#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_Start_position_hg18	i_TranscriptID	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
FRMPD2	143162	broad.mit.edu	37	10	49450338	49450338	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr10:49450338G>T	ENST00000374201.3	-	5	735	c.433C>A	c.(433-435)Cct>Act	p.P145T	FRMPD2_ENST00000407470.4_Missense_Mutation_p.P114T|FRMPD2_ENST00000305531.3_Missense_Mutation_p.P121T	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	145	KIND. {ECO:0000255|PROSITE- ProRule:PRU00709}.				tight junction assembly (GO:0070830)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)	1-phosphatidylinositol binding (GO:0005545)	p.P145T(1)		NS(2)|autonomic_ganglia(2)|breast(5)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(15)|lung(24)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	66				Kidney(211;0.201)		CGCCTGTGAGGCTGGTCTTCA	0.607																																					p.P145T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C433A	10						.						82.0	80.0	81.0					10																	49450338		2203	4300	6503	49120344	SO:0001583	missense	143162	exon5			AK123038	CCDS31195.1	10q11	2010-10-13			ENSG00000170324	ENSG00000170324			28572	protein-coding gene	gene with protein product		613323	"""PDZ domain containing 5C"""	PDZD5C, PDZK5C			Standard	NM_001018071		Approved	MGC35285	uc001jdv.3	Q68DX3	OTTHUMG00000018171	ENST00000374201.3:c.433C>A	10.37:g.49450338G>T	ENSP00000363317:p.Pro145Thr		49120344	NM_001018071	B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Missense_Mutation	SNP	ENST00000374201.3	37	CCDS31195.1	.	.	.	.	.	.	.	.	.	.	G	13.45	2.242180	0.39598	.	.	ENSG00000170324	ENST00000374201;ENST00000305531;ENST00000407470	T;T;T	0.63744	0.4;-0.06;-0.06	5.19	5.19	0.71726	KIND (2);	.	.	.	.	T	0.75064	0.3799	L	0.54908	1.71	0.32198	N	0.578201	D;P;D	0.89917	1.0;0.852;1.0	D;B;D	0.91635	0.999;0.353;0.999	T	0.79351	-0.1839	9	0.87932	D	0	.	14.2141	0.65781	0.0:0.0:1.0:0.0	.	121;145;114	Q68DX3-2;Q68DX3;F8WCT2	.;FRPD2_HUMAN;.	T	145;121;114	ENSP00000363317:P145T;ENSP00000307079:P121T;ENSP00000384339:P114T	ENSP00000307079:P121T	P	-	1	0	FRMPD2	49120344	1.000000	0.71417	0.996000	0.52242	0.316000	0.28119	3.237000	0.51344	2.430000	0.82344	0.655000	0.94253	CCT		0.607	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047923.3	NM_152428	
KCNC1	3746	broad.mit.edu	37	11	17757743	17757743	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr11:17757743C>T	ENST00000379472.3	+	1	224	c.194C>T	c.(193-195)gCg>gTg	p.A65V	KCNC1_ENST00000265969.6_Missense_Mutation_p.A65V	NM_004976.4	NP_004967.1	P48547	KCNC1_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 1	65					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|voltage-gated potassium channel activity (GO:0005249)	p.A65V(1)		breast(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(7)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	33					Dalfampridine(DB06637)	GGCGTCTTCGCGCACATCCTG	0.677																																					p.A65V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C194T	11						.						53.0	47.0	49.0					11																	17757743		2200	4293	6493	17714319	SO:0001583	missense	3746	exon1			M96747	CCDS7827.1, CCDS44547.1	11p15	2012-07-05			ENSG00000129159	ENSG00000129159		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6233	protein-coding gene	gene with protein product		176258				8449507, 16382104	Standard	NM_004976		Approved	Kv3.1	uc009yhc.1	P48547	OTTHUMG00000166359	ENST00000379472.3:c.194C>T	11.37:g.17757743C>T	ENSP00000368785:p.Ala65Val		17714319	NM_004976	K4DI87	Missense_Mutation	SNP	ENST00000379472.3	37	CCDS7827.1	.	.	.	.	.	.	.	.	.	.	C	36	5.600299	0.96614	.	.	ENSG00000129159	ENST00000265969;ENST00000379472	T;T	0.77229	-1.08;-1.08	5.03	5.03	0.67393	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.000000	0.85682	D	0.000000	T	0.81456	0.4826	M	0.79343	2.45	0.80722	D	1	P;D	0.61697	0.922;0.99	B;P	0.45377	0.236;0.478	D	0.85029	0.0916	10	0.59425	D	0.04	.	18.3563	0.90358	0.0:1.0:0.0:0.0	.	65;65	Q3KNS8;P48547	.;KCNC1_HUMAN	V	65	ENSP00000265969:A65V;ENSP00000368785:A65V	ENSP00000265969:A65V	A	+	2	0	KCNC1	17714319	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.818000	0.86416	2.327000	0.79052	0.491000	0.48974	GCG		0.677	KCNC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389389.1	NM_004976	
PRMT3	10196	broad.mit.edu	37	11	20424504	20424504	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr11:20424504C>T	ENST00000331079.6	+	8	962	c.745C>T	c.(745-747)Caa>Taa	p.Q249*	PRMT3_ENST00000437750.2_Nonsense_Mutation_p.Q187*	NM_001145167.1|NM_005788.3	NP_001138639.1|NP_005779	O60678	ANM3_HUMAN	protein arginine methyltransferase 3	249	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				histone arginine methylation (GO:0034969)|negative regulation of protein ubiquitination (GO:0031397)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|ribosome (GO:0005840)	histone-arginine N-methyltransferase activity (GO:0008469)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|modified amino acid binding (GO:0072341)|protein-arginine N-methyltransferase activity (GO:0016274)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)	p.Q249*(1)		endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|prostate(1)	17						TTTCATATACCAAAATCCACA	0.348																																					p.Q249X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C745T	11						.						146.0	152.0	150.0					11																	20424504		2203	4300	6503	20381080	SO:0001587	stop_gained	10196	exon8			AF059531	CCDS7853.1, CCDS44554.1	11p15.1	2008-02-05	2006-02-16	2006-02-16	ENSG00000185238	ENSG00000185238		"""Protein arginine methyltransferases"""	30163	protein-coding gene	gene with protein product		603190	"""HMT1 hnRNP methyltransferase-like 3 (S. cerevisiae)"""	HRMT1L3		9642256	Standard	NM_005788		Approved		uc001mqb.3	O60678	OTTHUMG00000166022	ENST00000331079.6:c.745C>T	11.37:g.20424504C>T	ENSP00000331879:p.Gln249*		20381080	NM_005788	B4DUC7	Nonsense_Mutation	SNP	ENST00000331079.6	37	CCDS7853.1	.	.	.	.	.	.	.	.	.	.	C	36	5.884236	0.97062	.	.	ENSG00000185238	ENST00000331079;ENST00000541255;ENST00000437750	.	.	.	5.55	5.55	0.83447	.	0.215890	0.47852	D	0.000203	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09084	T	0.74	-18.0696	17.2632	0.87078	0.0:1.0:0.0:0.0	.	.	.	.	X	249;249;187	.	ENSP00000331879:Q249X	Q	+	1	0	PRMT3	20381080	0.988000	0.35896	1.000000	0.80357	0.982000	0.71751	1.343000	0.33930	2.610000	0.88304	0.585000	0.79938	CAA		0.348	PRMT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387489.1	NM_005788	
GYS2	2998	broad.mit.edu	37	12	21721886	21721886	+	Nonsense_Mutation	SNP	G	G	A	rs121918419		TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr12:21721886G>A	ENST00000261195.2	-	5	990	c.736C>T	c.(736-738)Cga>Tga	p.R246*		NM_021957.3	NP_068776.2	P54840	GYS2_HUMAN	glycogen synthase 2 (liver)	246					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|ectoplasm (GO:0043265)	glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein homodimerization activity (GO:0042803)	p.R246*(1)		NS(1)|breast(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(14)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						ACGGAAGCTCGCTCCATGCAG	0.423																																					p.R246X	Colon(149;9 1820 3690 10544 50424)											.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C736T	12	GRCh37	CM980965	GYS2	M	rs121918419	.						161.0	154.0	156.0					12																	21721886		2203	4300	6503	21613153	SO:0001587	stop_gained	2998	exon5				CCDS8690.1	12p12.2-p11.2	2013-02-22			ENSG00000111713	ENSG00000111713	2.4.1.11	"""Glycosyltransferase group 1 domain containing"""	4707	protein-coding gene	gene with protein product		138571					Standard	NM_021957		Approved		uc001rfb.3	P54840	OTTHUMG00000169135	ENST00000261195.2:c.736C>T	12.37:g.21721886G>A	ENSP00000261195:p.Arg246*		21613153	NM_021957	A0AVD8	Nonsense_Mutation	SNP	ENST00000261195.2	37	CCDS8690.1	.	.	.	.	.	.	.	.	.	.	G	39	7.668078	0.98422	.	.	ENSG00000111713	ENST00000261195	.	.	.	5.16	4.25	0.50352	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.9125	15.0535	0.71894	0.0:0.0:0.8571:0.1429	.	.	.	.	X	246	.	ENSP00000261195:R246X	R	-	1	2	GYS2	21613153	1.000000	0.71417	0.995000	0.50966	0.995000	0.86356	3.419000	0.52728	1.363000	0.46019	0.655000	0.94253	CGA		0.423	GYS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402396.1	NM_021957	
DIP2B	57609	broad.mit.edu	37	12	51084911	51084911	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr12:51084911C>G	ENST00000301180.5	+	13	1665	c.1631C>G	c.(1630-1632)tCg>tGg	p.S544W		NM_173602.2	NP_775873.2	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B (Drosophila)	544						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	catalytic activity (GO:0003824)	p.S544W(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(15)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	60						CAAGCTCTGTCGCAGGCCTGC	0.453																																					p.S544W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1631G	12						.						122.0	101.0	109.0					12																	51084911		2203	4300	6503	49371178	SO:0001583	missense	57609	exon13			AB040896	CCDS31799.1	12q13.12	2012-10-02	2006-01-13		ENSG00000066084	ENSG00000066084			29284	protein-coding gene	gene with protein product		611379					Standard	XM_005269044		Approved	KIAA1463, FLJ34278	uc001rwv.3	Q9P265	OTTHUMG00000169475	ENST00000301180.5:c.1631C>G	12.37:g.51084911C>G	ENSP00000301180:p.Ser544Trp		49371178	NM_173602	Q6B011|Q8N1L5|Q8NB38	Missense_Mutation	SNP	ENST00000301180.5	37	CCDS31799.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.597109	0.87055	.	.	ENSG00000066084	ENST00000301180	T	0.43294	0.95	5.25	5.25	0.73442	AMP-dependent synthetase/ligase (1);	0.053655	0.85682	D	0.000000	T	0.56171	0.1967	L	0.36672	1.1	0.80722	D	1	D	0.64830	0.994	D	0.68765	0.96	T	0.56226	-0.8014	10	0.59425	D	0.04	-12.122	19.0398	0.92993	0.0:1.0:0.0:0.0	.	544	Q9P265	DIP2B_HUMAN	W	544	ENSP00000301180:S544W	ENSP00000301180:S544W	S	+	2	0	DIP2B	49371178	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.840000	0.69402	2.745000	0.94114	0.555000	0.69702	TCG		0.453	DIP2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404243.1	NM_173602	
TMBIM4	51643	broad.mit.edu	37	12	66546128	66546128	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr12:66546128C>T	ENST00000358230.3	-	3	355	c.235G>A	c.(235-237)Gga>Aga	p.G79R	TMBIM4_ENST00000539652.1_Missense_Mutation_p.G79R|TMBIM4_ENST00000398033.4_Missense_Mutation_p.G79R|TMBIM4_ENST00000542724.1_Missense_Mutation_p.G48R|TMBIM4_ENST00000556010.1_Missense_Mutation_p.G79R|TMBIM4_ENST00000286424.7_Missense_Mutation_p.G126R|TMBIM4_ENST00000544599.1_5'UTR	NM_016056.2	NP_057140.2	Q9HC24	LFG4_HUMAN	transmembrane BAX inhibitor motif containing 4	79					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|regulation of calcium-mediated signaling (GO:0050848)	Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)		p.G79R(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|ovary(1)|prostate(2)	9				GBM - Glioblastoma multiforme(28;0.0745)		CCCAGAGATCCGAGGGCAAAC	0.328																																					p.G79R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G235A	12						.						88.0	84.0	85.0					12																	66546128		1828	4080	5908	64832395	SO:0001583	missense	51643	exon3			AF113127	CCDS41805.1, CCDS61187.1, CCDS73493.1	12q14.3	2014-05-09			ENSG00000155957	ENSG00000155957			24257	protein-coding gene	gene with protein product						11042152, 10810093	Standard	NM_001282609		Approved	CGI-119, S1R, ZPRO, LFG4, GAAP	uc001stc.3	Q9HC24	OTTHUMG00000168973	ENST00000358230.3:c.235G>A	12.37:g.66546128C>T	ENSP00000350965:p.Gly79Arg		64832395	NM_016056	Q542Z6|Q9UHY5|Q9Y3C2	Missense_Mutation	SNP	ENST00000358230.3	37	CCDS41805.1	.	.	.	.	.	.	.	.	.	.	C	16.80	3.223162	0.58668	.	.	ENSG00000155957	ENST00000556010;ENST00000358230;ENST00000426857;ENST00000286424;ENST00000398033;ENST00000539043;ENST00000539427;ENST00000542724	T;T;T;T;T	0.46819	0.86;0.86;0.86;0.86;0.86	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.77322	0.4113	M	0.92784	3.345	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.993	D;D;D;D;D	0.77557	0.99;0.97;0.99;0.969;0.939	T	0.81961	-0.0693	9	.	.	.	-9.9146	18.9861	0.92771	0.0:1.0:0.0:0.0	.	79;126;79;48;79	E7EWY5;G3XAA5;E7EQ00;G3V1M2;Q9HC24	.;.;.;.;TMBI4_HUMAN	R	79;79;79;126;79;79;125;48	ENSP00000451688:G79R;ENSP00000350965:G79R;ENSP00000286424:G126R;ENSP00000381114:G79R;ENSP00000441291:G48R	.	G	-	1	0	TMBIM4	64832395	1.000000	0.71417	0.886000	0.34754	0.043000	0.13939	5.849000	0.69465	2.785000	0.95823	0.591000	0.81541	GGA		0.328	TMBIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401832.2	NM_016056	
GRIP1	23426	broad.mit.edu	37	12	66909497	66909497	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr12:66909497A>G	ENST00000398016.3	-	7	694	c.626T>C	c.(625-627)aTt>aCt	p.I209T	GRIP1_ENST00000359742.4_Missense_Mutation_p.I209T|GRIP1_ENST00000286445.7_Missense_Mutation_p.I209T	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.I209T(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)		AAGAAGCCGAATTCCATCCAC	0.438																																					p.I209T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T626C	12						.						160.0	159.0	160.0					12																	66909497		1955	4156	6111	65195764	SO:0001583	missense	23426	exon7			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.626T>C	12.37:g.66909497A>G	ENSP00000381098:p.Ile209Thr		65195764	NM_001178074	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Missense_Mutation	SNP	ENST00000398016.3	37	CCDS41807.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.34|16.34	3.095345|3.095345	0.56075|0.56075	.|.	.|.	ENSG00000155974|ENSG00000155974	ENST00000538164|ENST00000398016;ENST00000359742;ENST00000286445;ENST00000540854;ENST00000538211;ENST00000540433;ENST00000536215;ENST00000545666	.|T;T;T;T;T;T;T;T	.|0.24723	.|1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84	5.81|5.81	5.81|5.81	0.92471|0.92471	.|PDZ/DHR/GLGF (4);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.22044|0.22044	0.0531|0.0531	N|N	0.11756|0.11756	0.17|0.17	0.80722|0.80722	D|D	1|1	.|B;B;B	.|0.24186	.|0.005;0.099;0.04	.|B;B;B	.|0.39339	.|0.009;0.297;0.138	T|T	0.18618|0.18618	-1.0331|-1.0331	5|9	.|.	.|.	.|.	-17.8109|-17.8109	16.1564|16.1564	0.81670|0.81670	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|209;209;209	.|F5H4N6;Q9Y3R0;Q9Y3R0-3	.|.;GRIP1_HUMAN;.	L|T	24|209;209;209;80;209;153;153;182	.|ENSP00000381098:I209T;ENSP00000352780:I209T;ENSP00000286445:I209T;ENSP00000443006:I80T;ENSP00000446047:I209T;ENSP00000446024:I153T;ENSP00000446011:I153T;ENSP00000439124:I182T	.|.	F|I	-|-	1|2	0|0	GRIP1|GRIP1	65195764|65195764	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.900000|0.900000	0.52787|0.52787	8.923000|8.923000	0.92808|0.92808	2.228000|2.228000	0.72767|0.72767	0.477000|0.477000	0.44152|0.44152	TTC|ATT		0.438	GRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401975.2		
GLIPR1L2	144321	broad.mit.edu	37	12	75785031	75785031	+	Silent	SNP	G	G	A			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr12:75785031G>A	ENST00000550916.1	+	1	182	c.135G>A	c.(133-135)ttG>ttA	p.L45L	GLIPR1L2_ENST00000435775.1_Silent_p.L45L|GLIPR1L2_ENST00000547164.1_Silent_p.L45L|GLIPR1L2_ENST00000378692.3_5'UTR|GLIPR1L2_ENST00000441218.1_5'Flank|GLIPR1L2_ENST00000320460.4_Silent_p.L45L|GLIPR1L2_ENST00000378689.2_Silent_p.L45L|CAPS2_ENST00000442339.2_5'Flank	NM_001270396.1	NP_001257325.1	Q4G1C9	GRPL2_HUMAN	GLI pathogenesis-related 1 like 2	45						integral component of membrane (GO:0016021)		p.L45L(2)		kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16						CCAGATTTTTGCCAGACGAGG	0.567											OREG0021999	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L45L												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G135A	12						.						107.0	92.0	97.0					12																	75785031		2203	4300	6503	74071298	SO:0001819	synonymous_variant	144321	exon1			BC029557	CCDS9010.1, CCDS58258.1	12q21.1	2014-06-03				ENSG00000180481			28592	protein-coding gene	gene with protein product		610394				12477932	Standard	NM_001270396		Approved	MGC39497	uc001sxr.2	Q4G1C9	OTTHUMG00000169756	ENST00000550916.1:c.135G>A	12.37:g.75785031G>A		1163	74071298	NM_152436	Q6MZS1|Q8N6N0|Q8NA43	Silent	SNP	ENST00000550916.1	37	CCDS58258.1																																																																																				0.567	GLIPR1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405718.1	NM_152436	
C12orf29	91298	broad.mit.edu	37	12	88439502	88439502	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr12:88439502C>T	ENST00000356891.3	+	5	768	c.565C>T	c.(565-567)Ctc>Ttc	p.L189F	C12orf29_ENST00000548757.2_3'UTR	NM_001009894.2	NP_001009894.2	Q8N999	CL029_HUMAN	chromosome 12 open reading frame 29	189					hematopoietic progenitor cell differentiation (GO:0002244)			p.L189F(1)		large_intestine(3)|lung(1)|ovary(1)	5						ACTTTCAGATCTCTTAGAACA	0.348																																					p.L189F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C565T	12						.						84.0	80.0	82.0					12																	88439502		2203	4300	6503	86963633	SO:0001583	missense	91298	exon5			AL137488	CCDS31866.1	12q21.32	2012-05-30			ENSG00000133641	ENSG00000133641			25322	protein-coding gene	gene with protein product						14702039	Standard	NM_001009894		Approved	DKFZp434N2030	uc001tao.3	Q8N999	OTTHUMG00000169870	ENST00000356891.3:c.565C>T	12.37:g.88439502C>T	ENSP00000349358:p.Leu189Phe		86963633	NM_001009894	Q569K5|Q6AWA8|Q6PEK5|Q8IYQ5|Q9NT75	Missense_Mutation	SNP	ENST00000356891.3	37	CCDS31866.1	.	.	.	.	.	.	.	.	.	.	C	16.06	3.016362	0.54468	.	.	ENSG00000133641	ENST00000356891	T	0.61627	0.09	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.51618	0.1685	L	0.58428	1.81	0.58432	D	0.999996	B	0.20671	0.047	B	0.18263	0.021	T	0.52230	-0.8603	10	0.52906	T	0.07	-9.2191	8.8233	0.35039	0.1502:0.7731:0.0:0.0767	.	189	Q8N999	CL029_HUMAN	F	189	ENSP00000349358:L189F	ENSP00000349358:L189F	L	+	1	0	C12orf29	86963633	0.999000	0.42202	1.000000	0.80357	0.995000	0.86356	4.311000	0.59147	2.666000	0.90696	0.655000	0.94253	CTC		0.348	C12orf29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406335.1	NM_001009894	
SRRM4	84530	broad.mit.edu	37	12	119592089	119592089	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr12:119592089G>A	ENST00000267260.4	+	12	1821	c.1433G>A	c.(1432-1434)cGg>cAg	p.R478Q		NM_194286.3	NP_919262.2	A7MD48	SRRM4_HUMAN	serine/arginine repetitive matrix 4	478	Arg-rich.|Ser-rich.				cell differentiation (GO:0030154)|mRNA processing (GO:0006397)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	mRNA binding (GO:0003729)	p.R478Q(1)		breast(2)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	24						TCGCAGCAGCGGGAGCGCGAG	0.662																																					p.R478Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1433A	12						.						14.0	18.0	17.0					12																	119592089		1858	4087	5945	118076472	SO:0001583	missense	84530	exon12			AB058756	CCDS44994.1	12q24.23	2009-09-22	2009-09-21	2009-09-21	ENSG00000139767	ENSG00000139767			29389	protein-coding gene	gene with protein product	"""neural-specific SR-related protein of 100 kDa"""	613103	"""KIAA1853"""	KIAA1853		19737518	Standard	NM_194286		Approved	nSR100	uc001txa.2	A7MD48	OTTHUMG00000168928	ENST00000267260.4:c.1433G>A	12.37:g.119592089G>A	ENSP00000267260:p.Arg478Gln		118076472	NM_194286	A8K5P6|B2RZH7|Q7Z5F0|Q96JH4	Missense_Mutation	SNP	ENST00000267260.4	37	CCDS44994.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.419091	0.83559	.	.	ENSG00000139767	ENST00000267260	T	0.22945	1.93	4.08	3.16	0.36331	.	0.808617	0.10639	N	0.651282	T	0.15046	0.0363	L	0.36672	1.1	0.09310	N	1	P	0.37997	0.614	B	0.26770	0.073	T	0.14699	-1.0463	9	.	.	.	-9.1346	5.0382	0.14445	0.1081:0.0:0.682:0.2099	.	478	A7MD48	SRRM4_HUMAN	Q	478	ENSP00000267260:R478Q	.	R	+	2	0	SRRM4	118076472	1.000000	0.71417	0.851000	0.33527	0.998000	0.95712	3.621000	0.54210	1.042000	0.40150	0.655000	0.94253	CGG		0.662	SRRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401640.2	NM_194286	
RXFP2	122042	broad.mit.edu	37	13	32376306	32376307	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr13:32376306_32376307insT	ENST00000298386.2	+	18	2100_2101	c.2029_2030insT	c.(2029-2031)attfs	p.I677fs	RXFP2_ENST00000380314.1_Frame_Shift_Ins_p.I653fs	NM_130806.3	NP_570718.1	Q8WXD0	RXFP2_HUMAN	relaxin/insulin-like family peptide receptor 2	677					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|oocyte maturation (GO:0001556)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	peptide hormone binding (GO:0017046)|protein-hormone receptor activity (GO:0016500)	p.L680fs*4(1)		cervix(1)|endometrium(2)|large_intestine(15)|lung(13)|prostate(1)|stomach(1)	33		Lung SC(185;0.0262)		all cancers(112;0.000559)|Epithelial(112;0.0017)|OV - Ovarian serous cystadenocarcinoma(117;0.0145)|BRCA - Breast invasive adenocarcinoma(63;0.0535)		CTGGATAGTGATTTTTTTCCTT	0.347																																					p.I677fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.2029_2030insT	13						.																																			31274307	SO:0001589	frameshift_variant	122042	exon18			AF403384	CCDS9342.1, CCDS53862.1	13q12.3	2012-08-08	2006-05-09	2006-05-09	ENSG00000133105	ENSG00000133105		"""GPCR / Class A : Relaxin family peptide receptors"""	17318	protein-coding gene	gene with protein product		606655	"""leucine-rich repeat-containing G protein-coupled receptor 8"""	LGR8		12217959, 12970298, 15956688, 16507880	Standard	NM_130806		Approved	GREAT, GPR106, INSL3R, RXFPR2	uc001utt.3	Q8WXD0	OTTHUMG00000016690	ENST00000298386.2:c.2036dupT	13.37:g.32376313_32376313dupT	ENSP00000298386:p.Ile677fs		31274306	NM_130806	B1ALE9|Q3KU23	Frame_Shift_Ins	INS	ENST00000298386.2	37	CCDS9342.1																																																																																				0.347	RXFP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044399.1	NM_130806	
