#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
SCD	6319	broad.mit.edu	37	10	102107859	102107859	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:102107859G>A	ENST00000370355.2	+	2	447	c.66G>A	c.(64-66)gcG>gcA	p.A22A	RP11-34D15.2_ENST00000429420.1_RNA	NM_005063.4	NP_005054.3	O00767	ACOD_HUMAN	stearoyl-CoA desaturase (delta-9-desaturase)	22					fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	iron ion binding (GO:0005506)|stearoyl-CoA 9-desaturase activity (GO:0004768)	p.A22A(1)		endometrium(1)|large_intestine(3)|lung(5)	9		Colorectal(252;0.0323)		Epithelial(162;1.97e-10)|all cancers(201;1.73e-08)		CCATTACAGCGCCTCCCTCCA	0.532																																					p.A22A	Colon(67;260 1459 9574 11663)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G66A	10						.						126.0	129.0	128.0					10																	102107859		2203	4300	6503	102097849	SO:0001819	synonymous_variant	6319	exon2			AF097514	CCDS7493.1	10q23-q24	2013-01-25			ENSG00000099194	ENSG00000099194	1.14.19.1	"""Fatty acid desaturases"""	10571	protein-coding gene	gene with protein product	"""acyl-CoA desaturase"", ""fatty acid desaturase"", ""delta-9-desaturase"""	604031	"""stearoyl-CoA desaturase opposite strand"""	SCDOS		7909540, 10229681	Standard	NM_005063		Approved	FADS5	uc001kqy.3	O00767	OTTHUMG00000018906	ENST00000370355.2:c.66G>A	10.37:g.102107859G>A			102097849	NM_005063	B2R5U0|D3DR68|Q16150|Q53GR9|Q5W037|Q5W038|Q6GSS4|Q96KF6|Q9BS07|Q9Y695	Silent	SNP	ENST00000370355.2	37	CCDS7493.1																																																																																				0.532	SCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049857.2	NM_005063	
SCD	6319	broad.mit.edu	37	10	102120595	102120595	+	Missense_Mutation	SNP	G	G	A	rs200630764		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:102120595G>A	ENST00000370355.2	+	6	1366	c.985G>A	c.(985-987)Gcc>Acc	p.A329T		NM_005063.4	NP_005054.3	O00767	ACOD_HUMAN	stearoyl-CoA desaturase (delta-9-desaturase)	329					fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	iron ion binding (GO:0005506)|stearoyl-CoA 9-desaturase activity (GO:0004768)	p.A329T(1)		endometrium(1)|large_intestine(3)|lung(5)	9		Colorectal(252;0.0323)		Epithelial(162;1.97e-10)|all cancers(201;1.73e-08)		TTGCATGGCCGCCCTCGGTCT	0.522																																					p.A329T	Colon(67;260 1459 9574 11663)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G985A	10						.						111.0	103.0	106.0					10																	102120595		2203	4300	6503	102110585	SO:0001583	missense	6319	exon6			AF097514	CCDS7493.1	10q23-q24	2013-01-25			ENSG00000099194	ENSG00000099194	1.14.19.1	"""Fatty acid desaturases"""	10571	protein-coding gene	gene with protein product	"""acyl-CoA desaturase"", ""fatty acid desaturase"", ""delta-9-desaturase"""	604031	"""stearoyl-CoA desaturase opposite strand"""	SCDOS		7909540, 10229681	Standard	NM_005063		Approved	FADS5	uc001kqy.3	O00767	OTTHUMG00000018906	ENST00000370355.2:c.985G>A	10.37:g.102120595G>A	ENSP00000359380:p.Ala329Thr		102110585	NM_005063	B2R5U0|D3DR68|Q16150|Q53GR9|Q5W037|Q5W038|Q6GSS4|Q96KF6|Q9BS07|Q9Y695	Missense_Mutation	SNP	ENST00000370355.2	37	CCDS7493.1	.	.	.	.	.	.	.	.	.	.	G	5.506	0.278419	0.10403	.	.	ENSG00000099194	ENST00000370355	T	0.46451	0.87	5.34	-0.821	0.10822	.	1.147710	0.06433	N	0.724574	T	0.30665	0.0772	L	0.42529	1.33	0.09310	N	1	B	0.31837	0.342	B	0.17433	0.018	T	0.19063	-1.0317	10	0.22706	T	0.39	-6.9311	10.2246	0.43218	0.0:0.4874:0.1803:0.3323	.	329	O00767	ACOD_HUMAN	T	329	ENSP00000359380:A329T	ENSP00000359380:A329T	A	+	1	0	SCD	102110585	0.000000	0.05858	0.004000	0.12327	0.153000	0.21895	0.172000	0.16704	0.229000	0.21039	-0.265000	0.10407	GCC		0.522	SCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049857.2	NM_005063	
PITX3	5309	broad.mit.edu	37	10	103991516	103991516	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:103991516G>A	ENST00000370002.3	-	3	303	c.150C>T	c.(148-150)ggC>ggT	p.G50G	PITX3_ENST00000539804.1_Silent_p.G50G	NM_005029.3	NP_005020.1	O75364	PITX3_HUMAN	paired-like homeodomain 3	50					dopaminergic neuron differentiation (GO:0071542)|lens development in camera-type eye (GO:0002088)|lens fiber cell differentiation (GO:0070306)|lens morphogenesis in camera-type eye (GO:0002089)|locomotory behavior (GO:0007626)|midbrain development (GO:0030901)|neuron development (GO:0048666)|organ morphogenesis (GO:0009887)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.G50G(1)		endometrium(1)|large_intestine(2)|lung(2)	5		Colorectal(252;0.00957)		Epithelial(162;4.97e-08)|all cancers(201;8.99e-07)		CTGGGGAGCCGCCGGGCAGCG	0.662																																					p.G50G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C150T	10						.						16.0	17.0	17.0					10																	103991516		2200	4298	6498	103981506	SO:0001819	synonymous_variant	5309	exon3				CCDS7532.1	10q24.32	2013-11-14	2007-07-12		ENSG00000107859	ENSG00000107859		"""Homeoboxes / PRD class"""	9006	protein-coding gene	gene with protein product		602669	"""paired-like homeodomain transcription factor 3"", ""anterior segment mesenchymal dysgenesis"""	ASMD		9620774	Standard	NM_005029		Approved		uc001kuu.1	O75364	OTTHUMG00000018952	ENST00000370002.3:c.150C>T	10.37:g.103991516G>A			103981506	NM_005029	Q5VZL2	Silent	SNP	ENST00000370002.3	37	CCDS7532.1																																																																																				0.662	PITX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050031.1		
ARL3	403	broad.mit.edu	37	10	104449653	104449653	+	Silent	SNP	A	A	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:104449653A>T	ENST00000260746.5	-	4	443	c.312T>A	c.(310-312)ggT>ggA	p.G104G		NM_004311.3	NP_004302.1	P36405	ARL3_HUMAN	ADP-ribosylation factor-like 3	104					cilium morphogenesis (GO:0060271)|cytokinesis (GO:0000910)|intraciliary transport (GO:0042073)|kidney development (GO:0001822)|photoreceptor cell development (GO:0042461)|post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)|spindle microtubule (GO:0005876)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|microtubule binding (GO:0008017)	p.G104G(1)		large_intestine(2)	2		Colorectal(252;0.122)		Epithelial(162;4.88e-09)|all cancers(201;1.29e-07)|BRCA - Breast invasive adenocarcinoma(275;0.22)		TATTTACCTGACCCGTCTCTT	0.328																																					p.G104G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T312A	10						.						47.0	51.0	49.0					10																	104449653		2203	4297	6500	104439643	SO:0001819	synonymous_variant	403	exon4			U07151	CCDS7538.1	10q23.3	2014-05-09			ENSG00000138175	ENSG00000138175		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	694	protein-coding gene	gene with protein product		604695				8034651, 10072593	Standard	NM_004311		Approved	ARFL3	uc001kwa.3	P36405	OTTHUMG00000018965	ENST00000260746.5:c.312T>A	10.37:g.104449653A>T			104439643	NM_004311	B2R6C7|Q53X83|Q5JSM2	Silent	SNP	ENST00000260746.5	37	CCDS7538.1																																																																																				0.328	ARL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050088.2	NM_004311	
SLK	9748	broad.mit.edu	37	10	105761255	105761255	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:105761255G>T	ENST00000369755.3	+	8	1463	c.918G>T	c.(916-918)gaG>gaT	p.E306D	SLK_ENST00000335753.4_Missense_Mutation_p.E306D	NM_014720.2	NP_055535.2	Q9H2G2	SLK_HUMAN	STE20-like kinase	306	Glu-rich.				apoptotic process (GO:0006915)|protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)	p.E306D(1)		kidney(1)|lung(1)|ovary(2)|skin(2)|stomach(2)	8		Colorectal(252;0.178)		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		TGATTGCAGAGGCGAAGGCTg	0.378																																					p.E306D	NSCLC(111;540 1651 1927 4474 17706)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G918T	10						.						90.0	78.0	82.0					10																	105761255		2203	4300	6503	105751245	SO:0001583	missense	9748	exon8				CCDS7553.1	10q25.1	2010-06-25	2010-06-25		ENSG00000065613	ENSG00000065613			11088	protein-coding gene	gene with protein product			"""SNF1 (sucrose nonfermenting, yeast, homolog)-like kinase, SNF1 sucrose nonfermenting like kinase (yeast)"", ""STE20-like kinase (yeast)"""			3526554	Standard	NM_014720		Approved	STK2, se20-9, KIAA0204	uc001kxo.1	Q9H2G2	OTTHUMG00000018999	ENST00000369755.3:c.918G>T	10.37:g.105761255G>T	ENSP00000358770:p.Glu306Asp		105751245	NM_014720	D3DRA0|D3DRA1|O00211|Q6P1Z4|Q86WU7|Q86WW1|Q92603|Q9NQL0|Q9NQL1	Missense_Mutation	SNP	ENST00000369755.3	37	CCDS7553.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.178511	0.78564	.	.	ENSG00000065613	ENST00000335753;ENST00000369755	T;T	0.21932	1.98;1.98	5.33	0.23	0.15372	Protein kinase-like domain (1);	0.050951	0.85682	D	0.000000	T	0.41373	0.1156	M	0.81497	2.545	0.80722	D	1	D;P	0.58970	0.984;0.752	D;P	0.65140	0.932;0.626	T	0.34153	-0.9840	10	0.66056	D	0.02	.	10.1877	0.43009	0.4859:0.0:0.5141:0.0	.	306;306	Q9H2G2-2;Q9H2G2	.;SLK_HUMAN	D	306	ENSP00000336824:E306D;ENSP00000358770:E306D	ENSP00000336824:E306D	E	+	3	2	SLK	105751245	1.000000	0.71417	0.999000	0.59377	0.978000	0.69477	0.494000	0.22467	0.065000	0.16485	0.462000	0.41574	GAG		0.378	SLK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050188.1	NM_014720	
SORCS3	22986	broad.mit.edu	37	10	106918670	106918670	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:106918670G>A	ENST00000369701.3	+	11	1877	c.1650G>A	c.(1648-1650)ctG>ctA	p.L550L		NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	550					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)	p.L550L(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		CCTTACATCTGCACCTGCAAC	0.468																																					p.L550L	NSCLC(116;1497 1690 7108 13108 14106)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1650A	10						.						111.0	94.0	100.0					10																	106918670		2203	4300	6503	106908660	SO:0001819	synonymous_variant	22986	exon11			AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.1650G>A	10.37:g.106918670G>A			106908660	NM_014978	Q5VXF9|Q9NQJ2	Silent	SNP	ENST00000369701.3	37	CCDS7558.1																																																																																				0.468	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978	
DIP2C	22982	broad.mit.edu	37	10	459992	459992	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:459992G>A	ENST00000280886.6	-	8	1005	c.918C>T	c.(916-918)cgC>cgT	p.R306R	DIP2C_ENST00000381496.3_Silent_p.R199R	NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	306						nucleus (GO:0005634)	catalytic activity (GO:0003824)	p.R306R(1)		breast(8)|endometrium(6)|kidney(10)|large_intestine(13)|lung(26)|ovary(3)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	81		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		GCTGCTCTCCGCGCATGGCCA	0.612																																					p.R306R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C918T	10						.						46.0	50.0	48.0					10																	459992		2202	4300	6502	449992	SO:0001819	synonymous_variant	22982	exon8			BC035216	CCDS7054.1	10p15.3	2006-01-13	2006-01-13	2006-01-13	ENSG00000151240	ENSG00000151240			29150	protein-coding gene	gene with protein product		611380	"""KIAA0934"""	KIAA0934			Standard	NM_014974		Approved		uc001ifp.3	Q9Y2E4	OTTHUMG00000017532	ENST00000280886.6:c.918C>T	10.37:g.459992G>A			449992	NM_014974	B4DPI5|Q5SS78	Silent	SNP	ENST00000280886.6	37	CCDS7054.1																																																																																				0.612	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974	
LARP4B	23185	broad.mit.edu	37	10	859147	859147	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:859147G>A	ENST00000316157.3	-	17	1976	c.1936C>T	c.(1936-1938)Cga>Tga	p.R646*	LARP4B_ENST00000469487.1_5'Flank	NM_015155.1	NP_055970.1	Q92615	LAR4B_HUMAN	La ribonucleoprotein domain family, member 4B	646					positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)	p.R646*(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(2)|skin(2)|urinary_tract(2)	38						CTGGGCTTTCGCAATTCCTGG	0.438																																					p.R646X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1936T	10						.						70.0	72.0	71.0					10																	859147		2203	4300	6503	849147	SO:0001587	stop_gained	23185	exon17			D86971	CCDS31131.1	10p15.3	2011-08-24	2009-06-09	2009-06-09	ENSG00000107929	ENSG00000107929		"""La ribonucleoprotein domain containing"""	28987	protein-coding gene	gene with protein product			"""KIAA0217"", ""La ribonucleoprotein domain family, member 5"""	KIAA0217, LARP5		9039502, 20573744	Standard	NM_015155		Approved		uc031ptb.1	Q92615	OTTHUMG00000017534	ENST00000316157.3:c.1936C>T	10.37:g.859147G>A	ENSP00000326128:p.Arg646*		849147	NM_015155	A7MD20|Q5T3R3|Q5T3R4|Q5T3R5|Q68CY4	Nonsense_Mutation	SNP	ENST00000316157.3	37	CCDS31131.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	36|36	5.894441|5.894441	0.97074|0.97074	.|.	.|.	ENSG00000107929|ENSG00000107929	ENST00000448368|ENST00000316157	.|.	.|.	.|.	6.07|6.07	1.4|1.4	0.22301|0.22301	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.42381|.	0.1200|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.29366|.	-1.0014|.	4|.	.|0.02654	.|T	.|1	5.9413|5.9413	16.7557|16.7557	0.85498|0.85498	0.0:0.0:0.4504:0.5496|0.0:0.0:0.4504:0.5496	.|.	.|.	.|.	.|.	V|X	246|646	.|.	.|ENSP00000326128:R646X	A|R	-|-	2|1	0|2	LARP4B|LARP4B	849147|849147	0.999000|0.999000	0.42202|0.42202	0.997000|0.997000	0.53966|0.53966	0.713000|0.713000	0.41058|0.41058	1.151000|1.151000	0.31651|0.31651	0.360000|0.360000	0.24265|0.24265	0.655000|0.655000	0.94253|0.94253	GCG|CGA		0.438	LARP4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046395.2	NM_015155	
NET1	10276	broad.mit.edu	37	10	5498100	5498100	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:5498100C>T	ENST00000355029.4	+	11	1390	c.1248C>T	c.(1246-1248)gtC>gtT	p.V416V	NET1_ENST00000484741.1_3'UTR|NET1_ENST00000380359.3_Silent_p.V362V|NET1_ENST00000542715.1_Silent_p.V235V	NM_001047160.2	NP_001040625.1	Q7Z628	ARHG8_HUMAN	neuroepithelial cell transforming 1	416	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to ionizing radiation (GO:0071479)|myoblast migration (GO:0051451)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.V362V(1)|p.V416V(1)		breast(4)|kidney(2)|large_intestine(9)|lung(5)|prostate(2)|skin(1)	23						CTCGGCCCGTCACACGGAACG	0.468																																					p.V362V												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1086T	10						.						88.0	90.0	89.0					10																	5498100		2203	4300	6503	5488100	SO:0001819	synonymous_variant	10276	exon9			AJ010046	CCDS7067.1, CCDS41483.1	10p15	2013-01-10	2008-09-12		ENSG00000173848	ENSG00000173848		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	14592	protein-coding gene	gene with protein product		606450				8649828	Standard	NR_073040		Approved	ARHGEF8, NET1A	uc001iia.4	Q7Z628	OTTHUMG00000017596	ENST00000355029.4:c.1248C>T	10.37:g.5498100C>T			5488100	NM_005863	Q12773|Q96D82|Q99903|Q9UEN6	Silent	SNP	ENST00000355029.4	37	CCDS41483.1																																																																																				0.468	NET1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000046553.3	NM_005863	
CALML5	51806	broad.mit.edu	37	10	5541131	5541131	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:5541131C>T	ENST00000380332.3	-	1	402	c.271G>A	c.(271-273)Gac>Aac	p.D91N		NM_017422.4	NP_059118.2	Q9NZT1	CALL5_HUMAN	calmodulin-like 5	91	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				epidermis development (GO:0008544)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.D91N(1)		biliary_tract(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|stomach(1)	8						CCATCCTGGTCGAAGGCGCGG	0.706																																					p.D91N	GBM(149;1055 3356 43077)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G271A	10						.						27.0	28.0	28.0					10																	5541131		2203	4299	6502	5531131	SO:0001583	missense	51806	exon1			AF172852	CCDS7068.1	10p15.1	2013-01-10			ENSG00000178372	ENSG00000178372		"""EF-hand domain containing"""	18180	protein-coding gene	gene with protein product	"""calmodulin-like skin protein"""	605183				10777582	Standard	NM_017422		Approved	CLSP	uc001iic.2	Q9NZT1	OTTHUMG00000017598	ENST00000380332.3:c.271G>A	10.37:g.5541131C>T	ENSP00000369689:p.Asp91Asn		5531131	NM_017422	Q5SQI3|Q8IXU8	Missense_Mutation	SNP	ENST00000380332.3	37	CCDS7068.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.153505	0.78114	.	.	ENSG00000178372	ENST00000380332	D	0.95821	-3.82	4.68	4.68	0.58851	EF-hand-like domain (1);	0.000000	0.64402	D	0.000011	D	0.98280	0.9430	H	0.94423	3.535	0.54753	D	0.999987	D	0.89917	1.0	D	0.85130	0.997	D	0.99123	1.0850	10	0.87932	D	0	-69.2141	15.1975	0.73104	0.0:1.0:0.0:0.0	.	91	Q9NZT1	CALL5_HUMAN	N	91	ENSP00000369689:D91N	ENSP00000369689:D91N	D	-	1	0	CALML5	5531131	1.000000	0.71417	0.377000	0.26055	0.208000	0.24298	5.253000	0.65452	2.535000	0.85469	0.655000	0.94253	GAC		0.706	CALML5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046556.1	NM_017422	
FBXO18	84893	broad.mit.edu	37	10	5937117	5937117	+	Intron	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:5937117G>A	ENST00000362091.4	+	1	116				FBXO18_ENST00000470089.1_Intron|FBXO18_ENST00000379999.5_Missense_Mutation_p.A41T|FBXO18_ENST00000397269.3_Intron	NM_001258453.1|NM_178150.2	NP_001245382.1|NP_835363.1	Q8NFZ0	FBX18_HUMAN	F-box protein, helicase, 18						DNA catabolic process, endonucleolytic (GO:0000737)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|positive regulation of protein phosphorylation (GO:0001934)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)	p.A41T(1)		NS(2)|breast(2)|kidney(2)|large_intestine(16)|lung(9)|ovary(2)|prostate(3)|skin(3)|stomach(1)	40						GAGGACGAGTGCCCACTTGCT	0.542																																					p.A41T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G121A	10						.						66.0	58.0	61.0					10																	5937117		2203	4300	6503	5977123	SO:0001627	intron_variant	84893	exon2			AK095343	CCDS7072.1, CCDS7073.1, CCDS73064.1	10p15.1	2004-08-24	2004-06-15		ENSG00000134452	ENSG00000134452		"""F-boxes /  ""other"""""	13620	protein-coding gene	gene with protein product		607222	"""F-box only protein 18"""			10531037, 11956208	Standard	NM_032807		Approved	FBH1, FLJ14590, Fbx18	uc001iit.4	Q8NFZ0	OTTHUMG00000017609	ENST00000362091.4:c.1+4808G>A	10.37:g.5937117G>A			5977123	NM_032807	Q5JVB0|Q5JVB1|Q7Z4Q6|Q7Z4R0|Q8N1P5|Q8N586|Q96E82|Q96K67|Q96SW7|Q9UFB2	Missense_Mutation	SNP	ENST00000362091.4	37	CCDS7072.1	.	.	.	.	.	.	.	.	.	.	G	12.55	1.970716	0.34754	.	.	ENSG00000134452	ENST00000379999	.	.	.	3.78	-0.0978	0.13631	.	1.628900	0.04297	N	0.346721	T	0.29288	0.0729	.	.	.	0.09310	N	0.999999	B	0.18310	0.027	B	0.19391	0.025	T	0.21930	-1.0231	8	0.35671	T	0.21	0.0442	6.119	0.20142	0.4574:0.0:0.5426:0.0	.	41	Q8NFZ0-2	.	T	41	.	ENSP00000369335:A41T	A	+	1	0	FBXO18	5977123	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	0.211000	0.17474	-0.019000	0.14055	0.655000	0.94253	GCC		0.542	FBXO18-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046596.1	NM_032807	
PRKCQ	5588	broad.mit.edu	37	10	6470269	6470269	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:6470269C>T	ENST00000263125.5	-	18	2120	c.2021G>A	c.(2020-2022)cGg>cAg	p.R674Q	PRKCQ_ENST00000397176.2_Missense_Mutation_p.R611Q|PRKCQ_ENST00000539722.1_Missense_Mutation_p.R549Q	NM_001282644.1|NM_006257.3	NP_001269573.1|NP_006248.1	Q04759	KPCT_HUMAN	protein kinase C, theta	674	AGC-kinase C-terminal.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of T cell apoptotic process (GO:0070233)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of T-helper 2 cell activation (GO:2000570)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of transcription, DNA-templated (GO:0006355)|rhodopsin mediated signaling pathway (GO:0016056)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)	p.R674Q(1)		NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(2)	45					Tamoxifen(DB00675)	AAATGACAGCCGGGGCTTCTC	0.443																																					p.R674Q	Ovarian(50;572 1126 10530 25349 30594)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2021A	10						.						200.0	209.0	206.0					10																	6470269		2203	4300	6503	6510275	SO:0001583	missense	5588	exon18			L07032	CCDS7079.1, CCDS55701.1, CCDS60482.1	10p15	2009-07-10			ENSG00000065675	ENSG00000065675	2.7.11.1		9410	protein-coding gene	gene with protein product		600448				8444877	Standard	NM_001282645		Approved		uc001ijj.2	Q04759	OTTHUMG00000017623	ENST00000263125.5:c.2021G>A	10.37:g.6470269C>T	ENSP00000263125:p.Arg674Gln		6510275	NM_006257	B4DF52|Q14DH6|Q3MJF1|Q64FY5|Q9H508|Q9H549	Missense_Mutation	SNP	ENST00000263125.5	37	CCDS7079.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.02|16.02	3.003629|3.003629	0.54254|0.54254	.|.	.|.	ENSG00000065675|ENSG00000065675	ENST00000397178|ENST00000263125;ENST00000397176;ENST00000539722	.|T;T;T	.|0.53423	.|0.62;0.62;0.62	5.56|5.56	5.56|5.56	0.83823|0.83823	.|Protein kinase, C-terminal (1);AGC-kinase, C-terminal (2);Protein kinase-like domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.57431|0.57431	0.2053|0.2053	L|L	0.31476|0.31476	0.935|0.935	0.80722|0.80722	D|D	1|1	.|B;P;D;D	.|0.89917	.|0.344;0.778;0.985;1.0	.|B;B;P;D	.|0.79108	.|0.052;0.11;0.63;0.992	T|T	0.49123|0.49123	-0.8972|-0.8972	5|10	.|0.20519	.|T	.|0.43	.|.	19.1513|19.1513	0.93491|0.93491	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|549;446;611;674	.|B4DF52;Q5JUN8;Q04759-2;Q04759	.|.;.;.;KPCT_HUMAN	S|Q	447|674;611;549	.|ENSP00000263125:R674Q;ENSP00000380361:R611Q;ENSP00000441752:R549Q	.|ENSP00000263125:R674Q	G|R	-|-	1|2	0|0	PRKCQ|PRKCQ	6510275|6510275	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.080000|0.080000	0.17528|0.17528	3.654000|3.654000	0.54453|0.54453	2.614000|2.614000	0.88457|0.88457	0.561000|0.561000	0.74099|0.74099	GGC|CGG		0.443	PRKCQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046665.1	NM_006257	
ITIH5	80760	broad.mit.edu	37	10	7679251	7679251	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:7679251C>T	ENST00000256861.6	-	5	670	c.592G>A	c.(592-594)Gca>Aca	p.A198T	ITIH5_ENST00000397145.2_Missense_Mutation_p.A198T|ITIH5_ENST00000434980.1_5'UTR|ITIH5_ENST00000397146.2_Missense_Mutation_p.A198T|ITIH5_ENST00000446830.2_5'UTR	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	198					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.A198T(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						TCCAGGGATGCGATGCCCGCG	0.657																																					p.A198T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G592A	10						.						74.0	75.0	75.0					10																	7679251		2203	4300	6503	7719257	SO:0001583	missense	80760	exon5					10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"""inter-alpha (globulin) inhibitor H5"""			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.592G>A	10.37:g.7679251C>T	ENSP00000256861:p.Ala198Thr		7719257	NM_030569	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Missense_Mutation	SNP	ENST00000256861.6	37		.	.	.	.	.	.	.	.	.	.	C	1.318	-0.600312	0.03744	.	.	ENSG00000123243	ENST00000256861;ENST00000397146;ENST00000397145	T;T;T	0.02323	4.85;4.34;4.34	5.88	-2.99	0.05497	.	1.028080	0.07646	N	0.931097	T	0.01800	0.0057	.	.	.	0.09310	N	1	B;B	0.17852	0.024;0.002	B;B	0.18263	0.021;0.001	T	0.48559	-0.9025	9	0.30078	T	0.28	-5.3303	1.9961	0.03457	0.1975:0.2695:0.0974:0.4357	.	198;198	G5E9D8;Q86UX2	.;ITIH5_HUMAN	T	198	ENSP00000256861:A198T;ENSP00000380333:A198T;ENSP00000380332:A198T	ENSP00000256861:A198T	A	-	1	0	ITIH5	7719257	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.144000	0.03197	-0.524000	0.06400	-0.140000	0.14226	GCA		0.657	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569	
ITIH2	3698	broad.mit.edu	37	10	7774342	7774342	+	Silent	SNP	C	C	T	rs553454623		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:7774342C>T	ENST00000358415.4	+	14	1855	c.1689C>T	c.(1687-1689)gaC>gaT	p.D563D	ITIH2_ENST00000379587.4_Silent_p.D552D	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	563					hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.D563D(1)		NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						CCCAGATGGACGACTTGCAGG	0.463																																					p.D563D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1689T	10						.						95.0	84.0	88.0					10																	7774342		2203	4300	6503	7814348	SO:0001819	synonymous_variant	3698	exon14			X07173	CCDS31141.1	10p14	2011-10-26	2011-10-26		ENSG00000151655	ENSG00000151655			6167	protein-coding gene	gene with protein product		146640	"""inter-alpha (globulin) inhibitor, H2 polypeptide"""			1385302, 10100603	Standard	NM_002216		Approved	H2P	uc001ijs.3	P19823	OTTHUMG00000017633	ENST00000358415.4:c.1689C>T	10.37:g.7774342C>T			7814348	NM_002216	Q14659|Q15484|Q5T986	Silent	SNP	ENST00000358415.4	37	CCDS31141.1																																																																																				0.463	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216	
FRMD4A	55691	broad.mit.edu	37	10	13698868	13698868	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:13698868C>T	ENST00000357447.2	-	22	3089	c.2721G>A	c.(2719-2721)ccG>ccA	p.P907P	FRMD4A_ENST00000358621.4_Silent_p.P892P|FRMD4A_ENST00000378503.1_Silent_p.P907P	NM_018027.3	NP_060497.3	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A	907					establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)		p.P907P(1)		breast(4)|endometrium(9)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	41						GGCCCAGCGACGGAGTCCGCA	0.756																																					p.P907P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2721A	10						.						11.0	14.0	13.0					10																	13698868		2105	3999	6104	13738874	SO:0001819	synonymous_variant	55691	exon22			AB037715	CCDS7101.1	10p14	2004-07-15	2004-07-15	2004-07-15	ENSG00000151474	ENSG00000151474			25491	protein-coding gene	gene with protein product			"""FERM domain containing 4"""	FRMD4		10718198	Standard	NM_018027		Approved	FLJ10210, KIAA1294, bA295P9.4	uc001ims.3	Q9P2Q2	OTTHUMG00000017708	ENST00000357447.2:c.2721G>A	10.37:g.13698868C>T			13738874	NM_018027	A7E2Y3|Q5T377	Silent	SNP	ENST00000357447.2	37	CCDS7101.1																																																																																				0.756	FRMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046889.1	NM_018027	
CACNB2	783	broad.mit.edu	37	10	18828550	18828550	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:18828550G>A	ENST00000324631.7	+	14	1940	c.1880G>A	c.(1879-1881)cGt>cAt	p.R627H	CACNB2_ENST00000377315.4_Missense_Mutation_p.R579H|CACNB2_ENST00000282343.8_Missense_Mutation_p.R599H|CACNB2_ENST00000396576.2_Missense_Mutation_p.R572H|RP11-499P20.2_ENST00000436485.1_RNA|CACNB2_ENST00000352115.6_Missense_Mutation_p.R603H|RP11-499P20.2_ENST00000425669.1_RNA|CACNB2_ENST00000377329.4_Missense_Mutation_p.R573H|CACNB2_ENST00000377331.2_Missense_Mutation_p.R575H|CACNB2_ENST00000377328.1_Missense_Mutation_p.R377H|CACNB2_ENST00000377319.3_Missense_Mutation_p.R534H	NM_201593.2|NM_201596.2	NP_963887.2|NP_963890.2	Q08289	CACB2_HUMAN	calcium channel, voltage-dependent, beta 2 subunit	627					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|neuromuscular junction development (GO:0007528)|positive regulation of calcium ion transport (GO:0051928)|synaptic transmission (GO:0007268)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|voltage-gated calcium channel complex (GO:0005891)	calcium channel activity (GO:0005262)|voltage-gated calcium channel activity (GO:0005245)	p.R572H(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(12)|prostate(1)|skin(3)|stomach(2)	31					Amlodipine(DB00381)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CAGCGCAGCCGTCATAAATCC	0.547																																					p.R627H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1880A	10						.						70.0	64.0	66.0					10																	18828550		2203	4300	6503	18868556	SO:0001583	missense	783	exon14			U95019	CCDS7125.1, CCDS7126.1, CCDS7127.1, CCDS7128.1, CCDS7129.1, CCDS41493.1, CCDS41494.1	10p12	2014-09-17			ENSG00000165995	ENSG00000165995		"""Calcium channel subunits"""	1402	protein-coding gene	gene with protein product		600003		MYSB, CACNLB2		9254841, 8494331	Standard	NM_201596		Approved		uc001ipr.2	Q08289	OTTHUMG00000017764	ENST00000324631.7:c.1880G>A	10.37:g.18828550G>A	ENSP00000320025:p.Arg627His		18868556	NM_201596	A6PVM5|A6PVM7|A6PVM8|O00304|Q5QJ99|Q5QJA0|Q5VVG9|Q5VVH0|Q5VWV6|Q6TME1|Q6TME2|Q6TME3|Q8WX81|Q96NZ3|Q96NZ4|Q96NZ5|Q9BWU2|Q9HD32|Q9Y340|Q9Y341	Missense_Mutation	SNP	ENST00000324631.7	37	CCDS7125.1	.	.	.	.	.	.	.	.	.	.	G	16.71	3.197455	0.58126	.	.	ENSG00000165995	ENST00000324631;ENST00000352115;ENST00000377328;ENST00000282343;ENST00000377331;ENST00000396576;ENST00000377319;ENST00000377329;ENST00000377315	D;T;D;D;T;D;D;D;D	0.85556	-1.85;1.94;-2.0;-1.83;1.94;-1.92;-1.89;-1.92;-1.92	5.7	5.7	0.88788	.	0.075439	0.53938	D	0.000045	D	0.86251	0.5888	N	0.11064	0.09	0.58432	D	0.999995	D;D;D;D;D;B;D;D;D;D;B;D;D	0.89917	0.998;1.0;1.0;1.0;1.0;0.136;1.0;1.0;1.0;1.0;0.025;1.0;1.0	D;D;D;D;D;B;D;D;D;D;B;D;D	0.87578	0.976;0.992;0.992;0.992;0.964;0.021;0.992;0.996;0.996;0.997;0.007;0.998;0.992	D	0.88348	0.2979	10	0.52906	T	0.07	-12.6196	19.8389	0.96675	0.0:0.0:1.0:0.0	.	541;599;377;579;549;573;583;534;575;599;589;603;627	B7Z1U5;Q5QJA0;A6PVM6;Q5VVH1;Q6TME1;Q08289-3;Q59H42;Q08289-6;A6PVM7;Q08289-4;Q08289-7;Q08289-8;Q08289	.;.;.;.;.;.;.;.;.;.;.;.;CACB2_HUMAN	H	627;603;377;599;575;572;534;573;579	ENSP00000320025:R627H;ENSP00000344474:R603H;ENSP00000366545:R377H;ENSP00000282343:R599H;ENSP00000366548:R575H;ENSP00000379821:R572H;ENSP00000366536:R534H;ENSP00000366546:R573H;ENSP00000366532:R579H	ENSP00000282343:R599H	R	+	2	0	CACNB2	18868556	1.000000	0.71417	0.991000	0.47740	0.982000	0.71751	4.748000	0.62148	2.703000	0.92315	0.655000	0.94253	CGT		0.547	CACNB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047072.2	NM_000724	
NEBL	10529	broad.mit.edu	37	10	21124457	21124457	+	Silent	SNP	T	T	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:21124457T>A	ENST00000377122.4	-	14	1830	c.1434A>T	c.(1432-1434)gcA>gcT	p.A478A	NEBL_ENST00000417816.2_Intron|NEBL_ENST00000377159.4_Intron	NM_006393.2	NP_006384.1	O76041	NEBL_HUMAN	nebulette	478					cardiac muscle thin filament assembly (GO:0071691)	extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|filamin binding (GO:0031005)|structural constituent of muscle (GO:0008307)|tropomyosin binding (GO:0005523)	p.A478A(1)		NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						TCGCTATCTCTGCAGCCTTCT	0.423																																					p.A478A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1434T	10						.						247.0	223.0	231.0					10																	21124457		2203	4300	6503	21164463	SO:0001819	synonymous_variant	10529	exon14			Y16241	CCDS7133.1, CCDS7134.1	10p12	2014-09-17			ENSG00000078114	ENSG00000078114			16932	protein-coding gene	gene with protein product		605491				9733644, 10470015	Standard	NM_213569		Approved		uc001iqi.3	O76041	OTTHUMG00000017788	ENST00000377122.4:c.1434A>T	10.37:g.21124457T>A			21164463	NM_006393	B0YJ45|Q2TBD0|Q70I54|Q9UIC4	Silent	SNP	ENST00000377122.4	37	CCDS7134.1																																																																																				0.423	NEBL-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047113.1	NM_006393	
KIAA1217	56243	broad.mit.edu	37	10	24816887	24816887	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:24816887delA	ENST00000376454.3	+	14	2951	c.2921delA	c.(2920-2922)gaafs	p.E974fs	KIAA1217_ENST00000458595.1_Frame_Shift_Del_p.E939fs|KIAA1217_ENST00000376462.1_Frame_Shift_Del_p.E894fs|KIAA1217_ENST00000307544.6_Frame_Shift_Del_p.E657fs|KIAA1217_ENST00000396445.1_Frame_Shift_Del_p.E657fs|KIAA1217_ENST00000430453.2_3'UTR|KIAA1217_ENST00000376452.3_Frame_Shift_Del_p.E939fs|KIAA1217_ENST00000396446.1_Frame_Shift_Del_p.E657fs|KIAA1217_ENST00000376451.2_Frame_Shift_Del_p.E657fs	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	974					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)		p.R976fs*8(1)|p.R976fs*16(1)		breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						AAATGGGAGGAAAAAAGGCAA	0.433																																					p.E974fs												.	.	2	Deletion - Frameshift(1)|Insertion - Frameshift(1)	large_intestine(2)	c.2921delA	10						.						108.0	109.0	108.0					10																	24816887		2203	4300	6503	24856893	SO:0001589	frameshift_variant	56243	exon14			BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"""sickle tail"""					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.2921delA	10.37:g.24816887delA	ENSP00000365637:p.Glu974fs		24856893	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Frame_Shift_Del	DEL	ENST00000376454.3	37	CCDS31165.1																																																																																				0.433	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590	
APBB1IP	54518	broad.mit.edu	37	10	26800769	26800769	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:26800769G>A	ENST00000376236.4	+	7	1080	c.625G>A	c.(625-627)Gag>Aag	p.E209K	RNA5SP307_ENST00000362863.1_RNA	NM_019043.3	NP_061916.3	Q7Z5R6	AB1IP_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	209	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				blood coagulation (GO:0007596)|platelet activation (GO:0030168)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)		p.E209K(1)|p.E209*(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(27)|skin(7)|upper_aerodigestive_tract(1)	45						CAACCTTTTCGAGAAAACTCA	0.483																																					p.E209K												APBB1IP,lung,NS,Substitution - Nonsense,0 	.	2	Substitution - Nonsense(1)|Substitution - Missense(1)	large_intestine(1)|lung(1)	c.G625A	10						.						156.0	146.0	149.0					10																	26800769		2203	4300	6503	26840775	SO:0001583	missense	54518	exon7			AB085852	CCDS31167.1	10p12.1	2013-01-10			ENSG00000077420	ENSG00000077420		"""Pleckstrin homology (PH) domain containing"""	17379	protein-coding gene	gene with protein product	"""Rap1-GTP-interacting adaptor molecule"""	609036				9407065	Standard	NM_019043		Approved	INAG1, RIAM	uc001iss.3	Q7Z5R6	OTTHUMG00000017841	ENST00000376236.4:c.625G>A	10.37:g.26800769G>A	ENSP00000365411:p.Glu209Lys		26840775	NM_019043	Q8IWS8|Q8IYL7|Q8IZZ7	Missense_Mutation	SNP	ENST00000376236.4	37	CCDS31167.1	.	.	.	.	.	.	.	.	.	.	G	35	5.533936	0.96460	.	.	ENSG00000077420	ENST00000445780;ENST00000376236	T	0.17213	2.29	5.65	5.65	0.86999	Ras-association (3);	0.043784	0.85682	D	0.000000	T	0.45856	0.1363	M	0.78801	2.425	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.75484	0.968;0.986	T	0.25537	-1.0129	10	0.41790	T	0.15	.	19.717	0.96124	0.0:0.0:1.0:0.0	.	209;209	B4E100;Q7Z5R6	.;AB1IP_HUMAN	K	209	ENSP00000365411:E209K	ENSP00000365411:E209K	E	+	1	0	APBB1IP	26840775	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.455000	0.97625	2.661000	0.90470	0.655000	0.94253	GAG		0.483	APBB1IP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047270.1	NM_019043	
PTCHD3	374308	broad.mit.edu	37	10	27692218	27692218	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:27692218A>C	ENST00000438700.3	-	3	1397	c.1280T>G	c.(1279-1281)gTg>gGg	p.V427G		NM_001034842.3	NP_001030014.2	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	427	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|sperm midpiece (GO:0097225)	hedgehog receptor activity (GO:0008158)	p.V427G(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	55						AAAGCCGCTCACCACTGCCAA	0.438																																					p.V427G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1280G	10						.						135.0	125.0	129.0					10																	27692218		2203	4300	6503	27732224	SO:0001583	missense	374308	exon3			AK126025	CCDS31173.1	10p12.1	2006-05-26			ENSG00000182077	ENSG00000182077			24776	protein-coding gene	gene with protein product		611791					Standard	NM_001034842		Approved	FLJ44037, PTR	uc001itu.2	Q3KNS1	OTTHUMG00000017860	ENST00000438700.3:c.1280T>G	10.37:g.27692218A>C	ENSP00000417658:p.Val427Gly		27732224	NM_001034842	I3L499|Q6ZU28	Missense_Mutation	SNP	ENST00000438700.3	37	CCDS31173.1	.	.	.	.	.	.	.	.	.	.	A	18.66	3.672689	0.67928	.	.	ENSG00000182077	ENST00000438700	D	0.92299	-3.01	4.09	4.09	0.47781	Sterol-sensing domain (1);	0.335103	0.28187	N	0.016273	D	0.93733	0.7997	M	0.77313	2.365	0.50313	D	0.999863	B	0.32862	0.387	P	0.45276	0.475	D	0.94338	0.7568	10	0.87932	D	0	-9.6919	13.2249	0.59909	1.0:0.0:0.0:0.0	.	427	Q3KNS1	PTHD3_HUMAN	G	427	ENSP00000417658:V427G	ENSP00000417658:V427G	V	-	2	0	PTCHD3	27732224	1.000000	0.71417	0.935000	0.37517	0.990000	0.78478	6.867000	0.75511	1.720000	0.51447	0.459000	0.35465	GTG		0.438	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541	
MKX	283078	broad.mit.edu	37	10	28030318	28030318	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:28030318C>T	ENST00000375790.5	-	3	736	c.304G>A	c.(304-306)Gag>Aag	p.E102K	MKX_ENST00000419761.1_Missense_Mutation_p.E102K			Q8IYA7	MKX_HUMAN	mohawk homeobox	102					collagen fibril organization (GO:0030199)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|positive regulation of collagen biosynthetic process (GO:0032967)|tendon cell differentiation (GO:0035990)|tendon sheath development (GO:0002932)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.E102K(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(2)|skin(2)	16						AGTATCTTCTCGGTCTTGGTG	0.602																																					p.E102K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G304A	10						.						181.0	135.0	150.0					10																	28030318		2203	4300	6503	28070324	SO:0001583	missense	283078	exon3			BC036207	CCDS7156.1	10p12.1	2011-06-20	2006-03-31	2006-03-31	ENSG00000150051	ENSG00000150051		"""Homeoboxes / TALE class"""	23729	protein-coding gene	gene with protein product		601332	"""chromosome 10 open reading frame 48"", ""iroquois homeobox protein-like 1"""	C10orf48, IRXL1		16408284	Standard	NM_173576		Approved	MGC39616	uc001itx.4	Q8IYA7	OTTHUMG00000017862	ENST00000375790.5:c.304G>A	10.37:g.28030318C>T	ENSP00000364946:p.Glu102Lys		28070324	NM_173576	B3KWM5	Missense_Mutation	SNP	ENST00000375790.5	37	CCDS7156.1	.	.	.	.	.	.	.	.	.	.	C	37	6.152070	0.97329	.	.	ENSG00000150051	ENST00000375790;ENST00000419761	D;D	0.85629	-2.01;-2.01	5.76	5.76	0.90799	Homeodomain-related (1);Homeobox (2);Homeobox KN domain (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.92211	0.7530	M	0.72624	2.21	0.80722	D	1	D	0.89917	1.0	D	0.72075	0.976	D	0.92347	0.5886	10	0.87932	D	0	-41.0287	19.9705	0.97284	0.0:1.0:0.0:0.0	.	102	Q8IYA7	MKX_HUMAN	K	102	ENSP00000364946:E102K;ENSP00000400896:E102K	ENSP00000364946:E102K	E	-	1	0	MKX	28070324	1.000000	0.71417	0.980000	0.43619	0.996000	0.88848	7.734000	0.84928	2.728000	0.93425	0.655000	0.94253	GAG		0.602	MKX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047332.3	NM_173576	
GDF2	2658	broad.mit.edu	37	10	48416404	48416404	+	Missense_Mutation	SNP	G	G	A	rs372529223		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:48416404G>A	ENST00000249598.1	-	1	449	c.290C>T	c.(289-291)aCg>aTg	p.T97M		NM_016204.1	NP_057288.1	Q9UK05	GDF2_HUMAN	growth differentiation factor 2	97					activin receptor signaling pathway (GO:0032924)|angiogenesis (GO:0001525)|blood vessel morphogenesis (GO:0048514)|BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|cellular iron ion homeostasis (GO:0006879)|cellular response to BMP stimulus (GO:0071773)|growth (GO:0040007)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of DNA replication (GO:0008156)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|ossification (GO:0001503)|osteoblast differentiation (GO:0001649)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.T97M(1)		breast(1)|endometrium(2)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	28						CTTATCGGACGTGTACCTGTT	0.582													G|||	1	0.000199681	0.0	0.0	5008	,	,		17934	0.0		0.0	False		,,,				2504	0.001				p.T97M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C290T	10						.	G	MET/THR	1,4405	2.1+/-5.4	0,1,2202	116.0	93.0	101.0		290	3.5	0.6	10		101	0,8600		0,0,4300	no	missense	GDF2	NM_016204.1	81	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	97/430	48416404	1,13005	2203	4300	6503	48036410	SO:0001583	missense	2658	exon1			AF156891	CCDS73118.1	10q11.22	2014-05-06			ENSG00000128802	ENSG00000263761		"""Endogenous ligands"""	4217	protein-coding gene	gene with protein product		605120				10849432	Standard	NM_016204		Approved	BMP-9, BMP9	uc001jfa.1	Q9UK05	OTTHUMG00000188320	ENST00000249598.1:c.290C>T	10.37:g.48416404G>A	ENSP00000249598:p.Thr97Met		48036410	NM_016204	Q5VSQ9|Q9Y571	Missense_Mutation	SNP	ENST00000249598.1	37	CCDS7219.1	.	.	.	.	.	.	.	.	.	.	G	10.60	1.394549	0.25205	2.27E-4	0.0	ENSG00000128802	ENST00000249598	T	0.65732	-0.17	5.37	3.45	0.39498	Transforming growth factor-beta, N-terminal (1);	0.299180	0.42548	D	0.000684	T	0.55657	0.1934	L	0.57536	1.79	0.39923	D	0.974186	B	0.20988	0.05	B	0.20384	0.029	T	0.53034	-0.8495	10	0.40728	T	0.16	.	9.9275	0.41501	0.1761:0.0:0.8239:0.0	.	97	Q9UK05	GDF2_HUMAN	M	97	ENSP00000249598:T97M	ENSP00000249598:T97M	T	-	2	0	GDF2	48036410	1.000000	0.71417	0.624000	0.29186	0.012000	0.07955	4.611000	0.61162	0.677000	0.31305	-0.137000	0.14449	ACG		0.582	GDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047891.1	NM_016204	
MAPK8	5599	broad.mit.edu	37	10	49633933	49633933	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:49633933A>G	ENST00000374189.1	+	8	872	c.691A>G	c.(691-693)Att>Gtt	p.I231V	MAPK8_ENST00000360332.3_Missense_Mutation_p.I231V|MAPK8_ENST00000374182.3_Missense_Mutation_p.I231V|MAPK8_ENST00000395611.3_Intron			P45983	MK08_HUMAN	mitogen-activated protein kinase 8	231	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nitric oxide (GO:0071732)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|JNK cascade (GO:0007254)|JUN phosphorylation (GO:0007258)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein binding (GO:0032091)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of deacetylase activity (GO:0090045)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of gene expression (GO:0010628)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|programmed necrotic cell death (GO:0097300)|regulation of histone deacetylation (GO:0031063)|regulation of protein localization (GO:0032880)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|response to cadmium ion (GO:0046686)|response to stress (GO:0006950)|response to UV (GO:0009411)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|JUN kinase activity (GO:0004705)|protein serine/threonine kinase activity (GO:0004674)	p.I231V(1)		breast(1)|central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(6)|liver(3)|lung(11)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	34		Ovarian(717;0.0221)|Lung SC(717;0.113)|all_neural(218;0.116)		Epithelial(53;3.46e-65)|Lung(62;0.125)		GATATTAGATATTGATCAGTG	0.303																																					p.I231V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A691G	10						.						82.0	78.0	79.0					10																	49633933		2203	4300	6503	49303939	SO:0001583	missense	5599	exon7			L26318	CCDS7223.1, CCDS7224.1, CCDS7225.1, CCDS7226.1, CCDS60527.1	10q11	2011-06-09			ENSG00000107643	ENSG00000107643	2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinases"""	6881	protein-coding gene	gene with protein product	"""JUN N-terminal kinase"""	601158		PRKM8		8137421, 8654373	Standard	NM_002750		Approved	JNK, JNK1, SAPK1	uc001jgp.3	P45983	OTTHUMG00000018172	ENST00000374189.1:c.691A>G	10.37:g.49633933A>G	ENSP00000363304:p.Ile231Val		49303939	NM_002750	B5BTZ5|B7ZLV4|D3DX88|D3DX92|Q15709|Q15712|Q15713|Q308M2	Missense_Mutation	SNP	ENST00000374189.1	37	CCDS7224.1	.	.	.	.	.	.	.	.	.	.	A	17.58	3.424583	0.62733	.	.	ENSG00000107643	ENST00000374189;ENST00000374182;ENST00000374179;ENST00000360332;ENST00000374176	T;T;T;T;T	0.64991	-0.13;-0.13;-0.13;-0.13;-0.13	5.73	5.73	0.89815	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.52141	0.1716	N	0.16656	0.425	0.80722	D	1	B;B;B;B	0.24576	0.032;0.106;0.045;0.013	B;B;B;B	0.32805	0.095;0.153;0.153;0.095	T	0.52177	-0.8610	10	0.51188	T	0.08	.	16.3123	0.82883	1.0:0.0:0.0:0.0	.	231;231;231;231	P45983-2;P45983;A1L4K2;P45983-3	.;MK08_HUMAN;.;.	V	231	ENSP00000363304:I231V;ENSP00000363297:I231V;ENSP00000363294:I231V;ENSP00000353483:I231V;ENSP00000363291:I231V	ENSP00000353483:I231V	I	+	1	0	MAPK8	49303939	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.287000	0.95975	2.308000	0.77769	0.533000	0.62120	ATT		0.303	MAPK8-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047931.1		
PCDH15	65217	broad.mit.edu	37	10	55587239	55587239	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:55587239C>T	ENST00000320301.6	-	32	4675	c.4281G>A	c.(4279-4281)ccG>ccA	p.P1427P	PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395433.1_Silent_p.P1402P|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000395445.1_Silent_p.P1434P|PCDH15_ENST00000414778.1_Silent_p.P1429P|PCDH15_ENST00000395432.2_Silent_p.P1387P|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000373965.2_Silent_p.P1434P|PCDH15_ENST00000437009.1_Silent_p.P1356P|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000395430.1_Silent_p.P1424P|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000395438.1_Silent_p.P1427P|PCDH15_ENST00000361849.3_Silent_p.P1427P|PCDH15_ENST00000409834.1_Silent_p.P1038P	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1427					equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)	p.P1427P(1)|p.P1432P(1)		NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				GTGCAGGAGCCGGCACTGCTG	0.567										HNSCC(58;0.16)																											p.P1387P												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G4161A	10						.						59.0	65.0	63.0					10																	55587239		2203	4300	6503	55257245	SO:0001819	synonymous_variant	65217	exon30			AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.4281G>A	10.37:g.55587239C>T			55257245	NM_001142767	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Silent	SNP	ENST00000320301.6	37	CCDS7248.1																																																																																				0.567	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056	
HERC4	26091	broad.mit.edu	37	10	69714393	69714393	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:69714393T>C	ENST00000395198.3	-	20	2567	c.2320A>G	c.(2320-2322)Agg>Ggg	p.R774G	HERC4_ENST00000277817.6_Missense_Mutation_p.R664G|HERC4_ENST00000373700.4_Missense_Mutation_p.R766G|HERC4_ENST00000412272.2_Missense_Mutation_p.R774G|HERC4_ENST00000395187.2_3'UTR|HERC4_ENST00000480158.1_5'UTR	NM_022079.2	NP_071362.1	Q5GLZ8	HERC4_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 4	774	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cell differentiation (GO:0030154)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.R774G(1)		NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	27						TCATAATACCTAAACATGCCG	0.368																																					p.R774G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2320G	10						.						117.0	114.0	115.0					10																	69714393		2203	4300	6503	69384399	SO:0001583	missense	26091	exon20			AY221963	CCDS7274.1, CCDS41533.1, CCDS60541.1, CCDS60542.1	10q21.3	2013-09-20	2012-02-23		ENSG00000148634	ENSG00000148634			24521	protein-coding gene	gene with protein product		609248	"""hect domain and RLD 4"""			10997877	Standard	NM_022079		Approved	DKFZP564G092, KIAA1593	uc001jng.4	Q5GLZ8	OTTHUMG00000018343	ENST00000395198.3:c.2320A>G	10.37:g.69714393T>C	ENSP00000378624:p.Arg774Gly		69384399	NM_022079	Q5GC98|Q5GC99|Q5GCA0|Q8IXP9|Q9HCH9	Missense_Mutation	SNP	ENST00000395198.3	37	CCDS41533.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.989995	0.74589	.	.	ENSG00000148634	ENST00000277817;ENST00000412272;ENST00000395198;ENST00000373700	T;T;T;T	0.57752	0.38;0.89;0.38;0.38	5.95	2.16	0.27623	HECT (4);	0.000000	0.85682	D	0.000000	T	0.67297	0.2878	M	0.61703	1.905	0.80722	D	1	D;P;P;P;P	0.67145	0.996;0.93;0.891;0.868;0.943	D;P;P;B;P	0.77557	0.99;0.646;0.719;0.391;0.674	T	0.67007	-0.5779	10	0.59425	D	0.04	.	13.471	0.61281	0.0:0.0:0.3753:0.6247	.	774;664;624;766;774	Q5GLZ8-3;Q5GLZ8-6;Q5VXS9;Q5GLZ8-2;Q5GLZ8	.;.;.;.;HERC4_HUMAN	G	664;774;774;766	ENSP00000277817:R664G;ENSP00000416504:R774G;ENSP00000378624:R774G;ENSP00000362804:R766G	ENSP00000277817:R664G	R	-	1	2	HERC4	69384399	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	2.206000	0.42779	0.113000	0.18004	0.533000	0.62120	AGG		0.368	HERC4-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359262.1	NM_015601	
DDX50	79009	broad.mit.edu	37	10	70673922	70673922	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:70673922G>A	ENST00000373585.3	+	7	1158	c.1051G>A	c.(1051-1053)Gtt>Att	p.V351I	RNU6-571P_ENST00000384128.1_RNA	NM_024045.1	NP_076950.1	Q9BQ39	DDX50_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 50	351						membrane (GO:0016020)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)	p.V351I(1)		breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	29						GGTTGACCTTGTTGGAAAAAT	0.353																																					p.V351I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1051A	10						.						65.0	61.0	62.0					10																	70673922		2203	4300	6503	70343928	SO:0001583	missense	79009	exon7			AF334103	CCDS7283.1	10q22.2	2010-09-30			ENSG00000107625	ENSG00000107625		"""DEAD-boxes"""	17906	protein-coding gene	gene with protein product		610373				11891046	Standard	NM_024045		Approved	GU2, MGC3199, GUB, RH-II/GuB	uc001jou.3	Q9BQ39	OTTHUMG00000018362	ENST00000373585.3:c.1051G>A	10.37:g.70673922G>A	ENSP00000362687:p.Val351Ile		70343928	NM_024045	Q5VX37|Q8WV76|Q9BWI8	Missense_Mutation	SNP	ENST00000373585.3	37	CCDS7283.1	.	.	.	.	.	.	.	.	.	.	G	3.950	-0.012451	0.07727	.	.	ENSG00000107625	ENST00000373585;ENST00000541832	T	0.22134	1.97	5.49	4.58	0.56647	DEAD-like helicase (1);	0.105878	0.64402	D	0.000003	T	0.10165	0.0249	N	0.13235	0.315	0.42146	D	0.99153	B;B	0.15930	0.015;0.0	B;B	0.20384	0.029;0.005	T	0.13845	-1.0494	10	0.06891	T	0.86	-12.6582	8.793	0.34863	0.1679:0.0:0.8321:0.0	.	351;351	Q9BQ39;B4DED6	DDX50_HUMAN;.	I	351	ENSP00000362687:V351I	ENSP00000362687:V351I	V	+	1	0	DDX50	70343928	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.933000	0.70130	2.745000	0.94114	0.462000	0.41574	GTT		0.353	DDX50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048363.1	NM_024045	
HK1	3098	broad.mit.edu	37	10	71119780	71119780	+	Silent	SNP	C	C	T	rs533615871		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:71119780C>T	ENST00000359426.6	+	3	458	c.354C>T	c.(352-354)atC>atT	p.I118I	HK1_ENST00000404387.2_Silent_p.I122I|HK1_ENST00000448642.2_Silent_p.I153I|HK1_ENST00000494253.1_3'UTR|HK1_ENST00000298649.3_Silent_p.I117I|HK1_ENST00000360289.2_Silent_p.I106I	NM_000188.2	NP_000179.2	P19367	HXK1_HUMAN	hexokinase 1	118	Hexokinase type-1 1.|Regulatory.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cell death (GO:0008219)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)	p.I122I(1)		breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(1)|urinary_tract(2)	35						CAGAGAACATCGTGCACGGCA	0.567																																					p.I122I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C366T	10						.						104.0	97.0	99.0					10																	71119780		2203	4300	6503	70789786	SO:0001819	synonymous_variant	3098	exon6			M75126	CCDS7289.1, CCDS7290.1, CCDS7291.1, CCDS7292.1	10q22	2014-09-17			ENSG00000156515	ENSG00000156515	2.7.1.1		4922	protein-coding gene	gene with protein product		142600					Standard	NM_033496		Approved		uc001jpi.4	P19367	OTTHUMG00000018380	ENST00000359426.6:c.354C>T	10.37:g.71119780C>T			70789786	NM_033498	E9PCK0|O43443|O43444|O75574|Q5VTC3|Q96HC8|Q9NNZ4|Q9NNZ5	Silent	SNP	ENST00000359426.6	37	CCDS7292.1																																																																																				0.567	HK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048429.2	NM_000188	
