#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
HPS1	3257	broad.mit.edu	37	10	100202989	100202989	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:100202989G>A	ENST00000325103.6	-	3	242	c.9C>T	c.(7-9)tgC>tgT	p.C3C	HPS1_ENST00000467246.1_5'UTR|HPS1_ENST00000361490.4_Silent_p.C3C|HPS1_ENST00000338546.5_Silent_p.C3C	NM_000195.3	NP_000186.2	Q92902	HPS1_HUMAN	Hermansky-Pudlak syndrome 1	3					blood coagulation (GO:0007596)|eye pigmentation (GO:0048069)|lysosome organization (GO:0007040)|melanocyte differentiation (GO:0030318)|positive regulation of natural killer cell activation (GO:0032816)|retina development in camera-type eye (GO:0060041)|secretion of lysosomal enzymes (GO:0033299)|visual perception (GO:0007601)	BLOC-3 complex (GO:0031085)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	protein dimerization activity (GO:0046983)	p.C3C(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.234)		Epithelial(162;3.87e-12)|all cancers(201;5.63e-10)		CCACCAAGACGCACTTCATCT	0.552									Hermansky-Pudlak syndrome																												p.C3C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C9T	10						.						110.0	99.0	103.0					10																	100202989		2203	4300	6503	100192979	SO:0001819	synonymous_variant	3257	exon3	Familial Cancer Database	HPS, HPS1-8	U79136	CCDS7475.1, CCDS7476.1	10q23.1-q23.3	2014-06-18		2002-05-01	ENSG00000107521	ENSG00000107521			5163	protein-coding gene	gene with protein product		604982	"""Hermansky-Pudlak syndrome"""	HPS		8541858, 7573033	Standard	NM_182639		Approved		uc021pwv.1	Q92902	OTTHUMG00000018876	ENST00000325103.6:c.9C>T	10.37:g.100202989G>A		Somatic		Capture	Illumina HiSeq	Phase_I	100192979	NM_182639	A8MRT2|O15402|O15502|Q5TAA3|Q8WXE5	Silent	SNP	ENST00000325103.6	37	CCDS7475.1																																																																																				0.552	HPS1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049776.1	NM_000195, NM_182637, NM_182638, NM_182639	
CNNM1	26507	broad.mit.edu	37	10	101147585	101147585	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:101147585G>A	ENST00000356713.4	+	8	2638	c.2349G>A	c.(2347-2349)cgG>cgA	p.R783R	CNNM1_ENST00000446890.1_Silent_p.R712R|CNNM1_ENST00000370528.3_Silent_p.R712R|CNNM1_ENST00000370534.4_Silent_p.R439R	NM_020348.2	NP_065081.2	Q9NRU3	CNNM1_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 1	783					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)	p.R418R(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)		AGATCACACGGCAGCAATATC	0.627																																					p.R783R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2349A	10						.						71.0	54.0	60.0					10																	101147585		2203	4300	6503	101137575	SO:0001819	synonymous_variant	26507	exon8			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.2349G>A	10.37:g.101147585G>A		Somatic		Capture	Illumina HiSeq	Phase_I	101137575	NM_020348	Q4QQG7|Q4QQH8|Q4QQP9|Q9NT45	Silent	SNP	ENST00000356713.4	37	CCDS7478.2																																																																																				0.627	CNNM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049792.2	NM_020348	
PDZD7	79955	broad.mit.edu	37	10	102777900	102777900	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:102777900C>A	ENST00000370215.3	-	9	1703	c.1478G>T	c.(1477-1479)aGc>aTc	p.S493I		NM_024895.4	NP_079171.1	Q9H5P4	PDZD7_HUMAN	PDZ domain containing 7	493						cilium (GO:0005929)|extracellular space (GO:0005615)|nucleus (GO:0005634)		p.S493I(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22				Epithelial(162;6.98e-09)|all cancers(201;3.55e-07)		CAGGCTCCCGCTGTCCAGTGT	0.597																																					p.S493I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1478T	10						.						115.0	103.0	107.0					10																	102777900		2203	4300	6503	102767890	SO:0001583	missense	79955	exon9			AK026862	CCDS31269.1, CCDS73182.1	10q24.32	2006-01-24		2006-01-24	ENSG00000186862	ENSG00000186862			26257	protein-coding gene	gene with protein product		612971		PDZK7		12477932	Standard	NM_024895		Approved	FLJ23209, bA108L7.8	uc021pxc.1	Q9H5P4	OTTHUMG00000018916	ENST00000370215.3:c.1478G>T	10.37:g.102777900C>A	ENSP00000359234:p.Ser493Ile	Somatic		Capture	Illumina HiSeq	Phase_I	102767890	NM_001195263	D5FJ77|Q8N321	Missense_Mutation	SNP	ENST00000370215.3	37	CCDS31269.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.09|13.09	2.133113|2.133113	0.37630|0.37630	.|.	.|.	ENSG00000186862|ENSG00000186862	ENST00000433616|ENST00000393462;ENST00000370215	.|T	.|0.11930	.|2.73	4.12|4.12	1.09|1.09	0.20402|0.20402	.|.	.|3.850710	.|0.00447	.|N	.|0.000098	T|T	0.10465|0.10465	0.0256|0.0256	L|L	0.27053|0.27053	0.805|0.805	0.09310|0.09310	N|N	1|1	.|B;B	.|0.23735	.|0.09;0.045	.|B;B	.|0.21151	.|0.009;0.033	T|T	0.31530|0.31530	-0.9940|-0.9940	5|10	.|0.62326	.|D	.|0.03	.|.	1.7506|1.7506	0.02971|0.02971	0.1488:0.3756:0.291:0.1845|0.1488:0.3756:0.291:0.1845	.|.	.|493;493	.|Q9H5P4;Q9H5P4-2	.|PDZD7_HUMAN;.	S|I	68|493	.|ENSP00000359234:S493I	.|ENSP00000359234:S493I	A|S	-|-	1|2	0|0	PDZD7|PDZD7	102767890|102767890	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.393000|0.393000	0.30537|0.30537	0.350000|0.350000	0.20079|0.20079	0.372000|0.372000	0.24591|0.24591	0.555000|0.555000	0.69702|0.69702	GCG|AGC		0.597	PDZD7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049883.1	NM_024895	
TMEM180	79847	broad.mit.edu	37	10	104233474	104233474	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:104233474G>T	ENST00000238936.4	+	8	1310	c.1073G>T	c.(1072-1074)aGc>aTc	p.S358I	TMEM180_ENST00000366277.2_Missense_Mutation_p.S87I	NM_024789.3	NP_079065.2	Q14CX5	TM180_HUMAN	transmembrane protein 180	358						integral component of membrane (GO:0016021)		p.S358I(1)		breast(3)|endometrium(2)|large_intestine(3)|lung(1)|ovary(3)|skin(1)	13		Colorectal(252;0.122)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		GACCACCTCAGCCTGCTGTGC	0.647																																					p.S358I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1073T	10						.						146.0	119.0	128.0					10																	104233474		2203	4300	6503	104223464	SO:0001583	missense	79847	exon8			AK026182	CCDS7535.1	10q24.32	2011-02-09	2006-10-12	2006-10-12	ENSG00000138111	ENSG00000138111			26196	protein-coding gene	gene with protein product				C10orf77		12477932	Standard	XM_006717971		Approved	FLJ22529, bA18I14.8	uc001kvt.3	Q14CX5	OTTHUMG00000018961	ENST00000238936.4:c.1073G>T	10.37:g.104233474G>T	ENSP00000238936:p.Ser358Ile	Somatic		Capture	Illumina HiSeq	Phase_I	104223464	NM_024789	Q6NWM8|Q6NWM9|Q6PEZ7|Q9H679	Missense_Mutation	SNP	ENST00000238936.4	37	CCDS7535.1	.	.	.	.	.	.	.	.	.	.	G	9.971	1.225561	0.22457	.	.	ENSG00000138111	ENST00000366277;ENST00000447593;ENST00000238936;ENST00000369930	T;D;T	0.86562	-1.34;-2.14;-1.34	5.71	4.7	0.59300	Major facilitator superfamily domain, general substrate transporter (1);	0.388231	0.31884	N	0.006903	T	0.64427	0.2597	N	0.02539	-0.55	0.22213	N	0.999284	B;B	0.15141	0.012;0.0	B;B	0.11329	0.006;0.003	T	0.48281	-0.9049	10	0.21540	T	0.41	.	3.2877	0.06937	0.1822:0.2919:0.5258:0.0	.	207;358	B4DWN6;Q14CX5	.;TM180_HUMAN	I	87;207;358;87	ENSP00000437572:S87I;ENSP00000238936:S358I;ENSP00000358946:S87I	ENSP00000238936:S358I	S	+	2	0	TMEM180	104223464	0.995000	0.38212	0.948000	0.38648	0.627000	0.37826	4.350000	0.59392	2.700000	0.92200	0.462000	0.41574	AGC		0.647	TMEM180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050075.2	NM_024789	
TRIM8	81603	broad.mit.edu	37	10	104416655	104416655	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:104416655C>T	ENST00000302424.7	+	6	1322	c.1200C>T	c.(1198-1200)taC>taT	p.Y400Y	TRIM8_ENST00000487927.1_3'UTR	NM_030912.2	NP_112174.2	Q9BZR9	TRIM8_HUMAN	tripartite motif containing 8	400					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|PML body (GO:0016605)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)	p.Y400Y(1)		endometrium(4)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15		Colorectal(252;0.122)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		GCGGCCAGTACGGGGCGGCGG	0.721																																					p.Y400Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1200T	10						.						38.0	45.0	43.0					10																	104416655		2198	4289	6487	104406645	SO:0001819	synonymous_variant	81603	exon6			AF281046	CCDS31274.1	10q24.3	2013-01-09	2011-01-25	2002-06-14	ENSG00000171206	ENSG00000171206		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	15579	protein-coding gene	gene with protein product	"""glioblastoma expressed ring finger protein"""	606125	"""ring finger protein 27"", ""tripartite motif-containing 8"""	RNF27		11118312, 12163497	Standard	NM_030912		Approved	GERP	uc001kvz.2	Q9BZR9	OTTHUMG00000018964	ENST00000302424.7:c.1200C>T	10.37:g.104416655C>T		Somatic		Capture	Illumina HiSeq	Phase_I	104406645	NM_030912	A6NI31|Q9C028	Silent	SNP	ENST00000302424.7	37	CCDS31274.1																																																																																				0.721	TRIM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050084.3	NM_030912	
USP6NL	9712	broad.mit.edu	37	10	11527059	11527059	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:11527059G>A	ENST00000609104.1	-	13	1230	c.836C>T	c.(835-837)aCa>aTa	p.T279I	USP6NL_ENST00000379237.2_Missense_Mutation_p.T302I|USP6NL_ENST00000277575.5_Missense_Mutation_p.T296I	NM_014688.2	NP_055503.1	Q92738	US6NL_HUMAN	USP6 N-terminal like	279	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				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.T296I(1)		endometrium(3)|kidney(2)|large_intestine(6)|lung(18)|prostate(1)|skin(1)|urinary_tract(1)	32						GAGGTTTAGTGTAAAGGGAGT	0.313																																					p.T279I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C836T	10						.						40.0	38.0	39.0					10																	11527059		1794	4002	5796	11567065	SO:0001583	missense	9712	exon13			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.836C>T	10.37:g.11527059G>A	ENSP00000476462:p.Thr279Ile	Somatic		Capture	Illumina HiSeq	Phase_I	11567065	NM_014688	A8KA79|Q15400|Q5VV10|Q7L0K9	Missense_Mutation	SNP	ENST00000609104.1	37	CCDS53492.1	.	.	.	.	.	.	.	.	.	.	G	14.33	2.503674	0.44558	.	.	ENSG00000148429	ENST00000535316;ENST00000277575;ENST00000379237	T;T	0.29917	1.55;1.55	5.35	4.43	0.53597	Rab-GAP/TBC domain (4);	0.098852	0.64402	D	0.000002	T	0.23766	0.0575	N	0.21240	0.645	0.47374	D	0.999408	B;B	0.28208	0.198;0.203	B;B	0.35899	0.213;0.135	T	0.07214	-1.0784	10	0.36615	T	0.2	.	10.4428	0.44474	0.0717:0.261:0.6673:0.0	.	279;296	Q92738;Q92738-2	US6NL_HUMAN;.	I	279;296;279	ENSP00000277575:T296I;ENSP00000368539:T279I	ENSP00000277575:T296I	T	-	2	0	USP6NL	11567065	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	4.514000	0.60482	1.348000	0.45733	0.591000	0.81541	ACA		0.313	USP6NL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000046764.3	NM_014688	
COL17A1	1308	broad.mit.edu	37	10	105801087	105801087	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:105801087C>T	ENST00000353479.5	-	38	2911	c.2621G>A	c.(2620-2622)gGc>gAc	p.G874D	COL17A1_ENST00000369733.3_Missense_Mutation_p.G874D	NM_000494.3	NP_000485.3	Q9UMD9	COHA1_HUMAN	collagen, type XVII, alpha 1	874	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.G874D(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)		TCCTGGTGGGCCTGGAATGGA	0.627																																					p.G874D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2621A	10						.						60.0	62.0	62.0					10																	105801087		2203	4300	6503	105791077	SO:0001583	missense	1308	exon38			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.2621G>A	10.37:g.105801087C>T	ENSP00000340937:p.Gly874Asp	Somatic		Capture	Illumina HiSeq	Phase_I	105791077	NM_000494	Q02802|Q5JV36|Q99018|Q9NQK9|Q9UC14	Missense_Mutation	SNP	ENST00000353479.5	37	CCDS7554.1	.	.	.	.	.	.	.	.	.	.	C	15.35	2.806375	0.50421	.	.	ENSG00000065618	ENST00000353479;ENST00000369733	D;D	0.94650	-3.26;-3.48	4.95	4.95	0.65309	.	0.000000	0.45867	D	0.000323	D	0.97692	0.9243	M	0.93062	3.375	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.98200	1.0467	10	0.87932	D	0	-13.6892	13.7333	0.62802	0.0:1.0:0.0:0.0	.	874	Q9UMD9	COHA1_HUMAN	D	874	ENSP00000340937:G874D;ENSP00000358748:G874D	ENSP00000340937:G874D	G	-	2	0	COL17A1	105791077	1.000000	0.71417	0.999000	0.59377	0.163000	0.22366	4.469000	0.60169	2.629000	0.89072	0.491000	0.48974	GGC		0.627	COL17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050181.1	NM_130778, NM_000494	
KIAA1598	57698	broad.mit.edu	37	10	118711511	118711511	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:118711511C>T	ENST00000355371.4	-	6	940	c.443G>A	c.(442-444)cGa>cAa	p.R148Q	KIAA1598_ENST00000260777.10_Missense_Mutation_p.R148Q|KIAA1598_ENST00000392901.4_Missense_Mutation_p.R88Q|KIAA1598_ENST00000392903.2_Missense_Mutation_p.R148Q|KIAA1598_ENST00000497044.1_5'UTR	NM_001127211.2|NM_001258298.1|NM_001258299.1	NP_001120683.1|NP_001245227.1|NP_001245228.1	A0MZ66	SHOT1_HUMAN	KIAA1598	148					axon guidance (GO:0007411)|regulation of establishment of cell polarity (GO:2000114)|regulation of neuron migration (GO:2001222)	axonal growth cone (GO:0044295)		p.R148Q(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(3)	10				all cancers(201;0.00494)		AATTTGATCTCGAAGTTCTGC	0.299																																					p.R148Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G443A	10						.						56.0	51.0	53.0					10																	118711511		2202	4300	6502	118701501	SO:0001583	missense	57698	exon6			BC022348	CCDS31293.1, CCDS44482.1, CCDS58097.1, CCDS73207.1, CCDS73208.1	10q26.12	2007-01-30			ENSG00000187164	ENSG00000187164			29319	protein-coding gene	gene with protein product		611171				10997877, 17030985	Standard	NM_001127211		Approved	shootin1, shootin-1	uc009xyw.4	A0MZ66	OTTHUMG00000019114	ENST00000355371.4:c.443G>A	10.37:g.118711511C>T	ENSP00000347532:p.Arg148Gln	Somatic		Capture	Illumina HiSeq	Phase_I	118701501	NM_018330	A8MYU7|B3KRD3|B3KRH2|B3KTE0|B3KTJ7|B3KTJ8|B4E3U1|B7Z7Z9|Q68DG1|Q6PIM5|Q9HCH4|Q9NUV0	Missense_Mutation	SNP	ENST00000355371.4	37	CCDS44482.1	.	.	.	.	.	.	.	.	.	.	C	11.68	1.709544	0.30322	.	.	ENSG00000187164	ENST00000392903;ENST00000260777;ENST00000355371;ENST00000392901	T;T;T;T	0.73575	3.02;1.58;3.02;-0.76	5.69	4.76	0.60689	.	0.128531	0.51477	N	0.000092	T	0.61788	0.2375	L	0.38175	1.15	0.42842	D	0.994055	B;B;B	0.11235	0.004;0.003;0.003	B;B;B	0.11329	0.006;0.003;0.005	T	0.55029	-0.8204	10	0.10377	T	0.69	-4.2585	11.9916	0.53178	0.0:0.9172:0.0:0.0828	.	148;148;118	A0MZ66;A0MZ66-2;A0MZ66-6	SHOT1_HUMAN;.;.	Q	148;148;148;88	ENSP00000376636:R148Q;ENSP00000260777:R148Q;ENSP00000347532:R148Q;ENSP00000376635:R88Q	ENSP00000260777:R148Q	R	-	2	0	KIAA1598	118701501	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.577000	0.36515	1.350000	0.45770	0.655000	0.94253	CGA		0.299	KIAA1598-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018330	
MKI67	4288	broad.mit.edu	37	10	129905806	129905806	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:129905806G>A	ENST00000368654.3	-	13	4673	c.4298C>T	c.(4297-4299)gCg>gTg	p.A1433V	MKI67_ENST00000368653.3_Missense_Mutation_p.A1073V	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1433	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.A1433V(2)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TTCCCTAAACGCGTTGATGCT	0.488																																					p.A1073V												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.C3218T	10						.						253.0	239.0	244.0					10																	129905806		2203	4300	6503	129795796	SO:0001583	missense	4288	exon12			X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.4298C>T	10.37:g.129905806G>A	ENSP00000357643:p.Ala1433Val	Somatic		Capture	Illumina HiSeq	Phase_I	129795796	NM_001145966	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	G	0.041	-1.282707	0.01398	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.02579	4.24;4.24	3.87	-7.75	0.01236	.	.	.	.	.	T	0.01124	0.0037	N	0.02315	-0.6	0.09310	N	1	B;B;B	0.12013	0.0;0.002;0.005	B;B;B	0.14023	0.001;0.002;0.01	T	0.50874	-0.8776	9	0.27785	T	0.31	.	7.9372	0.29937	0.2509:0.0:0.6262:0.1229	.	1432;1073;1433	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	V	1433;1073;1432	ENSP00000357643:A1433V;ENSP00000357642:A1073V	ENSP00000357642:A1073V	A	-	2	0	MKI67	129795796	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.327000	0.01113	-1.550000	0.01708	-2.070000	0.00385	GCG		0.488	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
LARP4B	23185	broad.mit.edu	37	10	859113	859113	+	Missense_Mutation	SNP	G	G	A	rs148067710		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:859113G>A	ENST00000316157.3	-	17	2010	c.1970C>T	c.(1969-1971)aCg>aTg	p.T657M	LARP4B_ENST00000469487.1_5'Flank	NM_015155.1	NP_055970.1	Q92615	LAR4B_HUMAN	La ribonucleoprotein domain family, member 4B	657					positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)	p.T657M(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(2)|skin(2)|urinary_tract(2)	38						CTCTTTACTCGTTCTCTGACA	0.493																																					p.T657M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1970T	10						.	G	MET/THR	1,4405	2.1+/-5.4	0,1,2202	86.0	84.0	85.0		1970	6.1	1.0	10	dbSNP_134	85	0,8600		0,0,4300	no	missense	LARP4B	NM_015155.1	81	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	657/739	859113	1,13005	2203	4300	6503	849113	SO:0001583	missense	23185	exon17			D86971	CCDS31131.1	10p15.3	2011-08-24	2009-06-09	2009-06-09	ENSG00000107929	ENSG00000107929		"""La ribonucleoprotein domain containing"""	28987	protein-coding gene	gene with protein product			"""KIAA0217"", ""La ribonucleoprotein domain family, member 5"""	KIAA0217, LARP5		9039502, 20573744	Standard	NM_015155		Approved		uc031ptb.1	Q92615	OTTHUMG00000017534	ENST00000316157.3:c.1970C>T	10.37:g.859113G>A	ENSP00000326128:p.Thr657Met	Somatic		Capture	Illumina HiSeq	Phase_I	849113	NM_015155	A7MD20|Q5T3R3|Q5T3R4|Q5T3R5|Q68CY4	Missense_Mutation	SNP	ENST00000316157.3	37	CCDS31131.1	.	.	.	.	.	.	.	.	.	.	G	16.26	3.071935	0.55646	2.27E-4	0.0	ENSG00000107929	ENST00000316157	T	0.32272	1.46	6.07	6.07	0.98685	.	0.249182	0.47093	D	0.000258	T	0.33000	0.0848	N	0.08118	0	0.46203	D	0.998923	D	0.67145	0.996	P	0.55303	0.773	T	0.33904	-0.9850	10	0.72032	D	0.01	33.1838	20.6439	0.99570	0.0:0.0:1.0:0.0	.	657	Q92615	LAR4B_HUMAN	M	657	ENSP00000326128:T657M	ENSP00000326128:T657M	T	-	2	0	LARP4B	849113	1.000000	0.71417	0.997000	0.53966	0.944000	0.59088	3.546000	0.53656	2.884000	0.98904	0.655000	0.94253	ACG		0.493	LARP4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046395.2	NM_015155	
ITIH5	80760	broad.mit.edu	37	10	7608141	7608141	+	Silent	SNP	G	G	A	rs142836742		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:7608141G>A	ENST00000256861.6	-	13	2457	c.2379C>T	c.(2377-2379)aaC>aaT	p.N793N	ITIH5_ENST00000397146.2_Intron|ITIH5_ENST00000298441.6_Silent_p.N579N|ITIH5_ENST00000446830.2_Silent_p.N575N	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	793					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.N793N(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						TGACATTGGCGTTGGCAGACA	0.602																																					p.N793N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2379T	10						.	G	,	0,4406		0,0,2203	108.0	85.0	93.0		2379,1737	-12.0	0.2	10	dbSNP_134	93	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	ITIH5	NM_030569.6,NM_032817.5	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	793/943,579/729	7608141	1,13005	2203	4300	6503	7648147	SO:0001819	synonymous_variant	80760	exon13					10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"""inter-alpha (globulin) inhibitor H5"""			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.2379C>T	10.37:g.7608141G>A		Somatic		Capture	Illumina HiSeq	Phase_I	7648147	NM_030569	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Silent	SNP	ENST00000256861.6	37																																																																																					0.602	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569	
FAM107B	83641	broad.mit.edu	37	10	14816460	14816460	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:14816460C>T	ENST00000181796.2	-	1	436	c.203G>A	c.(202-204)aGc>aAc	p.S68N		NM_031453.2	NP_113641.2	Q9H098	F107B_HUMAN	family with sequence similarity 107, member B	0					sensory perception of sound (GO:0007605)			p.S68N(1)		breast(7)|kidney(1)|large_intestine(4)|lung(7)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TCCTTCTGCGCTTGGGTGTCT	0.577																																					p.S68N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G203A	10						.						132.0	120.0	124.0					10																	14816460		2203	4300	6503	14856466	SO:0001583	missense	83641	exon1			AK127413	CCDS7102.1, CCDS60486.1	10p14	2006-01-17	2006-01-17	2005-11-20	ENSG00000065809	ENSG00000065809			23726	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 45"""	C10orf45		11230166	Standard	XM_005252616		Approved	FLJ45505, MGC11034	uc001ina.1	Q9H098	OTTHUMG00000017709	ENST00000181796.2:c.203G>A	10.37:g.14816460C>T	ENSP00000181796:p.Ser68Asn	Somatic		Capture	Illumina HiSeq	Phase_I	14856466	NM_031453	A8K1P4|D3DRT2|Q5T9K7|Q5T9K8|Q6ZSI4	Missense_Mutation	SNP	ENST00000181796.2	37	CCDS7102.1	.	.	.	.	.	.	.	.	.	.	C	2.663	-0.279404	0.05642	.	.	ENSG00000065809	ENST00000181796	T	0.49139	0.79	4.4	1.36	0.22044	.	0.821449	0.10295	N	0.691794	T	0.28400	0.0702	N	0.19112	0.55	0.09310	N	1	B	0.22346	0.068	B	0.21546	0.035	T	0.22138	-1.0225	10	0.35671	T	0.21	-8.4126	3.5025	0.07679	0.0:0.4183:0.1958:0.386	.	68	Q9H098-2	.	N	68	ENSP00000181796:S68N	ENSP00000181796:S68N	S	-	2	0	FAM107B	14856466	0.000000	0.05858	0.000000	0.03702	0.316000	0.28119	-1.123000	0.03263	0.101000	0.17610	0.655000	0.94253	AGC		0.577	FAM107B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000356966.1	NM_031453	
CUBN	8029	broad.mit.edu	37	10	16957158	16957158	+	Silent	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:16957158G>T	ENST00000377833.4	-	47	7289	c.7224C>A	c.(7222-7224)ggC>ggA	p.G2408G		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2408	CUB 17. {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.G2408G(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)	CACAGTATCTGCCCAAGATGT	0.423																																					p.G2408G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C7224A	10						.						103.0	94.0	97.0					10																	16957158		2203	4300	6503	16997164	SO:0001819	synonymous_variant	8029	exon47			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.7224C>A	10.37:g.16957158G>T		Somatic		Capture	Illumina HiSeq	Phase_I	16997164	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	37	CCDS7113.1																																																																																				0.423	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
PIP4K2A	5305	broad.mit.edu	37	10	22828900	22828900	+	Splice_Site	SNP	G	G	A	rs549534439		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:22828900G>A	ENST00000376573.4	-	9	1368	c.1140C>T	c.(1138-1140)ggC>ggT	p.G380G	PIP4K2A_ENST00000545335.1_Splice_Site_p.G321G|PIP4K2A_ENST00000323883.7_Splice_Site_p.G240G	NM_005028.4	NP_005019.2	P48426	PI42A_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, alpha	380	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				megakaryocyte development (GO:0035855)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|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)	p.G380G(1)		endometrium(4)|kidney(13)|large_intestine(4)|lung(6)|ovary(1)|skin(1)	29						AGATACTCACGCCATGTTTAA	0.458													G|||	1	0.000199681	0.0	0.0	5008	,	,		19194	0.0		0.0	False		,,,				2504	0.001				p.G380G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1140T	10						.						191.0	168.0	176.0					10																	22828900		2203	4300	6503	22868906	SO:0001630	splice_region_variant	5305	exon9			S78798	CCDS7141.1	10p12.2	2007-08-21	2007-08-14	2007-08-14	ENSG00000150867	ENSG00000150867			8997	protein-coding gene	gene with protein product		603140	"""phosphatidylinositol-4-phosphate 5-kinase, type II, alpha"""	PIP5K2A		7852364, 9367159	Standard	NM_005028		Approved	PIP5KIIA, PIP5KIIalpha	uc001irl.4	P48426	OTTHUMG00000017810	ENST00000376573.4:c.1140+1C>T	10.37:g.22828900G>A		Somatic		Capture	Illumina HiSeq	Phase_I	22868906	NM_005028	B0YJ66|B4DGX2|D3DRV1|P53807|Q5VUX3	Silent	SNP	ENST00000376573.4	37	CCDS7141.1																																																																																				0.458	PIP4K2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047193.1	NM_005028	Silent
KIAA1217	56243	broad.mit.edu	37	10	24508621	24508621	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:24508621G>A	ENST00000376454.3	+	2	167	c.137G>A	c.(136-138)cGc>cAc	p.R46H	KIAA1217_ENST00000458595.1_Missense_Mutation_p.R46H|KIAA1217_ENST00000376452.3_Missense_Mutation_p.R46H|KIAA1217_ENST00000376462.1_5'UTR	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	46					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)		p.R46H(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						ACCAAGGAACGCCTTTCTAAT	0.463																																					p.R46H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G137A	10						.						73.0	67.0	69.0					10																	24508621		2203	4300	6503	24548627	SO:0001583	missense	56243	exon2			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.137G>A	10.37:g.24508621G>A	ENSP00000365637:p.Arg46His	Somatic		Capture	Illumina HiSeq	Phase_I	24548627	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	18.46	3.629884	0.67015	.	.	ENSG00000120549	ENST00000376456;ENST00000458595;ENST00000376454;ENST00000376452	T;T;T;T	0.63096	-0.02;-0.02;-0.02;-0.02	5.87	4.91	0.64330	.	0.241275	0.27206	N	0.020431	T	0.51584	0.1683	N	0.22421	0.69	0.30705	N	0.749838	D;D;D;D	0.64830	0.983;0.971;0.994;0.983	P;B;P;P	0.51582	0.578;0.374;0.674;0.578	T	0.57493	-0.7802	10	0.52906	T	0.07	.	4.369	0.11239	0.0801:0.1284:0.5911:0.2004	.	46;46;46;46	Q5T5P2-7;A6NLF3;Q5T5P2;Q5T5P2-2	.;.;SKT_HUMAN;.	H	46	ENSP00000365639:R46H;ENSP00000392625:R46H;ENSP00000365637:R46H;ENSP00000365635:R46H	ENSP00000365635:R46H	R	+	2	0	KIAA1217	24548627	0.992000	0.36948	0.912000	0.35992	0.933000	0.57130	2.271000	0.43364	2.791000	0.96007	0.655000	0.94253	CGC		0.463	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590	
SVIL	6840	broad.mit.edu	37	10	29762863	29762863	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:29762863G>A	ENST00000355867.4	-	30	6185	c.5433C>T	c.(5431-5433)tgC>tgT	p.C1811C	SVIL_ENST00000535393.1_Silent_p.C725C|SVIL_ENST00000375400.3_Silent_p.C1385C|PTCHD3P1_ENST00000413405.1_RNA|PTCHD3P1_ENST00000446807.1_RNA|SVIL_ENST00000375398.2_Silent_p.C1811C|SVIL_ENST00000460007.1_5'UTR|PTCHD3P1_ENST00000414457.1_RNA|PTCHD3P1_ENST00000423223.1_RNA	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		
MTPAP	55149	broad.mit.edu	37	10	30602718	30602718	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:30602718C>T	ENST00000263063.4	-	9	1612	c.1569G>A	c.(1567-1569)cgG>cgA	p.R523R	MTPAP_ENST00000358107.4_Silent_p.R653R|MTPAP_ENST00000488290.1_5'UTR	NM_018109.3	NP_060579.3	Q9NVV4	PAPD1_HUMAN	mitochondrial poly(A) polymerase	523					cell death (GO:0008219)|histone mRNA catabolic process (GO:0071044)|mRNA polyadenylation (GO:0006378)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|poly(A) RNA binding (GO:0044822)|polynucleotide adenylyltransferase activity (GO:0004652)|protein homodimerization activity (GO:0042803)|UTP binding (GO:0002134)	p.R523R(1)|p.R653R(1)		breast(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	33						GCCCCCAGGGCCGATTACTTG	0.418																																					p.R523R												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G1569A	10						.						131.0	126.0	127.0					10																	30602718		2203	4300	6503	30642724	SO:0001819	synonymous_variant	55149	exon9			AL122121	CCDS7165.1	10p12.1	2014-01-30	2009-01-12	2009-01-12	ENSG00000107951	ENSG00000107951			25532	protein-coding gene	gene with protein product	"""TUTase1"""	613669	"""PAP associated domain containing 1"""	PAPD1		12239557, 15769737, 15547249	Standard	NM_018109		Approved	FLJ10486, mtPAP, SPAX4	uc001iva.4	Q9NVV4	OTTHUMG00000017895	ENST00000263063.4:c.1569G>A	10.37:g.30602718C>T		Somatic		Capture	Illumina HiSeq	Phase_I	30642724	NM_018109	D3DRX0|Q659E3|Q6P7E5|Q9HA74	Silent	SNP	ENST00000263063.4	37	CCDS7165.1																																																																																				0.418	MTPAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047426.2	NM_018109	
FZD8	8325	broad.mit.edu	37	10	35929113	35929113	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:35929113C>T	ENST00000374694.1	-	1	1249	c.1245G>A	c.(1243-1245)gtG>gtA	p.V415V	MIR4683_ENST00000579659.1_RNA	NM_031866.2	NP_114072.1	Q9H461	FZD8_HUMAN	frizzled class receptor 8	415					axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|gonad development (GO:0008406)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|T cell differentiation in thymus (GO:0033077)|vasculature development (GO:0001944)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.V415V(1)		central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	11						GCGACAAGATCACCCACCAGA	0.632																																					p.V415V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1245A	10						.						56.0	54.0	55.0					10																	35929113		2203	4300	6503	35969119	SO:0001819	synonymous_variant	8325	exon1			AB043703	CCDS7192.1	10p11.2	2014-01-29	2014-01-29		ENSG00000177283	ENSG00000177283		"""GPCR / Class F : Frizzled receptors"""	4046	protein-coding gene	gene with protein product		606146	"""frizzled (Drosophila) homolog 8"", ""frizzled homolog 8 (Drosophila)"", ""frizzled 8, seven transmembrane spanning receptor"", ""frizzled family receptor 8"""			11295046	Standard	NM_031866		Approved		uc001iyz.1	Q9H461	OTTHUMG00000017956	ENST00000374694.1:c.1245G>A	10.37:g.35929113C>T		Somatic		Capture	Illumina HiSeq	Phase_I	35969119	NM_031866		Silent	SNP	ENST00000374694.1	37	CCDS7192.1																																																																																				0.632	FZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047575.2	NM_031866	
BMS1	9790	broad.mit.edu	37	10	43315763	43315763	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:43315763G>A	ENST00000374518.5	+	16	2723	c.2660G>A	c.(2659-2661)cGc>cAc	p.R887H		NM_014753.3	NP_055568.3	Q14692	BMS1_HUMAN	BMS1 ribosome biogenesis factor	887					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)	p.R887H(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						ATGTACGTCCGCATTGAGATT	0.463																																					p.R887H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2660A	10						.						134.0	130.0	131.0					10																	43315763		2203	4300	6503	42635769	SO:0001583	missense	9790	exon16			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.2660G>A	10.37:g.43315763G>A	ENSP00000363642:p.Arg887His	Somatic		Capture	Illumina HiSeq	Phase_I	42635769	NM_014753	Q5QPT5|Q86XJ9	Missense_Mutation	SNP	ENST00000374518.5	37	CCDS7199.1	.	.	.	.	.	.	.	.	.	.	G	31	5.100189	0.94245	.	.	ENSG00000165733	ENST00000374518	T	0.20332	2.08	5.05	5.05	0.67936	Ribosome biogenesis protein BMS1/TSR1, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.58047	0.2095	M	0.92459	3.31	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.69363	-0.5165	10	0.59425	D	0.04	.	18.4608	0.90737	0.0:0.0:1.0:0.0	.	887	Q14692	BMS1_HUMAN	H	887	ENSP00000363642:R887H	ENSP00000363642:R887H	R	+	2	0	BMS1	42635769	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.609000	0.98334	2.352000	0.79861	0.454000	0.30748	CGC		0.463	BMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047690.2	NM_014753	
CSGALNACT2	55454	broad.mit.edu	37	10	43651094	43651094	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:43651094A>G	ENST00000374466.3	+	2	832	c.497A>G	c.(496-498)cAt>cGt	p.H166R	CSGALNACT2_ENST00000374464.1_Missense_Mutation_p.H166R	NM_018590.3	NP_061060.3	Q8N6G5	CGAT2_HUMAN	chondroitin sulfate N-acetylgalactosaminyltransferase 2	166					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050653)|dermatan sulfate proteoglycan biosynthetic process (GO:0050651)|dermatan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050652)|glycosaminoglycan metabolic process (GO:0030203)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047237)|metal ion binding (GO:0046872)	p.H166R(1)		endometrium(12)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						CTCACTCGCCATCCTGAAGAA	0.408																																					p.H166R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A497G	10						.						94.0	95.0	95.0					10																	43651094		2203	4300	6503	42971100	SO:0001583	missense	55454	exon2			AF116646	CCDS7201.1	10q11.21	2013-02-19			ENSG00000169826	ENSG00000169826		"""Beta 4-glycosyltransferases"""	24292	protein-coding gene	gene with protein product	"""chondroitin beta1,4 N-acetylgalactosaminyltransferase 2"""					12446672	Standard	NM_018590		Approved	GALNACT2, MGC40204, PRO0082, GALNACT-2	uc001jan.4	Q8N6G5	OTTHUMG00000018023	ENST00000374466.3:c.497A>G	10.37:g.43651094A>G	ENSP00000363590:p.His166Arg	Somatic		Capture	Illumina HiSeq	Phase_I	42971100	NM_018590	B3KWL7|Q6MZJ5|Q6MZP6|Q8TCH4|Q9P1I6	Missense_Mutation	SNP	ENST00000374466.3	37	CCDS7201.1	.	.	.	.	.	.	.	.	.	.	A	15.51	2.854924	0.51376	.	.	ENSG00000169826	ENST00000374466;ENST00000374464	T;T	0.19394	2.15;2.15	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.36138	0.0956	L	0.38692	1.165	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.83275	0.994;0.996	T	0.03684	-1.1013	10	0.23891	T	0.37	-21.0496	16.1547	0.81649	1.0:0.0:0.0:0.0	.	166;166	Q8N6G5;Q8N6G5-2	CGAT2_HUMAN;.	R	166	ENSP00000363590:H166R;ENSP00000363588:H166R	ENSP00000363588:H166R	H	+	2	0	CSGALNACT2	42971100	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.923000	0.92808	2.221000	0.72209	0.528000	0.53228	CAT		0.408	CSGALNACT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047693.1	NM_018590	
ZNF485	220992	broad.mit.edu	37	10	44112129	44112129	+	Missense_Mutation	SNP	C	C	A	rs138352256		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:44112129C>A	ENST00000361807.3	+	5	832	c.638C>A	c.(637-639)cCc>cAc	p.P213H	ZNF485_ENST00000374435.3_Missense_Mutation_p.P213H|ZNF485_ENST00000374437.2_Missense_Mutation_p.P122H	NM_145312.3	NP_660355.2	Q8NCK3	ZN485_HUMAN	zinc finger protein 485	213					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.P174H(1)|p.P213H(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	16						AGGGAGAAACCCCACAAATGC	0.388																																					p.P213H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C638A	10						.						52.0	55.0	54.0					10																	44112129		2203	4300	6503	43432135	SO:0001583	missense	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.638C>A	10.37:g.44112129C>A	ENSP00000354694:p.Pro213His	Somatic		Capture	Illumina HiSeq	Phase_I	43432135	NM_145312	B4DSE6|Q96CL0	Missense_Mutation	SNP	ENST00000361807.3	37	CCDS7205.2	.	.	.	.	.	.	.	.	.	.	C	8.928	0.962750	0.18583	.	.	ENSG00000198298	ENST00000361807;ENST00000374437;ENST00000374435	T;T;T	0.29397	1.57;1.57;1.57	2.02	0.0858	0.14443	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.56963	0.2021	M	0.91406	3.205	0.27435	N	0.95389	D	0.89917	1.0	D	0.81914	0.995	T	0.46707	-0.9172	9	0.87932	D	0	.	6.0956	0.20019	0.0:0.7017:0.0:0.2983	.	213	Q8NCK3	ZN485_HUMAN	H	213;122;213	ENSP00000354694:P213H;ENSP00000363560:P122H;ENSP00000363558:P213H	ENSP00000354694:P213H	P	+	2	0	ZNF485	43432135	0.000000	0.05858	0.014000	0.15608	0.542000	0.35054	0.688000	0.25422	0.009000	0.14813	0.462000	0.41574	CCC		0.388	ZNF485-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047719.2	NM_145312	
RASSF4	83937	broad.mit.edu	37	10	45486398	45486398	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:45486398C>T	ENST00000340258.5	+	9	801	c.688C>T	c.(688-690)Cgg>Tgg	p.R230W	RASSF4_ENST00000334940.6_Missense_Mutation_p.R239W|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.R230W(1)		NS(1)|endometrium(2)|large_intestine(6)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16						TTTTTCAGAGCGGACAAAATT	0.473																																					p.R230W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C688T	10						.						75.0	86.0	82.0					10																	45486398		2203	4300	6503	44806404	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.688C>T	10.37:g.45486398C>T	ENSP00000339692:p.Arg230Trp	Somatic		Capture	Illumina HiSeq	Phase_I	44806404	NM_032023	Q00425|Q5TFT8|Q9BQL3|Q9H071	Missense_Mutation	SNP	ENST00000340258.5	37	CCDS7208.1	.	.	.	.	.	.	.	.	.	.	C	19.95	3.921432	0.73213	.	.	ENSG00000107551	ENST00000334940;ENST00000340258;ENST00000374411	T;T	0.24350	1.86;1.86	5.82	-7.92	0.01160	Ras-association (3);	0.050792	0.85682	D	0.000000	T	0.46698	0.1406	M	0.80982	2.52	0.54753	D	0.99998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79108	0.927;0.992;0.93	T	0.67484	-0.5659	10	0.87932	D	0	-13.622	17.6734	0.88224	0.7816:0.1371:0.0813:0.0	.	239;321;230	Q9H2L5-2;Q59FL4;Q9H2L5	.;.;RASF4_HUMAN	W	239;230;321	ENSP00000334543:R239W;ENSP00000339692:R230W	ENSP00000334543:R239W	R	+	1	2	RASSF4	44806404	0.000000	0.05858	0.015000	0.15790	0.986000	0.74619	-1.245000	0.02899	-2.057000	0.00897	-0.188000	0.12872	CGG		0.473	RASSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047745.2	NM_032023	
OGDHL	55753	broad.mit.edu	37	10	50952124	50952124	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:50952124C>T	ENST00000374103.4	-	14	1862	c.1777G>A	c.(1777-1779)Gcc>Acc	p.A593T	OGDHL_ENST00000432695.1_Missense_Mutation_p.A384T|OGDHL_ENST00000419399.1_Missense_Mutation_p.A536T	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	593					glycolytic process (GO:0006096)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)	p.A593T(1)		central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	61						ATCCCCGTGGCTGGGCATGTC	0.587																																					p.A536T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1606A	10						.						105.0	88.0	94.0					10																	50952124		2203	4300	6503	50622130	SO:0001583	missense	55753	exon13			AK001713	CCDS7234.1, CCDS44390.1, CCDS44391.1	10q11.23	2013-09-20			ENSG00000197444	ENSG00000197444			25590	protein-coding gene	gene with protein product						10574462	Standard	NM_018245		Approved	FLJ10851	uc001jie.3	Q9ULD0	OTTHUMG00000018200	ENST00000374103.4:c.1777G>A	10.37:g.50952124C>T	ENSP00000363216:p.Ala593Thr	Somatic		Capture	Illumina HiSeq	Phase_I	50622130	NM_001143996	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Missense_Mutation	SNP	ENST00000374103.4	37	CCDS7234.1	.	.	.	.	.	.	.	.	.	.	C	11.53	1.665073	0.29604	.	.	ENSG00000197444	ENST00000374103;ENST00000419399;ENST00000432695	T;T;T	0.05580	3.42;3.42;3.42	5.5	-4.58	0.03410	.	0.404642	0.29246	N	0.012713	T	0.02267	0.0070	N	0.05383	-0.06	0.20638	N	0.999871	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.001	T	0.33929	-0.9849	10	0.39692	T	0.17	.	4.172	0.10334	0.0882:0.1625:0.4528:0.2965	.	536;384;593	Q9ULD0-2;Q9ULD0-3;Q9ULD0	.;.;OGDHL_HUMAN	T	593;536;384	ENSP00000363216:A593T;ENSP00000401356:A536T;ENSP00000390240:A384T	ENSP00000363216:A593T	A	-	1	0	OGDHL	50622130	0.000000	0.05858	0.079000	0.20413	0.762000	0.43233	-1.413000	0.02473	-0.440000	0.07211	-0.140000	0.14226	GCC		0.587	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245	
AGAP7P	653268	broad.mit.edu	37	10	51472582	51472582	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:51472582A>C	ENST00000374095.5	-	4	523	c.398T>G	c.(397-399)aTc>aGc	p.I133S		NM_001077685.1	NP_001071153.1	Q5VUJ5	AGAP7_HUMAN		133					regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.I133S(1)		kidney(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)	11						ATAATGCTGGATGGCTGTGCT	0.388																																					p.I133S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T398G	10						.						17.0	15.0	16.0					10																	51472582		1662	3162	4824	51142588	SO:0001583	missense	653268	exon4																														ENST00000374095.5:c.398T>G	10.37:g.51472582A>C	ENSP00000363208:p.Ile133Ser	Somatic		Capture	Illumina HiSeq	Phase_I	51142588	NM_001077685	A6NGH4	Missense_Mutation	SNP	ENST00000374095.5	37	CCDS41524.1	.	.	.	.	.	.	.	.	.	.	.	2.963	-0.214232	0.06101	.	.	ENSG00000204169	ENST00000374095	T	0.32988	1.43	0.861	-0.174	0.13319	.	0.165811	0.38381	N	0.001717	T	0.03651	0.0104	N	0.00055	-2.37	0.09310	N	0.999996	B	0.02656	0.0	B	0.01281	0.0	T	0.34800	-0.9814	10	0.06494	T	0.89	.	3.0902	0.06291	0.2553:0.5517:0.0:0.193	.	133	Q5VUJ5	AGAP7_HUMAN	S	133	ENSP00000363208:I133S	ENSP00000363208:I133S	I	-	2	0	AGAP7	51142588	1.000000	0.71417	0.960000	0.40013	0.007000	0.05969	2.153000	0.42282	-0.585000	0.05905	-2.876000	0.00098	ATC		0.388	AGAP7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048033.1		
FAM21A	387680	broad.mit.edu	37	10	51829309	51829309	+	Silent	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:51829309A>G	ENST00000282633.5	+	3	174	c.129A>G	c.(127-129)ctA>ctG	p.L43L	FAM21A_ENST00000351071.6_Silent_p.L43L|FAM21A_ENST00000314664.7_Silent_p.L43L|RP11-324H6.5_ENST00000456967.1_RNA|FAM21A_ENST00000492914.1_3'UTR	NM_001005751.1	NP_001005751.1	Q641Q2	FA21A_HUMAN	family with sequence similarity 21, member A	43					retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|membrane (GO:0016020)|WASH complex (GO:0071203)		p.L43L(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	15						TAAAATAGCTACTACAGTTTC	0.358																																					p.L43L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A129G	10						.						42.0	40.0	40.0					10																	51829309		1786	4031	5817	51499315	SO:0001819	synonymous_variant	387680	exon3			BC082258	CCDS41527.1	10q11.23	2014-06-19			ENSG00000099290	ENSG00000099290			23416	protein-coding gene	gene with protein product			"""family with sequence similarity 21, member B"""	FAM21B			Standard	XM_005269805		Approved	bA56A21.1, bA98I6.1, FLJ10824	uc001jjb.3	Q641Q2	OTTHUMG00000018225	ENST00000282633.5:c.129A>G	10.37:g.51829309A>G		Somatic		Capture	Illumina HiSeq	Phase_I	51499315	NM_001005751	A2A3S2|A2A3U6|Q6DHY0	Silent	SNP	ENST00000282633.5	37	CCDS41527.1																																																																																				0.358	FAM21A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276917.2	NM_001005751	
PCDH15	65217	broad.mit.edu	37	10	55780164	55780164	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:55780164C>T	ENST00000320301.6	-	20	2933	c.2539G>A	c.(2539-2541)Gac>Aac	p.D847N	PCDH15_ENST00000395438.1_Missense_Mutation_p.D847N|PCDH15_ENST00000395445.1_Missense_Mutation_p.D854N|PCDH15_ENST00000361849.3_Missense_Mutation_p.D847N|PCDH15_ENST00000409834.1_Missense_Mutation_p.D458N|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000373955.1_Missense_Mutation_p.D847N|PCDH15_ENST00000395430.1_Missense_Mutation_p.D847N|PCDH15_ENST00000437009.1_Missense_Mutation_p.D776N|PCDH15_ENST00000414778.1_Missense_Mutation_p.D852N|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000395432.2_Missense_Mutation_p.D810N|PCDH15_ENST00000395433.1_Missense_Mutation_p.D825N|PCDH15_ENST00000373965.2_Missense_Mutation_p.D854N|PCDH15_ENST00000395446.1_Intron	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	847	Cadherin 8. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)	p.D852N(1)|p.D847N(1)		NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				GCTCCAAGGTCGACATCTTTG	0.403										HNSCC(58;0.16)																											p.D810N												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2428A	10						.						126.0	127.0	127.0					10																	55780164		2203	4298	6501	55450170	SO:0001583	missense	65217	exon19			AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.2539G>A	10.37:g.55780164C>T	ENSP00000322604:p.Asp847Asn	Somatic		Capture	Illumina HiSeq	Phase_I	55450170	NM_001142767	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	37	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	C	33	5.264482	0.95399	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955	T;T;T;T;T;T;T;T;T;T;T;T	0.74002	-0.8;-0.8;-0.8;-0.8;-0.8;-0.8;-0.8;-0.8;-0.8;-0.8;-0.8;-0.8	5.92	5.92	0.95590	Cadherin (4);Cadherin-like (1);	.	.	.	.	D	0.90160	0.6925	M	0.93106	3.38	0.80722	D	1	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	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.91635	0.999;0.996;0.997;0.997;0.997;0.996;0.999;0.982;0.993;0.996;0.996;0.993;0.969;0.996	D	0.91586	0.5283	9	0.87932	D	0	.	19.922	0.97089	0.0:1.0:0.0:0.0	.	825;847;847;852;776;810;847;847;854;854;847;852;847;847	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	N	854;852;847;847;458;854;810;847;825;847;847;852;776;847	ENSP00000363076:D854N;ENSP00000410304:D852N;ENSP00000378826:D847N;ENSP00000386693:D458N;ENSP00000378832:D854N;ENSP00000378820:D810N;ENSP00000354950:D847N;ENSP00000378821:D825N;ENSP00000322604:D847N;ENSP00000378818:D847N;ENSP00000412628:D776N;ENSP00000363066:D847N	ENSP00000322604:D847N	D	-	1	0	PCDH15	55450170	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.076000	0.76806	2.794000	0.96219	0.650000	0.86243	GAC		0.403	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056	
FAM13C	220965	broad.mit.edu	37	10	61012600	61012600	+	Silent	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:61012600T>C	ENST00000373868.2	-	12	1578	c.1491A>G	c.(1489-1491)aaA>aaG	p.K497K	FAM13C_ENST00000468840.2_Silent_p.K414K|FAM13C_ENST00000277705.6_Silent_p.K517K|FAM13C_ENST00000435852.2_Silent_p.K497K|FAM13C_ENST00000442566.3_Silent_p.K518K|FAM13C_ENST00000373867.3_Silent_p.K413K|FAM13C_ENST00000419214.2_Silent_p.K399K	NM_198215.3	NP_937858.2	Q8NE31	FA13C_HUMAN	family with sequence similarity 13, member C	497								p.K497K(1)		NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(19)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						GAGCTGGTGGTTTTACTTCTT	0.453																																					p.K414K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1242G	10						.						172.0	151.0	158.0					10																	61012600		2203	4300	6503	60682606	SO:0001819	synonymous_variant	220965	exon13			U79304	CCDS31207.1, CCDS44406.1, CCDS7255.1, CCDS53538.1	10q21	2009-09-15	2009-01-20	2009-01-20	ENSG00000148541	ENSG00000148541			19371	protein-coding gene	gene with protein product			"""family with sequence similarity 13, member C1"""	FAM13C1			Standard	NM_001001971		Approved		uc001jkn.3	Q8NE31	OTTHUMG00000018277	ENST00000373868.2:c.1491A>G	10.37:g.61012600T>C		Somatic		Capture	Illumina HiSeq	Phase_I	60682606	NM_001143773	B7ZB77|Q5T631|Q6P2M3|Q99787	Silent	SNP	ENST00000373868.2	37	CCDS7255.1																																																																																				0.453	FAM13C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048162.2		
EGR2	1959	broad.mit.edu	37	10	64573913	64573913	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:64573913T>G	ENST00000242480.3	-	2	810	c.485A>C	c.(484-486)gAc>gCc	p.D162A	EGR2_ENST00000493899.2_5'Flank|EGR2_ENST00000439032.1_Missense_Mutation_p.D162A|EGR2_ENST00000411732.1_Missense_Mutation_p.D112A	NM_000399.3|NM_001136177.1	NP_000390.2|NP_001129649.1	P11161	EGR2_HUMAN	early growth response 2	162					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.D162A(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)					GTACAGGTGGTCCAGGTCAGG	0.632																																					p.D162A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A485C	10						.						104.0	101.0	102.0					10																	64573913		2203	4300	6503	64243919	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.485A>C	10.37:g.64573913T>G	ENSP00000242480:p.Asp162Ala	Somatic		Capture	Illumina HiSeq	Phase_I	64243919	NM_000399	B2R724|B3KRD7|Q68CZ5|Q8IV26|Q9UNA6	Missense_Mutation	SNP	ENST00000242480.3	37	CCDS7267.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.120627	0.77323	.	.	ENSG00000122877	ENST00000242480;ENST00000439032;ENST00000411732;ENST00000432380	T;T;T	0.12672	2.66;2.66;2.68	5.14	5.14	0.70334	.	0.102020	0.64402	D	0.000003	T	0.19604	0.0471	L	0.38175	1.15	0.52501	D	0.999954	P;P	0.50819	0.939;0.905	P;P	0.50934	0.654;0.46	T	0.00653	-1.1625	10	0.72032	D	0.01	-23.9138	14.7913	0.69844	0.0:0.0:0.0:1.0	.	112;162	P11161-2;P11161	.;EGR2_HUMAN	A	162;162;112;175	ENSP00000242480:D162A;ENSP00000402040:D162A;ENSP00000387634:D112A	ENSP00000242480:D162A	D	-	2	0	EGR2	64243919	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.900000	0.56295	2.146000	0.66826	0.528000	0.53228	GAC		0.632	EGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048245.2	NM_000399	
JMJD1C	221037	broad.mit.edu	37	10	64968176	64968176	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:64968176G>T	ENST00000399262.2	-	10	3471	c.3253C>A	c.(3253-3255)Cct>Act	p.P1085T	JMJD1C_ENST00000402544.1_Missense_Mutation_p.P866T|JMJD1C_ENST00000399251.1_Missense_Mutation_p.P866T|JMJD1C_ENST00000542921.1_Missense_Mutation_p.P903T	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	1085					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)	p.P1085T(1)|p.P866T(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					AAACTCTGAGGCACTGAGTGC	0.368																																					p.P866T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C2596A	10						.						202.0	191.0	194.0					10																	64968176		1872	4112	5984	64638182	SO:0001583	missense	221037	exon7			L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"""thyroid hormone receptor interactor 8"""	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.3253C>A	10.37:g.64968176G>T	ENSP00000382204:p.Pro1085Thr	Somatic		Capture	Illumina HiSeq	Phase_I	64638182	NM_004241	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	37	CCDS41532.1	.	.	.	.	.	.	.	.	.	.	G	12.91	2.079488	0.36662	.	.	ENSG00000171988	ENST00000399262;ENST00000402544;ENST00000399251;ENST00000542921	T;T;T;T	0.55052	0.89;0.54;2.45;0.89	5.59	3.72	0.42706	.	0.388548	0.29668	N	0.011509	T	0.41305	0.1153	L	0.51422	1.61	0.34815	D	0.738107	B;B;B	0.30021	0.265;0.265;0.265	B;B;B	0.28139	0.086;0.058;0.079	T	0.43814	-0.9368	10	0.12103	T	0.63	-5.9905	9.5616	0.39373	0.2165:0.0:0.7835:0.0	.	626;1085;903	A6PW35;Q15652;A0T124	.;JHD2C_HUMAN;.	T	1085;866;866;903	ENSP00000382204:P1085T;ENSP00000384990:P866T;ENSP00000382195:P866T;ENSP00000444682:P903T	ENSP00000382195:P866T	P	-	1	0	JMJD1C	64638182	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.533000	0.45667	0.697000	0.31718	0.563000	0.77884	CCT		0.368	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241	
ADAMTS14	140766	broad.mit.edu	37	10	72513565	72513565	+	Silent	SNP	G	G	A	rs370803022		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:72513565G>A	ENST00000373207.1	+	19	2739	c.2739G>A	c.(2737-2739)acG>acA	p.T913T	ADAMTS14_ENST00000373208.1_Silent_p.T916T	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	913	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.T916T(1)		NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						GGTGGGTGACGGAGGAGTGGG	0.617																																					p.T913T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2739A	10						.	G	,	0,4394		0,0,2197	15.0	12.0	13.0		2739,2748	-6.1	0.1	10		13	4,8574		0,4,4285	no	coding-synonymous,coding-synonymous	ADAMTS14	NM_080722.3,NM_139155.2	,	0,4,6482	AA,AG,GG		0.0466,0.0,0.0308	,	913/1224,916/1227	72513565	4,12968	2197	4289	6486	72183571	SO:0001819	synonymous_variant	140766	exon19			AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14899	protein-coding gene	gene with protein product		607506	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"""			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.2739G>A	10.37:g.72513565G>A		Somatic		Capture	Illumina HiSeq	Phase_I	72183571	NM_080722	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Silent	SNP	ENST00000373207.1	37	CCDS7306.1																																																																																				0.617	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722	
MICU1	10367	broad.mit.edu	37	10	74293517	74293517	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:74293517C>T	ENST00000361114.5	-	5	620	c.524G>A	c.(523-525)cGc>cAc	p.R175H	MICU1_ENST00000398761.4_Missense_Mutation_p.R175H|MICU1_ENST00000401998.3_Missense_Mutation_p.R175H	NM_001195518.1|NM_006077.3	NP_001182447.1|NP_006068.2	Q9BPX6	MICU1_HUMAN	mitochondrial calcium uptake 1	175					calcium ion import (GO:0070509)|calcium ion transmembrane import into mitochondrion (GO:0036444)|defense response (GO:0006952)|mitochondrial calcium ion homeostasis (GO:0051560)|mitochondrial calcium ion transport (GO:0006851)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|protein homooligomerization (GO:0051260)	calcium channel complex (GO:0034704)|integral component of mitochondrial membrane (GO:0032592)|intracellular (GO:0005622)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|uniplex complex (GO:1990246)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)	p.R175H(1)									TCCATCAAAGCGTTTTATTAT	0.294																																					p.R175H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G524A	10						.						74.0	74.0	74.0					10																	74293517		1800	4065	5865	73963523	SO:0001583	missense	10367	exon5			Y17711	CCDS55714.1, CCDS55715.1	10q22.1	2013-01-10	2011-06-23	2011-06-23	ENSG00000107745	ENSG00000107745		"""EF-hand domain containing"""	1530	protein-coding gene	gene with protein product		605084	"""calcium binding atopy-related autoantigen 1"""	CBARA1		9806765, 20693986	Standard	NM_006077		Approved	CALC, EFHA3, FLJ12684	uc001jtb.2	Q9BPX6	OTTHUMG00000018437	ENST00000361114.5:c.524G>A	10.37:g.74293517C>T	ENSP00000354415:p.Arg175His	Somatic		Capture	Illumina HiSeq	Phase_I	73963523	NM_006077	A8MV96|B3KN20|B4DJH9|B4DPI1|B5MBY3|D3YTJ3|O75785|Q9H9N6|Q9UFX0	Missense_Mutation	SNP	ENST00000361114.5	37	CCDS55715.1	.	.	.	.	.	.	.	.	.	.	C	17.71	3.457643	0.63401	.	.	ENSG00000107745	ENST00000361114;ENST00000398761;ENST00000401998	T;T;T	0.80824	-1.35;-1.42;-1.35	5.54	5.54	0.83059	EF-hand-like domain (1);	0.056684	0.64402	D	0.000001	T	0.73202	0.3557	L	0.56124	1.755	0.80722	D	1	P	0.41546	0.754	B	0.26693	0.072	T	0.75659	-0.3241	10	0.38643	T	0.18	.	17.2732	0.87109	0.0:1.0:0.0:0.0	.	175	Q9BPX6	MICU1_HUMAN	H	175	ENSP00000354415:R175H;ENSP00000381745:R175H;ENSP00000384068:R175H	ENSP00000354415:R175H	R	-	2	0	MICU1	73963523	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	4.191000	0.58372	2.610000	0.88304	0.557000	0.71058	CGC		0.294	MICU1-002	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048586.1	NM_006077	
USP54	159195	broad.mit.edu	37	10	75279710	75279710	+	Silent	SNP	C	C	T	rs369618128		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:75279710C>T	ENST00000339859.4	-	18	2623	c.2523G>A	c.(2521-2523)acG>acA	p.T841T	USP54_ENST00000428547.1_Silent_p.T691T|RP11-137L10.6_ENST00000597958.1_RNA|RP11-137L10.6_ENST00000593790.1_RNA|USP54_ENST00000497106.1_Intron|RP11-137L10.6_ENST00000600206.1_RNA|USP54_ENST00000422491.2_Silent_p.T23T|RP11-137L10.6_ENST00000595069.1_RNA|USP54_ENST00000408019.1_Silent_p.T841T|USP54_ENST00000394811.2_5'UTR			Q70EL1	UBP54_HUMAN	ubiquitin specific peptidase 54	841					ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitinyl hydrolase activity (GO:0036459)	p.T841T(1)		breast(5)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)	30	Prostate(51;0.0112)					CTCTGCTGTGCGTGCTACAGC	0.443																																					p.T841T	Colon(195;880 2046 8854 25025 38456)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2523A	10						.	C		1,4109		0,1,2054	35.0	37.0	36.0		2523	-1.8	1.0	10		36	0,8434		0,0,4217	no	coding-synonymous	USP54	NM_152586.3		0,1,6271	TT,TC,CC		0.0,0.0243,0.0080		841/1685	75279710	1,12543	2055	4217	6272	74949716	SO:0001819	synonymous_variant	159195	exon17			AJ583820	CCDS7329.2	10q22.3	2006-09-26	2005-08-08	2004-01-30	ENSG00000166348	ENSG00000166348		"""Ubiquitin-specific peptidases"""	23513	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 29"", ""ubiquitin specific protease 54"""	C10orf29		14715245	Standard	NM_152586		Approved	FLJ37318, bA137L10.3, bA137L10.4	uc001juo.3	Q70EL1	OTTHUMG00000018469	ENST00000339859.4:c.2523G>A	10.37:g.75279710C>T		Somatic		Capture	Illumina HiSeq	Phase_I	74949716	NM_152586	A1L4Q4|A3KFK3|A3KFK5|A3KFK6|A3KFK7|A6PVS4|A6PVS5|A6PVS6|A6PVS7|B3KVY1|B9ZVM1|Q5F2F4|Q6P1N6|Q6ZSP1|Q6ZSR1|Q6ZTM0|Q8N1X2	Silent	SNP	ENST00000339859.4	37	CCDS7329.2																																																																																				0.443	USP54-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316563.2	NM_152586	
DYDC2	84332	broad.mit.edu	37	10	82126597	82126597	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:82126597G>A	ENST00000372199.1	+	6	1022	c.424G>A	c.(424-426)Gct>Act	p.A142T	DYDC2_ENST00000372198.1_Missense_Mutation_p.A156T|DYDC2_ENST00000256039.2_Missense_Mutation_p.A142T|DYDC2_ENST00000372197.1_Missense_Mutation_p.A142T|DYDC2_ENST00000444807.2_Missense_Mutation_p.A142T			Q96IM9	DYDC2_HUMAN	DPY30 domain containing 2	142								p.A142T(1)		breast(1)|large_intestine(3)|lung(6)|skin(1)	11			Colorectal(32;0.229)			TTCAGAGTCTGCTGGCCAGAT	0.478																																					p.A142T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G424A	10						.						112.0	116.0	115.0					10																	82126597		2203	4300	6503	82116577	SO:0001583	missense	84332	exon5			BC018606	CCDS7367.1, CCDS58088.1	10q23.1	2006-06-16			ENSG00000133665	ENSG00000133665			23468	protein-coding gene	gene with protein product						12477932	Standard	NM_032372		Approved	bA36D19.6, MGC16186	uc031pwk.1	Q96IM9	OTTHUMG00000018610	ENST00000372199.1:c.424G>A	10.37:g.82126597G>A	ENSP00000361273:p.Ala142Thr	Somatic		Capture	Illumina HiSeq	Phase_I	82116577	NM_032372	D3DWD6|Q5QP07|Q5QP11	Missense_Mutation	SNP	ENST00000372199.1	37	CCDS7367.1	.	.	.	.	.	.	.	.	.	.	G	11.30	1.599013	0.28534	.	.	ENSG00000133665	ENST00000372199;ENST00000372198;ENST00000372197;ENST00000444807;ENST00000256039	T;T;T;T;T	0.52526	0.71;0.66;0.71;0.71;0.71	4.2	-1.46	0.08800	.	1.761320	0.03217	N	0.176998	T	0.27489	0.0675	N	0.14661	0.345	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.13388	-1.0511	10	0.46703	T	0.11	0.358	1.0854	0.01651	0.2161:0.3386:0.2676:0.1777	.	142	Q96IM9	DYDC2_HUMAN	T	142;156;142;142;142	ENSP00000361273:A142T;ENSP00000361272:A156T;ENSP00000361271:A142T;ENSP00000410285:A142T;ENSP00000256039:A142T	ENSP00000256039:A142T	A	+	1	0	DYDC2	82116577	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.255000	0.08769	-0.274000	0.09232	-0.136000	0.14681	GCT		0.478	DYDC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000049063.1	NM_032372	
LGI1	9211	broad.mit.edu	37	10	95557002	95557002	+	Silent	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:95557002C>A	ENST00000371418.4	+	8	1376	c.1116C>A	c.(1114-1116)tcC>tcA	p.S372S	LGI1_ENST00000371413.3_Intron|LGI1_ENST00000542308.1_Silent_p.S324S	NM_005097.2	NP_005088.1	O95970	LGI1_HUMAN	leucine-rich, glioma inactivated 1	372					axon guidance (GO:0007411)|cell proliferation (GO:0008283)|nervous system development (GO:0007399)|neuron projection development (GO:0031175)|positive regulation of cell growth (GO:0030307)|positive regulation of synaptic transmission (GO:0050806)|protein homooligomerization (GO:0051260)	cell junction (GO:0030054)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|synapse (GO:0045202)	receptor binding (GO:0005102)	p.S372S(1)		central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(18)|ovary(2)|skin(1)	29		Colorectal(252;0.124)				CCCATCAATCCTTACACGCGT	0.413																																					p.S372S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1116A	10						.						91.0	83.0	86.0					10																	95557002		2203	4300	6503	95546992	SO:0001819	synonymous_variant	9211	exon8			AF055636	CCDS7431.1	10q24	2008-08-01	2002-06-05		ENSG00000108231	ENSG00000108231			6572	protein-coding gene	gene with protein product		604619	"""epilepsy, partial"""	EPT		9879993, 11978770, 15079011	Standard	NM_005097		Approved	IB1099, ETL1, EPITEMPIN	uc001kjc.4	O95970	OTTHUMG00000018777	ENST00000371418.4:c.1116C>A	10.37:g.95557002C>A		Somatic		Capture	Illumina HiSeq	Phase_I	95546992	NM_005097	A8K0Z1|B4E1S0|Q5W001|Q5W002|Q8NI23|Q96LF5	Silent	SNP	ENST00000371418.4	37	CCDS7431.1																																																																																				0.413	LGI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049445.1	NM_005097	
PLCE1	51196	broad.mit.edu	37	10	95892086	95892086	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:95892086C>T	ENST00000371380.3	+	2	1597	c.1362C>T	c.(1360-1362)cgC>cgT	p.R454R	PLCE1_ENST00000260766.3_Silent_p.R454R|PLCE1_ENST00000371385.3_Silent_p.R146R|PLCE1_ENST00000371375.1_Silent_p.R146R			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	454					activation of MAPK activity (GO:0000187)|calcium-mediated signaling (GO:0019722)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|diacylglycerol biosynthetic process (GO:0006651)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerulus development (GO:0032835)|heart development (GO:0007507)|inositol phosphate metabolic process (GO:0043647)|inositol phosphate-mediated signaling (GO:0048016)|lipid catabolic process (GO:0016042)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipid metabolic process (GO:0006644)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of GTPase activity (GO:0043547)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of protein kinase activity (GO:0045859)|regulation of Ras protein signal transduction (GO:0046578)|regulation of smooth muscle contraction (GO:0006940)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|guanyl-nucleotide exchange factor activity (GO:0005085)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|Ras GTPase binding (GO:0017016)|receptor signaling protein activity (GO:0005057)	p.R454R(1)		liver(1)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.0458)				GTGAGTATCGCGCCACCCTCC	0.507																																					p.R146R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C438T	10						.						151.0	155.0	154.0					10																	95892086		2118	4231	6349	95882076	SO:0001819	synonymous_variant	51196	exon2				CCDS41552.1, CCDS53555.1	10q23	2010-02-22			ENSG00000138193	ENSG00000138193	3.1.4.11		17175	protein-coding gene	gene with protein product	"""nephrosis type 3"""	608414				11022047, 11022048	Standard	NM_016341		Approved	KIAA1516, PLCE, NPHS3	uc001kjk.3	Q9P212	OTTHUMG00000018789	ENST00000371380.3:c.1362C>T	10.37:g.95892086C>T		Somatic		Capture	Illumina HiSeq	Phase_I	95882076	NM_001165979	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Silent	SNP	ENST00000371380.3	37	CCDS41552.1																																																																																				0.507	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	NM_016341	
CYP2C19	1557	broad.mit.edu	37	10	96534945	96534945	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:96534945T>G	ENST00000371321.3	+	2	381	c.299T>G	c.(298-300)tTc>tGc	p.F100C	CYP2C19_ENST00000464755.1_3'UTR	NM_000769.1	NP_000760	P33261	CP2CJ_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 19	100					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|heterocycle metabolic process (GO:0046483)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	(R)-limonene 6-monooxygenase activity (GO:0052741)|(S)-limonene 6-monooxygenase activity (GO:0018675)|(S)-limonene 7-monooxygenase activity (GO:0018676)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxygen binding (GO:0019825)|steroid hydroxylase activity (GO:0008395)	p.F100C(1)		central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	43		Colorectal(252;0.09)		all cancers(201;6.02e-07)|KIRC - Kidney renal clear cell carcinoma(50;0.0672)|Kidney(138;0.0838)	Acenocoumarol(DB01418)|Acetylsalicylic acid(DB00945)|Adinazolam(DB00546)|Almotriptan(DB00918)|Aminoglutethimide(DB00357)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amoxicillin(DB01060)|Amprenavir(DB00701)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Arformoterol(DB01274)|Artemether(DB06697)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Benzatropine(DB00245)|Bicalutamide(DB01128)|Bifonazole(DB04794)|Bortezomib(DB00188)|Bromazepam(DB01558)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carisoprodol(DB00395)|Chloramphenicol(DB00446)|Chlorpropamide(DB00672)|Cholecalciferol(DB00169)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cisapride(DB00604)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clevidipine(DB04920)|Clobazam(DB00349)|Clomipramine(DB01242)|Clopidogrel(DB00758)|Clotiazepam(DB01559)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronabinol(DB00470)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enfuvirtide(DB00109)|Enzalutamide(DB08899)|Escitalopram(DB01175)|Esomeprazole(DB00736)|Estradiol(DB00783)|Ethanol(DB00898)|Ethotoin(DB00754)|Etoricoxib(DB01628)|Etravirine(DB06414)|Famotidine(DB00927)|Felbamate(DB00949)|Fluconazole(DB00196)|Flunitrazepam(DB01544)|Fluoxetine(DB00472)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Fosphenytoin(DB01320)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Gliclazide(DB01120)|Glucosamine(DB01296)|Glyburide(DB01016)|Guanfacine(DB01018)|Haloperidol(DB00502)|Hexobarbital(DB01355)|Ibuprofen(DB01050)|Ifosfamide(DB01181)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Indomethacin(DB00328)|Isoniazid(DB00951)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Levomilnacipran(DB08918)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Losartan(DB00678)|Lovastatin(DB00227)|LULICONAZOLE(DB08933)|Lumiracoxib(DB01283)|MACITENTAN(DB08932)|Melatonin(DB01065)|Memantine(DB01043)|Meprobamate(DB00371)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methsuximide(DB05246)|Methylphenobarbital(DB00849)|Metoprolol(DB00264)|Miconazole(DB01110)|Moclobemide(DB01171)|Modafinil(DB00745)|Nelfinavir(DB00220)|Nicardipine(DB00622)|Nicotine(DB00184)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Norethindrone(DB00717)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ospemifene(DB04938)|Oxcarbazepine(DB00776)|Oxiconazole(DB00239)|Pantoprazole(DB00213)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Pentobarbital(DB00312)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phensuximide(DB00832)|Phenytoin(DB00252)|Pimozide(DB01100)|Pioglitazone(DB01132)|Pipotiazine(DB01621)|Podofilox(DB01179)|Prasugrel(DB06209)|Praziquantel(DB01058)|Prednisone(DB00635)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Propofol(DB00818)|Propranolol(DB00571)|Quazepam(DB01589)|Quetiapine(DB01224)|Quinine(DB00468)|Rabeprazole(DB01129)|Ramelteon(DB00980)|Ranitidine(DB00863)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sitaxentan(DB06268)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Tamoxifen(DB00675)|Tapentadol(DB06204)|Telmisartan(DB00966)|Temazepam(DB00231)|Teniposide(DB00444)|Terbinafine(DB00857)|Testosterone(DB00624)|Thalidomide(DB01041)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Timolol(DB00373)|Tioconazole(DB01007)|Tipranavir(DB00932)|Tofacitinib(DB08895)|Tolbutamide(DB01124)|Tolterodine(DB01036)|Topiramate(DB00273)|Torasemide(DB00214)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Trimethadione(DB00347)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zidovudine(DB00495)|Zolpidem(DB00425)|Zonisamide(DB00909)	AGAGGCCATTTCCCACTGGCT	0.498																																					p.F100C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T299G	10						.						217.0	203.0	208.0					10																	96534945		2203	4300	6503	96524935	SO:0001583	missense	1557	exon2			M61854	CCDS7436.1	10q24	2007-12-14	2003-01-14		ENSG00000165841	ENSG00000165841		"""Cytochrome P450s"""	2621	protein-coding gene	gene with protein product		124020	"""cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 19"""	CYP2C		2009263, 8530044	Standard	NM_000769		Approved	P450IIC19, CPCJ	uc010qnz.2	P33261	OTTHUMG00000018799	ENST00000371321.3:c.299T>G	10.37:g.96534945T>G	ENSP00000360372:p.Phe100Cys	Somatic		Capture	Illumina HiSeq	Phase_I	96524935	NM_000769	P33259|Q8WZB1|Q8WZB2|Q9UCD4	Missense_Mutation	SNP	ENST00000371321.3	37	CCDS7436.1	.	.	.	.	.	.	.	.	.	.	T	9.971	1.225408	0.22457	.	.	ENSG00000165841	ENST00000371321	T	0.68331	-0.32	3.74	1.17	0.20885	.	0.538541	0.15937	U	0.237389	T	0.68348	0.2991	M	0.87097	2.86	0.09310	N	1	B	0.26002	0.139	B	0.34824	0.19	T	0.64015	-0.6506	10	0.56958	D	0.05	.	4.1629	0.10293	0.1786:0.1075:0.0:0.7138	.	100	P33261	CP2CJ_HUMAN	C	100	ENSP00000360372:F100C	ENSP00000360372:F100C	F	+	2	0	CYP2C19	96524935	0.033000	0.19621	0.000000	0.03702	0.020000	0.10135	2.382000	0.44345	0.004000	0.14682	0.333000	0.21579	TTC		0.498	CYP2C19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049490.1	NM_000769	
DPYSL4	10570	broad.mit.edu	37	10	134015504	134015504	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:134015504G>A	ENST00000338492.4	+	11	1329	c.1165G>A	c.(1165-1167)Gcc>Acc	p.A389T	DPYSL4_ENST00000368627.1_Missense_Mutation_p.A289T|DPYSL4_ENST00000368629.1_Missense_Mutation_p.A289T	NM_006426.2	NP_006417.2	O14531	DPYL4_HUMAN	dihydropyrimidinase-like 4	389					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.A389T(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)		TACAAATGCTGCCAAAATCTT	0.567																																					p.A389T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1165A	10						.						105.0	104.0	105.0					10																	134015504		2203	4300	6503	133865494	SO:0001583	missense	10570	exon11			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.1165G>A	10.37:g.134015504G>A	ENSP00000339850:p.Ala389Thr	Somatic		Capture	Illumina HiSeq	Phase_I	133865494	NM_006426	B2RMQ1|D3DRG5|O00240|Q5T0Q7	Missense_Mutation	SNP	ENST00000338492.4	37	CCDS7665.1	.	.	.	.	.	.	.	.	.	.	G	33	5.219356	0.95139	.	.	ENSG00000151640	ENST00000338492;ENST00000368629;ENST00000368627	D;D;D	0.95482	-3.72;-3.72;-3.72	4.48	4.48	0.54585	Amidohydrolase 1 (1);Metal-dependent hydrolase, composite domain (1);	0.000000	0.85682	D	0.000000	D	0.98397	0.9467	H	0.97265	3.97	0.50813	D	0.999895	D	0.69078	0.997	P	0.60886	0.88	D	0.99847	1.1067	10	0.87932	D	0	-22.3051	17.4178	0.87505	0.0:0.0:1.0:0.0	.	389	O14531	DPYL4_HUMAN	T	389;289;289	ENSP00000339850:A389T;ENSP00000357618:A289T;ENSP00000357616:A289T	ENSP00000339850:A389T	A	+	1	0	DPYSL4	133865494	1.000000	0.71417	0.998000	0.56505	0.929000	0.56500	9.134000	0.94467	2.317000	0.78254	0.650000	0.86243	GCC		0.567	DPYSL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051050.2		
PAOX	196743	broad.mit.edu	37	10	135193855	135193855	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:135193855delG	ENST00000278060.5	+	2	617	c.534delG	c.(532-534)aagfs	p.K178fs	PAOX_ENST00000368535.2_3'UTR|PAOX_ENST00000480071.2_Frame_Shift_Del_p.K178fs|PAOX_ENST00000357296.3_Frame_Shift_Del_p.K178fs|PAOX_ENST00000368539.4_Intron|AL360181.1_ENST00000597657.1_5'Flank	NM_152911.2	NP_690875.1	Q6QHF9	PAOX_HUMAN	polyamine oxidase (exo-N4-amino)	316					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)|positive regulation of spermidine biosynthetic process (GO:1901307)|putrescine biosynthetic process (GO:0009446)|putrescine catabolic process (GO:0009447)|small molecule metabolic process (GO:0044281)|spermidine catabolic process (GO:0046203)|spermine catabolic process (GO:0046208)|xenobiotic metabolic process (GO:0006805)	peroxisomal matrix (GO:0005782)	N(1),N(12)-diacetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity (GO:0052899)|N1-acetylspermidine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity (GO:0052904)|N1-acetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity (GO:0052903)|polyamine oxidase activity (GO:0046592)|receptor binding (GO:0005102)|spermidine:oxygen oxidoreductase (3-aminopropanal-forming) activity (GO:0052902)|spermine:oxygen oxidoreductase (spermidine-forming) activity (GO:0052901)	p.K178fs*2(2)		cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|urinary_tract(2)	23		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;4.39e-07)|OV - Ovarian serous cystadenocarcinoma(35;1.21e-06)|Epithelial(32;1.94e-06)		AGACCAGGAAGCTGAAGCTGG	0.617																																					p.K178fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.534delG	10						.						35.0	35.0	35.0					10																	135193855		2200	4300	6500	135043845	SO:0001589	frameshift_variant	196743	exon2			BC032778	CCDS7682.1, CCDS7683.1, CCDS7684.1	10q26.3	2003-11-13			ENSG00000148832	ENSG00000148832			20837	protein-coding gene	gene with protein product		615853				12660232	Standard	NM_207127		Approved	PAO	uc001lmv.3	Q6QHF9	OTTHUMG00000019318	ENST00000278060.5:c.534delG	10.37:g.135193855delG	ENSP00000278060:p.Lys178fs	Somatic		Capture	Illumina HiSeq	Phase_I	135043845	NM_152911	D3DXI6|Q5VWY0|Q6QHF5|Q6QHF6|Q6QHF7|Q6QHF8|Q6QHG0|Q6QHG1|Q6QHG2|Q6QHG3|Q6QHG4|Q6QHG5|Q6QHG6|Q86WP9|Q8N555|Q8NCX3	Frame_Shift_Del	DEL	ENST00000278060.5	37	CCDS7683.1																																																																																				0.617	PAOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051146.2	NM_152911	
IFIT1	3434	broad.mit.edu	37	10	91163033	91163033	+	Frame_Shift_Del	DEL	A	A	-	rs74435957		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr10:91163033delA	ENST00000371804.3	+	2	1168	c.1001delA	c.(1000-1002)gaafs	p.E334fs	LIPA_ENST00000371837.1_Intron|IFIT1_ENST00000546318.1_Frame_Shift_Del_p.E303fs	NM_001270927.1|NM_001548.4	NP_001257856.1|NP_001539.3	P09914	IFIT1_HUMAN	interferon-induced protein with tetratricopeptide repeats 1	334					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.K336fs*9(1)		breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(2)|prostate(2)|upper_aerodigestive_tract(1)	15						TCTGCAGTGGAAAAAAAGCCC	0.393																																					p.E334fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1001delA	10						.						45.0	45.0	45.0					10																	91163033		2203	4299	6502	91153013	SO:0001589	frameshift_variant	3434	exon2			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.1001delA	10.37:g.91163033delA	ENSP00000360869:p.Glu334fs	Somatic		Capture	Illumina HiSeq	Phase_I	91153013	NM_001548	B3KS50|D3DR31|Q5T7J1|Q96QM5	Frame_Shift_Del	DEL	ENST00000371804.3	37	CCDS31243.1																																																																																				0.393	IFIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049302.1	NM_001548	
EIF4G2	1982	broad.mit.edu	37	11	10822534	10822534	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:10822534C>T	ENST00000526148.1	-	15	2024	c.1514G>A	c.(1513-1515)cGc>cAc	p.R505H	EIF4G2_ENST00000525681.1_Missense_Mutation_p.R505H|EIF4G2_ENST00000339995.5_Missense_Mutation_p.R505H|EIF4G2_ENST00000396525.2_Missense_Mutation_p.R467H|SNORD97_ENST00000459187.1_RNA|RP11-685M7.5_ENST00000532365.1_RNA	NM_001172705.1	NP_001166176			eukaryotic translation initiation factor 4 gamma, 2									p.R505H(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	43				all cancers(16;2.8e-07)|Epithelial(150;4.18e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		TGTTTGAGTGCGTGGTGGTTG	0.438																																					p.R505H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1514A	11						.						224.0	208.0	213.0					11																	10822534		2201	4294	6495	10779110	SO:0001583	missense	1982	exon15			U73824	CCDS31428.1, CCDS41618.1	11p15	2005-09-29			ENSG00000110321	ENSG00000110321			3297	protein-coding gene	gene with protein product		602325				9030685, 9032289	Standard	NM_001042559		Approved	DAP5, NAT1, p97	uc001mjc.3	P78344	OTTHUMG00000165823	ENST00000526148.1:c.1514G>A	11.37:g.10822534C>T	ENSP00000433664:p.Arg505His	Somatic		Capture	Illumina HiSeq	Phase_I	10779110	NM_001418		Missense_Mutation	SNP	ENST00000526148.1	37	CCDS31428.1	.	.	.	.	.	.	.	.	.	.	C	17.43	3.387523	0.61956	.	.	ENSG00000110321	ENST00000526148;ENST00000525681;ENST00000339995;ENST00000396525;ENST00000429377;ENST00000531180	T;T;T;T;T	0.48836	2.15;2.15;2.15;2.21;0.8	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.50120	0.1597	L	0.40543	1.245	0.43145	D	0.994903	D;B;D	0.67145	0.986;0.096;0.996	B;B;P	0.51170	0.36;0.006;0.661	T	0.26710	-1.0095	9	0.12103	T	0.63	-4.0016	20.3206	0.98668	0.0:1.0:0.0:0.0	.	467;505;578	P78344-2;P78344;B4DZF2	.;IF4G2_HUMAN;.	H	505;505;505;467;578;10	ENSP00000433664:R505H;ENSP00000433371:R505H;ENSP00000340281:R505H;ENSP00000379778:R467H;ENSP00000433561:R10H	ENSP00000340281:R505H	R	-	2	0	EIF4G2	10779110	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.415000	0.73328	2.809000	0.96659	0.655000	0.94253	CGC		0.438	EIF4G2-006	KNOWN	alternative_5_UTR|non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386603.1	NM_001418	
KDELC2	143888	broad.mit.edu	37	11	108350130	108350130	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:108350130C>T	ENST00000323468.5	-	6	1256	c.1191G>A	c.(1189-1191)tcG>tcA	p.S397S	KDELC2_ENST00000532730.1_Intron|KDELC2_ENST00000375648.1_Silent_p.S341S|KDELC2_ENST00000434945.2_Silent_p.S341S	NM_153705.4	NP_714916.3	Q7Z4H8	KDEL2_HUMAN	KDEL (Lys-Asp-Glu-Leu) containing 2	397						endoplasmic reticulum (GO:0005783)		p.S397S(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	13		all_cancers(61;1.38e-11)|all_epithelial(67;3.16e-07)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;6.93e-06)|BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|all cancers(92;0.00016)|OV - Ovarian serous cystadenocarcinoma(223;0.132)|Colorectal(284;0.14)		CATAATATGGCGAGTCCTGCT	0.393																																					p.S397S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1191A	11						.						83.0	80.0	81.0					11																	108350130		1868	4115	5983	107855340	SO:0001819	synonymous_variant	143888	exon6			AF533708	CCDS41711.1	11q32	2010-11-18			ENSG00000178202	ENSG00000178202			28496	protein-coding gene	gene with protein product						12975309	Standard	NM_153705		Approved	MGC33424	uc001pkj.2	Q7Z4H8	OTTHUMG00000166535	ENST00000323468.5:c.1191G>A	11.37:g.108350130C>T		Somatic		Capture	Illumina HiSeq	Phase_I	107855340	NM_153705	Q6UWW2|Q6ZUM9|Q8N7L8|Q8NE24	Silent	SNP	ENST00000323468.5	37	CCDS41711.1																																																																																				0.393	KDELC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390273.1	NM_153705	
EXPH5	23086	broad.mit.edu	37	11	108382998	108382998	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:108382998T>A	ENST00000265843.4	-	6	3346	c.3236A>T	c.(3235-3237)aAt>aTt	p.N1079I	EXPH5_ENST00000428840.1_Missense_Mutation_p.N1003I|EXPH5_ENST00000443411.1_Missense_Mutation_p.N891I|EXPH5_ENST00000525344.1_Missense_Mutation_p.N1072I|EXPH5_ENST00000524840.1_5'Flank	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	1079					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)	p.N1079I(1)		breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		GGAACATTCATTCGCTGACTC	0.423																																					p.N1079I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3236T	11						.						105.0	106.0	106.0					11																	108382998		2201	4298	6499	107888208	SO:0001583	missense	23086	exon6				CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.3236A>T	11.37:g.108382998T>A	ENSP00000265843:p.Asn1079Ile	Somatic		Capture	Illumina HiSeq	Phase_I	107888208	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	.	.	.	.	.	.	.	.	.	.	T	10.97	1.501724	0.26949	.	.	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000526312;ENST00000533052	T;T;T;T;T;T	0.04049	4.31;4.24;4.09;4.31;4.16;3.72	5.5	-6.24	0.02046	.	0.923729	0.09356	N	0.813427	T	0.02304	0.0071	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.45877	-0.9231	10	0.72032	D	0.01	0.0283	2.7283	0.05220	0.1103:0.1857:0.4082:0.2958	.	1079	Q8NEV8	EXPH5_HUMAN	I	1079;1003;891;1072;1003;891	ENSP00000265843:N1079I;ENSP00000391966:N1003I;ENSP00000411390:N891I;ENSP00000432546:N1072I;ENSP00000432683:N1003I;ENSP00000446434:N891I	ENSP00000265843:N1079I	N	-	2	0	EXPH5	107888208	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.986000	0.03747	-0.745000	0.04772	-1.656000	0.00753	AAT		0.423	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
ALG9	79796	broad.mit.edu	37	11	111711402	111711402	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:111711402G>A	ENST00000531154.1	-	10	1108	c.636C>T	c.(634-636)ggC>ggT	p.G212G	ALG9_ENST00000527228.1_5'UTR|ALG9_ENST00000398006.2_Silent_p.G212G|ALG9_ENST00000524880.1_3'UTR	NM_024740.2	NP_079016.2	Q9H6U8	ALG9_HUMAN	ALG9, alpha-1,2-mannosyltransferase	383					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	dol-P-Man:Man(6)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase activity (GO:0052926)|dol-P-Man:Man(8)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase activity (GO:0052918)	p.G212G(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;6.81e-07)|BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|all cancers(92;1.3e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0587)		GAGCCACAGCGCCACAGAGAC	0.393																																					p.R384C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1150T	11						.						97.0	102.0	100.0					11																	111711402		1903	4123	6026	111216612	SO:0001819	synonymous_variant	79796	exon10				CCDS41714.1, CCDS53709.1, CCDS73379.1, CCDS73380.1	11q23	2013-02-26	2013-02-26	2004-08-26	ENSG00000086848	ENSG00000086848	2.4.1.259, 2.4.1.261	"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"""	15672	protein-coding gene	gene with protein product	"""dolichyl-P-Man:Man(6)GlcNAc(2)-PP-dolichol alpha-1,2-mannosyltransferase"", ""dolichyl-P-Man:Man(8)GlcNAc(2)-PP-dolichol alpha-1,2-mannosyltransferase"", ""dol-P-Man dependent alpha-1,2-mannosyltransferase"""	606941	"""disrupted in bipolar affective disorder 1"", ""asparagine-linked glycosylation 9 homolog (yeast, alpha 1,2 mannosyltransferase)"", ""asparagine-linked glycosylation 9, alpha- 1,2-mannosyltransferase homolog (S. cerevisiae, alpha- 1,2-mannosyltransferase)"", ""asparagine-linked glycosylation 9, alpha-1,2-mannosyltransferase homolog (S. cerevisiae)"""	DIBD1		12030331, 15148656	Standard	NM_024740		Approved		uc021qql.1	Q9H6U8	OTTHUMG00000166819	ENST00000531154.1:c.636C>T	11.37:g.111711402G>A		Somatic		Capture	Illumina HiSeq	Phase_I	111216612	NM_024740	Q6ZMD5|Q7Z4R4|Q96GS7|Q96PB9|Q9H068	Silent	SNP	ENST00000531154.1	37	CCDS41714.1																																																																																				0.393	ALG9-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000391485.1	NM_024740	
DKK3	27122	broad.mit.edu	37	11	11989956	11989956	+	Missense_Mutation	SNP	G	G	A	rs377759604		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:11989956G>A	ENST00000396505.2	-	5	752	c.514C>T	c.(514-516)Cgg>Tgg	p.R172W	DKK3_ENST00000450094.2_Missense_Mutation_p.R144W|DKK3_ENST00000326932.4_Missense_Mutation_p.R172W|DKK3_ENST00000525493.1_Missense_Mutation_p.R172W|DKK3_ENST00000527132.1_Intron	NM_015881.5	NP_056965.3	Q9UBP4	DKK3_HUMAN	dickkopf WNT signaling pathway inhibitor 3	172	DKK-type Cys-1.				adrenal gland development (GO:0030325)|anatomical structure morphogenesis (GO:0009653)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of transcription, DNA-templated (GO:0045892)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)		p.R172W(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(1)|pancreas(1)	8				Epithelial(150;0.000502)		CTCTGGCCCCGGCATGGCTGG	0.647																																					p.R172W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C514T	11						.	G	TRP/ARG,TRP/ARG,TRP/ARG	0,4402		0,0,2201	58.0	53.0	55.0		514,514,514	4.5	1.0	11		55	1,8587	1.2+/-3.3	0,1,4293	no	missense,missense,missense	DKK3	NM_001018057.1,NM_013253.4,NM_015881.5	101,101,101	0,1,6494	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	172/351,172/351,172/351	11989956	1,12989	2201	4294	6495	11946532	SO:0001583	missense	27122	exon4			AF177396	CCDS7808.1	11p15.3	2013-05-15	2013-05-15		ENSG00000050165	ENSG00000050165			2893	protein-coding gene	gene with protein product	"""regulated in glioma"""	605416	"""dickkopf (Xenopus laevis) homolog 3"", ""dickkopf 3 homolog (Xenopus laevis)"""			10570958	Standard	XM_006718177		Approved	REIC, RIG	uc001mjv.3	Q9UBP4	OTTHUMG00000165709	ENST00000396505.2:c.514C>T	11.37:g.11989956G>A	ENSP00000379762:p.Arg172Trp	Somatic		Capture	Illumina HiSeq	Phase_I	11946532	NM_001018057	A8K1I2|D3DQW1|Q9ULB7	Missense_Mutation	SNP	ENST00000396505.2	37	CCDS7808.1	.	.	.	.	.	.	.	.	.	.	G	16.31	3.086040	0.55861	0.0	1.16E-4	ENSG00000050165	ENST00000396505;ENST00000326932;ENST00000366345;ENST00000525493;ENST00000450094;ENST00000326914;ENST00000533813;ENST00000534511	T;T;T;T;T;T	0.49139	1.9;1.9;1.91;1.24;1.68;0.79	5.45	4.46	0.54185	Dickkopf, N-terminal cysteine-rich (1);	0.300218	0.34245	N	0.004130	T	0.57198	0.2037	L	0.44542	1.39	0.36164	D	0.848322	D;D;D	0.89917	1.0;1.0;1.0	D;P;D	0.70935	0.971;0.874;0.965	T	0.65755	-0.6091	10	0.87932	D	0	-21.3197	10.5167	0.44894	0.0:0.0:0.6256:0.3744	.	172;144;172	F6SYF8;E7EUD0;Q9UBP4	.;.;DKK3_HUMAN	W	172;172;115;172;144;16;172;144	ENSP00000379762:R172W;ENSP00000314910:R172W;ENSP00000433112:R172W;ENSP00000398365:R144W;ENSP00000435269:R172W;ENSP00000436645:R144W	ENSP00000314730:R16W	R	-	1	2	DKK3	11946532	1.000000	0.71417	1.000000	0.80357	0.361000	0.29550	2.424000	0.44714	2.550000	0.86006	0.655000	0.94253	CGG		0.647	DKK3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385863.1	NM_013253	
DKK3	27122	broad.mit.edu	37	11	12020303	12020303	+	Silent	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:12020303T>C	ENST00000396505.2	-	4	613	c.375A>G	c.(373-375)caA>caG	p.Q125Q	DKK3_ENST00000450094.2_Intron|DKK3_ENST00000326932.4_Silent_p.Q125Q|DKK3_ENST00000525493.1_Silent_p.Q125Q|DKK3_ENST00000527132.1_Intron	NM_015881.5	NP_056965.3	Q9UBP4	DKK3_HUMAN	dickkopf WNT signaling pathway inhibitor 3	125					adrenal gland development (GO:0030325)|anatomical structure morphogenesis (GO:0009653)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of transcription, DNA-templated (GO:0045892)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)		p.Q125Q(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(1)|pancreas(1)	8				Epithelial(150;0.000502)		AAAAGACCATTTGTCCAGTCT	0.413																																					p.Q125Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A375G	11						.						193.0	170.0	178.0					11																	12020303		2201	4294	6495	11976879	SO:0001819	synonymous_variant	27122	exon3			AF177396	CCDS7808.1	11p15.3	2013-05-15	2013-05-15		ENSG00000050165	ENSG00000050165			2893	protein-coding gene	gene with protein product	"""regulated in glioma"""	605416	"""dickkopf (Xenopus laevis) homolog 3"", ""dickkopf 3 homolog (Xenopus laevis)"""			10570958	Standard	XM_006718177		Approved	REIC, RIG	uc001mjv.3	Q9UBP4	OTTHUMG00000165709	ENST00000396505.2:c.375A>G	11.37:g.12020303T>C		Somatic		Capture	Illumina HiSeq	Phase_I	11976879	NM_001018057	A8K1I2|D3DQW1|Q9ULB7	Silent	SNP	ENST00000396505.2	37	CCDS7808.1																																																																																				0.413	DKK3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385863.1	NM_013253	
TIMM8B	26521	broad.mit.edu	37	11	111956086	111956086	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:111956086C>T	ENST00000504148.2	-	2	256	c.185G>A	c.(184-186)cGc>cAc	p.R62H	TIMM8B_ENST00000541231.1_Missense_Mutation_p.R77H|SDHD_ENST00000528048.1_5'Flank|SDHD_ENST00000375549.3_5'Flank|SDHD_ENST00000532699.1_5'Flank|SDHD_ENST00000528182.1_5'Flank|SDHD_ENST00000526592.1_5'Flank|SDHD_ENST00000528021.1_5'Flank|TIMM8B_ENST00000507614.1_5'UTR|SDHD_ENST00000525291.1_5'Flank	NM_012459.2	NP_036591.2	Q9Y5J9	TIM8B_HUMAN	translocase of inner mitochondrial membrane 8 homolog B (yeast)	62					cellular protein metabolic process (GO:0044267)|chaperone-mediated protein transport (GO:0072321)|protein targeting to mitochondrion (GO:0006626)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space protein transporter complex (GO:0042719)	zinc ion binding (GO:0008270)	p.R62H(1)		large_intestine(1)	1		all_cancers(61;1.84e-10)|all_epithelial(67;9.33e-06)|Melanoma(852;4.01e-05)|all_hematologic(158;0.000885)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0512)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)		Epithelial(105;6.01e-07)|BRCA - Breast invasive adenocarcinoma(274;6.17e-07)|all cancers(92;1.03e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0512)		GTCAATGAAGCGGTCTACACA	0.502																																					p.R77H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G230A	11						.						145.0	115.0	125.0					11																	111956086		2201	4297	6498	111461296	SO:0001583	missense	26521	exon2			AF150087	CCDS8357.1, CCDS8357.2	11q23.1-q23.2	2010-11-23	2001-11-28		ENSG00000150779	ENSG00000150779			11818	protein-coding gene	gene with protein product	"""mitochondrial import inner membrane translocase subunit Tim8 B"""	606659	"""translocase of inner mitochondrial membrane 8 (yeast) homolog B"""			10552927	Standard	NM_012459		Approved	TIM8B, DDP2, FLJ21744, MGC102866, MGC117373	uc001pmx.3	Q9Y5J9	OTTHUMG00000162261	ENST00000504148.2:c.185G>A	11.37:g.111956086C>T	ENSP00000422122:p.Arg62His	Somatic		Capture	Illumina HiSeq	Phase_I	111461296	NM_012459	B0YJA5|Q3KQS9|Q9UN04	Missense_Mutation	SNP	ENST00000504148.2	37		.	.	.	.	.	.	.	.	.	.	C	22.7	4.324173	0.81580	.	.	ENSG00000150779	ENST00000504148;ENST00000541231	T;T	0.72505	-0.66;-0.66	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.68522	0.3010	.	.	.	0.80722	D	1	P	0.34757	0.467	B	0.34991	0.193	T	0.71087	-0.4694	9	0.66056	D	0.02	-14.7104	18.3499	0.90335	0.0:1.0:0.0:0.0	.	62	Q9Y5J9	TIM8B_HUMAN	H	62;77	ENSP00000422122:R62H;ENSP00000438455:R77H	ENSP00000422122:R62H	R	-	2	0	TIMM8B	111461296	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.179000	0.65043	2.645000	0.89757	0.549000	0.68633	CGC		0.502	TIMM8B-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000368270.2	NM_012459	
MICAL2	9645	broad.mit.edu	37	11	12229576	12229576	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:12229576G>A	ENST00000256194.4	+	5	767	c.479G>A	c.(478-480)cGc>cAc	p.R160H	MICAL2_ENST00000342902.5_Missense_Mutation_p.R160H|MICAL2_ENST00000527195.1_3'UTR|MICAL2_ENST00000527546.1_Missense_Mutation_p.R160H|MICAL2_ENST00000537344.1_Missense_Mutation_p.R160H|MICAL2_ENST00000379612.3_Missense_Mutation_p.R160H	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	160	Monooxygenase domain. {ECO:0000250}.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|heart development (GO:0007507)|heart looping (GO:0001947)|oxidation-reduction process (GO:0055114)|positive regulation of transcription via serum response element binding (GO:0010735)|sulfur oxidation (GO:0019417)	nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|NADPH:sulfur oxidoreductase activity (GO:0043914)|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.R160H(2)		breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	47				Epithelial(150;0.00552)		ACAGGTATTCGCCAACTACAG	0.483																																					p.R160H												.	.	2	Substitution - Missense(2)	upper_aerodigestive_tract(1)|large_intestine(1)	c.G479A	11						.						255.0	214.0	228.0					11																	12229576		2201	4294	6495	12186152	SO:0001583	missense	9645	exon5			AB018293	CCDS7809.1, CCDS60726.1, CCDS60727.1, CCDS60728.1	11p15.3	2014-08-12	2013-03-26		ENSG00000133816	ENSG00000133816			24693	protein-coding gene	gene with protein product		608881				12110185	Standard	XM_005253249		Approved	KIAA0750	uc001mjz.3	O94851	OTTHUMG00000165744	ENST00000256194.4:c.479G>A	11.37:g.12229576G>A	ENSP00000256194:p.Arg160His	Somatic		Capture	Illumina HiSeq	Phase_I	12186152	NM_014632	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Missense_Mutation	SNP	ENST00000256194.4	37	CCDS7809.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.005992	0.93287	.	.	ENSG00000133816	ENST00000537344;ENST00000256194;ENST00000527546;ENST00000342902;ENST00000379612	T;T;T;T;T	0.08193	3.12;3.12;3.12;3.12;3.12	5.64	5.64	0.86602	.	0.063637	0.64402	D	0.000004	T	0.40067	0.1102	M	0.92026	3.265	0.58432	D	0.999999	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;1.0;1.0	D;D;D;D;D;D	0.81914	0.988;0.933;0.978;0.952;0.995;0.981	T	0.43393	-0.9394	10	0.87932	D	0	.	19.4873	0.95035	0.0:0.0:1.0:0.0	.	160;160;160;160;160;160	G3XAC8;B7Z849;Q5KTR3;Q5KTR4;O94851;B4DGZ0	.;.;.;.;MICA2_HUMAN;.	H	160	ENSP00000441689:R160H;ENSP00000256194:R160H;ENSP00000433965:R160H;ENSP00000344894:R160H;ENSP00000368932:R160H	ENSP00000256194:R160H	R	+	2	0	MICAL2	12186152	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	6.202000	0.72131	2.937000	0.99478	0.650000	0.86243	CGC		0.483	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632	
SORL1	6653	broad.mit.edu	37	11	121485685	121485685	+	Missense_Mutation	SNP	G	G	A	rs545335743	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:121485685G>A	ENST00000260197.7	+	41	5654	c.5525G>A	c.(5524-5526)cGc>cAc	p.R1842H	SORL1_ENST00000534286.1_Missense_Mutation_p.R752H|SORL1_ENST00000527934.1_Missense_Mutation_p.R457H|SORL1_ENST00000525532.1_Missense_Mutation_p.R786H|SORL1_ENST00000532694.1_Missense_Mutation_p.R688H	NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	1842	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell death (GO:0008219)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902960)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of neurofibrillary tangle assembly (GO:1902997)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of tau-protein kinase activity (GO:1902948)|positive regulation of choline O-acetyltransferase activity (GO:1902771)|positive regulation of early endosome to recycling endosome transport (GO:1902955)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|positive regulation of protein localization to early endosome (GO:1902966)|post-Golgi vesicle-mediated transport (GO:0006892)|protein maturation (GO:0051604)|protein retention in Golgi apparatus (GO:0045053)|protein targeting (GO:0006605)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|receptor-mediated endocytosis (GO:0006898)|regulation of smooth muscle cell migration (GO:0014910)|signal transduction (GO:0007165)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|nuclear envelope lumen (GO:0005641)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)|beta-amyloid binding (GO:0001540)|low-density lipoprotein particle binding (GO:0030169)|transmembrane signaling receptor activity (GO:0004888)	p.R1842H(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)		AGAGGGGTTCGCCCACCTGCA	0.547													G|||	4	0.000798722	0.0	0.0	5008	,	,		17549	0.0		0.0	False		,,,				2504	0.0041				p.R1842H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5525A	11						.						106.0	87.0	93.0					11																	121485685		2202	4299	6501	120990895	SO:0001583	missense	6653	exon41			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.5525G>A	11.37:g.121485685G>A	ENSP00000260197:p.Arg1842His	Somatic		Capture	Illumina HiSeq	Phase_I	120990895	NM_003105	B2RNX7|Q92856	Missense_Mutation	SNP	ENST00000260197.7	37	CCDS8436.1	.	.	.	.	.	.	.	.	.	.	G	14.77	2.634251	0.47049	.	.	ENSG00000137642	ENST00000260197;ENST00000525532;ENST00000532694;ENST00000534286;ENST00000527934	T;T;T;T;T	0.54479	0.57;0.57;0.57;0.57;0.57	5.91	5.01	0.66863	Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.125890	0.51477	D	0.000099	T	0.36193	0.0958	L	0.29908	0.895	0.21064	N	0.999798	B;P	0.40266	0.004;0.71	B;B	0.34385	0.003;0.181	T	0.29701	-1.0003	10	0.45353	T	0.12	.	9.2551	0.37579	0.2177:0.0:0.7823:0.0	.	457;1842	E9PKB0;Q92673	.;SORL_HUMAN	H	1842;786;688;752;457	ENSP00000260197:R1842H;ENSP00000434634:R786H;ENSP00000432131:R688H;ENSP00000436447:R752H;ENSP00000435405:R457H	ENSP00000260197:R1842H	R	+	2	0	SORL1	120990895	0.370000	0.25047	0.972000	0.41901	0.976000	0.68499	2.023000	0.41040	1.510000	0.48803	0.655000	0.94253	CGC		0.547	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105	
NTM	50863	broad.mit.edu	37	11	131781481	131781481	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:131781481G>A	ENST00000374786.1	+	1	585	c.106G>A	c.(106-108)Gcc>Acc	p.A36T	NTM_ENST00000425719.2_Missense_Mutation_p.A36T|NTM_ENST00000374784.1_Missense_Mutation_p.A36T|NTM_ENST00000427481.2_Missense_Mutation_p.A27T|NTM_ENST00000374791.3_Missense_Mutation_p.A36T|NTM_ENST00000539799.1_Missense_Mutation_p.A36T	NM_001144058.1|NM_016522.2	NP_001137530.1|NP_057606.1	Q9P121	NTRI_HUMAN	neurotrimin	36					cell adhesion (GO:0007155)|neuron recognition (GO:0008038)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.A36T(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						CAGCGGAGATGCCACCTTCCC	0.602											OREG0021537	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A36T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G106A	11						.						89.0	83.0	85.0					11																	131781481		2201	4292	6493	131286691	SO:0001583	missense	50863	exon1			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.106G>A	11.37:g.131781481G>A	ENSP00000363918:p.Ala36Thr	Somatic	1590	Capture	Illumina HiSeq	Phase_I	131286691	NM_001144058	A0MTT2|Q6UXJ3|Q86VJ9	Missense_Mutation	SNP	ENST00000374786.1	37	CCDS8491.1	.	.	.	.	.	.	.	.	.	.	G	19.58	3.854711	0.71719	.	.	ENSG00000182667	ENST00000374791;ENST00000436745;ENST00000539799;ENST00000550167;ENST00000427481;ENST00000374786;ENST00000425719;ENST00000374784	T;T;T;T;T;T;T	0.60040	0.24;0.24;0.22;0.24;0.27;0.24;0.22	5.28	5.28	0.74379	.	0.072326	0.53938	D	0.000045	T	0.55800	0.1943	L	0.36672	1.1	0.43417	D	0.995566	P;B;B;P;B;P	0.39131	0.661;0.254;0.059;0.464;0.07;0.609	B;B;B;B;B;B	0.42087	0.297;0.375;0.037;0.232;0.087;0.287	T	0.59731	-0.7399	10	0.59425	D	0.04	-22.0091	18.8959	0.92423	0.0:0.0:1.0:0.0	.	36;27;36;36;36;36	B7Z1Z5;B7Z1I4;Q9P121-4;Q9P121;Q9P121-3;Q9P121-2	.;.;.;NTRI_HUMAN;.;.	T	36;27;36;27;27;36;36;36	ENSP00000363923:A36T;ENSP00000437668:A36T;ENSP00000448104:A27T;ENSP00000416320:A27T;ENSP00000363918:A36T;ENSP00000396722:A36T;ENSP00000363916:A36T	ENSP00000363916:A36T	A	+	1	0	NTM	131286691	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.530000	0.73816	2.479000	0.83701	0.561000	0.74099	GCC		0.602	NTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141937.1	NM_016522	
OR51A7	119687	broad.mit.edu	37	11	4929305	4929305	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:4929305G>A	ENST00000359350.4	+	1	706	c.706G>A	c.(706-708)Gcc>Acc	p.A236T	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001004749.1	NP_001004749.1	Q8NH64	O51A7_HUMAN	olfactory receptor, family 51, subfamily A, member 7	236						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A236T(1)		breast(1)|endometrium(1)|large_intestine(7)|lung(13)|ovary(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		GAGGCTTAAGGCCCTAAATAC	0.483																																					p.A236T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G706A	11						.						235.0	206.0	216.0					11																	4929305		2201	4298	6499	4885881	SO:0001583	missense	119687	exon1			AB065525	CCDS31364.1	11p15.4	2012-08-09			ENSG00000176895	ENSG00000176895		"""GPCR / Class A : Olfactory receptors"""	15188	protein-coding gene	gene with protein product							Standard	NM_001004749		Approved		uc010qyq.2	Q8NH64	OTTHUMG00000066502	ENST00000359350.4:c.706G>A	11.37:g.4929305G>A	ENSP00000352305:p.Ala236Thr	Somatic		Capture	Illumina HiSeq	Phase_I	4885881	NM_001004749	Q6IFH8	Missense_Mutation	SNP	ENST00000359350.4	37	CCDS31364.1	.	.	.	.	.	.	.	.	.	.	G	9.204	1.029281	0.19512	.	.	ENSG00000176895	ENST00000359350;ENST00000545959;ENST00000544684	T	0.46819	0.86	5.02	4.11	0.48088	GPCR, rhodopsin-like superfamily (1);	0.290426	0.24703	N	0.036295	T	0.49626	0.1568	M	0.69823	2.125	0.24759	N	0.992939	B	0.18166	0.026	B	0.29077	0.098	T	0.48559	-0.9025	10	0.45353	T	0.12	.	12.2537	0.54611	0.0828:0.0:0.9172:0.0	.	236	Q8NH64	O51A7_HUMAN	T	236;236;225	ENSP00000352305:A236T	ENSP00000352305:A236T	A	+	1	0	OR51A7	4885881	0.017000	0.18338	0.175000	0.22980	0.116000	0.19942	1.847000	0.39299	1.335000	0.45486	0.655000	0.94253	GCC		0.483	OR51A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142175.1	NM_001004749	
OR56A4	120793	broad.mit.edu	37	11	6024122	6024122	+	Missense_Mutation	SNP	A	A	T	rs370692842		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:6024122A>T	ENST00000330728.4	-	1	302	c.257T>A	c.(256-258)cTc>cAc	p.L86H		NM_001005179.2	NP_001005179.2	Q8NGH8	O56A4_HUMAN	olfactory receptor, family 56, subfamily A, member 4	34						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L86H(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|skin(1)|urinary_tract(1)	32		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;7.01e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GAGAAGGCTGAGGGGCAGAGA	0.587																																					p.L86H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T257A	11						.						82.0	78.0	79.0					11																	6024122		2201	4296	6497	5980698	SO:0001583	missense	120793	exon1			BK004255	CCDS31404.1	11p15.4	2012-08-09			ENSG00000183389	ENSG00000183389		"""GPCR / Class A : Olfactory receptors"""	14791	protein-coding gene	gene with protein product							Standard	NM_001005179		Approved		uc010qzv.2	Q8NGH8	OTTHUMG00000165376	ENST00000330728.4:c.257T>A	11.37:g.6024122A>T	ENSP00000328215:p.Leu86His	Somatic		Capture	Illumina HiSeq	Phase_I	5980698	NM_001005179	B9EH17	Missense_Mutation	SNP	ENST00000330728.4	37	CCDS31404.1	.	.	.	.	.	.	.	.	.	.	A	17.50	3.405737	0.62288	.	.	ENSG00000183389	ENST00000330728	T	0.00406	7.55	3.62	3.62	0.41486	.	0.336410	0.16300	U	0.220517	T	0.01287	0.0042	M	0.87381	2.88	0.34486	D	0.704413	D	0.76494	0.999	D	0.70016	0.967	T	0.48990	-0.8985	10	0.87932	D	0	.	11.4561	0.50183	1.0:0.0:0.0:0.0	.	34	Q8NGH8	O56A4_HUMAN	H	86	ENSP00000328215:L86H	ENSP00000328215:L86H	L	-	2	0	OR56A4	5980698	0.989000	0.36119	1.000000	0.80357	0.833000	0.47200	6.278000	0.72614	1.629000	0.50426	0.454000	0.30748	CTC		0.587	OR56A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383756.2	NM_001005179	
CNGA4	1262	broad.mit.edu	37	11	6261771	6261771	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:6261771C>T	ENST00000379936.2	+	4	862	c.747C>T	c.(745-747)ggC>ggT	p.G249G	CNGA4_ENST00000533426.1_Intron	NM_001037329.3	NP_001032406.1	Q8IV77	CNGA4_HUMAN	cyclic nucleotide gated channel alpha 4	249					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.G249G(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)		TCATGGTGGGCGACTTCCTGC	0.537																																					p.G249G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C747T	11						.						79.0	73.0	75.0					11																	6261771		2201	4296	6497	6218347	SO:0001819	synonymous_variant	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.747C>T	11.37:g.6261771C>T		Somatic		Capture	Illumina HiSeq	Phase_I	6218347	NM_001037329		Silent	SNP	ENST00000379936.2	37	CCDS31408.1																																																																																				0.537	CNGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383765.2	NM_001037329	
OR2AG2	338755	broad.mit.edu	37	11	6789862	6789862	+	Silent	SNP	G	G	A	rs145583606	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:6789862G>A	ENST00000338569.2	-	1	424	c.327C>T	c.(325-327)agC>agT	p.S109S		NM_001004490.1	NP_001004490.1	A6NM03	O2AG2_HUMAN	olfactory receptor, family 2, subfamily AG, member 2	109						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S109S(1)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(13)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	28		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.15e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		GGTCCTCAGCGCTACCCATTG	0.522													A|||	6	0.00119808	0.0	0.0	5008	,	,		21854	0.006		0.0	False		,,,				2504	0.0				p.S109S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C327T	11						.	A		0,4402		0,0,2201	92.0	79.0	83.0		327	-0.5	0.1	11	dbSNP_134	83	1,8591		0,1,4295	no	coding-synonymous	OR2AG2	NM_001004490.1		0,1,6496	AA,AG,GG		0.0116,0.0,0.0077		109/317	6789862	1,12993	2201	4296	6497	6746438	SO:0001819	synonymous_variant	338755	exon1			AB065539	CCDS31413.1	11p15.4	2012-08-09		2004-03-10	ENSG00000188124	ENSG00000188124		"""GPCR / Class A : Olfactory receptors"""	15143	protein-coding gene	gene with protein product				OR2AG2P			Standard	NM_001004490		Approved		uc001meq.1	A6NM03	OTTHUMG00000165868	ENST00000338569.2:c.327C>T	11.37:g.6789862G>A		Somatic		Capture	Illumina HiSeq	Phase_I	6746438	NM_001004490		Silent	SNP	ENST00000338569.2	37	CCDS31413.1																																																																																				0.522	OR2AG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386775.1	NM_001004490	
PPFIBP2	8495	broad.mit.edu	37	11	7654130	7654130	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:7654130G>A	ENST00000299492.4	+	12	1489	c.1101G>A	c.(1099-1101)ggG>ggA	p.G367G	PPFIBP2_ENST00000533792.1_Silent_p.G209G|PPFIBP2_ENST00000530181.1_Silent_p.G224G|PPFIBP2_ENST00000528883.1_Silent_p.G255G|PPFIBP2_ENST00000530582.1_3'UTR	NM_003621.3	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	367					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)	DNA binding (GO:0003677)|integrase activity (GO:0008907)	p.G367G(1)		breast(8)|cervix(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)		CTACAGTGGGGCCACCTCCAT	0.572																																					p.G367G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1101A	11						.						114.0	91.0	99.0					11																	7654130		2201	4296	6497	7610706	SO:0001819	synonymous_variant	8495	exon12			AF034803	CCDS31419.1, CCDS58116.1, CCDS58117.1	11p15.4	2013-01-10			ENSG00000166387	ENSG00000166387		"""Sterile alpha motif (SAM) domain containing"""	9250	protein-coding gene	gene with protein product		603142				9624153	Standard	NM_003621		Approved	Cclp1	uc001mfj.5	Q8ND30	OTTHUMG00000165617	ENST00000299492.4:c.1101G>A	11.37:g.7654130G>A		Somatic		Capture	Illumina HiSeq	Phase_I	7610706	NM_003621	B7Z433|E9PK77|O75337|Q8WW26	Silent	SNP	ENST00000299492.4	37	CCDS31419.1	.	.	.	.	.	.	.	.	.	.	G	4.958	0.177872	0.09443	.	.	ENSG00000166387	ENST00000534409	.	.	.	5.11	1.94	0.25998	.	.	.	.	.	T	0.51941	0.1704	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40739	-0.9547	4	.	.	.	-8.0208	5.3128	0.15839	0.187:0.1654:0.6477:0.0	.	.	.	.	T	47	.	.	A	+	1	0	PPFIBP2	7610706	0.978000	0.34361	0.996000	0.52242	0.405000	0.30901	0.667000	0.25112	0.543000	0.28864	0.491000	0.48974	GCC		0.572	PPFIBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385345.2	NM_003621	
PDE3B	5140	broad.mit.edu	37	11	14880716	14880716	+	Missense_Mutation	SNP	G	G	A	rs146384818		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:14880716G>A	ENST00000282096.4	+	13	3001	c.2648G>A	c.(2647-2649)cGt>cAt	p.R883H	PDE3B_ENST00000455098.2_Missense_Mutation_p.R832H	NM_000922.3	NP_000913.2	Q13370	PDE3B_HUMAN	phosphodiesterase 3B, cGMP-inhibited	883	Catalytic. {ECO:0000250}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cellular response to insulin stimulus (GO:0032869)|endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of lipid catabolic process (GO:0050995)|regulation of insulin secretion (GO:0050796)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|guanyl-nucleotide exchange factor complex (GO:0032045)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)|protein kinase B binding (GO:0043422)	p.R883H(1)		NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39					Caffeine(DB00201)	AAGCGCTTTCGTTTTTTAGTC	0.383																																					p.R883H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2648A	11						.	G	HIS/ARG	1,4399	2.1+/-5.4	0,1,2199	160.0	141.0	147.0		2648	5.5	1.0	11	dbSNP_134	147	0,8588		0,0,4294	no	missense	PDE3B	NM_000922.3	29	0,1,6493	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	883/1113	14880716	1,12987	2200	4294	6494	14837292	SO:0001583	missense	5140	exon13			U38178	CCDS7817.1	11p15.2	2008-03-18			ENSG00000152270	ENSG00000152270	3.1.4.17	"""Phosphodiesterases"""	8779	protein-coding gene	gene with protein product		602047				8884271, 16395595	Standard	NM_000922		Approved	HcGIP1	uc001mln.3	Q13370	OTTHUMG00000165898	ENST00000282096.4:c.2648G>A	11.37:g.14880716G>A	ENSP00000282096:p.Arg883His	Somatic		Capture	Illumina HiSeq	Phase_I	14837292	NM_000922	B7ZM37|O00639|Q14408|Q6SEI4	Missense_Mutation	SNP	ENST00000282096.4	37	CCDS7817.1	.	.	.	.	.	.	.	.	.	.	G	33	5.251424	0.95305	2.27E-4	0.0	ENSG00000152270	ENST00000282096;ENST00000455098	T;T	0.80393	-1.37;-1.37	5.54	5.54	0.83059	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	D	0.92277	0.7550	M	0.91140	3.18	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.93530	0.6869	10	0.87932	D	0	.	19.4868	0.95032	0.0:0.0:1.0:0.0	.	832;883	B7ZM37;Q13370	.;PDE3B_HUMAN	H	883;832	ENSP00000282096:R883H;ENSP00000388644:R832H	ENSP00000282096:R883H	R	+	2	0	PDE3B	14837292	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.476000	0.97823	2.598000	0.87819	0.563000	0.77884	CGT		0.383	PDE3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386974.1	NM_000922	
SOX6	55553	broad.mit.edu	37	11	16340073	16340073	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:16340073G>A	ENST00000352083.6	-	3	441	c.364C>T	c.(364-366)Cgc>Tgc	p.R122C	SOX6_ENST00000527619.1_Missense_Mutation_p.R125C|SOX6_ENST00000533658.1_5'UTR|SOX6_ENST00000528252.1_Missense_Mutation_p.R122C|SOX6_ENST00000396356.3_Missense_Mutation_p.R122C|SOX6_ENST00000316399.6_Missense_Mutation_p.R122C|SOX6_ENST00000528429.1_Missense_Mutation_p.R122C			P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6	122					astrocyte differentiation (GO:0048708)|cardiac muscle cell differentiation (GO:0055007)|cartilage development (GO:0051216)|cell morphogenesis (GO:0000902)|cellular response to transforming growth factor beta stimulus (GO:0071560)|erythrocyte development (GO:0048821)|gene silencing (GO:0016458)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oligodendrocyte cell fate specification (GO:0021778)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|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)|transcription regulatory region DNA binding (GO:0044212)	p.R122C(1)		NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(23)|ovary(3)|pancreas(1)|prostate(2)	43						CCTTTGCGGCGCTCTGGGGTT	0.502																																					p.R122C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C364T	11						.						196.0	183.0	187.0					11																	16340073		2200	4294	6494	16296649	SO:0001583	missense	55553	exon3			AF309034	CCDS7821.1, CCDS53604.1, CCDS53605.1	11p15.3	2008-02-05						"""SRY (sex determining region Y)-boxes"""	16421	protein-coding gene	gene with protein product		607257				11255018	Standard	NM_033326		Approved		uc001mme.3	P35712		ENST00000352083.6:c.364C>T	11.37:g.16340073G>A	ENSP00000339876:p.Arg122Cys	Somatic		Capture	Illumina HiSeq	Phase_I	16296649	NM_033326	Q86VX7|Q9BXQ3|Q9BXQ4|Q9BXQ5|Q9H0I8	Missense_Mutation	SNP	ENST00000352083.6	37		.	.	.	.	.	.	.	.	.	.	G	32	5.126131	0.94429	.	.	ENSG00000110693	ENST00000316399;ENST00000352083;ENST00000396356;ENST00000528252;ENST00000527619;ENST00000528429;ENST00000533411;ENST00000526673	D;D;D;D;D;D	0.98947	-5.26;-5.22;-5.26;-4.94;-4.94;-5.22	5.28	5.28	0.74379	.	0.063248	0.64402	D	0.000006	D	0.99067	0.9680	M	0.76574	2.34	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;0.998;0.999;1.0;0.995	D	0.99875	1.1102	10	0.87932	D	0	.	19.2735	0.94021	0.0:0.0:1.0:0.0	.	122;122;122;122;125	E9PQ78;E9PQL4;P35712-3;P35712;P35712-2	.;.;.;SOX6_HUMAN;.	C	122;122;122;122;125;122;122;122	ENSP00000324948:R122C;ENSP00000339876:R122C;ENSP00000379644:R122C;ENSP00000432134:R122C;ENSP00000434455:R125C;ENSP00000433233:R122C	ENSP00000324948:R122C	R	-	1	0	SOX6	16296649	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.341000	0.97041	2.632000	0.89209	0.591000	0.81541	CGC		0.502	SOX6-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000386811.1	NM_033326	
TMEM86A	144110	broad.mit.edu	37	11	18723413	18723413	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:18723413G>A	ENST00000280734.2	+	3	676	c.580G>A	c.(580-582)Gcc>Acc	p.A194T		NM_153347.1	NP_699178.1	Q8N2M4	TM86A_HUMAN	transmembrane protein 86A	194						integral component of membrane (GO:0016021)		p.A194T(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|skin(2)	11						CCTGACCATCGCCCTCAACAA	0.577																																					p.A194T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G580A	11						.						112.0	94.0	100.0					11																	18723413		2199	4293	6492	18679989	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.580G>A	11.37:g.18723413G>A	ENSP00000280734:p.Ala194Thr	Somatic		Capture	Illumina HiSeq	Phase_I	18679989	NM_153347	Q96AJ0	Missense_Mutation	SNP	ENST00000280734.2	37	CCDS7844.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.833959	0.91036	.	.	ENSG00000151117	ENST00000535380;ENST00000280734	T	0.30981	1.51	5.55	5.55	0.83447	.	0.162422	0.56097	D	0.000040	T	0.53384	0.1793	M	0.92412	3.305	0.80722	D	1	P	0.45176	0.852	P	0.45276	0.475	T	0.64732	-0.6338	9	.	.	.	-1.8768	19.6982	0.96039	0.0:0.0:1.0:0.0	.	194	Q8N2M4	TM86A_HUMAN	T	194	ENSP00000280734:A194T	.	A	+	1	0	TMEM86A	18679989	1.000000	0.71417	0.992000	0.48379	0.825000	0.46686	9.246000	0.95438	2.894000	0.99253	0.655000	0.94253	GCC		0.577	TMEM86A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387812.1	NM_153347	
SLC6A5	9152	broad.mit.edu	37	11	20623191	20623191	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:20623191G>A	ENST00000525748.1	+	2	793	c.520G>A	c.(520-522)Gtg>Atg	p.V174M		NM_004211.3	NP_004202.2	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 5	174					glycine import (GO:0036233)|synaptic transmission (GO:0007268)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine:sodium symporter activity (GO:0015375)|neurotransmitter:sodium symporter activity (GO:0005328)	p.V174M(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(34)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	63					Glycine(DB00145)	CCCGGGCAGCGTGGCCACCGT	0.667																																					p.V174M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G520A	11						.						67.0	60.0	63.0					11																	20623191		2203	4300	6503	20579767	SO:0001583	missense	9152	exon2			AF085412	CCDS7854.1	11p15.1	2013-07-19	2013-07-19		ENSG00000165970	ENSG00000165970		"""Solute carriers"""	11051	protein-coding gene	gene with protein product	"""glycine transporter 2"""	604159	"""solute carrier family 6 (neurotransmitter transporter, glycine), member 5"""	NET1		9845349	Standard	NM_004211		Approved	GLYT2	uc001mqd.3	Q9Y345	OTTHUMG00000166024	ENST00000525748.1:c.520G>A	11.37:g.20623191G>A	ENSP00000434364:p.Val174Met	Somatic		Capture	Illumina HiSeq	Phase_I	20579767	NM_004211	O95288|Q4VAM7|Q9BX77	De_novo_Start_OutOfFrame	SNP	ENST00000525748.1	37	CCDS7854.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.999392	0.74818	.	.	ENSG00000165970	ENST00000525748	T	0.73469	-0.75	5.44	4.54	0.55810	.	1.882680	0.02088	N	0.052959	T	0.66317	0.2777	L	0.29908	0.895	0.50813	D	0.999892	D	0.56035	0.974	B	0.37508	0.252	T	0.58521	-0.7622	10	0.72032	D	0.01	.	11.11	0.48226	0.0863:0.0:0.9137:0.0	.	174	Q9Y345	SC6A5_HUMAN	M	174	ENSP00000434364:V174M	ENSP00000298923:V174M	V	+	1	0	SLC6A5	20579767	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	3.972000	0.56838	1.302000	0.44855	0.455000	0.32223	GTG		0.667	SLC6A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387497.2	NM_004211	
LUZP2	338645	broad.mit.edu	37	11	24750823	24750823	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:24750823C>T	ENST00000336930.6	+	2	237	c.171C>T	c.(169-171)gtC>gtT	p.V57V	LUZP2_ENST00000531187.1_3'UTR|LUZP2_ENST00000533227.1_5'UTR			Q86TE4	LUZP2_HUMAN	leucine zipper protein 2	57						extracellular region (GO:0005576)		p.V57V(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(11)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	32						GAATTAAAGTCAATCTTCAGG	0.378																																					p.V57V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C171T	11						.						70.0	73.0	72.0					11																	24750823		2203	4299	6502	24707399	SO:0001819	synonymous_variant	338645	exon2			AL832641	CCDS31446.1, CCDS58128.1	11p14.3	2005-09-18			ENSG00000187398	ENSG00000187398			23206	protein-coding gene	gene with protein product		608178				12856284	Standard	NM_001009909		Approved		uc001mqs.3	Q86TE4	OTTHUMG00000166109	ENST00000336930.6:c.171C>T	11.37:g.24750823C>T		Somatic		Capture	Illumina HiSeq	Phase_I	24707399	NM_001009909	A2RUB8|E9PN53|Q6UXE7|Q6ZS65	Silent	SNP	ENST00000336930.6	37	CCDS31446.1																																																																																				0.378	LUZP2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387861.1	NM_001009909	
LGR4	55366	broad.mit.edu	37	11	27389696	27389696	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:27389696G>A	ENST00000379214.4	-	18	3017	c.2574C>T	c.(2572-2574)tgC>tgT	p.C858C	LGR4_ENST00000389858.4_Silent_p.C834C	NM_018490.2	NP_060960.2	Q9BXB1	LGR4_HUMAN	leucine-rich repeat containing G protein-coupled receptor 4	858					bone mineralization (GO:0030282)|bone remodeling (GO:0046849)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cell differentiation involved in metanephros development (GO:0072202)|epithelial cell proliferation (GO:0050673)|innate immune response (GO:0045087)|male genitalia development (GO:0030539)|metanephric glomerulus development (GO:0072224)|metanephric nephron tubule morphogenesis (GO:0072282)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast differentiation (GO:0001649)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)	p.C858C(1)		NS(3)|breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(10)|ovary(1)	32						CGCAGCAGTCGCAAACAGTCA	0.458																																					p.C858C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2574T	11						.						133.0	127.0	129.0					11																	27389696		2202	4299	6501	27346272	SO:0001819	synonymous_variant	55366	exon18			AF257182	CCDS31449.1	11p14-p13	2012-08-21	2011-01-25	2004-11-12	ENSG00000205213	ENSG00000205213		"""GPCR / Class A : Orphans"""	13299	protein-coding gene	gene with protein product		606666	"""G protein-coupled receptor 48"", ""leucine-rich repeat-containing G protein-coupled receptor 4"""	GPR48		10894923	Standard	NM_018490		Approved		uc001mrj.4	Q9BXB1	OTTHUMG00000133508	ENST00000379214.4:c.2574C>T	11.37:g.27389696G>A		Somatic		Capture	Illumina HiSeq	Phase_I	27346272	NM_018490	A6NCH3|G5E9B3|Q8N537|Q9NYD1	Silent	SNP	ENST00000379214.4	37	CCDS31449.1																																																																																				0.458	LGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257467.1	NM_018490	
KCNA4	3739	broad.mit.edu	37	11	30032726	30032726	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:30032726C>A	ENST00000328224.6	-	2	2733	c.1500G>T	c.(1498-1500)gaG>gaT	p.E500D	KCNA4_ENST00000526518.1_5'Flank	NM_002233.3	NP_002224.1	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 4	500					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	potassium ion binding (GO:0030955)|voltage-gated potassium channel activity (GO:0005249)	p.E500D(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(39)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	78					Dalfampridine(DB06637)	GTTCATCCGCCTCTGCAAAAT	0.522																																					p.E500D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1500T	11						.						57.0	59.0	58.0					11																	30032726		2161	4289	6450	29989302	SO:0001583	missense	3739	exon2			M55514	CCDS41629.1	11p14	2012-07-05	2002-07-10			ENSG00000182255		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6222	protein-coding gene	gene with protein product		176266	"""potassium voltage-gated channel, shaker-related subfamily, member 4-like"""	KCNA4L		2263489, 16382104	Standard	NM_002233		Approved	Kv1.4, HK1, HPCN2	uc001msk.3	P22459		ENST00000328224.6:c.1500G>T	11.37:g.30032726C>A	ENSP00000328511:p.Glu500Asp	Somatic		Capture	Illumina HiSeq	Phase_I	29989302	NM_002233		Missense_Mutation	SNP	ENST00000328224.6	37	CCDS41629.1	.	.	.	.	.	.	.	.	.	.	C	15.14	2.745269	0.49151	.	.	ENSG00000182255	ENST00000328224	D	0.98684	-5.07	5.57	2.24	0.28232	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99032	0.9669	H	0.96777	3.88	0.58432	D	0.999999	D	0.57257	0.979	P	0.57548	0.823	D	0.98521	1.0623	10	0.66056	D	0.02	.	6.6358	0.22881	0.0:0.4981:0.0:0.5018	.	500	P22459	KCNA4_HUMAN	D	500	ENSP00000328511:E500D	ENSP00000328511:E500D	E	-	3	2	KCNA4	29989302	1.000000	0.71417	0.998000	0.56505	0.955000	0.61496	2.187000	0.42602	0.634000	0.30469	0.650000	0.86243	GAG		0.522	KCNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388074.2	NM_002233	
KCNA4	3739	broad.mit.edu	37	11	30033223	30033223	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:30033223C>T	ENST00000328224.6	-	2	2236	c.1003G>A	c.(1003-1005)Gac>Aac	p.D335N	KCNA4_ENST00000526518.1_5'Flank	NM_002233.3	NP_002224.1	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 4	335					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	potassium ion binding (GO:0030955)|voltage-gated potassium channel activity (GO:0005249)	p.D335N(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(39)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	78					Dalfampridine(DB06637)	AGATCCCTGTCGTCCCTAAAC	0.517																																					p.D335N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1003A	11						.						86.0	78.0	81.0					11																	30033223		2048	4202	6250	29989799	SO:0001583	missense	3739	exon2			M55514	CCDS41629.1	11p14	2012-07-05	2002-07-10			ENSG00000182255		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6222	protein-coding gene	gene with protein product		176266	"""potassium voltage-gated channel, shaker-related subfamily, member 4-like"""	KCNA4L		2263489, 16382104	Standard	NM_002233		Approved	Kv1.4, HK1, HPCN2	uc001msk.3	P22459		ENST00000328224.6:c.1003G>A	11.37:g.30033223C>T	ENSP00000328511:p.Asp335Asn	Somatic		Capture	Illumina HiSeq	Phase_I	29989799	NM_002233		Missense_Mutation	SNP	ENST00000328224.6	37	CCDS41629.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.428234	0.83667	.	.	ENSG00000182255	ENST00000328224	T	0.71579	-0.58	5.16	5.16	0.70880	.	0.636212	0.15044	N	0.283675	T	0.61899	0.2384	L	0.43152	1.355	0.80722	D	1	P	0.38729	0.644	B	0.22880	0.042	T	0.67795	-0.5578	10	0.59425	D	0.04	.	18.6691	0.91504	0.0:1.0:0.0:0.0	.	335	P22459	KCNA4_HUMAN	N	335	ENSP00000328511:D335N	ENSP00000328511:D335N	D	-	1	0	KCNA4	29989799	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.976000	0.70484	2.412000	0.81896	0.655000	0.94253	GAC		0.517	KCNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388074.2	NM_002233	
ELP4	26610	broad.mit.edu	37	11	31805011	31805011	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:31805011C>T	ENST00000350638.5	+	10	1249	c.1214C>T	c.(1213-1215)gCc>gTc	p.A405V	Z83307.3_ENST00000606377.1_lincRNA|ELP4_ENST00000379163.5_Silent_p.R452R|ELP4_ENST00000395934.2_3'UTR	NM_019040.3	NP_061913.3	Q96EB1	ELP4_HUMAN	elongator acetyltransferase complex subunit 4	405					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|transcription elongation factor complex (GO:0008023)	phosphorylase kinase regulator activity (GO:0008607)	p.A405V(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(3)	20	Lung SC(675;0.225)					GCAGAATCCGCCAAGCGGCTG	0.527																																					p.A405V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1214T	11						.						71.0	78.0	76.0					11																	31805011		1924	4141	6065	31761587	SO:0001583	missense	26610	exon10			AJ276005	CCDS7875.2, CCDS73271.1, CCDS73272.1	11p13	2012-08-14	2012-08-08	2002-05-24	ENSG00000109911	ENSG00000109911		"""Elongator acetyltransferase complex subunits"""	1171	protein-coding gene	gene with protein product		606985	"""chromosome 11 open reading frame 19"", ""elongation protein 4 homolog (S. cerevisiae)"""	C11orf19		11889558, 11435442	Standard	XM_005252865		Approved	PAXNEB	uc001mtb.3	Q96EB1	OTTHUMG00000142919	ENST00000350638.5:c.1214C>T	11.37:g.31805011C>T	ENSP00000298937:p.Ala405Val	Somatic		Capture	Illumina HiSeq	Phase_I	31761587	NM_019040	B4E3W0|E7EPZ6|Q9H4E8|Q9NX11	Missense_Mutation	SNP	ENST00000350638.5	37	CCDS7875.2	.	.	.	.	.	.	.	.	.	.	C	21.3	4.124518	0.77436	.	.	ENSG00000109911	ENST00000350638	T	0.46451	0.87	5.73	5.73	0.89815	.	.	.	.	.	T	0.43211	0.1237	L	0.44542	1.39	0.80722	D	1	P	0.36683	0.565	B	0.38803	0.282	T	0.24333	-1.0163	9	0.45353	T	0.12	.	20.2786	0.98501	0.0:1.0:0.0:0.0	.	405	Q96EB1	ELP4_HUMAN	V	405	ENSP00000298937:A405V	ENSP00000298937:A405V	A	+	2	0	ELP4	31761587	1.000000	0.71417	0.467000	0.27180	0.933000	0.57130	4.994000	0.63901	2.868000	0.98415	0.557000	0.71058	GCC		0.527	ELP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286640.1	NM_019040	
CCDC73	493860	broad.mit.edu	37	11	32637659	32637659	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:32637659T>A	ENST00000335185.5	-	15	1245	c.1202A>T	c.(1201-1203)aAt>aTt	p.N401I	CCDC73_ENST00000534415.1_5'UTR	NM_001008391.2	NP_001008392.2	Q6ZRK6	CCD73_HUMAN	coiled-coil domain containing 73	401								p.N401I(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	51	Breast(20;0.112)					GTTTTCATTATTTACTTCTGG	0.284																																					p.N401I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1202T	11						.						56.0	52.0	53.0					11																	32637659		1803	4033	5836	32594235	SO:0001583	missense	493860	exon15			AK128159	CCDS41630.1	11p13	2006-02-11			ENSG00000186714	ENSG00000186714			23261	protein-coding gene	gene with protein product		612328					Standard	NM_001008391		Approved	NY-SAR-79	uc001mtv.4	Q6ZRK6	OTTHUMG00000166279	ENST00000335185.5:c.1202A>T	11.37:g.32637659T>A	ENSP00000335325:p.Asn401Ile	Somatic		Capture	Illumina HiSeq	Phase_I	32594235	NM_001008391	Q6P5Q7|Q6ZMW0|Q86WE7	Missense_Mutation	SNP	ENST00000335185.5	37	CCDS41630.1	.	.	.	.	.	.	.	.	.	.	T	16.86	3.239225	0.58995	.	.	ENSG00000186714	ENST00000335185	.	.	.	5.34	-1.18	0.09617	.	0.528557	0.18554	N	0.137822	T	0.45518	0.1346	L	0.56769	1.78	0.45567	D	0.998515	P;P	0.45078	0.85;0.825	B;P	0.46253	0.424;0.509	T	0.36504	-0.9745	9	0.33940	T	0.23	.	4.4318	0.11531	0.1746:0.4387:0.0:0.3866	.	391;401	Q6ZRK6-2;Q6ZRK6	.;CCD73_HUMAN	I	401	.	ENSP00000335325:N401I	N	-	2	0	CCDC73	32594235	0.581000	0.26741	0.994000	0.49952	0.923000	0.55619	-0.298000	0.08265	0.104000	0.17725	0.477000	0.44152	AAT		0.284	CCDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388874.2	NM_001008391	
LDLRAD3	143458	broad.mit.edu	37	11	36248835	36248835	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:36248835C>T	ENST00000315571.5	+	5	676	c.655C>T	c.(655-657)Cgc>Tgc	p.R219C	LDLRAD3_ENST00000528989.1_Missense_Mutation_p.R170C|LDLRAD3_ENST00000524419.1_Missense_Mutation_p.R209C|LDLRAD3_ENST00000529759.1_3'UTR	NM_174902.2	NP_777562.1	Q86YD5	LRAD3_HUMAN	low density lipoprotein receptor class A domain containing 3	219					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.R219C(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)				GCTGCTGTCCCGCCTGGTGGT	0.637																																					p.R219C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C655T	11						.						53.0	49.0	50.0					11																	36248835		2202	4298	6500	36205411	SO:0001583	missense	143458	exon5			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.655C>T	11.37:g.36248835C>T	ENSP00000318607:p.Arg219Cys	Somatic		Capture	Illumina HiSeq	Phase_I	36205411	NM_174902	B7Z1U3|B9EG81|Q8NBJ0	Missense_Mutation	SNP	ENST00000315571.5	37	CCDS31462.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.442173	0.83993	.	.	ENSG00000179241	ENST00000528989;ENST00000524419;ENST00000315571	D;D;D	0.95885	-3.76;-3.84;-3.49	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	D	0.95695	0.8600	L	0.32530	0.975	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.994;0.99	D	0.95221	0.8334	10	0.44086	T	0.13	.	13.4351	0.61079	0.1568:0.8432:0.0:0.0	.	209;170;219	E9PR86;B7Z1U3;Q86YD5	.;.;LRAD3_HUMAN	C	170;209;219	ENSP00000433954:R170C;ENSP00000434313:R209C;ENSP00000318607:R219C	ENSP00000318607:R219C	R	+	1	0	LDLRAD3	36205411	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.089000	0.57685	2.359000	0.80004	0.655000	0.94253	CGC		0.637	LDLRAD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389085.1	NM_174902	
ALX4	60529	broad.mit.edu	37	11	44297022	44297022	+	Missense_Mutation	SNP	C	C	T	rs104894193		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:44297022C>T	ENST00000329255.3	-	2	756	c.653G>A	c.(652-654)cGg>cAg	p.R218Q		NM_021926.3	NP_068745.2	Q9H161	ALX4_HUMAN	ALX homeobox 4	218			R -> Q (in PFM2). {ECO:0000269|PubMed:11137991}.		anterior/posterior pattern specification (GO:0009952)|digestive tract development (GO:0048565)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal system morphogenesis (GO:0048704)|hair follicle development (GO:0001942)|muscle organ development (GO:0007517)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of apoptotic process (GO:0042981)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R218Q(1)		central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	16						GAAGGTGGTCCGGTTCCGCCG	0.632																																					p.R218Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G653A	11	GRCh37	CM010011	ALX4	M	rs104894193	.						147.0	155.0	152.0					11																	44297022		2203	4299	6502	44253598	SO:0001583	missense	60529	exon2			AF294629	CCDS31468.1	11p11.2	2011-06-20	2008-11-04		ENSG00000052850	ENSG00000052850		"""Homeoboxes / PRD class"""	450	protein-coding gene	gene with protein product		605420	"""parietal foramina 2"", ""aristaless-like homeobox 4"""	PFM2		11017806, 8644736	Standard	NM_021926		Approved	FPP, PFM, KIAA1788	uc001myb.3	Q9H161	OTTHUMG00000166557	ENST00000329255.3:c.653G>A	11.37:g.44297022C>T	ENSP00000332744:p.Arg218Gln	Somatic		Capture	Illumina HiSeq	Phase_I	44253598	NM_021926	Q96JN7|Q9H198|Q9HAY9	Missense_Mutation	SNP	ENST00000329255.3	37	CCDS31468.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.099847	0.76983	.	.	ENSG00000052850	ENST00000329255	D	0.99150	-5.49	3.62	3.62	0.41486	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.204036	0.40908	N	0.000991	D	0.99600	0.9855	H	0.99286	4.5	0.80722	A	1	D	0.76494	0.999	D	0.70935	0.971	D	0.97329	0.9949	9	0.87932	D	0	.	15.4743	0.75465	0.0:1.0:0.0:0.0	.	218	Q9H161	ALX4_HUMAN	Q	218	ENSP00000332744:R218Q	ENSP00000332744:R218Q	R	-	2	0	ALX4	44253598	1.000000	0.71417	0.928000	0.36995	0.905000	0.53344	7.620000	0.83070	1.856000	0.53863	0.455000	0.32223	CGG		0.632	ALX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390399.1		
PHF21A	51317	broad.mit.edu	37	11	45986969	45986969	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:45986969G>A	ENST00000418153.2	-	9	1089	c.890C>T	c.(889-891)aCg>aTg	p.T297M	PHF21A_ENST00000257821.4_Missense_Mutation_p.T298M|PHF21A_ENST00000323180.6_Missense_Mutation_p.T298M|PHF21A_ENST00000527753.1_5'UTR			Q96BD5	PF21A_HUMAN	PHD finger protein 21A	297					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.T298M(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(10)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	29						CATGGGGAACGTTTTGGCTAT	0.537											OREG0020936	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T297M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C890T	11						.						147.0	106.0	120.0					11																	45986969		2202	4299	6501	45943545	SO:0001583	missense	51317	exon9			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.890C>T	11.37:g.45986969G>A	ENSP00000398824:p.Thr297Met	Somatic	935	Capture	Illumina HiSeq	Phase_I	45943545	NM_001101802	D3DQP5|Q6AWA2|Q9C0G7|Q9H8V9|Q9HAK6|Q9NZE9	Missense_Mutation	SNP	ENST00000418153.2	37	CCDS44578.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.033296	0.93575	.	.	ENSG00000135365	ENST00000257821;ENST00000323180;ENST00000418153	T;T;T	0.52526	0.66;0.66;0.66	6.17	6.17	0.99709	.	0.188503	0.56097	D	0.000028	T	0.65015	0.2651	L	0.54323	1.7	0.58432	D	0.999998	D;D;D	0.76494	0.992;0.998;0.999	P;P;P	0.62014	0.799;0.809;0.897	T	0.61441	-0.7062	10	0.54805	T	0.06	-5.9572	20.8794	0.99867	0.0:0.0:1.0:0.0	.	297;298;298	Q96BD5;Q96BD5-2;Q96BD5-3	PF21A_HUMAN;.;.	M	298;298;297	ENSP00000257821:T298M;ENSP00000323152:T298M;ENSP00000398824:T297M	ENSP00000257821:T298M	T	-	2	0	PHF21A	45943545	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.778000	0.75043	2.941000	0.99782	0.655000	0.94253	ACG		0.537	PHF21A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392583.1	NM_016621	
NDUFS3	4722	broad.mit.edu	37	11	47602418	47602418	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:47602418T>A	ENST00000263774.4	+	4	345	c.263T>A	c.(262-264)aTc>aAc	p.I88N	KBTBD4_ENST00000395288.2_5'Flank|KBTBD4_ENST00000526005.1_5'Flank|NDUFS3_ENST00000533507.1_3'UTR|NDUFS3_ENST00000534716.2_Missense_Mutation_p.I88N|KBTBD4_ENST00000533290.1_5'Flank|NDUFS3_ENST00000528192.1_Missense_Mutation_p.I88N|KBTBD4_ENST00000525720.1_5'Flank|NDUFS3_ENST00000534208.1_3'UTR|KBTBD4_ENST00000430070.2_5'Flank	NM_004551.2	NP_004542.1	O75489	NDUS3_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 3, 30kDa (NADH-coenzyme Q reductase)	88					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.I88N(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)	9					Doxorubicin(DB00997)	GAGGTCTGTATCCATCCTGAT	0.502																																					p.I88N	Pancreas(15;551 601 22438 23457 52512)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T263A	11						.						213.0	180.0	191.0					11																	47602418		2201	4298	6499	47558994	SO:0001583	missense	4722	exon4			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.263T>A	11.37:g.47602418T>A	ENSP00000263774:p.Ile88Asn	Somatic		Capture	Illumina HiSeq	Phase_I	47558994	NM_004551	B2R9J1|B4DFM8|Q9UNQ8	Missense_Mutation	SNP	ENST00000263774.4	37	CCDS7941.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.616055	0.87359	.	.	ENSG00000213619	ENST00000263774;ENST00000528192;ENST00000530295;ENST00000534716	D;D;D	0.88664	-2.41;-2.41;-2.41	5.9	5.9	0.94986	.	0.096980	0.64402	D	0.000001	D	0.94883	0.8346	M	0.85041	2.73	0.80722	D	1	D;D;D	0.76494	0.999;0.978;0.961	D;P;P	0.74348	0.983;0.794;0.824	D	0.95492	0.8570	10	0.87932	D	0	-11.2834	16.3322	0.83039	0.0:0.0:0.0:1.0	.	88;88;14	B4DFM8;O75489;Q9UF24	.;NDUS3_HUMAN;.	N	88;88;66;88	ENSP00000263774:I88N;ENSP00000432099:I88N;ENSP00000434970:I88N	ENSP00000263774:I88N	I	+	2	0	NDUFS3	47558994	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	7.698000	0.84413	2.251000	0.74343	0.528000	0.53228	ATC		0.502	NDUFS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391749.1	NM_004551	
OR4D6	219983	broad.mit.edu	37	11	59225222	59225222	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:59225222G>A	ENST00000300127.2	+	1	812	c.789G>A	c.(787-789)atG>atA	p.M263I		NM_001004708.1	NP_001004708.1	Q8NGJ1	OR4D6_HUMAN	olfactory receptor, family 4, subfamily D, member 6	263			M -> T (in dbSNP:rs1453541).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.M263I(1)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	34						GGCCCTTCATGACGCTGCCCA	0.527																																					p.M263I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G789A	11						.						115.0	110.0	111.0					11																	59225222		2201	4295	6496	58981798	SO:0001583	missense	219983	exon1			AB065803	CCDS31562.1	11q12.1	2012-08-09			ENSG00000166884	ENSG00000166884		"""GPCR / Class A : Olfactory receptors"""	15175	protein-coding gene	gene with protein product							Standard	NM_001004708		Approved		uc010rku.2	Q8NGJ1	OTTHUMG00000167340	ENST00000300127.2:c.789G>A	11.37:g.59225222G>A	ENSP00000300127:p.Met263Ile	Somatic		Capture	Illumina HiSeq	Phase_I	58981798	NM_001004708	B2RNP7|Q6IFF5|Q96R74	Missense_Mutation	SNP	ENST00000300127.2	37	CCDS31562.1	.	.	.	.	.	.	.	.	.	.	G	7.206	0.594413	0.13875	.	.	ENSG00000166884	ENST00000300127	T	0.00036	8.86	6.01	-12.0	0.00017	GPCR, rhodopsin-like superfamily (1);	0.805216	0.11028	N	0.607551	T	0.00073	0.0002	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.54050	-0.8351	10	0.52906	T	0.07	-1.5571	16.3563	0.83236	0.0:0.5689:0.3235:0.1076	.	263	Q8NGJ1	OR4D6_HUMAN	I	263	ENSP00000300127:M263I	ENSP00000300127:M263I	M	+	3	0	OR4D6	58981798	0.000000	0.05858	0.000000	0.03702	0.090000	0.18270	-2.750000	0.00793	-2.949000	0.00294	-0.262000	0.10625	ATG		0.527	OR4D6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394234.1	NM_001004708	
DDB1	1642	broad.mit.edu	37	11	61097052	61097052	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:61097052C>T	ENST00000301764.7	-	4	729	c.332G>A	c.(331-333)cGc>cAc	p.R111H	DDB1_ENST00000545930.1_5'Flank|DDB1_ENST00000450997.2_Intron	NM_001923.4	NP_001914.3	Q16531	DDB1_HUMAN	damage-specific DNA binding protein 1, 127kDa	111	Interaction with CDT1.|WD repeat beta-propeller A.				DNA repair (GO:0006281)|histone H2A monoubiquitination (GO:0035518)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of mitotic cell cycle phase transition (GO:1901990)|UV-damage excision repair (GO:0070914)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)	p.R111H(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	48						GCGGCCAATGCGGTCCTGAGA	0.507								Nucleotide excision repair (NER)																													p.R111H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G332A	11						.						24.0	22.0	22.0					11																	61097052		2203	4299	6502	60853628	SO:0001583	missense	1642	exon4			AJ002955	CCDS31576.1	11q12-q13	2014-09-17	2002-08-29		ENSG00000167986	ENSG00000167986			2717	protein-coding gene	gene with protein product		600045	"""damage-specific DNA binding protein 1 (127kD)"""			8530102, 10574459	Standard	NM_001923		Approved	XPE	uc001nrc.5	Q16531	OTTHUMG00000168209	ENST00000301764.7:c.332G>A	11.37:g.61097052C>T	ENSP00000301764:p.Arg111His	Somatic		Capture	Illumina HiSeq	Phase_I	60853628	NM_001923	A6NG77|B2R648|B4DG00|O15176|Q13289|Q58F96	Missense_Mutation	SNP	ENST00000301764.7	37	CCDS31576.1	.	.	.	.	.	.	.	.	.	.	C	17.99	3.522294	0.64747	.	.	ENSG00000167986	ENST00000301764;ENST00000539426;ENST00000535283;ENST00000542337	T;T;T;T	0.45668	0.89;0.89;0.89;0.89	5.0	5.0	0.66597	.	0.051676	0.85682	D	0.000000	T	0.57533	0.2060	M	0.80982	2.52	0.80722	D	1	B;P	0.48407	0.169;0.91	B;P	0.48795	0.024;0.59	T	0.65076	-0.6256	10	0.59425	D	0.04	-13.2997	18.6709	0.91512	0.0:1.0:0.0:0.0	.	111;111	B7Z2A1;Q16531	.;DDB1_HUMAN	H	111;55;55;111	ENSP00000301764:R111H;ENSP00000445554:R55H;ENSP00000441825:R55H;ENSP00000444105:R111H	ENSP00000301764:R111H	R	-	2	0	DDB1	60853628	1.000000	0.71417	0.980000	0.43619	0.775000	0.43874	5.731000	0.68554	2.480000	0.83734	0.563000	0.77884	CGC		0.507	DDB1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398816.1	NM_001923	
SYVN1	84447	broad.mit.edu	37	11	64898618	64898618	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:64898618C>T	ENST00000377190.3	-	9	903	c.809G>A	c.(808-810)cGc>cAc	p.R270H	SYVN1_ENST00000526060.1_Missense_Mutation_p.R270H|SYVN1_ENST00000307289.6_Missense_Mutation_p.R219H|SYVN1_ENST00000526121.1_5'UTR|SYVN1_ENST00000294256.8_Missense_Mutation_p.R270H	NM_172230.2	NP_757385.1	Q86TM6	SYVN1_HUMAN	synovial apoptosis inhibitor 1, synoviolin	270	Interaction with p53/TP53.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|in utero embryonic development (GO:0001701)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|zinc ion binding (GO:0008270)	p.R270H(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22						GTTCATGTTGCGGATGGCTCG	0.552																																					p.R270H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G809A	11						.						88.0	78.0	81.0					11																	64898618		2201	4297	6498	64655194	SO:0001583	missense	84447	exon9			AB085847	CCDS8097.1, CCDS31605.1	11q13	2013-01-09			ENSG00000162298	ENSG00000162298		"""RING-type (C3HC4) zinc fingers"""	20738	protein-coding gene	gene with protein product	"""HMG-coA reductase degradation 1 homolog (S. cerevisiae)"""	608046				12975321	Standard	NM_032431		Approved	HRD1, DER3	uc001odb.3	Q86TM6		ENST00000377190.3:c.809G>A	11.37:g.64898618C>T	ENSP00000366395:p.Arg270His	Somatic		Capture	Illumina HiSeq	Phase_I	64655194	NM_032431	Q8N3K3|Q8N6E8|Q96JL5|Q96PK3	Missense_Mutation	SNP	ENST00000377190.3	37	CCDS31605.1	.	.	.	.	.	.	.	.	.	.	C	19.25	3.792078	0.70452	.	.	ENSG00000162298	ENST00000377190;ENST00000294256;ENST00000434219;ENST00000307289;ENST00000526060;ENST00000531018	T;T;T;T	0.12465	2.68;2.68;2.85;2.68	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.18676	0.0448	M	0.67625	2.065	0.80722	D	1	P;P;P	0.50617	0.89;0.937;0.895	B;B;B	0.40444	0.329;0.271;0.14	T	0.02844	-1.1103	10	0.56958	D	0.05	-21.0838	16.0806	0.81003	0.0:1.0:0.0:0.0	.	219;270;270	Q86TM6-2;Q86TM6-3;Q86TM6	.;.;SYVN1_HUMAN	H	270;270;270;219;270;210	ENSP00000366395:R270H;ENSP00000294256:R270H;ENSP00000302035:R219H;ENSP00000436984:R270H	ENSP00000294256:R270H	R	-	2	0	SYVN1	64655194	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.809000	0.62591	2.379000	0.81126	0.563000	0.77884	CGC		0.552	SYVN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385274.1	NM_032431	
MAP3K11	4296	broad.mit.edu	37	11	65367034	65367034	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:65367034delG	ENST00000530153.1	-	9	1787	c.1266delC	c.(1264-1266)cccfs	p.P422fs	MAP3K11_ENST00000532507.1_Frame_Shift_Del_p.P95fs|MAP3K11_ENST00000534432.1_5'UTR|MAP3K11_ENST00000309100.3_Frame_Shift_Del_p.P679fs					mitogen-activated protein kinase kinase kinase 11									p.T680fs*>168(1)		breast(3)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(14)|skin(1)	24						GCGTTGGCGTGGGGGGTGTTG	0.761																																					p.P679fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2037delC	11						.			6,3940		1,4,1968	9.0	13.0	11.0			-3.1	0.0	11		12	22,7752		6,10,3871	no	frameshift	MAP3K11	NM_002419.3		7,14,5839	A1A1,A1R,RR		0.283,0.1521,0.2389			65367034	28,11692	2096	4138	6234	65123610	SO:0001589	frameshift_variant	4296	exon9				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.1266delC	11.37:g.65367034delG	ENSP00000433886:p.Pro422fs	Somatic		Capture	Illumina HiSeq	Phase_I	65123610	NM_002419		Frame_Shift_Del	DEL	ENST00000530153.1	37																																																																																					0.761	MAP3K11-004	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000390233.2		
CTSW	1521	broad.mit.edu	37	11	65649948	65649948	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:65649948G>T	ENST00000307886.3	+	5	535	c.489G>T	c.(487-489)gaG>gaT	p.E163D	CTSW_ENST00000528419.1_Missense_Mutation_p.E163D	NM_001335.3	NP_001326	P56202	CATW_HUMAN	cathepsin W	163					immune response (GO:0006955)	membrane (GO:0016020)	cysteine-type peptidase activity (GO:0008234)	p.E163D(1)		central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(5)	9				READ - Rectum adenocarcinoma(159;0.168)		GCAACATAGAGACCCTGTGGC	0.647																																					p.E163D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G489T	11						.						82.0	86.0	85.0					11																	65649948		2201	4296	6497	65406524	SO:0001583	missense	1521	exon5			AF055903	CCDS8117.1	11q13.1	2008-02-01	2006-12-05		ENSG00000172543	ENSG00000172543		"""Cathepsins"""	2546	protein-coding gene	gene with protein product		602364	"""cathepsin W (lymphopain)"""			9108299, 9675123	Standard	NM_001335		Approved		uc001ogc.1	P56202	OTTHUMG00000166663	ENST00000307886.3:c.489G>T	11.37:g.65649948G>T	ENSP00000311300:p.Glu163Asp	Somatic		Capture	Illumina HiSeq	Phase_I	65406524	NM_001335	Q86VT4	Missense_Mutation	SNP	ENST00000307886.3	37	CCDS8117.1	.	.	.	.	.	.	.	.	.	.	G	18.05	3.537150	0.65085	.	.	ENSG00000172543	ENST00000307886;ENST00000528419;ENST00000526034	T;T;T	0.46819	0.86;0.86;0.86	5.69	3.84	0.44239	Peptidase C1A, papain C-terminal (2);	0.077254	0.52532	D	0.000072	T	0.72622	0.3483	M	0.93197	3.39	0.35606	D	0.808257	D;D	0.89917	0.998;1.0	D;D	0.81914	0.995;0.977	T	0.80264	-0.1455	10	0.66056	D	0.02	.	8.5631	0.33523	0.176:0.0:0.824:0.0	.	163;163	P56202;E9PI30	CATW_HUMAN;.	D	163;163;162	ENSP00000311300:E163D;ENSP00000436568:E163D;ENSP00000434267:E162D	ENSP00000311300:E163D	E	+	3	2	CTSW	65406524	1.000000	0.71417	1.000000	0.80357	0.591000	0.36615	1.928000	0.40104	0.763000	0.33175	0.655000	0.94253	GAG		0.647	CTSW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391042.1	NM_001335	
TBC1D10C	374403	broad.mit.edu	37	11	67176565	67176565	+	Frame_Shift_Del	DEL	C	C	-	rs147560025		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:67176565delC	ENST00000542590.1	+	8	968	c.954delC	c.(952-954)atcfs	p.I318fs	TBC1D10C_ENST00000526387.1_Frame_Shift_Del_p.P255fs|TBC1D10C_ENST00000312390.5_Frame_Shift_Del_p.I318fs			Q8IV04	TB10C_HUMAN	TBC1 domain family, member 10C	318					retrograde transport, endosome to Golgi (GO:0042147)	filopodium membrane (GO:0031527)|membrane (GO:0016020)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)	p.A321fs*100(2)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	16			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)			TTCGAGCCATCCCCCCCGCGC	0.687																																					p.I318fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.954delC	11						.																																			66933141	SO:0001589	frameshift_variant	374403	exon9			BC035630	CCDS8162.1, CCDS58150.1	11q13.1	2013-07-09			ENSG00000175463	ENSG00000175463			24702	protein-coding gene	gene with protein product		610831				17230191, 20404108	Standard	NM_001256508		Approved	FLJ00332, Carabin, EPI64C	uc001ola.4	Q8IV04	OTTHUMG00000167139	ENST00000542590.1:c.954delC	11.37:g.67176565delC	ENSP00000443654:p.Ile318fs	Somatic		Capture	Illumina HiSeq	Phase_I	66933141	NM_198517	G3V1D6	Frame_Shift_Del	DEL	ENST00000542590.1	37	CCDS8162.1																																																																																				0.687	TBC1D10C-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395492.2	NM_198517	
INPPL1	3636	broad.mit.edu	37	11	71939802	71939802	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:71939802G>A	ENST00000298229.2	+	4	633	c.429G>A	c.(427-429)ccG>ccA	p.P143P	INPPL1_ENST00000538751.1_5'UTR|INPPL1_ENST00000541756.1_5'UTR	NM_001567.3	NP_001558.3	O15357	SHIP2_HUMAN	inositol polyphosphate phosphatase-like 1	143					actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|endochondral ossification (GO:0001958)|endocytosis (GO:0006897)|glucose metabolic process (GO:0006006)|immune system process (GO:0002376)|inositol phosphate metabolic process (GO:0043647)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|post-embryonic development (GO:0009791)|response to insulin (GO:0032868)|ruffle assembly (GO:0097178)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|SH2 domain binding (GO:0042169)	p.P143P(1)		breast(2)|endometrium(9)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						CGCTGCCCCCGCGCTCTGGCT	0.672																																					p.P143P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G429A	11						.						27.0	35.0	32.0					11																	71939802		2200	4293	6493	71617450	SO:0001819	synonymous_variant	3636	exon4			Y14385	CCDS8213.1	11q23	2013-02-14			ENSG00000165458	ENSG00000165458		"""Sterile alpha motif (SAM) domain containing"", ""SH2 domain containing"""	6080	protein-coding gene	gene with protein product	"""51C protein"""	600829				8530088	Standard	NM_001567		Approved	SHIP2	uc001osf.3	O15357	OTTHUMG00000167879	ENST00000298229.2:c.429G>A	11.37:g.71939802G>A		Somatic		Capture	Illumina HiSeq	Phase_I	71617450	NM_001567	B2RTX5|Q13577|Q13578	Silent	SNP	ENST00000298229.2	37	CCDS8213.1																																																																																				0.672	INPPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396789.1	NM_001567	
ARRB1	408	broad.mit.edu	37	11	74980000	74980000	+	Silent	SNP	G	G	A	rs150290364	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:74980000G>A	ENST00000420843.2	-	14	1123	c.1026C>T	c.(1024-1026)gaC>gaT	p.D342D	ARRB1_ENST00000393505.4_Silent_p.D342D|ARRB1_ENST00000360025.3_Silent_p.D334D	NM_004041.4	NP_004032.2	P49407	ARRB1_HUMAN	arrestin, beta 1	342	Interaction with TRAF6.				activation of MAPK activity (GO:0000187)|apoptotic DNA fragmentation (GO:0006309)|blood coagulation (GO:0007596)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor internalization (GO:0002031)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of GTPase activity (GO:0034260)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein ubiquitination (GO:0031397)|Notch signaling pathway (GO:0007219)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of GTPase activity (GO:0043547)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H4 acetylation (GO:0090240)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of receptor internalization (GO:0002092)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-Golgi vesicle-mediated transport (GO:0006892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|stress fiber assembly (GO:0043149)|transcription from RNA polymerase II promoter (GO:0006366)	basolateral plasma membrane (GO:0016323)|chromatin (GO:0000785)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|pseudopodium (GO:0031143)	angiotensin receptor binding (GO:0031701)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|enzyme inhibitor activity (GO:0004857)|GTPase activator activity (GO:0005096)|insulin-like growth factor receptor binding (GO:0005159)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)	p.D334D(1)		breast(4)|large_intestine(2)|lung(4)|prostate(1)	11						CCACGGCCACGTCGCTGAAAC	0.592																																					p.D334D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1002T	11						.	G	,	6,4394	11.4+/-27.6	0,6,2194	107.0	98.0	101.0		1026,1002	-8.7	0.1	11	dbSNP_134	101	0,8586		0,0,4293	no	coding-synonymous,coding-synonymous	ARRB1	NM_004041.4,NM_020251.3	,	0,6,6487	AA,AG,GG		0.0,0.1364,0.0462	,	342/419,334/411	74980000	6,12980	2200	4293	6493	74657648	SO:0001819	synonymous_variant	408	exon13			BC003636	CCDS31640.1, CCDS44684.1	11q13	2008-12-11			ENSG00000137486	ENSG00000137486			711	protein-coding gene	gene with protein product	"""arrestin 2"""	107940		ARR1		8486659	Standard	NM_004041		Approved		uc001owe.2	P49407	OTTHUMG00000165444	ENST00000420843.2:c.1026C>T	11.37:g.74980000G>A		Somatic		Capture	Illumina HiSeq	Phase_I	74657648	NM_020251	B6V9G8|O75625|O75630|Q2PP20|Q9BTK8	Silent	SNP	ENST00000420843.2	37	CCDS44684.1	.	.	.	.	.	.	.	.	.	.	G	4.533	0.099037	0.08681	0.001364	0.0	ENSG00000137486	ENST00000532447	.	.	.	4.36	-8.72	0.00845	.	.	.	.	.	T	0.64125	0.2570	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.73442	-0.3981	4	.	.	.	-17.0269	17.7008	0.88294	0.7866:0.0:0.2134:0.0	.	.	.	.	C	159	.	.	R	-	1	0	ARRB1	74657648	0.000000	0.05858	0.077000	0.20336	0.612000	0.37316	-2.165000	0.01274	-2.653000	0.00423	-1.250000	0.01514	CGT		0.592	ARRB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384092.3	NM_004041	
C11orf30	56946	broad.mit.edu	37	11	76256898	76256898	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:76256898C>T	ENST00000529032.1	+	19	3331	c.3331C>T	c.(3331-3333)Cgc>Tgc	p.R1111C	C11orf30_ENST00000334736.3_Missense_Mutation_p.R1111C|C11orf30_ENST00000343878.3_Intron|C11orf30_ENST00000533248.1_Missense_Mutation_p.R1020C|C11orf30_ENST00000525919.1_Missense_Mutation_p.R1112C|C11orf30_ENST00000525038.1_Missense_Mutation_p.R1112C|C11orf30_ENST00000524767.1_Missense_Mutation_p.R1126C|C11orf30_ENST00000524490.1_Missense_Mutation_p.R1013C			Q7Z589	EMSY_HUMAN	chromosome 11 open reading frame 30	1111					chromatin modification (GO:0016568)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.R1111C(3)		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						TTTTGAGGGGCGCCAGCCTCC	0.453																																					p.R1111C												.	.	3	Substitution - Missense(3)	large_intestine(2)|lung(1)	c.C3331T	11						.						70.0	72.0	71.0					11																	76256898		2200	4292	6492	75934546	SO:0001583	missense	56946	exon20			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.3331C>T	11.37:g.76256898C>T	ENSP00000432327:p.Arg1111Cys	Somatic		Capture	Illumina HiSeq	Phase_I	75934546	NM_020193	B7ZKT8|B7ZKU0|B7ZKU2|Q17RM7|Q4G109|Q8NBU6|Q8TE50|Q9H8I9|Q9NRH0	Missense_Mutation	SNP	ENST00000529032.1	37	CCDS8244.1	.	.	.	.	.	.	.	.	.	.	C	15.29	2.790075	0.50102	.	.	ENSG00000158636	ENST00000524490;ENST00000334736;ENST00000393457;ENST00000524767;ENST00000533248;ENST00000525919;ENST00000525038;ENST00000529032	.	.	.	5.5	4.57	0.56435	.	0.379291	0.30329	N	0.009866	T	0.52677	0.1749	N	0.08118	0	0.80722	D	1	D;P;P;P;P;P	0.76494	0.999;0.923;0.923;0.804;0.564;0.804	D;B;B;B;B;B	0.69654	0.965;0.17;0.17;0.165;0.109;0.165	T	0.63211	-0.6688	9	0.56958	D	0.05	-0.0182	15.6293	0.76888	0.1384:0.8616:0.0:0.0	.	1020;1112;1126;1112;1013;1111	B7ZKT8;B7ZKU2;B7ZKU0;Q17RM7;E9PMC9;Q7Z589	.;.;.;.;.;EMSY_HUMAN	C	1013;1111;793;1126;1020;1112;1112;1111	.	ENSP00000334130:R1111C	R	+	1	0	C11orf30	75934546	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.634000	0.46528	1.505000	0.48720	0.650000	0.86243	CGC		0.453	C11orf30-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383288.2	NM_020193	
FAT3	120114	broad.mit.edu	37	11	92534138	92534138	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:92534138C>T	ENST00000298047.6	+	9	7976	c.7959C>T	c.(7957-7959)atC>atT	p.I2653I	FAT3_ENST00000525166.1_Silent_p.I2503I|FAT3_ENST00000409404.2_Silent_p.I2653I			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	2653	Cadherin 24. {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.I2653I(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)				TCCTGGAAATCGATCCTGACA	0.463										TCGA Ovarian(4;0.039)																											p.I2653I												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C7959T	11						.						36.0	34.0	35.0					11																	92534138		1875	4104	5979	92173786	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.7959C>T	11.37:g.92534138C>T		Somatic		Capture	Illumina HiSeq	Phase_I	92173786	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																					0.463	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
MAML2	84441	broad.mit.edu	37	11	95724856	95724856	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:95724856C>A	ENST00000524717.1	-	3	3455	c.2171G>T	c.(2170-2172)gGc>gTc	p.G724V		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	724					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)	p.G724V(1)	CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				TGGACTGGGGCCTGTGTTCTG	0.433			T	"""MECT1, CRTC3"""	salivary gland mucoepidermoid																																p.G724V			Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2171T	11						.						94.0	90.0	92.0					11																	95724856		1879	4095	5974	95364504	SO:0001583	missense	84441	exon3			AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"""mastermind (Drosophila)-like 2"""			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.2171G>T	11.37:g.95724856C>A	ENSP00000434552:p.Gly724Val	Somatic		Capture	Illumina HiSeq	Phase_I	95364504	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Missense_Mutation	SNP	ENST00000524717.1	37	CCDS44714.1	.	.	.	.	.	.	.	.	.	.	C	18.10	3.547982	0.65311	.	.	ENSG00000184384	ENST00000524717;ENST00000440572	T;T	0.54279	0.58;0.58	5.46	5.46	0.80206	.	0.494497	0.18723	N	0.132980	T	0.64571	0.2610	L	0.54323	1.7	0.54753	D	0.999981	D	0.64830	0.994	P	0.59825	0.864	T	0.64960	-0.6284	10	0.59425	D	0.04	-4.6525	14.2681	0.66135	0.0:0.727:0.273:0.0	.	724	Q8IZL2	MAML2_HUMAN	V	724	ENSP00000434552:G724V;ENSP00000412394:G724V	ENSP00000412394:G724V	G	-	2	0	MAML2	95364504	1.000000	0.71417	0.998000	0.56505	0.963000	0.63663	1.908000	0.39907	2.577000	0.86979	0.557000	0.71058	GGC		0.433	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1		
OPCML	4978	broad.mit.edu	37	11	132527171	132527171	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr11:132527171G>A	ENST00000331898.7	-	2	789	c.211C>T	c.(211-213)Cgc>Tgc	p.R71C	OPCML_ENST00000529038.1_5'UTR|OPCML_ENST00000374778.4_Missense_Mutation_p.R30C|OPCML_ENST00000524381.1_Missense_Mutation_p.R64C|OPCML_ENST00000541867.1_Missense_Mutation_p.R71C	NM_002545.3	NP_002536.1	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion molecule-like	71	Ig-like C2-type 1.				cell adhesion (GO:0007155)|neuron recognition (GO:0008038)|opioid receptor signaling pathway (GO:0038003)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	opioid receptor activity (GO:0004985)	p.R71C(2)|p.R64C(1)		endometrium(5)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|skin(2)|urinary_tract(8)	47	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		ATGGTGCTGCGGTTTAGCCAG	0.542																																					p.R64C												.	.	3	Substitution - Missense(3)	endometrium(2)|large_intestine(1)	c.C190T	11						.						151.0	111.0	125.0					11																	132527171		2201	4297	6498	132032381	SO:0001583	missense	4978	exon3			BX537377	CCDS8492.1, CCDS31722.1	11q25	2013-01-11	2001-11-28		ENSG00000183715	ENSG00000183715		"""Immunoglobulin superfamily / I-set domain containing"""	8143	protein-coding gene	gene with protein product	"""IgLON family member 1"""	600632	"""opioid-binding protein/cell adhesion molecule-like"""			8244387	Standard	XM_005271578		Approved	OPCM, OBCAM, IGLON1	uc001qgs.3	Q14982	OTTHUMG00000163658	ENST00000331898.7:c.211C>T	11.37:g.132527171G>A	ENSP00000330862:p.Arg71Cys	Somatic		Capture	Illumina HiSeq	Phase_I	132032381	NM_001012393	B2CZX2|B7ZLQ1|Q17RN7|Q7Z3W6	Missense_Mutation	SNP	ENST00000331898.7	37	CCDS8492.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.028776	0.93518	.	.	ENSG00000183715	ENST00000331898;ENST00000524381;ENST00000374778;ENST00000416724;ENST00000541867	T;T;T;T	0.28069	1.63;1.63;1.63;1.63	5.92	5.02	0.67125	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.057400	0.64402	N	0.000001	T	0.65913	0.2737	M	0.93594	3.435	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	T	0.76642	-0.2884	10	0.87932	D	0	-7.4602	15.0633	0.71973	0.0678:0.0:0.9322:0.0	.	71;64;71;71	B7ZLQ1;Q7Z3W6;B7ZLQ0;Q14982	.;.;.;OPCM_HUMAN	C	71;64;30;64;71	ENSP00000330862:R71C;ENSP00000434750:R64C;ENSP00000363910:R30C;ENSP00000445496:R71C	ENSP00000330862:R71C	R	-	1	0	OPCML	132032381	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.799000	0.99117	1.521000	0.48983	0.655000	0.94253	CGC		0.542	OPCML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374689.3	NM_001012393	
GTF2H3	2967	broad.mit.edu	37	12	124123861	124123862	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:124123861_124123862insG	ENST00000543341.2	+	2	95_96	c.64_65insG	c.(64-66)tggfs	p.W22fs	GTF2H3_ENST00000228955.7_Intron	NM_001271867.1|NM_001516.3	NP_001258796.1|NP_001507.2	Q13889	TF2H3_HUMAN	general transcription factor IIH, polypeptide 3, 34kDa	22					7-methylguanosine mRNA capping (GO:0006370)|ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|gene expression (GO:0010467)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|translation (GO:0006412)|viral process (GO:0016032)	core TFIIH complex (GO:0000439)|holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|sequence-specific DNA binding transcription factor activity (GO:0003700)|translation factor activity, nucleic acid binding (GO:0008135)	p.Q25fs*66(1)		breast(2)|endometrium(1)|large_intestine(4)|lung(2)|urinary_tract(1)	10	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.1e-05)|Epithelial(86;0.000388)|all cancers(50;0.00362)		CCCAATTTGGTGGGGAAAGCAA	0.322								Nucleotide excision repair (NER)																													p.W22fs	Melanoma(176;111 2022 3038 14733 36962)											.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.64_65insG	12						.																																			122689815	SO:0001589	frameshift_variant	2967	exon2			Z30093	CCDS9252.1, CCDS61275.1, CCDS73544.1	12q24.31	2012-11-05	2002-08-29		ENSG00000111358	ENSG00000111358		"""General transcription factors"", ""General transcription factor IIH complex subunits"""	4657	protein-coding gene	gene with protein product		601750	"""general transcription factor IIH, polypeptide 3 (34kD subunit)"""			8194529	Standard	NM_001516		Approved	BTF2, TFIIH, P34	uc001ufo.2	Q13889	OTTHUMG00000168697	ENST00000543341.2:c.68dupG	12.37:g.124123865_124123865dupG	ENSP00000445162:p.Trp22fs	Somatic		Capture	Illumina HiSeq	Phase_I	122689814	NM_001516	B2R819|B4DNZ6|Q7L0G0|Q96AT7	Frame_Shift_Ins	INS	ENST00000543341.2	37	CCDS9252.1																																																																																				0.322	GTF2H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400641.2	NM_001516	
CLEC12A	160364	broad.mit.edu	37	12	10124283	10124283	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:10124283A>G	ENST00000304361.4	+	1	270	c.88A>G	c.(88-90)Aaa>Gaa	p.K30E	CLEC12A_ENST00000355690.4_Missense_Mutation_p.K40E|CLEC12A_ENST00000434319.2_Missense_Mutation_p.K30E|CLEC12A_ENST00000350667.4_Missense_Mutation_p.K30E	NM_138337.5|NM_201623.3	NP_612210.4|NP_963917.2	Q5QGZ9	CL12A_HUMAN	C-type lectin domain family 12, member A	30						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.K30E(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	16						ATTTGGGGAAAAAGGTAAGAT	0.318																																					p.K30E	Melanoma(197;1487 2125 16611 22221 34855)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A88G	12						.						83.0	91.0	88.0					12																	10124283		2203	4299	6502	10015550	SO:0001583	missense	160364	exon1			AY498550	CCDS8608.1, CCDS8609.1, CCDS55803.1, CCDS73442.1	12p13.31	2010-08-17			ENSG00000172322	ENSG00000172322		"""C-type lectin domain containing"""	31713	protein-coding gene	gene with protein product		612088					Standard	NM_201623		Approved	CLL-1, MICL	uc001qwq.3	Q5QGZ9		ENST00000304361.4:c.88A>G	12.37:g.10124283A>G	ENSP00000302804:p.Lys30Glu	Somatic		Capture	Illumina HiSeq	Phase_I	10015550	NM_138337	B2RA16|Q6P4H1|Q6RH77|Q6RH78|Q8TDQ6	Missense_Mutation	SNP	ENST00000304361.4	37	CCDS8608.1	.	.	.	.	.	.	.	.	.	.	A	8.465	0.856104	0.17106	.	.	ENSG00000172322	ENST00000355690;ENST00000396507;ENST00000304361;ENST00000434319;ENST00000350667	T;T;T;T;T	0.06768	4.55;3.26;4.56;4.0;4.27	4.12	2.97	0.34412	.	.	.	.	.	T	0.04861	0.0131	N	0.25890	0.77	0.26457	N	0.975509	P;B;B	0.36412	0.552;0.067;0.2	B;B;B	0.30105	0.111;0.012;0.051	T	0.37753	-0.9692	9	0.20519	T	0.43	.	6.349	0.21365	0.8887:0.0:0.1113:0.0	.	30;30;40	Q5QGZ9-4;Q5QGZ9;Q5QGZ9-1	.;CL12A_HUMAN;.	E	40;30;30;30;30	ENSP00000347916:K40E;ENSP00000379764:K30E;ENSP00000302804:K30E;ENSP00000405244:K30E;ENSP00000345448:K30E	ENSP00000302804:K30E	K	+	1	0	CLEC12A	10015550	0.733000	0.28132	0.724000	0.30704	0.309000	0.27889	0.934000	0.28910	0.918000	0.36919	0.533000	0.62120	AAA		0.318	CLEC12A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399545.1	NM_138337	
STAB2	55576	broad.mit.edu	37	12	104144415	104144415	+	Missense_Mutation	SNP	C	C	A	rs143368827		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:104144415C>A	ENST00000388887.2	+	60	6701	c.6497C>A	c.(6496-6498)cCg>cAg	p.P2166Q	RP11-341G23.4_ENST00000551299.1_RNA	NM_017564.9	NP_060034.9			stabilin 2									p.P2166Q(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						AACTGTGAGCCGGAGCAGCTG	0.542																																					p.P2166Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C6497A	12						.						102.0	92.0	96.0					12																	104144415		2203	4300	6503	102668545	SO:0001583	missense	55576	exon60			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.6497C>A	12.37:g.104144415C>A	ENSP00000373539:p.Pro2166Gln	Somatic		Capture	Illumina HiSeq	Phase_I	102668545	NM_017564		Missense_Mutation	SNP	ENST00000388887.2	37	CCDS31888.1	.	.	.	.	.	.	.	.	.	.	C	14.83	2.652719	0.47362	.	.	ENSG00000136011	ENST00000388887;ENST00000258495	T	0.64438	-0.1	5.32	3.23	0.37069	.	0.306880	0.30101	N	0.010403	T	0.43634	0.1256	L	0.47716	1.5	0.19775	N	0.99996	P	0.36874	0.572	B	0.31442	0.13	T	0.17440	-1.0369	10	0.15499	T	0.54	.	4.3143	0.10986	0.0:0.5199:0.0:0.4801	.	2166	Q8WWQ8	STAB2_HUMAN	Q	2166;853	ENSP00000373539:P2166Q	ENSP00000258495:P853Q	P	+	2	0	STAB2	102668545	0.800000	0.28916	0.947000	0.38551	0.808000	0.45660	1.750000	0.38329	1.238000	0.43771	0.555000	0.69702	CCG		0.542	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
TDG	6996	broad.mit.edu	37	12	104376700	104376700	+	Missense_Mutation	SNP	A	A	C	rs61937630		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	A	A	A	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:104376700A>C	ENST00000392872.3	+	5	836	c.602A>C	c.(601-603)aAa>aCa	p.K201T	TDG_ENST00000266775.9_Missense_Mutation_p.K197T|AC078819.1_ENST00000401157.1_RNA|TDG_ENST00000542036.1_Missense_Mutation_p.K25Q|TDG_ENST00000544861.1_Missense_Mutation_p.K58T	NM_003211.4	NP_003202.3	Q13569	TDG_HUMAN	thymine-DNA glycosylase	201					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|chromatin modification (GO:0016568)|depyrimidination (GO:0045008)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|embryo development (GO:0009790)|mismatch repair (GO:0006298)|negative regulation of chromatin binding (GO:0035562)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression, epigenetic (GO:0040029)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|double-stranded DNA binding (GO:0003690)|mismatched DNA binding (GO:0030983)|protein homodimerization activity (GO:0042803)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|RNA polymerase II transcription cofactor activity (GO:0001104)|structure-specific DNA binding (GO:0043566)	p.K201T(1)		large_intestine(2)|lung(14)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(302;0.00114)		CCCGGCAGCAAAGATCTCTCC	0.458								Base excision repair (BER), DNA glycosylases																													p.K201T												.	.	1	Substitution - Missense(1)	skin(1)	c.A602C	12						.						81.0	78.0	79.0					12																	104376700		2203	4300	6503	102900830	SO:0001583	missense	6996	exon5			U51166	CCDS9095.1	12q24.1	2014-05-14			ENSG00000139372	ENSG00000139372	3.2.2.29		11700	protein-coding gene	gene with protein product	"""G/T mismatch-specific thymine DNA glycosylase"""	601423				8662714, 9299239	Standard	NM_003211		Approved		uc001tkg.3	Q13569	OTTHUMG00000168418	ENST00000392872.3:c.602A>C	12.37:g.104376700A>C	ENSP00000376611:p.Lys201Thr	None		Capture	Illumina HiSeq	Phase_I	102900830	NM_003211	Q8IUZ6|Q8IZM3	Missense_Mutation	SNP	ENST00000392872.3	37	CCDS9095.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.68|17.68	3.450099|3.450099	0.63290|0.63290	.|.	.|.	ENSG00000139372|ENSG00000139372	ENST00000542036|ENST00000392872;ENST00000266775;ENST00000544861;ENST00000537100	T|T;T;T;T	0.22539|0.45276	1.95|0.9;0.9;0.9;0.9	5.4|5.4	5.4|5.4	0.78164|0.78164	.|Uracil-DNA glycosylase-like (3);	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.47116|0.47116	0.1428|0.1428	L|L	0.36672|0.36672	1.1|1.1	0.29181|0.29181	N|N	0.876493|0.876493	B|P;P	0.22346|0.42692	0.068|0.787;0.787	B|P;P	0.12837|0.52159	0.008|0.691;0.581	T|T	0.42699|0.42699	-0.9436|-0.9436	10|10	0.87932|0.31617	D|T	0|0.26	-25.7328|-25.7328	15.4266|15.4266	0.75055|0.75055	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	rs61937630|rs61937630	25|201;201	B4DI29|B2R848;Q13569	.|.;TDG_HUMAN	Q|T	25|201;197;58;194	ENSP00000439054:K25Q|ENSP00000376611:K201T;ENSP00000266775:K197T;ENSP00000445899:K58T;ENSP00000439825:K194T	ENSP00000439054:K25Q|ENSP00000266775:K197T	K|K	+|+	1|2	0|0	TDG|TDG	102900830|102900830	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.736000|0.736000	0.42039|0.42039	9.271000|9.271000	0.95698|0.95698	2.037000|2.037000	0.60232|0.60232	0.460000|0.460000	0.39030|0.39030	AAG|AAA		0.458	TDG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399673.2		
RFX4	5992	broad.mit.edu	37	12	107103190	107103190	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:107103190C>T	ENST00000392842.1	+	9	1330	c.916C>T	c.(916-918)Cga>Tga	p.R306*	RP11-144F15.1_ENST00000551505.1_Intron|RFX4_ENST00000229387.5_Nonsense_Mutation_p.R212*|RFX4_ENST00000357881.4_Nonsense_Mutation_p.R315*	NM_213594.2	NP_998759.1	Q33E94	RFX4_HUMAN	regulatory factor X, 4 (influences HLA class II expression)	306					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.R306*(1)|p.R315*(1)		NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(20)|pancreas(1)|upper_aerodigestive_tract(1)	35						AGAAAACTTGCGAAACATCAA	0.398																																					p.R212X												.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C634T	12						.						86.0	75.0	79.0					12																	107103190		2203	4300	6503	105627320	SO:0001587	stop_gained	5992	exon5			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.916C>T	12.37:g.107103190C>T	ENSP00000376585:p.Arg306*	Somatic		Capture	Illumina HiSeq	Phase_I	105627320	NM_032491	A8K5Y0|B2RDW4|Q33DW6|Q33DW7|Q33E95|Q6YM53|Q8MHQ1|Q8NC78|Q8NDF9|Q8SNA1|Q96S80|Q9BXI0	Nonsense_Mutation	SNP	ENST00000392842.1	37	CCDS9106.1	.	.	.	.	.	.	.	.	.	.	C	39	7.428677	0.98279	.	.	ENSG00000111783	ENST00000392842;ENST00000357881;ENST00000266774;ENST00000551640;ENST00000229387	.	.	.	5.59	4.68	0.58851	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05436	T	0.98	-8.515	15.4125	0.74937	0.1443:0.8557:0.0:0.0	.	.	.	.	X	306;315;315;251;212	.	ENSP00000229387:R212X	R	+	1	2	RFX4	105627320	1.000000	0.71417	0.992000	0.48379	0.990000	0.78478	2.987000	0.49378	1.294000	0.44707	0.650000	0.86243	CGA		0.398	RFX4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402707.1	NM_032491	
OAS3	4940	broad.mit.edu	37	12	113386914	113386914	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:113386914G>A	ENST00000228928.7	+	6	1457	c.1278G>A	c.(1276-1278)ccG>ccA	p.P426P	RP1-71H24.1_ENST00000552784.1_RNA	NM_006187.2	NP_006178.2	Q9Y6K5	OAS3_HUMAN	2'-5'-oligoadenylate synthetase 3, 100kDa	426	OAS domain 2.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|nucleobase-containing compound metabolic process (GO:0006139)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)	p.P426P(1)		breast(3)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|skin(2)	27						ACCTGAAGCCGAGCCCCCAGT	0.577																																					p.P426P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1278A	12						.						53.0	59.0	57.0					12																	113386914		2070	4194	6264	111871297	SO:0001819	synonymous_variant	4940	exon6			AF063613	CCDS44981.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111331			8088	protein-coding gene	gene with protein product		603351	"""2'-5'-oligoadenylate synthetase 3 (100 kD)"""			9790745	Standard	NM_006187		Approved		uc001tug.3	Q9Y6K5	OTTHUMG00000169795	ENST00000228928.7:c.1278G>A	12.37:g.113386914G>A		Somatic		Capture	Illumina HiSeq	Phase_I	111871297	NM_006187	Q2HJ14|Q9H3P5	Silent	SNP	ENST00000228928.7	37	CCDS44981.1																																																																																				0.577	OAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405920.1		
TPCN1	53373	broad.mit.edu	37	12	113707613	113707613	+	Silent	SNP	G	G	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:113707613G>C	ENST00000335509.6	+	7	1025	c.711G>C	c.(709-711)ctG>ctC	p.L237L	TPCN1_ENST00000541517.1_Silent_p.L309L|TPCN1_ENST00000550785.1_Silent_p.L309L|TPCN1_ENST00000392569.4_Silent_p.L169L	NM_017901.4	NP_060371.2	Q9ULQ1	TPC1_HUMAN	two pore segment channel 1	237					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.L237L(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						ACATCCTCCTGCTGCTGCTGT	0.597																																					p.L237L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G711C	12						.						162.0	126.0	138.0					12																	113707613		2203	4300	6503	112191996	SO:0001819	synonymous_variant	53373	exon7			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.711G>C	12.37:g.113707613G>C		Somatic		Capture	Illumina HiSeq	Phase_I	112191996	NM_017901	A7E258|Q86XS9|Q8NC20	Silent	SNP	ENST00000335509.6	37	CCDS31908.1																																																																																				0.597	TPCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405156.3	NM_017901	
PLBD2	196463	broad.mit.edu	37	12	113812683	113812683	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:113812683T>C	ENST00000280800.3	+	5	761	c.730T>C	c.(730-732)Tgt>Cgt	p.C244R	PLBD2_ENST00000545182.2_Missense_Mutation_p.C244R|PLBD2_ENST00000547163.1_3'UTR	NM_173542.3	NP_775813.2	Q8NHP8	PLBL2_HUMAN	phospholipase B domain containing 2	244					lipid catabolic process (GO:0016042)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	hydrolase activity (GO:0016787)	p.C244R(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(7)|prostate(1)	13						CTCTGGCTCCTGTTCTGCCCT	0.582																																					p.C244R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T730C	12						.						106.0	91.0	96.0					12																	113812683		2203	4300	6503	112297066	SO:0001583	missense	196463	exon5			BC030618	CCDS9168.1, CCDS53834.1	12q24.13	2013-10-11				ENSG00000151176			27283	protein-coding gene	gene with protein product	"""PLB homolog 2 (Dictyostelium)"", ""mannose-6-phosphate protein associated protein p76"""					17105447, 15193148, 19019078	Standard	NM_001159727		Approved	p76	uc001tve.2	Q8NHP8	OTTHUMG00000169567	ENST00000280800.3:c.730T>C	12.37:g.113812683T>C	ENSP00000280800:p.Cys244Arg	Somatic		Capture	Illumina HiSeq	Phase_I	112297066	NM_001159727	F5H5E2	Missense_Mutation	SNP	ENST00000280800.3	37	CCDS9168.1	.	.	.	.	.	.	.	.	.	.	T	14.91	2.677260	0.47886	.	.	ENSG00000151176	ENST00000545182;ENST00000280800	T;T	0.38722	1.12;1.12	4.93	3.7	0.42460	.	0.049031	0.85682	D	0.000000	T	0.71970	0.3403	H	0.95679	3.705	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.98;1.0	T	0.79885	-0.1614	10	0.87932	D	0	-51.0932	11.3315	0.49479	0.0:0.0:0.1521:0.8479	.	244;244	F5H5E2;Q8NHP8	.;PLBL2_HUMAN	R	244	ENSP00000443463:C244R;ENSP00000280800:C244R	ENSP00000280800:C244R	C	+	1	0	PLBD2	112297066	1.000000	0.71417	0.991000	0.47740	0.165000	0.22458	5.855000	0.69510	1.858000	0.53909	0.334000	0.21626	TGT		0.582	PLBD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404835.1	NM_173542	
MED13L	23389	broad.mit.edu	37	12	116457746	116457746	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:116457746C>T	ENST00000281928.3	-	6	863	c.657G>A	c.(655-657)acG>acA	p.T219T		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	219						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.T219T(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)		GGCCTGTTAGCGTCCCATTTA	0.408																																					p.T219T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G657A	12						.						129.0	112.0	118.0					12																	116457746		2203	4300	6503	114942129	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.657G>A	12.37:g.116457746C>T		Somatic		Capture	Illumina HiSeq	Phase_I	114942129	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Silent	SNP	ENST00000281928.3	37	CCDS9177.1																																																																																				0.408	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3		
CCDC64	92558	broad.mit.edu	37	12	120436390	120436390	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:120436390C>T	ENST00000397558.2	+	2	495	c.495C>T	c.(493-495)ggC>ggT	p.G165G		NM_207311.2	NP_997194.2	Q6ZP65	BICR1_HUMAN	coiled-coil domain containing 64	165					Golgi to secretory granule transport (GO:0055107)|neuron projection development (GO:0031175)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	dynactin binding (GO:0034452)|Rab GTPase binding (GO:0017137)	p.G165G(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(2)|lung(4)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	22	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AGTGGGAAGGCCGAGTGTCAG	0.483																																					p.G165G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C495T	12						.						73.0	80.0	78.0					12																	120436390		2017	4182	6199	118920773	SO:0001819	synonymous_variant	92558	exon2			U88834, AK129960	CCDS41845.1	12q24.23	2006-01-24				ENSG00000135127			28095	protein-coding gene	gene with protein product							Standard	NM_207311		Approved	FLJ26450	uc001txl.1	Q6ZP65	OTTHUMG00000169311	ENST00000397558.2:c.495C>T	12.37:g.120436390C>T		Somatic		Capture	Illumina HiSeq	Phase_I	118920773	NM_207311	A8MUC8|B4DWL0|B5MDJ0|O95000	Silent	SNP	ENST00000397558.2	37	CCDS41845.1																																																																																				0.483	CCDC64-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000403390.2	NM_207311	
HPD	3242	broad.mit.edu	37	12	122292611	122292611	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:122292611T>C	ENST00000289004.4	-	7	447	c.412A>G	c.(412-414)Acg>Gcg	p.T138A	HPD_ENST00000543163.1_Missense_Mutation_p.T99A|RP11-7M8.2_ENST00000543848.1_RNA	NM_002150.2	NP_002141	P32754	HPPD_HUMAN	4-hydroxyphenylpyruvate dioxygenase	138					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)	4-hydroxyphenylpyruvate dioxygenase activity (GO:0003868)|metal ion binding (GO:0046872)	p.T138A(1)		breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(8)|urinary_tract(1)	18	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000105)|Epithelial(86;0.000352)|BRCA - Breast invasive adenocarcinoma(302;0.225)	Nitisinone(DB00348)	GAACTCACCGTCTGCAGCACA	0.597																																					p.T138A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A412G	12						.						201.0	171.0	181.0					12																	122292611		2203	4300	6503	120776994	SO:0001583	missense	3242	exon7			BC014790	CCDS9224.1, CCDS53839.1	12q24.31	2013-09-19			ENSG00000158104	ENSG00000158104	1.13.11.27		5147	protein-coding gene	gene with protein product	"""glyoxalase domain containing 3"""	609695		PPD			Standard	NM_001171993		Approved	4-HPPD, 4HPPD, GLOD3	uc001ubj.3	P32754	OTTHUMG00000169081	ENST00000289004.4:c.412A>G	12.37:g.122292611T>C	ENSP00000289004:p.Thr138Ala	Somatic		Capture	Illumina HiSeq	Phase_I	120776994	NM_002150	A8K461|B3KQ63|Q13234	Missense_Mutation	SNP	ENST00000289004.4	37	CCDS9224.1	.	.	.	.	.	.	.	.	.	.	T	16.75	3.209065	0.58343	.	.	ENSG00000158104	ENST00000289004;ENST00000545969;ENST00000543163	T;T	0.63096	-0.02;-0.02	5.29	5.29	0.74685	.	0.229208	0.44097	D	0.000490	T	0.54759	0.1878	L	0.41906	1.305	0.80722	D	1	B	0.06786	0.001	B	0.20955	0.032	T	0.51212	-0.8734	10	0.38643	T	0.18	-11.6818	14.395	0.67005	0.0:0.0:0.0:1.0	.	138	P32754	HPPD_HUMAN	A	138;135;99	ENSP00000289004:T138A;ENSP00000441677:T99A	ENSP00000289004:T138A	T	-	1	0	HPD	120776994	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	7.437000	0.80417	2.005000	0.58758	0.383000	0.25322	ACG		0.597	HPD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402184.1	NM_002150	
CLIP1	6249	broad.mit.edu	37	12	122757612	122757612	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:122757612C>T	ENST00000540338.1	-	25	4168	c.4127G>A	c.(4126-4128)cGc>cAc	p.R1376H	CLIP1_ENST00000536634.1_5'UTR|CLIP1_ENST00000358808.2_Missense_Mutation_p.R1365H|CLIP1_ENST00000537178.1_Missense_Mutation_p.R1330H|CLIP1_ENST00000540539.1_Missense_Mutation_p.R55H|CLIP1_ENST00000302528.7_Missense_Mutation_p.R1365H|CLIP1_ENST00000361654.4_Missense_Mutation_p.R1254H|CLIP1_ENST00000545889.1_Missense_Mutation_p.R951H			P30622	CLIP1_HUMAN	CAP-GLY domain containing linker protein 1	1376					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.R1365H(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)		ACAGAAGAGGCGAGGTTTCTT	0.438																																					p.R1330H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3989A	12						.						141.0	114.0	123.0					12																	122757612		2203	4300	6503	121323565	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.4127G>A	12.37:g.122757612C>T	ENSP00000439093:p.Arg1376His	Somatic		Capture	Illumina HiSeq	Phase_I	121323565	NM_198240	A0AVD3|Q17RS4|Q29RG0	Missense_Mutation	SNP	ENST00000540338.1	37	CCDS58285.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.896977	0.91962	.	.	ENSG00000130779	ENST00000545889;ENST00000302528;ENST00000358808;ENST00000542885;ENST00000392458;ENST00000537178;ENST00000540539;ENST00000540338	T;T;T;T;T;T	0.30981	1.51;1.51;1.51;1.51;1.51;1.51	5.86	5.86	0.93980	.	0.239817	0.40064	N	0.001183	T	0.62624	0.2443	M	0.84082	2.675	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.65594	-0.6130	10	0.87932	D	0	-8.5441	20.2019	0.98263	0.0:1.0:0.0:0.0	.	1330;1365;1376	P30622-2;P30622-1;P30622	.;.;CLIP1_HUMAN	H	951;1365;1365;1097;409;1330;55;1376	ENSP00000438743:R951H;ENSP00000303585:R1365H;ENSP00000351665:R1365H;ENSP00000445531:R1330H;ENSP00000437617:R55H;ENSP00000439093:R1376H	ENSP00000303585:R1365H	R	-	2	0	CLIP1	121323565	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.346000	0.79347	2.776000	0.95493	0.655000	0.94253	CGC		0.438	CLIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401625.1	NM_002956	
MANSC1	54682	broad.mit.edu	37	12	12483418	12483418	+	Missense_Mutation	SNP	G	G	A	rs201432430		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:12483418G>A	ENST00000535902.1	-	4	1402	c.839C>T	c.(838-840)aCg>aTg	p.T280M	MANSC1_ENST00000545735.1_Missense_Mutation_p.T199M|MANSC1_ENST00000396349.3_Missense_Mutation_p.T246M			Q9H8J5	MANS1_HUMAN	MANSC domain containing 1	280	Thr-rich.					integral component of membrane (GO:0016021)		p.T281fs*1(1)|p.T280M(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|skin(1)|stomach(4)	23		Prostate(47;0.0865)		BRCA - Breast invasive adenocarcinoma(232;0.185)		AATGAGGGTCGTGGGAGGCTG	0.547													G|||	1	0.000199681	0.0	0.0	5008	,	,		18510	0.001		0.0	False		,,,				2504	0.0				p.T280M												.	.	2	Substitution - Missense(1)|Insertion - Frameshift(1)	large_intestine(2)	c.C839T	12						.	G	MET/THR	0,4406		0,0,2203	88.0	82.0	84.0		839	2.0	0.0	12		84	2,8598	2.2+/-6.3	0,2,4298	no	missense	MANSC1	NM_018050.2	81	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	280/432	12483418	2,13004	2203	4300	6503	12374685	SO:0001583	missense	54682	exon4			AK001160	CCDS8648.1	12p13.2	2006-04-12				ENSG00000111261			25505	protein-coding gene	gene with protein product						12975309	Standard	NM_018050		Approved	FLJ10298, LOH12CR3	uc001rai.1	Q9H8J5		ENST00000535902.1:c.839C>T	12.37:g.12483418G>A	ENSP00000438205:p.Thr280Met	Somatic		Capture	Illumina HiSeq	Phase_I	12374685	NM_018050	Q8NEC1|Q9NW60	Missense_Mutation	SNP	ENST00000535902.1	37	CCDS8648.1	.	.	.	.	.	.	.	.	.	.	G	15.86	2.957441	0.53400	0.0	2.33E-4	ENSG00000111261	ENST00000535902;ENST00000396349;ENST00000355566;ENST00000545735	T;T;T	0.38560	1.49;1.63;1.13	4.99	1.96	0.26148	.	1.452760	0.04711	N	0.417712	T	0.41282	0.1152	L	0.27053	0.805	0.09310	N	1	D;D;D	0.76494	0.999;0.997;0.997	P;P;P	0.50082	0.63;0.63;0.63	T	0.35151	-0.9800	10	0.72032	D	0.01	-5.251	8.5407	0.33390	0.0:0.302:0.5391:0.1589	.	214;246;280	B4DQ82;Q9NW60;Q9H8J5	.;.;MANS1_HUMAN	M	280;246;199;199	ENSP00000438205:T280M;ENSP00000379638:T246M;ENSP00000445303:T199M	ENSP00000347765:T199M	T	-	2	0	MANSC1	12374685	0.023000	0.18921	0.000000	0.03702	0.249000	0.25844	1.410000	0.34691	0.095000	0.17434	0.491000	0.48974	ACG		0.547	MANSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400144.1	NM_018050	
DNAH10	196385	broad.mit.edu	37	12	124366273	124366273	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:124366273G>T	ENST00000409039.3	+	50	8407	c.8382G>T	c.(8380-8382)atG>atT	p.M2794I		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2794	AAA 4. {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)			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)		TCATCCGCATGGACCGCGGCC	0.547																																					p.M2794I												.	.	0			c.G8382T	12						.						23.0	25.0	24.0					12																	124366273		1743	3637	5380	122932226	SO:0001583	missense	196385	exon50			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.8382G>T	12.37:g.124366273G>T	ENSP00000386770:p.Met2794Ile	None		Capture	Illumina HiSeq	Phase_I	122932226	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	G	15.25	2.776532	0.49786	.	.	ENSG00000197653	ENST00000409039	T	0.40756	1.02	5.57	5.57	0.84162	Dynein heavy chain, P-loop containing D4 domain (1);	0.060071	0.64402	U	0.000004	T	0.43389	0.1245	L	0.53671	1.685	0.52501	D	0.999955	B	0.18013	0.025	B	0.25759	0.063	T	0.25606	-1.0127	10	0.21014	T	0.42	.	19.5927	0.95522	0.0:0.0:1.0:0.0	.	2794	Q8IVF4	DYH10_HUMAN	I	2794	ENSP00000386770:M2794I	ENSP00000386770:M2794I	M	+	3	0	DNAH10	122932226	1.000000	0.71417	0.997000	0.53966	0.609000	0.37215	4.428000	0.59894	2.635000	0.89317	0.558000	0.71614	ATG		0.547	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
SLC6A13	6540	broad.mit.edu	37	12	330230	330230	+	Missense_Mutation	SNP	G	G	A	rs537041083		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:330230G>A	ENST00000343164.4	-	15	1745	c.1693C>T	c.(1693-1695)Cgt>Tgt	p.R565C	SLC6A13_ENST00000445055.2_Missense_Mutation_p.R473C|SLC6A13_ENST00000539668.1_5'Flank	NM_016615.4	NP_057699.2	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 13	565					neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)	p.R565C(1)		NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(1)	28	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)			ATGAGCTGACGGATTCTCTGC	0.652													G|||	1	0.000199681	0.0	0.0	5008	,	,		17972	0.0		0.001	False		,,,				2504	0.0				p.R473C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1417T	12						.						48.0	54.0	52.0					12																	330230		2203	4300	6503	200491	SO:0001583	missense	6540	exon13			U76343	CCDS8502.1, CCDS53729.1, CCDS58198.1	12p13.33	2013-07-19	2013-07-19		ENSG00000010379	ENSG00000010379		"""Solute carriers"""	11046	protein-coding gene	gene with protein product	"""GABA transporter 2"""	615097	"""solute carrier family 6 (neurotransmitter transporter, GABA), member 13"""				Standard	NM_001243392		Approved	GAT2	uc001qic.2	Q9NSD5	OTTHUMG00000168053	ENST00000343164.4:c.1693C>T	12.37:g.330230G>A	ENSP00000339260:p.Arg565Cys	Somatic		Capture	Illumina HiSeq	Phase_I	200491	NM_001190997	B4DJL1|Q8TCC2|Q8WW56	Missense_Mutation	SNP	ENST00000343164.4	37	CCDS8502.1	.	.	.	.	.	.	.	.	.	.	G	13.75	2.329246	0.41197	.	.	ENSG00000010379	ENST00000445055;ENST00000313154;ENST00000343164	T;T	0.74737	-0.84;-0.87	4.32	4.32	0.51571	.	0.555420	0.18263	N	0.146579	T	0.57095	0.2030	N	0.08118	0	0.80722	D	1	B;B;B	0.20988	0.028;0.037;0.05	B;B;B	0.13407	0.009;0.009;0.006	T	0.58515	-0.7623	10	0.62326	D	0.03	.	15.1566	0.72746	0.0:0.0:1.0:0.0	.	473;544;565	B4DJL1;B4DJS3;Q9NSD5	.;.;S6A13_HUMAN	C	473;544;565	ENSP00000407104:R473C;ENSP00000339260:R565C	ENSP00000318097:R544C	R	-	1	0	SLC6A13	200491	0.996000	0.38824	0.988000	0.46212	0.555000	0.35460	4.195000	0.58400	2.244000	0.73946	0.448000	0.29417	CGT		0.652	SLC6A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397801.1	NM_016615	
CACNA2D4	93589	broad.mit.edu	37	12	1910242	1910242	+	Silent	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:1910242A>G	ENST00000382722.5	-	31	3197	c.2835T>C	c.(2833-2835)agT>agC	p.S945S	CACNA2D4_ENST00000538450.1_Silent_p.S75S|CACNA2D4_ENST00000585708.1_Silent_p.S881S|CACNA2D4_ENST00000586184.1_Silent_p.S945S|CACNA2D4_ENST00000588077.1_Silent_p.S881S|CACNA2D4_ENST00000538027.2_Silent_p.S90S|CACNA2D4_ENST00000587995.1_Silent_p.S920S	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	945					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.S945S(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)		TGTGGTGGTGACTCGAGGGTT	0.607											OREG0021569	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S945S	Colon(2;101 179 21030 23310 28141)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T2835C	12						.						97.0	115.0	109.0					12																	1910242		2202	4299	6501	1780503	SO:0001819	synonymous_variant	93589	exon31			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.2835T>C	12.37:g.1910242A>G		Somatic	599	Capture	Illumina HiSeq	Phase_I	1780503	NM_172364	Q7Z3S8|Q86XZ5|Q8IZS9	Silent	SNP	ENST00000382722.5	37	CCDS44785.1																																																																																				0.607	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398230.2		
CACNA2D4	93589	broad.mit.edu	37	12	2024074	2024074	+	Silent	SNP	G	G	A	rs375466678		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:2024074G>A	ENST00000382722.5	-	2	617	c.255C>T	c.(253-255)ggC>ggT	p.G85G	CACNA2D4_ENST00000585708.1_Silent_p.G21G|CACNA2D4_ENST00000586184.1_Silent_p.G85G|CACNA2D4_ENST00000588077.1_Silent_p.G21G|CACNA2D4_ENST00000585732.1_Silent_p.G85G|CACNA2D4_ENST00000587995.1_Silent_p.G85G	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	85					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.G85G(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)		ACAGGTCCCCGCCGAAGGTGT	0.542																																					p.G85G	Colon(2;101 179 21030 23310 28141)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C255T	12						.	G		0,4096		0,0,2048	118.0	130.0	126.0		255	1.2	0.1	12		126	1,8389		0,1,4194	no	coding-synonymous	CACNA2D4	NM_172364.4		0,1,6242	AA,AG,GG		0.0119,0.0,0.0080		85/1138	2024074	1,12485	2048	4195	6243	1894335	SO:0001819	synonymous_variant	93589	exon2			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.255C>T	12.37:g.2024074G>A		Somatic		Capture	Illumina HiSeq	Phase_I	1894335	NM_172364	Q7Z3S8|Q86XZ5|Q8IZS9	Silent	SNP	ENST00000382722.5	37	CCDS44785.1																																																																																				0.542	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398230.2		
FGF23	8074	broad.mit.edu	37	12	4481861	4481861	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:4481861C>A	ENST00000237837.1	-	2	359	c.214G>T	c.(214-216)Gcc>Tcc	p.A72S		NM_020638.2	NP_065689.1	Q9GZV9	FGF23_HUMAN	fibroblast growth factor 23	72					cell differentiation (GO:0030154)|cellular phosphate ion homeostasis (GO:0030643)|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)|negative regulation of bone mineralization (GO:0030502)|negative regulation of hormone secretion (GO:0046888)|negative regulation of osteoblast differentiation (GO:0045668)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphate ion homeostasis (GO:0055062)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vitamin D 24-hydroxylase activity (GO:0010980)|regulation of phosphate transport (GO:0010966)|vitamin D catabolic process (GO:0042369)	extracellular region (GO:0005576)|extracellular space (GO:0005615)		p.A72S(1)		NS(1)|breast(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	22			Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)|STAD - Stomach adenocarcinoma(119;0.206)			ATCATCAGGGCACCTATGGAG	0.473																																					p.A72S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G214T	12						.						121.0	106.0	111.0					12																	4481861		2203	4300	6503	4352122	SO:0001583	missense	8074	exon2			AF263537	CCDS8526.1	12p13	2008-07-04			ENSG00000118972	ENSG00000118972			3680	protein-coding gene	gene with protein product		605380				11032749, 18310961	Standard	NM_020638		Approved		uc001qmq.1	Q9GZV9	OTTHUMG00000168241	ENST00000237837.1:c.214G>T	12.37:g.4481861C>A	ENSP00000237837:p.Ala72Ser	Somatic		Capture	Illumina HiSeq	Phase_I	4352122	NM_020638	Q4V758	Missense_Mutation	SNP	ENST00000237837.1	37	CCDS8526.1	.	.	.	.	.	.	.	.	.	.	C	16.53	3.148120	0.57151	.	.	ENSG00000118972	ENST00000237837	T	0.81078	-1.45	4.47	4.47	0.54385	.	0.054275	0.64402	D	0.000001	D	0.87653	0.6231	L	0.56769	1.78	0.42809	D	0.99395	D	0.69078	0.997	D	0.75020	0.985	D	0.89176	0.3540	10	0.66056	D	0.02	-15.7637	17.3456	0.87308	0.0:1.0:0.0:0.0	.	72	Q9GZV9	FGF23_HUMAN	S	72	ENSP00000237837:A72S	ENSP00000237837:A72S	A	-	1	0	FGF23	4352122	1.000000	0.71417	1.000000	0.80357	0.311000	0.27955	5.188000	0.65093	2.322000	0.78497	0.549000	0.68633	GCC		0.473	FGF23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398936.1		
KCNA5	3741	broad.mit.edu	37	12	5154333	5154333	+	Silent	SNP	C	C	T	rs72546671	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:5154333C>T	ENST00000252321.3	+	1	1249	c.1020C>T	c.(1018-1020)ctC>ctT	p.L340L		NM_002234.3	NP_002225.2	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 5	340					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.L340L(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)	TCGAGCTGCTCGTGCGCTTCT	0.617													C|||	28	0.00559105	0.0212	0.0	5008	,	,		16600	0.0		0.0	False		,,,				2504	0.0				p.L340L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1020T	12						.	C		75,4331	67.6+/-105.2	3,69,2131	97.0	85.0	89.0		1020	-9.7	0.2	12	dbSNP_130	89	0,8600		0,0,4300	no	coding-synonymous	KCNA5	NM_002234.2		3,69,6431	TT,TC,CC		0.0,1.7022,0.5767		340/614	5154333	75,12931	2203	4300	6503	5024594	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.1020C>T	12.37:g.5154333C>T		Somatic		Capture	Illumina HiSeq	Phase_I	5024594	NM_002234	Q4KKT8|Q4VAJ1|Q4VAJ2|Q9UDA4	Silent	SNP	ENST00000252321.3	37	CCDS8536.1																																																																																				0.617	KCNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398925.2	NM_002234	
LTBR	4055	broad.mit.edu	37	12	6493550	6493550	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:6493550delC	ENST00000228918.4	+	1	352	c.26delC	c.(25-27)gccfs	p.A9fs	LTBR_ENST00000543190.1_5'UTR|LTBR_ENST00000541102.1_5'Flank|LTBR_ENST00000546296.1_Intron|LTBR_ENST00000539925.1_Intron	NM_002342.2	NP_002333.1	P36941	TNR3_HUMAN	lymphotoxin beta receptor (TNFR superfamily, member 3)	9					apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of JNK cascade (GO:0046330)|signal transduction (GO:0007165)|viral process (GO:0016032)	integral component of membrane (GO:0016021)	identical protein binding (GO:0042802)|ubiquitin protein ligase binding (GO:0031625)	p.G11fs*85(1)		breast(1)|cervix(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)	15						GCCACCTCTGCCCCCGGCCTG	0.741																																					p.A9fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.26delC	12						.						3.0	4.0	4.0					12																	6493550		1983	3936	5919	6363811	SO:0001589	frameshift_variant	4055	exon1			L04270	CCDS8544.1, CCDS59233.1	12p13	2013-05-22				ENSG00000111321		"""Tumor necrosis factor receptor superfamily"""	6718	protein-coding gene	gene with protein product		600979		D12S370		8171323, 8486360	Standard	NM_002342		Approved	TNFCR, TNFR-RP, TNFR2-RP, TNF-R-III, TNFRSF3	uc001qny.2	P36941		ENST00000228918.4:c.26delC	12.37:g.6493550delC	ENSP00000228918:p.Ala9fs	Somatic		Capture	Illumina HiSeq	Phase_I	6363811	NM_002342	B7Z1D2|D3DUR2|F5GXE7	Frame_Shift_Del	DEL	ENST00000228918.4	37	CCDS8544.1																																																																																				0.741	LTBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399422.1		
ACRBP	84519	broad.mit.edu	37	12	6749518	6749518	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:6749518G>A	ENST00000229243.2	-	7	1341	c.1248C>T	c.(1246-1248)atC>atT	p.I416I	ACRBP_ENST00000414226.2_Silent_p.I383I|ACRBP_ENST00000542357.1_5'UTR	NM_032489.2	NP_115878.2			acrosin binding protein									p.I416I(1)		NS(1)|breast(1)|central_nervous_system(1)|large_intestine(8)|lung(5)|ovary(1)	17						CCTGGTTGCCGATGGACAGGC	0.657																																					p.I416I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1248T	12						.						57.0	62.0	60.0					12																	6749518		2203	4300	6503	6619779	SO:0001819	synonymous_variant	84519	exon7			AB051833	CCDS8554.1	12p13.31	2009-03-12			ENSG00000111644	ENSG00000111644			17195	protein-coding gene	gene with protein product	"""proacrosin binding protein sp32"", ""cancer/testis antigen 23"""	608352				11248070	Standard	NM_032489		Approved	SP32, OY-TES-1, CT23	uc001qpu.1	Q8NEB7	OTTHUMG00000168715	ENST00000229243.2:c.1248C>T	12.37:g.6749518G>A		Somatic		Capture	Illumina HiSeq	Phase_I	6619779	NM_032489		Silent	SNP	ENST00000229243.2	37	CCDS8554.1																																																																																				0.657	ACRBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400703.1	NM_032489	
PTPN6	5777	broad.mit.edu	37	12	7064026	7064026	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:7064026G>A	ENST00000318974.9	+	4	629	c.385G>A	c.(385-387)Gag>Aag	p.E129K	PTPN6_ENST00000456013.1_Missense_Mutation_p.E129K|PTPN6_ENST00000447931.2_Missense_Mutation_p.E90K|PTPN6_ENST00000399448.1_Missense_Mutation_p.E131K	NM_002831.5	NP_002822.2	P29350	PTN6_HUMAN	protein tyrosine phosphatase, non-receptor type 6	129	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.E129K(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|prostate(3)	18						GGCCAAGGGCGAGCCCTGGAC	0.637																																					p.E129K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G385A	12						.						47.0	53.0	51.0					12																	7064026		2135	4252	6387	6934287	SO:0001583	missense	5777	exon4				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.385G>A	12.37:g.7064026G>A	ENSP00000326010:p.Glu129Lys	Somatic		Capture	Illumina HiSeq	Phase_I	6934287	NM_002831	A8K306|G3V0F8|Q969V8|Q9UK67	Missense_Mutation	SNP	ENST00000318974.9	37	CCDS44820.1	.	.	.	.	.	.	.	.	.	.	G	9.618	1.133168	0.21041	.	.	ENSG00000111679	ENST00000399448;ENST00000447931;ENST00000538715;ENST00000318974;ENST00000456013;ENST00000542462	D;D;D;D;D;D	0.88046	-2.33;-2.33;-2.33;-2.33;-2.33;-2.33	5.07	5.07	0.68467	SH2 motif (4);	0.353403	0.28465	N	0.015242	T	0.66137	0.2759	N	0.02854	-0.475	0.47547	D	0.999452	B;B;B;B;B	0.16802	0.019;0.007;0.003;0.002;0.008	B;B;B;B;B	0.14023	0.01;0.002;0.004;0.004;0.007	T	0.64037	-0.6501	10	0.02654	T	1	.	9.7753	0.40614	0.1287:0.0:0.8713:0.0	.	117;90;129;129;131	B4DPS0;P29350-2;G3V0F8;P29350;Q53XS4	.;.;.;PTN6_HUMAN;.	K	131;90;129;129;129;88	ENSP00000382376:E131K;ENSP00000415979:E90K;ENSP00000438740:E129K;ENSP00000326010:E129K;ENSP00000391592:E129K;ENSP00000440114:E88K	ENSP00000326010:E129K	E	+	1	0	PTPN6	6934287	1.000000	0.71417	0.978000	0.43139	0.956000	0.61745	3.844000	0.55873	2.373000	0.80994	0.491000	0.48974	GAG		0.637	PTPN6-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400023.1	NM_002831	
A2M	2	broad.mit.edu	37	12	9262615	9262615	+	Missense_Mutation	SNP	C	C	T	rs369574498		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:9262615C>T	ENST00000318602.7	-	6	828	c.521G>A	c.(520-522)cGc>cAc	p.R174H		NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	174					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|stem cell differentiation (GO:0048863)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	calcium-dependent protein binding (GO:0048306)|enzyme binding (GO:0019899)|growth factor binding (GO:0019838)|interleukin-1 binding (GO:0019966)|interleukin-8 binding (GO:0019959)|protease binding (GO:0002020)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|tumor necrosis factor binding (GO:0043120)	p.R174H(1)		breast(1)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(17)|lung(30)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	77					Bacitracin(DB00626)|Becaplermin(DB00102)|Ocriplasmin(DB08888)	TTGTGCGATGCGATTTCCTTT	0.423																																					p.R174H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G521A	12						.	C	HIS/ARG	0,3972		0,0,1986	107.0	112.0	110.0		521	5.8	1.0	12		110	1,8437		0,1,4218	no	missense	A2M	NM_000014.4	29	0,1,6204	TT,TC,CC		0.0119,0.0,0.0081	probably-damaging	174/1475	9262615	1,12409	1986	4219	6205	9153882	SO:0001583	missense	2	exon6			BX647329, X68728, M11313	CCDS44827.1	12p13.31	2010-02-24			ENSG00000175899	ENSG00000175899			7	protein-coding gene	gene with protein product		103950					Standard	XM_006719056		Approved	FWP007, S863-7, CPAMD5	uc001qvk.1	P01023	OTTHUMG00000150267	ENST00000318602.7:c.521G>A	12.37:g.9262615C>T	ENSP00000323929:p.Arg174His	Somatic		Capture	Illumina HiSeq	Phase_I	9153882	NM_000014	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Missense_Mutation	SNP	ENST00000318602.7	37	CCDS44827.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.593523	0.86953	0.0	1.19E-4	ENSG00000175899	ENST00000318602;ENST00000540099	T	0.75050	-0.9	5.82	5.82	0.92795	Alpha-2-macroglobulin, N-terminal (1);	0.069386	0.64402	D	0.000010	D	0.89518	0.6738	M	0.93283	3.4	0.40438	D	0.980015	D	0.89917	1.0	D	0.77004	0.989	D	0.91998	0.5608	10	0.87932	D	0	.	15.5992	0.76611	0.0:1.0:0.0:0.0	.	174	P01023	A2MG_HUMAN	H	174;189	ENSP00000323929:R174H	ENSP00000323929:R174H	R	-	2	0	A2M	9153882	0.990000	0.36364	1.000000	0.80357	0.979000	0.70002	2.980000	0.49321	2.752000	0.94435	0.655000	0.94253	CGC		0.423	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014	
GRIN2B	2904	broad.mit.edu	37	12	13768577	13768577	+	Silent	SNP	C	C	T	rs200607718		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:13768577C>T	ENST00000609686.1	-	6	1559	c.1350G>A	c.(1348-1350)ccG>ccA	p.P450P		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	450					behavioral fear response (GO:0001662)|behavioral response to pain (GO:0048266)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|glutamate receptor signaling pathway (GO:0007215)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning (GO:0007612)|learning or memory (GO:0007611)|memory (GO:0007613)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic plasticity (GO:0048167)|response to ethanol (GO:0045471)|sensory organ development (GO:0007423)|startle response (GO:0001964)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|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)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)	p.P450P(1)		NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(12)|liver(1)|lung(70)|ovary(4)|prostate(6)|skin(10)|upper_aerodigestive_tract(5)|urinary_tract(1)	143					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Haloperidol(DB00502)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	TGATGTAACCCGGCTCCTCGT	0.353																																					p.P450P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1350A	12						.						128.0	142.0	138.0					12																	13768577		2203	4300	6503	13659844	SO:0001819	synonymous_variant	2904	exon6				CCDS8662.1	12p13.1	2014-07-16			ENSG00000273079			"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4586	protein-coding gene	gene with protein product		138252		NMDAR2B		1350383	Standard	NM_000834		Approved	GluN2B	uc001rbt.2	Q13224	OTTHUMG00000137373	ENST00000609686.1:c.1350G>A	12.37:g.13768577C>T		Somatic		Capture	Illumina HiSeq	Phase_I	13659844	NM_000834	Q12919|Q13220|Q13225|Q14CU4|Q9UM56	Silent	SNP	ENST00000609686.1	37	CCDS8662.1																																																																																				0.353	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268014.2		
ARHGDIB	397	broad.mit.edu	37	12	15100826	15100826	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:15100826C>A	ENST00000228945.4	-	4	467	c.323G>T	c.(322-324)aGa>aTa	p.R108I	ARHGDIB_ENST00000541644.1_Missense_Mutation_p.R108I|ARHGDIB_ENST00000541546.1_Missense_Mutation_p.R108I|ARHGDIB_ENST00000539131.1_5'UTR	NM_001175.4	NP_001166.3	P52566	GDIR2_HUMAN	Rho GDP dissociation inhibitor (GDI) beta	108					actin cytoskeleton organization (GO:0030036)|cellular component movement (GO:0006928)|immune response (GO:0006955)|multicellular organismal development (GO:0007275)|negative regulation of cell adhesion (GO:0007162)|regulation of catalytic activity (GO:0050790)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	GTPase activator activity (GO:0005096)|Rho GDP-dissociation inhibitor activity (GO:0005094)	p.R108I(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	15						AATTTTGACTCTATATTCAGA	0.338																																					p.R108I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G323T	12						.						158.0	153.0	155.0					12																	15100826		2202	4300	6502	14992093	SO:0001583	missense	397	exon4			L07916	CCDS8671.1	12p12.3	2014-01-30				ENSG00000111348		"""Endogenous ligands"""	679	protein-coding gene	gene with protein product		602843		RAP1GN1, GDIA2, GDID4		8434008, 8356058	Standard	NM_001175		Approved	Ly-GDI, RhoGDI2	uc001rcq.1	P52566		ENST00000228945.4:c.323G>T	12.37:g.15100826C>A	ENSP00000228945:p.Arg108Ile	Somatic		Capture	Illumina HiSeq	Phase_I	14992093	NM_001175	B5BU79	Missense_Mutation	SNP	ENST00000228945.4	37	CCDS8671.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.51|12.51	1.960053|1.960053	0.34565|0.34565	.|.	.|.	ENSG00000111348|ENSG00000111348	ENST00000228945;ENST00000541644;ENST00000541546;ENST00000545895;ENST00000541380|ENST00000536592	.|.	.|.	.|.	5.23|5.23	0.619|0.619	0.17630|0.17630	Immunoglobulin E-set (1);|.	0.095734|.	0.64402|.	D|.	0.000001|.	T|.	0.77611|.	0.4156|.	M|M	0.92784|0.92784	3.345|3.345	0.80722|0.80722	D|D	1|1	P|.	0.36577|.	0.558|.	B|.	0.38428|.	0.273|.	T|.	0.76969|.	-0.2762|.	9|.	0.62326|.	D|.	0.03|.	-0.3334|-0.3334	8.3901|8.3901	0.32522|0.32522	0.0:0.599:0.0:0.401|0.0:0.599:0.0:0.401	.|.	108|.	P52566|.	GDIR2_HUMAN|.	I|Y	108|101	.|.	ENSP00000228945:R108I|.	R|X	-|-	2|3	0|2	ARHGDIB|ARHGDIB	14992093|14992093	0.998000|0.998000	0.40836|0.40836	0.980000|0.980000	0.43619|0.43619	0.178000|0.178000	0.23041|0.23041	0.608000|0.608000	0.24223|0.24223	0.035000|0.035000	0.15519|0.15519	-0.469000|-0.469000	0.05056|0.05056	AGA|TAG		0.338	ARHGDIB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400871.1	NM_001175	
C12orf77	196415	broad.mit.edu	37	12	25148935	25148935	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:25148935C>T	ENST00000549828.1	-	3	417	c.213G>A	c.(211-213)acG>acA	p.T71T	C12orf77_ENST00000434912.3_Silent_p.T16T|C12orf77_ENST00000549262.1_Silent_p.T16T	NM_001101339.1	NP_001094809.1	C9JDV5	CL097_HUMAN	chromosome 12 open reading frame 77	71								p.T71T(2)		endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)	7						TGCTGTCCAGCGTCTGCACGT	0.478																																					p.T71T												.	.	2	Substitution - coding silent(2)	large_intestine(1)|prostate(1)	c.G213A	12						.						87.0	89.0	89.0					12																	25148935		1964	4159	6123	25040202	SO:0001819	synonymous_variant	196415	exon3			BC046192	CCDS44846.1	12p12.1	2009-09-30			ENSG00000226397	ENSG00000226397			27282	protein-coding gene	gene with protein product						12477932	Standard	NM_001101339		Approved		uc001rgf.3	C9JDV5	OTTHUMG00000170185	ENST00000549828.1:c.213G>A	12.37:g.25148935C>T		Somatic		Capture	Illumina HiSeq	Phase_I	25040202	NM_001101339		Silent	SNP	ENST00000549828.1	37	CCDS44846.1																																																																																				0.478	C12orf77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407827.1	NM_001101339	
PPFIBP1	8496	broad.mit.edu	37	12	27830005	27830005	+	Intron	SNP	C	C	T	rs371335870		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:27830005C>T	ENST00000318304.8	+	18	1916				PPFIBP1_ENST00000228425.6_Nonsense_Mutation_p.R531*|PPFIBP1_ENST00000542629.1_Intron|PPFIBP1_ENST00000537927.1_Intron	NM_001198916.1|NM_177444.2	NP_001185845.1|NP_803193	Q86W92	LIPB1_HUMAN	PTPRF interacting protein, binding protein 1 (liprin beta 1)						cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)		p.R531*(2)	PPFIBP1/ALK(3)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(13)|prostate(2)|skin(1)	32	Lung SC(9;0.0873)					AGATCGTAAACGAAGTGCCAG	0.502																																					p.R531X												.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C1591T	12						.	C	,,stop/ARG,	1,4405	2.1+/-5.4	0,1,2202	347.0	286.0	307.0		,,1591,	5.4	1.0	12		307	0,8600		0,0,4300	no	intron,intron,stop-gained,intron	PPFIBP1	NM_001198915.1,NM_001198916.1,NM_003622.3,NM_177444.2	,,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,,	,,531/1006,	27830005	1,13005	2203	4300	6503	27721272	SO:0001627	intron_variant	8496	exon19			AF034802	CCDS8713.1, CCDS55812.1, CCDS55813.1, CCDS55814.1	12p12.1	2013-01-10						"""Sterile alpha motif (SAM) domain containing"""	9249	protein-coding gene	gene with protein product		603141				9624153, 11836260	Standard	NM_003622		Approved	L2, hSGT2, hSgt2p, SGT2	uc001ric.2	Q86W92		ENST00000318304.8:c.1633+473C>T	12.37:g.27830005C>T		Somatic		Capture	Illumina HiSeq	Phase_I	27721272	NM_003622	O75336|Q86X70|Q9NY03|Q9ULJ0	Nonsense_Mutation	SNP	ENST00000318304.8	37	CCDS55812.1	.	.	.	.	.	.	.	.	.	.	C	40	8.381988	0.98786	2.27E-4	0.0	ENSG00000110841	ENST00000228425	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	.	19.0495	0.93038	0.0:1.0:0.0:0.0	.	.	.	.	X	531	.	ENSP00000228425:R531X	R	+	1	2	PPFIBP1	27721272	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.205000	0.42770	2.832000	0.97577	0.655000	0.94253	CGA		0.502	PPFIBP1-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402877.1	NM_003622	
KLHL42	57542	broad.mit.edu	37	12	27944696	27944696	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:27944696G>A	ENST00000381271.2	+	2	1239	c.928G>A	c.(928-930)Gcc>Acc	p.A310T		NM_020782.1	NP_065833.1	Q9P2K6	KLH42_HUMAN	kelch-like family member 42	310					mitotic nuclear division (GO:0007067)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of microtubule-based process (GO:0032886)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.A310T(1)									CGGAGGGCAGGCCGTTTCTAA	0.483																																					p.A310T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G928A	12						.						220.0	209.0	213.0					12																	27944696		2203	4300	6503	27835963	SO:0001583	missense	57542	exon2			AB037761	CCDS31763.1	12p11.22	2013-04-24	2013-02-22	2013-01-30	ENSG00000087448	ENSG00000087448		"""Kelch-like"""	29252	protein-coding gene	gene with protein product			"""kelch domain containing 5"""	KLHDC5		19261606	Standard	NM_020782		Approved	KIAA1340, Ctb9	uc001rij.3	Q9P2K6	OTTHUMG00000169217	ENST00000381271.2:c.928G>A	12.37:g.27944696G>A	ENSP00000370671:p.Ala310Thr	Somatic		Capture	Illumina HiSeq	Phase_I	27835963	NM_020782	Q2VPK1|Q8N334	Missense_Mutation	SNP	ENST00000381271.2	37	CCDS31763.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.33|14.33	2.502605|2.502605	0.44455|0.44455	.|.	.|.	ENSG00000087448|ENSG00000087448	ENST00000381271|ENST00000543254	T|.	0.75477|.	-0.94|.	4.86|4.86	3.9|3.9	0.45041|0.45041	Kelch-type beta propeller (1);|.	0.319828|.	0.34291|.	N|.	0.004094|.	T|T	0.23611|0.23611	0.0571|0.0571	N|N	0.20328|0.20328	0.56|0.56	0.28792|0.28792	N|N	0.899253|0.899253	B|.	0.15719|.	0.014|.	B|.	0.16289|.	0.015|.	T|T	0.08452|0.08452	-1.0721|-1.0721	10|5	0.05721|.	T|.	0.95|.	.|.	5.6935|5.6935	0.17843|0.17843	0.1003:0.0:0.6417:0.2579|0.1003:0.0:0.6417:0.2579	.|.	310|.	Q9P2K6|.	KLDC5_HUMAN|.	T|D	310|131	ENSP00000370671:A310T|.	ENSP00000370671:A310T|.	A|G	+|+	1|2	0|0	KLHDC5|KLHDC5	27835963|27835963	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	2.078000|2.078000	0.41567|0.41567	2.505000|2.505000	0.84491|0.84491	0.650000|0.650000	0.86243|0.86243	GCC|GGC		0.483	KLHL42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402904.1	NM_020782	
PDZRN4	29951	broad.mit.edu	37	12	41967346	41967346	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:41967346G>A	ENST00000402685.2	+	10	2773	c.2765G>A	c.(2764-2766)cGg>cAg	p.R922Q	PDZRN4_ENST00000298919.7_Missense_Mutation_p.R662Q|PDZRN4_ENST00000539469.2_Missense_Mutation_p.R664Q	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	922							ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R664Q(1)		breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				AAGGAAGAGCGGAGTGGCATG	0.527																																					p.R922Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2765A	12						.						94.0	87.0	89.0					12																	41967346		2203	4300	6503	40253613	SO:0001583	missense	29951	exon10			AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"""RING-type (C3HC4) zinc fingers"""	30552	protein-coding gene	gene with protein product	"""similar to semaF cytoplasmic domain associated protein 3"""	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.2765G>A	12.37:g.41967346G>A	ENSP00000384197:p.Arg922Gln	Somatic		Capture	Illumina HiSeq	Phase_I	40253613	NM_001164595	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Missense_Mutation	SNP	ENST00000402685.2	37	CCDS53777.1	.	.	.	.	.	.	.	.	.	.	G	33	5.217828	0.95104	.	.	ENSG00000165966	ENST00000402685;ENST00000539469;ENST00000298919	T;T;T	0.38722	1.12;1.12;1.12	5.34	5.34	0.76211	.	0.000000	0.64402	D	0.000001	T	0.70561	0.3238	M	0.85041	2.73	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	0.74359	-0.3691	10	0.87932	D	0	-29.5889	19.939	0.97151	0.0:0.0:1.0:0.0	.	922;662;664	Q6ZMN7;Q6ZMN7-4;Q6ZMN7-2	PZRN4_HUMAN;.;.	Q	922;664;662	ENSP00000384197:R922Q;ENSP00000439990:R664Q;ENSP00000298919:R662Q	ENSP00000298919:R662Q	R	+	2	0	PDZRN4	40253613	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	9.813000	0.99286	2.890000	0.99128	0.650000	0.86243	CGG		0.527	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377	
TWF1	5756	broad.mit.edu	37	12	44193253	44193253	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:44193253G>T	ENST00000395510.2	-	5	560	c.431C>A	c.(430-432)cCt>cAt	p.P144H	TWF1_ENST00000325127.4_Missense_Mutation_p.P178H|TWF1_ENST00000552521.1_Missense_Mutation_p.P46H|TWF1_ENST00000547564.1_5'Flank|TWF1_ENST00000548315.1_Missense_Mutation_p.P144H	NM_001242397.1|NM_002822.4	NP_001229326.1|NP_002813.3	Q12792	TWF1_HUMAN	twinfilin actin-binding protein 1	144					barbed-end actin filament capping (GO:0051016)|negative regulation of actin filament polymerization (GO:0030837)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of actin phosphorylation (GO:0043538)|sequestering of actin monomers (GO:0042989)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|myofibril (GO:0030016)|perinuclear region of cytoplasm (GO:0048471)|ruffle membrane (GO:0032587)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.P144H(1)		endometrium(2)|large_intestine(6)|lung(4)|prostate(1)|stomach(1)	14	all_cancers(12;0.00125)	Lung NSC(34;0.0804)|all_lung(34;0.181)		GBM - Glioblastoma multiforme(48;0.0474)		CAGTGGGGCAGGGGAAGATTG	0.338																																					p.P178H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C533A	12						.						76.0	74.0	75.0					12																	44193253		2203	4300	6503	42479520	SO:0001583	missense	5756	exon5			U02680	CCDS31780.1, CCDS31780.2, CCDS55818.1	12q12	2013-04-25	2013-04-25	2006-11-13					9620	protein-coding gene	gene with protein product		610932	"""protein tyrosine kinase 9"", ""PTK9 protein tyrosine kinase 9"", ""twinfilin, actin-binding protein, homolog 1 (Drosophila)"""	PTK9		7507208	Standard	NM_002822		Approved	A6	uc001rob.3	Q12792		ENST00000395510.2:c.431C>A	12.37:g.44193253G>T	ENSP00000378886:p.Pro144His	Somatic		Capture	Illumina HiSeq	Phase_I	42479520	NM_002822	A8K5A8|B3KXS6|B4DLX9|Q59G07|Q5U0B1|Q6FHJ1|Q6FHL6|Q6NUK9|Q86XL6|Q8TCD3	Missense_Mutation	SNP	ENST00000395510.2	37	CCDS31780.2	.	.	.	.	.	.	.	.	.	.	G	32	5.105732	0.94292	.	.	ENSG00000151239	ENST00000552521;ENST00000395510;ENST00000325127;ENST00000548315;ENST00000546662	D;T;T;T;T	0.83755	-1.76;1.46;1.46;1.46;1.38	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	D	0.93074	0.7795	M	0.88775	2.98	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.992	D	0.93369	0.6733	10	0.87932	D	0	-19.2412	20.3931	0.98965	0.0:0.0:1.0:0.0	.	144;144	Q12792-3;Q12792	.;TWF1_HUMAN	H	46;144;178;144;182	ENSP00000448750:P46H;ENSP00000378886:P144H;ENSP00000321058:P178H;ENSP00000449428:P144H;ENSP00000448221:P182H	ENSP00000321058:P178H	P	-	2	0	TWF1	42479520	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.219000	0.78000	2.824000	0.97209	0.655000	0.94253	CCT		0.338	TWF1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403956.1	NM_002822	
PLEKHA8P1	51054	broad.mit.edu	37	12	45567094	45567094	+	RNA	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:45567094G>A	ENST00000256692.5	-	0	1591					NR_037144.1		O95397	PKHA9_HUMAN	pleckstrin homology domain containing, family A member 8 pseudogene 1							cytoplasm (GO:0005737)	glycolipid binding (GO:0051861)|glycolipid transporter activity (GO:0017089)	p.A352V(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(10)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						GGTTAACGCGGCCACAAAATC	0.493																																					.												.	.	1	Substitution - Missense(1)	large_intestine(1)	.	12						.						104.0	97.0	99.0					12																	45567094		2203	4300	6503	43853361			51054	.			AF103731		12q12	2010-11-24	2010-11-24	2010-11-24	ENSG00000134297	ENSG00000134297			30222	pseudogene	pseudogene	"""putative glycolipid transfer protein"""		"""pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 9"""	PLEKHA9		12477932	Standard	NR_037144		Approved	FLJ14156	uc001rom.2	O95397			12.37:g.45567094G>A		Somatic		Capture	Illumina HiSeq	Phase_I	43853361	.		Missense_Mutation	SNP	ENST00000256692.5	37																																																																																					0.493	PLEKHA8P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000404814.1	NR_037144	
SCAF11	9169	broad.mit.edu	37	12	46315893	46315893	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:46315893G>A	ENST00000369367.3	-	15	4563	c.4330C>T	c.(4330-4332)Cgg>Tgg	p.R1444W	SCAF11_ENST00000550629.1_Intron|SCAF11_ENST00000465950.1_Missense_Mutation_p.R1129W|SCAF11_ENST00000549162.1_Missense_Mutation_p.R1252W|SCAF11_ENST00000419565.2_Missense_Mutation_p.R1444W	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	1444					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.R1444W(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(17)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	69						CTCCCCTTCCGTGAATATTTG	0.388																																					p.R1444W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4330T	12						.						151.0	148.0	149.0					12																	46315893		2203	4300	6503	44602160	SO:0001583	missense	9169	exon15			Y11251	CCDS8748.2	12q13.11	2013-01-09	2011-01-10	2011-01-10	ENSG00000139218	ENSG00000139218		"""RING-type (C3HC4) zinc fingers"""	10784	protein-coding gene	gene with protein product		603668	"""splicing factor, arginine/serine-rich 2, interacting protein"", ""serine/arginine-rich splicing factor 2, interacting protein"""	SFRS2IP, SRSF2IP		9224939, 9447963	Standard	NM_004719		Approved	SIP1, SRRP129, CASP11	uc001rox.3	Q99590	OTTHUMG00000149930	ENST00000369367.3:c.4330C>T	12.37:g.46315893G>A	ENSP00000358374:p.Arg1444Trp	Somatic		Capture	Illumina HiSeq	Phase_I	44602160	NM_004719	A6NEU9|A6NLW5|Q8IW59	Missense_Mutation	SNP	ENST00000369367.3	37	CCDS8748.2	.	.	.	.	.	.	.	.	.	.	G	19.30	3.802079	0.70682	.	.	ENSG00000139218	ENST00000465950;ENST00000369367;ENST00000549162;ENST00000419565	T;T;T;T	0.66280	-0.2;1.37;-0.2;1.37	4.93	4.04	0.47022	.	0.000000	0.50627	D	0.000111	T	0.75265	0.3826	M	0.63843	1.955	0.58432	D	0.999991	D	0.89917	1.0	D	0.79784	0.993	T	0.78006	-0.2373	10	0.87932	D	0	-11.1683	13.379	0.60757	0.0766:0.0:0.9234:0.0	.	1444	Q99590	SCAFB_HUMAN	W	1129;1444;1252;1444	ENSP00000449812:R1129W;ENSP00000358374:R1444W;ENSP00000448864:R1252W;ENSP00000413036:R1444W	ENSP00000358374:R1444W	R	-	1	2	SCAF11	44602160	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	7.262000	0.78410	1.204000	0.43247	0.563000	0.77884	CGG		0.388	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313992.2	NM_004719	
KMT2D	8085	broad.mit.edu	37	12	49445837	49445837	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:49445837C>T	ENST00000301067.7	-	10	1628	c.1629G>A	c.(1627-1629)tcG>tcA	p.S543S		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	543	15 X 5 AA repeats of S/P-P-P-E/P-E/A.|Pro-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.S543S(1)									GGGACAGGGGCGATGCTTCAG	0.592																																					p.S543S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1629A	12						.						81.0	89.0	86.0					12																	49445837		2094	4207	6301	47732104	SO:0001819	synonymous_variant	8085	exon10			AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.1629G>A	12.37:g.49445837C>T		Somatic		Capture	Illumina HiSeq	Phase_I	47732104	NM_003482	O14687	Silent	SNP	ENST00000301067.7	37	CCDS44873.1																																																																																				0.592	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
DNAJC22	79962	broad.mit.edu	37	12	49745217	49745217	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:49745217T>C	ENST00000549441.2	+	4	2162	c.958T>C	c.(958-960)Ttc>Ctc	p.F320L	DNAJC22_ENST00000395069.3_Missense_Mutation_p.F320L			Q8N4W6	DJC22_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 22	320	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.					integral component of membrane (GO:0016021)		p.F320L(2)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|liver(2)|lung(1)|ovary(1)|pancreas(1)	10						ACAGAGGCACTTCCTGGAGAT	0.552																																					p.F320L												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T958C	12						.						56.0	56.0	56.0					12																	49745217		2203	4300	6503	48031484	SO:0001583	missense	79962	exon3			AK055747	CCDS8785.1	12q13.12	2011-09-02		2008-07-08	ENSG00000178401	ENSG00000178401		"""Heat shock proteins / DNAJ (HSP40)"""	25802	protein-coding gene	gene with protein product	"""wurst homolog (Drosophila)"""					17558392	Standard	NM_024902		Approved	wus, FLJ13236	uc001rua.3	Q8N4W6		ENST00000549441.2:c.958T>C	12.37:g.49745217T>C	ENSP00000446830:p.Phe320Leu	Somatic		Capture	Illumina HiSeq	Phase_I	48031484	NM_024902	B3KP54	Missense_Mutation	SNP	ENST00000549441.2	37	CCDS8785.1	.	.	.	.	.	.	.	.	.	.	T	34	5.314549	0.95655	.	.	ENSG00000178401	ENST00000549441;ENST00000395069	T;T	0.46063	0.88;0.88	5.5	5.5	0.81552	Heat shock protein DnaJ, N-terminal (5);	0.000000	0.85682	D	0.000000	T	0.63965	0.2556	M	0.74647	2.275	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.67956	-0.5536	10	0.87932	D	0	-18.0439	13.6117	0.62083	0.0:0.0:0.0:1.0	.	320	Q8N4W6	DJC22_HUMAN	L	320	ENSP00000446830:F320L;ENSP00000378508:F320L	ENSP00000378508:F320L	F	+	1	0	DNAJC22	48031484	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.439000	0.66556	2.313000	0.78055	0.454000	0.30748	TTC		0.552	DNAJC22-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404302.2	NM_024902	
SPATS2	65244	broad.mit.edu	37	12	49893910	49893910	+	Missense_Mutation	SNP	G	G	A	rs377665993		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:49893910G>A	ENST00000553127.1	+	10	1274	c.761G>A	c.(760-762)cGg>cAg	p.R254Q	SPATS2_ENST00000552557.1_3'UTR|SPATS2_ENST00000321898.6_Missense_Mutation_p.R254Q|SPATS2_ENST00000552918.1_Missense_Mutation_p.R254Q			Q86XZ4	SPAS2_HUMAN	spermatogenesis associated, serine-rich 2	254						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.R254Q(1)		breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(1)|prostate(1)|urinary_tract(4)	21						TCTCTTGCACGGTATCGAGTT	0.358																																					p.R254Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G761A	12						.	G	GLN/ARG	1,4405		0,1,2202	74.0	73.0	74.0		761	6.1	1.0	12		74	0,8600		0,0,4300	no	missense	SPATS2	NM_023071.3	43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	254/546	49893910	1,13005	2203	4300	6503	48180177	SO:0001583	missense	65244	exon9			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.761G>A	12.37:g.49893910G>A	ENSP00000448228:p.Arg254Gln	Somatic		Capture	Illumina HiSeq	Phase_I	48180177	NM_023071	A8K8G9|Q9H7D4|Q9H8Y7|Q9H8Z8	Missense_Mutation	SNP	ENST00000553127.1	37	CCDS31794.1	.	.	.	.	.	.	.	.	.	.	G	36	5.878675	0.97055	2.27E-4	0.0	ENSG00000123352	ENST00000553127;ENST00000321898;ENST00000552918;ENST00000395063	.	.	.	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.80686	0.4670	M	0.79258	2.445	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.81543	-0.0885	9	0.87932	D	0	-9.7194	18.1659	0.89727	0.0:0.0:1.0:0.0	.	254	Q86XZ4	SPAS2_HUMAN	Q	254	.	ENSP00000326841:R254Q	R	+	2	0	SPATS2	48180177	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	9.146000	0.94640	2.894000	0.99253	0.591000	0.81541	CGG		0.358	SPATS2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404023.1	NM_023071	
AQP5	362	broad.mit.edu	37	12	50356092	50356092	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:50356092G>A	ENST00000293599.6	+	1	440	c.292G>A	c.(292-294)Gcc>Acc	p.A98T	RP11-469H8.6_ENST00000552379.1_RNA|RP11-469H8.6_ENST00000550530.1_RNA|RP11-469H8.6_ENST00000550214.1_RNA	NM_001651.2	NP_001642.1	P55064	AQP5_HUMAN	aquaporin 5	98					camera-type eye morphogenesis (GO:0048593)|carbon dioxide transport (GO:0015670)|excretion (GO:0007588)|odontogenesis (GO:0042476)|pancreatic juice secretion (GO:0030157)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	water channel activity (GO:0015250)	p.A98T(1)		large_intestine(1)|lung(3)	4						GCTGGTGGGCGCCATTGCCGG	0.697																																					p.A98T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G292A	12						.						26.0	27.0	27.0					12																	50356092		2202	4299	6501	48642359	SO:0001583	missense	362	exon1			U46569	CCDS8793.1	12q13	2013-09-10				ENSG00000161798		"""Ion channels / Aquaporins"""	638	protein-coding gene	gene with protein product		600442				8621489, 23830519	Standard	NM_001651		Approved		uc001rvo.3	P55064	OTTHUMG00000169710	ENST00000293599.6:c.292G>A	12.37:g.50356092G>A	ENSP00000293599:p.Ala98Thr	Somatic		Capture	Illumina HiSeq	Phase_I	48642359	NM_001651	Q6FGW8	Missense_Mutation	SNP	ENST00000293599.6	37	CCDS8793.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.421168	0.83559	.	.	ENSG00000161798	ENST00000293599	D	0.96651	-4.08	3.69	2.79	0.32731	Aquaporin-like (2);	0.225469	0.30446	N	0.009619	D	0.98845	0.9610	H	0.99609	4.655	0.49213	D	0.999763	D	0.89917	1.0	D	0.77004	0.989	D	0.97509	1.0065	10	0.87932	D	0	-3.7444	8.9175	0.35590	0.1131:0.0:0.8869:0.0	.	98	P55064	AQP5_HUMAN	T	98	ENSP00000293599:A98T	ENSP00000293599:A98T	A	+	1	0	AQP5	48642359	1.000000	0.71417	0.307000	0.25127	0.872000	0.50106	9.601000	0.98297	0.903000	0.36546	0.462000	0.41574	GCC		0.697	AQP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405542.2	NM_001651	
ASIC1	41	broad.mit.edu	37	12	50471865	50471865	+	Silent	SNP	C	C	T	rs149923094	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:50471865C>T	ENST00000447966.2	+	5	1021	c.792C>T	c.(790-792)ggC>ggT	p.G264G	ASIC1_ENST00000228468.4_Silent_p.G264G|ASIC1_ENST00000552438.1_Silent_p.G298G	NM_001095.3	NP_001086.2	P78348	ASIC1_HUMAN	acid-sensing (proton-gated) ion channel 1	264					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.G264G(1)								Amiloride(DB00594)|Diclofenac(DB00586)	TGGGCTTTGGCGTGGCCCCAG	0.602													C|||	6	0.00119808	0.0	0.0	5008	,	,		18602	0.006		0.0	False		,,,				2504	0.0				p.G264G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C792T	12						.						151.0	133.0	139.0					12																	50471865		2203	4300	6503	48758132	SO:0001819	synonymous_variant	41	exon5			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.792C>T	12.37:g.50471865C>T		Somatic		Capture	Illumina HiSeq	Phase_I	48758132	NM_020039	A3KN86|E5KBL7|P78349|Q96CV2	Silent	SNP	ENST00000447966.2	37	CCDS44876.1	5	0.0022893772893772895	0	0.0	0	0.0	5	0.008741258741258742	0	0.0	C	9.491	1.100655	0.20552	.	.	ENSG00000110881	ENST00000453327	.	.	.	4.09	-8.18	0.01053	.	.	.	.	.	T	0.35068	0.0919	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46133	-0.9213	4	.	.	.	-9.0027	5.4217	0.16403	0.0803:0.1342:0.1599:0.6257	.	.	.	.	V	132	.	.	A	+	2	0	ACCN2	48758132	0.000000	0.05858	0.785000	0.31869	0.998000	0.95712	-5.608000	0.00110	-1.881000	0.01123	0.563000	0.77884	GCG		0.602	ASIC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406004.2	NM_020039	
SLC11A2	4891	broad.mit.edu	37	12	51388340	51388340	+	Missense_Mutation	SNP	T	T	C	rs199762460		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:51388340T>C	ENST00000262051.7	-	11	1151	c.1064A>G	c.(1063-1065)gAc>gGc	p.D355G	SLC11A2_ENST00000541174.2_Missense_Mutation_p.D355G|SLC11A2_ENST00000546743.1_Missense_Mutation_p.D276G|SLC11A2_ENST00000262052.5_Missense_Mutation_p.D355G|SLC11A2_ENST00000547198.1_Missense_Mutation_p.D355G|SLC11A2_ENST00000394904.3_Missense_Mutation_p.D384G|SLC11A2_ENST00000547688.1_Missense_Mutation_p.D384G|SLC11A2_ENST00000545993.2_Missense_Mutation_p.D351G	NM_001174126.1|NM_001174127.1	NP_001167597.1|NP_001167598.1	P49281	NRAM2_HUMAN	solute carrier family 11 (proton-coupled divalent metal ion transporter), member 2	355					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cadmium ion transmembrane transport (GO:0070574)|cation transmembrane transport (GO:0098655)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|cellular response to iron ion (GO:0071281)|cellular response to oxidative stress (GO:0034599)|cellular response to tumor necrosis factor (GO:0071356)|cobalt ion transport (GO:0006824)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detection of oxygen (GO:0003032)|erythrocyte development (GO:0048821)|ferrous iron import (GO:0070627)|ferrous iron transport (GO:0015684)|heme biosynthetic process (GO:0006783)|lead ion transport (GO:0015692)|learning or memory (GO:0007611)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|multicellular organismal iron ion homeostasis (GO:0060586)|nickel cation transmembrane transport (GO:0035444)|nickel cation transport (GO:0015675)|response to cadmium ion (GO:0046686)|response to hypoxia (GO:0001666)|response to iron ion (GO:0010039)|response to lead ion (GO:0010288)|response to manganese ion (GO:0010042)|transmembrane transport (GO:0055085)|vanadium ion transport (GO:0015676)|zinc ion transmembrane transport (GO:0071577)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|basal part of cell (GO:0045178)|brush border (GO:0005903)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|paraferritin complex (GO:0070826)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)|vacuole (GO:0005773)	cadmium ion binding (GO:0046870)|cadmium ion transmembrane transporter activity (GO:0015086)|cobalt ion binding (GO:0050897)|cobalt ion transmembrane transporter activity (GO:0015087)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|ferrous iron transmembrane transporter activity (GO:0015093)|hydrogen ion transmembrane transporter activity (GO:0015078)|inorganic cation transmembrane transporter activity (GO:0022890)|iron ion binding (GO:0005506)|lead ion transmembrane transporter activity (GO:0015094)|manganese ion binding (GO:0030145)|manganese ion transmembrane transporter activity (GO:0005384)|nickel cation binding (GO:0016151)|nickel cation transmembrane transporter activity (GO:0015099)|solute:proton symporter activity (GO:0015295)|vanadium ion transmembrane transporter activity (GO:0015100)|zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)	p.D355G(1)		breast(2)|cervix(1)|endometrium(3)|kidney(16)|large_intestine(4)|lung(9)|upper_aerodigestive_tract(1)	36						TTTGTAGATGTCCACAGCCAG	0.403																																					p.D384G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1151G	12						.						128.0	110.0	116.0					12																	51388340		2203	4300	6503	49674607	SO:0001583	missense	4891	exon11			AB015355	CCDS8805.1, CCDS53791.1, CCDS53792.1, CCDS53793.1	12q13	2013-07-18	2013-07-18		ENSG00000110911	ENSG00000110911		"""Solute carriers"""	10908	protein-coding gene	gene with protein product		600523		NRAMP2		7613023	Standard	NM_000617		Approved	DCT1, DMT1	uc001rxk.2	P49281	OTTHUMG00000169493	ENST00000262051.7:c.1064A>G	12.37:g.51388340T>C	ENSP00000262051:p.Asp355Gly	Somatic		Capture	Illumina HiSeq	Phase_I	49674607	NM_001174125	B3KT08|B4DK84|F5H741|O43288|O60932|O94801|Q498Z5|Q8IUD7|Q96J35	Missense_Mutation	SNP	ENST00000262051.7	37	CCDS53792.1	.	.	.	.	.	.	.	.	.	.	T	17.33	3.363052	0.61403	.	.	ENSG00000110911	ENST00000262051;ENST00000547198;ENST00000262052;ENST00000394904;ENST00000547688;ENST00000541174;ENST00000545993;ENST00000546743	T;T;T;T;T;T;T;T	0.71579	-0.58;-0.58;-0.58;-0.58;-0.58;-0.58;-0.58;-0.58	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.69378	0.3104	L	0.56124	1.755	0.80722	D	1	B;B;B;B;B;B	0.23128	0.046;0.037;0.037;0.08;0.046;0.019	B;B;B;B;B;B	0.32022	0.139;0.085;0.085;0.132;0.097;0.044	T	0.67252	-0.5717	10	0.44086	T	0.13	-17.7796	14.6374	0.68699	0.0:0.0:0.0:1.0	.	318;351;384;355;204;355	B7Z9M2;F5H741;P49281-3;P49281-2;B3KY44;P49281	.;.;.;.;.;NRAM2_HUMAN	G	355;355;355;384;384;355;351;276	ENSP00000262051:D355G;ENSP00000446769:D355G;ENSP00000262052:D355G;ENSP00000378364:D384G;ENSP00000449200:D384G;ENSP00000444542:D355G;ENSP00000442810:D351G;ENSP00000446914:D276G	ENSP00000262051:D355G	D	-	2	0	SLC11A2	49674607	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.631000	0.83237	2.153000	0.67306	0.533000	0.62120	GAC		0.403	SLC11A2-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404383.1		
POU6F1	5463	broad.mit.edu	37	12	51584206	51584206	+	Frame_Shift_Del	DEL	G	G	-	rs369846174		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:51584206delG	ENST00000389243.4	-	11	1669	c.730delC	c.(730-732)cagfs	p.Q244fs	POU6F1_ENST00000333640.10_Frame_Shift_Del_p.Q244fs|POU6F1_ENST00000550824.1_Frame_Shift_Del_p.Q244fs			Q14863	PO6F1_HUMAN	POU class 6 homeobox 1	244					brain development (GO:0007420)|heart development (GO:0007507)|muscle organ development (GO:0007517)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q244fs*3(1)		breast(2)|cervix(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(1)	11						TCTATGGCCTGGGGGGTGAAG	0.562																																					p.Q244fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.730delC	12						.						116.0	115.0	115.0					12																	51584206		2203	4300	6503	49870473	SO:0001589	frameshift_variant	5463	exon6			AL832881	CCDS31803.1	12q13.13	2011-06-20	2007-07-13			ENSG00000184271		"""Homeoboxes / POU class"""	9224	protein-coding gene	gene with protein product			"""POU domain, class 6, transcription factor 1"""			7908264	Standard	NM_002702		Approved	BRN5, MPOU, TCFB1	uc001rxz.3	Q14863		ENST00000389243.4:c.730delC	12.37:g.51584206delG	ENSP00000373895:p.Gln244fs	Somatic		Capture	Illumina HiSeq	Phase_I	49870473	NM_002702	Q15944|Q6DK47|Q7Z7P6	Frame_Shift_Del	DEL	ENST00000389243.4	37	CCDS31803.1																																																																																				0.562	POU6F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405126.1	NM_002702	
BIN2	51411	broad.mit.edu	37	12	51696872	51696872	+	Splice_Site	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:51696872T>C	ENST00000267012.4	-	3	277	c.216A>G	c.(214-216)aaA>aaG	p.K72K	BIN2_ENST00000452142.2_Splice_Site_p.K72K|BIN2_ENST00000544402.1_Splice_Site_p.K46K|BIN2_ENST00000604560.1_Splice_Site_p.K45K	NM_016293.2	NP_057377.2	Q9UBW5	BIN2_HUMAN	bridging integrator 2	72	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				cell chemotaxis (GO:0060326)|membrane tubulation (GO:0097320)|phagocytosis, engulfment (GO:0006911)|podosome assembly (GO:0071800)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|podosome (GO:0002102)	phospholipid binding (GO:0005543)	p.K72K(1)		NS(2)|breast(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(3)	31						ATTGCCCACCTTTGACTGCAC	0.433																																					p.K72K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A216G	12						.						126.0	113.0	117.0					12																	51696872		2203	4300	6503	49983139	SO:0001630	splice_region_variant	51411	exon3			AF146531	CCDS8811.1	12q13.13	2012-01-23			ENSG00000110934	ENSG00000110934			1053	protein-coding gene	gene with protein product		605936				10903846	Standard	XM_005268957		Approved	BRAP-1	uc001ryg.3	Q9UBW5		ENST00000267012.4:c.217+1A>G	12.37:g.51696872T>C		Somatic		Capture	Illumina HiSeq	Phase_I	49983139	NM_016293	Q86VV0|Q9NWK4|Q9UKN4	Silent	SNP	ENST00000267012.4	37	CCDS8811.1																																																																																				0.433	BIN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000469800.1		Silent
ACVRL1	94	broad.mit.edu	37	12	52309928	52309928	+	Missense_Mutation	SNP	G	G	A	rs141764916		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:52309928G>A	ENST00000388922.4	+	8	1440	c.1157G>A	c.(1156-1158)cGc>cAc	p.R386H	ACVRL1_ENST00000419526.2_Missense_Mutation_p.R212H|ACVRL1_ENST00000550683.1_Missense_Mutation_p.R400H	NM_000020.2	NP_000011.2	P37023	ACVL1_HUMAN	activin A receptor type II-like 1	386	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|angiogenesis (GO:0001525)|artery development (GO:0060840)|blood circulation (GO:0008015)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|blood vessel maturation (GO:0001955)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|cellular response to transforming growth factor beta stimulus (GO:0071560)|endothelial tube morphogenesis (GO:0061154)|in utero embryonic development (GO:0001701)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of focal adhesion assembly (GO:0051895)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of blood pressure (GO:0008217)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of DNA replication (GO:0006275)|regulation of endothelial cell proliferation (GO:0001936)|regulation of transcription, DNA-templated (GO:0006355)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|venous blood vessel development (GO:0060841)|wound healing, spreading of epidermal cells (GO:0035313)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)	activin binding (GO:0048185)|activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type I (GO:0005025)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)	p.R386H(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	20				BRCA - Breast invasive adenocarcinoma(357;0.0991)	Adenosine triphosphate(DB00171)	GAGCAGATCCGCACGGACTGC	0.607																																					p.R386H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1157A	12	GRCh37	CM050996	ACVRL1	M	rs141764916	.	G	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	102.0	86.0	91.0		1157,1157	4.1	1.0	12	dbSNP_134	91	0,8600		0,0,4300	no	missense,missense	ACVRL1	NM_000020.2,NM_001077401.1	29,29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign	386/504,386/504	52309928	1,13005	2203	4300	6503	50596195	SO:0001583	missense	94	exon7			L17075	CCDS31804.1	12q13.13	2014-09-17			ENSG00000139567	ENSG00000139567			175	protein-coding gene	gene with protein product		601284		ACVRLK1, ORW2		8397373, 8640225	Standard	NM_000020		Approved	HHT2, ALK1, HHT	uc001rzk.3	P37023	OTTHUMG00000169507	ENST00000388922.4:c.1157G>A	12.37:g.52309928G>A	ENSP00000373574:p.Arg386His	Somatic		Capture	Illumina HiSeq	Phase_I	50596195	NM_001077401	A6NGA8	Missense_Mutation	SNP	ENST00000388922.4	37	CCDS31804.1	.	.	.	.	.	.	.	.	.	.	G	12.91	2.080528	0.36662	2.27E-4	0.0	ENSG00000139567	ENST00000388922;ENST00000267008;ENST00000550683;ENST00000548659;ENST00000419526	D;D;D	0.93488	-3.23;-3.23;-3.23	4.98	4.08	0.47627	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.45361	D	0.000370	D	0.89417	0.6709	L	0.42581	1.335	0.80722	D	1	B;B	0.22211	0.008;0.066	B;B	0.21546	0.007;0.035	D	0.86950	0.2085	10	0.72032	D	0.01	.	9.9878	0.41852	0.0763:0.1413:0.7825:0.0	.	212;386	E7EN07;P37023	.;ACVL1_HUMAN	H	386;386;400;212;212	ENSP00000373574:R386H;ENSP00000447884:R400H;ENSP00000392492:R212H	ENSP00000267008:R386H	R	+	2	0	ACVRL1	50596195	0.985000	0.35326	1.000000	0.80357	0.405000	0.30901	1.897000	0.39799	1.462000	0.47948	0.563000	0.77884	CGC		0.607	ACVRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404520.2		
KRT77	374454	broad.mit.edu	37	12	53096688	53096688	+	Silent	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:53096688G>T	ENST00000341809.3	-	1	559	c.531C>A	c.(529-531)tcC>tcA	p.S177S	KRT77_ENST00000537195.1_5'UTR	NM_175078.2	NP_778253.2	Q7Z794	K2C1B_HUMAN	keratin 77	177	Coil 1A.|Rod.					cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.S177S(1)		NS(2)|endometrium(2)|large_intestine(3)|lung(11)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25						tgtcaatgaaggaggcaaact	0.527																																					p.S177S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C531A	12						.						130.0	124.0	126.0					12																	53096688		2203	4300	6503	51382955	SO:0001819	synonymous_variant	374454	exon1			BK000975	CCDS8837.1	12q13.13	2013-06-25	2006-07-17	2006-07-17	ENSG00000189182	ENSG00000189182		"""-"", ""Intermediate filaments type II, keratins (basic)"""	20411	protein-coding gene	gene with protein product		611158	"""keratin 1B"""	KRT1B		11683385, 16831889	Standard	NM_175078		Approved		uc001saw.3	Q7Z794	OTTHUMG00000169450	ENST00000341809.3:c.531C>A	12.37:g.53096688G>T		Somatic		Capture	Illumina HiSeq	Phase_I	51382955	NM_175078	Q7RTS8	Silent	SNP	ENST00000341809.3	37	CCDS8837.1																																																																																				0.527	KRT77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404111.1	NM_175078	