TRPC4	7223	broad.mit.edu	37	13	38211560	38211560	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr13:38211560G>A	ENST00000379705.3	-	11	3271	c.2414C>T	c.(2413-2415)cCg>cTg	p.P805L	TRPC4_ENST00000379673.2_Intron|TRPC4_ENST00000447043.1_Intron|TRPC4_ENST00000426868.2_Intron|TRPC4_ENST00000355779.2_Intron|TRPC4_ENST00000338947.5_Missense_Mutation_p.P632L|TRPC4_ENST00000379679.1_Missense_Mutation_p.P632L|TRPC4_ENST00000379681.3_Missense_Mutation_p.P810L|TRPC4_ENST00000358477.2_Intron			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	805	Binds to ITPR1, ITPR2 and ITPR3.				axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|gamma-aminobutyric acid secretion (GO:0014051)|ion transmembrane transport (GO:0034220)|oligodendrocyte differentiation (GO:0048709)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|calcium channel complex (GO:0034704)|caveola (GO:0005901)|cell surface (GO:0009986)|cortical cytoskeleton (GO:0030863)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)	p.P805L(1)		NS(2)|breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(26)|lung(30)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	83				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		TGCTGATCTCGGATGAATCAG	0.438																																					p.P805L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2414T	13						.						87.0	84.0	85.0					13																	38211560		2203	4300	6503	37109560	SO:0001583	missense	7223	exon11			U40983	CCDS9365.1, CCDS45035.1, CCDS45036.1, CCDS45038.1, CCDS45039.1	13q13.3	2013-01-10			ENSG00000133107	ENSG00000133107		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	12336	protein-coding gene	gene with protein product		603651				8646775, 16382100	Standard	NM_016179		Approved	HTRP4, TRP4	uc010abx.3	Q9UBN4	OTTHUMG00000016752	ENST00000379705.3:c.2414C>T	13.37:g.38211560G>A	ENSP00000369027:p.Pro805Leu		37109560	NM_016179	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Missense_Mutation	SNP	ENST00000379705.3	37	CCDS9365.1	.	.	.	.	.	.	.	.	.	.	G	15.93	2.977027	0.53720	.	.	ENSG00000133107	ENST00000379705;ENST00000379681;ENST00000338947;ENST00000379679	T;T;T;T	0.65178	-0.14;-0.14;0.05;0.05	5.9	5.9	0.94986	.	0.320827	0.28853	N	0.013939	T	0.72732	0.3497	L	0.36672	1.1	0.80722	D	1	D;P;P	0.89917	1.0;0.726;0.931	D;B;B	0.79108	0.992;0.079;0.171	T	0.67518	-0.5650	10	0.31617	T	0.26	-21.0662	20.282	0.98514	0.0:0.0:1.0:0.0	.	810;632;805	Q9UBN4-5;Q9UBN4-6;Q9UBN4	.;.;TRPC4_HUMAN	L	805;810;632;632	ENSP00000369027:P805L;ENSP00000369003:P810L;ENSP00000342580:P632L;ENSP00000369001:P632L	ENSP00000342580:P632L	P	-	2	0	TRPC4	37109560	1.000000	0.71417	0.888000	0.34837	0.986000	0.74619	5.845000	0.69437	2.786000	0.95864	0.563000	0.77884	CCG		0.438	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306	
ARHGAP5	394	broad.mit.edu	37	14	32562357	32562357	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr14:32562357C>T	ENST00000345122.3	+	2	2797	c.2482C>T	c.(2482-2484)Cga>Tga	p.R828*	ARHGAP5_ENST00000432921.1_Nonsense_Mutation_p.R828*|ARHGAP5_ENST00000556611.1_Nonsense_Mutation_p.R828*|ARHGAP5_ENST00000433497.1_Intron|ARHGAP5_ENST00000396582.2_Intron|ARHGAP5_ENST00000539826.2_Nonsense_Mutation_p.R828*	NM_001030055.1	NP_001025226.1	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5	828					cell adhesion (GO:0007155)|GTP catabolic process (GO:0006184)|mammary gland development (GO:0030879)|positive regulation of cell migration (GO:0030335)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell size (GO:0008361)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)	p.R828*(1)		NS(2)|breast(10)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(12)|ovary(4)|skin(1)|stomach(1)|urinary_tract(4)	55	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		AAAAAGGAGGCGAATACAGAT	0.363																																					p.R828X	NSCLC(9;77 350 3443 29227 41353)											.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2482T	14						.						72.0	70.0	71.0					14																	32562357		2203	4300	6503	31632108	SO:0001587	stop_gained	394	exon2			U17032	CCDS32062.1, CCDS45095.1	14q12	2010-02-05						"""Rho GTPase activating proteins"""	675	protein-coding gene	gene with protein product		602680	"""growth factor independent 2"""	GFI2		8537347	Standard	XM_005267635		Approved	RhoGAP5, p190-B, p190BRhoGAP	uc001wrn.3	Q13017		ENST00000345122.3:c.2482C>T	14.37:g.32562357C>T	ENSP00000371897:p.Arg828*		31632108	NM_001030055	A1L375|A1L376|A8KAA1|D3DS89|D3DS90|Q05BE8|Q05BU8|Q59ER0|Q6DHZ3	Nonsense_Mutation	SNP	ENST00000345122.3	37	CCDS32062.1	.	.	.	.	.	.	.	.	.	.	C	42	9.203815	0.99099	.	.	ENSG00000100852	ENST00000556611;ENST00000539826;ENST00000345122;ENST00000432921	.	.	.	5.56	4.61	0.57282	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.9549	0.64142	0.2544:0.7456:0.0:0.0	.	.	.	.	X	828	.	ENSP00000371897:R828X	R	+	1	2	ARHGAP5	31632108	0.999000	0.42202	0.983000	0.44433	0.886000	0.51366	1.127000	0.31357	2.778000	0.95560	0.650000	0.86243	CGA		0.363	ARHGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409735.1	NM_001030055	
DACT1	51339	broad.mit.edu	37	14	59113156	59113156	+	Silent	SNP	G	G	A			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr14:59113156G>A	ENST00000335867.4	+	4	1839	c.1815G>A	c.(1813-1815)acG>acA	p.T605T	DACT1_ENST00000395153.3_Silent_p.T568T|DACT1_ENST00000556859.1_Silent_p.T324T|DACT1_ENST00000541264.2_Silent_p.T324T			Q9NYF0	DACT1_HUMAN	dishevelled-binding antagonist of beta-catenin 1	605					dendrite morphogenesis (GO:0048813)|embryonic hindgut morphogenesis (GO:0048619)|gastrulation with mouth forming second (GO:0001702)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of catenin import into nucleus (GO:0035412)|regulation of protein stability (GO:0031647)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|synapse organization (GO:0050808)|Wnt signaling pathway (GO:0016055)	beta-catenin destruction complex (GO:0030877)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|protein kinase A binding (GO:0051018)|protein kinase C binding (GO:0005080)	p.T605T(1)		endometrium(7)|kidney(3)|large_intestine(11)|lung(27)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	53						GGGAGAAAACGCGGGCCGGGA	0.617																																					p.T568T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1704A	14						.						16.0	20.0	18.0					14																	59113156		2193	4292	6485	58182909	SO:0001819	synonymous_variant	51339	exon4			AF251079	CCDS9736.1, CCDS41961.1	14q22.3	2013-05-15	2013-05-15		ENSG00000165617	ENSG00000165617			17748	protein-coding gene	gene with protein product		607861	"""dapper homolog 1, antagonist of beta-catenin (xenopus)"", ""dapper, antagonist of beta-catenin, homolog 1 (Xenopus laevis)"""			11970895	Standard	NM_001079520		Approved	DAPPER1, THYEX3, HDPR1, DAPPER, FRODO	uc001xdw.3	Q9NYF0	OTTHUMG00000140324	ENST00000335867.4:c.1815G>A	14.37:g.59113156G>A			58182909	NM_001079520	A8MYJ2|Q86TY0	Silent	SNP	ENST00000335867.4	37	CCDS9736.1																																																																																				0.617	DACT1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325515.1	NM_016651	
DICER1	23405	broad.mit.edu	37	14	95595891	95595891	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr14:95595891C>A	ENST00000526495.1	-	8	943	c.652G>T	c.(652-654)Gaa>Taa	p.E218*	DICER1_ENST00000343455.3_Nonsense_Mutation_p.E218*|DICER1_ENST00000393063.1_Nonsense_Mutation_p.E218*|DICER1_ENST00000541352.1_Nonsense_Mutation_p.E218*|DICER1_ENST00000527414.1_Nonsense_Mutation_p.E218*			Q9UPY3	DICER_HUMAN	dicer 1, ribonuclease type III	218	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.			E -> D (in Ref. 1; BAA78691). {ECO:0000305}.	angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac muscle cell development (GO:0055013)|cerebral cortex development (GO:0021987)|defense response to virus (GO:0051607)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|hair follicle cell proliferation (GO:0071335)|hair follicle morphogenesis (GO:0031069)|inner ear receptor cell development (GO:0060119)|intestinal epithelial cell development (GO:0060576)|lung development (GO:0030324)|mRNA stabilization (GO:0048255)|multicellular organism growth (GO:0035264)|negative regulation of Schwann cell proliferation (GO:0010626)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nerve development (GO:0021675)|neuron projection morphogenesis (GO:0048812)|olfactory bulb interneuron differentiation (GO:0021889)|peripheral nervous system myelin formation (GO:0032290)|positive regulation of gene expression (GO:0010628)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of myelination (GO:0031643)|positive regulation of Schwann cell differentiation (GO:0014040)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|production of siRNA involved in RNA interference (GO:0030422)|regulation of cell cycle (GO:0051726)|regulation of enamel mineralization (GO:0070173)|regulation of neuron differentiation (GO:0045664)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of viral genome replication (GO:0045069)|reproductive structure development (GO:0048608)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|spinal cord motor neuron differentiation (GO:0021522)|spindle assembly (GO:0051225)|spleen development (GO:0048536)|stem cell maintenance (GO:0019827)|targeting of mRNA for destruction involved in RNA interference (GO:0030423)|zygote asymmetric cell division (GO:0010070)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|growth cone (GO:0030426)|RISC complex (GO:0016442)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|ribonuclease III activity (GO:0004525)	p.E218*(1)		NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(13)|kidney(3)|large_intestine(10)|lung(33)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	75		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)		TCTTCCAATTCCTCTGGATCA	0.373			"""Mis F, N"""		"""sex cord-stromal tumour, TGCT, embryonal rhadomyosarcoma"""	pleuropulmonary blastoma			Familial Multinodular Goiter ;DICER 1 syndrome																												p.E218X		yes	Rec	yes	Familial Pleuropulmonary Blastoma	14	14q32.13	23405	"""dicer 1, ribonuclease type III """		"""E, M, O"""	.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G652T	14						.						73.0	73.0	73.0					14																	95595891		2203	4300	6503	94665644	SO:0001587	stop_gained	23405	exon5	Familial Cancer Database	Adolescent Multinodular Goiter, incl. Multinodular Euthyroid Goiter & Non-Medullary Thyroid Cancer;incl. Pleuropulmonary Blastoma, Familial ; Cystic Nephroma, Familial	AB028449	CCDS9931.1, CCDS55941.1	14q32.13	2014-09-17	2008-02-20		ENSG00000100697	ENSG00000100697			17098	protein-coding gene	gene with protein product	"""dicer 1, double-stranded RNA-specific endoribonuclease"""	606241	"""Dicer1, Dcr-1 homolog (Drosophila)"", ""multinodular goitre 1"""	MNG1		10051563, 10786632, 21205968	Standard	NM_177438		Approved	Dicer, KIAA0928, K12H4.8-LIKE, HERNA	uc001ydw.2	Q9UPY3	OTTHUMG00000166134	ENST00000526495.1:c.652G>T	14.37:g.95595891C>A	ENSP00000437256:p.Glu218*		94665644	NM_001195573	A7E2D3|B3KRG4|E0AD28|O95943|Q9UQ02	Nonsense_Mutation	SNP	ENST00000526495.1	37	CCDS9931.1	.	.	.	.	.	.	.	.	.	.	C	39	7.487613	0.98316	.	.	ENSG00000100697	ENST00000343455;ENST00000526495;ENST00000393063;ENST00000527414;ENST00000541352	.	.	.	5.57	5.57	0.84162	.	0.130205	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07990	T	0.79	-32.2177	19.9222	0.97091	0.0:1.0:0.0:0.0	.	.	.	.	X	218	.	ENSP00000343745:E218X	E	-	1	0	DICER1	94665644	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.367000	0.79558	2.779000	0.95612	0.650000	0.86243	GAA		0.373	DICER1-004	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387997.1		
BEGAIN	57596	broad.mit.edu	37	14	101005328	101005331	+	Frame_Shift_Del	DEL	CGTC	CGTC	-	rs147214195		TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	CGTC	CGTC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr14:101005328_101005331delCGTC	ENST00000355173.2	-	7	828_831	c.757_760delGACG	c.(757-762)gacgtgfs	p.DV253fs	BEGAIN_ENST00000443071.2_Frame_Shift_Del_p.DV253fs|CTD-2062F14.3_ENST00000553301.1_lincRNA|BEGAIN_ENST00000556751.1_Frame_Shift_Del_p.DV189fs	NM_020836.3	NP_065887.1	Q9BUH8	BEGIN_HUMAN	brain-enriched guanylate kinase-associated	253						cytoplasm (GO:0005737)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)		p.D253fs*65(1)		cervix(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|skin(2)|stomach(1)	14		Melanoma(154;0.212)				AGGAAGCCCACGTCGGTCACGGGC	0.711																																					p.253_254del	NSCLC(159;1889 2010 9965 27479 40101)											.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.757_760del	14						.																																			100075084	SO:0001589	frameshift_variant	57596	exon6			BC002607	CCDS9962.1	14q32.2	2012-12-07	2012-12-07			ENSG00000183092			24163	protein-coding gene	gene with protein product			"""brain-enriched guanylate kinase-associated homolog (rat)"""			10819331	Standard	NM_020836		Approved	KIAA1446	uc010txa.2	Q9BUH8		ENST00000355173.2:c.757_760delGACG	14.37:g.101005328_101005331delCGTC	ENSP00000347301:p.Asp253fs		100075081	NM_001159531	Q9NPU3|Q9P282	Frame_Shift_Del	DEL	ENST00000355173.2	37	CCDS9962.1																																																																																				0.711	BEGAIN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414329.1	NM_020836	
PPP1R13B	23368	broad.mit.edu	37	14	104245135	104245135	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr14:104245135G>A	ENST00000202556.9	-	4	583	c.301C>T	c.(301-303)Cga>Tga	p.R101*		NM_015316.2	NP_056131.2	Q96KQ4	ASPP1_HUMAN	protein phosphatase 1, regulatory subunit 13B	101					intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R101*(1)		endometrium(6)|kidney(2)|large_intestine(7)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.173)|all_epithelial(191;0.131)|Melanoma(154;0.155)				CTCTGAGTTCGTTGCTCTTGG	0.348																																					p.R101X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C301T	14						.						143.0	133.0	136.0					14																	104245135		1832	4098	5930	103314888	SO:0001587	stop_gained	23368	exon4			AB018314	CCDS41997.1	14q32.33	2013-01-10	2011-10-04		ENSG00000088808	ENSG00000088808		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	14950	protein-coding gene	gene with protein product		606455	"""protein phosphatase 1, regulatory (inhibitor) subunit 13B"""			9872452	Standard	NM_015316		Approved	p53BP2-like, KIAA0771, p85, ASPP1	uc001yof.1	Q96KQ4	OTTHUMG00000171647	ENST00000202556.9:c.301C>T	14.37:g.104245135G>A	ENSP00000202556:p.Arg101*		103314888	NM_015316	B2RMX5|O94870	Nonsense_Mutation	SNP	ENST00000202556.9	37	CCDS41997.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.224985	0.79576	.	.	ENSG00000088808	ENST00000202556;ENST00000555734;ENST00000553739	.	.	.	5.69	3.41	0.39046	.	0.155706	0.56097	D	0.000029	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	.	10.4405	0.44462	0.0:0.0:0.4059:0.5941	.	.	.	.	X	101;98;130	.	ENSP00000202556:R101X	R	-	1	2	PPP1R13B	103314888	0.121000	0.22262	0.846000	0.33378	0.999000	0.98932	1.172000	0.31908	0.560000	0.29169	0.655000	0.94253	CGA		0.348	PPP1R13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414591.1	NM_015316	
GDPGP1	390637	broad.mit.edu	37	15	90784306	90784306	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr15:90784306C>A	ENST00000558017.1	+	4	586	c.166C>A	c.(166-168)Caa>Aaa	p.Q56K	GDPGP1_ENST00000329600.6_Missense_Mutation_p.Q56K	NM_001013657.2	NP_001013679.2	Q6ZNW5	GDPP1_HUMAN	GDP-D-glucose phosphorylase 1	56					glucose metabolic process (GO:0006006)	cytoplasm (GO:0005737)	GDP-D-glucose phosphorylase activity (GO:0080048)|guanyl-nucleotide exchange factor activity (GO:0005085)|hydrolase activity (GO:0016787)|nucleotide binding (GO:0000166)|nucleotidyltransferase activity (GO:0016779)	p.Q56K(1)									TGCTCTGCCACAATCTCCCTT	0.557																																					p.Q56K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C166A	15						.						143.0	144.0	144.0					15																	90784306		2199	4298	6497	88585310	SO:0001583	missense	390637	exon4				CCDS32327.1	15q26.1	2012-05-04	2012-05-04	2012-05-04	ENSG00000183208	ENSG00000183208	2.7.7.78		34360	protein-coding gene	gene with protein product			"""chromosome 15 open reading frame 58"""	C15orf58		21507950	Standard	NM_001013657		Approved		uc002bpc.3	Q6ZNW5		ENST00000558017.1:c.166C>A	15.37:g.90784306C>A	ENSP00000452793:p.Gln56Lys		88585310	NM_001013657		Missense_Mutation	SNP	ENST00000558017.1	37	CCDS32327.1	.	.	.	.	.	.	.	.	.	.	C	0.360	-0.939762	0.02322	.	.	ENSG00000183208	ENST00000329600	T	0.21191	2.02	4.94	2.05	0.26809	.	1.630640	0.04499	N	0.380995	T	0.10766	0.0263	N	0.14661	0.345	0.09310	N	1	B	0.12013	0.005	B	0.10450	0.005	T	0.27400	-1.0075	10	0.06099	T	0.92	-0.0352	4.1615	0.10285	0.1837:0.6262:0.0:0.19	.	56	Q6ZNW5	VTC2_HUMAN	K	56	ENSP00000368405:Q56K	ENSP00000368405:Q56K	Q	+	1	0	C15orf58	88585310	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.386000	0.07370	0.281000	0.22233	-0.259000	0.10710	CAA		0.557	GDPGP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416973.1	NM_001013657	
CREBBP	1387	broad.mit.edu	37	16	3781797	3781797	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr16:3781797T>G	ENST00000262367.5	-	29	5679	c.4870A>C	c.(4870-4872)Acc>Ccc	p.T1624P	CREBBP_ENST00000382070.3_Missense_Mutation_p.T1586P	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1624	CBP/p300-type HAT. {ECO:0000255|PROSITE- ProRule:PRU01065}.|Interaction with TRERF1.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.T1624P(1)		NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		TTCTCCATGGTGGCATACAGC	0.607			"""T, N, F, Mis, O"""	"""MLL, MORF, RUNXBP2"""	"""ALL, AML, DLBCL, B-NHL """		Rubinstein-Taybi syndrome																														p.T1624P			Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A4870C	16						.						372.0	303.0	326.0					16																	3781797		2197	4300	6497	3721798	SO:0001583	missense	1387	exon29			U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"""Chromatin-modifying enzymes / K-acetyltransferases"""	2348	protein-coding gene	gene with protein product		600140	"""Rubinstein-Taybi syndrome"""	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.4870A>C	16.37:g.3781797T>G	ENSP00000262367:p.Thr1624Pro		3721798	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	t	16.60	3.169421	0.57584	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070	D;D	0.93906	-3.31;-3.31	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	D	0.96750	0.8939	M	0.84219	2.685	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.85130	0.997;0.997	D	0.97341	0.9957	10	0.72032	D	0.01	-24.8426	15.5057	0.75739	0.0:0.0:0.0:1.0	.	1654;1624	Q4LE28;Q92793	.;CBP_HUMAN	P	1624;1654;1586	ENSP00000262367:T1624P;ENSP00000371502:T1586P	ENSP00000262367:T1624P	T	-	1	0	CREBBP	3721798	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.040000	0.89188	2.071000	0.62044	0.459000	0.35465	ACC		0.607	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380	
GRIN2A	2903	broad.mit.edu	37	16	10274121	10274121	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr16:10274121C>T	ENST00000396573.2	-	3	457	c.148G>A	c.(148-150)Gaa>Aaa	p.E50K	GRIN2A_ENST00000330684.3_Missense_Mutation_p.E50K|GRIN2A_ENST00000404927.2_Missense_Mutation_p.E50K|GRIN2A_ENST00000396575.2_Missense_Mutation_p.E50K|GRIN2A_ENST00000562109.1_Missense_Mutation_p.E50K	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	50					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)	p.E50K(1)		NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GTTCGAAGTTCGCGCTCTGTC	0.682																																					p.E50K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G148A	16						.						55.0	60.0	58.0					16																	10274121		2197	4300	6497	10181622	SO:0001583	missense	2903	exon2				CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.148G>A	16.37:g.10274121C>T	ENSP00000379818:p.Glu50Lys		10181622	NM_001134408	O00669|Q17RZ6	Missense_Mutation	SNP	ENST00000396573.2	37	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	C	15.15	2.748373	0.49257	.	.	ENSG00000183454	ENST00000396573;ENST00000404927;ENST00000330684;ENST00000396575	D;D;D;D	0.86030	-2.06;-2.06;-2.06;-2.06	4.54	4.54	0.55810	.	0.189796	0.42821	D	0.000652	T	0.72614	0.3482	N	0.22421	0.69	0.80722	D	1	P;B;B	0.48640	0.913;0.021;0.082	B;B;B	0.34038	0.174;0.003;0.008	T	0.74575	-0.3620	9	.	.	.	.	16.2901	0.82747	0.0:1.0:0.0:0.0	.	50;50;50	Q547U9;Q17RZ6;Q12879	.;.;NMDE1_HUMAN	K	50	ENSP00000379818:E50K;ENSP00000385872:E50K;ENSP00000332549:E50K;ENSP00000379820:E50K	.	E	-	1	0	GRIN2A	10181622	1.000000	0.71417	0.996000	0.52242	0.984000	0.73092	4.772000	0.62324	2.088000	0.63022	0.561000	0.74099	GAA		0.682	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3		
CYLD	1540	broad.mit.edu	37	16	50783734	50783734	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr16:50783734C>T	ENST00000427738.3	+	2	330	c.125C>T	c.(124-126)cCg>cTg	p.P42L	CYLD_ENST00000569418.1_Missense_Mutation_p.P42L|CYLD_ENST00000311559.9_Missense_Mutation_p.P42L|CYLD_ENST00000540145.1_Missense_Mutation_p.P42L|CYLD_ENST00000398568.2_Missense_Mutation_p.P42L|CYLD_ENST00000568704.2_Missense_Mutation_p.P42L|CYLD_ENST00000564326.1_Missense_Mutation_p.P42L|CYLD_ENST00000566206.1_Missense_Mutation_p.P42L			Q9NQC7	CYLD_HUMAN	cylindromatosis (turban tumor syndrome)	42					cell cycle (GO:0007049)|innate immune response (GO:0045087)|necroptotic process (GO:0070266)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|protein K63-linked deubiquitination (GO:0070536)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of mitotic cell cycle (GO:0007346)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|microtubule (GO:0005874)|nucleus (GO:0005634)	Lys63-specific deubiquitinase activity (GO:0061578)|proline-rich region binding (GO:0070064)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.P42L(1)		central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(9)|lung(17)|pancreas(1)|skin(22)|upper_aerodigestive_tract(1)	62		all_cancers(37;0.0156)				CTTAAAGTACCGAAGGGAAGT	0.388			"""Mis, N, F, S"""		cylindroma	cylindroma			Multiple Trichoepithelioma, Familial;Familial Cylindromatosis																												p.P42L		yes	Rec	yes	Familial cylindromatosis	16	16q12-q13	1540	familial cylindromatosis gene		E	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C125T	16						.						101.0	96.0	97.0					16																	50783734		1857	4096	5953	49341235	SO:0001583	missense	1540	exon4	Familial Cancer Database	;FADC, Turban Tumor syndrome, Epithelioma Adenoides Cysticum of Brooke, Hereditary Multiple Benign Cystic Epithelioma, Dermal Eccrine Cylindromatosis, Brooke-Spiegler s.	AB020656	CCDS42164.1, CCDS45482.1	16q12-q13	2014-09-17							2584	protein-coding gene	gene with protein product	"""ubiquitin specific peptidase like 2"""	605018		CYLD1		7493027	Standard	NM_015247		Approved	KIAA0849, USPL2	uc002egq.1	Q9NQC7		ENST00000427738.3:c.125C>T	16.37:g.50783734C>T	ENSP00000392025:p.Pro42Leu		49341235	NM_015247	O94934|Q7L3N6|Q96EH0|Q9NZX9	Missense_Mutation	SNP	ENST00000427738.3	37	CCDS45482.1	.	.	.	.	.	.	.	.	.	.	C	11.53	1.665708	0.29604	.	.	ENSG00000083799	ENST00000540145;ENST00000311559;ENST00000427738;ENST00000398568	D;D;D;D	0.93763	-3.28;-3.28;-3.28;-3.28	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	D	0.90710	0.7085	N	0.14661	0.345	0.80722	D	1	P;D;D;P	0.54964	0.947;0.969;0.969;0.947	B;P;P;B	0.48400	0.373;0.576;0.576;0.373	D	0.91420	0.5158	10	0.56958	D	0.05	-16.9568	20.5827	0.99408	0.0:1.0:0.0:0.0	.	42;42;42;42	A8KAB0;F5H2R7;Q9NQC7-2;Q9NQC7	.;.;.;CYLD_HUMAN	L	42	ENSP00000445447:P42L;ENSP00000308928:P42L;ENSP00000392025:P42L;ENSP00000381574:P42L	ENSP00000308928:P42L	P	+	2	0	CYLD	49341235	1.000000	0.71417	0.921000	0.36526	0.021000	0.10359	5.478000	0.66806	2.941000	0.99782	0.655000	0.94253	CCG		0.388	CYLD-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422998.2		