HK1	3098	broad.mit.edu	37	10	71160866	71160866	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:71160866G>A	ENST00000359426.6	+	18	2833	c.2729G>A	c.(2728-2730)cGg>cAg	p.R910Q	HK1_ENST00000404387.2_Missense_Mutation_p.R914Q|HK1_ENST00000448642.2_Missense_Mutation_p.R945Q|HK1_ENST00000298649.3_Missense_Mutation_p.R909Q|HK1_ENST00000360289.2_Missense_Mutation_p.R898Q	NM_000188.2	NP_000179.2	P19367	HXK1_HUMAN	hexokinase 1	910	Catalytic.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cell death (GO:0008219)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)	p.R914Q(1)		breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(1)|urinary_tract(2)	35						GTGGGCGTGCGGTTACGCACA	0.622																																					p.R914Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2741A	10						.						44.0	39.0	41.0					10																	71160866		2203	4300	6503	70830872	SO:0001583	missense	3098	exon21			M75126	CCDS7289.1, CCDS7290.1, CCDS7291.1, CCDS7292.1	10q22	2014-09-17			ENSG00000156515	ENSG00000156515	2.7.1.1		4922	protein-coding gene	gene with protein product		142600					Standard	NM_033496		Approved		uc001jpi.4	P19367	OTTHUMG00000018380	ENST00000359426.6:c.2729G>A	10.37:g.71160866G>A	ENSP00000352398:p.Arg910Gln		70830872	NM_033498	E9PCK0|O43443|O43444|O75574|Q5VTC3|Q96HC8|Q9NNZ4|Q9NNZ5	Missense_Mutation	SNP	ENST00000359426.6	37	CCDS7292.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.772690	0.90108	.	.	ENSG00000156515	ENST00000360289;ENST00000448642;ENST00000404387;ENST00000298649;ENST00000359426;ENST00000405407	D;D;D;D;D	0.98178	-4.77;-4.77;-4.77;-4.77;-4.77	5.78	4.88	0.63580	.	0.000000	0.85682	D	0.000000	D	0.98356	0.9454	L	0.55834	1.745	0.80722	D	1	D;D;D;D;B	0.89917	0.965;0.995;1.0;1.0;0.076	B;B;D;D;B	0.80764	0.321;0.421;0.994;0.992;0.003	D	0.98561	1.0641	10	0.38643	T	0.18	-18.1761	15.3547	0.74418	0.0674:0.0:0.9326:0.0	.	910;909;945;914;898	P19367;P19367-2;E7ENR4;P19367-3;P19367-4	HXK1_HUMAN;.;.;.;.	Q	898;945;914;909;910;910	ENSP00000353433:R898Q;ENSP00000402103:R945Q;ENSP00000384774:R914Q;ENSP00000298649:R909Q;ENSP00000352398:R910Q	ENSP00000298649:R909Q	R	+	2	0	HK1	70830872	1.000000	0.71417	0.983000	0.44433	0.930000	0.56654	3.243000	0.51392	1.582000	0.49881	0.655000	0.94253	CGG		0.622	HK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048429.2	NM_000188	
AIFM2	84883	broad.mit.edu	37	10	71874802	71874802	+	Missense_Mutation	SNP	C	C	T	rs151190502	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:71874802C>T	ENST00000307864.1	-	8	1057	c.844G>A	c.(844-846)Gcc>Acc	p.A282T	AIFM2_ENST00000373248.1_Missense_Mutation_p.A282T|AIFM2_ENST00000482166.1_5'UTR	NM_001198696.1|NM_032797.5	NP_001185625.1|NP_116186.1	Q9BRQ8	AIFM2_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 2	282					apoptotic mitochondrial changes (GO:0008637)|positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|electron-transferring-flavoprotein dehydrogenase activity (GO:0004174)|flavin adenine dinucleotide binding (GO:0050660)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)	p.A282T(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|skin(2)|urinary_tract(2)	16						TCACCAATGGCGTAGACGTTG	0.587													C|||	2	0.000399361	0.0	0.0	5008	,	,		20111	0.002		0.0	False		,,,				2504	0.0				p.A282T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G844A	10						.	C	THR/ALA,THR/ALA	3,4403	6.2+/-15.9	0,3,2200	94.0	65.0	75.0		844,844	5.9	1.0	10	dbSNP_134	75	0,8600		0,0,4300	no	missense,missense	AIFM2	NM_001198696.1,NM_032797.5	58,58	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	probably-damaging,probably-damaging	282/374,282/374	71874802	3,13003	2203	4300	6503	71544808	SO:0001583	missense	84883	exon8			AK027403	CCDS7297.1	10q22.2	2006-11-16	2006-11-16	2006-11-16	ENSG00000042286	ENSG00000042286			21411	protein-coding gene	gene with protein product		605159	"""apoptosis-inducing factor (AIF)-like mitochondrion-associated inducer of death"""	AMID		12135761, 11980907, 15958387	Standard	NM_001198696		Approved	FLJ14497, PRG3	uc001jqp.2	Q9BRQ8	OTTHUMG00000018398	ENST00000307864.1:c.844G>A	10.37:g.71874802C>T	ENSP00000312370:p.Ala282Thr		71544808	NM_001198696	B3KXI0|Q63Z39	Missense_Mutation	SNP	ENST00000307864.1	37	CCDS7297.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.337360	0.81911	6.81E-4	0.0	ENSG00000042286	ENST00000373248;ENST00000307864;ENST00000395039	T;T	0.62639	0.01;0.01	5.93	5.93	0.95920	Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.84889	0.5572	M	0.93328	3.405	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	D	0.87992	0.2750	10	0.87932	D	0	-30.1341	18.1421	0.89643	0.0:1.0:0.0:0.0	.	282	Q9BRQ8	AIFM2_HUMAN	T	282;282;245	ENSP00000362345:A282T;ENSP00000312370:A282T	ENSP00000312370:A282T	A	-	1	0	AIFM2	71544808	1.000000	0.71417	0.970000	0.41538	0.043000	0.13939	7.167000	0.77562	2.826000	0.97356	0.655000	0.94253	GCC		0.587	AIFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048487.1	NM_032797	
ANXA7	310	broad.mit.edu	37	10	75139869	75139869	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:75139869T>A	ENST00000372921.5	-	10	1065	c.1009A>T	c.(1009-1011)Acc>Tcc	p.T337S	RP11-537A6.9_ENST00000427492.1_RNA|ANXA7_ENST00000535178.1_Missense_Mutation_p.T207S	NM_001156.3	NP_001147.1	P20073	ANXA7_HUMAN	annexin A7	359					autophagy (GO:0006914)|cell proliferation (GO:0008283)|cellular calcium ion homeostasis (GO:0006874)|cellular water homeostasis (GO:0009992)|epithelial cell differentiation (GO:0030855)|hemostasis (GO:0007599)|membrane fusion (GO:0061025)|negative regulation of gene expression (GO:0010629)|regulation of cell shape (GO:0008360)|response to calcium ion (GO:0051592)|response to organic cyclic compound (GO:0014070)|response to salt stress (GO:0009651)|social behavior (GO:0035176)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|integrin binding (GO:0005178)|poly(A) RNA binding (GO:0044822)	p.T359S(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	26	Prostate(51;0.0119)					GATTCATCGGTCCCTAGTCTC	0.458																																					p.T337S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1009T	10						.						241.0	238.0	239.0					10																	75139869		2203	4300	6503	74809875	SO:0001583	missense	310	exon10			J04543	CCDS7325.1, CCDS7326.1	10q22.2	2005-11-09			ENSG00000138279	ENSG00000138279		"""Annexins"""	545	protein-coding gene	gene with protein product		186360		ANX7		7515686	Standard	NM_001156		Approved		uc001jtz.2	P20073	OTTHUMG00000018463	ENST00000372921.5:c.1009A>T	10.37:g.75139869T>A	ENSP00000362012:p.Thr337Ser		74809875	NM_001156	Q5F2H3|Q5T0M6|Q5T0M7	Missense_Mutation	SNP	ENST00000372921.5	37	CCDS7325.1	.	.	.	.	.	.	.	.	.	.	T	29.5	5.011615	0.93346	.	.	ENSG00000138279	ENST00000372921;ENST00000372919;ENST00000535178	T;T;T	0.05786	3.39;3.39;3.39	6.17	6.17	0.99709	Annexin repeat, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.30355	0.0762	M	0.87269	2.87	0.48341	D	0.99963	D;D;D;D;D	0.89917	0.998;1.0;1.0;0.997;0.998	D;D;D;D;D	0.91635	0.997;0.999;0.997;0.995;0.997	T	0.04664	-1.0935	10	0.62326	D	0.03	.	14.7743	0.69713	0.0:0.0:0.0:1.0	.	337;337;264;337;359	Q53HM8;B2R7L2;B4DWU2;P20073-2;P20073	.;.;.;.;ANXA7_HUMAN	S	337;359;207	ENSP00000362012:T337S;ENSP00000362010:T359S;ENSP00000442864:T207S	ENSP00000362010:T359S	T	-	1	0	ANXA7	74809875	1.000000	0.71417	0.997000	0.53966	0.936000	0.57629	6.193000	0.72075	2.371000	0.80710	0.533000	0.62120	ACC		0.458	ANXA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048646.2	NM_001156	
DYDC1	143241	broad.mit.edu	37	10	82098324	82098324	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:82098324C>T	ENST00000372204.3	-	7	567	c.403G>A	c.(403-405)Gca>Aca	p.A135T	DYDC1_ENST00000372202.1_Missense_Mutation_p.A135T|DYDC1_ENST00000421924.2_Missense_Mutation_p.A135T	NM_138812.3	NP_620167.1	Q8WWB3	DYDC1_HUMAN	DPY30 domain containing 1	135								p.A135T(1)		kidney(1)|large_intestine(3)|skin(1)	5			Colorectal(32;0.229)			TCTAGTGTTGCTTCCTACAAT	0.299																																					p.A135T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G403A	10						.						159.0	146.0	151.0					10																	82098324		2203	4300	6503	82088304	SO:0001583	missense	143241	exon7			BC019250	CCDS7366.1	10q22.3	2006-02-01			ENSG00000170788	ENSG00000170788			23460	protein-coding gene	gene with protein product		615154					Standard	NM_138812		Approved	bA36D19.5, DPY30D1	uc031pwj.1	Q8WWB3	OTTHUMG00000018609	ENST00000372204.3:c.403G>A	10.37:g.82098324C>T	ENSP00000361278:p.Ala135Thr		82088304	NM_138812	A8K927|Q5QP03|Q5QP04|Q6WNP4|Q6ZU87	Missense_Mutation	SNP	ENST00000372204.3	37	CCDS7366.1	.	.	.	.	.	.	.	.	.	.	C	7.165	0.586445	0.13749	.	.	ENSG00000170788	ENST00000372204;ENST00000372202;ENST00000421924;ENST00000454362	.	.	.	4.67	-1.37	0.09056	.	2.101280	0.01934	N	0.041446	T	0.28928	0.0718	L	0.36672	1.1	0.09310	N	1	B;B	0.23442	0.085;0.049	B;B	0.16722	0.016;0.01	T	0.04825	-1.0924	9	0.13470	T	0.59	0.3627	3.9995	0.09574	0.4887:0.3173:0.0:0.194	.	135;135	A8K927;Q8WWB3	.;DYDC1_HUMAN	T	135	.	ENSP00000361276:A135T	A	-	1	0	DYDC1	82088304	0.000000	0.05858	0.000000	0.03702	0.236000	0.25371	-0.531000	0.06171	-0.127000	0.11661	0.655000	0.94253	GCA		0.299	DYDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049059.1	NM_138812	
LRIT2	340745	broad.mit.edu	37	10	85985222	85985222	+	Missense_Mutation	SNP	C	C	T	rs199853938		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:85985222C>T	ENST00000372113.4	-	1	60	c.55G>A	c.(55-57)Gca>Aca	p.A19T	LRIT2_ENST00000538192.1_Missense_Mutation_p.A19T	NM_001017924.2	NP_001017924.1	A6NDA9	LRIT2_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 2	19						integral component of membrane (GO:0016021)		p.A19T(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|prostate(6)|urinary_tract(1)	32						GGCTGAGCTGCGTGTGTATCC	0.458													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18579	0.0		0.0	False		,,,				2504	0.0				p.A19T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G55A	10						.	C	THR/ALA	3,4403	6.2+/-15.9	0,3,2200	74.0	72.0	73.0		55	-2.4	0.0	10		73	0,8600		0,0,4300	yes	missense	LRIT2	NM_001017924.2	58	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	benign	19/551	85985222	3,13003	2203	4300	6503	85975202	SO:0001583	missense	340745	exon1				CCDS31234.1, CCDS60581.1	10q23.2	2013-01-11	2007-06-19	2007-06-19	ENSG00000204033	ENSG00000204033		"""Immunoglobulin superfamily / I-set domain containing"""	23443	protein-coding gene	gene with protein product			"""leucine rich repeat containing 22"""	LRRC22			Standard	NM_001017924		Approved	AC022389.4	uc001kcy.3	A6NDA9	OTTHUMG00000018633	ENST00000372113.4:c.55G>A	10.37:g.85985222C>T	ENSP00000361185:p.Ala19Thr		85975202	NM_001017924	B7ZME6	Missense_Mutation	SNP	ENST00000372113.4	37	CCDS31234.1	.	.	.	.	.	.	.	.	.	.	C	4.002	-0.002289	0.07819	6.81E-4	0.0	ENSG00000204033	ENST00000372113;ENST00000538192	T;T	0.61627	0.49;0.09	5.87	-2.39	0.06602	.	0.249770	0.30219	N	0.010139	T	0.30230	0.0758	L	0.31294	0.92	0.09310	N	1	B;B	0.14438	0.01;0.01	B;B	0.06405	0.002;0.002	T	0.06144	-1.0843	10	0.13853	T	0.58	.	0.6736	0.00863	0.2696:0.3249:0.1348:0.2707	.	19;19	B7ZME6;A6NDA9	.;LRIT2_HUMAN	T	19	ENSP00000361185:A19T;ENSP00000438264:A19T	ENSP00000361185:A19T	A	-	1	0	LRIT2	85975202	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.001000	0.13038	-0.072000	0.12864	-0.136000	0.14681	GCA		0.458	LRIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049110.4	XM_291697	
EXOC6	54536	broad.mit.edu	37	10	94654776	94654776	+	Splice_Site	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:94654776T>C	ENST00000260762.6	+	4	425	c.411T>C	c.(409-411)ccT>ccC	p.P137P	EXOC6_ENST00000371543.1_Splice_Site_p.P137P|EXOC6_ENST00000371547.4_Splice_Site_p.P153P|EXOC6_ENST00000443748.2_Splice_Site_p.P137P|EXOC6_ENST00000371552.4_Splice_Site_p.P132P	NM_019053.4	NP_061926.3	Q8TAG9	EXOC6_HUMAN	exocyst complex component 6	137					cellular protein metabolic process (GO:0044267)|erythrocyte differentiation (GO:0030218)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	exocyst (GO:0000145)|plasma membrane (GO:0005886)		p.P137P(1)|p.P132P(1)		cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	26		Colorectal(252;0.123)				TATGCCTTCCTGGTGAGTTAA	0.318																																					p.P132P												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T396C	10						.						138.0	150.0	146.0					10																	94654776		2203	4300	6503	94644756	SO:0001630	splice_region_variant	54536	exon4			BC028395	CCDS7424.2, CCDS31247.1	10q23.33	2013-01-22	2006-11-07	2006-11-07	ENSG00000138190	ENSG00000138190			23196	protein-coding gene	gene with protein product		609672	"""SEC15-like 1 (S. cerevisiae)"""	SEC15L1		8889548	Standard	NM_001013848		Approved	SEC15L, FLJ1125, DKFZp761I2124, MGC33397, Sec15p, EXOC6A	uc001kig.3	Q8TAG9	OTTHUMG00000018767	ENST00000260762.6:c.412+1T>C	10.37:g.94654776T>C			94644756	NM_001013848	E9PHI3|Q5VXH8|Q9NZ24	Silent	SNP	ENST00000260762.6	37	CCDS7424.2																																																																																				0.318	EXOC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049410.2	NM_019053	Silent
CYP2C8	1558	broad.mit.edu	37	10	96824626	96824626	+	Silent	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:96824626A>G	ENST00000371270.3	-	4	667	c.573T>C	c.(571-573)gaT>gaC	p.D191D	CYP2C8_ENST00000539050.1_Silent_p.D105D|CYP2C8_ENST00000535898.1_Silent_p.D89D	NM_000770.3|NM_001198853.1|NM_001198855.1	NP_000761.3|NP_001185782.1|NP_001185784.1	P10632	CP2C8_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 8	191					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|omega-hydroxylase P450 pathway (GO:0097267)|organic acid metabolic process (GO:0006082)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|caffeine oxidase activity (GO:0034875)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)	p.D191D(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|skin(3)	21		Colorectal(252;0.0397)		all cancers(201;6.21e-05)	Abiraterone(DB05812)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Almotriptan(DB00918)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Antipyrine(DB01435)|Apixaban(DB06605)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bezafibrate(DB01393)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Candesartan(DB00796)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cisapride(DB00604)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dapsone(DB00250)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Domperidone(DB01184)|Eltrombopag(DB06210)|Enzalutamide(DB08899)|Erlotinib(DB00530)|Estradiol(DB00783)|Eszopiclone(DB00402)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Felodipine(DB01023)|Fenofibrate(DB01039)|Fluorouracil(DB00544)|Fluvastatin(DB01095)|Fosphenytoin(DB01320)|Gemfibrozil(DB01241)|Halofantrine(DB01218)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Ifosfamide(DB01181)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Liotrix(DB01583)|Loperamide(DB00836)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Methadone(DB00333)|Metronidazole(DB00916)|Mirtazapine(DB00370)|Mometasone(DB00764)|Montelukast(DB00471)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Naloxone(DB01183)|Naproxen(DB00788)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Omeprazole(DB00338)|Oxybutynin(DB01062)|Paclitaxel(DB01229)|Paramethadione(DB00617)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Perphenazine(DB00850)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quinidine(DB00908)|Quinine(DB00468)|Raloxifene(DB00481)|Regorafenib(DB08896)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Salmeterol(DB00938)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Simvastatin(DB00641)|Sitagliptin(DB01261)|Sorafenib(DB00398)|Spironolactone(DB00421)|Sulfadiazine(DB00359)|Sulfamethoxazole(DB01015)|Sulfaphenazole(DB06729)|Sulfinpyrazone(DB01138)|Tamoxifen(DB00675)|Tazarotene(DB00799)|Temazepam(DB00231)|Terbinafine(DB00857)|Testosterone(DB00624)|Theophylline(DB00277)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Torasemide(DB00214)|Trametinib(DB08911)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Verapamil(DB00661)|Vismodegib(DB08828)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zidovudine(DB00495)|Zopiclone(DB01198)	GAAAATTCTGATCTTTATAAT	0.413																																					p.D191D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T573C	10						.						89.0	86.0	87.0					10																	96824626		2203	4300	6503	96814616	SO:0001819	synonymous_variant	1558	exon4			M17397	CCDS7438.1, CCDS55721.1, CCDS73166.1	10q24.1	2007-12-14	2003-01-14		ENSG00000138115	ENSG00000138115		"""Cytochrome P450s"""	2622	protein-coding gene	gene with protein product		601129	"""cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 8"""			7841444	Standard	NM_001198853		Approved	CPC8	uc001kkb.3	P10632	OTTHUMG00000018804	ENST00000371270.3:c.573T>C	10.37:g.96824626A>G			96814616	NM_000770	A8K9N8|B0AZN2|B7Z1F6|Q5VX93|Q8WWB1|Q9UCZ9	Silent	SNP	ENST00000371270.3	37	CCDS7438.1																																																																																				0.413	CYP2C8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049499.2	NM_000770	
C10orf12	26148	broad.mit.edu	37	10	98742889	98742889	+	Missense_Mutation	SNP	G	G	A	rs141178994		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:98742889G>A	ENST00000286067.2	+	1	1849	c.1742G>A	c.(1741-1743)cGc>cAc	p.R581H		NM_015652.2	NP_056467.2	Q8N655	CJ012_HUMAN	chromosome 10 open reading frame 12	581								p.R581H(1)		NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(3)|prostate(2)|skin(2)|stomach(4)	45		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		GTCAATGAACGCCCCTCTGAG	0.522																																					p.R581H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1742A	10						.	G	HIS/ARG	0,4406		0,0,2203	48.0	55.0	53.0		1742	-3.3	0.0	10	dbSNP_134	53	1,8599	1.2+/-3.3	0,1,4299	no	missense	C10orf12	NM_015652.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	581/1248	98742889	1,13005	2203	4300	6503	98732879	SO:0001583	missense	26148	exon1			BC024315	CCDS7452.1	10q24.2	2014-03-11			ENSG00000155640	ENSG00000155640			23420	protein-coding gene	gene with protein product						24550272	Standard	NM_015652		Approved	DKFZP564P1916, FLJ13022	uc001kmv.3	Q8N655	OTTHUMG00000018840	ENST00000286067.2:c.1742G>A	10.37:g.98742889G>A	ENSP00000286067:p.Arg581His		98732879	NM_015652	Q9H945|Q9Y457	Missense_Mutation	SNP	ENST00000286067.2	37	CCDS7452.1	.	.	.	.	.	.	.	.	.	.	G	0.082	-1.182323	0.01633	0.0	1.16E-4	ENSG00000155640	ENST00000286067;ENST00000539886	T	0.06528	3.29	4.94	-3.26	0.05064	.	1.241240	0.05944	N	0.637619	T	0.02888	0.0086	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.46679	-0.9174	10	0.35671	T	0.21	0.7721	10.8904	0.46992	0.4179:0.0:0.5821:0.0	.	581	Q8N655	CJ012_HUMAN	H	581;415	ENSP00000286067:R581H	ENSP00000286067:R581H	R	+	2	0	C10orf12	98732879	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.007000	0.13174	-0.439000	0.07222	-1.267000	0.01435	CGC		0.522	C10orf12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049627.1	NM_015652	
SLIT1	6585	broad.mit.edu	37	10	98807471	98807471	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:98807471C>T	ENST00000266058.4	-	16	1855	c.1610G>A	c.(1609-1611)cGc>cAc	p.R537H	ARHGAP19-SLIT1_ENST00000453547.2_3'UTR|SLIT1_ENST00000371070.4_Missense_Mutation_p.R537H	NM_003061.2	NP_003052.2	O75093	SLIT1_HUMAN	slit homolog 1 (Drosophila)	537	LRRNT 3.				axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|dorsal/ventral axon guidance (GO:0033563)|establishment of nucleus localization (GO:0040023)|forebrain morphogenesis (GO:0048853)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of synapse assembly (GO:0051964)|retinal ganglion cell axon guidance (GO:0031290)|spinal cord development (GO:0021510)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)	p.R537H(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(37)|ovary(5)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	78		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		CTGGGGGATGCGCTCAGGGAT	0.622																																					p.R537H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1610A	10						.						81.0	82.0	82.0					10																	98807471		2203	4300	6503	98797461	SO:0001583	missense	6585	exon16			AB011537	CCDS7453.1	10q23.3-q24	2008-08-01	2001-11-28		ENSG00000187122	ENSG00000187122			11085	protein-coding gene	gene with protein product		603742	"""slit (Drosophila) homolog 1"""	SLIL1		9693030, 9813312	Standard	NM_003061		Approved	slit1, MEGF4, Slit-1, SLIT3	uc001kmw.2	O75093	OTTHUMG00000018843	ENST00000266058.4:c.1610G>A	10.37:g.98807471C>T	ENSP00000266058:p.Arg537His		98797461	NM_003061	Q5T0V1|Q8WWZ2|Q9UIL7	Missense_Mutation	SNP	ENST00000266058.4	37	CCDS7453.1	.	.	.	.	.	.	.	.	.	.	C	1.012	-0.687690	0.03328	.	.	ENSG00000187122	ENST00000266058;ENST00000371057;ENST00000371070;ENST00000314867	D;D;D	0.96587	-4.06;-4.06;-4.06	4.54	4.54	0.55810	Leucine-rich repeat-containing N-terminal (2);	0.105878	0.64402	D	0.000003	D	0.86781	0.6015	N	0.01424	-0.875	0.80722	D	1	B;B	0.10296	0.003;0.001	B;B	0.06405	0.002;0.001	D	0.83479	0.0063	10	0.02654	T	1	.	17.8601	0.88778	0.0:1.0:0.0:0.0	.	547;537	E7EWQ8;O75093	.;SLIT1_HUMAN	H	537;547;537;530	ENSP00000266058:R537H;ENSP00000360109:R537H;ENSP00000315005:R530H	ENSP00000266058:R537H	R	-	2	0	SLIT1	98797461	1.000000	0.71417	0.995000	0.50966	0.125000	0.20455	2.785000	0.47782	2.517000	0.84864	0.563000	0.77884	CGC		0.622	SLIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049636.1	NM_003061	
ZDHHC16	84287	broad.mit.edu	37	10	99211894	99211894	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:99211894C>T	ENST00000370854.3	+	3	480	c.291C>T	c.(289-291)atC>atT	p.I97I	ZDHHC16_ENST00000370846.4_Silent_p.I97I|ZDHHC16_ENST00000345745.5_Intron|ZDHHC16_ENST00000370842.2_Silent_p.I97I|ZDHHC16_ENST00000393760.1_Silent_p.I97I|ZDHHC16_ENST00000353979.3_Silent_p.I97I|ZDHHC16_ENST00000495735.1_3'UTR|ZDHHC16_ENST00000352634.4_Silent_p.I97I	NM_032327.2	NP_115703.2	Q969W1	ZDH16_HUMAN	zinc finger, DHHC-type containing 16	97					apoptotic process (GO:0006915)|protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.I97I(1)		kidney(4)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	14		Colorectal(252;0.0846)		Epithelial(162;5.81e-10)|all cancers(201;4.19e-08)		TTGTAGCTATCGCCTACCTGT	0.542																																					p.I97I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C291T	10						.						172.0	121.0	138.0					10																	99211894		2203	4300	6503	99201884	SO:0001819	synonymous_variant	84287	exon3			AF258563	CCDS7460.1, CCDS7461.1, CCDS7462.1, CCDS7463.1, CCDS73176.1	10q24.1	2008-05-02			ENSG00000171307	ENSG00000171307		"""Zinc fingers, DHHC-type"""	20714	protein-coding gene	gene with protein product						12021275	Standard	NM_198043		Approved	APH2	uc001knk.3	Q969W1	OTTHUMG00000018847	ENST00000370854.3:c.291C>T	10.37:g.99211894C>T			99201884	NM_198043	D3DR52|D3DR53|D3DR54|Q5JTG7|Q5JTH0|Q8N4Z6|Q8WY84|Q9BSV3	Silent	SNP	ENST00000370854.3	37	CCDS7460.1	.	.	.	.	.	.	.	.	.	.	C	7.126	0.578970	0.13686	.	.	ENSG00000171307	ENST00000420089;ENST00000417044	.	.	.	5.55	-6.78	0.01721	.	.	.	.	.	T	0.53384	0.1793	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58387	-0.7645	4	.	.	.	-0.1517	11.6333	0.51189	0.0849:0.2911:0.0:0.6241	.	.	.	.	L	73;39	.	.	S	+	2	0	ZDHHC16	99201884	0.024000	0.19004	0.892000	0.35008	0.837000	0.47467	-0.704000	0.05058	-1.252000	0.02491	-1.069000	0.02264	TCG		0.542	ZDHHC16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049658.2	NM_032327	
MMS19	64210	broad.mit.edu	37	10	99228140	99228140	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:99228140G>C	ENST00000438925.2	-	13	1422	c.1087C>G	c.(1087-1089)Ccg>Gcg	p.P363A	MMS19_ENST00000355839.6_Missense_Mutation_p.P320A|MMS19_ENST00000327277.7_5'UTR|MMS19_ENST00000483626.1_5'Flank|MMS19_ENST00000370782.2_Missense_Mutation_p.P363A|MMS19_ENST00000327238.10_Intron	NM_022362.4	NP_071757.4	Q96T76	MMS19_HUMAN	MMS19 nucleotide excision repair homolog (S. cerevisiae)	363					cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|iron-sulfur cluster assembly (GO:0016226)|nucleotide-excision repair (GO:0006289)|phosphorelay signal transduction system (GO:0000160)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	CIA complex (GO:0097361)|cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|membrane (GO:0016020)|MMXD complex (GO:0071817)|nucleus (GO:0005634)|spindle (GO:0005819)	estrogen receptor binding (GO:0030331)|protein binding, bridging (GO:0030674)|receptor signaling complex scaffold activity (GO:0030159)|transcription coactivator activity (GO:0003713)	p.P363A(1)		endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|stomach(1)	16		Colorectal(252;0.0846)		Epithelial(162;3.33e-10)|all cancers(201;2.74e-08)		TTCATGTCCGGTTCACACAGG	0.577								Direct reversal of damage																													p.P363A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1087G	10						.						63.0	52.0	56.0					10																	99228140		2203	4300	6503	99218130	SO:0001583	missense	64210	exon13			AF007151	CCDS7464.1, CCDS73177.1	10q24-q25	2007-08-15	2007-08-15	2007-08-15	ENSG00000155229	ENSG00000155229			13824	protein-coding gene	gene with protein product	"""MET18 homolog (S. cerevisiae)"""	614777		MMS19L		11071939	Standard	NM_022362		Approved	MET18, hMMS19	uc001kns.4	Q96T76	OTTHUMG00000018857	ENST00000438925.2:c.1087C>G	10.37:g.99228140G>C	ENSP00000412698:p.Pro363Ala		99218130	NM_022362	B0QZ75|B3KPE5|B4DQX2|B4E2I3|D3DR55|F8W9Y2|Q17RZ8|Q5T455|Q66K82|Q7L4W8|Q969Z1|Q96DF1|Q96MR1|Q96RK5|Q96SK1|Q9BUE2|Q9BYS9	Missense_Mutation	SNP	ENST00000438925.2	37	CCDS7464.1	.	.	.	.	.	.	.	.	.	.	G	19.36	3.812197	0.70797	.	.	ENSG00000155229	ENST00000438925;ENST00000370782;ENST00000422291;ENST00000355839	T;T;T	0.67523	-0.27;-0.27;-0.27	5.05	5.05	0.67936	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.80110	0.4563	M	0.67953	2.075	0.80722	D	1	D;D;D	0.89917	0.993;1.0;1.0	P;D;D	0.97110	0.869;1.0;0.999	T	0.76085	-0.3088	10	0.25751	T	0.34	.	18.5916	0.91215	0.0:0.0:1.0:0.0	.	384;363;320	B4DQX2;Q96T76;B4E2I3	.;MMS19_HUMAN;.	A	363;363;342;320	ENSP00000412698:P363A;ENSP00000359818:P363A;ENSP00000348097:P320A	ENSP00000348097:P320A	P	-	1	0	MMS19	99218130	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	7.562000	0.82300	2.630000	0.89119	0.514000	0.50259	CCG		0.577	MMS19-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049706.2		
VAX1	11023	broad.mit.edu	37	10	118897421	118897421	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr10:118897421G>A	ENST00000369206.5	-	1	146	c.147C>T	c.(145-147)ggC>ggT	p.G49G	VAX1_ENST00000277905.2_Silent_p.G49G	NM_001112704.1	NP_001106175.1	Q5SQQ9	VAX1_HUMAN	ventral anterior homeobox 1	49					axon guidance (GO:0007411)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|palate development (GO:0060021)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G49G(1)		endometrium(1)|large_intestine(1)|lung(8)|ovary(2)	12				all cancers(201;0.0108)		CTGAGAAGGCGCCCTGCGGCT	0.647																																					p.G49G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C147T	10						.						37.0	45.0	42.0					10																	118897421		2203	4300	6503	118887411	SO:0001819	synonymous_variant	11023	exon1			AK127095	CCDS7597.1, CCDS44483.1	10q26.11	2011-06-20			ENSG00000148704	ENSG00000148704		"""Homeoboxes / ANTP class : NKL subclass"""	12660	protein-coding gene	gene with protein product		604294				9636075, 10485894	Standard	NM_199131		Approved		uc009xyx.3	Q5SQQ9	OTTHUMG00000019117	ENST00000369206.5:c.147C>T	10.37:g.118897421G>A			118887411	NM_199131	B1AVW5|Q6ZSX0	Silent	SNP	ENST00000369206.5	37	CCDS44483.1																																																																																				0.647	VAX1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050559.3	XM_301242	
EPS8L2	64787	broad.mit.edu	37	11	723304	723305	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:723304_723305insC	ENST00000533256.1	+	16	1780_1781	c.1405_1406insC	c.(1405-1407)accfs	p.T469fs	AP006621.9_ENST00000527021.2_RNA|EPS8L2_ENST00000318562.8_Frame_Shift_Ins_p.T469fs|EPS8L2_ENST00000526198.1_Frame_Shift_Ins_p.T485fs|EPS8L2_ENST00000530636.1_Frame_Shift_Ins_p.T469fs			Q9H6S3	ES8L2_HUMAN	EPS8-like 2	469					positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	actin binding (GO:0003779)	p.D473fs*30(1)		NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|pancreas(1)|prostate(2)|soft_tissue(1)|urinary_tract(1)	13		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;4.37e-27)|Epithelial(43;2.81e-26)|OV - Ovarian serous cystadenocarcinoma(40;1.33e-20)|BRCA - Breast invasive adenocarcinoma(625;4.29e-05)|Lung(200;0.0582)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TTCAGAGCCCACCCCCCCGGGG	0.584											OREG0020659	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T469fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1405_1406insC	11						.			17,4247		0,17,2115						-1.4	0.0			78	21,8233		1,19,4107	no	frameshift	EPS8L2	NM_022772.3		1,36,6222	A1A1,A1R,RR		0.2544,0.3987,0.3036				38,12480				713305	SO:0001589	frameshift_variant	64787	exon15			AF318331	CCDS31328.1	11p15.5	2008-02-05				ENSG00000177106			21296	protein-coding gene	gene with protein product		614988				12620401	Standard	NM_022772		Approved	FLJ21935, FLJ22171, MGC3088	uc001lqt.3	Q9H6S3		ENST00000533256.1:c.1412dupC	11.37:g.723311_723311dupC	ENSP00000435585:p.Thr469fs	590	713304	NM_022772	B3KSX1|B7ZKL3|Q53GM8|Q8WYW7|Q96K06|Q9H6K9	Frame_Shift_Ins	INS	ENST00000533256.1	37	CCDS31328.1																																																																																				0.584	EPS8L2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382344.1	NM_022772	
DYNC2H1	79659	broad.mit.edu	37	11	103005080	103005080	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:103005080C>T	ENST00000375735.2	+	15	2281	c.2137C>T	c.(2137-2139)Cgg>Tgg	p.R713W	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.R713W|DYNC2H1_ENST00000334267.7_Missense_Mutation_p.R713W	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	713	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.R713W(1)		NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		TGATCTGCTTCGGCAGCAACA	0.373																																					p.R713W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2137T	11						.						152.0	148.0	149.0					11																	103005080		1861	4096	5957	102510290	SO:0001583	missense	79659	exon15			AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"""Cytoplasmic dyneins"""	2962	protein-coding gene	gene with protein product		603297	"""dynein, cytoplasmic, heavy polypeptide 2"""	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.2137C>T	11.37:g.103005080C>T	ENSP00000364887:p.Arg713Trp		102510290	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	c	16.82	3.229622	0.58777	.	.	ENSG00000187240	ENST00000375735;ENST00000334267;ENST00000398093	T;T;T	0.37235	1.5;1.21;1.5	5.64	4.73	0.59995	.	0.244724	0.31156	U	0.008154	T	0.64951	0.2645	M	0.84683	2.71	0.44247	D	0.997095	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.83275	0.992;0.978;0.996	T	0.72663	-0.4225	10	0.87932	D	0	.	16.0173	0.80450	0.1356:0.8644:0.0:0.0	.	713;713;713	Q8NCM8-3;Q8NCM8;Q8NCM8-2	.;DYHC2_HUMAN;.	W	713	ENSP00000364887:R713W;ENSP00000334021:R713W;ENSP00000381167:R713W	ENSP00000334021:R713W	R	+	1	2	DYNC2H1	102510290	1.000000	0.71417	1.000000	0.80357	0.357000	0.29423	4.394000	0.59671	1.376000	0.46267	0.486000	0.48141	CGG		0.373	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
DYNC2H1	79659	broad.mit.edu	37	11	103059361	103059361	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:103059361C>T	ENST00000375735.2	+	44	7420	c.7276C>T	c.(7276-7278)Cgt>Tgt	p.R2426C	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.R2426C|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	2426	AAA 3. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		TTCCATCGTTCGTCTTTGTTC	0.308																																					p.R2426C												.	.	0			c.C7276T	11						.						96.0	92.0	93.0					11																	103059361		1815	4066	5881	102564571	SO:0001583	missense	79659	exon44			AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"""Cytoplasmic dyneins"""	2962	protein-coding gene	gene with protein product		603297	"""dynein, cytoplasmic, heavy polypeptide 2"""	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.7276C>T	11.37:g.103059361C>T	ENSP00000364887:p.Arg2426Cys		102564571	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.236045	0.79800	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.31247	1.5;1.5	5.75	5.75	0.90469	ATPase, AAA+ type, core (1);	.	.	.	.	T	0.53738	0.1815	M	0.78456	2.415	0.80722	D	1	D;D	0.69078	0.997;0.994	P;P	0.57324	0.818;0.783	T	0.49560	-0.8927	9	0.35671	T	0.21	.	19.9381	0.97149	0.0:1.0:0.0:0.0	.	2426;2426	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	C	2426	ENSP00000364887:R2426C;ENSP00000381167:R2426C	ENSP00000364887:R2426C	R	+	1	0	DYNC2H1	102564571	1.000000	0.71417	1.000000	0.80357	0.507000	0.33981	7.714000	0.84703	2.701000	0.92244	0.585000	0.79938	CGT		0.308	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
PDGFD	80310	broad.mit.edu	37	11	103797822	103797822	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:103797822G>A	ENST00000393158.2	-	6	984	c.805C>T	c.(805-807)Cgt>Tgt	p.R269C	PDGFD_ENST00000302251.5_Missense_Mutation_p.R263C			Q9GZP0	PDGFD_HUMAN	platelet derived growth factor D	269					cellular response to amino acid stimulus (GO:0071230)|multicellular organismal development (GO:0007275)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell division (GO:0051781)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)		p.R269C(2)		biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)|prostate(3)|upper_aerodigestive_tract(1)	23		Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Melanoma(852;0.0563)|all_neural(303;0.165)		BRCA - Breast invasive adenocarcinoma(274;0.00136)|Epithelial(105;0.111)		CAACTGTAACGCTTGGCATCA	0.463																																					p.R263C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C787T	11						.						162.0	139.0	147.0					11																	103797822		2202	4299	6501	103303032	SO:0001583	missense	80310	exon6			AF113216	CCDS8326.1, CCDS41703.1	11q22.3	2008-02-05			ENSG00000170962	ENSG00000170962			30620	protein-coding gene	gene with protein product	"""spinal cord derived growth factor B"""	609673				11162582, 11980634	Standard	NM_033135		Approved	SCDGF-B, MSTP036, IEGF	uc001phq.3	Q9GZP0	OTTHUMG00000165953	ENST00000393158.2:c.805C>T	11.37:g.103797822G>A	ENSP00000376865:p.Arg269Cys		103303032	NM_033135	A8K9T6|Q9BWV5	Missense_Mutation	SNP	ENST00000393158.2	37	CCDS41703.1	.	.	.	.	.	.	.	.	.	.	G	18.34	3.601483	0.66445	.	.	ENSG00000170962	ENST00000393158;ENST00000302251	T;T	0.34667	1.36;1.35	5.87	3.92	0.45320	Platelet-derived growth factor (PDGF) (1);	0.052614	0.64402	D	0.000001	T	0.54532	0.1864	L	0.53249	1.67	0.54753	D	0.999987	D;D	0.89917	1.0;1.0	D;D	0.73708	0.981;0.938	T	0.57010	-0.7884	10	0.72032	D	0.01	-13.4421	14.9698	0.71223	0.0:0.0:0.7394:0.2606	.	269;263	Q9GZP0;Q9GZP0-2	PDGFD_HUMAN;.	C	269;263	ENSP00000376865:R269C;ENSP00000302193:R263C	ENSP00000302193:R263C	R	-	1	0	PDGFD	103303032	1.000000	0.71417	0.993000	0.49108	0.652000	0.38707	3.651000	0.54431	0.744000	0.32741	0.650000	0.86243	CGT		0.463	PDGFD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387231.2	NM_025208	
DDI1	414301	broad.mit.edu	37	11	103907731	103907731	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:103907731C>A	ENST00000302259.3	+	1	424	c.181C>A	c.(181-183)Ctg>Atg	p.L61M	PDGFD_ENST00000302251.5_Intron|PDGFD_ENST00000393158.2_Intron	NM_001001711.2	NP_001001711.1	Q8WTU0	DDI1_HUMAN	DNA-damage inducible 1 homolog 1 (S. cerevisiae)	61	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.						aspartic-type endopeptidase activity (GO:0004190)	p.L61M(2)		central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(12)|liver(2)|lung(21)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00648)|Melanoma(852;0.055)|all_neural(303;0.164)		BRCA - Breast invasive adenocarcinoma(274;0.00128)|Epithelial(105;0.0631)|all cancers(92;0.169)		CCACTGTTCCCTGGGCTCCTA	0.587																																					p.L61M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C181A	11						.						147.0	136.0	140.0					11																	103907731		2202	4299	6501	103412941	SO:0001583	missense	414301	exon1				CCDS31660.1	11q22.3	2010-05-04	2010-05-04			ENSG00000170967			18961	protein-coding gene	gene with protein product			"""DDI1, DNA-damage inducible 1, homolog 1 (S. cerevisiae)"""				Standard	NM_001001711		Approved	FLJ36017	uc001phr.2	Q8WTU0		ENST00000302259.3:c.181C>A	11.37:g.103907731C>A	ENSP00000302805:p.Leu61Met		103412941	NM_001001711	Q7Z4U6|Q8WTS3	Missense_Mutation	SNP	ENST00000302259.3	37	CCDS31660.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.06|14.06	2.424083|2.424083	0.43020|0.43020	.|.	.|.	ENSG00000170967|ENSG00000170962	ENST00000302259|ENST00000529268	T|T	0.67345|0.31510	-0.26|1.49	4.97|4.97	1.0|1.0	0.19881|0.19881	Ubiquitin supergroup (1);Ubiquitin (2);|.	0.000000|.	0.64402|.	D|.	0.000001|.	T|T	0.49474|0.49474	0.1559|0.1559	M|M	0.88181|0.88181	2.935|2.935	0.36935|0.36935	D|D	0.892092|0.892092	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	T|T	0.55503|0.55503	-0.8131|-0.8131	10|7	0.59425|0.62326	D|D	0.04|0.03	-26.0553|-26.0553	7.0825|7.0825	0.25239|0.25239	0.0:0.63:0.0:0.37|0.0:0.63:0.0:0.37	.|.	61|.	Q8WTU0|.	DDI1_HUMAN|.	M|H	61|8	ENSP00000302805:L61M|ENSP00000432909:Q8H	ENSP00000302805:L61M|ENSP00000432909:Q8H	L|Q	+|-	1|3	2|2	DDI1|PDGFD	103412941|103412941	0.005000|0.005000	0.15991|0.15991	0.879000|0.879000	0.34478|0.34478	0.284000|0.284000	0.27059|0.27059	-0.291000|-0.291000	0.08343|0.08343	0.104000|0.104000	0.17725|0.17725	0.655000|0.655000	0.94253|0.94253	CTG|CAG		0.587	DDI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387326.1	NM_001001711	
GRIA4	2893	broad.mit.edu	37	11	105797568	105797568	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:105797568G>A	ENST00000530497.1	+	12	1949	c.1949G>A	c.(1948-1950)cGa>cAa	p.R650Q	GRIA4_ENST00000393127.2_Missense_Mutation_p.R650Q|GRIA4_ENST00000525187.1_Missense_Mutation_p.R650Q|GRIA4_ENST00000282499.5_Missense_Mutation_p.R650Q			P48058	GRIA4_HUMAN	glutamate receptor, ionotropic, AMPA 4	650					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|vesicle (GO:0031982)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)	p.R650Q(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(24)|liver(2)|lung(25)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	82		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)		ACGGTTGAGCGAATGGTCTCT	0.433																																					p.R650Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1949A	11						.						111.0	106.0	108.0					11																	105797568		2201	4298	6499	105302778	SO:0001583	missense	2893	exon13			U16129	CCDS8333.1, CCDS41706.1, CCDS41707.1	11q22	2012-08-29	2012-02-03		ENSG00000152578	ENSG00000152578		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4574	protein-coding gene	gene with protein product		138246	"""glutamate receptor, ionotrophic, AMPA 4"""	GLUR4			Standard	NM_001077244		Approved	GluA4, GLURD	uc001pix.2	P48058	OTTHUMG00000166236	ENST00000530497.1:c.1949G>A	11.37:g.105797568G>A	ENSP00000435775:p.Arg650Gln		105302778	NM_001077243	Q86XE8	Missense_Mutation	SNP	ENST00000530497.1	37	CCDS8333.1	.	.	.	.	.	.	.	.	.	.	G	36	5.911308	0.97093	.	.	ENSG00000152578	ENST00000282499;ENST00000393127;ENST00000530497;ENST00000525187	T;T;T;T	0.56275	0.47;0.47;0.47;0.47	5.87	5.87	0.94306	Ionotropic glutamate receptor (2);	0.000000	0.64402	D	0.000015	T	0.77150	0.4088	M	0.83774	2.66	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.78437	-0.2204	10	0.87932	D	0	.	20.5827	0.99408	0.0:0.0:1.0:0.0	.	650;650	P48058;G3V164	GRIA4_HUMAN;.	Q	650	ENSP00000282499:R650Q;ENSP00000376835:R650Q;ENSP00000435775:R650Q;ENSP00000432180:R650Q	ENSP00000282499:R650Q	R	+	2	0	GRIA4	105302778	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	9.813000	0.99286	2.941000	0.99782	0.655000	0.94253	CGA		0.433	GRIA4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388593.1		
CUL5	8065	broad.mit.edu	37	11	107925674	107925674	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:107925674G>A	ENST00000393094.2	+	7	1388	c.772G>A	c.(772-774)Gtt>Att	p.V258I		NM_003478.3	NP_003469.2	Q93034	CUL5_HUMAN	cullin 5	258					calcium ion transmembrane transport (GO:0070588)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cytosolic calcium ion homeostasis (GO:0051480)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|protein ubiquitination (GO:0016567)|response to osmotic stress (GO:0006970)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	Cul5-RING ubiquitin ligase complex (GO:0031466)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|receptor activity (GO:0004872)|ubiquitin protein ligase binding (GO:0031625)	p.V258I(1)		endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(1)|prostate(1)|skin(1)	23		all_cancers(61;7.09e-10)|all_epithelial(67;2.97e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|Melanoma(852;4.48e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;3.58e-05)|Epithelial(105;4.68e-05)|all cancers(92;0.00122)|OV - Ovarian serous cystadenocarcinoma(223;0.217)		ATGTAACTCCGTTGAAGCAGT	0.299																																					p.V258I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G772A	11						.						59.0	58.0	58.0					11																	107925674		2201	4296	6497	107430884	SO:0001583	missense	8065	exon7			X81882	CCDS31668.1	11q22.3	2011-05-24			ENSG00000166266	ENSG00000166266			2556	protein-coding gene	gene with protein product		601741				8681378, 9037604	Standard	XM_005271682		Approved	VACM-1	uc001pjv.3	Q93034	OTTHUMG00000166369	ENST00000393094.2:c.772G>A	11.37:g.107925674G>A	ENSP00000376808:p.Val258Ile		107430884	NM_003478	A8K960|O14766|Q9BZC6	Missense_Mutation	SNP	ENST00000393094.2	37	CCDS31668.1	.	.	.	.	.	.	.	.	.	.	G	16.15	3.040960	0.55003	.	.	ENSG00000166266	ENST00000393094	T	0.29142	1.58	6.02	6.02	0.97574	Cullin, N-terminal (1);Cullin repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.19644	0.0472	N	0.04746	-0.17	0.80722	D	1	B	0.13145	0.007	B	0.09377	0.004	T	0.08371	-1.0725	10	0.27785	T	0.31	-18.2681	20.5407	0.99260	0.0:0.0:1.0:0.0	.	258	Q93034	CUL5_HUMAN	I	258	ENSP00000376808:V258I	ENSP00000376808:V258I	V	+	1	0	CUL5	107430884	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.827000	0.99397	2.865000	0.98341	0.655000	0.94253	GTT		0.299	CUL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389429.1		
EXPH5	23086	broad.mit.edu	37	11	108380955	108380955	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:108380955G>T	ENST00000265843.4	-	6	5389	c.5279C>A	c.(5278-5280)cCt>cAt	p.P1760H	EXPH5_ENST00000443411.1_Missense_Mutation_p.P1572H|EXPH5_ENST00000525344.1_Missense_Mutation_p.P1753H|EXPH5_ENST00000428840.1_Missense_Mutation_p.P1684H	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	1760					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)	p.P1760H(1)		breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		TTTCTGTGCAGGCTCCAGTGG	0.522																																					p.P1760H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5279A	11						.						66.0	72.0	70.0					11																	108380955		2201	4298	6499	107886165	SO:0001583	missense	23086	exon6				CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.5279C>A	11.37:g.108380955G>T	ENSP00000265843:p.Pro1760His		107886165	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	.	.	.	.	.	.	.	.	.	.	G	19.90	3.913195	0.72983	.	.	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000439956;ENST00000526312	T;T;T;T;T	0.03242	4.22;4.15;4.0;4.22;4.06	6.17	5.27	0.74061	.	0.507866	0.20049	N	0.100351	T	0.13543	0.0328	M	0.65975	2.015	0.09310	N	1	D	0.67145	0.996	P	0.59288	0.855	T	0.02975	-1.1087	10	0.87932	D	0	-6.4526	13.7527	0.62917	0.0702:0.0:0.9298:0.0	.	1760	Q8NEV8	EXPH5_HUMAN	H	1760;1684;1572;1753;590;1684	ENSP00000265843:P1760H;ENSP00000391966:P1684H;ENSP00000411390:P1572H;ENSP00000432546:P1753H;ENSP00000432683:P1684H	ENSP00000265843:P1760H	P	-	2	0	EXPH5	107886165	0.005000	0.15991	0.284000	0.24805	0.069000	0.16628	1.464000	0.35288	1.633000	0.50488	0.655000	0.94253	CCT		0.522	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
NCAM1	4684	broad.mit.edu	37	11	113105875	113105875	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:113105875C>T	ENST00000533760.1	+	13	2029	c.1430C>T	c.(1429-1431)aCg>aTg	p.T477M	NCAM1_ENST00000316851.7_Missense_Mutation_p.T595M|NCAM1_ENST00000401611.2_Missense_Mutation_p.T604M|NCAM1_ENST00000397957.4_3'UTR	NM_001242608.1	NP_001229537.1	P13591	NCAM1_HUMAN	neural cell adhesion molecule 1	605	Ig-like C2-type 5.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|interferon-gamma-mediated signaling pathway (GO:0060333)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)	p.T595M(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(27)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	49		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		GAGTTCAAGACGCAGCCAGTC	0.617																																					p.D595D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1785T	11						.						27.0	32.0	30.0					11																	113105875		2016	4149	6165	112611085	SO:0001583	missense	4684	exon13				CCDS73384.1, CCDS73385.1, CCDS73386.1, CCDS73387.1, CCDS73388.1	11q23.2	2013-02-11			ENSG00000149294	ENSG00000149294		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7656	protein-coding gene	gene with protein product		116930					Standard	NM_000615		Approved	NCAM, CD56	uc021qqp.1	P13591	OTTHUMG00000167196	ENST00000533760.1:c.1430C>T	11.37:g.113105875C>T	ENSP00000473281:p.Thr477Met		112611085	NM_001076682	A8K8T8|P13592|P13593|Q05C58|Q15829|Q16180|Q16209|Q59FL7|Q86X47|Q96CJ3	Missense_Mutation	SNP	ENST00000533760.1	37		.	.	.	.	.	.	.	.	.	.	C	29.0	4.964939	0.92855	.	.	ENSG00000149294	ENST00000531044;ENST00000401611;ENST00000316851;ENST00000433634	T;T	0.64991	0.45;-0.13	5.84	5.84	0.93424	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.000000	0.85682	U	0.000000	T	0.81754	0.4889	.	.	.	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.82963	-0.0196	9	0.87932	D	0	-21.0644	20.1336	0.98010	0.0:1.0:0.0:0.0	.	605;595;605;595	P13591-5;P13591-1;P13591;P13591-3	.;.;NCAM1_HUMAN;.	M	477;604;595;39	ENSP00000384055:T604M;ENSP00000318472:T595M	ENSP00000318472:T595M	T	+	2	0	NCAM1	112611085	1.000000	0.71417	0.989000	0.46669	0.980000	0.70556	7.629000	0.83207	2.767000	0.95098	0.591000	0.81541	ACG		0.617	NCAM1-003	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000394068.2	NM_000615	
SIDT2	51092	broad.mit.edu	37	11	117066527	117066527	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:117066527G>A	ENST00000324225.4	+	25	2863	c.2332G>A	c.(2332-2334)Gca>Aca	p.A778T	SIDT2_ENST00000532062.1_Missense_Mutation_p.A70T|SIDT2_ENST00000431081.2_Missense_Mutation_p.A775T	NM_001040455.1	NP_001035545.1	Q8NBJ9	SIDT2_HUMAN	SID1 transmembrane family, member 2	778					cell morphogenesis (GO:0000902)|dsRNA transport (GO:0033227)|glucose homeostasis (GO:0042593)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to glucose (GO:0009749)|type B pancreatic cell development (GO:0003323)|type B pancreatic cell proliferation (GO:0044342)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	RNA transmembrane transporter activity (GO:0051033)	p.A778T(1)		NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	36	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000219)|all cancers(92;0.00144)		GAAAACCCCTGCAGAGTCGAG	0.587																																					p.A778T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2332A	11						.						180.0	186.0	184.0					11																	117066527		2201	4296	6497	116571737	SO:0001583	missense	51092	exon25			AF151799	CCDS31682.1	11q23.3	2008-02-05			ENSG00000149577	ENSG00000149577			24272	protein-coding gene	gene with protein product						10810093, 12975309	Standard	NM_001040455		Approved	CGI-40	uc001pqh.1	Q8NBJ9	OTTHUMG00000167065	ENST00000324225.4:c.2332G>A	11.37:g.117066527G>A	ENSP00000314023:p.Ala778Thr		116571737	NM_001040455	Q8NBY7|Q9Y357	Missense_Mutation	SNP	ENST00000324225.4	37	CCDS31682.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.819056	0.90873	.	.	ENSG00000149577	ENST00000324225;ENST00000278951;ENST00000431081;ENST00000392956;ENST00000525478;ENST00000532062	T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87	4.16	4.16	0.48862	.	0.000000	0.85682	D	0.000000	T	0.70263	0.3204	M	0.89715	3.055	0.80722	D	1	D;D;D;D	0.76494	0.998;0.986;0.999;0.999	D;P;D;D	0.72982	0.976;0.801;0.979;0.979	T	0.78957	-0.1999	10	0.87932	D	0	-11.3982	16.6056	0.84827	0.0:0.0:1.0:0.0	.	799;775;778;799	Q8NBJ9-2;F5H8L4;Q8NBJ9;C9JBG5	.;.;SIDT2_HUMAN;.	T	778;799;775;132;79;70	ENSP00000314023:A778T;ENSP00000278951:A799T;ENSP00000399635:A775T;ENSP00000435890:A79T;ENSP00000432432:A70T	ENSP00000278951:A799T	A	+	1	0	SIDT2	116571737	1.000000	0.71417	0.766000	0.31476	0.621000	0.37620	9.480000	0.97931	2.322000	0.78497	0.563000	0.77884	GCA		0.587	SIDT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392836.1	NM_015996	
TREH	11181	broad.mit.edu	37	11	118533639	118533639	+	Missense_Mutation	SNP	C	C	T	rs573986675		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:118533639C>T	ENST00000529101.1	-	4	419	c.374G>A	c.(373-375)cGt>cAt	p.R125H	TREH_ENST00000264029.4_Missense_Mutation_p.R125H|TREH_ENST00000530256.1_Missense_Mutation_p.V5M|TREH_ENST00000525958.1_Missense_Mutation_p.R125H|TREH_ENST00000397925.1_Missense_Mutation_p.R125H			O43280	TREA_HUMAN	trehalase (brush-border membrane glycoprotein)	125					carbohydrate metabolic process (GO:0005975)|organ morphogenesis (GO:0009887)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|trehalose catabolic process (GO:0005993)|trehalose metabolic process (GO:0005991)	anchored component of plasma membrane (GO:0046658)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	alpha,alpha-trehalase activity (GO:0004555)	p.R125H(1)		NS(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|urinary_tract(1)	13	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.16e-05)		TGCCCAGGCACGCAGTTTGGC	0.577													C|||	1	0.000199681	0.0	0.0014	5008	,	,		19862	0.0		0.0	False		,,,				2504	0.0				p.R125H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G374A	11						.						30.0	32.0	31.0					11																	118533639		1989	4153	6142	118038849	SO:0001583	missense	11181	exon4			AB000824	CCDS73401.1, CCDS73402.1	11q23.3	2008-07-21				ENSG00000118094	3.2.1.28		12266	protein-coding gene	gene with protein product	"""alpha,alpha-trehalase"", ""alpha,alpha-trehalose glucohydrolase"""	275360				9427547	Standard	NM_007180		Approved	TRE, TREA, MGC129621	uc001pty.1	O43280		ENST00000529101.1:c.374G>A	11.37:g.118533639C>T	ENSP00000435095:p.Arg125His		118038849	NM_007180	Q32MB9|Q53FY8	Missense_Mutation	SNP	ENST00000529101.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.31|12.31	1.900158|1.900158	0.33535|0.33535	.|.	.|.	ENSG00000118094|ENSG00000118094	ENST00000529101;ENST00000264029;ENST00000525958;ENST00000397925|ENST00000530256;ENST00000450700	T;T;T;T|T	0.27402|0.15603	1.67;1.67;1.67;1.67|2.41	4.59|4.59	4.59|4.59	0.56863|0.56863	.|.	0.179711|.	0.44902|.	D|.	0.000413|.	T|T	0.11750|0.11750	0.0286|0.0286	.|.	.|.	.|.	0.18873|0.18873	N|N	0.999981|0.999981	D;D|P	0.89917|0.46220	1.0;0.996|0.874	D;D|B	0.76071|0.33521	0.987;0.913|0.165	T|T	0.16276|0.16276	-1.0408|-1.0408	9|8	0.56958|0.66056	D|D	0.05|0.02	-9.9945|-9.9945	10.0901|10.0901	0.42443|0.42443	0.2001:0.7999:0.0:0.0|0.2001:0.7999:0.0:0.0	.|.	125;125|5	E9PNA2;O43280|E9PPK1	.;TREA_HUMAN|.	H|M	125|5	ENSP00000435095:R125H;ENSP00000264029:R125H;ENSP00000432853:R125H;ENSP00000381020:R125H|ENSP00000432640:V5M	ENSP00000264029:R125H|ENSP00000398042:V5M	R|V	-|-	2|1	0|0	TREH|TREH	118038849|118038849	0.837000|0.837000	0.29446|0.29446	0.911000|0.911000	0.35937|0.35937	0.442000|0.442000	0.32017|0.32017	3.061000|3.061000	0.49963|0.49963	2.412000|2.412000	0.81896|0.81896	0.555000|0.555000	0.69702|0.69702	CGT|GTG		0.577	TREH-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000389639.1	NM_007180	