HOXC12	3228	broad.mit.edu	37	12	54350153	54350153	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:54350153C>T	ENST00000243103.3	+	2	748	c.652C>T	c.(652-654)Cgc>Tgc	p.R218C	AC012531.23_ENST00000603432.1_lincRNA	NM_173860.1	NP_776272.1	P31275	HXC12_HUMAN	homeobox C12	218					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.R218C(1)		large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)	12						TCGGAAGAAGCGCAAGCCCTA	0.597																																					p.R218C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C652T	12						.						87.0	90.0	89.0					12																	54350153		2203	4300	6503	52636420	SO:0001583	missense	3228	exon2			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.652C>T	12.37:g.54350153C>T	ENSP00000243103:p.Arg218Cys	Somatic		Capture	Illumina HiSeq	Phase_I	52636420	NM_173860	Q9BXJ6	Missense_Mutation	SNP	ENST00000243103.3	37	CCDS8866.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.296831	0.81025	.	.	ENSG00000123407	ENST00000243103	D	0.99186	-5.53	4.35	4.35	0.52113	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.083554	0.48286	D	0.000192	D	0.99591	0.9852	H	0.99565	4.63	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.97617	1.0133	10	0.87932	D	0	.	11.3119	0.49368	0.1824:0.8176:0.0:0.0	.	218	P31275	HXC12_HUMAN	C	218	ENSP00000243103:R218C	ENSP00000243103:R218C	R	+	1	0	HOXC12	52636420	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.857000	0.55972	2.135000	0.66039	0.462000	0.41574	CGC		0.597	HOXC12-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358868.2	NM_173860	
SLC16A7	9194	broad.mit.edu	37	12	60168560	60168560	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:60168560G>A	ENST00000261187.4	+	4	648	c.484G>A	c.(484-486)Gct>Act	p.A162T	SLC16A7_ENST00000552024.1_Missense_Mutation_p.A162T|SLC16A7_ENST00000547379.1_Missense_Mutation_p.A162T|SLC16A7_ENST00000543448.1_Missense_Mutation_p.A63T|SLC16A7_ENST00000552432.1_Missense_Mutation_p.A162T	NM_004731.4	NP_004722.2	O60669	MOT2_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 7	162					lactate transmembrane transport (GO:0035873)|pyruvate transmembrane transport (GO:1901475)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	lactate transmembrane transporter activity (GO:0015129)|pyruvate secondary active transmembrane transporter activity (GO:0005477)|pyruvate transmembrane transporter activity (GO:0050833)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)	p.A162T(1)		endometrium(1)|large_intestine(14)|liver(2)|lung(11)|ovary(1)|skin(1)	30				GBM - Glioblastoma multiforme(3;0.0303)	Gamma Hydroxybutyric Acid(DB01440)|Niflumic Acid(DB04552)|Probenecid(DB01032)|Pyruvic acid(DB00119)	AAGTTCATTGGCTCCTTTCAA	0.438																																					p.A162T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G484A	12						.						79.0	78.0	78.0					12																	60168560		2203	4300	6503	58454827	SO:0001583	missense	9194	exon4			AF049608	CCDS8961.1	12q14.1	2013-07-18	2013-07-18		ENSG00000118596	ENSG00000118596		"""Solute carriers"""	10928	protein-coding gene	gene with protein product		603654	"""solute carrier family 16 (monocarboxylic acid transporters), member 7"""			9786900	Standard	NM_004731		Approved	MCT2	uc001sqt.4	O60669	OTTHUMG00000169923	ENST00000261187.4:c.484G>A	12.37:g.60168560G>A	ENSP00000261187:p.Ala162Thr	Somatic		Capture	Illumina HiSeq	Phase_I	58454827	NM_004731	Q8NEM3|Q9UPB3	Missense_Mutation	SNP	ENST00000261187.4	37	CCDS8961.1	.	.	.	.	.	.	.	.	.	.	G	36	5.784738	0.96937	.	.	ENSG00000118596	ENST00000552432;ENST00000547379;ENST00000552024;ENST00000548610;ENST00000261187;ENST00000543448;ENST00000548444	T;T;T;T;T;T;T	0.59224	0.28;0.28;0.28;0.28;0.28;0.28;0.28	6.06	6.06	0.98353	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.78541	0.4299	M	0.84156	2.68	0.80722	D	1	D	0.56287	0.975	D	0.63488	0.915	T	0.77587	-0.2532	9	.	.	.	.	20.6397	0.99537	0.0:0.0:1.0:0.0	.	162	O60669	MOT2_HUMAN	T	162;162;162;162;162;63;47	ENSP00000449547:A162T;ENSP00000448071:A162T;ENSP00000448742:A162T;ENSP00000446722:A162T;ENSP00000261187:A162T;ENSP00000443731:A63T;ENSP00000447814:A47T	.	A	+	1	0	SLC16A7	58454827	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	9.869000	0.99810	2.880000	0.98712	0.650000	0.86243	GCT		0.438	SLC16A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406587.1	NM_004731	
MON2	23041	broad.mit.edu	37	12	62918894	62918894	+	Silent	SNP	G	G	A	rs150576914	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:62918894G>A	ENST00000393632.2	+	10	1531	c.1140G>A	c.(1138-1140)caG>caA	p.Q380Q	MON2_ENST00000546600.1_Silent_p.Q380Q|MON2_ENST00000393630.3_Silent_p.Q380Q|MON2_ENST00000393629.2_Silent_p.Q380Q|MON2_ENST00000552115.1_Silent_p.Q380Q|MON2_ENST00000280379.6_Silent_p.Q380Q|MON2_ENST00000552738.1_Silent_p.Q380Q	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	380					actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)	p.Q380Q(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		ATATGAAACAGCATTCTACCA	0.333													G|||	2	0.000399361	0.0008	0.0014	5008	,	,		16782	0.0		0.0	False		,,,				2504	0.0				p.Q380Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1140A	12						.	G		7,4399	12.9+/-30.5	0,7,2196	98.0	93.0	95.0		1140	-3.2	0.9	12	dbSNP_134	95	0,8600		0,0,4300	no	coding-synonymous	MON2	NM_015026.2		0,7,6496	AA,AG,GG		0.0,0.1589,0.0538		380/1718	62918894	7,12999	2203	4300	6503	61205161	SO:0001819	synonymous_variant	23041	exon10				CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"""MON2 homolog (yeast)"""			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.1140G>A	12.37:g.62918894G>A		Somatic		Capture	Illumina HiSeq	Phase_I	61205161	NM_015026	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Silent	SNP	ENST00000393632.2	37	CCDS31849.1																																																																																				0.333	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026	
DPY19L2	283417	broad.mit.edu	37	12	63954370	63954370	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:63954370G>A	ENST00000324472.4	-	22	2382	c.2199C>T	c.(2197-2199)agC>agT	p.S733S	DPY19L2_ENST00000413230.2_Silent_p.S180S	NM_173812.4	NP_776173.3	Q6NUT2	D19L2_HUMAN	dpy-19-like 2 (C. elegans)	733					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nucleus (GO:0005634)	transferase activity, transferring glycosyl groups (GO:0016757)	p.S733S(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	45			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		CGAGCAGGACGCTACATAAGG	0.433																																					p.S733S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2199T	12						.						84.0	72.0	76.0					12																	63954370		2203	4300	6503	62240637	SO:0001819	synonymous_variant	283417	exon22				CCDS31851.1	12q14.2	2012-11-14			ENSG00000177990	ENSG00000177990			19414	protein-coding gene	gene with protein product	"""spermatogenesis associated 34"""	613893				12975309	Standard	XM_006719348		Approved	FLJ32949, SPATA34	uc001srp.1	Q6NUT2	OTTHUMG00000168712	ENST00000324472.4:c.2199C>T	12.37:g.63954370G>A		Somatic		Capture	Illumina HiSeq	Phase_I	62240637	NM_173812	A4FVC1|B4E191|Q3ZCX2|Q6UWG8|Q96LZ9	Silent	SNP	ENST00000324472.4	37	CCDS31851.1																																																																																				0.433	DPY19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400689.2	NM_173812	
GRIP1	23426	broad.mit.edu	37	12	66849198	66849198	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:66849198T>G	ENST00000398016.3	-	10	1257	c.1189A>C	c.(1189-1191)Aaa>Caa	p.K397Q	GRIP1_ENST00000286445.7_Missense_Mutation_p.K449Q|GRIP1_ENST00000359742.4_Missense_Mutation_p.K449Q	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.K397Q(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)		CATGAGCTTTTGAAGTCTTTC	0.478																																					p.K397Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1189C	12						.						154.0	150.0	151.0					12																	66849198		1900	4116	6016	65135465	SO:0001583	missense	23426	exon10			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.1189A>C	12.37:g.66849198T>G	ENSP00000381098:p.Lys397Gln	Somatic		Capture	Illumina HiSeq	Phase_I	65135465	NM_001178074	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Missense_Mutation	SNP	ENST00000398016.3	37	CCDS41807.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.31|16.31	3.086131|3.086131	0.55861|0.55861	.|.	.|.	ENSG00000155974|ENSG00000155974	ENST00000398016;ENST00000359742;ENST00000286445;ENST00000538211;ENST00000540433|ENST00000543172	T;T;T;T;T|.	0.21543|.	2.0;2.02;2.02;2.0;2.08|.	5.51|5.51	5.51|5.51	0.81932|0.81932	.|.	0.101024|.	0.64402|.	D|.	0.000002|.	T|T	0.73908|0.73908	0.3647|0.3647	M|M	0.69823|0.69823	2.125|2.125	0.58432|0.58432	D|D	0.999996|0.999996	P;B;D|.	0.76494|.	0.694;0.317;0.999|.	P;B;D|.	0.71870|.	0.452;0.124;0.975|.	T|T	0.74000|0.74000	-0.3805|-0.3805	9|5	.|.	.|.	.|.	-19.7388|-19.7388	15.9405|15.9405	0.79750|0.79750	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	397;397;449|.	F5H4N6;Q9Y3R0-3;Q9Y3R0-2|.	.;.;.|.	Q|P	397;449;449;397;341|216	ENSP00000381098:K397Q;ENSP00000352780:K449Q;ENSP00000286445:K449Q;ENSP00000446047:K397Q;ENSP00000446024:K341Q|.	.|.	K|Q	-|-	1|2	0|0	GRIP1|GRIP1	65135465|65135465	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.920000|0.920000	0.55202|0.55202	8.040000|8.040000	0.89188|0.89188	2.234000|2.234000	0.73211|0.73211	0.459000|0.459000	0.35465|0.35465	AAA|CAA		0.478	GRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401975.2		
DYRK2	8445	broad.mit.edu	37	12	68051020	68051020	+	Silent	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:68051020T>C	ENST00000344096.3	+	3	746	c.333T>C	c.(331-333)ctT>ctC	p.L111L	RP11-335O4.3_ENST00000425371.2_RNA|DYRK2_ENST00000393555.3_Silent_p.L38L	NM_006482.2	NP_006473.2	Q92630	DYRK2_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	111					cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of NFAT protein import into nucleus (GO:0051534)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of glycogen biosynthetic process (GO:0045725)|protein phosphorylation (GO:0006468)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|ubiquitin binding (GO:0043130)	p.L111L(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	30			Lung(24;6.81e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(7;0.000573)		CAAATGGGCTTACAACAGTGG	0.547																																					p.L38L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T114C	12						.						100.0	83.0	89.0					12																	68051020		2203	4300	6503	66337287	SO:0001819	synonymous_variant	8445	exon2			Y09216	CCDS8978.1, CCDS8979.1	12q15	2008-07-03				ENSG00000127334			3093	protein-coding gene	gene with protein product		603496				9748265	Standard	NM_003583		Approved		uc001str.4	Q92630		ENST00000344096.3:c.333T>C	12.37:g.68051020T>C		Somatic		Capture	Illumina HiSeq	Phase_I	66337287	NM_003583	B2R9V9|Q9BRB5	Silent	SNP	ENST00000344096.3	37	CCDS8978.1																																																																																				0.547	DYRK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402218.1		
PTPRB	5787	broad.mit.edu	37	12	70980841	70980841	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:70980841C>T	ENST00000261266.5	-	7	1632	c.1603G>A	c.(1603-1605)Gtc>Atc	p.V535I	PTPRB_ENST00000538708.1_Missense_Mutation_p.V535I|PTPRB_ENST00000334414.6_Missense_Mutation_p.V753I|PTPRB_ENST00000550857.1_Missense_Mutation_p.V445I|PTPRB_ENST00000551525.1_Missense_Mutation_p.V752I|PTPRB_ENST00000451516.2_Missense_Mutation_p.V445I|PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000550358.1_Missense_Mutation_p.V753I	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	535	Fibronectin type-III 6. {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.V535I(1)|p.V753I(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)			ATACTGGTGACTGTAGCCATG	0.388																																					p.V753I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2257A	12						.						111.0	106.0	107.0					12																	70980841		1861	4098	5959	69267108	SO:0001583	missense	5787	exon9			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.1603G>A	12.37:g.70980841C>T	ENSP00000261266:p.Val535Ile	Somatic		Capture	Illumina HiSeq	Phase_I	69267108	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Missense_Mutation	SNP	ENST00000261266.5	37	CCDS44944.1	.	.	.	.	.	.	.	.	.	.	C	16.26	3.072011	0.55646	.	.	ENSG00000127329	ENST00000334414;ENST00000451516;ENST00000550358;ENST00000544694;ENST00000538708;ENST00000550857;ENST00000261266;ENST00000551525;ENST00000548122	T;T;T;T;T;T;T;T	0.70749	-0.51;-0.51;-0.51;-0.51;-0.51;-0.51;-0.51;-0.51	5.12	5.12	0.69794	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.73281	0.3567	M	0.66506	2.035	0.46678	D	0.999151	P;P;B;P;B;P;P	0.35383	0.498;0.498;0.092;0.482;0.421;0.476;0.498	B;B;B;B;B;B;B	0.44085	0.44;0.44;0.152;0.309;0.31;0.437;0.44	T	0.69658	-0.5086	10	0.22706	T	0.39	.	13.8788	0.63670	0.0:0.9238:0.0:0.0761	.	445;535;632;752;753;535;753	P23467-2;F5H3G6;Q6ZR19;F8VSD5;P23467-3;P23467;F8VU56	.;.;.;.;.;PTPRB_HUMAN;.	I	753;445;753;753;535;445;535;752;632	ENSP00000334928:V753I;ENSP00000393028:V445I;ENSP00000448058:V753I;ENSP00000438927:V535I;ENSP00000447302:V445I;ENSP00000261266:V535I;ENSP00000448349:V752I;ENSP00000446982:V632I	ENSP00000261266:V535I	V	-	1	0	PTPRB	69267108	0.963000	0.33076	0.997000	0.53966	0.989000	0.77384	2.158000	0.42329	2.368000	0.80403	0.557000	0.71058	GTC		0.388	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1		
ACSS3	79611	broad.mit.edu	37	12	81528724	81528724	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:81528724A>C	ENST00000548058.1	+	3	1496	c.586A>C	c.(586-588)Agt>Cgt	p.S196R	ACSS3_ENST00000261206.3_Missense_Mutation_p.S195R			Q9H6R3	ACSS3_HUMAN	acyl-CoA synthetase short-chain family member 3	196						mitochondrion (GO:0005739)	acetate-CoA ligase activity (GO:0003987)|ATP binding (GO:0005524)	p.S196R(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(7)|liver(3)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	51						TGCCATCCACAGTCTCATATT	0.418																																					p.S196R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A586C	12						.						181.0	148.0	159.0					12																	81528724		2203	4300	6503	80052855	SO:0001583	missense	79611	exon3				CCDS9022.1	12q21.31	2014-08-08			ENSG00000111058	ENSG00000111058		"""Acyl-CoA synthetase family"""	24723	protein-coding gene	gene with protein product		614356				17762044	Standard	NM_024560		Approved	FLJ21963	uc001szl.1	Q9H6R3	OTTHUMG00000170179	ENST00000548058.1:c.586A>C	12.37:g.81528724A>C	ENSP00000449535:p.Ser196Arg	Somatic		Capture	Illumina HiSeq	Phase_I	80052855	NM_024560	Q8NC66	Missense_Mutation	SNP	ENST00000548058.1	37	CCDS9022.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.680722	0.88542	.	.	ENSG00000111058	ENST00000549175;ENST00000548058;ENST00000261206	T;T;T	0.42900	0.96;0.96;0.96	5.83	5.83	0.93111	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	T	0.77136	0.4086	H	0.97390	3.995	0.80722	D	1	D	0.76494	0.999	D	0.75020	0.985	D	0.85802	0.1374	10	0.87932	D	0	-25.0503	16.194	0.82011	1.0:0.0:0.0:0.0	.	196	Q9H6R3	ACSS3_HUMAN	R	88;196;195	ENSP00000447748:S88R;ENSP00000449535:S196R;ENSP00000261206:S195R	ENSP00000261206:S195R	S	+	1	0	ACSS3	80052855	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.271000	0.95698	2.225000	0.72522	0.460000	0.39030	AGT		0.418	ACSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407794.1	NM_024560	
SLC6A15	55117	broad.mit.edu	37	12	85270295	85270295	+	Missense_Mutation	SNP	C	C	T	rs139565834	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:85270295C>T	ENST00000266682.5	-	6	1389	c.848G>A	c.(847-849)cGc>cAc	p.R283H	SLC6A15_ENST00000552192.1_Missense_Mutation_p.R176H|SLC6A15_ENST00000551388.1_5'UTR	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15	283					amino acid transport (GO:0006865)|ion transport (GO:0006811)|leucine transport (GO:0015820)|neurotransmitter transport (GO:0006836)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)|proline:sodium symporter activity (GO:0005298)	p.R283H(1)		kidney(1)|large_intestine(18)|lung(15)|ovary(1)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	44						AAACATGTGGCGAATGCCATC	0.308													C|||	4	0.000798722	0.003	0.0	5008	,	,		14763	0.0		0.0	False		,,,				2504	0.0				p.R283H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G848A	12						.	C	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	80.0	79.0	79.0		527,848	4.2	1.0	12	dbSNP_134	79	0,8592		0,0,4296	yes	missense,missense	SLC6A15	NM_001146335.1,NM_182767.4	29,29	0,1,6498	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	176/624,283/731	85270295	1,12997	2203	4296	6499	83794426	SO:0001583	missense	55117	exon6			AF265577	CCDS9026.1, CCDS9027.1, CCDS53816.1	12q21.31	2013-07-15	2008-09-02		ENSG00000072041	ENSG00000072041		"""Solute carriers"""	13621	protein-coding gene	gene with protein product	"""homolog of rat orphan transporter v7-3"", ""sodium/chloride dependent neurotransmitter transporter Homo sapiens orphan neurotransmitter transporter NTT7"""	607971	"""solute carrier family 6 (neurotransmitter transporter), member 15"""			10471414, 11112352, 16185194	Standard	NM_182767		Approved	hv7-3, NTT73, FLJ10316, V7-3, SBAT1	uc001szv.4	Q9H2J7	OTTHUMG00000169742	ENST00000266682.5:c.848G>A	12.37:g.85270295C>T	ENSP00000266682:p.Arg283His	Somatic		Capture	Illumina HiSeq	Phase_I	83794426	NM_182767	A8K592|B7Z2P7|E7ESJ5|Q9H9F5	Missense_Mutation	SNP	ENST00000266682.5	37	CCDS9026.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	12.88	2.071239	0.36566	2.27E-4	0.0	ENSG00000072041	ENST00000266682;ENST00000552192	T;T	0.74842	-0.88;-0.88	5.97	4.16	0.48862	.	0.148736	0.64402	N	0.000013	T	0.62171	0.2406	L	0.60845	1.875	0.80722	D	1	B	0.18863	0.031	B	0.15484	0.013	T	0.61312	-0.7088	10	0.33940	T	0.23	.	12.6403	0.56707	0.0:0.8668:0.0:0.1332	.	283	Q9H2J7	S6A15_HUMAN	H	283;176	ENSP00000266682:R283H;ENSP00000450145:R176H	ENSP00000266682:R283H	R	-	2	0	SLC6A15	83794426	0.993000	0.37304	0.996000	0.52242	0.452000	0.32318	1.750000	0.38329	0.864000	0.35578	0.655000	0.94253	CGC		0.308	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	NM_018057, NM_182767	
PLXNC1	10154	broad.mit.edu	37	12	94673303	94673303	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:94673303G>A	ENST00000258526.4	+	22	3902	c.3653G>A	c.(3652-3654)cGg>cAg	p.R1218Q	RP11-1105G2.3_ENST00000547927.1_5'Flank|RP11-1105G2.4_ENST00000550111.1_RNA|PLXNC1_ENST00000545312.1_5'UTR|RP11-1105G2.3_ENST00000551941.1_Intron|PLXNC1_ENST00000547057.1_Missense_Mutation_p.R265Q	NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	1218					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)	p.R1218Q(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(12)|lung(30)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						GATGTCTGTCGGAATATTTCA	0.398																																					p.R1218Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3653A	12						.						105.0	101.0	102.0					12																	94673303		2203	4300	6503	93197434	SO:0001583	missense	10154	exon22			AF030339	CCDS9049.1	12q23	2009-04-17				ENSG00000136040		"""CD molecules"", ""Plexins"""	9106	protein-coding gene	gene with protein product		604259					Standard	NR_037687		Approved	VESPR, CD232	uc001tdc.3	O60486	OTTHUMG00000170235	ENST00000258526.4:c.3653G>A	12.37:g.94673303G>A	ENSP00000258526:p.Arg1218Gln	Somatic		Capture	Illumina HiSeq	Phase_I	93197434	NM_005761	Q59H25	Missense_Mutation	SNP	ENST00000258526.4	37	CCDS9049.1	.	.	.	.	.	.	.	.	.	.	G	8.052	0.766147	0.15983	.	.	ENSG00000136040	ENST00000258526;ENST00000547057	T;T	0.12774	3.38;2.65	5.28	5.28	0.74379	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	1.946260	0.02572	N	0.097915	T	0.03053	0.0090	N	0.00399	-1.545	0.80722	D	1	B;P	0.46220	0.024;0.874	B;B	0.31495	0.001;0.131	T	0.52881	-0.8516	10	0.06891	T	0.86	.	7.7051	0.28646	0.1342:0.0:0.8658:0.0	.	265;1218	B4DHQ7;O60486	.;PLXC1_HUMAN	Q	1218;265	ENSP00000258526:R1218Q;ENSP00000446720:R265Q	ENSP00000258526:R1218Q	R	+	2	0	PLXNC1	93197434	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.429000	0.44758	2.750000	0.94351	0.655000	0.94253	CGG		0.398	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2		
ANO4	121601	broad.mit.edu	37	12	101473037	101473037	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:101473037A>G	ENST00000392977.3	+	15	1589	c.1379A>G	c.(1378-1380)gAc>gGc	p.D460G	ANO4_ENST00000392979.3_Missense_Mutation_p.D425G|ANO4_ENST00000299222.9_Missense_Mutation_p.D27G|ANO4_ENST00000550015.1_Missense_Mutation_p.D27G			Q32M45	ANO4_HUMAN	anoctamin 4	460					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.D425G(1)		NS(1)|biliary_tract(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(4)|prostate(5)|skin(7)|stomach(2)|urinary_tract(1)	78						GATTTGATAGACTGGGAAGAA	0.428										HNSCC(74;0.22)																											p.D425G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1274G	12						.						143.0	139.0	141.0					12																	101473037		2203	4300	6503	99997168	SO:0001583	missense	121601	exon14			AK091540	CCDS31884.1, CCDS66445.1	12q23.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000151572	ENSG00000151572		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	23837	protein-coding gene	gene with protein product		610111	"""transmembrane protein 16D"""	TMEM16D		12739008, 15067359, 24692353	Standard	NM_178826		Approved	FLJ34221, FLJ34272, FLJ35277	uc001thw.2	Q32M45		ENST00000392977.3:c.1379A>G	12.37:g.101473037A>G	ENSP00000376703:p.Asp460Gly	Somatic		Capture	Illumina HiSeq	Phase_I	99997168	NM_178826	Q8NAJ0|Q8NB39|Q8NB53	Missense_Mutation	SNP	ENST00000392977.3	37		.	.	.	.	.	.	.	.	.	.	A	15.66	2.899550	0.52227	.	.	ENSG00000151572	ENST00000392979;ENST00000299222;ENST00000392977;ENST00000550015	T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	T	0.50718	0.1632	N	0.17872	0.535	0.80722	D	1	P;P;P	0.43477	0.808;0.65;0.454	P;B;B	0.44990	0.466;0.393;0.221	T	0.45308	-0.9270	10	0.13470	T	0.59	.	15.261	0.73621	1.0:0.0:0.0:0.0	.	27;460;425	Q32M45-3;Q32M45;Q32M45-2	.;ANO4_HUMAN;.	G	425;27;460;27	ENSP00000376705:D425G;ENSP00000299222:D27G;ENSP00000376703:D460G;ENSP00000450192:D27G	ENSP00000299222:D27G	D	+	2	0	ANO4	99997168	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.618000	0.90932	2.064000	0.61679	0.533000	0.62120	GAC		0.428	ANO4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409295.1	NM_178826	
SETD1B	23067	broad.mit.edu	37	12	122242658	122242658	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:122242658delC	ENST00000604567.1	+	2	83	c.15delC	c.(13-15)cacfs	p.H5fs	SETD1B_ENST00000542440.1_Frame_Shift_Del_p.H5fs|SETD1B_ENST00000267197.5_Frame_Shift_Del_p.H5fs|RP11-347I19.8_ENST00000609067.1_lincRNA|RHOF_ENST00000545544.1_5'Flank			Q9UPS6	SET1B_HUMAN	SET domain containing 1B	5					histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone-lysine N-methyltransferase activity (GO:0018024)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.H8fs*27(2)		NS(1)|endometrium(6)|kidney(2)|prostate(2)	11						AGAACAGTCACCCCCCCCACC	0.632																																					p.H5fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.15delC	12						.						37.0	44.0	42.0					12																	122242658		692	1591	2283	120727041	SO:0001589	frameshift_variant	23067	exon1			AB028999	CCDS53838.1	12q24.31	2013-02-12			ENSG00000139718	ENSG00000139718		"""Chromatin-modifying enzymes / K-methyltransferases"", ""RNA binding motif (RRM) containing"""	29187	protein-coding gene	gene with protein product		611055				10470851, 17355966	Standard	NM_015048		Approved	KIAA1076, Set1B, KMT2G	uc001ubi.3	Q9UPS6	OTTHUMG00000169080	ENST00000604567.1:c.15delC	12.37:g.122242658delC	ENSP00000474253:p.His5fs	Somatic		Capture	Illumina HiSeq	Phase_I	120727041	NM_015048	F6MFW1	Frame_Shift_Del	DEL	ENST00000604567.1	37																																																																																					0.632	SETD1B-002	PUTATIVE	non_canonical_U12|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000468264.1	XM_037523	
TMEM132D	121256	broad.mit.edu	37	12	129694171	129694171	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr12:129694171T>C	ENST00000422113.2	-	5	1663	c.1337A>G	c.(1336-1338)aAg>aGg	p.K446R	RP11-669N7.3_ENST00000542578.1_lincRNA	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	446					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)		p.K446R(1)		NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		GGCCACCGTCTTCCCCGTGAG	0.587																																					p.K446R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1337G	12						.						98.0	78.0	84.0					12																	129694171		2203	4300	6503	128260124	SO:0001583	missense	121256	exon5			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.1337A>G	12.37:g.129694171T>C	ENSP00000408581:p.Lys446Arg	Somatic		Capture	Illumina HiSeq	Phase_I	128260124	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	37	CCDS9266.1	.	.	.	.	.	.	.	.	.	.	T	17.44	3.390755	0.62066	.	.	ENSG00000151952	ENST00000422113	T	0.18960	2.18	5.3	5.3	0.74995	.	0.000000	0.64402	D	0.000001	T	0.19046	0.0457	L	0.47190	1.495	0.36062	D	0.841555	P	0.40619	0.724	B	0.34452	0.183	T	0.19811	-1.0294	9	.	.	.	-41.5871	15.2632	0.73640	0.0:0.0:0.0:1.0	.	446	Q14C87	T132D_HUMAN	R	446	ENSP00000408581:K446R	.	K	-	2	0	TMEM132D	128260124	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	2.291000	0.43540	1.981000	0.57761	0.533000	0.62120	AAG		0.587	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448	
FGF14	2259	broad.mit.edu	37	13	102375233	102375233	+	Missense_Mutation	SNP	G	G	A	rs199536239		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr13:102375233G>A	ENST00000376143.4	-	5	691	c.692C>T	c.(691-693)gCg>gTg	p.A231V	FGF14_ENST00000376131.4_Missense_Mutation_p.A236V|ITGBL1_ENST00000415285.1_3'UTR	NM_004115.3	NP_004106.1	Q92915	FGF14_HUMAN	fibroblast growth factor 14	231					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cell-cell signaling (GO:0007267)|JNK cascade (GO:0007254)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|positive regulation of sodium ion transport (GO:0010765)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)	p.A236V(2)|p.A231V(2)|p.A236E(1)|p.A231E(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)	29	all_neural(89;0.0239)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					TATTGCAGACGCACTTGTGCT	0.483																																					p.A236V												.	.	6	Substitution - Missense(6)	large_intestine(4)|lung(2)	c.C707T	13						.	G	VAL/ALA,VAL/ALA	0,4406		0,0,2203	293.0	213.0	240.0		692,707	5.1	1.0	13		240	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	FGF14	NM_004115.3,NM_175929.2	64,64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	231/248,236/253	102375233	1,13005	2203	4300	6503	101173234	SO:0001583	missense	2259	exon5				CCDS9500.1, CCDS9501.1	13q34	2008-02-05			ENSG00000102466	ENSG00000102466			3671	protein-coding gene	gene with protein product		601515				8790420, 17236779	Standard	NM_175929		Approved	FHF4, SCA27	uc001vpf.2	Q92915	OTTHUMG00000017303	ENST00000376143.4:c.692C>T	13.37:g.102375233G>A	ENSP00000365313:p.Ala231Val	Somatic		Capture	Illumina HiSeq	Phase_I	101173234	NM_175929	Q86YN7|Q96QX6	Missense_Mutation	SNP	ENST00000376143.4	37	CCDS9501.1	.	.	.	.	.	.	.	.	.	.	G	12.05	1.821101	0.32237	0.0	1.16E-4	ENSG00000102466	ENST00000376131;ENST00000376143	T;T	0.77750	-1.12;-1.06	5.92	5.08	0.68730	.	0.462575	0.24879	N	0.034872	T	0.61527	0.2354	N	0.08118	0	0.50039	D	0.999848	B;B	0.20459	0.045;0.006	B;B	0.22386	0.039;0.006	T	0.56450	-0.7977	10	0.28530	T	0.3	.	15.3981	0.74812	0.0669:0.0:0.9331:0.0	.	236;231	Q92915-2;Q92915	.;FGF14_HUMAN	V	236;231	ENSP00000365301:A236V;ENSP00000365313:A231V	ENSP00000365301:A236V	A	-	2	0	FGF14	101173234	1.000000	0.71417	0.991000	0.47740	0.993000	0.82548	4.839000	0.62810	1.515000	0.48885	0.563000	0.77884	GCG		0.483	FGF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045679.2		
ZMYM2	7750	broad.mit.edu	37	13	20641083	20641083	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr13:20641083C>T	ENST00000382874.2	+	21	3415	c.3225C>T	c.(3223-3225)ggC>ggT	p.G1075G	ZMYM2_ENST00000494061.2_3'UTR|ZMYM2_ENST00000382869.3_Silent_p.G1075G|ZMYM2_ENST00000382871.2_Silent_p.G1075G	NM_001190964.1	NP_001177893.1	Q9UBW7	ZMYM2_HUMAN	zinc finger, MYM-type 2	1075					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.G1075G(1)|p.G1073G(1)		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)		ATACGTATGGCGTAAATGCAT	0.368																																					p.G1075G												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C3225T	13						.						127.0	118.0	121.0					13																	20641083		1863	4096	5959	19539083	SO:0001819	synonymous_variant	7750	exon20			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.3225C>T	13.37:g.20641083C>T		Somatic		Capture	Illumina HiSeq	Phase_I	19539083	NM_197968	A6NDG0|A6NI02|O43212|O43434|O60898|Q5W0Q4|Q5W0T3|Q63HP0|Q8NE39|Q9H0V5|Q9H538|Q9UEU2	Silent	SNP	ENST00000382874.2	37	CCDS45016.1																																																																																				0.368	ZMYM2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044051.2	NM_003453	
MICU2	221154	broad.mit.edu	37	13	22095388	22095388	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr13:22095388A>C	ENST00000382374.4	-	6	658	c.593T>G	c.(592-594)tTt>tGt	p.F198C		NM_152726.2	NP_689939.1	Q8IYU8	MICU2_HUMAN	mitochondrial calcium uptake 2	198	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				mitochondrial calcium ion transport (GO:0006851)|negative regulation of mitochondrial calcium ion concentration (GO:0051562)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)	calcium channel complex (GO:0034704)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|uniplex complex (GO:1990246)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)	p.F198C(1)									ACTTACCTTAAAAAATTCCCT	0.299																																					p.F198C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T593G	13						.						75.0	71.0	72.0					13																	22095388		2203	4299	6502	20993388	SO:0001583	missense	221154	exon6			AK091907	CCDS9297.1	13q12.11	2013-03-13	2013-03-13	2013-03-13	ENSG00000165487	ENSG00000165487		"""EF-hand domain containing"""	31830	protein-coding gene	gene with protein product		610632	"""EF hand domain family A1"", ""EF-hand domain family, member A1"""	EFHA1		23409044	Standard	NM_152726		Approved		uc001uof.3	Q8IYU8	OTTHUMG00000067414	ENST00000382374.4:c.593T>G	13.37:g.22095388A>C	ENSP00000371811:p.Phe198Cys	Somatic		Capture	Illumina HiSeq	Phase_I	20993388	NM_152726	Q8N0T6|Q8NAX8	Missense_Mutation	SNP	ENST00000382374.4	37	CCDS9297.1	.	.	.	.	.	.	.	.	.	.	A	16.77	3.213837	0.58452	.	.	ENSG00000165487	ENST00000382374	T	0.80304	-1.36	5.49	2.94	0.34122	EF-hand-like domain (1);	0.284737	0.40385	N	0.001102	T	0.78978	0.4369	M	0.63428	1.95	0.37929	D	0.931932	D	0.58620	0.983	P	0.46479	0.518	T	0.79014	-0.1976	10	0.54805	T	0.06	-14.0788	10.0151	0.42010	0.7305:0.0:0.0:0.2695	.	198	Q8IYU8	EFHA1_HUMAN	C	198	ENSP00000371811:F198C	ENSP00000371811:F198C	F	-	2	0	EFHA1	20993388	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	3.464000	0.53057	0.326000	0.23384	-0.468000	0.05107	TTT		0.299	MICU2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144355.1	NM_152726	
LNX2	222484	broad.mit.edu	37	13	28143253	28143253	+	Missense_Mutation	SNP	G	G	A	rs199501730		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr13:28143253G>A	ENST00000316334.3	-	3	697	c.568C>T	c.(568-570)Cgg>Tgg	p.R190W		NM_153371.3	NP_699202.1	Q8N448	LNX2_HUMAN	ligand of numb-protein X 2	190					protein homooligomerization (GO:0051260)		zinc ion binding (GO:0008270)	p.R190W(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	31		Lung SC(185;0.0156)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.113)|all cancers(112;0.127)|Epithelial(112;0.248)		GTCAAGTGCCGCTCCACAGGC	0.547																																					p.R190W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C568T	13						.						235.0	226.0	229.0					13																	28143253		2203	4300	6503	27041253	SO:0001583	missense	222484	exon3			AL138699	CCDS9323.1	13q12.2	2013-01-09	2004-01-22	2004-01-23	ENSG00000139517	ENSG00000139517		"""RING-type (C3HC4) zinc fingers"""	20421	protein-coding gene	gene with protein product		609733	"""PDZ domain containing ring finger 1"""	PDZRN1			Standard	NM_153371		Approved	MGC46315	uc001url.4	Q8N448	OTTHUMG00000016634	ENST00000316334.3:c.568C>T	13.37:g.28143253G>A	ENSP00000325929:p.Arg190Trp	Somatic		Capture	Illumina HiSeq	Phase_I	27041253	NM_153371	Q5W0P0|Q6ZMH2|Q96SH4	Missense_Mutation	SNP	ENST00000316334.3	37	CCDS9323.1	.	.	.	.	.	.	.	.	.	.	G	18.73	3.685996	0.68157	.	.	ENSG00000139517	ENST00000316334	T	0.05855	3.38	5.74	3.91	0.45181	.	0.389734	0.26503	N	0.024005	T	0.12902	0.0313	M	0.67953	2.075	0.30387	N	0.781337	P	0.49961	0.93	P	0.48677	0.586	T	0.02736	-1.1117	10	0.87932	D	0	.	10.4726	0.44646	0.0:0.1272:0.5939:0.2789	.	190	Q8N448	LNX2_HUMAN	W	190	ENSP00000325929:R190W	ENSP00000325929:R190W	R	-	1	2	LNX2	27041253	0.876000	0.30132	0.004000	0.12327	0.133000	0.20885	2.300000	0.43620	0.792000	0.33850	0.563000	0.77884	CGG		0.547	LNX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044302.2		
PAN3	255967	broad.mit.edu	37	13	28834683	28834683	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr13:28834683C>T	ENST00000380958.3	+	8	1500	c.1348C>T	c.(1348-1350)Cga>Tga	p.R450*	PAN3_ENST00000399613.1_Nonsense_Mutation_p.R250*|PAN3_ENST00000282391.5_Nonsense_Mutation_p.R138*	NM_175854.7	NP_787050.6			PAN3 poly(A) specific ribonuclease subunit									p.R250*(1)		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)		TGATGAACTCCGACAGGTATG	0.398																																					p.R450X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1348T	13						.						122.0	108.0	113.0					13																	28834683		2203	4300	6503	27732683	SO:0001587	stop_gained	255967	exon8			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.1348C>T	13.37:g.28834683C>T	ENSP00000370345:p.Arg450*	Somatic		Capture	Illumina HiSeq	Phase_I	27732683	NM_175854		Nonsense_Mutation	SNP	ENST00000380958.3	37	CCDS9329.2	.	.	.	.	.	.	.	.	.	.	C	37	6.372475	0.97515	.	.	ENSG00000152520	ENST00000380958;ENST00000399613;ENST00000282391	.	.	.	5.71	4.81	0.61882	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.6159	12.0133	0.53299	0.3353:0.6647:0.0:0.0	.	.	.	.	X	450;250;138	.	ENSP00000282391:R138X	R	+	1	2	PAN3	27732683	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.923000	0.48868	2.686000	0.91538	0.585000	0.79938	CGA		0.398	PAN3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044318.4	NM_175854	
FLT1	2321	broad.mit.edu	37	13	29008056	29008056	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr13:29008056C>T	ENST00000282397.4	-	6	964	c.713G>A	c.(712-714)cGc>cAc	p.R238H	FLT1_ENST00000541932.1_Missense_Mutation_p.R238H|FLT1_ENST00000539099.1_Missense_Mutation_p.R238H	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	238	Ig-like C2-type 3.				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.R238H(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)	TTTGACTGGGCGTGGTGTGCT	0.383																																					p.R238H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G713A	13						.						142.0	144.0	143.0					13																	29008056		2203	4300	6503	27906056	SO:0001583	missense	2321	exon6			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.713G>A	13.37:g.29008056C>T	ENSP00000282397:p.Arg238His	Somatic		Capture	Illumina HiSeq	Phase_I	27906056	NM_002019	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Missense_Mutation	SNP	ENST00000282397.4	37	CCDS9330.1	.	.	.	.	.	.	.	.	.	.	C	7.232	0.599477	0.13939	.	.	ENSG00000102755	ENST00000282397;ENST00000541932;ENST00000539099	T;T;T	0.12465	2.68;2.68;2.68	5.56	1.22	0.21188	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Tyrosine-protein kinase, vascular endothelial growth factor receptor 1 (VEGFR1), N-terminal (1);Immunoglobulin-like fold (1);	0.629398	0.17418	N	0.174954	T	0.05135	0.0137	N	0.03154	-0.405	0.09310	N	1	P;P;P;P	0.51057	0.633;0.941;0.633;0.794	B;B;B;B	0.41988	0.229;0.372;0.177;0.271	T	0.33574	-0.9863	10	0.32370	T	0.25	.	5.9937	0.19480	0.0:0.4933:0.2692:0.2375	.	238;238;238;238	P17948-4;P17948-3;P17948-2;P17948	.;.;.;VGFR1_HUMAN	H	238	ENSP00000282397:R238H;ENSP00000437631:R238H;ENSP00000442630:R238H	ENSP00000282397:R238H	R	-	2	0	FLT1	27906056	0.000000	0.05858	0.047000	0.18901	0.254000	0.26022	0.026000	0.13599	0.291000	0.22468	-0.156000	0.13503	CGC		0.383	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1		
PDS5B	23047	broad.mit.edu	37	13	33344297	33344297	+	Silent	SNP	C	C	T	rs200532241		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr13:33344297C>T	ENST00000315596.10	+	32	3849	c.3663C>T	c.(3661-3663)ccC>ccT	p.P1221P		NM_015032.3	NP_055847.1	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)	1221					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.P1221P(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)		AAAAAACGCCCGTCACAGAAC	0.403																																					p.P1221P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3663T	13						.	C		2,3764		0,2,1881	65.0	67.0	66.0		3663	-4.2	0.0	13		66	2,8214		0,2,4106	no	coding-synonymous	PDS5B	NM_015032.3		0,4,5987	TT,TC,CC		0.0243,0.0531,0.0334		1221/1448	33344297	4,11978	1883	4108	5991	32242297	SO:0001819	synonymous_variant	23047	exon32			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.3663C>T	13.37:g.33344297C>T		Somatic		Capture	Illumina HiSeq	Phase_I	32242297	NM_015032	Q5R3S3|Q5W0K8|Q6NSC3|Q8IXT6|Q9H5N8|Q9Y2I5|Q9Y451	Silent	SNP	ENST00000315596.10	37	CCDS41878.1																																																																																				0.403	PDS5B-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044428.3	NM_015032	
NBEA	26960	broad.mit.edu	37	13	36241642	36241642	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr13:36241642C>T	ENST00000400445.3	+	56	9067	c.8533C>T	c.(8533-8535)Cga>Tga	p.R2845*	NBEA_ENST00000537702.1_Nonsense_Mutation_p.R638*|NBEA_ENST00000540320.1_Nonsense_Mutation_p.R2845*|NBEA_ENST00000379939.2_Nonsense_Mutation_p.R2842*|NBEA_ENST00000310336.4_Nonsense_Mutation_p.R2845*|NBEA_ENST00000379922.3_Nonsense_Mutation_p.R423*	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	2845					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)		p.R2845*(1)		NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		TGAACGAGGGCGATTCAGTAA	0.428																																					p.R2845X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C8533T	13						.						180.0	176.0	177.0					13																	36241642		1889	4123	6012	35139642	SO:0001587	stop_gained	26960	exon56			AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"""A-kinase anchor proteins"", ""WD repeat domain containing"""	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.8533C>T	13.37:g.36241642C>T	ENSP00000383295:p.Arg2845*	Somatic		Capture	Illumina HiSeq	Phase_I	35139642	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Nonsense_Mutation	SNP	ENST00000400445.3	37	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	C	42	9.430291	0.99169	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518;ENST00000402346;ENST00000537702;ENST00000379922	.	.	.	5.73	5.73	0.89815	.	0.139473	0.56097	D	0.000038	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.16896	T	0.51	.	13.3704	0.60709	0.2752:0.7248:0.0:0.0	.	.	.	.	X	2845;2845;2842;2845;1474;423;638;423	.	ENSP00000308534:R2845X	R	+	1	2	NBEA	35139642	0.987000	0.35691	0.995000	0.50966	0.989000	0.77384	2.755000	0.47540	2.700000	0.92200	0.655000	0.94253	CGA		0.428	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678	
DCLK1	9201	broad.mit.edu	37	13	36686117	36686117	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr13:36686117C>T	ENST00000360631.3	-	3	823	c.612G>A	c.(610-612)ctG>ctA	p.L204L	DCLK1_ENST00000255448.4_Silent_p.L204L|DCLK1_ENST00000379892.4_Silent_p.L204L			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	204	Doublecortin 2. {ECO:0000255|PROSITE- ProRule:PRU00072}.				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.L204L(3)		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)		TCTTGTTCAGCAGAATCCTGA	0.527																																					p.L204L												.	.	3	Substitution - coding silent(3)	large_intestine(2)|ovary(1)	c.G612A	13						.						185.0	159.0	168.0					13																	36686117		2203	4300	6503	35584117	SO:0001819	synonymous_variant	9201	exon3			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.612G>A	13.37:g.36686117C>T		Somatic		Capture	Illumina HiSeq	Phase_I	35584117	NM_004734	B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Silent	SNP	ENST00000360631.3	37																																																																																					0.527	DCLK1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000044487.1	NM_004734	
COG6	57511	broad.mit.edu	37	13	40298682	40298682	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr13:40298682C>T	ENST00000455146.3	+	17	1780	c.1730C>T	c.(1729-1731)aCa>aTa	p.T577I	COG6_ENST00000416691.1_Missense_Mutation_p.T577I	NM_020751.2	NP_065802.1	Q9Y2V7	COG6_HUMAN	component of oligomeric golgi complex 6	577					glycosylation (GO:0070085)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)		p.T577I(1)		NS(1)|kidney(2)|large_intestine(5)|lung(4)|skin(1)	13		Lung NSC(96;0.000124)|Breast(139;0.0199)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.03e-09)|Epithelial(112;7e-07)|OV - Ovarian serous cystadenocarcinoma(117;0.00015)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.0168)		GATTCTGTGACACTGAAGGCT	0.299																																					p.T577I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1730T	13						.						91.0	96.0	94.0					13																	40298682		2203	4299	6502	39196682	SO:0001583	missense	57511	exon17			AK026638	CCDS9370.1, CCDS45042.1	13q13.2	2011-08-01			ENSG00000133103	ENSG00000133103		"""Components of oligomeric golgi complex"""	18621	protein-coding gene	gene with protein product		606977				11980916	Standard	NM_020751		Approved	COD2, KIAA1134	uc001uxh.2	Q9Y2V7	OTTHUMG00000016768	ENST00000455146.3:c.1730C>T	13.37:g.40298682C>T	ENSP00000397441:p.Thr577Ile	Somatic		Capture	Illumina HiSeq	Phase_I	39196682	NM_001145079	Q5T0U1|Q6AI19|Q86V49|Q9ULT5	Missense_Mutation	SNP	ENST00000455146.3	37	CCDS9370.1	.	.	.	.	.	.	.	.	.	.	C	14.37	2.514014	0.44763	.	.	ENSG00000133103	ENST00000416691;ENST00000255468;ENST00000455146	T;T	0.56103	0.48;0.48	5.47	5.47	0.80525	.	0.205916	0.52532	D	0.000064	T	0.46927	0.1418	L	0.34521	1.04	0.34185	D	0.671437	B;B	0.27316	0.175;0.033	B;B	0.28465	0.09;0.023	T	0.56860	-0.7909	10	0.51188	T	0.08	-19.0406	18.6794	0.91541	0.0:1.0:0.0:0.0	.	598;577	Q5T0U2;Q9Y2V7	.;COG6_HUMAN	I	577;608;577	ENSP00000403733:T577I;ENSP00000397441:T577I	ENSP00000255468:T608I	T	+	2	0	COG6	39196682	1.000000	0.71417	0.997000	0.53966	0.813000	0.45954	5.145000	0.64839	2.717000	0.92951	0.650000	0.86243	ACA		0.299	COG6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044622.3		
NEK5	341676	broad.mit.edu	37	13	52639603	52639603	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr13:52639603G>A	ENST00000355568.4	-	22	2206	c.2067C>T	c.(2065-2067)agC>agT	p.S689S		NM_199289.1	NP_954983.1	Q6P3R8	NEK5_HUMAN	NIMA-related kinase 5	689					positive regulation of cysteine-type endopeptidase activity (GO:2001056)|positive regulation of striated muscle cell differentiation (GO:0051155)		ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.S689S(1)		breast(5)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(11)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	39		Breast(56;0.00173)|Lung NSC(96;0.0168)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;3.7e-08)		GACGACTGACGCTAAGCACAG	0.552																																					p.S689S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2067T	13						.						188.0	150.0	163.0					13																	52639603		2203	4300	6503	51537604	SO:0001819	synonymous_variant	341676	exon22			BC063885	CCDS31979.1	13q14.2	2012-11-15	2012-11-15		ENSG00000197168	ENSG00000197168			7748	protein-coding gene	gene with protein product			"""NIMA (never in mitosis gene a)-related kinase 5"""			9552363	Standard	XM_006719807		Approved		uc001vge.3	Q6P3R8	OTTHUMG00000016957	ENST00000355568.4:c.2067C>T	13.37:g.52639603G>A		Somatic		Capture	Illumina HiSeq	Phase_I	51537604	NM_199289	Q5TAP5	Silent	SNP	ENST00000355568.4	37	CCDS31979.1																																																																																				0.552	NEK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045045.3	NM_199289	
KLF12	11278	broad.mit.edu	37	13	74269761	74269761	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr13:74269761C>T	ENST00000377669.2	-	7	1101	c.1075G>A	c.(1075-1077)Gct>Act	p.A359T	KLF12_ENST00000377666.4_Missense_Mutation_p.A359T	NM_007249.4	NP_009180.3	Q9Y4X4	KLF12_HUMAN	Kruppel-like factor 12	359					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.A359T(1)		central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	16		Prostate(6;0.00217)|Breast(118;0.0838)		GBM - Glioblastoma multiforme(99;0.00677)		TCTGAACGAGCGAACTTCCAG	0.498																																					p.A359T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1075A	13						.						132.0	107.0	116.0					13																	74269761		2203	4300	6503	73167762	SO:0001583	missense	11278	exon8			AJ243274	CCDS9449.1	13q22	2013-01-08			ENSG00000118922	ENSG00000118922		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	6346	protein-coding gene	gene with protein product	"""KLF12 zinc finger transcriptional repressor"", ""AP-2rep transcription factor"", ""AP-2 repressor"""	607531				10704285	Standard	NM_007249		Approved	AP-2rep, HSPC122, AP2REP	uc001vjf.3	Q9Y4X4	OTTHUMG00000017078	ENST00000377669.2:c.1075G>A	13.37:g.74269761C>T	ENSP00000366897:p.Ala359Thr	Somatic		Capture	Illumina HiSeq	Phase_I	73167762	NM_007249	A8K5T2|L0R3J4|Q5VZM7|Q9UHZ0	Missense_Mutation	SNP	ENST00000377669.2	37	CCDS9449.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.686172	0.88639	.	.	ENSG00000118922	ENST00000377669;ENST00000342812;ENST00000377666	T;T	0.36157	1.27;1.27	6.03	6.03	0.97812	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	0.21022	0.0506	N	0.04880	-0.145	0.80722	D	1	P	0.46656	0.882	B	0.36289	0.221	T	0.06110	-1.0845	10	0.35671	T	0.21	.	20.5568	0.99304	0.0:1.0:0.0:0.0	.	359	Q9Y4X4	KLF12_HUMAN	T	359	ENSP00000366897:A359T;ENSP00000366894:A359T	ENSP00000344057:A359T	A	-	1	0	KLF12	73167762	1.000000	0.71417	0.997000	0.53966	0.983000	0.72400	7.818000	0.86416	2.861000	0.98227	0.655000	0.94253	GCT		0.498	KLF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045271.2	NM_007249	
SLITRK6	84189	broad.mit.edu	37	13	86368390	86368390	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr13:86368390C>T	ENST00000400286.2	-	2	2852	c.2254G>A	c.(2254-2256)Gcc>Acc	p.A752T		NM_032229.2	NP_115605.2	Q9H5Y7	SLIK6_HUMAN	SLIT and NTRK-like family, member 6	752					adult locomotory behavior (GO:0008344)|auditory behavior (GO:0031223)|auditory receptor cell morphogenesis (GO:0002093)|axonogenesis (GO:0007409)|cochlea development (GO:0090102)|innervation (GO:0060384)|lens development in camera-type eye (GO:0002088)|linear vestibuloocular reflex (GO:0060007)|multicellular organism growth (GO:0035264)|sensory perception of sound (GO:0007605)|startle response (GO:0001964)|synapse assembly (GO:0007416)|vestibulocochlear nerve development (GO:0021562)|visual perception (GO:0007601)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)		p.A752T(1)		breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(18)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_neural(89;0.117)|Medulloblastoma(90;0.163)			GBM - Glioblastoma multiforme(99;0.0456)		AATGAGCTGGCATCTTGGAAG	0.383																																					p.A752T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2254A	13						.						226.0	215.0	219.0					13																	86368390		1850	4096	5946	85266391	SO:0001583	missense	84189	exon2			AK026427	CCDS41903.1	13q31.1	2006-04-12			ENSG00000184564	ENSG00000184564			23503	protein-coding gene	gene with protein product		609681				14557068	Standard	NM_032229		Approved	FLJ22774	uc001vll.1	Q9H5Y7	OTTHUMG00000017157	ENST00000400286.2:c.2254G>A	13.37:g.86368390C>T	ENSP00000383143:p.Ala752Thr	Somatic		Capture	Illumina HiSeq	Phase_I	85266391	NM_032229	A8K9S8|Q495Q0|Q6AW93|Q9HAA8|Q9NT60	Missense_Mutation	SNP	ENST00000400286.2	37	CCDS41903.1	.	.	.	.	.	.	.	.	.	.	C	3.639	-0.073919	0.07184	.	.	ENSG00000184564	ENST00000400286	T	0.57752	0.38	5.84	5.84	0.93424	.	0.266969	0.30820	U	0.008801	T	0.32585	0.0834	N	0.12182	0.205	0.48696	D	0.999694	P	0.34864	0.473	B	0.32393	0.145	T	0.28073	-1.0055	10	0.02654	T	1	-7.6492	18.719	0.91686	0.0:1.0:0.0:0.0	.	752	Q9H5Y7	SLIK6_HUMAN	T	752	ENSP00000383143:A752T	ENSP00000383143:A752T	A	-	1	0	SLITRK6	85266391	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	3.060000	0.49955	2.760000	0.94817	0.655000	0.94253	GCC		0.383	SLITRK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045404.2	NM_032229	
IPO5	3843	broad.mit.edu	37	13	98673377	98673377	+	Missense_Mutation	SNP	G	G	A	rs370003102		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr13:98673377G>A	ENST00000490680.1	+	25	3262	c.3197G>A	c.(3196-3198)cGc>cAc	p.R1066H	IPO5_ENST00000539640.1_Missense_Mutation_p.R941H|IPO5_ENST00000261574.5_Missense_Mutation_p.R1084H			O00410	IPO5_HUMAN	importin 5	1066					cellular response to amino acid stimulus (GO:0071230)|negative regulation of catalytic activity (GO:0043086)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein import into nucleus (GO:0042307)|ribosomal protein import into nucleus (GO:0006610)|viral process (GO:0016032)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	GTPase inhibitor activity (GO:0005095)|poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|Ran GTPase binding (GO:0008536)	p.R1084H(1)		breast(2)|endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	27						AATGTCGTTCGCCAAGTACAG	0.408																																					p.R1084H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3251A	13						.	G	HIS/ARG	0,4406		0,0,2203	119.0	122.0	121.0		3251	5.6	1.0	13		121	1,8599	1.2+/-3.3	0,1,4299	no	missense	IPO5	NM_002271.4	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	1084/1116	98673377	1,13005	2203	4300	6503	97471378	SO:0001583	missense	3843	exon28			U72761	CCDS31999.1	13q32.2	2012-05-02	2008-04-15	2008-04-15	ENSG00000065150	ENSG00000065150		"""Importins"""	6402	protein-coding gene	gene with protein product		602008	"""karyopherin (importin) beta 3"", ""RAN binding protein 5"""	KPNB3, RANBP5		9114010, 9271386, 17005651	Standard	NM_002271		Approved	IMB3, MGC2068, Pse1	uc001vne.3	O00410	OTTHUMG00000017244	ENST00000490680.1:c.3197G>A	13.37:g.98673377G>A	ENSP00000418393:p.Arg1066His	Somatic		Capture	Illumina HiSeq	Phase_I	97471378	NM_002271	B4DZA0|O15257|Q5T578|Q86XC7	Missense_Mutation	SNP	ENST00000490680.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	35|35	5.529863|5.529863	0.96446|0.96446	0.0|0.0	1.16E-4|1.16E-4	ENSG00000065150|ENSG00000065150	ENST00000469360|ENST00000261574;ENST00000357602;ENST00000490680;ENST00000539640	.|T;T;T;T	.|0.11063	.|2.81;2.82;2.82;2.81	5.6|5.6	5.6|5.6	0.85130|0.85130	.|.	.|0.047841	.|0.85682	.|D	.|0.000000	T|T	0.39279|0.39279	0.1072|0.1072	M|M	0.83953|0.83953	2.67|2.67	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.74348	.|0.983	T|T	0.26643|0.26643	-1.0097|-1.0097	5|10	.|0.72032	.|D	.|0.01	-21.8652|-21.8652	19.6223|19.6223	0.95663|0.95663	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1084	.|O00410-3	.|.	T|H	1068|1084;1066;1066;941	.|ENSP00000261574:R1084H;ENSP00000350219:R1066H;ENSP00000418393:R1066H;ENSP00000445126:R941H	.|ENSP00000261574:R1084H	A|R	+|+	1|2	0|0	IPO5|IPO5	97471378|97471378	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	9.817000|9.817000	0.99352|0.99352	2.616000|2.616000	0.88540|0.88540	0.655000|0.655000	0.94253|0.94253	GCC|CGC		0.408	IPO5-006	NOVEL	alternative_5_UTR|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000354655.1	NM_002271	
ING1	3621	broad.mit.edu	37	13	111372142	111372142	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr13:111372142T>C	ENST00000375774.3	+	2	1594	c.1132T>C	c.(1132-1134)Tgg>Cgg	p.W378R	ING1_ENST00000338450.7_Missense_Mutation_p.W191R|ING1_ENST00000333219.7_Missense_Mutation_p.W235R|ING1_ENST00000375775.3_Missense_Mutation_p.W166R	NM_005537.4	NP_005528.3	Q9UK53	ING1_HUMAN	inhibitor of growth family, member 1	378					cell cycle (GO:0007049)|chromatin modification (GO:0016568)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell death (GO:0010941)	nucleus (GO:0005634)	methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.W235R(1)		endometrium(4)|large_intestine(6)|lung(1)|ovary(1)	12	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.188)			CCCCATCGAGTGGTTCCACTT	0.587																																					p.W235R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T703C	13						.						81.0	71.0	74.0					13																	111372142		2203	4300	6503	110170143	SO:0001583	missense	3621	exon2				CCDS9515.1, CCDS9516.1, CCDS9517.1, CCDS9518.1	13q34	2013-01-28			ENSG00000153487	ENSG00000153487		"""Zinc fingers, PHD-type"""	6062	protein-coding gene	gene with protein product	"""inhibitor of growth 1"", ""tumor suppressor ING1"", ""growth inhibitor ING1"", ""growth inhibitory protein ING1"""	601566				8944021, 9186514	Standard	NM_198219		Approved	p33ING1, p33ING1b, p24ING1c, p33, p47, p47ING1a	uc001vri.3	Q9UK53	OTTHUMG00000017346	ENST00000375774.3:c.1132T>C	13.37:g.111372142T>C	ENSP00000364929:p.Trp378Arg	Somatic		Capture	Illumina HiSeq	Phase_I	110170143	NM_198219	O00532|O43658|Q53ZR3|Q5T9G8|Q5T9G9|Q5T9H0|Q5T9H1|Q9H007|Q9HD98|Q9HD99|Q9NS83|Q9P0U6|Q9UBC6|Q9UIJ1|Q9UIJ2|Q9UIJ3|Q9UIJ4|Q9UK52	Missense_Mutation	SNP	ENST00000375774.3	37	CCDS9517.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.243556	0.79912	.	.	ENSG00000153487	ENST00000338450;ENST00000333219;ENST00000375775;ENST00000375774	T;T;T;T	0.58940	0.3;0.3;0.3;0.3	5.5	5.5	0.81552	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	0.87120	0.6098	H	0.99609	4.655	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.97110	1.0;0.999;0.994	D	0.92873	0.6316	10	0.72032	D	0.01	-40.1282	15.5913	0.76530	0.0:0.0:0.0:1.0	.	378;235;191	Q9UK53;Q5T9H0;Q9UK53-4	ING1_HUMAN;.;.	R	191;235;166;378	ENSP00000345202:W191R;ENSP00000328436:W235R;ENSP00000364930:W166R;ENSP00000364929:W378R	ENSP00000328436:W235R	W	+	1	0	ING1	110170143	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.529000	0.81952	2.089000	0.63090	0.402000	0.26972	TGG		0.587	ING1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045770.2	NM_005537	
RPGRIP1	57096	broad.mit.edu	37	14	21794267	21794267	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr14:21794267C>A	ENST00000400017.2	+	16	2645	c.2645C>A	c.(2644-2646)cCt>cAt	p.P882H	RPGRIP1_ENST00000206660.6_Missense_Mutation_p.P882H|RPGRIP1_ENST00000382933.4_Intron|RPGRIP1_ENST00000556336.1_Intron|RPGRIP1_ENST00000557771.1_Missense_Mutation_p.P844H|RPGRIP1_ENST00000307974.4_Missense_Mutation_p.P241H	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	882	C2.				eye photoreceptor cell development (GO:0042462)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	axoneme (GO:0005930)|nonmotile primary cilium (GO:0031513)		p.P498H(1)		breast(3)|endometrium(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(4)|pancreas(1)|prostate(3)|stomach(1)	39	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		GACTTAGAGCCTGGCTCGTAT	0.493																																					p.P882H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2645A	14						.						91.0	86.0	88.0					14																	21794267		1904	4112	6016	20864107	SO:0001583	missense	57096	exon16			AF227257	CCDS45080.1	14q11.2	2013-06-06			ENSG00000092200	ENSG00000092200			13436	protein-coding gene	gene with protein product		605446		RPGRIP		10958647, 10958648	Standard	NM_020366		Approved	RGI1, LCA6, CORD13	uc001wag.3	Q96KN7	OTTHUMG00000170758	ENST00000400017.2:c.2645C>A	14.37:g.21794267C>A	ENSP00000382895:p.Pro882His	Somatic		Capture	Illumina HiSeq	Phase_I	20864107	NM_020366	Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Missense_Mutation	SNP	ENST00000400017.2	37	CCDS45080.1	.	.	.	.	.	.	.	.	.	.	C	16.16	3.045750	0.55110	.	.	ENSG00000092200	ENST00000557771;ENST00000400017;ENST00000206660;ENST00000555587;ENST00000307974	D;D;D;D;T	0.87966	-2.32;-2.32;-2.32;-2.32;-0.34	4.87	3.9	0.45041	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.120324	0.56097	D	0.000029	D	0.90570	0.7044	M	0.62723	1.935	0.30666	N	0.753935	D;D;D;D;D	0.71674	0.998;0.997;0.997;0.998;0.997	P;D;P;P;P	0.63877	0.874;0.919;0.874;0.874;0.817	D	0.88085	0.2809	10	0.59425	D	0.04	-8.9138	12.2287	0.54476	0.0:0.9033:0.0:0.0967	.	265;241;357;498;882	Q96KN7-2;Q96KN7-3;G3V3I7;Q96KN7-5;Q96KN7	.;.;.;.;RPGR1_HUMAN	H	844;882;882;357;241	ENSP00000451219:P844H;ENSP00000382895:P882H;ENSP00000206660:P882H;ENSP00000451262:P357H;ENSP00000309721:P241H	ENSP00000206660:P882H	P	+	2	0	RPGRIP1	20864107	0.241000	0.23857	1.000000	0.80357	0.896000	0.52359	0.827000	0.27421	2.534000	0.85438	0.655000	0.94253	CCT		0.493	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410258.1	NM_020366	
SLC22A17	51310	broad.mit.edu	37	14	23821250	23821250	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr14:23821250C>T	ENST00000206544.8	-	1	510	c.174G>A	c.(172-174)tcG>tcA	p.S58S	SLC22A17_ENST00000354772.3_Silent_p.S58S|SLC22A17_ENST00000474057.1_5'UTR|SLC22A17_ENST00000397260.3_De_novo_Start_OutOfFrame|SLC22A17_ENST00000397267.1_Silent_p.S58S	NM_020372.2	NP_065105.2	Q8WUG5	S22AH_HUMAN	solute carrier family 22, member 17	58					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.S58S(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)		AGCCGCTGCACGAGGGGTCGG	0.672																																					p.S58S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G174A	14						.						26.0	22.0	24.0					14																	23821250		2200	4299	6499	22891090	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.174G>A	14.37:g.23821250C>T		Somatic		Capture	Illumina HiSeq	Phase_I	22891090	NM_020372	A4UA13|A8MUT0|Q2TAB0|Q5BKY8|Q86U04|Q9H1D3|Q9NQD5	De_novo_Start_OutOfFrame	SNP	ENST00000206544.8	37	CCDS9593.1																																																																																				0.672	SLC22A17-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157223.3	NM_020372	
NFATC4	4776	broad.mit.edu	37	14	24842912	24842912	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr14:24842912C>T	ENST00000250373.4	+	5	1712	c.1571C>T	c.(1570-1572)gCg>gTg	p.A524V	NFATC4_ENST00000553879.1_Missense_Mutation_p.A454V|NFATC4_ENST00000553708.1_Missense_Mutation_p.A524V|NFATC4_ENST00000555393.1_5'Flank|NFATC4_ENST00000556169.1_Missense_Mutation_p.A512V|NFATC4_ENST00000413692.2_Missense_Mutation_p.A587V|NFATC4_ENST00000554966.1_Missense_Mutation_p.A537V|NFATC4_ENST00000557767.1_5'Flank|NFATC4_ENST00000554591.1_Missense_Mutation_p.A587V|NFATC4_ENST00000555590.1_Missense_Mutation_p.A537V|NFATC4_ENST00000554473.1_Missense_Mutation_p.A59V|NFATC4_ENST00000556279.1_Missense_Mutation_p.A556V|NFATC4_ENST00000554050.1_Missense_Mutation_p.A524V|NFATC4_ENST00000556759.1_Missense_Mutation_p.A59V|NFATC4_ENST00000554661.1_Missense_Mutation_p.A454V|NFATC4_ENST00000555167.1_Missense_Mutation_p.A59V|NFATC4_ENST00000555453.1_Missense_Mutation_p.A512V|NFATC4_ENST00000424781.2_Missense_Mutation_p.A537V|NFATC4_ENST00000557451.1_Missense_Mutation_p.A454V|NFATC4_ENST00000555802.1_5'Flank|NFATC4_ENST00000553469.1_Missense_Mutation_p.A556V|NFATC4_ENST00000422617.3_Missense_Mutation_p.A512V|NFATC4_ENST00000539237.2_Missense_Mutation_p.A556V|NFATC4_ENST00000554344.1_Missense_Mutation_p.A454V	NM_004554.4	NP_004545.2	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4	524	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				cellular respiration (GO:0045333)|cellular response to lithium ion (GO:0071285)|cellular response to UV (GO:0034644)|heart development (GO:0007507)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of synaptic plasticity (GO:0048167)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	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 coactivator activity (GO:0003713)	p.A524V(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(7)|liver(4)|lung(12)|ovary(1)|skin(2)	34				GBM - Glioblastoma multiforme(265;0.018)		ATTGACTGCGCGGGAATCCTG	0.547																																					p.A587V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1760T	14						.						105.0	111.0	109.0					14																	24842912		2203	4300	6503	23912752	SO:0001583	missense	4776	exon6			BC053855	CCDS9629.1, CCDS45089.1, CCDS55909.1, CCDS55910.1, CCDS55911.1, CCDS73625.1	14q11.2	2009-11-24			ENSG00000100968	ENSG00000100968		"""Nuclear factor of activated T-cells"""	7778	protein-coding gene	gene with protein product		602699				7749981	Standard	NM_004554		Approved	NFAT3	uc010tok.2	Q14934	OTTHUMG00000029351	ENST00000250373.4:c.1571C>T	14.37:g.24842912C>T	ENSP00000250373:p.Ala524Val	Somatic		Capture	Illumina HiSeq	Phase_I	23912752	NM_001136022	B4DDG5|B4DY55|B5B2U7|B5B2U8|B5B2U9|B5B2V0|B5B2V1|B5B2V2|B5B2V3|B5B2V4|B5B2V5|B5B2V7|B5B2V8|B5B2V9|B5B2W0|B5B2W1|B5B2W2|B5B2W3|B5B2W4|B5B2W5|B5B2W6|B5B2W7|B5B2W8|B5B2W9|B5B2X0|Q7Z598|Q96H68	Missense_Mutation	SNP	ENST00000250373.4	37	CCDS9629.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.078900	0.76528	.	.	ENSG00000100968	ENST00000413692;ENST00000554591;ENST00000555590;ENST00000554966;ENST00000424781;ENST00000539237;ENST00000556279;ENST00000553469;ENST00000554050;ENST00000250373;ENST00000553708;ENST00000553879;ENST00000554344;ENST00000554661;ENST00000556169;ENST00000557451;ENST00000422617;ENST00000555453;ENST00000554473;ENST00000556759;ENST00000555167	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.37584	1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19;1.19	4.58	4.58	0.56647	Rel homology (3);p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.43366	0.1244	N	0.13003	0.285	0.80722	D	1	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	0.91635	0.994;0.994;0.964;0.996;0.964;0.948;0.994;0.998;0.998;0.996;0.948;0.948;0.999;0.974;0.969	T	0.50833	-0.8781	10	0.87932	D	0	-4.9326	15.2561	0.73585	0.0:1.0:0.0:0.0	.	512;512;556;556;537;537;537;587;587;512;454;556;501;587;524	Q14934-17;Q14934-9;Q14934-14;Q14934-4;Q14934-15;Q14934-6;Q14934-7;Q14934-2;Q14934-3;Q14934-10;Q14934-12;Q14934-5;B4DU09;Q14934-11;Q14934	.;.;.;.;.;.;.;.;.;.;.;.;.;.;NFAC4_HUMAN	V	587;587;537;537;537;556;556;556;524;524;524;454;454;454;512;454;512;512;59;59;59	ENSP00000388910:A587V;ENSP00000452039:A587V;ENSP00000451224:A537V;ENSP00000450644:A537V;ENSP00000388668:A537V;ENSP00000439350:A556V;ENSP00000452270:A556V;ENSP00000451502:A556V;ENSP00000451151:A524V;ENSP00000250373:A524V;ENSP00000450590:A524V;ENSP00000452349:A454V;ENSP00000450469:A454V;ENSP00000450733:A454V;ENSP00000451454:A512V;ENSP00000451284:A454V;ENSP00000396788:A512V;ENSP00000450686:A512V;ENSP00000450810:A59V;ENSP00000451183:A59V;ENSP00000451395:A59V	ENSP00000250373:A524V	A	+	2	0	NFATC4	23912752	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.580000	0.82523	2.515000	0.84797	0.655000	0.94253	GCG		0.547	NFATC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073206.6	NM_004554	
COCH	1690	broad.mit.edu	37	14	31354636	31354636	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr14:31354636C>T	ENST00000396618.3	+	10	826	c.770C>T	c.(769-771)aCg>aTg	p.T257M	COCH_ENST00000475087.1_Missense_Mutation_p.T257M|RP11-829H16.3_ENST00000556786.1_RNA|RP11-829H16.3_ENST00000468444.2_RNA|COCH_ENST00000460581.2_Missense_Mutation_p.T145M|RP11-829H16.3_ENST00000555421.1_RNA|RP11-829H16.3_ENST00000555108.1_RNA|COCH_ENST00000382493.4_Missense_Mutation_p.T108M|COCH_ENST00000216361.4_Missense_Mutation_p.T257M	NM_004086.2	NP_004077.1	O43405	COCH_HUMAN	cochlin	257	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				defense response to bacterium (GO:0042742)|positive regulation of innate immune response (GO:0045089)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)		p.T257M(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|pancreas(1)|skin(3)	19	Hepatocellular(127;0.0877)|Breast(36;0.148)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805)	GBM - Glioblastoma multiforme(265;0.00645)		AAATTCTTCACGGTAGATGCT	0.433																																					p.T257M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C770T	14						.						114.0	106.0	109.0					14																	31354636		2203	4300	6503	30424387	SO:0001583	missense	1690	exon10				CCDS9640.1	14q11.2-q13	2013-05-01	2013-05-01		ENSG00000100473	ENSG00000100473			2180	protein-coding gene	gene with protein product		603196	"""coagulation factor C (Limulus polyphemus homolog); cochlin"", ""coagulation factor C homolog, cochlin (Limulus polyphemus)"""	DFNA31, DFNA9		9806553	Standard	NM_004086		Approved	COCH-5B2	uc001wqp.2	O43405	OTTHUMG00000029432	ENST00000396618.3:c.770C>T	14.37:g.31354636C>T	ENSP00000379862:p.Thr257Met	Somatic		Capture	Illumina HiSeq	Phase_I	30424387	NM_004086	A8K9K9|D3DS84|Q96IU6	Missense_Mutation	SNP	ENST00000396618.3	37	CCDS9640.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.04|17.04	3.288257|3.288257	0.59976|0.59976	.|.	.|.	ENSG00000100473|ENSG00000100473	ENST00000468826|ENST00000216361;ENST00000396618;ENST00000475087;ENST00000555881;ENST00000460581;ENST00000542225;ENST00000382493	.|D;D;D;D;D;D	.|0.84070	.|-1.8;-1.8;-1.8;-1.8;-1.8;-1.8	5.6|5.6	5.6|5.6	0.85130|0.85130	.|von Willebrand factor, type A (3);	.|0.485962	.|0.23964	.|N	.|0.042834	D|D	0.88644|0.88644	0.6492|0.6492	L|L	0.55213|0.55213	1.73|1.73	0.36926|0.36926	D|D	0.891658|0.891658	.|D;D;D	.|0.65815	.|0.991;0.995;0.995	.|P;P;P	.|0.60236	.|0.871;0.807;0.807	D|D	0.90866|0.90866	0.4742|0.4742	5|10	.|0.87932	.|D	.|0	-11.7736|-11.7736	19.6182|19.6182	0.95643|0.95643	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|108;257;257	.|E7EN67;Q96IU6;O43405	.|.;.;COCH_HUMAN	W|M	141|257;257;257;139;145;145;108	.|ENSP00000216361:T257M;ENSP00000379862:T257M;ENSP00000451528:T257M;ENSP00000452569:T139M;ENSP00000451713:T145M;ENSP00000371933:T108M	.|ENSP00000216361:T257M	R|T	+|+	1|2	2|0	COCH|COCH	30424387|30424387	0.786000|0.786000	0.28738|0.28738	0.968000|0.968000	0.41197|0.41197	0.799000|0.799000	0.45148|0.45148	1.260000|1.260000	0.32968|0.32968	2.626000|2.626000	0.88956|0.88956	0.650000|0.650000	0.86243|0.86243	CGG|ACG		0.433	COCH-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276608.1	NM_004086	
HEATR5A	25938	broad.mit.edu	37	14	31828207	31828207	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr14:31828207G>A	ENST00000389961.3	-	14	2109	c.2110C>T	c.(2110-2112)Cag>Tag	p.Q704*	HEATR5A_ENST00000439348.1_Nonsense_Mutation_p.Q704*|HEATR5A_ENST00000439727.1_Nonsense_Mutation_p.Q417*|HEATR5A_ENST00000404677.3_Nonsense_Mutation_p.Q710*|HEATR5A_ENST00000543095.2_Nonsense_Mutation_p.Q710*			Q86XA9	HTR5A_HUMAN	HEAT repeat containing 5A	704								p.Q704*(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)	26	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)		GCTGCCACCTGAATATCAGGG	0.413																																					p.Q417X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1249T	14						.						70.0	68.0	69.0					14																	31828207		1902	4121	6023	30897958	SO:0001587	stop_gained	25938	exon9			AB037737		14q12	2012-04-19	2007-01-02	2007-01-02	ENSG00000129493	ENSG00000129493			20276	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 125"""	C14orf125			Standard	NM_015473		Approved	DKFZP434I1735	uc001wrf.4	Q86XA9	OTTHUMG00000169043	ENST00000389961.3:c.2110C>T	14.37:g.31828207G>A	ENSP00000374611:p.Gln704*	Somatic		Capture	Illumina HiSeq	Phase_I	30897958	NM_015473	Q68DD8|Q6P3S5|Q6P5R9|Q9H8D7|Q9NXB7|Q9P2N0|Q9UFQ3	Nonsense_Mutation	SNP	ENST00000389961.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	37|37	6.346192|6.346192	0.97494|0.97494	.|.	.|.	ENSG00000129493|ENSG00000129493	ENST00000389961;ENST00000439348;ENST00000439727;ENST00000543095;ENST00000404677|ENST00000550366	.|.	.|.	.|.	5.29|5.29	5.29|5.29	0.74685|0.74685	.|.	0.297228|.	0.32563|.	N|.	0.005932|.	.|T	.|0.76097	.|0.3940	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.74665	.|-0.3589	.|3	0.38643|.	T|.	0.18|.	.|.	19.3018|19.3018	0.94146|0.94146	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|L	704;704;417;710;710|352	.|.	ENSP00000374611:Q704X|.	Q|S	-|-	1|2	0|0	HEATR5A|HEATR5A	30897958|30897958	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	4.309000|4.309000	0.59135|0.59135	2.636000|2.636000	0.89361|0.89361	0.563000|0.563000	0.77884|0.77884	CAG|TCA		0.413	HEATR5A-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015473	
FAM179B	23116	broad.mit.edu	37	14	45431988	45431988	+	Missense_Mutation	SNP	C	C	T	rs140361174		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr14:45431988C>T	ENST00000361577.3	+	1	578	c.364C>T	c.(364-366)Cgg>Tgg	p.R122W	FAM179B_ENST00000361462.2_Missense_Mutation_p.R122W|FAM179B_ENST00000382233.2_Missense_Mutation_p.R122W|KLHL28_ENST00000553817.1_5'Flank|KLHL28_ENST00000355081.2_5'Flank|KLHL28_ENST00000396128.4_5'Flank	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	122								p.R122W(1)		endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						TGCTTTGCCGCGGCGGGGCGG	0.612																																					p.R122W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C364T	14						.	C	TRP/ARG	0,4390		0,0,2195	58.0	68.0	64.0		364	4.0	1.0	14	dbSNP_134	64	2,8574		0,2,4286	no	missense	FAM179B	NM_015091.2	101	0,2,6481	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	122/1721	45431988	2,12964	2195	4288	6483	44501738	SO:0001583	missense	23116	exon1			AB007883	CCDS9681.1	14q21.3	2008-07-21	2008-07-21	2008-07-21	ENSG00000198718	ENSG00000198718			19959	protein-coding gene	gene with protein product			"""KIAA0423"""	KIAA0423			Standard	XM_005267451		Approved		uc001wvv.3	Q9Y4F4	OTTHUMG00000140264	ENST00000361577.3:c.364C>T	14.37:g.45431988C>T	ENSP00000355045:p.Arg122Trp	Somatic		Capture	Illumina HiSeq	Phase_I	44501738	NM_015091	Q68D66|Q6PG27	Missense_Mutation	SNP	ENST00000361577.3	37	CCDS9681.1	.	.	.	.	.	.	.	.	.	.	C	16.87	3.241545	0.58995	0.0	2.33E-4	ENSG00000198718	ENST00000429476;ENST00000361577;ENST00000361462;ENST00000382233	T;T;T	0.58358	0.34;0.34;0.34	4.88	3.99	0.46301	Armadillo-like helical (1);	0.000000	0.42682	D	0.000672	T	0.56381	0.1981	N	0.24115	0.695	0.33120	D	0.54162	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.81914	0.995;0.995;0.995;0.995	T	0.67688	-0.5606	10	0.87932	D	0	-7.4667	10.523	0.44931	0.193:0.807:0.0:0.0	.	122;122;122;122	Q9Y4F4-3;G3XAE9;Q9Y4F4;Q9Y4F4-2	.;.;F179B_HUMAN;.	W	122	ENSP00000355045:R122W;ENSP00000354917:R122W;ENSP00000371668:R122W	ENSP00000354917:R122W	R	+	1	2	FAM179B	44501738	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.396000	0.34531	1.270000	0.44297	-0.152000	0.13540	CGG		0.612	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781	
FANCM	57697	broad.mit.edu	37	14	45605362	45605362	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr14:45605362C>T	ENST00000267430.5	+	1	213	c.128C>T	c.(127-129)cCa>cTa	p.P43L	FANCM_ENST00000556036.1_Missense_Mutation_p.P43L|FKBP3_ENST00000216330.3_5'Flank|FANCM_ENST00000542564.2_Missense_Mutation_p.P43L|FKBP3_ENST00000396062.3_5'Flank	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	43					DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)	p.P43L(1)		breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						GCGCCTTTGCCAGCAGCAGCG	0.622								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.P43L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C128T	14						.						53.0	53.0	53.0					14																	45605362		2203	4300	6503	44675112	SO:0001583	missense	57697	exon1	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"""Fanconi anemia, complementation groups"""	23168	protein-coding gene	gene with protein product		609644	"""KIAA1596"""	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.128C>T	14.37:g.45605362C>T	ENSP00000267430:p.Pro43Leu	Somatic		Capture	Illumina HiSeq	Phase_I	44675112	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	37	CCDS32070.1	.	.	.	.	.	.	.	.	.	.	C	13.81	2.348395	0.41599	.	.	ENSG00000187790	ENST00000556036;ENST00000267430;ENST00000542564	T;T;T	0.11821	2.74;2.81;2.84	4.99	3.15	0.36227	.	1.260730	0.05704	N	0.594663	T	0.15132	0.0365	L	0.50333	1.59	0.09310	N	1	B;B;B	0.25609	0.001;0.001;0.13	B;B;B	0.26416	0.003;0.001;0.069	T	0.41124	-0.9526	10	0.20046	T	0.44	.	8.5339	0.33351	0.0:0.7588:0.1545:0.0867	.	43;43;43	B2RTQ9;Q8IYD8;Q8IYD8-2	.;FANCM_HUMAN;.	L	43	ENSP00000450596:P43L;ENSP00000267430:P43L;ENSP00000442493:P43L	ENSP00000267430:P43L	P	+	2	0	FANCM	44675112	0.095000	0.21747	0.092000	0.20876	0.505000	0.33919	2.558000	0.45879	0.506000	0.28125	0.462000	0.41574	CCA		0.622	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128	
SOS2	6655	broad.mit.edu	37	14	50647396	50647396	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr14:50647396T>C	ENST00000216373.5	-	7	1137	c.863A>G	c.(862-864)cAa>cGa	p.Q288R	SOS2_ENST00000543680.1_Missense_Mutation_p.Q288R|SOS2_ENST00000555794.1_5'Flank	NM_006939.2	NP_008870.2	Q07890	SOS2_HUMAN	son of sevenless homolog 2 (Drosophila)	288	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.Q288R(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)					ATCAAATGCTTGCTCCTATTT	0.338																																					p.Q288R												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A863G	14						.						60.0	60.0	60.0					14																	50647396		2203	4299	6502	49717146	SO:0001583	missense	6655	exon7			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.863A>G	14.37:g.50647396T>C	ENSP00000216373:p.Gln288Arg	Somatic		Capture	Illumina HiSeq	Phase_I	49717146	NM_006939	B7ZKT6|D3DSB4|Q15503|Q17RN1	Missense_Mutation	SNP	ENST00000216373.5	37	CCDS9697.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.155623	0.78114	.	.	ENSG00000100485	ENST00000216373;ENST00000543680	T;T	0.62941	-0.01;-0.01	5.6	5.6	0.85130	Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	T	0.63355	0.2504	L	0.41236	1.265	0.80722	D	1	P;P	0.43231	0.801;0.801	P;P	0.48063	0.565;0.565	T	0.65940	-0.6046	10	0.56958	D	0.05	.	15.829	0.78736	0.0:0.0:0.0:1.0	.	288;288	B7ZKT6;Q07890	.;SOS2_HUMAN	R	288	ENSP00000216373:Q288R;ENSP00000445328:Q288R	ENSP00000216373:Q288R	Q	-	2	0	SOS2	49717146	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.145000	0.64839	2.122000	0.65172	0.529000	0.55759	CAA		0.338	SOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276878.2		
ERO1L	30001	broad.mit.edu	37	14	53133179	53133179	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr14:53133179C>T	ENST00000395686.3	-	7	766	c.543G>A	c.(541-543)ttG>ttA	p.L181L		NM_014584.1	NP_055399.1	Q96HE7	ERO1A_HUMAN	ERO1-like (S. cerevisiae)	181					4-hydroxyproline metabolic process (GO:0019471)|brown fat cell differentiation (GO:0050873)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|chaperone mediated protein folding requiring cofactor (GO:0051085)|endoplasmic reticulum unfolded protein response (GO:0030968)|extracellular matrix organization (GO:0030198)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|protein folding (GO:0006457)|protein maturation by protein folding (GO:0022417)|release of sequestered calcium ion into cytosol (GO:0051209)|response to endoplasmic reticulum stress (GO:0034976)|response to temperature stimulus (GO:0009266)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor (GO:0016671)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)	p.L181L(1)	ERO1L/FERMT2(2)	breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	12	Breast(41;0.226)					GATTAAGAAGCAAATCTACAT	0.353																																					p.L181L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G543A	14						.						77.0	76.0	76.0					14																	53133179		2203	4300	6503	52202929	SO:0001819	synonymous_variant	30001	exon7			AF081886	CCDS9709.1	14q22.1	2010-10-06	2001-11-28		ENSG00000197930	ENSG00000197930			13280	protein-coding gene	gene with protein product		615435	"""ERO1 (S. cerevisiae)-like"""			10671517	Standard	NM_014584		Approved	ERO1A, ERO1-alpha	uc001wzv.3	Q96HE7	OTTHUMG00000140301	ENST00000395686.3:c.543G>A	14.37:g.53133179C>T		Somatic		Capture	Illumina HiSeq	Phase_I	52202929	NM_014584	A8K9X4|A8MYW1|Q7LD45|Q9P1Q9|Q9UKV6	Silent	SNP	ENST00000395686.3	37	CCDS9709.1																																																																																				0.353	ERO1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276892.1	NM_014584	
SYT16	83851	broad.mit.edu	37	14	62463202	62463202	+	Silent	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr14:62463202A>G	ENST00000430451.2	+	1	662	c.465A>G	c.(463-465)caA>caG	p.Q155Q	SYT16_ENST00000446982.2_Silent_p.Q155Q	NM_031914.2	NP_114120.2	Q17RD7	SYT16_HUMAN	synaptotagmin XVI	155					exocytosis (GO:0006887)			p.Q155Q(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	35				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)		GTGGCCTTCAACATGGCTTTG	0.463																																					p.Q155Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A465G	14						.						125.0	119.0	121.0					14																	62463202		1873	4120	5993	61532955	SO:0001819	synonymous_variant	83851	exon1			BC040924	CCDS45121.1	14q23.2	2014-07-02	2005-07-15	2005-07-15	ENSG00000139973	ENSG00000139973		"""Synaptotagmins"""	23142	protein-coding gene	gene with protein product	"""synaptotagmin XIV-related"", "" chr14 synaptotagmin"""	610950	"""synaptotagmin XIV-like"""	SYT14L		11543631	Standard	NM_031914		Approved	yt14r, CHR14SYT, Strep14	uc001xfu.1	Q17RD7	OTTHUMG00000171106	ENST00000430451.2:c.465A>G	14.37:g.62463202A>G		Somatic		Capture	Illumina HiSeq	Phase_I	61532955	NM_031914	B4DZH2|B7ZL60|C9J8I3|Q707N2|Q7Z441|Q8IUU0|Q9BQR8	Silent	SNP	ENST00000430451.2	37	CCDS45121.1																																																																																				0.463	SYT16-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000411700.1	NM_031914	
SYNE2	23224	broad.mit.edu	37	14	64518324	64518324	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr14:64518324G>A	ENST00000344113.4	+	48	7905	c.7693G>A	c.(7693-7695)Gca>Aca	p.A2565T	SYNE2_ENST00000554584.1_Missense_Mutation_p.A2598T|SYNE2_ENST00000358025.3_Missense_Mutation_p.A2565T|SYNE2_ENST00000357395.3_5'UTR	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	2565					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.A2565T(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)		AAAATTCATAGCATCCATAGA	0.313																																					p.A2565T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G7693A	14						.						44.0	40.0	42.0					14																	64518324		1794	4073	5867	63588077	SO:0001583	missense	23224	exon48			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.7693G>A	14.37:g.64518324G>A	ENSP00000341781:p.Ala2565Thr	Somatic		Capture	Illumina HiSeq	Phase_I	63588077	NM_015180	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	37	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	G	3.985	-0.005643	0.07773	.	.	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	T;T;T	0.56444	1.26;1.26;0.46	5.9	3.11	0.35812	.	0.740727	0.12335	N	0.478059	T	0.30603	0.0770	N	0.19112	0.55	0.35785	D	0.821983	B;B	0.16802	0.011;0.019	B;B	0.14578	0.005;0.011	T	0.21348	-1.0248	10	0.17832	T	0.49	.	2.6545	0.05008	0.2078:0.1266:0.5346:0.1309	.	2565;2565	Q8WXH0;Q8WXH0-2	SYNE2_HUMAN;.	T	2565;2565;2598;2598	ENSP00000350719:A2565T;ENSP00000341781:A2565T;ENSP00000452570:A2598T	ENSP00000261678:A2598T	A	+	1	0	SYNE2	63588077	0.189000	0.23263	0.658000	0.29665	0.133000	0.20885	0.676000	0.25247	0.406000	0.25560	-0.175000	0.13238	GCA		0.313	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
SPTB	6710	broad.mit.edu	37	14	65271701	65271701	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-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_ENST00000556626.1_Missense_Mutation_p.R86C|SPTB_ENST00000542895.1_Missense_Mutation_p.R86C|SPTB_ENST00000389722.3_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		
SLC39A9	55334	broad.mit.edu	37	14	69925187	69925187	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr14:69925187C>T	ENST00000336643.5	+	7	1479	c.801C>T	c.(799-801)ggC>ggT	p.G267G	SLC39A9_ENST00000557046.1_Silent_p.G244G|SLC39A9_ENST00000555245.1_3'UTR|SLC39A9_ENST00000031146.4_Silent_p.G201G|SLC39A9_ENST00000556605.1_Intron	NM_018375.4	NP_060845.2	Q9NUM3	S39A9_HUMAN	solute carrier family 39, member 9	267					zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)	p.G267G(1)		breast(1)|endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|skin(1)|stomach(1)	14				all cancers(60;0.00299)|BRCA - Breast invasive adenocarcinoma(234;0.0145)|OV - Ovarian serous cystadenocarcinoma(108;0.0373)		CTGAGGTGGGCGGAATAGGGC	0.597																																					p.G267G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C801T	14						.						69.0	70.0	70.0					14																	69925187		2203	4300	6503	68994940	SO:0001819	synonymous_variant	55334	exon7				CCDS9795.1, CCDS58327.1, CCDS58328.1	14q24.1	2013-07-17	2013-07-17			ENSG00000029364		"""Solute carriers"""	20182	protein-coding gene	gene with protein product							Standard	NM_018375		Approved	FLJ11274	uc001xle.3	Q9NUM3		ENST00000336643.5:c.801C>T	14.37:g.69925187C>T		Somatic		Capture	Illumina HiSeq	Phase_I	68994940	NM_018375	G3V5J8|Q53HN3|Q5MJQ0|Q6P2Q1|Q86WY2	Silent	SNP	ENST00000336643.5	37	CCDS9795.1																																																																																				0.597	SLC39A9-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412446.1	NM_018375	
PCNX	22990	broad.mit.edu	37	14	71444757	71444757	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr14:71444757G>A	ENST00000304743.2	+	6	2149	c.1703G>A	c.(1702-1704)cGg>cAg	p.R568Q	PCNX_ENST00000439984.3_Missense_Mutation_p.R568Q|PCNX_ENST00000238570.5_Missense_Mutation_p.R568Q	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	568						integral component of membrane (GO:0016021)		p.R568Q(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)		GGAAAAAAACGGGCTAGCAGT	0.478																																					p.R568Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1703A	14						.						103.0	103.0	103.0					14																	71444757		2203	4300	6503	70514510	SO:0001583	missense	22990	exon6			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.1703G>A	14.37:g.71444757G>A	ENSP00000304192:p.Arg568Gln	Somatic		Capture	Illumina HiSeq	Phase_I	70514510	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Missense_Mutation	SNP	ENST00000304743.2	37	CCDS9806.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.013946	0.75161	.	.	ENSG00000100731	ENST00000304743;ENST00000238570;ENST00000439984	T;T;T	0.01215	5.16;5.16;5.16	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.03651	0.0104	L	0.29908	0.895	0.58432	D	0.999999	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.85130	0.978;0.978;0.997	T	0.71174	-0.4670	10	0.12766	T	0.61	.	20.2069	0.98280	0.0:0.0:1.0:0.0	.	568;568;568	B2RTR6;Q96RV3;Q96RV3-2	.;PCX1_HUMAN;.	Q	568	ENSP00000304192:R568Q;ENSP00000238570:R568Q;ENSP00000396617:R568Q	ENSP00000238570:R568Q	R	+	2	0	PCNX	70514510	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	9.230000	0.95299	2.779000	0.95612	0.655000	0.94253	CGG		0.478	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982	
DCAF4	26094	broad.mit.edu	37	14	73412700	73412700	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr14:73412700T>G	ENST00000358377.2	+	7	863	c.643T>G	c.(643-645)Ttc>Gtc	p.F215V	DCAF4_ENST00000553457.1_Missense_Mutation_p.F115V|DCAF4_ENST00000394234.2_Missense_Mutation_p.F115V|DCAF4_ENST00000509153.1_Missense_Mutation_p.F154V|DCAF4_ENST00000555042.1_Missense_Mutation_p.F215V|DCAF4_ENST00000353777.3_Missense_Mutation_p.F154V	NM_001163509.1|NM_015604.3	NP_001156981.1|NP_056419.2	Q8WV16	DCAF4_HUMAN	DDB1 and CUL4 associated factor 4	215					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)		p.F215V(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|skin(1)	22						GCTCAAGGTGTTCATGCACGA	0.512																																					p.F154V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T460G	14						.						186.0	167.0	174.0					14																	73412700		2203	4300	6503	72482453	SO:0001583	missense	26094	exon5			BC018979	CCDS9809.1, CCDS9810.1, CCDS41968.1, CCDS41968.2, CCDS55926.1	14q24.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000119599		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	20229	protein-coding gene	gene with protein product			"""WD repeat domain 21"", ""WD repeat domain 21A"""	WDR21, WDR21A			Standard	NM_015604		Approved	DKFZp434K114	uc010ttr.2	Q8WV16		ENST00000358377.2:c.643T>G	14.37:g.73412700T>G	ENSP00000351147:p.Phe215Val	Somatic		Capture	Illumina HiSeq	Phase_I	72482453	NM_181341	B4DUT6|G3V522|Q86U31|Q8IV10|Q96K22|Q9Y4P5	Missense_Mutation	SNP	ENST00000358377.2	37	CCDS9809.1	.	.	.	.	.	.	.	.	.	.	T	8.474	0.858236	0.17178	.	.	ENSG00000119599	ENST00000358377;ENST00000353777;ENST00000394234;ENST00000509153;ENST00000555042;ENST00000553457	T;T;T;T;T;T	0.69435	0.61;-0.23;-0.4;0.61;0.22;1.35	6.04	0.575	0.17374	.	0.622716	0.17934	N	0.157073	T	0.37156	0.0993	N	0.08118	0	0.26909	N	0.966942	B;B;B;B;B;B	0.16802	0.019;0.018;0.018;0.018;0.012;0.01	B;B;B;B;B;B	0.28385	0.041;0.053;0.089;0.089;0.013;0.053	T	0.13602	-1.0503	10	0.18710	T	0.47	.	0.7467	0.00983	0.2322:0.2943:0.2764:0.1971	.	154;193;215;215;154;215	B4DUT6;B4DN30;Q8WV16-2;G3V522;Q86SY2;Q8WV16	.;.;.;.;.;DCAF4_HUMAN	V	215;154;115;154;215;115	ENSP00000351147:F215V;ENSP00000345176:F154V;ENSP00000377781:F115V;ENSP00000426178:F154V;ENSP00000452131:F215V;ENSP00000451186:F115V	ENSP00000345176:F154V	F	+	1	0	DCAF4	72482453	1.000000	0.71417	0.115000	0.21578	0.380000	0.30137	3.316000	0.51960	0.097000	0.17492	-0.366000	0.07423	TTC		0.512	DCAF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361058.1	NM_015604	
NRXN3	9369	broad.mit.edu	37	14	79933617	79933617	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr14:79933617C>T	ENST00000557594.1	+	2	1254	c.301C>T	c.(301-303)Cca>Tca	p.P101S	NRXN3_ENST00000335750.5_Missense_Mutation_p.P733S|NRXN3_ENST00000554719.1_Missense_Mutation_p.P733S|NRXN3_ENST00000428277.2_Missense_Mutation_p.P101S|NRXN3_ENST00000556003.1_3'UTR|NRXN3_ENST00000281127.7_Missense_Mutation_p.P101S	NM_001272020.1	NP_001258949.1	Q9HDB5	NRX3B_HUMAN	neurexin 3	101	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.P733S(1)|p.P101S(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)		CTACACCTGGCCAGCCAATGA	0.567																																					p.P101S												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C301T	14						.						107.0	87.0	94.0					14																	79933617		2203	4300	6503	79003370	SO:0001583	missense	9369	exon2			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.301C>T	14.37:g.79933617C>T	ENSP00000451672:p.Pro101Ser	Somatic		Capture	Illumina HiSeq	Phase_I	79003370	NM_138970	A5PKW8|A8MPU5|B3KPM7|Q6NUR0|Q8IUD8	Missense_Mutation	SNP	ENST00000557594.1	37		.	.	.	.	.	.	.	.	.	.	C	35	5.445297	0.96187	.	.	ENSG00000021645	ENST00000330071;ENST00000332068;ENST00000554719;ENST00000335750;ENST00000557594;ENST00000281127;ENST00000428277	T;T;T;T;T	0.81078	-1.45;-1.45;0.94;0.94;0.94	5.93	5.93	0.95920	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	0.000000	0.85682	D	0.000000	D	0.89497	0.6732	M	0.73430	2.235	0.80722	D	1	P;P;D;D	0.56521	0.932;0.92;0.976;0.973	P;P;D;P	0.65573	0.808;0.619;0.936;0.731	D	0.88023	0.2770	9	.	.	.	.	20.3312	0.98718	0.0:1.0:0.0:0.0	.	101;101;101;733	Q9HDB5-4;Q9HDB5-2;Q9HDB5;Q9Y4C0-3	.;.;NRX3B_HUMAN;.	S	1106;1095;733;733;101;101;101	ENSP00000451648:P733S;ENSP00000338349:P733S;ENSP00000451672:P101S;ENSP00000281127:P101S;ENSP00000394426:P101S	.	P	+	1	0	NRXN3	79003370	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.015000	0.70791	2.797000	0.96272	0.655000	0.94253	CCA		0.567	NRXN3-004	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000413790.1	NM_001105250	
RPS6KA5	9252	broad.mit.edu	37	14	91356840	91356840	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr14:91356840G>A	ENST00000261991.3	-	14	2000	c.1827C>T	c.(1825-1827)ggC>ggT	p.G609G	RPS6KA5_ENST00000536315.2_Silent_p.G530G	NM_004755.2	NP_004746.2	O75582	KS6A5_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 5	609	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|epidermal growth factor receptor signaling pathway (GO:0007173)|histone H2A-S1 phosphorylation (GO:0043990)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-S28 phosphorylation (GO:0043988)|histone phosphorylation (GO:0016572)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|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 cytokine production (GO:0001818)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.G609G(2)		endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0148)|Melanoma(154;0.099)|all_epithelial(191;0.146)		Epithelial(152;0.182)|BRCA - Breast invasive adenocarcinoma(234;0.201)		CCAAAATGACGCCCAAGCTCC	0.463																																					p.G609G												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1827T	14						.						54.0	51.0	52.0					14																	91356840		2203	4300	6503	90426593	SO:0001819	synonymous_variant	9252	exon14			AF074393	CCDS9893.1, CCDS45149.1	14q31-q32.1	2011-04-05	2002-08-29			ENSG00000100784			10434	protein-coding gene	gene with protein product		603607	"""ribosomal protein S6 kinase, 90kD, polypeptide 5"""			9687510, 10702687	Standard	NM_004755		Approved	MSK1, RLPK	uc001xys.2	O75582		ENST00000261991.3:c.1827C>T	14.37:g.91356840G>A		Somatic		Capture	Illumina HiSeq	Phase_I	90426593	NM_004755	O95316|Q96AF7	Silent	SNP	ENST00000261991.3	37	CCDS9893.1																																																																																				0.463	RPS6KA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411442.2	NM_004755	
CLMN	79789	broad.mit.edu	37	14	95669462	95669462	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr14:95669462C>T	ENST00000298912.4	-	9	2337	c.2224G>A	c.(2224-2226)Gct>Act	p.A742T		NM_024734.3	NP_079010.2	Q96JQ2	CLMN_HUMAN	calmin (calponin-like, transmembrane)	742					negative regulation of cell proliferation (GO:0008285)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)		p.A742T(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(17)|prostate(3)|skin(3)	44				Epithelial(152;0.193)		TCTACATAAGCCTCCAAAACT	0.527																																					p.A742T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2224A	14						.						38.0	41.0	40.0					14																	95669462		2203	4300	6503	94739215	SO:0001583	missense	79789	exon9			AB033014	CCDS9933.1	14q32.13	2012-10-02			ENSG00000165959	ENSG00000165959			19972	protein-coding gene	gene with protein product		611121				11386753	Standard	NM_024734		Approved	FLJ12383, KIAA1188, KIAA0500	uc001yef.2	Q96JQ2	OTTHUMG00000171629	ENST00000298912.4:c.2224G>A	14.37:g.95669462C>T	ENSP00000298912:p.Ala742Thr	Somatic		Capture	Illumina HiSeq	Phase_I	94739215	NM_024734	B2RAR7|Q9H713|Q9HA23|Q9HA57|Q9UFP4|Q9ULN2	Missense_Mutation	SNP	ENST00000298912.4	37	CCDS9933.1	.	.	.	.	.	.	.	.	.	.	C	17.38	3.374312	0.61735	.	.	ENSG00000165959	ENST00000298912	D	0.97575	-4.44	5.22	5.22	0.72569	.	0.000000	0.41294	D	0.000917	D	0.97414	0.9154	M	0.65498	2.005	0.80722	D	1	D	0.59767	0.986	P	0.55615	0.78	D	0.97804	1.0246	10	0.66056	D	0.02	.	15.528	0.75928	0.0:1.0:0.0:0.0	.	742	Q96JQ2	CLMN_HUMAN	T	742	ENSP00000298912:A742T	ENSP00000298912:A742T	A	-	1	0	CLMN	94739215	1.000000	0.71417	0.985000	0.45067	0.117000	0.20001	3.431000	0.52814	2.438000	0.82558	0.555000	0.69702	GCT		0.527	CLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414518.2		
CLMN	79789	broad.mit.edu	37	14	95670599	95670599	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr14:95670599G>A	ENST00000298912.4	-	9	1200	c.1087C>T	c.(1087-1089)Cgc>Tgc	p.R363C		NM_024734.3	NP_079010.2	Q96JQ2	CLMN_HUMAN	calmin (calponin-like, transmembrane)	363					negative regulation of cell proliferation (GO:0008285)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)		p.R363C(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(17)|prostate(3)|skin(3)	44				Epithelial(152;0.193)		CCATCCAGGCGGAATTCCTTC	0.542																																					p.R363C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1087T	14						.						145.0	148.0	147.0					14																	95670599		2203	4300	6503	94740352	SO:0001583	missense	79789	exon9			AB033014	CCDS9933.1	14q32.13	2012-10-02			ENSG00000165959	ENSG00000165959			19972	protein-coding gene	gene with protein product		611121				11386753	Standard	NM_024734		Approved	FLJ12383, KIAA1188, KIAA0500	uc001yef.2	Q96JQ2	OTTHUMG00000171629	ENST00000298912.4:c.1087C>T	14.37:g.95670599G>A	ENSP00000298912:p.Arg363Cys	Somatic		Capture	Illumina HiSeq	Phase_I	94740352	NM_024734	B2RAR7|Q9H713|Q9HA23|Q9HA57|Q9UFP4|Q9ULN2	Missense_Mutation	SNP	ENST00000298912.4	37	CCDS9933.1	.	.	.	.	.	.	.	.	.	.	G	11.42	1.632617	0.29068	.	.	ENSG00000165959	ENST00000298912	D	0.92249	-3.0	5.41	-5.36	0.02689	.	2.078530	0.02088	N	0.052948	T	0.75117	0.3806	N	0.01352	-0.895	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.68209	-0.5469	10	0.38643	T	0.18	.	4.48	0.11762	0.2587:0.0:0.3663:0.375	.	363	Q96JQ2	CLMN_HUMAN	C	363	ENSP00000298912:R363C	ENSP00000298912:R363C	R	-	1	0	CLMN	94740352	0.000000	0.05858	0.000000	0.03702	0.140000	0.21249	-0.813000	0.04491	-0.575000	0.05982	-0.302000	0.09304	CGC		0.542	CLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414518.2		
GLRX5	51218	broad.mit.edu	37	14	96010336	96010336	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr14:96010336C>T	ENST00000331334.4	+	2	845	c.348C>T	c.(346-348)ggC>ggT	p.G116G	GLRX5_ENST00000553672.1_3'UTR	NM_016417.2	NP_057501.2	Q86SX6	GLRX5_HUMAN	glutaredoxin 5	116	Glutaredoxin. {ECO:0000255|PROSITE- ProRule:PRU00686}.				cell redox homeostasis (GO:0045454)|hemopoiesis (GO:0030097)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|protein disulfide oxidoreductase activity (GO:0015035)	p.G116G(1)		large_intestine(1)|lung(1)	2		all_cancers(154;0.135)		Epithelial(152;0.133)|COAD - Colon adenocarcinoma(157;0.21)|all cancers(159;0.212)		ACCTCAATGGCGAGTTTGTAG	0.453																																					p.G116G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C348T	14						.						94.0	94.0	94.0					14																	96010336		2203	4300	6503	95080089	SO:0001819	synonymous_variant	51218	exon2			AF113691	CCDS9936.1	14q32.2	2007-08-16	2007-08-16	2005-11-11		ENSG00000182512			20134	protein-coding gene	gene with protein product		609588	"""chromosome 14 open reading frame 87"", ""glutaredoxin 5 homolog (S. cerevisiae)"""	C14orf87			Standard	NM_016417		Approved	PR01238, GRX5	uc001yem.1	Q86SX6		ENST00000331334.4:c.348C>T	14.37:g.96010336C>T		Somatic		Capture	Illumina HiSeq	Phase_I	95080089	NM_016417	Q0X088|Q3YML0|Q86WY3|Q8IZ54	Silent	SNP	ENST00000331334.4	37	CCDS9936.1																																																																																				0.453	GLRX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414550.1		
AMN	81693	broad.mit.edu	37	14	103389067	103389067	+	Splice_Site	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr14:103389067C>T	ENST00000299155.5	+	1	75	c.42C>T	c.(40-42)tgC>tgT	p.C14C		NM_030943.3	NP_112205.2	Q9BXJ7	AMNLS_HUMAN	amnion associated transmembrane protein	14					cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|excretion (GO:0007588)|Golgi to plasma membrane protein transport (GO:0043001)|lipoprotein metabolic process (GO:0042157)|multicellular organismal development (GO:0007275)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)	p.C14C(1)		kidney(2)|large_intestine(1)|lung(2)|skin(1)	6				Colorectal(3;0.00739)|READ - Rectum adenocarcinoma(2;0.0336)|Epithelial(152;0.0363)|all cancers(159;0.147)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TGCAGCTCTGCGGTGAGCCGG	0.692																																					p.C14C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C42T	14						.						27.0	21.0	23.0					14																	103389067		2182	4280	6462	102458820	SO:0001630	splice_region_variant	81693	exon1			AF328788	CCDS9977.1	14q32.32	2014-09-17	2012-12-07		ENSG00000166126	ENSG00000166126			14604	protein-coding gene	gene with protein product		605799	"""amnionless homolog (mouse)"""			11279523	Standard	NM_030943		Approved	amnionless	uc001ymg.4	Q9BXJ7		ENST00000299155.5:c.43+1C>T	14.37:g.103389067C>T		Somatic		Capture	Illumina HiSeq	Phase_I	102458820	NM_030943	Q6UX83	Silent	SNP	ENST00000299155.5	37	CCDS9977.1																																																																																				0.692	AMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415704.1		Silent
INF2	64423	broad.mit.edu	37	14	105169757	105169758	+	Frame_Shift_Del	DEL	GC	GC	-			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	GC	GC					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr14:105169757_105169758delGC	ENST00000392634.4	+	4	745_746	c.633_634delGC	c.(631-636)ctgcgcfs	p.R212fs	INF2_ENST00000330634.7_Frame_Shift_Del_p.R212fs|INF2_ENST00000398337.4_Frame_Shift_Del_p.R212fs	NM_022489.3	NP_071934.3	Q27J81	INF2_HUMAN	inverted formin, FH2 and WH2 domain containing	212	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|regulation of cellular component size (GO:0032535)|regulation of mitochondrial fission (GO:0090140)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)		p.R214fs*38(1)|p.R214fs*>21(1)		large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)		CCGAGGACCTGCGCGCGCGCAC	0.644																																					p.211_212del												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.633_634del	14						.																																			104240803	SO:0001589	frameshift_variant	64423	exon4			AK025709	CCDS9989.2, CCDS45173.1	14q32.33	2009-09-07	2007-11-29	2007-11-29	ENSG00000203485	ENSG00000203485			23791	protein-coding gene	gene with protein product	"""inverted formin 2"""	610982	"""chromosome 14 open reading frame 151"", ""chromosome 14 open reading frame 173"""	C14orf151, C14orf173		16818491	Standard	NM_001031714		Approved	MGC13251	uc001ypb.2	Q27J81	OTTHUMG00000029811	ENST00000392634.4:c.633_634delGC	14.37:g.105169765_105169766delGC	ENSP00000376410:p.Arg212fs	Somatic		Capture	Illumina HiSeq	Phase_I	104240802	NM_032714	Q27J83|Q69YL8|Q6P1X7|Q6PK22|Q86TR7|Q9BRM1|Q9H6N1	Frame_Shift_Del	DEL	ENST00000392634.4	37	CCDS9989.2																																																																																				0.644	INF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074371.4	NM_022489	
RNF31	55072	broad.mit.edu	37	14	24629764	24629764	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr14:24629764delC	ENST00000324103.6	+	21	3521	c.3201delC	c.(3199-3201)atcfs	p.I1067fs	IRF9_ENST00000396864.3_5'Flank|RNF31_ENST00000559275.1_Frame_Shift_Del_p.I916fs|RP11-468E2.4_ENST00000558468.1_Frame_Shift_Del_p.I542fs|RNA5SP383_ENST00000362934.1_RNA|RNF31_ENST00000382687.3_Frame_Shift_Del_p.I916fs|IRF9_ENST00000557894.1_5'Flank	NM_017999.4	NP_060469.4	Q96EP0	RNF31_HUMAN	ring finger protein 31	1067	LDD domain.				CD40 signaling pathway (GO:0023035)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein linear polyubiquitination (GO:0097039)|protein polyubiquitination (GO:0000209)|T cell receptor signaling pathway (GO:0050852)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|LUBAC complex (GO:0071797)	ligase activity (GO:0016874)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R1069fs*>4(1)		breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|prostate(4)|skin(2)|soft_tissue(1)	39				GBM - Glioblastoma multiforme(265;0.00861)		GACAGAGTATCCCCCGCAGGC	0.557											OREG0022619	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I1067fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.3201delC	14						.						39.0	45.0	43.0					14																	24629764		1896	4115	6011	23699604	SO:0001589	frameshift_variant	55072	exon21			AK000973	CCDS41931.1	14q11.2	2012-09-20			ENSG00000092098	ENSG00000092098		"""RING-type (C3HC4) zinc fingers"""	16031	protein-coding gene	gene with protein product	"""HOIL-1-interacting protein"""	612487				10422847	Standard	NM_017999		Approved	ZIBRA, FLJ10111, FLJ23501, HOIP	uc001wmn.1	Q96EP0	OTTHUMG00000028798	ENST00000324103.6:c.3201delC	14.37:g.24629764delC	ENSP00000315112:p.Ile1067fs	Somatic	772	Capture	Illumina HiSeq	Phase_I	23699604	NM_017999	A0A962|Q86VI2|Q8TEI0|Q96GB4|Q96NF1|Q9H5F1|Q9NWD2	Frame_Shift_Del	DEL	ENST00000324103.6	37	CCDS41931.1																																																																																				0.557	RNF31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071921.3	NM_017999	
MPP5	64398	broad.mit.edu	37	14	67783612	67783612	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr14:67783612delA	ENST00000261681.4	+	10	1950	c.1289delA	c.(1288-1290)gaafs	p.E430fs	ATP6V1D_ENST00000553974.1_Intron|MPP5_ENST00000555925.1_Frame_Shift_Del_p.E396fs	NM_022474.3	NP_071919.2	Q8N3R9	MPP5_HUMAN	membrane protein, palmitoylated 5 (MAGUK p55 subfamily member 5)	430					cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|establishment of protein localization to plasma membrane (GO:0090002)|morphogenesis of an epithelial sheet (GO:0002011)|myelin assembly (GO:0032288)|peripheral nervous system myelin maintenance (GO:0032287)|protein localization to myelin sheath abaxonal region (GO:0035750)|tight junction assembly (GO:0070830)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lateral loop (GO:0043219)|myelin sheath adaxonal region (GO:0035749)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein domain specific binding (GO:0019904)	p.K431fs*34(1)		cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|skin(1)	18				all cancers(60;0.000388)|OV - Ovarian serous cystadenocarcinoma(108;0.00762)|BRCA - Breast invasive adenocarcinoma(234;0.0106)		AAGGAGCCAGAAAAATCAGGT	0.368																																					p.E430fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1289delA	14						.						56.0	54.0	55.0					14																	67783612		2203	4300	6503	66853365	SO:0001589	frameshift_variant	64398	exon10			AK022677	CCDS9779.1, CCDS58325.1	14q23.3	2008-08-11				ENSG00000072415			18669	protein-coding gene	gene with protein product	"""stardust"""	606958				11927608	Standard	NM_022474		Approved	PALS1, FLJ12615	uc001xjc.4	Q8N3R9		ENST00000261681.4:c.1289delA	14.37:g.67783612delA	ENSP00000261681:p.Glu430fs	Somatic		Capture	Illumina HiSeq	Phase_I	66853365	NM_022474	A1L380|Q7Z631|Q86T98|Q8N7I5|Q9H9Q0	Frame_Shift_Del	DEL	ENST00000261681.4	37	CCDS9779.1																																																																																				0.368	MPP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412498.1	NM_022474	
CSPG4	1464	broad.mit.edu	37	15	75968542	75968543	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr15:75968542_75968543insC	ENST00000308508.5	-	10	6409_6410	c.6317_6318insG	c.(6316-6318)ggcfs	p.G2106fs	CTD-2026K11.1_ENST00000569467.1_RNA|AC105020.1_ENST00000435356.1_5'Flank	NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	2106	Cysteine-containing.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)	p.S2107fs*13(1)		breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						CCAGCTGGCTGCCCCCGGGCTC	0.748																																					p.G2106fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.6318_6319insG	15						.																																			73755598	SO:0001589	frameshift_variant	1464	exon10			X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.6318dupG	15.37:g.75968547_75968547dupC	ENSP00000312506:p.Gly2106fs	Somatic		Capture	Illumina HiSeq	Phase_I	73755597	NM_001897	D3DW77|Q92675	Frame_Shift_Ins	INS	ENST00000308508.5	37	CCDS10284.1																																																																																				0.748	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
MAGEL2	54551	broad.mit.edu	37	15	23890644	23890644	+	Missense_Mutation	SNP	C	C	T	rs372951342		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr15:23890644C>T	ENST00000532292.1	-	1	531	c.437G>A	c.(436-438)cGc>cAc	p.R146H		NM_019066.4	NP_061939.3	Q9UJ55	MAGL2_HUMAN	MAGE-like 2	29					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)			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)		AAAGATCATGCGGTCTTTTGA	0.602																																					p.R749H												.	.	0			c.G2246A	15						.						34.0	37.0	36.0					15																	23890644		1976	4150	6126	21441737	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.437G>A	15.37:g.23890644C>T	ENSP00000433433:p.Arg146His	Somatic		Capture	Illumina HiSeq	Phase_I	21441737	NM_019066		Missense_Mutation	SNP	ENST00000532292.1	37		.	.	.	.	.	.	.	.	.	.	C	17.19	3.326703	0.60743	.	.	ENSG00000254585	ENST00000532292	.	.	.	4.08	3.16	0.36331	.	.	.	.	.	T	0.29850	0.0746	N	0.24115	0.695	0.28267	N	0.924599	.	.	.	.	.	.	T	0.18493	-1.0335	5	.	.	.	.	7.6247	0.28206	0.0:0.8866:0.0:0.1134	.	.	.	.	T	178	.	.	A	-	1	0	MAGEL2	21441737	0.077000	0.21312	0.947000	0.38551	0.768000	0.43524	0.768000	0.26590	1.290000	0.44636	0.655000	0.94253	GCA		0.602	MAGEL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395182.2	NM_019066	
UBE3A	7337	broad.mit.edu	37	15	25599677	25599677	+	Missense_Mutation	SNP	G	G	A	rs144567527		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr15:25599677G>A	ENST00000397954.2	-	8	2286	c.2287C>T	c.(2287-2289)Cgg>Tgg	p.R763W	UBE3A_ENST00000428984.2_Missense_Mutation_p.R740W|UBE3A_ENST00000566215.1_Missense_Mutation_p.R740W|UBE3A_ENST00000232165.3_Missense_Mutation_p.R760W|UBE3A_ENST00000438097.1_Missense_Mutation_p.R740W|SNHG14_ENST00000554726.1_RNA			Q05086	UBE3A_HUMAN	ubiquitin protein ligase E3A	763					androgen receptor signaling pathway (GO:0030521)|brain development (GO:0007420)|ovarian follicle development (GO:0001541)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland growth (GO:0060736)|protein autoubiquitination (GO:0051865)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|proteolysis (GO:0006508)|sperm entry (GO:0035037)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)	p.R763W(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(13)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	38		all_cancers(20;3.47e-21)|Breast(32;0.00123)		all cancers(64;2.78e-08)|Epithelial(43;8.85e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0155)|Lung(196;0.0616)		TTTCTTACCCGGCTTCCACAT	0.353																																					p.R760W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2278T	15						.	G	TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	142.0	147.0	145.0		2287,2218,2278	4.7	1.0	15	dbSNP_134	145	1,8597	1.2+/-3.3	0,1,4298	no	missense,missense,missense	UBE3A	NM_000462.3,NM_130838.1,NM_130839.2	101,101,101	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	763/876,740/853,760/873	25599677	1,13003	2203	4299	6502	23150770	SO:0001583	missense	7337	exon10			AF002224	CCDS32177.1, CCDS45191.1, CCDS45192.1	15q11.2	2014-09-17	2008-07-31		ENSG00000114062	ENSG00000114062	6.3.2.19		12496	protein-coding gene	gene with protein product	"""Angelman syndrome"""	601623	"""human papilloma virus E6-associated protein"""	EPVE6AP, HPVE6A		8221889	Standard	NM_130838		Approved	AS, ANCR, E6-AP, FLJ26981	uc001zas.3	Q05086		ENST00000397954.2:c.2287C>T	15.37:g.25599677G>A	ENSP00000381045:p.Arg763Trp	Somatic		Capture	Illumina HiSeq	Phase_I	23150770	NM_130839	A8K8Z9|P78355|Q93066|Q9UEP4|Q9UEP5|Q9UEP6|Q9UEP7|Q9UEP8|Q9UEP9	Missense_Mutation	SNP	ENST00000397954.2	37	CCDS45192.1	.	.	.	.	.	.	.	.	.	.	G	18.95	3.731587	0.69189	0.0	1.16E-4	ENSG00000114062	ENST00000232165;ENST00000356465;ENST00000397954;ENST00000438097;ENST00000428984	T;T;T;T	0.58358	0.34;0.34;0.34;0.34	5.65	4.73	0.59995	HECT (4);	0.000000	0.85682	D	0.000000	T	0.72930	0.3522	M	0.82823	2.61	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.74023	0.937;0.982	T	0.77239	-0.2661	10	0.72032	D	0.01	.	12.9105	0.58177	0.0:0.0:0.5539:0.4461	.	760;763	Q05086-3;Q05086	.;UBE3A_HUMAN	W	760;760;763;740;740	ENSP00000232165:R760W;ENSP00000381045:R763W;ENSP00000411258:R740W;ENSP00000401265:R740W	ENSP00000232165:R760W	R	-	1	2	UBE3A	23150770	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.280000	0.51677	1.355000	0.45865	-0.293000	0.09583	CGG		0.353	UBE3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000434203.1	NM_000462	
RYR3	6263	broad.mit.edu	37	15	34115266	34115266	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr15:34115266T>G	ENST00000389232.4	+	81	11135	c.11065T>G	c.(11065-11067)Tct>Gct	p.S3689A	RYR3_ENST00000415757.3_Missense_Mutation_p.S3684A	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3689					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.S3688A(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)		TCTTATGCAGTCTTGCAGGTA	0.438																																					p.S3689A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T11065G	15						.						111.0	105.0	107.0					15																	34115266		1848	4093	5941	31902558	SO:0001583	missense	6263	exon81				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.11065T>G	15.37:g.34115266T>G	ENSP00000373884:p.Ser3689Ala	Somatic		Capture	Illumina HiSeq	Phase_I	31902558	NM_001036	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	T	16.41	3.116787	0.56505	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D	0.87491	-2.26	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	D	0.89663	0.6780	L	0.61218	1.895	0.42513	D	0.992974	D;P	0.57257	0.979;0.853	P;B	0.56563	0.801;0.41	D	0.90379	0.4386	10	0.66056	D	0.02	.	10.6977	0.45909	0.1423:0.0:0.0:0.8577	.	3684;3689	Q15413-2;Q15413	.;RYR3_HUMAN	A	3689;3688;3684	ENSP00000373884:S3689A	ENSP00000354735:S3684A	S	+	1	0	RYR3	31902558	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.946000	0.70234	2.243000	0.73865	0.533000	0.62120	TCT		0.438	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
THBS1	7057	broad.mit.edu	37	15	39885817	39885817	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr15:39885817C>A	ENST00000260356.5	+	19	3380	c.3215C>A	c.(3214-3216)cCt>cAt	p.P1072H	CTD-2033D15.1_ENST00000560769.1_RNA	NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	1072	TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				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.P1072H(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)		ACCACAGGGCCTGGCGAGCAC	0.582																																					p.P1072H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3215A	15						.						106.0	106.0	106.0					15																	39885817		2200	4297	6497	37673109	SO:0001583	missense	7057	exon19				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.3215C>A	15.37:g.39885817C>A	ENSP00000260356:p.Pro1072His	Somatic		Capture	Illumina HiSeq	Phase_I	37673109	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Missense_Mutation	SNP	ENST00000260356.5	37	CCDS32194.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.970625	0.92919	.	.	ENSG00000137801	ENST00000260356	D	0.97850	-4.57	5.77	5.77	0.91146	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Thrombospondin, C-terminal (2);	0.000000	0.35772	N	0.002990	D	0.98880	0.9621	M	0.85197	2.74	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.983;1.0	D	0.99686	1.1000	10	0.87932	D	0	-10.3622	19.9729	0.97289	0.0:1.0:0.0:0.0	.	987;1072	B4E3J7;P07996	.;TSP1_HUMAN	H	1072	ENSP00000260356:P1072H	ENSP00000260356:P1072H	P	+	2	0	THBS1	37673109	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	7.814000	0.86154	2.714000	0.92807	0.655000	0.94253	CCT		0.582	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	
EIF2AK4	440275	broad.mit.edu	37	15	40321616	40321616	+	Silent	SNP	C	C	T	rs181699370	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr15:40321616C>T	ENST00000263791.5	+	34	4555	c.4512C>T	c.(4510-4512)tcC>tcT	p.S1504S	EIF2AK4_ENST00000382727.2_Silent_p.S1476S	NM_001013703.2	NP_001013725.2	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha kinase 4	1504					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.S1504S(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)		GAGAAGCTTCCGATAATCTTG	0.333													C|||	4	0.000798722	0.0008	0.0	5008	,	,		18105	0.0		0.001	False		,,,				2504	0.002				p.S1504S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4512T	15						.	C		0,3678		0,0,1839	111.0	109.0	110.0		4512	-1.5	1.0	15		110	1,8153		0,1,4076	no	coding-synonymous	EIF2AK4	NM_001013703.2		0,1,5915	TT,TC,CC		0.0123,0.0,0.0085		1504/1650	40321616	1,11831	1839	4077	5916	38108908	SO:0001819	synonymous_variant	440275	exon34			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.4512C>T	15.37:g.40321616C>T		Somatic		Capture	Illumina HiSeq	Phase_I	38108908	NM_001013703	C9JEC4|Q69YL7|Q6DC97|Q96GN6|Q9H5K1|Q9NSQ3|Q9NSZ5|Q9UJ56	Silent	SNP	ENST00000263791.5	37	CCDS42016.1																																																																																				0.333	EIF2AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418395.1		
BUB1B	701	broad.mit.edu	37	15	40477537	40477537	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr15:40477537T>C	ENST00000287598.6	+	7	1118	c.923T>C	c.(922-924)cTg>cCg	p.L308P	BUB1B_ENST00000412359.3_Missense_Mutation_p.L322P	NM_001211.5	NP_001202	O60566	BUB1B_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase B	308					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|protein localization to chromosome, centromeric region (GO:0071459)|protein localization to kinetochore (GO:0034501)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|condensed chromosome kinetochore (GO:0000777)|condensed chromosome outer kinetochore (GO:0000940)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|perinuclear region of cytoplasm (GO:0048471)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.L308P(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(1)|stomach(2)|urinary_tract(2)	36		all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556)		GAGAATGAGCTGCAAGCAGGC	0.502			"""Mis, N, F, S"""			rhabdomyosarcoma			Mosaic Variegated Aneuploidy Syndrome																												p.L308P		yes	Rec		Mosaic variegated aneuploidy	15	15q15	701	BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast)		M	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T923C	15						.						103.0	103.0	103.0					15																	40477537		2203	4300	6503	38264829	SO:0001583	missense	701	exon7	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	AF107297	CCDS10053.1	15q15	2014-09-17	2013-01-17		ENSG00000156970	ENSG00000156970			1149	protein-coding gene	gene with protein product		602860	"""budding uninhibited by benzimidazoles 1 (yeast homolog), beta"", ""budding uninhibited by benzimidazoles 1 homolog beta (yeast)"""			9889005	Standard	NM_001211		Approved	BUBR1, MAD3L, Bub1A, SSK1	uc001zkx.4	O60566	OTTHUMG00000129877	ENST00000287598.6:c.923T>C	15.37:g.40477537T>C	ENSP00000287598:p.Leu308Pro	Somatic		Capture	Illumina HiSeq	Phase_I	38264829	NM_001211	B2R6U0|B4DL09|B4DLG3|O60501|O60627|O60758|O75389|Q59HH6|Q8WV50|Q96KM4	Missense_Mutation	SNP	ENST00000287598.6	37	CCDS10053.1	.	.	.	.	.	.	.	.	.	.	T	20.5	3.996844	0.74818	.	.	ENSG00000156970	ENST00000287598;ENST00000412359;ENST00000442874	T;T	0.16073	2.37;2.38	6.04	6.04	0.98038	.	0.104145	0.42821	D	0.000653	T	0.39600	0.1084	M	0.65975	2.015	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.76575	0.988;0.972	T	0.06162	-1.0842	10	0.30078	T	0.28	-8.4442	15.1474	0.72667	0.0:0.0:0.0:1.0	.	322;308	O60566-3;O60566	.;BUB1B_HUMAN	P	308;322;254	ENSP00000287598:L308P;ENSP00000398470:L322P	ENSP00000287598:L308P	L	+	2	0	BUB1B	38264829	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.342000	0.52159	2.317000	0.78254	0.459000	0.35465	CTG		0.502	BUB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252122.4		
PLCB2	5330	broad.mit.edu	37	15	40582788	40582788	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr15:40582788C>T	ENST00000260402.3	-	29	3448	c.3199G>A	c.(3199-3201)Gcc>Acc	p.A1067T	PLCB2_ENST00000557821.1_Missense_Mutation_p.A1063T|PLCB2_ENST00000456256.2_Missense_Mutation_p.A1052T	NM_001284297.1|NM_004573.2	NP_001271226.1|NP_004564.2	Q00722	PLCB2_HUMAN	phospholipase C, beta 2	1067					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.A1063T(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)		CTCTCCTGGGCCATCTTGTCT	0.572																																					p.A1067T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3199A	15						.						219.0	229.0	226.0					15																	40582788		2011	4165	6176	38370080	SO:0001583	missense	5330	exon29				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.3199G>A	15.37:g.40582788C>T	ENSP00000260402:p.Ala1067Thr	Somatic		Capture	Illumina HiSeq	Phase_I	38370080	NM_004573	A8K6J2|B9EGH5	Missense_Mutation	SNP	ENST00000260402.3	37	CCDS42020.1	.	.	.	.	.	.	.	.	.	.	C	11.48	1.651822	0.29336	.	.	ENSG00000137841	ENST00000260402;ENST00000456256	T;T	0.45276	0.9;0.9	4.3	3.38	0.38709	PLC-beta, C-terminal (1);	0.286493	0.33253	N	0.005119	T	0.30603	0.0770	L	0.40543	1.245	0.80722	D	1	B;B;B	0.16802	0.015;0.004;0.019	B;B;B	0.11329	0.006;0.005;0.006	T	0.11743	-1.0575	10	0.49607	T	0.09	.	6.4731	0.22020	0.1795:0.7272:0.0:0.0933	.	1052;1063;1067	B9EGH5;Q00722-2;Q00722	.;.;PLCB2_HUMAN	T	1067;1052	ENSP00000260402:A1067T;ENSP00000411991:A1052T	ENSP00000260402:A1067T	A	-	1	0	PLCB2	38370080	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	1.624000	0.37018	0.997000	0.38969	0.561000	0.74099	GCC		0.572	PLCB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418430.1		
PLA2G4E	123745	broad.mit.edu	37	15	42294861	42294861	+	Silent	SNP	G	G	A	rs140988671	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr15:42294861G>A	ENST00000399518.3	-	6	1086	c.600C>T	c.(598-600)ggC>ggT	p.G200G	PLA2G4E_ENST00000413860.2_Silent_p.G171G	NM_001206670.1	NP_001193599.1	Q3MJ16	PA24E_HUMAN	phospholipase A2, group IVE	182					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|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)	cytosol (GO:0005829)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)	p.G171G(1)		NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|stomach(1)	16		all_cancers(109;8.09e-13)|all_epithelial(112;2.03e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.0273)		OV - Ovarian serous cystadenocarcinoma(18;7.61e-18)|GBM - Glioblastoma multiforme(94;3.07e-06)		CCACCAGCACGCCATTGGTGA	0.532													G|||	2	0.000399361	0.0	0.0014	5008	,	,		18103	0.0		0.001	False		,,,				2504	0.0				p.G171G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C513T	15						.						56.0	61.0	59.0					15																	42294861		1978	4140	6118	40082153	SO:0001819	synonymous_variant	123745	exon5				CCDS55962.1	15q15.1	2008-09-19			ENSG00000188089	ENSG00000188089	3.1.1.4		24791	protein-coding gene	gene with protein product						15866882	Standard	NM_001206670		Approved	FLJ45651	uc021sjp.1	Q3MJ16	OTTHUMG00000130371	ENST00000399518.3:c.600C>T	15.37:g.42294861G>A		Somatic		Capture	Illumina HiSeq	Phase_I	40082153	NM_001080490	Q6ZSC0	Silent	SNP	ENST00000399518.3	37	CCDS55962.1																																																																																				0.532	PLA2G4E-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252738.2	NM_198442	
CCNDBP1	23582	broad.mit.edu	37	15	43482281	43482281	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr15:43482281C>T	ENST00000300213.4	+	5	602	c.360C>T	c.(358-360)ggC>ggT	p.G120G	CCNDBP1_ENST00000356633.5_Intron|EPB42_ENST00000563128.1_Intron	NM_012142.4	NP_036274.3	O95273	CCDB1_HUMAN	cyclin D-type binding-protein 1	120	Interaction with RPLP0.|Interaction with TCF3.|Required for interaction with CCND1.				cell cycle (GO:0007049)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.G120G(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)	13		all_cancers(109;3.31e-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;8.42e-07)		TGGTACGGGGCGCCACCCTGG	0.507																																					p.G120G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C360T	15						.						81.0	73.0	76.0					15																	43482281		2203	4299	6502	41269573	SO:0001819	synonymous_variant	23582	exon5			AF082569	CCDS10092.1	15q14-q15	2008-07-18			ENSG00000166946	ENSG00000166946			1587	protein-coding gene	gene with protein product	"""D-type cyclin-interacting protein 1"", ""MAID protein"", ""HHM Protein"", ""grap2 cyclin interacting protein"""	607089				10801854	Standard	NM_012142		Approved	DIP1, GCIP	uc001zqv.3	O95273	OTTHUMG00000130703	ENST00000300213.4:c.360C>T	15.37:g.43482281C>T		Somatic		Capture	Illumina HiSeq	Phase_I	41269573	NM_012142	A8K3Q0|A8K3U2|Q6ZQN9|Q7Z519|Q8NBS7|Q8NBY2|Q9NS19|Q9NYH3|Q9UHX9	Silent	SNP	ENST00000300213.4	37	CCDS10092.1																																																																																				0.507	CCNDBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253203.1	NM_012142	
ZSCAN29	146050	broad.mit.edu	37	15	43656467	43656467	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr15:43656467C>T	ENST00000396976.2	-	4	1470	c.1336G>A	c.(1336-1338)Gct>Act	p.A446T	ZSCAN29_ENST00000396972.1_Intron|ZSCAN29_ENST00000562072.1_Missense_Mutation_p.A445T|ZSCAN29_ENST00000568898.1_Intron	NM_152455.3	NP_689668.3	Q8IWY8	ZSC29_HUMAN	zinc finger and SCAN domain containing 29	446					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)	p.A446T(1)		cervix(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(7)|skin(2)	24		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-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;8.97e-07)		AACCTCTCAGCCACTGCTCCA	0.478																																					p.A446T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1336A	15						.						100.0	96.0	97.0					15																	43656467		2201	4299	6500	41443759	SO:0001583	missense	146050	exon4			AF525399	CCDS10095.2	15q15.3	2013-01-08	2007-03-08	2007-03-08	ENSG00000140265	ENSG00000140265		"""-"", ""Zinc fingers, C2H2-type"""	26673	protein-coding gene	gene with protein product			"""zinc finger protein 690"""	ZNF690		12434312	Standard	NM_152455		Approved	FLJ35867, Zfp690	uc001zrk.1	Q8IWY8	OTTHUMG00000130767	ENST00000396976.2:c.1336G>A	15.37:g.43656467C>T	ENSP00000380174:p.Ala446Thr	Somatic		Capture	Illumina HiSeq	Phase_I	41443759	NM_152455	B3KVB9|Q32M75|Q32M76|Q8NA40	Missense_Mutation	SNP	ENST00000396976.2	37	CCDS10095.2	.	.	.	.	.	.	.	.	.	.	C	27.1	4.798210	0.90538	.	.	ENSG00000140265	ENST00000396976	T	0.54279	0.58	5.22	5.22	0.72569	.	0.000000	0.64402	D	0.000003	T	0.77896	0.4199	M	0.91406	3.205	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.997	T	0.80322	-0.1431	10	0.42905	T	0.14	-8.0138	16.3111	0.82872	0.0:1.0:0.0:0.0	.	445;446	C9K0J8;Q8IWY8	.;ZSC29_HUMAN	T	446	ENSP00000380174:A446T	ENSP00000380174:A446T	A	-	1	0	ZSCAN29	41443759	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.576000	0.53878	2.715000	0.92844	0.655000	0.94253	GCT		0.478	ZSCAN29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253278.1	NM_152455	
ZNF280D	54816	broad.mit.edu	37	15	56970878	56970878	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr15:56970878C>T	ENST00000267807.7	-	11	1362	c.1146G>A	c.(1144-1146)acG>acA	p.T382T	ZNF280D_ENST00000559237.1_Silent_p.T369T|ZNF280D_ENST00000559000.1_Silent_p.T369T|ZNF280D_ENST00000396245.1_Silent_p.T86T	NM_017661.2	NP_060131.2	Q6N043	Z280D_HUMAN	zinc finger protein 280D	382					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.T382T(1)		endometrium(5)|kidney(4)|large_intestine(7)|lung(12)|ovary(1)|skin(1)	30				all cancers(107;0.0399)|GBM - Glioblastoma multiforme(80;0.0787)		ATTCATGGGGCGTATGTGTAC	0.393																																					p.T382T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1146A	15						.						167.0	146.0	153.0					15																	56970878		2192	4292	6484	54758170	SO:0001819	synonymous_variant	54816	exon11			AB046804	CCDS32245.1, CCDS42041.1, CCDS58364.1	15q21.2	2008-05-02	2007-09-20	2007-09-20					25953	protein-coding gene	gene with protein product			"""suppressor of hairy wing homolog 4 (Drosophila)"""	SUHW4		10997877	Standard	XM_005254481		Approved	FLJ20086, ZNF634	uc002adu.3	Q6N043		ENST00000267807.7:c.1146G>A	15.37:g.56970878C>T		Somatic		Capture	Illumina HiSeq	Phase_I	54758170	NM_017661	A1L495|B2RMT6|Q6MZM6|Q6N085|Q6P2R6|Q7Z6J5|Q9H0U5|Q9HCI8|Q9NXS0	Silent	SNP	ENST00000267807.7	37	CCDS32245.1																																																																																				0.393	ZNF280D-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418891.2	XM_370867	
CA12	771	broad.mit.edu	37	15	63637685	63637685	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr15:63637685G>A	ENST00000178638.3	-	4	860	c.420C>T	c.(418-420)ttC>ttT	p.F140F	CA12_ENST00000422263.2_Silent_p.F80F|CA12_ENST00000344366.3_Silent_p.F140F	NM_001218.3	NP_001209.1	O43570	CAH12_HUMAN	carbonic anhydrase XII	140					bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)	p.F140F(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(2)	16					Benzthiazide(DB00562)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Zonisamide(DB00909)	CCTCGGCGGCGAAGTGCTGTC	0.642																																					p.F140F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C420T	15						.						52.0	49.0	50.0					15																	63637685		2203	4300	6503	61424738	SO:0001819	synonymous_variant	771	exon4			AF051882	CCDS10185.1, CCDS10186.1	15q22	2004-01-19			ENSG00000074410	ENSG00000074410		"""Carbonic anhydrases"""	1371	protein-coding gene	gene with protein product		603263				9636197	Standard	NM_001218		Approved	HsT18816	uc002amc.3	O43570	OTTHUMG00000132881	ENST00000178638.3:c.420C>T	15.37:g.63637685G>A		Somatic		Capture	Illumina HiSeq	Phase_I	61424738	NM_001218	B2RE24|Q53YE5|Q9BWG2	Silent	SNP	ENST00000178638.3	37	CCDS10185.1																																																																																				0.642	CA12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256370.1	NM_001218	
DPP8	54878	broad.mit.edu	37	15	65766554	65766554	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr15:65766554C>T	ENST00000341861.5	-	12	3157	c.1577G>A	c.(1576-1578)gGa>gAa	p.G526E	DPP8_ENST00000321118.7_Missense_Mutation_p.G526E|DPP8_ENST00000358939.4_Missense_Mutation_p.G510E|DPP8_ENST00000321147.6_Missense_Mutation_p.G526E|DPP8_ENST00000559233.1_Missense_Mutation_p.G526E|DPP8_ENST00000300141.6_Missense_Mutation_p.G510E|DPP8_ENST00000339244.5_Intron	NM_197960.2	NP_932064.1	Q6V1X1	DPP8_HUMAN	dipeptidyl-peptidase 8	526					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.G510E(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						TACATTAGATCCATGCCGGCC	0.343																																					p.G510E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1529A	15						.						99.0	90.0	93.0					15																	65766554		2201	4299	6500	63553607	SO:0001583	missense	54878	exon12			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.1577G>A	15.37:g.65766554C>T	ENSP00000339208:p.Gly526Glu	Somatic		Capture	Illumina HiSeq	Phase_I	63553607	NM_017743	Q7Z4C8|Q7Z4D3|Q7Z4E1|Q8IWG7|Q8NEM5|Q96JX1|Q9HBM2|Q9HBM3|Q9HBM4|Q9HBM5|Q9NXF4	Missense_Mutation	SNP	ENST00000341861.5	37	CCDS10207.1	.	.	.	.	.	.	.	.	.	.	C	19.92	3.917052	0.73098	.	.	ENSG00000074603	ENST00000341861;ENST00000358939;ENST00000300141;ENST00000321147;ENST00000321118;ENST00000395652	T;T;T;T;T;T	0.29655	1.56;1.56;1.56;1.56;1.56;1.56	4.64	4.64	0.57946	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.000000	0.64402	D	0.000002	T	0.54271	0.1848	M	0.68317	2.08	0.80722	D	1	D;B;D;D	0.71674	0.997;0.033;0.971;0.998	D;B;P;D	0.70227	0.947;0.018;0.89;0.968	T	0.57974	-0.7718	10	0.56958	D	0.05	-3.5847	17.8789	0.88834	0.0:1.0:0.0:0.0	.	510;510;526;526	Q6V1X1-3;Q6V1X1-4;Q6V1X1-2;Q6V1X1	.;.;.;DPP8_HUMAN	E	526;510;510;526;526;526	ENSP00000339208:G526E;ENSP00000351817:G510E;ENSP00000300141:G510E;ENSP00000318111:G526E;ENSP00000316373:G526E;ENSP00000379013:G526E	ENSP00000300141:G510E	G	-	2	0	DPP8	63553607	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.351000	0.79395	2.285000	0.76669	0.491000	0.48974	GGA		0.343	DPP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256847.1	NM_017743	
CCDC33	80125	broad.mit.edu	37	15	74622573	74622573	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr15:74622573A>G	ENST00000398814.3	+	12	1765	c.1334A>G	c.(1333-1335)gAc>gGc	p.D445G	CCDC33_ENST00000321288.5_Missense_Mutation_p.D648G|CCDC33_ENST00000558821.1_Missense_Mutation_p.D38G|CCDC33_ENST00000268082.4_Missense_Mutation_p.D38G	NM_025055.3	NP_079331.3	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33	648								p.D445G(1)		breast(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						ATGGCAGAGGACATCCTGTCT	0.622																																					p.D445G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1334G	15						.						39.0	46.0	44.0					15																	74622573		2038	4188	6226	72409626	SO:0001583	missense	80125	exon12			BC025689	CCDS42058.1, CCDS42059.1, CCDS73753.1	15q24.1	2009-08-06				ENSG00000140481			26552	protein-coding gene	gene with protein product	"""cancer/testis antigen 61"""					12477932	Standard	NM_025055		Approved	FLJ32855, CT61	uc002axo.4	Q8N5R6		ENST00000398814.3:c.1334A>G	15.37:g.74622573A>G	ENSP00000381795:p.Asp445Gly	Somatic		Capture	Illumina HiSeq	Phase_I	72409626	NM_025055	A8K3U4|A8MPQ6|A8MV61|A8MVU9|B3KQ49|Q8TAX6|Q9H5Q6	Missense_Mutation	SNP	ENST00000398814.3	37	CCDS42058.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.198856	0.79015	.	.	ENSG00000140481	ENST00000321288;ENST00000398814;ENST00000321374;ENST00000268082	T;T;T;T	0.37584	1.28;1.58;1.24;1.19	4.69	4.69	0.59074	.	0.000000	0.85682	D	0.000000	T	0.60405	0.2266	M	0.80616	2.505	0.41898	D	0.990404	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.999;0.996;0.998	T	0.66496	-0.5909	10	0.87932	D	0	.	11.6967	0.51548	1.0:0.0:0.0:0.0	.	38;38;648;445	Q8N5R6-4;Q8N5R6-5;C9JFX2;Q8N5R6-6	.;.;.;.	G	648;445;38;38	ENSP00000325012:D648G;ENSP00000381795:D445G;ENSP00000325661:D38G;ENSP00000268082:D38G	ENSP00000268082:D38G	D	+	2	0	CCDC33	72409626	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	4.495000	0.60353	1.757000	0.51966	0.523000	0.50628	GAC		0.622	CCDC33-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419491.2	NM_182791	
CYP1A2	1544	broad.mit.edu	37	15	75047188	75047188	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr15:75047188G>A	ENST00000343932.4	+	7	1373	c.1310G>A	c.(1309-1311)gGc>gAc	p.G437D		NM_000761.3	NP_000752.2	P05177	CP1A2_HUMAN	cytochrome P450, family 1, subfamily A, polypeptide 2	437					alkaloid metabolic process (GO:0009820)|arachidonic acid metabolic process (GO:0019369)|cellular respiration (GO:0045333)|cellular response to cadmium ion (GO:0071276)|dibenzo-p-dioxin metabolic process (GO:0018894)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|heterocycle metabolic process (GO:0046483)|hydrogen peroxide biosynthetic process (GO:0050665)|lung development (GO:0030324)|methylation (GO:0032259)|monocarboxylic acid metabolic process (GO:0032787)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|oxidative deethylation (GO:0071615)|oxidative demethylation (GO:0070989)|porphyrin-containing compound metabolic process (GO:0006778)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)|response to estradiol (GO:0032355)|response to lipopolysaccharide (GO:0032496)|small molecule metabolic process (GO:0044281)|steroid catabolic process (GO:0006706)|toxin biosynthetic process (GO:0009403)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|caffeine oxidase activity (GO:0034875)|demethylase activity (GO:0032451)|electron carrier activity (GO:0009055)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)	p.G437D(1)		breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	33					"""""""Insulin(DB00071)|Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Agomelatine(DB06594)|Albendazole(DB00518)|Alitretinoin(DB00523)|Almotriptan(DB00918)|Alosetron(DB00969)|Aminoglutethimide(DB00357)|Aminophenazone(DB01424)|Aminophylline(DB01223)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Anagrelide(DB00261)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Asenapine(DB06216)|Atropine(DB00572)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzyl alcohol(DB06770)|Betaxolol(DB00195)|Bortezomib(DB00188)|Bromazepam(DB01558)|Bromocriptine(DB01200)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Caffeine(DB00201)|Carbamazepine(DB00564)|Carmustine(DB00262)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clenbuterol(DB01407)|Clevidipine(DB04920)|Clobetasol propionate(DB01013)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Conjugated Estrogens(DB00286)|Cyclobenzaprine(DB00924)|Dacarbazine(DB00851)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Diazepam(DB00829)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Domperidone(DB01184)|Dopamine(DB00988)|Doxepin(DB01142)|Duloxetine(DB00476)|Edetic Acid(DB00974)|Efavirenz(DB00625)|Eltrombopag(DB06210)|Enoxacin(DB00467)|Epinephrine(DB00668)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estrone(DB00655)|Estropipate(DB04574)|Ethanol(DB00898)|Etoposide(DB00773)|Etoricoxib(DB01628)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Frovatriptan(DB00998)|Gemfibrozil(DB01241)|Griseofulvin(DB00400)|Guanabenz(DB00629)|Haloperidol(DB00502)|Hesperetin(DB01094)|Hexobarbital(DB01355)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Imiquimod(DB00724)|inhaled insulin(DB05278)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Levobupivacaine(DB01002)|Levofloxacin(DB01137)|Lidocaine(DB00281)|Lomefloxacin(DB00978)|Lopinavir(DB01601)|Lorcaserin(DB04871)|Losartan(DB00678)|Lumiracoxib(DB01283)|Malathion(DB00772)|Maprotiline(DB00934)|Meclizine(DB00737)|Melatonin(DB01065)|Menadione(DB00170)|Methadone(DB00333)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Modafinil(DB00745)|Nabumetone(DB00461)|Nafcillin(DB00607)|Naproxen(DB00788)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niclosamide(DB06803)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitric Oxide(DB00435)|Nitroprusside(DB00325)|Norepinephrine(DB00368)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ofloxacin(DB01165)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxaliplatin(DB00526)|Oxtriphylline(DB01303)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Pefloxacin(DB00487)|Pentamidine(DB00738)|Pentoxifylline(DB00806)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phentermine(DB00191)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Pimozide(DB01100)|Pipotiazine(DB01621)|Pomalidomide(DB08910)|Praziquantel(DB01058)|Primaquine(DB01087)|Primidone(DB00794)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Pyrazinamide(DB00339)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ramelteon(DB00980)|Ranitidine(DB00863)|Rasagiline(DB01367)|Rifabutin(DB00615)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Riluzole(DB00740)|Ritonavir(DB00503)|Rizatriptan(DB00953)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Roxithromycin(DB00778)|Secobarbital(DB00418)|Selegiline(DB01037)|Sertraline(DB01104)|SIMEPREVIR(DB06290)|Sorafenib(DB00398)|Streptozocin(DB00428)|Sulindac(DB00605)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Tenofovir(DB00300)|Terbinafine(DB00857)|Thalidomide(DB01041)|Theobromine(DB01412)|Theophylline(DB00277)|Thiabendazole(DB00730)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tizanidine(DB00697)|Tocainide(DB01056)|Toremifene(DB00539)|Tranylcypromine(DB00752)|Triamterene(DB00384)|Trifluoperazine(DB00831)|Valproic Acid(DB00313)|Vemurafenib(DB08881)|Verapamil(DB00661)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zileuton(DB00744)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)|Zolpidem(DB00425)"""	ACCGCCGATGGCACTGCCATT	0.597																																					p.G437D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1310A	15						.						101.0	94.0	97.0					15																	75047188		2197	4296	6493	72834241	SO:0001583	missense	1544	exon7			AF182274	CCDS32293.1	15q24.1	2013-11-11	2003-01-14		ENSG00000140505	ENSG00000140505	1.14.14.1	"""Cytochrome P450s"""	2596	protein-coding gene	gene with protein product		124060	"""cytochrome P450, subfamily I (aromatic compound-inducible), polypeptide 2"""			15128046	Standard	NM_000761		Approved	P3-450, CP12	uc002ayr.1	P05177	OTTHUMG00000172901	ENST00000343932.4:c.1310G>A	15.37:g.75047188G>A	ENSP00000342007:p.Gly437Asp	Somatic		Capture	Illumina HiSeq	Phase_I	72834241	NM_000761	Q16754|Q6NWU5|Q9BXX7|Q9UK49	Missense_Mutation	SNP	ENST00000343932.4	37	CCDS32293.1	.	.	.	.	.	.	.	.	.	.	G	10.34	1.322610	0.23994	.	.	ENSG00000140505	ENST00000343932	T	0.71341	-0.56	4.42	2.39	0.29439	.	0.102480	0.64402	D	0.000002	T	0.70413	0.3221	M	0.84846	2.72	0.52501	D	0.999951	B	0.14012	0.009	B	0.20577	0.03	T	0.66968	-0.5789	10	0.66056	D	0.02	.	7.8511	0.29455	0.2294:0.0:0.7706:0.0	.	437	P05177-2	.	D	437	ENSP00000342007:G437D	ENSP00000342007:G437D	G	+	2	0	CYP1A2	72834241	0.990000	0.36364	0.001000	0.08648	0.038000	0.13279	2.596000	0.46205	0.380000	0.24823	0.455000	0.32223	GGC		0.597	CYP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421263.2	NM_000761	
KIAA1024	23251	broad.mit.edu	37	15	79750663	79750663	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr15:79750663G>A	ENST00000305428.3	+	2	2249	c.2174G>A	c.(2173-2175)aGc>aAc	p.S725N		NM_015206.2	NP_056021.1	Q9UPX6	K1024_HUMAN	KIAA1024	725						integral component of membrane (GO:0016021)		p.S725N(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(2)|pancreas(2)|prostate(1)	49						AAAATTGCCAGCATCTCCAAC	0.512																																					p.S725N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2174A	15						.						86.0	82.0	83.0					15																	79750663		2196	4293	6489	77537718	SO:0001583	missense	23251	exon2			AB028947	CCDS32306.1	15q25.1	2007-12-12				ENSG00000169330			29172	protein-coding gene	gene with protein product						10470851	Standard	NM_015206		Approved		uc002bew.1	Q9UPX6		ENST00000305428.3:c.2174G>A	15.37:g.79750663G>A	ENSP00000307461:p.Ser725Asn	Somatic		Capture	Illumina HiSeq	Phase_I	77537718	NM_015206	A7MD43	Missense_Mutation	SNP	ENST00000305428.3	37	CCDS32306.1	.	.	.	.	.	.	.	.	.	.	G	17.54	3.416320	0.62511	.	.	ENSG00000169330	ENST00000305428	T	0.35236	1.32	5.68	5.68	0.88126	.	0.183165	0.56097	D	0.000024	T	0.34571	0.0902	L	0.48642	1.525	0.58432	D	0.999993	P	0.42692	0.787	B	0.37091	0.241	T	0.06954	-1.0798	9	.	.	.	.	19.7911	0.96458	0.0:0.0:1.0:0.0	.	725	Q9UPX6	K1024_HUMAN	N	725	ENSP00000307461:S725N	.	S	+	2	0	KIAA1024	77537718	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	5.070000	0.64376	2.681000	0.91329	0.655000	0.94253	AGC		0.512	KIAA1024-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416718.1	NM_015206	
IL16	3603	broad.mit.edu	37	15	81571914	81571914	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr15:81571914C>T	ENST00000302987.4	+	7	880	c.880C>T	c.(880-882)Ctc>Ttc	p.L294F	IL16_ENST00000394660.2_Missense_Mutation_p.L294F			Q14005	IL16_HUMAN	interleukin 16	294	Interaction with GRIN2A.|PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.L294F(2)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						CAAAAAGGGGCTCCTCACCCT	0.562																																					p.L294F												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C880T	15						.						24.0	26.0	25.0					15																	81571914		1932	4128	6060	79358969	SO:0001583	missense	3603	exon8			U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"""Interleukins and interleukin receptors"""	5980	protein-coding gene	gene with protein product	"""prointerleukin 16"", ""lymphocyte chemoattractant factor"""	603035	"""interleukin 16 (lymphocyte chemoattractant factor)"""			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.880C>T	15.37:g.81571914C>T	ENSP00000302935:p.Leu294Phe	Somatic		Capture	Illumina HiSeq	Phase_I	79358969	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Missense_Mutation	SNP	ENST00000302987.4	37	CCDS42069.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.173349	0.78452	.	.	ENSG00000172349	ENST00000394655;ENST00000394660;ENST00000355368;ENST00000302987	T;T	0.27557	1.66;1.66	4.96	4.96	0.65561	PDZ/DHR/GLGF (4);	0.000000	0.39407	N	0.001362	T	0.47600	0.1454	L	0.46157	1.445	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.77557	0.99;0.982	T	0.36890	-0.9729	10	0.51188	T	0.08	.	14.0617	0.64804	0.0:0.8492:0.1508:0.0	.	294;294	Q14005;Q14005-2	IL16_HUMAN;.	F	294;294;126;294	ENSP00000378155:L294F;ENSP00000302935:L294F	ENSP00000302935:L294F	L	+	1	0	IL16	79358969	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.190000	0.50973	2.570000	0.86706	0.591000	0.81541	CTC		0.562	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217	
WHAMM	123720	broad.mit.edu	37	15	83499641	83499641	+	Silent	SNP	T	T	A	rs200993177|rs369423285	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr15:83499641T>A	ENST00000286760.4	+	9	2031	c.1932T>A	c.(1930-1932)ccT>ccA	p.P644P		NM_001080435.1	NP_001073904.1	Q8TF30	WHAMM_HUMAN	WAS protein homolog associated with actin, golgi membranes and microtubules	644	Mediates actin nucleation. {ECO:0000269|PubMed:18614018}.|Pro-rich.				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.P644P(4)		endometrium(6)|large_intestine(5)|lung(1)|prostate(1)	13						ctcctcctcctccaccaccac	0.562																																					p.P644P												.	.	4	Substitution - coding silent(4)	large_intestine(2)|endometrium(2)	c.T1932A	15						.						22.0	24.0	23.0					15																	83499641		1914	4096	6010	81296695	SO:0001819	synonymous_variant	123720	exon9			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.1932T>A	15.37:g.83499641T>A		Somatic		Capture	Illumina HiSeq	Phase_I	81296695	NM_001080435	Q8N1J9	Silent	SNP	ENST00000286760.4	37	CCDS45333.1																																																																																				0.562	WHAMM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418463.1		
SLC28A1	9154	broad.mit.edu	37	15	85478574	85478574	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr15:85478574G>A	ENST00000286749.3	+	14	1496	c.1406G>A	c.(1405-1407)cGg>cAg	p.R469Q	SLC28A1_ENST00000394573.1_Missense_Mutation_p.R469Q|SLC28A1_ENST00000537624.1_Missense_Mutation_p.R469Q|SLC28A1_ENST00000537216.1_Missense_Mutation_p.R469Q|SLC28A1_ENST00000538177.1_Intron			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	469					nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside transmembrane transporter activity (GO:0005337)|nucleoside:sodium symporter activity (GO:0005415)	p.R469Q(1)		breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	41			BRCA - Breast invasive adenocarcinoma(143;0.0587)		Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495)	TACATCCTGCGGCCTGTAGCC	0.602																																					p.R469Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1406A	15						.						109.0	88.0	95.0					15																	85478574		2203	4299	6502	83279578	SO:0001583	missense	9154	exon15			U62967	CCDS10334.1, CCDS10335.1, CCDS73777.1	15q25.3	2013-07-17	2013-07-17		ENSG00000156222	ENSG00000156222		"""Solute carriers"""	11001	protein-coding gene	gene with protein product		606207	"""solute carrier family 28 (sodium-coupled nucleoside transporter), member 1"""			9124315	Standard	NM_004213		Approved	CNT1	uc002blg.3	O00337	OTTHUMG00000148668	ENST00000286749.3:c.1406G>A	15.37:g.85478574G>A	ENSP00000286749:p.Arg469Gln	Somatic		Capture	Illumina HiSeq	Phase_I	83279578	NM_004213	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Missense_Mutation	SNP	ENST00000286749.3	37	CCDS10334.1	.	.	.	.	.	.	.	.	.	.	G	15.70	2.909690	0.52439	.	.	ENSG00000156222	ENST00000537216;ENST00000537624;ENST00000286749;ENST00000394573	T;T;T;T	0.06528	3.29;3.29;3.29;3.29	5.12	5.12	0.69794	Na dependent nucleoside transporter, C-terminal (1);	0.047516	0.85682	D	0.000000	T	0.07954	0.0199	L	0.56396	1.775	0.80722	D	1	P;B;P	0.39903	0.694;0.131;0.471	B;B;B	0.35770	0.21;0.04;0.21	T	0.07712	-1.0758	10	0.42905	T	0.14	-28.0831	11.0516	0.47894	0.0:0.0:0.815:0.185	.	469;469;469	B7Z533;F5H560;O00337	.;.;S28A1_HUMAN	Q	469	ENSP00000440546:R469Q;ENSP00000444700:R469Q;ENSP00000286749:R469Q;ENSP00000378074:R469Q	ENSP00000286749:R469Q	R	+	2	0	SLC28A1	83279578	1.000000	0.71417	1.000000	0.80357	0.777000	0.43975	5.175000	0.65021	2.663000	0.90544	0.400000	0.26472	CGG		0.602	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2		
TICRR	90381	broad.mit.edu	37	15	90143884	90143884	+	Silent	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr15:90143884A>G	ENST00000268138.7	+	9	2226	c.2121A>G	c.(2119-2121)ggA>ggG	p.G707G	TICRR_ENST00000560985.1_Silent_p.G706G			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	707					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.G707G(1)									AGAATCTAGGAAAAAAACTGG	0.299																																					p.G707G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A2121G	15						.						40.0	37.0	38.0					15																	90143884		1803	4069	5872	87944888	SO:0001819	synonymous_variant	90381	exon9			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.2121A>G	15.37:g.90143884A>G		Somatic		Capture	Illumina HiSeq	Phase_I	87944888	NM_152259	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Silent	SNP	ENST00000268138.7	37	CCDS10352.2																																																																																				0.299	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259	
SV2B	9899	broad.mit.edu	37	15	91832844	91832844	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr15:91832844G>A	ENST00000394232.1	+	12	2272	c.1802G>A	c.(1801-1803)gGg>gAg	p.G601E	SV2B_ENST00000545111.2_Missense_Mutation_p.G450E|SV2B_ENST00000330276.4_Missense_Mutation_p.G601E	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	601					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)	p.G601E(1)		NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(17)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			CTGTTCTGTGGGACAAGCATT	0.532																																					p.G601E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1802A	15						.						161.0	135.0	144.0					15																	91832844		2198	4298	6496	89633848	SO:0001583	missense	9899	exon13			AB018278	CCDS10370.1, CCDS53972.1	15q26.1	2005-01-10			ENSG00000185518	ENSG00000185518			16874	protein-coding gene	gene with protein product		185861				9872452, 7681585	Standard	NM_014848		Approved	KIAA0735, HsT19680	uc002bqv.3	Q7L1I2	OTTHUMG00000149833	ENST00000394232.1:c.1802G>A	15.37:g.91832844G>A	ENSP00000377779:p.Gly601Glu	Somatic		Capture	Illumina HiSeq	Phase_I	89633848	NM_014848	B4DH30|C6G489|O94840|Q6IAR8	Missense_Mutation	SNP	ENST00000394232.1	37	CCDS10370.1	.	.	.	.	.	.	.	.	.	.	.	33	5.277895	0.95459	.	.	ENSG00000185518	ENST00000545111;ENST00000394232;ENST00000330276	T;T;T	0.61859	0.07;0.07;0.07	5.46	5.46	0.80206	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.78786	0.4338	M	0.85777	2.775	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.77435	-0.2589	10	0.33940	T	0.23	-24.647	18.3099	0.90195	0.0:0.0:1.0:0.0	.	601	Q7L1I2	SV2B_HUMAN	E	450;601;601	ENSP00000443243:G450E;ENSP00000377779:G601E;ENSP00000332818:G601E	ENSP00000332818:G601E	G	+	2	0	SV2B	89633848	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.396000	0.73234	2.731000	0.93534	0.650000	0.86243	GGG		0.532	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313494.3	NM_014848	
SLCO3A1	28232	broad.mit.edu	37	15	92669418	92669418	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr15:92669418C>T	ENST00000318445.6	+	6	1516	c.1302C>T	c.(1300-1302)tgC>tgT	p.C434C	SLCO3A1_ENST00000424469.2_Silent_p.C434C|SLCO3A1_ENST00000555549.1_3'UTR	NM_013272.3	NP_037404.2	Q9UIG8	SO3A1_HUMAN	solute carrier organic anion transporter family, member 3A1	434					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.C434C(1)		breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)|skin(2)	25	Lung NSC(78;0.0158)|all_lung(78;0.0255)		BRCA - Breast invasive adenocarcinoma(143;0.0841)		Alprostadil(DB00770)|Aminohippurate(DB00345)|Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Iloprost(DB01088)|Methotrexate(DB00563)	CCACTGCTTGCTACGTCTCCT	0.587																																					p.C434C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1302T	15						.						217.0	161.0	180.0					15																	92669418		2198	4298	6496	90470422	SO:0001819	synonymous_variant	28232	exon6			AB031050	CCDS10371.1, CCDS45354.1	15q26	2013-05-22	2003-11-25	2003-11-26	ENSG00000176463	ENSG00000176463		"""Solute carriers"""	10952	protein-coding gene	gene with protein product		612435	"""solute carrier family 21 (organic anion transporter), member 11"""	SLC21A11			Standard	NM_001145044		Approved	OATP-D, OATP3A1	uc002bqx.2	Q9UIG8	OTTHUMG00000149846	ENST00000318445.6:c.1302C>T	15.37:g.92669418C>T		Somatic		Capture	Illumina HiSeq	Phase_I	90470422	NM_013272	A8K4A7|B3KPY5|B3KUR7|C6G486|Q9BW73|Q9GZV2	Silent	SNP	ENST00000318445.6	37	CCDS10371.1																																																																																				0.587	SLCO3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313529.1	NM_013272	
PGPEP1L	145814	broad.mit.edu	37	15	99511878	99511878	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr15:99511878G>A	ENST00000378919.6	-	5	625	c.420C>T	c.(418-420)ggC>ggT	p.G140G	PGPEP1L_ENST00000535714.1_Silent_p.G86G|RP11-654A16.3_ENST00000559468.1_RNA	NM_001102612.2	NP_001096082.2	A6NFU8	PGPIL_HUMAN	pyroglutamyl-peptidase I-like	140							cysteine-type peptidase activity (GO:0008234)	p.G140G(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(2)|skin(1)|stomach(1)	14						GTGCCGCGCAGCCCTTTCCAT	0.542																																					p.G140G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C420T	15						.						27.0	28.0	27.0					15																	99511878		1998	4155	6153	97329401	SO:0001819	synonymous_variant	145814	exon5				CCDS53977.1, CCDS58400.1	15q26.3	2010-02-16			ENSG00000183571	ENSG00000183571			27080	protein-coding gene	gene with protein product							Standard	NM_001102612		Approved		uc002bum.3	A6NFU8		ENST00000378919.6:c.420C>T	15.37:g.99511878G>A		Somatic		Capture	Illumina HiSeq	Phase_I	97329401	NM_001102612	H0YF86	Missense_Mutation	SNP	ENST00000378919.6	37	CCDS53977.1																																																																																				0.542	PGPEP1L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415703.1	NM_001102612.2	
MEF2A	4205	broad.mit.edu	37	15	100215617	100215617	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr15:100215617C>T	ENST00000557785.1	+	7	973	c.624C>T	c.(622-624)agC>agT	p.S208S	MEF2A_ENST00000354410.5_Silent_p.S210S|MEF2A_ENST00000453228.2_Silent_p.S208S|MEF2A_ENST00000449277.2_Silent_p.S140S|MEF2A_ENST00000558812.1_Silent_p.S140S|MEF2A_ENST00000557942.1_Silent_p.S208S|MEF2A_ENST00000338042.6_Silent_p.S208S	NM_001171894.1	NP_001165365.1	Q02078	MEF2A_HUMAN	myocyte enhancer factor 2A	210					apoptotic process (GO:0006915)|cardiac conduction (GO:0061337)|cellular response to calcium ion (GO:0071277)|dendrite morphogenesis (GO:0048813)|ERK5 cascade (GO:0070375)|heart development (GO:0007507)|innate immune response (GO:0045087)|MAPK cascade (GO:0000165)|mitochondrial genome maintenance (GO:0000002)|mitochondrion distribution (GO:0048311)|muscle cell differentiation (GO:0042692)|muscle organ development (GO:0007517)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ventricular cardiac myofibril assembly (GO:0055005)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)	p.S210S(1)|p.S208S(1)		endometrium(2)|large_intestine(2)|lung(7)|ovary(1)	12	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00085)			GGATGTTGAGCACTACAGACC	0.433																																					p.S210S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C630T	15						.						161.0	168.0	166.0					15																	100215617		1955	4148	6103	98033140	SO:0001819	synonymous_variant	4205	exon7				CCDS45362.1, CCDS45363.1, CCDS53978.1, CCDS58401.1	15q26	2008-02-05	2007-04-24			ENSG00000068305		"""Myocyte enhancer factors"""	6993	protein-coding gene	gene with protein product		600660				1516833	Standard	NM_005587		Approved	RSRFC4, RSRFC9	uc002bvf.3	Q02078		ENST00000557785.1:c.624C>T	15.37:g.100215617C>T		Somatic		Capture	Illumina HiSeq	Phase_I	98033140	NM_005587	B4DFQ7|F6XG23|O43814|Q14223|Q14224|Q59GX4|Q7Z6C9|Q96D14	Silent	SNP	ENST00000557785.1	37	CCDS53978.1																																																																																				0.433	MEF2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415985.1		
ADAMTS17	170691	broad.mit.edu	37	15	100672242	100672242	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr15:100672242C>T	ENST00000268070.4	-	12	1796	c.1691G>A	c.(1690-1692)cGc>cAc	p.R564H	RP11-90E5.1_ENST00000560128.1_RNA	NM_139057.2	NP_620688.2	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 17	564	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R564H(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)	50	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)		CTGCCTGAAGCGGGCTCCCGT	0.632											OREG0023513	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R564H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1691A	15						.						60.0	61.0	61.0					15																	100672242		2203	4300	6503	98489765	SO:0001583	missense	170691	exon12			AJ315735	CCDS10383.1	15q24	2014-01-28	2005-08-19		ENSG00000140470	ENSG00000140470		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17109	protein-coding gene	gene with protein product		607511	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 17"""			11867212	Standard	NM_139057		Approved	FLJ32769, FLJ16363	uc002bvv.1	Q8TE56	OTTHUMG00000149867	ENST00000268070.4:c.1691G>A	15.37:g.100672242C>T	ENSP00000268070:p.Arg564His	Somatic	1353	Capture	Illumina HiSeq	Phase_I	98489765	NM_139057	Q2I7G4|Q6ZN75	Missense_Mutation	SNP	ENST00000268070.4	37	CCDS10383.1	.	.	.	.	.	.	.	.	.	.	C	16.66	3.186244	0.57909	.	.	ENSG00000140470	ENST00000268070;ENST00000378898	T	0.57907	0.37	5.24	5.24	0.73138	.	0.068715	0.64402	D	0.000018	T	0.43077	0.1231	N	0.21142	0.635	0.53688	D	0.999972	B;B	0.18863	0.021;0.031	B;B	0.14578	0.011;0.007	T	0.27088	-1.0084	10	0.48119	T	0.1	.	18.8106	0.92056	0.0:1.0:0.0:0.0	.	321;564	Q8TE56-2;Q8TE56	.;ATS17_HUMAN	H	564;321	ENSP00000268070:R564H	ENSP00000268070:R564H	R	-	2	0	ADAMTS17	98489765	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	3.386000	0.52492	2.423000	0.82170	0.561000	0.74099	CGC		0.632	ADAMTS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313595.1	NM_139057	
ADAMTS17	170691	broad.mit.edu	37	15	100802560	100802560	+	Silent	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr15:100802560A>G	ENST00000268070.4	-	5	975	c.870T>C	c.(868-870)cgT>cgC	p.R290R	ADAMTS17_ENST00000559976.1_5'Flank	NM_139057.2	NP_620688.2	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 17	290	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R290R(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)	50	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)		GACTTACGGGACGTTGTCGTA	0.478																																					p.R290R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T870C	15						.						153.0	146.0	148.0					15																	100802560		2203	4300	6503	98620083	SO:0001819	synonymous_variant	170691	exon5			AJ315735	CCDS10383.1	15q24	2014-01-28	2005-08-19		ENSG00000140470	ENSG00000140470		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17109	protein-coding gene	gene with protein product		607511	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 17"""			11867212	Standard	NM_139057		Approved	FLJ32769, FLJ16363	uc002bvv.1	Q8TE56	OTTHUMG00000149867	ENST00000268070.4:c.870T>C	15.37:g.100802560A>G		Somatic		Capture	Illumina HiSeq	Phase_I	98620083	NM_139057	Q2I7G4|Q6ZN75	Silent	SNP	ENST00000268070.4	37	CCDS10383.1																																																																																				0.478	ADAMTS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313595.1	NM_139057	
RAB40C	57799	broad.mit.edu	37	16	677579	677580	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:677579_677580insC	ENST00000248139.3	+	6	1006_1007	c.803_804insC	c.(802-807)agccccfs	p.SP268fs	RAB40C_ENST00000535977.1_Frame_Shift_Ins_p.SP268fs|RAB40C_ENST00000539661.1_Frame_Shift_Ins_p.SP268fs|RAB40C_ENST00000538492.1_Frame_Shift_Ins_p.SP268fs	NM_021168.4	NP_066991.3	Q96S21	RB40C_HUMAN	RAB40C, member RAS oncogene family	268					protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)	p.Q271fs*7(1)		NS(1)|endometrium(2)|large_intestine(1)|lung(1)|prostate(1)	6		Hepatocellular(780;0.0218)				CCACCCCAGAGCCCCCCCCAGA	0.678																																					p.S268fs	Melanoma(123;1631 1690 28262 44104 44957)											.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.803_804insC	16						.																																			617581	SO:0001589	frameshift_variant	57799	exon7			Z84779	CCDS10413.1	16p13.3	2008-07-28	2003-10-14		ENSG00000197562	ENSG00000197562		"""RAB, member RAS oncogene"""	18285	protein-coding gene	gene with protein product			"""RAS-like, family 8, member C"""	RASL8C		11697911, 18485483	Standard	NM_021168		Approved	RARL	uc021szv.1	Q96S21	OTTHUMG00000047854	ENST00000248139.3:c.811dupC	16.37:g.677587_677587dupC	ENSP00000248139:p.Ser268fs	Somatic		Capture	Illumina HiSeq	Phase_I	617580	NM_001172664	A2IDE2|D3DU54|O60795|Q4TT41|Q5PXE8|Q6PIU5	Frame_Shift_Ins	INS	ENST00000248139.3	37	CCDS10413.1																																																																																				0.678	RAB40C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109079.4	NM_021168	
NOMO1	23420	broad.mit.edu	37	16	14976480	14976480	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:14976480G>T	ENST00000287667.7	+	26	3228	c.3057G>T	c.(3055-3057)aaG>aaT	p.K1019N		NM_014287.3	NP_055102.3	Q15155	NOMO1_HUMAN	NODAL modulator 1	1019						integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)	p.K1019N(1)		endometrium(6)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|skin(2)	30						TTCAGCTCAAGGCAGAAGGCA	0.582																																					p.K1019N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3057T	16						.						53.0	55.0	54.0					16																	14976480		1988	4002	5990	14883981	SO:0001583	missense	23420	exon26			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.3057G>T	16.37:g.14976480G>T	ENSP00000287667:p.Lys1019Asn	Somatic		Capture	Illumina HiSeq	Phase_I	14883981	NM_014287	P78421|Q8IW21|Q96DG0	Missense_Mutation	SNP	ENST00000287667.7	37	CCDS10556.1	.	.	.	.	.	.	.	.	.	.	.	11.64	1.699230	0.30142	.	.	ENSG00000103512	ENST00000287667;ENST00000456867;ENST00000536948	T	0.36878	1.23	2.91	2.91	0.33838	Carbohydrate-binding-like fold (1);Immunoglobulin-like fold (1);	0.061256	0.64402	D	0.000004	T	0.20577	0.0495	L	0.39898	1.24	0.46149	D	0.998895	P	0.38335	0.627	B	0.29663	0.105	T	0.03493	-1.1031	10	0.25751	T	0.34	-26.3279	5.9584	0.19286	0.1486:0.0:0.8514:0.0	.	1019	Q15155	NOMO1_HUMAN	N	1019;1019;852	ENSP00000287667:K1019N	ENSP00000287667:K1019N	K	+	3	2	NOMO1	14883981	1.000000	0.71417	1.000000	0.80357	0.539000	0.34962	3.853000	0.55941	1.628000	0.50416	0.184000	0.17185	AAG		0.582	NOMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207065.1		
ERI2	112479	broad.mit.edu	37	16	20814829	20814829	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:20814829A>C	ENST00000357967.4	-	3	143	c.101T>G	c.(100-102)tTt>tGt	p.F34C	ERI2_ENST00000563117.1_5'UTR|ERI2_ENST00000564349.1_5'UTR|AC004381.6_ENST00000261377.6_5'Flank|ERI2_ENST00000568251.1_5'Flank|ERI2_ENST00000300005.3_Missense_Mutation_p.F34C|ERI2_ENST00000569729.1_Missense_Mutation_p.F34C|ERI2_ENST00000389345.5_5'UTR	NM_001142725.1	NP_001136197.1	A8K979	ERI2_HUMAN	ERI1 exoribonuclease family member 2	34							exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.F34C(2)		endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|prostate(2)	11						TAAGTAGTCAAACAACTGCTC	0.398																																					p.F34C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T101G	16						.						87.0	72.0	77.0					16																	20814829		2201	4300	6501	20722330	SO:0001583	missense	112479	exon3			BC010503	CCDS10590.1, CCDS45436.1	16p12.3	2014-02-18	2009-10-07	2008-12-16	ENSG00000196678	ENSG00000196678		"""Enhanced RNAi three prime mRNA exonucleases"""	30541	protein-coding gene	gene with protein product	"""enhanced RNAi three prime mRNA exonuclease homolog 2 (C.elegans)"", ""exoribonuclease 2"", ""zinc finger, GRF-type containing 5"""		"""exonuclease domain containing 1"""	EXOD1		10819331	Standard	NM_080663		Approved	KIAA1504, MGC16943, ZGRF5	uc010vbb.1	A8K979	OTTHUMG00000131557	ENST00000357967.4:c.101T>G	16.37:g.20814829A>C	ENSP00000350651:p.Phe34Cys	Somatic		Capture	Illumina HiSeq	Phase_I	20722330	NM_080663	Q6ZSJ2|Q96FR9|Q9P224|Q9Y6V3	Missense_Mutation	SNP	ENST00000357967.4	37	CCDS45436.1	.	.	.	.	.	.	.	.	.	.	A	19.48	3.834845	0.71373	.	.	ENSG00000196678	ENST00000300005;ENST00000357967	T;T	0.45276	0.9;0.9	5.76	3.49	0.39957	Ribonuclease H-like (1);	0.106284	0.64402	D	0.000004	T	0.47544	0.1451	L	0.27053	0.805	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	P;D;D	0.71184	0.879;0.944;0.972	T	0.44003	-0.9356	10	0.87932	D	0	-8.6229	9.9509	0.41638	0.6855:0.0:0.0:0.3145	.	34;34;34	A8K979;A8K979-3;A8K979-4	ERI2_HUMAN;.;.	C	34	ENSP00000300005:F34C;ENSP00000350651:F34C	ENSP00000300005:F34C	F	-	2	0	ERI2	20722330	1.000000	0.71417	0.995000	0.50966	0.995000	0.86356	4.131000	0.57970	0.418000	0.25898	0.533000	0.62120	TTT		0.398	ERI2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_080663	
LYRM1	57149	broad.mit.edu	37	16	20926937	20926937	+	Silent	SNP	G	G	A	rs147140909	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:20926937G>A	ENST00000396052.2	+	4	460	c.60G>A	c.(58-60)gcG>gcA	p.A20A	LYRM1_ENST00000219168.4_Silent_p.A20A|LYRM1_ENST00000439021.1_Silent_p.A20A|LYRM1_ENST00000568663.1_Silent_p.A20A|LYRM1_ENST00000562740.1_Intron|LYRM1_ENST00000567954.1_Silent_p.A20A|LYRM1_ENST00000569023.1_Silent_p.A20A|LYRM1_ENST00000412082.2_Intron			O43325	LYRM1_HUMAN	LYR motif containing 1	20						mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.A20A(2)		large_intestine(1)|prostate(1)	2						TCAGGCTTGCGAGGAAATGGC	0.448													G|||	4	0.000798722	0.003	0.0	5008	,	,		17578	0.0		0.0	False		,,,				2504	0.0				p.A20A												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G60A	16						.	G	,,	9,4393	16.8+/-37.8	0,9,2192	110.0	105.0	107.0		60,60,60	-5.6	0.9	16	dbSNP_134	107	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	LYRM1	NM_001128301.1,NM_001128302.1,NM_020424.3	,,	0,12,6489	AA,AG,GG		0.0349,0.2045,0.0923	,,	20/123,20/123,20/123	20926937	12,12990	2201	4300	6501	20834438	SO:0001819	synonymous_variant	57149	exon2				CCDS10593.1	16p12.2	2008-02-05			ENSG00000102897	ENSG00000102897		"""LYR motif containing"""	25074	protein-coding gene	gene with protein product		614709				10493829	Standard	NM_020424		Approved	A211C6.1	uc010bwl.3	O43325	OTTHUMG00000131554	ENST00000396052.2:c.60G>A	16.37:g.20926937G>A		Somatic		Capture	Illumina HiSeq	Phase_I	20834438	NM_020424	B2R4M5	Silent	SNP	ENST00000396052.2	37	CCDS10593.1																																																																																				0.448	LYRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254416.1	NM_020424	
DNAH3	55567	broad.mit.edu	37	16	21093001	21093001	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:21093001G>A	ENST00000261383.3	-	20	2924	c.2925C>T	c.(2923-2925)tgC>tgT	p.C975C	DNAH3_ENST00000415178.1_Silent_p.C975C	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	975	Stem. {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)|microtubule motor activity (GO:0003777)	p.C975C(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)		TATTTGAGAGGCAGGTCGTTT	0.443																																					p.C975C												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C2925T	16						.						192.0	184.0	187.0					16																	21093001		2201	4300	6501	21000502	SO:0001819	synonymous_variant	55567	exon20			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.2925C>T	16.37:g.21093001G>A		Somatic		Capture	Illumina HiSeq	Phase_I	21000502	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Silent	SNP	ENST00000261383.3	37	CCDS10594.1																																																																																				0.443	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
ECI1	1632	broad.mit.edu	37	16	2290103	2290103	+	Silent	SNP	C	C	T	rs201856225		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:2290103C>T	ENST00000301729.4	-	7	833	c.786G>A	c.(784-786)acG>acA	p.T262T	ECI1_ENST00000570258.1_Silent_p.T203T|ECI1_ENST00000562238.1_Silent_p.T245T|RP11-304L19.11_ENST00000565709.1_RNA	NM_001919.3	NP_001910.2	P42126	ECI1_HUMAN	enoyl-CoA delta isomerase 1	262					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	dodecenoyl-CoA delta-isomerase activity (GO:0004165)|intramolecular oxidoreductase activity (GO:0016860)	p.T262T(1)		endometrium(1)|large_intestine(2)|lung(6)	9						GGCGGCTGGCCGTGGCCTTTC	0.562													C|||	1	0.000199681	0.0	0.0	5008	,	,		16384	0.001		0.0	False		,,,				2504	0.0				p.T245T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G735A	16						.						62.0	61.0	62.0					16																	2290103		2198	4300	6498	2230104	SO:0001819	synonymous_variant	1632	exon7				CCDS10464.1, CCDS58410.1	16p13.3	2011-03-15	2011-03-15	2011-03-15	ENSG00000167969	ENSG00000167969	5.3.3.8		2703	protein-coding gene	gene with protein product	"""3,2 trans-enoyl-CoA isomerase"""	600305	"""dodecenoyl-Coenzyme A delta isomerase (3,2 trans-enoyl-Coenzyme A isomerase)"", ""dodecenoyl-CoA isomerase"""	DCI		7829074	Standard	NM_001178029		Approved		uc002cpr.3	P42126	OTTHUMG00000128830	ENST00000301729.4:c.786G>A	16.37:g.2290103C>T		Somatic		Capture	Illumina HiSeq	Phase_I	2230104	NM_001178029	A8K512|Q13290|Q7Z2L6|Q7Z2L7|Q9BUB8|Q9BW05|Q9UDG6	Silent	SNP	ENST00000301729.4	37	CCDS10464.1																																																																																				0.562	ECI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250768.1		
OTOA	146183	broad.mit.edu	37	16	21737952	21737952	+	Silent	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:21737952A>G	ENST00000286149.4	+	18	2032	c.2031A>G	c.(2029-2031)tcA>tcG	p.S677S	OTOA_ENST00000388956.4_Silent_p.S584S|OTOA_ENST00000388958.3_Silent_p.S663S|OTOA_ENST00000388957.3_Silent_p.S339S			Q7RTW8	OTOAN_HUMAN	otoancorin	677					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|proteinaceous extracellular matrix (GO:0005578)		p.S663S(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)	46				GBM - Glioblastoma multiforme(48;0.0414)		AAAAGACTTCAGTCCTCAGGA	0.552																																					p.S663S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1989G	16						.						102.0	97.0	99.0					16																	21737952		2198	4300	6498	21645453	SO:0001819	synonymous_variant	146183	exon18			AK057335	CCDS10600.2, CCDS32403.1, CCDS53994.1	16p12.2	2009-08-18	2002-07-05		ENSG00000155719	ENSG00000155719			16378	protein-coding gene	gene with protein product	"""cancer/testis antigen 108"""	607038	"""deafness, autosomal recessive 22"""	DFNB22		11972037, 19088187	Standard	NM_170664		Approved	CT108	uc002djh.3	Q7RTW8	OTTHUMG00000090721	ENST00000286149.4:c.2031A>G	16.37:g.21737952A>G		Somatic		Capture	Illumina HiSeq	Phase_I	21645453	NM_144672	A1L3A8|A2VDI0|B3KWU3|E9PF51|Q8NA86|Q96M76	Silent	SNP	ENST00000286149.4	37																																																																																					0.552	OTOA-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000430021.1		
USP31	57478	broad.mit.edu	37	16	23116808	23116808	+	Missense_Mutation	SNP	C	C	A	rs199941759		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:23116808C>A	ENST00000219689.7	-	5	1042	c.1043G>T	c.(1042-1044)aGa>aTa	p.R348I		NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	0	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)	p.R348I(1)		breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		TTCCCGAAGTCTGGCGACAGT	0.473																																					p.R348I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1043T	16						.						125.0	106.0	112.0					16																	23116808		2197	4300	6497	23024309	SO:0001583	missense	57478	exon5			AB033029	CCDS10607.1	16p12.3	2008-02-05	2005-08-08		ENSG00000103404	ENSG00000103404		"""Ubiquitin-specific peptidases"""	20060	protein-coding gene	gene with protein product			"""ubiquitin specific protease 31"""			12838346	Standard	NM_020718		Approved	KIAA1203	uc002dll.3	Q70CQ4	OTTHUMG00000094793	ENST00000219689.7:c.1043G>T	16.37:g.23116808C>A	ENSP00000219689:p.Arg348Ile	Somatic		Capture	Illumina HiSeq	Phase_I	23024309	NM_020718	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000219689.7	37	CCDS10607.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.138070	0.77775	.	.	ENSG00000103404	ENST00000219689	T	0.08634	3.07	4.69	3.72	0.42706	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	U	0.000000	T	0.17831	0.0428	L	0.42245	1.32	0.80722	D	1	D	0.65815	0.995	D	0.65874	0.939	T	0.00896	-1.1523	10	0.38643	T	0.18	-8.0737	12.2959	0.54847	0.0:0.9161:0.0:0.0839	.	348	Q70CQ4	UBP31_HUMAN	I	348	ENSP00000219689:R348I	ENSP00000219689:R348I	R	-	2	0	USP31	23024309	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.607000	0.61133	2.157000	0.67596	0.655000	0.94253	AGA		0.473	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718	
GTF3C1	2975	broad.mit.edu	37	16	27497443	27497443	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:27497443G>A	ENST00000356183.4	-	24	3748	c.3733C>T	c.(3733-3735)Cgc>Tgc	p.R1245C	GTF3C1_ENST00000561623.1_Missense_Mutation_p.R1245C	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	1245					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.R1245C(3)		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						TCATGGTAGCGCAGCCTTTTG	0.562																																					p.R1245C												.	.	3	Substitution - Missense(3)	liver(2)|large_intestine(1)	c.C3733T	16						.						208.0	195.0	200.0					16																	27497443		2197	4300	6497	27404944	SO:0001583	missense	2975	exon24			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.3733C>T	16.37:g.27497443G>A	ENSP00000348510:p.Arg1245Cys	Somatic		Capture	Illumina HiSeq	Phase_I	27404944	NM_001520	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Missense_Mutation	SNP	ENST00000356183.4	37	CCDS32414.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.695907	0.88830	.	.	ENSG00000077235	ENST00000356183;ENST00000388971	T	0.26957	1.7	5.15	5.15	0.70609	.	0.192006	0.47852	D	0.000210	T	0.53351	0.1791	M	0.76574	2.34	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.987;0.999	T	0.56469	-0.7974	10	0.59425	D	0.04	-13.5363	18.2358	0.89949	0.0:0.0:1.0:0.0	.	1245;1245	Q12789;Q12789-3	TF3C1_HUMAN;.	C	1245;1241	ENSP00000348510:R1245C	ENSP00000348510:R1245C	R	-	1	0	GTF3C1	27404944	1.000000	0.71417	0.944000	0.38274	0.848000	0.48234	5.576000	0.67437	2.398000	0.81561	0.561000	0.74099	CGC		0.562	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520	
KREMEN2	79412	broad.mit.edu	37	16	3014609	3014609	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:3014609A>G	ENST00000303746.5	+	1	665	c.88A>G	c.(88-90)Agt>Ggt	p.S30G	KREMEN2_ENST00000575769.1_Missense_Mutation_p.S30G|KREMEN2_ENST00000571007.1_Missense_Mutation_p.S30G|KREMEN2_ENST00000572045.1_Missense_Mutation_p.S30G|KREMEN2_ENST00000319500.6_Missense_Mutation_p.S30G|KREMEN2_ENST00000575885.1_Missense_Mutation_p.S30G			Q8NCW0	KREM2_HUMAN	kringle containing transmembrane protein 2	30					Wnt signaling pathway (GO:0016055)	integral component of membrane (GO:0016021)		p.S30G(1)		central_nervous_system(2)|endometrium(1)|large_intestine(1)	4						GAGCCTGCACAGTCCAGGTAA	0.687																																					p.S30G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A88G	16						.						41.0	44.0	43.0					16																	3014609		2197	4299	6496	2954610	SO:0001583	missense	79412	exon1			BC003533	CCDS10483.1, CCDS10484.1, CCDS58412.1, CCDS58413.1	16p13.11	2008-08-04			ENSG00000131650	ENSG00000131650			18797	protein-coding gene	gene with protein product		609899				12050670	Standard	NM_172229		Approved	MGC10791, KRM2	uc002csg.3	Q8NCW0	OTTHUMG00000128976	ENST00000303746.5:c.88A>G	16.37:g.3014609A>G	ENSP00000304422:p.Ser30Gly	Somatic		Capture	Illumina HiSeq	Phase_I	2954610	NM_172229	B4DXF6|I3L2S2|Q8N2J4|Q8NCW1|Q96GL8|Q9BTP9	Missense_Mutation	SNP	ENST00000303746.5	37	CCDS10483.1	.	.	.	.	.	.	.	.	.	.	A	13.71	2.317586	0.40996	.	.	ENSG00000131650	ENST00000303746;ENST00000319500	T;T	0.62941	-0.01;-0.01	4.68	4.68	0.58851	Kringle (1);Kringle-like fold (1);	0.670270	0.13039	N	0.418680	T	0.48909	0.1526	L	0.27053	0.805	0.25363	N	0.988768	B;B;B;B;B;B	0.28291	0.172;0.131;0.206;0.206;0.206;0.075	B;B;B;B;B;B	0.31101	0.058;0.058;0.124;0.124;0.124;0.04	T	0.36065	-0.9763	10	0.23891	T	0.37	.	10.8321	0.46667	1.0:0.0:0.0:0.0	.	30;30;30;30;30;30	B4DXF6;Q53F67;Q8NCW0-2;Q8NCW0-4;Q8NCW0-3;Q8NCW0	.;.;.;.;.;KREM2_HUMAN	G	30	ENSP00000304422:S30G;ENSP00000322079:S30G	ENSP00000304422:S30G	S	+	1	0	KREMEN2	2954610	0.006000	0.16342	0.870000	0.34147	0.902000	0.53008	1.092000	0.30927	1.874000	0.54306	0.459000	0.35465	AGT		0.687	KREMEN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250964.2	NM_145347	
GSG1L	146395	broad.mit.edu	37	16	27818828	27818828	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:27818828C>T	ENST00000447459.2	-	6	962	c.878G>A	c.(877-879)cGc>cAc	p.R293H	GSG1L_ENST00000380898.2_Missense_Mutation_p.R156H|GSG1L_ENST00000569166.1_Missense_Mutation_p.R156H|GSG1L_ENST00000395724.3_Missense_Mutation_p.R242H|GSG1L_ENST00000380897.3_Missense_Mutation_p.R138H	NM_001109763.1	NP_001103233.1	Q6UXU4	GSG1L_HUMAN	GSG1-like	293					regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)	asymmetric synapse (GO:0032279)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R293H(1)|p.R138H(1)		endometrium(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(4)	17						TCTCTCGTGGCGGCAGTCTAA	0.493																																					p.R138H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G413A	16						.						87.0	69.0	75.0					16																	27818828		2196	4300	6496	27726329	SO:0001583	missense	146395	exon5			AK128775	CCDS10631.1, CCDS45450.1	16p11.2	2014-01-20			ENSG00000169181	ENSG00000169181			28283	protein-coding gene	gene with protein product						22813734	Standard	NM_001109763		Approved	MGC18079, PRO19651, KTSR5831	uc002doz.2	Q6UXU4	OTTHUMG00000131676	ENST00000447459.2:c.878G>A	16.37:g.27818828C>T	ENSP00000394954:p.Arg293His	Somatic		Capture	Illumina HiSeq	Phase_I	27726329	NM_144675	Q7Z6F8|Q8TB81	Missense_Mutation	SNP	ENST00000447459.2	37	CCDS45450.1	.	.	.	.	.	.	.	.	.	.	C	18.01	3.527181	0.64860	.	.	ENSG00000169181	ENST00000447459;ENST00000395724;ENST00000380898;ENST00000380897	T;T	0.39229	1.18;1.09	3.81	3.81	0.43845	.	0.550774	0.18179	N	0.149212	T	0.41811	0.1175	N	0.11201	0.11	0.33495	D	0.589224	D;D;D	0.76494	0.999;0.999;0.998	D;D;D	0.77004	0.984;0.989;0.964	T	0.49716	-0.8910	10	0.34782	T	0.22	-4.02	11.5171	0.50529	0.0:1.0:0.0:0.0	.	242;156;293	Q6UXU4-3;Q6UXU4-4;Q6UXU4	.;.;GSG1L_HUMAN	H	293;242;156;138	ENSP00000394954:R293H;ENSP00000379074:R242H	ENSP00000370282:R138H	R	-	2	0	GSG1L	27726329	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	1.176000	0.31957	2.426000	0.82243	0.561000	0.74099	CGC		0.493	GSG1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433832.2	NM_144675	
KCTD13	253980	broad.mit.edu	37	16	29918413	29918413	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:29918413G>A	ENST00000568000.1	-	6	1771	c.770C>T	c.(769-771)gCc>gTc	p.A257V		NM_178863.3	NP_849194.1	Q8WZ19	BACD1_HUMAN	potassium channel tetramerization domain containing 13	257					cell migration (GO:0016477)|DNA replication (GO:0006260)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of DNA replication (GO:0045740)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein homooligomerization (GO:0051260)|protein ubiquitination (GO:0016567)|stress fiber assembly (GO:0043149)	Cul3-RING ubiquitin ligase complex (GO:0031463)|nucleus (GO:0005634)	GTP-Rho binding (GO:0017049)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(2)	7						GAAGATCCGGGCCTCTGGAAA	0.657																																					p.A257V												.	.	0			c.C770T	16						.						34.0	34.0	34.0					16																	29918413		2196	4300	6496	29825914	SO:0001583	missense	253980	exon6			AF289573	CCDS10661.1	16p11.2	2013-06-20	2013-06-20		ENSG00000174943	ENSG00000174943			22234	protein-coding gene	gene with protein product	"""polymerase delta-interacting protein 1"", ""TNFAIP1-like"""	608947	"""potassium channel tetramerisation domain containing 13"""			11593007	Standard	NM_178863		Approved	PDIP1, FKSG86, POLDIP1	uc002duv.4	Q8WZ19	OTTHUMG00000132120	ENST00000568000.1:c.770C>T	16.37:g.29918413G>A	ENSP00000455785:p.Ala257Val	None		Capture	Illumina HiSeq	Phase_I	29825914	NM_178863	A8K0R5|Q96P93|Q96SA1	Missense_Mutation	SNP	ENST00000568000.1	37	CCDS10661.1	.	.	.	.	.	.	.	.	.	.	G	34	5.346978	0.95807	.	.	ENSG00000174943	ENST00000308768	T	0.61510	0.1	4.61	4.61	0.57282	.	0.000000	0.47852	D	0.000203	T	0.75838	0.3904	M	0.79011	2.435	0.80722	D	1	D	0.71674	0.998	D	0.70935	0.971	T	0.80006	-0.1563	10	0.87932	D	0	-0.9525	16.3758	0.83387	0.0:0.0:1.0:0.0	.	257	Q8WZ19	BACD1_HUMAN	V	257	ENSP00000311202:A257V	ENSP00000311202:A257V	A	-	2	0	KCTD13	29825914	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	9.625000	0.98406	2.392000	0.81423	0.460000	0.39030	GCC		0.657	KCTD13-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255162.2	NM_178863	
ZNF688	146542	broad.mit.edu	37	16	30582414	30582414	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:30582414G>T	ENST00000223459.6	-	2	1331	c.227C>A	c.(226-228)tCt>tAt	p.S76Y	ZNF688_ENST00000395219.1_Missense_Mutation_p.S62Y|ZNF688_ENST00000567855.1_Missense_Mutation_p.S76Y|AC002310.7_ENST00000492040.1_RNA|ZNF688_ENST00000563707.1_Intron|AC002310.7_ENST00000486926.1_RNA	NM_145271.3	NP_660314.1	P0C7X2	ZN688_HUMAN	zinc finger protein 688	76	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.S76Y(1)		endometrium(3)|large_intestine(2)|lung(2)|ovary(1)	8						TTCCATCCAAGAGATGAGGGC	0.632																																					p.S76Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C227A	16						.						36.0	38.0	37.0					16																	30582414		2197	4300	6497	30489915	SO:0001583	missense	146542	exon2			AK122680	CCDS10684.1	16p11.2	2013-01-08			ENSG00000229809	ENSG00000229809		"""Zinc fingers, C2H2-type"", ""-"""	30489	protein-coding gene	gene with protein product						10493829	Standard	XM_005255139		Approved		uc002dys.2	P0C7X2	OTTHUMG00000132408	ENST00000223459.6:c.227C>A	16.37:g.30582414G>T	ENSP00000223459:p.Ser76Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	30489915	NM_145271	A8MV39|B3KV51|O75701|Q8IW91|Q8WV14|Q96MN0	Missense_Mutation	SNP	ENST00000223459.6	37	CCDS10684.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.554254	0.86231	.	.	ENSG00000229809	ENST00000395219;ENST00000223459	T;T	0.11495	2.77;5.56	5.2	5.2	0.72013	Krueppel-associated box (3);	.	.	.	.	T	0.28433	0.0703	L	0.53617	1.68	0.39896	D	0.973833	D;D	0.89917	0.999;1.0	D;D	0.85130	0.995;0.997	T	0.00463	-1.1724	9	0.87932	D	0	.	14.4281	0.67230	0.0:0.0:1.0:0.0	.	76;62	P0C7X2;A8MV39	ZN688_HUMAN;.	Y	62;76	ENSP00000378645:S62Y;ENSP00000223459:S76Y	ENSP00000223459:S76Y	S	-	2	0	ZNF688	30489915	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.545000	0.53648	2.861000	0.98227	0.655000	0.94253	TCT		0.632	ZNF688-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255544.2	NM_145271	
NETO2	81831	broad.mit.edu	37	16	47163238	47163238	+	Silent	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:47163238G>T	ENST00000562435.1	-	3	513	c.129C>A	c.(127-129)acC>acA	p.T43T	NETO2_ENST00000303155.5_Silent_p.T43T	NM_018092.4	NP_060562.3	Q8NC67	NETO2_HUMAN	neuropilin (NRP) and tolloid (TLL)-like 2	43					regulation of kainate selective glutamate receptor activity (GO:2000312)	kainate selective glutamate receptor complex (GO:0032983)|postsynaptic density (GO:0014069)		p.T43T(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(8)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	29		all_cancers(37;0.00114)|all_lung(18;0.00432)|Lung NSC(13;0.0384)|Breast(268;0.174)				TGCCACACTGGGTTGCAGGAA	0.403										HNSCC(25;0.065)																											p.T43T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C129A	16						.						159.0	150.0	153.0					16																	47163238		2202	4300	6502	45720739	SO:0001819	synonymous_variant	81831	exon3			AK001292	CCDS10727.1, CCDS58460.1	16q11.2	2008-08-04			ENSG00000171208	ENSG00000171208			14644	protein-coding gene	gene with protein product		607974				11943477	Standard	NM_018092		Approved	FLJ10430, NEOT2	uc002eer.2	Q8NC67	OTTHUMG00000133101	ENST00000562435.1:c.129C>A	16.37:g.47163238G>T		Somatic		Capture	Illumina HiSeq	Phase_I	45720739	NM_018092	J3KNF1|Q7Z381|Q8ND51|Q96SP4|Q9NVY8	Silent	SNP	ENST00000562435.1	37	CCDS10727.1																																																																																				0.403	NETO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256766.2	NM_018092	
ABCC12	94160	broad.mit.edu	37	16	48119527	48119527	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:48119527G>A	ENST00000311303.3	-	27	4150	c.3805C>T	c.(3805-3807)Cga>Tga	p.R1269*	ABCC12_ENST00000448542.1_3'UTR|ABCC12_ENST00000532355.1_5'UTR|ABCC12_ENST00000416054.1_3'UTR	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	1269	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.					integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)	p.R1269*(1)		NS(1)|breast(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|liver(1)|lung(43)|ovary(2)|prostate(3)|skin(7)|urinary_tract(1)	90		all_cancers(37;0.0474)|all_lung(18;0.047)				AGAAGAGCTCGGGCCACACAA	0.443																																					p.R1269X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C3805T	16						.						164.0	162.0	162.0					16																	48119527		2201	4300	6501	46677028	SO:0001587	stop_gained	94160	exon27			AY040220	CCDS10730.1	16q12.1	2012-03-14			ENSG00000140798	ENSG00000140798		"""ATP binding cassette transporters / subfamily C"""	14640	protein-coding gene	gene with protein product		607041				11435397, 11483364	Standard	NM_033226		Approved	MRP9	uc002efc.1	Q96J65	OTTHUMG00000133143	ENST00000311303.3:c.3805C>T	16.37:g.48119527G>A	ENSP00000311030:p.Arg1269*	Somatic		Capture	Illumina HiSeq	Phase_I	46677028	NM_033226	Q49AL2|Q8TAF0|Q8TEY2	Nonsense_Mutation	SNP	ENST00000311303.3	37	CCDS10730.1	.	.	.	.	.	.	.	.	.	.	G	45	11.954805	0.99621	.	.	ENSG00000140798	ENST00000311303	.	.	.	5.59	3.51	0.40186	.	0.136740	0.51477	D	0.000096	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.4151	0.21712	0.094:0.0:0.5717:0.3343	.	.	.	.	X	1269	.	ENSP00000311030:R1269X	R	-	1	2	ABCC12	46677028	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	1.921000	0.40035	1.369000	0.46134	-0.137000	0.14449	CGA		0.443	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226	
GLYR1	84656	broad.mit.edu	37	16	4855260	4855260	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:4855260C>T	ENST00000321919.9	-	16	1715	c.1639G>A	c.(1639-1641)Gtg>Atg	p.V547M	GLYR1_ENST00000436648.5_Missense_Mutation_p.V466M|GLYR1_ENST00000381983.3_Missense_Mutation_p.V530M|GLYR1_ENST00000591451.1_Missense_Mutation_p.V541M|ROGDI_ENST00000322048.7_5'Flank	NM_032569.3	NP_115958	Q49A26	GLYR1_HUMAN	glyoxylate reductase 1 homolog (Arabidopsis)	547					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.V547M(1)		endometrium(1)|kidney(1)|large_intestine(7)|lung(6)|prostate(2)|skin(1)|urinary_tract(1)	19						GCTCGGTACACGGCGGACATA	0.587																																					p.V547M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1639A	16						.						125.0	105.0	112.0					16																	4855260		2197	4300	6497	4795261	SO:0001583	missense	84656	exon16			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.1639G>A	16.37:g.4855260C>T	ENSP00000322716:p.Val547Met	Somatic		Capture	Illumina HiSeq	Phase_I	4795261	NM_032569	B4DL47|C9JJ40|C9JJ60|Q5U632|Q6P1Q2|Q6V3W7|Q9BTI1|Q9BXK2	Missense_Mutation	SNP	ENST00000321919.9	37	CCDS10524.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.298509	0.81025	.	.	ENSG00000140632	ENST00000321919;ENST00000381983;ENST00000436648	T;T;T	0.35048	1.33;1.33;1.33	4.72	4.72	0.59763	Dehydrogenase, multihelical (1);6-phosphogluconate dehydrogenase, C-terminal-like (1);	0.000000	0.85682	D	0.000000	T	0.65428	0.2690	M	0.86502	2.82	0.80722	D	1	D;D;D;D	0.89917	0.998;1.0;0.998;1.0	P;D;P;D	0.79108	0.906;0.989;0.906;0.992	T	0.73139	-0.4077	10	0.66056	D	0.02	-15.2145	16.467	0.84081	0.0:1.0:0.0:0.0	.	466;541;530;547	Q49A26-5;Q49A26-3;Q49A26-2;Q49A26	.;.;.;GLYR1_HUMAN	M	547;530;466	ENSP00000322716:V547M;ENSP00000371413:V530M;ENSP00000390276:V466M	ENSP00000322716:V547M	V	-	1	0	GLYR1	4795261	1.000000	0.71417	0.997000	0.53966	0.817000	0.46193	7.703000	0.84585	2.159000	0.67721	0.655000	0.94253	GTG		0.587	GLYR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251717.2	NM_032569	
UBN1	29855	broad.mit.edu	37	16	4908663	4908663	+	Splice_Site	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:4908663C>T	ENST00000396658.4	+	3	1134	c.431C>T	c.(430-432)gCg>gTg	p.A144V	UBN1_ENST00000545171.1_Splice_Site_p.A144V|UBN1_ENST00000262376.6_Splice_Site_p.A144V|UBN1_ENST00000590769.1_Splice_Site_p.A144V	NM_016936.3	NP_058632.2	Q9NPG3	UBN1_HUMAN	ubinuclein 1	144	Sufficient for interaction with HIRA.				chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of phosphatase activity (GO:0010923)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|tight junction (GO:0005923)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A144V(1)		NS(1)|endometrium(6)|kidney(4)|large_intestine(10)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38						AACTCTGAGGCGGTAAGTAGT	0.493																																					p.A144V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C431T	16						.						118.0	100.0	106.0					16																	4908663		2197	4300	6497	4848664	SO:0001630	splice_region_variant	29855	exon3			AF108460	CCDS10525.1, CCDS73822.1	16p13.3	2010-11-09			ENSG00000118900	ENSG00000118900			12506	protein-coding gene	gene with protein product		609771				10725330	Standard	XM_005255277		Approved		uc002cyb.3	Q9NPG3	OTTHUMG00000129531	ENST00000396658.4:c.432+1C>T	16.37:g.4908663C>T		Somatic		Capture	Illumina HiSeq	Phase_I	4848664	NM_016936	B7Z6D3|D3DUE8|Q13079|Q9P1P7	Missense_Mutation	SNP	ENST00000396658.4	37	CCDS10525.1	.	.	.	.	.	.	.	.	.	.	C	36	5.854264	0.97030	.	.	ENSG00000118900	ENST00000262376;ENST00000545171;ENST00000396658	T;T;T	0.58652	0.9;0.32;0.9	5.63	5.63	0.86233	.	0.049540	0.85682	D	0.000000	T	0.78811	0.4342	M	0.80746	2.51	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.989;0.993	T	0.80725	-0.1254	10	0.72032	D	0.01	-18.5987	19.6772	0.95941	0.0:1.0:0.0:0.0	.	144;144	Q9NPG3-2;Q9NPG3	.;UBN1_HUMAN	V	144	ENSP00000262376:A144V;ENSP00000442379:A144V;ENSP00000379894:A144V	ENSP00000262376:A144V	A	+	2	0	UBN1	4848664	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.601000	0.82783	2.653000	0.90120	0.557000	0.71058	GCG		0.493	UBN1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251719.1	NM_016936	Missense_Mutation
ABCC11	85320	broad.mit.edu	37	16	48221301	48221301	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:48221301G>T	ENST00000394747.1	-	20	3093	c.2744C>A	c.(2743-2745)cCa>cAa	p.P915Q	ABCC11_ENST00000537808.1_3'UTR|ABCC11_ENST00000353782.5_Missense_Mutation_p.P915Q|ABCC11_ENST00000565329.1_5'UTR|ABCC11_ENST00000394748.1_Missense_Mutation_p.P915Q|ABCC11_ENST00000356608.2_Missense_Mutation_p.P915Q	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	915	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				organic anion transport (GO:0015711)|purine nucleotide transport (GO:0015865)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|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)|purine nucleotide transmembrane transporter activity (GO:0015216)	p.P915Q(1)		breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(3)|prostate(2)|skin(5)|urinary_tract(2)	83		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)			Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032)	CCGGCCTATTGGGATGGTGTC	0.527																																					p.P915Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2744A	16						.						36.0	35.0	35.0					16																	48221301		2201	4300	6501	46778802	SO:0001583	missense	85320	exon21			AF367202	CCDS10732.1, CCDS10733.1	16q12	2012-03-14			ENSG00000121270	ENSG00000121270		"""ATP binding cassette transporters / subfamily C"""	14639	protein-coding gene	gene with protein product		607040				11483364, 11435397	Standard	NM_033151		Approved	MRP8	uc002efg.1	Q96J66	OTTHUMG00000133146	ENST00000394747.1:c.2744C>A	16.37:g.48221301G>T	ENSP00000378230:p.Pro915Gln	Somatic		Capture	Illumina HiSeq	Phase_I	46778802	NM_145186	Q8TDJ0|Q96JA6|Q9BX80	Missense_Mutation	SNP	ENST00000394747.1	37	CCDS10732.1	.	.	.	.	.	.	.	.	.	.	G	33	5.217866	0.95104	.	.	ENSG00000121270	ENST00000353782;ENST00000356608;ENST00000394748;ENST00000394747	D;D;D;D	0.89746	-2.56;-2.56;-2.56;-2.56	5.09	4.1	0.47936	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.125121	0.53938	N	0.000045	D	0.94545	0.8243	M	0.88704	2.975	0.80722	D	1	D;D	0.89917	0.976;1.0	P;D	0.91635	0.698;0.999	D	0.94666	0.7852	10	0.87932	D	0	-6.4388	10.9414	0.47275	0.0:0.0:0.8125:0.1875	.	915;915	Q96J66-2;Q96J66	.;ABCCB_HUMAN	Q	915	ENSP00000311326:P915Q;ENSP00000349017:P915Q;ENSP00000378231:P915Q;ENSP00000378230:P915Q	ENSP00000311326:P915Q	P	-	2	0	ABCC11	46778802	1.000000	0.71417	0.016000	0.15963	0.919000	0.55068	5.482000	0.66833	1.193000	0.43086	0.563000	0.77884	CCA		0.527	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583	
RPGRIP1L	23322	broad.mit.edu	37	16	53721802	53721802	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:53721802T>C	ENST00000379925.3	-	5	655	c.605A>G	c.(604-606)gAa>gGa	p.E202G	RPGRIP1L_ENST00000262135.4_Missense_Mutation_p.E202G|RPGRIP1L_ENST00000563746.1_Missense_Mutation_p.E202G|RPGRIP1L_ENST00000564374.1_Missense_Mutation_p.E202G	NM_015272.2	NP_056087.2	Q68CZ1	FTM_HUMAN	RPGRIP1-like	202					camera-type eye development (GO:0043010)|cerebellum development (GO:0021549)|cilium assembly (GO:0042384)|corpus callosum development (GO:0022038)|determination of left/right symmetry (GO:0007368)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|establishment or maintenance of cell polarity (GO:0007163)|head development (GO:0060322)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lateral ventricle development (GO:0021670)|liver development (GO:0001889)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|neural tube patterning (GO:0021532)|nose development (GO:0043584)|olfactory bulb development (GO:0021772)|pericardium development (GO:0060039)|regulation of smoothened signaling pathway (GO:0008589)	axoneme (GO:0005930)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	thromboxane A2 receptor binding (GO:0031870)	p.E202G(1)		endometrium(6)|kidney(3)|large_intestine(9)|lung(19)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(2)	46		all_cancers(37;0.0973)				TCTGGCTTCTTCAAGTAAACT	0.299																																					p.E202G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A605G	16						.						134.0	145.0	141.0					16																	53721802		2198	4297	6495	52279303	SO:0001583	missense	23322	exon5				CCDS32447.1, CCDS45486.1	16q12.2	2014-09-17				ENSG00000103494			29168	protein-coding gene	gene with protein product	"""fantom homolog"", ""Meckel syndrome, type 5"", ""protein phosphatase 1, regulatory subunit 134"""	610937				10231032	Standard	NM_015272		Approved	KIAA1005, CORS3, JBTS7, MKS5, NPHP8, FTM, PPP1R134	uc002ehp.3	Q68CZ1		ENST00000379925.3:c.605A>G	16.37:g.53721802T>C	ENSP00000369257:p.Glu202Gly	Somatic		Capture	Illumina HiSeq	Phase_I	52279303	NM_001127897	A0PJ88|Q9Y2K8	Missense_Mutation	SNP	ENST00000379925.3	37	CCDS32447.1	.	.	.	.	.	.	.	.	.	.	T	17.68	3.449342	0.63178	.	.	ENSG00000103494	ENST00000379925;ENST00000262135	T;T	0.80738	-0.08;-1.41	5.38	5.38	0.77491	.	0.216541	0.47093	D	0.000253	T	0.81725	0.4883	L	0.56769	1.78	0.80722	D	1	P;B;P;P	0.49307	0.701;0.425;0.922;0.867	B;B;B;P	0.47376	0.23;0.23;0.424;0.545	D	0.84033	0.0360	10	0.66056	D	0.02	-11.3115	14.664	0.68893	0.0:0.0:0.0:1.0	.	202;202;202;202	B4E3M8;B7ZKJ9;Q68CZ1;Q68CZ1-2	.;.;FTM_HUMAN;.	G	202	ENSP00000369257:E202G;ENSP00000262135:E202G	ENSP00000262135:E202G	E	-	2	0	RPGRIP1L	52279303	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.144000	0.71762	2.173000	0.68751	0.528000	0.53228	GAA		0.299	RPGRIP1L-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422187.1	NM_015272	
IRX5	10265	broad.mit.edu	37	16	54966800	54966800	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:54966800G>A	ENST00000394636.4	+	2	977	c.640G>A	c.(640-642)Gag>Aag	p.E214K	IRX5_ENST00000558597.1_Missense_Mutation_p.E148K|CTD-3032H12.2_ENST00000560487.1_lincRNA|IRX5_ENST00000320990.5_Missense_Mutation_p.E214K|IRX5_ENST00000560154.1_Intron			P78411	IRX5_HUMAN	iroquois homeobox 5	214					embryonic cranial skeleton morphogenesis (GO:0048701)|gonad development (GO:0008406)|neuron maturation (GO:0042551)|regulation of heart rate (GO:0002027)|regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|retinal bipolar neuron differentiation (GO:0060040)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|vitamin D binding (GO:0005499)	p.E214K(1)		kidney(3)|large_intestine(6)|lung(4)|prostate(1)	14						GGGCGACCCCGAGGGCCCCGA	0.652																																					p.E214K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G640A	16						.						63.0	80.0	75.0					16																	54966800		2198	4300	6498	53524301	SO:0001583	missense	10265	exon2			U90309	CCDS10751.1, CCDS58462.1	16q12.2	2011-06-20	2007-07-13		ENSG00000176842	ENSG00000176842		"""Homeoboxes / TALE class"""	14361	protein-coding gene	gene with protein product		606195					Standard	NM_005853		Approved	IRX-2a	uc002ehv.3	P78411	OTTHUMG00000133201	ENST00000394636.4:c.640G>A	16.37:g.54966800G>A	ENSP00000378132:p.Glu214Lys	Somatic		Capture	Illumina HiSeq	Phase_I	53524301	NM_005853	H0YMS7|P78416|Q7Z2E1	Missense_Mutation	SNP	ENST00000394636.4	37	CCDS10751.1	.	.	.	.	.	.	.	.	.	.	G	9.084	0.999942	0.19121	.	.	ENSG00000176842	ENST00000394636;ENST00000320990	T;T	0.59638	0.29;0.25	4.14	3.14	0.36123	.	0.365106	0.28062	N	0.016757	T	0.33904	0.0879	N	0.22421	0.69	0.37939	D	0.932278	P	0.43352	0.804	B	0.32724	0.151	T	0.25398	-1.0133	10	0.10902	T	0.67	-9.8677	11.7885	0.52055	0.0:0.0:0.8224:0.1776	.	214	P78411	IRX5_HUMAN	K	214	ENSP00000378132:E214K;ENSP00000316250:E214K	ENSP00000316250:E214K	E	+	1	0	IRX5	53524301	1.000000	0.71417	0.868000	0.34077	0.565000	0.35776	5.878000	0.69682	0.884000	0.36064	0.655000	0.94253	GAG		0.652	IRX5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256911.2		
MMP2	4313	broad.mit.edu	37	16	55513487	55513487	+	Silent	SNP	G	G	A	rs146220690	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:55513487G>A	ENST00000219070.4	+	1	605	c.96G>A	c.(94-96)tcG>tcA	p.S32S	MMP2_ENST00000543485.1_5'Flank|MMP2_ENST00000570308.1_Intron|MMP2_ENST00000437642.2_5'Flank	NM_004530.4	NP_004521.1	P08253	MMP2_HUMAN	matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)	32					angiogenesis (GO:0001525)|blood vessel maturation (GO:0001955)|bone trabecula formation (GO:0060346)|cellular protein metabolic process (GO:0044267)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|positive regulation of innate immune response (GO:0045089)|proteolysis (GO:0006508)|response to hypoxia (GO:0001666)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|sarcomere (GO:0030017)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)	p.S32S(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|liver(2)|lung(23)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	58		Renal(780;0.00183)|Breast(268;0.00354)|Hepatocellular(780;0.00826)|all_neural(199;0.0189)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0185)|all cancers(182;7.16e-45)|Epithelial(162;5.26e-37)|GBM - Glioblastoma multiforme(240;9e-08)|Kidney(780;0.00227)|BRCA - Breast invasive adenocarcinoma(181;0.00786)	Captopril(DB01197)|Marimastat(DB00786)	CCGCGCCGTCGCCCATCATCA	0.657																																					p.S32S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G96A	16						.						23.0	23.0	23.0					16																	55513487		2195	4296	6491	54070988	SO:0001819	synonymous_variant	4313	exon1				CCDS10752.1, CCDS45487.1	16q13-q21	2008-02-05	2005-08-08		ENSG00000087245	ENSG00000087245	3.4.24.24		7166	protein-coding gene	gene with protein product		120360	"""matrix metalloproteinase 2 (gelatinase A, 72kD gelatinase, 72kD type IV collagenase)"", ""matrix metalloproteinase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)"""	CLG4, CLG4A			Standard	NM_004530		Approved	TBE-1	uc002ehz.4	P08253	OTTHUMG00000133202	ENST00000219070.4:c.96G>A	16.37:g.55513487G>A		Somatic		Capture	Illumina HiSeq	Phase_I	54070988	NM_004530	B2R6U1|B4DWH3|E9PE45|Q9UCJ8	Silent	SNP	ENST00000219070.4	37	CCDS10752.1																																																																																				0.657	MMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256913.3		
SLC6A2	6530	broad.mit.edu	37	16	55725891	55725891	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:55725891T>C	ENST00000379906.2	+	5	1100	c.845T>C	c.(844-846)gTc>gCc	p.V282A	SLC6A2_ENST00000561820.1_Missense_Mutation_p.V282A|SLC6A2_ENST00000568943.1_Missense_Mutation_p.V282A|SLC6A2_ENST00000219833.8_Missense_Mutation_p.V282A|SLC6A2_ENST00000566163.1_Intron|SLC6A2_ENST00000567238.1_Missense_Mutation_p.V177A|SLC6A2_ENST00000414754.3_Missense_Mutation_p.V282A	NM_001043.3	NP_001034.1	P23975	SC6A2_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 2	282					monoamine transport (GO:0015844)|norepinephrine transport (GO:0015874)|response to drug (GO:0042493)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	monoamine transmembrane transporter activity (GO:0008504)|norepinephrine:sodium symporter activity (GO:0005334)	p.V282A(2)		breast(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(20)|ovary(3)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(181;0.01)|Kidney(780;0.0267)	Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Bupropion(DB01156)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Diethylpropion(DB00937)|Dopamine(DB00988)|Doxepin(DB01142)|Droxidopa(DB06262)|Duloxetine(DB00476)|Ephedra(DB01363)|Ephedrine(DB01364)|Ergotamine(DB00696)|Escitalopram(DB01175)|Ginkgo biloba(DB01381)|Guanadrel(DB00226)|Guanethidine(DB01170)|Imipramine(DB00458)|Iobenguane(DB06704)|Ketamine(DB01221)|Levomilnacipran(DB08918)|Levonordefrin(DB06707)|Loxapine(DB00408)|Maprotiline(DB00934)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Milnacipran(DB04896)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Orphenadrine(DB01173)|Paroxetine(DB00715)|Pethidine(DB00454)|Phendimetrazine(DB01579)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Reboxetine(DB00234)|Sibutramine(DB01105)|Tapentadol(DB06204)|Tramadol(DB00193)|Trimipramine(DB00726)|Venlafaxine(DB00285)	GTCCATGGCGTCACGCTGCCC	0.582																																					p.V282A												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T845C	16						.						142.0	93.0	109.0					16																	55725891		2198	4300	6498	54283392	SO:0001583	missense	6530	exon5				CCDS10754.1, CCDS54011.1, CCDS58463.1	16q12.2	2013-07-19	2013-07-19		ENSG00000103546	ENSG00000103546		"""Solute carriers"""	11048	protein-coding gene	gene with protein product	"""norepinephrine transporter"""	163970	"""solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2"""	NET1, NAT1, SLC6A5		2008212	Standard	NM_001043		Approved	NET	uc021tio.1	P23975	OTTHUMG00000133208	ENST00000379906.2:c.845T>C	16.37:g.55725891T>C	ENSP00000369237:p.Val282Ala	Somatic		Capture	Illumina HiSeq	Phase_I	54283392	NM_001172504	B2R707|B4DX48|Q96KH8	Missense_Mutation	SNP	ENST00000379906.2	37	CCDS10754.1	.	.	.	.	.	.	.	.	.	.	T	14.30	2.493474	0.44352	.	.	ENSG00000103546	ENST00000414754;ENST00000379906;ENST00000219833	T;T;T	0.78246	-1.16;-1.16;-1.16	4.92	4.92	0.64577	.	0.345832	0.34200	N	0.004167	T	0.69842	0.3156	L	0.37507	1.11	0.39908	D	0.973986	B;B;B	0.14438	0.01;0.005;0.003	B;B;B	0.21546	0.035;0.035;0.021	T	0.66544	-0.5897	10	0.31617	T	0.26	.	14.5223	0.67859	0.0:0.0:0.0:1.0	.	282;177;282	Q96KH8;B4DX48;P23975	.;.;SC6A2_HUMAN	A	282	ENSP00000394956:V282A;ENSP00000369237:V282A;ENSP00000219833:V282A	ENSP00000219833:V282A	V	+	2	0	SLC6A2	54283392	1.000000	0.71417	0.906000	0.35671	0.889000	0.51656	5.703000	0.68340	1.967000	0.57214	0.533000	0.62120	GTC		0.582	SLC6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256922.2		
CDH11	1009	broad.mit.edu	37	16	64981827	64981827	+	Silent	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:64981827A>G	ENST00000268603.4	-	13	2685	c.2070T>C	c.(2068-2070)ttT>ttC	p.F690F	CDH11_ENST00000394156.3_3'UTR|CDH11_ENST00000566827.1_Silent_p.F564F	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	690					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.F690F(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		TGCGGGGGATAAATCCATTGA	0.493			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																											p.F690F			Dom	yes		16	16q22.1	1009	"""cadherin 11, type 2, OB-cadherin (osteoblast)"""		M	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T2070C	16						.						142.0	137.0	139.0					16																	64981827		2203	4300	6503	63539328	SO:0001819	synonymous_variant	1009	exon13			D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"""Cadherins / Major cadherins"""	1750	protein-coding gene	gene with protein product	"""OB-Cadherin"""	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.2070T>C	16.37:g.64981827A>G		Somatic		Capture	Illumina HiSeq	Phase_I	63539328	NM_001797	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Silent	SNP	ENST00000268603.4	37	CCDS10803.1																																																																																				0.493	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664	
CDH11	1009	broad.mit.edu	37	16	65005580	65005580	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:65005580G>A	ENST00000268603.4	-	11	2159	c.1544C>T	c.(1543-1545)gCa>gTa	p.A515V	CDH11_ENST00000394156.3_Missense_Mutation_p.A515V|CDH11_ENST00000566827.1_Missense_Mutation_p.A389V	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	515	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A515V(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		CTTGTCATCTGCACTAATTGT	0.408			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																											p.A515V			Dom	yes		16	16q22.1	1009	"""cadherin 11, type 2, OB-cadherin (osteoblast)"""		M	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1544T	16						.						106.0	101.0	103.0					16																	65005580		2203	4300	6503	63563081	SO:0001583	missense	1009	exon11			D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"""Cadherins / Major cadherins"""	1750	protein-coding gene	gene with protein product	"""OB-Cadherin"""	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.1544C>T	16.37:g.65005580G>A	ENSP00000268603:p.Ala515Val	Somatic		Capture	Illumina HiSeq	Phase_I	63563081	NM_001797	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Missense_Mutation	SNP	ENST00000268603.4	37	CCDS10803.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.567248	0.86439	.	.	ENSG00000140937	ENST00000268603;ENST00000394156;ENST00000538390	T;T	0.68624	1.57;-0.34	5.88	5.88	0.94601	Cadherin (3);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.81697	0.4877	M	0.71920	2.185	0.80722	D	1	D;P	0.89917	1.0;0.866	D;P	0.85130	0.997;0.468	T	0.79262	-0.1876	10	0.39692	T	0.17	.	19.211	0.93755	0.0:0.0:1.0:0.0	.	515;515	P55287-2;P55287	.;CAD11_HUMAN	V	515;515;498	ENSP00000268603:A515V;ENSP00000377711:A515V	ENSP00000268603:A515V	A	-	2	0	CDH11	63563081	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.405000	0.97313	2.789000	0.95967	0.655000	0.94253	GCA		0.408	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664	
HAS3	3038	broad.mit.edu	37	16	69148722	69148722	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:69148722C>T	ENST00000306560.1	+	4	1371	c.1215C>T	c.(1213-1215)cgC>cgT	p.R405R	HAS3_ENST00000219322.3_Intron|HAS3_ENST00000569188.1_Silent_p.R405R	NM_005329.2	NP_005320.2	O00219	HYAS3_HUMAN	hyaluronan synthase 3	405					carbohydrate metabolic process (GO:0005975)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|positive regulation of hyaluranon cable assembly (GO:1900106)|positive regulation of transcription, DNA-templated (GO:0045893)|small molecule metabolic process (GO:0044281)	hyaluranon cable (GO:0036117)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronan synthase activity (GO:0050501)	p.R405R(1)		cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|urinary_tract(2)	16		Ovarian(137;0.101)		OV - Ovarian serous cystadenocarcinoma(108;0.0694)		ACCGGGGCCGCATCTGGAACA	0.542																																					p.R405R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1215T	16						.						117.0	110.0	112.0					16																	69148722		2198	4300	6498	67706223	SO:0001819	synonymous_variant	3038	exon4			BC021853	CCDS10870.1, CCDS10871.1	16q22.1	2013-02-22			ENSG00000103044	ENSG00000103044	2.4.1.212	"""Glycosyltransferase family 2 domain containing"""	4820	protein-coding gene	gene with protein product		602428				9169154, 9083017	Standard	NM_005329		Approved		uc010cfh.3	O00219	OTTHUMG00000137562	ENST00000306560.1:c.1215C>T	16.37:g.69148722C>T		Somatic		Capture	Illumina HiSeq	Phase_I	67706223	NM_005329	A8K5T5|Q8WTZ0|Q9NYP0	Silent	SNP	ENST00000306560.1	37	CCDS10871.1																																																																																				0.542	HAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268898.2	NM_138612	
CIRH1A	84916	broad.mit.edu	37	16	69187487	69187487	+	Splice_Site	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:69187487C>T	ENST00000314423.7	+	9	1180	c.1003C>T	c.(1003-1005)Cga>Tga	p.R335*	CIRH1A_ENST00000352319.4_Splice_Site_p.R335*|CIRH1A_ENST00000563094.1_Splice_Site_p.R335*			Q969X6	CIR1A_HUMAN	cirrhosis, autosomal recessive 1A (cirhin)	335					maturation of SSU-rRNA (GO:0030490)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|t-UTP complex (GO:0034455)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(4)|prostate(1)|urinary_tract(1)	16				OV - Ovarian serous cystadenocarcinoma(108;0.125)		TTGGATATAGCGATGTCTCAT	0.418																																					p.R335X	Melanoma(69;1156 1278 4951 8715 52012)											.	.	0			c.C1003T	16						.						102.0	86.0	92.0					16																	69187487		2198	4300	6498	67744988	SO:0001630	splice_region_variant	84916	exon9			AB075868	CCDS10872.1	16q22	2014-04-07			ENSG00000141076	ENSG00000141076		"""WD repeat domain containing"""	1983	protein-coding gene	gene with protein product	"""UTP4, small subunit (SSU) processome component, homolog (yeast)"""	607456				10820129, 20385600	Standard	NM_032830		Approved	NAIC, FLJ14728, KIAA1988, TEX292, CIRHIN, UTP4	uc002ews.4	Q969X6	OTTHUMG00000137570	ENST00000314423.7:c.1003-1C>T	16.37:g.69187487C>T		None		Capture	Illumina HiSeq	Phase_I	67744988	NM_032830	Q8NCD9|Q8TF14|Q96SP0|Q96SR9|Q96SZ9|Q96T13|Q9BWK6	Nonsense_Mutation	SNP	ENST00000314423.7	37	CCDS10872.1	.	.	.	.	.	.	.	.	.	.	C	36	5.865044	0.97043	.	.	ENSG00000141076	ENST00000314423;ENST00000352319	.	.	.	5.27	3.24	0.37175	.	0.189223	0.44688	D	0.000424	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.9645	0.47403	0.3393:0.6607:0.0:0.0	.	.	.	.	X	335	.	.	R	+	1	2	CIRH1A	67744988	1.000000	0.71417	1.000000	0.80357	0.606000	0.37113	1.452000	0.35156	0.651000	0.30788	0.563000	0.77884	CGA		0.418	CIRH1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268950.2	NM_032830	Nonsense_Mutation
WWP2	11060	broad.mit.edu	37	16	69965751	69965751	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:69965751T>C	ENST00000359154.2	+	16	1741	c.1640T>C	c.(1639-1641)aTc>aCc	p.I547T	WWP2_ENST00000568684.1_Missense_Mutation_p.I108T|WWP2_ENST00000448661.1_Missense_Mutation_p.I547T|WWP2_ENST00000542271.1_Missense_Mutation_p.I431T|WWP2_ENST00000544162.1_3'UTR|WWP2_ENST00000356003.2_Missense_Mutation_p.I547T|MIR140_ENST00000385282.1_RNA	NM_001270454.1|NM_007014.4	NP_001257383.1|NP_008945.2	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase 2	547	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cellular protein modification process (GO:0006464)|negative regulation of gene expression (GO:0010629)|negative regulation of protein transport (GO:0051224)|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 transporter activity (GO:0032410)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|RNA polymerase II transcription factor binding (GO:0001085)|transcription factor binding (GO:0008134)|ubiquitin-protein transferase activity (GO:0004842)	p.I547T(1)		breast(4)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						CTCTACATCATCATGCGTGGC	0.627																																					p.I108T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T323C	16						.						100.0	106.0	104.0					16																	69965751		2198	4300	6498	68523252	SO:0001583	missense	11060	exon6			BC013645	CCDS10885.1, CCDS58475.1, CCDS58476.1, CCDS58477.1	16q22.1	2008-02-05			ENSG00000198373	ENSG00000198373			16804	protein-coding gene	gene with protein product		602308				9169421, 12167593	Standard	NM_007014		Approved	AIP2	uc002exv.2	O00308	OTTHUMG00000137573	ENST00000359154.2:c.1640T>C	16.37:g.69965751T>C	ENSP00000352069:p.Ile547Thr	Somatic		Capture	Illumina HiSeq	Phase_I	68523252	NM_199424	A6NEP1|B2R706|B4DTL5|F5H213|H3BRF3|I3RSG8|Q6ZTQ5|Q96CZ2|Q9BWN6	Missense_Mutation	SNP	ENST00000359154.2	37	CCDS10885.1	.	.	.	.	.	.	.	.	.	.	T	17.02	3.280889	0.59758	.	.	ENSG00000198373	ENST00000359154;ENST00000545099;ENST00000448661;ENST00000356003;ENST00000544162;ENST00000542271	T;T;T;T	0.75367	-0.93;-0.93;-0.93;-0.93	5.27	5.27	0.74061	HECT (3);	0.000000	0.85682	D	0.000000	T	0.52996	0.1769	N	0.03930	-0.32	0.80722	D	1	B	0.27765	0.188	B	0.30029	0.11	T	0.53655	-0.8408	9	.	.	.	.	15.4847	0.75557	0.0:0.0:0.0:1.0	.	547	O00308	WWP2_HUMAN	T	547;108;547;547;434;431	ENSP00000352069:I547T;ENSP00000396871:I547T;ENSP00000348283:I547T;ENSP00000445616:I431T	.	I	+	2	0	WWP2	68523252	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.961000	0.87903	2.117000	0.64856	0.459000	0.35465	ATC		0.627	WWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268954.1	NM_007014	
DDX19A	55308	broad.mit.edu	37	16	70399018	70399018	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:70399018C>T	ENST00000302243.7	+	7	751	c.588C>T	c.(586-588)gcC>gcT	p.A196A	RP11-529K1.3_ENST00000567706.1_Intron|DDX19A_ENST00000443119.2_Silent_p.A106A|DDX19A_ENST00000417604.2_Silent_p.A165A	NM_018332.3	NP_060802.1	Q9NUU7	DD19A_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 19A	196	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.|N-terminal lobe. {ECO:0000250}.				mRNA transport (GO:0051028)|positive regulation of apoptotic process (GO:0043065)|protein transport (GO:0015031)|response to zinc ion (GO:0010043)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)	p.A196A(1)		breast(1)|endometrium(1)|large_intestine(5)|lung(3)|urinary_tract(1)	11		Ovarian(137;0.221)				TTGCCTATGCCGTTCGAGGCA	0.488																																					p.A196A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C588T	16						.						102.0	91.0	95.0					16																	70399018		2198	4300	6498	68956519	SO:0001819	synonymous_variant	55308	exon7			AF183422	CCDS10889.1	16q22.1	2012-02-23	2012-02-23	2005-07-13	ENSG00000168872	ENSG00000168872		"""DEAD-boxes"""	25628	protein-coding gene	gene with protein product			"""DEAD (Asp-Glu-Ala-As) box polypeptide 19-like"""	DDX19L		12477932	Standard	NM_018332		Approved	FLJ11126		Q9NUU7	OTTHUMG00000137579	ENST00000302243.7:c.588C>T	16.37:g.70399018C>T		Somatic		Capture	Illumina HiSeq	Phase_I	68956519	NM_018332	B2RPL0|B4DRZ7|Q53FM0	Silent	SNP	ENST00000302243.7	37	CCDS10889.1																																																																																				0.488	DDX19A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268967.2	NM_018332	
DHX38	9785	broad.mit.edu	37	16	72137643	72137643	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:72137643G>A	ENST00000268482.3	+	13	2289	c.1780G>A	c.(1780-1782)Gcc>Acc	p.A594T	DHX38_ENST00000536867.1_Intron	NM_014003.3	NP_054722.2	Q92620	PRP16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 38	594	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				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.A594T(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)				CATGTCAGTGGCCAAGAGAGT	0.557																																					p.A594T	Melanoma(97;711 1442 7855 13832 28836)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1780A	16						.						52.0	47.0	49.0					16																	72137643		2198	4300	6498	70695144	SO:0001583	missense	9785	exon13			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.1780G>A	16.37:g.72137643G>A	ENSP00000268482:p.Ala594Thr	Somatic		Capture	Illumina HiSeq	Phase_I	70695144	NM_014003	B4DVG8|D3DWS7|O75212|Q96HN7	Missense_Mutation	SNP	ENST00000268482.3	37	CCDS10907.1	.	.	.	.	.	.	.	.	.	.	G	36	5.711487	0.96821	.	.	ENSG00000140829	ENST00000268482	T	0.35789	1.29	5.22	5.22	0.72569	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.81583	0.4853	H	0.99977	5.165	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.91367	0.5116	10	0.87932	D	0	.	19.1592	0.93524	0.0:0.0:1.0:0.0	.	594	Q92620	PRP16_HUMAN	T	594	ENSP00000268482:A594T	ENSP00000268482:A594T	A	+	1	0	DHX38	70695144	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.700000	0.98707	2.586000	0.87340	0.563000	0.77884	GCC		0.557	DHX38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269004.3	NM_014003	
RFWD3	55159	broad.mit.edu	37	16	74662417	74662417	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:74662417C>T	ENST00000361070.4	-	11	1999	c.1902G>A	c.(1900-1902)gaG>gaA	p.E634E	RFWD3_ENST00000571750.1_Silent_p.E634E	NM_018124.3	NP_060594.3	Q6PCD5	RFWD3_HUMAN	ring finger and WD repeat domain 3	634					DNA repair (GO:0006281)|mitotic G1 DNA damage checkpoint (GO:0031571)|protein ubiquitination (GO:0016567)|regulation of DNA damage checkpoint (GO:2000001)|response to ionizing radiation (GO:0010212)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|MDM2/MDM4 family protein binding (GO:0097371)|p53 binding (GO:0002039)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E634E(1)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	26						AGCCCCCTGGCTCCAAGGGCA	0.522																																					p.E634E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1902A	16						.						114.0	113.0	114.0					16																	74662417		2198	4300	6498	73219918	SO:0001819	synonymous_variant	55159	exon11			AK001382	CCDS32486.1	16q22.3	2013-01-09						"""WD repeat domain containing"", ""RING-type (C3HC4) zinc fingers"""	25539	protein-coding gene	gene with protein product		614151				21504906	Standard	XM_005256021		Approved	FLJ10520, RNF201	uc002fda.3	Q6PCD5		ENST00000361070.4:c.1902G>A	16.37:g.74662417C>T		Somatic		Capture	Illumina HiSeq	Phase_I	73219918	NM_018124	A8K585|B2RE35|D3DUJ8|Q5XKR3|Q9H9Q3|Q9NVT4	Silent	SNP	ENST00000361070.4	37	CCDS32486.1																																																																																				0.522	RFWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436506.2	NM_018124	
CENPN	55839	broad.mit.edu	37	16	81060181	81060181	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:81060181C>T	ENST00000305850.5	+	9	1538	c.748C>T	c.(748-750)Cga>Tga	p.R250*	CENPN_ENST00000428963.2_Nonsense_Mutation_p.R216*|CENPN_ENST00000393335.3_Nonsense_Mutation_p.R250*|RP11-303E16.3_ENST00000566390.1_RNA|RP11-303E16.3_ENST00000562315.1_RNA|CENPN_ENST00000439957.3_Nonsense_Mutation_p.R230*|RP11-303E16.3_ENST00000561808.1_RNA	NM_001100624.2|NM_001270474.1	NP_001094094.2|NP_001257403.1	Q96H22	CENPN_HUMAN	centromere protein N	250					CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.R230*(1)		breast(1)|large_intestine(5)|lung(4)	10						GAGAGTCCAACGAATAACTCA	0.318																																					p.R250X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C748T	16						.						113.0	108.0	110.0					16																	81060181		1822	4071	5893	79617682	SO:0001587	stop_gained	55839	exon9			AK026313	CCDS10931.1, CCDS42199.1, CCDS42200.1, CCDS58482.1, CCDS58483.1	16q23.2	2013-11-05	2006-06-15	2006-06-15	ENSG00000166451	ENSG00000166451			30873	protein-coding gene	gene with protein product		611509	"""chromosome 16 open reading frame 60"""	C16orf60		16622419	Standard	NM_001100625		Approved	FLJ13607, FLJ22660, BM039	uc002ffy.4	Q96H22	OTTHUMG00000137628	ENST00000305850.5:c.748C>T	16.37:g.81060181C>T	ENSP00000305608:p.Arg250*	Somatic		Capture	Illumina HiSeq	Phase_I	79617682	NM_001100625	A8MZE6|B3KN53|B4DJD1|B4DPY7|C9JJM5|D3DUK8|E7ES30|E7ETS3|Q9NZ83	Nonsense_Mutation	SNP	ENST00000305850.5	37	CCDS42200.1	.	.	.	.	.	.	.	.	.	.	C	14.27	2.484737	0.44147	.	.	ENSG00000166451	ENST00000305850;ENST00000439957;ENST00000393335;ENST00000428963	.	.	.	5.25	1.46	0.22682	.	0.337495	0.35466	N	0.003199	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.0412	13.9653	0.64205	0.4846:0.5154:0.0:0.0	.	.	.	.	X	250;230;250;216	.	ENSP00000305608:R250X	R	+	1	2	CENPN	79617682	0.712000	0.27916	0.297000	0.24988	0.316000	0.28119	1.273000	0.33121	0.490000	0.27771	-0.397000	0.06425	CGA		0.318	CENPN-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269051.1	NM_018455	
MBTPS1	8720	broad.mit.edu	37	16	84088186	84088186	+	Silent	SNP	T	T	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:84088186T>A	ENST00000343411.3	-	23	3522	c.3027A>T	c.(3025-3027)ggA>ggT	p.G1009G		NM_003791.2	NP_003782.1	Q14703	MBTP1_HUMAN	membrane-bound transcription factor peptidase, site 1	1009					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cholesterol metabolic process (GO:0008203)|endoplasmic reticulum unfolded protein response (GO:0030968)|lipid metabolic process (GO:0006629)|lysosome organization (GO:0007040)|proteolysis (GO:0006508)|regulation of transcription factor import into nucleus (GO:0042990)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)	p.G1009G(1)		NS(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(10)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						CCACCATGGCTCCCAGGAAGG	0.602																																					p.G1009G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A3027T	16						.						82.0	70.0	74.0					16																	84088186		2200	4300	6500	82645687	SO:0001819	synonymous_variant	8720	exon23			D42053	CCDS10941.1	16q24	2008-08-04	2005-08-17		ENSG00000140943	ENSG00000140943			15456	protein-coding gene	gene with protein product		603355	"""membrane-bound transcription factor protease, site 1"""			9809072, 10944850	Standard	NM_003791		Approved	S1P, KIAA0091, SKI-1, PCSK8	uc002fhi.3	Q14703	OTTHUMG00000137639	ENST00000343411.3:c.3027A>T	16.37:g.84088186T>A		Somatic		Capture	Illumina HiSeq	Phase_I	82645687	NM_003791	A8K6V8|Q24JQ2|Q9UF67	Silent	SNP	ENST00000343411.3	37	CCDS10941.1																																																																																				0.602	MBTPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269080.2	NM_003791	
CRISPLD2	83716	broad.mit.edu	37	16	84900530	84900530	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:84900530C>T	ENST00000262424.5	+	7	961	c.737C>T	c.(736-738)aCg>aTg	p.T246M	CRISPLD2_ENST00000564567.1_Missense_Mutation_p.T246M|CRISPLD2_ENST00000567845.1_Missense_Mutation_p.T245M	NM_031476.3	NP_113664.1	Q9H0B8	CRLD2_HUMAN	cysteine-rich secretory protein LCCL domain containing 2	246					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.T246M(1)		endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)	18						AAACCTGAAACGGACGAGATG	0.448																																					p.T246M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C737T	16						.						105.0	92.0	96.0					16																	84900530		2199	4300	6499	83458031	SO:0001583	missense	83716	exon7			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.737C>T	16.37:g.84900530C>T	ENSP00000262424:p.Thr246Met	Somatic		Capture	Illumina HiSeq	Phase_I	83458031	NM_031476	D3DUM0|Q6P590|Q6UWH0|Q6UXC6|Q96IB1|Q96K61	Missense_Mutation	SNP	ENST00000262424.5	37	CCDS10949.1	.	.	.	.	.	.	.	.	.	.	C	7.784	0.710136	0.15239	.	.	ENSG00000103196	ENST00000262424	T	0.65732	-0.17	5.66	4.7	0.59300	.	0.344507	0.33631	N	0.004711	T	0.70684	0.3252	M	0.75264	2.295	0.21473	N	0.999679	D;D;D	0.76494	0.965;0.998;0.999	P;P;P	0.57057	0.459;0.812;0.742	T	0.64193	-0.6465	10	0.49607	T	0.09	.	8.0405	0.30519	0.0:0.8157:0.0:0.1843	.	246;246;246	Q9H0B8;Q9H0B8-2;Q9H0B8-3	CRLD2_HUMAN;.;.	M	246	ENSP00000262424:T246M	ENSP00000262424:T246M	T	+	2	0	CRISPLD2	83458031	0.356000	0.24930	0.010000	0.14722	0.001000	0.01503	0.575000	0.23729	1.362000	0.46000	0.655000	0.94253	ACG		0.448	CRISPLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269086.2	NM_031476	
ZDHHC7	55625	broad.mit.edu	37	16	85015579	85015579	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:85015579C>T	ENST00000313732.4	-	4	689	c.337G>A	c.(337-339)Gct>Act	p.A113T	ZDHHC7_ENST00000569488.1_Intron|ZDHHC7_ENST00000564466.1_Missense_Mutation_p.A150T	NM_017740.2	NP_060210.2	Q9NXF8	ZDHC7_HUMAN	zinc finger, DHHC-type containing 7	113					peptidyl-L-cysteine S-palmitoylation (GO:0018230)|protein palmitoylation (GO:0018345)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.A113T(1)		large_intestine(6)|lung(4)	10						TCTTTCGTAGCGTTTCCTTTG	0.512																																					p.A113T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G337A	16						.						142.0	145.0	144.0					16																	85015579		2199	4300	6499	83573080	SO:0001583	missense	55625	exon4			AK000286	CCDS10950.1, CCDS45538.1	16q23.1	2010-02-09			ENSG00000153786	ENSG00000153786		"""Zinc fingers, DHHC-type"""	18459	protein-coding gene	gene with protein product	"""Sertoli cell gene with zinc finger domain-&#946;"""	614604					Standard	NM_017740		Approved	FLJ10792, ZNF370, FLJ20279, SERZ-B, SERZ1	uc002fiq.2	Q9NXF8	OTTHUMG00000137645	ENST00000313732.4:c.337G>A	16.37:g.85015579C>T	ENSP00000315604:p.Ala113Thr	Somatic		Capture	Illumina HiSeq	Phase_I	83573080	NM_017740	D3DUM1|Q8WV42|Q9NVD8	Missense_Mutation	SNP	ENST00000313732.4	37	CCDS10950.1	.	.	.	.	.	.	.	.	.	.	C	18.59	3.657886	0.67586	.	.	ENSG00000153786	ENST00000313732;ENST00000344861	T;T	0.36699	1.87;1.24	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.58807	0.2148	M	0.64997	1.995	0.80722	D	1	P;D	0.89917	0.943;1.0	P;D	0.74674	0.576;0.984	T	0.58317	-0.7657	10	0.54805	T	0.06	-2.262	18.4162	0.90571	0.0:1.0:0.0:0.0	.	150;113	Q9NXF8-2;Q9NXF8	.;ZDHC7_HUMAN	T	113;150	ENSP00000315604:A113T;ENSP00000341681:A150T	ENSP00000315604:A113T	A	-	1	0	ZDHHC7	83573080	1.000000	0.71417	0.132000	0.22025	0.004000	0.04260	7.642000	0.83385	2.658000	0.90341	0.655000	0.94253	GCT		0.512	ZDHHC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269087.1	NM_017740	
GSE1	23199	broad.mit.edu	37	16	85706054	85706054	+	Missense_Mutation	SNP	G	G	A	rs368544307		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:85706054G>A	ENST00000253458.7	+	16	3739	c.3563G>A	c.(3562-3564)cGg>cAg	p.R1188Q	GSE1_ENST00000393243.1_Missense_Mutation_p.R1115Q|GSE1_ENST00000405402.2_Missense_Mutation_p.R1084Q|GSE1_ENST00000471070.1_3'UTR	NM_014615.2	NP_055430.1	Q14687	GSE1_HUMAN	Gse1 coiled-coil protein	1188								p.R1188Q(1)									GAAAGGGAGCGGCTCCAGGCA	0.532																																					p.R1084Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3251A	16						.	G	GLN/ARG,GLN/ARG	0,4396		0,0,2198	59.0	49.0	52.0		3251,3563	5.9	1.0	16		52	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	KIAA0182	NM_001134473.1,NM_014615.2	43,43	0,1,6497	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	1084/1114,1188/1218	85706054	1,12995	2198	4300	6498	84263555	SO:0001583	missense	23199	exon15			D80004	CCDS10952.1, CCDS45539.1, CCDS62007.1	16q24.1	2012-12-07	2012-12-07	2012-10-02	ENSG00000131149	ENSG00000131149			28979	protein-coding gene	gene with protein product	"""genetic suppressor element 1"""		"""KIAA0182"", ""Gse1 coiled-coil protein homolog (mouse)"""	KIAA0182		8724849, 8786132	Standard	NM_014615		Approved		uc002fix.4	Q14687	OTTHUMG00000137650	ENST00000253458.7:c.3563G>A	16.37:g.85706054G>A	ENSP00000253458:p.Arg1188Gln	Somatic		Capture	Illumina HiSeq	Phase_I	84263555	NM_001134473	D3DUM4|Q8IY61|Q96GA4|Q9BW09	Missense_Mutation	SNP	ENST00000253458.7	37	CCDS10952.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.4|22.4	4.281295|4.281295	0.80692|0.80692	0.0|0.0	1.16E-4|1.16E-4	ENSG00000131149|ENSG00000131149	ENST00000412692|ENST00000405402;ENST00000253458;ENST00000393243	.|T;T;T	.|0.33438	.|1.41;1.41;1.41	5.89|5.89	5.89|5.89	0.94794|0.94794	.|.	.|0.180182	.|0.47093	.|D	.|0.000244	T|T	0.53642|0.53642	0.1809|0.1809	M|M	0.62723|0.62723	1.935|1.935	0.39186|0.39186	D|D	0.962873|0.962873	.|D;D;D	.|0.71674	.|0.998;0.998;0.997	.|P;P;P	.|0.62089	.|0.898;0.898;0.793	T|T	0.54629|0.54629	-0.8265|-0.8265	5|10	.|0.72032	.|D	.|0.01	-24.3256|-24.3256	20.2617|20.2617	0.98447|0.98447	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1084;1115;1188	.|Q14687-2;Q14687-3;Q14687	.|.;.;GSE1_HUMAN	S|Q	957|1084;1188;1115	.|ENSP00000384839:R1084Q;ENSP00000253458:R1188Q;ENSP00000376934:R1115Q	.|ENSP00000253458:R1188Q	G|R	+|+	1|2	0|0	KIAA0182|KIAA0182	84263555|84263555	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.875000|0.875000	0.50365|0.50365	5.858000|5.858000	0.69532|0.69532	2.793000|2.793000	0.96121|0.96121	0.655000|0.655000	0.94253|0.94253	GGC|CGG		0.532	GSE1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325527.1	NM_014615	
FBXO31	79791	broad.mit.edu	37	16	87393909	87393909	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:87393909T>C	ENST00000311635.7	-	2	416	c.404A>G	c.(403-405)tAt>tGt	p.Y135C	RP11-178L8.9_ENST00000602779.1_RNA	NM_001282683.1|NM_024735.3	NP_001269612.1|NP_079011.3	Q5XUX0	FBX31_HUMAN	F-box protein 31	135					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.Y135C(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)		ACGCTTCGCATAGACGTCCCG	0.408																																					p.Y135C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A404G	16						.						134.0	117.0	123.0					16																	87393909		2198	4300	6498	85951410	SO:0001583	missense	79791	exon2			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.404A>G	16.37:g.87393909T>C	ENSP00000310841:p.Tyr135Cys	Somatic		Capture	Illumina HiSeq	Phase_I	85951410	NM_024735	Q5K680|Q8WYV1|Q96D73|Q9UFV4	Missense_Mutation	SNP	ENST00000311635.7	37	CCDS32501.1	.	.	.	.	.	.	.	.	.	.	T	18.21	3.573414	0.65765	.	.	ENSG00000103264	ENST00000311635	T	0.70631	-0.5	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.75140	0.3809	L	0.27053	0.805	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.66196	0.942;0.912	T	0.78823	-0.2052	10	0.87932	D	0	-8.3194	15.8578	0.78994	0.0:0.0:0.0:1.0	.	135;27	Q5XUX0;Q5XUX0-2	FBX31_HUMAN;.	C	135	ENSP00000310841:Y135C	ENSP00000310841:Y135C	Y	-	2	0	FBXO31	85951410	1.000000	0.71417	0.940000	0.37924	0.481000	0.33189	6.500000	0.73687	2.147000	0.66899	0.533000	0.62120	TAT		0.408	FBXO31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430799.2	NM_024735	
DEF8	54849	broad.mit.edu	37	16	90030983	90030983	+	Splice_Site	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr16:90030983G>A	ENST00000268676.7	+	12	1525	c.1436G>A	c.(1435-1437)aGg>aAg	p.R479K	DEF8_ENST00000569453.1_Splice_Site_p.R418K|DEF8_ENST00000563594.1_Splice_Site_p.R418K|DEF8_ENST00000570182.1_Splice_Site_p.R408K|DEF8_ENST00000567874.1_Splice_Site_p.R358K|DEF8_ENST00000563795.1_Splice_Site_p.R401K	NM_207514.2	NP_997397.1	Q6ZN54	DEFI8_HUMAN	differentially expressed in FDCP 8 homolog (mouse)	479					intracellular signal transduction (GO:0035556)		zinc ion binding (GO:0008270)	p.R479K(1)		central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12		all_cancers(9;7.59e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.0019)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0274)		GTCTTCCACAGGTGGGTGTGG	0.687																																					p.R479K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1436A	16						.						28.0	23.0	25.0					16																	90030983		2182	4283	6465	88558484	SO:0001630	splice_region_variant	54849	exon12			AK131370	CCDS10989.1, CCDS45555.1, CCDS58493.1, CCDS58494.1, CCDS58495.1, CCDS58496.1	16q24.3	2011-01-31			ENSG00000140995	ENSG00000140995			25969	protein-coding gene	gene with protein product						12477932	Standard	NM_207514		Approved	FLJ20186	uc002fpn.2	Q6ZN54	OTTHUMG00000138989	ENST00000268676.7:c.1436+1G>A	16.37:g.90030983G>A		Somatic		Capture	Illumina HiSeq	Phase_I	88558484	NM_207514	B3KT65|B4DK62|B4E0S9|B7Z3H6|H3BUG7|Q8N8N3|Q9NXL0	Missense_Mutation	SNP	ENST00000268676.7	37	CCDS10989.1	.	.	.	.	.	.	.	.	.	.	g	21.0	4.089415	0.76756	.	.	ENSG00000140995	ENST00000268676	T	0.41400	1.0	5.22	5.22	0.72569	Zinc finger, RING-type (1);Protein kinase C-like, phorbol ester/diacylglycerol binding (1);	0.000000	0.85682	D	0.000000	T	0.29524	0.0736	N	0.16602	0.42	0.80722	D	1	B;B;B;P	0.35684	0.28;0.234;0.28;0.515	B;B;B;B	0.35039	0.09;0.028;0.09;0.194	T	0.07102	-1.0790	10	0.24483	T	0.36	-12.8243	17.5674	0.87923	0.0:0.0:1.0:0.0	.	418;358;408;479	Q6ZN54-5;Q6ZN54-4;Q6ZN54-3;Q6ZN54	.;.;.;DEFI8_HUMAN	K	479	ENSP00000268676:R479K	ENSP00000268676:R479K	R	+	2	0	DEF8	88558484	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	9.016000	0.93645	2.453000	0.82957	0.651000	0.88453	AGG		0.687	DEF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000272878.1	NM_207514	Missense_Mutation
MYH8	4626	broad.mit.edu	37	17	10322011	10322011	+	Silent	SNP	C	C	T	rs376637883		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:10322011C>T	ENST00000403437.2	-	5	556	c.462G>A	c.(460-462)ccG>ccA	p.P154P	RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	154	Myosin motor.				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.P154P(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						AGATGTGGGGCGGGGCCTCCT	0.522									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling																												p.P154P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G462A	17						.	C		2,4404	4.2+/-10.8	0,2,2201	107.0	118.0	114.0		462	-1.2	1.0	17		114	0,8596		0,0,4298	no	coding-synonymous	MYH8	NM_002472.2		0,2,6499	TT,TC,CC		0.0,0.0454,0.0154		154/1938	10322011	2,13000	2203	4298	6501	10262736	SO:0001819	synonymous_variant	4626	exon5	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.462G>A	17.37:g.10322011C>T		Somatic		Capture	Illumina HiSeq	Phase_I	10262736	NM_002472	Q14910	Silent	SNP	ENST00000403437.2	37	CCDS11153.1																																																																																				0.522	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472	
PRPF8	10594	broad.mit.edu	37	17	1578592	1578592	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:1578592C>T	ENST00000572621.1	-	19	3179	c.2914G>A	c.(2914-2916)Gag>Aag	p.E972K	PRPF8_ENST00000304992.6_Missense_Mutation_p.E972K			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	972	Reverse transcriptase homology domain.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)	p.E972K(1)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		ACATTGCACTCGCCTTCACTC	0.527																																					p.E972K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2914A	17						.						160.0	128.0	139.0					17																	1578592		2203	4300	6503	1525342	SO:0001583	missense	10594	exon20			AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231			17340	protein-coding gene	gene with protein product		607300	"""PRP8 pre-mRNA processing factor 8 homolog (yeast)"", ""PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)"""	RP13		11468273, 10411133	Standard	NM_006445		Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.2914G>A	17.37:g.1578592C>T	ENSP00000460348:p.Glu972Lys	Somatic		Capture	Illumina HiSeq	Phase_I	1525342	NM_006445	O14547|O75965	Missense_Mutation	SNP	ENST00000572621.1	37	CCDS11010.1	.	.	.	.	.	.	.	.	.	.	C	34	5.302005	0.95601	.	.	ENSG00000174231	ENST00000304992	T	0.81078	-1.45	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.81361	0.4806	M	0.68728	2.09	0.80722	D	1	B	0.10296	0.003	B	0.13407	0.009	T	0.75243	-0.3386	10	0.45353	T	0.12	-4.8239	20.2562	0.98421	0.0:1.0:0.0:0.0	.	972	Q6P2Q9	PRP8_HUMAN	K	972	ENSP00000304350:E972K	ENSP00000304350:E972K	E	-	1	0	PRPF8	1525342	1.000000	0.71417	0.985000	0.45067	0.877000	0.50540	7.818000	0.86416	2.797000	0.96272	0.563000	0.77884	GAG		0.527	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438412.2		
DNAH9	1770	broad.mit.edu	37	17	11790240	11790240	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:11790240C>T	ENST00000262442.4	+	57	11138	c.11070C>T	c.(11068-11070)aaC>aaT	p.N3690N	DNAH9_ENST00000396001.2_3'UTR|DNAH9_ENST00000454412.2_Silent_p.N3690N|DNAH9_ENST00000608377.1_Silent_p.N2N	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	3690					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.N3690N(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)		TCATCATGAACGACCTCAGCA	0.488																																					p.N2N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C6T	17						.						124.0	103.0	110.0					17																	11790240		2203	4300	6503	11730965	SO:0001819	synonymous_variant	1770	exon3			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.11070C>T	17.37:g.11790240C>T		Somatic		Capture	Illumina HiSeq	Phase_I	11730965	NM_004662	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																				0.488	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
TRPV2	51393	broad.mit.edu	37	17	16331649	16331649	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:16331649C>T	ENST00000338560.7	+	9	1768	c.1369C>T	c.(1369-1371)Cgc>Tgc	p.R457C	TRPV2_ENST00000583241.1_3'UTR|TRPV2_ENST00000577397.1_Missense_Mutation_p.R27C|AC093484.4_ENST00000441875.1_RNA	NM_016113.4	NP_057197.2	Q9Y5S1	TRPV2_HUMAN	transient receptor potential cation channel, subfamily V, member 2	457					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|positive regulation of axon extension (GO:0045773)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|response to temperature stimulus (GO:0009266)|sensory perception (GO:0007600)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axonal growth cone (GO:0044295)|cell body (GO:0044297)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|growth cone membrane (GO:0032584)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|ion channel activity (GO:0005216)|ion transmembrane transporter activity (GO:0015075)	p.R457C(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|stomach(3)	28				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		CTTCTGGCGGCGCCACGTGTT	0.582											OREG0024202	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R457C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1369T	17						.						186.0	170.0	176.0					17																	16331649		2203	4300	6503	16272374	SO:0001583	missense	51393	exon9			AF129112	CCDS32576.1	17p11.2	2013-01-10			ENSG00000187688	ENSG00000187688		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	18082	protein-coding gene	gene with protein product		606676				10201375, 16382100	Standard	NM_016113		Approved	VRL, VRL-1, VRL1	uc002gpy.3	Q9Y5S1	OTTHUMG00000058989	ENST00000338560.7:c.1369C>T	17.37:g.16331649C>T	ENSP00000342222:p.Arg457Cys	Somatic	709	Capture	Illumina HiSeq	Phase_I	16272374	NM_016113	A6NML2|A8K0Z0|Q9Y670	Missense_Mutation	SNP	ENST00000338560.7	37	CCDS32576.1	.	.	.	.	.	.	.	.	.	.	C	15.97	2.988987	0.53934	.	.	ENSG00000187688	ENST00000338560	D	0.90004	-2.6	5.57	4.55	0.56014	Ion transport (1);	0.044877	0.85682	D	0.000000	D	0.94095	0.8107	M	0.82630	2.6	0.53688	D	0.999972	D	0.89917	1.0	D	0.83275	0.996	D	0.94211	0.7459	10	0.66056	D	0.02	-36.9794	12.8081	0.57626	0.2186:0.7814:0.0:0.0	.	457	Q9Y5S1	TRPV2_HUMAN	C	457	ENSP00000342222:R457C	ENSP00000342222:R457C	R	+	1	0	TRPV2	16272374	0.995000	0.38212	0.890000	0.34922	0.772000	0.43724	1.582000	0.36568	2.627000	0.88993	0.650000	0.86243	CGC		0.582	TRPV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130464.2	NM_016113	
TNFRSF13B	23495	broad.mit.edu	37	17	16843010	16843010	+	Missense_Mutation	SNP	C	C	T	rs372816963		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:16843010C>T	ENST00000261652.2	-	5	745	c.733G>A	c.(733-735)Gca>Aca	p.A245T	TNFRSF13B_ENST00000437538.2_Missense_Mutation_p.A199T|TNFRSF13B_ENST00000581616.2_5'Flank|TNFRSF13B_ENST00000579315.1_Intron|TNFRSF13B_ENST00000583789.1_Missense_Mutation_p.A199T	NM_012452.2	NP_036584.1	O14836	TR13B_HUMAN	tumor necrosis factor receptor superfamily, member 13B	245					B cell homeostasis (GO:0001782)|cell surface receptor signaling pathway (GO:0007166)|hematopoietic progenitor cell differentiation (GO:0002244)|negative regulation of B cell proliferation (GO:0030889)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)	p.A245T(1)		endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(7)|skin(1)	16						GGCGTGACTGCGCTCTCCTGC	0.667									IgA Deficiency, Selective																												p.A245T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G733A	17						.	C	THR/ALA	0,4406		0,0,2203	35.0	33.0	34.0		733	0.9	0.0	17		34	1,8599	1.2+/-3.3	0,1,4299	no	missense	TNFRSF13B	NM_012452.2	58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	245/294	16843010	1,13005	2203	4300	6503	16783735	SO:0001583	missense	23495	exon5	Familial Cancer Database	IGAD1, IGAD2	AF023614	CCDS11181.1	17p11.2	2014-09-17			ENSG00000240505	ENSG00000240505		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	18153	protein-coding gene	gene with protein product		604907				9311921	Standard	NM_012452		Approved	TACI, CD267	uc002gqs.1	O14836	OTTHUMG00000059262	ENST00000261652.2:c.733G>A	17.37:g.16843010C>T	ENSP00000261652:p.Ala245Thr	Somatic		Capture	Illumina HiSeq	Phase_I	16783735	NM_012452	B2R8B0|B7Z6V8|Q32LX4|Q7Z6F5	Missense_Mutation	SNP	ENST00000261652.2	37	CCDS11181.1	.	.	.	.	.	.	.	.	.	.	C	7.470	0.646502	0.14451	0.0	1.16E-4	ENSG00000240505	ENST00000437538;ENST00000261652	D;D	0.93076	-3.16;-3.13	3.12	0.895	0.19247	.	0.669254	0.13622	N	0.374350	D	0.85703	0.5758	L	0.38175	1.15	0.09310	N	1	P;P	0.40931	0.733;0.614	B;B	0.35413	0.202;0.1	T	0.76626	-0.2890	10	0.44086	T	0.13	-4.6595	4.1945	0.10437	0.2242:0.6397:0.0:0.1361	.	199;245	O14836-2;O14836	.;TR13B_HUMAN	T	199;245	ENSP00000413453:A199T;ENSP00000261652:A245T	ENSP00000261652:A245T	A	-	1	0	TNFRSF13B	16783735	0.001000	0.12720	0.032000	0.17829	0.005000	0.04900	-0.451000	0.06795	0.096000	0.17463	-0.480000	0.04831	GCA		0.667	TNFRSF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131474.2		
DRG2	1819	broad.mit.edu	37	17	17997275	17997275	+	Silent	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:17997275C>A	ENST00000225729.3	+	2	351	c.213C>A	c.(211-213)ccC>ccA	p.P71P	DRG2_ENST00000395726.4_Silent_p.P71P|DRG2_ENST00000583355.1_Silent_p.P71P	NM_001388.4	NP_001379.1	P55039	DRG2_HUMAN	developmentally regulated GTP binding protein 2	71	OBG-type G. {ECO:0000255|PROSITE- ProRule:PRU01047}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)	p.P71P(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	14	all_neural(463;0.228)					TTGGATTTCCCTCTGTGGGTA	0.572																																					p.P71P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C213A	17						.						170.0	139.0	150.0					17																	17997275		2203	4300	6503	17938000	SO:0001819	synonymous_variant	1819	exon2			X80754	CCDS11191.1	17p13-p12	2008-07-18	2001-11-28		ENSG00000108591	ENSG00000108591			3030	protein-coding gene	gene with protein product		602986	"""developmentally regulated GTP-binding protein 2"""			9605870, 7929244	Standard	NM_001388		Approved		uc002gsh.2	P55039	OTTHUMG00000059399	ENST00000225729.3:c.213C>A	17.37:g.17997275C>A		Somatic		Capture	Illumina HiSeq	Phase_I	17938000	NM_001388	B2R8G5|Q53Y50|Q9BWB2	Silent	SNP	ENST00000225729.3	37	CCDS11191.1																																																																																				0.572	DRG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132075.3	NM_001388	