SCARF1	8578	broad.mit.edu	37	17	1549810	1549810	+	5'Flank	SNP	G	G	A			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr17:1549810G>A	ENST00000263071.4	-	0	0				SCARF1_ENST00000571272.1_5'Flank|SCARF1_ENST00000574545.1_5'Flank|SCARF1_ENST00000348987.3_5'Flank|RILP_ENST00000301336.6_Missense_Mutation_p.P378S	NM_003693.2|NM_145350.1	NP_003684.2|NP_663325.1	Q14162	SREC_HUMAN	scavenger receptor class F, member 1						cell adhesion (GO:0007155)|cholesterol catabolic process (GO:0006707)|dendrite development (GO:0016358)|neuron remodeling (GO:0016322)|positive regulation of axon regeneration (GO:0048680)|positive regulation of neuron projection development (GO:0010976)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	endocytic vesicle membrane (GO:0030666)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	low-density lipoprotein particle binding (GO:0030169)|scavenger receptor activity (GO:0005044)|transmembrane signaling receptor activity (GO:0004888)	p.P378S(1)		cervix(1)|endometrium(3)|kidney(2)|lung(9)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		TCAGGAGCTGGAGACTGTGGT	0.612																																					p.P378S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1132T	17						.						142.0	126.0	131.0					17																	1549810		2203	4300	6503	1496560	SO:0001631	upstream_gene_variant	83547	exon8			D63483	CCDS11007.1, CCDS45564.1	17p13.3	2008-07-18			ENSG00000074660	ENSG00000074660			16820	protein-coding gene	gene with protein product	"""scavenger receptor expressed by endothelial cells"", ""acetyl LDL receptor"""	607873				9395444, 8590280	Standard	NM_003693		Approved	SREC, KIAA0149	uc002fsz.2	Q14162	OTTHUMG00000090555		17.37:g.1549810G>A	Exception_encountered		1496560	NM_031430	A8MQ05|O43701|Q8NHD2|Q8NHD3|Q8NHD4|Q8NHD5	Missense_Mutation	SNP	ENST00000263071.4	37	CCDS11007.1	.	.	.	.	.	.	.	.	.	.	G	11.63	1.696029	0.30052	.	.	ENSG00000167705	ENST00000301336	T	0.32753	1.44	4.54	1.3	0.21679	.	2.844620	0.01361	N	0.012224	T	0.26122	0.0637	L	0.40543	1.245	0.09310	N	1	B	0.17038	0.02	B	0.12837	0.008	T	0.19679	-1.0298	10	0.49607	T	0.09	-4.1008	3.0733	0.06237	0.3317:0.0:0.4782:0.1902	.	378	Q96NA2	RILP_HUMAN	S	378	ENSP00000301336:P378S	ENSP00000301336:P378S	P	-	1	0	RILP	1496560	0.008000	0.16893	0.029000	0.17559	0.004000	0.04260	0.367000	0.20382	0.402000	0.25451	0.561000	0.74099	CCA		0.612	SCARF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207081.4	NM_003693	
CLUH	23277	broad.mit.edu	37	17	2595379	2595379	+	Silent	SNP	G	G	A			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr17:2595379G>A	ENST00000570628.2	-	23	3561	c.3456C>T	c.(3454-3456)gtC>gtT	p.V1152V	CLUH_ENST00000538975.1_Silent_p.V1152V|CLUH_ENST00000435359.1_Silent_p.V1152V			O75153	CLU_HUMAN	clustered mitochondria (cluA/CLU1) homolog	1152					intracellular distribution of mitochondria (GO:0048312)	cytoplasm (GO:0005737)		p.V1153V(1)									AGACTCGGGCGACAAGGTGGT	0.697																																					p.V1152V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3456T	17						.						10.0	11.0	10.0					17																	2595379		2005	4156	6161	2542129	SO:0001819	synonymous_variant	23277	exon23			AB014564	CCDS45572.1	17p13.3	2012-12-18	2012-11-30	2012-11-30	ENSG00000132361	ENSG00000132361			29094	protein-coding gene	gene with protein product			"""KIAA0664"""	KIAA0664			Standard	XM_005256567		Approved	CLU1	uc002fuy.1	O75153	OTTHUMG00000177575	ENST00000570628.2:c.3456C>T	17.37:g.2595379G>A			2542129	NM_015229	Q6AHY2|Q6P3X7|Q6ZUG8|Q8N4U7|Q9BTA3|Q9H979	Silent	SNP	ENST00000570628.2	37	CCDS45572.1																																																																																				0.697	CLUH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437807.2	NM_015229	
ANKFN1	162282	broad.mit.edu	37	17	54428171	54428171	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr17:54428171T>A	ENST00000318698.2	+	4	277	c.242T>A	c.(241-243)cTc>cAc	p.L81H	ANKFN1_ENST00000566473.2_Missense_Mutation_p.L81H	NM_153228.2	NP_694960.2	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain containing 1	81								p.L81H(1)		NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(11)|lung(27)|ovary(1)|prostate(1)|skin(1)	53						AATTTACATCTCTGTCAGTCA	0.413																																					p.L81H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T242A	17						.						108.0	107.0	108.0					17																	54428171		2203	4300	6503	51783170	SO:0001583	missense	162282	exon4			AK095654	CCDS32686.1	17q23.2	2014-02-12	2005-11-15		ENSG00000153930	ENSG00000153930		"""Ankyrin repeat domain containing"", ""Fibronectin type III domain containing"""	26766	protein-coding gene	gene with protein product							Standard	NM_153228		Approved	FLJ38335	uc002iun.1	Q8N957	OTTHUMG00000155010	ENST00000318698.2:c.242T>A	17.37:g.54428171T>A	ENSP00000321627:p.Leu81His		51783170	NM_153228		Missense_Mutation	SNP	ENST00000318698.2	37	CCDS32686.1	.	.	.	.	.	.	.	.	.	.	T	18.70	3.680375	0.68042	.	.	ENSG00000153930	ENST00000318698	T	0.25579	1.79	5.57	4.5	0.54988	.	0.191693	0.45361	D	0.000366	T	0.30823	0.0777	L	0.46157	1.445	0.37317	D	0.909386	D	0.58620	0.983	P	0.50231	0.635	T	0.26744	-1.0094	10	0.62326	D	0.03	-10.9744	10.9177	0.47146	0.0:0.0728:0.0:0.9272	.	81	Q8N957	ANKF1_HUMAN	H	81	ENSP00000321627:L81H	ENSP00000321627:L81H	L	+	2	0	ANKFN1	51783170	1.000000	0.71417	0.998000	0.56505	0.977000	0.68977	3.231000	0.51294	2.114000	0.64651	0.533000	0.62120	CTC		0.413	ANKFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338043.1	NM_153228	
SMAD4	4089	broad.mit.edu	37	18	48573522	48573551	+	In_Frame_Del	DEL	GCAAAAAGAGCAATTGAAAGTTTGGTAAAG	GCAAAAAGAGCAATTGAAAGTTTGGTAAAG	-			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	GCAAAAAGAGCAATTGAAAGTTTGGTAAAG	GCAAAAAGAGCAATTGAAAGTTTGGTAAAG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr18:48573522_48573551delGCAAAAAGAGCAATTGAAAGTTTGGTAAAG	ENST00000342988.3	+	2	644_673	c.106_135delGCAAAAAGAGCAATTGAAAGTTTGGTAAAG	c.(106-135)gcaaaaagagcaattgaaagtttggtaaagdel	p.AKRAIESLVK36del	RP11-729L2.2_ENST00000590722.2_3'UTR|SMAD4_ENST00000398417.2_In_Frame_Del_p.AKRAIESLVK36del|SMAD4_ENST00000452201.2_In_Frame_Del_p.AKRAIESLVK36del|SMAD4_ENST00000588745.1_In_Frame_Del_p.AKRAIESLVK36del	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	36	MH1. {ECO:0000255|PROSITE- ProRule:PRU00438}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(5)|p.E41fs*8(1)|p.L43S(1)|p.A36_K45delAKRAIESLVK(1)|p.V44G(1)|p.A39T(1)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		TGAAACATTTGCAAAAAGAGCAATTGAAAGTTTGGTAAAGAAGCTGAAGG	0.361																																					p.36_45del												.	.	46	Whole gene deletion(36)|Unknown(5)|Substitution - Missense(3)|Complex - frameshift(1)|Deletion - In frame(1)	pancreas(28)|large_intestine(5)|stomach(3)|breast(3)|lung(2)|oesophagus(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|NS(1)	c.106_135del	18						.																																			46827549	SO:0001651	inframe_deletion	4089	exon2			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"""SMADs"""	6770	protein-coding gene	gene with protein product		600993	"""MAD, mothers against decapentaplegic homolog 4 (Drosophila)"", ""SMAD, mothers against DPP homolog 4 (Drosophila)"""	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.106_135delGCAAAAAGAGCAATTGAAAGTTTGGTAAAG	18.37:g.48573522_48573551delGCAAAAAGAGCAATTGAAAGTTTGGTAAAG	ENSP00000341551:p.Ala36_Lys45del		46827520	NM_005359	A8K405	In_Frame_Del	DEL	ENST00000342988.3	37	CCDS11950.1																																																																																				0.361	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359	
MAG	4099	broad.mit.edu	37	19	35802892	35802892	+	Missense_Mutation	SNP	G	G	A	rs138056630		TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr19:35802892G>A	ENST00000392213.3	+	10	1847	c.1688G>A	c.(1687-1689)cGc>cAc	p.R563H	MAG_ENST00000361922.4_Missense_Mutation_p.R563H|MAG_ENST00000537831.2_Missense_Mutation_p.R538H|MAG_ENST00000593348.1_3'UTR	NM_002361.3	NP_002352.1	P20916	MAG_HUMAN	myelin associated glycoprotein	563					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)|negative regulation of axonogenesis (GO:0050771)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of axonogenesis (GO:0050770)|substantia nigra development (GO:0021762)	integral component of membrane (GO:0016021)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)	carbohydrate binding (GO:0030246)	p.R563H(2)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(10)|lung(11)|skin(2)|upper_aerodigestive_tract(2)	34	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)	Renal(1328;0.242)	Epithelial(14;3.14e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.5e-18)|all cancers(14;1.5e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			AGCGACTTCCGCATCTCTGGG	0.617																																					p.R538H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1613A	19						.		HIS/ARG,HIS/ARG,HIS/ARG	0,4406		0,0,2203	45.0	34.0	38.0		1613,1688,1688	5.3	1.0	19	dbSNP_134	38	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	MAG	NM_001199216.1,NM_002361.3,NM_080600.2	29,29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	538/602,563/627,563/583	35802892	1,13005	2203	4300	6503	40494732	SO:0001583	missense	4099	exon10			M29273	CCDS12455.1, CCDS12456.1, CCDS56090.1	19q13.1	2013-01-29			ENSG00000105695	ENSG00000105695		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6783	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 4A"""	159460		GMA		2476987, 8432525	Standard	NM_080600		Approved	SIGLEC4A, SIGLEC-4A, S-MAG	uc002nyy.2	P20916		ENST00000392213.3:c.1688G>A	19.37:g.35802892G>A	ENSP00000376048:p.Arg563His		40494732	NM_001199216	B7Z2E5|F5GYC0|Q567S4	Missense_Mutation	SNP	ENST00000392213.3	37	CCDS12455.1	.	.	.	.	.	.	.	.	.	.	g	17.74	3.463523	0.63513	0.0	1.16E-4	ENSG00000105695	ENST00000262624;ENST00000361922;ENST00000392213;ENST00000537831	T;T;T	0.65732	-0.07;-0.17;-0.15	5.26	5.26	0.73747	.	0.158554	0.44902	D	0.000401	T	0.55878	0.1948	N	0.14661	0.345	0.30827	N	0.737125	D;B;B	0.71674	0.998;0.0;0.002	P;B;B	0.51193	0.662;0.0;0.001	T	0.61647	-0.7020	10	0.49607	T	0.09	.	16.3569	0.83237	0.0:0.0:1.0:0.0	.	600;563;563	Q59GD9;P20916;Q567S4	.;MAG_HUMAN;.	H	600;563;563;538	ENSP00000355234:R563H;ENSP00000376048:R563H;ENSP00000440695:R538H	ENSP00000262624:R600H	R	+	2	0	MAG	40494732	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.592000	0.53993	2.466000	0.83321	0.556000	0.70494	CGC		0.617	MAG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466071.1	NM_080600	
FFAR1	2864	broad.mit.edu	37	19	35842982	35842982	+	Silent	SNP	G	G	A			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr19:35842982G>A	ENST00000246553.2	+	1	538	c.528G>A	c.(526-528)ccG>ccA	p.P176P		NM_005303.2	NP_005294.1	O14842	FFAR1_HUMAN	free fatty acid receptor 1	176					energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|positive regulation of GTPase activity (GO:0043547)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|guanyl-nucleotide exchange factor activity (GO:0005085)|lipid binding (GO:0008289)	p.P176P(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;4.58e-20)|OV - Ovarian serous cystadenocarcinoma(14;6.67e-19)|all cancers(14;2.01e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)		Icosapent(DB00159)	CCTGGGACCCGGCCTCTGCCG	0.667																																					p.P176P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G528A	19						.						29.0	32.0	31.0					19																	35842982		2202	4300	6502	40534822	SO:0001819	synonymous_variant	2864	exon1			AF024687	CCDS12458.1	19q13.1	2012-08-08	2006-02-15	2006-02-15	ENSG00000126266	ENSG00000126266		"""GPCR / Class A : Fatty acid receptors"""	4498	protein-coding gene	gene with protein product		603820	"""G protein-coupled receptor 40"""	GPR40		15684720	Standard	NM_005303		Approved	FFA1R	uc002nzc.2	O14842		ENST00000246553.2:c.528G>A	19.37:g.35842982G>A			40534822	NM_005303	Q0VAS2|Q4VBL4	Silent	SNP	ENST00000246553.2	37	CCDS12458.1																																																																																				0.667	FFAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466112.2	NM_005303	
CCDC9	26093	broad.mit.edu	37	19	47767873	47767873	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr19:47767873G>A	ENST00000221922.6	+	6	698	c.476G>A	c.(475-477)cGg>cAg	p.R159Q		NM_015603.2	NP_056418.1	Q9Y3X0	CCDC9_HUMAN	coiled-coil domain containing 9	159							poly(A) RNA binding (GO:0044822)	p.R159Q(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|urinary_tract(1)	12		all_cancers(25;0.0432)|all_epithelial(76;0.00812)|Medulloblastoma(540;0.0208)|all_neural(266;0.0416)|Hepatocellular(1079;0.114)		OV - Ovarian serous cystadenocarcinoma(262;8.51e-95)|Epithelial(262;1.15e-92)|all cancers(93;7.67e-84)|GBM - Glioblastoma multiforme(486;0.024)|STAD - Stomach adenocarcinoma(1328;0.183)		TGGGAGGAGCGGCGCAGGCAG	0.612																																					p.R159Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G476A	19						.						62.0	50.0	54.0					19																	47767873		2202	4300	6502	52459713	SO:0001583	missense	26093	exon6			AL050284	CCDS12698.1	19q13.33	2008-02-05				ENSG00000105321			24560	protein-coding gene	gene with protein product						11230166	Standard	NM_015603		Approved	DKFZP586M1019	uc010xym.2	Q9Y3X0		ENST00000221922.6:c.476G>A	19.37:g.47767873G>A	ENSP00000221922:p.Arg159Gln		52459713	NM_015603		Missense_Mutation	SNP	ENST00000221922.6	37	CCDS12698.1	.	.	.	.	.	.	.	.	.	.	g	18.82	3.704589	0.68615	.	.	ENSG00000105321	ENST00000221922;ENST00000504556	T	0.29655	1.56	4.63	4.63	0.57726	.	0.115808	0.56097	D	0.000031	T	0.49098	0.1537	L	0.53249	1.67	0.41567	D	0.988666	D	0.76494	0.999	D	0.64144	0.922	T	0.52343	-0.8588	10	0.72032	D	0.01	-21.2322	16.3937	0.83548	0.0:0.0:1.0:0.0	.	159	Q9Y3X0	CCDC9_HUMAN	Q	159;141	ENSP00000221922:R159Q	ENSP00000221922:R159Q	R	+	2	0	CCDC9	52459713	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.661000	0.68025	2.416000	0.81992	0.561000	0.74099	CGG		0.612	CCDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466917.1	NM_015603	
SAFB	6294	broad.mit.edu	37	19	5668250	5668250	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr19:5668250G>T	ENST00000292123.5	+	21	2803	c.2696G>T	c.(2695-2697)gGc>gTc	p.G899V	SAFB_ENST00000454510.1_Missense_Mutation_p.G832V|SAFB_ENST00000433404.1_Missense_Mutation_p.G731V|SAFB_ENST00000592224.1_Missense_Mutation_p.G900V|SAFB_ENST00000588852.1_Missense_Mutation_p.G901V|SAFB_ENST00000538656.1_Missense_Mutation_p.G743V	NM_001201338.1|NM_001201339.1|NM_002967.3	NP_001188267.1|NP_001188268.1|NP_002958.2	Q15424	SAFB1_HUMAN	scaffold attachment factor B	899	Gly-rich.|Interaction with SAFB2.				chromatin organization (GO:0006325)|growth (GO:0040007)|hormone metabolic process (GO:0042445)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.G899V(1)		breast(3)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(6)|ovary(2)|skin(1)	23				UCEC - Uterine corpus endometrioid carcinoma (162;0.000222)		GGGTTTGGAGGCCAGAGCCGG	0.637																																					p.G899V	Colon(88;338 1345 6184 8214 20897)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2696T	19						.						36.0	42.0	40.0					19																	5668250		2203	4299	6502	5619250	SO:0001583	missense	6294	exon21			L43631	CCDS12142.1, CCDS56077.1, CCDS59339.1, CCDS59340.1	19p13.3-p13.2	2013-02-12				ENSG00000160633		"""RNA binding motif (RRM) containing"""	10520	protein-coding gene	gene with protein product	"""Hsp27 ERE-TATA binding protein"""	602895				9605873, 8600450	Standard	NM_002967		Approved	HET, SAFB1	uc002mcg.3	Q15424		ENST00000292123.5:c.2696G>T	19.37:g.5668250G>T	ENSP00000292123:p.Gly899Val		5619250	NM_002967	A0AV56|B7Z5B6|B7ZLP6|F5H0H3|O60406|Q59HH8	Missense_Mutation	SNP	ENST00000292123.5	37	CCDS12142.1	.	.	.	.	.	.	.	.	.	.	G	12.37	1.919110	0.33908	.	.	ENSG00000160633	ENST00000454510;ENST00000540206;ENST00000433404;ENST00000292123;ENST00000538656	T;T;T;T	0.12361	2.72;2.87;2.74;2.69	5.23	4.17	0.49024	.	0.151009	0.31542	N	0.007470	T	0.16557	0.0398	L	0.43152	1.355	0.58432	D	0.999992	P;D;P;P;P;P;P	0.54047	0.906;0.964;0.944;0.906;0.906;0.906;0.906	B;P;P;B;B;B;B	0.48425	0.36;0.577;0.563;0.36;0.36;0.36;0.36	T	0.00273	-1.1858	10	0.66056	D	0.02	-23.1321	10.2438	0.43328	0.0773:0.1374:0.7853:0.0	.	700;743;832;898;901;899;900	B7Z1C7;B7Z2F6;F5H0H3;B7ZLP5;A0AV56;Q15424;B7ZLP6	.;.;.;.;.;SAFB1_HUMAN;.	V	832;796;731;899;743	ENSP00000415895:G832V;ENSP00000404545:G731V;ENSP00000292123:G899V;ENSP00000438880:G743V	ENSP00000292123:G899V	G	+	2	0	SAFB	5619250	0.996000	0.38824	0.821000	0.32701	0.304000	0.27724	1.949000	0.40313	2.606000	0.88127	0.585000	0.79938	GGC		0.637	SAFB-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000451641.2		
FLT3LG	2323	broad.mit.edu	37	19	49979038	49979038	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr19:49979038G>A	ENST00000594009.1	+	2	203	c.124G>A	c.(124-126)Gct>Act	p.A42T	FLT3LG_ENST00000597551.1_Missense_Mutation_p.A42T|FLT3LG_ENST00000204637.2_De_novo_Start_OutOfFrame|FLT3LG_ENST00000596435.1_Missense_Mutation_p.A42T|FLT3LG_ENST00000600429.1_Missense_Mutation_p.A42T|FLT3LG_ENST00000595510.1_De_novo_Start_OutOfFrame|CTD-3148I10.15_ENST00000595815.1_RNA|FLT3LG_ENST00000344019.3_Missense_Mutation_p.A42T|CTD-3148I10.9_ENST00000599536.1_Intron	NM_001204503.1	NP_001191432.1	P49771	FLT3L_HUMAN	fms-related tyrosine kinase 3 ligand	42					embryonic hemopoiesis (GO:0035162)|lymphocyte differentiation (GO:0030098)|positive regulation of cell proliferation (GO:0008284)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of protein phosphorylation (GO:0001934)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|intrinsic component of external side of plasma membrane (GO:0031233)|membrane (GO:0016020)	receptor binding (GO:0005102)	p.A42T(1)		large_intestine(2)|lung(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	10		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00154)|GBM - Glioblastoma multiforme(486;0.0246)		CTCCGACTTCGCTGTCAAAAT	0.592																																					p.A42T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G124A	19						.						88.0	67.0	74.0					19																	49979038		2203	4300	6503	54670850	SO:0001583	missense	2323	exon3			U04806	CCDS12767.1, CCDS62753.1	19q13.3	2014-01-30				ENSG00000090554		"""Endogenous ligands"""	3766	protein-coding gene	gene with protein product		600007				8145851, 7824267	Standard	NM_001204502		Approved		uc010yau.2	P49771		ENST00000594009.1:c.124G>A	19.37:g.49979038G>A	ENSP00000469613:p.Ala42Thr		54670850	NM_001459	A0AVC2|B9EGH2|Q05C96	Missense_Mutation	SNP	ENST00000594009.1	37	CCDS12767.1	.	.	.	.	.	.	.	.	.	.	g	12.62	1.991185	0.35131	.	.	ENSG00000090554	ENST00000204637;ENST00000344019	.	.	.	4.18	-3.18	0.05186	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	697.833000	0.01355	U	0.012036	T	0.20414	0.0491	L	0.27053	0.805	0.09310	N	1	P	0.37663	0.604	B	0.30495	0.116	T	0.12941	-1.0528	9	0.25751	T	0.34	-5.2691	4.8488	0.13526	0.2872:0.292:0.4208:0.0	.	42	P49771	FLT3L_HUMAN	T	42	.	ENSP00000204637:A42T	A	+	1	0	FLT3LG	54670850	0.000000	0.05858	0.027000	0.17364	0.208000	0.24298	-1.404000	0.02494	-0.223000	0.09943	0.544000	0.68410	GCT		0.592	FLT3LG-007	KNOWN	alternative_3_UTR|alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465305.1		
CTTNBP2NL	55917	broad.mit.edu	37	1	112958850	112958850	+	Silent	SNP	G	G	A			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr1:112958850G>A	ENST00000271277.6	+	3	288	c.63G>A	c.(61-63)gaG>gaA	p.E21E		NM_018704.2	NP_061174.1	Q9P2B4	CT2NL_HUMAN	CTTNBP2 N-terminal like	21					negative regulation of transmembrane transport (GO:0034763)|negative regulation of transporter activity (GO:0032410)|protein dephosphorylation (GO:0006470)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	protein phosphatase 2A binding (GO:0051721)	p.E21E(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	29		all_cancers(81;0.00064)|all_epithelial(167;0.000415)|all_lung(203;0.00045)|Lung NSC(69;0.000705)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTGAAGGAGAGCTTGAAGCAA	0.343																																					p.E21E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G63A	1						.						92.0	92.0	92.0					1																	112958850		2203	4300	6503	112760373	SO:0001819	synonymous_variant	55917	exon3			AB037854	CCDS845.1	1p13.2	2008-02-05			ENSG00000143079	ENSG00000143079			25330	protein-coding gene	gene with protein product		615100				10718198	Standard	NM_018704		Approved	DKFZp547A023	uc001ebx.3	Q9P2B4	OTTHUMG00000011154	ENST00000271277.6:c.63G>A	1.37:g.112958850G>A			112760373	NM_018704	B3KMS5|Q96B40	Silent	SNP	ENST00000271277.6	37	CCDS845.1																																																																																				0.343	CTTNBP2NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030686.1	NM_018704	
NRAS	4893	broad.mit.edu	37	1	115258747	115258747	+	Missense_Mutation	SNP	C	C	T	rs121913237		TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr1:115258747C>T	ENST00000369535.4	-	2	288	c.35G>A	c.(34-36)gGt>gAt	p.G12D	CSDE1_ENST00000483407.1_5'Flank	NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	12			G -> C (in leukemia). {ECO:0000269|PubMed:2998510}.|G -> D (in KNEN). {ECO:0000269|PubMed:22499344}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(375)|p.G12V(59)|p.G12A(42)|p.G12N(2)|p.G12E(1)|p.G12P(1)|p.G12Y(1)		NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		CCCAACACCACCTGCTCCAAC	0.493	G12D(697_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(HEC151_ENDOMETRIUM)|G12D(KE37_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(P12ICHIKAWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(TYKNU_OVARY)	50	Mis		"""melanoma, MM, AML, thyroid"""				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																											p.G12D			Dom	yes		1	1p13.2	4893	neuroblastoma RAS viral (v-ras) oncogene homolog		"""L, E"""	NRAS,haematopoietic_and_lymphoid_tissue,NS,Substitution - Missense,0 	.	481	Substitution - Missense(481)	haematopoietic_and_lymphoid_tissue(375)|skin(59)|large_intestine(21)|testis(5)|thyroid(4)|central_nervous_system(3)|endometrium(3)|biliary_tract(3)|ovary(3)|soft_tissue(2)|lung(2)|prostate(1)	c.G35A	1						.	C	ASP/GLY	0,4406		0,0,2203	206.0	184.0	191.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	35	5.6	1.0	1	dbSNP_133	191	1,8599	1.2+/-3.3	0,1,4299	no	missense	NRAS	NM_002524.4	94	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	12/190	115258747	1,13005	2203	4300	6503	115060270	SO:0001583	missense	4893	exon2	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.35G>A	1.37:g.115258747C>T	ENSP00000358548:p.Gly12Asp		115060270	NM_002524	Q14971|Q15104|Q15282	Missense_Mutation	SNP	ENST00000369535.4	37	CCDS877.1	.	.	.	.	.	.	.	.	.	.	C	35	5.524414	0.96431	0.0	1.16E-4	ENSG00000213281	ENST00000369535	T	0.78595	-1.19	5.58	5.58	0.84498	Small GTP-binding protein domain (1);	0.000000	0.56097	U	0.000025	D	0.85252	0.5654	M	0.92604	3.325	0.80722	D	1	B	0.32467	0.372	B	0.42827	0.399	D	0.86173	0.1601	10	0.87932	D	0	.	19.3769	0.94514	0.0:1.0:0.0:0.0	.	12	P01111	RASN_HUMAN	D	12	ENSP00000358548:G12D	ENSP00000358548:G12D	G	-	2	0	NRAS	115060270	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.651000	0.83577	2.906000	0.99361	0.655000	0.94253	GGT		0.493	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033395.2	NM_002524	