HYOU1	10525	broad.mit.edu	37	11	118916330	118916330	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:118916330C>T	ENST00000404233.3	-	26	3099	c.2975G>A	c.(2974-2976)cGg>cAg	p.R992Q	RP11-110I1.6_ENST00000531886.1_RNA|HYOU1_ENST00000525859.1_Missense_Mutation_p.R930Q|HYOU1_ENST00000529972.1_Missense_Mutation_p.R930Q	NM_001130991.1|NM_006389.3	NP_001124463.1|NP_006380.1	Q9Y4L1	HYOU1_HUMAN	hypoxia up-regulated 1	992					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|response to ischemia (GO:0002931)|response to stress (GO:0006950)	endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ATP binding (GO:0005524)	p.R992Q(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(10)|prostate(1)|skin(2)	33	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.78e-05)		CTTCAAAGGCCGCTTCTGTCC	0.502																																					p.R992Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2975A	11						.						147.0	150.0	149.0					11																	118916330		2200	4295	6495	118421540	SO:0001583	missense	10525	exon26			U65785	CCDS8408.1	11q23.1-q23.3	2011-09-02			ENSG00000149428	ENSG00000149428		"""Heat shock proteins / HSP70"""	16931	protein-coding gene	gene with protein product	"""glucose-regulated protein 170"""	601746				9020069, 10037731	Standard	XM_005271390		Approved	ORP150, HSP12A, Grp170	uc001pux.3	Q9Y4L1	OTTHUMG00000166354	ENST00000404233.3:c.2975G>A	11.37:g.118916330C>T	ENSP00000384144:p.Arg992Gln		118421540	NM_006389	A8C1Z0|B7Z909|Q2I204|Q53H25	Missense_Mutation	SNP	ENST00000404233.3	37	CCDS8408.1	.	.	.	.	.	.	.	.	.	.	C	11.14	1.549890	0.27652	.	.	ENSG00000149428	ENST00000404233;ENST00000353883;ENST00000529972;ENST00000535579;ENST00000525859;ENST00000544701	T;T;T	0.01430	4.9;4.9;4.9	5.54	-6.89	0.01660	.	1.486100	0.04083	N	0.309880	T	0.01254	0.0041	L	0.29908	0.895	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.001;0.001	T	0.46414	-0.9193	10	0.26408	T	0.33	0.2487	7.5231	0.27639	0.0:0.1606:0.4102:0.4292	.	984;974;992;992	B3KXH0;B7Z2N4;Q9Y4L1;A8C1Z0	.;.;HYOU1_HUMAN;.	Q	992;984;930;841;930;973	ENSP00000384144:R992Q;ENSP00000437313:R930Q;ENSP00000433397:R930Q	ENSP00000278752:R984Q	R	-	2	0	HYOU1	118421540	0.000000	0.05858	0.000000	0.03702	0.328000	0.28507	-1.431000	0.02432	-1.224000	0.02581	-0.119000	0.15052	CGG		0.502	HYOU1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389353.1	NM_006389	
ABCG4	64137	broad.mit.edu	37	11	119020754	119020754	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:119020754G>A	ENST00000449422.2	+	2	267	c.79G>A	c.(79-81)Ggg>Agg	p.G27R	ABCG4_ENST00000307417.3_Missense_Mutation_p.G27R|ABCG4_ENST00000531739.1_Missense_Mutation_p.G27R	NM_001142505.1	NP_001135977.1	Q9H172	ABCG4_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 4	27					cholesterol efflux (GO:0033344)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.G27R(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(28)|ovary(2)|prostate(1)|skin(1)	44	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		GCTGGAGGACGGGGCGGAACC	0.682																																					p.G27R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G79A	11						.						51.0	56.0	54.0					11																	119020754		2200	4295	6495	118525964	SO:0001583	missense	64137	exon2			AJ300465	CCDS8415.1	11q23	2012-03-14			ENSG00000172350	ENSG00000172350		"""ATP binding cassette transporters / subfamily G"""	13884	protein-coding gene	gene with protein product	"""putative ABC transporter"", ""ATP-binding cassette, subfamily G, member 4"""	607784				11435397	Standard	NM_022169		Approved	WHITE2	uc001pvs.3	Q9H172	OTTHUMG00000166169	ENST00000449422.2:c.79G>A	11.37:g.119020754G>A	ENSP00000406874:p.Gly27Arg		118525964	NM_001142505	A8K1B5|Q8WWH0|Q8WWH1|Q8WWH2	Missense_Mutation	SNP	ENST00000449422.2	37	CCDS8415.1	.	.	.	.	.	.	.	.	.	.	G	14.62	2.590501	0.46214	.	.	ENSG00000172350	ENST00000307417;ENST00000524604;ENST00000449422;ENST00000531739	T;T;T;T	0.06294	3.32;3.32;3.32;3.32	4.72	3.72	0.42706	.	0.309957	0.29646	N	0.011571	T	0.06917	0.0176	M	0.65498	2.005	0.35050	D	0.760545	B	0.02656	0.0	B	0.01281	0.0	T	0.13019	-1.0525	10	0.27082	T	0.32	-23.2403	3.8759	0.09056	0.1592:0.2552:0.5856:0.0	.	27	Q9H172	ABCG4_HUMAN	R	27	ENSP00000304111:G27R;ENSP00000431915:G27R;ENSP00000406874:G27R;ENSP00000434318:G27R	ENSP00000304111:G27R	G	+	1	0	ABCG4	118525964	1.000000	0.71417	1.000000	0.80357	0.861000	0.49209	2.270000	0.43355	2.450000	0.82876	0.650000	0.86243	GGG		0.682	ABCG4-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388215.1	NM_022169	
HSPA8	3312	broad.mit.edu	37	11	122931851	122931851	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:122931851A>G	ENST00000532636.1	-	2	301	c.182T>C	c.(181-183)aTg>aCg	p.M61T	HSPA8_ENST00000526862.1_5'Flank|HSPA8_ENST00000227378.3_Missense_Mutation_p.M61T|SNORD14E_ENST00000364009.1_RNA|HSPA8_ENST00000534624.1_Missense_Mutation_p.M61T|SNORD14C_ENST00000365382.1_RNA|HSPA8_ENST00000453788.2_Missense_Mutation_p.M61T|HSPA8_ENST00000533540.1_Missense_Mutation_p.M61T|HSPA8_ENST00000534319.1_5'Flank|HSPA8_ENST00000526110.1_Missense_Mutation_p.M61T|SNORD14D_ENST00000384390.1_RNA			P11142	HSP7C_HUMAN	heat shock 70kDa protein 8	61					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone mediated protein folding requiring cofactor (GO:0051085)|clathrin coat disassembly (GO:0072318)|gene expression (GO:0010467)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|negative regulation of fibril organization (GO:1902904)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotransmitter secretion (GO:0007269)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|protein refolding (GO:0042026)|regulation of cell cycle (GO:0051726)|response to unfolded protein (GO:0006986)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	blood microparticle (GO:0072562)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Prp19 complex (GO:0000974)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|MHC class II protein complex binding (GO:0023026)|poly(A) RNA binding (GO:0044822)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)	p.M61T(1)		breast(1)|central_nervous_system(7)|endometrium(1)|kidney(9)|large_intestine(4)|lung(13)|upper_aerodigestive_tract(1)	36		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		GGTGGGGTTCATTGCAACTTG	0.433																																					p.M61T	Colon(21;486 594 5900 6733 14272)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T182C	11						.						74.0	64.0	68.0					11																	122931851		2202	4299	6501	122437061	SO:0001583	missense	3312	exon2			Y00371	CCDS8440.1, CCDS44754.1	11q24.1	2011-09-02	2002-08-29		ENSG00000109971	ENSG00000109971		"""Heat shock proteins / HSP70"""	5241	protein-coding gene	gene with protein product		600816	"""heat shock 70kD protein 8"""	HSPA10		8530083, 3037489	Standard	NM_006597		Approved	HSC71, HSC70, HSP73	uc001pyo.3	P11142	OTTHUMG00000166030	ENST00000532636.1:c.182T>C	11.37:g.122931851A>G	ENSP00000437125:p.Met61Thr		122437061	NM_153201	Q9H3R6	Missense_Mutation	SNP	ENST00000532636.1	37	CCDS8440.1	.	.	.	.	.	.	.	.	.	.	A	13.47	2.247115	0.39697	.	.	ENSG00000109971	ENST00000532636;ENST00000533540;ENST00000534624;ENST00000453788;ENST00000227378;ENST00000526110;ENST00000528292;ENST00000525463;ENST00000525624;ENST00000534567;ENST00000527387;ENST00000532182;ENST00000524590;ENST00000530391	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.03580	5.6;5.6;5.6;5.6;5.6;5.6;5.6;3.88;5.6;5.6;5.6;5.6;5.6;5.6	4.42	4.42	0.53409	.	0.043631	0.85682	D	0.000000	T	0.09069	0.0224	N	0.20986	0.625	0.80722	D	1	B;P;B;B;P	0.37276	0.332;0.589;0.022;0.007;0.589	P;P;B;B;P	0.57009	0.509;0.811;0.062;0.037;0.811	T	0.33343	-0.9872	10	0.87932	D	0	-31.7108	13.9807	0.64304	1.0:0.0:0.0:0.0	.	61;61;61;61;61	B4DTX2;Q53GZ6;E7ET08;P11142-2;P11142	.;.;.;.;HSP7C_HUMAN	T	61;61;61;61;61;61;1;61;61;61;61;61;61;61	ENSP00000437125:M61T;ENSP00000437189:M61T;ENSP00000432083:M61T;ENSP00000404372:M61T;ENSP00000227378:M61T;ENSP00000433584:M61T;ENSP00000432884:M1T;ENSP00000436762:M61T;ENSP00000435154:M61T;ENSP00000431641:M61T;ENSP00000436183:M61T;ENSP00000434415:M61T;ENSP00000434565:M61T;ENSP00000434851:M61T	ENSP00000227378:M61T	M	-	2	0	HSPA8	122437061	1.000000	0.71417	0.989000	0.46669	0.951000	0.60555	9.337000	0.96545	1.748000	0.51833	0.397000	0.26171	ATG		0.433	HSPA8-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387515.1		
TIRAP	114609	broad.mit.edu	37	11	126162460	126162460	+	Silent	SNP	A	A	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:126162460A>T	ENST00000392680.2	+	5	561	c.156A>T	c.(154-156)tcA>tcT	p.S52S	RP11-712L6.5_ENST00000528876.1_5'Flank|TIRAP_ENST00000392678.3_Silent_p.S52S|TIRAP_ENST00000392679.1_Silent_p.S52S|RP11-712L6.7_ENST00000533378.1_RNA	NM_001039661.1	NP_001034750.1	P58753	TIRAP_HUMAN	toll-interleukin 1 receptor (TIR) domain containing adaptor protein	52					3'-UTR-mediated mRNA stabilization (GO:0070935)|cell surface receptor signaling pathway (GO:0007166)|cellular response to bacterial lipopeptide (GO:0071221)|cellular response to lipoteichoic acid (GO:0071223)|defense response to Gram-positive bacterium (GO:0050830)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine (C-X-C motif) ligand 1 production (GO:2000340)|positive regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000343)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-15 production (GO:0032738)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of toll-like receptor 2 signaling pathway (GO:0034137)|positive regulation of toll-like receptor 3 signaling pathway (GO:0034141)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of innate immune response (GO:0045088)|regulation of interferon-beta production (GO:0032648)|response to lipopolysaccharide (GO:0032496)|TIRAP-dependent toll-like receptor 4 signaling pathway (GO:0035665)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein binding, bridging (GO:0030674)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|Toll-like receptor 2 binding (GO:0035663)|Toll-like receptor 4 binding (GO:0035662)	p.S52S(1)		breast(1)|endometrium(1)|large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	6	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00948)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.0604)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0739)		AGCCTACCTCACAGGACAGCC	0.597																																					p.S52S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A156T	11						.						117.0	100.0	106.0					11																	126162460		2201	4298	6499	125667670	SO:0001819	synonymous_variant	114609	exon5			AF378129	CCDS8472.1, CCDS41731.1	11q24.2	2008-02-05	2002-01-14		ENSG00000150455	ENSG00000150455			17192	protein-coding gene	gene with protein product	"""MyD88 adapter-like"""	606252	"""Toll-interleukin 1 receptor (TIR) domain-containing adaptor protein"""			11526399, 11544529	Standard	XM_005271399		Approved	Mal, wyatt	uc001qdl.1	P58753	OTTHUMG00000140373	ENST00000392680.2:c.156A>T	11.37:g.126162460A>T			125667670	NM_001039661	B3KW65|Q56UH9|Q56UI0|Q8N5E5	Silent	SNP	ENST00000392680.2	37	CCDS8472.1																																																																																				0.597	TIRAP-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000277092.1	NM_148910	
TIRAP	114609	broad.mit.edu	37	11	126162545	126162545	+	Missense_Mutation	SNP	C	C	T	rs138228187	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:126162545C>T	ENST00000392680.2	+	5	646	c.241C>T	c.(241-243)Cgc>Tgc	p.R81C	RP11-712L6.5_ENST00000528876.1_5'Flank|TIRAP_ENST00000392678.3_Missense_Mutation_p.R81C|TIRAP_ENST00000392679.1_Missense_Mutation_p.R81C|RP11-712L6.7_ENST00000533378.1_RNA	NM_001039661.1	NP_001034750.1	P58753	TIRAP_HUMAN	toll-interleukin 1 receptor (TIR) domain containing adaptor protein	81					3'-UTR-mediated mRNA stabilization (GO:0070935)|cell surface receptor signaling pathway (GO:0007166)|cellular response to bacterial lipopeptide (GO:0071221)|cellular response to lipoteichoic acid (GO:0071223)|defense response to Gram-positive bacterium (GO:0050830)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine (C-X-C motif) ligand 1 production (GO:2000340)|positive regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000343)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-15 production (GO:0032738)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of toll-like receptor 2 signaling pathway (GO:0034137)|positive regulation of toll-like receptor 3 signaling pathway (GO:0034141)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of innate immune response (GO:0045088)|regulation of interferon-beta production (GO:0032648)|response to lipopolysaccharide (GO:0032496)|TIRAP-dependent toll-like receptor 4 signaling pathway (GO:0035665)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein binding, bridging (GO:0030674)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|Toll-like receptor 2 binding (GO:0035663)|Toll-like receptor 4 binding (GO:0035662)	p.R81C(3)		breast(1)|endometrium(1)|large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	6	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00948)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.0604)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0739)		TGGCAGTAGTCGCTGGAGCAA	0.607													C|||	3	0.000599042	0.0	0.0	5008	,	,		18124	0.002		0.0	False		,,,				2504	0.001				p.R81C												.	.	3	Substitution - Missense(3)	endometrium(2)|large_intestine(1)	c.C241T	11						.						86.0	71.0	76.0					11																	126162545		2201	4297	6498	125667755	SO:0001583	missense	114609	exon5			AF378129	CCDS8472.1, CCDS41731.1	11q24.2	2008-02-05	2002-01-14		ENSG00000150455	ENSG00000150455			17192	protein-coding gene	gene with protein product	"""MyD88 adapter-like"""	606252	"""Toll-interleukin 1 receptor (TIR) domain-containing adaptor protein"""			11526399, 11544529	Standard	XM_005271399		Approved	Mal, wyatt	uc001qdl.1	P58753	OTTHUMG00000140373	ENST00000392680.2:c.241C>T	11.37:g.126162545C>T	ENSP00000376447:p.Arg81Cys		125667755	NM_001039661	B3KW65|Q56UH9|Q56UI0|Q8N5E5	Missense_Mutation	SNP	ENST00000392680.2	37	CCDS8472.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	C	20.4	3.983175	0.74474	.	.	ENSG00000150455	ENST00000392679;ENST00000279992;ENST00000392678;ENST00000392680	T;T;T	0.02579	4.24;4.24;4.24	5.41	5.41	0.78517	Toll/interleukin-1 receptor homology (TIR) domain (1);	0.059532	0.64402	D	0.000006	T	0.15955	0.0384	M	0.69823	2.125	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.00090	-1.2086	10	0.72032	D	0.01	-0.0428	19.1929	0.93674	0.0:1.0:0.0:0.0	.	81;81	P58753;Q56UH9	TIRAP_HUMAN;.	C	81	ENSP00000376446:R81C;ENSP00000376445:R81C;ENSP00000376447:R81C	ENSP00000279992:R81C	R	+	1	0	TIRAP	125667755	0.998000	0.40836	0.997000	0.53966	0.343000	0.28985	4.063000	0.57499	2.523000	0.85059	0.655000	0.94253	CGC		0.607	TIRAP-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000277092.1	NM_148910	
ATHL1	80162	broad.mit.edu	37	11	292614	292614	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:292614C>T	ENST00000409548.2	+	6	1210	c.1095C>T	c.(1093-1095)gtC>gtT	p.V365V	ATHL1_ENST00000409479.1_Silent_p.V365V|ATHL1_ENST00000409655.1_Silent_p.V188V	NM_025092.4	NP_079368.3	Q32M88	ATHL1_HUMAN	ATH1, acid trehalase-like 1 (yeast)	365					carbohydrate metabolic process (GO:0005975)		hydrolase activity, acting on glycosyl bonds (GO:0016798)	p.V188V(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(7)|prostate(1)|skin(3)	17		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;5.38e-28)|Epithelial(43;3.25e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		TTTACGGAGTCCAGGAGGTCC	0.607																																					p.V365V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1095T	11						.						110.0	79.0	89.0					11																	292614		2203	4300	6503	282614	SO:0001819	synonymous_variant	80162	exon6			AK090428	CCDS31322.2	11p15.5	2005-10-27			ENSG00000142102	ENSG00000142102			26210	protein-coding gene	gene with protein product							Standard	NM_025092		Approved	FLJ22635	uc010qvu.2	Q32M88	OTTHUMG00000153218	ENST00000409548.2:c.1095C>T	11.37:g.292614C>T			282614	NM_025092	Q658X8|Q8TEG9|Q9H635	Silent	SNP	ENST00000409548.2	37	CCDS31322.2																																																																																				0.607	ATHL1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330164.3	NM_025092	
CDHR5	53841	broad.mit.edu	37	11	617483	617483	+	Silent	SNP	G	G	A	rs369218232		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:617483G>A	ENST00000358353.3	-	16	2728	c.2406C>T	c.(2404-2406)gaC>gaT	p.D802D	IRF7_ENST00000348655.6_5'Flank|IRF7_ENST00000397566.1_5'Flank|IRF7_ENST00000397574.2_5'Flank|IRF7_ENST00000397562.3_5'Flank|IRF7_ENST00000330243.5_5'Flank|IRF7_ENST00000525445.1_5'Flank|CDHR5_ENST00000397542.2_Silent_p.D802D|CDHR5_ENST00000349570.7_Silent_p.D608D|IRF7_ENST00000397570.1_5'Flank			Q9HBB8	CDHR5_HUMAN	cadherin-related family member 5	802					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)	p.D802D(1)		NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	23						GAACGACCACGTCTGCCTCCG	0.706																																					p.D608D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1824T	11						.	G	,,	0,4402		0,0,2201	54.0	47.0	50.0		2388,2406,1824	-3.9	0.0	11		50	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	CDHR5	NM_001171968.1,NM_021924.4,NM_031264.3	,,	0,2,6499	AA,AG,GG		0.0233,0.0,0.0154	,,	796/840,802/846,608/652	617483	2,13000	2201	4300	6501	607483	SO:0001819	synonymous_variant	53841	exon14			AF258675	CCDS7707.1, CCDS7708.1	11p15.5	2011-07-01	2010-01-25	2010-01-25	ENSG00000099834	ENSG00000099834		"""Cadherins / Cadherin-related"""	7521	protein-coding gene	gene with protein product		606839	"""mucin and cadherin-like"", ""mucin-like protocadherin"""	MUCDHL, MUPCDH		11031102, 10801787	Standard	NM_021924		Approved	FLJ20219, MU-PCDH	uc001lqj.3	Q9HBB8	OTTHUMG00000132018	ENST00000358353.3:c.2406C>T	11.37:g.617483G>A			607483	NM_031264	C9J7X1|Q9H746|Q9HAU3|Q9HBB5|Q9HBB6|Q9HBB7|Q9NX86|Q9NXI9	Silent	SNP	ENST00000358353.3	37	CCDS7707.1																																																																																				0.706	CDHR5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255023.2	NM_021924	
CDHR5	53841	broad.mit.edu	37	11	618999	618999	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:618999delC	ENST00000358353.3	-	14	1882	c.1560delG	c.(1558-1560)gggfs	p.G520fs	IRF7_ENST00000397574.2_5'Flank|CDHR5_ENST00000397542.2_Frame_Shift_Del_p.G520fs|CDHR5_ENST00000349570.7_Intron|IRF7_ENST00000397570.1_5'Flank			Q9HBB8	CDHR5_HUMAN	cadherin-related family member 5	520					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)	p.P522fs*253(1)		NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	23						CACCCGGGGGCCCCCCGGGTG	0.682																																					p.G520fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1560delG	11						.						53.0	69.0	64.0					11																	618999		2203	4299	6502	608999	SO:0001589	frameshift_variant	53841	exon13			AF258675	CCDS7707.1, CCDS7708.1	11p15.5	2011-07-01	2010-01-25	2010-01-25	ENSG00000099834	ENSG00000099834		"""Cadherins / Cadherin-related"""	7521	protein-coding gene	gene with protein product		606839	"""mucin and cadherin-like"", ""mucin-like protocadherin"""	MUCDHL, MUPCDH		11031102, 10801787	Standard	NM_021924		Approved	FLJ20219, MU-PCDH	uc001lqj.3	Q9HBB8	OTTHUMG00000132018	ENST00000358353.3:c.1560delG	11.37:g.618999delC	ENSP00000351118:p.Gly520fs		608999	NM_021924	C9J7X1|Q9H746|Q9HAU3|Q9HBB5|Q9HBB6|Q9HBB7|Q9NX86|Q9NXI9	Frame_Shift_Del	DEL	ENST00000358353.3	37	CCDS7707.1																																																																																				0.682	CDHR5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255023.2	NM_021924	
NUP98	4928	broad.mit.edu	37	11	3803313	3803313	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:3803313delC	ENST00000324932.7	-	2	455	c.35delG	c.(34-36)ggtfs	p.G13fs	NUP98_ENST00000397007.4_Frame_Shift_Del_p.G13fs|NUP98_ENST00000397004.4_Frame_Shift_Del_p.G13fs|NUP98_ENST00000355260.3_Frame_Shift_Del_p.G13fs|NUP98_ENST00000359171.4_Frame_Shift_Del_p.G13fs|RNU7-50P_ENST00000459175.1_RNA	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	13	FG repeats 1.|Gly/Thr-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore organization (GO:0006999)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654)	peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)	p.G12fs*171(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		ACCTGTGCCACCCCCAAAGGG	0.373			T	"""HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"""	AML																																p.G12fs			Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.35delG	11						.						85.0	82.0	83.0					11																	3803313		2201	4298	6499	3759889	SO:0001589	frameshift_variant	4928	exon2			AF071076, AF231130, BC012906, BG773331	CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1	11p15	2008-02-26	2002-08-29		ENSG00000110713	ENSG00000110713			8068	protein-coding gene	gene with protein product		601021	"""nucleoporin 98kD"""			9166830	Standard	NM_139131		Approved	NUP96	uc001lyh.3	P52948	OTTHUMG00000011846	ENST00000324932.7:c.35delG	11.37:g.3803313delC	ENSP00000316032:p.Gly13fs		3759889	NM_005387	Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Frame_Shift_Del	DEL	ENST00000324932.7	37	CCDS7746.1																																																																																				0.373	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320	
OR51G1	79324	broad.mit.edu	37	11	4945423	4945423	+	Silent	SNP	G	G	A	rs199614723		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:4945423G>A	ENST00000321961.2	-	1	214	c.147C>T	c.(145-147)caC>caT	p.H49H	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001005237.1	NP_001005237.1	Q8NGK1	O51G1_HUMAN	olfactory receptor, family 51, subfamily G, member 1	49						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H49H(1)		NS(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(3)|skin(4)|soft_tissue(1)	25		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.58e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		TACAAATGACGTGGAGAATGG	0.502													G|||	1	0.000199681	0.0008	0.0	5008	,	,		21304	0.0		0.0	False		,,,				2504	0.0				p.H49H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C147T	11						.	G		1,4401	4.2+/-10.8	0,1,2200	118.0	90.0	99.0		147	-4.8	0.8	11		99	0,8596		0,0,4298	no	coding-synonymous	OR51G1	NM_001005237.1		0,1,6498	AA,AG,GG		0.0,0.0227,0.0077		49/322	4945423	1,12997	2201	4298	6499	4901999	SO:0001819	synonymous_variant	79324	exon1			AB065793	CCDS31366.1	11p15.4	2012-08-09			ENSG00000176879	ENSG00000176879		"""GPCR / Class A : Olfactory receptors"""	14738	protein-coding gene	gene with protein product				OR51G3P			Standard	NM_001005237		Approved		uc010qyr.2	Q8NGK1	OTTHUMG00000066532	ENST00000321961.2:c.147C>T	11.37:g.4945423G>A			4901999	NM_001005237	B9EGW8|Q6IFH6	Silent	SNP	ENST00000321961.2	37	CCDS31366.1																																																																																				0.502	OR51G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142345.1	NM_001005237	
OR51A4	401666	broad.mit.edu	37	11	4968155	4968155	+	Missense_Mutation	SNP	T	T	C	rs1817206		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	C	Unknown	Valid	Germline	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:4968155T>C	ENST00000380373.2	-	1	201	c.176A>G	c.(175-177)gAg>gGg	p.E59G	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001005329.1	NP_001005329.1	Q8NGJ6	O51A4_HUMAN	olfactory receptor, family 51, subfamily A, member 4	59						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(3)|lung(15)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		GTACATGGGCTCATGCAAGGA	0.428																																					p.E59G												.	.	0			c.A176G	11						.						187.0	169.0	175.0					11																	4968155		2198	4298	6496	4924731	SO:0001583	missense	401666	exon1			AB065798	CCDS31367.1	11p15.4	2012-08-09			ENSG00000205497	ENSG00000205497		"""GPCR / Class A : Olfactory receptors"""	14795	protein-coding gene	gene with protein product							Standard	NM_001005329		Approved		uc010qys.2	Q8NGJ6	OTTHUMG00000066614	ENST00000380373.2:c.176A>G	11.37:g.4968155T>C	ENSP00000369731:p.Glu59Gly		4924731	NM_001005329		Missense_Mutation	SNP	ENST00000380373.2	37	CCDS31367.1	27	0.012362637362637362	18	0.036585365853658534	1	0.0027624309392265192	2	0.0034965034965034965	6	0.0079155672823219	T	18.26	3.583935	0.65992	.	.	ENSG00000205497	ENST00000380373	T	0.00360	7.86	3.56	3.56	0.40772	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00271	0.0008	M	0.93150	3.385	0.26475	N	0.975206	D	0.63046	0.992	D	0.65773	0.938	T	0.35992	-0.9766	9	0.72032	D	0.01	.	6.3245	0.21237	0.2208:0.0:0.0:0.7792	.	59	Q8NGJ6	O51A4_HUMAN	G	59	ENSP00000369731:E59G	ENSP00000369731:E59G	E	-	2	0	OR51A4	4924731	0.004000	0.15560	0.912000	0.35992	0.945000	0.59286	1.544000	0.36158	1.620000	0.50308	0.462000	0.41574	GAG		0.428	OR51A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142821.1	NM_001005329	
OR52N4	390072	broad.mit.edu	37	11	5776371	5776371	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:5776371A>T	ENST00000317254.3	+	1	449	c.401A>T	c.(400-402)tAt>tTt	p.Y134F	TRIM5_ENST00000380027.1_Intron	NM_001005175.2	NP_001005175.3	Q8NGI2	O52N4_HUMAN	olfactory receptor, family 52, subfamily N, member 4 (gene/pseudogene)	134						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Y134F(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;1.87e-10)|LUSC - Lung squamous cell carcinoma(625;0.114)|BRCA - Breast invasive adenocarcinoma(625;0.135)|Lung(200;0.197)		CCCTTACGCTATTCAACTATC	0.498																																					p.Y134F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A401T	11						.						153.0	151.0	151.0					11																	5776371		2201	4297	6498	5732947	SO:0001583	missense	390072	exon1			AB065813	CCDS44528.1	11p15.4	2013-10-10	2013-10-10		ENSG00000181074	ENSG00000181074		"""GPCR / Class A : Olfactory receptors"""	15230	protein-coding gene	gene with protein product			"""olfactory receptor, family 52, subfamily N, member 4"""				Standard	NM_001005175		Approved		uc001mbu.3	Q8NGI2	OTTHUMG00000066887	ENST00000317254.3:c.401A>T	11.37:g.5776371A>T	ENSP00000323224:p.Tyr134Phe		5732947	NM_001005175	B2RNP8|Q6IF77	Missense_Mutation	SNP	ENST00000317254.3	37	CCDS44528.1	.	.	.	.	.	.	.	.	.	.	A	15.38	2.815588	0.50527	.	.	ENSG00000181074	ENST00000317254	T	0.30448	1.53	5.97	5.97	0.96955	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44483	D	0.000457	T	0.70745	0.3259	H	0.97896	4.1	0.31707	N	0.639984	D	0.89917	1.0	D	0.74674	0.984	D	0.84044	0.0366	10	0.87932	D	0	.	15.2763	0.73745	1.0:0.0:0.0:0.0	.	134	Q8NGI2	O52N4_HUMAN	F	134	ENSP00000323224:Y134F	ENSP00000323224:Y134F	Y	+	2	0	OR52N4	5732947	0.980000	0.34600	0.981000	0.43875	0.021000	0.10359	9.058000	0.93896	2.286000	0.76751	0.455000	0.32223	TAT		0.498	OR52N4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143350.1	NM_001005175	
OR52N5	390075	broad.mit.edu	37	11	5799164	5799164	+	Missense_Mutation	SNP	G	G	A	rs372078375		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:5799164G>A	ENST00000317093.2	-	1	733	c.701C>T	c.(700-702)gCg>gTg	p.A234V	TRIM5_ENST00000380027.1_Intron	NM_001001922.2	NP_001001922.2	Q8NH56	O52N5_HUMAN	olfactory receptor, family 52, subfamily N, member 5	234						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A234V(1)		endometrium(2)|large_intestine(3)|liver(1)|lung(17)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.05e-11)|LUSC - Lung squamous cell carcinoma(625;0.112)|BRCA - Breast invasive adenocarcinoma(625;0.135)|Lung(200;0.195)		GAGGCTGATCGCTGCCTTGAG	0.438																																					p.A234V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C701T	11						.						114.0	107.0	109.0					11																	5799164		2118	4088	6206	5755740	SO:0001583	missense	390075	exon1			AB065535	CCDS31397.1	11p15.4	2012-08-09			ENSG00000181009	ENSG00000181009		"""GPCR / Class A : Olfactory receptors"""	15231	protein-coding gene	gene with protein product							Standard	NM_001001922		Approved	OR52N5Q	uc010qzn.2	Q8NH56	OTTHUMG00000168799	ENST00000317093.2:c.701C>T	11.37:g.5799164G>A	ENSP00000322866:p.Ala234Val		5755740	NM_001001922	B9EH12|Q6IFG2	Missense_Mutation	SNP	ENST00000317093.2	37	CCDS31397.1	.	.	.	.	.	.	.	.	.	.	G	0.003	-2.519489	0.00149	.	.	ENSG00000181009	ENST00000317093	T	0.00011	9.37	3.72	2.58	0.30949	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.00011	-3.01	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.38415	-0.9662	9	0.02654	T	1	.	8.344	0.32261	0.9014:0.0:0.0986:0.0	.	234	Q8NH56	O52N5_HUMAN	V	234	ENSP00000322866:A234V	ENSP00000322866:A234V	A	-	2	0	OR52N5	5755740	0.130000	0.22417	0.197000	0.23402	0.090000	0.18270	4.000000	0.57039	0.592000	0.29728	-0.513000	0.04457	GCG		0.438	OR52N5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401141.1	NM_001001922	
DCHS1	8642	broad.mit.edu	37	11	6651124	6651124	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:6651124C>A	ENST00000299441.3	-	11	5225	c.4814G>T	c.(4813-4815)cGg>cTg	p.R1605L	RP11-732A19.6_ENST00000526633.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	1605	Cadherin 15. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R1605L(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GTCCAACGGCCGCACCACGGA	0.652																																					p.R1605L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4814T	11						.						40.0	41.0	41.0					11																	6651124		2200	4295	6495	6607700	SO:0001583	missense	8642	exon11			AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"""Cadherins / Cadherin-related"""	13681	protein-coding gene	gene with protein product	"""cadherin-related family member 6"""	603057	"""protocadherin 16"", ""dachsous 1 (Drosophila)"""	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.4814G>T	11.37:g.6651124C>A	ENSP00000299441:p.Arg1605Leu		6607700	NM_003737	O15098	Missense_Mutation	SNP	ENST00000299441.3	37	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	C	11.53	1.665899	0.29604	.	.	ENSG00000166341	ENST00000299441	T	0.01725	4.67	4.95	3.05	0.35203	Cadherin (4);Cadherin-like (1);	0.158403	0.29853	N	0.011028	T	0.03434	0.0099	M	0.76002	2.32	0.28535	N	0.912392	B	0.23377	0.084	B	0.24006	0.05	T	0.12734	-1.0536	10	0.37606	T	0.19	.	11.7396	0.51786	0.1246:0.8041:0.0:0.0713	.	1605	Q96JQ0	PCD16_HUMAN	L	1605	ENSP00000299441:R1605L	ENSP00000299441:R1605L	R	-	2	0	DCHS1	6607700	0.984000	0.35163	0.668000	0.29813	0.006000	0.05464	2.222000	0.42926	0.288000	0.22398	-2.619000	0.00157	CGG		0.652	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737	
WEE1	7465	broad.mit.edu	37	11	9608076	9608076	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:9608076G>A	ENST00000450114.2	+	9	1804	c.1551G>A	c.(1549-1551)ccG>ccA	p.P517P	WEE1_ENST00000299613.6_Silent_p.P303P	NM_003390.3	NP_003381.1	P30291	WEE1_HUMAN	WEE1 G2 checkpoint kinase	517	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood coagulation (GO:0007596)|establishment of cell polarity (GO:0030010)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|neuron projection morphogenesis (GO:0048812)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.P517P(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	23				all cancers(16;4.59e-09)|Epithelial(150;3.15e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0484)		AACCTCTTCCGAGAAATGGAG	0.403																																					p.P303P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G909A	11						.						105.0	100.0	102.0					11																	9608076		2201	4294	6495	9564652	SO:0001819	synonymous_variant	7465	exon9			X62048	CCDS7800.1, CCDS44536.1	11p15.4	2013-10-21	2013-10-21		ENSG00000166483	ENSG00000166483			12761	protein-coding gene	gene with protein product		193525	"""wee1+ (S. pombe) homolog"", ""WEE1 homolog (S. pombe)"""			1840647	Standard	NM_003390		Approved		uc001mhs.3	P30291	OTTHUMG00000165863	ENST00000450114.2:c.1551G>A	11.37:g.9608076G>A			9564652	NM_001143976	B3KVE1|D3DQV0	Silent	SNP	ENST00000450114.2	37	CCDS7800.1																																																																																				0.403	WEE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386757.1	NM_003390	
PIK3C2A	5286	broad.mit.edu	37	11	17190693	17190693	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:17190693G>T	ENST00000265970.7	-	1	595	c.596C>A	c.(595-597)cCt>cAt	p.P199H	PIK3C2A_ENST00000540361.1_Intron|PIK3C2A_ENST00000531428.1_Intron	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	199					clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|exocytosis (GO:0006887)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|small molecule metabolic process (GO:0044281)|vascular smooth muscle contraction (GO:0014829)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol binding (GO:0035091)	p.P199H(1)		central_nervous_system(4)|endometrium(5)|kidney(5)|large_intestine(7)|lung(24)|ovary(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	58						AGGTGTCAAAGGATATGAGAA	0.408																																					p.P199H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C596A	11						.						64.0	65.0	65.0					11																	17190693		2200	4293	6493	17147269	SO:0001583	missense	5286	exon1			Y13367	CCDS7824.1	11p15.5-p14	2012-07-13	2012-07-13			ENSG00000011405	2.7.1.154		8971	protein-coding gene	gene with protein product		603601	"""phosphoinositide-3-kinase, class 2, alpha polypeptide"""			9337861	Standard	NM_002645		Approved	PI3K-C2alpha	uc001mmq.4	O00443		ENST00000265970.7:c.596C>A	11.37:g.17190693G>T	ENSP00000265970:p.Pro199His		17147269	NM_002645	B0LPH2|B4E2G4|Q14CQ9	Missense_Mutation	SNP	ENST00000265970.7	37	CCDS7824.1	.	.	.	.	.	.	.	.	.	.	G	18.81	3.702569	0.68501	.	.	ENSG00000011405	ENST00000265970;ENST00000544896	T	0.64803	-0.12	5.53	5.53	0.82687	.	0.308537	0.36740	N	0.002427	T	0.68210	0.2976	L	0.29908	0.895	0.80722	D	1	D;D	0.76494	0.999;0.991	D;P	0.66979	0.948;0.707	T	0.71290	-0.4637	10	0.87932	D	0	-9.5336	14.3006	0.66346	0.0:0.0:0.8514:0.1486	.	199;199	F5H5W9;O00443	.;P3C2A_HUMAN	H	199	ENSP00000265970:P199H	ENSP00000265970:P199H	P	-	2	0	PIK3C2A	17147269	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.075000	0.57584	2.591000	0.87537	0.591000	0.81541	CCT		0.408	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645	
ABCC8	6833	broad.mit.edu	37	11	17414672	17414672	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:17414672G>A	ENST00000389817.3	-	39	4680	c.4612C>T	c.(4612-4614)Cga>Tga	p.R1538*	ABCC8_ENST00000302539.4_Nonsense_Mutation_p.R1539*			Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 8	1538	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium ion transmembrane transporter activity (GO:0015079)|sulfonylurea receptor activity (GO:0008281)	p.R1538*(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(38)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	67				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Chlorpropamide(DB00672)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Gliquidone(DB01251)|Glyburide(DB01016)|Glycodiazine(DB01382)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolbutamide(DB01124)	GTGTGCACTCGATGCTGGGCA	0.647																																					p.R1538X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C4612T	11						.						61.0	49.0	53.0					11																	17414672		2200	4293	6493	17371248	SO:0001587	stop_gained	6833	exon39			L78207	CCDS31437.1, CCDS73264.1	11p15.1	2014-09-17			ENSG00000006071	ENSG00000006071		"""ATP binding cassette transporters / subfamily C"""	59	protein-coding gene	gene with protein product	"""sulfonylurea receptor (hyperinsulinemia)"""	600509		SUR, HRINS		7920639, 7716548	Standard	NM_000352		Approved	HI, PHHI, SUR1, MRP8, ABC36, HHF1, TNDM2	uc001mnc.3	Q09428	OTTHUMG00000166316	ENST00000389817.3:c.4612C>T	11.37:g.17414672G>A	ENSP00000374467:p.Arg1538*		17371248	NM_000352	A6NMX8|E3UYX6|O75948|Q16583	Nonsense_Mutation	SNP	ENST00000389817.3	37	CCDS31437.1	.	.	.	.	.	.	.	.	.	.	G	43	9.951471	0.99303	.	.	ENSG00000006071	ENST00000389817;ENST00000302539	.	.	.	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.7391	0.91767	0.0:0.0:1.0:0.0	.	.	.	.	X	1538;1539	.	ENSP00000303960:R1539X	R	-	1	2	ABCC8	17371248	1.000000	0.71417	0.995000	0.50966	0.610000	0.37248	5.303000	0.65738	2.430000	0.82344	0.561000	0.74099	CGA		0.647	ABCC8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389093.1	NM_000352	
KCNC1	3746	broad.mit.edu	37	11	17793340	17793340	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:17793340G>A	ENST00000379472.3	+	2	729	c.699G>A	c.(697-699)gtG>gtA	p.V233V	KCNC1_ENST00000265969.6_Silent_p.V233V	NM_004976.4	NP_004967.1	P48547	KCNC1_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 1	233					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.V233V(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)	GCACGCAAGTGCGCTACTACC	0.577																																					p.V233V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G699A	11						.						263.0	211.0	229.0					11																	17793340		2200	4293	6493	17749916	SO:0001819	synonymous_variant	3746	exon2			M96747	CCDS7827.1, CCDS44547.1	11p15	2012-07-05			ENSG00000129159	ENSG00000129159		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6233	protein-coding gene	gene with protein product		176258				8449507, 16382104	Standard	NM_004976		Approved	Kv3.1	uc009yhc.1	P48547	OTTHUMG00000166359	ENST00000379472.3:c.699G>A	11.37:g.17793340G>A			17749916	NM_004976	K4DI87	Silent	SNP	ENST00000379472.3	37	CCDS7827.1																																																																																				0.577	KCNC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389389.1	NM_004976	
IMMP1L	196294	broad.mit.edu	37	11	31451881	31451881	+	IGR	SNP	C	C	A	rs181756989		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:31451881C>A	ENST00000278200.1	-	0	795				DNAJC24_ENST00000465995.1_Missense_Mutation_p.A128E	NM_144981.1	NP_659418.1	Q96LU5	IMP1L_HUMAN	IMP1 inner mitochondrial membrane peptidase-like (S. cerevisiae)						protein processing involved in protein targeting to mitochondrion (GO:0006627)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	serine-type peptidase activity (GO:0008236)	p.A128E(1)		breast(1)|cervix(1)|large_intestine(1)|lung(4)	7	Lung SC(675;0.225)					AAGGATGAAGCGGAAGAAGTT	0.338													C|||	1	0.000199681	0.0	0.0	5008	,	,		15746	0.0		0.001	False		,,,				2504	0.0				p.A128E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C383A	11						.						176.0	168.0	171.0					11																	31451881		1866	4104	5970	31408457	SO:0001628	intergenic_variant	120526	exon5				CCDS7874.1	11p13	2014-07-30			ENSG00000148950	ENSG00000148950			26317	protein-coding gene	gene with protein product		612323					Standard	NM_144981		Approved	FLJ25059	uc001msy.1	Q96LU5	OTTHUMG00000166226		11.37:g.31451881C>A			31408457	NM_181706	D3DQZ7|Q96SH9	Missense_Mutation	SNP	ENST00000278200.1	37	CCDS7874.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	15.95	2.983886	0.53827	.	.	ENSG00000170946	ENST00000465995	T	0.32515	1.45	5.35	2.19	0.27852	Zinc finger, DPH-type (2);	0.512035	0.21664	N	0.070971	T	0.34019	0.0883	M	0.64997	1.995	0.26778	N	0.969655	P	0.47191	0.891	P	0.48524	0.58	T	0.13150	-1.0520	10	0.49607	T	0.09	.	5.993	0.19478	0.0:0.5289:0.2409:0.2302	.	127	Q6P3W2	DJC24_HUMAN	E	128	ENSP00000417548:A128E	ENSP00000417548:A128E	A	+	2	0	DNAJC24	31408457	0.067000	0.21026	0.885000	0.34714	0.853000	0.48598	0.253000	0.18296	0.522000	0.28464	0.650000	0.86243	GCG		0.338	IMMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388496.1	NM_144981	
RAG1	5896	broad.mit.edu	37	11	36594979	36594979	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:36594979C>A	ENST00000299440.5	+	2	237	c.125C>A	c.(124-126)cCt>cAt	p.P42H		NM_000448.2	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	42	Interaction with importin alpha-1.				adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|DNA recombination (GO:0006310)|histone monoubiquitination (GO:0010390)|immune response (GO:0006955)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|pre-B cell allelic exclusion (GO:0002331)|protein autoubiquitination (GO:0051865)|regulation of T cell differentiation (GO:0045580)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.P42H(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	65	all_lung(20;0.226)	all_hematologic(20;0.107)				GAAAAGACACCTGAAGAAGCT	0.458									Familial Hemophagocytic Lymphohistiocytosis																												p.P42H	Pancreas(43;321 1249 3212 48200)|Esophageal Squamous(38;49 1003 17530 24363)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C125A	11						.						50.0	55.0	54.0					11																	36594979		2202	4298	6500	36551555	SO:0001583	missense	5896	exon2	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	M29474	CCDS7902.1	11p13	2014-09-17				ENSG00000166349		"""RING-type (C3HC4) zinc fingers"""	9831	protein-coding gene	gene with protein product	"""recombination activating protein 1"", ""RING finger protein 74"", ""V(D)J recombination-activating protein 1"""	179615				1612612, 1283330	Standard	NM_000448		Approved	RNF74, MGC43321	uc001mwu.4	P15918		ENST00000299440.5:c.125C>A	11.37:g.36594979C>A	ENSP00000299440:p.Pro42His		36551555	NM_000448	E9PPC4|Q8IY72|Q8NER2	Missense_Mutation	SNP	ENST00000299440.5	37	CCDS7902.1	.	.	.	.	.	.	.	.	.	.	C	13.94	2.386078	0.42308	.	.	ENSG00000166349	ENST00000534663;ENST00000299440	T;T	0.81247	-1.47;-1.44	6.14	6.14	0.99180	.	0.056365	0.64402	D	0.000001	D	0.85159	0.5633	M	0.82823	2.61	0.58432	D	0.999996	P	0.38167	0.621	B	0.39419	0.299	D	0.85906	0.1437	10	0.87932	D	0	.	20.8597	0.99761	0.0:1.0:0.0:0.0	.	42	P15918	RAG1_HUMAN	H	42	ENSP00000434610:P42H;ENSP00000299440:P42H	ENSP00000299440:P42H	P	+	2	0	RAG1	36551555	0.230000	0.23740	0.224000	0.23877	0.523000	0.34469	4.382000	0.59594	2.937000	0.99478	0.650000	0.86243	CCT		0.458	RAG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389535.1	NM_000448	
LRRC4C	57689	broad.mit.edu	37	11	40136434	40136434	+	Missense_Mutation	SNP	C	C	T	rs74858686	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:40136434C>T	ENST00000278198.2	-	2	3372	c.1409G>A	c.(1408-1410)cGg>cAg	p.R470Q	LRRC4C_ENST00000527150.1_Missense_Mutation_p.R470Q|LRRC4C_ENST00000528697.1_Missense_Mutation_p.R470Q|LRRC4C_ENST00000530763.1_Missense_Mutation_p.R470Q			Q9HCJ2	LRC4C_HUMAN	leucine rich repeat containing 4C	470					regulation of axonogenesis (GO:0050770)	cell junction (GO:0030054)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)		p.R470Q(1)		NS(2)|central_nervous_system(3)|endometrium(1)|large_intestine(14)|lung(43)|ovary(5)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	86		all_lung(304;0.0575)|Lung NSC(402;0.138)				ATCTGTGGTCCGTGCCTCATC	0.517													C|||	17	0.00339457	0.0015	0.0	5008	,	,		20552	0.0149		0.0	False		,,,				2504	0.0				p.R470Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1409A	11						.	C	GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	130.0	118.0	122.0		1409	5.8	1.0	11	dbSNP_131	122	0,8600		0,0,4300	yes	missense	LRRC4C	NM_020929.1	43	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	benign	470/641	40136434	2,13004	2203	4300	6503	40093010	SO:0001583	missense	57689	exon2			AB046800	CCDS31464.1	11p12	2013-01-14				ENSG00000148948		"""Immunoglobulin superfamily / I-set domain containing"""	29317	protein-coding gene	gene with protein product		608817				14595443	Standard	NM_020929		Approved	KIAA1580, NGL-1	uc031pzu.1	Q9HCJ2		ENST00000278198.2:c.1409G>A	11.37:g.40136434C>T	ENSP00000278198:p.Arg470Gln		40093010	NM_020929	A8K0T1|Q7L0N3	Missense_Mutation	SNP	ENST00000278198.2	37	CCDS31464.1	5	0.0022893772893772895	0	0.0	0	0.0	5	0.008741258741258742	0	0.0	C	7.365	0.625735	0.14257	4.54E-4	0.0	ENSG00000148948	ENST00000278198;ENST00000527150;ENST00000528697;ENST00000530763	T;T;T;T	0.57107	0.42;0.42;0.42;0.42	5.84	5.84	0.93424	.	0.259107	0.38005	N	0.001849	T	0.32882	0.0844	L	0.41824	1.3	0.39554	D	0.969015	B	0.10296	0.003	B	0.01281	0.0	T	0.23297	-1.0192	10	0.12103	T	0.63	.	12.3703	0.55252	0.0:0.9158:0.0:0.0842	.	470	Q9HCJ2	LRC4C_HUMAN	Q	470	ENSP00000278198:R470Q;ENSP00000436976:R470Q;ENSP00000437132:R470Q;ENSP00000434761:R470Q	ENSP00000278198:R470Q	R	-	2	0	LRRC4C	40093010	1.000000	0.71417	0.994000	0.49952	0.943000	0.58893	4.025000	0.57225	2.760000	0.94817	0.655000	0.94253	CGG		0.517	LRRC4C-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389499.1	NM_020929	
ACCS	84680	broad.mit.edu	37	11	44104992	44104992	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:44104992T>G	ENST00000263776.8	+	14	1707	c.1273T>G	c.(1273-1275)Ttt>Gtt	p.F425V		NM_001127219.1|NM_032592.3	NP_001120691.1|NP_115981.1	Q96QU6	1A1L1_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)	425					biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)	p.F425V(1)		breast(4)|endometrium(3)|large_intestine(11)|lung(15)|ovary(1)|skin(1)	35						CAAGGGCACCTTTGAGGAGGA	0.572																																					p.F425V	Esophageal Squamous(158;148 1889 8077 23160 41213)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1273G	11						.						62.0	57.0	59.0					11																	44104992		2203	4300	6503	44061568	SO:0001583	missense	84680	exon14			AY026508	CCDS7907.1	11p11	2008-03-12	2008-01-28		ENSG00000110455	ENSG00000110455			23989	protein-coding gene	gene with protein product		608405				11470512	Standard	NM_032592		Approved	PHACS, ACS	uc009yks.1	Q96QU6	OTTHUMG00000166427	ENST00000263776.8:c.1273T>G	11.37:g.44104992T>G	ENSP00000263776:p.Phe425Val		44061568	NM_032592	B4E219|Q8WUL4|Q96LX5	Missense_Mutation	SNP	ENST00000263776.8	37	CCDS7907.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.401571	0.83120	.	.	ENSG00000110455	ENST00000263776	T	0.21361	2.01	5.91	5.91	0.95273	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.162467	0.56097	D	0.000025	T	0.44932	0.1317	M	0.67397	2.05	0.80722	D	1	D	0.53619	0.961	D	0.64410	0.925	T	0.38090	-0.9677	10	0.87932	D	0	-4.9024	16.0098	0.80391	0.0:0.0:0.0:1.0	.	425	Q96QU6	1A1L1_HUMAN	V	425	ENSP00000263776:F425V	ENSP00000263776:F425V	F	+	1	0	ACCS	44061568	1.000000	0.71417	1.000000	0.80357	0.704000	0.40688	7.315000	0.78998	2.254000	0.74563	0.533000	0.62120	TTT		0.572	ACCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389721.1	NM_032592	
MAPK8IP1	9479	broad.mit.edu	37	11	45926729	45926729	+	Silent	SNP	C	C	T	rs544815653		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:45926729C>T	ENST00000241014.2	+	11	2162	c.1992C>T	c.(1990-1992)ccC>ccT	p.P664P	RP11-618K13.2_ENST00000533218.1_RNA|MAPK8IP1_ENST00000395629.2_Silent_p.P654P	NM_005456.3	NP_005447.1	Q9UQF2	JIP1_HUMAN	mitogen-activated protein kinase 8 interacting protein 1	664	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				JUN phosphorylation (GO:0007258)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|positive regulation of signal transduction (GO:0009967)|regulation of JNK cascade (GO:0046328)|regulation of transcription, DNA-templated (GO:0006355)|vesicle-mediated transport (GO:0016192)	axonal growth cone (GO:0044295)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic growth cone (GO:0044294)|dentate gyrus mossy fiber (GO:0044302)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	kinesin binding (GO:0019894)|MAP-kinase scaffold activity (GO:0005078)|protein kinase inhibitor activity (GO:0004860)	p.P664P(2)		breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(2)	24				GBM - Glioblastoma multiforme(35;0.231)		CCAAGCACCCCGCCGACCACC	0.632													c|||	1	0.000199681	0.0	0.0	5008	,	,		15782	0.0		0.001	False		,,,				2504	0.0				p.P664P												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1992T	11						.						59.0	57.0	58.0					11																	45926729		2203	4299	6502	45883305	SO:0001819	synonymous_variant	9479	exon11				CCDS7916.1	11p11.2	2009-07-24			ENSG00000121653	ENSG00000121653			6882	protein-coding gene	gene with protein product		604641		PRKM8IP		9235893, 9442013	Standard	NM_005456		Approved	IB1, JIP-1, JIP1	uc001nbr.3	Q9UQF2	OTTHUMG00000134324	ENST00000241014.2:c.1992C>T	11.37:g.45926729C>T			45883305	NM_005456	D3DQP4|O43407	Silent	SNP	ENST00000241014.2	37	CCDS7916.1																																																																																				0.632	MAPK8IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259405.1	NM_005456	
CKAP5	9793	broad.mit.edu	37	11	46774923	46774923	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:46774923A>G	ENST00000529230.1	-	37	5040	c.4994T>C	c.(4993-4995)aTc>aCc	p.I1665T	CKAP5_ENST00000415402.1_Missense_Mutation_p.I1665T|MIR5582_ENST00000579697.1_RNA|CKAP5_ENST00000312055.5_Missense_Mutation_p.I1605T|CKAP5_ENST00000354558.3_Missense_Mutation_p.I1605T			Q14008	CKAP5_HUMAN	cytoskeleton associated protein 5	1665					centrosome organization (GO:0051297)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|RNA transport (GO:0050658)|spindle organization (GO:0007051)	centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|protein complex (GO:0043234)|spindle pole (GO:0000922)		p.I1665T(1)		breast(1)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	43						CACAGAGCGGATGACCTGTTG	0.502																																					p.I1665T	Ovarian(4;85 273 2202 4844 13323)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T4994C	11						.						183.0	149.0	161.0					11																	46774923		2201	4299	6500	46731499	SO:0001583	missense	9793	exon37				CCDS7924.1, CCDS31477.1	11p11.2	2006-09-20			ENSG00000175216	ENSG00000175216			28959	protein-coding gene	gene with protein product		611142				7788527, 8536682	Standard	NM_014756		Approved	ch-TOG, KIAA0097, TOG, TOGp	uc001ndi.2	Q14008	OTTHUMG00000166599	ENST00000529230.1:c.4994T>C	11.37:g.46774923A>G	ENSP00000432768:p.Ile1665Thr		46731499	NM_001008938	Q05D70|Q0VAX7|Q0VAX8|Q14668|Q2TA89|Q6NSH4	Missense_Mutation	SNP	ENST00000529230.1	37	CCDS31477.1	.	.	.	.	.	.	.	.	.	.	A	14.99	2.700540	0.48307	.	.	ENSG00000175216	ENST00000529230;ENST00000415402;ENST00000312055;ENST00000354558	T;T;T;T	0.49720	0.83;0.81;0.77;0.77	5.61	5.61	0.85477	Armadillo-like helical (1);Armadillo-type fold (1);	0.141968	0.64402	D	0.000006	T	0.40839	0.1133	L	0.46157	1.445	0.39458	D	0.967518	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.09377	0.004;0.003;0.001	T	0.36407	-0.9749	10	0.52906	T	0.07	-1.5122	10.1858	0.42998	0.9258:0.0:0.0742:0.0	.	1665;1605;1665	Q14008-3;Q14008-2;Q14008	.;.;CKAP5_HUMAN	T	1665;1665;1605;1605	ENSP00000432768:I1665T;ENSP00000395302:I1665T;ENSP00000310227:I1605T;ENSP00000346566:I1605T	ENSP00000310227:I1605T	I	-	2	0	CKAP5	46731499	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	7.515000	0.81761	2.133000	0.65898	0.533000	0.62120	ATC		0.502	CKAP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390679.1	NM_014756	
NR1H3	10062	broad.mit.edu	37	11	47290160	47290160	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:47290160C>T	ENST00000467728.1	+	9	2495	c.1257C>T	c.(1255-1257)agC>agT	p.S419S	MADD_ENST00000395344.3_5'Flank|RP11-17G12.3_ENST00000543925.1_RNA|MADD_ENST00000402799.1_5'Flank|MADD_ENST00000406482.1_5'Flank|NR1H3_ENST00000529540.1_3'UTR|MADD_ENST00000342922.4_5'Flank|NR1H3_ENST00000395397.3_Silent_p.S374S|NR1H3_ENST00000441012.2_Silent_p.S419S|MADD_ENST00000402192.2_5'Flank|MADD_ENST00000407859.3_5'Flank|MADD_ENST00000349238.3_5'Flank|MADD_ENST00000311027.5_5'Flank|MADD_ENST00000395336.3_5'Flank|NR1H3_ENST00000527949.1_Silent_p.S268S|RP11-17G12.3_ENST00000545474.1_RNA|NR1H3_ENST00000405853.3_Silent_p.S359S|NR1H3_ENST00000405576.1_Silent_p.S314S|NR1H3_ENST00000481889.2_Silent_p.S438S|NR1H3_ENST00000407404.1_Silent_p.S359S			Q13133	NR1H3_HUMAN	nuclear receptor subfamily 1, group H, member 3	419	Ligand-binding. {ECO:0000255}.				apoptotic cell clearance (GO:0043277)|cellular lipid metabolic process (GO:0044255)|cellular response to lipopolysaccharide (GO:0071222)|cholesterol homeostasis (GO:0042632)|gene expression (GO:0010467)|lipid homeostasis (GO:0055088)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of lipid transport (GO:0032369)|negative regulation of macrophage activation (GO:0043031)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of pinocytosis (GO:0048550)|negative regulation of proteolysis (GO:0045861)|negative regulation of secretion of lysosomal enzymes (GO:0090341)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of cholesterol transport (GO:0032376)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cholesterol homeostasis (GO:2000188)|regulation of circadian rhythm (GO:0042752)|response to progesterone (GO:0032570)|sterol homeostasis (GO:0055092)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|steroid hormone receptor activity (GO:0003707)|sterol response element binding (GO:0032810)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.S419S(1)		endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|ovary(5)	20						CCCTGAGCAGCGTCCACTCAG	0.557																																					p.S374S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1122T	11						.						125.0	115.0	118.0					11																	47290160		2201	4298	6499	47246736	SO:0001819	synonymous_variant	10062	exon9			U22662	CCDS7929.1, CCDS44584.1, CCDS44585.1, CCDS73285.1	11p11.2	2013-01-16			ENSG00000025434	ENSG00000025434		"""Nuclear hormone receptors"""	7966	protein-coding gene	gene with protein product	"""liver X receptor-alpha"""	602423				8621574, 7744246	Standard	NM_005693		Approved	LXR-a, RLD-1	uc009ylm.3	Q13133	OTTHUMG00000150628	ENST00000467728.1:c.1257C>T	11.37:g.47290160C>T			47246736	NM_001130102	A8K3J9|D3DQR1|Q8IW13|Q96H87	Silent	SNP	ENST00000467728.1	37	CCDS7929.1																																																																																				0.557	NR1H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319214.3		