USP22	23326	broad.mit.edu	37	17	20919098	20919098	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:20919098C>T	ENST00000261497.4	-	6	1008	c.805G>A	c.(805-807)Gcg>Acg	p.A269T	USP22_ENST00000455117.2_Intron|USP22_ENST00000537526.2_Missense_Mutation_p.A257T	NM_015276.1	NP_056091.1	Q9UPT9	UBP22_HUMAN	ubiquitin specific peptidase 22	269	USP.				cell cycle (GO:0007049)|chromatin organization (GO:0006325)|embryo development (GO:0009790)|histone deubiquitination (GO:0016578)|histone H4 acetylation (GO:0043967)|histone ubiquitination (GO:0016574)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|protein deubiquitination (GO:0016579)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	SAGA complex (GO:0000124)	enzyme binding (GO:0019899)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|transcription coactivator activity (GO:0003713)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.A491T(1)		endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	15						TCCAGGGCCGCGATGAGGAAC	0.632																																					p.A269T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G805A	17						.						45.0	54.0	51.0					17																	20919098		2037	4180	6217	20859690	SO:0001583	missense	23326	exon6			AB028986	CCDS42285.1	17p11.2	2006-11-24	2005-08-08		ENSG00000124422	ENSG00000124422		"""Ubiquitin-specific peptidases"""	12621	protein-coding gene	gene with protein product		612116	"""ubiquitin specific protease 22"", ""ubiquitin specific peptidase 3-like"""	USP3L		12838346	Standard	NM_015276		Approved	KIAA1063	uc002gym.4	Q9UPT9	OTTHUMG00000133621	ENST00000261497.4:c.805G>A	17.37:g.20919098C>T	ENSP00000261497:p.Ala269Thr	Somatic		Capture	Illumina HiSeq	Phase_I	20859690	NM_015276	A0JNS3|Q2NLE2|Q6MZY4|Q8TBS8|Q96IW5	Missense_Mutation	SNP	ENST00000261497.4	37	CCDS42285.1	.	.	.	.	.	.	.	.	.	.	c	27.8	4.862183	0.91511	.	.	ENSG00000124422	ENST00000455117;ENST00000537526;ENST00000261497	T;T	0.30714	1.52;1.52	3.72	3.72	0.42706	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.64402	D	0.000001	T	0.47875	0.1469	L	0.54323	1.7	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.74023	0.953;0.982	T	0.38286	-0.9668	10	0.22706	T	0.39	.	15.8267	0.78711	0.0:1.0:0.0:0.0	.	257;269	Q9UPT9-2;Q9UPT9	.;UBP22_HUMAN	T	337;257;269	ENSP00000440950:A257T;ENSP00000261497:A269T	ENSP00000261497:A269T	A	-	1	0	USP22	20859690	1.000000	0.71417	0.767000	0.31495	0.812000	0.45895	6.439000	0.73430	1.788000	0.52465	0.563000	0.77884	GCG		0.632	USP22-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444169.1		
SLC46A1	113235	broad.mit.edu	37	17	26722963	26722963	+	3'UTR	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:26722963C>T	ENST00000440501.1	-	0	5184				SLC46A1_ENST00000584729.1_5'UTR|SARM1_ENST00000457710.3_Missense_Mutation_p.P621S|SLC46A1_ENST00000321666.5_3'UTR|SARM1_ENST00000379061.4_3'UTR	NM_080669.4	NP_542400.2	Q96NT5	PCFT_HUMAN	solute carrier family 46 (folate transporter), member 1						cellular iron ion homeostasis (GO:0006879)|folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|heme transporter activity (GO:0015232)|methotrexate transporter activity (GO:0015350)	p.P653S(1)		lung(5)	5	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Folic Acid(DB00158)|Methotrexate(DB00563)|Sulfasalazine(DB00795)	GAACATTGTGCCCATCATTGA	0.542																																					p.A654V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1961T	17						.						96.0	89.0	92.0					17																	26722963		2203	4300	6503	23747090	SO:0001624	3_prime_UTR_variant	23098	exon8			AK054669	CCDS74019.1, CCDS74020.1	17q11.2	2014-09-17	2007-09-24			ENSG00000076351		"""Solute carriers"""	30521	protein-coding gene	gene with protein product	"""heme carrier protein 1"", ""proton-coupled folate transporter"""	611672	"""solute carrier family 46, member 1"""			16143108, 17129779	Standard	XM_005277786		Approved	HCP1, MGC9564, PCFT	uc002hbf.2	Q96NT5		ENST00000440501.1:c.*3709G>A	17.37:g.26722963C>T		Somatic		Capture	Illumina HiSeq	Phase_I	23747090	NM_015077	Q1HE20|Q86T92|Q8TEG3|Q96FL0	Missense_Mutation	SNP	ENST00000440501.1	37		.	.	.	.	.	.	.	.	.	.	C	32	5.120293	0.94385	.	.	ENSG00000004139	ENST00000457710;ENST00000003834	.	.	.	4.68	4.68	0.58851	Toll/interleukin-1 receptor homology (TIR) domain (2);	0.000000	0.85682	D	0.000000	T	0.80602	0.4654	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84268	0.0487	8	0.87932	D	0	-26.8028	17.6006	0.88024	0.0:1.0:0.0:0.0	.	655	Q6SZW1	SARM1_HUMAN	S	653;621	.	ENSP00000003834:P621S	P	+	1	0	SARM1	23747090	1.000000	0.71417	0.993000	0.49108	0.961000	0.63080	7.810000	0.86072	2.138000	0.66242	0.561000	0.74099	CCC		0.542	SLC46A1-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_080669	
SPAG5	10615	broad.mit.edu	37	17	26919547	26919547	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:26919547C>T	ENST00000321765.5	-	3	1047	c.715G>A	c.(715-717)Gcc>Acc	p.A239T		NM_006461.3	NP_006452.3	Q96R06	SPAG5_HUMAN	sperm associated antigen 5	239					chromosome segregation (GO:0007059)|mitotic sister chromatid segregation (GO:0000070)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|microtubule plus-end (GO:0035371)|mitotic spindle (GO:0072686)		p.A239T(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43	Lung NSC(42;0.00431)					GGCAAGAAGGCGTTACTTTCA	0.493																																					p.A239T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G715A	17						.						129.0	117.0	121.0					17																	26919547		2203	4300	6503	23943674	SO:0001583	missense	10615	exon3			AF063308	CCDS32594.1	17q11.2	2008-07-18			ENSG00000076382	ENSG00000076382			13452	protein-coding gene	gene with protein product	"""mitotic spindle coiled-coil related protein"", ""astrin"", ""mitotic spindle associated protein p126"""	615562				11549262	Standard	NM_006461		Approved	DEEPEST, MAP126, hMAP126	uc002hbq.3	Q96R06	OTTHUMG00000166586	ENST00000321765.5:c.715G>A	17.37:g.26919547C>T	ENSP00000323300:p.Ala239Thr	Somatic		Capture	Illumina HiSeq	Phase_I	23943674	NM_006461	O95213|Q9BWE8|Q9NT17|Q9UFE6	Missense_Mutation	SNP	ENST00000321765.5	37	CCDS32594.1	.	.	.	.	.	.	.	.	.	.	c	5.596	0.294730	0.10567	.	.	ENSG00000076382	ENST00000321765	T	0.20069	2.1	5.22	-5.6	0.02497	.	1.565570	0.03696	N	0.247894	T	0.10078	0.0247	N	0.13043	0.29	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.26395	-1.0104	10	0.40728	T	0.16	5.7588	2.8024	0.05418	0.1298:0.2392:0.1168:0.5142	.	239	Q96R06	SPAG5_HUMAN	T	239	ENSP00000323300:A239T	ENSP00000323300:A239T	A	-	1	0	SPAG5	23943674	0.000000	0.05858	0.003000	0.11579	0.272000	0.26649	-0.663000	0.05299	-0.611000	0.05709	-0.735000	0.03563	GCC		0.493	SPAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390564.2	NM_006461	
OR1D2	4991	broad.mit.edu	37	17	2995508	2995508	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:2995508C>T	ENST00000331459.1	-	1	782	c.783G>A	c.(781-783)aaG>aaA	p.K261K		NM_002548.2	NP_002539.2	P34982	OR1D2_HUMAN	olfactory receptor, family 1, subfamily D, member 2	261					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|G-protein coupled receptor signaling pathway (GO:0007186)|protein import into nucleus, translocation (GO:0000060)|sensory perception of smell (GO:0007608)|single fertilization (GO:0007338)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(2)|large_intestine(2)|lung(10)|ovary(1)	15						TATGGAGGGGCTTTAGGTATA	0.488																																					p.K261K												.	.	0			c.G783A	17						.						104.0	98.0	100.0					17																	2995508		2203	4300	6503	2942258	SO:0001819	synonymous_variant	4991	exon1			U04678	CCDS11019.1	17p13.3	2012-08-09			ENSG00000184166	ENSG00000184166		"""GPCR / Class A : Olfactory receptors"""	8183	protein-coding gene	gene with protein product		164342		OLFR1		1370859, 1840504	Standard	NM_002548		Approved	OR17-4	uc010vrb.2	P34982	OTTHUMG00000090619	ENST00000331459.1:c.783G>A	17.37:g.2995508C>T		None		Capture	Illumina HiSeq	Phase_I	2942258	NM_002548	Q6IFL8|Q96RA4|Q9UM78	Silent	SNP	ENST00000331459.1	37	CCDS11019.1																																																																																				0.488	OR1D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207207.1	NM_002548	
SUPT6H	6830	broad.mit.edu	37	17	27031032	27031032	+	IGR	SNP	C	C	T	rs377488532		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:27031032C>T	ENST00000314616.6	+	0	6518				PROCA1_ENST00000579650.1_5'Flank|PROCA1_ENST00000301039.2_Silent_p.A185A|PROCA1_ENST00000581289.1_3'UTR|PROCA1_ENST00000439862.3_Silent_p.A187A	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)						chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A185A(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)					TGGTGATGGGCGCTGTGGAGT	0.597																																					p.A185A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G555A	17						.	C		1,4403	2.1+/-5.4	0,1,2201	28.0	27.0	27.0		555	-4.4	0.9	17		27	0,8600		0,0,4300	no	coding-synonymous	PROCA1	NM_152465.1		0,1,6501	TT,TC,CC		0.0,0.0227,0.0077		185/337	27031032	1,13003	2202	4300	6502	24055159	SO:0001628	intergenic_variant	147011	exon4			U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"""SH2 domain containing"""	11470	protein-coding gene	gene with protein product		601333	"""suppressor of Ty (S.cerevisiae) 6 homolog"""			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85			17.37:g.27031032C>T		Somatic		Capture	Illumina HiSeq	Phase_I	24055159	NM_152465	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Silent	SNP	ENST00000314616.6	37	CCDS32596.1																																																																																				0.597	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170	
TMEM132E	124842	broad.mit.edu	37	17	32964220	32964220	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:32964220T>C	ENST00000321639.5	+	10	2252	c.1924T>C	c.(1924-1926)Tcc>Ccc	p.S642P		NM_207313.1	NP_997196.1	Q6IEE7	T132E_HUMAN	transmembrane protein 132E	642						integral component of membrane (GO:0016021)		p.S642P(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(28)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	57				BRCA - Breast invasive adenocarcinoma(366;0.231)		CCTCTGGCTCTCCTACAGTGA	0.582																																					p.S642P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1924C	17						.						76.0	72.0	73.0					17																	32964220		2203	4300	6503	29988333	SO:0001583	missense	124842	exon10			BN000149	CCDS11283.1	17q12	2012-11-01			ENSG00000181291	ENSG00000181291			26991	protein-coding gene	gene with protein product							Standard	NM_207313		Approved		uc002hif.3	Q6IEE7	OTTHUMG00000132927	ENST00000321639.5:c.1924T>C	17.37:g.32964220T>C	ENSP00000316532:p.Ser642Pro	Somatic		Capture	Illumina HiSeq	Phase_I	29988333	NM_207313	Q8WUF4|Q8WVA5	Missense_Mutation	SNP	ENST00000321639.5	37	CCDS11283.1	.	.	.	.	.	.	.	.	.	.	T	16.31	3.086477	0.55861	.	.	ENSG00000181291	ENST00000321639	T	0.16073	2.37	4.7	4.7	0.59300	.	0.269957	0.38326	N	0.001723	T	0.17534	0.0421	L	0.61218	1.895	0.37491	D	0.916394	B	0.32620	0.378	B	0.32393	0.145	T	0.08269	-1.0730	10	0.33141	T	0.24	-40.4328	9.015	0.36164	0.1644:0.0:0.0:0.8356	.	642	Q6IEE7	T132E_HUMAN	P	642	ENSP00000316532:S642P	ENSP00000316532:S642P	S	+	1	0	TMEM132E	29988333	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.063000	0.49978	1.973000	0.57446	0.523000	0.50628	TCC		0.582	TMEM132E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256440.2	NM_207313	
UNC45B	146862	broad.mit.edu	37	17	33501381	33501381	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:33501381C>A	ENST00000268876.5	+	14	2054	c.1957C>A	c.(1957-1959)Ctg>Atg	p.L653M	UNC45B_ENST00000394570.2_Missense_Mutation_p.L651M|UNC45B_ENST00000591048.1_Missense_Mutation_p.L572M|UNC45B_ENST00000433649.1_Missense_Mutation_p.L651M|UNC45B_ENST00000378449.1_Missense_Mutation_p.L572M	NM_173167.2	NP_775259.1	Q8IWX7	UN45B_HUMAN	unc-45 homolog B (C. elegans)	653					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.L653M(1)		breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(10)|lung(24)|ovary(3)|prostate(2)|skin(1)|stomach(1)|urinary_tract(3)	59		Ovarian(249;0.17)				CAAGGAGCTGCTGGCCAGGTG	0.622																																					p.L653M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1957A	17						.						55.0	55.0	55.0					17																	33501381		2203	4300	6503	30525494	SO:0001583	missense	146862	exon14			AW755253	CCDS11292.1, CCDS45648.1	17q12	2008-02-05	2005-11-17	2005-11-17	ENSG00000141161	ENSG00000141161			14304	protein-coding gene	gene with protein product		611220	"""cardiomyopathy associated 4"""	CMYA4		12356907	Standard	NM_001267052		Approved	UNC45	uc002hja.3	Q8IWX7	OTTHUMG00000132931	ENST00000268876.5:c.1957C>A	17.37:g.33501381C>A	ENSP00000268876:p.Leu653Met	Somatic		Capture	Illumina HiSeq	Phase_I	30525494	NM_173167	Q495Q8|Q495Q9	Missense_Mutation	SNP	ENST00000268876.5	37	CCDS11292.1	.	.	.	.	.	.	.	.	.	.	C	16.47	3.132028	0.56828	.	.	ENSG00000141161	ENST00000394570;ENST00000268876;ENST00000433649;ENST00000378449	T;T;T	0.70399	-0.48;-0.48;-0.48	4.7	3.73	0.42828	Armadillo-like helical (1);Armadillo-type fold (1);	0.081179	0.49916	D	0.000135	T	0.74015	0.3661	L	0.58810	1.83	0.33216	D	0.554031	P;D;P	0.55800	0.835;0.973;0.954	P;P;P	0.61533	0.63;0.89;0.779	T	0.78481	-0.2187	10	0.59425	D	0.04	-14.332	3.9756	0.09473	0.2188:0.6043:0.0:0.1769	.	572;651;653	Q8IWX7-2;Q8IWX7-3;Q8IWX7	.;.;UN45B_HUMAN	M	653;653;651;572	ENSP00000268876:L653M;ENSP00000412840:L651M;ENSP00000367710:L572M	ENSP00000268876:L653M	L	+	1	2	UNC45B	30525494	0.998000	0.40836	1.000000	0.80357	0.983000	0.72400	0.756000	0.26419	2.606000	0.88127	0.591000	0.81541	CTG		0.622	UNC45B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256458.2	NM_173167	
SYNRG	11276	broad.mit.edu	37	17	35896149	35896149	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:35896149G>A	ENST00000339208.6	-	19	3738	c.3598C>T	c.(3598-3600)Cag>Tag	p.Q1200*	SYNRG_ENST00000345615.4_Nonsense_Mutation_p.Q1122*|SYNRG_ENST00000346661.4_Nonsense_Mutation_p.Q1200*|SYNRG_ENST00000585472.1_Nonsense_Mutation_p.Q1121*|SYNRG_ENST00000394378.2_Nonsense_Mutation_p.Q1122*|SYNRG_ENST00000502449.2_Nonsense_Mutation_p.Q1077*|SYNRG_ENST00000591288.1_Nonsense_Mutation_p.Q994*	NM_001163544.1|NM_001163545.1|NM_007247.4	NP_001157016.1|NP_001157017.1|NP_009178.3	Q9UMZ2	SYNRG_HUMAN	synergin, gamma	1200					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.Q1200*(2)		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						TTCAGCAACTGCTGGAGTTTC	0.493																																					p.Q1200X												.	.	2	Substitution - Nonsense(2)	large_intestine(1)|skin(1)	c.C3598T	17						.						178.0	145.0	156.0					17																	35896149		2203	4300	6503	32970262	SO:0001587	stop_gained	11276	exon19			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.3598C>T	17.37:g.35896149G>A	ENSP00000343610:p.Gln1200*	Somatic		Capture	Illumina HiSeq	Phase_I	32970262	NM_007247	A8MWU4|B7ZKZ2|B7ZKZ3|Q17RI2|Q5BKU5|Q6ZT17	Nonsense_Mutation	SNP	ENST00000339208.6	37	CCDS11321.1	.	.	.	.	.	.	.	.	.	.	G	42	9.783440	0.99263	.	.	ENSG00000006114	ENST00000346661;ENST00000339208;ENST00000345615;ENST00000502449;ENST00000394378	.	.	.	5.65	5.65	0.86999	.	0.121890	0.56097	D	0.000023	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	-8.1041	20.0887	0.97806	0.0:0.0:1.0:0.0	.	.	.	.	X	1200;994;1200;1122;1122	.	ENSP00000343610:Q994X	Q	-	1	0	SYNRG	32970262	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.126000	0.64721	2.825000	0.97269	0.655000	0.94253	CAG		0.493	SYNRG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256811.2	NM_007247	
LASP1	3927	broad.mit.edu	37	17	37034433	37034433	+	Splice_Site	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:37034433C>T	ENST00000318008.6	+	2	495	c.164C>T	c.(163-165)gCa>gTa	p.A55V	LASP1_ENST00000433206.2_Splice_Site_p.R27R|LASP1_ENST00000435347.3_Splice_Site_p.A55V	NM_006148.2	NP_006139.1	Q14847	LASP1_HUMAN	LIM and SH3 protein 1	55	LIM zinc-binding. {ECO:0000255|PROSITE- ProRule:PRU00125}.				ion transport (GO:0006811)|positive regulation of signal transduction (GO:0009967)	cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	ion transmembrane transporter activity (GO:0015075)|SH3/SH2 adaptor activity (GO:0005070)|zinc ion binding (GO:0008270)	p.A55V(1)		breast(1)|large_intestine(2)|lung(4)|urinary_tract(2)	9						TACTGCAACGCGTGAGTCCTG	0.547			T	MLL	AML																																p.A55V			Dom	yes		17	17q11-q21.3	3927	LIM and SH3 protein 1		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C164T	17						.						119.0	91.0	100.0					17																	37034433		2203	4300	6503	34287959	SO:0001630	splice_region_variant	3927	exon2				CCDS11331.1, CCDS62164.1	17q11-q21.3	2008-07-18			ENSG00000002834	ENSG00000002834			6513	protein-coding gene	gene with protein product		602920				7490069	Standard	NM_006148		Approved	MLN50, Lasp-1	uc010cvq.3	Q14847	OTTHUMG00000133182	ENST00000318008.6:c.164+1C>T	17.37:g.37034433C>T		Somatic		Capture	Illumina HiSeq	Phase_I	34287959	NM_006148	B4DGQ0|Q96ED2|Q96IG0	Missense_Mutation	SNP	ENST00000318008.6	37	CCDS11331.1	.	.	.	.	.	.	.	.	.	.	C	17.91	3.504814	0.64410	.	.	ENSG00000002834	ENST00000318008;ENST00000443937;ENST00000435347;ENST00000419929	D;D;D;T	0.87729	-2.29;-2.29;-2.29;2.48	5.72	5.72	0.89469	Zinc finger, LIM-type (4);	0.100483	0.64402	D	0.000002	D	0.82733	0.5101	L	0.33753	1.03	0.80722	D	1	B;B	0.24483	0.056;0.104	B;B	0.24155	0.016;0.051	T	0.77621	-0.2519	10	0.37606	T	0.19	.	18.4408	0.90666	0.0:1.0:0.0:0.0	.	55;55	B4DJI4;Q14847	.;LASP1_HUMAN	V	55;55;55;19	ENSP00000325240:A55V;ENSP00000414803:A55V;ENSP00000392853:A55V;ENSP00000391897:A19V	ENSP00000325240:A55V	A	+	2	0	LASP1	34287959	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	4.770000	0.62309	2.709000	0.92574	0.561000	0.74099	GCA		0.547	LASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256890.3	NM_006148	Missense_Mutation
NT5C3B	115024	broad.mit.edu	37	17	39991473	39991473	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:39991473G>A	ENST00000435506.2	-	3	232	c.163C>T	c.(163-165)Cga>Tga	p.R55*	RN7SL871P_ENST00000583512.1_RNA|KLHL10_ENST00000293303.4_5'Flank|NT5C3B_ENST00000521789.1_Nonsense_Mutation_p.R22*|NT5C3B_ENST00000269534.8_Nonsense_Mutation_p.R47*			Q969T7	5NT3B_HUMAN	5'-nucleotidase, cytosolic IIIB	55					nucleotide metabolic process (GO:0009117)	cytoplasm (GO:0005737)	5'-nucleotidase activity (GO:0008253)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)	p.R47*(2)									GAAGGGCATCGCTTTCCATTA	0.398																																					p.R55X												.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C163T	17						.						123.0	109.0	114.0					17																	39991473		2203	4300	6503	37244999	SO:0001587	stop_gained	115024	exon3				CCDS11410.1, CCDS11410.2	17q21.2	2013-01-31	2013-01-31	2013-01-31	ENSG00000141698	ENSG00000141698	3.1.3.5		28300	protein-coding gene	gene with protein product			"""5'-nucleotidase, cytosolic III-like"""	NT5C3L		23223233	Standard	NM_052935		Approved	MGC20781	uc021txo.1	Q969T7	OTTHUMG00000133499	ENST00000435506.2:c.163C>T	17.37:g.39991473G>A	ENSP00000389948:p.Arg55*	Somatic		Capture	Illumina HiSeq	Phase_I	37244999	NM_052935	A8MWB9|C9JKC4|Q7L3B7	Nonsense_Mutation	SNP	ENST00000435506.2	37	CCDS11410.2	.	.	.	.	.	.	.	.	.	.	G	23.8	4.459824	0.84317	.	.	ENSG00000141698	ENST00000269534;ENST00000521789;ENST00000393911;ENST00000435506;ENST00000415460	.	.	.	4.56	1.09	0.20402	.	0.062956	0.64402	D	0.000013	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	1.8599	12.7824	0.57485	0.0:0.0:0.435:0.5649	.	.	.	.	X	47;22;89;55;55	.	ENSP00000269534:R47X	R	-	1	2	NT5C3L	37244999	0.979000	0.34478	0.995000	0.50966	0.988000	0.76386	1.004000	0.29822	0.492000	0.27815	0.558000	0.71614	CGA		0.398	NT5C3B-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257430.2	NM_052935	
CNTNAP1	8506	broad.mit.edu	37	17	40843962	40843962	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:40843962G>A	ENST00000264638.4	+	16	2700	c.2483G>A	c.(2482-2484)gGc>gAc	p.G828D	CTD-3193K9.3_ENST00000592440.1_RNA	NM_003632.2	NP_003623.1	P78357	CNTP1_HUMAN	contactin associated protein 1	828	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon cargo transport (GO:0008088)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytoskeleton organization (GO:0007010)|neuromuscular process controlling balance (GO:0050885)|neuromuscular process controlling posture (GO:0050884)|neuron projection morphogenesis (GO:0048812)|neuronal action potential propagation (GO:0019227)|paranodal junction assembly (GO:0030913)|positive regulation of signal transduction (GO:0009967)|protein localization to paranode region of axon (GO:0002175)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|paranode region of axon (GO:0033270)|voltage-gated potassium channel complex (GO:0008076)	receptor activity (GO:0004872)|SH3 domain binding (GO:0017124)|SH3/SH2 adaptor activity (GO:0005070)	p.G828D(1)		NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(11)|lung(15)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.143)		AATATGGGGGGCCCTTACTGC	0.602																																					p.G828D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2483A	17						.						101.0	111.0	107.0					17																	40843962		2203	4300	6503	38097488	SO:0001583	missense	8506	exon16			U87223	CCDS11436.1	17q21	2008-07-18				ENSG00000108797			8011	protein-coding gene	gene with protein product	"""neurexin 4"""	602346		NRXN4		9118959	Standard	NM_003632		Approved	p190, Caspr, CNTNAP	uc002iay.3	P78357		ENST00000264638.4:c.2483G>A	17.37:g.40843962G>A	ENSP00000264638:p.Gly828Asp	Somatic		Capture	Illumina HiSeq	Phase_I	38097488	NM_003632		Missense_Mutation	SNP	ENST00000264638.4	37	CCDS11436.1	.	.	.	.	.	.	.	.	.	.	G	14.32	2.500382	0.44455	.	.	ENSG00000108797	ENST00000264638	T	0.77489	-1.1	5.5	5.5	0.81552	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.271889	0.33110	N	0.005265	T	0.56411	0.1983	N	0.04090	-0.28	0.41293	D	0.986997	B	0.15719	0.014	B	0.15484	0.013	T	0.55218	-0.8175	10	0.10902	T	0.67	.	15.2546	0.73576	0.0:0.0:1.0:0.0	.	828	P78357	CNTP1_HUMAN	D	828	ENSP00000264638:G828D	ENSP00000264638:G828D	G	+	2	0	CNTNAP1	38097488	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	4.940000	0.63533	2.755000	0.94549	0.655000	0.94253	GGC		0.602	CNTNAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452342.1	NM_003632	
CNTD1	124817	broad.mit.edu	37	17	40959844	40959844	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:40959844G>A	ENST00000588408.1	+	6	1060	c.784G>A	c.(784-786)Gca>Aca	p.A262T	CNTD1_ENST00000588527.1_Missense_Mutation_p.A179T|CNTD1_ENST00000315066.5_3'UTR	NM_173478.2	NP_775749.2	Q8N815	CNTD1_HUMAN	cyclin N-terminal domain containing 1	262								p.A262T(1)		central_nervous_system(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	10		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		AATCATTGCAGCAAGTGCTTT	0.413																																					p.A262T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G784A	17						.						140.0	124.0	129.0					17																	40959844		2203	4300	6503	38213370	SO:0001583	missense	124817	exon6			AK097456	CCDS11440.1	17q21.31	2014-07-03	2006-03-31	2006-03-31	ENSG00000176563	ENSG00000176563			26847	protein-coding gene	gene with protein product			"""cyclin N-terminal domain containing"""	CNTD		24891606	Standard	NM_173478		Approved	FLJ40137	uc002ibm.4	Q8N815		ENST00000588408.1:c.784G>A	17.37:g.40959844G>A	ENSP00000465204:p.Ala262Thr	Somatic		Capture	Illumina HiSeq	Phase_I	38213370	NM_173478	Q658Q6|Q8NEP1	Missense_Mutation	SNP	ENST00000588408.1	37	CCDS11440.1	.	.	.	.	.	.	.	.	.	.	G	18.83	3.706338	0.68615	.	.	ENSG00000176563	ENST00000315066	.	.	.	5.92	5.92	0.95590	.	0.116151	0.64402	D	0.000008	T	0.43366	0.1244	L	0.50333	1.59	0.40186	D	0.977357	P	0.42692	0.787	B	0.33121	0.158	T	0.43130	-0.9410	9	0.33141	T	0.24	-12.085	13.9307	0.63994	0.0778:0.0:0.9222:0.0	.	262	Q8N815	CNTD1_HUMAN	T	262	.	ENSP00000316647:A262T	A	+	1	0	CNTD1	38213370	0.999000	0.42202	1.000000	0.80357	0.998000	0.95712	3.284000	0.51708	2.811000	0.96726	0.555000	0.69702	GCA		0.413	CNTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452398.1	NM_173478	
BECN1	8678	broad.mit.edu	37	17	40970591	40970591	+	Silent	SNP	G	G	A	rs111283520	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:40970591G>A	ENST00000361523.4	-	6	591	c.459C>T	c.(457-459)aaC>aaT	p.N153N	BECN1_ENST00000438274.3_Intron|BECN1_ENST00000590099.1_Silent_p.N153N	NM_003766.3	NP_003757.1	Q14457	BECN1_HUMAN	beclin 1, autophagy related	153					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.N153N(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)		TTTCAGTGACGTTGAGCTGAG	0.517																																					p.N153N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C459T	17						.	G		0,4406		0,0,2203	97.0	86.0	90.0		459	0.4	1.0	17	dbSNP_132	90	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	BECN1	NM_003766.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		153/451	40970591	1,13005	2203	4300	6503	38224117	SO:0001819	synonymous_variant	8678	exon6			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.459C>T	17.37:g.40970591G>A		Somatic		Capture	Illumina HiSeq	Phase_I	38224117	NM_003766	B2R6N7|O75595|Q9UNA8	Silent	SNP	ENST00000361523.4	37	CCDS11441.1																																																																																				0.517	BECN1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452405.1	NM_003766	
VAT1	10493	broad.mit.edu	37	17	41170617	41170617	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:41170617A>G	ENST00000420567.3	-	2	330	c.185T>C	c.(184-186)aTg>aCg	p.M62T	VAT1_ENST00000587173.1_Missense_Mutation_p.M128T|VAT1_ENST00000355653.3_Missense_Mutation_p.M196T			P54219	VMAT1_HUMAN	vesicle amine transport 1	0					monoamine transport (GO:0015844)|neurotransmitter transport (GO:0006836)|transmembrane transport (GO:0055085)	clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	drug transmembrane transporter activity (GO:0015238)|monoamine transmembrane transporter activity (GO:0008504)	p.M196T(1)		endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|upper_aerodigestive_tract(1)	9		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.156)	Ephedra(DB01363)|Methamphetamine(DB01577)|Norepinephrine(DB00368)|Reserpine(DB00206)	ACCTGCAGCCATGTGTACCAA	0.547																																					p.M196T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T587C	17						.						85.0	86.0	86.0					17																	41170617		2203	4300	6503	38424143	SO:0001583	missense	10493	exon2			U18009	CCDS11451.1	17q21	2013-08-23	2013-08-23			ENSG00000108828			16919	protein-coding gene	gene with protein product		604631	"""vesicle amine transport protein 1 homolog (T. californica)"""			7774926, 8938427	Standard	NM_006373		Approved	VATI, FLJ20230	uc002icm.1	Q99536		ENST00000420567.3:c.185T>C	17.37:g.41170617A>G	ENSP00000408553:p.Met62Thr	Somatic		Capture	Illumina HiSeq	Phase_I	38424143	NM_006373	E9PDJ5|Q9BRE4	Missense_Mutation	SNP	ENST00000420567.3	37		.	.	.	.	.	.	.	.	.	.	A	10.99	1.506707	0.26949	.	.	ENSG00000108828	ENST00000355653;ENST00000542468;ENST00000420567;ENST00000315674	T;T	0.40756	1.02;1.02	5.64	5.64	0.86602	GroES-like (1);Quinone oxidoreductase/zeta-crystallin, conserved site (1);	0.123332	0.64402	D	0.000001	T	0.34861	0.0912	N	0.08118	0	0.49389	D	0.99978	D;B	0.54772	0.968;0.017	P;B	0.50970	0.655;0.029	T	0.30357	-0.9981	10	0.38643	T	0.18	-20.9663	15.8621	0.79032	1.0:0.0:0.0:0.0	.	128;196	B4DPX4;Q99536	.;VAT1_HUMAN	T	196;103;62;196	ENSP00000347872:M196T;ENSP00000408553:M62T	ENSP00000326121:M196T	M	-	2	0	VAT1	38424143	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.287000	0.78681	2.139000	0.66308	0.459000	0.35465	ATG		0.547	VAT1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000453104.1	NM_006373	
MPP3	4356	broad.mit.edu	37	17	41901373	41901373	+	Splice_Site	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:41901373C>T	ENST00000398389.4	-	10	775	c.610G>A	c.(610-612)Gcc>Acc	p.A204T	MPP3_ENST00000398393.1_Splice_Site_p.A229T	NM_001932.4	NP_001923.2	Q13368	MPP3_HUMAN	membrane protein, palmitoylated 3 (MAGUK p55 subfamily member 3)	204	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	guanylate kinase activity (GO:0004385)	p.A204T(1)		endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	26		Breast(137;0.00394)		BRCA - Breast invasive adenocarcinoma(366;0.119)		TGGGACTGGGCCTGAAACGAA	0.522																																					p.A204T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G610A	17						.						121.0	123.0	122.0					17																	41901373		1923	4129	6052	39256899	SO:0001630	splice_region_variant	4356	exon10				CCDS42344.1	17q12-q21	2008-07-18			ENSG00000161647	ENSG00000161647			7221	protein-coding gene	gene with protein product	"""MAGUK p55 subfamily member 3"", ""discs, large (Drosophila) homolog 3"", ""membrane protein palmitoylated 3"""	601114		DLG3		8824795	Standard	NR_003562		Approved		uc002iei.4	Q13368	OTTHUMG00000133838	ENST00000398389.4:c.610-1G>A	17.37:g.41901373C>T		Somatic		Capture	Illumina HiSeq	Phase_I	39256899	NM_001932	B2R7N0|D3DX47|Q4GX05|Q6PGR3|Q86SV1	Missense_Mutation	SNP	ENST00000398389.4	37	CCDS42344.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.068711	0.76301	.	.	ENSG00000161647	ENST00000398393;ENST00000398389;ENST00000356492	T;T	0.26518	1.73;1.73	4.71	4.71	0.59529	Src homology-3 domain (1);PDZ/DHR/GLGF (4);	0.063203	0.64402	D	0.000004	T	0.26521	0.0648	N	0.25957	0.775	0.53688	D	0.999977	P;P;P	0.45176	0.852;0.688;0.688	B;P;P	0.45712	0.388;0.491;0.491	T	0.06250	-1.0837	10	0.66056	D	0.02	.	17.8567	0.88765	0.0:1.0:0.0:0.0	.	229;204;229	B4DS20;Q13368;D3DX46	.;MPP3_HUMAN;.	T	229;204;229	ENSP00000381430:A229T;ENSP00000381425:A204T	ENSP00000348885:A229T	A	-	1	0	MPP3	39256899	1.000000	0.71417	1.000000	0.80357	0.816000	0.46133	5.770000	0.68873	2.432000	0.82394	0.467000	0.42956	GCC		0.522	MPP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258371.1	NM_001932	Missense_Mutation
KANSL1	284058	broad.mit.edu	37	17	44144936	44144936	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:44144936G>T	ENST00000262419.6	-	5	2101	c.1631C>A	c.(1630-1632)cCt>cAt	p.P544H	KANSL1_ENST00000572904.1_Missense_Mutation_p.P544H|KANSL1_ENST00000432791.1_Missense_Mutation_p.P544H|KANSL1_ENST00000575318.1_Missense_Mutation_p.P544H|KANSL1_ENST00000574590.1_Missense_Mutation_p.P544H|KANSL1_ENST00000393476.3_De_novo_Start_OutOfFrame	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	544					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.P544H(1)									TCCATTGACAGGTCTGAGTGC	0.413																																					p.P544H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1631A	17						.						128.0	114.0	119.0					17																	44144936		2203	4300	6503	41500758	SO:0001583	missense	284058	exon5			BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.1631C>A	17.37:g.44144936G>T	ENSP00000262419:p.Pro544His	Somatic		Capture	Illumina HiSeq	Phase_I	41500758	NM_015443	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Missense_Mutation	SNP	ENST00000262419.6	37	CCDS11503.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.107479	0.77096	.	.	ENSG00000120071	ENST00000262419;ENST00000432791	T;T	0.51071	0.72;0.72	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.65974	0.2743	M	0.62723	1.935	0.80722	D	1	D;D	0.89917	1.0;0.997	D;D	0.81914	0.995;0.994	T	0.68372	-0.5426	10	0.66056	D	0.02	-12.832	15.5344	0.75990	0.0:0.0:1.0:0.0	.	544;544	C9JHY2;Q7Z3B3	.;K1267_HUMAN	H	544	ENSP00000262419:P544H;ENSP00000387393:P544H	ENSP00000262419:P544H	P	-	2	0	KIAA1267	41500758	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	6.683000	0.74533	2.432000	0.82394	0.655000	0.94253	CCT		0.413	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
NPEPPS	9520	broad.mit.edu	37	17	45691040	45691040	+	Nonsense_Mutation	SNP	T	T	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:45691040T>A	ENST00000322157.4	+	19	2481	c.2244T>A	c.(2242-2244)taT>taA	p.Y748*	RP11-580I16.2_ENST00000582066.1_RNA|RP11-580I16.2_ENST00000582389.1_RNA|NPEPPS_ENST00000530173.1_Nonsense_Mutation_p.Y744*|NPEPPS_ENST00000544660.1_Nonsense_Mutation_p.Y668*	NM_006310.3	NP_006301.3	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive	748					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.Y748*(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						TGTAGGTCTATCTGACTGTTT	0.318																																					p.Y748X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.T2244A	17						.						179.0	152.0	161.0					17																	45691040		1842	4097	5939	43046039	SO:0001587	stop_gained	9520	exon19			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.2244T>A	17.37:g.45691040T>A	ENSP00000320324:p.Tyr748*	Somatic		Capture	Illumina HiSeq	Phase_I	43046039	NM_006310	B7Z463|Q6P145|Q9NP16|Q9UEM2	Nonsense_Mutation	SNP	ENST00000322157.4	37	CCDS45721.1	.	.	.	.	.	.	.	.	.	.	T	37	6.399002	0.97537	.	.	ENSG00000141279	ENST00000530173;ENST00000322157;ENST00000544660	.	.	.	5.3	0.686	0.18015	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.2208	0.31541	0.0:0.296:0.0:0.704	.	.	.	.	X	744;748;668	.	ENSP00000320324:Y748X	Y	+	3	2	NPEPPS	43046039	1.000000	0.71417	0.998000	0.56505	0.950000	0.60333	0.483000	0.22292	0.044000	0.15775	0.528000	0.53228	TAT		0.318	NPEPPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384269.1	NM_006310	
OSBPL7	114881	broad.mit.edu	37	17	45896352	45896352	+	Splice_Site	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:45896352C>T	ENST00000007414.3	-	5	560	c.369G>A	c.(367-369)aaG>aaA	p.K123K	OSBPL7_ENST00000392507.3_Splice_Site_p.K123K	NM_145798.2	NP_665741.1	Q9BZF2	OSBL7_HUMAN	oxysterol binding protein-like 7	123	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cellular response to cholesterol (GO:0071397)|lipid transport (GO:0006869)|positive regulation of proteasomal protein catabolic process (GO:1901800)	autophagic vacuole (GO:0005776)|cytosol (GO:0005829)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)	p.K123K(1)		autonomic_ganglia(1)|endometrium(6)|kidney(2)|large_intestine(5)|liver(2)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32						GGGATGTCACCTTGAGGTGGT	0.572																																					p.K123K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G369A	17						.						161.0	109.0	127.0					17																	45896352		2203	4300	6503	43251351	SO:0001630	splice_region_variant	114881	exon5			AF392446	CCDS11515.1	17q21	2013-01-10				ENSG00000006025		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16387	protein-coding gene	gene with protein product		606735				14593528, 11735225	Standard	NM_145798		Approved	ORP7, MGC71150	uc002ilx.1	Q9BZF2		ENST00000007414.3:c.369+1G>A	17.37:g.45896352C>T		Somatic		Capture	Illumina HiSeq	Phase_I	43251351	NM_145798	D3DTT6|Q6PIV6	Silent	SNP	ENST00000007414.3	37	CCDS11515.1																																																																																				0.572	OSBPL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441367.1	NM_017731	Silent
SAMD14	201191	broad.mit.edu	37	17	48195610	48195610	+	Missense_Mutation	SNP	C	C	T	rs200210474		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:48195610C>T	ENST00000330175.4	-	3	442	c.125G>A	c.(124-126)cGg>cAg	p.R42Q	SAMD14_ENST00000503131.1_Missense_Mutation_p.R42Q|SAMD14_ENST00000503734.1_5'UTR	NM_001257359.1	NP_001244288.1	Q8IZD0	SAM14_HUMAN	sterile alpha motif domain containing 14	42								p.R42Q(1)		breast(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(3)|prostate(1)|urinary_tract(1)	15						CCGGTGTCTCCGGCCCTTGGC	0.667																																					p.R42Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G125A	17						.	C	GLN/ARG	0,4406		0,0,2203	41.0	44.0	43.0		125	5.3	1.0	17		43	2,8598	2.2+/-6.3	0,2,4298	yes	missense	SAMD14	NM_174920.2	43	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	42/446	48195610	2,13004	2203	4300	6503	45550609	SO:0001583	missense	201191	exon3				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.125G>A	17.37:g.48195610C>T	ENSP00000329144:p.Arg42Gln	Somatic		Capture	Illumina HiSeq	Phase_I	45550609	NM_174920	A5D8V1|Q8N2X0	Missense_Mutation	SNP	ENST00000330175.4	37	CCDS58562.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.323216	0.81580	0.0	2.33E-4	ENSG00000167100	ENST00000330175;ENST00000285206;ENST00000503131	.	.	.	5.29	5.29	0.74685	.	0.000000	0.56097	D	0.000021	T	0.48960	0.1529	L	0.47716	1.5	0.36630	D	0.876258	P;D	0.56287	0.943;0.975	B;B	0.42738	0.126;0.396	T	0.59690	-0.7407	9	0.44086	T	0.13	-18.8357	15.8415	0.78848	0.0:1.0:0.0:0.0	.	42;42	Q8IZD0;Q8IZD0-2	SAM14_HUMAN;.	Q	42;54;42	.	ENSP00000285206:R54Q	R	-	2	0	SAMD14	45550609	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.880000	0.48530	2.461000	0.83175	0.557000	0.71058	CGG		0.667	SAMD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366661.1	NM_174920	
PSMB6	5694	broad.mit.edu	37	17	4700837	4700837	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:4700837C>T	ENST00000270586.3	+	3	326	c.275C>T	c.(274-276)gCt>gTt	p.A92V		NM_001270481.1|NM_002798.2	NP_001257410.1|NP_002789.1	P28072	PSB6_HUMAN	proteasome (prosome, macropain) subunit, beta type, 6	92					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	endopeptidase activity (GO:0004175)|threonine-type endopeptidase activity (GO:0004298)	p.A92V(1)		endometrium(3)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	11						GTAGCTGATGCTGTCACCTAC	0.537																																					p.A92V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C275T	17						.						82.0	73.0	76.0					17																	4700837		2203	4300	6503	4647795	SO:0001583	missense	5694	exon3			BC000835	CCDS11056.1, CCDS73944.1	17p13	2004-02-18			ENSG00000142507	ENSG00000142507		"""Proteasome (prosome, macropain) subunits"""	9543	protein-coding gene	gene with protein product		600307				8066462, 1888762	Standard	NM_002798		Approved	Y, DELTA	uc002fzb.4	P28072	OTTHUMG00000090777	ENST00000270586.3:c.275C>T	17.37:g.4700837C>T	ENSP00000270586:p.Ala92Val	Somatic		Capture	Illumina HiSeq	Phase_I	4647795	NM_002798	Q96J55	Missense_Mutation	SNP	ENST00000270586.3	37	CCDS11056.1	.	.	.	.	.	.	.	.	.	.	C	13.52	2.261334	0.39995	.	.	ENSG00000142507	ENST00000270586	T	0.21932	1.98	5.65	4.67	0.58626	.	0.053881	0.64402	D	0.000001	T	0.11110	0.0271	N	0.04063	-0.285	0.47341	D	0.99939	B	0.19935	0.04	B	0.15052	0.012	T	0.10474	-1.0628	10	0.35671	T	0.21	-24.1441	14.5214	0.67853	0.0:0.8528:0.1472:0.0	.	92	P28072	PSB6_HUMAN	V	92	ENSP00000270586:A92V	ENSP00000270586:A92V	A	+	2	0	PSMB6	4647795	0.995000	0.38212	0.824000	0.32777	0.947000	0.59692	3.511000	0.53400	1.616000	0.50265	0.655000	0.94253	GCT		0.537	PSMB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207559.2	NM_002798	
ABCC3	8714	broad.mit.edu	37	17	48753891	48753891	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:48753891G>A	ENST00000285238.8	+	23	3400	c.3320G>A	c.(3319-3321)aGc>aAc	p.S1107N		NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	1107	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)	p.S1107N(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Doxorubicin(DB00997)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indomethacin(DB00328)|Lamivudine(DB00709)|Leucovorin(DB00650)|Methotrexate(DB00563)|Metyrapone(DB01011)|Nifedipine(DB01115)|Omeprazole(DB00338)|Phenobarbital(DB01174)|Probenecid(DB01032)|Rifampicin(DB01045)|Sulfinpyrazone(DB01138)|Verapamil(DB00661)|Vincristine(DB00541)	ATCATGGCCAGCACGCCGCTC	0.552																																					p.S1107N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3320A	17						.						187.0	145.0	159.0					17																	48753891		2203	4300	6503	46108890	SO:0001583	missense	8714	exon23			Y17151	CCDS32681.1, CCDS45739.1	17q21	2012-03-14			ENSG00000108846	ENSG00000108846		"""ATP binding cassette transporters / subfamily C"""	54	protein-coding gene	gene with protein product	"""canalicular multispecific organic anion transporter 2"""	604323				8894702, 9827529	Standard	NM_003786		Approved	MRP3, cMOAT2, EST90757, MLP2, MOAT-D	uc002isl.3	O15438	OTTHUMG00000162245	ENST00000285238.8:c.3320G>A	17.37:g.48753891G>A	ENSP00000285238:p.Ser1107Asn	Somatic		Capture	Illumina HiSeq	Phase_I	46108890	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Missense_Mutation	SNP	ENST00000285238.8	37	CCDS32681.1	.	.	.	.	.	.	.	.	.	.	G	15.32	2.799246	0.50208	.	.	ENSG00000108846	ENST00000285238	D	0.94497	-3.44	5.21	3.19	0.36642	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	0.96673	0.8914	M	0.80982	2.52	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96008	0.8999	10	0.87932	D	0	-20.3596	10.7478	0.46191	0.0719:0.1318:0.7963:0.0	.	1107	O15438	MRP3_HUMAN	N	1107	ENSP00000285238:S1107N	ENSP00000285238:S1107N	S	+	2	0	ABCC3	46108890	1.000000	0.71417	1.000000	0.80357	0.041000	0.13682	4.001000	0.57046	0.567000	0.29293	0.655000	0.94253	AGC		0.552	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038	
CA10	56934	broad.mit.edu	37	17	50008401	50008401	+	Missense_Mutation	SNP	C	C	A	rs267604958		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:50008401C>A	ENST00000285273.4	-	4	1339	c.228G>T	c.(226-228)atG>atT	p.M76I	CA10_ENST00000451037.2_Missense_Mutation_p.M76I|CA10_ENST00000340813.6_Missense_Mutation_p.M82I|CA10_ENST00000442502.2_Missense_Mutation_p.M76I|CA10_ENST00000570565.1_Start_Codon_SNP_p.M1I	NM_001082533.1	NP_001076002.1	Q9NS85	CAH10_HUMAN	carbonic anhydrase X	76					brain development (GO:0007420)			p.M76I(2)		cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(21)|ovary(1)|skin(3)|stomach(2)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)		Zonisamide(DB00909)	GGTCGAAGATCATGTGACTGG	0.498																																					p.M76I												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G228T	17						.						277.0	259.0	265.0					17																	50008401		2203	4300	6503	47363400	SO:0001583	missense	56934	exon3			AF288385	CCDS32684.1	17q21	2012-08-21			ENSG00000154975	ENSG00000154975		"""Carbonic anhydrases"""	1369	protein-coding gene	gene with protein product		604642				8673298, 9921901	Standard	NM_020178		Approved	CARPX, CA-RPX, HUCEP-15	uc002itx.4	Q9NS85	OTTHUMG00000177544	ENST00000285273.4:c.228G>T	17.37:g.50008401C>A	ENSP00000285273:p.Met76Ile	Somatic		Capture	Illumina HiSeq	Phase_I	47363400	NM_020178	B2R7J0|B4DGL6	Missense_Mutation	SNP	ENST00000285273.4	37	CCDS32684.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.996016	0.74703	.	.	ENSG00000154975	ENST00000442502;ENST00000285273;ENST00000451037;ENST00000340813	T;T;T;T	0.71222	-0.55;-0.55;-0.55;-0.55	5.93	5.93	0.95920	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.000000	0.85682	D	0.000000	T	0.49966	0.1588	N	0.03268	-0.37	0.58432	D	0.999999	B;B	0.15473	0.013;0.013	B;B	0.12837	0.008;0.008	T	0.48103	-0.9064	9	.	.	.	.	19.3421	0.94347	0.0:1.0:0.0:0.0	.	76;82	Q9NS85;Q68D28	CAH10_HUMAN;.	I	76;76;76;82	ENSP00000390666:M76I;ENSP00000285273:M76I;ENSP00000405388:M76I;ENSP00000340363:M82I	.	M	-	3	0	CA10	47363400	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.298000	0.78815	2.826000	0.97356	0.655000	0.94253	ATG		0.498	CA10-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000437480.1	NM_020178	
MMD	23531	broad.mit.edu	37	17	53471796	53471796	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:53471796C>T	ENST00000262065.3	-	7	912	c.616G>A	c.(616-618)Gcc>Acc	p.A206T		NM_012329.2	NP_036461.2	Q15546	PAQRB_HUMAN	monocyte to macrophage differentiation-associated	206					cytolysis (GO:0019835)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|membrane (GO:0016020)	receptor activity (GO:0004872)	p.A206T(1)		breast(1)|large_intestine(1)|lung(4)|prostate(1)	7						TGCCAGATGGCGTGGGCAAAT	0.488																																					p.A206T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G616A	17						.						112.0	102.0	105.0					17																	53471796		2203	4300	6503	50826795	SO:0001583	missense	23531	exon7			X85750	CCDS11586.1	17q	2008-05-02				ENSG00000108960			7153	protein-coding gene	gene with protein product		604467				7503749, 16044242	Standard	NM_012329		Approved	MMA, PAQR11	uc002iui.3	Q15546		ENST00000262065.3:c.616G>A	17.37:g.53471796C>T	ENSP00000262065:p.Ala206Thr	Somatic		Capture	Illumina HiSeq	Phase_I	50826795	NM_012329	B2R6X9|D3DTY6|Q8TAN7	Missense_Mutation	SNP	ENST00000262065.3	37	CCDS11586.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.044585	0.93685	.	.	ENSG00000108960	ENST00000262065	T	0.32023	1.47	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.57961	0.2089	M	0.72624	2.21	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.55263	-0.8168	10	0.59425	D	0.04	-50.3384	19.6068	0.95584	0.0:1.0:0.0:0.0	.	206	Q15546	PAQRB_HUMAN	T	206	ENSP00000262065:A206T	ENSP00000262065:A206T	A	-	1	0	MMD	50826795	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.811000	0.86092	2.876000	0.98609	0.643000	0.83706	GCC		0.488	MMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439214.1		
TRIM25	7706	broad.mit.edu	37	17	54969484	54969484	+	Silent	SNP	C	C	T	rs142382736		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:54969484C>T	ENST00000316881.4	-	9	1519	c.1470G>A	c.(1468-1470)ccG>ccA	p.P490P	RP11-670E13.5_ENST00000574826.1_RNA|MIR3614_ENST00000581261.1_RNA|TRIM25_ENST00000537230.1_Silent_p.P490P|TRIM25_ENST00000573108.1_5'Flank	NM_005082.4	NP_005073.2	Q14258	TRI25_HUMAN	tripartite motif containing 25	490	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|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 ubiquitination (GO:0016567)|regulation of viral entry into host cell (GO:0046596)|regulation of viral release from host cell (GO:1902186)|response to estrogen (GO:0043627)|response to vitamin D (GO:0033280)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.P490P(1)		breast(2)|endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Breast(9;6.15e-08)					TCTGGGGATGCGGCCGGTAGT	0.532													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18961	0.0		0.0	False		,,,				2504	0.0				p.P490P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1470A	17						.	C		0,4406		0,0,2203	78.0	75.0	76.0		1470	-9.7	0.8	17	dbSNP_134	76	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TRIM25	NM_005082.4		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		490/631	54969484	2,13004	2203	4300	6503	52324483	SO:0001819	synonymous_variant	7706	exon9			D21205	CCDS11591.1	17q23.1	2013-01-09	2011-01-25	2004-03-30				"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	12932	protein-coding gene	gene with protein product		600453	"""zinc finger protein 147 (estrogen-responsive finger protein)"", ""tripartite motif-containing 25"""	ZNF147		7789997	Standard	NM_005082		Approved	EFP, RNF147	uc002iut.3	Q14258		ENST00000316881.4:c.1470G>A	17.37:g.54969484C>T		Somatic		Capture	Illumina HiSeq	Phase_I	52324483	NM_005082		Silent	SNP	ENST00000316881.4	37	CCDS11591.1																																																																																				0.532	TRIM25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440609.1	NM_005082	
RPS6KB1	6198	broad.mit.edu	37	17	58024051	58024051	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:58024051G>A	ENST00000225577.4	+	15	1501	c.1480G>A	c.(1480-1482)Gca>Aca	p.A494T	RPS6KB1_ENST00000406116.3_Intron|RPS6KB1_ENST00000393021.3_Missense_Mutation_p.A441T|RP11-178C3.1_ENST00000591035.1_Intron|RPS6KB1_ENST00000443572.2_Missense_Mutation_p.A471T	NM_001272042.1|NM_001272044.1|NM_001272060.1|NM_003161.2	NP_001258971.1|NP_001258973.1|NP_001258989.1|NP_003152.1	P23443	KS6B1_HUMAN	ribosomal protein S6 kinase, 70kDa, polypeptide 1	494	Autoinhibitory domain.				aging (GO:0007568)|apoptotic process (GO:0006915)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|G1/S transition of mitotic cell cycle (GO:0000082)|germ cell development (GO:0007281)|insulin receptor signaling pathway (GO:0008286)|long-term memory (GO:0007616)|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)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of skeletal muscle tissue growth (GO:0048633)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of translation (GO:0045727)|positive regulation of translational initiation (GO:0045948)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|regulation of glucose import (GO:0046324)|response to drug (GO:0042493)|response to electrical stimulus involved in regulation of muscle adaptation (GO:0014878)|response to ethanol (GO:0045471)|response to glucagon (GO:0033762)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to leucine (GO:0043201)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|response to testosterone (GO:0033574)|response to toxic substance (GO:0009636)|response to tumor necrosis factor (GO:0034612)|response to wounding (GO:0009611)|signal transduction (GO:0007165)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|TOR signaling (GO:0031929)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	ATP binding (GO:0005524)|peptide binding (GO:0042277)|protein kinase activity (GO:0004672)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ribosomal protein S6 kinase activity (GO:0004711)	p.A494T(1)		endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	14	all_cancers(5;1.63e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;3.57e-12)|all cancers(12;6.41e-11)			GGAAGCATCGGCACCACTTCC	0.498																																					p.A494T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1480A	17						.						77.0	64.0	68.0					17																	58024051		2203	4300	6503	55378833	SO:0001583	missense	6198	exon15			M60724	CCDS11621.1, CCDS62271.1, CCDS62272.1, CCDS62273.1	17q23.1	2011-04-05	2002-08-29		ENSG00000108443	ENSG00000108443			10436	protein-coding gene	gene with protein product		608938	"""ribosomal protein S6 kinase, 70kD, polypeptide 1"""	STK14A		1922062	Standard	NM_003161		Approved	S6K1, p70(S6K)-alpha, PS6K	uc002ixy.4	P23443	OTTHUMG00000150642	ENST00000225577.4:c.1480G>A	17.37:g.58024051G>A	ENSP00000225577:p.Ala494Thr	Somatic		Capture	Illumina HiSeq	Phase_I	55378833	NM_003161	B2R779|B4DLT4|B4DTG1|E7ESB8|F6UYM1|Q7Z721	Missense_Mutation	SNP	ENST00000225577.4	37	CCDS11621.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.192753	0.78902	.	.	ENSG00000108443	ENST00000443572;ENST00000225577;ENST00000393021	T;T;T	0.71222	-0.55;-0.37;-0.34	5.23	5.23	0.72850	.	0.046113	0.85682	D	0.000000	T	0.68081	0.2962	L	0.48642	1.525	0.80722	D	1	P;P	0.48407	0.908;0.91	B;B	0.43916	0.436;0.388	T	0.65721	-0.6099	10	0.23302	T	0.38	.	18.7992	0.92008	0.0:0.0:1.0:0.0	.	471;494	F6UYM1;P23443	.;KS6B1_HUMAN	T	471;494;441	ENSP00000441993:A471T;ENSP00000225577:A494T;ENSP00000376744:A441T	ENSP00000225577:A494T	A	+	1	0	RPS6KB1	55378833	1.000000	0.71417	0.998000	0.56505	0.967000	0.64934	9.410000	0.97335	2.430000	0.82344	0.655000	0.94253	GCA		0.498	RPS6KB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319324.1	NM_003161	
ALOX12	239	broad.mit.edu	37	17	6900228	6900228	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:6900228C>T	ENST00000251535.6	+	2	272	c.219C>T	c.(217-219)gaC>gaT	p.D73D	AC027763.2_ENST00000399541.2_Intron|RP11-589P10.5_ENST00000573222.1_lincRNA|RP11-589P10.7_ENST00000572547.1_RNA	NM_000697.2	NP_000688.2	P18054	LOX12_HUMAN	arachidonate 12-lipoxygenase	73	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				aging (GO:0007568)|arachidonic acid metabolic process (GO:0019369)|cellular component movement (GO:0006928)|cellular response to lipid (GO:0071396)|establishment of skin barrier (GO:0061436)|fatty acid oxidation (GO:0019395)|hepoxilin biosynthetic process (GO:0051122)|hepoxilin metabolic process (GO:0051121)|leukotriene A4 metabolic process (GO:1901751)|linoleic acid metabolic process (GO:0043651)|lipoxin A4 biosynthetic process (GO:2001303)|lipoxin B4 biosynthetic process (GO:2001306)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of platelet aggregation (GO:0090331)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of gene expression (GO:0010628)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of vasodilation (GO:0045909)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|superoxide anion generation (GO:0042554)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|sarcolemma (GO:0042383)	arachidonate 12-lipoxygenase activity (GO:0004052)|hepoxilin A3 synthase activity (GO:0051120)|hepoxilin-epoxide hydrolase activity (GO:0047977)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)	p.D73D(1)		breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(4)|ovary(1)|prostate(3)|urinary_tract(1)	19						GGCTGGTGGACGACGCGTGGT	0.662																																					p.D73D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C219T	17						.						82.0	59.0	67.0					17																	6900228		2203	4300	6503	6840952	SO:0001819	synonymous_variant	239	exon2			M35418	CCDS11084.1	17p13.1	2010-01-14			ENSG00000108839	ENSG00000108839	1.13.11.31	"""Arachidonate lipoxygenases"""	429	protein-coding gene	gene with protein product	"""platelet 12-LOX"""	152391				1570320	Standard	NM_000697		Approved	12S-LOX	uc002gdx.4	P18054	OTTHUMG00000102088	ENST00000251535.6:c.219C>T	17.37:g.6900228C>T		Somatic		Capture	Illumina HiSeq	Phase_I	6840952	NM_000697	O95569|Q6ISF8|Q9UQM4	Silent	SNP	ENST00000251535.6	37	CCDS11084.1																																																																																				0.662	ALOX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219922.2		
ABCA8	10351	broad.mit.edu	37	17	66937099	66937099	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:66937099C>A	ENST00000269080.2	-	3	238	c.101G>T	c.(100-102)tGg>tTg	p.W34L	ABCA8_ENST00000430352.2_Missense_Mutation_p.W34L|ABCA8_ENST00000586539.1_Missense_Mutation_p.W34L	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	34					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)	p.W34L(1)		breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					TGAATTCAGCCATTCCTATAT	0.313																																					p.W34L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G101T	17						.						36.0	37.0	37.0					17																	66937099		2203	4299	6502	64448694	SO:0001583	missense	10351	exon3			AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"""ATP binding cassette transporters / subfamily A"""	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.101G>T	17.37:g.66937099C>A	ENSP00000269080:p.Trp34Leu	Somatic		Capture	Illumina HiSeq	Phase_I	64448694	NM_007168	A1L3U3|C9JQE6|Q86WW0	Missense_Mutation	SNP	ENST00000269080.2	37	CCDS11680.1	.	.	.	.	.	.	.	.	.	.	C	5.262	0.233841	0.09969	.	.	ENSG00000141338	ENST00000269080;ENST00000430352;ENST00000428549	D;D	0.83837	-1.77;-1.77	5.23	4.24	0.50183	.	0.329786	0.22583	N	0.058189	T	0.81437	0.4822	M	0.62016	1.91	0.38871	D	0.956706	B;B;B;B	0.31581	0.329;0.18;0.033;0.175	B;B;B;B	0.40375	0.327;0.261;0.036;0.162	T	0.75599	-0.3262	10	0.13470	T	0.59	.	10.8246	0.46625	0.1883:0.8116:0.0:0.0	.	34;34;34;34	A1L3U3;B4DJ11;C9JQE6;O94911	.;.;.;ABCA8_HUMAN	L	34	ENSP00000269080:W34L;ENSP00000402814:W34L	ENSP00000269080:W34L	W	-	2	0	ABCA8	64448694	0.075000	0.21258	0.945000	0.38365	0.117000	0.20001	0.057000	0.14279	1.395000	0.46643	0.655000	0.94253	TGG		0.313	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168	
CDC42EP4	23580	broad.mit.edu	37	17	71282504	71282504	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:71282504C>T	ENST00000335793.3	-	2	530	c.136G>A	c.(136-138)Gcc>Acc	p.A46T	CDC42EP4_ENST00000581014.1_Intron|CDC42EP4_ENST00000439510.2_Missense_Mutation_p.A46T			Q9H3Q1	BORG4_HUMAN	CDC42 effector protein (Rho GTPase binding) 4	46					positive regulation of pseudopodium assembly (GO:0031274)|regulation of cell shape (GO:0008360)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	GTP-Rho binding (GO:0017049)|poly(A) RNA binding (GO:0044822)	p.A46T(1)		cervix(2)|endometrium(3)|large_intestine(1)|lung(7)|urinary_tract(1)	14			LUSC - Lung squamous cell carcinoma(166;0.0352)|Lung(188;0.0711)			TCCCCAAAGGCGTCTCCGGCC	0.647																																					p.A46T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G136A	17						.						38.0	40.0	39.0					17																	71282504		2203	4300	6503	68794099	SO:0001583	missense	23580	exon2			AB042237	CCDS11695.1	17q24-q25	2008-07-18				ENSG00000179604			17147	protein-coding gene	gene with protein product	"""Cdc42 effector protein 4"", ""binder of Rho GTPases 4"""	605468				11035016, 10490598	Standard	NM_012121		Approved	CEP4, KAIA1777, BORG4, MGC3740, MGC17125	uc002jjo.3	Q9H3Q1		ENST00000335793.3:c.136G>A	17.37:g.71282504C>T	ENSP00000338258:p.Ala46Thr	Somatic		Capture	Illumina HiSeq	Phase_I	68794099	NM_012121	B3KUS7|O95828|Q96FT3	Missense_Mutation	SNP	ENST00000335793.3	37	CCDS11695.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.999421	0.74818	.	.	ENSG00000179604	ENST00000335793;ENST00000439510	D;D	0.83673	-1.75;-1.75	5.1	5.1	0.69264	PAK-box/P21-Rho-binding (1);	0.054431	0.64402	D	0.000001	D	0.89213	0.6651	L	0.61387	1.9	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.991;0.999	D	0.86135	0.1577	10	0.19147	T	0.46	-16.8816	18.1001	0.89503	0.0:1.0:0.0:0.0	.	46;46	B3KUS7;Q9H3Q1	.;BORG4_HUMAN	T	46	ENSP00000338258:A46T;ENSP00000404270:A46T	ENSP00000338258:A46T	A	-	1	0	CDC42EP4	68794099	1.000000	0.71417	0.825000	0.32803	0.009000	0.06853	7.649000	0.83500	2.378000	0.81104	0.585000	0.79938	GCC		0.647	CDC42EP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441898.1	NM_012121	
SDK2	54549	broad.mit.edu	37	17	71354323	71354323	+	Missense_Mutation	SNP	C	C	T	rs146597384		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:71354323C>T	ENST00000392650.3	-	40	5488	c.5488G>A	c.(5488-5490)Gtg>Atg	p.V1830M	SDK2_ENST00000388726.3_Missense_Mutation_p.V1811M|SDK2_ENST00000410094.1_5'UTR	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	1830	Fibronectin type-III 13. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				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						ATGATGGGCACGCCAGGCGGT	0.652																																					p.V1830M												.	.	0			c.G5488A	17						.	C	MET/VAL	0,4406		0,0,2203	128.0	118.0	121.0		5488	4.1	1.0	17	dbSNP_134	121	2,8598	2.2+/-6.3	0,2,4298	no	missense	SDK2	NM_001144952.1	21	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	1830/2173	71354323	2,13004	2203	4300	6503	68865918	SO:0001583	missense	54549	exon40			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.5488G>A	17.37:g.71354323C>T	ENSP00000376421:p.Val1830Met	None		Capture	Illumina HiSeq	Phase_I	68865918	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Missense_Mutation	SNP	ENST00000392650.3	37	CCDS45769.1	.	.	.	.	.	.	.	.	.	.	C	12.60	1.987639	0.35036	0.0	2.33E-4	ENSG00000069188	ENST00000409227;ENST00000392650;ENST00000388726;ENST00000424778;ENST00000316893;ENST00000410094	T;T;T	0.60797	0.16;0.16;0.16	5.12	4.06	0.47325	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.299519	0.31734	N	0.007160	T	0.37598	0.1009	N	0.16266	0.395	0.32151	N	0.58424	P;P;B	0.43169	0.8;0.468;0.413	B;B;B	0.38056	0.258;0.264;0.172	T	0.51036	-0.8756	10	0.39692	T	0.17	.	10.6128	0.45432	0.0:0.8683:0.0:0.1317	.	1830;1830;1811	Q58EX2-2;Q58EX2;Q58EX2-3	.;SDK2_HUMAN;.	M	1454;1830;1811;987;1830;171	ENSP00000376421:V1830M;ENSP00000373378:V1811M;ENSP00000407098:V987M	ENSP00000324967:V1830M	V	-	1	0	SDK2	68865918	0.976000	0.34144	0.993000	0.49108	0.212000	0.24457	2.454000	0.44979	2.377000	0.81083	0.655000	0.94253	GTG		0.652	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064	
DNAI2	64446	broad.mit.edu	37	17	72297264	72297264	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:72297264A>G	ENST00000311014.6	+	8	1011	c.944A>G	c.(943-945)gAa>gGa	p.E315G	DNAI2_ENST00000446837.2_Missense_Mutation_p.E315G|DNAI2_ENST00000307504.5_Missense_Mutation_p.E172G|DNAI2_ENST00000579490.1_Missense_Mutation_p.E372G|DNAI2_ENST00000582036.1_Missense_Mutation_p.E315G			Q9GZS0	DNAI2_HUMAN	dynein, axonemal, intermediate chain 2	315					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.E315G(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						GAACAGTTGGAAAATGCCTTG	0.552									Kartagener syndrome																												p.E315G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A944G	17						.						215.0	190.0	198.0					17																	72297264		2203	4300	6503	69808859	SO:0001583	missense	64446	exon8	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.944A>G	17.37:g.72297264A>G	ENSP00000308312:p.Glu315Gly	Somatic		Capture	Illumina HiSeq	Phase_I	69808859	NM_023036	C9J0S6|Q8IUW4|Q9H179|Q9NT53	Missense_Mutation	SNP	ENST00000311014.6	37	CCDS11697.1	.	.	.	.	.	.	.	.	.	.	A	11.51	1.661616	0.29515	.	.	ENSG00000171595	ENST00000311014;ENST00000307504;ENST00000446837	T;T;T	0.14893	2.47;2.47;2.47	5.56	5.56	0.83823	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.241826	0.49305	D	0.000150	T	0.15565	0.0375	L	0.38692	1.165	0.46437	D	0.999049	B	0.12013	0.005	B	0.11329	0.006	T	0.06023	-1.0850	10	0.21540	T	0.41	-25.0359	15.7696	0.78157	1.0:0.0:0.0:0.0	.	315	Q9GZS0	DNAI2_HUMAN	G	315;172;315	ENSP00000308312:E315G;ENSP00000302929:E172G;ENSP00000400252:E315G	ENSP00000302929:E172G	E	+	2	0	DNAI2	69808859	1.000000	0.71417	0.852000	0.33557	0.309000	0.27889	5.852000	0.69488	2.123000	0.65237	0.529000	0.55759	GAA		0.552	DNAI2-001	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442537.1	NM_023036	
C17orf77	146723	broad.mit.edu	37	17	72588737	72588737	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:72588737G>A	ENST00000392620.1	+	3	914	c.552G>A	c.(550-552)agG>agA	p.R184R	CD300LD_ENST00000375352.1_5'Flank|C17orf77_ENST00000328023.2_Silent_p.R184R	NM_152460.2	NP_689673.2	Q96MU5	CQ077_HUMAN	chromosome 17 open reading frame 77	184						extracellular region (GO:0005576)		p.R184R(1)		breast(2)|large_intestine(2)|lung(5)|prostate(1)|stomach(1)	11						AGGAGTGCAGGGAGAGGAGCA	0.607																																					p.R184R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G552A	17						.						91.0	81.0	84.0					17																	72588737		2203	4300	6503	70100332	SO:0001819	synonymous_variant	146723	exon3				CCDS32721.1	17q25.1	2006-01-16			ENSG00000182352	ENSG00000182352			26480	protein-coding gene	gene with protein product							Standard	NM_152460		Approved	FLJ31882	uc002jla.1	Q96MU5	OTTHUMG00000067611	ENST00000392620.1:c.552G>A	17.37:g.72588737G>A		Somatic		Capture	Illumina HiSeq	Phase_I	70100332	NM_152460		Silent	SNP	ENST00000392620.1	37	CCDS32721.1																																																																																				0.607	C17orf77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145090.2	NM_152460	
NUP85	79902	broad.mit.edu	37	17	73228057	73228057	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:73228057G>T	ENST00000245544.4	+	14	1450	c.1379G>T	c.(1378-1380)cGg>cTg	p.R460L	NUP85_ENST00000579298.1_Missense_Mutation_p.R415L|NUP85_ENST00000540768.1_Missense_Mutation_p.R63L|NUP85_ENST00000541827.1_Missense_Mutation_p.R414L|NUP85_ENST00000579324.1_Missense_Mutation_p.R348L|NUP85_ENST00000447371.2_Missense_Mutation_p.R292L	NM_024844.3	NP_079120.1	Q9BW27	NUP85_HUMAN	nucleoporin 85kDa	460					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.R460L(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)			TGTGAGCAGCGGCAGATGACT	0.607																																					p.R460L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1379T	17						.						43.0	41.0	41.0					17																	73228057		2203	4300	6503	70739652	SO:0001583	missense	79902	exon14			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.1379G>T	17.37:g.73228057G>T	ENSP00000245544:p.Arg460Leu	Somatic		Capture	Illumina HiSeq	Phase_I	70739652	NM_024844	B4DMQ3|B4DPW1|Q8NDI4|Q9H9U1	Missense_Mutation	SNP	ENST00000245544.4	37	CCDS32730.1	.	.	.	.	.	.	.	.	.	.	G	16.74	3.205878	0.58234	.	.	ENSG00000125450	ENST00000245544;ENST00000541827;ENST00000447371;ENST00000540768	.	.	.	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.71005	0.3289	L	0.60845	1.875	0.80722	D	1	P;P	0.52170	0.916;0.951	P;P	0.57244	0.617;0.816	T	0.64368	-0.6424	9	0.11182	T	0.66	-24.5811	19.1635	0.93544	0.0:0.0:1.0:0.0	.	414;460	B4DMQ3;Q9BW27	.;NUP85_HUMAN	L	460;414;292;63	.	ENSP00000245544:R460L	R	+	2	0	NUP85	70739652	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.163000	0.94750	2.606000	0.88127	0.561000	0.74099	CGG		0.607	NUP85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446619.1	NM_024844	
TNFSF12	8742	broad.mit.edu	37	17	7460159	7460159	+	Silent	SNP	C	C	T	rs559336720		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:7460159C>T	ENST00000293825.6	+	6	701	c.438C>T	c.(436-438)taC>taT	p.Y146Y	TNFSF13_ENST00000338784.4_5'Flank|TNFSF13_ENST00000380535.4_5'Flank|TNFSF13_ENST00000396545.4_5'Flank|TNFSF12_ENST00000557233.1_Silent_p.Y146Y|TNFSF13_ENST00000349228.4_5'Flank|TNFSF13_ENST00000396542.1_5'Flank|TNFSF12_ENST00000462811.1_3'UTR|TNFSF12-TNFSF13_ENST00000293826.4_Silent_p.Y146Y|TNFSF13_ENST00000483039.1_5'Flank	NM_003809.2	NP_003800.1	O43508	TNF12_HUMAN	tumor necrosis factor (ligand) superfamily, member 12	146					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|endothelial cell migration (GO:0043542)|immune response (GO:0006955)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)	cytokine activity (GO:0005125)|receptor binding (GO:0005102)	p.Y146Y(2)		central_nervous_system(1)|endometrium(3)|large_intestine(5)|prostate(2)	11		Prostate(122;0.157)				CTCTGCGCTACAACCGCCAGA	0.562													C|||	1	0.000199681	0.0	0.0	5008	,	,		15632	0.0		0.0	False		,,,				2504	0.001				p.Y146Y												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C438T	17						.						58.0	53.0	54.0					17																	7460159		2203	4300	6503	7400883	SO:0001819	synonymous_variant	407977	exon6			AF030099	CCDS11109.1	17p13.1	2008-02-01			ENSG00000239697	ENSG00000239697		"""Tumor necrosis factor (ligand) superfamily"""	11927	protein-coding gene	gene with protein product		602695				9405449, 9560343	Standard	NM_003809		Approved	TWEAK, DR3LG, APO3L		O43508	OTTHUMG00000108148	ENST00000293825.6:c.438C>T	17.37:g.7460159C>T		Somatic		Capture	Illumina HiSeq	Phase_I	7400883	NM_172089	Q8IZK7|Q8WUZ7	Silent	SNP	ENST00000293825.6	37	CCDS11109.1																																																																																				0.562	TNFSF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226951.2	NM_003809	
TP53	7157	broad.mit.edu	37	17	7577120	7577120	+	Missense_Mutation	SNP	C	C	T	rs28934576		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:7577120C>T	ENST00000269305.4	-	8	1007	c.818G>A	c.(817-819)cGt>cAt	p.R273H	TP53_ENST00000455263.2_Missense_Mutation_p.R273H|TP53_ENST00000413465.2_Intron|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.R273H|TP53_ENST00000420246.2_Missense_Mutation_p.R273H|TP53_ENST00000445888.2_Missense_Mutation_p.R273H	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	273	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17224074, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:9450901}.|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; abolishes sequence-specific DNA binding; does not induce SNAI1 degradation; dbSNP:rs28934576). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1699228, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7682763, ECO:0000269|Ref.14}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> S (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R273H(521)|p.R273L(93)|p.R273P(32)|p.0?(8)|p.?(2)|p.R273fs*32(2)|p.R273_C275delRVC(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.R273S(1)|p.E258fs*71(1)|p.R273fs*72(1)|p.R273fs*71(1)|p.F270_D281del12(1)|p.R273fs*33(1)|p.E271_R273delEVR(1)|p.V272_K292del21(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGCACAAACACGCACCTCAAA	0.542	R273H(EN_ENDOMETRIUM)|R273H(HEC59_ENDOMETRIUM)|R273H(HEC6_ENDOMETRIUM)|R273H(HT29_LARGE_INTESTINE)|R273H(HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(MDAMB468_BREAST)|R273H(MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(NCIH1155_LUNG)|R273H(NCIH1793_LUNG)|R273H(NCIH1975_LUNG)|R273H(NCIH2405_LUNG)|R273H(NCIH508_LARGE_INTESTINE)|R273H(OC314_OVARY)|R273H(PANC1_PANCREAS)|R273H(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SKMEL30_SKIN)|R273H(SNB19_CENTRAL_NERVOUS_SYSTEM)|R273H(SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SUIT2_PANCREAS)|R273H(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273H(SW1783_CENTRAL_NERVOUS_SYSTEM)|R273H(SW480_LARGE_INTESTINE)|R273H(SW620_LARGE_INTESTINE)|R273H(U251MG_CENTRAL_NERVOUS_SYSTEM)	111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			C|||	1	0.000199681	0.0	0.0	5008	,	,		18620	0.0		0.001	False		,,,				2504	0.0				p.R273H	Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	TP53,central_nervous_system,brain,Substitution - Missense,-1 	.	669	Substitution - Missense(647)|Whole gene deletion(8)|Deletion - Frameshift(6)|Deletion - In frame(5)|Unknown(2)|Insertion - Frameshift(1)	large_intestine(136)|lung(99)|breast(74)|ovary(59)|upper_aerodigestive_tract(55)|central_nervous_system(46)|oesophagus(35)|haematopoietic_and_lymphoid_tissue(30)|stomach(26)|urinary_tract(25)|pancreas(15)|endometrium(13)|liver(12)|skin(11)|bone(9)|biliary_tract(7)|penis(4)|cervix(2)|genital_tract(2)|NS(2)|soft_tissue(2)|vulva(1)|thyroid(1)|fallopian_tube(1)|prostate(1)|thymus(1)	c.G818A	17	GRCh37	CM004342|CM010472|CM920677	TP53	M	rs28934576	.						67.0	58.0	61.0					17																	7577120		2203	4300	6503	7517845	SO:0001583	missense	7157	exon8	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.818G>A	17.37:g.7577120C>T	ENSP00000269305:p.Arg273His	Somatic		Capture	Illumina HiSeq	Phase_I	7517845	NM_001126114	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	18.03	3.532510	0.64972	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99868	-7.32;-7.32;-7.32;-7.32;-7.32;-7.32	4.92	4.92	0.64577	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99822	0.9921	M	0.79475	2.455	0.80722	A	1	P;D;P;P	0.89917	0.631;1.0;0.831;0.48	B;D;P;B	0.77004	0.274;0.989;0.516;0.242	D	0.96531	0.9393	9	0.72032	D	0.01	-11.9995	15.662	0.77193	0.0:1.0:0.0:0.0	rs28934576	273;273;273;273	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	H	273;273;273;273;273;262;141	ENSP00000352610:R273H;ENSP00000269305:R273H;ENSP00000398846:R273H;ENSP00000391127:R273H;ENSP00000391478:R273H;ENSP00000425104:R141H	ENSP00000269305:R273H	R	-	2	0	TP53	7517845	1.000000	0.71417	0.068000	0.19968	0.665000	0.39181	7.587000	0.82613	2.556000	0.86216	0.462000	0.41574	CGT		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
GGA3	23163	broad.mit.edu	37	17	73237110	73237110	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:73237110C>T	ENST00000245541.6	-	11	1191	c.975G>A	c.(973-975)acG>acA	p.T325T	GGA3_ENST00000351904.7_Silent_p.T292T|GGA3_ENST00000579743.1_5'Flank|GGA3_ENST00000582486.1_Silent_p.T253T|GGA3_ENST00000537686.1_3'UTR|GGA3_ENST00000538886.1_Silent_p.T203T|GGA3_ENST00000578348.1_Silent_p.T203T|GGA3_ENST00000582717.1_Silent_p.T253T	NM_138619.2	NP_619525.1	Q9NZ52	GGA3_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 3	325	Unstructured hinge.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|endosome (GO:0005768)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)	p.T325T(1)		breast(2)|endometrium(3)|large_intestine(4)|liver(1)|lung(4)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	20			all cancers(21;2.39e-06)|Epithelial(20;2.38e-05)			GGTCGATGAGCGTGCCTTGGT	0.572											OREG0024730	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T292T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G876A	17						.						135.0	131.0	132.0					17																	73237110		2203	4300	6503	70748705	SO:0001819	synonymous_variant	23163	exon10			AF190864	CCDS11716.1, CCDS11717.1, CCDS54164.1, CCDS58597.1	17q25	2010-02-12	2010-02-12			ENSG00000125447			17079	protein-coding gene	gene with protein product		606006				10747089, 10749927	Standard	NR_033345		Approved	KIAA0154	uc002jni.2	Q9NZ52		ENST00000245541.6:c.975G>A	17.37:g.73237110C>T		Somatic	1143	Capture	Illumina HiSeq	Phase_I	70748705	NM_014001	B7Z7E2|B7Z7M9|J3KRN0|Q15017|Q6IS16|Q9UJY3	Silent	SNP	ENST00000245541.6	37	CCDS11717.1																																																																																				0.572	GGA3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446645.1	NM_138619	
SLC26A11	284129	broad.mit.edu	37	17	78210814	78210814	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:78210814A>G	ENST00000361193.3	+	8	1104	c.824A>G	c.(823-825)gAg>gGg	p.E275G	SLC26A11_ENST00000572725.1_Missense_Mutation_p.E275G|SLC26A11_ENST00000411502.3_Missense_Mutation_p.E275G|SLC26A11_ENST00000546047.2_Missense_Mutation_p.E275G	NM_001166347.1|NM_173626.3	NP_001159819.1|NP_775897.3			solute carrier family 26 (anion exchanger), member 11									p.E275G(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)			CTAACAGGGGAGACAGCTGAG	0.622																																					p.E275G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A824G	17						.						101.0	82.0	89.0					17																	78210814		2203	4300	6503	75825409	SO:0001583	missense	284129	exon7				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.824A>G	17.37:g.78210814A>G	ENSP00000355384:p.Glu275Gly	Somatic		Capture	Illumina HiSeq	Phase_I	75825409	NM_001166349		Missense_Mutation	SNP	ENST00000361193.3	37	CCDS11771.2	.	.	.	.	.	.	.	.	.	.	A	12.59	1.985105	0.35036	.	.	ENSG00000181045	ENST00000411502;ENST00000546047;ENST00000361193	D;D;D	0.93906	-3.31;-3.31;-3.31	5.06	2.79	0.32731	Sulphate transporter (1);	0.643908	0.17090	N	0.187438	D	0.88937	0.6573	L	0.48642	1.525	0.09310	N	1	B	0.25235	0.121	B	0.30943	0.122	T	0.78056	-0.2353	10	0.30854	T	0.27	-12.649	5.7665	0.18229	0.7054:0.1524:0.1422:0.0	.	275	Q86WA9	S2611_HUMAN	G	275	ENSP00000403998:E275G;ENSP00000440724:E275G;ENSP00000355384:E275G	ENSP00000355384:E275G	E	+	2	0	SLC26A11	75825409	0.999000	0.42202	0.047000	0.18901	0.769000	0.43574	4.030000	0.57260	0.724000	0.32296	0.383000	0.25322	GAG		0.622	SLC26A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257281.1		
ASPSCR1	79058	broad.mit.edu	37	17	79943408	79943408	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:79943408A>G	ENST00000306739.4	+	4	396	c.299A>G	c.(298-300)gAt>gGt	p.D100G	ASPSCR1_ENST00000580534.1_Missense_Mutation_p.D23G|ASPSCR1_ENST00000581647.1_Missense_Mutation_p.D100G|ASPSCR1_ENST00000306729.7_Missense_Mutation_p.D100G	NM_024083.3	NP_076988.1	Q9BZE9	ASPC1_HUMAN	alveolar soft part sarcoma chromosome region, candidate 1	100					glucose homeostasis (GO:0042593)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|regulation of glucose import (GO:0046324)	cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)		p.D100G(2)	ASPSCR1/TFE3(167)	breast(2)|large_intestine(2)	4	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)			CAGCTGGACGATGGCTCGAGG	0.512			T	TFE3	alveolar soft part sarcoma																																p.D100G			Dom	yes		17	17q25	79058	"""alveolar soft part sarcoma chromosome region, candidate 1"""		M	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A299G	17						.						105.0	92.0	97.0					17																	79943408		2203	4300	6503	77536697	SO:0001583	missense	79058	exon4			AF324219	CCDS11796.1, CCDS58611.1	17q25	2011-06-28				ENSG00000169696		"""UBX domain containing"""	13825	protein-coding gene	gene with protein product	"""UBX domain protein 9"""	606236				11244503, 10506710	Standard	NM_024083		Approved	ASPS, ASPL, UBXD9, UBXN9	uc002kcy.3	Q9BZE9		ENST00000306739.4:c.299A>G	17.37:g.79943408A>G	ENSP00000302176:p.Asp100Gly	Somatic		Capture	Illumina HiSeq	Phase_I	77536697	NM_024083	A8K3K9|Q7Z6N7|Q8WV59|Q96LS5|Q96M40	Missense_Mutation	SNP	ENST00000306739.4	37	CCDS11796.1	.	.	.	.	.	.	.	.	.	.	A	8.485	0.860702	0.17178	.	.	ENSG00000169696	ENST00000306739;ENST00000306729;ENST00000344865	T;T	0.26518	1.73;1.73	5.44	5.44	0.79542	.	0.101061	0.64402	D	0.000004	T	0.53867	0.1823	M	0.85462	2.755	0.47994	D	0.999565	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.87578	0.998;0.998;0.998;0.994;0.998	T	0.60357	-0.7279	10	0.66056	D	0.02	-21.0303	11.8769	0.52552	1.0:0.0:0.0:0.0	.	23;23;100;100;23	Q9BZE9-3;Q9BZE9-4;Q9BZE9-2;Q9BZE9;C9JAL9	.;.;.;ASPC1_HUMAN;.	G	100;100;23	ENSP00000302176:D100G;ENSP00000306625:D100G	ENSP00000306625:D100G	D	+	2	0	ASPSCR1	77536697	1.000000	0.71417	0.890000	0.34922	0.118000	0.20060	5.267000	0.65530	2.060000	0.61445	0.383000	0.25322	GAT		0.512	ASPSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441972.1	NM_024083	
ABR	29	broad.mit.edu	37	17	915088	915088	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:915088G>A	ENST00000302538.5	-	19	2245	c.2099C>T	c.(2098-2100)gCc>gTc	p.A700V	ABR_ENST00000574437.1_Missense_Mutation_p.A654V|ABR_ENST00000536794.2_Missense_Mutation_p.A482V|ABR_ENST00000291107.2_Missense_Mutation_p.A663V|ABR_ENST00000544583.2_Missense_Mutation_p.A654V|ABR_ENST00000572441.1_Intron|ABR_ENST00000543210.2_Missense_Mutation_p.A151V	NM_001282149.1|NM_021962.3	NP_001269078.1|NP_068781.2	Q12979	ABR_HUMAN	active BCR-related	700	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|brain development (GO:0007420)|inner ear morphogenesis (GO:0042472)|negative regulation of cell migration (GO:0030336)|negative regulation of inflammatory response (GO:0050728)|negative regulation of neutrophil degranulation (GO:0043314)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phagocytosis (GO:0050766)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to lipopolysaccharide (GO:0032496)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|Rac GTPase activator activity (GO:0030675)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.A700V(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)		AGACTCACTGGCATCGAAGAC	0.642																																					p.A700V	Esophageal Squamous(197;2016 2115 4129 29033 46447)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2099T	17						.						139.0	108.0	118.0					17																	915088		2203	4300	6503	861838	SO:0001583	missense	29	exon19			L19704	CCDS10999.1, CCDS11000.1, CCDS54060.1, CCDS58497.1, CCDS73936.1	17p13	2013-01-10	2012-02-27		ENSG00000159842	ENSG00000159842		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	81	protein-coding gene	gene with protein product		600365	"""active BCR-related gene"""			2587217, 7479768	Standard	NM_001092		Approved	MDB	uc002fsd.4	Q12979	OTTHUMG00000090313	ENST00000302538.5:c.2099C>T	17.37:g.915088G>A	ENSP00000303909:p.Ala700Val	Somatic		Capture	Illumina HiSeq	Phase_I	861838	NM_021962	B3KW89|B7Z6H7|D3DTH3|D3DTH4|F5H3S2|F5H8B3|Q13693|Q13694	Missense_Mutation	SNP	ENST00000302538.5	37	CCDS10999.1	.	.	.	.	.	.	.	.	.	.	G	12.47	1.947932	0.34377	.	.	ENSG00000159842	ENST00000302538;ENST00000544583;ENST00000291107;ENST00000536794;ENST00000543210;ENST00000382259	T;T;T;T;T	0.19532	2.14;2.14;2.14;2.14;2.14	5.96	5.96	0.96718	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.118233	0.56097	D	0.000021	T	0.19366	0.0465	N	0.26130	0.795	0.50171	D	0.999853	B;B;P;B;B;B	0.46784	0.001;0.206;0.884;0.122;0.001;0.003	B;B;B;B;B;B	0.42959	0.014;0.086;0.403;0.059;0.009;0.014	T	0.01578	-1.1320	10	0.21540	T	0.41	.	19.034	0.92970	0.0:0.0:1.0:0.0	.	482;151;308;663;610;700	B7Z683;F5H3S2;Q6ZT60;Q12979-2;B7Z2X0;Q12979	.;.;.;.;.;ABR_HUMAN	V	700;654;663;482;151;309	ENSP00000303909:A700V;ENSP00000442048:A654V;ENSP00000291107:A663V;ENSP00000437429:A482V;ENSP00000445198:A151V	ENSP00000291107:A663V	A	-	2	0	ABR	861838	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	4.818000	0.62657	2.843000	0.97960	0.650000	0.86243	GCC		0.642	ABR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206675.4		
C17orf59	54785	broad.mit.edu	37	17	8092633	8092633	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:8092633C>T	ENST00000389017.4	-	1	931	c.826G>A	c.(826-828)Gac>Aac	p.D276N	MIR3676_ENST00000579470.1_RNA	NM_017622.2	NP_060092.2	Q96GS4	CQ059_HUMAN	chromosome 17 open reading frame 59	276								p.D142N(1)		large_intestine(2)|lung(3)|urinary_tract(1)	6						AGCAGACGGTCCACCCGGCCT	0.682																																					p.D276N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G826A	17						.																																			8033358	SO:0001583	missense	54785	exon1			BC018880	CCDS11133.2	17p13.1	2005-12-16			ENSG00000196544	ENSG00000196544			25939	protein-coding gene	gene with protein product						12477932	Standard	NM_017622		Approved	FLJ20014	uc010vut.2	Q96GS4	OTTHUMG00000153930	ENST00000389017.4:c.826G>A	17.37:g.8092633C>T	ENSP00000373669:p.Asp276Asn	Somatic		Capture	Illumina HiSeq	Phase_I	8033358	NM_017622	Q53HS4|Q9NXW8	Missense_Mutation	SNP	ENST00000389017.4	37	CCDS11133.2	.	.	.	.	.	.	.	.	.	.	C	27.6	4.845846	0.91277	.	.	ENSG00000196544	ENST00000389017	.	.	.	5.48	5.48	0.80851	.	0.109690	0.64402	D	0.000008	T	0.68668	0.3026	L	0.49126	1.545	0.58432	D	0.999996	D	0.69078	0.997	D	0.64321	0.924	T	0.69327	-0.5174	9	0.54805	T	0.06	-24.3552	14.8546	0.70326	0.0:1.0:0.0:0.0	.	276	Q96GS4	CQ059_HUMAN	N	276	.	ENSP00000373669:D276N	D	-	1	0	C17orf59	8033358	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.608000	0.61141	2.592000	0.87571	0.561000	0.74099	GAC		0.682	C17orf59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333072.1	NM_017622	
PIK3R5	23533	broad.mit.edu	37	17	8791611	8791611	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:8791611C>T	ENST00000447110.1	-	10	1617	c.1493G>A	c.(1492-1494)cGc>cAc	p.R498H	PIK3R5_ENST00000584803.1_Missense_Mutation_p.R498H|PIK3R5_ENST00000581552.1_Missense_Mutation_p.R498H	NM_001142633.2|NM_001251851.1|NM_001251852.1|NM_001251853.1|NM_001251855.1	NP_001136105.1|NP_001238780.1|NP_001238781.1|NP_001238782.1|NP_001238784.1	Q8WYR1	PI3R5_HUMAN	phosphoinositide-3-kinase, regulatory subunit 5	498					blood coagulation (GO:0007596)|cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|small molecule metabolic process (GO:0044281)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|G-protein beta/gamma-subunit complex binding (GO:0031683)	p.R498H(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(14)|prostate(3)|skin(4)|urinary_tract(1)	34						GCGCTGGGGGCGTGAAGCAGG	0.657																																					p.R498H	NSCLC(18;589 615 7696 20311 50332)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1493A	17						.						35.0	38.0	37.0					17																	8791611		2203	4300	6503	8732336	SO:0001583	missense	23533	exon10			AF128881	CCDS11147.1, CCDS73986.1	17p13.1	2011-10-13	2008-02-04		ENSG00000141506	ENSG00000141506			30035	protein-coding gene	gene with protein product		611317				12507995	Standard	NM_014308		Approved	P101-PI3K, p101	uc002glt.3	Q8WYR1	OTTHUMG00000108197	ENST00000447110.1:c.1493G>A	17.37:g.8791611C>T	ENSP00000392812:p.Arg498His	Somatic		Capture	Illumina HiSeq	Phase_I	8732336	NM_014308	B0LPH4|D3DTS3|Q5G936|Q5G938|Q5G939|Q8IZ23|Q9Y2Y2	Missense_Mutation	SNP	ENST00000447110.1	37	CCDS11147.1	.	.	.	.	.	.	.	.	.	.	C	6.141	0.394228	0.11638	.	.	ENSG00000141506	ENST00000269300;ENST00000447110	T	0.77620	-1.11	5.48	3.12	0.35913	.	0.719133	0.14504	N	0.315566	T	0.53594	0.1806	N	0.04880	-0.145	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.38067	-0.9678	10	0.25106	T	0.35	-10.5507	6.6596	0.23007	0.0:0.676:0.0:0.324	.	498	Q8WYR1	PI3R5_HUMAN	H	498	ENSP00000392812:R498H	ENSP00000269300:R498H	R	-	2	0	PIK3R5	8732336	0.153000	0.22777	0.730000	0.30809	0.143000	0.21401	0.966000	0.29331	1.280000	0.44463	0.650000	0.86243	CGC		0.657	PIK3R5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000227003.2	NM_014308	
MEIS3P1	4213	broad.mit.edu	37	17	15690295	15690297	+	lincRNA	DEL	CTT	CTT	-	rs200526826	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	CTT	CTT					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:15690295_15690297delCTT	ENST00000582780.1	-	0	694																											CTGAGAGGCCCTTCTTCTCCTCC	0.591														765	0.152756	0.1377	0.1787	5008	,	,		16962	0.1687		0.0467	False		,,,				2504	0.2474				.												.	.	0			.	17						.																																			15631022			4213	.																															17.37:g.15690298_15690300delCTT		Somatic		Capture	Illumina HiSeq	Phase_I	15631020	.		In_Frame_Del	DEL	ENST00000582780.1	37																																																																																					0.591	CTD-3157E16.1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000444653.1		
FOXK2	3607	broad.mit.edu	37	17	80540765	80540765	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr17:80540765G>T	ENST00000335255.5	+	5	1232	c.1058G>T	c.(1057-1059)aGg>aTg	p.R353M	snoU13_ENST00000459591.1_RNA	NM_004514.3	NP_004505.2	Q01167	FOXK2_HUMAN	forkhead box K2	353	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.R353M(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)			CGACGGCCTAGGGGCGTGCCC	0.502																																					p.R353M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1058T	17						.						49.0	51.0	50.0					17																	80540765		2203	4300	6503	78134054	SO:0001583	missense	3607	exon5			U58196	CCDS11813.1	17q25	2006-12-15	2004-03-09	2004-03-10	ENSG00000141568	ENSG00000141568		"""Forkhead boxes"""	6036	protein-coding gene	gene with protein product		147685	"""interleukin enhancer binding factor 1"""	ILF, ILF1		3260003	Standard	NM_004514		Approved		uc002kfn.3	Q01167	OTTHUMG00000140374	ENST00000335255.5:c.1058G>T	17.37:g.80540765G>T	ENSP00000335677:p.Arg353Met	Somatic		Capture	Illumina HiSeq	Phase_I	78134054	NM_004514	A6NEP5|Q13622|Q13623|Q13624	Missense_Mutation	SNP	ENST00000335255.5	37	CCDS11813.1	.	.	.	.	.	.	.	.	.	.	G	33	5.196854	0.94960	.	.	ENSG00000141568	ENST00000535184;ENST00000335255;ENST00000531030;ENST00000526383	D;D;D	0.96745	-3.79;-4.11;-3.94	6.07	6.07	0.98685	Transcription factor, fork head (1);	0.000000	0.85682	D	0.000000	D	0.98388	0.9464	M	0.89904	3.07	0.80722	D	1	P;D	0.53462	0.916;0.96	P;P	0.60473	0.875;0.867	D	0.98532	1.0628	10	0.72032	D	0.01	.	20.6439	0.99570	0.0:0.0:1.0:0.0	.	353;353	Q01167;Q01167-2	FOXK2_HUMAN;.	M	349;353;164;233	ENSP00000335677:R353M;ENSP00000433167:R164M;ENSP00000432663:R233M	ENSP00000335677:R353M	R	+	2	0	FOXK2	78134054	1.000000	0.71417	0.994000	0.49952	0.994000	0.84299	9.678000	0.98647	2.884000	0.98904	0.655000	0.94253	AGG		0.502	FOXK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277099.2	NM_181430	
AQP4	361	broad.mit.edu	37	18	24445649	24445649	+	Missense_Mutation	SNP	C	C	G	rs375551135		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr18:24445649C>G	ENST00000383168.4	-	1	133	c.5G>C	c.(4-6)aGt>aCt	p.S2T	AQP4-AS1_ENST00000579964.1_RNA|AQP4-AS1_ENST00000582605.1_RNA|AQP4_ENST00000581374.1_5'Flank|AQP4-AS1_ENST00000578701.1_RNA|AQP4-AS1_ENST00000568797.1_RNA|AQP4_ENST00000440832.3_5'Flank	NM_001650.4|NM_004028.3	NP_001641.1|NP_004019.1	P55087	AQP4_HUMAN	aquaporin 4	2					carbon dioxide transport (GO:0015670)|cellular response to estradiol stimulus (GO:0071392)|cellular response to interferon-gamma (GO:0071346)|female pregnancy (GO:0007565)|hyperosmotic salinity response (GO:0042538)|multicellular organismal water homeostasis (GO:0050891)|protein homooligomerization (GO:0051260)|renal water absorption (GO:0070295)|response to glucocorticoid (GO:0051384)|response to radiation (GO:0009314)|sensory perception of sound (GO:0007605)|transmembrane transport (GO:0055085)|transport (GO:0006810)|water transport (GO:0006833)	basolateral plasma membrane (GO:0016323)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)	porin activity (GO:0015288)|water channel activity (GO:0015250)|water transmembrane transporter activity (GO:0005372)	p.S2T(1)		kidney(2)|large_intestine(3)|lung(5)|skin(1)	11	all_cancers(21;0.0172)|Lung NSC(5;0.00299)|all_lung(6;0.00747)|Ovarian(20;0.124)					GGGTCTGTCACTCATGCCTTC	0.522																																					p.S2T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5C	18						.						103.0	103.0	103.0					18																	24445649		2203	4300	6503	22699647	SO:0001583	missense	361	exon1			U63622	CCDS11889.1, CCDS58617.1	18q11.2-q12.1	2005-09-20			ENSG00000171885	ENSG00000171885		"""Ion channels / Aquaporins"""	637	protein-coding gene	gene with protein product		600308				7528931	Standard	NM_001650		Approved	MIWC	uc002kwa.3	P55087	OTTHUMG00000131955	ENST00000383168.4:c.5G>C	18.37:g.24445649C>G	ENSP00000372654:p.Ser2Thr	Somatic		Capture	Illumina HiSeq	Phase_I	22699647	NM_001650	P78564	Missense_Mutation	SNP	ENST00000383168.4	37	CCDS11889.1	.	.	.	.	.	.	.	.	.	.	C	15.80	2.939260	0.52972	.	.	ENSG00000171885	ENST00000383168;ENST00000440832;ENST00000383170	D	0.86230	-2.09	5.04	5.04	0.67666	.	0.809444	0.11000	N	0.610552	D	0.83376	0.5241	L	0.36672	1.1	0.80722	D	1	P	0.38535	0.635	B	0.33339	0.162	T	0.83320	-0.0018	10	0.72032	D	0.01	.	18.8734	0.92325	0.0:1.0:0.0:0.0	.	2	P55087	AQP4_HUMAN	T	2;2;9	ENSP00000372654:S2T	ENSP00000372654:S2T	S	-	2	0	AQP4	22699647	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.541000	0.60670	2.719000	0.93026	0.655000	0.94253	AGT		0.522	AQP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254914.2	NM_001650, NM_004028	
CHST9	83539	broad.mit.edu	37	18	24496351	24496351	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr18:24496351C>A	ENST00000284224.8	-	6	1481	c.1204G>T	c.(1204-1206)Gat>Tat	p.D402Y	AQP4-AS1_ENST00000579964.1_RNA|AQP4-AS1_ENST00000582605.1_RNA|CHST9_ENST00000581714.1_Missense_Mutation_p.D402Y|AQP4-AS1_ENST00000578701.1_RNA|AQP4-AS1_ENST00000568797.1_RNA|CHST9_ENST00000580774.1_3'UTR	NM_031422.5	NP_113610.2	Q7L1S5	CHST9_HUMAN	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 9	402					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|hormone biosynthetic process (GO:0042446)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)	p.D402Y(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|skin(3)	28	all_lung(6;0.0145)|Ovarian(20;0.124)					GTTCTTTCATCGGAAGAGTGC	0.363																																					p.D402Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1204T	18						.						146.0	136.0	139.0					18																	24496351		1840	4090	5930	22750349	SO:0001583	missense	83539	exon6			AF239821	CCDS42422.1, CCDS58618.1	18q11.2	2011-04-28			ENSG00000154080	ENSG00000154080		"""Sulfotransferases, membrane-bound"""	19898	protein-coding gene	gene with protein product		610191				11139592, 11445554	Standard	NM_031422		Approved	GALNAC4ST-2, GALNAC-4-ST2	uc002kwe.4	Q7L1S5		ENST00000284224.8:c.1204G>T	18.37:g.24496351C>A	ENSP00000284224:p.Asp402Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	22750349	NM_031422	Q6UX69|Q9BXH3|Q9BXH4|Q9BZW9	Missense_Mutation	SNP	ENST00000284224.8	37	CCDS42422.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.932603	0.73442	.	.	ENSG00000154080	ENST00000284224	T	0.73469	-0.75	6.07	6.07	0.98685	.	0.073354	0.56097	D	0.000021	T	0.75788	0.3897	N	0.08118	0	0.80722	D	1	D	0.76494	0.999	D	0.76575	0.988	T	0.77453	-0.2582	10	0.37606	T	0.19	-26.7158	20.6593	0.99626	0.0:1.0:0.0:0.0	.	402	Q7L1S5	CHST9_HUMAN	Y	402	ENSP00000284224:D402Y	ENSP00000284224:D402Y	D	-	1	0	CHST9	22750349	1.000000	0.71417	0.991000	0.47740	0.986000	0.74619	5.755000	0.68750	2.885000	0.99019	0.655000	0.94253	GAT		0.363	CHST9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446549.1	NM_031422	
CDH2	1000	broad.mit.edu	37	18	25565573	25565573	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr18:25565573G>C	ENST00000269141.3	-	12	2317	c.1894C>G	c.(1894-1896)Cca>Gca	p.P632A	CDH2_ENST00000399380.3_Missense_Mutation_p.P601A	NM_001792.3	NP_001783.2	P19022	CADH2_HUMAN	cadherin 2, type 1, N-cadherin (neuronal)	632	Cadherin 5. {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.P632A(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						CCAGCATTTGGATCAATGTCA	0.388																																					p.P632A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1894G	18						.						93.0	92.0	92.0					18																	25565573		2203	4300	6503	23819571	SO:0001583	missense	1000	exon12			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.1894C>G	18.37:g.25565573G>C	ENSP00000269141:p.Pro632Ala	Somatic		Capture	Illumina HiSeq	Phase_I	23819571	NM_001792	A8MWK3|B0YIY6|Q14923|Q8N173	Missense_Mutation	SNP	ENST00000269141.3	37	CCDS11891.1	.	.	.	.	.	.	.	.	.	.	G	17.16	3.318076	0.60524	.	.	ENSG00000170558	ENST00000269141;ENST00000399380	T;T	0.54071	0.59;0.59	5.96	5.96	0.96718	Cadherin (3);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.71854	0.3389	M	0.77820	2.39	0.80722	D	1	D;P	0.61697	0.99;0.954	P;P	0.59171	0.853;0.448	T	0.70824	-0.4767	10	0.46703	T	0.11	.	20.394	0.98981	0.0:0.0:1.0:0.0	.	601;632	A8MWK3;P19022	.;CADH2_HUMAN	A	632;601	ENSP00000269141:P632A;ENSP00000382312:P601A	ENSP00000269141:P632A	P	-	1	0	CDH2	23819571	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.414000	0.97362	2.830000	0.97506	0.585000	0.79938	CCA		0.388	CDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133246.3	NM_001792	
DSG1	1828	broad.mit.edu	37	18	28906963	28906963	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr18:28906963G>A	ENST00000257192.4	+	3	423	c.211G>A	c.(211-213)Gcc>Acc	p.A71T		NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	71	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell-cell junction assembly (GO:0007043)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|protein stabilization (GO:0050821)|response to progesterone (GO:0032570)|single organismal cell-cell adhesion (GO:0016337)	apical plasma membrane (GO:0016324)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)|toxic substance binding (GO:0015643)	p.A71T(1)		NS(2)|central_nervous_system(2)|endometrium(5)|kidney(7)|large_intestine(11)|lung(36)|ovary(3)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	76			OV - Ovarian serous cystadenocarcinoma(10;0.00559)			GAACCCAATCGCCAAAGTAGG	0.413																																					p.A71T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G211A	18						.						110.0	104.0	106.0					18																	28906963		2203	4300	6503	27160961	SO:0001583	missense	1828	exon3			X56654	CCDS11896.1	18q12.1	2014-05-13			ENSG00000134760	ENSG00000134760		"""Cadherins / Major cadherins"""	3048	protein-coding gene	gene with protein product		125670		DSG		1889810	Standard	NM_001942		Approved	CDHF4	uc002kwp.3	Q02413	OTTHUMG00000131983	ENST00000257192.4:c.211G>A	18.37:g.28906963G>A	ENSP00000257192:p.Ala71Thr	Somatic		Capture	Illumina HiSeq	Phase_I	27160961	NM_001942	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	CCDS11896.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.171890	0.78452	.	.	ENSG00000134760	ENST00000257192	T	0.49139	0.79	5.34	5.34	0.76211	Cadherin (3);Cadherin-like (1);	0.000000	0.56097	D	0.000039	T	0.69771	0.3148	M	0.72624	2.21	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.72683	-0.4219	10	0.72032	D	0.01	.	19.0554	0.93062	0.0:0.0:1.0:0.0	.	71	Q02413	DSG1_HUMAN	T	71	ENSP00000257192:A71T	ENSP00000257192:A71T	A	+	1	0	DSG1	27160961	1.000000	0.71417	0.998000	0.56505	0.462000	0.32619	6.473000	0.73572	2.494000	0.84150	0.557000	0.71058	GCC		0.413	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942	
COLEC12	81035	broad.mit.edu	37	18	331693	331693	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr18:331693G>T	ENST00000400256.3	-	8	2245	c.2038C>A	c.(2038-2040)Ctg>Atg	p.L680M		NM_130386.2	NP_569057	Q5KU26	COL12_HUMAN	collectin sub-family member 12	680	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				carbohydrate mediated signaling (GO:0009756)|defense response (GO:0006952)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)|phagocytosis, recognition (GO:0006910)|protein homooligomerization (GO:0051260)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galactose binding (GO:0005534)|low-density lipoprotein particle binding (GO:0030169)|metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)	p.L680M(1)		cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	46		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)				GTCCCATCCAGCCACTTCCAT	0.483																																					p.L680M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2038A	18						.						138.0	118.0	124.0					18																	331693		2203	4300	6503	321693	SO:0001583	missense	81035	exon8			AB038518	CCDS32782.1	18p11.32	2013-09-19			ENSG00000158270	ENSG00000158270		"""Collectins"""	16016	protein-coding gene	gene with protein product		607621				11162630	Standard	NM_130386		Approved	SRCL, CL-P1, SCARA4	uc002kkm.3	Q5KU26	OTTHUMG00000178145	ENST00000400256.3:c.2038C>A	18.37:g.331693G>T	ENSP00000383115:p.Leu680Met	Somatic		Capture	Illumina HiSeq	Phase_I	321693	NM_130386	Q6P9F2|Q8TCR2|Q8WZA4|Q9BY85|Q9BYH7	Missense_Mutation	SNP	ENST00000400256.3	37	CCDS32782.1	.	.	.	.	.	.	.	.	.	.	G	17.83	3.484509	0.63962	.	.	ENSG00000158270	ENST00000400256	T	0.18174	2.23	5.73	5.73	0.89815	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.000000	0.64402	D	0.000001	T	0.30324	0.0761	L	0.37466	1.105	0.50039	D	0.999843	D	0.69078	0.997	D	0.87578	0.998	T	0.00664	-1.1620	10	0.35671	T	0.21	-11.5067	12.6318	0.56661	0.1189:0.0:0.8811:0.0	.	680	Q5KU26	COL12_HUMAN	M	680	ENSP00000383115:L680M	ENSP00000383115:L680M	L	-	1	2	COLEC12	321693	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.419000	0.34793	2.714000	0.92807	0.591000	0.81541	CTG		0.483	COLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440746.1		
SLC39A6	25800	broad.mit.edu	37	18	33694256	33694256	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr18:33694256G>A	ENST00000590986.1	-	7	1936	c.1647C>T	c.(1645-1647)ggC>ggT	p.G549G	SLC39A6_ENST00000440549.2_Silent_p.G274G|SLC39A6_ENST00000269187.5_Silent_p.G549G			Q13433	S39A6_HUMAN	solute carrier family 39 (zinc transporter), member 6	549	His-rich.				cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)|zinc ion transmembrane import (GO:0071578)|zinc ion transmembrane transport (GO:0071577)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|lamellipodium membrane (GO:0031258)|plasma membrane (GO:0005886)	zinc ion transmembrane transporter activity (GO:0005385)	p.G549G(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(4)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	41						CGTCTGACTGGCCGAGTGTAT	0.468																																					p.G274G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C822T	18						.						233.0	240.0	238.0					18																	33694256		2177	4276	6453	31948254	SO:0001819	synonymous_variant	25800	exon6			U41060	CCDS42428.1, CCDS45854.1	18q12.2	2013-05-22				ENSG00000141424		"""Solute carriers"""	18607	protein-coding gene	gene with protein product		608731	"""solute carrier family 39 (metal ion transporter), member 6"""			12659941, 12839489	Standard	NM_012319		Approved	LIV-1	uc010dmy.3	Q13433		ENST00000590986.1:c.1647C>T	18.37:g.33694256G>A		Somatic		Capture	Illumina HiSeq	Phase_I	31948254	NM_001099406	B4DR49|B4E224|Q8IXR3|Q96HP5	Silent	SNP	ENST00000590986.1	37	CCDS42428.1																																																																																				0.468	SLC39A6-004	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000444136.1		
DCC	1630	broad.mit.edu	37	18	50994337	50994337	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr18:50994337G>A	ENST00000442544.2	+	25	4309	c.3693G>A	c.(3691-3693)cgG>cgA	p.R1231R	DCC_ENST00000581580.1_Silent_p.R866R	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	1231					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)	p.R1231R(1)		NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		GAGCCCCCCGGGCCAAGCTCA	0.493																																					p.R1231R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3693A	18						.						77.0	74.0	75.0					18																	50994337		2203	4300	6503	49248335	SO:0001819	synonymous_variant	1630	exon25			X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2701	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 1"""	120470	"""deleted in colorectal carcinoma"""			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.3693G>A	18.37:g.50994337G>A		Somatic		Capture	Illumina HiSeq	Phase_I	49248335	NM_005215		Silent	SNP	ENST00000442544.2	37	CCDS11952.1																																																																																				0.493	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215	
CDH20	28316	broad.mit.edu	37	18	59212348	59212348	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr18:59212348A>G	ENST00000262717.4	+	10	2017	c.1619A>G	c.(1618-1620)aAc>aGc	p.N540S	CDH20_ENST00000538374.1_Missense_Mutation_p.N540S|CDH20_ENST00000536675.2_Missense_Mutation_p.N540S			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	540	Cadherin 5. {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.N540S(1)		breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|skin(3)	61		Colorectal(73;0.186)				GCTGCTAACAACCCCAACTTT	0.502																																					p.N540S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1619G	18						.						196.0	156.0	169.0					18																	59212348		2203	4300	6503	57363328	SO:0001583	missense	28316	exon9			AF217289	CCDS11977.1	18q21.33	2010-01-26			ENSG00000101542	ENSG00000101542		"""Cadherins / Major cadherins"""	1760	protein-coding gene	gene with protein product		605807				10995570	Standard	NM_031891		Approved	CDH7L3, Cdh7	uc010dps.1	Q9HBT6	OTTHUMG00000132768	ENST00000262717.4:c.1619A>G	18.37:g.59212348A>G	ENSP00000262717:p.Asn540Ser	Somatic		Capture	Illumina HiSeq	Phase_I	57363328	NM_031891	Q495S3	Missense_Mutation	SNP	ENST00000262717.4	37	CCDS11977.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.568232	0.86439	.	.	ENSG00000101542	ENST00000536675;ENST00000538374;ENST00000262717	T;T;T	0.50813	0.73;0.73;0.73	6.01	6.01	0.97437	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.59197	0.2176	L	0.39326	1.205	0.80722	D	1	D	0.62365	0.991	D	0.63283	0.913	T	0.59600	-0.7424	10	0.54805	T	0.06	.	16.5285	0.84344	1.0:0.0:0.0:0.0	.	540	Q9HBT6	CAD20_HUMAN	S	540	ENSP00000444767:N540S;ENSP00000442226:N540S;ENSP00000262717:N540S	ENSP00000262717:N540S	N	+	2	0	CDH20	57363328	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.469000	0.80959	2.307000	0.77673	0.528000	0.53228	AAC		0.502	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256141.2	NM_031891	
BCL2	596	broad.mit.edu	37	18	60985895	60985895	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr18:60985895G>A	ENST00000398117.1	-	1	1466	c.5C>T	c.(4-6)gCg>gTg	p.A2V	BCL2_ENST00000333681.4_Missense_Mutation_p.A2V|BCL2_ENST00000589955.1_Missense_Mutation_p.A2V|BCL2_ENST00000444484.1_Missense_Mutation_p.A2V	NM_000633.2	NP_000624.2	P10415	BCL2_HUMAN	B-cell CLL/lymphoma 2	2					actin filament organization (GO:0007015)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|axonogenesis (GO:0007409)|B cell homeostasis (GO:0001782)|B cell lineage commitment (GO:0002326)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|behavioral fear response (GO:0001662)|branching involved in ureteric bud morphogenesis (GO:0001658)|CD8-positive, alpha-beta T cell lineage commitment (GO:0043375)|cell aging (GO:0007569)|cell growth (GO:0016049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to organic substance (GO:0071310)|cochlear nucleus development (GO:0021747)|defense response to virus (GO:0051607)|developmental growth (GO:0048589)|digestive tract morphogenesis (GO:0048546)|ear development (GO:0043583)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|female pregnancy (GO:0007565)|focal adhesion assembly (GO:0048041)|gland morphogenesis (GO:0022612)|glomerulus development (GO:0032835)|hair follicle morphogenesis (GO:0031069)|homeostasis of number of cells within a tissue (GO:0048873)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|melanin metabolic process (GO:0006582)|melanocyte differentiation (GO:0030318)|mesenchymal cell development (GO:0014031)|metanephros development (GO:0001656)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of autophagy (GO:0010507)|negative regulation of calcium ion transport into cytosol (GO:0010523)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cellular pH reduction (GO:0032848)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of mitochondrial depolarization (GO:0051902)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of myeloid cell apoptotic process (GO:0033033)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of retinal cell programmed cell death (GO:0046671)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|oocyte development (GO:0048599)|organ growth (GO:0035265)|ossification (GO:0001503)|ovarian follicle development (GO:0001541)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|pigment granule organization (GO:0048753)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of catalytic activity (GO:0043085)|positive regulation of cell growth (GO:0030307)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron maturation (GO:0014042)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of skeletal muscle fiber development (GO:0048743)|positive regulation of smooth muscle cell migration (GO:0014911)|post-embryonic development (GO:0009791)|protein dephosphorylation (GO:0006470)|protein polyubiquitination (GO:0000209)|reactive oxygen species metabolic process (GO:0072593)|regulation of calcium ion transport (GO:0051924)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glycoprotein biosynthetic process (GO:0010559)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of nitrogen utilization (GO:0006808)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|regulation of protein stability (GO:0031647)|regulation of transmembrane transporter activity (GO:0022898)|regulation of viral genome replication (GO:0045069)|release of cytochrome c from mitochondria (GO:0001836)|renal system process (GO:0003014)|response to acid chemical (GO:0001101)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to gamma radiation (GO:0010332)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to iron ion (GO:0010039)|response to ischemia (GO:0002931)|response to nicotine (GO:0035094)|response to radiation (GO:0009314)|response to toxic substance (GO:0009636)|response to UV-B (GO:0010224)|single organismal cell-cell adhesion (GO:0016337)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|myelin sheath (GO:0043209)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|pore complex (GO:0046930)	BH3 domain binding (GO:0051434)|channel activity (GO:0015267)|channel inhibitor activity (GO:0016248)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin protein ligase binding (GO:0031625)	p.A2V(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(106)|kidney(1)|large_intestine(1)|lung(3)	113		all_hematologic(56;1.18e-20)|Prostate(75;0.0872)		Lung(128;0.0234)|READ - Rectum adenocarcinoma(59;0.0935)	Docetaxel(DB01248)|Ibuprofen(DB01050)|Paclitaxel(DB01229)|Rasagiline(DB01367)	CCCAGCGTGCGCCATCCTTCC	0.577			T	IGH@	"""NHL, CLL"""																																p.A2V			Dom	yes		18	18q21.3	596	B-cell CLL/lymphoma 2		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5T	18						.						58.0	64.0	62.0					18																	60985895		1925	4038	5963	59136875	SO:0001583	missense	596	exon2			M14745	CCDS11981.1, CCDS45882.1	18q21.3	2014-03-07			ENSG00000171791	ENSG00000171791		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	990	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 50"""	151430					Standard	XM_006722523		Approved	Bcl-2, PPP1R50	uc002lit.1	P10415	OTTHUMG00000132791	ENST00000398117.1:c.5C>T	18.37:g.60985895G>A	ENSP00000381185:p.Ala2Val	Somatic		Capture	Illumina HiSeq	Phase_I	59136875	NM_000633	C9JHD5|P10416|Q13842|Q16197	Missense_Mutation	SNP	ENST00000398117.1	37	CCDS11981.1	.	.	.	.	.	.	.	.	.	.	G	19.23	3.787811	0.70337	.	.	ENSG00000171791	ENST00000398117;ENST00000333681;ENST00000444484	T;T;T	0.15372	2.43;2.43;2.44	4.48	2.68	0.31781	.	0.000000	0.56097	D	0.000037	T	0.30978	0.0782	L	0.46157	1.445	0.38644	D	0.951686	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.986	T	0.05649	-1.0872	10	0.87932	D	0	-15.6376	9.828	0.40923	0.0774:0.1399:0.7827:0.0	.	2;2	C9JHD5;P10415	.;BCL2_HUMAN	V	2	ENSP00000381185:A2V;ENSP00000329623:A2V;ENSP00000404214:A2V	ENSP00000329623:A2V	A	-	2	0	BCL2	59136875	1.000000	0.71417	0.998000	0.56505	0.963000	0.63663	4.951000	0.63610	0.509000	0.28195	-0.216000	0.12614	GCG		0.577	BCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256199.1	NM_000633, NM_000657	
SERPINB2	5055	broad.mit.edu	37	18	61558697	61558697	+	Missense_Mutation	SNP	G	G	A	rs553765342	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr18:61558697G>A	ENST00000299502.4	+	2	99	c.19G>A	c.(19-21)Gca>Aca	p.A7T	SERPINB2_ENST00000457692.1_Missense_Mutation_p.A7T	NM_002575.2	NP_002566.1	P05120	PAI2_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 2	7					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.A7T(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)	TCTTTGTGTGGCAAACACACT	0.458													G|||	2	0.000399361	0.0	0.0	5008	,	,		21135	0.0		0.0	False		,,,				2504	0.002				p.A7T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G19A	18						.						110.0	106.0	107.0					18																	61558697		2203	4300	6503	59709677	SO:0001583	missense	5055	exon2			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.19G>A	18.37:g.61558697G>A	ENSP00000299502:p.Ala7Thr	Somatic		Capture	Illumina HiSeq	Phase_I	59709677	NM_002575	Q96E96	Missense_Mutation	SNP	ENST00000299502.4	37	CCDS11989.1	.	.	.	.	.	.	.	.	.	.	G	17.92	3.507569	0.64410	.	.	ENSG00000197632	ENST00000404622;ENST00000299502;ENST00000457692;ENST00000413956;ENST00000443281	D;D;D;D;D	0.85773	-2.03;-2.03;-2.03;-2.03;-2.03	5.44	5.44	0.79542	Serpin domain (2);	0.056867	0.64402	D	0.000001	D	0.91975	0.7458	M	0.79693	2.465	0.58432	D	0.999999	D	0.69078	0.997	D	0.70487	0.969	D	0.92486	0.5996	10	0.87932	D	0	.	14.6374	0.68699	0.0:0.0:1.0:0.0	.	7	P05120	PAI2_HUMAN	T	7	ENSP00000385397:A7T;ENSP00000299502:A7T;ENSP00000401645:A7T;ENSP00000402386:A7T;ENSP00000397096:A7T	ENSP00000299502:A7T	A	+	1	0	SERPINB2	59709677	1.000000	0.71417	0.890000	0.34922	0.396000	0.30629	4.395000	0.59678	2.834000	0.97654	0.650000	0.86243	GCA		0.458	SERPINB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134009.1	NM_002575	
DSEL	92126	broad.mit.edu	37	18	65181151	65181151	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr18:65181151A>G	ENST00000310045.7	-	2	2198	c.725T>C	c.(724-726)tTa>tCa	p.L242S	RP11-638L3.1_ENST00000583687.1_lincRNA|CTD-2541J13.2_ENST00000581951.1_RNA|CTD-2541J13.2_ENST00000583493.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	232					carbohydrate metabolic process (GO:0005975)|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 membrane (GO:0016021)	isomerase activity (GO:0016853)|sulfotransferase activity (GO:0008146)	p.L242S(1)		NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(25)|lung(23)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)				CCCTGTGAGTAATGCTATCAT	0.413																																					p.L242S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T725C	18						.						95.0	95.0	95.0					18																	65181151		2203	4300	6503	63332131	SO:0001583	missense	92126	exon2			AF480435	CCDS11995.1	18q22.1	2007-01-29	2007-01-29	2007-01-29	ENSG00000171451	ENSG00000171451			18144	protein-coding gene	gene with protein product		611125	"""chromosome 18 open reading frame 4"""	C18orf4		16505484	Standard	NM_032160		Approved	NCAG1, FLJ11477	uc002lke.1	Q8IZU8	OTTHUMG00000132804	ENST00000310045.7:c.725T>C	18.37:g.65181151A>G	ENSP00000310565:p.Leu242Ser	Somatic		Capture	Illumina HiSeq	Phase_I	63332131	NM_032160	Q17RH1|Q6P5Z3	Missense_Mutation	SNP	ENST00000310045.7	37	CCDS11995.1	.	.	.	.	.	.	.	.	.	.	A	19.43	3.825923	0.71143	.	.	ENSG00000171451	ENST00000310045;ENST00000397964	T	0.55234	0.53	4.75	4.75	0.60458	.	0.316966	0.26180	U	0.025877	T	0.56470	0.1987	M	0.68593	2.085	0.46631	D	0.999139	B	0.29301	0.241	B	0.35813	0.211	T	0.61955	-0.6956	10	0.87932	D	0	.	14.5674	0.68188	1.0:0.0:0.0:0.0	.	232	Q8IZU8	DSEL_HUMAN	S	242;232	ENSP00000310565:L242S	ENSP00000310565:L242S	L	-	2	0	DSEL	63332131	1.000000	0.71417	0.940000	0.37924	0.994000	0.84299	9.113000	0.94321	1.921000	0.55644	0.454000	0.30748	TTA		0.413	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160	
TMX3	54495	broad.mit.edu	37	18	66344240	66344240	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr18:66344240G>T	ENST00000299608.2	-	16	1611	c.1295C>A	c.(1294-1296)cCc>cAc	p.P432H		NM_019022.3	NP_061895.3	Q96JJ7	TMX3_HUMAN	thioredoxin-related transmembrane protein 3	432					cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein disulfide isomerase activity (GO:0003756)	p.P432H(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	17						TCCACTGCTGGGCTCCTGCTG	0.403																																					p.P432H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1295A	18						.						177.0	140.0	153.0					18																	66344240		2203	4300	6503	64495220	SO:0001583	missense	54495	exon16			BX647846	CCDS32840.1	18q22	2011-10-19	2009-02-23	2009-02-23		ENSG00000166479		"""Protein disulfide isomerases"""	24718	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 13"""		"""thioredoxin domain containing 10"""	TXNDC10		15623505	Standard	NM_019022		Approved	FLJ20793, KIAA1830, PDIA13	uc002lkf.3	Q96JJ7		ENST00000299608.2:c.1295C>A	18.37:g.66344240G>T	ENSP00000299608:p.Pro432His	Somatic		Capture	Illumina HiSeq	Phase_I	64495220	NM_019022	B3KV75|Q52LT7|Q8N5J0|Q9NWJ9	Missense_Mutation	SNP	ENST00000299608.2	37	CCDS32840.1	.	.	.	.	.	.	.	.	.	.	G	4.516	0.095801	0.08681	.	.	ENSG00000166479	ENST00000299608	T	0.09630	2.96	5.61	1.44	0.22558	.	0.912769	0.09540	N	0.788450	T	0.05227	0.0139	N	0.08118	0	0.18873	N	0.999989	B	0.06786	0.001	B	0.06405	0.002	T	0.37526	-0.9702	10	0.48119	T	0.1	.	4.4355	0.11549	0.0828:0.2204:0.5206:0.1762	.	432	Q96JJ7	TMX3_HUMAN	H	432	ENSP00000299608:P432H	ENSP00000299608:P432H	P	-	2	0	TMX3	64495220	0.200000	0.23398	0.060000	0.19600	0.022000	0.10575	1.705000	0.37867	0.699000	0.31761	-0.142000	0.14014	CCC		0.403	TMX3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420155.1	NM_019022	
TMX3	54495	broad.mit.edu	37	18	66354971	66354971	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr18:66354971G>A	ENST00000299608.2	-	10	985	c.669C>T	c.(667-669)atC>atT	p.I223I	TMX3_ENST00000566887.1_5'Flank	NM_019022.3	NP_061895.3	Q96JJ7	TMX3_HUMAN	thioredoxin-related transmembrane protein 3	223					cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein disulfide isomerase activity (GO:0003756)	p.I223I(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	17						TTTCCCTGTTGATCCATGATG	0.343																																					p.I223I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C669T	18						.						159.0	144.0	149.0					18																	66354971		2203	4300	6503	64505951	SO:0001819	synonymous_variant	54495	exon10			BX647846	CCDS32840.1	18q22	2011-10-19	2009-02-23	2009-02-23		ENSG00000166479		"""Protein disulfide isomerases"""	24718	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 13"""		"""thioredoxin domain containing 10"""	TXNDC10		15623505	Standard	NM_019022		Approved	FLJ20793, KIAA1830, PDIA13	uc002lkf.3	Q96JJ7		ENST00000299608.2:c.669C>T	18.37:g.66354971G>A		Somatic		Capture	Illumina HiSeq	Phase_I	64505951	NM_019022	B3KV75|Q52LT7|Q8N5J0|Q9NWJ9	Silent	SNP	ENST00000299608.2	37	CCDS32840.1																																																																																				0.343	TMX3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420155.1	NM_019022	
RTTN	25914	broad.mit.edu	37	18	67759356	67759356	+	Missense_Mutation	SNP	C	C	G	rs376532876		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr18:67759356C>G	ENST00000255674.6	-	30	4419	c.4133G>C	c.(4132-4134)cGg>cCg	p.R1378P	RTTN_ENST00000454359.1_3'UTR|RTTN_ENST00000437017.1_Missense_Mutation_p.R1378P	NM_173630.3	NP_775901.3	Q86VV8	RTTN_HUMAN	rotatin	1378					determination of left/right symmetry (GO:0007368)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)		p.R1378P(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(35)|ovary(4)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Esophageal squamous(42;0.129)				CTCTGGGTCCCGATCAACCCA	0.453																																					p.R1378P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4133C	18						.						74.0	67.0	69.0					18																	67759356		1896	4110	6006	65910336	SO:0001583	missense	25914	exon30			AL117635	CCDS42443.1	18q22.1	2008-08-01				ENSG00000176225			18654	protein-coding gene	gene with protein product		610436				11900971	Standard	NM_173630		Approved	DKFZP434G145	uc002lkp.2	Q86VV8		ENST00000255674.6:c.4133G>C	18.37:g.67759356C>G	ENSP00000255674:p.Arg1378Pro	Somatic		Capture	Illumina HiSeq	Phase_I	65910336	NM_173630	Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	Missense_Mutation	SNP	ENST00000255674.6	37	CCDS42443.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.699734	0.88924	.	.	ENSG00000176225	ENST00000255674;ENST00000437017	T;T	0.65178	-0.14;-0.14	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	T	0.78767	0.4335	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80970	-0.1144	10	0.87932	D	0	.	18.8474	0.92212	0.0:1.0:0.0:0.0	.	1378	Q86VV8	RTTN_HUMAN	P	1378	ENSP00000255674:R1378P;ENSP00000399520:R1378P	ENSP00000255674:R1378P	R	-	2	0	RTTN	65910336	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.138000	0.77305	2.524000	0.85096	0.585000	0.79938	CGG		0.453	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442988.1	NM_173630	
ARHGAP28	79822	broad.mit.edu	37	18	6876175	6876175	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr18:6876175T>G	ENST00000383472.4	+	10	1362	c.1258T>G	c.(1258-1260)Ttt>Gtt	p.F420V	ARHGAP28_ENST00000262227.3_Missense_Mutation_p.F368V|ARHGAP28_ENST00000532996.1_Missense_Mutation_p.F243V|ARHGAP28_ENST00000419673.2_Missense_Mutation_p.F261V|ARHGAP28_ENST00000418986.1_Missense_Mutation_p.F261V|ARHGAP28_ENST00000314319.3_Missense_Mutation_p.F261V|ARHGAP28_ENST00000400091.2_Missense_Mutation_p.F420V|ARHGAP28_ENST00000531294.1_Missense_Mutation_p.F256V|RP11-146G7.2_ENST00000583659.1_RNA			Q9P2N2	RHG28_HUMAN	Rho GTPase activating protein 28	420	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)	p.F420V(1)|p.F261V(1)		breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	37		Colorectal(10;0.168)				TGAAGGAATTTTTCGACTTTC	0.373																																					p.F261V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T781G	18						.						148.0	142.0	144.0					18																	6876175		2203	4300	6503	6866175	SO:0001583	missense	79822	exon9			BC033668	CCDS32785.1	18p11.23	2011-06-29				ENSG00000088756		"""Rho GTPase activating proteins"""	25509	protein-coding gene	gene with protein product		610592				10718198	Standard	NM_001010000		Approved	KIAA1314, FLJ10312	uc002kne.3	Q9P2N2		ENST00000383472.4:c.1258T>G	18.37:g.6876175T>G	ENSP00000372964:p.Phe420Val	Somatic		Capture	Illumina HiSeq	Phase_I	6866175	NM_001010000	A8MQB7|A8MU88|Q6P160|Q8N4T3|Q9NW53	Missense_Mutation	SNP	ENST00000383472.4	37		.	.	.	.	.	.	.	.	.	.	T	20.1	3.935758	0.73442	.	.	ENSG00000088756	ENST00000400091;ENST00000262227;ENST00000419673;ENST00000531294;ENST00000314319;ENST00000418986;ENST00000532996;ENST00000383472	T;T;T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07;-0.07;-0.07	5.74	4.44	0.53790	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.108221	0.64402	D	0.000004	T	0.64972	0.2647	M	0.83483	2.645	0.34113	D	0.663226	P;P;P;B	0.41498	0.752;0.599;0.544;0.393	B;P;B;B	0.45167	0.388;0.472;0.341;0.406	T	0.77051	-0.2731	10	0.72032	D	0.01	.	4.0891	0.09962	0.0:0.2111:0.0:0.7889	.	420;252;261;368	Q9P2N2;E9PRP2;F6VKJ9;Q9P2N2-2	RHG28_HUMAN;.;.;.	V	420;368;261;256;261;261;252;243	ENSP00000382963:F420V;ENSP00000262227:F368V;ENSP00000392660:F261V;ENSP00000437262:F256V;ENSP00000313506:F261V;ENSP00000406907:F261V	ENSP00000262227:F368V	F	+	1	0	ARHGAP28	6866175	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	2.399000	0.44495	2.317000	0.78254	0.459000	0.35465	TTT		0.373	ARHGAP28-006	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442123.3	XM_371108	
LRRC30	339291	broad.mit.edu	37	18	7231888	7231888	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr18:7231888T>A	ENST00000383467.2	+	1	766	c.752T>A	c.(751-753)cTc>cAc	p.L251H		NM_001105581.1	NP_001099051.1	A6NM36	LRC30_HUMAN	leucine rich repeat containing 30	251								p.L251H(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(13)|ovary(1)|prostate(1)|skin(3)	31						CCGAGCGAACTCCACCTGCTG	0.572																																					p.L251H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T752A	18						.						78.0	82.0	81.0					18																	7231888		2016	4189	6205	7221888	SO:0001583	missense	339291	exon1				CCDS42409.1	18p11.23	2005-01-06				ENSG00000206422			30219	protein-coding gene	gene with protein product							Standard	NM_001105581		Approved		uc010wzk.2	A6NM36		ENST00000383467.2:c.752T>A	18.37:g.7231888T>A	ENSP00000372959:p.Leu251His	Somatic		Capture	Illumina HiSeq	Phase_I	7221888	NM_001105581		Missense_Mutation	SNP	ENST00000383467.2	37	CCDS42409.1	.	.	.	.	.	.	.	.	.	.	T	15.86	2.957591	0.53400	.	.	ENSG00000206422	ENST00000383467	T	0.31510	1.49	5.8	5.8	0.92144	.	0.103199	0.64402	D	0.000003	T	0.65668	0.2713	M	0.92077	3.27	0.53688	D	0.999977	D	0.89917	1.0	D	0.77004	0.989	T	0.75172	-0.3411	10	0.87932	D	0	.	16.1547	0.81649	0.0:0.0:0.0:1.0	.	251	A6NM36	LRC30_HUMAN	H	251	ENSP00000372959:L251H	ENSP00000372959:L251H	L	+	2	0	LRRC30	7221888	1.000000	0.71417	0.996000	0.52242	0.074000	0.17049	7.698000	0.84413	2.221000	0.72209	0.528000	0.53228	CTC		0.572	LRRC30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442140.1	XM_292678	
NETO1	81832	broad.mit.edu	37	18	70416299	70416299	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr18:70416299G>T	ENST00000327305.6	-	10	2223	c.1566C>A	c.(1564-1566)agC>agA	p.S522R	RNA5SP460_ENST00000516789.1_RNA|NETO1_ENST00000299430.2_Missense_Mutation_p.S521R|NETO1_ENST00000583169.1_Missense_Mutation_p.S522R	NM_138966.3	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin (NRP) and tolloid (TLL)-like 1	522					memory (GO:0007613)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|receptor localization to synapse (GO:0097120)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|visual learning (GO:0008542)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|kainate selective glutamate receptor complex (GO:0032983)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)		p.S522R(1)		NS(3)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(36)|ovary(2)|prostate(3)|skin(3)|stomach(1)	63		Esophageal squamous(42;0.129)		READ - Rectum adenocarcinoma(1;0.0487)		ATTCATGTTTGCTTAGAGACC	0.343																																					p.S522R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1566A	18						.						246.0	208.0	221.0					18																	70416299		2203	4300	6503	68567279	SO:0001583	missense	81832	exon10			AF448838	CCDS12000.1, CCDS42444.1	18q22.2	2008-08-01			ENSG00000166342	ENSG00000166342			13823	protein-coding gene	gene with protein product		607973				11943477, 12810072	Standard	NM_138999		Approved	BTCL1, BCTL1	uc002lkw.3	Q8TDF5	OTTHUMG00000132834	ENST00000327305.6:c.1566C>A	18.37:g.70416299G>T	ENSP00000313088:p.Ser522Arg	Somatic		Capture	Illumina HiSeq	Phase_I	68567279	NM_138966	Q86W85|Q8ND78|Q8TDF4	Missense_Mutation	SNP	ENST00000327305.6	37	CCDS12000.1	.	.	.	.	.	.	.	.	.	.	G	15.91	2.971284	0.53614	.	.	ENSG00000166342	ENST00000327305;ENST00000299430	T;T	0.26067	1.76;1.76	5.6	5.6	0.85130	.	0.000000	0.64402	D	0.000001	T	0.29783	0.0744	L	0.44542	1.39	0.80722	D	1	P;B	0.35908	0.527;0.392	B;B	0.37989	0.262;0.084	T	0.06006	-1.0851	10	0.87932	D	0	-3.8228	19.6075	0.95586	0.0:0.0:1.0:0.0	.	521;522	Q8TDF5-2;Q8TDF5	.;NETO1_HUMAN	R	522;521	ENSP00000313088:S522R;ENSP00000299430:S521R	ENSP00000299430:S521R	S	-	3	2	NETO1	68567279	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.429000	0.97481	2.640000	0.89533	0.585000	0.79938	AGC		0.343	NETO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256301.2	NM_138999	
CTDP1	9150	broad.mit.edu	37	18	77473101	77473101	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr18:77473101G>A	ENST00000299543.7	+	7	1140	c.993G>A	c.(991-993)gcG>gcA	p.A331A	CTDP1_ENST00000075430.7_Silent_p.A331A	NM_001202504.1|NM_004715.4	NP_001189433.1|NP_004706.3	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	331	FCP1 homology. {ECO:0000255|PROSITE- ProRule:PRU00336}.				exit from mitosis (GO:0010458)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|protein dephosphorylation (GO:0006470)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	CTD phosphatase activity (GO:0008420)|DNA-directed RNA polymerase activity (GO:0003899)	p.A331A(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(2)|urinary_tract(1)	35		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)		ATATGAATGCGCCCCCTGGGT	0.433																																					p.A331A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G993A	18						.						67.0	65.0	66.0					18																	77473101		2203	4300	6503	75574089	SO:0001819	synonymous_variant	9150	exon7			AF081287	CCDS12017.1, CCDS12018.1, CCDS74239.1	18q23	2014-09-17			ENSG00000060069	ENSG00000060069		"""Serine/threonine phosphatases / CTD aspartate-based phosphatases"""	2498	protein-coding gene	gene with protein product		604927				9405607, 9765293	Standard	NM_004715		Approved	FCP1	uc002lnh.2	Q9Y5B0	OTTHUMG00000132920	ENST00000299543.7:c.993G>A	18.37:g.77473101G>A		Somatic		Capture	Illumina HiSeq	Phase_I	75574089	NM_048368	A8MY97|Q7Z644|Q96BZ1|Q9Y6F5	Silent	SNP	ENST00000299543.7	37	CCDS12017.1																																																																																				0.433	CTDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256432.1	NM_004715	
NDUFB7	4713	broad.mit.edu	37	19	14677654	14677654	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:14677654C>T	ENST00000215565.2	-	2	265	c.204G>A	c.(202-204)aaG>aaA	p.K68K		NM_004146.5	NP_004137.2	P17568	NDUB7_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7, 18kDa	68					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 intermembrane space (GO:0005758)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)	p.K68K(1)		endometrium(3)|large_intestine(2)|lung(2)|ovary(1)	8						CACGCTTGCACTTGAGCAGCC	0.652																																					p.K68K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G204A	19						.						58.0	48.0	52.0					19																	14677654		2192	4282	6474	14538654	SO:0001819	synonymous_variant	4713	exon2				CCDS12314.1	19p13.12	2011-07-04	2002-08-29		ENSG00000099795	ENSG00000099795		"""Mitochondrial respiratory chain complex / Complex I"""	7702	protein-coding gene	gene with protein product	"""NADH-ubiquinone oxidoreductase B18 subunit"", ""complex I B18 subunit"""	603842	"""NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7 (18kD, B18)"""			9763677, 10830904	Standard	NM_004146		Approved	B18, CI-B18, MGC2480	uc002mzg.3	P17568		ENST00000215565.2:c.204G>A	19.37:g.14677654C>T		Somatic		Capture	Illumina HiSeq	Phase_I	14538654	NM_004146	Q6ICN9|Q9UI16	Silent	SNP	ENST00000215565.2	37	CCDS12314.1																																																																																				0.652	NDUFB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466025.1	NM_004146	
BRD4	23476	broad.mit.edu	37	19	15349966	15349966	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:15349966C>T	ENST00000263377.2	-	18	3907	c.3686G>A	c.(3685-3687)cGc>cAc	p.R1229H		NM_058243.2	NP_490597.1	O60885	BRD4_HUMAN	bromodomain containing 4	1229	C-terminal (CTD) 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.R1229H(1)		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)			CCGAGCGGCGCGGCGGAACTG	0.642			T	C15orf55	lethal midline carcinoma of young people																																p.R1229H			Dom	yes		19	19p13.1	23476	bromodomain containing 4		E	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3686A	19						.						30.0	31.0	30.0					19																	15349966		2203	4299	6502	15210966	SO:0001583	missense	23476	exon18			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.3686G>A	19.37:g.15349966C>T	ENSP00000263377:p.Arg1229His	Somatic		Capture	Illumina HiSeq	Phase_I	15210966	NM_058243	O60433|Q4G0X8|Q86YS8|Q96PD3	Missense_Mutation	SNP	ENST00000263377.2	37	CCDS12328.1	.	.	.	.	.	.	.	.	.	.	c	9.807	1.181987	0.21787	.	.	ENSG00000141867	ENST00000263377	T	0.18657	2.2	4.76	3.71	0.42584	.	0.126644	0.36303	N	0.002666	T	0.34193	0.0889	L	0.46157	1.445	0.80722	D	1	D	0.76494	0.999	P	0.58928	0.848	T	0.10683	-1.0619	10	0.87932	D	0	-16.2448	13.8287	0.63366	0.0:0.8449:0.1551:0.0	.	1229	O60885	BRD4_HUMAN	H	1229	ENSP00000263377:R1229H	ENSP00000263377:R1229H	R	-	2	0	BRD4	15210966	1.000000	0.71417	0.744000	0.31058	0.046000	0.14306	7.314000	0.78988	0.961000	0.38030	-0.324000	0.08512	CGC		0.642	BRD4-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465800.3	NM_058243	
AKAP8	10270	broad.mit.edu	37	19	15471697	15471697	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:15471697G>A	ENST00000269701.2	-	12	1549	c.1489C>T	c.(1489-1491)Cgg>Tgg	p.R497W		NM_005858.3	NP_005849.1	O43823	AKAP8_HUMAN	A kinase (PRKA) anchor protein 8	497					mitotic chromosome condensation (GO:0007076)|mitotic nuclear division (GO:0007067)|signal transduction (GO:0007165)	condensed chromosome (GO:0000793)|female pronucleus (GO:0001939)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.R497W(1)		breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)	26						TGCAGGTGCCGCTGGAGGAGC	0.622																																					p.R497W	GBM(190;1671 2163 3274 27186 30476)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1489T	19						.						71.0	55.0	61.0					19																	15471697		2203	4300	6503	15332697	SO:0001583	missense	10270	exon12			Y11997	CCDS12329.1	19p13.12	2012-05-16			ENSG00000105127	ENSG00000105127		"""A-kinase anchor proteins"""	378	protein-coding gene	gene with protein product	"""A-kinase anchor protein, 95kDa"""	604692				9473338	Standard	NM_005858		Approved	AKAP95, DKFZp586B1222	uc002nav.3	O43823		ENST00000269701.2:c.1489C>T	19.37:g.15471697G>A	ENSP00000269701:p.Arg497Trp	Somatic		Capture	Illumina HiSeq	Phase_I	15332697	NM_005858		Missense_Mutation	SNP	ENST00000269701.2	37	CCDS12329.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.065670	0.76187	.	.	ENSG00000105127	ENST00000269701	T	0.48201	0.82	5.87	4.82	0.62117	.	0.000000	0.50627	D	0.000119	T	0.56411	0.1983	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.60900	-0.7171	10	0.87932	D	0	-14.0584	13.5541	0.61749	0.0:0.0:0.7173:0.2826	.	497	O43823	AKAP8_HUMAN	W	497	ENSP00000269701:R497W	ENSP00000269701:R497W	R	-	1	2	AKAP8	15332697	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	2.598000	0.46223	1.468000	0.48064	0.655000	0.94253	CGG		0.622	AKAP8-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461293.3	NM_005858	
UNC13A	23025	broad.mit.edu	37	19	17743622	17743622	+	Missense_Mutation	SNP	C	C	T	rs75595663	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:17743622C>T	ENST00000519716.2	-	28	3396	c.3397G>A	c.(3397-3399)Gcc>Acc	p.A1133T	UNC13A_ENST00000252773.7_Missense_Mutation_p.A1133T|UNC13A_ENST00000550896.1_Missense_Mutation_p.A1131T|UNC13A_ENST00000551649.1_Missense_Mutation_p.A1133T|UNC13A_ENST00000552293.1_Missense_Mutation_p.A1133T|UNC13A_ENST00000428389.2_Missense_Mutation_p.A1221T	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	1133	MHD1. {ECO:0000255|PROSITE- ProRule:PRU00587}.				beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)	p.A1133T(1)		breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						TCCTTGAAGGCGGGAAGTTCC	0.552																																					p.A1133T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3397A	19						.						107.0	113.0	111.0					19																	17743622		2130	4254	6384	17604622	SO:0001583	missense	23025	exon27			AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.3397G>A	19.37:g.17743622C>T	ENSP00000429562:p.Ala1133Thr	Somatic		Capture	Illumina HiSeq	Phase_I	17604622	NM_001080421	E5RHY9	Missense_Mutation	SNP	ENST00000519716.2	37	CCDS46013.2	.	.	.	.	.	.	.	.	.	.	c	8.833	0.940363	0.18281	.	.	ENSG00000130477	ENST00000519716;ENST00000428389;ENST00000252773;ENST00000551649;ENST00000552293;ENST00000550896	T;T;T;T;T;T	0.80566	-1.38;-1.39;-1.38;-1.25;-1.25;-1.38	3.63	-0.725	0.11174	Munc13 homology 1 (1);	0.684102	0.13889	N	0.355725	T	0.60869	0.2302	L	0.28344	0.845	0.19300	N	0.99998	B	0.06786	0.001	B	0.06405	0.002	T	0.39014	-0.9634	10	0.15499	T	0.54	.	3.8778	0.09064	0.2746:0.472:0.0:0.2533	.	1133	Q9UPW8	UN13A_HUMAN	T	1133;1221;1133;1133;1133;1131	ENSP00000429562:A1133T;ENSP00000400409:A1221T;ENSP00000252773:A1133T;ENSP00000447236:A1133T;ENSP00000447572:A1133T;ENSP00000446831:A1131T	ENSP00000252773:A1133T	A	-	1	0	UNC13A	17604622	0.001000	0.12720	0.987000	0.45799	0.590000	0.36582	-0.016000	0.12613	0.079000	0.16929	0.298000	0.19748	GCC		0.552	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604	
RPL18A	6142	broad.mit.edu	37	19	17972210	17972210	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:17972210C>T	ENST00000222247.5	+	2	208	c.127C>T	c.(127-129)Cgc>Tgc	p.R43C	RPL18A_ENST00000600147.1_Missense_Mutation_p.R43C|SNORA68_ENST00000384437.1_RNA|RPL18A_ENST00000599870.1_Missense_Mutation_p.R14C|RPL18A_ENST00000599898.1_Intron	NM_000980.3	NP_000971.1	Q02543	RL18A_HUMAN	ribosomal protein L18a	43					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)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)	p.R43C(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|upper_aerodigestive_tract(1)	5						CGCCAAGTCCCGCTTCTGGTA	0.562																																					p.R43C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C127T	19						.						35.0	34.0	34.0					19																	17972210		2203	4279	6482	17833210	SO:0001583	missense	6142	exon2			AB007175	CCDS12367.1	19p13.11	2011-04-06			ENSG00000105640	ENSG00000105640		"""L ribosomal proteins"""	10311	protein-coding gene	gene with protein product	"""60S ribosomal protein L18a"", ""ribosomal protein L18a-like protein"""	604178				9582194	Standard	NM_000980		Approved	L18A	uc002nhp.3	Q02543		ENST00000222247.5:c.127C>T	19.37:g.17972210C>T	ENSP00000222247:p.Arg43Cys	Somatic		Capture	Illumina HiSeq	Phase_I	17833210	NM_000980		Missense_Mutation	SNP	ENST00000222247.5	37	CCDS12367.1	.	.	.	.	.	.	.	.	.	.	C	15.64	2.893764	0.52121	.	.	ENSG00000105640	ENST00000420197;ENST00000222247	.	.	.	4.11	1.78	0.24846	Ribosomal protein L18a/LX (1);	0.063063	0.64402	U	0.000006	T	0.80265	0.4591	M	0.93638	3.44	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.80346	-0.1421	9	0.87932	D	0	.	7.0801	0.25227	0.1693:0.7295:0.0:0.1012	.	43	Q02543	RL18A_HUMAN	C	43	.	ENSP00000222247:R43C	R	+	1	0	RPL18A	17833210	1.000000	0.71417	1.000000	0.80357	0.211000	0.24417	5.817000	0.69229	0.866000	0.35629	-0.251000	0.11542	CGC		0.562	RPL18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466679.1	NM_000980	
IL12RB1	3594	broad.mit.edu	37	19	18180425	18180425	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:18180425C>T	ENST00000600835.2	-	11	1418	c.1120G>A	c.(1120-1122)Gtg>Atg	p.V374M	IL12RB1_ENST00000593993.2_Missense_Mutation_p.V374M			P42701	I12R1_HUMAN	interleukin 12 receptor, beta 1	374	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-23-mediated signaling pathway (GO:0038155)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|interleukin-12 receptor complex (GO:0042022)|interleukin-23 receptor complex (GO:0072536)	cytokine receptor activity (GO:0004896)	p.V374M(1)		endometrium(1)|kidney(1)|lung(3)|pancreas(1)|skin(2)	8						TCCTGGCCCACAGGCTGCCAT	0.622																																					p.V374M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1120A	19						.						61.0	68.0	66.0					19																	18180425		2041	4183	6224	18041425	SO:0001583	missense	3594	exon10			U03187	CCDS32957.1, CCDS54232.1	19p13.1	2014-09-17						"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	5971	protein-coding gene	gene with protein product		601604		IL12RB		9284929	Standard	XM_005259893		Approved	CD212	uc002nhw.1	P42701		ENST00000600835.2:c.1120G>A	19.37:g.18180425C>T	ENSP00000470788:p.Val374Met	Somatic		Capture	Illumina HiSeq	Phase_I	18041425	NM_005535	A8K308|B2RPF1|B7ZKK3|Q8N6Q7	Missense_Mutation	SNP	ENST00000600835.2	37	CCDS54232.1	.	.	.	.	.	.	.	.	.	.	C	8.810	0.934960	0.18206	.	.	ENSG00000096996	ENST00000430026	T	0.80480	-1.38	4.0	-0.51	0.11973	.	1.089450	0.07069	N	0.835180	T	0.61489	0.2351	N	0.08118	0	0.09310	N	1	P;P	0.51791	0.948;0.913	B;B	0.43990	0.438;0.254	T	0.54853	-0.8231	10	0.37606	T	0.19	-0.2729	3.6224	0.08100	0.3335:0.2001:0.4664:0.0	.	374;374	P42701-2;P42701	.;I12R1_HUMAN	M	374	ENSP00000403103:V374M	ENSP00000403103:V374M	V	-	1	0	IL12RB1	18041425	0.000000	0.05858	0.001000	0.08648	0.053000	0.15095	-0.066000	0.11598	-0.086000	0.12550	-0.662000	0.03851	GTG		0.622	IL12RB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466525.3		
GIPC3	126326	broad.mit.edu	37	19	3590070	3590070	+	Missense_Mutation	SNP	C	C	T	rs149028750	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:3590070C>T	ENST00000322315.5	+	6	866	c.821C>T	c.(820-822)gCg>gTg	p.A274V		NM_133261.2	NP_573568.1	Q8TF64	GIPC3_HUMAN	GIPC PDZ domain containing family, member 3	274								p.A274V(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	10				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0025)|STAD - Stomach adenocarcinoma(1328;0.18)		AAGAAGACAGCGAGCGCCCAG	0.662													C|||	2	0.000399361	0.0	0.0	5008	,	,		12674	0.0		0.002	False		,,,				2504	0.0				p.A274V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C821T	19						.	C	VAL/ALA	0,4406		0,0,2203	38.0	43.0	41.0		821	-8.6	0.0	19	dbSNP_134	41	1,8597	1.2+/-3.3	0,1,4298	no	missense	GIPC3	NM_133261.2	64	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	benign	274/313	3590070	1,13003	2203	4299	6502	3541070	SO:0001583	missense	126326	exon6			AB073738	CCDS32871.1	19p13.3	2011-11-29				ENSG00000179855			18183	protein-coding gene	gene with protein product		608792	"""chromosome 19 open reading frame 64"", ""deafness, autosomal recessive 72"", ""deafness, autosomal recessive 15"""	C19orf64, DFNB72, DFNB15		11836571, 21326233	Standard	NM_133261		Approved	DFNB95	uc002lyd.4	Q8TF64		ENST00000322315.5:c.821C>T	19.37:g.3590070C>T	ENSP00000319254:p.Ala274Val	Somatic		Capture	Illumina HiSeq	Phase_I	3541070	NM_133261	O75227	Missense_Mutation	SNP	ENST00000322315.5	37	CCDS32871.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	7.584	0.669315	0.14776	0.0	1.16E-4	ENSG00000179855	ENST00000322315	T	0.81330	-1.48	4.28	-8.56	0.00904	.	0.863329	0.10101	N	0.715924	T	0.54481	0.1861	N	0.11427	0.14	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.39840	-0.9594	10	0.26408	T	0.33	-0.8751	6.602	0.22705	0.0906:0.5347:0.2554:0.1193	.	274	Q8TF64	GIPC3_HUMAN	V	274	ENSP00000319254:A274V	ENSP00000319254:A274V	A	+	2	0	GIPC3	3541070	0.000000	0.05858	0.002000	0.10522	0.625000	0.37756	-1.491000	0.02302	-3.461000	0.00159	-0.458000	0.05436	GCG		0.662	GIPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394577.1	NM_133261	
ZNF99	7652	broad.mit.edu	37	19	22941143	22941143	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:22941143G>T	ENST00000596209.1	-	4	1658	c.1568C>A	c.(1567-1569)gCc>gAc	p.A523D	ZNF99_ENST00000397104.3_Missense_Mutation_p.A432D	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	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)	p.A432D(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				TTTTCTAAGGGCTGAGAAATG	0.343																																					p.A432D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1295A	19						.						35.0	36.0	36.0					19																	22941143		1986	4183	6169	22732983	SO:0001583	missense	7652	exon5			BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"""Zinc fingers, C2H2-type"", ""-"""	13175	protein-coding gene	gene with protein product		603981	"""zinc finger protein 99 (F8281)"", ""chromosome 19 open reading frame 9"""	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.1568C>A	19.37:g.22941143G>T	ENSP00000472969:p.Ala523Asp	Somatic		Capture	Illumina HiSeq	Phase_I	22732983	NM_001080409	M0R335	Missense_Mutation	SNP	ENST00000596209.1	37	CCDS59369.1	.	.	.	.	.	.	.	.	.	.	-	0.052	-1.246287	0.01481	.	.	ENSG00000213973	ENST00000397104	T	0.19394	2.15	0.975	0.975	0.19721	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09949	0.0244	N	0.11255	0.115	0.09310	N	1	B	0.29835	0.258	B	0.27500	0.08	T	0.35400	-0.9790	9	0.22109	T	0.4	.	8.8169	0.35000	0.0:0.0:1.0:0.0	.	432	A8MXY4	ZNF99_HUMAN	D	432	ENSP00000380293:A432D	ENSP00000380293:A432D	A	-	2	0	ZNF99	22732983	0.000000	0.05858	0.010000	0.14722	0.064000	0.16182	-1.619000	0.02048	0.450000	0.26774	0.194000	0.17425	GCC		0.343	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124	
RHPN2	85415	broad.mit.edu	37	19	33482773	33482773	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:33482773C>T	ENST00000254260.3	-	13	1635	c.1600G>A	c.(1600-1602)Gcc>Acc	p.A534T	RHPN2_ENST00000400226.4_Missense_Mutation_p.A383T|RHPN2_ENST00000588683.1_5'Flank	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	534	PDZ.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)		p.A534T(1)		NS(1)|breast(3)|central_nervous_system(5)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(3)|urinary_tract(1)	44	Esophageal squamous(110;0.137)					TGAACGGGGGCGTTCCCTCTC	0.522																																					p.A534T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1600A	19						.						71.0	62.0	65.0					19																	33482773		2203	4300	6503	38174613	SO:0001583	missense	85415	exon13			AF268032	CCDS12427.1	19q13.12	2008-02-05				ENSG00000131941			19974	protein-coding gene	gene with protein product						12221077	Standard	NM_033103		Approved		uc002nuf.3	Q8IUC4		ENST00000254260.3:c.1600G>A	19.37:g.33482773C>T	ENSP00000254260:p.Ala534Thr	Somatic		Capture	Illumina HiSeq	Phase_I	38174613	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1	.	.	.	.	.	.	.	.	.	.	C	13.13	2.146126	0.37923	.	.	ENSG00000131941	ENST00000254260;ENST00000544458;ENST00000400226	T;T	0.29655	1.56;1.56	5.22	-0.477	0.12097	PDZ/DHR/GLGF (2);	0.352815	0.33534	N	0.004810	T	0.17280	0.0415	L	0.39020	1.185	0.23030	N	0.998409	B	0.14805	0.011	B	0.09377	0.004	T	0.10567	-1.0624	10	0.40728	T	0.16	0.7111	2.4928	0.04615	0.1981:0.4356:0.0873:0.2791	.	534	Q8IUC4	RHPN2_HUMAN	T	534;264;383	ENSP00000254260:A534T;ENSP00000402244:A383T	ENSP00000254260:A534T	A	-	1	0	RHPN2	38174613	0.000000	0.05858	0.691000	0.30163	0.841000	0.47740	-1.113000	0.03296	-0.305000	0.08831	-0.150000	0.13652	GCC		0.522	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103	
PEPD	5184	broad.mit.edu	37	19	34002017	34002017	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:34002017G>A	ENST00000244137.7	-	3	279	c.246C>T	c.(244-246)tgC>tgT	p.C82C	PEPD_ENST00000436370.3_Intron|PEPD_ENST00000397032.4_Silent_p.C82C	NM_000285.3	NP_000276.2	P12955	PEPD_HUMAN	peptidase D	82					cellular amino acid metabolic process (GO:0006520)|collagen catabolic process (GO:0030574)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)	aminopeptidase activity (GO:0004177)|dipeptidase activity (GO:0016805)|manganese ion binding (GO:0030145)|metallocarboxypeptidase activity (GO:0004181)	p.C82C(1)		endometrium(3)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)	17	Esophageal squamous(110;0.137)					TGACACCATAGCAGCCTGGCT	0.562																																					p.C82C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C246T	19						.						59.0	68.0	65.0					19																	34002017		2116	4224	6340	38693857	SO:0001819	synonymous_variant	5184	exon3			BC015027	CCDS42544.1, CCDS54244.1, CCDS54245.1	19q13.11	2008-02-05				ENSG00000124299	3.4.13.9		8840	protein-coding gene	gene with protein product	"""prolidase"""	613230				2925654, 1972707	Standard	NM_000285		Approved		uc002nur.4	P12955		ENST00000244137.7:c.246C>T	19.37:g.34002017G>A		Somatic		Capture	Illumina HiSeq	Phase_I	38693857	NM_000285	A8K3Z1|A8K416|A8K696|A8MX47|B4DDB7|B4DGJ1|E9PCE8|Q8TBN9|Q9BT75	Silent	SNP	ENST00000244137.7	37	CCDS42544.1																																																																																				0.562	PEPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451432.3	NM_000285	
ZNF599	148103	broad.mit.edu	37	19	35250135	35250135	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:35250135C>T	ENST00000329285.8	-	4	1944	c.1571G>A	c.(1570-1572)cGg>cAg	p.R524Q		NM_001007248.2	NP_001007249.1	Q96NL3	ZN599_HUMAN	zinc finger protein 599	524					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.R524Q(1)		endometrium(3)|large_intestine(10)|lung(8)|ovary(1)|pancreas(1)|skin(1)	24	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			CCTATTATGCCGAACAAAATT	0.423																																					p.R524Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1571A	19						.						105.0	106.0	106.0					19																	35250135		2203	4300	6503	39941975	SO:0001583	missense	148103	exon4			AK055225	CCDS32991.1	19q13.13	2013-01-08				ENSG00000153896		"""Zinc fingers, C2H2-type"", ""-"""	26408	protein-coding gene	gene with protein product							Standard	NM_001007248		Approved	FLJ30663	uc010edn.1	Q96NL3		ENST00000329285.8:c.1571G>A	19.37:g.35250135C>T	ENSP00000333802:p.Arg524Gln	Somatic		Capture	Illumina HiSeq	Phase_I	39941975	NM_001007248	Q569K0|Q5PRG1	Missense_Mutation	SNP	ENST00000329285.8	37	CCDS32991.1	.	.	.	.	.	.	.	.	.	.	C	0.006	-2.098207	0.00360	.	.	ENSG00000153896	ENST00000392231;ENST00000329285;ENST00000392229	T	0.26223	1.75	2.61	0.429	0.16506	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.11836	0.0288	L	0.28649	0.875	0.09310	N	1	P	0.39250	0.665	B	0.33890	0.172	T	0.16719	-1.0393	9	0.06891	T	0.86	.	4.9731	0.14127	0.0:0.5574:0.0:0.4426	.	524	Q96NL3	ZN599_HUMAN	Q	523;524;298	ENSP00000333802:R524Q	ENSP00000333802:R524Q	R	-	2	0	ZNF599	39941975	0.000000	0.05858	0.049000	0.19019	0.031000	0.12232	-1.634000	0.02020	0.174000	0.19809	0.655000	0.94253	CGG		0.423	ZNF599-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460648.2	XM_086046	
GRAMD1A	57655	broad.mit.edu	37	19	35501253	35501253	+	Silent	SNP	C	C	T	rs76289022		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:35501253C>T	ENST00000317991.5	+	6	687	c.495C>T	c.(493-495)aaC>aaT	p.N165N	GRAMD1A_ENST00000424536.2_Silent_p.N165N|GRAMD1A_ENST00000411896.2_Silent_p.N158N|GRAMD1A_ENST00000599564.1_Silent_p.N252N|GRAMD1A_ENST00000504615.2_5'UTR	NM_020895.3	NP_065946.2	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A	165						integral component of membrane (GO:0016021)		p.N165N(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	19	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			TGATCCCCAACGCCATCCAGA	0.607													C|||	1	0.000199681	0.0	0.0	5008	,	,		17426	0.001		0.0	False		,,,				2504	0.0				p.N158N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C474T	19						.						81.0	90.0	87.0					19																	35501253		2021	4187	6208	40193093	SO:0001819	synonymous_variant	57655	exon5			AK074864	CCDS42546.1, CCDS46046.1	19q13.13	2008-02-05	2005-11-02	2005-11-02		ENSG00000089351			29305	protein-coding gene	gene with protein product			"""KIAA1533"""	KIAA1533		10819331	Standard	NM_020895		Approved	FLJ90346	uc010xse.1	Q96CP6		ENST00000317991.5:c.495C>T	19.37:g.35501253C>T		Somatic		Capture	Illumina HiSeq	Phase_I	40193093	NM_001136199	A6NKY7|Q8NC77|Q9P1Z5	De_novo_Start_InFrame	SNP	ENST00000317991.5	37	CCDS42546.1																																																																																				0.607	GRAMD1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461557.1	NM_020895	
FFAR2	2867	broad.mit.edu	37	19	35941518	35941518	+	Missense_Mutation	SNP	G	G	A	rs147802928	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:35941518G>A	ENST00000599180.2	+	2	982	c.902G>A	c.(901-903)cGc>cAc	p.R301H	FFAR2_ENST00000601590.1_Intron|FFAR2_ENST00000246549.2_Missense_Mutation_p.R301H			O15552	FFAR2_HUMAN	free fatty acid receptor 2	301					cell surface pattern recognition receptor signaling pathway (GO:0002752)|cellular response to fatty acid (GO:0071398)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|leukocyte chemotaxis involved in inflammatory response (GO:0002232)|lipid storage (GO:0019915)|mucosal immune response (GO:0002385)|positive regulation of acute inflammatory response to non-antigenic stimulus (GO:0002879)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine production involved in immune response (GO:0002720)|positive regulation of interleukin-8 secretion (GO:2000484)|regulation of acute inflammatory response (GO:0002673)|regulation of peptide hormone secretion (GO:0090276)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)	p.R301H(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(6)|skin(1)|urinary_tract(1)	22	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			CTGTTGGGACGCAGAGGCAAA	0.572													G|||	8	0.00159744	0.0053	0.0014	5008	,	,		18993	0.0		0.0	False		,,,				2504	0.0				p.R301H	GBM(40;139 809 9833 23358 48736)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G902A	19						.	G	HIS/ARG	25,4381	30.8+/-60.4	1,23,2179	74.0	75.0	75.0		902	3.8	0.0	19	dbSNP_134	75	6,8594	5.7+/-21.5	0,6,4294	yes	missense	FFAR2	NM_005306.2	29	1,29,6473	AA,AG,GG		0.0698,0.5674,0.2384	possibly-damaging	301/331	35941518	31,12975	2203	4300	6503	40633358	SO:0001583	missense	2867	exon1			AF024690	CCDS12461.1	19q13.1	2012-08-08	2006-02-15	2006-02-15		ENSG00000126262		"""GPCR / Class A : Fatty acid receptors"""	4501	protein-coding gene	gene with protein product		603823	"""G protein-coupled receptor 43"""	GPR43		9344866	Standard	NM_005306		Approved	FFA2R	uc010eea.3	O15552		ENST00000599180.2:c.902G>A	19.37:g.35941518G>A	ENSP00000473159:p.Arg301His	Somatic		Capture	Illumina HiSeq	Phase_I	40633358	NM_005306	B0M0J9|Q4VAZ3|Q4VAZ5|Q4VBL5	Missense_Mutation	SNP	ENST00000599180.2	37	CCDS12461.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	13.52	2.260415	0.39995	0.005674	6.98E-4	ENSG00000126262	ENST00000246549	T	0.68624	-0.34	4.85	3.81	0.43845	.	0.444083	0.19863	N	0.104381	T	0.51500	0.1678	L	0.51422	1.61	0.09310	N	1	D	0.64830	0.994	P	0.44477	0.451	T	0.48581	-0.9023	10	0.27082	T	0.32	-3.8436	10.4645	0.44600	0.0:0.0:0.6457:0.3543	.	301	O15552	FFAR2_HUMAN	H	301	ENSP00000246549:R301H	ENSP00000246549:R301H	R	+	2	0	FFAR2	40633358	0.179000	0.23135	0.021000	0.16686	0.286000	0.27126	1.665000	0.37449	1.389000	0.46526	0.563000	0.77884	CGC		0.572	FFAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466120.3	NM_005306	
ANKRD24	170961	broad.mit.edu	37	19	4210269	4210269	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:4210269G>A	ENST00000600132.1	+	13	1235	c.959G>A	c.(958-960)cGa>cAa	p.R320Q	ANKRD24_ENST00000595096.1_3'UTR|ANKRD24_ENST00000262970.5_Missense_Mutation_p.R410Q|ANKRD24_ENST00000318934.4_Missense_Mutation_p.R320Q|RN7SL84P_ENST00000578969.1_RNA	NM_133475.1	NP_597732.1	Q8TF21	ANR24_HUMAN	ankyrin repeat domain 24	320								p.R185Q(1)|p.R320Q(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)		CAGGATGATCGAGATGCCTAT	0.657																																					p.R320Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G959A	19						.						34.0	45.0	41.0					19																	4210269		2042	4183	6225	4161269	SO:0001583	missense	170961	exon13			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.959G>A	19.37:g.4210269G>A	ENSP00000471252:p.Arg320Gln	Somatic		Capture	Illumina HiSeq	Phase_I	4161269	NM_133475	O75268|O95781	Missense_Mutation	SNP	ENST00000600132.1	37	CCDS45925.1	.	.	.	.	.	.	.	.	.	.	G	2.642	-0.284020	0.05642	.	.	ENSG00000089847	ENST00000318934;ENST00000262970	T;T	0.31247	1.55;1.5	4.45	-0.576	0.11731	.	.	.	.	.	T	0.15435	0.0372	N	0.16478	0.41	0.09310	N	1	B;B	0.23490	0.029;0.086	B;B	0.10450	0.002;0.005	T	0.27971	-1.0058	9	0.22706	T	0.39	-2.3003	7.4531	0.27250	0.4198:0.0:0.5802:0.0	.	320;410	Q8TF21;Q8TF21-2	ANR24_HUMAN;.	Q	320;410	ENSP00000321731:R320Q;ENSP00000262970:R410Q	ENSP00000262970:R410Q	R	+	2	0	ANKRD24	4161269	0.001000	0.12720	0.003000	0.11579	0.188000	0.23474	0.830000	0.27462	-0.320000	0.08640	-0.461000	0.05368	CGA		0.657	ANKRD24-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458188.1	XM_114000	
NFKBID	84807	broad.mit.edu	37	19	36386982	36386982	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:36386982C>T	ENST00000396901.1	-	9	1079	c.506G>A	c.(505-507)cGc>cAc	p.R169H	NFKBID_ENST00000352614.2_Missense_Mutation_p.R321H|NFKBID_ENST00000606253.1_Missense_Mutation_p.R169H|NFKBID_ENST00000585544.1_5'Flank	NM_139239.1	NP_640332.1	Q8NI38	IKBD_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, delta	169					inflammatory response (GO:0006954)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell differentiation in thymus (GO:0033085)|positive regulation of thymocyte apoptotic process (GO:0070245)	nucleus (GO:0005634)		p.R169H(1)		breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	14						GTCGGAAGGGCGCATAGCAAC	0.627																																					p.R169H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G506A	19						.						103.0	123.0	116.0					19																	36386982		2100	4204	6304	41078822	SO:0001583	missense	84807	exon9			AF385434	CCDS42552.1	19q13.12	2013-01-10				ENSG00000167604		"""Ankyrin repeat domain containing"""	15671	protein-coding gene	gene with protein product						12477932	Standard	NM_139239		Approved	TA-NFKBH, IkappaBNS	uc002oci.1	Q8NI38		ENST00000396901.1:c.506G>A	19.37:g.36386982C>T	ENSP00000380109:p.Arg169His	Somatic		Capture	Illumina HiSeq	Phase_I	41078822	NM_139239	Q8NI39|Q9BRG9	Missense_Mutation	SNP	ENST00000396901.1	37	CCDS42552.1	.	.	.	.	.	.	.	.	.	.	C	1.790	-0.479843	0.04383	.	.	ENSG00000167604	ENST00000352614;ENST00000396901	T;T	0.55760	0.5;1.12	5.04	-2.18	0.07037	Ankyrin repeat-containing domain (3);	0.785725	0.12398	N	0.472400	T	0.22666	0.0547	N	0.04203	-0.255	0.09310	N	0.999992	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.10965	-1.0607	10	0.35671	T	0.21	.	3.6681	0.08264	0.3953:0.2514:0.0:0.3533	.	321;169	Q8NI38-2;Q8NI38	.;IKBD_HUMAN	H	321;169	ENSP00000252985:R321H;ENSP00000380109:R169H	ENSP00000252985:R321H	R	-	2	0	NFKBID	41078822	0.018000	0.18449	0.105000	0.21289	0.382000	0.30200	-0.045000	0.12003	-0.227000	0.09884	0.491000	0.48974	CGC		0.627	NFKBID-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000452927.3	NM_032721	
ZNF585B	92285	broad.mit.edu	37	19	37677527	37677527	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:37677527G>A	ENST00000532828.2	-	5	1163	c.912C>T	c.(910-912)ggC>ggT	p.G304G	CTC-454I21.3_ENST00000585860.2_Intron|ZNF585B_ENST00000312908.5_5'UTR|ZNF585B_ENST00000531805.1_Silent_p.G249G|ZNF585B_ENST00000527838.1_3'UTR	NM_152279.3	NP_689492.3	Q52M93	Z585B_HUMAN	zinc finger protein 585B	304					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)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G304G(1)		NS(1)|breast(3)|endometrium(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TGAAGGATTTGCCACAGTTAT	0.408																																					p.G304G	Melanoma(93;882 1454 18863 28917 48427)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C912T	19						.						255.0	236.0	243.0					19																	37677527		2203	4300	6503	42369367	SO:0001819	synonymous_variant	92285	exon5			AK027834	CCDS12500.1	19q13.13	2013-01-08				ENSG00000245680		"""Zinc fingers, C2H2-type"", ""-"""	30948	protein-coding gene	gene with protein product						12477932	Standard	NM_152279		Approved	FLJ14928, SZFP41	uc002ofq.3	Q52M93		ENST00000532828.2:c.912C>T	19.37:g.37677527G>A		Somatic		Capture	Illumina HiSeq	Phase_I	42369367	NM_152279	Q8IZD3|Q96JW6	Silent	SNP	ENST00000532828.2	37	CCDS12500.1																																																																																				0.408	ZNF585B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388272.2	NM_152279	
PLIN4	729359	broad.mit.edu	37	19	4512470	4512470	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:4512470G>A	ENST00000301286.3	-	3	1459	c.1460C>T	c.(1459-1461)gCt>gTt	p.A487V		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	487	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)		p.A415V(1)		NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						AGTGGACACAGCATCTTTAGT	0.612																																					p.A487V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1460T	19						.						114.0	124.0	121.0					19																	4512470		1993	4160	6153	4463470	SO:0001583	missense	729359	exon3			AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"""Perilipins"""	29393	protein-coding gene	gene with protein product		613247	"""KIAA1881"""	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.1460C>T	19.37:g.4512470G>A	ENSP00000301286:p.Ala487Val	Somatic		Capture	Illumina HiSeq	Phase_I	4463470	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	.	.	.	.	.	.	.	.	.	.	G	12.43	1.935293	0.34189	.	.	ENSG00000167676	ENST00000301286	T	0.05649	3.41	5.38	4.34	0.51931	.	0.398470	0.21372	N	0.075604	T	0.06462	0.0166	L	0.41236	1.265	0.09310	N	1	B	0.16396	0.017	B	0.13407	0.009	T	0.21177	-1.0253	10	0.32370	T	0.25	-5.9471	11.1651	0.48539	0.0894:0.0:0.9106:0.0	.	487	Q96Q06	PLIN4_HUMAN	V	487	ENSP00000301286:A487V	ENSP00000301286:A487V	A	-	2	0	PLIN4	4463470	0.009000	0.17119	0.005000	0.12908	0.001000	0.01503	1.473000	0.35387	2.536000	0.85505	0.549000	0.68633	GCT		0.612	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
HKR1	284459	broad.mit.edu	37	19	37853619	37853619	+	Nonsense_Mutation	SNP	C	C	T	rs374853630		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:37853619C>T	ENST00000324411.4	+	6	1191	c.922C>T	c.(922-924)Cga>Tga	p.R308*	HKR1_ENST00000591134.1_Intron|HKR1_ENST00000544914.1_Nonsense_Mutation_p.R35*|HKR1_ENST00000392153.3_Nonsense_Mutation_p.R289*|HKR1_ENST00000591471.1_Nonsense_Mutation_p.R35*|HKR1_ENST00000589392.1_Nonsense_Mutation_p.R290*|HKR1_ENST00000541583.2_Nonsense_Mutation_p.R247*	NM_181786.2	NP_861451.1	P10072	HKR1_HUMAN	HKR1, GLI-Kruppel zinc finger family member	308					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)	p.R308*(1)		cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GGAATGTGGGCGAGGCTTTAC	0.502																																					p.R308X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C922T	19						.	C	stop/ARG	1,4405	2.1+/-5.4	0,1,2202	92.0	84.0	87.0		922	0.9	1.0	19		87	0,8600		0,0,4300	no	stop-gained	HKR1	NM_181786.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		308/660	37853619	1,13005	2203	4300	6503	42545459	SO:0001587	stop_gained	284459	exon6			M20675	CCDS12502.1	19q13.13	2013-01-08	2010-05-04			ENSG00000181666		"""Zinc fingers, C2H2-type"", ""-"""	4928	protein-coding gene	gene with protein product	"""oncogene HKR1"""	165250	"""GLI-Kruppel family member HKR1"""			2850480, 9813242	Standard	NM_181786		Approved	ZNF875	uc002ogb.3	P10072		ENST00000324411.4:c.922C>T	19.37:g.37853619C>T	ENSP00000315505:p.Arg308*	Somatic		Capture	Illumina HiSeq	Phase_I	42545459	NM_181786	A8MRS7|Q6PJD0|Q9BSW9|Q9UM09	Nonsense_Mutation	SNP	ENST00000324411.4	37	CCDS12502.1	.	.	.	.	.	.	.	.	.	.	C	37	6.282603	0.97440	2.27E-4	0.0	ENSG00000181666	ENST00000544914;ENST00000392153;ENST00000542144;ENST00000324411;ENST00000541583	.	.	.	3.37	0.889	0.19212	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	-5.3909	9.1681	0.37063	0.6087:0.3913:0.0:0.0	.	.	.	.	X	35;289;344;308;247	.	ENSP00000315505:R308X	R	+	1	2	HKR1	42545459	0.005000	0.15991	0.985000	0.45067	0.994000	0.84299	0.771000	0.26633	0.720000	0.32209	0.650000	0.86243	CGA		0.502	HKR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458375.1	NM_181786	
NUMBL	9253	broad.mit.edu	37	19	41186951	41186951	+	Silent	SNP	G	G	A	rs112715509	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:41186951G>A	ENST00000252891.4	-	6	578	c.411C>T	c.(409-411)gtC>gtT	p.V137V	NUMBL_ENST00000540131.1_Silent_p.V96V|NUMBL_ENST00000599594.1_5'Flank|NUMBL_ENST00000598779.1_Silent_p.V96V	NM_004756.3	NP_004747.1	Q9Y6R0	NUMBL_HUMAN	numb homolog (Drosophila)-like	137	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				adherens junction organization (GO:0034332)|axonogenesis (GO:0007409)|cytokine-mediated signaling pathway (GO:0019221)|lateral ventricle development (GO:0021670)|nervous system development (GO:0007399)|neuroblast division in subventricular zone (GO:0021849)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of neurogenesis (GO:0050769)|protein metabolic process (GO:0019538)	cytoplasm (GO:0005737)		p.V137V(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)	16			Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105)			TGGTCTGGTCGACCAGAAGAT	0.532																																					p.V137V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C411T	19						.	G		2,4404	4.2+/-10.8	0,2,2201	102.0	98.0	100.0		411	-7.5	0.8	19	dbSNP_132	100	0,8600		0,0,4300	no	coding-synonymous	NUMBL	NM_004756.3		0,2,6501	AA,AG,GG		0.0,0.0454,0.0154		137/610	41186951	2,13004	2203	4300	6503	45878791	SO:0001819	synonymous_variant	9253	exon6			AF015401	CCDS12561.1	19q13.13-q13.2	2008-07-17	2001-11-28			ENSG00000105245			8061	protein-coding gene	gene with protein product		604018	"""numb (Drosophila) homolog-like"""			9225980, 9303539	Standard	XM_006723471		Approved	NUMB-R, CTG3a, CAG3A, TNRC23, NUMBR, NUMBLIKE	uc002oon.3	Q9Y6R0		ENST00000252891.4:c.411C>T	19.37:g.41186951G>A		Somatic		Capture	Illumina HiSeq	Phase_I	45878791	NM_004756	Q7Z4J9	Silent	SNP	ENST00000252891.4	37	CCDS12561.1																																																																																				0.532	NUMBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462749.2	NM_004756	
CYP2A13	1553	broad.mit.edu	37	19	41594395	41594395	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:41594395C>A	ENST00000330436.3	+	1	19	c.19C>A	c.(19-21)Ctt>Att	p.L7I		NM_000766.4	NP_000757.2	Q16696	CP2AD_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 13	7					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)	p.L7I(1)		breast(3)|endometrium(6)|kidney(4)|large_intestine(8)|lung(13)|ovary(3)|prostate(3)|skin(2)	42					Methoxsalen(DB00553)|Nicotine(DB00184)|Testosterone(DB00624)	CTCAGGGCTGCTTCTGGTGAC	0.572																																					p.L7I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C19A	19						.						67.0	55.0	59.0					19																	41594395		2203	4300	6503	46286235	SO:0001583	missense	1553	exon1			U22028	CCDS12571.1	19q13.2	2013-11-11	2003-01-14		ENSG00000197838	ENSG00000197838		"""Cytochrome P450s"""	2608	protein-coding gene	gene with protein product		608055	"""cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 13"""			7668294, 15128046	Standard	NM_000766		Approved	CPAD, CYP2A	uc002opt.4	Q16696	OTTHUMG00000182762	ENST00000330436.3:c.19C>A	19.37:g.41594395C>A	ENSP00000332679:p.Leu7Ile	Somatic		Capture	Illumina HiSeq	Phase_I	46286235	NM_000766	Q53YR8|Q6R569|Q6R570|Q9H2X2	Missense_Mutation	SNP	ENST00000330436.3	37	CCDS12571.1	.	.	.	.	.	.	.	.	.	.	.	10.99	1.508252	0.27036	.	.	ENSG00000197838	ENST00000330436	T	0.71579	-0.58	3.3	3.3	0.37823	.	0.567073	0.16323	U	0.219443	T	0.65512	0.2698	L	0.60455	1.87	0.22989	N	0.998469	D	0.56968	0.978	P	0.47470	0.548	T	0.54833	-0.8234	10	0.18710	T	0.47	.	6.6519	0.22967	0.0:0.8652:0.0:0.1348	.	7	Q16696	CP2AD_HUMAN	I	7	ENSP00000332679:L7I	ENSP00000332679:L7I	L	+	1	0	CYP2A13	46286235	0.460000	0.25776	0.875000	0.34327	0.964000	0.63967	0.954000	0.29175	1.860000	0.53959	0.430000	0.28490	CTT		0.572	CYP2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463505.1	NM_000766	
ZNF574	64763	broad.mit.edu	37	19	42584302	42584302	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:42584302G>A	ENST00000600245.1	+	2	2199	c.1544G>A	c.(1543-1545)cGc>cAc	p.R515H	ZNF574_ENST00000359044.4_Missense_Mutation_p.R515H|ZNF574_ENST00000222339.7_Missense_Mutation_p.R605H|CTB-59C6.3_ENST00000594531.1_RNA			Q6ZN55	ZN574_HUMAN	zinc finger protein 574	515					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.R515H(1)		endometrium(4)|kidney(1)|large_intestine(3)|lung(6)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	20		Prostate(69;0.059)				AACCACCTGCGCACACACACA	0.602																																					p.R515H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1544A	19						.						177.0	197.0	190.0					19																	42584302		2203	4300	6503	47276142	SO:0001583	missense	64763	exon2			AK074788	CCDS12596.1	19q13.2	2013-09-20			ENSG00000105732	ENSG00000105732		"""Zinc fingers, C2H2-type"""	26166	protein-coding gene	gene with protein product						12477932	Standard	NM_022752		Approved	FLJ22059	uc002osm.4	Q6ZN55	OTTHUMG00000182751	ENST00000600245.1:c.1544G>A	19.37:g.42584302G>A	ENSP00000469029:p.Arg515His	Somatic		Capture	Illumina HiSeq	Phase_I	47276142	NM_022752	Q6IPE0|Q6ZN10|Q7L5Z5|Q8NCE3|Q9H6N0	Missense_Mutation	SNP	ENST00000600245.1	37	CCDS12596.1	.	.	.	.	.	.	.	.	.	.	G	12.09	1.834563	0.32421	.	.	ENSG00000105732	ENST00000222339;ENST00000359044;ENST00000535775	T;T	0.25749	1.78;1.78	5.02	5.02	0.67125	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.072293	0.56097	D	0.000032	T	0.46132	0.1377	M	0.75777	2.31	0.36189	D	0.849969	D;D	0.89917	0.999;1.0	P;P	0.62014	0.82;0.897	T	0.59440	-0.7454	10	0.87932	D	0	-20.8962	10.9824	0.47501	0.0:0.0:0.6983:0.3017	.	515;604	Q6ZN55;Q6ZN55-2	ZN574_HUMAN;.	H	605;515;122	ENSP00000222339:R605H;ENSP00000351939:R515H	ENSP00000222339:R605H	R	+	2	0	ZNF574	47276142	0.960000	0.32886	0.988000	0.46212	0.027000	0.11550	1.775000	0.38584	2.340000	0.79590	0.650000	0.86243	CGC		0.602	ZNF574-002	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463458.1	NM_022752	
GSK3A	2931	broad.mit.edu	37	19	42736814	42736814	+	Silent	SNP	C	C	T	rs201146173		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:42736814C>T	ENST00000222330.3	-	9	1246	c.1119G>A	c.(1117-1119)ccG>ccA	p.P373P	GSK3A_ENST00000398249.4_Silent_p.P291P	NM_019884.2	NP_063937.2	P49840	GSK3A_HUMAN	glycogen synthase kinase 3 alpha	373	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cardiac left ventricle morphogenesis (GO:0003214)|cell migration (GO:0016477)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|cellular response to interleukin-3 (GO:0036016)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|endoplasmic reticulum unfolded protein response (GO:0030968)|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)|glycogen metabolic process (GO:0005977)|hypermethylation of CpG island (GO:0044027)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell growth involved in cardiac muscle cell development (GO:0061052)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transferase activity (GO:0051348)|negative regulation of type B pancreatic cell development (GO:2000077)|negative regulation of UDP-glucose catabolic process (GO:0010905)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of adrenergic receptor signaling pathway (GO:0071879)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of heart contraction (GO:0045823)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein phosphorylation (GO:0006468)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of systemic arterial blood pressure (GO:0003073)|Wnt signaling pathway (GO:0016055)	beta-catenin destruction complex (GO:0030877)|cytosol (GO:0005829)	ATP binding (GO:0005524)|protein kinase A catalytic subunit binding (GO:0034236)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)	p.P373P(1)		endometrium(3)|large_intestine(3)|lung(6)|ovary(3)|prostate(2)|skin(1)|urinary_tract(1)	19		Prostate(69;0.00682)				TGGCCTCTGGCGGCGTTCGAG	0.587													C|||	1	0.000199681	0.0	0.0	5008	,	,		16763	0.001		0.0	False		,,,				2504	0.0				p.P373P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1119A	19						.						54.0	54.0	54.0					19																	42736814		2203	4300	6503	47428654	SO:0001819	synonymous_variant	2931	exon9				CCDS12599.1	19q13	2008-02-15			ENSG00000105723	ENSG00000105723			4616	protein-coding gene	gene with protein product		606784				9809441	Standard	NM_019884		Approved		uc002otb.1	P49840	OTTHUMG00000150722	ENST00000222330.3:c.1119G>A	19.37:g.42736814C>T		Somatic		Capture	Illumina HiSeq	Phase_I	47428654	NM_019884	O14959	Silent	SNP	ENST00000222330.3	37	CCDS12599.1																																																																																				0.587	GSK3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319782.1		
LYPD3	27076	broad.mit.edu	37	19	43965903	43965903	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:43965903G>T	ENST00000244333.3	-	5	729	c.641C>A	c.(640-642)tCc>tAc	p.S214Y		NM_014400.2	NP_055215.2	O95274	LYPD3_HUMAN	LY6/PLAUR domain containing 3	214	UPAR/Ly6 2.				cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)		p.S214Y(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|pancreas(1)|upper_aerodigestive_tract(2)	11		Prostate(69;0.0153)				CTGGCAACAGGAGCCACTGAG	0.612																																					p.S214Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C641A	19						.						82.0	83.0	83.0					19																	43965903		2203	4300	6503	48657743	SO:0001583	missense	27076	exon5			AF082889	CCDS12620.1	19q13.31	2008-02-05				ENSG00000124466			24880	protein-coding gene	gene with protein product		609484				11179665, 11245483	Standard	NM_014400		Approved	C4.4A	uc002owl.1	O95274		ENST00000244333.3:c.641C>A	19.37:g.43965903G>T	ENSP00000244333:p.Ser214Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	48657743	NM_014400	Q9UJ74	Missense_Mutation	SNP	ENST00000244333.3	37	CCDS12620.1	.	.	.	.	.	.	.	.	.	.	G	18.57	3.652831	0.67472	.	.	ENSG00000124466	ENST00000244333;ENST00000377995	T	0.71934	-0.61	4.18	4.18	0.49190	CD59 antigen (1);	0.108239	0.40640	N	0.001045	T	0.76716	0.4026	L	0.41824	1.3	0.36837	D	0.887212	D	0.89917	1.0	D	0.81914	0.995	T	0.81152	-0.1063	10	0.59425	D	0.04	.	12.7694	0.57412	0.0:0.0:1.0:0.0	.	214	O95274	LYPD3_HUMAN	Y	214;162	ENSP00000244333:S214Y	ENSP00000244333:S214Y	S	-	2	0	LYPD3	48657743	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	4.529000	0.60588	2.289000	0.77006	0.603000	0.83216	TCC		0.612	LYPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463177.1	NM_014400	
IRGQ	126298	broad.mit.edu	37	19	44097051	44097051	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:44097051G>A	ENST00000602269.1	-	2	1184	c.999C>T	c.(997-999)ggC>ggT	p.G333G	L34079.2_ENST00000594374.1_Silent_p.G46G|IRGQ_ENST00000601520.1_5'UTR|IRGQ_ENST00000422989.1_Silent_p.G333G			Q8WZA9	IRGQ_HUMAN	immunity-related GTPase family, Q	333	IRG-type G.							p.G333G(1)		endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(3)	18		Prostate(69;0.0199)				CCTCGCCCTCGCCGTCTGTGC	0.617																																					p.G333G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C999T	19						.						142.0	138.0	139.0					19																	44097051		2203	4300	6503	48788891	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.999C>T	19.37:g.44097051G>A		Somatic		Capture	Illumina HiSeq	Phase_I	48788891	NM_001007561	B2RNP3	Silent	SNP	ENST00000602269.1	37	CCDS33040.1																																																																																				0.617	IRGQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463205.1	NM_001007561	
PLAUR	5329	broad.mit.edu	37	19	44160746	44160746	+	Silent	SNP	G	G	T	rs377260231		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:44160746G>T	ENST00000340093.3	-	4	586	c.357C>A	c.(355-357)tcC>tcA	p.S119S	PLAUR_ENST00000601723.1_Silent_p.S119S|PLAUR_ENST00000221264.4_Silent_p.S119S|PLAUR_ENST00000339082.3_Silent_p.S119S	NM_002659.3	NP_002650.1	Q03405	UPAR_HUMAN	plasminogen activator, urokinase receptor	119	UPAR/Ly6 2.				attachment of GPI anchor to protein (GO:0016255)|blood coagulation (GO:0007596)|C-terminal protein lipidation (GO:0006501)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|chemotaxis (GO:0006935)|fibrinolysis (GO:0042730)|post-translational protein modification (GO:0043687)|regulation of proteolysis (GO:0030162)|signal transduction (GO:0007165)|urokinase plasminogen activator signaling pathway (GO:0038195)	anchored component of membrane (GO:0031225)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|receptor activity (GO:0004872)|urokinase plasminogen activator receptor activity (GO:0030377)	p.S119S(2)		endometrium(1)|kidney(4)|large_intestine(5)|lung(5)|ovary(1)|stomach(1)|urinary_tract(3)	20		Prostate(69;0.0153)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)|Urokinase(DB00013)	ATGAGCCACAGGAAATGCATT	0.612																																					p.S119S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C357A	19						.						85.0	79.0	81.0					19																	44160746		2203	4300	6503	48852586	SO:0001819	synonymous_variant	5329	exon4				CCDS12628.1, CCDS33041.1, CCDS33042.1, CCDS74386.1	19q13	2012-03-15			ENSG00000011422	ENSG00000011422		"""CD molecules"""	9053	protein-coding gene	gene with protein product	"""urokinase-type plasminogen activator (uPA) receptor"", ""urokinase plasminogen activator surface receptor"""	173391					Standard	NM_002659		Approved	URKR, UPAR, CD87	uc002oxf.2	Q03405		ENST00000340093.3:c.357C>A	19.37:g.44160746G>T		Somatic		Capture	Illumina HiSeq	Phase_I	48852586	NM_001005377	A8K409|Q12876|Q15845|Q16887|Q6IB52|Q9BWT0|Q9NYC8|Q9UD69|Q9UEA6|Q9UM92|Q9UMV0	Silent	SNP	ENST00000340093.3	37	CCDS12628.1																																																																																				0.612	PLAUR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463571.1	NM_002659	
ZNF226	7769	broad.mit.edu	37	19	44676353	44676353	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:44676353A>G	ENST00000590089.1	+	5	495	c.128A>G	c.(127-129)aAc>aGc	p.N43S	ZNF226_ENST00000337433.5_Missense_Mutation_p.N43S|ZNF226_ENST00000588742.1_Missense_Mutation_p.N43S|ZNF226_ENST00000413984.2_Missense_Mutation_p.N43S|ZNF226_ENST00000588795.1_Missense_Mutation_p.N43S|ZNF226_ENST00000589160.1_Missense_Mutation_p.N43S|ZNF226_ENST00000454662.2_Missense_Mutation_p.N43S|ZNF226_ENST00000588883.1_Missense_Mutation_p.N43S|ZNF226_ENST00000300823.6_Missense_Mutation_p.N43S			Q9NYT6	ZN226_HUMAN	zinc finger protein 226	43	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.N43S(1)					Prostate(69;0.0352)|all_neural(266;0.202)				AACTTTAGGAACCTGCTGTCA	0.547																																					p.N43S	Pancreas(115;581 1665 13228 19278 50070)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A128G	19						.						146.0	147.0	147.0					19																	44676353		2203	4300	6503	49368193	SO:0001583	missense	7769	exon5			AF024707	CCDS46102.1, CCDS46103.1	19q13.31	2013-01-08	2012-09-11	2012-09-11	ENSG00000167380	ENSG00000167380		"""Zinc fingers, C2H2-type"", ""-"""	13019	protein-coding gene	gene with protein product							Standard	NM_001146220		Approved		uc002oyp.3	Q9NYT6		ENST00000590089.1:c.128A>G	19.37:g.44676353A>G	ENSP00000465121:p.Asn43Ser	Somatic		Capture	Illumina HiSeq	Phase_I	49368193	NM_001146220	Q8WWE6|Q96TE6|Q9NS44	Missense_Mutation	SNP	ENST00000590089.1	37	CCDS46102.1	.	.	.	.	.	.	.	.	.	.	A	17.74	3.464968	0.63513	.	.	ENSG00000167380	ENST00000300823;ENST00000337433;ENST00000413984;ENST00000454662	T;T;T;T	0.02525	4.26;4.26;4.26;4.26	4.32	4.32	0.51571	Krueppel-associated box (4);	.	.	.	.	T	0.14527	0.0351	M	0.85299	2.745	0.26103	N	0.980799	D;D	0.89917	0.998;1.0	P;D	0.97110	0.901;1.0	T	0.08027	-1.0742	9	0.87932	D	0	.	6.625	0.22824	0.8935:0.0:0.1065:0.0	.	43;43	Q9NYT6;Q8WWE6	ZN226_HUMAN;.	S	43	ENSP00000300823:N43S;ENSP00000336719:N43S;ENSP00000407474:N43S;ENSP00000393265:N43S	ENSP00000300823:N43S	N	+	2	0	ZNF226	49368193	0.798000	0.28890	0.997000	0.53966	0.996000	0.88848	0.956000	0.29202	1.957000	0.56846	0.529000	0.55759	AAC		0.547	ZNF226-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460712.1		
ERCC1	2067	broad.mit.edu	37	19	45918163	45918163	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:45918163C>T	ENST00000300853.3	-	7	1249	c.658G>A	c.(658-660)Gcg>Acg	p.A220T	ERCC1_ENST00000588738.1_5'Flank|ERCC1_ENST00000423698.2_Missense_Mutation_p.A148T|ERCC1_ENST00000340192.7_Missense_Mutation_p.A220T|ERCC1_ENST00000589165.1_Missense_Mutation_p.A220T|ERCC1_ENST00000591636.1_Intron|ERCC1_ENST00000013807.5_Missense_Mutation_p.A220T	NM_001983.3	NP_001974.1	P07992	ERCC1_HUMAN	excision repair cross-complementation group 1	220	HhH2, dimerization with ERCC4.				cell proliferation (GO:0008283)|chromosome organization (GO:0051276)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|male gonad development (GO:0008584)|mitotic recombination (GO:0006312)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|negative regulation of telomere maintenance (GO:0032205)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|nucleotide-excision repair, DNA incision, 5'-to lesion (GO:0006296)|oogenesis (GO:0048477)|post-embryonic hemopoiesis (GO:0035166)|pyrimidine dimer repair by nucleotide-excision repair (GO:0000720)|replicative cell aging (GO:0001302)|response to nutrient (GO:0007584)|response to oxidative stress (GO:0006979)|response to sucrose (GO:0009744)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)|syncytium formation (GO:0006949)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	cytoplasm (GO:0005737)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	damaged DNA binding (GO:0003684)|endonuclease activity (GO:0004519)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|single-stranded DNA binding (GO:0003697)	p.A220T(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(2)|ovary(2)|skin(1)	15		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0247)		AGGAGGTCCGCTGGTTTCTGC	0.627								Nucleotide excision repair (NER)																													p.A220T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G658A	19						.						112.0	95.0	101.0					19																	45918163		2203	4300	6503	50610003	SO:0001583	missense	2067	exon7				CCDS12662.1, CCDS12663.1, CCDS54279.1	19q13.32	2014-03-07	2014-03-07			ENSG00000012061			3433	protein-coding gene	gene with protein product		126380	"""excision repair cross-complementing rodent repair deficiency, complementation group 1 (includes overlapping antisense sequence)"""			6462228	Standard	NM_001983		Approved	RAD10	uc002pbs.2	P07992		ENST00000300853.3:c.658G>A	19.37:g.45918163C>T	ENSP00000300853:p.Ala220Thr	Somatic		Capture	Illumina HiSeq	Phase_I	50610003	NM_001983	B2RC01|B3KRR0|Q7Z7F5|Q96S40	Missense_Mutation	SNP	ENST00000300853.3	37	CCDS12662.1	.	.	.	.	.	.	.	.	.	.	C	16.14	3.037709	0.54896	.	.	ENSG00000012061	ENST00000300853;ENST00000340192;ENST00000423698;ENST00000013807	T;T;T;T	0.48836	0.84;0.8;0.9;0.82	5.21	4.15	0.48705	RuvA domain 2-like (1);Restriction endonuclease, type II-like (1);	0.054529	0.64402	D	0.000001	T	0.43166	0.1235	M	0.72118	2.19	0.53688	D	0.999975	B;B;P;P	0.47910	0.441;0.401;0.902;0.831	B;B;B;B	0.35312	0.092;0.052;0.2;0.2	T	0.52616	-0.8552	10	0.66056	D	0.02	-18.4128	11.9994	0.53222	0.0:0.8255:0.1745:0.0	.	220;148;220;220	Q7Z7F5;B3KRR0;Q96S40;P07992	.;.;.;ERCC1_HUMAN	T	220;220;148;220	ENSP00000300853:A220T;ENSP00000345203:A220T;ENSP00000394875:A148T;ENSP00000013807:A220T	ENSP00000013807:A220T	A	-	1	0	ERCC1	50610003	1.000000	0.71417	0.038000	0.18304	0.575000	0.36095	4.900000	0.63252	1.310000	0.45006	0.505000	0.49811	GCG		0.627	ERCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459542.1	NM_001983	
RSPH6A	81492	broad.mit.edu	37	19	46307703	46307703	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:46307703C>T	ENST00000221538.3	-	3	1602	c.1460G>A	c.(1459-1461)cGc>cAc	p.R487H	RSPH6A_ENST00000597055.1_Missense_Mutation_p.R487H|RSPH6A_ENST00000600188.1_Missense_Mutation_p.R223H	NM_030785.3	NP_110412.1	Q9H0K4	RSH6A_HUMAN	radial spoke head 6 homolog A (Chlamydomonas)	487						intracellular (GO:0005622)		p.R487H(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						GGCCGAGATGCGGGCTATCTG	0.632																																					p.R487H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1460A	19						.						48.0	46.0	47.0					19																	46307703		2203	4300	6503	50999543	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.1460G>A	19.37:g.46307703C>T	ENSP00000221538:p.Arg487His	Somatic		Capture	Illumina HiSeq	Phase_I	50999543	NM_030785	Q53FE2|Q6PEZ9	Missense_Mutation	SNP	ENST00000221538.3	37	CCDS12675.1	.	.	.	.	.	.	.	.	.	.	C	16.36	3.100393	0.56183	.	.	ENSG00000104941	ENST00000221538	T	0.60920	0.15	3.8	2.74	0.32292	.	0.129101	0.53938	D	0.000051	T	0.77592	0.4153	M	0.91038	3.17	0.39212	D	0.963349	D	0.89917	1.0	D	0.67231	0.95	D	0.83439	0.0042	10	0.87932	D	0	0.3611	11.6332	0.51187	0.0:0.8179:0.1821:0.0	.	487	Q9H0K4	RSH6A_HUMAN	H	487	ENSP00000221538:R487H	ENSP00000221538:R487H	R	-	2	0	RSPH6A	50999543	1.000000	0.71417	0.994000	0.49952	0.255000	0.26057	5.440000	0.66563	1.178000	0.42870	0.456000	0.33151	CGC		0.632	RSPH6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461657.1		
PGLYRP1	8993	broad.mit.edu	37	19	46522868	46522868	+	Missense_Mutation	SNP	G	G	A	rs555905155		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:46522868G>A	ENST00000008938.4	-	2	368	c.325C>T	c.(325-327)Cgt>Tgt	p.R109C	CCDC61_ENST00000601763.1_Intron|MIR769_ENST00000390225.1_RNA	NM_005091.2	NP_005082.1	O75594	PGRP1_HUMAN	peptidoglycan recognition protein 1	109					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|immune response (GO:0006955)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)	p.R109C(1)		endometrium(2)|large_intestine(3)|lung(3)|ovary(2)	10		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.0036)|GBM - Glioblastoma multiforme(486;0.022)|Epithelial(262;0.208)		TTCCAGCCACGGCCCTCGTAT	0.587													G|||	1	0.000199681	0.0	0.0	5008	,	,		17181	0.0		0.0	False		,,,				2504	0.001				p.R109C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C325T	19						.						62.0	54.0	57.0					19																	46522868		2203	4300	6503	51214708	SO:0001583	missense	8993	exon2			AF076483	CCDS12680.1	19q13.2-q13.3	2008-02-05	2004-03-17	2004-03-19		ENSG00000008438			8904	protein-coding gene	gene with protein product		604963	"""peptidoglycan recognition protein"""	TNFSF3L, PGLYRP		9707603, 12669421	Standard	NM_005091		Approved	TAG7, PGRP, PGRP-S, PGRPS	uc002pdx.2	O75594		ENST00000008938.4:c.325C>T	19.37:g.46522868G>A	ENSP00000008938:p.Arg109Cys	Somatic		Capture	Illumina HiSeq	Phase_I	51214708	NM_005091	Q4VB36	Missense_Mutation	SNP	ENST00000008938.4	37	CCDS12680.1	.	.	.	.	.	.	.	.	.	.	G	13.08	2.130326	0.37630	.	.	ENSG00000008438	ENST00000008938	T	0.57907	0.37	5.01	3.96	0.45880	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (4);	0.110599	0.38897	N	0.001535	T	0.76227	0.3958	M	0.92649	3.33	0.50467	D	0.999876	D	0.89917	1.0	D	0.97110	1.0	T	0.79381	-0.1827	10	0.52906	T	0.07	-39.4179	10.7716	0.46325	0.0:0.0:0.8097:0.1903	.	109	O75594	PGRP1_HUMAN	C	109	ENSP00000008938:R109C	ENSP00000008938:R109C	R	-	1	0	PGLYRP1	51214708	1.000000	0.71417	0.998000	0.56505	0.031000	0.12232	3.252000	0.51461	1.093000	0.41377	-0.187000	0.12897	CGT		0.587	PGLYRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461695.1	NM_005091	
MEIS3	56917	broad.mit.edu	37	19	47910380	47910380	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:47910380C>T	ENST00000558555.1	-	10	1137	c.950G>A	c.(949-951)cGg>cAg	p.R317Q	MEIS3_ENST00000441740.2_Missense_Mutation_p.R300Q|MEIS3_ENST00000559524.1_Missense_Mutation_p.R363Q|MEIS3_ENST00000331559.5_Missense_Mutation_p.R346Q|MEIS3_ENST00000560253.1_5'UTR|MEIS3_ENST00000561293.1_Missense_Mutation_p.R363Q|MEIS3_ENST00000561096.1_Missense_Mutation_p.R405Q			Q99687	MEIS3_HUMAN	Meis homeobox 3	317					negative regulation of apoptotic signaling pathway (GO:2001234)|positive regulation of protein kinase B signaling (GO:0051897)	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.R363Q(1)		breast(1)|large_intestine(5)|lung(11)|prostate(1)|skin(2)	20		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;0.000198)|OV - Ovarian serous cystadenocarcinoma(262;0.000439)|Epithelial(262;0.0113)|GBM - Glioblastoma multiforme(486;0.0223)		GATGCGTCTCCGGGCGTTAAT	0.602																																					p.R363Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1088A	19						.						64.0	36.0	46.0					19																	47910380		2203	4300	6503	52602192	SO:0001583	missense	56917	exon10			BC025404	CCDS33064.1, CCDS46132.1, CCDS74406.1	19q13.32	2012-10-02	2007-02-15		ENSG00000105419	ENSG00000105419		"""Homeoboxes / TALE class"""	29537	protein-coding gene	gene with protein product			"""Meis1, myeloid ecotropic viral integration site 1 homolog 3 (mouse)"""			8950991	Standard	NM_020160		Approved	MRG2, DKFZp547H236	uc002pgt.4	Q99687	OTTHUMG00000172280	ENST00000558555.1:c.950G>A	19.37:g.47910380C>T	ENSP00000454073:p.Arg317Gln	Somatic		Capture	Illumina HiSeq	Phase_I	52602192	NM_020160	A8K1N5|Q6NT73|Q8TC66|Q9NPW2	Missense_Mutation	SNP	ENST00000558555.1	37		.	.	.	.	.	.	.	.	.	.	C	34	5.349934	0.95830	.	.	ENSG00000105419	ENST00000331559;ENST00000441740	D	0.99841	-7.09	4.24	4.24	0.50183	Homeodomain-related (1);Homeobox (2);Homeobox KN domain (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99900	0.9952	H	0.98701	4.305	0.51482	D	0.999927	D;D;D;P;D	0.89917	1.0;0.999;0.986;0.942;1.0	D;D;D;B;D	0.85130	0.997;0.986;0.927;0.288;0.997	D	0.96096	0.9065	10	0.87932	D	0	-25.285	14.5053	0.67748	0.0:1.0:0.0:0.0	.	209;317;300;363;192	Q8TCW1;Q99687;Q99687-3;Q99687-2;Q59FK5	.;MEIS3_HUMAN;.;.;.	Q	363;300	ENSP00000388667:R300Q	ENSP00000333552:R363Q	R	-	2	0	MEIS3	52602192	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	6.870000	0.75526	2.365000	0.80145	0.436000	0.28706	CGG		0.602	MEIS3-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000417642.1	XM_085929	
CRX	1406	broad.mit.edu	37	19	48343113	48343113	+	Silent	SNP	C	C	T	rs550083287		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:48343113C>T	ENST00000221996.7	+	4	995	c.789C>T	c.(787-789)ccC>ccT	p.P263P	TPRX2P_ENST00000535362.1_Intron|CRX_ENST00000539067.1_Silent_p.P263P	NM_000554.4	NP_000545.1	O43186	CRX_HUMAN	cone-rod homeobox	263					circadian rhythm (GO:0007623)|organ morphogenesis (GO:0009887)|positive regulation of photoreceptor cell differentiation (GO:0046534)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|leucine zipper domain binding (GO:0043522)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P263P(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|urinary_tract(1)	23		all_cancers(25;2.76e-09)|all_epithelial(76;7.01e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000266)|all cancers(93;0.000788)|Epithelial(262;0.0226)|GBM - Glioblastoma multiforme(486;0.0521)		CCTACAGCCCCGTGGATAGCT	0.617													C|||	1	0.000199681	0.0008	0.0	5008	,	,		16101	0.0		0.0	False		,,,				2504	0.0				p.P263P	Pancreas(57;461 1196 22201 40716 47188)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C789T	19	GRCh37	CD013149	CRX	D		.						88.0	96.0	93.0					19																	48343113		2203	4299	6502	53034925	SO:0001819	synonymous_variant	1406	exon4			AF024711	CCDS12706.1	19q13.3	2013-01-08				ENSG00000105392		"""Homeoboxes / PRD class"""	2383	protein-coding gene	gene with protein product	"""orthodenticle homeobox 3"""	602225		CORD2		9390563, 9537410	Standard	NM_000554		Approved	CRD, LCA7, OTX3	uc002phq.4	O43186		ENST00000221996.7:c.789C>T	19.37:g.48343113C>T		Somatic		Capture	Illumina HiSeq	Phase_I	53034925	NM_000554	Q0QD45	Silent	SNP	ENST00000221996.7	37	CCDS12706.1																																																																																				0.617	CRX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409812.4	NM_000554	
HRC	3270	broad.mit.edu	37	19	49657283	49657283	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:49657283C>A	ENST00000252825.4	-	1	1398	c.1212G>T	c.(1210-1212)gaG>gaT	p.E404D	HRC_ENST00000595625.1_Missense_Mutation_p.E404D	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	404					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.E404D(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)		CTTGGAAGTCCTCTTCATCAC	0.527																																					p.E404D	Melanoma(37;75 1097 24567 25669 30645)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1212T	19						.						115.0	109.0	111.0					19																	49657283		2203	4300	6503	54349095	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.1212G>T	19.37:g.49657283C>A	ENSP00000252825:p.Glu404Asp	Somatic		Capture	Illumina HiSeq	Phase_I	54349095	NM_002152	Q504Y6	Missense_Mutation	SNP	ENST00000252825.4	37	CCDS12759.1	.	.	.	.	.	.	.	.	.	.	C	2.525	-0.309863	0.05458	.	.	ENSG00000130528	ENST00000252825;ENST00000391863;ENST00000434964	T	0.35789	1.29	3.39	-0.194	0.13240	.	.	.	.	.	T	0.18425	0.0442	N	0.16368	0.405	0.09310	N	0.999999	B	0.20780	0.048	B	0.18871	0.023	T	0.21415	-1.0246	9	0.31617	T	0.26	-11.0114	4.3078	0.10956	0.0:0.5598:0.1941:0.2461	.	404	P23327	SRCH_HUMAN	D	404;103;374	ENSP00000252825:E404D	ENSP00000252825:E404D	E	-	3	2	HRC	54349095	0.522000	0.26266	0.088000	0.20740	0.002000	0.02628	-0.588000	0.05774	0.107000	0.17824	-1.373000	0.01185	GAG		0.527	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152	
TSKS	60385	broad.mit.edu	37	19	50243051	50243051	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:50243051G>A	ENST00000246801.3	-	11	1843	c.1761C>T	c.(1759-1761)ggC>ggT	p.G587G	TSKS_ENST00000358830.3_Silent_p.G387G	NM_021733.1	NP_068379.1	Q9UJT2	TSKS_HUMAN	testis-specific serine kinase substrate	587					negative regulation of phosphatase activity (GO:0010923)	centriole (GO:0005814)	protein kinase binding (GO:0019901)	p.G587G(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|prostate(3)|skin(3)	38		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(134;0.0145)		CAGGGGCTGAGCCCCCCTGTT	0.557																																					p.G587G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1761T	19						.						97.0	97.0	97.0					19																	50243051		2203	4300	6503	54934863	SO:0001819	synonymous_variant	60385	exon11			BC058862	CCDS12780.1	19q13.3	2014-06-13							30719	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 161"""	608253				11444856, 18495105	Standard	NM_021733		Approved	TSSKS, PPP1R161	uc002ppm.3	Q9UJT2		ENST00000246801.3:c.1761C>T	19.37:g.50243051G>A		Somatic		Capture	Illumina HiSeq	Phase_I	54934863	NM_021733	Q8WXJ0	Silent	SNP	ENST00000246801.3	37	CCDS12780.1																																																																																				0.557	TSKS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465795.1	NM_021733	
ZNF473	25888	broad.mit.edu	37	19	50542421	50542421	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:50542421T>G	ENST00000595661.1	+	4	508	c.13T>G	c.(13-15)Ttt>Gtt	p.F5V	ZNF473_ENST00000601364.1_Missense_Mutation_p.F5V|ZNF473_ENST00000391821.2_Missense_Mutation_p.F5V|ZNF473_ENST00000445728.3_De_novo_Start_OutOfFrame|ZNF473_ENST00000270617.3_Missense_Mutation_p.F5V			Q8WTR7	ZN473_HUMAN	zinc finger protein 473	5					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.F5V(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)		GTTTCAGGAATTTGTGACCCT	0.582																																					p.F5V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T13G	19						.						158.0	139.0	146.0					19																	50542421		2203	4300	6503	55234233	SO:0001583	missense	25888	exon3			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.13T>G	19.37:g.50542421T>G	ENSP00000472808:p.Phe5Val	Somatic		Capture	Illumina HiSeq	Phase_I	55234233	NM_001006656	A8K8T7|Q9ULS9|Q9Y4Q7	Missense_Mutation	SNP	ENST00000595661.1	37	CCDS33077.1	.	.	.	.	.	.	.	.	.	.	T	6.383	0.438807	0.12104	.	.	ENSG00000142528	ENST00000270617;ENST00000391821	T;T	0.00753	5.74;5.74	4.87	-3.1	0.05315	Krueppel-associated box (1);	1.238380	0.05977	N	0.643538	T	0.00608	0.0020	L	0.32530	0.975	0.09310	N	0.999999	B	0.22003	0.063	B	0.18871	0.023	T	0.47935	-0.9078	10	0.15066	T	0.55	-1.9768	0.4628	0.00519	0.3642:0.2298:0.1244:0.2816	.	5	Q8WTR7	ZN473_HUMAN	V	5	ENSP00000270617:F5V;ENSP00000375697:F5V	ENSP00000270617:F5V	F	+	1	0	ZNF473	55234233	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-1.995000	0.01472	-0.882000	0.03987	0.528000	0.53228	TTT		0.582	ZNF473-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464833.1	XM_046390	
MYH14	79784	broad.mit.edu	37	19	50779294	50779294	+	Missense_Mutation	SNP	C	C	T	rs373919106		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:50779294C>T	ENST00000596571.1	+	25	3391	c.3391C>T	c.(3391-3393)Cgg>Tgg	p.R1131W	MYH14_ENST00000601313.1_Missense_Mutation_p.R1172W|MYH14_ENST00000598205.1_Missense_Mutation_p.R1139W|MYH14_ENST00000425460.1_Missense_Mutation_p.R1139W|MYH14_ENST00000376970.2_Missense_Mutation_p.R1164W|MYH14_ENST00000262269.8_Missense_Mutation_p.R1172W|MYH14_ENST00000440075.2_Missense_Mutation_p.R1172W			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1131					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.R1172W(1)|p.R1131W(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)		GAAATCCCTGCGGGAGGCTCA	0.677																																					p.R1139W												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C3415T	19						.						13.0	17.0	16.0					19																	50779294		1978	4162	6140	55471106	SO:0001583	missense	79784	exon27			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.3391C>T	19.37:g.50779294C>T	ENSP00000472819:p.Arg1131Trp	Somatic		Capture	Illumina HiSeq	Phase_I	55471106	NM_001077186	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	37	CCDS59411.1	.	.	.	.	.	.	.	.	.	.	C	15.58	2.874422	0.51695	.	.	ENSG00000105357	ENST00000301415;ENST00000440075;ENST00000376970;ENST00000425460;ENST00000376965;ENST00000262269	T;T;T;T	0.79653	-1.29;-1.29;-1.29;-1.29	4.0	1.63	0.23807	Myosin tail (1);	.	.	.	.	D	0.86916	0.6048	M	0.71581	2.175	0.54753	D	0.999986	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.86838	0.2015	9	0.87932	D	0	.	10.4099	0.44287	0.3458:0.6542:0.0:0.0	.	1172;1131;1139	Q7Z406-2;Q7Z406;Q7Z406-6	.;MYH14_HUMAN;.	W	1131;1172;1164;1139;1131;1172	ENSP00000406273:R1172W;ENSP00000366169:R1164W;ENSP00000407879:R1139W;ENSP00000262269:R1172W	ENSP00000262269:R1172W	R	+	1	2	MYH14	55471106	0.996000	0.38824	0.988000	0.46212	0.268000	0.26511	1.177000	0.31969	1.031000	0.39867	0.455000	0.32223	CGG		0.677	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	
POLD1	5424	broad.mit.edu	37	19	50909579	50909579	+	Splice_Site	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:50909579G>T	ENST00000440232.2	+	11	1436	c.1383G>T	c.(1381-1383)caG>caT	p.Q461H	POLD1_ENST00000595904.1_Splice_Site_p.Q461H|POLD1_ENST00000599857.1_Splice_Site_p.Q461H	NM_001256849.1|NM_002691.3	NP_001243778.1|NP_002682.2	P28340	DPOD1_HUMAN	polymerase (DNA directed), delta 1, catalytic subunit	461			Q -> H (found in a colorectal sample; somatic mutation). {ECO:0000269|PubMed:23263490}.		base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|fatty acid homeostasis (GO:0055089)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)|response to UV (GO:0009411)|small molecule metabolic process (GO:0044281)|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)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|delta DNA polymerase complex (GO:0043625)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)	p.Q461H(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		ACATGCTGCAGGTATGGGCGG	0.662								DNA polymerases (catalytic subunits)																													p.Q461H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1383T	19						.						48.0	47.0	47.0					19																	50909579		2203	4300	6503	55601391	SO:0001630	splice_region_variant	5424	exon11				CCDS12795.1	19q13.3	2014-09-17	2012-05-18		ENSG00000062822	ENSG00000062822		"""DNA polymerases"""	9175	protein-coding gene	gene with protein product	"""CDC2 homolog (S. cerevisiae)"""	174761	"""polymerase (DNA directed), delta 1, catalytic subunit (125kD)"""	POLD		1722322	Standard	NM_001256849		Approved	CDC2	uc002psc.5	P28340		ENST00000440232.2:c.1383+1G>T	19.37:g.50909579G>T		Somatic		Capture	Illumina HiSeq	Phase_I	55601391	NM_002691	Q8NER3|Q96H98	Missense_Mutation	SNP	ENST00000440232.2	37	CCDS12795.1	.	.	.	.	.	.	.	.	.	.	G	15.53	2.861909	0.51482	.	.	ENSG00000062822	ENST00000440232;ENST00000376930	T	0.10192	2.9	4.28	4.28	0.50868	DNA-directed DNA polymerase, family B, exonuclease domain (1);Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.11580	0.0282	L	0.39467	1.215	0.80722	D	1	B;B	0.09022	0.002;0.002	B;B	0.18263	0.021;0.021	T	0.07462	-1.0771	10	0.40728	T	0.16	-39.3601	15.9971	0.80260	0.0:0.0:1.0:0.0	.	461;461	E7EVW0;P28340	.;DPOD1_HUMAN	H	461;462	ENSP00000406046:Q461H	ENSP00000366129:Q462H	Q	+	3	2	POLD1	55601391	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	8.594000	0.90836	2.399000	0.81585	0.655000	0.94253	CAG		0.662	POLD1-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464732.1		Missense_Mutation
FAM71E1	112703	broad.mit.edu	37	19	50979095	50979095	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:50979095C>T	ENST00000600100.1	-	2	719	c.355G>A	c.(355-357)Gta>Ata	p.V119I	EMC10_ENST00000334976.6_5'Flank|EMC10_ENST00000376918.3_5'Flank|FAM71E1_ENST00000595790.1_Missense_Mutation_p.V119I|EMC10_ENST00000598585.1_5'Flank			Q6IPT2	F71E1_HUMAN	family with sequence similarity 71, member E1	119								p.V119I(1)		breast(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.0077)|GBM - Glioblastoma multiforme(134;0.026)		CCTACCTGTACGAAGTTGCTC	0.627																																					p.V119I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G355A	19						.						47.0	47.0	47.0					19																	50979095		2203	4300	6503	55670907	SO:0001583	missense	112703	exon2				CCDS33081.1	19q13.33	2007-11-20				ENSG00000142530			25107	protein-coding gene	gene with protein product							Standard	XM_005258472		Approved		uc002psg.3	Q6IPT2		ENST00000600100.1:c.355G>A	19.37:g.50979095C>T	ENSP00000472421:p.Val119Ile	Somatic		Capture	Illumina HiSeq	Phase_I	55670907	NM_138411	Q96EJ5|Q9BSM9	Missense_Mutation	SNP	ENST00000600100.1	37		.	.	.	.	.	.	.	.	.	.	C	11.79	1.742734	0.30865	.	.	ENSG00000142530	ENST00000391816;ENST00000270620	T;T	0.10382	2.91;2.88	4.53	2.37	0.29283	.	0.099262	0.42294	D	0.000728	T	0.07052	0.0179	N	0.11789	0.175	0.23649	N	0.997207	D;D	0.61697	0.99;0.985	P;P	0.50570	0.539;0.644	T	0.27331	-1.0077	10	0.11485	T	0.65	-16.5582	6.7858	0.23672	0.0:0.6983:0.0:0.3016	.	119;119	Q6IPT2;Q6IPT2-2	F71E1_HUMAN;.	I	119	ENSP00000375692:V119I;ENSP00000270620:V119I	ENSP00000270620:V119I	V	-	1	0	FAM71E1	55670907	0.999000	0.42202	0.999000	0.59377	0.572000	0.35998	1.042000	0.30303	0.460000	0.27045	0.455000	0.32223	GTA		0.627	FAM71E1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000464754.2		
RPL36	25873	broad.mit.edu	37	19	5692093	5692093	+	IGR	SNP	C	C	T	rs138631909		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:5692093C>T	ENST00000577222.1	+	0	874				LONP1_ENST00000590729.1_Missense_Mutation_p.D814N|LONP1_ENST00000540670.2_Missense_Mutation_p.D748N|LONP1_ENST00000360614.3_Missense_Mutation_p.D944N|LONP1_ENST00000585374.1_Missense_Mutation_p.D830N|LONP1_ENST00000593119.1_Missense_Mutation_p.D880N			Q9Y3U8	RL36_HUMAN	ribosomal protein L36						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)|membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.D944N(1)		breast(1)|upper_aerodigestive_tract(1)	2						AAGGCGATGTCGAAGATCTCC	0.657													C|||	1	0.000199681	0.0	0.0	5008	,	,		16383	0.0		0.001	False		,,,				2504	0.0				p.D944N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2830A	19						.	C	ASN/ASP	0,4406		0,0,2203	142.0	119.0	127.0		2830	-5.7	0.0	19	dbSNP_134	127	1,8599	1.2+/-3.3	0,1,4299	no	missense	LONP1	NM_004793.2	23	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	944/960	5692093	1,13005	2203	4300	6503	5643093	SO:0001628	intergenic_variant	9361	exon18				CCDS12147.1	19p13.2	2011-04-06				ENSG00000130255		"""L ribosomal proteins"""	13631	protein-coding gene	gene with protein product							Standard	NM_033643		Approved	DKFZp566B023, L36	uc002mcv.3	Q9Y3U8			19.37:g.5692093C>T		Somatic		Capture	Illumina HiSeq	Phase_I	5643093	NM_004793	B2R4Y1|D6W634|Q6FIG1|Q9UQF6	Missense_Mutation	SNP	ENST00000577222.1	37	CCDS12147.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	7.919	0.738242	0.15574	0.0	1.16E-4	ENSG00000196365	ENST00000360614;ENST00000358403;ENST00000540670	T;T	0.30448	1.53;1.53	3.9	-5.72	0.02406	Ribosomal protein S5 domain 2-type fold (1);Peptidase S16, Lon C-terminal (1);	2.240520	0.02637	N	0.104931	T	0.15782	0.0380	N	0.20845	0.615	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.18618	-1.0331	10	0.10377	T	0.69	-2.7766	6.1574	0.20346	0.0:0.3617:0.3836:0.2547	.	944;880;944	E5KMH8;Q8N8K8;P36776	.;.;LONM_HUMAN	N	944;908;748	ENSP00000353826:D944N;ENSP00000441523:D748N	ENSP00000351177:D908N	D	-	1	0	LONP1	5643093	0.000000	0.05858	0.000000	0.03702	0.118000	0.20060	-0.040000	0.12104	-1.248000	0.02503	-1.411000	0.01122	GAC		0.657	RPL36-001	KNOWN	alternative_5_UTR|overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442561.1	NM_015414	
LRRC4B	94030	broad.mit.edu	37	19	51022488	51022488	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:51022488C>T	ENST00000599957.1	-	3	679	c.482G>A	c.(481-483)cGg>cAg	p.R161Q	LRRC4B_ENST00000389201.3_Missense_Mutation_p.R161Q			Q9NT99	LRC4B_HUMAN	leucine rich repeat containing 4B	161					positive regulation of synapse assembly (GO:0051965)	cell junction (GO:0030054)|cerebellar mossy fiber (GO:0044300)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)		p.R161Q(1)		breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|liver(1)|lung(11)|prostate(4)|skin(1)|urinary_tract(1)	30		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00284)|GBM - Glioblastoma multiforme(134;0.0188)		CCAGAGCTCCCGCAGCTTGGA	0.667																																					p.R161Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G482A	19						.						58.0	63.0	61.0					19																	51022488		2202	4300	6502	55714300	SO:0001583	missense	94030	exon3			BC032460	CCDS42595.1	19q13.33	2014-01-30	2004-06-14	2004-06-16	ENSG00000131409	ENSG00000131409		"""Immunoglobulin superfamily / I-set domain containing"", ""Endogenous ligands"""	25042	protein-coding gene	gene with protein product	"""netrin-G3 ligand"""		"""leucine-rich repeats and immunoglobulin-like domains 4"""	LRIG4		11441184	Standard	NM_001080457		Approved	DKFZp761A179, HSM	uc002pss.3	Q9NT99		ENST00000599957.1:c.482G>A	19.37:g.51022488C>T	ENSP00000471502:p.Arg161Gln	Somatic		Capture	Illumina HiSeq	Phase_I	55714300	NM_001080457	Q3ZCQ4|Q58F20	Missense_Mutation	SNP	ENST00000599957.1	37	CCDS42595.1	.	.	.	.	.	.	.	.	.	.	C	17.69	3.452262	0.63290	.	.	ENSG00000131409	ENST00000389201;ENST00000535879	D	0.91011	-2.77	3.96	3.96	0.45880	.	0.000000	0.56097	U	0.000035	T	0.78868	0.4351	N	0.17278	0.47	0.45354	D	0.998341	P	0.48503	0.911	B	0.39617	0.305	T	0.75631	-0.3251	10	0.20519	T	0.43	.	7.6699	0.28453	0.0:0.8857:0.0:0.1143	.	161	Q9NT99	LRC4B_HUMAN	Q	161	ENSP00000373853:R161Q	ENSP00000373853:R161Q	R	-	2	0	LRRC4B	55714300	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.700000	0.61803	2.235000	0.73313	0.491000	0.48974	CGG		0.667	LRRC4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464907.1	NM_001080457	
IGLON5	402665	broad.mit.edu	37	19	51828609	51828609	+	Missense_Mutation	SNP	G	G	A	rs527614882		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:51828609G>A	ENST00000270642.8	+	4	401	c.401G>A	c.(400-402)cGc>cAc	p.R134H		NM_001101372.1	NP_001094842.1	A6NGN9	IGLO5_HUMAN	IgLON family member 5	134	Ig-like C2-type 2.					extracellular region (GO:0005576)		p.R134H(1)		large_intestine(5)|lung(6)|prostate(1)	12						GTCCCTGCCCGCATTGTGAAC	0.647													G|||	1	0.000199681	0.0	0.0	5008	,	,		13032	0.001		0.0	False		,,,				2504	0.0				p.R134H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G401A	19						.						30.0	33.0	32.0					19																	51828609		2103	4221	6324	56520421	SO:0001583	missense	402665	exon4				CCDS46158.1	19q13.33	2013-01-29			ENSG00000142549	ENSG00000142549		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	34550	protein-coding gene	gene with protein product							Standard	NM_001101372		Approved	LOC402665	uc002pwc.2	A6NGN9	OTTHUMG00000154422	ENST00000270642.8:c.401G>A	19.37:g.51828609G>A	ENSP00000270642:p.Arg134His	Somatic		Capture	Illumina HiSeq	Phase_I	56520421	NM_001101372		Missense_Mutation	SNP	ENST00000270642.8	37	CCDS46158.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.158369	0.78114	.	.	ENSG00000142549	ENST00000270642	T	0.36878	1.23	4.13	4.13	0.48395	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.278980	0.31673	N	0.007256	T	0.52517	0.1739	M	0.69523	2.12	0.44899	D	0.997913	D	0.69078	0.997	D	0.65773	0.938	T	0.55095	-0.8194	10	0.62326	D	0.03	-8.9374	7.8867	0.29655	0.1151:0.0:0.8849:0.0	.	134	A6NGN9	IGLO5_HUMAN	H	134	ENSP00000270642:R134H	ENSP00000270642:R134H	R	+	2	0	IGLON5	56520421	1.000000	0.71417	1.000000	0.80357	0.793000	0.44817	1.993000	0.40747	1.857000	0.53885	0.313000	0.20887	CGC		0.647	IGLON5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335149.1	NM_001101372	
IGLON5	402665	broad.mit.edu	37	19	51830995	51830995	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:51830995C>T	ENST00000270642.8	+	7	777	c.777C>T	c.(775-777)agC>agT	p.S259S		NM_001101372.1	NP_001094842.1	A6NGN9	IGLO5_HUMAN	IgLON family member 5	259	Ig-like C2-type 3.					extracellular region (GO:0005576)		p.S259S(1)		large_intestine(5)|lung(6)|prostate(1)	12						GGCTGAGCAGCGGCACGGCCG	0.701																																					p.S259S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C777T	19						.						8.0	9.0	9.0					19																	51830995		1930	4074	6004	56522807	SO:0001819	synonymous_variant	402665	exon7				CCDS46158.1	19q13.33	2013-01-29			ENSG00000142549	ENSG00000142549		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	34550	protein-coding gene	gene with protein product							Standard	NM_001101372		Approved	LOC402665	uc002pwc.2	A6NGN9	OTTHUMG00000154422	ENST00000270642.8:c.777C>T	19.37:g.51830995C>T		Somatic		Capture	Illumina HiSeq	Phase_I	56522807	NM_001101372		Silent	SNP	ENST00000270642.8	37	CCDS46158.1																																																																																				0.701	IGLON5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335149.1	NM_001101372	
SIGLEC10	89790	broad.mit.edu	37	19	51917730	51917730	+	Missense_Mutation	SNP	G	G	A	rs201868126		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:51917730G>A	ENST00000339313.5	-	9	1771	c.1655C>T	c.(1654-1656)gCg>gTg	p.A552V	SIGLEC10_ENST00000442846.3_Missense_Mutation_p.A309V|SIGLEC10_ENST00000439889.2_Missense_Mutation_p.A494V|SIGLEC10_ENST00000436984.2_Missense_Mutation_p.A409V|SIGLEC10_ENST00000432469.2_Missense_Mutation_p.A374V|SIGLEC10_ENST00000353836.5_Missense_Mutation_p.A457V|CTD-2616J11.3_ENST00000532473.1_RNA|SIGLEC10_ENST00000525998.1_Missense_Mutation_p.A367V|SIGLEC10_ENST00000356298.5_Missense_Mutation_p.A552V|CTD-2616J11.2_ENST00000526996.1_RNA|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000441969.3_Missense_Mutation_p.A399V			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	552					cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.A552V(1)|p.A494V(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		TCCCAGAAACGCTCCGTTGGA	0.592													g|||	1	0.000199681	0.0	0.0	5008	,	,		18490	0.0		0.001	False		,,,				2504	0.0				p.A457V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1370T	19						.	G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	1,4405		0,1,2202	102.0	90.0	94.0		1481,1370,1226,1196,1121,926,1655	-7.1	0.0	19	dbSNP_132	94	0,8600		0,0,4300	no	missense,missense,missense,missense,missense,missense,missense	SIGLEC10	NM_001171156.1,NM_001171157.1,NM_001171158.1,NM_001171159.1,NM_001171160.1,NM_001171161.1,NM_033130.4	64,64,64,64,64,64,64	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign,benign,benign,benign,benign,benign	494/640,457/603,409/555,399/545,374/520,309/455,552/698	51917730	1,13005	2203	4300	6503	56609542	SO:0001583	missense	89790	exon8			AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15620	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 10 Ig-like lectin 7"", ""siglec-like gene 2"""	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.1655C>T	19.37:g.51917730G>A	ENSP00000345243:p.Ala552Val	Somatic		Capture	Illumina HiSeq	Phase_I	56609542	NM_001171157	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Missense_Mutation	SNP	ENST00000339313.5	37	CCDS12832.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	.	13.06	2.125026	0.37533	2.27E-4	0.0	ENSG00000142512	ENST00000353836;ENST00000432469;ENST00000442846;ENST00000356298;ENST00000441969;ENST00000525998;ENST00000439889;ENST00000436984;ENST00000339313	T;T;T;T;T;T;T;T;T	0.55234	0.9;2.12;1.49;0.68;1.96;1.72;0.53;1.89;0.68	4.89	-7.07	0.01563	.	1.605430	0.03806	N	0.265217	T	0.34221	0.0890	N	0.25245	0.725	0.09310	N	1	B;P;B;P;B;B;B;B	0.35551	0.423;0.488;0.209;0.509;0.314;0.314;0.009;0.022	B;B;B;B;B;B;B;B	0.25614	0.038;0.028;0.018;0.06;0.041;0.062;0.004;0.014	T	0.18999	-1.0319	10	0.30854	T	0.27	.	15.3152	0.74069	0.329:0.0:0.671:0.0	.	409;367;457;309;457;399;494;552	C9JM10;E9PL79;B7ZL04;C9JJ33;Q96LC7-2;Q96LC7-6;Q96LC7-3;Q96LC7	.;.;.;.;.;.;.;SIG10_HUMAN	V	457;374;309;552;399;367;494;409;552	ENSP00000342389:A457V;ENSP00000396742:A374V;ENSP00000395475:A309V;ENSP00000348646:A552V;ENSP00000408387:A399V;ENSP00000431444:A367V;ENSP00000389132:A494V;ENSP00000414324:A409V;ENSP00000345243:A552V	ENSP00000345243:A552V	A	-	2	0	SIGLEC10	56609542	0.000000	0.05858	0.000000	0.03702	0.071000	0.16799	-0.831000	0.04405	-1.538000	0.01734	-0.459000	0.05422	GCG		0.592	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
SIGLEC8	27181	broad.mit.edu	37	19	51955708	51955708	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:51955708G>A	ENST00000321424.3	-	7	1491	c.1425C>T	c.(1423-1425)atC>atT	p.I475I	SIGLEC8_ENST00000340550.5_Silent_p.I382I|SIGLEC8_ENST00000430817.1_Silent_p.I366I	NM_014442.2	NP_055257.2	Q9NYZ4	SIGL8_HUMAN	sialic acid binding Ig-like lectin 8	475					cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)	p.I475I(1)		NS(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(11)|liver(3)|lung(15)|ovary(2)|skin(4)|stomach(3)|urinary_tract(2)	50		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000627)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		CTCGCTTGTGGATCTTGATCT	0.507																																					p.I475I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1425T	19						.						131.0	118.0	123.0					19																	51955708		2203	4300	6503	56647520	SO:0001819	synonymous_variant	27181	exon7			AF195092	CCDS33086.1	19q13.33-q13.41	2013-01-29			ENSG00000105366	ENSG00000105366		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10877	protein-coding gene	gene with protein product		605639				10625619	Standard	XR_243922		Approved	SIGLEC-8, SAF2, SIGLEC8L, MGC59785	uc002pwt.3	Q9NYZ4		ENST00000321424.3:c.1425C>T	19.37:g.51955708G>A		Somatic		Capture	Illumina HiSeq	Phase_I	56647520	NM_014442	Q7Z728	Silent	SNP	ENST00000321424.3	37	CCDS33086.1																																																																																				0.507	SIGLEC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463648.2	NM_014442	
MYADM	91663	broad.mit.edu	37	19	54377543	54377543	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:54377543G>A	ENST00000391769.2	+	3	1040	c.760G>A	c.(760-762)Gcc>Acc	p.A254T	MYADM_ENST00000391768.2_Missense_Mutation_p.A254T|AC008440.5_ENST00000413496.2_RNA|MYADM_ENST00000391770.4_Missense_Mutation_p.A254T|MYADM_ENST00000336967.3_Missense_Mutation_p.A254T|MYADM_ENST00000391771.1_Missense_Mutation_p.A254T	NM_001020821.1	NP_001018657.1	Q96S97	MYADM_HUMAN	myeloid-associated differentiation marker	254	MARVEL 2. {ECO:0000255|PROSITE- ProRule:PRU00581}.				establishment of endothelial barrier (GO:0061028)|membrane raft organization (GO:0031579)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of gene expression (GO:0010629)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of protein kinase C signaling (GO:0090038)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of cell migration (GO:0030335)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|protein targeting to plasma membrane (GO:0072661)	cell-cell junction (GO:0005911)|cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.A254T(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	12	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.0488)		CTATGCCACCGCCCTTGTTCT	0.617																																					p.A254T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G760A	19						.						86.0	79.0	82.0					19																	54377543		2203	4300	6503	59069355	SO:0001583	missense	91663	exon3			AF087882	CCDS12866.1	19q13.33-q13.4	2004-07-23			ENSG00000179820	ENSG00000179820			7544	protein-coding gene	gene with protein product		609959				10733104, 12075932	Standard	NM_001020818		Approved		uc002qcl.3	Q96S97	OTTHUMG00000060775	ENST00000391769.2:c.760G>A	19.37:g.54377543G>A	ENSP00000375649:p.Ala254Thr	Somatic		Capture	Illumina HiSeq	Phase_I	59069355	NM_001020820	B2RE58|Q542Z1|Q7Z507|Q8N9R4|Q96CS6|Q96SK9	Missense_Mutation	SNP	ENST00000391769.2	37	CCDS12866.1	.	.	.	.	.	.	.	.	.	.	G	18.12	3.552548	0.65425	.	.	ENSG00000179820	ENST00000336967;ENST00000391770;ENST00000439000;ENST00000391771;ENST00000415619;ENST00000391769;ENST00000391768	T;T;T;T;T;T	0.38560	1.13;1.13;1.13;1.13;1.13;1.13	4.3	4.3	0.51218	Marvel (1);MARVEL-like domain (1);	0.000000	0.85682	D	0.000000	T	0.62708	0.2450	M	0.79475	2.455	0.80722	D	1	D	0.76494	0.999	D	0.63597	0.916	T	0.69390	-0.5158	10	0.87932	D	0	-13.4599	14.6581	0.68850	0.0:0.0:1.0:0.0	.	254	Q96S97	MYADM_HUMAN	T	254;254;254;254;217;254;254	ENSP00000337222:A254T;ENSP00000375650:A254T;ENSP00000416919:A254T;ENSP00000375651:A254T;ENSP00000375649:A254T;ENSP00000375648:A254T	ENSP00000337222:A254T	A	+	1	0	MYADM	59069355	1.000000	0.71417	0.033000	0.17914	0.189000	0.23516	9.650000	0.98490	2.133000	0.65898	0.305000	0.20034	GCC		0.617	MYADM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134337.1	NM_138373	
CACNG7	59284	broad.mit.edu	37	19	54418709	54418709	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:54418709C>T	ENST00000391767.1	+	4	586	c.374C>T	c.(373-375)cCg>cTg	p.P125L	CACNG7_ENST00000391766.1_Missense_Mutation_p.P125L|CACNG7_ENST00000468076.1_3'UTR|CACNG7_ENST00000222212.2_Missense_Mutation_p.P125L			P62955	CCG7_HUMAN	calcium channel, voltage-dependent, gamma subunit 7	125					calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.P125L(1)		NS(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0711)		CACATCCGCCCGCAGAGGACC	0.597																																					p.P125L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C374T	19						.						115.0	101.0	105.0					19																	54418709		2203	4300	6503	59110521	SO:0001583	missense	59284	exon3			AF288387	CCDS12868.1	19q13.4	2008-05-02			ENSG00000105605	ENSG00000105605		"""Calcium channel subunits"""	13626	protein-coding gene	gene with protein product		606899				11170751	Standard	NM_031896		Approved		uc002qcr.2	P62955	OTTHUMG00000064852	ENST00000391767.1:c.374C>T	19.37:g.54418709C>T	ENSP00000375647:p.Pro125Leu	Somatic		Capture	Illumina HiSeq	Phase_I	59110521	NM_031896	Q52LL8|Q8VBX3|Q8WXS6|Q9BXT1	Missense_Mutation	SNP	ENST00000391767.1	37	CCDS12868.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.313362	0.81358	.	.	ENSG00000105605	ENST00000391767;ENST00000222212;ENST00000391766	D;D;D	0.86230	-2.09;-2.09;-2.09	3.91	3.91	0.45181	.	0.000000	0.85682	D	0.000000	D	0.91314	0.7261	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.70227	0.968	D	0.89612	0.3842	10	0.31617	T	0.26	-9.9231	14.2221	0.65833	0.0:1.0:0.0:0.0	.	125	P62955	CCG7_HUMAN	L	125	ENSP00000375647:P125L;ENSP00000222212:P125L;ENSP00000375646:P125L	ENSP00000222212:P125L	P	+	2	0	CACNG7	59110521	1.000000	0.71417	0.963000	0.40424	0.979000	0.70002	7.180000	0.77674	2.469000	0.83416	0.563000	0.77884	CCG		0.597	CACNG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139240.2		
LENG1	79165	broad.mit.edu	37	19	54660546	54660546	+	Missense_Mutation	SNP	C	C	T	rs377766733		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:54660546C>T	ENST00000222224.3	-	3	716	c.530G>A	c.(529-531)cGc>cAc	p.R177H		NM_024316.1	NP_077292.1	Q96BZ8	LENG1_HUMAN	leukocyte receptor cluster (LRC) member 1	177								p.R177H(2)		breast(1)|endometrium(3)|large_intestine(2)|lung(1)|ovary(1)	8	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					CTTTCTGCTGCGACTGCCTTC	0.597													C|||	1	0.000199681	0.0	0.0	5008	,	,		17659	0.0		0.0	False		,,,				2504	0.001				p.R177H												.	.	2	Substitution - Missense(2)	large_intestine(1)|breast(1)	c.G530A	19						.	C	HIS/ARG	0,4406		0,0,2203	98.0	89.0	92.0		530	-7.6	0.0	19		92	1,8599	1.2+/-3.3	0,1,4299	no	missense	LENG1	NM_024316.1	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	177/265	54660546	1,13005	2203	4300	6503	59352358	SO:0001583	missense	79165	exon3			AF211966	CCDS12881.1	19q13.4	2008-02-05			ENSG00000105617	ENSG00000105617			15502	protein-coding gene	gene with protein product						10941842	Standard	NM_024316		Approved		uc002qdm.3	Q96BZ8	OTTHUMG00000066486	ENST00000222224.3:c.530G>A	19.37:g.54660546C>T	ENSP00000222224:p.Arg177His	Somatic		Capture	Illumina HiSeq	Phase_I	59352358	NM_024316	Q9HCU7	Missense_Mutation	SNP	ENST00000222224.3	37	CCDS12881.1	.	.	.	.	.	.	.	.	.	.	C	9.854	1.194373	0.22037	0.0	1.16E-4	ENSG00000105617	ENST00000222224	T	0.44881	0.91	5.67	-7.59	0.01308	.	8.658420	0.00166	N	0.000000	T	0.12987	0.0315	N	0.00419	-1.52	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31806	-0.9930	10	0.38643	T	0.18	3.2812	10.0563	0.42248	0.0:0.3447:0.4104:0.2449	.	177	Q96BZ8	LENG1_HUMAN	H	177	ENSP00000222224:R177H	ENSP00000222224:R177H	R	-	2	0	LENG1	59352358	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.005000	0.03674	-1.299000	0.02344	-0.320000	0.08662	CGC		0.597	LENG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142159.1	NM_024316	
LILRB1	10859	broad.mit.edu	37	19	55143986	55143986	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:55143986C>A	ENST00000396331.1	+	7	1090	c.733C>A	c.(733-735)Cag>Aag	p.Q245K	LILRB1_ENST00000396315.1_Missense_Mutation_p.Q245K|LILRB1_ENST00000427581.2_Missense_Mutation_p.Q281K|LILRB1_ENST00000396332.4_Missense_Mutation_p.Q245K|LILRB1_ENST00000324602.7_Missense_Mutation_p.Q245K|LILRB1_ENST00000434867.2_Missense_Mutation_p.Q245K|LILRB1_ENST00000396327.3_Missense_Mutation_p.Q245K|LILRB1_ENST00000396321.2_Missense_Mutation_p.Q245K|LILRB1_ENST00000396317.1_Missense_Mutation_p.Q245K|LILRB1_ENST00000418536.2_Missense_Mutation_p.Q245K|LILRB1_ENST00000448689.1_Missense_Mutation_p.Q245K	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	245	Ig-like C2-type 3.				cellular response to lipopolysaccharide (GO:0071222)|defense response to virus (GO:0051607)|dendritic cell differentiation (GO:0097028)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma production (GO:0032609)|interferon-gamma secretion (GO:0072643)|negative regulation of alpha-beta T cell activation (GO:0046636)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of CD8-positive, alpha-beta T cell activation (GO:2001186)|negative regulation of cell cycle (GO:0045786)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of endocytosis (GO:0045806)|negative regulation of interferon-beta secretion (GO:0035548)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-12 secretion (GO:2001183)|negative regulation of mononuclear cell proliferation (GO:0032945)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of osteoclast development (GO:2001205)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transforming growth factor-beta secretion (GO:2001202)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of gamma-delta T cell activation involved in immune response (GO:2001193)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor internalization (GO:0031623)|regulation of immune response (GO:0050776)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	HLA-A specific inhibitory MHC class I receptor activity (GO:0030107)|HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)|MHC class I protein binding (GO:0042288)|MHC class I receptor activity (GO:0032393)|protein homodimerization activity (GO:0042803)|protein phosphatase 1 binding (GO:0008157)|SH2 domain binding (GO:0042169)	p.Q245K(2)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74				GBM - Glioblastoma multiforme(193;0.0188)		CCTGACTCTGCAGTGTGGCTC	0.562										HNSCC(37;0.09)																											p.Q245K												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.C733A	19						.						96.0	102.0	100.0					19																	55143986		2203	4300	6503	59835798	SO:0001583	missense	10859	exon6			AF009220	CCDS42614.1, CCDS42615.1, CCDS42616.1, CCDS42617.1, CCDS62803.1	19q13.4	2013-01-11						"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6605	protein-coding gene	gene with protein product		604811				9285411, 9382880	Standard	XM_006726246		Approved	LIR-1, ILT2, MIR-7, CD85, LIR1, CD85j	uc002qgm.3	Q8NHL6		ENST00000396331.1:c.733C>A	19.37:g.55143986C>A	ENSP00000379622:p.Gln245Lys	Somatic		Capture	Illumina HiSeq	Phase_I	59835798	NM_001081639	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Missense_Mutation	SNP	ENST00000396331.1	37	CCDS42617.1	.	.	.	.	.	.	.	.	.	.	C	12.41	1.929904	0.34096	.	.	ENSG00000104972	ENST00000396321;ENST00000418536;ENST00000448689;ENST00000396331;ENST00000396327;ENST00000324602;ENST00000434867;ENST00000396332;ENST00000427581;ENST00000396317;ENST00000396315	T;T;T;T;T;T;T;T;T;T;T	0.11930	2.73;2.73;2.73;2.73;2.73;2.73;2.73;2.73;2.73;2.73;2.73	1.49	1.49	0.22878	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.798013	0.10674	N	0.647173	T	0.37919	0.1021	M	0.86502	2.82	0.09310	N	1	D;D;D;P;D	0.71674	0.996;0.993;0.997;0.918;0.998	D;D;D;P;D	0.91635	0.975;0.963;0.971;0.882;0.999	T	0.06881	-1.0802	10	0.87932	D	0	.	6.4456	0.21875	0.0:1.0:0.0:0.0	.	245;245;245;245;245	A8MVE2;Q8NHL6-3;A2IXV4;Q8NHL6-2;Q8NHL6	.;.;.;.;LIRB1_HUMAN	K	245;245;245;245;245;245;245;245;281;245;245	ENSP00000379614:Q245K;ENSP00000391514:Q245K;ENSP00000409968:Q245K;ENSP00000379622:Q245K;ENSP00000379618:Q245K;ENSP00000315997:Q245K;ENSP00000405243:Q245K;ENSP00000379623:Q245K;ENSP00000395004:Q281K;ENSP00000379610:Q245K;ENSP00000379608:Q245K	ENSP00000315997:Q245K	Q	+	1	0	LILRB1	59835798	0.012000	0.17670	0.004000	0.12327	0.015000	0.08874	1.380000	0.34351	1.136000	0.42199	0.184000	0.17185	CAG		0.562	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4		
KIR3DL2	3812	broad.mit.edu	37	19	55363495	55363495	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:55363495T>C	ENST00000326321.3	+	3	146	c.113T>C	c.(112-114)gTg>gCg	p.V38A	KIR3DL2_ENST00000270442.5_Missense_Mutation_p.V38A|KIR3DL1_ENST00000402254.2_Intron	NM_006737.3	NP_006728.2	P43630	KI3L2_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 2	38					cellular defense response (GO:0006968)|regulation of immune response (GO:0050776)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.V38A(1)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	23				GBM - Glioblastoma multiforme(193;0.0192)		CCCAGCACTGTGGTGCCTCGA	0.572																																					p.V38A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T113C	19						.						7.0	7.0	7.0					19																	55363495		1952	3801	5753	60055307	SO:0001583	missense	3812	exon3			L41270	CCDS12906.1, CCDS58677.1	19q13.4	2014-05-22			ENSG00000240403	ENSG00000240403		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6339	protein-coding gene	gene with protein product		604947				7716543, 8662091	Standard	NM_006737		Approved	cl-5, nkat4, nkat4a, nkat4b, CD158K	uc002qho.4	P43630	OTTHUMG00000065935	ENST00000326321.3:c.113T>C	19.37:g.55363495T>C	ENSP00000325525:p.Val38Ala	Somatic		Capture	Illumina HiSeq	Phase_I	60055307	NM_006737	Q13238|Q14947|Q14948|Q92684|Q95366|Q95367|Q95368	Missense_Mutation	SNP	ENST00000326321.3	37	CCDS12906.1	.	.	.	.	.	.	.	.	.	.	t	11.33	1.607479	0.28623	.	.	ENSG00000240403	ENST00000326321;ENST00000270442	T;T	0.14022	2.54;2.54	1.62	0.559	0.17272	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	3.753350	0.02314	U	0.072415	T	0.38374	0.1038	M	0.89840	3.065	0.09310	N	1	B;P	0.39022	0.426;0.655	P;P	0.53490	0.675;0.727	T	0.15037	-1.0451	10	0.87932	D	0	.	3.3822	0.07259	0.0:0.2349:0.0:0.7651	.	38;38	Q95366;P43630	.;KI3L2_HUMAN	A	38	ENSP00000325525:V38A;ENSP00000270442:V38A	ENSP00000270442:V38A	V	+	2	0	KIR3DL2	60055307	0.011000	0.17503	0.000000	0.03702	0.016000	0.09150	0.812000	0.27211	0.116000	0.18110	0.155000	0.16302	GTG		0.572	KIR3DL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000141241.1		
NLRP8	126205	broad.mit.edu	37	19	56490889	56490889	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:56490889C>T	ENST00000291971.3	+	9	3077	c.3006C>T	c.(3004-3006)tgC>tgT	p.C1002C	NLRP8_ENST00000590542.1_Silent_p.C983C	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	1002					neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)	p.C1002C(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)		TGACCTTGTGCGAGGCCTTCT	0.483																																					p.C1002C												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C3006T	19						.						118.0	115.0	116.0					19																	56490889		2203	4300	6503	61182701	SO:0001819	synonymous_variant	126205	exon9			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.3006C>T	19.37:g.56490889C>T		Somatic		Capture	Illumina HiSeq	Phase_I	61182701	NM_176811	Q7RTR4	Silent	SNP	ENST00000291971.3	37	CCDS12937.1																																																																																				0.483	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811	
ACER1	125981	broad.mit.edu	37	19	6306858	6306858	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:6306858A>G	ENST00000301452.4	-	6	739	c.662T>C	c.(661-663)aTg>aCg	p.M221T		NM_133492.2	NP_597999.1	Q8TDN7	ACER1_HUMAN	alkaline ceramidase 1	221					cell differentiation (GO:0030154)|cellular response to calcium ion (GO:0071277)|ceramide catabolic process (GO:0046514)|epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)|regulation of lipid metabolic process (GO:0019216)|response to alkaline pH (GO:0010446)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ceramidase activity (GO:0017040)|dihydroceramidase activity (GO:0071633)	p.M221T(1)		NS(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|pancreas(1)	15						CATGGTGACCATGCCATAAGG	0.602																																					p.M221T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T662C	19						.						75.0	54.0	61.0					19																	6306858		2203	4300	6503	6257858	SO:0001583	missense	125981	exon6			AF347024	CCDS12161.1	19p13.3	2013-01-25	2008-12-19	2008-12-19	ENSG00000167769	ENSG00000167769	3.5.1.23	"""Alkaline ceramidase"""	18356	protein-coding gene	gene with protein product		613491	"""N-acylsphingosine amidohydrolase (alkaline ceramidase) 3"""	ASAH3		12783875	Standard	NM_133492		Approved		uc002mel.2	Q8TDN7		ENST00000301452.4:c.662T>C	19.37:g.6306858A>G	ENSP00000301452:p.Met221Thr	Somatic		Capture	Illumina HiSeq	Phase_I	6257858	NM_133492		Missense_Mutation	SNP	ENST00000301452.4	37	CCDS12161.1	.	.	.	.	.	.	.	.	.	.	A	2.499	-0.315651	0.05422	.	.	ENSG00000167769	ENST00000301452	T	0.40476	1.03	5.49	4.48	0.54585	.	0.474948	0.25037	N	0.033635	T	0.22627	0.0546	N	0.16478	0.41	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.15694	-1.0428	10	0.22706	T	0.39	-14.7729	5.2102	0.15312	0.7592:0.0:0.0844:0.1564	.	221	Q8TDN7	ACER1_HUMAN	T	221	ENSP00000301452:M221T	ENSP00000301452:M221T	M	-	2	0	ACER1	6257858	0.011000	0.17503	0.038000	0.18304	0.478000	0.33099	1.073000	0.30691	0.919000	0.36945	0.533000	0.62120	ATG		0.602	ACER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452982.1	NM_133492	
TNFSF14	8740	broad.mit.edu	37	19	6669971	6669971	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:6669971C>T	ENST00000599359.1	-	2	491	c.110G>A	c.(109-111)cGg>cAg	p.R37Q	TNFSF14_ENST00000245912.3_Splice_Site_p.R37Q|TNFSF14_ENST00000326176.9_Splice_Site_p.R37Q			O43557	TNF14_HUMAN	tumor necrosis factor (ligand) superfamily, member 14	37					apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|immune response (GO:0006955)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of T cell chemotaxis (GO:0010820)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|receptor binding (GO:0005102)	p.R37Q(1)		breast(1)|kidney(2)|large_intestine(4)|liver(1)|lung(4)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	18						CAGACCCACCCGGGCCACACT	0.632																																					p.R37Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G110A	19						.						120.0	107.0	112.0					19																	6669971		2203	4300	6503	6620971	SO:0001583	missense	8740	exon2			AF036581	CCDS12171.1, CCDS45939.1	19p13.3	2008-02-05				ENSG00000125735		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"""	11930	protein-coding gene	gene with protein product		604520				9462508	Standard	NM_172014		Approved	LIGHT, LTg, HVEM-L, CD258	uc002mfk.2	O43557		ENST00000599359.1:c.110G>A	19.37:g.6669971C>T	ENSP00000469049:p.Arg37Gln	Somatic		Capture	Illumina HiSeq	Phase_I	6620971	NM_003807	A8K7M2|C9J5H4|O75476|Q6FHA1|Q8WVF8|Q96LD2	Missense_Mutation	SNP	ENST00000599359.1	37	CCDS12171.1	.	.	.	.	.	.	.	.	.	.	C	3.765	-0.048870	0.07407	.	.	ENSG00000125735	ENST00000245912;ENST00000326176	T;T	0.35421	1.31;1.31	5.04	-10.1	0.00402	.	1.572510	0.03885	N	0.277665	T	0.12092	0.0294	N	0.00823	-1.155	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.04013	0.001;0.001	T	0.40776	-0.9545	10	0.48119	T	0.1	-7.7551	13.3845	0.60789	0.0:0.1184:0.0999:0.7817	.	37;37	O43557;O43557-2	TNF14_HUMAN;.	Q	37	ENSP00000245912:R37Q;ENSP00000326940:R37Q	ENSP00000245912:R37Q	R	-	2	0	TNFSF14	6620971	0.004000	0.15560	0.000000	0.03702	0.004000	0.04260	-0.526000	0.06207	-2.051000	0.00904	-1.129000	0.01985	CGG		0.632	TNFSF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457863.1		
C3	718	broad.mit.edu	37	19	6712610	6712610	+	Missense_Mutation	SNP	C	C	T	rs373511900		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:6712610C>T	ENST00000245907.6	-	10	1120	c.1028G>A	c.(1027-1029)cGc>cAc	p.R343H		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	343					complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)	p.R343H(1)		breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	GATCCCGCTGCGCTCTGCCTG	0.582																																					p.R343H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1028A	19						.	C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	212.0	184.0	193.0		1028	-1.7	0.0	19		193	0,8600		0,0,4300	no	missense	C3	NM_000064.2	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	343/1664	6712610	1,13005	2203	4300	6503	6663610	SO:0001583	missense	718	exon10			J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"""Complement system"", ""Endogenous ligands"""	1318	protein-coding gene	gene with protein product	"""C3a anaphylatoxin"", ""complement component C3a"", ""complement component C3b"", ""prepro-C3"""	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.1028G>A	19.37:g.6712610C>T	ENSP00000245907:p.Arg343His	Somatic		Capture	Illumina HiSeq	Phase_I	6663610	NM_000064	A7E236	Missense_Mutation	SNP	ENST00000245907.6	37	CCDS32883.1	.	.	.	.	.	.	.	.	.	.	C	10.44	1.351592	0.24512	2.27E-4	0.0	ENSG00000125730	ENST00000245907	T	0.33216	1.42	5.13	-1.73	0.08081	.	1.455980	0.03434	N	0.208227	T	0.28234	0.0697	M	0.71296	2.17	0.09310	N	1	B	0.25609	0.13	B	0.20955	0.032	T	0.12293	-1.0553	10	0.15066	T	0.55	.	4.0249	0.09683	0.3691:0.3609:0.0:0.27	.	343	P01024	CO3_HUMAN	H	343	ENSP00000245907:R343H	ENSP00000245907:R343H	R	-	2	0	C3	6663610	0.000000	0.05858	0.006000	0.13384	0.692000	0.40212	-0.993000	0.03720	-0.071000	0.12886	0.561000	0.74099	CGC		0.582	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064	
ZNF557	79230	broad.mit.edu	37	19	7075716	7075716	+	Nonsense_Mutation	SNP	G	G	T	rs565026462	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:7075716G>T	ENST00000439035.2	+	4	301	c.61G>T	c.(61-63)Gga>Tga	p.G21*	ZNF557_ENST00000414706.1_Nonsense_Mutation_p.G28*|ZNF557_ENST00000252840.6_Nonsense_Mutation_p.G28*			Q8N988	ZN557_HUMAN	zinc finger protein 557	21					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.G28*(1)		endometrium(6)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	17				Lung(535;0.179)		CACAGAGGGCGGAGAGCTGGT	0.522																																					p.G21X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G61T	19						.						154.0	160.0	158.0					19																	7075716		2203	4300	6503	7026716	SO:0001587	stop_gained	79230	exon4			AK095524	CCDS42485.1, CCDS45945.1	19p13.2	2013-09-20			ENSG00000130544	ENSG00000130544		"""Zinc fingers, C2H2-type"", ""-"""	28632	protein-coding gene	gene with protein product						12477932	Standard	NM_024341		Approved	MGC4054	uc002mgc.3	Q8N988	OTTHUMG00000181977	ENST00000439035.2:c.61G>T	19.37:g.7075716G>T	ENSP00000398965:p.Gly21*	Somatic		Capture	Illumina HiSeq	Phase_I	7026716	NM_001044388	Q6PEJ3|Q9BTZ1	Nonsense_Mutation	SNP	ENST00000439035.2	37	CCDS45945.1	.	.	.	.	.	.	.	.	.	.	.	33	5.209569	0.95069	.	.	ENSG00000130544	ENST00000252840;ENST00000414706;ENST00000439035	.	.	.	1.08	1.08	0.20341	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	.	8.0181	0.30393	0.0:0.0:1.0:0.0	.	.	.	.	X	28;28;21	.	ENSP00000252840:G28X	G	+	1	0	ZNF557	7026716	0.001000	0.12720	0.010000	0.14722	0.089000	0.18198	-0.052000	0.11865	0.889000	0.36185	0.313000	0.20887	GGA		0.522	ZNF557-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458502.1	NM_024341	
ACTL9	284382	broad.mit.edu	37	19	8808697	8808697	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:8808697C>T	ENST00000324436.3	-	1	475	c.355G>A	c.(355-357)Gtc>Atc	p.V119I		NM_178525.3	NP_848620.3	Q8TC94	ACTL9_HUMAN	actin-like 9	119						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.V119I(1)		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						CAGTCCACGACGATGCCGCTG	0.706																																					p.V119I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G355A	19						.						25.0	30.0	28.0					19																	8808697		2201	4298	6499	8669697	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.355G>A	19.37:g.8808697C>T	ENSP00000316674:p.Val119Ile	Somatic		Capture	Illumina HiSeq	Phase_I	8669697	NM_178525	A8K893|Q6X960	Missense_Mutation	SNP	ENST00000324436.3	37	CCDS12207.1	.	.	.	.	.	.	.	.	.	.	C	3.012	-0.203641	0.06180	.	.	ENSG00000181786	ENST00000324436	D	0.95069	-3.6	4.0	-0.834	0.10779	.	1.052430	0.07596	N	0.922856	D	0.86234	0.5884	N	0.14661	0.345	0.28316	N	0.922437	B	0.16603	0.018	B	0.14578	0.011	T	0.75246	-0.3385	10	0.45353	T	0.12	.	3.9188	0.09234	0.1646:0.3825:0.0:0.4529	.	119	Q8TC94	ACTL9_HUMAN	I	119	ENSP00000316674:V119I	ENSP00000316674:V119I	V	-	1	0	ACTL9	8669697	0.017000	0.18338	0.392000	0.26245	0.098000	0.18820	-0.463000	0.06696	-0.110000	0.12022	0.462000	0.41574	GTC		0.706	ACTL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459953.1	NM_178525	
OR2Z1	284383	broad.mit.edu	37	19	8842180	8842180	+	Missense_Mutation	SNP	G	G	A	rs373819151		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:8842180G>A	ENST00000324060.2	+	1	865	c.790G>A	c.(790-792)Gcc>Acc	p.A264T		NM_001004699.1	NP_001004699.1	Q8NG97	OR2Z1_HUMAN	olfactory receptor, family 2, subfamily Z, member 1	264						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A264T(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						GGTGCCTTGCGCCTACCACAG	0.552																																					p.A264T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G790A	19						.	G	THR/ALA	0,4406		0,0,2203	179.0	145.0	156.0		790	-1.1	0.2	19		156	1,8599	2.2+/-6.3	0,1,4299	no	missense	OR2Z1	NM_001004699.1	58	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	264/315	8842180	1,13005	2203	4300	6503	8703180	SO:0001583	missense	284383	exon1			AC008753	CCDS32895.1	19p13.2	2013-09-20	2002-11-13		ENSG00000181733	ENSG00000181733		"""GPCR / Class A : Olfactory receptors"""	15391	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily Z, member 2"""	OR2Z2			Standard	NM_001004699		Approved		uc010xkg.2	Q8NG97	OTTHUMG00000182195	ENST00000324060.2:c.790G>A	19.37:g.8842180G>A	ENSP00000316284:p.Ala264Thr	Somatic		Capture	Illumina HiSeq	Phase_I	8703180	NM_001004699	B9EH50|Q6IFK0|Q96R25	Missense_Mutation	SNP	ENST00000324060.2	37	CCDS32895.1	.	.	.	.	.	.	.	.	.	.	G	7.556	0.663709	0.14710	0.0	1.16E-4	ENSG00000181733	ENST00000324060	T	0.00099	8.73	4.67	-1.08	0.09936	GPCR, rhodopsin-like superfamily (1);	1.416960	0.04216	N	0.332618	T	0.00073	0.0002	N	0.04636	-0.2	0.09310	N	1	B	0.12630	0.006	B	0.13407	0.009	T	0.14868	-1.0457	10	0.62326	D	0.03	.	4.5004	0.11862	0.1929:0.0:0.3208:0.4862	.	264	Q8NG97	OR2Z1_HUMAN	T	264	ENSP00000316284:A264T	ENSP00000316284:A264T	A	+	1	0	OR2Z1	8703180	0.000000	0.05858	0.216000	0.23742	0.112000	0.19704	0.270000	0.18607	0.136000	0.18733	-0.320000	0.08662	GCC		0.552	OR2Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459954.1		
MUC16	94025	broad.mit.edu	37	19	9089600	9089600	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:9089600C>T	ENST00000397910.4	-	1	2418	c.2215G>A	c.(2215-2217)Gcg>Acg	p.A739T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	739	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.A739T(2)		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						GTGCTGGTCGCTGACACTTTA	0.493																																					p.A739T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2215A	19						.						149.0	150.0	150.0					19																	9089600		2134	4254	6388	8950600	SO:0001583	missense	94025	exon1			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.2215G>A	19.37:g.9089600C>T	ENSP00000381008:p.Ala739Thr	Somatic		Capture	Illumina HiSeq	Phase_I	8950600	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	5.928	0.355335	0.11239	.	.	ENSG00000181143	ENST00000397910	T	0.02709	4.19	1.55	0.408	0.16377	.	.	.	.	.	T	0.01287	0.0042	N	0.08118	0	.	.	.	P	0.41041	0.736	B	0.28784	0.094	T	0.47100	-0.9143	8	0.87932	D	0	.	5.0001	0.14261	0.3497:0.6503:0.0:0.0	.	739	B5ME49	.	T	739	ENSP00000381008:A739T	ENSP00000381008:A739T	A	-	1	0	MUC16	8950600	0.000000	0.05858	0.001000	0.08648	0.216000	0.24613	-0.755000	0.04782	0.192000	0.20272	0.197000	0.17608	GCG		0.493	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
C19orf66	55337	broad.mit.edu	37	19	10202224	10202224	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:10202224delC	ENST00000253110.11	+	7	859	c.561delC	c.(559-561)ctcfs	p.L187fs	C19orf66_ENST00000591813.1_Intron|C19orf66_ENST00000397881.3_Frame_Shift_Del_p.L136fs|CTD-2240E14.4_ENST00000589622.1_RNA	NM_018381.2	NP_060851.2	Q9NUL5	CS066_HUMAN	chromosome 19 open reading frame 66	187								p.P189fs*67(1)		large_intestine(3)|skin(1)	4						CACGGATCCTCCCCCCGCGCT	0.711																																					p.L187fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.561delC	19						.						10.0	15.0	13.0					19																	10202224		1870	3826	5696	10063224	SO:0001589	frameshift_variant	55337	exon7				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.561delC	19.37:g.10202224delC	ENSP00000253110:p.Leu187fs	Somatic		Capture	Illumina HiSeq	Phase_I	10063224	NM_018381	A8MQT9|Q4G188|Q8IYH6|Q8N8V1	Frame_Shift_Del	DEL	ENST00000253110.11	37	CCDS45957.1																																																																																				0.711	C19orf66-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451129.1	NM_018381	
ZNF486	90649	broad.mit.edu	37	19	20308052	20308052	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:20308052delA	ENST00000335117.8	+	4	590	c.533delA	c.(532-534)gaafs	p.E178fs	CTC-260E6.6_ENST00000585498.1_RNA|CTC-260E6.6_ENST00000593655.1_RNA|CTC-260E6.6_ENST00000586657.1_RNA	NM_052852.3	NP_443084.2	Q96H40	ZN486_HUMAN	zinc finger protein 486	178					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.K171fs*3(1)|p.K180fs*3(1)		endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	11						AGACATACTGAAAAAAAACCT	0.303																																					p.E178fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.533delA	19						.						40.0	45.0	44.0					19																	20308052		2042	4226	6268	20169052	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.533delA	19.37:g.20308052delA	ENSP00000335042:p.Glu178fs	Somatic		Capture	Illumina HiSeq	Phase_I	20169052	NM_052852	Q0VG00	Frame_Shift_Del	DEL	ENST00000335117.8	37	CCDS46029.1																																																																																				0.303	ZNF486-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447843.2	NM_052852	
HIF3A	64344	broad.mit.edu	37	19	46815858	46815858	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:46815858delG	ENST00000377670.4	+	8	1004	c.973delG	c.(973-975)gggfs	p.G326fs	HIF3A_ENST00000244303.6_Frame_Shift_Del_p.G257fs|HIF3A_ENST00000420102.2_Frame_Shift_Del_p.G275fs|HIF3A_ENST00000600383.1_Frame_Shift_Del_p.G257fs|HIF3A_ENST00000472815.1_Frame_Shift_Del_p.G257fs|HIF3A_ENST00000339613.2_Frame_Shift_Del_p.G270fs|HIF3A_ENST00000300862.3_Frame_Shift_Del_p.G324fs	NM_152795.3	NP_690008.2	Q9Y2N7	HIF3A_HUMAN	hypoxia inducible factor 3, alpha subunit	326					cellular response to hypoxia (GO:0071456)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|transcription from RNA polymerase II promoter (GO:0006366)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.G324fs*15(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(14)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	33		Ovarian(192;0.00965)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00204)|all cancers(93;0.0107)|GBM - Glioblastoma multiforme(486;0.0489)|Epithelial(262;0.136)		AGTGGTGTCAGGGGGACGGGG	0.617																																					p.G325fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.973delG	19						.						73.0	77.0	76.0					19																	46815858		2203	4300	6503	51507698	SO:0001589	frameshift_variant	64344	exon8			AK027725	CCDS12681.2, CCDS12682.1, CCDS42580.1, CCDS42580.2	19q13	2013-05-21			ENSG00000124440	ENSG00000124440		"""Basic helix-loop-helix proteins"""	15825	protein-coding gene	gene with protein product		609976				11573933, 11734856	Standard	NM_152794		Approved	IPAS, MOP7, PASD7, bHLHe17	uc002peh.3	Q9Y2N7	OTTHUMG00000141296	ENST00000377670.4:c.973delG	19.37:g.46815858delG	ENSP00000366898:p.Gly326fs	Somatic		Capture	Illumina HiSeq	Phase_I	51507698	NM_152795	B0M185|B4DNA2|Q58A43|Q66K72|Q8WXA1|Q96K34|Q9H7Z9|Q9HAI2	Frame_Shift_Del	DEL	ENST00000377670.4	37	CCDS12681.2																																																																																				0.617	HIF3A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280556.3		