HRNR	388697	broad.mit.edu	37	1	152187584	152187584	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr1:152187584C>T	ENST00000368801.2	-	3	6596	c.6521G>A	c.(6520-6522)cGa>cAa	p.R2174Q	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	2174					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.R2174Q(1)		autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGACCCTTGTCGGCCGTGGCC	0.637																																					p.R2174Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G6521A	1						.						73.0	90.0	84.0					1																	152187584		1566	3253	4819	150454208	SO:0001583	missense	388697	exon3			AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.6521G>A	1.37:g.152187584C>T	ENSP00000357791:p.Arg2174Gln		150454208	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	-	8.310	0.821969	0.16678	.	.	ENSG00000197915	ENST00000368801	T	0.01998	4.51	3.22	-4.67	0.03319	.	.	.	.	.	T	0.00271	0.0008	N	0.02247	-0.625	0.09310	N	1	B	0.10296	0.003	B	0.01281	0.0	T	0.40905	-0.9538	9	0.12103	T	0.63	.	6.5485	0.22420	0.1153:0.3449:0.0:0.5398	.	2174	Q86YZ3	HORN_HUMAN	Q	2174	ENSP00000357791:R2174Q	ENSP00000357791:R2174Q	R	-	2	0	HRNR	150454208	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.323000	0.01117	-1.798000	0.01250	-3.112000	0.00062	CGA		0.637	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
SPRR3	6707	broad.mit.edu	37	1	152975749	152975749	+	Missense_Mutation	SNP	G	G	A	rs374824766		TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr1:152975749G>A	ENST00000295367.4	+	2	295	c.253G>A	c.(253-255)Gtc>Atc	p.V85I	SPRR3_ENST00000331860.3_Missense_Mutation_p.V85I|SPRR3_ENST00000542696.1_Missense_Mutation_p.V85I	NM_001097589.1	NP_001091058.1	Q9UBC9	SPRR3_HUMAN	small proline-rich protein 3	85	14 X 8 AA approximate tandem repeats.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	structural molecule activity (GO:0005198)	p.V85I(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	11	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			TTGTACCAAGGTCCCTGAGCC	0.597													G|||	1	0.000199681	0.0	0.0014	5008	,	,		17452	0.0		0.0	False		,,,				2504	0.0				p.V85I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G253A	1						.	G	ILE/VAL,ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	66.0	56.0	59.0		253,253	-1.2	0.0	1		59	0,8598		0,0,4299	no	missense,missense	SPRR3	NM_001097589.1,NM_005416.2	29,29	0,1,6501	AA,AG,GG		0.0,0.0227,0.0077	benign,benign	85/170,85/170	152975749	1,13003	2203	4299	6502	151242373	SO:0001583	missense	6707	exon2			AY118269	CCDS1033.1	1q21-q22	2008-02-05			ENSG00000163209	ENSG00000163209			11268	protein-coding gene	gene with protein product		182271				8325635	Standard	NM_005416		Approved		uc001faz.4	Q9UBC9	OTTHUMG00000013872	ENST00000295367.4:c.253G>A	1.37:g.152975749G>A	ENSP00000295367:p.Val85Ile		151242373	NM_001097589	A5YKK8|B2R4G8|D3DV32|O75597|Q4ZGI7|Q5T525|Q8NET7|Q9UDG3	Missense_Mutation	SNP	ENST00000295367.4	37	CCDS1033.1	.	.	.	.	.	.	.	.	.	.	G	8.952	0.968506	0.18659	2.27E-4	0.0	ENSG00000163209	ENST00000331860;ENST00000443178;ENST00000295367;ENST00000542696	T;T;T;T	0.15718	2.65;2.65;2.65;2.4	4.79	-1.17	0.09648	.	.	.	.	.	T	0.04363	0.0120	L	0.55990	1.75	0.09310	N	1	B;B	0.24426	0.075;0.103	B;B	0.25614	0.058;0.062	T	0.41822	-0.9487	9	0.30078	T	0.28	.	2.2186	0.03967	0.2589:0.1297:0.4793:0.1321	.	77;85	F5GZ12;Q9UBC9	.;SPRR3_HUMAN	I	85	ENSP00000330391:V85I;ENSP00000402016:V85I;ENSP00000295367:V85I;ENSP00000441477:V85I	ENSP00000295367:V85I	V	+	1	0	SPRR3	151242373	0.000000	0.05858	0.000000	0.03702	0.096000	0.18686	-0.196000	0.09532	-0.076000	0.12775	-0.244000	0.11960	GTC		0.597	SPRR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038910.1	NM_005416	
BCAN	63827	broad.mit.edu	37	1	156621423	156621423	+	Silent	SNP	C	C	T	rs147038529	byFrequency	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr1:156621423C>T	ENST00000329117.5	+	7	1575	c.1239C>T	c.(1237-1239)gaC>gaT	p.D413D	RP11-284F21.7_ENST00000448869.1_RNA|BCAN_ENST00000361588.5_Silent_p.D413D	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican	413	Glu-rich.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hippocampus development (GO:0021766)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)	p.D413D(1)		cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	55	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TCATGGAGGACGGAGGAGGTG	0.562													C|||	4	0.000798722	0.0	0.0	5008	,	,		19892	0.001		0.0	False		,,,				2504	0.0031				p.D413D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1239T	1						.	C	,	0,4406		0,0,2203	91.0	89.0	90.0		1239,1239	-0.6	0.9	1	dbSNP_134	90	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous	BCAN	NM_021948.4,NM_198427.1	,	0,5,6498	TT,TC,CC		0.0581,0.0,0.0384	,	413/912,413/672	156621423	5,13001	2203	4300	6503	154888047	SO:0001819	synonymous_variant	63827	exon7			BC027971	CCDS1149.1, CCDS1150.1	1q31	2013-05-07			ENSG00000132692	ENSG00000132692		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	23059	protein-coding gene	gene with protein product	"""chondroitin sulfate proteoglycan 7"", ""brevican proteoglycan"""	600347				11054543, 11873941	Standard	NM_021948		Approved	BEHAB, MGC13038, CSPG7	uc001fpp.3	Q96GW7	OTTHUMG00000033322	ENST00000329117.5:c.1239C>T	1.37:g.156621423C>T			154888047	NM_021948	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	Silent	SNP	ENST00000329117.5	37	CCDS1149.1																																																																																				0.562	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081844.2	NM_021948	
XPR1	9213	broad.mit.edu	37	1	180601397	180601397	+	Silent	SNP	C	C	A			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr1:180601397C>A	ENST00000367590.4	+	1	258	c.60C>A	c.(58-60)atC>atA	p.I20I	XPR1_ENST00000367589.3_Silent_p.I20I	NM_004736.3	NP_004727.2	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor 1	20	SPX. {ECO:0000255|PROSITE- ProRule:PRU00714}.				G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)	p.I20I(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	35						AGCAATACATCCAGTATGAGG	0.642																																					p.I20I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C60A	1						.						59.0	49.0	53.0					1																	180601397		2203	4300	6503	178868020	SO:0001819	synonymous_variant	9213	exon1			AF099082	CCDS1340.1, CCDS44284.1	1q25.1	2013-07-18	2010-04-23		ENSG00000143324	ENSG00000143324			12827	protein-coding gene	gene with protein product		605237	"""xenotropic and polytropic retrovirus receptor"""			9990033	Standard	NM_004736		Approved	SYG1, X3	uc001goi.3	Q9UBH6	OTTHUMG00000035116	ENST00000367590.4:c.60C>A	1.37:g.180601397C>A			178868020	NM_001135669	O95719|Q7L8K9|Q8IW20|Q9NT19|Q9UFB9	Silent	SNP	ENST00000367590.4	37	CCDS1340.1																																																																																				0.642	XPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084996.2	NM_004736	
OPRD1	4985	broad.mit.edu	37	1	29185620	29185620	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr1:29185620G>A	ENST00000234961.2	+	2	624	c.382G>A	c.(382-384)Gac>Aac	p.D128N		NM_000911.3	NP_000902.3	P41143	OPRD_HUMAN	opioid receptor, delta 1	128					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adult locomotory behavior (GO:0008344)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|cellular response to toxic substance (GO:0097237)|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)|negative regulation of gene expression (GO:0010629)|negative regulation of protein oligomerization (GO:0032460)|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 CREB transcription factor activity (GO:0032793)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein import into nucleus, translocation (GO:0000060)|regulation of calcium ion transport (GO:0051924)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of sensory perception of pain (GO:0051930)	axon terminus (GO:0043679)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	enkephalin receptor activity (GO:0038046)|opioid receptor activity (GO:0004985)	p.D128N(1)		breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15		Colorectal(325;3.46e-05)|Lung NSC(340;0.000947)|all_lung(284;0.00131)|Renal(390;0.00758)|Breast(348;0.00765)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;1.29e-07)|COAD - Colon adenocarcinoma(152;7.51e-06)|STAD - Stomach adenocarcinoma(196;0.00306)|BRCA - Breast invasive adenocarcinoma(304;0.0241)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)	Alvimopan(DB06274)|Amitriptyline(DB00321)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diphenoxylate(DB01081)|Fentanyl(DB00813)|Heroin(DB01452)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	GCTCTCCATCGACTACTACAA	0.582																																					p.D128N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G382A	1						.						166.0	139.0	148.0					1																	29185620		2203	4300	6503	29058207	SO:0001583	missense	4985	exon2			U10504	CCDS329.1	1p36.1-p34.3	2012-08-08			ENSG00000116329	ENSG00000116329		"""GPCR / Class A : Opioid receptors"""	8153	protein-coding gene	gene with protein product		165195				8415697	Standard	NM_000911		Approved		uc001brf.1	P41143	OTTHUMG00000003646	ENST00000234961.2:c.382G>A	1.37:g.29185620G>A	ENSP00000234961:p.Asp128Asn		29058207	NM_000911	B5B0B8	Missense_Mutation	SNP	ENST00000234961.2	37	CCDS329.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.833597	0.91036	.	.	ENSG00000116329	ENST00000234961;ENST00000536280	T	0.37752	1.18	4.46	4.46	0.54185	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.57227	0.2039	M	0.90650	3.135	0.80722	D	1	P	0.36144	0.539	P	0.46253	0.509	T	0.66670	-0.5865	10	0.72032	D	0.01	.	14.6367	0.68694	0.0:0.0:1.0:0.0	.	128	P41143	OPRD_HUMAN	N	128	ENSP00000234961:D128N	ENSP00000234961:D128N	D	+	1	0	OPRD1	29058207	1.000000	0.71417	0.996000	0.52242	0.978000	0.69477	9.657000	0.98554	2.315000	0.78130	0.462000	0.41574	GAC		0.582	OPRD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010330.1	NM_000911	
FMN2	56776	broad.mit.edu	37	1	240370671	240370671	+	Nonsense_Mutation	SNP	T	T	A			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr1:240370671T>A	ENST00000319653.9	+	5	2789	c.2559T>A	c.(2557-2559)tgT>tgA	p.C853*		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	853	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.C996*(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			AAAACAGCTGTAACATCCCAT	0.577																																					p.C853X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.T2559A	1						.						117.0	111.0	113.0					1																	240370671		2203	4300	6503	238437294	SO:0001587	stop_gained	56776	exon5			AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2559T>A	1.37:g.240370671T>A	ENSP00000318884:p.Cys853*		238437294	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Nonsense_Mutation	SNP	ENST00000319653.9	37	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	T	32	5.107287	0.94292	.	.	ENSG00000155816	ENST00000319653	.	.	.	4.09	1.75	0.24633	.	0.969977	0.08476	N	0.940277	.	.	.	.	.	.	0.18873	N	0.999981	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.2323	0.31605	0.0:0.1661:0.0:0.8339	.	.	.	.	X	853	.	.	C	+	3	2	FMN2	238437294	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	0.238000	0.18004	0.249000	0.21456	0.454000	0.30748	TGT		0.577	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
SNPH	9751	broad.mit.edu	37	20	1285648	1285648	+	Silent	SNP	C	C	T			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr20:1285648C>T	ENST00000381873.3	+	6	671	c.435C>T	c.(433-435)ctC>ctT	p.L145L	SNPH_ENST00000381867.1_Silent_p.L189L	NM_014723.2	NP_055538.2	O15079	SNPH_HUMAN	syntaphilin	145					brain development (GO:0007420)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|synaptic vesicle docking involved in exocytosis (GO:0016081)	cell junction (GO:0030054)|cytoplasmic microtubule (GO:0005881)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|presynaptic membrane (GO:0042734)	syntaxin-1 binding (GO:0017075)	p.L145L(1)|p.L189L(1)		endometrium(2)|large_intestine(4)|lung(10)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						TCAAGCAGCTCAAGCAGGTCA	0.562																																					p.L145L												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C435T	20						.						131.0	118.0	122.0					20																	1285648		2203	4300	6503	1233648	SO:0001819	synonymous_variant	9751	exon6				CCDS13012.1	20p13	2008-07-02			ENSG00000101298	ENSG00000101298			15931	protein-coding gene	gene with protein product		604942				10707983	Standard	NM_014723		Approved	bA314N13.5	uc002wes.3	O15079	OTTHUMG00000031662	ENST00000381873.3:c.435C>T	20.37:g.1285648C>T			1233648	NM_014723	Q8IYI3	Silent	SNP	ENST00000381873.3	37	CCDS13012.1																																																																																				0.562	SNPH-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145240.2	NM_014723	
ZNF335	63925	broad.mit.edu	37	20	44588071	44588071	+	Splice_Site	SNP	C	C	T	rs543763444		TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr20:44588071C>T	ENST00000322927.2	-	15	2122	c.2022G>A	c.(2020-2022)ggG>ggA	p.G674G	ZNF335_ENST00000426788.1_Splice_Site_p.G519G	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	674					brain development (GO:0007420)|brain morphogenesis (GO:0048854)|cerebral cortex neuron differentiation (GO:0021895)|histone H3-K4 trimethylation (GO:0080182)|in utero embryonic development (GO:0001701)|neuron projection morphogenesis (GO:0048812)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of neurogenesis (GO:0050769)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription regulatory region DNA binding (GO:0044212)	p.G674G(1)		NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51		Myeloproliferative disorder(115;0.0122)				AGGGCTTGGCCCCTGGAGGCA	0.582													C|||	1	0.000199681	0.0	0.0	5008	,	,		19061	0.0		0.0	False		,,,				2504	0.001				p.G674G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2022A	20						.						44.0	30.0	35.0					20																	44588071		2203	4300	6503	44021478	SO:0001630	splice_region_variant	63925	exon15			AK026157	CCDS13389.1	20q13.12	2011-09-12			ENSG00000198026	ENSG00000198026		"""Zinc fingers, C2H2-type"""	15807	protein-coding gene	gene with protein product	"""NRC-interacting factor 1"""	610827				12215545, 19131338	Standard	NM_022095		Approved	bA465L10.2, NIF-1	uc002xqw.3	Q9H4Z2	OTTHUMG00000032637	ENST00000322927.2:c.2021-1G>A	20.37:g.44588071C>T			44021478	NM_022095	B4DLG7|Q548D0|Q9H684	Silent	SNP	ENST00000322927.2	37	CCDS13389.1																																																																																				0.582	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1	NM_022095	Silent
PTGIS	5740	broad.mit.edu	37	20	48129710	48129710	+	Silent	SNP	G	G	A	rs561620152		TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr20:48129710G>A	ENST00000244043.4	-	8	1142	c.1113C>T	c.(1111-1113)gaC>gaT	p.D371D	PTGIS_ENST00000478971.1_5'UTR	NM_000961.3	NP_000952.1	Q16647	PTGIS_HUMAN	prostaglandin I2 (prostacyclin) synthase	371					apoptotic signaling pathway (GO:0097190)|arachidonic acid metabolic process (GO:0019369)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cyclooxygenase pathway (GO:0019371)|icosanoid metabolic process (GO:0006690)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|positive regulation of angiogenesis (GO:0045766)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)|prostaglandin-I synthase activity (GO:0008116)	p.D371D(1)		endometrium(1)|kidney(1)|large_intestine(7)|lung(6)|ovary(3)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(12;2.37e-05)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Epoprostenol(DB01240)|Phenylbutazone(DB00812)	ATTCTCGCCCGTCTGCCATGG	0.602													G|||	1	0.000199681	0.0	0.0014	5008	,	,		16866	0.0		0.0	False		,,,				2504	0.0				p.D371D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1113T	20						.						97.0	86.0	89.0					20																	48129710		2203	4300	6503	47563117	SO:0001819	synonymous_variant	5740	exon8				CCDS13419.1	20q13	2013-11-18			ENSG00000124212	ENSG00000124212	5.3.99.4	"""Cytochrome P450s"""	9603	protein-coding gene	gene with protein product	"""cytochrome P450, family 8, subfamily A, polypeptide 1"""	601699				8812456	Standard	NM_000961		Approved	PGIS, CYP8A1	uc002xut.3	Q16647	OTTHUMG00000033077	ENST00000244043.4:c.1113C>T	20.37:g.48129710G>A			47563117	NM_000961	Q3MII8|Q9HAX2|Q9HAX3|Q9HAX4	Silent	SNP	ENST00000244043.4	37	CCDS13419.1																																																																																				0.602	PTGIS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080496.2		
MLC1	23209	broad.mit.edu	37	22	50515832	50515832	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr22:50515832T>C	ENST00000311597.5	-	6	1129	c.523A>G	c.(523-525)Aag>Gag	p.K175E	MLC1_ENST00000535444.1_Missense_Mutation_p.K96E|MLC1_ENST00000395876.2_Missense_Mutation_p.K175E|MLC1_ENST00000431262.2_Missense_Mutation_p.K145E|MLC1_ENST00000538737.1_Missense_Mutation_p.K141E|MLC1_ENST00000450140.2_Missense_Mutation_p.K123E	NM_015166.3	NP_055981.1	Q15049	MLC1_HUMAN	megalencephalic leukoencephalopathy with subcortical cysts 1	175	Poly-Lys.				caveolin-mediated endocytosis (GO:0072584)|cellular response to cholesterol (GO:0071397)|ion transport (GO:0006811)|positive regulation of intracellular transport (GO:0032388)|protein oligomerization (GO:0051259)|regulation of response to osmotic stress (GO:0047484)|transport (GO:0006810)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	protein complex binding (GO:0032403)|protein transporter activity (GO:0008565)|transporter activity (GO:0005215)	p.K175E(2)		endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(3)	18		all_cancers(38;7.69e-11)|all_epithelial(38;9.52e-10)|all_lung(38;3.67e-05)|Breast(42;0.000776)|Lung NSC(38;0.000946)|Ovarian(80;0.0365)|Lung SC(80;0.113)		READ - Rectum adenocarcinoma(2;0.000669)|Colorectal(2;0.00242)|LUAD - Lung adenocarcinoma(64;0.0695)|BRCA - Breast invasive adenocarcinoma(115;0.216)		GCACCCACCTTCTTTTTCTTG	0.632																																					p.K175E												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.A523G	22						.						74.0	55.0	61.0					22																	50515832		2203	4300	6503	48857959	SO:0001583	missense	23209	exon6			D25217	CCDS14083.1	22q13.33	2007-03-20			ENSG00000100427	ENSG00000100427			17082	protein-coding gene	gene with protein product		605908				7584026, 7584028	Standard	XR_430476		Approved	MLC, KIAA0027, LVM, VL	uc003bjg.1	Q15049	OTTHUMG00000150236	ENST00000311597.5:c.523A>G	22.37:g.50515832T>C	ENSP00000310375:p.Lys175Glu		48857959	NM_015166	B3KW61|B7Z659|Q5JZ83|Q8TAG4|Q96RP5|Q9UGY8	Missense_Mutation	SNP	ENST00000311597.5	37	CCDS14083.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.283129	0.80803	.	.	ENSG00000100427	ENST00000395876;ENST00000311597;ENST00000538737;ENST00000431262;ENST00000535444;ENST00000450140;ENST00000442311	D;D;D;D;D;D;D	0.88431	-2.38;-2.38;-2.38;-2.38;-2.38;-2.38;-2.38	3.55	3.55	0.40652	.	0.102504	0.64402	D	0.000004	D	0.90758	0.7099	L	0.43923	1.385	0.58432	D	0.999997	D;D;D;D	0.71674	0.998;0.998;0.996;0.998	D;D;D;D	0.78314	0.991;0.991;0.987;0.991	D	0.90691	0.4613	10	0.87932	D	0	-8.3487	9.9004	0.41344	0.0:0.0:0.0:1.0	.	141;145;123;175	F5H1B9;B7Z659;B7Z1X1;Q15049	.;.;.;MLC1_HUMAN	E	175;175;141;145;96;123;145	ENSP00000379216:K175E;ENSP00000310375:K175E;ENSP00000445805:K141E;ENSP00000415877:K145E;ENSP00000438910:K96E;ENSP00000412448:K123E;ENSP00000401385:K145E	ENSP00000310375:K175E	K	-	1	0	MLC1	48857959	1.000000	0.71417	0.995000	0.50966	0.853000	0.48598	4.473000	0.60196	1.360000	0.45960	0.533000	0.62120	AAG		0.632	MLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316979.2	NM_015166	
ANKMY1	51281	broad.mit.edu	37	2	241463566	241463567	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr2:241463566_241463567insC	ENST00000272972.3	-	7	1514_1515	c.1300_1301insG	c.(1300-1302)gacfs	p.D434fs	ANKMY1_ENST00000462004.1_5'Flank|ANKMY1_ENST00000403283.1_Frame_Shift_Ins_p.D372fs|ANKMY1_ENST00000391987.1_Frame_Shift_Ins_p.D434fs|ANKMY1_ENST00000373320.4_Frame_Shift_Ins_p.D204fs|ANKMY1_ENST00000373318.2_Frame_Shift_Ins_p.D293fs|ANKMY1_ENST00000361678.4_Frame_Shift_Ins_p.D293fs|ANKMY1_ENST00000405523.3_Frame_Shift_Ins_p.D293fs|ANKMY1_ENST00000401804.1_Frame_Shift_Ins_p.D523fs|ANKMY1_ENST00000406958.1_Intron|ANKMY1_ENST00000536462.1_Frame_Shift_Ins_p.D246fs|ANKMY1_ENST00000405002.1_Frame_Shift_Ins_p.D204fs	NM_016552.2	NP_057636.2	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1	434							metal ion binding (GO:0046872)	p.D434fs*17(1)		central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	30		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)		CAACGGGGAGTCCCCCTTCAGA	0.639																																					p.D293fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.878_879insG	2						.																																			241112240	SO:0001589	frameshift_variant	51281	exon6			AB034636	CCDS2535.1, CCDS2536.1, CCDS63184.1, CCDS63185.1, CCDS74681.1	2q37.3	2013-01-10			ENSG00000144504	ENSG00000144504		"""Zinc fingers, MYND-type"", ""Ankyrin repeat domain containing"""	20987	protein-coding gene	gene with protein product							Standard	XM_005247020		Approved	FLJ20499, ZMYND13	uc002vyz.1	Q9P2S6	OTTHUMG00000133355	ENST00000272972.3:c.1301dupG	2.37:g.241463571_241463571dupC	ENSP00000272972:p.Asp434fs		241112239	NM_017844	B2RB78|Q4ZFV3|Q8IYX5|Q8NDK5|Q9H0V8|Q9NX10	Frame_Shift_Ins	INS	ENST00000272972.3	37	CCDS2536.1																																																																																				0.639	ANKMY1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257187.2	NM_017844	
PXDN	7837	broad.mit.edu	37	2	1653119	1653119	+	Silent	SNP	G	G	A			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr2:1653119G>A	ENST00000252804.4	-	17	2483	c.2433C>T	c.(2431-2433)gaC>gaT	p.D811D		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	811					extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.D811D(1)		breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		TGAACTGCTCGTCGGGTGTGA	0.667																																					p.D811D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2433T	2						.						56.0	65.0	62.0					2																	1653119		2179	4273	6452	1632126	SO:0001819	synonymous_variant	7837	exon17			AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"""Immunoglobulin superfamily / I-set domain containing"""	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.2433C>T	2.37:g.1653119G>A			1632126	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Silent	SNP	ENST00000252804.4	37	CCDS46221.1																																																																																				0.667	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455	