MADD	8567	broad.mit.edu	37	11	47312255	47312255	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:47312255G>T	ENST00000311027.5	+	20	3414	c.3249G>T	c.(3247-3249)atG>atT	p.M1083I	MADD_ENST00000395344.3_Missense_Mutation_p.M1020I|MADD_ENST00000402799.1_Missense_Mutation_p.M1020I|MADD_ENST00000406482.1_Missense_Mutation_p.M1020I|MADD_ENST00000342922.4_Missense_Mutation_p.M1063I|MADD_ENST00000405573.2_5'Flank|MADD_ENST00000402192.2_Missense_Mutation_p.M1063I|MADD_ENST00000407859.3_Missense_Mutation_p.M1040I|MADD_ENST00000349238.3_Missense_Mutation_p.M1083I|MADD_ENST00000395336.3_Missense_Mutation_p.M1083I	NM_003682.3	NP_003673.3			MAP-kinase activating death domain									p.M1083I(1)		breast(7)|central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(19)|lung(26)|ovary(6)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	84				Lung(87;0.182)		CAAAGGCTATGGCACAACTGA	0.517																																					p.M1083I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3249T	11						.						61.0	60.0	60.0					11																	47312255		2201	4298	6499	47268831	SO:0001583	missense	8567	exon20			AB002356	CCDS7930.1, CCDS7931.1, CCDS7932.1, CCDS41642.1, CCDS44586.1, CCDS44587.1, CCDS44588.1, CCDS44589.1, CCDS44590.1	11p11.2	2012-10-04			ENSG00000110514	ENSG00000110514		"""DENN/MADD domain containing"""	6766	protein-coding gene	gene with protein product		603584				9115275, 9796103	Standard	NM_130476		Approved	DENN, KIAA0358, RAB3GEP	uc001ner.1	Q8WXG6	OTTHUMG00000150350	ENST00000311027.5:c.3249G>T	11.37:g.47312255G>T	ENSP00000310933:p.Met1083Ile		47268831	NM_003682		Missense_Mutation	SNP	ENST00000311027.5	37	CCDS7930.1	.	.	.	.	.	.	.	.	.	.	G	14.93	2.682389	0.47991	.	.	ENSG00000110514	ENST00000342922;ENST00000395342;ENST00000402799;ENST00000406482;ENST00000349238;ENST00000311027;ENST00000407859;ENST00000395344;ENST00000395336;ENST00000402192	T;T;T;T;T;T;T;T;T	0.05319	3.59;3.46;3.46;3.59;3.57;3.46;3.46;3.57;3.59	5.41	5.41	0.78517	.	0.662303	0.16492	N	0.212054	T	0.06325	0.0163	N	0.22421	0.69	0.80722	D	1	B;B;B;B;B;B;B;B;B;B	0.28850	0.033;0.019;0.143;0.225;0.056;0.056;0.082;0.225;0.088;0.141	B;B;B;B;B;B;B;B;B;B	0.31614	0.03;0.03;0.133;0.104;0.066;0.041;0.104;0.104;0.063;0.104	T	0.49588	-0.8924	10	0.26408	T	0.33	-11.3033	15.0842	0.72138	0.0:0.2589:0.7411:0.0	.	1020;1020;1083;1020;1020;1020;1083;1040;1083;1063	B5MEE5;A8K8S7;Q8WXG6-7;F8W9P9;Q8WXG6-6;Q8WXG6-5;Q8WXG6-2;Q8WXG6-4;Q8WXG6;Q8WXG6-3	.;.;.;.;.;.;.;.;MADD_HUMAN;.	I	1063;1020;1020;1020;1083;1083;1040;1020;1083;1063	ENSP00000343902:M1063I;ENSP00000385585:M1020I;ENSP00000384435:M1020I;ENSP00000304505:M1083I;ENSP00000310933:M1083I;ENSP00000384204:M1040I;ENSP00000378753:M1020I;ENSP00000378745:M1083I;ENSP00000384287:M1063I	ENSP00000310933:M1083I	M	+	3	0	MADD	47268831	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.520000	0.45554	2.691000	0.91804	0.563000	0.77884	ATG		0.517	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1		
PTPRJ	5795	broad.mit.edu	37	11	48157663	48157663	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:48157663C>T	ENST00000418331.2	+	9	2040	c.1688C>T	c.(1687-1689)cCt>cTt	p.P563L		NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	563	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				contact inhibition (GO:0060242)|heart development (GO:0007507)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of vascular permeability (GO:0043116)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of cell adhesion (GO:0045785)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion (GO:0030155)|vasculogenesis (GO:0001570)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|mitogen-activated protein kinase binding (GO:0051019)|phosphatase activity (GO:0016791)|platelet-derived growth factor receptor binding (GO:0005161)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)	p.P563L(1)		breast(3)|endometrium(7)|kidney(7)|large_intestine(5)|lung(15)|ovary(1)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						TGGAAGAGCCCTGACGGTGCT	0.522																																					p.P563L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1688T	11						.						152.0	129.0	137.0					11																	48157663		2201	4298	6499	48114239	SO:0001583	missense	5795	exon9			U10886	CCDS7945.1, CCDS44596.1	11p11.2	2013-02-11			ENSG00000149177	ENSG00000149177		"""CD molecules"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9673	protein-coding gene	gene with protein product		600925				7937872, 7994032	Standard	NM_001098503		Approved	DEP1, HPTPeta, CD148	uc001ngp.4	Q12913	OTTHUMG00000166573	ENST00000418331.2:c.1688C>T	11.37:g.48157663C>T	ENSP00000400010:p.Pro563Leu		48114239	NM_002843	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Missense_Mutation	SNP	ENST00000418331.2	37	CCDS7945.1	.	.	.	.	.	.	.	.	.	.	C	10.77	1.442599	0.25987	.	.	ENSG00000149177	ENST00000418331	T	0.62498	0.02	5.61	-2.15	0.07102	Fibronectin, type III (4);Immunoglobulin-like fold (1);	.	.	.	.	T	0.49949	0.1587	L	0.50333	1.59	0.09310	N	1	B	0.25667	0.131	B	0.28553	0.091	T	0.50709	-0.8796	9	0.66056	D	0.02	.	3.4476	0.07486	0.3312:0.226:0.3605:0.0823	.	563	Q12913	PTPRJ_HUMAN	L	563	ENSP00000400010:P563L	ENSP00000400010:P563L	P	+	2	0	PTPRJ	48114239	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.080000	0.11339	0.008000	0.14787	-0.291000	0.09656	CCT		0.522	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1		
SMTNL1	219537	broad.mit.edu	37	11	57310546	57310546	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:57310546C>T	ENST00000399154.2	+	1	431	c.431C>T	c.(430-432)gCc>gTc	p.A144V	SMTNL1_ENST00000457912.1_Missense_Mutation_p.A162V|SMTNL1_ENST00000527972.1_Missense_Mutation_p.A144V			A8MU46	SMTL1_HUMAN	smoothelin-like 1	144	Glu-rich.				negative regulation of vasodilation (GO:0045908)|positive regulation of vasoconstriction (GO:0045907)	contractile fiber (GO:0043292)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.A162V(1)		endometrium(2)|large_intestine(1)|lung(4)|ovary(1)	8						GAGAAAGAGGCCAAACCTGAA	0.532																																					p.A144V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C431T	11						.						37.0	39.0	38.0					11																	57310546		2054	4191	6245	57067122	SO:0001583	missense	219537	exon1			BX116227		11q12.1	2006-02-02				ENSG00000214872			32394	protein-coding gene	gene with protein product	"""calponin homology-associated smooth muscle protein"""	613664				15327999	Standard	NM_001105565		Approved	CHASM	uc021qjh.1	A8MU46		ENST00000399154.2:c.431C>T	11.37:g.57310546C>T	ENSP00000382108:p.Ala144Val		57067122	NM_001105565		Missense_Mutation	SNP	ENST00000399154.2	37		.	.	.	.	.	.	.	.	.	.	C	15.16	2.750151	0.49257	.	.	ENSG00000214872	ENST00000457912;ENST00000527972;ENST00000399154	T;T;T	0.02682	4.2;4.2;4.21	5.3	5.3	0.74995	.	0.273229	0.19243	U	0.119120	T	0.03053	0.0090	L	0.32530	0.975	0.09310	N	1	P	0.45126	0.851	B	0.37550	0.253	T	0.45469	-0.9259	10	0.62326	D	0.03	-5.2644	12.2208	0.54433	0.0:0.8284:0.1716:0.0	.	162	C9J621	.	V	162;144;144	ENSP00000406485:A162V;ENSP00000432651:A144V;ENSP00000382108:A144V	ENSP00000382108:A144V	A	+	2	0	SMTNL1	57067122	0.022000	0.18835	0.049000	0.19019	0.049000	0.14656	0.909000	0.28558	2.490000	0.84030	0.655000	0.94253	GCC		0.532	SMTNL1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_166203	
ZDHHC5	25921	broad.mit.edu	37	11	57466281	57466281	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:57466281G>T	ENST00000287169.3	+	11	2735	c.1373G>T	c.(1372-1374)aGc>aTc	p.S458I	ZDHHC5_ENST00000527985.1_Missense_Mutation_p.S405I	NM_015457.2	NP_056272.2	Q9C0B5	ZDHC5_HUMAN	zinc finger, DHHC-type containing 5	458					protein palmitoylation (GO:0018345)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.S458I(1)		endometrium(6)|kidney(3)|large_intestine(3)|lung(5)|skin(1)	18						TCCTATAAGAGCCTGGCCAAC	0.567																																					p.S458I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1373T	11						.						90.0	72.0	78.0					11																	57466281		2201	4296	6497	57222857	SO:0001583	missense	25921	exon11			AB051535	CCDS7965.1	11q13.1	2008-05-02			ENSG00000156599	ENSG00000156599		"""Zinc fingers, DHHC-type"""	18472	protein-coding gene	gene with protein product		614586				11214970	Standard	NM_015457		Approved	KIAA1748, ZNF375	uc001nkx.1	Q9C0B5	OTTHUMG00000167198	ENST00000287169.3:c.1373G>T	11.37:g.57466281G>T	ENSP00000287169:p.Ser458Ile		57222857	NM_015457	Q2TGF0|Q6ZMF0|Q8TAK8|Q9H923|Q9UFI7	Missense_Mutation	SNP	ENST00000287169.3	37	CCDS7965.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.042104	0.75732	.	.	ENSG00000156599	ENST00000527985;ENST00000287169;ENST00000529447	T;T;D	0.87491	-0.08;0.91;-2.26	5.09	5.09	0.68999	.	0.163209	0.53938	D	0.000043	D	0.90497	0.7023	L	0.49778	1.585	0.80722	D	1	D	0.59357	0.985	P	0.58520	0.84	D	0.91383	0.5129	10	0.87932	D	0	-19.7213	18.2951	0.90143	0.0:0.0:1.0:0.0	.	458	Q9C0B5	ZDHC5_HUMAN	I	405;458;292	ENSP00000432202:S405I;ENSP00000287169:S458I;ENSP00000435722:S292I	ENSP00000287169:S458I	S	+	2	0	ZDHHC5	57222857	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.988000	0.93501	2.656000	0.90262	0.563000	0.77884	AGC		0.567	ZDHHC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393694.1	NM_015457	
MRPL16	54948	broad.mit.edu	37	11	59573825	59573825	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	None	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:59573825C>T	ENST00000300151.4	-	4	964	c.751G>A	c.(751-753)Gtg>Atg	p.V251M		NM_017840.3	NP_060310.1	Q9NX20	RM16_HUMAN	mitochondrial ribosomal protein L16	251					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|endometrium(1)|liver(1)|lung(8)	11						ACTCACTACACACGTTTGGGC	0.468																																					p.V251M												.	.	0			c.G751A	11						.						182.0	172.0	175.0					11																	59573825		2201	4295	6496	59330401	SO:0001583	missense	54948	exon4			AF183428	CCDS7976.1	11q12.1	2012-09-13			ENSG00000166902	ENSG00000166902		"""Mitochondrial ribosomal proteins / large subunits"""	14476	protein-coding gene	gene with protein product		611829					Standard	NM_017840		Approved	FLJ20484, PNAS-111	uc001noh.2	Q9NX20	OTTHUMG00000167410	ENST00000300151.4:c.751G>A	11.37:g.59573825C>T	ENSP00000300151:p.Val251Met		59330401	NM_017840	Q9BYD0|Q9HB70	Missense_Mutation	SNP	ENST00000300151.4	37	CCDS7976.1	.	.	.	.	.	.	.	.	.	.	C	18.66	3.671398	0.67814	.	.	ENSG00000166902	ENST00000300151	T	0.30448	1.53	6.07	5.16	0.70880	.	0.053328	0.85682	D	0.000000	T	0.55970	0.1954	M	0.74258	2.255	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.61292	-0.7092	10	0.87932	D	0	.	14.2394	0.65948	0.0:0.9282:0.0:0.0718	.	251	Q9NX20	RM16_HUMAN	M	251	ENSP00000300151:V251M	ENSP00000300151:V251M	V	-	1	0	MRPL16	59330401	0.999000	0.42202	0.937000	0.37676	0.524000	0.34500	4.180000	0.58296	1.581000	0.49865	0.655000	0.94253	GTG		0.468	MRPL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394521.1	NM_017840	
MS4A10	341116	broad.mit.edu	37	11	60561505	60561505	+	Missense_Mutation	SNP	G	G	A	rs200380093		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:60561505G>A	ENST00000308287.1	+	5	517	c.421G>A	c.(421-423)Gtc>Atc	p.V141I		NM_206893.3	NP_996776.2	Q96PG2	M4A10_HUMAN	membrane-spanning 4-domains, subfamily A, member 10	141						integral component of membrane (GO:0016021)		p.V141I(1)		endometrium(1)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|skin(2)	21						TGGCCTCTTCGTCATCTCCAA	0.517																																					p.V141I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G421A	11						.	G	ILE/VAL	0,4406		0,0,2203	142.0	127.0	132.0		421	2.0	0.0	11		132	1,8597	1.2+/-3.3	0,1,4298	yes	missense	MS4A10	NM_206893.3	29	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	141/268	60561505	1,13003	2203	4299	6502	60318081	SO:0001583	missense	341116	exon5			AK122633	CCDS7992.1	11q12.2	2008-02-05				ENSG00000172689			13368	protein-coding gene	gene with protein product		608403				11486273, 11401424	Standard	NM_206893		Approved	CD20L7, MS4A9	uc001npz.1	Q96PG2		ENST00000308287.1:c.421G>A	11.37:g.60561505G>A	ENSP00000311862:p.Val141Ile		60318081	NM_206893	B2RP45|Q96PG3	Missense_Mutation	SNP	ENST00000308287.1	37	CCDS7992.1	.	.	.	.	.	.	.	.	.	.	G	7.886	0.731322	0.15507	0.0	1.16E-4	ENSG00000172689	ENST00000308287	T	0.02050	4.48	4.87	2.0	0.26442	.	0.463445	0.16144	N	0.227570	T	0.01092	0.0036	N	0.11870	0.19	0.09310	N	1	P	0.47253	0.892	B	0.37692	0.256	T	0.33777	-0.9855	10	0.02654	T	1	-18.0706	6.9355	0.24464	0.2928:0.0:0.7072:0.0	.	141	Q96PG2	M4A10_HUMAN	I	141	ENSP00000311862:V141I	ENSP00000311862:V141I	V	+	1	0	MS4A10	60318081	0.250000	0.23951	0.017000	0.16124	0.024000	0.10985	0.753000	0.26376	0.139000	0.18822	-0.140000	0.14226	GTC		0.517	MS4A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395619.1	NM_206893	
NXF1	10482	broad.mit.edu	37	11	62568866	62568866	+	Missense_Mutation	SNP	C	C	T	rs373618263		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:62568866C>T	ENST00000532297.1	-	9	1362	c.733G>A	c.(733-735)Gtt>Att	p.V245I	NXF1_ENST00000531131.1_Missense_Mutation_p.V108I|NXF1_ENST00000531709.2_Missense_Mutation_p.V245I|NXF1_ENST00000439713.2_Missense_Mutation_p.V245I|NXF1_ENST00000294172.2_Missense_Mutation_p.V245I			Q9UBU9	NXF1_HUMAN	nuclear RNA export factor 1	245					gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear inclusion body (GO:0042405)|nuclear pore (GO:0005643)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)	mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.V245I(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(9)|lung(13)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TTCAGGACAACGTCAATGTTC	0.498																																					p.V245I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G733A	11						.	C	ILE/VAL,ILE/VAL	1,4401	2.1+/-5.4	0,1,2200	80.0	69.0	73.0		733,733	5.3	1.0	11		73	0,8598		0,0,4299	no	missense,missense	NXF1	NM_001081491.1,NM_006362.4	29,29	0,1,6499	TT,TC,CC		0.0,0.0227,0.0077	benign,benign	245/357,245/620	62568866	1,12999	2201	4299	6500	62325442	SO:0001583	missense	10482	exon8			AF112880	CCDS8037.1, CCDS44629.1	11q12-q13	2008-07-21			ENSG00000162231	ENSG00000162231			8071	protein-coding gene	gene with protein product	"""tip associating protein"""	602647				9175835, 9660949	Standard	NM_001081491		Approved	TAP, Mex67, DKFZp667O0311	uc001nvf.1	Q9UBU9	OTTHUMG00000167612	ENST00000532297.1:c.733G>A	11.37:g.62568866C>T	ENSP00000436679:p.Val245Ile		62325442	NM_006362	B4E269|Q99799|Q9UQL2	Missense_Mutation	SNP	ENST00000532297.1	37	CCDS8037.1	.	.	.	.	.	.	.	.	.	.	C	8.076	0.771280	0.16051	2.27E-4	0.0	ENSG00000162231	ENST00000294172;ENST00000532297;ENST00000530875;ENST00000439713	T;T;T;T	0.27557	1.66;1.66;1.66;1.66	5.27	5.27	0.74061	.	0.134478	0.51477	D	0.000097	T	0.09862	0.0242	N	0.01122	-1.005	0.54753	D	0.99998	B;B;D;B	0.57899	0.001;0.0;0.981;0.002	B;B;B;B	0.41646	0.002;0.001;0.362;0.001	T	0.24368	-1.0162	10	0.11182	T	0.66	-20.5138	11.4714	0.50270	0.1796:0.8203:0.0:0.0	.	108;288;258;245	B4E227;E9PIN3;Q59E96;Q9UBU9	.;.;.;NXF1_HUMAN	I	245;245;288;245	ENSP00000294172:V245I;ENSP00000436679:V245I;ENSP00000435742:V288I;ENSP00000408864:V245I	ENSP00000294172:V245I	V	-	1	0	NXF1	62325442	0.971000	0.33674	0.966000	0.40874	0.948000	0.59901	2.812000	0.47994	2.466000	0.83321	0.655000	0.94253	GTT		0.498	NXF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395365.2	NM_006362	
WDR74	54663	broad.mit.edu	37	11	62603451	62603451	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:62603451C>T	ENST00000525239.1	-	5	888	c.351G>A	c.(349-351)aaG>aaA	p.K117K	WDR74_ENST00000525752.1_Silent_p.K60K|RP11-727F15.9_ENST00000535817.1_RNA|WDR74_ENST00000540620.1_5'UTR|RP11-727F15.9_ENST00000535867.1_RNA|WDR74_ENST00000278856.4_Silent_p.K117K|WDR74_ENST00000311713.7_Silent_p.K117K|WDR74_ENST00000529106.1_Silent_p.K117K			Q6RFH5	WDR74_HUMAN	WD repeat domain 74	117					blastocyst formation (GO:0001825)|RNA metabolic process (GO:0016070)	nucleolus (GO:0005730)|nucleus (GO:0005634)		p.K117N(2)|p.K117K(1)		kidney(2)|large_intestine(1)|liver(1)|lung(3)|ovary(1)	8						AGGATGTGTCCTTGTCCTTGT	0.527																																					p.K117K												.	.	3	Substitution - Missense(2)|Substitution - coding silent(1)	large_intestine(3)	c.G351A	11						.						91.0	89.0	90.0					11																	62603451		1969	4169	6138	62360027	SO:0001819	synonymous_variant	54663	exon5				CCDS44630.1	11q12.3	2013-01-09				ENSG00000133316		"""WD repeat domain containing"""	25529	protein-coding gene	gene with protein product							Standard	NM_018093		Approved	FLJ10439	uc001nvm.2	Q6RFH5		ENST00000525239.1:c.351G>A	11.37:g.62603451C>T			62360027	NM_018093	A8K8G5|Q9BRC9|Q9H6X8|Q9NVY2	Silent	SNP	ENST00000525239.1	37	CCDS44630.1	.	.	.	.	.	.	.	.	.	.	C	3.467	-0.108715	0.06924	.	.	ENSG00000133316	ENST00000535048	.	.	.	4.96	-1.53	0.08611	.	.	.	.	.	T	0.40473	0.1118	.	.	.	0.32036	N	0.598927	.	.	.	.	.	.	T	0.49818	-0.8899	4	.	.	.	-25.3561	9.1529	0.36973	0.0:0.4956:0.0:0.5044	.	.	.	.	R	109	.	.	G	-	1	0	WDR74	62360027	0.394000	0.25246	0.015000	0.15790	0.003000	0.03518	-0.624000	0.05540	-0.378000	0.07918	0.655000	0.94253	GGA		0.527	WDR74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395678.1	NM_018093	
CHRM1	1128	broad.mit.edu	37	11	62678422	62678422	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:62678422T>C	ENST00000306960.3	-	2	692	c.151A>G	c.(151-153)Aag>Gag	p.K51E	AP000438.2_ENST00000543624.1_RNA	NM_000738.2	NP_000729.2	P11229	ACM1_HUMAN	cholinergic receptor, muscarinic 1	51					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cognition (GO:0050890)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|neuromuscular synaptic transmission (GO:0007274)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of ion transport (GO:0043270)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of locomotion (GO:0040012)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)	p.K51E(1)		large_intestine(5)|lung(3)|stomach(1)	9					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Benzatropine(DB00245)|Biperiden(DB00810)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbachol(DB00411)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Citalopram(DB00215)|Clidinium(DB00771)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyclopentolate(DB00979)|Cycrimine(DB00942)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Doxylamine(DB00366)|Escitalopram(DB01175)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Flupentixol(DB00875)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methantheline(DB00940)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metoclopramide(DB01233)|Minaprine(DB00805)|Molindone(DB01618)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Oxyphenonium(DB00219)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pirenzepine(DB00670)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propantheline(DB00782)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Trospium(DB00209)|Ziprasidone(DB00246)	GTGTTGACCTTGAAAGAGATG	0.542																																					p.K51E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A151G	11						.						131.0	108.0	116.0					11																	62678422		2201	4298	6499	62434998	SO:0001583	missense	1128	exon2			Y00508	CCDS8040.1	11q12-q13	2012-08-08				ENSG00000168539		"""Cholinergic receptors"", ""GPCR / Class A : Cholinergic receptors, muscarinic"""	1950	protein-coding gene	gene with protein product	"""acetylcholine receptor, muscarinic 1"""	118510					Standard	NM_000738		Approved		uc001nwi.3	P11229		ENST00000306960.3:c.151A>G	11.37:g.62678422T>C	ENSP00000306490:p.Lys51Glu		62434998	NM_000738	Q96RH1	Missense_Mutation	SNP	ENST00000306960.3	37	CCDS8040.1	.	.	.	.	.	.	.	.	.	.	T	18.05	3.537535	0.65085	.	.	ENSG00000168539	ENST00000306960;ENST00000543973;ENST00000536524	T;T;T	0.37411	1.2;1.2;1.2	4.5	3.35	0.38373	GPCR, rhodopsin-like superfamily (1);	0.095502	0.41294	D	0.000916	T	0.47451	0.1446	M	0.62209	1.925	0.41576	D	0.988717	D	0.55385	0.971	P	0.56343	0.796	T	0.44892	-0.9298	10	0.56958	D	0.05	-20.4768	9.479	0.38889	0.0:0.0:0.1785:0.8215	.	51	P11229	ACM1_HUMAN	E	51	ENSP00000306490:K51E;ENSP00000441188:K51E;ENSP00000444482:K51E	ENSP00000306490:K51E	K	-	1	0	CHRM1	62434998	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.031000	0.70911	0.743000	0.32719	0.383000	0.25322	AAG		0.542	CHRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396178.1	NM_000738	
SLC22A25	387601	broad.mit.edu	37	11	62985141	62985141	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:62985141G>A	ENST00000306494.6	-	3	572	c.573C>T	c.(571-573)gcC>gcT	p.A191A	SLC22A25_ENST00000403374.2_Silent_p.A25A|SLC22A10_ENST00000525620.1_Intron|SLC22A10_ENST00000535888.1_Intron	NM_199352.3	NP_955384.3			solute carrier family 22, member 25									p.A191A(1)		NS(2)|breast(2)|endometrium(4)|kidney(2)|large_intestine(7)|lung(7)|ovary(3)|skin(7)	34						TGGGAGCAAAGGCCGCACAGG	0.478																																					p.A191A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C573T	11						.						80.0	70.0	73.0					11																	62985141		2201	4298	6499	62741717	SO:0001819	synonymous_variant	387601	exon3			AY437532	CCDS31592.1	11q12.3	2014-05-20			ENSG00000196600	ENSG00000196600		"""Solute carriers"""	32935	protein-coding gene	gene with protein product		610792	"""MGI:2442751, MGI:2385316, MGI:3042283, MGI:3645714, MGI:3605624, MGI:2442750"""			17714910	Standard	NM_199352		Approved	UST6, HIMTP, MGC120420	uc001nwr.1	Q6T423	OTTHUMG00000165340	ENST00000306494.6:c.573C>T	11.37:g.62985141G>A			62741717	NM_199352		Silent	SNP	ENST00000306494.6	37	CCDS31592.1																																																																																				0.478	SLC22A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383519.3	NM_199352	
SLC22A10	387775	broad.mit.edu	37	11	63057780	63057780	+	Missense_Mutation	SNP	G	G	A	rs374307478		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:63057780G>A	ENST00000332793.6	+	1	145	c.143G>A	c.(142-144)cGt>cAt	p.R48H	SLC22A10_ENST00000525620.1_Intron|SLC22A10_ENST00000526800.1_5'UTR|SLC22A10_ENST00000535888.1_Intron|SLC22A10_ENST00000544661.1_De_novo_Start_OutOfFrame	NM_001039752.3	NP_001034841.3	Q63ZE4	S22AA_HUMAN	solute carrier family 22, member 10	48						integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)	p.R48H(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28					Conjugated Estrogens(DB00286)|Probenecid(DB01032)|Salicylic acid(DB00936)	CCTGGTCATCGTTGCTGGGTC	0.428																																					p.R48H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G143A	11						.	G	HIS/ARG	0,4398		0,0,2199	96.0	105.0	102.0		143	2.0	1.0	11		102	1,8595	1.2+/-3.3	0,1,4297	no	missense	SLC22A10	NM_001039752.3	29	0,1,6496	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	48/542	63057780	1,12993	2199	4298	6497	62814356	SO:0001583	missense	387775	exon1			AP003420	CCDS41661.1	11q12.3	2013-05-22	2008-01-11		ENSG00000184999	ENSG00000184999		"""Solute carriers"""	18057	protein-coding gene	gene with protein product		607580	"""solute carrier family 22 (organic anion/cation transporter), member 10"""			11327718	Standard	NM_001039752		Approved	OAT5, hOAT5	uc009yor.3	Q63ZE4	OTTHUMG00000165197	ENST00000332793.6:c.143G>A	11.37:g.63057780G>A	ENSP00000327569:p.Arg48His		62814356	NM_001039752	Q68CJ0	Missense_Mutation	SNP	ENST00000332793.6	37	CCDS41661.1	.	.	.	.	.	.	.	.	.	.	G	11.71	1.719478	0.30503	0.0	1.16E-4	ENSG00000184999	ENST00000332793	T	0.54479	0.57	2.89	1.96	0.26148	.	0.227351	0.36740	U	0.002427	T	0.34308	0.0893	L	0.41906	1.305	0.80722	D	1	P	0.41345	0.746	B	0.34138	0.176	T	0.06058	-1.0848	10	0.23891	T	0.37	.	7.7091	0.28667	0.1333:0.0:0.8667:0.0	.	48	Q63ZE4	S22AA_HUMAN	H	48	ENSP00000327569:R48H	ENSP00000327569:R48H	R	+	2	0	SLC22A10	62814356	0.985000	0.35326	0.971000	0.41717	0.748000	0.42578	1.023000	0.30065	0.577000	0.29470	0.579000	0.79373	CGT		0.428	SLC22A10-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382622.3	NM_001039752	
MARK2	2011	broad.mit.edu	37	11	63669758	63669758	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:63669758G>A	ENST00000509502.2	+	12	1554	c.1091G>A	c.(1090-1092)cGc>cAc	p.R364H	MARK2_ENST00000350490.7_Missense_Mutation_p.R397H|MARK2_ENST00000513765.2_Missense_Mutation_p.R364H|MARK2_ENST00000408948.3_Missense_Mutation_p.R364H|MARK2_ENST00000361128.5_Missense_Mutation_p.R397H|MARK2_ENST00000315032.8_Missense_Mutation_p.R397H|MARK2_ENST00000377809.4_Missense_Mutation_p.R397H|MARK2_ENST00000508192.1_Missense_Mutation_p.R397H|MARK2_ENST00000413835.2_Missense_Mutation_p.R397H|MARK2_ENST00000425897.2_Missense_Mutation_p.R364H|MARK2_ENST00000402010.2_Missense_Mutation_p.R397H|MARK2_ENST00000377810.3_Missense_Mutation_p.R364H|MARK2_ENST00000502399.3_Missense_Mutation_p.R397H	NM_017490.3	NP_059672.2			MAP/microtubule affinity-regulating kinase 2									p.R364Q(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33						AAGGTACAGCGCAGCGTGTCG	0.582																																					p.R364H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1091A	11						.						80.0	70.0	73.0					11																	63669758		2201	4297	6498	63426334	SO:0001583	missense	2011	exon12			BC008771	CCDS8051.1, CCDS41665.1, CCDS8051.2, CCDS53649.1, CCDS53650.1, CCDS53651.1	11q13.1	2013-06-27	2002-07-26	2002-08-01	ENSG00000072518	ENSG00000072518			3332	protein-coding gene	gene with protein product	"""ELKL motif kinase 1"", ""serine/threonine kinase"", ""protein-serine/threonine kinase"", ""Ser/Thr protein kinase PAR-1B"""	600526	"""ELKL motif kinase"""	EMK1		9730619, 10516437	Standard	NM_017490		Approved	PAR-1, Par1b, PAR-1B	uc001nxw.3	Q7KZI7	OTTHUMG00000160504	ENST00000509502.2:c.1091G>A	11.37:g.63669758G>A	ENSP00000423974:p.Arg364His		63426334	NM_017490		Missense_Mutation	SNP	ENST00000509502.2	37	CCDS41665.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.781616	0.90282	.	.	ENSG00000072518	ENST00000402010;ENST00000315032;ENST00000377809;ENST00000413835;ENST00000377810;ENST00000508192;ENST00000361128;ENST00000350490;ENST00000502399;ENST00000509502;ENST00000513765;ENST00000408948;ENST00000425897	T;T;T;T;T;T;T;T;T;T;T;T	0.35973	1.28;1.28;1.28;1.28;1.28;1.28;1.28;1.28;1.28;1.28;1.28;1.28	5.07	4.13	0.48395	.	0.000000	0.85682	D	0.000000	T	0.61974	0.2390	M	0.86268	2.805	0.80722	D	1	D;D;D;D;D;D	0.89917	0.998;1.0;1.0;1.0;0.999;1.0	P;D;D;D;D;D	0.83275	0.886;0.988;0.947;0.996;0.932;0.987	T	0.67397	-0.5681	10	0.66056	D	0.02	.	11.729	0.51726	0.0907:0.0:0.9093:0.0	.	364;364;397;397;397;397	E7ETY4;Q7KZI7-14;Q7KZI7-15;Q7KZI7-5;Q7KZI7;Q7KZI7-16	.;.;.;.;MARK2_HUMAN;.	H	397;397;397;397;364;397;397;397;397;364;364;364;364	ENSP00000385751:R397H;ENSP00000326632:R397H;ENSP00000367040:R397H;ENSP00000389184:R397H;ENSP00000367041:R364H;ENSP00000425765:R397H;ENSP00000355091:R397H;ENSP00000294247:R397H;ENSP00000423974:R364H;ENSP00000421075:R364H;ENSP00000386128:R364H;ENSP00000415494:R364H	ENSP00000326632:R397H	R	+	2	0	MARK2	63426334	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.583000	0.98217	1.295000	0.44724	0.555000	0.69702	CGC		0.582	MARK2-003	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000360862.2	NM_017490	
VEGFB	7423	broad.mit.edu	37	11	64004663	64004663	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:64004663delA	ENST00000309422.2	+	5	675	c.379delA	c.(379-381)aaafs	p.K129fs	RP11-783K16.14_ENST00000539963.1_RNA|VEGFB_ENST00000426086.2_Frame_Shift_Del_p.K129fs|RP11-783K16.14_ENST00000534988.1_RNA	NM_001243733.1|NM_003377.4	NP_001230662.1|NP_003368.1	P49765	VEGFB_HUMAN	vascular endothelial growth factor B	129					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|coronary vasculature development (GO:0060976)|induction of positive chemotaxis (GO:0050930)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|negative regulation of neuron apoptotic process (GO:0043524)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of cell division (GO:0051781)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of mast cell chemotaxis (GO:0060754)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation of vascular wound healing (GO:0035470)|protein O-linked glycosylation (GO:0006493)|response to drug (GO:0042493)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	chemoattractant activity (GO:0042056)|heparin binding (GO:0008201)|vascular endothelial growth factor receptor 1 binding (GO:0043183)	p.K129fs*5(2)		endometrium(2)|large_intestine(2)|prostate(1)|stomach(1)	6					Aflibercept(DB08885)	TTTCAGACCTAAAAAAAAGGA	0.473																																					p.K127fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.379delA	11						.						137.0	121.0	126.0					11																	64004663		2201	4297	6498	63761239	SO:0001589	frameshift_variant	7423	exon5			BC008818	CCDS8062.1, CCDS58144.1	11q13	2005-09-29				ENSG00000173511			12681	protein-coding gene	gene with protein product		601398		VRF		8637916, 8919691	Standard	NM_001243733		Approved	VEGFL	uc001nyw.3	P49765		ENST00000309422.2:c.379delA	11.37:g.64004663delA	ENSP00000311127:p.Lys129fs		63761239	NM_003377	Q16528	Frame_Shift_Del	DEL	ENST00000309422.2	37	CCDS8062.1																																																																																				0.473	VEGFB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396393.2	NM_003377	
PLCB3	5331	broad.mit.edu	37	11	64029898	64029898	+	Silent	SNP	C	C	T	rs185360102		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:64029898C>T	ENST00000540288.1	+	18	2161	c.2058C>T	c.(2056-2058)aaC>aaT	p.N686N	PLCB3_ENST00000325234.5_Silent_p.N619N|PLCB3_ENST00000279230.6_Silent_p.N686N	NM_000932.2	NP_000923.1	Q01970	PLCB3_HUMAN	phospholipase C, beta 3 (phosphatidylinositol-specific)	686	PI-PLC Y-box. {ECO:0000255|PROSITE- ProRule:PRU00271}.				inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|regulation of systemic arterial blood pressure (GO:0003073)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)	p.N686N(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|urinary_tract(1)	33						TGCAGCTCAACGCGGGCGTTT	0.632													C|||	1	0.000199681	0.0	0.0014	5008	,	,		17778	0.0		0.0	False		,,,				2504	0.0				p.N619N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1857T	11						.						81.0	89.0	87.0					11																	64029898		2201	4297	6498	63786474	SO:0001819	synonymous_variant	5331	exon16			Z26649	CCDS8064.1, CCDS53654.1	11q13	2008-03-18			ENSG00000149782	ENSG00000149782	3.1.4.11		9056	protein-coding gene	gene with protein product		600230				7849701	Standard	NM_000932		Approved		uc009ypg.2	Q01970	OTTHUMG00000167816	ENST00000540288.1:c.2058C>T	11.37:g.64029898C>T			63786474	NM_001184883	A5PKZ6|G5E960|Q8N1A4	Silent	SNP	ENST00000540288.1	37	CCDS8064.1																																																																																				0.632	PLCB3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396405.1		
CDC42BPG	55561	broad.mit.edu	37	11	64594813	64594813	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:64594813C>T	ENST00000342711.5	-	33	4207	c.4208G>A	c.(4207-4209)cGc>cAc	p.R1403H		NM_017525.2	NP_059995.2			CDC42 binding protein kinase gamma (DMPK-like)									p.R1403H(1)		central_nervous_system(1)|lung(3)	4						GCTCTTGGTGCGGAACAGCTG	0.652																																					p.R1403H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4208A	11						.						83.0	94.0	90.0					11																	64594813		2201	4297	6498	64351389	SO:0001583	missense	55561	exon33			AY648038	CCDS31601.1	11q13	2013-01-10			ENSG00000171219	ENSG00000171219		"""Pleckstrin homology (PH) domain containing"""	29829	protein-coding gene	gene with protein product		613991				9341881, 15194684	Standard	NM_017525		Approved	HSMDPKIN, MRCKgamma, DMPK2, kappa-200	uc001obs.4	Q6DT37	OTTHUMG00000045365	ENST00000342711.5:c.4208G>A	11.37:g.64594813C>T	ENSP00000345133:p.Arg1403His		64351389	NM_017525		Missense_Mutation	SNP	ENST00000342711.5	37	CCDS31601.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.813769	0.90790	.	.	ENSG00000171219	ENST00000342711	T	0.72051	-0.62	4.82	4.82	0.62117	.	0.000000	0.45126	D	0.000399	D	0.83876	0.5349	M	0.81942	2.565	0.42186	D	0.991703	D	0.89917	1.0	D	0.68621	0.959	D	0.86739	0.1953	10	0.87932	D	0	.	15.8054	0.78501	0.0:1.0:0.0:0.0	.	1403	Q6DT37	MRCKG_HUMAN	H	1403	ENSP00000345133:R1403H	ENSP00000345133:R1403H	R	-	2	0	CDC42BPG	64351389	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.284000	0.51708	2.409000	0.81822	0.561000	0.74099	CGC		0.652	CDC42BPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105352.4	XM_290516	
ATG2A	23130	broad.mit.edu	37	11	64671070	64671070	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:64671070A>T	ENST00000377264.3	-	25	3639	c.3527T>A	c.(3526-3528)cTg>cAg	p.L1176Q	ATG2A_ENST00000421419.2_Missense_Mutation_p.L1176Q	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	1176					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)		p.L1176Q(1)		breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(19)|ovary(3)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	55						ACCTCGCCGCAGGTCCAGGGT	0.701											OREG0004027	type=REGULATORY REGION|Gene=BC053596|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.L1176Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T3527A	11						.						17.0	12.0	13.0					11																	64671070		1933	3789	5722	64427646	SO:0001583	missense	23130	exon25				CCDS31602.1	11q13.1	2014-02-12	2012-06-06		ENSG00000110046	ENSG00000110046			29028	protein-coding gene	gene with protein product			"""ATG2 autophagy related 2 homolog A (S. cerevisiae)"""			21887408	Standard	NM_015104		Approved	KIAA0404	uc001obx.3	Q2TAZ0	OTTHUMG00000066831	ENST00000377264.3:c.3527T>A	11.37:g.64671070A>T	ENSP00000366475:p.Leu1176Gln	1078	64427646	NM_015104	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Missense_Mutation	SNP	ENST00000377264.3	37	CCDS31602.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.632881	0.87660	.	.	ENSG00000110046	ENST00000421419;ENST00000377264	T;T	0.11385	2.79;2.78	5.13	5.13	0.70059	.	0.000000	0.64402	D	0.000008	T	0.33294	0.0858	M	0.76838	2.35	0.58432	D	0.999998	D	0.89917	1.0	D	0.87578	0.998	T	0.05632	-1.0873	10	0.54805	T	0.06	.	13.1808	0.59653	1.0:0.0:0.0:0.0	.	1176	Q2TAZ0	ATG2A_HUMAN	Q	1176	ENSP00000410522:L1176Q;ENSP00000366475:L1176Q	ENSP00000366475:L1176Q	L	-	2	0	ATG2A	64427646	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.847000	0.92166	2.065000	0.61736	0.459000	0.35465	CTG		0.701	ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000143224.1	NM_015104	
PPP2R5B	5526	broad.mit.edu	37	11	64695605	64695605	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:64695605A>G	ENST00000164133.2	+	5	1188	c.566A>G	c.(565-567)tAt>tGt	p.Y189C		NM_006244.3	NP_006235.1	Q15173	2A5B_HUMAN	protein phosphatase 2, regulatory subunit B', beta	189					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)	p.Y189C(1)		central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(2)	21						GCCAAGAGATATGTGGATCAA	0.562																																					p.Y189C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A566G	11						.						127.0	120.0	123.0					11																	64695605		2201	4297	6498	64452181	SO:0001583	missense	5526	exon5			L42374	CCDS8085.1	11q12	2010-06-18	2010-04-14		ENSG00000068971	ENSG00000068971		"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9310	protein-coding gene	gene with protein product	"""PP2A, B subunit, B' beta isoform"", ""PP2A, B subunit, B56 beta isoform"", ""PP2A, B subunit, PR61 beta isoform"", ""PP2A, B subunit, R5 beta isoform"", ""serine/threonine protein phosphatase 2A, 56 kDa regulatory subunit, beta isoform"""	601644	"""protein phosphatase 2, regulatory subunit B (B56), beta isoform"", ""protein phosphatase 2, regulatory subunit B', beta isoform"""			7592815	Standard	NM_006244		Approved	FLJ35411, B56B, PR61B	uc001oby.3	Q15173	OTTHUMG00000150043	ENST00000164133.2:c.566A>G	11.37:g.64695605A>G	ENSP00000164133:p.Tyr189Cys		64452181	NM_006244	Q13853	Missense_Mutation	SNP	ENST00000164133.2	37	CCDS8085.1	.	.	.	.	.	.	.	.	.	.	A	15.72	2.917380	0.52546	.	.	ENSG00000068971	ENST00000526559;ENST00000164133;ENST00000359279;ENST00000532850;ENST00000527441	.	.	.	3.47	3.47	0.39725	Armadillo-type fold (1);	0.327444	0.29403	N	0.012256	T	0.71771	0.3379	M	0.90922	3.16	0.58432	D	0.999995	B	0.20368	0.044	B	0.22880	0.042	T	0.76019	-0.3112	9	0.87932	D	0	-1.4257	10.6363	0.45567	1.0:0.0:0.0:0.0	.	189	Q15173	2A5B_HUMAN	C	189;189;216;103;189	.	ENSP00000164133:Y189C	Y	+	2	0	PPP2R5B	64452181	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.652000	0.91083	1.846000	0.53633	0.449000	0.29647	TAT		0.562	PPP2R5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385465.1	NM_006244	
BATF2	116071	broad.mit.edu	37	11	64756725	64756725	+	Missense_Mutation	SNP	C	C	T	rs377505280		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:64756725C>T	ENST00000301887.4	-	3	831	c.701G>A	c.(700-702)cGt>cAt	p.R234H	BATF2_ENST00000435842.2_Missense_Mutation_p.R149H|BATF2_ENST00000527716.1_Missense_Mutation_p.R210H	NM_138456.3	NP_612465.3	Q8N1L9	BATF2_HUMAN	basic leucine zipper transcription factor, ATF-like 2	234					defense response to protozoan (GO:0042832)|myeloid dendritic cell differentiation (GO:0043011)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R234H(1)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(1)|ovary(1)|skin(1)	9						GCTCTGCAGACGTGCAAGCCC	0.642													C|||	1	0.000199681	0.0	0.0	5008	,	,		18813	0.0		0.0	False		,,,				2504	0.001				p.R234H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G701A	11						.						49.0	48.0	48.0					11																	64756725		2201	4297	6498	64513301	SO:0001583	missense	116071	exon3			AK092453	CCDS8087.1, CCDS73317.1	11q13.1	2013-01-10			ENSG00000168062	ENSG00000168062		"""basic leucine zipper proteins"""	25163	protein-coding gene	gene with protein product		614983					Standard	NM_138456		Approved	MGC20410	uc001ocf.1	Q8N1L9	OTTHUMG00000165633	ENST00000301887.4:c.701G>A	11.37:g.64756725C>T	ENSP00000301887:p.Arg234His		64513301	NM_138456	D9IC56|Q8NAF4|Q8NAL8|Q96EH4	Missense_Mutation	SNP	ENST00000301887.4	37	CCDS8087.1	.	.	.	.	.	.	.	.	.	.	C	11.39	1.625275	0.28889	.	.	ENSG00000168062	ENST00000301887;ENST00000435842;ENST00000527716	T	0.44881	0.91	4.28	-4.29	0.03721	.	2.198590	0.02182	N	0.060599	T	0.22437	0.0541	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.09552	-1.0669	10	0.54805	T	0.06	23.2412	1.1251	0.01733	0.131:0.2686:0.2571:0.3433	.	234	Q8N1L9	BATF2_HUMAN	H	234;149;210	ENSP00000301887:R234H	ENSP00000301887:R234H	R	-	2	0	BATF2	64513301	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-0.656000	0.05342	-1.066000	0.03164	0.555000	0.69702	CGT		0.642	BATF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385478.2	NM_138456	
MUS81	80198	broad.mit.edu	37	11	65632497	65632497	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:65632497C>A	ENST00000308110.4	+	13	1631	c.1282C>A	c.(1282-1284)Cta>Ata	p.L428I	MUS81_ENST00000533035.1_Missense_Mutation_p.L353I|EFEMP2_ENST00000532648.1_5'Flank	NM_025128.4	NP_079404.3	Q96NY9	MUS81_HUMAN	MUS81 structure-specific endonuclease subunit	428					DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	intercellular bridge (GO:0045171)|nucleus (GO:0005634)	3'-flap endonuclease activity (GO:0048257)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L428I(1)		endometrium(1)|kidney(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	13				READ - Rectum adenocarcinoma(159;0.166)		GGGCCACACCCTACGCAGCCG	0.642								Homologous recombination																													p.L428I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1282A	11						.						67.0	77.0	74.0					11																	65632497		2201	4296	6497	65389073	SO:0001583	missense	80198	exon13				CCDS8115.1	11q13	2013-07-03	2013-07-03			ENSG00000172732			29814	protein-coding gene	gene with protein product	"""SLX3 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	606591	"""MUS81 endonuclease homolog (yeast)"", ""MUS81 endonuclease homolog (S. cerevisiae)"""			11741546, 12374758	Standard	NM_025128		Approved	FLJ44872, SLX3	uc001ofv.4	Q96NY9		ENST00000308110.4:c.1282C>A	11.37:g.65632497C>A	ENSP00000307853:p.Leu428Ile		65389073	NM_025128	Q9H7D9	Missense_Mutation	SNP	ENST00000308110.4	37	CCDS8115.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.42|18.42	3.620182|3.620182	0.66787|0.66787	.|.	.|.	ENSG00000172732|ENSG00000172732	ENST00000533035;ENST00000308110;ENST00000437855|ENST00000529374	T;T|.	0.17691|.	2.26;2.48|.	4.93|4.93	4.02|4.02	0.46733|0.46733	.|.	0.139477|.	0.48767|.	D|.	0.000161|.	T|T	0.74906|0.74906	0.3778|0.3778	M|M	0.85777|0.85777	2.775|2.775	0.53688|0.53688	D|D	0.999977|0.999977	P|.	0.49862|.	0.929|.	P|.	0.52881|.	0.712|.	T|T	0.76782|0.76782	-0.2832|-0.2832	10|5	0.45353|.	T|.	0.12|.	-14.8189|-14.8189	9.9164|9.9164	0.41436|0.41436	0.0:0.9028:0.0:0.0972|0.0:0.9028:0.0:0.0972	.|.	428|.	Q96NY9|.	MUS81_HUMAN|.	I|H	353;428;428|353	ENSP00000432287:L353I;ENSP00000307853:L428I|.	ENSP00000307853:L428I|.	L|P	+|+	1|2	2|0	MUS81|MUS81	65389073|65389073	0.986000|0.986000	0.35501|0.35501	0.543000|0.543000	0.28128|0.28128	0.733000|0.733000	0.41908|0.41908	1.679000|1.679000	0.37597|0.37597	1.412000|1.412000	0.46977|0.46977	0.561000|0.561000	0.74099|0.74099	CTA|CCT		0.642	MUS81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390941.3	NM_025128	
ACTN3	89	broad.mit.edu	37	11	66326798	66326798	+	lincRNA	SNP	C	C	T	rs369128953		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:66326798C>T	ENST00000504911.1	-	0	220				ACTN3_ENST00000513398.1_RNA|ACTN3_ENST00000502692.1_RNA																							CCTTTGAGAGCGACCTGGCGG	0.692																																					p.S456S												.	.	0			c.C1368T	11						.			0,4384		0,0,2192	27.0	31.0	30.0		1368	-1.9	1.0	11		30	1,8577		0,1,4288	no	coding-synonymous	ACTN3	NM_001104.1		0,1,6480	TT,TC,CC		0.0117,0.0,0.0077		456/902	66326798	1,12961	2192	4289	6481	66083374			89	exon12																															11.37:g.66326798C>T			66083374	NM_001104		Silent	SNP	ENST00000504911.1	37																																																																																					0.692	CTD-3074O7.2-001	KNOWN	basic|exp_conf	lincRNA	lincRNA	OTTHUMT00000362463.1		
C11orf80	79703	broad.mit.edu	37	11	66555636	66555636	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:66555636C>T	ENST00000360962.4	+	5	536	c.529C>T	c.(529-531)Cag>Tag	p.Q177*	C11orf80_ENST00000346672.4_Nonsense_Mutation_p.Q22*|C11orf80_ENST00000532565.2_5'UTR|C11orf80_ENST00000540737.1_Nonsense_Mutation_p.Q11*|C11orf80_ENST00000525449.2_Nonsense_Mutation_p.Q22*|C11orf80_ENST00000527634.1_Intron|C11orf80_ENST00000527368.1_3'UTR	NM_024650.3	NP_078926.3	Q8N6T0	CK080_HUMAN	chromosome 11 open reading frame 80	177								p.Q177*(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	14						CACAGAAATACAGTCCATACT	0.433																																					p.Q177X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C529T	11						.						78.0	73.0	75.0					11																	66555636		1873	4110	5983	66312212	SO:0001587	stop_gained	79703	exon5					11q13.2	2012-05-30			ENSG00000173715	ENSG00000173715			26197	protein-coding gene	gene with protein product						18160775	Standard	NM_024650		Approved	FLJ22531	uc021qmd.1	Q8N6T0	OTTHUMG00000167164	ENST00000360962.4:c.529C>T	11.37:g.66555636C>T	ENSP00000354227:p.Gln177*		66312212	NM_024650	Q9H677	Nonsense_Mutation	SNP	ENST00000360962.4	37	CCDS53664.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.551077	0.86127	.	.	ENSG00000173715	ENST00000525908;ENST00000360962;ENST00000346672;ENST00000528340;ENST00000540737;ENST00000525449	.	.	.	5.38	5.38	0.77491	.	0.141555	0.32785	N	0.005643	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	14.6458	0.68759	0.0:1.0:0.0:0.0	.	.	.	.	X	128;177;22;11;11;22	.	ENSP00000317408:Q22X	Q	+	1	0	C11orf80	66312212	0.123000	0.22298	0.417000	0.26559	0.542000	0.35054	2.019000	0.41001	2.538000	0.85594	0.655000	0.94253	CAG		0.433	C11orf80-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_024650	
RCE1	9986	broad.mit.edu	37	11	66613395	66613395	+	Silent	SNP	C	C	T	rs11538048	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:66613395C>T	ENST00000309657.3	+	8	863	c.819C>T	c.(817-819)tgC>tgT	p.C273C	PC_ENST00000528224.1_5'Flank|RCE1_ENST00000525356.1_Silent_p.C150C|RCE1_ENST00000524506.1_Silent_p.C252C	NM_001032279.1|NM_005133.2	NP_001027450.1|NP_005124.1	Q9Y256	FACE2_HUMAN	Ras converting CAAX endopeptidase 1	273					CAAX-box protein processing (GO:0071586)|proteolysis (GO:0006508)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	cysteine-type endopeptidase activity (GO:0004197)|metalloendopeptidase activity (GO:0004222)	p.C273C(1)		breast(2)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)	10						CAGCTGTTTGCGCGGCCTTGG	0.622													C|||	11	0.00219649	0.0068	0.0029	5008	,	,		17476	0.0		0.0	False		,,,				2504	0.0				p.C273C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C819T	11						.	C	,	41,4359	43.1+/-76.7	0,41,2159	111.0	102.0	105.0		507,819	-9.9	0.0	11	dbSNP_120	105	0,8590		0,0,4295	no	coding-synonymous,coding-synonymous	RCE1	NM_001032279.1,NM_005133.2	,	0,41,6454	TT,TC,CC		0.0,0.9318,0.3156	,	169/226,273/330	66613395	41,12949	2200	4295	6495	66369971	SO:0001819	synonymous_variant	9986	exon8			AF121951	CCDS8151.1	11q13	2013-10-18	2013-10-18	2001-06-29	ENSG00000173653	ENSG00000173653			13721	protein-coding gene	gene with protein product	"""farnesylated protein-converting enzyme 2"", ""prenyl protein-specific endoprotease 2"", ""RCE1 homolog, prenyl protein protease"", ""CAAX prenyl protease 2"""	605385	"""RCE1 (S. Cerevisiae) homolog, prenyl protein protease"", ""RCE1 homolog, prenyl protein peptidase (S. cerevisiae)"", ""RCE1 homolog, prenyl protein protease (S. cerevisiae)"""	RCE1A, RCE1B		10085068, 10373325	Standard	NM_005133		Approved	hRCE1, FACE-2, FACE2	uc001ojk.1	Q9Y256	OTTHUMG00000167098	ENST00000309657.3:c.819C>T	11.37:g.66613395C>T			66369971	NM_005133	Q52LZ9	Silent	SNP	ENST00000309657.3	37	CCDS8151.1																																																																																				0.622	RCE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393105.1	NM_005133	
RPS6KB2	6199	broad.mit.edu	37	11	67200479	67200479	+	Missense_Mutation	SNP	G	G	A	rs370932588		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:67200479G>A	ENST00000312629.5	+	8	718	c.673G>A	c.(673-675)Gtc>Atc	p.V225I	RPS6KB2_ENST00000539188.1_3'UTR|AP003419.16_ENST00000535922.1_RNA	NM_003952.2	NP_003943.2	Q9UBS0	KS6B2_HUMAN	ribosomal protein S6 kinase, 70kDa, polypeptide 2	225	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of translational initiation (GO:0045948)|protein kinase B signaling (GO:0043491)|signal transduction (GO:0007165)|translation (GO:0006412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|peptide binding (GO:0042277)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ribosomal protein S6 kinase activity (GO:0004711)	p.V225I(2)		breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|prostate(3)|salivary_gland(1)|stomach(2)	25			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)			TGAGGGCGCCGTCACTCACAC	0.622																																					p.V225I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G673A	11						.	G	ILE/VAL	0,4132		0,0,2066	40.0	45.0	43.0		673	2.9	0.6	11		43	1,8395		0,1,4197	no	missense	RPS6KB2	NM_003952.2	29	0,1,6263	AA,AG,GG		0.0119,0.0,0.0080	benign	225/483	67200479	1,12527	2066	4198	6264	66957055	SO:0001583	missense	6199	exon8			AB019245	CCDS41677.1	11q13.1	2011-04-05	2002-08-29		ENSG00000175634	ENSG00000175634			10437	protein-coding gene	gene with protein product		608939	"""ribosomal protein S6 kinase, 70kD, polypeptide 2"""			9878560, 9804755	Standard	XM_005274164		Approved	p70S6Kb, P70-BETA, STK14B, KLS	uc001old.3	Q9UBS0	OTTHUMG00000167673	ENST00000312629.5:c.673G>A	11.37:g.67200479G>A	ENSP00000308413:p.Val225Ile		66957055	NM_003952	B2RMZ9|B4DML8|O94809|Q9UEC1	Missense_Mutation	SNP	ENST00000312629.5	37	CCDS41677.1	.	.	.	.	.	.	.	.	.	.	G	11.25	1.582363	0.28180	0.0	1.19E-4	ENSG00000175634	ENST00000312629	T	0.65549	-0.16	4.76	2.87	0.33458	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.159443	0.40728	N	0.001040	T	0.41351	0.1155	N	0.11000	0.08	0.80722	D	1	P;P	0.43938	0.822;0.743	B;B	0.43123	0.409;0.273	T	0.12993	-1.0526	9	.	.	.	.	9.1265	0.36818	0.1847:0.0:0.8153:0.0	.	225;225	Q9BRS0;Q9UBS0	.;KS6B2_HUMAN	I	225	ENSP00000308413:V225I	.	V	+	1	0	RPS6KB2	66957055	0.999000	0.42202	0.576000	0.28549	0.989000	0.77384	2.827000	0.48112	0.588000	0.29660	0.561000	0.74099	GTC		0.622	RPS6KB2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395508.1	NM_003952	
TCIRG1	10312	broad.mit.edu	37	11	67814983	67814983	+	Missense_Mutation	SNP	G	G	A	rs140963213	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:67814983G>A	ENST00000265686.3	+	11	1357	c.1249G>A	c.(1249-1251)Gcc>Acc	p.A417T	TCIRG1_ENST00000532635.1_Missense_Mutation_p.A201T	NM_006019.3	NP_006010.2	Q13488	VPP3_HUMAN	T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 subunit A3	417					ATP hydrolysis coupled proton transport (GO:0015991)|cellular defense response (GO:0006968)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of cell proliferation (GO:0008284)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	hydrogen ion transmembrane transporter activity (GO:0015078)|transporter activity (GO:0005215)	p.A417T(1)		breast(1)|endometrium(4)|large_intestine(3)|lung(4)|ovary(3)|prostate(1)	16						GTTCCTGTTCGCCCTGGCCAT	0.647													G|||	6	0.00119808	0.0015	0.0	5008	,	,		16229	0.0		0.004	False		,,,				2504	0.0				p.A417T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1249A	11						.	G	THR/ALA,THR/ALA	5,4395	9.9+/-24.2	0,5,2195	133.0	96.0	108.0		1249,601	4.1	1.0	11	dbSNP_134	108	42,8546	28.5+/-78.6	0,42,4252	yes	missense,missense	TCIRG1	NM_006019.3,NM_006053.3	58,58	0,47,6447	AA,AG,GG		0.4891,0.1136,0.3619	probably-damaging,probably-damaging	417/831,201/615	67814983	47,12941	2200	4294	6494	67571559	SO:0001583	missense	10312	exon11			AF025374	CCDS8177.1, CCDS53670.1	11q13.2	2014-09-17	2006-01-20		ENSG00000110719	ENSG00000110719		"""ATPases / V-type"""	11647	protein-coding gene	gene with protein product	"""T-cell immune response cDNA 7"""	604592	"""T-cell, immune regulator 1"", ""T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein a isoform 3"", ""T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein A3"""			8579597, 9806637	Standard	NM_006019		Approved	TIRC7, OC-116, OC116, ATP6N1C, Atp6i, a3, ATP6V0A3	uc001one.3	Q13488	OTTHUMG00000167358	ENST00000265686.3:c.1249G>A	11.37:g.67814983G>A	ENSP00000265686:p.Ala417Thr		67571559	NM_006019	O75877|Q8WVC5	Missense_Mutation	SNP	ENST00000265686.3	37	CCDS8177.1	6	0.0027472527472527475	2	0.0040650406504065045	0	0.0	0	0.0	4	0.005277044854881266	G	29.7	5.024742	0.93518	0.001136	0.004891	ENSG00000110719	ENST00000265686;ENST00000532635	D;D	0.91843	-2.92;-2.92	4.07	4.07	0.47477	.	0.164083	0.53938	D	0.000056	D	0.94348	0.8183	M	0.84156	2.68	0.58432	D	0.999997	D	0.89917	1.0	D	0.75020	0.985	D	0.94242	0.7486	10	0.56958	D	0.05	-19.2839	14.9965	0.71436	0.0:0.0:1.0:0.0	.	417	Q13488	VPP3_HUMAN	T	417;201	ENSP00000265686:A417T;ENSP00000434407:A201T	ENSP00000265686:A417T	A	+	1	0	TCIRG1	67571559	0.027000	0.19231	0.996000	0.52242	0.932000	0.56968	0.534000	0.23098	2.092000	0.63282	0.462000	0.41574	GCC		0.647	TCIRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394305.1	NM_006019	