ZNF264	9422	broad.mit.edu	37	19	57723920	57723920	+	Silent	SNP	C	C	T	rs145421065		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr19:57723920C>T	ENST00000263095.6	+	4	1869	c.1455C>T	c.(1453-1455)tgC>tgT	p.C485C	ZNF264_ENST00000536056.1_Silent_p.C485C	NM_003417.4	NP_003408.1	O43296	ZN264_HUMAN	zinc finger protein 264	485					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.C485C(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(8)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	27		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0135)		CCTATGAGTGCGTGGAGTGTG	0.522																																					p.C485C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1455T	19						.	T		0,4406		0,0,2203	64.0	64.0	64.0		1455	0.1	0.3	19	dbSNP_134	64	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ZNF264	NM_003417.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		485/628	57723920	1,13005	2203	4300	6503	62415732	SO:0001819	synonymous_variant	9422	exon4			AB007872	CCDS33127.1	19q13.4	2013-01-08				ENSG00000083844		"""Zinc fingers, C2H2-type"", ""-"""	13057	protein-coding gene	gene with protein product		604668				9455477	Standard	NM_003417		Approved	KIAA0412	uc002qob.3	O43296		ENST00000263095.6:c.1455C>T	19.37:g.57723920C>T		Somatic		Capture	Illumina HiSeq	Phase_I	62415732	NM_003417	A8K8Y9|Q9P1V0	Silent	SNP	ENST00000263095.6	37	CCDS33127.1																																																																																				0.522	ZNF264-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465080.1		
GPR88	54112	broad.mit.edu	37	1	101004897	101004897	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:101004897G>A	ENST00000315033.4	+	2	814	c.375G>A	c.(373-375)acG>acA	p.T125T		NM_022049.2	NP_071332.2	Q9GZN0	GPR88_HUMAN	G protein-coupled receptor 88	125					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.T125T(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)		TCGGACTCACGGTGTCCCTCC	0.731																																					p.T125T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G375A	1						.						16.0	21.0	19.0					1																	101004897		2135	4250	6385	100777485	SO:0001819	synonymous_variant	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.375G>A	1.37:g.101004897G>A		Somatic		Capture	Illumina HiSeq	Phase_I	100777485	NM_022049	Q29S24|Q6VN48	Silent	SNP	ENST00000315033.4	37	CCDS772.1																																																																																				0.731	GPR88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030212.1	NM_022049	
OLFM3	118427	broad.mit.edu	37	1	102302527	102302527	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:102302527C>T	ENST00000338858.5	-	2	183	c.184G>A	c.(184-186)Gat>Aat	p.D62N	OLFM3_ENST00000359814.3_Missense_Mutation_p.D62N|OLFM3_ENST00000462354.1_5'UTR|OLFM3_ENST00000536598.1_5'UTR|OLFM3_ENST00000370103.4_Missense_Mutation_p.D42N			Q96PB7	NOE3_HUMAN	olfactomedin 3	62					eye photoreceptor cell development (GO:0042462)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)				breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(24)|ovary(3)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	43		all_epithelial(167;1.87e-06)|all_lung(203;8.12e-05)|Lung NSC(277;0.000189)		all cancers(265;0.0843)|Epithelial(280;0.0921)|COAD - Colon adenocarcinoma(174;0.145)		CACCGCCCATCAGGATCCTGA	0.488																																					p.D42N												.	.	0			c.G124A	1						.						94.0	85.0	88.0					1																	102302527		2203	4300	6503	102075115	SO:0001583	missense	118427	exon2			AF397392	CCDS30781.1, CCDS72832.1	1p22	2008-05-23			ENSG00000118733	ENSG00000118733			17990	protein-coding gene	gene with protein product	"""optimedin"""	607567				12019210, 16115881	Standard	NM_001288821		Approved	NOE3	uc001dug.2	Q96PB7	OTTHUMG00000010941	ENST00000338858.5:c.184G>A	1.37:g.102302527C>T	ENSP00000345192:p.Asp62Asn	None		Capture	Illumina HiSeq	Phase_I	102075115	NM_058170	Q5T3V6|Q6IMI7|Q6IMI8|Q6IMI9|Q6IMJ1|Q8TBG1|Q96PB2|Q96PB3|Q96PB4|Q96PB5|Q96PB6	Missense_Mutation	SNP	ENST00000338858.5	37		.	.	.	.	.	.	.	.	.	.	C	26.9	4.780932	0.90282	.	.	ENSG00000118733	ENST00000370103;ENST00000338858;ENST00000359814	D;D;T	0.93189	-3.18;-3.18;0.58	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	D	0.95708	0.8604	M	0.63843	1.955	0.80722	D	1	D;D	0.69078	0.996;0.997	D;D	0.80764	0.969;0.994	D	0.93875	0.7166	10	0.37606	T	0.19	.	20.2789	0.98501	0.0:1.0:0.0:0.0	.	42;62	Q5T3V6;Q96PB7	.;NOE3_HUMAN	N	42;62;62	ENSP00000359121:D42N;ENSP00000345192:D62N;ENSP00000352867:D62N	ENSP00000345192:D62N	D	-	1	0	OLFM3	102075115	1.000000	0.71417	0.992000	0.48379	0.638000	0.38207	7.794000	0.85869	2.788000	0.95919	0.650000	0.86243	GAT		0.488	OLFM3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000030142.1		
VAV3	10451	broad.mit.edu	37	1	108507301	108507301	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:108507301G>A	ENST00000370056.4	-	1	465	c.191C>T	c.(190-192)cCg>cTg	p.P64L	VAV3_ENST00000527011.1_Missense_Mutation_p.P64L|VAV3_ENST00000371846.4_5'UTR|VAV3-AS1_ENST00000438318.1_RNA	NM_006113.4	NP_006104.4	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor	64	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of signal transduction (GO:0009967)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|vesicle fusion (GO:0006906)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|SH3/SH2 adaptor activity (GO:0005070)	p.P64L(1)		NS(2)|breast(5)|endometrium(4)|kidney(2)|large_intestine(14)|lung(20)|ovary(6)|prostate(3)|stomach(1)|urinary_tract(1)	58		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		GGACATCTGCGGCCTCAGGTT	0.597																																					p.P64L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C191T	1						.						32.0	35.0	34.0					1																	108507301		2203	4300	6503	108308824	SO:0001583	missense	10451	exon1			AF118886	CCDS785.1, CCDS44181.1	1p13.3	2013-02-14	2007-07-25		ENSG00000134215	ENSG00000134215		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	12659	protein-coding gene	gene with protein product		605541	"""vav 3 oncogene"""				Standard	NM_001079874		Approved		uc001dvk.1	Q9UKW4	OTTHUMG00000010995	ENST00000370056.4:c.191C>T	1.37:g.108507301G>A	ENSP00000359073:p.Pro64Leu	Somatic		Capture	Illumina HiSeq	Phase_I	108308824	NM_006113	B1AMM0|B1APV5|B4E232|B7ZLR1|E9PQ97|O60498|O95230|Q9Y5X8	Missense_Mutation	SNP	ENST00000370056.4	37	CCDS785.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	29.8|29.8	5.039254|5.039254	0.93630|0.93630	.|.	.|.	ENSG00000134215|ENSG00000134215	ENST00000370056;ENST00000527011|ENST00000490388	T;T|.	0.60920|.	0.15;0.15|.	4.95|4.95	4.95|4.95	0.65309|0.65309	Calponin homology domain (5);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.85509|0.85509	0.5713|0.5713	H|H	0.95611|0.95611	3.695|3.695	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	0.998;0.986;1.0|.	D;P;D|.	0.97110|.	0.996;0.87;1.0|.	D|D	0.90034|0.90034	0.4137|0.4137	10|5	0.87932|.	D|.	0|.	.|.	16.8237|16.8237	0.85925|0.85925	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	64;64;64|.	B7ZLR1;E9PQ97;Q9UKW4|.	.;.;VAV3_HUMAN|.	L|C	64|59	ENSP00000359073:P64L;ENSP00000432540:P64L|.	ENSP00000359073:P64L|.	P|R	-|-	2|1	0|0	VAV3|VAV3	108308824|108308824	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.978000|0.978000	0.69477|0.69477	9.212000|9.212000	0.95126|0.95126	2.329000|2.329000	0.79093|0.79093	0.456000|0.456000	0.33151|0.33151	CCG|CGC		0.597	VAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030242.2	NM_006113	
PRPF38B	55119	broad.mit.edu	37	1	109241987	109241987	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:109241987G>A	ENST00000370025.4	+	6	1255	c.986G>A	c.(985-987)cGc>cAc	p.R329H	PRPF38B_ENST00000370021.1_Missense_Mutation_p.R218H	NM_018061.2	NP_060531.2	Q5VTL8	PR38B_HUMAN	pre-mRNA processing factor 38B	329	Arg-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)	p.R329H(1)		NS(1)|kidney(3)|large_intestine(5)|lung(8)|prostate(1)|skin(1)	19		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0149)|Lung(183;0.0888)|COAD - Colon adenocarcinoma(174;0.113)|Epithelial(280;0.161)		GAACGCAGGCGCAGCAGAAGT	0.502																																					p.R329H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G986A	1						.						80.0	78.0	78.0					1																	109241987		2203	4300	6503	109043510	SO:0001583	missense	55119	exon6			AL833950	CCDS788.1	1p13.3	2013-10-03	2013-10-03		ENSG00000134186	ENSG00000134186			25512	protein-coding gene	gene with protein product			"""PRP38 pre-mRNA processing factor 38 (yeast) domain containing B"""				Standard	NM_018061		Approved	FLJ10330, NET1	uc001dvv.4	Q5VTL8	OTTHUMG00000010991	ENST00000370025.4:c.986G>A	1.37:g.109241987G>A	ENSP00000359042:p.Arg329His	Somatic		Capture	Illumina HiSeq	Phase_I	109043510	NM_018061	Q05DD6|Q32Q58|Q5VTL9|Q6PK39|Q7Z6E2|Q86WF3|Q8IWG9|Q9NW40	Missense_Mutation	SNP	ENST00000370025.4	37	CCDS788.1	.	.	.	.	.	.	.	.	.	.	G	4.437	0.080947	0.08533	.	.	ENSG00000134186	ENST00000370025;ENST00000370021	T;T	0.14022	3.93;2.54	5.69	-6.24	0.02046	.	0.394934	0.25845	N	0.027933	T	0.04272	0.0118	L	0.27053	0.805	0.33564	D	0.59769	B	0.06786	0.001	B	0.04013	0.001	T	0.01305	-1.1390	10	0.52906	T	0.07	.	23.4742	0.99983	0.0825:0.0:0.9175:0.0	.	329	Q5VTL8	PR38B_HUMAN	H	329;218	ENSP00000359042:R329H;ENSP00000359038:R218H	ENSP00000359038:R218H	R	+	2	0	PRPF38B	109043510	0.044000	0.20184	0.002000	0.10522	0.441000	0.31987	0.114000	0.15520	-1.776000	0.01285	-0.948000	0.02665	CGC		0.502	PRPF38B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030231.1	NM_018061	
CLCC1	23155	broad.mit.edu	37	1	109482352	109482352	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:109482352C>A	ENST00000369971.2	-	9	1076	c.947G>T	c.(946-948)gGa>gTa	p.G316V	AKNAD1_ENST00000357393.4_Intron|CLCC1_ENST00000356970.2_Missense_Mutation_p.G316V|CLCC1_ENST00000348264.2_Missense_Mutation_p.G131V|CLCC1_ENST00000369976.1_Intron|CLCC1_ENST00000369969.2_Missense_Mutation_p.G195V|CLCC1_ENST00000369970.3_Missense_Mutation_p.G266V|CLCC1_ENST00000415331.1_Missense_Mutation_p.G266V|CLCC1_ENST00000482889.1_5'UTR|CLCC1_ENST00000369968.2_Missense_Mutation_p.G131V|CLCC1_ENST00000302500.4_Missense_Mutation_p.G195V	NM_001048210.1	NP_001041675.1	Q96S66	CLCC1_HUMAN	chloride channel CLIC-like 1	316						chloride channel complex (GO:0034707)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	chloride channel activity (GO:0005254)	p.G266V(1)		autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|liver(1)|skin(1)	14		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.231)		AGTTCCTTTTCCAATATGCTT	0.408																																					p.G316V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G947T	1						.						103.0	92.0	96.0					1																	109482352		2203	4300	6503	109283875	SO:0001583	missense	23155	exon9			AB018304	CCDS793.1, CCDS41362.1, CCDS60214.1, CCDS60215.1	1p13.3	2008-02-05			ENSG00000121940	ENSG00000121940			29675	protein-coding gene	gene with protein product	"""Mid1-related chloride channel (yeast)"""					9872452, 11279057	Standard	NM_001048210		Approved	MCLC	uc001dwf.2	Q96S66	OTTHUMG00000011732	ENST00000369971.2:c.947G>T	1.37:g.109482352C>A	ENSP00000358988:p.Gly316Val	Somatic		Capture	Illumina HiSeq	Phase_I	109283875	NM_001048210	O94861|Q8WYP8|Q8WYP9|Q9BU25	Missense_Mutation	SNP	ENST00000369971.2	37	CCDS41362.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.858170	0.91433	.	.	ENSG00000121940	ENST00000356970;ENST00000369971;ENST00000415331;ENST00000369969;ENST00000369968;ENST00000369970;ENST00000348264;ENST00000302500	T;T;T;T;T;T;T;T	0.62105	0.05;0.05;0.05;0.05;0.05;0.05;0.05;0.05	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.77075	0.4077	M	0.78801	2.425	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;1.0;1.0	T	0.79526	-0.1767	10	0.62326	D	0.03	-25.0215	18.8082	0.92047	0.0:1.0:0.0:0.0	.	131;195;266;316	Q96S66-4;Q96S66-3;Q96S66-2;Q96S66	.;.;.;CLCC1_HUMAN	V	316;316;266;195;131;266;131;195	ENSP00000349456:G316V;ENSP00000358988:G316V;ENSP00000411591:G266V;ENSP00000358986:G195V;ENSP00000358985:G131V;ENSP00000358987:G266V;ENSP00000337243:G131V;ENSP00000306552:G195V	ENSP00000306552:G195V	G	-	2	0	CLCC1	109283875	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.333000	0.79214	2.429000	0.82318	0.591000	0.81541	GGA		0.408	CLCC1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032405.1	NM_015127	
SARS	6301	broad.mit.edu	37	1	109778615	109778615	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:109778615A>G	ENST00000234677.2	+	8	1061	c.986A>G	c.(985-987)tAc>tGc	p.Y329C	SARS_ENST00000369923.4_Missense_Mutation_p.Y329C	NM_006513.3	NP_006504.2	P49591	SYSC_HUMAN	seryl-tRNA synthetase	329					gene expression (GO:0010467)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)|seryl-tRNA aminoacylation (GO:0006434)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)|tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|RNA binding (GO:0003723)|serine-tRNA ligase activity (GO:0004828)	p.Y329C(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	17		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0301)|Lung(183;0.0677)|COAD - Colon adenocarcinoma(174;0.116)|Epithelial(280;0.233)	L-Serine(DB00133)	CAGTTTGTGTACTCATCACCC	0.488																																					p.Y329C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A986G	1						.						97.0	90.0	93.0					1																	109778615		2203	4300	6503	109580138	SO:0001583	missense	6301	exon8			BC009390	CCDS795.1	1p13.3	2011-07-01			ENSG00000031698	ENSG00000031698	6.1.1.11	"""Aminoacyl tRNA synthetases / Class II"""	10537	protein-coding gene	gene with protein product	"""serine tRNA ligase 1, cytoplasmic"""	607529				9431993	Standard	NM_006513		Approved	SERS	uc001dwu.2	P49591	OTTHUMG00000011726	ENST00000234677.2:c.986A>G	1.37:g.109778615A>G	ENSP00000234677:p.Tyr329Cys	Somatic		Capture	Illumina HiSeq	Phase_I	109580138	NM_006513	B2R6Y9|Q5T5C8|Q9NSE3	Missense_Mutation	SNP	ENST00000234677.2	37	CCDS795.1	.	.	.	.	.	.	.	.	.	.	a	20.8	4.054783	0.75960	.	.	ENSG00000031698	ENST00000234677;ENST00000369923	T;T	0.77620	-1.11;-1.11	5.88	5.88	0.94601	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (G/ H/ P/ S), conserved domain (1);	0.000000	0.85682	D	0.000000	T	0.81758	0.4890	L	0.56340	1.77	0.80722	D	1	D;D;D;D	0.76494	0.973;0.973;0.999;0.973	P;P;D;P	0.64506	0.852;0.852;0.926;0.852	D	0.84372	0.0544	10	0.87932	D	0	-15.7747	15.9558	0.79886	1.0:0.0:0.0:0.0	.	329;329;329;329	Q0VGA5;Q53HA4;Q5T5C7;P49591	.;.;.;SYSC_HUMAN	C	329	ENSP00000234677:Y329C;ENSP00000358939:Y329C	ENSP00000234677:Y329C	Y	+	2	0	SARS	109580138	1.000000	0.71417	0.987000	0.45799	0.673000	0.39480	5.111000	0.64628	2.250000	0.74265	0.533000	0.62120	TAC		0.488	SARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032394.2	NM_006513	
MTOR	2475	broad.mit.edu	37	1	11204730	11204730	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:11204730C>T	ENST00000361445.4	-	34	4923	c.4847G>A	c.(4846-4848)cGc>cAc	p.R1616H	MTOR-AS1_ENST00000420480.1_RNA|MTOR-AS1_ENST00000445982.1_RNA|MTOR_ENST00000495435.1_5'UTR	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	1616	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)	p.R1616H(1)		breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	CCAGATCTGGCGGATGATCTC	0.582																																					p.R1616H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4847A	1						.						92.0	86.0	88.0					1																	11204730		2203	4300	6503	11127317	SO:0001583	missense	2475	exon34			L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"""FK506 binding protein 12-rapamycin associated protein 2"", ""rapamycin target protein"", ""FKBP12-rapamycin complex-associated protein 1"", ""FKBP-rapamycin associated protein"", ""rapamycin associated protein FRAP2"", ""dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)"", ""rapamycin and FKBP12 target 1"", ""mammalian target of rapamycin"""	601231	"""FK506 binding protein 12-rapamycin associated protein 1"""	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.4847G>A	1.37:g.11204730C>T	ENSP00000354558:p.Arg1616His	Somatic		Capture	Illumina HiSeq	Phase_I	11127317	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	ENST00000361445.4	37	CCDS127.1	.	.	.	.	.	.	.	.	.	.	C	35	5.494877	0.96339	.	.	ENSG00000198793	ENST00000361445;ENST00000539766	T	0.67865	-0.29	5.81	5.81	0.92471	PIK-related kinase (1);PIK-related kinase, FAT (1);Armadillo-like helical (1);	0.000000	0.85682	D	0.000000	D	0.84705	0.5531	M	0.85462	2.755	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	D	0.86147	0.1585	10	0.87932	D	0	-26.5251	20.0826	0.97783	0.0:1.0:0.0:0.0	.	1616	P42345	MTOR_HUMAN	H	1616	ENSP00000354558:R1616H	ENSP00000354558:R1616H	R	-	2	0	MTOR	11127317	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.365000	0.79537	2.746000	0.94184	0.655000	0.94253	CGC		0.582	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958	
RBM15	64783	broad.mit.edu	37	1	110883472	110883472	+	Missense_Mutation	SNP	G	G	A	rs113985065		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:110883472G>A	ENST00000369784.3	+	1	2345	c.1445G>A	c.(1444-1446)cGc>cAc	p.R482H	RP5-1074L1.1_ENST00000449169.1_RNA|RBM15_ENST00000602849.1_Missense_Mutation_p.R482H|RBM15_ENST00000487146.2_Missense_Mutation_p.R482H	NM_022768.4	NP_073605.4	Q96T37	RBM15_HUMAN	RNA binding motif protein 15	482	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				negative regulation of myeloid cell differentiation (GO:0045638)|patterning of blood vessels (GO:0001569)|placenta blood vessel development (GO:0060674)|positive regulation of transcription of Notch receptor target (GO:0007221)|spleen development (GO:0048536)|ventricular septum morphogenesis (GO:0060412)|viral process (GO:0016032)	membrane (GO:0016020)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R482L(1)|p.R482H(1)		ovary(3)	3		all_cancers(81;2.89e-06)|all_epithelial(167;2.96e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Breast(1374;0.0634)		BRCA - Breast invasive adenocarcinoma(282;0.000224)|Epithelial(280;0.000476)|Kidney(133;0.000539)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|all cancers(265;0.00144)|Lung(183;0.0238)|Colorectal(144;0.103)|LUSC - Lung squamous cell carcinoma(189;0.135)		GGCACCATACGCACCATAGAC	0.557			T	MKL1	acute megakaryocytic leukemia																																p.R482H			Dom	yes		1	1p13	64783	RNA binding motif protein 15		L	.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G1445A	1						.						77.0	78.0	77.0					1																	110883472		2203	4300	6503	110684995	SO:0001583	missense	64783	exon1			AF368063	CCDS822.1, CCDS59198.1	1p13	2013-02-12			ENSG00000162775	ENSG00000162775		"""RNA binding motif (RRM) containing"""	14959	protein-coding gene	gene with protein product	"""one twenty-two"""	606077				11431691, 11344311	Standard	NM_001201545		Approved	OTT, OTT1	uc001dzl.1	Q96T37	OTTHUMG00000011284	ENST00000369784.3:c.1445G>A	1.37:g.110883472G>A	ENSP00000358799:p.Arg482His	Somatic		Capture	Illumina HiSeq	Phase_I	110684995	NM_022768	A1A693|Q3ZB86|Q4V760|Q5D058|Q5T613|Q86VW9|Q96PE4|Q96SC5|Q96SC6|Q96SC9|Q96SD0|Q96T38|Q9BRA5|Q9H6R8|Q9H9Y0	Missense_Mutation	SNP	ENST00000369784.3	37	CCDS822.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.364949	0.82463	.	.	ENSG00000162775	ENST00000369784	T	0.06294	3.32	4.94	4.94	0.65067	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.000000	0.47093	D	0.000245	T	0.22282	0.0537	M	0.83223	2.63	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.87578	0.98;0.998	T	0.02411	-1.1163	10	0.87932	D	0	-6.7304	18.3212	0.90239	0.0:0.0:1.0:0.0	.	482;482	Q96T37-3;Q96T37	.;RBM15_HUMAN	H	482	ENSP00000358799:R482H	ENSP00000358799:R482H	R	+	2	0	RBM15	110684995	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.263000	0.95617	2.563000	0.86464	0.655000	0.94253	CGC		0.557	RBM15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000031114.2	NM_022768	
DENND2D	79961	broad.mit.edu	37	1	111737331	111737331	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:111737331C>T	ENST00000357640.4	-	7	892	c.663G>A	c.(661-663)cgG>cgA	p.R221R	DENND2D_ENST00000369752.5_Silent_p.R218R|DENND2D_ENST00000473682.1_5'Flank	NM_024901.3	NP_079177.2	Q9H6A0	DEN2D_HUMAN	DENN/MADD domain containing 2D	221	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)	cytoplasm (GO:0005737)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.R221R(1)		breast(1)|endometrium(1)|kidney(7)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	25		all_cancers(81;0.00198)|all_epithelial(167;0.000686)|all_lung(203;0.00318)|Lung NSC(277;0.00499)		Lung(183;0.0162)|Colorectal(144;0.069)|all cancers(265;0.0757)|LUSC - Lung squamous cell carcinoma(189;0.0845)|Epithelial(280;0.114)|COAD - Colon adenocarcinoma(174;0.14)		AGTCCAGGGGCCGTGTCAGTG	0.502																																					p.R221R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G663A	1						.						75.0	85.0	82.0					1																	111737331		2203	4300	6503	111538854	SO:0001819	synonymous_variant	79961	exon7				CCDS831.1, CCDS60219.1	1p13.3	2014-02-12	2005-08-17		ENSG00000162777	ENSG00000162777		"""DENN/MADD domain containing"""	26192	protein-coding gene	gene with protein product		615111				12477932	Standard	NM_024901		Approved	FLJ22457, RP5-1180E21.2	uc001eal.2	Q9H6A0	OTTHUMG00000012356	ENST00000357640.4:c.663G>A	1.37:g.111737331C>T		Somatic		Capture	Illumina HiSeq	Phase_I	111538854	NM_024901	Q5T5V6|Q9BSU0	Silent	SNP	ENST00000357640.4	37	CCDS831.1																																																																																				0.502	DENND2D-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000034456.1	NM_024901	
CSDE1	7812	broad.mit.edu	37	1	115263257	115263257	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:115263257A>C	ENST00000358528.4	-	17	2381	c.1955T>G	c.(1954-1956)gTc>gGc	p.V652G	CSDE1_ENST00000438362.2_Missense_Mutation_p.V698G|CSDE1_ENST00000483407.1_5'Flank|CSDE1_ENST00000339438.6_Missense_Mutation_p.V621G|CSDE1_ENST00000261443.5_Missense_Mutation_p.V621G|CSDE1_ENST00000530886.1_Missense_Mutation_p.V522G|CSDE1_ENST00000369530.1_Missense_Mutation_p.V667G|CSDE1_ENST00000534699.1_Missense_Mutation_p.V652G	NM_001007553.2	NP_001007554.1	O75534	CSDE1_HUMAN	cold shock domain containing E1, RNA-binding	652	CSD 8.				male gonad development (GO:0008584)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|regulation of transcription, DNA-templated (GO:0006355)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.V652G(1)		NS(1)|breast(4)|endometrium(11)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	51	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTGGAACTTGACGCTCTCCCC	0.493																																					p.V667G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2000G	1						.						218.0	177.0	191.0					1																	115263257		2203	4300	6503	115064780	SO:0001583	missense	7812	exon17				CCDS30811.1, CCDS30812.1, CCDS44197.1, CCDS55626.1	1p13.2	2011-11-02			ENSG00000009307	ENSG00000009307			29905	protein-coding gene	gene with protein product	"""upstream of NRAS"""	191510				2204029, 10048485	Standard	NM_007158		Approved	D1S155E, UNR	uc001efi.3	O75534	OTTHUMG00000012060	ENST00000358528.4:c.1955T>G	1.37:g.115263257A>C	ENSP00000351329:p.Val652Gly	Somatic		Capture	Illumina HiSeq	Phase_I	115064780	NM_001130523	A8K281|E9PGZ0|G5E9Q2|O94961|Q5TF04|Q5TF05|Q68DF1|Q68DI9|Q9Y2S4	Missense_Mutation	SNP	ENST00000358528.4	37	CCDS30812.1	.	.	.	.	.	.	.	.	.	.	A	28.1	4.889659	0.91889	.	.	ENSG00000009307	ENST00000339438;ENST00000438362;ENST00000358528;ENST00000261443;ENST00000530886;ENST00000369530;ENST00000534699	.	.	.	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.74366	0.3707	M	0.72118	2.19	0.80722	D	1	D;D;D	0.76494	0.999;0.998;0.981	D;D;D	0.78314	0.991;0.981;0.978	T	0.77953	-0.2394	9	0.87932	D	0	-5.4765	16.6406	0.85098	1.0:0.0:0.0:0.0	.	667;652;698	E9PGZ0;O75534;G5E9Q2	.;CSDE1_HUMAN;.	G	621;698;652;621;522;667;652	.	ENSP00000261443:V621G	V	-	2	0	CSDE1	115064780	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.691000	0.91279	2.326000	0.78906	0.533000	0.62120	GTC		0.493	CSDE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033397.1	NM_007158	
FAM46C	54855	broad.mit.edu	37	1	118166184	118166184	+	Missense_Mutation	SNP	G	G	A	rs371434677		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:118166184G>A	ENST00000369448.3	+	2	941	c.694G>A	c.(694-696)Gcc>Acc	p.A232T		NM_017709.3	NP_060179.2	Q5VWP2	FA46C_HUMAN	family with sequence similarity 46, member C	232								p.A232T(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)	15	Lung SC(450;0.225)	all_cancers(81;0.000101)|all_lung(203;3.4e-06)|all_epithelial(167;4.98e-06)|Lung NSC(69;2.33e-05)		Lung(183;0.0576)|LUSC - Lung squamous cell carcinoma(189;0.192)|Colorectal(144;0.247)		CAGACTGATCGCCACCAAGAA	0.517			"""Mis, F, O"""		MM					Multiple Myeloma(3;1.13e-06)																											p.A232T			Rec	yes		1	1p12	54855	"""family with sequence similarity 46, member C"""		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G694A	1						.	G	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	74.0	80.0	78.0		694	4.8	1.0	1		78	0,8600		0,0,4300	no	missense	FAM46C	NM_017709.3	58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging	232/392	118166184	1,13005	2203	4300	6503	117967707	SO:0001583	missense	54855	exon2			BC036516	CCDS896.1	1p12	2008-02-05			ENSG00000183508	ENSG00000183508			24712	protein-coding gene	gene with protein product		613952				12477932	Standard	NM_017709		Approved	FLJ20202	uc001ehe.3	Q5VWP2	OTTHUMG00000013703	ENST00000369448.3:c.694G>A	1.37:g.118166184G>A	ENSP00000358458:p.Ala232Thr	Somatic		Capture	Illumina HiSeq	Phase_I	117967707	NM_017709	A3KMG2|Q8NE25|Q9NXK0	Missense_Mutation	SNP	ENST00000369448.3	37	CCDS896.1	.	.	.	.	.	.	.	.	.	.	G	15.31	2.794336	0.50102	2.27E-4	0.0	ENSG00000183508	ENST00000369448	T	0.26223	1.75	5.72	4.81	0.61882	Domain of unknown function DUF1693 (1);	0.260851	0.32785	N	0.005641	T	0.16981	0.0408	M	0.80616	2.505	0.58432	D	0.999996	B	0.18863	0.031	B	0.11329	0.006	T	0.07558	-1.0766	10	0.54805	T	0.06	-10.0494	8.798	0.34892	0.0752:0.0:0.7759:0.1488	.	232	Q5VWP2	FA46C_HUMAN	T	232	ENSP00000358458:A232T	ENSP00000358458:A232T	A	+	1	0	FAM46C	117967707	1.000000	0.71417	1.000000	0.80357	0.602000	0.36980	5.517000	0.67061	1.426000	0.47256	-0.251000	0.11542	GCC		0.517	FAM46C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038424.1	NM_017709	
VPS13D	55187	broad.mit.edu	37	1	12368635	12368635	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:12368635C>T	ENST00000358136.3	+	27	6717	c.6587C>T	c.(6586-6588)aCa>aTa	p.T2196I	VPS13D_ENST00000356315.4_Missense_Mutation_p.T2196I	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)									p.T2196I(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)		GTGCGACAGACAGGAGGAAGC	0.453																																					p.T2196I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C6587T	1						.						161.0	158.0	159.0					1																	12368635		2203	4300	6503	12291222	SO:0001583	missense	55187	exon27			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.6587C>T	1.37:g.12368635C>T	ENSP00000350854:p.Thr2196Ile	Somatic		Capture	Illumina HiSeq	Phase_I	12291222	NM_018156		Missense_Mutation	SNP	ENST00000358136.3	37	CCDS30588.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.27|16.27	3.075208|3.075208	0.55646|0.55646	.|.	.|.	ENSG00000048707|ENSG00000048707	ENST00000011700|ENST00000356315;ENST00000358136	.|T;T	.|0.38722	.|1.12;1.12	5.61|5.61	5.61|5.61	0.85477|0.85477	.|.	.|0.163455	.|0.52532	.|D	.|0.000064	.|T	.|0.35653	.|0.0939	L|L	0.44542|0.44542	1.39|1.39	0.80722|0.80722	D|D	1|1	.|B;B	.|0.28470	.|0.213;0.136	.|B;B	.|0.26202	.|0.067;0.03	.|T	.|0.11227	.|-1.0596	.|10	.|0.37606	.|T	.|0.19	.|.	12.9182|12.9182	0.58216|0.58216	0.0:0.9258:0.0:0.0742|0.0:0.9258:0.0:0.0742	.|.	.|2196;2196	.|Q5THJ4-2;Q5THJ4	.|.;VP13D_HUMAN	X|I	1019|2196	.|ENSP00000348666:T2196I;ENSP00000350854:T2196I	.|ENSP00000348666:T2196I	Q|T	+|+	1|2	0|0	VPS13D|VPS13D	12291222|12291222	0.997000|0.997000	0.39634|0.39634	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	3.601000|3.601000	0.54059|0.54059	2.636000|2.636000	0.89361|0.89361	0.650000|0.650000	0.86243|0.86243	CAG|ACA		0.453	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378	
TBX15	6913	broad.mit.edu	37	1	119427666	119427666	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:119427666G>T	ENST00000369429.3	-	8	1507	c.1498C>A	c.(1498-1500)Cac>Aac	p.H500N	TBX15_ENST00000207157.3_Missense_Mutation_p.H394N			Q96SF7	TBX15_HUMAN	T-box 15	500					embryonic cranial skeleton morphogenesis (GO:0048701)	Tle3-Aes complex (GO:0070722)	RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.H394N(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(19)|ovary(1)|pancreas(1)|skin(5)	37	all_neural(166;0.117)	all_cancers(81;0.000692)|all_lung(203;3.05e-06)|Lung NSC(69;2.13e-05)|all_epithelial(167;0.000237)		Lung(183;0.044)|LUSC - Lung squamous cell carcinoma(189;0.141)		TGCTGCATGTGGCTGCCCCCG	0.557																																					p.H394N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1180A	1						.						62.0	54.0	57.0					1																	119427666		2203	4300	6503	119229189	SO:0001583	missense	6913	exon8			AK127536	CCDS30816.1	1p11.1	2008-02-05	2004-10-05		ENSG00000092607	ENSG00000092607		"""T-boxes"""	11594	protein-coding gene	gene with protein product		604127	"""T-box 14"""	TBX14		9693034	Standard	XM_005271162		Approved		uc001ehl.1	Q96SF7	OTTHUMG00000012263	ENST00000369429.3:c.1498C>A	1.37:g.119427666G>T	ENSP00000358437:p.His500Asn	Somatic		Capture	Illumina HiSeq	Phase_I	119229189	NM_152380	Q08E76|Q5JT54|Q5T9S7	Missense_Mutation	SNP	ENST00000369429.3	37		.	.	.	.	.	.	.	.	.	.	G	14.91	2.676542	0.47886	.	.	ENSG00000092607	ENST00000344218;ENST00000207157;ENST00000369429;ENST00000449873	D;D;T	0.87571	-2.27;-2.15;-1.11	5.31	5.31	0.75309	.	0.050646	0.85682	D	0.000000	T	0.77398	0.4124	L	0.36672	1.1	0.80722	D	1	P;P	0.48998	0.918;0.863	B;P	0.44422	0.428;0.449	T	0.76263	-0.3023	10	0.11485	T	0.65	.	19.1626	0.93539	0.0:0.0:1.0:0.0	.	297;500	E9PCG3;Q96SF7	.;TBX15_HUMAN	N	297;394;500;228	ENSP00000207157:H394N;ENSP00000358437:H500N;ENSP00000398625:H228N	ENSP00000207157:H394N	H	-	1	0	TBX15	119229189	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.802000	0.91910	2.768000	0.95171	0.561000	0.74099	CAC		0.557	TBX15-002	PUTATIVE	not_organism_supported|upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000034351.1	NM_152380	
ANKRD35	148741	broad.mit.edu	37	1	145558910	145558910	+	Missense_Mutation	SNP	G	G	A	rs186195553	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:145558910G>A	ENST00000355594.4	+	7	616	c.529G>A	c.(529-531)Gcc>Acc	p.A177T	ANKRD35_ENST00000544626.1_3'UTR	NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	177								p.A177T(1)		NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(16)|ovary(4)|prostate(3)|skin(2)|urinary_tract(1)	47	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GCAGCGAGGCGCCCGAGTTAA	0.547													G|||	3	0.000599042	0.0	0.0	5008	,	,		18008	0.0		0.003	False		,,,				2504	0.0				p.A177T	Melanoma(9;127 754 22988 51047)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G529A	1						.	G	THR/ALA	0,4406		0,0,2203	84.0	81.0	82.0		529	5.7	1.0	1		82	2,8598	2.2+/-6.3	0,2,4298	no	missense	ANKRD35	NM_144698.3	58	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	177/1002	145558910	2,13004	2203	4300	6503	144270267	SO:0001583	missense	148741	exon7			AK091120	CCDS72867.1, CCDS72868.1	1q21.1	2013-01-10			ENSG00000198483	ENSG00000198483		"""Ankyrin repeat domain containing"""	26323	protein-coding gene	gene with protein product							Standard	NM_144698		Approved	FLJ25124	uc001eob.1	Q8N283	OTTHUMG00000013743	ENST00000355594.4:c.529G>A	1.37:g.145558910G>A	ENSP00000347802:p.Ala177Thr	Somatic		Capture	Illumina HiSeq	Phase_I	144270267	NM_144698	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Missense_Mutation	SNP	ENST00000355594.4	37	CCDS919.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	33	5.263758	0.95399	0.0	2.33E-4	ENSG00000198483	ENST00000453670;ENST00000355594	T	0.61510	0.1	5.65	5.65	0.86999	Ankyrin repeat-containing domain (4);	0.000000	0.47455	D	0.000228	T	0.78578	0.4305	M	0.92412	3.305	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.83223	-0.0067	10	0.72032	D	0.01	-12.0547	15.233	0.73407	0.0:0.0:1.0:0.0	.	177	Q8N283	ANR35_HUMAN	T	86;177	ENSP00000347802:A177T	ENSP00000347802:A177T	A	+	1	0	ANKRD35	144270267	1.000000	0.71417	0.964000	0.40570	0.911000	0.54048	4.990000	0.63876	2.663000	0.90544	0.655000	0.94253	GCC		0.547	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698	
GPR89A	653519	broad.mit.edu	37	1	145816723	145816723	+	Silent	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:145816723T>C	ENST00000313835.9	-	3	263	c.120A>G	c.(118-120)gtA>gtG	p.V40V	GPR89A_ENST00000462900.2_Silent_p.V15V|GPR89A_ENST00000534502.1_Silent_p.V15V|GPR89A_ENST00000454423.3_5'UTR			B7ZAQ6	GPHRA_HUMAN	G protein-coupled receptor 89A	40					intracellular pH reduction (GO:0051452)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein transport (GO:0015031)|regulation of anion transport (GO:0044070)|signal transduction (GO:0007165)	Golgi cisterna membrane (GO:0032580)|Golgi-associated vesicle membrane (GO:0030660)|integral component of membrane (GO:0016021)	signal transducer activity (GO:0004871)|voltage-gated anion channel activity (GO:0008308)	p.V40V(1)		breast(1)|large_intestine(3)|lung(1)|skin(1)	6	all_hematologic(18;0.00473)|Acute lymphoblastic leukemia(18;0.0786)		KIRC - Kidney renal clear cell carcinoma(6;0.0764)|Kidney(552;0.118)|Colorectal(543;0.229)			AGATCACCTGTACAACATACT	0.378																																					p.V15V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A45G	1						.						15.0	17.0	16.0					1																	145816723		2097	4210	6307	144528080	SO:0001819	synonymous_variant	653519	exon4			AB097024	CCDS72857.1, CCDS72858.1	1q21.1	2008-12-17	2007-06-06	2007-06-06	ENSG00000117262	ENSG00000117262			31984	protein-coding gene	gene with protein product		612821					Standard	NM_001097612		Approved	UNQ192	uc001eot.2	B7ZAQ6	OTTHUMG00000013738	ENST00000313835.9:c.120A>G	1.37:g.145816723T>C		Somatic		Capture	Illumina HiSeq	Phase_I	144528080	NM_001097613	A6NN37|B2RUV3|B3KMN3|B4DLT3|B4DXE7|Q53FQ9|Q5T2V8|Q5T5P5|Q659E2|Q6NVY5|Q9P0S4|Q9Y302	Silent	SNP	ENST00000313835.9	37	CCDS41377.1																																																																																				0.378	GPR89A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038507.2	NM_001097612	
HIST2H2BF	440689	broad.mit.edu	37	1	149783854	149783854	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:149783854G>C	ENST00000369167.1	-	1	60	c.25C>G	c.(25-27)Cct>Gct	p.P9A	HIST2H2BF_ENST00000545683.1_Missense_Mutation_p.P9A|RP11-196G18.21_ENST00000420462.1_RNA|HIST2H2BF_ENST00000427880.2_Missense_Mutation_p.P9A|HIST2H2BF_ENST00000469483.1_5'UTR	NM_001024599.4	NP_001019770.1	Q5QNW6	H2B2F_HUMAN	histone cluster 2, H2bf	9					chromatin organization (GO:0006325)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.P9A(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	Breast(34;0.0124)|all_hematologic(923;0.127)					TTGGGAGCAGGAGCGGATTTC	0.507																																					p.P9A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C25G	1						.						66.0	72.0	70.0					1																	149783854		2203	4298	6501	148050478	SO:0001583	missense	440689	exon1			BC110793	CCDS30846.1, CCDS53359.1	1q21.2	2013-06-03	2006-10-11		ENSG00000203814	ENSG00000203814		"""Histones / Replication-dependent"""	24700	protein-coding gene	gene with protein product			"""histone 2, H2bf"""				Standard	NM_001161334		Approved		uc010pbj.2	Q5QNW6	OTTHUMG00000183159	ENST00000369167.1:c.25C>G	1.37:g.149783854G>C	ENSP00000358164:p.Pro9Ala	Somatic		Capture	Illumina HiSeq	Phase_I	148050478	NM_001024599	A8K0U9|B4DLA9	Missense_Mutation	SNP	ENST00000369167.1	37	CCDS30846.1	.	.	.	.	.	.	.	.	.	.	G	14.48	2.549087	0.45383	.	.	ENSG00000203814	ENST00000545683;ENST00000427880;ENST00000369167	T;T;T	0.22134	1.97;1.97;1.97	3.56	3.56	0.40772	Histone-fold (2);	0.000000	0.48286	D	0.000197	T	0.27349	0.0671	M	0.63428	1.95	0.41263	D	0.986792	D;B;B	0.56968	0.978;0.202;0.202	P;B;B	0.55999	0.789;0.057;0.057	T	0.05954	-1.0854	10	0.66056	D	0.02	.	14.937	0.70964	0.0:0.0:1.0:0.0	.	9;9;9	B4DR52;B4DLA9;Q5QNW6	.;.;H2B2F_HUMAN	A	9	ENSP00000445831:P9A;ENSP00000407461:P9A;ENSP00000358164:P9A	ENSP00000358164:P9A	P	-	1	0	HIST2H2BF	148050478	1.000000	0.71417	0.999000	0.59377	0.479000	0.33129	5.931000	0.70113	2.287000	0.76781	0.195000	0.17529	CCT		0.507	HIST2H2BF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033453.2	NM_001024599	
SF3B4	10262	broad.mit.edu	37	1	149895450	149895450	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:149895450C>T	ENST00000271628.8	-	6	1843	c.1259G>A	c.(1258-1260)gGc>gAc	p.G420D		NM_005850.4	NP_005841.1	Q15427	SF3B4_HUMAN	splicing factor 3b, subunit 4, 49kDa	420					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.G420D(1)		endometrium(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(1)	17	Breast(34;0.0009)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)			AGGGAGAGGGCCTCGAAGTGG	0.577																																					p.G420D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1259A	1						.						9.0	11.0	10.0					1																	149895450		2177	4249	6426	148162074	SO:0001583	missense	10262	exon6			L35013	CCDS72900.1	1q21.2	2013-02-12	2002-08-29		ENSG00000143368	ENSG00000143368		"""RNA binding motif (RRM) containing"""	10771	protein-coding gene	gene with protein product		605593	"""splicing factor 3b, subunit 4, 49kD"""			7958871	Standard	NM_005850		Approved	SAP49, SF3b49, Hsh49	uc001etk.2	Q15427	OTTHUMG00000012208	ENST00000271628.8:c.1259G>A	1.37:g.149895450C>T	ENSP00000271628:p.Gly420Asp	Somatic		Capture	Illumina HiSeq	Phase_I	148162074	NM_005850	Q5SZ63	Missense_Mutation	SNP	ENST00000271628.8	37	CCDS941.1	.	.	.	.	.	.	.	.	.	.	C	15.16	2.751363	0.49257	.	.	ENSG00000143368	ENST00000271628	T	0.22743	1.94	4.07	4.07	0.47477	.	0.279051	0.40385	N	0.001119	T	0.06050	0.0157	N	0.22421	0.69	0.35480	D	0.798094	B	0.31655	0.334	B	0.20384	0.029	T	0.12941	-1.0528	10	0.87932	D	0	.	10.7131	0.45995	0.1908:0.8092:0.0:0.0	.	420	Q15427	SF3B4_HUMAN	D	420	ENSP00000271628:G420D	ENSP00000271628:G420D	G	-	2	0	SF3B4	148162074	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	2.730000	0.47335	2.255000	0.74692	0.655000	0.94253	GGC		0.577	SF3B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033753.1	NM_005850	
TARS2	80222	broad.mit.edu	37	1	150470120	150470120	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:150470120C>T	ENST00000369064.3	+	10	1169	c.1135C>T	c.(1135-1137)Cag>Tag	p.Q379*	TARS2_ENST00000369054.2_Nonsense_Mutation_p.Q249*|TARS2_ENST00000463555.1_3'UTR|TARS2_ENST00000606933.1_Nonsense_Mutation_p.Q297*|TARS2_ENST00000438568.2_3'UTR	NM_025150.3	NP_079426.2	Q9BW92	SYTM_HUMAN	threonyl-tRNA synthetase 2, mitochondrial (putative)	379					gene expression (GO:0010467)|mitochondrial threonyl-tRNA aminoacylation (GO:0070159)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|threonine-tRNA ligase activity (GO:0004829)	p.Q379*(1)		cervix(1)|endometrium(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	35	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.51e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)		L-Threonine(DB00156)	GTTTGCCGTGCAGCCCCCAGG	0.547																																					p.Q379X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1135T	1						.						73.0	64.0	67.0					1																	150470120		2203	4300	6503	148736744	SO:0001587	stop_gained	80222	exon10			BC007824	CCDS952.1, CCDS60251.1, CCDS60252.1	1q21.2	2012-10-26	2007-02-23	2007-02-23	ENSG00000143374	ENSG00000143374	6.1.1.3	"""Aminoacyl tRNA synthetases / Class II"""	30740	protein-coding gene	gene with protein product	"""threonine tRNA ligase 2, mitochondrial"""	612805	"""threonyl-tRNA synthetase-like 1"""	TARSL1			Standard	NM_001271895		Approved	FLJ12528	uc001euq.4	Q9BW92	OTTHUMG00000012809	ENST00000369064.3:c.1135C>T	1.37:g.150470120C>T	ENSP00000358060:p.Gln379*	Somatic		Capture	Illumina HiSeq	Phase_I	148736744	NM_025150	Q53GW7|Q96I50|Q9H9V2	Nonsense_Mutation	SNP	ENST00000369064.3	37	CCDS952.1	.	.	.	.	.	.	.	.	.	.	C	9.848	1.192986	0.21954	.	.	ENSG00000143374	ENST00000369054;ENST00000369064;ENST00000369051;ENST00000369052	.	.	.	5.53	2.49	0.30216	.	0.536597	0.20384	N	0.093388	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.19590	T	0.45	-11.7414	11.2218	0.48860	0.5002:0.4998:0.0:0.0	.	.	.	.	X	249;379;104;104	.	ENSP00000358047:Q104X	Q	+	1	0	TARS2	148736744	0.966000	0.33281	0.990000	0.47175	0.058000	0.15608	1.147000	0.31602	0.370000	0.24538	0.655000	0.94253	CAG		0.547	TARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035847.1	NM_025150	
FLG	2312	broad.mit.edu	37	1	152275899	152275899	+	Silent	SNP	G	G	A	rs149624484	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:152275899G>A	ENST00000368799.1	-	3	11498	c.11463C>T	c.(11461-11463)gaC>gaT	p.D3821D	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3821	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.D3821D(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)			GCCTGGAGCCGTCTCCTGACT	0.582									Ichthyosis				G|||	21	0.00419329	0.0159	0.0	5008	,	,		19925	0.0		0.0	False		,,,				2504	0.0				p.D3821D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C11463T	1						.	G		60,4346	57.4+/-93.9	0,60,2143	331.0	327.0	328.0		11463	-3.6	0.0	1	dbSNP_134	328	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	FLG	NM_002016.1		0,62,6441	AA,AG,GG		0.0233,1.3618,0.4767		3821/4062	152275899	62,12944	2203	4300	6503	150542523	SO:0001819	synonymous_variant	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.11463C>T	1.37:g.152275899G>A		Somatic		Capture	Illumina HiSeq	Phase_I	150542523	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																				0.582	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
LCE1D	353134	broad.mit.edu	37	1	152770545	152770545	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:152770545G>A	ENST00000326233.6	+	2	318	c.275G>A	c.(274-276)tGc>tAc	p.C92Y		NM_178352.2	NP_848129.1	Q5T752	LCE1D_HUMAN	late cornified envelope 1D	92	Cys-rich.				cellular response to calcium ion (GO:0071277)|cognition (GO:0050890)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)		p.C92Y(1)		large_intestine(1)	1	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCTGACTGCTGCAGCCAGCCC	0.667																																					p.C92Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G275A	1						.						30.0	28.0	29.0					1																	152770545		2020	3773	5793	151037169	SO:0001583	missense	353134	exon2				CCDS1025.1	1q21.3	2008-02-05			ENSG00000172155	ENSG00000172155		"""Late cornified envelopes"""	29465	protein-coding gene	gene with protein product		612606				11698679	Standard	NM_178352		Approved	LEP4	uc009wnp.3	Q5T752	OTTHUMG00000012444	ENST00000326233.6:c.275G>A	1.37:g.152770545G>A	ENSP00000316737:p.Cys92Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	151037169	NM_178352		Missense_Mutation	SNP	ENST00000326233.6	37	CCDS1025.1	.	.	.	.	.	.	.	.	.	.	G	10.67	1.416369	0.25552	.	.	ENSG00000172155	ENST00000326233	T	0.05717	3.4	4.52	4.52	0.55395	.	0.000000	0.38548	N	0.001641	T	0.12987	0.0315	M	0.77616	2.38	0.27389	N	0.95521	D	0.64830	0.994	P	0.62184	0.899	T	0.01074	-1.1460	10	0.87932	D	0	.	13.0644	0.59025	0.0:0.0:1.0:0.0	.	92	Q5T752	LCE1D_HUMAN	Y	92	ENSP00000316737:C92Y	ENSP00000316737:C92Y	C	+	2	0	LCE1D	151037169	0.997000	0.39634	0.998000	0.56505	0.880000	0.50808	4.521000	0.60532	2.197000	0.70478	0.555000	0.69702	TGC		0.667	LCE1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034657.2	NM_178352	
GATAD2B	57459	broad.mit.edu	37	1	153800716	153800716	+	Silent	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:153800716C>A	ENST00000368655.4	-	2	351	c.108G>T	c.(106-108)ggG>ggT	p.G36G		NM_020699.2	NP_065750.1	Q8WXI9	P66B_HUMAN	GATA zinc finger domain containing 2B	36					ATP-dependent chromatin remodeling (GO:0043044)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.G36G(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(5)|lung(12)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	38	all_lung(78;1.34e-32)|Lung NSC(65;1.04e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			TGGCCTCATGCCCCTCCATTT	0.493																																					p.G36G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G108T	1						.						172.0	158.0	163.0					1																	153800716		2203	4300	6503	152067340	SO:0001819	synonymous_variant	57459	exon2			AF411836	CCDS1054.1	1q21.3	2013-01-25			ENSG00000143614	ENSG00000143614		"""GATA zinc finger domain containing"""	30778	protein-coding gene	gene with protein product	"""transcription repressor p66 beta component of the MeCP1 complex"""	614998				10574461, 11756549	Standard	NM_020699		Approved	P66beta	uc001fdb.4	Q8WXI9	OTTHUMG00000037162	ENST00000368655.4:c.108G>T	1.37:g.153800716C>A		Somatic		Capture	Illumina HiSeq	Phase_I	152067340	NM_020699	D3DUZ2|Q5VUR2|Q7LG68|Q9ULS0	Silent	SNP	ENST00000368655.4	37	CCDS1054.1																																																																																				0.493	GATAD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090305.1	NM_020699	
UBAP2L	9898	broad.mit.edu	37	1	154224083	154224083	+	Missense_Mutation	SNP	G	G	A	rs375698253		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:154224083G>A	ENST00000361546.2	+	13	1660	c.1618G>A	c.(1618-1620)Gcc>Acc	p.A540T	UBAP2L_ENST00000428931.1_Missense_Mutation_p.A540T|UBAP2L_ENST00000271877.7_Missense_Mutation_p.A551T|AL590431.1_ENST00000517008.1_RNA|UBAP2L_ENST00000343815.6_Missense_Mutation_p.A540T			Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like	540					binding of sperm to zona pellucida (GO:0007339)		poly(A) RNA binding (GO:0044822)			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)			CACCACGAGCGCCTCTTCAAG	0.488																																					p.A540T												.	.	0			c.G1618A	1						.	G	THR/ALA,THR/ALA	0,4406		0,0,2203	83.0	85.0	84.0		1618,1618	2.2	1.0	1		84	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	UBAP2L	NM_014847.3,NM_001127320.1	58,58	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign,benign	540/1088,540/984	154224083	2,13004	2203	4300	6503	152490707	SO:0001583	missense	9898	exon14			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.1618G>A	1.37:g.154224083G>A	ENSP00000355343:p.Ala540Thr	None		Capture	Illumina HiSeq	Phase_I	152490707	NM_014847	B4E0U8|Q5VU75|Q5VU76|Q9BTU3|Q9UGL2|Q9UGL3|Q9UGL4|Q9UGL5	Missense_Mutation	SNP	ENST00000361546.2	37	CCDS1063.1	.	.	.	.	.	.	.	.	.	.	G	13.02	2.111910	0.37242	0.0	2.33E-4	ENSG00000143569	ENST00000343815;ENST00000428931;ENST00000456955;ENST00000433006;ENST00000271877;ENST00000361546	T;T;T;T	0.11495	2.77;2.78;2.77;2.78	5.09	2.17	0.27698	.	0.105637	0.64402	N	0.000003	T	0.00936	0.0031	N	0.01048	-1.04	0.28560	N	0.911185	B;B;B;B;B	0.17667	0.023;0.003;0.0;0.0;0.002	B;B;B;B;B	0.08055	0.003;0.002;0.001;0.001;0.001	T	0.48364	-0.9042	10	0.29301	T	0.29	-0.1644	8.1893	0.31359	0.1443:0.1296:0.7261:0.0	.	454;551;533;540;540	B4DZJ6;F8W726;Q14157-4;Q14157-1;Q14157	.;.;.;.;UBP2L_HUMAN	T	540;540;36;36;551;540	ENSP00000345308:A540T;ENSP00000389445:A540T;ENSP00000271877:A551T;ENSP00000355343:A540T	ENSP00000271877:A551T	A	+	1	0	UBAP2L	152490707	0.998000	0.40836	1.000000	0.80357	0.999000	0.98932	2.766000	0.47629	0.411000	0.25702	0.650000	0.86243	GCC		0.488	UBAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087673.1	NM_014847	
NES	10763	broad.mit.edu	37	1	156639459	156639459	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:156639459C>A	ENST00000368223.3	-	4	4653	c.4521G>T	c.(4519-4521)ttG>ttT	p.L1507F		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	1507	Tail.				brain development (GO:0007420)|cell projection morphogenesis (GO:0048858)|central nervous system development (GO:0007417)|embryonic camera-type eye development (GO:0031076)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of catalytic activity (GO:0043086)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein binding (GO:0032091)|positive regulation of intermediate filament depolymerization (GO:0030844)|positive regulation of neural precursor cell proliferation (GO:2000179)|stem cell proliferation (GO:0072089)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	intermediate filament binding (GO:0019215)|structural molecule activity (GO:0005198)	p.L1507F(1)		central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(30)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(4)	64	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CCTCCCTCTCCAAGGAAACAG	0.607																																					p.L1507F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4521T	1						.						56.0	55.0	55.0					1																	156639459		2203	4300	6503	154906083	SO:0001583	missense	10763	exon4			X65964	CCDS1151.1	1q23	2013-01-16			ENSG00000132688	ENSG00000132688		"""Intermediate filaments type IV"""	7756	protein-coding gene	gene with protein product		600915				1478958, 9104587	Standard	NM_006617		Approved	FLJ21841	uc001fpq.3	P48681	OTTHUMG00000034299	ENST00000368223.3:c.4521G>T	1.37:g.156639459C>A	ENSP00000357206:p.Leu1507Phe	Somatic		Capture	Illumina HiSeq	Phase_I	154906083	NM_006617	O00552|Q3LIF5|Q5SYZ6	Missense_Mutation	SNP	ENST00000368223.3	37	CCDS1151.1	.	.	.	.	.	.	.	.	.	.	C	12.46	1.945778	0.34377	.	.	ENSG00000132688	ENST00000368223	D	0.89415	-2.51	4.59	1.7	0.24286	.	0.368268	0.15575	N	0.255248	D	0.84188	0.5417	M	0.65498	2.005	0.09310	N	0.999997	D	0.60160	0.987	P	0.52672	0.706	T	0.76173	-0.3056	10	0.54805	T	0.06	.	7.3407	0.26635	0.0:0.6421:0.0:0.3579	.	1507	P48681	NEST_HUMAN	F	1507	ENSP00000357206:L1507F	ENSP00000357206:L1507F	L	-	3	2	NES	154906083	0.000000	0.05858	0.300000	0.25030	0.348000	0.29142	-0.087000	0.11215	0.065000	0.16485	0.557000	0.71058	TTG		0.607	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617	
FCRL3	115352	broad.mit.edu	37	1	157666084	157666084	+	Missense_Mutation	SNP	C	C	T	rs115596233	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:157666084C>T	ENST00000368184.3	-	7	1169	c.878G>A	c.(877-879)cGg>cAg	p.R293Q	FCRL3_ENST00000368186.5_Missense_Mutation_p.R293Q|FCRL3_ENST00000473231.1_5'UTR|RP11-367J7.3_ENST00000453692.1_RNA	NM_052939.3	NP_443171.2	Q96P31	FCRL3_HUMAN	Fc receptor-like 3	293	Ig-like C2-type 4.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R293Q(1)		autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(1)|large_intestine(13)|lung(31)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)	69	all_hematologic(112;0.0378)					TCCGGTGGGCCGGATCTCTAG	0.527													C|||	4	0.000798722	0.0	0.0	5008	,	,		17338	0.004		0.0	False		,,,				2504	0.0				p.R293Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G878A	1						.						91.0	87.0	89.0					1																	157666084		2203	4300	6503	155932708	SO:0001583	missense	115352	exon7			AF459027	CCDS1167.1	1q21-q22	2013-01-11			ENSG00000160856	ENSG00000160856		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18506	protein-coding gene	gene with protein product		606510				11493702, 12014205	Standard	XR_241065		Approved	FCRH3, IRTA3, IFGP3, SPAP2a, SPAP2, SPAP2b, SPAP2c, SPAP2d, SPAP2e, CD307c	uc001frb.3	Q96P31	OTTHUMG00000019400	ENST00000368184.3:c.878G>A	1.37:g.157666084C>T	ENSP00000357167:p.Arg293Gln	Somatic		Capture	Illumina HiSeq	Phase_I	155932708	NM_052939	A0N0M4|A8MTH7|D3DVD2|Q5VXZ8|Q8N6S2|Q96LA4|Q96P27|Q96P28|Q96P29|Q96P30	Missense_Mutation	SNP	ENST00000368184.3	37	CCDS1167.1	.	.	.	.	.	.	.	.	.	.	C	3.512	-0.099580	0.07010	.	.	ENSG00000160856	ENST00000368186;ENST00000368184;ENST00000292392	T;T	0.12039	2.72;2.72	5.21	-1.8	0.07907	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.154170	0.06622	N	0.757571	T	0.00724	0.0024	N	0.00339	-1.615	0.09310	N	0.999996	B;B;B	0.18166	0.026;0.008;0.021	B;B;B	0.14578	0.011;0.01;0.004	T	0.47315	-0.9127	10	0.06757	T	0.87	.	9.3535	0.38153	0.0:0.4073:0.0:0.5927	.	293;198;293	Q96P31;D3DVD1;Q96P31-6	FCRL3_HUMAN;.;.	Q	293	ENSP00000357169:R293Q;ENSP00000357167:R293Q	ENSP00000292392:R293Q	R	-	2	0	FCRL3	155932708	0.113000	0.22115	0.463000	0.27130	0.125000	0.20455	-0.529000	0.06186	-0.574000	0.05990	-0.351000	0.07748	CGG		0.527	FCRL3-006	NOVEL	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051419.2	NM_052939	
OR6N1	128372	broad.mit.edu	37	1	158736049	158736049	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:158736049C>T	ENST00000335094.2	-	1	443	c.424G>A	c.(424-426)Gca>Aca	p.A142T		NM_001005185.1	NP_001005185.1	Q8NGY5	OR6N1_HUMAN	olfactory receptor, family 6, subfamily N, member 1	142						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A142T(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(22)|ovary(1)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_hematologic(112;0.0378)					GCAATCTCTGCACAAAGTGTT	0.532																																					p.A142T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G424A	1						.						39.0	45.0	43.0					1																	158736049		2203	4300	6503	157002673	SO:0001583	missense	128372	exon1			BK004199	CCDS30905.1	1q23.1	2012-08-09			ENSG00000197403	ENSG00000197403		"""GPCR / Class A : Olfactory receptors"""	15034	protein-coding gene	gene with protein product							Standard	NM_001005185		Approved		uc010piq.2	Q8NGY5	OTTHUMG00000022774	ENST00000335094.2:c.424G>A	1.37:g.158736049C>T	ENSP00000335535:p.Ala142Thr	Somatic		Capture	Illumina HiSeq	Phase_I	157002673	NM_001005185	Q5VUU8|Q96R35	Missense_Mutation	SNP	ENST00000335094.2	37	CCDS30905.1	.	.	.	.	.	.	.	.	.	.	C	5.551	0.286609	0.10513	.	.	ENSG00000197403	ENST00000335094	T	0.37752	1.18	4.89	0.0811	0.14423	GPCR, rhodopsin-like superfamily (1);	1.058580	0.07437	N	0.896672	T	0.05960	0.0155	N	0.17248	0.465	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.39210	-0.9625	10	0.10902	T	0.67	-1.3383	5.9925	0.19474	0.1265:0.5556:0.0:0.3178	.	142	Q8NGY5	OR6N1_HUMAN	T	142	ENSP00000335535:A142T	ENSP00000335535:A142T	A	-	1	0	OR6N1	157002673	0.000000	0.05858	0.018000	0.16275	0.885000	0.51271	-2.033000	0.01425	0.080000	0.16959	0.655000	0.94253	GCA		0.532	OR6N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059067.1	NM_001005185	
SLAMF9	89886	broad.mit.edu	37	1	159922231	159922231	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:159922231C>T	ENST00000368093.3	-	3	601	c.485G>A	c.(484-486)gGc>gAc	p.G162D	SLAMF9_ENST00000368092.3_Intron|SLAMF9_ENST00000466773.1_5'UTR	NM_033438.3	NP_254273.2	Q96A28	SLAF9_HUMAN	SLAM family member 9	162	Ig-like C2-type.					integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.G162D(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	13	all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			CATATCCATGCCTGCCTTCTC	0.577																																					p.G162D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G485A	1						.						148.0	141.0	144.0					1																	159922231		2203	4300	6503	158188855	SO:0001583	missense	89886	exon3			AY034613	CCDS1191.1, CCDS53392.1	1q23.1	2013-01-11			ENSG00000162723	ENSG00000162723		"""Immunoglobulin superfamily / V-set domain containing"""	18430	protein-coding gene	gene with protein product		608589				11685473	Standard	NM_033438		Approved	CD2F-10, CD84-H1, SF2001	uc001fus.3	Q96A28	OTTHUMG00000024074	ENST00000368093.3:c.485G>A	1.37:g.159922231C>T	ENSP00000357072:p.Gly162Asp	Somatic		Capture	Illumina HiSeq	Phase_I	158188855	NM_033438	Q5JRQ9|Q5JRR0|Q6UWG1	Missense_Mutation	SNP	ENST00000368093.3	37	CCDS1191.1	.	.	.	.	.	.	.	.	.	.	C	15.05	2.718083	0.48622	.	.	ENSG00000162723	ENST00000368093	T	0.62232	0.04	4.89	1.89	0.25635	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.212247	0.32687	N	0.005772	T	0.49795	0.1578	M	0.73319	2.225	0.21915	N	0.999473	P	0.52463	0.953	P	0.51866	0.682	T	0.46857	-0.9161	9	.	.	.	-22.0148	6.2227	0.20691	0.0:0.6543:0.0:0.3457	.	162	Q96A28	SLAF9_HUMAN	D	162	ENSP00000357072:G162D	.	G	-	2	0	SLAMF9	158188855	0.031000	0.19500	0.029000	0.17559	0.638000	0.38207	0.534000	0.23098	0.096000	0.17463	-0.142000	0.14014	GGC		0.577	SLAMF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060630.1	NM_033438	
KCNJ10	3766	broad.mit.edu	37	1	160012105	160012105	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:160012105G>A	ENST00000368089.3	-	2	444	c.218C>T	c.(217-219)gCg>gTg	p.A73V	KCNJ10_ENST00000509700.1_5'Flank	NM_002241.4	NP_002232.2	P78508	KCJ10_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 10	73					adult walking behavior (GO:0007628)|central nervous system myelination (GO:0022010)|inflammatory response (GO:0006954)|L-glutamate uptake involved in synaptic transmission (GO:0051935)|membrane hyperpolarization (GO:0060081)|optic nerve development (GO:0021554)|potassium ion homeostasis (GO:0055075)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of resting membrane potential (GO:0060075)|regulation of sensory perception of pain (GO:0051930)|response to blue light (GO:0009637)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|synaptic transmission (GO:0007268)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP-activated inward rectifier potassium channel activity (GO:0015272)	p.A73V(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)	17	all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)		Yohimbine(DB01392)	TGCAAAGGTCGCAGAGAAGAG	0.572																																					p.A73V	GBM(167;1368 2014 14817 36425 43215)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C218T	1						.						163.0	141.0	148.0					1																	160012105		2203	4300	6503	158278729	SO:0001583	missense	3766	exon2			U52155	CCDS1193.1	1q23.2	2011-07-05			ENSG00000177807	ENSG00000177807		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6256	protein-coding gene	gene with protein product		602208				9367690, 8995301, 16382105	Standard	NM_002241		Approved	Kir4.1, Kir1.2	uc001fuw.2	P78508	OTTHUMG00000024073	ENST00000368089.3:c.218C>T	1.37:g.160012105G>A	ENSP00000357068:p.Ala73Val	Somatic		Capture	Illumina HiSeq	Phase_I	158278729	NM_002241	A3KME7|Q5VUT9|Q8N4I7|Q92808	Missense_Mutation	SNP	ENST00000368089.3	37	CCDS1193.1	.	.	.	.	.	.	.	.	.	.	G	17.93	3.509046	0.64410	.	.	ENSG00000177807	ENST00000368089	D	0.95656	-3.77	5.17	5.17	0.71159	Potassium channel, inwardly rectifying, Kir, conserved region 2 (2);	0.000000	0.85682	D	0.000000	D	0.94981	0.8376	L	0.54323	1.7	0.80722	D	1	D	0.58620	0.983	P	0.54499	0.754	D	0.94198	0.7447	10	0.44086	T	0.13	.	16.2022	0.82088	0.0:0.0:1.0:0.0	.	73	P78508	IRK10_HUMAN	V	73	ENSP00000357068:A73V	ENSP00000357068:A73V	A	-	2	0	KCNJ10	158278729	0.998000	0.40836	0.862000	0.33874	0.988000	0.76386	6.616000	0.74205	2.688000	0.91661	0.591000	0.81541	GCG		0.572	KCNJ10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060629.1	NM_002241	
HSPA6	3310	broad.mit.edu	37	1	161494949	161494949	+	Silent	SNP	G	G	A	rs370008079	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:161494949G>A	ENST00000309758.4	+	1	914	c.501G>A	c.(499-501)gcG>gcA	p.A167A	RP11-25K21.6_ENST00000537821.2_RNA	NM_002155.3	NP_002146.2	P17066	HSP76_HUMAN	heat shock 70kDa protein 6 (HSP70B')	167					ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)	blood microparticle (GO:0072562)|centriole (GO:0005814)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)	p.A167A(1)		endometrium(3)|large_intestine(5)|lung(9)|prostate(2)|skin(2)	21	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			GGGCCATCGCGGGGCTCAACG	0.657													g|||	3	0.000599042	0.0	0.0	5008	,	,		17597	0.0		0.0	False		,,,				2504	0.0031				p.A167A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G501A	1						.						30.0	34.0	33.0					1																	161494949		2203	4298	6501	159761573	SO:0001819	synonymous_variant	3310	exon1				CCDS1231.1	1q23.3	2011-09-02	2002-08-29		ENSG00000173110	ENSG00000173110		"""Heat shock proteins / HSP70"""	5239	protein-coding gene	gene with protein product		140555	"""heat shock 70kD protein 6 (HSP70B')"""			1346391	Standard	NM_002155		Approved		uc001gaq.3	P17066	OTTHUMG00000034461	ENST00000309758.4:c.501G>A	1.37:g.161494949G>A		Somatic		Capture	Illumina HiSeq	Phase_I	159761573	NM_002155	Q1HBA8|Q8IYK7|Q9BT95	Silent	SNP	ENST00000309758.4	37	CCDS1231.1																																																																																				0.657	HSPA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083308.1	NM_002155	
Unknown	0	broad.mit.edu	37	1	16134112	16134112	+	IGR	SNP	G	G	A	rs377310211	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:16134112G>A								FBLIM1 (21023 upstream) : RP11-169K16.9 (26447 downstream)																							CTCCGGATTCGGTAAGCATCT	0.473																																					p.T11T												.	.	0			c.C33T	1						.	G		1,4405	2.1+/-5.4	0,1,2202	78.0	75.0	76.0		33	-3.3	0.0	1		76	0,8600		0,0,4300	no	coding-synonymous	UQCRHL	NM_001089591.1		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		11/92	16134112	1,13005	2203	4300	6503	16006699	SO:0001628	intergenic_variant	440567	exon1																															1.37:g.16134112G>A		Somatic		Capture	Illumina HiSeq	Phase_I	16006699	NM_001089591		Silent	SNP		37																																																																																				0	0.473								
ATF6	22926	broad.mit.edu	37	1	161789443	161789443	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:161789443G>A	ENST00000367942.3	+	8	997	c.930G>A	c.(928-930)caG>caA	p.Q310Q		NM_007348.3	NP_031374.2	P18850	ATF6A_HUMAN	activating transcription factor 6	310	Basic motif.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				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)|positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response (GO:0006990)|protein folding (GO:0006457)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to stress (GO:0006950)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(14)|ovary(3)|skin(1)|stomach(1)	34	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.00953)		Pseudoephedrine(DB00852)	TAAGGAGACAGCAACGTATGA	0.363																																					p.Q310Q												.	.	0			c.G930A	1						.						55.0	57.0	57.0					1																	161789443		2203	4300	6503	160056067	SO:0001819	synonymous_variant	22926	exon8			AB015856	CCDS1235.1	1q22-q23	2013-01-10			ENSG00000118217	ENSG00000118217		"""basic leucine zipper proteins"""	791	protein-coding gene	gene with protein product	"""activating transcription factor 6 alpha"""	605537				9837962, 9271374, 11256944	Standard	NM_007348		Approved	ATF6A	uc001gbs.3	P18850	OTTHUMG00000023961	ENST00000367942.3:c.930G>A	1.37:g.161789443G>A		None		Capture	Illumina HiSeq	Phase_I	160056067	NM_007348	O15139|Q5VW62|Q6IPB5|Q9UEC9	Silent	SNP	ENST00000367942.3	37	CCDS1235.1																																																																																				0.363	ATF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060304.2	NM_007348	
SPEN	23013	broad.mit.edu	37	1	16203109	16203109	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:16203109G>A	ENST00000375759.3	+	3	1021	c.817G>A	c.(817-819)Ggc>Agc	p.G273S	SPEN_ENST00000471538.1_3'UTR	NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	273	Arg-rich.|Ser-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|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)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)	p.G273S(1)		NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		TAGCGGCAGCGGCTCTAGAAG	0.502																																					p.G273S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G817A	1						.						56.0	53.0	54.0					1																	16203109		2200	4296	6496	16075696	SO:0001583	missense	23013	exon3				CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"""RNA binding motif (RRM) containing"""	17575	protein-coding gene	gene with protein product		613484	"""SPEN homolog, transcriptional regulator (Drosophila)"", ""spen homolog, transcriptional regulator (Drosophila)"""			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.817G>A	1.37:g.16203109G>A	ENSP00000364912:p.Gly273Ser	Somatic		Capture	Illumina HiSeq	Phase_I	16075696	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	37	CCDS164.1	.	.	.	.	.	.	.	.	.	.	G	19.59	3.856694	0.71834	.	.	ENSG00000065526	ENST00000375759;ENST00000438066;ENST00000375753	T;T	0.37752	2.91;1.18	5.78	5.78	0.91487	.	.	.	.	.	T	0.46541	0.1398	N	0.24115	0.695	0.80722	D	1	D	0.89917	1.0	D	0.72338	0.977	T	0.19192	-1.0313	9	0.17369	T	0.5	-14.9686	20.0118	0.97458	0.0:0.0:1.0:0.0	.	273	Q96T58	MINT_HUMAN	S	273;232;232	ENSP00000364912:G273S;ENSP00000388021:G232S	ENSP00000364906:G232S	G	+	1	0	SPEN	16075696	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.797000	0.62503	2.744000	0.94065	0.563000	0.77884	GGC		0.502	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001	
ATF6	22926	broad.mit.edu	37	1	161823046	161823046	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:161823046G>A	ENST00000367942.3	+	12	1533	c.1466G>A	c.(1465-1467)aGa>aAa	p.R489K	ATF6_ENST00000476437.1_3'UTR	NM_007348.3	NP_031374.2	P18850	ATF6A_HUMAN	activating transcription factor 6	489	Interaction with THBS4.				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)|positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response (GO:0006990)|protein folding (GO:0006457)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to stress (GO:0006950)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)	p.R489K(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(14)|ovary(3)|skin(1)|stomach(1)	34	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.00953)		Pseudoephedrine(DB00852)	TGGGTTCATAGACATGAAGTA	0.308																																					p.R489K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1466A	1						.						76.0	76.0	76.0					1																	161823046		2203	4300	6503	160089670	SO:0001583	missense	22926	exon12			AB015856	CCDS1235.1	1q22-q23	2013-01-10			ENSG00000118217	ENSG00000118217		"""basic leucine zipper proteins"""	791	protein-coding gene	gene with protein product	"""activating transcription factor 6 alpha"""	605537				9837962, 9271374, 11256944	Standard	NM_007348		Approved	ATF6A	uc001gbs.3	P18850	OTTHUMG00000023961	ENST00000367942.3:c.1466G>A	1.37:g.161823046G>A	ENSP00000356919:p.Arg489Lys	Somatic		Capture	Illumina HiSeq	Phase_I	160089670	NM_007348	O15139|Q5VW62|Q6IPB5|Q9UEC9	Missense_Mutation	SNP	ENST00000367942.3	37	CCDS1235.1	.	.	.	.	.	.	.	.	.	.	G	34	5.307695	0.95629	.	.	ENSG00000118217	ENST00000367942	T	0.18174	2.23	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.28632	0.0709	M	0.71581	2.175	0.47621	D	0.999475	D;D	0.71674	0.998;0.976	P;P	0.56823	0.807;0.492	T	0.01874	-1.1256	9	0.62326	D	0.03	-4.9828	17.4774	0.87662	0.0:0.0:1.0:0.0	.	489;490	P18850;Q59H30	ATF6A_HUMAN;.	K	489	ENSP00000356919:R489K	ENSP00000356919:R489K	R	+	2	0	ATF6	160089670	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.343000	0.79319	2.726000	0.93360	0.655000	0.94253	AGA		0.308	ATF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060304.2	NM_007348	
PBX1	5087	broad.mit.edu	37	1	164790779	164790779	+	Silent	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:164790779T>C	ENST00000420696.2	+	8	1304	c.1116T>C	c.(1114-1116)gaT>gaC	p.D372D	PBX1_ENST00000560641.1_Silent_p.D267D|PBX1_ENST00000401534.1_Missense_Mutation_p.Y335H|PBX1_ENST00000540236.1_Silent_p.D372D|PBX1_ENST00000540246.1_Silent_p.D267D|PBX1_ENST00000367897.1_Missense_Mutation_p.Y335H|PBX1_ENST00000559240.1_Silent_p.D281D	NM_001204961.1|NM_001204963.1|NM_002585.3	NP_001191890.1|NP_001191892.1|NP_002576.1	P40424	PBX1_HUMAN	pre-B-cell leukemia homeobox 1	372					adrenal gland development (GO:0030325)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic hemopoiesis (GO:0035162)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system development (GO:0048706)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|proximal/distal pattern formation (GO:0009954)|regulation of ossification (GO:0030278)|sex differentiation (GO:0007548)|spleen development (GO:0048536)|steroid biosynthetic process (GO:0006694)|thymus development (GO:0048538)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	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 positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.D372D(1)	EWSR1/PBX1(3)	large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	4						TTTAGGTGGATACCCTTCGCC	0.493			T	"""TCF3, EWSR1"""	"""pre B-ALL, myoepithelioma"""																																p.D372D			Dom	yes		1	1q23	5087	pre-B-cell leukemia transcription factor 1		"""L, M"""	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1116C	1						.						144.0	134.0	138.0					1																	164790779		2203	4300	6503	163057403	SO:0001819	synonymous_variant	5087	exon8			M86546	CCDS1246.1, CCDS55654.1	1q23.3	2011-06-20	2007-01-30		ENSG00000185630	ENSG00000185630		"""Homeoboxes / TALE class"""	8632	protein-coding gene	gene with protein product		176310	"""pre-B-cell leukemia transcription factor 1"""				Standard	NM_002585		Approved		uc001gct.3	P40424	OTTHUMG00000034307	ENST00000420696.2:c.1116T>C	1.37:g.164790779T>C		Somatic		Capture	Illumina HiSeq	Phase_I	163057403	NM_002585	B4DSC1|F5H4U9|Q5T488	Missense_Mutation	SNP	ENST00000420696.2	37	CCDS1246.1	.	.	.	.	.	.	.	.	.	.	T	14.34	2.506113	0.44558	.	.	ENSG00000185630	ENST00000367897;ENST00000401534	D;D	0.87103	-2.21;-2.21	5.41	5.41	0.78517	.	.	.	.	.	T	0.67287	0.2877	.	.	.	0.20638	N	0.999871	P	0.38863	0.65	B	0.31751	0.135	T	0.69405	-0.5154	7	0.17369	T	0.5	-14.0142	15.1057	0.72319	0.0:0.0:0.0:1.0	.	335	Q53YC7	.	H	335	ENSP00000356872:Y335H;ENSP00000384856:Y335H	ENSP00000356872:Y335H	Y	+	1	0	PBX1	163057403	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.587000	0.82613	2.044000	0.60594	0.460000	0.39030	TAC		0.493	PBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082864.4	NM_002585	
POU2F1	5451	broad.mit.edu	37	1	167343356	167343356	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:167343356G>A	ENST00000541643.3	+	7	507	c.345G>A	c.(343-345)acG>acA	p.T115T	POU2F1_ENST00000367865.1_3'UTR|POU2F1_ENST00000367866.2_Silent_p.T138T|POU2F1_ENST00000420254.3_Silent_p.T115T|POU2F1_ENST00000452019.1_Silent_p.T115T|POU2F1_ENST00000429375.2_Intron|POU2F1_ENST00000367862.5_Silent_p.T127T			P14859	PO2F1_HUMAN	POU class 2 homeobox 1	115					gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T115T(1)		breast(2)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	30						TTACTTTGACGCCTGCCCAGC	0.502																																					p.T138T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G414A	1						.						64.0	58.0	60.0					1																	167343356		2203	4300	6503	165609980	SO:0001819	synonymous_variant	5451	exon6			BC001664	CCDS1259.1, CCDS1259.2, CCDS55655.1, CCDS55656.1	1q24.2	2011-06-20	2007-07-13		ENSG00000143190	ENSG00000143190		"""Homeoboxes / POU class"""	9212	protein-coding gene	gene with protein product		164175	"""POU domain class 2, transcription factor 1"""	OTF1		1887216	Standard	NM_002697		Approved	OCT1	uc001gee.3	P14859	OTTHUMG00000034436	ENST00000541643.3:c.345G>A	1.37:g.167343356G>A		Somatic		Capture	Illumina HiSeq	Phase_I	165609980	NM_002697	B1AL91|B1AL93|B4E029|J3KP77|Q5TBT7|Q6PK46|Q8NEU9|Q9BPV1	Silent	SNP	ENST00000541643.3	37																																																																																					0.502	POU2F1-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_002697	
PRRC2C	23215	broad.mit.edu	37	1	171501776	171501776	+	Missense_Mutation	SNP	C	C	T	rs374981644		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:171501776C>T	ENST00000338920.4	+	12	1780	c.1543C>T	c.(1543-1545)Cgt>Tgt	p.R515C	PRRC2C_ENST00000392078.3_Missense_Mutation_p.R517C|PRRC2C_ENST00000476522.1_3'UTR|PRRC2C_ENST00000426496.2_Missense_Mutation_p.R515C|PRRC2C_ENST00000367742.3_Missense_Mutation_p.R517C	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	515	Glu-rich.				hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.R517C(1)									AGAACGGGAGCGTGAGAAAGA	0.463													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19948	0.0		0.0	False		,,,				2504	0.0				p.R515C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1543T	1						.	C	CYS/ARG	0,4276		0,0,2138	36.0	35.0	35.0		1543	4.6	1.0	1		35	2,8300		0,2,4149	no	missense	PRRC2C	NM_015172.3	180	0,2,6287	TT,TC,CC		0.0241,0.0,0.0159	probably-damaging	515/2818	171501776	2,12576	2138	4151	6289	169768400	SO:0001583	missense	23215	exon12			AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"""BAT2 domain containing 1"", ""HLA-B associated transcript 2-like 2"""	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.1543C>T	1.37:g.171501776C>T	ENSP00000343629:p.Arg515Cys	Somatic		Capture	Illumina HiSeq	Phase_I	169768400	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Missense_Mutation	SNP	ENST00000338920.4	37	CCDS1296.2	.	.	.	.	.	.	.	.	.	.	C	6.021	0.372279	0.11409	0.0	2.41E-4	ENSG00000117523	ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920;ENST00000392080;ENST00000483654	T;T;T;T	0.08370	3.1;3.1;3.1;3.1	5.55	4.61	0.57282	.	0.179120	0.27043	N	0.021219	T	0.11324	0.0276	L	0.57536	1.79	0.09310	N	0.999995	D;D	0.71674	0.998;0.997	P;P	0.56700	0.804;0.549	T	0.01074	-1.1460	10	0.66056	D	0.02	.	14.4648	0.67477	0.2552:0.7448:0.0:0.0	.	515;517	Q9Y520-4;E7EPN9	.;.	C	517;515;515;517;515;271;273	ENSP00000375928:R517C;ENSP00000410219:R515C;ENSP00000356716:R517C;ENSP00000343629:R515C	ENSP00000343629:R515C	R	+	1	0	PRRC2C	169768400	0.833000	0.29383	0.992000	0.48379	0.027000	0.11550	1.524000	0.35942	2.602000	0.87976	0.650000	0.86243	CGT		0.463	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172	
TNN	63923	broad.mit.edu	37	1	175046559	175046559	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:175046559G>A	ENST00000239462.4	+	2	118	c.5G>A	c.(4-6)aGt>aAt	p.S2N		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	2					axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)		p.S2N(1)		NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		CCAAGGATGAGTCTCCAGGAG	0.572																																					p.S2N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5A	1						.						97.0	105.0	103.0					1																	175046559		2200	4295	6495	173313182	SO:0001583	missense	63923	exon2			AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.5G>A	1.37:g.175046559G>A	ENSP00000239462:p.Ser2Asn	Somatic		Capture	Illumina HiSeq	Phase_I	173313182	NM_022093	B9EGP3|Q5R360	Missense_Mutation	SNP	ENST00000239462.4	37	CCDS30943.1	.	.	.	.	.	.	.	.	.	.	G	9.478	1.097417	0.20552	.	.	ENSG00000120332	ENST00000239462;ENST00000539081	T	0.25749	1.78	5.07	5.07	0.68467	.	0.518661	0.21847	N	0.068228	T	0.13243	0.0321	N	0.08118	0	0.21064	N	0.999791	B;B	0.28128	0.201;0.189	B;B	0.24541	0.039;0.054	T	0.13791	-1.0496	10	0.59425	D	0.04	.	9.9988	0.41916	0.0933:0.0:0.9067:0.0	.	2;2	B3KXB6;Q9UQP3	.;TENN_HUMAN	N	2	ENSP00000239462:S2N	ENSP00000239462:S2N	S	+	2	0	TNN	173313182	1.000000	0.71417	0.943000	0.38184	0.021000	0.10359	3.488000	0.53229	2.513000	0.84729	0.655000	0.94253	AGT		0.572	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527	
BRINP2	57795	broad.mit.edu	37	1	177245363	177245363	+	Missense_Mutation	SNP	C	C	T	rs368347121		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:177245363C>T	ENST00000361539.4	+	6	1117	c.805C>T	c.(805-807)Cgt>Tgt	p.R269C	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	269	MACPF.				cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	extracellular region (GO:0005576)		p.R269C(1)									TGAGTATCTGCGTGAGCGCTT	0.562																																					p.R269C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C805T	1						.	C	CYS/ARG	0,4406		0,0,2203	66.0	61.0	63.0		805	5.1	1.0	1		63	1,8599	1.2+/-3.3	0,1,4299	no	missense	FAM5B	NM_021165.2	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	269/784	177245363	1,13005	2203	4300	6503	175511986	SO:0001583	missense	57795	exon6				CCDS1320.1	1q24	2013-08-06	2013-08-06	2013-07-31	ENSG00000198797	ENSG00000198797			13746	protein-coding gene	gene with protein product			"""family with sequence similarity 5, member B"""	FAM5B		15193423	Standard	NM_021165		Approved	DBCCR1L2	uc001glf.3	Q9C0B6	OTTHUMG00000034953	ENST00000361539.4:c.805C>T	1.37:g.177245363C>T	ENSP00000354481:p.Arg269Cys	Somatic		Capture	Illumina HiSeq	Phase_I	175511986	NM_021165	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Missense_Mutation	SNP	ENST00000361539.4	37	CCDS1320.1	.	.	.	.	.	.	.	.	.	.	C	19.40	3.820383	0.71028	0.0	1.16E-4	ENSG00000198797	ENST00000536589;ENST00000361539	T	0.18810	2.19	6.07	5.08	0.68730	Membrane attack complex component/perforin (MACPF) domain (1);	0.052850	0.85682	D	0.000000	T	0.47135	0.1429	M	0.69823	2.125	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;P;P	0.74023	0.982;0.899;0.719	T	0.42865	-0.9426	10	0.87932	D	0	-12.1511	17.7481	0.88426	0.1596:0.8404:0.0:0.0	.	19;164;269	F5H8E0;Q9C0B6-2;Q9C0B6	.;.;FAM5B_HUMAN	C	19;269	ENSP00000354481:R269C	ENSP00000354481:R269C	R	+	1	0	FAM5B	175511986	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.551000	0.45820	2.884000	0.98904	0.655000	0.94253	CGT		0.562	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165	
HMCN1	83872	broad.mit.edu	37	1	186113380	186113380	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:186113380C>A	ENST00000271588.4	+	90	14229	c.14000C>A	c.(13999-14001)gCa>gAa	p.A4667E	HMCN1_ENST00000367492.2_Missense_Mutation_p.A4667E	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	4667	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				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.A4667E(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						CAGACAAGAGCAAGACTTTGT	0.478																																					p.A4667E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C14000A	1						.						156.0	157.0	157.0					1																	186113380		2203	4300	6503	184380003	SO:0001583	missense	83872	exon90			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.14000C>A	1.37:g.186113380C>A	ENSP00000271588:p.Ala4667Glu	Somatic		Capture	Illumina HiSeq	Phase_I	184380003	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	C	7.115	0.576797	0.13686	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.51574	0.7;0.7	5.42	0.682	0.17992	.	0.901972	0.09791	N	0.755419	T	0.16300	0.0392	N	0.00980	-1.08	0.09310	N	1	B	0.27316	0.175	B	0.23852	0.049	T	0.19549	-1.0302	10	0.30854	T	0.27	.	5.1327	0.14919	0.0:0.4378:0.1468:0.4154	.	4667	Q96RW7	HMCN1_HUMAN	E	4667	ENSP00000271588:A4667E;ENSP00000356462:A4667E	ENSP00000271588:A4667E	A	+	2	0	HMCN1	184380003	0.001000	0.12720	0.047000	0.18901	0.026000	0.11368	0.834000	0.27518	0.319000	0.23209	0.650000	0.86243	GCA		0.478	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
HMCN1	83872	broad.mit.edu	37	1	186151419	186151419	+	Splice_Site	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:186151419G>T	ENST00000271588.4	+	105	16643	c.16414G>T	c.(16414-16416)Gat>Tat	p.D5472Y	HMCN1_ENST00000367492.2_Splice_Site_p.D5355Y	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	5472					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.D5472Y(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						GACATGCCAAGGTGAGAAAAC	0.413																																					p.D5472Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G16414T	1						.						101.0	94.0	96.0					1																	186151419		2203	4300	6503	184418042	SO:0001630	splice_region_variant	83872	exon105			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.16414+1G>T	1.37:g.186151419G>T		Somatic		Capture	Illumina HiSeq	Phase_I	184418042	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.168564	0.78339	.	.	ENSG00000143341	ENST00000271588;ENST00000367492;ENST00000414277	D;D;D	0.99868	-7.32;-7.32;-7.32	5.42	5.42	0.78866	EGF-like calcium-binding, conserved site (1);Growth factor, receptor (1);	0.000000	0.85682	D	0.000000	D	0.99912	0.9958	H	0.96208	3.785	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96228	0.9166	10	0.87932	D	0	.	19.2127	0.93763	0.0:0.0:1.0:0.0	.	5472	Q96RW7	HMCN1_HUMAN	Y	5472;5355;147	ENSP00000271588:D5472Y;ENSP00000356462:D5355Y;ENSP00000406205:D147Y	ENSP00000271588:D5472Y	D	+	1	0	HMCN1	184418042	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	9.562000	0.98145	2.528000	0.85240	0.563000	0.77884	GAT		0.413	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	Missense_Mutation
TPR	7175	broad.mit.edu	37	1	186306274	186306274	+	Silent	SNP	C	C	T	rs150466145	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:186306274C>T	ENST00000367478.4	-	32	4673	c.4377G>A	c.(4375-4377)tcG>tcA	p.S1459S		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	1459					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.S1460S(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)		AGGACTGAGCCGATGTCTCCA	0.383			T	NTRK1	papillary thyroid								C|||	5	0.000998403	0.0038	0.0	5008	,	,		19023	0.0		0.0	False		,,,				2504	0.0				p.S1459S			Dom	yes		1	1q25	7175	translocated promoter region		E	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G4377A	1						.	C		3,3829		0,3,1913	121.0	105.0	110.0		4377	-5.4	0.7	1	dbSNP_134	110	1,8247		0,1,4123	no	coding-synonymous	TPR	NM_003292.2		0,4,6036	TT,TC,CC		0.0121,0.0783,0.0331		1459/2364	186306274	4,12076	1916	4124	6040	184572897	SO:0001819	synonymous_variant	7175	exon32			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.4377G>A	1.37:g.186306274C>T		Somatic		Capture	Illumina HiSeq	Phase_I	184572897	NM_003292	Q15655|Q5SWY0|Q99968	Silent	SNP	ENST00000367478.4	37	CCDS41446.1																																																																																				0.383	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292	
CDC73	79577	broad.mit.edu	37	1	193094336	193094336	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:193094336C>T	ENST00000367435.3	+	2	410	c.226C>T	c.(226-228)Cga>Tga	p.R76*		NM_024529.4	NP_078805.3	Q6P1J9	CDC73_HUMAN	cell division cycle 73	76					cell cycle (GO:0007049)|cellular response to lipopolysaccharide (GO:0071222)|endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|mRNA polyadenylation (GO:0006378)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|protein destabilization (GO:0031648)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|nucleus (GO:0005634)	RNA polymerase II core binding (GO:0000993)	p.R76*(2)		breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(14)|ovary(1)|pancreas(1)|parathyroid(51)|skin(1)|upper_aerodigestive_tract(1)	87						TGTTTATGTCCGACGTGCAGC	0.383																																					p.R76X												CDC73,parathyroid,NS,Substitution - Nonsense,0 	.	2	Substitution - Nonsense(2)	large_intestine(1)|parathyroid(1)	c.C226T	1						.						143.0	142.0	142.0					1																	193094336		2203	4300	6503	191360959	SO:0001587	stop_gained	79577	exon2			AF312865	CCDS1382.1	1q25	2014-09-17	2013-01-17	2005-07-20	ENSG00000134371	ENSG00000134371			16783	protein-coding gene	gene with protein product	"""Paf1/RNA polymerase II complex component"""	607393	"""chromosome 1 open reading frame 28"", ""hyperparathyroidism 2 (with jaw tumor)"", ""cell division cycle 73, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)"", ""hyperparathyroidism 1"""	C1orf28, HRPT2, HRPT1		11318611, 15632063, 18755853	Standard	NM_024529		Approved	parafibromin, FIHP	uc001gtb.3	Q6P1J9	OTTHUMG00000035676	ENST00000367435.3:c.226C>T	1.37:g.193094336C>T	ENSP00000356405:p.Arg76*	Somatic		Capture	Illumina HiSeq	Phase_I	191360959	NM_024529	A6NLZ8|B2RBR2|Q6PK51|Q96A07|Q9H245|Q9H5L7	Nonsense_Mutation	SNP	ENST00000367435.3	37	CCDS1382.1	.	.	.	.	.	.	.	.	.	.	C	38	6.907276	0.97924	.	.	ENSG00000134371	ENST00000367435;ENST00000445394	.	.	.	5.88	4.95	0.65309	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.888	16.2736	0.82632	0.1335:0.8665:0.0:0.0	.	.	.	.	X	76	.	ENSP00000356405:R76X	R	+	1	2	CDC73	191360959	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	4.722000	0.61958	1.439000	0.47511	0.655000	0.94253	CGA		0.383	CDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086696.2	NM_024529	
CDC73	79577	broad.mit.edu	37	1	193107258	193107258	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:193107258G>A	ENST00000367435.3	+	6	651	c.467G>A	c.(466-468)cGt>cAt	p.R156H	MIR1278_ENST00000408753.1_RNA	NM_024529.4	NP_078805.3	Q6P1J9	CDC73_HUMAN	cell division cycle 73	156					cell cycle (GO:0007049)|cellular response to lipopolysaccharide (GO:0071222)|endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|mRNA polyadenylation (GO:0006378)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|protein destabilization (GO:0031648)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|nucleus (GO:0005634)	RNA polymerase II core binding (GO:0000993)	p.R156H(1)		breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(14)|ovary(1)|pancreas(1)|parathyroid(51)|skin(1)|upper_aerodigestive_tract(1)	87						TTGGCTGCCCGTTTGGAGGGT	0.343																																					p.R156H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G467A	1						.						141.0	143.0	142.0					1																	193107258		2203	4300	6503	191373881	SO:0001583	missense	79577	exon6			AF312865	CCDS1382.1	1q25	2014-09-17	2013-01-17	2005-07-20	ENSG00000134371	ENSG00000134371			16783	protein-coding gene	gene with protein product	"""Paf1/RNA polymerase II complex component"""	607393	"""chromosome 1 open reading frame 28"", ""hyperparathyroidism 2 (with jaw tumor)"", ""cell division cycle 73, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)"", ""hyperparathyroidism 1"""	C1orf28, HRPT2, HRPT1		11318611, 15632063, 18755853	Standard	NM_024529		Approved	parafibromin, FIHP	uc001gtb.3	Q6P1J9	OTTHUMG00000035676	ENST00000367435.3:c.467G>A	1.37:g.193107258G>A	ENSP00000356405:p.Arg156His	Somatic		Capture	Illumina HiSeq	Phase_I	191373881	NM_024529	A6NLZ8|B2RBR2|Q6PK51|Q96A07|Q9H245|Q9H5L7	Missense_Mutation	SNP	ENST00000367435.3	37	CCDS1382.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.557199	0.86231	.	.	ENSG00000134371	ENST00000367435;ENST00000445394	D	0.85629	-2.01	5.9	4.99	0.66335	.	0.000000	0.85682	D	0.000000	D	0.91680	0.7370	M	0.76838	2.35	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	D	0.91415	0.5154	10	0.40728	T	0.16	-1.5716	15.3032	0.73972	0.0671:0.0:0.9329:0.0	.	156	Q6P1J9	CDC73_HUMAN	H	156	ENSP00000356405:R156H	ENSP00000356405:R156H	R	+	2	0	CDC73	191373881	1.000000	0.71417	0.982000	0.44146	0.949000	0.60115	9.426000	0.97469	1.520000	0.48965	-0.156000	0.13503	CGT		0.343	CDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086696.2	NM_024529	
F13B	2165	broad.mit.edu	37	1	197024863	197024863	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:197024863A>G	ENST00000367412.1	-	8	1379	c.1336T>C	c.(1336-1338)Tcc>Ccc	p.S446P		NM_001994.2	NP_001985.2	P05160	F13B_HUMAN	coagulation factor XIII, B polypeptide	446	Sushi 7. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation (GO:0007596)	extracellular region (GO:0005576)		p.S446P(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(5)|liver(1)|lung(40)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	66						ACAGGTGGGGATGACCATTTT	0.373																																					p.S446P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1336C	1						.						138.0	134.0	135.0					1																	197024863		2203	4300	6503	195291486	SO:0001583	missense	2165	exon8			M14057	CCDS1388.1	1q31-q32.1	2012-10-02			ENSG00000143278	ENSG00000143278			3534	protein-coding gene	gene with protein product		134580				2339067, 2271707	Standard	NM_001994		Approved	FXIIIB	uc001gtt.1	P05160	OTTHUMG00000036519	ENST00000367412.1:c.1336T>C	1.37:g.197024863A>G	ENSP00000356382:p.Ser446Pro	Somatic		Capture	Illumina HiSeq	Phase_I	195291486	NM_001994	A8K3E5|Q5VYL5	Missense_Mutation	SNP	ENST00000367412.1	37	CCDS1388.1	.	.	.	.	.	.	.	.	.	.	A	12.80	2.047634	0.36085	.	.	ENSG00000143278	ENST00000367412	T	0.63913	-0.07	5.84	-9.13	0.00704	Complement control module (2);Sushi/SCR/CCP (3);	0.267662	0.20107	N	0.099102	T	0.31513	0.0799	N	0.20357	0.565	0.09310	N	1	B	0.17852	0.024	B	0.22152	0.038	T	0.08806	-1.0704	10	0.28530	T	0.3	.	3.2055	0.06665	0.138:0.1864:0.4268:0.2487	.	446	P05160	F13B_HUMAN	P	446	ENSP00000356382:S446P	ENSP00000356382:S446P	S	-	1	0	F13B	195291486	0.000000	0.05858	0.233000	0.24025	0.968000	0.65278	-1.856000	0.01662	-1.224000	0.02581	-0.346000	0.07831	TCC		0.373	F13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088821.2	NM_001994	
CRB1	23418	broad.mit.edu	37	1	197390428	197390428	+	Silent	SNP	C	C	T	rs35193230	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:197390428C>T	ENST00000367400.3	+	6	1605	c.1470C>T	c.(1468-1470)ggC>ggT	p.G490G	CRB1_ENST00000476483.1_3'UTR|CRB1_ENST00000544212.1_5'UTR|CRB1_ENST00000543483.1_Silent_p.G189G|CRB1_ENST00000367399.2_Silent_p.G378G|CRB1_ENST00000535699.1_Silent_p.G421G|CRB1_ENST00000538660.1_Silent_p.G490G|CRB1_ENST00000367397.1_5'UTR	NM_201253.2	NP_957705.1	P82279	CRUM1_HUMAN	crumbs family member 1, photoreceptor morphogenesis associated	490	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|plasma membrane organization (GO:0007009)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.G490G(3)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(13)|kidney(4)|large_intestine(21)|lung(58)|ovary(7)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	132						CATTTGAGGGCGATGGCTTCC	0.517													C|||	12	0.00239617	0.0076	0.0014	5008	,	,		19803	0.0		0.0	False		,,,				2504	0.001				p.G490G												.	.	3	Substitution - coding silent(3)	large_intestine(3)	c.C1470T	1						.	C	,	35,4371	40.8+/-73.8	0,35,2168	104.0	93.0	97.0		1134,1470	-0.9	0.0	1	dbSNP_126	97	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	CRB1	NM_001193640.1,NM_201253.2	,	0,37,6466	TT,TC,CC		0.0233,0.7944,0.2845	,	378/1295,490/1407	197390428	37,12969	2203	4300	6503	195657051	SO:0001819	synonymous_variant	23418	exon6				CCDS1390.1, CCDS53454.1, CCDS58052.1, CCDS58053.1	1q31-q32.1	2014-02-06	2014-02-06		ENSG00000134376	ENSG00000134376			2343	protein-coding gene	gene with protein product		604210	"""crumbs (Drosophila) homolog 1"", ""crumbs homolog 1 (Drosophila)"""	RP12		10373321, 10508521	Standard	NM_201253		Approved	LCA8	uc001gtz.3	P82279	OTTHUMG00000035663	ENST00000367400.3:c.1470C>T	1.37:g.197390428C>T		Somatic		Capture	Illumina HiSeq	Phase_I	195657051	NM_201253	A2A308|B7Z5T2|B9EG71|Q5K3A6|Q5TC28|Q5VUT1|Q6N027|Q8WWY0|Q8WWY1	Silent	SNP	ENST00000367400.3	37	CCDS1390.1																																																																																				0.517	CRB1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086565.2	NM_201253	
LHX9	56956	broad.mit.edu	37	1	197881673	197881673	+	Silent	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:197881673T>C	ENST00000367390.3	+	1	39	c.12T>C	c.(10-12)ggT>ggC	p.G4G	LHX9_ENST00000606127.1_3'UTR|LHX9_ENST00000367391.1_Silent_p.G4G	NM_001014434.1	NP_001014434.1	Q9NQ69	LHX9_HUMAN	LIM homeobox 9	0					cell proliferation (GO:0008283)|female gonad development (GO:0008585)|gonad morphogenesis (GO:0035262)|male gonad development (GO:0008584)|motor neuron axon guidance (GO:0008045)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.G4G(1)		endometrium(8)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(2)|skin(1)|stomach(1)	35						TGCTGAACGGTACCACTCTAG	0.557																																					p.G4G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T12C	1						.						265.0	238.0	247.0					1																	197881673		2203	4300	6503	196148296	SO:0001819	synonymous_variant	56956	exon1			AJ277915	CCDS1393.1, CCDS30962.1	1q31.1	2011-06-20			ENSG00000143355	ENSG00000143355		"""Homeoboxes / LIM class"""	14222	protein-coding gene	gene with protein product		606066					Standard	NM_020204		Approved		uc001guk.1	Q9NQ69	OTTHUMG00000035656	ENST00000367390.3:c.12T>C	1.37:g.197881673T>C		Somatic		Capture	Illumina HiSeq	Phase_I	196148296	NM_001014434	Q5VUE2|Q5VUE3|Q5VUE6|Q86UH2|Q9BYU6|Q9NQ70	Silent	SNP	ENST00000367390.3	37	CCDS30962.1																																																																																				0.557	LHX9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000086544.1	NM_020204	
KDM5B	10765	broad.mit.edu	37	1	202702824	202702824	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:202702824G>A	ENST00000367265.3	-	23	4778	c.3614C>T	c.(3613-3615)gCg>gTg	p.A1205V	KDM5B_ENST00000367264.2_Missense_Mutation_p.A1241V	NM_006618.3	NP_006609.3	Q9UGL1	KDM5B_HUMAN	lysine (K)-specific demethylase 5B	1205					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.A1205V(1)		breast(2)|ovary(2)|skin(1)|urinary_tract(1)	6						ACTGGGTACCGCCACACAACT	0.512																																					p.A1205V												.	.	1	Substitution - Missense(1)	lung(1)	c.C3614T	1						.						55.0	56.0	56.0					1																	202702824		2203	4300	6503	200969447	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.3614C>T	1.37:g.202702824G>A	ENSP00000356234:p.Ala1205Val	None		Capture	Illumina HiSeq	Phase_I	200969447	NM_006618	O95811|Q15752|Q9Y3Q5	Missense_Mutation	SNP	ENST00000367265.3	37	CCDS30974.1	.	.	.	.	.	.	.	.	.	.	G	16.25	3.070931	0.55646	.	.	ENSG00000117139	ENST00000367265;ENST00000538292;ENST00000367264;ENST00000235790	D;D;D	0.84730	-1.89;-1.89;-1.89	6.09	4.24	0.50183	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);	0.322125	0.37219	N	0.002192	T	0.78811	0.4342	L	0.50333	1.59	0.28817	N	0.897909	P;B	0.40360	0.714;0.139	B;B	0.31101	0.124;0.046	T	0.74368	-0.3688	10	0.66056	D	0.02	-7.7423	13.0547	0.58973	0.1298:0.0:0.8702:0.0	.	1241;1205	Q9UGL1-2;Q9UGL1	.;KDM5B_HUMAN	V	1205;1047;1241;1047	ENSP00000356234:A1205V;ENSP00000356233:A1241V;ENSP00000235790:A1047V	ENSP00000235790:A1047V	A	-	2	0	KDM5B	200969447	0.983000	0.35010	0.739000	0.30968	0.799000	0.45148	2.542000	0.45744	0.919000	0.36945	-0.148000	0.13756	GCG		0.512	KDM5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099184.2	NM_006618	
ADORA1	134	broad.mit.edu	37	1	203134419	203134419	+	Silent	SNP	G	G	A	rs143331026		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:203134419G>A	ENST00000367236.4	+	3	1293	c.372G>A	c.(370-372)gcG>gcA	p.A124A	ADORA1_ENST00000337894.4_Silent_p.A124A|ADORA1_ENST00000472535.1_3'UTR|ADORA1_ENST00000367235.1_3'UTR|ADORA1_ENST00000309502.3_Silent_p.A124A	NM_001048230.1	NP_001041695.1	P30542	AA1R_HUMAN	adenosine A1 receptor	124					activation of MAPKK activity (GO:0000186)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|apoptotic signaling pathway (GO:0097190)|cell-cell signaling (GO:0007267)|cognition (GO:0050890)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|inflammatory response (GO:0006954)|lipid catabolic process (GO:0016042)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood pressure (GO:0045776)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of cell proliferation (GO:0008285)|negative regulation of circadian sleep/wake cycle, non-REM sleep (GO:0042323)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of heart contraction (GO:0045822)|negative regulation of hormone secretion (GO:0046888)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of mucus secretion (GO:0070256)|negative regulation of neurotrophin production (GO:0032900)|negative regulation of renal sodium excretion (GO:0035814)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|negative regulation of vasodilation (GO:0045908)|nervous system development (GO:0007399)|phagocytosis (GO:0006909)|positive regulation of blood pressure (GO:0045777)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of nucleoside transport (GO:0032244)|positive regulation of peptide secretion (GO:0002793)|positive regulation of potassium ion transport (GO:0043268)|positive regulation of protein dephosphorylation (GO:0035307)|protein targeting to membrane (GO:0006612)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of glomerular filtration (GO:0003093)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|relaxation of vascular smooth muscle (GO:0060087)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|temperature homeostasis (GO:0001659)	asymmetric synapse (GO:0032279)|axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	G-protein coupled adenosine receptor activity (GO:0001609)|phospholipase C activity (GO:0004629)|purine nucleoside binding (GO:0001883)	p.A124A(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(9)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	25					Adenosine(DB00640)|Aminophylline(DB01223)|Caffeine(DB00201)|Defibrotide(DB04932)|Dyphylline(DB00651)|Enprofylline(DB00824)|Gabapentin(DB00996)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Theobromine(DB01412)|Theophylline(DB00277)	CCCGGAGGGCGGCGGTGGCCA	0.657																																					p.A124A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G372A	1						.	G	,	3,4403	6.2+/-15.9	0,3,2200	37.0	44.0	42.0		372,372	-9.5	0.2	1	dbSNP_134	42	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ADORA1	NM_000674.2,NM_001048230.1	,	0,3,6500	AA,AG,GG		0.0,0.0681,0.0231	,	124/327,124/327	203134419	3,13003	2203	4300	6503	201401042	SO:0001819	synonymous_variant	134	exon3			BC026340	CCDS1434.1	1q32.1	2012-08-08			ENSG00000163485	ENSG00000163485		"""GPCR / Class A : Adenosine receptors"""	262	protein-coding gene	gene with protein product		102775				1662665, 2541503	Standard	NM_001048230		Approved	RDC7	uc001gzf.1	P30542	OTTHUMG00000042125	ENST00000367236.4:c.372G>A	1.37:g.203134419G>A		Somatic		Capture	Illumina HiSeq	Phase_I	201401042	NM_001048230	A6NFY5|A6NGP4|A8K1L3|B3KXQ4|D2CGD0|Q6FHK3|Q8TAM8	Missense_Mutation	SNP	ENST00000367236.4	37	CCDS1434.1																																																																																				0.657	ADORA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100273.1	NM_000674	
CHI3L1	1116	broad.mit.edu	37	1	203151978	203151978	+	Silent	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:203151978T>C	ENST00000255409.3	-	6	593	c.468A>G	c.(466-468)gaA>gaG	p.E156E		NM_001276.2	NP_001267.2	P36222	CH3L1_HUMAN	chitinase 3-like 1 (cartilage glycoprotein-39)	156					activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cellular response to tumor necrosis factor (GO:0071356)|chitin catabolic process (GO:0006032)|inflammatory response (GO:0006954)|interleukin-8 secretion (GO:0072606)|lung development (GO:0030324)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase B signaling (GO:0051897)|response to interleukin-1 (GO:0070555)|response to interleukin-6 (GO:0070741)|response to mechanical stimulus (GO:0009612)|response to tumor necrosis factor (GO:0034612)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|extracellular matrix structural constituent (GO:0005201)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)	p.E156E(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|skin(1)	18						CGGCCTTCATTTCCTAGATGG	0.547																																					p.E156E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A468G	1						.						55.0	50.0	52.0					1																	203151978		2203	4300	6503	201418601	SO:0001819	synonymous_variant	1116	exon6			BC008568	CCDS1435.1	1q32.1	2008-02-05			ENSG00000133048	ENSG00000133048			1932	protein-coding gene	gene with protein product		601525				8245017, 9244440	Standard	NM_001276		Approved	GP39, YKL40	uc001gzi.2	P36222	OTTHUMG00000042122	ENST00000255409.3:c.468A>G	1.37:g.203151978T>C		Somatic		Capture	Illumina HiSeq	Phase_I	201418601	NM_001276	B2R7B0|P30923|Q8IVA4|Q96HI7	Silent	SNP	ENST00000255409.3	37	CCDS1435.1																																																																																				0.547	CHI3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100265.1	NM_001276	
KIF17	57576	broad.mit.edu	37	1	20991165	20991165	+	Missense_Mutation	SNP	C	C	T	rs574381737		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:20991165C>T	ENST00000247986.2	-	15	3312	c.3002G>A	c.(3001-3003)cGg>cAg	p.R1001Q	KIF17_ENST00000490034.1_5'UTR|KIF17_ENST00000400463.3_Missense_Mutation_p.R1000Q|KIF17_ENST00000375044.1_Missense_Mutation_p.R901Q			Q9P2E2	KIF17_HUMAN	kinesin family member 17	1001					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.R1001Q(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)		GCGGAAGGGCCGGGGCTGGGG	0.597																																					p.R1000Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2999A	1						.						76.0	83.0	80.0					1																	20991165		2203	4300	6503	20863752	SO:0001583	missense	57576	exon15			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.3002G>A	1.37:g.20991165C>T	ENSP00000247986:p.Arg1001Gln	Somatic		Capture	Illumina HiSeq	Phase_I	20863752	NM_001122819	A2A3Q7|A2A3Q8|O95077|Q53YS6|Q5VWA9|Q6GSA8|Q8N411	Missense_Mutation	SNP	ENST00000247986.2	37	CCDS213.1	.	.	.	.	.	.	.	.	.	.	C	33	5.276556	0.95459	.	.	ENSG00000117245	ENST00000375044;ENST00000400463;ENST00000247986;ENST00000321188	D;D;D	0.84800	-1.9;-1.62;-1.6	5.21	5.21	0.72293	.	0.000000	0.30185	U	0.010210	D	0.90800	0.7111	L	0.59436	1.845	0.34801	D	0.736713	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.991;0.997;0.994	D	0.93890	0.7179	10	0.66056	D	0.02	.	16.2816	0.82692	0.0:1.0:0.0:0.0	.	1001;1000;1001	B0I1R5;Q9P2E2-3;Q9P2E2	.;.;KIF17_HUMAN	Q	901;1000;1001;382	ENSP00000364184:R901Q;ENSP00000383311:R1000Q;ENSP00000247986:R1001Q	ENSP00000247986:R1001Q	R	-	2	0	KIF17	20863752	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.273000	0.65564	2.446000	0.82766	0.655000	0.94253	CGG		0.597	KIF17-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276995.1	NM_020816	
NFASC	23114	broad.mit.edu	37	1	204943867	204943867	+	Missense_Mutation	SNP	C	C	T	rs531423904		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:204943867C>T	ENST00000401399.1	+	13	1673	c.1474C>T	c.(1474-1476)Cgc>Tgc	p.R492C	NFASC_ENST00000403080.1_Missense_Mutation_p.R492C|NFASC_ENST00000513543.1_Missense_Mutation_p.R503C|NFASC_ENST00000367171.4_Missense_Mutation_p.R492C|NFASC_ENST00000367170.4_Missense_Mutation_p.R492C|NFASC_ENST00000539706.1_Missense_Mutation_p.R503C|NFASC_ENST00000338586.6_Missense_Mutation_p.R492C|NFASC_ENST00000360049.4_Missense_Mutation_p.R503C|NFASC_ENST00000367172.4_Missense_Mutation_p.R492C|NFASC_ENST00000367169.4_Missense_Mutation_p.R492C|NFASC_ENST00000404076.1_Missense_Mutation_p.R486C|NFASC_ENST00000404907.1_Missense_Mutation_p.R503C|NFASC_ENST00000339876.6_Missense_Mutation_p.R492C|NFASC_ENST00000338515.6_Missense_Mutation_p.R492C			O94856	NFASC_HUMAN	neurofascin	492	Ig-like C2-type 5.				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.R492S(2)|p.R503C(1)|p.R503S(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)			TAAGATGATCCGCAAAGAGGA	0.507													C|||	1	0.000199681	0.0	0.0	5008	,	,		21518	0.0		0.0	False		,,,				2504	0.001				p.R503C												.	.	4	Substitution - Missense(4)	lung(3)|large_intestine(1)	c.C1507T	1						.						155.0	145.0	149.0					1																	204943867		2203	4300	6503	203210490	SO:0001583	missense	23114	exon12			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.1474C>T	1.37:g.204943867C>T	ENSP00000385637:p.Arg492Cys	Somatic		Capture	Illumina HiSeq	Phase_I	203210490	NM_001160331	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Missense_Mutation	SNP	ENST00000401399.1	37	CCDS53460.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.767538	0.90020	.	.	ENSG00000163531	ENST00000367172;ENST00000367171;ENST00000367170;ENST00000338515;ENST00000339876;ENST00000338586;ENST00000295776;ENST00000539706;ENST00000360049;ENST00000367169;ENST00000403080;ENST00000404076;ENST00000401399;ENST00000404907;ENST00000513543;ENST00000430393	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.68025	-0.3;1.53;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;1.53;1.53;-0.3;-0.3;-0.3;-0.3	5.8	5.8	0.92144	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.376178	0.22679	N	0.056966	T	0.76399	0.3982	L	0.49699	1.58	0.58432	D	0.999999	D;P;P;D;D;D;D	0.89917	1.0;0.917;0.948;0.998;0.998;0.998;0.976	D;B;P;D;P;P;P	0.66497	0.943;0.399;0.45;0.944;0.648;0.866;0.66	T	0.76961	-0.2765	10	0.66056	D	0.02	.	14.5461	0.68032	0.1465:0.8535:0.0:0.0	.	492;503;503;492;492;503;492	O94856;O94856-11;O94856-8;F8W791;O94856-9;O94856-3;O94856-2	NFASC_HUMAN;.;.;.;.;.;.	C	492;492;492;492;492;492;503;503;503;492;492;486;492;503;503;479	ENSP00000356140:R492C;ENSP00000356139:R492C;ENSP00000356138:R492C;ENSP00000342128:R492C;ENSP00000344786:R492C;ENSP00000343509:R492C;ENSP00000438614:R503C;ENSP00000353154:R503C;ENSP00000356137:R492C;ENSP00000384875:R492C;ENSP00000385676:R486C;ENSP00000385637:R492C;ENSP00000384061:R503C;ENSP00000425908:R503C;ENSP00000415031:R479C	ENSP00000295776:R503C	R	+	1	0	NFASC	203210490	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	4.772000	0.62324	2.764000	0.94973	0.485000	0.47835	CGC		0.507	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388	
KCNH1	3756	broad.mit.edu	37	1	210857381	210857381	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:210857381G>A	ENST00000271751.4	-	11	2239	c.2212C>T	c.(2212-2214)Cgg>Tgg	p.R738W	KCNH1_ENST00000367007.4_Missense_Mutation_p.R711W			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	738	Calmodulin-binding.				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.R738W(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)		AAGAGGCGCCGGACAGGGTGG	0.577																																					p.R711W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2131T	1						.						43.0	46.0	45.0					1																	210857381		2203	4300	6503	208924004	SO:0001583	missense	3756	exon11			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.2212C>T	1.37:g.210857381G>A	ENSP00000271751:p.Arg738Trp	Somatic		Capture	Illumina HiSeq	Phase_I	208924004	NM_002238	B1AQ26|O76035|Q14CL3	Missense_Mutation	SNP	ENST00000271751.4	37	CCDS1496.1	.	.	.	.	.	.	.	.	.	.	G	17.95	3.512692	0.64522	.	.	ENSG00000143473	ENST00000271751;ENST00000367007	T;T	0.20069	2.1;2.1	4.49	3.33	0.38152	.	0.000000	0.85682	D	0.000000	T	0.45836	0.1362	M	0.79011	2.435	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76575	0.98;0.988	T	0.46034	-0.9220	10	0.87932	D	0	.	12.6424	0.56716	0.0:0.0:0.7522:0.2478	.	711;738	Q14CL3;O95259	.;KCNH1_HUMAN	W	738;711	ENSP00000271751:R738W;ENSP00000355974:R711W	ENSP00000271751:R738W	R	-	1	2	KCNH1	208924004	1.000000	0.71417	0.953000	0.39169	0.983000	0.72400	4.279000	0.58953	0.526000	0.28541	0.462000	0.41574	CGG		0.577	KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238	
HLX	3142	broad.mit.edu	37	1	221057801	221057801	+	Missense_Mutation	SNP	A	A	C	rs554006386		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	A	A	A	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:221057801A>C	ENST00000366903.6	+	4	2723	c.1222A>C	c.(1222-1224)Aag>Cag	p.K408Q	HLX_ENST00000549319.1_Missense_Mutation_p.K194Q	NM_021958.3	NP_068777.1	Q14774	HLX_HUMAN	H2.0-like homeobox	408	Ser-rich.				cell differentiation (GO:0030154)|embryonic digestive tract morphogenesis (GO:0048557)|enteric nervous system development (GO:0048484)|liver development (GO:0001889)|multicellular organismal development (GO:0007275)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|positive regulation of cell proliferation (GO:0008284)|positive regulation of organ growth (GO:0046622)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(9)|lung(11)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	32				GBM - Glioblastoma multiforme(131;0.00914)		AACAGTTATTAAGGCCCCGGT	0.637													A|||	1	0.000199681	0.0008	0.0	5008	,	,		15574	0.0		0.0	False		,,,				2504	0.0				p.K408Q												.	.	0			c.A1222C	1						.						59.0	51.0	54.0					1																	221057801		2203	4300	6503	219124424	SO:0001583	missense	3142	exon4			BC033808	CCDS1527.1	1q41	2011-06-20	2007-07-26	2007-07-26	ENSG00000136630	ENSG00000136630		"""Homeoboxes / ANTP class : NKL subclass"""	4978	protein-coding gene	gene with protein product		142995	"""H2.0 (Drosophila)-like homeo box 1"", ""H2.0-like homeobox 1 (Drosophila)"", ""H2.0-like homeobox 1"""	HLX1		1676597, 7806220	Standard	NM_021958		Approved	HB24	uc001hmv.4	Q14774	OTTHUMG00000037352	ENST00000366903.6:c.1222A>C	1.37:g.221057801A>C	ENSP00000355870:p.Lys408Gln	None		Capture	Illumina HiSeq	Phase_I	219124424	NM_021958	B2R8A8|Q15988|Q59HE7|Q9NZ75	Missense_Mutation	SNP	ENST00000366903.6	37	CCDS1527.1	.	.	.	.	.	.	.	.	.	.	A	18.05	3.536000	0.64972	.	.	ENSG00000136630	ENST00000366903;ENST00000427693;ENST00000549319	D;D;T	0.93133	-2.62;-3.17;3.48	4.83	4.83	0.62350	.	0.000000	0.56097	D	0.000031	D	0.92535	0.7629	L	0.29908	0.895	0.29828	N	0.830234	D	0.69078	0.997	P	0.60789	0.879	D	0.88473	0.3063	10	0.30078	T	0.28	-16.3248	12.2028	0.54335	1.0:0.0:0.0:0.0	.	408	Q14774	HLX_HUMAN	Q	408;141;194	ENSP00000355870:K408Q;ENSP00000408248:K141Q;ENSP00000449882:K194Q	ENSP00000355870:K408Q	K	+	1	0	HLX	219124424	0.870000	0.30015	1.000000	0.80357	0.722000	0.41435	0.082000	0.14847	1.937000	0.56155	0.402000	0.26972	AAG		0.637	HLX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090902.3	NM_021958	
DISP1	84976	broad.mit.edu	37	1	223177026	223177026	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:223177026C>T	ENST00000284476.6	+	8	2451	c.2287C>T	c.(2287-2289)Cgt>Tgt	p.R763C		NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)	763					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.R763C(3)		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)		TCCTTTTGAGCGTTATGATGC	0.483																																					p.R763C												.	.	3	Substitution - Missense(3)	large_intestine(2)|endometrium(1)	c.C2287T	1						.						81.0	78.0	79.0					1																	223177026		2203	4300	6503	221243649	SO:0001583	missense	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.2287C>T	1.37:g.223177026C>T	ENSP00000284476:p.Arg763Cys	Somatic		Capture	Illumina HiSeq	Phase_I	221243649	NM_032890	Q8N7C2|Q96I92|Q9H698|Q9H8H9|Q9UFA2	Missense_Mutation	SNP	ENST00000284476.6	37	CCDS1536.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.292790	0.80914	.	.	ENSG00000154309	ENST00000284476	D	0.94000	-3.33	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	D	0.96312	0.8797	M	0.61703	1.905	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.96198	0.9143	10	0.72032	D	0.01	-31.3579	20.0016	0.97412	0.0:1.0:0.0:0.0	.	763	Q96F81	DISP1_HUMAN	C	763	ENSP00000284476:R763C	ENSP00000284476:R763C	R	+	1	0	DISP1	221243649	1.000000	0.71417	0.671000	0.29857	0.981000	0.71138	7.776000	0.85560	2.802000	0.96397	0.655000	0.94253	CGT		0.483	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	NM_032890	
CELA3A	10136	broad.mit.edu	37	1	22331997	22331997	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:22331997A>G	ENST00000290122.3	+	3	206	c.187A>G	c.(187-189)Atc>Gtc	p.I63V	RN7SL768P_ENST00000584415.1_RNA|CELA3A_ENST00000374663.1_Missense_Mutation_p.I63V	NM_005747.4	NP_005738.4	P09093	CEL3A_HUMAN	chymotrypsin-like elastase family, member 3A	63	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.			I -> T (in Ref. 4; AAH05918). {ECO:0000305}.	cholesterol metabolic process (GO:0008203)|digestion (GO:0007586)|proteolysis (GO:0006508)		serine-type endopeptidase activity (GO:0004252)	p.I63V(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						CGGTAGCCTCATCGCCCCCGA	0.627											OREG0013211	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I63V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A187G	1						.						82.0	97.0	92.0					1																	22331997		2197	4300	6497	22204584	SO:0001583	missense	10136	exon3			D00306	CCDS220.1	1p36.12	2009-05-05	2009-05-05	2009-05-05	ENSG00000142789	ENSG00000142789			15944	protein-coding gene	gene with protein product	"""protease E"""		"""elastase 3A, pancreatic (protease E)"", ""elastase 3A, pancreatic"""	ELA3A		2826474, 2460440	Standard	NM_005747		Approved	ELA3		P09093	OTTHUMG00000002755	ENST00000290122.3:c.187A>G	1.37:g.22331997A>G	ENSP00000290122:p.Ile63Val	Somatic	755	Capture	Illumina HiSeq	Phase_I	22204584	NM_005747	B1AQ53|Q9BRW4	Missense_Mutation	SNP	ENST00000290122.3	37	CCDS220.1	.	.	.	.	.	.	.	.	.	.	A	8.823	0.938023	0.18206	.	.	ENSG00000142789	ENST00000290122;ENST00000374663;ENST00000374661	T;D	0.96011	1.73;-3.88	3.73	2.59	0.31030	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.91952	0.7451	L	0.37800	1.135	0.38502	D	0.948258	P;B	0.37083	0.581;0.051	B;B	0.41946	0.371;0.124	D	0.88812	0.3292	9	0.52906	T	0.07	-47.1977	6.9548	0.24565	0.8853:0.0:0.1147:0.0	.	63;63	B1AQ52;P09093	.;CEL3A_HUMAN	V	63;63;79	ENSP00000290122:I63V;ENSP00000363795:I63V	ENSP00000290122:I63V	I	+	1	0	CELA3A	22204584	1.000000	0.71417	0.234000	0.24042	0.021000	0.10359	6.903000	0.75703	0.509000	0.28195	0.329000	0.21502	ATC		0.627	CELA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007791.1	NM_005747	
DISP1	84976	broad.mit.edu	37	1	223179256	223179256	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:223179256C>A	ENST00000284476.6	+	8	4681	c.4517C>A	c.(4516-4518)cCt>cAt	p.P1506H		NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)	1506					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.P1506H(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)		GCCAATGTGCCTGCTGTATTA	0.383																																					p.P1506H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4517A	1						.						53.0	49.0	51.0					1																	223179256		2203	4300	6503	221245879	SO:0001583	missense	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.4517C>A	1.37:g.223179256C>A	ENSP00000284476:p.Pro1506His	Somatic		Capture	Illumina HiSeq	Phase_I	221245879	NM_032890	Q8N7C2|Q96I92|Q9H698|Q9H8H9|Q9UFA2	Missense_Mutation	SNP	ENST00000284476.6	37	CCDS1536.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.646432	0.87958	.	.	ENSG00000154309	ENST00000284476	D	0.96992	-4.2	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	D	0.96959	0.9007	L	0.34521	1.04	0.58432	D	0.999996	D	0.89917	1.0	D	0.87578	0.998	D	0.97969	1.0342	10	0.87932	D	0	-17.7009	19.4334	0.94781	0.0:1.0:0.0:0.0	.	1506	Q96F81	DISP1_HUMAN	H	1506	ENSP00000284476:P1506H	ENSP00000284476:P1506H	P	+	2	0	DISP1	221245879	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.001000	0.76297	2.585000	0.87301	0.655000	0.94253	CCT		0.383	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	NM_032890	
TP53BP2	7159	broad.mit.edu	37	1	223987705	223987705	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:223987705G>A	ENST00000343537.7	-	11	1672	c.1381C>T	c.(1381-1383)Cgt>Tgt	p.R461C	TP53BP2_ENST00000391879.2_5'UTR|TP53BP2_ENST00000391878.2_Missense_Mutation_p.R332C|TP53BP2_ENST00000498843.1_5'UTR	NM_001031685.2	NP_001026855.2	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein 2	455					cell cycle (GO:0007049)|central nervous system development (GO:0007417)|embryo development ending in birth or egg hatching (GO:0009792)|heart development (GO:0007507)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)|positive regulation of signal transduction (GO:0009967)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|SH3/SH2 adaptor activity (GO:0005070)	p.R332C(1)		NS(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(2)	29				GBM - Glioblastoma multiforme(131;0.0958)		GAGAACGGACGCACTTTCTTC	0.428																																					p.R461C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1381T	1						.						202.0	171.0	182.0					1																	223987705		2203	4300	6503	222054328	SO:0001583	missense	7159	exon11			U09582	CCDS1538.1, CCDS44319.1	1q41	2014-06-24	2014-06-24		ENSG00000143514	ENSG00000143514		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	12000	protein-coding gene	gene with protein product		602143	"""tumor protein p53-binding protein, 2"""			8668206, 8016121	Standard	NM_005426		Approved	PPP1R13A, ASPP2, 53BP2	uc010pvb.2	Q13625	OTTHUMG00000037379	ENST00000343537.7:c.1381C>T	1.37:g.223987705G>A	ENSP00000341957:p.Arg461Cys	Somatic		Capture	Illumina HiSeq	Phase_I	222054328	NM_001031685	B4DG66|Q12892|Q86X75|Q96KQ3	Missense_Mutation	SNP	ENST00000343537.7	37	CCDS44319.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.155174	0.78114	.	.	ENSG00000143514	ENST00000391878;ENST00000343537	T;T	0.51071	0.72;0.89	5.8	5.8	0.92144	.	0.099352	0.64402	D	0.000001	T	0.67126	0.2860	M	0.71581	2.175	0.80722	D	1	D;D	0.89917	1.0;0.999	P;P	0.60117	0.869;0.676	T	0.67665	-0.5612	10	0.59425	D	0.04	.	20.0693	0.97712	0.0:0.0:1.0:0.0	.	461;455	B4DG66;Q13625	.;ASPP2_HUMAN	C	332;461	ENSP00000375750:R332C;ENSP00000341957:R461C	ENSP00000341957:R461C	R	-	1	0	TP53BP2	222054328	1.000000	0.71417	0.585000	0.28666	0.091000	0.18340	9.194000	0.94962	2.758000	0.94735	0.563000	0.77884	CGT		0.428	TP53BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090985.3	NM_001031685, NM_005426	
PARP1	142	broad.mit.edu	37	1	226552791	226552791	+	Missense_Mutation	SNP	C	C	T	rs190105316		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:226552791C>T	ENST00000366794.5	-	19	2713	c.2570G>A	c.(2569-2571)cGa>cAa	p.R857Q	PARP1_ENST00000490921.1_5'UTR	NM_001618.3	NP_001609.2	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase 1	857	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				base-excision repair (GO:0006284)|cellular response to insulin stimulus (GO:0032869)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|gene expression (GO:0010467)|macrophage differentiation (GO:0030225)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein ADP-ribosylation (GO:0006471)|protein autoprocessing (GO:0016540)|protein poly-ADP-ribosylation (GO:0070212)|regulation of growth rate (GO:0040009)|signal transduction involved in regulation of gene expression (GO:0023019)|telomere maintenance (GO:0000723)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NAD binding (GO:0051287)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.R857Q(1)		breast(2)|endometrium(4)|kidney(4)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	44	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		CAGCAATCTTCGGTTATGAAG	0.532								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA					C|||	1	0.000199681	0.0008	0.0	5008	,	,		20110	0.0		0.0	False		,,,				2504	0.0				p.R857Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2570A	1						.						73.0	71.0	71.0					1																	226552791		2203	4300	6503	224619414	SO:0001583	missense	142	exon19			BC037545	CCDS1554.1	1q41-q42	2010-02-16	2008-07-28	2004-08-26	ENSG00000143799	ENSG00000143799	2.4.2.30	"""Poly (ADP-ribose) polymerases"""	270	protein-coding gene	gene with protein product		173870	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)"", ""poly (ADP-ribose) polymerase family, member 1"""	PPOL, ADPRT		10964595	Standard	NM_001618		Approved	PARP	uc001hqd.4	P09874	OTTHUMG00000037556	ENST00000366794.5:c.2570G>A	1.37:g.226552791C>T	ENSP00000355759:p.Arg857Gln	Somatic		Capture	Illumina HiSeq	Phase_I	224619414	NM_001618	B1ANJ4|Q8IUZ9	Missense_Mutation	SNP	ENST00000366794.5	37	CCDS1554.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	37	6.149560	0.97324	.	.	ENSG00000143799	ENST00000366794	T	0.15718	2.4	5.84	5.84	0.93424	Poly(ADP-ribose) polymerase, catalytic domain (2);	0.050091	0.85682	D	0.000000	T	0.52041	0.1710	M	0.90483	3.12	0.80722	D	1	D	0.76494	0.999	D	0.68192	0.956	T	0.59773	-0.7391	10	0.87932	D	0	.	20.1379	0.98040	0.0:1.0:0.0:0.0	.	857	P09874	PARP1_HUMAN	Q	857	ENSP00000355759:R857Q	ENSP00000355759:R857Q	R	-	2	0	PARP1	224619414	1.000000	0.71417	0.967000	0.41034	0.996000	0.88848	7.794000	0.85869	2.779000	0.95612	0.655000	0.94253	CGA		0.532	PARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091519.1	NM_001618	
SNAP47	116841	broad.mit.edu	37	1	227935847	227935847	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:227935847C>T	ENST00000366759.4	+	2	959	c.545C>T	c.(544-546)gCg>gTg	p.A182V	SNAP47_ENST00000366760.1_Intron|SNAP47_ENST00000315781.5_Missense_Mutation_p.A182V|SNAP47-AS1_ENST00000413347.2_RNA	NM_053052.3	NP_444280.2	Q5SQN1	SNP47_HUMAN	synaptosomal-associated protein, 47kDa	182	t-SNARE coiled-coil homology 1. {ECO:0000255|PROSITE-ProRule:PRU00202}.				long-term synaptic potentiation (GO:0060291)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)		p.A182V(1)		endometrium(1)|large_intestine(5)|liver(2)|lung(6)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	17						GAGGACACGGCGAGGGTCCTG	0.652																																					p.A182V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C545T	1						.						30.0	32.0	32.0					1																	227935847		2203	4300	6503	226002470	SO:0001583	missense	116841	exon2			AY090635	CCDS1562.1	1q42.13	2013-10-11	2008-10-27	2008-10-27	ENSG00000143740	ENSG00000143740			30669	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 142"""	C1orf142		16621800	Standard	NM_053052		Approved	SVAP1, SNAP-47	uc001hrf.2	Q5SQN1	OTTHUMG00000037697	ENST00000366759.4:c.545C>T	1.37:g.227935847C>T	ENSP00000355721:p.Ala182Val	Somatic		Capture	Illumina HiSeq	Phase_I	226002470	NM_053052	B6EDE0|Q5HYB5|Q5TBZ3|Q8N558|Q8TB31|Q8TCW8|Q8WV46|Q96CQ3|Q96FE1|Q96I66|Q96NU3|Q9BT10|Q9BVB2	Missense_Mutation	SNP	ENST00000366759.4	37	CCDS1562.1	.	.	.	.	.	.	.	.	.	.	C	13.99	2.402879	0.42613	.	.	ENSG00000143740	ENST00000366759;ENST00000315781	T;T	0.15952	2.38;2.38	4.12	4.12	0.48240	Target SNARE coiled-coil domain (1);	0.123969	0.52532	D	0.000066	T	0.35624	0.0938	M	0.77820	2.39	0.20074	N	0.999939	D;D	0.71674	0.998;0.998	P;P	0.60236	0.794;0.871	T	0.13495	-1.0507	10	0.72032	D	0.01	-6.4913	9.8791	0.41222	0.0:0.7914:0.2086:0.0	.	182;182	Q5SQN1;Q5SQN1-2	SNP47_HUMAN;.	V	182	ENSP00000355721:A182V;ENSP00000314157:A182V	ENSP00000314157:A182V	A	+	2	0	SNAP47	226002470	1.000000	0.71417	0.014000	0.15608	0.015000	0.08874	4.220000	0.58567	2.143000	0.66587	0.591000	0.81541	GCG		0.652	SNAP47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091961.1	NM_053052	
OBSCN	84033	broad.mit.edu	37	1	228503690	228503690	+	Silent	SNP	C	C	T	rs568898759		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:228503690C>T	ENST00000422127.1	+	50	13199	c.13155C>T	c.(13153-13155)aaC>aaT	p.N4385N	OBSCN_ENST00000366709.4_Silent_p.N1504N|OBSCN_ENST00000284548.11_Silent_p.N4385N|OBSCN_ENST00000366707.4_Silent_p.N2019N|OBSCN_ENST00000570156.2_Silent_p.N5342N	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4385	Ig-like 45.				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.N4967N(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)				CCTCGGAGAACGCCGAGGTGG	0.662													C|||	1	0.000199681	0.0	0.0	5008	,	,		13753	0.0		0.0	False		,,,				2504	0.001				p.N4385N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C13155T	1						.						28.0	34.0	32.0					1																	228503690		2109	4192	6301	226570313	SO:0001819	synonymous_variant	84033	exon50			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.13155C>T	1.37:g.228503690C>T		Somatic		Capture	Illumina HiSeq	Phase_I	226570313	NM_052843	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																				0.662	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
OBSCN	84033	broad.mit.edu	37	1	228506933	228506933	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:228506933G>A	ENST00000422127.1	+	54	14524	c.14480G>A	c.(14479-14481)gGc>gAc	p.G4827D	OBSCN_ENST00000366709.4_Missense_Mutation_p.G1946D|OBSCN_ENST00000284548.11_Missense_Mutation_p.G4827D|OBSCN_ENST00000366707.4_Missense_Mutation_p.G2461D|OBSCN_ENST00000570156.2_Missense_Mutation_p.G5784D	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4827					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.G5409D(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)				GGGAGGCCAGGCACCTCACCA	0.602																																					p.G4827D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G14480A	1						.						17.0	20.0	19.0					1																	228506933		2030	4171	6201	226573556	SO:0001583	missense	84033	exon54			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.14480G>A	1.37:g.228506933G>A	ENSP00000409493:p.Gly4827Asp	Somatic		Capture	Illumina HiSeq	Phase_I	226573556	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	17.68	3.449836	0.63290	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.63096	0.38;-0.02;0.04;0.53	4.02	2.01	0.26516	.	1.200320	0.06017	N	0.650528	T	0.61961	0.2389	N	0.24115	0.695	0.09310	N	1	P;D	0.65815	0.906;0.995	B;P	0.61592	0.276;0.891	T	0.52540	-0.8562	10	0.16420	T	0.52	.	8.6156	0.33829	0.0:0.1663:0.6613:0.1724	.	4827;4827	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	D	4827;4827;2461;1946	ENSP00000284548:G4827D;ENSP00000409493:G4827D;ENSP00000355668:G2461D;ENSP00000355670:G1946D	ENSP00000284548:G4827D	G	+	2	0	OBSCN	226573556	0.117000	0.22190	0.000000	0.03702	0.085000	0.17905	2.733000	0.47360	0.296000	0.22592	0.306000	0.20318	GGC		0.602	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
URB2	9816	broad.mit.edu	37	1	229783335	229783335	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:229783335C>G	ENST00000258243.2	+	7	4121	c.3985C>G	c.(3985-3987)Ctg>Gtg	p.L1329V		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	1329						aggresome (GO:0016235)|nucleolus (GO:0005730)|nucleus (GO:0005634)		p.L1329V(1)		breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(6)	73						CCTGGCTGCACTGCTGCGGCA	0.567																																					p.L1329V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3985G	1						.						77.0	69.0	72.0					1																	229783335		2203	4300	6503	227849958	SO:0001583	missense	9816	exon7			D50923	CCDS31052.1	1q42.13	2009-11-06	2008-10-01	2008-10-01	ENSG00000135763	ENSG00000135763			28967	protein-coding gene	gene with protein product	"""nucleolar preribosomal-associated protein 1"""		"""KIAA0133"""	KIAA0133		8590280	Standard	NM_014777		Approved	NPA2, NET10	uc001hts.1	Q14146	OTTHUMG00000039464	ENST00000258243.2:c.3985C>G	1.37:g.229783335C>G	ENSP00000258243:p.Leu1329Val	Somatic		Capture	Illumina HiSeq	Phase_I	227849958	NM_014777	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	37	CCDS31052.1	.	.	.	.	.	.	.	.	.	.	C	13.11	2.140722	0.37825	.	.	ENSG00000135763	ENST00000258243	T	0.45668	0.89	5.58	-1.45	0.08828	Nucleolar 27S pre-rRNA processing, Urb2/Npa2, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.57227	0.2039	M	0.71581	2.175	0.39422	D	0.966938	D	0.89917	1.0	D	0.97110	1.0	T	0.58411	-0.7641	9	.	.	.	-14.0995	11.9571	0.52986	0.0:0.5973:0.0:0.4027	.	1329	Q14146	URB2_HUMAN	V	1329	ENSP00000258243:L1329V	.	L	+	1	2	URB2	227849958	0.086000	0.21541	0.044000	0.18714	0.296000	0.27459	0.508000	0.22692	-0.143000	0.11334	-0.291000	0.09656	CTG		0.567	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777	
SIPA1L2	57568	broad.mit.edu	37	1	232577125	232577125	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:232577125C>T	ENST00000366630.1	-	13	3912	c.3554G>A	c.(3553-3555)gGc>gAc	p.G1185D	SIPA1L2_ENST00000308942.4_Missense_Mutation_p.G259D|SIPA1L2_ENST00000262861.4_Missense_Mutation_p.G1185D			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	1185					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				GGAAGGTGGGCCATGCCATTT	0.413																																					p.G1185D												.	.	0			c.G3554A	1						.						182.0	189.0	187.0					1																	232577125		1831	4092	5923	230643748	SO:0001583	missense	57568	exon12			AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.3554G>A	1.37:g.232577125C>T	ENSP00000355589:p.Gly1185Asp	None		Capture	Illumina HiSeq	Phase_I	230643748	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	37	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	C	16.16	3.044014	0.55110	.	.	ENSG00000116991	ENST00000366630;ENST00000262861;ENST00000308942	T;T;T	0.78816	-1.21;-1.21;2.75	6.17	6.17	0.99709	.	0.234533	0.36740	N	0.002439	T	0.71863	0.3390	L	0.33485	1.01	0.38347	D	0.944225	B;P	0.50943	0.012;0.94	B;P	0.45071	0.003;0.468	T	0.73088	-0.4093	10	0.34782	T	0.22	-37.8672	15.125	0.72475	0.0:0.7555:0.2445:0.0	.	1185;259	Q9P2F8;Q9P2F8-2	SI1L2_HUMAN;.	D	1185;1185;259	ENSP00000355589:G1185D;ENSP00000262861:G1185D;ENSP00000309102:G259D	ENSP00000262861:G1185D	G	-	2	0	SIPA1L2	230643748	1.000000	0.71417	0.995000	0.50966	0.996000	0.88848	3.940000	0.56599	2.941000	0.99782	0.655000	0.94253	GGC		0.413	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839	
RYR2	6262	broad.mit.edu	37	1	237758805	237758805	+	Missense_Mutation	SNP	C	C	T	rs564869863	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:237758805C>T	ENST00000366574.2	+	34	4761	c.4444C>T	c.(4444-4446)Cgc>Tgc	p.R1482C	RYR2_ENST00000360064.6_Missense_Mutation_p.R1480C|RYR2_ENST00000542537.1_Missense_Mutation_p.R1466C	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1482	4 X approximate repeats.|B30.2/SPRY 3. {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.R1480C(3)		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)			CAGCATCAAACGCAGCAACTG	0.438													C|||	2	0.000399361	0.0	0.0	5008	,	,		20969	0.001		0.0	False		,,,				2504	0.001				p.R1482C												.	.	3	Substitution - Missense(3)	large_intestine(2)|pancreas(1)	c.C4444T	1						.						77.0	79.0	78.0					1																	237758805		2011	4169	6180	235825428	SO:0001583	missense	6262	exon34			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.4444C>T	1.37:g.237758805C>T	ENSP00000355533:p.Arg1482Cys	Somatic		Capture	Illumina HiSeq	Phase_I	235825428	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	C	17.48	3.401264	0.62288	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	T;T;T	0.62232	0.04;0.04;0.04	5.0	5.0	0.66597	SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.267390	0.30446	N	0.009610	T	0.73916	0.3648	M	0.66378	2.025	0.80722	D	1	D	0.76494	0.999	P	0.57679	0.825	T	0.73500	-0.3963	10	0.39692	T	0.17	.	18.4746	0.90788	0.0:1.0:0.0:0.0	.	1482	Q92736	RYR2_HUMAN	C	1482;1480;1466	ENSP00000355533:R1482C;ENSP00000353174:R1480C;ENSP00000443798:R1466C	ENSP00000353174:R1480C	R	+	1	0	RYR2	235825428	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.618000	0.61211	2.598000	0.87819	0.655000	0.94253	CGC		0.438	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	237870450	237870450	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:237870450C>T	ENST00000366574.2	+	68	10099	c.9782C>T	c.(9781-9783)gCc>gTc	p.A3261V	RYR2_ENST00000360064.6_Missense_Mutation_p.A3259V|RYR2_ENST00000542537.1_Missense_Mutation_p.A3245V|RYR2_ENST00000609119.1_3'UTR	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	3261					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.A3259V(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)			CCAGAACGGGCCGAGATGTGC	0.473																																					p.A3261V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C9782T	1						.						71.0	70.0	70.0					1																	237870450		2057	4189	6246	235937073	SO:0001583	missense	6262	exon68			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.9782C>T	1.37:g.237870450C>T	ENSP00000355533:p.Ala3261Val	Somatic		Capture	Illumina HiSeq	Phase_I	235937073	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	C	8.540	0.873143	0.17322	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537;ENST00000542288	T;D;T	0.96716	-0.23;-4.1;-0.23	5.72	4.8	0.61643	.	0.177397	0.34628	N	0.003818	D	0.93115	0.7808	L	0.47716	1.5	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	D	0.84998	0.0898	10	0.48119	T	0.1	-6.4092	9.7011	0.40187	0.0:0.7543:0.1192:0.1265	.	3261	Q92736	RYR2_HUMAN	V	3261;3259;3245;216	ENSP00000355533:A3261V;ENSP00000353174:A3259V;ENSP00000443798:A3245V	ENSP00000353174:A3259V	A	+	2	0	RYR2	235937073	0.000000	0.05858	0.125000	0.21846	0.122000	0.20287	0.869000	0.27996	2.711000	0.92665	0.655000	0.94253	GCC		0.473	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
C1orf100	200159	broad.mit.edu	37	1	244538715	244538715	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:244538715A>G	ENST00000308105.4	+	3	211	c.98A>G	c.(97-99)tAc>tGc	p.Y33C	RP11-518L10.5_ENST00000417765.1_RNA|C1orf100_ENST00000366537.1_Missense_Mutation_p.Y33C	NM_001012970.1	NP_001012988.1	Q5SVJ3	CA100_HUMAN	chromosome 1 open reading frame 100	33								p.Y33C(1)		endometrium(1)|large_intestine(2)|lung(2)|prostate(1)|skin(1)	7	all_cancers(71;3.94e-05)|all_epithelial(71;0.000138)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|all_lung(81;0.0736)|Ovarian(71;0.0761)|Lung NSC(105;0.103)		all cancers(7;8.19e-08)|GBM - Glioblastoma multiforme(7;2.05e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.000984)			CAAGGCTATTACCCTGGGCAG	0.458																																					p.Y33C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A98G	1						.						87.0	80.0	82.0					1																	244538715		2203	4300	6503	242605338	SO:0001583	missense	200159	exon3			BC054479	CCDS31079.1, CCDS60465.1	1q44	2008-02-05			ENSG00000173728	ENSG00000173728			30435	protein-coding gene	gene with protein product							Standard	NM_001276348		Approved		uc001iah.4	Q5SVJ3	OTTHUMG00000040104	ENST00000308105.4:c.98A>G	1.37:g.244538715A>G	ENSP00000311218:p.Tyr33Cys	Somatic		Capture	Illumina HiSeq	Phase_I	242605338	NM_001012970	Q5SVJ4	Missense_Mutation	SNP	ENST00000308105.4	37	CCDS31079.1	.	.	.	.	.	.	.	.	.	.	A	12.31	1.900593	0.33535	.	.	ENSG00000173728	ENST00000366537;ENST00000308105	.	.	.	5.35	1.35	0.21983	.	1.208830	0.05782	N	0.608875	T	0.55178	0.1904	M	0.62723	1.935	0.09310	N	1	D;D	0.65815	0.995;0.995	P;P	0.60415	0.874;0.874	T	0.30446	-0.9978	9	0.59425	D	0.04	-13.7529	5.245	0.15493	0.4704:0.1529:0.0:0.3767	.	33;33	Q5SVJ3-2;Q5SVJ3	.;CA100_HUMAN	C	33	.	ENSP00000311218:Y33C	Y	+	2	0	C1orf100	242605338	0.002000	0.14202	0.001000	0.08648	0.320000	0.28249	1.032000	0.30178	0.023000	0.15187	0.460000	0.39030	TAC		0.458	C1orf100-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096712.1	NM_001012970	
PANK4	55229	broad.mit.edu	37	1	2452293	2452293	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:2452293G>A	ENST00000378466.3	-	4	487	c.475C>T	c.(475-477)Ctc>Ttc	p.L159F	PANK4_ENST00000435556.3_Intron|PANK4_ENST00000491212.1_5'Flank	NM_018216.1	NP_060686.1	Q9NVE7	PANK4_HUMAN	pantothenate kinase 4	159					coenzyme A biosynthetic process (GO:0015937)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)	p.L159F(1)		breast(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	23	all_cancers(77;0.000158)|all_epithelial(69;8.01e-05)|all_lung(157;0.0212)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.18e-20)|all_lung(118;1.67e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;1.54e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-23)|GBM - Glioblastoma multiforme(42;2.81e-08)|Colorectal(212;4.25e-05)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.00445)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.201)		ATGTTCTTGAGCACGAAGTTG	0.537																																					p.L159F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C475T	1						.						130.0	129.0	129.0					1																	2452293		2203	4300	6503	2442153	SO:0001583	missense	55229	exon4			AK001644	CCDS42.1	1p36.32	2008-02-05			ENSG00000157881	ENSG00000157881			19366	protein-coding gene	gene with protein product		606162				11479594	Standard	XR_241034		Approved	FLJ10782	uc001ajm.1	Q9NVE7	OTTHUMG00000000791	ENST00000378466.3:c.475C>T	1.37:g.2452293G>A	ENSP00000367727:p.Leu159Phe	Somatic		Capture	Illumina HiSeq	Phase_I	2442153	NM_018216	B9DI84|Q53EU3|Q5TA84|Q7RTX3|Q9H3X5	Missense_Mutation	SNP	ENST00000378466.3	37	CCDS42.1	.	.	.	.	.	.	.	.	.	.	G	16.33	3.091725	0.55968	.	.	ENSG00000157881	ENST00000378466	D	0.99652	-6.3	4.91	0.946	0.19549	.	0.178143	0.38959	N	0.001519	D	0.99576	0.9847	M	0.92649	3.33	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99877	1.1106	10	0.72032	D	0.01	-17.338	8.775	0.34756	0.3086:0.0:0.6914:0.0	.	159	Q9NVE7	PANK4_HUMAN	F	159	ENSP00000367727:L159F	ENSP00000367727:L159F	L	-	1	0	PANK4	2442153	1.000000	0.71417	0.936000	0.37596	0.373000	0.29922	1.167000	0.31847	-0.081000	0.12662	-0.251000	0.11542	CTC		0.537	PANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002082.1		
KIF26B	55083	broad.mit.edu	37	1	245849626	245849626	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:245849626C>T	ENST00000407071.2	+	12	3781	c.3341C>T	c.(3340-3342)gCg>gTg	p.A1114V	KIF26B_ENST00000366518.4_Missense_Mutation_p.A733V	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	1114					establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.A1114V(2)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			TCCGGCGTGGCGTCTAGGGAG	0.622																																					p.A1114V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C3341T	1						.						66.0	74.0	72.0					1																	245849626		1943	4135	6078	243916249	SO:0001583	missense	55083	exon12			AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"""Kinesins"""	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.3341C>T	1.37:g.245849626C>T	ENSP00000385545:p.Ala1114Val	Somatic		Capture	Illumina HiSeq	Phase_I	243916249	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Missense_Mutation	SNP	ENST00000407071.2	37	CCDS44342.1	.	.	.	.	.	.	.	.	.	.	C	2.753	-0.259491	0.05791	.	.	ENSG00000162849	ENST00000407071;ENST00000366518;ENST00000413001	T;T	0.76186	-1.0;-1.0	5.76	-2.66	0.06077	.	.	.	.	.	T	0.43897	0.1268	N	0.02111	-0.68	0.09310	N	1	B;B	0.10296	0.003;0.003	B;B	0.04013	0.001;0.001	T	0.34204	-0.9838	9	0.08599	T	0.76	.	13.8666	0.63592	0.0:0.6039:0.0:0.3961	.	733;1114	B7WPD9;Q2KJY2	.;KI26B_HUMAN	V	1114;733;730	ENSP00000385545:A1114V;ENSP00000355475:A733V	ENSP00000355475:A733V	A	+	2	0	KIF26B	243916249	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.134000	0.15932	-0.383000	0.07858	-1.079000	0.02226	GCG		0.622	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354	
ZNF670	93474	broad.mit.edu	37	1	247201099	247201099	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:247201099C>T	ENST00000366503.2	-	4	980	c.822G>A	c.(820-822)acG>acA	p.T274T		NM_001204220.1|NM_033213.4	NP_001191149.1|NP_149990.1	Q9BS34	ZN670_HUMAN	zinc finger protein 670	274					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.T274T(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	17	all_cancers(71;4.01e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00427)			CTCCAGTATGCGTTCTTTCAT	0.423																																					p.T274T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G822A	1						.						123.0	123.0	123.0					1																	247201099		2203	4300	6503	245267722	SO:0001819	synonymous_variant	93474	exon4				CCDS31087.1	1q44	2013-01-08			ENSG00000135747	ENSG00000135747		"""Zinc fingers, C2H2-type"", ""-"""	28167	protein-coding gene	gene with protein product						12477932	Standard	NM_033213		Approved	MGC12466	uc001icd.2	Q9BS34	OTTHUMG00000040868	ENST00000366503.2:c.822G>A	1.37:g.247201099C>T		Somatic		Capture	Illumina HiSeq	Phase_I	245267722	NM_033213		Silent	SNP	ENST00000366503.2	37	CCDS31087.1																																																																																				0.423	ZNF670-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098183.3	NM_033213	
OR2G2	81470	broad.mit.edu	37	1	247752206	247752206	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:247752206G>A	ENST00000320065.1	+	1	545	c.545G>A	c.(544-546)tGc>tAc	p.C182Y	RP11-978I15.10_ENST00000446347.1_RNA|RP11-978I15.10_ENST00000435333.1_RNA	NM_001001915.1	NP_001001915.1	Q8NGZ5	OR2G2_HUMAN	olfactory receptor, family 2, subfamily G, member 2	182						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.C182Y(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)			CATTTCATCTGCGAGGTCCCT	0.537																																					p.C182Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G545A	1						.						177.0	170.0	172.0					1																	247752206		2203	4300	6503	245818829	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.545G>A	1.37:g.247752206G>A	ENSP00000326349:p.Cys182Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	245818829	NM_001001915	Q5JQT2|Q6IEZ0	Missense_Mutation	SNP	ENST00000320065.1	37	CCDS31092.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.964308	0.74131	.	.	ENSG00000177489	ENST00000320065	T	0.61980	0.06	4.29	4.29	0.51040	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40818	U	0.001012	D	0.83403	0.5247	M	0.93898	3.47	0.40524	D	0.980863	D	0.89917	1.0	D	0.97110	1.0	D	0.88482	0.3069	10	0.87932	D	0	.	14.3294	0.66545	0.0:0.0:1.0:0.0	.	182	Q8NGZ5	OR2G2_HUMAN	Y	182	ENSP00000326349:C182Y	ENSP00000326349:C182Y	C	+	2	0	OR2G2	245818829	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.346000	0.79347	2.206000	0.71126	0.591000	0.81541	TGC		0.537	OR2G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097623.1		
OR11L1	391189	broad.mit.edu	37	1	248004952	248004952	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:248004952C>A	ENST00000355784.2	-	1	302	c.247G>T	c.(247-249)Gcc>Tcc	p.A83S		NM_001001959.1	NP_001001959.1	Q8NGX0	O11L1_HUMAN	olfactory receptor, family 11, subfamily L, member 1	83						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A83S(1)		NS(1)|endometrium(4)|kidney(5)|large_intestine(5)|lung(35)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	57	all_cancers(71;8.78e-05)|all_epithelial(71;9.15e-06)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.0786)|Lung NSC(105;0.0858)		OV - Ovarian serous cystadenocarcinoma(106;0.0319)			AGCAGGTTGGCTAGGAGAAGG	0.592																																					p.A83S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G247T	1						.						71.0	60.0	64.0					1																	248004952		2203	4300	6503	246071575	SO:0001583	missense	391189	exon1			AB065646	CCDS31098.1	1q44	2013-09-24			ENSG00000197591	ENSG00000197591		"""GPCR / Class A : Olfactory receptors"""	14998	protein-coding gene	gene with protein product							Standard	NM_001001959		Approved		uc001idn.1	Q8NGX0	OTTHUMG00000040193	ENST00000355784.2:c.247G>T	1.37:g.248004952C>A	ENSP00000348033:p.Ala83Ser	Somatic		Capture	Illumina HiSeq	Phase_I	246071575	NM_001001959		Missense_Mutation	SNP	ENST00000355784.2	37	CCDS31098.1	.	.	.	.	.	.	.	.	.	.	C	9.614	1.132012	0.21041	.	.	ENSG00000197591	ENST00000355784	T	0.00392	7.58	4.2	0.853	0.19001	GPCR, rhodopsin-like superfamily (1);	0.730437	0.11158	N	0.593307	T	0.00210	0.0006	N	0.17474	0.49	0.09310	N	1	B	0.16802	0.019	B	0.18561	0.022	T	0.21930	-1.0231	10	0.38643	T	0.18	.	9.384	0.38331	0.3903:0.4883:0.1214:0.0	.	83	Q8NGX0	O11L1_HUMAN	S	83	ENSP00000348033:A83S	ENSP00000348033:A83S	A	-	1	0	OR11L1	246071575	0.000000	0.05858	0.212000	0.23672	0.740000	0.42216	-0.498000	0.06420	0.460000	0.27045	0.543000	0.68304	GCC		0.592	OR11L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096850.1	NM_001001959	
OR2M3	127062	broad.mit.edu	37	1	248367073	248367073	+	Missense_Mutation	SNP	G	G	A	rs138010167	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:248367073G>A	ENST00000456743.1	+	1	742	c.704G>A	c.(703-705)cGc>cAc	p.R235H		NM_001004689.1	NP_001004689.1	Q8NG83	OR2M3_HUMAN	olfactory receptor, family 2, subfamily M, member 3	235						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R235H(2)		endometrium(6)|large_intestine(4)|lung(33)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	50	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;0.0245)			GAGGGTCGTCGCAAAGCTTTT	0.468													g|||	2	0.000399361	0.0	0.0	5008	,	,		20996	0.001		0.001	False		,,,				2504	0.0				p.R235H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G704A	1						.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	257.0	244.0	248.0		704	-3.3	0.0	1	dbSNP_134	248	0,8600		0,0,4300	no	missense	OR2M3	NM_001004689.1	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	235/313	248367073	1,13005	2203	4300	6503	246433696	SO:0001583	missense	127062	exon1				CCDS31107.1	1q44	2012-08-09		2004-03-10	ENSG00000228198	ENSG00000228198		"""GPCR / Class A : Olfactory receptors"""	8269	protein-coding gene	gene with protein product				OR2M6, OR2M3P			Standard	NM_001004689		Approved	OST003	uc010pzg.2	Q8NG83	OTTHUMG00000040459	ENST00000456743.1:c.704G>A	1.37:g.248367073G>A	ENSP00000389625:p.Arg235His	Somatic		Capture	Illumina HiSeq	Phase_I	246433696	NM_001004689	B9EH06|Q6IEY0	Missense_Mutation	SNP	ENST00000456743.1	37	CCDS31107.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	6.305	0.424298	0.11928	2.27E-4	0.0	ENSG00000228198	ENST00000456743	T	0.00034	8.87	2.25	-3.31	0.04988	GPCR, rhodopsin-like superfamily (1);	1.276350	0.06104	N	0.665935	T	0.00073	0.0002	N	0.04508	-0.205	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.04386	-1.0955	10	0.41790	T	0.15	.	7.4052	0.26987	0.6672:0.0:0.3328:0.0	.	235	Q8NG83	OR2M3_HUMAN	H	235	ENSP00000389625:R235H	ENSP00000389625:R235H	R	+	2	0	OR2M3	246433696	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-2.791000	0.00767	-0.925000	0.03775	0.398000	0.26397	CGC		0.468	OR2M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097355.1	NM_001004689	
OR2T11	127077	broad.mit.edu	37	1	248790149	248790149	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:248790149C>T	ENST00000330803.2	-	1	342	c.281G>A	c.(280-282)tGt>tAt	p.C94Y		NM_001001964.1	NP_001001964.1	Q8NH01	O2T11_HUMAN	olfactory receptor, family 2, subfamily T, member 11 (gene/pseudogene)	94						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.C94Y(1)		breast(1)|large_intestine(5)|lung(20)|skin(2)	28	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CTGGATGCCACAGGCCACAAA	0.498																																					p.C94Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G281A	1						.						70.0	66.0	68.0					1																	248790149		2053	4230	6283	246856772	SO:0001583	missense	127077	exon1			BK004476	CCDS31122.1	1q44	2013-10-10	2013-10-10		ENSG00000183130	ENSG00000183130		"""GPCR / Class A : Olfactory receptors"""	19574	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily T, member 11"""				Standard	NM_001001964		Approved	OR2T11Q	uc001ier.1	Q8NH01	OTTHUMG00000040384	ENST00000330803.2:c.281G>A	1.37:g.248790149C>T	ENSP00000328934:p.Cys94Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	246856772	NM_001001964	Q6IEY6	Missense_Mutation	SNP	ENST00000330803.2	37	CCDS31122.1	.	.	.	.	.	.	.	.	.	.	.	16.88	3.244495	0.59103	.	.	ENSG00000183130	ENST00000330803	T	0.00547	6.66	4.62	3.7	0.42460	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47852	D	0.000210	T	0.04272	0.0118	H	0.97415	4	0.38382	D	0.94515	D	0.89917	1.0	D	0.91635	0.999	T	0.04481	-1.0948	10	0.87932	D	0	.	13.1223	0.59334	0.1615:0.8385:0.0:0.0	.	94	Q8NH01	O2T11_HUMAN	Y	94	ENSP00000328934:C94Y	ENSP00000328934:C94Y	C	-	2	0	OR2T11	246856772	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	6.436000	0.73417	1.122000	0.41944	0.655000	0.94253	TGT		0.498	OR2T11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097134.1	NM_001001964	
C1orf174	339448	broad.mit.edu	37	1	3809534	3809534	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:3809534C>T	ENST00000361605.3	-	2	140	c.42G>A	c.(40-42)gcG>gcA	p.A14A	C1orf174_ENST00000486765.1_5'UTR	NM_207356.2	NP_997239.2	Q8IYL3	CA174_HUMAN	chromosome 1 open reading frame 174	14						nucleus (GO:0005634)		p.A14A(1)		endometrium(1)|large_intestine(5)|lung(4)|prostate(1)	11	all_cancers(77;0.0395)|Ovarian(185;0.0634)|all_lung(157;0.222)|Lung NSC(156;0.227)	all_cancers(23;5.09e-25)|all_epithelial(116;9.35e-17)|all_lung(118;1.09e-06)|Lung NSC(185;0.000139)|all_neural(13;0.00287)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0219)|all_hematologic(16;0.027)|Colorectal(325;0.0276)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.0743)|Ovarian(437;0.127)		Epithelial(90;1.55e-39)|OV - Ovarian serous cystadenocarcinoma(86;5.99e-23)|GBM - Glioblastoma multiforme(42;2.22e-17)|Colorectal(212;1.08e-05)|COAD - Colon adenocarcinoma(227;5.49e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.000365)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.19)		CTTTCAAGCGCGCTGAAGACC	0.552																																					p.A14A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G42A	1						.						75.0	63.0	67.0					1																	3809534		2203	4300	6503	3799394	SO:0001819	synonymous_variant	339448	exon2			BC035643	CCDS53.1	1p36.32	2012-07-25			ENSG00000198912	ENSG00000198912			27915	protein-coding gene	gene with protein product						12477932	Standard	NM_207356		Approved	RP13-531C17.2	uc001alf.3	Q8IYL3	OTTHUMG00000003739	ENST00000361605.3:c.42G>A	1.37:g.3809534C>T		Somatic		Capture	Illumina HiSeq	Phase_I	3799394	NM_207356	A8K0C8|A8MUG9|Q5SR20|Q6NX36	Silent	SNP	ENST00000361605.3	37	CCDS53.1																																																																																				0.552	C1orf174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010539.1	NM_207356	
PER3	8863	broad.mit.edu	37	1	7848183	7848183	+	Missense_Mutation	SNP	C	C	T	rs375445968		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:7848183C>T	ENST00000361923.2	+	4	644	c.469C>T	c.(469-471)Cgt>Tgt	p.R157C	PER3_ENST00000377532.3_Missense_Mutation_p.R157C|PER3_ENST00000377541.1_Missense_Mutation_p.R157C	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	157	PAS 1. {ECO:0000255|PROSITE- ProRule:PRU00140}.				circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)	p.R157C(1)		breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		GATCCTGAATCGTAAGAAAGA	0.428																																					p.R157C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C469T	1						.						136.0	138.0	137.0					1																	7848183		2203	4300	6503	7770770	SO:0001583	missense	8863	exon4			BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"""period (Drosophila) homolog 3"", ""period homolog 3 (Drosophila)"""			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.469C>T	1.37:g.7848183C>T	ENSP00000355031:p.Arg157Cys	Somatic		Capture	Illumina HiSeq	Phase_I	7770770	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	37	CCDS89.1	.	.	.	.	.	.	.	.	.	.	C	2.430	-0.331064	0.05314	.	.	ENSG00000049246	ENST00000377541;ENST00000377532;ENST00000361923	T;T;T	0.26067	1.76;3.38;3.44	4.96	2.62	0.31277	PAS (1);	0.285984	0.39759	N	0.001280	T	0.05456	0.0144	N	0.00182	-1.905	0.29974	N	0.818271	B;B;B;B	0.14012	0.006;0.005;0.009;0.006	B;B;B;B	0.10450	0.001;0.001;0.005;0.001	T	0.21827	-1.0234	10	0.23891	T	0.37	.	8.3213	0.32130	0.0:0.1699:0.0:0.8301	.	157;157;157;157	A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;PER3_HUMAN	C	157	ENSP00000366764:R157C;ENSP00000366755:R157C;ENSP00000355031:R157C	ENSP00000355031:R157C	R	+	1	0	PER3	7770770	0.996000	0.38824	0.372000	0.25991	0.857000	0.48899	2.599000	0.46231	0.758000	0.33059	-0.312000	0.09012	CGT		0.428	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
CLSTN1	22883	broad.mit.edu	37	1	9801205	9801205	+	Missense_Mutation	SNP	G	G	A	rs375763180		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:9801205G>A	ENST00000377298.4	-	10	2258	c.1466C>T	c.(1465-1467)cCg>cTg	p.P489L	CLSTN1_ENST00000361311.4_Missense_Mutation_p.P479L|CLSTN1_ENST00000377288.3_Missense_Mutation_p.P489L	NM_001009566.1	NP_001009566.1	O94985	CSTN1_HUMAN	calsyntenin 1	489					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	beta-amyloid binding (GO:0001540)|calcium ion binding (GO:0005509)|kinesin binding (GO:0019894)|X11-like protein binding (GO:0042988)	p.P489L(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(9)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	36	all_lung(157;0.222)	all_lung(284;4.03e-05)|Lung NSC(185;6.93e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;8.36e-08)|COAD - Colon adenocarcinoma(227;1.93e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419)		TGGATGGAGCGGGTAATCCTC	0.542													G|||	1	0.000199681	0.0	0.0	5008	,	,		19724	0.0		0.0	False		,,,				2504	0.001				p.P479L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1436T	1						.	G	LEU/PRO,LEU/PRO	0,4406		0,0,2203	125.0	113.0	117.0		1466,1436	5.4	0.3	1		117	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	CLSTN1	NM_001009566.1,NM_014944.3	98,98	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	489/982,479/972	9801205	1,13005	2203	4300	6503	9723792	SO:0001583	missense	22883	exon9			AB020718	CCDS105.1, CCDS30580.1	1p36.22	2011-07-01			ENSG00000171603	ENSG00000171603		"""Cadherins / Cadherin-related"""	17447	protein-coding gene	gene with protein product	"""cadherin-related family member 12"""	611321				10048485	Standard	XM_005263432		Approved	CSTN1, KIAA0911, CDHR12	uc001aqh.3	O94985	OTTHUMG00000001451	ENST00000377298.4:c.1466C>T	1.37:g.9801205G>A	ENSP00000366513:p.Pro489Leu	Somatic		Capture	Illumina HiSeq	Phase_I	9723792	NM_014944	A8K183|Q5SR52|Q5UE58|Q71MN0|Q8N4K9	Missense_Mutation	SNP	ENST00000377298.4	37	CCDS30580.1	.	.	.	.	.	.	.	.	.	.	G	15.75	2.926119	0.52759	0.0	1.16E-4	ENSG00000171603	ENST00000377298;ENST00000361311;ENST00000435891;ENST00000377288;ENST00000539822	T;T;T;T	0.49139	0.79;0.79;0.79;0.79	5.37	5.37	0.77165	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.66954	0.2842	M	0.62723	1.935	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	0.62676	-0.6804	10	0.31617	T	0.26	-16.4801	19.1089	0.93309	0.0:0.0:1.0:0.0	.	489;479;489	B4E3Q1;O94985-2;O94985	.;.;CSTN1_HUMAN	L	489;479;309;489;489	ENSP00000366513:P489L;ENSP00000354997:P479L;ENSP00000401934:P309L;ENSP00000366502:P489L	ENSP00000354997:P479L	P	-	2	0	CLSTN1	9723792	1.000000	0.71417	0.291000	0.24904	0.044000	0.14063	9.869000	0.99810	2.520000	0.84964	0.655000	0.94253	CCG		0.542	CLSTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004239.1		
SEPN1	57190	broad.mit.edu	37	1	26135539	26135539	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:26135539G>A	ENST00000374315.1	+	5	706	c.668G>A	c.(667-669)aGc>aAc	p.S223N	SEPN1_ENST00000354177.4_Missense_Mutation_p.S223N|SEPN1_ENST00000361547.2_Missense_Mutation_p.S257N	NM_206926.1	NP_996809.1	Q9NZV5	SELN_HUMAN	selenoprotein N, 1	257						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	calcium ion binding (GO:0005509)	p.S257N(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	19		Colorectal(325;3.46e-05)|Lung NSC(340;0.00038)|all_lung(284;0.00051)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0505)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0421)|OV - Ovarian serous cystadenocarcinoma(117;1.26e-25)|Colorectal(126;3.01e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|BRCA - Breast invasive adenocarcinoma(304;0.00099)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0143)|READ - Rectum adenocarcinoma(331;0.0649)		CGGCTCCTGAGCATGTTCCAC	0.647																																					p.S257N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G770A	1						.						69.0	76.0	74.0					1																	26135539		2062	4190	6252	26008126	SO:0001583	missense	57190	exon6			AF166125	CCDS41282.1, CCDS41283.1	1p36.13	2014-09-17	2004-02-13		ENSG00000162430	ENSG00000162430		"""EF-hand domain containing"""	15999	protein-coding gene	gene with protein product		606210	"""rigid spine muscular dystrophy 1"""	RSMD1, MDRS1		10608886	Standard	NM_020451		Approved	selN, RSS	uc021ojl.1	Q9NZV5	OTTHUMG00000007375	ENST00000374315.1:c.668G>A	1.37:g.26135539G>A	ENSP00000363434:p.Ser223Asn	Somatic		Capture	Illumina HiSeq	Phase_I	26008126	NM_020451	A6NJG8|A8MQ64|Q6PI70|Q969F6|Q9NUI6	Missense_Mutation	SNP	ENST00000374315.1	37	CCDS41283.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.544361	0.86022	.	.	ENSG00000162430	ENST00000361547;ENST00000354177;ENST00000374315	D;D;D	0.89746	-2.56;-2.55;-2.54	5.84	5.84	0.93424	.	0.116646	0.85682	D	0.000000	D	0.90501	0.7024	M	0.63428	1.95	0.58432	D	0.999999	P;P	0.46395	0.868;0.877	P;P	0.49226	0.603;0.494	D	0.90883	0.4755	10	0.62326	D	0.03	-20.927	15.5923	0.76543	0.0:0.137:0.863:0.0	.	223;257	Q9NZV5-2;Q9NZV5	.;SELN_HUMAN	N	257;223;223	ENSP00000355141:S257N;ENSP00000346109:S223N;ENSP00000363434:S223N	ENSP00000346109:S223N	S	+	2	0	SEPN1	26008126	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.221000	0.72243	2.768000	0.95171	0.561000	0.74099	AGC		0.647	SEPN1-002	KNOWN	basic|appris_candidate_longest|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000019315.2	NM_020451	
LIN28A	79727	broad.mit.edu	37	1	26738004	26738004	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:26738004C>T	ENST00000326279.6	+	2	273	c.159C>T	c.(157-159)ttC>ttT	p.F53F	LIN28A_ENST00000254231.4_Silent_p.F53F	NM_024674.4	NP_078950.1	Q9H9Z2	LN28A_HUMAN	lin-28 homolog A (C. elegans)	53	CSD.				germ cell development (GO:0007281)|miRNA catabolic process (GO:0010587)|negative regulation of glial cell differentiation (GO:0045686)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of translation (GO:0045727)|pre-miRNA processing (GO:0031054)|regulation of gene silencing by miRNA (GO:0060964)|regulation of transcription, DNA-templated (GO:0006355)|RNA 3'-end processing (GO:0031123)|stem cell maintenance (GO:0019827)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|miRNA binding (GO:0035198)|mRNA binding (GO:0003729)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.F53F(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)	8						GCATGGGGTTCGGCTTCCTGT	0.687																																					p.F53F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C159T	1						.						47.0	52.0	50.0					1																	26738004		2202	4299	6501	26610591	SO:0001819	synonymous_variant	79727	exon2			AF521099	CCDS280.1	1p35.3	2013-01-09	2010-04-06	2010-04-06	ENSG00000131914	ENSG00000131914		"""Zinc fingers, CCHC domain containing"""	15986	protein-coding gene	gene with protein product		611043	"""lin-28 homolog (C. elegans)"""	LIN28		12798299	Standard	XM_006710899		Approved	LIN-28, FLJ12457, ZCCHC1, CSDD1	uc001bmj.3	Q9H9Z2	OTTHUMG00000003550	ENST00000326279.6:c.159C>T	1.37:g.26738004C>T		Somatic		Capture	Illumina HiSeq	Phase_I	26610591	NM_024674		Silent	SNP	ENST00000326279.6	37	CCDS280.1																																																																																				0.687	LIN28A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009891.2	NM_024674	
WDTC1	23038	broad.mit.edu	37	1	27587578	27587578	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:27587578C>T	ENST00000319394.3	+	2	568	c.33C>T	c.(31-33)atC>atT	p.I11I	WDTC1_ENST00000361771.3_Silent_p.I11I	NM_001276252.1|NM_015023.3	NP_001263181.1|NP_055838.2	Q8N5D0	WDTC1_HUMAN	WD and tetratricopeptide repeats 1	11					cellular chemical homeostasis (GO:0055082)|cellular response to insulin stimulus (GO:0032869)|glucose metabolic process (GO:0006006)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|regulation of cell size (GO:0008361)	cytosol (GO:0005829)|nucleus (GO:0005634)	enzyme inhibitor activity (GO:0004857)	p.I11I(1)		central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|skin(1)	21		all_cancers(24;3.12e-19)|all_epithelial(13;4.18e-18)|Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.00257)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0443)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;1.02e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00201)|STAD - Stomach adenocarcinoma(196;0.00321)|READ - Rectum adenocarcinoma(331;0.0476)		GAGACCTCATCCGTAGGCAGA	0.413																																					p.I11I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C33T	1						.						115.0	110.0	112.0					1																	27587578		2203	4300	6503	27460165	SO:0001819	synonymous_variant	23038	exon2			AK023778	CCDS296.1, CCDS60044.1	1p35.3	2013-01-11			ENSG00000142784	ENSG00000142784		"""DDB1 and CUL4 associated factors"", ""WD repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29175	protein-coding gene	gene with protein product	"""adipose homolog (Drosophila)"", ""DDB1 and CUL4 associated factor 9"""					12717455, 19238144	Standard	NM_015023		Approved	KIAA1037, ADP, DCAF9	uc009vst.3	Q8N5D0	OTTHUMG00000004273	ENST00000319394.3:c.33C>T	1.37:g.27587578C>T		Somatic		Capture	Illumina HiSeq	Phase_I	27460165	NM_015023	D3DPL5|Q5SSC5|Q9NV87|Q9UPW4	Silent	SNP	ENST00000319394.3	37																																																																																					0.413	WDTC1-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015023	
RCC1	1104	broad.mit.edu	37	1	28858745	28858745	+	Silent	SNP	G	G	T	rs202047602		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:28858745G>T	ENST00000373833.6	+	7	609	c.324G>T	c.(322-324)tcG>tcT	p.S108S	RCC1_ENST00000398958.2_Silent_p.S108S|RCC1_ENST00000373831.3_Silent_p.S139S|RCC1_ENST00000373832.1_Silent_p.S108S|RCC1_ENST00000429051.1_3'UTR			P18754	RCC1_HUMAN	regulator of chromosome condensation 1	108					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.S108S(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)		TGGAGGGCTCGGAGATGGTCC	0.582																																					p.S108S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G324T	1						.						91.0	74.0	80.0					1																	28858745		2203	4300	6503	28731332	SO:0001819	synonymous_variant	1104	exon4			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.324G>T	1.37:g.28858745G>T		Somatic		Capture	Illumina HiSeq	Phase_I	28731332	NM_001269	Q16269|Q6NT97	Silent	SNP	ENST00000373833.6	37	CCDS323.1																																																																																				0.582	RCC1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010323.3	NM_001269	
CSMD2	114784	broad.mit.edu	37	1	34383774	34383774	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:34383774C>T	ENST00000373381.4	-	5	1017	c.841G>A	c.(841-843)Gcc>Acc	p.A281T		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	241	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A241T(1)		NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				AACACCAGGGCGATGGTGTCC	0.567																																					p.A241T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G721A	1						.						106.0	88.0	94.0					1																	34383774		2203	4300	6503	34156361	SO:0001583	missense	114784	exon5			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.841G>A	1.37:g.34383774C>T	ENSP00000362479:p.Ala281Thr	Somatic		Capture	Illumina HiSeq	Phase_I	34156361	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		.	.	.	.	.	.	.	.	.	.	C	13.57	2.277212	0.40294	.	.	ENSG00000121904	ENST00000373381	T	0.17370	2.28	5.48	5.48	0.80851	CUB (5);	0.000000	0.64402	D	0.000001	T	0.23846	0.0577	N	0.13371	0.34	0.80722	D	1	P;D	0.67145	0.706;0.996	B;D	0.66196	0.2;0.942	T	0.09975	-1.0650	10	0.18276	T	0.48	.	18.3364	0.90290	0.0:1.0:0.0:0.0	.	241;281	Q7Z408;E7EUA6	CSMD2_HUMAN;.	T	281	ENSP00000362479:A281T	ENSP00000241312:A241T	A	-	1	0	CSMD2	34156361	1.000000	0.71417	1.000000	0.80357	0.533000	0.34776	5.913000	0.69957	2.591000	0.87537	0.478000	0.44815	GCC		0.567	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896	
SFPQ	6421	broad.mit.edu	37	1	35653648	35653648	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:35653648G>A	ENST00000357214.5	-	7	1839	c.1741C>T	c.(1741-1743)Cgt>Tgt	p.R581C		NM_005066.2	NP_005057.1	P23246	SFPQ_HUMAN	splicing factor proline/glutamine-rich	581					alternative mRNA splicing, via spliceosome (GO:0000380)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H3 deacetylation (GO:0070932)|mRNA processing (GO:0006397)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902177)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|histone deacetylase binding (GO:0042826)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.R581C(1)	SFPQ/TFE3(6)	NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(4)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	25		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.196)				TCACGTTGACGAATCATCATC	0.438			T	TFE3	papillary renal cell																																p.R581C			Dom	yes		1	1p34.3	6421	splicing factor proline/glutamine rich(polypyrimidine tract binding protein associated)		E	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1741T	1						.						388.0	334.0	352.0					1																	35653648		2203	4300	6503	35426235	SO:0001583	missense	6421	exon7			X70944	CCDS388.1	1p34.3	2014-06-13	2010-05-04		ENSG00000116560	ENSG00000116560		"""RNA binding motif (RRM) containing"""	10774	protein-coding gene	gene with protein product	"""polypyrimidine tract binding protein associated"", ""protein phosphatase 1, regulatory subunit 140"""	605199	"""splicing factor proline/glutamine rich (polypyrimidine tract-binding protein-associated)"""			8449401	Standard	NM_005066		Approved	PSF, PPP1R140	uc001bys.3	P23246	OTTHUMG00000004157	ENST00000357214.5:c.1741C>T	1.37:g.35653648G>A	ENSP00000349748:p.Arg581Cys	Somatic		Capture	Illumina HiSeq	Phase_I	35426235	NM_005066	P30808|Q5SZ71	Missense_Mutation	SNP	ENST00000357214.5	37	CCDS388.1	.	.	.	.	.	.	.	.	.	.	G	35	5.422185	0.96111	.	.	ENSG00000116560	ENST00000357214	D	0.92911	-3.13	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	D	0.91352	0.7272	L	0.50333	1.59	0.80722	D	1	D	0.58970	0.984	P	0.45474	0.482	D	0.90231	0.4279	9	.	.	.	-7.7665	20.0656	0.97703	0.0:0.0:1.0:0.0	.	581	P23246	SFPQ_HUMAN	C	581	ENSP00000349748:R581C	.	R	-	1	0	SFPQ	35426235	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.638000	0.83328	2.752000	0.94435	0.555000	0.69702	CGT		0.438	SFPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011984.4	NM_005066	
ZMYM4	9202	broad.mit.edu	37	1	35835643	35835643	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:35835643G>A	ENST00000314607.6	+	6	934	c.854G>A	c.(853-855)gGc>gAc	p.G285D	ZMYM4_ENST00000373297.2_Missense_Mutation_p.G285D|ZMYM4_ENST00000482131.1_3'UTR	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	285					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.G285D(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2)	54		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TATAGTCATGGCCAACAGCAA	0.353																																					p.G285D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G854A	1						.						61.0	61.0	61.0					1																	35835643		2203	4300	6503	35608230	SO:0001583	missense	9202	exon6			AB007885	CCDS389.1	1p34-p32	2013-01-08	2005-12-19	2005-12-19	ENSG00000146463	ENSG00000146463		"""Zinc fingers, MYM type"""	13055	protein-coding gene	gene with protein product		613568	"""zinc finger protein 262"""	ZNF262		10449923	Standard	NM_005095		Approved	KIAA0425, ZNF198L3, MYM	uc001byt.3	Q5VZL5	OTTHUMG00000004241	ENST00000314607.6:c.854G>A	1.37:g.35835643G>A	ENSP00000322915:p.Gly285Asp	Somatic		Capture	Illumina HiSeq	Phase_I	35608230	NM_005095	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	Missense_Mutation	SNP	ENST00000314607.6	37	CCDS389.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.23|16.23	3.064768|3.064768	0.55432|0.55432	.|.	.|.	ENSG00000146463|ENSG00000146463	ENST00000314607;ENST00000373297|ENST00000457946	T;T|.	0.23754|.	1.95;1.89|.	5.63|5.63	5.63|5.63	0.86233|0.86233	.|.	0.149615|.	0.43579|.	D|.	0.000544|.	T|.	0.43322|.	0.1242|.	N|N	0.14661|0.14661	0.345|0.345	0.34192|0.34192	D|D	0.672208|0.672208	B|.	0.16166|.	0.016|.	B|.	0.14023|.	0.01|.	T|.	0.52975|.	-0.8503|.	10|.	0.12766|.	T|.	0.61|.	-7.6158|-7.6158	15.1904|15.1904	0.73038|0.73038	0.0:0.1404:0.8596:0.0|0.0:0.1404:0.8596:0.0	.|.	285|.	Q5VZL5|.	ZMYM4_HUMAN|.	D|X	285|33	ENSP00000322915:G285D;ENSP00000362394:G285D|.	ENSP00000322915:G285D|.	G|W	+|+	2|3	0|0	ZMYM4|ZMYM4	35608230|35608230	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	3.901000|3.901000	0.56303|0.56303	2.652000|2.652000	0.90054|0.90054	0.591000|0.591000	0.81541|0.81541	GGC|TGG		0.353	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012207.3	NM_005095	
PSMB2	5690	broad.mit.edu	37	1	36096876	36096876	+	Splice_Site	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:36096876C>A	ENST00000373237.3	-	3	695	c.284G>T	c.(283-285)cGg>cTg	p.R95L		NM_002794.4	NP_002785.1	P49721	PSB2_HUMAN	proteasome (prosome, macropain) subunit, beta type, 2	95					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|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 complex (GO:0000502)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)	p.R95L(1)		endometrium(1)|large_intestine(2)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)			Bortezomib(DB00188)|Carfilzomib(DB08889)	ATTACTTACCCGACTCCGAAG	0.388																																					p.R70L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G209T	1						.						68.0	68.0	68.0					1																	36096876		2203	4300	6503	35869463	SO:0001630	splice_region_variant	5690	exon3			D26599	CCDS394.1, CCDS72755.1	1p34.2	2008-02-05			ENSG00000126067	ENSG00000126067		"""Proteasome (prosome, macropain) subunits"""	9539	protein-coding gene	gene with protein product		602175				7918633	Standard	NM_002794		Approved	HC7-I	uc001bzf.2	P49721	OTTHUMG00000004169	ENST00000373237.3:c.285+1G>T	1.37:g.36096876C>A		Somatic		Capture	Illumina HiSeq	Phase_I	35869463	NM_001199779	D3DPS0|P31145|Q9BWZ9	Missense_Mutation	SNP	ENST00000373237.3	37	CCDS394.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.338343	0.81911	.	.	ENSG00000126067	ENST00000373237	T	0.25085	1.82	5.64	5.64	0.86602	.	0.052410	0.85682	D	0.000000	T	0.40094	0.1103	M	0.84511	2.7	0.80722	D	1	B;B;B	0.28350	0.208;0.124;0.048	B;B;B	0.30179	0.112;0.076;0.069	T	0.39583	-0.9607	10	0.87932	D	0	.	18.2699	0.90064	0.0:1.0:0.0:0.0	.	70;95;127	B7Z478;P49721;Q59FJ0	.;PSB2_HUMAN;.	L	95	ENSP00000362334:R95L	ENSP00000362334:R95L	R	-	2	0	PSMB2	35869463	1.000000	0.71417	1.000000	0.80357	0.865000	0.49528	7.467000	0.80930	2.832000	0.97577	0.655000	0.94253	CGG		0.388	PSMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012016.1	NM_002794	Missense_Mutation
AGO1	26523	broad.mit.edu	37	1	36385189	36385189	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:36385189G>A	ENST00000373204.4	+	19	2768	c.2555G>A	c.(2554-2556)cGc>cAc	p.R852H	AGO1_ENST00000373206.1_Missense_Mutation_p.R777H	NM_012199.2	NP_036331.1	Q9UL18	AGO1_HUMAN	argonaute RISC catalytic component 1	852					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)|nuclear-transcribed mRNA catabolic process (GO:0000956)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R852H(1)									GATACTCTGCGCACCATGTAC	0.572																																					p.R852H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2555A	1						.						55.0	54.0	54.0					1																	36385189		2203	4300	6503	36157776	SO:0001583	missense	26523	exon19			AF093097	CCDS398.1	1p34.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000092847	ENSG00000092847		"""Argonaute/PIWI family"""	3262	protein-coding gene	gene with protein product	"""argonaute 1"""	606228	"""eukaryotic translation initiation factor 2C, 1"""	EIF2C1		10534406, 12906857	Standard	NM_012199		Approved	hAGO1	uc001bzl.3	Q9UL18	OTTHUMG00000007381	ENST00000373204.4:c.2555G>A	1.37:g.36385189G>A	ENSP00000362300:p.Arg852His	Somatic		Capture	Illumina HiSeq	Phase_I	36157776	NM_012199	Q5TA57|Q6P4S0	Missense_Mutation	SNP	ENST00000373204.4	37	CCDS398.1	.	.	.	.	.	.	.	.	.	.	G	14.80	2.642462	0.47153	.	.	ENSG00000092847	ENST00000373206;ENST00000373204	T;T	0.09911	2.93;2.93	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.09992	0.0245	N	0.19112	0.55	0.80722	D	1	B	0.13594	0.008	B	0.09377	0.004	T	0.17018	-1.0383	10	0.46703	T	0.11	-9.2036	19.6069	0.95585	0.0:0.0:1.0:0.0	.	852	Q9UL18	AGO1_HUMAN	H	777;852	ENSP00000362302:R777H;ENSP00000362300:R852H	ENSP00000362300:R852H	R	+	2	0	EIF2C1	36157776	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	8.018000	0.88722	2.706000	0.92434	0.655000	0.94253	CGC		0.572	AGO1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019337.3		
AGO3	192669	broad.mit.edu	37	1	36475180	36475180	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:36475180G>T	ENST00000373191.4	+	9	1483	c.1134G>T	c.(1132-1134)gaG>gaT	p.E378D	AGO3_ENST00000246314.6_Missense_Mutation_p.E144D|RP4-665N4.8_ENST00000479395.2_RNA|RP4-665N4.8_ENST00000466576.2_RNA	NM_024852.3	NP_079128.2	Q9H9G7	AGO3_HUMAN	argonaute RISC catalytic component 3	378					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)|mRNA catabolic process (GO:0006402)|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)|regulation of stem cell proliferation (GO:0072091)	cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)	p.E378D(1)									ATAGACAAGAGGAAATTAGCA	0.378																																					p.E144D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G432T	1						.						93.0	87.0	89.0					1																	36475180		2203	4300	6503	36247767	SO:0001583	missense	192669	exon7			AB046787	CCDS399.1, CCDS400.1	1p34	2013-06-03	2013-02-15	2013-02-15	ENSG00000126070	ENSG00000126070		"""Argonaute/PIWI family"""	18421	protein-coding gene	gene with protein product	"""argonaute 3"""	607355	"""eukaryotic translation initiation factor 2C, 3"""	EIF2C3		12906857	Standard	NM_024852		Approved	hAGO3, FLJ12765	uc001bzp.3	Q9H9G7	OTTHUMG00000184172	ENST00000373191.4:c.1134G>T	1.37:g.36475180G>T	ENSP00000362287:p.Glu378Asp	Somatic		Capture	Illumina HiSeq	Phase_I	36247767	NM_177422	B1ALI0|Q5TA55|Q9H1U6	Missense_Mutation	SNP	ENST00000373191.4	37	CCDS399.1	.	.	.	.	.	.	.	.	.	.	G	15.75	2.926297	0.52759	.	.	ENSG00000126070	ENST00000373191;ENST00000246314	T;T	0.10477	2.87;2.88	6.06	2.08	0.27032	Argonaute/Dicer protein, PAZ (1);	0.044704	0.85682	N	0.000000	T	0.08670	0.0215	L	0.41961	1.31	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.19484	-1.0304	10	0.31617	T	0.26	-9.0431	7.3344	0.26601	0.2483:0.1112:0.6405:0.0	.	378	Q9H9G7	AGO3_HUMAN	D	378;144	ENSP00000362287:E378D;ENSP00000246314:E144D	ENSP00000246314:E144D	E	+	3	2	EIF2C3	36247767	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.496000	0.45346	0.444000	0.26612	0.655000	0.94253	GAG		0.378	AGO3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019831.4	NM_024852	
STK40	83931	broad.mit.edu	37	1	36820947	36820947	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:36820947G>T	ENST00000373129.3	-	6	836	c.430C>A	c.(430-432)Ctc>Atc	p.L144I	STK40_ENST00000482458.1_5'UTR|STK40_ENST00000373130.3_Missense_Mutation_p.L149I|STK40_ENST00000359297.2_Missense_Mutation_p.L144I|STK40_ENST00000373132.3_Missense_Mutation_p.L144I	NM_032017.1	NP_114406.1	Q8N2I9	STK40_HUMAN	serine/threonine kinase 40	144	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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.L144I(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)				TGAGCACAGAGGCAGTCCAGG	0.542																																					p.L144I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C430A	1						.						314.0	273.0	287.0					1																	36820947		2203	4300	6503	36593534	SO:0001583	missense	83931	exon6			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.430C>A	1.37:g.36820947G>T	ENSP00000362221:p.Leu144Ile	Somatic		Capture	Illumina HiSeq	Phase_I	36593534	NM_032017	D3DPS8|Q5VTK8|Q5VTK9|Q6ZMN1|Q8N2J8|Q8N3I6|Q96HN6|Q96I44|Q9BSA3|Q9H7H6	Missense_Mutation	SNP	ENST00000373129.3	37	CCDS407.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.672290	0.88348	.	.	ENSG00000196182	ENST00000373129;ENST00000359297;ENST00000373130;ENST00000373132	T;T;T;T	0.74315	-0.83;1.94;1.94;-0.83	5.91	5.91	0.95273	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.80576	0.4649	L	0.53561	1.675	0.48830	D	0.999715	D;D;D	0.63046	0.99;0.99;0.992	P;P;P	0.61070	0.814;0.814;0.883	T	0.80195	-0.1483	10	0.51188	T	0.08	-16.2269	12.5742	0.56355	0.0751:0.0:0.9249:0.0	.	144;149;144	Q8N2I9-3;Q8N2I9-4;Q8N2I9	.;.;STK40_HUMAN	I	144;144;149;144	ENSP00000362221:L144I;ENSP00000352245:L144I;ENSP00000362222:L149I;ENSP00000362224:L144I	ENSP00000352245:L144I	L	-	1	0	STK40	36593534	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.390000	0.66261	2.804000	0.96469	0.462000	0.41574	CTC		0.542	STK40-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022592.1	NM_032017	
MACF1	23499	broad.mit.edu	37	1	39783045	39783045	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:39783045C>T	ENST00000372915.3	+	28	3850	c.3763C>T	c.(3763-3765)Cgt>Tgt	p.R1255C	MACF1_ENST00000361689.2_Missense_Mutation_p.R1255C|MACF1_ENST00000545844.1_Missense_Mutation_p.R1255C|MACF1_ENST00000567887.1_Missense_Mutation_p.R1287C|MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000564288.1_Missense_Mutation_p.R1250C|MACF1_ENST00000317713.7_Missense_Mutation_p.R1255C|MACF1_ENST00000539005.1_Missense_Mutation_p.R1255C			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	1255					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.R1255C(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)			GCTGCAGGAGCGTTGGCACCG	0.527																																					p.R1255C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3763T	1						.						81.0	78.0	79.0					1																	39783045		2203	4300	6503	39555632	SO:0001583	missense	23499	exon30			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.3763C>T	1.37:g.39783045C>T	ENSP00000362006:p.Arg1255Cys	Somatic		Capture	Illumina HiSeq	Phase_I	39555632	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.6|24.6	4.553339|4.553339	0.86127|0.86127	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000372925|ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000524432;ENST00000530262	.|T;T;T;T;T;T;T	.|0.40476	.|1.03;1.03;1.03;1.03;1.03;1.03;1.03	5.75|5.75	5.75|5.75	0.90469|0.90469	.|.	.|.	.|.	.|.	.|.	T|T	0.69278|0.69278	0.3093|0.3093	M|M	0.81497|0.81497	2.545|2.545	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|0.987;0.999;1.0	.|P;D;D	.|0.91635	.|0.781;0.931;0.999	T|T	0.72023|0.72023	-0.4415|-0.4415	5|9	.|0.87932	.|D	.|0	.|.	19.994|19.994	0.97377|0.97377	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1255;1255;1220	.|F8W8Q1;Q9UPN3-2;Q9UPN3-3	.|.;.;.	V|C	388|1255;1255;1255;1255;1255;1213;1404	.|ENSP00000439537:R1255C;ENSP00000362006:R1255C;ENSP00000354573:R1255C;ENSP00000313438:R1255C;ENSP00000444364:R1255C;ENSP00000435070:R1213C;ENSP00000437059:R1404C	.|ENSP00000313438:R1255C	A|R	+|+	2|1	0|0	MACF1|MACF1	39555632|39555632	0.999000|0.999000	0.42202|0.42202	0.978000|0.978000	0.43139|0.43139	0.992000|0.992000	0.81027|0.81027	4.079000|4.079000	0.57613|0.57613	2.729000|2.729000	0.93468|0.93468	0.558000|0.558000	0.71614|0.71614	GCG|CGT		0.527	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	39802867	39802867	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:39802867G>T	ENST00000372915.3	+	37	10181	c.10094G>T	c.(10093-10095)cGg>cTg	p.R3365L	MACF1_ENST00000289893.4_Missense_Mutation_p.R1800L|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000567887.1_Missense_Mutation_p.R3397L|MACF1_ENST00000476350.1_Intron|MACF1_ENST00000564288.1_Missense_Mutation_p.R3360L|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000539005.1_Intron			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	3365					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.R1800L(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)			GTATTTACCCGGCAACTCTGT	0.408																																					p.R1800L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5399T	1						.						145.0	133.0	137.0					1																	39802867		2203	4300	6503	39575454	SO:0001583	missense	23499	exon2			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.10094G>T	1.37:g.39802867G>T	ENSP00000362006:p.Arg3365Leu	Somatic		Capture	Illumina HiSeq	Phase_I	39575454	NM_033044	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.	.	.	.	.	.	.	.	.	.	G	15.13	2.741724	0.49151	.	.	ENSG00000127603	ENST00000372915;ENST00000289893	T;T	0.64085	-0.08;0.95	5.41	5.41	0.78517	.	0.533022	0.17032	N	0.189668	T	0.62429	0.2427	L	0.32530	0.975	0.58432	D	0.999999	D	0.63046	0.992	P	0.62298	0.9	T	0.56019	-0.8048	10	0.20519	T	0.43	.	7.4465	0.27213	0.2063:0.0:0.7937:0.0	.	3365	Q9UPN3	MACF1_HUMAN	L	3365;1800	ENSP00000362006:R3365L;ENSP00000289893:R1800L	ENSP00000289893:R1800L	R	+	2	0	MACF1	39575454	1.000000	0.71417	0.784000	0.31847	0.930000	0.56654	3.902000	0.56310	2.524000	0.85096	0.557000	0.71058	CGG		0.408	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
NT5C1A	84618	broad.mit.edu	37	1	40129063	40129063	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:40129063C>T	ENST00000235628.1	-	4	476	c.477G>A	c.(475-477)ccG>ccA	p.P159P		NM_032526.1	NP_115915.1	Q9BXI3	5NT1A_HUMAN	5'-nucleotidase, cytosolic IA	159					adenosine metabolic process (GO:0046085)|dephosphorylation (GO:0016311)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|purine nucleobase metabolic process (GO:0006144)|purine nucleoside monophosphate catabolic process (GO:0009128)|purine nucleotide catabolic process (GO:0006195)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	5'-nucleotidase activity (GO:0008253)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)	p.P159P(1)		breast(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(2)	15	Lung NSC(20;3.81e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;4.3e-17)|all cancers(16;8.48e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			GGTAGCAGATCGGGCTGTTCC	0.542																																					p.P159P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G477A	1						.						134.0	118.0	123.0					1																	40129063		2203	4300	6503	39901650	SO:0001819	synonymous_variant	84618	exon4			AF331801	CCDS440.1	1p34.3-p33	2008-07-18			ENSG00000116981	ENSG00000116981			17819	protein-coding gene	gene with protein product	"""cytosolic 5' nucleotidase, type 1A"", ""AMP-specific 5'-NT"", ""cytosolic 5'-nucleotidase IA"""	610525				11133996, 11690631	Standard	NM_032526		Approved	CN-I, CN-IA, CN1A, CN1, MGC119199, MGC119201	uc001cdq.1	Q9BXI3	OTTHUMG00000009244	ENST00000235628.1:c.477G>A	1.37:g.40129063C>T		Somatic		Capture	Illumina HiSeq	Phase_I	39901650	NM_032526	Q3SYB9|Q5TG98|Q9BWT8	Silent	SNP	ENST00000235628.1	37	CCDS440.1																																																																																				0.542	NT5C1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025626.1	NM_032526	
RLF	6018	broad.mit.edu	37	1	40703416	40703416	+	Silent	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:40703416C>A	ENST00000372771.4	+	8	3069	c.3042C>A	c.(3040-3042)ccC>ccA	p.P1014P		NM_012421.3	NP_036553.2	Q13129	RLF_HUMAN	rearranged L-myc fusion	1014					chromosome organization (GO:0051276)|DNA integration (GO:0015074)|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)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.P1014P(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(18)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(4)|urinary_tract(2)	68	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;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)			AACCTAAACCCTGCTCAGATA	0.388																																					p.P1014P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3042A	1						.						57.0	56.0	56.0					1																	40703416		2203	4300	6503	40476003	SO:0001819	synonymous_variant	6018	exon8				CCDS448.1	1p32	2010-05-07	2005-08-16		ENSG00000117000	ENSG00000117000		"""Zinc fingers, C2H2-type"""	10025	protein-coding gene	gene with protein product		180610	"""rearranged L-myc fusion sequence"""			1649386	Standard	NM_012421		Approved	ZNF292L, Zn-15L	uc001cfc.4	Q13129	OTTHUMG00000005763	ENST00000372771.4:c.3042C>A	1.37:g.40703416C>A		Somatic		Capture	Illumina HiSeq	Phase_I	40476003	NM_012421	Q14CQ1|Q9NU60	Silent	SNP	ENST00000372771.4	37	CCDS448.1																																																																																				0.388	RLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015767.1	NM_012421	
CLDN19	149461	broad.mit.edu	37	1	43204199	43204199	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:43204199G>A	ENST00000296387.1	-	2	471	c.281C>T	c.(280-282)gCc>gTc	p.A94V	CLDN19_ENST00000539749.1_Missense_Mutation_p.A94V|CLDN19_ENST00000372539.3_Missense_Mutation_p.A94V	NM_001123395.1|NM_148960.2	NP_001116867.1|NP_683763.2	Q8N6F1	CLD19_HUMAN	claudin 19	94					apical junction assembly (GO:0043297)|calcium-independent cell-cell adhesion (GO:0016338)|neuronal action potential propagation (GO:0019227)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	apical junction complex (GO:0043296)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)	p.A94V(1)		breast(2)|large_intestine(1)|lung(2)|skin(1)	6	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				GAGGACCATGGCCACGAAGCC	0.652																																					p.A94V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C281T	1						.						92.0	74.0	80.0					1																	43204199		2203	4300	6503	42976786	SO:0001583	missense	149461	exon2			AK096063	CCDS471.1, CCDS44125.1, CCDS53306.1	1p34.2	2008-05-14			ENSG00000164007	ENSG00000164007		"""Claudins"""	2040	protein-coding gene	gene with protein product		610036					Standard	NM_148960		Approved		uc001cht.1	Q8N6F1	OTTHUMG00000007524	ENST00000296387.1:c.281C>T	1.37:g.43204199G>A	ENSP00000296387:p.Ala94Val	Somatic		Capture	Illumina HiSeq	Phase_I	42976786	NM_148960	B7Z5I2|F5H5P9|Q5QT57|Q8N8X0	Missense_Mutation	SNP	ENST00000296387.1	37	CCDS471.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.266729	0.80358	.	.	ENSG00000164007	ENST00000296387;ENST00000539749;ENST00000372539	D;D;D	0.90004	-2.6;-2.6;-2.6	4.89	1.73	0.24493	.	0.163434	0.53938	D	0.000050	D	0.92802	0.7711	M	0.74258	2.255	0.33655	D	0.608988	D;P;P	0.58970	0.984;0.921;0.936	D;P;P	0.63703	0.917;0.743;0.868	D	0.94959	0.8106	10	0.87932	D	0	.	14.0314	0.64617	0.0:0.6746:0.3254:0.0	.	94;94;94	F5H5P9;Q8N6F1-2;Q8N6F1	.;.;CLD19_HUMAN	V	94	ENSP00000296387:A94V;ENSP00000443229:A94V;ENSP00000361617:A94V	ENSP00000296387:A94V	A	-	2	0	CLDN19	42976786	0.994000	0.37717	1.000000	0.80357	0.777000	0.43975	0.932000	0.28884	0.444000	0.26612	0.313000	0.20887	GCC		0.652	CLDN19-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019788.1	NM_148960	
EIF2B3	8891	broad.mit.edu	37	1	45407190	45407190	+	Missense_Mutation	SNP	T	T	C	rs151056457	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:45407190T>C	ENST00000360403.2	-	4	568	c.442A>G	c.(442-444)Aaa>Gaa	p.K148E	EIF2B3_ENST00000372183.3_Missense_Mutation_p.K148E|EIF2B3_ENST00000480675.1_5'UTR	NM_001261418.1|NM_020365.4	NP_001248347.1|NP_065098.1	Q9NR50	EI2BG_HUMAN	eukaryotic translation initiation factor 2B, subunit 3 gamma, 58kDa	148					cellular protein metabolic process (GO:0044267)|cellular response to stimulus (GO:0051716)|gene expression (GO:0010467)|negative regulation of translational initiation in response to stress (GO:0032057)|oligodendrocyte development (GO:0014003)|positive regulation of GTPase activity (GO:0043547)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to peptide hormone (GO:0043434)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation initiation factor 2B complex (GO:0005851)	guanyl-nucleotide exchange factor activity (GO:0005085)|nucleotidyltransferase activity (GO:0016779)|translation initiation factor activity (GO:0003743)	p.K148E(1)		endometrium(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)	17	Acute lymphoblastic leukemia(166;0.155)					GCTTTTTTTTTCCCCTTTTGA	0.368													T|||	5	0.000998403	0.0015	0.0	5008	,	,		20377	0.002		0.0	False		,,,				2504	0.001				p.K148E	Colon(26;357 658 2581 11857 12657)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A442G	1						.																																			45179777	SO:0001583	missense	8891	exon4			AF257077	CCDS517.1, CCDS53313.1, CCDS72775.1	1p34.1	2008-02-05	2002-08-29		ENSG00000070785	ENSG00000070785			3259	protein-coding gene	gene with protein product		606273	"""eukaryotic translation initiation factor 2B, subunit 3 (gamma, 58kD)"""			10900014	Standard	NM_020365		Approved	EIF2Bgamma, EIF-2B	uc001cmt.3	Q9NR50	OTTHUMG00000008585	ENST00000360403.2:c.442A>G	1.37:g.45407190T>C	ENSP00000353575:p.Lys148Glu	Somatic		Capture	Illumina HiSeq	Phase_I	45179777	NM_001166588	B2RBH8|D3DPZ2|Q5QP89|Q5QP90|Q8NDB5|Q8WV57|Q9H850	Missense_Mutation	SNP	ENST00000360403.2	37	CCDS517.1	4	0.0018315018315018315	2	0.0040650406504065045	0	0.0	2	0.0034965034965034965	0	0.0	T	24.8	4.567602	0.86439	.	.	ENSG00000070785	ENST00000360403;ENST00000372183;ENST00000372182	D;D;D	0.93019	-3.15;-2.65;-1.8	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	D	0.96466	0.8847	M	0.84683	2.71	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.992	D;D;D	0.77557	0.99;0.956;0.917	D	0.95605	0.8666	10	0.17832	T	0.49	-7.2339	15.4686	0.75422	0.0:0.0:0.0:1.0	.	148;148;148	Q9NR50-2;Q9NR50-3;Q9NR50	.;.;EI2BG_HUMAN	E	148	ENSP00000353575:K148E;ENSP00000361257:K148E;ENSP00000361256:K148E	ENSP00000353575:K148E	K	-	1	0	EIF2B3	45179777	1.000000	0.71417	0.993000	0.49108	0.808000	0.45660	4.634000	0.61325	2.063000	0.61619	0.482000	0.46254	AAA		0.368	EIF2B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023724.1	NM_020365	
NASP	4678	broad.mit.edu	37	1	46080716	46080716	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:46080716G>A	ENST00000350030.3	+	10	1785	c.1698G>A	c.(1696-1698)caG>caA	p.Q566Q	NASP_ENST00000372052.4_Silent_p.Q200Q|NASP_ENST00000537798.1_Silent_p.Q502Q|NASP_ENST00000530073.1_3'UTR|NASP_ENST00000402363.3_Silent_p.Q568Q|NASP_ENST00000351223.3_Silent_p.Q227Q	NM_002482.3	NP_002473.2	P49321	NASP_HUMAN	nuclear autoantigenic sperm protein (histone-binding)	566	Glu-rich (acidic).				blastocyst development (GO:0001824)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone exchange (GO:0043486)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	Hsp90 protein binding (GO:0051879)	p.Q568Q(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	17	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.211)					AGGAGTTCCAGTCCTGCCTTA	0.468																																					p.Q502Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1506A	1						.						54.0	53.0	53.0					1																	46080716		2203	4300	6503	45853303	SO:0001819	synonymous_variant	4678	exon8			M97856	CCDS524.1, CCDS525.1, CCDS55597.1	1p34.1	2013-01-10			ENSG00000132780	ENSG00000132780		"""Tetratricopeptide (TTC) repeat domain containing"""	7644	protein-coding gene	gene with protein product		603185				1426632	Standard	NM_002482		Approved	FLB7527, FLJ31599, FLJ35510, MGC19722, MGC20372, MGC2297, DKFZp547F162, PRO1999	uc001coi.2	P49321	OTTHUMG00000007826	ENST00000350030.3:c.1698G>A	1.37:g.46080716G>A		Somatic		Capture	Illumina HiSeq	Phase_I	45853303	NM_001195193	A8K6H2|B4DQP3|D3DQ07|F5H3J2|Q53GW5|Q5T622|Q5T625|Q96A69|Q9BTW2	Silent	SNP	ENST00000350030.3	37	CCDS524.1	.	.	.	.	.	.	.	.	.	.	G	7.181	0.589517	0.13812	.	.	ENSG00000132780	ENST00000531612	.	.	.	5.3	5.3	0.74995	.	.	.	.	.	T	0.60314	0.2259	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58025	-0.7709	4	.	.	.	-9.8764	9.2298	0.37430	0.0763:0.1471:0.7767:0.0	.	.	.	.	N	91	.	.	S	+	2	0	NASP	45853303	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	4.129000	0.57957	2.635000	0.89317	0.655000	0.94253	AGT		0.468	NASP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021533.2	NM_002482	
CCDC17	149483	broad.mit.edu	37	1	46088016	46088016	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:46088016C>A	ENST00000528266.1	-	7	1011	c.864G>T	c.(862-864)agG>agT	p.R288S	CCDC17_ENST00000445048.2_Intron|CCDC17_ENST00000421127.2_Missense_Mutation_p.R279S|CCDC17_ENST00000343901.2_Missense_Mutation_p.R256S|CCDC17_ENST00000464739.1_Intron			Q96LX7	CCD17_HUMAN	coiled-coil domain containing 17	288								p.R256S(1)		kidney(1)|large_intestine(1)|lung(1)|ovary(2)	5	Acute lymphoblastic leukemia(166;0.155)					TGGCACCTGCCCTTCCTGCGA	0.597																																					p.R288S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G864T	1						.						52.0	48.0	50.0					1																	46088016		2203	4300	6503	45860603	SO:0001583	missense	149483	exon7				CCDS44131.1, CCDS44131.2, CCDS53314.1	1p34.1	2014-02-12			ENSG00000159588	ENSG00000159588			26574	protein-coding gene	gene with protein product							Standard	NM_001190182		Approved	FLJ33084	uc010olt.2	Q96LX7	OTTHUMG00000007822	ENST00000528266.1:c.864G>T	1.37:g.46088016C>A	ENSP00000432172:p.Arg288Ser	Somatic		Capture	Illumina HiSeq	Phase_I	45860603	NM_001114938	A1A4Y7|B4DNX7|B4E1Q5|C9J8L2|Q0P683|Q5T629	Missense_Mutation	SNP	ENST00000528266.1	37	CCDS44131.2	.	.	.	.	.	.	.	.	.	.	C	16.92	3.255853	0.59321	.	.	ENSG00000159588	ENST00000421127;ENST00000343901;ENST00000528266	T;T;T	0.19669	2.14;2.14;2.13	5.0	0.0115	0.14087	.	0.677323	0.15132	N	0.278794	T	0.17746	0.0426	L	0.42245	1.32	0.09310	N	1	P;P;P	0.52316	0.952;0.557;0.782	P;B;B	0.46659	0.523;0.085;0.349	T	0.11084	-1.0602	10	0.51188	T	0.08	-2.5844	3.7665	0.08624	0.1647:0.5017:0.0:0.3336	.	288;279;256	Q96LX7;Q96LX7-5;F2Z395	CCD17_HUMAN;.;.	S	279;256;288	ENSP00000389415:R279S;ENSP00000341451:R256S;ENSP00000432172:R288S	ENSP00000341451:R256S	R	-	3	2	CCDC17	45860603	.	.	0.000000	0.03702	0.179000	0.23085	.	.	-0.068000	0.12953	0.655000	0.94253	AGG		0.597	CCDC17-008	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386833.1	NM_152500	
MAST2	23139	broad.mit.edu	37	1	46494524	46494524	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:46494524A>C	ENST00000361297.2	+	18	2420	c.2137A>C	c.(2137-2139)Att>Ctt	p.I713L	MAST2_ENST00000372009.2_Missense_Mutation_p.I643L	NM_015112.2	NP_055927.2			microtubule associated serine/threonine kinase 2									p.I713L(1)		breast(1)|lung(3)|ovary(5)|stomach(2)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					GGCCATGGGCATTATCCTGTA	0.572																																					p.I713L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2137C	1						.						191.0	194.0	193.0					1																	46494524		2029	4198	6227	46267111	SO:0001583	missense	23139	exon18			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.2137A>C	1.37:g.46494524A>C	ENSP00000354671:p.Ile713Leu	Somatic		Capture	Illumina HiSeq	Phase_I	46267111	NM_015112		Missense_Mutation	SNP	ENST00000361297.2	37	CCDS41326.1	.	.	.	.	.	.	.	.	.	.	A	16.72	3.200993	0.58234	.	.	ENSG00000086015	ENST00000361297;ENST00000372009;ENST00000432341;ENST00000372008	T;T;T	0.26223	1.75;1.75;1.75	4.83	-0.163	0.13363	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.126249	0.51477	D	0.000081	T	0.23410	0.0566	L	0.52573	1.65	0.42236	D	0.99191	B;B;B;B	0.30763	0.015;0.095;0.294;0.072	B;B;B;B	0.33799	0.014;0.12;0.109;0.17	T	0.12167	-1.0558	10	0.87932	D	0	-1.7582	10.7438	0.46168	0.5004:0.0:0.4996:0.0	.	643;387;643;713	Q6P0Q8-2;E7EWL1;E7ERL6;Q6P0Q8	.;.;.;MAST2_HUMAN	L	713;643;387;598	ENSP00000354671:I713L;ENSP00000361079:I643L;ENSP00000361078:I598L	ENSP00000354671:I713L	I	+	1	0	MAST2	46267111	0.555000	0.26530	0.990000	0.47175	0.983000	0.72400	0.672000	0.25187	0.009000	0.14813	0.459000	0.35465	ATT		0.572	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112	
CYP4A11	1579	broad.mit.edu	37	1	47395796	47395796	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:47395796G>A	ENST00000310638.4	-	12	1582	c.1551C>T	c.(1549-1551)gaC>gaT	p.D517D	CYP4A11_ENST00000462347.1_Silent_p.D419D|CYP4A11_ENST00000371904.4_Silent_p.D518D	NM_000778.3	NP_000769.2	Q02928	CP4AB_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 11	517			NGIHLRLRRLPNPCEDKDQL -> MESTCVSGGSLTLVKTR TSFEGLHLPSCLPDPRFCPLPVCPYPVFCLPTFPSSHLPAV PQSACPSLSHLSPGLPTCLSTCLLPTCISCWEKS (in CYP4A11V).		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.D517D(1)		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)	CTCAAAGCTGGTCCTTGTCTT	0.562																																					p.D517D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1551T	1						.						73.0	60.0	64.0					1																	47395796		2203	4300	6503	47168383	SO:0001819	synonymous_variant	1579	exon12			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.1551C>T	1.37:g.47395796G>A		Somatic		Capture	Illumina HiSeq	Phase_I	47168383	NM_000778	Q06766|Q16865|Q16866|Q5VSP8|Q86SU6|Q8IWY5	Silent	SNP	ENST00000310638.4	37	CCDS543.1																																																																																				0.562	CYP4A11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022022.1	NM_000778	
SPATA6	54558	broad.mit.edu	37	1	48865129	48865129	+	Missense_Mutation	SNP	C	C	T	rs377106164		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:48865129C>T	ENST00000371847.3	-	7	838	c.674G>A	c.(673-675)cGc>cAc	p.R225H	SPATA6_ENST00000371843.3_Missense_Mutation_p.R225H|SPATA6_ENST00000463938.1_5'UTR|SPATA6_ENST00000396199.3_Missense_Mutation_p.R153H	NM_019073.2	NP_061946.1	Q9NWH7	SPAT6_HUMAN	spermatogenesis associated 6	225					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)		p.R225H(1)		breast(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	21						CTCACACATGCGTCTTTTTGT	0.408																																					p.R225H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G674A	1						.						232.0	236.0	235.0					1																	48865129		2203	4300	6503	48637716	SO:0001583	missense	54558	exon7			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.674G>A	1.37:g.48865129C>T	ENSP00000360913:p.Arg225His	Somatic		Capture	Illumina HiSeq	Phase_I	48637716	NM_019073	Q5T3N7|Q8WUE6	Missense_Mutation	SNP	ENST00000371847.3	37	CCDS551.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.674826	0.88445	.	.	ENSG00000132122	ENST00000371847;ENST00000371843;ENST00000396199;ENST00000371841	T;T;T;T	0.55413	2.25;2.23;2.13;0.52	5.68	5.68	0.88126	.	0.068283	0.64402	D	0.000018	T	0.66954	0.2842	L	0.41824	1.3	0.44188	D	0.997001	D;D;D;D	0.89917	0.983;0.973;1.0;1.0	P;P;D;D	0.85130	0.723;0.632;0.997;0.997	T	0.68424	-0.5412	10	0.87932	D	0	.	18.7846	0.91949	0.0:1.0:0.0:0.0	.	153;153;225;225	B4DX17;A8MU33;Q9NWH7-2;Q9NWH7	.;.;.;SPAT6_HUMAN	H	225;225;153;66	ENSP00000360913:R225H;ENSP00000360909:R225H;ENSP00000379502:R153H;ENSP00000360907:R66H	ENSP00000360907:R66H	R	-	2	0	SPATA6	48637716	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	4.660000	0.61511	2.683000	0.91414	0.555000	0.69702	CGC		0.408	SPATA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021347.1	NM_019073	
EPS15	2060	broad.mit.edu	37	1	51913719	51913719	+	Splice_Site	SNP	G	G	A	rs201144796		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:51913719G>A	ENST00000371733.3	-	9	746	c.650C>T	c.(649-651)aCg>aTg	p.T217M	EPS15_ENST00000371730.2_Splice_Site_p.T217M	NM_001981.2	NP_001972.1	P42566	EPS15_HUMAN	epidermal growth factor receptor pathway substrate 15	217	Interaction with DAB2. {ECO:0000250}.				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?(1)|p.T217M(1)		endometrium(3)|kidney(5)|large_intestine(8)|lung(13)|prostate(2)|skin(1)|stomach(1)|urinary_tract(2)	35						TATACTGACCGTTTTTCTCTT	0.463			T	MLL	ALL																																p.T217M			Dom	yes		1	1p32	2060	epidermal growth factor receptor pathway substrate 15 (AF1p)		L	.	.	2	Substitution - Missense(1)|Whole gene deletion(1)	large_intestine(1)|central_nervous_system(1)	c.C650T	1						.						169.0	160.0	163.0					1																	51913719		2203	4300	6503	51686307	SO:0001630	splice_region_variant	2060	exon9			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.651+1C>T	1.37:g.51913719G>A		Somatic		Capture	Illumina HiSeq	Phase_I	51686307	NM_001981	B2R8J7|D3DPJ2|Q5SRH4	Missense_Mutation	SNP	ENST00000371733.3	37	CCDS557.1	.	.	.	.	.	.	.	.	.	.	G	19.85	3.903031	0.72754	.	.	ENSG00000085832	ENST00000371730;ENST00000371733	T;T	0.24151	1.9;1.87	5.97	5.05	0.67936	EPS15 homology (EH) (1);EF-hand-like domain (1);	0.000000	0.33235	N	0.005129	T	0.22820	0.0551	L	0.31926	0.97	0.80722	D	1	P;D	0.59767	0.476;0.986	B;P	0.47206	0.093;0.541	T	0.00559	-1.1671	10	0.62326	D	0.03	.	8.1866	0.31343	0.135:0.1302:0.7348:0.0	.	217;217	B1AUU8;P42566	.;EPS15_HUMAN	M	217	ENSP00000360795:T217M;ENSP00000360798:T217M	ENSP00000360795:T217M	T	-	2	0	EPS15	51686307	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.262000	0.32992	2.836000	0.97738	0.655000	0.94253	ACG		0.463	EPS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022422.1	NM_001981	Missense_Mutation
C1orf177	163747	broad.mit.edu	37	1	55277736	55277736	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:55277736C>T	ENST00000371273.3	+	6	651	c.636C>T	c.(634-636)ccC>ccT	p.P212P	C1orf177_ENST00000358193.3_Silent_p.P212P	NM_001110533.1	NP_001104003	Q3ZCV2	CA177_HUMAN	chromosome 1 open reading frame 177	212								p.P212P(1)		breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(6)|prostate(2)	17						GTCTGGGACCCGGCACCTACT	0.617																																					p.P212P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C636T	1						.						91.0	99.0	96.0					1																	55277736		2203	4300	6503	55050324	SO:0001819	synonymous_variant	163747	exon6			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.636C>T	1.37:g.55277736C>T		Somatic		Capture	Illumina HiSeq	Phase_I	55050324	NM_001110533	B7WPL2|Q8N7Y9	Silent	SNP	ENST00000371273.3	37	CCDS44153.1																																																																																				0.617	C1orf177-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027674.1	NM_152607	
HOOK1	51361	broad.mit.edu	37	1	60338540	60338540	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:60338540C>T	ENST00000371208.3	+	22	2347	c.2090C>T	c.(2089-2091)gCg>gTg	p.A697V	HOOK1_ENST00000395561.2_Missense_Mutation_p.A655V|HOOK1_ENST00000465876.1_3'UTR	NM_015888.4	NP_056972.1	Q9UJC3	HOOK1_HUMAN	hook microtubule-tethering protein 1	697	Sufficient for interaction with AKTIP and VPS18.				early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)|spermatid development (GO:0007286)	FHF complex (GO:0070695)|microtubule (GO:0005874)	identical protein binding (GO:0042802)	p.A697V(1)		biliary_tract(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|urinary_tract(1)	29	all_cancers(7;0.000129)					GACACTGGTGCGTGCACTCCT	0.458																																					p.A697V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2090T	1						.						30.0	27.0	28.0					1																	60338540		1854	3523	5377	60111128	SO:0001583	missense	51361	exon22			AF044923	CCDS612.1	1p32.1	2013-08-21	2013-08-21		ENSG00000134709	ENSG00000134709			19884	protein-coding gene	gene with protein product		607820	"""hook homolog 1 (Drosophila)"""			9927460	Standard	XM_005270922		Approved	HK1	uc001czo.3	Q9UJC3	OTTHUMG00000008990	ENST00000371208.3:c.2090C>T	1.37:g.60338540C>T	ENSP00000360252:p.Ala697Val	Somatic		Capture	Illumina HiSeq	Phase_I	60111128	NM_015888	A8K8E9|A8MU44|B4DX15|O60561|Q5TG44	Missense_Mutation	SNP	ENST00000371208.3	37	CCDS612.1	.	.	.	.	.	.	.	.	.	.	C	10.75	1.438478	0.25900	.	.	ENSG00000134709	ENST00000371208;ENST00000395561	T;T	0.32753	1.86;1.44	5.69	3.84	0.44239	.	0.809322	0.10861	N	0.626074	T	0.28830	0.0715	L	0.44542	1.39	0.09310	N	1	B	0.28026	0.198	B	0.28784	0.094	T	0.19353	-1.0308	10	0.46703	T	0.11	.	11.3647	0.49664	0.0:0.8506:0.0:0.1494	.	697	Q9UJC3	HOOK1_HUMAN	V	697;655	ENSP00000360252:A697V;ENSP00000378928:A655V	ENSP00000360252:A697V	A	+	2	0	HOOK1	60111128	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.943000	0.29030	0.759000	0.33084	0.591000	0.81541	GCG		0.458	HOOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024934.1	NM_015888	
FPGT	8790	broad.mit.edu	37	1	74671305	74671305	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:74671305C>T	ENST00000609362.1	+	4	1611	c.1574C>T	c.(1573-1575)gCa>gTa	p.A525V	FPGT-TNNI3K_ENST00000370899.3_Intron|FPGT_ENST00000524915.1_Intron|FPGT_ENST00000370898.3_Missense_Mutation_p.A538V|TNNI3K_ENST00000370891.2_Intron|FPGT-TNNI3K_ENST00000533006.1_Intron|FPGT_ENST00000370894.5_3'UTR|FPGT-TNNI3K_ENST00000370895.1_Intron|FPGT-TNNI3K_ENST00000557284.2_Intron|FPGT_ENST00000534056.1_Missense_Mutation_p.A271V|FPGT-TNNI3K_ENST00000370893.1_Intron	NM_003838.4	NP_003829.3	O14772	FPGT_HUMAN	fucose-1-phosphate guanylyltransferase	525					fucose metabolic process (GO:0006004)	cytoplasm (GO:0005737)	catalytic activity (GO:0003824)|fucose-1-phosphate guanylyltransferase activity (GO:0047341)|GTP binding (GO:0005525)	p.A525V(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	39						TTGTGGACTGCACGCATTTTC	0.393																																					p.A271V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C812T	1						.						169.0	155.0	160.0					1																	74671305		2203	4300	6503	74443893	SO:0001583	missense	8790	exon5			AF017445	CCDS663.1, CCDS663.2	1p31.1	2013-09-24			ENSG00000254685	ENSG00000254685	2.7.7.30		3825	protein-coding gene	gene with protein product		603609				9804772	Standard	NM_003838		Approved	GFPP		O14772	OTTHUMG00000009571	ENST00000609362.1:c.1574C>T	1.37:g.74671305C>T	ENSP00000476680:p.Ala525Val	Somatic		Capture	Illumina HiSeq	Phase_I	74443893	NM_001199328	A6NMH3|B4DRX2|B4E2Y7|E9PNQ2|Q8N5J7	Missense_Mutation	SNP	ENST00000609362.1	37	CCDS663.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.369092	0.82463	.	.	ENSG00000254685	ENST00000370898;ENST00000534056	T;T	0.59906	0.23;0.23	5.1	5.1	0.69264	L-fucokinase (1);	.	.	.	.	T	0.74238	0.3690	M	0.82056	2.57	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.977;0.999;0.998	T	0.78204	-0.2295	9	0.66056	D	0.02	.	18.5202	0.90950	0.0:1.0:0.0:0.0	.	271;150;525	E9PNQ2;B4E2Y7;O14772	.;.;FPGT_HUMAN	V	525;271	ENSP00000359935:A525V;ENSP00000432819:A271V	ENSP00000359935:A525V	A	+	2	0	TNNI3K	74443893	0.999000	0.42202	1.000000	0.80357	0.989000	0.77384	3.701000	0.54793	2.351000	0.79841	0.563000	0.77884	GCA		0.393	FPGT-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
ERICH3	127254	broad.mit.edu	37	1	75038435	75038435	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:75038435C>A	ENST00000326665.5	-	14	3177	c.2959G>T	c.(2959-2961)Gtt>Ttt	p.V987F	C1orf173_ENST00000433746.2_5'UTR	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		987	Glu-rich.							p.V987F(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						GTTCTCATAACCTCTTTTCTC	0.542																																					p.V987F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2959T	1						.						122.0	108.0	113.0					1																	75038435		2203	4300	6503	74811023	SO:0001583	missense	127254	exon14																														ENST00000326665.5:c.2959G>T	1.37:g.75038435C>A	ENSP00000322609:p.Val987Phe	Somatic		Capture	Illumina HiSeq	Phase_I	74811023	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Missense_Mutation	SNP	ENST00000326665.5	37	CCDS30755.1	.	.	.	.	.	.	.	.	.	.	C	11.97	1.798847	0.31777	.	.	ENSG00000178965	ENST00000326665	T	0.15017	2.46	4.8	0.472	0.16758	.	.	.	.	.	T	0.02418	0.0074	N	0.14661	0.345	0.09310	N	1	B	0.14012	0.009	B	0.17433	0.018	T	0.44862	-0.9300	9	0.52906	T	0.07	-0.8227	1.9301	0.03325	0.2608:0.4392:0.1372:0.1629	.	987	Q5RHP9	CA173_HUMAN	F	987	ENSP00000322609:V987F	ENSP00000322609:V987F	V	-	1	0	C1orf173	74811023	0.000000	0.05858	0.000000	0.03702	0.226000	0.24999	0.421000	0.21280	-0.192000	0.10432	0.407000	0.27541	GTT		0.542	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1		
LPHN2	23266	broad.mit.edu	37	1	82416777	82416777	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:82416777C>A	ENST00000370728.1	+	10	2213	c.1568C>A	c.(1567-1569)tCa>tAa	p.S523*	LPHN2_ENST00000319517.6_Nonsense_Mutation_p.S523*|LPHN2_ENST00000370727.1_Nonsense_Mutation_p.S523*|LPHN2_ENST00000469377.2_Intron|LPHN2_ENST00000370730.1_Nonsense_Mutation_p.S523*|LPHN2_ENST00000370725.1_Nonsense_Mutation_p.S523*|LPHN2_ENST00000370715.1_Nonsense_Mutation_p.S523*|LPHN2_ENST00000271029.4_Nonsense_Mutation_p.S523*|LPHN2_ENST00000370723.1_Nonsense_Mutation_p.S523*|LPHN2_ENST00000359929.3_Nonsense_Mutation_p.S523*|LPHN2_ENST00000370721.1_Nonsense_Mutation_p.S461*|LPHN2_ENST00000370717.2_Nonsense_Mutation_p.S523*|LPHN2_ENST00000370713.1_Nonsense_Mutation_p.S523*|LPHN2_ENST00000394879.1_Nonsense_Mutation_p.S523*|LPHN2_ENST00000335786.5_Nonsense_Mutation_p.S523*			O95490	LPHN2_HUMAN	latrophilin 2	523					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)	p.S523*(1)		NS(3)|breast(6)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(37)|ovary(3)|pancreas(1)|prostate(3)|skin(22)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	119				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)		AACTGTACCTCACACTGGGTG	0.418																																					p.S523X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1568A	1						.						109.0	104.0	106.0					1																	82416777		2203	4300	6503	82189365	SO:0001587	stop_gained	23266	exon7			AJ131581	CCDS689.1, CCDS72811.1	1p31.1	2014-08-08	2003-03-17	2003-05-02	ENSG00000117114	ENSG00000117114		"""-"", ""GPCR / Class B : Orphans"""	18582	protein-coding gene	gene with protein product		607018	"""latrophilin 1"""	LPHH1		10760572	Standard	XR_248786		Approved	KIAA0786, LEC1	uc001diu.3	O95490	OTTHUMG00000009844	ENST00000370728.1:c.1568C>A	1.37:g.82416777C>A	ENSP00000359763:p.Ser523*	Somatic		Capture	Illumina HiSeq	Phase_I	82189365	NM_012302	A5XEI2|B1ALT8|B1ALT9|B1ALU0|B1ALU2|B1ALU4|B1ALU5|B1ALU6|O94882|Q5VX76|Q9UKY5|Q9UKY6	Nonsense_Mutation	SNP	ENST00000370728.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	45|45	11.457952|11.457952	0.99563|0.99563	.|.	.|.	ENSG00000117114|ENSG00000117114	ENST00000449420|ENST00000370721;ENST00000370728;ENST00000370730;ENST00000370727;ENST00000370725;ENST00000370723;ENST00000359929;ENST00000370715;ENST00000370713;ENST00000319517;ENST00000370717;ENST00000394879;ENST00000271029;ENST00000335786	.|.	.|.	.|.	5.96|5.96	5.96|5.96	0.96718|0.96718	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.34716|.	0.0907|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.34254|.	-0.9836|.	3|.	.|0.02654	.|T	.|1	.|.	20.4192|20.4192	0.99033|0.99033	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	N|X	391|461;523;523;523;523;523;523;523;523;523;523;523;523;523	.|.	.|ENSP00000271029:S523X	H|S	+|+	1|2	0|0	LPHN2|LPHN2	82189365|82189365	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.818000|7.818000	0.86416|0.86416	2.831000|2.831000	0.97527|0.97527	0.650000|0.650000	0.86243|0.86243	CAC|TCA		0.418	LPHN2-007	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000027188.1	NM_012302	
RPF1	80135	broad.mit.edu	37	1	84948638	84948638	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:84948638G>A	ENST00000370654.5	+	3	341	c.326G>A	c.(325-327)cGa>cAa	p.R109Q	RPF1_ENST00000370656.1_Missense_Mutation_p.R109Q	NM_025065.6	NP_079341.2	Q9H9Y2	RPF1_HUMAN	ribosome production factor 1 homolog (S. cerevisiae)	109					rRNA processing (GO:0006364)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)	p.R109Q(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(5)|lung(2)|prostate(1)	14						GACAACCAGCGAGTGTATGAT	0.328																																					p.R109Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G326A	1						.						112.0	104.0	106.0					1																	84948638		2203	4300	6503	84721226	SO:0001583	missense	80135	exon3			AF322053	CCDS695.1	1p22.3	2009-09-25	2009-09-25	2009-09-25	ENSG00000117133	ENSG00000117133			30350	protein-coding gene	gene with protein product	"""RNA processing factor 1"", ""ribosome production factor 1"""		"""brix domain containing 5"""	BXDC5		11864606	Standard	NM_025065		Approved		uc001djv.4	Q9H9Y2	OTTHUMG00000009857	ENST00000370654.5:c.326G>A	1.37:g.84948638G>A	ENSP00000359688:p.Arg109Gln	Somatic		Capture	Illumina HiSeq	Phase_I	84721226	NM_025065	Q5VSK7|Q6AHX1|Q8WXZ8	Missense_Mutation	SNP	ENST00000370654.5	37	CCDS695.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.759407	0.89932	.	.	ENSG00000117133	ENST00000370656;ENST00000370654	D;T	0.84730	-1.89;1.22	5.93	5.01	0.66863	.	0.146337	0.50627	D	0.000103	D	0.93916	0.8053	H	0.95079	3.62	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	D	0.95648	0.8704	10	0.66056	D	0.02	-6.8429	16.4785	0.84151	0.0:0.0:0.8677:0.1323	.	109	Q9H9Y2	RPF1_HUMAN	Q	109	ENSP00000359690:R109Q;ENSP00000359688:R109Q	ENSP00000359688:R109Q	R	+	2	0	RPF1	84721226	1.000000	0.71417	0.997000	0.53966	0.698000	0.40448	8.895000	0.92512	1.490000	0.48466	-0.181000	0.13052	CGA		0.328	RPF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027238.1	NM_025065	
MCOLN3	55283	broad.mit.edu	37	1	85487818	85487818	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:85487818C>T	ENST00000370589.2	-	11	1307	c.1255G>A	c.(1255-1257)Gca>Aca	p.A419T	MCOLN3_ENST00000474447.1_5'UTR|WDR63_ENST00000370596.1_Intron|MCOLN3_ENST00000341115.4_Missense_Mutation_p.A363T	NM_018298.10	NP_060768.8	Q8TDD5	MCLN3_HUMAN	mucolipin 3	419					auditory receptor cell differentiation (GO:0042491)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|locomotory behavior (GO:0007626)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A419T(1)		endometrium(6)|kidney(3)|large_intestine(9)|lung(12)|prostate(3)|skin(1)	34				all cancers(265;0.00957)|Epithelial(280;0.0254)		ATCATAGCTGCACAGCAGCAG	0.448																																					p.A419T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1255A	1						.						100.0	96.0	97.0					1																	85487818		2203	4300	6503	85260406	SO:0001583	missense	55283	exon11			AF475085	CCDS701.1, CCDS58009.1	1p22.3	2011-12-16			ENSG00000055732	ENSG00000055732		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	13358	protein-coding gene	gene with protein product		607400				16382100	Standard	NM_018298		Approved	TRPML3, FLJ11006, TRP-ML3	uc001dkp.3	Q8TDD5	OTTHUMG00000009955	ENST00000370589.2:c.1255G>A	1.37:g.85487818C>T	ENSP00000359621:p.Ala419Thr	Somatic		Capture	Illumina HiSeq	Phase_I	85260406	NM_018298	Q5T4H5|Q5T4H6|Q9NV09	Missense_Mutation	SNP	ENST00000370589.2	37	CCDS701.1	.	.	.	.	.	.	.	.	.	.	C	35	5.444831	0.96187	.	.	ENSG00000055732	ENST00000370589;ENST00000302814;ENST00000370588;ENST00000341115	T;T	0.69175	-0.38;-0.38	5.7	5.7	0.88788	Polycystin cation channel, PKD1/PKD2 (1);	0.000000	0.85682	D	0.000000	T	0.80854	0.4703	M	0.82630	2.6	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.77811	-0.2449	10	0.33141	T	0.24	-20.0808	19.8414	0.96690	0.0:1.0:0.0:0.0	.	363;419	Q8TDD5-2;Q8TDD5	.;MCLN3_HUMAN	T	419;419;363;363	ENSP00000359621:A419T;ENSP00000342698:A363T	ENSP00000304843:A419T	A	-	1	0	MCOLN3	85260406	1.000000	0.71417	0.997000	0.53966	0.977000	0.68977	7.441000	0.80485	2.680000	0.91292	0.563000	0.77884	GCA		0.448	MCOLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027569.2	NM_018298	
BCAR3	8412	broad.mit.edu	37	1	94140341	94140341	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:94140341C>T	ENST00000370244.1	-	4	434	c.146G>A	c.(145-147)gGc>gAc	p.G49D	BCAR3_ENST00000260502.6_Missense_Mutation_p.G49D|BCAR3_ENST00000370243.1_Missense_Mutation_p.G49D	NM_001261408.1	NP_001248337.1	O75815	BCAR3_HUMAN	breast cancer anti-estrogen resistance 3	49					lens morphogenesis in camera-type eye (GO:0002089)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)	p.G49D(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)	25		all_lung(203;0.00145)|Lung NSC(277;0.00662)		all cancers(265;0.0126)|GBM - Glioblastoma multiforme(16;0.0467)|Epithelial(280;0.166)		TGGAAGGGTGCCATGTATAGA	0.557																																					p.G49D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G146A	1						.						82.0	72.0	75.0					1																	94140341		2203	4300	6503	93912929	SO:0001583	missense	8412	exon2			U92715	CCDS745.1, CCDS58010.1	1p22.1	2013-02-14			ENSG00000137936	ENSG00000137936		"""SH2 domain containing"""	973	protein-coding gene	gene with protein product		604704				9582273	Standard	NM_001261408		Approved	NSP2, SH2D3B	uc001dpz.4	O75815	OTTHUMG00000010301	ENST00000370244.1:c.146G>A	1.37:g.94140341C>T	ENSP00000359264:p.Gly49Asp	Somatic		Capture	Illumina HiSeq	Phase_I	93912929	NM_003567	D3DT43|Q5TEW3|Q6UW40|Q9BR50	Missense_Mutation	SNP	ENST00000370244.1	37	CCDS745.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.150578	0.78001	.	.	ENSG00000137936	ENST00000260502;ENST00000370244;ENST00000370243	T;T;T	0.38077	1.16;1.16;1.16	5.83	5.83	0.93111	.	0.000000	0.64402	D	0.000001	T	0.30727	0.0774	L	0.34521	1.04	0.80722	D	1	P	0.45011	0.848	P	0.47102	0.537	T	0.07908	-1.0748	10	0.87932	D	0	-0.5439	20.1338	0.98010	0.0:1.0:0.0:0.0	.	49	O75815	BCAR3_HUMAN	D	49	ENSP00000260502:G49D;ENSP00000359264:G49D;ENSP00000359263:G49D	ENSP00000260502:G49D	G	-	2	0	BCAR3	93912929	1.000000	0.71417	0.997000	0.53966	0.979000	0.70002	6.013000	0.70776	2.770000	0.95276	0.655000	0.94253	GGC		0.557	BCAR3-003	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028420.1		
SNX7	51375	broad.mit.edu	37	1	99150475	99150475	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:99150475C>A	ENST00000306121.3	+	2	224	c.215C>A	c.(214-216)cCt>cAt	p.P72H	SNX7_ENST00000529992.1_Missense_Mutation_p.P72H|SNX7_ENST00000370189.5_Missense_Mutation_p.P8H	NM_015976.4	NP_057060.2	Q9UNH6	SNX7_HUMAN	sorting nexin 7	8	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				apoptotic process (GO:0006915)|intracellular protein transport (GO:0006886)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)	p.P72H(1)|p.P8H(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	13		all_epithelial(167;7.64e-07)|all_lung(203;0.0006)|Lung NSC(277;0.00137)		Epithelial(280;0.0521)|all cancers(265;0.0687)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.207)|Colorectal(170;0.234)		TCCTTCAGCCCTATGATGCCA	0.338																																					p.P72H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C215A	1						.						119.0	108.0	112.0					1																	99150475		2203	4300	6503	98923063	SO:0001583	missense	51375	exon2			AF121857	CCDS755.2, CCDS756.1, CCDS756.2	1p21	2008-05-22			ENSG00000162627	ENSG00000162627		"""Sorting nexins"""	14971	protein-coding gene	gene with protein product		614904					Standard	NM_015976		Approved		uc010ouc.2	Q9UNH6	OTTHUMG00000010723	ENST00000306121.3:c.215C>A	1.37:g.99150475C>A	ENSP00000304429:p.Pro72His	Somatic		Capture	Illumina HiSeq	Phase_I	98923063	NM_152238	A8KAF3|D3DT50|Q53FQ3|Q5VT09|Q5VT10|Q86U82|Q8WVD4|Q96FW9|Q9Y3Z7	Missense_Mutation	SNP	ENST00000306121.3	37	CCDS755.2	.	.	.	.	.	.	.	.	.	.	C	16.89	3.248707	0.59103	.	.	ENSG00000162627	ENST00000370189;ENST00000529992;ENST00000306121;ENST00000454199	T;T;T;T	0.57595	1.39;1.94;1.33;0.39	5.39	3.51	0.40186	.	0.000000	0.85682	D	0.000000	T	0.50718	0.1632	L	0.44542	1.39	0.43531	D	0.995814	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.74348	0.968;0.983;0.964	T	0.55412	-0.8145	10	0.66056	D	0.02	-20.5152	10.3183	0.43751	0.1352:0.7947:0.0:0.0701	.	72;72;8	E9PNL2;Q9UNH6-3;Q9UNH6-2	.;.;.	H	8;72;72;8	ENSP00000359208:P8H;ENSP00000434731:P72H;ENSP00000304429:P72H;ENSP00000388266:P8H	ENSP00000304429:P72H	P	+	2	0	SNX7	98923063	1.000000	0.71417	0.581000	0.28614	0.756000	0.42949	6.193000	0.72075	0.641000	0.30601	0.650000	0.86243	CCT		0.338	SNX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029609.2		
PGBD2	267002	broad.mit.edu	37	1	249211210	249211210	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr1:249211210G>T	ENST00000329291.5	+	3	574	c.427G>T	c.(427-429)Ggc>Tgc	p.G143C	PGBD2_ENST00000355360.4_Intron|PGBD2_ENST00000539153.1_Missense_Mutation_p.G140C|PGBD2_ENST00000462488.1_Intron	NM_170725.2	NP_733843.1	Q6P3X8	PGBD2_HUMAN	piggyBac transposable element derived 2	143										NS(1)|endometrium(3)|lung(6)|ovary(1)|skin(3)	14	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;0.012)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			GAGTCCCGTGGGCCTTTTTGA	0.408																																					p.G143C												.	.	0			c.G427T	1						.						63.0	71.0	69.0					1																	249211210		2201	4300	6501	247177833	SO:0001583	missense	267002	exon3			AF229602	CCDS31128.1, CCDS31129.1	1q	2008-02-05			ENSG00000185220	ENSG00000185220			19399	protein-coding gene	gene with protein product							Standard	XM_005270333		Approved		uc001ifh.3	Q6P3X8	OTTHUMG00000040424	ENST00000329291.5:c.427G>T	1.37:g.249211210G>T	ENSP00000331643:p.Gly143Cys	None		Capture	Illumina HiSeq	Phase_I	247177833	NM_170725	B3KVR8|Q6MZF8	Missense_Mutation	SNP	ENST00000329291.5	37	CCDS31128.1	.	.	.	.	.	.	.	.	.	.	G	14.32	2.500695	0.44455	.	.	ENSG00000185220	ENST00000329291;ENST00000539153	T;T	0.18338	2.22;2.22	4.18	2.25	0.28309	.	0.237462	0.21552	U	0.072715	T	0.18923	0.0454	N	0.22421	0.69	0.21719	N	0.999575	D;D	0.69078	0.997;0.994	P;P	0.60345	0.849;0.873	T	0.04140	-1.0974	10	0.56958	D	0.05	-26.7899	5.5814	0.17252	0.11:0.2027:0.6873:0.0	.	140;143	F5H4U7;Q6P3X8	.;PGBD2_HUMAN	C	143;140	ENSP00000331643:G143C;ENSP00000439950:G140C	ENSP00000331643:G143C	G	+	1	0	PGBD2	247177833	1.000000	0.71417	0.575000	0.28536	0.793000	0.44817	3.798000	0.55522	0.509000	0.28195	0.655000	0.94253	GGC		0.408	PGBD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000097318.1		
HCK	3055	broad.mit.edu	37	20	30640229	30640230	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr20:30640229_30640230insG	ENST00000375852.2	+	1	166_167	c.2_3insG	c.(1-6)ctggggfs	p.LG1fs	RNA5SP482_ENST00000391269.1_RNA|HCK_ENST00000375862.2_Frame_Shift_Ins_p.LG1fs|HCK_ENST00000518730.1_5'UTR|HCK_ENST00000534862.1_5'UTR|HCK_ENST00000520553.1_5'UTR|HCK_ENST00000538448.1_5'UTR			P08631	HCK_HUMAN	HCK proto-oncogene, Src family tyrosine kinase	1					cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|innate immune response-activating signal transduction (GO:0002758)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte degranulation (GO:0043299)|leukocyte migration involved in immune response (GO:0002522)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|mesoderm development (GO:0007498)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell proliferation (GO:0008284)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of defense response to virus by virus (GO:0050690)|regulation of inflammatory response (GO:0050727)|regulation of phagocytosis (GO:0050764)|regulation of podosome assembly (GO:0071801)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|respiratory burst after phagocytosis (GO:0045728)|viral process (GO:0016032)	caveola (GO:0005901)|cell projection (GO:0042995)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|nucleus (GO:0005634)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)	p.R4fs*38(1)		NS(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(4)	36			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)		Bosutinib(DB06616)	GCTGCCGAGCTGGGGGGGCGCT	0.723																																					p.L1fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.2_3insG	20						.																																			30103891	SO:0001589	frameshift_variant	3055	exon1			AK026432	CCDS33460.1, CCDS54453.1, CCDS54455.1, CCDS54456.1	20q11-q12	2014-06-25	2014-06-25		ENSG00000101336	ENSG00000101336		"""SH2 domain containing"""	4840	protein-coding gene	gene with protein product		142370	"""hemopoietic cell kinase"""			3496523	Standard	NM_002110		Approved	JTK9	uc002wxh.3	P08631	OTTHUMG00000032204	ENST00000375852.2:c.9dupG	20.37:g.30640236_30640236dupG	ENSP00000365012:p.Leu1fs	Somatic		Capture	Illumina HiSeq	Phase_I	30103890	NM_002110	A8K1I1|B4DQB6|E1P5M2|Q29RX1|Q2VPE2|Q504R5|Q5T7K1|Q5T7K2|Q96CC0|Q9H5Y5|Q9NUA4|Q9UMJ5	Frame_Shift_Ins	INS	ENST00000375852.2	37	CCDS33460.1																																																																																				0.723	HCK-001	KNOWN	NAGNAG_splice_site|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078603.4		
ESF1	51575	broad.mit.edu	37	20	13763614	13763614	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr20:13763614C>T	ENST00000202816.1	-	2	280	c.173G>A	c.(172-174)cGc>cAc	p.R58H	NDUFAF5_ENST00000463598.1_5'Flank|NDUFAF5_ENST00000378106.5_5'Flank	NM_001276380.1|NM_016649.3	NP_001263309.1|NP_057733.2	Q9H501	ESF1_HUMAN	ESF1, nucleolar pre-rRNA processing protein, homolog (S. cerevisiae)	58					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R58H(1)		endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|skin(1)|stomach(1)	31						GCTAATGGGGCGCCCTCTTTT	0.413																																					p.R58H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G173A	20						.						82.0	81.0	81.0					20																	13763614		2203	4300	6503	13711614	SO:0001583	missense	51575	exon2				CCDS13117.1	20p12.1	2007-02-12	2006-11-13	2006-11-13	ENSG00000089048	ENSG00000089048			15898	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 6"""	C20orf6			Standard	NM_016649		Approved	bA526K24.1	uc002wok.2	Q9H501	OTTHUMG00000031906	ENST00000202816.1:c.173G>A	20.37:g.13763614C>T	ENSP00000202816:p.Arg58His	Somatic		Capture	Illumina HiSeq	Phase_I	13711614	NM_016649	Q86X92|Q9H9Q5|Q9HA35|Q9NX93|Q9P1S6	Missense_Mutation	SNP	ENST00000202816.1	37	CCDS13117.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.327812	0.81690	.	.	ENSG00000089048	ENST00000202816;ENST00000541185	T	0.45668	0.89	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.73458	0.3589	M	0.92604	3.325	0.58432	D	0.999995	D	0.89917	1.0	D	0.87578	0.998	T	0.81562	-0.0876	10	0.87932	D	0	.	17.9232	0.88973	0.0:1.0:0.0:0.0	.	58	Q9H501	ESF1_HUMAN	H	58	ENSP00000202816:R58H	ENSP00000202816:R58H	R	-	2	0	ESF1	13711614	1.000000	0.71417	0.128000	0.21923	0.560000	0.35617	6.091000	0.71406	2.306000	0.77630	0.591000	0.81541	CGC		0.413	ESF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078049.1	NM_016649	
KIF16B	55614	broad.mit.edu	37	20	16360626	16360626	+	Missense_Mutation	SNP	G	G	A	rs543632299		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr20:16360626G>A	ENST00000354981.2	-	19	2178	c.2021C>T	c.(2020-2022)gCg>gTg	p.A674V	KIF16B_ENST00000378003.2_5'UTR|KIF16B_ENST00000355755.3_Missense_Mutation_p.A674V|KIF16B_ENST00000408042.1_Missense_Mutation_p.A674V	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	674	Glu-rich.				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.A674V(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						TTCCTTCTCCGCAAGTAAATC	0.502																																					p.A674V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2021T	20						.						131.0	117.0	121.0					20																	16360626		2203	4300	6503	16308626	SO:0001583	missense	55614	exon19			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.2021C>T	20.37:g.16360626G>A	ENSP00000347076:p.Ala674Val	Somatic		Capture	Illumina HiSeq	Phase_I	16308626	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	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.21|13.21	2.170550|2.170550	0.38315|0.38315	.|.	.|.	ENSG00000089177|ENSG00000089177	ENST00000354981;ENST00000355755;ENST00000377997;ENST00000408042|ENST00000450176	T;T;T|.	0.18502|.	2.21;2.21;2.21|.	5.58|5.58	4.63|4.63	0.57726|0.57726	.|.	0.174942|.	0.49305|.	D|.	0.000149|.	T|T	0.63616|0.63616	0.2526|0.2526	L|L	0.53249|0.53249	1.67|1.67	0.80722|0.80722	D|D	1|1	P;D;P;P|.	0.56968|.	0.956;0.978;0.883;0.926|.	B;P;B;B|.	0.46208|.	0.146;0.507;0.146;0.069|.	T|T	0.61715|0.61715	-0.7006|-0.7006	10|5	0.10377|.	T|.	0.69|.	.|.	14.1994|14.1994	0.65693|0.65693	0.0716:0.0:0.9284:0.0|0.0716:0.0:0.9284:0.0	.|.	674;674;674;674|.	Q96L93-4;Q96L93-2;Q96L93-6;Q96L93|.	.;.;.;KI16B_HUMAN|.	V|W	674|109	ENSP00000347076:A674V;ENSP00000347995:A674V;ENSP00000384164:A674V|.	ENSP00000347076:A674V|.	A|R	-|-	2|1	0|2	KIF16B|KIF16B	16308626|16308626	1.000000|1.000000	0.71417|0.71417	0.028000|0.028000	0.17463|0.17463	0.078000|0.078000	0.17371|0.17371	5.578000|5.578000	0.67450|0.67450	1.364000|1.364000	0.46038|0.46038	0.655000|0.655000	0.94253|0.94253	GCG|CGG		0.502	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683	
TMC2	117532	broad.mit.edu	37	20	2597798	2597798	+	Missense_Mutation	SNP	C	C	T	rs200272296		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr20:2597798C>T	ENST00000358864.1	+	16	2036	c.2021C>T	c.(2020-2022)gCg>gTg	p.A674V	TMC2_ENST00000496948.1_3'UTR	NM_080751.2	NP_542789.2	Q8TDI7	TMC2_HUMAN	transmembrane channel-like 2	674					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)	p.A674V(1)		NS(1)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						CAGTGCTGGGCGGTGATGAGC	0.567													C|||	1	0.000199681	0.0	0.0	5008	,	,		20791	0.001		0.0	False		,,,				2504	0.0				p.A674V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2021T	20						.						172.0	126.0	142.0					20																	2597798		2203	4300	6503	2545798	SO:0001583	missense	117532	exon16			AF417580	CCDS13029.2	20p13	2010-08-05	2003-02-23		ENSG00000149488	ENSG00000149488			16527	protein-coding gene	gene with protein product		606707	"""transmembrane, cochlear expressed, 2"""	C20orf145		11850618, 12906855	Standard	XM_005260660		Approved	dJ686C3.3	uc002wgf.1	Q8TDI7	OTTHUMG00000031698	ENST00000358864.1:c.2021C>T	20.37:g.2597798C>T	ENSP00000351732:p.Ala674Val	Somatic		Capture	Illumina HiSeq	Phase_I	2545798	NM_080751	Q5JXT0|Q5JXT1|Q6UWW4|Q6ZS41|Q8N9F3|Q9BYN2|Q9BYN3|Q9BYN4|Q9BYN5	Missense_Mutation	SNP	ENST00000358864.1	37	CCDS13029.2	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	33	5.284200	0.95517	.	.	ENSG00000149488	ENST00000358864	T	0.64438	-0.1	5.35	5.35	0.76521	.	0.101582	0.64402	D	0.000002	T	0.78742	0.4331	M	0.70842	2.15	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80641	-0.1292	10	0.87932	D	0	-3.1957	16.9259	0.86176	0.0:1.0:0.0:0.0	.	674	Q8TDI7	TMC2_HUMAN	V	674	ENSP00000351732:A674V	ENSP00000351732:A674V	A	+	2	0	TMC2	2545798	1.000000	0.71417	0.967000	0.41034	0.976000	0.68499	7.818000	0.86416	2.656000	0.90262	0.650000	0.86243	GCG		0.567	TMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077601.2		
CRNKL1	51340	broad.mit.edu	37	20	20023121	20023121	+	Missense_Mutation	SNP	G	G	A	rs577483196		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr20:20023121G>A	ENST00000377340.2	-	9	1526	c.1495C>T	c.(1495-1497)Cgc>Tgc	p.R499C	CRNKL1_ENST00000536226.1_Missense_Mutation_p.R338C|CRNKL1_ENST00000377327.4_Missense_Mutation_p.R487C	NM_001278628.1|NM_016652.4	NP_001265557.1|NP_057736.4	Q9BZJ0	CRNL1_HUMAN	crooked neck pre-mRNA splicing factor 1	499	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.R499C(1)		breast(2)|cervix(2)|endometrium(7)|large_intestine(11)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(6)	45						TCTACCAAGCGCAAGTAATCA	0.448													G|||	1	0.000199681	0.0	0.0	5008	,	,		18645	0.0		0.0	False		,,,				2504	0.001				p.R499C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1495T	20						.						130.0	120.0	123.0					20																	20023121		2203	4300	6503	19971121	SO:0001583	missense	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.1495C>T	20.37:g.20023121G>A	ENSP00000366557:p.Arg499Cys	Somatic		Capture	Illumina HiSeq	Phase_I	19971121	NM_016652	A8K9T4|Q5JY64|Q8WYI5|Q9BZI9|Q9BZJ1|Q9BZJ2|Q9GZW7|Q9H8F8|Q9NQH5|Q9NYD8	Missense_Mutation	SNP	ENST00000377340.2	37	CCDS33446.1	.	.	.	.	.	.	.	.	.	.	G	31	5.063101	0.93898	.	.	ENSG00000101343	ENST00000377327;ENST00000377340;ENST00000536226	T;T;T	0.35789	1.29;1.29;1.29	5.93	5.93	0.95920	Tetratricopeptide-like helical (1);	0.046777	0.85682	D	0.000000	T	0.68879	0.3049	H	0.94847	3.59	0.80722	D	1	D	0.89917	1.0	P	0.62184	0.899	T	0.77694	-0.2492	10	0.87932	D	0	-10.4676	16.6005	0.84815	0.0:0.0:0.8694:0.1306	.	499	Q9BZJ0	CRNL1_HUMAN	C	487;499;338	ENSP00000366544:R487C;ENSP00000366557:R499C;ENSP00000440733:R338C	ENSP00000366544:R487C	R	-	1	0	CRNKL1	19971121	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.630000	0.74272	2.797000	0.96272	0.655000	0.94253	CGC		0.448	CRNKL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000127787.1		
DNMT3B	1789	broad.mit.edu	37	20	31395624	31395624	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr20:31395624G>A	ENST00000328111.2	+	23	2798	c.2477G>A	c.(2476-2478)cGc>cAc	p.R826H	DNMT3B_ENST00000348286.2_Missense_Mutation_p.R743H|DNMT3B_ENST00000443239.3_Missense_Mutation_p.R701H|DNMT3B_ENST00000456297.2_Missense_Mutation_p.R667H|DNMT3B_ENST00000201963.3_Missense_Mutation_p.R818H|DNMT3B_ENST00000353855.2_Missense_Mutation_p.R806H|DNMT3B_ENST00000344505.4_Silent_p.P766P	NM_006892.3	NP_008823.1	Q9UBC3	DNM3B_HUMAN	DNA (cytosine-5-)-methyltransferase 3 beta	826	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation on cytosine within a CG sequence (GO:0010424)|methylation-dependent chromatin silencing (GO:0006346)|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)|positive regulation of neuron differentiation (GO:0045666)|protein complex localization (GO:0031503)|regulation of gene expression by genetic imprinting (GO:0006349)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA-methyltransferase activity (GO:0009008)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)|unmethylated CpG binding (GO:0045322)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(16)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CGTGGTGCCCGCCAGAAGCTG	0.582																																					p.R806H												.	.	0			c.G2417A	20						.						133.0	124.0	127.0					20																	31395624		2203	4300	6503	30859285	SO:0001583	missense	1789	exon22				CCDS13204.1, CCDS13205.1, CCDS13206.1, CCDS13207.1, CCDS56183.1, CCDS56184.1	20q11.2	2014-09-17			ENSG00000088305	ENSG00000088305			2979	protein-coding gene	gene with protein product		602900				9662389, 10433969	Standard	NM_006892		Approved		uc002wyc.3	Q9UBC3	OTTHUMG00000032226	ENST00000328111.2:c.2477G>A	20.37:g.31395624G>A	ENSP00000328547:p.Arg826His	None		Capture	Illumina HiSeq	Phase_I	30859285	NM_175848	A2A2E2|B4DSM8|B4DSU1|E1P5M6|E1P5M7|E7EN63|E9PBF2|Q9UBD4|Q9UJQ5|Q9UKA6|Q9UNE5|Q9Y5R9|Q9Y5S0	Missense_Mutation	SNP	ENST00000328111.2	37	CCDS13205.1	.	.	.	.	.	.	.	.	.	.	G	36	5.615110	0.96649	.	.	ENSG00000088305	ENST00000328111;ENST00000353855;ENST00000348286;ENST00000443239;ENST00000456297;ENST00000201963	D;D;D;D;D;D	0.97186	-4.28;-4.28;-4.28;-4.28;-4.28;-4.28	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	D	0.98686	0.9559	M	0.88570	2.965	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	0.996;0.996;0.994;0.999;0.998;0.999;0.999	D	0.99285	1.0897	10	0.87932	D	0	-29.9786	18.5892	0.91202	0.0:0.0:1.0:0.0	.	667;701;462;818;743;806;826	E9PBF2;E7EN63;B3KM53;Q9UBC3-6;Q9UBC3-3;Q9UBC3-2;Q9UBC3	.;.;.;.;.;.;DNM3B_HUMAN	H	826;806;743;701;667;818	ENSP00000328547:R826H;ENSP00000313397:R806H;ENSP00000337764:R743H;ENSP00000403169:R701H;ENSP00000412305:R667H;ENSP00000201963:R818H	ENSP00000201963:R818H	R	+	2	0	DNMT3B	30859285	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	9.657000	0.98554	2.941000	0.99782	0.655000	0.94253	CGC		0.582	DNMT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078643.2	NM_006892	
BPIFB3	359710	broad.mit.edu	37	20	31657706	31657706	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr20:31657706C>T	ENST00000375494.3	+	11	1162	c.1162C>T	c.(1162-1164)Cgt>Tgt	p.R388C		NM_182658.1	NP_872599.1	P59826	BPIB3_HUMAN	BPI fold containing family B, member 3	388					innate immune response (GO:0045087)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)	p.R388C(1)									CATGACTGTGCGTGCCCAGCT	0.577																																					p.R388C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1162T	20						.						251.0	226.0	234.0					20																	31657706		2203	4300	6503	31121367	SO:0001583	missense	359710	exon11			AF549189	CCDS13212.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186190	ENSG00000186190		"""BPI fold containing"""	16178	protein-coding gene	gene with protein product		615717	"""chromosome 20 open reading frame 185"""	C20orf185		11971875, 21787333	Standard	NM_182658		Approved	dJ726C3.4, LPLUNC3, RYA3	uc002wym.1	P59826	OTTHUMG00000032234	ENST00000375494.3:c.1162C>T	20.37:g.31657706C>T	ENSP00000364643:p.Arg388Cys	Somatic		Capture	Illumina HiSeq	Phase_I	31121367	NM_182658	Q5TDX7	Missense_Mutation	SNP	ENST00000375494.3	37	CCDS13212.1	.	.	.	.	.	.	.	.	.	.	C	9.908	1.208837	0.22205	.	.	ENSG00000186190	ENST00000375494	T	0.07114	3.22	4.34	3.24	0.37175	.	0.456780	0.20154	N	0.098085	T	0.07324	0.0185	N	0.22421	0.69	0.27560	N	0.950214	D	0.54047	0.964	P	0.45946	0.498	T	0.14839	-1.0458	10	0.56958	D	0.05	-1.5609	7.9452	0.29982	0.776:0.224:0.0:0.0	.	388	P59826	BPIB3_HUMAN	C	388	ENSP00000364643:R388C	ENSP00000364643:R388C	R	+	1	0	BPIFB3	31121367	0.786000	0.28738	0.573000	0.28510	0.004000	0.04260	2.492000	0.45311	0.808000	0.34231	-0.467000	0.05162	CGT		0.577	BPIFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078654.2	NM_182658	
SNTA1	6640	broad.mit.edu	37	20	32000128	32000128	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr20:32000128G>A	ENST00000217381.2	-	5	1285	c.1014C>T	c.(1012-1014)gcC>gcT	p.A338A		NM_003098.2	NP_003089.1	Q13424	SNTA1_HUMAN	syntrophin, alpha 1	338	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				muscle contraction (GO:0006936)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|neuromuscular junction development (GO:0007528)|regulation of heart rate (GO:0002027)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of vasoconstriction by circulating norepinephrine (GO:0003117)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|ventricular cardiac muscle cell action potential (GO:0086005)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular (GO:0005622)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	ATPase binding (GO:0051117)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)	p.A338A(1)		breast(1)|large_intestine(4)|liver(1)|lung(4)|skin(1)|stomach(1)|urinary_tract(1)	13						GGGCAGTACGGGCTGGCCGGC	0.657																																					p.A338A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1014T	20						.						18.0	22.0	21.0					20																	32000128		2201	4296	6497	31463789	SO:0001819	synonymous_variant	6640	exon5			U40571	CCDS13220.1	20q11.2	2014-09-17	2012-06-15		ENSG00000101400	ENSG00000101400			11167	protein-coding gene	gene with protein product	"""pro-TGF-alpha cytoplasmic domain-interacting protein 1"", ""dystrophin-associated protein A1, 59kDa, acidic component"""	601017	"""syntrophin, alpha 1 (dystrophin-associated protein A1, 59kD, acidic component)"""	SNT1		8576247, 8612778	Standard	NM_003098		Approved	TACIP1, LQT12	uc002wzd.1	Q13424	OTTHUMG00000032259	ENST00000217381.2:c.1014C>T	20.37:g.32000128G>A		Somatic		Capture	Illumina HiSeq	Phase_I	31463789	NM_003098	A8K7H9|B4DX40|E1P5N1|Q16438	Silent	SNP	ENST00000217381.2	37	CCDS13220.1																																																																																				0.657	SNTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078704.2	NM_003098	
ZNF341	84905	broad.mit.edu	37	20	32379126	32379126	+	Missense_Mutation	SNP	G	G	A	rs371648715		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr20:32379126G>A	ENST00000375200.1	+	15	2733	c.2368G>A	c.(2368-2370)Ggc>Agc	p.G790S	RP4-553F4.6_ENST00000439444.1_RNA|RP4-553F4.6_ENST00000423074.1_RNA|RP4-553F4.6_ENST00000443171.1_RNA|ZNF341_ENST00000342427.2_Missense_Mutation_p.G783S	NM_001282933.1	NP_001269862.1	Q9BYN7	ZN341_HUMAN	zinc finger protein 341	790					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.G783S(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	31						GGCTGTCCCCGGCAAGCCGCC	0.701																																					p.G783S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2347A	20						.	G	SER/GLY	2,4402		0,2,2200	25.0	28.0	27.0		2347	3.1	1.0	20		27	0,8594		0,0,4297	no	missense	ZNF341	NM_032819.3	56	0,2,6497	AA,AG,GG		0.0,0.0454,0.0154	benign	783/848	32379126	2,12996	2202	4297	6499	31842787	SO:0001583	missense	84905	exon15			AK027550	CCDS13227.1, CCDS74719.1	20q11.22	2013-01-08			ENSG00000131061	ENSG00000131061		"""Zinc fingers, C2H2-type"""	15992	protein-coding gene	gene with protein product							Standard	NM_001282933		Approved	dJ553F4.3	uc002wzx.3	Q9BYN7	OTTHUMG00000032275	ENST00000375200.1:c.2368G>A	20.37:g.32379126G>A	ENSP00000364346:p.Gly790Ser	Somatic		Capture	Illumina HiSeq	Phase_I	31842787	NM_032819	A2RUF4|B2RXE5|B7ZM09|Q5JXM8|Q96ST5	Missense_Mutation	SNP	ENST00000375200.1	37		.	.	.	.	.	.	.	.	.	.	G	9.972	1.225694	0.22542	4.54E-4	0.0	ENSG00000131061	ENST00000342427;ENST00000375200	T;T	0.08634	3.32;3.07	5.06	3.08	0.35506	.	0.502824	0.18782	N	0.131309	T	0.05135	0.0137	N	0.19112	0.55	0.27198	N	0.960241	B;B;B;B	0.26002	0.002;0.139;0.008;0.014	B;B;B;B	0.12156	0.001;0.007;0.002;0.006	T	0.27606	-1.0069	10	0.46703	T	0.11	-19.134	7.3998	0.26956	0.2968:0.0:0.7032:0.0	.	731;642;790;783	Q504V9;B3KU97;Q9BYN7;Q9BYN7-2	.;.;ZN341_HUMAN;.	S	783;790	ENSP00000344308:G783S;ENSP00000364346:G790S	ENSP00000344308:G783S	G	+	1	0	ZNF341	31842787	0.994000	0.37717	0.979000	0.43373	0.253000	0.25986	2.370000	0.44240	1.273000	0.44346	0.491000	0.48974	GGC		0.701	ZNF341-201	KNOWN	basic	protein_coding	protein_coding			
EDEM2	55741	broad.mit.edu	37	20	33734701	33734701	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr20:33734701T>G	ENST00000374492.3	-	2	250	c.145A>C	c.(145-147)Agc>Cgc	p.S49R	EDEM2_ENST00000541621.1_5'Flank|EDEM2_ENST00000542871.1_5'UTR|EDEM2_ENST00000374491.3_Intron|EDEM2_ENST00000540582.1_Missense_Mutation_p.S8R	NM_018217.2	NP_060687.2	Q9BV94	EDEM2_HUMAN	ER degradation enhancer, mannosidase alpha-like 2	49					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.S49R(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	22			BRCA - Breast invasive adenocarcinoma(18;0.00936)			TCCAGGTAGCTGTCGTAGGCG	0.602																																					p.S49R	Esophageal Squamous(51;906 1021 24535 36410 39145)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A145C	20						.						108.0	62.0	77.0					20																	33734701		2203	4300	6503	33198362	SO:0001583	missense	55741	exon2			AK001645	CCDS13247.1, CCDS46592.1	20q11.22	2006-03-31	2006-03-31	2006-03-31	ENSG00000088298	ENSG00000088298			15877	protein-coding gene	gene with protein product		610302	"""chromosome 20 open reading frame 31"""	C20orf49, C20orf31		15537790, 15579471	Standard	NM_018217		Approved	FLJ10783, bA4204.1	uc002xbo.2	Q9BV94	OTTHUMG00000032322	ENST00000374492.3:c.145A>C	20.37:g.33734701T>G	ENSP00000363616:p.Ser49Arg	Somatic		Capture	Illumina HiSeq	Phase_I	33198362	NM_018217	B4DTG9|Q6GU33|Q6IA89|Q6UWZ4|Q9H4U0|Q9H886|Q9NTL9|Q9NVE6	Missense_Mutation	SNP	ENST00000374492.3	37	CCDS13247.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.409994	0.83340	.	.	ENSG00000088298	ENST00000374492;ENST00000540582	T;T	0.47177	0.85;0.85	5.08	5.08	0.68730	.	0.139599	0.64402	D	0.000004	T	0.62392	0.2424	M	0.84326	2.69	0.47737	D	0.999501	P;P	0.50617	0.937;0.87	P;P	0.53360	0.628;0.724	T	0.68503	-0.5391	10	0.66056	D	0.02	-19.7985	11.5769	0.50866	0.0:0.0:0.1488:0.8512	.	8;49	F5GZ44;Q9BV94	.;EDEM2_HUMAN	R	49;8	ENSP00000363616:S49R;ENSP00000441548:S8R	ENSP00000363616:S49R	S	-	1	0	EDEM2	33198362	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.729000	0.68538	2.144000	0.66660	0.448000	0.29417	AGC		0.602	EDEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078842.2	NM_018217	