NPHP1	4867	broad.mit.edu	37	2	110922274	110922274	+	Silent	SNP	C	C	T			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr2:110922274C>T	ENST00000393272.3	-	8	859	c.762G>A	c.(760-762)gcG>gcA	p.A254A	NPHP1_ENST00000355301.4_Silent_p.A192A|NPHP1_ENST00000417665.1_Silent_p.A254A|NPHP1_ENST00000445609.2_Silent_p.A254A|NPHP1_ENST00000316534.4_Silent_p.A254A	NM_000272.3|NM_207181.2	NP_000263.2|NP_997064.2	O15259	NPHP1_HUMAN	nephronophthisis 1 (juvenile)	254					actin cytoskeleton organization (GO:0030036)|cell projection organization (GO:0030030)|cellular protein localization (GO:0034613)|excretion (GO:0007588)|photoreceptor cell outer segment organization (GO:0035845)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|spermatid differentiation (GO:0048515)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|motile cilium (GO:0031514)|photoreceptor connecting cilium (GO:0032391)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)	p.A254A(1)		autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(2)	24						CCTCTGAAATCGCTTTCTGAA	0.448																																					p.A254A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G762A	2						.						106.0	117.0	113.0					2																	110922274		2203	4300	6503	110279563	SO:0001819	synonymous_variant	4867	exon8			AF023674	CCDS2086.1, CCDS46384.1, CCDS46385.1, CCDS46386.1	2q13	2014-01-28			ENSG00000144061	ENSG00000144061			7905	protein-coding gene	gene with protein product	"""nephrocystin-1"""	607100		NPH1			Standard	NM_000272		Approved	JBTS4, SLSN1	uc002tfm.4	O15259	OTTHUMG00000131195	ENST00000393272.3:c.762G>A	2.37:g.110922274C>T			110279563	NM_001128178	O14837	Silent	SNP	ENST00000393272.3	37	CCDS46385.1																																																																																				0.448	NPHP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253919.3	NM_000272	
LRP2	4036	broad.mit.edu	37	2	170103911	170103911	+	Nonsense_Mutation	SNP	G	G	T	rs575919892	byFrequency	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr2:170103911G>T	ENST00000263816.3	-	20	3170	c.2885C>A	c.(2884-2886)tCg>tAg	p.S962*	LRP2_ENST00000443831.1_Nonsense_Mutation_p.S825*	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	962					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.S962*(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)"""	GACATCATACGATTTCAAATG	0.398																																					p.S962X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2885A	2						.						130.0	111.0	117.0					2																	170103911		2203	4300	6503	169812157	SO:0001587	stop_gained	4036	exon20				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.2885C>A	2.37:g.170103911G>T	ENSP00000263816:p.Ser962*		169812157	NM_004525	O00711|Q16215	Nonsense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	G	39	7.840649	0.98519	.	.	ENSG00000081479	ENST00000263816;ENST00000443831	.	.	.	5.8	3.98	0.46160	.	0.268999	0.37955	N	0.001880	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	.	11.672	0.51408	0.147:0.0:0.853:0.0	.	.	.	.	X	962;825	.	ENSP00000263816:S962X	S	-	2	0	LRP2	169812157	1.000000	0.71417	0.081000	0.20488	0.198000	0.23893	5.393000	0.66279	0.769000	0.33313	0.491000	0.48974	TCG		0.398	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
BZW1	9689	broad.mit.edu	37	2	201684819	201684819	+	Nonsense_Mutation	SNP	A	A	T			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr2:201684819A>T	ENST00000409600.1	+	10	1536	c.1081A>T	c.(1081-1083)Aaa>Taa	p.K361*	BZW1_ENST00000452790.2_Nonsense_Mutation_p.K393*|BZW1_ENST00000409226.1_Nonsense_Mutation_p.K365*	NM_001207067.1|NM_014670.3	NP_001193996.1|NP_055485.2	Q7L1Q6	BZW1_HUMAN	basic leucine zipper and W2 domains 1	361	W2. {ECO:0000255|PROSITE- ProRule:PRU00695}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.K295*(1)		breast(1)|kidney(2)|large_intestine(1)|lung(2)	6						AGCCTTCCAGAAAATAGTGGT	0.318																																					p.K295X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.A883T	2						.						31.0	26.0	27.0					2																	201684819		1792	4060	5852	201393064	SO:0001587	stop_gained	9689	exon10			D13630	CCDS56154.1, CCDS56155.1, CCDS56156.1	2q33	2010-04-09			ENSG00000082153	ENSG00000082153			18380	protein-coding gene	gene with protein product						10964520, 11524015	Standard	NM_001207067		Approved	BZAP45, KIAA0005	uc021vus.1	Q7L1Q6	OTTHUMG00000154560	ENST00000409600.1:c.1081A>T	2.37:g.201684819A>T	ENSP00000386474:p.Lys361*		201393064	NM_014670	B4DLZ8|B4DWF7|Q14281|Q15394|Q9BUY0	Nonsense_Mutation	SNP	ENST00000409600.1	37	CCDS56156.1	.	.	.	.	.	.	.	.	.	.	A	36	5.852422	0.97030	.	.	ENSG00000082153	ENST00000409600;ENST00000409226;ENST00000452790	.	.	.	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-20.5923	16.3786	0.83431	1.0:0.0:0.0:0.0	.	.	.	.	X	361;365;393	.	ENSP00000386837:K365X	K	+	1	0	BZW1	201393064	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.230000	0.95299	2.323000	0.78572	0.528000	0.53228	AAA		0.318	BZW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335975.1	NM_014670	
COL6A3	1293	broad.mit.edu	37	2	238270462	238270462	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr2:238270462C>T	ENST00000295550.4	-	15	6528	c.6076G>A	c.(6076-6078)Gag>Aag	p.E2026K	COL6A3_ENST00000347401.3_Missense_Mutation_p.E1825K|COL6A3_ENST00000346358.4_Missense_Mutation_p.E1826K|COL6A3_ENST00000353578.4_Missense_Mutation_p.E1820K|COL6A3_ENST00000409809.1_Missense_Mutation_p.E1820K|COL6A3_ENST00000472056.1_Missense_Mutation_p.E1419K	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2026	Nonhelical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.E2026K(1)|p.E2026*(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)		CAAGCTTTCTCGGCAATGTTG	0.522																																					p.E1419K												.	.	2	Substitution - Nonsense(1)|Substitution - Missense(1)	large_intestine(1)|lung(1)	c.G4255A	2						.						72.0	74.0	73.0					2																	238270462		2203	4300	6503	237935201	SO:0001583	missense	1293	exon12			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.6076G>A	2.37:g.238270462C>T	ENSP00000295550:p.Glu2026Lys		237935201	NM_057166	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	15.61	2.883668	0.51908	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	T;T;T;T;T;T	0.37235	1.21;1.21;1.21;1.21;1.21;1.21	5.38	5.38	0.77491	.	0.000000	0.53938	D	0.000058	T	0.64843	0.2635	M	0.83118	2.625	0.54753	D	0.999987	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.85130	0.994;0.997;0.912	T	0.64918	-0.6294	10	0.37606	T	0.19	.	19.1613	0.93533	0.0:1.0:0.0:0.0	.	1419;1820;2026	E9PFQ6;P12111-2;P12111	.;.;CO6A3_HUMAN	K	2026;1825;1820;1419;1820;1826	ENSP00000295550:E2026K;ENSP00000315609:E1825K;ENSP00000315873:E1820K;ENSP00000418285:E1419K;ENSP00000386844:E1820K;ENSP00000295546:E1826K	ENSP00000295550:E2026K	E	-	1	0	COL6A3	237935201	1.000000	0.71417	0.980000	0.43619	0.864000	0.49448	5.583000	0.67484	2.513000	0.84729	0.650000	0.86243	GAG		0.522	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
EHD3	30845	broad.mit.edu	37	2	31457617	31457617	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr2:31457617G>A	ENST00000322054.5	+	1	415	c.130G>A	c.(130-132)Gag>Aag	p.E44K	EHD3_ENST00000541626.1_Missense_Mutation_p.E44K	NM_014600.2	NP_055415.1	Q9NZN3	EHD3_HUMAN	EH-domain containing 3	44					blood coagulation (GO:0007596)|endocytic recycling (GO:0032456)|protein homooligomerization (GO:0051260)|protein targeting to plasma membrane (GO:0072661)|regulation of cardiac muscle cell membrane potential (GO:0086036)	cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)	p.E44K(2)		NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(11)|lung(12)|ovary(1)|skin(3)	33	Acute lymphoblastic leukemia(172;0.155)					CCGCTTCCACGAGTTCCACTC	0.587																																					p.E44K												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G130A	2						.						107.0	101.0	103.0					2																	31457617		2203	4300	6503	31311121	SO:0001583	missense	30845	exon1			AF181264	CCDS1774.1	2p21	2013-01-10			ENSG00000013016	ENSG00000013016		"""EF-hand domain containing"""	3244	protein-coding gene	gene with protein product		605891		PAST3		10673336	Standard	NM_014600		Approved		uc002rnu.3	Q9NZN3	OTTHUMG00000099365	ENST00000322054.5:c.130G>A	2.37:g.31457617G>A	ENSP00000327116:p.Glu44Lys		31311121	NM_014600	B4DFR5|D6W574|Q8N514|Q9NZB3	Missense_Mutation	SNP	ENST00000322054.5	37	CCDS1774.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.456198	0.84209	.	.	ENSG00000013016	ENST00000541626;ENST00000322054	T;T	0.32023	1.47;2.22	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.32376	0.0827	M	0.68317	2.08	0.80722	D	1	P;B	0.39326	0.668;0.351	B;B	0.29942	0.109;0.069	T	0.33292	-0.9874	10	0.52906	T	0.07	-50.6122	18.4785	0.90802	0.0:0.0:1.0:0.0	.	44;44	B4DFR5;Q9NZN3	.;EHD3_HUMAN	K	44	ENSP00000440685:E44K;ENSP00000327116:E44K	ENSP00000327116:E44K	E	+	1	0	EHD3	31311121	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	5.996000	0.70639	2.600000	0.87896	0.561000	0.74099	GAG		0.587	EHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216810.1	NM_014600	
DYSF	8291	broad.mit.edu	37	2	71827854	71827854	+	Missense_Mutation	SNP	G	G	A	rs2303603	byFrequency	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr2:71827854G>A	ENST00000258104.3	+	34	4002	c.3725G>A	c.(3724-3726)cGc>cAc	p.R1242H	DYSF_ENST00000429174.2_Missense_Mutation_p.R1242H|DYSF_ENST00000409651.1_Missense_Mutation_p.R1274H|DYSF_ENST00000413539.2_Missense_Mutation_p.R1273H|DYSF_ENST00000410020.3_Missense_Mutation_p.R1260H|DYSF_ENST00000409582.3_Missense_Mutation_p.R1259H|DYSF_ENST00000409762.1_Missense_Mutation_p.R1259H|DYSF_ENST00000479049.2_3'UTR|DYSF_ENST00000409744.1_Missense_Mutation_p.R1229H|DYSF_ENST00000410041.1_Missense_Mutation_p.R1260H|DYSF_ENST00000409366.1_Missense_Mutation_p.R1243H|DYSF_ENST00000394120.2_Missense_Mutation_p.R1243H	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1242	C2 4. {ECO:0000255|PROSITE- ProRule:PRU00041}.		R -> H (in dbSNP:rs2303603).		plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)	p.R1242H(1)		autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						TTTATGGGTCGCTGCATCTGT	0.592													G|||	12	0.00239617	0.0008	0.0	5008	,	,		19005	0.0099		0.0	False		,,,				2504	0.001				p.R1274H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3821A	2						.	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,HIS/ARG,HIS/ARG	6,4400	11.4+/-27.6	0,6,2197	86.0	90.0	89.0		3728,3683,3683,3725,3818,3776,3776,3821,3728,3686,3779,3686,3779,3725	5.7	1.0	2	dbSNP_100	89	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	DYSF	NM_001130455.1,NM_001130976.1,NM_001130977.1,NM_001130978.1,NM_001130979.1,NM_001130980.1,NM_001130981.1,NM_001130982.1,NM_001130983.1,NM_001130984.1,NM_001130985.1,NM_001130986.1,NM_001130987.1,NM_003494.3	29,29,29,29,29,29,29,29,29,29,29,29,29,29	0,6,6497	AA,AG,GG		0.0,0.1362,0.0461	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	1243/2082,1228/2067,1228/2088,1242/2102,1273/2112,1259/2098,1259/2119,1274/2113,1243/2103,1229/2089,1260/2099,1229/2068,1260/2120,1242/2081	71827854	6,13000	2203	4300	6503	71681362	SO:0001583	missense	8291	exon35			AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.3725G>A	2.37:g.71827854G>A	ENSP00000258104:p.Arg1242His		71681362	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Missense_Mutation	SNP	ENST00000258104.3	37	CCDS1918.1	7	0.003205128205128205	0	0.0	0	0.0	7	0.012237762237762238	0	0.0	G	18.40	3.616276	0.66672	0.001362	0.0	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	T;T;T;T;T;T;T;T;T;T;T	0.70164	-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46;-0.46	5.66	5.66	0.87406	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.048208	0.85682	D	0.000000	T	0.78672	0.4320	M	0.84156	2.68	0.58432	D	0.999999	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.999;0.997;0.997;0.995;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;P;P;P;D;D;D;D;D;D;D;D;D;D	0.74023	0.944;0.9;0.9;0.9;0.969;0.969;0.981;0.981;0.969;0.969;0.969;0.944;0.969;0.982	T	0.82719	-0.0318	10	0.59425	D	0.04	-11.4755	17.2321	0.86987	0.0:0.0:1.0:0.0	rs2303603;rs2303603	1274;1260;1243;1229;1260;1229;1259;1228;1273;1259;1242;1228;1243;1242	O75923-8;O75923-13;O75923-10;O75923-9;O75923-11;O75923-12;O75923-5;O75923-6;O75923-2;O75923-7;O75923-4;O75923-3;O75923-14;O75923	.;.;.;.;.;.;.;.;.;.;.;.;.;DYSF_HUMAN	H	1273;1259;1259;1242;1242;1274;1243;1229;1243;1260;1260	ENSP00000407046:R1273H;ENSP00000387137:R1259H;ENSP00000386547:R1259H;ENSP00000398305:R1242H;ENSP00000258104:R1242H;ENSP00000386683:R1274H;ENSP00000377678:R1243H;ENSP00000386285:R1229H;ENSP00000386512:R1243H;ENSP00000386881:R1260H;ENSP00000386617:R1260H	ENSP00000258104:R1242H	R	+	2	0	DYSF	71681362	1.000000	0.71417	1.000000	0.80357	0.227000	0.25037	7.531000	0.81973	2.675000	0.91044	0.655000	0.94253	CGC		0.592	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494	
REV1	51455	broad.mit.edu	37	2	100019562	100019562	+	Silent	SNP	C	C	T			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr2:100019562C>T	ENST00000258428.3	-	20	3402	c.3174G>A	c.(3172-3174)aaG>aaA	p.K1058K	RP11-527J8.1_ENST00000608144.1_RNA|REV1_ENST00000465835.1_5'UTR|REV1_ENST00000393445.3_Silent_p.K1057K	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	1058					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|error-prone translesion synthesis (GO:0042276)|response to UV (GO:0009411)	nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|deoxycytidyl transferase activity (GO:0017125)|DNA-directed DNA polymerase activity (GO:0003887)|magnesium ion binding (GO:0000287)	p.K1058K(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(12)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GTAAAGGATTCTTTGGCACTA	0.358								Direct reversal of damage																													p.K1058K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3174A	2						.						31.0	28.0	29.0					2																	100019562		2201	4297	6498	99385994	SO:0001819	synonymous_variant	51455	exon20			AF206019	CCDS2045.1, CCDS42722.1	2q11.1-q11.2	2012-05-18	2012-05-18	2006-11-07	ENSG00000135945	ENSG00000135945		"""DNA polymerases"""	14060	protein-coding gene	gene with protein product		606134	"""REV1 (yeast homolog)- like"", ""REV1-like (yeast)"", ""REV1 homolog (S. cerevisiae)"""	REV1L		10536157	Standard	XM_005263968		Approved		uc002tad.3	Q9UBZ9	OTTHUMG00000130636	ENST00000258428.3:c.3174G>A	2.37:g.100019562C>T			99385994	NM_016316	O95941|Q53SI7|Q9C0J4|Q9NUP2	Silent	SNP	ENST00000258428.3	37	CCDS2045.1																																																																																				0.358	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253123.2	NM_016316	
COL6A3	1293	broad.mit.edu	37	2	238283278	238283278	+	Silent	SNP	G	G	A	rs112815265	byFrequency	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr2:238283278G>A	ENST00000295550.4	-	8	3908	c.3456C>T	c.(3454-3456)tcC>tcT	p.S1152S	COL6A3_ENST00000392003.2_Silent_p.S745S|COL6A3_ENST00000347401.3_Silent_p.S951S|COL6A3_ENST00000346358.4_Silent_p.S952S|COL6A3_ENST00000353578.4_Silent_p.S946S|COL6A3_ENST00000409809.1_Silent_p.S946S|COL6A3_ENST00000472056.1_Silent_p.S545S|COL6A3_ENST00000392004.3_Silent_p.S946S	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1152	Nonhelical region.|VWFA 6. {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.S1152S(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)		TCACGACCACGGAGGGGTTCC	0.607													G|||	20	0.00399361	0.0151	0.0	5008	,	,		22302	0.0		0.0	False		,,,				2504	0.0				p.S545S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1635T	2						.	G	,,,,	61,4345	59.9+/-96.7	0,61,2142	81.0	69.0	73.0		3456,2235,2838,1635,2838	-10.4	0.0	2	dbSNP_132	73	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057164.4,NM_057165.4,NM_057166.4,NM_057167.3	,,,,	0,61,6442	AA,AG,GG		0.0,1.3845,0.469	,,,,	1152/3178,745/1037,946/1238,545/2571,946/2972	238283278	61,12945	2203	4300	6503	237948017	SO:0001819	synonymous_variant	1293	exon5			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.3456C>T	2.37:g.238283278G>A			237948017	NM_057166	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																				0.607	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
GNB4	59345	broad.mit.edu	37	3	179143987	179143988	+	Start_Codon_Ins	INS	-	-	T			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	-	-	-	-	-	-	Unknown	Wildtype	None	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr3:179143987_179143988insT	ENST00000232564.3	-	0	287_288				GNB4_ENST00000468623.1_Start_Codon_Ins	NM_021629.3	NP_067642.1	Q9HAV0	GBB4_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 4						cell death (GO:0008219)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)|signal transducer activity (GO:0004871)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	16	all_cancers(143;2.01e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.237)			CAGTTCGCTCATTTTTTCAATT	0.366																																					p.M1fs	Melanoma(105;1405 1491 7265 20440 33721)											.	.	0			c.2_3insA	3						.																																			180626682	SO:0001582	initiator_codon_variant	59345	exon2			AF300648	CCDS3230.1	3q27.1	2013-01-10			ENSG00000114450	ENSG00000114450		"""WD repeat domain containing"""	20731	protein-coding gene	gene with protein product		610863				10644457, 11842130	Standard	NM_021629		Approved		uc003fjv.4	Q9HAV0	OTTHUMG00000157440	ENST00000232564.3:c.2dupA	3.37:g.179143993_179143993dupT			180626681	NM_021629	B3KMH5|D3DNR8	Frame_Shift_Ins	INS	ENST00000232564.3	37	CCDS3230.1																																																																																				0.366	GNB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258218.1	NM_021629	
NMD3	51068	broad.mit.edu	37	3	160964220	160964220	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr3:160964220G>A	ENST00000460469.1	+	11	1569	c.1114G>A	c.(1114-1116)Gga>Aga	p.G372R	NMD3_ENST00000351193.2_Missense_Mutation_p.G372R|NMD3_ENST00000472947.1_Missense_Mutation_p.G372R			Q96D46	NMD3_HUMAN	NMD3 ribosome export adaptor	372					protein transport (GO:0015031)|ribosomal large subunit export from nucleus (GO:0000055)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|ribosomal large subunit binding (GO:0043023)	p.G372R(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(10)|ovary(1)|skin(1)|urinary_tract(2)	25			Lung(72;0.00111)|LUSC - Lung squamous cell carcinoma(72;0.00156)			TCTAAATCCCGGAGACCTGGT	0.368																																					p.G372R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1114A	3						.						75.0	75.0	75.0					3																	160964220		2203	4300	6503	162446914	SO:0001583	missense	51068	exon12			BC013317	CCDS3194.1	3q26.1	2013-08-06	2013-08-06		ENSG00000169251	ENSG00000169251			24250	protein-coding gene	gene with protein product		611021	"""NMD3 homolog (S. cerevisiae)"""			10810093, 23782956, 12773398	Standard	NM_015938		Approved	CGI-07	uc003feb.1	Q96D46	OTTHUMG00000159063	ENST00000460469.1:c.1114G>A	3.37:g.160964220G>A	ENSP00000419004:p.Gly372Arg		162446914	NM_015938	D3DNM7|Q9Y2Z6	Missense_Mutation	SNP	ENST00000460469.1	37	CCDS3194.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.598462	0.87055	.	.	ENSG00000169251	ENST00000351193;ENST00000472947;ENST00000460469;ENST00000540137	T;T;T	0.71579	-0.48;-0.58;-0.48	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	D	0.88448	0.6439	M	0.93939	3.475	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.998;0.999	D	0.91181	0.4976	10	0.87932	D	0	-6.7637	18.1915	0.89808	0.0:0.0:1.0:0.0	.	372;372;372	B3KT11;C9JA08;Q96D46	.;.;NMD3_HUMAN	R	372;372;372;252	ENSP00000307525:G372R;ENSP00000417559:G372R;ENSP00000419004:G372R	ENSP00000307525:G372R	G	+	1	0	NMD3	162446914	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.796000	0.91877	2.709000	0.92574	0.655000	0.94253	GGA		0.368	NMD3-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353114.1	NM_015938	
TNIK	23043	broad.mit.edu	37	3	170912360	170912360	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr3:170912360G>T	ENST00000436636.2	-	5	715	c.371C>A	c.(370-372)aCg>aAg	p.T124K	TNIK_ENST00000470834.1_Missense_Mutation_p.T124K|TNIK_ENST00000284483.8_Missense_Mutation_p.T124K|TNIK_ENST00000475336.1_Missense_Mutation_p.T124K|TNIK_ENST00000369326.5_Missense_Mutation_p.T124K|TNIK_ENST00000460047.1_Missense_Mutation_p.T124K|TNIK_ENST00000488470.1_Missense_Mutation_p.T124K|TNIK_ENST00000357327.5_Missense_Mutation_p.T124K|TNIK_ENST00000341852.6_Missense_Mutation_p.T124K|TNIK_ENST00000538048.1_Missense_Mutation_p.T124K	NM_015028.2	NP_055843.1	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase	124	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|activation of JNKK activity (GO:0007256)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite morphogenesis (GO:0048814)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.T124K(2)		cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(22)|ovary(5)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)	62	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			CTCTTTCAACGTGTTACCTTT	0.468																																					p.T124K												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C371A	3						.						219.0	223.0	222.0					3																	170912360		1984	4150	6134	172395054	SO:0001583	missense	23043	exon5			AF172264	CCDS46956.1, CCDS54673.1, CCDS54674.1, CCDS54675.1, CCDS54676.1, CCDS54677.1, CCDS54678.1, CCDS54679.1	3q26.31	2008-01-23			ENSG00000154310	ENSG00000154310			30765	protein-coding gene	gene with protein product		610005				9628581, 10521462	Standard	NR_027767		Approved	KIAA0551	uc003fhh.2	Q9UKE5	OTTHUMG00000159036	ENST00000436636.2:c.371C>A	3.37:g.170912360G>T	ENSP00000399511:p.Thr124Lys		172395054	NM_001161565	A7E2A3|A8K4U1|D3DNQ6|O60298|Q8WUY7|Q9UKD8|Q9UKD9|Q9UKE0|Q9UKE1|Q9UKE2|Q9UKE3|Q9UKE4	Missense_Mutation	SNP	ENST00000436636.2	37	CCDS46956.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.357794	0.82243	.	.	ENSG00000154310	ENST00000436636;ENST00000369326;ENST00000538048;ENST00000341852;ENST00000284483;ENST00000475336;ENST00000357327;ENST00000460047;ENST00000488470;ENST00000470834;ENST00000468757	T;T;T;T;T;T;T;T;T;T;T	0.64085	1.89;1.89;1.89;1.89;1.89;1.89;1.89;1.89;1.89;1.89;-0.08	6.07	6.07	0.98685	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.051368	0.85682	D	0.000000	T	0.57755	0.2075	N	0.13352	0.335	0.80722	D	1	B;P;P;D;P;P;P;P	0.57899	0.083;0.726;0.942;0.981;0.726;0.726;0.942;0.768	B;B;B;P;B;B;B;B	0.48921	0.016;0.08;0.423;0.595;0.08;0.08;0.423;0.13	T	0.63773	-0.6561	10	0.87932	D	0	.	20.6593	0.99626	0.0:0.0:1.0:0.0	.	124;124;124;124;124;124;124;124	Q9UKE5-8;Q9UKE5-6;Q9UKE5-7;Q9UKE5-5;Q9UKE5-4;Q9UKE5-2;Q9UKE5-3;Q9UKE5	.;.;.;.;.;.;.;TNIK_HUMAN	K	124;124;124;124;124;124;124;124;124;124;98	ENSP00000399511:T124K;ENSP00000358332:T124K;ENSP00000443278:T124K;ENSP00000345352:T124K;ENSP00000284483:T124K;ENSP00000418156:T124K;ENSP00000349880:T124K;ENSP00000418916:T124K;ENSP00000418378:T124K;ENSP00000419990:T124K;ENSP00000417338:T98K	ENSP00000284483:T124K	T	-	2	0	TNIK	172395054	1.000000	0.71417	0.973000	0.42090	0.718000	0.41266	9.835000	0.99442	2.885000	0.99019	0.655000	0.94253	ACG		0.468	TNIK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352973.2	XM_039796	