LRP5	4041	broad.mit.edu	37	11	68177405	68177405	+	Silent	SNP	C	C	T	rs145456776	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:68177405C>T	ENST00000294304.7	+	10	2221	c.2115C>T	c.(2113-2115)aaC>aaT	p.N705N		NM_002335.2	NP_002326.2	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein 5	705	Beta-propeller 3.				adipose tissue development (GO:0060612)|anatomical structure regression (GO:0060033)|anterior/posterior pattern specification (GO:0009952)|apoptotic process involved in patterning of blood vessels (GO:1902262)|bone marrow development (GO:0048539)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in gastrulation (GO:0042074)|cell-cell signaling involved in mammary gland development (GO:0060764)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocytosis (GO:0006897)|extracellular matrix-cell signaling (GO:0035426)|gastrulation with mouth forming second (GO:0001702)|glucose catabolic process (GO:0006007)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|osteoblast development (GO:0002076)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mitosis (GO:0045840)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of bone remodeling (GO:0046850)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to peptide hormone (GO:0043434)|retina morphogenesis in camera-type eye (GO:0060042)|retinal blood vessel morphogenesis (GO:0061304)|somatic stem cell maintenance (GO:0035019)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	coreceptor activity (GO:0015026)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.N705N(1)		autonomic_ganglia(1)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(24)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						CCTTCATGAACGGGAGCTCGG	0.552																																					p.N705N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2115T	11						.	C		0,4400		0,0,2200	84.0	82.0	83.0		2115	-5.7	0.7	11	dbSNP_134	83	3,8585	3.0+/-9.4	0,3,4291	no	coding-synonymous	LRP5	NM_002335.2		0,3,6491	TT,TC,CC		0.0349,0.0,0.0231		705/1616	68177405	3,12985	2200	4294	6494	67933981	SO:0001819	synonymous_variant	4041	exon10			AF064548	CCDS8181.1	11q13.4	2014-01-28	2003-03-12		ENSG00000162337	ENSG00000162337		"""Low density lipoprotein receptors"""	6697	protein-coding gene	gene with protein product		603506	"""osteoporosis pseudoglioma syndrome"", ""exudative vitreoretinopathy 1"""	LRP7, OPPG, EVR1		9714764, 10049586	Standard	XM_005273994		Approved	LR3, BMND1, HBM, OPS, OPTA1, VBCH2, EVR4	uc001ont.3	O75197	OTTHUMG00000167570	ENST00000294304.7:c.2115C>T	11.37:g.68177405C>T			67933981	NM_002335	Q96TD6|Q9UES7|Q9UP66	Silent	SNP	ENST00000294304.7	37	CCDS8181.1																																																																																				0.552	LRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395088.1	NM_002335	
FOLR1	2348	broad.mit.edu	37	11	71906439	71906439	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:71906439G>A	ENST00000393679.1	+	3	729	c.293G>A	c.(292-294)cGg>cAg	p.R98Q	FOLR1_ENST00000393676.3_Missense_Mutation_p.R98Q|FOLR1_ENST00000393681.2_Missense_Mutation_p.R98Q|FOLR1_ENST00000312293.4_Missense_Mutation_p.R98Q|RP11-807H22.7_ENST00000378140.3_RNA			P15328	FOLR1_HUMAN	folate receptor 1 (adult)	98					cell death (GO:0008219)|folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|receptor-mediated endocytosis (GO:0006898)	anchored component of external side of plasma membrane (GO:0031362)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|receptor activity (GO:0004872)	p.R98Q(1)		cervix(2)|endometrium(1)|large_intestine(7)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	14					Methotrexate(DB00563)	GCCTGCAAACGGCATTTCATC	0.542																																					p.R98Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G293A	11						.						173.0	168.0	170.0					11																	71906439		2200	4293	6493	71584087	SO:0001583	missense	2348	exon4			J05013	CCDS8211.1	11q13.3-q14.1	2010-04-09			ENSG00000110195	ENSG00000110195			3791	protein-coding gene	gene with protein product		136430		FOLR		1717147	Standard	NM_000802		Approved		uc001osa.2	P15328		ENST00000393679.1:c.293G>A	11.37:g.71906439G>A	ENSP00000377284:p.Arg98Gln		71584087	NM_016724	Q53EW2|Q6FGT8|Q6LC90|Q9UCT2	Missense_Mutation	SNP	ENST00000393679.1	37	CCDS8211.1	.	.	.	.	.	.	.	.	.	.	g	15.84	2.952236	0.53293	.	.	ENSG00000110195	ENST00000312293;ENST00000393681;ENST00000393679;ENST00000393676	T;T;T;T	0.76968	-1.06;-1.06;-1.06;-1.06	5.19	1.06	0.20224	Folate receptor-like (1);	0.606207	0.17753	N	0.163179	T	0.71074	0.3297	M	0.86651	2.83	0.26250	N	0.978748	P	0.42039	0.769	B	0.35607	0.206	T	0.61912	-0.6965	10	0.29301	T	0.29	-19.5055	1.686	0.02842	0.3213:0.1264:0.423:0.1293	.	98	P15328	FOLR1_HUMAN	Q	98	ENSP00000308137:R98Q;ENSP00000377286:R98Q;ENSP00000377284:R98Q;ENSP00000377281:R98Q	ENSP00000308137:R98Q	R	+	2	0	FOLR1	71584087	0.000000	0.05858	0.058000	0.19502	0.951000	0.60555	0.002000	0.13061	0.004000	0.14682	-0.253000	0.11424	CGG		0.542	FOLR1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396773.1	NM_016725	
GDPD5	81544	broad.mit.edu	37	11	75153437	75153437	+	Missense_Mutation	SNP	C	C	T	rs377131289		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:75153437C>T	ENST00000336898.3	-	12	1975	c.1138G>A	c.(1138-1140)Gtg>Atg	p.V380M	GDPD5_ENST00000529721.1_Missense_Mutation_p.V380M|GDPD5_ENST00000526177.1_Missense_Mutation_p.V242M|GDPD5_ENST00000533784.1_Missense_Mutation_p.V261M|GDPD5_ENST00000376282.3_Missense_Mutation_p.V261M|GDPD5_ENST00000443276.2_3'UTR|GDPD5_ENST00000533805.1_Missense_Mutation_p.V135M	NM_030792.6	NP_110419.5	Q8WTR4	GDPD5_HUMAN	glycerophosphodiester phosphodiesterase domain containing 5	380	GP-PDE.				cerebral cortex neuron differentiation (GO:0021895)|glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)|negative regulation of Notch signaling pathway (GO:0045746)|neuron projection development (GO:0031175)|positive regulation of neuron differentiation (GO:0045666)|regulation of timing of cell differentiation (GO:0048505)|spinal cord motor neuron differentiation (GO:0021522)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)	p.V380M(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(3)|skin(2)	20						GAGTGCAGCACGGCCTCCAGA	0.667																																					p.V380M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1138A	11						.		MET/VAL	1,4373		0,1,2186	22.0	21.0	22.0		1138	-10.7	0.1	11		22	0,8572		0,0,4286	no	missense	GDPD5	NM_030792.6	21	0,1,6472	TT,TC,CC		0.0,0.0229,0.0077	possibly-damaging	380/606	75153437	1,12945	2187	4286	6473	74831085	SO:0001583	missense	81544	exon12			AF318377	CCDS8238.1	11q13.4-q13.5	2011-01-25				ENSG00000158555			28804	protein-coding gene	gene with protein product		609632				18667693, 17275818	Standard	NM_030792		Approved	PP1665, GDE2	uc001owp.4	Q8WTR4		ENST00000336898.3:c.1138G>A	11.37:g.75153437C>T	ENSP00000337972:p.Val380Met		74831085	NM_030792	Q49AQ5|Q6UX76|Q7Z4S0|Q8N781|Q8NCB7|Q8TB77	Missense_Mutation	SNP	ENST00000336898.3	37	CCDS8238.1	.	.	.	.	.	.	.	.	.	.	c	14.92	2.680590	0.47886	2.29E-4	0.0	ENSG00000158555	ENST00000526177;ENST00000533784;ENST00000529721;ENST00000336898;ENST00000533805;ENST00000376282	T;T;T;T;T;T	0.13196	2.61;2.61;2.61;2.61;2.61;2.61	5.37	-10.7	0.00240	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	0.456846	0.22780	N	0.055739	T	0.09949	0.0244	L	0.56199	1.76	0.42010	D	0.990937	D;P	0.52996	0.957;0.486	P;B	0.44897	0.463;0.214	T	0.50575	-0.8812	10	0.87932	D	0	-3.1753	7.2066	0.25911	0.1269:0.1848:0.5868:0.1015	.	261;380	Q8WTR4-2;Q8WTR4	.;GDPD5_HUMAN	M	242;261;380;380;135;261	ENSP00000434050:V242M;ENSP00000437049:V261M;ENSP00000433214:V380M;ENSP00000337972:V380M;ENSP00000435196:V135M;ENSP00000365459:V261M	ENSP00000337972:V380M	V	-	1	0	GDPD5	74831085	0.000000	0.05858	0.094000	0.20943	0.883000	0.51084	-0.547000	0.06055	-1.710000	0.01397	0.450000	0.29827	GTG		0.667	GDPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384409.1	NM_030792	
DDIAS	220042	broad.mit.edu	37	11	82643116	82643116	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:82643116A>G	ENST00000533655.1	+	6	948	c.736A>G	c.(736-738)Act>Gct	p.T246A	C11orf82_ENST00000329143.3_5'UTR|C11orf82_ENST00000525388.1_3'UTR|C11orf82_ENST00000528759.1_3'UTR|C11orf82_ENST00000525361.1_Intron|C11orf82_ENST00000430323.2_Missense_Mutation_p.T246A	NM_145018.3	NP_659455.3	Q8IXT1	DDIAS_HUMAN		246					apoptotic process (GO:0006915)|cellular response to cytokine stimulus (GO:0071345)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to hydroperoxide (GO:0071447)|cellular response to UV (GO:0034644)|hemopoiesis (GO:0030097)|mitotic cell cycle arrest (GO:0071850)|negative regulation of fibroblast apoptotic process (GO:2000270)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.T246A(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(17)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	33						ACTTGAATTCACTTGCATTGT	0.383																																					p.T246A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A736G	11						.						76.0	78.0	77.0					11																	82643116		2203	4300	6503	82320764	SO:0001583	missense	220042	exon6																														ENST00000533655.1:c.736A>G	11.37:g.82643116A>G	ENSP00000435421:p.Thr246Ala		82320764	NM_145018	Q96LK6|Q9H856	Missense_Mutation	SNP	ENST00000533655.1	37	CCDS8263.1	.	.	.	.	.	.	.	.	.	.	A	10.44	1.351650	0.24512	.	.	ENSG00000165490	ENST00000430323;ENST00000533655	T;T	0.20738	2.05;2.05	5.66	3.35	0.38373	.	0.513400	0.21306	N	0.076727	T	0.27313	0.0670	M	0.66939	2.045	0.58432	D	0.999991	P	0.52316	0.952	P	0.46796	0.527	T	0.01657	-1.1302	9	.	.	.	.	9.7193	0.40293	0.8604:0.0:0.1396:0.0	.	246	Q8IXT1	NOXIN_HUMAN	A	246	ENSP00000414687:T246A;ENSP00000435421:T246A	.	T	+	1	0	C11orf82	82320764	1.000000	0.71417	0.178000	0.23040	0.073000	0.16967	2.870000	0.48451	0.439000	0.26476	0.460000	0.39030	ACT		0.383	C11orf82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391936.1		
CTSC	1075	broad.mit.edu	37	11	88068132	88068132	+	Silent	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:88068132A>G	ENST00000227266.5	-	2	405	c.291T>C	c.(289-291)aaT>aaC	p.N97N	CTSC_ENST00000524463.1_Silent_p.N97N|CTSC_ENST00000393301.4_5'UTR|CTSC_ENST00000529974.1_Silent_p.N97N	NM_001814.4	NP_001805	P53634	CATC_HUMAN	cathepsin C	97					aging (GO:0007568)|immune response (GO:0006955)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of proteolysis involved in cellular protein catabolic process (GO:1903052)|proteolysis (GO:0006508)|response to organic substance (GO:0010033)|T cell mediated cytotoxicity (GO:0001913)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)	chaperone binding (GO:0051087)|chloride ion binding (GO:0031404)|cysteine-type peptidase activity (GO:0008234)|peptidase activator activity involved in apoptotic process (GO:0016505)|phosphatase binding (GO:0019902)|serine-type endopeptidase activity (GO:0004252)	p.N97N(1)		large_intestine(7)|lung(8)|ovary(2)|prostate(3)|skin(2)	22		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				ACTTGTAGTCATTCAACACAA	0.378																																					p.N97N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T291C	11						.						127.0	117.0	120.0					11																	88068132		2201	4299	6500	87707780	SO:0001819	synonymous_variant	1075	exon2			AK223038	CCDS8282.1, CCDS31654.1, CCDS44693.1	11q14.2	2014-09-17			ENSG00000109861	ENSG00000109861	3.4.14.1	"""Cathepsins"""	2528	protein-coding gene	gene with protein product	"""dipeptidyl peptidase 1"""	602365		PLS, PALS		7649281, 9092576	Standard	NM_148170		Approved	DPP1	uc001pck.4	P53634	OTTHUMG00000167290	ENST00000227266.5:c.291T>C	11.37:g.88068132A>G			87707780	NM_001114173	A8K7V2|B5MDD5|Q2HIY8|Q53G93|Q71E75|Q71E76|Q7M4N9|Q7Z3G7|Q7Z5U7|Q8WY99|Q8WYA7|Q8WYA8	Silent	SNP	ENST00000227266.5	37	CCDS8282.1	.	.	.	.	.	.	.	.	.	.	A	10.75	1.438356	0.25900	.	.	ENSG00000109861	ENST00000527018	.	.	.	5.84	-2.2	0.06994	.	.	.	.	.	T	0.39733	0.1089	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.27331	-1.0077	4	.	.	.	.	2.1696	0.03846	0.3274:0.1375:0.3829:0.1522	.	.	.	.	T	54	.	.	M	-	2	0	CTSC	87707780	0.852000	0.29690	0.990000	0.47175	0.989000	0.77384	0.022000	0.13511	-0.403000	0.07622	0.533000	0.62120	ATG		0.378	CTSC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394019.2	NM_001814	
ST3GAL4	6484	broad.mit.edu	37	11	126278027	126278027	+	Silent	SNP	C	C	T	rs141211562		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr11:126278027C>T	ENST00000526727.1	+	6	749	c.375C>T	c.(373-375)aaC>aaT	p.N125N	ST3GAL4_ENST00000530591.1_Silent_p.N121N|ST3GAL4_ENST00000356132.4_Silent_p.N131N|ST3GAL4_ENST00000444328.2_Silent_p.N125N|ST3GAL4_ENST00000392669.2_Silent_p.N125N|ST3GAL4_ENST00000227495.6_Silent_p.N121N|ST3GAL4_ENST00000449406.2_Silent_p.N114N|ST3GAL4_ENST00000534083.1_Silent_p.N125N|ST3GAL4_ENST00000534457.1_Silent_p.N120N|ST3GAL4_ENST00000526756.1_3'UTR|ST3GAL4_ENST00000532243.1_Silent_p.N124N			Q11206	SIA4C_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 4	125					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cognition (GO:0050890)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	beta-galactoside (CMP) alpha-2,3-sialyltransferase activity (GO:0003836)|monosialoganglioside sialyltransferase activity (GO:0047288)	p.N121N(1)		endometrium(1)|large_intestine(2)|lung(5)|stomach(1)	9	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.138)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0767)		TCGTGGGGAACGGGCACCGGC	0.577																																					p.N121N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C363T	11						.	C		0,4402		0,0,2201	122.0	120.0	121.0		363	-4.1	0.9	11	dbSNP_134	121	2,8594	2.2+/-6.3	0,2,4296	no	coding-synonymous	ST3GAL4	NM_006278.1		0,2,6497	TT,TC,CC		0.0233,0.0,0.0154		121/330	126278027	2,12996	2201	4298	6499	125783237	SO:0001819	synonymous_variant	6484	exon7			X74570	CCDS8474.1, CCDS58193.1, CCDS58194.1	11q23-q24	2013-03-01	2003-01-14	2005-02-07	ENSG00000110080	ENSG00000110080	2.4.99.4	"""Sialyltransferases"""	10864	protein-coding gene	gene with protein product	"""ST3Gal IV"""	104240	"""sialyltransferase 4C (beta-galactosidase alpha-2,3-sialytransferase)"""	CGS23, SIAT4, NANTA3, SIAT4C		8557707, 8288606	Standard	NM_006278		Approved	STZ, SAT3, FLJ11867	uc001qds.3	Q11206	OTTHUMG00000165830	ENST00000526727.1:c.375C>T	11.37:g.126278027C>T			125783237	NM_006278	A8K6B2|O60497|Q8N6A6|Q8NFG7|Q96QQ9	De_novo_Start_OutOfFrame	SNP	ENST00000526727.1	37	CCDS58193.1																																																																																				0.577	ST3GAL4-003	PUTATIVE	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386470.1	NM_006278	
KLRK1	22914	broad.mit.edu	37	12	10525786	10525786	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:10525786G>A	ENST00000240618.6	-	8	718	c.578C>T	c.(577-579)gCc>gTc	p.A193V	RP11-277P12.20_ENST00000500682.1_RNA|KLRC4-KLRK1_ENST00000539300.1_3'UTR|KLRK1_ENST00000540818.1_Missense_Mutation_p.A193V	NM_001199805.1|NM_007360.3	NP_001186734.1|NP_031386.2	P26718	NKG2D_HUMAN	killer cell lectin-like receptor subfamily K, member 1	193	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell differentiation (GO:0030154)|innate immune response (GO:0045087)|natural killer cell activation (GO:0030101)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)	p.A193V(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|skin(1)	9						AAAGCTCGAGGCATAGAGTGC	0.363																																					p.A193V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C578T	12						.						168.0	151.0	157.0					12																	10525786		2203	4300	6503	10417053	SO:0001583	missense	22914	exon13			AJ001687	CCDS8623.1	12p13.2-p12.3	2010-02-17	2003-02-19		ENSG00000213809	ENSG00000213809		"""Killer cell lectin-like receptors"", ""CD molecules"""	18788	protein-coding gene	gene with protein product		611817	"""DNA segment on chromosome 12 (unique) 2489 expressed sequence"""	D12S2489E		9683661, 2007850	Standard	NM_007360		Approved	NKG2D, KLR, NKG2-D, CD314	uc009zhj.3	P26718	OTTHUMG00000168574	ENST00000240618.6:c.578C>T	12.37:g.10525786G>A	ENSP00000240618:p.Ala193Val		10417053	NM_001199805	A8K7K5|A8K7P4|Q9NR41	Missense_Mutation	SNP	ENST00000240618.6	37	CCDS8623.1	.	.	.	.	.	.	.	.	.	.	G	12.00	1.808033	0.31961	.	.	ENSG00000213809	ENST00000240618;ENST00000540818	T;T	0.28255	1.62;1.62	5.59	4.71	0.59529	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.102830	0.43416	D	0.000575	T	0.17746	0.0426	N	0.04203	-0.255	0.30441	N	0.776166	D	0.64830	0.994	P	0.47346	0.544	T	0.04481	-1.0948	10	0.17832	T	0.49	.	12.3813	0.55309	0.0:0.8215:0.1785:0.0	.	193	P26718	NKG2D_HUMAN	V	193	ENSP00000240618:A193V;ENSP00000446003:A193V	ENSP00000240618:A193V	A	-	2	0	KLRK1	10417053	0.998000	0.40836	1.000000	0.80357	0.083000	0.17756	1.052000	0.30429	1.366000	0.46076	-0.171000	0.13296	GCC		0.363	KLRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400269.1	NM_007360	
PAH	5053	broad.mit.edu	37	12	103245493	103245493	+	Nonsense_Mutation	SNP	G	G	C	rs62642910		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:103245493G>C	ENST00000553106.1	-	8	1356	c.884C>G	c.(883-885)tCa>tGa	p.S295*	PAH_ENST00000307000.2_Nonsense_Mutation_p.S290*	NM_000277.1	NP_000268.1	P00439	PH4H_HUMAN	phenylalanine hydroxylase	295					catecholamine biosynthetic process (GO:0042423)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|neurotransmitter biosynthetic process (GO:0042136)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|phenylalanine 4-monooxygenase activity (GO:0004505)	p.S295*(1)		endometrium(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(5)|skin(2)|urinary_tract(1)	27					Droxidopa(DB06262)|Epinephrine(DB00668)|L-Phenylalanine(DB00120)|Norepinephrine(DB00368)|Tetrahydrobiopterin(DB00360)	GCTGCGATCTGAAAACAAGGG	0.483																																					p.S295X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C884G	12	GRCh37	CM990998	PAH	M	rs62642910	.						86.0	82.0	83.0					12																	103245493		2203	4300	6503	101769623	SO:0001587	stop_gained	5053	exon8			U49897	CCDS9092.1	12q22-q24.2	2010-04-27				ENSG00000171759	1.14.16.1		8582	protein-coding gene	gene with protein product	"""phenylalanine 4-monooxygenase"""	612349				2063869	Standard	NM_000277		Approved	PH	uc001tjq.1	P00439		ENST00000553106.1:c.884C>G	12.37:g.103245493G>C	ENSP00000448059:p.Ser295*		101769623	NM_000277	Q16717|Q8TC14	Nonsense_Mutation	SNP	ENST00000553106.1	37	CCDS9092.1	.	.	.	.	.	.	.	.	.	.	G	43	10.427575	0.99403	.	.	ENSG00000171759	ENST00000553106;ENST00000307000	.	.	.	5.51	5.51	0.81932	.	0.113998	0.64402	D	0.000017	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-10.362	19.7791	0.96410	0.0:0.0:1.0:0.0	rs62642910	.	.	.	X	295;290	.	ENSP00000303500:S290X	S	-	2	0	PAH	101769623	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.420000	0.97426	2.763000	0.94921	0.650000	0.86243	TCA		0.483	PAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406692.1		
POLR3B	55703	broad.mit.edu	37	12	106804719	106804719	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:106804719G>A	ENST00000228347.4	+	12	1304	c.1082G>A	c.(1081-1083)cGa>cAa	p.R361Q	POLR3B_ENST00000549195.1_3'UTR|POLR3B_ENST00000539066.1_Missense_Mutation_p.R303Q	NM_018082.5	NP_060552.4	Q9NW08	RPC2_HUMAN	polymerase (RNA) III (DNA directed) polypeptide B	361					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)	p.R361Q(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(22)|ovary(1)|prostate(3)|skin(3)|urinary_tract(2)	57						GGTAACAAGCGACTGGAATTG	0.348																																					p.R361Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1082A	12						.						91.0	92.0	92.0					12																	106804719		2203	4300	6503	105328849	SO:0001583	missense	55703	exon12			AY092084	CCDS9105.1, CCDS53824.1	12q23.3	2014-08-12			ENSG00000013503	ENSG00000013503		"""RNA polymerase subunits"""	30348	protein-coding gene	gene with protein product		614366				12391170	Standard	NM_018082		Approved	RPC2, FLJ10388	uc001tlp.3	Q9NW08	OTTHUMG00000170077	ENST00000228347.4:c.1082G>A	12.37:g.106804719G>A	ENSP00000228347:p.Arg361Gln		105328849	NM_018082	A8K6H0|B3KV73|F5H1E6|Q9NW59	Missense_Mutation	SNP	ENST00000228347.4	37	CCDS9105.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.532310	0.85812	.	.	ENSG00000013503	ENST00000228347;ENST00000551370;ENST00000539066;ENST00000549569;ENST00000549195	T;T;T	0.77489	-1.1;-1.1;-1.1	5.42	4.53	0.55603	RNA polymerase, beta subunit, protrusion (1);RNA polymerase Rpb2, domain 2 (1);	0.000000	0.85682	D	0.000000	D	0.90635	0.7063	M	0.93854	3.465	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.92986	0.6410	10	0.87932	D	0	-12.2144	14.5055	0.67750	0.0711:0.0:0.9289:0.0	.	361	Q9NW08	RPC2_HUMAN	Q	361;361;303;119;24	ENSP00000228347:R361Q;ENSP00000445721:R303Q;ENSP00000448398:R119Q	ENSP00000228347:R361Q	R	+	2	0	POLR3B	105328849	1.000000	0.71417	0.992000	0.48379	0.758000	0.43043	9.368000	0.97152	1.430000	0.47334	-0.266000	0.10368	CGA		0.348	POLR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407166.1	NM_018082	
OAS3	4940	broad.mit.edu	37	12	113382362	113382362	+	Missense_Mutation	SNP	C	C	T	rs199852899		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:113382362C>T	ENST00000228928.7	+	3	721	c.542C>T	c.(541-543)gCg>gTg	p.A181V	OAS3_ENST00000548514.1_Missense_Mutation_p.A181V|OAS3_ENST00000546638.1_3'UTR|RP1-71H24.1_ENST00000552784.1_RNA	NM_006187.2	NP_006178.2	Q9Y6K5	OAS3_HUMAN	2'-5'-oligoadenylate synthetase 3, 100kDa	181	OAS domain 1.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|nucleobase-containing compound metabolic process (GO:0006139)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)	p.A181V(1)		breast(3)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|skin(2)	27						GGCGAGCATGCGGCCTGCTTC	0.577																																					p.A181V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C542T	12						.	C	VAL/ALA	0,4080		0,0,2040	58.0	63.0	61.0		542	2.7	0.0	12		61	4,8384		0,4,4190	yes	missense	OAS3	NM_006187.2	64	0,4,6230	TT,TC,CC		0.0477,0.0,0.0321	possibly-damaging	181/1088	113382362	4,12464	2040	4194	6234	111866745	SO:0001583	missense	4940	exon3			AF063613	CCDS44981.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111331			8088	protein-coding gene	gene with protein product		603351	"""2'-5'-oligoadenylate synthetase 3 (100 kD)"""			9790745	Standard	NM_006187		Approved		uc001tug.3	Q9Y6K5	OTTHUMG00000169795	ENST00000228928.7:c.542C>T	12.37:g.113382362C>T	ENSP00000228928:p.Ala181Val		111866745	NM_006187	Q2HJ14|Q9H3P5	Missense_Mutation	SNP	ENST00000228928.7	37	CCDS44981.1	.	.	.	.	.	.	.	.	.	.	C	13.79	2.342931	0.41498	0.0	4.77E-4	ENSG00000111331	ENST00000228928;ENST00000548514;ENST00000323881	T;T	0.08546	3.08;3.08	3.57	2.65	0.31530	-oligoadenylate synthetase 1, domain 2/C-terminal (2);-5&apos (2);2&apos (2);	.	.	.	.	T	0.21022	0.0506	M	0.62723	1.935	0.09310	N	0.999998	D;D	0.76494	0.971;0.999	P;D	0.63597	0.649;0.916	T	0.03394	-1.1041	9	0.72032	D	0.01	.	8.8632	0.35269	0.0:0.7692:0.2308:0.0	.	181;181	Q9Y6K5;F8VS35	OAS3_HUMAN;.	V	181	ENSP00000228928:A181V;ENSP00000448388:A181V	ENSP00000228928:A181V	A	+	2	0	OAS3	111866745	0.003000	0.15002	0.005000	0.12908	0.326000	0.28443	1.824000	0.39072	0.790000	0.33803	0.655000	0.94253	GCG		0.577	OAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405920.1		
KSR2	283455	broad.mit.edu	37	12	117962830	117962830	+	Silent	SNP	G	G	A	rs540286777		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:117962830G>A	ENST00000339824.5	-	14	2773	c.2046C>T	c.(2044-2046)caC>caT	p.H682H	KSR2_ENST00000302438.5_Silent_p.H379H|KSR2_ENST00000425217.1_Silent_p.H653H|KSR2_ENST00000545002.1_5'UTR			Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2	682	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.H714H(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(25)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GCCAGCGGCCGTGGTACACTT	0.607													G|||	1	0.000199681	0.0	0.0	5008	,	,		19594	0.001		0.0	False		,,,				2504	0.0				p.H653H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1959T	12						.						54.0	58.0	57.0					12																	117962830		2087	4206	6293	116447213	SO:0001819	synonymous_variant	283455	exon14			AY345972	CCDS61250.1	12q24.22-q24.23	2014-08-12			ENSG00000171435	ENSG00000171435			18610	protein-coding gene	gene with protein product		610737				12471243	Standard	NM_173598		Approved	FLJ25965	uc001two.2	Q6VAB6	OTTHUMG00000169020	ENST00000339824.5:c.2046C>T	12.37:g.117962830G>A			116447213	NM_173598	A0PJT2|Q3B828|Q8N775	Silent	SNP	ENST00000339824.5	37																																																																																					0.607	KSR2-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401987.2	NM_173598	
CCDC60	160777	broad.mit.edu	37	12	119978425	119978425	+	Nonsense_Mutation	SNP	C	C	T	rs78597191	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:119978425C>T	ENST00000327554.2	+	14	2023	c.1558C>T	c.(1558-1560)Cga>Tga	p.R520*	RP11-768F21.1_ENST00000509470.2_lincRNA	NM_178499.3	NP_848594.2	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60	520								p.R520*(1)		endometrium(4)|kidney(3)|large_intestine(8)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)		ACAGTTTGTGCGAGAACACAT	0.512													C|||	10	0.00199681	0.0068	0.0014	5008	,	,		22171	0.0		0.0	False		,,,				2504	0.0				p.R520X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1558T	12						.	C	stop/ARG	39,4367	43.1+/-76.7	1,37,2165	120.0	114.0	116.0		1558	3.5	0.9	12	dbSNP_131	116	0,8600		0,0,4300	yes	stop-gained	CCDC60	NM_178499.3		1,37,6465	TT,TC,CC		0.0,0.8852,0.2999		520/551	119978425	39,12967	2203	4300	6503	118462808	SO:0001587	stop_gained	160777	exon14			BC040553	CCDS9190.1	12q24.23	2006-02-03			ENSG00000183273	ENSG00000183273			28610	protein-coding gene	gene with protein product						12477932	Standard	NM_178499		Approved	MGC39827	uc001txe.3	Q8IWA6	OTTHUMG00000168943	ENST00000327554.2:c.1558C>T	12.37:g.119978425C>T	ENSP00000333374:p.Arg520*		118462808	NM_178499		Nonsense_Mutation	SNP	ENST00000327554.2	37	CCDS9190.1	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	C	41	8.937452	0.99010	0.008852	0.0	ENSG00000183273	ENST00000327554	.	.	.	5.4	3.5	0.40072	.	0.108649	0.37906	N	0.001896	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-12.8815	11.8074	0.52163	0.339:0.661:0.0:0.0	.	.	.	.	X	520	.	.	R	+	1	2	CCDC60	118462808	0.905000	0.30787	0.898000	0.35279	0.997000	0.91878	1.651000	0.37302	0.768000	0.33290	0.655000	0.94253	CGA		0.512	CCDC60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401680.1	NM_178499	
SPPL3	121665	broad.mit.edu	37	12	121206174	121206174	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:121206174G>A	ENST00000353487.2	-	8	1230	c.727C>T	c.(727-729)Cgt>Tgt	p.R243C		NM_139015.4	NP_620584.2	Q8TCT6	SPPL3_HUMAN	signal peptide peptidase like 3	244						Golgi-associated vesicle membrane (GO:0030660)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|rough endoplasmic reticulum (GO:0005791)	aspartic endopeptidase activity, intramembrane cleaving (GO:0042500)|protein homodimerization activity (GO:0042803)	p.R243C(1)				all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GGAACATCACGCCCAACATTG	0.547																																					p.R243C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C727T	12						.						129.0	120.0	123.0					12																	121206174		2203	4300	6503	119690557	SO:0001583	missense	121665	exon8				CCDS9208.1	12q24.31	2012-02-21			ENSG00000157837	ENSG00000157837			30424	protein-coding gene	gene with protein product	"""intramembrane protease 2"", ""presenilin-like protein 4"""	608240				12139484	Standard	NM_139015		Approved	IMP2, PSL4, MGC90402, MGC126674, MGC126676, DKFZP586C1324	uc001tzd.3	Q8TCT6	OTTHUMG00000169232	ENST00000353487.2:c.727C>T	12.37:g.121206174G>A	ENSP00000288680:p.Arg243Cys		119690557	NM_139015	Q3MJ04|Q8TAU4|Q96DD9	Missense_Mutation	SNP	ENST00000353487.2	37	CCDS9208.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.241329	0.79912	.	.	ENSG00000157837	ENST00000353487;ENST00000405631	T	0.19105	2.17	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.33294	0.0858	L	0.41236	1.265	0.80722	D	1	D;D	0.76494	0.999;0.999	D;P	0.63033	0.91;0.877	T	0.01205	-1.1419	10	0.39692	T	0.17	-23.6268	13.192	0.59717	0.0:0.0:0.7325:0.2675	.	244;243	Q8TCT6;Q3MJ04	PSL4_HUMAN;.	C	243;242	ENSP00000288680:R243C	ENSP00000288680:R243C	R	-	1	0	AC069214.1	119690557	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	4.874000	0.63064	2.503000	0.84419	0.591000	0.81541	CGT		0.547	SPPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402980.2	NM_139015	
RNF34	80196	broad.mit.edu	37	12	121861198	121861198	+	Missense_Mutation	SNP	G	G	A	rs369744966		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:121861198G>A	ENST00000392464.2	+	6	1007	c.938G>A	c.(937-939)cGg>cAg	p.R313Q	RNF34_ENST00000361234.5_Missense_Mutation_p.R313Q|RNF34_ENST00000392465.3_Missense_Mutation_p.R314Q|RNF34_ENST00000555076.1_Missense_Mutation_p.G6S					ring finger protein 34, E3 ubiquitin protein ligase									p.R314Q(1)		breast(1)|large_intestine(1)	2	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000432)|Epithelial(86;0.00233)		GATGGCGAGCGGCTGCAGCTG	0.607													G|||	1	0.000199681	0.0	0.0	5008	,	,		17509	0.0		0.001	False		,,,				2504	0.0				p.R313Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G938A	12						.	G	GLN/ARG,GLN/ARG	0,4406		0,0,2203	71.0	53.0	59.0		941,938	5.1	1.0	12		59	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	RNF34	NM_194271.1,NM_025126.2	43,43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	314/374,313/373	121861198	1,13005	2203	4300	6503	120345581	SO:0001583	missense	80196	exon6			AF306709, AB084914	CCDS9221.1, CCDS31915.1, CCDS73538.1	12q24.31	2012-02-23	2012-02-23			ENSG00000170633		"""RING-type (C3HC4) zinc fingers"""	17297	protein-coding gene	gene with protein product		608299	"""ring finger protein 34"""			12118383	Standard	NM_025126		Approved	RIFF, FLJ21786, RIF	uc001ual.2	Q969K3		ENST00000392464.2:c.938G>A	12.37:g.121861198G>A	ENSP00000376257:p.Arg313Gln		120345581	NM_025126		Missense_Mutation	SNP	ENST00000392464.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.00|16.00	2.998204|2.998204	0.54147|0.54147	0.0|0.0	1.16E-4|1.16E-4	ENSG00000170633|ENSG00000170633	ENST00000555076|ENST00000361234;ENST00000392465;ENST00000392464;ENST00000354795	.|T;T;T	.|0.36157	.|1.27;1.27;1.48	6.06|6.06	5.07|5.07	0.68467|0.68467	.|.	.|0.430462	.|0.27327	.|N	.|0.019865	T|T	0.21841|0.21841	0.0526|0.0526	N|N	0.22421|0.22421	0.69|0.69	0.23298|0.23298	N|N	0.99796|0.99796	.|B;B	.|0.18610	.|0.017;0.029	.|B;B	.|0.09377	.|0.002;0.004	T|T	0.10989|0.10989	-1.0606|-1.0606	5|10	.|0.15066	.|T	.|0.55	-27.9282|-27.9282	10.3469|10.3469	0.43911|0.43911	0.161:0.0:0.839:0.0|0.161:0.0:0.839:0.0	.|.	.|313;314	.|Q969K3;Q969K3-2	.|RNF34_HUMAN;.	S|Q	6|313;314;313;314	.|ENSP00000355137:R313Q;ENSP00000376258:R314Q;ENSP00000376257:R313Q	.|ENSP00000346850:R314Q	G|R	+|+	1|2	0|0	RNF34|RNF34	120345581|120345581	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.982000|0.982000	0.71751|0.71751	3.055000|3.055000	0.49916|0.49916	2.879000|2.879000	0.98667|0.98667	0.650000|0.650000	0.86243|0.86243	GGC|CGG		0.607	RNF34-005	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000413892.1	NM_194271	
KDM2B	84678	broad.mit.edu	37	12	121986794	121986794	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:121986794G>A	ENST00000377071.4	-	6	743	c.671C>T	c.(670-672)cCg>cTg	p.P224L	KDM2B_ENST00000538046.2_Missense_Mutation_p.P224L|KDM2B_ENST00000377069.4_Missense_Mutation_p.P193L|KDM2B_ENST00000536437.1_Missense_Mutation_p.P107L	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	224	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				embryonic camera-type eye morphogenesis (GO:0048596)|forebrain development (GO:0030900)|fourth ventricle development (GO:0021592)|hindbrain development (GO:0030902)|histone demethylation (GO:0016577)|histone H2A monoubiquitination (GO:0035518)|initiation of neural tube closure (GO:0021993)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K36 specific) (GO:0051864)|rRNA binding (GO:0019843)|zinc ion binding (GO:0008270)	p.P224L(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	19						TTTCACTTTCGGGTACTTCAT	0.582																																					p.P224L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C671T	12						.						176.0	185.0	182.0					12																	121986794		2019	4175	6194	120471177	SO:0001583	missense	84678	exon6			AJ459424	CCDS41849.1, CCDS41850.1	12q24.31	2014-02-18	2009-04-06	2009-04-06	ENSG00000089094	ENSG00000089094		"""F-boxes / Leucine-rich repeats"", ""Chromatin-modifying enzymes / K-demethylases"""	13610	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1B"""	609078	"""F-box and leucine-rich repeat protein 10"""	FBXL10		10799292	Standard	NM_032590		Approved	PCCX2, CXXC2, Fbl10, JHDM1B	uc001uat.3	Q8NHM5	OTTHUMG00000169071	ENST00000377071.4:c.671C>T	12.37:g.121986794G>A	ENSP00000366271:p.Pro224Leu		120471177	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Missense_Mutation	SNP	ENST00000377071.4	37	CCDS41850.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.190455	0.78789	.	.	ENSG00000089094	ENST00000397480;ENST00000377069;ENST00000377071;ENST00000536437;ENST00000397478;ENST00000261824;ENST00000446152;ENST00000539394;ENST00000539371	T;T;T;T;T	0.71934	-0.61;-0.61;-0.61;-0.61;-0.61	5.11	5.11	0.69529	Transcription factor jumonji/aspartyl beta-hydroxylase (2);	0.206896	0.34507	N	0.003914	D	0.88948	0.6576	H	0.94620	3.56	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.997;0.999;1.0;0.999	D	0.91805	0.5455	10	0.87932	D	0	-28.0661	18.7254	0.91711	0.0:0.0:1.0:0.0	.	224;107;224;193	E7EML5;Q1RLM7;Q8NHM5;A8MRS1	.;.;KDM2B_HUMAN;.	L	224;193;224;107;224;224;187;107;193	ENSP00000366269:P193L;ENSP00000366271:P224L;ENSP00000445196:P107L;ENSP00000398279:P187L;ENSP00000440373:P107L	ENSP00000261824:P224L	P	-	2	0	KDM2B	120471177	1.000000	0.71417	0.996000	0.52242	0.508000	0.34012	9.259000	0.95561	2.649000	0.89929	0.655000	0.94253	CCG		0.582	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590	
BCL7A	605	broad.mit.edu	37	12	122492725	122492725	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:122492725C>T	ENST00000261822.4	+	5	660	c.454C>T	c.(454-456)Cag>Tag	p.Q152*	BCL7A_ENST00000538010.1_Nonsense_Mutation_p.Q152*	NM_001024808.1	NP_001019979.1	Q4VC05	BCL7A_HUMAN	B-cell CLL/lymphoma 7A	152					negative regulation of transcription, DNA-templated (GO:0045892)			p.Q152*(1)		haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000202)|Epithelial(86;0.000386)|BRCA - Breast invasive adenocarcinoma(302;0.231)		TTCTGATGAGCAGAATTCACA	0.527			T	MYC	BNHL						OREG0022214	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q152X	GBM(17;197 467 16477 23242 44349)		Dom	yes		12	12q24.1	605	B-cell CLL/lymphoma 7A		L	.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C454T	12						.						128.0	137.0	134.0					12																	122492725		2203	4300	6503	120977108	SO:0001587	stop_gained	605	exon5			X89984	CCDS9226.1, CCDS53841.1	12q24.1	2008-07-03			ENSG00000110987	ENSG00000110987			1004	protein-coding gene	gene with protein product		601406		BCL7		8605326, 9931421	Standard	NM_020993		Approved		uc001ubo.3	Q4VC05	OTTHUMG00000168951	ENST00000261822.4:c.454C>T	12.37:g.122492725C>T	ENSP00000261822:p.Gln152*	1519	120977108	NM_020993	B4DJN6|B7ZB21|Q13843|Q14CT7	Nonsense_Mutation	SNP	ENST00000261822.4	37	CCDS53841.1	.	.	.	.	.	.	.	.	.	.	C	37	6.383169	0.97524	.	.	ENSG00000110987	ENST00000538010;ENST00000261822	.	.	.	5.92	5.92	0.95590	.	0.116875	0.64402	D	0.000016	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	.	20.3214	0.98679	0.0:1.0:0.0:0.0	.	.	.	.	X	152	.	ENSP00000261822:Q152X	Q	+	1	0	BCL7A	120977108	1.000000	0.71417	1.000000	0.80357	0.657000	0.38888	5.296000	0.65698	2.804000	0.96469	0.655000	0.94253	CAG		0.527	BCL7A-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000401712.1		
KNTC1	9735	broad.mit.edu	37	12	123028753	123028753	+	Silent	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:123028753T>C	ENST00000333479.7	+	8	783	c.606T>C	c.(604-606)caT>caC	p.H202H	KNTC1_ENST00000450485.2_Intron	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	202					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|protein complex assembly (GO:0006461)|regulation of exit from mitosis (GO:0007096)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)		p.H202H(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(8)|large_intestine(12)|lung(20)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	72	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		AAAATTATCATACTCTTGGTT	0.308																																					p.H202H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T606C	12						.						157.0	152.0	154.0					12																	123028753		1809	4077	5886	121594706	SO:0001819	synonymous_variant	9735	exon8				CCDS45002.1	12q24.31	2013-01-17			ENSG00000184445	ENSG00000184445			17255	protein-coding gene	gene with protein product	"""rough deal homolog (Drosophila)"""	607363				11146660, 11590237	Standard	NM_014708		Approved	KIAA0166, ROD	uc001ucv.3	P50748	OTTHUMG00000168861	ENST00000333479.7:c.606T>C	12.37:g.123028753T>C			121594706	NM_014708	A7E2C4|B3KSG2	Silent	SNP	ENST00000333479.7	37	CCDS45002.1																																																																																				0.308	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2		
RILPL2	196383	broad.mit.edu	37	12	123915113	123915113	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:123915113G>A	ENST00000280571.8	-	2	729	c.433C>T	c.(433-435)Cgc>Tgc	p.R145C		NM_145058.1	NP_659495.1	Q969X0	RIPL2_HUMAN	Rab interacting lysosomal protein-like 2	145	RILP-like.				epithelial cell morphogenesis (GO:0003382)|intracellular protein transport (GO:0006886)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|primary cilium (GO:0072372)	identical protein binding (GO:0042802)	p.R145C(1)		endometrium(1)|large_intestine(2)|lung(2)|skin(1)	6	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000546)|Epithelial(86;0.00179)|all cancers(50;0.0168)		AGTTTGTTGCGTTCCTGCAGC	0.592																																					p.R145C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C433T	12						.						138.0	125.0	130.0					12																	123915113		2203	4300	6503	122481066	SO:0001583	missense	196383	exon2			AB085763	CCDS9248.1	12q24.31	2007-11-27				ENSG00000150977			28787	protein-coding gene	gene with protein product		614093				14668488	Standard	NM_145058		Approved	MGC7036, FLJ30380, FLJ32372	uc001uey.1	Q969X0		ENST00000280571.8:c.433C>T	12.37:g.123915113G>A	ENSP00000280571:p.Arg145Cys		122481066	NM_145058		Missense_Mutation	SNP	ENST00000280571.8	37	CCDS9248.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.320553	0.81469	.	.	ENSG00000150977	ENST00000280571	T	0.69175	-0.38	6.04	5.12	0.69794	.	0.149706	0.64402	D	0.000020	D	0.82305	0.5008	M	0.79805	2.47	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.84119	0.0405	10	0.87932	D	0	.	15.733	0.77819	0.0:0.0:0.7558:0.2442	.	145	Q969X0	RIPL2_HUMAN	C	145	ENSP00000280571:R145C	ENSP00000280571:R145C	R	-	1	0	RILPL2	122481066	1.000000	0.71417	0.998000	0.56505	0.982000	0.71751	4.055000	0.57441	2.870000	0.98441	0.637000	0.83480	CGC		0.592	RILPL2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_145058	
GPRC5A	9052	broad.mit.edu	37	12	13061924	13061924	+	Silent	SNP	C	C	T	rs200045600		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:13061924C>T	ENST00000014914.5	+	2	1631	c.741C>T	c.(739-741)tcC>tcT	p.S247S	GPRC5A_ENST00000542056.1_Intron	NM_003979.3	NP_003970.1	Q8NFJ5	RAI3_HUMAN	G protein-coupled receptor, class C, group 5, member A	247					signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.S247S(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	18		Prostate(47;0.141)		BRCA - Breast invasive adenocarcinoma(232;0.0708)	Tretinoin(DB00755)	TCCTCAGCTCCGCCTTGGCTG	0.552													C|||	1	0.000199681	0.0	0.0	5008	,	,		21770	0.001		0.0	False		,,,				2504	0.0				p.S247S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C741T	12						.						114.0	92.0	99.0					12																	13061924		2203	4300	6503	12953191	SO:0001819	synonymous_variant	9052	exon2			AF095448	CCDS8657.1	12p13-p12.3	2014-01-30	2014-01-30	2005-05-03		ENSG00000013588		"""GPCR / Class C : Orphans"""	9836	protein-coding gene	gene with protein product		604138	"""retinoic acid induced 3"", ""G protein-coupled receptor, family C, group 5, member A"""	RAI3, GPCR5A		9857033	Standard	NM_003979		Approved	RAIG1	uc001rba.3	Q8NFJ5		ENST00000014914.5:c.741C>T	12.37:g.13061924C>T			12953191	NM_003979	B3KV45|O95357	Silent	SNP	ENST00000014914.5	37	CCDS8657.1																																																																																				0.552	GPRC5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400682.1		
HEBP1	50865	broad.mit.edu	37	12	13128358	13128358	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:13128358G>A	ENST00000014930.4	-	4	612	c.454C>T	c.(454-456)Cgt>Tgt	p.R152C	RP11-392P7.6_ENST00000545914.1_RNA|RP11-392P7.6_ENST00000542078.1_RNA|RP11-392P7.6_ENST00000536029.1_RNA|RP11-392P7.6_ENST00000543515.2_RNA|HEBP1_ENST00000540916.1_5'UTR	NM_015987.4	NP_057071.2	Q9NRV9	HEBP1_HUMAN	heme binding protein 1	152					circadian rhythm (GO:0007623)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	heme binding (GO:0020037)	p.R152C(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(1)|urinary_tract(1)	7		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.153)		AGGGCAGCACGCAGACGGGTG	0.587																																					p.R152C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C454T	12						.						99.0	76.0	84.0					12																	13128358		2203	4300	6503	13019625	SO:0001583	missense	50865	exon4			AF117615	CCDS31749.1	12p13.2	2014-01-30			ENSG00000013583	ENSG00000013583		"""Endogenous ligands"""	17176	protein-coding gene	gene with protein product		605826				10640688	Standard	NM_015987		Approved	HEBP, HBP	uc001rbd.3	Q9NRV9	OTTHUMG00000168771	ENST00000014930.4:c.454C>T	12.37:g.13128358G>A	ENSP00000014930:p.Arg152Cys		13019625	NM_015987	A8K1G2|Q9Y5Z5	Missense_Mutation	SNP	ENST00000014930.4	37	CCDS31749.1	.	.	.	.	.	.	.	.	.	.	G	17.26	3.344272	0.61073	.	.	ENSG00000013583	ENST00000014930	T	0.24908	1.83	4.76	3.88	0.44766	Regulatory factor, effector, bacterial (1);	0.366612	0.29722	N	0.011380	T	0.42268	0.1195	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	P	0.61722	0.893	T	0.32268	-0.9913	10	0.56958	D	0.05	-14.8694	8.0054	0.30321	0.0855:0.0:0.756:0.1585	.	152	Q9NRV9	HEBP1_HUMAN	C	152	ENSP00000014930:R152C	ENSP00000014930:R152C	R	-	1	0	HEBP1	13019625	0.724000	0.28038	0.813000	0.32504	0.595000	0.36748	1.363000	0.34159	1.365000	0.46057	0.655000	0.94253	CGT		0.587	HEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401001.1		
NCOR2	9612	broad.mit.edu	37	12	124887093	124887093	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:124887093C>T	ENST00000405201.1	-	14	1497	c.1497G>A	c.(1495-1497)caG>caA	p.Q499Q	NCOR2_ENST00000356219.3_Silent_p.Q499Q|NCOR2_ENST00000404121.2_Silent_p.Q69Q|NCOR2_ENST00000404621.1_Silent_p.Q498Q|NCOR2_ENST00000397355.1_Silent_p.Q499Q|NCOR2_ENST00000429285.2_Silent_p.Q498Q			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	499	Poly-Gln.				cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)	p.Q499Q(9)		breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		gctgctgctgctgttgttgct	0.617																																					p.Q499Q												.	.	9	Substitution - coding silent(9)	endometrium(4)|large_intestine(3)|kidney(2)	c.G1497A	12						.						9.0	10.0	10.0					12																	124887093		2051	4183	6234	123453046	SO:0001819	synonymous_variant	9612	exon16			U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"""nuclear receptor co-repressor 2"""			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.1497G>A	12.37:g.124887093C>T			123453046	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Silent	SNP	ENST00000405201.1	37	CCDS41858.2																																																																																				0.617	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	
CCDC77	84318	broad.mit.edu	37	12	542408	542408	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:542408C>T	ENST00000239830.4	+	9	920	c.741C>T	c.(739-741)atC>atT	p.I247I	CCDC77_ENST00000540180.1_Silent_p.I215I|CCDC77_ENST00000422000.1_Silent_p.I215I|CCDC77_ENST00000412006.2_Silent_p.I215I|CCDC77_ENST00000540344.1_3'UTR	NM_032358.3	NP_115734.1	Q9BR77	CCD77_HUMAN	coiled-coil domain containing 77	247						centrosome (GO:0005813)|membrane (GO:0016020)		p.I247I(1)		cervix(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(10;0.0149)|all_epithelial(11;0.035)|all_lung(10;0.111)|Ovarian(42;0.142)|Lung NSC(10;0.156)		OV - Ovarian serous cystadenocarcinoma(31;0.00123)|BRCA - Breast invasive adenocarcinoma(9;0.033)			AAGGGCTCATCGAGGACAGAC	0.468																																					p.I215I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C645T	12						.						131.0	121.0	124.0					12																	542408		2203	4300	6503	412669	SO:0001819	synonymous_variant	84318	exon7			AK027638	CCDS8503.1, CCDS44781.1	12p13.33	2006-02-16			ENSG00000120647	ENSG00000120647			28203	protein-coding gene	gene with protein product						12477932	Standard	NM_001130148		Approved	MGC13183	uc001qig.3	Q9BR77	OTTHUMG00000129214	ENST00000239830.4:c.741C>T	12.37:g.542408C>T			412669	NM_001130148	B4DDE8	Silent	SNP	ENST00000239830.4	37	CCDS8503.1																																																																																				0.468	CCDC77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251296.1	NM_032358	
FBXL14	144699	broad.mit.edu	37	12	1702349	1702349	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:1702349T>G	ENST00000339235.3	-	1	982	c.884A>C	c.(883-885)cAg>cCg	p.Q295P	WNT5B_ENST00000537031.1_Intron|FBXL14_ENST00000543278.1_5'Flank	NM_152441.2	NP_689654.1	Q8N1E6	FXL14_HUMAN	F-box and leucine-rich repeat protein 14	295					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)	p.Q295P(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	8	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00115)			AGCCAGACTCTGGTCTCCCAC	0.587																																					p.Q295P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A884C	12						.						81.0	68.0	73.0					12																	1702349		2203	4300	6503	1572610	SO:0001583	missense	144699	exon1			BC028132	CCDS8509.1	12p13.33	2011-06-09			ENSG00000171823	ENSG00000171823		"""F-boxes / Leucine-rich repeats"""	28624	protein-coding gene	gene with protein product		609081				12477932	Standard	NM_152441		Approved	MGC40195, Fbl14	uc001qjh.3	Q8N1E6	OTTHUMG00000090369	ENST00000339235.3:c.884A>C	12.37:g.1702349T>G	ENSP00000344855:p.Gln295Pro		1572610	NM_152441		Missense_Mutation	SNP	ENST00000339235.3	37	CCDS8509.1	.	.	.	.	.	.	.	.	.	.	T	14.09	2.430533	0.43122	.	.	ENSG00000171823	ENST00000339235	T	0.02525	4.26	4.71	4.71	0.59529	.	0.000000	0.85682	D	0.000000	T	0.04724	0.0128	M	0.62154	1.92	0.58432	D	0.999999	P	0.42827	0.791	B	0.37650	0.255	T	0.50750	-0.8791	10	0.33141	T	0.24	.	14.3439	0.66646	0.0:0.0:0.0:1.0	.	295	Q8N1E6	FXL14_HUMAN	P	295	ENSP00000344855:Q295P	ENSP00000344855:Q295P	Q	-	2	0	FBXL14	1572610	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.776000	0.85560	1.946000	0.56461	0.528000	0.53228	CAG		0.587	FBXL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206741.1	NM_152441	
CACNA1C	775	broad.mit.edu	37	12	2800144	2800144	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:2800144G>A	ENST00000347598.4	+	49	6340	c.6340G>A	c.(6340-6342)Gcc>Acc	p.A2114T	CACNA1C_ENST00000399606.1_Missense_Mutation_p.A2086T|CACNA1C_ENST00000399644.1_Missense_Mutation_p.A2066T|CACNA1C_ENST00000399649.1_Missense_Mutation_p.A2072T|CACNA1C_ENST00000344100.3_Missense_Mutation_p.A2107T|CACNA1C_ENST00000399637.1_Missense_Mutation_p.A2085T|CACNA1C_ENST00000399603.1_Missense_Mutation_p.A2066T|CACNA1C_ENST00000399655.1_Missense_Mutation_p.A2066T|CACNA1C_ENST00000399597.1_Missense_Mutation_p.A2066T|CACNA1C-AS1_ENST00000501371.1_RNA|CACNA1C_ENST00000399638.1_Missense_Mutation_p.A2094T|CACNA1C_ENST00000399621.1_Missense_Mutation_p.A2085T|CACNA1C_ENST00000399617.1_Missense_Mutation_p.A2101T|CACNA1C_ENST00000399601.1_Missense_Mutation_p.A2066T|CACNA1C-AS1_ENST00000541673.1_RNA|CACNA1C_ENST00000406454.3_Missense_Mutation_p.A2137T|CACNA1C_ENST00000399595.1_Missense_Mutation_p.A2074T|CACNA1C_ENST00000402845.3_Missense_Mutation_p.A2085T|CACNA1C_ENST00000327702.7_Missense_Mutation_p.A2101T|CACNA1C_ENST00000399629.1_Missense_Mutation_p.A2083T|CACNA1C_ENST00000335762.5_Missense_Mutation_p.A2091T|CACNA1C_ENST00000399634.1_Missense_Mutation_p.A2137T|CACNA1C_ENST00000399591.1_Missense_Mutation_p.A2074T|CACNA1C_ENST00000399641.1_Missense_Mutation_p.A2066T|CACNA1C-AS1_ENST00000544517.1_RNA	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	2149					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.A2179T(1)|p.A2107T(1)|p.A1601T(1)		NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	GCTGGCCGACGCCTGCGACAT	0.612																																					p.A2066T												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.G6196A	12						.						13.0	16.0	15.0					12																	2800144		2006	4171	6177	2670405	SO:0001583	missense	775	exon47			AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.6340G>A	12.37:g.2800144G>A	ENSP00000266376:p.Ala2114Thr		2670405	NM_001129842	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Missense_Mutation	SNP	ENST00000347598.4	37	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.008438	0.93346	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.61980	0.06;0.06;0.06;0.06;0.06;0.06;0.06;0.06;0.06;0.06;0.06;0.06;0.06;0.06;0.06;0.06;0.06;0.06;0.06;0.06;0.06;0.06	4.58	4.58	0.56647	.	0.060120	0.64402	D	0.000005	T	0.81118	0.4756	M	0.83774	2.66	0.51482	D	0.99992	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.988;1.0;1.0;1.0;1.0;1.0;1.0;0.999;1.0;0.989;1.0;0.997;0.993;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;P;D;D;D;D;D;D;D;D;P;D;D;D;D;D;D;D	0.97110	1.0;0.996;0.992;0.999;0.996;0.998;0.997;0.998;0.748;0.999;0.996;0.996;0.996;0.998;0.981;0.995;0.996;0.819;0.996;0.943;0.923;0.998;0.996;0.996;0.992	D	0.84472	0.0600	10	0.87932	D	0	.	17.926	0.88983	0.0:0.0:1.0:0.0	.	757;2107;2063;2149;2101;2085;2066;2083;2094;2066;2086;2066;2097;2114;2066;2101;2137;2074;2072;2074;2055;2085;2085;2066;2066	B7Z7Z5;Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-28;Q13936-11;E9PDJ1;E9PDJ0;F5GY28;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;Q13936-12	.;.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	T	2091;2066;2066;2094;2066;2085;2085;2074;2066;2114;2086;2066;2107;2083;2101;2072;2085;2066;2137;2101;2137;2074;1967	ENSP00000336982:A2091T;ENSP00000382563:A2066T;ENSP00000382552:A2066T;ENSP00000382547:A2094T;ENSP00000382506:A2066T;ENSP00000382530:A2085T;ENSP00000382546:A2085T;ENSP00000382500:A2074T;ENSP00000382549:A2066T;ENSP00000266376:A2114T;ENSP00000382515:A2086T;ENSP00000382510:A2066T;ENSP00000341092:A2107T;ENSP00000382537:A2083T;ENSP00000329877:A2101T;ENSP00000382557:A2072T;ENSP00000385724:A2085T;ENSP00000382512:A2066T;ENSP00000382542:A2137T;ENSP00000382526:A2101T;ENSP00000385896:A2137T;ENSP00000382504:A2074T	ENSP00000323129:A1967T	A	+	1	0	CACNA1C	2670405	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.482000	0.97935	2.545000	0.85829	0.655000	0.94253	GCC		0.612	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719	