FAM83C	128876	broad.mit.edu	37	20	33874684	33874684	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr20:33874684C>T	ENST00000374408.3	-	4	1994	c.1898G>A	c.(1897-1899)aGc>aAc	p.S633N	FAM83C-AS1_ENST00000429167.1_RNA|EIF6_ENST00000374443.3_5'Flank|EIF6_ENST00000462894.1_5'Flank|EIF6_ENST00000374450.3_5'Flank|EIF6_ENST00000374436.3_5'Flank	NM_178468.5	NP_848563.1	Q9BQN1	FA83C_HUMAN	family with sequence similarity 83, member C	633								p.S633N(1)		central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(18;0.00252)			GTCCAGCTGGCTGTGCCCCAG	0.647																																					p.S633N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1898A	20						.						44.0	42.0	43.0					20																	33874684		2203	4300	6503	33338098	SO:0001583	missense	128876	exon4			AL121753	CCDS13251.1	20q11.22	2011-04-01	2006-03-23	2006-03-23	ENSG00000125998	ENSG00000125998			16121	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 128"""	C20orf128			Standard	NM_178468		Approved	dJ614O4.7	uc021wck.1	Q9BQN1	OTTHUMG00000032332	ENST00000374408.3:c.1898G>A	20.37:g.33874684C>T	ENSP00000363529:p.Ser633Asn	Somatic		Capture	Illumina HiSeq	Phase_I	33338098	NM_178468	Q14D67|Q5JWN6|Q8N276	Missense_Mutation	SNP	ENST00000374408.3	37	CCDS13251.1	.	.	.	.	.	.	.	.	.	.	C	13.84	2.356243	0.41700	.	.	ENSG00000125998	ENST00000374408	T	0.10763	2.84	4.66	4.66	0.58398	.	0.281220	0.30060	N	0.010502	T	0.14098	0.0341	L	0.61218	1.895	0.28160	N	0.929022	B	0.18461	0.028	B	0.14023	0.01	T	0.05209	-1.0899	10	0.72032	D	0.01	-3.752	13.0833	0.59125	0.0:0.8385:0.1615:0.0	.	633	Q9BQN1	FA83C_HUMAN	N	633	ENSP00000363529:S633N	ENSP00000363529:S633N	S	-	2	0	FAM83C	33338098	1.000000	0.71417	1.000000	0.80357	0.791000	0.44710	1.490000	0.35573	2.541000	0.85698	0.561000	0.74099	AGC		0.647	FAM83C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078854.3		
RBM12	10137	broad.mit.edu	37	20	34242973	34242973	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr20:34242973T>C	ENST00000374114.3	-	3	535	c.272A>G	c.(271-273)gAa>gGa	p.E91G	CPNE1_ENST00000397443.1_Intron|RP1-309K20.6_ENST00000541176.2_Intron|CPNE1_ENST00000397442.1_Intron|RBM12_ENST00000359646.1_Missense_Mutation_p.E91G|CPNE1_ENST00000397445.1_Intron|RBM12_ENST00000374104.3_Missense_Mutation_p.E91G|CPNE1_ENST00000317677.5_5'Flank|CPNE1_ENST00000317619.3_Intron|CPNE1_ENST00000352393.4_Intron|CPNE1_ENST00000397446.1_Intron	NM_001198838.1|NM_001198840.1|NM_006047.5	NP_001185767.1|NP_001185769.1|NP_006038.2	Q9NTZ6	RBM12_HUMAN	RNA binding motif protein 12	91						nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.E91G(1)		breast(3)|endometrium(7)|kidney(1)|large_intestine(3)|lung(14)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			GTTGGCAGTTTCAAAACGCCT	0.438											OREG0004046	type=REGULATORY REGION|Gene=RBM12|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.E91G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A272G	20						.						180.0	169.0	173.0					20																	34242973		2203	4300	6503	33706387	SO:0001583	missense	10137	exon3			AJ289772	CCDS13261.1	20q11.21	2013-02-12			ENSG00000244462	ENSG00000244462		"""RNA binding motif (RRM) containing"""	9898	protein-coding gene	gene with protein product		607179				11435693	Standard	NM_006047		Approved	HRIHFB2091, KIAA0765, SWAN	uc021wcq.1	Q9NTZ6	OTTHUMG00000032350	ENST00000374114.3:c.272A>G	20.37:g.34242973T>C	ENSP00000363228:p.Glu91Gly	Somatic	846	Capture	Illumina HiSeq	Phase_I	33706387	NM_152838	B3KRU2|E1P5R6|O94865|Q8N3B1|Q9H196	Missense_Mutation	SNP	ENST00000374114.3	37	CCDS13261.1	.	.	.	.	.	.	.	.	.	.	T	13.45	2.239635	0.39598	.	.	ENSG00000244462	ENST00000374114;ENST00000359646;ENST00000374104;ENST00000424458;ENST00000431148;ENST00000435161	T;T;T;T;T;T	0.25414	2.37;2.37;2.37;1.8;2.14;2.16	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.38241	0.1033	L	0.27053	0.805	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.13388	-1.0511	10	0.44086	T	0.13	-11.5866	15.6958	0.77494	0.0:0.0:0.0:1.0	.	91	Q9NTZ6	RBM12_HUMAN	G	91	ENSP00000363228:E91G;ENSP00000352668:E91G;ENSP00000363217:E91G;ENSP00000411036:E91G;ENSP00000392642:E91G;ENSP00000411692:E91G	ENSP00000352668:E91G	E	-	2	0	RBM12	33706387	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.294000	0.78760	2.288000	0.76882	0.528000	0.53228	GAA		0.438	RBM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078894.1	NM_006047	
RALGAPB	57148	broad.mit.edu	37	20	37146428	37146428	+	Splice_Site	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr20:37146428T>C	ENST00000262879.6	+	9	1486	c.1202T>C	c.(1201-1203)gTt>gCt	p.V401A	RALGAPB_ENST00000397042.3_Splice_Site_p.V401A|RALGAPB_ENST00000537204.1_Splice_Site_p.V401A|RALGAPB_ENST00000397038.1_Splice_Site_p.V179A|RALGAPB_ENST00000397040.1_Splice_Site_p.V401A|MIR548O2_ENST00000583129.1_RNA			Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit (non-catalytic)	401					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)|Ral protein signal transduction (GO:0032484)|regulation of exocyst localization (GO:0060178)		protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)	p.V401A(1)		breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(29)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						GTCTAATAGGTTAGTACTGCT	0.433																																					p.V401A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1202C	20						.						112.0	105.0	107.0					20																	37146428		2203	4300	6503	36579842	SO:0001630	splice_region_variant	57148	exon9			AB033045	CCDS13305.1, CCDS63272.1	20q11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000170471	ENSG00000170471			29221	protein-coding gene	gene with protein product			"""KIAA1219"""	KIAA1219		19520869	Standard	XM_005260462		Approved	DKFZp781M2411, RalGAPbeta	uc002xiw.3	Q86X10	OTTHUMG00000140270	ENST00000262879.6:c.1201-1T>C	20.37:g.37146428T>C		Somatic		Capture	Illumina HiSeq	Phase_I	36579842	NM_020336	A2A2E8|A2A2E9|Q5TG31|Q8N3D1|Q8WWC0|Q9H3X8|Q9UJR1|Q9ULK1|Q9Y3G9	Missense_Mutation	SNP	ENST00000262879.6	37	CCDS13305.1	.	.	.	.	.	.	.	.	.	.	T	9.955	1.221299	0.22457	.	.	ENSG00000170471	ENST00000262879;ENST00000397042;ENST00000304939;ENST00000397038;ENST00000537204;ENST00000397040;ENST00000438490	.	.	.	5.28	4.16	0.48862	.	0.247198	0.40818	N	0.001014	T	0.29783	0.0744	N	0.08118	0	0.39143	D	0.962081	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.001;0.001;0.001;0.001	T	0.14364	-1.0475	9	0.30854	T	0.27	.	9.9628	0.41706	0.0:0.1351:0.0:0.8649	.	401;229;401;401;401	B4E2E8;A2A2F0;Q86X10-4;A2A2E9;Q86X10	.;.;.;.;RLGPB_HUMAN	A	401;401;401;179;401;401;229	.	ENSP00000262879:V401A	V	+	2	0	RALGAPB	36579842	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	0.790000	0.26900	2.122000	0.65172	0.454000	0.30748	GTT		0.433	RALGAPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079191.1	NM_020336	Missense_Mutation
CSNK2A1	1457	broad.mit.edu	37	20	469335	469335	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr20:469335C>A	ENST00000217244.3	-	11	1186	c.811G>T	c.(811-813)Gat>Tat	p.D271Y	CSNK2A1_ENST00000400227.3_Missense_Mutation_p.D271Y|CSNK2A1_ENST00000349736.5_Missense_Mutation_p.D271Y|CSNK2A1_ENST00000400217.2_Missense_Mutation_p.D135Y	NM_177559.2	NP_808227.1	P68400	CSK21_HUMAN	casein kinase 2, alpha 1 polypeptide	271	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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.D271Y(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)			CCCAAGATATCATTGAAACGT	0.358																																					p.D271Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G811T	20						.						144.0	126.0	132.0					20																	469335		2203	4300	6503	417335	SO:0001583	missense	1457	exon10			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.811G>T	20.37:g.469335C>A	ENSP00000217244:p.Asp271Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	417335	NM_001895	B4DYS6|D3DVV8|P19138|P20426|Q14013|Q5U065	Missense_Mutation	SNP	ENST00000217244.3	37	CCDS13003.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.801367	0.90538	.	.	ENSG00000101266	ENST00000400227;ENST00000349736;ENST00000217244;ENST00000381973;ENST00000400217	T;T;T;T	0.42131	3.37;3.37;3.37;0.98	5.44	5.44	0.79542	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	0.57932	0.2087	L	0.39898	1.24	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	T	0.58612	-0.7606	10	0.87932	D	0	-3.4933	18.4336	0.90636	0.0:1.0:0.0:0.0	.	271	P68400	CSK21_HUMAN	Y	271;271;271;271;135	ENSP00000383086:D271Y;ENSP00000339247:D271Y;ENSP00000217244:D271Y;ENSP00000383076:D135Y	ENSP00000217244:D271Y	D	-	1	0	CSNK2A1	417335	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.604000	0.82830	2.832000	0.97577	0.655000	0.94253	GAT		0.358	CSNK2A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077466.1	NM_001895	
SLC32A1	140679	broad.mit.edu	37	20	37353697	37353697	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr20:37353697C>T	ENST00000217420.1	+	1	593	c.330C>T	c.(328-330)ggC>ggT	p.G110G		NM_080552.2	NP_542119.1	Q9H598	VIAAT_HUMAN	solute carrier family 32 (GABA vesicular transporter), member 1	110					aging (GO:0007568)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell tip (GO:0051286)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cone cell pedicle (GO:0044316)|dendrite (GO:0030425)|dendrite terminus (GO:0044292)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	gamma-aminobutyric acid:proton symporter activity (GO:0015495)|glycine transmembrane transporter activity (GO:0015187)	p.G110G(1)		breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(16)|urinary_tract(1)	38		Myeloproliferative disorder(115;0.00878)			Glycine(DB00145)	AATTCGGGGGCCACGACAAGC	0.657																																					p.G110G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C330T	20						.						42.0	46.0	45.0					20																	37353697		2155	4232	6387	36787111	SO:0001819	synonymous_variant	140679	exon1			AL133519	CCDS13307.1	20q11	2013-05-22			ENSG00000101438	ENSG00000101438		"""Solute carriers"""	11018	protein-coding gene	gene with protein product			"""vesicular inhibitory amino acid transporter"""	VIAAT		19843525	Standard	NM_080552		Approved	VGAT, bA122O1.1	uc002xjc.3	Q9H598	OTTHUMG00000032457	ENST00000217420.1:c.330C>T	20.37:g.37353697C>T		Somatic		Capture	Illumina HiSeq	Phase_I	36787111	NM_080552	Q8N489	Silent	SNP	ENST00000217420.1	37	CCDS13307.1																																																																																				0.657	SLC32A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079206.1	NM_080552	
TNNC2	7125	broad.mit.edu	37	20	44452741	44452741	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr20:44452741C>T	ENST00000372555.3	-	5	432	c.340G>A	c.(340-342)Gag>Aag	p.E114K	TNNC2_ENST00000372557.1_Missense_Mutation_p.E99K	NM_003279.2	NP_003270.1	P02585	TNNC2_HUMAN	troponin C type 2 (fast)	114	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.			E -> G (in Ref. 3; AAA91854). {ECO:0000305}.	muscle filament sliding (GO:0030049)|regulation of muscle contraction (GO:0006937)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|troponin complex (GO:0005861)	calcium ion binding (GO:0005509)	p.E114K(1)		endometrium(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	5		Myeloproliferative disorder(115;0.0122)			Felodipine(DB01023)	GCCAGCTCCTCCGGGTCGATG	0.642																																					p.E114K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G340A	20						.						132.0	123.0	126.0					20																	44452741		2203	4300	6503	43886148	SO:0001583	missense	7125	exon5				CCDS13375.1	20q12-q13.11	2013-01-10	2005-09-12		ENSG00000101470	ENSG00000101470		"""EF-hand domain containing"""	11944	protein-coding gene	gene with protein product		191039	"""troponin C2, fast"""			2373703	Standard	NM_003279		Approved		uc002xpr.3	P02585	OTTHUMG00000032623	ENST00000372555.3:c.340G>A	20.37:g.44452741C>T	ENSP00000361636:p.Glu114Lys	Somatic		Capture	Illumina HiSeq	Phase_I	43886148	NM_003279	Q6FH92	Missense_Mutation	SNP	ENST00000372555.3	37	CCDS13375.1	.	.	.	.	.	.	.	.	.	.	C	16.98	3.270200	0.59540	.	.	ENSG00000101470	ENST00000372557;ENST00000372555	T;T	0.66099	-0.19;-0.19	4.12	4.12	0.48240	EF-hand-like domain (1);	0.057016	0.64402	D	0.000002	T	0.44201	0.1282	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.17098	0.017	T	0.47142	-0.9140	10	0.87932	D	0	-24.7625	15.0859	0.72151	0.0:1.0:0.0:0.0	.	114	P02585	TNNC2_HUMAN	K	99;114	ENSP00000361638:E99K;ENSP00000361636:E114K	ENSP00000361636:E114K	E	-	1	0	TNNC2	43886148	1.000000	0.71417	0.947000	0.38551	0.683000	0.39861	5.797000	0.69087	2.132000	0.65825	0.305000	0.20034	GAG		0.642	TNNC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079524.3	NM_003279	
SNX21	90203	broad.mit.edu	37	20	44469293	44469293	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr20:44469293G>A	ENST00000491381.1	+	4	531	c.463G>A	c.(463-465)Gtg>Atg	p.V155M	SNX21_ENST00000372541.1_Silent_p.P149P|SNX21_ENST00000342644.5_Missense_Mutation_p.V155M|SNX21_ENST00000462307.1_Silent_p.P158P|SNX21_ENST00000372542.1_Missense_Mutation_p.V146M|SNX21_ENST00000344780.4_3'UTR			Q969T3	SNX21_HUMAN	sorting nexin family member 21	155	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|pancreas(1)	7		Myeloproliferative disorder(115;0.0122)				CACCCTCGCCGTGATCGGCCC	0.647																																					p.V155M												.	.	0			c.G463A	20						.						85.0	88.0	87.0					20																	44469293		2203	4300	6503	43902700	SO:0001583	missense	90203	exon4			AK095851	CCDS13376.1, CCDS13377.1, CCDS42883.1	20q13.12	2013-01-10	2006-07-24	2006-07-24	ENSG00000124104	ENSG00000124104		"""Sorting nexins"", ""Tetratricopeptide (TTC) repeat domain containing"""	16154	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 161"""	C20orf161		12461558, 12459172	Standard	NM_152897		Approved	dJ337O18.4, SNX-L	uc002xpv.1	Q969T3	OTTHUMG00000032624	ENST00000491381.1:c.463G>A	20.37:g.44469293G>A	ENSP00000418593:p.Val155Met	None		Capture	Illumina HiSeq	Phase_I	43902700	NM_152897	Q5JZH5|Q5JZH6|Q5JZH7|Q8WUR6|Q9BR16	Missense_Mutation	SNP	ENST00000491381.1	37	CCDS13377.1	.	.	.	.	.	.	.	.	.	.	G	17.10	3.302681	0.60195	.	.	ENSG00000124104	ENST00000491381;ENST00000342644;ENST00000372542	T;T;T	0.35973	1.28;1.28;1.28	4.34	3.34	0.38264	Phox homologous domain (4);	0.150978	0.43919	D	0.000501	T	0.46946	0.1419	.	.	.	0.80722	D	1	P;D;D	0.63046	0.909;0.992;0.992	B;P;P	0.58210	0.348;0.781;0.835	T	0.45600	-0.9250	9	0.56958	D	0.05	-16.776	6.9173	0.24367	0.0:0.267:0.5766:0.1565	.	146;155;155	Q5JZH3;Q969T3;Q5JZH5	.;SNX21_HUMAN;.	M	155;155;146	ENSP00000418593:V155M;ENSP00000344586:V155M;ENSP00000361620:V146M	ENSP00000344586:V155M	V	+	1	0	SNX21	43902700	1.000000	0.71417	1.000000	0.80357	0.786000	0.44442	1.861000	0.39438	2.254000	0.74563	0.462000	0.41574	GTG		0.647	SNX21-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079534.1	NM_033421	
RASSF2	9770	broad.mit.edu	37	20	4776521	4776521	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr20:4776521C>T	ENST00000379400.3	-	5	422	c.227G>A	c.(226-228)cGc>cAc	p.R76H	RASSF2_ENST00000478553.1_5'Flank|RASSF2_ENST00000379376.2_Missense_Mutation_p.R76H	NM_014737.2	NP_055552.1	P50749	RASF2_HUMAN	Ras association (RalGDS/AF-6) domain family member 2	76					bone remodeling (GO:0046849)|cell cycle (GO:0007049)|epidermal growth factor receptor signaling pathway via I-kappaB kinase/NF-kappaB cascade (GO:0038168)|homeostasis of number of cells (GO:0048872)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|ossification (GO:0001503)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R76H(1)		endometrium(3)|kidney(2)|large_intestine(8)|lung(12)|ovary(3)|pancreas(2)|prostate(2)|skin(2)	34						GGGTCGAATGCGTTCGTTGTC	0.622																																					p.R76H	Melanoma(158;1891 3343 50738)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G227A	20						.						135.0	125.0	128.0					20																	4776521		2203	4300	6503	4724521	SO:0001583	missense	9770	exon4			D79990	CCDS13083.1	20p13	2011-08-12	2008-02-22		ENSG00000101265	ENSG00000101265			9883	protein-coding gene	gene with protein product	"""centromere protein 34"""	609492				8724849, 15806169	Standard	NM_014737		Approved	KIAA0168, CENP-34	uc002wld.3	P50749	OTTHUMG00000031790	ENST00000379400.3:c.227G>A	20.37:g.4776521C>T	ENSP00000368710:p.Arg76His	Somatic		Capture	Illumina HiSeq	Phase_I	4724521	NM_170774	A6NIX9|A8K5Z3|Q17S06|Q53HD0|Q6AHZ2|Q8IZA5	Missense_Mutation	SNP	ENST00000379400.3	37	CCDS13083.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.790660	0.90367	.	.	ENSG00000101265	ENST00000379400;ENST00000379376	T;T	0.10860	2.83;2.83	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.31136	0.0787	M	0.84326	2.69	0.80722	D	1	D	0.76494	0.999	P	0.60173	0.87	T	0.08764	-1.0706	10	0.17369	T	0.5	.	17.3318	0.87267	0.0:1.0:0.0:0.0	.	76	P50749	RASF2_HUMAN	H	76	ENSP00000368710:R76H;ENSP00000368684:R76H	ENSP00000368684:R76H	R	-	2	0	RASSF2	4724521	1.000000	0.71417	1.000000	0.80357	0.499000	0.33736	7.351000	0.79395	2.665000	0.90641	0.563000	0.77884	CGC		0.622	RASSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077828.1	NM_014737	
CSE1L	1434	broad.mit.edu	37	20	47682765	47682765	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr20:47682765C>T	ENST00000262982.2	+	4	388	c.265C>T	c.(265-267)Cga>Tga	p.R89*	CSE1L_ENST00000396192.3_Nonsense_Mutation_p.R89*|CSE1L_ENST00000542325.1_Intron	NM_001256135.1|NM_001316.3	NP_001243064.1|NP_001307.2	P55060	XPO2_HUMAN	CSE1 chromosome segregation 1-like (yeast)	89	Importin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00115}.				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.R89*(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)			TGAAGCCGATCGAGTGGCCAT	0.423																																					p.R89X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C265T	20						.						96.0	89.0	91.0					20																	47682765		2203	4300	6503	47116172	SO:0001587	stop_gained	1434	exon4			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.265C>T	20.37:g.47682765C>T	ENSP00000262982:p.Arg89*	Somatic		Capture	Illumina HiSeq	Phase_I	47116172	NM_001316	A3RLL6|B2R5T4|E1P5Y0|F8W904|O75432|Q32M40|Q9H5B7|Q9NTS0|Q9UP98|Q9UP99|Q9UPA0	Nonsense_Mutation	SNP	ENST00000262982.2	37	CCDS13412.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.890084	0.91889	.	.	ENSG00000124207	ENST00000262982;ENST00000396192	.	.	.	5.62	3.55	0.40652	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.6972	13.6813	0.62487	0.386:0.614:0.0:0.0	.	.	.	.	X	89	.	ENSP00000262982:R89X	R	+	1	2	CSE1L	47116172	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.250000	0.51445	1.340000	0.45581	0.655000	0.94253	CGA		0.423	CSE1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080345.2	NM_001316	
TMEM230	29058	broad.mit.edu	37	20	5090082	5090082	+	5'UTR	SNP	G	G	A	rs145815993	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr20:5090082G>A	ENST00000379286.2	-	0	415				TMEM230_ENST00000202834.7_5'UTR|TMEM230_ENST00000342308.5_Missense_Mutation_p.R62C|TMEM230_ENST00000379283.2_5'UTR|TMEM230_ENST00000492419.1_5'UTR|TMEM230_ENST00000379279.2_5'UTR|TMEM230_ENST00000379277.2_5'UTR	NM_001009924.1	NP_001009924.1	Q96A57	TM230_HUMAN	transmembrane protein 230							integral component of membrane (GO:0016021)		p.R62C(1)									ATCATAACACGCTGACACAGC	0.438																																					p.R62C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C184T	20						.	G	CYS/ARG,,,	4,4402	8.1+/-20.4	0,4,2199	62.0	55.0	57.0		184,,,	-3.2	0.3	20	dbSNP_134	57	0,8600		0,0,4300	no	missense,utr-5,utr-5,utr-5	C20orf30	NM_001009923.1,NM_001009924.1,NM_001009925.1,NM_014145.4	180,,,	0,4,6499	AA,AG,GG		0.0,0.0908,0.0308	benign,,,	62/184,,,	5090082	4,13002	2203	4300	6503	5038082	SO:0001623	5_prime_UTR_variant	29058	exon3			AF161392	CCDS13086.1, CCDS33438.1	20p13	2012-03-16	2012-03-16	2012-03-16	ENSG00000089063	ENSG00000089063			15876	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 30"""	C20orf30			Standard	XM_005260713		Approved	HSPC274	uc002wlk.3	Q96A57	OTTHUMG00000031796	ENST00000379286.2:c.-6C>T	20.37:g.5090082G>A		Somatic		Capture	Illumina HiSeq	Phase_I	5038082	NM_001009923	B2RDM8|D3DVZ9|Q0VGC8|Q5TDS5|Q96ES2|Q9P0A7	Missense_Mutation	SNP	ENST00000379286.2	37	CCDS13086.1	.	.	.	.	.	.	.	.	.	.	G	4.274	0.049974	0.08243	9.08E-4	0.0	ENSG00000089063	ENST00000342308	T	0.17370	2.28	4.92	-3.19	0.05171	.	0.831596	0.10389	N	0.680657	T	0.10035	0.0246	.	.	.	0.18873	N	0.999984	B	0.09022	0.002	B	0.04013	0.001	T	0.30090	-0.9990	9	0.36615	T	0.2	0.5147	7.3117	0.26477	0.5802:0.1297:0.2901:0.0	.	62	Q96A57-2	.	C	62	ENSP00000341364:R62C	ENSP00000341364:R62C	R	-	1	0	C20orf30	5038082	0.000000	0.05858	0.262000	0.24481	0.298000	0.27526	-0.087000	0.11215	-0.839000	0.04212	-0.482000	0.04802	CGT		0.438	TMEM230-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077846.1		
ZFP64	55734	broad.mit.edu	37	20	50705172	50705172	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr20:50705172C>T	ENST00000361387.2	-	8	1047	c.987G>A	c.(985-987)ccG>ccA	p.P329P	ZFP64_ENST00000371518.2_Silent_p.P329P|ZFP64_ENST00000371523.4_Silent_p.P110P|ZFP64_ENST00000477786.1_5'Flank	NM_199427.2	NP_955459.2	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	286					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.P329P(1)		breast(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						CACACTTGTGCGGTTTGTCTC	0.478																																					p.P329P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G987A	20						.						117.0	104.0	108.0					20																	50705172		2203	4300	6503	50138579	SO:0001819	synonymous_variant	55734	exon8			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	ENST00000361387.2:c.987G>A	20.37:g.50705172C>T		Somatic		Capture	Illumina HiSeq	Phase_I	50138579	NM_199427	Q9NTS7|Q9NVH4	Silent	SNP	ENST00000361387.2	37	CCDS13439.1	.	.	.	.	.	.	.	.	.	.	C	8.314	0.822850	0.16678	.	.	ENSG00000020256	ENST00000456175	.	.	.	4.49	-8.97	0.00758	.	.	.	.	.	T	0.50667	0.1629	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61744	-0.7000	4	.	.	.	.	11.5333	0.50622	0.0:0.3394:0.4568:0.2038	.	.	.	.	T	35	.	.	A	-	1	0	ZFP64	50138579	0.000000	0.05858	0.640000	0.29408	0.996000	0.88848	-4.207000	0.00274	-2.453000	0.00541	-0.126000	0.14955	GCA		0.478	ZFP64-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079743.2	NM_018197	
APCDD1L	164284	broad.mit.edu	37	20	57036332	57036332	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr20:57036332C>T	ENST00000371149.3	-	4	1250	c.1020G>A	c.(1018-1020)acG>acA	p.T340T	APCDD1L_ENST00000439429.1_Silent_p.T351T|APCDD1L_ENST00000491015.1_5'UTR	NM_153360.1	NP_699191.1	Q8NCL9	APCDL_HUMAN	adenomatosis polyposis coli down-regulated 1-like	340						integral component of membrane (GO:0016021)				large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(1)	18	Lung NSC(12;0.000856)|all_lung(29;0.0025)		BRCA - Breast invasive adenocarcinoma(13;5.6e-11)|Epithelial(14;1.67e-07)|all cancers(14;1.48e-06)			TGGTGGATGGCGTGCCCCTGG	0.657																																					p.T340T												.	.	0			c.G1020A	20						.						31.0	31.0	31.0					20																	57036332		2202	4299	6501	56469738	SO:0001819	synonymous_variant	164284	exon4			AK074647	CCDS13467.1	20q13.32	2006-07-07			ENSG00000198768	ENSG00000198768			26892	protein-coding gene	gene with protein product							Standard	NM_153360		Approved	FLJ90166	uc002xze.1	Q8NCL9	OTTHUMG00000032845	ENST00000371149.3:c.1020G>A	20.37:g.57036332C>T		None		Capture	Illumina HiSeq	Phase_I	56469738	NM_153360		Silent	SNP	ENST00000371149.3	37	CCDS13467.1																																																																																				0.657	APCDD1L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000079881.2	NM_153360	
TRMT6	51605	broad.mit.edu	37	20	5922605	5922605	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr20:5922605G>A	ENST00000203001.2	-	8	1234	c.1104C>T	c.(1102-1104)aaC>aaT	p.N368N	TRMT6_ENST00000473131.1_5'UTR|TRMT6_ENST00000453074.2_Silent_p.N198N	NM_015939.3	NP_057023.2	Q9UJA5	TRM6_HUMAN	tRNA methyltransferase 6 homolog (S. cerevisiae)	368					regulation of translational initiation (GO:0006446)|tRNA processing (GO:0008033)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743)	p.N368N(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)	15						ACCCATCTGCGTTTCTTTCAC	0.453																																					p.N368N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1104T	20						.						235.0	226.0	229.0					20																	5922605		2203	4300	6503	5870605	SO:0001819	synonymous_variant	51605	exon8			AK000613	CCDS13093.1, CCDS63225.1	20p12.3	2009-01-12			ENSG00000089195	ENSG00000089195			20900	protein-coding gene	gene with protein product						16043508	Standard	NM_001281467		Approved	GCD10, MGC5029, Gcd10p, CGI-09	uc002wmh.1	Q9UJA5	OTTHUMG00000031816	ENST00000203001.2:c.1104C>T	20.37:g.5922605G>A		Somatic		Capture	Illumina HiSeq	Phase_I	5870605	NM_015939	B4DUV6|Q76P92|Q9BQV5|Q9ULR7|Q9Y2Z8	Silent	SNP	ENST00000203001.2	37	CCDS13093.1																																																																																				0.453	TRMT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077889.2		
MCM8	84515	broad.mit.edu	37	20	5935882	5935882	+	Silent	SNP	T	T	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr20:5935882T>G	ENST00000378896.3	+	5	848	c.471T>G	c.(469-471)ggT>ggG	p.G157G	MCM8_ENST00000378883.1_Silent_p.G157G|MCM8_ENST00000378886.2_Silent_p.G157G|MCM8_ENST00000265187.4_Silent_p.G157G	NM_001281520.1|NM_032485.4|NM_182802.1	NP_001268449.1|NP_115874.3|NP_877954.1	Q9UJA3	MCM8_HUMAN	minichromosome maintenance complex component 8	157					cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)|G1/S transition of mitotic cell cycle (GO:0000082)|male gamete generation (GO:0048232)|mitotic cell cycle (GO:0000278)	MCM8-MCM9 complex (GO:0097362)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.G157G(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	23						CTTGCATGGGTTTGGCAATAC	0.363																																					p.G157G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T471G	20						.						179.0	168.0	172.0					20																	5935882		2203	4300	6503	5883882	SO:0001819	synonymous_variant	84515	exon5			AJ439063	CCDS13094.1, CCDS13095.1, CCDS63226.1, CCDS63227.1	20p12.3	2007-04-04	2007-04-04	2003-07-09	ENSG00000125885	ENSG00000125885			16147	protein-coding gene	gene with protein product	"""REC homolog (Drosophila)"""	608187	"""chromosome 20 open reading frame 154"""	C20orf154		12527764	Standard	NM_032485		Approved	MGC4816, MGC12866, MGC119522, MGC119523, dJ967N21.5, REC	uc002wmi.3	Q9UJA3	OTTHUMG00000031822	ENST00000378896.3:c.471T>G	20.37:g.5935882T>G		Somatic		Capture	Illumina HiSeq	Phase_I	5883882	NM_032485	B2RBG7|D3DW08|E7EQU7|Q495R4|Q495R6|Q495R7|Q86US4|Q969I5	Silent	SNP	ENST00000378896.3	37	CCDS13094.1																																																																																				0.363	MCM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077900.1	NM_032485	
APCDD1L	164284	broad.mit.edu	37	20	57045788	57045788	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr20:57045788G>A	ENST00000371149.3	-	2	295	c.65C>T	c.(64-66)gCg>gTg	p.A22V	APCDD1L_ENST00000439429.1_Missense_Mutation_p.A33V	NM_153360.1	NP_699191.1	Q8NCL9	APCDL_HUMAN	adenomatosis polyposis coli down-regulated 1-like	22						integral component of membrane (GO:0016021)		p.A22V(1)		large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(1)	18	Lung NSC(12;0.000856)|all_lung(29;0.0025)		BRCA - Breast invasive adenocarcinoma(13;5.6e-11)|Epithelial(14;1.67e-07)|all cancers(14;1.48e-06)			CTCCCCAGCCGCCGGTGCAGT	0.682																																					p.A22V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C65T	20						.						9.0	9.0	9.0					20																	57045788		2088	4069	6157	56479194	SO:0001583	missense	164284	exon2			AK074647	CCDS13467.1	20q13.32	2006-07-07			ENSG00000198768	ENSG00000198768			26892	protein-coding gene	gene with protein product							Standard	NM_153360		Approved	FLJ90166	uc002xze.1	Q8NCL9	OTTHUMG00000032845	ENST00000371149.3:c.65C>T	20.37:g.57045788G>A	ENSP00000360191:p.Ala22Val	Somatic		Capture	Illumina HiSeq	Phase_I	56479194	NM_153360		Missense_Mutation	SNP	ENST00000371149.3	37	CCDS13467.1	.	.	.	.	.	.	.	.	.	.	G	14.54	2.566603	0.45694	.	.	ENSG00000198768	ENST00000371149;ENST00000439429;ENST00000425773	T;T;T	0.34275	2.42;2.47;1.37	4.5	1.45	0.22620	.	1.108010	0.07018	N	0.826328	T	0.25680	0.0625	L	0.36672	1.1	0.09310	N	1	B;B	0.12013	0.005;0.005	B;B	0.06405	0.002;0.002	T	0.33523	-0.9865	10	0.56958	D	0.05	-1.3348	1.2941	0.02066	0.2682:0.1465:0.4354:0.1499	.	33;22	F5H6V6;Q8NCL9	.;APCDL_HUMAN	V	22;33;33	ENSP00000360191:A22V;ENSP00000413261:A33V;ENSP00000396856:A33V	ENSP00000360191:A22V	A	-	2	0	APCDD1L	56479194	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.263000	0.18478	0.123000	0.18342	0.655000	0.94253	GCG		0.682	APCDD1L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000079881.2	NM_153360	
LTN1	26046	broad.mit.edu	37	21	30359137	30359137	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr21:30359137G>A	ENST00000361371.5	-	2	240	c.161C>T	c.(160-162)gCt>gTt	p.A54V	LTN1_ENST00000389195.2_Missense_Mutation_p.A100V|LTN1_ENST00000389194.2_Missense_Mutation_p.A100V			O94822	LTN1_HUMAN	listerin E3 ubiquitin protein ligase 1	54					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.A54V(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						AATTTCTTCAGCTCCTTGAAT	0.413																																					p.A100V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C299T	21						.						88.0	89.0	88.0					21																	30359137		2203	4300	6503	29281008	SO:0001583	missense	26046	exon2			AK001915	CCDS33527.1, CCDS33527.2	21q21.3	2013-01-09	2010-09-17	2010-09-17	ENSG00000198862	ENSG00000198862		"""RING-type (C3HC4) zinc fingers"""	13082	protein-coding gene	gene with protein product	"""listerin"""	613083	"""chromosome 21 open reading frame 98"", ""zinc finger protein 294"", ""ring finger protein 160"""	C21orf98, C21orf10, ZNF294, RNF160		20835226, 19196968	Standard	NM_015565		Approved	KIAA0714, FLJ11053, LISTERIN	uc002ymr.2	O94822	OTTHUMG00000078803	ENST00000361371.5:c.161C>T	21.37:g.30359137G>A	ENSP00000354977:p.Ala54Val	Somatic		Capture	Illumina HiSeq	Phase_I	29281008	NM_015565	A6NL41|A7E2D0|B2RTS0|C9J7U3|J3KPL4|Q05C47|Q9H8M4|Q9NUY5|Q9P0E9	Missense_Mutation	SNP	ENST00000361371.5	37		.	.	.	.	.	.	.	.	.	.	G	16.03	3.008416	0.54361	.	.	ENSG00000198862	ENST00000389194;ENST00000361371;ENST00000446611;ENST00000389195	T;T;T	0.26067	2.11;2.12;1.76	4.83	4.83	0.62350	.	0.062993	0.64402	D	0.000007	T	0.19087	0.0458	N	0.17082	0.46	0.58432	D	0.999999	P	0.48503	0.911	B	0.42282	0.382	T	0.03259	-1.1055	10	0.25751	T	0.34	.	18.1275	0.89590	0.0:0.0:1.0:0.0	.	54	O94822	LTN1_HUMAN	V	100;54;54;100	ENSP00000373846:A100V;ENSP00000354977:A54V;ENSP00000373847:A100V	ENSP00000354977:A54V	A	-	2	0	LTN1	29281008	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.081000	0.64444	2.514000	0.84764	0.561000	0.74099	GCT		0.413	LTN1-008	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000472108.1	NM_015565	
CLDN17	26285	broad.mit.edu	37	21	31538885	31538885	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr21:31538885G>A	ENST00000286808.3	-	1	86	c.51C>T	c.(49-51)ggC>ggT	p.G17G		NM_012131.2	NP_036263.1	P56750	CLD17_HUMAN	claudin 17	17					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)	p.G17G(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(6)|lung(9)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	23						TCCCCACCATGCCAAGGAACC	0.483																																					p.G17G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C51T	21						.						68.0	67.0	68.0					21																	31538885		2203	4300	6503	30460756	SO:0001819	synonymous_variant	26285	exon1			AJ250712	CCDS13586.1	21q22.1	2008-07-31			ENSG00000156282	ENSG00000156282		"""Claudins"""	2038	protein-coding gene	gene with protein product						12736707	Standard	NM_012131		Approved	MGC126552, MGC126554	uc011acv.2	P56750	OTTHUMG00000081873	ENST00000286808.3:c.51C>T	21.37:g.31538885G>A		Somatic		Capture	Illumina HiSeq	Phase_I	30460756	NM_012131	Q3MJB5|Q6UY37	Silent	SNP	ENST00000286808.3	37	CCDS13586.1																																																																																				0.483	CLDN17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000182261.1	NM_012131	
KRTAP19-2	337969	broad.mit.edu	37	21	31859611	31859611	+	Silent	SNP	G	G	A	rs144891171		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr21:31859611G>A	ENST00000334055.3	-	1	144	c.57C>T	c.(55-57)tgC>tgT	p.C19C		NM_181608.1	NP_853639.1	Q3LHN2	KR192_HUMAN	keratin associated protein 19-2	19						intermediate filament (GO:0005882)		p.C19C(1)|p.C19*(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(1)	5						CTTCATAGCCGCAGCCATAGC	0.547													-|||	1	0.000199681	0.0	0.0	5008	,	,		15832	0.0		0.001	False		,,,				2504	0.0				p.C19C												.	.	2	Substitution - Nonsense(1)|Substitution - coding silent(1)	large_intestine(2)	c.C57T	21						.	A		0,4406		0,0,2203	157.0	154.0	155.0		57	4.4	0.0	21	dbSNP_134	155	15,8585		0,15,4285	no	coding-synonymous	KRTAP19-2	NM_181608.1		0,15,6488	AA,AG,GG		0.1744,0.0,0.1153		19/53	31859611	15,12991	2203	4300	6503	30781482	SO:0001819	synonymous_variant	337969	exon1			AP001708	CCDS13595.1	21q22.1	2006-03-13			ENSG00000186965	ENSG00000186965		"""Keratin associated proteins"""	18937	protein-coding gene	gene with protein product						12359730	Standard	NM_181608		Approved	KAP19.2	uc011acy.2	Q3LHN2	OTTHUMG00000057772	ENST00000334055.3:c.57C>T	21.37:g.31859611G>A		Somatic		Capture	Illumina HiSeq	Phase_I	30781482	NM_181608		Silent	SNP	ENST00000334055.3	37	CCDS13595.1																																																																																				0.547	KRTAP19-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128224.3		
TIAM1	7074	broad.mit.edu	37	21	32624154	32624154	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr21:32624154C>T	ENST00000286827.3	-	6	1786	c.1315G>A	c.(1315-1317)Gcc>Acc	p.A439T	TIAM1_ENST00000469412.1_5'UTR|TIAM1_ENST00000541036.1_Missense_Mutation_p.A439T	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	439	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)			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						ACGGCCAGGGCGCCGGCCTTG	0.642																																					p.A439T												.	.	0			c.G1315A	21						.						69.0	71.0	70.0					21																	32624154		2203	4300	6503	31546025	SO:0001583	missense	7074	exon6				CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.1315G>A	21.37:g.32624154C>T	ENSP00000286827:p.Ala439Thr	None		Capture	Illumina HiSeq	Phase_I	31546025	NM_003253	B7ZLR6|F5GZ53|Q17RT7	Missense_Mutation	SNP	ENST00000286827.3	37	CCDS13609.1	.	.	.	.	.	.	.	.	.	.	C	16.44	3.125032	0.56721	.	.	ENSG00000156299	ENST00000286827;ENST00000399841;ENST00000541036	T;T	0.42131	1.0;0.98	4.62	4.62	0.57501	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.207799	0.40908	D	0.000987	T	0.28962	0.0719	N	0.14661	0.345	0.46149	D	0.998896	B;B;B;B	0.24426	0.084;0.049;0.103;0.103	B;B;B;B	0.15052	0.007;0.012;0.012;0.012	T	0.07888	-1.0749	10	0.44086	T	0.13	.	17.6527	0.88169	0.0:1.0:0.0:0.0	.	439;439;280;439	F5GZ53;B7ZLR6;E9PD83;Q13009	.;.;.;TIAM1_HUMAN	T	439;280;439	ENSP00000286827:A439T;ENSP00000441570:A439T	ENSP00000286827:A439T	A	-	1	0	TIAM1	31546025	0.860000	0.29831	0.909000	0.35828	0.918000	0.54935	3.415000	0.52700	2.381000	0.81170	0.655000	0.94253	GCC		0.642	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253	
PDE9A	5152	broad.mit.edu	37	21	44152188	44152188	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr21:44152188G>T	ENST00000291539.6	+	6	511	c.451G>T	c.(451-453)Gaa>Taa	p.E151*	PDE9A_ENST00000328862.6_Nonsense_Mutation_p.E125*|PDE9A_ENST00000398229.3_Intron|PDE9A_ENST00000398224.3_Nonsense_Mutation_p.E24*|PDE9A_ENST00000335440.6_Intron|PDE9A_ENST00000349112.3_Intron|PDE9A_ENST00000335512.4_Nonsense_Mutation_p.E91*|PDE9A_ENST00000398232.3_Nonsense_Mutation_p.E84*|PDE9A_ENST00000398225.3_Nonsense_Mutation_p.E110*|PDE9A_ENST00000380328.2_Intron|PDE9A_ENST00000470987.1_3'UTR|PDE9A_ENST00000398234.3_Nonsense_Mutation_p.E50*|PDE9A_ENST00000398236.3_Nonsense_Mutation_p.E65*|AP001627.1_ENST00000437426.1_RNA|PDE9A_ENST00000398227.3_Intron|PDE9A_ENST00000539837.1_Intron	NM_002606.2	NP_002597.1	O76083	PDE9A_HUMAN	phosphodiesterase 9A	151					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.E151*(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)	AGAGAGAGAAGAATTAATCCA	0.488																																					p.E65X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G193T	21						.						94.0	87.0	89.0					21																	44152188		2203	4300	6503	43025257	SO:0001587	stop_gained	5152	exon4			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.451G>T	21.37:g.44152188G>T	ENSP00000291539:p.Glu151*	Somatic		Capture	Illumina HiSeq	Phase_I	43025257	NM_001001574	B2RBI5|B4DFI5|D3DSJ8|D3DSJ9|O75490|O75491|O95225|Q53Y40|Q5QD39|Q86SF7|Q86SI6|Q86SJ3|Q86WN3|Q86WN4|Q86WN5|Q86WN6|Q86WN7|Q86WN8|Q86WN9|Q86WP0	Nonsense_Mutation	SNP	ENST00000291539.6	37	CCDS13690.1	.	.	.	.	.	.	.	.	.	.	G	35	5.530058	0.96446	.	.	ENSG00000160191	ENST00000335512;ENST00000291539;ENST00000398232;ENST00000398234;ENST00000398236;ENST00000328862;ENST00000398225;ENST00000398224	.	.	.	5.15	5.15	0.70609	.	7739.210000	0.00166	N	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	.	16.4177	0.83748	0.0:0.0:1.0:0.0	.	.	.	.	X	91;151;84;50;65;125;110;24	.	ENSP00000291539:E151X	E	+	1	0	PDE9A	43025257	1.000000	0.71417	0.991000	0.47740	0.425000	0.31504	4.809000	0.62591	2.385000	0.81259	0.650000	0.86243	GAA		0.488	PDE9A-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195466.1		
TRPM2	7226	broad.mit.edu	37	21	45786703	45786703	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr21:45786703C>T	ENST00000397928.1	+	4	935	c.490C>T	c.(490-492)Ctg>Ttg	p.L164L	TRPM2_ENST00000300481.9_Silent_p.L164L|TRPM2_ENST00000300482.5_Silent_p.L164L|TRPM2_ENST00000397932.2_Silent_p.L164L	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	164					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)	p.L164L(1)		breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						GCACTGGGGGCTGGACGTCCC	0.607																																					p.L164L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C490T	21						.						64.0	59.0	61.0					21																	45786703		2203	4300	6503	44611131	SO:0001819	synonymous_variant	7226	exon4			AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Nudix motif containing"""	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.490C>T	21.37:g.45786703C>T		Somatic		Capture	Illumina HiSeq	Phase_I	44611131	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Silent	SNP	ENST00000397928.1	37	CCDS13710.1																																																																																				0.607	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307	
COL18A1	80781	broad.mit.edu	37	21	46888602	46888602	+	Silent	SNP	A	A	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr21:46888602A>C	ENST00000359759.4	+	2	1819	c.1798A>C	c.(1798-1800)Aga>Cga	p.R600R	COL18A1_ENST00000400337.2_Silent_p.R185R|COL18A1_ENST00000355480.5_Silent_p.R365R			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	600	Laminin G-like.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)	p.R365R(1)		breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		GGAGTTCCAGAGAATGCCGCT	0.662																																					p.R365R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1093C	21						.						45.0	49.0	48.0					21																	46888602		2028	4170	6198	45713030	SO:0001819	synonymous_variant	80781	exon2				CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.1798A>C	21.37:g.46888602A>C		Somatic		Capture	Illumina HiSeq	Phase_I	45713030	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	37																																																																																					0.662	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
FTCD	10841	broad.mit.edu	37	21	47571510	47571510	+	Missense_Mutation	SNP	C	C	T	rs148763241		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr21:47571510C>T	ENST00000291670.5	-	5	641	c.598G>A	c.(598-600)Gcg>Acg	p.A200T	FTCD_ENST00000355384.2_Missense_Mutation_p.A200T|FTCD_ENST00000397746.3_Missense_Mutation_p.A200T|FTCD-AS1_ENST00000446649.1_RNA|FTCD_ENST00000397743.1_Missense_Mutation_p.A200T|FTCD_ENST00000359679.2_Missense_Mutation_p.A200T|FTCD_ENST00000397748.1_Missense_Mutation_p.A200T|FTCD_ENST00000498355.2_5'UTR	NM_006657.2	NP_006648.1	O95954	FTCD_HUMAN	formimidoyltransferase cyclodeaminase	200	Formiminotransferase C-subdomain. {ECO:0000250}.				cellular nitrogen compound metabolic process (GO:0034641)|cytoskeleton organization (GO:0007010)|folic acid-containing compound metabolic process (GO:0006760)|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)|tetrahydrofolate interconversion (GO:0035999)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	folic acid binding (GO:0005542)|formimidoyltetrahydrofolate cyclodeaminase activity (GO:0030412)|glutamate formimidoyltransferase activity (GO:0030409)	p.A200T(1)		endometrium(1)|large_intestine(2)|lung(9)|pancreas(1)|prostate(3)|skin(3)	19	Breast(49;0.214)			Colorectal(79;0.235)	Tetrahydrofolic acid(DB00116)	AGGTTGAGCGCGATGCGGTGG	0.647																																					p.A200T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G598A	21						.	C	THR/ALA,THR/ALA	0,4406		0,0,2203	64.0	68.0	67.0		598,598	4.2	1.0	21	dbSNP_134	67	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	FTCD	NM_006657.2,NM_206965.1	58,58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	200/542,200/542	47571510	1,13005	2203	4300	6503	46395938	SO:0001583	missense	10841	exon5			U91541	CCDS13731.1	21q22.3	2013-06-10	2013-06-10		ENSG00000160282	ENSG00000160282	2.1.2.5, 4.3.1.4		3974	protein-coding gene	gene with protein product		606806	"""formiminotransferase cyclodeaminase"""			10029623, 10773664	Standard	NM_006657		Approved		uc002zif.3	O95954	OTTHUMG00000090488	ENST00000291670.5:c.598G>A	21.37:g.47571510C>T	ENSP00000291670:p.Ala200Thr	Somatic		Capture	Illumina HiSeq	Phase_I	46395938	NM_006657	B9EGD0|Q86V03|Q9HCT4|Q9HCT5|Q9HCT6|Q9UHJ2	Missense_Mutation	SNP	ENST00000291670.5	37	CCDS13731.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.763582	0.89932	0.0	1.16E-4	ENSG00000160282	ENST00000291670;ENST00000397748;ENST00000359679;ENST00000355384;ENST00000397746;ENST00000397743	D;D;D;D;D;D	0.85702	-2.02;-2.02;-2.02;-2.02;-2.02;-2.02	4.23	4.23	0.50019	Formiminotransferas, N- and C-terminal subdomains (1);Formiminotransferase, C-terminal subdomain (2);Formiminotransferase catalytic domain (1);	0.061950	0.64402	U	0.000005	D	0.94634	0.8270	H	0.95679	3.705	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.994;0.999	D	0.96554	0.9410	10	0.87932	D	0	.	16.6242	0.84937	0.0:1.0:0.0:0.0	.	200;200;200	B7WPK3;O95954-2;O95954	.;.;FTCD_HUMAN	T	200	ENSP00000291670:A200T;ENSP00000380856:A200T;ENSP00000352707:A200T;ENSP00000347545:A200T;ENSP00000380854:A200T;ENSP00000380851:A200T	ENSP00000291670:A200T	A	-	1	0	FTCD	46395938	1.000000	0.71417	0.987000	0.45799	0.456000	0.32438	7.593000	0.82686	1.875000	0.54330	0.467000	0.42956	GCG		0.647	FTCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206962.1	NM_006657	
TPTE	7179	broad.mit.edu	37	21	10951380	10951380	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr21:10951380G>A	ENST00000361285.4	-	10	661	c.332C>T	c.(331-333)gCc>gTc	p.A111V	TPTE_ENST00000342420.5_Missense_Mutation_p.A73V|TPTE_ENST00000298232.7_Missense_Mutation_p.A93V|TPTE_ENST00000415664.2_5'UTR	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	111					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.A93V(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		AATTAGGTCGGCAAGGATGAG	0.328																																					p.A93V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C278T	21						.						132.0	138.0	136.0					21																	10951380		2203	4300	6503	9973251	SO:0001583	missense	7179	exon9			AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	12023	protein-coding gene	gene with protein product	"""PTEN-related tyrosine phosphatase"", ""cancer/testis antigen 44"""	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.332C>T	21.37:g.10951380G>A	ENSP00000355208:p.Ala111Val	Somatic		Capture	Illumina HiSeq	Phase_I	9973251	NM_199259	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Missense_Mutation	SNP	ENST00000361285.4	37	CCDS13560.2	.	.	.	.	.	.	.	.	.	.	.	0.009	-1.816203	0.00595	.	.	ENSG00000166157	ENST00000298232;ENST00000361285;ENST00000342420;ENST00000328758	D;D;D	0.97232	-4.3;-4.3;-4.3	1.8	-1.73	0.08081	.	0.490245	0.19981	N	0.101761	D	0.87720	0.6248	N	0.16903	0.455	0.09310	N	1	B;B;B	0.19445	0.035;0.035;0.036	B;B;B	0.18561	0.022;0.022;0.01	T	0.78750	-0.2082	10	0.02654	T	1	-2.0E-4	1.9594	0.03383	0.3981:0.0:0.3394:0.2625	.	73;93;111	P56180-3;P56180-2;P56180	.;.;TPTE_HUMAN	V	93;111;73;93	ENSP00000298232:A93V;ENSP00000355208:A111V;ENSP00000344441:A73V	ENSP00000298232:A93V	A	-	2	0	TPTE	9973251	0.000000	0.05858	0.000000	0.03702	0.037000	0.13140	0.443000	0.21644	-0.509000	0.06532	0.194000	0.17425	GCC		0.328	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1		
NCAM2	4685	broad.mit.edu	37	21	22782728	22782728	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr21:22782728delA	ENST00000400546.1	+	10	1579	c.1330delA	c.(1330-1332)aaafs	p.K444fs	NCAM2_ENST00000284894.7_Frame_Shift_Del_p.K302fs	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	444	Ig-like C2-type 5.				axonal fasciculation (GO:0007413)|neuron cell-cell adhesion (GO:0007158)|sensory perception of smell (GO:0007608)	axon (GO:0030424)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.N445fs*5(1)		breast(4)|cervix(2)|endometrium(8)|kidney(6)|large_intestine(22)|liver(4)|lung(49)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	108		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		CTTACCTGCTAAAAACACGAC	0.318																																					p.K444fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1330delA	21						.						78.0	78.0	78.0					21																	22782728		1835	4076	5911	21704599	SO:0001589	frameshift_variant	4685	exon10				CCDS42910.1	21q21	2013-02-11			ENSG00000154654	ENSG00000154654		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7657	protein-coding gene	gene with protein product		602040				9226371	Standard	NM_004540		Approved	NCAM21, MGC51008	uc002yld.2	O15394	OTTHUMG00000078121	ENST00000400546.1:c.1330delA	21.37:g.22782728delA	ENSP00000383392:p.Lys444fs	Somatic		Capture	Illumina HiSeq	Phase_I	21704599	NM_004540	A8MQ06|B7Z841|Q7Z7F2	Frame_Shift_Del	DEL	ENST00000400546.1	37	CCDS42910.1																																																																																				0.318	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540	
DIP2A	23181	broad.mit.edu	37	21	47974139	47974139	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr21:47974139G>A	ENST00000417564.2	+	26	3109	c.3088G>A	c.(3088-3090)Gcc>Acc	p.A1030T	DIP2A_ENST00000318711.7_Missense_Mutation_p.A1031T|DIP2A_ENST00000427143.2_Missense_Mutation_p.A966T|DIP2A_ENST00000400274.1_Missense_Mutation_p.A1026T			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	1030					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.A1030T(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)		TGAGAGAGTGGCCGCGGCTCT	0.592																																					p.A966T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2896A	21						.						88.0	102.0	97.0					21																	47974139		2144	4248	6392	46798567	SO:0001583	missense	23181	exon24			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.3088G>A	21.37:g.47974139G>A	ENSP00000392066:p.Ala1030Thr	Somatic		Capture	Illumina HiSeq	Phase_I	46798567	NM_001146114	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Missense_Mutation	SNP	ENST00000417564.2	37	CCDS46655.1	.	.	.	.	.	.	.	.	.	.	G	34	5.318133	0.95682	.	.	ENSG00000160305	ENST00000400274;ENST00000427143;ENST00000318711;ENST00000417564	T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29	5.76	5.76	0.90799	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	T	0.72827	0.3509	M	0.62154	1.92	0.80722	D	1	P;P;P	0.51537	0.678;0.946;0.698	B;P;P	0.48524	0.361;0.549;0.58	T	0.75889	-0.3158	10	0.72032	D	0.01	-21.1018	18.9518	0.92643	0.0:0.0:1.0:0.0	.	1031;966;1030	E9PER1;E7EMA5;Q14689	.;.;DIP2A_HUMAN	T	1026;966;1031;1030	ENSP00000383133:A1026T;ENSP00000400528:A966T;ENSP00000323633:A1031T;ENSP00000392066:A1030T	ENSP00000323633:A1031T	A	+	1	0	DIP2A	46798567	1.000000	0.71417	0.856000	0.33681	0.821000	0.46438	7.795000	0.85887	2.718000	0.92993	0.650000	0.86243	GCC		0.592	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151	
TXNRD2	10587	broad.mit.edu	37	22	19902744	19902744	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr22:19902744G>T	ENST00000400521.1	-	7	590	c.584C>A	c.(583-585)cCc>cAc	p.P195H	TXNRD2_ENST00000400518.1_Missense_Mutation_p.P165H|TXNRD2_ENST00000334363.9_Missense_Mutation_p.P195H|TXNRD2_ENST00000535882.1_Missense_Mutation_p.P194H|TXNRD2_ENST00000542719.1_Missense_Mutation_p.P165H|TXNRD2_ENST00000491939.1_5'UTR|TXNRD2_ENST00000400519.1_Missense_Mutation_p.P194H	NM_006440.3	NP_006431.2	Q9NNW7	TRXR2_HUMAN	thioredoxin reductase 2	195					cell redox homeostasis (GO:0045454)|heart development (GO:0007507)|hemopoiesis (GO:0030097)|response to oxygen radical (GO:0000305)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|NADP binding (GO:0050661)|thioredoxin-disulfide reductase activity (GO:0004791)	p.P195H(1)		breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|urinary_tract(2)	30	Colorectal(54;0.0993)					CACGTGCGTGGGGTATCTCGG	0.572																																					p.P195H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C584A	22						.						52.0	62.0	58.0					22																	19902744		2056	4189	6245	18282744	SO:0001583	missense	10587	exon7			AF106697	CCDS42981.1, CCDS63402.1	22q11.21	2014-09-17			ENSG00000184470	ENSG00000184470			18155	protein-coding gene	gene with protein product	"""thioredoxin reductase beta"", ""selenoprotein Z"""	606448				9923614, 10215850, 11012661	Standard	NM_006440		Approved	TR, TRXR2, TR3	uc021wlj.1	Q9NNW7	OTTHUMG00000149975	ENST00000400521.1:c.584C>A	22.37:g.19902744G>T	ENSP00000383365:p.Pro195His	Somatic		Capture	Illumina HiSeq	Phase_I	18282744	NM_006440	O95840|Q96IJ2|Q9H2Z5|Q9NZV3|Q9NZV4|Q9P2Y0|Q9P2Y1|Q9UQU8	Missense_Mutation	SNP	ENST00000400521.1	37	CCDS42981.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.257094	0.80246	.	.	ENSG00000184470	ENST00000400518;ENST00000538798;ENST00000400521;ENST00000400525;ENST00000540474;ENST00000400519;ENST00000535882;ENST00000542719;ENST00000334363	T;T;T;T;T;T;T	0.54071	0.59;0.59;0.59;0.59;0.59;0.59;0.59	4.58	4.58	0.56647	Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain (1);	0.063969	0.64402	D	0.000005	T	0.80059	0.4554	M	0.93550	3.43	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	0.85919	0.1445	10	0.87932	D	0	-2.4482	17.9344	0.89008	0.0:0.0:1.0:0.0	.	195;195;163;194	Q9NNW7;E7EWK1;Q6M1B7;D3YTF9	TRXR2_HUMAN;.;.;.	H	165;195;195;172;99;194;194;165;195	ENSP00000383362:P165H;ENSP00000383365:P195H;ENSP00000383369:P172H;ENSP00000383363:P194H;ENSP00000439314:P194H;ENSP00000439570:P165H;ENSP00000334451:P195H	ENSP00000334451:P195H	P	-	2	0	TXNRD2	18282744	1.000000	0.71417	0.967000	0.41034	0.660000	0.38997	8.199000	0.89731	2.547000	0.85894	0.505000	0.49811	CCC		0.572	TXNRD2-003	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000314903.3	NM_006440	
PI4KA	5297	broad.mit.edu	37	22	21147503	21147503	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr22:21147503A>G	ENST00000572273.1	-	19	2362	c.2132T>C	c.(2131-2133)gTa>gCa	p.V711A	PI4KA_ENST00000466162.1_5'UTR|PI4KA_ENST00000255882.6_Missense_Mutation_p.V769A			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	711					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)	p.V711A(2)		breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			AGGAATGAGTACTCCCAAGTT	0.353																																					p.V711A	GBM(136;1332 1831 3115 23601 50806)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T2132C	22						.						126.0	116.0	119.0					22																	21147503		2203	4300	6503	19477503	SO:0001583	missense	5297	exon19			L36151	CCDS33603.1, CCDS33603.2	22q11.21	2011-05-25	2007-08-14	2007-08-02	ENSG00000241973	ENSG00000241973			8983	protein-coding gene	gene with protein product		600286		PIK4CA		7961848, 8662589	Standard	NM_002650		Approved	PI4K-ALPHA, pi4K230	uc002zsz.5	P42356	OTTHUMG00000167440	ENST00000572273.1:c.2132T>C	22.37:g.21147503A>G	ENSP00000458238:p.Val711Ala	Somatic		Capture	Illumina HiSeq	Phase_I	19477503	NM_058004	Q7Z625|Q9UPG2	Missense_Mutation	SNP	ENST00000572273.1	37		.	.	.	.	.	.	.	.	.	.	A	27.6	4.841701	0.91197	.	.	ENSG00000241973	ENST00000255882	.	.	.	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	T	0.73337	0.3574	M	0.67397	2.05	0.80722	D	1	D	0.65815	0.995	P	0.58013	0.831	T	0.76244	-0.3030	9	0.56958	D	0.05	-23.2532	15.0241	0.71653	1.0:0.0:0.0:0.0	.	711	P42356	PI4KA_HUMAN	A	711	.	ENSP00000255882:V711A	V	-	2	0	PI4KA	19477503	1.000000	0.71417	0.752000	0.31206	0.987000	0.75469	8.976000	0.93442	2.143000	0.66587	0.533000	0.62120	GTA		0.353	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004	
ZNF280B	140883	broad.mit.edu	37	22	22842926	22842926	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr22:22842926A>C	ENST00000406426.1	-	4	1540	c.798T>G	c.(796-798)agT>agG	p.S266R	ZNF280B_ENST00000360412.2_Missense_Mutation_p.S266R			Q86YH2	Z280B_HUMAN	zinc finger protein 280B	266					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.S266R(1)		autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(2)	22	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		GACTTGTTAGACTCAAAATGT	0.378																																					p.S266R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T798G	22						.						116.0	108.0	111.0					22																	22842926		2203	4300	6503	21172926	SO:0001583	missense	140883	exon4			AK097608	CCDS13799.1	22q11.2	2007-09-20	2007-09-20	2007-09-20	ENSG00000198477	ENSG00000275004			23022	protein-coding gene	gene with protein product			"""zinc finger protein 279"", ""suppressor of hairy wing homolog 2 (Drosophila)"""	ZNF279, SUHW2		9074928	Standard	NM_080764		Approved	5'OY11.1, ZNF632	uc002zwc.1	Q86YH2	OTTHUMG00000151066	ENST00000406426.1:c.798T>G	22.37:g.22842926A>C	ENSP00000385998:p.Ser266Arg	Somatic		Capture	Illumina HiSeq	Phase_I	21172926	NM_080764		Missense_Mutation	SNP	ENST00000406426.1	37	CCDS13799.1	.	.	.	.	.	.	.	.	.	.	A	2.801	-0.249078	0.05867	.	.	ENSG00000198477	ENST00000406426;ENST00000360412	T;T	0.03358	3.96;3.96	4.28	-0.389	0.12455	.	.	.	.	.	T	0.04952	0.0133	M	0.67953	2.075	0.09310	N	1	B	0.19331	0.035	B	0.22753	0.041	T	0.39143	-0.9628	9	0.72032	D	0.01	-1.0815	3.2073	0.06670	0.5181:0.0:0.3052:0.1768	.	266	Q86YH2	Z280B_HUMAN	R	266	ENSP00000385998:S266R;ENSP00000353586:S266R	ENSP00000353586:S266R	S	-	3	2	ZNF280B	21172926	0.000000	0.05858	0.000000	0.03702	0.137000	0.21094	-0.245000	0.08890	-0.247000	0.09597	0.533000	0.62120	AGT		0.378	ZNF280B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321170.2	NM_080764	
GNAZ	2781	broad.mit.edu	37	22	23465358	23465358	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr22:23465358A>G	ENST00000248996.4	+	3	1474	c.808A>G	c.(808-810)Aac>Gac	p.N270D	RTDR1_ENST00000216036.4_Intron	NM_002073.2	NP_002064.1	P19086	GNAZ_HUMAN	guanine nucleotide binding protein (G protein), alpha z polypeptide	270					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|receptor signaling protein activity (GO:0005057)|signal transducer activity (GO:0004871)	p.N270D(1)		endometrium(3)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(5)|urinary_tract(1)	19	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.166)		CCTCTTCCTGAACAAGAAGGA	0.547																																					p.N270D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A808G	22						.						92.0	87.0	89.0					22																	23465358		2203	4300	6503	21795358	SO:0001583	missense	2781	exon3				CCDS13804.1	22q11.1-q11.2	2008-06-10			ENSG00000128266	ENSG00000128266			4395	protein-coding gene	gene with protein product		139160				2115889	Standard	NM_002073		Approved		uc002zwu.1	P19086	OTTHUMG00000150611	ENST00000248996.4:c.808A>G	22.37:g.23465358A>G	ENSP00000248996:p.Asn270Asp	Somatic		Capture	Illumina HiSeq	Phase_I	21795358	NM_002073	B2R6C1|Q4QRJ6	Missense_Mutation	SNP	ENST00000248996.4	37	CCDS13804.1	.	.	.	.	.	.	.	.	.	.	A	31	5.069330	0.93950	.	.	ENSG00000128266	ENST00000248996;ENST00000456059	D	0.93906	-3.31	5.14	5.14	0.70334	.	0.216956	0.46758	D	0.000279	D	0.98077	0.9366	H	0.98487	4.245	0.80722	D	1	D	0.53885	0.963	D	0.75484	0.986	D	0.99395	1.0926	10	0.87932	D	0	.	14.4404	0.67311	1.0:0.0:0.0:0.0	.	270	P19086	GNAZ_HUMAN	D	270;218	ENSP00000248996:N270D	ENSP00000248996:N270D	N	+	1	0	GNAZ	21795358	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.082000	0.94059	2.085000	0.62840	0.533000	0.62120	AAC		0.547	GNAZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319073.1	NM_002073	
ZNF70	7621	broad.mit.edu	37	22	24086368	24086368	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr22:24086368G>A	ENST00000341976.3	-	2	1420	c.960C>T	c.(958-960)agC>agT	p.S320S		NM_021916.2	NP_068735.1	Q9UC06	ZNF70_HUMAN	zinc finger protein 70	320					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.S320S(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|urinary_tract(1)	21						TGAGGTTGGAGCTCTGGCTGA	0.552																																					p.S320S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C960T	22						.						133.0	116.0	122.0					22																	24086368		2203	4300	6503	22416368	SO:0001819	synonymous_variant	7621	exon2			X60077	CCDS13812.1	22q11.23	2013-01-08	2006-05-12		ENSG00000187792	ENSG00000187792		"""Zinc fingers, C2H2-type"""	13140	protein-coding gene	gene with protein product		194544	"""zinc finger protein 70 (Cos17)"""			1639391	Standard	NM_021916		Approved	Cos17, MGC48959	uc002zxs.3	Q9UC06	OTTHUMG00000150739	ENST00000341976.3:c.960C>T	22.37:g.24086368G>A		Somatic		Capture	Illumina HiSeq	Phase_I	22416368	NM_021916		Silent	SNP	ENST00000341976.3	37	CCDS13812.1																																																																																				0.552	ZNF70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319881.1	NM_021916	
SUSD2	56241	broad.mit.edu	37	22	24584248	24584248	+	Silent	SNP	G	G	A	rs536911780		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr22:24584248G>A	ENST00000358321.3	+	14	2658	c.2397G>A	c.(2395-2397)gcG>gcA	p.A799A		NM_019601.3	NP_062547.1	Q9UGT4	SUSD2_HUMAN	sushi domain containing 2	799					immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)	p.A799A(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	26						CGGTGGTGGCGGCGGTTGCGC	0.682																																					p.A799A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2397A	22						.						57.0	59.0	58.0					22																	24584248		2203	4299	6502	22914248	SO:0001819	synonymous_variant	56241	exon14			AK026431	CCDS13824.1	22q11-q12	2005-08-16			ENSG00000099994	ENSG00000099994			30667	protein-coding gene	gene with protein product		615825				12477932	Standard	NM_019601		Approved	BK65A6.2, FLJ22778	uc002zzn.1	Q9UGT4	OTTHUMG00000150792	ENST00000358321.3:c.2397G>A	22.37:g.24584248G>A		Somatic		Capture	Illumina HiSeq	Phase_I	22914248	NM_019601	Q9H5Y6	Silent	SNP	ENST00000358321.3	37	CCDS13824.1																																																																																				0.682	SUSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320088.1	NM_019601	
SPECC1L	23384	broad.mit.edu	37	22	24807589	24807589	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr22:24807589A>G	ENST00000314328.9	+	15	3406	c.3121A>G	c.(3121-3123)Aat>Gat	p.N1041D	SPECC1L_ENST00000437398.1_Missense_Mutation_p.N1041D|SPECC1L-ADORA2A_ENST00000358654.2_3'UTR|SPECC1L_ENST00000541492.1_Intron	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	1041	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.			N -> K (in Ref. 4; BAA21574). {ECO:0000305}.	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.N1041D(1)		breast(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(6)|ovary(1)|prostate(1)|skin(3)|stomach(2)|urinary_tract(1)	27						CAGCAGCTGGAATGATGGGCT	0.493																																					p.N1041D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3121G	22						.						132.0	119.0	123.0					22																	24807589		2203	4300	6503	23137589	SO:0001583	missense	23384	exon14			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.3121A>G	22.37:g.24807589A>G	ENSP00000325785:p.Asn1041Asp	Somatic		Capture	Illumina HiSeq	Phase_I	23137589	NM_001145468	B7Z758|F5H1H6|O15081	Missense_Mutation	SNP	ENST00000314328.9	37	CCDS33619.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.477335	0.84640	.	.	ENSG00000100014	ENST00000437398;ENST00000314328	D;D	0.94931	-3.56;-3.56	5.65	5.65	0.86999	Calponin homology domain (5);	0.000000	0.85682	D	0.000000	D	0.97445	0.9164	M	0.87381	2.88	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.98085	1.0406	10	0.66056	D	0.02	-37.4973	15.0577	0.71927	1.0:0.0:0.0:0.0	.	1041	Q69YQ0	CYTSA_HUMAN	D	1041	ENSP00000393363:N1041D;ENSP00000325785:N1041D	ENSP00000325785:N1041D	N	+	1	0	SPECC1L	23137589	1.000000	0.71417	1.000000	0.80357	0.725000	0.41563	8.625000	0.90965	2.154000	0.67381	0.459000	0.35465	AAT		0.493	SPECC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319986.2	NM_015330	
ADORA2A	135	broad.mit.edu	37	22	24836791	24836791	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr22:24836791G>A	ENST00000337539.7	+	3	1032	c.573G>A	c.(571-573)ctG>ctA	p.L191L	ADORA2A-AS1_ENST00000427813.2_RNA|SPECC1L-ADORA2A_ENST00000358654.2_3'UTR|ADORA2A-AS1_ENST00000543438.1_RNA|ADORA2A-AS1_ENST00000326341.4_RNA|ADORA2A_ENST00000496497.1_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	191					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.L191L(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)	TGCCCCTGCTGCTCATGCTGG	0.612																																					p.L191L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G573A	22						.						189.0	177.0	181.0					22																	24836791		2203	4300	6503	23166791	SO:0001819	synonymous_variant	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.573G>A	22.37:g.24836791G>A		Somatic		Capture	Illumina HiSeq	Phase_I	23166791	NM_000675	B2R7E0	Silent	SNP	ENST00000337539.7	37	CCDS13826.1																																																																																				0.612	ADORA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319971.2	NM_000675	
MYO18B	84700	broad.mit.edu	37	22	26173670	26173670	+	Missense_Mutation	SNP	G	G	A	rs547076224		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr22:26173670G>A	ENST00000407587.2	+	8	2159	c.1990G>A	c.(1990-1992)Gct>Act	p.A664T	MYO18B_ENST00000335473.7_Missense_Mutation_p.A664T|MYO18B_ENST00000536101.1_Missense_Mutation_p.A664T			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	664	Myosin motor.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.A664T(1)		NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						CTGGAGTGGCGCTGGGAAGAC	0.632													G|||	1	0.000199681	0.0	0.0	5008	,	,		19129	0.0		0.0	False		,,,				2504	0.001				p.A664T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1990A	22						.						79.0	88.0	85.0					22																	26173670		2101	4215	6316	24503670	SO:0001583	missense	84700	exon8			AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.1990G>A	22.37:g.26173670G>A	ENSP00000386096:p.Ala664Thr	Somatic		Capture	Illumina HiSeq	Phase_I	24503670	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		.	.	.	.	.	.	.	.	.	.	G	10.83	1.461995	0.26248	.	.	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.81659	-1.52;-1.52;-1.52	5.38	1.76	0.24704	Myosin head, motor domain (3);	0.122006	0.56097	D	0.000033	T	0.79094	0.4388	M	0.83312	2.635	0.09310	N	0.999999	B;P;P;P	0.48589	0.367;0.564;0.912;0.508	B;B;B;B	0.38921	0.066;0.184;0.285;0.116	T	0.74535	-0.3633	10	0.51188	T	0.08	.	13.4392	0.61104	0.0:0.0:0.5229:0.4771	.	177;664;664;664	Q8IUG5-2;Q8IUG5;F5GXR6;F5GYU7	.;MY18B_HUMAN;.;.	T	664	ENSP00000441229:A664T;ENSP00000334563:A664T;ENSP00000386096:A664T	ENSP00000334563:A664T	A	+	1	0	MYO18B	24503670	0.026000	0.19158	0.376000	0.26042	0.026000	0.11368	0.781000	0.26774	1.227000	0.43598	0.655000	0.94253	GCT		0.632	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
SF3A1	10291	broad.mit.edu	37	22	30742466	30742466	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr22:30742466G>A	ENST00000215793.8	-	3	382	c.228C>T	c.(226-228)atC>atT	p.I76I	SF3A1_ENST00000439242.1_Silent_p.I76I	NM_005877.4	NP_005868.1	Q15459	SF3A1_HUMAN	splicing factor 3a, subunit 1, 120kDa	76					gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U2-type spliceosomal complex (GO:0005684)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.I76I(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|urinary_tract(1)	29						TGGGGTTGTTGATCTCGTTCT	0.493																																					p.I76I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C228T	22						.						202.0	196.0	198.0					22																	30742466		2203	4300	6503	29072466	SO:0001819	synonymous_variant	10291	exon3			X85237	CCDS13875.1	22q12.2	2014-09-17	2002-08-29		ENSG00000099995	ENSG00000099995			10765	protein-coding gene	gene with protein product		605595	"""splicing factor 3a, subunit 1, 120kD"""			7489498	Standard	NM_005877		Approved	SF3a120, SAP114, PRPF21, Prp21	uc003ahl.3	Q15459	OTTHUMG00000151005	ENST00000215793.8:c.228C>T	22.37:g.30742466G>A		Somatic		Capture	Illumina HiSeq	Phase_I	29072466	NM_001005409	E9PAW1	Silent	SNP	ENST00000215793.8	37	CCDS13875.1																																																																																				0.493	SF3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320916.2	NM_005877	
SFI1	9814	broad.mit.edu	37	22	32000320	32000320	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr22:32000320G>A	ENST00000400288.2	+	19	2012	c.1907G>A	c.(1906-1908)cGg>cAg	p.R636Q	SFI1_ENST00000443011.1_Missense_Mutation_p.R483Q|SFI1_ENST00000540643.1_Missense_Mutation_p.R581Q|SFI1_ENST00000443326.1_Missense_Mutation_p.R554Q|SFI1_ENST00000432498.1_Missense_Mutation_p.R605Q|SFI1_ENST00000400289.1_Missense_Mutation_p.R554Q|SFI1_ENST00000414585.1_Missense_Mutation_p.R483Q	NM_001007467.2	NP_001007468.1	A8K8P3	SFI1_HUMAN	Sfi1 homolog, spindle assembly associated (yeast)	636					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)	p.R636Q(1)		NS(2)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)	38						GGAGCGGAGCGGCAGAAGCTG	0.632											OREG0003526	type=REGULATORY REGION|Gene=SFI1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.R605Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1814A	22						.						11.0	14.0	13.0					22																	32000320		2058	4194	6252	30330320	SO:0001583	missense	9814	exon18			AB011114	CCDS43004.1, CCDS43005.1, CCDS58803.1, CCDS58804.1	22q12.2	2014-06-13			ENSG00000198089	ENSG00000198089			29064	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 139"""	612765				14504268	Standard	NM_001007467		Approved	KIAA0542, PISD, PPP1R139	uc003ale.4	A8K8P3	OTTHUMG00000030249	ENST00000400288.2:c.1907G>A	22.37:g.32000320G>A	ENSP00000383145:p.Arg636Gln	Somatic	829	Capture	Illumina HiSeq	Phase_I	30330320	NM_014775	A1L373|A1L387|A2A2L2|B1AKL9|B5MDB7|B7Z1V6|B7Z8G3|B7ZBE2|B7ZBE3|O60289|Q2TAN8|Q5W1B5|Q86TK0|Q8N4U8|Q8N8C1|Q8WU14	Missense_Mutation	SNP	ENST00000400288.2	37	CCDS43004.1	.	.	.	.	.	.	.	.	.	.	G	11.21	1.571632	0.28003	.	.	ENSG00000198089	ENST00000432498;ENST00000540643;ENST00000443326;ENST00000421060;ENST00000414585;ENST00000443011;ENST00000400289;ENST00000400288	T;T;T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5;1.5;1.5	5.4	-2.29	0.06805	.	0.741063	0.13048	N	0.417902	T	0.12732	0.0309	N	0.08118	0	0.09310	N	1	B;B;B;B;B;P	0.50710	0.221;0.236;0.41;0.403;0.115;0.938	B;B;B;B;B;B	0.40602	0.024;0.032;0.053;0.049;0.016;0.334	T	0.31916	-0.9926	10	0.22706	T	0.39	.	9.637	0.39814	0.6506:0.0:0.3494:0.0	.	581;554;554;605;636;612	A8K8P3-9;A8K8P3-10;A8K8P3-3;A8K8P3-2;A8K8P3;A8K8P3-5	.;.;.;.;SFI1_HUMAN;.	Q	605;581;554;612;483;483;554;636	ENSP00000402679:R605Q;ENSP00000443025:R581Q;ENSP00000416469:R554Q;ENSP00000397148:R483Q;ENSP00000401199:R483Q;ENSP00000383146:R554Q;ENSP00000383145:R636Q	ENSP00000383145:R636Q	R	+	2	0	SFI1	30330320	0.123000	0.22298	0.001000	0.08648	0.011000	0.07611	0.275000	0.18698	-0.693000	0.05121	-0.251000	0.11542	CGG		0.632	SFI1-023	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337180.3	NM_014775	
KDELR3	11015	broad.mit.edu	37	22	38882283	38882283	+	IGR	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr22:38882283C>T	ENST00000216014.4	+	0	1728				DDX17_ENST00000444597.1_Missense_Mutation_p.G68D|DDX17_ENST00000381633.3_Missense_Mutation_p.G539D|DDX17_ENST00000396821.3_Missense_Mutation_p.G618D	NM_006855.2	NP_006846.1	O43731	ERD23_HUMAN	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 3						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)|protein retention in ER lumen (GO:0006621)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ER retention sequence binding (GO:0046923)	p.G616D(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)	13	Melanoma(58;0.0286)					ATAGCCACTGCCATTAGCATA	0.532																																					p.G618D	Ovarian(11;103 529 24120 28493 32980)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1853A	22						.						81.0	71.0	74.0					22																	38882283		2203	4300	6503	37212229	SO:0001628	intergenic_variant	10521	exon13			AL035081	CCDS13972.1, CCDS46705.1	22q13	2008-05-02			ENSG00000100196	ENSG00000100196			6306	protein-coding gene	gene with protein product							Standard	NM_006855		Approved		uc003avu.3	O43731	OTTHUMG00000153520		22.37:g.38882283C>T		Somatic		Capture	Illumina HiSeq	Phase_I	37212229	NM_001098504	A8K7T7|B8ZZ26|O95557|Q4V750|Q4V767|Q53FP4|Q53GK1	Missense_Mutation	SNP	ENST00000216014.4	37	CCDS13972.1	.	.	.	.	.	.	.	.	.	.	C	11.98	1.801480	0.31869	.	.	ENSG00000100201	ENST00000396821;ENST00000381633;ENST00000415748;ENST00000444597;ENST00000403230;ENST00000404499	T;T;T	0.30981	1.53;1.58;1.51	5.53	5.53	0.82687	.	0.734778	0.13399	N	0.390796	T	0.43919	0.1269	L	0.39898	1.24	0.80722	D	1	P;P;D	0.54207	0.689;0.793;0.965	B;B;P	0.55055	0.16;0.303;0.767	T	0.24440	-1.0160	10	0.59425	D	0.04	-9.103	17.6592	0.88187	0.0:1.0:0.0:0.0	.	620;616;70	Q59F66;Q92841-4;Q9UQL5	.;.;.	D	618;539;70;68;616;620	ENSP00000380033:G618D;ENSP00000371046:G539D;ENSP00000385536:G616D	ENSP00000371046:G539D	G	-	2	0	DDX17	37212229	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.004000	0.49513	2.583000	0.87209	0.655000	0.94253	GGC		0.532	KDELR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331474.1		
APOBEC3G	60489	broad.mit.edu	37	22	39482525	39482525	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr22:39482525G>A	ENST00000407997.3	+	6	1334	c.977G>A	c.(976-978)cGc>cAc	p.R326H	APOBEC3G_ENST00000452957.2_Missense_Mutation_p.R326H	NM_021822.3	NP_068594.1	Q9HC16	ABC3G_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3G	326	Necessary for homooligomerization.				base conversion or substitution editing (GO:0016553)|cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral process (GO:0048525)|positive regulation of defense response to virus by host (GO:0002230)|viral process (GO:0016032)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|ribonucleoprotein complex (GO:0030529)	cytidine deaminase activity (GO:0004126)|deoxycytidine deaminase activity (GO:0047844)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.R326H(2)		central_nervous_system(1)|large_intestine(4)|lung(5)|skin(1)|stomach(1)	12	Melanoma(58;0.04)					GAGGGGCTGCGCACCCTGGCC	0.522																																					p.R326H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G977A	22						.						106.0	116.0	112.0					22																	39482525		2203	4300	6503	37812471	SO:0001583	missense	60489	exon6			AF182420	CCDS13984.1	22q13.1-q13.2	2008-05-15			ENSG00000239713	ENSG00000239713		"""Apolipoprotein B mRNA editing enzymes"""	17357	protein-coding gene	gene with protein product		607113				11863358	Standard	NM_021822		Approved	CEM15, MDS019, dJ494G10.1, FLJ12740, bK150C2.7		Q9HC16	OTTHUMG00000151081	ENST00000407997.3:c.977G>A	22.37:g.39482525G>A	ENSP00000385057:p.Arg326His	Somatic		Capture	Illumina HiSeq	Phase_I	37812471	NM_021822	B2RDR9|Q45F02|Q5TF77|Q7Z2N1|Q7Z2N4|Q9H9H8	Missense_Mutation	SNP	ENST00000407997.3	37	CCDS13984.1	.	.	.	.	.	.	.	.	.	.	.	8.930	0.963236	0.18583	.	.	ENSG00000239713	ENST00000452957;ENST00000407997	T;T	0.71579	-0.58;-0.58	1.53	0.487	0.16842	APOBEC-like, C-terminal (1);Cytidine deaminase-like (1);	.	.	.	.	T	0.75095	0.3803	M	0.66439	2.03	0.09310	N	1	D	0.59357	0.985	P	0.58780	0.845	T	0.62243	-0.6895	9	0.51188	T	0.08	.	5.7265	0.18017	0.1943:0.0:0.8057:0.0	.	326	Q9HC16	ABC3G_HUMAN	H	326	ENSP00000413376:R326H;ENSP00000385057:R326H	ENSP00000385057:R326H	R	+	2	0	APOBEC3G	37812471	0.043000	0.20138	0.004000	0.12327	0.015000	0.08874	1.271000	0.33098	0.204000	0.20548	0.460000	0.39030	CGC		0.522	APOBEC3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321219.1	NM_021822	
MIEF1	54471	broad.mit.edu	37	22	39909927	39909927	+	Missense_Mutation	SNP	G	G	A	rs559558267	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr22:39909927G>A	ENST00000325301.2	+	6	1415	c.991G>A	c.(991-993)Gcc>Acc	p.A331T	MIEF1_ENST00000402881.1_Missense_Mutation_p.A331T|MIEF1_ENST00000404569.1_Missense_Mutation_p.A331T	NM_019008.4	NP_061881.2	Q9NQG6	MID51_HUMAN	mitochondrial elongation factor 1	331					mitochondrial fission (GO:0000266)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein targeting to membrane (GO:0090314)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ADP binding (GO:0043531)|GDP binding (GO:0019003)|identical protein binding (GO:0042802)	p.A331T(1)									ACACCGGCTAGCCCAGTATGA	0.612											OREG0026577	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	331	0.0660942	0.028	0.0836	5008	,	,		18174	0.1438		0.0865	False		,,,				2504	0.0041				p.A331T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G991A	22						.						72.0	69.0	70.0					22																	39909927		2203	4300	6503	38239873	SO:0001583	missense	54471	exon6			AL365515	CCDS13995.1	22q13.1	2013-09-23	2013-09-23	2013-09-23	ENSG00000100335	ENSG00000100335			25979	protein-coding gene	gene with protein product		615497	"""Smith-Magenis syndrome chromosome region, candidate 7-like"""	SMCR7L		21508961, 21701560	Standard	NM_019008		Approved	FLJ20232, MiD51	uc003axx.3	Q9NQG6	OTTHUMG00000151105	ENST00000325301.2:c.991G>A	22.37:g.39909927G>A	ENSP00000327124:p.Ala331Thr	Somatic	889	Capture	Illumina HiSeq	Phase_I	38239873	NM_019008	Q7L890|Q9BUI3	Missense_Mutation	SNP	ENST00000325301.2	37	CCDS13995.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.825409	0.90955	.	.	ENSG00000100335	ENST00000402881;ENST00000325301;ENST00000404569	T;T;T	0.07800	3.16;3.16;3.16	6.07	6.07	0.98685	.	0.044485	0.85682	D	0.000000	T	0.23688	0.0573	L	0.56769	1.78	0.49798	D	0.999825	P;D	0.76494	0.924;0.999	P;D	0.63113	0.723;0.911	T	0.00009	-1.2468	10	0.46703	T	0.11	-22.0508	16.051	0.80763	0.0:0.1333:0.8667:0.0	.	331;331	Q9NQG6;B0QY95	MID51_HUMAN;.	T	331	ENSP00000385110:A331T;ENSP00000327124:A331T;ENSP00000385191:A331T	ENSP00000327124:A331T	A	+	1	0	SMCR7L	38239873	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.865000	0.87049	2.884000	0.98904	0.655000	0.94253	GCC		0.612	MIEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321325.1	NM_019008	
MEI1	150365	broad.mit.edu	37	22	42177341	42177341	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr22:42177341T>C	ENST00000401548.3	+	23	2909	c.2869T>C	c.(2869-2871)Tcc>Ccc	p.S957P	MEI1_ENST00000400107.1_Missense_Mutation_p.S290P|MEI1_ENST00000540880.1_3'UTR|MEI1_ENST00000300398.4_5'UTR	NM_152513.3	NP_689726.3			meiosis inhibitor 1									p.S963P(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						CCTGCAGCCCTCCTTCAACTT	0.572																																					p.S957P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2869C	22						.						44.0	44.0	44.0					22																	42177341		1967	4168	6135	40507287	SO:0001583	missense	150365	exon23			AK092934	CCDS46718.1	22q13.2	2013-10-11			ENSG00000167077	ENSG00000167077			28613	protein-coding gene	gene with protein product	"""spermatogenesis associated 38"""	608797				16683055	Standard	XM_006724154		Approved	MGC40042, SPATA38	uc003baz.1	Q5TIA1	OTTHUMG00000030083	ENST00000401548.3:c.2869T>C	22.37:g.42177341T>C	ENSP00000384115:p.Ser957Pro	Somatic		Capture	Illumina HiSeq	Phase_I	40507287	NM_152513		Missense_Mutation	SNP	ENST00000401548.3	37	CCDS46718.1	.	.	.	.	.	.	.	.	.	.	T	19.56	3.851521	0.71719	.	.	ENSG00000167077	ENST00000401548;ENST00000400107;ENST00000419798	T;T	0.65178	-0.14;-0.14	5.4	4.31	0.51392	.	0.362700	0.29451	N	0.012114	T	0.71929	0.3398	L	0.56769	1.78	0.80722	D	1	D;D;D;D	0.76494	0.993;0.998;0.999;0.999	P;D;D;D	0.68943	0.878;0.919;0.961;0.961	T	0.73244	-0.4044	10	0.56958	D	0.05	.	9.9178	0.41446	0.0:0.0:0.1708:0.8292	.	290;200;325;957	Q5TIA1-3;Q5TIA1-5;Q5TIA1-2;Q5TIA1	.;.;.;MEI1_HUMAN	P	957;290;67	ENSP00000384115:S957P;ENSP00000382978:S290P	ENSP00000382978:S290P	S	+	1	0	MEI1	40507287	0.904000	0.30761	1.000000	0.80357	0.999000	0.98932	0.722000	0.25925	2.053000	0.61076	0.533000	0.62120	TCC		0.572	MEI1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000074937.3	NM_152513	
POLDIP3	84271	broad.mit.edu	37	22	42988073	42988073	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr22:42988073A>C	ENST00000252115.5	-	7	1013	c.909T>G	c.(907-909)tgT>tgG	p.C303W	POLDIP3_ENST00000451060.2_Missense_Mutation_p.C147W|POLDIP3_ENST00000339677.6_Intron|POLDIP3_ENST00000348657.2_Missense_Mutation_p.C274W|POLDIP3_ENST00000491021.1_5'UTR	NM_032311.3	NP_115687.2	Q9BY77	PDIP3_HUMAN	polymerase (DNA-directed), delta interacting protein 3	303	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				poly(A)+ mRNA export from nucleus (GO:0016973)|positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.C303W(1)		biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|upper_aerodigestive_tract(1)	16						TGAGGGCCCCACACACACAGA	0.557																																					p.C274W	Ovarian(52;967 1128 5875 19997 42537)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T822G	22						.						132.0	121.0	125.0					22																	42988073		2203	4300	6503	41318017	SO:0001583	missense	84271	exon6				CCDS14038.1, CCDS14039.1, CCDS74873.1	22q13.31	2013-02-12			ENSG00000100227	ENSG00000100227		"""RNA binding motif (RRM) containing"""	23782	protein-coding gene	gene with protein product		611520				12522211	Standard	NM_032311		Approved	PDIP46, KIAA1649	uc003bcu.3	Q9BY77	OTTHUMG00000150887	ENST00000252115.5:c.909T>G	22.37:g.42988073A>C	ENSP00000252115:p.Cys303Trp	Somatic		Capture	Illumina HiSeq	Phase_I	41318017	NM_178136	A8K6F8|A8K6V9|Q009A7|Q5H972|Q6PGN6|Q7Z6Z0|Q9NSP5|Q9NSP6	Missense_Mutation	SNP	ENST00000252115.5	37	CCDS14038.1	.	.	.	.	.	.	.	.	.	.	A	18.90	3.721739	0.68959	.	.	ENSG00000100227	ENST00000348657;ENST00000252115;ENST00000451060	T;T;T	0.16073	2.37;2.37;2.37	6.08	0.464	0.16706	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.39733	0.1089	M	0.80332	2.49	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.91635	0.999;0.999;0.994;0.999	T	0.27020	-1.0086	10	0.87932	D	0	-11.5197	11.2478	0.49006	0.621:0.0:0.3789:0.0	.	320;299;274;303	B4E0L0;Q96DI9;Q9BY77-2;Q9BY77	.;.;.;PDIP3_HUMAN	W	274;303;147	ENSP00000252116:C274W;ENSP00000252115:C303W;ENSP00000397927:C147W	ENSP00000252115:C303W	C	-	3	2	POLDIP3	41318017	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	1.757000	0.38400	-0.024000	0.13941	0.533000	0.62120	TGT		0.557	POLDIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320433.1	NM_032311	
ARHGAP8	23779	broad.mit.edu	37	22	45210580	45210580	+	Missense_Mutation	SNP	G	G	A	rs562703546	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr22:45210580G>A	ENST00000389774.2	+	6	562	c.421G>A	c.(421-423)Gtg>Atg	p.V141M	ARHGAP8_ENST00000389773.5_Missense_Mutation_p.V232M|PRR5-ARHGAP8_ENST00000352766.7_Missense_Mutation_p.V320M|ARHGAP8_ENST00000517296.3_Missense_Mutation_p.V320M|ARHGAP8_ENST00000356099.6_Missense_Mutation_p.V110M|ARHGAP8_ENST00000336963.4_Missense_Mutation_p.V110M|PRR5-ARHGAP8_ENST00000361473.5_Missense_Mutation_p.V241M	NM_001017526.1	NP_001017526.1	P85298	RHG08_HUMAN	Rho GTPase activating protein 8	141	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)	p.V141M(1)|p.V146M(1)		breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(9)|prostate(1)|skin(7)	29		all_neural(38;0.00409)|Ovarian(80;0.00976)|Glioma(61;0.0649)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0204)		GGCCCTCTACGTGGTGCACCC	0.577													G|||	2	0.000399361	0.0	0.0	5008	,	,		17251	0.0		0.0	False		,,,				2504	0.002				p.V232M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G694A	22						.						137.0	111.0	120.0					22																	45210580		2203	4300	6503	43589244	SO:0001583	missense	553158	exon8			AF177331	CCDS14060.2, CCDS33664.1, CCDS56233.1	22q13.3	2010-05-11			ENSG00000241484	ENSG00000241484		"""Rho GTPase activating proteins"""	677	protein-coding gene	gene with protein product		609405				10591208	Standard	NM_001198726		Approved	FLJ20185, BPGAP1		P85298	OTTHUMG00000030234	ENST00000389774.2:c.421G>A	22.37:g.45210580G>A	ENSP00000374424:p.Val141Met	Somatic		Capture	Illumina HiSeq	Phase_I	43589244	NM_181334	A6ZJ79|A6ZJ80|O75983|O95695|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Missense_Mutation	SNP	ENST00000389774.2	37	CCDS33664.1	.	.	.	.	.	.	.	.	.	.	G	13.20	2.165433	0.38217	.	.	ENSG00000248405;ENSG00000248405;ENSG00000241484;ENSG00000241484;ENSG00000241484;ENSG00000241484;ENSG00000241484;ENSG00000241484	ENST00000361473;ENST00000352766;ENST00000517296;ENST00000389773;ENST00000389774;ENST00000336963;ENST00000356099;ENST00000412433	T;T;T;T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54;1.54;1.54;1.54	4.43	-1.56	0.08532	Cellular retinaldehyde-binding/triple function, C-terminal (5);	.	.	.	.	T	0.39600	0.1084	L	0.43152	1.355	0.23546	N	0.997441	D;D;D;D;D;B;D	0.76494	0.998;0.993;0.999;0.998;0.993;0.29;0.999	D;D;D;D;D;B;D	0.71870	0.975;0.964;0.938;0.975;0.913;0.115;0.939	T	0.27020	-1.0086	9	0.87932	D	0	.	5.9095	0.19020	0.4708:0.1337:0.3956:0.0	.	146;110;146;141;151;320;241	B7ZMA4;A6ZJ79;A2RU51;P85298;Q6PCC7;B1AHC4;B1AHC3	.;.;.;RHG08_HUMAN;.;.;.	M	241;320;320;232;141;110;110;110	ENSP00000354732:V241M;ENSP00000262731:V320M;ENSP00000429240:V320M;ENSP00000374423:V232M;ENSP00000374424:V141M;ENSP00000337287:V110M;ENSP00000348407:V110M;ENSP00000402775:V110M	ENSP00000337287:V110M	V	+	1	0	PRR5-ARHGAP8;ARHGAP8	43589244	0.209000	0.23505	0.002000	0.10522	0.241000	0.25554	0.470000	0.22084	-0.350000	0.08262	-0.131000	0.14894	GTG		0.577	ARHGAP8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000075088.4	NM_017701	
CELSR1	9620	broad.mit.edu	37	22	46790131	46790131	+	Missense_Mutation	SNP	A	A	C	rs199586660	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-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	
ZBED4	9889	broad.mit.edu	37	22	50277770	50277770	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr22:50277770A>G	ENST00000216268.5	+	2	937	c.460A>G	c.(460-462)Acc>Gcc	p.T154A		NM_014838.2	NP_055653.2	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	154						cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T154A(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	44		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)|BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		AGACTTGAGTACCAGTTGTCT	0.512																																					p.T154A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A460G	22						.						76.0	71.0	73.0					22																	50277770		2203	4300	6503	48663774	SO:0001583	missense	9889	exon2			AB014537	CCDS33677.1	22q13.33	2013-05-03			ENSG00000100426	ENSG00000100426		"""Zinc fingers, BED-type"""	20721	protein-coding gene	gene with protein product		612552				23533661	Standard	NM_014838		Approved	KIAA0637	uc003bix.2	O75132	OTTHUMG00000150291	ENST00000216268.5:c.460A>G	22.37:g.50277770A>G	ENSP00000216268:p.Thr154Ala	Somatic		Capture	Illumina HiSeq	Phase_I	48663774	NM_014838	B2RZH1|Q1ECU0|Q9UGG8	Missense_Mutation	SNP	ENST00000216268.5	37	CCDS33677.1	.	.	.	.	.	.	.	.	.	.	A	19.82	3.898182	0.72639	.	.	ENSG00000100426	ENST00000216268	T	0.76186	-1.0	5.31	5.31	0.75309	Zinc finger, BED-type predicted (3);	0.000000	0.85682	D	0.000000	D	0.86543	0.5958	M	0.80982	2.52	0.58432	D	0.999998	D	0.76494	0.999	D	0.83275	0.996	D	0.88501	0.3082	10	0.87932	D	0	-7.6206	15.4245	0.75041	1.0:0.0:0.0:0.0	.	154	O75132	ZBED4_HUMAN	A	154	ENSP00000216268:T154A	ENSP00000216268:T154A	T	+	1	0	ZBED4	48663774	1.000000	0.71417	0.989000	0.46669	0.403000	0.30841	8.342000	0.90049	2.229000	0.72834	0.528000	0.53228	ACC		0.512	ZBED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317408.2	NM_014838	
PLXNB2	23654	broad.mit.edu	37	22	50721513	50721513	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr22:50721513delC	ENST00000449103.1	-	17	2922	c.2782delG	c.(2782-2784)gtgfs	p.V928fs	PLXNB2_ENST00000496720.1_5'Flank|PLXNB2_ENST00000359337.4_Frame_Shift_Del_p.V928fs			O15031	PLXB2_HUMAN	plexin B2	928	IPT/TIG 2.				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.V971fs*3(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)		GTCACCCGCACGTCCTCCTGG	0.682																																					p.V928fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2782delG	22						.						18.0	24.0	22.0					22																	50721513		2016	4170	6186	49063640	SO:0001589	frameshift_variant	23654	exon16				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.2782delG	22.37:g.50721513delC	ENSP00000409171:p.Val928fs	Somatic		Capture	Illumina HiSeq	Phase_I	49063640	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Frame_Shift_Del	DEL	ENST00000449103.1	37	CCDS43035.1																																																																																				0.682	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401	
MAP4K4	9448	broad.mit.edu	37	2	102448201	102448201	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:102448201C>A	ENST00000347699.4	+	7	527	c.527C>A	c.(526-528)gCt>gAt	p.A176D	MAP4K4_ENST00000324219.4_Missense_Mutation_p.A176D|MAP4K4_ENST00000456652.1_Intron|MAP4K4_ENST00000350198.4_Missense_Mutation_p.A176D|MAP4K4_ENST00000425019.1_Missense_Mutation_p.A176D|MAP4K4_ENST00000302217.5_Intron|MAP4K4_ENST00000413150.2_Missense_Mutation_p.A176D|MAP4K4_ENST00000350878.4_Missense_Mutation_p.A156D	NM_001242559.1|NM_145687.3	NP_001229488.1|NP_663720.1	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase kinase 4	176	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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.A176D(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						GGTGTGAGTGCTCAGCTGGAC	0.483											OREG0014845	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A176D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C527A	2						.						83.0	78.0	79.0					2																	102448201		1947	4166	6113	101814633	SO:0001583	missense	9448	exon7			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.527C>A	2.37:g.102448201C>A	ENSP00000314363:p.Ala176Asp	Somatic	1366	Capture	Illumina HiSeq	Phase_I	101814633	NM_145687	O75172|Q9NST7	Missense_Mutation	SNP	ENST00000347699.4	37	CCDS56130.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.667087	0.88251	.	.	ENSG00000071054	ENST00000425019;ENST00000324219;ENST00000350198;ENST00000413150;ENST00000347699;ENST00000417294;ENST00000350878	T;T;T;T;T;T;T	0.66099	1.79;1.79;1.79;1.79;1.79;1.79;-0.19	6.06	6.06	0.98353	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	0.82935	0.5145	M	0.84773	2.715	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;0.999;0.999;0.999;0.998;0.998	D;D;D;D;D;D;D;D;D;D	0.97110	1.0;0.999;0.997;0.999;0.999;0.99;0.993;0.98;0.982;0.982	D	0.84011	0.0348	10	0.87932	D	0	.	20.6244	0.99512	0.0:1.0:0.0:0.0	.	156;176;176;156;176;176;176;176;176;176	B7Z388;B7Z3V5;E7ENQ1;E7ESS2;O95819-4;O95819;E7EN19;G3XAA2;O95819-2;G5E948	.;.;.;.;.;M4K4_HUMAN;.;.;.;.	D	176;176;176;176;176;138;156	ENSP00000392830:A176D;ENSP00000313644:A176D;ENSP00000281111:A176D;ENSP00000389752:A176D;ENSP00000314363:A176D;ENSP00000409720:A138D;ENSP00000343658:A156D	ENSP00000313644:A176D	A	+	2	0	MAP4K4	101814633	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.689000	0.84165	2.879000	0.98667	0.650000	0.86243	GCT		0.483	MAP4K4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339839.1	NM_004834	
SLC9A2	6549	broad.mit.edu	37	2	103274214	103274214	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:103274214C>A	ENST00000233969.2	+	2	623	c.481C>A	c.(481-483)Cca>Aca	p.P161T		NM_003048.3	NP_003039.2	Q9UBY0	SL9A2_HUMAN	solute carrier family 9, subfamily A (NHE2, cation proton antiporter 2), member 2	161					ion transport (GO:0006811)|protein localization (GO:0008104)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)	p.P161T(1)		breast(5)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42						GCCCACTCGCCCATTCTTTGA	0.478																																					p.P161T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C481A	2						.						324.0	305.0	312.0					2																	103274214		2203	4300	6503	102640646	SO:0001583	missense	6549	exon2				CCDS2062.1	2q11.2	2013-05-22	2012-03-22		ENSG00000115616	ENSG00000115616		"""Solute carriers"""	11072	protein-coding gene	gene with protein product		600530	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 2"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 2"""	NHE2			Standard	NM_003048		Approved		uc002tca.3	Q9UBY0	OTTHUMG00000130778	ENST00000233969.2:c.481C>A	2.37:g.103274214C>A	ENSP00000233969:p.Pro161Thr	Somatic		Capture	Illumina HiSeq	Phase_I	102640646	NM_003048	B2RMS2	Missense_Mutation	SNP	ENST00000233969.2	37	CCDS2062.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.351622	0.82132	.	.	ENSG00000115616	ENST00000233969	T	0.14516	2.5	5.93	5.93	0.95920	Cation/H+ exchanger (1);	0.101113	0.64402	D	0.000001	T	0.29061	0.0722	L	0.54863	1.705	0.45250	D	0.998259	D	0.52996	0.957	P	0.56434	0.798	T	0.00263	-1.1866	10	0.21540	T	0.41	.	20.3507	0.98813	0.0:1.0:0.0:0.0	.	161	Q9UBY0	SL9A2_HUMAN	T	161	ENSP00000233969:P161T	ENSP00000233969:P161T	P	+	1	0	SLC9A2	102640646	0.966000	0.33281	0.827000	0.32855	0.941000	0.58515	3.889000	0.56212	2.808000	0.96608	0.655000	0.94253	CCA		0.478	SLC9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253292.2		
EDAR	10913	broad.mit.edu	37	2	109513587	109513587	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:109513587G>A	ENST00000258443.2	-	12	1553	c.1123C>T	c.(1123-1125)Cgc>Tgc	p.R375C	EDAR_ENST00000409271.1_Missense_Mutation_p.R407C|EDAR_ENST00000376651.1_Missense_Mutation_p.R407C	NM_022336.3	NP_071731.1	Q9UNE0	EDAR_HUMAN	ectodysplasin A receptor	375	Death.		R -> H (in ECTD10B; the mutant protein does not interact with EDARADD and is functionally inactive). {ECO:0000269|PubMed:15373768}.		apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|epidermis development (GO:0008544)|hair follicle development (GO:0001942)|odontogenesis of dentin-containing tooth (GO:0042475)|pigmentation (GO:0043473)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|salivary gland cavitation (GO:0060662)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.R375C(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	16						GCGAGGTGGCGCCACGTTTTC	0.567																																					p.R375C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1123T	2						.						89.0	77.0	81.0					2																	109513587		2203	4300	6503	108880019	SO:0001583	missense	10913	exon12			AF130988	CCDS2081.1	2q13	2013-05-22	2004-08-09		ENSG00000135960	ENSG00000135960		"""Tumor necrosis factor receptor superfamily"""	2895	protein-coding gene	gene with protein product		604095	"""ectodysplasin 1, anhidrotic receptor"""	ED3, DL		10431241, 9375732	Standard	NM_022336		Approved	ED5, EDA3, Edar, ED1R, EDA1R	uc002teq.4	Q9UNE0	OTTHUMG00000130982	ENST00000258443.2:c.1123C>T	2.37:g.109513587G>A	ENSP00000258443:p.Arg375Cys	Somatic		Capture	Illumina HiSeq	Phase_I	108880019	NM_022336	B2R9H2|B4DLC5|D3DX74|E9PC98|Q52LL5|Q9UND9	Missense_Mutation	SNP	ENST00000258443.2	37	CCDS2081.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.241092	0.79912	.	.	ENSG00000135960	ENST00000409271;ENST00000258443;ENST00000376651	D;D;D	0.87179	-2.22;-2.22;-2.22	5.64	5.64	0.86602	Death (1);DEATH-like (2);	0.000000	0.85682	D	0.000000	D	0.89546	0.6746	N	0.19112	0.55	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.91119	0.4928	10	0.87932	D	0	-43.2992	19.7209	0.96143	0.0:0.0:1.0:0.0	.	407;375	E9PC98;Q9UNE0	.;EDAR_HUMAN	C	407;375;407	ENSP00000386371:R407C;ENSP00000258443:R375C;ENSP00000365839:R407C	ENSP00000258443:R375C	R	-	1	0	EDAR	108880019	1.000000	0.71417	1.000000	0.80357	0.725000	0.41563	6.993000	0.76245	2.651000	0.90000	0.650000	0.86243	CGC		0.567	EDAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253595.1		
MERTK	10461	broad.mit.edu	37	2	112779062	112779062	+	Silent	SNP	C	C	T	rs149178674		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:112779062C>T	ENST00000295408.4	+	17	2510	c.2253C>T	c.(2251-2253)ggC>ggT	p.G751G	MERTK_ENST00000421804.2_Silent_p.G751G|MERTK_ENST00000409780.1_Silent_p.G575G			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	751	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic cell clearance (GO:0043277)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|leukocyte migration (GO:0050900)|natural killer cell differentiation (GO:0001779)|negative regulation of lymphocyte activation (GO:0051250)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of phagocytosis (GO:0050766)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|secretion by cell (GO:0032940)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|rhabdomere (GO:0016028)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.G751G(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(10)	46						TTTACAGTGGCGATTATTACC	0.478																																					p.G751G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2253T	2						.	C		1,4405	2.1+/-5.4	0,1,2202	151.0	145.0	147.0		2253	-10.5	0.1	2	dbSNP_134	147	0,8600		0,0,4300	no	coding-synonymous	MERTK	NM_006343.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		751/1000	112779062	1,13005	2203	4300	6503	112495533	SO:0001819	synonymous_variant	10461	exon17			U08023	CCDS2094.1	2q14.1	2014-06-26	2014-06-26		ENSG00000153208	ENSG00000153208		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7027	protein-coding gene	gene with protein product		604705	"""c-mer proto-oncogene tyrosine kinase"""			8086340, 10343112	Standard	XM_005263565		Approved	mer, RP38	uc002thk.1	Q12866	OTTHUMG00000131278	ENST00000295408.4:c.2253C>T	2.37:g.112779062C>T		Somatic		Capture	Illumina HiSeq	Phase_I	112495533	NM_006343	Q9HBB4	Silent	SNP	ENST00000295408.4	37	CCDS2094.1																																																																																				0.478	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2		
CHCHD5	84269	broad.mit.edu	37	2	113343607	113343607	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:113343607G>A	ENST00000324913.5	+	2	266	c.59G>A	c.(58-60)gGc>gAc	p.G20D	CHCHD5_ENST00000409719.1_Missense_Mutation_p.G20D|CHCHD5_ENST00000489052.1_3'UTR	NM_032309.2	NP_115685.1	Q9BSY4	CHCH5_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 5	20						mitochondrion (GO:0005739)		p.G20D(1)		NS(1)|endometrium(1)|large_intestine(4)|urinary_tract(1)	7						GAGCAGTATGGCCAGTGTGTG	0.617																																					p.G20D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G59A	2						.						55.0	59.0	57.0					2																	113343607		2203	4300	6503	113060078	SO:0001583	missense	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.59G>A	2.37:g.113343607G>A	ENSP00000325655:p.Gly20Asp	Somatic		Capture	Illumina HiSeq	Phase_I	113060078	NM_032309	Q585T4|Q8N8C4	Missense_Mutation	SNP	ENST00000324913.5	37	CCDS2098.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.735157	0.89482	.	.	ENSG00000125611	ENST00000324913;ENST00000409719	T;T	0.16324	2.35;2.35	5.64	4.75	0.60458	.	0.085529	0.48767	D	0.000162	T	0.26629	0.0651	L	0.32530	0.975	0.53005	D	0.999961	D;D	0.62365	0.991;0.978	P;P	0.61940	0.896;0.746	T	0.00380	-1.1776	10	0.72032	D	0.01	-27.278	11.9335	0.52860	0.0839:0.0:0.9161:0.0	.	20;20	Q8N8C4;Q9BSY4	.;CHCH5_HUMAN	D	20	ENSP00000325655:G20D;ENSP00000386994:G20D	ENSP00000325655:G20D	G	+	2	0	CHCHD5	113060078	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.864000	0.62990	2.833000	0.97629	0.650000	0.86243	GGC		0.617	CHCHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254081.2	NM_032309	
INSIG2	51141	broad.mit.edu	37	2	118854176	118854176	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:118854176G>A	ENST00000245787.4	+	2	250	c.44G>A	c.(43-45)gGc>gAc	p.G15D	INSIG2_ENST00000485520.1_Intron	NM_016133.2	NP_057217.2	Q9Y5U4	INSI2_HUMAN	insulin induced gene 2	15					cholesterol biosynthetic process (GO:0006695)|cranial suture morphogenesis (GO:0060363)|inner ear morphogenesis (GO:0042472)|middle ear morphogenesis (GO:0042474)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of steroid biosynthetic process (GO:0010894)|palate development (GO:0060021)|response to fatty acid (GO:0070542)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)|triglyceride metabolic process (GO:0006641)	endoplasmic reticulum membrane (GO:0005789)|SREBP-SCAP-Insig complex (GO:0032937)		p.G15D(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(5)|ovary(1)	13						AAAAAGTGTGGCCCATATATT	0.398																																					p.G15D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G44A	2						.						123.0	120.0	121.0					2																	118854176		2203	4300	6503	118570646	SO:0001583	missense	51141	exon2			AF527632	CCDS2122.1	2q14.1	2008-02-05			ENSG00000125629	ENSG00000125629			20452	protein-coding gene	gene with protein product		608660				12242332	Standard	NM_016133		Approved		uc002tlk.3	Q9Y5U4	OTTHUMG00000058518	ENST00000245787.4:c.44G>A	2.37:g.118854176G>A	ENSP00000245787:p.Gly15Asp	Somatic		Capture	Illumina HiSeq	Phase_I	118570646	NM_016133	A8K5W8|Q8TBI8	Missense_Mutation	SNP	ENST00000245787.4	37	CCDS2122.1	.	.	.	.	.	.	.	.	.	.	G	18.94	3.729616	0.69074	.	.	ENSG00000125629	ENST00000245787	.	.	.	5.65	5.65	0.86999	.	0.306369	0.34603	N	0.003838	T	0.56352	0.1979	L	0.39898	1.24	0.80722	D	1	B	0.30793	0.295	B	0.31614	0.133	T	0.52230	-0.8603	9	0.36615	T	0.2	.	17.6855	0.88255	0.0:0.0:1.0:0.0	.	15	Q9Y5U4	INSI2_HUMAN	D	15	.	ENSP00000245787:G15D	G	+	2	0	INSIG2	118570646	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.364000	0.79526	2.941000	0.99782	0.655000	0.94253	GGC		0.398	INSIG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129624.1	NM_016133	
SMPD4	55627	broad.mit.edu	37	2	130912765	130912765	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:130912765G>A	ENST00000409031.1	-	15	2622	c.1474C>T	c.(1474-1476)Ctc>Ttc	p.L492F	SMPD4_ENST00000443958.2_Missense_Mutation_p.L156F|SMPD4_ENST00000426662.2_Missense_Mutation_p.L128F|SMPD4_ENST00000339679.7_Missense_Mutation_p.L350F|SMPD4_ENST00000453750.1_Missense_Mutation_p.L241F|SMPD4_ENST00000431183.2_Missense_Mutation_p.L390F|SMPD4_ENST00000473720.1_5'Flank|SMPD4_ENST00000351288.6_Missense_Mutation_p.L463F|SMPD4_ENST00000452225.2_Missense_Mutation_p.L233F	NM_017951.4	NP_060421.2	Q9NXE4	NSMA3_HUMAN	sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)	453					cellular response to tumor necrosis factor (GO:0071356)|ceramide biosynthetic process (GO:0046513)|glycerophospholipid catabolic process (GO:0046475)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)|sphingomyelin phosphodiesterase D activity (GO:0050290)	p.L492F(1)		breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(17)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29	Colorectal(110;0.1)				Phosphatidylserine(DB00144)	TCTGTGCGGAGCGCGCGGTTC	0.592																																					p.L492F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1474T	2						.						95.0	88.0	91.0					2																	130912765		2203	4300	6503	130629235	SO:0001583	missense	55627	exon15			AF052134	CCDS2156.2, CCDS42751.1, CCDS54398.1	2q21.1	2009-11-06			ENSG00000136699	ENSG00000136699			32949	protein-coding gene	gene with protein product		610457				16517606	Standard	NM_001171083		Approved	FLJ20297, FLJ20756, nSMase-3, KIAA1418, NSMASE3, NET13	uc002tqr.2	Q9NXE4	OTTHUMG00000131624	ENST00000409031.1:c.1474C>T	2.37:g.130912765G>A	ENSP00000386531:p.Leu492Phe	Somatic		Capture	Illumina HiSeq	Phase_I	130629235	NM_017951	B4DM23|B4DQ31|B4DRB8|B4DWK7|B4E0L6|E7ESA2|E9PCE6|Q6FI76|Q6P1P7|Q6ZT43|Q9H0M2|Q9NW20|Q9NWL2|Q9P2C9	Missense_Mutation	SNP	ENST00000409031.1	37	CCDS42751.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	14.08|14.08	2.428925|2.428925	0.43122|0.43122	.|.	.|.	ENSG00000136699|ENSG00000136699	ENST00000430682|ENST00000351288;ENST00000409031;ENST00000431183;ENST00000453750;ENST00000443958;ENST00000339679;ENST00000452225;ENST00000426662;ENST00000457039;ENST00000449159;ENST00000451542	.|.	.|.	.|.	4.24|4.24	4.24|4.24	0.50183|0.50183	.|.	.|0.136554	.|0.49916	.|D	.|0.000127	T|T	0.69441|0.69441	0.3111|0.3111	L|L	0.57536|0.57536	1.79|1.79	0.43569|0.43569	D|D	0.995893|0.995893	.|P;P;P;P;D;D;D;D;D	.|0.76494	.|0.775;0.909;0.724;0.724;0.964;0.999;0.998;0.998;0.999	.|P;P;B;B;P;D;D;D;D	.|0.80764	.|0.58;0.58;0.442;0.348;0.66;0.929;0.954;0.971;0.994	T|T	0.66131|0.66131	-0.6000|-0.6000	6|9	0.02654|0.22109	T|T	1|0.4	.|.	14.1436|14.1436	0.65336|0.65336	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|128;233;390;350;241;424;453;492;499	.|B4E0L6;B4DQ31;E7ESA2;B4E0T5;B4DM23;Q9NXE4-2;Q9NXE4;B1PBA3;Q9NXE4-4	.|.;.;.;.;.;.;NSMA3_HUMAN;.;.	V|F	173|463;492;390;241;156;350;233;128;89;28;234	.|.	ENSP00000406325:A173V|ENSP00000339721:L350F	A|L	-|-	2|1	0|0	SMPD4|SMPD4	130629235|130629235	1.000000|1.000000	0.71417|0.71417	0.781000|0.781000	0.31783|0.31783	0.214000|0.214000	0.24535|0.24535	3.736000|3.736000	0.55052|0.55052	1.886000|1.886000	0.54624|0.54624	0.305000|0.305000	0.20034|0.20034	GCT|CTC		0.592	SMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254516.3	NM_017751	
TUBA3E	112714	broad.mit.edu	37	2	130951638	130951638	+	Silent	SNP	G	G	T	rs141240951	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	G	G	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:130951638G>T	ENST00000312988.7	-	4	877	c.777C>A	c.(775-777)ctC>ctA	p.L259L		NM_207312.2	NP_997195	Q6PEY2	TBA3E_HUMAN	tubulin, alpha 3e	259					microtubule-based process (GO:0007017)|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.L259L(1)		endometrium(4)|kidney(7)|large_intestine(6)|lung(9)|skin(2)	28	Colorectal(110;0.1)					GGTACGGCACGAGGTTGGTCT	0.602																																					p.L259L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C777A	2						.						203.0	144.0	164.0					2																	130951638		2203	4300	6503	130668108	SO:0001819	synonymous_variant	112714	exon4			BC057811	CCDS2158.1	2q21.1	2007-03-16			ENSG00000152086	ENSG00000152086		"""Tubulins"""	20765	protein-coding gene	gene with protein product							Standard	NM_207312		Approved		uc002tqv.3	Q6PEY2	OTTHUMG00000131626	ENST00000312988.7:c.777C>A	2.37:g.130951638G>T		LOH		Capture	Illumina HiSeq	Phase_I	130668108	NM_207312		Silent	SNP	ENST00000312988.7	37	CCDS2158.1																																																																																				0.602	TUBA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254519.1	NM_207312	
CXCR4	7852	broad.mit.edu	37	2	136872795	136872795	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:136872795G>A	ENST00000241393.3	-	2	807	c.703C>T	c.(703-705)Cgc>Tgc	p.R235C	CXCR4_ENST00000466288.1_5'UTR|CXCR4_ENST00000409817.1_Missense_Mutation_p.R239C	NM_003467.2	NP_003458.1	P61073	CXCR4_HUMAN	chemokine (C-X-C motif) receptor 4	235					activation of MAPK activity (GO:0000187)|ameboidal cell migration (GO:0001667)|apoptotic process (GO:0006915)|brain development (GO:0007420)|calcium-mediated signaling (GO:0019722)|cellular response to cytokine stimulus (GO:0071345)|chemokine-mediated signaling pathway (GO:0070098)|dendritic cell chemotaxis (GO:0002407)|entry into host cell (GO:0030260)|G-protein coupled receptor signaling pathway (GO:0007186)|germ cell development (GO:0007281)|germ cell migration (GO:0008354)|inflammatory response (GO:0006954)|motor neuron axon guidance (GO:0008045)|myelin maintenance (GO:0043217)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|neutrophil activation (GO:0042119)|patterning of blood vessels (GO:0001569)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of oligodendrocyte differentiation (GO:0048714)|regulation of cell migration (GO:0030334)|regulation of chemotaxis (GO:0050920)|response to hypoxia (GO:0001666)|response to virus (GO:0009615)|T cell proliferation (GO:0042098)|viral process (GO:0016032)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|C-X-C chemokine receptor activity (GO:0016494)|coreceptor activity (GO:0015026)|G-protein coupled receptor activity (GO:0004930)|myosin light chain binding (GO:0032027)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|virus receptor activity (GO:0001618)	p.R239C(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.155)	Framycetin(DB00452)|Plerixafor(DB06809)	AGGGCCTTGCGCTTCTGGTGG	0.522																																					p.R235C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C703T	2						.						169.0	155.0	160.0					2																	136872795		2203	4300	6503	136589265	SO:0001583	missense	7852	exon2			AF005058	CCDS33295.1, CCDS46420.1	2q21	2014-09-17	2002-08-22		ENSG00000121966	ENSG00000121966		"""CD molecules"", ""GPCR / Class A : Chemokine receptors : C-X-C motif"""	2561	protein-coding gene	gene with protein product		162643	"""chemokine (C-X-C motif), receptor 4 (fusin)"""			9599023, 9379028	Standard	NM_001008540		Approved	LESTR, NPY3R, HM89, NPYY3R, D2S201E, fusin, HSY3RR, NPYR, CD184	uc002tuz.3	P61073	OTTHUMG00000153583	ENST00000241393.3:c.703C>T	2.37:g.136872795G>A	ENSP00000241393:p.Arg235Cys	Somatic		Capture	Illumina HiSeq	Phase_I	136589265	NM_003467	B2R5N0|O60835|P30991|P56438|Q53S69|Q9BXA0|Q9UKN2	Missense_Mutation	SNP	ENST00000241393.3	37	CCDS46420.1	.	.	.	.	.	.	.	.	.	.	G	16.43	3.119740	0.56613	.	.	ENSG00000121966	ENST00000409817;ENST00000241393;ENST00000537957	T;T	0.74002	-0.8;-0.8	6.17	4.35	0.52113	GPCR, rhodopsin-like superfamily (1);	0.092545	0.64402	D	0.000001	D	0.86514	0.5951	M	0.86343	2.81	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.78314	0.984;0.991	D	0.87388	0.2361	10	0.72032	D	0.01	.	11.4376	0.50076	0.0645:0.0:0.8089:0.1267	.	235;239	P61073;P61073-2	CXCR4_HUMAN;.	C	239;235;105	ENSP00000386884:R239C;ENSP00000241393:R235C	ENSP00000241393:R235C	R	-	1	0	CXCR4	136589265	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.175000	0.65021	0.897000	0.36392	-0.136000	0.14681	CGC		0.522	CXCR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331732.1		
THSD7B	80731	broad.mit.edu	37	2	137814184	137814184	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:137814184C>T	ENST00000409968.1	+	3	512	c.334C>T	c.(334-336)Cac>Tac	p.H112Y	THSD7B_ENST00000543459.1_5'Flank|THSD7B_ENST00000272643.3_Missense_Mutation_p.H112Y|THSD7B_ENST00000413152.2_Missense_Mutation_p.H81Y			Q9C0I4	THS7B_HUMAN	thrombospondin, type I, domain containing 7B	112	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.					integral component of membrane (GO:0016021)		p.H112Y(1)		NS(3)|breast(3)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(14)|lung(57)|ovary(4)|pancreas(3)|prostate(11)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	134				BRCA - Breast invasive adenocarcinoma(221;0.19)		TTCTGACTGGCACCACTGTGT	0.552																																					p.H81Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C241T	2						.						92.0	100.0	97.0					2																	137814184		2046	4204	6250	137530654	SO:0001583	missense	80731	exon2					2q22.1	2006-11-24			ENSG00000144229	ENSG00000144229			29348	protein-coding gene	gene with protein product						11214970	Standard	NM_001080427		Approved	KIAA1679	uc002tva.1	Q9C0I4	OTTHUMG00000153590	ENST00000409968.1:c.334C>T	2.37:g.137814184C>T	ENSP00000387145:p.His112Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	137530654	NM_001080427		Missense_Mutation	SNP	ENST00000409968.1	37		.	.	.	.	.	.	.	.	.	.	C	14.50	2.553292	0.45487	.	.	ENSG00000144229	ENST00000409968;ENST00000272643;ENST00000413152	T;T;T	0.60672	0.17;0.17;0.17	6.07	5.15	0.70609	.	0.412741	0.30547	N	0.009381	T	0.41259	0.1151	L	0.36672	1.1	0.80722	D	1	B	0.09022	0.002	B	0.12837	0.008	T	0.34030	-0.9845	9	.	.	.	.	4.891	0.13726	0.1363:0.5654:0.2213:0.077	.	81	C9JKN6	.	Y	112;112;81	ENSP00000387145:H112Y;ENSP00000272643:H112Y;ENSP00000413841:H81Y	.	H	+	1	0	THSD7B	137530654	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	1.496000	0.35638	2.890000	0.99128	0.585000	0.79938	CAC		0.552	THSD7B-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000331769.2	XM_046570.9	
HNMT	3176	broad.mit.edu	37	2	138738852	138738852	+	Intron	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:138738852G>A	ENST00000280097.3	+	2	372				HNMT_ENST00000410115.1_Intron|HNMT_ENST00000329366.4_Missense_Mutation_p.R86H|HNMT_ENST00000485653.1_Intron	NM_006895.2	NP_008826.1	P50135	HNMT_HUMAN	histamine N-methyltransferase						brain development (GO:0007420)|hyperosmotic response (GO:0006972)|respiratory gaseous exchange (GO:0007585)|response to amine (GO:0014075)|response to cocaine (GO:0042220)|response to glucocorticoid (GO:0051384)|response to interleukin-1 (GO:0070555)|response to tumor cell (GO:0002347)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|nucleus (GO:0005634)	histamine N-methyltransferase activity (GO:0046539)	p.R86H(1)		NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.125)	Amodiaquine(DB00613)|Chlorhexidine(DB00878)|Histamine Phosphate(DB00667)|Quinacrine(DB01103)	TGTAGCACCCGTCAGAAAGAC	0.473																																					p.R86H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G257A	2						.						111.0	109.0	110.0					2																	138738852		2203	4300	6503	138455322	SO:0001627	intron_variant	3176	exon3				CCDS2181.1, CCDS33296.1, CCDS33297.1	2q22.1	2008-02-05			ENSG00000150540	ENSG00000150540	2.1.1.8		5028	protein-coding gene	gene with protein product		605238					Standard	NM_001024074		Approved		uc002tvf.3	P50135	OTTHUMG00000131751	ENST00000280097.3:c.190+11065G>A	2.37:g.138738852G>A		Somatic		Capture	Illumina HiSeq	Phase_I	138455322	NM_001024075	B2R9J3|Q546Z6|Q7Z7I2|Q8IU56|Q8WW98|Q9BRW6	Missense_Mutation	SNP	ENST00000280097.3	37	CCDS2181.1	.	.	.	.	.	.	.	.	.	.	G	9.851	1.193796	0.22037	.	.	ENSG00000150540	ENST00000329366	.	.	.	3.78	-4.51	0.03483	.	.	.	.	.	T	0.27489	0.0675	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.28332	-1.0047	7	0.87932	D	0	.	7.1757	0.25742	0.6542:0.1431:0.2027:0.0	.	86	P50135-2	.	H	86	.	ENSP00000333259:R86H	R	+	2	0	HNMT	138455322	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.642000	0.05427	-1.088000	0.03077	-1.047000	0.02352	CGT		0.473	HNMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254673.1		
LRP1B	53353	broad.mit.edu	37	2	141298623	141298623	+	Silent	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:141298623A>G	ENST00000389484.3	-	45	8403	c.7432T>C	c.(7432-7434)Ttg>Ctg	p.L2478L		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2478	EGF-like 10. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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.L2478L(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)		AAAAGGCACAAGTCATGGCAG	0.403										TSP Lung(27;0.18)																											p.L2478L	Colon(99;50 2074 2507 20106)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T7432C	2						.						125.0	117.0	120.0					2																	141298623		2203	4300	6503	141015093	SO:0001819	synonymous_variant	53353	exon45			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.7432T>C	2.37:g.141298623A>G		Somatic		Capture	Illumina HiSeq	Phase_I	141015093	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																				0.403	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
NEB	4703	broad.mit.edu	37	2	152346914	152346914	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:152346914G>T	ENST00000172853.10	-	147	19848	c.19701C>A	c.(19699-19701)agC>agA	p.S6567R	NEB_ENST00000498015.2_5'Flank|NEB_ENST00000604864.1_Missense_Mutation_p.S8423R|NEB_ENST00000509223.2_Missense_Mutation_p.S336R|RIF1_ENST00000457745.1_Intron|NEB_ENST00000397336.2_Missense_Mutation_p.S398R|NEB_ENST00000397345.3_Missense_Mutation_p.S8423R|NEB_ENST00000427231.2_Missense_Mutation_p.S8423R|NEB_ENST00000409198.1_Missense_Mutation_p.S6567R|NEB_ENST00000603639.1_Missense_Mutation_p.S8423R			P20929	NEBU_HUMAN	nebulin	6567	Interaction with SVIL.				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.S6567R(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)		CACCCCCGTCGCTGTAAGTCG	0.547																																					p.S8423R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C25269A	2						.						63.0	66.0	65.0					2																	152346914		1986	4158	6144	152055160	SO:0001583	missense	4703	exon180			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.19701C>A	2.37:g.152346914G>T	ENSP00000172853:p.Ser6567Arg	Somatic		Capture	Illumina HiSeq	Phase_I	152055160	NM_001164507	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.02|15.02	2.708043|2.708043	0.48412|0.48412	.|.	.|.	ENSG00000183091|ENSG00000183091	ENST00000397337;ENST00000434685|ENST00000409198;ENST00000397345;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853;ENST00000397336;ENST00000509223	.|T;T;T;T;T;T;T	.|0.07908	.|3.29;3.34;3.34;3.15;3.29;3.89;4.08	5.53|5.53	-2.53|-2.53	0.06326|0.06326	.|.	.|0.075920	.|0.85682	.|D	.|0.000000	T|T	0.21921|0.21921	0.0528|0.0528	M|M	0.72894|0.72894	2.215|2.215	0.58432|0.58432	D|D	0.999999|0.999999	.|D;D;D;D;D;P	.|0.89917	.|0.999;1.0;0.999;0.965;1.0;0.773	.|D;D;D;P;D;P	.|0.91635	.|0.992;0.999;0.977;0.527;0.997;0.584	T|T	0.00036|0.00036	-1.2253|-1.2253	5|10	.|0.72032	.|D	.|0.01	.|.	10.8674|10.8674	0.46864|0.46864	0.5479:0.0:0.4521:0.0|0.5479:0.0:0.4521:0.0	.|.	.|336;398;336;6567;2905;8423	.|B7Z6B9;B7Z6P9;B7Z6N8;P20929;Q14215;F8WCL5	.|.;.;.;NEBU_HUMAN;.;.	E|R	557;664|6567;8423;8423;2523;2905;6567;398;336	.|ENSP00000386259:S6567R;ENSP00000380505:S8423R;ENSP00000416578:S8423R;ENSP00000410961:S2905R;ENSP00000172853:S6567R;ENSP00000380497:S398R;ENSP00000427083:S336R	.|ENSP00000172853:S6567R	A|S	-|-	2|3	0|2	NEB|NEB	152055160|152055160	0.972000|0.972000	0.33761|0.33761	0.254000|0.254000	0.24359|0.24359	0.102000|0.102000	0.19082|0.19082	0.136000|0.136000	0.15974|0.15974	-0.956000|-0.956000	0.03631|0.03631	-0.258000|-0.258000	0.10820|0.10820	GCG|AGC		0.547	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
NEB	4703	broad.mit.edu	37	2	152408313	152408313	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:152408313G>A	ENST00000172853.10	-	101	14927	c.14780C>T	c.(14779-14781)gCt>gTt	p.A4927V	NEB_ENST00000604864.1_Missense_Mutation_p.A6628V|NEB_ENST00000397345.3_Missense_Mutation_p.A6628V|NEB_ENST00000427231.2_Missense_Mutation_p.A6628V|NEB_ENST00000409198.1_Missense_Mutation_p.A4927V|NEB_ENST00000603639.1_Missense_Mutation_p.A6628V			P20929	NEBU_HUMAN	nebulin	4927					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.A4927V(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)		GGTAGTTGGAGCCACTTTGCC	0.512																																					p.A6628V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C19883T	2						.						109.0	102.0	104.0					2																	152408313		1966	4149	6115	152116559	SO:0001583	missense	4703	exon129			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.14780C>T	2.37:g.152408313G>A	ENSP00000172853:p.Ala4927Val	Somatic		Capture	Illumina HiSeq	Phase_I	152116559	NM_001164507	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	G	10.52	1.373393	0.24857	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853	T;T;T;T;T	0.06687	3.4;3.4;3.39;3.27;3.4	6.06	5.17	0.71159	.	0.260506	0.42548	D	0.000694	T	0.18882	0.0453	L	0.47716	1.5	0.80722	D	1	B;D	0.71674	0.005;0.998	B;D	0.75484	0.014;0.986	T	0.01930	-1.1245	10	0.15066	T	0.55	.	12.8699	0.57958	0.1282:0.0:0.8718:0.0	.	4927;1358	P20929;Q14215	NEBU_HUMAN;.	V	4927;6628;6628;976;1358;4927	ENSP00000386259:A4927V;ENSP00000380505:A6628V;ENSP00000416578:A6628V;ENSP00000410961:A1358V;ENSP00000172853:A4927V	ENSP00000172853:A4927V	A	-	2	0	NEB	152116559	1.000000	0.71417	0.994000	0.49952	0.984000	0.73092	4.244000	0.58728	2.882000	0.98803	0.655000	0.94253	GCT		0.512	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
NEB	4703	broad.mit.edu	37	2	152500575	152500575	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:152500575G>A	ENST00000172853.10	-	57	7860	c.7713C>T	c.(7711-7713)gaC>gaT	p.D2571D	NEB_ENST00000604864.1_Silent_p.D2571D|NEB_ENST00000397345.3_Silent_p.D2571D|NEB_ENST00000427231.2_Silent_p.D2571D|NEB_ENST00000409198.1_Silent_p.D2571D|NEB_ENST00000603639.1_Silent_p.D2571D			P20929	NEBU_HUMAN	nebulin	2571					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.D2571D(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)		TCATCTTGGGGTCATCTTCAA	0.488																																					p.D2571D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C7713T	2						.						310.0	298.0	302.0					2																	152500575		1944	4140	6084	152208821	SO:0001819	synonymous_variant	4703	exon57			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.7713C>T	2.37:g.152500575G>A		Somatic		Capture	Illumina HiSeq	Phase_I	152208821	NM_001164507	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																					0.488	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
NEB	4703	broad.mit.edu	37	2	152528930	152528930	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:152528930C>T	ENST00000172853.10	-	37	4399	c.4252G>A	c.(4252-4254)Gcc>Acc	p.A1418T	NEB_ENST00000604864.1_Missense_Mutation_p.A1418T|NEB_ENST00000397345.3_Missense_Mutation_p.A1418T|NEB_ENST00000427231.2_Missense_Mutation_p.A1418T|NEB_ENST00000409198.1_Missense_Mutation_p.A1418T|NEB_ENST00000603639.1_Missense_Mutation_p.A1418T			P20929	NEBU_HUMAN	nebulin	1418					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.A1418T(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)		AGACTCATGGCGTCAGGTAGG	0.443																																					p.A1418T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4252A	2						.						170.0	158.0	162.0					2																	152528930		2045	4201	6246	152237176	SO:0001583	missense	4703	exon37			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.4252G>A	2.37:g.152528930C>T	ENSP00000172853:p.Ala1418Thr	Somatic		Capture	Illumina HiSeq	Phase_I	152237176	NM_001164507	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	C	8.833	0.940383	0.18281	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.32023	1.47;1.47;1.47;1.47	5.92	5.04	0.67666	.	0.127845	0.53938	D	0.000051	T	0.34337	0.0894	M	0.79475	2.455	0.09310	N	0.999995	P	0.48162	0.906	B	0.38842	0.283	T	0.38845	-0.9642	10	0.38643	T	0.18	.	13.5257	0.61593	0.1242:0.7563:0.1195:0.0	.	1418	P20929	NEBU_HUMAN	T	1418	ENSP00000386259:A1418T;ENSP00000380505:A1418T;ENSP00000416578:A1418T;ENSP00000172853:A1418T	ENSP00000172853:A1418T	A	-	1	0	NEB	152237176	0.672000	0.27530	0.276000	0.24689	0.076000	0.17211	0.856000	0.27818	1.499000	0.48617	0.650000	0.86243	GCC		0.443	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
ACVR1	90	broad.mit.edu	37	2	158594162	158594162	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:158594162C>A	ENST00000263640.3	-	11	1840	c.1411G>T	c.(1411-1413)Gcc>Tcc	p.A471S	ACVR1_ENST00000410057.2_Missense_Mutation_p.A471S|ACVR1_ENST00000409283.2_Missense_Mutation_p.A471S|AC019186.1_ENST00000447019.1_lincRNA|ACVR1_ENST00000434821.1_Missense_Mutation_p.A471S	NM_001105.4	NP_001096.1	Q04771	ACVR1_HUMAN	activin A receptor, type I	471	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|acute inflammatory response (GO:0002526)|atrial septum primum morphogenesis (GO:0003289)|BMP signaling pathway (GO:0030509)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to glucocorticoid stimulus (GO:0071385)|determination of left/right symmetry (GO:0007368)|embryonic heart tube morphogenesis (GO:0003143)|endocardial cushion cell fate commitment (GO:0061445)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation with mouth forming second (GO:0001702)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|mesoderm formation (GO:0001707)|mitral valve morphogenesis (GO:0003183)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of signal transduction (GO:0009968)|neural crest cell migration (GO:0001755)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|peptidyl-threonine phosphorylation (GO:0018107)|pharyngeal system development (GO:0060037)|positive regulation of bone mineralization (GO:0030501)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of ossification (GO:0030278)|regulation of skeletal muscle tissue development (GO:0048641)|smooth muscle cell differentiation (GO:0051145)|transforming growth factor beta receptor signaling pathway (GO:0007179)|urogenital system development (GO:0001655)	activin receptor complex (GO:0048179)|apical part of cell (GO:0045177)|integral component of plasma membrane (GO:0005887)	activin binding (GO:0048185)|activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|peptide hormone binding (GO:0017046)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type I (GO:0005025)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)	p.A471S(1)		endometrium(4)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(2)	19				BRCA - Breast invasive adenocarcinoma(221;0.104)	Adenosine triphosphate(DB00171)	ATTAGCTTGGCCAGAGAGGTT	0.418																																					p.A471S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1411T	2						.						139.0	129.0	132.0					2																	158594162		2203	4300	6503	158302408	SO:0001583	missense	90	exon11				CCDS2206.1	2q23-q24	2008-06-13			ENSG00000115170	ENSG00000115170			171	protein-coding gene	gene with protein product		102576		ACVRLK2		8397373	Standard	NM_001105		Approved	SKR1, ALK2, ACVR1A	uc010fog.2	Q04771	OTTHUMG00000131967	ENST00000263640.3:c.1411G>T	2.37:g.158594162C>A	ENSP00000263640:p.Ala471Ser	Somatic		Capture	Illumina HiSeq	Phase_I	158302408	NM_001111067		Missense_Mutation	SNP	ENST00000263640.3	37	CCDS2206.1	.	.	.	.	.	.	.	.	.	.	C	11.52	1.661865	0.29515	.	.	ENSG00000115170	ENST00000263640;ENST00000409283;ENST00000434821;ENST00000410057	T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17	6.16	6.16	0.99307	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.140531	0.64402	D	0.000004	T	0.60547	0.2277	N	0.25485	0.75	0.80722	D	1	B	0.24675	0.109	B	0.40982	0.345	T	0.51293	-0.8724	10	0.12103	T	0.63	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	471	Q04771	ACVR1_HUMAN	S	471	ENSP00000263640:A471S;ENSP00000387273:A471S;ENSP00000405004:A471S;ENSP00000387127:A471S	ENSP00000263640:A471S	A	-	1	0	ACVR1	158302408	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.937000	0.99478	0.650000	0.86243	GCC		0.418	ACVR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254927.1	NM_001105	
GRB14	2888	broad.mit.edu	37	2	165365358	165365358	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:165365358G>A	ENST00000263915.3	-	7	1359	c.821C>T	c.(820-822)cCg>cTg	p.P274L	GRB14_ENST00000543549.1_Missense_Mutation_p.P187L	NM_004490.2	NP_004481.2	Q14449	GRB14_HUMAN	growth factor receptor-bound protein 14	274	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				blood coagulation (GO:0007596)|leukocyte migration (GO:0050900)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)	p.P274L(1)		breast(3)|endometrium(2)|large_intestine(6)|lung(10)|ovary(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32						CAAATGCCGCGGTTCCTTAAA	0.328																																					p.P274L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C821T	2						.						75.0	77.0	76.0					2																	165365358		2203	4300	6503	165073604	SO:0001583	missense	2888	exon7				CCDS2222.1	2q22-q24	2013-02-14			ENSG00000115290	ENSG00000115290		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	4565	protein-coding gene	gene with protein product		601524				8812444	Standard	XM_005246477		Approved		uc002ucl.3	Q14449	OTTHUMG00000132135	ENST00000263915.3:c.821C>T	2.37:g.165365358G>A	ENSP00000263915:p.Pro274Leu	Somatic		Capture	Illumina HiSeq	Phase_I	165073604	NM_004490	B7Z7F9|Q7Z6I1	Missense_Mutation	SNP	ENST00000263915.3	37	CCDS2222.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.081964	0.76528	.	.	ENSG00000115290	ENST00000263915;ENST00000543549;ENST00000446413	T;T;T	0.78595	-1.19;-1.19;-1.19	5.93	5.93	0.95920	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.047272	0.85682	D	0.000000	D	0.88625	0.6487	M	0.79123	2.44	0.80722	D	1	D;D	0.89917	0.999;1.0	P;D	0.81914	0.899;0.995	D	0.89101	0.3489	10	0.87932	D	0	-11.7154	18.5116	0.90918	0.0:0.0:1.0:0.0	.	187;274	B7Z7F9;Q14449	.;GRB14_HUMAN	L	274;187;229	ENSP00000263915:P274L;ENSP00000443699:P187L;ENSP00000416786:P229L	ENSP00000263915:P274L	P	-	2	0	GRB14	165073604	1.000000	0.71417	1.000000	0.80357	0.627000	0.37826	9.188000	0.94921	2.803000	0.96430	0.650000	0.86243	CCG		0.328	GRB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255180.2		
SCN9A	6335	broad.mit.edu	37	2	167084213	167084213	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:167084213C>T	ENST00000409435.1	-	22	4226	c.4227G>A	c.(4225-4227)acG>acA	p.T1409T	SCN9A_ENST00000409672.1_Silent_p.T1398T|SCN9A_ENST00000375387.4_Silent_p.T1410T|AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Silent_p.T1410T			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	1409					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)	p.T1398T(1)		NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	ACATAATAATCGTCCATCCCT	0.274																																					p.T1398T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G4194A	2						.						55.0	50.0	52.0					2																	167084213		1796	4050	5846	166792459	SO:0001819	synonymous_variant	6335	exon23			X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10597	protein-coding gene	gene with protein product		603415	"""sodium channel, voltage-gated, type IX, alpha polypeptide"""			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.4227G>A	2.37:g.167084213C>T		Somatic		Capture	Illumina HiSeq	Phase_I	166792459	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Silent	SNP	ENST00000409435.1	37	CCDS46441.1																																																																																				0.274	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977	
XIRP2	129446	broad.mit.edu	37	2	168107296	168107296	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:168107296C>T	ENST00000409195.1	+	9	9483	c.9394C>T	c.(9394-9396)Cga>Tga	p.R3132*	XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000295237.9_Nonsense_Mutation_p.R3132*|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409273.1_Nonsense_Mutation_p.R2910*	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2957					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)		p.R3132*(1)		NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TACTGCCCGACGAACAGAAAA	0.433																																					p.R2910X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C8728T	2						.						79.0	76.0	77.0					2																	168107296		1854	4085	5939	167815542	SO:0001587	stop_gained	129446	exon7			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.9394C>T	2.37:g.168107296C>T	ENSP00000386840:p.Arg3132*	Somatic		Capture	Illumina HiSeq	Phase_I	167815542	NM_001199144	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Nonsense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	C	48	14.509185	0.99798	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	.	.	.	5.88	1.93	0.25924	.	0.235594	0.36444	N	0.002586	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.3638	9.5944	0.39565	0.4152:0.5188:0.0:0.0661	.	.	.	.	X	3132;3132;2910;546	.	ENSP00000295237:R3132X	R	+	1	2	XIRP2	167815542	0.726000	0.28059	0.012000	0.15200	0.025000	0.11179	1.235000	0.32671	0.066000	0.16515	0.557000	0.71058	CGA		0.433	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
STK39	27347	broad.mit.edu	37	2	168931676	168931676	+	Silent	SNP	A	A	G	rs201897996		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:168931676A>G	ENST00000355999.4	-	11	1860	c.1155T>C	c.(1153-1155)agT>agC	p.S385S	STK39_ENST00000487143.1_5'UTR	NM_013233.2	NP_037365.2	Q9UEW8	STK39_HUMAN	serine threonine kinase 39	385					cellular hypotonic response (GO:0071476)|intracellular signal transduction (GO:0035556)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of rubidium ion transmembrane transporter activity (GO:2000687)|negative regulation of rubidium ion transport (GO:2000681)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of potassium ion transport (GO:0043268)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|response to stress (GO:0006950)|signal transduction by phosphorylation (GO:0023014)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)	p.S385S(2)		central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(3)|prostate(2)|skin(2)	13						TCTCGTCGTCACTCCACTCCC	0.443																																					p.S385S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T1155C	2						.						195.0	192.0	193.0					2																	168931676		1978	4174	6152	168639922	SO:0001819	synonymous_variant	27347	exon11			AF099989	CCDS42770.1	2q24.3	2010-06-25	2010-06-25		ENSG00000198648	ENSG00000198648			17717	protein-coding gene	gene with protein product	"""STE20/SPS1 homolog (yeast)"""	607648				10980603	Standard	NM_013233		Approved	DCHT, SPAK	uc002uea.3	Q9UEW8	OTTHUMG00000133745	ENST00000355999.4:c.1155T>C	2.37:g.168931676A>G		Somatic		Capture	Illumina HiSeq	Phase_I	168639922	NM_013233	O14774|Q53S90|Q53SL7|Q53SS1|Q9UER4|X5D9C8	Silent	SNP	ENST00000355999.4	37	CCDS42770.1																																																																																				0.443	STK39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258112.2	NM_013233	
STK39	27347	broad.mit.edu	37	2	169038578	169038578	+	Silent	SNP	A	A	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:169038578A>C	ENST00000355999.4	-	2	936	c.231T>G	c.(229-231)gtT>gtG	p.V77V		NM_013233.2	NP_037365.2	Q9UEW8	STK39_HUMAN	serine threonine kinase 39	77	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular hypotonic response (GO:0071476)|intracellular signal transduction (GO:0035556)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of rubidium ion transmembrane transporter activity (GO:2000687)|negative regulation of rubidium ion transport (GO:2000681)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of potassium ion transport (GO:0043268)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|response to stress (GO:0006950)|signal transduction by phosphorylation (GO:0023014)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)	p.V77V(2)		central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(3)|prostate(2)|skin(2)	13						GGGCTGCCTGAACCACAGCAG	0.413																																					p.V77V												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T231G	2						.						175.0	161.0	165.0					2																	169038578		1954	4154	6108	168746824	SO:0001819	synonymous_variant	27347	exon2			AF099989	CCDS42770.1	2q24.3	2010-06-25	2010-06-25		ENSG00000198648	ENSG00000198648			17717	protein-coding gene	gene with protein product	"""STE20/SPS1 homolog (yeast)"""	607648				10980603	Standard	NM_013233		Approved	DCHT, SPAK	uc002uea.3	Q9UEW8	OTTHUMG00000133745	ENST00000355999.4:c.231T>G	2.37:g.169038578A>C		Somatic		Capture	Illumina HiSeq	Phase_I	168746824	NM_013233	O14774|Q53S90|Q53SL7|Q53SS1|Q9UER4|X5D9C8	Silent	SNP	ENST00000355999.4	37	CCDS42770.1																																																																																				0.413	STK39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258112.2	NM_013233	
LRP2	4036	broad.mit.edu	37	2	170083026	170083026	+	Missense_Mutation	SNP	C	C	T	rs145060665	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:170083026C>T	ENST00000263816.3	-	32	5585	c.5300G>A	c.(5299-5301)aGc>aAc	p.S1767N		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1767					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.S1767N(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)"""	AGCATCATTGCTCTTCACCTC	0.358																																					p.S1767N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5300A	2						.	C	ASN/SER	5,4401	9.9+/-24.2	0,5,2198	126.0	120.0	122.0		5300	4.0	1.0	2	dbSNP_134	122	0,8600		0,0,4300	yes	missense	LRP2	NM_004525.2	46	0,5,6498	TT,TC,CC		0.0,0.1135,0.0384	probably-damaging	1767/4656	170083026	5,13001	2203	4300	6503	169791272	SO:0001583	missense	4036	exon32				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.5300G>A	2.37:g.170083026C>T	ENSP00000263816:p.Ser1767Asn	Somatic		Capture	Illumina HiSeq	Phase_I	169791272	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	C	16.16	3.044254	0.55110	0.001135	0.0	ENSG00000081479	ENST00000263816	D	0.89746	-2.56	5.83	4.0	0.46444	Six-bladed beta-propeller, TolB-like (1);	0.236617	0.50627	D	0.000115	D	0.88127	0.6353	L	0.61036	1.89	0.80722	D	1	P	0.47762	0.9	P	0.45946	0.498	D	0.85792	0.1368	10	0.18710	T	0.47	.	14.9814	0.71313	0.0:0.392:0.6079:0.0	.	1767	P98164	LRP2_HUMAN	N	1767	ENSP00000263816:S1767N	ENSP00000263816:S1767N	S	-	2	0	LRP2	169791272	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	1.927000	0.40094	1.464000	0.47987	0.655000	0.94253	AGC		0.358	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
LRP2	4036	broad.mit.edu	37	2	170137025	170137025	+	Silent	SNP	G	G	A	rs369145798	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:170137025G>A	ENST00000263816.3	-	11	1461	c.1176C>T	c.(1174-1176)ggC>ggT	p.G392G	LRP2_ENST00000443831.1_Silent_p.G392G	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	392					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.G392G(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)"""	TGGAGGCCTCGCCAACTAAAT	0.448													G|||	3	0.000599042	0.0023	0.0	5008	,	,		19979	0.0		0.0	False		,,,				2504	0.0				p.G392G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1176T	2						.	G		1,4405	2.1+/-5.4	0,1,2202	40.0	40.0	40.0		1176	-10.8	0.0	2		40	0,8600		0,0,4300	no	coding-synonymous	LRP2	NM_004525.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		392/4656	170137025	1,13005	2203	4300	6503	169845271	SO:0001819	synonymous_variant	4036	exon11				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.1176C>T	2.37:g.170137025G>A		Somatic		Capture	Illumina HiSeq	Phase_I	169845271	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																				0.448	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
PPIG	9360	broad.mit.edu	37	2	170465267	170465267	+	Splice_Site	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:170465267A>G	ENST00000260970.3	+	7	596	c.376A>G	c.(376-378)Ata>Gta	p.I126V	PPIG_ENST00000448752.2_Splice_Site_p.I126V|PPIG_ENST00000409714.3_Splice_Site_p.I111V|PPIG_ENST00000462903.1_Splice_Site_p.I126V	NM_004792.2	NP_004783.2	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G (cyclophilin G)	126	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				protein folding (GO:0006457)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)	p.I126V(1)		NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(17)|ovary(2)|stomach(1)|urinary_tract(1)	43					L-Proline(DB00172)	ACAGTTCTTCATGTAAGTATT	0.438																																					p.I126V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A376G	2						.						85.0	84.0	84.0					2																	170465267		2203	4300	6503	170173513	SO:0001630	splice_region_variant	9360	exon7			X99717	CCDS2235.1	2q31.1	2010-07-23	2006-01-12		ENSG00000138398	ENSG00000138398	6.1.1.16		14650	protein-coding gene	gene with protein product	"""SR-related CTD-associated factor 10"""	606093	"""peptidyl-prolyl isomerase G (cyclophilin G)"""			8973360, 9153302	Standard	NM_004792		Approved	CARS-Cyp, SRCyp, SCAF10	uc002uez.3	Q13427	OTTHUMG00000132206	ENST00000260970.3:c.377+1A>G	2.37:g.170465267A>G		Somatic		Capture	Illumina HiSeq	Phase_I	170173513	NM_004792	D3DPC5|D3DPC6|O00706|Q53R40|Q53SN4|Q96DG9	Missense_Mutation	SNP	ENST00000260970.3	37	CCDS2235.1	.	.	.	.	.	.	.	.	.	.	A	17.15	3.315796	0.60524	.	.	ENSG00000138398	ENST00000260970;ENST00000530133;ENST00000433207;ENST00000409714;ENST00000462903;ENST00000448752;ENST00000414307	T;T;T;T;T;T	0.62232	0.04;0.04;0.04;0.04;0.04;0.04	5.06	5.06	0.68205	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (4);Cyclophilin-like (1);	0.046992	0.85682	D	0.000000	T	0.68439	0.3001	M	0.66297	2.02	0.58432	D	0.999996	B;B;B;P;P	0.42735	0.232;0.147;0.147;0.788;0.627	B;B;B;B;P	0.47528	0.181;0.071;0.071;0.382;0.549	T	0.71961	-0.4434	10	0.54805	T	0.06	-19.0411	15.0955	0.72232	1.0:0.0:0.0:0.0	.	122;111;111;126;126	C9JM79;E9PG73;Q2NKQ6;Q13427-2;Q13427	.;.;.;.;PPIG_HUMAN	V	126;126;122;111;126;126;126	ENSP00000260970:I126V;ENSP00000408683:I122V;ENSP00000386245:I111V;ENSP00000435987:I126V;ENSP00000407083:I126V;ENSP00000402222:I126V	ENSP00000260970:I126V	I	+	1	0	PPIG	170173513	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.359000	0.79477	2.018000	0.59344	0.477000	0.44152	ATA		0.438	PPIG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255264.2		Missense_Mutation
DYNC1I2	1781	broad.mit.edu	37	2	172582555	172582555	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:172582555T>G	ENST00000397119.3	+	9	901	c.734T>G	c.(733-735)tTt>tGt	p.F245C	DYNC1I2_ENST00000409773.1_Missense_Mutation_p.F245C|DYNC1I2_ENST00000358002.6_Missense_Mutation_p.F237C|DYNC1I2_ENST00000409453.1_Missense_Mutation_p.F245C|DYNC1I2_ENST00000263811.4_Missense_Mutation_p.F239C|DYNC1I2_ENST00000508530.1_Missense_Mutation_p.F219C|DYNC1I2_ENST00000409197.1_Missense_Mutation_p.F219C|DYNC1I2_ENST00000410079.3_Missense_Mutation_p.F237C|DYNC1I2_ENST00000340296.4_Missense_Mutation_p.F219C|DYNC1I2_ENST00000409317.1_Missense_Mutation_p.F239C|DYNC1I2_ENST00000534253.2_Missense_Mutation_p.F245C	NM_001378.1	NP_001369.1	Q13409	DC1I2_HUMAN	dynein, cytoplasmic 1, intermediate chain 2	245					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|G2/M transition of mitotic cell cycle (GO:0000086)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|transport (GO:0006810)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|microtubule (GO:0005874)|vesicle (GO:0031982)	microtubule motor activity (GO:0003777)	p.F245C(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)	15			OV - Ovarian serous cystadenocarcinoma(117;0.198)			AACATCTTCTTTGACTATAGT	0.318																																					p.F245C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T734G	2						.						25.0	24.0	25.0					2																	172582555		1804	4076	5880	172290801	SO:0001583	missense	1781	exon9			AK055491	CCDS46450.1, CCDS63054.1, CCDS63056.1, CCDS63057.1	2q31.1	2013-01-10	2005-11-24	2005-11-24	ENSG00000077380	ENSG00000077380		"""Cytoplasmic dyneins"", ""WD repeat domain containing"""	2964	protein-coding gene	gene with protein product		603331	"""dynein, cytoplasmic, intermediate polypeptide 2"""	DNCI2		10049579, 16260502	Standard	NM_001378		Approved		uc002uha.2	Q13409	OTTHUMG00000154061	ENST00000397119.3:c.734T>G	2.37:g.172582555T>G	ENSP00000380308:p.Phe245Cys	Somatic		Capture	Illumina HiSeq	Phase_I	172290801	NM_001378	B7ZA04|D3DPD4|D3DPD5|D3DPD6|Q32LY9|Q53S84|Q5BJF8|Q7Z4X1|Q96NG7|Q96S87|Q9BXZ5|Q9NT58	Missense_Mutation	SNP	ENST00000397119.3	37	CCDS46450.1	.	.	.	.	.	.	.	.	.	.	T	18.97	3.734964	0.69189	.	.	ENSG00000077380	ENST00000452242;ENST00000340296;ENST00000534253;ENST00000263811;ENST00000397119;ENST00000410079;ENST00000508530;ENST00000409197;ENST00000409317;ENST00000409773;ENST00000409453;ENST00000358002;ENST00000435234	T;T;T;T;T;T;T;T;T;T;T	0.76060	-0.83;-0.99;-0.84;-0.76;-0.61;-0.61;-0.83;-0.84;-0.76;-0.63;-0.61	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	D	0.85031	0.5604	M	0.74881	2.28	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.975;0.975;0.975;0.999	D;P;P;P;D	0.66847	0.947;0.854;0.854;0.854;0.928	D	0.84453	0.0589	10	0.38643	T	0.18	-18.4268	16.4781	0.84144	0.0:0.0:0.0:1.0	.	237;239;219;219;245	B7ZA04;Q13409-2;Q13409-6;Q13409-3;Q13409	.;.;.;.;DC1I2_HUMAN	C	239;219;245;239;245;237;219;219;239;245;245;237;219	ENSP00000339430:F219C;ENSP00000433791:F245C;ENSP00000263811:F239C;ENSP00000380308:F245C;ENSP00000386522:F237C;ENSP00000423339:F219C;ENSP00000386397:F219C;ENSP00000386591:F239C;ENSP00000386415:F245C;ENSP00000386886:F245C;ENSP00000350692:F237C	ENSP00000263811:F239C	F	+	2	0	DYNC1I2	172290801	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.013000	0.88655	2.288000	0.76882	0.528000	0.53228	TTT		0.318	DYNC1I2-001	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333683.2	NM_001378	
TTN	7273	broad.mit.edu	37	2	179424742	179424742	+	Missense_Mutation	SNP	C	C	T	rs199788826	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:179424742C>T	ENST00000591111.1	-	276	81418	c.81194G>A	c.(81193-81195)cGa>cAa	p.R27065Q	TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R19833Q|TTN_ENST00000589042.1_Missense_Mutation_p.R28706Q|TTN_ENST00000342992.6_Missense_Mutation_p.R26138Q|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R19766Q|TTN_ENST00000460472.2_Missense_Mutation_p.R19641Q|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA			Q8WZ42	TITIN_HUMAN	titin	27065	Fibronectin type-III 97. {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.R19833Q(1)|p.R26136Q(1)|p.R19641Q(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)			TTCTGTCCCTCGTAAGCTCTG	0.423													C|||	4	0.000798722	0.0	0.0	5008	,	,		21562	0.0		0.0	False		,,,				2504	0.0041				p.E19641K												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.G58921A	2						.						72.0	69.0	70.0					2																	179424742		1862	4090	5952	179132988	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.81194G>A	2.37:g.179424742C>T	ENSP00000465570:p.Arg27065Gln	Somatic		Capture	Illumina HiSeq	Phase_I	179132988	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	13.34	2.208667	0.39003	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.55760	0.5;0.5;0.5;0.5	5.87	4.07	0.47477	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.36413	0.0966	N	0.26130	0.795	0.29479	N	0.856479	P;P;P;B	0.36944	0.574;0.574;0.574;0.271	B;B;B;B	0.28139	0.086;0.086;0.086;0.086	T	0.31447	-0.9943	9	0.87932	D	0	.	10.6386	0.45579	0.0:0.8005:0.0:0.1995	.	19641;19766;19833;27065	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	Q	26138;19641;19833;19766;19638	ENSP00000343764:R26138Q;ENSP00000434586:R19641Q;ENSP00000340554:R19833Q;ENSP00000352154:R19766Q	ENSP00000340554:R19833Q	R	-	2	0	TTN	179132988	1.000000	0.71417	0.883000	0.34634	0.985000	0.73830	3.174000	0.50847	0.919000	0.36945	0.655000	0.94253	CGA		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	broad.mit.edu	37	2	179425740	179425740	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:179425740C>T	ENST00000591111.1	-	276	80420	c.80196G>A	c.(80194-80196)gaG>gaA	p.E26732E	TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Silent_p.E19500E|TTN_ENST00000589042.1_Silent_p.E28373E|TTN_ENST00000342992.6_Silent_p.E25805E|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Silent_p.E19433E|TTN_ENST00000460472.2_Silent_p.E19308E|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA			Q8WZ42	TITIN_HUMAN	titin	26732	Ig-like 128.				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.E19308E(1)|p.E19500E(1)|p.E25803E(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)			TCTTAAGGACCTCTCCAGCTT	0.428																																					p.R19308K												.	.	3	Substitution - coding silent(3)	large_intestine(3)	c.G57923A	2						.						184.0	171.0	175.0					2																	179425740		1937	4126	6063	179133986	SO:0001819	synonymous_variant	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.80196G>A	2.37:g.179425740C>T		Somatic		Capture	Illumina HiSeq	Phase_I	179133986	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																																																																																					0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	broad.mit.edu	37	2	179446655	179446655	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:179446655G>A	ENST00000591111.1	-	265	61742	c.61518C>T	c.(61516-61518)gcC>gcT	p.A20506A	TTN-AS1_ENST00000590743.1_RNA|RP11-171I2.2_ENST00000603521.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Silent_p.A13274A|TTN_ENST00000589042.1_Silent_p.A22147A|TTN_ENST00000342992.6_Silent_p.A19579A|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Silent_p.A13207A|TTN_ENST00000460472.2_Silent_p.A13082A|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA			Q8WZ42	TITIN_HUMAN	titin	20506	Fibronectin type-III 48. {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.A19577A(1)|p.A13082A(1)|p.A13274A(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)			GAGCATAAGCGGCCTTGGATG	0.438																																					p.P13082L												.	.	3	Substitution - coding silent(3)	large_intestine(3)	c.C39245T	2						.						76.0	73.0	74.0					2																	179446655		1921	4132	6053	179154901	SO:0001819	synonymous_variant	7273	exon143			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.61518C>T	2.37:g.179446655G>A		Somatic		Capture	Illumina HiSeq	Phase_I	179154901	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																																																																																					0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
SESTD1	91404	broad.mit.edu	37	2	180036889	180036889	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:180036889C>T	ENST00000428443.3	-	5	643	c.327G>A	c.(325-327)acG>acA	p.T109T	SESTD1_ENST00000486468.1_5'UTR	NM_178123.4	NP_835224.3	Q86VW0	SESD1_HUMAN	SEC14 and spectrin domains 1	109	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.						phosphatidic acid binding (GO:0070300)|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)			breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(3)	30			OV - Ovarian serous cystadenocarcinoma(117;0.0344)|Epithelial(96;0.0531)|all cancers(119;0.147)			AACAAAAATGCGTTACTTTCT	0.308																																					p.T109T												.	.	0			c.G327A	2						.						92.0	96.0	95.0					2																	180036889		2203	4300	6503	179745134	SO:0001819	synonymous_variant	91404	exon5			AK096232	CCDS33338.1	2q31.3	2014-01-28			ENSG00000187231	ENSG00000187231			18379	protein-coding gene	gene with protein product						12837271	Standard	NM_178123		Approved	DKFZp434O0515, Solo	uc002uni.4	Q86VW0	OTTHUMG00000154554	ENST00000428443.3:c.327G>A	2.37:g.180036889C>T		None		Capture	Illumina HiSeq	Phase_I	179745134	NM_178123	Q53R38|Q53SP3|Q5GM69|Q8N6M1|Q96LQ2	Silent	SNP	ENST00000428443.3	37	CCDS33338.1																																																																																				0.308	SESTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335916.2	NM_178123	
MFSD6	54842	broad.mit.edu	37	2	191301134	191301134	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:191301134C>T	ENST00000392328.1	+	3	703	c.379C>T	c.(379-381)Cgc>Tgc	p.R127C	MFSD6_ENST00000281416.7_Missense_Mutation_p.R127C	NM_017694.3	NP_060164.3	Q6ZSS7	MFSD6_HUMAN	major facilitator superfamily domain containing 6	127					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.R127C(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(3)|stomach(1)	23						AGTTGCAGACCGCTTTAAAAA	0.438																																					p.R127C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C379T	2						.						74.0	72.0	73.0					2																	191301134		2203	4300	6503	191009379	SO:0001583	missense	54842	exon3				CCDS2306.1	2q32.2	2008-10-29			ENSG00000151690	ENSG00000151690			24711	protein-coding gene	gene with protein product		613476					Standard	NM_017694		Approved	FLJ20160	uc002urz.2	Q6ZSS7	OTTHUMG00000132671	ENST00000392328.1:c.379C>T	2.37:g.191301134C>T	ENSP00000376141:p.Arg127Cys	Somatic		Capture	Illumina HiSeq	Phase_I	191009379	NM_017694	D3KSZ4|Q86TH2|Q9NXM3	Missense_Mutation	SNP	ENST00000392328.1	37	CCDS2306.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.424628	0.83667	.	.	ENSG00000151690	ENST00000392328;ENST00000445546;ENST00000281416	D;T;D	0.85629	-2.01;-1.41;-2.01	5.39	5.39	0.77823	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	D	0.95639	0.8582	H	0.98178	4.165	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96952	0.9695	10	0.87932	D	0	-19.3267	18.3329	0.90276	0.0:1.0:0.0:0.0	.	127	Q6ZSS7	MFSD6_HUMAN	C	127	ENSP00000376141:R127C;ENSP00000403762:R127C;ENSP00000281416:R127C	ENSP00000281416:R127C	R	+	1	0	MFSD6	191009379	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.651000	0.83577	2.810000	0.96702	0.650000	0.86243	CGC		0.438	MFSD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255931.1		
MFSD6	54842	broad.mit.edu	37	2	191301397	191301397	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:191301397G>T	ENST00000392328.1	+	3	966	c.642G>T	c.(640-642)ttG>ttT	p.L214F	MFSD6_ENST00000281416.7_Missense_Mutation_p.L214F	NM_017694.3	NP_060164.3	Q6ZSS7	MFSD6_HUMAN	major facilitator superfamily domain containing 6	214					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.L214F(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(3)|stomach(1)	23						CCGTTACTTTGCCAACAGCTC	0.433																																					p.L214F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G642T	2						.						83.0	85.0	85.0					2																	191301397		2203	4300	6503	191009642	SO:0001583	missense	54842	exon3				CCDS2306.1	2q32.2	2008-10-29			ENSG00000151690	ENSG00000151690			24711	protein-coding gene	gene with protein product		613476					Standard	NM_017694		Approved	FLJ20160	uc002urz.2	Q6ZSS7	OTTHUMG00000132671	ENST00000392328.1:c.642G>T	2.37:g.191301397G>T	ENSP00000376141:p.Leu214Phe	Somatic		Capture	Illumina HiSeq	Phase_I	191009642	NM_017694	D3KSZ4|Q86TH2|Q9NXM3	Missense_Mutation	SNP	ENST00000392328.1	37	CCDS2306.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.713191	0.00094	.	.	ENSG00000151690	ENST00000392328;ENST00000281416	T;T	0.32515	1.45;1.45	5.54	-6.19	0.02078	Major facilitator superfamily domain, general substrate transporter (1);	1.136750	0.06137	N	0.671706	T	0.09598	0.0236	N	0.03324	-0.35	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.28396	-1.0045	10	0.09084	T	0.74	-0.2749	4.9113	0.13823	0.0947:0.2901:0.4548:0.1604	.	214	Q6ZSS7	MFSD6_HUMAN	F	214	ENSP00000376141:L214F;ENSP00000281416:L214F	ENSP00000281416:L214F	L	+	3	2	MFSD6	191009642	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.054000	0.03496	-1.397000	0.02068	-1.069000	0.02264	TTG		0.433	MFSD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255931.1		
DNAH7	56171	broad.mit.edu	37	2	196889164	196889164	+	Silent	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:196889164G>T	ENST00000312428.6	-	8	832	c.732C>A	c.(730-732)gcC>gcA	p.A244A	DNAH7_ENST00000410072.1_Silent_p.A244A	NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	244	Stem. {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.A244A(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						CAGCACGATGGGCTGGAAGTT	0.299																																					p.A244A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C732A	2						.						86.0	85.0	85.0					2																	196889164		1821	4080	5901	196597409	SO:0001819	synonymous_variant	56171	exon8			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.732C>A	2.37:g.196889164G>T		Somatic		Capture	Illumina HiSeq	Phase_I	196597409	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Silent	SNP	ENST00000312428.6	37	CCDS42794.1																																																																																				0.299	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897	
CCNYL1	151195	broad.mit.edu	37	2	208611934	208611934	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:208611934A>G	ENST00000295414.3	+	8	1014	c.803A>G	c.(802-804)gAc>gGc	p.D268G	CCNYL1_ENST00000392209.3_Missense_Mutation_p.D198G|CCNYL1_ENST00000339882.5_Missense_Mutation_p.D217G			Q8N7R7	CCYL1_HUMAN	cyclin Y-like 1	268					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)			p.D198G(1)		endometrium(1)|large_intestine(1)|lung(3)	5				LUSC - Lung squamous cell carcinoma(261;0.0731)|Epithelial(149;0.139)|Lung(261;0.14)		ACAGTTGAGGACATGTGAGTT	0.378																																					p.D198G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A593G	2						.						104.0	95.0	98.0					2																	208611934		2203	4300	6503	208320179	SO:0001583	missense	151195	exon9			AK095479	CCDS2377.1, CCDS46503.1	2q33.3	2008-02-05			ENSG00000163249	ENSG00000163249			26868	protein-coding gene	gene with protein product							Standard	NM_152523		Approved	FLJ40432	uc002vci.3	Q8N7R7	OTTHUMG00000132946	ENST00000295414.3:c.803A>G	2.37:g.208611934A>G	ENSP00000295414:p.Asp268Gly	Somatic		Capture	Illumina HiSeq	Phase_I	208320179	NM_152523	Q6NX60	Missense_Mutation	SNP	ENST00000295414.3	37		.	.	.	.	.	.	.	.	.	.	A	26.0	4.691259	0.88735	.	.	ENSG00000163249	ENST00000392209;ENST00000295414;ENST00000339882;ENST00000420321	T;T;T;T	0.12465	2.68;2.68;2.68;2.68	5.42	5.42	0.78866	Cyclin, N-terminal (1);Cyclin-like (3);	0.000000	0.85682	U	0.000000	T	0.41213	0.1149	M	0.87328	2.875	0.80722	D	1	D;D	0.59767	0.965;0.986	P;P	0.61874	0.89;0.895	T	0.47898	-0.9081	10	0.72032	D	0.01	.	15.9034	0.79400	1.0:0.0:0.0:0.0	.	217;268	Q8N7R7-2;Q8N7R7	.;CCYL1_HUMAN	G	198;268;217;78	ENSP00000376045:D198G;ENSP00000295414:D268G;ENSP00000342344:D217G;ENSP00000396072:D78G	ENSP00000295414:D268G	D	+	2	0	CCNYL1	208320179	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.247000	0.95444	2.210000	0.71456	0.444000	0.29173	GAC		0.378	CCNYL1-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000337062.1	NM_152523	
IDH1	3417	broad.mit.edu	37	2	209116179	209116179	+	Missense_Mutation	SNP	G	G	A	rs555882127		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:209116179G>A	ENST00000415913.1	-	3	478	c.97C>T	c.(97-99)Ccc>Tcc	p.P33S	IDH1_ENST00000446179.1_Missense_Mutation_p.P33S|IDH1_ENST00000345146.2_Missense_Mutation_p.P33S	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	33					2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.P33S(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		TCCACGTAGGGAAAAATGAGT	0.423			Mis		gliobastoma								G|||	1	0.000199681	0.0	0.0	5008	,	,		16229	0.0		0.0	False		,,,				2504	0.001				p.P33S	Pancreas(158;264 1958 3300 35450 36047)		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C97T	2						.						69.0	66.0	67.0					2																	209116179		2203	4300	6503	208824424	SO:0001583	missense	3417	exon3				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.97C>T	2.37:g.209116179G>A	ENSP00000390265:p.Pro33Ser	Somatic		Capture	Illumina HiSeq	Phase_I	208824424	NM_005896	Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.996120	0.93167	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282;ENST00000417583;ENST00000451391	T;T;T;T;T;T	0.77358	-1.09;-1.09;-1.09;-1.09;-1.09;-1.09	5.21	5.21	0.72293	Isopropylmalate dehydrogenase-like domain (2);	0.050326	0.85682	D	0.000000	D	0.90834	0.7121	M	0.91510	3.215	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.92613	0.6101	10	0.66056	D	0.02	-5.5475	18.7632	0.91862	0.0:0.0:1.0:0.0	.	33	O75874	IDHC_HUMAN	S	33	ENSP00000260985:P33S;ENSP00000410513:P33S;ENSP00000390265:P33S;ENSP00000391075:P33S;ENSP00000409045:P33S;ENSP00000396787:P33S	ENSP00000260985:P33S	P	-	1	0	IDH1	208824424	1.000000	0.71417	0.979000	0.43373	0.992000	0.81027	9.262000	0.95591	2.423000	0.82170	0.650000	0.86243	CCC		0.423	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1		
PTH2R	5746	broad.mit.edu	37	2	209353841	209353841	+	Missense_Mutation	SNP	G	G	A	rs553009188		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:209353841G>A	ENST00000272847.2	+	11	1394	c.1181G>A	c.(1180-1182)cGc>cAc	p.R394H	AC019185.4_ENST00000424628.1_RNA|PTH2R_ENST00000413482.1_3'UTR	NM_005048.2	NP_005039.1	P49190	PTH2R_HUMAN	parathyroid hormone 2 receptor	394					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	parathyroid hormone receptor activity (GO:0004991)	p.R394H(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(21)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43				Epithelial(149;0.0684)|Lung(261;0.0785)|LUSC - Lung squamous cell carcinoma(261;0.0836)	Preotact(DB05829)	TGGGAGATCCGCATGCACTGT	0.488																																					p.R394H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1181A	2						.						192.0	171.0	178.0					2																	209353841		2203	4300	6503	209062086	SO:0001583	missense	5746	exon11			BC036811	CCDS2383.1	2q33	2012-08-10	2007-08-24	2007-08-24	ENSG00000144407	ENSG00000144407		"""GPCR / Class B : Parathyroid hormone receptors"""	9609	protein-coding gene	gene with protein product		601469	"""parathyroid hormone receptor 2"""	PTHR2			Standard	NM_005048		Approved		uc002vdb.4	P49190	OTTHUMG00000132960	ENST00000272847.2:c.1181G>A	2.37:g.209353841G>A	ENSP00000272847:p.Arg394His	Somatic		Capture	Illumina HiSeq	Phase_I	209062086	NM_005048	Q8N429	Missense_Mutation	SNP	ENST00000272847.2	37	CCDS2383.1	.	.	.	.	.	.	.	.	.	.	G	19.05	3.751743	0.69533	.	.	ENSG00000144407	ENST00000272847	T	0.46451	0.87	5.75	5.75	0.90469	GPCR, family 2-like (1);	0.000000	0.45606	D	0.000351	T	0.65790	0.2725	M	0.74647	2.275	0.44880	D	0.997892	D;D	0.89917	1.0;1.0	D;D	0.83275	0.994;0.996	T	0.64795	-0.6323	9	.	.	.	.	17.4417	0.87566	0.0:0.0:1.0:0.0	.	283;394	B4DFN8;P49190	.;PTH2R_HUMAN	H	394	ENSP00000272847:R394H	.	R	+	2	0	PTH2R	209062086	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.048000	0.49862	2.712000	0.92718	0.591000	0.81541	CGC		0.488	PTH2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256519.2	NM_005048	
APOB	338	broad.mit.edu	37	2	21252574	21252574	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:21252574C>T	ENST00000233242.1	-	12	1681	c.1554G>A	c.(1552-1554)aaG>aaA	p.K518K	APOB_ENST00000399256.4_Silent_p.K518K	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	518	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)	p.K518K(1)		NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCAGTGATGGCTTTGTACTTT	0.433																																					p.K518K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1554A	2						.						199.0	182.0	188.0					2																	21252574		2203	4300	6503	21106079	SO:0001819	synonymous_variant	338	exon12			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.1554G>A	2.37:g.21252574C>T		Somatic		Capture	Illumina HiSeq	Phase_I	21106079	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Silent	SNP	ENST00000233242.1	37	CCDS1703.1																																																																																				0.433	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
MAP2	4133	broad.mit.edu	37	2	210560965	210560965	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:210560965A>T	ENST00000360351.4	+	7	4577	c.4071A>T	c.(4069-4071)gaA>gaT	p.E1357D	MAP2_ENST00000447185.1_Missense_Mutation_p.E1353D|MAP2_ENST00000199940.6_Intron|MAP2_ENST00000361559.4_Intron|MAP2_ENST00000392194.1_Intron	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	1357					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)	p.E1357D(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	CTGAGAGAGAAGAGGTTGCAC	0.498																																					p.E1357D	Pancreas(27;423 979 28787 29963)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A4071T	2						.						78.0	90.0	86.0					2																	210560965		2203	4299	6502	210269210	SO:0001583	missense	4133	exon7				CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"""A-kinase anchor proteins"""	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.4071A>T	2.37:g.210560965A>T	ENSP00000353508:p.Glu1357Asp	Somatic		Capture	Illumina HiSeq	Phase_I	210269210	NM_002374	Q17S04|Q8IUX2|Q99975|Q99976	Missense_Mutation	SNP	ENST00000360351.4	37	CCDS2384.1	.	.	.	.	.	.	.	.	.	.	A	15.48	2.846522	0.51164	.	.	ENSG00000078018	ENST00000360351;ENST00000447185	T;T	0.24723	1.84;1.84	5.82	0.752	0.18398	MAP2/Tau projection (1);	0.102493	0.42964	D	0.000627	T	0.39627	0.1085	M	0.61703	1.905	0.41646	D	0.989103	D;D	0.76494	0.998;0.999	D;D	0.80764	0.99;0.994	T	0.15809	-1.0424	10	0.62326	D	0.03	-12.5564	5.2649	0.15593	0.55:0.1438:0.3062:0.0	.	1353;1357	P11137-3;P11137	.;MAP2_HUMAN	D	1357;1353	ENSP00000353508:E1357D;ENSP00000392164:E1353D	ENSP00000353508:E1357D	E	+	3	2	MAP2	210269210	1.000000	0.71417	0.996000	0.52242	0.848000	0.48234	2.165000	0.42396	0.109000	0.17891	0.528000	0.53228	GAA		0.498	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538	
RNF25	64320	broad.mit.edu	37	2	219538364	219538364	+	5'Flank	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:219538364T>C	ENST00000295704.2	-	0	0				STK36_ENST00000392105.3_Missense_Mutation_p.F34S|STK36_ENST00000440309.1_Missense_Mutation_p.F34S|STK36_ENST00000392106.2_Missense_Mutation_p.F34S|STK36_ENST00000295709.3_Missense_Mutation_p.F34S	NM_022453.2	NP_071898.2	Q96BH1	RNF25_HUMAN	ring finger protein 25						positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|NF-kappaB binding (GO:0051059)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.F34S(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24		Renal(207;0.0474)		Epithelial(149;6.99e-07)|all cancers(144;0.000129)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCCCTGAAGTTCATCCCAAAA	0.463																																					p.F34S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T101C	2						.						60.0	60.0	60.0					2																	219538364		2203	4300	6503	219246608	SO:0001631	upstream_gene_variant	27148	exon3				CCDS2420.1	2q35	2008-02-05			ENSG00000163481	ENSG00000163481		"""RING-type (C3HC4) zinc fingers"""	14662	protein-coding gene	gene with protein product						12748188	Standard	NM_022453		Approved	AO7, FLJ13906	uc002vit.3	Q96BH1	OTTHUMG00000133077		2.37:g.219538364T>C	Exception_encountered	Somatic		Capture	Illumina HiSeq	Phase_I	219246608	NM_015690	A8K0D6|Q53HQ5|Q9H874	Missense_Mutation	SNP	ENST00000295704.2	37	CCDS2420.1	.	.	.	.	.	.	.	.	.	.	T	29.9	5.049648	0.93740	.	.	ENSG00000163482	ENST00000295709;ENST00000392106;ENST00000392105;ENST00000440309;ENST00000424080	T;T;T;T;D	0.82526	1.87;1.87;1.87;1.87;-1.62	5.71	5.71	0.89125	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	0.47852	D	0.000215	D	0.84813	0.5555	N	0.17312	0.475	0.80722	D	1	D;D	0.89917	1.0;0.978	D;D	0.91635	0.999;0.963	D	0.87648	0.2526	10	0.87932	D	0	-24.6872	16.0044	0.80349	0.0:0.0:0.0:1.0	.	34;34	Q9NRP7-2;Q9NRP7	.;STK36_HUMAN	S	34	ENSP00000295709:F34S;ENSP00000375955:F34S;ENSP00000375954:F34S;ENSP00000394095:F34S;ENSP00000403527:F34S	ENSP00000295709:F34S	F	+	2	0	STK36	219246608	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.813000	0.86123	2.191000	0.70037	0.528000	0.53228	TTC		0.463	RNF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256721.1	NM_022453	
SLC4A3	6508	broad.mit.edu	37	2	220497674	220497674	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:220497674A>C	ENST00000358055.3	+	9	1732	c.1220A>C	c.(1219-1221)gAc>gCc	p.D407A	SLC4A3_ENST00000373760.2_Missense_Mutation_p.D407A|SLC4A3_ENST00000273063.6_Missense_Mutation_p.D434A|SLC4A3_ENST00000373762.3_Missense_Mutation_p.D434A|SLC4A3_ENST00000317151.3_Missense_Mutation_p.D407A			P48751	B3A3_HUMAN	solute carrier family 4 (anion exchanger), member 3	407					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)	p.D434A(1)		breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	51		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		ATTGTGTCTGACCAGATCCGG	0.647																																					p.D407A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1220C	2						.						80.0	68.0	72.0					2																	220497674		2203	4300	6503	220205918	SO:0001583	missense	6508	exon9				CCDS2445.1, CCDS2446.1	2q35	2013-07-19	2013-07-19		ENSG00000114923	ENSG00000114923		"""Solute carriers"""	11029	protein-coding gene	gene with protein product	"""Anion exchanger 3, neuronal"""	106195	"""solute carrier family 4, anion exchanger, member 3"""			8001971	Standard	NM_005070		Approved	AE3, SLC2C	uc002vmo.4	P48751	OTTHUMG00000059238	ENST00000358055.3:c.1220A>C	2.37:g.220497674A>C	ENSP00000350756:p.Asp407Ala	Somatic		Capture	Illumina HiSeq	Phase_I	220205918	NM_005070	A6H8L2|A8K1Q9|B7ZVX6|B9EGD1|Q6YIQ9	Missense_Mutation	SNP	ENST00000358055.3	37	CCDS2445.1	.	.	.	.	.	.	.	.	.	.	A	27.5	4.838494	0.91117	.	.	ENSG00000114923	ENST00000358055;ENST00000373760;ENST00000273063;ENST00000373762;ENST00000317151;ENST00000413743	T;T;T;T;T;T	0.69926	-0.44;-0.44;-0.44;-0.44;-0.44;-0.44	4.72	4.72	0.59763	Bicarbonate transporter, cytoplasmic (2);Phosphotransferase/anion transporter (1);	0.053566	0.64402	D	0.000001	T	0.82250	0.4996	M	0.89287	3.02	0.80722	D	1	D;D	0.56035	0.974;0.968	P;P	0.60541	0.876;0.804	D	0.86261	0.1655	10	0.87932	D	0	.	14.2312	0.65892	1.0:0.0:0.0:0.0	.	407;434	P48751;P48751-3	B3A3_HUMAN;.	A	407;407;434;434;407;209	ENSP00000350756:D407A;ENSP00000362865:D407A;ENSP00000273063:D434A;ENSP00000362867:D434A;ENSP00000314006:D407A;ENSP00000414722:D209A	ENSP00000273063:D434A	D	+	2	0	SLC4A3	220205918	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	9.331000	0.96430	1.758000	0.51981	0.523000	0.50628	GAC		0.647	SLC4A3-009	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316472.1	NM_005070	
SLC4A3	6508	broad.mit.edu	37	2	220499297	220499297	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:220499297C>T	ENST00000358055.3	+	12	2229	c.1717C>T	c.(1717-1719)Cgc>Tgc	p.R573C	SLC4A3_ENST00000373760.2_Missense_Mutation_p.R573C|SLC4A3_ENST00000273063.6_Missense_Mutation_p.R600C|SLC4A3_ENST00000373762.3_Missense_Mutation_p.R600C|SLC4A3_ENST00000317151.3_Missense_Mutation_p.R573C			P48751	B3A3_HUMAN	solute carrier family 4 (anion exchanger), member 3	573					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)	p.R600C(1)		breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	51		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CGAGCTTGGGCGCTCCATTGC	0.602																																					p.R573C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1717T	2						.						69.0	57.0	61.0					2																	220499297		2203	4300	6503	220207541	SO:0001583	missense	6508	exon12				CCDS2445.1, CCDS2446.1	2q35	2013-07-19	2013-07-19		ENSG00000114923	ENSG00000114923		"""Solute carriers"""	11029	protein-coding gene	gene with protein product	"""Anion exchanger 3, neuronal"""	106195	"""solute carrier family 4, anion exchanger, member 3"""			8001971	Standard	NM_005070		Approved	AE3, SLC2C	uc002vmo.4	P48751	OTTHUMG00000059238	ENST00000358055.3:c.1717C>T	2.37:g.220499297C>T	ENSP00000350756:p.Arg573Cys	Somatic		Capture	Illumina HiSeq	Phase_I	220207541	NM_005070	A6H8L2|A8K1Q9|B7ZVX6|B9EGD1|Q6YIQ9	Missense_Mutation	SNP	ENST00000358055.3	37	CCDS2445.1	.	.	.	.	.	.	.	.	.	.	C	32	5.184361	0.94885	.	.	ENSG00000114923	ENST00000358055;ENST00000373760;ENST00000273063;ENST00000373762;ENST00000317151	D;D;D;D;D	0.85088	-1.94;-1.94;-1.94;-1.94;-1.94	4.75	4.75	0.60458	Bicarbonate transporter, cytoplasmic (2);Phosphotransferase/anion transporter (1);	0.000000	0.85682	D	0.000000	D	0.95017	0.8387	H	0.96398	3.815	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	0.96627	0.9464	10	0.87932	D	0	.	17.9543	0.89063	0.0:1.0:0.0:0.0	.	277;573;600	P48751-2;P48751;P48751-3	.;B3A3_HUMAN;.	C	573;573;600;600;573	ENSP00000350756:R573C;ENSP00000362865:R573C;ENSP00000273063:R600C;ENSP00000362867:R600C;ENSP00000314006:R573C	ENSP00000273063:R600C	R	+	1	0	SLC4A3	220207541	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.534000	0.82004	2.471000	0.83476	0.655000	0.94253	CGC		0.602	SLC4A3-009	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316472.1	NM_005070	
SLC4A3	6508	broad.mit.edu	37	2	220504356	220504356	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:220504356C>T	ENST00000358055.3	+	20	3688	c.3176C>T	c.(3175-3177)gCg>gTg	p.A1059V	SLC4A3_ENST00000373760.2_Missense_Mutation_p.A1059V|SLC4A3_ENST00000273063.6_Missense_Mutation_p.A1086V|SLC4A3_ENST00000373762.3_Missense_Mutation_p.A1086V|SLC4A3_ENST00000317151.3_Missense_Mutation_p.A1059V			P48751	B3A3_HUMAN	solute carrier family 4 (anion exchanger), member 3	1059	Membrane (anion exchange).				bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)	p.A1086V(1)		breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	51		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CATGTCAATGCGTTGACAGTG	0.652																																					p.A1059V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3176T	2						.						71.0	61.0	65.0					2																	220504356		2203	4300	6503	220212600	SO:0001583	missense	6508	exon20				CCDS2445.1, CCDS2446.1	2q35	2013-07-19	2013-07-19		ENSG00000114923	ENSG00000114923		"""Solute carriers"""	11029	protein-coding gene	gene with protein product	"""Anion exchanger 3, neuronal"""	106195	"""solute carrier family 4, anion exchanger, member 3"""			8001971	Standard	NM_005070		Approved	AE3, SLC2C	uc002vmo.4	P48751	OTTHUMG00000059238	ENST00000358055.3:c.3176C>T	2.37:g.220504356C>T	ENSP00000350756:p.Ala1059Val	Somatic		Capture	Illumina HiSeq	Phase_I	220212600	NM_005070	A6H8L2|A8K1Q9|B7ZVX6|B9EGD1|Q6YIQ9	Missense_Mutation	SNP	ENST00000358055.3	37	CCDS2445.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.144332	0.77888	.	.	ENSG00000114923	ENST00000358055;ENST00000373760;ENST00000273063;ENST00000373762;ENST00000356251;ENST00000317151	D;D;D;D;D	0.81579	-1.51;-1.51;-1.51;-1.51;-1.51	4.38	4.38	0.52667	Bicarbonate transporter, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.92519	0.7624	H	0.94264	3.515	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.87578	0.985;0.998;0.995	D	0.94709	0.7890	10	0.87932	D	0	.	17.5373	0.87835	0.0:1.0:0.0:0.0	.	763;1059;1086	P48751-2;P48751;P48751-3	.;B3A3_HUMAN;.	V	1059;1059;1086;1086;319;1059	ENSP00000350756:A1059V;ENSP00000362865:A1059V;ENSP00000273063:A1086V;ENSP00000362867:A1086V;ENSP00000314006:A1059V	ENSP00000273063:A1086V	A	+	2	0	SLC4A3	220212600	1.000000	0.71417	0.331000	0.25455	0.278000	0.26855	7.439000	0.80444	2.431000	0.82371	0.539000	0.68188	GCG		0.652	SLC4A3-009	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316472.1	NM_005070	
SPHKAP	80309	broad.mit.edu	37	2	228846527	228846527	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:228846527T>C	ENST00000392056.3	-	12	5055	c.5009A>G	c.(5008-5010)gAt>gGt	p.D1670G	SPHKAP_ENST00000344657.5_Missense_Mutation_p.D1641G	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	1670						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)	p.D1689G(1)		NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		ATGGAAGATATCACCCACTTT	0.478																																					p.D1670G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A5009G	2						.						103.0	93.0	97.0					2																	228846527		2203	4300	6503	228554771	SO:0001583	missense	80309	exon12				CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"""A-kinase anchor proteins"""	30619	protein-coding gene	gene with protein product	"""sphingosine kinase type 1-interacting protein"""	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.5009A>G	2.37:g.228846527T>C	ENSP00000375909:p.Asp1670Gly	Somatic		Capture	Illumina HiSeq	Phase_I	228554771	NM_001142644	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	37	CCDS46537.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.612119	0.87258	.	.	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.07216	3.21;3.21	5.85	5.85	0.93711	A-kinase anchor 110kDa, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.29976	0.0750	M	0.73598	2.24	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.989	T	0.01215	-1.1416	10	0.59425	D	0.04	.	15.4167	0.74974	0.0:0.0:0.0:1.0	.	1670;1641	Q2M3C7;Q2M3C7-2	SPKAP_HUMAN;.	G	1670;1641	ENSP00000375909:D1670G;ENSP00000339886:D1641G	ENSP00000339886:D1641G	D	-	2	0	SPHKAP	228554771	1.000000	0.71417	0.996000	0.52242	0.990000	0.78478	6.362000	0.73077	2.238000	0.73509	0.533000	0.62120	GAT		0.478	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623	
DNER	92737	broad.mit.edu	37	2	230312076	230312076	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:230312076G>A	ENST00000341772.4	-	8	1576	c.1442C>T	c.(1441-1443)aCg>aTg	p.T481M		NM_139072.3	NP_620711.3	Q8NFT8	DNER_HUMAN	delta/notch-like EGF repeat containing	481	EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00076}.				central nervous system development (GO:0007417)|endocytosis (GO:0006897)|glial cell differentiation (GO:0010001)|neuron migration (GO:0001764)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|skeletal muscle fiber development (GO:0048741)|synapse assembly (GO:0007416)	dendrite (GO:0030425)|early endosome (GO:0005769)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|clathrin binding (GO:0030276)|transmembrane signaling receptor activity (GO:0004888)	p.T481M(1)		NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	63		all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175)		Epithelial(121;1.4e-11)|all cancers(144;7.7e-09)|LUSC - Lung squamous cell carcinoma(224;0.034)|Lung(119;0.0375)		GCTGCGGCACGTGCCATGAGC	0.572																																					p.T481M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1442T	2						.						44.0	39.0	41.0					2																	230312076		2203	4300	6503	230020320	SO:0001583	missense	92737	exon8			AY358891	CCDS33390.1	2q36.3	2006-10-26			ENSG00000187957	ENSG00000187957			24456	protein-coding gene	gene with protein product		607299				11950833, 11997712	Standard	NM_139072		Approved	UNQ26, bet	uc002vpv.3	Q8NFT8	OTTHUMG00000153637	ENST00000341772.4:c.1442C>T	2.37:g.230312076G>A	ENSP00000345229:p.Thr481Met	Somatic		Capture	Illumina HiSeq	Phase_I	230020320	NM_139072	A6NP39|Q53R88|Q53TP7|Q53TQ5|Q8IYT0|Q8TB42|Q9NTF1|Q9UDM2	Missense_Mutation	SNP	ENST00000341772.4	37	CCDS33390.1	.	.	.	.	.	.	.	.	.	.	G	12.47	1.946237	0.34377	.	.	ENSG00000187957	ENST00000341772;ENST00000543700	D	0.87650	-2.28	4.94	1.89	0.25635	EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.290858	0.38164	N	0.001791	T	0.79082	0.4386	L	0.51853	1.615	0.26855	N	0.968081	B	0.19817	0.039	B	0.19391	0.025	T	0.64097	-0.6487	10	0.30854	T	0.27	.	3.6932	0.08354	0.4378:0.1902:0.3721:0.0	.	481	Q8NFT8	DNER_HUMAN	M	481;199	ENSP00000345229:T481M	ENSP00000345229:T481M	T	-	2	0	DNER	230020320	1.000000	0.71417	0.998000	0.56505	0.784000	0.44337	3.436000	0.52856	0.579000	0.29504	0.655000	0.94253	ACG		0.572	DNER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331902.1	NM_139072	
DNER	92737	broad.mit.edu	37	2	230450598	230450598	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:230450598C>T	ENST00000341772.4	-	4	957	c.823G>A	c.(823-825)Gcc>Acc	p.A275T	DNER_ENST00000482831.1_5'UTR	NM_139072.3	NP_620711.3	Q8NFT8	DNER_HUMAN	delta/notch-like EGF repeat containing	275					central nervous system development (GO:0007417)|endocytosis (GO:0006897)|glial cell differentiation (GO:0010001)|neuron migration (GO:0001764)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|skeletal muscle fiber development (GO:0048741)|synapse assembly (GO:0007416)	dendrite (GO:0030425)|early endosome (GO:0005769)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|clathrin binding (GO:0030276)|transmembrane signaling receptor activity (GO:0004888)	p.A275T(1)		NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	63		all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175)		Epithelial(121;1.4e-11)|all cancers(144;7.7e-09)|LUSC - Lung squamous cell carcinoma(224;0.034)|Lung(119;0.0375)		TTCCCCAAGGCGAGCATCTCC	0.502																																					p.A275T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G823A	2						.						79.0	78.0	79.0					2																	230450598		2203	4300	6503	230158842	SO:0001583	missense	92737	exon4			AY358891	CCDS33390.1	2q36.3	2006-10-26			ENSG00000187957	ENSG00000187957			24456	protein-coding gene	gene with protein product		607299				11950833, 11997712	Standard	NM_139072		Approved	UNQ26, bet	uc002vpv.3	Q8NFT8	OTTHUMG00000153637	ENST00000341772.4:c.823G>A	2.37:g.230450598C>T	ENSP00000345229:p.Ala275Thr	Somatic		Capture	Illumina HiSeq	Phase_I	230158842	NM_139072	A6NP39|Q53R88|Q53TP7|Q53TQ5|Q8IYT0|Q8TB42|Q9NTF1|Q9UDM2	Missense_Mutation	SNP	ENST00000341772.4	37	CCDS33390.1	.	.	.	.	.	.	.	.	.	.	C	0.065	-1.215070	0.01542	.	.	ENSG00000187957	ENST00000341772;ENST00000543700	D	0.84589	-1.87	5.67	-0.939	0.10408	.	0.726926	0.13778	N	0.363455	T	0.66626	0.2808	N	0.14661	0.345	0.09310	N	0.999999	B	0.09022	0.002	B	0.04013	0.001	T	0.48990	-0.8985	10	0.12766	T	0.61	.	6.4887	0.22103	0.1845:0.5669:0.0:0.2486	.	275	Q8NFT8	DNER_HUMAN	T	275;3	ENSP00000345229:A275T	ENSP00000345229:A275T	A	-	1	0	DNER	230158842	0.002000	0.14202	0.002000	0.10522	0.024000	0.10985	0.022000	0.13511	-0.863000	0.04084	-1.731000	0.00696	GCC		0.502	DNER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331902.1	NM_139072	
TRIP12	9320	broad.mit.edu	37	2	230693967	230693967	+	Silent	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:230693967A>G	ENST00000283943.5	-	7	1426	c.1248T>C	c.(1246-1248)ttT>ttC	p.F416F	TRIP12_ENST00000389045.3_Silent_p.F119F|TRIP12_ENST00000389044.4_Silent_p.F464F|TRIP12_ENST00000543084.1_Intron	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	416					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)	p.F416F(1)		breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		CAAGAGGACCAAATAGGTGAG	0.413																																					p.F416F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1248C	2						.						76.0	75.0	75.0					2																	230693967		2203	4300	6503	230402211	SO:0001819	synonymous_variant	9320	exon7			L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.1248T>C	2.37:g.230693967A>G		Somatic		Capture	Illumina HiSeq	Phase_I	230402211	NM_004238	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Silent	SNP	ENST00000283943.5	37	CCDS33391.1																																																																																				0.413	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238	
CHRND	1144	broad.mit.edu	37	2	233400011	233400011	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:233400011C>T	ENST00000258385.3	+	12	1575	c.1543C>T	c.(1543-1545)Cgc>Tgc	p.R515C	CHRND_ENST00000457943.2_Missense_Mutation_p.R321C|CHRND_ENST00000543200.1_Missense_Mutation_p.R500C	NM_000751.2	NP_000742.1	Q07001	ACHD_HUMAN	cholinergic receptor, nicotinic, delta (muscle)	515					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|muscle contraction (GO:0006936)|musculoskeletal movement (GO:0050881)|neuromuscular process (GO:0050905)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|skeletal muscle tissue growth (GO:0048630)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)	p.R515C(1)		breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)	34		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;1.89e-16)|BRCA - Breast invasive adenocarcinoma(100;0.00078)|Lung(119;0.00579)|LUSC - Lung squamous cell carcinoma(224;0.00754)	Galantamine(DB00674)	GCAGGACAAGCGCTTCATCTA	0.612																																					p.R515C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1543T	2						.						74.0	74.0	74.0					2																	233400011		2203	4300	6503	233108255	SO:0001583	missense	1144	exon12			X55019	CCDS2494.1, CCDS58754.1	2q37.1	2012-02-11	2012-02-07		ENSG00000135902	ENSG00000135902		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1965	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, delta (muscle)"""	100720	"""cholinergic receptor, nicotinic, delta"""	ACHRD			Standard	NM_000751		Approved		uc002vsw.4	Q07001	OTTHUMG00000133261	ENST00000258385.3:c.1543C>T	2.37:g.233400011C>T	ENSP00000258385:p.Arg515Cys	Somatic		Capture	Illumina HiSeq	Phase_I	233108255	NM_000751	A8K661|B4DT92|Q52LH4	Missense_Mutation	SNP	ENST00000258385.3	37	CCDS2494.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.376349	0.82682	.	.	ENSG00000135902	ENST00000543200;ENST00000258385;ENST00000457943	D;T;D	0.89485	-1.52;-1.39;-2.52	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	D	0.94125	0.8116	M	0.75447	2.3	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.996;0.996;0.996;0.996	D	0.94764	0.7939	10	0.87932	D	0	.	16.7779	0.85556	0.0:1.0:0.0:0.0	.	321;500;515;515	B4E3W4;B4DT92;A8K661;Q07001	.;.;.;ACHD_HUMAN	C	500;515;321	ENSP00000438380:R500C;ENSP00000258385:R515C;ENSP00000391055:R321C	ENSP00000258385:R515C	R	+	1	0	CHRND	233108255	1.000000	0.71417	1.000000	0.80357	0.713000	0.41058	6.643000	0.74334	2.389000	0.81357	0.655000	0.94253	CGC		0.612	CHRND-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257038.2		
GIGYF2	26058	broad.mit.edu	37	2	233621005	233621005	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:233621005G>A	ENST00000409547.1	+	8	651	c.340G>A	c.(340-342)Gtg>Atg	p.V114M	GIGYF2_ENST00000409480.1_Missense_Mutation_p.V114M|GIGYF2_ENST00000409451.3_Missense_Mutation_p.V114M|GIGYF2_ENST00000373566.3_Missense_Mutation_p.V114M|GIGYF2_ENST00000373563.4_Missense_Mutation_p.V114M|GIGYF2_ENST00000409196.3_Missense_Mutation_p.V114M	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	114					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.V114M(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		AGGAACAGTGGTGGGGGCTCC	0.438																																					p.V114M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G340A	2						.						62.0	66.0	64.0					2																	233621005		2203	4300	6503	233329249	SO:0001583	missense	26058	exon5			U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"""Trinucleotide (CAG) repeat containing"""	11960	protein-coding gene	gene with protein product	"""GYF domain containing 2"""	612003	"""PERQ amino acid rich, with GYF domain 2"", ""PERQ amino acid rich, with GYF domain 3"", ""trinucleotide repeat containing 15"", ""Parkinson disease (autosomal recessive, early onset) 11"""	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.340G>A	2.37:g.233621005G>A	ENSP00000386537:p.Val114Met	Somatic		Capture	Illumina HiSeq	Phase_I	233329249	NM_001103148	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Missense_Mutation	SNP	ENST00000409547.1	37	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.176285	0.78564	.	.	ENSG00000204120	ENST00000373566;ENST00000414511;ENST00000373563;ENST00000428883;ENST00000409480;ENST00000409547;ENST00000535418;ENST00000423659;ENST00000409196;ENST00000409451;ENST00000440945	T;T;T;T;T;T;T;T;T	0.80033	-0.68;-0.68;-1.33;-0.68;-0.68;-0.84;-0.72;-0.68;-0.9	5.63	5.63	0.86233	.	0.281661	0.33834	N	0.004510	D	0.85919	0.5809	L	0.40543	1.245	0.80722	D	1	D;D;D	0.64830	0.994;0.976;0.989	D;P;D	0.65987	0.92;0.656;0.94	D	0.85834	0.1393	10	0.52906	T	0.07	-12.1168	19.6755	0.95930	0.0:0.0:1.0:0.0	.	114;114;114	A6H8W4;Q6Y7W6;E9PBB0	.;PERQ2_HUMAN;.	M	114	ENSP00000362667:V114M;ENSP00000362664:V114M;ENSP00000402712:V114M;ENSP00000386765:V114M;ENSP00000386537:V114M;ENSP00000404195:V114M;ENSP00000387070:V114M;ENSP00000387170:V114M;ENSP00000410297:V114M	ENSP00000362664:V114M	V	+	1	0	GIGYF2	233329249	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.970000	0.88000	2.652000	0.90054	0.563000	0.77884	GTG		0.438	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146	
GBX2	2637	broad.mit.edu	37	2	237074763	237074763	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:237074763C>T	ENST00000306318.4	-	2	1238	c.841G>A	c.(841-843)Gcc>Acc	p.A281T	GBX2_ENST00000551105.1_3'UTR|AC079135.1_ENST00000415226.1_RNA|GBX2_ENST00000465889.1_5'UTR|AC079135.1_ENST00000483218.1_RNA	NM_001485.2	NP_001476.2	P52951	GBX2_HUMAN	gastrulation brain homeobox 2	281					autonomic nervous system development (GO:0048483)|axon guidance (GO:0007411)|cerebellar granule cell precursor proliferation (GO:0021930)|cerebellum development (GO:0021549)|forebrain neuron development (GO:0021884)|inner ear morphogenesis (GO:0042472)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|patterning of blood vessels (GO:0001569)|rhombomere 2 development (GO:0021568)|thalamus development (GO:0021794)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	7		Breast(86;0.00235)|Renal(207;0.00339)|all_hematologic(139;0.00357)|all_lung(227;0.0616)|Acute lymphoblastic leukemia(138;0.0775)|Ovarian(221;0.089)|Lung NSC(271;0.179)		Epithelial(121;4.5e-25)|OV - Ovarian serous cystadenocarcinoma(60;5.16e-11)|BRCA - Breast invasive adenocarcinoma(100;3.4e-05)|Lung(119;0.00195)|LUSC - Lung squamous cell carcinoma(224;0.00471)		AGGGCGTGGGCGATCTGCGAG	0.597																																					p.A281T												.	.	0			c.G841A	2						.						84.0	87.0	86.0					2																	237074763		2203	4300	6503	236739502	SO:0001583	missense	2637	exon2			AF118452	CCDS2515.1	2q37.2	2012-03-09	2005-12-22		ENSG00000168505	ENSG00000168505		"""Homeoboxes / ANTP class : HOXL subclass"""	4186	protein-coding gene	gene with protein product		601135	"""gastrulation brain homeo box 2"""			9346236, 8838315	Standard	XM_005246071		Approved		uc002vvw.1	P52951	OTTHUMG00000133294	ENST00000306318.4:c.841G>A	2.37:g.237074763C>T	ENSP00000302251:p.Ala281Thr	None		Capture	Illumina HiSeq	Phase_I	236739502	NM_001485	B2RPH7|O43833|Q53RX5|Q9Y5Y1	Missense_Mutation	SNP	ENST00000306318.4	37	CCDS2515.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.650752	0.87958	.	.	ENSG00000168505	ENST00000306318	D	0.98164	-4.76	4.66	4.66	0.58398	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99375	0.9780	H	0.97758	4.07	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98383	1.0559	10	0.87932	D	0	-15.3226	17.5569	0.87894	0.0:1.0:0.0:0.0	.	281	P52951	GBX2_HUMAN	T	281	ENSP00000302251:A281T	ENSP00000302251:A281T	A	-	1	0	GBX2	236739502	1.000000	0.71417	1.000000	0.80357	0.556000	0.35491	5.995000	0.70631	2.133000	0.65898	0.561000	0.74099	GCC		0.597	GBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257078.3	NM_001485	
COL6A3	1293	broad.mit.edu	37	2	238268788	238268788	+	Silent	SNP	C	C	T	rs368711215		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:238268788C>T	ENST00000295550.4	-	17	6677	c.6225G>A	c.(6223-6225)ccG>ccA	p.P2075P	COL6A3_ENST00000409809.1_Silent_p.P1869P|COL6A3_ENST00000346358.4_Silent_p.P1875P|COL6A3_ENST00000353578.4_Silent_p.P1869P|COL6A3_ENST00000347401.3_Silent_p.P1874P|COL6A3_ENST00000472056.1_Silent_p.P1468P	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2075	Collagen-like 1.|Triple-helical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.P2075P(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)		TCACACCAGGCGGACCACGCT	0.602													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19799	0.0		0.0	False		,,,				2504	0.0				p.P1468P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G4404A	2						.	C	,,	1,4405	2.1+/-5.4	0,1,2202	166.0	126.0	139.0		6225,4404,5607	-10.7	0.0	2		139	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057166.4,NM_057167.3	,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,	2075/3178,1468/2571,1869/2972	238268788	1,13005	2203	4300	6503	237933527	SO:0001819	synonymous_variant	1293	exon14			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.6225G>A	2.37:g.238268788C>T		Somatic		Capture	Illumina HiSeq	Phase_I	237933527	NM_057166	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																				0.602	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
COL6A3	1293	broad.mit.edu	37	2	238289624	238289624	+	Missense_Mutation	SNP	C	C	T	rs372255458		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:238289624C>T	ENST00000295550.4	-	5	2283	c.1831G>A	c.(1831-1833)Gcc>Acc	p.A611T	COL6A3_ENST00000409809.1_Missense_Mutation_p.A405T|COL6A3_ENST00000346358.4_Missense_Mutation_p.A611T|COL6A3_ENST00000353578.4_Missense_Mutation_p.A405T|COL6A3_ENST00000347401.3_Missense_Mutation_p.A410T|COL6A3_ENST00000392003.2_Missense_Mutation_p.A204T|COL6A3_ENST00000392004.3_Missense_Mutation_p.A405T|COL6A3_ENST00000472056.1_Missense_Mutation_p.A204T	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	611	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.A611T(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)		TGCAATGGGGCGGCTCGGAAC	0.582																																					p.A204T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G610A	2						.	C	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	0,4406		0,0,2203	61.0	53.0	56.0		1213,610,1213,610,1831	4.4	0.0	2		56	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense	COL6A3	NM_057167.3,NM_057166.4,NM_057165.4,NM_057164.4,NM_004369.3	58,58,58,58,58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign,benign,benign	405/2972,204/2571,405/1238,204/1037,611/3178	238289624	1,13005	2203	4300	6503	237954363	SO:0001583	missense	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.1831G>A	2.37:g.238289624C>T	ENSP00000295550:p.Ala611Thr	Somatic		Capture	Illumina HiSeq	Phase_I	237954363	NM_057166	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	6.522	0.464485	0.12402	0.0	1.16E-4	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358;ENST00000392004;ENST00000392003;ENST00000433762	D;D;D;D;D;D;T;T;T	0.88586	-2.4;-2.37;-2.35;-2.36;-2.35;-2.35;0.15;0.02;0.17	5.27	4.4	0.53042	von Willebrand factor, type A (2);	0.839591	0.10116	N	0.714003	T	0.81837	0.4907	L	0.29908	0.895	0.09310	N	1	B;P;B;B;B;B	0.38535	0.106;0.635;0.03;0.03;0.407;0.039	B;B;B;B;B;B	0.38458	0.04;0.274;0.025;0.041;0.065;0.013	T	0.67829	-0.5569	10	0.15066	T	0.55	.	9.1507	0.36962	0.0:0.6557:0.2607:0.0836	.	611;204;204;405;405;611	E9PCV6;E9PFQ6;A8MT30;E9PGQ9;P12111-2;P12111	.;.;.;.;.;CO6A3_HUMAN	T	611;410;405;204;405;611;405;204;611	ENSP00000295550:A611T;ENSP00000315609:A410T;ENSP00000315873:A405T;ENSP00000418285:A204T;ENSP00000386844:A405T;ENSP00000295546:A611T;ENSP00000375861:A405T;ENSP00000375860:A204T;ENSP00000389539:A611T	ENSP00000295550:A611T	A	-	1	0	COL6A3	237954363	0.000000	0.05858	0.010000	0.14722	0.022000	0.10575	0.127000	0.15790	1.362000	0.46000	0.655000	0.94253	GCC		0.582	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
RAB17	64284	broad.mit.edu	37	2	238483670	238483670	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:238483670C>T	ENST00000264601.3	-	6	1260	c.631G>A	c.(631-633)Gcc>Acc	p.A211T	RAB17_ENST00000409822.1_Missense_Mutation_p.A84T|RAB17_ENST00000409576.1_Intron|RAB17_ENST00000538644.1_Missense_Mutation_p.A84T	NM_022449.3	NP_071894.1	Q9H0T7	RAB17_HUMAN	RAB17, member RAS oncogene family	211					cilium assembly (GO:0042384)|endocytic recycling (GO:0032456)|establishment of melanosome localization (GO:0032401)|filopodium assembly (GO:0046847)|GTP catabolic process (GO:0006184)|immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor (GO:0002415)|melanosome transport (GO:0032402)|protein transport (GO:0015031)|regulation of dendrite development (GO:0050773)|regulation of filopodium assembly (GO:0051489)|regulation of synapse assembly (GO:0051963)|small GTPase mediated signal transduction (GO:0007264)|transcytosis (GO:0045056)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|dendrite (GO:0030425)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|melanosome (GO:0042470)|neuronal cell body (GO:0043025)|recycling endosome (GO:0055037)|recycling endosome membrane (GO:0055038)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.A211T(1)		haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(1)	4		Renal(207;0.00272)|Breast(86;0.00297)|all_hematologic(139;0.182)|Ovarian(221;0.221)		Epithelial(121;9.36e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.26e-10)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000354)|Lung(119;0.011)|LUSC - Lung squamous cell carcinoma(224;0.026)		ACCTAGTGGGCGCAGCATTTG	0.637																																					p.A211T	Colon(56;987 1029 6466 13943 27336)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G631A	2						.																																			238148409	SO:0001583	missense	64284	exon6			AK022600	CCDS2520.1	2q37.3	2008-05-23			ENSG00000124839	ENSG00000124839		"""RAB, member RAS oncogene"""	16523	protein-coding gene	gene with protein product		602206				9624171	Standard	NM_022449		Approved		uc002vwz.2	Q9H0T7	OTTHUMG00000133299	ENST00000264601.3:c.631G>A	2.37:g.238483670C>T	ENSP00000264601:p.Ala211Thr	Somatic		Capture	Illumina HiSeq	Phase_I	238148409	NM_022449	Q53QV6|Q6IA73|Q6PJZ0|Q9BVU1|Q9H9U9	Missense_Mutation	SNP	ENST00000264601.3	37	CCDS2520.1	.	.	.	.	.	.	.	.	.	.	C	11.01	1.511926	0.27036	.	.	ENSG00000124839	ENST00000264601;ENST00000538644;ENST00000409822	T;T;T	0.63913	-0.07;2.19;2.19	2.9	1.08	0.20341	.	1.055870	0.07493	N	0.905883	T	0.39410	0.1077	N	0.08118	0	0.09310	N	1	B	0.17667	0.023	B	0.08055	0.003	T	0.31779	-0.9931	10	0.72032	D	0.01	-25.4247	4.95	0.14009	0.0:0.7092:0.0:0.2908	.	211	Q9H0T7	RAB17_HUMAN	T	211;84;84	ENSP00000264601:A211T;ENSP00000443461:A84T;ENSP00000386589:A84T	ENSP00000264601:A211T	A	-	1	0	RAB17	238148409	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.359000	0.07632	0.277000	0.22141	-0.258000	0.10820	GCC		0.637	RAB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257084.2		
PASK	23178	broad.mit.edu	37	2	242066283	242066283	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:242066283C>T	ENST00000405260.1	-	10	2745	c.2047G>A	c.(2047-2049)Gtt>Att	p.V683I	PASK_ENST00000544142.1_Missense_Mutation_p.V497I|PASK_ENST00000403638.3_Missense_Mutation_p.V683I|PASK_ENST00000539818.1_Missense_Mutation_p.V467I|PASK_ENST00000358649.4_Missense_Mutation_p.V683I|PASK_ENST00000234040.4_Missense_Mutation_p.V683I	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	683					negative regulation of glycogen biosynthetic process (GO:0045719)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of energy homeostasis (GO:2000505)|regulation of glucagon secretion (GO:0070092)|regulation of respiratory gaseous exchange (GO:0043576)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)	p.V683I(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(20)|ovary(4)|prostate(4)|skin(1)|stomach(1)|urinary_tract(2)	53		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		TCTGTCGGAACGAGTTCGGCG	0.617																																					p.V683I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2047A	2						.						100.0	108.0	105.0					2																	242066283		2203	4300	6503	241714956	SO:0001583	missense	23178	exon10			U79240	CCDS2545.1, CCDS58758.1, CCDS58759.1	2q37.3	2008-05-23			ENSG00000115687	ENSG00000115687			17270	protein-coding gene	gene with protein product		607505				11688972, 11459942, 15148392	Standard	NM_001252119		Approved	PASKIN, KIAA0135, STK37	uc010fzl.2	Q96RG2	OTTHUMG00000133392	ENST00000405260.1:c.2047G>A	2.37:g.242066283C>T	ENSP00000384016:p.Val683Ile	Somatic		Capture	Illumina HiSeq	Phase_I	241714956	NM_015148	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Missense_Mutation	SNP	ENST00000405260.1	37	CCDS2545.1	.	.	.	.	.	.	.	.	.	.	C	10.53	1.376865	0.24857	.	.	ENSG00000115687	ENST00000234040;ENST00000544142;ENST00000405260;ENST00000358649;ENST00000539818;ENST00000403638	T;T;T;T;T;T	0.70749	-0.51;-0.5;-0.51;-0.46;-0.49;0.44	3.83	0.483	0.16820	.	0.927514	0.08917	N	0.874958	T	0.47078	0.1426	L	0.29908	0.895	0.09310	N	1	P;B;B;B;B	0.52316	0.952;0.007;0.009;0.007;0.005	B;B;B;B;B	0.35413	0.202;0.002;0.007;0.006;0.003	T	0.34551	-0.9824	10	0.13470	T	0.59	.	5.0165	0.14339	0.0:0.559:0.2132:0.2279	.	648;497;683;683;683	B7Z7R6;F5GYW7;Q96RG2-2;G5E9F1;Q96RG2	.;.;.;.;PASK_HUMAN	I	683;497;683;683;467;683	ENSP00000234040:V683I;ENSP00000441374:V497I;ENSP00000384016:V683I;ENSP00000351475:V683I;ENSP00000443083:V467I;ENSP00000384438:V683I	ENSP00000234040:V683I	V	-	1	0	PASK	241714956	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.008000	0.13197	0.048000	0.15891	-0.224000	0.12420	GTT		0.617	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148	
OTOF	9381	broad.mit.edu	37	2	26684998	26684998	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:26684998G>C	ENST00000272371.2	-	42	5370	c.5244C>G	c.(5242-5244)gaC>gaG	p.D1748E	OTOF_ENST00000402415.3_Missense_Mutation_p.D1058E|OTOF_ENST00000338581.6_Missense_Mutation_p.D981E|OTOF_ENST00000339598.3_Missense_Mutation_p.D981E|OTOF_ENST00000403946.3_Missense_Mutation_p.D1748E	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	1748					membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)	p.D1748E(1)|p.D981E(1)		NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGAAGTCGTCGTCCTCCAAGA	0.607																																					p.D981E	GBM(102;732 1451 20652 24062 31372)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C2943G	2						.						180.0	163.0	169.0					2																	26684998		2203	4300	6503	26538502	SO:0001583	missense	9381	exon25			AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.5244C>G	2.37:g.26684998G>C	ENSP00000272371:p.Asp1748Glu	Somatic		Capture	Illumina HiSeq	Phase_I	26538502	NM_194323	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Missense_Mutation	SNP	ENST00000272371.2	37	CCDS1725.1	.	.	.	.	.	.	.	.	.	.	G	19.02	3.746820	0.69418	.	.	ENSG00000115155	ENST00000338581;ENST00000339598;ENST00000402415;ENST00000272371;ENST00000403946	D;D;D;D;D	0.82711	-1.64;-1.64;-1.64;-1.64;-1.64	5.06	-2.42	0.06542	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.83585	0.5286	L	0.38838	1.175	0.49915	D	0.999831	D;D;D;D	0.89917	1.0;0.993;0.96;0.993	D;D;P;D	0.79108	0.992;0.954;0.85;0.954	T	0.80908	-0.1172	10	0.56958	D	0.05	-31.2221	11.7463	0.51821	0.8111:0.0:0.1889:0.0	.	1748;981;1058;981	Q9HC10;Q9HC10-2;Q9HC10-3;Q9HC10-4	OTOF_HUMAN;.;.;.	E	981;981;1058;1748;1748	ENSP00000345137:D981E;ENSP00000344521:D981E;ENSP00000383906:D1058E;ENSP00000272371:D1748E;ENSP00000385255:D1748E	ENSP00000272371:D1748E	D	-	3	2	OTOF	26538502	0.223000	0.23663	0.955000	0.39395	0.966000	0.64601	-0.302000	0.08221	-0.345000	0.08325	-0.258000	0.10820	GAC		0.607	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		
CAD	790	broad.mit.edu	37	2	27456389	27456389	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:27456389G>T	ENST00000403525.1	+	19	3156	c.3012G>T	c.(3010-3012)gaG>gaT	p.E1004D	CAD_ENST00000264705.4_Missense_Mutation_p.E1067D			O76075	DFFB_HUMAN	carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	0					apoptotic chromosome condensation (GO:0030263)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)	p.E1067D(1)		NS(1)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(40)|ovary(6)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	92	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGTGGAGGGAGCTCAGTGACC	0.587																																					p.E1067D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3201T	2						.						40.0	44.0	42.0					2																	27456389		2203	4300	6503	27309893	SO:0001583	missense	790	exon20			D78586	CCDS1742.1	2p22-p21	2012-10-02			ENSG00000084774	ENSG00000084774	2.1.3.2, 3.5.2.-		1424	protein-coding gene	gene with protein product		114010				8619816, 2565865	Standard	NM_004341		Approved		uc002rji.3	P27708	OTTHUMG00000097070	ENST00000403525.1:c.3012G>T	2.37:g.27456389G>T	ENSP00000384510:p.Glu1004Asp	Somatic		Capture	Illumina HiSeq	Phase_I	27309893	NM_004341	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Missense_Mutation	SNP	ENST00000403525.1	37		.	.	.	.	.	.	.	.	.	.	G	20.6	4.011434	0.75046	.	.	ENSG00000084774	ENST00000264705;ENST00000403525	D;D	0.97232	-4.3;-4.3	6.17	3.01	0.34805	ATP-grasp fold (1);ATP-grasp fold, subdomain 1 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);	0.000000	0.85682	D	0.000000	D	0.98137	0.9385	M	0.90425	3.115	0.58432	D	0.999997	D;P	0.54397	0.966;0.956	P;P	0.59115	0.852;0.622	D	0.98417	1.0575	10	0.87932	D	0	-13.0373	12.0248	0.53365	0.2235:0.0:0.7764:0.0	.	1004;1067	F8VPD4;P27708	.;PYR1_HUMAN	D	1067;1004	ENSP00000264705:E1067D;ENSP00000384510:E1004D	ENSP00000264705:E1067D	E	+	3	2	CAD	27309893	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	2.418000	0.44662	0.938000	0.37419	0.655000	0.94253	GAG		0.587	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1		
PLB1	151056	broad.mit.edu	37	2	28812544	28812544	+	Silent	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:28812544A>G	ENST00000327757.5	+	28	1967	c.1923A>G	c.(1921-1923)gaA>gaG	p.E641E	PLB1_ENST00000422425.2_Silent_p.E630E|PLB1_ENST00000329020.6_Silent_p.E329E	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	641	4 X 308-326 AA approximate repeats.				glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)	p.E641E(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(31)|ovary(6)|prostate(1)|skin(7)|stomach(2)	69	Acute lymphoblastic leukemia(172;0.155)					GTGACCAGGAAGGATTGCCTG	0.468																																					p.E630E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1890G	2						.						90.0	82.0	85.0					2																	28812544		2203	4300	6503	28666048	SO:0001819	synonymous_variant	151056	exon27				CCDS33168.1, CCDS54340.1	2p23.3	2014-03-14			ENSG00000163803	ENSG00000163803	3.1.1.4, 3.1.1.5		30041	protein-coding gene	gene with protein product		610179				12150957	Standard	NM_153021		Approved	PLB, FLJ30866	uc002rmb.2	Q6P1J6	OTTHUMG00000152014	ENST00000327757.5:c.1923A>G	2.37:g.28812544A>G		Somatic		Capture	Illumina HiSeq	Phase_I	28666048	NM_001170585	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Silent	SNP	ENST00000327757.5	37	CCDS33168.1	.	.	.	.	.	.	.	.	.	.	A	2.879	-0.232157	0.05983	.	.	ENSG00000163803	ENST00000404858	.	.	.	5.99	-1.67	0.08238	.	.	.	.	.	T	0.41213	0.1149	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.24190	-1.0167	4	.	.	.	-17.4282	2.3188	0.04205	0.4197:0.1176:0.3422:0.1205	.	.	.	.	R	629	.	.	K	+	2	0	PLB1	28666048	0.278000	0.24230	0.740000	0.30986	0.145000	0.21501	-0.468000	0.06656	-0.615000	0.05679	-1.082000	0.02213	AAG		0.468	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2		
FAM179A	165186	broad.mit.edu	37	2	29249724	29249724	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:29249724G>A	ENST00000379558.4	+	14	2210	c.1859G>A	c.(1858-1860)cGg>cAg	p.R620Q	FAM179A_ENST00000465300.1_3'UTR|FAM179A_ENST00000403861.2_Missense_Mutation_p.R565Q	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	620								p.R620Q(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						TTCAGCCACCGGAACCCCTTG	0.582																																					p.R620Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1859A	2						.						27.0	29.0	28.0					2																	29249724		1967	4147	6114	29103228	SO:0001583	missense	165186	exon14			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.1859G>A	2.37:g.29249724G>A	ENSP00000368876:p.Arg620Gln	Somatic		Capture	Illumina HiSeq	Phase_I	29103228	NM_199280	Q6ZUF5	Missense_Mutation	SNP	ENST00000379558.4	37	CCDS1769.2	.	.	.	.	.	.	.	.	.	.	G	14.33	2.504385	0.44558	.	.	ENSG00000189350	ENST00000401723;ENST00000379558;ENST00000403861	T;T;T	0.48836	0.8;0.8;0.8	4.81	4.81	0.61882	Armadillo-like helical (1);Armadillo-type fold (1);CLASP N-terminal domain (1);	0.000000	0.46442	D	0.000297	T	0.62122	0.2402	L	0.43152	1.355	0.33517	D	0.591892	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	T	0.70857	-0.4758	10	0.48119	T	0.1	.	17.4884	0.87694	0.0:0.0:1.0:0.0	.	565;620	F8W8E4;Q6ZUX3	.;F179A_HUMAN	Q	55;620;565	ENSP00000384897:R55Q;ENSP00000368876:R620Q;ENSP00000384699:R565Q	ENSP00000368876:R620Q	R	+	2	0	FAM179A	29103228	1.000000	0.71417	1.000000	0.80357	0.205000	0.24178	4.450000	0.60041	2.233000	0.73108	0.561000	0.74099	CGG		0.582	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280	
C2orf71	388939	broad.mit.edu	37	2	29294142	29294142	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:29294142G>T	ENST00000331664.5	-	1	2985	c.2986C>A	c.(2986-2988)Ccc>Acc	p.P996T		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	996					response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)		p.P996T(1)		NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						GTCCTCGTGGGAGAGGCCTTT	0.642																																					p.P996T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2986A	2						.						38.0	41.0	40.0					2																	29294142		1926	4125	6051	29147646	SO:0001583	missense	388939	exon1				CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.2986C>A	2.37:g.29294142G>T	ENSP00000332809:p.Pro996Thr	Somatic		Capture	Illumina HiSeq	Phase_I	29147646	NM_001029883		Missense_Mutation	SNP	ENST00000331664.5	37	CCDS42669.1	.	.	.	.	.	.	.	.	.	.	G	12.50	1.957109	0.34565	.	.	ENSG00000179270	ENST00000331664	T	0.30182	1.54	5.29	5.29	0.74685	.	0.156624	0.45126	D	0.000382	T	0.56140	0.1965	M	0.65498	2.005	0.33850	D	0.632523	D	0.89917	1.0	D	0.79108	0.992	T	0.67209	-0.5728	10	0.62326	D	0.03	-23.0235	18.9378	0.92592	0.0:0.0:1.0:0.0	.	996	A6NGG8	CB071_HUMAN	T	996	ENSP00000332809:P996T	ENSP00000332809:P996T	P	-	1	0	C2orf71	29147646	1.000000	0.71417	1.000000	0.80357	0.275000	0.26752	1.972000	0.40540	2.469000	0.83416	0.491000	0.48974	CCC		0.642	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883	
CRIM1	51232	broad.mit.edu	37	2	36668428	36668428	+	Missense_Mutation	SNP	G	G	A	rs138252009		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:36668428G>A	ENST00000280527.2	+	3	900	c.533G>A	c.(532-534)cGc>cAc	p.R178H		NM_016441.2	NP_057525.1	Q9NZV1	CRIM1_HUMAN	cysteine rich transmembrane BMP regulator 1 (chordin-like)	178					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.R178H(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)				TCCAAGGCCCGCTGTGAAGTC	0.522																																					p.R178H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G533A	2						.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	98.0	91.0	94.0		533	4.8	1.0	2	dbSNP_134	94	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	178/1037	36668428	1,13005	2203	4300	6503	36521932	SO:0001583	missense	51232	exon3			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.533G>A	2.37:g.36668428G>A	ENSP00000280527:p.Arg178His	Somatic		Capture	Illumina HiSeq	Phase_I	36521932	NM_016441	Q2M2G4|Q59GH0|Q7LCQ5|Q9H318	Missense_Mutation	SNP	ENST00000280527.2	37	CCDS1783.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.209021	0.79240	2.27E-4	0.0	ENSG00000150938	ENST00000280527;ENST00000426856	T	0.05025	3.51	4.81	4.81	0.61882	.	0.142660	0.46758	D	0.000272	T	0.20455	0.0492	L	0.54323	1.7	0.50467	D	0.999874	D	0.76494	0.999	D	0.70016	0.967	T	0.00253	-1.1875	10	0.46703	T	0.11	-16.3434	17.0663	0.86559	0.0:0.0:1.0:0.0	.	178	Q9NZV1	CRIM1_HUMAN	H	178;70	ENSP00000280527:R178H	ENSP00000280527:R178H	R	+	2	0	CRIM1	36521932	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.678000	0.91211	2.480000	0.83734	0.650000	0.86243	CGC		0.522	CRIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216878.2	NM_016441	
SOS1	6654	broad.mit.edu	37	2	39249784	39249784	+	Missense_Mutation	SNP	C	C	A	rs543119480		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:39249784C>A	ENST00000426016.1	-	11	1871	c.1785G>T	c.(1783-1785)aaG>aaT	p.K595N	SOS1_ENST00000472480.1_5'Flank|SOS1_ENST00000395038.2_Missense_Mutation_p.K595N|SOS1_ENST00000402219.2_Missense_Mutation_p.K595N			Q07889	SOS1_HUMAN	son of sevenless homolog 1 (Drosophila)	595					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|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)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|Ras protein signal transduction (GO:0007265)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	DNA binding (GO:0003677)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.K595N(1)		autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	75		all_hematologic(82;0.21)				GAATTCCAGCCTTGGGCTGCA	0.408									Noonan syndrome																												p.K595N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1785T	2						.						90.0	91.0	91.0					2																	39249784		2203	4300	6503	39103288	SO:0001583	missense	6654	exon10	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	L13857	CCDS1802.1	2p21	2014-09-17	2002-11-05		ENSG00000115904	ENSG00000115904		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11187	protein-coding gene	gene with protein product		182530	"""gingival fibromatosis, hereditary, 1"""	GINGF		8276400, 10995566	Standard	NM_005633		Approved	HGF, GF1	uc002rrk.4	Q07889	OTTHUMG00000102109	ENST00000426016.1:c.1785G>T	2.37:g.39249784C>A	ENSP00000387784:p.Lys595Asn	Somatic		Capture	Illumina HiSeq	Phase_I	39103288	NM_005633	A8K2G3|B4DXG2	Missense_Mutation	SNP	ENST00000426016.1	37	CCDS1802.1	.	.	.	.	.	.	.	.	.	.	C	7.544	0.661332	0.14645	.	.	ENSG00000115904	ENST00000426016;ENST00000402219;ENST00000543698;ENST00000395038;ENST00000263879	T;T;T	0.28895	1.59;1.59;1.59	5.78	-0.0362	0.13889	Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.27313	0.0670	L	0.45581	1.43	0.80722	D	1	P;B	0.50369	0.934;0.026	P;B	0.47075	0.536;0.028	T	0.07028	-1.0794	10	0.19147	T	0.46	.	10.1568	0.42827	0.0:0.3707:0.0:0.6293	.	327;595	F5GX06;Q07889	.;SOS1_HUMAN	N	595;595;327;595;595	ENSP00000387784:K595N;ENSP00000384675:K595N;ENSP00000378479:K595N	ENSP00000263879:K595N	K	-	3	2	SOS1	39103288	0.999000	0.42202	0.999000	0.59377	0.992000	0.81027	0.620000	0.24403	0.056000	0.16144	-0.262000	0.10625	AAG		0.408	SOS1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219948.3	NM_005633	
SLC8A1	6546	broad.mit.edu	37	2	40366802	40366802	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:40366802C>T	ENST00000403092.1	-	10	2317	c.2284G>A	c.(2284-2286)Gac>Aac	p.D762N	SLC8A1_ENST00000405269.1_Missense_Mutation_p.D726N|SLC8A1-AS1_ENST00000597170.1_RNA|SLC8A1-AS1_ENST00000597385.1_RNA|SLC8A1_ENST00000406785.2_Missense_Mutation_p.D726N|SLC8A1_ENST00000405901.3_Missense_Mutation_p.D757N|SLC8A1-AS1_ENST00000593878.1_RNA|SLC8A1_ENST00000408028.2_Missense_Mutation_p.D754N|SLC8A1-AS1_ENST00000599268.1_RNA|SLC8A1_ENST00000406391.2_Missense_Mutation_p.D726N|SLC8A1-AS1_ENST00000593848.1_RNA|SLC8A1-AS1_ENST00000444629.1_RNA|SLC8A1-AS1_ENST00000599740.1_RNA|SLC8A1-AS1_ENST00000435515.1_RNA|SLC8A1-AS1_ENST00000596532.1_RNA|SLC8A1_ENST00000542756.1_Missense_Mutation_p.D757N|SLC8A1_ENST00000332839.4_Missense_Mutation_p.D762N|SLC8A1_ENST00000542024.1_Missense_Mutation_p.D726N|SLC8A1-AS1_ENST00000599956.1_RNA|SLC8A1_ENST00000402441.1_Missense_Mutation_p.D726N|SLC8A1-AS1_ENST00000598247.1_RNA|SLC8A1-AS1_ENST00000601679.1_RNA			P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 1	762	Poly-Asp.				blood coagulation (GO:0007596)|calcium ion export (GO:1901660)|calcium ion homeostasis (GO:0055074)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|cardiac muscle cell development (GO:0055013)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular response to caffeine (GO:0071313)|cellular response to reactive oxygen species (GO:0034614)|cellular sodium ion homeostasis (GO:0006883)|cytosolic calcium ion transport (GO:0060401)|embryonic heart tube development (GO:0035050)|embryonic placenta development (GO:0001892)|heart morphogenesis (GO:0003007)|ion transport (GO:0006811)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|muscle contraction (GO:0006936)|muscle fiber development (GO:0048747)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|post-embryonic development (GO:0009791)|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 the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|relaxation of smooth muscle (GO:0044557)|sodium ion export (GO:0071436)|sodium ion import (GO:0097369)|transmembrane transport (GO:0055085)|vascular smooth muscle contraction (GO:0014829)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|calcium:sodium antiporter activity (GO:0005432)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)	p.D762N(1)		NS(1)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|liver(1)|lung(57)|ovary(2)|pancreas(1)|skin(7)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)	100					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	CATTCATCGTCGTCATCATCT	0.507																																					p.D757N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2269A	2						.						165.0	146.0	152.0					2																	40366802		2203	4300	6503	40220306	SO:0001583	missense	6546	exon8				CCDS1806.1, CCDS46264.1, CCDS46265.1, CCDS59430.1	2p22.1	2013-07-15			ENSG00000183023	ENSG00000183023		"""Solute carriers"""	11068	protein-coding gene	gene with protein product	"""Na+/Ca++ exchanger"""	182305		NCX1		1559714	Standard	NM_021097		Approved		uc002rrx.3	P32418	OTTHUMG00000102183	ENST00000403092.1:c.2284G>A	2.37:g.40366802C>T	ENSP00000384763:p.Asp762Asn	Somatic		Capture	Illumina HiSeq	Phase_I	40220306	NM_001112800	A8K6N1|D6W595|O95849|Q4QQG6|Q587I6|Q59GN4|Q9UBL8|Q9UD55|Q9UDN1|Q9UDN2|Q9UKX6	Missense_Mutation	SNP	ENST00000403092.1	37	CCDS1806.1	.	.	.	.	.	.	.	.	.	.	C	17.68	3.449924	0.63290	.	.	ENSG00000183023	ENST00000406785;ENST00000378715;ENST00000542756;ENST00000403092;ENST00000405901;ENST00000402441;ENST00000405269;ENST00000332839;ENST00000408028;ENST00000535962;ENST00000406391;ENST00000542024	T;T;T;T;T;T;T;T;T;T	0.30182	1.55;1.58;1.58;1.58;1.55;1.55;1.58;1.54;1.55;1.55	5.16	5.16	0.70880	.	0.051425	0.64402	D	0.000001	T	0.49406	0.1555	L	0.49126	1.545	0.80722	D	1	D;D;D;D	0.89917	0.992;1.0;0.997;0.995	D;D;D;P	0.69654	0.936;0.965;0.918;0.787	T	0.47873	-0.9083	10	0.59425	D	0.04	.	16.17	0.81801	0.0:1.0:0.0:0.0	.	726;749;757;762	P32418-2;P32418-3;F6VPY9;P32418	.;.;.;NAC1_HUMAN	N	726;762;757;762;757;726;726;762;754;749;726;726	ENSP00000383886:D726N;ENSP00000440727:D757N;ENSP00000384763:D762N;ENSP00000385678:D757N;ENSP00000385188:D726N;ENSP00000385535:D726N;ENSP00000332931:D762N;ENSP00000384908:D754N;ENSP00000385811:D726N;ENSP00000443515:D726N	ENSP00000332931:D762N	D	-	1	0	SLC8A1	40220306	1.000000	0.71417	0.280000	0.24747	0.080000	0.17528	7.711000	0.84669	2.391000	0.81399	0.563000	0.77884	GAC		0.507	SLC8A1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326065.1	NM_021097	
SLC3A1	6519	broad.mit.edu	37	2	44531312	44531312	+	Silent	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:44531312T>C	ENST00000260649.6	+	7	1243	c.1167T>C	c.(1165-1167)agT>agC	p.S389S	SLC3A1_ENST00000409294.1_Silent_p.S9S|SLC3A1_ENST00000409740.3_Silent_p.S20S|SLC3A1_ENST00000409387.1_Silent_p.S389S|SLC3A1_ENST00000409380.1_Silent_p.S111S|SLC3A1_ENST00000409741.1_Silent_p.S389S|SLC3A1_ENST00000409229.3_Silent_p.S389S	NM_000341.3	NP_000332.2	Q07837	SLC31_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 1	389					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|basic amino acid transport (GO:0015802)|carbohydrate metabolic process (GO:0005975)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)|vacuolar membrane (GO:0005774)	amino acid transmembrane transporter activity (GO:0015171)|basic amino acid transmembrane transporter activity (GO:0015174)|catalytic activity (GO:0003824)|cation binding (GO:0043169)|L-cystine transmembrane transporter activity (GO:0015184)	p.S389S(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(3)	26		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)			L-Cystine(DB00138)	ATGCAGAGAGTATTGACAGGA	0.473																																					p.S389S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1167C	2						.						196.0	170.0	179.0					2																	44531312		2203	4300	6503	44384816	SO:0001819	synonymous_variant	6519	exon7				CCDS1819.1	2p16.3	2013-07-19	2013-07-19		ENSG00000138079	ENSG00000138079		"""Solute carriers"""	11025	protein-coding gene	gene with protein product		104614	"""solute carrier family 3 (cystine, dibasic and neutral amino acid transporters, activator of cystine, dibasic and neutral amino acid transport), member 1"""			8486766, 9186880	Standard	NM_000341		Approved	CSNU1, D2H, RBAT, ATR1, NBAT	uc002ruc.4	Q07837	OTTHUMG00000128759	ENST00000260649.6:c.1167T>C	2.37:g.44531312T>C		Somatic		Capture	Illumina HiSeq	Phase_I	44384816	NM_000341	A8K0S1|O00658|Q15295|Q4J6B4|Q4J6B5|Q4J6B6|Q4J6B7|Q4J6B8|Q4J6B9|Q52M92|Q52M94	Silent	SNP	ENST00000260649.6	37	CCDS1819.1																																																																																				0.473	SLC3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250676.1	NM_000341	
TTC7A	57217	broad.mit.edu	37	2	47301054	47301054	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:47301054G>A	ENST00000319190.5	+	20	2937	c.2569G>A	c.(2569-2571)Gag>Aag	p.E857K	C2orf61_ENST00000464527.2_Intron|TTC7A_ENST00000394850.2_Missense_Mutation_p.E881K|TTC7A_ENST00000263737.6_Missense_Mutation_p.E503K|RP11-761B3.1_ENST00000422269.1_Intron|TTC7A_ENST00000409245.1_Missense_Mutation_p.E823K|AC073283.7_ENST00000421759.1_RNA	NM_020458.2	NP_065191.2	Q9ULT0	TTC7A_HUMAN	tetratricopeptide repeat domain 7A	857					cellular iron ion homeostasis (GO:0006879)|hemopoiesis (GO:0030097)			p.E857K(1)		breast(4)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			CATCCCCAGAGAGCTCTGACG	0.672																																					p.E857K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2569A	2						.						29.0	26.0	27.0					2																	47301054		2201	4299	6500	47154558	SO:0001583	missense	57217	exon20			AB032966	CCDS33193.1, CCDS74510.1, CCDS74511.1	2p16.3	2013-01-10	2004-06-02	2004-06-02	ENSG00000068724	ENSG00000068724		"""Tetratricopeptide (TTC) repeat domain containing"""	19750	protein-coding gene	gene with protein product		609332	"""tetratricopeptide repeat domain 7"""	TTC7		10574461	Standard	XM_005264439		Approved	KIAA1140	uc002rvo.3	Q9ULT0	OTTHUMG00000153121	ENST00000319190.5:c.2569G>A	2.37:g.47301054G>A	ENSP00000316699:p.Glu857Lys	Somatic		Capture	Illumina HiSeq	Phase_I	47154558	NM_020458	Q6PIX4|Q8ND67|Q9BUS3	Missense_Mutation	SNP	ENST00000319190.5	37	CCDS33193.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.721313	0.89205	.	.	ENSG00000068724	ENST00000409245;ENST00000319190;ENST00000394850;ENST00000263737;ENST00000434093	T;T;T;T	0.30981	1.9;1.91;1.52;1.51	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.48040	0.1478	L	0.50333	1.59	0.80722	D	1	D;P;D;D	0.67145	0.996;0.949;0.996;0.97	P;P;D;P	0.65443	0.883;0.694;0.935;0.839	T	0.19712	-1.0297	10	0.20519	T	0.43	-20.092	18.5332	0.91000	0.0:0.0:1.0:0.0	.	881;823;857;823	Q2T9J9;B3KPK7;Q9ULT0;G5E9G4	.;.;TTC7A_HUMAN;.	K	823;857;881;503;684	ENSP00000386307:E823K;ENSP00000316699:E857K;ENSP00000378320:E881K;ENSP00000263737:E503K	ENSP00000263737:E503K	E	+	1	0	TTC7A	47154558	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	3.462000	0.53042	2.495000	0.84180	0.561000	0.74099	GAG		0.672	TTC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329667.2	XM_372927	
MSH2	4436	broad.mit.edu	37	2	47643533	47643533	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:47643533G>A	ENST00000233146.2	+	6	1264	c.1041G>A	c.(1039-1041)aaG>aaA	p.K347K	MSH2_ENST00000406134.1_Silent_p.K347K|MSH2_ENST00000543555.1_Silent_p.K281K	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	347					ATP catabolic process (GO:0006200)|B cell differentiation (GO:0030183)|B cell mediated immunity (GO:0019724)|cell cycle arrest (GO:0007050)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|intra-S DNA damage checkpoint (GO:0031573)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|isotype switching (GO:0045190)|maintenance of DNA repeat elements (GO:0043570)|male gonad development (GO:0008584)|meiotic gene conversion (GO:0006311)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reciprocal meiotic recombination (GO:0045128)|oxidative phosphorylation (GO:0006119)|positive regulation of helicase activity (GO:0051096)|postreplication repair (GO:0006301)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSalpha complex (GO:0032301)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|guanine/thymine mispair binding (GO:0032137)|heteroduplex DNA loop binding (GO:0000404)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|Y-form DNA binding (GO:0000403)	p.0?(2)|p.?(1)|p.K347K(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(5)|large_intestine(50)|lung(18)|ovary(5)|prostate(2)|skin(3)|small_intestine(1)|stomach(2)|urinary_tract(1)	112		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AGTGGATTAAGCAGCCTCTCA	0.408			"""D, Mis, N, F, S"""		"""colorectal, endometrial, ovarian"""	"""colorectal, endometrial, ovarian"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.K347K		yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p22-p21	4436	mutS homolog 2 (E. coli)		E	.	.	4	Whole gene deletion(2)|Substitution - coding silent(1)|Unknown(1)	haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)	c.G1041A	2						.						130.0	130.0	130.0					2																	47643533		2203	4300	6503	47497037	SO:0001819	synonymous_variant	4436	exon6	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U03911	CCDS1834.1, CCDS58709.1	2p21	2014-09-17	2013-09-12		ENSG00000095002	ENSG00000095002			7325	protein-coding gene	gene with protein product		609309	"""mutS (E. coli) homolog 2 (colon cancer, nonpolyposis type 1)"", ""mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)"""	COCA1		8484120, 9843200	Standard	NM_000251		Approved	HNPCC, HNPCC1	uc002rvy.2	P43246	OTTHUMG00000128861	ENST00000233146.2:c.1041G>A	2.37:g.47643533G>A		Somatic		Capture	Illumina HiSeq	Phase_I	47497037	NM_000251	B4E2Z2|O75488	Silent	SNP	ENST00000233146.2	37	CCDS1834.1																																																																																				0.408	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3		
MSH6	2956	broad.mit.edu	37	2	48026204	48026204	+	Missense_Mutation	SNP	G	G	A	rs267608056|rs63750440		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:48026204G>A	ENST00000234420.5	+	4	1234	c.1082G>A	c.(1081-1083)cGc>cAc	p.R361H	MSH6_ENST00000538136.1_Missense_Mutation_p.R59H|FBXO11_ENST00000405808.1_Intron|MSH6_ENST00000540021.1_Missense_Mutation_p.R231H	NM_000179.2	NP_000170.1	P52701	MSH6_HUMAN	mutS homolog 6	361					ATP catabolic process (GO:0006200)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|response to UV (GO:0009411)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|MutSalpha complex (GO:0032301)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|guanine/thymine mispair binding (GO:0032137)|methylated histone binding (GO:0035064)|mismatched DNA binding (GO:0030983)	p.0?(2)|p.R361H(1)		breast(8)|central_nervous_system(29)|cervix(1)|endometrium(32)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(75)|lung(25)|ovary(3)|prostate(3)|skin(10)|stomach(22)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	229		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GACAGTAGTCGCCCTACTGTT	0.453			"""Mis, N, F, S"""		colorectal	"""colorectal, endometrial, ovarian"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.R361H		yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p16	2956	mutS homolog 6 (E. coli)		E	.	.	3	Whole gene deletion(2)|Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)	c.G1082A	2						.						91.0	92.0	92.0					2																	48026204		2203	4300	6503	47879708	SO:0001583	missense	2956	exon4	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	U54777	CCDS1836.1, CCDS62906.1, CCDS62907.1	2p16	2014-09-17	2013-09-12		ENSG00000116062	ENSG00000116062			7329	protein-coding gene	gene with protein product		600678	"""mutS (E. coli) homolog 6"", ""mutS homolog 6 (E. coli)"""	GTBP		7604266	Standard	NM_000179		Approved		uc002rwd.4	P52701	OTTHUMG00000129129	ENST00000234420.5:c.1082G>A	2.37:g.48026204G>A	ENSP00000234420:p.Arg361His	Somatic		Capture	Illumina HiSeq	Phase_I	47879708	NM_000179	B4DF41|B4E3I4|F5H2F9|O43706|O43917|Q8TCX4|Q9BTB5	Missense_Mutation	SNP	ENST00000234420.5	37	CCDS1836.1	.	.	.	.	.	.	.	.	.	.	G	12.93	2.084128	0.36758	.	.	ENSG00000116062	ENST00000234420;ENST00000544857;ENST00000540021;ENST00000538136	D;D;D	0.87650	-1.91;-2.05;-2.28	4.09	4.09	0.47781	.	0.437004	0.23266	N	0.050064	T	0.77232	0.4100	N	0.08118	0	0.24714	N	0.993181	P;P;P	0.44521	0.789;0.837;0.829	B;B;P	0.45794	0.036;0.243;0.493	T	0.70457	-0.4866	10	0.45353	T	0.12	-3.9883	10.5136	0.44876	0.0:0.2699:0.7301:0.0	rs63750440	231;361;361	B4DF41;P52701;P52701-2	.;MSH6_HUMAN;.	H	361;359;231;59	ENSP00000234420:R361H;ENSP00000446475:R231H;ENSP00000438580:R59H	ENSP00000234420:R361H	R	+	2	0	MSH6	47879708	0.956000	0.32656	0.458000	0.27068	0.846000	0.48090	5.290000	0.65661	2.118000	0.64928	0.655000	0.94253	CGC		0.453	MSH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251180.4	NM_000179	
ACTG2	72	broad.mit.edu	37	2	74140692	74140692	+	Missense_Mutation	SNP	C	C	T	rs78001248		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:74140692C>T	ENST00000409624.1	+	7	1175	c.532C>T	c.(532-534)Cgc>Tgc	p.R178C	ACTG2_ENST00000409731.3_Missense_Mutation_p.R135C|ACTG2_ENST00000345517.3_Missense_Mutation_p.R178C			P63267	ACTH_HUMAN	actin, gamma 2, smooth muscle, enteric	178			R -> C (in VSCM; interferes with proper polymerization into thin filaments leading to impaired contractility of the smooth muscle). {ECO:0000269|PubMed:24337657, ECO:0000269|PubMed:24676022}.|R -> H (in VSCM). {ECO:0000269|PubMed:24676022}.|R -> L (in VSCM; interferes with proper polymerization into thin filaments leading to impaired contractility of the smooth muscle). {ECO:0000269|PubMed:24337657}.		muscle contraction (GO:0006936)	blood microparticle (GO:0072562)|cell periphery (GO:0071944)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)	p.R178C(1)		large_intestine(3)|lung(14)|skin(1)	18						TGCCATCATGCGCCTGGACTT	0.557																																					p.R178C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C532T	2						.						143.0	126.0	132.0					2																	74140692		2203	4300	6503	73994200	SO:0001583	missense	72	exon6				CCDS1930.1, CCDS56124.1	2p13.1	2008-05-20			ENSG00000163017	ENSG00000163017			145	protein-coding gene	gene with protein product		102545		ACTL3, ACTA3		1710027, 1673027	Standard	NM_001199893		Approved	ACTSG	uc002sjw.3	P63267	OTTHUMG00000129813	ENST00000409624.1:c.532C>T	2.37:g.74140692C>T	ENSP00000386857:p.Arg178Cys	Somatic		Capture	Illumina HiSeq	Phase_I	73994200	NM_001615	B2R7E7|B4E315|D6W5H8|E9PG30|P12718|Q504R1|Q6FI22	Missense_Mutation	SNP	ENST00000409624.1	37	CCDS1930.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.055284	0.75960	.	.	ENSG00000163017	ENST00000409731;ENST00000345517;ENST00000409624	D;D;D	0.95137	-3.62;-3.62;-3.62	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	D	0.96932	0.8998	H	0.99357	4.53	0.80722	D	1	P;B	0.44309	0.832;0.118	B;B	0.39185	0.293;0.231	D	0.98579	1.0649	10	0.87932	D	0	.	17.4481	0.87584	0.0:1.0:0.0:0.0	.	135;178	E9PG30;P63267	.;ACTH_HUMAN	C	135;178;178	ENSP00000386929:R135C;ENSP00000295137:R178C;ENSP00000386857:R178C	ENSP00000295137:R178C	R	+	1	0	ACTG2	73994200	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.609000	0.82925	2.733000	0.93635	0.557000	0.71058	CGC		0.557	ACTG2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328086.1	NM_001615	
SLC4A5	57835	broad.mit.edu	37	2	74454676	74454676	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:74454676A>G	ENST00000377634.4	-	27	3331	c.2932T>C	c.(2932-2934)Tca>Cca	p.S978P	SLC4A5_ENST00000346834.4_Intron|SLC4A5_ENST00000357822.5_Missense_Mutation_p.S978P|SLC4A5_ENST00000359484.4_Intron|SLC4A5_ENST00000377632.1_Intron|SLC4A5_ENST00000394019.2_Intron|SLC4A5_ENST00000358683.4_Intron|SLC4A5_ENST00000423644.1_Intron|RP11-287D1.3_ENST00000451608.2_3'UTR|SLC4A5_ENST00000483195.1_Intron					solute carrier family 4 (sodium bicarbonate cotransporter), member 5									p.S978P(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						TTGAATtctgaccctccggtc	0.408																																					p.S978P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2932C	2						.						72.0	71.0	72.0					2																	74454676		2203	4300	6503	74308184	SO:0001583	missense	57835	exon22			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.2932T>C	2.37:g.74454676A>G	ENSP00000366861:p.Ser978Pro	Somatic		Capture	Illumina HiSeq	Phase_I	74308184	NM_021196		Missense_Mutation	SNP	ENST00000377634.4	37	CCDS1936.1	.	.	.	.	.	.	.	.	.	.	A	7.471	0.646726	0.14516	.	.	ENSG00000188687	ENST00000451608;ENST00000357822;ENST00000377634	T;T	0.77229	-1.08;-1.08	3.9	1.44	0.22558	Bicarbonate transporter, C-terminal (1);	9.680060	0.00166	U	0.000010	T	0.60301	0.2258	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.49254	-0.8959	10	0.30078	T	0.28	.	6.0982	0.20033	0.6821:0.0:0.3179:0.0	.	978	Q9BY07	S4A5_HUMAN	P	978	ENSP00000350475:S978P;ENSP00000366861:S978P	ENSP00000350475:S978P	S	-	1	0	SLC4A5	74308184	0.000000	0.05858	0.038000	0.18304	0.037000	0.13140	0.151000	0.16283	0.303000	0.22785	0.533000	0.62120	TCA		0.408	SLC4A5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206583.3		
MRPL53	116540	broad.mit.edu	37	2	74699727	74699727	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:74699727A>T	ENST00000258105.7	-	1	722	c.61T>A	c.(61-63)Tgt>Agt	p.C21S	MRPL53_ENST00000409710.1_Missense_Mutation_p.C21S	NM_053050.4	NP_444278.1	Q96EL3	RM53_HUMAN	mitochondrial ribosomal protein L53	21						mitochondrion (GO:0005739)|ribosome (GO:0005840)		p.M450K(1)|p.C21S(1)		central_nervous_system(1)|large_intestine(2)|lung(1)|urinary_tract(1)	5						TCGAAGGGACAGAACTGAACC	0.602																																					p.C21S												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T61A	2						.						111.0	99.0	103.0					2																	74699727		2203	4300	6503	74553235	SO:0001583	missense	116540	exon1			BC012163	CCDS1944.1	2p13.1	2012-09-13			ENSG00000204822	ENSG00000204822		"""Mitochondrial ribosomal proteins / large subunits"""	16684	protein-coding gene	gene with protein product		611857				11551941	Standard	NM_053050		Approved		uc002sln.3	Q96EL3	OTTHUMG00000129961	ENST00000258105.7:c.61T>A	2.37:g.74699727A>T	ENSP00000258105:p.Cys21Ser	Somatic		Capture	Illumina HiSeq	Phase_I	74553235	NM_053050		Missense_Mutation	SNP	ENST00000258105.7	37	CCDS1944.1	.	.	.	.	.	.	.	.	.	.	A	10.94	1.493338	0.26774	.	.	ENSG00000204822	ENST00000258105;ENST00000409710	T;T	0.72051	0.95;-0.62	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.76392	0.3981	L	0.50919	1.6	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	T	0.71543	-0.4561	10	0.12766	T	0.61	-29.143	11.3777	0.49737	1.0:0.0:0.0:0.0	.	21	Q96EL3	RM53_HUMAN	S	21	ENSP00000258105:C21S;ENSP00000386920:C21S	ENSP00000258105:C21S	C	-	1	0	MRPL53	74553235	1.000000	0.71417	0.998000	0.56505	0.014000	0.08584	4.445000	0.60007	2.174000	0.68829	0.533000	0.62120	TGT		0.602	MRPL53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252225.2	NM_053050	
HTRA2	27429	broad.mit.edu	37	2	74757324	74757324	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:74757324G>A	ENST00000258080.3	+	1	821	c.191G>A	c.(190-192)gGg>gAg	p.G64E	HTRA2_ENST00000352222.3_Missense_Mutation_p.G64E|HTRA2_ENST00000467961.1_Intron|AUP1_ENST00000377526.3_5'Flank	NM_013247.4	NP_037379.1	O43464	HTRA2_HUMAN	HtrA serine peptidase 2	64					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.G64E(1)		endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	12						TTGTCTGTTGGGGTCACTGAA	0.667																																					p.G64E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G191A	2						.						12.0	14.0	14.0					2																	74757324		2194	4287	6481	74610832	SO:0001583	missense	27429	exon1				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.191G>A	2.37:g.74757324G>A	ENSP00000258080:p.Gly64Glu	Somatic		Capture	Illumina HiSeq	Phase_I	74610832	NM_013247	Q9HBZ4|Q9P0Y3|Q9P0Y4	Missense_Mutation	SNP	ENST00000258080.3	37	CCDS1951.1	.	.	.	.	.	.	.	.	.	.	g	15.12	2.739159	0.49045	.	.	ENSG00000115317	ENST00000258080;ENST00000352222;ENST00000437202	T;T;T	0.15718	2.4;2.4;2.4	4.05	4.05	0.47172	.	0.080123	0.49305	D	0.000159	T	0.23054	0.0557	N	0.24115	0.695	0.34959	D	0.751977	P;P;D;P	0.59767	0.89;0.933;0.986;0.802	B;P;P;B	0.58130	0.338;0.659;0.833;0.338	T	0.23583	-1.0184	10	0.72032	D	0.01	-15.2358	14.5212	0.67851	0.0:0.0:1.0:0.0	.	64;64;64;64	A8K7G2;O43464-3;O43464-2;O43464	.;.;.;HTRA2_HUMAN	E	64;64;51	ENSP00000258080:G64E;ENSP00000312893:G64E;ENSP00000399166:G51E	ENSP00000258080:G64E	G	+	2	0	HTRA2	74610832	0.952000	0.32445	0.993000	0.49108	0.248000	0.25809	2.167000	0.42415	2.547000	0.85894	0.457000	0.33378	GGG		0.667	HTRA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252219.2	NM_013247	
POLR1A	25885	broad.mit.edu	37	2	86308732	86308732	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:86308732C>T	ENST00000263857.6	-	8	1293	c.915G>A	c.(913-915)ccG>ccA	p.P305P	POLR1A_ENST00000409681.1_Silent_p.P305P			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	305					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)|DNA-directed RNA polymerase I complex (GO:0005736)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)	p.P305P(1)		NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						ACCTTGAGGGCGGCACCACCA	0.423																																					p.P305P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G915A	2						.						87.0	81.0	83.0					2																	86308732		1852	4100	5952	86162243	SO:0001819	synonymous_variant	25885	exon8			AK025568	CCDS42706.1	2p11.2	2013-01-21			ENSG00000068654	ENSG00000068654		"""RNA polymerase subunits"""	17264	protein-coding gene	gene with protein product						9236775	Standard	NM_015425		Approved	DKFZP586M0122, FLJ21915, RPO1-4, RPA1	uc002sqs.3	O95602	OTTHUMG00000153165	ENST00000263857.6:c.915G>A	2.37:g.86308732C>T		Somatic		Capture	Illumina HiSeq	Phase_I	86162243	NM_015425	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Silent	SNP	ENST00000263857.6	37	CCDS42706.1																																																																																				0.423	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425	
POLR1A	25885	broad.mit.edu	37	2	86315788	86315788	+	Missense_Mutation	SNP	C	C	T	rs375330613		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:86315788C>T	ENST00000263857.6	-	6	1009	c.631G>A	c.(631-633)Ggg>Agg	p.G211R	POLR1A_ENST00000409681.1_Missense_Mutation_p.G211R			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	211					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)|DNA-directed RNA polymerase I complex (GO:0005736)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)	p.G211R(1)		NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						ACGGATCGCCCGGTCCTGTGC	0.517																																					p.G211R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G631A	2						.	C	ARG/GLY	1,3935		0,1,1967	111.0	101.0	104.0		631	6.2	1.0	2		104	0,8294		0,0,4147	no	missense	POLR1A	NM_015425.3	125	0,1,6114	TT,TC,CC		0.0,0.0254,0.0082	benign	211/1721	86315788	1,12229	1968	4147	6115	86169299	SO:0001583	missense	25885	exon6			AK025568	CCDS42706.1	2p11.2	2013-01-21			ENSG00000068654	ENSG00000068654		"""RNA polymerase subunits"""	17264	protein-coding gene	gene with protein product						9236775	Standard	NM_015425		Approved	DKFZP586M0122, FLJ21915, RPO1-4, RPA1	uc002sqs.3	O95602	OTTHUMG00000153165	ENST00000263857.6:c.631G>A	2.37:g.86315788C>T	ENSP00000263857:p.Gly211Arg	Somatic		Capture	Illumina HiSeq	Phase_I	86169299	NM_015425	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Missense_Mutation	SNP	ENST00000263857.6	37	CCDS42706.1	.	.	.	.	.	.	.	.	.	.	C	7.613	0.675252	0.14841	2.54E-4	0.0	ENSG00000068654	ENST00000263857;ENST00000409681	T;T	0.66460	-0.21;-0.21	6.17	6.17	0.99709	RNA polymerase Rpb1, domain 1 (1);	0.205916	0.52532	D	0.000076	T	0.53658	0.1810	L	0.38838	1.175	0.37264	D	0.907094	B;B	0.28258	0.152;0.205	B;B	0.25140	0.038;0.058	T	0.54282	-0.8317	10	0.25106	T	0.35	-38.5118	10.4826	0.44702	0.0:0.7938:0.1355:0.0707	.	211;211	B9ZVN9;O95602	.;RPA1_HUMAN	R	211	ENSP00000263857:G211R;ENSP00000386300:G211R	ENSP00000263857:G211R	G	-	1	0	POLR1A	86169299	0.987000	0.35691	0.980000	0.43619	0.035000	0.12851	3.057000	0.49931	2.941000	0.99782	0.655000	0.94253	GGG		0.517	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425	
ITPRIPL1	150771	broad.mit.edu	37	2	96993099	96993099	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:96993099C>A	ENST00000439118.2	+	3	981	c.730C>A	c.(730-732)Cca>Aca	p.P244T	ITPRIPL1_ENST00000361124.4_Missense_Mutation_p.P252T|ITPRIPL1_ENST00000536814.1_Missense_Mutation_p.P236T|ITPRIPL1_ENST00000542887.1_Missense_Mutation_p.P236T	NM_001008949.2	NP_001008949.1	Q6GPH6	IPIL1_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein-like 1	244						integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.P252T(1)		breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						CATTGTCCCCCCACAGGGCAC	0.582																																					p.P236T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C706A	2						.						37.0	40.0	39.0					2																	96993099		2203	4300	6503	96356826	SO:0001583	missense	150771	exon2				CCDS33250.1, CCDS46360.1, CCDS54378.1	2q11.2	2011-04-28	2011-04-28	2008-08-11	ENSG00000198885	ENSG00000198885			29371	protein-coding gene	gene with protein product			"""KIAA1754-like"", ""inositol 1,4,5-triphosphate receptor interacting protein-like 1"""	KIAA1754L		12477932	Standard	NM_178495		Approved		uc010yul.2	Q6GPH6	OTTHUMG00000155230	ENST00000439118.2:c.730C>A	2.37:g.96993099C>A	ENSP00000389308:p.Pro244Thr	Somatic		Capture	Illumina HiSeq	Phase_I	96356826	NM_001163523	F5H1L8|Q8NE61	Missense_Mutation	SNP	ENST00000439118.2	37	CCDS46360.1	.	.	.	.	.	.	.	.	.	.	C	12.92	2.081804	0.36758	.	.	ENSG00000198885	ENST00000536814;ENST00000439118;ENST00000361124;ENST00000542887	T;T;T;T	0.37752	1.21;1.2;1.18;1.21	5.24	5.24	0.73138	.	0.000000	0.48767	D	0.000165	T	0.50205	0.1602	L	0.29908	0.895	0.48135	D	0.999591	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.52245	-0.8601	10	0.87932	D	0	-20.5596	17.7609	0.88464	0.0:1.0:0.0:0.0	.	252;244	Q6GPH6-2;Q6GPH6	.;IPIL1_HUMAN	T	236;244;252;236	ENSP00000439566:P236T;ENSP00000389308:P244T;ENSP00000355121:P252T;ENSP00000438212:P236T	ENSP00000355121:P252T	P	+	1	0	ITPRIPL1	96356826	1.000000	0.71417	0.154000	0.22540	0.034000	0.12701	6.252000	0.72447	2.706000	0.92434	0.655000	0.94253	CCA		0.582	ITPRIPL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000338896.1	NM_178495	
FARP2	9855	broad.mit.edu	37	2	242402855	242402855	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr2:242402855C>T	ENST00000264042.3	+	16	1953	c.1783C>T	c.(1783-1785)Cgc>Tgc	p.R595C	FARP2_ENST00000373287.4_Missense_Mutation_p.R595C|FARP2_ENST00000545004.1_Missense_Mutation_p.R595C	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	595	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton reorganization (GO:0031532)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|neuron remodeling (GO:0016322)|osteoclast differentiation (GO:0030316)|podosome assembly (GO:0071800)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of integrin activation (GO:0033623)|regulation of Rac GTPase activity (GO:0032314)|semaphorin-plexin signaling pathway (GO:0071526)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R595C(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	43		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		AGGCTTCCTGCGCGAGGTGGA	0.592																																					p.R595C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1783T	2						.						98.0	80.0	86.0					2																	242402855		2203	4300	6503	242051528	SO:0001583	missense	9855	exon16			AB018336	CCDS33424.1, CCDS63197.1	2q37.3	2013-01-10			ENSG00000006607	ENSG00000006607		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	16460	protein-coding gene	gene with protein product						9872452, 12351724	Standard	NM_001282984		Approved	KIAA0793, FIR, PLEKHC3, FRG	uc002wbi.2	O94887	OTTHUMG00000151574	ENST00000264042.3:c.1783C>T	2.37:g.242402855C>T	ENSP00000264042:p.Arg595Cys	Somatic		Capture	Illumina HiSeq	Phase_I	242051528	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Missense_Mutation	SNP	ENST00000264042.3	37	CCDS33424.1	.	.	.	.	.	.	.	.	.	.	C	16.01	3.002624	0.54254	.	.	ENSG00000006607	ENST00000264042;ENST00000545004;ENST00000373287	T;T;T	0.63913	-0.07;-0.07;-0.07	5.25	3.26	0.37387	Dbl homology (DH) domain (5);	0.603345	0.16535	N	0.210218	T	0.50343	0.1610	L	0.39245	1.2	0.34476	D	0.703387	B;B;B	0.17465	0.017;0.017;0.022	B;B;B	0.12837	0.005;0.005;0.008	T	0.58387	-0.7645	10	0.56958	D	0.05	.	8.0778	0.30726	0.2375:0.6699:0.0:0.0926	.	595;595;595	O94887-2;F5GZ84;O94887	.;.;FARP2_HUMAN	C	595	ENSP00000264042:R595C;ENSP00000443876:R595C;ENSP00000362384:R595C	ENSP00000264042:R595C	R	+	1	0	FARP2	242051528	0.967000	0.33354	0.699000	0.30290	0.992000	0.81027	2.618000	0.46393	1.200000	0.43188	-0.140000	0.14226	CGC		0.592	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1		