HRG	3273	broad.mit.edu	37	3	186395244	186395244	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr3:186395244C>T	ENST00000232003.4	+	7	1230	c.1150C>T	c.(1150-1152)Cac>Tac	p.H384Y		NM_000412.2	NP_000403.1	P04196	HRG_HUMAN	histidine-rich glycoprotein	384	His/Pro-rich (HRR).				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|defense response to fungus (GO:0050832)|fibrinolysis (GO:0042730)|heme export (GO:0097037)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel remodeling (GO:2000504)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of immune response to tumor cell (GO:0002839)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet activation (GO:0010543)|regulation of protein complex assembly (GO:0043254)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|response to organic cyclic compound (GO:0014070)	blood microparticle (GO:0072562)|endolysosome (GO:0036019)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|phagolysosome membrane (GO:0061474)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heme binding (GO:0020037)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|immunoglobulin binding (GO:0019865)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)	p.H384Y(1)		breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(12)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)		tccccatggacaccaccccca	0.542																																					p.H384Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1150T	3						.						200.0	122.0	149.0					3																	186395244		2201	4299	6500	187877938	SO:0001583	missense	3273	exon7				CCDS3280.1	3q27	2008-07-18			ENSG00000113905	ENSG00000113905			5181	protein-coding gene	gene with protein product	"""histidine-proline rich glycoprotein"", ""thrombophilia due to elevated HRG"""	142640				1678514	Standard	NM_000412		Approved	HRGP, HPRG	uc003fqq.3	P04196	OTTHUMG00000156578	ENST00000232003.4:c.1150C>T	3.37:g.186395244C>T	ENSP00000232003:p.His384Tyr		187877938	NM_000412	B9EK35|D3DNU7	Missense_Mutation	SNP	ENST00000232003.4	37	CCDS3280.1	.	.	.	.	.	.	.	.	.	.	C	13.10	2.135263	0.37728	.	.	ENSG00000113905	ENST00000232003	T	0.20200	2.09	4.61	4.61	0.57282	.	0.000000	0.53938	D	0.000043	T	0.33702	0.0872	M	0.81341	2.54	0.09310	N	1	D	0.56968	0.978	P	0.51657	0.676	T	0.33954	-0.9848	10	0.10377	T	0.69	-3.4222	13.1572	0.59524	0.0:1.0:0.0:0.0	.	384	P04196	HRG_HUMAN	Y	384	ENSP00000232003:H384Y	ENSP00000232003:H384Y	H	+	1	0	HRG	187877938	0.002000	0.14202	0.016000	0.15963	0.007000	0.05969	1.660000	0.37397	2.561000	0.86390	0.455000	0.32223	CAC		0.542	HRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344655.1	NM_000412	
EIF4A2	1974	broad.mit.edu	37	3	186506990	186506990	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr3:186506990C>G	ENST00000323963.5	+	11	1220	c.1156C>G	c.(1156-1158)Cgt>Ggt	p.R386G	SNORA63_ENST00000363548.1_RNA|SNORA4_ENST00000584302.1_RNA|EIF4A2_ENST00000440191.2_Missense_Mutation_p.R387G|EIF4A2_ENST00000356531.5_Missense_Mutation_p.R291G|SNORA81_ENST00000408493.2_RNA|SNORA63_ENST00000363450.1_RNA			Q14240	IF4A2_HUMAN	eukaryotic translation initiation factor 4A2	386	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|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)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743)	p.R386S(1)|p.R386G(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|urinary_tract(1)	28	all_cancers(143;2.68e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.07e-20)	GBM - Glioblastoma multiforme(93;0.0704)		GAGGATTCTTCGTGACATTGA	0.428			T	BCL6	NHL																																p.R386G			Dom	yes		3	3q27.3	1974	"""eukaryotic translation initiation factor 4A, isoform 2"""		L	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1156G	3						.						196.0	203.0	200.0					3																	186506990		2203	4300	6503	187989684	SO:0001583	missense	1974	exon11			D30655	CCDS3282.1	3q28	2012-02-23	2010-02-10		ENSG00000156976	ENSG00000156976	3.6.1.1	"""DEAD-boxes"""	3284	protein-coding gene	gene with protein product		601102	"""eukaryotic translation initiation factor 4A, isoform 2"""	EIF4F		8521730	Standard	NM_001967		Approved	DDX2B, EIF4A, BM-010	uc003fqs.3	Q14240	OTTHUMG00000156564	ENST00000323963.5:c.1156C>G	3.37:g.186506990C>G	ENSP00000326381:p.Arg386Gly		187989684	NM_001967	D3DNU9|Q53XJ6|Q96B90|Q96EA8	Missense_Mutation	SNP	ENST00000323963.5	37	CCDS3282.1	.	.	.	.	.	.	.	.	.	.	C	14.16	2.451485	0.43531	.	.	ENSG00000156976	ENST00000323963;ENST00000440191;ENST00000356531	T;T;T	0.05199	3.48;3.48;3.48	5.87	5.87	0.94306	Helicase, C-terminal (1);	0.052166	0.85682	D	0.000000	T	0.08313	0.0207	N	0.22421	0.69	0.80722	D	1	B;B;B	0.28820	0.079;0.224;0.143	B;B;B	0.35655	0.047;0.207;0.137	T	0.29458	-1.0011	10	0.72032	D	0.01	-4.0502	18.0718	0.89410	0.0:1.0:0.0:0.0	.	291;387;386	Q9NZE6;Q14240-2;Q14240	.;.;IF4A2_HUMAN	G	386;387;291	ENSP00000326381:R386G;ENSP00000398370:R387G;ENSP00000348925:R291G	ENSP00000326381:R386G	R	+	1	0	EIF4A2	187989684	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.340000	0.79292	2.941000	0.99782	0.655000	0.94253	CGT		0.428	EIF4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344609.1	NM_001967	
CAV3	859	broad.mit.edu	37	3	8787233	8787233	+	Missense_Mutation	SNP	G	G	A	rs116840789		TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr3:8787233G>A	ENST00000343849.2	+	2	213	c.136G>A	c.(136-138)Gca>Aca	p.A46T	CAV3_ENST00000472766.1_Intron|SSUH2_ENST00000478513.1_5'Flank|CAV3_ENST00000397368.2_Missense_Mutation_p.A46T	NM_001234.4|NM_033337.2	NP_001225.1|NP_203123.1	P56539	CAV3_HUMAN	caveolin 3	46			A -> T (in LGMD1C and RMD; decreased surface expression of the CAV3 protein). {ECO:0000269|PubMed:11001938, ECO:0000269|PubMed:11431690, ECO:0000269|PubMed:15580566}.|A -> V (in RMD). {ECO:0000269|PubMed:11431690}.		actin filament organization (GO:0007015)|cardiac muscle cell development (GO:0055013)|caveola assembly (GO:0070836)|cell differentiation (GO:0030154)|cell growth (GO:0016049)|cholesterol homeostasis (GO:0042632)|cytoplasmic microtubule organization (GO:0031122)|endocytosis (GO:0006897)|establishment of protein localization to plasma membrane (GO:0090002)|glucose homeostasis (GO:0042593)|heart trabecula formation (GO:0060347)|membrane raft organization (GO:0031579)|muscle cell cellular homeostasis (GO:0046716)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of cell growth involved in cardiac muscle cell development (GO:0061052)|negative regulation of cell size (GO:0045792)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sarcomere organization (GO:0060299)|nucleus localization (GO:0051647)|plasma membrane organization (GO:0007009)|plasma membrane repair (GO:0001778)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein localization (GO:0008104)|protein localization to plasma membrane (GO:0072659)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of calcium ion import (GO:0090279)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart contraction (GO:0008016)|regulation of heart rate (GO:0002027)|regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900825)|regulation of membrane potential (GO:0042391)|regulation of nerve growth factor receptor activity (GO:0051394)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase B signaling (GO:0051896)|regulation of signal transduction by receptor internalization (GO:0038009)|regulation of skeletal muscle contraction (GO:0014819)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|T-tubule organization (GO:0033292)|triglyceride metabolic process (GO:0006641)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|dystrophin-associated glycoprotein complex (GO:0016010)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	calcium channel regulator activity (GO:0005246)|connexin binding (GO:0071253)|ion channel binding (GO:0044325)|potassium channel inhibitor activity (GO:0019870)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein complex scaffold (GO:0032947)|sodium channel regulator activity (GO:0017080)	p.A46T(1)		breast(1)|kidney(2)|large_intestine(4)|lung(3)|prostate(1)	11						AGACGTGATCGCAGAGCCTGT	0.562																																					p.A46T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G136A	3	GRCh37	CM003421	CAV3	M	rs116840789	.						77.0	64.0	68.0					3																	8787233		2203	4300	6503	8762233	SO:0001583	missense	859	exon2			AF043101	CCDS2569.1	3p25	2014-09-17			ENSG00000182533	ENSG00000182533			1529	protein-coding gene	gene with protein product	"""M-caveolin"""	601253				9536092, 9537420	Standard	NM_033337		Approved	VIP-21, LGMD1C, VIP21, LQT9	uc003brb.3	P56539	OTTHUMG00000090519	ENST00000343849.2:c.136G>A	3.37:g.8787233G>A	ENSP00000341940:p.Ala46Thr		8762233	NM_001234	A8K777|Q3T1A4	Missense_Mutation	SNP	ENST00000343849.2	37	CCDS2569.1	.	.	.	.	.	.	.	.	.	.	G	17.71	3.456011	0.63401	.	.	ENSG00000182533	ENST00000343849;ENST00000397368	D;D	0.94793	-3.52;-3.52	4.75	4.75	0.60458	Caveolin, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.97838	0.9290	M	0.92367	3.3	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98874	1.0767	10	0.87932	D	0	-10.3419	16.4843	0.84180	0.0:0.0:1.0:0.0	.	46	P56539	CAV3_HUMAN	T	46	ENSP00000341940:A46T;ENSP00000380525:A46T	ENSP00000341940:A46T	A	+	1	0	CAV3	8762233	1.000000	0.71417	0.829000	0.32907	0.026000	0.11368	9.181000	0.94874	2.451000	0.82905	0.460000	0.39030	GCA		0.562	CAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207008.2	NM_033337	
TRANK1	9881	broad.mit.edu	37	3	36896710	36896710	+	Silent	SNP	C	C	T			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr3:36896710C>T	ENST00000429976.2	-	12	4618	c.4371G>A	c.(4369-4371)aaG>aaA	p.K1457K	TRANK1_ENST00000301807.6_Silent_p.K907K|TRANK1_ENST00000428977.2_Silent_p.K907K	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	1457							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)	p.K907K(2)|p.K1457K(1)		NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						TCTTCTTGGGCTTCCGGACAG	0.542																																					p.K1457K												.	.	3	Substitution - coding silent(3)	large_intestine(3)	c.G4371A	3						.						75.0	73.0	74.0					3																	36896710		2017	4187	6204	36871714	SO:0001819	synonymous_variant	9881	exon12			AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29011	protein-coding gene	gene with protein product	"""lupus brain antigen 1"", ""KIAA0342"""					9205841	Standard	NM_014831		Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000429976.2:c.4371G>A	3.37:g.36896710C>T			36871714	NM_014831	Q8N8K0	Silent	SNP	ENST00000429976.2	37	CCDS46789.2																																																																																				0.542	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831	
CAMP	820	broad.mit.edu	37	3	48265948	48265948	+	Silent	SNP	C	C	T	rs201842351		TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr3:48265948C>T	ENST00000576243.1	+	2	446	c.306C>T	c.(304-306)gaC>gaT	p.D102D	CAMP_ENST00000296435.2_Silent_p.D105D			P49913	CAMP_HUMAN	cathelicidin antimicrobial peptide	102					antibacterial humoral response (GO:0019731)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to peptidoglycan (GO:0071224)|cellular response to tumor necrosis factor (GO:0071356)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|killing by host of symbiont cells (GO:0051873)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of growth of symbiont on or near host surface (GO:0044140)|phagosome maturation (GO:0090382)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein phosphorylation (GO:0001934)	cell projection (GO:0042995)|cell wall (GO:0005618)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|specific granule (GO:0042581)		p.D102D(1)		endometrium(2)|large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6				BRCA - Breast invasive adenocarcinoma(193;0.000614)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		TCAAGAAGGACGGGGTGAGGC	0.612													C|||	1	0.000199681	0.0008	0.0	5008	,	,		15192	0.0		0.0	False		,,,				2504	0.0				p.D102D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C306T	3						.						47.0	45.0	46.0					3																	48265948		2203	4300	6503	48240952	SO:0001819	synonymous_variant	820	exon2			BC055089	CCDS2762.1, CCDS2762.2	3p21.3	2014-01-30			ENSG00000164047	ENSG00000164047		"""Endogenous ligands"""	1472	protein-coding gene	gene with protein product		600474				7624374	Standard	NM_004345		Approved	CAP18, FALL39, FALL-39, LL37	uc003csj.3	P49913	OTTHUMG00000133526	ENST00000576243.1:c.306C>T	3.37:g.48265948C>T			48240952	NM_004345	Q71SN9	Silent	SNP	ENST00000576243.1	37																																																																																					0.612	CAMP-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_004345	
SLC25A20	788	broad.mit.edu	37	3	48900021	48900021	+	Silent	SNP	A	A	G			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr3:48900021A>G	ENST00000319017.4	-	5	687	c.489T>C	c.(487-489)ttT>ttC	p.F163F	SLC25A20_ENST00000430379.1_Silent_p.F90F|SLC25A20_ENST00000544097.1_Silent_p.F113F	NM_000387.5	NP_000378.1	O43772	MCAT_HUMAN	solute carrier family 25 (carnitine/acylcarnitine translocase), member 20	163					carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)		p.F163F(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(5)|prostate(1)	13				BRCA - Breast invasive adenocarcinoma(193;0.000168)|Kidney(197;0.00231)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)	L-Carnitine(DB00583)	CTCGGATCCCAAACTCCTGGT	0.522																																					p.F163F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T489C	3						.						131.0	113.0	119.0					3																	48900021		2203	4300	6503	48875025	SO:0001819	synonymous_variant	788	exon5			Y10319	CCDS2779.1	3p21.31	2013-05-22			ENSG00000178537	ENSG00000178537		"""Solute carriers"""	1421	protein-coding gene	gene with protein product	"""carnitine-acylcarnitine carrier"", ""carnitine/acylcarnitine translocase"""	613698		CACT		9399886, 9533014	Standard	NM_000387		Approved	CAC	uc003cva.4	O43772	OTTHUMG00000133538	ENST00000319017.4:c.489T>C	3.37:g.48900021A>G			48875025	NM_000387	B2R7F4|Q9UIQ2	Silent	SNP	ENST00000319017.4	37	CCDS2779.1																																																																																				0.522	SLC25A20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257516.2	NM_000387	
FGF12	2257	broad.mit.edu	37	3	192125881	192125881	+	Silent	SNP	G	G	A			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr3:192125881G>A	ENST00000454309.2	-	1	957	c.132C>T	c.(130-132)caC>caT	p.H44H	FGF12_ENST00000264730.3_Intron|FGF12_ENST00000430714.1_Intron|FGF12_ENST00000450716.1_Intron|FGF12_ENST00000445105.2_Intron	NM_021032.4	NP_066360.1	P61328	FGF12_HUMAN	fibroblast growth factor 12	44					adult locomotory behavior (GO:0008344)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell-cell signaling (GO:0007267)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|JNK cascade (GO:0007254)|negative regulation of cation channel activity (GO:2001258)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|positive regulation of sodium ion transport (GO:0010765)|regulation of membrane depolarization (GO:0003254)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	extracellular space (GO:0005615)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)|ion channel binding (GO:0044325)|sodium channel regulator activity (GO:0017080)	p.H44H(1)		endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	30	all_cancers(143;1.72e-08)|Ovarian(172;0.0634)|Breast(254;0.247)	Lung NSC(153;0.21)	LUSC - Lung squamous cell carcinoma(58;5.45e-06)|Lung(62;6.17e-06)	GBM - Glioblastoma multiforme(46;0.00032)		CCCCGAGGACGTGCCTCTCGC	0.682																																					p.H44H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C132T	3						.						70.0	81.0	77.0					3																	192125881		2199	4283	6482	193608575	SO:0001819	synonymous_variant	2257	exon1			U66197	CCDS3301.1, CCDS46983.1	3q28	2008-07-18			ENSG00000114279	ENSG00000114279			3668	protein-coding gene	gene with protein product	"""fibroblast growth factor 12B"", ""fibroblast growth factor homologous factor 1"", ""myocyte-activating factor"", ""fibroblast growth factor FGF-12b"""	601513		FGF12B		8790420, 9345906	Standard	NM_021032		Approved	FHF1	uc003fsx.3	P61328	OTTHUMG00000156132	ENST00000454309.2:c.132C>T	3.37:g.192125881G>A			193608575	NM_021032	B2R6B7|B2R976|O35339|P70376|Q8TBG5|Q92912|Q93001	Silent	SNP	ENST00000454309.2	37	CCDS3301.1																																																																																				0.682	FGF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343160.1	NM_021032	
ADH5	128	broad.mit.edu	37	4	99997898	99997898	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr4:99997898C>T	ENST00000296412.8	-	5	571	c.521G>A	c.(520-522)tGt>tAt	p.C174Y	ADH5_ENST00000512991.1_5'UTR	NM_000671.3	NP_000662.3			alcohol dehydrogenase 5 (class III), chi polypeptide									p.C174Y(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)	13				OV - Ovarian serous cystadenocarcinoma(123;2.5e-07)		TGAAATGCCACAACCTAGAAG	0.413																																					p.C174Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G521A	4						.						72.0	66.0	68.0					4																	99997898		1897	4128	6025	100216921	SO:0001583	missense	128	exon5			M29872	CCDS47111.1	4q23	2012-07-13	2003-06-19		ENSG00000197894	ENSG00000197894	1.1.1.284	"""Alcohol dehydrogenases"""	253	protein-coding gene	gene with protein product		103710	"""formaldehyde dehydrogenase"""	FDH		1446828, 6424546	Standard	NM_000671		Approved	ADH-3, ADHX	uc003hui.3	P11766	OTTHUMG00000161230	ENST00000296412.8:c.521G>A	4.37:g.99997898C>T	ENSP00000296412:p.Cys174Tyr		100216921	NM_000671		Missense_Mutation	SNP	ENST00000296412.8	37	CCDS47111.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.672429	0.88348	.	.	ENSG00000197894	ENST00000296412;ENST00000503130	T;T	0.25250	1.81;1.81	5.1	5.1	0.69264	GroES-like (1);	0.000000	0.85682	D	0.000000	T	0.71290	0.3322	H	0.99312	4.51	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	0.84237	0.0470	9	.	.	.	-28.9543	19.0691	0.93125	0.0:1.0:0.0:0.0	.	174;174;174	Q5U043;Q6IRT1;P11766	.;.;ADHX_HUMAN	Y	174;161	ENSP00000296412:C174Y;ENSP00000427049:C161Y	.	C	-	2	0	ADH5	100216921	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.802000	0.75175	2.822000	0.97130	0.650000	0.86243	TGT		0.413	ADH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364224.1	NM_000671	
APC	324	broad.mit.edu	37	5	112151204	112151204	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr5:112151204C>T	ENST00000457016.1	+	9	1227	c.847C>T	c.(847-849)Cga>Tga	p.R283*	APC_ENST00000508376.2_Nonsense_Mutation_p.R283*|APC_ENST00000257430.4_Nonsense_Mutation_p.R283*			P25054	APC_HUMAN	adenomatous polyposis coli	283	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R283*(11)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TTCAACTACACGAATGGACCA	0.383		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.R265X	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	APC,large_intestine,NS,Substitution - Nonsense,0 	.	11	Substitution - Nonsense(11)	large_intestine(11)	c.C793T	5	GRCh37	CM920030	APC	M		.						108.0	98.0	102.0					5																	112151204		2202	4300	6502	112179103	SO:0001587	stop_gained	324	exon7	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.847C>T	5.37:g.112151204C>T	ENSP00000413133:p.Arg283*		112179103	NM_001127511	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	40	8.381748	0.98786	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.11	4.22	0.49857	.	0.134048	0.50627	D	0.000103	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.044	12.9775	0.58546	0.2942:0.7058:0.0:0.0	.	.	.	.	X	283;265;283;283;283	.	ENSP00000257430:R283X	R	+	1	2	APC	112179103	1.000000	0.71417	0.953000	0.39169	0.976000	0.68499	5.216000	0.65246	1.244000	0.43870	0.650000	0.86243	CGA		0.383	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
APC	324	broad.mit.edu	37	5	112175423	112175423	+	Nonsense_Mutation	SNP	C	C	T	rs121913329		TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr5:112175423C>T	ENST00000457016.1	+	16	4512	c.4132C>T	c.(4132-4134)Cag>Tag	p.Q1378*	APC_ENST00000508376.2_Nonsense_Mutation_p.Q1378*|APC_ENST00000257430.4_Nonsense_Mutation_p.Q1378*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1378	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.Q1378*(47)|p.Q1378fs*7(2)|p.Y1376fs*41(1)|p.?(1)|p.Q1378fs*5(1)|p.Q1378fs*8(1)|p.K1192fs*3(1)|p.Y1376fs*5(1)|p.Y1376fs*1(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		ACACTATGTTCAGGAGACCCC	0.468		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.Q1360X	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	APC,large_intestine,NS,Substitution - Nonsense,0 	.	56	Substitution - Nonsense(47)|Deletion - Frameshift(6)|Unknown(1)|Complex - frameshift(1)|Insertion - Frameshift(1)	large_intestine(49)|stomach(5)|soft_tissue(1)|skin(1)	c.C4078T	5						.						91.0	87.0	88.0					5																	112175423		2202	4300	6502	112203322	SO:0001587	stop_gained	324	exon14	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4132C>T	5.37:g.112175423C>T	ENSP00000413133:p.Gln1378*		112203322	NM_001127511	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	41	8.764727	0.98945	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-8.1139	20.4898	0.99202	0.0:1.0:0.0:0.0	.	.	.	.	X	1378	.	.	Q	+	1	0	APC	112203322	1.000000	0.71417	0.999000	0.59377	0.831000	0.47069	5.761000	0.68801	2.941000	0.99782	0.655000	0.94253	CAG		0.468	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
DMXL1	1657	broad.mit.edu	37	5	118506749	118506749	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr5:118506749G>T	ENST00000311085.8	+	24	6343	c.6263G>T	c.(6262-6264)gGc>gTc	p.G2088V	DMXL1_ENST00000539542.1_Missense_Mutation_p.G2088V	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	2088								p.G2088V(1)		breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		TCTGCATTTGGCAGAAATGAA	0.388																																					p.G2088V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G6263T	5						.						89.0	88.0	88.0					5																	118506749		2202	4300	6502	118534648	SO:0001583	missense	1657	exon24			AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"""WD repeat domain containing"""	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.6263G>T	5.37:g.118506749G>T	ENSP00000309690:p.Gly2088Val		118534648	NM_005509		Missense_Mutation	SNP	ENST00000311085.8	37	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	G	6.186	0.402504	0.11696	.	.	ENSG00000172869	ENST00000311085;ENST00000539542	T;T	0.78126	-1.15;-1.15	5.5	3.73	0.42828	.	0.679068	0.16067	N	0.231203	T	0.61048	0.2316	N	0.14661	0.345	0.09310	N	1	B;B	0.25235	0.018;0.121	B;B	0.24155	0.019;0.051	T	0.45425	-0.9262	10	0.23302	T	0.38	-0.001	11.6131	0.51072	0.1454:0.0:0.8546:0.0	.	2088;2088	F5H269;Q9Y485	.;DMXL1_HUMAN	V	2088	ENSP00000309690:G2088V;ENSP00000439479:G2088V	ENSP00000309690:G2088V	G	+	2	0	DMXL1	118534648	0.000000	0.05858	0.002000	0.10522	0.661000	0.39034	0.334000	0.19787	0.694000	0.31654	0.563000	0.77884	GGC		0.388	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509	