NTF3	4908	broad.mit.edu	37	12	5541508	5541508	+	Splice_Site	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:5541508G>A	ENST00000423158.3	+	1	230	c.18G>A	c.(16-18)acG>acA	p.T6T	NTF3_ENST00000535299.1_3'UTR	NM_001102654.1	NP_001096124.1	P20783	NTF3_HUMAN	neurotrophin 3	0					activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell-cell signaling (GO:0007267)|enteric nervous system development (GO:0048484)|epidermis development (GO:0008544)|glial cell fate determination (GO:0007403)|induction of positive chemotaxis (GO:0050930)|mechanoreceptor differentiation (GO:0042490)|myelination (GO:0042552)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|nerve development (GO:0021675)|nervous system development (GO:0007399)|neuromuscular synaptic transmission (GO:0007274)|peripheral nervous system development (GO:0007422)|positive chemotaxis (GO:0050918)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of glial cell differentiation (GO:0045687)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of receptor internalization (GO:0002092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of synaptic transmission (GO:0050804)|signal transduction (GO:0007165)|smooth muscle cell differentiation (GO:0051145)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasmic membrane-bounded vesicle (GO:0016023)|extracellular region (GO:0005576)	chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|receptor binding (GO:0005102)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(3)|upper_aerodigestive_tract(1)	22						CTTTTGCCACGGTAAGGGGAG	0.632																																					p.T6T	GBM(194;1104 2182 8339 9578 18493)											.	.	0			c.G18A	12						.						55.0	58.0	57.0					12																	5541508		1929	4134	6063	5411769	SO:0001630	splice_region_variant	4908	exon1				CCDS8538.1, CCDS44806.1	12p13	2014-01-30			ENSG00000185652	ENSG00000185652		"""Endogenous ligands"""	8023	protein-coding gene	gene with protein product		162660				1889806	Standard	NM_002527		Approved	NGF2	uc001qnk.4	P20783	OTTHUMG00000168649	ENST00000423158.3:c.18+1G>A	12.37:g.5541508G>A			5411769	NM_001102654	B7Z1T5|Q6FH50	Silent	SNP	ENST00000423158.3	37	CCDS44806.1																																																																																				0.632	NTF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400484.2		Silent
PLEKHG6	55200	broad.mit.edu	37	12	6424300	6424300	+	Missense_Mutation	SNP	G	G	A	rs370357030		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:6424300G>A	ENST00000396988.3	+	4	654	c.424G>A	c.(424-426)Gag>Aag	p.E142K	PLEKHG6_ENST00000449001.2_Missense_Mutation_p.E110K|PLEKHG6_ENST00000536531.1_Missense_Mutation_p.E142K|PLEKHG6_ENST00000011684.7_Missense_Mutation_p.E142K	NM_001144856.1	NP_001138328.1	Q3KR16	PKHG6_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 6	142						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.E142K(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|skin(4)	23						CCTGACCATCGAGAAGTCCTG	0.612																																					p.E110K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G328A	12						.	G	LYS/GLU,LYS/GLU,LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	59.0	56.0	57.0		424,328,424	5.0	1.0	12		57	0,8600		0,0,4300	no	missense,missense,missense	PLEKHG6	NM_001144856.1,NM_001144857.1,NM_018173.3	56,56,56	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging	142/791,110/759,142/791	6424300	1,13005	2203	4300	6503	6294561	SO:0001583	missense	55200	exon3			AK001527	CCDS8541.1, CCDS44808.1	12p13.31	2013-01-11			ENSG00000008323	ENSG00000008323		"""Pleckstrin homology (PH) domain containing"""	25562	protein-coding gene	gene with protein product		611743					Standard	NM_018173		Approved	FLJ10665	uc001qnr.3	Q3KR16	OTTHUMG00000168266	ENST00000396988.3:c.424G>A	12.37:g.6424300G>A	ENSP00000380185:p.Glu142Lys		6294561	NM_001144857	Q3SWR1|Q8N1P1|Q8WYY1|Q9H8F4|Q9NVK9	Missense_Mutation	SNP	ENST00000396988.3	37	CCDS8541.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.038713	0.93630	2.27E-4	0.0	ENSG00000008323	ENST00000011684;ENST00000536531;ENST00000396988;ENST00000449001	T;T;T;T	0.69561	-0.29;-0.2;-0.29;-0.41	5.0	5.0	0.66597	.	0.000000	0.52532	D	0.000067	T	0.71517	0.3349	L	0.27053	0.805	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.996;0.998;0.986	T	0.74393	-0.3680	10	0.72032	D	0.01	-18.7132	13.6539	0.62327	0.0:0.0:1.0:0.0	.	110;142;142	Q3KR16-2;F5H731;Q3KR16	.;.;PKHG6_HUMAN	K	142;142;142;110	ENSP00000011684:E142K;ENSP00000442836:E142K;ENSP00000380185:E142K;ENSP00000393194:E110K	ENSP00000011684:E142K	E	+	1	0	PLEKHG6	6294561	1.000000	0.71417	0.994000	0.49952	0.933000	0.57130	6.354000	0.73036	2.600000	0.87896	0.591000	0.81541	GAG		0.612	PLEKHG6-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399031.1	NM_018173	
IFFO1	25900	broad.mit.edu	37	12	6665016	6665016	+	Silent	SNP	C	C	T	rs139597321		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:6665016C>T	ENST00000396840.2	-	1	221	c.180G>A	c.(178-180)ccG>ccA	p.P60P	NOP2_ENST00000542015.1_5'Flank|IFFO1_ENST00000356896.4_Silent_p.P60P|IFFO1_ENST00000336604.4_Silent_p.P60P			Q0D2I5	IFFO1_HUMAN	intermediate filament family orphan 1	60						intermediate filament (GO:0005882)		p.P60P(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	20						TGGCGGCAggcggggccgggc	0.721																																					p.P60P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G180A	12						.						28.0	31.0	30.0					12																	6665016		2201	4300	6501	6535277	SO:0001819	synonymous_variant	25900	exon1			AF124432	CCDS8550.1, CCDS41741.1, CCDS8550.2, CCDS73425.1	12p13.31	2013-01-16	2008-09-11	2008-09-11	ENSG00000010295	ENSG00000010295		"""Intermediate filament family orphans"""	24970	protein-coding gene	gene with protein product		610495	"""intermediate filament family orphan"""	IFFO		8771189, 3052284	Standard	NM_001193457		Approved	HOM-TES-103	uc010sfe.2	Q0D2I5	OTTHUMG00000141264	ENST00000396840.2:c.180G>A	12.37:g.6665016C>T			6535277	NM_001193457	Q24JT6|Q7L5J9|Q7Z5X4|Q9BQ46	Silent	SNP	ENST00000396840.2	37																																																																																					0.721	IFFO1-008	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000280428.1	NM_080730	
GNB3	2784	broad.mit.edu	37	12	6948237	6948237	+	5'Flank	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:6948237C>T	ENST00000229264.3	+	0	0				LEPREL2_ENST00000251761.8_RNA|LEPREL2_ENST00000538102.1_RNA|LEPREL2_ENST00000606935.1_RNA|LEPREL2_ENST00000396725.2_RNA|GNB3_ENST00000435982.2_5'Flank	NM_002075.2	NP_002066.1	P16520	GBB3_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 3						cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|GTP catabolic process (GO:0006184)|regulation of blood pressure (GO:0008217)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cell body (GO:0044297)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	GTPase activity (GO:0003924)|GTPase binding (GO:0051020)|signal transducer activity (GO:0004871)	p.A659V(1)		cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)|stomach(1)	20						GGGGTGTGGGCCGTGACTCGG	0.667																																					p.P660S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1978T	12						.						36.0	42.0	40.0					12																	6948237		2097	4209	6306	6818498	SO:0001631	upstream_gene_variant	10536	exon14				CCDS8564.1, CCDS73427.1	12p13	2013-01-10			ENSG00000111664	ENSG00000111664		"""WD repeat domain containing"""	4400	protein-coding gene	gene with protein product		139130				11770079, 16600389	Standard	XM_005253680		Approved		uc001qrd.3	P16520	OTTHUMG00000168517		12.37:g.6948237C>T	Exception_encountered		6818498	NM_014262	Q96B71|Q9BQC0	Missense_Mutation	SNP	ENST00000229264.3	37	CCDS8564.1	.	.	.	.	.	.	.	.	.	.	C	35	5.491273	0.96339	.	.	ENSG00000110811	ENST00000451242;ENST00000396725;ENST00000290510	T;T	0.59772	0.24;0.24	4.99	4.99	0.66335	Oxoglutarate/iron-dependent oxygenase (1);Prolyl 4-hydroxylase, alpha subunit (1);	0.050842	0.85682	D	0.000000	T	0.77831	0.4189	.	.	.	0.80722	D	1	D	0.76494	0.999	D	0.72338	0.977	T	0.81720	-0.0804	9	0.87932	D	0	-12.8366	18.2817	0.90101	0.0:1.0:0.0:0.0	.	660	Q8IVL6	P3H3_HUMAN	V	87;659;475	ENSP00000379951:A659V;ENSP00000290510:A475V	ENSP00000290510:A475V	A	+	2	0	LEPREL2	6818498	1.000000	0.71417	0.991000	0.47740	0.969000	0.65631	5.783000	0.68982	2.319000	0.78375	0.561000	0.74099	GCC		0.667	GNB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400006.1	NM_002075	
LRRC23	10233	broad.mit.edu	37	12	7021987	7021987	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:7021987C>T	ENST00000007969.8	+	7	1072	c.852C>T	c.(850-852)gaC>gaT	p.D284D	LRRC23_ENST00000323702.5_Intron|ENO2_ENST00000538763.1_5'Flank|LRRC23_ENST00000429740.1_Intron|ENO2_ENST00000545045.2_5'Flank|ENO2_ENST00000541477.1_5'Flank|LRRC23_ENST00000443597.2_Silent_p.D284D|ENO2_ENST00000544774.1_5'Flank|LRRC23_ENST00000436789.1_Intron|ENO2_ENST00000535366.1_5'Flank|ENO2_ENST00000229277.1_5'Flank	NM_001135217.1|NM_201650.2	NP_001128689.1|NP_964013.1	Q53EV4	LRC23_HUMAN	leucine rich repeat containing 23	284	LRRCT.							p.D284D(2)		NS(1)|breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|stomach(1)	13						CATGCACGGACGAAACCAGCT	0.602																																					p.D284D												.	.	2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	c.C852T	12						.						119.0	114.0	116.0					12																	7021987		2203	4300	6503	6892248	SO:0001819	synonymous_variant	10233	exon7			BC014450	CCDS8568.1, CCDS8569.1	12p13	2006-02-02			ENSG00000010626	ENSG00000010626			19138	protein-coding gene	gene with protein product						11830501, 11826754	Standard	NM_201650		Approved	B7, LRPB7	uc001qrp.3	Q53EV4	OTTHUMG00000156668	ENST00000007969.8:c.852C>T	12.37:g.7021987C>T			6892248	NM_001135217	A8K8C6|D3DUT1|Q8N6K6|Q92977|Q99620	Silent	SNP	ENST00000007969.8	37	CCDS8569.1																																																																																				0.602	LRRC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345214.1	NM_006992	
C1RL	51279	broad.mit.edu	37	12	7249400	7249400	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:7249400delG	ENST00000266542.4	-	6	1143	c.1051delC	c.(1051-1053)ctgfs	p.L351fs	C1RL_ENST00000544702.1_3'UTR|C1RL_ENST00000545280.1_Intron|C1RL_ENST00000504702.2_Intron	NM_016546.2	NP_057630.2	Q9NZP8	C1RL_HUMAN	complement component 1, r subcomponent-like	351	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)	p.L351fs*35(2)		breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						TTGGGGCCCAGGGGGATGCTG	0.617																																					p.L351fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.1051delC	12						.						85.0	72.0	77.0					12																	7249400		2203	4300	6503	7140542	SO:0001589	frameshift_variant	51279	exon6			AF178985	CCDS8573.1, CCDS73431.1	12p13.31	2008-02-05				ENSG00000139178			21265	protein-coding gene	gene with protein product		608974				12838346	Standard	XM_005253385		Approved	C1r-LP, C1RL1	uc001qsn.3	Q9NZP8		ENST00000266542.4:c.1051delC	12.37:g.7249400delG	ENSP00000266542:p.Leu351fs		7140542	NM_016546	Q53GX9	Frame_Shift_Del	DEL	ENST00000266542.4	37	CCDS8573.1																																																																																				0.617	C1RL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398367.1	NM_016546	
CD163L1	283316	broad.mit.edu	37	12	7550907	7550907	+	Missense_Mutation	SNP	C	C	T	rs201614670		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:7550907C>T	ENST00000313599.3	-	7	1739	c.1682G>A	c.(1681-1683)gGa>gAa	p.G561E	CD163L1_ENST00000416109.2_Missense_Mutation_p.G571E|CD163L1_ENST00000396630.1_Missense_Mutation_p.G561E			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	561	SRCR 5. {ECO:0000255|PROSITE- ProRule:PRU00196}.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)	p.G561E(1)		breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						ATTATGCTTTCCCCATCCACT	0.383																																					p.G561E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1682A	12						.						183.0	174.0	177.0					12																	7550907		2203	4300	6503	7442174	SO:0001583	missense	283316	exon7			AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"""CD163 antigen-like 1"""			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.1682G>A	12.37:g.7550907C>T	ENSP00000315945:p.Gly561Glu		7442174	NM_174941	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Missense_Mutation	SNP	ENST00000313599.3	37	CCDS8577.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.608702	0.87258	.	.	ENSG00000177675	ENST00000313599;ENST00000416109;ENST00000396630	T;T;T	0.35789	1.29;1.29;1.29	2.77	2.77	0.32553	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.573338	0.13609	N	0.375240	T	0.58075	0.2097	M	0.75150	2.29	0.35925	D	0.832128	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.66444	-0.5922	10	0.52906	T	0.07	.	11.679	0.51446	0.0:1.0:0.0:0.0	.	571;561	E7EVK4;Q9NR16	.;C163B_HUMAN	E	561;571;561	ENSP00000315945:G561E;ENSP00000393474:G571E;ENSP00000379871:G561E	ENSP00000315945:G561E	G	-	2	0	CD163L1	7442174	0.998000	0.40836	0.994000	0.49952	0.751000	0.42716	3.762000	0.55250	1.463000	0.47967	0.460000	0.39030	GGA		0.383	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941	
A2M	2	broad.mit.edu	37	12	9264973	9264973	+	Splice_Site	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:9264973C>A	ENST00000318602.7	-	3	737	c.430G>T	c.(430-432)Gtg>Ttg	p.V144L		NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	144					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|stem cell differentiation (GO:0048863)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	calcium-dependent protein binding (GO:0048306)|enzyme binding (GO:0019899)|growth factor binding (GO:0019838)|interleukin-1 binding (GO:0019966)|interleukin-8 binding (GO:0019959)|protease binding (GO:0002020)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|tumor necrosis factor binding (GO:0043120)	p.V144L(1)		breast(1)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(17)|lung(30)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	77					Bacitracin(DB00626)|Becaplermin(DB00102)|Ocriplasmin(DB08888)	TTCTTCATACCTGTCTGCCCT	0.438																																					p.V144L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G430T	12						.						89.0	83.0	85.0					12																	9264973		1923	4159	6082	9156240	SO:0001630	splice_region_variant	2	exon3			BX647329, X68728, M11313	CCDS44827.1	12p13.31	2010-02-24			ENSG00000175899	ENSG00000175899			7	protein-coding gene	gene with protein product		103950					Standard	XM_006719056		Approved	FWP007, S863-7, CPAMD5	uc001qvk.1	P01023	OTTHUMG00000150267	ENST00000318602.7:c.430+1G>T	12.37:g.9264973C>A			9156240	NM_000014	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Missense_Mutation	SNP	ENST00000318602.7	37	CCDS44827.1	.	.	.	.	.	.	.	.	.	.	C	16.15	3.040868	0.55003	.	.	ENSG00000175899	ENST00000318602;ENST00000540099;ENST00000404455	D;D	0.83673	-1.75;-1.75	5.53	5.53	0.82687	Alpha-2-macroglobulin, N-terminal (1);	0.089570	0.46758	D	0.000261	D	0.93161	0.7822	M	0.93328	3.405	0.45318	D	0.998313	D	0.89917	1.0	D	0.91635	0.999	D	0.94493	0.7703	9	.	.	.	.	14.9503	0.71067	0.0:1.0:0.0:0.0	.	144	P01023	A2MG_HUMAN	L	144;159;144	ENSP00000323929:V144L;ENSP00000385710:V144L	.	V	-	1	0	A2M	9156240	1.000000	0.71417	1.000000	0.80357	0.020000	0.10135	4.512000	0.60469	2.608000	0.88229	0.650000	0.86243	GTG		0.438	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014	Missense_Mutation
GSG1	83445	broad.mit.edu	37	12	13243456	13243456	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:13243456C>T	ENST00000432710.2	-	2	477	c.345G>A	c.(343-345)gaG>gaA	p.E115E	GSG1_ENST00000537302.1_Silent_p.E102E|GSG1_ENST00000396310.2_Silent_p.E99E|GSG1_ENST00000324458.8_Silent_p.E115E|GSG1_ENST00000337630.6_Silent_p.E102E|GSG1_ENST00000457134.2_Silent_p.E102E|GSG1_ENST00000396302.3_Silent_p.E102E|GSG1_ENST00000351606.6_Silent_p.E115E	NM_001206842.1	NP_001193771.1	Q2KHT4	GSG1_HUMAN	germ cell associated 1	102						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.E102E(1)		endometrium(1)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(1)	10		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.15)		CCACAGTTTCCTCACAGGATA	0.552																																					p.E102E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G306A	12						.						62.0	61.0	61.0					12																	13243456		2203	4300	6503	13134723	SO:0001819	synonymous_variant	83445	exon2			BC001796	CCDS8659.2, CCDS44835.1, CCDS44836.1, CCDS55806.1, CCDS55807.1, CCDS55808.1	12p13.31	2007-12-03			ENSG00000111305	ENSG00000111305			19716	protein-coding gene	gene with protein product							Standard	NM_031289		Approved	MGC3146	uc001rbn.3	Q2KHT4	OTTHUMG00000150148	ENST00000432710.2:c.345G>A	12.37:g.13243456C>T			13134723	NM_153823	Q8N4M3|Q8NBR4|Q8NBS0|Q8NBT1|Q96LP9|Q96SI6|Q9BUY4	Silent	SNP	ENST00000432710.2	37	CCDS55808.1																																																																																				0.552	GSG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316546.1	NM_031289	
ATF7IP	55729	broad.mit.edu	37	12	14578226	14578226	+	Silent	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:14578226A>G	ENST00000540793.1	+	1	1532	c.1377A>G	c.(1375-1377)ccA>ccG	p.P459P	ATF7IP_ENST00000536444.1_Silent_p.P459P|ATF7IP_ENST00000261168.4_Silent_p.P459P|ATF7IP_ENST00000541654.1_3'UTR|ATF7IP_ENST00000543189.1_Silent_p.P459P|ATF7IP_ENST00000544627.1_Silent_p.P467P			Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting protein	459	Glu-rich.				DNA methylation (GO:0006306)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045898)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)		p.P459P(1)		cervix(1)|endometrium(7)|kidney(5)|large_intestine(10)|liver(2)|lung(22)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	54						CTCTCCTTCCAATCGATGAGA	0.373																																					p.P459P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1377G	12						.						59.0	61.0	60.0					12																	14578226		2203	4300	6503	14469493	SO:0001819	synonymous_variant	55729	exon2			AJ242978	CCDS8663.1, CCDS66326.1, CCDS66327.1, CCDS73449.1	12p13.1	2005-11-18				ENSG00000171681			20092	protein-coding gene	gene with protein product		613644				10976766, 10777215	Standard	XM_005253424		Approved	FLJ10688, p621	uc001rbw.3	Q6VMQ6		ENST00000540793.1:c.1377A>G	12.37:g.14578226A>G			14469493	NM_018179	F5GX74|G3V1U0|Q4G0T9|Q6P3T3|Q86XW5|Q9NVJ9|Q9NWC2|Q9Y4X8	Silent	SNP	ENST00000540793.1	37	CCDS8663.1																																																																																				0.373	ATF7IP-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401400.1	NM_018179	
DERA	51071	broad.mit.edu	37	12	16185550	16185550	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:16185550C>T	ENST00000428559.2	+	7	924	c.712C>T	c.(712-714)Cgg>Tgg	p.R238W	DERA_ENST00000532573.1_3'UTR|DERA_ENST00000532964.1_Missense_Mutation_p.R195W|DERA_ENST00000526530.1_Missense_Mutation_p.R150W	NM_015954.2	NP_057038.2	Q9Y315	DEOC_HUMAN	deoxyribose-phosphate aldolase (putative)	238					deoxyribonucleoside catabolic process (GO:0046121)|deoxyribonucleotide catabolic process (GO:0009264)|deoxyribose phosphate catabolic process (GO:0046386)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	deoxyribose-phosphate aldolase activity (GO:0004139)	p.R238W(1)		endometrium(1)|large_intestine(2)|lung(3)|skin(1)	7		Hepatocellular(102;0.121)				AGTAATGCTGCGGGCCATTAG	0.343																																					p.R238W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C712T	12						.						43.0	39.0	40.0					12																	16185550		1794	4058	5852	16076817	SO:0001583	missense	51071	exon7			AF132960	CCDS44838.1, CCDS73451.1	12p12.3	2010-06-24	2010-06-24		ENSG00000023697	ENSG00000023697	4.1.2.4		24269	protein-coding gene	gene with protein product			"""2-deoxyribose-5-phosphate aldolase homolog (C. elegans)"""			12546782	Standard	XM_006719083		Approved	CGI-26, DEOC	uc001rde.3	Q9Y315	OTTHUMG00000165537	ENST00000428559.2:c.712C>T	12.37:g.16185550C>T	ENSP00000416583:p.Arg238Trp		16076817	NM_015954	Q53HN9|Q6PHW2	Missense_Mutation	SNP	ENST00000428559.2	37	CCDS44838.1	.	.	.	.	.	.	.	.	.	.	C	17.05	3.289254	0.59976	.	.	ENSG00000023697	ENST00000428559;ENST00000532964;ENST00000533447;ENST00000526530	.	.	.	5.58	3.72	0.42706	Aldolase-type TIM barrel (1);	0.052194	0.85682	N	0.000000	T	0.78509	0.4294	M	0.85777	2.775	0.80722	D	1	P;D	0.89917	0.947;1.0	P;D	0.97110	0.636;1.0	T	0.79220	-0.1893	9	0.72032	D	0.01	-19.0244	9.3046	0.37867	0.258:0.6742:0.0:0.0677	.	150;238	B4DKS9;Q9Y315	.;DEOC_HUMAN	W	238;195;150;150	.	ENSP00000416583:R238W	R	+	1	2	DERA	16076817	1.000000	0.71417	0.989000	0.46669	0.955000	0.61496	1.696000	0.37773	0.805000	0.34159	0.557000	0.71058	CGG		0.343	DERA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384731.1	NM_015954	
PDE3A	5139	broad.mit.edu	37	12	20522791	20522791	+	Silent	SNP	G	G	A	rs148318159		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:20522791G>A	ENST00000359062.3	+	1	613	c.573G>A	c.(571-573)gcG>gcA	p.A191A	RP11-284H19.1_ENST00000535755.1_RNA	NM_000921.4|NM_001244683.1	NP_000912.3|NP_001231612.1	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited	191					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP-mediated signaling (GO:0019934)|diterpenoid metabolic process (GO:0016101)|lipid metabolic process (GO:0006629)|negative regulation of apoptotic process (GO:0043066)|negative regulation of vascular permeability (GO:0043116)|oocyte maturation (GO:0001556)|positive regulation of oocyte development (GO:0060282)|positive regulation of vascular permeability (GO:0043117)|regulation of meiosis (GO:0040020)|response to cAMP (GO:0051591)|response to drug (GO:0042493)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)	p.A191A(1)		NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(7)|lung(29)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	58	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Caffeine(DB00201)|Cilostazol(DB01166)|Enoximone(DB04880)|Ibudilast(DB05266)|Levosimendan(DB00922)|Milrinone(DB00235)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Tofisopam(DB08811)	TCCCCGCCGCGGGGGTGGTGC	0.692																																					p.A191A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G573A	12						.	G		1,4401		0,1,2200	16.0	19.0	18.0		573	2.5	1.0	12	dbSNP_134	18	0,8586		0,0,4293	no	coding-synonymous	PDE3A	NM_000921.4		0,1,6493	AA,AG,GG		0.0,0.0227,0.0077		191/1142	20522791	1,12987	2201	4293	6494	20414058	SO:0001819	synonymous_variant	5139	exon1				CCDS31754.1	12p12.2	2011-04-15			ENSG00000172572	ENSG00000172572	3.1.4.17	"""Phosphodiesterases"""	8778	protein-coding gene	gene with protein product		123805				1315035, 10679291	Standard	NM_000921		Approved	CGI-PDE	uc001reh.2	Q14432	OTTHUMG00000168962	ENST00000359062.3:c.573G>A	12.37:g.20522791G>A			20414058	NM_000921	O60865|Q13348|Q17RD1	Silent	SNP	ENST00000359062.3	37	CCDS31754.1																																																																																				0.692	PDE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401756.2		
LRMP	4033	broad.mit.edu	37	12	25232370	25232370	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:25232370C>T	ENST00000354454.3	+	7	939	c.110C>T	c.(109-111)tCg>tTg	p.S37L	LRMP_ENST00000547044.1_Missense_Mutation_p.S37L|LRMP_ENST00000548766.1_Missense_Mutation_p.S37L	NM_006152.3	NP_006143.2	Q12912	LRMP_HUMAN	lymphoid-restricted membrane protein	93					immune system process (GO:0002376)|single fertilization (GO:0007338)|vesicle fusion (GO:0006906)|vesicle targeting (GO:0006903)	chromosome (GO:0005694)|cytoskeleton (GO:0005856)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleus (GO:0005634)		p.S37L(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	19	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Colorectal(261;0.11)					CACACTTCATCGACAGACGGT	0.373																																					p.S37L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C110T	12						.						159.0	153.0	155.0					12																	25232370		2203	4300	6503	25123637	SO:0001583	missense	4033	exon7				CCDS8701.1	12p12.1	2012-05-16			ENSG00000118308	ENSG00000118308			6690	protein-coding gene	gene with protein product		602003				8021504	Standard	NM_006152		Approved	JAW1	uc010sja.2	Q12912	OTTHUMG00000170192	ENST00000354454.3:c.110C>T	12.37:g.25232370C>T	ENSP00000346442:p.Ser37Leu		25123637	NM_006152	A0AVM2|B4E077|Q8N301	Missense_Mutation	SNP	ENST00000354454.3	37	CCDS8701.1	.	.	.	.	.	.	.	.	.	.	C	14.76	2.630637	0.46944	.	.	ENSG00000118308	ENST00000550945;ENST00000557489;ENST00000354454;ENST00000548766;ENST00000554942;ENST00000547044	T;T;T;T;T;T	0.16196	2.36;2.36;2.36;2.36;2.36;2.36	4.82	4.82	0.62117	.	0.211018	0.34156	N	0.004213	T	0.38374	0.1038	M	0.63428	1.95	0.34681	D	0.724674	D	0.89917	1.0	D	0.87578	0.998	T	0.49995	-0.8879	10	0.72032	D	0.01	-13.2752	13.5997	0.62011	0.0:1.0:0.0:0.0	.	93	Q12912	LRMP_HUMAN	L	37	ENSP00000448534:S37L;ENSP00000452116:S37L;ENSP00000346442:S37L;ENSP00000446496:S37L;ENSP00000450634:S37L;ENSP00000450246:S37L	ENSP00000346442:S37L	S	+	2	0	LRMP	25123637	0.525000	0.26290	0.858000	0.33744	0.708000	0.40852	3.222000	0.51223	2.668000	0.90789	0.591000	0.81541	TCG		0.373	LRMP-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407870.1	NM_006152	
RASSF8	11228	broad.mit.edu	37	12	26217762	26217762	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:26217762A>C	ENST00000405154.2	+	3	634	c.435A>C	c.(433-435)aaA>aaC	p.K145N	RASSF8_ENST00000381352.3_Missense_Mutation_p.K145N|RASSF8_ENST00000542865.1_Missense_Mutation_p.K145N|RASSF8_ENST00000541490.1_Missense_Mutation_p.K145N|RASSF8_ENST00000282884.9_Missense_Mutation_p.K145N	NM_001164748.1	NP_001158220.1	Q8NHQ8	RASF8_HUMAN	Ras association (RalGDS/AF-6) domain family (N-terminal) member 8	145					signal transduction (GO:0007165)			p.K145N(1)		cervix(2)|endometrium(1)|large_intestine(6)|lung(15)|urinary_tract(1)	25	Colorectal(261;0.0847)					TTTTTGGAAAAGGTAAAGAAA	0.398																																					p.K145N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A435C	12						.						75.0	76.0	76.0					12																	26217762		2203	4300	6503	26109029	SO:0001583	missense	11228	exon4			U82396	CCDS8705.1, CCDS53765.1	12p12.3	2013-05-30	2008-02-22	2005-09-14	ENSG00000123094	ENSG00000123094			13232	protein-coding gene	gene with protein product		608231	"""chromosome 12 open reading frame 2"""	C12orf2			Standard	NM_007211		Approved	HoJ-1	uc001rgx.3	Q8NHQ8	OTTHUMG00000169087	ENST00000405154.2:c.435A>C	12.37:g.26217762A>C	ENSP00000384491:p.Lys145Asn		26109029	NM_007211	A8K1Z0|O95647|Q5SCI2|Q76KB6	Missense_Mutation	SNP	ENST00000405154.2	37	CCDS53765.1	.	.	.	.	.	.	.	.	.	.	A	12.33	1.905281	0.33628	.	.	ENSG00000123094	ENST00000381352;ENST00000405154;ENST00000542865;ENST00000541490;ENST00000542004;ENST00000541218;ENST00000282884;ENST00000545413	T;T;T;T;T;T;T;T	0.50277	1.34;1.34;1.34;1.34;0.76;0.77;1.34;0.75	4.92	3.77	0.43336	.	0.192412	0.53938	D	0.000041	T	0.41789	0.1174	L	0.48642	1.525	0.44762	D	0.99776	P;P	0.51933	0.949;0.608	P;B	0.45946	0.498;0.146	T	0.15263	-1.0443	10	0.27082	T	0.32	-11.7116	8.8526	0.35210	0.8406:0.0:0.1594:0.0	.	145;145	Q8NHQ8-2;Q8NHQ8	.;RASF8_HUMAN	N	145	ENSP00000370756:K145N;ENSP00000384491:K145N;ENSP00000439839:K145N;ENSP00000443096:K145N;ENSP00000442485:K145N;ENSP00000445970:K145N;ENSP00000282884:K145N;ENSP00000443696:K145N	ENSP00000282884:K145N	K	+	3	2	RASSF8	26109029	0.989000	0.36119	0.973000	0.42090	0.963000	0.63663	0.301000	0.19174	0.848000	0.35191	0.533000	0.62120	AAA		0.398	RASSF8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402209.2	NM_007211	
PPFIBP1	8496	broad.mit.edu	37	12	27835563	27835563	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:27835563T>C	ENST00000318304.8	+	23	2475	c.2192T>C	c.(2191-2193)aTt>aCt	p.I731T	PPFIBP1_ENST00000542629.1_Missense_Mutation_p.I700T|PPFIBP1_ENST00000228425.6_Missense_Mutation_p.I725T|PPFIBP1_ENST00000537927.1_Missense_Mutation_p.I578T	NM_001198916.1|NM_177444.2	NP_001185845.1|NP_803193	Q86W92	LIPB1_HUMAN	PTPRF interacting protein, binding protein 1 (liprin beta 1)	731	SAM 2. {ECO:0000255|PROSITE- ProRule:PRU00184}.				cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)		p.I725T(1)|p.I731T(1)	PPFIBP1/ALK(3)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(13)|prostate(2)|skin(1)	32	Lung SC(9;0.0873)					TTGGATGACATTGGCCTCCCT	0.418																																					p.I578T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T1733C	12						.						146.0	141.0	143.0					12																	27835563		2203	4300	6503	27726830	SO:0001583	missense	8496	exon21			AF034802	CCDS8713.1, CCDS55812.1, CCDS55813.1, CCDS55814.1	12p12.1	2013-01-10						"""Sterile alpha motif (SAM) domain containing"""	9249	protein-coding gene	gene with protein product		603141				9624153, 11836260	Standard	NM_003622		Approved	L2, hSGT2, hSgt2p, SGT2	uc001ric.2	Q86W92		ENST00000318304.8:c.2192T>C	12.37:g.27835563T>C	ENSP00000314724:p.Ile731Thr		27726830	NM_001198915	O75336|Q86X70|Q9NY03|Q9ULJ0	Missense_Mutation	SNP	ENST00000318304.8	37	CCDS55812.1	.	.	.	.	.	.	.	.	.	.	T	17.97	3.518064	0.64634	.	.	ENSG00000110841	ENST00000540114;ENST00000537927;ENST00000318304;ENST00000542629;ENST00000228425	T;T;T;T;T	0.59364	0.27;0.27;0.27;0.27;0.27	5.26	5.26	0.73747	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.000000	0.34484	U	0.003928	T	0.76716	0.4026	M	0.80616	2.505	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	T	0.79339	-0.1844	10	0.52906	T	0.07	-18.5508	14.8559	0.70338	0.0:0.0:0.0:1.0	.	578;562;731;725;700	Q86W92-3;F5GZP6;Q86W92;Q86W92-2;Q86W92-4	.;.;LIPB1_HUMAN;.;.	T	562;578;731;700;725	ENSP00000444304:I562T;ENSP00000445425:I578T;ENSP00000314724:I731T;ENSP00000443442:I700T;ENSP00000228425:I725T	ENSP00000228425:I725T	I	+	2	0	PPFIBP1	27726830	1.000000	0.71417	0.988000	0.46212	0.360000	0.29518	7.900000	0.87376	1.985000	0.57927	0.533000	0.62120	ATT		0.418	PPFIBP1-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402877.1	NM_003622	
DNM1L	10059	broad.mit.edu	37	12	32891212	32891212	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:32891212C>G	ENST00000549701.1	+	16	1763	c.1689C>G	c.(1687-1689)agC>agG	p.S563R	DNM1L_ENST00000381000.4_Intron|DNM1L_ENST00000414834.2_Missense_Mutation_p.S360R|DNM1L_ENST00000547312.1_Intron|DNM1L_ENST00000553257.1_Missense_Mutation_p.S576R|DNM1L_ENST00000358214.5_Intron|DNM1L_ENST00000452533.2_Missense_Mutation_p.S537R|DNM1L_ENST00000266481.6_Intron|YARS2_ENST00000551673.1_Intron			O00429	DNM1L_HUMAN	dynamin 1-like	563	B domain.|Interaction with GSK3B.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|dynamin polymerization involved in mitochondrial fission (GO:0003374)|endocytosis (GO:0006897)|GTP catabolic process (GO:0006184)|membrane fission involved in mitochondrial fission (GO:0090149)|membrane fusion (GO:0061025)|mitochondrial fission (GO:0000266)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrion morphogenesis (GO:0070584)|necroptotic process (GO:0070266)|peroxisome fission (GO:0016559)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein secretion (GO:0050714)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein homotetramerization (GO:0051289)|protein localization to mitochondrion (GO:0070585)|regulation of mitochondrion organization (GO:0010821)|regulation of peroxisome organization (GO:1900063)|regulation of protein oligomerization (GO:0032459)|release of cytochrome c from mitochondria (GO:0001836)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)|protein complex (GO:0043234)|synapse (GO:0045202)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)	p.S563R(1)		cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	23	Lung NSC(5;2.15e-06)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					TTCAGGACAGCAGAAGAGAAA	0.328																																					p.S563R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1689G	12						.						85.0	90.0	88.0					12																	32891212		2203	4299	6502	32782479	SO:0001583	missense	10059	exon16			AF000430	CCDS8728.1, CCDS8729.1, CCDS8730.1, CCDS61095.1, CCDS61096.1, CCDS61098.1, CCDS61099.1	12p11.21	2012-10-02			ENSG00000087470	ENSG00000087470			2973	protein-coding gene	gene with protein product		603850				9348079, 9731200	Standard	NM_012062		Approved	DRP1, DVLP, HDYNIV, DYMPLE, VPS1	uc001rld.2	O00429	OTTHUMG00000169451	ENST00000549701.1:c.1689C>G	12.37:g.32891212C>G	ENSP00000450399:p.Ser563Arg		32782479	NM_012062	A8K4X9|B4DGC9|B4DSU8|J3KPI2|O14541|O60709|Q59GN9|Q7L6B3|Q8TBT7|Q9BWM1|Q9Y5J2	Missense_Mutation	SNP	ENST00000549701.1	37	CCDS8729.1	.	.	.	.	.	.	.	.	.	.	C	12.42	1.933256	0.34096	.	.	ENSG00000087470	ENST00000452533;ENST00000553257;ENST00000549701;ENST00000414834	D;D;D;T	0.90069	-2.61;-2.61;-2.61;-1.24	5.53	5.53	0.82687	.	.	.	.	.	T	0.79076	0.4385	N	0.08118	0	0.80722	D	1	B;B;B	0.23058	0.079;0.057;0.037	B;B;B	0.18871	0.023;0.016;0.007	T	0.74237	-0.3730	9	0.30078	T	0.28	.	16.6496	0.85185	0.0:1.0:0.0:0.0	.	360;590;563	B4DGC9;D3DUW6;O00429	.;.;DNM1L_HUMAN	R	537;576;563;360	ENSP00000415131:S537R;ENSP00000449089:S576R;ENSP00000450399:S563R;ENSP00000404160:S360R	ENSP00000404160:S360R	S	+	3	2	DNM1L	32782479	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.945000	0.40273	2.605000	0.88082	0.655000	0.94253	AGC		0.328	DNM1L-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404124.1	NM_012062	
SYT10	341359	broad.mit.edu	37	12	33579360	33579360	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:33579360delA	ENST00000228567.3	-	2	518	c.222delT	c.(220-222)tttfs	p.F74fs	SYT10_ENST00000535526.1_5'UTR|SYT10_ENST00000567656.1_5'Flank	NM_198992.3	NP_945343.1	Q6XYQ8	SYT10_HUMAN	synaptotagmin X	74					regulation of calcium ion-dependent exocytosis (GO:0017158)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)	p.F74fs*16(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(3)|skin(4)|urinary_tract(1)	42	Lung NSC(5;8.37e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0334)					TCCAGAAGACAAAAAGTGAGA	0.418																																					p.F74fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.222delT	12						.						63.0	61.0	62.0					12																	33579360		2203	4300	6503	33470627	SO:0001589	frameshift_variant	341359	exon2			AY198413	CCDS8732.1	12p11	2013-01-21			ENSG00000110975	ENSG00000110975		"""Synaptotagmins"""	19266	protein-coding gene	gene with protein product							Standard	NM_198992		Approved		uc001rll.1	Q6XYQ8	OTTHUMG00000169269	ENST00000228567.3:c.222delT	12.37:g.33579360delA	ENSP00000228567:p.Phe74fs		33470627	NM_198992	Q495U2	Frame_Shift_Del	DEL	ENST00000228567.3	37	CCDS8732.1																																																																																				0.418	SYT10-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403222.1	NM_198992	
PRICKLE1	144165	broad.mit.edu	37	12	42860065	42860065	+	Missense_Mutation	SNP	G	G	A	rs372213429		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:42860065G>A	ENST00000455697.1	-	6	991	c.706C>T	c.(706-708)Cgc>Tgc	p.R236C	RP11-328C8.4_ENST00000547824.1_RNA|PRICKLE1_ENST00000548696.1_Missense_Mutation_p.R236C|PRICKLE1_ENST00000345127.3_Missense_Mutation_p.R236C|PRICKLE1_ENST00000552240.1_Missense_Mutation_p.R236C|PRICKLE1_ENST00000445766.2_Missense_Mutation_p.R236C	NM_001144882.1|NM_001144883.1	NP_001138354.1|NP_001138355.1	Q96MT3	PRIC1_HUMAN	prickle homolog 1 (Drosophila)	236	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell myoblast differentiation (GO:2000691)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.R236C(1)		NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(13)|ovary(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	47	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)		CAGAAGGGGCGGCCGTCCTTC	0.547																																					p.R236C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C706T	12						.	G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	93.0	80.0	84.0		706,706,706,706	5.2	1.0	12		84	0,8600		0,0,4300	no	missense,missense,missense,missense	PRICKLE1	NM_001144881.1,NM_001144882.1,NM_001144883.1,NM_153026.2	180,180,180,180	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	236/832,236/832,236/832,236/832	42860065	1,13005	2203	4300	6503	41146332	SO:0001583	missense	144165	exon6			AK056499	CCDS8742.1	12p11-q12	2010-08-13	2006-09-12			ENSG00000139174			17019	protein-coding gene	gene with protein product		608500	"""prickle-like 1 (Drosophila)"""			12525887, 18976727	Standard	NM_153026		Approved	FLJ31937, EPM1B	uc010skv.2	Q96MT3		ENST00000455697.1:c.706C>T	12.37:g.42860065G>A	ENSP00000401060:p.Arg236Cys		41146332	NM_001144882	Q14C83|Q71QF8|Q96N00	Missense_Mutation	SNP	ENST00000455697.1	37	CCDS8742.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.231401	0.79688	2.27E-4	0.0	ENSG00000139174	ENST00000455697;ENST00000445766;ENST00000548696;ENST00000345127;ENST00000552240	D;D;D;D;D	0.88354	-2.37;-2.37;-2.37;-2.37;-2.37	5.18	5.18	0.71444	Zinc finger, LIM-type (4);	0.098090	0.64402	D	0.000001	D	0.95701	0.8602	M	0.91768	3.24	0.80722	D	1	D	0.89917	1.0	D	0.70016	0.967	D	0.96424	0.9314	10	0.87932	D	0	-13.9958	19.0641	0.93103	0.0:0.0:1.0:0.0	.	236	Q96MT3	PRIC1_HUMAN	C	236	ENSP00000401060:R236C;ENSP00000398947:R236C;ENSP00000448359:R236C;ENSP00000345064:R236C;ENSP00000449819:R236C	ENSP00000345064:R236C	R	-	1	0	PRICKLE1	41146332	0.997000	0.39634	1.000000	0.80357	0.982000	0.71751	3.018000	0.49625	2.590000	0.87494	0.561000	0.74099	CGC		0.547	PRICKLE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404069.1		
ADCY6	112	broad.mit.edu	37	12	49176823	49176823	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:49176823C>T	ENST00000307885.4	-	1	1089	c.395G>A	c.(394-396)cGt>cAt	p.R132H	ADCY6_ENST00000357869.3_Missense_Mutation_p.R132H|ADCY6_ENST00000550422.1_Missense_Mutation_p.R132H	NM_015270.3	NP_056085.1	O43306	ADCY6_HUMAN	adenylate cyclase 6	132					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|dopamine receptor signaling pathway (GO:0007212)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|negative regulation of neuron projection development (GO:0010977)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)	p.R132H(1)		breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(16)|prostate(1)|skin(1)|urinary_tract(1)	29						CTTGGCCGAACGGAACTGCTT	0.667																																					p.R132H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G395A	12						.						41.0	45.0	44.0					12																	49176823		2202	4300	6502	47463090	SO:0001583	missense	112	exon1				CCDS8767.1, CCDS8768.1	12q12-q13	2013-02-04				ENSG00000174233	4.6.1.1	"""Adenylate cyclases"""	237	protein-coding gene	gene with protein product		600294					Standard	NM_015270		Approved	AC6	uc001rsh.4	O43306		ENST00000307885.4:c.395G>A	12.37:g.49176823C>T	ENSP00000311405:p.Arg132His		47463090	NM_015270	Q9NR75|Q9UDB0	Missense_Mutation	SNP	ENST00000307885.4	37	CCDS8767.1	.	.	.	.	.	.	.	.	.	.	C	14.19	2.460832	0.43736	.	.	ENSG00000174233	ENST00000357869;ENST00000550422;ENST00000307885	T;T;T	0.77229	-1.08;-1.08;-1.08	4.69	3.78	0.43462	.	0.148834	0.47455	D	0.000222	T	0.54647	0.1871	N	0.03608	-0.345	0.41763	D	0.989722	D;B	0.57899	0.981;0.008	P;B	0.45037	0.467;0.002	T	0.57791	-0.7750	10	0.41790	T	0.15	.	6.5897	0.22639	0.0:0.7377:0.0:0.2623	.	132;132	O43306-2;O43306	.;ADCY6_HUMAN	H	132	ENSP00000350536:R132H;ENSP00000446730:R132H;ENSP00000311405:R132H	ENSP00000311405:R132H	R	-	2	0	ADCY6	47463090	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	2.389000	0.44407	2.427000	0.82271	0.462000	0.41574	CGT		0.667	ADCY6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408863.1	NM_020983	
CACNB3	784	broad.mit.edu	37	12	49220595	49220595	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:49220595C>T	ENST00000301050.2	+	11	1147	c.948C>T	c.(946-948)acC>acT	p.T316T	CACNB3_ENST00000547392.1_Silent_p.T289T|CACNB3_ENST00000536187.2_Silent_p.T315T|CACNB3_ENST00000540990.1_Silent_p.T303T|CACNB3_ENST00000547230.1_Silent_p.T275T	NM_000725.3	NP_000716.2	P54284	CACB3_HUMAN	calcium channel, voltage-dependent, beta 3 subunit	316					axon guidance (GO:0007411)|calcium ion transport (GO:0006816)|membrane depolarization (GO:0051899)|synaptic transmission (GO:0007268)|T cell receptor signaling pathway (GO:0050852)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|membrane (GO:0016020)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.T316T(1)		autonomic_ganglia(1)|breast(1)|large_intestine(5)|lung(4)|prostate(1)	12					Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	AGCACCTGACCGTACAGATGA	0.612																																					p.T316T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C948T	12						.						172.0	175.0	174.0					12																	49220595		2203	4300	6503	47506862	SO:0001819	synonymous_variant	784	exon11				CCDS8769.1, CCDS55821.1, CCDS55822.1, CCDS55823.1	12q13	2008-05-02				ENSG00000167535		"""Calcium channel subunits"""	1403	protein-coding gene	gene with protein product		601958		CACNLB3		8119293	Standard	NM_000725		Approved		uc010sly.2	P54284		ENST00000301050.2:c.948C>T	12.37:g.49220595C>T			47506862	NM_000725	A8K0Z4|B7Z4Q1|B7Z973|B7ZAK8|F5GZW7|F5H2P6|F8VSG3|Q13913	Silent	SNP	ENST00000301050.2	37	CCDS8769.1																																																																																				0.612	CACNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408886.1		
SCN8A	6334	broad.mit.edu	37	12	52145173	52145173	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:52145173C>T	ENST00000354534.6	+	14	2344	c.2166C>T	c.(2164-2166)tgC>tgT	p.C722C	SCN8A_ENST00000550891.1_Silent_p.C722C|SCN8A_ENST00000545061.1_Silent_p.C722C	NM_001177984.2|NM_014191.3	NP_001171455.1|NP_055006.1	Q9UQD0	SCN8A_HUMAN	sodium channel, voltage gated, type VIII, alpha subunit	722					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|membrane depolarization during action potential (GO:0086010)|muscle organ development (GO:0007517)|myelination (GO:0042552)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|neuronal action potential (GO:0019228)|peripheral nervous system development (GO:0007422)|response to toxic substance (GO:0009636)|sensory perception of sound (GO:0007605)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ATP binding (GO:0005524)|voltage-gated sodium channel activity (GO:0005248)	p.C722C(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55				BRCA - Breast invasive adenocarcinoma(357;0.181)	Valproic Acid(DB00313)	GCCCGCCATGCTGGTATAAAT	0.458																																					p.C722C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2166T	12						.						158.0	146.0	150.0					12																	52145173		1905	4105	6010	50431440	SO:0001819	synonymous_variant	6334	exon14			AB027567	CCDS44891.1, CCDS53794.1	12q13.1	2012-02-26	2007-01-23			ENSG00000196876		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10596	protein-coding gene	gene with protein product		600702	"""sodium channel, voltage gated, type VIII, alpha polypeptide"""	MED		7670495, 9828131, 16382098	Standard	NM_014191		Approved	Nav1.6, NaCh6, PN4, CerIII	uc001ryw.4	Q9UQD0		ENST00000354534.6:c.2166C>T	12.37:g.52145173C>T			50431440	NM_014191	B9VWG8|O95788|Q9NYX2|Q9UPB2	Silent	SNP	ENST00000354534.6	37	CCDS44891.1																																																																																				0.458	SCN8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404372.3	NM_014191	
ACVR1B	91	broad.mit.edu	37	12	52378994	52378994	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:52378994A>G	ENST00000257963.4	+	6	1075	c.998A>G	c.(997-999)cAt>cGt	p.H333R	ACVR1B_ENST00000415850.2_Missense_Mutation_p.H333R|ACVR1B_ENST00000563121.1_3'UTR|ACVR1B_ENST00000541224.1_Missense_Mutation_p.H374R|ACVR1B_ENST00000426655.2_Missense_Mutation_p.H333R|ACVR1B_ENST00000542485.1_Missense_Mutation_p.H281R|RNU6-574P_ENST00000384265.1_RNA	NM_004302.4|NM_020328.3	NP_004293.1|NP_064733.3	P36896	ACV1B_HUMAN	activin A receptor, type IB	333	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|central nervous system development (GO:0007417)|development of primary female sexual characteristics (GO:0046545)|extrinsic apoptotic signaling pathway (GO:0097191)|G1/S transition of mitotic cell cycle (GO:0000082)|hair follicle development (GO:0001942)|in utero embryonic development (GO:0001701)|negative regulation of cell growth (GO:0030308)|nodal signaling pathway (GO:0038092)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of trophoblast cell migration (GO:1901165)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|inhibin binding (GO:0034711)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)|ubiquitin protein ligase binding (GO:0031625)	p.H333R(1)|p.H374R(1)		breast(5)|endometrium(4)|kidney(5)|large_intestine(12)|lung(10)|ovary(1)|pancreas(6)|prostate(1)	44				BRCA - Breast invasive adenocarcinoma(357;0.104)	Adenosine triphosphate(DB00171)	GGAATTGCTCATCGAGACTTA	0.443																																					p.H281R												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A842G	12						.						75.0	72.0	73.0					12																	52378994		2203	4300	6503	50665261	SO:0001583	missense	91	exon6				CCDS8816.1, CCDS44893.1, CCDS44894.1, CCDS44893.2, CCDS44894.2	12q13	2006-11-09			ENSG00000135503	ENSG00000135503			172	protein-coding gene	gene with protein product		601300		ACVRLK4		8397373	Standard	NM_020327		Approved	ALK4, SKR2, ActRIB	uc010snn.2	P36896	OTTHUMG00000167920	ENST00000257963.4:c.998A>G	12.37:g.52378994A>G	ENSP00000257963:p.His333Arg		50665261	NM_020327	B7Z5L8|B7Z5W5|Q15479|Q15480|Q15481|Q15482	Missense_Mutation	SNP	ENST00000257963.4	37	CCDS8816.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.078141	0.76528	.	.	ENSG00000135503	ENST00000257963;ENST00000541224;ENST00000426655;ENST00000415850;ENST00000542485	D;D;D;D;D	0.98889	-5.21;-5.21;-5.21;-5.21;-5.21	4.76	4.76	0.60689	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.99396	0.9787	H	0.96547	3.84	0.80722	D	1	D;D;D;D	0.89917	0.968;0.991;1.0;1.0	D;D;D;D	0.85130	0.924;0.95;0.982;0.997	D	0.98440	1.0586	10	0.87932	D	0	.	14.7556	0.69560	1.0:0.0:0.0:0.0	.	374;333;333;333	P36896-4;P36896;P36896-2;P36896-3	.;ACV1B_HUMAN;.;.	R	333;374;333;333;281	ENSP00000257963:H333R;ENSP00000442656:H374R;ENSP00000390477:H333R;ENSP00000397550:H333R;ENSP00000442885:H281R	ENSP00000257963:H333R	H	+	2	0	ACVR1B	50665261	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.139000	0.94554	2.138000	0.66242	0.460000	0.39030	CAT		0.443	ACVR1B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397000.1	NM_020328	
KRT83	3889	broad.mit.edu	37	12	52711471	52711471	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:52711471G>A	ENST00000293670.3	-	4	806	c.744C>T	c.(742-744)taC>taT	p.Y248Y		NM_002282.3	NP_002273.3	P78385	KRT83_HUMAN	keratin 83	248	Coil 1B.|Rod.				aging (GO:0007568)|epidermis development (GO:0008544)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.Y248Y(1)		NS(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(4)|stomach(7)|upper_aerodigestive_tract(1)	32	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		TCACCTCCTCGTACAGCCGCC	0.632																																					p.Y248Y	GBM(41;747 834 12702 24089 39393)|Esophageal Squamous(97;805 1414 12559 28198 31861)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C744T	12						.						82.0	79.0	80.0					12																	52711471		2203	4300	6503	50997738	SO:0001819	synonymous_variant	3889	exon4			X99141	CCDS8823.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000170523	ENSG00000170523		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6460	protein-coding gene	gene with protein product	"""hard keratin type II"""	602765	"""keratin, hair, basic, 3"""	KRTHB3		9084137, 16831889	Standard	NM_002282		Approved	Hb-3	uc001saf.2	P78385	OTTHUMG00000169632	ENST00000293670.3:c.744C>T	12.37:g.52711471G>A			50997738	NM_002282	A1A4S9|B2RC21|Q6NT21|Q9NSB3	Silent	SNP	ENST00000293670.3	37	CCDS8823.1																																																																																				0.632	KRT83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405182.1	NM_002282	
KRT85	3891	broad.mit.edu	37	12	52757185	52757185	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:52757185C>T	ENST00000257901.3	-	5	871	c.796G>A	c.(796-798)Gtt>Att	p.V266I	KRT85_ENST00000544265.1_Missense_Mutation_p.V54I	NM_002283.3	NP_002274.1	P78386	KRT85_HUMAN	keratin 85	266	Coil 1B.|Rod.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.V266I(1)		NS(1)|breast(1)|endometrium(6)|kidney(1)|large_intestine(7)|liver(1)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	36	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		GCTTGGAGAACGCGGATCTCC	0.562																																					p.V266I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G796A	12						.						128.0	77.0	94.0					12																	52757185		2203	4300	6503	51043452	SO:0001583	missense	3891	exon5			X99140	CCDS8824.1, CCDS73472.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000135443	ENSG00000135443		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6462	protein-coding gene	gene with protein product	"""hard keratin type II"""	602767	"""keratin, hair, basic, 5"""	KRTHB5		9084137, 16831889	Standard	NM_002283		Approved	Hb-5	uc001sag.3	P78386	OTTHUMG00000169633	ENST00000257901.3:c.796G>A	12.37:g.52757185C>T	ENSP00000257901:p.Val266Ile		51043452	NM_002283	Q9NSB1	Missense_Mutation	SNP	ENST00000257901.3	37	CCDS8824.1	.	.	.	.	.	.	.	.	.	.	C	12.80	2.047815	0.36085	.	.	ENSG00000135443	ENST00000257901;ENST00000544265	D;D	0.88741	-2.42;-2.42	4.83	-0.405	0.12392	Filament (1);	0.524687	0.17187	N	0.183664	T	0.79263	0.4416	L	0.39020	1.185	0.09310	N	1	B	0.10296	0.003	B	0.13407	0.009	T	0.61407	-0.7069	10	0.19590	T	0.45	.	6.6891	0.23161	0.0:0.396:0.3197:0.2843	.	266	P78386	KRT85_HUMAN	I	266;54	ENSP00000257901:V266I;ENSP00000440240:V54I	ENSP00000257901:V266I	V	-	1	0	KRT85	51043452	0.031000	0.19500	0.000000	0.03702	0.882000	0.50991	0.824000	0.27379	-0.121000	0.11787	0.555000	0.69702	GTT		0.562	KRT85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405184.1	NM_002283	
KRT75	9119	broad.mit.edu	37	12	52827678	52827678	+	Silent	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:52827678T>C	ENST00000252245.5	-	1	631	c.411A>G	c.(409-411)caA>caG	p.Q137Q		NM_004693.2	NP_004684.2	O95678	K2C75_HUMAN	keratin 75	137	Head.				hematopoietic progenitor cell differentiation (GO:0002244)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.Q137Q(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(10)|prostate(1)|skin(1)	28				BRCA - Breast invasive adenocarcinoma(357;0.192)		TGGGGTCGATTTGCAGGTGAA	0.597																																					p.Q137Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A411G	12						.						135.0	136.0	136.0					12																	52827678		2203	4300	6503	51113945	SO:0001819	synonymous_variant	9119	exon1			Y19212	CCDS8827.1	12q13.13	2013-06-25			ENSG00000170454	ENSG00000170454		"""-"", ""Intermediate filaments type II, keratins (basic)"""	24431	protein-coding gene	gene with protein product		609025				9856802, 10692104, 16831889	Standard	NM_004693		Approved	K6HF	uc001saj.2	O95678	OTTHUMG00000169592	ENST00000252245.5:c.411A>G	12.37:g.52827678T>C			51113945	NM_004693	B4DQU4|Q9NSA9	Silent	SNP	ENST00000252245.5	37	CCDS8827.1																																																																																				0.597	KRT75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404968.1	NM_004693	
KRT6C	286887	broad.mit.edu	37	12	52865929	52865929	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:52865929C>T	ENST00000252250.6	-	2	723	c.676G>A	c.(676-678)Gac>Aac	p.D226N		NM_173086.4	NP_775109.2	P48668	K2C6C_HUMAN	keratin 6C	226	Coil 1B.|Rod.				intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.D226N(1)		cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|prostate(2)|skin(2)	23				BRCA - Breast invasive adenocarcinoma(357;0.0828)		ACGATGCTGTCCAGCTGCCTC	0.592																																					p.D226N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G676A	12						.						129.0	83.0	99.0					12																	52865929		2202	4275	6477	51152196	SO:0001583	missense	286887	exon2			L42611	CCDS8829.1	12q13.13	2013-01-16	2006-07-17	2006-07-17	ENSG00000170465	ENSG00000170465		"""-"", ""Intermediate filaments type II, keratins (basic)"""	20406	protein-coding gene	gene with protein product		612315	"""keratin 6E"""	KRT6E		7543104, 16831889	Standard	NM_173086		Approved		uc001sal.4	P48668	OTTHUMG00000169596	ENST00000252250.6:c.676G>A	12.37:g.52865929C>T	ENSP00000252250:p.Asp226Asn		51152196	NM_173086	A1L4L5|P48666|Q2TAZ9|Q7RTN9	Missense_Mutation	SNP	ENST00000252250.6	37	CCDS8829.1	.	.	.	.	.	.	.	.	.	.	C	16.33	3.093684	0.56075	.	.	ENSG00000170465	ENST00000252250;ENST00000411979	T	0.79352	-1.26	2.89	1.97	0.26223	Filament (1);	0.194061	0.35646	N	0.003068	T	0.80803	0.4693	M	0.88377	2.95	0.31778	N	0.63128	P	0.40211	0.707	B	0.43867	0.434	T	0.82321	-0.0515	10	0.56958	D	0.05	.	8.5584	0.33496	0.0:0.7249:0.0:0.275	.	226	P48668	K2C6C_HUMAN	N	226;211	ENSP00000252250:D226N	ENSP00000252250:D226N	D	-	1	0	KRT6C	51152196	1.000000	0.71417	0.764000	0.31436	0.565000	0.35776	1.742000	0.38248	0.739000	0.32628	0.407000	0.27541	GAC		0.592	KRT6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404976.1	NM_173086	