SLC6A11	6538	broad.mit.edu	37	3	10858058	10858058	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:10858058G>A	ENST00000254488.2	+	1	174	c.108G>A	c.(106-108)gcG>gcA	p.A36A	SLC6A11_ENST00000454147.1_Silent_p.A36A	NM_014229.1	NP_055044.1	P48066	S6A11_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 11	36					brain development (GO:0007420)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter binding (GO:0042165)|neurotransmitter:sodium symporter activity (GO:0005328)	p.A36A(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(13)|ovary(1)|skin(4)	35				OV - Ovarian serous cystadenocarcinoma(96;0.229)	Clobazam(DB00349)	cggcgcccgcgcgccacccgc	0.736																																					p.A36A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G108A	3						.						10.0	7.0	8.0					3																	10858058		2130	4131	6261	10833058	SO:0001819	synonymous_variant	6538	exon1			S75989	CCDS2602.1	3p25.3	2013-07-19	2013-07-19		ENSG00000132164	ENSG00000132164		"""Solute carriers"""	11044	protein-coding gene	gene with protein product	"""GABA transporter 3"""	607952	"""solute carrier family 6 (neurotransmitter transporter, GABA), member 11"""			7874447	Standard	NM_014229		Approved	GAT3	uc003bvz.3	P48066	OTTHUMG00000129718	ENST00000254488.2:c.108G>A	3.37:g.10858058G>A		Somatic		Capture	Illumina HiSeq	Phase_I	10833058	NM_014229	B2R6U6|Q8IYC9	Silent	SNP	ENST00000254488.2	37	CCDS2602.1																																																																																				0.736	SLC6A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251927.1	NM_014229	
COL8A1	1295	broad.mit.edu	37	3	99513759	99513759	+	Silent	SNP	G	G	A	rs200329310		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:99513759G>A	ENST00000261037.3	+	5	1394	c.1014G>A	c.(1012-1014)ctG>ctA	p.L338L	COL8A1_ENST00000273342.4_Silent_p.L338L	NM_001850.4	NP_001841.2	P27658	CO8A1_HUMAN	collagen, type VIII, alpha 1	338	Triple-helical region (COL1).				angiogenesis (GO:0001525)|camera-type eye morphogenesis (GO:0048593)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	collagen type VIII trimer (GO:0005591)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)				breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(15)|skin(5)|upper_aerodigestive_tract(1)	27						AGCAAGGACTGCCAGGGCTAC	0.627																																					p.L338L												.	.	0			c.G1014A	3						.						28.0	33.0	31.0					3																	99513759		2203	4299	6502	100996449	SO:0001819	synonymous_variant	1295	exon4			AF170702	CCDS2934.1	3q11.1-q13.2	2013-01-16			ENSG00000144810	ENSG00000144810		"""Collagens"""	2215	protein-coding gene	gene with protein product		120251	"""chromosome 3 open reading frame 7"""	C3orf7		2029894	Standard	NM_001850		Approved	MGC9568	uc003dth.2	P27658	OTTHUMG00000148669	ENST00000261037.3:c.1014G>A	3.37:g.99513759G>A		None		Capture	Illumina HiSeq	Phase_I	100996449	NM_020351	D3DN42|Q53XI6|Q96D07	Silent	SNP	ENST00000261037.3	37	CCDS2934.1																																																																																				0.627	COL8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309001.1	NM_001850	
MORC1	27136	broad.mit.edu	37	3	108776288	108776288	+	Silent	SNP	G	G	A	rs369056513		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:108776288G>A	ENST00000483760.1	-	13	1120	c.1077C>T	c.(1075-1077)aaC>aaT	p.N359N	MORC1_ENST00000232603.5_Silent_p.N359N					MORC family CW-type zinc finger 1									p.N359N(1)		breast(7)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(47)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	105						GGTTTTCTACGTTCACTCCAT	0.343													G|||	1	0.000199681	0.0	0.0	5008	,	,		18701	0.0		0.0	False		,,,				2504	0.001				p.N359N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1077T	3						.	G		0,4406		0,0,2203	121.0	114.0	117.0		1077	2.8	1.0	3		117	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MORC1	NM_014429.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		359/985	108776288	1,13005	2203	4300	6503	110258978	SO:0001819	synonymous_variant	27136	exon13			AF084946	CCDS2955.1	3q13	2011-10-26	2005-06-15	2005-06-15	ENSG00000114487	ENSG00000114487			7198	protein-coding gene	gene with protein product	"""cancer/testis antigen 33"""	603205	"""microrchidia (mouse) homolog"", ""microrchidia homolog (mouse)"""	MORC		10369865	Standard	NM_014429		Approved	ZCW6, CT33	uc003dxl.3	Q86VD1	OTTHUMG00000159209	ENST00000483760.1:c.1077C>T	3.37:g.108776288G>A		Somatic		Capture	Illumina HiSeq	Phase_I	110258978	NM_014429		Silent	SNP	ENST00000483760.1	37																																																																																					0.343	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1		
ATG7	10533	broad.mit.edu	37	3	11354804	11354804	+	Silent	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:11354804T>C	ENST00000354449.3	+	6	463	c.438T>C	c.(436-438)taT>taC	p.Y146Y	ATG7_ENST00000446450.2_Intron|ATG7_ENST00000354956.5_Silent_p.Y146Y	NM_006395.2	NP_006386.1	O95352	ATG7_HUMAN	autophagy related 7	146					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.Y146Y(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						ACTTCTACTATTGGTTTTGCT	0.363																																					p.Y146Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T438C	3						.						132.0	124.0	127.0					3																	11354804		2203	4300	6503	11329804	SO:0001819	synonymous_variant	10533	exon6			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.438T>C	3.37:g.11354804T>C		Somatic		Capture	Illumina HiSeq	Phase_I	11329804	NM_006395	B4E170|E9PB95|Q7L8L0|Q9BWP2|Q9UFH4	Silent	SNP	ENST00000354449.3	37	CCDS2605.1																																																																																				0.363	ATG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251951.3	NM_006395	
PHLDB2	90102	broad.mit.edu	37	3	111667781	111667781	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:111667781C>T	ENST00000431670.2	+	10	2901	c.2490C>T	c.(2488-2490)ggC>ggT	p.G830G	PHLDB2_ENST00000393923.3_Silent_p.G814G|PHLDB2_ENST00000393925.3_Silent_p.G830G|PHLDB2_ENST00000481953.1_Silent_p.G787G|PHLDB2_ENST00000412622.1_Silent_p.G787G|PHLDB2_ENST00000495180.1_Intron	NM_001134438.1	NP_001127910.1	Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B, member 2	830						cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(8)|lung(23)|ovary(6)|skin(7)|stomach(1)	55						CCTTTTAGGGCTATATCAGTG	0.438																																					p.G830G												.	.	0			c.C2490T	3						.						76.0	75.0	76.0					3																	111667781		2203	4300	6503	113150471	SO:0001819	synonymous_variant	90102	exon10				CCDS2962.1, CCDS46885.1, CCDS46886.1	3q13.13	2013-01-10			ENSG00000144824	ENSG00000144824		"""Pleckstrin homology (PH) domain containing"""	29573	protein-coding gene	gene with protein product		610298				12376540	Standard	NM_145753		Approved	LL5beta, FLJ21791, LL5b	uc003dyg.3	Q86SQ0	OTTHUMG00000159282	ENST00000431670.2:c.2490C>T	3.37:g.111667781C>T		None		Capture	Illumina HiSeq	Phase_I	113150471	NM_001134439	A5PKZ3|Q59EA8|Q68CY3|Q6NT98|Q8N8U8|Q8NAB1|Q8NCU5	Silent	SNP	ENST00000431670.2	37	CCDS46886.1																																																																																				0.438	PHLDB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354337.1	NM_145753	
CD200R1L	344807	broad.mit.edu	37	3	112545858	112545858	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:112545858A>T	ENST00000398214.1	-	4	886	c.661T>A	c.(661-663)Tcc>Acc	p.S221T	CD200R1L_ENST00000488794.1_Missense_Mutation_p.S200T|CD200R1L_ENST00000448932.1_Missense_Mutation_p.S200T	NM_001008784.2	NP_001008784.2	Q6Q8B3	MO2R2_HUMAN	CD200 receptor 1-like	221	Ig-like C2-type.					integral component of membrane (GO:0016021)		p.S221T(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|urinary_tract(2)	19						AACTTTACGGACAGACTCTTG	0.458																																					p.S221T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T661A	3						.						66.0	70.0	69.0					3																	112545858		2196	4299	6495	114028548	SO:0001583	missense	344807	exon4			AY284976	CCDS43131.1, CCDS56267.1	3q13.2	2014-05-15	2008-10-08		ENSG00000206531	ENSG00000206531		"""Immunoglobulin superfamily / C2-set domain containing"""	24665	protein-coding gene	gene with protein product	"""CD200 receptor 2"""						Standard	NM_001008784		Approved	CD200RLa, CD200R2	uc003dzi.1	Q6Q8B3	OTTHUMG00000159283	ENST00000398214.1:c.661T>A	3.37:g.112545858A>T	ENSP00000381272:p.Ser221Thr	Somatic		Capture	Illumina HiSeq	Phase_I	114028548	NM_001008784	Q6WHB7	Missense_Mutation	SNP	ENST00000398214.1	37	CCDS43131.1	.	.	.	.	.	.	.	.	.	.	A	9.818	1.185126	0.21870	.	.	ENSG00000206531	ENST00000398214;ENST00000488794;ENST00000448932	T;T;T	0.22743	1.94;1.96;1.96	4.35	0.34	0.15985	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.560672	0.17797	N	0.161714	T	0.14098	0.0341	L	0.60455	1.87	0.09310	N	1	P	0.43633	0.813	B	0.35413	0.202	T	0.18587	-1.0332	10	0.24483	T	0.36	.	4.6357	0.12523	0.4677:0.1692:0.0:0.3631	.	221	Q6Q8B3	MO2R2_HUMAN	T	221;200;200	ENSP00000381272:S221T;ENSP00000418413:S200T;ENSP00000415132:S200T	ENSP00000381272:S221T	S	-	1	0	CD200R1L	114028548	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-0.135000	0.10420	-0.029000	0.13827	-0.291000	0.09656	TCC		0.458	CD200R1L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354365.1	NM_001008784	
SIDT1	54847	broad.mit.edu	37	3	113320478	113320478	+	Silent	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:113320478A>G	ENST00000264852.4	+	11	1815	c.1089A>G	c.(1087-1089)acA>acG	p.T363T	SIDT1_ENST00000393830.3_Silent_p.T363T	NM_017699.2	NP_060169.2	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1	363			T -> I (in dbSNP:rs33990195).		dsRNA transport (GO:0033227)	integral component of membrane (GO:0016021)	RNA transmembrane transporter activity (GO:0051033)	p.T363T(1)		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						CTGCCAGCACACCCGAAGGGA	0.423																																					p.T363T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1089G	3						.						116.0	103.0	107.0					3																	113320478		2203	4300	6503	114803168	SO:0001819	synonymous_variant	54847	exon11			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.1089A>G	3.37:g.113320478A>G		Somatic		Capture	Illumina HiSeq	Phase_I	114803168	NM_017699	Q17RR4	Silent	SNP	ENST00000264852.4	37	CCDS2974.1																																																																																				0.423	SIDT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317564.1	NM_017699	
ILDR1	286676	broad.mit.edu	37	3	121712753	121712753	+	Silent	SNP	G	G	A	rs371152020		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:121712753G>A	ENST00000344209.5	-	7	969	c.843C>T	c.(841-843)atC>atT	p.I281I	ILDR1_ENST00000462014.1_Silent_p.I249I|ILDR1_ENST00000460554.1_5'UTR|ILDR1_ENST00000273691.3_Silent_p.I237I|ILDR1_ENST00000393631.1_Silent_p.I192I	NM_001199799.1	NP_001186728.1	Q86SU0	ILDR1_HUMAN	immunoglobulin-like domain containing receptor 1	281					positive regulation of peptide hormone secretion (GO:0090277)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-density lipoprotein particle receptor activity (GO:0070506)	p.I281I(1)|p.I237I(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				GBM - Glioblastoma multiforme(114;0.156)		CACCATTGGCGATGGGAGGCT	0.547																																					p.I237I												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C711T	3						.	G	,,	1,4405	2.1+/-5.4	0,1,2202	67.0	64.0	65.0		843,576,711	-1.5	0.0	3		65	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	ILDR1	NM_001199799.1,NM_001199800.1,NM_175924.3	,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,	281/547,192/458,237/503	121712753	1,13005	2203	4300	6503	123195443	SO:0001819	synonymous_variant	286676	exon6			BC044240	CCDS3008.1, CCDS56270.1, CCDS56271.1	3q21.1	2013-10-11			ENSG00000145103	ENSG00000145103			28741	protein-coding gene	gene with protein product		609739	"""deafness, autosomal recessive 42"""	DFNB42		15641023, 21255762	Standard	NM_175924		Approved	MGC50831	uc003ees.3	Q86SU0	OTTHUMG00000159481	ENST00000344209.5:c.843C>T	3.37:g.121712753G>A		Somatic		Capture	Illumina HiSeq	Phase_I	123195443	NM_175924	Q6ZP61|Q7Z578	Silent	SNP	ENST00000344209.5	37	CCDS56271.1																																																																																				0.547	ILDR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355666.1	NM_175924	
PDIA5	10954	broad.mit.edu	37	3	122842976	122842976	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:122842976C>T	ENST00000316218.7	+	9	768	c.673C>T	c.(673-675)Cgc>Tgc	p.R225C		NM_006810.3	NP_006801.1	Q14554	PDIA5_HUMAN	protein disulfide isomerase family A, member 5	225	Thioredoxin 1. {ECO:0000255|PROSITE- ProRule:PRU00691}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|oxidation-reduction process (GO:0055114)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	oxidoreductase activity (GO:0016491)|protein disulfide isomerase activity (GO:0003756)	p.R225C(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	21				GBM - Glioblastoma multiforme(114;0.0427)		GTACAGCGTGCGCGGCTTCCC	0.537																																					p.R225C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C673T	3						.						78.0	71.0	73.0					3																	122842976		2203	4300	6503	124325666	SO:0001583	missense	10954	exon9			AK054963	CCDS3020.1	3q21.1	2009-11-20	2005-06-29		ENSG00000065485	ENSG00000065485	5.3.4.1	"""Protein disulfide isomerases"""	24811	protein-coding gene	gene with protein product			"""protein disulfide isomerase-associated 5"""			7556671	Standard	NM_006810		Approved	PDIR, FLJ30401	uc003egc.2	Q14554	OTTHUMG00000159558	ENST00000316218.7:c.673C>T	3.37:g.122842976C>T	ENSP00000323313:p.Arg225Cys	Somatic		Capture	Illumina HiSeq	Phase_I	124325666	NM_006810	D3DN95|Q9BV43	Missense_Mutation	SNP	ENST00000316218.7	37	CCDS3020.1	.	.	.	.	.	.	.	.	.	.	C	19.14	3.769373	0.69992	.	.	ENSG00000065485	ENST00000316218	T	0.64618	-0.11	5.27	4.4	0.53042	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.135590	0.50627	D	0.000104	T	0.81489	0.4833	M	0.91090	3.175	0.53005	D	0.999969	D	0.76494	0.999	D	0.65140	0.932	D	0.85623	0.1265	10	0.56958	D	0.05	.	14.5045	0.67743	0.0:0.8539:0.1461:0.0	.	225	Q14554	PDIA5_HUMAN	C	225	ENSP00000323313:R225C	ENSP00000323313:R225C	R	+	1	0	PDIA5	124325666	1.000000	0.71417	0.843000	0.33291	0.972000	0.66771	5.165000	0.64959	1.440000	0.47531	0.655000	0.94253	CGC		0.537	PDIA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356192.1	NM_006810	
MYLK	4638	broad.mit.edu	37	3	123456231	123456231	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:123456231T>C	ENST00000475616.1	-	5	747	c.748A>G	c.(748-750)Atc>Gtc	p.I250V	MYLK_ENST00000360772.3_Missense_Mutation_p.I250V|MYLK_ENST00000359169.1_Missense_Mutation_p.I250V|MYLK_ENST00000360304.3_Missense_Mutation_p.I250V|MYLK_ENST00000346322.5_Missense_Mutation_p.I250V			Q15746	MYLK_HUMAN	myosin light chain kinase	250					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.I250V(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)		ATACCTTGGATGGAAAGTTCA	0.572																																					p.I250V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A748G	3						.						237.0	166.0	190.0					3																	123456231		2203	4300	6503	124938921	SO:0001583	missense	4638	exon8			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.748A>G	3.37:g.123456231T>C	ENSP00000418335:p.Ile250Val	Somatic		Capture	Illumina HiSeq	Phase_I	124938921	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	1.543	-0.541169	0.04053	.	.	ENSG00000065534	ENST00000360772;ENST00000360304;ENST00000359169;ENST00000346322;ENST00000475616	T;T;T;T;T	0.57752	0.38;0.38;0.38;0.38;0.38	5.07	3.89	0.44902	Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.15046	0.0363	N	0.00605	-1.335	0.80722	D	1	B;B;B;B;B;B	0.20780	0.009;0.048;0.002;0.017;0.002;0.012	B;B;B;B;B;B	0.19666	0.015;0.015;0.002;0.015;0.002;0.026	T	0.21211	-1.0252	9	0.02654	T	1	.	4.0615	0.09841	0.0:0.1637:0.1857:0.6507	.	250;250;250;250;250;250	Q15746-6;Q15746-5;Q15746-4;Q15746-3;Q15746-2;Q15746	.;.;.;.;.;MYLK_HUMAN	V	250	ENSP00000354004:I250V;ENSP00000353452:I250V;ENSP00000352088:I250V;ENSP00000320622:I250V;ENSP00000418335:I250V	ENSP00000320622:I250V	I	-	1	0	MYLK	124938921	1.000000	0.71417	0.996000	0.52242	0.662000	0.39071	1.176000	0.31957	0.917000	0.36895	0.460000	0.39030	ATC		0.572	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025	
PLXNA1	5361	broad.mit.edu	37	3	126740973	126740973	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:126740973C>T	ENST00000393409.2	+	21	4084	c.4084C>T	c.(4084-4086)Ctg>Ttg	p.L1362L	PLXNA1_ENST00000251772.4_Silent_p.L1339L	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	1362					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.L1339L(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)		CGGGCAGCTGCTGACCAAGAA	0.617																																					p.L1362L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4084T	3						.						71.0	57.0	62.0					3																	126740973		2203	4300	6503	128223663	SO:0001819	synonymous_variant	5361	exon21			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.4084C>T	3.37:g.126740973C>T		Somatic		Capture	Illumina HiSeq	Phase_I	128223663	NM_032242		Silent	SNP	ENST00000393409.2	37	CCDS33847.2																																																																																				0.617	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356451.1	NM_032242	
RHO	6010	broad.mit.edu	37	3	129251163	129251163	+	Silent	SNP	C	C	T	rs147005807		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:129251163C>T	ENST00000296271.3	+	3	694	c.600C>T	c.(598-600)aaC>aaT	p.N200N		NM_000539.3	NP_000530.1	P08100	OPSD_HUMAN	rhodopsin	200					G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction, visible light (GO:0007603)|protein phosphorylation (GO:0006468)|protein-chromophore linkage (GO:0018298)|red, far-red light phototransduction (GO:0009585)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|retinoid metabolic process (GO:0001523)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	cell-cell junction (GO:0005911)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)|photoreceptor inner segment membrane (GO:0060342)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|rough endoplasmic reticulum membrane (GO:0030867)	G-protein coupled receptor activity (GO:0004930)|metal ion binding (GO:0046872)|photoreceptor activity (GO:0009881)|retinal binding (GO:0016918)	p.N200N(1)		breast(1)|endometrium(1)|large_intestine(10)|lung(6)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	22		all_neural(597;0.0227)|Myeloproliferative disorder(1037;0.0255)|Prostate(884;0.183)		GBM - Glioblastoma multiforme(114;2.58e-05)|Lung(219;0.0234)	Halothane(DB01159)	AGGTCAACAACGAGTCTTTTG	0.537																																					p.N200N	Esophageal Squamous(118;214 1623 30842 43234 46940)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C600T	3						.	C		1,4405	2.1+/-5.4	0,1,2202	296.0	235.0	256.0		600	-6.9	0.7	3	dbSNP_134	256	0,8600		0,0,4300	no	coding-synonymous	RHO	NM_000539.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		200/349	129251163	1,13005	2203	4300	6503	130733853	SO:0001819	synonymous_variant	6010	exon3			AB065668	CCDS3063.1	3q21-q24	2014-01-28	2008-04-16		ENSG00000163914	ENSG00000163914		"""GPCR / Class A : Opsin receptors"""	10012	protein-coding gene	gene with protein product	"""opsin 2, rod pigment"""	180380	"""retinitis pigmentosa 4, autosomal dominant"""	RP4		2016091	Standard	NM_000539		Approved	OPN2, CSNBAD1	uc003emt.3	P08100	OTTHUMG00000159542	ENST00000296271.3:c.600C>T	3.37:g.129251163C>T		Somatic		Capture	Illumina HiSeq	Phase_I	130733853	NM_000539	Q16414|Q2M249	Silent	SNP	ENST00000296271.3	37	CCDS3063.1																																																																																				0.537	RHO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356101.1	NM_000539	
COL6A6	131873	broad.mit.edu	37	3	130345356	130345356	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:130345356G>T	ENST00000358511.6	+	24	4937	c.4906G>T	c.(4906-4908)Gga>Tga	p.G1636*	COL6A6_ENST00000453409.2_Nonsense_Mutation_p.G1636*	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	1636	Triple-helical region.				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.G1636*(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						GGGAGAAAAAGGAGCTGTTGG	0.418																																					p.G1636X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G4906T	3						.						167.0	168.0	168.0					3																	130345356		1875	4110	5985	131828046	SO:0001587	stop_gained	131873	exon24			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.4906G>T	3.37:g.130345356G>T	ENSP00000351310:p.Gly1636*	Somatic		Capture	Illumina HiSeq	Phase_I	131828046	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Nonsense_Mutation	SNP	ENST00000358511.6	37	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	G	42	9.686405	0.99238	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	.	.	.	5.17	5.17	0.71159	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	14.5357	0.67958	0.0:0.0:1.0:0.0	.	.	.	.	X	1636	.	ENSP00000351310:G1636X	G	+	1	0	COL6A6	131828046	1.000000	0.71417	0.874000	0.34290	0.159000	0.22180	4.826000	0.62715	2.576000	0.86940	0.650000	0.86243	GGA		0.418	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608	
ASTE1	28990	broad.mit.edu	37	3	130743851	130743851	+	Silent	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:130743851G>T	ENST00000264992.3	-	3	741	c.300C>A	c.(298-300)atC>atA	p.I100I	NEK11_ENST00000429253.2_5'Flank|NEK11_ENST00000356918.4_5'Flank|NEK11_ENST00000383366.4_5'Flank|NEK11_ENST00000507910.1_5'Flank|NEK11_ENST00000510769.1_5'Flank|NEK11_ENST00000412440.2_5'Flank|ASTE1_ENST00000514044.1_Silent_p.I100I|NEK11_ENST00000511262.1_5'Flank|NEK11_ENST00000510688.1_5'Flank	NM_014065.2	NP_054784.2	Q2TB18	ASTE1_HUMAN	asteroid homolog 1 (Drosophila)	100					DNA repair (GO:0006281)		nuclease activity (GO:0004518)	p.I100I(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)	22						GGGCCATCTGGATCTTCTCTC	0.418																																					p.I100I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C300A	3						.						119.0	116.0	117.0					3																	130743851		2203	4300	6503	132226541	SO:0001819	synonymous_variant	28990	exon3			AF113539	CCDS3068.1, CCDS75007.1	3q21.3	2005-11-17			ENSG00000034533	ENSG00000034533			25021	protein-coding gene	gene with protein product							Standard	NM_014065		Approved	HT001	uc003env.1	Q2TB18	OTTHUMG00000159644	ENST00000264992.3:c.300C>A	3.37:g.130743851G>T		Somatic		Capture	Illumina HiSeq	Phase_I	132226541	NM_014065	B4DFL9|Q3MIB6|Q8N6G4|Q96JY1|Q9UHX6	Silent	SNP	ENST00000264992.3	37	CCDS3068.1																																																																																				0.418	ASTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356659.1	NM_014065	
ACKR4	51554	broad.mit.edu	37	3	132320115	132320115	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:132320115G>A	ENST00000249887.2	+	2	970	c.874G>A	c.(874-876)Gca>Aca	p.A292T	ACAD11_ENST00000545291.1_Intron|ACAD11_ENST00000264990.6_Intron|ACAD11_ENST00000355458.3_Intron	NM_016557.2|NM_178445.2	NP_057641.1|NP_848540.1	Q9NPB9	ACKR4_HUMAN	atypical chemokine receptor 4	292					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)|scavenger receptor activity (GO:0005044)	p.A292T(1)									AGAAAGCATCGCACTCTTTCA	0.463																																					p.A292T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G874A	3						.						231.0	226.0	227.0					3																	132320115		2202	4298	6500	133802805	SO:0001583	missense	51554	exon1			AF110640	CCDS3075.1	3q22	2013-07-17	2013-07-16	2013-07-16	ENSG00000129048	ENSG00000129048		"""GPCR / Class A : Chemokine receptors : Atypical"""	1611	protein-coding gene	gene with protein product		606065	"""chemokine (C-C motif) receptor-like 1"""	CCRL1		10767544, 16148	Standard	NM_016557		Approved	CCR11, CCBP2, VSHK1, CCX-CKR, PPR1	uc003eow.3	Q9NPB9	OTTHUMG00000159768	ENST00000249887.2:c.874G>A	3.37:g.132320115G>A	ENSP00000249887:p.Ala292Thr	Somatic		Capture	Illumina HiSeq	Phase_I	133802805	NM_178445	B2R9U7	Missense_Mutation	SNP	ENST00000249887.2	37	CCDS3075.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.327316	0.81690	.	.	ENSG00000129048	ENST00000249887	T	0.39229	1.09	5.56	4.68	0.58851	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.69415	0.3108	M	0.86502	2.82	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.77005	-0.2748	10	0.87932	D	0	.	16.3902	0.83532	0.0:0.1319:0.868:0.0	.	292	Q9NPB9	CCRL1_HUMAN	T	292	ENSP00000249887:A292T	ENSP00000249887:A292T	A	+	1	0	CCRL1	133802805	1.000000	0.71417	0.393000	0.26258	0.911000	0.54048	9.869000	0.99810	1.346000	0.45694	0.655000	0.94253	GCA		0.463	ACKR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357238.2	NM_016557	
C3orf36	80111	broad.mit.edu	37	3	133647302	133647302	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:133647302C>T	ENST00000408895.2	-	1	1354	c.346G>A	c.(346-348)Gcc>Acc	p.A116T		NM_025041.2	NP_079317.2	Q3SXR2	CC036_HUMAN	chromosome 3 open reading frame 36	116								p.A116T(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)	6						CCTGAGAGGGCGCAGAGTGGG	0.652																																					p.A116T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G346A	3						.						30.0	33.0	32.0					3																	133647302		2203	4300	6503	135129992	SO:0001583	missense	80111	exon1			AK025826	CCDS3083.1	3q22.1	2011-09-30			ENSG00000221972	ENSG00000221972			26170	protein-coding gene	gene with protein product						12477932	Standard	NM_025041		Approved	FLJ22173	uc003epz.1	Q3SXR2		ENST00000408895.2:c.346G>A	3.37:g.133647302C>T	ENSP00000386219:p.Ala116Thr	Somatic		Capture	Illumina HiSeq	Phase_I	135129992	NM_025041	Q3SXR3|Q9H6K8	Missense_Mutation	SNP	ENST00000408895.2	37	CCDS3083.1	.	.	.	.	.	.	.	.	.	.	C	4.421	0.077787	0.08485	.	.	ENSG00000221972	ENST00000408895	.	.	.	1.71	-0.195	0.13236	.	.	.	.	.	T	0.16128	0.0388	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.20638	-1.0269	8	0.87932	D	0	.	2.8693	0.05611	0.2018:0.3089:0.4893:0.0	.	116	Q3SXR2	CC036_HUMAN	T	116	.	ENSP00000386219:A116T	A	-	1	0	C3orf36	135129992	0.000000	0.05858	0.001000	0.08648	0.043000	0.13939	0.135000	0.15952	-0.069000	0.12931	-0.702000	0.03669	GCC		0.652	C3orf36-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_025041	
CEP63	80254	broad.mit.edu	37	3	134267983	134267983	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:134267983G>A	ENST00000337090.3	+	10	1320	c.1147G>A	c.(1147-1149)Gca>Aca	p.A383T	CEP63_ENST00000606977.1_Missense_Mutation_p.A383T|CEP63_ENST00000354446.3_Missense_Mutation_p.A337T|CEP63_ENST00000332047.5_Missense_Mutation_p.A337T|CEP63_ENST00000383229.3_Missense_Mutation_p.A383T|CEP63_ENST00000513612.2_Missense_Mutation_p.A383T			Q96MT8	CEP63_HUMAN	centrosomal protein 63kDa	383					centriole replication (GO:0007099)|DNA damage checkpoint (GO:0000077)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|signal transduction in response to DNA damage (GO:0042770)|spindle assembly (GO:0051225)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|spindle pole (GO:0000922)				kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						GAGGATGGAAGCACATAACAA	0.363																																					p.A337T												.	.	0			c.G1009A	3						.						104.0	95.0	98.0					3																	134267983		2203	4300	6503	135750673	SO:0001583	missense	80254	exon9			AK056465	CCDS3086.1, CCDS43152.1, CCDS43153.1, CCDS43154.1	3q22.1	2014-02-20			ENSG00000182923	ENSG00000182923			25815	protein-coding gene	gene with protein product		614724				14654843, 24240477	Standard	NM_001042383		Approved	FLJ13386	uc003eqo.1	Q96MT8	OTTHUMG00000159725	ENST00000337090.3:c.1147G>A	3.37:g.134267983G>A	ENSP00000336524:p.Ala383Thr	None		Capture	Illumina HiSeq	Phase_I	135750673	NM_001042383	D3DND8|D3DND9|D3DNE0|Q96CR0|Q9H8F5|Q9H8N0	Missense_Mutation	SNP	ENST00000337090.3	37	CCDS3086.1	.	.	.	.	.	.	.	.	.	.	G	9.976	1.226845	0.22542	.	.	ENSG00000182923	ENST00000332047;ENST00000354446;ENST00000337090;ENST00000383229;ENST00000513612;ENST00000514678	T;T;T;T;T;T	0.33438	1.47;1.83;2.21;1.49;2.21;1.41	5.73	1.76	0.24704	.	0.989402	0.08232	N	0.977455	T	0.17066	0.0410	N	0.14661	0.345	0.18873	N	0.999985	B;B;B;B	0.20671	0.002;0.001;0.047;0.0	B;B;B;B	0.17979	0.003;0.004;0.02;0.002	T	0.33777	-0.9855	10	0.22706	T	0.39	0.0433	6.6335	0.22869	0.155:0.2734:0.5717:0.0	.	383;383;337;337	Q96MT8;Q96MT8-2;Q96MT8-4;Q96MT8-3	CEP63_HUMAN;.;.;.	T	337;337;383;383;383;56	ENSP00000328382:A337T;ENSP00000346432:A337T;ENSP00000336524:A383T;ENSP00000372716:A383T;ENSP00000426129:A383T;ENSP00000427526:A56T	ENSP00000328382:A337T	A	+	1	0	CEP63	135750673	0.996000	0.38824	0.285000	0.24819	0.944000	0.59088	1.494000	0.35616	0.029000	0.15352	0.655000	0.94253	GCA		0.363	CEP63-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000470139.1	NM_025180	
STAG1	10274	broad.mit.edu	37	3	136323198	136323198	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:136323198G>A	ENST00000383202.2	-	4	506	c.250C>T	c.(250-252)Cct>Tct	p.P84S	STAG1_ENST00000434713.2_5'UTR|STAG1_ENST00000236698.5_Missense_Mutation_p.P84S|STAG1_ENST00000480733.1_Missense_Mutation_p.P84S	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	84					chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.P84S(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						AATGTGACAGGCTCCCCTTCC	0.428																																					p.P84S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C250T	3						.						159.0	152.0	155.0					3																	136323198		2203	4300	6503	137805888	SO:0001583	missense	10274	exon4			Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007			11354	protein-coding gene	gene with protein product		604358				9305759	Standard	XM_006713471		Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000383202.2:c.250C>T	3.37:g.136323198G>A	ENSP00000372689:p.Pro84Ser	Somatic		Capture	Illumina HiSeq	Phase_I	137805888	NM_005862	O00539|Q6P275	Missense_Mutation	SNP	ENST00000383202.2	37	CCDS3090.1	.	.	.	.	.	.	.	.	.	.	G	1.973	-0.436136	0.04636	.	.	ENSG00000118007	ENST00000383202;ENST00000236698;ENST00000480733	T;T	0.23754	1.9;1.89	5.81	4.03	0.46877	.	0.051582	0.85682	N	0.000000	T	0.25644	0.0624	L	0.61218	1.895	0.80722	D	1	B;B;B	0.14012	0.0;0.009;0.0	B;B;B	0.19946	0.002;0.027;0.007	T	0.04855	-1.0922	10	0.15499	T	0.54	.	11.9736	0.53078	0.1412:0.0:0.8588:0.0	.	84;84;84	C9JJQ0;Q6P275;Q8WVM7	.;.;STAG1_HUMAN	S	84	ENSP00000372689:P84S;ENSP00000236698:P84S	ENSP00000236698:P84S	P	-	1	0	STAG1	137805888	1.000000	0.71417	0.935000	0.37517	0.215000	0.24574	9.276000	0.95745	0.799000	0.34018	0.655000	0.94253	CCT		0.428	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862	
ESYT3	83850	broad.mit.edu	37	3	138179496	138179496	+	Missense_Mutation	SNP	C	C	T	rs201949984		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:138179496C>T	ENST00000389567.4	+	7	968	c.782C>T	c.(781-783)gCg>gTg	p.A261V	ESYT3_ENST00000289135.4_Missense_Mutation_p.A261V	NM_031913.3	NP_114119.2	A0FGR9	ESYT3_HUMAN	extended synaptotagmin-like protein 3	261	Glycerophospholipid-binding barrel-like domain. {ECO:0000250}.				lipid transport (GO:0006869)	extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|organelle membrane contact site (GO:0044232)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(1)|endometrium(5)|large_intestine(7)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	25						CTGCTGGATGCGCCGGGAATC	0.597													C|||	1	0.000199681	0.0	0.0	5008	,	,		19533	0.001		0.0	False		,,,				2504	0.0				p.A261V												.	.	0			c.C782T	3						.						151.0	157.0	155.0					3																	138179496		2203	4300	6503	139662186	SO:0001583	missense	83850	exon7			AJ303366	CCDS3101.2	3q22.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000158220	ENSG00000158220		"""Synaptotagmins"""	24295	protein-coding gene	gene with protein product			"""family with sequence similarity 62 (C2 domain containing), member C"""	FAM62C		11543631, 17672888	Standard	NM_031913		Approved	CHR3SYT	uc003esk.3	A0FGR9	OTTHUMG00000147354	ENST00000389567.4:c.782C>T	3.37:g.138179496C>T	ENSP00000374218:p.Ala261Val	None		Capture	Illumina HiSeq	Phase_I	139662186	NM_031913	A8K0G5|Q6ZV21|Q8NDZ5|Q9BQR9	Missense_Mutation	SNP	ENST00000389567.4	37	CCDS3101.2	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	10.13	1.266681	0.23136	.	.	ENSG00000158220	ENST00000389567;ENST00000289135	T;T	0.21932	1.98;1.98	5.09	3.26	0.37387	.	0.381626	0.30528	N	0.009423	T	0.07324	0.0185	N	0.02916	-0.46	0.09310	N	0.999999	B	0.20052	0.041	B	0.11329	0.006	T	0.36841	-0.9731	10	0.16896	T	0.51	-9.7295	7.0086	0.24849	0.0:0.7081:0.0:0.2919	.	261	A0FGR9	ESYT3_HUMAN	V	261	ENSP00000374218:A261V;ENSP00000289135:A261V	ENSP00000289135:A261V	A	+	2	0	ESYT3	139662186	0.000000	0.05858	0.164000	0.22755	0.776000	0.43924	-0.173000	0.09854	0.512000	0.28257	0.549000	0.68633	GCG		0.597	ESYT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303993.1	NM_031913	
TRIM42	287015	broad.mit.edu	37	3	140419802	140419802	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:140419802C>T	ENST00000286349.3	+	5	2349	c.2158C>T	c.(2158-2160)Cag>Tag	p.Q720*		NM_152616.4	NP_689829.3	Q8IWZ5	TRI42_HUMAN	tripartite motif containing 42	720						intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.Q720*(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						GTCTGCCCTCCAGAAGCACTT	0.463																																					p.Q720X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2158T	3						.						114.0	93.0	100.0					3																	140419802		2203	4300	6503	141902492	SO:0001587	stop_gained	287015	exon5			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.2158C>T	3.37:g.140419802C>T	ENSP00000286349:p.Gln720*	Somatic		Capture	Illumina HiSeq	Phase_I	141902492	NM_152616	A1L4B4|Q8N832|Q8NDL3	Nonsense_Mutation	SNP	ENST00000286349.3	37	CCDS3113.1	.	.	.	.	.	.	.	.	.	.	C	39	7.595109	0.98381	.	.	ENSG00000155890	ENST00000286349	.	.	.	5.91	5.03	0.67393	.	0.376195	0.23033	N	0.052703	.	.	.	.	.	.	0.31900	N	0.616053	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	-10.0294	9.9942	0.41889	0.0:0.9112:0.0:0.0888	.	.	.	.	X	720	.	ENSP00000286349:Q720X	Q	+	1	0	TRIM42	141902492	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.763000	0.38461	2.793000	0.96121	0.655000	0.94253	CAG		0.463	TRIM42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359531.2	NM_152616	
SLC9A9	285195	broad.mit.edu	37	3	143371166	143371166	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:143371166T>C	ENST00000316549.6	-	6	894	c.686A>G	c.(685-687)gAc>gGc	p.D229G		NM_173653.3	NP_775924.1	Q8IVB4	SL9A9_HUMAN	solute carrier family 9, subfamily A (NHE9, cation proton antiporter 9), member 9	229					ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|recycling endosome (GO:0055037)	sodium:proton antiporter activity (GO:0015385)	p.D229G(1)		breast(2)|endometrium(5)|kidney(2)|large_intestine(13)|lung(29)|ovary(2)|skin(3)|stomach(1)	57						CAGGTCAGGGTCGACGTGCAG	0.463																																					p.D229G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A686G	3						.						121.0	93.0	103.0					3																	143371166		2203	4300	6503	144853856	SO:0001583	missense	285195	exon6			AY254100	CCDS33872.1	3q23-q24	2014-01-28	2012-03-22		ENSG00000181804	ENSG00000181804		"""Solute carriers"""	20653	protein-coding gene	gene with protein product		608396	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 9"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 9"""			14569117	Standard	NM_173653		Approved	FLJ35613, NHE9	uc003evn.3	Q8IVB4	OTTHUMG00000159373	ENST00000316549.6:c.686A>G	3.37:g.143371166T>C	ENSP00000320246:p.Asp229Gly	Somatic		Capture	Illumina HiSeq	Phase_I	144853856	NM_173653	A6NMQ9|Q3LIC2|Q5JPI6|Q5WA58|Q8NAB9	Missense_Mutation	SNP	ENST00000316549.6	37	CCDS33872.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.251419	0.80135	.	.	ENSG00000181804	ENST00000316549;ENST00000450105	T	0.16196	2.36	5.53	5.53	0.82687	Cation/H+ exchanger (1);	0.000000	0.85682	D	0.000000	T	0.50854	0.1640	M	0.91612	3.225	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.61874	-0.6973	10	0.87932	D	0	.	14.7802	0.69760	0.0:0.0:0.0:1.0	.	229	Q8IVB4	SL9A9_HUMAN	G	229;112	ENSP00000320246:D229G	ENSP00000320246:D229G	D	-	2	0	SLC9A9	144853856	1.000000	0.71417	0.954000	0.39281	0.875000	0.50365	7.116000	0.77119	2.324000	0.78689	0.533000	0.62120	GAC		0.463	SLC9A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354994.1	NM_173653	
METTL6	131965	broad.mit.edu	37	3	15457355	15457355	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:15457355T>C	ENST00000443029.1	-	4	695	c.455A>G	c.(454-456)gAt>gGt	p.D152G	METTL6_ENST00000383790.3_Missense_Mutation_p.D152G|METTL6_ENST00000383789.5_Missense_Mutation_p.D152G|METTL6_ENST00000450816.2_Missense_Mutation_p.D107G			Q8TCB7	METL6_HUMAN	methyltransferase like 6	152							methyltransferase activity (GO:0008168)	p.D152G(1)		endometrium(1)|kidney(1)|large_intestine(9)|lung(3)|prostate(1)	15						CATAACAACATCCACAGACTC	0.398																																					p.D152G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A455G	3						.						136.0	133.0	134.0					3																	15457355		2027	4205	6232	15432359	SO:0001583	missense	131965	exon4			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.455A>G	3.37:g.15457355T>C	ENSP00000407613:p.Asp152Gly	Somatic		Capture	Illumina HiSeq	Phase_I	15432359	NM_152396	Q96LU4	Missense_Mutation	SNP	ENST00000443029.1	37	CCDS43056.1	.	.	.	.	.	.	.	.	.	.	T	18.07	3.540910	0.65085	.	.	ENSG00000206562	ENST00000383790;ENST00000450816;ENST00000453819;ENST00000383789	T;T;T;T	0.22945	1.93;1.93;1.93;1.93	6.16	6.16	0.99307	Methyltransferase type 12 (1);	0.000000	0.85682	D	0.000000	T	0.63885	0.2549	H	0.99011	4.4	0.80722	D	1	P;P;P	0.50066	0.931;0.749;0.931	P;P;P	0.53988	0.651;0.627;0.739	T	0.79105	-0.1940	10	0.62326	D	0.03	-24.2237	16.4675	0.84087	0.0:0.0:0.0:1.0	.	107;152;152	B4DDX3;Q8TCB7-2;Q8TCB7	.;.;METL6_HUMAN	G	152;107;59;152	ENSP00000373300:D152G;ENSP00000410726:D107G;ENSP00000412006:D59G;ENSP00000373299:D152G	ENSP00000373299:D152G	D	-	2	0	METTL6	15432359	1.000000	0.71417	0.957000	0.39632	0.016000	0.09150	8.007000	0.88571	2.367000	0.80283	0.528000	0.53228	GAT		0.398	METTL6-007	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346373.1	NM_152396	
MED12L	116931	broad.mit.edu	37	3	150903121	150903121	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:150903121C>T	ENST00000474524.1	+	11	1537	c.1499C>T	c.(1498-1500)gCg>gTg	p.A500V	MED12L_ENST00000422248.2_Missense_Mutation_p.A500V|RNA5SP145_ENST00000363124.1_RNA|MED12L_ENST00000273432.4_Missense_Mutation_p.A360V|MED12L_ENST00000309237.4_Missense_Mutation_p.A500V	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	500						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.A500V(1)		NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			CATTAGGTTGCGCCCAACGAT	0.517																																					p.A500V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1499T	3						.						105.0	87.0	93.0					3																	150903121		2203	4300	6503	152385811	SO:0001583	missense	116931	exon11			AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"""			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.1499C>T	3.37:g.150903121C>T	ENSP00000417235:p.Ala500Val	Somatic		Capture	Illumina HiSeq	Phase_I	152385811	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	37	CCDS33876.1	.	.	.	.	.	.	.	.	.	.	C	18.10	3.549340	0.65311	.	.	ENSG00000144893	ENST00000422248;ENST00000309237;ENST00000474524;ENST00000273432	T;T;T;T	0.30714	1.52;1.52;1.52;1.52	5.51	5.51	0.81932	Mediator complex, subunit Med12, LCEWAV-domain (1);	0.188818	0.47455	D	0.000231	T	0.48502	0.1503	L	0.37630	1.12	0.45995	D	0.998807	D;D;D;D	0.89917	0.994;0.995;0.991;1.0	P;P;P;D	0.76071	0.8;0.858;0.666;0.987	T	0.46748	-0.9169	10	0.72032	D	0.01	-13.9009	19.0129	0.92881	0.0:1.0:0.0:0.0	.	360;500;500;500	F8WAE6;Q86YW9;Q86YW9-2;Q86YW9-3	.;MD12L_HUMAN;.;.	V	500;500;500;360	ENSP00000403308:A500V;ENSP00000310760:A500V;ENSP00000417235:A500V;ENSP00000273432:A360V	ENSP00000273432:A360V	A	+	2	0	MED12L	152385811	0.988000	0.35896	0.971000	0.41717	0.120000	0.20174	3.970000	0.56824	2.589000	0.87451	0.591000	0.81541	GCG		0.517	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002	
NLGN1	22871	broad.mit.edu	37	3	173993280	173993280	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:173993280T>G	ENST00000457714.1	+	5	1251	c.822T>G	c.(820-822)caT>caG	p.H274Q	NLGN1_ENST00000361589.4_Missense_Mutation_p.H274Q|NLGN1_ENST00000545397.1_Missense_Mutation_p.H274Q|NLGN1_ENST00000401917.3_Missense_Mutation_p.H314Q|NLGN1_ENST00000466350.1_3'UTR	NM_014932.2	NP_055747.1	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	291					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|calcium-dependent cell-cell adhesion (GO:0016339)|cytoskeletal matrix organization at active zone (GO:0048789)|establishment of protein localization (GO:0045184)|heterophilic cell-cell adhesion (GO:0007157)|N-methyl-D-aspartate receptor clustering (GO:0097114)|nervous system development (GO:0007399)|neurexin clustering (GO:0097115)|neuron cell-cell adhesion (GO:0007158)|neuronal signal transduction (GO:0023041)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|positive regulation of synaptic vesicle exocytosis (GO:2000302)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|protein homooligomerization (GO:0051260)|protein localization to synapse (GO:0035418)|protein targeting (GO:0006605)|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)|regulation of neuron differentiation (GO:0045664)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|synapse assembly (GO:0007416)|synaptic vesicle clustering (GO:0097091)|synaptic vesicle targeting (GO:0016080)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|filopodium tip (GO:0032433)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|PDZ domain binding (GO:0030165)|protein dimerization activity (GO:0046983)|receptor activity (GO:0004872)	p.H274Q(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(2)|lung(54)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	83	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			CTTTATCCCATTATTCTGAAG	0.423																																					p.H274Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T822G	3						.						83.0	80.0	81.0					3																	173993280		2203	4299	6502	175475974	SO:0001583	missense	22871	exon5			AB028993	CCDS3222.1	3q26.32	2008-07-18			ENSG00000169760	ENSG00000169760			14291	protein-coding gene	gene with protein product		600568				10767552, 10819331	Standard	NM_014932		Approved	KIAA1070	uc003fio.1	Q8N2Q7	OTTHUMG00000157005	ENST00000457714.1:c.822T>G	3.37:g.173993280T>G	ENSP00000392500:p.His274Gln	Somatic		Capture	Illumina HiSeq	Phase_I	175475974	NM_014932	Q9UPT2	Missense_Mutation	SNP	ENST00000457714.1	37	CCDS3222.1	.	.	.	.	.	.	.	.	.	.	T	17.13	3.310458	0.60414	.	.	ENSG00000169760	ENST00000457714;ENST00000361589;ENST00000415045;ENST00000545397;ENST00000401917	T;T;T;T;T	0.71222	-0.33;-0.33;-0.55;-0.33;-0.34	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.75627	0.3875	N	0.25890	0.77	0.58432	D	0.999995	D;D	0.76494	0.999;0.993	D;P	0.78314	0.991;0.874	T	0.77357	-0.2618	10	0.51188	T	0.08	.	15.7739	0.78193	0.0:0.0:0.0:1.0	.	314;274	D2X2H5;Q8N2Q7-2	.;.	Q	274;274;314;274;314	ENSP00000392500:H274Q;ENSP00000354541:H274Q;ENSP00000410374:H314Q;ENSP00000441108:H274Q;ENSP00000385750:H314Q	ENSP00000354541:H274Q	H	+	3	2	NLGN1	175475974	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.886000	0.56190	2.367000	0.80283	0.528000	0.53228	CAT		0.423	NLGN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347054.3	NM_014932	
ZMAT3	64393	broad.mit.edu	37	3	178785282	178785282	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:178785282C>A	ENST00000311417.2	-	2	1000	c.259G>T	c.(259-261)Gct>Tct	p.A87S	ZMAT3_ENST00000432729.1_Missense_Mutation_p.A87S	NM_022470.3	NP_071915.1			zinc finger, matrin-type 3									p.A87S(1)		breast(1)|endometrium(1)|large_intestine(6)|lung(2)|ovary(2)|prostate(1)|skin(1)	14	all_cancers(143;3.31e-18)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;6.74e-27)|GBM - Glioblastoma multiforme(14;0.00448)|BRCA - Breast invasive adenocarcinoma(182;0.0527)			TGATAATGAGCCTGGGCTTGC	0.493																																					p.A87S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G259T	3						.						153.0	152.0	153.0					3																	178785282		2203	4300	6503	180267976	SO:0001583	missense	64393	exon3			AK122768	CCDS3224.1, CCDS46962.1	3q26.32	2012-10-05	2010-09-15		ENSG00000172667	ENSG00000172667		"""Zinc fingers, matrin-type"""	29983	protein-coding gene	gene with protein product		606452				9400996, 11689294	Standard	NM_022470		Approved	WIG1, MGC10613, FLJ12296, WIG-1, PAG608	uc003fjg.3	Q9HA38	OTTHUMG00000157290	ENST00000311417.2:c.259G>T	3.37:g.178785282C>A	ENSP00000311221:p.Ala87Ser	Somatic		Capture	Illumina HiSeq	Phase_I	180267976	NM_152240		Missense_Mutation	SNP	ENST00000311417.2	37	CCDS3224.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.156256	0.78114	.	.	ENSG00000172667	ENST00000311417;ENST00000432729;ENST00000414084	T;T;T	0.18810	2.19;2.19;2.19	5.86	5.86	0.93980	Zinc finger, C2H2-like (1);Zinc finger, U1-type (1);	0.000000	0.85682	D	0.000000	T	0.36496	0.0969	L	0.31752	0.955	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	T	0.01935	-1.1244	10	0.23891	T	0.37	-25.9012	20.1931	0.98233	0.0:1.0:0.0:0.0	.	87;87	Q9HA38-2;Q9HA38	.;ZMAT3_HUMAN	S	87	ENSP00000311221:A87S;ENSP00000396506:A87S;ENSP00000398920:A87S	ENSP00000311221:A87S	A	-	1	0	ZMAT3	180267976	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.487000	0.81328	2.771000	0.95319	0.563000	0.77884	GCT		0.493	ZMAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348336.2	NM_152240	
KLHL6	89857	broad.mit.edu	37	3	183273160	183273160	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:183273160G>T	ENST00000341319.3	-	1	317	c.282C>A	c.(280-282)agC>agA	p.S94R		NM_130446.2	NP_569713.2	Q8WZ60	KLHL6_HUMAN	kelch-like family member 6	94	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.			S -> G (in Ref. 1; BAG37078). {ECO:0000305}.	B cell receptor signaling pathway (GO:0050853)|germinal center formation (GO:0002467)			p.S94R(1)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44	all_cancers(143;9.2e-12)|Ovarian(172;0.0172)		all cancers(12;1.29e-44)|Epithelial(37;1.24e-38)|LUSC - Lung squamous cell carcinoma(7;2.58e-24)|Lung(8;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.32e-22)			TGAAATAGTTGCTGGCTGCGG	0.522																																					p.S94R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C282A	3						.						86.0	77.0	80.0					3																	183273160		2203	4300	6503	184755854	SO:0001583	missense	89857	exon1			AF441792	CCDS3245.2	3q27.3	2013-01-30	2013-01-30		ENSG00000172578	ENSG00000172578		"""Kelch-like"", ""BTB/POZ domain containing"""	18653	protein-coding gene	gene with protein product	"""kelch-like protein KLHL6"""	614214	"""kelch-like 6 (Drosophila)"""			11214971, 12617994	Standard	NM_130446		Approved	FLJ00029	uc003flr.3	Q8WZ60	OTTHUMG00000148673	ENST00000341319.3:c.282C>A	3.37:g.183273160G>T	ENSP00000341342:p.Ser94Arg	Somatic		Capture	Illumina HiSeq	Phase_I	184755854	NM_130446	B2RB31|D3DNS8|Q8N5I1|Q8N892	Missense_Mutation	SNP	ENST00000341319.3	37	CCDS3245.2	.	.	.	.	.	.	.	.	.	.	G	21.0	4.079203	0.76528	.	.	ENSG00000172578	ENST00000341319	D	0.85861	-2.04	5.56	4.67	0.58626	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.95529	0.8547	H	0.98866	4.355	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	D	0.96934	0.9683	10	0.87932	D	0	.	14.8077	0.69971	0.0705:0.0:0.9295:0.0	.	94	Q8WZ60	KLHL6_HUMAN	R	94	ENSP00000341342:S94R	ENSP00000341342:S94R	S	-	3	2	KLHL6	184755854	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.073000	0.57570	2.608000	0.88229	0.655000	0.94253	AGC		0.522	KLHL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309024.1	NM_130446	
FAM131A	131408	broad.mit.edu	37	3	184062488	184062488	+	Silent	SNP	C	C	T	rs150189351	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:184062488C>T	ENST00000310585.4	+	3	2102	c.738C>T	c.(736-738)ggC>ggT	p.G246G	FAM131A_ENST00000383847.2_Silent_p.G277G|FAM131A_ENST00000453072.1_Silent_p.G192G|EIF2B5_ENST00000444495.1_Intron|FAM131A_ENST00000340957.5_Silent_p.G192G|FAM131A_ENST00000450976.1_Silent_p.G192G|FAM131A_ENST00000418281.1_Silent_p.G154G			Q6UXB0	F131A_HUMAN	family with sequence similarity 131, member A	246						extracellular region (GO:0005576)		p.G246G(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(9)|skin(1)	14	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			AGCTGCTGGGCGATGAGCTGC	0.667													C|||	3	0.000599042	0.0023	0.0	5008	,	,		15733	0.0		0.0	False		,,,				2504	0.0				p.G192G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C576T	3						.	C	,	3,4403	6.2+/-15.9	0,3,2200	57.0	66.0	63.0		576,831	-7.7	0.0	3	dbSNP_134	63	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	FAM131A	NM_001171093.1,NM_144635.4	,	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	,	192/282,277/367	184062488	3,13003	2203	4300	6503	185545182	SO:0001819	synonymous_variant	131408	exon6			BC026221	CCDS3262.1, CCDS3262.2, CCDS54689.1	3q27.1	2007-03-20	2007-03-20	2007-03-20	ENSG00000175182	ENSG00000175182			28308	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 40"""	C3orf40		12975309	Standard	NM_144635		Approved	MGC21688	uc003foe.3	Q6UXB0	OTTHUMG00000156206	ENST00000310585.4:c.738C>T	3.37:g.184062488C>T		Somatic		Capture	Illumina HiSeq	Phase_I	185545182	NM_001171093	D3DNT6|G5E9B1|Q8TA84	Silent	SNP	ENST00000310585.4	37																																																																																					0.667	FAM131A-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000343462.1	NM_144635	
MAP3K13	9175	broad.mit.edu	37	3	185184669	185184669	+	Missense_Mutation	SNP	C	C	T	rs202042288		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:185184669C>T	ENST00000265026.3	+	10	1895	c.1561C>T	c.(1561-1563)Cgt>Tgt	p.R521C	MAP3K13_ENST00000535426.1_Missense_Mutation_p.R377C|MAP3K13_ENST00000443863.1_Missense_Mutation_p.R377C|MAP3K13_ENST00000446828.1_Missense_Mutation_p.R314C|MAP3K13_ENST00000424227.1_Missense_Mutation_p.R521C	NM_004721.4	NP_004712.1			mitogen-activated protein kinase kinase kinase 13									p.R521C(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)			ACACCCTGTTCGTCCTATCAT	0.483																																					p.R521C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1561T	3						.						150.0	120.0	130.0					3																	185184669		2203	4300	6503	186667363	SO:0001583	missense	9175	exon10			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.1561C>T	3.37:g.185184669C>T	ENSP00000265026:p.Arg521Cys	Somatic		Capture	Illumina HiSeq	Phase_I	186667363	NM_004721		Missense_Mutation	SNP	ENST00000265026.3	37	CCDS3270.1	.	.	.	.	.	.	.	.	.	.	C	18.43	3.621470	0.66787	.	.	ENSG00000073803	ENST00000446828;ENST00000424227;ENST00000443863;ENST00000535426;ENST00000265026	T;T;T;T;T	0.24908	1.83;1.83;1.83;1.83;1.83	5.56	3.51	0.40186	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.37183	0.0994	L	0.32530	0.975	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.988;0.996;0.982	T	0.19614	-1.0300	10	0.87932	D	0	.	11.0257	0.47743	0.1691:0.7532:0.0:0.0777	.	377;314;521	O43283-4;O43283-5;O43283	.;.;M3K13_HUMAN	C	314;521;377;377;521	ENSP00000411483:R314C;ENSP00000399910:R521C;ENSP00000409325:R377C;ENSP00000439257:R377C;ENSP00000265026:R521C	ENSP00000265026:R521C	R	+	1	0	MAP3K13	186667363	0.999000	0.42202	1.000000	0.80357	0.964000	0.63967	1.891000	0.39738	1.485000	0.48380	0.655000	0.94253	CGT		0.483	MAP3K13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345268.1	NM_004721	
BCL6	604	broad.mit.edu	37	3	187444640	187444640	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:187444640C>T	ENST00000406870.2	-	7	1953	c.1587G>A	c.(1585-1587)gaG>gaA	p.E529E	RP11-211G3.3_ENST00000449623.1_Intron|BCL6_ENST00000450123.2_Intron|RP11-211G3.3_ENST00000437407.1_Intron|BCL6_ENST00000232014.4_Silent_p.E529E	NM_001706.4	NP_001697.2	P41182	BCL6_HUMAN	B-cell CLL/lymphoma 6	529					actin cytoskeleton organization (GO:0030036)|B cell differentiation (GO:0030183)|cell morphogenesis (GO:0000902)|cellular response to DNA damage stimulus (GO:0006974)|erythrocyte development (GO:0048821)|germinal center formation (GO:0002467)|inflammatory response (GO:0006954)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of isotype switching to IgE isotypes (GO:0048294)|negative regulation of mast cell cytokine production (GO:0032764)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cellular component movement (GO:0051272)|protein import into nucleus, translocation (GO:0000060)|regulation of germinal center formation (GO:0002634)|regulation of immune response (GO:0050776)|regulation of inflammatory response (GO:0050727)|regulation of memory T cell differentiation (GO:0043380)|regulation of Rho GTPase activity (GO:0032319)|Rho protein signal transduction (GO:0007266)|spermatogenesis (GO:0007283)|type 2 immune response (GO:0042092)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|metal ion binding (GO:0046872)|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 (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E529E(1)		central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(9)|lung(10)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	40	all_cancers(143;9.45e-12)|Ovarian(172;0.0418)		OV - Ovarian serous cystadenocarcinoma(80;1.76e-18)	GBM - Glioblastoma multiforme(93;0.0141)		GTGAGGCCTCCTCAGAGAAGC	0.597			"""T, Mis"""	"""IG loci, ZNFN1A1, LCP1, PIM1, TFRC, CIITA, NACA, HSPCB, HSPCA, HIST1H4I, IL21R,  POU2AF1, ARHH, EIF4A2, SFRS3"""	"""NHL, CLL"""																																p.E529E			Dom	yes		3	3q27	604	B-cell CLL/lymphoma 6		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1587A	3						.						121.0	99.0	107.0					3																	187444640		2203	4300	6503	188927334	SO:0001819	synonymous_variant	604	exon7				CCDS3289.1, CCDS46975.1	3q27	2013-01-09	2008-08-01		ENSG00000113916	ENSG00000113916		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	1001	protein-coding gene	gene with protein product		109565	"""zinc finger protein 51"""	ZNF51			Standard	NM_001130845		Approved	ZBTB27, LAZ3, BCL5, BCL6A	uc003frq.2	P41182	OTTHUMG00000156441	ENST00000406870.2:c.1587G>A	3.37:g.187444640C>T		Somatic		Capture	Illumina HiSeq	Phase_I	188927334	NM_001130845	A7E241|B8PSA7|D3DNV5	Silent	SNP	ENST00000406870.2	37	CCDS3289.1																																																																																				0.597	BCL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344202.1	NM_138931	
KCNH8	131096	broad.mit.edu	37	3	19498291	19498291	+	Silent	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:19498291A>G	ENST00000328405.2	+	11	2123	c.1857A>G	c.(1855-1857)tcA>tcG	p.S619S		NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	619					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.S619S(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						CAAATCTATCAATTAAGGACC	0.383																																					p.S619S	NSCLC(124;1625 1765 8018 24930 42026)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1857G	3						.						123.0	118.0	120.0					3																	19498291		2203	4300	6503	19473295	SO:0001819	synonymous_variant	131096	exon11			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.1857A>G	3.37:g.19498291A>G		Somatic		Capture	Illumina HiSeq	Phase_I	19473295	NM_144633	B7Z2I7|Q59GQ6	Silent	SNP	ENST00000328405.2	37	CCDS2632.1																																																																																				0.383	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633	
CLDN16	10686	broad.mit.edu	37	3	190126108	190126108	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:190126108C>A	ENST00000264734.2	+	4	846	c.598C>A	c.(598-600)Cca>Aca	p.P200T	CLDN16_ENST00000456423.1_Intron	NM_006580.3	NP_006571.1	Q9Y5I7	CLD16_HUMAN	claudin 16	200					calcium-independent cell-cell adhesion (GO:0016338)|cellular metal ion homeostasis (GO:0006875)|excretion (GO:0007588)|magnesium ion transport (GO:0015693)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|magnesium ion transmembrane transporter activity (GO:0015095)|structural molecule activity (GO:0005198)	p.P200T(1)		breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|skin(1)	19	all_cancers(143;3.61e-10)|Ovarian(172;0.0991)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.018)		TTCAGGTACCCCAGGAATCAT	0.378																																					p.P200T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C598A	3						.						282.0	269.0	273.0					3																	190126108		2203	4300	6503	191608802	SO:0001583	missense	10686	exon4			AF152101	CCDS3296.1	3q28	2008-12-10			ENSG00000113946	ENSG00000113946		"""Claudins"""	2037	protein-coding gene	gene with protein product	"""paracellin-1"", ""hypomagnesemia 3, with hypercalciuria and nephrocalcinosis"""	603959				10390358	Standard	NM_006580		Approved	PCLN1, HOMG3	uc003fsi.3	Q9Y5I7	OTTHUMG00000156215	ENST00000264734.2:c.598C>A	3.37:g.190126108C>A	ENSP00000264734:p.Pro200Thr	Somatic		Capture	Illumina HiSeq	Phase_I	191608802	NM_006580		Missense_Mutation	SNP	ENST00000264734.2	37	CCDS3296.1	.	.	.	.	.	.	.	.	.	.	C	13.03	2.114760	0.37339	.	.	ENSG00000113946	ENST00000264734	D	0.88124	-2.34	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.92331	0.7567	M	0.68317	2.08	0.80722	D	1	D	0.76494	0.999	D	0.72338	0.977	D	0.89877	0.4027	10	0.25106	T	0.35	-1.6241	18.6648	0.91485	0.0:1.0:0.0:0.0	.	200	Q9Y5I7	CLD16_HUMAN	T	200	ENSP00000264734:P200T	ENSP00000264734:P200T	P	+	1	0	CLDN16	191608802	0.998000	0.40836	1.000000	0.80357	0.325000	0.28411	5.650000	0.67944	2.641000	0.89580	0.557000	0.71058	CCA		0.378	CLDN16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343519.1	NM_006580	
SMCO1	255798	broad.mit.edu	37	3	196236519	196236519	+	Silent	SNP	C	C	T	rs371593591		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:196236519C>T	ENST00000397537.2	-	2	228	c.72G>A	c.(70-72)gcG>gcA	p.A24A		NM_001077657.1	NP_001071125.1	Q147U7	SMCO1_HUMAN	single-pass membrane protein with coiled-coil domains 1	24						integral component of membrane (GO:0016021)		p.A24A(1)									GTGTTTCTAACGCTTGGAGTT	0.408																																					p.A24A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G72A	3						.	C		0,3738		0,0,1869	236.0	212.0	219.0		72	-1.7	1.0	3		219	1,8231		0,1,4115	no	coding-synonymous	C3orf43	NM_001077657.1		0,1,5984	TT,TC,CC		0.0121,0.0,0.0084		24/215	196236519	1,11969	1869	4116	5985	197720916	SO:0001819	synonymous_variant	255798	exon2			AK123917	CCDS43192.1	3q29	2013-03-08	2013-03-08	2013-03-08	ENSG00000214097	ENSG00000214097			27407	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 43"""	C3orf43			Standard	NM_001077657		Approved	FLJ41923, DKFZp313B0440		Q147U7	OTTHUMG00000155581	ENST00000397537.2:c.72G>A	3.37:g.196236519C>T		Somatic		Capture	Illumina HiSeq	Phase_I	197720916	NM_001077657	B3KW20	Silent	SNP	ENST00000397537.2	37	CCDS43192.1																																																																																				0.408	SMCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340776.1	NM_001006109	
EFHB	151651	broad.mit.edu	37	3	19925952	19925952	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:19925952A>G	ENST00000295824.9	-	11	2250	c.2089T>C	c.(2089-2091)Tac>Cac	p.Y697H	EFHB_ENST00000344838.4_Missense_Mutation_p.Y567H	NM_144715.3	NP_653316.3	Q8N7U6	EFHB_HUMAN	EF-hand domain family, member B	697							calcium ion binding (GO:0005509)	p.Y697H(1)		breast(2)|endometrium(4)|kidney(1)|lung(17)|prostate(1)|urinary_tract(1)	26						GTCTTATAGTAGTTGGAAACT	0.373																																					p.Y697H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2089C	3						.						111.0	111.0	111.0					3																	19925952		2203	4300	6503	19900956	SO:0001583	missense	151651	exon11			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.2089T>C	3.37:g.19925952A>G	ENSP00000295824:p.Tyr697His	Somatic		Capture	Illumina HiSeq	Phase_I	19900956	NM_144715	A6ND25|A8MPR3|Q6ZWK9|Q8IV58|Q96LQ6	Missense_Mutation	SNP	ENST00000295824.9	37	CCDS33715.2	.	.	.	.	.	.	.	.	.	.	A	0.105	-1.146809	0.01714	.	.	ENSG00000163576	ENST00000295824;ENST00000344838	T;T	0.21031	2.03;2.06	5.15	-9.97	0.00440	.	1.296690	0.04980	N	0.465390	T	0.05227	0.0139	N	0.02011	-0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.25433	-1.0132	9	.	.	.	2.2954	4.5777	0.12241	0.2817:0.4481:0.1433:0.1269	.	567;697	Q8N7U6-3;Q8N7U6	.;EFHB_HUMAN	H	697;567	ENSP00000295824:Y697H;ENSP00000342263:Y567H	.	Y	-	1	0	EFHB	19900956	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.406000	0.07187	-1.842000	0.01181	-2.300000	0.00261	TAC		0.373	EFHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318673.2	NM_144715	
MFI2	4241	broad.mit.edu	37	3	196743988	196743988	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:196743988G>A	ENST00000296350.5	-	7	999	c.886C>T	c.(886-888)Ctc>Ttc	p.L296F		NM_005929.5	NP_005920.2	P08582	TRFM_HUMAN	antigen p97 (melanoma associated) identified by monoclonal antibodies 133.2 and 96.5	296	Transferrin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00741}.				cellular iron ion homeostasis (GO:0006879)|iron ion import (GO:0097286)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of extracellular matrix disassembly (GO:0090091)|positive regulation of plasminogen activation (GO:0010756)	anchored component of plasma membrane (GO:0046658)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ferric iron binding (GO:0008199)|iron ion binding (GO:0005506)	p.L296F(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|prostate(1)	20	all_cancers(143;3.95e-09)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.55e-24)|all cancers(36;2.87e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00536)		CCTTCGTTGAGCAGCCGGAAG	0.682																																					p.L296F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C886T	3						.						31.0	33.0	33.0					3																	196743988		2203	4300	6503	198228385	SO:0001583	missense	4241	exon7				CCDS3325.1, CCDS3326.1	3q28-q29	2012-10-02			ENSG00000163975	ENSG00000163975		"""CD molecules"""	7037	protein-coding gene	gene with protein product	"""melanotransferrin"", ""membrane-bound transferrin-like protein"""	155750					Standard	NM_033316		Approved	CD228, FLJ38863, MAP97, MGC4856, MTF1	uc003fxk.4	P08582	OTTHUMG00000155518	ENST00000296350.5:c.886C>T	3.37:g.196743988G>A	ENSP00000296350:p.Leu296Phe	Somatic		Capture	Illumina HiSeq	Phase_I	198228385	NM_005929	Q9BQE2	Missense_Mutation	SNP	ENST00000296350.5	37	CCDS3325.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.874650	0.91664	.	.	ENSG00000163975	ENST00000296350	T	0.44482	0.92	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.65729	0.2719	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.66256	-0.5969	10	0.59425	D	0.04	-36.2061	18.7965	0.91995	0.0:0.0:1.0:0.0	.	296	P08582	TRFM_HUMAN	F	296	ENSP00000296350:L296F	ENSP00000296350:L296F	L	-	1	0	MFI2	198228385	1.000000	0.71417	0.999000	0.59377	0.975000	0.68041	8.669000	0.91163	2.687000	0.91594	0.462000	0.41574	CTC		0.682	MFI2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340458.1		
LMCD1	29995	broad.mit.edu	37	3	8607140	8607140	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:8607140C>T	ENST00000157600.3	+	5	978	c.746C>T	c.(745-747)gCg>gTg	p.A249V	LMCD1-AS1_ENST00000439407.1_RNA|LMCD1_ENST00000454244.1_Missense_Mutation_p.A176V|LMCD1_ENST00000397386.3_Missense_Mutation_p.A137V	NM_014583.2	NP_055398.1	Q9NZU5	LMCD1_HUMAN	LIM and cysteine-rich domains 1	249	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				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.A249V(1)		breast(2)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)	16				OV - Ovarian serous cystadenocarcinoma(96;0.124)		TGCAAGGGAGCGGCCCCTCCT	0.607																																					p.A249V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C746T	3						.						104.0	112.0	110.0					3																	8607140		2203	4300	6503	8582140	SO:0001583	missense	29995	exon5			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.746C>T	3.37:g.8607140C>T	ENSP00000157600:p.Ala249Val	Somatic		Capture	Illumina HiSeq	Phase_I	8582140	NM_014583	B4DG80	Missense_Mutation	SNP	ENST00000157600.3	37	CCDS33688.1	.	.	.	.	.	.	.	.	.	.	T	8.020	0.759449	0.15846	.	.	ENSG00000071282	ENST00000157600;ENST00000454244;ENST00000397386	T;T;T	0.47869	0.86;0.84;0.83	5.51	-6.7	0.01766	Zinc finger, LIM-type (4);	0.914911	0.09086	N	0.850548	T	0.37544	0.1007	L	0.35593	1.075	0.09310	N	1	B;B	0.11235	0.004;0.0	B;B	0.10450	0.005;0.001	T	0.14200	-1.0481	10	0.25106	T	0.35	-3.9651	21.6104	0.99957	0.0:0.7833:0.0:0.2167	.	137;249	B4DEY6;Q9NZU5	.;LMCD1_HUMAN	V	249;176;137	ENSP00000157600:A249V;ENSP00000396515:A176V;ENSP00000380542:A137V	ENSP00000157600:A249V	A	+	2	0	LMCD1	8582140	0.000000	0.05858	0.000000	0.03702	0.664000	0.39144	-4.103000	0.00294	-1.595000	0.01613	-0.332000	0.08345	GCG		0.607	LMCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337854.1	NM_014583	
PLCD1	5333	broad.mit.edu	37	3	38061759	38061759	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:38061759C>T	ENST00000334661.4	-	2	341	c.119G>A	c.(118-120)cGc>cAc	p.R40H	PLCD1_ENST00000479619.1_5'Flank|PLCD1_ENST00000463876.1_Missense_Mutation_p.R61H	NM_006225.3	NP_006216.2	P51178	PLCD1_HUMAN	phospholipase C, delta 1	40	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.|Substrate binding. {ECO:0000250}.				angiogenesis (GO:0001525)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|labyrinthine layer blood vessel development (GO:0060716)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTPase activating protein binding (GO:0032794)|phosphatidic acid binding (GO:0070300)|phosphatidylinositol phosphate binding (GO:1901981)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylserine binding (GO:0001786)|signal transducer activity (GO:0004871)	p.R40Q(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.0519)|Kidney(284;0.0653)		CTTGTAGAAGCGCTCTCTCCT	0.597																																					p.R40H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G119A	3						.						96.0	86.0	89.0					3																	38061759		2203	4300	6503	38036763	SO:0001583	missense	5333	exon2				CCDS2671.1, CCDS46793.1	3p22-p21.3	2013-01-10			ENSG00000187091	ENSG00000187091	3.1.4.11	"""EF-hand domain containing"""	9060	protein-coding gene	gene with protein product		602142				9345909	Standard	NM_001130964		Approved		uc003chm.3	P51178	OTTHUMG00000130813	ENST00000334661.4:c.119G>A	3.37:g.38061759C>T	ENSP00000335600:p.Arg40His	Somatic		Capture	Illumina HiSeq	Phase_I	38036763	NM_006225	B3KR14|Q86VN8	Missense_Mutation	SNP	ENST00000334661.4	37	CCDS2671.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.197150	0.79015	.	.	ENSG00000187091	ENST00000463876;ENST00000334661	T;T	0.71103	-0.54;-0.54	5.22	5.22	0.72569	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.85682	D	0.000000	D	0.86397	0.5923	M	0.84948	2.725	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.88326	0.2965	10	0.87932	D	0	.	19.1602	0.93527	0.0:1.0:0.0:0.0	.	40;61	P51178;B3KR14	PLCD1_HUMAN;.	H	61;40	ENSP00000430344:R61H;ENSP00000335600:R40H	ENSP00000335600:R40H	R	-	2	0	PLCD1	38036763	1.000000	0.71417	0.998000	0.56505	0.003000	0.03518	7.710000	0.84655	2.601000	0.87937	0.561000	0.74099	CGC		0.597	PLCD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253359.2		
SCN5A	6331	broad.mit.edu	37	3	38663938	38663938	+	Silent	SNP	G	G	A	rs587781159		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:38663938G>A	ENST00000333535.4	-	4	584	c.435C>T	c.(433-435)tgC>tgT	p.C145C	SCN5A_ENST00000423572.2_Silent_p.C145C|SCN5A_ENST00000413689.1_Silent_p.C145C|SCN5A_ENST00000455624.2_Silent_p.C145C|SCN5A_ENST00000449557.2_Silent_p.C145C|SCN5A_ENST00000425664.1_Silent_p.C145C|SCN5A_ENST00000414099.2_Silent_p.C145C|SCN5A_ENST00000443581.1_Silent_p.C145C|SCN5A_ENST00000451551.2_Silent_p.C145C|SCN5A_ENST00000450102.2_Silent_p.C145C			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	145					AV node cell to bundle of His cell communication (GO:0086067)|brainstem development (GO:0003360)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cardiac ventricle development (GO:0003231)|cellular response to calcium ion (GO:0071277)|cerebellum development (GO:0021549)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during SA node cell action potential (GO:0086046)|neuronal action potential (GO:0019228)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of action potential (GO:0045760)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|telencephalon development (GO:0021537)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	ankyrin binding (GO:0030506)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)	p.C145C(1)		NS(3)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|lung(27)|ovary(6)|pancreas(3)|prostate(10)|skin(9)|upper_aerodigestive_tract(4)	107	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909)	CCATGAACACGCAGTTGGTGA	0.602																																					p.C145C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C435T	3						.						90.0	101.0	97.0					3																	38663938		2179	4268	6447	38638942	SO:0001819	synonymous_variant	6331	exon4			AJ310893	CCDS46796.1, CCDS46797.1, CCDS46798.1, CCDS46799.1, CCDS54569.1, CCDS54570.1	3p21	2014-09-17	2007-01-23		ENSG00000183873	ENSG00000183873		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10593	protein-coding gene	gene with protein product	"""long QT syndrome 3"""	600163	"""sodium channel, voltage-gated, type V, alpha (long QT syndrome 3)"""	CMD1E		7842012, 15466643, 16382098	Standard	NM_198056		Approved	Nav1.5, LQT3, HB1, HBBD, PFHB1, IVF, HB2, HH1, SSS1, CDCD2, CMPD2, ICCD	uc021wvl.1	Q14524	OTTHUMG00000156166	ENST00000333535.4:c.435C>T	3.37:g.38663938G>A		Somatic		Capture	Illumina HiSeq	Phase_I	38638942	NM_001099405	A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Silent	SNP	ENST00000333535.4	37	CCDS46796.1																																																																																				0.602	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056	
SLC25A38	54977	broad.mit.edu	37	3	39431018	39431018	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:39431018C>T	ENST00000273158.4	+	2	479	c.102C>T	c.(100-102)ggC>ggT	p.G34G		NM_017875.2	NP_060345.2			solute carrier family 25, member 38									p.G34G(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(6)|skin(1)|stomach(1)	11				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		TCCTGTGTGGCTCCATCAGTG	0.522																																					p.G34G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C102T	3						.						209.0	174.0	186.0					3																	39431018		2203	4300	6503	39406022	SO:0001819	synonymous_variant	54977	exon2			BC013194	CCDS2685.1	3p22.1	2013-05-22			ENSG00000144659	ENSG00000144659		"""Solute carriers"""	26054	protein-coding gene	gene with protein product		610819				16949250	Standard	NM_017875		Approved	FLJ20551	uc003cjo.2	Q96DW6	OTTHUMG00000131289	ENST00000273158.4:c.102C>T	3.37:g.39431018C>T		Somatic		Capture	Illumina HiSeq	Phase_I	39406022	NM_017875		Silent	SNP	ENST00000273158.4	37	CCDS2685.1																																																																																				0.522	SLC25A38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254057.3	NM_017875	
VIPR1	7433	broad.mit.edu	37	3	42573785	42573785	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:42573785C>T	ENST00000325123.4	+	10	1083	c.970C>T	c.(970-972)Cgg>Tgg	p.R324W	VIPR1-AS1_ENST00000598837.1_RNA|VIPR1-AS1_ENST00000600342.1_RNA|VIPR1-AS1_ENST00000610022.1_RNA|VIPR1-AS1_ENST00000593611.1_RNA|VIPR1-AS1_ENST00000596630.1_RNA|VIPR1-AS1_ENST00000602176.1_RNA|VIPR1-AS1_ENST00000608869.1_RNA|VIPR1-AS1_ENST00000601312.1_RNA|VIPR1_ENST00000438259.2_Missense_Mutation_p.R114W|VIPR1-AS1_ENST00000452639.3_RNA|VIPR1_ENST00000543411.1_Missense_Mutation_p.R276W|VIPR1-AS1_ENST00000593621.1_RNA|VIPR1_ENST00000433647.1_Missense_Mutation_p.R283W	NM_001251885.1|NM_004624.3	NP_001238814.1|NP_004615.2	P32241	VIPR1_HUMAN	vasoactive intestinal peptide receptor 1	324					digestion (GO:0007586)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|muscle contraction (GO:0006936)|positive regulation of cell proliferation (GO:0008284)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	vasoactive intestinal polypeptide receptor activity (GO:0004999)	p.R324W(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|ovary(2)|skin(1)|urinary_tract(3)	18				KIRC - Kidney renal clear cell carcinoma(284;0.241)		TCAGAAACTGCGGCCCCCAGA	0.557																																					p.R324W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C970T	3						.						146.0	137.0	140.0					3																	42573785		2203	4300	6503	42548789	SO:0001583	missense	7433	exon10			AH005329	CCDS2698.1, CCDS58827.1, CCDS58828.1, CCDS58829.1	3p22	2012-08-10			ENSG00000114812	ENSG00000114812		"""GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"""	12694	protein-coding gene	gene with protein product	"""VIP and PACAP receptor 1"""	192321				7708752	Standard	NM_004624		Approved	VPAC1, RDC1, HVR1, VPAC1R	uc003clf.2	P32241	OTTHUMG00000131792	ENST00000325123.4:c.970C>T	3.37:g.42573785C>T	ENSP00000327246:p.Arg324Trp	Somatic		Capture	Illumina HiSeq	Phase_I	42548789	NM_004624	A5JUT9|B3KPV1|B4DEB5|B4DGI4|F5H1F5|G3V0I1|Q15871|Q6P2M6	Missense_Mutation	SNP	ENST00000325123.4	37	CCDS2698.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.583006	0.86748	.	.	ENSG00000114812	ENST00000433647;ENST00000543411;ENST00000438259;ENST00000325123	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	4.61	4.61	0.57282	GPCR, family 2-like (1);	0.414384	0.25068	N	0.033392	T	0.58906	0.2155	M	0.64170	1.965	0.28980	N	0.888691	D;D;D;D	0.61697	0.988;0.988;0.99;0.988	P;P;P;P	0.58820	0.846;0.72;0.609;0.846	T	0.60047	-0.7339	10	0.87932	D	0	.	17.4441	0.87574	0.0:1.0:0.0:0.0	.	297;114;276;324	B4DNY6;B4DEB5;F5H1F5;P32241	.;.;.;VIPR1_HUMAN	W	283;276;114;324	ENSP00000394950:R283W;ENSP00000445701:R276W;ENSP00000415371:R114W;ENSP00000327246:R324W	ENSP00000327246:R324W	R	+	1	2	VIPR1	42548789	1.000000	0.71417	0.983000	0.44433	0.991000	0.79684	5.088000	0.64486	2.110000	0.64415	0.655000	0.94253	CGG		0.557	VIPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254728.4	NM_004624	
NBEAL2	23218	broad.mit.edu	37	3	47046044	47046044	+	Silent	SNP	G	G	A	rs371080261		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:47046044G>A	ENST00000450053.3	+	38	6437	c.6258G>A	c.(6256-6258)gcG>gcA	p.A2086A	NBEAL2_ENST00000383740.2_Silent_p.A365A|NBEAL2_ENST00000292309.5_Silent_p.A1902A	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	2086	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.				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.A2086A(1)|p.A1463A(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)		ACACCATTGCGGGGCGGACCT	0.587																																					p.A2086A												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G6258A	3						.	G		1,4171		0,1,2085	97.0	109.0	105.0		6258	-9.9	0.4	3		105	0,8444		0,0,4222	no	coding-synonymous	NBEAL2	NM_015175.1		0,1,6307	AA,AG,GG		0.0,0.024,0.0079		2086/2755	47046044	1,12615	2086	4222	6308	47021048	SO:0001819	synonymous_variant	23218	exon38			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.6258G>A	3.37:g.47046044G>A		Somatic		Capture	Illumina HiSeq	Phase_I	47021048	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Silent	SNP	ENST00000450053.3	37	CCDS46817.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.354|8.354	0.831507|0.831507	0.16820|0.16820	2.4E-4|2.4E-4	0.0|0.0	ENSG00000160796|ENSG00000160796	ENST00000443829|ENST00000416683	.|.	.|.	.|.	4.96|4.96	-9.87|-9.87	0.00470|0.00470	.|.	.|.	.|.	.|.	.|.	T|T	0.41305|0.41305	0.1153|0.1153	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.46219|0.46219	-0.9207|-0.9207	4|4	.|.	.|.	.|.	.|.	4.3817|4.3817	0.11297|0.11297	0.4918:0.2404:0.1873:0.0805|0.4918:0.2404:0.1873:0.0805	.|.	.|.	.|.	.|.	R|Q	455|1374	.|.	.|.	G|R	+|+	1|2	0|0	NBEAL2|NBEAL2	47021048|47021048	0.000000|0.000000	0.05858|0.05858	0.393000|0.393000	0.26258|0.26258	0.982000|0.982000	0.71751|0.71751	-1.753000|-1.753000	0.01818|0.01818	-2.237000|-2.237000	0.00712|0.00712	-0.291000|-0.291000	0.09656|0.09656	GGG|CGG		0.587	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064	
MAP4	4134	broad.mit.edu	37	3	47958466	47958466	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:47958466A>G	ENST00000360240.6	-	7	1369	c.851T>C	c.(850-852)tTa>tCa	p.L284S	MAP4_ENST00000426837.2_Missense_Mutation_p.L301S|MAP4_ENST00000383737.4_Missense_Mutation_p.L284S|MAP4_ENST00000395734.3_Missense_Mutation_p.L284S	NM_002375.4	NP_002366.2	P27816	MAP4_HUMAN	microtubule-associated protein 4	284	17 X 14 AA tandem repeats.				cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|microtubule sliding (GO:0051012)|mitotic spindle organization (GO:0007052)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|microtubule cytoskeleton (GO:0015630)|mitotic spindle (GO:0072686)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)	p.L284S(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(2)	32				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)	Docetaxel(DB01248)|Paclitaxel(DB01229)	TGTCACATCTAATTTGGTGGG	0.488																																					p.L284S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T851C	3						.						390.0	333.0	352.0					3																	47958466		2203	4300	6503	47933470	SO:0001583	missense	4134	exon7				CCDS33750.1, CCDS46818.1, CCDS46821.1	3p21	2008-07-18			ENSG00000047849	ENSG00000047849			6862	protein-coding gene	gene with protein product		157132				1905296	Standard	NM_002375		Approved		uc003csb.2	P27816	OTTHUMG00000156828	ENST00000360240.6:c.851T>C	3.37:g.47958466A>G	ENSP00000353375:p.Leu284Ser	Somatic		Capture	Illumina HiSeq	Phase_I	47933470	NM_001134364	Q13082|Q59FT2|Q68D74|Q6ZUW9|Q86V26|Q96A76|Q96NS9	Missense_Mutation	SNP	ENST00000360240.6	37	CCDS33750.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.48|10.48	1.361835|1.361835	0.24684|0.24684	.|.	.|.	ENSG00000047849|ENSG00000047849	ENST00000383737;ENST00000395734;ENST00000426837;ENST00000360240|ENST00000423088	T;T;T;T|.	0.07444|.	3.2;3.19;3.19;3.19|.	4.35|4.35	-1.67|-1.67	0.08238|0.08238	.|.	.|.	.|.	.|.	.|.	T|.	0.06416|.	0.0165|.	N|N	0.00666|0.00666	-1.275|-1.275	0.09310|0.09310	N|N	1|1	B;B;B|.	0.13145|.	0.002;0.007;0.007|.	B;B;B|.	0.14023|.	0.005;0.007;0.01|.	T|.	0.31420|.	-0.9944|.	9|.	0.18710|.	T|.	0.47|.	2.9431|2.9431	0.8|0.8	0.01074|0.01074	0.3405:0.1587:0.3391:0.1617|0.3405:0.1587:0.3391:0.1617	.|.	261;284;284|.	C9JFC3;P27816-6;P27816|.	.;.;MAP4_HUMAN|.	S|Q	284;284;301;284|253	ENSP00000373243:L284S;ENSP00000379083:L284S;ENSP00000407602:L301S;ENSP00000353375:L284S|.	ENSP00000353375:L284S|.	L|X	-|-	2|1	0|0	MAP4|MAP4	47933470|47933470	0.675000|0.675000	0.27558|0.27558	0.000000|0.000000	0.03702|0.03702	0.112000|0.112000	0.19704|0.19704	0.665000|0.665000	0.25083|0.25083	-0.466000|-0.466000	0.06943|0.06943	-0.326000|-0.326000	0.08463|0.08463	TTA|TAG		0.488	MAP4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346085.1	NM_002375	
NCKIPSD	51517	broad.mit.edu	37	3	48712036	48712036	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:48712036G>A	ENST00000294129.2	-	13	2229	c.2110C>T	c.(2110-2112)Cgc>Tgc	p.R704C	NCKIPSD_ENST00000341520.4_Intron|NCKIPSD_ENST00000416649.2_Missense_Mutation_p.R697C|RP11-572O6.1_ENST00000607025.1_lincRNA	NM_016453.2	NP_057537.1	Q9NZQ3	SPN90_HUMAN	NCK interacting protein with SH3 domain	704					cytoskeleton organization (GO:0007010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|NLS-bearing protein import into nucleus (GO:0006607)|signal transduction (GO:0007165)	cytosol (GO:0005829)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	cytoskeletal protein binding (GO:0008092)	p.R704C(1)		endometrium(1)|large_intestine(3)|lung(6)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		ACAATCATGCGGTCCATCTGG	0.617																																					p.R704C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2110T	3						.						107.0	90.0	96.0					3																	48712036		2203	4300	6503	48687040	SO:0001583	missense	51517	exon13			AF178432	CCDS2776.1, CCDS46827.1	3p21	2008-07-18			ENSG00000213672	ENSG00000213672			15486	protein-coding gene	gene with protein product	"""dia interacting protein"", ""diaphanous protein interacting protein"", ""SH3 protein interacting with Nck, 90 kDa"""	606671				10648423, 10619843	Standard	NM_016453		Approved	AF3P21, SPIN90, ORF1, WISH, WASLBP, DIP1	uc003cun.3	Q9NZQ3	OTTHUMG00000133542	ENST00000294129.2:c.2110C>T	3.37:g.48712036G>A	ENSP00000294129:p.Arg704Cys	Somatic		Capture	Illumina HiSeq	Phase_I	48687040	NM_016453	B4DFL5|Q6GU34|Q6SPF3|Q8TC10|Q9UGM8	Missense_Mutation	SNP	ENST00000294129.2	37	CCDS2776.1	.	.	.	.	.	.	.	.	.	.	g	22.5	4.297523	0.81025	.	.	ENSG00000213672	ENST00000416649;ENST00000294129	T;T	0.36157	1.27;1.28	5.42	4.49	0.54785	.	.	.	.	.	T	0.36826	0.0981	L	0.36672	1.1	0.80722	D	1	D;D	0.61697	0.983;0.99	B;P	0.50109	0.427;0.631	T	0.16217	-1.0410	9	0.72032	D	0.01	.	11.5488	0.50708	0.0:0.0:0.6454:0.3546	.	704;697	Q9NZQ3;Q9NZQ3-3	SPN90_HUMAN;.	C	697;704	ENSP00000389059:R697C;ENSP00000294129:R704C	ENSP00000294129:R704C	R	-	1	0	NCKIPSD	48687040	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	6.251000	0.72441	2.556000	0.86216	0.543000	0.68304	CGC		0.617	NCKIPSD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257520.1	NM_016453	
USP4	7375	broad.mit.edu	37	3	49343174	49343174	+	Missense_Mutation	SNP	C	C	T	rs546430537		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:49343174C>T	ENST00000265560.4	-	9	1148	c.1102G>A	c.(1102-1104)Gcc>Acc	p.A368T	USP4_ENST00000351842.4_Missense_Mutation_p.A321T|USP4_ENST00000488520.1_5'UTR	NM_003363.3	NP_003354.2	Q13107	UBP4_HUMAN	ubiquitin specific peptidase 4 (proto-oncogene)	368	USP.				negative regulation of protein ubiquitination (GO:0031397)|protein deubiquitination (GO:0016579)|protein localization to cell surface (GO:0034394)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	adenosine receptor binding (GO:0031685)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.A368T(1)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33		Ovarian(412;0.00308)|Myeloproliferative disorder(1037;0.0255)|Hepatocellular(537;0.121)		OV - Ovarian serous cystadenocarcinoma(275;4.74e-26)|Kidney(197;2.22e-07)|KIRC - Kidney renal clear cell carcinoma(197;5.14e-06)|BRCA - Breast invasive adenocarcinoma(193;9.46e-05)		GCCACATGGGCGTCCCTTCCA	0.468													C|||	1	0.000199681	0.0	0.0	5008	,	,		19913	0.0		0.001	False		,,,				2504	0.0				p.A321T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G961A	3						.						109.0	96.0	100.0					3																	49343174		2203	4300	6503	49318178	SO:0001583	missense	7375	exon8			U20657	CCDS2793.1, CCDS2794.1, CCDS58832.1	3p21.3	2005-10-11	2005-08-08		ENSG00000114316	ENSG00000114316		"""Ubiquitin-specific peptidases"""	12627	protein-coding gene	gene with protein product		603486	"""ubiquitin specific protease 4 (proto-oncogene)"""	UNP		12838346, 9464533	Standard	NM_199443		Approved	Unph	uc003cwq.2	Q13107	OTTHUMG00000156825	ENST00000265560.4:c.1102G>A	3.37:g.49343174C>T	ENSP00000265560:p.Ala368Thr	Somatic		Capture	Illumina HiSeq	Phase_I	49318178	NM_199443	A8K6Y0|C9IY91|O43452|O43453|Q08AK8	Missense_Mutation	SNP	ENST00000265560.4	37	CCDS2793.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	7.515|7.515	0.655527|0.655527	0.14580|0.14580	.|.	.|.	ENSG00000114316|ENSG00000114316	ENST00000351842;ENST00000265560|ENST00000431357	T;T|.	0.02763|.	4.17;4.17|.	5.92|5.92	-2.84|-2.84	0.05751|0.05751	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);|.	0.489265|.	0.25744|.	N|.	0.028593|.	T|T	0.17831|0.17831	0.0428|0.0428	N|N	0.03000|0.03000	-0.44|-0.44	0.37648|0.37648	D|D	0.922301|0.922301	B;B;B|.	0.06786|.	0.001;0.0;0.001|.	B;B;B|.	0.06405|.	0.001;0.001;0.002|.	T|T	0.15896|0.15896	-1.0421|-1.0421	10|5	0.06625|.	T|.	0.88|.	-0.1686|-0.1686	5.4956|5.4956	0.16802|0.16802	0.2739:0.2441:0.0:0.4819|0.2739:0.2441:0.0:0.4819	.|.	321;368;368|.	Q13107-2;Q13107;Q08AK7|.	.;UBP4_HUMAN;.|.	T|H	321;368|124	ENSP00000341028:A321T;ENSP00000265560:A368T|.	ENSP00000265560:A368T|.	A|R	-|-	1|2	0|0	USP4|USP4	49318178|49318178	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.744000|0.744000	0.42396|0.42396	-0.866000|-0.866000	0.04245|0.04245	-0.424000|-0.424000	0.07382|0.07382	0.557000|0.557000	0.71058|0.71058	GCC|CGC		0.468	USP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346069.1	NM_199443	
SEMA3G	56920	broad.mit.edu	37	3	52475406	52475406	+	Silent	SNP	G	G	A	rs368237957		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:52475406G>A	ENST00000231721.2	-	7	686	c.687C>T	c.(685-687)gcC>gcT	p.A229A		NM_020163.1	NP_064548.1	Q9NS98	SEM3G_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3G	229	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)	p.A229A(1)		kidney(1)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)	18				BRCA - Breast invasive adenocarcinoma(193;1.69e-05)|Kidney(197;0.00173)|KIRC - Kidney renal clear cell carcinoma(197;0.00196)|OV - Ovarian serous cystadenocarcinoma(275;0.0333)		GGATCCGGGCGGCCATCACAA	0.612																																					p.A229A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C687T	3						.	G		0,4406		0,0,2203	55.0	45.0	48.0		687	-8.8	0.0	3		48	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SEMA3G	NM_020163.1		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		229/783	52475406	1,13005	2203	4300	6503	52450446	SO:0001819	synonymous_variant	56920	exon7				CCDS2856.1	3p21.1	2013-01-11			ENSG00000010319	ENSG00000010319		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	30400	protein-coding gene	gene with protein product						11214971	Standard	XM_005265327		Approved	FLJ00014, sem2	uc003dea.1	Q9NS98	OTTHUMG00000158570	ENST00000231721.2:c.687C>T	3.37:g.52475406G>A		Somatic		Capture	Illumina HiSeq	Phase_I	52450446	NM_020163	Q7L9D9|Q9H7Q3	Silent	SNP	ENST00000231721.2	37	CCDS2856.1																																																																																				0.612	SEMA3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351354.1	NM_020163	
ITIH1	3697	broad.mit.edu	37	3	52819193	52819193	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:52819193G>A	ENST00000273283.2	+	12	1565	c.1541G>A	c.(1540-1542)cGc>cAc	p.R514H	ITIH1_ENST00000537050.1_Missense_Mutation_p.R226H|ITIH1_ENST00000542827.1_Missense_Mutation_p.R514H|ITIH1_ENST00000405128.3_5'Flank|ITIH1_ENST00000540715.1_Missense_Mutation_p.R372H	NM_002215.3	NP_002206.2	P19827	ITIH1_HUMAN	inter-alpha-trypsin inhibitor heavy chain 1	514	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.R514H(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)		GTGGCCGGGCGCATTGCTGAC	0.572																																					p.R372H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1115A	3						.						134.0	123.0	127.0					3																	52819193		2203	4300	6503	52794233	SO:0001583	missense	3697	exon10				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.1541G>A	3.37:g.52819193G>A	ENSP00000273283:p.Arg514His	Somatic		Capture	Illumina HiSeq	Phase_I	52794233	NM_001166434	A8K9N5|B2RAH9|B7Z558|B7Z8C0|F5H165|F5H7Y8|P78455|Q01746|Q562G1	Missense_Mutation	SNP	ENST00000273283.2	37	CCDS2864.1	.	.	.	.	.	.	.	.	.	.	G	16.34	3.095707	0.56075	.	.	ENSG00000055957	ENST00000542827;ENST00000273283;ENST00000540715;ENST00000537050;ENST00000428133	T;T;T;T;T	0.13420	2.59;2.59;2.59;2.59;2.59	4.88	3.92	0.45320	.	0.055516	0.64402	D	0.000001	T	0.17365	0.0417	M	0.85197	2.74	0.34732	D	0.729813	P;B;P	0.47841	0.901;0.333;0.752	B;B;B	0.35813	0.211;0.02;0.189	T	0.43130	-0.9410	10	0.87932	D	0	-16.6527	9.8078	0.40803	0.1717:0.0:0.8283:0.0	.	372;115;514	F5H165;Q9P1C5;P19827	.;.;ITIH1_HUMAN	H	514;514;372;226;67	ENSP00000442584:R514H;ENSP00000273283:R514H;ENSP00000443973:R372H;ENSP00000443847:R226H;ENSP00000395836:R67H	ENSP00000273283:R514H	R	+	2	0	ITIH1	52794233	0.510000	0.26171	1.000000	0.80357	0.990000	0.78478	1.821000	0.39041	2.557000	0.86248	0.543000	0.68304	CGC		0.572	ITIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317522.1	NM_002215	
IL17RB	55540	broad.mit.edu	37	3	53892823	53892823	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:53892823C>T	ENST00000288167.3	+	9	834	c.825C>T	c.(823-825)ggC>ggT	p.G275G	RP11-884K10.7_ENST00000607783.1_RNA	NM_018725.3	NP_061195.2	Q9NRM6	I17RB_HUMAN	interleukin 17 receptor B	275					cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|regulation of cell growth (GO:0001558)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	cytokine receptor activity (GO:0004896)	p.G275G(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)	13				BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)		CACAAACAGGCGTCCCTTTCC	0.502																																					p.G275G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C825T	3						.						90.0	80.0	84.0					3																	53892823		2203	4300	6503	53867863	SO:0001819	synonymous_variant	55540	exon9			AF212365	CCDS2874.1	3p21.1	2008-02-05		2003-07-09	ENSG00000056736	ENSG00000056736		"""Interleukins and interleukin receptors"""	18015	protein-coding gene	gene with protein product		605458	"""interleukin 17B receptor"""	IL17BR		10749887, 10815801	Standard	NM_018725		Approved	IL17RH1, EVI27, CRL4	uc003dha.3	Q9NRM6	OTTHUMG00000158280	ENST00000288167.3:c.825C>T	3.37:g.53892823C>T		Somatic		Capture	Illumina HiSeq	Phase_I	53867863	NM_018725	Q9BPZ0|Q9NRL4|Q9NRM5	Silent	SNP	ENST00000288167.3	37	CCDS2874.1																																																																																				0.502	IL17RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350563.1	NM_172234	
ARL6IP5	10550	broad.mit.edu	37	3	69153744	69153744	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:69153744G>A	ENST00000273258.3	+	3	628	c.524G>A	c.(523-525)gGc>gAc	p.G175D	ARL6IP5_ENST00000478935.1_Intron	NM_006407.3	NP_006398.1	O75915	PRAF3_HUMAN	ADP-ribosylation factor-like 6 interacting protein 5	175	Targeting to endoplasmic reticulum membrane. {ECO:0000250}.				intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|L-glutamate transport (GO:0015813)|negative regulation of mitochondrial membrane potential (GO:0010917)|negative regulation of transport (GO:0051051)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of stress-activated MAPK cascade (GO:0032874)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				biliary_tract(1)|endometrium(1)|large_intestine(2)|ovary(1)|prostate(1)|urinary_tract(1)	7		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.78e-05)|Epithelial(33;0.000818)|LUSC - Lung squamous cell carcinoma(21;0.0118)|Lung(16;0.0189)|KIRC - Kidney renal clear cell carcinoma(39;0.203)|Kidney(39;0.238)		CAGGAAGAAGGCATCAACAGA	0.453																																					p.G175D												.	.	0			c.G524A	3						.						102.0	91.0	95.0					3																	69153744		2203	4300	6503	69236434	SO:0001583	missense	10550	exon3			AF070523	CCDS2912.1	3p14	2014-05-12	2014-05-12		ENSG00000144746	ENSG00000144746			16937	protein-coding gene	gene with protein product	"""PRA1 domain family 3"""	605709				11242046, 11042152	Standard	NM_006407		Approved	PRAF3, JWA, GTRAP3-18, DERP11, HSPC127	uc003dnr.3	O75915	OTTHUMG00000158773	ENST00000273258.3:c.524G>A	3.37:g.69153744G>A	ENSP00000273258:p.Gly175Asp	None		Capture	Illumina HiSeq	Phase_I	69236434	NM_006407	B2R6V5|Q53ES3|Q5KU08	Missense_Mutation	SNP	ENST00000273258.3	37	CCDS2912.1	.	.	.	.	.	.	.	.	.	.	G	1.401	-0.578067	0.03854	.	.	ENSG00000144746	ENST00000273258	T	0.42900	0.96	5.69	-11.4	0.00090	.	0.580762	0.21315	N	0.076577	T	0.16514	0.0397	N	0.08118	0	0.09310	N	0.999999	B	0.13145	0.007	B	0.12156	0.007	T	0.15350	-1.0440	10	0.14656	T	0.56	-1.6262	16.7633	0.85517	0.2163:0.1956:0.5881:0.0	.	175	O75915	PRAF3_HUMAN	D	175	ENSP00000273258:G175D	ENSP00000273258:G175D	G	+	2	0	ARL6IP5	69236434	0.000000	0.05858	0.000000	0.03702	0.064000	0.16182	-1.481000	0.02323	-3.891000	0.00094	-1.105000	0.02106	GGC		0.453	ARL6IP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352132.1	NM_006407	
FOXP1	27086	broad.mit.edu	37	3	71247427	71247427	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:71247427G>A	ENST00000318789.4	-	6	631	c.106C>T	c.(106-108)Cgg>Tgg	p.R36W	FOXP1_ENST00000475937.1_Missense_Mutation_p.R36W|FOXP1_ENST00000468577.1_Missense_Mutation_p.R36W|FOXP1_ENST00000318779.3_Missense_Mutation_p.R36W|FOXP1_ENST00000498215.1_Missense_Mutation_p.R36W|FOXP1_ENST00000484350.1_Missense_Mutation_p.R36W|FOXP1_ENST00000493089.1_Missense_Mutation_p.R36W	NM_001244810.1|NM_001244813.1|NM_032682.5	NP_001231739.1|NP_001231742.1|NP_116071.2	Q9H334	FOXP1_HUMAN	forkhead box P1	36					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R36W(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)		CCGTTGGACCGCCCCTCCCGA	0.622			T	PAX5	ALL																																p.R36W			Dom	yes		3	3p14.1	27086	forkhead box P1		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C106T	3						.						87.0	94.0	92.0					3																	71247427		2203	4300	6503	71330117	SO:0001583	missense	27086	exon6			AF146696	CCDS2914.1, CCDS33785.1, CCDS58837.1, CCDS58838.1, CCDS58839.1, CCDS74963.1, CCDS74964.1	3p14.1	2008-07-18			ENSG00000114861	ENSG00000114861		"""Forkhead boxes"""	3823	protein-coding gene	gene with protein product	"""fork head-related protein like B"", ""glutamine-rich factor 1"", ""PAX5/FOXP1 fusion protein"""	605515				8265594, 11751404	Standard	NM_032682		Approved	QRF1, 12CC4, HSPC215, hFKH1B	uc003doj.3	Q9H334	OTTHUMG00000158803	ENST00000318789.4:c.106C>T	3.37:g.71247427G>A	ENSP00000318902:p.Arg36Trp	Somatic		Capture	Illumina HiSeq	Phase_I	71330117	NM_032682	A3QVP8|B3KV70|G5E9V8|Q8NAN6|Q9BSG9|Q9H332|Q9H333|Q9P0R1	Missense_Mutation	SNP	ENST00000318789.4	37	CCDS2914.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.787804	0.90367	.	.	ENSG00000114861	ENST00000318789;ENST00000475937;ENST00000339693;ENST00000493089;ENST00000498215;ENST00000484350;ENST00000468577;ENST00000318779	D;D;D;D;D;D;T	0.89939	-2.56;-2.56;-2.56;-2.56;-2.59;-2.36;-0.11	5.77	3.66	0.41972	.	0.000000	0.85682	D	0.000000	D	0.91297	0.7256	L	0.43152	1.355	0.52501	D	0.999953	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;0.996;0.988;0.973;0.973	D	0.91861	0.5499	10	0.87932	D	0	.	12.3329	0.55049	0.0:0.0:0.4436:0.5564	.	36;36;36;36;36	Q9BSG9;A3KMG1;G5E9V8;Q8NAN6;Q9H334	.;.;.;.;FOXP1_HUMAN	W	36	ENSP00000318902:R36W;ENSP00000419393:R36W;ENSP00000418524:R36W;ENSP00000418102:R36W;ENSP00000417857:R36W;ENSP00000418883:R36W;ENSP00000318721:R36W	ENSP00000318721:R36W	R	-	1	2	FOXP1	71330117	0.977000	0.34250	0.619000	0.29118	0.970000	0.65996	1.743000	0.38258	1.513000	0.48852	0.655000	0.94253	CGG		0.622	FOXP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352250.1	NM_032682	
EPHA3	2042	broad.mit.edu	37	3	89390124	89390124	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:89390124G>A	ENST00000336596.2	+	4	1098	c.873G>A	c.(871-873)ccG>ccA	p.P291P	EPHA3_ENST00000452448.2_Silent_p.P291P|EPHA3_ENST00000494014.1_Silent_p.P291P	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	291	Cys-rich.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)	p.P291P(4)		NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		CTAAGTGCCCGCCTCACAGTT	0.438										TSP Lung(6;0.00050)																											p.P291P												.	.	4	Substitution - coding silent(4)	large_intestine(2)|lung(2)	c.G873A	3						.						164.0	158.0	160.0					3																	89390124		2203	4300	6503	89472814	SO:0001819	synonymous_variant	2042	exon4			M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3387	protein-coding gene	gene with protein product		179611	"""EphA3"""	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.873G>A	3.37:g.89390124G>A		None		Capture	Illumina HiSeq	Phase_I	89472814	NM_005233	Q9H2V3|Q9H2V4	Silent	SNP	ENST00000336596.2	37	CCDS2922.1																																																																																				0.438	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233	
EPHA3	2042	broad.mit.edu	37	3	89468417	89468417	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:89468417G>A	ENST00000336596.2	+	11	2176	c.1951G>A	c.(1951-1953)Gcc>Acc	p.A651T	EPHA3_ENST00000494014.1_Missense_Mutation_p.A651T	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	651	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)	p.A651T(1)		NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		GATTTCAGTGGCCATTAAGAC	0.423										TSP Lung(6;0.00050)																											p.A651T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1951A	3						.						91.0	90.0	90.0					3																	89468417		2203	4300	6503	89551107	SO:0001583	missense	2042	exon11			M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3387	protein-coding gene	gene with protein product		179611	"""EphA3"""	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.1951G>A	3.37:g.89468417G>A	ENSP00000337451:p.Ala651Thr	Somatic		Capture	Illumina HiSeq	Phase_I	89551107	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	37	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.047187	0.75846	.	.	ENSG00000044524	ENST00000336596;ENST00000494014	T;T	0.80480	-1.38;-1.38	5.56	5.56	0.83823	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	D	0.93713	0.7991	H	0.96996	3.92	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.95419	0.8505	9	.	.	.	.	19.5365	0.95255	0.0:0.0:1.0:0.0	.	651	P29320	EPHA3_HUMAN	T	651	ENSP00000337451:A651T;ENSP00000419190:A651T	.	A	+	1	0	EPHA3	89551107	1.000000	0.71417	1.000000	0.80357	0.141000	0.21300	9.869000	0.99810	2.614000	0.88457	0.563000	0.77884	GCC		0.423	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233	
GABRR3	200959	broad.mit.edu	37	3	97705715	97705715	+	RNA	SNP	A	A	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:97705715A>C	ENST00000472788.1	-	0	1217					NM_001105580.2	NP_001099050.1	A8MPY1	GBRR3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, rho 3 (gene/pseudogene)						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.F86V(1)		large_intestine(2)|lung(1)	3					Adinazolam(DB00546)|Bromazepam(DB01558)|Cinolazepam(DB01594)|Clotiazepam(DB01559)|Diazepam(DB00829)|Estazolam(DB01215)|Fludiazepam(DB01567)|Flurazepam(DB00690)|Halazepam(DB00801)|Midazolam(DB00683)|Nitrazepam(DB01595)|Oxazepam(DB00842)|Prazepam(DB01588)|Quazepam(DB01589)|Temazepam(DB00231)|Triazolam(DB00897)	CTTCTCATGAAGTCTTCTGAG	0.428																																					p.F406V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1216G	3						.						71.0	64.0	66.0					3																	97705715		1884	4105	5989	99188405			200959	exon9			Y18994	CCDS54617.1	3q11.2	2014-03-25	2014-03-25		ENSG00000183185	ENSG00000183185		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	17969	protein-coding gene	gene with protein product	"""GABA(A) receptor, rho 3"""		"""gamma-aminobutyric acid (GABA) receptor, rho 3"", ""gamma-aminobutyric acid (GABA) A receptor, rho 3"""			10542332	Standard	NM_001105580		Approved		uc021xbp.1	A8MPY1	OTTHUMG00000159135		3.37:g.97705715A>C		Somatic		Capture	Illumina HiSeq	Phase_I	99188405	NM_001105580	Q9UIV9	Missense_Mutation	SNP	ENST00000472788.1	37																																																																																					0.428	GABRR3-002	KNOWN	not_organism_supported|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000353445.2		
OR5H1	26341	broad.mit.edu	37	3	97852131	97852131	+	Missense_Mutation	SNP	T	T	G	rs371242000		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:97852131T>G	ENST00000354565.2	+	1	590	c.590T>G	c.(589-591)cTa>cGa	p.L197R	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005338.1	NP_001005338.1	A6NKK0	OR5H1_HUMAN	olfactory receptor, family 5, subfamily H, member 1	197						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L197R(1)		breast(1)|endometrium(7)|kidney(8)|large_intestine(3)|lung(13)|ovary(1)|skin(1)	34						ATTAATTTTCTAATGGTTTTT	0.308																																					p.L197R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T590G	3						.						25.0	29.0	28.0					3																	97852131		2196	4292	6488	99334821	SO:0001583	missense	26341	exon1			X64988	CCDS33797.1	3q12.1	2012-08-09			ENSG00000231192	ENSG00000231192		"""GPCR / Class A : Olfactory receptors"""	8346	protein-coding gene	gene with protein product						1370859	Standard	NM_001005338		Approved	HTPCRX14, HSHTPCRX14	uc011bgt.2	A6NKK0	OTTHUMG00000160070	ENST00000354565.2:c.590T>G	3.37:g.97852131T>G	ENSP00000346575:p.Leu197Arg	Somatic		Capture	Illumina HiSeq	Phase_I	99334821	NM_001005338		Missense_Mutation	SNP	ENST00000354565.2	37	CCDS33797.1	.	.	.	.	.	.	.	.	.	.	T	8.543	0.873757	0.17322	.	.	ENSG00000231192	ENST00000354565	T	0.00216	8.53	3.57	3.57	0.40892	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36703	N	0.002454	T	0.00496	0.0016	M	0.81802	2.56	0.09310	N	1	D	0.63046	0.992	D	0.70487	0.969	T	0.35624	-0.9781	10	0.72032	D	0.01	.	10.1009	0.42504	0.0:0.0:0.0:1.0	.	197	A6NKK0	OR5H1_HUMAN	R	197	ENSP00000346575:L197R	ENSP00000346575:L197R	L	+	2	0	OR5H1	99334821	0.143000	0.22626	0.004000	0.12327	0.034000	0.12701	3.752000	0.55172	1.481000	0.48307	0.164000	0.16699	CTA		0.308	OR5H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359100.2	NM_001005338	
LMLN	89782	broad.mit.edu	37	3	197707247	197707247	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr3:197707247G>A	ENST00000330198.4	+	6	622	c.600G>A	c.(598-600)gtG>gtA	p.V200V	LMLN_ENST00000482695.1_Silent_p.V148V|LMLN_ENST00000332636.5_Silent_p.V148V|LMLN_ENST00000420910.2_Silent_p.V200V	NM_033029.3	NP_149018.2	Q96KR4	LMLN_HUMAN	leishmanolysin-like (metallopeptidase M8 family)	200					cell adhesion (GO:0007155)|mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|lipid particle (GO:0005811)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)	p.V200V(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;9.84e-24)|all cancers(36;3.18e-22)|OV - Ovarian serous cystadenocarcinoma(49;5.35e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.111)		CAGTGGGTGTGCCAGACCAAG	0.532																																					p.V200V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G600A	3						.						145.0	137.0	140.0					3																	197707247		2203	4300	6503	199191644	SO:0001819	synonymous_variant	89782	exon6			AJ312398	CCDS3332.1, CCDS46988.1	3q29	2008-02-04			ENSG00000185621	ENSG00000185621	3.4.24.36		15991	protein-coding gene	gene with protein product		609380					Standard	NM_033029		Approved	Gp63, Msp	uc010iar.3	Q96KR4	OTTHUMG00000155375	ENST00000330198.4:c.600G>A	3.37:g.197707247G>A		Somatic		Capture	Illumina HiSeq	Phase_I	199191644	NM_033029	B3LDG9|B3LDH0|C9J796|F8WB28|Q96KR5	Silent	SNP	ENST00000330198.4	37	CCDS3332.1																																																																																				0.532	LMLN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339701.1	NM_033029	
ETNPPL	64850	broad.mit.edu	37	4	109681432	109681432	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr4:109681432A>T	ENST00000296486.3	-	2	241	c.87T>A	c.(85-87)gaT>gaA	p.D29E	ETNPPL_ENST00000510706.1_5'UTR|ETNPPL_ENST00000411864.2_Missense_Mutation_p.D29E|ETNPPL_ENST00000512646.1_Intron	NM_001146590.1|NM_031279.3	NP_001140062.1|NP_112569.2	Q8TBG4	AT2L1_HUMAN	ethanolamine-phosphate phospho-lyase	29						mitochondrion (GO:0005739)	ethanolamine-phosphate phospho-lyase activity (GO:0050459)|pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)	p.D29E(1)									TTTTGATGGGATCCGATGCAA	0.428																																					p.D29E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T87A	4						.						102.0	100.0	101.0					4																	109681432		2203	4300	6503	109900881	SO:0001583	missense	64850	exon2			AJ298293	CCDS3682.1, CCDS54792.1, CCDS54793.1	4q25	2013-06-12	2013-06-12	2013-06-12	ENSG00000164089	ENSG00000164089	4.2.3.2		14404	protein-coding gene	gene with protein product		614682	"""alanine-glyoxylate aminotransferase 2-like 1"""	AGXT2L1		7592550, 22241472	Standard	NM_031279		Approved		uc003hzc.3	Q8TBG4	OTTHUMG00000161036	ENST00000296486.3:c.87T>A	4.37:g.109681432A>T	ENSP00000296486:p.Asp29Glu	Somatic		Capture	Illumina HiSeq	Phase_I	109900881	NM_001146590	B7Z1Y0|E9PBY0|Q9H174	Missense_Mutation	SNP	ENST00000296486.3	37	CCDS3682.1	.	.	.	.	.	.	.	.	.	.	A	16.85	3.237831	0.58886	.	.	ENSG00000164089	ENST00000296486;ENST00000411864	T;T	0.42900	0.96;0.96	5.31	1.52	0.23074	.	0.000000	0.85682	D	0.000000	T	0.59238	0.2179	M	0.88704	2.975	0.80722	D	1	B;D	0.61080	0.369;0.989	B;P	0.56612	0.259;0.802	T	0.62756	-0.6787	9	.	.	.	-30.9447	9.205	0.37285	0.607:0.0:0.393:0.0	.	29;29	Q8TBG4-2;Q8TBG4	.;AT2L1_HUMAN	E	29	ENSP00000296486:D29E;ENSP00000392269:D29E	.	D	-	3	2	AGXT2L1	109900881	0.996000	0.38824	1.000000	0.80357	0.986000	0.74619	0.392000	0.20801	0.342000	0.23796	0.460000	0.39030	GAT		0.428	ETNPPL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363508.1	NM_031279	
PDE5A	8654	broad.mit.edu	37	4	120488258	120488258	+	Silent	SNP	G	G	A	rs199732889		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr4:120488258G>A	ENST00000354960.3	-	4	1192	c.873C>T	c.(871-873)aaC>aaT	p.N291N	PDE5A_ENST00000264805.5_Silent_p.N249N|PDE5A_ENST00000394439.1_Silent_p.N239N|SNORA11_ENST00000408318.1_RNA	NM_001083.3	NP_001074.2	O76074	PDE5A_HUMAN	phosphodiesterase 5A, cGMP-specific	291	GAF 1.				blood coagulation (GO:0007596)|cGMP catabolic process (GO:0046069)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of oocyte development (GO:0060282)|relaxation of cardiac muscle (GO:0055119)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)	p.N291N(2)		breast(4)|endometrium(2)|kidney(3)|large_intestine(8)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	27					Avanafil(DB06237)|Caffeine(DB00201)|Dipyridamole(DB00975)|Pentoxifylline(DB00806)|Sildenafil(DB00203)|Tadalafil(DB00820)|Theophylline(DB00277)|Udenafil(DB06267)|Vardenafil(DB00862)	ATGTCCCACCGTTTCCTGATT	0.358													G|||	1	0.000199681	0.0	0.0	5008	,	,		16959	0.001		0.0	False		,,,				2504	0.0				p.N239N												.	.	2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	c.C717T	4						.						168.0	152.0	158.0					4																	120488258		2203	4300	6503	120707706	SO:0001819	synonymous_variant	8654	exon4			D89094	CCDS3713.1, CCDS34055.1	4q27	2008-05-15			ENSG00000138735	ENSG00000138735	3.1.4.17	"""Phosphodiesterases"""	8784	protein-coding gene	gene with protein product		603310				9714779, 9642111	Standard	NM_033437		Approved		uc003idh.3	O76074	OTTHUMG00000132971	ENST00000354960.3:c.873C>T	4.37:g.120488258G>A		Somatic		Capture	Illumina HiSeq	Phase_I	120707706	NM_033437	A0AV69|A8K2C4|O75026|O75887|Q86UI0|Q86V66|Q9Y6Z6	Silent	SNP	ENST00000354960.3	37	CCDS3713.1																																																																																				0.358	PDE5A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256529.1	NM_001083	
KIAA1109	84162	broad.mit.edu	37	4	123229145	123229145	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr4:123229145T>A	ENST00000264501.4	+	58	10256	c.9883T>A	c.(9883-9885)Tgg>Agg	p.W3295R	KIAA1109_ENST00000455637.1_Missense_Mutation_p.W3295R|KIAA1109_ENST00000388738.3_Missense_Mutation_p.W3295R			Q2LD37	K1109_HUMAN	KIAA1109	3295					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.W3295R(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						CTATGACAACTGGAATGAACA	0.383																																					p.W3295R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T9883A	4						.						174.0	170.0	171.0					4																	123229145		1860	4104	5964	123448595	SO:0001583	missense	84162	exon56			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.9883T>A	4.37:g.123229145T>A	ENSP00000264501:p.Trp3295Arg	Somatic		Capture	Illumina HiSeq	Phase_I	123448595	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.7|25.7	4.662506|4.662506	0.88251|0.88251	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000419325|ENST00000264501;ENST00000388738;ENST00000455637	.|T;T;T	.|0.73047	.|-0.71;-0.71;-0.71	5.92|5.92	5.92|5.92	0.95590|0.95590	.|.	.|0.000000	.|0.64402	.|D	.|0.000001	D|D	0.82646|0.82646	0.5082|0.5082	M|M	0.62723|0.62723	1.935|1.935	0.58432|0.58432	D|D	0.999996|0.999996	.|D;D	.|0.76494	.|0.999;0.999	.|D;D	.|0.85130	.|0.997;0.996	D|D	0.84305|0.84305	0.0507|0.0507	5|10	.|0.87932	.|D	.|0	.|.	16.3631|16.3631	0.83280|0.83280	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|3295;3295	.|Q2LD37-6;Q2LD37	.|.;K1109_HUMAN	Q|R	1252|3295	.|ENSP00000264501:W3295R;ENSP00000373390:W3295R;ENSP00000389925:W3295R	.|ENSP00000264501:W3295R	L|W	+|+	2|1	0|0	KIAA1109|KIAA1109	123448595|123448595	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	7.943000|7.943000	0.87716|0.87716	2.266000|2.266000	0.75297|0.75297	0.533000|0.533000	0.62120|0.62120	CTG|TGG		0.383	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797	
FAT4	79633	broad.mit.edu	37	4	126237573	126237573	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr4:126237573T>G	ENST00000394329.3	+	1	20	c.7T>G	c.(7-9)Tta>Gta	p.L3V		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	3					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.L3V(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						GACCATGGACTTAGCACCAGA	0.512											OREG0016317	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L3V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T7G	4						.						138.0	144.0	142.0					4																	126237573		1919	4142	6061	126457023	SO:0001583	missense	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.7T>G	4.37:g.126237573T>G	ENSP00000377862:p.Leu3Val	Somatic	1548	Capture	Illumina HiSeq	Phase_I	126457023	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	T	13.63	2.294180	0.40594	.	.	ENSG00000196159	ENST00000394329	T	0.73897	-0.79	4.16	1.68	0.24146	.	.	.	.	.	T	0.56934	0.2019	N	0.22421	0.69	0.80722	D	1	B	0.23316	0.083	B	0.18871	0.023	T	0.50841	-0.8780	9	0.87932	D	0	.	6.7058	0.23250	0.0:0.1994:0.0:0.8006	.	3	Q6V0I7	FAT4_HUMAN	V	3	ENSP00000377862:L3V	ENSP00000377862:L3V	L	+	1	2	FAT4	126457023	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	1.449000	0.35123	0.251000	0.21505	0.374000	0.22700	TTA		0.512	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
PCDH10	57575	broad.mit.edu	37	4	134072407	134072407	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr4:134072407C>T	ENST00000264360.5	+	1	1938	c.1112C>T	c.(1111-1113)gCg>gTg	p.A371V	RP11-9G1.3_ENST00000505289.1_lincRNA	NM_032961.1	NP_116586.1	Q9P2E7	PCD10_HUMAN	protocadherin 10	371	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.A371V(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)		AGTGAGGGCGCGGCGCCCGGC	0.622																																					p.A371V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1112T	4						.						77.0	79.0	78.0					4																	134072407		2203	4300	6503	134291857	SO:0001583	missense	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.1112C>T	4.37:g.134072407C>T	ENSP00000264360:p.Ala371Val	Somatic		Capture	Illumina HiSeq	Phase_I	134291857	NM_032961	Q4W5F6|Q96SF0	Missense_Mutation	SNP	ENST00000264360.5	37	CCDS34063.1	.	.	.	.	.	.	.	.	.	.	C	18.34	3.601503	0.66445	.	.	ENSG00000138650	ENST00000264360;ENST00000394248	T	0.01804	4.63	4.68	4.68	0.58851	Cadherin (3);Cadherin-like (1);	0.000000	0.44902	D	0.000402	T	0.04272	0.0118	L	0.55481	1.735	0.80722	D	1	D;P	0.58620	0.983;0.762	P;B	0.47162	0.54;0.318	T	0.49943	-0.8885	10	0.52906	T	0.07	.	17.3997	0.87456	0.0:1.0:0.0:0.0	.	371;371	Q9P2E7;Q96SF0	PCD10_HUMAN;.	V	371	ENSP00000264360:A371V	ENSP00000264360:A371V	A	+	2	0	PCDH10	134291857	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.846000	0.69444	2.423000	0.82170	0.561000	0.74099	GCG		0.622	PCDH10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000364457.2	NM_032961	
PCDH18	54510	broad.mit.edu	37	4	138449694	138449694	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr4:138449694A>G	ENST00000344876.4	-	3	3064	c.2678T>C	c.(2677-2679)aTa>aCa	p.I893T	PCDH18_ENST00000510305.1_Missense_Mutation_p.I104T|PCDH18_ENST00000511115.1_Missense_Mutation_p.I73T|PCDH18_ENST00000412923.2_Missense_Mutation_p.I892T|PCDH18_ENST00000507846.1_Missense_Mutation_p.I672T	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	893	Interaction with DAB1. {ECO:0000250}.				brain development (GO:0007420)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.I893T(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(27)|lung(21)|ovary(2)|pancreas(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86	all_hematologic(180;0.24)					CAGCCTATCTATTGGAGAATC	0.448																																					p.I893T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2678C	4						.						203.0	219.0	214.0					4																	138449694		2203	4300	6503	138669144	SO:0001583	missense	54510	exon3			AL137471	CCDS34064.1, CCDS75193.1	4q28.3	2010-01-26			ENSG00000189184	ENSG00000189184		"""Cadherins / Protocadherins : Non-clustered"""	14268	protein-coding gene	gene with protein product		608287				10835267, 11549318	Standard	XM_005263070		Approved	KIAA1562, PCDH68L	uc003ihe.4	Q9HCL0	OTTHUMG00000161348	ENST00000344876.4:c.2678T>C	4.37:g.138449694A>G	ENSP00000355082:p.Ile893Thr	Somatic		Capture	Illumina HiSeq	Phase_I	138669144	NM_019035	A8K7K3|B7ZKT1|Q52LS2	Missense_Mutation	SNP	ENST00000344876.4	37	CCDS34064.1	.	.	.	.	.	.	.	.	.	.	A	15.35	2.807787	0.50421	.	.	ENSG00000189184	ENST00000344876;ENST00000412923;ENST00000507846;ENST00000510305;ENST00000511115	T;T;T;T;T	0.55052	0.63;0.64;0.54;1.45;1.46	5.56	4.37	0.52481	.	0.000000	0.47093	D	0.000260	T	0.39064	0.1064	L	0.51422	1.61	0.40673	D	0.982237	P;B;B;B	0.44044	0.825;0.118;0.257;0.255	B;B;B;B	0.36092	0.217;0.026;0.053;0.038	T	0.37174	-0.9717	10	0.06365	T	0.9	.	11.9578	0.52991	0.8698:0.0:0.0:0.1301	.	73;672;892;893	B4DLR6;D6RIG4;Q9HCL0-2;Q9HCL0	.;.;.;PCD18_HUMAN	T	893;892;672;104;73	ENSP00000355082:I893T;ENSP00000390688:I892T;ENSP00000425903:I672T;ENSP00000424269:I104T;ENSP00000425647:I73T	ENSP00000355082:I893T	I	-	2	0	PCDH18	138669144	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.904000	0.92590	0.919000	0.36945	0.533000	0.62120	ATA		0.448	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035	
PCDH18	54510	broad.mit.edu	37	4	138450957	138450957	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr4:138450957C>T	ENST00000344876.4	-	1	2672	c.2286G>A	c.(2284-2286)gtG>gtA	p.V762V	PCDH18_ENST00000510305.1_Intron|PCDH18_ENST00000511115.1_Intron|PCDH18_ENST00000412923.2_Silent_p.V762V|PCDH18_ENST00000507846.1_Silent_p.V542V	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	762					brain development (GO:0007420)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V762V(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(27)|lung(21)|ovary(2)|pancreas(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86	all_hematologic(180;0.24)					TTATGGTAGGCACCAATGTGA	0.512																																					p.V762V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2286A	4						.						204.0	171.0	182.0					4																	138450957		2203	4300	6503	138670407	SO:0001819	synonymous_variant	54510	exon1			AL137471	CCDS34064.1, CCDS75193.1	4q28.3	2010-01-26			ENSG00000189184	ENSG00000189184		"""Cadherins / Protocadherins : Non-clustered"""	14268	protein-coding gene	gene with protein product		608287				10835267, 11549318	Standard	XM_005263070		Approved	KIAA1562, PCDH68L	uc003ihe.4	Q9HCL0	OTTHUMG00000161348	ENST00000344876.4:c.2286G>A	4.37:g.138450957C>T		Somatic		Capture	Illumina HiSeq	Phase_I	138670407	NM_019035	A8K7K3|B7ZKT1|Q52LS2	Silent	SNP	ENST00000344876.4	37	CCDS34064.1																																																																																				0.512	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035	
FBXW7	55294	broad.mit.edu	37	4	153251907	153251907	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr4:153251907G>A	ENST00000281708.4	-	7	2328	c.1099C>T	c.(1099-1101)Cga>Tga	p.R367*	FBXW7_ENST00000603548.1_Nonsense_Mutation_p.R367*|FBXW7_ENST00000603841.1_Nonsense_Mutation_p.R367*|FBXW7_ENST00000393956.3_Nonsense_Mutation_p.R191*|FBXW7_ENST00000263981.5_Nonsense_Mutation_p.R287*|FBXW7_ENST00000296555.5_Nonsense_Mutation_p.R249*	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	367					cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.R367*(10)|p.R287*(3)|p.R128*(3)|p.?(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				AGTTCTCCTCGCCTCCAGTTA	0.388			"""Mis, N, D, F"""		"""colorectal, endometrial, T-ALL"""																																p.R287X			Rec	yes		4	4q31.3	55294	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"""		"""E, L"""	FBXW7,central_nervous_system,brain,Substitution - Nonsense,0 	.	17	Substitution - Nonsense(16)|Unknown(1)	large_intestine(10)|upper_aerodigestive_tract(4)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|endometrium(1)	c.C859T	4						.						335.0	288.0	304.0					4																	153251907		2203	4300	6503	153471357	SO:0001587	stop_gained	55294	exon6			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	16712	protein-coding gene	gene with protein product	"""archipelago homolog (Drosophila)"""	606278	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"", ""F-box and WD repeat domain containing 7"""			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1099C>T	4.37:g.153251907G>A	ENSP00000281708:p.Arg367*	Somatic		Capture	Illumina HiSeq	Phase_I	153471357	NM_018315	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Nonsense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	G	37	6.344024	0.97489	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	.	.	.	6.07	5.22	0.72569	.	0.052867	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11794	T	0.64	-12.733	16.6928	0.85326	0.0:0.0:0.8693:0.1307	.	.	.	.	X	367;249;287;191	.	ENSP00000263981:R287X	R	-	1	2	FBXW7	153471357	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.642000	0.46596	1.556000	0.49512	0.650000	0.86243	CGA		0.388	FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1		
DCHS2	54798	broad.mit.edu	37	4	155254305	155254305	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr4:155254305C>T	ENST00000357232.4	-	9	1557	c.1558G>A	c.(1558-1560)Gcc>Acc	p.A520T	DCHS2_ENST00000339452.1_Missense_Mutation_p.A1019T|DCHS2_ENST00000507542.1_5'UTR	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	520	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.A520T(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)		TGCGGGCTGGCGATGGAGTAC	0.652																																					p.A1019T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3055A	4						.						35.0	37.0	36.0					4																	155254305		2203	4300	6503	155473755	SO:0001583	missense	54798	exon5			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.1558G>A	4.37:g.155254305C>T	ENSP00000349768:p.Ala520Thr	Somatic		Capture	Illumina HiSeq	Phase_I	155473755	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	C	9.992	1.230968	0.22542	.	.	ENSG00000197410	ENST00000357232;ENST00000339452;ENST00000544161	T;T	0.51325	0.71;0.71	5.6	3.87	0.44632	Cadherin (4);Cadherin-like (1);	0.204155	0.31760	N	0.007109	T	0.26340	0.0643	N	0.16130	0.375	0.23636	N	0.997239	B;B	0.31655	0.334;0.14	B;B	0.27262	0.078;0.06	T	0.12293	-1.0553	10	0.12766	T	0.61	.	11.8828	0.52586	0.0:0.8595:0.0:0.1405	.	1019;520	E9PC11;Q6V1P9	.;PCD23_HUMAN	T	520;1019;1019	ENSP00000349768:A520T;ENSP00000345062:A1019T	ENSP00000345062:A1019T	A	-	1	0	DCHS2	155473755	0.004000	0.15560	0.049000	0.19019	0.004000	0.04260	1.132000	0.31418	1.378000	0.46305	-0.219000	0.12488	GCC		0.652	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
GUCY1A3	2982	broad.mit.edu	37	4	156632157	156632157	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr4:156632157G>A	ENST00000296518.7	+	6	1049	c.840G>A	c.(838-840)tcG>tcA	p.S280S	GUCY1A3_ENST00000506455.1_Silent_p.S280S|GUCY1A3_ENST00000513574.1_Silent_p.S280S|GUCY1A3_ENST00000393832.3_Silent_p.S22S|GUCY1A3_ENST00000511108.1_Silent_p.S280S|GUCY1A3_ENST00000455639.2_Silent_p.S280S|GUCY1A3_ENST00000511507.1_Silent_p.S280S			Q02108	GCYA3_HUMAN	guanylate cyclase 1, soluble, alpha 3	280					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of cGMP biosynthetic process (GO:0030828)|regulation of blood pressure (GO:0008217)|relaxation of vascular smooth muscle (GO:0060087)|response to defense-related host nitric oxide production (GO:0052565)	guanylate cyclase complex, soluble (GO:0008074)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)|receptor activity (GO:0004872)	p.S280S(2)		central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|liver(2)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.17)		TTCCCACATCGCTATTCTGCA	0.463																																					p.S280S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G840A	4						.						100.0	95.0	97.0					4																	156632157		2203	4300	6503	156851607	SO:0001819	synonymous_variant	2982	exon6				CCDS34085.1, CCDS54812.1	4q31.3-q33	2008-03-18				ENSG00000164116	4.6.1.2		4685	protein-coding gene	gene with protein product		139396		GUC1A3		1352257	Standard	NM_001130687		Approved	GC-SA3	uc003iow.3	Q02108		ENST00000296518.7:c.840G>A	4.37:g.156632157G>A		Somatic		Capture	Illumina HiSeq	Phase_I	156851607	NM_001130682	D3DP19|D6RDW3|O43843|Q8TAH3	Silent	SNP	ENST00000296518.7	37	CCDS34085.1																																																																																				0.463	GUCY1A3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365786.2		
FAM198B	51313	broad.mit.edu	37	4	159092400	159092400	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr4:159092400G>A	ENST00000296530.8	-	2	749	c.128C>T	c.(127-129)gCg>gTg	p.A43V	RP11-597D13.9_ENST00000503611.1_RNA|RP11-597D13.9_ENST00000514381.1_RNA|FAM198B_ENST00000585682.1_Missense_Mutation_p.A43V|FAM198B_ENST00000589306.1_Intron|RP11-597D13.9_ENST00000509463.1_RNA|FAM198B_ENST00000393807.5_Missense_Mutation_p.A43V|RP11-597D13.9_ENST00000505532.1_RNA|FAM198B_ENST00000592057.1_Missense_Mutation_p.A43V	NM_016613.6	NP_057697.2	Q6UWH4	F198B_HUMAN	family with sequence similarity 198, member B	43						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.A43V(2)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(14)|skin(2)|urinary_tract(1)	26						GATGGCACACGCAGTGCCCAG	0.642																																					p.A43V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C128T	4						.						41.0	44.0	43.0					4																	159092400		2202	4299	6501	159311850	SO:0001583	missense	51313	exon2				CCDS3798.1, CCDS34087.1	4q32.1	2012-11-29	2009-10-19	2009-10-19	ENSG00000164125	ENSG00000164125			25312	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 18"""	C4orf18		12975309	Standard	NM_001031700		Approved	FLJ38155, DKFZp434L142	uc003ipr.4	Q6UWH4	OTTHUMG00000161537	ENST00000296530.8:c.128C>T	4.37:g.159092400G>A	ENSP00000296530:p.Ala43Val	Somatic		Capture	Illumina HiSeq	Phase_I	159311850	NM_001128424	Q498Z3|Q6IAF9|Q6ZMF2|Q86XL0	Missense_Mutation	SNP	ENST00000296530.8	37	CCDS3798.1	.	.	.	.	.	.	.	.	.	.	G	16.50	3.141474	0.57044	.	.	ENSG00000164125	ENST00000337222;ENST00000296530;ENST00000393807;ENST00000417442	T;T	0.30714	1.52;1.52	5.21	5.21	0.72293	.	0.317511	0.34245	N	0.004131	T	0.53222	0.1783	L	0.60455	1.87	0.50632	D	0.999883	D;D;D	0.89917	1.0;0.977;0.977	D;B;B	0.87578	0.998;0.314;0.314	T	0.42616	-0.9441	10	0.36615	T	0.2	-4.0887	18.9456	0.92621	0.0:0.0:1.0:0.0	.	43;43;43	Q6UWH4-3;Q6UWH4-2;Q6UWH4	.;.;F198B_HUMAN	V	43	ENSP00000296530:A43V;ENSP00000377396:A43V	ENSP00000296530:A43V	A	-	2	0	FAM198B	159311850	1.000000	0.71417	0.990000	0.47175	0.798000	0.45092	4.374000	0.59543	2.705000	0.92388	0.655000	0.94253	GCG		0.642	FAM198B-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365230.1	NM_001031700, NM_016613	
ETFDH	2110	broad.mit.edu	37	4	159601706	159601706	+	Missense_Mutation	SNP	G	G	T	rs150105001		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr4:159601706G>T	ENST00000511912.1	+	2	454	c.122G>T	c.(121-123)cGa>cTa	p.R41L	ETFDH_ENST00000307738.5_Intron	NM_001281738.1|NM_004453.2	NP_001268667.1|NP_004444.2	Q16134	ETFD_HUMAN	electron-transferring-flavoprotein dehydrogenase	41					cellular metabolic process (GO:0044237)|electron transport chain (GO:0022900)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|respiratory electron transport chain (GO:0022904)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)	4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|electron-transferring-flavoprotein dehydrogenase activity (GO:0004174)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, oxidizing metal ions with flavin as acceptor (GO:0043783)|quinone binding (GO:0048038)|ubiquinone binding (GO:0048039)	p.R41Q(1)|p.R41L(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|prostate(1)|skin(3)	28	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0172)		ACTGTGCCTCGAATTACTACC	0.353																																					p.R41L												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G122T	4						.						122.0	112.0	115.0					4																	159601706		2203	4299	6502	159821156	SO:0001583	missense	2110	exon2			S69232	CCDS3800.1, CCDS64090.1	4q32-q35	2008-08-26			ENSG00000171503	ENSG00000171503			3483	protein-coding gene	gene with protein product		231675					Standard	NM_004453		Approved	ETFQO	uc003iqb.3	Q16134	OTTHUMG00000161684	ENST00000511912.1:c.122G>T	4.37:g.159601706G>T	ENSP00000426638:p.Arg41Leu	Somatic		Capture	Illumina HiSeq	Phase_I	159821156	NM_004453	B4E3R9|J3KND9|Q7Z347	Missense_Mutation	SNP	ENST00000511912.1	37	CCDS3800.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.2|24.2	4.506747|4.506747	0.85282|0.85282	.|.	.|.	ENSG00000171503|ENSG00000171503	ENST00000512251|ENST00000511912	.|D	.|0.95001	.|-3.58	5.48|5.48	-1.16|-1.16	0.09678|0.09678	.|.	.|0.206985	.|0.52532	.|D	.|0.000074	.|D	.|0.90528	.|0.7032	L|L	0.54323|0.54323	1.7|1.7	0.80722|0.80722	D|D	1|1	.|B	.|0.17268	.|0.021	.|B	.|0.11329	.|0.006	.|T	.|0.79361	.|-0.1835	.|10	0.87932|0.45353	D|T	0|0.12	-11.7494|-11.7494	10.6135|10.6135	0.45436|0.45436	0.4443:0.0:0.5557:0.0|0.4443:0.0:0.5557:0.0	.|.	.|41	.|Q16134	.|ETFD_HUMAN	X|L	21|41	.|ENSP00000426638:R41L	ENSP00000425661:E21X|ENSP00000426638:R41L	E|R	+|+	1|2	0|0	ETFDH|ETFDH	159821156|159821156	0.999000|0.999000	0.42202|0.42202	0.833000|0.833000	0.33012|0.33012	0.783000|0.783000	0.44284|0.44284	2.898000|2.898000	0.48672|0.48672	-0.533000|-0.533000	0.06323|0.06323	-0.964000|-0.964000	0.02622|0.02622	GAA|CGA		0.353	ETFDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365718.2		
CPE	1363	broad.mit.edu	37	4	166388931	166388931	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr4:166388931A>G	ENST00000402744.4	+	3	876	c.596A>G	c.(595-597)tAc>tGc	p.Y199C		NM_001873.2	NP_001864.1	P16870	CBPE_HUMAN	carboxypeptidase E	199					cardiac left ventricle morphogenesis (GO:0003214)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|insulin processing (GO:0030070)|metabolic process (GO:0008152)|neuropeptide signaling pathway (GO:0007218)|protein localization to membrane (GO:0072657)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)	carboxypeptidase activity (GO:0004180)|cell adhesion molecule binding (GO:0050839)|metallocarboxypeptidase activity (GO:0004181)|neurexin family protein binding (GO:0042043)|zinc ion binding (GO:0008270)	p.Y199C(1)		endometrium(2)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	26	all_hematologic(180;0.221)	Prostate(90;0.0962)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.137)	"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	AGGATAGTGTACGTGAATGAG	0.418																																					p.Y199C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A596G	4						.						77.0	74.0	75.0					4																	166388931		2203	4300	6503	166608381	SO:0001583	missense	1363	exon3			X51405	CCDS3810.1	4q32.3	2012-02-10			ENSG00000109472	ENSG00000109472	3.4.17.10		2303	protein-coding gene	gene with protein product	"""carboxypeptidase H"", ""enkephalin convertase"", ""insulin granule-associated carboxypeptidase"", ""cobalt-stimulated chromaffin granule carboxypeptidase"""	114855				2334405	Standard	NM_001873		Approved		uc003irg.4	P16870	OTTHUMG00000150252	ENST00000402744.4:c.596A>G	4.37:g.166388931A>G	ENSP00000386104:p.Tyr199Cys	Somatic		Capture	Illumina HiSeq	Phase_I	166608381	NM_001873	A8K4N1|B3KR42|B4DFN4|D3DP33|Q9UIU9	Missense_Mutation	SNP	ENST00000402744.4	37	CCDS3810.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.962162	0.74016	.	.	ENSG00000109472	ENST00000513982;ENST00000402744;ENST00000261510;ENST00000431967;ENST00000511992	T;T;T;T	0.10763	2.84;2.84;2.84;2.84	5.34	5.34	0.76211	Peptidase M14, carboxypeptidase A (2);	0.000000	0.85682	D	0.000000	T	0.17238	0.0414	L	0.60957	1.885	0.80722	D	1	P	0.42993	0.797	B	0.43478	0.421	T	0.00728	-1.1591	10	0.87932	D	0	-10.6645	15.3065	0.73995	1.0:0.0:0.0:0.0	.	199	P16870	CBPE_HUMAN	C	87;199;163;87;87	ENSP00000424830:Y87C;ENSP00000386104:Y199C;ENSP00000416601:Y87C;ENSP00000423699:Y87C	ENSP00000261510:Y163C	Y	+	2	0	CPE	166608381	1.000000	0.71417	0.988000	0.46212	0.905000	0.53344	8.615000	0.90920	2.016000	0.59253	0.528000	0.53228	TAC		0.418	CPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317094.2	NM_001873	
TENM3	55714	broad.mit.edu	37	4	183721022	183721022	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr4:183721022A>G	ENST00000511685.1	+	28	7741	c.7618A>G	c.(7618-7620)Acc>Gcc	p.T2540A	TENM3_ENST00000406950.2_Missense_Mutation_p.T2540A			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	2540					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.T2540A(1)									CCTGCACTTCACCATCGAGGG	0.627																																					p.T2540A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A7618G	4						.						36.0	41.0	40.0					4																	183721022		2195	4285	6480	183958016	SO:0001583	missense	55714	exon27			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.7618A>G	4.37:g.183721022A>G	ENSP00000424226:p.Thr2540Ala	Somatic		Capture	Illumina HiSeq	Phase_I	183958016	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	37	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	A	15.99	2.994178	0.54041	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	D;D	0.86769	-2.17;-2.17	4.48	4.48	0.54585	.	.	.	.	.	D	0.92984	0.7767	M	0.82517	2.595	0.58432	D	0.999999	D	0.58970	0.984	D	0.65443	0.935	D	0.93987	0.7263	9	0.72032	D	0.01	.	14.2179	0.65805	1.0:0.0:0.0:0.0	.	2540	Q9P273	TEN3_HUMAN	A	2540	ENSP00000424226:T2540A;ENSP00000385276:T2540A	ENSP00000385276:T2540A	T	+	1	0	ODZ3	183958016	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.087000	0.94110	2.010000	0.58986	0.455000	0.32223	ACC		0.627	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1		
ACSL1	2180	broad.mit.edu	37	4	185681621	185681621	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr4:185681621G>A	ENST00000515030.1	-	18	1997	c.1672C>T	c.(1672-1674)Cac>Tac	p.H558Y	ACSL1_ENST00000507295.1_Missense_Mutation_p.H524Y|ACSL1_ENST00000454703.2_Missense_Mutation_p.H387Y|ACSL1_ENST00000281455.2_Missense_Mutation_p.H558Y|ACSL1_ENST00000437665.3_Missense_Mutation_p.H387Y|ACSL1_ENST00000504342.1_Missense_Mutation_p.H558Y|ACSL1_ENST00000513317.1_Missense_Mutation_p.H558Y			P33121	ACSL1_HUMAN	acyl-CoA synthetase long-chain family member 1	558					adiponectin-activated signaling pathway (GO:0033211)|alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|linoleic acid metabolic process (GO:0043651)|lipid biosynthetic process (GO:0008610)|long-chain fatty acid import (GO:0044539)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|response to oleic acid (GO:0034201)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|unsaturated fatty acid metabolic process (GO:0033559)|xenobiotic catabolic process (GO:0042178)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|liver(1)|lung(17)|ovary(2)|prostate(1)|skin(2)	38		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Colorectal(36;0.00172)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0315)|all_neural(102;0.107)|Medulloblastoma(177;0.146)		all cancers(43;1.33e-28)|Epithelial(43;5.3e-25)|OV - Ovarian serous cystadenocarcinoma(60;4.88e-11)|Colorectal(24;3.59e-06)|STAD - Stomach adenocarcinoma(60;2.72e-05)|GBM - Glioblastoma multiforme(59;2.83e-05)|BRCA - Breast invasive adenocarcinoma(30;7.66e-05)|COAD - Colon adenocarcinoma(29;0.000538)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.0419)	Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	TTAAATATGTGCTTTTTCCGG	0.468																																					p.H558Y												.	.	0			c.C1672T	4						.						327.0	349.0	341.0					4																	185681621		2203	4300	6503	185918615	SO:0001583	missense	2180	exon18			BC026290	CCDS3839.1, CCDS68825.1, CCDS68826.1, CCDS75213.1	4q35.1	2014-08-08	2004-02-19	2004-02-20	ENSG00000151726	ENSG00000151726	6.2.1.3	"""Acyl-CoA synthetase family"""	3569	protein-coding gene	gene with protein product	"""lignoceroyl-CoA synthase"", ""long-chain fatty-acid-coenzyme A ligase 1"""	152425	"""fatty-acid-Coenzyme A ligase, long-chain 2"""	FACL2		2341402, 1531127	Standard	XM_005262828		Approved	LACS2, LACS, ACS1, LACS1, FACL1	uc003iwu.1	P33121	OTTHUMG00000160547	ENST00000515030.1:c.1672C>T	4.37:g.185681621G>A	ENSP00000422607:p.His558Tyr	None		Capture	Illumina HiSeq	Phase_I	185918615	NM_001995	B7Z452|D3DP57|P41215|Q8N8V7|Q8TA99	Missense_Mutation	SNP	ENST00000515030.1	37	CCDS3839.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.694186	0.88735	.	.	ENSG00000151726	ENST00000454703;ENST00000515030;ENST00000503407;ENST00000281455;ENST00000507295;ENST00000437665;ENST00000504342;ENST00000513317	T;T;T;T;T;T;T;T	0.10860	2.83;2.83;2.83;2.83;2.83;2.83;2.83;2.83	5.63	5.63	0.86233	AMP-dependent synthetase/ligase (1);	0.088049	0.85682	D	0.000000	T	0.39886	0.1095	M	0.86268	2.805	0.80722	D	1	P;P;P;P	0.49090	0.868;0.919;0.919;0.901	D;D;P;P	0.64506	0.926;0.912;0.832;0.741	T	0.26087	-1.0113	10	0.87932	D	0	-18.1838	19.7533	0.96277	0.0:0.0:1.0:0.0	.	524;558;558;548	E7EPM6;B7Z452;P33121;P33121-2	.;.;ACSL1_HUMAN;.	Y	387;558;154;558;524;387;558;558	ENSP00000407165:H387Y;ENSP00000422607:H558Y;ENSP00000425098:H154Y;ENSP00000281455:H558Y;ENSP00000426244:H524Y;ENSP00000405687:H387Y;ENSP00000425006:H558Y;ENSP00000426150:H558Y	ENSP00000281455:H558Y	H	-	1	0	ACSL1	185918615	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.410000	0.66381	2.673000	0.90976	0.650000	0.86243	CAC		0.468	ACSL1-011	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361112.2	NM_001995	
JAKMIP1	152789	broad.mit.edu	37	4	6083424	6083424	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr4:6083424C>T	ENST00000282924.5	-	6	1498	c.1013G>A	c.(1012-1014)cGg>cAg	p.R338Q	JAKMIP1_ENST00000409021.3_Missense_Mutation_p.R338Q|JAKMIP1_ENST00000410077.2_Missense_Mutation_p.R173Q|JAKMIP1_ENST00000457227.2_5'UTR|JAKMIP1_ENST00000409371.3_Missense_Mutation_p.R173Q|JAKMIP1_ENST00000409831.1_Missense_Mutation_p.R338Q	NM_144720.3	NP_653321.1	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein 1	338	Mediates association with microtubules.				cognition (GO:0050890)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|microtubule (GO:0005874)|ribonucleoprotein complex (GO:0030529)	GABA receptor binding (GO:0050811)|RNA binding (GO:0003723)	p.R338Q(2)		NS(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						CTTGTTCATCCGCTTGTTCTT	0.507																																					p.R338Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1013A	4						.						150.0	140.0	144.0					4																	6083424		2203	4300	6503	6134325	SO:0001583	missense	152789	exon6			AK056126	CCDS3385.1, CCDS47005.1	4p16.1	2013-10-11	2009-08-13		ENSG00000152969	ENSG00000152969			26460	protein-coding gene	gene with protein product		611195				18941173	Standard	NM_144720		Approved	MARLIN1, JAMIP1, Gababrbp, FLJ31564	uc010idb.1	Q96N16	OTTHUMG00000125491	ENST00000282924.5:c.1013G>A	4.37:g.6083424C>T	ENSP00000282924:p.Arg338Gln	Somatic		Capture	Illumina HiSeq	Phase_I	6134325	NM_144720	A6H2J2|A6H2J3|A6H2J4|A6H2J5|A8MTK6|B4DHZ8|B8ZZR7|D3DVT0|Q86Y69|Q8N7G3	Missense_Mutation	SNP	ENST00000282924.5	37	CCDS3385.1	.	.	.	.	.	.	.	.	.	.	C	19.21	3.783979	0.70222	.	.	ENSG00000152969	ENST00000409021;ENST00000409371;ENST00000418227;ENST00000425341;ENST00000429819;ENST00000282924;ENST00000409831;ENST00000410077	T;T;T;T;T	0.36340	1.66;1.29;1.65;1.65;1.26	4.41	4.41	0.53225	.	0.000000	0.64402	D	0.000007	T	0.59945	0.2231	M	0.77820	2.39	0.35944	D	0.833394	D;D;D;D;D	0.89917	0.999;1.0;0.999;0.999;1.0	P;D;P;P;D	0.81914	0.771;0.995;0.905;0.905;0.995	T	0.67492	-0.5657	10	0.30078	T	0.28	.	16.3932	0.83546	0.0:1.0:0.0:0.0	.	173;338;173;338;338	B4DHZ8;F2Z2K5;Q96N16-5;Q96N16-2;Q96N16	.;.;.;.;JKIP1_HUMAN	Q	338;173;338;338;230;338;338;173	ENSP00000386711:R338Q;ENSP00000387042:R173Q;ENSP00000282924:R338Q;ENSP00000386925:R338Q;ENSP00000386745:R173Q	ENSP00000282924:R338Q	R	-	2	0	JAKMIP1	6134325	0.998000	0.40836	0.551000	0.28230	0.470000	0.32858	4.195000	0.58400	2.185000	0.69588	0.555000	0.69702	CGG		0.507	JAKMIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246816.2	NM_144720	
CCDC149	91050	broad.mit.edu	37	4	24839844	24839844	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr4:24839844G>A	ENST00000389609.4	-	6	566	c.423C>T	c.(421-423)ggC>ggT	p.G141G	CCDC149_ENST00000428116.2_Intron|CCDC149_ENST00000504487.1_Silent_p.G141G|CCDC149_ENST00000502801.1_Intron	NM_173463.4	NP_775734.2	Q6ZUS6	CC149_HUMAN	coiled-coil domain containing 149	86								p.G86G(1)		cervix(1)|endometrium(1)|large_intestine(2)|lung(3)	7		Breast(46;0.173)				AGTGTCGCACGCCGATTGCTT	0.483																																					p.G141G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C423T	4						.						156.0	140.0	146.0					4																	24839844		2203	4300	6503	24448942	SO:0001819	synonymous_variant	91050	exon6				CCDS33967.1, CCDS47036.1, CCDS33967.2	4p15.2	2008-03-03				ENSG00000181982			25405	protein-coding gene	gene with protein product						17457313	Standard	NM_173463		Approved	DKFZp761B107	uc003grc.3	Q6ZUS6		ENST00000389609.4:c.423C>T	4.37:g.24839844G>A		Somatic		Capture	Illumina HiSeq	Phase_I	24448942	NM_173463	A6NJE7|B4DK90|B4DZG3|G5EA04|Q6NW41|Q8N3K8	Silent	SNP	ENST00000389609.4	37	CCDS33967.2																																																																																				0.483	CCDC149-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000360157.1	NM_173463	
SEL1L3	23231	broad.mit.edu	37	4	25823623	25823623	+	Missense_Mutation	SNP	C	C	T	rs115625644	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr4:25823623C>T	ENST00000399878.3	-	7	1407	c.1285G>A	c.(1285-1287)Gcc>Acc	p.A429T	SEL1L3_ENST00000502949.1_Missense_Mutation_p.A276T|SEL1L3_ENST00000264868.5_Missense_Mutation_p.A394T	NM_015187.3	NP_056002.2	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3 (C. elegans)	429						integral component of membrane (GO:0016021)		p.A276T(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(2)	14						CTCACCTGGGCGGGGTGCAGA	0.547													C|||	5	0.000998403	0.0038	0.0	5008	,	,		16156	0.0		0.0	False		,,,				2504	0.0				p.A429T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1285A	4						.	C	THR/ALA	5,3869		0,5,1932	28.0	29.0	29.0		1285	0.1	0.0	4	dbSNP_132	29	0,8268		0,0,4134	yes	missense	SEL1L3	NM_015187.3	58	0,5,6066	TT,TC,CC		0.0,0.1291,0.0412	benign	429/1133	25823623	5,12137	1937	4134	6071	25432721	SO:0001583	missense	23231	exon7			BC009945	CCDS47037.1, CCDS75113.1	4p15.2	2009-09-24			ENSG00000091490	ENSG00000091490			29108	protein-coding gene	gene with protein product	"""KIAA0746 protein"""					9872452	Standard	XM_005248143		Approved	KIAA0746	uc003gru.4	Q68CR1	OTTHUMG00000160331	ENST00000399878.3:c.1285G>A	4.37:g.25823623C>T	ENSP00000382767:p.Ala429Thr	Somatic		Capture	Illumina HiSeq	Phase_I	25432721	NM_015187	A0PJH6|A8K0X2|O94847|Q6P999|Q96G59	Missense_Mutation	SNP	ENST00000399878.3	37	CCDS47037.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	5.949	0.359180	0.11239	0.001291	0.0	ENSG00000091490	ENST00000399878;ENST00000264868;ENST00000502949	T;T;T	0.17213	2.29;2.29;2.29	5.81	0.124	0.14714	.	0.956909	0.08782	N	0.894549	T	0.07188	0.0182	L	0.28274	0.84	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41179	-0.9523	10	0.20519	T	0.43	1.8775	5.7932	0.18371	0.0:0.5196:0.1245:0.356	.	429	Q68CR1	SE1L3_HUMAN	T	429;394;276	ENSP00000382767:A429T;ENSP00000264868:A394T;ENSP00000425438:A276T	ENSP00000264868:A394T	A	-	1	0	SEL1L3	25432721	0.000000	0.05858	0.000000	0.03702	0.487000	0.33371	0.036000	0.13819	-0.335000	0.08451	-0.880000	0.02959	GCC		0.547	SEL1L3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360261.1	NM_015187	
RFC1	5981	broad.mit.edu	37	4	39322085	39322085	+	Missense_Mutation	SNP	G	G	A	rs111155341		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr4:39322085G>A	ENST00000381897.1	-	9	1146	c.1013C>T	c.(1012-1014)tCa>tTa	p.S338L	RFC1_ENST00000349703.2_Missense_Mutation_p.S338L|RFC1_ENST00000418436.1_5'UTR	NM_001204747.1|NM_002913.4	NP_001191676.1|NP_002904.3	P35251	RFC1_HUMAN	replication factor C (activator 1) 1, 145kDa	338					DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription, DNA-templated (GO:0045893)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|telomere maintenance via telomerase (GO:0007004)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	cell junction (GO:0030054)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA clamp loader activity (GO:0003689)|double-stranded DNA binding (GO:0003690)|enzyme activator activity (GO:0008047)|sequence-specific DNA binding (GO:0043565)	p.S338L(1)		haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						TTTTCTTTTTGAGGCCACAGG	0.353																																					p.S338L	Colon(109;59 1555 12203 17579 39824)|Esophageal Squamous(18;360 542 16186 28570 51157)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1013T	4						.						46.0	45.0	45.0					4																	39322085		2200	4299	6499	38998480	SO:0001583	missense	5981	exon9			L23320	CCDS3450.1, CCDS56329.1	4p14-p13	2010-04-21	2002-08-29		ENSG00000035928	ENSG00000035928		"""ATPases / AAA-type"""	9969	protein-coding gene	gene with protein product		102579	"""replication factor C (activator 1) 1 (145kD)"""			8114700	Standard	NM_002913		Approved	A1, PO-GA, RFC140, MHCBFB	uc003gty.2	P35251	OTTHUMG00000099363	ENST00000381897.1:c.1013C>T	4.37:g.39322085G>A	ENSP00000371321:p.Ser338Leu	Somatic		Capture	Illumina HiSeq	Phase_I	38998480	NM_002913	A8K6E7|Q5XKF5|Q6PKU0|Q86V41|Q86V46	Missense_Mutation	SNP	ENST00000381897.1	37	CCDS56329.1	.	.	.	.	.	.	.	.	.	.	G	10.96	1.498245	0.26861	.	.	ENSG00000035928	ENST00000381897;ENST00000349703	T;T	0.56275	0.47;0.47	5.91	4.18	0.49190	.	1.002150	0.08039	N	0.994715	T	0.46112	0.1376	L	0.40543	1.245	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.10450	0.002;0.005	T	0.33111	-0.9881	10	0.39692	T	0.17	-0.5805	10.4885	0.44737	0.2091:0.0:0.7909:0.0	.	338;338	P35251;P35251-2	RFC1_HUMAN;.	L	338	ENSP00000371321:S338L;ENSP00000261424:S338L	ENSP00000261424:S338L	S	-	2	0	RFC1	38998480	0.025000	0.19082	0.510000	0.27712	0.693000	0.40251	2.051000	0.41307	1.506000	0.48736	0.655000	0.94253	TCA		0.353	RFC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216808.1	NM_002913	
ATP10D	57205	broad.mit.edu	37	4	47537964	47537964	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr4:47537964A>C	ENST00000273859.3	+	7	1198	c.929A>C	c.(928-930)aAg>aCg	p.K310T	ATP10D_ENST00000504445.1_Missense_Mutation_p.K310T	NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	310					cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|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.K310T(1)		NS(2)|endometrium(5)|kidney(5)|large_intestine(14)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	66						CCACGGTATAAGCGCAGCAAA	0.423																																					p.K310T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A929C	4						.						114.0	103.0	107.0					4																	47537964		2203	4300	6503	47232721	SO:0001583	missense	57205	exon7			AB040920	CCDS3476.1	4p12	2010-04-20	2007-09-19		ENSG00000145246	ENSG00000145246		"""ATPases / P-type"""	13549	protein-coding gene	gene with protein product			"""ATPase, Class V, type 10D"""			12532265	Standard	NM_020453		Approved	ATPVD, KIAA1487	uc003gxk.1	Q9P241	OTTHUMG00000160784	ENST00000273859.3:c.929A>C	4.37:g.47537964A>C	ENSP00000273859:p.Lys310Thr	Somatic		Capture	Illumina HiSeq	Phase_I	47232721	NM_020453	A2RRC8|D6REN2|Q8NC70|Q96SR3	Missense_Mutation	SNP	ENST00000273859.3	37	CCDS3476.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.052311	0.75960	.	.	ENSG00000145246	ENST00000273859;ENST00000504445	D;D	0.90788	-2.73;-2.73	5.31	5.31	0.75309	ATPase, P-type, ATPase-associated domain (1);	0.000000	0.85682	D	0.000000	D	0.97269	0.9107	H	0.98407	4.225	0.58432	D	0.99999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.98730	1.0712	10	0.87932	D	0	-25.6454	14.7496	0.69516	1.0:0.0:0.0:0.0	.	310;310	Q9P241;Q6PEW3	AT10D_HUMAN;.	T	310	ENSP00000273859:K310T;ENSP00000420909:K310T	ENSP00000273859:K310T	K	+	2	0	ATP10D	47232721	1.000000	0.71417	0.914000	0.36105	0.563000	0.35712	9.287000	0.95975	2.129000	0.65627	0.460000	0.39030	AAG		0.423	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453	
LNX1	84708	broad.mit.edu	37	4	54344819	54344819	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr4:54344819C>T	ENST00000263925.7	-	8	1890	c.1576G>A	c.(1576-1578)Gca>Aca	p.A526T	FIP1L1_ENST00000507166.1_Intron|LNX1_ENST00000306888.2_Missense_Mutation_p.A430T	NM_001126328.2	NP_001119800.1	Q8TBB1	LNX1_HUMAN	ligand of numb-protein X 1, E3 ubiquitin protein ligase	526	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				protein homooligomerization (GO:0051260)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.A430T(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|endometrium(3)|large_intestine(11)|lung(6)|ovary(3)|urinary_tract(4)	32	all_neural(26;0.153)		GBM - Glioblastoma multiforme(3;8.2e-46)|LUSC - Lung squamous cell carcinoma(32;0.0134)			CTATGTGATGCTCCCCCTGCG	0.463																																					p.A526T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1576A	4						.						172.0	166.0	168.0					4																	54344819		2203	4300	6503	54039576	SO:0001583	missense	84708	exon8			AF237782	CCDS3492.1, CCDS47057.1	4q12	2013-01-09	2012-02-23	2005-11-04	ENSG00000072201	ENSG00000072201		"""RING-type (C3HC4) zinc fingers"""	6657	protein-coding gene	gene with protein product		609732	"""ligand of numb-protein X"", ""ligand of numb-protein X 1"""	LNX		11521506, 11782429	Standard	NM_032622		Approved	MPDZ, PDZRN2	uc003hag.5	Q8TBB1	OTTHUMG00000102099	ENST00000263925.7:c.1576G>A	4.37:g.54344819C>T	ENSP00000263925:p.Ala526Thr	Somatic		Capture	Illumina HiSeq	Phase_I	54039576	NM_001126328	Q4W5K7|Q8N4C2|Q96MJ7|Q9BY20	Missense_Mutation	SNP	ENST00000263925.7	37	CCDS47057.1	.	.	.	.	.	.	.	.	.	.	C	12.49	1.954075	0.34471	.	.	ENSG00000072201	ENST00000306888;ENST00000538207;ENST00000263925	T;T	0.27104	1.69;1.69	4.98	4.14	0.48551	PDZ/DHR/GLGF (4);	0.141793	0.64402	N	0.000005	T	0.19725	0.0474	L	0.33137	0.985	0.47407	D	0.999413	B;B	0.33807	0.426;0.03	B;B	0.35770	0.21;0.049	T	0.03335	-1.1047	10	0.13108	T	0.6	.	13.5755	0.61873	0.0:0.9252:0.0:0.0748	.	526;430	Q8TBB1;Q8TBB1-2	LNX1_HUMAN;.	T	430;364;526	ENSP00000302879:A430T;ENSP00000263925:A526T	ENSP00000263925:A526T	A	-	1	0	LNX1	54039576	1.000000	0.71417	0.986000	0.45419	0.482000	0.33219	2.694000	0.47035	1.461000	0.47929	0.655000	0.94253	GCA		0.463	LNX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219934.2		
KDR	3791	broad.mit.edu	37	4	55968633	55968633	+	Missense_Mutation	SNP	G	G	A	rs200338299		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr4:55968633G>A	ENST00000263923.4	-	14	2325	c.2030C>T	c.(2029-2031)aCg>aTg	p.T677M		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	677	Ig-like C2-type 7.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|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 endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|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)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|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.T677M(1)		NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	AATACTTGTCGTCTGATTCTC	0.443			Mis		"""NSCLC, angiosarcoma"""					TSP Lung(20;0.16)			G|||	1	0.000199681	0.0	0.0	5008	,	,		18066	0.0		0.001	False		,,,				2504	0.0				p.T677M			Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2030T	4						.						183.0	152.0	162.0					4																	55968633		2203	4300	6503	55663390	SO:0001583	missense	3791	exon14			AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.2030C>T	4.37:g.55968633G>A	ENSP00000263923:p.Thr677Met	Somatic		Capture	Illumina HiSeq	Phase_I	55663390	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	ENST00000263923.4	37	CCDS3497.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	13.06	2.124355	0.37533	.	.	ENSG00000128052	ENST00000263923	T	0.68624	-0.34	6.02	6.02	0.97574	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.105383	0.64402	D	0.000003	D	0.83326	0.5230	M	0.81802	2.56	0.46044	D	0.998835	D	0.89917	1.0	D	0.78314	0.991	T	0.81230	-0.1027	10	0.39692	T	0.17	.	20.1146	0.97924	0.0:0.0:1.0:0.0	.	677	P35968	VGFR2_HUMAN	M	677	ENSP00000263923:T677M	ENSP00000263923:T677M	T	-	2	0	KDR	55663390	1.000000	0.71417	0.971000	0.41717	0.177000	0.22998	4.984000	0.63838	2.855000	0.98099	0.655000	0.94253	ACG		0.443	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1		
LPHN3	23284	broad.mit.edu	37	4	62910254	62910254	+	Silent	SNP	G	G	A	rs182596389	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr4:62910254G>A	ENST00000514591.1	+	24	3926	c.3597G>A	c.(3595-3597)gcG>gcA	p.A1199A	LPHN3_ENST00000506700.1_Silent_p.A1190A|LPHN3_ENST00000504896.1_Silent_p.A1199A|LPHN3_ENST00000509896.1_Silent_p.A1267A|LPHN3_ENST00000506720.1_Silent_p.A1267A|LPHN3_ENST00000508693.1_Silent_p.A1267A|LPHN3_ENST00000506746.1_Silent_p.A1258A|LPHN3_ENST00000508946.1_Silent_p.A1199A|LPHN3_ENST00000507625.1_Silent_p.A1258A|LPHN3_ENST00000512091.2_Silent_p.A1199A|LPHN3_ENST00000514996.1_Silent_p.A1190A|LPHN3_ENST00000511324.1_Silent_p.A1258A|LPHN3_ENST00000545650.1_Silent_p.A1199A|LPHN3_ENST00000514157.1_Silent_p.A1190A|LPHN3_ENST00000507164.1_Silent_p.A1258A			Q9HAR2	LPHN3_HUMAN	latrophilin 3	1177					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)	p.A1199A(5)		breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						ACAGTTCAGCGTCACTCAACA	0.368													G|||	6	0.00119808	0.0045	0.0	5008	,	,		16079	0.0		0.0	False		,,,				2504	0.0				p.A1199A												.	.	5	Substitution - coding silent(5)	large_intestine(5)	c.G3597A	4						.	G		16,3770		0,16,1877	45.0	42.0	43.0		3597	-5.4	0.9	4		43	1,8249		0,1,4124	no	coding-synonymous	LPHN3	NM_015236.4		0,17,6001	AA,AG,GG		0.0121,0.4226,0.1412		1199/1470	62910254	17,12019	1893	4125	6018	62592849	SO:0001819	synonymous_variant	23284	exon22			AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"""-"", ""GPCR / Class B : Orphans"""	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.3597G>A	4.37:g.62910254G>A		Somatic		Capture	Illumina HiSeq	Phase_I	62592849	NM_015236	E9PE04|O94867|Q9NWK5	Silent	SNP	ENST00000514591.1	37	CCDS54768.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	7.943	0.743102	0.15642	0.004226	1.21E-4	ENSG00000150471	ENST00000502815	.	.	.	5.95	-5.37	0.02681	.	.	.	.	.	T	0.46852	0.1414	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46162	-0.9211	4	.	.	.	.	5.8064	0.18442	0.6148:0.0803:0.1569:0.148	.	.	.	.	I	648	.	.	V	+	1	0	LPHN3	62592849	0.001000	0.12720	0.919000	0.36401	0.993000	0.82548	-1.345000	0.02637	-0.951000	0.03654	-0.244000	0.11960	GTC		0.368	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1		
TECRL	253017	broad.mit.edu	37	4	65188429	65188429	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr4:65188429C>A	ENST00000381210.3	-	4	523	c.413G>T	c.(412-414)gGt>gTt	p.G138V	TECRL_ENST00000507440.1_Missense_Mutation_p.G138V|TECRL_ENST00000513125.1_5'Flank	NM_001010874.4	NP_001010874.2	Q5HYJ1	TECRL_HUMAN	trans-2,3-enoyl-CoA reductase-like	138					lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	oxidoreductase activity, acting on the CH-CH group of donors (GO:0016627)	p.G138V(1)		endometrium(2)|kidney(5)|large_intestine(7)|lung(30)|prostate(1)|skin(1)|stomach(1)	47						GACTTGTTGACCTAGGTCTGT	0.328																																					p.G138V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G413T	4						.						73.0	73.0	73.0					4																	65188429		2203	4300	6503	64871024	SO:0001583	missense	253017	exon4			AL833108	CCDS33990.1	4q13.1	2009-07-21			ENSG00000205678	ENSG00000205678			27365	protein-coding gene	gene with protein product	"""glycoprotein, synaptic 2-like"""					12477932	Standard	NM_001010874		Approved	GPSN2L, SRD5A2L2, DKFZp313D0829, DKFZp313B2333, TERL	uc003hcv.3	Q5HYJ1	OTTHUMG00000160680	ENST00000381210.3:c.413G>T	4.37:g.65188429C>A	ENSP00000370607:p.Gly138Val	Somatic		Capture	Illumina HiSeq	Phase_I	64871024	NM_001010874		Missense_Mutation	SNP	ENST00000381210.3	37	CCDS33990.1	.	.	.	.	.	.	.	.	.	.	C	14.67	2.603559	0.46423	.	.	ENSG00000205678	ENST00000507440;ENST00000381210;ENST00000509536	T;T;T	0.39787	1.06;1.06;1.06	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.71871	0.3391	M	0.91972	3.26	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	T	0.77960	-0.2391	10	0.87932	D	0	-0.0784	15.4919	0.75611	0.0:1.0:0.0:0.0	.	138;138	Q6IN47;Q5HYJ1	.;TECRL_HUMAN	V	138	ENSP00000426043:G138V;ENSP00000370607:G138V;ENSP00000422497:G138V	ENSP00000370607:G138V	G	-	2	0	TECRL	64871024	1.000000	0.71417	1.000000	0.80357	0.011000	0.07611	4.729000	0.62008	2.728000	0.93425	0.585000	0.79938	GGT		0.328	TECRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361705.4	NM_001010874	
UBA6	55236	broad.mit.edu	37	4	68514929	68514929	+	Splice_Site	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr4:68514929G>A	ENST00000322244.5	-	14	1164	c.1105C>T	c.(1105-1107)Cct>Tct	p.P369S		NM_018227.5	NP_060697.4	A0AVT1	UBA6_HUMAN	ubiquitin-like modifier activating enzyme 6	369					protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|FAT10 activating enzyme activity (GO:0019780)|ligase activity (GO:0016874)	p.P369S(1)		central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(6)|liver(1)|lung(23)|skin(2)|upper_aerodigestive_tract(2)	44						TTTACATCAGGCTAAAACAAA	0.383																																					p.P369S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1105T	4						.						76.0	77.0	77.0					4																	68514929		2203	4300	6503	68197524	SO:0001630	splice_region_variant	55236	exon14			AK094164	CCDS3516.1	4q13.2	2008-02-05	2007-11-30	2007-11-30	ENSG00000033178	ENSG00000033178		"""Ubiquitin-like modifier activating enzymes"""	25581	protein-coding gene	gene with protein product	"""UBA6, ubiquitin-activating enzyme E1"""	611361	"""ubiquitin-activating enzyme E1-like 2"""	UBE1L2		17580310	Standard	NM_018227		Approved	FLJ10808	uc003hdg.4	A0AVT1	OTTHUMG00000129299	ENST00000322244.5:c.1105-1C>T	4.37:g.68514929G>A		Somatic		Capture	Illumina HiSeq	Phase_I	68197524	NM_018227	A6N8M7|B2RAV3|Q4W5K0|Q6UV21|Q86T78|Q86TC7|Q8N5T3|Q8N9E4|Q9H3T7|Q9NVC9	Missense_Mutation	SNP	ENST00000322244.5	37	CCDS3516.1	.	.	.	.	.	.	.	.	.	.	G	1.775	-0.483453	0.04383	.	.	ENSG00000033178	ENST00000322244	T	0.27890	1.64	5.08	5.08	0.68730	Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.222634	0.48286	D	0.000190	T	0.17238	0.0414	N	0.11789	0.175	0.80722	D	1	B	0.31435	0.323	B	0.24006	0.05	T	0.07809	-1.0753	10	0.10377	T	0.69	-31.3202	18.4296	0.90620	0.0:0.0:1.0:0.0	.	369	A0AVT1	UBA6_HUMAN	S	369	ENSP00000313454:P369S	ENSP00000313454:P369S	P	-	1	0	UBA6	68197524	1.000000	0.71417	1.000000	0.80357	0.077000	0.17291	6.134000	0.71689	2.525000	0.85131	0.484000	0.47621	CCT		0.383	UBA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251429.2	NM_018227	Missense_Mutation
AMBN	258	broad.mit.edu	37	4	71472192	71472192	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr4:71472192C>T	ENST00000322937.6	+	13	1192	c.1089C>T	c.(1087-1089)ggC>ggT	p.G363G	AMBN_ENST00000449493.2_Silent_p.G348G	NM_016519.5	NP_057603.1	Q9NP70	AMBN_HUMAN	ameloblastin (enamel matrix protein)	363					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|odontogenesis of dentin-containing tooth (GO:0042475)	proteinaceous extracellular matrix (GO:0005578)	growth factor activity (GO:0008083)|structural constituent of tooth enamel (GO:0030345)	p.G363G(2)		NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(1)	29			Lung(101;0.235)			ACATTCCCGGCCTGCCAAGGA	0.557																																					p.G363G												.	.	2	Substitution - coding silent(2)	large_intestine(1)|prostate(1)	c.C1089T	4						.						48.0	49.0	48.0					4																	71472192		2203	4300	6503	71506781	SO:0001819	synonymous_variant	258	exon13			AF209780	CCDS3543.1	4q21	2006-11-28	2006-04-27		ENSG00000178522	ENSG00000178522			452	protein-coding gene	gene with protein product		601259	"""ameloblastin, enamel matrix protein"""			9126491	Standard	NM_016519		Approved		uc003hfl.3	Q9NP70	OTTHUMG00000129913	ENST00000322937.6:c.1089C>T	4.37:g.71472192C>T		Somatic		Capture	Illumina HiSeq	Phase_I	71506781	NM_016519	Q3B862|Q9H2X1|Q9H4L1	Silent	SNP	ENST00000322937.6	37	CCDS3543.1																																																																																				0.557	AMBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252165.1	NM_016519	
ABCG2	9429	broad.mit.edu	37	4	89053006	89053006	+	Silent	SNP	A	A	G	rs199578838		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr4:89053006A>G	ENST00000237612.3	-	4	872	c.327T>C	c.(325-327)aaT>aaC	p.N109N	ABCG2_ENST00000515655.1_Silent_p.N109N	NM_004827.2	NP_004818.2	Q9UNQ0	ABCG2_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 2 (Junior blood group)	109	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular iron ion homeostasis (GO:0006879)|drug export (GO:0046618)|drug transmembrane transport (GO:0006855)|embryonic process involved in female pregnancy (GO:0060136)|heme transport (GO:0015886)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|response to iron ion (GO:0010039)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|urate metabolic process (GO:0046415)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|heme transporter activity (GO:0015232)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)	p.N109N(1)		breast(5)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(13)|lung(10)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.02e-05)	Afatinib(DB08916)|Apixaban(DB06605)|Buprenorphine(DB00921)|Cabazitaxel(DB06772)|Carboplatin(DB00958)|Cisplatin(DB00515)|Cladribine(DB00242)|Clofarabine(DB00631)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Diethylstilbestrol(DB00255)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gefitinib(DB00317)|Glyburide(DB01016)|Hesperetin(DB01094)|Hydrocortisone(DB00741)|Imatinib(DB00619)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Methotrexate(DB00563)|Mitoxantrone(DB01204)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Nilotinib(DB04868)|Nitrofurantoin(DB00698)|Novobiocin(DB01051)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Prazosin(DB00457)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rilpivirine(DB08864)|Riluzole(DB00740)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Teniposide(DB00444)|Teriflunomide(DB08880)|Testosterone(DB00624)|Topotecan(DB01030)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vincristine(DB00541)|Vismodegib(DB08828)|Zafirlukast(DB00549)|Zidovudine(DB00495)	GCGGTGCTCCATTTATCAGAA	0.388																																					p.N109N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T327C	4						.						98.0	91.0	94.0					4																	89053006		2203	4300	6503	89272030	SO:0001819	synonymous_variant	9429	exon4			AF103796	CCDS3628.1, CCDS58910.1	4q22.1	2014-08-27	2014-08-27		ENSG00000118777	ENSG00000118777		"""CD molecules"", ""ATP binding cassette transporters / subfamily G"""	74	protein-coding gene	gene with protein product		603756	"""ATP-binding cassette, sub-family G (WHITE), member 2"""			8894702, 9861027	Standard	NM_001257386		Approved	EST157481, MXR, BCRP, ABCP, CD338	uc003hrg.3	Q9UNQ0	OTTHUMG00000130601	ENST00000237612.3:c.327T>C	4.37:g.89053006A>G		Somatic		Capture	Illumina HiSeq	Phase_I	89272030	NM_004827	A0A1W3|A8K1T5|O95374|Q4W5I3|Q53ZQ1|Q569L4|Q5YLG4|Q86V64|Q8IX16|Q96LD6|Q96TA8|Q9BY73|Q9NUS0	Silent	SNP	ENST00000237612.3	37	CCDS3628.1																																																																																				0.388	ABCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253051.1	NM_004827	
FAM13A	10144	broad.mit.edu	37	4	89658653	89658653	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr4:89658653G>A	ENST00000264344.5	-	21	2823	c.2616C>T	c.(2614-2616)ggC>ggT	p.G872G	FAM13A_ENST00000503556.1_Silent_p.G532G|FAM13A_ENST00000511976.1_Silent_p.G458G|FAM13A_ENST00000508369.1_Silent_p.G546G|FAM13A_ENST00000395002.2_Intron|FAM13A_ENST00000513837.1_Silent_p.G518G	NM_014883.3	NP_055698.2	O94988	FA13A_HUMAN	family with sequence similarity 13, member A	872					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	55						AAGCAGTTTCGCCCTCGATAA	0.547																																					p.G872G												.	.	0			c.C2616T	4						.						103.0	99.0	100.0					4																	89658653		2203	4300	6503	89877676	SO:0001819	synonymous_variant	10144	exon21			AB020721	CCDS34029.1, CCDS43251.1, CCDS58911.1, CCDS58912.1, CCDS58913.1	4q22.1	2011-09-07	2009-01-20	2009-01-20	ENSG00000138640	ENSG00000138640		"""Rho GTPase activating proteins"""	19367	protein-coding gene	gene with protein product		613299	"""family with sequence similarity 13, member A1"""	FAM13A1			Standard	NM_014883		Approved	KIAA0914, ARHGAP48	uc003hse.2	O94988	OTTHUMG00000161006	ENST00000264344.5:c.2616C>T	4.37:g.89658653G>A		None		Capture	Illumina HiSeq	Phase_I	89877676	NM_014883	B4DLC1|Q24JP0|Q5PR21|Q8NBA3	Silent	SNP	ENST00000264344.5	37	CCDS34029.1																																																																																				0.547	FAM13A-022	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363371.1		
SNCA	6622	broad.mit.edu	37	4	90743454	90743454	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr4:90743454C>A	ENST00000394986.1	-	4	670	c.249G>T	c.(247-249)gaG>gaT	p.E83D	SNCA_ENST00000505199.1_Missense_Mutation_p.E69D|SNCA_ENST00000506244.1_Missense_Mutation_p.E83D|SNCA_ENST00000502987.1_Missense_Mutation_p.E83D|SNCA_ENST00000508895.1_Missense_Mutation_p.E83D|SNCA_ENST00000420646.2_Missense_Mutation_p.E83D|SNCA_ENST00000336904.3_Missense_Mutation_p.E83D|SNCA_ENST00000345009.4_Missense_Mutation_p.E83D|SNCA_ENST00000394989.2_Missense_Mutation_p.E69D|SNCA_ENST00000394991.3_Missense_Mutation_p.E83D			P37840	SYUA_HUMAN	synuclein, alpha (non A4 component of amyloid precursor)	83					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|adult locomotory behavior (GO:0008344)|aging (GO:0007568)|behavioral response to cocaine (GO:0048148)|cellular response to copper ion (GO:0071280)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to oxidative stress (GO:0034599)|dopamine biosynthetic process (GO:0042416)|dopamine uptake involved in synaptic transmission (GO:0051583)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|long-term synaptic potentiation (GO:0060291)|microglial cell activation (GO:0001774)|mitochondrial ATP synthesis coupled electron transport (GO:0042775)|mitochondrial membrane organization (GO:0007006)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dopamine metabolic process (GO:0045963)|negative regulation of dopamine uptake involved in synaptic transmission (GO:0051585)|negative regulation of exocytosis (GO:0045920)|negative regulation of histone acetylation (GO:0035067)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of monooxygenase activity (GO:0032769)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of norepinephrine uptake (GO:0051622)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of serotonin uptake (GO:0051612)|negative regulation of thrombin receptor signaling pathway (GO:0070495)|negative regulation of transporter activity (GO:0032410)|neutral lipid metabolic process (GO:0006638)|oxidation-reduction process (GO:0055114)|phospholipid metabolic process (GO:0006644)|positive regulation of endocytosis (GO:0045807)|positive regulation of glutathione peroxidase activity (GO:1903284)|positive regulation of hydrogen peroxide catabolic process (GO:1903285)|positive regulation of inositol phosphate biosynthetic process (GO:0060732)|positive regulation of neurotransmitter secretion (GO:0001956)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of receptor recycling (GO:0001921)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|protein destabilization (GO:0031648)|receptor internalization (GO:0031623)|regulation of acyl-CoA biosynthetic process (GO:0050812)|regulation of dopamine secretion (GO:0014059)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of glutamate secretion (GO:0014048)|regulation of locomotion (GO:0040012)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of macrophage activation (GO:0043030)|regulation of neuron death (GO:1901214)|regulation of phospholipase activity (GO:0010517)|response to drug (GO:0042493)|response to interferon-gamma (GO:0034341)|response to interleukin-1 (GO:0070555)|response to iron(II) ion (GO:0010040)|response to lipopolysaccharide (GO:0032496)|response to magnesium ion (GO:0032026)|synapse organization (GO:0050808)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular region (GO:0005576)|fibril (GO:0043205)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|inclusion body (GO:0016234)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nuclear outer membrane (GO:0005640)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ribosome (GO:0005840)|rough endoplasmic reticulum (GO:0005791)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	alpha-tubulin binding (GO:0043014)|calcium ion binding (GO:0005509)|copper ion binding (GO:0005507)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|dynein binding (GO:0045502)|ferrous iron binding (GO:0008198)|histone binding (GO:0042393)|Hsp70 protein binding (GO:0030544)|identical protein binding (GO:0042802)|kinesin binding (GO:0019894)|magnesium ion binding (GO:0000287)|oxidoreductase activity (GO:0016491)|phospholipid binding (GO:0005543)|phosphoprotein binding (GO:0051219)|tau protein binding (GO:0048156)|zinc ion binding (GO:0008270)	p.E83D(1)		kidney(1)|large_intestine(2)|lung(4)|ovary(1)	8		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.42e-05)		TCCCTGCTCCCTCCACTGTCT	0.498																																					p.E83D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G249T	4						.						211.0	155.0	174.0					4																	90743454		2203	4300	6503	90962477	SO:0001583	missense	6622	exon4			L08850	CCDS3634.1, CCDS43252.1	4q21.3-q22	2014-05-22			ENSG00000145335	ENSG00000145335		"""Parkinson disease"""	11138	protein-coding gene	gene with protein product		163890	"""Parkinson disease (autosomal dominant, Lewy body) 4"""	PARK1, PARK4		8248242, 14593171	Standard	NM_000345		Approved	NACP, PD1, alpha-synuclein	uc003hsr.3	P37840	OTTHUMG00000130948	ENST00000394986.1:c.249G>T	4.37:g.90743454C>A	ENSP00000378437:p.Glu83Asp	Somatic		Capture	Illumina HiSeq	Phase_I	90962477	NM_001146054	A8K2A4|Q13701|Q4JHI3|Q6IAU6	Missense_Mutation	SNP	ENST00000394986.1	37	CCDS3634.1	.	.	.	.	.	.	.	.	.	.	C	19.05	3.752122	0.69533	.	.	ENSG00000145335	ENST00000394989;ENST00000420646;ENST00000345009;ENST00000394986;ENST00000394991;ENST00000336904;ENST00000508895;ENST00000506244;ENST00000505199;ENST00000502987	D;D;D;D;D;D;D;D;D;D	0.86297	-2.1;-2.1;-2.1;-2.1;-2.1;-2.1;-2.1;-2.1;-2.1;-2.1	4.21	0.0525	0.14302	.	0.000000	0.85682	D	0.000000	D	0.90017	0.6883	M	0.64997	1.995	0.37324	D	0.909699	P;P;D	0.61697	0.552;0.81;0.99	P;P;D	0.70935	0.656;0.889;0.971	D	0.89066	0.3466	10	0.72032	D	0.01	2.6457	9.5516	0.39313	0.0:0.1705:0.0:0.8295	.	69;83;83	P37840-3;P37840;P37840-2	.;SYUA_HUMAN;.	D	69;83;83;83;83;83;83;83;69;83	ENSP00000378440:E69D;ENSP00000396241:E83D;ENSP00000343683:E83D;ENSP00000378437:E83D;ENSP00000378442:E83D;ENSP00000338345:E83D;ENSP00000426955:E83D;ENSP00000422238:E83D;ENSP00000421485:E69D;ENSP00000426034:E83D	ENSP00000338345:E83D	E	-	3	2	SNCA	90962477	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	1.248000	0.32827	0.005000	0.14708	0.563000	0.77884	GAG		0.498	SNCA-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253547.2		
LRP2BP	55805	broad.mit.edu	37	4	186295381	186295381	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr4:186295381C>T	ENST00000328559.7	-	5	1298	c.487G>A	c.(487-489)Gca>Aca	p.A163T	LRP2BP_ENST00000510776.1_Missense_Mutation_p.A137T|LRP2BP_ENST00000362004.3_Missense_Mutation_p.A165T|LRP2BP_ENST00000505916.1_Missense_Mutation_p.A163T|RP11-714G18.1_ENST00000514884.1_RNA	NM_018409.3	NP_060879.2	Q9P2M1	LR2BP_HUMAN	LRP2 binding protein	163						cytoplasm (GO:0005737)		p.A163T(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)		TTGTCTGCTGCGATAAGCCAC	0.438																																					p.A163T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G487A	4						.						164.0	153.0	157.0					4																	186295381		2203	4300	6503	186532375	SO:0001583	missense	55805	exon5			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.487G>A	4.37:g.186295381C>T	ENSP00000332681:p.Ala163Thr	Somatic		Capture	Illumina HiSeq	Phase_I	186532375	NM_018409	A6NJR7|A7E219|B3KX83|Q9NSN6	Missense_Mutation	SNP	ENST00000328559.7	37	CCDS3840.1	.	.	.	.	.	.	.	.	.	.	C	31	5.075609	0.94000	.	.	ENSG00000109771	ENST00000362004;ENST00000328559;ENST00000510776;ENST00000505916	T;T;T;T	0.64085	-0.08;-0.08;-0.08;-0.08	5.33	5.33	0.75918	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	D	0.84714	0.5533	M	0.92219	3.285	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.88015	0.2765	10	0.72032	D	0.01	-11.6398	19.3842	0.94550	0.0:1.0:0.0:0.0	.	137;163	G5E9Z9;Q9P2M1	.;LR2BP_HUMAN	T	165;163;137;163	ENSP00000354846:A165T;ENSP00000332681:A163T;ENSP00000424610:A137T;ENSP00000426203:A163T	ENSP00000332681:A163T	A	-	1	0	LRP2BP	186532375	1.000000	0.71417	0.997000	0.53966	0.687000	0.40016	6.515000	0.73751	2.644000	0.89710	0.655000	0.94253	GCA		0.438	LRP2BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360679.2	NM_018409	
CCT5	22948	broad.mit.edu	37	5	10261684	10261684	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:10261684G>A	ENST00000280326.4	+	8	1426	c.1006G>A	c.(1006-1008)Gca>Aca	p.A336T	CCT5_ENST00000506600.1_Missense_Mutation_p.A243T|CCT5_ENST00000515676.1_Missense_Mutation_p.A298T|CCT5_ENST00000503026.1_Missense_Mutation_p.A315T|CCT5_ENST00000515390.1_Missense_Mutation_p.A281T	NM_012073.3	NP_036205.1	P48643	TCPE_HUMAN	chaperonin containing TCP1, subunit 5 (epsilon)	336					'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)|response to virus (GO:0009615)	cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleolus (GO:0005730)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|G-protein beta-subunit binding (GO:0031681)	p.A336T(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(2)	26						GATTGCCATCGCAACAGGAGG	0.498																																					p.A336T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1006A	5						.						202.0	213.0	209.0					5																	10261684		2203	4300	6503	10314684	SO:0001583	missense	22948	exon8			D43950	CCDS3877.1	5p15.2	2014-09-17			ENSG00000150753	ENSG00000150753		"""Heat Shock Proteins / Chaperonins"""	1618	protein-coding gene	gene with protein product		610150					Standard	NM_012073		Approved	KIAA0098	uc003jeq.3	P48643	OTTHUMG00000131042	ENST00000280326.4:c.1006G>A	5.37:g.10261684G>A	ENSP00000280326:p.Ala336Thr	Somatic		Capture	Illumina HiSeq	Phase_I	10314684	NM_012073	A8JZY8|A8K2X8|B4DYD8	Missense_Mutation	SNP	ENST00000280326.4	37	CCDS3877.1	.	.	.	.	.	.	.	.	.	.	G	15.81	2.944352	0.53079	.	.	ENSG00000150753	ENST00000280326;ENST00000503026;ENST00000515390;ENST00000440011;ENST00000515676;ENST00000506600	T;T;T;T;T	0.80304	-1.36;-1.36;-1.36;-1.36;-1.36	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	D	0.86740	0.6005	M	0.80616	2.505	0.80722	D	1	P;B;D;P;P;P	0.65815	0.633;0.336;0.995;0.52;0.52;0.52	B;B;P;B;B;B	0.51055	0.347;0.162;0.657;0.384;0.384;0.384	D	0.88928	0.3371	10	0.87932	D	0	-24.9254	18.2379	0.89956	0.0:0.0:1.0:0.0	.	243;281;185;334;336;336	B4DYD8;E7ENZ3;B4DZY9;Q9BU08;A8K2X8;P48643	.;.;.;.;.;TCPE_HUMAN	T	336;315;281;309;298;243	ENSP00000280326:A336T;ENSP00000423318:A315T;ENSP00000426923:A281T;ENSP00000427297:A298T;ENSP00000423052:A243T	ENSP00000280326:A336T	A	+	1	0	CCT5	10314684	1.000000	0.71417	0.179000	0.23059	0.179000	0.23085	9.196000	0.94978	2.532000	0.85374	0.563000	0.77884	GCA		0.498	CCT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253688.2		
TSLP	85480	broad.mit.edu	37	5	110407656	110407656	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	T	T	T	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:110407656T>C	ENST00000344895.3	+	1	267	c.68T>C	c.(67-69)gTa>gCa	p.V23A	TSLP_ENST00000420978.2_Missense_Mutation_p.V23A|TSLP_ENST00000379706.4_5'Flank	NM_033035.4	NP_149024.1	Q969D9	TSLP_HUMAN	thymic stromal lymphopoietin	23						extracellular space (GO:0005615)				breast(1)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|stomach(1)	11		all_cancers(142;2.72e-05)|all_epithelial(76;4.39e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0417)|Ovarian(225;0.0443)|Colorectal(57;0.0464)|all_lung(232;0.0507)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.24e-08)|Epithelial(69;1.54e-07)|all cancers(49;1.73e-05)|COAD - Colon adenocarcinoma(37;0.109)		TTACAACTTGTAGGGCTGGTG	0.388																																					p.V23A												.	.	0			c.T68C	5						.						194.0	179.0	184.0					5																	110407656		2202	4300	6502	110435555	SO:0001583	missense	85480	exon1			BC040592	CCDS4101.1	5q22.1	2007-08-24			ENSG00000145777	ENSG00000145777			30743	protein-coding gene	gene with protein product		607003				11418668, 11480573	Standard	NM_033035		Approved		uc003kpb.2	Q969D9	OTTHUMG00000128791	ENST00000344895.3:c.68T>C	5.37:g.110407656T>C	ENSP00000339804:p.Val23Ala	None		Capture	Illumina HiSeq	Phase_I	110435555	NM_033035	Q8IW99	Missense_Mutation	SNP	ENST00000344895.3	37	CCDS4101.1	.	.	.	.	.	.	.	.	.	.	T	15.37	2.812745	0.50527	.	.	ENSG00000145777	ENST00000420978;ENST00000344895	.	.	.	5.71	1.97	0.26223	.	0.316331	0.22910	N	0.054143	T	0.33411	0.0862	L	0.29908	0.895	0.80722	D	1	P	0.36144	0.539	B	0.30782	0.12	T	0.12477	-1.0546	9	0.87932	D	0	-7.7444	6.0374	0.19716	0.0:0.414:0.0:0.586	.	23	Q969D9	TSLP_HUMAN	A	23	.	ENSP00000339804:V23A	V	+	2	0	TSLP	110435555	0.947000	0.32204	0.992000	0.48379	0.818000	0.46254	0.878000	0.28126	0.412000	0.25729	-0.408000	0.06270	GTA		0.388	TSLP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250717.1	NM_033035	
TSLP	85480	broad.mit.edu	37	5	110411737	110411737	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:110411737C>T	ENST00000344895.3	+	4	644	c.445C>T	c.(445-447)Cgt>Tgt	p.R149C	TSLP_ENST00000420978.2_Missense_Mutation_p.R149C|TSLP_ENST00000379706.4_Missense_Mutation_p.R53C|CTC-551A13.2_ENST00000507269.3_RNA	NM_033035.4	NP_149024.1	Q969D9	TSLP_HUMAN	thymic stromal lymphopoietin	149						extracellular space (GO:0005615)		p.R149C(1)		breast(1)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|stomach(1)	11		all_cancers(142;2.72e-05)|all_epithelial(76;4.39e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0417)|Ovarian(225;0.0443)|Colorectal(57;0.0464)|all_lung(232;0.0507)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.24e-08)|Epithelial(69;1.54e-07)|all cancers(49;1.73e-05)|COAD - Colon adenocarcinoma(37;0.109)		AGGATTGTGGCGTCGCTTCAA	0.358																																					p.R149C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C445T	5						.						128.0	127.0	127.0					5																	110411737		2202	4300	6502	110439636	SO:0001583	missense	85480	exon4			BC040592	CCDS4101.1	5q22.1	2007-08-24			ENSG00000145777	ENSG00000145777			30743	protein-coding gene	gene with protein product		607003				11418668, 11480573	Standard	NM_033035		Approved		uc003kpb.2	Q969D9	OTTHUMG00000128791	ENST00000344895.3:c.445C>T	5.37:g.110411737C>T	ENSP00000339804:p.Arg149Cys	Somatic		Capture	Illumina HiSeq	Phase_I	110439636	NM_033035	Q8IW99	Missense_Mutation	SNP	ENST00000344895.3	37	CCDS4101.1	.	.	.	.	.	.	.	.	.	.	C	12.16	1.853633	0.32791	.	.	ENSG00000145777	ENST00000420978;ENST00000344895;ENST00000379706	.	.	.	4.52	-3.2	0.05156	.	1.227270	0.05823	N	0.616158	T	0.36138	0.0956	N	0.24115	0.695	0.22240	N	0.999264	D	0.76494	0.999	P	0.60949	0.881	T	0.33752	-0.9856	9	0.72032	D	0.01	0.738	4.3574	0.11185	0.1232:0.2383:0.4831:0.1554	.	149	Q969D9	TSLP_HUMAN	C	149;149;53	.	ENSP00000339804:R149C	R	+	1	0	TSLP	110439636	0.002000	0.14202	0.004000	0.12327	0.228000	0.25075	-0.654000	0.05354	-0.702000	0.05056	-0.165000	0.13383	CGT		0.358	TSLP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250717.1	NM_033035	
YTHDC2	64848	broad.mit.edu	37	5	112874845	112874845	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:112874845G>T	ENST00000161863.4	+	8	1390	c.1177G>T	c.(1177-1179)Gaa>Taa	p.E393*	YTHDC2_ENST00000515883.1_Nonsense_Mutation_p.E393*	NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	393					ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)	p.E393*(1)		NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		TACAAACAAAGAAATGTTAAA	0.234																																					p.E393X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G1177T	5						.						13.0	15.0	14.0					5																	112874845		2033	4171	6204	112902744	SO:0001587	stop_gained	64848	exon8			AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188			24721	protein-coding gene	gene with protein product						12477932	Standard	NM_022828		Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	ENST00000161863.4:c.1177G>T	5.37:g.112874845G>T	ENSP00000161863:p.Glu393*	Somatic		Capture	Illumina HiSeq	Phase_I	112902744	NM_022828	B2RP66	Nonsense_Mutation	SNP	ENST00000161863.4	37	CCDS4113.1	.	.	.	.	.	.	.	.	.	.	G	38	6.892921	0.97916	.	.	ENSG00000047188	ENST00000161863;ENST00000515883;ENST00000511372	.	.	.	5.34	4.46	0.54185	.	0.292912	0.37261	N	0.002171	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	.	15.3016	0.73955	0.0:0.0:0.8586:0.1414	.	.	.	.	X	393;393;303	.	ENSP00000161863:E393X	E	+	1	0	YTHDC2	112902744	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	7.532000	0.81985	1.210000	0.43336	-0.321000	0.08615	GAA		0.234	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828	
DTWD2	285605	broad.mit.edu	37	5	118176772	118176772	+	Missense_Mutation	SNP	C	C	T	rs140154641		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:118176772C>T	ENST00000510708.1	-	6	770	c.737G>A	c.(736-738)cGc>cAc	p.R246H	DTWD2_ENST00000515439.3_Missense_Mutation_p.R150H|DTWD2_ENST00000304058.4_Missense_Mutation_p.R180H	NM_173666.2	NP_775937.1	Q8NBA8	DTWD2_HUMAN	DTW domain containing 2	246								p.R246H(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)	13		all_epithelial(76;0.0982)|Prostate(80;0.121)		OV - Ovarian serous cystadenocarcinoma(64;0.000228)|Epithelial(69;0.000941)|all cancers(49;0.00939)		TTGAAGAGGGCGAAGCAAAGT	0.363																																					p.R246H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G737A	5						.	C	HIS/ARG	1,4403	2.1+/-5.4	0,1,2201	64.0	55.0	58.0		737	4.5	1.0	5	dbSNP_134	58	0,8600		0,0,4300	no	missense	DTWD2	NM_173666.2	29	0,1,6501	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	246/299	118176772	1,13003	2202	4300	6502	118204671	SO:0001583	missense	285605	exon6				CCDS34216.1	5q23.1	2008-02-05			ENSG00000169570	ENSG00000169570			19334	protein-coding gene	gene with protein product							Standard	NM_173666		Approved	FLJ33977	uc003ksa.3	Q8NBA8	OTTHUMG00000162956	ENST00000510708.1:c.737G>A	5.37:g.118176772C>T	ENSP00000425048:p.Arg246His	Somatic		Capture	Illumina HiSeq	Phase_I	118204671	NM_173666		Missense_Mutation	SNP	ENST00000510708.1	37	CCDS34216.1	.	.	.	.	.	.	.	.	.	.	C	17.34	3.364196	0.61513	2.27E-4	0.0	ENSG00000169570	ENST00000304058;ENST00000510708;ENST00000515439	.	.	.	5.42	4.54	0.55810	DTW (1);	0.000000	0.85682	D	0.000000	T	0.56949	0.2020	M	0.62154	1.92	0.58432	D	0.999998	B	0.31351	0.32	B	0.23716	0.048	T	0.59322	-0.7476	9	0.40728	T	0.16	-11.4893	14.2256	0.65858	0.0:0.9257:0.0:0.0743	.	246	Q8NBA8	DTWD2_HUMAN	H	180;246;150	.	ENSP00000302892:R180H	R	-	2	0	DTWD2	118204671	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.930000	0.48924	2.539000	0.85634	0.650000	0.86243	CGC		0.363	DTWD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371167.2	NM_173666	
SLC27A6	28965	broad.mit.edu	37	5	128320963	128320963	+	Missense_Mutation	SNP	C	C	T	rs201991962		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:128320963C>T	ENST00000262462.4	+	2	1629	c.619C>T	c.(619-621)Cgc>Tgc	p.R207C	SLC27A6_ENST00000506176.1_Missense_Mutation_p.R207C|SLC27A6_ENST00000395266.1_Missense_Mutation_p.R207C			Q9Y2P4	S27A6_HUMAN	solute carrier family 27 (fatty acid transporter), member 6	207				R -> H (in Ref. 4; CAD97625). {ECO:0000305}.	long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty acid transport (GO:0015909)|transmembrane transport (GO:0055085)|very long-chain fatty acid metabolic process (GO:0000038)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	long-chain fatty acid-CoA ligase activity (GO:0004467)|nucleotide binding (GO:0000166)|very long-chain fatty acid-CoA ligase activity (GO:0031957)	p.R207C(1)		NS(2)|endometrium(1)|kidney(3)|large_intestine(11)|liver(1)|lung(20)|prostate(1)|skin(4)|stomach(1)	44		all_cancers(142;0.0483)|Prostate(80;0.055)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.171)|OV - Ovarian serous cystadenocarcinoma(64;0.186)		GCCCGTGCCACGCAGCCACCA	0.418																																					p.R207C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C619T	5						.	C	CYS/ARG,CYS/ARG	0,4406		0,0,2203	112.0	95.0	100.0		619,619	3.6	0.0	5		100	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	SLC27A6	NM_001017372.1,NM_014031.3	180,180	0,4,6499	TT,TC,CC		0.0465,0.0,0.0308	possibly-damaging,possibly-damaging	207/620,207/620	128320963	4,13002	2203	4300	6503	128348862	SO:0001583	missense	28965	exon2			AF064254	CCDS4145.1	5q23.3	2013-05-22			ENSG00000113396	ENSG00000113396		"""Acyl-CoA synthetase family"", ""Solute carriers"""	11000	protein-coding gene	gene with protein product	"""fatty-acid-Coenzyme A ligase, very long-chain 2"""	604196				12556534, 10479480	Standard	XM_005271967		Approved	FATP6, VLCS-H1, FACVL2, ACSVL2	uc003kuy.3	Q9Y2P4	OTTHUMG00000128991	ENST00000262462.4:c.619C>T	5.37:g.128320963C>T	ENSP00000262462:p.Arg207Cys	Somatic		Capture	Illumina HiSeq	Phase_I	128348862	NM_001017372	Q6IAM5|Q7Z6E6|Q86YF6	Missense_Mutation	SNP	ENST00000262462.4	37	CCDS4145.1	.	.	.	.	.	.	.	.	.	.	C	11.15	1.554148	0.27739	0.0	4.65E-4	ENSG00000113396	ENST00000508645;ENST00000262462;ENST00000395266;ENST00000506176	T;T;T;T	0.44881	2.82;0.91;0.91;0.91	4.43	3.56	0.40772	AMP-dependent synthetase/ligase (1);	0.508589	0.23347	N	0.049169	T	0.49423	0.1556	L	0.49571	1.57	0.19575	N	0.999968	D	0.69078	0.997	P	0.58970	0.849	T	0.31223	-0.9951	9	.	.	.	-16.4716	9.4056	0.38460	0.0:0.7306:0.1835:0.0859	.	207	Q9Y2P4	S27A6_HUMAN	C	26;207;207;207	ENSP00000421759:R26C;ENSP00000262462:R207C;ENSP00000378684:R207C;ENSP00000421024:R207C	.	R	+	1	0	SLC27A6	128348862	0.001000	0.12720	0.042000	0.18584	0.015000	0.08874	0.987000	0.29603	1.472000	0.48140	0.650000	0.86243	CGC		0.418	SLC27A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250980.1	NM_014031	
DNAH5	1767	broad.mit.edu	37	5	13717565	13717565	+	Silent	SNP	C	C	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:13717565C>G	ENST00000265104.4	-	73	12668	c.12564G>C	c.(12562-12564)gtG>gtC	p.V4188V		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4188	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.V4188V(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)					GCAGGAAAGCCACTGCGTACA	0.547									Kartagener syndrome																												p.V4188V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G12564C	5						.						65.0	59.0	61.0					5																	13717565		2203	4300	6503	13770565	SO:0001819	synonymous_variant	1767	exon73	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.12564G>C	5.37:g.13717565C>G		Somatic		Capture	Illumina HiSeq	Phase_I	13770565	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																				0.547	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
DNAH5	1767	broad.mit.edu	37	5	13721259	13721259	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:13721259C>T	ENST00000265104.4	-	71	12233	c.12129G>A	c.(12127-12129)acG>acA	p.T4043T		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4043	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.T4043T(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)					AGATGAGTGGCGTCCGTGGAT	0.502									Kartagener syndrome																												p.T4043T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G12129A	5						.						121.0	122.0	121.0					5																	13721259		2203	4300	6503	13774259	SO:0001819	synonymous_variant	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.12129G>A	5.37:g.13721259C>T		Somatic		Capture	Illumina HiSeq	Phase_I	13774259	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																				0.502	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
DNAH5	1767	broad.mit.edu	37	5	13871054	13871054	+	Missense_Mutation	SNP	C	C	T	rs73055857	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:13871054C>T	ENST00000265104.4	-	24	3760	c.3656G>A	c.(3655-3657)cGc>cAc	p.R1219H	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1219	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.R1219H(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)					GTTACAGTGGCGTCCAATGAC	0.383									Kartagener syndrome				C|||	4	0.000798722	0.0008	0.0	5008	,	,		17329	0.0		0.0	False		,,,				2504	0.0031				p.R1219H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3656A	5						.	C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	100.0	101.0	100.0		3656	4.1	0.9	5	dbSNP_130	100	0,8600		0,0,4300	yes	missense	DNAH5	NM_001369.2	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	1219/4625	13871054	1,13005	2203	4300	6503	13924054	SO:0001583	missense	1767	exon24	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.3656G>A	5.37:g.13871054C>T	ENSP00000265104:p.Arg1219His	Somatic		Capture	Illumina HiSeq	Phase_I	13924054	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	8.550	0.875279	0.17395	2.27E-4	0.0	ENSG00000039139	ENST00000265104	T	0.24151	1.87	5.84	4.06	0.47325	.	0.580298	0.19269	N	0.118465	T	0.23330	0.0564	L	0.48362	1.52	0.09310	N	1	B	0.12013	0.005	B	0.09377	0.004	T	0.13764	-1.0497	10	0.46703	T	0.11	.	11.3789	0.49746	0.0:0.763:0.0:0.237	.	1219	Q8TE73	DYH5_HUMAN	H	1219	ENSP00000265104:R1219H	ENSP00000265104:R1219H	R	-	2	0	DNAH5	13924054	0.606000	0.26949	0.941000	0.38009	0.403000	0.30841	0.714000	0.25808	1.473000	0.48159	-0.150000	0.13652	CGC		0.383	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
CDC25C	995	broad.mit.edu	37	5	137665272	137665272	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:137665272G>T	ENST00000323760.6	-	3	537	c.259C>A	c.(259-261)Ctt>Att	p.L87I	CDC25C_ENST00000415130.2_Intron|CDC25C_ENST00000348983.3_Intron|CDC25C_ENST00000513970.1_Missense_Mutation_p.L87I|CDC25C_ENST00000514555.1_Missense_Mutation_p.L87I|CDC25C_ENST00000357274.3_Intron|CDC25C_ENST00000356505.3_Missense_Mutation_p.L87I	NM_001790.3	NP_001781.2	P30307	MPIP3_HUMAN	cell division cycle 25C	87					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|peptidyl-tyrosine dephosphorylation (GO:0035335)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|WW domain binding (GO:0050699)	p.L87I(1)		endometrium(2)|kidney(3)|large_intestine(5)|lung(5)|skin(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			GAAGTGGTAAGCTGAGTGGCA	0.443																																					p.L87I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C259A	5						.						170.0	166.0	167.0					5																	137665272		2203	4300	6503	137693171	SO:0001583	missense	995	exon3			M34065	CCDS4202.1, CCDS4203.1	5q31	2013-01-17	2013-01-17		ENSG00000158402	ENSG00000158402		"""Protein tyrosine phosphatases / Class III Cys-based PTPs"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1727	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 60"""	157680	"""cell division cycle 25C"", ""cell division cycle 25 homolog C (S. cerevisiae)"", ""cell division cycle 25 homolog C (S. pombe)"""	CDC25		1703321	Standard	XM_005272145		Approved	PPP1R60	uc003lcp.1	P30307	OTTHUMG00000129203	ENST00000323760.6:c.259C>A	5.37:g.137665272G>T	ENSP00000321656:p.Leu87Ile	Somatic		Capture	Illumina HiSeq	Phase_I	137693171	NM_001790	D3DQB8|Q96PL3|Q9H168|Q9H2E8|Q9H2E9|Q9H2F1	Missense_Mutation	SNP	ENST00000323760.6	37	CCDS4202.1	.	.	.	.	.	.	.	.	.	.	G	10.34	1.322865	0.23994	.	.	ENSG00000158402	ENST00000323760;ENST00000356505;ENST00000513970;ENST00000534892;ENST00000514555;ENST00000503022;ENST00000510119	T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97	4.4	-1.94	0.07571	.	0.764676	0.11327	N	0.575452	T	0.30854	0.0778	L	0.56769	1.78	0.09310	N	1	P;P;P;P	0.42296	0.775;0.666;0.573;0.58	B;B;B;B	0.39660	0.306;0.162;0.23;0.142	T	0.17561	-1.0365	10	0.22706	T	0.39	-0.2367	3.3045	0.06994	0.3281:0.0:0.3789:0.2931	.	104;104;87;87	G3V1P6;B4DX61;P30307-2;P30307	.;.;.;MPIP3_HUMAN	I	87;87;87;104;87;87;104	ENSP00000321656:L87I;ENSP00000348898:L87I;ENSP00000424795:L87I;ENSP00000425470:L87I;ENSP00000427251:L87I;ENSP00000427105:L104I	ENSP00000321656:L87I	L	-	1	0	CDC25C	137693171	0.005000	0.15991	0.059000	0.19551	0.948000	0.59901	-0.175000	0.09825	-0.722000	0.04922	-0.253000	0.11424	CTT		0.443	CDC25C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251280.1		
PCDHB1	29930	broad.mit.edu	37	5	140431248	140431248	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:140431248C>T	ENST00000306549.3	+	1	270	c.193C>T	c.(193-195)Cgg>Tgg	p.R65W		NM_013340.2	NP_037472.2	Q9Y5F3	PCDB1_HUMAN	protocadherin beta 1	65	Cadherin 1. {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.R65W(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|liver(1)|lung(13)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	53			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCGCGGGGCGCGGCTGGTTTC	0.572																																					p.R65W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C193T	5						.						47.0	50.0	49.0					5																	140431248		2203	4300	6503	140411432	SO:0001583	missense	29930	exon1			AF152488	CCDS4243.1	5q31	2010-01-26			ENSG00000171815	ENSG00000171815		"""Cadherins / Protocadherins : Clustered"""	8680	other	protocadherin		606327				10380929	Standard	NM_013340		Approved	PCDH-BETA1	uc003lik.1	Q9Y5F3	OTTHUMG00000129627	ENST00000306549.3:c.193C>T	5.37:g.140431248C>T	ENSP00000307234:p.Arg65Trp	Somatic		Capture	Illumina HiSeq	Phase_I	140411432	NM_013340	Q2M257	Missense_Mutation	SNP	ENST00000306549.3	37	CCDS4243.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.269870	0.80469	.	.	ENSG00000171815	ENST00000306549	T	0.38887	1.11	5.81	-0.863	0.10669	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	0.338512	0.21027	N	0.081414	T	0.67692	0.2920	H	0.97983	4.12	0.09310	N	1	D	0.71674	0.998	P	0.59643	0.861	T	0.60801	-0.7191	10	0.87932	D	0	.	7.2627	0.26212	0.5173:0.3236:0.1008:0.0583	.	65	Q9Y5F3	PCDB1_HUMAN	W	65	ENSP00000307234:R65W	ENSP00000307234:R65W	R	+	1	2	PCDHB1	140411432	0.458000	0.25760	0.471000	0.27229	0.965000	0.64279	1.697000	0.37784	-0.162000	0.10964	-0.165000	0.13383	CGG		0.572	PCDHB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251822.2	NM_013340	
PCDHB7	56129	broad.mit.edu	37	5	140554034	140554034	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:140554034G>A	ENST00000231137.3	+	1	1792	c.1618G>A	c.(1618-1620)Gcg>Acg	p.A540T		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	540	Cadherin 5. {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.A540T(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGGCTCCCCCGCGCTGAGCAG	0.697																																					p.A540T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1618A	5						.						45.0	50.0	48.0					5																	140554034		2201	4298	6499	140534218	SO:0001583	missense	56129	exon1			AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"""Cadherins / Protocadherins : Clustered"""	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.1618G>A	5.37:g.140554034G>A	ENSP00000231137:p.Ala540Thr	Somatic		Capture	Illumina HiSeq	Phase_I	140534218	NM_018940	A1L3Y8	Missense_Mutation	SNP	ENST00000231137.3	37	CCDS4249.1	.	.	.	.	.	.	.	.	.	.	g	16.57	3.159255	0.57368	.	.	ENSG00000113212	ENST00000231137;ENST00000543636	T	0.03181	4.02	4.3	2.38	0.29361	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.11665	0.0284	L	0.52266	1.64	0.34654	D	0.721994	D	0.89917	1.0	D	0.75484	0.986	T	0.06643	-1.0815	9	0.62326	D	0.03	.	10.5437	0.45047	0.0:0.5191:0.3461:0.1347	.	540	Q9Y5E2	PCDB7_HUMAN	T	540;323	ENSP00000231137:A540T	ENSP00000231137:A540T	A	+	1	0	PCDHB7	140534218	0.116000	0.22171	0.968000	0.41197	0.508000	0.34012	0.205000	0.17356	0.317000	0.23160	0.449000	0.29647	GCG		0.697	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940	
PCDHB10	56126	broad.mit.edu	37	5	140573826	140573826	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:140573826C>T	ENST00000239446.4	+	1	1885	c.1701C>T	c.(1699-1701)aaC>aaT	p.N567N		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	567					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.N567N(1)		breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGCTGCAGAACGGCTCCGCGC	0.726																																					p.N567N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1701T	5						.						8.0	11.0	10.0					5																	140573826		1804	3787	5591	140554010	SO:0001819	synonymous_variant	56126	exon1			AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"""Cadherins / Protocadherins : Clustered"""	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.1701C>T	5.37:g.140573826C>T		Somatic		Capture	Illumina HiSeq	Phase_I	140554010	NM_018930	Q96T99	Silent	SNP	ENST00000239446.4	37	CCDS4252.1																																																																																				0.726	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930	
PCDHB11	56125	broad.mit.edu	37	5	140579817	140579817	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:140579817C>T	ENST00000354757.3	+	1	470	c.470C>T	c.(469-471)gCg>gTg	p.A157V	PCDHB11_ENST00000536699.1_Intron	NM_018931.2	NP_061754.1	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11	157	Cadherin 2. {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.A157V(1)		NS(2)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTAGAAAGTGCGAAGGATTTA	0.393																																					p.A157V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C470T	5						.						94.0	103.0	100.0					5																	140579817		2203	4300	6503	140560001	SO:0001583	missense	56125	exon1			AF152490	CCDS4253.1	5q31	2010-01-26			ENSG00000197479	ENSG00000197479		"""Cadherins / Protocadherins : Clustered"""	8682	other	protocadherin	"""cadherin ME2"""	606337				10380929	Standard	NM_018931		Approved	PCDH-BETA11, ME2	uc003liy.3	Q9Y5F2	OTTHUMG00000129618	ENST00000354757.3:c.470C>T	5.37:g.140579817C>T	ENSP00000346802:p.Ala157Val	Somatic		Capture	Illumina HiSeq	Phase_I	140560001	NM_018931	B4DSF7|Q2M223	Missense_Mutation	SNP	ENST00000354757.3	37	CCDS4253.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.497282	0.85069	.	.	ENSG00000197479	ENST00000354757	T	0.59364	0.27	2.8	1.9	0.25705	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.74489	0.3723	M	0.82630	2.6	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.75869	-0.3165	9	0.62326	D	0.03	.	11.3665	0.49675	0.0:0.8142:0.1858:0.0	.	157	Q9Y5F2	PCDBB_HUMAN	V	157	ENSP00000346802:A157V	ENSP00000346802:A157V	A	+	2	0	PCDHB11	140560001	1.000000	0.71417	0.002000	0.10522	0.720000	0.41350	4.488000	0.60300	0.480000	0.27534	0.467000	0.42956	GCG		0.393	PCDHB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251813.1	NM_018931	
PCDHGA1	56114	broad.mit.edu	37	5	140712342	140712342	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:140712342G>A	ENST00000517417.1	+	1	2091	c.2091G>A	c.(2089-2091)gcG>gcA	p.A697A	PCDHGA1_ENST00000378105.3_Silent_p.A697A	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	697					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A697A(1)		breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|lung(32)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGTGGCGGCGGCCGCGGTCT	0.672																																					p.A697A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2091A	5						.						73.0	84.0	80.0					5																	140712342		2203	4297	6500	140692526	SO:0001819	synonymous_variant	56114	exon1			AF152318	CCDS54922.1	5q31	2010-01-26				ENSG00000204956		"""Cadherins / Protocadherins : Clustered"""	8696	other	protocadherin		606288				10380929	Standard	NM_018912		Approved	PCDH-GAMMA-A1		Q9Y5H4		ENST00000517417.1:c.2091G>A	5.37:g.140712342G>A		Somatic		Capture	Illumina HiSeq	Phase_I	140692526	NM_031993	Q2M273|Q9Y5D6	Silent	SNP	ENST00000517417.1	37	CCDS54922.1																																																																																				0.672	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912	
PCDHGA7	56108	broad.mit.edu	37	5	140764450	140764450	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:140764450G>A	ENST00000518325.1	+	1	1984	c.1984G>A	c.(1984-1986)Gtg>Atg	p.V662M	PCDHGA2_ENST00000394576.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018920.2	NP_061743.1	Q9Y5G6	PCDG7_HUMAN	protocadherin gamma subfamily A, 7	662	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.V662M(2)		NS(1)|biliary_tract(1)|endometrium(8)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|skin(1)|stomach(3)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CACACTCACCGTGGCTGTGGC	0.637																																					p.V662M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1984A	5						.						34.0	43.0	40.0					5																	140764450		2195	4293	6488	140744634	SO:0001583	missense	56108	exon1			AF152514	CCDS54927.1, CCDS75336.1	5q31	2010-01-26				ENSG00000253537		"""Cadherins / Protocadherins : Clustered"""	8705	other	protocadherin		606294				10380929	Standard	NM_018920		Approved	PCDH-GAMMA-A7		Q9Y5G6		ENST00000518325.1:c.1984G>A	5.37:g.140764450G>A	ENSP00000430024:p.Val662Met	Somatic		Capture	Illumina HiSeq	Phase_I	140744634	NM_032087	B2RN87|Q9Y5D0	Missense_Mutation	SNP	ENST00000518325.1	37	CCDS54927.1	.	.	.	.	.	.	.	.	.	.	.	16.69	3.193324	0.58017	.	.	ENSG00000253537	ENST00000518325	T	0.69685	-0.42	5.01	5.01	0.66863	Cadherin (4);Cadherin-like (1);	.	.	.	.	D	0.83317	0.5228	M	0.93062	3.375	0.30202	N	0.798502	D;D	0.71674	0.989;0.998	P;P	0.59115	0.852;0.846	D	0.83565	0.0109	9	0.72032	D	0.01	.	14.0097	0.64488	0.0:0.1515:0.8485:0.0	.	662;662	Q9Y5G6;Q9Y5G6-2	PCDG7_HUMAN;.	M	662	ENSP00000430024:V662M	ENSP00000430024:V662M	V	+	1	0	PCDHGA7	140744634	0.941000	0.31946	0.922000	0.36590	0.547000	0.35210	1.432000	0.34936	2.484000	0.83849	0.655000	0.94253	GTG		0.637	PCDHGA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374744.1	NM_018920	
PCDHGA12	26025	broad.mit.edu	37	5	140811927	140811927	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:140811927C>T	ENST00000252085.3	+	1	1743	c.1601C>T	c.(1600-1602)gCg>gTg	p.A534V	PCDHGB3_ENST00000576222.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA7_ENST00000518325.1_Intron	NM_003735.2|NM_032094.1	NP_003726.1|NP_115265.1	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12	534	Cadherin 5. {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.A534V(4)		breast(2)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(23)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	58			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAAGTGATGGCGCGGGACAAC	0.597																																					p.A534V												.	.	4	Substitution - Missense(4)	large_intestine(2)|breast(2)	c.C1601T	5						.						123.0	137.0	132.0					5																	140811927		2203	4300	6503	140792111	SO:0001583	missense	26025	exon1			AF152506	CCDS4260.1, CCDS75346.1	5q31	2010-01-26	2002-05-23		ENSG00000253159	ENSG00000253159		"""Cadherins / Protocadherins : Clustered"""	8699	other	protocadherin	"""fibroblast cadherin FIB3"""	603059	"""cadherin 21"""	CDH21		10380929	Standard	NM_003735		Approved	KIAA0588, FIB3, PCDH-GAMMA-A12		O60330	OTTHUMG00000129611	ENST00000252085.3:c.1601C>T	5.37:g.140811927C>T	ENSP00000252085:p.Ala534Val	Somatic		Capture	Illumina HiSeq	Phase_I	140792111	NM_032094	O15100|Q6UW70|Q9Y5D7	Missense_Mutation	SNP	ENST00000252085.3	37	CCDS4260.1	.	.	.	.	.	.	.	.	.	.	c	12.89	2.072333	0.36566	.	.	ENSG00000253159	ENST00000252085	T	0.73363	-0.74	5.23	5.23	0.72850	Cadherin (5);Cadherin-like (1);	.	.	.	.	D	0.87224	0.6124	M	0.90082	3.085	0.35553	D	0.804033	D;D	0.89917	0.999;1.0	D;D	0.70016	0.967;0.954	D	0.91456	0.5185	9	0.49607	T	0.09	.	12.6273	0.56636	0.0:0.9133:0.0:0.0867	.	534;534	O60330-2;O60330	.;PCDGC_HUMAN	V	534	ENSP00000252085:A534V	ENSP00000252085:A534V	A	+	2	0	PCDHGA12	140792111	0.437000	0.25593	0.075000	0.20258	0.021000	0.10359	1.108000	0.31123	2.436000	0.82500	0.561000	0.74099	GCG		0.597	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735	
TRIO	7204	broad.mit.edu	37	5	14287023	14287023	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:14287023C>T	ENST00000344204.4	+	4	415	c.391C>T	c.(391-393)Cgt>Tgt	p.R131C	TRIO_ENST00000537187.1_Missense_Mutation_p.R131C|TRIO_ENST00000509967.2_Missense_Mutation_p.R82C	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	131	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				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.R131C(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)					CGTGGACATGCGTGGGTCCAA	0.557																																					p.R131C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C391T	5						.						111.0	98.0	102.0					5																	14287023		2203	4300	6503	14340023	SO:0001583	missense	7204	exon4			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.391C>T	5.37:g.14287023C>T	ENSP00000339299:p.Arg131Cys	Somatic		Capture	Illumina HiSeq	Phase_I	14340023	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Missense_Mutation	SNP	ENST00000344204.4	37	CCDS3883.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.479966	0.84747	.	.	ENSG00000038382	ENST00000344204;ENST00000537187;ENST00000509967	T;T;T	0.64085	-0.08;-0.08;-0.08	5.55	5.55	0.83447	Cellular retinaldehyde-binding/triple function, C-terminal (4);	0.000000	0.85682	D	0.000000	D	0.85762	0.5772	H	0.94964	3.605	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.89374	0.3677	10	0.87932	D	0	.	19.505	0.95111	0.0:1.0:0.0:0.0	.	82;131	F5H228;O75962	.;TRIO_HUMAN	C	131;131;82	ENSP00000339299:R131C;ENSP00000446348:R131C;ENSP00000445592:R82C	ENSP00000339299:R131C	R	+	1	0	TRIO	14340023	1.000000	0.71417	0.999000	0.59377	0.953000	0.61014	7.818000	0.86416	2.616000	0.88540	0.585000	0.79938	CGT		0.557	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118	
FCHSD1	89848	broad.mit.edu	37	5	141029014	141029014	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:141029014C>T	ENST00000435817.2	-	5	373	c.323G>A	c.(322-324)cGt>cAt	p.R108H	FCHSD1_ENST00000519800.1_Missense_Mutation_p.R106H|FCHSD1_ENST00000523856.1_5'Flank|FCHSD1_ENST00000522126.1_Missense_Mutation_p.R32H|FCHSD1_ENST00000522783.1_Missense_Mutation_p.R106H	NM_033449.2	NP_258260.1	Q86WN1	FCSD1_HUMAN	FCH and double SH3 domains 1	108								p.R108H(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)			TGCTAGGTCACGGTATCGGTC	0.642																																					p.R108H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G323A	5						.						112.0	127.0	122.0					5																	141029014		2099	4225	6324	141009198	SO:0001583	missense	89848	exon5			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.323G>A	5.37:g.141029014C>T	ENSP00000399259:p.Arg108His	Somatic		Capture	Illumina HiSeq	Phase_I	141009198	NM_033449	Q6UX75|Q86Y77|Q9NXX8	Missense_Mutation	SNP	ENST00000435817.2	37	CCDS47295.1	.	.	.	.	.	.	.	.	.	.	c	25.1	4.604746	0.87157	.	.	ENSG00000197948	ENST00000435817;ENST00000522126;ENST00000522783;ENST00000519800	T;T;T;T	0.14266	2.52;2.52;2.52;2.52	5.19	5.19	0.71726	.	0.070347	0.52532	D	0.000068	T	0.32315	0.0825	L	0.54323	1.7	0.43118	D	0.994835	D	0.89917	1.0	D	0.71184	0.972	T	0.01844	-1.1262	10	0.59425	D	0.04	-11.8432	15.428	0.75069	0.0:1.0:0.0:0.0	.	108	Q86WN1	FCSD1_HUMAN	H	108;32;106;106	ENSP00000399259:R108H;ENSP00000427796:R32H;ENSP00000428677:R106H;ENSP00000428776:R106H	ENSP00000399259:R108H	R	-	2	0	FCHSD1	141009198	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.309000	0.59135	2.412000	0.81896	0.556000	0.70494	CGT		0.642	FCHSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375282.2	NM_033449	
TCERG1	10915	broad.mit.edu	37	5	145851091	145851091	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:145851091C>A	ENST00000296702.5	+	9	1591	c.1553C>A	c.(1552-1554)gCc>gAc	p.A518D	TCERG1_ENST00000394421.2_Missense_Mutation_p.A497D	NM_006706.3	NP_006697.2	O14776	TCRG1_HUMAN	transcription elongation regulator 1	518					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription coactivator activity (GO:0003713)	p.A518D(1)		breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(18)|lung(9)|ovary(2)|prostate(3)|skin(1)	46		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GAAAAGGCTGCCCAGAAGGCA	0.383																																					p.A497D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1490A	5						.						112.0	117.0	115.0					5																	145851091		2203	4300	6503	145831284	SO:0001583	missense	10915	exon8			AF017789	CCDS4282.1, CCDS43379.1	5q31	2010-01-25	2002-01-24	2002-01-25	ENSG00000113649	ENSG00000113649			15630	protein-coding gene	gene with protein product	"""transcription factor CA150"", ""co-activator of 150 kDa"", ""TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"", ""TATA box-binding protein-associated factor 2S"""	605409	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"""	TAF2S		9315662, 11003711	Standard	XM_005268365		Approved	CA150, Urn1	uc003lob.3	O14776	OTTHUMG00000129683	ENST00000296702.5:c.1553C>A	5.37:g.145851091C>A	ENSP00000296702:p.Ala518Asp	Somatic		Capture	Illumina HiSeq	Phase_I	145831284	NM_001040006	Q2NKN2|Q59EA1	Missense_Mutation	SNP	ENST00000296702.5	37	CCDS4282.1	.	.	.	.	.	.	.	.	.	.	C	33	5.276598	0.95459	.	.	ENSG00000113649	ENST00000296702;ENST00000394421	T;T	0.79454	-1.27;-1.27	5.78	5.78	0.91487	.	0.050481	0.85682	D	0.000000	D	0.86079	0.5847	M	0.71581	2.175	0.80722	D	1	D;D;D	0.63880	0.988;0.993;0.963	P;P;P	0.58620	0.842;0.794;0.527	D	0.84824	0.0798	10	0.42905	T	0.14	-11.232	20.0143	0.97474	0.0:1.0:0.0:0.0	.	497;497;518	B7Z921;O14776-2;O14776	.;.;TCRG1_HUMAN	D	518;497	ENSP00000296702:A518D;ENSP00000377943:A497D	ENSP00000296702:A518D	A	+	2	0	TCERG1	145831284	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.633000	0.83260	2.740000	0.93945	0.313000	0.20887	GCC		0.383	TCERG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251886.1	NM_001040006	
ARHGEF37	389337	broad.mit.edu	37	5	148996287	148996287	+	Missense_Mutation	SNP	G	G	A	rs202046872	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:148996287G>A	ENST00000333677.6	+	5	779	c.616G>A	c.(616-618)Gtg>Atg	p.V206M		NM_001001669.2	NP_001001669.2	A1IGU5	ARH37_HUMAN	Rho guanine nucleotide exchange factor (GEF) 37	206	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.					cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.V206M(1)		large_intestine(5)|lung(6)|ovary(1)|prostate(2)|stomach(3)	17						CCTCCAGGACGTGAACACCAA	0.502													G|||	4	0.000798722	0.0	0.0014	5008	,	,		22998	0.0		0.0	False		,,,				2504	0.0031				p.V206M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G616A	5						.	G	MET/VAL	0,3932		0,0,1966	114.0	108.0	110.0		616	3.6	0.9	5		110	2,8318		0,2,4158	yes	missense	ARHGEF37	NM_001001669.2	21	0,2,6124	AA,AG,GG		0.024,0.0,0.0163	probably-damaging	206/676	148996287	2,12250	1966	4160	6126	148976480	SO:0001583	missense	389337	exon5			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.616G>A	5.37:g.148996287G>A	ENSP00000328083:p.Val206Met	Somatic		Capture	Illumina HiSeq	Phase_I	148976480	NM_001001669	Q6ZW51	Missense_Mutation	SNP	ENST00000333677.6	37	CCDS43385.1	.	.	.	.	.	.	.	.	.	.	G	18.31	3.596140	0.66332	0.0	2.4E-4	ENSG00000183111	ENST00000333677	T	0.68331	-0.32	5.42	3.56	0.40772	Dbl homology (DH) domain (5);	0.203945	0.42420	D	0.000711	T	0.80053	0.4553	M	0.81682	2.555	0.48087	D	0.999586	D	0.89917	1.0	D	0.79784	0.993	T	0.81470	-0.0918	10	0.59425	D	0.04	-6.5766	10.6722	0.45766	0.0716:0.1337:0.7947:0.0	.	206	A1IGU5	ARH37_HUMAN	M	206	ENSP00000328083:V206M	ENSP00000328083:V206M	V	+	1	0	ARHGEF37	148976480	0.989000	0.36119	0.890000	0.34922	0.891000	0.51852	1.816000	0.38992	1.374000	0.46228	0.655000	0.94253	GTG		0.502	ARHGEF37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373763.1	NM_001001669	
NMUR2	56923	broad.mit.edu	37	5	151784441	151784441	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:151784441C>T	ENST00000255262.3	-	1	399	c.234G>A	c.(232-234)acG>acA	p.T78T	NMUR2_ENST00000518933.1_Intron	NM_020167.4	NP_064552.3	Q9GZQ4	NMUR2_HUMAN	neuromedin U receptor 2	78					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|arachidonic acid secretion (GO:0050482)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell-cell signaling (GO:0007267)|central nervous system development (GO:0007417)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|feeding behavior (GO:0007631)|grooming behavior (GO:0007625)|inositol phosphate-mediated signaling (GO:0048016)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|reduction of food intake in response to dietary excess (GO:0002023)|regulation of smooth muscle contraction (GO:0006940)|response to pain (GO:0048265)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|GTP binding (GO:0005525)|intracellular calcium activated chloride channel activity (GO:0005229)|neuromedin U binding (GO:0042924)|neuromedin U receptor activity (GO:0001607)	p.T78T(2)		breast(1)|endometrium(1)|kidney(2)|large_intestine(12)|liver(1)|lung(15)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	44		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)	Kidney(363;0.000106)|KIRC - Kidney renal clear cell carcinoma(527;0.000672)			AGTTGGTGGGCGTCTTCATAG	0.562																																					p.T78T												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G234A	5						.						105.0	102.0	103.0					5																	151784441		2203	4300	6503	151764634	SO:0001819	synonymous_variant	56923	exon1			AF242874	CCDS4321.1	5q33.1	2012-08-08		2004-05-28	ENSG00000132911	ENSG00000132911		"""GPCR / Class A : Neuromedin U receptors"""	16454	protein-coding gene	gene with protein product		605108		NMU2R		8940772, 10894543	Standard	NM_020167		Approved		uc003luv.2	Q9GZQ4	OTTHUMG00000130131	ENST00000255262.3:c.234G>A	5.37:g.151784441C>T		Somatic		Capture	Illumina HiSeq	Phase_I	151764634	NM_020167	Q7LC54|Q96AM5|Q9NRA6	Silent	SNP	ENST00000255262.3	37	CCDS4321.1																																																																																				0.562	NMUR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252439.1	NM_020167	
SGCD	6444	broad.mit.edu	37	5	156184625	156184625	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:156184625G>T	ENST00000435422.3	+	7	1093	c.606G>T	c.(604-606)gaG>gaT	p.E202D	SGCD_ENST00000337851.4_Missense_Mutation_p.E203D|SGCD_ENST00000517913.1_Missense_Mutation_p.E203D|SGCD_ENST00000447401.1_Missense_Mutation_p.E203D	NM_001128209.1	NP_001121681.1	Q92629	SGCD_HUMAN	sarcoglycan, delta (35kDa dystrophin-associated glycoprotein)	202					muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)		p.E203D(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(16)|prostate(1)	24	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TAGTGATGGAGGCCCCAAAAG	0.458																																					p.E203D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G609T	5						.						51.0	51.0	51.0					5																	156184625		1861	4111	5972	156117203	SO:0001583	missense	6444	exon8			BX537948	CCDS47325.1, CCDS47326.1, CCDS47327.1	5q33-q34	2014-09-17	2002-08-29						10807	protein-coding gene	gene with protein product		601411	"""sarcoglycan, delta (35kD dystrophin-associated glycoprotein)"""			8776597, 8841194, 10974018	Standard	NM_000337		Approved	DAGD, LGMD2F, CMD1L	uc003lwd.4	Q92629		ENST00000435422.3:c.606G>T	5.37:g.156184625G>T	ENSP00000403003:p.Glu202Asp	Somatic		Capture	Illumina HiSeq	Phase_I	156117203	NM_172244	A8K9S9|Q53XA5|Q99644	Missense_Mutation	SNP	ENST00000435422.3	37	CCDS47327.1	.	.	.	.	.	.	.	.	.	.	G	14.70	2.614465	0.46631	.	.	ENSG00000170624	ENST00000517913;ENST00000435422;ENST00000337851;ENST00000447401	D;D;D;D	0.94537	-3.45;-3.45;-3.45;-3.45	5.56	0.294	0.15747	.	0.000000	0.85682	D	0.000000	D	0.92453	0.7604	N	0.17723	0.515	0.53005	D	0.999967	D;D;D	0.67145	0.992;0.99;0.996	D;D;D	0.77004	0.989;0.98;0.987	D	0.87291	0.2299	10	0.18276	T	0.48	.	10.2915	0.43599	0.4307:0.0:0.5693:0.0	.	202;203;203	Q92629;Q92629-2;Q92629-3	SGCD_HUMAN;.;.	D	203;202;203;203	ENSP00000429378:E203D;ENSP00000403003:E202D;ENSP00000338343:E203D;ENSP00000408324:E203D	ENSP00000338343:E203D	E	+	3	2	SGCD	156117203	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	0.897000	0.28390	0.110000	0.17919	-0.136000	0.14681	GAG		0.458	SGCD-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000373469.3		
CYFIP2	26999	broad.mit.edu	37	5	156810327	156810327	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:156810327T>C	ENST00000521420.1	+	27	3180	c.3089T>C	c.(3088-3090)cTc>cCc	p.L1030P	CYFIP2_ENST00000347377.6_Missense_Mutation_p.L1056P|CYFIP2_ENST00000377576.3_Missense_Mutation_p.L1056P|CYFIP2_ENST00000435847.2_Missense_Mutation_p.L755P|CYFIP2_ENST00000442283.2_3'UTR|CTB-47B11.3_ENST00000520658.1_RNA|CYFIP2_ENST00000522463.1_Missense_Mutation_p.L860P|CTB-47B11.3_ENST00000508443.1_RNA|CYFIP2_ENST00000541131.1_Missense_Mutation_p.L981P|CYFIP2_ENST00000318218.6_Missense_Mutation_p.L1081P					cytoplasmic FMR1 interacting protein 2									p.L1081P(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)			TATGCCCCGCTCCACCTGGTC	0.542																																					p.L1056P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T3167C	5						.						38.0	40.0	39.0					5																	156810327		1882	4107	5989	156742905	SO:0001583	missense	26999	exon28			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.3089T>C	5.37:g.156810327T>C	ENSP00000430904:p.Leu1030Pro	Somatic		Capture	Illumina HiSeq	Phase_I	156742905	NM_001037333		Missense_Mutation	SNP	ENST00000521420.1	37		.	.	.	.	.	.	.	.	.	.	T	21.0	4.083855	0.76642	.	.	ENSG00000055163	ENST00000318218;ENST00000522463;ENST00000521420;ENST00000347377;ENST00000377576;ENST00000541131;ENST00000435847	T;T;T;T;T;T;T	0.35421	1.31;1.31;1.31;1.31;1.31;1.31;1.31	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.63885	0.2549	M	0.85373	2.75	0.80722	D	1	D;D;D;D;P;D	0.89917	0.96;0.989;0.961;1.0;0.771;0.971	P;D;P;D;P;P	0.76071	0.864;0.981;0.882;0.987;0.485;0.798	T	0.69818	-0.5042	10	0.56958	D	0.05	-7.0949	14.9354	0.70951	0.0:0.0:0.0:1.0	.	920;860;1030;1056;1056;1081	A8MUM2;E7EW33;E7EVJ5;E7EVF4;Q96F07-2;Q96F07	.;.;.;.;.;CYFP2_HUMAN	P	1081;860;1030;1056;1056;981;755	ENSP00000325817:L1081P;ENSP00000428009:L860P;ENSP00000430904:L1030P;ENSP00000313567:L1056P;ENSP00000366799:L1056P;ENSP00000444645:L981P;ENSP00000403793:L755P	ENSP00000325817:L1081P	L	+	2	0	CYFIP2	156742905	1.000000	0.71417	0.810000	0.32431	0.683000	0.39861	7.887000	0.87295	1.921000	0.55644	0.460000	0.39030	CTC		0.542	CYFIP2-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000373710.1	NM_001037332	
MYO10	4651	broad.mit.edu	37	5	16818214	16818214	+	Silent	SNP	G	G	A	rs200910595	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:16818214G>A	ENST00000513610.1	-	3	637	c.183C>T	c.(181-183)aaC>aaT	p.N61N	MYO10_ENST00000507288.1_Silent_p.N61N	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	61					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						CGCCCTCCTCGTTCGTGGGGT	0.458													G|||	7	0.00139776	0.0	0.0	5008	,	,		15440	0.0		0.0	False		,,,				2504	0.0072				p.N61N												.	.	0			c.C183T	5						.	G		5,3973		0,5,1984	70.0	70.0	70.0		183	-8.7	0.0	5		70	1,8305		0,1,4152	no	coding-synonymous	MYO10	NM_012334.2		0,6,6136	AA,AG,GG		0.012,0.1257,0.0488		61/2059	16818214	6,12278	1989	4153	6142	16871214	SO:0001819	synonymous_variant	4651	exon3			AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"""Myosins / Myosin superfamily : Class X"", ""Pleckstrin homology (PH) domain containing"""	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.183C>T	5.37:g.16818214G>A		None		Capture	Illumina HiSeq	Phase_I	16871214	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	37	CCDS54834.1																																																																																				0.458	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334	
TENM2	57451	broad.mit.edu	37	5	167642231	167642231	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:167642231C>T	ENST00000518659.1	+	21	4071	c.4032C>T	c.(4030-4032)tgC>tgT	p.C1344C	TENM2_ENST00000403607.2_Silent_p.C1168C|TENM2_ENST00000545108.1_Silent_p.C1343C|TENM2_ENST00000519204.1_Silent_p.C1223C|TENM2_ENST00000520394.1_Silent_p.C1105C	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	1344					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.C1177C(1)									AAGCCCGCTGCGGGGATGGAG	0.567																																					p.C1335C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4005T	5						.						101.0	106.0	105.0					5																	167642231		1957	4140	6097	167574809	SO:0001819	synonymous_variant	57451	exon21			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.4032C>T	5.37:g.167642231C>T		Somatic		Capture	Illumina HiSeq	Phase_I	167574809	NM_001122679	Q9ULU2	Silent	SNP	ENST00000518659.1	37																																																																																					0.567	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679	
DOCK2	1794	broad.mit.edu	37	5	169472853	169472853	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:169472853C>T	ENST00000256935.8	+	39	3990	c.3910C>T	c.(3910-3912)Ctg>Ttg	p.L1304L	DOCK2_ENST00000540750.1_Silent_p.L365L|DOCK2_ENST00000523351.1_3'UTR|DOCK2_ENST00000520908.1_Silent_p.L796L	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1304	DHR-2.|Interaction with CRKL.				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.L1304L(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)			GTGCAAGGAGCTGGCGGAACA	0.567																																					p.L1304L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3910T	5						.						188.0	167.0	174.0					5																	169472853		2203	4300	6503	169405431	SO:0001819	synonymous_variant	1794	exon39			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.3910C>T	5.37:g.169472853C>T		Somatic		Capture	Illumina HiSeq	Phase_I	169405431	NM_004946	Q2M3I0|Q96AK7	Silent	SNP	ENST00000256935.8	37	CCDS4371.1																																																																																				0.567	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946	
BOD1	91272	broad.mit.edu	37	5	173036273	173036273	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:173036273T>C	ENST00000311086.4	-	3	750	c.527A>G	c.(526-528)gAc>gGc	p.D176G	BOD1_ENST00000285908.5_Intron|BOD1_ENST00000471339.1_5'Flank|BOD1_ENST00000480951.1_Intron	NM_138369.2	NP_612378.1	Q96IK1	BOD1_HUMAN	biorientation of chromosomes in cell division 1	176					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|kinetochore (GO:0000776)		p.D176G(1)		endometrium(1)|large_intestine(2)|lung(2)|ovary(2)	7						AGCTGGAGGGTCCTGGCCTTC	0.512																																					p.D176G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A527G	5						.						97.0	94.0	95.0					5																	173036273		2203	4300	6503	172968879	SO:0001583	missense	91272	exon3			AY303777	CCDS4389.1, CCDS54951.1	5q35.2	2013-10-11	2009-03-04	2009-03-04	ENSG00000145919	ENSG00000145919			25114	protein-coding gene	gene with protein product	"""biorientation defective 1"""		"""family with sequence similarity 44, member B"""	FAM44B		17938248	Standard	NM_138369		Approved		uc003mcq.2	Q96IK1	OTTHUMG00000130540	ENST00000311086.4:c.527A>G	5.37:g.173036273T>C	ENSP00000309644:p.Asp176Gly	Somatic		Capture	Illumina HiSeq	Phase_I	172968879	NM_138369	B4DXH8|Q9BTW1	Missense_Mutation	SNP	ENST00000311086.4	37	CCDS4389.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.124932	0.77436	.	.	ENSG00000145919	ENST00000311086	.	.	.	5.86	4.63	0.57726	.	0.156460	0.56097	D	0.000022	T	0.42698	0.1214	N	0.19112	0.55	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.38222	-0.9671	9	0.56958	D	0.05	-19.8745	12.7596	0.57356	0.0:0.0:0.1367:0.8633	.	176	Q96IK1	BOD1_HUMAN	G	176	.	ENSP00000309644:D176G	D	-	2	0	BOD1	172968879	1.000000	0.71417	0.989000	0.46669	0.916000	0.54674	4.381000	0.59587	2.241000	0.73720	0.533000	0.62120	GAC		0.512	BOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252963.1	NM_138369	
SFXN1	94081	broad.mit.edu	37	5	174937118	174937118	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:174937118G>A	ENST00000321442.5	+	4	596	c.342G>A	c.(340-342)acG>acA	p.T114T	SFXN1_ENST00000502393.1_Silent_p.T114T	NM_022754.5	NP_073591.2	Q9H9B4	SFXN1_HUMAN	sideroflexin 1	114					erythrocyte differentiation (GO:0030218)|iron ion homeostasis (GO:0055072)|iron ion transport (GO:0006826)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)	p.T114T(1)		endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|skin(3)	15	all_cancers(89;0.00922)|Renal(175;0.000269)|Lung NSC(126;0.00515)|all_lung(126;0.00873)	Medulloblastoma(196;0.0399)|all_neural(177;0.0663)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			TTAGGACTACGCCGGCTGTGC	0.542																																					p.T114T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G342A	5						.						169.0	122.0	138.0					5																	174937118		2203	4300	6503	174869724	SO:0001819	synonymous_variant	94081	exon4			AF327346	CCDS4394.1	5q35.3	2008-02-05			ENSG00000164466	ENSG00000164466		"""Sideroflexins"""	16085	protein-coding gene	gene with protein product		615569					Standard	NM_022754		Approved	FLJ12876	uc003mda.2	Q9H9B4	OTTHUMG00000130555	ENST00000321442.5:c.342G>A	5.37:g.174937118G>A		Somatic		Capture	Illumina HiSeq	Phase_I	174869724	NM_022754	B3KPW3|D3DQN2|Q9HA53	Silent	SNP	ENST00000321442.5	37	CCDS4394.1																																																																																				0.542	SFXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252980.2	NM_022754	
PROP1	5626	broad.mit.edu	37	5	177422915	177422915	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:177422915C>T	ENST00000308304.2	-	1	328	c.20G>A	c.(19-21)cGc>cAc	p.R7H		NM_006261.4	NP_006252	O75360	PROP1_HUMAN	PROP paired-like homeobox 1	7					blood vessel development (GO:0001568)|canonical Wnt signaling pathway (GO:0060070)|cell migration (GO:0016477)|central nervous system development (GO:0007417)|dorsal/ventral pattern formation (GO:0009953)|hypophysis morphogenesis (GO:0048850)|hypothalamus cell differentiation (GO:0021979)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|somatotropin secreting cell differentiation (GO:0060126)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)	p.R7H(1)		endometrium(1)|large_intestine(2)|lung(9)|stomach(1)	13	all_cancers(89;0.00176)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	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)			CTCAGCCTGGCGCCTCCTTTC	0.617																																					p.R7H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G20A	5						.						74.0	65.0	68.0					5																	177422915		2203	4300	6503	177355521	SO:0001583	missense	5626	exon1			AF076215	CCDS4430.1	5q35.3	2011-06-20	2007-07-12		ENSG00000175325	ENSG00000175325		"""Homeoboxes / PRD class"""	9455	protein-coding gene	gene with protein product		601538	"""prophet of Pit1, paired-like homeodomain transcription factor"""			9462743	Standard	NM_006261		Approved		uc003mif.1	O75360	OTTHUMG00000130887	ENST00000308304.2:c.20G>A	5.37:g.177422915C>T	ENSP00000311290:p.Arg7His	Somatic		Capture	Illumina HiSeq	Phase_I	177355521	NM_006261		Missense_Mutation	SNP	ENST00000308304.2	37	CCDS4430.1	.	.	.	.	.	.	.	.	.	.	.	9.395	1.076529	0.20227	.	.	ENSG00000175325	ENST00000308304	D	0.89050	-2.46	2.12	1.2	0.21068	.	1.042410	0.07632	N	0.928852	T	0.76176	0.3951	N	0.14661	0.345	0.09310	N	1	P	0.37708	0.606	B	0.29176	0.099	T	0.66674	-0.5864	10	0.54805	T	0.06	1.7359	6.5442	0.22397	0.0:0.696:0.304:0.0	.	7	O75360	PROP1_HUMAN	H	7	ENSP00000311290:R7H	ENSP00000311290:R7H	R	-	2	0	PROP1	177355521	0.000000	0.05858	0.001000	0.08648	0.018000	0.09664	-1.049000	0.03514	0.452000	0.26830	0.561000	0.74099	CGC		0.617	PROP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253472.1	NM_006261	
GRM6	2916	broad.mit.edu	37	5	178416347	178416347	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:178416347C>T	ENST00000517717.1	-	6	1110	c.1072G>A	c.(1072-1074)Gcc>Acc	p.A358T	RP11-281O15.4_ENST00000519491.1_RNA|GRM6_ENST00000231188.5_Missense_Mutation_p.A358T			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6	358					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|detection of light stimulus involved in visual perception (GO:0050908)|detection of visible light (GO:0009584)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|locomotory behavior (GO:0007626)|positive regulation of calcium ion import (GO:0090280)|regulation of synaptic transmission, glutamatergic (GO:0051966)|retina development in camera-type eye (GO:0060041)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|new growing cell tip (GO:0035841)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|protein homodimerization activity (GO:0042803)	p.A358T(1)		NS(2)|breast(4)|endometrium(9)|large_intestine(12)|lung(21)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	55	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|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)	all cancers(165;0.245)		CAGAACTCGGCGAACCAGATG	0.547																																					p.A358T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1072A	5						.						104.0	103.0	103.0					5																	178416347		2203	4300	6503	178348953	SO:0001583	missense	2916	exon5			U82083	CCDS4442.1	5q35	2014-01-28						"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4598	protein-coding gene	gene with protein product		604096				9215706	Standard	NM_000843		Approved	GPRC1F, mGlu6, MGLUR6, CSNB1B	uc003mjr.3	O15303	OTTHUMG00000130889	ENST00000517717.1:c.1072G>A	5.37:g.178416347C>T	ENSP00000430767:p.Ala358Thr	Somatic		Capture	Illumina HiSeq	Phase_I	178348953	NM_000843		Missense_Mutation	SNP	ENST00000517717.1	37	CCDS4442.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.467955	0.84533	.	.	ENSG00000113262	ENST00000319065;ENST00000231188;ENST00000517717	D;D	0.86297	-2.1;-2.1	5.07	5.07	0.68467	Extracellular ligand-binding receptor (1);	.	.	.	.	D	0.85164	0.5634	M	0.69358	2.11	0.53005	D	0.999966	B	0.27316	0.175	B	0.21708	0.036	T	0.81775	-0.0778	9	0.23302	T	0.38	.	16.3378	0.83071	0.0:1.0:0.0:0.0	.	358	O15303	GRM6_HUMAN	T	390;358;358	ENSP00000231188:A358T;ENSP00000430767:A358T	ENSP00000231188:A358T	A	-	1	0	GRM6	178348953	1.000000	0.71417	0.588000	0.28705	0.790000	0.44656	3.960000	0.56752	2.518000	0.84900	0.655000	0.94253	GCC		0.547	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2		
AHRR	57491	broad.mit.edu	37	5	434432	434432	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:434432C>T	ENST00000505113.1	+	11	1633	c.1589C>T	c.(1588-1590)aCg>aTg	p.T530M	AHRR_ENST00000506456.1_Missense_Mutation_p.T386M|AHRR_ENST00000512529.1_Missense_Mutation_p.T376M|AHRR_ENST00000316418.5_Missense_Mutation_p.T548M	NM_001242412.1	NP_001229341.1	A9YTQ3	AHRR_HUMAN	aryl-hydrocarbon receptor repressor	530					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of protein sumoylation (GO:0033235)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)	p.T544M(1)		breast(2)|endometrium(4)|large_intestine(1)|lung(12)|prostate(1)	20			Epithelial(17;0.0011)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00354)|Lung(60;0.0863)			TGTGGTCCGACGCTGCTGCTA	0.622																																					p.T548M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1643T	5						.						75.0	84.0	81.0					5																	434432		2203	4299	6502	487432	SO:0001583	missense	57491	exon12			AB033060	CCDS43297.1, CCDS56355.1	5p15.33	2013-05-21	2003-09-11	2003-09-12	ENSG00000063438	ENSG00000063438		"""Basic helix-loop-helix proteins"""	346	protein-coding gene	gene with protein product		606517	"""aryl hydrocarbon receptor regulator"""	AHH, AHHR		1070014, 11423533	Standard	NM_020731		Approved	KIAA1234, bHLHe77	uc003jaw.3	A9YTQ3	OTTHUMG00000162171	ENST00000505113.1:c.1589C>T	5.37:g.434432C>T	ENSP00000424601:p.Thr530Met	Somatic		Capture	Illumina HiSeq	Phase_I	487432	NM_020731	A7MBN5|D6RAZ1|Q9HAZ3|Q9ULI6	Missense_Mutation	SNP	ENST00000505113.1	37	CCDS56355.1	.	.	.	.	.	.	.	.	.	.	C	6.903	0.536094	0.13188	.	.	ENSG00000063438	ENST00000505113;ENST00000316418;ENST00000512529;ENST00000506456;ENST00000511487	T;T;T;T;T	0.39406	2.35;2.34;2.02;2.02;1.08	4.17	0.0868	0.14448	.	1.341060	0.04546	N	0.388964	T	0.19886	0.0478	N	0.04508	-0.205	0.09310	N	1	B;B;B	0.22604	0.029;0.043;0.072	B;B;B	0.09377	0.003;0.002;0.004	T	0.13308	-1.0514	10	0.33141	T	0.24	.	4.3219	0.11022	0.0:0.2999:0.1698:0.5303	.	386;530;548	D6RE68;A9YTQ3;A9YTQ3-2	.;AHRR_HUMAN;.	M	530;548;376;386;185	ENSP00000424601:T530M;ENSP00000323816:T548M;ENSP00000424880:T376M;ENSP00000426932:T386M;ENSP00000426076:T185M	ENSP00000323816:T548M	T	+	2	0	AHRR	487432	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.420000	0.21263	-0.158000	0.11040	0.549000	0.68633	ACG		0.622	AHRR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367720.1	NM_020731	
SLC9A3	6550	broad.mit.edu	37	5	476449	476449	+	Silent	SNP	G	G	A	rs558562725		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:476449G>A	ENST00000264938.3	-	13	1944	c.1935C>T	c.(1933-1935)gaC>gaT	p.D645D	CTD-2228K2.7_ENST00000607286.1_RNA|SLC9A3_ENST00000514375.1_Silent_p.D636D|CTD-2228K2.7_ENST00000606288.1_RNA|CTD-2228K2.7_ENST00000606319.1_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	645	Interaction with PDZD3. {ECO:0000250}.				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.D645D(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)			CCTGTTTCTCGTCCTCCGTGG	0.612													g|||	1	0.000199681	0.0	0.0	5008	,	,		16843	0.001		0.0	False		,,,				2504	0.0				p.D645D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1935T	5						.						127.0	123.0	124.0					5																	476449		2203	4300	6503	529449	SO:0001819	synonymous_variant	6550	exon13				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.1935C>T	5.37:g.476449G>A		Somatic		Capture	Illumina HiSeq	Phase_I	529449	NM_004174	B7ZKR2|E9PF67|Q3MIW3	Silent	SNP	ENST00000264938.3	37	CCDS3855.1																																																																																				0.612	SLC9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206677.2	NM_004174	
ADCY2	108	broad.mit.edu	37	5	7817087	7817087	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:7817087C>T	ENST00000338316.4	+	23	3081	c.2992C>T	c.(2992-2994)Cga>Tga	p.R998*	ADCY2_ENST00000537121.1_Nonsense_Mutation_p.R818*	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	998					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)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)	p.R998*(1)		NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						CTTCAAATTGCGAGTGGGTAC	0.478											OREG0016499	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R998X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2992T	5						.						184.0	136.0	153.0					5																	7817087		2203	4300	6503	7870087	SO:0001587	stop_gained	108	exon23			AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"""Adenylate cyclases"""	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.2992C>T	5.37:g.7817087C>T	ENSP00000342952:p.Arg998*	Somatic	644	Capture	Illumina HiSeq	Phase_I	7870087	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Nonsense_Mutation	SNP	ENST00000338316.4	37	CCDS3872.2	.	.	.	.	.	.	.	.	.	.	C	40	7.988714	0.98596	.	.	ENSG00000078295	ENST00000338316;ENST00000382532;ENST00000541993;ENST00000537121	.	.	.	5.6	4.7	0.59300	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.8655	0.79060	0.1361:0.8639:0.0:0.0	.	.	.	.	X	998;151;831;818	.	ENSP00000342952:R998X	R	+	1	2	ADCY2	7870087	0.052000	0.20516	1.000000	0.80357	0.739000	0.42172	0.411000	0.21115	2.652000	0.90054	0.561000	0.74099	CGA		0.478	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546	
CDH6	1004	broad.mit.edu	37	5	31323111	31323111	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:31323111G>T	ENST00000265071.2	+	12	2334	c.2069G>T	c.(2068-2070)aGg>aTg	p.R690M		NM_004932.3	NP_004923.1	P55285	CADH6_HUMAN	cadherin 6, type 2, K-cadherin (fetal kidney)	690					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.R690M(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						AAATTACGAAGGGACATTGTG	0.498																																					p.R690M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2069T	5						.						89.0	82.0	85.0					5																	31323111		2203	4300	6503	31358868	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.2069G>T	5.37:g.31323111G>T	ENSP00000265071:p.Arg690Met	Somatic		Capture	Illumina HiSeq	Phase_I	31358868	NM_004932	A8K5H5|Q9BWS0	Missense_Mutation	SNP	ENST00000265071.2	37	CCDS3894.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.744767	0.89663	.	.	ENSG00000113361	ENST00000265071	T	0.78246	-1.16	5.52	5.52	0.82312	Cadherin, cytoplasmic domain (1);	0.000000	0.85682	D	0.000000	D	0.88559	0.6469	M	0.74881	2.28	0.58432	D	0.999999	D	0.89917	1.0	D	0.83275	0.996	D	0.89052	0.3456	10	0.87932	D	0	.	19.8024	0.96513	0.0:0.0:1.0:0.0	.	690	P55285	CADH6_HUMAN	M	690	ENSP00000265071:R690M	ENSP00000265071:R690M	R	+	2	0	CDH6	31358868	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	9.328000	0.96403	2.752000	0.94435	0.655000	0.94253	AGG		0.498	CDH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207355.2	NM_004932	
ADAMTS12	81792	broad.mit.edu	37	5	33588882	33588882	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:33588882G>A	ENST00000504830.1	-	18	3022	c.2687C>T	c.(2686-2688)gCg>gTg	p.A896V	ADAMTS12_ENST00000352040.3_Missense_Mutation_p.A811V|ADAMTS12_ENST00000504582.1_5'UTR	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	896	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.A896V(1)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						CCCGCATGTCGCCGAGCATGC	0.592										HNSCC(64;0.19)	OREG0016553	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A896V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2687T	5						.						76.0	69.0	72.0					5																	33588882		2203	4300	6503	33624639	SO:0001583	missense	81792	exon18			AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14605	protein-coding gene	gene with protein product		606184	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"""			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.2687C>T	5.37:g.33588882G>A	ENSP00000422554:p.Ala896Val	Somatic	841	Capture	Illumina HiSeq	Phase_I	33624639	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	37	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	G	7.211	0.595455	0.13875	.	.	ENSG00000151388	ENST00000504830;ENST00000352040	T;T	0.34667	1.35;1.35	5.98	3.17	0.36434	.	0.503424	0.24245	N	0.040237	T	0.19525	0.0469	N	0.17594	0.5	0.35047	D	0.760271	B;B	0.27351	0.176;0.083	B;B	0.23150	0.039;0.044	T	0.19745	-1.0296	10	0.22109	T	0.4	.	8.937	0.35706	0.1292:0.0:0.7481:0.1226	.	811;896	P58397-3;P58397	.;ATS12_HUMAN	V	896;811	ENSP00000422554:A896V;ENSP00000344847:A811V	ENSP00000344847:A811V	A	-	2	0	ADAMTS12	33624639	0.607000	0.26958	0.000000	0.03702	0.075000	0.17131	3.311000	0.51919	0.379000	0.24794	0.591000	0.81541	GCG		0.592	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955	
TTC23L	153657	broad.mit.edu	37	5	34867155	34867155	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:34867155C>A	ENST00000505624.1	+	7	924	c.821C>A	c.(820-822)gCc>gAc	p.A274D	TTC23L_ENST00000514080.1_3'UTR	NM_144725.3	NP_653326.3	Q6PF05	TT23L_HUMAN	tetratricopeptide repeat domain 23-like	274								p.A274D(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(9)|prostate(2)|stomach(1)|urinary_tract(1)	22						CACAACCAGGCCATCCAGTAC	0.582																																					p.A274D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C821A	5						.						36.0	39.0	38.0					5																	34867155		1982	4149	6131	34902912	SO:0001583	missense	153657	exon7				CCDS54840.1	5p13.2	2008-07-14			ENSG00000205838	ENSG00000205838			26355	protein-coding gene	gene with protein product						12477932	Standard	NM_144725		Approved	FLJ25439	uc003jiu.3	Q6PF05	OTTHUMG00000162020	ENST00000505624.1:c.821C>A	5.37:g.34867155C>A	ENSP00000422188:p.Ala274Asp	Somatic		Capture	Illumina HiSeq	Phase_I	34902912	NM_144725	Q6RGS4|Q8N7R3|Q96LJ2	Missense_Mutation	SNP	ENST00000505624.1	37	CCDS54840.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.033669	0.75504	.	.	ENSG00000205838	ENST00000505624;ENST00000535797	D	0.92397	-3.03	5.28	4.39	0.52855	Tetratricopeptide-like helical (1);	0.059695	0.64402	D	0.000003	D	0.95357	0.8493	M	0.71581	2.175	0.42377	D	0.992478	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.95920	0.8930	10	0.87932	D	0	-21.2886	14.5812	0.68292	0.0:0.8526:0.1474:0.0	.	274;205;274	Q6PF05-2;B4DEX1;Q6PF05	.;.;TT23L_HUMAN	D	274	ENSP00000422188:A274D	ENSP00000425242:A274D	A	+	2	0	TTC23L	34902912	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	2.572000	0.45999	1.384000	0.46424	0.655000	0.94253	GCC		0.582	TTC23L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366819.1	NM_144725	
LMBRD2	92255	broad.mit.edu	37	5	36122432	36122432	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:36122432G>T	ENST00000296603.4	-	9	1532	c.1070C>A	c.(1069-1071)tCg>tAg	p.S357*		NM_001007527.1	NP_001007528.1	Q68DH5	LMBD2_HUMAN	LMBR1 domain containing 2	357						integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.S357*(1)		breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_lung(31;0.000146)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TGGCTCTGGCGATTGAAAGGT	0.303																																					p.S357X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1070A	5						.						101.0	101.0	101.0					5																	36122432		2203	4300	6503	36158189	SO:0001587	stop_gained	92255	exon9				CCDS34145.1	5p13.2	2008-02-05			ENSG00000164187	ENSG00000164187			25287	protein-coding gene	gene with protein product							Standard	NM_001007527		Approved	DKFZp434H2226	uc003jkb.1	Q68DH5	OTTHUMG00000162150	ENST00000296603.4:c.1070C>A	5.37:g.36122432G>T	ENSP00000296603:p.Ser357*	Somatic		Capture	Illumina HiSeq	Phase_I	36158189	NM_001007527	B3KRB6|Q9NTC7	Nonsense_Mutation	SNP	ENST00000296603.4	37	CCDS34145.1	.	.	.	.	.	.	.	.	.	.	G	41	8.627336	0.98890	.	.	ENSG00000164187	ENST00000296603;ENST00000546130	.	.	.	5.69	5.69	0.88448	.	0.322050	0.29715	N	0.011383	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	-3.1663	14.642	0.68732	0.0:0.0:0.8546:0.1454	.	.	.	.	X	357;251	.	ENSP00000296603:S357X	S	-	2	0	LMBRD2	36158189	0.986000	0.35501	0.221000	0.23827	0.898000	0.52572	5.014000	0.64029	2.657000	0.90304	0.650000	0.86243	TCG		0.303	LMBRD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367552.1	NM_001007527	
PRKAA1	5562	broad.mit.edu	37	5	40777678	40777678	+	Silent	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:40777678A>G	ENST00000397128.2	-	2	146	c.138T>C	c.(136-138)caT>caC	p.H46H	PRKAA1_ENST00000296800.4_Silent_p.H37H|PRKAA1_ENST00000354209.3_Silent_p.H46H	NM_006251.5|NM_206907.3	NP_006242.5|NP_996790.3	Q13131	AAPK1_HUMAN	protein kinase, AMP-activated, alpha 1 catalytic subunit	46	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|cell cycle arrest (GO:0007050)|cellular response to ethanol (GO:0071361)|cellular response to glucose starvation (GO:0042149)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|cholesterol biosynthetic process (GO:0006695)|cold acclimation (GO:0009631)|fatty acid biosynthetic process (GO:0006633)|fatty acid homeostasis (GO:0055089)|fatty acid oxidation (GO:0019395)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glucose import in response to insulin stimulus (GO:2001274)|negative regulation of glucosylceramide biosynthetic process (GO:0046318)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of gene expression (GO:0010628)|positive regulation of glycolytic process (GO:0045821)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|regulation of energy homeostasis (GO:2000505)|regulation of transcription, DNA-templated (GO:0006355)|regulation of vesicle-mediated transport (GO:0060627)|response to activity (GO:0014823)|response to caffeine (GO:0031000)|response to camptothecin (GO:1901563)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	AMP-activated protein kinase complex (GO:0031588)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)	[acetyl-CoA carboxylase] kinase activity (GO:0050405)|[hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity (GO:0047322)|AMP-activated protein kinase activity (GO:0004679)|ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|chromatin binding (GO:0003682)|histone serine kinase activity (GO:0035174)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|tau-protein kinase activity (GO:0050321)	p.H46H(1)		breast(1)	1					Acetylsalicylic acid(DB00945)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Phenformin(DB00914)	CAGTCAATTCATGTTTGCCAA	0.378																																					p.H46H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T138C	5						.						57.0	54.0	55.0					5																	40777678		1817	4077	5894	40813435	SO:0001819	synonymous_variant	5562	exon2				CCDS3932.2, CCDS3933.2	5p13.1	2012-10-03			ENSG00000132356	ENSG00000132356			9376	protein-coding gene	gene with protein product	"""AMPK, alpha, 1"""	602739				8557660	Standard	XM_006714481		Approved	AMPKa1	uc003jmb.3	Q13131	OTTHUMG00000162269	ENST00000397128.2:c.138T>C	5.37:g.40777678A>G		Somatic		Capture	Illumina HiSeq	Phase_I	40813435	NM_006251	A8MTQ6|B2R7E1|O00286|Q5D0E1|Q86VS1|Q9UNQ4	Silent	SNP	ENST00000397128.2	37	CCDS3932.2																																																																																				0.378	PRKAA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253833.2	NM_006251	