PCDHAC1	56135	broad.mit.edu	37	5	140306632	140306632	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr5:140306632C>T	ENST00000253807.2	+	1	155	c.155C>T	c.(154-156)tCg>tTg	p.S52L	PCDHA12_ENST00000398631.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHAC1_ENST00000409700.3_Missense_Mutation_p.S52L|PCDHA13_ENST00000289272.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA4_ENST00000512229.2_Intron	NM_018898.3	NP_061721.2	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1	52	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.S52L(1)		NS(2)|breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|liver(2)|lung(13)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	65			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTATGTCCTCGCGGAACTTT	0.647																																					p.S52L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C155T	5						.						50.0	58.0	55.0					5																	140306632		2203	4300	6503	140286816	SO:0001583	missense	56135	exon1			AF152473	CCDS4241.1	5q31	2010-11-26			ENSG00000248383	ENSG00000248383		"""Cadherins / Protocadherins : Clustered"""	8676	other	complex locus constituent	"""PCDH-ALPHA-C1"""	606320				10380929	Standard	NM_018898		Approved			Q9H158	OTTHUMG00000129603	ENST00000253807.2:c.155C>T	5.37:g.140306632C>T	ENSP00000253807:p.Ser52Leu		140286816	NM_031882	Q9Y5F5|Q9Y5I5	Missense_Mutation	SNP	ENST00000253807.2	37	CCDS4241.1	.	.	.	.	.	.	.	.	.	.	C	10.38	1.334264	0.24253	.	.	ENSG00000248383	ENST00000409700;ENST00000253807	T;T	0.29397	1.57;1.57	5.29	-1.31	0.09230	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.14527	0.0351	N	0.19112	0.55	0.09310	N	1	B;B	0.17852	0.024;0.001	B;B	0.13407	0.009;0.005	T	0.25606	-1.0127	9	0.29301	T	0.29	.	1.7717	0.03013	0.1448:0.3418:0.2948:0.2187	.	52;52	Q9H158;Q9H158-2	PCDC1_HUMAN;.	L	52	ENSP00000386356:S52L;ENSP00000253807:S52L	ENSP00000253807:S52L	S	+	2	0	PCDHAC1	140286816	0.000000	0.05858	0.027000	0.17364	0.492000	0.33523	0.297000	0.19101	-0.231000	0.09825	-0.367000	0.07326	TCG		0.647	PCDHAC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251798.1	NM_018898	
PREP	5550	broad.mit.edu	37	6	105726167	105726167	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr6:105726167C>T	ENST00000369110.3	-	15	2177	c.1985G>A	c.(1984-1986)cGc>cAc	p.R662H	RP3-355L5.4_ENST00000452363.1_RNA	NM_002726.4	NP_002717.3	P48147	PPCE_HUMAN	prolyl endopeptidase	662					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)|serine-type peptidase activity (GO:0008236)	p.R662H(1)		breast(1)|endometrium(2)|large_intestine(7)|lung(12)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		all_cancers(87;0.000128)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0344)|Lung NSC(302;0.191)|Colorectal(196;0.202)			Oxytocin(DB00107)	CTTCCTGCTGCGGCCCACGAT	0.602																																					p.R662H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1985A	6						.						87.0	77.0	80.0					6																	105726167		2203	4300	6503	105832860	SO:0001583	missense	5550	exon15				CCDS5053.1	6q22	2008-02-05			ENSG00000085377	ENSG00000085377	3.4.21.26		9358	protein-coding gene	gene with protein product		600400				7959018	Standard	NM_002726		Approved		uc003prc.3	P48147	OTTHUMG00000015297	ENST00000369110.3:c.1985G>A	6.37:g.105726167C>T	ENSP00000358106:p.Arg662His		105832860	NM_002726	Q8N6D4	Missense_Mutation	SNP	ENST00000369110.3	37	CCDS5053.1	.	.	.	.	.	.	.	.	.	.	C	17.33	3.361232	0.61403	.	.	ENSG00000085377	ENST00000369110	T	0.32023	1.47	6.01	6.01	0.97437	Peptidase S9, prolyl oligopeptidase, catalytic domain (1);	0.100830	0.64402	D	0.000001	T	0.07279	0.0184	N	0.03050	-0.425	0.54753	D	0.999988	B	0.06786	0.001	B	0.04013	0.001	T	0.11792	-1.0573	10	0.42905	T	0.14	-19.0418	13.6832	0.62499	0.0:0.9299:0.0:0.0701	.	662	P48147	PPCE_HUMAN	H	662	ENSP00000358106:R662H	ENSP00000358106:R662H	R	-	2	0	PREP	105832860	0.999000	0.42202	1.000000	0.80357	0.997000	0.91878	2.645000	0.46621	2.861000	0.98227	0.650000	0.86243	CGC		0.602	PREP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041658.1		
KPNA5	3841	broad.mit.edu	37	6	117013507	117013507	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr6:117013507G>C	ENST00000368564.1	+	4	440	c.292G>C	c.(292-294)Gat>Cat	p.D98H	KPNA5_ENST00000356348.1_Missense_Mutation_p.D98H			O15131	IMA6_HUMAN	karyopherin alpha 5 (importin alpha 6)	95					cytokine-mediated signaling pathway (GO:0019221)|NLS-bearing protein import into nucleus (GO:0006607)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)	protein transporter activity (GO:0008565)	p.D98H(1)		breast(6)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0298)|all cancers(137;0.0461)|OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.212)		TAATAATGCTGATCAACAGCT	0.279																																					p.D98H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G292C	6						.						78.0	84.0	82.0					6																	117013507		2201	4281	6482	117120200	SO:0001583	missense	3841	exon4			AF005361	CCDS5111.1	6q22.2	2013-02-14			ENSG00000196911	ENSG00000196911		"""Importins"", ""Armadillo repeat containing"""	6398	protein-coding gene	gene with protein product		604545				9395085	Standard	NM_002269		Approved	SRP6, IPOA6	uc003pxh.3	O15131	OTTHUMG00000015448	ENST00000368564.1:c.292G>C	6.37:g.117013507G>C	ENSP00000357552:p.Asp98His		117120200	NM_002269	B2RAI5|Q86X23	Missense_Mutation	SNP	ENST00000368564.1	37	CCDS5111.1	.	.	.	.	.	.	.	.	.	.	G	16.72	3.200077	0.58126	.	.	ENSG00000196911	ENST00000368564;ENST00000413340;ENST00000356348	T;T;T	0.32272	1.46;1.46;1.46	5.85	4.99	0.66335	Armadillo-like helical (1);Armadillo-type fold (1);	0.351990	0.27846	N	0.017613	T	0.21103	0.0508	L	0.57536	1.79	0.47245	D	0.999369	B	0.23249	0.082	B	0.32624	0.149	T	0.09443	-1.0674	10	0.72032	D	0.01	.	11.7495	0.51841	0.1409:0.0:0.8591:0.0	.	95	O15131	IMA5_HUMAN	H	98;95;98	ENSP00000357552:D98H;ENSP00000396791:D95H;ENSP00000348704:D98H	ENSP00000348704:D98H	D	+	1	0	KPNA5	117120200	1.000000	0.71417	0.931000	0.37212	0.993000	0.82548	6.344000	0.72991	1.483000	0.48342	0.484000	0.47621	GAT		0.279	KPNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041967.1	NM_002269	
ME1	4199	broad.mit.edu	37	6	84117499	84117499	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr6:84117499G>A	ENST00000369705.3	-	2	316	c.200C>T	c.(199-201)tCt>tTt	p.S67F	ME1_ENST00000541327.1_Intron|ME1_ENST00000543031.1_Intron	NM_002395.4	NP_002386.1	P48163	MAOX_HUMAN	malic enzyme 1, NADP(+)-dependent, cytosolic	67					carbohydrate metabolic process (GO:0005975)|cellular lipid metabolic process (GO:0044255)|malate metabolic process (GO:0006108)|NADP biosynthetic process (GO:0006741)|protein tetramerization (GO:0051262)|response to carbohydrate (GO:0009743)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ADP binding (GO:0043531)|electron carrier activity (GO:0009055)|malate dehydrogenase (decarboxylating) (NAD+) activity (GO:0004471)|malate dehydrogenase (decarboxylating) (NADP+) activity (GO:0004473)|malic enzyme activity (GO:0004470)|manganese ion binding (GO:0030145)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|oxaloacetate decarboxylase activity (GO:0008948)	p.S67F(1)		NS(2)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36		all_cancers(76;1.28e-06)|Acute lymphoblastic leukemia(125;5.03e-07)|all_hematologic(105;0.000238)|all_epithelial(107;0.00218)		BRCA - Breast invasive adenocarcinoma(397;0.0641)		GTCAAAGTCAGAGTTCAGATG	0.358																																					p.S67F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C200T	6						.						124.0	127.0	126.0					6																	84117499		2203	4300	6503	84174218	SO:0001583	missense	4199	exon2			X77244	CCDS34492.1	6q12	2012-10-02			ENSG00000065833	ENSG00000065833	1.1.1.40		6983	protein-coding gene	gene with protein product		154250				8187880	Standard	NM_002395		Approved		uc003pjy.3	P48163	OTTHUMG00000015111	ENST00000369705.3:c.200C>T	6.37:g.84117499G>A	ENSP00000358719:p.Ser67Phe		84174218	NM_002395	B4DZ70|Q16797|Q16855|Q53F72|Q5VWA2|Q9BWX8|Q9H1W3|Q9UIY4	Missense_Mutation	SNP	ENST00000369705.3	37	CCDS34492.1	.	.	.	.	.	.	.	.	.	.	G	14.19	2.462708	0.43736	.	.	ENSG00000065833	ENST00000369705	T	0.30714	1.52	5.43	5.43	0.79202	Malic enzyme, N-terminal (1);	0.465267	0.26237	N	0.025532	T	0.36880	0.0983	M	0.75884	2.315	0.80722	D	1	D	0.57257	0.979	P	0.51895	0.683	T	0.28427	-1.0044	10	0.59425	D	0.04	-17.6751	14.8086	0.69977	0.0:0.1438:0.8562:0.0	.	67	P48163	MAOX_HUMAN	F	67	ENSP00000358719:S67F	ENSP00000358719:S67F	S	-	2	0	ME1	84174218	0.958000	0.32768	0.840000	0.33206	0.270000	0.26580	2.560000	0.45896	2.540000	0.85666	0.650000	0.86243	TCT		0.358	ME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041350.1		
PNRC1	10957	broad.mit.edu	37	6	89790819	89790819	+	Missense_Mutation	SNP	C	C	T	rs370396619		TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr6:89790819C>T	ENST00000336032.3	+	1	323	c.206C>T	c.(205-207)aCc>aTc	p.T69I	PNRC1_ENST00000354922.3_5'Flank|PNRC1_ENST00000369472.1_Intron|RP11-63L7.5_ENST00000606729.1_RNA	NM_006813.2	NP_006804.1	Q12796	PNRC1_HUMAN	proline-rich nuclear receptor coactivator 1	69					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.T69I(1)		endometrium(1)|large_intestine(2)|lung(3)	6		all_cancers(76;3.64e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00527)		BRCA - Breast invasive adenocarcinoma(108;0.102)		CCGTGTCTGACCCCCCAGCCT	0.697										Multiple Myeloma(7;0.094)																											p.T69I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C206T	6						.	C	ILE/THR	1,4403		0,1,2201	15.0	17.0	16.0		206	1.1	0.0	6		16	0,8594		0,0,4297	no	missense	PNRC1	NM_006813.2	89	0,1,6498	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	69/328	89790819	1,12997	2202	4297	6499	89847538	SO:0001583	missense	10957	exon1			U03105	CCDS5018.1	6q16.1	2008-02-05	2003-09-25	2003-09-26	ENSG00000146278	ENSG00000146278			17278	protein-coding gene	gene with protein product		606714	"""proline rich 2"""	PROL2		7578250	Standard	NM_006813		Approved	B4-2, PRR2	uc003pmv.3	Q12796	OTTHUMG00000015191	ENST00000336032.3:c.206C>T	6.37:g.89790819C>T	ENSP00000336931:p.Thr69Ile		89847538	NM_006813	B2R6Q0|E1P515|Q5T7J6|Q7Z5N0	Missense_Mutation	SNP	ENST00000336032.3	37	CCDS5018.1	.	.	.	.	.	.	.	.	.	.	C	6.761	0.509247	0.12883	2.27E-4	0.0	ENSG00000146278	ENST00000336032	T	0.45668	0.89	4.93	1.08	0.20341	.	0.694212	0.14281	N	0.329559	T	0.12347	0.0300	L	0.44542	1.39	0.09310	N	0.999996	B;B	0.26809	0.032;0.16	B;B	0.24701	0.055;0.055	T	0.25641	-1.0126	10	0.62326	D	0.03	-2.6068	1.6683	0.02806	0.1695:0.4833:0.1642:0.183	.	69;69	Q12796;Q7Z5N0	PNRC1_HUMAN;.	I	69	ENSP00000336931:T69I	ENSP00000336931:T69I	T	+	2	0	PNRC1	89847538	0.810000	0.29049	0.001000	0.08648	0.002000	0.02628	0.710000	0.25748	0.009000	0.14813	-0.266000	0.10368	ACC		0.697	PNRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041471.1	NM_006813	
RAET1E	135250	broad.mit.edu	37	6	150210703	150210703	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr6:150210703C>T	ENST00000357183.4	-	3	535	c.403G>A	c.(403-405)Ggt>Agt	p.G135S	RAET1E-AS1_ENST00000605899.1_RNA|RP11-244K5.8_ENST00000606915.1_RNA|RAET1E_ENST00000532335.1_Missense_Mutation_p.G135S|RAET1E_ENST00000529948.1_Missense_Mutation_p.G135S|RAET1E_ENST00000367363.3_Missense_Mutation_p.G99S|RAET1E-AS1_ENST00000446954.2_RNA	NM_139165.2	NP_631904.1	Q8TD07	N2DL4_HUMAN	retinoic acid early transcript 1E	135	MHC class I alpha-2 like.				antigen processing and presentation (GO:0019882)|natural killer cell mediated cytotoxicity (GO:0042267)|regulation of immune response (GO:0050776)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	natural killer cell lectin-like receptor binding (GO:0046703)	p.G135S(1)		cervix(1)|kidney(2)|large_intestine(3)|lung(3)|skin(1)	10		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.58e-12)		CAGGATGCACCAGTGCACCGT	0.468																																					p.G135S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G403A	6						.						138.0	111.0	120.0					6																	150210703		2203	4300	6503	150252396	SO:0001583	missense	135250	exon3			AF359243	CCDS5221.1, CCDS59042.1, CCDS59043.1, CCDS59044.1	6q24.3	2011-02-09			ENSG00000164520	ENSG00000164520			16793	protein-coding gene	gene with protein product		609243				11827464	Standard	NM_139165		Approved	LETAL, bA350J20.7, ULBP4	uc003qnl.1	Q8TD07	OTTHUMG00000015796	ENST00000357183.4:c.403G>A	6.37:g.150210703C>T	ENSP00000349709:p.Gly135Ser		150252396	NM_139165	A6YF59|Q5VYB7|Q5VYB8|Q8TEZ2|Q96L41	Missense_Mutation	SNP	ENST00000357183.4	37	CCDS5221.1	.	.	.	.	.	.	.	.	.	.	C	5.745	0.321930	0.10900	.	.	ENSG00000164520	ENST00000532335;ENST00000357183;ENST00000367363;ENST00000529948	T;T;T;T	0.09073	3.02;3.02;3.3;3.02	3.68	0.928	0.19443	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.828547	0.10470	N	0.670900	T	0.04137	0.0115	N	0.20845	0.615	0.09310	N	1	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.79108	0.992;0.99;0.947	T	0.35699	-0.9778	10	0.15952	T	0.53	-1.9559	5.6483	0.17602	0.0:0.6443:0.0:0.3557	.	135;99;135	Q8TD07;Q8TD07-2;Q8TD07-3	N2DL4_HUMAN;.;.	S	135;135;99;135	ENSP00000437067:G135S;ENSP00000349709:G135S;ENSP00000356332:G99S;ENSP00000432366:G135S	ENSP00000349709:G135S	G	-	1	0	RAET1E	150252396	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.451000	0.06795	0.188000	0.20168	-0.350000	0.07774	GGT		0.468	RAET1E-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042659.1	NM_139165	
FERD3L	222894	broad.mit.edu	37	7	19184981	19184981	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr7:19184981G>A	ENST00000275461.3	-	1	63	c.5C>T	c.(4-6)gCg>gTg	p.A2V	AC003986.5_ENST00000452700.1_RNA	NM_152898.2	NP_690862.1	Q96RJ6	FER3L_HUMAN	Fer3-like bHLH transcription factor	2					cell development (GO:0048468)|floor plate development (GO:0033504)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of neurogenesis (GO:0050767)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.A2V(1)		breast(1)|endometrium(4)|large_intestine(8)|lung(16)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	35						CGGATAGGCCGCCATCGCTTC	0.637																																					p.A2V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5T	7						.						24.0	24.0	24.0					7																	19184981		2203	4293	6496	19151506	SO:0001583	missense	222894	exon1			AF369897	CCDS5368.1	7p21.3	2013-10-17	2013-10-17		ENSG00000146618	ENSG00000146618		"""Basic helix-loop-helix proteins"""	16660	protein-coding gene	gene with protein product			"""Fer3-like (Drosophila)"""			11472856, 12217327	Standard	NM_152898		Approved	NATO3, N-TWIST, bHLHa31	uc003suo.1	Q96RJ6	OTTHUMG00000090823	ENST00000275461.3:c.5C>T	7.37:g.19184981G>A	ENSP00000275461:p.Ala2Val		19151506	NM_152898	Q495K0	Missense_Mutation	SNP	ENST00000275461.3	37	CCDS5368.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.099521	0.76983	.	.	ENSG00000146618	ENST00000275461	D	0.96967	-4.19	5.66	4.73	0.59995	.	0.447693	0.23173	N	0.051119	D	0.90625	0.7060	N	0.24115	0.695	0.28576	N	0.910386	B	0.24533	0.105	B	0.15052	0.012	D	0.83667	0.0164	10	0.87932	D	0	-1.0028	5.9963	0.19495	0.096:0.0:0.7134:0.1906	.	2	Q96RJ6	FER3L_HUMAN	V	2	ENSP00000275461:A2V	ENSP00000275461:A2V	A	-	2	0	FERD3L	19151506	1.000000	0.71417	0.999000	0.59377	0.979000	0.70002	2.085000	0.41634	2.682000	0.91365	0.650000	0.86243	GCG		0.637	FERD3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207627.1		
FAM188B	84182	broad.mit.edu	37	7	30825451	30825451	+	Missense_Mutation	SNP	C	C	T	rs111491161	byFrequency	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr7:30825451C>T	ENST00000265299.6	+	4	583	c.506C>T	c.(505-507)cCg>cTg	p.P169L	INMT-FAM188B_ENST00000458257.1_3'UTR	NM_032222.2	NP_115598.2	Q4G0A6	F188B_HUMAN	family with sequence similarity 188, member B	169								p.P169L(1)|p.P169Q(1)		endometrium(1)|large_intestine(5)|lung(19)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CAGACGGTCCCGGGTGAAACT	0.473													C|||	5	0.000998403	0.0	0.0	5008	,	,		19374	0.0		0.0	False		,,,				2504	0.0051				p.P169L												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.C506T	7						.	C	LEU/PRO	0,3748		0,0,1874	104.0	108.0	107.0		506	3.4	0.0	7	dbSNP_132	107	3,8229		0,3,4113	yes	missense	FAM188B	NM_032222.2	98	0,3,5987	TT,TC,CC		0.0364,0.0,0.025	benign	169/758	30825451	3,11977	1874	4116	5990	30791976	SO:0001583	missense	84182	exon4			AK026027	CCDS43565.1	7p14.3	2010-08-17	2009-07-14	2009-07-14	ENSG00000106125	ENSG00000106125			21916	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 67"""	C7orf67			Standard	NM_032222		Approved	FLJ22374	uc003tbt.3	Q4G0A6	OTTHUMG00000152800	ENST00000265299.6:c.506C>T	7.37:g.30825451C>T	ENSP00000265299:p.Pro169Leu		30791976	NM_032222	Q71AZ7|Q9H6D2	Missense_Mutation	SNP	ENST00000265299.6	37	CCDS43565.1	.	.	.	.	.	.	.	.	.	.	C	1.198	-0.633358	0.03584	0.0	3.64E-4	ENSG00000106125	ENST00000265299	T	0.22336	1.96	5.19	3.36	0.38483	.	1.198200	0.05747	N	0.602442	T	0.11410	0.0278	N	0.04043	-0.29	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.24799	-1.0150	10	0.87932	D	0	0.0788	5.8434	0.18647	0.1905:0.7113:0.0:0.0983	.	169	Q4G0A6	F188B_HUMAN	L	169	ENSP00000265299:P169L	ENSP00000265299:P169L	P	+	2	0	FAM188B	30791976	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	0.078000	0.14761	0.749000	0.32854	0.650000	0.86243	CCG		0.473	FAM188B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327962.1	NM_032222	
PILRB	29990	broad.mit.edu	37	7	99956564	99956564	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G	G	G	G	G	Unknown	Wildtype	None	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr7:99956564G>A	ENST00000452089.1	+	7	1375	c.316G>A	c.(316-318)Gag>Aag	p.E106K	PILRB_ENST00000610247.1_Missense_Mutation_p.E106K|PILRB_ENST00000448382.1_Missense_Mutation_p.G158E|PILRB_ENST00000444073.1_Missense_Mutation_p.E106K|PILRB_ENST00000609309.1_Missense_Mutation_p.E106K|STAG3L5P-PVRIG2P-PILRB_ENST00000310771.4_RNA			Q9UKJ0	PILRB_HUMAN	paired immunoglobin-like type 2 receptor beta	106	Ig-like V-type.				activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)				endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	13	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					AGAGGGTCAGGAGAGCGGCTT	0.572																																					p.E106K												.	.	0			c.G316A	7						.						111.0	118.0	116.0					7																	99956564		2203	4300	6503	99794500	SO:0001583	missense	29990	exon2			AF161081, AJ400845	CCDS43622.1	7q22.1	2014-05-16			ENSG00000121716	ENSG00000121716		"""Immunoglobulin superfamily / V-set domain containing"""	18297	protein-coding gene	gene with protein product		605342				10660620	Standard	NM_178238		Approved	FDFACT1, FDFACT2	uc022ail.1	Q9UKJ0	OTTHUMG00000155363	ENST00000452089.1:c.316G>A	7.37:g.99956564G>A	ENSP00000391748:p.Glu106Lys		99794500	NM_178238	Q69YF9|Q9HBS0	Missense_Mutation	SNP	ENST00000452089.1	37	CCDS43622.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0.044|0.044	-1.274521|-1.274521	0.01410|0.01410	.|.	.|.	ENSG00000121716|ENSG00000121716	ENST00000310771;ENST00000420688;ENST00000452089;ENST00000457519;ENST00000443526;ENST00000419749;ENST00000422808;ENST00000438028;ENST00000444073;ENST00000413850;ENST00000438231|ENST00000444874;ENST00000448382;ENST00000431140	T;T;T;T;T;T;T;T;T|.	0.21543|.	2.0;2.0;2.0;2.0;2.0;2.0;2.0;2.0;2.0|.	2.76|2.76	-4.0|-4.0	0.04057|0.04057	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	2.881560|.	0.00958|.	N|.	0.003068|.	T|T	0.12263|0.12263	0.0298|0.0298	N|N	0.03324|0.03324	-0.35|-0.35	0.09310|0.09310	N|N	1|1	B|B	0.09022|0.02656	0.002|0.0	B|B	0.08055|0.01281	0.003|0.0	T|T	0.22068|0.22068	-1.0227|-1.0227	9|7	.|.	.|.	.|.	.|.	4.9812|4.9812	0.14166|0.14166	0.4444:0.2669:0.2887:0.0|0.4444:0.2669:0.2887:0.0	.|.	106|36	Q9UKJ0|Q9UKJ0-2	PILRB_HUMAN|.	K|E	106;106;106;106;106;106;106;25;106;211;106|36;158;36	ENSP00000311153:E106K;ENSP00000391748:E106K;ENSP00000411261:E106K;ENSP00000403757:E106K;ENSP00000404321:E106K;ENSP00000389856:E106K;ENSP00000409411:E25K;ENSP00000410764:E106K;ENSP00000408425:E106K|.	.|.	E|G	+|+	1|2	0|0	PILRB|PILRB	99794500|99794500	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-0.612000|-0.612000	0.05616|0.05616	-1.969000|-1.969000	0.01005|0.01005	-2.316000|-2.316000	0.00254|0.00254	GAG|GGA		0.572	PILRB-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339923.2	NM_178238	
FAM71F1	84691	broad.mit.edu	37	7	128356894	128356894	+	Missense_Mutation	SNP	G	G	A	rs150827355		TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr7:128356894G>A	ENST00000315184.5	+	2	330	c.277G>A	c.(277-279)Gtc>Atc	p.V93I	FAM71F1_ENST00000469348.1_3'UTR|FAM71F1_ENST00000485070.1_Missense_Mutation_p.R14H	NM_001282788.1|NM_032599.2	NP_001269717.1|NP_115988.1	Q96KD3	F71F1_HUMAN	family with sequence similarity 71, member F1	93								p.V93I(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	18						TTGGAGAGACGTCTACAAAGC	0.567													g|||	1	0.000199681	0.0008	0.0	5008	,	,		18165	0.0		0.0	False		,,,				2504	0.0				p.V93I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G277A	7						.	G	ILE/VAL	7,4399	11.4+/-27.6	0,7,2196	113.0	99.0	104.0		277	0.6	0.8	7	dbSNP_134	104	0,8600		0,0,4300	yes	missense	FAM71F1	NM_032599.2	29	0,7,6496	AA,AG,GG		0.0,0.1589,0.0538	benign	93/345	128356894	7,12999	2203	4300	6503	128144130	SO:0001583	missense	84691	exon2			AF367470	CCDS5804.1, CCDS64763.1	7q32.1	2007-11-20	2007-11-20	2007-11-20	ENSG00000135248	ENSG00000135248			30704	protein-coding gene	gene with protein product			"""family with sequence similarity 137, member A"""	FAM137A		12477932	Standard	XM_005250645		Approved	NYD-SP18	uc003vno.1	Q96KD3	OTTHUMG00000158276	ENST00000315184.5:c.277G>A	7.37:g.128356894G>A	ENSP00000326652:p.Val93Ile		128144130	NM_032599	Q8IY75|Q8NA48	Missense_Mutation	SNP	ENST00000315184.5	37	CCDS5804.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	0.012|0.012	-1.669821|-1.669821	0.00758|0.00758	0.001589|0.001589	0.0|0.0	ENSG00000135248|ENSG00000135248	ENST00000485070|ENST00000315184	T|T	0.27890|0.09163	1.64|3.01	5.54|5.54	0.609|0.609	0.17575|0.17575	.|.	.|0.442134	.|0.21524	.|N	.|0.073163	T|T	0.03390|0.03390	0.0098|0.0098	N|N	0.02225|0.02225	-0.63|-0.63	0.09310|0.09310	N|N	0.999998|0.999998	B;B|B;B	0.02656|0.02656	0.0;0.0|0.0;0.0	B;B|B;B	0.01281|0.01281	0.0;0.0|0.0;0.0	T|T	0.45011|0.45011	-0.9290|-0.9290	9|10	0.87932|0.19147	D|T	0|0.46	-6.9303|-6.9303	7.4229|7.4229	0.27081|0.27081	0.6428:0.0:0.3572:0.0|0.6428:0.0:0.3572:0.0	.|.	17;14|93;93	B4DY15;Q8NA48|Q96KD3-2;Q96KD3	.;.|.;F71F1_HUMAN	H|I	14|93	ENSP00000418192:R14H|ENSP00000326652:V93I	ENSP00000418192:R14H|ENSP00000326652:V93I	R|V	+|+	2|1	0|0	FAM71F1|FAM71F1	128144130|128144130	1.000000|1.000000	0.71417|0.71417	0.802000|0.802000	0.32245|0.32245	0.107000|0.107000	0.19398|0.19398	1.236000|1.236000	0.32683|0.32683	0.076000|0.076000	0.16826|0.16826	-0.374000|-0.374000	0.07098|0.07098	CGT|GTC		0.567	FAM71F1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350544.2	NM_032599	