KRT4	3851	broad.mit.edu	37	12	53203200	53203200	+	Silent	SNP	G	G	A	rs369207280		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:53203200G>A	ENST00000551956.1	-	4	1293	c.801C>T	c.(799-801)gaC>gaT	p.D267D	KRT4_ENST00000458244.2_Silent_p.D247D|KRT4_ENST00000293774.4_Silent_p.D341D			P19013	K2C4_HUMAN	keratin 4	281	Coil 1B.|Rod.				cytoskeleton organization (GO:0007010)|epithelial cell differentiation (GO:0030855)|negative regulation of epithelial cell proliferation (GO:0050680)	cell surface (GO:0009986)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)	p.D341D(1)		endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|prostate(2)|skin(2)	29						AGTTGATCTCGTCATTAAGAC	0.557																																					p.D341D	Pancreas(190;284 2995 41444 45903)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1023T	12						.						132.0	142.0	139.0					12																	53203200		2187	4298	6485	51489467	SO:0001819	synonymous_variant	3851	exon4				CCDS41787.1, CCDS41787.2	12q13.13	2013-01-16			ENSG00000170477	ENSG00000170477		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6441	protein-coding gene	gene with protein product	"""cytokeratin 4"", ""keratin, type II cytoskeletal 4"""	123940		CYK4		16831889	Standard	NM_002272		Approved	CK4, K4	uc031qhk.1	P19013		ENST00000551956.1:c.801C>T	12.37:g.53203200G>A			51489467	NM_002272	F8VS64|Q6GTR8|Q96LA7|Q9BTL1	Silent	SNP	ENST00000551956.1	37	CCDS41787.2																																																																																				0.557	KRT4-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405931.1	NM_002272	
KRT18	3875	broad.mit.edu	37	12	53346086	53346086	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:53346086G>T	ENST00000388835.3	+	6	1342	c.1132G>T	c.(1132-1134)Gcc>Tcc	p.A378S	KRT18_ENST00000550600.1_Missense_Mutation_p.A378S|KRT8_ENST00000546897.1_5'Flank|AC107016.2_ENST00000581256.1_RNA|KRT8_ENST00000552551.1_5'Flank|KRT8_ENST00000549198.1_5'Flank|KRT18_ENST00000388837.2_Missense_Mutation_p.A378S	NM_000224.2	NP_000215.1	P05783	K1C18_HUMAN	keratin 18	378	Coil 2.|Interaction with DNAJB6.|Rod.				anatomical structure morphogenesis (GO:0009653)|cell cycle (GO:0007049)|extrinsic apoptotic signaling pathway (GO:0097191)|Golgi to plasma membrane CFTR protein transport (GO:0043000)|hepatocyte apoptotic process (GO:0097284)|intermediate filament cytoskeleton organization (GO:0045104)|negative regulation of apoptotic process (GO:0043066)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|viral process (GO:0016032)	cell periphery (GO:0071944)|centriolar satellite (GO:0034451)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|scaffold protein binding (GO:0097110)|structural molecule activity (GO:0005198)	p.A378S(1)		central_nervous_system(1)|large_intestine(2)|lung(4)|prostate(3)|skin(1)	11						GGCTGAGATCGCCACCTACCG	0.607																																					p.A378S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1132T	12						.						16.0	19.0	18.0					12																	53346086		2198	4292	6490	51632353	SO:0001583	missense	3875	exon7				CCDS31809.1	12q13	2013-01-16			ENSG00000111057	ENSG00000111057		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6430	protein-coding gene	gene with protein product		148070				1705144, 16831889	Standard	NM_000224		Approved		uc001sbg.3	P05783	OTTHUMG00000169882	ENST00000388835.3:c.1132G>T	12.37:g.53346086G>T	ENSP00000373487:p.Ala378Ser		51632353	NM_199187	Q53G38|Q5U0N8|Q9BW26	Missense_Mutation	SNP	ENST00000388835.3	37	CCDS31809.1	.	.	.	.	.	.	.	.	.	.	g	15.09	2.729281	0.48833	.	.	ENSG00000111057	ENST00000388837;ENST00000550600;ENST00000388835	D;D;D	0.90504	-2.68;-2.68;-2.68	4.0	1.97	0.26223	Filament (1);Intermediate filament protein, conserved site (1);	0.653554	0.14080	N	0.342775	D	0.91509	0.7319	M	0.86953	2.85	0.32584	N	0.528122	B;B	0.30824	0.296;0.201	B;B	0.42738	0.275;0.396	D	0.88159	0.2856	10	0.35671	T	0.21	.	3.2493	0.06808	0.2903:0.2188:0.491:0.0	.	378;378	F8VZY9;P05783	.;K1C18_HUMAN	S	378	ENSP00000373489:A378S;ENSP00000447278:A378S;ENSP00000373487:A378S	ENSP00000373487:A378S	A	+	1	0	KRT18	51632353	0.045000	0.20229	0.978000	0.43139	0.990000	0.78478	0.922000	0.28734	0.540000	0.28808	0.561000	0.74099	GCC		0.607	KRT18-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406405.1	NM_199187	
MAP3K12	7786	broad.mit.edu	37	12	53875005	53875005	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:53875005G>A	ENST00000267079.2	-	15	2766	c.2541C>T	c.(2539-2541)agC>agT	p.S847S	MAP3K12_ENST00000547035.1_Silent_p.S880S|MAP3K12_ENST00000547488.1_Silent_p.S880S	NM_001193511.1|NM_006301.3	NP_001180440.1|NP_006292.3	Q12852	M3K12_HUMAN	mitogen-activated protein kinase kinase kinase 12	847					histone phosphorylation (GO:0016572)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)	p.S847S(2)|p.S880S(1)		NS(2)|breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	37						AGGCATCAACGCTGTTGGAGT	0.438																																					p.S880S												.	.	3	Substitution - coding silent(3)	endometrium(2)|large_intestine(1)	c.C2640T	12						.						70.0	62.0	65.0					12																	53875005		2203	4300	6503	52161272	SO:0001819	synonymous_variant	7786	exon14			U07358	CCDS8860.1, CCDS55831.1	12q13.13	2013-10-30			ENSG00000139625	ENSG00000139625		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6851	protein-coding gene	gene with protein product	"""dual leucine zipper kinase DLK"""	600447		ZPK		8037767	Standard	NM_006301		Approved	MUK, DLK, ZPKP1, MEKK12	uc001sdn.2	Q12852	OTTHUMG00000169854	ENST00000267079.2:c.2541C>T	12.37:g.53875005G>A			52161272	NM_001193511	B3KSS9|G3V1Y2|Q86VQ5|Q8WY25	Silent	SNP	ENST00000267079.2	37	CCDS8860.1																																																																																				0.438	MAP3K12-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406267.1	NM_006301	
ITGA5	3678	broad.mit.edu	37	12	54812766	54812766	+	Splice_Site	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:54812766C>T	ENST00000293379.4	-	1	478	c.217G>A	c.(217-219)Ggg>Agg	p.G73R	RP11-753H16.3_ENST00000550474.1_RNA|RP11-753H16.5_ENST00000552785.1_RNA|RP11-753H16.3_ENST00000552053.1_RNA	NM_002205.2	NP_002196.2	P08648	ITA5_HUMAN	integrin, alpha 5 (fibronectin receptor, alpha polypeptide)	73					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|memory (GO:0007613)|negative regulation of anoikis (GO:2000811)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|viral process (GO:0016032)|wound healing, spreading of epidermal cells (GO:0035313)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	metal ion binding (GO:0046872)|platelet-derived growth factor receptor binding (GO:0005161)|vascular endothelial growth factor receptor 2 binding (GO:0043184)	p.G73R(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	34						CTCACTCACCCGTCTGTTCCC	0.672																																					p.G73R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G217A	12						.						15.0	20.0	18.0					12																	54812766		2058	4128	6186	53099033	SO:0001630	splice_region_variant	3678	exon1				CCDS8880.1	12q11-q13	2010-03-23				ENSG00000161638		"""CD molecules"", ""Integrins"""	6141	protein-coding gene	gene with protein product		135620		FNRA		2454952	Standard	NM_002205		Approved	CD49e	uc001sga.3	P08648	OTTHUMG00000169841	ENST00000293379.4:c.218+1G>A	12.37:g.54812766C>T			53099033	NM_002205	Q96HA5	Missense_Mutation	SNP	ENST00000293379.4	37	CCDS8880.1	.	.	.	.	.	.	.	.	.	.	C	8.743	0.919477	0.17982	.	.	ENSG00000161638	ENST00000293379	T	0.44083	0.93	3.69	3.69	0.42338	.	0.378995	0.26746	N	0.022720	T	0.23171	0.0560	N	0.20401	0.57	0.38330	D	0.943771	B	0.21071	0.051	B	0.17979	0.02	T	0.08106	-1.0738	10	0.06494	T	0.89	.	11.2197	0.48846	0.0:1.0:0.0:0.0	.	73	P08648	ITA5_HUMAN	R	73	ENSP00000293379:G73R	ENSP00000293379:G73R	G	-	1	0	ITGA5	53099033	0.822000	0.29219	0.998000	0.56505	0.908000	0.53690	1.253000	0.32886	2.371000	0.80710	0.462000	0.41574	GGG		0.672	ITGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406174.1		Missense_Mutation
LRP1	4035	broad.mit.edu	37	12	57574574	57574574	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:57574574C>T	ENST00000243077.3	+	33	5977	c.5511C>T	c.(5509-5511)gaC>gaT	p.D1837D		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	1837					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)	p.D1837D(1)		NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	AGGTCTATGACGAGAGCATCC	0.657																																					p.D1837D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C5511T	12						.						82.0	76.0	78.0					12																	57574574		2203	4300	6503	55860841	SO:0001819	synonymous_variant	4035	exon33			X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.5511C>T	12.37:g.57574574C>T			55860841	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																				0.657	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
SHMT2	6472	broad.mit.edu	37	12	57626004	57626004	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:57626004G>A	ENST00000328923.3	+	5	975	c.523G>A	c.(523-525)Ggc>Agc	p.G175S	SHMT2_ENST00000449049.3_Missense_Mutation_p.G154S|SHMT2_ENST00000554600.1_3'UTR|SHMT2_ENST00000553474.1_Missense_Mutation_p.G154S|SHMT2_ENST00000557487.1_Missense_Mutation_p.G175S|SHMT2_ENST00000393827.4_Silent_p.T69T|SHMT2_ENST00000414700.3_Missense_Mutation_p.G154S	NM_001166356.1|NM_005412.5	NP_001159828.1|NP_005403.2	P34897	GLYM_HUMAN	serine hydroxymethyltransferase 2 (mitochondrial)	175					glycine biosynthetic process from serine (GO:0019264)|L-serine biosynthetic process (GO:0006564)|one-carbon metabolic process (GO:0006730)|positive regulation of cell proliferation (GO:0008284)|protein homotetramerization (GO:0051289)|tetrahydrofolate interconversion (GO:0035999)	extracellular vesicular exosome (GO:0070062)|microtubule cytoskeleton (GO:0015630)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|chromatin binding (GO:0003682)|glycine hydroxymethyltransferase activity (GO:0004372)|L-allo-threonine aldolase activity (GO:0008732)|pyridoxal phosphate binding (GO:0030170)	p.G175S(1)		breast(1)|central_nervous_system(1)|large_intestine(4)|liver(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	15					Glycine(DB00145)|Tetrahydrofolic acid(DB00116)	TCTCACCCACGGCTACATGTC	0.552																																					p.G154S	Esophageal Squamous(150;1369 2416 49071 49364)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G460A	12						.						135.0	111.0	119.0					12																	57626004		2203	4300	6503	55912271	SO:0001583	missense	6472	exon5			AK223555	CCDS8934.1, CCDS53805.1, CCDS55837.1	12q12-q14	2006-03-27				ENSG00000182199	2.1.2.1		10852	protein-coding gene	gene with protein product		138450		SHMT		8999870	Standard	NM_005412		Approved		uc001snf.2	P34897		ENST00000328923.3:c.523G>A	12.37:g.57626004G>A	ENSP00000333667:p.Gly175Ser		55912271	NM_001166359	B7Z9F1|E7EQ19|E7EU43|O00740|Q8N1A5	Missense_Mutation	SNP	ENST00000328923.3	37	CCDS8934.1	.	.	.	.	.	.	.	.	.	.	G	34	5.299352	0.95574	.	.	ENSG00000182199	ENST00000328923;ENST00000557487;ENST00000555634;ENST00000556689;ENST00000414700;ENST00000554310;ENST00000557427;ENST00000553474;ENST00000554975;ENST00000449049	T;T;T;T;T;T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2;-0.2;-0.2;-0.2;-0.2;-0.2	4.95	4.95	0.65309	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.84973	0.5591	H	0.94542	3.55	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.89003	0.3423	10	0.87932	D	0	-10.2043	17.4978	0.87723	0.0:0.0:1.0:0.0	.	184;175;106;175	B4DWA7;Q8N1A5;B4DP88;P34897	.;.;.;GLYM_HUMAN	S	175;175;14;175;154;154;154;154;154;154	ENSP00000333667:G175S;ENSP00000452315:G175S;ENSP00000450930:G14S;ENSP00000452035:G175S;ENSP00000406881:G154S;ENSP00000450893:G154S;ENSP00000452045:G154S;ENSP00000452419:G154S;ENSP00000452404:G154S;ENSP00000413770:G154S	ENSP00000333667:G175S	G	+	1	0	SHMT2	55912271	1.000000	0.71417	0.999000	0.59377	0.700000	0.40528	7.818000	0.86416	2.735000	0.93741	0.655000	0.94253	GGC		0.552	SHMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412525.2	NM_005412	
R3HDM2	22864	broad.mit.edu	37	12	57663776	57663776	+	Splice_Site	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:57663776G>A	ENST00000347140.3	-	15	1694	c.1304C>T	c.(1303-1305)gCa>gTa	p.A435V	R3HDM2_ENST00000546843.1_5'Flank|R3HDM2_ENST00000403821.2_Splice_Site_p.A469V|RP11-123K3.4_ENST00000548184.1_3'UTR|R3HDM2_ENST00000402412.1_Splice_Site_p.A449V|R3HDM2_ENST00000441731.2_Splice_Site_p.A130V|R3HDM2_ENST00000358907.2_Splice_Site_p.A435V|R3HDM2_ENST00000413953.2_Splice_Site_p.A162V			Q9Y2K5	R3HD2_HUMAN	R3H domain containing 2	435	Gln-rich.					nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.A96V(1)|p.A435V(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	22						GAGGTCATCTGCCTGTTGAGA	0.463																																					p.A435V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1304T	12						.						113.0	111.0	112.0					12																	57663776		2203	4300	6503	55950043	SO:0001630	splice_region_variant	22864	exon13			AB023219	CCDS8937.2	12q13.3	2012-11-19			ENSG00000179912	ENSG00000179912			29167	protein-coding gene	gene with protein product							Standard	NM_014925		Approved	KIAA1002	uc009zpm.1	Q9Y2K5	OTTHUMG00000171568	ENST00000347140.3:c.1303-1C>T	12.37:g.57663776G>A			55950043	NM_014925	Q2M1T9|Q3ZCT5	Missense_Mutation	SNP	ENST00000347140.3	37	CCDS8937.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.15|16.15	3.042861|3.042861	0.55003|0.55003	.|.	.|.	ENSG00000179912|ENSG00000179912	ENST00000413953;ENST00000393811;ENST00000347140;ENST00000402412;ENST00000358907;ENST00000441731;ENST00000429355;ENST00000403821|ENST00000466401	T;T;T;T;T;T;T;T|.	0.44881|.	0.93;0.93;1.95;1.95;1.95;0.91;1.52;1.91|.	4.98|4.98	4.98|4.98	0.66077|0.66077	.|.	0.648253|.	0.15072|.	N|.	0.282160|.	T|.	0.54175|.	0.1842|.	N|N	0.22421|0.22421	0.69|0.69	0.80722|0.80722	D|D	1|1	B;B;B;B;B|.	0.28713|.	0.167;0.22;0.104;0.104;0.137|.	B;B;B;B;B|.	0.28011|.	0.085;0.073;0.024;0.024;0.085|.	T|.	0.47787|.	-0.9090|.	10|.	0.25106|.	T|.	0.35|.	-8.8016|-8.8016	17.5663|17.5663	0.87921|0.87921	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	162;469;449;435;162|.	B4DDZ2;B5MCG9;B5MCU0;Q9Y2K5;E9PAL1|.	.;.;.;R3HD2_HUMAN;.|.	V|X	162;162;435;449;435;130;200;469|33	ENSP00000409146:A162V;ENSP00000377400:A162V;ENSP00000317903:A435V;ENSP00000385839:A449V;ENSP00000351784:A435V;ENSP00000408536:A130V;ENSP00000394676:A200V;ENSP00000385169:A469V|.	ENSP00000317903:A435V|.	A|Q	-|-	2|1	0|0	R3HDM2|R3HDM2	55950043|55950043	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	3.680000|3.680000	0.54641|0.54641	2.773000|2.773000	0.95371|0.95371	0.650000|0.650000	0.86243|0.86243	GCA|CAG		0.463	R3HDM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326570.2	NM_014925	Missense_Mutation
MBD6	114785	broad.mit.edu	37	12	57920575	57920575	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:57920575G>A	ENST00000355673.3	+	7	2003	c.1647G>A	c.(1645-1647)caG>caA	p.Q549Q	MBD6_ENST00000431731.2_Silent_p.Q549Q	NM_052897.3	NP_443129.3	Q96DN6	MBD6_HUMAN	methyl-CpG binding domain protein 6	549	Pro-rich.					chromocenter (GO:0010369)|nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.Q549Q(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)|urinary_tract(1)	31						GTCTGGGGCAGCCTCCACCTT	0.627																																					p.Q549Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1647A	12						.						69.0	58.0	62.0					12																	57920575		2203	4299	6502	56206842	SO:0001819	synonymous_variant	114785	exon7			AB067474	CCDS8944.1	12q13.2	2008-02-05				ENSG00000166987			20445	protein-coding gene	gene with protein product						12529184	Standard	NM_052897		Approved	KIAA1887	uc001soj.1	Q96DN6		ENST00000355673.3:c.1647G>A	12.37:g.57920575G>A			56206842	NM_052897	Q8N3M0|Q8NA81|Q96Q00	Silent	SNP	ENST00000355673.3	37	CCDS8944.1																																																																																				0.627	MBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407250.1		
CYP27B1	1594	broad.mit.edu	37	12	58158889	58158889	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:58158889G>A	ENST00000228606.4	-	4	904	c.695C>T	c.(694-696)aCg>aTg	p.T232M	CYP27B1_ENST00000546496.1_5'Flank	NM_000785.3	NP_000776.1	O15528	CP27B_HUMAN	cytochrome P450, family 27, subfamily B, polypeptide 1	232					bone mineralization (GO:0030282)|calcitriol biosynthetic process from calciol (GO:0036378)|calcium ion homeostasis (GO:0055074)|calcium ion transport (GO:0006816)|decidualization (GO:0046697)|G1 to G0 transition (GO:0070314)|negative regulation of calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of vitamin D 24-hydroxylase activity (GO:0010980)|positive regulation of vitamin D receptor signaling pathway (GO:0070564)|regulation of bone mineralization (GO:0030500)|response to estrogen (GO:0043627)|response to interferon-gamma (GO:0034341)|response to lipopolysaccharide (GO:0032496)|response to vitamin D (GO:0033280)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D catabolic process (GO:0042369)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	calcidiol 1-monooxygenase activity (GO:0004498)|heme binding (GO:0020037)|iron ion binding (GO:0005506)	p.T232M(1)		central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|urinary_tract(1)	15	all_cancers(7;8.09e-80)|Lung NSC(6;2.26e-27)|all_lung(6;1.99e-25)|all_epithelial(6;3.62e-18)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)		GBM - Glioblastoma multiforme(5;1.97e-113)|all cancers(5;1.54e-78)|BRCA - Breast invasive adenocarcinoma(9;0.0294)		Alfacalcidol(DB01436)|Calcidiol(DB00146)|Corticotropin(DB01285)|Ergocalciferol(DB00153)	GGTCAACAGCGTGGACACAAA	0.657											OREG0021953	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T232M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C695T	12						.						59.0	53.0	55.0					12																	58158889		2203	4300	6503	56445156	SO:0001583	missense	1594	exon4			AB006987	CCDS8954.1	12q14.1	2013-11-13	2003-01-14		ENSG00000111012	ENSG00000111012		"""Cytochrome P450s"""	2606	protein-coding gene	gene with protein product	"""VDDR I"", ""1alpha(OH)ase"", ""25-Hydroxyvitamin D3 1alpha-hydroxylase"""	609506	"""cytochrome P450, subfamily XXVIIB (25-hydroxyvitamin D-1-alpha-hydroxylase), polypeptide 1"""	VDD1, PDDR		9295274, 9344864	Standard	NM_000785		Approved	CYP1, P450c1	uc001spz.1	O15528	OTTHUMG00000170457	ENST00000228606.4:c.695C>T	12.37:g.58158889G>A	ENSP00000228606:p.Thr232Met	1028	56445156	NM_000785	B2RC61|Q548T3	Missense_Mutation	SNP	ENST00000228606.4	37	CCDS8954.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.739429	0.89573	.	.	ENSG00000111012	ENST00000228606	T	0.69561	-0.41	5.06	5.06	0.68205	.	0.000000	0.85682	D	0.000000	T	0.80082	0.4558	M	0.69358	2.11	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	T	0.78732	-0.2089	10	0.39692	T	0.17	.	17.3428	0.87301	0.0:0.0:1.0:0.0	.	232	O15528	CP27B_HUMAN	M	232	ENSP00000228606:T232M	ENSP00000228606:T232M	T	-	2	0	CYP27B1	56445156	1.000000	0.71417	0.998000	0.56505	0.883000	0.51084	7.205000	0.77881	2.625000	0.88918	0.561000	0.74099	ACG		0.657	CYP27B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409248.1	NM_000785	
WIF1	11197	broad.mit.edu	37	12	65445153	65445153	+	Silent	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:65445153T>C	ENST00000286574.4	-	10	1490	c.1116A>G	c.(1114-1116)ccA>ccG	p.P372P		NM_007191.4	NP_009122.2	Q9Y5W5	WIF1_HUMAN	WNT inhibitory factor 1	372					multicellular organismal development (GO:0007275)|positive regulation of fat cell differentiation (GO:0045600)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)		p.P372P(1)		cervix(1)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|stomach(1)|urinary_tract(1)	21			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0231)		TGGATTCAGGTGGATCCCGCC	0.502			T	HMGA2	pleomorphic salivary gland adenoma																																p.P372P	Esophageal Squamous(148;1595 1816 48559 49439 49664)		Dom	yes		12	12q14.3	11197	WNT inhibitory factor 1		E	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1116G	12						.						73.0	71.0	72.0					12																	65445153		2203	4300	6503	63731420	SO:0001819	synonymous_variant	11197	exon10			AF122922	CCDS8971.1	12q14.2	2008-04-11			ENSG00000156076	ENSG00000156076			18081	protein-coding gene	gene with protein product		605186				10201374	Standard	NM_007191		Approved		uc001ssk.3	Q9Y5W5	OTTHUMG00000168832	ENST00000286574.4:c.1116A>G	12.37:g.65445153T>C			63731420	NM_007191	Q6UXI1|Q8WVG4	Silent	SNP	ENST00000286574.4	37	CCDS8971.1																																																																																				0.502	WIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401258.2		
LLPH	84298	broad.mit.edu	37	12	66517749	66517749	+	Silent	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:66517749T>C	ENST00000266604.2	-	3	331	c.261A>G	c.(259-261)ctA>ctG	p.L87L	TMBIM4_ENST00000556010.1_3'UTR|TMBIM4_ENST00000539652.1_3'UTR|LLPH_ENST00000446587.2_Silent_p.L87L	NM_032338.3	NP_115714.1	Q9BRT6	LLPH_HUMAN	LLP homolog, long-term synaptic facilitation (Aplysia)	87	Lys-rich.						poly(A) RNA binding (GO:0044822)	p.L87L(1)		central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(1)|skin(1)	5						CATGCTGGTCTAGAAGAGTCT	0.378																																					p.L87L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A261G	12						.						74.0	67.0	69.0					12																	66517749		2202	4297	6499	64804016	SO:0001819	synonymous_variant	84298	exon3			AK057947	CCDS8974.1	12q14.3	2014-05-09	2008-10-02	2008-10-02	ENSG00000139233	ENSG00000139233			28229	protein-coding gene	gene with protein product	"""human LAPS18-like protein"""		"""chromosome 12 open reading frame 31"""	C12orf31		12477932	Standard	NM_032338		Approved	MGC14817, hLLP	uc010ssw.2	Q9BRT6	OTTHUMG00000168959	ENST00000266604.2:c.261A>G	12.37:g.66517749T>C			64804016	NM_032338	Q3B766	Silent	SNP	ENST00000266604.2	37	CCDS8974.1																																																																																				0.378	LLPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401752.1	NM_032338	
TPH2	121278	broad.mit.edu	37	12	72372833	72372833	+	Missense_Mutation	SNP	C	C	T	rs120074176		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:72372833C>T	ENST00000333850.3	+	7	1048	c.907C>T	c.(907-909)Cgg>Tgg	p.R303W		NM_173353.3	NP_775489.2	Q8IWU9	TPH2_HUMAN	tryptophan hydroxylase 2	303			R -> W (in ADHD7; has severely reduced solubility and is completely inactive; loss of function may lead to a reduced serotonin synthesis which in turn makes the mutation carriers susceptible to ADHD and possibly other psychiatric disorders). {ECO:0000269|PubMed:18347598}.		aromatic amino acid family metabolic process (GO:0009072)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to lithium ion (GO:0071285)|circadian rhythm (GO:0007623)|indolalkylamine biosynthetic process (GO:0046219)|response to activity (GO:0014823)|response to calcium ion (GO:0051592)|response to estrogen (GO:0043627)|response to glucocorticoid (GO:0051384)|response to nutrient levels (GO:0031667)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|neuron projection (GO:0043005)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|tryptophan 5-monooxygenase activity (GO:0004510)	p.R303W(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	41					L-Tryptophan(DB00150)	CCAGTACATCCGGCATGGCTC	0.542																																					p.R303W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C907T	12	GRCh37	CM084847	TPH2	M	rs120074176	.	C	TRP/ARG	0,4406		0,0,2203	144.0	140.0	141.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	907	4.5	1.0	12	dbSNP_132	141	1,8599	1.2+/-3.3	0,1,4299	no	missense	TPH2	NM_173353.3	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	303/491	72372833	1,13005	2203	4300	6503	70659100	SO:0001583	missense	121278	exon7			AY098914	CCDS31859.1	12q15	2008-02-07				ENSG00000139287	1.14.16.4		20692	protein-coding gene	gene with protein product		607478				12511643	Standard	NM_173353		Approved	NTPH, FLJ37295	uc009zrw.1	Q8IWU9		ENST00000333850.3:c.907C>T	12.37:g.72372833C>T	ENSP00000329093:p.Arg303Trp		70659100	NM_173353	A6NGA4|Q14CB0	Missense_Mutation	SNP	ENST00000333850.3	37	CCDS31859.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.234280	0.79688	0.0	1.16E-4	ENSG00000139287	ENST00000333850	D	0.99943	-8.48	5.47	4.5	0.54988	Aromatic amino acid hydroxylase, C-terminal (3);	0.054169	0.85682	D	0.000000	D	0.99953	0.9980	H	0.98256	4.185	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96096	0.9065	10	0.87932	D	0	-9.4935	14.4487	0.67370	0.2308:0.7692:0.0:0.0	.	303	Q8IWU9	TPH2_HUMAN	W	303	ENSP00000329093:R303W	ENSP00000329093:R303W	R	+	1	2	TPH2	70659100	0.889000	0.30405	0.991000	0.47740	0.969000	0.65631	1.703000	0.37846	2.570000	0.86706	0.555000	0.69702	CGG		0.542	TPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405234.1	NM_173353	
KCNC2	3747	broad.mit.edu	37	12	75442029	75442029	+	Missense_Mutation	SNP	G	G	A	rs199735865		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:75442029G>A	ENST00000549446.1	-	4	2364	c.1684C>T	c.(1684-1686)Cgc>Tgc	p.R562C	KCNC2_ENST00000540018.1_Intron|KCNC2_ENST00000550433.1_Missense_Mutation_p.R562C|KCNC2_ENST00000341669.3_Missense_Mutation_p.R562C|KCNC2_ENST00000548513.1_Missense_Mutation_p.R562C|KCNC2_ENST00000298972.1_Missense_Mutation_p.R562C|KCNC2_ENST00000393288.2_Missense_Mutation_p.R562C|KCNC2_ENST00000548243.1_5'UTR|KCNC2_ENST00000350228.2_Intron	NM_001260497.1|NM_139137.3	NP_001247426.1|NP_631875.1	Q96PR1	KCNC2_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 2	562					action potential (GO:0001508)|energy reserve metabolic process (GO:0006112)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.R562C(2)		breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(28)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	54					Dalfampridine(DB06637)	GTACTAGAGCGTCTGATGGGG	0.512																																					p.R562C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1684T	12						.						222.0	177.0	193.0					12																	75442029		2203	4300	6503	73728296	SO:0001583	missense	3747	exon4			AF268896	CCDS9005.1, CCDS9006.1, CCDS9007.1, CCDS58255.1, CCDS58256.1, CCDS58257.1	12q14.1	2012-07-05						"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6234	protein-coding gene	gene with protein product		176256				8111118, 16382104	Standard	NM_139136		Approved	Kv3.2	uc001sxg.2	Q96PR1	OTTHUMG00000169717	ENST00000549446.1:c.1684C>T	12.37:g.75442029G>A	ENSP00000449253:p.Arg562Cys		73728296	NM_139137	B7Z231|F5H030|J3KPP5|Q4LE77|Q86W09|Q8N1V9|Q96PR0	Missense_Mutation	SNP	ENST00000549446.1	37	CCDS9007.1	.	.	.	.	.	.	.	.	.	.	G	16.37	3.103252	0.56183	.	.	ENSG00000166006	ENST00000550433;ENST00000548513;ENST00000549446;ENST00000341669;ENST00000298972;ENST00000393288	D;D;D;D;D;D	0.97752	-4.5;-4.48;-4.46;-4.5;-4.48;-4.52	5.55	5.55	0.83447	.	0.362760	0.27249	N	0.020222	D	0.97467	0.9171	L	0.36672	1.1	0.58432	D	0.999997	B;B;D	0.89917	0.039;0.109;1.0	B;B;P	0.59288	0.012;0.014;0.855	D	0.97524	1.0075	10	0.44086	T	0.13	.	19.4922	0.95054	0.0:0.0:1.0:0.0	.	562;562;562	Q96PR1-2;Q96PR1;Q96PR1-3	.;KCNC2_HUMAN;.	C	562	ENSP00000448301:R562C;ENSP00000449941:R562C;ENSP00000449253:R562C;ENSP00000340121:R562C;ENSP00000298972:R562C;ENSP00000376966:R562C	ENSP00000298972:R562C	R	-	1	0	KCNC2	73728296	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.805000	0.55575	2.604000	0.88044	0.585000	0.79938	CGC		0.512	KCNC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405581.2	NM_153748	
KRR1	11103	broad.mit.edu	37	12	75902207	75902207	+	Silent	SNP	C	C	T	rs115154800	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:75902207C>T	ENST00000229214.4	-	2	128	c.105G>A	c.(103-105)acG>acA	p.T35T	KRR1_ENST00000438169.2_Silent_p.T35T	NM_007043.6	NP_008974.5	Q13601	KRR1_HUMAN	KRR1, small subunit (SSU) processome component, homolog (yeast)	35					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)	p.T35T(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(1)|ovary(1)|pancreas(1)|urinary_tract(1)	11						CATCAGGAACCGTAAGGAGTT	0.398													C|||	4	0.000798722	0.003	0.0	5008	,	,		18594	0.0		0.0	False		,,,				2504	0.0				p.T35T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G105A	12						.	C		9,4397	15.5+/-35.6	0,9,2194	56.0	55.0	55.0		105	2.2	1.0	12	dbSNP_132	55	0,8600		0,0,4300	no	coding-synonymous	KRR1	NM_007043.6		0,9,6494	TT,TC,CC		0.0,0.2043,0.0692		35/382	75902207	9,12997	2203	4300	6503	74188474	SO:0001819	synonymous_variant	11103	exon2			U55766	CCDS9012.1	12q	2011-03-15	2006-05-18	2006-05-18	ENSG00000111615	ENSG00000111615			5176	protein-coding gene	gene with protein product		612817	"""HIV-1 rev binding protein 2"", ""HIV-1 Rev binding protein 2"""	HRB2		7505766, 11027267, 11359931, 8675026	Standard	NM_007043		Approved	RIP-1	uc001sxt.3	Q13601	OTTHUMG00000169759	ENST00000229214.4:c.105G>A	12.37:g.75902207C>T			74188474	NM_007043	A0FIK6|A0JLP0|B2R989|E7EUQ0|Q8NEA8|Q8TC37|Q96AT5	Silent	SNP	ENST00000229214.4	37	CCDS9012.1																																																																																				0.398	KRR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405727.1	NM_007043	
NAV3	89795	broad.mit.edu	37	12	78598824	78598824	+	Missense_Mutation	SNP	G	G	A	rs552595814	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:78598824G>A	ENST00000397909.2	+	39	7117	c.6944G>A	c.(6943-6945)cGa>cAa	p.R2315Q	NAV3_ENST00000228327.6_Missense_Mutation_p.R2293Q|NAV3_ENST00000536525.2_Missense_Mutation_p.R2293Q|NAV3_ENST00000266692.7_Missense_Mutation_p.R2116Q|NAV3_ENST00000541270.1_Missense_Mutation_p.R145Q			Q8IVL0	NAV3_HUMAN	neuron navigator 3	2315						membrane (GO:0016020)|nuclear envelope (GO:0005635)		p.R2293L(1)|p.R2293Q(1)		NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						CTTCAGCTGCGACCAGAAGAT	0.507										HNSCC(70;0.22)			G|||	2	0.000399361	0.0015	0.0	5008	,	,		14473	0.0		0.0	False		,,,				2504	0.0				p.R2293Q												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G6878A	12						.						77.0	80.0	79.0					12																	78598824		2055	4193	6248	77122955	SO:0001583	missense	89795	exon38			AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 1"", ""steerin 3"""	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.6944G>A	12.37:g.78598824G>A	ENSP00000381007:p.Arg2315Gln		77122955	NM_014903	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	37		.	.	.	.	.	.	.	.	.	.	G	19.82	3.897911	0.72639	.	.	ENSG00000067798	ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692;ENST00000541270	T;T;T;T;T	0.49432	1.45;1.45;1.45;1.42;0.78	5.4	5.4	0.78164	.	0.000000	0.36628	U	0.002497	T	0.69682	0.3138	M	0.74881	2.28	0.80722	D	1	D;D;D;D	0.89917	1.0;0.998;1.0;1.0	D;D;D;D	0.91635	0.999;0.986;0.99;0.996	T	0.67604	-0.5628	10	0.35671	T	0.21	-9.3303	19.1641	0.93546	0.0:0.0:1.0:0.0	.	2293;2116;2315;2293	E7EUC6;Q8IVL0-3;Q8IVL0;Q8IVL0-2	.;.;NAV3_HUMAN;.	Q	2293;2315;2293;2116;145	ENSP00000446132:R2293Q;ENSP00000381007:R2315Q;ENSP00000228327:R2293Q;ENSP00000266692:R2116Q;ENSP00000444918:R145Q	ENSP00000228327:R2293Q	R	+	2	0	NAV3	77122955	1.000000	0.71417	0.588000	0.28705	0.010000	0.07245	9.869000	0.99810	2.532000	0.85374	0.591000	0.81541	CGA		0.507	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383	
DUSP6	1848	broad.mit.edu	37	12	89744697	89744698	+	Frame_Shift_Del	DEL	CC	CC	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	CC	CC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:89744697_89744698delCC	ENST00000279488.7	-	2	1736_1737	c.505_506delGG	c.(505-507)ggcfs	p.G169fs	DUSP6_ENST00000547140.1_5'UTR|DUSP6_ENST00000547291.1_Frame_Shift_Del_p.G44fs|DUSP6_ENST00000308385.6_Intron	NM_001946.2	NP_001937.2	Q16828	DUS6_HUMAN	dual specificity phosphatase 6	169					cell differentiation (GO:0030154)|dorsal/ventral pattern formation (GO:0009953)|inactivation of MAPK activity (GO:0000188)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of apoptotic process (GO:0043065)|regulation of endodermal cell fate specification (GO:0042663)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of heart growth (GO:0060420)|response to drug (GO:0042493)|response to nitrosative stress (GO:0051409)|response to organic cyclic compound (GO:0014070)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)	p.G169fs*6(1)		large_intestine(5)|lung(8)|skin(2)|urinary_tract(1)	16						GATCCGCAGGCCCCCGAGCCCC	0.594																																					p.169_169del	Colon(132;3456 5224)											.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.505_506del	12						.																																			88268829	SO:0001589	frameshift_variant	1848	exon2			BC037236	CCDS9033.1, CCDS9034.1	12q22-q23	2011-06-09				ENSG00000139318		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	3072	protein-coding gene	gene with protein product		602748				8626780, 9205128	Standard	NM_001946		Approved	MKP-3, PYST1	uc001tay.3	Q16828		ENST00000279488.7:c.505_506delGG	12.37:g.89744699_89744700delCC	ENSP00000279488:p.Gly169fs		88268828	NM_001946	O75109|Q53Y75|Q9BSH6	Frame_Shift_Del	DEL	ENST00000279488.7	37	CCDS9033.1																																																																																				0.594	DUSP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406534.2	NM_001946, NM_022652	
FAM71C	196472	broad.mit.edu	37	12	100042176	100042176	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:100042176G>A	ENST00000324341.1	+	1	646	c.224G>A	c.(223-225)cGc>cAc	p.R75H	ANKS1B_ENST00000547010.1_Intron|ANKS1B_ENST00000547776.2_Intron|ANKS1B_ENST00000329257.7_Intron	NM_153364.3	NP_699195.1	Q8NEG0	FA71C_HUMAN	family with sequence similarity 71, member C	75								p.R75H(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				OV - Ovarian serous cystadenocarcinoma(2;0.00733)|Epithelial(2;0.0385)|all cancers(2;0.19)		GGCATCGTTCGCACCAGCCCC	0.537																																					p.R75H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G224A	12						.						119.0	100.0	106.0					12																	100042176		2203	4300	6503	98566307	SO:0001583	missense	196472	exon1				CCDS9072.1	12q23.1	2006-02-03				ENSG00000180219			28594	protein-coding gene	gene with protein product						12477932	Standard	NM_153364		Approved	MGC39520	uc001tgn.3	Q8NEG0		ENST00000324341.1:c.224G>A	12.37:g.100042176G>A	ENSP00000315247:p.Arg75His		98566307	NM_153364	B2R6Y6	Missense_Mutation	SNP	ENST00000324341.1	37	CCDS9072.1	.	.	.	.	.	.	.	.	.	.	G	0.565	-0.843547	0.02671	.	.	ENSG00000180219	ENST00000324341	T	0.10005	2.92	3.94	1.13	0.20643	.	1.096330	0.06984	N	0.820517	T	0.05914	0.0154	N	0.12182	0.205	0.18873	N	0.999981	B	0.11235	0.004	B	0.09377	0.004	T	0.44726	-0.9309	9	.	.	.	-4.6689	5.8961	0.18939	0.3384:0.0:0.6616:0.0	.	75	Q8NEG0	FA71C_HUMAN	H	75	ENSP00000315247:R75H	.	R	+	2	0	FAM71C	98566307	0.000000	0.05858	0.362000	0.25862	0.105000	0.19272	-0.120000	0.10660	0.242000	0.21303	-0.263000	0.10527	CGC		0.537	FAM71C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408458.1	NM_153364	
ANKS1B	56899	broad.mit.edu	37	12	100200457	100200457	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:100200457G>T	ENST00000547776.2	-	4	393	c.394C>A	c.(394-396)Cta>Ata	p.L132I	ANKS1B_ENST00000547010.1_Intron|ANKS1B_ENST00000329257.7_Missense_Mutation_p.L132I	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	132						cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)	p.L132I(1)		NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		GCACAGTGTAGGGCAGTTTCA	0.353																																					p.L132I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C394A	12						.						96.0	91.0	92.0					12																	100200457		1884	4119	6003	98724588	SO:0001583	missense	56899	exon4			AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10						"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	24600	protein-coding gene	gene with protein product		607815				10490826, 12415113	Standard	NM_020140		Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.394C>A	12.37:g.100200457G>T	ENSP00000449629:p.Leu132Ile		98724588	NM_152788	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Missense_Mutation	SNP	ENST00000547776.2	37	CCDS55872.1	.	.	.	.	.	.	.	.	.	.	G	16.93	3.259301	0.59321	.	.	ENSG00000185046	ENST00000547776;ENST00000329257;ENST00000549866	T;T;T	0.77098	-0.51;-0.51;-1.07	5.29	3.43	0.39272	Ankyrin repeat-containing domain (4);	0.000000	0.64402	D	0.000015	D	0.85097	0.5619	M	0.71581	2.175	0.80722	D	1	D;D	0.89917	0.996;1.0	D;D	0.87578	0.994;0.998	D	0.84479	0.0604	9	.	.	.	-5.6448	10.5313	0.44977	0.262:0.0:0.738:0.0	.	132;132	F8VVQ4;Q7Z6G8	.;ANS1B_HUMAN	I	132	ENSP00000449629:L132I;ENSP00000331381:L132I;ENSP00000449894:L132I	.	L	-	1	2	ANKS1B	98724588	0.903000	0.30736	0.423000	0.26634	0.893000	0.52053	1.317000	0.33631	1.213000	0.43380	0.557000	0.71058	CTA		0.353	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140	
MMP17	4326	broad.mit.edu	37	12	132325232	132325232	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr12:132325232G>A	ENST00000360564.1	+	4	639	c.537G>A	c.(535-537)gcG>gcA	p.A179A	MMP17_ENST00000535291.1_Silent_p.A95A	NM_016155.4	NP_057239.4	Q9ULZ9	MMP17_HUMAN	matrix metallopeptidase 17 (membrane-inserted)	179					positive regulation of catalytic activity (GO:0043085)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.A179A(1)		endometrium(1)|large_intestine(3)|lung(1)	5	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.82e-07)|Epithelial(86;1.51e-06)|all cancers(50;2.35e-05)	Marimastat(DB00786)	ACGAGGTGGCGGGCAGCGCCG	0.662																																					p.A179A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G537A	12						.						90.0	79.0	83.0					12																	132325232		2203	4299	6502	130891185	SO:0001819	synonymous_variant	4326	exon4			X89576	CCDS31927.1	12q24.3	2005-08-08	2005-08-08		ENSG00000198598	ENSG00000198598			7163	protein-coding gene	gene with protein product		602285	"""matrix metalloproteinase 17 (membrane-inserted)"""			9878265	Standard	NM_016155		Approved	MT4-MMP	uc001ujc.1	Q9ULZ9	OTTHUMG00000168050	ENST00000360564.1:c.537G>A	12.37:g.132325232G>A			130891185	NM_016155	Q14850	Silent	SNP	ENST00000360564.1	37	CCDS31927.1																																																																																				0.662	MMP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397757.1	NM_016155	
SLC46A3	283537	broad.mit.edu	37	13	29287157	29287158	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr13:29287157_29287158insT	ENST00000266943.6	-	3	1088_1089	c.719_720insA	c.(718-720)aacfs	p.N240fs	SLC46A3_ENST00000380814.4_Frame_Shift_Ins_p.N240fs	NM_001135919.1|NM_181785.3	NP_001129391.1|NP_861450.1	Q7Z3Q1	S46A3_HUMAN	solute carrier family 46, member 3	240					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.N240fs*11(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(2)|prostate(1)|skin(1)	15		Lung SC(185;0.0367)		all cancers(112;0.159)		GGTAAAATAGGTTTTTGAAGCC	0.322																																					p.N240fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.720_721insA	13						.																																			28185158	SO:0001589	frameshift_variant	283537	exon3				CCDS9332.1, CCDS45021.1	13q12.3	2013-05-22	2007-03-29		ENSG00000139508	ENSG00000139508		"""Solute carriers"""	27501	protein-coding gene	gene with protein product							Standard	NM_001135919		Approved	DKFZp686A1775, FLJ42613	uc001usj.3	Q7Z3Q1	OTTHUMG00000016650	ENST00000266943.6:c.720dupA	13.37:g.29287162_29287162dupT	ENSP00000266943:p.Asn240fs		28185157	NM_181785	Q3ZCV8|Q6NUK5|Q6P9B3|Q6ZVG5|Q96QA1	Frame_Shift_Ins	INS	ENST00000266943.6	37	CCDS9332.1																																																																																				0.322	SLC46A3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276111.1	NM_181785	
PCID2	55795	broad.mit.edu	37	13	113833328	113833328	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr13:113833328G>A	ENST00000337344.4	-	13	1138	c.1062C>T	c.(1060-1062)gaC>gaT	p.D354D	PCID2_ENST00000375457.2_Silent_p.D352D|PCID2_ENST00000375479.2_Silent_p.D354D|PCID2_ENST00000375459.1_Silent_p.D352D|PCID2_ENST00000375477.1_Silent_p.D354D|PCID2_ENST00000493650.1_5'UTR|PCID2_ENST00000246505.5_Silent_p.D408D	NM_001127202.2	NP_001120674.1	Q5JVF3	PCID2_HUMAN	PCI domain containing 2	354	PCI.				negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity (GO:2000117)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mRNA stability (GO:0043488)|spleen development (GO:0048536)			p.D408D(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)	20	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_lung(25;0.216)|all_epithelial(44;0.234)	all cancers(43;0.104)			CAATGTCCACGTCCTCCACCT	0.463																																					p.D354D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1062T	13						.						147.0	120.0	129.0					13																	113833328		2203	4300	6503	112881329	SO:0001819	synonymous_variant	55795	exon13			AK002167	CCDS9532.2, CCDS58301.1, CCDS58302.1	13q34	2006-03-31			ENSG00000126226	ENSG00000126226			25653	protein-coding gene	gene with protein product		613713				12477932	Standard	NM_001127203		Approved	FLJ11305	uc031qnm.1	Q5JVF3	OTTHUMG00000017385	ENST00000337344.4:c.1062C>T	13.37:g.113833328G>A			112881329	NM_018386	A6NK09|Q3ZCX1|Q5TC57|Q5TC58|Q9H7K1|Q9HBZ7|Q9NUK6|Q9NVY1|Q9NW44|Q9NWH3	Silent	SNP	ENST00000337344.4	37	CCDS9532.2																																																																																				0.463	PCID2-002	KNOWN	alternative_3_UTR|non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045897.1	NM_018386	
LAMP1	3916	broad.mit.edu	37	13	113975974	113975974	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr13:113975974C>T	ENST00000332556.4	+	8	1240	c.1046C>T	c.(1045-1047)gCg>gTg	p.A349V	LAMP1_ENST00000397181.3_Missense_Mutation_p.A296V	NM_005561.3	NP_005552.3	P11279	LAMP1_HUMAN	lysosomal-associated membrane protein 1	349	Second lumenal domain.				autophagic cell death (GO:0048102)|autophagy (GO:0006914)|establishment of protein localization to organelle (GO:0072594)|Golgi to lysosome transport (GO:0090160)|granzyme-mediated apoptotic signaling pathway (GO:0008626)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|protein stabilization (GO:0050821)|regulation of organelle transport along microtubule (GO:1902513)	alveolar lamellar body (GO:0097208)|cytolytic granule (GO:0044194)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|melanosome (GO:0042470)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|phagolysosome membrane (GO:0061474)|sarcolemma (GO:0042383)	enzyme binding (GO:0019899)	p.A349V(1)		NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(2)|prostate(1)|skin(1)|stomach(2)	16	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.025)|GBM - Glioblastoma multiforme(44;0.206)|Epithelial(84;0.246)			GTCACGAAGGCGTTTTCAGTC	0.582																																					p.A349V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1046T	13						.						106.0	116.0	112.0					13																	113975974		2117	4210	6327	113023975	SO:0001583	missense	3916	exon8			J03263	CCDS41909.1	13q34	2011-11-24			ENSG00000185896	ENSG00000185896		"""CD molecules"""	6499	protein-coding gene	gene with protein product		153330					Standard	NM_005561		Approved	CD107a	uc001vtm.1	P11279	OTTHUMG00000017380	ENST00000332556.4:c.1046C>T	13.37:g.113975974C>T	ENSP00000333298:p.Ala349Val		113023975	NM_005561	B4DWL3|Q8WU33|Q96I40|Q9BRD2|Q9NP13	Missense_Mutation	SNP	ENST00000332556.4	37	CCDS41909.1	.	.	.	.	.	.	.	.	.	.	C	5.500	0.277313	0.10403	.	.	ENSG00000185896	ENST00000332556;ENST00000397181	T;T	0.35605	1.3;1.3	5.27	0.988	0.19796	.	1.144700	0.06218	N	0.686192	T	0.30166	0.0756	L	0.56124	1.755	0.09310	N	1	P;B	0.50369	0.934;0.381	B;B	0.41332	0.354;0.08	T	0.24368	-1.0162	10	0.29301	T	0.29	-18.5131	3.3326	0.07089	0.2853:0.4283:0.2041:0.0823	.	296;349	B4DWL3;P11279	.;LAMP1_HUMAN	V	349;296	ENSP00000333298:A349V;ENSP00000415354:A296V	ENSP00000333298:A349V	A	+	2	0	LAMP1	113023975	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.407000	0.07178	0.579000	0.29504	0.549000	0.68633	GCG		0.582	LAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045876.2		
GPR12	2835	broad.mit.edu	37	13	27333856	27333856	+	Missense_Mutation	SNP	C	C	G	rs369035674		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr13:27333856C>G	ENST00000381436.2	-	1	571	c.109G>C	c.(109-111)Gag>Cag	p.E37Q	GPR12_ENST00000405846.3_Missense_Mutation_p.E37Q			P47775	GPR12_HUMAN	G protein-coupled receptor 12	37					cellular calcium ion homeostasis (GO:0006874)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|phosphatidylcholine binding (GO:0031210)	p.E37Q(1)		endometrium(7)|kidney(2)|large_intestine(6)|lung(14)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33	Colorectal(5;5.77e-05)	Breast(139;0.198)		Epithelial(112;9.37e-07)|OV - Ovarian serous cystadenocarcinoma(117;1.16e-06)|all cancers(112;8.31e-06)|GBM - Glioblastoma multiforme(144;0.00121)|Lung(94;0.111)|LUSC - Lung squamous cell carcinoma(192;0.184)		GGCTCTGGCTCTACGGCAGGA	0.542																																					p.E37Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G109C	13						.	C	GLN/GLU	0,4406		0,0,2203	73.0	76.0	75.0		109	0.3	0.0	13		75	1,8599	1.2+/-3.3	0,1,4299	no	missense	GPR12	NM_005288.3	29	0,1,6502	GG,GC,CC		0.0116,0.0,0.0077	benign	37/335	27333856	1,13005	2203	4300	6503	26231856	SO:0001583	missense	2835	exon2			U18548	CCDS9319.1	13q12	2014-06-12			ENSG00000132975	ENSG00000132975		"""GPCR / Class A : Orphans"""	4466	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 84"""	600752				8262253, 8530049	Standard	NM_005288		Approved	GPCR21, PPP1R84	uc010aal.3	P47775	OTTHUMG00000016620	ENST00000381436.2:c.109G>C	13.37:g.27333856C>G	ENSP00000370844:p.Glu37Gln		26231856	NM_005288	Q5T8P3	Missense_Mutation	SNP	ENST00000381436.2	37	CCDS9319.1	.	.	.	.	.	.	.	.	.	.	C	0.794	-0.757872	0.03019	0.0	1.16E-4	ENSG00000132975	ENST00000405846;ENST00000381436	T;T	0.37058	1.22;1.22	5.23	0.334	0.15948	.	2.343680	0.01580	N	0.021029	T	0.31544	0.0800	L	0.36672	1.1	0.09310	N	0.999996	B	0.02656	0.0	B	0.01281	0.0	T	0.19451	-1.0305	10	0.33940	T	0.23	.	8.9387	0.35715	0.0:0.6141:0.2007:0.1852	.	37	P47775	GPR12_HUMAN	Q	37	ENSP00000384932:E37Q;ENSP00000370844:E37Q	ENSP00000370844:E37Q	E	-	1	0	GPR12	26231856	0.537000	0.26386	0.005000	0.12908	0.039000	0.13416	1.133000	0.31430	-0.570000	0.06022	-1.598000	0.00824	GAG		0.542	GPR12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044257.2		
FLT1	2321	broad.mit.edu	37	13	29008278	29008278	+	Missense_Mutation	SNP	G	G	A	rs201044311		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr13:29008278G>A	ENST00000282397.4	-	5	844	c.593C>T	c.(592-594)aCg>aTg	p.T198M	FLT1_ENST00000541932.1_Missense_Mutation_p.T198M|FLT1_ENST00000539099.1_Missense_Mutation_p.T198M	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	198	Ig-like C2-type 2.				blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)	p.T198M(1)		NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TTCTTTGTACGTTGCATTTGA	0.408													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18661	0.0		0.0	False		,,,				2504	0.0				p.T198M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C593T	13						.						182.0	146.0	158.0					13																	29008278		2203	4300	6503	27906278	SO:0001583	missense	2321	exon5			AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3763	protein-coding gene	gene with protein product	"""vascular endothelial growth factor receptor 1"", ""vascular permeability factor receptor"""	165070	"""fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"""	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.593C>T	13.37:g.29008278G>A	ENSP00000282397:p.Thr198Met		27906278	NM_002019	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Missense_Mutation	SNP	ENST00000282397.4	37	CCDS9330.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	15.90	2.968284	0.53614	.	.	ENSG00000102755	ENST00000282397;ENST00000541932;ENST00000539099	T;T;T	0.15603	2.41;2.41;2.41	5.78	4.9	0.64082	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.237802	0.41605	D	0.000855	T	0.35248	0.0925	L	0.55103	1.725	0.53688	D	0.999978	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.996;0.996;0.996;0.989	T	0.01375	-1.1371	10	0.18710	T	0.47	.	16.2754	0.82642	0.0:0.0:0.8671:0.1329	.	198;198;198;198	P17948-4;P17948-3;P17948-2;P17948	.;.;.;VGFR1_HUMAN	M	198	ENSP00000282397:T198M;ENSP00000437631:T198M;ENSP00000442630:T198M	ENSP00000282397:T198M	T	-	2	0	FLT1	27906278	1.000000	0.71417	0.121000	0.21740	0.357000	0.29423	6.808000	0.75206	2.742000	0.94016	0.650000	0.86243	ACG		0.408	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1		
FRY	10129	broad.mit.edu	37	13	32776571	32776571	+	Missense_Mutation	SNP	G	G	A	rs200315543		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr13:32776571G>A	ENST00000380250.3	+	31	4421	c.3925G>A	c.(3925-3927)Ggc>Agc	p.G1309S		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	1309						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G1309S(1)		NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		TGGAACACACGGCCCGCTGCC	0.498																																					p.G1309S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3925A	13						.						87.0	88.0	87.0					13																	32776571		1974	4150	6124	31674571	SO:0001583	missense	10129	exon31			AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"""chromosome 13 open reading frame 14"""	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.3925G>A	13.37:g.32776571G>A	ENSP00000369600:p.Gly1309Ser		31674571	NM_023037	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	37	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	G	1.744	-0.491060	0.04322	.	.	ENSG00000073910	ENST00000380250;ENST00000380257	T	0.20738	2.05	5.39	4.54	0.55810	.	0.000000	0.85682	D	0.000000	T	0.10465	0.0256	N	0.12569	0.235	0.80722	D	1	B	0.28378	0.209	B	0.28784	0.094	T	0.06110	-1.0845	10	0.02654	T	1	.	13.5025	0.61465	0.075:0.0:0.925:0.0	.	1309	Q5TBA9	FRY_HUMAN	S	1309;148	ENSP00000369600:G1309S	ENSP00000369600:G1309S	G	+	1	0	FRY	31674571	1.000000	0.71417	0.839000	0.33178	0.011000	0.07611	4.366000	0.59492	2.548000	0.85928	0.455000	0.32223	GGC		0.498	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037	
STARD13	90627	broad.mit.edu	37	13	33703571	33703571	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr13:33703571G>T	ENST00000336934.5	-	5	1359	c.1243C>A	c.(1243-1245)Ctc>Atc	p.L415I	STARD13_ENST00000399365.3_Missense_Mutation_p.L297I|STARD13_ENST00000255486.4_Missense_Mutation_p.L407I	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	415					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)	p.L415I(1)		breast(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	40	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		GTGGGAGAGAGGCTTTCAATA	0.527																																					p.L415I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1243A	13						.						42.0	45.0	44.0					13																	33703571		2203	4300	6503	32601571	SO:0001583	missense	90627	exon5			AL049801	CCDS9348.1, CCDS9349.1, CCDS9350.1	13q13.1	2013-08-13	2007-08-16		ENSG00000133121	ENSG00000133121		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	19164	protein-coding gene	gene with protein product		609866	"""START domain containing 13"", ""long intergenic non-protein coding RNA 464"""	LINC00464		8812419	Standard	NM_178006		Approved	GT650, DLC2, ARHGAP37	uc001uuw.3	Q9Y3M8	OTTHUMG00000016708	ENST00000336934.5:c.1243C>A	13.37:g.33703571G>T	ENSP00000338785:p.Leu415Ile		32601571	NM_178006	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Missense_Mutation	SNP	ENST00000336934.5	37	CCDS9348.1	.	.	.	.	.	.	.	.	.	.	G	17.98	3.521393	0.64747	.	.	ENSG00000133121	ENST00000399365;ENST00000255486;ENST00000336934;ENST00000399364	T;T;T	0.09630	2.96;2.98;2.98	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.39200	0.1069	M	0.83223	2.63	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;0.998;0.991	D;D;D;D	0.97110	1.0;0.976;0.946;0.931	T	0.12477	-1.0546	10	0.45353	T	0.12	.	19.5851	0.95487	0.0:0.0:1.0:0.0	.	407;380;415;407	Q9Y3M8-5;Q9Y3M8-4;Q9Y3M8;Q9Y3M8-2	.;.;STA13_HUMAN;.	I	297;407;415;407	ENSP00000382300:L297I;ENSP00000255486:L407I;ENSP00000338785:L415I	ENSP00000255486:L407I	L	-	1	0	STARD13	32601571	1.000000	0.71417	0.997000	0.53966	0.912000	0.54170	5.384000	0.66225	2.632000	0.89209	0.561000	0.74099	CTC		0.527	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466	