PARP8	79668	broad.mit.edu	37	5	50084395	50084395	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:50084395C>T	ENST00000281631.5	+	10	867	c.709C>T	c.(709-711)Cga>Tga	p.R237*	PARP8_ENST00000505554.1_Nonsense_Mutation_p.R216*|PARP8_ENST00000503750.2_Nonsense_Mutation_p.R237*|PARP8_ENST00000511363.2_3'UTR|PARP8_ENST00000514067.2_Nonsense_Mutation_p.R237*|PARP8_ENST00000505697.2_Nonsense_Mutation_p.R237*|PARP8_ENST00000514342.2_5'UTR	NM_001178056.1|NM_024615.3	NP_001171527.1|NP_078891.2	Q8N3A8	PARP8_HUMAN	poly (ADP-ribose) polymerase family, member 8	237						intracellular (GO:0005622)	NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.R237*(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Lung NSC(810;0.0305)|Breast(144;0.222)				CACAAAAGAGCGATTTGGATT	0.363																																					p.R237X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C709T	5						.						128.0	109.0	115.0					5																	50084395		2203	4300	6503	50120152	SO:0001587	stop_gained	79668	exon11			AL834477	CCDS3954.1, CCDS54849.1	5q11.2	2010-02-16			ENSG00000151883	ENSG00000151883		"""Poly (ADP-ribose) polymerases"""	26124	protein-coding gene	gene with protein product						15273990	Standard	NM_001178055		Approved	FLJ21308, pART16	uc003joo.3	Q8N3A8	OTTHUMG00000096969	ENST00000281631.5:c.709C>T	5.37:g.50084395C>T	ENSP00000281631:p.Arg237*	Somatic		Capture	Illumina HiSeq	Phase_I	50120152	NM_001178055	Q3KRB7|Q6DHZ1|Q9H754	Nonsense_Mutation	SNP	ENST00000281631.5	37	CCDS3954.1	.	.	.	.	.	.	.	.	.	.	C	37	6.488727	0.97607	.	.	ENSG00000151883	ENST00000505697;ENST00000503750;ENST00000281631;ENST00000514067;ENST00000505554	.	.	.	5.44	3.34	0.38264	.	0.060114	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-10.2493	11.6833	0.51470	0.5685:0.4315:0.0:0.0	.	.	.	.	X	237;237;237;237;216	.	.	R	+	1	2	PARP8	50120152	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.033000	0.41136	1.399000	0.46721	0.561000	0.74099	CGA		0.363	PARP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214035.3	NM_024615	
PELO	53918	broad.mit.edu	37	5	52097435	52097435	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:52097435G>A	ENST00000274311.2	+	3	1904	c.919G>A	c.(919-921)Gca>Aca	p.A307T	ITGA1_ENST00000282588.6_Intron|ITGA1_ENST00000504086.1_Intron|PELO_ENST00000506949.1_3'UTR	NM_015946.4	NP_057030.3	Q9BRX2	PELO_HUMAN	pelota homolog (Drosophila)	307					cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|chromosome organization (GO:0051276)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|nuclear-transcribed mRNA catabolic process, non-stop decay (GO:0070481)|RNA surveillance (GO:0071025)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)	11		Lung NSC(810;4.94e-05)|Breast(144;0.0848)				TGAAGCCATGGCAATTGACAC	0.493																																					p.A307T												.	.	0			c.G919A	5						.						97.0	83.0	87.0					5																	52097435		2203	4300	6503	52133192	SO:0001583	missense	53918	exon3				CCDS3956.1	5q11.2	2008-07-18	2001-11-28		ENSG00000152684	ENSG00000152684			8829	protein-coding gene	gene with protein product		605757	"""pelota (Drosophila) homolog"""			11060452	Standard	NM_015946		Approved		uc003jos.3	Q9BRX2	OTTHUMG00000096973	ENST00000274311.2:c.919G>A	5.37:g.52097435G>A	ENSP00000274311:p.Ala307Thr	None		Capture	Illumina HiSeq	Phase_I	52133192	NM_015946	Q9GZS6|Q9Y306	Missense_Mutation	SNP	ENST00000274311.2	37	CCDS3956.1	.	.	.	.	.	.	.	.	.	.	G	33	5.246016	0.95272	.	.	ENSG00000152684	ENST00000274311	T	0.74842	-0.88	5.91	5.91	0.95273	eRF1 domain 3 (1);	0.000000	0.85682	U	0.000000	D	0.92338	0.7569	H	0.98370	4.215	0.80722	D	1	D	0.71674	0.998	D	0.79108	0.992	D	0.94636	0.7826	10	0.87932	D	0	-7.6461	19.9	0.96981	0.0:0.0:1.0:0.0	.	307	Q9BRX2	PELO_HUMAN	T	307	ENSP00000274311:A307T	ENSP00000274311:A307T	A	+	1	0	PELO	52133192	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.609000	0.90898	2.794000	0.96219	0.655000	0.94253	GCA		0.493	PELO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214040.1	NM_015946	
SNX18	112574	broad.mit.edu	37	5	53839138	53839138	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:53839138T>C	ENST00000381410.4	+	2	1941	c.1751T>C	c.(1750-1752)tTc>tCc	p.F584S	SNX18_ENST00000343017.6_3'UTR	NM_001102575.1	NP_001096045.1	Q96RF0	SNX18_HUMAN	sorting nexin 18	0	BAR.				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.F584S(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)				ATTCACCACTTCCATCAAATT	0.418																																					p.F584S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1751C	5						.						97.0	96.0	96.0					5																	53839138		1942	4129	6071	53874895	SO:0001583	missense	112574	exon2			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	ENST00000381410.4:c.1751T>C	5.37:g.53839138T>C	ENSP00000370817:p.Phe584Ser	Somatic		Capture	Illumina HiSeq	Phase_I	53874895	NM_001102575	B4E2B3|H7BXX3|Q05BB3|Q0VG02	Missense_Mutation	SNP	ENST00000381410.4	37	CCDS43317.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.124617	0.77436	.	.	ENSG00000178996	ENST00000381410	T	0.24538	1.85	5.72	5.72	0.89469	.	.	.	.	.	T	0.53126	0.1777	.	.	.	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	T	0.58188	-0.7680	8	0.87932	D	0	.	16.0101	0.80396	0.0:0.0:0.0:1.0	.	584	Q96RF0-2	.	S	584	ENSP00000370817:F584S	ENSP00000370817:F584S	F	+	2	0	SNX18	53874895	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.683000	0.84093	2.171000	0.68590	0.533000	0.62120	TTC		0.418	SNX18-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214073.2		
HTR1A	3350	broad.mit.edu	37	5	63256686	63256686	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:63256686G>A	ENST00000323865.3	-	1	1094	c.861C>T	c.(859-861)ggC>ggT	p.G287G	RP11-158J3.2_ENST00000502882.1_RNA	NM_000524.3	NP_000515.2	P08908	5HT1A_HUMAN	5-hydroxytryptamine (serotonin) receptor 1A, G protein-coupled	287					adenylate cyclase-inhibiting serotonin receptor signaling pathway (GO:0007198)|behavioral fear response (GO:0001662)|cell proliferation (GO:0008283)|exploration behavior (GO:0035640)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cell proliferation (GO:0008284)|regulation of behavior (GO:0050795)|regulation of dopamine metabolic process (GO:0042053)|regulation of hormone secretion (GO:0046883)|regulation of serotonin secretion (GO:0014062)|serotonin metabolic process (GO:0042428)|serotonin receptor signaling pathway (GO:0007210)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin receptor activity (GO:0004993)	p.G287G(1)		cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(29)|ovary(2)|pancreas(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	56		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0575)|Colorectal(97;0.234)		Lung(70;0.105)	Acepromazine(DB01614)|Alprenolol(DB00866)|Alverine(DB01616)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bopindolol(DB08807)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinitapride(DB08810)|Clozapine(DB00363)|Desipramine(DB01151)|Dopamine(DB00988)|Doxepin(DB01142)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Methysergide(DB00247)|Mianserin(DB06148)|Molindone(DB01618)|Naratriptan(DB00952)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Ondansetron(DB00904)|Paliperidone(DB01267)|Penbutolol(DB01359)|Pergolide(DB01186)|Pindolol(DB00960)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Propranolol(DB00571)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sumatriptan(DB00669)|Thioproperazine(DB01622)|Trazodone(DB00656)|Trimipramine(DB00726)|Vilazodone(DB06684)|Yohimbine(DB01392)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)	CCAGGGCGGCGCCATCGTCAC	0.657																																					p.G287G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C861T	5						.						42.0	39.0	40.0					5																	63256686		2203	4300	6503	63292442	SO:0001819	synonymous_variant	3350	exon1			AF498978	CCDS34168.1	5q11.2-q13	2012-08-08	2012-02-03			ENSG00000178394		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5286	protein-coding gene	gene with protein product		109760	"""5-hydroxytryptamine (serotonin) receptor 1A"""	ADRB2RL1, ADRBRL1		2591972, 12969265	Standard	NM_000524		Approved	5-HT1A	uc011cqt.3	P08908		ENST00000323865.3:c.861C>T	5.37:g.63256686G>A		Somatic		Capture	Illumina HiSeq	Phase_I	63292442	NM_000524	Q6LAE7	Silent	SNP	ENST00000323865.3	37	CCDS34168.1																																																																																				0.657	HTR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368397.1	NM_000524	
TRIM23	373	broad.mit.edu	37	5	64910016	64910016	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:64910016T>A	ENST00000231524.9	-	3	646	c.275A>T	c.(274-276)aAt>aTt	p.N92I	TRIM23_ENST00000381018.3_Missense_Mutation_p.N92I|TRIM23_ENST00000274327.7_Missense_Mutation_p.N92I	NM_001656.3	NP_001647.1	P36406	TRI23_HUMAN	tripartite motif containing 23	92					GTP catabolic process (GO:0006184)|positive regulation of catalytic activity (GO:0043085)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	enzyme activator activity (GO:0008047)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.N92I(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	28		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Breast(144;0.0433)|Ovarian(174;0.0545)|Colorectal(97;0.234)		Lung(70;0.00473)		TAAAGCAAAATTTTTTTTCAA	0.358																																					p.N92I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A275T	5						.						99.0	105.0	103.0					5																	64910016		2203	4300	6503	64945772	SO:0001583	missense	373	exon3			L04510	CCDS3986.1, CCDS3987.1, CCDS43322.1	5q12.3	2013-01-09	2011-01-25	2004-06-04	ENSG00000113595	ENSG00000113595		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	660	protein-coding gene	gene with protein product		601747	"""ADP-ribosylation factor domain protein 1, 64kDa"", ""tripartite motif-containing 23"""	ARFD1		8473324	Standard	NM_001656		Approved	ARD1, RNF46	uc003jty.3	P36406	OTTHUMG00000097802	ENST00000231524.9:c.275A>T	5.37:g.64910016T>A	ENSP00000231524:p.Asn92Ile	Somatic		Capture	Illumina HiSeq	Phase_I	64945772	NM_033228	Q9BZY4|Q9BZY5	Missense_Mutation	SNP	ENST00000231524.9	37	CCDS3987.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.564029	0.86335	.	.	ENSG00000113595	ENST00000231524;ENST00000381018;ENST00000274327	D;D;D	0.95035	-3.59;-3.59;-3.59	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	D	0.97964	0.9330	H	0.94964	3.605	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	D	0.99226	1.0880	10	0.87932	D	0	.	14.865	0.70406	0.0:0.0:0.0:1.0	.	92;92;92	P36406;P36406-2;P36406-3	TRI23_HUMAN;.;.	I	92	ENSP00000231524:N92I;ENSP00000370406:N92I;ENSP00000274327:N92I	ENSP00000231524:N92I	N	-	2	0	TRIM23	64945772	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.384000	0.79751	1.923000	0.55706	0.477000	0.44152	AAT		0.358	TRIM23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215058.2	NM_001656	
ENC1	8507	broad.mit.edu	37	5	73930729	73930729	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:73930729G>A	ENST00000302351.4	-	2	2712	c.1582C>T	c.(1582-1584)Cgc>Tgc	p.R528C	ENC1_ENST00000537006.1_Missense_Mutation_p.R528C|ENC1_ENST00000510316.1_Missense_Mutation_p.R455C|ENC1_ENST00000509284.1_5'Flank	NM_003633.3	NP_003624.1	O14682	ENC1_HUMAN	ectodermal-neural cortex 1 (with BTB domain)	528				YTAAAVLGNQIFIMGGDTEFSACSAYKFNSETYQWTKVGDV TAKRMSCHAVASGNKLYVVGGYFGIQRCKTLDCYDPTLDVW NSITTVPYSLIPTAFVSTWKHLPS -> IHSQASCPGGTQD FLLWGVIQNFSACFCL (in Ref. 1; AAC39532). {ECO:0000305}.	multicellular organismal development (GO:0007275)|negative regulation of translation (GO:0017148)|nervous system development (GO:0007399)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)		p.R528C(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	20		all_lung(232;0.0154)|Lung NSC(167;0.0331)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;1.45e-59)		CAGCTCATGCGCTTTGCTGTC	0.478																																					p.R528C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1582T	5						.						97.0	91.0	93.0					5																	73930729		2203	4300	6503	73966485	SO:0001583	missense	8507	exon2			AF059611	CCDS4021.1, CCDS58958.1	5q13	2013-01-30	2013-01-30		ENSG00000171617	ENSG00000171617		"""Kelch-like"", ""BTB/POZ domain containing"""	3345	protein-coding gene	gene with protein product	"""kelch-like family member 37"""	605173	"""ectodermal-neural cortex 1 (with BTB-like domain)"""	NRPB		9305847, 9566959	Standard	NM_003633		Approved	PIG10, ENC-1, TP53I10, KLHL37	uc003kdc.5	O14682	OTTHUMG00000102059	ENST00000302351.4:c.1582C>T	5.37:g.73930729G>A	ENSP00000306356:p.Arg528Cys	Somatic		Capture	Illumina HiSeq	Phase_I	73966485	NM_003633	B4DHJ1|E9PFU0|O75464|Q9UPG9	Missense_Mutation	SNP	ENST00000302351.4	37	CCDS4021.1	.	.	.	.	.	.	.	.	.	.	G	14.85	2.659426	0.47467	.	.	ENSG00000171617	ENST00000302351;ENST00000510316;ENST00000537006	D;D;D	0.85411	-1.98;-1.98;-1.98	5.93	5.03	0.67393	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	D	0.89598	0.6761	M	0.91249	3.19	0.80722	D	1	P	0.50710	0.938	P	0.45829	0.494	D	0.91804	0.5454	10	0.72032	D	0.01	.	14.8976	0.70654	0.0:0.0:0.7439:0.2561	.	528	O14682	ENC1_HUMAN	C	528;455;528	ENSP00000306356:R528C;ENSP00000423804:R455C;ENSP00000446289:R528C	ENSP00000306356:R528C	R	-	1	0	ENC1	73966485	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.001000	0.57046	2.815000	0.96918	0.561000	0.74099	CGC		0.478	ENC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219862.2	NM_003633	
S100Z	170591	broad.mit.edu	37	5	76171269	76171269	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:76171269C>A	ENST00000317593.4	+	3	317	c.85C>A	c.(85-87)Ctc>Atc	p.L29I	S100Z_ENST00000513010.1_Missense_Mutation_p.L29I	NM_130772.3	NP_570128.2	Q8WXG8	S100Z_HUMAN	S100 calcium binding protein Z	29	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)	p.L29I(1)		large_intestine(1)|ovary(1)	2		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;8.91e-51)|Epithelial(54;5.43e-45)|all cancers(79;1.82e-40)		GAGATTCAAGCTCAGCAAGGG	0.512																																					p.L29I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C85A	5						.						92.0	97.0	96.0					5																	76171269		1974	4144	6118	76207025	SO:0001583	missense	170591	exon3			AF437876	CCDS43333.1	5q13.3	2014-08-12	2006-09-11		ENSG00000171643	ENSG00000171643		"""S100 calcium binding proteins"", ""EF-hand domain containing"""	30367	protein-coding gene	gene with protein product		610103	"""S100 calcium binding protein, zeta"""			11747429	Standard	NM_130772		Approved	Gm625, S100-zeta	uc003keq.4	Q8WXG8	OTTHUMG00000162441	ENST00000317593.4:c.85C>A	5.37:g.76171269C>A	ENSP00000320430:p.Leu29Ile	Somatic		Capture	Illumina HiSeq	Phase_I	76207025	NM_130772		Missense_Mutation	SNP	ENST00000317593.4	37	CCDS43333.1	.	.	.	.	.	.	.	.	.	.	C	18.98	3.738197	0.69304	.	.	ENSG00000171643	ENST00000513010;ENST00000317593	T;T	0.37915	1.17;1.17	5.55	3.74	0.42951	S100/CaBP-9k-type, calcium binding, subdomain (1);EF-hand-like domain (1);	0.060810	0.64402	D	0.000003	T	0.55673	0.1935	.	.	.	0.43540	D	0.99583	D	0.89917	1.0	D	0.97110	1.0	T	0.55560	-0.8122	9	0.87932	D	0	.	6.2023	0.20583	0.1405:0.6532:0.1351:0.0712	.	29	Q8WXG8	S100Z_HUMAN	I	29	ENSP00000426768:L29I;ENSP00000320430:L29I	ENSP00000320430:L29I	L	+	1	0	S100Z	76207025	1.000000	0.71417	1.000000	0.80357	0.666000	0.39218	3.758000	0.55220	0.682000	0.31407	0.650000	0.86243	CTC		0.512	S100Z-002	KNOWN	alternative_3_UTR|alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368927.1	NM_130772	
AGGF1	55109	broad.mit.edu	37	5	76358925	76358925	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:76358925C>T	ENST00000312916.7	+	14	2375	c.1993C>T	c.(1993-1995)Cca>Tca	p.P665S		NM_018046.4	NP_060516.2	Q8N302	AGGF1_HUMAN	angiogenic factor with G patch and FHA domains 1	665	G-patch. {ECO:0000255|PROSITE- ProRule:PRU00092}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|RNA processing (GO:0006396)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	nucleic acid binding (GO:0003676)	p.P665S(2)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(2)	20		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;4.51e-51)|Epithelial(54;2.2e-45)|all cancers(79;6.68e-41)		GACAGGCAAACCATCCTCATT	0.433																																					p.P665S												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.C1993T	5						.						227.0	244.0	238.0					5																	76358925		2203	4300	6503	76394681	SO:0001583	missense	55109	exon14			AK001145	CCDS4035.1	5q13.3	2013-10-11			ENSG00000164252	ENSG00000164252		"""G patch domain containing"""	24684	protein-coding gene	gene with protein product		608464				18564129, 17103452	Standard	NM_018046		Approved	VG5Q, HSU84971, FLJ10283, GPATC7, GPATCH7	uc003ket.3	Q8N302	OTTHUMG00000102132	ENST00000312916.7:c.1993C>T	5.37:g.76358925C>T	ENSP00000316109:p.Pro665Ser	Somatic		Capture	Illumina HiSeq	Phase_I	76394681	NM_018046	O00581|Q53YS3|Q9BU84|Q9NW66	Missense_Mutation	SNP	ENST00000312916.7	37	CCDS4035.1	.	.	.	.	.	.	.	.	.	.	C	13.53	2.263230	0.39995	.	.	ENSG00000164252	ENST00000312916	T	0.37752	1.18	5.35	3.45	0.39498	D111/G-patch (1);	0.341930	0.34700	N	0.003758	T	0.36138	0.0956	M	0.79123	2.44	0.80722	D	1	B	0.31680	0.335	B	0.28139	0.086	T	0.31420	-0.9944	10	0.08179	T	0.78	-0.015	15.3457	0.74334	0.0:0.7361:0.2639:0.0	.	665	Q8N302	AGGF1_HUMAN	S	665	ENSP00000316109:P665S	ENSP00000316109:P665S	P	+	1	0	AGGF1	76394681	0.000000	0.05858	0.943000	0.38184	0.979000	0.70002	0.409000	0.21082	1.247000	0.43917	0.650000	0.86243	CCA		0.433	AGGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219971.2	NM_018046	
CMYA5	202333	broad.mit.edu	37	5	79041088	79041088	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:79041088A>G	ENST00000446378.2	+	4	10809	c.10778A>G	c.(10777-10779)gAg>gGg	p.E3593G		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	3593	B-box coiled-coil; BBC.				negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)		p.E3593G(1)		NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		GAACAGAATGAGGAAATGATG	0.388																																					p.E3593G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A10778G	5						.						63.0	62.0	63.0					5																	79041088		1869	4109	5978	79076844	SO:0001583	missense	202333	exon4			AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"""Tripartite motif containing / Tripartite motif containing"", ""A-kinase anchor proteins"", ""Fibronectin type III domain containing"""	14305	protein-coding gene	gene with protein product	"""genethonin-3"", ""tripartite motif-containing 76"""	612193	"""chromosome 5 open reading frame 10"""	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.10778A>G	5.37:g.79041088A>G	ENSP00000394770:p.Glu3593Gly	Somatic		Capture	Illumina HiSeq	Phase_I	79076844	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.481247	0.84747	.	.	ENSG00000164309	ENST00000446378	T	0.42900	0.96	5.58	5.58	0.84498	.	0.000000	0.51477	D	0.000090	T	0.60090	0.2242	L	0.49126	1.545	0.58432	D	0.99999	D	0.89917	1.0	D	0.91635	0.999	T	0.62732	-0.6792	10	0.87932	D	0	.	16.0556	0.80801	1.0:0.0:0.0:0.0	.	3593	Q8N3K9	CMYA5_HUMAN	G	3593	ENSP00000394770:E3593G	ENSP00000394770:E3593G	E	+	2	0	CMYA5	79076844	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.246000	0.89828	2.239000	0.73571	0.533000	0.62120	GAG		0.388	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
EDIL3	10085	broad.mit.edu	37	5	83356181	83356181	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:83356181C>T	ENST00000296591.5	-	9	1493	c.1075G>A	c.(1075-1077)Gac>Aac	p.D359N	EDIL3_ENST00000380138.3_Missense_Mutation_p.D349N|EDIL3_ENST00000510271.1_5'UTR	NM_005711.3	NP_005702.3	O43854	EDIL3_HUMAN	EGF-like repeats and discoidin I-like domains 3	359	F5/8 type C 2. {ECO:0000255|PROSITE- ProRule:PRU00081}.				cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)	p.D359N(1)		cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|prostate(5)|skin(3)	31		Lung NSC(167;0.000121)|all_lung(232;0.000154)|Ovarian(174;0.0425)		OV - Ovarian serous cystadenocarcinoma(54;4.3e-40)|Epithelial(54;4.79e-32)|all cancers(79;1.54e-26)		CCTTGCTTGTCCAGCCGAGCT	0.468																																					p.D359N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1075A	5						.						148.0	136.0	140.0					5																	83356181		2203	4300	6503	83391937	SO:0001583	missense	10085	exon9			U70312	CCDS4062.1, CCDS64195.1	5q14	2008-02-05			ENSG00000164176	ENSG00000164176			3173	protein-coding gene	gene with protein product		606018				9420328	Standard	NM_005711		Approved	DEL1	uc003kio.1	O43854	OTTHUMG00000119047	ENST00000296591.5:c.1075G>A	5.37:g.83356181C>T	ENSP00000296591:p.Asp359Asn	Somatic		Capture	Illumina HiSeq	Phase_I	83391937	NM_005711	B2R763|O43855|Q5D094|Q8N610	Missense_Mutation	SNP	ENST00000296591.5	37	CCDS4062.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.446775	0.84101	.	.	ENSG00000164176	ENST00000296591;ENST00000380138	D;D	0.99226	-5.59;-5.59	5.96	5.96	0.96718	Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	D	0.98642	0.9545	N	0.16790	0.44	0.80722	D	1	B;D;D	0.67145	0.0;0.996;0.97	B;D;D	0.77004	0.001;0.989;0.937	D	0.98368	1.0552	10	0.21540	T	0.41	-33.2493	20.422	0.99049	0.0:1.0:0.0:0.0	.	136;349;359	B7Z865;O43854-2;O43854	.;.;EDIL3_HUMAN	N	359;349	ENSP00000296591:D359N;ENSP00000369483:D349N	ENSP00000296591:D359N	D	-	1	0	EDIL3	83391937	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.487000	0.81328	2.832000	0.97577	0.655000	0.94253	GAC		0.468	EDIL3-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239258.1	NM_005711	
PDLIM4	8572	broad.mit.edu	37	5	131606779	131606779	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:131606779delC	ENST00000253754.3	+	4	563	c.499delC	c.(499-501)cccfs	p.P168fs	PDLIM4_ENST00000484620.1_3'UTR|PDLIM4_ENST00000379018.3_Frame_Shift_Del_p.P168fs|P4HA2_ENST00000471826.1_Intron	NM_001131027.1|NM_003687.3	NP_001124499.1|NP_003678.2	P50479	PDLI4_HUMAN	PDZ and LIM domain 4	168							zinc ion binding (GO:0008270)	p.S169fs*50(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|urinary_tract(1)	10			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TGTGTCTCCACCCCCCAGGTA	0.592																																					p.P167fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.499delC	5						.						134.0	132.0	133.0					5																	131606779		2203	4300	6503	131634678	SO:0001589	frameshift_variant	8572	exon4			AF153882	CCDS4152.1, CCDS47261.1	5q31.1	2008-02-05			ENSG00000131435	ENSG00000131435			16501	protein-coding gene	gene with protein product		603422				9573374	Standard	NM_001131027		Approved	RIL	uc003kwn.3	P50479	OTTHUMG00000059645	ENST00000253754.3:c.499delC	5.37:g.131606779delC	ENSP00000253754:p.Pro168fs	Somatic		Capture	Illumina HiSeq	Phase_I	131634678	NM_001131027	B2R8U1|Q53Y39|Q96AT8|Q9BTW8|Q9Y292	Frame_Shift_Del	DEL	ENST00000253754.3	37	CCDS4152.1																																																																																				0.592	PDLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132644.2	NM_003687	
CD74	972	broad.mit.edu	37	5	149786524	149786524	+	Splice_Site	SNP	C	C	A	rs112157732		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:149786524C>A	ENST00000009530.7	-	3	300		c.e3-1		CD74_ENST00000377795.3_Splice_Site|CD74_ENST00000524315.1_Splice_Site|CD74_ENST00000353334.6_Splice_Site			P04233	HG2A_HUMAN	CD74 molecule, major histocompatibility complex, class II invariant chain						activation of MAPK activity (GO:0000187)|antigen processing and presentation of endogenous antigen (GO:0019883)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell proliferation (GO:0008283)|chaperone mediated protein folding requiring cofactor (GO:0051085)|defense response (GO:0006952)|immunoglobulin mediated immune response (GO:0016064)|intracellular protein transport (GO:0006886)|macrophage migration inhibitory factor signaling pathway (GO:0035691)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of mature B cell apoptotic process (GO:0002906)|negative regulation of peptide secretion (GO:0002792)|negative regulation of T cell differentiation (GO:0045581)|negative thymic T cell selection (GO:0045060)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000343)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of type 2 immune response (GO:0002830)|positive thymic T cell selection (GO:0045059)|prostaglandin biosynthetic process (GO:0001516)|protein complex assembly (GO:0006461)|regulation of macrophage activation (GO:0043030)|signal transduction (GO:0007165)|T cell selection (GO:0045058)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)|macrophage migration inhibitory factor receptor complex (GO:0035692)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|multivesicular body (GO:0005771)|NOS2-CD74 complex (GO:0035693)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)|vacuole (GO:0005773)	beta-amyloid binding (GO:0001540)|cytokine binding (GO:0019955)|cytokine receptor activity (GO:0004896)|identical protein binding (GO:0042802)|macrophage migration inhibitory factor binding (GO:0035718)|MHC class II protein binding (GO:0042289)|MHC class II protein binding, via antigen binding groove (GO:0042658)|MHC class II protein complex binding (GO:0023026)|protein binding involved in protein folding (GO:0044183)	p.?(1)		breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)	5		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGCTTGGGAGCTGTGGGGACA	0.657			T	ROS1	NSCLC																																.			Dom	yes		5	5q32	972	"""CD74 molecule, major histocompatibility complex, class II invariant chain"""		E	.	.	1	Unknown(1)	large_intestine(1)	.	5						.						22.0	27.0	26.0					5																	149786524		2202	4300	6502	149766717	SO:0001630	splice_region_variant	972	.				CCDS34276.1, CCDS47308.1, CCDS47309.1	5q32	2012-09-20	2006-03-28		ENSG00000019582	ENSG00000019582		"""CD molecules"""	1697	protein-coding gene	gene with protein product	"""HLA-DR-gamma"", ""Ia-associated invariant chain"", ""gamma chain of class II antigens"", ""MHC HLA-DR gamma chain"""	142790	"""CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)"""	DHLAG		6324166, 3001652	Standard	NM_004355		Approved		uc003lsc.3	P04233	OTTHUMG00000163559	ENST00000009530.7:c.299-1G>T	5.37:g.149786524C>A		Somatic		Capture	Illumina HiSeq	Phase_I	149766717	.	A8K7R1|B4DNE8|D3DQG3|D3DQG4|Q14597|Q29832|Q5U0J8|Q8SNA0|Q8WLP6	Splice_Site	SNP	ENST00000009530.7	37	CCDS47309.1	.	.	.	.	.	.	.	.	.	.	C	18.24	3.579790	0.65992	.	.	ENSG00000019582	ENST00000377795;ENST00000353334;ENST00000518797;ENST00000524315;ENST00000009530	.	.	.	5.04	5.04	0.67666	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.8823	0.63688	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CD74	149766717	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	3.790000	0.55461	2.327000	0.79052	0.561000	0.74099	.		0.657	CD74-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374178.1	NM_004355	Intron
ADAMTS2	9509	broad.mit.edu	37	5	178548689	178548689	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr5:178548689C>T	ENST00000251582.7	-	21	3252	c.3151G>A	c.(3151-3153)Gac>Aac	p.D1051N		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	1051					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.D1051N(1)		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)		ATGGGCGAGTCGGGGTCCGGG	0.622																																					p.D1051N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3151A	5						.						185.0	197.0	193.0					5																	178548689		2203	4300	6503	178481295	SO:0001583	missense	9509	exon21			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.3151G>A	5.37:g.178548689C>T	ENSP00000251582:p.Asp1051Asn	Somatic		Capture	Illumina HiSeq	Phase_I	178481295	NM_014244		Missense_Mutation	SNP	ENST00000251582.7	37	CCDS4444.1	.	.	.	.	.	.	.	.	.	.	C	13.24	2.179342	0.38511	.	.	ENSG00000087116	ENST00000251582	T	0.59502	0.26	5.74	3.94	0.45596	.	0.097300	0.44285	N	0.000465	T	0.50360	0.1611	L	0.60455	1.87	0.80722	D	1	B	0.09022	0.002	B	0.04013	0.001	T	0.39981	-0.9587	10	0.21540	T	0.41	.	11.0356	0.47799	0.0:0.8468:0.0:0.1532	.	1051	O95450	ATS2_HUMAN	N	1051	ENSP00000251582:D1051N	ENSP00000251582:D1051N	D	-	1	0	ADAMTS2	178481295	0.997000	0.39634	0.067000	0.19924	0.793000	0.44817	3.346000	0.52190	0.750000	0.32877	0.555000	0.69702	GAC		0.622	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244	
SIM1	6492	broad.mit.edu	37	6	100841712	100841712	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:100841712G>A	ENST00000369208.3	-	11	2003	c.1221C>T	c.(1219-1221)ggC>ggT	p.G407G	SIM1_ENST00000262901.4_Silent_p.G407G			P81133	SIM1_HUMAN	single-minded family bHLH transcription factor 1	407	Single-minded C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00632}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.G407G(1)		breast(1)|central_nervous_system(4)|endometrium(5)|kidney(1)|large_intestine(15)|lung(34)|ovary(4)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	79		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)		AGGGACTTCCGCCCCACTGGC	0.547																																					p.G407G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1221T	6						.						38.0	37.0	37.0					6																	100841712		2203	4299	6502	100948433	SO:0001819	synonymous_variant	6492	exon10			U70212	CCDS5045.1	6q16.3	2013-10-17	2013-10-17		ENSG00000112246	ENSG00000112246		"""Basic helix-loop-helix proteins"""	10882	protein-coding gene	gene with protein product		603128	"""single-minded (Drosophila) homolog 1"", ""single-minded homolog 1 (Drosophila)"""			9199934, 11448938	Standard	NM_005068		Approved	bHLHe14	uc003pqj.4	P81133	OTTHUMG00000015275	ENST00000369208.3:c.1221C>T	6.37:g.100841712G>A		Somatic		Capture	Illumina HiSeq	Phase_I	100948433	NM_005068	Q5TDP7	Silent	SNP	ENST00000369208.3	37	CCDS5045.1																																																																																				0.547	SIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041628.3	NM_005068	
AIM1	202	broad.mit.edu	37	6	107006442	107006442	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:107006442A>G	ENST00000369066.3	+	16	5060	c.4573A>G	c.(4573-4575)Aat>Gat	p.N1525D	AIM1_ENST00000535438.1_Missense_Mutation_p.N344D	NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)		p.N1525D(1)		breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		AGAAACTGTCAATCTCCGATC	0.353																																					p.N1525D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A4573G	6						.						106.0	95.0	98.0					6																	107006442		2203	4300	6503	107113135	SO:0001583	missense	202	exon16			U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"""suppression of tumorigenicity 4"", ""beta-gamma crystallin domain containing 1"""	601797	"""suppression of tumorigenicity 4 (malignant melanoma)"""	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.4573A>G	6.37:g.107006442A>G	ENSP00000358062:p.Asn1525Asp	Somatic		Capture	Illumina HiSeq	Phase_I	107113135	NM_001624	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000369066.3	37	CCDS34506.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.181941	0.78677	.	.	ENSG00000112297	ENST00000369066;ENST00000535438	T;T	0.75821	-0.97;-0.97	5.81	5.81	0.92471	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.040834	0.85682	D	0.000000	T	0.78904	0.4357	L	0.49350	1.555	0.58432	D	0.999999	D;D	0.76494	0.999;0.993	D;D	0.71656	0.974;0.973	T	0.80425	-0.1388	10	0.52906	T	0.07	.	16.1699	0.81801	1.0:0.0:0.0:0.0	.	344;1525	B4DU04;Q9Y4K1	.;AIM1_HUMAN	D	1525;344	ENSP00000358062:N1525D;ENSP00000439183:N344D	ENSP00000358062:N1525D	N	+	1	0	AIM1	107113135	1.000000	0.71417	0.980000	0.43619	0.576000	0.36127	7.882000	0.87258	2.217000	0.71921	0.533000	0.62120	AAT		0.353	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1		
NEDD9	4739	broad.mit.edu	37	6	11191156	11191156	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:11191156C>T	ENST00000379446.5	-	5	1112	c.946G>A	c.(946-948)Gca>Aca	p.A316T	RP3-510L9.1_ENST00000500636.2_RNA|NEDD9_ENST00000504387.1_Missense_Mutation_p.A316T	NM_001271033.1|NM_006403.3	NP_001257962.1|NP_006394.1	Q14511	CASL_HUMAN	neural precursor cell expressed, developmentally down-regulated 9	316					actin filament bundle assembly (GO:0051017)|cell adhesion (GO:0007155)|cytoskeleton organization (GO:0007010)|integrin-mediated signaling pathway (GO:0007229)|mitotic nuclear division (GO:0007067)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle pole (GO:0000922)		p.A316T(4)		endometrium(3)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	Breast(50;0.0768)|Ovarian(93;0.152)	all_hematologic(90;0.135)	Epithelial(50;0.0647)|all cancers(50;0.179)			ACATCATATGCGTCGTTCTGA	0.572																																					p.A316T												.	.	4	Substitution - Missense(4)	large_intestine(4)	c.G946A	6						.						71.0	74.0	73.0					6																	11191156		2203	4300	6503	11299142	SO:0001583	missense	4739	exon5			L43821	CCDS4520.1, CCDS34340.1, CCDS47373.1, CCDS75400.1	6p25-p24	2011-04-13			ENSG00000111859	ENSG00000111859		"""Cas scaffolding proteins"""	7733	protein-coding gene	gene with protein product	"""Cas scaffolding protein family member 2"", ""Cas-like"""	602265					Standard	NM_182966		Approved	HEF1, CAS-L, CASS2	uc003mzv.2	Q14511	OTTHUMG00000014255	ENST00000379446.5:c.946G>A	6.37:g.11191156C>T	ENSP00000368759:p.Ala316Thr	Somatic		Capture	Illumina HiSeq	Phase_I	11299142	NM_006403	A8K9G7|A8MSJ9|G5E9Y9|Q5T9R4|Q5XKI0	Missense_Mutation	SNP	ENST00000379446.5	37	CCDS4520.1	.	.	.	.	.	.	.	.	.	.	C	14.75	2.627474	0.46944	.	.	ENSG00000111859	ENST00000379446;ENST00000504387	T;T	0.39592	1.07;1.19	5.94	5.94	0.96194	.	0.290933	0.37577	N	0.002028	T	0.23094	0.0558	L	0.57536	1.79	0.80722	D	1	P;P;P	0.52577	0.81;0.825;0.954	B;B;B	0.35039	0.194;0.145;0.163	T	0.19353	-1.0308	10	0.10377	T	0.69	-23.9187	20.3633	0.98874	0.0:1.0:0.0:0.0	.	316;316;316	G5E9Y9;A8K9G7;Q14511	.;.;CASL_HUMAN	T	316	ENSP00000368759:A316T;ENSP00000422871:A316T	ENSP00000368759:A316T	A	-	1	0	NEDD9	11299142	0.998000	0.40836	0.239000	0.24122	0.059000	0.15707	3.460000	0.53028	2.826000	0.97356	0.561000	0.74099	GCA		0.572	NEDD9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039853.2	NM_006403	
PDSS2	57107	broad.mit.edu	37	6	107531649	107531649	+	Silent	SNP	G	G	A	rs375546963		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:107531649G>A	ENST00000369037.4	-	6	1279	c.1002C>T	c.(1000-1002)atC>atT	p.I334I	PDSS2_ENST00000453874.2_Intron	NM_020381.3	NP_065114.3	Q86YH6	DLP1_HUMAN	prenyl (decaprenyl) diphosphate synthase, subunit 2	334					isoprenoid biosynthetic process (GO:0008299)|protein heterotetramerization (GO:0051290)|regulation of body fluid levels (GO:0050878)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	protein heterodimerization activity (GO:0046982)|trans-hexaprenyltranstransferase activity (GO:0000010)|trans-octaprenyltranstransferase activity (GO:0050347)	p.I334I(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(3)	19	Breast(9;0.0127)	all_cancers(87;3.63e-05)|Acute lymphoblastic leukemia(125;2.86e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.0108)|Colorectal(196;0.156)|Lung NSC(302;0.211)	BRCA - Breast invasive adenocarcinoma(8;0.0101)|all cancers(7;0.243)	BRCA - Breast invasive adenocarcinoma(108;0.112)|OV - Ovarian serous cystadenocarcinoma(136;0.173)|all cancers(137;0.191)		TTACCTCTCCGATCTGTTTAA	0.333																																					p.I334I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1002T	6						.	G		0,4406		0,0,2203	97.0	106.0	103.0		1002	-6.9	0.0	6		103	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PDSS2	NM_020381.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		334/400	107531649	1,13005	2203	4300	6503	107638342	SO:0001819	synonymous_variant	57107	exon6			AF254956	CCDS5059.1	6q21	2006-02-14	2006-02-14	2006-02-14	ENSG00000164494	ENSG00000164494			23041	protein-coding gene	gene with protein product		610564	"""chromosome 6 open reading frame 210"""	C6orf210		16262699	Standard	NM_020381		Approved	bA59I9.3	uc003prt.2	Q86YH6	OTTHUMG00000059359	ENST00000369037.4:c.1002C>T	6.37:g.107531649G>A		Somatic		Capture	Illumina HiSeq	Phase_I	107638342	NM_020381	Q33DR4|Q4G158|Q5VU38|Q5VU39|Q9NR58	Silent	SNP	ENST00000369037.4	37	CCDS5059.1																																																																																				0.333	PDSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131954.1	NM_020381	
RSPH4A	345895	broad.mit.edu	37	6	116949178	116949178	+	Silent	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:116949178A>G	ENST00000229554.5	+	3	1445	c.1308A>G	c.(1306-1308)gaA>gaG	p.E436E	RSPH4A_ENST00000368581.4_Silent_p.E436E|RSPH4A_ENST00000368580.4_Intron	NM_001010892.2	NP_001010892.1	Q5TD94	RSH4A_HUMAN	radial spoke head 4 homolog A (Chlamydomonas)	436					axoneme assembly (GO:0035082)|cilium movement (GO:0003341)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|radial spoke (GO:0001534)		p.E436E(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						TTTGCAATGAACCAGGAAGAC	0.393									Kartagener syndrome																												p.E436E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1308G	6						.						79.0	77.0	78.0					6																	116949178		2203	4300	6503	117055871	SO:0001819	synonymous_variant	345895	exon3	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome		CCDS34521.1, CCDS55051.1	6q22.1	2012-05-03	2009-02-17	2009-02-17	ENSG00000111834	ENSG00000111834			21558	protein-coding gene	gene with protein product		612647	"""radial spokehead-like 3"""	RSHL3		19200523	Standard	NM_001010892		Approved	dJ412I7.1, FLJ37974, RSPH6B, CILD11	uc003pxe.2	Q5TD94	OTTHUMG00000015444	ENST00000229554.5:c.1308A>G	6.37:g.116949178A>G		Somatic		Capture	Illumina HiSeq	Phase_I	117055871	NM_001161664	B4DSI1|Q3KP24|Q5TD95	Silent	SNP	ENST00000229554.5	37	CCDS34521.1																																																																																				0.393	RSPH4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041960.1	NM_001010892	
RFX6	222546	broad.mit.edu	37	6	117244360	117244360	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:117244360C>A	ENST00000332958.2	+	14	1544	c.1528C>A	c.(1528-1530)Ctc>Atc	p.L510I		NM_173560.3	NP_775831.2	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	510					endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|pancreatic A cell differentiation (GO:0003310)|pancreatic D cell differentiation (GO:0003311)|pancreatic epsilon cell differentiation (GO:0090104)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin secretion (GO:0050796)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell differentiation (GO:0003309)	nucleus (GO:0005634)	transcription regulatory region DNA binding (GO:0044212)	p.L510I(1)		cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(29)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	59						AATGCATAATCTCACCTTGAA	0.348																																					p.L510I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1528A	6						.						153.0	142.0	146.0					6																	117244360		2203	4300	6503	117351053	SO:0001583	missense	222546	exon14			BC039248	CCDS5113.1	6q22.31	2008-08-04	2008-08-04	2008-08-04	ENSG00000185002	ENSG00000185002			21478	protein-coding gene	gene with protein product		612659	"""regulatory factor X domain containing 1"""	RFXDC1			Standard	NM_173560		Approved	MGC33442, dJ955L16.1	uc003pxm.3	Q8HWS3	OTTHUMG00000015449	ENST00000332958.2:c.1528C>A	6.37:g.117244360C>A	ENSP00000332208:p.Leu510Ile	Somatic		Capture	Illumina HiSeq	Phase_I	117351053	NM_173560	Q5T6B3	Missense_Mutation	SNP	ENST00000332958.2	37	CCDS5113.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.490482	0.84962	.	.	ENSG00000185002	ENST00000332958	T	0.73789	-0.78	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	D	0.83834	0.5340	M	0.85462	2.755	0.54753	D	0.999981	D	0.71674	0.998	D	0.70487	0.969	D	0.85970	0.1476	10	0.72032	D	0.01	-13.697	12.5859	0.56416	0.0:0.9236:0.0:0.0764	.	510	Q8HWS3	RFX6_HUMAN	I	510	ENSP00000332208:L510I	ENSP00000332208:L510I	L	+	1	0	RFX6	117351053	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.697000	0.68295	2.634000	0.89283	0.561000	0.74099	CTC		0.348	RFX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041970.2	NM_173560	
ROS1	6098	broad.mit.edu	37	6	117609955	117609955	+	Silent	SNP	G	G	A	rs565892633		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:117609955G>A	ENST00000368508.3	-	43	6942	c.6744C>T	c.(6742-6744)ggC>ggT	p.G2248G	ROS1_ENST00000368507.3_Silent_p.G2242G	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	2248				EDGDVICLNSDDIMP -> KFDSSEFSSFRCTVN (in Ref. 3; AAA60277). {ECO:0000305}.	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.G2248G(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)		AAATCACATCGCCATCTTCAC	0.313			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""								G|||	1	0.000199681	0.0	0.0	5008	,	,		20286	0.0		0.0	False		,,,				2504	0.001				p.G2248G			Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"""O, E"""	.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C6744T	6						.						60.0	58.0	59.0					6																	117609955		2203	4300	6503	117716648	SO:0001819	synonymous_variant	6098	exon43			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.6744C>T	6.37:g.117609955G>A		Somatic		Capture	Illumina HiSeq	Phase_I	117716648	NM_002944	Q15368|Q5TDB5	Silent	SNP	ENST00000368508.3	37	CCDS5116.1																																																																																				0.313	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1		
SOGA3	387104	broad.mit.edu	37	6	127796634	127796634	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:127796634T>C	ENST00000525778.1	-	6	3282	c.2537A>G	c.(2536-2538)tAc>tGc	p.Y846C	SOGA3_ENST00000465909.2_Missense_Mutation_p.Y846C|SOGA3_ENST00000368268.2_Missense_Mutation_p.Y846C|SOGA3_ENST00000481848.2_Missense_Mutation_p.Y846C|SOGA3_ENST00000556132.1_Missense_Mutation_p.Y846C|SOGA3_ENST00000474293.2_5'UTR			Q5TF21	SOGA3_HUMAN	SOGA family member 3	846					regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)		p.Y846C(1)									GTTGGCCACGTAGATGCGCGC	0.642																																					p.Y846C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2537G	6						.						89.0	102.0	97.0					6																	127796634		2185	4284	6469	127838327	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.2537A>G	6.37:g.127796634T>C	ENSP00000434570:p.Tyr846Cys	Somatic		Capture	Illumina HiSeq	Phase_I	127838327	NM_001012279		Missense_Mutation	SNP	ENST00000525778.1	37	CCDS43505.1	.	.	.	.	.	.	.	.	.	.	T	16.76	3.212541	0.58452	.	.	ENSG00000214338	ENST00000556132;ENST00000368268;ENST00000525778;ENST00000465909	T;T;T;T	0.29397	1.57;1.57;1.57;1.57	5.6	5.6	0.85130	.	0.056424	0.64402	D	0.000001	T	0.26810	0.0656	L	0.44542	1.39	0.58432	D	0.999998	D	0.57899	0.981	P	0.55749	0.783	T	0.02885	-1.1098	10	0.34782	T	0.22	-10.6283	11.5328	0.50620	0.134:0.0:0.0:0.866	.	846	Q5TF21	CF174_HUMAN	C	846	ENSP00000451768:Y846C;ENSP00000357251:Y846C;ENSP00000434570:Y846C;ENSP00000435559:Y846C	ENSP00000435559:Y846C	Y	-	2	0	C6orf174	127838327	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.996000	0.57009	2.134000	0.65973	0.379000	0.24179	TAC		0.642	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	129634174	129634174	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:129634174G>A	ENST00000421865.2	+	23	3392	c.3343G>A	c.(3343-3345)Gcc>Acc	p.A1115T		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	1115	Laminin EGF-like 13. {ECO:0000255|PROSITE-ProRule:PRU00460}.				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.A1115T(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)		TGGGACAGATGCCACAACCTG	0.483																																					p.A1115T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3343A	6						.						143.0	135.0	137.0					6																	129634174		2203	4300	6503	129675867	SO:0001583	missense	3908	exon23			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.3343G>A	6.37:g.129634174G>A	ENSP00000400365:p.Ala1115Thr	Somatic		Capture	Illumina HiSeq	Phase_I	129675867	NM_001079823	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	37	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	G	8.216	0.801500	0.16397	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	T	0.32753	1.44	5.92	4.04	0.47022	EGF-like, laminin (2);	0.824630	0.11569	N	0.550994	T	0.05868	0.0153	N	0.10782	0.045	0.25587	N	0.986731	B;B	0.21225	0.053;0.053	B;B	0.24848	0.056;0.056	T	0.38693	-0.9649	10	0.15499	T	0.54	.	9.1417	0.36908	0.0835:0.305:0.6115:0.0	.	1115;1115	A6NF00;P24043	.;LAMA2_HUMAN	T	1115	ENSP00000400365:A1115T	ENSP00000346769:A1115T	A	+	1	0	LAMA2	129675867	0.335000	0.24748	0.747000	0.31113	0.104000	0.19210	2.451000	0.44952	1.514000	0.48869	0.650000	0.86243	GCC		0.483	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1		
MAP7	9053	broad.mit.edu	37	6	136683766	136683766	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:136683766T>C	ENST00000354570.3	-	11	1758	c.1348A>G	c.(1348-1350)Acc>Gcc	p.T450A	MAP7_ENST00000454590.1_Missense_Mutation_p.T472A|MAP7_ENST00000544465.1_Missense_Mutation_p.T435A|RP3-406A7.3_ENST00000571188.1_RNA|MAP7_ENST00000438100.2_Missense_Mutation_p.T435A|MAP7_ENST00000432797.2_Missense_Mutation_p.T304A	NM_001198616.1|NM_001198617.1|NM_001198619.1|NM_003980.4	NP_001185545.1|NP_001185546.1|NP_001185548.1|NP_003971.1	Q14244	MAP7_HUMAN	microtubule-associated protein 7	450	Pro-rich.				cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|establishment or maintenance of cell polarity (GO:0007163)|fertilization (GO:0009566)|germ cell development (GO:0007281)|glycosphingolipid metabolic process (GO:0006687)|homeostasis of number of cells (GO:0048872)|Leydig cell differentiation (GO:0033327)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|nucleus organization (GO:0006997)|organ growth (GO:0035265)|protein localization to plasma membrane (GO:0072659)|response to osmotic stress (GO:0006970)|response to retinoic acid (GO:0032526)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)|structural molecule activity (GO:0005198)	p.T450A(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(11)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00199)|OV - Ovarian serous cystadenocarcinoma(155;0.00643)		atggctggggtggggaccggg	0.627																																					p.T472A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1414G	6						.						23.0	24.0	24.0					6																	136683766		2203	4300	6503	136725459	SO:0001583	missense	9053	exon12			X73882	CCDS5178.1, CCDS56452.1, CCDS56453.1, CCDS56454.1, CCDS56455.1, CCDS75527.1, CCDS75528.1, CCDS75529.1	6q23.2	2008-07-28			ENSG00000135525	ENSG00000135525			6869	protein-coding gene	gene with protein product		604108				8408219	Standard	NM_003980		Approved	E-MAP-115	uc011edg.2	Q14244	OTTHUMG00000015646	ENST00000354570.3:c.1348A>G	6.37:g.136683766T>C	ENSP00000346581:p.Thr450Ala	Somatic		Capture	Illumina HiSeq	Phase_I	136725459	NM_001198614	B7Z290|B7Z400|B7Z5S7|B7Z9U7|C9JPS0|E9PCP3|F5H1E2|Q7Z6S0|Q8TAU5|Q9NY82|Q9NY83	Missense_Mutation	SNP	ENST00000354570.3	37	CCDS5178.1	.	.	.	.	.	.	.	.	.	.	T	10.42	1.346314	0.24426	.	.	ENSG00000135525	ENST00000354570;ENST00000454590;ENST00000544465;ENST00000438100;ENST00000432797;ENST00000345567	T;T;T;T;T	0.28666	1.6;1.6;1.6;1.6;1.6	5.6	0.117	0.14652	.	1.345310	0.06074	N	0.660577	T	0.01287	0.0042	N	0.00246	-1.78	0.09310	N	1	B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B	0.04013	0.0;0.0;0.0;0.0;0.001;0.001;0.0	T	0.34304	-0.9834	10	0.07990	T	0.79	5.364	0.319	0.00300	0.2478:0.3145:0.173:0.2647	.	435;472;435;472;356;413;450	B7Z290;B7ZB64;F5H1E2;E9PCP3;F8W783;Q14244-2;Q14244	.;.;.;.;.;.;MAP7_HUMAN	A	450;472;435;435;304;356	ENSP00000346581:T450A;ENSP00000414712:T472A;ENSP00000445737:T435A;ENSP00000400790:T435A;ENSP00000414879:T304A	ENSP00000344217:T356A	T	-	1	0	MAP7	136725459	0.000000	0.05858	0.035000	0.18076	0.692000	0.40212	0.018000	0.13422	0.069000	0.16605	0.454000	0.30748	ACC		0.627	MAP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042382.2	NM_003980	
PLAGL1	5325	broad.mit.edu	37	6	144263735	144263735	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:144263735C>T	ENST00000360537.2	-	5	2131	c.218G>A	c.(217-219)cGg>cAg	p.R73Q	PLAGL1_ENST00000392309.1_Missense_Mutation_p.R73Q|PLAGL1_ENST00000416623.1_Missense_Mutation_p.R73Q|PLAGL1_ENST00000392307.1_Missense_Mutation_p.R21Q|PLAGL1_ENST00000437412.1_Missense_Mutation_p.R21Q|PLAGL1_ENST00000367571.1_Missense_Mutation_p.R73Q|PLAGL1_ENST00000444202.1_Missense_Mutation_p.R73Q|PLAGL1_ENST00000367572.1_Missense_Mutation_p.R21Q|PLAGL1_ENST00000429150.1_Missense_Mutation_p.R73Q|PLAGL1_ENST00000354765.2_Missense_Mutation_p.R73Q			Q9UM63	PLAL1_HUMAN	pleiomorphic adenoma gene-like 1	73					apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|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)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|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.R73Q(1)		endometrium(1)|large_intestine(4)|lung(2)|prostate(1)|skin(3)|stomach(2)	13				OV - Ovarian serous cystadenocarcinoma(155;5.74e-07)|GBM - Glioblastoma multiforme(68;0.0885)		GTGGTCTTTCCGGTTGAACGT	0.498											OREG0017707	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R21Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G62A	6						.						133.0	122.0	126.0					6																	144263735		2203	4300	6503	144305428	SO:0001583	missense	5325	exon6			U81992	CCDS5202.1, CCDS5203.1	6q24-q25	2013-01-08			ENSG00000118495	ENSG00000118495		"""Zinc fingers, C2H2-type"""	9046	protein-coding gene	gene with protein product		603044				9722527, 9671765	Standard	NM_006718		Approved	ZAC, LOT1	uc003qkf.3	Q9UM63	OTTHUMG00000015738	ENST00000360537.2:c.218G>A	6.37:g.144263735C>T	ENSP00000353734:p.Arg73Gln	Somatic	1685	Capture	Illumina HiSeq	Phase_I	144305428	NM_001080955	B2RBA4|B2RCM8|E1P595|E1P597|O76019|Q7Z3V8|Q92981|Q96JR9|Q9UIZ0	Missense_Mutation	SNP	ENST00000360537.2	37	CCDS5202.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.249875	0.80024	.	.	ENSG00000118495	ENST00000360537;ENST00000354765;ENST00000444202;ENST00000429150;ENST00000392309;ENST00000416623;ENST00000437412;ENST00000392307;ENST00000367572;ENST00000367571;ENST00000417959	T;T;T;T;T;T;T;T;T;T;T	0.28255	1.62;1.62;1.62;1.62;1.62;1.62;3.19;3.19;3.19;1.62;3.19	6.16	4.38	0.52667	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000012	T	0.16854	0.0405	N	0.20685	0.6	0.43172	D	0.994975	D	0.56035	0.974	P	0.54401	0.751	T	0.03212	-1.1060	10	0.31617	T	0.26	-43.7992	10.7222	0.46046	0.1322:0.8005:0.0:0.0673	.	73	Q9UM63	PLAL1_HUMAN	Q	73;73;73;73;73;73;21;21;21;73;21	ENSP00000353734:R73Q;ENSP00000346810:R73Q;ENSP00000400929:R73Q;ENSP00000398409:R73Q;ENSP00000376125:R73Q;ENSP00000400060:R73Q;ENSP00000392418:R21Q;ENSP00000376124:R21Q;ENSP00000356544:R21Q;ENSP00000356543:R73Q;ENSP00000395960:R21Q	ENSP00000346810:R73Q	R	-	2	0	PLAGL1	144305428	1.000000	0.71417	0.982000	0.44146	0.709000	0.40893	7.757000	0.85209	0.917000	0.36895	-0.142000	0.14014	CGG		0.498	PLAGL1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042541.1		
SHPRH	257218	broad.mit.edu	37	6	146240543	146240543	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:146240543G>A	ENST00000367505.2	-	22	4357	c.4093C>T	c.(4093-4095)Cgt>Tgt	p.R1365C	SHPRH_ENST00000275233.7_Missense_Mutation_p.R1365C|SHPRH_ENST00000367503.3_Missense_Mutation_p.R1369C|SHPRH_ENST00000438092.2_Missense_Mutation_p.R1369C			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	1365					DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R1369C(1)		breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		CTAGGATCACGCACTCTTAGT	0.438																																					p.R1369C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4105T	6						.						193.0	183.0	187.0					6																	146240543		1974	4172	6146	146282236	SO:0001583	missense	257218	exon22			AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"""RING-type (C3HC4) zinc fingers"""	19336	protein-coding gene	gene with protein product		608048	"""SNF2 histone linker PHD RING helicase"""			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.4093C>T	6.37:g.146240543G>A	ENSP00000356475:p.Arg1365Cys	Somatic		Capture	Illumina HiSeq	Phase_I	146282236	NM_173082	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Missense_Mutation	SNP	ENST00000367505.2	37	CCDS43513.2	.	.	.	.	.	.	.	.	.	.	G	33	5.235400	0.95207	.	.	ENSG00000146414	ENST00000367505;ENST00000367503;ENST00000438092;ENST00000275233	T;T;T;T	0.76709	-1.04;-1.04;-1.04;-1.04	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	D	0.85080	0.5615	L	0.59436	1.845	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.959;0.998;0.999	D	0.85425	0.1145	10	0.72032	D	0.01	-19.5766	19.744	0.96245	0.0:0.0:1.0:0.0	.	564;1365;1369	B3KX98;Q149N8;Q149N8-4	.;SHPRH_HUMAN;.	C	1365;1369;1369;1365	ENSP00000356475:R1365C;ENSP00000356473:R1369C;ENSP00000412797:R1369C;ENSP00000275233:R1365C	ENSP00000275233:R1365C	R	-	1	0	SHPRH	146282236	1.000000	0.71417	0.939000	0.37840	0.979000	0.70002	9.420000	0.97426	2.746000	0.94184	0.561000	0.74099	CGT		0.438	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082	
GRM1	2911	broad.mit.edu	37	6	146480607	146480607	+	Missense_Mutation	SNP	G	G	A	rs553512718		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:146480607G>A	ENST00000282753.1	+	2	1059	c.824G>A	c.(823-825)cGc>cAc	p.R275H	GRM1_ENST00000492807.2_Missense_Mutation_p.R275H|GRM1_ENST00000392299.2_Missense_Mutation_p.R275H|GRM1_ENST00000507907.1_Missense_Mutation_p.R275H|GRM1_ENST00000355289.4_Missense_Mutation_p.R275H|GRM1_ENST00000361719.2_Missense_Mutation_p.R275H			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	275					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)	p.R275H(1)		NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		CGACTCTTGCGCAAACTCCGA	0.577													G|||	1	0.000199681	0.0	0.0	5008	,	,		18937	0.001		0.0	False		,,,				2504	0.0				p.R275H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G824A	6						.						93.0	84.0	87.0					6																	146480607		2203	4300	6503	146522300	SO:0001583	missense	2911	exon3			U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4593	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 85"""	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.824G>A	6.37:g.146480607G>A	ENSP00000282753:p.Arg275His	Somatic		Capture	Illumina HiSeq	Phase_I	146522300	NM_001114329	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Missense_Mutation	SNP	ENST00000282753.1	37	CCDS5209.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.838921	0.91117	.	.	ENSG00000152822	ENST00000361719;ENST00000392299;ENST00000492807;ENST00000282753;ENST00000355289;ENST00000507907	D;D;D;D;D;D	0.83419	-1.72;-1.72;-1.72;-1.72;-1.72;-1.72	5.32	5.32	0.75619	Extracellular ligand-binding receptor (1);	0.053988	0.64402	D	0.000002	D	0.82398	0.5028	L	0.53671	1.685	0.53688	D	0.999976	P;D;P;P	0.64830	0.932;0.994;0.945;0.932	P;P;P;P	0.58780	0.537;0.845;0.667;0.537	D	0.84833	0.0803	10	0.72032	D	0.01	.	9.6698	0.40006	0.1545:0.0:0.8455:0.0	.	275;275;270;275	F8W805;Q13255;Q59HC2;Q13255-2	.;GRM1_HUMAN;.;.	H	275	ENSP00000354896:R275H;ENSP00000376119:R275H;ENSP00000424095:R275H;ENSP00000282753:R275H;ENSP00000347437:R275H;ENSP00000425599:R275H	ENSP00000282753:R275H	R	+	2	0	GRM1	146522300	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.432000	0.73400	2.495000	0.84180	0.655000	0.94253	CGC		0.577	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838	
ESR1	2099	broad.mit.edu	37	6	152332911	152332911	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:152332911C>A	ENST00000206249.3	+	5	1579	c.1217C>A	c.(1216-1218)cCt>cAt	p.P406H	ESR1_ENST00000406599.1_Intron|ESR1_ENST00000338799.5_Missense_Mutation_p.P406H|ESR1_ENST00000440973.1_Missense_Mutation_p.P406H|ESR1_ENST00000456483.2_Missense_Mutation_p.P294H|ESR1_ENST00000427531.2_Missense_Mutation_p.P233H|ESR1_ENST00000443427.1_Missense_Mutation_p.P406H	NM_000125.3	NP_000116.2	P03372	ESR1_HUMAN	estrogen receptor 1	406	Interaction with AKAP13.|Self-association.|Steroid-binding.|Transactivation AF-2.				androgen metabolic process (GO:0008209)|antral ovarian follicle growth (GO:0001547)|cellular response to estradiol stimulus (GO:0071392)|chromatin remodeling (GO:0006338)|epithelial cell development (GO:0002064)|epithelial cell proliferation involved in mammary gland duct elongation (GO:0060750)|gene expression (GO:0010467)|intracellular estrogen receptor signaling pathway (GO:0030520)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|male gonad development (GO:0008584)|mammary gland alveolus development (GO:0060749)|mammary gland branching involved in pregnancy (GO:0060745)|negative regulation of gene expression (GO:0010629)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|uterus development (GO:0060065)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|transcriptionally active chromatin (GO:0035327)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enzyme binding (GO:0019899)|estrogen receptor activity (GO:0030284)|estrogen response element binding (GO:0034056)|estrogen-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0038052)|identical protein binding (GO:0042802)|nitric-oxide synthase regulator activity (GO:0030235)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.P406H(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(19)|ovary(1)|prostate(2)|skin(1)	49		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Allylestrenol(DB01431)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Estropipate(DB04574)|Ethinyl Estradiol(DB00977)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Ospemifene(DB04938)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)|Trilostane(DB01108)	CTGTTTGCTCCTAACTTGCTC	0.468																																					p.P406H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1217A	6						.						131.0	117.0	122.0					6																	152332911		2203	4300	6503	152374604	SO:0001583	missense	2099	exon6			X03635	CCDS5234.1	6q24-q27	2013-01-16			ENSG00000091831	ENSG00000091831		"""Nuclear hormone receptors"""	3467	protein-coding gene	gene with protein product		133430		ESR		3754034	Standard	NM_000125		Approved	NR3A1, Era	uc003qon.4	P03372	OTTHUMG00000016103	ENST00000206249.3:c.1217C>A	6.37:g.152332911C>A	ENSP00000206249:p.Pro406His	Somatic		Capture	Illumina HiSeq	Phase_I	152374604	NM_001122740	Q13511|Q14276|Q5T5H7|Q6MZQ9|Q9NU51|Q9UDZ7|Q9UIS7	Missense_Mutation	SNP	ENST00000206249.3	37	CCDS5234.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.2|21.2	4.112590|4.112590	0.77210|0.77210	.|.	.|.	ENSG00000091831|ENSG00000091831	ENST00000427531|ENST00000440973;ENST00000338799;ENST00000456483;ENST00000431219;ENST00000443427;ENST00000206249;ENST00000431590;ENST00000544394;ENST00000415488	.|D;D;D;D;D;T;T	.|0.96685	.|-4.09;-4.09;-4.09;-4.09;-4.09;1.17;0.61	5.42|5.42	5.42|5.42	0.78866|0.78866	.|Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	.|0.118691	.|0.64402	.|D	.|0.000018	D|D	0.98560|0.98560	0.9519|0.9519	M|M	0.91038|0.91038	3.17|3.17	0.58432|0.58432	D|D	0.999999|0.999999	.|D;D;D;D;D;D	.|0.89917	.|1.0;1.0;0.987;1.0;1.0;1.0	.|D;D;P;D;D;D	.|0.83275	.|0.996;0.982;0.813;0.981;0.983;0.99	D|D	0.99544|0.99544	1.0964|1.0964	5|10	.|0.87932	.|D	.|0	.|.	19.21|19.21	0.93749|0.93749	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|310;187;101;405;406;406	.|B0QYW6;E7EVR3;C8CJL6;A8KAF4;G4XH65;P03372	.|.;.;.;.;.;ESR1_HUMAN	I|H	311|406;406;294;187;406;406;334;233;79	.|ENSP00000405330:P406H;ENSP00000342630:P406H;ENSP00000415934:P294H;ENSP00000387500:P406H;ENSP00000206249:P406H;ENSP00000445454:P233H;ENSP00000401995:P79H	.|ENSP00000206249:P406H	L|P	+|+	1|2	2|0	ESR1|ESR1	152374604|152374604	0.958000|0.958000	0.32768|0.32768	0.998000|0.998000	0.56505|0.56505	0.998000|0.998000	0.95712|0.95712	2.193000|2.193000	0.42658|0.42658	2.541000|2.541000	0.85698|0.85698	0.591000|0.591000	0.81541|0.81541	CTA|CCT		0.468	ESR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043308.1		
SYNE1	23345	broad.mit.edu	37	6	152473137	152473137	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:152473137T>C	ENST00000367255.5	-	134	24870	c.24269A>G	c.(24268-24270)gAc>gGc	p.D8090G	SYNE1_ENST00000423061.1_Missense_Mutation_p.D8019G|SYNE1_ENST00000347037.5_5'UTR|SYNE1_ENST00000354674.4_Missense_Mutation_p.D245G|SYNE1_ENST00000539504.1_Missense_Mutation_p.D245G|SYNE1_ENST00000448038.1_Missense_Mutation_p.D8019G|SYNE1_ENST00000341594.5_Missense_Mutation_p.D7702G|SYNE1_ENST00000265368.4_Missense_Mutation_p.D8090G|SYNE1_ENST00000356820.4_Missense_Mutation_p.D2614G	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	8090					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.D8090G(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)		TTGCAGGTTGTCCCATCTCTG	0.522										HNSCC(10;0.0054)																											p.D2614G												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A7841G	6						.						164.0	106.0	126.0					6																	152473137		2203	4300	6503	152514830	SO:0001583	missense	23345	exon49			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.24269A>G	6.37:g.152473137T>C	ENSP00000356224:p.Asp8090Gly	Somatic		Capture	Illumina HiSeq	Phase_I	152514830	NM_015293	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	T	27.5	4.838524	0.91117	.	.	ENSG00000131018	ENST00000367255;ENST00000539504;ENST00000367257;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000313630;ENST00000367247;ENST00000367251;ENST00000354674	T;T;T;T;T;T;T;T;T;T	0.53206	1.24;0.63;0.63;1.24;1.24;1.24;1.24;0.63;0.63;0.63	5.72	5.72	0.89469	.	0.000000	0.56097	D	0.000021	T	0.64068	0.2565	M	0.81802	2.56	0.80722	D	1	D;D;D;D;P	0.63880	0.988;0.988;0.993;0.988;0.867	D;D;D;D;P	0.69307	0.919;0.919;0.963;0.919;0.722	T	0.70178	-0.4943	10	0.72032	D	0.01	.	16.0168	0.80445	0.0:0.0:0.0:1.0	.	8090;8090;8019;8019;292	Q8NF91;E7EQI5;Q8NF91-4;E9PEL9;B7Z9Y6	SYNE1_HUMAN;.;.;.;.	G	8090;245;736;8019;8090;8019;7702;2614;252;247;1012;245	ENSP00000356224:D8090G;ENSP00000441052:D245G;ENSP00000356226:D736G;ENSP00000396024:D8019G;ENSP00000265368:D8090G;ENSP00000390975:D8019G;ENSP00000341887:D7702G;ENSP00000349276:D2614G;ENSP00000356220:D1012G;ENSP00000346701:D245G	ENSP00000265368:D8090G	D	-	2	0	SYNE1	152514830	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.841000	0.86834	2.194000	0.70268	0.528000	0.53228	GAC		0.522	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
SYNE1	23345	broad.mit.edu	37	6	152583315	152583315	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:152583315G>A	ENST00000367255.5	-	101	19425	c.18824C>T	c.(18823-18825)cCt>cTt	p.P6275L	SYNE1_ENST00000423061.1_Missense_Mutation_p.P6204L|SYNE1_ENST00000448038.1_Missense_Mutation_p.P6204L|SYNE1_ENST00000341594.5_Missense_Mutation_p.P5887L|SYNE1_ENST00000265368.4_Missense_Mutation_p.P6275L|SYNE1_ENST00000356820.4_Missense_Mutation_p.P799L	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	6275					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.P6275L(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)		TAACACATCAGGTTTTTCGCT	0.393										HNSCC(10;0.0054)																											p.P799L												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C2396T	6						.						103.0	98.0	100.0					6																	152583315		2203	4300	6503	152625008	SO:0001583	missense	23345	exon16			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.18824C>T	6.37:g.152583315G>A	ENSP00000356224:p.Pro6275Leu	Somatic		Capture	Illumina HiSeq	Phase_I	152625008	NM_015293	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	16.07	3.018864	0.54576	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820	T;T;T;T;T;T	0.54479	0.66;0.65;0.57;0.65;0.78;2.68	5.96	5.07	0.68467	.	0.217104	0.32430	N	0.006113	T	0.37461	0.1004	L	0.54323	1.7	0.43536	D	0.995828	B;B;P	0.34800	0.339;0.339;0.469	B;B;B	0.30572	0.055;0.055;0.117	T	0.41052	-0.9530	10	0.51188	T	0.08	.	17.2517	0.87044	0.0:0.1252:0.8748:0.0	.	6275;6275;6204	Q8NF91;E7EQI5;Q8NF91-4	SYNE1_HUMAN;.;.	L	6275;6204;6275;6204;5887;799	ENSP00000356224:P6275L;ENSP00000396024:P6204L;ENSP00000265368:P6275L;ENSP00000390975:P6204L;ENSP00000341887:P5887L;ENSP00000349276:P799L	ENSP00000265368:P6275L	P	-	2	0	SYNE1	152625008	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.808000	0.38912	2.831000	0.97527	0.650000	0.86243	CCT		0.393	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
DTNBP1	84062	broad.mit.edu	37	6	15533514	15533514	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:15533514C>T	ENST00000344537.5	-	8	796	c.624G>A	c.(622-624)gaG>gaA	p.E208E	DTNBP1_ENST00000462989.2_Silent_p.E52E|DTNBP1_ENST00000338950.5_Silent_p.E208E|DTNBP1_ENST00000355917.3_Silent_p.E209E	NM_032122.4	NP_115498.2	Q96EV8	DTBP1_HUMAN	dystrobrevin binding protein 1	208	Dysbindin.				actin cytoskeleton reorganization (GO:0031532)|anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|blood coagulation (GO:0007596)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|neuron projection development (GO:0031175)|neuron projection morphogenesis (GO:0048812)|platelet dense granule organization (GO:0060155)|positive regulation of gene expression (GO:0010628)|positive regulation of neurotransmitter secretion (GO:0001956)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of dopamine secretion (GO:0014059)	axon (GO:0030424)|BLOC-1 complex (GO:0031083)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|growth cone (GO:0030426)|neuron projection (GO:0043005)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)|synaptic vesicle membrane (GO:0030672)		p.E208E(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|skin(2)	14	Breast(50;0.0289)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.211)			ACAGGTACTGCTCCATGTCCT	0.612									Hermansky-Pudlak syndrome																												p.E208E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G624A	6						.						140.0	119.0	126.0					6																	15533514		2203	4300	6503	15641493	SO:0001819	synonymous_variant	84062	exon8	Familial Cancer Database	HPS, HPS1-8	AF394226	CCDS4534.1, CCDS4535.1, CCDS75404.1, CCDS75405.1	6p22.3	2013-09-27			ENSG00000047579	ENSG00000047579		"""Biogenesis of lysosomal organelles complex-1 subunits"""	17328	protein-coding gene	gene with protein product	"""dysbindin-1"", ""biogenesis of lysosomal organelles complex-1, subunit 8"""	607145				11316798	Standard	NM_032122		Approved	Dysbindin, My031, HPS7, DBND, BLOC1S8	uc003nbm.3	Q96EV8	OTTHUMG00000014295	ENST00000344537.5:c.624G>A	6.37:g.15533514C>T		Somatic		Capture	Illumina HiSeq	Phase_I	15641493	NM_032122	A8K3V3|Q5THY3|Q5THY4|Q96NV2|Q9H0U2|Q9H3J5	Silent	SNP	ENST00000344537.5	37	CCDS4534.1																																																																																				0.612	DTNBP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000039933.2	NM_032122	
OPRM1	4988	broad.mit.edu	37	6	154360922	154360922	+	Silent	SNP	C	C	T	rs200915701		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:154360922C>T	ENST00000330432.7	+	1	480	c.243C>T	c.(241-243)tgC>tgT	p.C81C	OPRM1_ENST00000524163.1_Silent_p.C81C|OPRM1_ENST00000428397.2_Silent_p.C81C|OPRM1_ENST00000337049.4_Silent_p.C81C|OPRM1_ENST00000360422.4_Silent_p.C81C|OPRM1_ENST00000419506.2_Silent_p.C81C|OPRM1_ENST00000520708.1_Intron|OPRM1_ENST00000523520.1_3'UTR|OPRM1_ENST00000452687.2_Silent_p.C81C|OPRM1_ENST00000518759.1_Intron|OPRM1_ENST00000434900.2_Silent_p.C174C|OPRM1_ENST00000414028.2_Silent_p.C81C|OPRM1_ENST00000435918.2_Silent_p.C81C|OPRM1_ENST00000229768.5_Silent_p.C81C	NM_000914.3	NP_000905.3	P35372	OPRM_HUMAN	opioid receptor, mu 1	81					adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavioral response to ethanol (GO:0048149)|calcium ion transmembrane transport (GO:0070588)|cellular response to stress (GO:0033554)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|locomotory behavior (GO:0007626)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of Wnt protein secretion (GO:0061358)|neuropeptide signaling pathway (GO:0007218)|opioid receptor signaling pathway (GO:0038003)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neurogenesis (GO:0050769)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-endorphin receptor activity (GO:0004979)|G-protein alpha-subunit binding (GO:0001965)|G-protein coupled receptor activity (GO:0004930)|morphine receptor activity (GO:0038047)|voltage-gated calcium channel activity (GO:0005245)	p.C81C(2)|p.C174C(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(15)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	33		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;9.26e-11)|BRCA - Breast invasive adenocarcinoma(81;0.0154)	Alfentanil(DB00802)|Alvimopan(DB06274)|Amitriptyline(DB00321)|Anileridine(DB00913)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dezocine(DB01209)|Diphenoxylate(DB01081)|Ethylmorphine(DB01466)|Fentanyl(DB00813)|Heroin(DB01452)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levallorphan(DB00504)|Levomethadyl Acetate(DB01227)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Methadyl Acetate(DB01433)|Methylnaltrexone(DB06800)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Ondansetron(DB00904)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Pentazocine(DB00652)|Pethidine(DB00454)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	CCATCGTGTGCGTGGTGGGGC	0.617																																					p.C81C												.	.	3	Substitution - coding silent(3)	large_intestine(3)	c.C243T	6						.	C	,,,,,,,,,,,	1,4025		0,1,2012	75.0	77.0	76.0		243,243,243,243,522,,,243,243,243,243,243	1.5	1.0	6		76	0,8360		0,0,4180	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron,intron,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OPRM1	NM_000914.3,NM_001008503.1,NM_001008504.2,NM_001008505.1,NM_001145279.2,NM_001145280.2,NM_001145281.1,NM_001145282.1,NM_001145283.1,NM_001145284.2,NM_001145285.1,NM_001145286.1	,,,,,,,,,,,	0,1,6192	TT,TC,CC		0.0,0.0248,0.0081	,,,,,,,,,,,	81/401,81/419,81/393,81/447,174/494,,,81/407,81/398,81/404,81/390,81/421	154360922	1,12385	2013	4180	6193	154402615	SO:0001819	synonymous_variant	4988	exon1			L29301	CCDS43517.1, CCDS43518.1, CCDS47503.1, CCDS47504.1, CCDS47505.1, CCDS47506.1, CCDS47507.1, CCDS47508.1, CCDS55071.1, CCDS55068.1, CCDS55069.1, CCDS55070.1	6q24-q25	2012-08-08			ENSG00000112038	ENSG00000112038		"""GPCR / Class A : Opioid receptors"""	8156	protein-coding gene	gene with protein product		600018					Standard	NM_001145285		Approved	MOR1	uc003qpo.1	P35372	OTTHUMG00000015870	ENST00000330432.7:c.243C>T	6.37:g.154360922C>T		Somatic		Capture	Illumina HiSeq	Phase_I	154402615	NM_000914	B0FXJ1|B2R9S7|B8Q1L7|B8Q1L8|B8Q1L9|E7EWZ3|G8XRH6|G8XRH8|Q12930|Q4VWM1|Q4VWM2|Q4VWM3|Q4VWM4|Q4VWM6|Q4VWX6|Q5TDA1|Q6UPP1|Q6UQ80|Q7Z2D8|Q86V80|Q8IWW3|Q8IWW4|Q9UCZ4|Q9UN57	Silent	SNP	ENST00000330432.7	37	CCDS55070.1																																																																																				0.617	OPRM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042786.2	NM_000914	
WTAP	9589	broad.mit.edu	37	6	160176145	160176145	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:160176145G>A	ENST00000358372.4	+	8	2450	c.693G>A	c.(691-693)gaG>gaA	p.E231E	SOD2_ENST00000546087.1_Intron	NM_001270531.1|NM_004906.4	NP_001257460.1|NP_004897.2	Q15007	FL2D_HUMAN	Wilms tumor 1 associated protein	231					cell cycle (GO:0007049)|mRNA methylation (GO:0080009)|mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	MIS complex (GO:0036396)|nuclear membrane (GO:0031965)|nuclear speck (GO:0016607)|nucleus (GO:0005634)		p.E231E(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)|skin(1)|urinary_tract(1)	18		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.75e-18)|BRCA - Breast invasive adenocarcinoma(81;5.93e-06)		AGCTGAAGGAGACACGCCAGC	0.517																																					p.E231E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G693A	6						.						63.0	57.0	59.0					6																	160176145		2203	4300	6503	160096135	SO:0001819	synonymous_variant	9589	exon8			AJ276706	CCDS5266.1, CCDS5267.1, CCDS75542.1	6q25-q27	2008-02-05			ENSG00000146457	ENSG00000146457			16846	protein-coding gene	gene with protein product		605442				7788527, 11001926	Standard	NM_004906		Approved	KIAA0105, MGC3925	uc003qsl.4	Q15007	OTTHUMG00000015933	ENST00000358372.4:c.693G>A	6.37:g.160176145G>A		Somatic		Capture	Illumina HiSeq	Phase_I	160096135	NM_004906	Q5TCL8|Q5TCL9|Q96T28|Q9BYJ7|Q9H4E2	Silent	SNP	ENST00000358372.4	37	CCDS5266.1																																																																																				0.517	WTAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042905.1	NM_152857	
MLLT4	4301	broad.mit.edu	37	6	168351875	168351875	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:168351875C>T	ENST00000447894.2	+	29	3820	c.3820C>T	c.(3820-3822)Cgt>Tgt	p.R1274C	MLLT4_ENST00000400822.3_Missense_Mutation_p.R1273C|MLLT4_ENST00000366806.2_Missense_Mutation_p.R1274C|MLLT4_ENST00000392112.1_Missense_Mutation_p.R1257C|MLLT4_ENST00000344191.4_Missense_Mutation_p.R1274C|MLLT4_ENST00000392108.3_Missense_Mutation_p.R1274C|MLLT4_ENST00000351017.4_Missense_Mutation_p.R1281C			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	1274					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)	p.R1274C(1)|p.R1258C(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(13)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		GCGTGTTACACGTTCCCAAGA	0.358			T	MLL	AL																																p.R1274C			Dom	yes		6	6q27	4301	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"""		L	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C3820T	6						.						55.0	57.0	57.0					6																	168351875		2203	4300	6503	168094724	SO:0001583	missense	4301	exon29			AB011399	CCDS47517.1, CCDS75553.1	6q27	2008-02-05	2001-11-28		ENSG00000130396	ENSG00000130396			7137	protein-coding gene	gene with protein product		159559	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4"""			8242616	Standard	NM_001040000		Approved	AF-6, AF6	uc021zij.1	P55196	OTTHUMG00000016031	ENST00000447894.2:c.3820C>T	6.37:g.168351875C>T	ENSP00000404595:p.Arg1274Cys	Somatic		Capture	Illumina HiSeq	Phase_I	168094724	NM_001040000	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Missense_Mutation	SNP	ENST00000447894.2	37		.	.	.	.	.	.	.	.	.	.	C	22.3	4.265601	0.80358	.	.	ENSG00000130396	ENST00000344191;ENST00000351017;ENST00000392108;ENST00000366806;ENST00000392112;ENST00000341575;ENST00000400822;ENST00000447894	T;T;T;T;T;T;T	0.05081	3.71;3.6;3.71;3.7;3.5;3.6;3.6	5.5	5.5	0.81552	.	0.134569	0.49916	D	0.000131	T	0.11879	0.0289	L	0.57536	1.79	0.58432	D	0.999996	D;D;D;D	0.89917	0.996;1.0;0.999;0.999	P;P;P;P	0.62184	0.719;0.899;0.897;0.851	T	0.00175	-1.1955	10	0.72032	D	0.01	-22.0132	13.0344	0.58862	0.0:0.9263:0.0:0.0737	.	1274;1273;1274;1258	P55196;P55196-5;P55196-6;P55196-2	AFAD_HUMAN;.;.;.	C	1274;1281;1274;1274;1257;1274;1273;1274	ENSP00000341118:R1274C;ENSP00000252692:R1281C;ENSP00000375956:R1274C;ENSP00000355771:R1274C;ENSP00000375960:R1257C;ENSP00000383623:R1273C;ENSP00000404595:R1274C	ENSP00000345834:R1274C	R	+	1	0	MLLT4	168094724	1.000000	0.71417	0.656000	0.29637	0.977000	0.68977	4.208000	0.58486	2.735000	0.93741	0.655000	0.94253	CGT		0.358	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936	
EXOC2	55770	broad.mit.edu	37	6	637755	637755	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:637755T>C	ENST00000230449.4	-	2	199	c.64A>G	c.(64-66)Acg>Gcg	p.T22A	EXOC2_ENST00000448181.3_Intron	NM_018303.5	NP_060773.3	Q96KP1	EXOC2_HUMAN	exocyst complex component 2	22	IPT/TIG.				cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.T22A(1)		breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|liver(1)|lung(16)|ovary(4)|pancreas(1)|prostate(2)	46	Ovarian(93;0.0733)	Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897)		OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14)		GTGACCTTCGTCCATGGTATC	0.532																																					p.T22A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A64G	6						.						135.0	132.0	133.0					6																	637755		2203	4300	6503	582755	SO:0001583	missense	55770	exon2			AJ420556	CCDS34327.1	6p25.3	2013-01-22	2005-11-01	2005-11-01	ENSG00000112685	ENSG00000112685			24968	protein-coding gene	gene with protein product		615329	"""SEC5-like 1 (S. cerevisiae)"""	SEC5L1		12575951, 12459492	Standard	NM_018303		Approved	FLJ11026, Sec5p	uc003mtd.4	Q96KP1	OTTHUMG00000137437	ENST00000230449.4:c.64A>G	6.37:g.637755T>C	ENSP00000230449:p.Thr22Ala	Somatic		Capture	Illumina HiSeq	Phase_I	582755	NM_018303	B2RBE6|Q5JPC8|Q96AN6|Q9NUZ8|Q9UJM7	Missense_Mutation	SNP	ENST00000230449.4	37	CCDS34327.1	.	.	.	.	.	.	.	.	.	.	T	26.9	4.777163	0.90195	.	.	ENSG00000112685	ENST00000230449;ENST00000443083	T;T	0.64991	-0.13;-0.13	5.29	5.29	0.74685	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.81004	0.4733	M	0.92649	3.33	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.86055	0.1528	10	0.72032	D	0.01	-14.1175	15.4966	0.75658	0.0:0.0:0.0:1.0	.	22	Q96KP1	EXOC2_HUMAN	A	22	ENSP00000230449:T22A;ENSP00000406400:T22A	ENSP00000230449:T22A	T	-	1	0	EXOC2	582755	1.000000	0.71417	0.996000	0.52242	0.827000	0.46813	7.384000	0.79751	2.119000	0.64992	0.460000	0.39030	ACG		0.532	EXOC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039627.1	NM_018303	
RIOK1	83732	broad.mit.edu	37	6	7393451	7393451	+	Missense_Mutation	SNP	A	A	G	rs368069269		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:7393451A>G	ENST00000379834.2	+	2	698	c.191A>G	c.(190-192)gAc>gGc	p.D64G		NM_031480.2|NM_153005.1	NP_113668.2|NP_694550.1	Q9BRS2	RIOK1_HUMAN	RIO kinase 1	64							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.D57G(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	19	Ovarian(93;0.0418)					gagggttatgacgatgatgat	0.433																																					p.D64G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A191G	6						.						188.0	158.0	168.0					6																	7393451		2203	4300	6503	7338450	SO:0001583	missense	83732	exon2			BC006104	CCDS4500.1	6p24.3	2012-12-10	2012-12-10		ENSG00000124784	ENSG00000124784			18656	protein-coding gene	gene with protein product			"""RIO kinase 1 (yeast)"""				Standard	NM_031480		Approved	AD034, FLJ30006, bA288G3.1, RRP10	uc003mxn.3	Q9BRS2	OTTHUMG00000014207	ENST00000379834.2:c.191A>G	6.37:g.7393451A>G	ENSP00000369162:p.Asp64Gly	Somatic		Capture	Illumina HiSeq	Phase_I	7338450	NM_031480	B2RB28|Q8NDC8|Q96NV9	Missense_Mutation	SNP	ENST00000379834.2	37	CCDS4500.1	.	.	.	.	.	.	.	.	.	.	A	8.625	0.892308	0.17613	.	.	ENSG00000124784	ENST00000379834	T	0.06608	3.28	4.7	4.7	0.59300	.	0.000000	0.85682	D	0.000000	T	0.03220	0.0094	M	0.72118	2.19	0.20821	N	0.999846	B	0.27498	0.18	B	0.23574	0.047	T	0.25433	-1.0132	10	0.37606	T	0.19	.	8.8415	0.35144	0.8108:0.1892:0.0:0.0	.	64	Q9BRS2	RIOK1_HUMAN	G	64	ENSP00000369162:D64G	ENSP00000369162:D64G	D	+	2	0	RIOK1	7338450	0.980000	0.34600	0.005000	0.12908	0.287000	0.27160	2.735000	0.47377	1.879000	0.54435	0.533000	0.62120	GAC		0.433	RIOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039780.2	NM_031480	
LRRC16A	55604	broad.mit.edu	37	6	25520554	25520554	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:25520554G>A	ENST00000329474.6	+	23	2325	c.1957G>A	c.(1957-1959)Gct>Act	p.A653T		NM_001173977.1|NM_017640.5	NP_001167448.1|NP_060110.4	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	653					actin filament organization (GO:0007015)|barbed-end actin filament uncapping (GO:0051638)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|lamellipodium assembly (GO:0030032)|negative regulation of barbed-end actin filament capping (GO:2000813)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of lamellipodium organization (GO:1902745)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|ruffle organization (GO:0031529)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|lamellipodium (GO:0030027)|nucleus (GO:0005634)	protein complex binding (GO:0032403)	p.A653T(1)		breast(4)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	50						AACAGAAGACGCTCTGCAAAA	0.308																																					p.A653T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1957A	6						.						45.0	41.0	42.0					6																	25520554		1794	4052	5846	25628533	SO:0001583	missense	55604	exon23			AK000055	CCDS54973.1	6p22.1	2010-09-10	2008-02-12	2008-02-12	ENSG00000079691	ENSG00000079691			21581	protein-coding gene	gene with protein product	"""capping protein, Arp2/3, and Myosin-I Linker homolog 1 (Dictyostelium)"""	609593	"""leucine rich repeat containing 16"""	LRRC16		19846667	Standard	NM_017640		Approved	dJ501N12.1, FLJ20048, CARMIL, CARMIL1	uc011djw.2	Q5VZK9	OTTHUMG00000014393	ENST00000329474.6:c.1957G>A	6.37:g.25520554G>A	ENSP00000331983:p.Ala653Thr	Somatic		Capture	Illumina HiSeq	Phase_I	25628533	NM_017640	B8X1J0|Q6ZUH5|Q6ZW07|Q9NXU7	Missense_Mutation	SNP	ENST00000329474.6	37	CCDS54973.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.843449	0.91197	.	.	ENSG00000079691	ENST00000329474;ENST00000399313	T	0.49139	0.79	4.57	4.57	0.56435	.	0.000000	0.85682	D	0.000000	T	0.43831	0.1265	L	0.55990	1.75	0.80722	D	1	D;D;D	0.57257	0.979;0.968;0.974	P;B;P	0.51516	0.558;0.439;0.672	T	0.27157	-1.0082	10	0.28530	T	0.3	.	17.7325	0.88382	0.0:0.0:1.0:0.0	.	653;653;653	Q5VZK9;B2RTQ5;Q5VZK9-2	LR16A_HUMAN;.;.	T	653	ENSP00000331983:A653T	ENSP00000331983:A653T	A	+	1	0	LRRC16A	25628533	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	9.065000	0.93941	2.224000	0.72417	0.650000	0.86243	GCT		0.308	LRRC16A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040045.2	NM_017640	
PRSS16	10279	broad.mit.edu	37	6	27220721	27220721	+	Silent	SNP	C	C	T	rs191407230	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:27220721C>T	ENST00000230582.3	+	9	1158	c.1143C>T	c.(1141-1143)ttC>ttT	p.F381F	PRSS16_ENST00000421826.2_Silent_p.F124F|PRSS16_ENST00000377456.2_Intron	NM_005865.3	NP_005856.1	Q9NQE7	TSSP_HUMAN	protease, serine, 16 (thymus)	381					protein catabolic process (GO:0030163)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|lysosome (GO:0005764)	serine-type peptidase activity (GO:0008236)	p.F381F(1)		central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	26						GTACCGAGTTCGGCTTCTGTA	0.507													C|||	2	0.000399361	0.0015	0.0	5008	,	,		21194	0.0		0.0	False		,,,				2504	0.0				p.F381F	NSCLC(178;1118 2105 17078 23587 44429)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1143T	6						.	C		1,4405	2.1+/-5.4	0,1,2202	209.0	178.0	188.0		1143	-7.3	0.9	6		188	0,8600		0,0,4300	no	coding-synonymous	PRSS16	NM_005865.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		381/515	27220721	1,13005	2203	4300	6503	27328700	SO:0001819	synonymous_variant	10279	exon9			AF052514	CCDS4623.1	6p21	2010-05-07			ENSG00000112812	ENSG00000112812		"""Serine peptidases / Serine peptidases"""	9480	protein-coding gene	gene with protein product		607169				10527559	Standard	NM_005865		Approved	TSSP	uc003nja.3	Q9NQE7	OTTHUMG00000016167	ENST00000230582.3:c.1143C>T	6.37:g.27220721C>T		Somatic		Capture	Illumina HiSeq	Phase_I	27328700	NM_005865	O75416	Silent	SNP	ENST00000230582.3	37	CCDS4623.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	8.864	0.947645	0.18356	2.27E-4	0.0	ENSG00000112812	ENST00000485993;ENST00000475106	.	.	.	4.26	-7.33	0.01431	.	.	.	.	.	T	0.37293	0.0998	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56896	-0.7903	4	.	.	.	-26.3792	11.6689	0.51389	0.0:0.535:0.0:0.465	.	.	.	.	W	134;160	.	.	R	+	1	2	PRSS16	27328700	0.105000	0.21958	0.949000	0.38748	0.911000	0.54048	-2.253000	0.01184	-1.143000	0.02866	-1.012000	0.02466	CGG		0.507	PRSS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043418.2		
HLA-C	3107	broad.mit.edu	37	6	31238154	31238154	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:31238154C>A	ENST00000376228.5	-	4	742	c.728G>T	c.(727-729)cGg>cTg	p.R243L	HLA-C_ENST00000383329.3_Missense_Mutation_p.R243L	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	243	Alpha-3.|Ig-like C1-type.				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 exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)	p.R243L(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						CTCCCCATCCCGCTGCCAGGT	0.632																																					p.R243L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G728T	6						.						38.0	37.0	37.0					6																	31238154		2198	4286	6484	31346133	SO:0001583	missense	3107	exon4			M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.728G>T	6.37:g.31238154C>A	ENSP00000365402:p.Arg243Leu	Somatic		Capture	Illumina HiSeq	Phase_I	31346133	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	.	.	.	.	.	.	.	.	.	.	.	5.093	0.202806	0.09652	.	.	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	T;T	0.03065	4.06;4.06	2.67	-0.601	0.11638	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.232985	0.21532	U	0.073034	T	0.01029	0.0034	L	0.46819	1.47	0.20873	N	0.999831	B;B;B;B	0.26577	0.153;0.019;0.066;0.019	B;B;B;B	0.26416	0.069;0.022;0.042;0.022	T	0.45381	-0.9265	10	0.87932	D	0	.	1.0722	0.01623	0.2389:0.4:0.2131:0.148	.	243;243;243;243	A2AEA4;A6H578;A2AEA2;P10321	.;.;.;1C07_HUMAN	L	243;243;243;280	ENSP00000365402:R243L;ENSP00000372819:R243L	ENSP00000365402:R243L	R	-	2	0	HLA-C	31346133	0.000000	0.05858	0.981000	0.43875	0.450000	0.32258	-0.485000	0.06520	-0.130000	0.11599	0.298000	0.19748	CGG		0.632	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
NFKBIL1	4795	broad.mit.edu	37	6	31526322	31526322	+	Silent	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:31526322C>A	ENST00000376148.4	+	4	1194	c.1080C>A	c.(1078-1080)ggC>ggA	p.G360G	NFKBIL1_ENST00000376145.4_Silent_p.G345G	NM_005007.3	NP_004998.3	Q9UBC1	IKBL1_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 1	360					cellular response to lipopolysaccharide (GO:0071222)|cytoplasmic sequestering of transcription factor (GO:0042994)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of tumor necrosis factor production (GO:0032720)	cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)		p.G360G(1)		breast(1)|endometrium(2)|large_intestine(1)|lung(2)|skin(1)	7						GGGAGCTGGGCCGTGTGATGG	0.612																																					p.G322G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C966A	6						.						15.0	9.0	11.0					6																	31526322		1504	2691	4195	31634301	SO:0001819	synonymous_variant	4795	exon4			X77909	CCDS4700.1, CCDS47399.1, CCDS47400.1	6p21.3	2010-02-17			ENSG00000204498	ENSG00000204498			7800	protein-coding gene	gene with protein product		601022		NFKBIL		8081366	Standard	NM_005007		Approved	IKBL	uc003nub.3	Q9UBC1	OTTHUMG00000031038	ENST00000376148.4:c.1080C>A	6.37:g.31526322C>A		Somatic		Capture	Illumina HiSeq	Phase_I	31634301	NM_001144963	A6NL91|B4DUW1|Q14625|Q5HYU4|Q5RJ72|Q5ST96|Q5STV4|Q5STV5|Q9UBX4	Silent	SNP	ENST00000376148.4	37	CCDS4700.1																																																																																				0.612	NFKBIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076036.3	NM_005007	
TAP1	6890	broad.mit.edu	37	6	32818271	32818271	+	Silent	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:32818271T>C	ENST00000354258.4	-	5	1415	c.1254A>G	c.(1252-1254)gaA>gaG	p.E418E	TAP1_ENST00000425148.2_Silent_p.E157E|PSMB9_ENST00000395330.1_Intron	NM_000593.5	NP_000584.2	Q03518	TAP1_HUMAN	transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)	418	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|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)|cytosol to ER transport (GO:0046967)|defense response (GO:0006952)|intracellular transport of viral protein in host cell (GO:0019060)|peptide transport (GO:0015833)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)|TAP complex (GO:0042825)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|MHC class Ib protein binding (GO:0023029)|peptide antigen binding (GO:0042605)|peptide transporter activity (GO:0015197)|protein homodimerization activity (GO:0042803)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)	p.E418E(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(4)|prostate(1)|skin(1)	21					Lapatinib(DB01259)	TTGCCAGAGATTCCCGCACCT	0.537																																					p.E418E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1254G	6						.						60.0	66.0	64.0					6																	32818271		2203	4300	6503	32926249	SO:0001819	synonymous_variant	6890	exon5				CCDS4758.1	6p21.3	2014-09-17			ENSG00000168394	ENSG00000168394		"""ATP binding cassette transporters / subfamily B"""	43	protein-coding gene	gene with protein product		170260		ABCB2		1529427, 1946428	Standard	NM_000593		Approved	PSF1, RING4, D6S114E	uc003ocg.3	Q03518	OTTHUMG00000031067	ENST00000354258.4:c.1254A>G	6.37:g.32818271T>C		Somatic		Capture	Illumina HiSeq	Phase_I	32926249	NM_000593	Q16149|Q96CP4	Silent	SNP	ENST00000354258.4	37	CCDS4758.1																																																																																				0.537	TAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076087.2	NM_000593	
HLA-DMB	3109	broad.mit.edu	37	6	32903331	32903331	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:32903331G>A	ENST00000418107.2	-	4	983	c.721C>T	c.(721-723)Cgg>Tgg	p.R241W	AL645941.1_ENST00000390777.1_RNA	NM_002118.4	NP_002109.2	P28068	DMB_HUMAN	major histocompatibility complex, class II, DM beta	241					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|immune response (GO:0006955)|MHC class II protein complex assembly (GO:0002399)|peptide antigen assembly with MHC class II protein complex (GO:0002503)|positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001190)|positive regulation of T cell proliferation (GO:0042102)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)	MHC class II protein complex binding (GO:0023026)			breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13						CCAGCTCTCCGCCAGCTGATC	0.552																																					p.R241W												.	.	0			c.C721T	6						.						98.0	110.0	105.0					6																	32903331		1509	2709	4218	33011309	SO:0001583	missense	3109	exon4				CCDS4760.1	6p21.3	2014-05-16			ENSG00000242574	ENSG00000242574		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4935	protein-coding gene	gene with protein product		142856				1922365	Standard	NM_002118		Approved	D6S221E, RING7	uc003ocl.2	P28068	OTTHUMG00000031176	ENST00000418107.2:c.721C>T	6.37:g.32903331G>A	ENSP00000398890:p.Arg241Trp	None		Capture	Illumina HiSeq	Phase_I	33011309	NM_002118	O77936|Q13012|Q29751|Q58ZE2|Q5SNZ8|Q5STC4|Q9XRX2	Missense_Mutation	SNP	ENST00000418107.2	37	CCDS4760.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.89|11.89	1.772941|1.772941	0.31411|0.31411	.|.	.|.	ENSG00000242574|ENSG00000242574	ENST00000414017|ENST00000446948;ENST00000418107	.|T	.|0.01272	.|5.07	4.81|4.81	2.0|2.0	0.26442|0.26442	.|.	.|0.125959	.|0.36002	.|N	.|0.002858	T|T	0.00906|0.00906	0.0030|0.0030	M|M	0.82517|0.82517	2.595|2.595	0.80722|0.80722	D|D	1|1	.|B;B	.|0.32382	.|0.368;0.175	.|B;B	.|0.25759	.|0.063;0.032	T|T	0.49661|0.49661	-0.8916|-0.8916	5|10	.|0.87932	.|D	.|0	.|.	4.5211|4.5211	0.11959|0.11959	0.1875:0.0:0.6377:0.1748|0.1875:0.0:0.6377:0.1748	.|.	.|130;241	.|B0V062;P28068	.|.;DMB_HUMAN	V|W	130|241	.|ENSP00000398890:R241W	.|ENSP00000398890:R241W	A|R	-|-	2|1	0|2	HLA-DMB|HLA-DMB	33011309|33011309	0.954000|0.954000	0.32549|0.32549	0.998000|0.998000	0.56505|0.56505	0.792000|0.792000	0.44763|0.44763	0.312000|0.312000	0.19397|0.19397	0.319000|0.319000	0.23209|0.23209	-0.558000|-0.558000	0.04189|0.04189	GCG|CGG		0.552	HLA-DMB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076340.2	NM_002118	
PPARD	5467	broad.mit.edu	37	6	35393666	35393666	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:35393666G>A	ENST00000311565.4	+	9	1485	c.1136G>A	c.(1135-1137)cGt>cAt	p.R379H	PPARD_ENST00000418635.2_Missense_Mutation_p.R281H|PPARD_ENST00000540939.1_Missense_Mutation_p.R276H|PPARD_ENST00000448077.2_Missense_Mutation_p.R340H|PPARD_ENST00000360694.3_Missense_Mutation_p.R379H	NM_001171818.1	NP_001165289.1	Q03181	PPARD_HUMAN	peroxisome proliferator-activated receptor delta	379	Ligand-binding.				adipose tissue development (GO:0060612)|anagen (GO:0042640)|apoptotic signaling pathway (GO:0097190)|axon ensheathment (GO:0008366)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cell-substrate adhesion (GO:0031589)|cellular response to hypoxia (GO:0071456)|cholesterol metabolic process (GO:0008203)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|fatty acid beta-oxidation (GO:0006635)|fatty acid catabolic process (GO:0009062)|fatty acid transport (GO:0015908)|gene expression (GO:0010467)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|heart development (GO:0007507)|intracellular receptor signaling pathway (GO:0030522)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)|lipid metabolic process (GO:0006629)|mRNA transcription (GO:0009299)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of inflammatory response (GO:0050728)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|phospholipid biosynthetic process (GO:0008654)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epidermis development (GO:0045684)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of insulin secretion (GO:0032024)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasodilation (GO:0045909)|proteoglycan metabolic process (GO:0006029)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to activity (GO:0014823)|response to glucose (GO:0009749)|response to vitamin A (GO:0033189)|transcription initiation from RNA polymerase II promoter (GO:0006367)|vitamin A metabolic process (GO:0006776)|wound healing (GO:0042060)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|drug binding (GO:0008144)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|linoleic acid binding (GO:0070539)|lipid binding (GO:0008289)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.R379H(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|large_intestine(4)|liver(2)|lung(9)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23					Bezafibrate(DB01393)|Icosapent(DB00159)|Sulindac(DB00605)|Treprostinil(DB00374)	ACCATCCTGCGTGCCCTCGAA	0.627																																					p.R379H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1136A	6						.						112.0	98.0	103.0					6																	35393666		2203	4300	6503	35501644	SO:0001583	missense	5467	exon9			L07592	CCDS4803.1, CCDS4804.1, CCDS54994.1, CCDS54995.1	6p21.2	2013-01-16	2006-10-17		ENSG00000112033	ENSG00000112033		"""Nuclear hormone receptors"""	9235	protein-coding gene	gene with protein product		600409	"""peroxisome proliferative activated receptor, delta"""			1333051	Standard	NM_177435		Approved	NUC1, NUCII, FAAR, NR1C2	uc003okm.3	Q03181	OTTHUMG00000014567	ENST00000311565.4:c.1136G>A	6.37:g.35393666G>A	ENSP00000310928:p.Arg379His	Somatic		Capture	Illumina HiSeq	Phase_I	35501644	NM_001171818	A8K6J6|B4E3V3|B6ZGS1|B7Z3W1|E9PE18|Q5D1P0|Q7Z5K0|Q9BUD4	Missense_Mutation	SNP	ENST00000311565.4	37	CCDS4803.1	.	.	.	.	.	.	.	.	.	.	G	12.39	1.922548	0.33908	.	.	ENSG00000112033	ENST00000448077;ENST00000360694;ENST00000418635;ENST00000311565;ENST00000540939	D;D;D;D;D	0.96802	-4.13;-4.13;-4.13;-4.13;-4.13	5.05	2.1	0.27182	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.453737	0.25708	N	0.028835	T	0.81997	0.4941	N	0.04335	-0.225	0.38358	D	0.944533	D;P;P	0.53151	0.958;0.882;0.95	P;B;B	0.44359	0.447;0.443;0.443	T	0.80141	-0.1506	10	0.17832	T	0.49	.	8.4014	0.32588	0.349:0.0:0.651:0.0	.	281;340;379	E9PE18;B7Z3W1;Q03181	.;.;PPARD_HUMAN	H	340;379;281;379;276	ENSP00000414372:R340H;ENSP00000353916:R379H;ENSP00000413314:R281H;ENSP00000310928:R379H;ENSP00000443759:R276H	ENSP00000310928:R379H	R	+	2	0	PPARD	35501644	0.997000	0.39634	0.995000	0.50966	0.982000	0.71751	1.886000	0.39688	0.434000	0.26340	0.561000	0.74099	CGT		0.627	PPARD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040288.1	NM_006238	
GLTSCR1L	23506	broad.mit.edu	37	6	42832478	42832478	+	Missense_Mutation	SNP	A	A	G	rs372192707		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:42832478A>G	ENST00000314073.5	+	13	2710	c.2534A>G	c.(2533-2535)cAt>cGt	p.H845R	GLTSCR1L_ENST00000394168.1_Missense_Mutation_p.H845R			Q6AI39	GSC1L_HUMAN	GLTSCR1-like	845								p.H845R(1)									AGTGACCAGCATGGCAGTAAA	0.502																																					p.H845R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2534G	6						.						126.0	107.0	114.0					6																	42832478		2203	4300	6503	42940456	SO:0001583	missense	23506	exon12			AL833540	CCDS34451.1	6p21.1	2012-11-29	2012-11-29	2012-11-29	ENSG00000112624	ENSG00000112624			21111	protein-coding gene	gene with protein product			"""KIAA0240"""	KIAA0240			Standard	XM_005248972		Approved		uc003osp.1	Q6AI39	OTTHUMG00000014706	ENST00000314073.5:c.2534A>G	6.37:g.42832478A>G	ENSP00000313933:p.His845Arg	Somatic		Capture	Illumina HiSeq	Phase_I	42940456	NM_015349	A1L3W2|Q5TFZ3|Q92514	Missense_Mutation	SNP	ENST00000314073.5	37	CCDS34451.1	.	.	.	.	.	.	.	.	.	.	A	11.83	1.756675	0.31137	.	.	ENSG00000112624	ENST00000394167;ENST00000314073;ENST00000394168	T;T	0.41400	1.0;1.0	5.07	-0.958	0.10347	.	0.352452	0.28114	N	0.016552	T	0.12220	0.0297	N	0.24115	0.695	0.27237	N	0.959242	B	0.19200	0.034	B	0.18871	0.023	T	0.30707	-0.9969	10	0.41790	T	0.15	-0.199	13.9062	0.63836	0.4915:0.5085:0.0:0.0	.	845	Q6AI39	K0240_HUMAN	R	845	ENSP00000313933:H845R;ENSP00000377723:H845R	ENSP00000313933:H845R	H	+	2	0	KIAA0240	42940456	0.846000	0.29590	0.937000	0.37676	0.979000	0.70002	1.486000	0.35530	-0.008000	0.14320	0.533000	0.62120	CAT		0.502	GLTSCR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040562.3	NM_015349	
SRF	6722	broad.mit.edu	37	6	43141726	43141726	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:43141726C>A	ENST00000265354.4	+	2	1013	c.655C>A	c.(655-657)Ctc>Atc	p.L219I	SRF_ENST00000457278.2_Missense_Mutation_p.L15I	NM_003131.2	NP_003122.1	P11831	SRF_HUMAN	serum response factor (c-fos serum response element-binding transcription factor)	219	Involved in dimerization.				angiogenesis involved in wound healing (GO:0060055)|associative learning (GO:0008306)|cardiac myofibril assembly (GO:0055003)|cardiac vascular smooth muscle cell differentiation (GO:0060947)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-matrix adhesion (GO:0007160)|cellular response to glucose stimulus (GO:0071333)|cellular senescence (GO:0090398)|contractile actin filament bundle assembly (GO:0030038)|developmental growth (GO:0048589)|dorsal aorta morphogenesis (GO:0035912)|epithelial cell-cell adhesion (GO:0090136)|epithelial structure maintenance (GO:0010669)|erythrocyte development (GO:0048821)|eyelid development in camera-type eye (GO:0061029)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula formation (GO:0060347)|hematopoietic stem cell differentiation (GO:0060218)|hippocampus development (GO:0021766)|long term synaptic depression (GO:0060292)|long-term memory (GO:0007616)|megakaryocyte development (GO:0035855)|mesoderm formation (GO:0001707)|morphogenesis of an epithelial sheet (GO:0002011)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|neuron development (GO:0048666)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|patterning of blood vessels (GO:0001569)|platelet activation (GO:0030168)|platelet formation (GO:0030220)|positive regulation of cell differentiation (GO:0045597)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription by glucose (GO:0046016)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription via serum response element binding (GO:0010735)|positive thymic T cell selection (GO:0045059)|primitive streak formation (GO:0090009)|regulation of cell adhesion (GO:0030155)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of water loss via skin (GO:0033561)|response to cytokine (GO:0034097)|response to hormone (GO:0009725)|response to hypoxia (GO:0001666)|response to toxic substance (GO:0009636)|sarcomere organization (GO:0045214)|skin morphogenesis (GO:0043589)|stress fiber assembly (GO:0043149)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)|tight junction assembly (GO:0070830)|transcription from RNA polymerase II promoter (GO:0006366)|trophectodermal cell differentiation (GO:0001829)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|serum response element binding (GO:0010736)|transcription factor binding (GO:0008134)	p.L219I(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)	12			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.011)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)			TCAGACCTGCCTCAACTCGCC	0.562																																					p.L219I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C655A	6						.						174.0	133.0	147.0					6																	43141726		2203	4300	6503	43249704	SO:0001583	missense	6722	exon2			J03161	CCDS4889.1	6p	2008-02-05			ENSG00000112658	ENSG00000112658			11291	protein-coding gene	gene with protein product		600589				3203386	Standard	NM_003131		Approved	MCM1	uc003oui.3	P11831	OTTHUMG00000014722	ENST00000265354.4:c.655C>A	6.37:g.43141726C>A	ENSP00000265354:p.Leu219Ile	Somatic		Capture	Illumina HiSeq	Phase_I	43249704	NM_003131	Q5T648	Missense_Mutation	SNP	ENST00000265354.4	37	CCDS4889.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.611060	0.87258	.	.	ENSG00000112658	ENST00000265354;ENST00000457278	D	0.89681	-2.55	5.11	5.11	0.69529	Transcription factor, MADS-box (1);	0.000000	0.85682	D	0.000000	D	0.92325	0.7565	M	0.72894	2.215	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.93090	0.6499	10	0.72032	D	0.01	-0.2676	12.9175	0.58214	0.0:0.922:0.0:0.078	.	219	P11831	SRF_HUMAN	I	219;15	ENSP00000265354:L219I	ENSP00000265354:L219I	L	+	1	0	SRF	43249704	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.353000	0.59411	2.371000	0.80710	0.561000	0.74099	CTC		0.562	SRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040581.1	NM_003131	
VEGFA	7422	broad.mit.edu	37	6	43749782	43749782	+	Missense_Mutation	SNP	G	G	A	rs369593555		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:43749782G>A	ENST00000523873.1	+	7	673	c.635G>A	c.(634-636)cGt>cAt	p.R212H	VEGFA_ENST00000457104.2_Intron|VEGFA_ENST00000372067.3_Missense_Mutation_p.R351H|VEGFA_ENST00000523950.1_Missense_Mutation_p.R171H|VEGFA_ENST00000520948.1_Missense_Mutation_p.R195H|VEGFA_ENST00000518689.1_Missense_Mutation_p.R189H|VEGFA_ENST00000372064.4_Intron|VEGFA_ENST00000324450.6_Intron|VEGFA_ENST00000372055.4_Missense_Mutation_p.R392H|VEGFA_ENST00000417285.2_Missense_Mutation_p.R351H|VEGFA_ENST00000425836.2_Missense_Mutation_p.R375H|VEGFA_ENST00000523125.1_Missense_Mutation_p.R171H|VEGFA_ENST00000413642.3_Missense_Mutation_p.R369H|VEGFA_ENST00000518824.1_Missense_Mutation_p.R171H|VEGFA_ENST00000482630.2_Missense_Mutation_p.R351H|VEGFA_ENST00000372077.4_Intron|VEGFA_ENST00000230480.6_Missense_Mutation_p.R143H			P15692	VEGFA_HUMAN	vascular endothelial growth factor A	212					activation of protein kinase activity (GO:0032147)|angiogenesis (GO:0001525)|artery morphogenesis (GO:0048844)|basophil chemotaxis (GO:0002575)|blood coagulation (GO:0007596)|branching morphogenesis of an epithelial tube (GO:0048754)|camera-type eye morphogenesis (GO:0048593)|cardiac muscle fiber development (GO:0048739)|cardiac vascular smooth muscle cell development (GO:0060948)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to hypoxia (GO:0071456)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|commissural neuron axon guidance (GO:0071679)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|dopaminergic neuron differentiation (GO:0071542)|endothelial cell chemotaxis (GO:0035767)|epithelial cell differentiation (GO:0030855)|eye photoreceptor cell development (GO:0042462)|growth (GO:0040007)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|induction of positive chemotaxis (GO:0050930)|kidney development (GO:0001822)|lactation (GO:0007595)|lung development (GO:0030324)|lymph vessel morphogenesis (GO:0036303)|macrophage differentiation (GO:0030225)|mammary gland alveolus development (GO:0060749)|mesoderm development (GO:0007498)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|outflow tract morphogenesis (GO:0003151)|ovarian follicle development (GO:0001541)|patterning of blood vessels (GO:0001569)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|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 cellular component movement (GO:0051272)|positive regulation of CREB transcription factor activity (GO:0032793)|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 epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mast cell chemotaxis (GO:0060754)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine autophosphorylation (GO:1900086)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein localization to early endosome (GO:1902966)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of receptor internalization (GO:0002092)|positive regulation of retinal ganglion cell axon guidance (GO:1902336)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation of vascular permeability (GO:0043117)|post-embryonic camera-type eye development (GO:0031077)|primitive erythrocyte differentiation (GO:0060319)|regulation of cell shape (GO:0008360)|regulation of retinal ganglion cell axon guidance (GO:0090259)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to hypoxia (GO:0001666)|surfactant homeostasis (GO:0043129)|tube formation (GO:0035148)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|VEGF-activated neuropilin signaling pathway (GO:0038190)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	chemoattractant activity (GO:0042056)|cytokine activity (GO:0005125)|extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|neuropilin binding (GO:0038191)|platelet-derived growth factor receptor binding (GO:0005161)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor agonist activity (GO:0048018)|vascular endothelial growth factor receptor 1 binding (GO:0043183)|vascular endothelial growth factor receptor 2 binding (GO:0043184)|vascular endothelial growth factor receptor binding (GO:0005172)	p.R392H(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)	9	all_cancers(18;5.46e-07)|all_epithelial(2;5.96e-08)|Lung NSC(15;0.000157)|all_lung(25;0.000486)|Hepatocellular(11;0.00309)		all cancers(41;0.000413)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0742)|OV - Ovarian serous cystadenocarcinoma(102;0.196)		Aflibercept(DB08885)|Bevacizumab(DB00112)|Carvedilol(DB01136)|Dalteparin(DB06779)|Gliclazide(DB01120)|Minocycline(DB01017)|Ranibizumab(DB01270)|Vandetanib(DB05294)	ACAGACTCGCGTTGCAAGGCG	0.517																																					p.R351H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1052A	6						.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,,HIS/ARG,,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,,HIS/ARG,,,,HIS/ARG	0,4406		0,0,2203	98.0	86.0	90.0		1175,1106,1052,1052,,1052,,635,584,566,512,512,,512,,,,1124	5.8	1.0	6		90	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,intron,missense,intron,missense,missense,missense,missense,missense,intron,missense,intron,intron,intron,missense	VEGFA	NM_001025366.2,NM_001025367.2,NM_001025368.2,NM_001025369.2,NM_001025370.2,NM_001033756.2,NM_001171622.1,NM_001171623.1,NM_001171624.1,NM_001171625.1,NM_001171626.1,NM_001171627.1,NM_001171628.1,NM_001171629.1,NM_001171630.1,NM_001204384.1,NM_001204385.1,NM_003376.5	29,29,29,29,,29,,29,29,29,29,29,,29,,,,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,,probably-damaging,,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,,probably-damaging,,,,probably-damaging	392/413,369/390,351/372,351/355,,351/372,,212/233,195/216,189/210,171/192,171/175,,171/192,,,,375/396	43749782	1,13005	2203	4300	6503	43857760	SO:0001583	missense	7422	exon6			AB021221	CCDS34457.1, CCDS4907.2, CCDS34458.1, CCDS47432.1, CCDS47433.1, CCDS47434.1, CCDS47435.1, CCDS55007.1, CCDS55008.1, CCDS55009.1, CCDS55010.1, CCDS55011.1, CCDS55012.1, CCDS55013.1, CCDS55014.1, CCDS55015.1, CCDS69125.1	6p12	2008-02-05	2006-10-31	2006-10-31	ENSG00000112715	ENSG00000112715			12680	protein-coding gene	gene with protein product		192240	"""vascular endothelial growth factor"""	VEGF		8786112	Standard	NM_001025366		Approved	VEGF-A, VPF	uc003owh.3	P15692	OTTHUMG00000014745	ENST00000523873.1:c.635G>A	6.37:g.43749782G>A	ENSP00000430479:p.Arg212His	Somatic		Capture	Illumina HiSeq	Phase_I	43857760	NM_001025369	B5BU86|H0Y2S8|H0Y407|H0Y414|H0Y462|H0Y8N2|H3BLW7|O60720|O75875|Q074Z4|Q16889|Q5UB46|Q6P0P5|Q96KJ0|Q96L82|Q96NW5|Q9H1W8|Q9H1W9|Q9UH58|Q9UL23	Missense_Mutation	SNP	ENST00000523873.1	37	CCDS55010.1	.	.	.	.	.	.	.	.	.	.	G	13.17	2.156162	0.38021	0.0	1.16E-4	ENSG00000112715	ENST00000372067;ENST00000417285;ENST00000413642;ENST00000372055;ENST00000482630;ENST00000425836;ENST00000520948;ENST00000523873;ENST00000523950;ENST00000518689;ENST00000523125;ENST00000518824;ENST00000230480;ENST00000520265	.	.	.	5.83	5.83	0.93111	.	0.158958	0.53938	D	0.000043	T	0.59307	0.2184	N	0.24115	0.695	0.47862	D	0.999533	P;D;P;D;P	0.89917	0.923;1.0;0.923;1.0;0.939	B;D;B;D;B	0.91635	0.304;0.999;0.304;0.997;0.441	T	0.61515	-0.7047	9	0.49607	T	0.09	-3.7466	19.1066	0.93299	0.0:0.0:1.0:0.0	.	171;392;189;375;351	P15692-8;P15692-14;P15692-3;P15692-13;P15692-11	.;.;.;.;.	H	351;351;369;392;351;375;195;212;171;189;171;171;143;91	.	ENSP00000230480:R143H	R	+	2	0	VEGFA	43857760	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.391000	0.79828	2.769000	0.95229	0.655000	0.94253	CGT		0.517	VEGFA-021	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000374460.1	NM_001025366	
TMEM63B	55362	broad.mit.edu	37	6	44115123	44115123	+	Silent	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:44115123C>A	ENST00000259746.9	+	12	1056	c.873C>A	c.(871-873)gcC>gcA	p.A291A	TMEM63B_ENST00000323267.6_Silent_p.A291A			Q5T3F8	CSCL2_HUMAN	transmembrane protein 63B	291					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	nucleotide binding (GO:0000166)	p.A291A(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(2)|prostate(2)|stomach(4)	35	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0215)			GGAAGAAGGCCGAGCGGGGAA	0.602																																					p.A291A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C873A	6						.						114.0	96.0	102.0					6																	44115123		2203	4300	6503	44223101	SO:0001819	synonymous_variant	55362	exon12			BC022095	CCDS34461.1	6p21.1	2008-02-05	2005-07-25	2005-07-25	ENSG00000137216	ENSG00000137216			17735	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 110"""	C6orf110			Standard	XM_005249211		Approved	DKFZp434P0531, dJ421H19.2	uc003owr.3	Q5T3F8	OTTHUMG00000014757	ENST00000259746.9:c.873C>A	6.37:g.44115123C>A		Somatic		Capture	Illumina HiSeq	Phase_I	44223101	NM_018426	B9EGU3|Q5T3F9|Q6AHX4|Q6P5A0|Q8N219|Q8NDE1|Q9NSG5	Silent	SNP	ENST00000259746.9	37	CCDS34461.1	.	.	.	.	.	.	.	.	.	.	C	8.457	0.854387	0.17106	.	.	ENSG00000137216	ENST00000371893	.	.	.	4.53	-9.07	0.00724	.	.	.	.	.	T	0.17450	0.0419	.	.	.	0.53005	D	0.99996	.	.	.	.	.	.	T	0.40794	-0.9544	4	.	.	.	.	2.8624	0.05591	0.283:0.0859:0.1467:0.4844	.	.	.	.	Q	220	.	.	P	+	2	0	TMEM63B	44223101	0.000000	0.05858	0.164000	0.22755	0.954000	0.61252	-3.685000	0.00393	-2.797000	0.00353	-0.898000	0.02899	CCG		0.602	TMEM63B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040712.2	XM_166410	
PKHD1	5314	broad.mit.edu	37	6	51799070	51799070	+	Missense_Mutation	SNP	C	C	T	rs375949362		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:51799070C>T	ENST00000371117.3	-	37	6234	c.5959G>A	c.(5959-5961)Gcc>Acc	p.A1987T	PKHD1_ENST00000340994.4_Missense_Mutation_p.A1987T	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	1987	G8 1. {ECO:0000255|PROSITE- ProRule:PRU00817}.				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.A1987T(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)					ACAAGGATGGCGTGTGCCCTG	0.542											OREG0017491	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1	0.000199681	0.0	0.0014	5008	,	,		19865	0.0		0.0	False		,,,				2504	0.0				p.A1987T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5959A	6						.	C	THR/ALA,THR/ALA	0,4406		0,0,2203	113.0	105.0	108.0		5959,5959	-0.9	0.1	6		108	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	PKHD1	NM_138694.3,NM_170724.2	58,58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	1987/4075,1987/3397	51799070	1,13005	2203	4300	6503	51907029	SO:0001583	missense	5314	exon37			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.5959G>A	6.37:g.51799070C>T	ENSP00000360158:p.Ala1987Thr	Somatic	980	Capture	Illumina HiSeq	Phase_I	51907029	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	C	10.54	1.378129	0.24944	0.0	1.16E-4	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.89050	-2.46;-2.46	5.59	-0.93	0.10441	G8 domain (2);	0.848896	0.10708	N	0.643186	T	0.65770	0.2723	L	0.34521	1.04	0.09310	N	1	P;P;P	0.45474	0.859;0.714;0.529	B;B;B	0.35655	0.207;0.08;0.102	T	0.57271	-0.7840	10	0.29301	T	0.29	.	10.5006	0.44804	0.3684:0.5613:0.0703:0.0	.	1987;1987;1987	A8MVM9;P08F94-2;P08F94	.;.;PKHD1_HUMAN	T	1987	ENSP00000360158:A1987T;ENSP00000341097:A1987T	ENSP00000341097:A1987T	A	-	1	0	PKHD1	51907029	0.035000	0.19736	0.057000	0.19452	0.924000	0.55760	0.083000	0.14871	-0.165000	0.10908	0.655000	0.94253	GCC		0.542	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
LRRC1	55227	broad.mit.edu	37	6	53778716	53778716	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:53778716C>T	ENST00000370888.1	+	11	1332	c.1055C>T	c.(1054-1056)gCa>gTa	p.A352V		NM_018214.4	NP_060684.4	Q9BTT6	LRRC1_HUMAN	leucine rich repeat containing 1	352						cytoplasm (GO:0005737)|membrane (GO:0016020)		p.A352V(1)		cervix(1)|endometrium(3)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20	Lung NSC(77;0.0147)			BRCA - Breast invasive adenocarcinoma(397;0.0745)		CGGATACCTGCAGAGGTGTCA	0.458																																					p.A352V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1055T	6						.						87.0	86.0	86.0					6																	53778716		1977	4154	6131	53886675	SO:0001583	missense	55227	exon11			AF332199	CCDS4953.2	6p12.2	2014-07-30	2003-11-19		ENSG00000137269	ENSG00000137269			14307	protein-coding gene	gene with protein product		608195	"""leucine-rich repeat-containing 1"""				Standard	NM_018214		Approved	dJ523E19.1, LANO, FLJ10775, FLJ11834	uc003pcd.1	Q9BTT6	OTTHUMG00000014885	ENST00000370888.1:c.1055C>T	6.37:g.53778716C>T	ENSP00000359925:p.Ala352Val	Somatic		Capture	Illumina HiSeq	Phase_I	53886675	NM_018214	Q5TGN3|Q9HAC0|Q9NVF1	Missense_Mutation	SNP	ENST00000370888.1	37	CCDS4953.2	.	.	.	.	.	.	.	.	.	.	C	18.27	3.587472	0.66105	.	.	ENSG00000137269	ENST00000370888	T	0.77229	-1.08	4.74	4.74	0.60224	.	0.162448	0.42172	D	0.000757	T	0.56731	0.2005	L	0.28740	0.885	0.80722	D	1	B	0.14805	0.011	B	0.14023	0.01	T	0.55250	-0.8170	10	0.33940	T	0.23	.	16.8882	0.86081	0.0:1.0:0.0:0.0	.	352	Q9BTT6	LRRC1_HUMAN	V	352	ENSP00000359925:A352V	ENSP00000359925:A352V	A	+	2	0	LRRC1	53886675	0.858000	0.29795	0.997000	0.53966	0.892000	0.51952	7.259000	0.78381	2.466000	0.83321	0.655000	0.94253	GCA		0.458	LRRC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040970.2	NM_025168	
HMGCLL1	54511	broad.mit.edu	37	6	55443836	55443836	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:55443836G>A	ENST00000398661.2	-	1	149	c.18C>T	c.(16-18)tcC>tcT	p.S6S	HMGCLL1_ENST00000370850.2_Silent_p.S6S|HMGCLL1_ENST00000428842.1_Silent_p.S6S|HMGCLL1_ENST00000274901.4_Silent_p.S6S|HMGCLL1_ENST00000358072.5_Silent_p.S6S|HMGCLL1_ENST00000308161.4_Silent_p.S6S|HMGCLL1_ENST00000508459.1_Silent_p.S6S	NM_019036.2	NP_061909.2	Q8TB92	HMGC2_HUMAN	3-hydroxymethyl-3-methylglutaryl-CoA lyase-like 1	6					ketone body biosynthetic process (GO:0046951)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	hydroxymethylglutaryl-CoA lyase activity (GO:0004419)|metal ion binding (GO:0046872)	p.S6S(2)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	31	Lung NSC(77;0.0875)		LUSC - Lung squamous cell carcinoma(124;0.23)			GCTTCACCGCGGATGGCACAT	0.687																																					p.S6S	Ovarian(35;840 893 7837 15538 42887)											.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C18T	6						.						21.0	23.0	23.0					6																	55443836		1993	4146	6139	55551795	SO:0001819	synonymous_variant	54511	exon1			AK055075	CCDS43474.1, CCDS43475.1, CCDS75472.1, CCDS75473.1	6p12.1	2010-04-30	2010-04-30		ENSG00000146151	ENSG00000146151			21359	protein-coding gene	gene with protein product			"""3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase-like 1"""			8619474, 9110174	Standard	NM_001042406		Approved	DKFZP434G1411, bA418P12.1	uc003pcn.3	Q8TB92	OTTHUMG00000014902	ENST00000398661.2:c.18C>T	6.37:g.55443836G>A		Somatic		Capture	Illumina HiSeq	Phase_I	55551795	NM_019036	B1AQ42|B3KNV0|B7Z1S7|F8W793|Q6ZSA9	Silent	SNP	ENST00000398661.2	37	CCDS43475.1																																																																																				0.687	HMGCLL1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360290.1	XM_166383	
DOPEY1	23033	broad.mit.edu	37	6	83828614	83828614	+	Missense_Mutation	SNP	G	G	A	rs149504271	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:83828614G>A	ENST00000349129.2	+	8	1048	c.788G>A	c.(787-789)cGa>cAa	p.R263Q	DOPEY1_ENST00000536812.1_3'UTR|DOPEY1_ENST00000369739.3_Missense_Mutation_p.R263Q|DOPEY1_ENST00000237163.5_Missense_Mutation_p.R263Q	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	263					protein transport (GO:0015031)			p.R263Q(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)		CAGGCCACTCGACCGGATATG	0.373																																					p.R263Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G788A	6						.	G	GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	230.0	204.0	213.0		788,788	5.5	1.0	6	dbSNP_134	213	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	DOPEY1	NM_001199942.1,NM_015018.3	43,43	0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231	probably-damaging,probably-damaging	263/2477,263/2466	83828614	3,13003	2203	4300	6503	83885333	SO:0001583	missense	23033	exon8			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.788G>A	6.37:g.83828614G>A	ENSP00000195654:p.Arg263Gln	Somatic		Capture	Illumina HiSeq	Phase_I	83885333	NM_015018	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Missense_Mutation	SNP	ENST00000349129.2	37	CCDS4996.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.798826	0.90538	2.27E-4	2.33E-4	ENSG00000083097	ENST00000349129;ENST00000237163;ENST00000369739	T;T;T	0.24908	1.84;1.84;1.83	5.49	5.49	0.81192	Dopey, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.29620	0.0739	L	0.28694	0.88	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.68192	0.956;0.956	T	0.01791	-1.1273	10	0.30854	T	0.27	.	19.3608	0.94436	0.0:0.0:1.0:0.0	.	263;263	B2RWN9;Q5JWR5	.;DOP1_HUMAN	Q	263	ENSP00000195654:R263Q;ENSP00000237163:R263Q;ENSP00000358754:R263Q	ENSP00000237163:R263Q	R	+	2	0	DOPEY1	83885333	1.000000	0.71417	1.000000	0.80357	0.557000	0.35523	9.476000	0.97823	2.572000	0.86782	0.650000	0.86243	CGA		0.373	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018	
CEP162	22832	broad.mit.edu	37	6	84895045	84895045	+	Missense_Mutation	SNP	G	G	A	rs148340487		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:84895045G>A	ENST00000403245.3	-	13	1637	c.1523C>T	c.(1522-1524)gCg>gTg	p.A508V	KIAA1009_ENST00000461137.1_5'UTR|KIAA1009_ENST00000257766.4_Missense_Mutation_p.A432V	NM_014895.2	NP_055710.2												p.A508V(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	43		all_cancers(76;1.5e-06)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00258)		BRCA - Breast invasive adenocarcinoma(397;0.089)		CCTAACTGACGCATATAATCC	0.418																																					p.A508V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1523T	6						.	G	VAL/ALA	0,4406		0,0,2203	161.0	161.0	161.0		1523	4.4	1.0	6	dbSNP_134	161	1,8599	1.2+/-3.3	0,1,4299	no	missense	KIAA1009	NM_014895.2	64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	508/1404	84895045	1,13005	2203	4300	6503	84951764	SO:0001583	missense	22832	exon13																														ENST00000403245.3:c.1523C>T	6.37:g.84895045G>A	ENSP00000385215:p.Ala508Val	Somatic		Capture	Illumina HiSeq	Phase_I	84951764	NM_014895		Missense_Mutation	SNP	ENST00000403245.3	37	CCDS34494.2	.	.	.	.	.	.	.	.	.	.	G	14.45	2.539014	0.45176	0.0	1.16E-4	ENSG00000135315	ENST00000257766;ENST00000403245	T;T	0.21361	2.01;2.01	5.34	4.41	0.53225	.	0.186153	0.38217	N	0.001777	T	0.16214	0.0390	L	0.59436	1.845	0.28733	N	0.90237	D;D	0.61697	0.972;0.99	P;P	0.53649	0.469;0.731	T	0.05194	-1.0900	10	0.33141	T	0.24	-9.0904	7.0636	0.25139	0.0915:0.1758:0.7327:0.0	.	508;508	Q5TB80;C9JFM9	QN1_HUMAN;.	V	432;508	ENSP00000257766:A432V;ENSP00000385215:A508V	ENSP00000257766:A432V	A	-	2	0	KIAA1009	84951764	0.981000	0.34729	0.981000	0.43875	0.248000	0.25809	0.978000	0.29488	2.662000	0.90505	0.637000	0.83480	GCG		0.418	KIAA1009-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317315.1		
ZNF292	23036	broad.mit.edu	37	6	87969085	87969085	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:87969085C>A	ENST00000369577.3	+	8	5781	c.5738C>A	c.(5737-5739)gCt>gAt	p.A1913D	ZNF292_ENST00000339907.4_Missense_Mutation_p.A1908D	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	1913						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.A1913D(1)|p.A1768D(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)		AACTACAGTGCTATGACAAAG	0.323																																					p.A1913D												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C5738A	6						.						33.0	33.0	33.0					6																	87969085		1857	4099	5956	88025804	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.5738C>A	6.37:g.87969085C>A	ENSP00000358590:p.Ala1913Asp	Somatic		Capture	Illumina HiSeq	Phase_I	88025804	NM_015021	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Missense_Mutation	SNP	ENST00000369577.3	37	CCDS47457.1	.	.	.	.	.	.	.	.	.	.	C	16.18	3.050511	0.55218	.	.	ENSG00000188994	ENST00000369577;ENST00000339907	T;T	0.42131	0.98;0.98	5.87	5.87	0.94306	Zinc finger, C2H2-like (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.097321	0.64402	D	0.000001	T	0.52240	0.1722	L	0.56769	1.78	0.45822	D	0.998697	D	0.89917	1.0	D	0.76575	0.988	T	0.20773	-1.0265	10	0.14656	T	0.56	.	20.5827	0.99408	0.0:1.0:0.0:0.0	.	1913	O60281	ZN292_HUMAN	D	1913;1908	ENSP00000358590:A1913D;ENSP00000342847:A1908D	ENSP00000342847:A1908D	A	+	2	0	ZNF292	88025804	1.000000	0.71417	0.998000	0.56505	0.980000	0.70556	3.999000	0.57031	2.941000	0.99782	0.655000	0.94253	GCT		0.323	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021	
SRSF12	135295	broad.mit.edu	37	6	89816897	89816897	+	Missense_Mutation	SNP	C	C	T	rs191899999		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:89816897C>T	ENST00000452027.2	-	2	339	c.146G>A	c.(145-147)cGc>cAc	p.R49H		NM_080743.4	NP_542781.3	Q8WXF0	SRS12_HUMAN	serine/arginine-rich splicing factor 12	49	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cytoplasmic transport (GO:0016482)|mRNA 5'-splice site recognition (GO:0000395)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|spliceosomal tri-snRNP complex assembly (GO:0000244)	nucleoplasm (GO:0005654)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RS domain binding (GO:0050733)|unfolded protein binding (GO:0051082)	p.R49H(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(4)	8						TCCTCTTGGGCGGCGAGTGTA	0.388													C|||	1	0.000199681	0.0	0.0014	5008	,	,		18073	0.0		0.0	False		,,,				2504	0.0				p.R49H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G146A	6						.						106.0	115.0	112.0					6																	89816897		2172	4296	6468	89873616	SO:0001583	missense	135295	exon2			AF449428	CCDS47459.1	6q16.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000154548	ENSG00000154548		"""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	21220	protein-coding gene	gene with protein product	"""splicing factor, arginine/serine-rich 19"", ""SR splicing factor 12"""		"""splicing factor, arginine/serine-rich 13B"""	SFRS13B		11684676, 20516191	Standard	NM_080743		Approved	SRrp35, SFRS19	uc021zcq.1	Q8WXF0	OTTHUMG00000015192	ENST00000452027.2:c.146G>A	6.37:g.89816897C>T	ENSP00000414302:p.Arg49His	Somatic		Capture	Illumina HiSeq	Phase_I	89873616	NM_080743	B2RA22|Q5T7K0|Q8WW25	Missense_Mutation	SNP	ENST00000452027.2	37	CCDS47459.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	15.19	2.759532	0.49468	.	.	ENSG00000154548	ENST00000452027	T	0.18960	2.18	5.34	4.46	0.54185	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.182482	0.37715	N	0.001966	T	0.13072	0.0317	M	0.72353	2.195	0.40032	D	0.975542	P	0.39601	0.68	B	0.30855	0.121	T	0.06303	-1.0834	10	0.59425	D	0.04	.	15.4196	0.75000	0.0:0.8602:0.1398:0.0	.	49	Q8WXF0	SRS12_HUMAN	H	49	ENSP00000414302:R49H	ENSP00000414302:R49H	R	-	2	0	SRSF12	89873616	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.829000	0.48128	1.607000	0.50170	0.650000	0.86243	CGC		0.388	SRSF12-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041474.2	NM_080743	
ANKRD6	22881	broad.mit.edu	37	6	90312802	90312802	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:90312802G>A	ENST00000522441.1	+	4	915	c.274G>A	c.(274-276)Gcg>Acg	p.A92T	ANKRD6_ENST00000339746.4_Missense_Mutation_p.A92T|ANKRD6_ENST00000485637.1_Missense_Mutation_p.A92T|ANKRD6_ENST00000369408.5_Missense_Mutation_p.A92T|ANKRD6_ENST00000447838.2_Missense_Mutation_p.A92T|ANKRD6_ENST00000520793.1_Missense_Mutation_p.A92T|ANKRD6_ENST00000520886.2_3'UTR	NM_001242811.1	NP_001229740.1	Q9Y2G4	ANKR6_HUMAN	ankyrin repeat domain 6	92					negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of JNK cascade (GO:0046330)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.A92T(1)		NS(1)|endometrium(3)|large_intestine(7)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|stomach(2)	21		all_cancers(76;1.22e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;1.83e-05)|Lung NSC(302;0.239)		BRCA - Breast invasive adenocarcinoma(108;0.0209)		GGAGATCATCGCGGCGCTCAT	0.612																																					p.A92T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G274A	6						.						40.0	47.0	45.0					6																	90312802		2106	4210	6316	90369521	SO:0001583	missense	22881	exon4			AB023174	CCDS47460.1, CCDS56441.1, CCDS56442.1, CCDS56443.1	6q14.2-q16.1	2013-03-20			ENSG00000135299	ENSG00000135299		"""Ankyrin repeat domain containing"""	17280	protein-coding gene	gene with protein product		610583					Standard	NM_001242809		Approved	KIAA0957	uc003pni.4	Q9Y2G4	OTTHUMG00000015202	ENST00000522441.1:c.274G>A	6.37:g.90312802G>A	ENSP00000430985:p.Ala92Thr	Somatic		Capture	Illumina HiSeq	Phase_I	90369521	NM_014942	B3KUC3|Q5JUJ4|Q5JUJ5|Q8IUQ8|Q9NU24|Q9UFQ9	Missense_Mutation	SNP	ENST00000522441.1	37	CCDS56441.1	.	.	.	.	.	.	.	.	.	.	G	3.666	-0.068606	0.07228	.	.	ENSG00000135299	ENST00000369408;ENST00000339746;ENST00000447838;ENST00000465722;ENST00000523798;ENST00000522441;ENST00000485637;ENST00000522705;ENST00000520793	T;T;T;T;T;T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07	5.93	2.12	0.27331	Ankyrin repeat-containing domain (4);	0.224281	0.31145	N	0.008164	T	0.21427	0.0516	N	0.21324	0.655	0.35068	D	0.762215	B;B;B;B	0.16603	0.018;0.01;0.008;0.002	B;B;B;B	0.11329	0.006;0.006;0.003;0.006	T	0.03157	-1.1066	10	0.26408	T	0.33	-6.2945	5.3718	0.16144	0.1986:0.0:0.5545:0.2468	.	92;92;92;92	B3KUC3;Q9Y2G4;Q9Y2G4-1;C9JJE8	.;ANKR6_HUMAN;.;.	T	92	ENSP00000358416:A92T;ENSP00000345767:A92T;ENSP00000396771:A92T;ENSP00000429431:A92T;ENSP00000428377:A92T;ENSP00000430985:A92T;ENSP00000430954:A92T;ENSP00000428309:A92T;ENSP00000429782:A92T	ENSP00000345767:A92T	A	+	1	0	ANKRD6	90369521	0.605000	0.26941	0.067000	0.19924	0.024000	0.10985	0.876000	0.28092	0.102000	0.17638	-0.152000	0.13540	GCG		0.612	ANKRD6-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376594.1		
MDN1	23195	broad.mit.edu	37	6	90428742	90428742	+	Missense_Mutation	SNP	T	T	C	rs115774502		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:90428742T>C	ENST00000369393.3	-	42	6180	c.6065A>G	c.(6064-6066)tAc>tGc	p.Y2022C	MDN1_ENST00000428876.1_Missense_Mutation_p.Y2022C			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	2022					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)	p.Y2022C(1)		NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		AAGGACTGAGTAGCCCAACTG	0.502													T|||	1	0.000199681	0.0008	0.0	5008	,	,		20153	0.0		0.0	False		,,,				2504	0.0				p.Y2022C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A6065G	6						.	T	CYS/TYR	7,4399	12.9+/-30.5	0,7,2196	67.0	71.0	69.0		6065	4.5	1.0	6	dbSNP_132	69	0,8600		0,0,4300	yes	missense	MDN1	NM_014611.1	194	0,7,6496	CC,CT,TT		0.0,0.1589,0.0538	probably-damaging	2022/5597	90428742	7,12999	2203	4300	6503	90485463	SO:0001583	missense	23195	exon42			AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.6065A>G	6.37:g.90428742T>C	ENSP00000358400:p.Tyr2022Cys	Somatic		Capture	Illumina HiSeq	Phase_I	90485463	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	9.654	1.142343	0.21205	0.001589	0.0	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.03124	4.04;4.04	5.63	4.46	0.54185	.	0.284232	0.35207	N	0.003373	T	0.01835	0.0058	L	0.57536	1.79	0.41707	D	0.989431	B	0.23591	0.088	B	0.23716	0.048	T	0.39272	-0.9622	10	0.39692	T	0.17	.	7.1967	0.25858	0.1304:0.071:0.0:0.7986	.	2022	Q9NU22	MDN1_HUMAN	C	2022	ENSP00000358400:Y2022C;ENSP00000413970:Y2022C	ENSP00000358400:Y2022C	Y	-	2	0	MDN1	90485463	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	2.211000	0.42825	0.950000	0.37743	0.528000	0.53228	TAC		0.502	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
ADGB	79747	broad.mit.edu	37	6	147136327	147136327	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:147136327delA	ENST00000397944.3	+	36	5054	c.4978delA	c.(4978-4980)aaafs	p.K1663fs	ADGB_ENST00000367488.1_3'UTR|ADGB_ENST00000367493.3_3'UTR	NM_024694.3	NP_078970.3	Q8N7X0	ADGB_HUMAN	androglobin	1663					oxygen transport (GO:0015671)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)	p.K607fs*>6(1)|p.K608fs*>6(1)		breast(1)|endometrium(2)|kidney(2)	5						TGACACACAGAAAAAAAAGAA	0.443																																					p.K1660fs												.	.	2	Deletion - Frameshift(1)|Insertion - Frameshift(1)	large_intestine(2)	c.4978delA	6						.						10.0	11.0	10.0					6																	147136327		692	1591	2283	147178020	SO:0001589	frameshift_variant	79747	exon36			AK026774		6q24.2	2012-02-03	2012-02-03	2012-02-03	ENSG00000118492	ENSG00000118492			21212	protein-coding gene	gene with protein product		614630	"""chromosome 6 open reading frame 103"""	C6orf103		22115833	Standard	NM_024694		Approved	FLJ23121, dJ408K24.1	uc010khx.3	Q8N7X0	OTTHUMG00000015758	ENST00000397944.3:c.4978delA	6.37:g.147136327delA	ENSP00000381036:p.Lys1663fs	Somatic		Capture	Illumina HiSeq	Phase_I	147178020	NM_024694	Q5T402|Q5T904|Q5T905	Frame_Shift_Del	DEL	ENST00000397944.3	37																																																																																					0.443	ADGB-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376350.2	NM_024694	
SMOC2	64094	broad.mit.edu	37	6	168910644	168910644	+	Missense_Mutation	SNP	C	C	T	rs141002558		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr6:168910644C>T	ENST00000356284.2	+	2	354	c.134C>T	c.(133-135)gCg>gTg	p.A45V	SMOC2_ENST00000354536.5_Missense_Mutation_p.A45V	NM_001166412.1	NP_001159884.1	Q9H3U7	SMOC2_HUMAN	SPARC related modular calcium binding 2	45	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)|signal transduction (GO:0007165)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.A45V(2)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	32		Breast(66;0.000141)|Esophageal squamous(34;0.222)|Ovarian(120;0.231)		OV - Ovarian serous cystadenocarcinoma(33;1.31e-19)|BRCA - Breast invasive adenocarcinoma(81;3.06e-06)|GBM - Glioblastoma multiforme(31;0.00109)		TTGGACTGTGCGGGTTCGCCC	0.443													C|||	1	0.000199681	0.0008	0.0	5008	,	,		17259	0.0		0.0	False		,,,				2504	0.0				p.A45V												.	.	2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	c.C134T	6						.	C	VAL/ALA,VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	98.0	99.0	99.0		134,134	2.1	0.0	6	dbSNP_134	99	1,8599	2.2+/-6.3	0,1,4299	yes	missense,missense	SMOC2	NM_001166412.1,NM_022138.2	64,64	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	benign,benign	45/447,45/458	168910644	2,13004	2203	4300	6503	168653493	SO:0001583	missense	64094	exon2			AB014730	CCDS5307.1, CCDS55076.1	6q27	2013-01-10			ENSG00000112562	ENSG00000112562		"""EF-hand domain containing"""	20323	protein-coding gene	gene with protein product		607223				12031507	Standard	NM_022138		Approved	SMAP2	uc003qwr.2	Q9H3U7	OTTHUMG00000016050	ENST00000356284.2:c.134C>T	6.37:g.168910644C>T	ENSP00000348630:p.Ala45Val	Somatic		Capture	Illumina HiSeq	Phase_I	168653493	NM_001166412	B3KPS7|Q4G169|Q5TAT7|Q5TAT8|Q86VV9|Q96SF3|Q9H1L3|Q9H1L4|Q9H3U0|Q9H4F7|Q9HCV2	Missense_Mutation	SNP	ENST00000356284.2	37	CCDS55076.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	9.407	1.079580	0.20309	2.27E-4	1.16E-4	ENSG00000112562	ENST00000356284;ENST00000354536;ENST00000366793	T;T	0.29142	1.58;1.58	4.87	2.08	0.27032	Proteinase inhibitor I1, Kazal (1);Thyroglobulin type-1 (1);	0.659654	0.16319	N	0.219661	T	0.10337	0.0253	L	0.34521	1.04	0.09310	N	1	P;P	0.37038	0.535;0.579	B;B	0.37601	0.254;0.077	T	0.10660	-1.0620	10	0.40728	T	0.16	-7.055	11.4675	0.50248	0.0:0.7661:0.153:0.0809	.	45;45	Q9H3U7;Q9H3U7-2	SMOC2_HUMAN;.	V	45	ENSP00000348630:A45V;ENSP00000346537:A45V	ENSP00000346537:A45V	A	+	2	0	SMOC2	168653493	0.320000	0.24616	0.001000	0.08648	0.154000	0.21943	0.881000	0.28173	0.183000	0.20059	0.442000	0.29010	GCG		0.443	SMOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043201.1		
MUC17	140453	broad.mit.edu	37	7	100676662	100676662	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:100676662C>T	ENST00000306151.4	+	3	2029	c.1965C>T	c.(1963-1965)gaC>gaT	p.D655D		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	655	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.D655D(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)					CTCCTGTTGACTCCAACACTC	0.478																																					p.D655D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1965T	7						.						272.0	276.0	275.0					7																	100676662		2203	4300	6503	100463382	SO:0001819	synonymous_variant	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.1965C>T	7.37:g.100676662C>T		Somatic		Capture	Illumina HiSeq	Phase_I	100463382	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																				0.478	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
SERPINE1	5054	broad.mit.edu	37	7	100773742	100773742	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:100773742G>A	ENST00000223095.4	+	3	469	c.312G>A	c.(310-312)gaG>gaA	p.E104E	SERPINE1_ENST00000445463.2_Silent_p.E89E	NM_000602.4	NP_000593.1	P05121	PAI1_HUMAN	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1	104					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to lipopolysaccharide (GO:0071222)|chronological cell aging (GO:0001300)|defense response to Gram-negative bacterium (GO:0050829)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|gene expression (GO:0010467)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell migration (GO:0030336)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of plasminogen activation (GO:0010757)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell-matrix adhesion (GO:2000098)|negative regulation of vascular wound healing (GO:0061044)|negative regulation of wound healing (GO:0061045)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of leukotriene production involved in inflammatory response (GO:0035491)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of receptor activity (GO:0010469)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.E104E(1)		central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(3)	20	Lung NSC(181;0.136)|all_lung(186;0.182)				Alteplase(DB00009)|Anistreplase(DB00029)|Drotrecogin alfa(DB00055)|Reteplase(DB00015)|Tenecteplase(DB00031)|Urokinase(DB00013)	TGTACAAGGAGCTCATGGGGC	0.587																																					p.E104E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G312A	7						.						124.0	117.0	120.0					7																	100773742		2203	4300	6503	100560462	SO:0001819	synonymous_variant	5054	exon3			M16006	CCDS5711.1	7q22.1	2014-02-18	2005-08-18		ENSG00000106366	ENSG00000106366		"""Serine (or cysteine) peptidase inhibitors"""	8583	protein-coding gene	gene with protein product	"""plasminogen activator inhibitor, type I"""	173360	"""serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1"""	PLANH1, PAI1		3097076, 2891140, 24172014	Standard	NM_000602		Approved	PAI	uc003uxt.4	P05121	OTTHUMG00000157107	ENST00000223095.4:c.312G>A	7.37:g.100773742G>A		Somatic		Capture	Illumina HiSeq	Phase_I	100560462	NM_000602	B7Z4S0|F8WD53	Silent	SNP	ENST00000223095.4	37	CCDS5711.1																																																																																				0.587	SERPINE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347458.1	NM_000602	
FBXL13	222235	broad.mit.edu	37	7	102566734	102566734	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:102566734G>A	ENST00000313221.4	-	10	1291	c.865C>T	c.(865-867)Cga>Tga	p.R289*	FBXL13_ENST00000379308.3_Nonsense_Mutation_p.R289*|FBXL13_ENST00000436908.1_Nonsense_Mutation_p.R289*|FBXL13_ENST00000379306.3_Nonsense_Mutation_p.R289*|LRRC17_ENST00000249377.4_Intron|FBXL13_ENST00000379305.3_Nonsense_Mutation_p.R289*|LRRC17_ENST00000339431.4_Intron|FBXL13_ENST00000455112.2_Nonsense_Mutation_p.R289*|FBXL13_ENST00000393772.2_Nonsense_Mutation_p.R289*|FBXL13_ENST00000456695.1_Nonsense_Mutation_p.R289*	NM_145032.3	NP_659469.3	Q8NEE6	FXL13_HUMAN	F-box and leucine-rich repeat protein 13	289								p.R289*(1)		NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|skin(3)|stomach(1)	27						GGCAGGAGTCGCATCGTCCTG	0.463																																					p.R289X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C865T	7						.						71.0	65.0	67.0					7																	102566734		2203	4300	6503	102353970	SO:0001587	stop_gained	222235	exon10			BC031285	CCDS5726.1, CCDS47678.1, CCDS75649.1	7q22.1	2014-07-18			ENSG00000161040	ENSG00000161040		"""F-boxes / Leucine-rich repeats"""	21658	protein-coding gene	gene with protein product		609080					Standard	NM_145032		Approved	MGC21636, Fbl13	uc003vaq.2	Q8NEE6	OTTHUMG00000157224	ENST00000313221.4:c.865C>T	7.37:g.102566734G>A	ENSP00000321927:p.Arg289*	Somatic		Capture	Illumina HiSeq	Phase_I	102353970	NM_001111038	C9J565|C9J566|Q6UVW7|Q6UVW8|Q75MN5|Q86UJ5|Q8N7Y4|Q8TCL2|Q8WUF9|Q8WUG0	Nonsense_Mutation	SNP	ENST00000313221.4	37	CCDS5726.1	.	.	.	.	.	.	.	.	.	.	G	37	6.172072	0.97348	.	.	ENSG00000161040	ENST00000393772;ENST00000379308;ENST00000379306;ENST00000379305;ENST00000436908;ENST00000313221;ENST00000456695;ENST00000455112	.	.	.	5.27	-2.77	0.05877	.	0.205144	0.33753	N	0.004584	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.4764	0.90793	0.0:0.0:0.2311:0.7689	.	.	.	.	X	289	.	ENSP00000321927:R289X	R	-	1	2	FBXL13	102353970	0.933000	0.31639	0.989000	0.46669	0.986000	0.74619	-0.077000	0.11394	-0.345000	0.08325	-0.274000	0.10170	CGA		0.463	FBXL13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348001.1	NM_145032	
FBXL13	222235	broad.mit.edu	37	7	102572336	102572336	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:102572336T>G	ENST00000313221.4	-	9	1195	c.769A>C	c.(769-771)Aca>Cca	p.T257P	FBXL13_ENST00000379308.3_Missense_Mutation_p.T257P|FBXL13_ENST00000436908.1_Missense_Mutation_p.T257P|FBXL13_ENST00000379306.3_Missense_Mutation_p.T257P|LRRC17_ENST00000249377.4_Intron|FBXL13_ENST00000379305.3_Missense_Mutation_p.T257P|LRRC17_ENST00000339431.4_Intron|FBXL13_ENST00000455112.2_Missense_Mutation_p.T257P|FBXL13_ENST00000393772.2_Missense_Mutation_p.T257P|FBXL13_ENST00000456695.1_Missense_Mutation_p.T257P	NM_145032.3	NP_659469.3	Q8NEE6	FXL13_HUMAN	F-box and leucine-rich repeat protein 13	257								p.T257P(1)		NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|skin(3)|stomach(1)	27						ACTGTGAATGTTGGGCAGTCA	0.368																																					p.T257P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A769C	7						.						133.0	114.0	120.0					7																	102572336		2203	4300	6503	102359572	SO:0001583	missense	222235	exon9			BC031285	CCDS5726.1, CCDS47678.1, CCDS75649.1	7q22.1	2014-07-18			ENSG00000161040	ENSG00000161040		"""F-boxes / Leucine-rich repeats"""	21658	protein-coding gene	gene with protein product		609080					Standard	NM_145032		Approved	MGC21636, Fbl13	uc003vaq.2	Q8NEE6	OTTHUMG00000157224	ENST00000313221.4:c.769A>C	7.37:g.102572336T>G	ENSP00000321927:p.Thr257Pro	Somatic		Capture	Illumina HiSeq	Phase_I	102359572	NM_001111038	C9J565|C9J566|Q6UVW7|Q6UVW8|Q75MN5|Q86UJ5|Q8N7Y4|Q8TCL2|Q8WUF9|Q8WUG0	Missense_Mutation	SNP	ENST00000313221.4	37	CCDS5726.1	.	.	.	.	.	.	.	.	.	.	T	12.08	1.832088	0.32421	.	.	ENSG00000161040	ENST00000393772;ENST00000379308;ENST00000379306;ENST00000379305;ENST00000436908;ENST00000313221;ENST00000456695;ENST00000455112	T;T;T;T;T;T;T;T	0.02525	4.28;4.28;4.26;4.28;4.28;4.28;4.26;4.28	5.71	-1.89	0.07689	.	1.247040	0.05357	N	0.532935	T	0.03520	0.0101	L	0.47190	1.495	0.19300	N	0.999978	B;B;B;B	0.26400	0.027;0.148;0.08;0.121	B;B;B;B	0.32022	0.022;0.048;0.027;0.139	T	0.47661	-0.9100	10	0.32370	T	0.25	.	3.7612	0.08604	0.3472:0.3255:0.0:0.3273	.	257;257;257;257	Q8NEE6-3;Q8NEE6-4;Q8NEE6-2;Q8NEE6	.;.;.;FXL13_HUMAN	P	257	ENSP00000377367:T257P;ENSP00000368610:T257P;ENSP00000368608:T257P;ENSP00000368607:T257P;ENSP00000388608:T257P;ENSP00000321927:T257P;ENSP00000409716:T257P;ENSP00000391550:T257P	ENSP00000321927:T257P	T	-	1	0	FBXL13	102359572	0.028000	0.19301	0.014000	0.15608	0.828000	0.46876	0.332000	0.19751	-0.242000	0.09667	0.533000	0.62120	ACA		0.368	FBXL13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348001.1	NM_145032	
RELN	5649	broad.mit.edu	37	7	103338488	103338488	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:103338488C>T	ENST00000428762.1	-	10	1114	c.955G>A	c.(955-957)Gcc>Acc	p.A319T	RELN_ENST00000424685.2_Missense_Mutation_p.A319T|RELN_ENST00000343529.5_Missense_Mutation_p.A319T	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	319					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)	p.A319T(1)		NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		TCCCCTTTGGCGTCCTCAGGA	0.448																																					p.A319T	NSCLC(146;835 1944 15585 22231 52158)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G955A	7						.						203.0	189.0	194.0					7																	103338488		2203	4300	6503	103125724	SO:0001583	missense	5649	exon10				CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.955G>A	7.37:g.103338488C>T	ENSP00000392423:p.Ala319Thr	Somatic		Capture	Illumina HiSeq	Phase_I	103125724	NM_005045	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	c	18.03	3.531874	0.64972	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.26067	1.76;1.76;1.76	6.07	6.07	0.98685	.	0.055176	0.85682	D	0.000000	T	0.26521	0.0648	L	0.50333	1.59	0.39948	D	0.974498	P;P	0.39326	0.668;0.539	B;B	0.31495	0.131;0.062	T	0.03443	-1.1036	10	0.41790	T	0.15	.	20.6485	0.99592	0.0:1.0:0.0:0.0	.	319;319	P78509-2;P78509	.;RELN_HUMAN	T	319	ENSP00000392423:A319T;ENSP00000345694:A319T;ENSP00000388446:A319T	ENSP00000345694:A319T	A	-	1	0	RELN	103125724	0.991000	0.36638	0.974000	0.42286	0.995000	0.86356	2.968000	0.49224	2.891000	0.99171	0.651000	0.88453	GCC		0.448	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	
PHF14	9678	broad.mit.edu	37	7	11068366	11068366	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:11068366A>T	ENST00000403050.3	+	7	1828	c.1376A>T	c.(1375-1377)gAt>gTt	p.D459V	PHF14_ENST00000445996.2_Missense_Mutation_p.D174V	NM_014660.3	NP_055475.2	O94880	PHF14_HUMAN	PHD finger protein 14	459					lung alveolus development (GO:0048286)|negative regulation of mesenchymal cell proliferation involved in lung development (GO:2000791)|negative regulation of platelet-derived growth factor receptor-alpha signaling pathway (GO:2000584)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.D459V(1)		NS(2)|breast(1)|endometrium(4)|kidney(5)|large_intestine(5)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	35				UCEC - Uterine corpus endometrioid carcinoma (126;0.205)		ATTAGCTGTGATGCAGGGATG	0.438																																					p.D459V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1376T	7						.						127.0	122.0	124.0					7																	11068366		1955	4163	6118	11034891	SO:0001583	missense	9678	exon7			AB018326	CCDS47542.1	7p21.3	2013-01-28			ENSG00000106443	ENSG00000106443		"""Zinc fingers, PHD-type"""	22203	protein-coding gene	gene with protein product						9872452	Standard	NM_014660		Approved	KIAA0783	uc003sry.2	O94880	OTTHUMG00000150463	ENST00000403050.3:c.1376A>T	7.37:g.11068366A>T	ENSP00000385795:p.Asp459Val	Somatic		Capture	Illumina HiSeq	Phase_I	11034891	NM_014660	A7MCZ3|B4DI82	Missense_Mutation	SNP	ENST00000403050.3	37	CCDS47542.1	.	.	.	.	.	.	.	.	.	.	A	29.3	4.992130	0.93167	.	.	ENSG00000106443	ENST00000403050;ENST00000445996	T;T	0.71341	2.62;-0.56	5.31	5.31	0.75309	Zinc finger, PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.82697	0.5093	M	0.68593	2.085	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.99	D;D;D;D	0.87578	0.996;0.997;0.998;0.937	D	0.84850	0.0813	10	0.87932	D	0	.	15.5768	0.76397	1.0:0.0:0.0:0.0	.	174;174;459;459	O94880-2;B4DG57;A8MSQ1;O94880	.;.;.;PHF14_HUMAN	V	459;174	ENSP00000385795:D459V;ENSP00000403907:D174V	ENSP00000385795:D459V	D	+	2	0	PHF14	11034891	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.230000	0.95299	2.126000	0.65437	0.528000	0.53228	GAT		0.438	PHF14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318212.1	NM_014660	
COG5	10466	broad.mit.edu	37	7	107053073	107053073	+	Silent	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:107053073A>G	ENST00000347053.3	-	7	686	c.636T>C	c.(634-636)taT>taC	p.Y212Y	COG5_ENST00000475638.2_5'UTR|COG5_ENST00000297135.3_Silent_p.Y212Y|COG5_ENST00000393603.2_Silent_p.Y212Y	NM_181733.2	NP_859422.2	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5	212					intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)		p.Y212Y(1)		breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|skin(4)|stomach(1)	40						CTTGAGAAAGATAATCTGTTT	0.284																																					p.Y212Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T636C	7						.						33.0	33.0	33.0					7																	107053073		2203	4299	6502	106840309	SO:0001819	synonymous_variant	10466	exon7			AF058718	CCDS5742.1, CCDS5743.1, CCDS55152.1	7q31	2010-06-24	2001-12-07	2002-05-10	ENSG00000164597	ENSG00000164597		"""Components of oligomeric golgi complex"""	14857	protein-coding gene	gene with protein product		606821	"""golgi transport complex 1 (90 kDa subunit)"""	GOLTC1		9792665, 11980916	Standard	NM_006348		Approved	GTC90	uc003vec.2	Q9UP83	OTTHUMG00000023895	ENST00000347053.3:c.636T>C	7.37:g.107053073A>G		Somatic		Capture	Illumina HiSeq	Phase_I	106840309	NM_001161520	A4D0R6|A4D0R7|O14555|O95008|Q6NUL5	Silent	SNP	ENST00000347053.3	37	CCDS5743.1																																																																																				0.284	COG5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060216.4		
LRRN3	54674	broad.mit.edu	37	7	110763518	110763518	+	Silent	SNP	C	C	T	rs146797927	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:110763518C>T	ENST00000422987.3	+	2	1521	c.690C>T	c.(688-690)aaC>aaT	p.N230N	IMMP2L_ENST00000450877.1_Intron|IMMP2L_ENST00000331762.3_Intron|IMMP2L_ENST00000489381.1_Intron|IMMP2L_ENST00000405709.2_Intron|LRRN3_ENST00000451085.1_Silent_p.N230N|IMMP2L_ENST00000452895.1_Intron|LRRN3_ENST00000308478.5_Silent_p.N230N|IMMP2L_ENST00000437687.1_Intron|IMMP2L_ENST00000447215.1_Intron|IMMP2L_ENST00000415362.1_Intron	NM_018334.4	NP_060804.3	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3	230					positive regulation of protein phosphorylation (GO:0001934)	clathrin adaptor complex (GO:0030131)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.N230N(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(15)|lung(20)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)		TACCAGATAACGCCTTGGTTG	0.358													T|||	2	0.000399361	0.0	0.0	5008	,	,		18436	0.0		0.0	False		,,,				2504	0.002				p.N230N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C690T	7						.	T	,,,	0,4406		0,0,2203	68.0	70.0	69.0		690,690,690,	0.8	1.0	7	dbSNP_134	69	2,8596	816.0+/-406.9	0,2,4297	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	LRRN3,IMMP2L	NM_001099658.1,NM_001099660.1,NM_018334.4,NM_032549.3	,,,	0,2,6500	TT,TC,CC		0.0233,0.0,0.0154	,,,	230/709,230/709,230/709,	110763518	2,13002	2203	4299	6502	110550754	SO:0001819	synonymous_variant	54674	exon2			AB060967	CCDS5754.1	7q31.1	2013-02-11			ENSG00000173114	ENSG00000173114		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	17200	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 5"""					11549284	Standard	NM_001099660		Approved	NLRR3, FLJ11129, FIGLER5	uc003vfs.4	Q9H3W5	OTTHUMG00000155039	ENST00000422987.3:c.690C>T	7.37:g.110763518C>T		Somatic		Capture	Illumina HiSeq	Phase_I	110550754	NM_018334	O43377|Q6I9V8|Q8IYQ6	Silent	SNP	ENST00000422987.3	37	CCDS5754.1																																																																																				0.358	LRRN3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338171.2	NM_018334	
CFTR	1080	broad.mit.edu	37	7	117232172	117232172	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:117232172G>A	ENST00000003084.6	+	14	2083	c.1951G>A	c.(1951-1953)Gac>Aac	p.D651N	CFTR_ENST00000454343.1_Missense_Mutation_p.D590N	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	651			D -> N (in CF).		cellular response to cAMP (GO:0071320)|cellular response to hormone stimulus (GO:0032870)|chloride transmembrane transport (GO:1902476)|cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intracellular pH elevation (GO:0051454)|iodide transport (GO:0015705)|lung development (GO:0030324)|membrane hyperpolarization (GO:0060081)|positive regulation of vasodilation (GO:0045909)|positive regulation of voltage-gated chloride channel activity (GO:1902943)|respiratory gaseous exchange (GO:0007585)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to peptide hormone (GO:0043434)|sperm capacitation (GO:0048240)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vasodilation (GO:0042311)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|chloride channel complex (GO:0034707)|cytoplasmic vesicle membrane (GO:0030659)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-binding and phosphorylation-dependent chloride channel activity (GO:0005224)|bicarbonate transmembrane transporter activity (GO:0015106)|channel-conductance-controlling ATPase activity (GO:0005260)|chloride channel activity (GO:0005254)|chloride channel inhibitor activity (GO:0019869)|chloride transmembrane transporter activity (GO:0015108)|enzyme binding (GO:0019899)|PDZ domain binding (GO:0030165)	p.D651N(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(15)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(9)	69	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Crofelemer(DB04941)|Glyburide(DB01016)|Ibuprofen(DB01050)|Ivacaftor(DB08820)	TGATTCTTTCGACCAATTTAG	0.383									Cystic Fibrosis																												p.D651N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1951A	7	GRCh37	CM024682|CM983561	CFTR	M		.						66.0	66.0	66.0					7																	117232172		2203	4300	6503	117019408	SO:0001583	missense	1080	exon14	Familial Cancer Database	CF	M28668	CCDS5773.1	7q31-q32	2014-09-17	2006-09-18		ENSG00000001626	ENSG00000001626		"""Ion channels / Chloride channels : Cystic fibrosis transmembrane conductance regulators"", ""ATP binding cassette transporters / subfamily C"""	1884	protein-coding gene	gene with protein product	"""ATP-binding cassette sub-family C, member 7"""	602421	"""cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)"""	CF, ABCC7		2772657	Standard	XM_006715842		Approved	MRP7, ABC35, TNR-CFTR, dJ760C5.1, CFTR/MRP	uc003vjd.3	P13569	OTTHUMG00000023076	ENST00000003084.6:c.1951G>A	7.37:g.117232172G>A	ENSP00000003084:p.Asp651Asn	Somatic		Capture	Illumina HiSeq	Phase_I	117019408	NM_000492	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Missense_Mutation	SNP	ENST00000003084.6	37	CCDS5773.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.785978	0.90282	.	.	ENSG00000001626	ENST00000003084;ENST00000454343;ENST00000426809	D;D;D	0.97791	-4.54;-4.54;-4.54	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.98595	0.9530	M	0.83953	2.67	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.98871	1.0766	10	0.87932	D	0	-20.5633	13.2854	0.60241	0.0726:0.0:0.9274:0.0	.	651	P13569	CFTR_HUMAN	N	651;590;621	ENSP00000003084:D651N;ENSP00000403677:D590N;ENSP00000389119:D621N	ENSP00000003084:D651N	D	+	1	0	CFTR	117019408	1.000000	0.71417	0.997000	0.53966	0.969000	0.65631	9.135000	0.94478	2.802000	0.96397	0.563000	0.77884	GAC		0.383	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492	
CPED1	79974	broad.mit.edu	37	7	120740134	120740134	+	Missense_Mutation	SNP	C	C	T	rs145131821	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:120740134C>T	ENST00000310396.5	+	7	1371	c.904C>T	c.(904-906)Cgc>Tgc	p.R302C	CPED1_ENST00000423795.1_Missense_Mutation_p.R82C|CPED1_ENST00000450913.2_Missense_Mutation_p.R302C	NM_024913.4	NP_079189.4	A4D0V7	CPED1_HUMAN	cadherin-like and PC-esterase domain containing 1	302						endoplasmic reticulum (GO:0005783)		p.R302C(1)									AAAGAAAAAACGCTTCACTGT	0.428													C|||	5	0.000998403	0.0	0.0	5008	,	,		20007	0.0		0.0	False		,,,				2504	0.0051				p.R302C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C904T	7						.	C	CYS/ARG,CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	123.0	107.0	112.0		904,904	4.7	1.0	7	dbSNP_134	112	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	C7orf58	NM_001105533.1,NM_024913.4	180,180	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging,probably-damaging	302/784,302/1027	120740134	2,13004	2203	4300	6503	120527370	SO:0001583	missense	79974	exon7				CCDS34739.1, CCDS47690.1	7q31.31	2012-06-12	2012-06-12	2012-06-12	ENSG00000106034	ENSG00000106034			26159	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 58"""	C7orf58		20056006	Standard	NM_024913		Approved	FLJ21986	uc003vjq.4	A4D0V7	OTTHUMG00000156982	ENST00000310396.5:c.904C>T	7.37:g.120740134C>T	ENSP00000309772:p.Arg302Cys	Somatic		Capture	Illumina HiSeq	Phase_I	120527370	NM_024913	A8K1R3|Q6UXT1|Q86T76|Q86T84|Q8N2T5|Q96NC9	Missense_Mutation	SNP	ENST00000310396.5	37	CCDS34739.1	.	.	.	.	.	.	.	.	.	.	C	17.37	3.372506	0.61624	2.27E-4	1.16E-4	ENSG00000106034	ENST00000310396;ENST00000428526;ENST00000450913;ENST00000423795;ENST00000443817	T;T;T;T;T	0.33438	1.41;1.41;1.41;1.41;1.41	5.58	4.69	0.59074	.	0.250619	0.40818	N	0.001005	T	0.48624	0.1510	L	0.59436	1.845	0.80722	D	1	D;P;B	0.89917	1.0;0.56;0.217	D;B;B	0.87578	0.998;0.112;0.019	T	0.38564	-0.9655	10	0.48119	T	0.1	.	11.0198	0.47711	0.0:0.913:0.0:0.087	.	82;302;302	G5E9U2;A4D0V7-2;A4D0V7	.;.;CG058_HUMAN	C	302;302;302;82;82	ENSP00000309772:R302C;ENSP00000398082:R302C;ENSP00000406122:R302C;ENSP00000415573:R82C;ENSP00000391952:R82C	ENSP00000309772:R302C	R	+	1	0	C7orf58	120527370	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.211000	0.42825	2.641000	0.89580	0.585000	0.79938	CGC		0.428	CPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346959.1	NM_024913	
IQUB	154865	broad.mit.edu	37	7	123101577	123101577	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:123101577G>A	ENST00000466202.1	-	11	2417	c.1841C>T	c.(1840-1842)tCt>tTt	p.S614F	RP11-332K15.1_ENST00000419832.1_RNA|IQUB_ENST00000324698.6_Missense_Mutation_p.S614F	NM_001282855.1	NP_001269784.1	Q8NA54	IQUB_HUMAN	IQ motif and ubiquitin domain containing	614					cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	acrosomal vesicle (GO:0001669)|motile cilium (GO:0031514)		p.S614F(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(3)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)	45						GGATGATACAGAAAATTCTGT	0.358																																					p.S614F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1841T	7						.						67.0	65.0	66.0					7																	123101577		2203	4299	6502	122888813	SO:0001583	missense	154865	exon11			AK093153	CCDS5787.1	7q31.32	2010-03-19			ENSG00000164675	ENSG00000164675			21995	protein-coding gene	gene with protein product							Standard	NM_178827		Approved	FLJ35834	uc003vko.3	Q8NA54	OTTHUMG00000157347	ENST00000466202.1:c.1841C>T	7.37:g.123101577G>A	ENSP00000417769:p.Ser614Phe	Somatic		Capture	Illumina HiSeq	Phase_I	122888813	NM_178827	A4D0X0|Q49AL6|Q4G189|Q5BJD9|Q6NUH6|Q8N9Y2	Missense_Mutation	SNP	ENST00000466202.1	37	CCDS5787.1	.	.	.	.	.	.	.	.	.	.	G	10.03	1.238580	0.22711	.	.	ENSG00000164675	ENST00000466202;ENST00000324698	T;T	0.24538	1.85;1.85	5.94	5.04	0.67666	.	0.817135	0.11885	N	0.520142	T	0.30634	0.0771	L	0.46157	1.445	0.22648	N	0.998899	P	0.43287	0.802	B	0.41813	0.367	T	0.15838	-1.0423	10	0.62326	D	0.03	.	16.2762	0.82644	0.0:0.0:0.8664:0.1336	.	614	Q8NA54	IQUB_HUMAN	F	614	ENSP00000417769:S614F;ENSP00000324882:S614F	ENSP00000324882:S614F	S	-	2	0	IQUB	122888813	0.292000	0.24362	0.002000	0.10522	0.018000	0.09664	3.285000	0.51716	1.454000	0.47793	0.643000	0.83706	TCT		0.358	IQUB-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348529.1	NM_178827	
WASL	8976	broad.mit.edu	37	7	123332590	123332590	+	Silent	SNP	C	C	T	rs368113473		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:123332590C>T	ENST00000223023.4	-	9	1490	c.1158G>A	c.(1156-1158)ccG>ccA	p.P386P		NM_003941.2	NP_003932.3	O00401	WASL_HUMAN	Wiskott-Aldrich syndrome-like	386	Pro-rich.				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.P386P(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						CAGGCGGGGGCGGTGGCCCAG	0.607																																					p.P386P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1158A	7						.	C		0,4406		0,0,2203	45.0	51.0	49.0		1158	-8.1	0.9	7		49	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	WASL	NM_003941.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		386/506	123332590	1,13005	2203	4300	6503	123119826	SO:0001819	synonymous_variant	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.1158G>A	7.37:g.123332590C>T		Somatic		Capture	Illumina HiSeq	Phase_I	123119826	NM_003941	A1JUI9|Q7Z746	Silent	SNP	ENST00000223023.4	37	CCDS34743.1																																																																																				0.607	WASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348522.1	NM_003941	
TNPO3	23534	broad.mit.edu	37	7	128614928	128614928	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:128614928G>A	ENST00000265388.5	-	18	2410	c.2267C>T	c.(2266-2268)gCc>gTc	p.A756V	TNPO3_ENST00000482320.1_Missense_Mutation_p.A690V|TNPO3_ENST00000471234.1_Missense_Mutation_p.A692V|TNPO3_ENST00000471166.1_Missense_Mutation_p.A790V|TNPO3_ENST00000393245.1_Missense_Mutation_p.A790V			Q9Y5L0	TNPO3_HUMAN	transportin 3	756					splicing factor protein import into nucleus (GO:0035048)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	receptor activity (GO:0004872)	p.A756V(1)|p.A790V(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(3)	22						TTACCTGGTGGCTAGCCGGAA	0.453																																					p.A756V	Pancreas(147;583 2585 39696 52331)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C2267T	7						.						132.0	114.0	120.0					7																	128614928		2203	4300	6503	128402164	SO:0001583	missense	23534	exon18			AF145029	CCDS5809.1, CCDS55162.1	7q32.2	2014-02-03			ENSG00000064419	ENSG00000064419		"""Importins"""	17103	protein-coding gene	gene with protein product	"""importin 12"""	610032	"""limb girdle muscular dystrophy 1F (autosomal dominant)"""	LGMD1F		10366588, 10713112, 23543484, 23667635	Standard	NM_012470		Approved	TRN-SR, MTR10A, TRN-SR2, IPO12	uc003vol.2	Q9Y5L0	OTTHUMG00000158409	ENST00000265388.5:c.2267C>T	7.37:g.128614928G>A	ENSP00000265388:p.Ala756Val	Somatic		Capture	Illumina HiSeq	Phase_I	128402164	NM_012470	A4D1K9|C9IZM0|Q6NUM1|Q96G71|Q96GU9|Q9Y3R2	Missense_Mutation	SNP	ENST00000265388.5	37	CCDS5809.1	.	.	.	.	.	.	.	.	.	.	G	16.68	3.189584	0.57909	.	.	ENSG00000064419	ENST00000393245;ENST00000265388;ENST00000482320;ENST00000471234;ENST00000471166	T;T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.13;-0.15	5.96	5.96	0.96718	Armadillo-type fold (1);	0.219670	0.47455	D	0.000238	T	0.44030	0.1274	N	0.19112	0.55	0.58432	D	0.999996	B;B;B;B	0.25351	0.022;0.124;0.023;0.074	B;B;B;B	0.20184	0.006;0.021;0.028;0.028	T	0.35001	-0.9806	10	0.18710	T	0.47	.	11.211	0.48797	0.0823:0.0:0.9177:0.0	.	692;790;756;756	C9IZM0;C9J7E5;Q9Y5L0-3;Q9Y5L0	.;.;.;TNPO3_HUMAN	V	790;756;690;692;790	ENSP00000376936:A790V;ENSP00000265388:A756V;ENSP00000420089:A690V;ENSP00000418646:A692V;ENSP00000418267:A790V	ENSP00000265388:A756V	A	-	2	0	TNPO3	128402164	1.000000	0.71417	1.000000	0.80357	0.746000	0.42486	7.896000	0.87350	2.832000	0.97577	0.655000	0.94253	GCC		0.453	TNPO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350929.1	NM_012470	
CNOT4	4850	broad.mit.edu	37	7	135079001	135079001	+	Silent	SNP	C	C	T	rs374055552		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:135079001C>T	ENST00000315544.5	-	10	1575	c.1296G>A	c.(1294-1296)tcG>tcA	p.S432S	CNOT4_ENST00000414802.1_Intron|CNOT4_ENST00000541284.1_Silent_p.S432S|CNOT4_ENST00000423368.2_Silent_p.S432S|CNOT4_ENST00000361528.4_Silent_p.S429S|CNOT4_ENST00000451834.1_Silent_p.S429S|CNOT4_ENST00000356162.4_Intron|CNOT4_ENST00000428680.2_Silent_p.S429S	NM_001190848.1	NP_001177777.1	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	432					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.S429S(1)		autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)	22						GAGATGTGGGCGAAAGGGAAG	0.498																																					p.S432S	Ovarian(51;766 1130 5502 35047 50875)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1296A	7						.	C	,,,,,	1,3981		0,1,1990	139.0	143.0	141.0		1287,1296,1296,1287,1296,1287	-6.6	0.1	7		141	0,8336		0,0,4168	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CNOT4	NM_001008225.2,NM_001190847.1,NM_001190848.1,NM_001190849.1,NM_001190850.1,NM_013316.3	,,,,,	0,1,6158	TT,TC,CC		0.0,0.0251,0.0081	,,,,,	429/573,432/643,432/576,429/711,432/714,429/640	135079001	1,12317	1991	4168	6159	134729541	SO:0001819	synonymous_variant	4850	exon10			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	ENST00000315544.5:c.1296G>A	7.37:g.135079001C>T		Somatic		Capture	Illumina HiSeq	Phase_I	134729541	NM_001190850	B7Z6I4|E7ET38|F8VQP3|O95339|O95627|Q8IYM7|Q8NCL0|Q9NPQ1|Q9NZN6	Silent	SNP	ENST00000315544.5	37	CCDS55166.1																																																																																				0.498	CNOT4-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_013316	
PARP12	64761	broad.mit.edu	37	7	139724513	139724513	+	Silent	SNP	G	G	A	rs149371341		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:139724513G>A	ENST00000263549.3	-	12	2826	c.1953C>T	c.(1951-1953)tgC>tgT	p.C651C		NM_022750.2	NP_073587.1	Q9H0J9	PAR12_HUMAN	poly (ADP-ribose) polymerase family, member 12	651	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.					nucleus (GO:0005634)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)	p.C651C(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(1)	19	Melanoma(164;0.0142)					CACTGTTCACGCAGCTATCAT	0.592																																					p.C651C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1953T	7						.	G		0,4406		0,0,2203	149.0	125.0	134.0		1953	-2.3	1.0	7	dbSNP_134	134	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	PARP12	NM_022750.2		0,4,6499	AA,AG,GG		0.0465,0.0,0.0308		651/702	139724513	4,13002	2203	4300	6503	139370982	SO:0001819	synonymous_variant	64761	exon12			AL136766	CCDS5857.1	7q34	2014-01-28	2005-06-02	2005-06-02	ENSG00000059378	ENSG00000059378		"""Zinc fingers, CCCH-type domain containing"", ""Poly (ADP-ribose) polymerases"""	21919	protein-coding gene	gene with protein product		612481	"""zinc finger CCCH-type domain containing 1"""	ZC3HDC1		11230166, 12851707	Standard	NM_022750		Approved	FLJ22693, PARP-12, ZC3H1	uc003vvl.1	Q9H0J9	OTTHUMG00000157315	ENST00000263549.3:c.1953C>T	7.37:g.139724513G>A		Somatic		Capture	Illumina HiSeq	Phase_I	139370982	NM_022750	Q9H610|Q9NP36|Q9NTI3	Silent	SNP	ENST00000263549.3	37	CCDS5857.1																																																																																				0.592	PARP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348413.1	NM_022750	
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12068308}.|V -> E (in CRC; also found in sarcoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis; loss of regulation by PMRT5). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:12198537, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:23263490, ECO:0000269|PubMed:24455489}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	TCGAGATTTCACTGTAGCTAG	0.368	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												p.V600E	Colon(40;35 892 2973 5743 27438)		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	BRAF,pituitary,NS,Substitution - Missense,0 	.	15808	Substitution - Missense(15790)|Complex - deletion inframe(17)|Insertion - In frame(1)	thyroid(7476)|skin(3822)|large_intestine(3288)|NS(360)|haematopoietic_and_lymphoid_tissue(336)|ovary(211)|lung(58)|eye(57)|central_nervous_system(53)|soft_tissue(30)|biliary_tract(18)|liver(17)|prostate(13)|breast(10)|upper_aerodigestive_tract(9)|endometrium(8)|pancreas(8)|testis(7)|small_intestine(7)|genital_tract(4)|stomach(4)|bone(3)|autonomic_ganglia(2)|oesophagus(2)|urinary_tract(2)|adrenal_gland(2)|pituitary(1)	c.T1799A	7						.						112.0	104.0	107.0					7																	140453136		2203	4300	6503	140099605	SO:0001583	missense	673	exon15	Familial Cancer Database	CFC, CFCS	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1799T>A	7.37:g.140453136A>T	ENSP00000288602:p.Val600Glu	Somatic		Capture	Illumina HiSeq	Phase_I	140099605	NM_004333	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.486113|4.486113	0.84854|0.84854	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.81739|.	-1.53|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.61565|.	0.2357|.	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	D|.	0.55385|.	0.971|.	D|.	0.66351|.	0.943|.	T|.	0.58160|.	-0.7685|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	600|.	P15056|.	BRAF_HUMAN|.	E|R	600|208	ENSP00000288602:V600E|.	ENSP00000288602:V600E|.	V|X	-|-	2|1	0|0	BRAF|BRAF	140099605|140099605	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.197000|9.197000	0.94985|0.94985	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	GTG|TGA		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333	
CNTNAP2	26047	broad.mit.edu	37	7	148106517	148106517	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:148106517C>T	ENST00000361727.3	+	23	4266	c.3750C>T	c.(3748-3750)ggC>ggT	p.G1250G	CNTNAP2_ENST00000538075.1_Silent_p.G309G|CNTNAP2_ENST00000463592.2_3'UTR	NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2	1250					adult behavior (GO:0030534)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|cerebral cortex development (GO:0021987)|clustering of voltage-gated potassium channels (GO:0045163)|learning (GO:0007612)|limbic system development (GO:0021761)|neuron projection development (GO:0031175)|neuron recognition (GO:0008038)|protein localization to juxtaparanode region of axon (GO:0071205)|social behavior (GO:0035176)|striatum development (GO:0021756)|superior temporal gyrus development (GO:0071109)|thalamus development (GO:0021794)|transmission of nerve impulse (GO:0019226)|vocalization behavior (GO:0071625)	axolemma (GO:0030673)|axon (GO:0030424)|cell surface (GO:0009986)|dendrite (GO:0030425)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|voltage-gated potassium channel complex (GO:0008076)	enzyme binding (GO:0019899)	p.G1250G(1)		NS(3)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(105)|ovary(9)|pancreas(2)|prostate(5)|skin(7)|stomach(3)|upper_aerodigestive_tract(6)|urinary_tract(3)	188	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			CAGGACAAGGCCAAGCTATAA	0.408										HNSCC(39;0.1)																											p.G1250G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3750T	7						.						92.0	93.0	92.0					7																	148106517		2203	4300	6503	147737450	SO:0001819	synonymous_variant	26047	exon23			AF193613	CCDS5889.1	7q35	2008-02-04			ENSG00000174469	ENSG00000174469			13830	protein-coding gene	gene with protein product		604569				10624965, 10048485	Standard	NM_014141		Approved	Caspr2, KIAA0868, NRXN4	uc003weu.2	Q9UHC6	OTTHUMG00000152743	ENST00000361727.3:c.3750C>T	7.37:g.148106517C>T		Somatic		Capture	Illumina HiSeq	Phase_I	147737450	NM_014141	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	Silent	SNP	ENST00000361727.3	37	CCDS5889.1																																																																																				0.408	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327668.1		
CUL1	8454	broad.mit.edu	37	7	148497633	148497633	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:148497633C>T	ENST00000325222.4	+	22	2569	c.2290C>T	c.(2290-2292)Cga>Tga	p.R764*	CUL1_ENST00000409469.1_Nonsense_Mutation_p.R764*|CUL1_ENST00000602748.1_Nonsense_Mutation_p.R764*	NM_003592.2	NP_003583.2	Q13616	CUL1_HUMAN	cullin 1	764					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic cell cycle (GO:0000278)|negative regulation of cell proliferation (GO:0008285)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|viral process (GO:0016032)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|SCF ubiquitin ligase complex (GO:0019005)		p.R764*(1)		breast(2)|central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(10)|liver(2)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	40	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			ATATTTGGAGCGAGTGGATGG	0.388																																					p.R764X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2290T	7						.						114.0	104.0	107.0					7																	148497633		2203	4300	6503	148128566	SO:0001587	stop_gained	8454	exon22			U58087	CCDS34772.1	7q36.1	2011-05-24			ENSG00000055130	ENSG00000055130			2551	protein-coding gene	gene with protein product		603134				8681378	Standard	NM_003592		Approved		uc003wey.3	Q13616	OTTHUMG00000152776	ENST00000325222.4:c.2290C>T	7.37:g.148497633C>T	ENSP00000326804:p.Arg764*	Somatic		Capture	Illumina HiSeq	Phase_I	148128566	NM_003592	D3DWG3|O60719|Q08AL6|Q8IYW1	Nonsense_Mutation	SNP	ENST00000325222.4	37	CCDS34772.1	.	.	.	.	.	.	.	.	.	.	.	41	8.599199	0.98879	.	.	ENSG00000055130	ENST00000409469;ENST00000325222;ENST00000433865	.	.	.	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.6393	19.3349	0.94312	0.0:1.0:0.0:0.0	.	.	.	.	X	764;764;691	.	ENSP00000326804:R764X	R	+	1	2	CUL1	148128566	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	5.627000	0.67784	2.575000	0.86900	0.467000	0.42956	CGA		0.388	CUL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467785.1	NM_003592	
ZNF777	27153	broad.mit.edu	37	7	149128967	149128967	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:149128967G>A	ENST00000247930.4	-	6	2719	c.2396C>T	c.(2395-2397)gCg>gTg	p.A799V		NM_015694.2	NP_056509.2	Q9ULD5	ZN777_HUMAN	zinc finger protein 777	715					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.A799V(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)			GCCCGTGTGCGCGCGCTGGTG	0.677																																					p.A799V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2396T	7						.						30.0	34.0	33.0					7																	149128967		2202	4299	6501	148759900	SO:0001583	missense	27153	exon6			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.2396C>T	7.37:g.149128967G>A	ENSP00000247930:p.Ala799Val	Somatic		Capture	Illumina HiSeq	Phase_I	148759900	NM_015694	Q8N2R2|Q8N659	Missense_Mutation	SNP	ENST00000247930.4	37	CCDS43675.1	.	.	.	.	.	.	.	.	.	.	G	13.48	2.250251	0.39797	.	.	ENSG00000196453	ENST00000247930	T	0.07908	3.15	4.48	4.48	0.54585	.	.	.	.	.	T	0.06690	0.0171	.	.	.	0.32002	N	0.603175	P	0.41748	0.761	B	0.29716	0.106	T	0.11966	-1.0566	8	0.40728	T	0.16	-16.1715	14.6658	0.68907	0.0:0.0:1.0:0.0	.	799	Q9ULD5-2	.	V	799	ENSP00000247930:A799V	ENSP00000247930:A799V	A	-	2	0	ZNF777	148759900	0.715000	0.27946	1.000000	0.80357	0.408000	0.30992	2.613000	0.46351	2.042000	0.60477	0.313000	0.20887	GCG		0.677	ZNF777-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352708.1	NM_015694	
AOC1	26	broad.mit.edu	37	7	150558219	150558219	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:150558219C>T	ENST00000493429.1	+	7	2762	c.2178C>T	c.(2176-2178)gtC>gtT	p.V726V	AOC1_ENST00000480582.1_3'UTR|AOC1_ENST00000467291.1_Silent_p.V726V|AOC1_ENST00000416793.2_Silent_p.V745V|AOC1_ENST00000360937.4_Silent_p.V726V			P19801	AOC1_HUMAN	amine oxidase, copper containing 1	726					amine metabolic process (GO:0009308)|cellular response to azide (GO:0097185)|cellular response to copper ion (GO:0071280)|cellular response to copper ion starvation (GO:0035874)|cellular response to heparin (GO:0071504)|cellular response to histamine (GO:0071420)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|diamine oxidase activity (GO:0052597)|drug binding (GO:0008144)|heparin binding (GO:0008201)|histamine oxidase activity (GO:0052598)|methylputrescine oxidase activity (GO:0052599)|primary amine oxidase activity (GO:0008131)|propane-1,3-diamine oxidase activity (GO:0052600)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|receptor activity (GO:0004872)|sodium channel activity (GO:0005272)|zinc ion binding (GO:0008270)	p.V726V(1)								Amiloride(DB00594)	CCAACTACGTCCAGCGCTGGA	0.607																																					p.V726V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2178T	7						.						58.0	65.0	62.0					7																	150558219		2035	4182	6217	150189152	SO:0001819	synonymous_variant	26	exon5			AK092514	CCDS43679.1, CCDS64797.1	7q36.1	2013-06-19	2013-06-19	2013-06-19	ENSG00000002726	ENSG00000002726	1.4.3.22		80	protein-coding gene	gene with protein product	"""diamine oxidase"""	104610	"""amiloride binding protein 1 (amine oxidase (copper-containing))"""	ABP1		8182053	Standard	NM_001091		Approved	DAO	uc003wia.2	P19801	OTTHUMG00000158306	ENST00000493429.1:c.2178C>T	7.37:g.150558219C>T		Somatic		Capture	Illumina HiSeq	Phase_I	150189152	NM_001091	C9J690|Q16683|Q16684|Q56II4|Q6GU42	Silent	SNP	ENST00000493429.1	37	CCDS43679.1																																																																																				0.607	AOC1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350628.1	NM_001091	
ABCB8	11194	broad.mit.edu	37	7	150733024	150733024	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:150733024G>A	ENST00000297504.6	+	8	1100	c.1034G>A	c.(1033-1035)cGt>cAt	p.R345H	ABCB8_ENST00000477092.1_Missense_Mutation_p.R328H|ABCB8_ENST00000356058.4_Missense_Mutation_p.R365H|ABCB8_ENST00000358849.4_Missense_Mutation_p.R328H|ABCB8_ENST00000498578.1_Missense_Mutation_p.R328H|ABCB8_ENST00000542328.1_Missense_Mutation_p.R240H|ABCB8_ENST00000477719.1_Missense_Mutation_p.R328H			Q9NUT2	ABCB8_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 8	345	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)	p.R328Q(2)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Doxorubicin(DB00997)	CGGACTGTGCGTGCCTTCGCC	0.622																																					p.R328H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G983A	7						.						82.0	66.0	71.0					7																	150733024		2203	4300	6503	150363957	SO:0001583	missense	11194	exon7			AF047690	CCDS5913.1, CCDS64798.1, CCDS64799.1, CCDS64800.1	7q36.1	2012-05-16			ENSG00000197150	ENSG00000197150		"""ATP binding cassette transporters / subfamily B"""	49	protein-coding gene	gene with protein product	"""mitochondrial ABC protein"""	605464				8894702	Standard	NM_001282291		Approved	EST328128, M-ABC1, MABC1	uc003wik.4	Q9NUT2	OTTHUMG00000158686	ENST00000297504.6:c.1034G>A	7.37:g.150733024G>A	ENSP00000297504:p.Arg345His	Somatic		Capture	Illumina HiSeq	Phase_I	150363957	NM_007188	A5D8W3|B2RBL8|B3KND2|B4DG02|G3XAP3|O95787|Q53GM0	Missense_Mutation	SNP	ENST00000297504.6	37		.	.	.	.	.	.	.	.	.	.	G	16.64	3.178349	0.57692	.	.	ENSG00000197150	ENST00000358849;ENST00000360651;ENST00000297504;ENST00000542328;ENST00000498578;ENST00000356058;ENST00000477719;ENST00000477092	D;D;D;D;D;D;D	0.95518	-3.73;-3.73;-3.73;-3.73;-1.64;-1.64;-1.64	5.34	5.34	0.76211	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.115170	0.56097	D	0.000030	D	0.97548	0.9197	M	0.86573	2.825	0.53688	D	0.999977	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.83275	0.988;0.993;0.996;0.988;0.996;0.996	D	0.97688	1.0177	10	0.72032	D	0.01	1.4811	10.0475	0.42195	0.0917:0.0:0.9083:0.0	.	240;328;345;328;328;365	G3XAP3;A5D8W3;Q9NUT2;Q9NUT2-2;C9JTY4;E7ENE8	.;.;ABCB8_HUMAN;.;.;.	H	328;311;345;240;328;365;328;328	ENSP00000351717:R328H;ENSP00000297504:R345H;ENSP00000438776:R240H;ENSP00000418271:R328H;ENSP00000348353:R365H;ENSP00000419891:R328H;ENSP00000419558:R328H	ENSP00000297504:R345H	R	+	2	0	ABCB8	150363957	1.000000	0.71417	0.398000	0.26321	0.180000	0.23129	4.994000	0.63901	2.504000	0.84457	0.561000	0.74099	CGT		0.622	ABCB8-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351733.2	NM_007188	
KMT2C	58508	broad.mit.edu	37	7	151879428	151879428	+	Silent	SNP	C	C	T	rs375505060		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:151879428C>T	ENST00000262189.6	-	36	5735	c.5517G>A	c.(5515-5517)acG>acA	p.T1839T	KMT2C_ENST00000355193.2_Silent_p.T1839T	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	1839	Pro-rich.				histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|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)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.T1839T(2)									AAGATGTAGACGTAGGGGTAC	0.493																																					p.T1839T												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G5517A	7						.	C		2,4404	4.2+/-10.8	0,2,2201	176.0	164.0	168.0		5517	-10.6	0.0	7		168	0,8600		0,0,4300	no	coding-synonymous	MLL3	NM_170606.2		0,2,6501	TT,TC,CC		0.0,0.0454,0.0154		1839/4912	151879428	2,13004	2203	4300	6503	151510361	SO:0001819	synonymous_variant	58508	exon36			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.5517G>A	7.37:g.151879428C>T		Somatic		Capture	Illumina HiSeq	Phase_I	151510361	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Silent	SNP	ENST00000262189.6	37	CCDS5931.1																																																																																				0.493	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
MAD1L1	8379	broad.mit.edu	37	7	1937900	1937900	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:1937900G>A	ENST00000406869.1	-	18	2491	c.1934C>T	c.(1933-1935)aCg>aTg	p.T645M	MAD1L1_ENST00000265854.7_Missense_Mutation_p.T645M|MAD1L1_ENST00000399654.2_Missense_Mutation_p.T645M|MAD1L1_ENST00000402746.1_Missense_Mutation_p.T553M			Q9Y6D9	MD1L1_HUMAN	MAD1 mitotic arrest deficient-like 1 (yeast)	645					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|regulation of metaphase plate congression (GO:0090235)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|spindle (GO:0005819)		p.T645M(1)		central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(5)	36		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		CTGGTTCTCCGTGGTGATGTC	0.612																																					p.T645M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1934T	7						.						135.0	159.0	151.0					7																	1937900		2164	4256	6420	1904426	SO:0001583	missense	8379	exon18			U33822	CCDS43539.1	7p22	2013-01-17	2001-11-28		ENSG00000002822	ENSG00000002822			6762	protein-coding gene	gene with protein product		602686	"""MAD1 (mitotic arrest deficient, yeast, homolog)-like 1"""			10049595, 9546394	Standard	XM_005249876		Approved	HsMAD1, TXBP181, MAD1, PIG9, TP53I9	uc003slg.1	Q9Y6D9	OTTHUMG00000151493	ENST00000406869.1:c.1934C>T	7.37:g.1937900G>A	ENSP00000385334:p.Thr645Met	Somatic		Capture	Illumina HiSeq	Phase_I	1904426	NM_001013836	B3KR41|Q13312|Q75MI0|Q86UM4|Q9UNH0	Missense_Mutation	SNP	ENST00000406869.1	37	CCDS43539.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.428140	0.83667	.	.	ENSG00000002822	ENST00000402746;ENST00000399654;ENST00000406869;ENST00000442131;ENST00000265854;ENST00000450235;ENST00000437877	T;T;T;T;T;T	0.26810	1.71;1.71;1.71;1.71;1.71;1.71	5.59	4.7	0.59300	.	0.245051	0.41194	D	0.000923	T	0.47728	0.1461	M	0.65498	2.005	0.46586	D	0.99911	D;D;D	0.89917	0.999;1.0;0.998	D;D;P	0.68621	0.939;0.959;0.867	T	0.46176	-0.9210	10	0.48119	T	0.1	-11.2025	14.6044	0.68466	0.0:0.1618:0.8382:0.0	.	644;553;645	A4D218;B3KR41;Q9Y6D9	.;.;MD1L1_HUMAN	M	553;645;645;196;645;196;101	ENSP00000384155:T553M;ENSP00000382562:T645M;ENSP00000385334:T645M;ENSP00000265854:T645M;ENSP00000394886:T196M;ENSP00000394069:T101M	ENSP00000265854:T645M	T	-	2	0	MAD1L1	1904426	1.000000	0.71417	0.749000	0.31150	0.929000	0.56500	5.098000	0.64548	1.316000	0.45131	0.655000	0.94253	ACG		0.612	MAD1L1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322871.1	NM_003550	
BRAT1	221927	broad.mit.edu	37	7	2584654	2584654	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:2584654C>A	ENST00000340611.4	-	4	575	c.319G>T	c.(319-321)Gga>Tga	p.G107*		NM_152743.3	NP_689956.2	Q6PJG6	BRAT1_HUMAN	BRCA1-associated ATM activator 1	107					response to ionizing radiation (GO:0010212)	membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	23						CCGAGGGGTCCTGGCTCCCCA	0.667																																					p.G107X												.	.	0			c.G319T	7						.																																			2551180	SO:0001587	stop_gained	221927	exon4			BC015632	CCDS5334.1	7p22.3	2011-03-22	2011-02-28	2011-03-22	ENSG00000106009	ENSG00000106009			21701	protein-coding gene	gene with protein product	"""BRCA1-associated protein required for ATM activation protein 1"""	614506	"""chromosome 7 open reading frame 27"""	C7orf27, BAAT1		16452482	Standard	NM_152743		Approved	MGC22916	uc003smi.3	Q6PJG6	OTTHUMG00000119091	ENST00000340611.4:c.319G>T	7.37:g.2584654C>A	ENSP00000339637:p.Gly107*	None		Capture	Illumina HiSeq	Phase_I	2551180	NM_152743	A4D200|C9JY24|Q8IW85|Q8IZ43|Q8WVR8|Q96IV9|Q9H7J8|Q9UFA3	Nonsense_Mutation	SNP	ENST00000340611.4	37	CCDS5334.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.274114	0.80580	.	.	ENSG00000106009	ENST00000340611	.	.	.	5.28	2.46	0.29980	.	0.282783	0.34314	N	0.004079	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-13.119	7.0484	0.25059	0.0:0.7067:0.1411:0.1522	.	.	.	.	X	107	.	ENSP00000339637:G107X	G	-	1	0	BRAT1	2551180	0.969000	0.33509	0.001000	0.08648	0.005000	0.04900	3.624000	0.54231	0.220000	0.20860	-0.258000	0.10820	GGA		0.667	BRAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239305.2	NM_152743	
SDK1	221935	broad.mit.edu	37	7	4009043	4009043	+	Silent	SNP	G	G	A	rs149174821		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:4009043G>A	ENST00000404826.2	+	11	1840	c.1701G>A	c.(1699-1701)acG>acA	p.T567T	SDK1_ENST00000389531.3_Silent_p.T567T	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	567	Ig-like C2-type 5.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.T567T(1)		NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		CATCGGCCACGCTCACTGTGT	0.587																																					p.T567T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1701A	7						.	G		0,4406		0,0,2203	76.0	76.0	76.0		1701	-1.5	0.0	7	dbSNP_134	76	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SDK1	NM_152744.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		567/2214	4009043	1,13005	2203	4300	6503	3975569	SO:0001819	synonymous_variant	221935	exon11			AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19307	protein-coding gene	gene with protein product		607216	"""sidekick homolog 1 (chicken)"", ""sidekick homolog 1, cell adhesion molecule (chicken)"""			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.1701G>A	7.37:g.4009043G>A		Somatic		Capture	Illumina HiSeq	Phase_I	3975569	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Silent	SNP	ENST00000404826.2	37	CCDS34590.1																																																																																				0.587	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744	
ICA1	3382	broad.mit.edu	37	7	8178638	8178638	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:8178638C>T	ENST00000402384.3	-	11	1261	c.995G>A	c.(994-996)gGc>gAc	p.G332D	ICA1_ENST00000422063.2_Missense_Mutation_p.G361D|ICA1_ENST00000396675.3_Missense_Mutation_p.G332D|ICA1_ENST00000406470.2_Missense_Mutation_p.G332D|ICA1_ENST00000401396.1_Missense_Mutation_p.G320D|ICA1_ENST00000265577.7_Missense_Mutation_p.G331D			Q05084	ICA69_HUMAN	islet cell autoantigen 1, 69kDa	332					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|secretory granule membrane (GO:0030667)|synaptic vesicle membrane (GO:0030672)		p.G332D(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(8)|urinary_tract(1)	23		Ovarian(82;0.0612)		UCEC - Uterine corpus endometrioid carcinoma (126;0.246)		ATGTGTAGAGCCTTTGTCTAA	0.353																																					p.G332D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G995A	7						.						138.0	129.0	132.0					7																	8178638		2203	4300	6503	8145163	SO:0001583	missense	3382	exon11				CCDS34602.1, CCDS64595.1	7p22	2006-12-13	2002-08-29		ENSG00000003147	ENSG00000003147			5343	protein-coding gene	gene with protein product		147625	"""islet cell autoantigen 1 (69kD)"""			7918678, 8777998	Standard	NM_001276478		Approved	ICAp69	uc003srm.3	Q05084	OTTHUMG00000152008	ENST00000402384.3:c.995G>A	7.37:g.8178638C>T	ENSP00000385570:p.Gly332Asp	Somatic		Capture	Illumina HiSeq	Phase_I	8145163	NM_004968	A8K7U1|B3FTQ2|P78506|Q13824|Q96HG3	Missense_Mutation	SNP	ENST00000402384.3	37	CCDS34602.1	.	.	.	.	.	.	.	.	.	.	C	0.032	-1.330057	0.01298	.	.	ENSG00000003147	ENST00000402384;ENST00000406470;ENST00000265577;ENST00000396675;ENST00000401396;ENST00000422063	.	.	.	5.17	0.0618	0.14342	Islet cell autoantigen Ica1, C-terminal (1);	0.493857	0.26654	N	0.023187	T	0.20577	0.0495	N	0.19112	0.55	0.09310	N	1	B;B;B;B	0.14012	0.009;0.007;0.007;0.005	B;B;B;B	0.20577	0.03;0.023;0.023;0.025	T	0.20273	-1.0280	9	0.12430	T	0.62	-0.3951	5.739	0.18083	0.0:0.3173:0.4737:0.209	.	361;331;332;320	B3FTQ2;Q96HG3;Q05084;E9PDL4	.;.;ICA69_HUMAN;.	D	332;332;331;332;320;361	.	ENSP00000265577:G331D	G	-	2	0	ICA1	8145163	0.017000	0.18338	0.048000	0.18961	0.101000	0.19017	0.047000	0.14056	0.110000	0.17919	0.655000	0.94253	GGC		0.353	ICA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324793.1	NM_004968	
SNX13	23161	broad.mit.edu	37	7	17915375	17915375	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:17915375C>T	ENST00000409389.1	-	6	651	c.479G>A	c.(478-480)cGc>cAc	p.R160H	SNX13_ENST00000428135.3_Missense_Mutation_p.R160H			Q9Y5W8	SNX13_HUMAN	sorting nexin 13	160	PXA. {ECO:0000255|PROSITE- ProRule:PRU00147, ECO:0000255|PROSITE- ProRule:PRU00553}.				intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	early endosome (GO:0005769)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)	p.R160H(1)		breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(13)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(10;0.0261)|all_lung(11;0.0521)					ATCTACAATGCGTGTAGTAAA	0.299																																					p.R160H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G479A	7						.						129.0	113.0	118.0					7																	17915375		1828	4081	5909	17881900	SO:0001583	missense	23161	exon6			AF420470	CCDS47551.1	7p21.1	2008-03-11			ENSG00000071189	ENSG00000071189		"""Sorting nexins"""	21335	protein-coding gene	gene with protein product		606589				11485546, 11729322	Standard	NM_015132		Approved	RGS-PX1, KIAA0713	uc003stv.3	Q9Y5W8	OTTHUMG00000152730	ENST00000409389.1:c.479G>A	7.37:g.17915375C>T	ENSP00000386705:p.Arg160His	Somatic		Capture	Illumina HiSeq	Phase_I	17881900	NM_015132	B2RCI9|O94821|Q8WVZ2|Q8WXH8	Missense_Mutation	SNP	ENST00000409389.1	37		.	.	.	.	.	.	.	.	.	.	C	18.71	3.683083	0.68157	.	.	ENSG00000071189	ENST00000409389;ENST00000428135;ENST00000242044	T;T	0.21031	2.03;2.29	5.5	5.5	0.81552	Phox-associated domain (2);PX-associated, sorting nexin 13 (1);	0.000000	0.85682	D	0.000000	T	0.20618	0.0496	L	0.43152	1.355	0.80722	D	1	B;B;P	0.39352	0.381;0.437;0.669	B;B;B	0.32533	0.08;0.147;0.049	T	0.01930	-1.1245	10	0.46703	T	0.11	-4.3327	19.3999	0.94623	0.0:1.0:0.0:0.0	.	160;160;160	Q9Y5W8;B8ZZT9;Q9Y5W8-2	SNX13_HUMAN;.;.	H	160;160;208	ENSP00000386705:R160H;ENSP00000398789:R160H	ENSP00000242044:R208H	R	-	2	0	SNX13	17881900	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.085000	0.76875	2.565000	0.86533	0.655000	0.94253	CGC		0.299	SNX13-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000327608.1	NM_015132	
SNX10	29887	broad.mit.edu	37	7	26411524	26411524	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:26411524C>T	ENST00000338523.4	+	6	582	c.395C>T	c.(394-396)gCg>gTg	p.A132V	SNX10_ENST00000462993.1_3'UTR|SNX10_ENST00000409838.1_Missense_Mutation_p.A48V|AC004540.4_ENST00000451264.1_RNA|SNX10_ENST00000396376.1_Missense_Mutation_p.A132V|SNX10_ENST00000409367.1_Missense_Mutation_p.A92V|AC004540.4_ENST00000451368.1_RNA|SNX10_ENST00000446848.2_Missense_Mutation_p.A158V	NM_001199835.1|NM_013322.2	NP_001186764.1|NP_037454.2	Q9Y5X0	SNX10_HUMAN	sorting nexin 10	132					cilium assembly (GO:0042384)|endosome organization (GO:0007032)|intracellular protein transport (GO:0006886)|osteoclast differentiation (GO:0030316)|protein localization to centrosome (GO:0071539)|protein localization to cilium (GO:0061512)	cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extrinsic component of endosome membrane (GO:0031313)|nucleus (GO:0005634)	1-phosphatidylinositol binding (GO:0005545)|ATPase binding (GO:0051117)	p.A132V(1)		endometrium(1)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	6						GACATTGAGGCGTGTGTTTCT	0.383																																					p.A129V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C386T	7						.						127.0	123.0	125.0					7																	26411524		2203	4300	6503	26378049	SO:0001583	missense	29887	exon4			AF121860	CCDS5399.1, CCDS56470.1	7p15.2	2008-05-22			ENSG00000086300	ENSG00000086300		"""Sorting nexins"""	14974	protein-coding gene	gene with protein product		614780				17012226	Standard	NM_013322		Approved		uc010kuu.3	Q9Y5X0	OTTHUMG00000023650	ENST00000338523.4:c.395C>T	7.37:g.26411524C>T	ENSP00000343709:p.Ala132Val	Somatic		Capture	Illumina HiSeq	Phase_I	26378049	NM_001199837	E9PFH5|Q8IYT5	Missense_Mutation	SNP	ENST00000338523.4	37	CCDS5399.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.370690	0.82573	.	.	ENSG00000086300	ENST00000416246;ENST00000338523;ENST00000446848;ENST00000396376;ENST00000409367;ENST00000409838	T;T;T;T;T;T	0.66280	-0.15;0.41;0.38;0.41;-0.2;0.63	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.79528	0.4461	M	0.71206	2.165	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.73380	0.98;0.97	T	0.78497	-0.2181	10	0.51188	T	0.08	.	20.1356	0.98028	0.0:1.0:0.0:0.0	.	158;132	B4DJM0;Q9Y5X0	.;SNX10_HUMAN	V	158;132;158;132;92;48	ENSP00000408164:A158V;ENSP00000343709:A132V;ENSP00000395474:A158V;ENSP00000379661:A132V;ENSP00000387274:A92V;ENSP00000386540:A48V	ENSP00000343709:A132V	A	+	2	0	SNX10	26378049	1.000000	0.71417	0.967000	0.41034	0.835000	0.47333	6.885000	0.75606	2.755000	0.94549	0.650000	0.86243	GCG		0.383	SNX10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214120.1		
HOXA11	3207	broad.mit.edu	37	7	27222546	27222546	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:27222546G>A	ENST00000006015.3	-	2	882	c.811C>T	c.(811-813)Cgc>Tgc	p.R271C	HOXA11-AS_ENST00000522674.1_RNA|RP1-170O19.20_ENST00000470747.4_5'Flank|HOXA11-AS_ENST00000522863.1_RNA|HOXA11-AS_ENST00000520360.1_RNA|HOXA10_ENST00000396344.4_5'Flank|HOXA11-AS_ENST00000520395.1_RNA	NM_005523.5	NP_005514.1	P31270	HXA11_HUMAN	homeobox A11	271					anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|developmental growth (GO:0048589)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal joint morphogenesis (GO:0060272)|male gonad development (GO:0008584)|mesodermal cell fate specification (GO:0007501)|metanephros development (GO:0001656)|multicellular organismal development (GO:0007275)|organ induction (GO:0001759)|positive regulation of cell development (GO:0010720)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)|uterus development (GO:0060065)	nucleus (GO:0005634)|protein complex (GO:0043234)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)	p.R271C(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|skin(2)	16						AGTTGCAGGCGCTTCTCTTTG	0.478			T	NUP98	CML																																p.R271C			Dom	yes		7	7p15-p14.2	3207	homeo box A11		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C811T	7						.						89.0	93.0	91.0					7																	27222546		2203	4300	6503	27189071	SO:0001583	missense	3207	exon2				CCDS5411.1	7p15.2	2014-09-17	2005-12-22		ENSG00000005073	ENSG00000005073		"""Homeoboxes / ANTP class : HOXL subclass"""	5101	protein-coding gene	gene with protein product		142958	"""homeo box A11"""	HOX1I, HOX1		1973146, 1358459	Standard	NM_005523		Approved		uc003syx.3	P31270	OTTHUMG00000023437	ENST00000006015.3:c.811C>T	7.37:g.27222546G>A	ENSP00000006015:p.Arg271Cys	Somatic		Capture	Illumina HiSeq	Phase_I	27189071	NM_005523	A4D190	Missense_Mutation	SNP	ENST00000006015.3	37	CCDS5411.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.426259	0.83667	.	.	ENSG00000005073	ENST00000006015	D	0.97480	-4.4	5.91	5.91	0.95273	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99093	0.9688	H	0.96208	3.785	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99063	1.0831	10	0.87932	D	0	.	20.3052	0.98627	0.0:0.0:1.0:0.0	.	271	P31270	HXA11_HUMAN	C	271	ENSP00000006015:R271C	ENSP00000006015:R271C	R	-	1	0	HOXA11	27189071	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.558000	0.67319	2.808000	0.96608	0.655000	0.94253	CGC		0.478	HOXA11-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358754.1		
CDK13	8621	broad.mit.edu	37	7	40085541	40085541	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:40085541G>T	ENST00000181839.4	+	6	3065	c.2460G>T	c.(2458-2460)caG>caT	p.Q820H	CDK13_ENST00000484589.1_3'UTR|CDK13_ENST00000340829.5_Missense_Mutation_p.Q820H	NM_003718.4|NM_031267.3	NP_003709.3|NP_112557.2	Q14004	CDK13_HUMAN	cyclin-dependent kinase 13	820	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				alternative mRNA splicing, via spliceosome (GO:0000380)|hemopoiesis (GO:0030097)|multicellular organismal development (GO:0007275)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|positive regulation of cell proliferation (GO:0008284)|regulation of mitosis (GO:0007088)|viral process (GO:0016032)	cyclin K-CDK13 complex (GO:0002945)|extracellular space (GO:0005615)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)	p.Q820H(1)		cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(2)|prostate(2)|skin(5)|stomach(2)|urinary_tract(1)	49						TTATGAGACAGCTCATGGAGG	0.333																																					p.Q820H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2460T	7						.						137.0	146.0	143.0					7																	40085541		2203	4300	6503	40052066	SO:0001583	missense	8621	exon6			M80629	CCDS5461.1, CCDS5462.1	7p14.1	2011-11-08	2009-12-16	2009-12-16	ENSG00000065883	ENSG00000065883		"""Cyclin-dependent kinases"""	1733	protein-coding gene	gene with protein product	"""cholinesterase-related cell division controller"""	603309	"""cell division cycle 2-like 5 (cholinesterase-related cell division controller)"""	CDC2L5		1731328, 19884882	Standard	NM_003718		Approved	CHED, CDC2L, KIAA1791	uc003thh.4	Q14004	OTTHUMG00000023726	ENST00000181839.4:c.2460G>T	7.37:g.40085541G>T	ENSP00000181839:p.Gln820His	Somatic		Capture	Illumina HiSeq	Phase_I	40052066	NM_003718	Q53G78|Q6DKQ9|Q75MH4|Q75MH5|Q96JN4|Q9H4A0|Q9H4A1|Q9UDR4	Missense_Mutation	SNP	ENST00000181839.4	37	CCDS5461.1	.	.	.	.	.	.	.	.	.	.	G	16.66	3.183950	0.57800	.	.	ENSG00000065883	ENST00000181839;ENST00000340829	T;T	0.56611	0.45;0.45	4.71	0.565	0.17309	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	0.73544	0.3600	M	0.90759	3.145	0.58432	D	0.999997	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.97110	1.0;0.997;1.0	T	0.75510	-0.3292	8	.	.	.	-8.6215	10.6451	0.45615	0.3053:0.0:0.6947:0.0	.	206;820;820	Q9BVE2;Q14004-2;Q14004	.;.;CDK13_HUMAN	H	820	ENSP00000181839:Q820H;ENSP00000340557:Q820H	.	Q	+	3	2	CDK13	40052066	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	2.267000	0.43329	0.220000	0.20860	-0.157000	0.13467	CAG		0.333	CDK13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250726.2	NM_003718	
INHBA	3624	broad.mit.edu	37	7	41729399	41729399	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:41729399C>T	ENST00000242208.4	-	3	1376	c.1130G>A	c.(1129-1131)cGc>cAc	p.R377H	AC005027.3_ENST00000416150.1_RNA|INHBA_ENST00000464515.1_5'UTR|INHBA_ENST00000442711.1_Missense_Mutation_p.R377H	NM_002192.2	NP_002183.1	P08476	INHBA_HUMAN	inhibin, beta A	377				RMR -> AC (in Ref. 7; CAA51163). {ECO:0000305}.	activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to cholesterol (GO:0071397)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|defense response (GO:0006952)|endodermal cell differentiation (GO:0035987)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|eyelid development in camera-type eye (GO:0061029)|G1/S transition of mitotic cell cycle (GO:0000082)|growth (GO:0040007)|hair follicle development (GO:0001942)|hematopoietic progenitor cell differentiation (GO:0002244)|hemoglobin biosynthetic process (GO:0042541)|male gonad development (GO:0008584)|mesodermal cell differentiation (GO:0048333)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of phosphorylation (GO:0042326)|nervous system development (GO:0007399)|odontogenesis (GO:0042476)|ovarian follicle development (GO:0001541)|palate development (GO:0060021)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|positive regulation of ovulation (GO:0060279)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone secretion (GO:0042701)|regulation of follicle-stimulating hormone secretion (GO:0046880)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)	activin A complex (GO:0043509)|extracellular region (GO:0005576)|inhibin A complex (GO:0043512)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|hormone activity (GO:0005179)|identical protein binding (GO:0042802)|peptide hormone binding (GO:0017046)|type II activin receptor binding (GO:0070699)	p.R377H(1)		biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(15)|lung(26)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						GCCCCGCATGCGGTAGTGGTT	0.547										TSP Lung(11;0.080)																											p.R377H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1130A	7						.						130.0	115.0	120.0					7																	41729399		2203	4300	6503	41695924	SO:0001583	missense	3624	exon3				CCDS5464.1	7p15-p13	2014-01-30	2007-07-30		ENSG00000122641	ENSG00000122641		"""Endogenous ligands"""	6066	protein-coding gene	gene with protein product		147290	"""inhibin, beta A (activin A, activin AB alpha polypeptide)"""			3345731	Standard	NM_002192		Approved		uc003thr.3	P08476	OTTHUMG00000023574	ENST00000242208.4:c.1130G>A	7.37:g.41729399C>T	ENSP00000242208:p.Arg377His	Somatic		Capture	Illumina HiSeq	Phase_I	41695924	NM_002192	Q14599	Missense_Mutation	SNP	ENST00000242208.4	37	CCDS5464.1	.	.	.	.	.	.	.	.	.	.	.	23.6	4.430177	0.83776	.	.	ENSG00000122641	ENST00000242208;ENST00000442711	T;T	0.62498	0.02;0.02	5.86	5.86	0.93980	Transforming growth factor-beta, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.80486	0.4632	M	0.75264	2.295	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.79505	-0.1776	10	0.51188	T	0.08	-23.9854	20.1781	0.98191	0.0:1.0:0.0:0.0	.	377	P08476	INHBA_HUMAN	H	377	ENSP00000242208:R377H;ENSP00000397197:R377H	ENSP00000242208:R377H	R	-	2	0	INHBA	41695924	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.751000	0.85126	2.778000	0.95560	0.591000	0.81541	CGC		0.547	INHBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250793.1		
HECW1	23072	broad.mit.edu	37	7	43483896	43483896	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:43483896C>T	ENST00000395891.2	+	11	1730	c.1125C>T	c.(1123-1125)agC>agT	p.S375S	HECW1_ENST00000453890.1_Silent_p.S375S	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	375					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.S354S(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						TGATGGAAAGCGGCAGTGGGG	0.552																																					p.S375S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1125T	7						.						57.0	64.0	62.0					7																	43483896		2105	4225	6330	43450421	SO:0001819	synonymous_variant	23072	exon11			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.1125C>T	7.37:g.43483896C>T		Somatic		Capture	Illumina HiSeq	Phase_I	43450421	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Silent	SNP	ENST00000395891.2	37	CCDS5469.2																																																																																				0.552	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052	
DBNL	28988	broad.mit.edu	37	7	44096429	44096429	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:44096429A>T	ENST00000448521.1	+	5	499	c.401A>T	c.(400-402)aAg>aTg	p.K134M	DBNL_ENST00000494774.1_Missense_Mutation_p.K134M|DBNL_ENST00000497184.1_3'UTR|DBNL_ENST00000456905.1_Intron|DBNL_ENST00000452943.1_Missense_Mutation_p.K109M|DBNL_ENST00000440166.1_Missense_Mutation_p.K31M|DBNL_ENST00000468694.1_Missense_Mutation_p.K134M|DBNL_ENST00000490734.2_Missense_Mutation_p.K39M	NM_001014436.2	NP_001014436.1	Q9UJU6	DBNL_HUMAN	drebrin-like	134					activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|endocytosis (GO:0006897)|immune system process (GO:0002376)|neuron projection morphogenesis (GO:0048812)|podosome assembly (GO:0071800)|Rac protein signal transduction (GO:0016601)|synapse assembly (GO:0007416)	cell cortex (GO:0005938)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|podosome (GO:0002102)|postsynaptic density (GO:0014069)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|enzyme activator activity (GO:0008047)	p.K134M(1)		breast(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)|stomach(1)	12						AAGGTGGCCAAGGCTTCAGGT	0.617																																					p.K134M	NSCLC(68;573 1327 18604 34760 37992)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A401T	7						.						123.0	104.0	110.0					7																	44096429		2203	4300	6503	44062954	SO:0001583	missense	28988	exon5			AF151364	CCDS34622.1, CCDS34623.1, CCDS47579.1, CCDS64633.1, CCDS64634.1	7p13	2004-07-22			ENSG00000136279	ENSG00000136279			2696	protein-coding gene	gene with protein product		610106				10087302	Standard	NM_014063		Approved	SH3P7, HIP-55	uc003tjq.4	Q9UJU6	OTTHUMG00000155350	ENST00000448521.1:c.401A>T	7.37:g.44096429A>T	ENSP00000411701:p.Lys134Met	Somatic		Capture	Illumina HiSeq	Phase_I	44062954	NM_014063	A4D2I9|B4DEM2|C9J7P1|P84070|Q6IAI8|Q96F30|Q96K74|Q9HBN8|Q9NR72	Missense_Mutation	SNP	ENST00000448521.1	37	CCDS34623.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.7|22.7	4.329349|4.329349	0.81690|0.81690	.|.	.|.	ENSG00000136279|ENSG00000136279	ENST00000448521;ENST00000440166;ENST00000452943;ENST00000468694;ENST00000494774;ENST00000490734;ENST00000539475|ENST00000432854	T;T;T;T;T;T|.	0.37915|.	1.55;1.78;1.77;1.17;1.56;1.78|.	5.03|5.03	3.93|3.93	0.45458|0.45458	.|.	0.099213|.	0.64402|.	D|.	0.000002|.	T|T	0.63200|0.63200	0.2491|0.2491	M|M	0.71581|0.71581	2.175|2.175	0.52501|0.52501	D|D	0.999951|0.999951	D;D;D;D;D;D;D;D|.	0.89917|.	0.999;0.999;0.999;1.0;0.998;0.999;0.999;0.999|.	D;P;D;D;P;D;P;D|.	0.71414|.	0.94;0.905;0.966;0.973;0.855;0.973;0.905;0.968|.	T|T	0.60692|0.60692	-0.7213|-0.7213	10|5	0.87932|.	D|.	0|.	-39.6825|-39.6825	7.3086|7.3086	0.26461|0.26461	0.8837:0.0:0.1163:0.0|0.8837:0.0:0.1163:0.0	.|.	31;82;64;39;109;134;134;134|.	B4DEM2;B4DXL9;B4DDU5;C9J7P1;B4DDD6;Q9UJU6-3;Q9UJU6;Q9UJU6-2|.	.;.;.;.;.;.;DBNL_HUMAN;.|.	M|H	134;31;109;134;134;39;64|62	ENSP00000411701:K134M;ENSP00000415173:K31M;ENSP00000405343:K109M;ENSP00000417653:K134M;ENSP00000419992:K134M;ENSP00000417749:K39M|.	ENSP00000415173:K31M|.	K|Q	+|+	2|3	0|2	DBNL|DBNL	44062954|44062954	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	7.214000|7.214000	0.77958|0.77958	0.854000|0.854000	0.35336|0.35336	0.456000|0.456000	0.33151|0.33151	AAG|CAA		0.617	DBNL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339572.2	NM_014063	
NPC1L1	29881	broad.mit.edu	37	7	44574088	44574088	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:44574088G>A	ENST00000289547.4	-	6	2179	c.2124C>T	c.(2122-2124)tcC>tcT	p.S708S	NPC1L1_ENST00000381160.3_Silent_p.S708S|NPC1L1_ENST00000546276.1_Silent_p.S708S|NPC1L1_ENST00000423141.1_Silent_p.S708S	NM_013389.2	NP_037521.2	Q9UHC9	NPCL1_HUMAN	NPC1-like 1	708	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				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.S708S(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)	CAGCCCCCACGGACAGCACCA	0.562											OREG0018038	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S708S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2124T	7						.						131.0	115.0	120.0					7																	44574088		2203	4300	6503	44540613	SO:0001819	synonymous_variant	29881	exon6				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.2124C>T	7.37:g.44574088G>A		Somatic	925	Capture	Illumina HiSeq	Phase_I	44540613	NM_013389	A4D2J7|B7ZLE6|D3DVK9|Q17RV5|Q6R3Q4|Q9UHC8	Silent	SNP	ENST00000289547.4	37	CCDS5491.1																																																																																				0.562	NPC1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251256.1	NM_013389	
HUS1	3364	broad.mit.edu	37	7	48016330	48016330	+	Silent	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:48016330A>G	ENST00000258774.5	-	4	485	c.462T>C	c.(460-462)ccT>ccC	p.P154P	HUS1_ENST00000432325.1_Silent_p.P133P	NM_004507.3	NP_004498.1	O60921	HUS1_HUMAN	HUS1 checkpoint homolog (S. pombe)	154					cellular response to DNA damage stimulus (GO:0006974)|cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|embryo development (GO:0009790)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of DNA replication (GO:0008156)|protein phosphorylation (GO:0006468)|regulation of protein phosphorylation (GO:0001932)|response to UV (GO:0009411)	checkpoint clamp complex (GO:0030896)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.P154P(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|liver(1)|lung(3)|ovary(2)|prostate(1)	13		Breast(660;0.00139)				CACCTACATCAGGATCTGGGA	0.433								Direct reversal of damage;Other conserved DNA damage response genes																													p.P154P	Ovarian(103;466 1517 21788 34610 43890)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T462C	7						.						177.0	161.0	167.0					7																	48016330		2203	4300	6503	47982855	SO:0001819	synonymous_variant	3364	exon4			Y16893	CCDS34635.1	7p13-p12	2008-08-08	2001-11-28		ENSG00000136273	ENSG00000136273			5309	protein-coding gene	gene with protein product	"""hus1+-like protein"""	603760	"""HUS1 (S. pombe) checkpoint homolog"""			9878245, 9524127	Standard	NM_004507		Approved		uc003tod.2	O60921	OTTHUMG00000155645	ENST00000258774.5:c.462T>C	7.37:g.48016330A>G		Somatic		Capture	Illumina HiSeq	Phase_I	47982855	NM_004507	B4DFI9	Silent	SNP	ENST00000258774.5	37	CCDS34635.1																																																																																				0.433	HUS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340952.1	NM_004507	
C7orf57	136288	broad.mit.edu	37	7	48086156	48086156	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:48086156C>T	ENST00000348904.3	+	5	662	c.450C>T	c.(448-450)ttC>ttT	p.F150F	C7orf57_ENST00000430738.1_Silent_p.F195F|C7orf57_ENST00000539619.1_Silent_p.F150F|C7orf57_ENST00000420324.1_Silent_p.F195F|C7orf57_ENST00000435376.1_Silent_p.F28F	NM_001100159.2	NP_001093629.1	Q8NEG2	CG057_HUMAN	chromosome 7 open reading frame 57	150								p.F150F(1)		breast(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)	9						CCTTCGACTTCGACATGAAAA	0.493																																					p.F150F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C450T	7						.						60.0	56.0	57.0					7																	48086156		1944	4138	6082	48052681	SO:0001819	synonymous_variant	136288	exon5			BC031107	CCDS47583.1, CCDS59054.1, CCDS75594.1	7p12.3	2011-11-25			ENSG00000164746	ENSG00000164746			22247	protein-coding gene	gene with protein product							Standard	NM_001100159		Approved		uc003toh.5	Q8NEG2	OTTHUMG00000155808	ENST00000348904.3:c.450C>T	7.37:g.48086156C>T		Somatic		Capture	Illumina HiSeq	Phase_I	48052681	NM_001100159	C9JBJ8	Silent	SNP	ENST00000348904.3	37	CCDS47583.1																																																																																				0.493	C7orf57-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341745.1	NM_001100159	
ABCA13	154664	broad.mit.edu	37	7	48443384	48443384	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:48443384T>C	ENST00000435803.1	+	39	12002	c.11978T>C	c.(11977-11979)aTg>aCg	p.M3993T		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	3993	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.M3993T(1)|p.M3938T(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						TTCATGGGCATGTCGAGGACC	0.567																																					p.C3939R												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T11815C	7						.						98.0	99.0	99.0					7																	48443384		2006	4168	6174	48413930	SO:0001583	missense	154664	exon37			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.11978T>C	7.37:g.48443384T>C	ENSP00000411096:p.Met3993Thr	Somatic		Capture	Illumina HiSeq	Phase_I	48413930	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	T	3.067	-0.192064	0.06299	.	.	ENSG00000179869	ENST00000435803	D	0.93076	-3.16	6.17	-9.66	0.00534	ATPase, AAA+ type, core (1);ABC transporter-like (2);	1.315600	0.05332	N	0.528547	T	0.71609	0.3360	N	0.01576	-0.805	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.68108	-0.5496	10	0.11485	T	0.65	.	0.6152	0.00768	0.3205:0.114:0.2613:0.3042	.	1695;3993	Q86UQ4-3;Q86UQ4	.;ABCAD_HUMAN	T	3993	ENSP00000411096:M3993T	ENSP00000411096:M3993T	M	+	2	0	ABCA13	48413930	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.093000	0.11111	-1.256000	0.02478	-1.063000	0.02288	ATG		0.567	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
IKZF1	10320	broad.mit.edu	37	7	50468172	50468172	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:50468172G>A	ENST00000331340.3	+	8	1562	c.1407G>A	c.(1405-1407)gtG>gtA	p.V469V	IKZF1_ENST00000349824.4_Silent_p.V326V|IKZF1_ENST00000438033.1_Silent_p.V382V|IKZF1_ENST00000357364.4_Silent_p.V382V|IKZF1_ENST00000439701.1_Silent_p.V427V|IKZF1_ENST00000440768.2_3'UTR|IKZF1_ENST00000343574.5_Silent_p.V382V|IKZF1_ENST00000359197.5_Silent_p.V427V|IKZF1_ENST00000346667.4_Silent_p.V239V	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)	469	Required for binding PP1CC. {ECO:0000250}.				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.?(28)		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)				ACTGCCGGGTGCTCTTCCTGG	0.622			"""D,T"""	BCL6	"""ALL, DLBCL"""																																p.V469V			"""Rec,Dom"""	yes		7	7p12.2	10320	IKAROS family zinc finger 1		L	.	.	28	Unknown(28)	haematopoietic_and_lymphoid_tissue(28)	c.G1407A	7						.						49.0	53.0	52.0					7																	50468172		2183	4293	6476	50435666	SO:0001819	synonymous_variant	10320	exon8			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.1407G>A	7.37:g.50468172G>A		None		Capture	Illumina HiSeq	Phase_I	50435666	NM_006060	A4D260|B4E0Z1|D3DVM5|O00598|Q53XL2|Q69BM4|Q8WVA3	Silent	SNP	ENST00000331340.3	37																																																																																					0.622	IKZF1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000342242.1	NM_006060	
POM121L12	285877	broad.mit.edu	37	7	53103659	53103659	+	Missense_Mutation	SNP	C	C	T	rs201854361	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:53103659C>T	ENST00000408890.4	+	1	311	c.295C>T	c.(295-297)Cgc>Tgc	p.R99C		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	99								p.R99C(1)		endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						GGGCTGGAGGCGCCCTGCCCT	0.721													C|||	2	0.000399361	0.0015	0.0	5008	,	,		12766	0.0		0.0	False		,,,				2504	0.0				p.R99C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C295T	7						.	C	CYS/ARG	3,3863		0,3,1930	17.0	21.0	20.0		295	-3.8	0.0	7		20	0,8230		0,0,4115	no	missense	POM121L12	NM_182595.3	180	0,3,6045	TT,TC,CC		0.0,0.0776,0.0248	probably-damaging	99/297	53103659	3,12093	1933	4115	6048	53071153	SO:0001583	missense	285877	exon1				CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 12"""				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.295C>T	7.37:g.53103659C>T	ENSP00000386133:p.Arg99Cys	Somatic		Capture	Illumina HiSeq	Phase_I	53071153	NM_182595	Q8NDI9	Missense_Mutation	SNP	ENST00000408890.4	37	CCDS43584.1	4	0.0018315018315018315	2	0.0040650406504065045	0	0.0	0	0.0	2	0.002638522427440633	C	13.05	2.121394	0.37436	7.76E-4	0.0	ENSG00000221900	ENST00000408890	T	0.30448	1.53	2.69	-3.82	0.04281	.	.	.	.	.	T	0.19927	0.0479	L	0.46157	1.445	0.09310	N	1	B	0.26935	0.164	B	0.17722	0.019	T	0.28933	-1.0028	9	0.87932	D	0	.	2.6302	0.04941	0.3596:0.249:0.0:0.3914	.	99	Q8N7R1	P1L12_HUMAN	C	99	ENSP00000386133:R99C	ENSP00000386133:R99C	R	+	1	0	POM121L12	53071153	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.096000	0.03353	-0.696000	0.05098	-1.401000	0.01141	CGC		0.721	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595	
PSPH	5723	broad.mit.edu	37	7	56087384	56087384	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:56087384G>C	ENST00000395471.3	-	5	989	c.184C>G	c.(184-186)Ctc>Gtc	p.L62V	PSPH_ENST00000459834.1_Intron|PSPH_ENST00000275605.3_Missense_Mutation_p.L62V			P78330	SERB_HUMAN	phosphoserine phosphatase	62					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|dephosphorylation (GO:0016311)|L-serine biosynthetic process (GO:0006564)|L-serine metabolic process (GO:0006563)|response to mechanical stimulus (GO:0009612)|response to nutrient levels (GO:0031667)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)	calcium ion binding (GO:0005509)|magnesium ion binding (GO:0000287)|phosphoserine phosphatase activity (GO:0004647)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|ovary(1)|skin(1)	11	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			CGCTCTGTGAGAGCAGCTTTG	0.602																																					p.L62V												.	.	0			c.C184G	7						.						56.0	41.0	46.0					7																	56087384		2203	4300	6503	56054878	SO:0001583	missense	5723	exon5			Y10275	CCDS5522.1	7p11.2	2012-10-02			ENSG00000146733	ENSG00000146733	3.1.3.3		9577	protein-coding gene	gene with protein product		172480		PSP		6297854, 9188776	Standard	NM_004577		Approved		uc003trh.3	P78330	OTTHUMG00000023441	ENST00000395471.3:c.184C>G	7.37:g.56087384G>C	ENSP00000378854:p.Leu62Val	None		Capture	Illumina HiSeq	Phase_I	56054878	NM_004577	B2RCR5|Q7Z3S5	Missense_Mutation	SNP	ENST00000395471.3	37	CCDS5522.1	.	.	.	.	.	.	.	.	.	.	G	10.27	1.302976	0.23736	.	.	ENSG00000146733	ENST00000275605;ENST00000395471;ENST00000421626	D;D;D	0.89196	-1.98;-1.98;-2.48	4.5	2.5	0.30297	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);Phosphoserine phosphatase, domain 2 (1);	0.068931	0.56097	D	0.000026	D	0.95066	0.8402	H	0.94771	3.58	0.80722	D	1	B;B	0.31837	0.18;0.342	P;P	0.51742	0.551;0.678	D	0.94628	0.7819	10	0.87932	D	0	-17.7028	12.2133	0.54391	0.2286:0.0:0.7714:0.0	.	62;62	Q53EY1;P78330	.;SERB_HUMAN	V	62	ENSP00000275605:L62V;ENSP00000378854:L62V;ENSP00000398653:L62V	ENSP00000275605:L62V	L	-	1	0	PSPH	56054878	1.000000	0.71417	0.726000	0.30738	0.062000	0.15995	1.831000	0.39141	0.536000	0.28733	-1.094000	0.02160	CTC		0.602	PSPH-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343304.1	NM_004577	
BAZ1B	9031	broad.mit.edu	37	7	72891744	72891744	+	Silent	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:72891744A>G	ENST00000339594.4	-	7	2385	c.2047T>C	c.(2047-2049)Ttg>Ctg	p.L683L	BAZ1B_ENST00000404251.1_Silent_p.L683L	NM_032408.3	NP_115784.1	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	683					cellular response to DNA damage stimulus (GO:0006974)|chromatin assembly or disassembly (GO:0006333)|chromatin-mediated maintenance of transcription (GO:0048096)|double-strand break repair (GO:0006302)|heart morphogenesis (GO:0003007)|histone phosphorylation (GO:0016572)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone kinase activity (GO:0035173)|lysine-acetylated histone binding (GO:0070577)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|vitamin D receptor activator activity (GO:0071884)|zinc ion binding (GO:0008270)	p.L683L(1)		NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(5)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Lung NSC(55;0.0659)|all_lung(88;0.152)				TGCAGAGTCAAGGGGATTTCC	0.478																																					p.L683L	Esophageal Squamous(112;1167 1561 21085 43672 48228)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T2047C	7						.						126.0	117.0	120.0					7																	72891744		2203	4300	6503	72529680	SO:0001819	synonymous_variant	9031	exon7			AF084479	CCDS5549.1	7q11.23	2013-01-28			ENSG00000009954	ENSG00000009954		"""Zinc fingers, PHD-type"""	961	protein-coding gene	gene with protein product	"""Williams-Beuren syndrome chromosome region 9"", ""Williams-Beuren syndrome chromosome region 10"", ""transcription factor WSTF"""	605681		WBSCR9, WBSCR10		9858827, 9828126	Standard	NM_032408		Approved	WSTF	uc003tyc.3	Q9UIG0	OTTHUMG00000023847	ENST00000339594.4:c.2047T>C	7.37:g.72891744A>G		Somatic		Capture	Illumina HiSeq	Phase_I	72529680	NM_032408	B9EGK3|D3DXE9|O95039|O95247|O95277|Q6P1K4|Q86UJ6	Silent	SNP	ENST00000339594.4	37	CCDS5549.1																																																																																				0.478	BAZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252123.4	NM_032408	
PCLO	27445	broad.mit.edu	37	7	82387900	82387900	+	Silent	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:82387900T>C	ENST00000333891.9	-	25	15757	c.15420A>G	c.(15418-15420)caA>caG	p.Q5140Q		NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.Q5140Q(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						TTCAATGCGTTTGAGTAGGAC	0.378																																					p.Q5140Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A15420G	7						.						270.0	260.0	263.0					7																	82387900		1862	4088	5950	82225836	SO:0001819	synonymous_variant	27445	exon25			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.15420A>G	7.37:g.82387900T>C		Somatic		Capture	Illumina HiSeq	Phase_I	82225836	NM_033026		Silent	SNP	ENST00000333891.9	37	CCDS47630.1																																																																																				0.378	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
PCLO	27445	broad.mit.edu	37	7	82545733	82545733	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:82545733T>C	ENST00000333891.9	-	7	11906	c.11569A>G	c.(11569-11571)Aga>Gga	p.R3857G	PCLO_ENST00000423517.2_Missense_Mutation_p.R3857G|PCLO_ENST00000437081.1_Missense_Mutation_p.R577G	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.R3857G(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						GGAGCAGTTCTTGGTCGCTCA	0.468																																					p.R3857G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A11569G	7						.						380.0	375.0	377.0					7																	82545733		2030	4193	6223	82383669	SO:0001583	missense	27445	exon7			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.11569A>G	7.37:g.82545733T>C	ENSP00000334319:p.Arg3857Gly	Somatic		Capture	Illumina HiSeq	Phase_I	82383669	NM_033026		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	T	6.154	0.396545	0.11638	.	.	ENSG00000186472	ENST00000333891;ENST00000423517;ENST00000437081	T;T	0.17370	2.28;2.28	5.8	4.64	0.57946	.	.	.	.	.	T	0.36441	0.0967	M	0.63843	1.955	0.41456	D	0.988011	D;D;D	0.76494	0.986;0.999;0.999	P;D;D	0.65443	0.722;0.913;0.935	T	0.13469	-1.0508	9	0.87932	D	0	.	12.5653	0.56306	0.0:0.0:0.4345:0.5655	.	3788;3857;3857	Q9Y6V0;Q9Y6V0-5;Q9Y6V0-6	PCLO_HUMAN;.;.	G	3857;3857;577	ENSP00000334319:R3857G;ENSP00000388393:R3857G	ENSP00000334319:R3857G	R	-	1	2	PCLO	82383669	0.864000	0.29904	0.976000	0.42696	0.998000	0.95712	1.214000	0.32419	1.018000	0.39521	0.460000	0.39030	AGA		0.468	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
PEX1	5189	broad.mit.edu	37	7	92146641	92146641	+	Silent	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:92146641A>G	ENST00000248633.4	-	5	1283	c.1188T>C	c.(1186-1188)aaT>aaC	p.N396N	PEX1_ENST00000541751.1_5'UTR|PEX1_ENST00000438045.1_Intron|PEX1_ENST00000428214.1_Silent_p.N396N	NM_000466.2	NP_000457.1	O43933	PEX1_HUMAN	peroxisomal biogenesis factor 1	396					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.N396N(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)			ATTTGATGGCATTGTTCAATT	0.343																																					p.N396N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1188C	7						.						139.0	140.0	139.0					7																	92146641		2203	4300	6503	91984577	SO:0001819	synonymous_variant	5189	exon5			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.1188T>C	7.37:g.92146641A>G		Somatic		Capture	Illumina HiSeq	Phase_I	91984577	NM_000466	A4D1G3|A8KA90|B4DIM7|E9PE75|Q96S71|Q96S72|Q96S73|Q99994	Silent	SNP	ENST00000248633.4	37	CCDS5627.1																																																																																				0.343	PEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254066.3	NM_000466	
TAC1	6863	broad.mit.edu	37	7	97363077	97363077	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:97363077G>A	ENST00000319273.5	+	3	463	c.166G>A	c.(166-168)Gcc>Acc	p.A56T	TAC1_ENST00000346867.4_Missense_Mutation_p.A56T|TAC1_ENST00000350485.4_Missense_Mutation_p.A56T	NM_003182.2	NP_003173.1	P20366	TKN1_HUMAN	tachykinin, precursor 1	56					associative learning (GO:0008306)|cell-cell signaling (GO:0007267)|detection of abiotic stimulus (GO:0009582)|inflammatory response (GO:0006954)|insemination (GO:0007320)|long-term memory (GO:0007616)|negative regulation of heart rate (GO:0010459)|neuropeptide signaling pathway (GO:0007218)|positive regulation of action potential (GO:0045760)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of corticosterone secretion (GO:2000854)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of ossification (GO:0045778)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of saliva secretion (GO:0046878)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|regulation of blood pressure (GO:0008217)|response to hormone (GO:0009725)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|response to pain (GO:0048265)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)|tachykinin receptor signaling pathway (GO:0007217)	axon (GO:0030424)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)		p.A56T(1)		large_intestine(4)|lung(6)|urinary_tract(1)	11	all_cancers(62;3.95e-09)|all_epithelial(64;1.1e-09)|Esophageal squamous(72;0.00448)|Lung NSC(181;0.0358)|all_lung(186;0.0384)					GCAGAGAATCGCCCGGAGACC	0.592																																					p.A56T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G166A	7						.						97.0	88.0	91.0					7																	97363077		2203	4300	6503	97201013	SO:0001583	missense	6863	exon3			M68907	CCDS5649.1, CCDS5650.1, CCDS5651.1	7q21-q22	2013-02-26	2008-01-17		ENSG00000006128	ENSG00000006128		"""Endogenous ligands"""	11517	protein-coding gene	gene with protein product	"""substance K"", ""substance P"", ""neurokinin 1"", ""neurokinin 2"", ""neuromedin L"", ""neurokinin alpha"", ""neuropeptide K"", ""neuropeptide gamma"", ""preprotachykinin"""	162320	"""tachykinin, precursor 1 (substance K, substance P, neurokinin 1, neurokinin 2, neuromedin L, neurokinin alpha, neuropeptide K, neuropeptide gamma)"""	TAC2, NKNA		1708336	Standard	NM_003182		Approved	NPK	uc003uop.4	P20366	OTTHUMG00000154069	ENST00000319273.5:c.166G>A	7.37:g.97363077G>A	ENSP00000321106:p.Ala56Thr	Somatic		Capture	Illumina HiSeq	Phase_I	97201013	NM_013997	O60600|O60601|Q00072|Q53GH4|Q549V0|Q549V1|Q549V2|Q6FHM1	Missense_Mutation	SNP	ENST00000319273.5	37	CCDS5649.1	.	.	.	.	.	.	.	.	.	.	G	17.65	3.443030	0.63067	.	.	ENSG00000006128	ENST00000319273;ENST00000350485;ENST00000346867	.	.	.	5.47	4.59	0.56863	.	0.047118	0.85682	D	0.000000	T	0.55721	0.1938	N	0.24115	0.695	0.42695	D	0.993598	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.83275	0.988;0.996;0.992;0.994	T	0.51647	-0.8679	9	0.21014	T	0.42	-6.622	12.3545	0.55167	0.0824:0.0:0.9176:0.0	.	56;56;56;56	P20366-4;P20366-3;P20366-2;P20366	.;.;.;TKN1_HUMAN	T	56	.	ENSP00000321106:A56T	A	+	1	0	TAC1	97201013	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.255000	0.72466	1.456000	0.47831	0.561000	0.74099	GCC		0.592	TAC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333696.1	NM_003182	
SMURF1	57154	broad.mit.edu	37	7	98649880	98649880	+	Silent	SNP	C	C	T	rs138039130	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:98649880C>T	ENST00000361125.1	-	7	988	c.669G>A	c.(667-669)acG>acA	p.T223T	SMURF1_ENST00000480055.1_5'UTR|SMURF1_ENST00000361368.2_Silent_p.T223T	NM_020429.2	NP_065162.1	Q9HCE7	SMUF1_HUMAN	SMAD specific E3 ubiquitin protein ligase 1	223					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.T223T(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)			GGTTCTGGGGCGTCTGTAGTG	0.577													C|||	4	0.000798722	0.003	0.0	5008	,	,		17854	0.0		0.0	False		,,,				2504	0.0				p.T223T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G669A	7						.	C	,,	4,4402	9.9+/-24.2	0,4,2199	158.0	141.0	147.0		669,669,669	-4.4	0.9	7	dbSNP_134	147	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	SMURF1	NM_001199847.1,NM_020429.2,NM_181349.2	,,	0,4,6499	TT,TC,CC		0.0,0.0908,0.0308	,,	223/729,223/758,223/732	98649880	4,13002	2203	4300	6503	98487816	SO:0001819	synonymous_variant	57154	exon7			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.669G>A	7.37:g.98649880C>T		Somatic		Capture	Illumina HiSeq	Phase_I	98487816	NM_020429	A4D279|B7ZMB6|B9EGV3|O75853|Q547Q3|Q9UJT8	Silent	SNP	ENST00000361125.1	37	CCDS34690.1																																																																																				0.577	SMURF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000335001.2	NM_020429	
RINT1	60561	broad.mit.edu	37	7	105182902	105182902	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:105182902delA	ENST00000257700.2	+	4	552	c.321delA	c.(319-321)ttafs	p.L107fs	RINT1_ENST00000477285.1_3'UTR	NM_021930.4	NP_068749.3	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1	107					G2 DNA damage checkpoint (GO:0031572)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)		p.N109fs*28(1)		central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						GAAGTGCCTTAAAAAATGCAG	0.353																																					p.L107fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.321delA	7						.						70.0	75.0	73.0					7																	105182902		2203	4300	6503	104970138	SO:0001589	frameshift_variant	60561	exon4			AF317622	CCDS34726.1	7q22.2	2007-05-03			ENSG00000135249	ENSG00000135249			21876	protein-coding gene	gene with protein product		610089				11096100, 15029241	Standard	NM_021930		Approved	FLJ11785, RINT-1	uc003vda.1	Q6NUQ1	OTTHUMG00000157400	ENST00000257700.2:c.321delA	7.37:g.105182902delA	ENSP00000257700:p.Leu107fs	Somatic		Capture	Illumina HiSeq	Phase_I	104970138	NM_021930	Q75MG9|Q75MH0|Q96IW8|Q9H229|Q9HAD9	Frame_Shift_Del	DEL	ENST00000257700.2	37	CCDS34726.1																																																																																				0.353	RINT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348686.1	NM_021930	
PTPRN2	5799	broad.mit.edu	37	7	157449179	157449179	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr7:157449179C>T	ENST00000389418.4	-	14	2075	c.2066G>A	c.(2065-2067)cGc>cAc	p.R689H	PTPRN2_ENST00000389413.3_Missense_Mutation_p.R660H|PTPRN2_ENST00000404321.2_Missense_Mutation_p.R712H|PTPRN2_ENST00000409483.1_Missense_Mutation_p.R651H|PTPRN2_ENST00000389416.4_Missense_Mutation_p.R672H	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	689					negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.R689H(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		GCTGCTGATGCGTGACGTGTG	0.682																																					p.R660H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1979A	7						.						67.0	52.0	57.0					7																	157449179		2184	4281	6465	157141940	SO:0001583	missense	5799	exon13			AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.2066G>A	7.37:g.157449179C>T	ENSP00000374069:p.Arg689His	Somatic		Capture	Illumina HiSeq	Phase_I	157141940	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Missense_Mutation	SNP	ENST00000389418.4	37	CCDS5947.1	.	.	.	.	.	.	.	.	.	.	c	20.6	4.009854	0.75046	.	.	ENSG00000155093	ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	T;T;T;T;T	0.03663	3.86;3.91;3.85;3.86;3.85	4.53	4.53	0.55603	.	0.000000	0.64402	D	0.000013	T	0.20088	0.0483	M	0.79693	2.465	0.58432	D	0.999995	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.83275	0.996;0.99;0.992;0.959;0.981	T	0.01608	-1.1313	10	0.62326	D	0.03	.	17.2928	0.87162	0.0:1.0:0.0:0.0	.	712;651;660;672;689	Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932	.;.;.;.;PTPR2_HUMAN	H	651;660;672;689;712	ENSP00000387114:R651H;ENSP00000374064:R660H;ENSP00000374067:R672H;ENSP00000374069:R689H;ENSP00000385464:R712H	ENSP00000374064:R660H	R	-	2	0	PTPRN2	157141940	1.000000	0.71417	0.595000	0.28798	0.237000	0.25408	5.378000	0.66190	2.047000	0.60756	0.450000	0.29827	CGC		0.682	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1		
RP1L1	94137	broad.mit.edu	37	8	10468744	10468744	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:10468744G>T	ENST00000382483.3	-	4	3087	c.2864C>A	c.(2863-2865)gCt>gAt	p.A955D		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	955					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.A955D(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)		GCGGACCACAGCCTCTGGAGA	0.627																																					p.A955D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2864A	8						.						45.0	52.0	50.0					8																	10468744		2011	4169	6180	10506154	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.2864C>A	8.37:g.10468744G>T	ENSP00000371923:p.Ala955Asp	Somatic		Capture	Illumina HiSeq	Phase_I	10506154	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	G	14.66	2.602290	0.46423	.	.	ENSG00000183638	ENST00000382483	T	0.79141	-1.24	4.73	3.77	0.43336	.	0.233660	0.22120	N	0.064348	T	0.76241	0.3960	L	0.29908	0.895	0.09310	N	1	D	0.69078	0.997	P	0.58520	0.84	T	0.66803	-0.5831	10	0.72032	D	0.01	-8.6665	9.5772	0.39465	0.0:0.0:0.7167:0.2833	.	955	A6NKC6	.	D	955	ENSP00000371923:A955D	ENSP00000371923:A955D	A	-	2	0	RP1L1	10506154	0.179000	0.23135	0.006000	0.13384	0.002000	0.02628	2.175000	0.42491	2.441000	0.82636	0.462000	0.41574	GCT		0.627	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
RIMS2	9699	broad.mit.edu	37	8	105001534	105001534	+	Splice_Site	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:105001534C>T	ENST00000436393.2	+	15	2504	c.2263C>T	c.(2263-2265)Cgg>Tgg	p.R755W	RIMS2_ENST00000406091.3_Splice_Site_p.R977W|RIMS2_ENST00000262231.10_Splice_Site_p.R816W|RIMS2_ENST00000507740.1_Splice_Site_p.R769W			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	1039					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)	p.R769W(1)|p.R1044W(1)|p.R755W(1)		NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			TTGTTTTAGTCGGAATGTGGA	0.383										HNSCC(12;0.0054)																											p.R977W												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.C2929T	8						.						127.0	123.0	125.0					8																	105001534		1852	4097	5949	105070710	SO:0001630	splice_region_variant	9699	exon17			AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"""RAB3 interacting protein 3"""	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000436393.2:c.2262-1C>T	8.37:g.105001534C>T		Somatic		Capture	Illumina HiSeq	Phase_I	105070710	NM_001100117	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Missense_Mutation	SNP	ENST00000436393.2	37		.	.	.	.	.	.	.	.	.	.	C	15.84	2.950974	0.53186	.	.	ENSG00000176406	ENST00000504942;ENST00000329869;ENST00000406091;ENST00000402998;ENST00000262231;ENST00000507740;ENST00000408894;ENST00000436393	T;T;T;T;T;T	0.19806	2.12;2.64;2.26;2.3;2.22;2.57	5.54	-2.71	0.05986	.	.	.	.	.	T	0.31796	0.0808	L	0.40543	1.245	0.80722	D	1	D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0	D;D;D;D;D	0.75020	0.929;0.937;0.958;0.922;0.985	T	0.24404	-1.0161	9	0.62326	D	0.03	.	12.3313	0.55041	0.6863:0.2485:0.0:0.0652	.	1039;755;816;769;977	Q9UQ26;D6RA03;Q9UQ26-1;Q9UQ26-3;F8WD47	RIMS2_HUMAN;.;.;.;.	W	977;992;977;1039;816;769;769;755	ENSP00000427018:R977W;ENSP00000384892:R977W;ENSP00000262231:R816W;ENSP00000423559:R769W;ENSP00000386228:R769W;ENSP00000390665:R755W	ENSP00000262231:R816W	R	+	1	2	RIMS2	105070710	0.997000	0.39634	0.996000	0.52242	0.558000	0.35554	0.200000	0.17257	-0.098000	0.12285	-0.516000	0.04426	CGG		0.383	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	NM_001100117	Missense_Mutation
PKHD1L1	93035	broad.mit.edu	37	8	110441641	110441641	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:110441641A>G	ENST00000378402.5	+	26	3177	c.3073A>G	c.(3073-3075)Aga>Gga	p.R1025G		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	1025					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.R1027G(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)			TGGCTTATTCAGACAACATGT	0.323										HNSCC(38;0.096)																											p.R1025G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3073G	8						.						92.0	85.0	87.0					8																	110441641		1881	4092	5973	110510817	SO:0001583	missense	93035	exon26			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.3073A>G	8.37:g.110441641A>G	ENSP00000367655:p.Arg1025Gly	Somatic		Capture	Illumina HiSeq	Phase_I	110510817	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	A	11.03	1.518858	0.27211	.	.	ENSG00000205038	ENST00000378402	D	0.85556	-2.0	5.02	2.39	0.29439	.	0.349669	0.30118	N	0.010364	T	0.80486	0.4632	M	0.70595	2.14	0.24160	N	0.995667	B	0.31837	0.342	B	0.22601	0.04	T	0.72947	-0.4137	10	0.59425	D	0.04	.	8.8765	0.35348	0.6295:0.3705:0.0:0.0	.	1025	Q86WI1	PKHL1_HUMAN	G	1025	ENSP00000367655:R1025G	ENSP00000367655:R1025G	R	+	1	2	PKHD1L1	110510817	1.000000	0.71417	1.000000	0.80357	0.494000	0.33585	1.999000	0.40806	0.845000	0.35118	-0.323000	0.08544	AGA		0.323	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
BLK	640	broad.mit.edu	37	8	11412914	11412914	+	Missense_Mutation	SNP	G	G	T	rs111642844		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:11412914G>T	ENST00000259089.4	+	8	1285	c.693G>T	c.(691-693)caG>caT	p.Q231H	RP11-148O21.3_ENST00000527922.1_RNA|RP11-148O21.6_ENST00000602626.1_lincRNA|RP11-148O21.4_ENST00000528629.1_RNA|BLK_ENST00000529894.1_Missense_Mutation_p.Q160H	NM_001715.2	NP_001706.2	P51451	BLK_HUMAN	BLK proto-oncogene, Src family tyrosine kinase	231					B cell receptor signaling pathway (GO:0050853)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of insulin secretion (GO:0032024)	plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)	p.Q231H(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(4)|stomach(1)	27			STAD - Stomach adenocarcinoma(15;0.00391)	COAD - Colon adenocarcinoma(149;0.207)		CCTGGGCCCAGGATGAATGGG	0.612																																					p.Q231H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G693T	8						.						78.0	82.0	80.0					8																	11412914		2203	4300	6503	11450323	SO:0001583	missense	640	exon8			BC004473	CCDS5982.1	8p23-p22	2014-06-25	2014-06-25		ENSG00000136573	ENSG00000136573		"""SH2 domain containing"""	1057	protein-coding gene	gene with protein product		191305	"""B lymphoid tyrosine kinase"""			7845672	Standard	NM_001715		Approved	MGC10442	uc003wty.3	P51451	OTTHUMG00000090729	ENST00000259089.4:c.693G>T	8.37:g.11412914G>T	ENSP00000259089:p.Gln231His	Somatic		Capture	Illumina HiSeq	Phase_I	11450323	NM_001715	Q16291|Q96IN1	Missense_Mutation	SNP	ENST00000259089.4	37	CCDS5982.1	.	.	.	.	.	.	.	.	.	.	G	12.61	1.988928	0.35131	.	.	ENSG00000136573	ENST00000259089;ENST00000427279;ENST00000529894	T;T	0.11277	2.79;2.79	4.53	2.69	0.31865	Protein kinase-like domain (1);SH2 motif (1);	0.000000	0.38720	U	0.001584	T	0.11367	0.0277	L	0.60904	1.88	0.80722	D	1	B	0.18610	0.029	B	0.17979	0.02	T	0.05920	-1.0856	10	0.66056	D	0.02	.	7.2733	0.26268	0.2815:0.0:0.7185:0.0	.	231	P51451	BLK_HUMAN	H	231;231;160	ENSP00000259089:Q231H;ENSP00000433663:Q160H	ENSP00000259089:Q231H	Q	+	3	2	BLK	11450323	0.994000	0.37717	0.999000	0.59377	0.811000	0.45836	0.461000	0.21940	0.432000	0.26286	0.462000	0.41574	CAG		0.612	BLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207460.1		
CSMD3	114788	broad.mit.edu	37	8	113841956	113841956	+	Silent	SNP	G	G	A	rs373699127		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:113841956G>A	ENST00000297405.5	-	12	2062	c.1818C>T	c.(1816-1818)ggC>ggT	p.G606G	CSMD3_ENST00000352409.3_Silent_p.G606G|CSMD3_ENST00000343508.3_Silent_p.G566G|CSMD3_ENST00000455883.2_Silent_p.G502G	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	606	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.G606G(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						CGCCCCCATCGCCAATTGTCA	0.388										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.G606G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1818T	8						.	G	,,	1,4405	2.1+/-5.4	0,1,2202	107.0	96.0	100.0		1506,1818,1698	2.5	1.0	8		100	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	CSMD3	NM_052900.2,NM_198123.1,NM_198124.1	,,	0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231	,,	502/3539,606/3708,566/3668	113841956	3,13003	2203	4300	6503	113911132	SO:0001819	synonymous_variant	114788	exon12			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.1818C>T	8.37:g.113841956G>A		Somatic		Capture	Illumina HiSeq	Phase_I	113911132	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																				0.388	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