CSMD3	114788	broad.mit.edu	37	8	113988239	113988239	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr8:113988239A>T	ENST00000297405.5	-	7	1413	c.1169T>A	c.(1168-1170)cTt>cAt	p.L390H	CSMD3_ENST00000455883.2_Intron|CSMD3_ENST00000343508.3_Missense_Mutation_p.L350H|CSMD3_ENST00000352409.3_Missense_Mutation_p.L390H	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	390						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.L390H(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						TTCCTCGGAAAGTCTATGGAT	0.498										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.L390H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1169A	8						.						200.0	177.0	184.0					8																	113988239		2203	4300	6503	114057415	SO:0001583	missense	114788	exon7			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.1169T>A	8.37:g.113988239A>T	ENSP00000297405:p.Leu390His		114057415	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	A	14.99	2.701065	0.48307	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000352409	T;T;T	0.24151	1.9;1.89;1.87	6.17	4.96	0.65561	.	0.000000	0.51477	D	0.000089	T	0.13756	0.0333	N	0.22421	0.69	0.26616	N	0.972748	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.20371	-1.0277	10	0.14252	T	0.57	.	6.1014	0.20049	0.6342:0.0:0.0699:0.2958	.	390;350	Q7Z407;Q7Z407-2	CSMD3_HUMAN;.	H	350;390;390	ENSP00000345799:L350H;ENSP00000297405:L390H;ENSP00000343124:L390H	ENSP00000297405:L390H	L	-	2	0	CSMD3	114057415	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.077000	0.41557	2.371000	0.80710	0.533000	0.62120	CTT		0.498	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
ADAM7	8756	broad.mit.edu	37	8	24333986	24333986	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr8:24333986G>A	ENST00000175238.6	+	8	757	c.674G>A	c.(673-675)cGa>cAa	p.R225Q	RP11-624C23.1_ENST00000519689.1_RNA|ADAM7_ENST00000380789.1_Missense_Mutation_p.R225Q|ADAM7_ENST00000520720.1_5'UTR|RP11-624C23.1_ENST00000523578.1_RNA	NM_003817.3	NP_003808.2	Q9H2U9	ADAM7_HUMAN	ADAM metallopeptidase domain 7	225	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R225Q(1)		NS(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(24)|ovary(1)|skin(15)	64		Prostate(55;0.0181)		Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182)		CTAAGGAACCGAATTTGGGGA	0.333																																					p.R225Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G674A	8						.						114.0	106.0	109.0					8																	24333986		2203	4300	6503	24389876	SO:0001583	missense	8756	exon8			AF090327	CCDS6045.1	8p21.2	2005-08-18	2005-08-18		ENSG00000069206	ENSG00000069206		"""ADAM metallopeptidase domain containing"""	214	protein-coding gene	gene with protein product		607310	"""a disintegrin and metalloproteinase domain 7"""				Standard	NM_003817		Approved	GP-83, EAPI	uc003xeb.3	Q9H2U9	OTTHUMG00000097859	ENST00000175238.6:c.674G>A	8.37:g.24333986G>A	ENSP00000175238:p.Arg225Gln		24389876	NM_003817	A8K8X7|O75959|Q6PEJ6	Missense_Mutation	SNP	ENST00000175238.6	37	CCDS6045.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.681565	0.88542	.	.	ENSG00000069206	ENST00000175238;ENST00000380789;ENST00000335595	T;T	0.30448	1.53;1.53	5.38	5.38	0.77491	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.46145	D	0.000301	T	0.60881	0.2303	M	0.89715	3.055	0.80722	D	1	D	0.89917	1.0	D	0.65233	0.933	T	0.68277	-0.5451	10	0.66056	D	0.02	.	14.9792	0.71299	0.0:0.0:1.0:0.0	.	225	Q9H2U9	ADAM7_HUMAN	Q	225;225;40	ENSP00000175238:R225Q;ENSP00000370166:R225Q	ENSP00000175238:R225Q	R	+	2	0	ADAM7	24389876	0.999000	0.42202	0.992000	0.48379	0.993000	0.82548	4.931000	0.63469	2.697000	0.92050	0.591000	0.81541	CGA		0.333	ADAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215150.1	NM_003817	
RBM12B	389677	broad.mit.edu	37	8	94746933	94746933	+	Missense_Mutation	SNP	G	G	C	rs150172581	byFrequency	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr8:94746933G>C	ENST00000399300.2	-	3	1919	c.1706C>G	c.(1705-1707)cCg>cGg	p.P569R	RP11-10N23.4_ENST00000517998.1_RNA|RBM12B_ENST00000520961.1_Intron|RBM12B_ENST00000517700.1_Missense_Mutation_p.P569R	NM_203390.2	NP_976324.2	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	569							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.P569R(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	30	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			GAAGTCCTCCGGGGGGAACCT	0.587																																					p.P569R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1706G	8						.						65.0	67.0	66.0					8																	94746933		1847	4087	5934	94816109	SO:0001583	missense	389677	exon3				CCDS43755.1	8q22	2014-05-20			ENSG00000183808	ENSG00000183808		"""RNA binding motif (RRM) containing"""	32310	protein-coding gene	gene with protein product							Standard	NM_203390		Approved		uc003yfz.3	Q8IXT5	OTTHUMG00000164317	ENST00000399300.2:c.1706C>G	8.37:g.94746933G>C	ENSP00000382239:p.Pro569Arg		94816109	NM_203390	A8MYB5	Missense_Mutation	SNP	ENST00000399300.2	37	CCDS43755.1	.	.	.	.	.	.	.	.	.	.	G	1.083	-0.666463	0.03428	.	.	ENSG00000183808	ENST00000399300;ENST00000517700	T;T	0.06849	3.25;3.28	4.3	1.14	0.20703	.	.	.	.	.	T	0.11452	0.0279	N	0.24115	0.695	0.09310	N	1	D	0.64830	0.994	P	0.57283	0.817	T	0.23904	-1.0175	9	0.72032	D	0.01	.	8.5355	0.33360	0.0:0.3146:0.5234:0.162	.	569	Q8IXT5	RB12B_HUMAN	R	569	ENSP00000382239:P569R;ENSP00000427729:P569R	ENSP00000382239:P569R	P	-	2	0	RBM12B	94816109	0.010000	0.17322	0.003000	0.11579	0.377000	0.30045	1.683000	0.37638	-0.028000	0.13850	0.655000	0.94253	CCG		0.587	RBM12B-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383603.1	NM_203390	
TNFRSF11B	4982	broad.mit.edu	37	8	119945284	119945284	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr8:119945284C>A	ENST00000297350.4	-	2	664	c.286G>T	c.(286-288)Gag>Tag	p.E96*		NM_002546.3	NP_002537.3	O00300	TR11B_HUMAN	tumor necrosis factor receptor superfamily, member 11b	96					apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|negative regulation of bone resorption (GO:0045779)|negative regulation of odontogenesis of dentin-containing tooth (GO:0042489)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to magnesium ion (GO:0032026)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|receptor activity (GO:0004872)	p.E96*(1)		breast(1)|central_nervous_system(3)|endometrium(4)|large_intestine(6)|lung(7)|prostate(3)|skin(1)	25	all_cancers(13;3.71e-26)|Lung NSC(37;1.69e-07)|Ovarian(258;0.018)|all_neural(195;0.0592)|Hepatocellular(40;0.234)		STAD - Stomach adenocarcinoma(47;0.00193)			CGATTGCACTCCTGCTTGACG	0.567																																					p.E96X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G286T	8						.						119.0	106.0	111.0					8																	119945284		2203	4300	6503	120014465	SO:0001587	stop_gained	4982	exon2			U94332	CCDS6326.1	8q24	2008-07-31	2008-07-31		ENSG00000164761	ENSG00000164761		"""Tumor necrosis factor receptor superfamily"""	11909	protein-coding gene	gene with protein product		602643	"""osteoprotegerin"""	OPG		9108485	Standard	NM_002546		Approved	OCIF, TR1	uc003yon.4	O00300	OTTHUMG00000164969	ENST00000297350.4:c.286G>T	8.37:g.119945284C>A	ENSP00000297350:p.Glu96*		120014465	NM_002546	B2R9A8|O60236|Q53FX6|Q9UHP4	Nonsense_Mutation	SNP	ENST00000297350.4	37	CCDS6326.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.204176	0.79127	.	.	ENSG00000164761	ENST00000297350	.	.	.	6.17	6.17	0.99709	.	0.093368	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-31.8198	20.8794	0.99867	0.0:1.0:0.0:0.0	.	.	.	.	X	96	.	.	E	-	1	0	TNFRSF11B	120014465	1.000000	0.71417	1.000000	0.80357	0.488000	0.33401	2.887000	0.48586	2.941000	0.99782	0.655000	0.94253	GAG		0.567	TNFRSF11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381220.1		
NR4A3	8013	broad.mit.edu	37	9	102590767	102590768	+	Frame_Shift_Ins	INS	-	-	C	rs368591388		TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr9:102590767_102590768insC	ENST00000395097.2	+	3	1172_1173	c.443_444insC	c.(442-447)ttccccfs	p.FP148fs	NR4A3_ENST00000338488.4_Frame_Shift_Ins_p.FP148fs|NR4A3_ENST00000330847.1_Frame_Shift_Ins_p.FP159fs	NM_006981.3|NM_173200.2	NP_008912.2|NP_775292.1	Q92570	NR4A3_HUMAN	nuclear receptor subfamily 4, group A, member 3	148					gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|thyroid hormone receptor activity (GO:0004887)|zinc ion binding (GO:0008270)	p.Q162fs*89(1)	TCF12/NR4A3(2)|TAF15/NR4A3(33)|EWSR1/NR4A3(146)|TFG/NR4A3(2)				Acute lymphoblastic leukemia(62;0.0559)|all_hematologic(171;0.189)				ACGCCGGCCTTCCCCCCGCAGG	0.718			T	EWSR1	extraskeletal myxoid chondrosarcoma																																p.F148fs			Dom	yes		9	9q22	8013	"""nuclear receptor subfamily 4, group A, member 3 (NOR1)"""		M	.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.443_444insC	9						.																																			101630589	SO:0001589	frameshift_variant	8013	exon3			U12767	CCDS6742.1, CCDS6743.1, CCDS6744.1	9q22	2013-01-16			ENSG00000119508	ENSG00000119508		"""Nuclear hormone receptors"""	7982	protein-coding gene	gene with protein product		600542				8614405	Standard	NM_006981		Approved	CSMF, CHN, NOR1, MINOR	uc004baf.1	Q92570	OTTHUMG00000021030	ENST00000395097.2:c.449dupC	9.37:g.102590773_102590773dupC	ENSP00000378531:p.Phe148fs		101630588	NM_173199	A2A3I7|Q12935|Q14979|Q16420|Q4VXA8|Q4VXA9|Q9UEK2|Q9UEK3	Frame_Shift_Ins	INS	ENST00000395097.2	37	CCDS6743.1																																																																																				0.718	NR4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055482.1		
PRSS3	5646	broad.mit.edu	37	9	33750695	33750696	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr9:33750695_33750696insA	ENST00000361005.5	+	1	181_182	c.181_182insA	c.(181-183)gatfs	p.D61fs	PRSS3_ENST00000429677.3_5'Flank|PRSS3_ENST00000342836.4_De_novo_Start_OutOfFrame	NM_007343.3	NP_031369	P35030	TRY3_HUMAN	protease, serine, 3	61					cobalamin metabolic process (GO:0009235)|digestion (GO:0007586)|endothelial cell migration (GO:0043542)|innate immune response (GO:0045087)|proteolysis (GO:0006508)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.D61fs*16(1)		large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	13			LUSC - Lung squamous cell carcinoma(29;0.0176)			AGCGGCGCGGGATGCAGACGGC	0.733																																					p.D61fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.181_182insA	9						.																																			33740696	SO:0001589	frameshift_variant	5646	exon1				CCDS6545.1, CCDS47958.1, CCDS56570.1, CCDS56571.1	9p13	2010-05-07	2008-03-11		ENSG00000010438	ENSG00000010438	3.4.21.4	"""Serine peptidases / Serine peptidases"""	9486	protein-coding gene	gene with protein product	"""mesotrypsin"""	613578	"""protease, serine, 4 (trypsin 4, brain)"", ""protease, serine, 3 (mesotrypsin)"""	PRSS4		2326201, 8294000	Standard	NM_002771		Approved	TRY3, TRY4	uc003ztj.4	P35030	OTTHUMG00000019798	ENST00000361005.5:c.182dupA	9.37:g.33750696_33750696dupA	ENSP00000354280:p.Asp61fs		33740695	NM_007343	A8CED1|A8CED3|A9Z1Y4|E7ES07|F8W7P3|P15951|Q15665|Q5VXV0|Q6ISJ4|Q9UQV3	De_novo_Start_InFrame	INS	ENST00000361005.5	37	CCDS47958.1																																																																																				0.733	PRSS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052121.1	NM_002771	
ABHD17B	51104	broad.mit.edu	37	9	74489605	74489605	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr9:74489605C>T	ENST00000333421.6	-	2	503	c.392G>A	c.(391-393)gGt>gAt	p.G131D	ABHD17B_ENST00000377041.2_Missense_Mutation_p.G131D	NM_001025780.1	NP_001020951.1	Q5VST6	AB17B_HUMAN	abhydrolase domain containing 17B	131						extracellular region (GO:0005576)|membrane (GO:0016020)	hydrolase activity (GO:0016787)	p.G131D(1)									GGAACTGGCACCATATCCAGA	0.393																																					p.G131D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G392A	9						.						82.0	80.0	81.0					9																	74489605		2203	4300	6503	73679425	SO:0001583	missense	51104	exon2			AF151825	CCDS35042.1, CCDS35043.1	9q21.2	2013-03-15	2013-03-15	2013-03-15	ENSG00000107362	ENSG00000107362		"""Abhydrolase domain containing"""	24278	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 77"", ""family with sequence similarity 108, member B1"""	C9orf77, FAM108B1		10810093	Standard	XM_006717134		Approved	CGI-67	uc004ail.3	Q5VST6	OTTHUMG00000020001	ENST00000333421.6:c.392G>A	9.37:g.74489605C>T	ENSP00000330222:p.Gly131Asp		73679425	NM_001025780	A8KAJ5|Q5VST7|Q86YB6|Q8IY03|Q9Y377	Missense_Mutation	SNP	ENST00000333421.6	37	CCDS35043.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.950508	0.92660	.	.	ENSG00000107362	ENST00000377041;ENST00000333421	T;T	0.70631	-0.5;-0.5	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	D	0.91590	0.7343	H	0.98996	4.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94041	0.7309	10	0.87932	D	0	-13.852	20.5827	0.99408	0.0:1.0:0.0:0.0	.	131;131	Q5VST6;Q5VST6-2	F108B_HUMAN;.	D	131	ENSP00000366240:G131D;ENSP00000330222:G131D	ENSP00000330222:G131D	G	-	2	0	FAM108B1	73679425	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.776000	0.85560	2.941000	0.99782	0.655000	0.94253	GGT		0.393	ABHD17B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052625.1	NM_016014	
NUTM2F	54754	broad.mit.edu	37	9	97082793	97082793	+	Missense_Mutation	SNP	C	C	G	rs577940402		TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr9:97082793C>G	ENST00000253262.4	-	5	1085	c.1065G>C	c.(1063-1065)aaG>aaC	p.K355N	NUTM2F_ENST00000335456.7_Missense_Mutation_p.K355N|NUTM2F_ENST00000341207.4_Missense_Mutation_p.K355N	NM_017561.1	NP_060031.1	A1L443	NTM2F_HUMAN	NUT family member 2F	355	Pro-rich.							p.K236N(5)									GCAGGTGGGCCTTGGTCTCCG	0.706													.|||	1	0.000199681	0.0	0.0	5008	,	,		14002	0.0		0.0	False		,,,				2504	0.001				p.K355N												.	.	5	Substitution - Missense(5)	large_intestine(5)	c.G1065C	9						.						17.0	24.0	21.0					9																	97082793		1985	4123	6108	96122614	SO:0001583	missense	54754	exon5				CCDS47994.1	9q22.32	2013-05-02	2013-03-14	2013-05-02	ENSG00000130950	ENSG00000130950			23450	protein-coding gene	gene with protein product			"""family with sequence similarity 22, member F"""	FAM22F			Standard	NM_017561		Approved	DKFZp434I1117		A1L443	OTTHUMG00000020260	ENST00000253262.4:c.1065G>C	9.37:g.97082793C>G	ENSP00000253262:p.Lys355Asn		96122614	NM_017561	B6ZDF0|Q5SR58|Q5SR59|Q9UFB1	Missense_Mutation	SNP	ENST00000253262.4	37	CCDS47994.1	.	.	.	.	.	.	.	.	.	.	.	10.88	1.475748	0.26511	.	.	ENSG00000130950	ENST00000335456;ENST00000253262;ENST00000341207	T;T;T	0.24151	1.87;2.67;2.67	0.1	0.1	0.14510	.	.	.	.	.	T	0.30070	0.0753	N	0.24115	0.695	0.09310	N	1	D	0.57899	0.981	D	0.69824	0.966	T	0.14062	-1.0486	9	0.62326	D	0.03	.	5.97	0.19346	0.0:0.9994:0.0:6.0E-4	.	355	A1L443	FA22F_HUMAN	N	355	ENSP00000335067:K355N;ENSP00000253262:K355N;ENSP00000343865:K355N	ENSP00000253262:K355N	K	-	3	2	FAM22F	96122614	0.001000	0.12720	0.113000	0.21522	0.093000	0.18481	0.349000	0.20055	0.170000	0.19704	0.173000	0.16961	AAG		0.706	NUTM2F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053173.2	NM_017561	
C9orf156	51531	broad.mit.edu	37	9	100667076	100667076	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr9:100667076G>A	ENST00000375119.3	-	5	1341	c.1265C>T	c.(1264-1266)cCg>cTg	p.P422L		NM_016481.3	NP_057565.3	Q9BU70	NAP1_HUMAN	chromosome 9 open reading frame 156	422					viral process (GO:0016032)		hydrolase activity (GO:0016787)	p.P422L(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|prostate(1)|skin(1)	13		Acute lymphoblastic leukemia(62;0.158)				CTCAGAAGCCGGCTTGATCCT	0.512																																					p.P422L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1265T	9						.						110.0	104.0	106.0					9																	100667076		2203	4300	6503	99706897	SO:0001583	missense	51531	exon5			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.1265C>T	9.37:g.100667076G>A	ENSP00000364260:p.Pro422Leu		99706897	NM_016481	Q5T113|Q86SK0|Q9NXJ7|Q9P0Q7	Missense_Mutation	SNP	ENST00000375119.3	37	CCDS6730.1	.	.	.	.	.	.	.	.	.	.	G	0.240	-1.014664	0.02095	.	.	ENSG00000136932	ENST00000375119;ENST00000375118	T;T	0.33216	1.79;1.42	4.24	-1.05	0.10036	.	0.256838	0.39341	N	0.001389	T	0.08891	0.0220	N	0.20685	0.6	0.36852	D	0.887968	P;B	0.37061	0.58;0.445	B;B	0.26094	0.066;0.03	T	0.41910	-0.9482	10	0.02654	T	1	-0.0558	1.5151	0.02504	0.29:0.1251:0.4228:0.1621	.	276;422	Q5T114;Q9BU70	.;NAP1_HUMAN	L	422;276	ENSP00000364260:P422L;ENSP00000364259:P276L	ENSP00000364259:P276L	P	-	2	0	C9orf156	99706897	0.812000	0.29077	0.027000	0.17364	0.041000	0.13682	0.936000	0.28938	-0.195000	0.10382	-0.136000	0.14681	CCG		0.512	C9orf156-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055401.1	NM_016481	
SARDH	1757	broad.mit.edu	37	9	136529132	136529132	+	Missense_Mutation	SNP	G	G	A	rs563709194		TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454_PCR_WGA			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chr9:136529132G>A	ENST00000371872.4	-	21	2893	c.2636C>T	c.(2635-2637)tCg>tTg	p.S879L	SARDH_ENST00000422262.2_Missense_Mutation_p.S711L|SARDH_ENST00000439388.1_Missense_Mutation_p.S879L|SARDH_ENST00000371868.1_Missense_Mutation_p.S329L|SARDH_ENST00000469828.1_5'UTR	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	879					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|sarcosine dehydrogenase activity (GO:0008480)	p.S879L(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(13)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	44				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		AAAGTCCAGCGAGACCTAGGA	0.582													G|||	1	0.000199681	0.0008	0.0	5008	,	,		20900	0.0		0.0	False		,,,				2504	0.0				p.S879L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2636T	9						.						81.0	67.0	72.0					9																	136529132		2203	4300	6503	135518953	SO:0001583	missense	1757	exon21				CCDS6978.1	9q33-q34	2008-02-05			ENSG00000123453	ENSG00000123453	1.5.99.2		10536	protein-coding gene	gene with protein product		604455		DMGDHL1		10444331	Standard	NM_007101		Approved	SDH	uc004cep.4	Q9UL12	OTTHUMG00000020879	ENST00000371872.4:c.2636C>T	9.37:g.136529132G>A	ENSP00000360938:p.Ser879Leu		135518953	NM_007101	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Missense_Mutation	SNP	ENST00000371872.4	37	CCDS6978.1	.	.	.	.	.	.	.	.	.	.	G	16.17	3.046003	0.55110	.	.	ENSG00000123453	ENST00000371872;ENST00000371868;ENST00000439388;ENST00000422262	T;T;T;T	0.80909	-0.7;-1.43;-0.7;-1.1	4.97	4.97	0.65823	.	0.198406	0.44688	D	0.000431	D	0.84374	0.5458	L	0.55834	1.745	0.80722	D	1	D;D	0.58268	0.961;0.982	P;P	0.53649	0.49;0.731	D	0.86023	0.1508	10	0.62326	D	0.03	-14.4034	18.1878	0.89797	0.0:0.0:1.0:0.0	.	879;329	Q9UL12;Q5SYV2	SARDH_HUMAN;.	L	879;329;879;711	ENSP00000360938:S879L;ENSP00000360934:S329L;ENSP00000403084:S879L;ENSP00000415537:S711L	ENSP00000360934:S329L	S	-	2	0	SARDH	135518953	1.000000	0.71417	0.986000	0.45419	0.195000	0.23768	6.257000	0.72480	2.478000	0.83669	0.561000	0.74099	TCG		0.582	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1		
ATP7A	538	broad.mit.edu	37	X	77270225	77270225	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3973-01A-01W-0995-10	TCGA-AA-3973-10A-01W-0999-10	g.chrX:77270225C>T	ENST00000341514.6	+	11	2628	c.2473C>T	c.(2473-2475)Ctt>Ttt	p.L825F	ATP7A_ENST00000343533.5_Missense_Mutation_p.L747F|ATP7A_ENST00000350425.4_Intron	NM_000052.5	NP_000043.4	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide	825					blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|cartilage development (GO:0051216)|catecholamine metabolic process (GO:0006584)|cellular copper ion homeostasis (GO:0006878)|central nervous system neuron development (GO:0021954)|cerebellar Purkinje cell differentiation (GO:0021702)|collagen fibril organization (GO:0030199)|copper ion export (GO:0060003)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detoxification of copper ion (GO:0010273)|dopamine metabolic process (GO:0042417)|elastic fiber assembly (GO:0048251)|elastin biosynthetic process (GO:0051542)|epinephrine metabolic process (GO:0042414)|extracellular matrix organization (GO:0030198)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|lung alveolus development (GO:0048286)|mitochondrion organization (GO:0007005)|negative regulation of metalloenzyme activity (GO:0048553)|negative regulation of neuron apoptotic process (GO:0043524)|neuron projection morphogenesis (GO:0048812)|norepinephrine biosynthetic process (GO:0042421)|norepinephrine metabolic process (GO:0042415)|peptidyl-lysine modification (GO:0018205)|pigmentation (GO:0043473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of oxidoreductase activity (GO:0051353)|pyramidal neuron development (GO:0021860)|regulation of gene expression (GO:0010468)|regulation of oxidative phosphorylation (GO:0002082)|release of cytochrome c from mitochondria (GO:0001836)|removal of superoxide radicals (GO:0019430)|response to iron(III) ion (GO:0010041)|response to zinc ion (GO:0010043)|serotonin metabolic process (GO:0042428)|skin development (GO:0043588)|T-helper cell differentiation (GO:0042093)|transmembrane transport (GO:0055085)|tryptophan metabolic process (GO:0006568)|tyrosine metabolic process (GO:0006570)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|copper-dependent protein binding (GO:0032767)|copper-exporting ATPase activity (GO:0004008)|superoxide dismutase copper chaperone activity (GO:0016532)	p.L825F(2)		breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(26)|pancreas(1)|prostate(1)|urinary_tract(1)	53					Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	TATTGTAACTCTTGATTCTGA	0.303																																					p.L825F												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C2473T	X						.						129.0	120.0	123.0					X																	77270225		2203	4290	6493	77156881	SO:0001583	missense	538	exon11			L06133	CCDS35339.1, CCDS75997.1	Xq21.1	2012-10-22	2008-07-31		ENSG00000165240	ENSG00000165240	3.6.3.4	"""ATPases / P-type"""	869	protein-coding gene	gene with protein product	"""copper pump 1"", ""copper-transporting ATPase 1"""	300011	"""Menkes syndrome"""	MNK		10079817	Standard	NM_000052		Approved		uc004ecx.4	Q04656	OTTHUMG00000021885	ENST00000341514.6:c.2473C>T	X.37:g.77270225C>T	ENSP00000345728:p.Leu825Phe		77156881	NM_000052	B1AT72|O00227|O00745|Q9BYY8	Missense_Mutation	SNP	ENST00000341514.6	37	CCDS35339.1	.	.	.	.	.	.	.	.	.	.	C	13.21	2.170082	0.38315	.	.	ENSG00000165240	ENST00000343533;ENST00000341514	D;D	0.90563	-2.69;-2.69	4.74	1.91	0.25777	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.072199	0.56097	D	0.000034	D	0.86397	0.5923	L	0.56124	1.755	0.80722	D	1	B	0.18166	0.026	B	0.25884	0.064	T	0.77900	-0.2415	10	0.51188	T	0.08	-0.0175	7.3804	0.26851	0.1413:0.7307:0.0:0.128	.	825	Q04656	ATP7A_HUMAN	F	747;825	ENSP00000343026:L747F;ENSP00000345728:L825F	ENSP00000345728:L825F	L	+	1	0	ATP7A	77156881	0.048000	0.20356	0.972000	0.41901	0.993000	0.82548	0.430000	0.21428	0.042000	0.15717	0.468000	0.43344	CTT		0.303	ATP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057306.1	NM_000052	