SLC30A8	169026	broad.mit.edu	37	8	118183329	118183329	+	Missense_Mutation	SNP	G	G	A	rs139489847		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:118183329G>A	ENST00000456015.2	+	7	886	c.886G>A	c.(886-888)Ggg>Agg	p.G296R	SLC30A8_ENST00000519688.1_Missense_Mutation_p.G247R|SLC30A8_ENST00000521243.1_Missense_Mutation_p.G247R|SLC30A8_ENST00000427715.2_Missense_Mutation_p.G247R	NM_173851.2	NP_776250.2	Q8IWU4	ZNT8_HUMAN	solute carrier family 30 (zinc transporter), member 8	296					cellular zinc ion homeostasis (GO:0006882)|insulin secretion (GO:0030073)|positive regulation of insulin secretion (GO:0032024)|regulation of sequestering of zinc ion (GO:0061088)|regulation of vesicle-mediated transport (GO:0060627)|response to glucose (GO:0009749)|response to interferon-gamma (GO:0034341)|response to interleukin-1 (GO:0070555)|sequestering of zinc ion (GO:0032119)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|secretory granule membrane (GO:0030667)	protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)	p.G296R(1)		breast(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(18)|ovary(2)|pancreas(2)|skin(5)	41	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.203)			AGCAGTCGACGGGGTGCTGTC	0.448																																					p.G296R	Ovarian(162;1202 1922 6011 16223 52092)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G886A	8						.	G	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	0,4406		0,0,2203	181.0	166.0	171.0		739,739,739,739,886	4.2	1.0	8	dbSNP_134	171	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense,missense,missense	SLC30A8	NM_001172811.1,NM_001172813.1,NM_001172814.1,NM_001172815.1,NM_173851.2	125,125,125,125,125	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	247/321,247/321,247/321,247/321,296/370	118183329	1,13005	2203	4300	6503	118252510	SO:0001583	missense	169026	exon7				CCDS6322.1, CCDS55272.1	8q24.11	2014-08-12			ENSG00000164756			"""Solute carriers"""	20303	protein-coding gene	gene with protein product		611145					Standard	NM_001172811		Approved		uc003yoh.3	Q8IWU4	OTTHUMG00000164962	ENST00000456015.2:c.886G>A	8.37:g.118183329G>A	ENSP00000415011:p.Gly296Arg	Somatic		Capture	Illumina HiSeq	Phase_I	118252510	NM_173851	A0AVP9|A5YM39|B4DPE0|Q8TCL3	Missense_Mutation	SNP	ENST00000456015.2	37	CCDS6322.1	.	.	.	.	.	.	.	.	.	.	G	16.88	3.245068	0.59103	0.0	1.16E-4	ENSG00000164756	ENST00000521243;ENST00000427715;ENST00000519688;ENST00000456015	T;T;T;T	0.69561	-0.41;-0.41;-0.41;-0.41	5.07	4.17	0.49024	.	0.105222	0.64402	D	0.000005	D	0.82843	0.5125	M	0.88241	2.94	0.58432	D	0.999999	D	0.89917	1.0	D	0.85130	0.997	D	0.85585	0.1242	10	0.87932	D	0	-15.9366	12.0719	0.53622	0.0901:0.0:0.9099:0.0	.	296	Q8IWU4	ZNT8_HUMAN	R	247;247;247;296	ENSP00000428545:G247R;ENSP00000407505:G247R;ENSP00000431069:G247R;ENSP00000415011:G296R	ENSP00000407505:G247R	G	+	1	0	SLC30A8	118252510	1.000000	0.71417	0.986000	0.45419	0.150000	0.21749	5.766000	0.68843	2.528000	0.85240	0.655000	0.94253	GGG		0.448	SLC30A8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381205.1	NM_173851	
HAS2	3037	broad.mit.edu	37	8	122641065	122641065	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:122641065C>T	ENST00000303924.4	-	2	1053	c.516G>A	c.(514-516)acG>acA	p.T172T		NM_005328.2	NP_005319.1	Q92819	HYAS2_HUMAN	hyaluronan synthase 2	172					atrioventricular canal development (GO:0036302)|bone morphogenesis (GO:0060349)|cellular response to fluid shear stress (GO:0071498)|cellular response to interleukin-1 (GO:0071347)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|cellular response to tumor necrosis factor (GO:0071356)|endocardial cushion to mesenchymal transition (GO:0090500)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|hyaluronan biosynthetic process (GO:0030213)|kidney development (GO:0001822)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of monocyte aggregation (GO:1900625)|positive regulation of urine volume (GO:0035810)|renal water absorption (GO:0070295)|vasculogenesis (GO:0001570)	integral component of plasma membrane (GO:0005887)	hyaluronan synthase activity (GO:0050501)	p.T172T(2)	HAS2/PLAG1(10)	breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(19)|ovary(5)|skin(1)	38	Lung NSC(37;3.12e-08)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)|all_neural(195;0.142)		STAD - Stomach adenocarcinoma(47;0.00503)			AGACCAATTGCGTTACGTGTT	0.458																																					p.T172T												.	.	2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	c.G516A	8						.						357.0	310.0	326.0					8																	122641065		2203	4300	6503	122710246	SO:0001819	synonymous_variant	3037	exon2			U54804	CCDS6335.1	8q24.12	2013-02-22			ENSG00000170961	ENSG00000170961	2.4.1.212	"""Glycosyltransferase family 2 domain containing"""	4819	protein-coding gene	gene with protein product		601636				9169154	Standard	NM_005328		Approved		uc003yph.2	Q92819	OTTHUMG00000164953	ENST00000303924.4:c.516G>A	8.37:g.122641065C>T		Somatic		Capture	Illumina HiSeq	Phase_I	122710246	NM_005328	Q32MM3	Silent	SNP	ENST00000303924.4	37	CCDS6335.1																																																																																				0.458	HAS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381150.2	NM_005328	
DLC1	10395	broad.mit.edu	37	8	12943372	12943372	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:12943372C>T	ENST00000276297.4	-	18	4944	c.4535G>A	c.(4534-4536)cGg>cAg	p.R1512Q	DLC1_ENST00000358919.2_Missense_Mutation_p.R1075Q|DLC1_ENST00000512044.2_Missense_Mutation_p.R1109Q|DLC1_ENST00000510318.1_5'UTR|DLC1_ENST00000520226.1_Missense_Mutation_p.R1001Q	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	1512	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)	p.R1512Q(1)		NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						GAAGGAATCCCGGATCTTTAC	0.433																																					p.R1512Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4535A	8						.						194.0	172.0	179.0					8																	12943372		2203	4300	6503	12987743	SO:0001583	missense	10395	exon18			AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	2897	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 12"""	604258	"""deleted in liver cancer 1"""			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.4535G>A	8.37:g.12943372C>T	ENSP00000276297:p.Arg1512Gln	Somatic		Capture	Illumina HiSeq	Phase_I	12987743	NM_182643	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Missense_Mutation	SNP	ENST00000276297.4	37	CCDS5989.1	.	.	.	.	.	.	.	.	.	.	C	36	5.673562	0.96754	.	.	ENSG00000164741	ENST00000276297;ENST00000358919;ENST00000510318;ENST00000512044;ENST00000520226	T;T;T;T	0.32515	1.45;1.45;1.45;1.45	5.17	5.17	0.71159	Lipid-binding START (2);	0.000000	0.85682	D	0.000000	T	0.61515	0.2353	M	0.83223	2.63	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.992;1.0;0.998	T	0.65751	-0.6092	10	0.87932	D	0	.	19.24	0.93877	0.0:1.0:0.0:0.0	.	1512;1109;1075	Q96QB1;E9PDZ8;Q96QB1-1	RHG07_HUMAN;.;.	Q	1512;1075;451;1109;1001	ENSP00000276297:R1512Q;ENSP00000351797:R1075Q;ENSP00000422595:R1109Q;ENSP00000428028:R1001Q	ENSP00000276297:R1512Q	R	-	2	0	DLC1	12987743	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.651000	0.83577	2.865000	0.98341	0.655000	0.94253	CGG		0.433	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094	
DLC1	10395	broad.mit.edu	37	8	12957853	12957853	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:12957853G>A	ENST00000276297.4	-	9	2402	c.1993C>T	c.(1993-1995)Cgc>Tgc	p.R665C	DLC1_ENST00000358919.2_Missense_Mutation_p.R228C|DLC1_ENST00000512044.2_Missense_Mutation_p.R262C|DLC1_ENST00000520226.1_Missense_Mutation_p.R154C	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	665					actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)	p.R665C(1)		NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						AGCAGACTGCGCGTCTTGGAC	0.557																																					p.R665C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1993T	8						.						125.0	114.0	118.0					8																	12957853		2203	4300	6503	13002224	SO:0001583	missense	10395	exon9			AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	2897	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 12"""	604258	"""deleted in liver cancer 1"""			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.1993C>T	8.37:g.12957853G>A	ENSP00000276297:p.Arg665Cys	Somatic		Capture	Illumina HiSeq	Phase_I	13002224	NM_182643	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Missense_Mutation	SNP	ENST00000276297.4	37	CCDS5989.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.144978	0.77888	.	.	ENSG00000164741	ENST00000276297;ENST00000358919;ENST00000512044;ENST00000520226	T;T;T;T	0.06933	3.47;3.24;3.24;3.29	4.84	3.9	0.45041	.	0.187241	0.43747	D	0.000521	T	0.19167	0.0460	M	0.65975	2.015	0.80722	D	1	D;D;D	0.71674	0.996;0.986;0.998	P;P;P	0.56278	0.487;0.453;0.795	T	0.00100	-1.2065	10	0.87932	D	0	.	10.8829	0.46948	0.0:0.0:0.6434:0.3566	.	665;262;228	Q96QB1;E9PDZ8;Q96QB1-1	RHG07_HUMAN;.;.	C	665;228;262;154	ENSP00000276297:R665C;ENSP00000351797:R228C;ENSP00000422595:R262C;ENSP00000428028:R154C	ENSP00000276297:R665C	R	-	1	0	DLC1	13002224	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	4.575000	0.60908	2.683000	0.91414	0.655000	0.94253	CGC		0.557	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094	
FAM83A	84985	broad.mit.edu	37	8	124204115	124204115	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:124204115C>T	ENST00000518448.1	+	3	2567	c.553C>T	c.(553-555)Cgt>Tgt	p.R185C	FAM83A_ENST00000546351.1_Intron|FAM83A_ENST00000522648.1_Intron|FAM83A_ENST00000318462.6_Missense_Mutation_p.R185C|FAM83A_ENST00000276699.6_Missense_Mutation_p.R185C|FAM83A_ENST00000536633.1_Missense_Mutation_p.R185C			Q86UY5	FA83A_HUMAN	family with sequence similarity 83, member A	185								p.R185C(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(2)|skin(1)	17	Lung NSC(37;1.55e-09)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)			AGCCAACAAGCGTGGGGTGTT	0.542																																					p.R185C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C553T	8						.						259.0	226.0	237.0					8																	124204115		2203	4300	6503	124273296	SO:0001583	missense	84985	exon2			BC052300	CCDS6339.1, CCDS6340.1, CCDS75784.1	8q24.13	2014-03-13			ENSG00000147689	ENSG00000147689			28210	protein-coding gene	gene with protein product						22886303	Standard	XM_005251087		Approved	MGC14128, BJ-TSA-9	uc003ypx.3	Q86UY5	OTTHUMG00000165083	ENST00000518448.1:c.553C>T	8.37:g.124204115C>T	ENSP00000428876:p.Arg185Cys	Somatic		Capture	Illumina HiSeq	Phase_I	124273296	NM_032899	Q71HL2|Q8N7I1|Q96I47	Missense_Mutation	SNP	ENST00000518448.1	37	CCDS6340.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.644430	0.87859	.	.	ENSG00000147689	ENST00000518448;ENST00000536633;ENST00000318462;ENST00000276699	T;T;T;T	0.21361	2.01;2.01;2.01;2.01	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.56262	0.1973	M	0.89414	3.03	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.996;1.0	T	0.64071	-0.6493	10	0.87932	D	0	-21.8998	19.5428	0.95281	0.0:1.0:0.0:0.0	.	185;185	Q86UY5-3;Q86UY5	.;FA83A_HUMAN	C	185	ENSP00000428876:R185C;ENSP00000445218:R185C;ENSP00000323034:R185C;ENSP00000276699:R185C	ENSP00000276699:R185C	R	+	1	0	FAM83A	124273296	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	2.140000	0.42159	2.610000	0.88304	0.561000	0.74099	CGT		0.542	FAM83A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381737.1	NM_032899	
DLC1	10395	broad.mit.edu	37	8	13259103	13259103	+	Missense_Mutation	SNP	G	G	A	rs148727515		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:13259103G>A	ENST00000276297.4	-	3	1458	c.1049C>T	c.(1048-1050)gCg>gTg	p.A350V	DLC1_ENST00000316609.5_Missense_Mutation_p.A350V|DLC1_ENST00000511869.1_Missense_Mutation_p.A350V	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	350					actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)	p.A350V(4)		NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						GTCCAGCCGCGCCCTATCTCG	0.448																																					p.A350V												.	.	4	Substitution - Missense(4)	large_intestine(4)	c.C1049T	8						.	G	VAL/ALA,VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	142.0	125.0	131.0		1049,1049	1.5	0.1	8	dbSNP_134	131	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	DLC1	NM_024767.3,NM_182643.2	64,64	0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231	benign,benign	350/464,350/1529	13259103	3,13003	2203	4300	6503	13303474	SO:0001583	missense	10395	exon3			AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	2897	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 12"""	604258	"""deleted in liver cancer 1"""			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.1049C>T	8.37:g.13259103G>A	ENSP00000276297:p.Ala350Val	Somatic		Capture	Illumina HiSeq	Phase_I	13303474	NM_182643	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Missense_Mutation	SNP	ENST00000276297.4	37	CCDS5989.1	.	.	.	.	.	.	.	.	.	.	G	10.72	1.428410	0.25726	2.27E-4	2.33E-4	ENSG00000164741	ENST00000276297;ENST00000316609;ENST00000511869	T;T;T	0.12255	3.63;2.7;2.71	5.49	1.5	0.22942	.	0.547689	0.15331	N	0.268021	T	0.09379	0.0231	L	0.29908	0.895	0.09310	N	1	B;B;B	0.13145	0.007;0.002;0.004	B;B;B	0.08055	0.003;0.002;0.002	T	0.25606	-1.0127	10	0.48119	T	0.1	.	7.1816	0.25776	0.2095:0.1217:0.6688:0.0	.	350;350;350	E9PF76;Q96QB1-3;Q96QB1	.;.;RHG07_HUMAN	V	350	ENSP00000276297:A350V;ENSP00000321034:A350V;ENSP00000425878:A350V	ENSP00000276297:A350V	A	-	2	0	DLC1	13303474	0.031000	0.19500	0.104000	0.21259	0.836000	0.47400	1.955000	0.40372	0.391000	0.25143	-0.234000	0.12200	GCG		0.448	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094	
ADCY8	114	broad.mit.edu	37	8	131812793	131812793	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:131812793G>T	ENST00000286355.5	-	15	5031	c.2939C>A	c.(2938-2940)gCt>gAt	p.A980D	ADCY8_ENST00000377928.3_Missense_Mutation_p.A849D	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	980					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)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|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)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)	p.A980D(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			CACCCCAACAGCATCATAGGA	0.502										HNSCC(32;0.087)																											p.A980D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2939A	8						.						137.0	121.0	126.0					8																	131812793		2203	4300	6503	131881975	SO:0001583	missense	114	exon15			Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"""Adenylate cyclases"""	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.2939C>A	8.37:g.131812793G>T	ENSP00000286355:p.Ala980Asp	Somatic		Capture	Illumina HiSeq	Phase_I	131881975	NM_001115		Missense_Mutation	SNP	ENST00000286355.5	37	CCDS6363.1	.	.	.	.	.	.	.	.	.	.	G	3.702	-0.061341	0.07317	.	.	ENSG00000155897	ENST00000286355;ENST00000377928	T;T	0.80824	-1.42;-1.42	5.31	4.42	0.53409	Adenylyl cyclase class-3/4/guanylyl cyclase (4);	0.111193	0.64402	D	0.000008	T	0.62478	0.2431	N	0.02202	-0.64	0.26311	N	0.977822	B;P	0.43169	0.241;0.8	B;P	0.45232	0.122;0.474	T	0.57556	-0.7791	10	0.12766	T	0.61	.	15.0084	0.71530	0.0:0.1432:0.8568:0.0	.	849;980	E7EVL1;P40145	.;ADCY8_HUMAN	D	980;849	ENSP00000286355:A980D;ENSP00000367161:A849D	ENSP00000286355:A980D	A	-	2	0	ADCY8	131881975	0.847000	0.29606	0.778000	0.31720	0.008000	0.06430	3.302000	0.51849	1.207000	0.43291	-0.312000	0.09012	GCT		0.502	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1		
PHF20L1	51105	broad.mit.edu	37	8	133837585	133837585	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:133837585G>A	ENST00000395386.2	+	14	2012	c.1713G>A	c.(1711-1713)aaG>aaA	p.K571K	PHF20L1_ENST00000395390.2_Silent_p.K546K|CTC-137K3.1_ENST00000602328.1_RNA|PHF20L1_ENST00000220847.7_5'UTR	NM_016018.4	NP_057102.4	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1	571	Lys-rich.						zinc ion binding (GO:0008270)	p.K545K(1)		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)			agaagaagaagaaaaaaaaga	0.299																																					p.K571K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1713A	8						.						9.0	9.0	9.0					8																	133837585		1886	4101	5987	133906767	SO:0001819	synonymous_variant	51105	exon14			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.1713G>A	8.37:g.133837585G>A		Somatic		Capture	Illumina HiSeq	Phase_I	133906767	NM_016018	A8MZC9|Q86U89|Q86W43|Q96BT0|Q9H702|Q9HBK3|Q9NYR3|Q9Y381	Silent	SNP	ENST00000395386.2	37	CCDS6367.2																																																																																				0.299	PHF20L1-008	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308949.3	NM_016018	
TG	7038	broad.mit.edu	37	8	133898885	133898885	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:133898885G>A	ENST00000220616.4	+	9	1308	c.1268G>A	c.(1267-1269)cGc>cAc	p.R423H	TG_ENST00000377869.1_Missense_Mutation_p.R423H	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	423					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)		p.R423H(1)		NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		GGGCTTCTCCGCCCAATGGTG	0.532																																					p.R423H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1268A	8						.						115.0	122.0	119.0					8																	133898885		2203	4300	6503	133968067	SO:0001583	missense	7038	exon9			AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.1268G>A	8.37:g.133898885G>A	ENSP00000220616:p.Arg423His	Somatic		Capture	Illumina HiSeq	Phase_I	133968067	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	G	0.716	-0.785448	0.02907	.	.	ENSG00000042832	ENST00000377869;ENST00000220616;ENST00000535932	T;T	0.64618	-0.11;-0.11	5.81	-10.3	0.00346	.	19.832600	0.00166	N	0.000000	T	0.33614	0.0869	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.12837	-1.0532	10	0.25106	T	0.35	.	6.0271	0.19660	0.5722:0.0957:0.2048:0.1272	.	423	P01266	THYG_HUMAN	H	423	ENSP00000367100:R423H;ENSP00000220616:R423H	ENSP00000220616:R423H	R	+	2	0	TG	133968067	0.000000	0.05858	0.000000	0.03702	0.078000	0.17371	-0.034000	0.12225	-1.923000	0.01065	-1.686000	0.00732	CGC		0.532	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
SLA	6503	broad.mit.edu	37	8	134057315	134057315	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:134057315C>T	ENST00000338087.5	-	7	1217	c.398G>A	c.(397-399)cGc>cAc	p.R133H	SLA_ENST00000524345.1_Missense_Mutation_p.R25H|SLA_ENST00000427060.2_Missense_Mutation_p.R173H|TG_ENST00000542445.1_Intron|SLA_ENST00000517648.1_Intron|TG_ENST00000220616.4_Intron|TG_ENST00000519543.1_Intron|TG_ENST00000377869.1_Intron|SLA_ENST00000395352.3_Missense_Mutation_p.R150H	NM_001045556.2	NP_001039021.1	Q13239	SLAP1_HUMAN	Src-like-adaptor	133	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				positive regulation of signal transduction (GO:0009967)	endosome (GO:0005768)	SH3/SH2 adaptor activity (GO:0005070)	p.R133H(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(1)|lung(6)|prostate(1)|skin(1)	17	all_epithelial(106;3.51e-21)|Lung NSC(106;4.24e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0279)|Breast(495;0.037)	BRCA - Breast invasive adenocarcinoma(115;0.000701)			ACGGAAAATGCGGTAATGCTT	0.537																																					p.R133H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G398A	8						.						176.0	142.0	154.0					8																	134057315		2203	4300	6503	134126497	SO:0001583	missense	6503	exon7				CCDS6370.1, CCDS47922.1, CCDS47923.1, CCDS64977.1, CCDS64978.1	8q24.22	2013-09-19	2001-11-28		ENSG00000155926	ENSG00000155926		"""SH2 domain containing"""	10902	protein-coding gene	gene with protein product		601099	"""Src-like-adapter"""			8825655, 11179692	Standard	NM_001045556		Approved	SLA1	uc011ljd.2	Q13239	OTTHUMG00000164439	ENST00000338087.5:c.398G>A	8.37:g.134057315C>T	ENSP00000337548:p.Arg133His	Somatic		Capture	Illumina HiSeq	Phase_I	134126497	NM_001045556	B7Z4J2|B7Z4L6|Q6FI01|Q9UMQ8	Missense_Mutation	SNP	ENST00000338087.5	37	CCDS6370.1	.	.	.	.	.	.	.	.	.	.	C	33	5.222711	0.95139	.	.	ENSG00000155926	ENST00000338087;ENST00000427060;ENST00000395352;ENST00000524345;ENST00000522119	T;T;T;T;D	0.93488	1.34;1.34;1.34;1.34;-3.23	5.77	5.77	0.91146	SH2 motif (5);	0.046432	0.85682	D	0.000000	D	0.96491	0.8855	M	0.76574	2.34	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77004	0.989;0.989;0.989	D	0.96652	0.9482	10	0.87932	D	0	-29.5587	17.4758	0.87658	0.0:1.0:0.0:0.0	.	133;133;133	Q6FI01;Q5TZW1;Q13239	.;.;SLAP1_HUMAN	H	133;173;150;25;133	ENSP00000337548:R133H;ENSP00000394049:R173H;ENSP00000378759:R150H;ENSP00000427928:R25H;ENSP00000430596:R133H	ENSP00000337548:R133H	R	-	2	0	SLA	134126497	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.137000	0.77295	2.737000	0.93849	0.561000	0.74099	CGC		0.537	SLA-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378771.1		
KCNK9	51305	broad.mit.edu	37	8	140715170	140715170	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:140715170G>A	ENST00000520439.1	-	1	129	c.66C>T	c.(64-66)ggC>ggT	p.G22G	KCNK9_ENST00000303015.1_Silent_p.G22G	NM_001282534.1	NP_001269463.1	Q9NPC2	KCNK9_HUMAN	potassium channel, subfamily K, member 9	22					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.G22G(2)		NS(1)|endometrium(9)|kidney(1)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)	43	all_cancers(97;3.94e-14)|all_epithelial(106;4.81e-13)|Lung NSC(106;8.18e-05)|all_lung(105;0.00015)|Ovarian(258;0.00235)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;0.134)	BRCA - Breast invasive adenocarcinoma(115;0.0855)		Doxapram(DB00561)|Halothane(DB01159)	ACACGGCGGCGCCCACCAGCA	0.632																																					p.G22G												KCNK9,lung,NS,Substitution - coding silent,0 	.	2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	c.C66T	8						.						54.0	47.0	49.0					8																	140715170		2203	4300	6503	140784352	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.66C>T	8.37:g.140715170G>A		Somatic		Capture	Illumina HiSeq	Phase_I	140784352	NM_016601	Q2M290|Q540F2	Silent	SNP	ENST00000520439.1	37	CCDS6377.1																																																																																				0.632	KCNK9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378473.1	NM_016601	
DENND3	22898	broad.mit.edu	37	8	142204229	142204229	+	Missense_Mutation	SNP	C	C	A	rs61743929	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:142204229C>A	ENST00000262585.2	+	23	3772	c.3494C>A	c.(3493-3495)gCg>gAg	p.A1165E	DENND3_ENST00000519811.1_Missense_Mutation_p.A1245E|DENND3_ENST00000523308.1_Missense_Mutation_p.A215E|DENND3_ENST00000424248.1_Missense_Mutation_p.A1113E	NM_014957.2	NP_055772.2	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	1165					cellular protein catabolic process (GO:0044257)|endosome to lysosome transport (GO:0008333)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.A1165E(1)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(4)|stomach(2)|urinary_tract(1)	55	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)			GAGCTGGTGGCGCACATGGAC	0.622																																					p.A1165E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3494A	8						.						100.0	92.0	95.0					8																	142204229		2203	4299	6502	142273411	SO:0001583	missense	22898	exon23			AB020677	CCDS34947.1	8q24.3	2013-01-10				ENSG00000105339		"""DENN/MADD domain containing"", ""WD repeat domain containing"""	29134	protein-coding gene	gene with protein product						10048485	Standard	NM_014957		Approved	KIAA0870	uc003yvy.3	A2RUS2		ENST00000262585.2:c.3494C>A	8.37:g.142204229C>A	ENSP00000262585:p.Ala1165Glu	Somatic		Capture	Illumina HiSeq	Phase_I	142273411	NM_014957	B7ZM28|O94947|Q2TAM7|Q6ZMS6|Q96DK3	Missense_Mutation	SNP	ENST00000262585.2	37	CCDS34947.1	.	.	.	.	.	.	.	.	.	.	C	17.86	3.491658	0.64074	.	.	ENSG00000105339	ENST00000262585;ENST00000424248;ENST00000519811;ENST00000523308	T;T;T;T	0.37235	1.53;1.53;1.53;1.21	5.14	5.14	0.70334	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.103386	0.64402	D	0.000004	T	0.59715	0.2214	M	0.74881	2.28	0.50632	D	0.999885	D;D	0.89917	1.0;0.999	D;D	0.73708	0.981;0.967	T	0.64183	-0.6467	10	0.87932	D	0	-27.2176	14.5924	0.68378	0.0:0.8097:0.1903:0.0	.	1245;1165	E9PF32;A2RUS2	.;DEND3_HUMAN	E	1165;1113;1245;215	ENSP00000262585:A1165E;ENSP00000410594:A1113E;ENSP00000428714:A1245E;ENSP00000430912:A215E	ENSP00000262585:A1165E	A	+	2	0	DENND3	142273411	0.995000	0.38212	0.965000	0.40720	0.619000	0.37552	3.038000	0.49783	2.390000	0.81377	0.591000	0.81541	GCG		0.622	DENND3-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_014957	
TNFRSF10B	8795	broad.mit.edu	37	8	22888292	22888292	+	Missense_Mutation	SNP	C	C	T	rs529765232		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:22888292C>T	ENST00000276431.4	-	3	628	c.344G>A	c.(343-345)cGc>cAc	p.R115H	TNFRSF10B_ENST00000542226.1_5'UTR|TNFRSF10B_ENST00000519910.1_5'UTR|TNFRSF10B_ENST00000347739.3_Missense_Mutation_p.R115H	NM_003842.4|NM_147187.2	NP_003833.4|NP_671716.2	O14763	TR10B_HUMAN	tumor necrosis factor receptor superfamily, member 10b	115					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell surface receptor signaling pathway (GO:0007166)|cellular response to mechanical stimulus (GO:0071260)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of apoptotic process (GO:0042981)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to endoplasmic reticulum stress (GO:0034976)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|TRAIL binding (GO:0045569)	p.R115H(1)		NS(1)|endometrium(2)|large_intestine(7)|liver(1)|lung(3)|skin(1)	15		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0179)|COAD - Colon adenocarcinoma(73;0.0703)		CCTGGTGCAGCGCAAGCAGAA	0.478																																					p.R115H	GBM(94;1064 1342 1839 21060 42553)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G344A	8						.						129.0	107.0	114.0					8																	22888292		2203	4300	6503	22944237	SO:0001583	missense	8795	exon3			AF012628	CCDS6035.1, CCDS6036.1	8p22-p21	2006-02-22			ENSG00000120889	ENSG00000120889		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11905	protein-coding gene	gene with protein product		603612				9285725, 9311998	Standard	NM_003842		Approved	DR5, KILLER, TRICK2A, TRAIL-R2, TRICKB, CD262	uc003xcu.2	O14763	OTTHUMG00000097826	ENST00000276431.4:c.344G>A	8.37:g.22888292C>T	ENSP00000276431:p.Arg115His	Somatic		Capture	Illumina HiSeq	Phase_I	22944237	NM_003842	O14720|O15508|O15517|O15531|Q6UXM8|Q7Z360|Q9BVE0	Missense_Mutation	SNP	ENST00000276431.4	37	CCDS6035.1	.	.	.	.	.	.	.	.	.	.	c	12.17	1.856341	0.32791	.	.	ENSG00000120889	ENST00000276431;ENST00000347739	D;D	0.91686	-2.89;-2.89	2.75	-3.05	0.05396	TNFR/CD27/30/40/95 cysteine-rich region (4);	2.347290	0.01728	U	0.028664	D	0.93390	0.7892	M	0.62723	1.935	0.09310	N	0.999997	D;D	0.89917	1.0;0.999	P;P	0.62014	0.897;0.757	T	0.83068	-0.0144	10	0.37606	T	0.19	.	4.6489	0.12585	0.3609:0.3868:0.2523:0.0	.	115;115	O14763;O14763-2	TR10B_HUMAN;.	H	115	ENSP00000276431:R115H;ENSP00000317859:R115H	ENSP00000276431:R115H	R	-	2	0	TNFRSF10B	22944237	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.649000	0.05384	-0.840000	0.04206	-0.868000	0.02995	CGC		0.478	TNFRSF10B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215099.2	NM_147187	
ENTPD4	9583	broad.mit.edu	37	8	23297280	23297280	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:23297280T>A	ENST00000358689.4	-	9	1266	c.1031A>T	c.(1030-1032)aAc>aTc	p.N344I	ENTPD4_ENST00000521321.1_5'Flank|ENTPD4_ENST00000417069.2_Missense_Mutation_p.N336I|ENTPD4_ENST00000356206.6_Missense_Mutation_p.N336I	NM_001128930.2|NM_004901.4	NP_001122402.1|NP_004892.1	Q9Y227	ENTP4_HUMAN	ectonucleoside triphosphate diphosphohydrolase 4	344					UDP catabolic process (GO:0006256)	cytoplasmic vesicle (GO:0031410)|integral component of Golgi membrane (GO:0030173)|intracellular membrane-bounded organelle (GO:0043231)	uridine-diphosphatase activity (GO:0045134)	p.N344I(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	25		Prostate(55;0.114)		Colorectal(74;0.0161)|COAD - Colon adenocarcinoma(73;0.0649)		TTGAATGGTGTTGGCAAATAT	0.453																																					p.N344I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1031T	8						.						174.0	149.0	158.0					8																	23297280		2203	4300	6503	23353225	SO:0001583	missense	9583	exon9			AJ131358	CCDS6041.1, CCDS47827.1	8p21.3	2014-05-16	2004-09-22	2004-09-22	ENSG00000197217	ENSG00000197217			14573	protein-coding gene	gene with protein product		607577	"""lysosomal apyrase-like 1"""	LYSAL1		10393803, 9205841	Standard	NM_001128930		Approved	LALP70, LAP70, KIAA0392, NTPDase-4, UDPase	uc003xdl.3	Q9Y227	OTTHUMG00000097852	ENST00000358689.4:c.1031A>T	8.37:g.23297280T>A	ENSP00000351520:p.Asn344Ile	Somatic		Capture	Illumina HiSeq	Phase_I	23353225	NM_004901	D3DSS3|O15092	Missense_Mutation	SNP	ENST00000358689.4	37	CCDS6041.1	.	.	.	.	.	.	.	.	.	.	T	14.88	2.668211	0.47677	.	.	ENSG00000197217	ENST00000356206;ENST00000358689;ENST00000417069	T;T;T	0.12984	2.63;2.63;2.63	6.07	-5.43	0.02632	.	0.500084	0.26231	N	0.025576	T	0.15349	0.0370	L	0.49126	1.545	0.27794	N	0.942729	B;B;B	0.31705	0.336;0.042;0.052	B;B;B	0.37480	0.251;0.104;0.167	T	0.06463	-1.0825	10	0.45353	T	0.12	-7.8995	19.4545	0.94882	0.0:0.7192:0.0:0.2808	.	336;336;344	Q8NE73;Q9Y227-2;Q9Y227	.;.;ENTP4_HUMAN	I	336;344;336	ENSP00000348536:N336I;ENSP00000351520:N344I;ENSP00000408573:N336I	ENSP00000348536:N336I	N	-	2	0	ENTPD4	23353225	0.328000	0.24687	0.206000	0.23566	0.971000	0.66376	-0.316000	0.08071	-0.929000	0.03757	0.533000	0.62120	AAC		0.453	ENTPD4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215142.1	NM_004901	
STMN4	81551	broad.mit.edu	37	8	27098752	27098752	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	A	A	A	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:27098752A>G	ENST00000265770.7	-	4	273	c.137T>C	c.(136-138)gTc>gCc	p.V46A	STMN4_ENST00000350889.4_Missense_Mutation_p.V73A|STMN4_ENST00000523048.1_Missense_Mutation_p.V73A|STMN4_ENST00000519614.1_Missense_Mutation_p.V46A|STMN4_ENST00000522908.1_Missense_Mutation_p.V73A|STMN4_ENST00000519997.1_Missense_Mutation_p.V37A			Q9H169	STMN4_HUMAN	stathmin-like 4	46					regulation of microtubule polymerization or depolymerization (GO:0031110)	cell projection (GO:0042995)|Golgi apparatus (GO:0005794)				endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)	11		Ovarian(32;0.00167)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0214)|Epithelial(17;9.82e-10)|Colorectal(74;0.142)	Lomustine(DB01206)	GTCGGAAATGACGCACCAATT	0.562																																					p.V73A												.	.	0			c.T218C	8						.						170.0	139.0	150.0					8																	27098752		2203	4300	6503	27154669	SO:0001583	missense	81551	exon5				CCDS6055.1, CCDS64851.1, CCDS64852.1, CCDS64854.1	8p21.2	2006-12-09			ENSG00000015592	ENSG00000015592			16078	protein-coding gene	gene with protein product						11230166	Standard	NM_001283054		Approved	RB3	uc003xfj.3	Q9H169	OTTHUMG00000099461	ENST00000265770.7:c.137T>C	8.37:g.27098752A>G	ENSP00000265770:p.Val46Ala	None		Capture	Illumina HiSeq	Phase_I	27154669	NM_030795	B7Z2Z7|B7Z4I9|D3DSS8|D3DSS9|G5EA16|Q2TAB9	Missense_Mutation	SNP	ENST00000265770.7	37		.	.	.	.	.	.	.	.	.	.	A	15.55	2.867054	0.51588	.	.	ENSG00000015592	ENST00000350889;ENST00000519997;ENST00000265770;ENST00000523048;ENST00000519614;ENST00000522908	.	.	.	5.71	5.71	0.89125	.	0.052638	0.85682	D	0.000000	T	0.27967	0.0689	N	0.12182	0.205	0.40319	D	0.978801	B;B;B;B;B;B	0.15473	0.013;0.0;0.002;0.003;0.0;0.002	B;B;B;B;B;B	0.10450	0.005;0.0;0.004;0.002;0.0;0.004	T	0.20371	-1.0277	9	0.02654	T	1	-13.392	8.4735	0.32999	0.914:0.0:0.086:0.0	.	73;37;73;46;46;73	E7EVN3;B7Z2Z7;G5EA16;E5RIR6;Q9H169;Q9H169-2	.;.;.;.;STMN4_HUMAN;.	A	73;37;46;73;46;73	.	ENSP00000265770:V46A	V	-	2	0	STMN4	27154669	1.000000	0.71417	0.701000	0.30321	0.978000	0.69477	5.100000	0.64560	2.179000	0.69175	0.379000	0.24179	GTC		0.562	STMN4-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000375941.1	NM_030795	
EXTL3	2137	broad.mit.edu	37	8	28595088	28595088	+	Missense_Mutation	SNP	G	G	A	rs369382883		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:28595088G>A	ENST00000220562.4	+	5	3231	c.2329G>A	c.(2329-2331)Gca>Aca	p.A777T	EXTL3_ENST00000519886.1_Intron|EXTL3_ENST00000523149.1_Missense_Mutation_p.A393T	NM_001440.2	NP_001431.1	O43909	EXTL3_HUMAN	exostosin-like glycosyltransferase 3	777					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|positive regulation of cell growth (GO:0030307)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0001888)|metal ion binding (GO:0046872)	p.A777T(1)		biliary_tract(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(8)|ovary(1)|prostate(2)|skin(2)|soft_tissue(1)|urinary_tract(1)	36		Ovarian(32;0.069)		KIRC - Kidney renal clear cell carcinoma(542;0.107)|Kidney(114;0.129)|Colorectal(74;0.228)		CCGTTACCACGCATGGGACAT	0.537																																					p.A777T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2329A	8						.						198.0	161.0	174.0					8																	28595088		2203	4300	6503	28651007	SO:0001583	missense	2137	exon5			U76188	CCDS6070.1	8p22-p12	2013-03-01	2013-03-01		ENSG00000012232	ENSG00000012232	2.4.1.223	"""Exostosin glycosyltransferase family"""	3518	protein-coding gene	gene with protein product	"""REG receptor"", ""glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase"""	605744	"""exostoses (multiple)-like 3"""			9479495, 9450183, 11257457	Standard	NM_001440		Approved	botv, REGR	uc003xgz.2	O43909	OTTHUMG00000102146	ENST00000220562.4:c.2329G>A	8.37:g.28595088G>A	ENSP00000220562:p.Ala777Thr	Somatic		Capture	Illumina HiSeq	Phase_I	28651007	NM_001440	D3DST8|O00225|Q53XT3	Missense_Mutation	SNP	ENST00000220562.4	37	CCDS6070.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.22|18.22	3.575035|3.575035	0.65878|0.65878	.|.	.|.	ENSG00000012232|ENSG00000012232	ENST00000523149;ENST00000220562;ENST00000521532;ENST00000517738|ENST00000521473	T;T;T;T|.	0.76060|.	-0.99;-0.99;-0.99;-0.99|.	5.18|5.18	3.3|3.3	0.37823|0.37823	EXTL2, alpha-1,4-N-acetylhexosaminyltransferase (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.61299|0.61299	0.2336|0.2336	L|L	0.50919|0.50919	1.6|1.6	0.80722|0.80722	D|D	1|1	D|.	0.60575|.	0.988|.	P|.	0.58820|.	0.846|.	T|T	0.57353|0.57353	-0.7826|-0.7826	10|5	0.23302|.	T|.	0.38|.	-25.1625|-25.1625	13.9029|13.9029	0.63817|0.63817	0.0:0.0:0.722:0.278|0.0:0.0:0.722:0.278	.|.	777|.	O43909|.	EXTL3_HUMAN|.	T|H	393;777;75;23|110	ENSP00000428691:A393T;ENSP00000220562:A777T;ENSP00000431013:A75T;ENSP00000430652:A23T|.	ENSP00000220562:A777T|.	A|R	+|+	1|2	0|0	EXTL3|EXTL3	28651007|28651007	1.000000|1.000000	0.71417|0.71417	0.821000|0.821000	0.32701|0.32701	0.960000|0.960000	0.62799|0.62799	9.559000|9.559000	0.98135|0.98135	0.685000|0.685000	0.31468|0.31468	0.650000|0.650000	0.86243|0.86243	GCA|CGC		0.537	EXTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219987.3	NM_001440	
KAT6A	7994	broad.mit.edu	37	8	41836215	41836215	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:41836215G>A	ENST00000396930.3	-	7	1531	c.988C>T	c.(988-990)Cgc>Tgc	p.R330C	KAT6A_ENST00000406337.1_Missense_Mutation_p.R330C|KAT6A_ENST00000485568.1_Missense_Mutation_p.R330C|KAT6A_ENST00000265713.2_Missense_Mutation_p.R330C	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	330	Interaction with PML.|Interaction with RUNX1-1.				aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.R330C(1)									TTAGTATAGCGCCGTTTTATC	0.388																																					p.R330C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C988T	8						.						302.0	295.0	297.0					8																	41836215		2203	4300	6503	41955372	SO:0001583	missense	7994	exon7			U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"", ""Zinc fingers, PHD-type"""	13013	protein-coding gene	gene with protein product	"""Monocytic leukemia zinc finger protein"""	601408	"""runt-related transcription factor binding protein 2"", ""MYST histone acetyltransferase (monocytic leukemia) 3"""	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.988C>T	8.37:g.41836215G>A	ENSP00000380136:p.Arg330Cys	Somatic		Capture	Illumina HiSeq	Phase_I	41955372	NM_001099413	Q76L81	Missense_Mutation	SNP	ENST00000396930.3	37	CCDS6124.1	.	.	.	.	.	.	.	.	.	.	G	16.44	3.123452	0.56613	.	.	ENSG00000083168	ENST00000265713;ENST00000406337;ENST00000396930;ENST00000485568	T;T;T;D	0.85773	0.01;0.01;0.01;-2.03	5.47	5.47	0.80525	.	0.147419	0.48286	D	0.000190	D	0.90249	0.6951	L	0.45352	1.415	0.80722	D	1	D;D	0.89917	1.0;1.0	P;D	0.83275	0.84;0.996	D	0.90987	0.4832	10	0.87932	D	0	-6.3621	19.4191	0.94713	0.0:0.0:1.0:0.0	.	330;330	A5PLL3;Q92794	.;KAT6A_HUMAN	C	330	ENSP00000265713:R330C;ENSP00000385888:R330C;ENSP00000380136:R330C;ENSP00000430606:R330C	ENSP00000265713:R330C	R	-	1	0	KAT6A	41955372	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.496000	0.81526	2.572000	0.86782	0.644000	0.83932	CGC		0.388	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766	
PXDNL	137902	broad.mit.edu	37	8	52258473	52258473	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:52258473C>T	ENST00000356297.4	-	20	4036	c.3936G>A	c.(3934-3936)acG>acA	p.T1312T	PXDNL_ENST00000543296.1_Intron	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	1312					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.T1312T(1)		NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				GAGACTCTTGCGTCACTGCTC	0.408																																					p.T1312T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3936A	8						.						151.0	140.0	144.0					8																	52258473		1958	4154	6112	52421026	SO:0001819	synonymous_variant	137902	exon20				CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"""Immunoglobulin superfamily / I-set domain containing"""	26359	protein-coding gene	gene with protein product	"""polysomal ribonuclease 1 homolog (Xenopus)"""	615904	"""peroxidasin homolog-like (Drosophila)"""			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.3936G>A	8.37:g.52258473C>T		Somatic		Capture	Illumina HiSeq	Phase_I	52421026	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Silent	SNP	ENST00000356297.4	37	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	C	2.681	-0.275346	0.05679	.	.	ENSG00000147485	ENST00000522933	.	.	.	3.71	-7.42	0.01388	.	.	.	.	.	T	0.23886	0.0578	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.20240	-1.0281	4	.	.	.	.	6.3795	0.21525	0.2936:0.5055:0.0:0.2009	.	.	.	.	H	386	.	.	R	-	2	0	PXDNL	52421026	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.168000	0.01270	-2.465000	0.00533	-0.600000	0.04104	CGC		0.408	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	
NPBWR1	2831	broad.mit.edu	37	8	53853167	53853167	+	Missense_Mutation	SNP	C	C	T	rs567536404		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:53853167C>T	ENST00000331251.3	+	1	2177	c.700C>T	c.(700-702)Cgg>Tgg	p.R234W		NM_005285.3	NP_005276.2	P48145	NPBW1_HUMAN	neuropeptides B/W receptor 1	234					G-protein coupled receptor signaling pathway (GO:0007186)|opioid receptor signaling pathway (GO:0038003)|regulation of metabolic process (GO:0019222)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|opioid receptor activity (GO:0004985)	p.R234W(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)	17		Lung NSC(129;0.0222)|all_epithelial(80;0.0301)|all_lung(136;0.0431)				GCATGCCATGCGGCTGGACAG	0.672																																					p.R234W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C700T	8						.						30.0	17.0	21.0					8																	53853167		2192	4278	6470	54015720	SO:0001583	missense	2831	exon1			BC033145	CCDS6151.1	8p22-q21.13	2012-08-08	2006-02-15	2006-02-15		ENSG00000183729		"""GPCR / Class A : Neuropeptide receptors : W/B"""	4522	protein-coding gene	gene with protein product		600730	"""G protein-coupled receptor 7"""	GPR7		7590751, 12401809	Standard	NM_005285		Approved		uc011ldu.2	P48145		ENST00000331251.3:c.700C>T	8.37:g.53853167C>T	ENSP00000330284:p.Arg234Trp	Somatic		Capture	Illumina HiSeq	Phase_I	54015720	NM_005285	Q6NTC7	Missense_Mutation	SNP	ENST00000331251.3	37	CCDS6151.1	.	.	.	.	.	.	.	.	.	.	C	18.15	3.559979	0.65538	.	.	ENSG00000183729	ENST00000331251	T	0.40476	1.03	5.32	1.22	0.21188	GPCR, rhodopsin-like superfamily (1);	0.488214	0.17373	N	0.176592	T	0.65302	0.2678	M	0.86651	2.83	0.24137	N	0.995741	D	0.76494	0.999	D	0.63192	0.912	T	0.63355	-0.6656	10	0.72032	D	0.01	.	15.133	0.72539	0.4839:0.5161:0.0:0.0	.	234	P48145	NPBW1_HUMAN	W	234	ENSP00000330284:R234W	ENSP00000330284:R234W	R	+	1	2	NPBWR1	54015720	0.997000	0.39634	0.001000	0.08648	0.954000	0.61252	1.637000	0.37155	0.363000	0.24346	-0.834000	0.03071	CGG		0.672	NPBWR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378047.1	NM_005285	
TCEA1	6917	broad.mit.edu	37	8	54891668	54891668	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:54891668G>A	ENST00000521604.2	-	8	1145	c.742C>T	c.(742-744)Cat>Tat	p.H248Y	TCEA1_ENST00000396401.3_Missense_Mutation_p.H227Y|TCEA1_ENST00000521086.2_5'UTR|TCEA1_ENST00000522635.1_Missense_Mutation_p.H64Y	NM_006756.2	NP_006747.1	P23193	TCEA1_HUMAN	transcription elongation factor A (SII), 1	248	TFIIS central. {ECO:0000255|PROSITE- ProRule:PRU00651}.				DNA repair (GO:0006281)|erythrocyte differentiation (GO:0030218)|gene expression (GO:0010467)|nucleotide-excision repair (GO:0006289)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|regulation of DNA-templated transcription, elongation (GO:0032784)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.H64Y(1)		breast(1)|large_intestine(1)|lung(1)|skin(1)	4		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;9.1e-07)|Epithelial(17;9.44e-05)|all cancers(17;0.000699)			GCCATCTGATGCTCTCTGATG	0.433			T	PLAG1	salivary adenoma																																p.H227Y			Dom	yes		8	8q11.2	6917	"""transcription elongation factor A (SII), 1"""		E	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C679T	8						.						124.0	113.0	117.0					8																	54891668		1863	4116	5979	55054221	SO:0001583	missense	6917	exon7			X62585	CCDS47857.1, CCDS47858.1	8q11.2	2011-01-25			ENSG00000187735	ENSG00000187735		"""General transcription factors"""	11612	protein-coding gene	gene with protein product		601425		TCEA, GTF2S		8812434, 8112616	Standard	NM_006756		Approved	SII, TF2S, TFIIS	uc003xru.3	P23193	OTTHUMG00000164262	ENST00000521604.2:c.742C>T	8.37:g.54891668G>A	ENSP00000428426:p.His248Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	55054221	NM_201437	A6NF25|A8K339|Q15563|Q6FG87	Missense_Mutation	SNP	ENST00000521604.2	37	CCDS47858.1	.	.	.	.	.	.	.	.	.	.	G	13.10	2.136242	0.37728	.	.	ENSG00000187735	ENST00000396401;ENST00000521604;ENST00000522635	.	.	.	5.07	5.07	0.68467	Transcription elongation factor S-II, central domain (2);	0.098866	0.64402	D	0.000001	D	0.84866	0.5567	M	0.89904	3.07	0.80722	D	1	B;D;P	0.76494	0.204;0.999;0.852	B;D;P	0.68039	0.068;0.955;0.808	D	0.87783	0.2613	9	0.62326	D	0.03	-7.58	18.834	0.92153	0.0:0.0:1.0:0.0	.	64;227;248	B7Z4S1;P23193-2;P23193	.;.;TCEA1_HUMAN	Y	227;248;64	.	ENSP00000395483:H227Y	H	-	1	0	TCEA1	55054221	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.740000	0.98839	2.523000	0.85059	0.555000	0.69702	CAT		0.433	TCEA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377975.2	NM_006756	
CHD7	55636	broad.mit.edu	37	8	61655106	61655106	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:61655106C>A	ENST00000423902.2	+	2	1594	c.1115C>A	c.(1114-1116)tCa>tAa	p.S372*	CHD7_ENST00000525508.1_Nonsense_Mutation_p.S372*|CHD7_ENST00000524602.1_Nonsense_Mutation_p.S372*	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	372					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.S372*(1)		NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			CCCAGTGGCTCACTTAACCAA	0.488																																					p.S372X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1115A	8						.						84.0	84.0	84.0					8																	61655106		2121	4242	6363	61817660	SO:0001587	stop_gained	55636	exon2			AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"""CHARGE association"""	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.1115C>A	8.37:g.61655106C>A	ENSP00000392028:p.Ser372*	Somatic		Capture	Illumina HiSeq	Phase_I	61817660	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Nonsense_Mutation	SNP	ENST00000423902.2	37	CCDS47865.1	.	.	.	.	.	.	.	.	.	.	C	42	9.192423	0.99096	.	.	ENSG00000171316	ENST00000307121;ENST00000423902;ENST00000524602;ENST00000525508	.	.	.	5.67	5.67	0.87782	.	0.000000	0.35151	N	0.003409	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.8005	19.7706	0.96363	0.0:1.0:0.0:0.0	.	.	.	.	X	372	.	ENSP00000307304:S372X	S	+	2	0	CHD7	61817660	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.176000	0.58269	2.697000	0.92050	0.655000	0.94253	TCA		0.488	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762	
CHD7	55636	broad.mit.edu	37	8	61750779	61750779	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:61750779A>G	ENST00000423902.2	+	19	4977	c.4498A>G	c.(4498-4500)Att>Gtt	p.I1500V	CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	1500					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.I1500V(1)		NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			CACCATTACCATTGAGTCAGA	0.448																																					p.I1500V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A4498G	8						.						65.0	59.0	61.0					8																	61750779		1910	4124	6034	61913333	SO:0001583	missense	55636	exon19			AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"""CHARGE association"""	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.4498A>G	8.37:g.61750779A>G	ENSP00000392028:p.Ile1500Val	Somatic		Capture	Illumina HiSeq	Phase_I	61913333	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Missense_Mutation	SNP	ENST00000423902.2	37	CCDS47865.1	.	.	.	.	.	.	.	.	.	.	A	19.40	3.820648	0.71028	.	.	ENSG00000171316	ENST00000307121;ENST00000423902	D	0.84516	-1.86	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	D	0.83147	0.5191	L	0.42581	1.335	0.80722	D	1	B	0.17852	0.024	B	0.30646	0.118	T	0.81024	-0.1120	10	0.87932	D	0	-14.8166	15.5931	0.76554	1.0:0.0:0.0:0.0	.	1500	Q9P2D1	CHD7_HUMAN	V	1500	ENSP00000392028:I1500V	ENSP00000307304:I1500V	I	+	1	0	CHD7	61913333	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.287000	0.95975	2.150000	0.67090	0.533000	0.62120	ATT		0.448	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762	
MYBL1	4603	broad.mit.edu	37	8	67488288	67488288	+	Missense_Mutation	SNP	G	G	A	rs61753806	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:67488288G>A	ENST00000522677.3	-	10	1834	c.1424C>T	c.(1423-1425)gCg>gTg	p.A475V	MYBL1_ENST00000524176.2_Missense_Mutation_p.A475V|MYBL1_ENST00000517885.1_Missense_Mutation_p.A133V	NM_001080416.2|NM_001144755.1	NP_001073885.1|NP_001138227.1	P10243	MYBA_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 1	475	Negative regulatory domain. {ECO:0000250}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.A475V(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|skin(1)	25			Epithelial(68;0.00211)|all cancers(69;0.00726)|OV - Ovarian serous cystadenocarcinoma(28;0.00989)|BRCA - Breast invasive adenocarcinoma(89;0.0938)			ATGTTTTAGCGCCATATTACC	0.413													G|||	3	0.000599042	0.0023	0.0	5008	,	,		16297	0.0		0.0	False		,,,				2504	0.0				p.A475V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1424T	8						.	G	VAL/ALA,VAL/ALA	2,3902		0,2,1950	94.0	87.0	89.0		1424,1424	4.6	1.0	8	dbSNP_129	89	0,8290		0,0,4145	yes	missense,missense	MYBL1	NM_001080416.2,NM_001144755.1	64,64	0,2,6095	AA,AG,GG		0.0,0.0512,0.0164	benign,benign	475/753,475/693	67488288	2,12192	1952	4145	6097	67650842	SO:0001583	missense	4603	exon10			X13294	CCDS47867.1, CCDS55241.1	8q22	2013-07-09	2013-07-09		ENSG00000185697	ENSG00000185697			7547	protein-coding gene	gene with protein product		159405					Standard	XM_005251251		Approved	AMYB, A-myb	uc003xwj.3	P10243	OTTHUMG00000164559	ENST00000522677.3:c.1424C>T	8.37:g.67488288G>A	ENSP00000429633:p.Ala475Val	Somatic		Capture	Illumina HiSeq	Phase_I	67650842	NM_001080416	E7EW29|Q495F9	Missense_Mutation	SNP	ENST00000522677.3	37	CCDS47867.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	12.99	2.102573	0.37145	5.12E-4	0.0	ENSG00000185697	ENST00000522677;ENST00000517885;ENST00000524176	T;T;T	0.17854	2.76;2.25;2.27	5.46	4.59	0.56863	.	0.185273	0.49305	D	0.000160	T	0.11024	0.0269	N	0.22421	0.69	0.41109	D	0.985723	B;B;B	0.32781	0.02;0.384;0.02	B;B;B	0.22152	0.003;0.038;0.003	T	0.11131	-1.0600	10	0.44086	T	0.13	-7.9891	12.5083	0.55993	0.0771:0.0:0.9229:0.0	rs61753806	475;474;475	Q495F9;Q495G0;P10243	.;.;MYBA_HUMAN	V	475;133;475	ENSP00000429633:A475V;ENSP00000428265:A133V;ENSP00000428011:A475V	ENSP00000428265:A133V	A	-	2	0	MYBL1	67650842	1.000000	0.71417	0.997000	0.53966	0.279000	0.26890	6.646000	0.74348	1.320000	0.45209	-0.229000	0.12294	GCG		0.413	MYBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379221.3	XM_034274	
PRDM14	63978	broad.mit.edu	37	8	70964514	70964514	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:70964514C>T	ENST00000276594.2	-	8	1715	c.1514G>A	c.(1513-1515)cGc>cAc	p.R505H		NM_024504.3	NP_078780.1	Q9GZV8	PRD14_HUMAN	PR domain containing 14	505					cell fate specification (GO:0001708)|cell morphogenesis (GO:0000902)|fertilization (GO:0009566)|germ cell development (GO:0007281)|germ-line stem cell maintenance (GO:0030718)|histone H3-R26 methylation (GO:0034972)|homeostasis of number of cells within a tissue (GO:0048873)|inner cell mass cell fate commitment (GO:0001827)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|regulation of DNA methylation (GO:0044030)|regulation of gene expression, epigenetic (GO:0040029)|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.R505H(1)		NS(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Breast(64;0.193)		Epithelial(68;0.00508)|all cancers(69;0.0259)|OV - Ovarian serous cystadenocarcinoma(28;0.0405)			GATGTGTGTGCGGAGTATGCT	0.498																																					p.R505H	NSCLC(129;99 1813 5906 40656 46114)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1514A	8						.						116.0	110.0	112.0					8																	70964514		2203	4300	6503	71127068	SO:0001583	missense	63978	exon8			AF319458	CCDS6206.1	8q13.3	2013-01-08			ENSG00000147596	ENSG00000147596		"""Zinc fingers, C2H2-type"""	14001	protein-coding gene	gene with protein product		611781					Standard	NM_024504		Approved		uc003xym.3	Q9GZV8	OTTHUMG00000150495	ENST00000276594.2:c.1514G>A	8.37:g.70964514C>T	ENSP00000276594:p.Arg505His	Somatic		Capture	Illumina HiSeq	Phase_I	71127068	NM_024504	Q86UX9	Missense_Mutation	SNP	ENST00000276594.2	37	CCDS6206.1	.	.	.	.	.	.	.	.	.	.	C	31	5.088548	0.94100	.	.	ENSG00000147596	ENST00000276594	T	0.22539	1.95	6.07	5.2	0.72013	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	0.42381	0.1200	L	0.52823	1.66	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.31280	-0.9949	10	0.62326	D	0.03	-39.5438	15.3554	0.74423	0.0:0.9334:0.0:0.0666	.	505	Q9GZV8	PRD14_HUMAN	H	505	ENSP00000276594:R505H	ENSP00000276594:R505H	R	-	2	0	PRDM14	71127068	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.340000	0.79292	1.586000	0.49944	0.650000	0.86243	CGC		0.498	PRDM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318505.1		
KCNB2	9312	broad.mit.edu	37	8	73848484	73848484	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:73848484C>T	ENST00000523207.1	+	3	1482	c.894C>T	c.(892-894)cgC>cgT	p.R298R		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	298					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.R298R(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	ACGTGAGGCGCGTGGTCCAGA	0.527																																					p.R298R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C894T	8						.						87.0	84.0	85.0					8																	73848484		2203	4300	6503	74011038	SO:0001819	synonymous_variant	9312	exon3			U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.894C>T	8.37:g.73848484C>T		Somatic		Capture	Illumina HiSeq	Phase_I	74011038	NM_004770	Q7Z7D0|Q9BXD3	Silent	SNP	ENST00000523207.1	37	CCDS6209.1																																																																																				0.527	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770	
STAU2	27067	broad.mit.edu	37	8	74601019	74601019	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:74601019C>T	ENST00000521419.1	-	4	336	c.30G>A	c.(28-30)gaG>gaA	p.E10E	STAU2_ENST00000522695.1_Silent_p.E16E|STAU2_ENST00000521451.1_Intron|STAU2_ENST00000355780.5_Silent_p.E16E|STAU2_ENST00000519961.1_Silent_p.E48E|STAU2_ENST00000524300.1_Silent_p.E48E|STAU2_ENST00000522509.1_Silent_p.E16E|STAU2_ENST00000517542.1_Silent_p.E10E|STAU2_ENST00000522962.1_5'UTR|RP11-463D19.2_ENST00000358757.5_3'UTR|STAU2_ENST00000523558.1_Intron|RP11-463D19.1_ENST00000533978.1_lincRNA|STAU2_ENST00000524104.1_Silent_p.E16E|STAU2_ENST00000521727.1_Silent_p.E28E|STAU2_ENST00000521210.1_Intron			Q9NUL3	STAU2_HUMAN	staufen double-stranded RNA binding protein 2	48	DRBM 1. {ECO:0000255|PROSITE- ProRule:PRU00266}.				transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)	p.E16E(1)		breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(1)|lung(6)|ovary(1)	19	Breast(64;0.0138)		Epithelial(68;0.026)|BRCA - Breast invasive adenocarcinoma(89;0.0483)|all cancers(69;0.0972)			CCCATGTCTGCTCACCAAGAC	0.413																																					p.E16E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G48A	8						.						146.0	138.0	141.0					8																	74601019		2203	4300	6503	74763573	SO:0001819	synonymous_variant	27067	exon3			Y19062	CCDS6214.1, CCDS55244.1, CCDS55245.1, CCDS55246.1, CCDS55247.1, CCDS55248.1	8q21.11	2013-06-05	2013-06-05		ENSG00000040341	ENSG00000040341			11371	protein-coding gene	gene with protein product		605920	"""staufen (Drosophila, RNA-binding protein) homolog 2"", ""staufen, RNA binding protein, homolog 2 (Drosophila)"""			10585778	Standard	NM_014393		Approved	39K2	uc003xzm.3	Q9NUL3	OTTHUMG00000164499	ENST00000521419.1:c.30G>A	8.37:g.74601019C>T		Somatic		Capture	Illumina HiSeq	Phase_I	74763573	NM_001164384	B7Z1I6|B7Z292|B7Z8B4|E7ER74|E9PEI3|E9PF26|E9PF50|Q6AHY7|Q96HM0|Q96HM1|Q9NVI5|Q9UGG6	Silent	SNP	ENST00000521419.1	37																																																																																					0.413	STAU2-013	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000379012.2	NM_001164380	
ZFHX4	79776	broad.mit.edu	37	8	77763171	77763171	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:77763171G>T	ENST00000521891.2	+	10	4462	c.4014G>T	c.(4012-4014)aaG>aaT	p.K1338N	ZFHX4_ENST00000518282.1_Missense_Mutation_p.K1312N|ZFHX4_ENST00000050961.6_Missense_Mutation_p.K1293N|ZFHX4_ENST00000455469.2_Missense_Mutation_p.K1293N	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	1293					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.K1338N(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)			AGGATTCAAAGGCTAATGTGG	0.403										HNSCC(33;0.089)																											p.K1338N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4014T	8						.						52.0	50.0	51.0					8																	77763171		1845	4081	5926	77925726	SO:0001583	missense	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.4014G>T	8.37:g.77763171G>T	ENSP00000430497:p.Lys1338Asn	Somatic		Capture	Illumina HiSeq	Phase_I	77925726	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	G	11.66	1.705035	0.30232	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.52526	0.66;0.73;0.69;0.69	4.95	4.08	0.47627	.	0.000000	0.46442	U	0.000298	T	0.46852	0.1414	L	0.55481	1.735	0.47308	D	0.99938	P;D;P	0.56521	0.9;0.976;0.939	B;P;P	0.48677	0.382;0.544;0.586	T	0.36114	-0.9761	10	0.24483	T	0.36	.	10.2398	0.43305	0.1729:0.0:0.8271:0.0	.	1293;1293;1338	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	N	1338;1338;1293;1293;1312	ENSP00000430497:K1338N;ENSP00000399605:K1293N;ENSP00000050961:K1293N;ENSP00000430848:K1312N	ENSP00000050961:K1293N	K	+	3	2	ZFHX4	77925726	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.419000	0.34793	1.335000	0.45486	0.555000	0.69702	AAG		0.403	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721	
FABP5	2171	broad.mit.edu	37	8	82192834	82192834	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:82192834G>A	ENST00000297258.6	+	1	237	c.4G>A	c.(4-6)Gcc>Acc	p.A2T	FABP5_ENST00000396359.1_5'Flank|RP11-363E6.3_ENST00000517670.1_RNA|RP11-363E6.3_ENST00000518880.1_RNA	NM_001444.2	NP_001435.1	Q01469	FABP5_HUMAN	fatty acid binding protein 5 (psoriasis-associated)	2					epidermis development (GO:0008544)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|response to wounding (GO:0009611)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	fatty acid binding (GO:0005504)|lipid binding (GO:0008289)|transporter activity (GO:0005215)	p.A2T(1)		large_intestine(1)|lung(3)	4	Lung NSC(7;3.57e-05)|all_lung(9;0.00011)		Epithelial(68;0.102)			ACCCACCATGGCCACAGTTCA	0.662																																					p.A2T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4A	8						.						17.0	17.0	17.0					8																	82192834		2153	4230	6383	82355389	SO:0001583	missense	2171	exon1			M94856	CCDS6228.1	8q21.13	2013-03-01			ENSG00000164687	ENSG00000164687		"""Fatty acid binding protein family"""	3560	protein-coding gene	gene with protein product		605168				1512466	Standard	NM_001444		Approved	E-FABP, PA-FABP, KFABP	uc003yca.2	Q01469	OTTHUMG00000134313	ENST00000297258.6:c.4G>A	8.37:g.82192834G>A	ENSP00000297258:p.Ala2Thr	Somatic		Capture	Illumina HiSeq	Phase_I	82355389	NM_001444	B2R4K0	Missense_Mutation	SNP	ENST00000297258.6	37	CCDS6228.1	.	.	.	.	.	.	.	.	.	.	G	17.04	3.287059	0.59867	.	.	ENSG00000164687	ENST00000297258	T	0.13196	2.61	4.01	1.92	0.25849	.	0.571450	0.16283	N	0.221261	T	0.08492	0.0211	N	0.19112	0.55	0.80722	D	1	P	0.43392	0.805	B	0.39771	0.309	T	0.30238	-0.9985	10	0.39692	T	0.17	.	8.7063	0.34356	0.0:0.1636:0.6682:0.1682	.	2	Q01469	FABP5_HUMAN	T	2	ENSP00000297258:A2T	ENSP00000297258:A2T	A	+	1	0	FABP5	82355389	0.988000	0.35896	0.998000	0.56505	0.959000	0.62525	0.624000	0.24462	0.954000	0.37851	0.460000	0.39030	GCC		0.662	FABP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259329.1	NM_001444	
NBN	4683	broad.mit.edu	37	8	90960055	90960055	+	Missense_Mutation	SNP	T	T	C	rs372877871		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:90960055T>C	ENST00000265433.3	-	12	2065	c.1911A>G	c.(1909-1911)atA>atG	p.I637M	NBN_ENST00000409330.1_Missense_Mutation_p.I555M	NM_002485.4	NP_002476.2	O60934	NBN_HUMAN	nibrin	637					blastocyst growth (GO:0001832)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|DNA damage checkpoint (GO:0000077)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intrinsic apoptotic signaling pathway (GO:0097193)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mitotic cell cycle checkpoint (GO:0007093)|mitotic G2 DNA damage checkpoint (GO:0007095)|neuromuscular process controlling balance (GO:0050885)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|telomere maintenance (GO:0000723)	Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nuclear inclusion body (GO:0042405)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|replication fork (GO:0005657)|site of double-strand break (GO:0035861)	damaged DNA binding (GO:0003684)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)	p.I637M(1)		autonomic_ganglia(1)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(11;0.0344)			TTCTCACAGATATTTCTTTAG	0.303								Homologous recombination																													p.I637M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1911G	8						.	T	MET/ILE	0,4398		0,0,2199	75.0	70.0	72.0		1911	0.7	0.0	8		72	1,8589		0,1,4294	no	missense	NBN	NM_002485.4	10	0,1,6493	CC,CT,TT		0.0116,0.0,0.0077	possibly-damaging	637/755	90960055	1,12987	2199	4295	6494	91029231	SO:0001583	missense	4683	exon12			AF058696	CCDS6249.1	8q21-q24	2014-09-17	2005-06-02	2005-06-02	ENSG00000104320	ENSG00000104320			7652	protein-coding gene	gene with protein product		602667	"""Nijmegen breakage syndrome 1 (nibrin)"""	NBS, NBS1		9590181, 9590180	Standard	XM_005250923		Approved	ATV, AT-V2, AT-V1	uc003yej.1	O60934	OTTHUMG00000153546	ENST00000265433.3:c.1911A>G	8.37:g.90960055T>C	ENSP00000265433:p.Ile637Met	Somatic		Capture	Illumina HiSeq	Phase_I	91029231	NM_002485	B2R626|B2RNC5|O60672|Q32NF7|Q53FM6|Q63HR6|Q7LDM2	Missense_Mutation	SNP	ENST00000265433.3	37	CCDS6249.1	.	.	.	.	.	.	.	.	.	.	T	6.129	0.392007	0.11581	0.0	1.16E-4	ENSG00000104320	ENST00000265433;ENST00000409330	T;T	0.59364	1.98;0.27	4.6	0.673	0.17941	.	0.896444	0.09723	N	0.764099	T	0.30510	0.0767	N	0.14661	0.345	0.09310	N	1	P;P	0.37864	0.479;0.61	B;B	0.28139	0.055;0.086	T	0.14699	-1.0463	10	0.49607	T	0.09	-0.9194	2.7963	0.05402	0.3195:0.184:0.0:0.4966	.	637;637	A6H8Y5;O60934	.;NBN_HUMAN	M	637;555	ENSP00000265433:I637M;ENSP00000386924:I555M	ENSP00000265433:I637M	I	-	3	3	NBN	91029231	0.008000	0.16893	0.041000	0.18516	0.396000	0.30629	0.381000	0.20619	-0.033000	0.13736	0.482000	0.46254	ATA		0.303	NBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331583.3	NM_001024688	
TMEM67	91147	broad.mit.edu	37	8	94821103	94821103	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:94821103C>G	ENST00000453321.3	+	24	2533	c.2475C>G	c.(2473-2475)aaC>aaG	p.N825K	TMEM67_ENST00000409623.3_Missense_Mutation_p.N744K	NM_153704.5	NP_714915.3	Q5HYA8	MKS3_HUMAN	transmembrane protein 67	825					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of centrosome duplication (GO:0010826)	centrosome (GO:0005813)|ciliary membrane (GO:0060170)|cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)	filamin binding (GO:0031005)|unfolded protein binding (GO:0051082)	p.N815K(1)		breast(3)|endometrium(8)|kidney(5)|large_intestine(4)|liver(2)|lung(15)|ovary(2)|skin(1)|urinary_tract(1)	41	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.00896)			TGGTACCCAACACAGATGGTC	0.318																																					p.N825K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2475G	8						.						66.0	65.0	65.0					8																	94821103		2203	4300	6503	94890279	SO:0001583	missense	91147	exon24			BX648768	CCDS6258.2, CCDS47893.1	8q22.1	2014-09-17			ENSG00000164953	ENSG00000164953			28396	protein-coding gene	gene with protein product	"""Meckelin"""	609884	"""Meckel syndrome, type 3"""	MKS3		12384791, 16415887, 19508969	Standard	NM_153704		Approved	MGC26979, JBTS6, NPHP11	uc011lgk.2	Q5HYA8	OTTHUMG00000153119	ENST00000453321.3:c.2475C>G	8.37:g.94821103C>G	ENSP00000389998:p.Asn825Lys	Somatic		Capture	Illumina HiSeq	Phase_I	94890279	NM_153704	B3KRU5|B3KT47|G5E9H2|Q3ZCX3|Q7Z5T8|Q8IZ06	Missense_Mutation	SNP	ENST00000453321.3	37	CCDS6258.2	.	.	.	.	.	.	.	.	.	.	C	18.98	3.737356	0.69304	.	.	ENSG00000164953	ENST00000453321;ENST00000409623	D;D	0.97114	-4.25;-4.25	5.71	4.82	0.62117	.	0.000000	0.85682	D	0.000000	D	0.96920	0.8994	M	0.72894	2.215	0.80722	D	1	D;D;D	0.59357	0.968;0.975;0.985	P;P;P	0.52031	0.688;0.619;0.57	D	0.96459	0.9340	10	0.66056	D	0.02	-14.1212	10.7134	0.45997	0.0:0.8437:0.0:0.1563	.	825;744;744	Q5HYA8;B3KRU5;G5E9H2	MKS3_HUMAN;.;.	K	825;744	ENSP00000389998:N825K;ENSP00000386966:N744K	ENSP00000314488:N815K	N	+	3	2	TMEM67	94890279	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.653000	0.37323	1.379000	0.46325	0.591000	0.81541	AAC		0.318	TMEM67-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329641.2	NM_153704	
ESRP1	54845	broad.mit.edu	37	8	95704959	95704959	+	Silent	SNP	C	C	T	rs369829287	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:95704959C>T	ENST00000433389.2	+	14	2065	c.1875C>T	c.(1873-1875)agC>agT	p.S625S	ESRP1_ENST00000358397.5_Silent_p.S621S|ESRP1_ENST00000454170.2_Intron|ESRP1_ENST00000423620.2_Silent_p.S621S	NM_001034915.2|NM_017697.3	NP_001030087.2|NP_060167.2	Q6NXG1	ESRP1_HUMAN	epithelial splicing regulatory protein 1	625					mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)	p.S625S(2)|p.S621S(1)	ESRP1/RAF1(4)	NS(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)|urinary_tract(2)	20						CTAATCTTAGCGGTGTCCCTC	0.493													C|||	2	0.000399361	0.0	0.0029	5008	,	,		19022	0.0		0.0	False		,,,				2504	0.0				p.S625S												.	.	3	Substitution - coding silent(3)	large_intestine(3)	c.C1875T	8						.	C	,,,,	1,3823		0,1,1911	92.0	88.0	90.0		1863,,1863,,1875	5.2	1.0	8		90	0,8216		0,0,4108	no	coding-synonymous,intron,coding-synonymous,intron,coding-synonymous	ESRP1	NM_001034915.2,NM_001122825.1,NM_001122826.1,NM_001122827.1,NM_017697.3	,,,,	0,1,6019	TT,TC,CC		0.0,0.0262,0.0083	,,,,	621/678,,621/660,,625/682	95704959	1,12039	1912	4108	6020	95774135	SO:0001819	synonymous_variant	54845	exon14			AK000178	CCDS47895.1, CCDS47896.1, CCDS47897.1, CCDS47898.1	8q22.1	2013-02-12	2009-03-10	2009-03-10	ENSG00000104413	ENSG00000104413		"""RNA binding motif (RRM) containing"""	25966	protein-coding gene	gene with protein product		612959	"""RNA binding motif protein 35A"""	RBM35A		12477932	Standard	NM_017697		Approved	FLJ20171	uc003ygq.4	Q6NXG1	OTTHUMG00000164587	ENST00000433389.2:c.1875C>T	8.37:g.95704959C>T		Somatic		Capture	Illumina HiSeq	Phase_I	95774135	NM_017697	A6NHA8|A8MPX1|E9PB47|Q2M2B0|Q499G3|Q6PJ86|Q9NXL8	Silent	SNP	ENST00000433389.2	37	CCDS47897.1																																																																																				0.493	ESRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379326.1	NM_017697	
PTDSS1	9791	broad.mit.edu	37	8	97321838	97321838	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:97321838G>A	ENST00000517309.1	+	9	1387	c.1061G>A	c.(1060-1062)tGc>tAc	p.C354Y	Y_RNA_ENST00000362862.1_RNA|PTDSS1_ENST00000455950.2_Missense_Mutation_p.C208Y|PTDSS1_ENST00000522072.1_Missense_Mutation_p.C151Y	NM_014754.1	NP_055569.1	P48651	PTSS1_HUMAN	phosphatidylserine synthase 1	354					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylserine biosynthetic process (GO:0006659)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)	p.C354Y(1)		endometrium(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|stomach(1)	29	Breast(36;6.18e-05)				Phosphatidylserine(DB00144)	GGAACACAATGCTGGGTGTTT	0.433																																					p.C354Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1061A	8						.						95.0	89.0	91.0					8																	97321838		2203	4300	6503	97391014	SO:0001583	missense	9791	exon9			D14694	CCDS6271.1	8q22	2008-05-02			ENSG00000156471	ENSG00000156471			9587	protein-coding gene	gene with protein product		612792					Standard	NM_014754		Approved	KIAA0024, PSSA, PSS1	uc003yht.1	P48651	OTTHUMG00000164687	ENST00000517309.1:c.1061G>A	8.37:g.97321838G>A	ENSP00000430548:p.Cys354Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	97391014	NM_014754	E5RFC5|Q9BUQ5	Missense_Mutation	SNP	ENST00000517309.1	37	CCDS6271.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.848156	0.91277	.	.	ENSG00000156471	ENST00000517309;ENST00000455950;ENST00000522072	T;T;T	0.48201	0.84;0.86;0.82	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.73923	0.3649	M	0.87547	2.89	0.80722	D	1	D	0.71674	0.998	D	0.79108	0.992	T	0.77242	-0.2660	10	0.62326	D	0.03	-29.2984	18.224	0.89911	0.0:0.0:1.0:0.0	.	354	P48651	PTSS1_HUMAN	Y	354;208;151	ENSP00000430548:C354Y;ENSP00000401248:C208Y;ENSP00000430928:C151Y	ENSP00000401248:C208Y	C	+	2	0	PTDSS1	97391014	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.837000	0.99465	2.731000	0.93534	0.650000	0.86243	TGC		0.433	PTDSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379743.2		
GML	2765	broad.mit.edu	37	8	143928042	143928042	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr8:143928042G>A	ENST00000220940.1	+	4	503	c.413G>A	c.(412-414)aGg>aAg	p.R138K		NM_002066.2	NP_002057.1	Q99445	GML_HUMAN	glycosylphosphatidylinositol anchored molecule like	138					apoptotic process (GO:0006915)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|negative regulation of cell proliferation (GO:0008285)	anchored component of membrane (GO:0031225)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)		p.R138K(1)		NS(1)|central_nervous_system(2)|endometrium(1)|large_intestine(6)|lung(8)	18	all_cancers(97;4.26e-11)|all_epithelial(106;1.85e-08)|Lung NSC(106;0.000274)|all_lung(105;0.000755)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					GGAACTGTGAGGCTGGGGGTA	0.473																																					p.R138K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G413A	8						.						109.0	105.0	107.0					8																	143928042		2203	4300	6503	143925044	SO:0001583	missense	2765	exon4			D84290	CCDS6391.1	8q24.3	2014-05-14	2012-11-02						4375	protein-coding gene	gene with protein product		602370	"""GPI anchored molecule like protein"", ""glycosylphosphatidylinositol anchored molecule like protein"""			8934543, 9169150	Standard	NM_002066		Approved	LY6DL	uc003yxg.3	Q99445		ENST00000220940.1:c.413G>A	8.37:g.143928042G>A	ENSP00000220940:p.Arg138Lys	Somatic		Capture	Illumina HiSeq	Phase_I	143925044	NM_002066	A0AVF6|O00686|O00731	Missense_Mutation	SNP	ENST00000220940.1	37	CCDS6391.1	.	.	.	.	.	.	.	.	.	.	N	0.295	-0.977465	0.02197	.	.	ENSG00000104499	ENST00000220940	T	0.45276	0.9	3.52	-4.06	0.03986	.	2.237860	0.02245	N	0.066112	T	0.32466	0.0830	L	0.47716	1.5	0.09310	N	1	B	0.17268	0.021	B	0.15870	0.014	T	0.38457	-0.9660	10	0.05833	T	0.94	-39.2743	10.6131	0.45434	0.7199:0.0:0.2801:0.0	.	138	Q99445	GML_HUMAN	K	138	ENSP00000220940:R138K	ENSP00000220940:R138K	R	+	2	0	GML	143925044	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.805000	0.04530	-1.111000	0.02988	0.557000	0.71058	AGG		0.473	GML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379659.1	NM_002066	
PRRC2B	84726	broad.mit.edu	37	9	134350786	134350787	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:134350786_134350787insG	ENST00000357304.4	+	15	3325_3326	c.3270_3271insG	c.(3271-3273)gggfs	p.G1091fs	PRRC2B_ENST00000405995.1_Intron|PRRC2B_ENST00000458550.1_Intron|PRRC2B_ENST00000372249.1_5'UTR	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	1091							poly(A) RNA binding (GO:0044822)	p.V1093fs*41(2)		cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						GCCTCTGTGGTGGGGGGGTCCT	0.698																																					p.G1090fs												.	.	2	Insertion - Frameshift(2)	large_intestine(2)	c.3270_3271insG	9						.																																			133340608	SO:0001589	frameshift_variant	84726	exon15			AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"""KIAA0515"", ""HLA-B associated transcript 2-like"", ""HLA-B associated transcript 2-like 1"""	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.3277dupG	9.37:g.134350793_134350793dupG	ENSP00000349856:p.Gly1091fs	Somatic		Capture	Illumina HiSeq	Phase_I	133340607	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Frame_Shift_Ins	INS	ENST00000357304.4	37	CCDS48044.1																																																																																				0.698	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
FOXD4	2298	broad.mit.edu	37	9	118098	118098	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:118098G>A	ENST00000382500.2	-	1	319	c.22C>T	c.(22-24)Cgc>Tgc	p.R8C		NM_207305.4	NP_997188.2	Q12950	FOXD4_HUMAN	forkhead box D4	8					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R8C(1)		endometrium(5)|large_intestine(2)|lung(3)|prostate(1)|skin(3)	14	all_lung(41;0.218)	all_cancers(5;0.0395)|Acute lymphoblastic leukemia(5;1.91e-07)|all_hematologic(5;1.95e-06)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)		GAGCGAAGGCGCTCAGCTCTT	0.652																																					p.R8C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C22T	9						.						67.0	78.0	74.0					9																	118098		2199	4294	6493	108098	SO:0001583	missense	2298	exon1			U13223	CCDS34975.1	9p24.3	2014-09-17			ENSG00000170122	ENSG00000170122		"""Forkhead boxes"""	3805	protein-coding gene	gene with protein product		601092		FKHL9		7957066, 8825632, 12234674	Standard	NM_207305		Approved	FREAC5, FOXD4a	uc003zfz.4	Q12950	OTTHUMG00000021015	ENST00000382500.2:c.22C>T	9.37:g.118098G>A	ENSP00000371940:p.Arg8Cys	Somatic		Capture	Illumina HiSeq	Phase_I	108098	NM_207305	B2RN05|B9EGL7|Q5VVK1|Q8WXT6	Missense_Mutation	SNP	ENST00000382500.2	37	CCDS34975.1	.	.	.	.	.	.	.	.	.	.	.	10.61	1.397255	0.25205	.	.	ENSG00000170122	ENST00000382500	D	0.95656	-3.77	2.31	-1.07	0.09968	.	0.918410	0.08832	N	0.887090	D	0.88187	0.6369	N	0.24115	0.695	0.29714	N	0.839169	B	0.15719	0.014	B	0.04013	0.001	T	0.77723	-0.2481	10	0.37606	T	0.19	.	2.2431	0.04024	0.4508:0.0:0.3075:0.2416	.	8	Q12950	FOXD4_HUMAN	C	8	ENSP00000371940:R8C	ENSP00000371940:R8C	R	-	1	0	FOXD4	108098	0.000000	0.05858	0.103000	0.21229	0.112000	0.19704	0.266000	0.18534	-0.104000	0.12154	0.291000	0.19559	CGC		0.652	FOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055433.1	NM_207305	
ALDOB	229	broad.mit.edu	37	9	104187208	104187208	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:104187208G>T	ENST00000374855.4	-	8	1040	c.916C>A	c.(916-918)Ctg>Atg	p.L306M	ALDOB_ENST00000468981.3_5'Flank	NM_000035.3	NP_000026.2	P05062	ALDOB_HUMAN	aldolase B, fructose-bisphosphate	306					carbohydrate metabolic process (GO:0005975)|fructose 1,6-bisphosphate metabolic process (GO:0030388)|fructose catabolic process (GO:0006001)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|NADH oxidation (GO:0006116)|positive regulation of ATPase activity (GO:0032781)|small molecule metabolic process (GO:0044281)|vacuolar proton-transporting V-type ATPase complex assembly (GO:0070072)	centriolar satellite (GO:0034451)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)	ATPase binding (GO:0051117)|cytoskeletal protein binding (GO:0008092)|fructose binding (GO:0070061)|fructose-1-phosphate aldolase activity (GO:0061609)|fructose-bisphosphate aldolase activity (GO:0004332)|identical protein binding (GO:0042802)	p.L306L(1)|p.L306M(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|liver(1)|lung(5)|prostate(2)|skin(4)|urinary_tract(1)	24		Acute lymphoblastic leukemia(62;0.0559)				CTGGCCTGCAGGGCCCGTCCA	0.552																																					p.L306M												.	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|kidney(1)	c.C916A	9						.						83.0	81.0	82.0					9																	104187208		2203	4300	6503	103227029	SO:0001583	missense	229	exon8			X01098	CCDS6756.1	9q21.3-q22.2	2008-02-05			ENSG00000136872	ENSG00000136872	4.1.2.13		417	protein-coding gene	gene with protein product		612724					Standard	NM_000035		Approved		uc004bbk.2	P05062	OTTHUMG00000020378	ENST00000374855.4:c.916C>A	9.37:g.104187208G>T	ENSP00000363988:p.Leu306Met	Somatic		Capture	Illumina HiSeq	Phase_I	103227029	NM_000035	Q13741|Q13742|Q5T7D6	Missense_Mutation	SNP	ENST00000374855.4	37	CCDS6756.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.826254	0.90955	.	.	ENSG00000136872	ENST00000374855	D	0.93547	-3.24	5.67	5.67	0.87782	Aldolase-type TIM barrel (1);	0.000000	0.85682	D	0.000000	D	0.97219	0.9091	M	0.87758	2.905	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97279	0.9916	10	0.66056	D	0.02	-5.8024	19.1251	0.93380	0.0:0.0:1.0:0.0	.	306	P05062	ALDOB_HUMAN	M	306	ENSP00000363988:L306M	ENSP00000363988:L306M	L	-	1	2	ALDOB	103227029	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.751000	0.74893	2.838000	0.97847	0.561000	0.74099	CTG		0.552	ALDOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053434.2		
ZNF483	158399	broad.mit.edu	37	9	114290010	114290010	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	T	T	T	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:114290010T>C	ENST00000309235.5	+	2	493	c.335T>C	c.(334-336)gTa>gCa	p.V112A	ZNF483_ENST00000358151.4_Missense_Mutation_p.V112A|ZNF483_ENST00000355824.3_Missense_Mutation_p.V112A|ZNF483_ENST00000374374.3_Missense_Mutation_p.V112A	NM_133464.2	NP_597721.2	Q8TF39	ZN483_HUMAN	zinc finger protein 483	112	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				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)			breast(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(11)|ovary(1)|skin(5)	31						AGGATTTGGGTAAAGTCACAA	0.448																																					p.V112A												.	.	0			c.T335C	9						.						101.0	105.0	104.0					9																	114290010		2203	4300	6503	113329831	SO:0001583	missense	158399	exon2			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.335T>C	9.37:g.114290010T>C	ENSP00000311679:p.Val112Ala	None		Capture	Illumina HiSeq	Phase_I	113329831	NM_001007169	Q5VZN2|Q8NAE1	Missense_Mutation	SNP	ENST00000309235.5	37	CCDS35106.1	.	.	.	.	.	.	.	.	.	.	T	18.93	3.727905	0.69074	.	.	ENSG00000173258	ENST00000358151;ENST00000355824;ENST00000374374;ENST00000309235	T;T;T;T	0.10477	2.87;2.87;2.87;2.87	5.55	4.41	0.53225	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	0.184455	0.26522	N	0.023908	T	0.35068	0.0919	M	0.89163	3.01	0.31925	N	0.612971	P;D;P;B	0.71674	0.594;0.998;0.594;0.049	B;D;B;B	0.74348	0.326;0.983;0.326;0.119	T	0.52533	-0.8563	10	0.87932	D	0	-13.5358	8.6258	0.33888	0.0:0.0877:0.0:0.9123	.	112;112;112;112	Q6P088;Q5VZN3;Q8NAE1;Q8TF39	.;.;.;ZN483_HUMAN	A	112	ENSP00000350871:V112A;ENSP00000438048:V112A;ENSP00000363494:V112A;ENSP00000311679:V112A	ENSP00000311679:V112A	V	+	2	0	ZNF483	113329831	0.996000	0.38824	0.845000	0.33349	0.757000	0.42996	3.069000	0.50026	1.038000	0.40049	-0.363000	0.07495	GTA		0.448	ZNF483-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053641.1	XM_088567	
AKNA	80709	broad.mit.edu	37	9	117110115	117110115	+	Missense_Mutation	SNP	T	T	G	rs200970909	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	G	T	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:117110115T>G	ENST00000307564.4	-	16	3448	c.3287A>C	c.(3286-3288)cAc>cCc	p.H1096P	AKNA_ENST00000374088.3_Missense_Mutation_p.H1096P|AKNA_ENST00000374075.5_Missense_Mutation_p.H1015P|AKNA_ENST00000374079.4_Missense_Mutation_p.H41P|AKNA_ENST00000492875.1_5'Flank|AKNA_ENST00000223791.3_Missense_Mutation_p.H556P	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	1096					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						GAGTGGCTGGTGCAGGCTGTC	0.667													T|||	732	0.146166	0.0166	0.1484	5008	,	,		13441	0.2669		0.2177	False		,,,				2504	0.1217				p.H1096P												.	.	0			c.A3287C	9						.						15.0	13.0	14.0					9																	117110115		2104	4146	6250	116149936	SO:0001583	missense	80709	exon16			AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.3287A>C	9.37:g.117110115T>G	ENSP00000303769:p.His1096Pro	Germline		Capture	Illumina HiSeq	Phase_I	116149936	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Missense_Mutation	SNP	ENST00000307564.4	37	CCDS6805.1	.	.	.	.	.	.	.	.	.	.	T	15.80	2.939315	0.52972	.	.	ENSG00000106948	ENST00000307564;ENST00000374079;ENST00000320310;ENST00000374088;ENST00000223791;ENST00000374075	T;T;T;T;T	0.18810	2.68;2.19;2.68;2.46;2.68	5.44	1.69	0.24217	.	0.369253	0.23674	N	0.045684	T	0.22781	0.0550	L	0.42245	1.32	0.29941	N	0.821025	D;D	0.61697	0.99;0.987	P;P	0.55391	0.758;0.775	T	0.11891	-1.0569	10	0.62326	D	0.03	-12.6768	1.671	0.02811	0.1676:0.0943:0.1742:0.564	.	1096;1015	Q7Z591;Q7Z591-2	AKNA_HUMAN;.	P	1096;41;108;1096;556;1015	ENSP00000303769:H1096P;ENSP00000363192:H41P;ENSP00000363201:H1096P;ENSP00000223791:H556P;ENSP00000363188:H1015P	ENSP00000223791:H556P	H	-	2	0	AKNA	116149936	0.854000	0.29725	0.996000	0.52242	0.804000	0.45430	0.998000	0.29744	1.009000	0.39289	0.533000	0.62120	CAC		0.667	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767	
PAPPA	5069	broad.mit.edu	37	9	118950315	118950315	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:118950315C>T	ENST00000328252.3	+	2	1667	c.1298C>T	c.(1297-1299)aCg>aTg	p.T433M	PAPPA_ENST00000534838.1_5'Flank	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	433	Metalloprotease.				cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|female pregnancy (GO:0007565)|response to follicle-stimulating hormone (GO:0032354)|response to glucocorticoid (GO:0051384)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(9)|kidney(2)|large_intestine(23)|lung(33)|ovary(4)|pancreas(2)|prostate(5)|skin(7)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	98						CACACGCTGACGGGCCACGAC	0.612																																					p.T433M												.	.	0			c.C1298T	9						.						63.0	51.0	55.0					9																	118950315		2203	4300	6503	117990136	SO:0001583	missense	5069	exon2				CCDS6813.1	9q33.1	2014-03-05			ENSG00000182752	ENSG00000182752			8602	protein-coding gene	gene with protein product	"""insulin-like growth factor-dependent IGF binding protein-4 protease"", ""aspecific BCL2 ARE-binding protein 2"", ""differentially placenta 1 expressed protein"""	176385				7679961	Standard	NM_002581		Approved	PAPP-A, PAPPA1, IGFBP-4ase, PAPA, ASBABP2, DIPLA1	uc004bjn.3	Q13219	OTTHUMG00000021045	ENST00000328252.3:c.1298C>T	9.37:g.118950315C>T	ENSP00000330658:p.Thr433Met	None		Capture	Illumina HiSeq	Phase_I	117990136	NM_002581	B1AMF9|Q08371|Q68G52|Q9UDK7	Missense_Mutation	SNP	ENST00000328252.3	37	CCDS6813.1	.	.	.	.	.	.	.	.	.	.	C	16.88	3.245984	0.59103	.	.	ENSG00000182752	ENST00000328252	D	0.91577	-2.87	6.07	6.07	0.98685	Notch domain (2);	0.000000	0.85682	D	0.000000	D	0.95532	0.8548	M	0.75777	2.31	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95100	0.8229	10	0.87932	D	0	-19.7402	20.6593	0.99626	0.0:1.0:0.0:0.0	.	433	Q13219	PAPP1_HUMAN	M	433	ENSP00000330658:T433M	ENSP00000330658:T433M	T	+	2	0	PAPPA	117990136	1.000000	0.71417	0.919000	0.36401	0.108000	0.19459	7.786000	0.85741	2.885000	0.99019	0.655000	0.94253	ACG		0.612	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581	
OR1L4	254973	broad.mit.edu	37	9	125487038	125487038	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:125487038T>A	ENST00000259466.1	+	1	770	c.770T>A	c.(769-771)aTc>aAc	p.I257N		NM_001005235.1	NP_001005235.1	Q8NGR5	OR1L4_HUMAN	olfactory receptor, family 1, subfamily L, member 4	257						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I257N(1)		breast(2)|large_intestine(3)|lung(13)|prostate(1)|skin(1)	20						GGGAGTGTCATCTATGTCTAT	0.522																																					p.I257N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T770A	9						.						141.0	126.0	131.0					9																	125487038		2203	4300	6503	124526859	SO:0001583	missense	254973	exon1				CCDS35129.1	9q33.2	2013-09-20			ENSG00000136939	ENSG00000136939		"""GPCR / Class A : Olfactory receptors"""	8216	protein-coding gene	gene with protein product				OR1L5			Standard	NM_001005235		Approved	OR9-E	uc004bmu.1	Q8NGR5	OTTHUMG00000020620	ENST00000259466.1:c.770T>A	9.37:g.125487038T>A	ENSP00000259466:p.Ile257Asn	Somatic		Capture	Illumina HiSeq	Phase_I	124526859	NM_001005235	Q6IFN0|Q96R81	Missense_Mutation	SNP	ENST00000259466.1	37	CCDS35129.1	.	.	.	.	.	.	.	.	.	.	.	13.95	2.389146	0.42410	.	.	ENSG00000136939	ENST00000259466	T	0.42900	0.96	4.23	3.06	0.35304	GPCR, rhodopsin-like superfamily (1);	0.109140	0.40728	N	0.001040	T	0.60650	0.2285	M	0.81682	2.555	0.36129	D	0.846002	D	0.63046	0.992	D	0.63703	0.917	T	0.70081	-0.4970	10	0.87932	D	0	-18.767	10.0273	0.42079	0.0:0.0:0.1701:0.8299	.	257	Q8NGR5	OR1L4_HUMAN	N	257	ENSP00000259466:I257N	ENSP00000259466:I257N	I	+	2	0	OR1L4	124526859	0.000000	0.05858	0.999000	0.59377	0.604000	0.37047	0.360000	0.20250	0.657000	0.30906	0.248000	0.18094	ATC		0.522	OR1L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053951.1		
TYRP1	7306	broad.mit.edu	37	9	12694121	12694121	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:12694121G>A	ENST00000388918.5	+	2	254	c.125G>A	c.(124-126)tGc>tAc	p.C42Y	TYRP1_ENST00000381137.2_5'UTR|TYRP1_ENST00000381136.2_5'Flank	NM_000550.2	NP_000541.1	P17643	TYRP1_HUMAN	tyrosinase-related protein 1	42					acetoacetic acid metabolic process (GO:0043438)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome organization (GO:0032438)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)|melanosome membrane (GO:0033162)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, another compound as one donor, and incorporation of one atom of oxygen (GO:0016716)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.C42Y(1)		NS(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|stomach(1)	22		all_cancers(3;3.1e-05)|all_lung(3;1.7e-06)|Lung NSC(3;2.09e-06)|all_epithelial(3;0.000695)|all_hematologic(3;0.0033)|Acute lymphoblastic leukemia(23;0.0744)		GBM - Glioblastoma multiforme(50;9.85e-06)		GGTATGTGTTGCCCAGACCTG	0.587									Oculocutaneous Albinism																												p.C42Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G125A	9						.						72.0	64.0	67.0					9																	12694121		2203	4300	6503	12684121	SO:0001583	missense	7306	exon2	Familial Cancer Database		L33830	CCDS34990.1	9p23	2013-01-08			ENSG00000107165	ENSG00000107165			12450	protein-coding gene	gene with protein product		115501		TYRP, CAS2		9434945	Standard	NM_000550		Approved	GP75, CATB, TRP, b-PROTEIN, OCA3	uc003zkv.4	P17643	OTTHUMG00000021034	ENST00000388918.5:c.125G>A	9.37:g.12694121G>A	ENSP00000373570:p.Cys42Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	12684121	NM_000550	P78468|P78469|Q13721|Q15679	Missense_Mutation	SNP	ENST00000388918.5	37	CCDS34990.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.768303	0.90020	.	.	ENSG00000107165	ENST00000473763;ENST00000388918	T;D	0.99886	2.41;-7.52	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	D	0.99908	0.9956	M	0.90082	3.085	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96474	0.9351	10	0.87932	D	0	-12.2413	19.7987	0.96497	0.0:0.0:1.0:0.0	.	42	P17643	TYRP1_HUMAN	Y	42	ENSP00000419006:C42Y;ENSP00000373570:C42Y	ENSP00000373570:C42Y	C	+	2	0	TYRP1	12684121	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.318000	0.96334	2.767000	0.95098	0.655000	0.94253	TGC		0.587	TYRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055502.3	NM_000550	
OLFML2A	169611	broad.mit.edu	37	9	127572447	127572447	+	Missense_Mutation	SNP	G	G	A	rs372603527		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:127572447G>A	ENST00000373580.3	+	8	1715	c.1715G>A	c.(1714-1716)cGg>cAg	p.R572Q	OLFML2A_ENST00000288815.5_Missense_Mutation_p.R358Q	NM_182487.2	NP_872293.2	Q68BL7	OLM2A_HUMAN	olfactomedin-like 2A	572	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)	p.R572Q(1)		endometrium(5)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	25						CGGCTGCGGCGGAACTCCTAC	0.647																																					p.R572Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1715A	9						.						63.0	63.0	63.0					9																	127572447		2203	4300	6503	126612268	SO:0001583	missense	169611	exon8			AK092255	CCDS6857.2, CCDS65129.1	9q34.11	2008-02-05			ENSG00000185585	ENSG00000185585			27270	protein-coding gene	gene with protein product		615899				12477932	Standard	NM_001282715		Approved	FLJ00237	uc004bov.3	Q68BL7	OTTHUMG00000020663	ENST00000373580.3:c.1715G>A	9.37:g.127572447G>A	ENSP00000362682:p.Arg572Gln	Somatic		Capture	Illumina HiSeq	Phase_I	126612268	NM_182487	Q5JTM5|Q5JTM6|Q6UXW1|Q7Z5V3	Missense_Mutation	SNP	ENST00000373580.3	37	CCDS6857.2	.	.	.	.	.	.	.	.	.	.	G	36	5.788651	0.96945	.	.	ENSG00000185585	ENST00000342100;ENST00000373580;ENST00000288815	D;D	0.89485	-2.52;-2.52	6.07	6.07	0.98685	Olfactomedin-like (3);	0.000000	0.85682	D	0.000000	D	0.95085	0.8408	M	0.84846	2.72	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.69479	0.964;0.958	D	0.95036	0.8174	10	0.87932	D	0	.	19.2077	0.93739	0.0:0.0:1.0:0.0	.	358;572	Q68BL7-3;Q68BL7	.;OLM2A_HUMAN	Q	264;572;358	ENSP00000362682:R572Q;ENSP00000288815:R358Q	ENSP00000288815:R358Q	R	+	2	0	OLFML2A	126612268	1.000000	0.71417	0.976000	0.42696	0.945000	0.59286	9.869000	0.99810	2.884000	0.98904	0.655000	0.94253	CGG		0.647	OLFML2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054046.2	NM_182487	
STXBP1	6812	broad.mit.edu	37	9	130423447	130423447	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:130423447C>T	ENST00000373299.1	+	6	507	c.392C>T	c.(391-393)aCg>aTg	p.T131M	STXBP1_ENST00000373302.3_Missense_Mutation_p.T131M	NM_001032221.3	NP_001027392.1	P61764	STXB1_HUMAN	syntaxin binding protein 1	131					axon target recognition (GO:0007412)|energy reserve metabolic process (GO:0006112)|glutamate secretion (GO:0014047)|long term synaptic depression (GO:0060292)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter secretion (GO:0007269)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|protein stabilization (GO:0050821)|protein transport (GO:0015031)|regulation of insulin secretion (GO:0050796)|regulation of SNARE complex assembly (GO:0035542)|regulation of synaptic vesicle fusion to presynaptic membrane (GO:0031630)|regulation of synaptic vesicle priming (GO:0010807)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle maturation (GO:0016188)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|protein complex (GO:0043234)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|SNARE binding (GO:0000149)|syntaxin binding (GO:0019905)|syntaxin-1 binding (GO:0017075)	p.T131M(1)		breast(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(7)|skin(2)	23						AAAACTCTGACGGAAATCAAT	0.468																																					p.T131M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C392T	9						.						119.0	111.0	114.0					9																	130423447		2203	4300	6503	129463268	SO:0001583	missense	6812	exon6			AF004563	CCDS6874.1, CCDS35146.1	9q34.1	2008-07-21			ENSG00000136854	ENSG00000136854			11444	protein-coding gene	gene with protein product	"""syntaxin-binding protein 1"""	602926				9545644	Standard	NM_001032221		Approved	hUNC18, MUNC18-1, UNC18, rbSec1	uc004brk.2	P61764	OTTHUMG00000020713	ENST00000373299.1:c.392C>T	9.37:g.130423447C>T	ENSP00000362396:p.Thr131Met	Somatic		Capture	Illumina HiSeq	Phase_I	129463268	NM_003165	B1AM97|Q28208|Q62759|Q64320|Q96TG8	Missense_Mutation	SNP	ENST00000373299.1	37	CCDS35146.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.174633	0.78452	.	.	ENSG00000136854	ENST00000535154;ENST00000373302;ENST00000373299	T;T	0.76186	-1.0;-1.0	5.71	5.71	0.89125	.	0.046323	0.85682	D	0.000000	T	0.74951	0.3784	N	0.25647	0.755	0.38916	D	0.957646	P;P	0.52463	0.953;0.942	P;P	0.53954	0.738;0.62	T	0.79264	-0.1875	10	0.87932	D	0	-5.5208	17.3563	0.87336	0.0:1.0:0.0:0.0	.	131;131	P61764;P61764-2	STXB1_HUMAN;.	M	85;131;131	ENSP00000362399:T131M;ENSP00000362396:T131M	ENSP00000362396:T131M	T	+	2	0	STXBP1	129463268	0.997000	0.39634	1.000000	0.80357	0.997000	0.91878	3.355000	0.52262	2.689000	0.91719	0.655000	0.94253	ACG		0.468	STXBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054229.1	NM_003165	
ST6GALNAC6	30815	broad.mit.edu	37	9	130653157	130653157	+	Missense_Mutation	SNP	C	C	T	rs138204383	byFrequency	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:130653157C>T	ENST00000373146.1	-	5	642	c.463G>A	c.(463-465)Gtc>Atc	p.V155I	ST6GALNAC6_ENST00000373142.1_Missense_Mutation_p.V155I|ST6GALNAC6_ENST00000373144.3_Missense_Mutation_p.V121I|ST6GALNAC6_ENST00000542456.1_Intron|ST6GALNAC6_ENST00000291839.5_Missense_Mutation_p.V155I|ST6GALNAC6_ENST00000485320.1_5'UTR|ST6GALNAC6_ENST00000373141.1_Missense_Mutation_p.V121I			Q969X2	SIA7F_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 6	155					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.V155F(1)|p.V155I(1)		endometrium(3)|large_intestine(3)|lung(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						TGGGCCACGACGCGGTAGGTG	0.607																																					p.V155I												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G463A	9						.	C	ILE/VAL	4,4402	8.1+/-20.4	0,4,2199	91.0	83.0	85.0		463	5.6	0.9	9	dbSNP_134	85	0,8600		0,0,4300	yes	missense	ST6GALNAC6	NM_013443.3	29	0,4,6499	TT,TC,CC		0.0,0.0908,0.0308	possibly-damaging	155/334	130653157	4,13002	2203	4300	6503	129692978	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.463G>A	9.37:g.130653157C>T	ENSP00000362239:p.Val155Ile	Somatic		Capture	Illumina HiSeq	Phase_I	129692978	NM_013443	B3KQ01|Q5T9C4|Q5T9C5|Q9H8A2|Q9ULB8	Missense_Mutation	SNP	ENST00000373146.1	37	CCDS6882.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.034924	0.93575	9.08E-4	0.0	ENSG00000160408	ENST00000373146;ENST00000373141;ENST00000373142;ENST00000373144;ENST00000291839;ENST00000447681	T;T;T;T;T;T	0.29655	1.56;1.56;1.56;1.56;1.56;1.56	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.54791	0.1880	M	0.69185	2.1	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.67103	0.915;0.949	T	0.56257	-0.8009	10	0.87932	D	0	-19.7642	18.1812	0.89779	0.0:1.0:0.0:0.0	.	121;155	Q969X2-2;Q969X2	.;SIA7F_HUMAN	I	155;121;155;121;155;121	ENSP00000362239:V155I;ENSP00000362234:V121I;ENSP00000362235:V155I;ENSP00000362237:V121I;ENSP00000291839:V155I;ENSP00000405326:V121I	ENSP00000291839:V155I	V	-	1	0	ST6GALNAC6	129692978	0.998000	0.40836	0.927000	0.36925	0.717000	0.41224	3.768000	0.55295	2.640000	0.89533	0.651000	0.88453	GTC		0.607	ST6GALNAC6-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054278.1	NM_013443	
DNM1	1759	broad.mit.edu	37	9	130996371	130996371	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:130996371C>T	ENST00000372923.3	+	11	1499	c.1407C>T	c.(1405-1407)ggC>ggT	p.G469G	DNM1_ENST00000341179.7_Silent_p.G469G|DNM1_ENST00000393594.3_Silent_p.G469G|DNM1_ENST00000475805.1_Silent_p.G469G|DNM1_ENST00000486160.1_Silent_p.G469G	NM_004408.2	NP_004399.2	Q05193	DYN1_HUMAN	dynamin 1	469					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.G469G(2)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(15)|lung(6)|ovary(2)|urinary_tract(2)	32						AGCGCGAGGGCCGCACTAAGG	0.697																																					p.G469G	GBM(113;146 1575 2722 28670 29921)											.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1407T	9						.						19.0	18.0	18.0					9																	130996371		2169	4271	6440	130036192	SO:0001819	synonymous_variant	1759	exon11			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.1407C>T	9.37:g.130996371C>T		Somatic		Capture	Illumina HiSeq	Phase_I	130036192	NM_001005336	A6NLM6|Q5SYX0|Q5SYX2|Q6P3T6|Q86VD2	Silent	SNP	ENST00000372923.3	37	CCDS6895.1																																																																																				0.697	DNM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054367.1	NM_004408	
BRD3	8019	broad.mit.edu	37	9	136910513	136910513	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:136910513C>T	ENST00000303407.7	-	7	1302	c.1117G>A	c.(1117-1119)Gca>Aca	p.A373T	BRD3_ENST00000371834.2_Missense_Mutation_p.A373T|BRD3_ENST00000357885.2_Missense_Mutation_p.A373T	NM_007371.3	NP_031397.1	Q15059	BRD3_HUMAN	bromodomain containing 3	373	Bromo 2. {ECO:0000255|PROSITE- ProRule:PRU00035}.				chromatin modification (GO:0016568)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|lysine-acetylated histone binding (GO:0070577)	p.A373T(2)	BRD3/C15orf55(3)	kidney(1)|skin(1)|stomach(4)	6				OV - Ovarian serous cystadenocarcinoma(145;1.43e-08)|Epithelial(140;8.41e-08)|all cancers(34;5.21e-07)		AAGCCCTGTGCGTCTGGGTAC	0.592			T	C15orf55	lethal midline carcinoma of young people																																p.A373T			Dom	yes		9	9q34	8019	bromodomain containing 3		E	.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.G1117A	9						.						176.0	144.0	155.0					9																	136910513		2203	4300	6503	135900334	SO:0001583	missense	8019	exon7				CCDS6980.1	9q34	2010-12-23	2002-01-14		ENSG00000169925	ENSG00000169925			1104	protein-coding gene	gene with protein product	"""RING3-like"""	601541	"""bromodomain-containing 3"""			7584044, 8781126	Standard	NM_007371		Approved	RING3L, ORFX, KIAA0043	uc004cew.3	Q15059	OTTHUMG00000021004	ENST00000303407.7:c.1117G>A	9.37:g.136910513C>T	ENSP00000305918:p.Ala373Thr	Somatic		Capture	Illumina HiSeq	Phase_I	135900334	NM_007371	B1APD9|Q4G5Y3|Q5T1R7|Q8N5M3|Q92645	Missense_Mutation	SNP	ENST00000303407.7	37	CCDS6980.1	.	.	.	.	.	.	.	.	.	.	C	33	5.256591	0.95336	.	.	ENSG00000169925	ENST00000303407;ENST00000540795;ENST00000371834;ENST00000357885	T;T;T	0.33654	1.4;1.4;1.4	4.69	4.69	0.59074	Bromodomain (5);Bromodomain, conserved site (1);	0.000000	0.64402	D	0.000001	T	0.49440	0.1557	L	0.35793	1.09	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.67103	0.942;0.949	T	0.50972	-0.8764	10	0.54805	T	0.06	-18.9639	16.5874	0.84731	0.0:1.0:0.0:0.0	.	373;373	Q15059-2;Q15059	.;BRD3_HUMAN	T	373;52;373;373	ENSP00000305918:A373T;ENSP00000360900:A373T;ENSP00000350557:A373T	ENSP00000305918:A373T	A	-	1	0	BRD3	135900334	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	5.857000	0.69525	2.137000	0.66172	0.561000	0.74099	GCA		0.592	BRD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055390.4	NM_007371	
UBAC1	10422	broad.mit.edu	37	9	138839700	138839700	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:138839700C>T	ENST00000371756.3	-	4	602	c.385G>A	c.(385-387)Gcc>Acc	p.A129T	UBAC1_ENST00000465873.1_5'Flank	NM_016172.2	NP_057256.2	Q9BSL1	UBAC1_HUMAN	UBA domain containing 1	129					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)		p.A129T(1)		NS(1)|biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(6)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	25		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.1e-06)|Epithelial(140;7.79e-06)		GGCAGGTTGGCGGTGGCCCGC	0.567																																					p.A129T	NSCLC(78;973 1398 27381 29552 42415)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G385A	9						.						90.0	90.0	90.0					9																	138839700		2203	4300	6503	137979521	SO:0001583	missense	10422	exon4			AF176796	CCDS35177.1	9q34.3	2008-02-05	2007-04-20	2007-04-20	ENSG00000130560	ENSG00000130560			30221	protein-coding gene	gene with protein product		608129	"""ubiquitin associated domain containing 1"""	UBADC1		10857748, 8619474	Standard	NM_016172		Approved	GBDR1	uc004cgt.3	Q9BSL1	OTTHUMG00000020920	ENST00000371756.3:c.385G>A	9.37:g.138839700C>T	ENSP00000360821:p.Ala129Thr	Somatic		Capture	Illumina HiSeq	Phase_I	137979521	NM_016172	O75500|Q9UMW7	Missense_Mutation	SNP	ENST00000371756.3	37	CCDS35177.1	.	.	.	.	.	.	.	.	.	.	C	15.05	2.719296	0.48728	.	.	ENSG00000130560	ENST00000371756	T	0.23950	1.88	5.23	4.34	0.51931	.	0.173327	0.50627	D	0.000114	T	0.23846	0.0577	M	0.72118	2.19	0.53688	D	0.999976	P	0.50066	0.931	B	0.33295	0.161	T	0.10543	-1.0625	10	0.36615	T	0.2	-31.4109	12.8749	0.57984	0.0:0.9215:0.0:0.0785	.	129	Q9BSL1	UBAC1_HUMAN	T	129	ENSP00000360821:A129T	ENSP00000360821:A129T	A	-	1	0	UBAC1	137979521	0.998000	0.40836	0.686000	0.30086	0.374000	0.29953	3.859000	0.55987	1.198000	0.43158	0.655000	0.94253	GCC		0.567	UBAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055034.1	NM_016172	
RFX3	5991	broad.mit.edu	37	9	3262957	3262957	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:3262957C>T	ENST00000382004.3	-	14	1894	c.1583G>A	c.(1582-1584)cGt>cAt	p.R528H	RFX3_ENST00000358730.2_Missense_Mutation_p.R528H|RFX3_ENST00000302303.1_Missense_Mutation_p.R528H	NM_001282116.1|NM_134428.1	NP_001269045.1|NP_602304.1	P48380	RFX3_HUMAN	regulatory factor X, 3 (influences HLA class II expression)	528					cell maturation (GO:0048469)|cilium assembly (GO:0042384)|cilium-dependent cell motility (GO:0060285)|endocrine pancreas development (GO:0031018)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type B pancreatic cell development (GO:2000078)|regulation of insulin secretion (GO:0050796)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|type B pancreatic cell maturation (GO:0072560)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	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)|transcription regulatory region DNA binding (GO:0044212)	p.R528H(2)		central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(11)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(50;0.00124)|Lung(2;0.0337)		AAAGTCGACACGGTTGAGGTC	0.443																																					p.R528H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1583A	9						.						200.0	182.0	188.0					9																	3262957		2203	4300	6503	3252957	SO:0001583	missense	5991	exon14			AI811824	CCDS6449.1, CCDS6450.1, CCDS75809.1	9p24.2	2008-02-05			ENSG00000080298	ENSG00000080298			9984	protein-coding gene	gene with protein product		601337				8289803	Standard	XM_005251534		Approved		uc003zhr.3	P48380	OTTHUMG00000019456	ENST00000382004.3:c.1583G>A	9.37:g.3262957C>T	ENSP00000371434:p.Arg528His	Somatic		Capture	Illumina HiSeq	Phase_I	3252957	NM_134428	A8K0H5|D3DRH8|D3DRH9|Q5JTL7|Q5JTL8|Q6NW13|Q8WTU4|Q95HL5|Q95HL6	Missense_Mutation	SNP	ENST00000382004.3	37	CCDS6449.1	.	.	.	.	.	.	.	.	.	.	C	36	5.636797	0.96693	.	.	ENSG00000080298	ENST00000382004;ENST00000358730;ENST00000302303;ENST00000381986;ENST00000458034	T;T;T;T	0.47528	0.84;0.84;0.84;0.84	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.76435	0.3987	M	0.90252	3.1	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.981	T	0.79110	-0.1938	10	0.59425	D	0.04	-8.0028	20.4192	0.99033	0.0:1.0:0.0:0.0	.	528;528	P48380-2;P48380	.;RFX3_HUMAN	H	528;528;528;7;101	ENSP00000371434:R528H;ENSP00000351574:R528H;ENSP00000303847:R528H;ENSP00000400026:R101H	ENSP00000303847:R528H	R	-	2	0	RFX3	3252957	1.000000	0.71417	0.983000	0.44433	0.998000	0.95712	6.080000	0.71299	2.831000	0.97527	0.650000	0.86243	CGT		0.443	RFX3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051545.1	NM_002919	
INSL6	11172	broad.mit.edu	37	9	5163996	5163996	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:5163996C>A	ENST00000381641.3	-	2	624	c.559G>T	c.(559-561)Gaa>Taa	p.E187*	INSL6_ENST00000510407.1_Intron	NM_007179.2	NP_009110.2	Q9Y581	INSL6_HUMAN	insulin-like 6	187					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.E187*(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|lung(2)	15	all_hematologic(13;0.137)	Breast(48;0.147)|Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0128)|Lung(218;0.145)		ATGCTAAGTTCTTCTTTTGTA	0.318																																					p.E187X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G559T	9						.						104.0	100.0	101.0					9																	5163996		2203	4299	6502	5153996	SO:0001587	stop_gained	11172	exon2			AF156094	CCDS6458.1	9p24	2008-07-21			ENSG00000120210	ENSG00000120210			6089	protein-coding gene	gene with protein product	"""relaxin/insulin-like factor 1"""	606414				10819760	Standard	NM_007179		Approved	RIF1	uc003zix.3	Q9Y581	OTTHUMG00000019489	ENST00000381641.3:c.559G>T	9.37:g.5163996C>A	ENSP00000371054:p.Glu187*	Somatic		Capture	Illumina HiSeq	Phase_I	5153996	NM_007179	A0AVS0|Q9NS16	Nonsense_Mutation	SNP	ENST00000381641.3	37	CCDS6458.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.694066	0.88735	.	.	ENSG00000120210	ENST00000381641	.	.	.	4.35	4.35	0.52113	.	0.074552	0.51477	D	0.000082	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-26.0104	12.6781	0.56906	0.0:1.0:0.0:0.0	.	.	.	.	X	187	.	ENSP00000371054:E187X	E	-	1	0	INSL6	5153996	0.997000	0.39634	0.989000	0.46669	0.997000	0.91878	2.886000	0.48578	2.711000	0.92665	0.591000	0.81541	GAA		0.318	INSL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051608.3	NM_007179	
KIAA2026	158358	broad.mit.edu	37	9	5919744	5919744	+	Silent	SNP	C	C	T	rs367652443		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:5919744C>T	ENST00000399933.3	-	8	6251	c.6252G>A	c.(6250-6252)gcG>gcA	p.A2084A	KIAA2026_ENST00000381461.2_Silent_p.A2054A	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	2084								p.A1259A(1)		breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		GGAAGACAGACGCAGGACTTC	0.433													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18132	0.0		0.0	False		,,,				2504	0.0				p.A2084A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G6252A	9						.	C		3,3751		0,3,1874	48.0	49.0	49.0		6252	0.9	1.0	9		49	0,8230		0,0,4115	no	coding-synonymous	KIAA2026	NM_001017969.2		0,3,5989	TT,TC,CC		0.0,0.0799,0.025		2084/2104	5919744	3,11981	1877	4115	5992	5909744	SO:0001819	synonymous_variant	158358	exon8			AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.6252G>A	9.37:g.5919744C>T		Somatic		Capture	Illumina HiSeq	Phase_I	5909744	NM_001017969	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Silent	SNP	ENST00000399933.3	37																																																																																					0.433	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969	
IFNA16	3449	broad.mit.edu	37	9	21216889	21216889	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:21216889G>A	ENST00000380216.1	-	1	421	c.416C>T	c.(415-417)tCc>tTc	p.S139F		NM_002173.2	NP_002164.1	P05015	IFN16_HUMAN	interferon, alpha 16	139					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)	p.S139F(1)		central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	13				Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.116)		AGCCAGGATGGAGTCCTCATT	0.458																																					p.S139F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C416T	9						.						214.0	206.0	209.0					9																	21216889		2203	4300	6503	21206889	SO:0001583	missense	3449	exon1				CCDS34996.1	9p22	2010-12-10			ENSG00000147885	ENSG00000147885		"""Interferons"""	5421	protein-coding gene	gene with protein product		147580				1385305	Standard	NM_002173		Approved	IFN-alphaO	uc003zor.1	P05015	OTTHUMG00000019663	ENST00000380216.1:c.416C>T	9.37:g.21216889G>A	ENSP00000369564:p.Ser139Phe	Somatic		Capture	Illumina HiSeq	Phase_I	21206889	NM_002173	Q5VV12	Missense_Mutation	SNP	ENST00000380216.1	37	CCDS34996.1	.	.	.	.	.	.	.	.	.	.	-	10.94	1.493876	0.26774	.	.	ENSG00000147885	ENST00000380216	T	0.05855	3.38	2.62	2.62	0.31277	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.701085	0.13017	N	0.420417	T	0.26738	0.0654	M	0.89214	3.015	0.09310	N	1	D	0.54207	0.965	D	0.71870	0.975	T	0.02208	-1.1195	10	0.72032	D	0.01	.	8.8232	0.35039	0.0:0.0:1.0:0.0	.	139	P05015	IFN16_HUMAN	F	139	ENSP00000369564:S139F	ENSP00000369564:S139F	S	-	2	0	IFNA16	21206889	0.000000	0.05858	0.009000	0.14445	0.208000	0.24298	0.096000	0.15147	1.471000	0.48121	0.184000	0.17185	TCC		0.458	IFNA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051892.1	NM_002173	
TAF1L	138474	broad.mit.edu	37	9	32630111	32630111	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:32630111C>T	ENST00000242310.4	-	1	5556	c.5467G>A	c.(5467-5469)Ggg>Agg	p.G1823R		NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1823					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.G1823W(1)|p.G1823R(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)		TTTCCGTGCCCATCCTTGTGT	0.498																																					p.G1823R												.	.	2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	c.G5467A	9						.						196.0	142.0	160.0					9																	32630111		2203	4300	6503	32620111	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.5467G>A	9.37:g.32630111C>T	ENSP00000418379:p.Gly1823Arg	Somatic		Capture	Illumina HiSeq	Phase_I	32620111	NM_153809	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	37	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	C	10.38	1.334855	0.24253	.	.	ENSG00000122728	ENST00000242310	T	0.08102	3.13	0.479	0.479	0.16796	.	0.253650	0.34484	N	0.003924	T	0.04048	0.0113	N	0.08118	0	0.25863	N	0.983797	D	0.58620	0.983	B	0.43251	0.413	T	0.39643	-0.9604	10	0.87932	D	0	.	6.6915	0.23174	0.0:0.9998:0.0:2.0E-4	.	1823	Q8IZX4	TAF1L_HUMAN	R	1823	ENSP00000418379:G1823R	ENSP00000418379:G1823R	G	-	1	0	TAF1L	32620111	1.000000	0.71417	0.991000	0.47740	0.183000	0.23260	2.128000	0.42045	0.507000	0.28148	0.195000	0.17529	GGG		0.498	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2		
KIF24	347240	broad.mit.edu	37	9	34256069	34256069	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:34256069G>A	ENST00000402558.2	-	10	3560	c.3536C>T	c.(3535-3537)aCg>aTg	p.T1179M	KIF24_ENST00000345050.2_Missense_Mutation_p.T1045M|KIF24_ENST00000379174.3_Missense_Mutation_p.T1045M|KIF24_ENST00000379166.2_Missense_Mutation_p.T1179M			Q5T7B8	KIF24_HUMAN	kinesin family member 24	1179					ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)	centriole (GO:0005814)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.T1179M(1)|p.T661M(1)		breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(13)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	32			LUSC - Lung squamous cell carcinoma(29;0.0107)			ATCCAGCCCCGTCTCCTCTGC	0.562																																					p.T1179M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C3536T	9						.						79.0	76.0	77.0					9																	34256069		2203	4300	6503	34246069	SO:0001583	missense	347240	exon11			AK001795	CCDS6551.2	9p13.3	2013-01-10			ENSG00000186638	ENSG00000186638		"""Kinesins"", ""Sterile alpha motif (SAM) domain containing"""	19916	protein-coding gene	gene with protein product		613747	"""chromosome 9 open reading frame 48"""	C9orf48		12477932	Standard	NM_194313		Approved	bA571F15.4, FLJ10933, FLJ43884	uc003zua.4	Q5T7B8	OTTHUMG00000019810	ENST00000402558.2:c.3536C>T	9.37:g.34256069G>A	ENSP00000384433:p.Thr1179Met	Somatic		Capture	Illumina HiSeq	Phase_I	34246069	NM_194313	Q2TB93|Q5T7B5|Q5T7B7|Q6ZU97|Q6ZUZ2|Q86XZ0|Q9NV43	Missense_Mutation	SNP	ENST00000402558.2	37	CCDS6551.2	.	.	.	.	.	.	.	.	.	.	G	2.905	-0.226594	0.06022	.	.	ENSG00000186638	ENST00000402558;ENST00000379174;ENST00000379166;ENST00000345050	T;T;T;T	0.73681	-0.55;-0.77;-0.55;-0.77	5.01	-1.6	0.08426	.	0.711535	0.12209	N	0.489494	T	0.54382	0.1855	L	0.29908	0.895	0.09310	N	1	B	0.23185	0.081	B	0.16289	0.015	T	0.31110	-0.9955	9	.	.	.	.	5.572	0.17202	0.2665:0.2428:0.4907:0.0	.	1179	Q5T7B8	KIF24_HUMAN	M	1179;1045;1179;1045	ENSP00000384433:T1179M;ENSP00000368472:T1045M;ENSP00000368464:T1179M;ENSP00000340179:T1045M	.	T	-	2	0	KIF24	34246069	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.425000	0.21346	-0.509000	0.06532	-1.105000	0.02106	ACG		0.562	KIF24-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052150.5		
SIGMAR1	10280	broad.mit.edu	37	9	34635739	34635739	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:34635739C>T	ENST00000277010.4	-	4	635	c.562G>A	c.(562-564)Gac>Aac	p.D188N	SIGMAR1_ENST00000378892.1_Missense_Mutation_p.D99N|SIGMAR1_ENST00000461426.1_5'UTR|SIGMAR1_ENST00000477726.1_Missense_Mutation_p.D157N	NM_001282208.1|NM_005866.2	NP_001269137.1|NP_005857.1	Q99720	SGMR1_HUMAN	sigma non-opioid intracellular receptor 1	188					cell death (GO:0008219)|lipid transport (GO:0006869)|nervous system development (GO:0007399)|regulation of neuron apoptotic process (GO:0043523)	cell junction (GO:0030054)|cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lipid particle (GO:0005811)|nuclear envelope (GO:0005635)	drug binding (GO:0008144)|opioid receptor activity (GO:0004985)	p.D188N(1)		large_intestine(1)|lung(1)	2					Amitriptyline(DB00321)|Dextromethorphan(DB00514)|Nortriptyline(DB00540)|Pentazocine(DB00652)|Remoxipride(DB00409)	AAGACAGTGTCGGCCAGCGCG	0.627																																					p.D157N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G469A	9						.						124.0	107.0	113.0					9																	34635739		2203	4300	6503	34625739	SO:0001583	missense	10280	exon3			BC004899	CCDS6562.1, CCDS6563.1	9p13.3	2008-12-18	2008-12-18	2008-12-18	ENSG00000147955	ENSG00000147955			8157	protein-coding gene	gene with protein product		601978	"""opioid receptor, sigma 1"""	OPRS1		8954936, 9453537	Standard	NM_005866		Approved	SR-BP1	uc003zvb.3	Q99720	OTTHUMG00000019829	ENST00000277010.4:c.562G>A	9.37:g.34635739C>T	ENSP00000277010:p.Asp188Asn	Somatic		Capture	Illumina HiSeq	Phase_I	34625739	NM_147157	D3DRM7|O00673|O00725|Q0Z9W6|Q153Z1|Q2TSD1|Q53GN2|Q7Z653|Q8N7H3|Q9NYX0	Missense_Mutation	SNP	ENST00000277010.4	37	CCDS6562.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.802727	0.90623	.	.	ENSG00000147955	ENST00000378892;ENST00000277010;ENST00000360710;ENST00000477726	T;T;T	0.76839	-1.05;-1.05;-1.05	4.43	3.53	0.40419	.	0.000000	0.85682	D	0.000000	D	0.88001	0.6320	M	0.87456	2.885	0.52099	D	0.99994	D;D;D	0.89917	0.992;0.998;1.0	D;D;D	0.87578	0.929;0.944;0.998	D	0.88733	0.3238	10	0.72032	D	0.01	-31.7278	10.84	0.46708	0.0:0.907:0.0:0.093	.	157;188;168	A2A3U5;Q99720;Q99720-2	.;SGMR1_HUMAN;.	N	99;188;154;157	ENSP00000368170:D99N;ENSP00000277010:D188N;ENSP00000420022:D157N	ENSP00000277010:D188N	D	-	1	0	SIGMAR1	34625739	1.000000	0.71417	0.943000	0.38184	0.904000	0.53231	5.580000	0.67464	1.084000	0.41184	0.462000	0.41574	GAC		0.627	SIGMAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052204.1	NM_005866	
UNC13B	10497	broad.mit.edu	37	9	35399698	35399698	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:35399698T>C	ENST00000378495.3	+	35	4283	c.4061T>C	c.(4060-4062)gTc>gCc	p.V1354A	UNC13B_ENST00000396787.1_Missense_Mutation_p.V1366A|UNC13B_ENST00000378496.4_Missense_Mutation_p.V1354A	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)	1354	MHD2. {ECO:0000255|PROSITE- ProRule:PRU00588}.				apoptotic process (GO:0006915)|excretion (GO:0007588)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synaptic vesicle priming (GO:0010808)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|terminal bouton (GO:0043195)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)	p.V1354A(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(16)|liver(2)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			CAGTGTGCAGTCCTTGACCTC	0.532																																					p.V1354A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T4061C	9						.						230.0	202.0	211.0					9																	35399698		2203	4300	6503	35389698	SO:0001583	missense	10497	exon35			AF020202	CCDS6579.1	9p13.3	2008-05-15	2003-10-17	2003-10-17	ENSG00000198722	ENSG00000198722			12566	protein-coding gene	gene with protein product		605836	"""unc-13-like (C. elegans)"""	UNC13		9607201	Standard	NM_006377		Approved	hmunc13, Unc13h2	uc003zwq.3	O14795	OTTHUMG00000019856	ENST00000378495.3:c.4061T>C	9.37:g.35399698T>C	ENSP00000367756:p.Val1354Ala	Somatic		Capture	Illumina HiSeq	Phase_I	35389698	NM_006377	Q5VYM8	Missense_Mutation	SNP	ENST00000378495.3	37	CCDS6579.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.643467	0.87859	.	.	ENSG00000198722	ENST00000396787;ENST00000378495;ENST00000378496;ENST00000535471	T;T;T	0.75477	-0.94;-0.94;-0.94	5.55	5.55	0.83447	Mammalian uncoordinated homology 13, domain 2 (1);Mammalian uncoordinated homology 13, subgroup, domain 2 (1);	0.224693	0.46758	D	0.000271	T	0.70988	0.3287	L	0.61036	1.89	0.58432	D	0.999999	B;B	0.33940	0.433;0.092	B;B	0.28916	0.068;0.096	T	0.71646	-0.4530	10	0.42905	T	0.14	-9.9134	15.8615	0.79026	0.0:0.0:0.0:1.0	.	1354;1354	F8W8M9;O14795	.;UN13B_HUMAN	A	1366;1354;1354;941	ENSP00000380006:V1366A;ENSP00000367756:V1354A;ENSP00000367757:V1354A	ENSP00000367756:V1354A	V	+	2	0	UNC13B	35389698	1.000000	0.71417	0.911000	0.35937	0.973000	0.67179	7.781000	0.85668	2.333000	0.79357	0.533000	0.62120	GTC		0.532	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377	
UNC13B	10497	broad.mit.edu	37	9	35403891	35403891	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:35403891G>A	ENST00000378495.3	+	39	4859	c.4637G>A	c.(4636-4638)tGc>tAc	p.C1546Y	UNC13B_ENST00000396787.1_Missense_Mutation_p.C1577Y|UNC13B_ENST00000378496.4_Missense_Mutation_p.C1565Y|ATP8B5P_ENST00000430846.1_RNA	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)	1546					apoptotic process (GO:0006915)|excretion (GO:0007588)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synaptic vesicle priming (GO:0010808)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|terminal bouton (GO:0043195)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(16)|liver(2)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			GCCTGCTGGTGCCCCTTGGGC	0.562																																					p.C1546Y												.	.	0			c.G4637A	9						.						86.0	86.0	86.0					9																	35403891		2203	4300	6503	35393891	SO:0001583	missense	10497	exon39			AF020202	CCDS6579.1	9p13.3	2008-05-15	2003-10-17	2003-10-17	ENSG00000198722	ENSG00000198722			12566	protein-coding gene	gene with protein product		605836	"""unc-13-like (C. elegans)"""	UNC13		9607201	Standard	NM_006377		Approved	hmunc13, Unc13h2	uc003zwq.3	O14795	OTTHUMG00000019856	ENST00000378495.3:c.4637G>A	9.37:g.35403891G>A	ENSP00000367756:p.Cys1546Tyr	None		Capture	Illumina HiSeq	Phase_I	35393891	NM_006377	Q5VYM8	Missense_Mutation	SNP	ENST00000378495.3	37	CCDS6579.1	.	.	.	.	.	.	.	.	.	.	G	14.08	2.429621	0.43122	.	.	ENSG00000198722	ENST00000396787;ENST00000378495;ENST00000378496;ENST00000535471	T;T;T	0.73789	-0.78;-0.78;-0.78	6.17	5.28	0.74379	C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.74764	0.3759	L	0.31752	0.955	0.49483	D	0.999798	D;B	0.89917	1.0;0.007	D;B	0.91635	0.999;0.005	T	0.69866	-0.5029	10	0.09843	T	0.71	-14.3349	10.3351	0.43846	0.0668:0.0:0.7988:0.1343	.	1565;1546	F8W8M9;O14795	.;UN13B_HUMAN	Y	1577;1546;1565;1152	ENSP00000380006:C1577Y;ENSP00000367756:C1546Y;ENSP00000367757:C1565Y	ENSP00000367756:C1546Y	C	+	2	0	UNC13B	35393891	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	2.948000	0.49066	1.635000	0.50512	0.655000	0.94253	TGC		0.562	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377	
FBXO10	26267	broad.mit.edu	37	9	37537509	37537509	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:37537509C>A	ENST00000432825.2	-	3	1065	c.1017G>T	c.(1015-1017)gaG>gaT	p.E339D	FBXO10_ENST00000541829.1_Intron|RP11-613M10.8_ENST00000544475.1_5'UTR|FBXO10_ENST00000543968.1_5'Flank	NM_012166.2	NP_036298.2	Q9UK96	FBX10_HUMAN	F-box protein 10	339					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.E339D(1)		breast(1)|endometrium(5)|large_intestine(11)|lung(15)|prostate(1)|upper_aerodigestive_tract(1)	34				GBM - Glioblastoma multiforme(29;0.0107)		CACTACCCACCTCTGCCTCCT	0.602																																					p.E339D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1017T	9						.						22.0	24.0	23.0					9																	37537509		2095	4210	6305	37527509	SO:0001583	missense	26267	exon3			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.1017G>T	9.37:g.37537509C>A	ENSP00000403802:p.Glu339Asp	Somatic		Capture	Illumina HiSeq	Phase_I	37527509	NM_012166	Q08AL3|Q08AL4|Q5JRT8|Q9UKC3	Missense_Mutation	SNP	ENST00000432825.2	37	CCDS47966.1	.	.	.	.	.	.	.	.	.	.	C	8.558	0.877071	0.17395	.	.	ENSG00000147912	ENST00000432825	T	0.46063	0.88	5.49	-1.07	0.09968	.	0.191466	0.44483	D	0.000451	T	0.20861	0.0502	N	0.19112	0.55	0.24925	N	0.991959	B	0.25667	0.131	B	0.22386	0.039	T	0.19679	-1.0298	10	0.18710	T	0.47	-30.5384	7.8836	0.29637	0.1013:0.5079:0.0:0.3908	.	339	Q9UK96	FBX10_HUMAN	D	339	ENSP00000403802:E339D	ENSP00000276960:E339D	E	-	3	2	FBXO10	37527509	0.005000	0.15991	0.994000	0.49952	0.862000	0.49288	0.424000	0.21330	-0.164000	0.10927	-0.797000	0.03246	GAG		0.602	FBXO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052472.3		
TRPM3	80036	broad.mit.edu	37	9	73151090	73151090	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:73151090C>T	ENST00000377110.3	-	25	5146	c.4903G>A	c.(4903-4905)Gcc>Acc	p.A1635T	TRPM3_ENST00000423814.3_Missense_Mutation_p.A1662T|TRPM3_ENST00000377111.2_Intron|TRPM3_ENST00000358082.3_Missense_Mutation_p.A1497T|TRPM3_ENST00000396280.5_Missense_Mutation_p.A1484T|TRPM3_ENST00000408909.2_Missense_Mutation_p.A1494T|TRPM3_ENST00000377106.1_Missense_Mutation_p.A1507T|TRPM3_ENST00000396292.4_Missense_Mutation_p.A1507T|TRPM3_ENST00000357533.2_Missense_Mutation_p.A1639T|TRPM3_ENST00000396285.1_Missense_Mutation_p.A1494T|TRPM3_ENST00000360823.2_Missense_Mutation_p.A1497T|TRPM3_ENST00000377105.1_Missense_Mutation_p.A1494T			Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	1660					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)	p.A1507T(1)		NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						TAGCTGTTGGCGCGCTCTATC	0.552																																					p.A1635T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4903A	9						.						404.0	386.0	392.0					9																	73151090		2203	4300	6503	72340910	SO:0001583	missense	80036	exon25			AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17992	protein-coding gene	gene with protein product	"""melastatin 2"""	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377110.3:c.4903G>A	9.37:g.73151090C>T	ENSP00000366314:p.Ala1635Thr	Somatic		Capture	Illumina HiSeq	Phase_I	72340910	NM_001007471	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Missense_Mutation	SNP	ENST00000377110.3	37	CCDS43835.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.88|17.88	3.497094|3.497094	0.64186|0.64186	.|.	.|.	ENSG00000083067|ENSG00000083067	ENST00000377110;ENST00000377106;ENST00000360823;ENST00000377105;ENST00000357533;ENST00000408909;ENST00000396285;ENST00000396292;ENST00000358082;ENST00000423814|ENST00000396280	T;T;T;T;T;T;T;T;T;T|T	0.59364|0.70045	0.39;0.3;0.29;0.27;0.39;0.27;0.3;0.3;0.29;0.38|-0.45	5.77|5.77	5.77|5.77	0.91146|0.91146	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.69522|0.69522	0.3120|0.3120	L|L	0.27053|0.27053	0.805|0.805	0.58432|0.58432	D|D	0.999998|0.999998	D;D;P;D;D;D;D|.	0.76494|.	0.999;0.994;0.48;0.999;0.999;0.999;0.999|.	D;P;B;D;D;D;D|.	0.80764|.	0.994;0.736;0.068;0.978;0.99;0.99;0.978|.	T|T	0.71646|0.71646	-0.4530|-0.4530	10|7	0.05525|0.72032	T|D	0.97|0.01	-19.3908|-19.3908	19.9981|19.9981	0.97395|0.97395	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1635;1625;1639;1497;1494;1607;1494|.	Q9HCF6-2;Q9HCF6-4;A2A3F7;A2A3F4;G5E9G1;Q9HCF6-8;A2A3F3|.	.;.;.;.;.;.;.|.	T|H	1635;1507;1497;1494;1639;1494;1494;1507;1497;1662|1483	ENSP00000366314:A1635T;ENSP00000366310:A1507T;ENSP00000354066:A1497T;ENSP00000366309:A1494T;ENSP00000350140:A1639T;ENSP00000386127:A1494T;ENSP00000379581:A1494T;ENSP00000379587:A1507T;ENSP00000350791:A1497T;ENSP00000389542:A1662T|ENSP00000379576:R1483H	ENSP00000350140:A1639T|ENSP00000379576:R1483H	A|R	-|-	1|2	0|0	TRPM3|TRPM3	72340910|72340910	1.000000|1.000000	0.71417|0.71417	0.980000|0.980000	0.43619|0.43619	0.987000|0.987000	0.75469|0.75469	7.294000|7.294000	0.78760|0.78760	2.729000|2.729000	0.93468|0.93468	0.655000|0.655000	0.94253|0.94253	GCC|CGC		0.552	TRPM3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214158.3	NM_206945	
TLE4	7091	broad.mit.edu	37	9	82242304	82242304	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:82242304G>A	ENST00000376552.2	+	6	1349	c.331G>A	c.(331-333)Gtg>Atg	p.V111M	TLE4_ENST00000265284.6_Intron|TLE4_ENST00000455913.1_3'UTR|TLE4_ENST00000376544.3_Missense_Mutation_p.V111M|TLE4_ENST00000376537.4_Missense_Mutation_p.V111M|TLE4_ENST00000376520.4_Missense_Mutation_p.V111M|TLE4_ENST00000376534.4_5'UTR	NM_007005.3	NP_008936.2	Q04727	TLE4_HUMAN	transducin-like enhancer of split 4	111	Gln-rich (Q 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.V111M(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						GCAACAAGTGGTGCAGGCTGT	0.438																																					p.V111M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G331A	9						.						152.0	156.0	155.0					9																	82242304		2196	4299	6495	81432124	SO:0001583	missense	7091	exon6			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.331G>A	9.37:g.82242304G>A	ENSP00000365735:p.Val111Met	Somatic		Capture	Illumina HiSeq	Phase_I	81432124	NM_007005	F8W6T6|Q3ZCS1|Q5T1Y2|Q6PCB3|Q9BZ07|Q9BZ08|Q9BZ09|Q9NSL3|Q9ULF9	De_novo_Start_OutOfFrame	SNP	ENST00000376552.2	37	CCDS43837.1	.	.	.	.	.	.	.	.	.	.	G	15.47	2.843671	0.51164	.	.	ENSG00000106829	ENST00000376552;ENST00000376544;ENST00000376520;ENST00000399288;ENST00000435650;ENST00000414465;ENST00000376537;ENST00000425506;ENST00000428713	T;T;T;T;T;T;T	0.49432	0.79;0.78;0.84;0.81;0.84;0.84;1.4	5.57	5.57	0.84162	Groucho/TLE, N-terminal Q-rich domain (1);	0.000000	0.85682	D	0.000000	T	0.64897	0.2640	L	0.53249	1.67	0.80722	D	1	D;P;P	0.71674	0.998;0.723;0.87	D;P;P	0.65443	0.935;0.751;0.675	T	0.63462	-0.6632	10	0.49607	T	0.09	-16.3522	19.5503	0.95314	0.0:0.0:1.0:0.0	.	111;111;111	Q04727-2;Q04727-3;Q04727	.;.;TLE4_HUMAN	M	111;111;111;111;111;96;111;109;96	ENSP00000365735:V111M;ENSP00000365727:V111M;ENSP00000365703:V111M;ENSP00000415423:V111M;ENSP00000365720:V111M;ENSP00000412567:V109M;ENSP00000409313:V96M	ENSP00000365703:V111M	V	+	1	0	TLE4	81432124	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.009000	0.88606	2.619000	0.88677	0.561000	0.74099	GTG		0.438	TLE4-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052792.4	XM_212237	
NTRK2	4915	broad.mit.edu	37	9	87570408	87570408	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:87570408C>T	ENST00000323115.4	+	15	2453	c.2100C>T	c.(2098-2100)gaC>gaT	p.D700D	NTRK2_ENST00000277120.3_Silent_p.D716D|NTRK2_ENST00000376214.1_Silent_p.D716D|NTRK2_ENST00000376213.1_Silent_p.D700D			Q16620	NTRK2_HUMAN	neurotrophic tyrosine kinase, receptor, type 2	700	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of adenylate cyclase activity (GO:0007190)|aging (GO:0007568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|central nervous system neuron development (GO:0021954)|cerebral cortex development (GO:0021987)|circadian rhythm (GO:0007623)|feeding behavior (GO:0007631)|glutamate secretion (GO:0014047)|learning (GO:0007612)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mechanoreceptor differentiation (GO:0042490)|negative regulation of anoikis (GO:2000811)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular junction development (GO:0007528)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peripheral nervous system neuron development (GO:0048935)|positive regulation of axonogenesis (GO:0050772)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|regulation of dendrite development (GO:0050773)|regulation of neurotransmitter secretion (GO:0046928)|regulation of protein kinase B signaling (GO:0051896)|regulation of Rac GTPase activity (GO:0032314)|response to auditory stimulus (GO:0010996)|retinal rod cell development (GO:0046548)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vasculogenesis (GO:0001570)	cell surface (GO:0009986)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endosome (GO:0005768)|excitatory synapse (GO:0060076)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|receptor complex (GO:0043235)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|brain-derived neurotrophic factor binding (GO:0048403)|brain-derived neurotrophic factor-activated receptor activity (GO:0060175)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)	p.D716D(2)		breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	46					Amitriptyline(DB00321)	TGTCCCGGGACGTGTACAGCA	0.587										TSP Lung(25;0.17)																											p.D716D												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C2148T	9						.						50.0	51.0	50.0					9																	87570408		2203	4300	6503	86760228	SO:0001819	synonymous_variant	4915	exon19			AF410902	CCDS6671.1, CCDS35050.1, CCDS35051.1, CCDS35052.1, CCDS35053.1	9q22.1	2013-01-11			ENSG00000148053	ENSG00000148053	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"""	8032	protein-coding gene	gene with protein product		600456				7789988	Standard	NM_001018065		Approved	TRKB	uc004anz.1	Q16620	OTTHUMG00000020120	ENST00000323115.4:c.2100C>T	9.37:g.87570408C>T		Somatic		Capture	Illumina HiSeq	Phase_I	86760228	NM_006180	B1ANZ4|B4DFV9|Q16675|Q59GJ1|Q8WXJ5|Q8WXJ6|Q8WXJ7	Silent	SNP	ENST00000323115.4	37	CCDS35050.1																																																																																				0.587	NTRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052882.1		
DAPK1	1612	broad.mit.edu	37	9	90321833	90321833	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:90321833A>G	ENST00000408954.3	+	26	4182	c.3847A>G	c.(3847-3849)Atg>Gtg	p.M1283V	DAPK1_ENST00000472284.1_Missense_Mutation_p.M1283V|DAPK1_ENST00000491893.1_Missense_Mutation_p.M1217V|DAPK1_ENST00000469640.2_Missense_Mutation_p.M1308V|DAPK1_ENST00000358077.5_Missense_Mutation_p.M1283V	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	1283					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.M1284V(1)|p.M1283V(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						CAGCAGCATCATGTGCTTCGG	0.562									Chronic Lymphocytic Leukemia, Familial Clustering of																												p.M1283V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A3847G	9						.						54.0	63.0	60.0					9																	90321833		2145	4242	6387	89511653	SO:0001583	missense	1612	exon26	Familial Cancer Database	Familial CLL	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"""Ankyrin repeat domain containing"""	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.3847A>G	9.37:g.90321833A>G	ENSP00000386135:p.Met1283Val	Somatic		Capture	Illumina HiSeq	Phase_I	89511653	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Missense_Mutation	SNP	ENST00000408954.3	37	CCDS43842.1	.	.	.	.	.	.	.	.	.	.	A	0.043	-1.275901	0.01410	.	.	ENSG00000196730	ENST00000358077;ENST00000472284;ENST00000469640;ENST00000408954;ENST00000491893	T;T;T;T;T	0.62105	0.05;0.05;0.06;0.05;0.07	5.66	4.51	0.55191	.	0.251095	0.28047	N	0.016811	T	0.29882	0.0747	N	0.02916	-0.46	0.25008	N	0.991424	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.27088	-1.0084	10	0.02654	T	1	.	8.1691	0.31243	0.5004:0.3822:0.0:0.1175	.	1217;1283;1283	B7ZLE7;P53355-3;P53355	.;.;DAPK1_HUMAN	V	1283;1283;1308;1283;1217	ENSP00000350785:M1283V;ENSP00000417076:M1283V;ENSP00000418885:M1308V;ENSP00000386135:M1283V;ENSP00000419026:M1217V	ENSP00000350785:M1283V	M	+	1	0	DAPK1	89511653	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	2.244000	0.43124	1.063000	0.40649	-0.313000	0.08912	ATG		0.562	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	90500343	90500343	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:90500343C>T	ENST00000325643.5	+	4	1007	c.941C>T	c.(940-942)aCc>aTc	p.T314I		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	314					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)		p.T314I(1)									GAGGCTGCCACCACCTGGGGC	0.622																																					p.T314I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C941T	9						.						35.0	39.0	38.0					9																	90500343		2203	4300	6503	89690163	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.941C>T	9.37:g.90500343C>T	ENSP00000322640:p.Thr314Ile	Somatic		Capture	Illumina HiSeq	Phase_I	89690163	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Missense_Mutation	SNP	ENST00000325643.5	37	CCDS6676.1	.	.	.	.	.	.	.	.	.	.	.	11.60	1.685718	0.29962	.	.	ENSG00000177992	ENST00000325643	T	0.03468	3.92	2.19	-1.82	0.07857	.	0.951207	0.08642	N	0.915423	T	0.05731	0.0150	L	0.44542	1.39	0.09310	N	1	D	0.57899	0.981	P	0.52957	0.714	T	0.30794	-0.9966	10	0.41790	T	0.15	.	3.152	0.06492	0.4169:0.2587:0.3244:0.0	.	314	Q6ZUB1	CI079_HUMAN	I	314	ENSP00000322640:T314I	ENSP00000322640:T314I	T	+	2	0	C9orf79	89690163	0.008000	0.16893	0.000000	0.03702	0.002000	0.02628	0.059000	0.14322	-0.442000	0.07190	-0.474000	0.04947	ACC		0.622	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828	
SEMA4D	10507	broad.mit.edu	37	9	92006307	92006307	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:92006307C>T	ENST00000450295.1	-	9	1422	c.646G>A	c.(646-648)Gtg>Atg	p.V216M	SEMA4D_ENST00000438547.2_Missense_Mutation_p.V216M|SEMA4D_ENST00000420987.1_Missense_Mutation_p.V216M|SEMA4D_ENST00000422704.2_Missense_Mutation_p.V216M|SEMA4D_ENST00000356444.2_Missense_Mutation_p.V216M|SEMA4D_ENST00000343780.4_Missense_Mutation_p.V216M|SEMA4D_ENST00000339861.4_Missense_Mutation_p.V216M|SEMA4D_ENST00000455551.2_Missense_Mutation_p.V216M			Q92854	SEM4D_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	216	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.V216M(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						TTTCGGATCACGTCAGCAAAC	0.562																																					p.V216M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G646A	9						.						134.0	114.0	121.0					9																	92006307		2203	4300	6503	91196127	SO:0001583	missense	10507	exon11			U60800	CCDS6685.1, CCDS47991.1	9q22-q31	2013-01-11			ENSG00000187764	ENSG00000187764		"""Semaphorins"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10732	protein-coding gene	gene with protein product	"""M-sema G"""	601866	"""chromosome 9 open reading frame 164"""	SEMAJ, C9orf164		8876214, 8969198	Standard	NM_006378		Approved	CD100, coll-4, FLJ39737	uc004aqo.1	Q92854	OTTHUMG00000020185	ENST00000450295.1:c.646G>A	9.37:g.92006307C>T	ENSP00000416523:p.Val216Met	Somatic		Capture	Illumina HiSeq	Phase_I	91196127	NM_001142287	B2RPM6|Q7Z5S4|Q8N8B0	Missense_Mutation	SNP	ENST00000450295.1	37	CCDS6685.1	.	.	.	.	.	.	.	.	.	.	C	17.19	3.325876	0.60743	.	.	ENSG00000187764	ENST00000339861;ENST00000420987;ENST00000455551;ENST00000343780;ENST00000450295;ENST00000438547;ENST00000356444;ENST00000422704	T;T;T;T;T;T;T;T	0.31769	1.48;1.48;1.48;1.48;1.48;1.48;1.48;1.48	5.17	5.17	0.71159	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.51261	0.1664	L	0.49640	1.575	0.80722	D	1	D;D	0.89917	0.986;1.0	P;D	0.75020	0.528;0.985	T	0.45775	-0.9238	10	0.51188	T	0.08	.	18.853	0.92240	0.0:1.0:0.0:0.0	.	216;216	Q92854-2;Q92854	.;SEM4D_HUMAN	M	216	ENSP00000344923:V216M;ENSP00000391733:V216M;ENSP00000411981:V216M;ENSP00000343418:V216M;ENSP00000416523:V216M;ENSP00000405102:V216M;ENSP00000348822:V216M;ENSP00000388768:V216M	ENSP00000344923:V216M	V	-	1	0	SEMA4D	91196127	1.000000	0.71417	0.977000	0.42913	0.020000	0.10135	4.437000	0.59955	2.700000	0.92200	0.561000	0.74099	GTG		0.562	SEMA4D-018	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342411.1	NM_006378	
PTCH1	5727	broad.mit.edu	37	9	98231267	98231267	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:98231267C>T	ENST00000331920.6	-	14	2315	c.2016G>A	c.(2014-2016)acG>acA	p.T672T	PTCH1_ENST00000418258.1_Silent_p.T521T|PTCH1_ENST00000437951.1_Silent_p.T606T|PTCH1_ENST00000429896.2_Silent_p.T521T|PTCH1_ENST00000421141.1_Silent_p.T521T|PTCH1_ENST00000375274.2_Silent_p.T671T|PTCH1_ENST00000430669.2_Silent_p.T606T	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	672					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.T672T(4)|p.T671T(3)		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)				AGTACACGTGCGTGTGGGGGT	0.627																																					p.T521T												.	.	7	Substitution - coding silent(7)	large_intestine(7)	c.G1563A	9	GRCh37	CI050947	PTCH1	I		.						160.0	147.0	152.0					9																	98231267		2203	4300	6503	97271088	SO:0001819	synonymous_variant	5727	exon14			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.2016G>A	9.37:g.98231267C>T		Somatic		Capture	Illumina HiSeq	Phase_I	97271088	NM_001083605	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Silent	SNP	ENST00000331920.6	37	CCDS6714.1																																																																																				0.627	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264	
C9orf156	51531	broad.mit.edu	37	9	100672810	100672810	+	Silent	SNP	C	C	T	rs571150996		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:100672810C>T	ENST00000375119.3	-	4	574	c.498G>A	c.(496-498)ccG>ccA	p.P166P	C9orf156_ENST00000478126.1_5'UTR	NM_016481.3	NP_057565.3	Q9BU70	NAP1_HUMAN	chromosome 9 open reading frame 156	166	TsaA-like. {ECO:0000255|PROSITE- ProRule:PRU01003}.				viral process (GO:0016032)		hydrolase activity (GO:0016787)	p.P166P(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|prostate(1)|skin(1)	13		Acute lymphoblastic leukemia(62;0.158)				TCACATTTTGCGGTGAGTCAT	0.433													C|||	1	0.000199681	0.0	0.0	5008	,	,		21955	0.0		0.0	False		,,,				2504	0.001				p.P166P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G498A	9						.						138.0	132.0	134.0					9																	100672810		2203	4300	6503	99712631	SO:0001819	synonymous_variant	51531	exon4			AK023069	CCDS6730.1	9q31.1	2011-03-02			ENSG00000136932	ENSG00000136932			30967	protein-coding gene	gene with protein product	"""Nef (lentivirus myristoylated factor) associated protein 1"""						Standard	NM_016481		Approved	HSPC219, NAP1	uc004axv.1	Q9BU70	OTTHUMG00000021007	ENST00000375119.3:c.498G>A	9.37:g.100672810C>T		Somatic		Capture	Illumina HiSeq	Phase_I	99712631	NM_016481	Q5T113|Q86SK0|Q9NXJ7|Q9P0Q7	Silent	SNP	ENST00000375119.3	37	CCDS6730.1																																																																																				0.433	C9orf156-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055401.1	NM_016481	
MAN1B1	11253	broad.mit.edu	37	9	139994310	139994310	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chr9:139994310T>C	ENST00000371589.4	+	6	966	c.893T>C	c.(892-894)aTg>aCg	p.M298T	MAN1B1_ENST00000474902.1_Start_Codon_SNP_p.M1T	NM_016219.4	NP_057303.2	Q9UKM7	MA1B1_HUMAN	mannosidase, alpha, class 1B, member 1	298					cellular protein metabolic process (GO:0044267)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum quality control compartment (GO:0044322)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)	p.M298T(1)		autonomic_ganglia(1)|central_nervous_system(2)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(2)	14	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;3.08e-05)|Epithelial(140;0.000513)		CTGGACACCATGTGGATCTTG	0.602																																					p.M298T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T893C	9						.						154.0	133.0	140.0					9																	139994310		2203	4300	6503	139114131	SO:0001583	missense	11253	exon6			AF145732	CCDS7029.1	9q34.3	2014-05-27			ENSG00000177239	ENSG00000177239			6823	protein-coding gene	gene with protein product	"""endoplasmic reticulum alpha-mannosidase 1"", ""alpha 1,2-mannosidase"", ""endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase 1"", ""ER alpha 1,2-mannosidase"", ""Man9GlcNAc2-specific processing alpha-mannosidase"""	604346				10409699, 10521544	Standard	NM_016219		Approved	MANA-ER, MRT15	uc004cld.3	Q9UKM7	OTTHUMG00000020978	ENST00000371589.4:c.893T>C	9.37:g.139994310T>C	ENSP00000360645:p.Met298Thr	Somatic		Capture	Illumina HiSeq	Phase_I	139114131	NM_016219	Q5VSG3|Q9BRS9|Q9Y5K7	Missense_Mutation	SNP	ENST00000371589.4	37	CCDS7029.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.111290	0.77210	.	.	ENSG00000177239	ENST00000371589;ENST00000474902	T;T	0.72167	-0.63;-0.63	4.79	4.79	0.61399	.	0.000000	0.85682	U	0.000000	D	0.86431	0.5931	M	0.91818	3.245	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;0.994;0.99	D;D;D;D	0.79784	0.993;0.991;0.967;0.962	D	0.89353	0.3662	9	.	.	.	-35.5349	13.4846	0.61357	0.0:0.0:0.0:1.0	.	199;262;298;199	B4DPS9;B4DR05;Q9UKM7;Q68D80	.;.;MA1B1_HUMAN;.	T	298;1	ENSP00000360645:M298T;ENSP00000447256:M1T	.	M	+	2	0	MAN1B1	139114131	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.746000	0.85057	1.801000	0.52704	0.459000	0.35465	ATG		0.602	MAN1B1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055294.2	NM_016219	
RAB9B	51209	broad.mit.edu	37	X	103080335	103080335	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:103080335T>C	ENST00000243298.2	-	3	664	c.380A>G	c.(379-381)gAc>gGc	p.D127G		NM_016370.2	NP_057454.1	Q9NP90	RAB9B_HUMAN	RAB9B, member RAS oncogene family	127					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)	p.D127G(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(11)	14						ATCCTCTTTGTCTACCTTGTT	0.428																																					p.D127G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A380G	X						.						220.0	213.0	215.0					X																	103080335		2203	4300	6503	102966991	SO:0001583	missense	51209	exon3			AB036693	CCDS14515.1	Xq22.1-q22.3	2010-04-19			ENSG00000123570	ENSG00000123570		"""RAB, member RAS oncogene"""	14090	protein-coding gene	gene with protein product		300285				11043518	Standard	NM_016370		Approved	RAB9L	uc004ell.2	Q9NP90	OTTHUMG00000022112	ENST00000243298.2:c.380A>G	X.37:g.103080335T>C	ENSP00000243298:p.Asp127Gly	Somatic		Capture	Illumina HiSeq	Phase_I	102966991	NM_016370	B2R8M0|Q52LX2	Missense_Mutation	SNP	ENST00000243298.2	37	CCDS14515.1	.	.	.	.	.	.	.	.	.	.	T	17.43	3.387904	0.61956	.	.	ENSG00000123570	ENST00000243298	D	0.89939	-2.59	5.51	5.51	0.81932	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.96700	0.8923	H	0.98883	4.36	0.80722	D	1	D	0.71674	0.998	D	0.79108	0.992	D	0.97679	1.0171	10	0.87932	D	0	-0.6831	12.4598	0.55725	0.0:0.0:0.0:1.0	.	127	Q9NP90	RAB9B_HUMAN	G	127	ENSP00000243298:D127G	ENSP00000243298:D127G	D	-	2	0	RAB9B	102966991	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.036000	0.88901	1.849000	0.53698	0.486000	0.48141	GAC		0.428	RAB9B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057746.1		
PSMD10	5716	broad.mit.edu	37	X	107331191	107331191	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:107331191T>C	ENST00000217958.3	-	3	449	c.352A>G	c.(352-354)Agg>Ggg	p.R118G	PSMD10_ENST00000372296.1_Missense_Mutation_p.R77G|PSMD10_ENST00000361815.5_Missense_Mutation_p.R118G|PSMD10_ENST00000372295.1_Missense_Mutation_p.R77G|PSMD10_ENST00000340200.5_Missense_Mutation_p.R85G	NM_002814.3|NM_170750.2	NP_002805.1|NP_736606.1	O75832	PSD10_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 10	118	Interaction with RELA.				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)|cytoplasmic sequestering of NF-kappaB (GO:0007253)|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 DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of cell growth (GO:0030307)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome regulatory particle assembly (GO:0070682)|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)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	transcription factor binding (GO:0008134)	p.R118G(1)		endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9						ACCTCATGCCTGTTTTTCGAA	0.413																																					p.R118G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A352G	X						.						190.0	171.0	178.0					X																	107331191		2203	4300	6503	107217847	SO:0001583	missense	5716	exon3			AB009619	CCDS14536.1, CCDS14537.1	Xq22.3	2013-01-10			ENSG00000101843	ENSG00000101843		"""Proteasome (prosome, macropain) subunits"", ""Ankyrin repeat domain containing"""	9555	protein-coding gene	gene with protein product	"""gankyrin"""	300880				9714768	Standard	NM_002814		Approved	p28	uc004enp.2	O75832	OTTHUMG00000022177	ENST00000217958.3:c.352A>G	X.37:g.107331191T>C	ENSP00000217958:p.Arg118Gly	Somatic		Capture	Illumina HiSeq	Phase_I	107217847	NM_002814	Q5U0B2|Q8IZK9	Missense_Mutation	SNP	ENST00000217958.3	37	CCDS14536.1	.	.	.	.	.	.	.	.	.	.	T	13.91	2.376603	0.42105	.	.	ENSG00000101843	ENST00000217958;ENST00000372296;ENST00000372295;ENST00000361815;ENST00000340200	T;T;T;T;T	0.66460	-0.05;-0.05;-0.14;-0.05;-0.21	4.73	4.73	0.59995	Ankyrin repeat-containing domain (3);	0.188205	0.48767	D	0.000174	T	0.65668	0.2713	M	0.67953	2.075	0.39215	D	0.963394	B;B	0.32071	0.355;0.313	B;B	0.36134	0.218;0.107	T	0.65463	-0.6162	10	0.25751	T	0.34	-4.7849	13.4162	0.60970	0.0:0.0:0.0:1.0	.	118;118	Q8IZK9;O75832	.;PSD10_HUMAN	G	118;77;77;118;85	ENSP00000217958:R118G;ENSP00000361370:R77G;ENSP00000361369:R77G;ENSP00000354906:R118G;ENSP00000345963:R85G	ENSP00000217958:R118G	R	-	1	2	PSMD10	107217847	1.000000	0.71417	0.998000	0.56505	0.960000	0.62799	2.906000	0.48735	1.739000	0.51704	0.417000	0.27973	AGG		0.413	PSMD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057868.1	NM_170750	
TRPC5	7224	broad.mit.edu	37	X	111155731	111155731	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:111155731G>A	ENST00000262839.2	-	3	1606	c.688C>T	c.(688-690)Ctc>Ttc	p.L230F		NM_012471.2	NP_036603.1	Q9UL62	TRPC5_HUMAN	transient receptor potential cation channel, subfamily C, member 5	230					axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|nervous system development (GO:0007399)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)	p.L230F(1)		biliary_tract(1)|breast(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(38)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						ACCTTGCTGAGCTCCTTGAGC	0.547																																					p.L230F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C688T	X						.						164.0	154.0	157.0					X																	111155731		2203	4300	6503	111042387	SO:0001583	missense	7224	exon3			AF054568	CCDS14561.1	Xq23	2014-06-13			ENSG00000072315	ENSG00000072315		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12337	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 159"""	300334				10493832, 16382100	Standard	NM_012471		Approved	PPP1R159	uc004epl.1	Q9UL62	OTTHUMG00000022212	ENST00000262839.2:c.688C>T	X.37:g.111155731G>A	ENSP00000262839:p.Leu230Phe	Somatic		Capture	Illumina HiSeq	Phase_I	111042387	NM_012471	B2RP53|O75233|Q5JXY8|Q9Y514	Missense_Mutation	SNP	ENST00000262839.2	37	CCDS14561.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.810344	0.90707	.	.	ENSG00000072315	ENST00000262839	D	0.86297	-2.1	5.79	5.79	0.91817	Transient receptor potential II (1);	0.000000	0.85682	D	0.000000	D	0.95850	0.8649	H	0.95294	3.65	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96888	0.9651	10	0.87932	D	0	-15.7798	18.9736	0.92725	0.0:0.0:1.0:0.0	.	231;230	Q59G51;Q9UL62	.;TRPC5_HUMAN	F	230	ENSP00000262839:L230F	ENSP00000262839:L230F	L	-	1	0	TRPC5	111042387	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.869000	0.99810	2.429000	0.82318	0.513000	0.50165	CTC		0.547	TRPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057945.1	NM_012471	
DOCK11	139818	broad.mit.edu	37	X	117699982	117699982	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:117699982C>T	ENST00000276202.7	+	8	771	c.708C>T	c.(706-708)cgC>cgT	p.R236R	DOCK11_ENST00000276204.6_Silent_p.R236R	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	236	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R236R(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						CCAAAATGCGCCGTCATGCTT	0.343																																					p.R236R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C708T	X						.						129.0	128.0	129.0					X																	117699982		2203	4300	6503	117584010	SO:0001819	synonymous_variant	139818	exon8			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.708C>T	X.37:g.117699982C>T		Somatic		Capture	Illumina HiSeq	Phase_I	117584010	NM_144658	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Silent	SNP	ENST00000276202.7	37	CCDS35373.1																																																																																				0.343	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658	
ACTRT1	139741	broad.mit.edu	37	X	127185123	127185123	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:127185123G>A	ENST00000371124.3	-	1	1259	c.1063C>T	c.(1063-1065)Cag>Tag	p.Q355*		NM_138289.3	NP_612146.1	Q8TDG2	ACTT1_HUMAN	actin-related protein T1	355						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.Q355*(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(13)|ovary(2)|skin(3)	34						ACCCACATCTGCTTGAAACTG	0.473																																					p.Q355X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1063T	X						.						172.0	146.0	155.0					X																	127185123		2203	4300	6503	127012804	SO:0001587	stop_gained	139741	exon1			AF440739	CCDS14611.1	Xq25	2008-02-05	2005-11-22		ENSG00000123165	ENSG00000123165			24027	protein-coding gene	gene with protein product		300487				12243744	Standard	NM_138289		Approved	AIP1, KIAA0705, ARIP1, Arp-T1	uc004eum.3	Q8TDG2	OTTHUMG00000022359	ENST00000371124.3:c.1063C>T	X.37:g.127185123G>A	ENSP00000360165:p.Gln355*	Somatic		Capture	Illumina HiSeq	Phase_I	127012804	NM_138289	Q6X7C1|Q96L10	Nonsense_Mutation	SNP	ENST00000371124.3	37	CCDS14611.1	.	.	.	.	.	.	.	.	.	.	G	15.70	2.910802	0.52439	.	.	ENSG00000123165	ENST00000371124	.	.	.	3.58	0.63	0.17693	.	0.105804	0.41001	D	0.000976	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	2.922	0.05772	0.1111:0.1736:0.5346:0.1808	.	.	.	.	X	355	.	ENSP00000360165:Q355X	Q	-	1	0	ACTRT1	127012804	1.000000	0.71417	0.028000	0.17463	0.080000	0.17528	1.992000	0.40737	0.007000	0.14760	-0.191000	0.12829	CAG		0.473	ACTRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058192.1	NM_138289	
ACTRT1	139741	broad.mit.edu	37	X	127185349	127185349	+	Silent	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:127185349G>T	ENST00000371124.3	-	1	1033	c.837C>A	c.(835-837)gtC>gtA	p.V279V		NM_138289.3	NP_612146.1	Q8TDG2	ACTT1_HUMAN	actin-related protein T1	279						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.V279V(2)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(13)|ovary(2)|skin(3)	34						TGCTGCTGGAGACCATTTTTG	0.522																																					p.V279V												.	.	2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	c.C837A	X						.						107.0	102.0	104.0					X																	127185349		2203	4300	6503	127013030	SO:0001819	synonymous_variant	139741	exon1			AF440739	CCDS14611.1	Xq25	2008-02-05	2005-11-22		ENSG00000123165	ENSG00000123165			24027	protein-coding gene	gene with protein product		300487				12243744	Standard	NM_138289		Approved	AIP1, KIAA0705, ARIP1, Arp-T1	uc004eum.3	Q8TDG2	OTTHUMG00000022359	ENST00000371124.3:c.837C>A	X.37:g.127185349G>T		Somatic		Capture	Illumina HiSeq	Phase_I	127013030	NM_138289	Q6X7C1|Q96L10	Silent	SNP	ENST00000371124.3	37	CCDS14611.1																																																																																				0.522	ACTRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058192.1	NM_138289	
AIFM1	9131	broad.mit.edu	37	X	129283454	129283454	+	Silent	SNP	G	G	A	rs368967639		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:129283454G>A	ENST00000287295.3	-	3	569	c.339C>T	c.(337-339)gcC>gcT	p.A113A	AIFM1_ENST00000535724.1_Silent_p.A26A|AIFM1_ENST00000319908.3_Silent_p.A109A|AIFM1_ENST00000346424.2_Intron	NM_001130847.3|NM_004208.3	NP_001124319.1|NP_004199.1	O95831	AIFM1_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 1	113					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cell redox homeostasis (GO:0045454)|chromosome condensation (GO:0030261)|DNA catabolic process (GO:0006308)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitochondrial respiratory chain complex I assembly (GO:0032981)|neuron apoptotic process (GO:0051402)|neuron differentiation (GO:0030182)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic DNA fragmentation (GO:1902510)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|electron carrier activity (GO:0009055)|FAD binding (GO:0071949)|NAD(P)H oxidase activity (GO:0016174)|oxidoreductase activity, acting on NAD(P)H (GO:0016651)	p.A109A(1)|p.A113A(1)		central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|liver(2)|lung(8)|ovary(4)|prostate(2)|urinary_tract(1)	30					Flavin adenine dinucleotide(DB03147)	CAGATAACGCGGCCTTTTTCT	0.408																																					p.A109A												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C327T	X						.	G	,,,	0,3835		0,0,1632,571	239.0	196.0	211.0		339,339,327,	-2.6	0.0	X		211	1,6727		0,1,2427,1872	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	AIFM1	NM_001130847.3,NM_004208.3,NM_145812.2,NM_145813.2	,,,	0,1,4059,2443	AA,AG,GG,G		0.0149,0.0,0.0095	,,,	113/325,113/614,109/610,	129283454	1,10562	2203	4300	6503	129111135	SO:0001819	synonymous_variant	9131	exon3			AF100928	CCDS14618.1, CCDS14619.1, CCDS48167.1	Xq26.1	2014-01-30	2006-11-16	2006-11-16	ENSG00000156709	ENSG00000156709			8768	protein-coding gene	gene with protein product		300169	"""programmed cell death 8 (apoptosis-inducing factor)"", ""neuropathy, axonal, motor-sensory with deafness and mental retardation (Cowchock syndrome)"""	PDCD8, NAMSD		9989411, 23217327	Standard	NM_004208		Approved	AIF, CMTX4	uc004evg.3	O95831	OTTHUMG00000022392	ENST00000287295.3:c.339C>T	X.37:g.129283454G>A		Somatic		Capture	Illumina HiSeq	Phase_I	129111135	NM_145812	A4QPB4|B1ALN1|B2RB08|D3DTE9|Q1L6K4|Q1L6K6|Q2QKE4|Q5JUZ7|Q6I9X6|Q9Y3I3|Q9Y3I4	Silent	SNP	ENST00000287295.3	37	CCDS14618.1																																																																																				0.408	AIFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058247.2		
SLC25A14	9016	broad.mit.edu	37	X	129498703	129498703	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:129498703C>T	ENST00000218197.5	+	7	923	c.696C>T	c.(694-696)ggC>ggT	p.G232G	SLC25A14_ENST00000543953.1_Silent_p.G197G|SLC25A14_ENST00000545805.1_Silent_p.G232G|SLC25A14_ENST00000467496.1_3'UTR|SLC25A14_ENST00000361980.5_Silent_p.G229G|SLC25A14_ENST00000339231.3_Silent_p.G260G	NM_001282195.1|NM_001282196.1|NM_001282198.1	NP_001269124.1|NP_001269125.1|NP_001269127.1	O95258	UCP5_HUMAN	solute carrier family 25 (mitochondrial carrier, brain), member 14	232					aerobic respiration (GO:0009060)|mitochondrial transport (GO:0006839)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)		p.G232G(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)	22						GAATGATGGGCGATACAATTT	0.408																																					p.G232G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C696T	X						.						180.0	150.0	160.0					X																	129498703		2203	4300	6503	129326384	SO:0001819	synonymous_variant	9016	exon7			AF078544	CCDS14623.1, CCDS14624.1, CCDS76020.1, CCDS76021.1	Xq24	2013-05-22			ENSG00000102078	ENSG00000102078		"""Solute carriers"""	10984	protein-coding gene	gene with protein product		300242				9852133	Standard	XM_005262485		Approved	BMCP1, UCP5	uc004evp.1	O95258	OTTHUMG00000022394	ENST00000218197.5:c.696C>T	X.37:g.129498703C>T		Somatic		Capture	Illumina HiSeq	Phase_I	129326384	NM_003951	D3DTG2|Q0VDH7|Q9HC60|Q9HC61	Silent	SNP	ENST00000218197.5	37	CCDS14623.1																																																																																				0.408	SLC25A14-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058253.1	NM_022810, NM_003951	
IGSF1	3547	broad.mit.edu	37	X	130417005	130417005	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:130417005C>T	ENST00000361420.3	-	6	980	c.901G>A	c.(901-903)Gca>Aca	p.A301T	IGSF1_ENST00000370910.1_Missense_Mutation_p.A292T|IGSF1_ENST00000370904.1_Missense_Mutation_p.A292T|IGSF1_ENST00000370903.3_Missense_Mutation_p.A301T			Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1	301	Ig-like C2-type 3.				regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	coreceptor activity (GO:0015026)|inhibin binding (GO:0034711)|receptor activity (GO:0004872)	p.A301T(1)		breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|liver(1)|lung(37)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)	78						CTATATGATGCGTCATAGTAA	0.388																																					p.A292T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G874A	X						.						117.0	96.0	103.0					X																	130417005		2203	4300	6503	130244686	SO:0001583	missense	3547	exon5			AF034198	CCDS14629.1, CCDS14630.1, CCDS55490.1, CCDS55491.1	Xq25	2013-01-11			ENSG00000147255	ENSG00000147255		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5948	protein-coding gene	gene with protein product		300137				9521868, 9729118	Standard	NM_001555		Approved	KIAA0364, IGDC1, IGCD1, INHBP, MGC75490, PGSF2	uc004ewe.4	Q8N6C5	OTTHUMG00000022406	ENST00000361420.3:c.901G>A	X.37:g.130417005C>T	ENSP00000355010:p.Ala301Thr	Somatic		Capture	Illumina HiSeq	Phase_I	130244686	NM_001170962	B5MEG2|H9KV64|O15070|Q9NTC8	Missense_Mutation	SNP	ENST00000361420.3	37	CCDS14629.1	.	.	.	.	.	.	.	.	.	.	C	1.021	-0.684913	0.03328	.	.	ENSG00000147255	ENST00000370910;ENST00000361420;ENST00000370904;ENST00000370903	T;T;T;T	0.00711	5.8;5.8;5.8;5.8	4.14	3.27	0.37495	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	1.031110	0.07710	N	0.941984	T	0.00637	0.0021	N	0.11154	0.105	0.18873	N	0.999987	B;B	0.30526	0.283;0.248	B;B	0.27608	0.033;0.081	T	0.50030	-0.8875	10	0.17369	T	0.5	.	10.0122	0.41992	0.0:0.8906:0.0:0.1094	.	292;301	Q8N6C5-2;Q8N6C5	.;IGSF1_HUMAN	T	292;301;292;301	ENSP00000359947:A292T;ENSP00000355010:A301T;ENSP00000359941:A292T;ENSP00000359940:A301T	ENSP00000355010:A301T	A	-	1	0	IGSF1	130244686	0.173000	0.23056	0.897000	0.35233	0.008000	0.06430	1.020000	0.30027	0.534000	0.28695	-0.923000	0.02734	GCA		0.388	IGSF1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058288.1		
FAM127B	26071	broad.mit.edu	37	X	134186083	134186083	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:134186083G>A	ENST00000370775.2	-	1	122	c.56C>T	c.(55-57)gCg>gTg	p.A19V	FAM127B_ENST00000520964.1_5'UTR	NM_001078172.1	NP_001071640.1	Q9BWD3	F127B_HUMAN	family with sequence similarity 127, member B	19								p.A19V(2)		breast(3)|endometrium(2)|large_intestine(3)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14	Acute lymphoblastic leukemia(192;0.000127)					GCGACGCGCCGCGGGCCGGAG	0.677																																					p.A19V												.	.	2	Substitution - Missense(2)	upper_aerodigestive_tract(1)|large_intestine(1)	c.C56T	X						.						55.0	60.0	59.0					X																	134186083		1938	4100	6038	134013749	SO:0001583	missense	26071	exon1			AL117556	CCDS43998.1	Xq26.3	2014-05-16			ENSG00000203950	ENSG00000203950			24514	protein-coding gene	gene with protein product						9403077, 15716091	Standard	NM_001078172		Approved	DKFZP564B147, MAR8A, CXX1b	uc004eyf.3	Q9BWD3	OTTHUMG00000022466	ENST00000370775.2:c.56C>T	X.37:g.134186083G>A	ENSP00000375267:p.Ala19Val	Somatic		Capture	Illumina HiSeq	Phase_I	134013749	NM_001134321	A2A2V9|Q8TBU2	Missense_Mutation	SNP	ENST00000370775.2	37	CCDS43998.1	.	.	.	.	.	.	.	.	.	.	G	12.01	1.810433	0.32053	.	.	ENSG00000203950	ENST00000370775	T	0.33438	1.41	2.11	-0.548	0.11833	.	1.521300	0.05776	U	0.607834	T	0.18299	0.0439	N	0.22421	0.69	0.09310	N	1	D;B	0.56521	0.976;0.272	B;B	0.40134	0.32;0.074	T	0.21552	-1.0242	10	0.30078	T	0.28	.	6.1284	0.20192	0.0:0.0:0.3833:0.6167	.	17;19	Q6IPB9;Q9BWD3	.;F127B_HUMAN	V	19	ENSP00000375267:A19V	ENSP00000375267:A19V	A	-	2	0	FAM127B	134013749	0.001000	0.12720	0.021000	0.16686	0.078000	0.17371	0.153000	0.16323	-0.220000	0.09988	0.292000	0.19580	GCG		0.677	FAM127B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058393.2	NM_001078172	
AFF2	2334	broad.mit.edu	37	X	147743718	147743718	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:147743718C>A	ENST00000370460.2	+	3	949	c.470C>A	c.(469-471)cCt>cAt	p.P157H	AFF2_ENST00000342251.3_Missense_Mutation_p.P153H|AFF2_ENST00000370457.5_Missense_Mutation_p.P153H|AFF2_ENST00000370458.1_Missense_Mutation_p.P153H	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	157					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)	p.P157H(1)		breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					AAATCAAAACCTGAGTGGTCA	0.473																																					p.P157H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C470A	X						.						153.0	147.0	149.0					X																	147743718		2203	4300	6503	147551410	SO:0001583	missense	2334	exon3			U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"""fragile X mental retardation 2"""	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.470C>A	X.37:g.147743718C>A	ENSP00000359489:p.Pro157His	Somatic		Capture	Illumina HiSeq	Phase_I	147551410	NM_002025	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Missense_Mutation	SNP	ENST00000370460.2	37	CCDS14684.1	.	.	.	.	.	.	.	.	.	.	C	9.418	1.082207	0.20309	.	.	ENSG00000155966	ENST00000370460;ENST00000370457;ENST00000342251;ENST00000370458	T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22	5.63	5.63	0.86233	.	0.442134	0.23446	N	0.048088	T	0.61912	0.2385	N	0.12182	0.205	0.80722	D	1	P;P;P;D;D;P	0.61697	0.547;0.547;0.547;0.969;0.99;0.697	B;B;B;P;P;B	0.56823	0.346;0.346;0.346;0.708;0.807;0.313	T	0.65936	-0.6047	10	0.51188	T	0.08	.	12.1536	0.54064	0.0:0.92:0.0:0.08	.	157;153;153;153;157;153	P51816-6;P51816-3;P51816-2;P51816-5;P51816;P51816-4	.;.;.;.;AFF2_HUMAN;.	H	157;153;153;153	ENSP00000359489:P157H;ENSP00000359486:P153H;ENSP00000345459:P153H;ENSP00000359487:P153H	ENSP00000345459:P153H	P	+	2	0	AFF2	147551410	0.004000	0.15560	0.279000	0.24732	0.763000	0.43281	1.844000	0.39269	2.365000	0.80145	0.600000	0.82982	CCT		0.473	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025	
HMGB3	3149	broad.mit.edu	37	X	150156360	150156360	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:150156360G>A	ENST00000325307.7	+	5	672	c.576G>A	c.(574-576)gaG>gaA	p.E192E	HMGB3_ENST00000448905.2_Silent_p.E192E	NM_005342.2	NP_005333.2	O15347	HMGB3_HUMAN	high mobility group box 3	192	Asp/Glu-rich (acidic).				DNA recombination (GO:0006310)|multicellular organismal development (GO:0007275)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)	p.E192E(1)		endometrium(3)|large_intestine(2)|lung(2)|skin(1)	8	Acute lymphoblastic leukemia(192;6.56e-05)					aggaagaagaggaggaggagg	0.443																																					p.E192E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G576A	X						.						50.0	48.0	49.0					X																	150156360		2202	4299	6501	149907018	SO:0001819	synonymous_variant	3149	exon5			AF274572	CCDS35428.1	Xq28	2011-07-01	2011-04-05	2002-08-16	ENSG00000029993	ENSG00000029993		"""High-mobility group / Canonical"""	5004	protein-coding gene	gene with protein product	"""non-histone chromosomal protein"""	300193	"""high-mobility group (nonhistone chromosomal) protein 4"", ""high-mobility group box 3"""	HMG4		9598312	Standard	XM_005274665		Approved	HMG2A, MGC90319	uc004fep.3	O15347	OTTHUMG00000024162	ENST00000325307.7:c.576G>A	X.37:g.150156360G>A		Somatic		Capture	Illumina HiSeq	Phase_I	149907018	NM_005342	O95556|Q6NS40	Silent	SNP	ENST00000325307.7	37	CCDS35428.1																																																																																				0.443	HMGB3-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060867.1	NM_005342	
ZNF275	10838	broad.mit.edu	37	X	152612592	152612592	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:152612592G>T	ENST00000421401.3	+	4	626	c.449G>T	c.(448-450)aGc>aTc	p.S150I	ZNF275_ENST00000440091.1_Missense_Mutation_p.S180I|ZNF275_ENST00000370249.2_Missense_Mutation_p.S97I|ZNF275_ENST00000370251.3_Missense_Mutation_p.S150I			Q9NSD4	ZN275_HUMAN	zinc finger protein 275	150					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	16	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CACAGGAAAAGCCACGTAGCT	0.627																																					p.S150I												.	.	0			c.G449T	X						.						36.0	39.0	38.0					X																	152612592		2059	4169	6228	152265786	SO:0001583	missense	10838	exon4			BC041602		Xq28	2013-01-08			ENSG00000063587	ENSG00000063587		"""Zinc fingers, C2H2-type"", ""-"""	13069	protein-coding gene	gene with protein product							Standard	NM_001080485		Approved		uc004fhg.2	Q9NSD4	OTTHUMG00000067450	ENST00000421401.3:c.449G>T	X.37:g.152612592G>T	ENSP00000398977:p.Ser150Ile	None		Capture	Illumina HiSeq	Phase_I	152265786	NM_001080485	A6NE92	Missense_Mutation	SNP	ENST00000421401.3	37		.	.	.	.	.	.	.	.	.	.	G	2.930	-0.221150	0.06061	.	.	ENSG00000063587	ENST00000370251;ENST00000421401;ENST00000440091;ENST00000370249	T;T;T;T	0.25912	1.77;1.77;1.77;1.77	4.84	0.68	0.17980	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);	0.547048	0.16802	N	0.198927	T	0.07413	0.0187	N	0.02751	-0.505	0.26886	N	0.967431	B;B	0.25850	0.028;0.136	B;B	0.24541	0.037;0.054	T	0.39057	-0.9632	10	0.02654	T	1	-22.7458	6.5227	0.22285	0.0916:0.0:0.4705:0.4379	.	150;150	Q9NSD4;A6NFS0	ZN275_HUMAN;.	I	150;150;180;97	ENSP00000359271:S150I;ENSP00000398977:S150I;ENSP00000411097:S180I;ENSP00000359269:S97I	ENSP00000359269:S97I	S	+	2	0	ZNF275	152265786	0.000000	0.05858	0.951000	0.38953	0.676000	0.39594	-0.019000	0.12546	0.166000	0.19597	0.513000	0.50165	AGC		0.627	ZNF275-201	KNOWN	basic	protein_coding	protein_coding		NM_001080485	
AVPR2	554	broad.mit.edu	37	X	153171715	153171715	+	Missense_Mutation	SNP	G	G	A	rs368306347		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:153171715G>A	ENST00000358927.2	+	3	964	c.755G>A	c.(754-756)cGg>cAg	p.R252Q	AVPR2_ENST00000337474.5_Missense_Mutation_p.R252Q|AVPR2_ENST00000370049.1_Missense_Mutation_p.R252Q			P30518	V2R_HUMAN	arginine vasopressin receptor 2	252			R -> W (in dbSNP:rs61733407).		activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|excretion (GO:0007588)|hemostasis (GO:0007599)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|interferon-gamma production (GO:0032609)|negative regulation of renal sodium excretion (GO:0035814)|negative regulation of urine volume (GO:0035811)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of systemic arterial blood pressure (GO:0003084)|response to cytokine (GO:0034097)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	vasopressin receptor activity (GO:0005000)	p.R252Q(2)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	26	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)				Conivaptan(DB00872)|Desmopressin(DB00035)|Terlipressin(DB02638)|Tolvaptan(DB06212)|Vasopressin(DB00067)	AGGGGACGCCGGACAGGCAGC	0.652																																					p.R252Q												.	.	2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	c.G755A	X						.	G	GLN/ARG,GLN/ARG	1,3834		0,1,1631,571	83.0	72.0	76.0		755,755	0.2	0.0	X		76	0,6728		0,0,2428,1872	no	missense,missense	AVPR2	NM_000054.4,NM_001146151.1	43,43	0,1,4059,2443	AA,AG,GG,G		0.0,0.0261,0.0095	possibly-damaging,possibly-damaging	252/372,252/310	153171715	1,10562	2203	4300	6503	152824909	SO:0001583	missense	554	exon2			Z11687	CCDS14735.1, CCDS55539.1	Xq28	2014-09-17	2008-08-01		ENSG00000126895	ENSG00000126895		"""GPCR / Class A : Vasopressin and oxytocin receptors"""	897	protein-coding gene	gene with protein product	"""nephrogenic diabetes insipidus"""	300538		DIR3, DIR		1324225	Standard	NM_000054		Approved	V2R	uc004fjh.4	P30518	OTTHUMG00000024227	ENST00000358927.2:c.755G>A	X.37:g.153171715G>A	ENSP00000351805:p.Arg252Gln	Somatic		Capture	Illumina HiSeq	Phase_I	152824909	NM_000054	C5HF20|O43192|Q3MJD3|Q9UCV9	Missense_Mutation	SNP	ENST00000358927.2	37	CCDS14735.1	.	.	.	.	.	.	.	.	.	.	g	0.069	-1.205466	0.01568	2.61E-4	0.0	ENSG00000126895	ENST00000358927;ENST00000430697;ENST00000337474;ENST00000370049	T;T;T;T	0.77358	-1.09;-0.86;-1.09;-0.51	4.13	0.151	0.14888	GPCR, rhodopsin-like superfamily (1);	1.368180	0.04734	N	0.421642	T	0.66636	0.2809	L	0.41415	1.275	0.20563	N	0.999889	B;B	0.15141	0.012;0.007	B;B	0.11329	0.005;0.006	T	0.41106	-0.9527	10	0.23302	T	0.38	-13.4909	4.2092	0.10503	0.4162:0.0:0.4253:0.1585	.	252;252	P30518-2;P30518	.;V2R_HUMAN	Q	252	ENSP00000351805:R252Q;ENSP00000393513:R252Q;ENSP00000338072:R252Q;ENSP00000359066:R252Q	ENSP00000338072:R252Q	R	+	2	0	AVPR2	152824909	0.078000	0.21339	0.007000	0.13788	0.017000	0.09413	1.392000	0.34486	-0.062000	0.13088	-0.819000	0.03115	CGG		0.652	AVPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061127.2		
NLGN4X	57502	broad.mit.edu	37	X	5821415	5821415	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:5821415G>A	ENST00000381095.3	-	5	1931	c.1304C>T	c.(1303-1305)aCg>aTg	p.T435M	NLGN4X_ENST00000275857.6_Missense_Mutation_p.T435M|NLGN4X_ENST00000381093.2_Missense_Mutation_p.T455M|NLGN4X_ENST00000381092.1_Missense_Mutation_p.T435M|NLGN4X_ENST00000538097.1_Missense_Mutation_p.T435M	NM_001282145.1|NM_001282146.1|NM_181332.1	NP_001269074.1|NP_001269075.1|NP_851849.1	Q8N0W4	NLGNX_HUMAN	neuroligin 4, X-linked	435					adult behavior (GO:0030534)|brainstem development (GO:0003360)|cell-cell junction organization (GO:0045216)|cerebellum development (GO:0021549)|learning (GO:0007612)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|neuron cell-cell adhesion (GO:0007158)|neuron differentiation (GO:0030182)|organ growth (GO:0035265)|presynaptic membrane assembly (GO:0097105)|social behavior (GO:0035176)|synapse organization (GO:0050808)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|chloride ion binding (GO:0031404)|neurexin family protein binding (GO:0042043)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)	p.T435M(1)		breast(1)|cervix(2)|endometrium(4)|large_intestine(21)|lung(39)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	81						TTTCCGCCGCGTCTCCGGGTT	0.602																																					p.T435M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1304T	X						.						16.0	19.0	18.0					X																	5821415		2198	4289	6487	5831415	SO:0001583	missense	57502	exon5			AB033086	CCDS14126.1	Xp22.33	2008-02-05	2004-05-21	2004-05-26	ENSG00000146938	ENSG00000146938			14287	protein-coding gene	gene with protein product		300427	"""neuroligin 4"""	NLGN4		10574462	Standard	XM_005274564		Approved	KIAA1260, NLGN, HLNX	uc004crr.3	Q8N0W4	OTTHUMG00000021093	ENST00000381095.3:c.1304C>T	X.37:g.5821415G>A	ENSP00000370485:p.Thr435Met	Somatic		Capture	Illumina HiSeq	Phase_I	5831415	NM_020742	Q6UX10|Q9ULG0	Missense_Mutation	SNP	ENST00000381095.3	37	CCDS14126.1	.	.	.	.	.	.	.	.	.	.	G	4.818	0.152170	0.09185	.	.	ENSG00000146938	ENST00000381095;ENST00000381093;ENST00000275857;ENST00000381092;ENST00000538097	T;T;T;T;T	0.68479	-0.33;-0.33;-0.33;-0.33;-0.33	3.93	3.93	0.45458	Carboxylesterase, type B (1);	.	.	.	.	T	0.68742	0.3034	L	0.43152	1.355	0.53688	D	0.999971	P;D;P	0.63880	0.799;0.993;0.578	B;P;B	0.54372	0.147;0.75;0.261	T	0.68542	-0.5381	8	.	.	.	.	14.4947	0.67678	0.0:0.0:1.0:0.0	.	492;435;455	A6NMU8;Q8N0W4;Q8N0W4-2	.;NLGNX_HUMAN;.	M	435;455;435;435;435	ENSP00000370485:T435M;ENSP00000370483:T455M;ENSP00000275857:T435M;ENSP00000370482:T435M;ENSP00000439203:T435M	.	T	-	2	0	NLGN4X	5831415	1.000000	0.71417	0.003000	0.11579	0.003000	0.03518	8.442000	0.90317	1.579000	0.49836	0.600000	0.82982	ACG		0.602	NLGN4X-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055673.1	NM_020742	
NLGN4X	57502	broad.mit.edu	37	X	5821624	5821624	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:5821624G>A	ENST00000381095.3	-	5	1722	c.1095C>T	c.(1093-1095)taC>taT	p.Y365Y	NLGN4X_ENST00000275857.6_Silent_p.Y365Y|NLGN4X_ENST00000381093.2_Silent_p.Y385Y|NLGN4X_ENST00000381092.1_Silent_p.Y365Y|NLGN4X_ENST00000538097.1_Silent_p.Y365Y	NM_001282145.1|NM_001282146.1|NM_181332.1	NP_001269074.1|NP_001269075.1|NP_851849.1	Q8N0W4	NLGNX_HUMAN	neuroligin 4, X-linked	365					adult behavior (GO:0030534)|brainstem development (GO:0003360)|cell-cell junction organization (GO:0045216)|cerebellum development (GO:0021549)|learning (GO:0007612)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|neuron cell-cell adhesion (GO:0007158)|neuron differentiation (GO:0030182)|organ growth (GO:0035265)|presynaptic membrane assembly (GO:0097105)|social behavior (GO:0035176)|synapse organization (GO:0050808)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|chloride ion binding (GO:0031404)|neurexin family protein binding (GO:0042043)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)	p.Y365Y(1)		breast(1)|cervix(2)|endometrium(4)|large_intestine(21)|lung(39)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	81						GCATGATGTCGTAGTTGAGGA	0.607																																					p.Y365Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1095T	X						.						34.0	27.0	29.0					X																	5821624		2203	4294	6497	5831624	SO:0001819	synonymous_variant	57502	exon5			AB033086	CCDS14126.1	Xp22.33	2008-02-05	2004-05-21	2004-05-26	ENSG00000146938	ENSG00000146938			14287	protein-coding gene	gene with protein product		300427	"""neuroligin 4"""	NLGN4		10574462	Standard	XM_005274564		Approved	KIAA1260, NLGN, HLNX	uc004crr.3	Q8N0W4	OTTHUMG00000021093	ENST00000381095.3:c.1095C>T	X.37:g.5821624G>A		Somatic		Capture	Illumina HiSeq	Phase_I	5831624	NM_020742	Q6UX10|Q9ULG0	Silent	SNP	ENST00000381095.3	37	CCDS14126.1																																																																																				0.607	NLGN4X-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055673.1	NM_020742	
PNPLA4	8228	broad.mit.edu	37	X	7894159	7894159	+	Start_Codon_SNP	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:7894159A>G	ENST00000381042.4	-	2	172	c.2T>C	c.(1-3)aTg>aCg	p.M1T	PNPLA4_ENST00000537427.1_Intron|PNPLA4_ENST00000444736.1_Start_Codon_SNP_p.M1T	NM_004650.2	NP_004641.1	P41247	PLPL4_HUMAN	patatin-like phospholipase domain containing 4	1					lipid catabolic process (GO:0016042)		triglyceride lipase activity (GO:0004806)	p.M1T(1)		kidney(1)|large_intestine(3)|lung(2)|prostate(1)	7		Colorectal(8;0.0329)|Medulloblastoma(8;0.232)				GATGTGCTTCATTCTAGCTGT	0.418											OREG0019651	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.M1T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2C	X						.						66.0	44.0	51.0					X																	7894159		2203	4299	6502	7854159	SO:0001582	initiator_codon_variant	8228	exon2			U03886	CCDS14129.1, CCDS55368.1	Xp22.3	2014-03-14			ENSG00000006757	ENSG00000006757	3.1.1.3	"""Patatin-like phospholipase domain containing"""	24887	protein-coding gene	gene with protein product		300102				7806223, 16799181, 19029121	Standard	NM_004650		Approved	DXS1283E, GS2, iPLA2eta	uc011mhr.1	P41247	OTTHUMG00000021103	ENST00000381042.4:c.2T>C	X.37:g.7894159A>G	ENSP00000370430:p.Met1Thr	Somatic	645	Capture	Illumina HiSeq	Phase_I	7854159	NM_004650	A8K1H3|B4E362|Q8WW83	Missense_Mutation	SNP	ENST00000381042.4	37	CCDS14129.1	.	.	.	.	.	.	.	.	.	.	A	13.61	2.289044	0.40494	.	.	ENSG00000006757	ENST00000381042;ENST00000444736;ENST00000442940	T;T;T	0.37584	1.19;1.19;1.53	3.76	3.76	0.43208	Acyl transferase/acyl hydrolase/lysophospholipase (1);	0.000000	0.85682	D	0.000000	T	0.46483	0.1395	.	.	.	0.80722	D	1	D	0.57257	0.979	P	0.52554	0.702	T	0.51325	-0.8720	9	0.87932	D	0	-40.314	10.766	0.46295	1.0:0.0:0.0:0.0	.	1	P41247	PLPL4_HUMAN	T	1	ENSP00000370430:M1T;ENSP00000415245:M1T;ENSP00000406698:M1T	ENSP00000370430:M1T	M	-	2	0	PNPLA4	7854159	1.000000	0.71417	0.998000	0.56505	0.984000	0.73092	5.920000	0.70017	1.402000	0.46780	0.486000	0.48141	ATG		0.418	PNPLA4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055687.1	NM_004650	Missense_Mutation
ZRSR2	8233	broad.mit.edu	37	X	15808623	15808623	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:15808623C>A	ENST00000307771.7	+	1	29	c.5C>A	c.(4-6)gCt>gAt	p.A2D	ZRSR2_ENST00000380308.3_Missense_Mutation_p.A2D	NM_005089.3	NP_005080.1	Q15696	U2AFM_HUMAN	zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 2	2					mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)	U12-type spliceosomal complex (GO:0005689)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|pre-mRNA 3'-splice site binding (GO:0030628)	p.A2D(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(38)|kidney(1)|large_intestine(2)|ovary(2)	48	Hepatocellular(33;0.183)					GGCAAGATGGCTGCGCCCGAG	0.677			"""F, S, Mis"""		"""MDS, CLL"""																																p.A2D	NSCLC(197;1631 3042 5741 31152)		Rec	yes		X	Xp22.1	8233	"""zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 2"""		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5A	X						.						21.0	18.0	19.0					X																	15808623		2100	4094	6194	15718544	SO:0001583	missense	8233	exon1			BC050451	CCDS14172.1	Xp22.1	2014-09-17	2006-09-26	2006-09-26	ENSG00000169249	ENSG00000169249		"""Zinc fingers, CCCH-type domain containing"", ""RNA binding motif (RRM) containing"""	23019	protein-coding gene	gene with protein product		300028	"""U2(RNU2) small nuclear RNA auxiliary factor 1-like 2"", ""U2 small nuclear RNA auxiliary factor 1-like 2"""	U2AF1L2		8586425, 9237760, 15146077	Standard	NM_005089		Approved	U2AF1-RS2, URP	uc004cxg.4	Q15696	OTTHUMG00000021184	ENST00000307771.7:c.5C>A	X.37:g.15808623C>A	ENSP00000303015:p.Ala2Asp	Somatic		Capture	Illumina HiSeq	Phase_I	15718544	NM_005089	Q14D69	Missense_Mutation	SNP	ENST00000307771.7	37	CCDS14172.1	.	.	.	.	.	.	.	.	.	.	C	9.274	1.046353	0.19748	.	.	ENSG00000169249	ENST00000307771;ENST00000380308	T	0.27104	1.69	5.69	3.86	0.44501	.	0.478897	0.22724	N	0.056419	T	0.24236	0.0587	M	0.67953	2.075	0.28269	N	0.924499	B	0.34103	0.437	B	0.27608	0.081	T	0.15838	-1.0423	10	0.56958	D	0.05	.	8.46	0.32923	0.1734:0.6629:0.1637:0.0	.	2	Q15696	U2AFM_HUMAN	D	2	ENSP00000369664:A2D	ENSP00000303015:A2D	A	+	2	0	ZRSR2	15718544	0.990000	0.36364	0.099000	0.21106	0.112000	0.19704	3.486000	0.53215	0.518000	0.28383	0.529000	0.55759	GCT		0.677	ZRSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055889.1	NM_005089	
TXLNG	55787	broad.mit.edu	37	X	16850812	16850812	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:16850812A>G	ENST00000380122.5	+	6	992	c.931A>G	c.(931-933)Acg>Gcg	p.T311A	TXLNG_ENST00000398155.4_Missense_Mutation_p.T179A	NM_018360.2	NP_060830.2	Q9NUQ3	TXLNG_HUMAN	taxilin gamma	311					cell cycle (GO:0007049)|regulation of bone mineralization (GO:0030500)|regulation of cell cycle (GO:0051726)|regulation of cell cycle process (GO:0010564)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)	protein heterodimerization activity (GO:0046982)	p.T311A(1)		breast(2)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	15						ACTGCAGCAAACGACACAACT	0.388																																					p.T311A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A931G	X						.						128.0	110.0	116.0					X																	16850812		2203	4300	6503	16760733	SO:0001583	missense	55787	exon6			AK002071	CCDS14178.1, CCDS55373.1	Xp22.2	2014-05-07	2010-04-20	2010-04-20	ENSG00000086712	ENSG00000086712			18578	protein-coding gene	gene with protein product	"""lipopolysaccharide specific response-5 protein"", ""factor inhibiting activating transcription factor 4 (ATF4)-mediated transcription"""	300677	"""chromosome X open reading frame 15"""	CXorf15		15911876, 15184072, 16831913	Standard	NM_018360		Approved	FLJ11209, LSR5, FIAT, MGC126621, MGC126625, TXLNGX	uc004cxq.2	Q9NUQ3	OTTHUMG00000021196	ENST00000380122.5:c.931A>G	X.37:g.16850812A>G	ENSP00000369465:p.Thr311Ala	Somatic		Capture	Illumina HiSeq	Phase_I	16760733	NM_018360	Q2KQ75|Q5JNZ7|Q9P0X1	Missense_Mutation	SNP	ENST00000380122.5	37	CCDS14178.1	.	.	.	.	.	.	.	.	.	.	A	4.004	-0.001906	0.07819	.	.	ENSG00000086712	ENST00000380122;ENST00000398155	T;T	0.26223	1.75;1.75	5.28	4.11	0.48088	.	0.110828	0.64402	D	0.000012	T	0.05960	0.0155	N	0.00256	-1.76	0.41085	D	0.985555	B;B	0.18741	0.007;0.03	B;B	0.28139	0.004;0.086	T	0.32693	-0.9897	10	0.02654	T	1	-11.3578	10.1671	0.42886	0.9205:0.0:0.0795:0.0	.	179;311	Q9NUQ3-2;Q9NUQ3	.;TXLNG_HUMAN	A	311;179	ENSP00000369465:T311A;ENSP00000381222:T179A	ENSP00000369465:T311A	T	+	1	0	TXLNG	16760733	1.000000	0.71417	0.611000	0.29010	0.945000	0.59286	4.745000	0.62125	0.660000	0.30964	0.486000	0.48141	ACG		0.388	TXLNG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055912.1	NM_018360	
PHKA2	5256	broad.mit.edu	37	X	18944633	18944633	+	Missense_Mutation	SNP	G	G	A	rs191267737		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:18944633G>A	ENST00000379942.4	-	14	2062	c.1397C>T	c.(1396-1398)gCg>gTg	p.A466V		NM_000292.2	NP_000283.1	P46019	KPB2_HUMAN	phosphorylase kinase, alpha 2 (liver)	466					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61	Hepatocellular(33;0.183)					ATGAATGTCCGCGATACTCTG	0.458													G|||	1	0.000264901	0.0	0.0	3775	,	,		15190	0.001		0.0	False		,,,				2504	0.0				p.A466V												.	.	0			c.C1397T	X						.						175.0	138.0	150.0					X																	18944633		2203	4300	6503	18854554	SO:0001583	missense	5256	exon14				CCDS14190.1	Xp22.2-p22.1	2009-07-10			ENSG00000044446	ENSG00000044446	2.7.11.19		8926	protein-coding gene	gene with protein product		300798		PHK, PYK		2387090	Standard	NM_000292		Approved		uc004cyv.4	P46019	OTTHUMG00000021222	ENST00000379942.4:c.1397C>T	X.37:g.18944633G>A	ENSP00000369274:p.Ala466Val	None		Capture	Illumina HiSeq	Phase_I	18854554	NM_000292	A8K1T1|Q6LAJ5|Q7Z6W0|Q96CR3|Q9UDA1	Missense_Mutation	SNP	ENST00000379942.4	37	CCDS14190.1	1	6.027727546714888E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	16.32	3.091165	0.55968	.	.	ENSG00000044446	ENST00000379942	D	0.91180	-2.8	5.38	5.38	0.77491	Glycoside hydrolase 15-related (1);	0.207947	0.51477	D	0.000087	D	0.89298	0.6675	M	0.80982	2.52	0.54753	D	0.999983	P	0.37233	0.588	B	0.30572	0.117	D	0.89015	0.3431	10	0.41790	T	0.15	-14.0755	13.7211	0.62728	0.0:0.1504:0.8496:0.0	.	466	P46019	KPB2_HUMAN	V	466	ENSP00000369274:A466V	ENSP00000369274:A466V	A	-	2	0	PHKA2	18854554	1.000000	0.71417	0.887000	0.34795	0.469000	0.32828	7.271000	0.78506	2.383000	0.81215	0.600000	0.82982	GCG		0.458	PHKA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055960.1	NM_000292	
PHKA2	5256	broad.mit.edu	37	X	18966934	18966934	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:18966934G>C	ENST00000379942.4	-	5	1130	c.465C>G	c.(463-465)atC>atG	p.I155M		NM_000292.2	NP_000283.1	P46019	KPB2_HUMAN	phosphorylase kinase, alpha 2 (liver)	155					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)	p.I155M(1)		NS(1)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61	Hepatocellular(33;0.183)					GAGTGAAAATGATACGTAAGC	0.388																																					p.I155M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C465G	X						.						141.0	141.0	141.0					X																	18966934		2203	4300	6503	18876855	SO:0001583	missense	5256	exon5				CCDS14190.1	Xp22.2-p22.1	2009-07-10			ENSG00000044446	ENSG00000044446	2.7.11.19		8926	protein-coding gene	gene with protein product		300798		PHK, PYK		2387090	Standard	NM_000292		Approved		uc004cyv.4	P46019	OTTHUMG00000021222	ENST00000379942.4:c.465C>G	X.37:g.18966934G>C	ENSP00000369274:p.Ile155Met	Somatic		Capture	Illumina HiSeq	Phase_I	18876855	NM_000292	A8K1T1|Q6LAJ5|Q7Z6W0|Q96CR3|Q9UDA1	Missense_Mutation	SNP	ENST00000379942.4	37	CCDS14190.1	.	.	.	.	.	.	.	.	.	.	G	12.50	1.955984	0.34471	.	.	ENSG00000044446	ENST00000379942	D	0.90844	-2.74	5.91	-1.22	0.09494	Six-hairpin glycosidase (1);Six-hairpin glycosidase-like (1);Glycoside hydrolase 15-related (1);	0.000000	0.85682	D	0.000000	D	0.94984	0.8377	H	0.94264	3.515	0.58432	D	0.999993	D	0.89917	1.0	D	0.77557	0.99	D	0.91230	0.5013	10	0.87932	D	0	-17.8451	5.3729	0.16150	0.5939:0.0:0.2864:0.1197	.	155	P46019	KPB2_HUMAN	M	155	ENSP00000369274:I155M	ENSP00000369274:I155M	I	-	3	3	PHKA2	18876855	0.982000	0.34865	0.969000	0.41365	0.070000	0.16714	0.333000	0.19768	-0.597000	0.05813	-0.390000	0.06520	ATC		0.388	PHKA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055960.1	NM_000292	
SAT1	6303	broad.mit.edu	37	X	23802147	23802147	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:23802147delA	ENST00000379253.3	+	3	528	c.349delA	c.(349-351)aaafs	p.K119fs	SAT1_ENST00000379251.3_Frame_Shift_Del_p.K149fs|Y_RNA_ENST00000365402.1_RNA|SAT1_ENST00000379270.4_Intron|SAT1_ENST00000489394.1_Intron|RP13-314C10.5_ENST00000366134.2_RNA|SAT1_ENST00000379254.1_Intron			Q9H2B4	S26A1_HUMAN	spermidine/spermine N1-acetyltransferase 1	0					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|chloride transport (GO:0006821)|glycosaminoglycan metabolic process (GO:0030203)|ion transport (GO:0006811)|oxalate transport (GO:0019532)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|chloride transmembrane transporter activity (GO:0015108)|oxalate transmembrane transporter activity (GO:0019531)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)	p.N150fs*13(3)		breast(1)|endometrium(3)|kidney(3)|lung(3)	10						ACTACTGAGGAAAAAAAAAAA	0.398																																					.												.	.	3	Deletion - Frameshift(3)	large_intestine(3)	.	X						.																																			23712068	SO:0001589	frameshift_variant	6303	.			M55580	CCDS14207.1	Xp22.1	2011-11-16	2006-08-24	2006-08-24	ENSG00000130066	ENSG00000130066	2.3.1.57		10540	protein-coding gene	gene with protein product	"""diamine N-acetyltransferase 1"""	313020	"""spermidine/spermine N1-acetyltransferase"""	SAT		1985966, 1417826	Standard	NM_002970		Approved	SSAT	uc004dau.3	P21673	OTTHUMG00000021256	ENST00000379253.3:c.349delA	X.37:g.23802147delA	ENSP00000368555:p.Lys119fs	Somatic		Capture	Illumina HiSeq	Phase_I	23712068	.	A8K9N2|Q7Z5R3|Q96BK0	Frame_Shift_Del	DEL	ENST00000379253.3	37																																																																																					0.398	SAT1-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000056058.1	NM_002970	
ZFX	7543	broad.mit.edu	37	X	24225910	24225910	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:24225910T>C	ENST00000379177.1	+	8	1305	c.878T>C	c.(877-879)gTt>gCt	p.V293A	ZFX_ENST00000539115.1_Missense_Mutation_p.V64A|ZFX_ENST00000338565.3_Missense_Mutation_p.V243A|ZFX_ENST00000459724.1_3'UTR|ZFX_ENST00000379188.3_Missense_Mutation_p.V293A|ZFX_ENST00000304543.5_Missense_Mutation_p.V293A|ZFX_ENST00000540034.1_Missense_Mutation_p.V332A	NM_001178085.1|NM_003410.3	NP_001171556.1|NP_003401.2	P17010	ZFX_HUMAN	zinc finger protein, X-linked	293					death (GO:0016265)|fertilization (GO:0009566)|homeostasis of number of cells (GO:0048872)|multicellular organism growth (GO:0035264)|oocyte development (GO:0048599)|ovarian follicle development (GO:0001541)|parental behavior (GO:0060746)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription coactivator activity (GO:0003713)	p.V293A(1)		cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(2)|lung(4)|ovary(2)|prostate(1)	24						AGTATTCGTGTTCCCAGGGAA	0.413																																					p.V293A	Esophageal Squamous(20;306 562 7346 32868 37983)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T878C	X						.						254.0	206.0	222.0					X																	24225910		2203	4300	6503	24135831	SO:0001583	missense	7543	exon5				CCDS14211.1, CCDS55390.1	Xp22.1-p21.3	2013-01-08			ENSG00000005889	ENSG00000005889		"""Zinc fingers, C2H2-type"""	12869	protein-coding gene	gene with protein product		314980					Standard	NM_003410		Approved	ZNF926	uc022bua.1	P17010	OTTHUMG00000021264	ENST00000379177.1:c.878T>C	X.37:g.24225910T>C	ENSP00000368475:p.Val293Ala	Somatic		Capture	Illumina HiSeq	Phase_I	24135831	NM_001178095	B9EG97|O43668|Q8WYJ8	Missense_Mutation	SNP	ENST00000379177.1	37	CCDS14211.1	.	.	.	.	.	.	.	.	.	.	T	15.59	2.877642	0.51801	.	.	ENSG00000005889	ENST00000539115;ENST00000379188;ENST00000535562;ENST00000379177;ENST00000304543;ENST00000540034;ENST00000338565;ENST00000545937	T;T;T;T;T;T	0.48522	0.81;0.81;0.81;0.81;0.81;0.81	5.62	5.62	0.85841	Transcriptional activator, Zfx / Zfy domain (1);	0.192528	0.35646	N	0.003064	T	0.51618	0.1685	L	0.55481	1.735	0.26711	N	0.970973	B;B;B	0.33448	0.216;0.165;0.412	B;B;B	0.40982	0.174;0.089;0.345	T	0.55315	-0.8160	10	0.72032	D	0.01	-1.4984	15.0216	0.71635	0.0:0.0:0.0:1.0	.	332;293;297	B9EG97;P17010;Q59EB9	.;ZFX_HUMAN;.	A	64;293;62;293;293;332;243;88	ENSP00000438233:V64A;ENSP00000368486:V293A;ENSP00000368475:V293A;ENSP00000304985:V293A;ENSP00000441382:V332A;ENSP00000343384:V243A	ENSP00000304985:V293A	V	+	2	0	ZFX	24135831	1.000000	0.71417	0.999000	0.59377	0.940000	0.58332	3.550000	0.53691	1.998000	0.58463	0.481000	0.45027	GTT		0.413	ZFX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056084.1	NM_003410	
ARX	170302	broad.mit.edu	37	X	25033763	25033763	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:25033763C>T	ENST00000379044.4	-	1	302	c.92G>A	c.(91-93)aGc>aAc	p.S31N		NM_139058.2	NP_620689.1	Q96QS3	ARX_HUMAN	aristaless related homeobox	31					axon guidance (GO:0007411)|cell proliferation in forebrain (GO:0021846)|cerebral cortex GABAergic interneuron migration (GO:0021853)|cerebral cortex tangential migration (GO:0021800)|embryonic olfactory bulb interneuron precursor migration (GO:0021831)|epithelial cell fate commitment (GO:0072148)|globus pallidus development (GO:0021759)|lipid digestion (GO:0044241)|positive regulation of organ growth (GO:0046622)|regulation of cell proliferation (GO:0042127)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|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.S31N(1)		kidney(1)|large_intestine(2)|lung(1)	4						GCCCAGGATGCTGTCGATGCA	0.632																																					p.S31N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G92A	X						.						38.0	32.0	34.0					X																	25033763		2202	4300	6502	24943684	SO:0001583	missense	170302	exon1			AY038071	CCDS14215.1	Xp21.3	2011-06-20			ENSG00000004848	ENSG00000004848		"""Homeoboxes / PRD class"""	18060	protein-coding gene	gene with protein product	"""cancer/testis antigen 121"""	300382	"""mental retardation, X-linked 54"", ""mental retardation, X-linked 43"", ""mental retardation, X-linked 36"", ""mental retardation, X-linked 29"", ""mental retardation, X-linked 32"", ""mental retardation, X-linked 33"", ""mental retardation, X-linked 38"", ""mental retardation, X-linked 87"", ""mental retardation, X-linked 76"""	MRXS1, PRTS, MRX76, MRX54, MRX43, MRX36, MRX29, MRX32, MRX33, MRX38, MRX87		11889467, 15850492, 17480217	Standard	NM_139058		Approved	ISSX, CT121, EIEE1	uc004dbp.4	Q96QS3	OTTHUMG00000021275	ENST00000379044.4:c.92G>A	X.37:g.25033763C>T	ENSP00000368332:p.Ser31Asn	Somatic		Capture	Illumina HiSeq	Phase_I	24943684	NM_139058		Missense_Mutation	SNP	ENST00000379044.4	37	CCDS14215.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.164569	0.78339	.	.	ENSG00000004848	ENST00000379044	D	0.89617	-2.54	5.2	5.2	0.72013	.	0.000000	0.85682	U	0.000000	D	0.93284	0.7860	L	0.58101	1.795	0.49130	D	0.999759	D	0.69078	0.997	D	0.75484	0.986	D	0.94084	0.7347	10	0.87932	D	0	.	17.3936	0.87439	0.0:1.0:0.0:0.0	.	31	Q96QS3	ARX_HUMAN	N	31	ENSP00000368332:S31N	ENSP00000368332:S31N	S	-	2	0	ARX	24943684	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.828000	0.75308	2.139000	0.66308	0.600000	0.82982	AGC		0.632	ARX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056109.1		
DCAF8L1	139425	broad.mit.edu	37	X	27998574	27998574	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:27998574G>A	ENST00000441525.1	-	1	992	c.878C>T	c.(877-879)gCt>gTt	p.A293V		NM_001017930.1	NP_001017930.1	A6NGE4	DC8L1_HUMAN	DDB1 and CUL4 associated factor 8-like 1	293								p.A293V(1)		NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(24)|ovary(3)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	56						TGGCTCCAGAGCCAACTCGTG	0.512																																					p.A293V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C878T	X						.						80.0	69.0	73.0					X																	27998574		2202	4300	6502	27908495	SO:0001583	missense	139425	exon1				CCDS35222.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17	ENSG00000226372	ENSG00000226372		"""WD repeat domain containing"""	31810	protein-coding gene	gene with protein product			"""WD repeat domain 42B"""	WDR42B			Standard	NM_001017930		Approved		uc004dbx.1	A6NGE4	OTTHUMG00000021312	ENST00000441525.1:c.878C>T	X.37:g.27998574G>A	ENSP00000405222:p.Ala293Val	Somatic		Capture	Illumina HiSeq	Phase_I	27908495	NM_001017930	B3KXX1	Missense_Mutation	SNP	ENST00000441525.1	37	CCDS35222.1	.	.	.	.	.	.	.	.	.	.	G	19.40	3.819482	0.71028	.	.	ENSG00000226372	ENST00000441525	D	0.82893	-1.66	0.842	0.842	0.18927	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.063315	0.64402	D	0.000007	D	0.86506	0.5949	M	0.72576	2.205	0.43259	D	0.995192	D	0.69078	0.997	D	0.64506	0.926	D	0.84232	0.0467	10	0.52906	T	0.07	-4.6818	7.2758	0.26283	1.0E-4:0.0:0.9999:0.0	.	293	A6NGE4	DC8L1_HUMAN	V	293	ENSP00000405222:A293V	ENSP00000405222:A293V	A	-	2	0	DCAF8L1	27908495	1.000000	0.71417	0.981000	0.43875	0.413000	0.31143	5.657000	0.67996	0.691000	0.31592	0.284000	0.19432	GCT		0.512	DCAF8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056150.2	XM_066690	
MAGEB1	4112	broad.mit.edu	37	X	30269392	30269392	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:30269392C>A	ENST00000378981.3	+	4	1103	c.782C>A	c.(781-783)cCc>cAc	p.P261H	MAGEB1_ENST00000397548.2_Missense_Mutation_p.P261H|MAGEB1_ENST00000397550.1_Missense_Mutation_p.P261H	NM_002363.4	NP_002354.2	P43366	MAGB1_HUMAN	melanoma antigen family B, 1	261	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.							p.P261H(1)		NS(2)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(8)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	32						GAGCAGGTGCCCAACAGTGAT	0.493																																					p.P261H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C782A	X						.						103.0	90.0	94.0					X																	30269392		2202	4300	6502	30179313	SO:0001583	missense	4112	exon4				CCDS14222.1	Xp21.3	2009-03-17			ENSG00000214107	ENSG00000214107			6808	protein-coding gene	gene with protein product	"""DSS/AHC critical interval MAGE superfamily 10"", ""cancer/testis antigen family 3, member 1"""	300097				7761436, 9441743	Standard	NM_002363		Approved	MAGEL1, MAGE-Xp, DAM10, MGC9322, CT3.1	uc004dce.3	P43366	OTTHUMG00000021322	ENST00000378981.3:c.782C>A	X.37:g.30269392C>A	ENSP00000368264:p.Pro261His	Somatic		Capture	Illumina HiSeq	Phase_I	30179313	NM_002363	B2RC79|O00601|O75862|Q6FHJ0|Q96CW8	Missense_Mutation	SNP	ENST00000378981.3	37	CCDS14222.1	.	.	.	.	.	.	.	.	.	.	C	9.108	1.005830	0.19199	.	.	ENSG00000214107	ENST00000378981;ENST00000397550;ENST00000397548	T;T;T	0.06294	3.32;3.32;3.32	3.99	1.23	0.21249	.	0.258718	0.38720	N	0.001584	T	0.30885	0.0779	H	0.96861	3.895	0.09310	N	1	D	0.89917	1.0	D	0.85130	0.997	T	0.14615	-1.0466	10	0.87932	D	0	.	5.8696	0.18797	0.0:0.6225:0.2632:0.1143	.	261	P43366	MAGB1_HUMAN	H	261	ENSP00000368264:P261H;ENSP00000380683:P261H;ENSP00000380681:P261H	ENSP00000368264:P261H	P	+	2	0	MAGEB1	30179313	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	-0.373000	0.07494	0.126000	0.18424	0.600000	0.82982	CCC		0.493	MAGEB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056160.1	NM_002363	
TAB3	257397	broad.mit.edu	37	X	30877628	30877628	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:30877628G>A	ENST00000378933.1	-	2	255	c.78C>T	c.(76-78)ggC>ggT	p.G26G	TAB3_ENST00000378932.2_Silent_p.G26G|TAB3_ENST00000378930.3_Silent_p.G26G|TAB3_ENST00000288422.2_Silent_p.G26G	NM_152787.3	NP_690000.2	Q8N5C8	TAB3_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 3	26	CUE. {ECO:0000255|PROSITE- ProRule:PRU00468}.				activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)	p.G26G(1)		NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|skin(1)	27						GAGACACCACGCCCTCTGGAA	0.448																																					p.G26G	Pancreas(164;1598 1985 29022 43301 49529)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C78T	X						.						100.0	77.0	85.0					X																	30877628		2202	4300	6502	30787549	SO:0001819	synonymous_variant	257397	exon5			AY331591	CCDS14226.1	Xp21.2	2010-02-05	2010-02-05	2010-02-05	ENSG00000157625	ENSG00000157625			30681	protein-coding gene	gene with protein product	"""TAK1 binding protein 3"""	300480	"""mitogen-activated protein kinase kinase kinase 7 interacting protein 3"""	MAP3K7IP3		14633987, 14670075	Standard	XM_005274482		Approved		uc004dcj.3	Q8N5C8	OTTHUMG00000021329	ENST00000378933.1:c.78C>T	X.37:g.30877628G>A		Somatic		Capture	Illumina HiSeq	Phase_I	30787549	NM_152787	A6NDD9|Q6VQR0	Silent	SNP	ENST00000378933.1	37	CCDS14226.1																																																																																				0.448	TAB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056173.1	NM_152787	
DMD	1756	broad.mit.edu	37	X	31144783	31144783	+	Missense_Mutation	SNP	A	A	T	rs398123849		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:31144783A>T	ENST00000357033.4	-	78	11228	c.11022T>A	c.(11020-11022)aaT>aaA	p.N3674K	DMD_ENST00000378707.3_Missense_Mutation_p.N1214K|DMD_ENST00000474231.1_Intron|DMD_ENST00000378702.4_Missense_Mutation_p.N606K|DMD_ENST00000541735.1_Missense_Mutation_p.N1104K|DMD_ENST00000378680.2_Intron|DMD_ENST00000359836.1_Intron|DMD_ENST00000378677.2_Missense_Mutation_p.N3670K|DMD_ENST00000378723.3_Intron|DMD_ENST00000343523.2_Intron|DMD_ENST00000361471.4_Intron	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	3674					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.N1214K(1)|p.N3669K(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				TTCCAGGGGTATTTCTTCCTT	0.388																																					p.N606K												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T1818A	X						.						92.0	78.0	83.0					X																	31144783		2202	4300	6502	31054704	SO:0001583	missense	1756	exon17			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.11022T>A	X.37:g.31144783A>T	ENSP00000354923:p.Asn3674Lys	Somatic		Capture	Illumina HiSeq	Phase_I	31054704	NM_004015	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	37	CCDS14233.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.68|18.68	3.675361|3.675361	0.67928|0.67928	.|.	.|.	ENSG00000198947|ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280;ENST00000378707;ENST00000541735;ENST00000378702|ENST00000465285	T;T;T;T;T|.	0.60424|.	0.19;0.19;3.98;3.96;2.32|.	6.02|6.02	6.02|6.02	0.97574|0.97574	.|.	0.000000|.	0.39475|.	U|.	0.001359|.	T|T	0.62829|0.62829	0.2460|0.2460	L|L	0.46157|0.46157	1.445|1.445	0.39853|0.39853	D|D	0.973275|0.973275	P;P;P;P;P;B;P;B;B;B|.	0.44139|.	0.827;0.734;0.734;0.734;0.734;0.004;0.728;0.244;0.0;0.019|.	B;B;B;B;B;B;B;B;B;B|.	0.44133|.	0.442;0.257;0.257;0.257;0.257;0.004;0.081;0.041;0.002;0.011|.	T|T	0.62011|0.62011	-0.6944|-0.6944	10|5	0.72032|.	D|.	0.01|.	.|.	15.449|15.449	0.75257|0.75257	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	3666;3674;3670;2333;2330;1214;1104;3551;593;606|.	P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6;E7EQS5;F5GZY3;F5GZT3;Q6NSJ9;E9PDN1|.	.;DMD_HUMAN;.;.;.;.;.;.;.;.|.	K|N	3666;2333;2330;3670;3674;3674;3551;1214;1104;606|1413	ENSP00000367948:N3670K;ENSP00000354923:N3674K;ENSP00000367979:N1214K;ENSP00000444119:N1104K;ENSP00000367974:N606K|.	ENSP00000354923:N3674K|.	N|Y	-|-	3|1	2|0	DMD|DMD	31054704|31054704	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	6.778000|6.778000	0.75043|0.75043	2.032000|2.032000	0.59987|0.59987	0.481000|0.481000	0.45027|0.45027	AAT|TAC		0.388	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
DMD	1756	broad.mit.edu	37	X	31792124	31792124	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:31792124T>A	ENST00000357033.4	-	51	7701	c.7495A>T	c.(7495-7497)Atg>Ttg	p.M2499L	DMD_ENST00000359836.1_Missense_Mutation_p.M39L|DMD_ENST00000541735.1_Missense_Mutation_p.M39L|DMD_ENST00000378677.2_Missense_Mutation_p.M2495L|DMD_ENST00000343523.2_Missense_Mutation_p.M39L|DMD_ENST00000474231.1_Missense_Mutation_p.M39L|DMD_ENST00000378707.3_Missense_Mutation_p.M39L	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	2499					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.M2494L(1)|p.M39L(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				TCACCCACCATCACCCTCTGT	0.413																																					p.M39L												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A115T	X						.						106.0	97.0	100.0					X																	31792124		2202	4300	6502	31702045	SO:0001583	missense	1756	exon8			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.7495A>T	X.37:g.31792124T>A	ENSP00000354923:p.Met2499Leu	Somatic		Capture	Illumina HiSeq	Phase_I	31702045	NM_004021	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	37	CCDS14233.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.32|15.32	2.799140|2.799140	0.50208|0.50208	.|.	.|.	ENSG00000198947|ENSG00000198947	ENST00000465285|ENST00000534884;ENST00000378682;ENST00000378684;ENST00000358062;ENST00000378677;ENST00000357033;ENST00000359836;ENST00000343523;ENST00000542849;ENST00000535280;ENST00000378707;ENST00000541735;ENST00000474231	.|T;T;T;T;T;T;T;T	.|0.33654	.|1.4;1.4;1.4;1.4;1.4;1.4;1.4;1.4	5.08|5.08	5.08|5.08	0.68730|0.68730	.|.	.|0.185391	.|0.26362	.|U	.|0.024812	T|T	0.25457|0.25457	0.0619|0.0619	N|N	0.19112|0.19112	0.55|0.55	0.35276|0.35276	D|D	0.780892|0.780892	.|B;B;B;B;B;B;B;B;B;B	.|0.24920	.|0.114;0.065;0.059;0.017;0.039;0.0;0.004;0.004;0.017;0.014	.|B;B;B;B;B;B;B;B;B;B	.|0.26969	.|0.075;0.037;0.042;0.016;0.016;0.002;0.027;0.027;0.023;0.014	T|T	0.26849|0.26849	-1.0091|-1.0091	5|10	.|0.23891	.|T	.|0.37	.|.	14.0022|14.0022	0.64439|0.64439	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|2491;2499;2495;1158;1155;39;39;39;39;39	.|P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6;F8VX32;E7ESB2;E7EQS5;E7EQR9;F5GZY3	.|.;DMD_HUMAN;.;.;.;.;.;.;.;.	V|L	227|2491;1158;1155;195;2495;2499;39;39;2499;2376;39;39;39	.|ENSP00000350765:M195L;ENSP00000367948:M2495L;ENSP00000354923:M2499L;ENSP00000352894:M39L;ENSP00000340057:M39L;ENSP00000367979:M39L;ENSP00000444119:M39L;ENSP00000417123:M39L	.|ENSP00000340057:M39L	D|M	-|-	2|1	0|0	DMD|DMD	31702045|31702045	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	2.782000|2.782000	0.47758|0.47758	1.682000|1.682000	0.51000|0.51000	0.481000|0.481000	0.45027|0.45027	GAT|ATG		0.413	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
DMD	1756	broad.mit.edu	37	X	32466598	32466598	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:32466598A>G	ENST00000357033.4	-	27	3967	c.3761T>C	c.(3760-3762)cTg>cCg	p.L1254P	DMD_ENST00000378677.2_Missense_Mutation_p.L1250P	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	1254					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.L1249P(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				TTTCCCATTCAGCCTAGTGCA	0.418																																					p.L1254P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T3761C	X						.						179.0	138.0	152.0					X																	32466598		2202	4300	6502	32376519	SO:0001583	missense	1756	exon27			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.3761T>C	X.37:g.32466598A>G	ENSP00000354923:p.Leu1254Pro	Somatic		Capture	Illumina HiSeq	Phase_I	32376519	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	37	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.003175	0.74932	.	.	ENSG00000198947	ENST00000534884;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280	T;T	0.53857	0.6;0.6	4.94	4.94	0.65067	.	0.000000	0.28515	U	0.015073	T	0.62024	0.2394	L	0.32530	0.975	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	0.64257	-0.6450	10	0.54805	T	0.06	.	13.9383	0.64039	1.0:0.0:0.0:0.0	.	1246;1254;1250	P11532-4;P11532;E9PDN5	.;DMD_HUMAN;.	P	1246;1250;1254;1254;1131	ENSP00000367948:L1250P;ENSP00000354923:L1254P	ENSP00000354923:L1254P	L	-	2	0	DMD	32376519	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.634000	0.91002	1.736000	0.51660	0.441000	0.28932	CTG		0.418	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
CASK	8573	broad.mit.edu	37	X	41530769	41530769	+	Silent	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:41530769G>A	ENST00000378163.1	-	6	918	c.444C>T	c.(442-444)ctC>ctT	p.L148L	CASK_ENST00000378166.4_Silent_p.L148L|CASK_ENST00000378158.1_Silent_p.L148L|CASK_ENST00000421587.2_Silent_p.L148L|CASK_ENST00000361962.4_Silent_p.L148L|CASK_ENST00000442742.2_Silent_p.L148L|CASK_ENST00000378154.1_Silent_p.L148L|CASK_ENST00000318588.9_Silent_p.L148L			O14936	CSKP_HUMAN	calcium/calmodulin-dependent serine protein kinase (MAGUK family)	148	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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.L148L(1)		breast(3)|endometrium(5)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|ovary(3)|prostate(1)|stomach(1)	32						TTGAGGCAAGGAGAACACAGT	0.413																																					p.L148L	NSCLC(42;104 1086 3090 27189 35040)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C444T	X						.						56.0	54.0	55.0					X																	41530769		2203	4300	6503	41415713	SO:0001819	synonymous_variant	8573	exon6			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.444C>T	X.37:g.41530769G>A		Somatic		Capture	Illumina HiSeq	Phase_I	41415713	NM_001126054	A6NES1|B7ZKY0|O43215|Q17RI4|Q59HA0|Q5VT16|Q5VT17|Q5VT18|Q5VT19|Q66T42|Q9BYH6|Q9NYB2|Q9NYB3	Silent	SNP	ENST00000378163.1	37																																																																																					0.413	CASK-007	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000056285.1	NM_003688	
UBA1	7317	broad.mit.edu	37	X	47060930	47060930	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:47060930C>T	ENST00000335972.6	+	8	915	c.732C>T	c.(730-732)agC>agT	p.S244S	UBA1_ENST00000377351.4_Silent_p.S244S	NM_003334.3	NP_003325.2	P22314	UBA1_HUMAN	ubiquitin-like modifier activating enzyme 1	244	2 approximate repeats.				cell death (GO:0008219)|cellular response to DNA damage stimulus (GO:0006974)|modification-dependent protein catabolic process (GO:0019941)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)	p.S244S(1)		breast(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						GGTTTGAGAGCGGGGACTTTG	0.552																																					p.S244S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C732T	X						.						37.0	32.0	33.0					X																	47060930		2203	4300	6503	46945874	SO:0001819	synonymous_variant	7317	exon8			AF258566	CCDS14275.1	Xp11.23	2014-08-13	2007-11-30	2007-11-30	ENSG00000130985	ENSG00000130985	6.3.2.19	"""Ubiquitin-like modifier activating enzymes"""	12469	protein-coding gene	gene with protein product	"""UBA1, ubiquitin-activating enzyme E1 homolog (yeast)"", ""POC20 centriolar protein homolog (Chlamydomonas)"""	314370	"""ubiquitin-activating enzyme E1 (A1S9T and BN75 temperature sensitivity complementing)"", ""ubiquitin-activating enzyme E1"""	A1S9T, GXP1, UBE1		1845793	Standard	NM_153280		Approved	UBE1X, POC20, CFAP124	uc004dhj.4	P22314	OTTHUMG00000021436	ENST00000335972.6:c.732C>T	X.37:g.47060930C>T		Somatic		Capture	Illumina HiSeq	Phase_I	46945874	NM_153280	Q5JRR8|Q96E13	Silent	SNP	ENST00000335972.6	37	CCDS14275.1																																																																																				0.552	UBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056389.1	NM_003334	
PORCN	64840	broad.mit.edu	37	X	48369710	48369710	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:48369710G>A	ENST00000326194.6	+	2	207	c.164G>A	c.(163-165)aGc>aAc	p.S55N	PORCN_ENST00000355961.4_Missense_Mutation_p.S55N|PORCN_ENST00000355092.3_Missense_Mutation_p.S55N|PORCN_ENST00000367574.4_Intron|PORCN_ENST00000537758.1_Missense_Mutation_p.S55N|AF196972.9_ENST00000445586.1_RNA|PORCN_ENST00000486272.1_3'UTR|PORCN_ENST00000359882.4_Missense_Mutation_p.S55N|PORCN_ENST00000361988.3_Missense_Mutation_p.S55N	NM_203475.1	NP_982301.1	Q9H237	PORCN_HUMAN	porcupine homolog (Drosophila)	55	Leu-rich.				glycoprotein metabolic process (GO:0009100)|Wnt signaling pathway (GO:0016055)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|integral component of endoplasmic reticulum membrane (GO:0030176)	transferase activity, transferring acyl groups (GO:0016746)	p.S55N(1)		breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						AAGCATGCAAGCACCGTGGCA	0.552											OREG0019764	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S55N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G164A	X						.						136.0	114.0	121.0					X																	48369710		2203	4300	6503	48254654	SO:0001583	missense	64840	exon2			AF317058	CCDS14296.1, CCDS14297.1, CCDS14298.1, CCDS14299.1	Xp11.23	2014-02-05			ENSG00000102312	ENSG00000102312			17652	protein-coding gene	gene with protein product		300651	"""dermal hypoplasia, focal"""	DHOF		10866835, 12034504, 17546030	Standard	NM_203474		Approved	MG61, PORC, PPN, por	uc004djv.1	Q9H237	OTTHUMG00000024116	ENST00000326194.6:c.164G>A	X.37:g.48369710G>A	ENSP00000322304:p.Ser55Asn	Somatic	954	Capture	Illumina HiSeq	Phase_I	48254654	NM_203474	B2RBN8|B7ZAR3|Q14829|Q9H234|Q9H235|Q9H236|Q9UJU7	Missense_Mutation	SNP	ENST00000326194.6	37	CCDS14299.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.736532	0.89482	.	.	ENSG00000102312	ENST00000359882;ENST00000537758;ENST00000355961;ENST00000489940;ENST00000361988;ENST00000326194;ENST00000355092	D;D;D;D;D;D;D	0.97642	-3.47;-4.47;-3.48;-2.5;-3.48;-4.47;-3.47	5.7	5.7	0.88788	.	0.088915	0.85682	D	0.000000	D	0.97598	0.9213	L	0.60455	1.87	0.80722	D	1	D;D;D;D;D	0.76494	0.989;0.98;0.989;0.989;0.999	P;B;P;P;D	0.68943	0.663;0.445;0.663;0.663;0.961	D	0.97180	0.9850	10	0.38643	T	0.18	-13.1091	14.0646	0.64821	0.0:0.0:1.0:0.0	.	55;55;55;55;55	Q9H237-3;Q9H237;Q9H237-4;Q9H237-2;C9JWI5	.;PORCN_HUMAN;.;.;.	N	55	ENSP00000352946:S55N;ENSP00000446401:S55N;ENSP00000348233:S55N;ENSP00000419212:S55N;ENSP00000354978:S55N;ENSP00000322304:S55N;ENSP00000347207:S55N	ENSP00000322304:S55N	S	+	2	0	PORCN	48254654	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.598000	0.74122	2.393000	0.81446	0.594000	0.82650	AGC		0.552	PORCN-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000356990.1	NM_022825	
WDR13	64743	broad.mit.edu	37	X	48458718	48458718	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:48458718C>T	ENST00000218056.5	+	5	1040	c.535C>T	c.(535-537)Cgc>Tgc	p.R179C	WDR13_ENST00000376729.5_Missense_Mutation_p.R179C	NM_001166426.1|NM_017883.4	NP_001159898.1|NP_060353	Q9H1Z4	WDR13_HUMAN	WD repeat domain 13	179						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R179C(1)		endometrium(1)|large_intestine(4)|lung(4)|ovary(2)	11						CCCAAGGGTGCGCTTCGCCAA	0.602																																					p.R87C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C259T	X						.						75.0	55.0	62.0					X																	48458718		2203	4300	6503	48343662	SO:0001583	missense	64743	exon4			AF329819	CCDS14302.1	Xp11.23	2013-01-09			ENSG00000101940	ENSG00000101940		"""WD repeat domain containing"""	14352	protein-coding gene	gene with protein product		300512					Standard	NM_017883		Approved		uc004dkj.2	Q9H1Z4	OTTHUMG00000024119	ENST00000218056.5:c.535C>T	X.37:g.48458718C>T	ENSP00000218056:p.Arg179Cys	Somatic		Capture	Illumina HiSeq	Phase_I	48343662	NM_001166426	Q06DW8|Q06DX0|Q06DX1|Q9BUL7|Q9NWW4	Missense_Mutation	SNP	ENST00000218056.5	37	CCDS14302.1	.	.	.	.	.	.	.	.	.	.	C	17.60	3.428796	0.62844	.	.	ENSG00000101940	ENST00000376729;ENST00000218056	T;T	0.65549	-0.16;-0.16	4.93	4.93	0.64822	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.055033	0.85682	D	0.000000	T	0.63082	0.2481	L	0.46157	1.445	0.58432	D	0.999999	D;D	0.76494	0.999;0.986	P;P	0.49502	0.613;0.582	T	0.65747	-0.6093	10	0.48119	T	0.1	-22.6207	14.6671	0.68915	0.0:1.0:0.0:0.0	.	57;179	B4DVQ7;Q9H1Z4	.;WDR13_HUMAN	C	179	ENSP00000365919:R179C;ENSP00000218056:R179C	ENSP00000218056:R179C	R	+	1	0	WDR13	48343662	1.000000	0.71417	1.000000	0.80357	0.344000	0.29017	5.150000	0.64869	2.044000	0.60594	0.436000	0.28706	CGC		0.602	WDR13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060743.2		
GRIPAP1	56850	broad.mit.edu	37	X	48855871	48855871	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:48855871C>T	ENST00000376441.1	-	2	122	c.88G>A	c.(88-90)Gaa>Aaa	p.E30K	GRIPAP1_ENST00000376425.3_Missense_Mutation_p.E30K|GRIPAP1_ENST00000376444.3_Missense_Mutation_p.E30K|GRIPAP1_ENST00000376423.4_Missense_Mutation_p.E30K	NM_020137.3	NP_064522.3	Q4V328	GRAP1_HUMAN	GRIP1 associated protein 1	30						blood microparticle (GO:0072562)|endosome (GO:0005768)		p.E30K(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(2)	10						TTGCGTAGTTCATCTGAAAGC	0.557																																					p.E30K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G88A	X						.						139.0	106.0	117.0					X																	48855871		2203	4300	6503	48740815	SO:0001583	missense	56850	exon2			AB032993	CCDS35248.1	Xp11.23	2008-02-05			ENSG00000068400	ENSG00000068400			18706	protein-coding gene	gene with protein product		300408				10896157	Standard	NM_020137		Approved	GRASP-1, GRASP1, KIAA1167, MPMGp800B12492Q3, DKFZp434P0630	uc004dly.1	Q4V328	OTTHUMG00000033192	ENST00000376441.1:c.88G>A	X.37:g.48855871C>T	ENSP00000365624:p.Glu30Lys	Somatic		Capture	Illumina HiSeq	Phase_I	48740815	NM_020137	A6NL78|Q3MJ75|Q4V327|Q4V330|Q5HYG1|Q6N046|Q96DH8|Q9NQ43|Q9ULQ3	Missense_Mutation	SNP	ENST00000376441.1	37	CCDS35248.1	.	.	.	.	.	.	.	.	.	.	c	27.8	4.862171	0.91511	.	.	ENSG00000068400	ENST00000376425;ENST00000376444;ENST00000376441;ENST00000537291;ENST00000376423	T;T;T;T	0.26518	1.73;1.73;1.73;1.73	5.13	5.13	0.70059	.	0.124416	0.53938	D	0.000059	T	0.25754	0.0627	L	0.43152	1.355	0.41759	D	0.989707	P;P	0.50272	0.933;0.592	P;B	0.44811	0.461;0.226	T	0.02104	-1.1213	10	0.22706	T	0.39	-12.9154	14.4662	0.67485	0.0:1.0:0.0:0.0	.	30;30	Q4V328-2;Q4V328	.;GRAP1_HUMAN	K	30	ENSP00000365608:E30K;ENSP00000365627:E30K;ENSP00000365624:E30K;ENSP00000365606:E30K	ENSP00000365606:E30K	E	-	1	0	GRIPAP1	48740815	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.156000	0.71840	2.390000	0.81377	0.521000	0.50471	GAA		0.557	GRIPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080970.2	NM_207672	
PPP1R3F	89801	broad.mit.edu	37	X	49126720	49126720	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:49126720C>T	ENST00000055335.6	+	1	404	c.388C>T	c.(388-390)Cgc>Tgc	p.R130C	PPP1R3F_ENST00000495799.1_Intron|LL0XNC01-7P3.1_ENST00000602455.1_lincRNA|PPP1R3F_ENST00000438316.1_Intron|PPP1R3F_ENST00000466508.1_Intron	NM_033215.4	NP_149992.3	Q6ZSY5	PPR3F_HUMAN	protein phosphatase 1, regulatory subunit 3F	130	CBM21. {ECO:0000255|PROSITE- ProRule:PRU00491}.				regulation of glycogen (starch) synthase activity (GO:2000465)|regulation of glycogen biosynthetic process (GO:0005979)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycogen binding (GO:2001069)|protein phosphatase binding (GO:0019903)	p.R130C(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(4)	27	Ovarian(276;0.236)					CCGTCTGGAGCGCTTGGGGCG	0.771																																					p.R130C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C388T	X						.						3.0	3.0	3.0					X																	49126720		1639	3354	4993	49013664	SO:0001583	missense	89801	exon1				CCDS35254.1, CCDS55415.1	Xp11.23	2012-04-17	2011-10-04		ENSG00000049769	ENSG00000049769		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14944	protein-coding gene	gene with protein product			"""protein phosphatase 1, regulatory (inhibitor) subunit 3F"""			11948623	Standard	NM_033215		Approved	Hb2E	uc004dnh.2	Q6ZSY5	OTTHUMG00000024139	ENST00000055335.6:c.388C>T	X.37:g.49126720C>T	ENSP00000055335:p.Arg130Cys	Somatic		Capture	Illumina HiSeq	Phase_I	49013664	NM_033215	A2VDJ8|B3KPW2|E9PCM3	Missense_Mutation	SNP	ENST00000055335.6	37	CCDS35254.1	.	.	.	.	.	.	.	.	.	.	c	21.6	4.172961	0.78452	.	.	ENSG00000049769	ENST00000055335	T	0.59772	0.24	4.13	4.13	0.48395	Putative phosphatase regulatory subunit (1);	0.000000	0.37012	N	0.002297	T	0.68879	0.3049	L	0.52126	1.63	0.80722	D	1	D	0.89917	1.0	D	0.70935	0.971	T	0.72717	-0.4209	10	0.87932	D	0	-0.9117	13.438	0.61094	0.0:1.0:0.0:0.0	.	130	Q6ZSY5	PPR3F_HUMAN	C	130	ENSP00000055335:R130C	ENSP00000055335:R130C	R	+	1	0	PPP1R3F	49013664	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.776000	0.47709	1.821000	0.53095	0.515000	0.50301	CGC		0.771	PPP1R3F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060819.2	NM_033215	
HUWE1	10075	broad.mit.edu	37	X	53615446	53615446	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:53615446T>G	ENST00000342160.3	-	36	4967	c.4510A>C	c.(4510-4512)Aca>Cca	p.T1504P	HUWE1_ENST00000218328.8_Missense_Mutation_p.T1504P|HUWE1_ENST00000262854.6_Missense_Mutation_p.T1504P			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	1504					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.T1367P(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						GTGTCACTTGTTGTCAGGGGA	0.463																																					p.T1504P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A4510C	X						.						110.0	75.0	87.0					X																	53615446		2203	4300	6503	53632171	SO:0001583	missense	10075	exon37			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.4510A>C	X.37:g.53615446T>G	ENSP00000340648:p.Thr1504Pro	Somatic		Capture	Illumina HiSeq	Phase_I	53632171	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	37	CCDS35301.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.70|17.70	3.455177|3.455177	0.63401|0.63401	.|.	.|.	ENSG00000086758|ENSG00000086758	ENST00000427052|ENST00000342160;ENST00000262854;ENST00000218328	.|T;T;T	.|0.49720	.|1.05;1.05;0.77	5.83|5.83	5.83|5.83	0.93111|0.93111	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.35970|0.35970	0.0950|0.0950	N|N	0.19112|0.19112	0.55|0.55	0.58432|0.58432	D|D	0.999996|0.999996	.|B;B	.|0.25169	.|0.03;0.119	.|B;B	.|0.25405	.|0.018;0.06	T|T	0.20371|0.20371	-1.0277|-1.0277	5|10	.|0.62326	.|D	.|0.03	.|.	14.0422|14.0422	0.64684|0.64684	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|1504;1504	.|Q7Z6Z7;Q7Z6Z7-2	.|HUWE1_HUMAN;.	T|P	537|1504	.|ENSP00000340648:T1504P;ENSP00000262854:T1504P;ENSP00000218328:T1504P	.|ENSP00000218328:T1504P	N|T	-|-	2|1	0|0	HUWE1|HUWE1	53632171|53632171	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	7.708000|7.708000	0.84633|0.84633	1.962000|1.962000	0.57031|0.57031	0.486000|0.486000	0.48141|0.48141	AAC|ACA		0.463	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119	
USP51	158880	broad.mit.edu	37	X	55515254	55515254	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:55515254G>T	ENST00000500968.3	-	2	201	c.119C>A	c.(118-120)gCg>gAg	p.A40E	USP51_ENST00000586165.1_5'Flank	NM_201286.3	NP_958443.1	Q70EK9	UBP51_HUMAN	ubiquitin specific peptidase 51	40					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.A40E(1)		NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	30						CCCCGCCGCCGCCTCCTCCAT	0.647																																					p.A40E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C119A	X						.						16.0	17.0	16.0					X																	55515254		2189	4290	6479	55531979	SO:0001583	missense	158880	exon2			BF741256	CCDS14370.1	Xp11	2009-03-19	2005-08-08		ENSG00000247746	ENSG00000247746		"""Ubiquitin-specific peptidases"""	23086	protein-coding gene	gene with protein product			"""ubiquitin specific protease 51"""			12838346	Standard	NM_201286		Approved		uc004dun.2	Q70EK9	OTTHUMG00000021656	ENST00000500968.3:c.119C>A	X.37:g.55515254G>T	ENSP00000423333:p.Ala40Glu	Somatic		Capture	Illumina HiSeq	Phase_I	55531979	NM_201286	Q8IWJ8	Missense_Mutation	SNP	ENST00000500968.3	37	CCDS14370.1	.	.	.	.	.	.	.	.	.	.	.	0.068	-1.208820	0.01568	.	.	ENSG00000247746	ENST00000500968	T	0.08008	3.14	2.09	-0.62	0.11567	.	.	.	.	.	T	0.03011	0.0089	N	0.08118	0	0.20074	N	0.999936	B	0.02656	0.0	B	0.01281	0.0	T	0.45585	-0.9251	9	0.02654	T	1	.	6.0368	0.19712	0.0:0.0:0.4956:0.5044	.	40	Q70EK9	UBP51_HUMAN	E	40	ENSP00000423333:A40E	ENSP00000423333:A40E	A	-	2	0	USP51	55531979	0.762000	0.28451	0.692000	0.30179	0.183000	0.23260	-0.144000	0.10280	-0.206000	0.10203	-0.534000	0.04291	GCG		0.647	USP51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056871.2	NM_201286	
ZXDA	7789	broad.mit.edu	37	X	57935790	57935790	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:57935790C>T	ENST00000358697.4	-	1	1277	c.1065G>A	c.(1063-1065)gaG>gaA	p.E355E		NM_007156.4	NP_009087.1	P98168	ZXDA_HUMAN	zinc finger, X-linked, duplicated A	355	Required for interaction with ZXDC.				positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E355E(1)		breast(2)|endometrium(9)|kidney(1)|large_intestine(7)|lung(13)|ovary(2)|prostate(2)|skin(1)	37						AGTTCTCCTGCTCATGGCCCT	0.617																																					p.E355E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1065A	X						.						76.0	67.0	70.0					X																	57935790		2203	4300	6503	57952515	SO:0001819	synonymous_variant	7789	exon1			L14787	CCDS14376.1	Xp11.21	2013-01-08			ENSG00000198205	ENSG00000198205		"""Zinc fingers, C2H2-type"""	13198	protein-coding gene	gene with protein product	"""zinc finger protein 896"""	300235				8268913	Standard	NM_007156		Approved	ZNF896	uc004dve.3	P98168	OTTHUMG00000021688	ENST00000358697.4:c.1065G>A	X.37:g.57935790C>T		Somatic		Capture	Illumina HiSeq	Phase_I	57952515	NM_007156	Q9UJP7	Silent	SNP	ENST00000358697.4	37	CCDS14376.1																																																																																				0.617	ZXDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056925.1	NM_007156	
OPHN1	4983	broad.mit.edu	37	X	67293106	67293106	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:67293106C>T	ENST00000355520.5	-	20	2363	c.1722G>A	c.(1720-1722)ccG>ccA	p.P574P	OPHN1_ENST00000484842.1_5'UTR|OPHN1_ENST00000540071.1_Silent_p.P574P	NM_002547.2	NP_002538.1	O60890	OPHN1_HUMAN	oligophrenin 1	574					actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|negative regulation of proteasomal protein catabolic process (GO:1901799)|nervous system development (GO:0007399)|regulation of endocytosis (GO:0030100)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of synaptic transmission, glutamatergic (GO:0051966)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|substrate-dependent cell migration, cell extension (GO:0006930)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|terminal bouton (GO:0043195)	phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)	p.P574P(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(3)|skin(2)	31						GAGGCACTGGCGGTGCAGCGC	0.468																																					p.P574P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1722A	X						.						91.0	71.0	78.0					X																	67293106		2203	4300	6503	67209831	SO:0001819	synonymous_variant	4983	exon20			AJ001189	CCDS14388.1	Xq12	2011-07-04			ENSG00000079482	ENSG00000079482		"""Rho GTPase activating proteins"""	8148	protein-coding gene	gene with protein product		300127	"""mental retardation, X-linked 60"""	MRX60		9195162, 9582072	Standard	NM_002547		Approved	OPN1, ARHGAP41	uc004dww.4	O60890	OTTHUMG00000021744	ENST00000355520.5:c.1722G>A	X.37:g.67293106C>T		Somatic		Capture	Illumina HiSeq	Phase_I	67209831	NM_002547	B9EIP8|Q5JQ81|Q6PCC1|Q8WX47	Silent	SNP	ENST00000355520.5	37	CCDS14388.1																																																																																				0.468	OPHN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057011.1	NM_002547	
STARD8	9754	broad.mit.edu	37	X	67943585	67943585	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:67943585C>T	ENST00000252336.6	+	12	3049	c.2677C>T	c.(2677-2679)Cgg>Tgg	p.R893W	STARD8_ENST00000374599.3_Missense_Mutation_p.R973W|STARD8_ENST00000374597.3_Missense_Mutation_p.R893W	NM_014725.4	NP_055540.2	Q92502	STAR8_HUMAN	StAR-related lipid transfer (START) domain containing 8	893	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)	p.R893W(2)		NS(2)|breast(5)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(2)	50						GGATCTGCTGCGGGCCCAGGT	0.652																																					p.R893W												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C2677T	X						.						22.0	23.0	23.0					X																	67943585		2178	4271	6449	67860310	SO:0001583	missense	9754	exon12			D80011	CCDS14390.1, CCDS48134.1	Xq13.1	2011-09-13	2007-08-16		ENSG00000130052	ENSG00000130052		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	19161	protein-coding gene	gene with protein product		300689	"""START domain containing 8"""			8724849	Standard	NM_001142504		Approved	KIAA0189, ARHGAP38	uc004dxb.3	Q92502	OTTHUMG00000021748	ENST00000252336.6:c.2677C>T	X.37:g.67943585C>T	ENSP00000252336:p.Arg893Trp	Somatic		Capture	Illumina HiSeq	Phase_I	67860310	NM_014725	A8K6T2|D3DVT9|Q5JST0|Q68DG7	Missense_Mutation	SNP	ENST00000252336.6	37	CCDS14390.1	.	.	.	.	.	.	.	.	.	.	C	19.32	3.805861	0.70682	.	.	ENSG00000130052	ENST00000252336;ENST00000374599;ENST00000374597	T;T;T	0.30981	1.51;1.51;1.51	4.44	2.6	0.31112	Lipid-binding START (3);START-like domain (1);	0.184596	0.36200	N	0.002738	T	0.37100	0.0991	L	0.29908	0.895	0.38595	D	0.95051	D;D	0.89917	0.999;1.0	D;D	0.74348	0.972;0.983	T	0.25293	-1.0136	10	0.87932	D	0	.	6.7059	0.23250	0.0:0.7183:0.1771:0.1046	.	973;893	Q92502-2;Q92502	.;STAR8_HUMAN	W	893;973;893	ENSP00000252336:R893W;ENSP00000363727:R973W;ENSP00000363725:R893W	ENSP00000252336:R893W	R	+	1	2	STARD8	67860310	1.000000	0.71417	0.995000	0.50966	0.992000	0.81027	1.788000	0.38714	0.323000	0.23307	0.600000	0.82982	CGG		0.652	STARD8-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057026.2	NM_014725	
AWAT1	158833	broad.mit.edu	37	X	69459685	69459685	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:69459685C>T	ENST00000374521.3	+	6	774	c.733C>T	c.(733-735)Cgc>Tgc	p.R245C		NM_001013579.2	NP_001013597.1	Q58HT5	AWAT1_HUMAN	acyl-CoA wax alcohol acyltransferase 1	245					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	long-chain-alcohol O-fatty-acyltransferase activity (GO:0047196)	p.R325C(1)		breast(2)|central_nervous_system(1)|large_intestine(4)|lung(3)|ovary(4)|skin(1)	15						GAGCTGCTTCCGCCGTATCTT	0.507																																					p.R245C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C733T	X						.						136.0	124.0	128.0					X																	69459685		2203	4300	6503	69376410	SO:0001583	missense	158833	exon6			BC039181	CCDS35321.1	Xq13.1	2010-01-25	2009-02-23	2009-02-23	ENSG00000204195	ENSG00000204195			23252	protein-coding gene	gene with protein product		300924	"""diacylglycerol O-acyltransferase 2-like 3"""	DGAT2L3		14970677, 15671038	Standard	NM_001013579		Approved		uc004dxy.3	Q58HT5	OTTHUMG00000021773	ENST00000374521.3:c.733C>T	X.37:g.69459685C>T	ENSP00000363645:p.Arg245Cys	Somatic		Capture	Illumina HiSeq	Phase_I	69376410	NM_001013579	Q5JT21|Q6IEE4	Missense_Mutation	SNP	ENST00000374521.3	37	CCDS35321.1	.	.	.	.	.	.	.	.	.	.	C	13.67	2.306410	0.40795	.	.	ENSG00000204195	ENST00000374521	T	0.14893	2.47	5.39	3.59	0.41128	.	0.188045	0.37623	N	0.002004	T	0.21674	0.0522	M	0.82517	2.595	0.34852	D	0.741752	B	0.22346	0.068	B	0.15052	0.012	T	0.15009	-1.0452	10	0.87932	D	0	-8.522	6.7915	0.23701	0.1749:0.7328:0.0:0.0923	.	245	Q58HT5	AWAT1_HUMAN	C	245	ENSP00000363645:R245C	ENSP00000363645:R245C	R	+	1	0	AWAT1	69376410	1.000000	0.71417	0.019000	0.16419	0.912000	0.54170	2.706000	0.47135	0.599000	0.29845	0.544000	0.68410	CGC		0.507	AWAT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057066.3	NM_001013579	
KIF4A	24137	broad.mit.edu	37	X	69639929	69639929	+	Silent	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:69639929C>T	ENST00000374403.3	+	31	3595	c.3513C>T	c.(3511-3513)tgC>tgT	p.C1171C	GDPD2_ENST00000536730.1_5'Flank|GDPD2_ENST00000538649.1_5'Flank|GDPD2_ENST00000453994.2_5'Flank	NM_012310.4	NP_036442.3	O95239	KIF4A_HUMAN	kinesin family member 4A	1171	Globular.|Interaction with PRC1.				anterograde axon cargo transport (GO:0008089)|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)|organelle organization (GO:0006996)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)	p.C1171C(1)		breast(6)|endometrium(9)|kidney(3)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	51						AAGAGATGTGCGATGTGGAGC	0.502																																					p.C1171C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3513T	X						.						63.0	61.0	62.0					X																	69639929		2203	4300	6503	69556654	SO:0001819	synonymous_variant	24137	exon31			AF179308	CCDS14401.1	Xq13.1	2008-08-11			ENSG00000090889	ENSG00000090889		"""Kinesins"""	13339	protein-coding gene	gene with protein product	"""chromokinesin"""	300521				10773663	Standard	NM_012310		Approved	KIF4-G1, KIF4, HSA271784, FLJ12530, FLJ12655, FLJ14204, FLJ20631	uc004dyg.3	O95239	OTTHUMG00000021775	ENST00000374403.3:c.3513C>T	X.37:g.69639929C>T		Somatic		Capture	Illumina HiSeq	Phase_I	69556654	NM_012310	B2R7V5|D3DVU4|Q86TN3|Q86XX7|Q9NNY6|Q9NY24|Q9UMW3	Silent	SNP	ENST00000374403.3	37	CCDS14401.1																																																																																				0.502	KIF4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057068.1	NM_012310	
TEX11	56159	broad.mit.edu	37	X	69830357	69830357	+	Silent	SNP	A	A	G			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:69830357A>G	ENST00000395889.2	-	22	1988	c.1833T>C	c.(1831-1833)aaT>aaC	p.N611N	TEX11_ENST00000344304.3_Silent_p.N611N|TEX11_ENST00000374333.2_Silent_p.N596N|TEX11_ENST00000374320.2_Silent_p.N286N	NM_001003811.1	NP_001003811.1	Q8IYF3	TEX11_HUMAN	testis expressed 11	611					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.N596N(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)					ATTTACCTCTATTCAGGCAAG	0.333																																					p.N611N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1833C	X						.						158.0	154.0	155.0					X																	69830357		2203	4300	6503	69747082	SO:0001819	synonymous_variant	56159	exon22			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.1833T>C	X.37:g.69830357A>G		Somatic		Capture	Illumina HiSeq	Phase_I	69747082	NM_001003811	A8K8V6|Q5JQQ8|Q96LZ4|Q96M47|Q9BXU6	Silent	SNP	ENST00000395889.2	37	CCDS35323.1																																																																																				0.333	TEX11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359072.1		
SLC7A3	84889	broad.mit.edu	37	X	70148429	70148429	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:70148429C>T	ENST00000374299.3	-	4	728	c.584G>A	c.(583-585)gGc>gAc	p.G195D	SLC7A3_ENST00000298085.4_Missense_Mutation_p.G195D			Q8WY07	CTR3_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 3	195					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	arginine transmembrane transporter activity (GO:0015181)|L-lysine transmembrane transporter activity (GO:0015189)	p.G195D(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|urinary_tract(1)	31	Renal(35;0.156)				L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	AAGGTTCACGCCTGTGAACAC	0.517																																					p.G195D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G584A	X						.						58.0	46.0	50.0					X																	70148429		2203	4300	6503	70065154	SO:0001583	missense	84889	exon4			AF320612	CCDS14404.1	Xq12	2013-05-22			ENSG00000165349	ENSG00000165349		"""Solute carriers"""	11061	protein-coding gene	gene with protein product		300443				11591158	Standard	NM_001048164		Approved	CAT-3, ATRC3, FLJ14541	uc004dyn.3	Q8WY07	OTTHUMG00000021780	ENST00000374299.3:c.584G>A	X.37:g.70148429C>T	ENSP00000363417:p.Gly195Asp	Somatic		Capture	Illumina HiSeq	Phase_I	70065154	NM_032803	D3DVU7|Q5JQR2|Q8N185|Q8NCA7|Q96SZ7	Missense_Mutation	SNP	ENST00000374299.3	37	CCDS14404.1	.	.	.	.	.	.	.	.	.	.	C	13.21	2.169419	0.38315	.	.	ENSG00000165349	ENST00000374299;ENST00000298085	D;D	0.90004	-2.6;-2.6	5.07	-3.49	0.04724	Amino acid permease domain (1);	0.537282	0.21498	N	0.073576	D	0.93677	0.7980	M	0.93808	3.46	0.19300	N	0.999971	B	0.32302	0.363	P	0.50896	0.653	D	0.90293	0.4324	10	0.56958	D	0.05	.	11.1966	0.48717	0.373:0.1404:0.4867:0.0	.	195	Q8WY07	CTR3_HUMAN	D	195	ENSP00000363417:G195D;ENSP00000298085:G195D	ENSP00000298085:G195D	G	-	2	0	SLC7A3	70065154	0.000000	0.05858	0.000000	0.03702	0.285000	0.27093	0.085000	0.14912	-1.299000	0.02344	-0.587000	0.04127	GGC		0.517	SLC7A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057080.1	NM_032803	
MED12	9968	broad.mit.edu	37	X	70340986	70340986	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:70340986C>T	ENST00000374080.3	+	5	751	c.719C>T	c.(718-720)gCc>gTc	p.A240V	MED12_ENST00000374102.1_Missense_Mutation_p.A240V|MED12_ENST00000333646.6_Missense_Mutation_p.A240V			Q93074	MED12_HUMAN	mediator complex subunit 12	240					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.A240V(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)					GAGAAGCTGGCCATGTTCATG	0.562			"""M, S"""		uterine leiomyoma		Opitz-Kaveggia Syndrome																														p.A240V			Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C719T	X						.						85.0	83.0	84.0					X																	70340986		2074	4180	6254	70257711	SO:0001583	missense	9968	exon5			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.719C>T	X.37:g.70340986C>T	ENSP00000363193:p.Ala240Val	Somatic		Capture	Illumina HiSeq	Phase_I	70257711	NM_005120	O15410|O75557|Q9UHV6|Q9UND7	Missense_Mutation	SNP	ENST00000374080.3	37	CCDS43970.1	.	.	.	.	.	.	.	.	.	.	.	23.4	4.409669	0.83340	.	.	ENSG00000184634	ENST00000333646;ENST00000536756;ENST00000374102;ENST00000374080;ENST00000430072	T;T;T;T	0.58652	0.36;0.36;0.36;0.32	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.76285	0.3966	M	0.73962	2.25	0.80722	D	1	P;D;D;P	0.69078	0.508;0.997;0.992;0.548	B;D;D;B	0.75020	0.264;0.985;0.966;0.288	T	0.76274	-0.3019	10	0.46703	T	0.11	-14.4313	18.4857	0.90828	0.0:1.0:0.0:0.0	.	240;87;240;240	F5H3Y1;Q7Z3Z5;Q93074-3;Q93074	.;.;.;MED12_HUMAN	V	240;240;240;240;208	ENSP00000333125:A240V;ENSP00000363215:A240V;ENSP00000363193:A240V;ENSP00000414203:A208V	ENSP00000333125:A240V	A	+	2	0	MED12	70257711	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.434000	0.80377	2.562000	0.86427	0.600000	0.82982	GCC		0.562	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120	
GJB1	2705	broad.mit.edu	37	X	70444105	70444105	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:70444105G>A	ENST00000374022.3	+	2	643	c.548G>A	c.(547-549)cGc>cAc	p.R183H	GJB1_ENST00000361726.6_Missense_Mutation_p.R183H|GJB1_ENST00000374029.1_Missense_Mutation_p.R183H	NM_001097642.2	NP_001091111.1	P08034	CXB1_HUMAN	gap junction protein, beta 1, 32kDa	183			R -> C (in CMTX1). {ECO:0000269|PubMed:9187667, ECO:0000269|PubMed:9361298}.|R -> H (in CMTX1). {ECO:0000269|PubMed:10737979, ECO:0000269|PubMed:12477701, ECO:0000269|PubMed:9187667, ECO:0000269|PubMed:9361298}.|R -> S (in CMTX1). {ECO:0000269|PubMed:9187667, ECO:0000269|PubMed:9361298}.		cell death (GO:0008219)|cell-cell signaling (GO:0007267)|gap junction assembly (GO:0016264)|membrane organization (GO:0061024)|nervous system development (GO:0007399)|protein oligomerization (GO:0051259)|purine ribonucleotide transport (GO:0015868)|transport (GO:0006810)	connexon complex (GO:0005922)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	gap junction channel activity (GO:0005243)	p.R183H(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(1)	10	Renal(35;0.156)					TTCGTGTCCCGCCCCACCGAG	0.572																																					p.R183H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G548A	X	GRCh37	CM081653|CM970670	GJB1	M		.						108.0	72.0	84.0					X																	70444105		2203	4300	6503	70360830	SO:0001583	missense	2705	exon2			X04325	CCDS14408.1	Xq13.1	2014-09-17	2007-01-16		ENSG00000169562	ENSG00000169562		"""Ion channels / Gap junction proteins (connexins)"""	4283	protein-coding gene	gene with protein product	"""Charcot-Marie-Tooth neuropathy, X-linked"", ""connexin 32"""	304040	"""gap junction protein, beta 1, 32kD (connexin 32, Charcot-Marie-Tooth neuropathy, X-linked)"", ""gap junction protein, beta 1, 32kDa (connexin 32, Charcot-Marie-Tooth neuropathy, X-linked)"", ""gap junction protein, beta 1, 32kDa (connexin 32)"""	CMTX1, CMTX		1319395	Standard	NM_000166		Approved	CX32	uc004dzf.3	P08034	OTTHUMG00000021797	ENST00000374022.3:c.548G>A	X.37:g.70444105G>A	ENSP00000363134:p.Arg183His	Somatic		Capture	Illumina HiSeq	Phase_I	70360830	NM_000166	B2R8R2|D3DVV2|Q5U0S4	Missense_Mutation	SNP	ENST00000374022.3	37	CCDS14408.1	.	.	.	.	.	.	.	.	.	.	G	19.10	3.761907	0.69763	.	.	ENSG00000169562	ENST00000374029;ENST00000374022;ENST00000361726	D;D;D	0.97404	-4.37;-4.37;-4.37	4.99	4.99	0.66335	Gap junction protein, cysteine-rich domain (1);Connexin, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.98582	0.9526	M	0.87971	2.92	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99761	1.1021	10	0.72032	D	0.01	.	17.5026	0.87736	0.0:0.0:1.0:0.0	.	183	P08034	CXB1_HUMAN	H	183	ENSP00000363141:R183H;ENSP00000363134:R183H;ENSP00000354900:R183H	ENSP00000354900:R183H	R	+	2	0	GJB1	70360830	1.000000	0.71417	1.000000	0.80357	0.543000	0.35085	9.654000	0.98509	2.317000	0.78254	0.592000	0.82586	CGC		0.572	GJB1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057133.1	NM_000166	
NAP1L2	4674	broad.mit.edu	37	X	72433103	72433103	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:72433103G>T	ENST00000373517.3	-	1	1581	c.1226C>A	c.(1225-1227)tCa>tAa	p.S409*	NAP1L2_ENST00000536638.1_Nonsense_Mutation_p.S267*	NM_021963.3	NP_068798.1	Q9ULW6	NP1L2_HUMAN	nucleosome assembly protein 1-like 2	409					nucleosome assembly (GO:0006334)|positive regulation of histone H3-K14 acetylation (GO:0071442)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of neuron differentiation (GO:0045666)|regulation of stem cell division (GO:2000035)	nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.S409*(1)		NS(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(12)|skin(3)	29	Renal(35;0.156)					TGCATCACCTGAGAAAAATAA	0.358																																					p.S409X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1226A	X						.						65.0	61.0	62.0					X																	72433103		2203	4300	6503	72349828	SO:0001587	stop_gained	4674	exon1			AF136178	CCDS14423.1	Xq13	2008-02-05			ENSG00000186462	ENSG00000186462			7638	protein-coding gene	gene with protein product		300026				8789438	Standard	NM_021963		Approved	BPX, MGC26243	uc004ebi.3	Q9ULW6	OTTHUMG00000021827	ENST00000373517.3:c.1226C>A	X.37:g.72433103G>T	ENSP00000362616:p.Ser409*	Somatic		Capture	Illumina HiSeq	Phase_I	72349828	NM_021963	B2RE61|B4E161|Q8TAN6	Nonsense_Mutation	SNP	ENST00000373517.3	37	CCDS14423.1	.	.	.	.	.	.	.	.	.	.	g	38	6.723473	0.97788	.	.	ENSG00000186462	ENST00000373517;ENST00000536638	.	.	.	3.03	3.03	0.35002	.	0.058376	0.64402	U	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	-4.8024	11.1562	0.48489	0.0:0.0:1.0:0.0	.	.	.	.	X	409;267	.	ENSP00000362616:S409X	S	-	2	0	NAP1L2	72349828	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.144000	0.42197	1.758000	0.51981	0.513000	0.50165	TCA		0.358	NAP1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057225.1	NM_021963	
TBX22	50945	broad.mit.edu	37	X	79282348	79282348	+	Missense_Mutation	SNP	C	C	T	rs104894943		TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:79282348C>T	ENST00000373294.5	+	5	807	c.779C>T	c.(778-780)aCg>aTg	p.T260M	TBX22_ENST00000373296.3_Missense_Mutation_p.T260M|TBX22_ENST00000442340.1_Missense_Mutation_p.T140M|TBX22_ENST00000373291.1_Missense_Mutation_p.T140M	NM_016954.2	NP_058650.1	Q9Y458	TBX22_HUMAN	T-box 22	260			T -> M (in CPX). {ECO:0000269|PubMed:11559848}.		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.T260M(2)		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						ACCACAGTAACGGCTTACCAA	0.468																																					p.T260M												.	.	2	Substitution - Missense(2)	large_intestine(1)|breast(1)	c.C779T	X	GRCh37	CM013049	TBX22	M	rs104894943	.						90.0	69.0	76.0					X																	79282348		2203	4300	6503	79169004	SO:0001583	missense	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.779C>T	X.37:g.79282348C>T	ENSP00000362390:p.Thr260Met	Somatic		Capture	Illumina HiSeq	Phase_I	79169004	NM_001109878	Q5JZ06|Q96LC0|Q9HBF1	Missense_Mutation	SNP	ENST00000373294.5	37	CCDS14445.1	.	.	.	.	.	.	.	.	.	.	C	18.98	3.738338	0.69304	.	.	ENSG00000122145	ENST00000373296;ENST00000442340;ENST00000373294;ENST00000373291	D;D;D;D	0.92805	-3.11;-3.11;-3.11;-3.11	3.68	3.68	0.42216	p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.97192	0.9082	H	0.97158	3.95	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.98188	1.0461	10	0.87932	D	0	.	13.587	0.61937	0.0:1.0:0.0:0.0	.	260	Q9Y458	TBX22_HUMAN	M	260;140;260;140	ENSP00000362393:T260M;ENSP00000396394:T140M;ENSP00000362390:T260M;ENSP00000362388:T140M	ENSP00000362388:T140M	T	+	2	0	TBX22	79169004	1.000000	0.71417	0.937000	0.37676	0.976000	0.68499	6.801000	0.75170	1.824000	0.53156	0.594000	0.82650	ACG		0.468	TBX22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057334.1	NM_016954	
HDX	139324	broad.mit.edu	37	X	83599343	83599343	+	Silent	SNP	T	T	C			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:83599343T>C	ENST00000297977.5	-	6	1686	c.1575A>G	c.(1573-1575)ccA>ccG	p.P525P	HDX_ENST00000506585.2_Silent_p.P467P|HDX_ENST00000373177.2_Silent_p.P525P	NM_001177479.1|NM_144657.4	NP_001170950.1|NP_653258.2	Q7Z353	HDX_HUMAN	highly divergent homeobox	525						nucleus (GO:0005634)	DNA binding (GO:0003677)	p.P525P(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						CTTCCTCTCCTGGTGTGAGTG	0.463																																					p.P525P	Pancreas(53;231 1169 36156 43751 51139)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1575G	X						.						97.0	89.0	91.0					X																	83599343		2203	4300	6503	83485999	SO:0001819	synonymous_variant	139324	exon7			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.1575A>G	X.37:g.83599343T>C		Somatic		Capture	Illumina HiSeq	Phase_I	83485999	NM_001177479	A8K1Y5|B7ZL18|Q5JZB4|Q96NK7	Silent	SNP	ENST00000297977.5	37	CCDS35342.1																																																																																				0.463	HDX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057379.2	NM_144657	
AVPR2	554	broad.mit.edu	37	X	153172079	153172079	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3949-01A-01W-0995-10	TCGA-AA-3949-10A-01W-0995-10	g.chrX:153172079G>A	ENST00000358927.2	+	4	1222	c.1013G>A	c.(1012-1014)aGc>aAc	p.S338N	AVPR2_ENST00000337474.5_Missense_Mutation_p.S338N|AVPR2_ENST00000370049.1_3'UTR|ARHGAP4_ENST00000467421.1_5'Flank			P30518	V2R_HUMAN	arginine vasopressin receptor 2	338					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|excretion (GO:0007588)|hemostasis (GO:0007599)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|interferon-gamma production (GO:0032609)|negative regulation of renal sodium excretion (GO:0035814)|negative regulation of urine volume (GO:0035811)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of systemic arterial blood pressure (GO:0003084)|response to cytokine (GO:0034097)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	vasopressin receptor activity (GO:0005000)	p.S338N(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	26	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)				Conivaptan(DB00872)|Desmopressin(DB00035)|Terlipressin(DB02638)|Tolvaptan(DB06212)|Vasopressin(DB00067)	GAGCTGCGAAGCTTGCTCTGC	0.622																																					p.S338N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1013A	X						.						101.0	86.0	91.0					X																	153172079		2203	4300	6503	152825273	SO:0001583	missense	554	exon3			Z11687	CCDS14735.1, CCDS55539.1	Xq28	2014-09-17	2008-08-01		ENSG00000126895	ENSG00000126895		"""GPCR / Class A : Vasopressin and oxytocin receptors"""	897	protein-coding gene	gene with protein product	"""nephrogenic diabetes insipidus"""	300538		DIR3, DIR		1324225	Standard	NM_000054		Approved	V2R	uc004fjh.4	P30518	OTTHUMG00000024227	ENST00000358927.2:c.1013G>A	X.37:g.153172079G>A	ENSP00000351805:p.Ser338Asn	Somatic		Capture	Illumina HiSeq	Phase_I	152825273	NM_000054	C5HF20|O43192|Q3MJD3|Q9UCV9	Missense_Mutation	SNP	ENST00000358927.2	37	CCDS14735.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	1.804|1.804	-0.476341|-0.476341	0.04414|0.04414	.|.	.|.	ENSG00000126895|ENSG00000126895	ENST00000430697|ENST00000358927;ENST00000337474	T|T;T	0.77489|0.37584	-1.1|1.19;1.19	4.3|4.3	2.47|2.47	0.30058|0.30058	.|.	.|0.730119	.|0.13737	.|N	.|0.366230	T|T	0.29389|0.29389	0.0732|0.0732	L|L	0.57536|0.57536	1.79|1.79	0.09310|0.09310	N|N	1|1	.|B	.|0.12013	.|0.005	.|B	.|0.08055	.|0.003	T|T	0.25082|0.25082	-1.0142|-1.0142	7|10	0.52906|0.17369	T|T	0.07|0.5	.|.	6.6741|6.6741	0.23083|0.23083	0.3223:0.0:0.6777:0.0|0.3223:0.0:0.6777:0.0	.|.	.|338	.|P30518	.|V2R_HUMAN	T|N	309|338	ENSP00000393513:A309T|ENSP00000351805:S338N;ENSP00000338072:S338N	ENSP00000393513:A309T|ENSP00000338072:S338N	A|S	+|+	1|2	0|0	AVPR2|AVPR2	152825273|152825273	0.007000|0.007000	0.16637|0.16637	0.161000|0.161000	0.22692|0.22692	0.042000|0.042000	0.13812|0.13812	1.511000|1.511000	0.35801|0.35801	0.744000|0.744000	0.32741|0.32741	0.418000|0.418000	0.28097|0.28097	GCT|AGC		0.622	AVPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061127.2		