TRPC4	7223	broad.mit.edu	37	13	38211583	38211583	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr13:38211583delA	ENST00000379705.3	-	11	3248	c.2391delT	c.(2389-2391)tttfs	p.F797fs	TRPC4_ENST00000379679.1_Frame_Shift_Del_p.F624fs|TRPC4_ENST00000426868.2_Intron|TRPC4_ENST00000358477.2_Intron|TRPC4_ENST00000447043.1_Intron|TRPC4_ENST00000379673.2_Intron|TRPC4_ENST00000338947.5_Frame_Shift_Del_p.F624fs|TRPC4_ENST00000379681.3_Frame_Shift_Del_p.F802fs|TRPC4_ENST00000355779.2_Intron			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	797	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.F797fs*3(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)		TGGTTAAATCAAAAAGGCTGA	0.468																																					p.F797fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2391delT	13						.						84.0	82.0	83.0					13																	38211583		2203	4300	6503	37109583	SO:0001589	frameshift_variant	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.2391delT	13.37:g.38211583delA	ENSP00000369027:p.Phe797fs		37109583	NM_016179	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Frame_Shift_Del	DEL	ENST00000379705.3	37	CCDS9365.1																																																																																				0.468	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306	
SERP2	387923	broad.mit.edu	37	13	44953812	44953812	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr13:44953812G>C	ENST00000379179.3	+	2	304	c.120G>C	c.(118-120)tgG>tgC	p.W40C		NM_001010897.1	NP_001010897.1	Q8N6R1	SERP2_HUMAN	stress-associated endoplasmic reticulum protein family member 2	40					protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.W40C(1)		large_intestine(1)	1		all_hematologic(4;1.49e-06)|Acute lymphoblastic leukemia(4;1.5e-06)|Lung NSC(96;0.00043)|Breast(139;0.0044)|Prostate(109;0.0137)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)		GBM - Glioblastoma multiforme(144;0.00026)|BRCA - Breast invasive adenocarcinoma(63;0.123)		TGGGACCATGGCTGTTGGCAC	0.408																																					p.W40C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G120C	13						.						298.0	253.0	268.0					13																	44953812		2203	4300	6503	43851812	SO:0001583	missense	387923	exon2			BC029067	CCDS31965.1	13q14.11	2008-02-05	2007-12-07	2007-12-07	ENSG00000151778	ENSG00000151778			20607	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 21"""	C13orf21			Standard	NM_001010897		Approved	bA269C23.1	uc001uzj.3	Q8N6R1	OTTHUMG00000016833	ENST00000379179.3:c.120G>C	13.37:g.44953812G>C	ENSP00000368477:p.Trp40Cys		43851812	NM_001010897		Missense_Mutation	SNP	ENST00000379179.3	37	CCDS31965.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.757643	0.49468	.	.	ENSG00000151778	ENST00000379179	.	.	.	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.56337	0.1978	.	.	.	0.80722	D	1	B	0.18863	0.031	B	0.23852	0.049	T	0.50524	-0.8818	8	0.38643	T	0.18	.	16.7844	0.85570	0.0:0.0:1.0:0.0	.	40	Q8N6R1	SERP2_HUMAN	C	40	.	ENSP00000368477:W40C	W	+	3	0	SERP2	43851812	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.176000	0.89686	2.819000	0.97034	0.585000	0.79938	TGG		0.408	SERP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044736.1	NM_001010897	
GTF2F2	2963	broad.mit.edu	37	13	45694853	45694853	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr13:45694853C>T	ENST00000340473.6	+	1	204	c.63C>T	c.(61-63)gtC>gtT	p.V21V	7SK_ENST00000606815.1_RNA	NM_004128.2	NP_004119.1	P13984	T2FB_HUMAN	general transcription factor IIF, polypeptide 2, 30kDa	21					7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIIF complex (GO:0005674)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)	p.V21V(1)		breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|prostate(1)|upper_aerodigestive_tract(1)	10		Lung NSC(96;0.00115)|Prostate(109;0.00578)|Breast(139;0.0192)|Lung SC(185;0.0367)|Hepatocellular(98;0.133)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000647)		TGTGGCTAGTCAAGGTAATGT	0.567																																					p.V21V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C63T	13						.						28.0	22.0	24.0					13																	45694853		2162	4206	6368	44592853	SO:0001819	synonymous_variant	2963	exon1			X16901	CCDS9395.1	13q14	2012-01-23	2002-08-29		ENSG00000188342	ENSG00000188342		"""General transcription factors"""	4653	protein-coding gene	gene with protein product		189969	"""general transcription factor IIF, polypeptide 1 (74kD subunit)"""			8162052	Standard	NM_004128		Approved	TFIIF, BTF4, RAP30	uc001uzw.3	P13984	OTTHUMG00000016849	ENST00000340473.6:c.63C>T	13.37:g.45694853C>T			44592853	NM_004128	A6NNS5|Q5W0H3	Silent	SNP	ENST00000340473.6	37	CCDS9395.1																																																																																				0.567	GTF2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044767.2	NM_004128	
COG3	83548	broad.mit.edu	37	13	46065663	46065663	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr13:46065663A>G	ENST00000349995.5	+	10	1197	c.1085A>G	c.(1084-1086)cAc>cGc	p.H362R	COG3_ENST00000465942.1_3'UTR	NM_031431.3	NP_113619	Q96JB2	COG3_HUMAN	component of oligomeric golgi complex 3	362					ER to Golgi vesicle-mediated transport (GO:0006888)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)	p.H362R(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|stomach(1)	24		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)		AATAGAGATCACTGTGCCTTG	0.383																																					p.H362R	Ovarian(150;1048 1859 18083 21577 42700)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1085G	13						.						128.0	127.0	127.0					13																	46065663		2203	4300	6503	44963664	SO:0001583	missense	83548	exon10			AF131829	CCDS9398.1	13q14.11	2008-02-05			ENSG00000136152	ENSG00000136152		"""Components of oligomeric golgi complex"""	18619	protein-coding gene	gene with protein product		606975				11980916	Standard	NM_031431		Approved	SEC34	uc001vak.3	Q96JB2	OTTHUMG00000016855	ENST00000349995.5:c.1085A>G	13.37:g.46065663A>G	ENSP00000258654:p.His362Arg		44963664	NM_031431	B2RAW5|Q5VT70|Q8IXX4|Q9BZ92	Missense_Mutation	SNP	ENST00000349995.5	37	CCDS9398.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.287009	0.80803	.	.	ENSG00000136152	ENST00000349995	T	0.46063	0.88	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.60753	0.2293	M	0.78049	2.395	0.80722	D	1	D;D;P	0.71674	0.995;0.998;0.939	P;P;P	0.60682	0.854;0.878;0.62	T	0.59726	-0.7400	10	0.24483	T	0.36	-15.5372	15.0854	0.72148	1.0:0.0:0.0:0.0	.	199;362;362	B4E2F3;Q96JB2;Q96JB2-2	.;COG3_HUMAN;.	R	362	ENSP00000258654:H362R	ENSP00000258654:H362R	H	+	2	0	COG3	44963664	1.000000	0.71417	0.997000	0.53966	0.930000	0.56654	9.012000	0.93624	2.160000	0.67779	0.528000	0.53228	CAC		0.383	COG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044777.2		
FNDC3A	22862	broad.mit.edu	37	13	49719939	49719939	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr13:49719939T>C	ENST00000492622.2	+	8	1150	c.845T>C	c.(844-846)gTa>gCa	p.V282A	FNDC3A_ENST00000398316.3_Missense_Mutation_p.V226A|FNDC3A_ENST00000541916.1_Missense_Mutation_p.V282A	NM_001079673.1	NP_001073141.1	Q9Y2H6	FND3A_HUMAN	fibronectin type III domain containing 3A	282	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				fertilization (GO:0009566)|Sertoli cell development (GO:0060009)|single organismal cell-cell adhesion (GO:0016337)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	poly(A) RNA binding (GO:0044822)	p.V282A(1)		endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|prostate(5)|skin(2)|urinary_tract(1)	41		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)		GCAAGGACAGTAGTACTTACC	0.383																																					p.V282A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T845C	13						.						109.0	102.0	105.0					13																	49719939		2203	4300	6503	48617940	SO:0001583	missense	22862	exon8			AB023187	CCDS9413.2, CCDS41886.1	13q14.12	2013-02-11	2005-01-20	2005-01-22	ENSG00000102531	ENSG00000102531		"""Fibronectin type III domain containing"""	20296	protein-coding gene	gene with protein product		615794	"""fibronectin type III domain containing 3"""	FNDC3			Standard	NM_001079673		Approved	bA203I16.5, KIAA0970	uc001vcm.3	Q9Y2H6	OTTHUMG00000016911	ENST00000492622.2:c.845T>C	13.37:g.49719939T>C	ENSP00000417257:p.Val282Ala		48617940	NM_001079673	B4DYG1|Q5HYC9|Q5JVF8|Q5JVF9|Q6EVH3|Q6EVH4|Q6N020|Q6P9D5|Q6ZME4|Q9H1W1	Missense_Mutation	SNP	ENST00000492622.2	37	CCDS41886.1	.	.	.	.	.	.	.	.	.	.	T	4.982	0.182457	0.09495	.	.	ENSG00000102531	ENST00000492622;ENST00000337156;ENST00000541916;ENST00000398316	T;T;T	0.47177	0.85;0.85;0.85	5.4	5.4	0.78164	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.104292	0.40640	N	0.001059	T	0.24392	0.0591	N	0.05050	-0.12	0.40797	D	0.983306	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.13407	0.002;0.005;0.009	T	0.15752	-1.0426	10	0.18276	T	0.48	-18.8441	9.3328	0.38032	0.0:0.0889:0.0:0.9111	.	226;282;282	Q9Y2H6-2;G5E9X3;Q9Y2H6	.;.;FND3A_HUMAN	A	282;218;282;226	ENSP00000417257:V282A;ENSP00000441831:V282A;ENSP00000381362:V226A	ENSP00000338579:V218A	V	+	2	0	FNDC3A	48617940	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	2.308000	0.43690	2.170000	0.68504	0.482000	0.46254	GTA		0.383	FNDC3A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354845.2	NM_014923	
RCBTB1	55213	broad.mit.edu	37	13	50134143	50134143	+	Missense_Mutation	SNP	C	C	T	rs374135653		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr13:50134143C>T	ENST00000378302.2	-	5	615	c.355G>A	c.(355-357)Gtc>Atc	p.V119I	RCBTB1_ENST00000546015.1_Missense_Mutation_p.V119I|RCBTB1_ENST00000258646.3_Missense_Mutation_p.V119I	NM_018191.3	NP_060661.3	Q8NDN9	RCBT1_HUMAN	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 1	119					cell cycle (GO:0007049)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.V119I(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|urinary_tract(1)	16		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;4.7e-09)		CAGACCTGGACGGGAGCAATG	0.502																																					p.V119I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G355A	13						.						226.0	218.0	221.0					13																	50134143		2203	4300	6503	49032144	SO:0001583	missense	55213	exon5			AF334406	CCDS9418.1	13q14	2013-01-08			ENSG00000136144	ENSG00000136144		"""BTB/POZ domain containing"""	18243	protein-coding gene	gene with protein product		607867				11306461	Standard	XM_005266441		Approved	FLJ10716, CLLD7, CLLL7	uc001vde.1	Q8NDN9	OTTHUMG00000016915	ENST00000378302.2:c.355G>A	13.37:g.50134143C>T	ENSP00000367552:p.Val119Ile		49032144	NM_018191	Q8IY29|Q969U9	Missense_Mutation	SNP	ENST00000378302.2	37	CCDS9418.1	.	.	.	.	.	.	.	.	.	.	c	3.660	-0.069738	0.07228	.	.	ENSG00000136144	ENST00000258646;ENST00000378302;ENST00000546015	D;D;D	0.86097	-2.07;-2.07;-2.07	5.08	1.05	0.20165	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.291582	0.38959	N	0.001505	T	0.74336	0.3703	L	0.35854	1.095	0.25564	N	0.986962	B	0.09022	0.002	B	0.06405	0.002	T	0.56408	-0.7984	10	0.20046	T	0.44	-5.199	9.4803	0.38898	0.0:0.393:0.0:0.607	.	119	Q8NDN9	RCBT1_HUMAN	I	119	ENSP00000258646:V119I;ENSP00000367552:V119I;ENSP00000443293:V119I	ENSP00000258646:V119I	V	-	1	0	RCBTB1	49032144	0.090000	0.21635	0.998000	0.56505	0.896000	0.52359	0.327000	0.19663	-0.039000	0.13602	-0.415000	0.06103	GTC		0.502	RCBTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044912.2	NM_018191	
NEK5	341676	broad.mit.edu	37	13	52639571	52639571	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr13:52639571G>A	ENST00000355568.4	-	22	2238	c.2099C>T	c.(2098-2100)cCg>cTg	p.P700L		NM_199289.1	NP_954983.1	Q6P3R8	NEK5_HUMAN	NIMA-related kinase 5	700					positive regulation of cysteine-type endopeptidase activity (GO:2001056)|positive regulation of striated muscle cell differentiation (GO:0051155)		ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.P700L(1)		breast(5)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(11)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	39		Breast(56;0.00173)|Lung NSC(96;0.0168)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;3.7e-08)		TGGGCTGTACGGGTCCTTGGT	0.502																																					p.P700L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2099T	13						.						203.0	161.0	175.0					13																	52639571		2203	4300	6503	51537572	SO:0001583	missense	341676	exon22			BC063885	CCDS31979.1	13q14.2	2012-11-15	2012-11-15		ENSG00000197168	ENSG00000197168			7748	protein-coding gene	gene with protein product			"""NIMA (never in mitosis gene a)-related kinase 5"""			9552363	Standard	XM_006719807		Approved		uc001vge.3	Q6P3R8	OTTHUMG00000016957	ENST00000355568.4:c.2099C>T	13.37:g.52639571G>A	ENSP00000347767:p.Pro700Leu		51537572	NM_199289	Q5TAP5	Missense_Mutation	SNP	ENST00000355568.4	37	CCDS31979.1	.	.	.	.	.	.	.	.	.	.	G	10.74	1.435240	0.25813	.	.	ENSG00000197168	ENST00000355568	T	0.74002	-0.8	3.83	2.03	0.26663	.	0.251154	0.27966	N	0.017131	T	0.62660	0.2446	M	0.61703	1.905	0.09310	N	1	B	0.15473	0.013	B	0.10450	0.005	T	0.42050	-0.9474	10	0.11182	T	0.66	.	5.0338	0.14423	0.1203:0.2285:0.6512:0.0	.	700	Q6P3R8	NEK5_HUMAN	L	700	ENSP00000347767:P700L	ENSP00000347767:P700L	P	-	2	0	NEK5	51537572	0.000000	0.05858	0.001000	0.08648	0.070000	0.16714	0.303000	0.19210	0.553000	0.29044	0.563000	0.77884	CCG		0.502	NEK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045045.3	NM_199289	
DIAPH3	81624	broad.mit.edu	37	13	60435635	60435635	+	Silent	SNP	C	C	T	rs201539656		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr13:60435635C>T	ENST00000400324.4	-	22	2863	c.2643G>A	c.(2641-2643)acG>acA	p.T881T	DIAPH3_ENST00000400320.1_Silent_p.T835T|DIAPH3_ENST00000377908.2_Silent_p.T870T|DIAPH3_ENST00000400319.1_Silent_p.T811T|DIAPH3_ENST00000400330.1_Silent_p.T881T|DIAPH3_ENST00000465066.1_5'UTR|DIAPH3_ENST00000267215.4_Silent_p.T881T	NM_001042517.1|NM_001258366.1	NP_001035982.1|NP_001245295.1	Q9NSV4	DIAP3_HUMAN	diaphanous-related formin 3	881	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.T881T(1)		cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|liver(1)|lung(20)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		AATGAAGTAGCGTTGTTTTCT	0.348																																					p.T618T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1854A	13						.	C	,	1,3661		0,1,1830	151.0	137.0	141.0		2643,1854	-5.5	0.6	13		141	0,8158		0,0,4079	no	coding-synonymous,coding-synonymous	DIAPH3	NM_001042517.1,NM_030932.3	,	0,1,5909	TT,TC,CC		0.0,0.0273,0.0085	,	881/1194,618/850	60435635	1,11819	1831	4079	5910	59333636	SO:0001819	synonymous_variant	81624	exon16			AL137718	CCDS41898.1, CCDS58294.1, CCDS58295.1, CCDS58296.1, CCDS58297.1, CCDS73579.1, CCDS73580.1	13q21.2	2013-05-24	2013-05-24		ENSG00000139734	ENSG00000139734			15480	protein-coding gene	gene with protein product		614567	"""diaphanous (Drosophila, homolog) 3"", ""auditory neuropathy, autosomal dominant 1"", ""diaphanous homolog 3 (Drosophila)"""	AUNA1		14767582, 20624953	Standard	NM_030932		Approved	DRF3, FLJ34705, AN, NSDAN	uc001vht.4	Q9NSV4	OTTHUMG00000017004	ENST00000400324.4:c.2643G>A	13.37:g.60435635C>T			59333636	NM_030932	A2A3B8|A2A3B9|A2A3C0|Q18P99|Q18PA0|Q18PA1|Q2KPB6|Q3ZK23|Q5JTP8|Q5T2S7|Q5XKF6|Q6MZF0|Q6NUP0|Q86VS4|Q8NAV4	Silent	SNP	ENST00000400324.4	37	CCDS41898.1																																																																																				0.348	DIAPH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045166.3	NM_001042517	
SLITRK1	114798	broad.mit.edu	37	13	84455253	84455253	+	Silent	SNP	G	G	A	rs370805552		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr13:84455253G>A	ENST00000377084.2	-	1	1275	c.390C>T	c.(388-390)gaC>gaT	p.D130D		NM_001281503.1|NM_052910.1	NP_001268432.1|NP_443142.1	Q96PX8	SLIK1_HUMAN	SLIT and NTRK-like family, member 1	130					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|homeostatic process (GO:0042592)|multicellular organism growth (GO:0035264)	integral component of membrane (GO:0016021)		p.D130D(2)		NS(2)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(36)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	80	Medulloblastoma(90;0.18)	Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.07)		ATTCCAGATCGTCCAGCCCCA	0.473																																					p.D130D												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C390T	13						.	G		1,4405	2.1+/-5.4	0,1,2202	63.0	68.0	67.0		390	3.6	1.0	13		67	0,8600		0,0,4300	no	coding-synonymous	SLITRK1	NM_052910.1		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		130/697	84455253	1,13005	2203	4300	6503	83353254	SO:0001819	synonymous_variant	114798	exon1			AB067497	CCDS9464.1	13q31.1	2004-01-08	2004-01-08		ENSG00000178235	ENSG00000178235			20297	protein-coding gene	gene with protein product		609678	"""leucine rich repeat containing 12"""	LRRC12		14557068, 12975309	Standard	NM_001281503		Approved	KIAA1910	uc001vlk.3	Q96PX8	OTTHUMG00000017149	ENST00000377084.2:c.390C>T	13.37:g.84455253G>A			83353254	NM_052910	Q5U5I6|Q96SF9	Silent	SNP	ENST00000377084.2	37	CCDS9464.1																																																																																				0.473	SLITRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045396.1	NM_052910	
GPC6	10082	broad.mit.edu	37	13	95034788	95034788	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr13:95034788G>A	ENST00000377047.4	+	7	1888	c.1273G>A	c.(1273-1275)Ggg>Agg	p.G425R		NM_005708.3	NP_005699.1	Q9Y625	GPC6_HUMAN	glypican 6	425					carbohydrate metabolic process (GO:0005975)|cell migration (GO:0016477)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.G425R(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	38	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				ATGCTGGAACGGGCACAGCAA	0.552																																					p.G425R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1273A	13						.						129.0	119.0	122.0					13																	95034788		2203	4300	6503	93832789	SO:0001583	missense	10082	exon7			AF111178	CCDS9469.1	13q32	2008-02-05			ENSG00000183098	ENSG00000183098		"""Proteoglycans / Cell Surface : Glypicans"""	4454	protein-coding gene	gene with protein product	"""glypican proteoglycan 6"""	604404				10329016	Standard	NM_005708		Approved		uc001vlt.3	Q9Y625	OTTHUMG00000017205	ENST00000377047.4:c.1273G>A	13.37:g.95034788G>A	ENSP00000366246:p.Gly425Arg		93832789	NM_005708	A8K279|Q96SG5|Q96SG8|Q9H1P4	Missense_Mutation	SNP	ENST00000377047.4	37	CCDS9469.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.883261	0.91740	.	.	ENSG00000183098	ENST00000377047	D	0.81908	-1.55	5.74	5.74	0.90152	.	0.051766	0.85682	D	0.000000	D	0.93109	0.7806	M	0.92026	3.265	0.50813	D	0.999895	D	0.89917	1.0	D	0.79108	0.992	D	0.94118	0.7377	10	0.87932	D	0	.	18.0853	0.89455	0.0:0.0:1.0:0.0	.	425	Q9Y625	GPC6_HUMAN	R	425	ENSP00000366246:G425R	ENSP00000366246:G425R	G	+	1	0	GPC6	93832789	1.000000	0.71417	0.990000	0.47175	0.960000	0.62799	7.996000	0.88334	2.708000	0.92522	0.650000	0.86243	GGG		0.552	GPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045460.4	NM_005708	
SOX21	11166	broad.mit.edu	37	13	95364138	95364138	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr13:95364138G>A	ENST00000376945.2	-	1	251	c.166C>T	c.(166-168)Ccg>Tcg	p.P56S	SOX21-AS1_ENST00000438290.2_lincRNA	NM_007084.2	NP_009015.1	Q9Y651	SOX21_HUMAN	SRY (sex determining region Y)-box 21	56					hair follicle development (GO:0001942)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P56S(1)		large_intestine(3)|lung(1)|prostate(1)|skin(1)	6	all_neural(89;0.0646)|Medulloblastoma(90;0.163)					TCGATGAACGGCCGCTTCTCC	0.622																																					p.P56S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C166T	13						.						97.0	93.0	94.0					13																	95364138		2203	4300	6503	94162139	SO:0001583	missense	11166	exon1			AF107044	CCDS9473.1	13q31-q32	2008-07-18			ENSG00000125285	ENSG00000125285		"""SRY (sex determining region Y)-boxes"""	11197	protein-coding gene	gene with protein product	"""SRY-box 21"""	604974				10441749	Standard	NM_007084		Approved	SOX25	uc001vma.3	Q9Y651	OTTHUMG00000017209	ENST00000376945.2:c.166C>T	13.37:g.95364138G>A	ENSP00000366144:p.Pro56Ser		94162139	NM_007084	P35715|Q15504|Q5TBS1	Missense_Mutation	SNP	ENST00000376945.2	37	CCDS9473.1	.	.	.	.	.	.	.	.	.	.	G	15.55	2.865592	0.51588	.	.	ENSG00000125285	ENST00000376945	D	0.98313	-4.86	3.17	3.17	0.36434	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.000000	0.64402	U	0.000001	D	0.99115	0.9695	M	0.93638	3.44	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.99260	1.0890	10	0.87932	D	0	.	14.2526	0.66031	0.0:0.0:1.0:0.0	.	56	Q9Y651	SOX21_HUMAN	S	56	ENSP00000366144:P56S	ENSP00000366144:P56S	P	-	1	0	SOX21	94162139	1.000000	0.71417	1.000000	0.80357	0.070000	0.16714	9.119000	0.94362	1.459000	0.47892	0.491000	0.48974	CCG		0.622	SOX21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045467.4	NM_007084	
FARP1	10160	broad.mit.edu	37	13	99020449	99020449	+	Splice_Site	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr13:99020449G>T	ENST00000319562.6	+	5	663	c.398G>T	c.(397-399)aGg>aTg	p.R133M	FARP1_ENST00000376586.2_Splice_Site_p.R133M|FARP1_ENST00000595437.1_Splice_Site_p.R133M	NM_005766.2	NP_005757.1	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)	133	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				dendrite morphogenesis (GO:0048813)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|synapse assembly (GO:0007416)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|synapse (GO:0045202)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R133M(3)		breast(3)|endometrium(6)|kidney(6)|large_intestine(13)|lung(16)|ovary(1)|skin(3)|urinary_tract(1)	49	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			GAACTCACAAGGTTAGTGGTT	0.358																																					p.R133M												.	.	3	Substitution - Missense(3)	endometrium(2)|large_intestine(1)	c.G398T	13						.						103.0	92.0	96.0					13																	99020449		2203	4300	6503	97818450	SO:0001630	splice_region_variant	10160	exon5			AB008430	CCDS9487.1, CCDS32000.1, CCDS66572.1	13q32.2	2013-01-10			ENSG00000152767	ENSG00000152767		"""Rho guanine nucleotide exchange factors"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Pleckstrin homology (PH) domain containing"""	3591	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 75"""	602654				9425278	Standard	NM_005766		Approved	CDEP, PLEKHC2, MGC87400, PPP1R75	uc001vnj.3	Q9Y4F1	OTTHUMG00000017248	ENST00000319562.6:c.398+1G>T	13.37:g.99020449G>T			97818450	NM_005766	Q5JVI9|Q6IQ29	Missense_Mutation	SNP	ENST00000319562.6	37	CCDS9487.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.383202	0.82792	.	.	ENSG00000152767	ENST00000376586;ENST00000319562	T;T	0.79749	-1.3;-1.3	5.91	5.91	0.95273	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.000000	0.85682	D	0.000000	D	0.93236	0.7845	H	0.95151	3.63	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.94526	0.7731	10	0.87932	D	0	.	19.07	0.93130	0.0:0.0:1.0:0.0	.	133;133	Q9Y4F1;C9JME2	FARP1_HUMAN;.	M	133	ENSP00000365771:R133M;ENSP00000322926:R133M	ENSP00000322926:R133M	R	+	2	0	FARP1	97818450	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.465000	0.73538	2.793000	0.96121	0.655000	0.94253	AGG		0.358	FARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045541.3	NM_005766	Missense_Mutation
UBAC2	337867	broad.mit.edu	37	13	100020095	100020095	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr13:100020095G>A	ENST00000403766.3	+	8	997	c.862G>A	c.(862-864)Gta>Ata	p.V288I	UBAC2_ENST00000376440.2_Missense_Mutation_p.V253I|UBAC2_ENST00000460562.1_3'UTR	NM_001144072.1	NP_001137544.1	Q8NBM4	UBAC2_HUMAN	UBA domain containing 2	288					protein localization to endoplasmic reticulum (GO:0070972)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.V253I(1)		breast(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)	10	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					GCGACAAAACGTAAACTATCA	0.443																																					p.V288I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G862A	13						.						106.0	99.0	101.0					13																	100020095		2203	4300	6503	98818096	SO:0001583	missense	337867	exon8			AK055110	CCDS9490.1, CCDS45064.1	13q32.3	2012-02-01	2007-04-20	2007-04-20	ENSG00000134882	ENSG00000134882			20486	protein-coding gene	gene with protein product			"""phosphoglycerate dehydrogenase like 1"""	PHGDHL1			Standard	NM_177967		Approved	FLJ30548, RP11-178C10.1	uc001voa.4	Q8NBM4	OTTHUMG00000017267	ENST00000403766.3:c.862G>A	13.37:g.100020095G>A	ENSP00000383911:p.Val288Ile		98818096	NM_001144072	B3KNV7|Q0VAB5|Q5W0W6|Q5W0W9|Q6GQR2|Q6P4B0|Q8N2E8|Q96NW2	Missense_Mutation	SNP	ENST00000403766.3	37	CCDS45064.1	.	.	.	.	.	.	.	.	.	.	G	0.749	-0.773579	0.02951	.	.	ENSG00000134882	ENST00000403766;ENST00000355700;ENST00000376440	.	.	.	5.43	-4.56	0.03431	UBA-like (1);	0.991212	0.08211	N	0.980669	T	0.17619	0.0423	N	0.03115	-0.41	0.09310	N	1	B;B;B;B	0.18013	0.0;0.025;0.0;0.0	B;B;B;B	0.09377	0.0;0.004;0.0;0.0	T	0.32134	-0.9918	8	.	.	.	-1.6505	12.3455	0.55118	0.4107:0.0:0.5893:0.0	.	218;253;288;288	B7Z6T7;Q8NBM4-2;A8K2S7;Q8NBM4	.;.;.;UBAC2_HUMAN	I	288;154;253	.	.	V	+	1	0	UBAC2	98818096	0.017000	0.18338	0.011000	0.14972	0.045000	0.14185	0.016000	0.13377	-0.795000	0.04462	-2.227000	0.00293	GTA		0.443	UBAC2-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045588.1	NM_177967	
TMCO3	55002	broad.mit.edu	37	13	114174959	114174959	+	Silent	SNP	C	C	T	rs139542574		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr13:114174959C>T	ENST00000434316.2	+	8	1613	c.1254C>T	c.(1252-1254)ctC>ctT	p.L418L	TMCO3_ENST00000375391.1_Intron|TMCO3_ENST00000474393.1_3'UTR	NM_017905.4	NP_060375.4	Q6UWJ1	TMCO3_HUMAN	transmembrane and coiled-coil domains 3	418						integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)	p.L418L(1)		NS(1)|endometrium(4)|large_intestine(9)|liver(1)|lung(8)|prostate(1)|stomach(1)	25	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0145)|all_epithelial(44;0.00286)|all_lung(25;0.0273)|Breast(118;0.0411)|Lung NSC(25;0.0983)	all cancers(43;0.0317)			CCGTGCTCCTCGGCATGCTGG	0.537																																					p.L418L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1254T	13						.	C		1,4405	2.1+/-5.4	0,1,2202	91.0	83.0	86.0		1254	-9.9	0.7	13	dbSNP_134	86	0,8600		0,0,4300	no	coding-synonymous	TMCO3	NM_017905.4		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		418/678	114174959	1,13005	2203	4300	6503	113222960	SO:0001819	synonymous_variant	55002	exon8			BC012564	CCDS9537.1	13q34	2008-02-05	2005-07-22	2005-07-22	ENSG00000150403	ENSG00000150403			20329	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 11"""	C13orf11			Standard	NM_017905		Approved	FLJ20623	uc001vtu.4	Q6UWJ1	OTTHUMG00000017389	ENST00000434316.2:c.1254C>T	13.37:g.114174959C>T			113222960	NM_017905	Q5JSB1|Q6NUN1|Q8NG29|Q8TCI6|Q96EA6|Q9NWT2	Silent	SNP	ENST00000434316.2	37	CCDS9537.1																																																																																				0.537	TMCO3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045931.3	NM_017905	
INF2	64423	broad.mit.edu	37	14	105174184	105174185	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:105174184_105174185insC	ENST00000392634.4	+	8	1692_1693	c.1580_1581insC	c.(1579-1584)agccccfs	p.SP527fs	INF2_ENST00000330634.7_Frame_Shift_Ins_p.SP527fs	NM_022489.3	NP_071934.3	Q27J81	INF2_HUMAN	inverted formin, FH2 and WH2 domain containing	527					actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|regulation of cellular component size (GO:0032535)|regulation of mitochondrial fission (GO:0090140)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)		p.V530fs*50(1)		large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)		TGCACCTGCAGCCCCCCCGTGG	0.718																																					p.S527fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1580_1581insC	14						.																																			104245230	SO:0001589	frameshift_variant	64423	exon8			AK025709	CCDS9989.2, CCDS45173.1	14q32.33	2009-09-07	2007-11-29	2007-11-29	ENSG00000203485	ENSG00000203485			23791	protein-coding gene	gene with protein product	"""inverted formin 2"""	610982	"""chromosome 14 open reading frame 151"", ""chromosome 14 open reading frame 173"""	C14orf151, C14orf173		16818491	Standard	NM_001031714		Approved	MGC13251	uc001ypb.2	Q27J81	OTTHUMG00000029811	ENST00000392634.4:c.1587dupC	14.37:g.105174191_105174191dupC	ENSP00000376410:p.Ser527fs		104245229	NM_001031714	Q27J83|Q69YL8|Q6P1X7|Q6PK22|Q86TR7|Q9BRM1|Q9H6N1	Frame_Shift_Ins	INS	ENST00000392634.4	37	CCDS9989.2																																																																																				0.718	INF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074371.4	NM_022489	
ACOT4	122970	broad.mit.edu	37	14	74060511	74060512	+	Frame_Shift_Ins	INS	-	-	TCAA	rs79684878|rs373880503	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	-	-	-	TCAA	-	TCAA	Unknown	Valid	Germline	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:74060511_74060512insTCAA	ENST00000326303.4	+	2	817_818	c.563_564insTCAA	c.(562-567)ctagctfs	p.A189fs		NM_152331.3	NP_689544.3	Q8N9L9	ACOT4_HUMAN	acyl-CoA thioesterase 4	189				ALAY -> DLQS (in Ref. 1; BAC04313). {ECO:0000305}.	acyl-CoA metabolic process (GO:0006637)|dicarboxylic acid catabolic process (GO:0043649)|dicarboxylic acid metabolic process (GO:0043648)|long-chain fatty acid metabolic process (GO:0001676)|saturated monocarboxylic acid metabolic process (GO:0032788)|short-chain fatty acid metabolic process (GO:0046459)|succinyl-CoA metabolic process (GO:0006104)|unsaturated monocarboxylic acid metabolic process (GO:0032789)|very long-chain fatty acid metabolic process (GO:0000038)	peroxisome (GO:0005777)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)|succinyl-CoA hydrolase activity (GO:0004778)			endometrium(1)|large_intestine(3)|lung(4)	8				BRCA - Breast invasive adenocarcinoma(234;0.00331)		ACGTTGGCTCTAGCTTATTATA	0.495														6	0.00119808	0.0	0.0	5008	,	,		16663	0.0		0.006	False		,,,				2504	0.0				p.L188fs												.	.	0			c.563_564insTCAA	14						.																																			73130265	SO:0001589	frameshift_variant	122970	exon2			BC031799	CCDS9817.1	14q24.1	2011-02-16			ENSG00000177465	ENSG00000177465		"""Acyl CoA thioesterases"""	19748	protein-coding gene	gene with protein product		614314				16103133, 16940157	Standard	NM_152331		Approved	FLJ31235, PTE-Ib, PTE2B	uc001xoo.3	Q8N9L9	OTTHUMG00000169485	Exception_encountered	14.37:g.74060511_74060512insTCAA	ENSP00000323071:p.Ala189fs		73130264	NM_152331	Q17RF4|Q5BKT6|Q86TX0|Q86TX1|Q96N88	Frame_Shift_Ins	INS	ENST00000326303.4	37	CCDS9817.1																																																																																				0.495	ACOT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404298.2	NM_152331	
BEGAIN	57596	broad.mit.edu	37	14	101004865	101004865	+	Missense_Mutation	SNP	C	C	T	rs201975523	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:101004865C>T	ENST00000355173.2	-	7	1294	c.1223G>A	c.(1222-1224)cGg>cAg	p.R408Q	BEGAIN_ENST00000443071.2_Missense_Mutation_p.R408Q|CTD-2062F14.3_ENST00000553301.1_lincRNA|BEGAIN_ENST00000556751.1_Missense_Mutation_p.R344Q	NM_020836.3	NP_065887.1	Q9BUH8	BEGIN_HUMAN	brain-enriched guanylate kinase-associated	408						cytoplasm (GO:0005737)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)		p.R408Q(1)		cervix(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|skin(2)|stomach(1)	14		Melanoma(154;0.212)				CCCGGGGAGCCGGGCGGTCCC	0.741													C|||	2	0.000399361	0.0	0.0	5008	,	,		12350	0.002		0.0	False		,,,				2504	0.0				p.R408Q	NSCLC(159;1889 2010 9965 27479 40101)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1223A	14						.						5.0	7.0	6.0					14																	101004865		2052	4109	6161	100074618	SO:0001583	missense	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.1223G>A	14.37:g.101004865C>T	ENSP00000347301:p.Arg408Gln		100074618	NM_001159531	Q9NPU3|Q9P282	Missense_Mutation	SNP	ENST00000355173.2	37	CCDS9962.1	4	0.0018315018315018315	1	0.0020325203252032522	0	0.0	3	0.005244755244755245	0	0.0	C	3.467	-0.108778	0.06924	.	.	ENSG00000183092	ENST00000355173;ENST00000556751;ENST00000443071	.	.	.	4.5	2.31	0.28768	.	0.885835	0.09906	N	0.740506	T	0.10809	0.0264	L	0.36672	1.1	0.22648	N	0.998899	P	0.47106	0.89	B	0.36335	0.222	T	0.08534	-1.0717	9	0.10902	T	0.67	.	1.6341	0.02738	0.3122:0.3824:0.0:0.3054	.	408	Q9BUH8	BEGIN_HUMAN	Q	408;344;408	.	ENSP00000347301:R408Q	R	-	2	0	BEGAIN	100074618	0.590000	0.26815	0.195000	0.23364	0.005000	0.04900	1.520000	0.35899	2.053000	0.61076	0.455000	0.32223	CGG		0.741	BEGAIN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414329.1	NM_020836	
DYNC1H1	1778	broad.mit.edu	37	14	102466397	102466397	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:102466397C>T	ENST00000360184.4	+	17	4040	c.3876C>T	c.(3874-3876)gaC>gaT	p.D1292D		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	1292	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)	p.D1292D(1)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						GGCTGAAGGACGACAGAGAGA	0.542																																					p.D1292D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3876T	14						.						112.0	101.0	104.0					14																	102466397		2203	4300	6503	101536150	SO:0001819	synonymous_variant	1778	exon17			AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"""Cytoplasmic dyneins"""	2961	protein-coding gene	gene with protein product		600112	"""dynein, cytoplasmic, heavy polypeptide 1"""	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.3876C>T	14.37:g.102466397C>T			101536150	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	37	CCDS9966.1																																																																																				0.542	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
TRAF3	7187	broad.mit.edu	37	14	103371797	103371797	+	Silent	SNP	C	C	T	rs141356642		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:103371797C>T	ENST00000560371.1	+	11	1600	c.1383C>T	c.(1381-1383)aaC>aaT	p.N461N	TRAF3_ENST00000539721.1_Silent_p.N378N|TRAF3_ENST00000347662.4_Silent_p.N436N|TRAF3_ENST00000351691.5_Silent_p.N436N|TRAF3_ENST00000392745.2_Silent_p.N461N	NM_003300.3|NM_145725.2	NP_003291.2|NP_663777.1	Q13114	TRAF3_HUMAN	TNF receptor-associated factor 3	461	MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.				apoptotic process (GO:0006915)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|regulation of apoptotic process (GO:0042981)|regulation of cytokine production (GO:0001817)|regulation of defense response to virus (GO:0050688)|regulation of interferon-beta production (GO:0032648)|regulation of proteolysis (GO:0030162)|signal transduction (GO:0007165)|Toll signaling pathway (GO:0008063)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endosome (GO:0005768)|mitochondrion (GO:0005739)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.N461N(1)		breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|liver(2)|lung(7)|ovary(1)|prostate(2)	30		all_cancers(154;7.87e-06)|all_epithelial(191;0.0024)		Epithelial(152;9.92e-24)|all cancers(159;2.23e-21)|OV - Ovarian serous cystadenocarcinoma(161;7.85e-12)|Colorectal(3;0.0971)		TCTACCTGAACGGGGACGGGA	0.532																																					p.N461N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1383T	14						.	C	,,,	1,4405	2.1+/-5.4	0,1,2202	197.0	175.0	182.0		1134,1383,1383,1308	-5.0	0.9	14	dbSNP_134	182	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRAF3	NM_001199427.1,NM_003300.3,NM_145725.2,NM_145726.2	,,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,,	378/486,461/569,461/569,436/544	103371797	1,13005	2203	4300	6503	102441550	SO:0001819	synonymous_variant	7187	exon12			U21092	CCDS9975.1, CCDS9976.1, CCDS55946.1	14q32.32	2014-09-17				ENSG00000131323			12033	protein-coding gene	gene with protein product		601896				7530216, 7859281	Standard	NM_145725		Approved	CAP-1, CD40bp, CRAF1, LAP1	uc001ymd.2	Q13114		ENST00000560371.1:c.1383C>T	14.37:g.103371797C>T			102441550	NM_145725	B7Z8C4|Q12990|Q13076|Q13947|Q6AZX1|Q9UNL1	Silent	SNP	ENST00000560371.1	37	CCDS9975.1																																																																																				0.532	TRAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415735.1	NM_145725	
MARK3	4140	broad.mit.edu	37	14	103969433	103969433	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:103969433G>A	ENST00000429436.2	+	18	2641	c.2131G>A	c.(2131-2133)Gtg>Atg	p.V711M	MARK3_ENST00000303622.9_Missense_Mutation_p.V687M|MARK3_ENST00000335102.5_Missense_Mutation_p.V734M|MARK3_ENST00000216288.7_Missense_Mutation_p.V671M|MARK3_ENST00000416682.2_Missense_Mutation_p.V710M|MARK3_ENST00000440884.3_Missense_Mutation_p.V617M|MARK3_ENST00000553942.1_Missense_Mutation_p.V702M	NM_001128918.1|NM_001128919.1	NP_001122390.1|NP_001122391.1	P27448	MARK3_HUMAN	MAP/microtubule affinity-regulating kinase 3	711	KA1. {ECO:0000255|PROSITE- ProRule:PRU00565}.					plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.V671M(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30		Melanoma(154;0.155)	Epithelial(46;0.241)			GGAGAACCTCGTGCAGTGGGA	0.537																																					p.V702M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2104A	14						.						62.0	64.0	63.0					14																	103969433		2029	4209	6238	103039186	SO:0001583	missense	4140	exon17			M80359	CCDS41993.1, CCDS45165.1, CCDS45166.1, CCDS45167.1, CCDS55947.1	14q32.32	2014-04-07			ENSG00000075413	ENSG00000075413			6897	protein-coding gene	gene with protein product		602678				9533022	Standard	NM_002376		Approved	CTAK1, KP78, PAR-1A	uc001ymz.4	P27448	OTTHUMG00000171789	ENST00000429436.2:c.2131G>A	14.37:g.103969433G>A	ENSP00000411397:p.Val711Met		103039186	NM_001128919	O60219|Q86TT8|Q8TB41|Q8WX83|Q96RG1|Q9UMY9|Q9UN34	Missense_Mutation	SNP	ENST00000429436.2	37	CCDS45165.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.299701	0.81136	.	.	ENSG00000075413	ENST00000335102;ENST00000411530;ENST00000440884;ENST00000416682;ENST00000429436;ENST00000303622;ENST00000216288;ENST00000553942;ENST00000556744	T;T;T;T;T;T;T;T	0.47177	0.85;0.85;0.85;0.85;0.85;0.85;0.85;0.85	6.17	6.17	0.99709	Kinase-associated KA1 (4);	0.000000	0.85682	D	0.000000	T	0.74038	0.3664	M	0.85099	2.735	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;0.998;1.0;1.0;0.977;1.0;1.0;0.998	D;D;P;D;D;P;D;D;P	0.97110	0.996;1.0;0.864;0.982;0.992;0.809;0.999;0.995;0.876	T	0.70761	-0.4784	10	0.36615	T	0.2	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	718;289;710;420;671;711;617;702;687	P27448-7;A2SY06;P27448-2;B4DKN1;P27448-6;P27448;Q86TT8;P27448-4;P27448-3	.;.;.;.;.;MARK3_HUMAN;.;.;.	M	734;403;617;710;711;687;671;702;289	ENSP00000335347:V734M;ENSP00000402104:V617M;ENSP00000408092:V710M;ENSP00000411397:V711M;ENSP00000303698:V687M;ENSP00000216288:V671M;ENSP00000450772:V702M;ENSP00000451623:V289M	ENSP00000216288:V702M	V	+	1	0	MARK3	103039186	1.000000	0.71417	1.000000	0.80357	0.350000	0.29205	9.807000	0.99171	2.941000	0.99782	0.655000	0.94253	GTG		0.537	MARK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415144.1	NM_001128918	
TEP1	7011	broad.mit.edu	37	14	20854727	20854727	+	Missense_Mutation	SNP	G	G	A	rs548257852		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:20854727G>A	ENST00000262715.5	-	19	2780	c.2740C>T	c.(2740-2742)Cgg>Tgg	p.R914W	TEP1_ENST00000556935.1_Missense_Mutation_p.R806W	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	914					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)	p.R914W(1)		NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		AGCAGGTCCCGCTCCCCATGC	0.607													G|||	1	0.000199681	0.0	0.0	5008	,	,		17255	0.0		0.001	False		,,,				2504	0.0				p.R914W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2740T	14						.						41.0	40.0	41.0					14																	20854727		2203	4300	6503	19924567	SO:0001583	missense	7011	exon19				CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"""WD repeat domain containing"""	11726	protein-coding gene	gene with protein product	"""TROVE domain family, member 1"""	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.2740C>T	14.37:g.20854727G>A	ENSP00000262715:p.Arg914Trp		19924567	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	CCDS9548.1	.	.	.	.	.	.	.	.	.	.	G	31	5.074655	0.94000	.	.	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935	T;T	0.75821	-0.97;-0.97	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	D	0.90800	0.7111	H	0.96301	3.8	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	D	0.93699	0.7014	10	0.87932	D	0	-26.4549	17.5272	0.87804	0.0:0.0:1.0:0.0	.	806;264;914	G3V5X7;G3V2A4;Q99973	.;.;TEP1_HUMAN	W	914;914;806	ENSP00000262715:R914W;ENSP00000452574:R806W	ENSP00000262715:R914W	R	-	1	2	TEP1	19924567	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.547000	0.82146	2.423000	0.82170	0.655000	0.94253	CGG		0.607	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
OR6S1	341799	broad.mit.edu	37	14	21109808	21109808	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:21109808C>T	ENST00000320704.3	-	1	42	c.43G>A	c.(43-45)Gtc>Atc	p.V15I		NM_001001968.1	NP_001001968.1	Q8NH40	OR6S1_HUMAN	olfactory receptor, family 6, subfamily S, member 1	15						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V15I(1)		kidney(1)|large_intestine(3)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	all_cancers(95;0.00304)		Epithelial(56;1.23e-06)|all cancers(55;1.01e-05)	GBM - Glioblastoma multiforme(265;0.0135)		CCTGCCAGGACGAACTCTGTT	0.453																																					p.V15I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G43A	14						.						114.0	120.0	118.0					14																	21109808		2203	4300	6503	20179648	SO:0001583	missense	341799	exon1			AL163636	CCDS32038.1	14q11.2	2013-09-24			ENSG00000181803	ENSG00000181803		"""GPCR / Class A : Olfactory receptors"""	15363	protein-coding gene	gene with protein product							Standard	NM_001001968		Approved	OR6S1Q	uc001vxv.1	Q8NH40	OTTHUMG00000171010	ENST00000320704.3:c.43G>A	14.37:g.21109808C>T	ENSP00000313110:p.Val15Ile		20179648	NM_001001968	Q6IFJ9	Missense_Mutation	SNP	ENST00000320704.3	37	CCDS32038.1	.	.	.	.	.	.	.	.	.	.	C	0.284	-0.984377	0.02180	.	.	ENSG00000181803	ENST00000320704	T	0.04194	3.68	5.84	-2.51	0.06365	.	1.127120	0.06800	N	0.788498	T	0.02267	0.0070	N	0.11364	0.135	0.23616	N	0.997287	B	0.02656	0.0	B	0.04013	0.001	T	0.45948	-0.9226	10	0.02654	T	1	-1.7924	7.6901	0.28563	0.0:0.4214:0.1172:0.4613	.	15	Q8NH40	OR6S1_HUMAN	I	15	ENSP00000313110:V15I	ENSP00000313110:V15I	V	-	1	0	OR6S1	20179648	0.000000	0.05858	0.491000	0.27477	0.553000	0.35397	-1.567000	0.02146	-0.734000	0.04843	-0.140000	0.14226	GTC		0.453	OR6S1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411227.1		
TPPP2	122664	broad.mit.edu	37	14	21499252	21499252	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:21499252G>C	ENST00000321760.6	+	3	403	c.255G>C	c.(253-255)aaG>aaC	p.K85N	TPPP2_ENST00000530140.2_Missense_Mutation_p.K85N|NDRG2_ENST00000403829.3_Intron|AL161668.5_ENST00000533984.1_lincRNA|TPPP2_ENST00000460647.2_Missense_Mutation_p.K85N|RP11-998D10.1_ENST00000531638.1_5'Flank	NM_173846.4	NP_776245.2	P59282	TPPP2_HUMAN	tubulin polymerization-promoting protein family member 2	85						cytoplasm (GO:0005737)		p.K85N(1)		endometrium(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9	all_cancers(95;0.000759)		OV - Ovarian serous cystadenocarcinoma(11;6.85e-11)|Epithelial(56;9.49e-09)|all cancers(55;3.84e-08)	GBM - Glioblastoma multiforme(265;0.0191)		TCAAAGGGAAGAGTCCAGATG	0.527																																					p.K85N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G255C	14						.						108.0	101.0	104.0					14																	21499252		2203	4300	6503	20569092	SO:0001583	missense	122664	exon3			AY072034	CCDS9566.1	14q11.2	2014-01-21	2007-05-02	2007-05-02	ENSG00000179636	ENSG00000179636			19293	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 8"""	C14orf8		15590652, 17105200	Standard	NM_173846		Approved	p25beta, p18, CT152	uc001vzh.3	P59282	OTTHUMG00000029642	ENST00000321760.6:c.255G>C	14.37:g.21499252G>C	ENSP00000317595:p.Lys85Asn		20569092	NM_173846	Q2VYF3	Missense_Mutation	SNP	ENST00000321760.6	37	CCDS9566.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.75|12.75	2.031072|2.031072	0.35797|0.35797	.|.	.|.	ENSG00000179636|ENSG00000179636	ENST00000321760;ENST00000460647;ENST00000530140;ENST00000472458;ENST00000481535|ENST00000555751	T;T;T;T;T|.	0.47869|.	0.83;0.83;0.83;0.83;0.83|.	4.84|4.84	1.71|1.71	0.24356|0.24356	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.75722|0.75722	0.3888|0.3888	M|M	0.90252|0.90252	3.1|3.1	0.48632|0.48632	D|D	0.99968|0.99968	D|.	0.62365|.	0.991|.	D|.	0.72338|.	0.977|.	T|T	0.75614|0.75614	-0.3257|-0.3257	10|5	0.39692|.	T|.	0.17|.	-15.6196|-15.6196	7.7479|7.7479	0.28879|0.28879	0.3328:0.0:0.6672:0.0|0.3328:0.0:0.6672:0.0	.|.	85|.	P59282|.	TPPP2_HUMAN|.	N|T	85;85;85;85;80|24	ENSP00000317595:K85N;ENSP00000427504:K85N;ENSP00000435356:K85N;ENSP00000423171:K85N;ENSP00000421438:K80N|.	ENSP00000317595:K85N|.	K|R	+|+	3|2	2|0	TPPP2|TPPP2	20569092|20569092	0.991000|0.991000	0.36638|0.36638	0.143000|0.143000	0.22291|0.22291	0.066000|0.066000	0.16364|0.16364	1.480000|1.480000	0.35464|0.35464	0.593000|0.593000	0.29745|0.29745	0.655000|0.655000	0.94253|0.94253	AAG|AGA		0.527	TPPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073914.3	NM_173846	
ARHGEF40	55701	broad.mit.edu	37	14	21543850	21543850	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:21543850G>A	ENST00000298694.4	+	5	1792	c.1665G>A	c.(1663-1665)ccG>ccA	p.P555P	ARHGEF40_ENST00000298693.3_Silent_p.P555P			Q8TER5	ARH40_HUMAN	Rho guanine nucleotide exchange factor (GEF) 40	555						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.P555P(1)		large_intestine(4)|ovary(3)|upper_aerodigestive_tract(2)	9						TTACCCCACCGTGCCCTCCTG	0.617																																					p.P555P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1665A	14						.						90.0	92.0	91.0					14																	21543850		2203	4300	6503	20613690	SO:0001819	synonymous_variant	55701	exon5				CCDS32041.1	14q11.2	2012-07-24			ENSG00000165801	ENSG00000165801		"""Rho guanine nucleotide exchange factors"""	25516	protein-coding gene	gene with protein product		610018				16143467	Standard	NM_001278529		Approved	solo, FLJ10357	uc001vzp.3	Q8TER5		ENST00000298694.4:c.1665G>A	14.37:g.21543850G>A			20613690	NM_018071	A5PL07|Q9BWP5|Q9H7L6|Q9NTF9|Q9NW24	Silent	SNP	ENST00000298694.4	37	CCDS32041.1																																																																																				0.617	ARHGEF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413122.1		
SUPT16H	11198	broad.mit.edu	37	14	21831294	21831294	+	Silent	SNP	T	T	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:21831294T>G	ENST00000216297.2	-	13	1748	c.1410A>C	c.(1408-1410)gcA>gcC	p.A470A		NM_007192.3	NP_009123.1	Q9Y5B9	SP16H_HUMAN	suppressor of Ty 16 homolog (S. cerevisiae)	470					DNA repair (GO:0006281)|DNA replication (GO:0006260)|gene expression (GO:0010467)|nucleosome disassembly (GO:0006337)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.A470A(1)		breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_cancers(95;0.00115)		Epithelial(56;1.62e-06)|all cancers(55;1.49e-05)	GBM - Glioblastoma multiforme(265;0.0159)		GCTTCTCTTCTGCAGTCATTT	0.398																																					p.A470A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1410C	14						.						148.0	142.0	144.0					14																	21831294		2203	4300	6503	20901134	SO:0001819	synonymous_variant	11198	exon13			AF152961	CCDS9569.1	14q11.1	2008-08-13	2001-11-28		ENSG00000092201	ENSG00000092201			11465	protein-coding gene	gene with protein product	"""facilitates chromatin remodeling 140 kDa subunit"""	605012	"""suppressor of Ty (S.cerevisiae) 16 homolog"""			9489704, 11239457	Standard	NM_007192		Approved	FACT, FACTP140, SPT16/CDC68, FLJ14010, FLJ10857, CDC68	uc001wao.2	Q9Y5B9	OTTHUMG00000029685	ENST00000216297.2:c.1410A>C	14.37:g.21831294T>G			20901134	NM_007192	Q6GMT8|Q6P2F1|Q6PJM1|Q9NRX0	Silent	SNP	ENST00000216297.2	37	CCDS9569.1																																																																																				0.398	SUPT16H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074025.2		
CHD8	57680	broad.mit.edu	37	14	21854022	21854022	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:21854022G>T	ENST00000557364.1	-	38	7759	c.7496C>A	c.(7495-7497)cCc>cAc	p.P2499H	RP11-524O1.4_ENST00000565098.1_RNA|CHD8_ENST00000430710.3_Missense_Mutation_p.P2220H|CHD8_ENST00000399982.2_Missense_Mutation_p.P2499H|SUPT16H_ENST00000555943.1_5'Flank|SUPT16H_ENST00000216297.2_5'Flank			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	2499	His-rich.				ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|canonical Wnt signaling pathway (GO:0060070)|DNA duplex unwinding (GO:0032508)|in utero embryonic development (GO:0001701)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)	p.P2499H(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(33)|ovary(6)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	85	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		gtgggggtgggggtggtggtg	0.562																																					p.P2220H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C6659A	14						.						19.0	20.0	20.0					14																	21854022		1876	3975	5851	20923862	SO:0001583	missense	57680	exon38			AB046784	CCDS45081.1, CCDS53885.1	14q11.2	2008-02-05	2004-06-22	2004-06-23		ENSG00000100888			20153	protein-coding gene	gene with protein product		610528	"""helicase with SNF2 domain 1"""	HELSNF1		10997877	Standard	NM_020920		Approved	KIAA1564, DUPLIN	uc001war.2	Q9HCK8		ENST00000557364.1:c.7496C>A	14.37:g.21854022G>T	ENSP00000451601:p.Pro2499His		20923862	NM_020920	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Missense_Mutation	SNP	ENST00000557364.1	37	CCDS53885.1	.	.	.	.	.	.	.	.	.	.	G	10.69	1.420229	0.25552	.	.	ENSG00000100888	ENST00000430710;ENST00000399982;ENST00000262707;ENST00000557364	D;D;D	0.89810	-2.56;-2.57;-2.57	5.26	4.29	0.51040	.	0.000000	0.47093	D	0.000242	T	0.76905	0.4053	N	0.08118	0	0.25093	N	0.990842	B	0.02656	0.0	B	0.04013	0.001	T	0.65660	-0.6114	10	0.36615	T	0.2	-3.2478	12.028	0.53382	0.0:0.0:0.7911:0.2089	.	2220	Q9HCK8-2	.	H	2220;2499;2219;2499	ENSP00000406288:P2220H;ENSP00000382863:P2499H;ENSP00000451601:P2499H	ENSP00000262707:P2219H	P	-	2	0	CHD8	20923862	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	1.024000	0.30077	2.461000	0.83175	0.655000	0.94253	CCC		0.562	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920	
LRP10	26020	broad.mit.edu	37	14	23346171	23346171	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:23346171G>A	ENST00000359591.4	+	7	2268	c.1577G>A	c.(1576-1578)cGt>cAt	p.R526H	LRP10_ENST00000546834.1_Missense_Mutation_p.R526H|LRP10_ENST00000470660.1_3'UTR	NM_014045.3	NP_054764.2	Q7Z4F1	LRP10_HUMAN	low density lipoprotein receptor-related protein 10	526					endocytosis (GO:0006897)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.R526H(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(7)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(2)	32	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.00549)		GGCAACCTGCGTTCTCTGCTA	0.622																																					p.R526H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1577A	14						.						63.0	58.0	60.0					14																	23346171		2203	4300	6503	22416011	SO:0001583	missense	26020	exon7			AF131760	CCDS9578.1	14q11.2	2013-05-29			ENSG00000197324	ENSG00000197324		"""Low density lipoprotein receptors"""	14553	protein-coding gene	gene with protein product		609921				11123907	Standard	XM_005267510		Approved	DKFZP564C1940, MGC8675, LRP9, MST087, MSTP087	uc001whd.3	Q7Z4F1	OTTHUMG00000028705	ENST00000359591.4:c.1577G>A	14.37:g.23346171G>A	ENSP00000352601:p.Arg526His		22416011	NM_014045	A8K4R5|D3DS31|O95882|Q14CK7|Q86T02|Q8NCZ4|Q9HC42|Q9UG33	Missense_Mutation	SNP	ENST00000359591.4	37	CCDS9578.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.212288	0.79240	.	.	ENSG00000197324	ENST00000359591;ENST00000546834	D;D	0.96459	-3.96;-4.02	5.13	5.13	0.70059	.	0.056744	0.64402	D	0.000001	D	0.97542	0.9195	M	0.62723	1.935	0.51767	D	0.999938	D	0.89917	1.0	D	0.83275	0.996	D	0.98136	1.0433	10	0.87932	D	0	-13.9664	15.8424	0.78861	0.0:0.0:1.0:0.0	.	526	Q7Z4F1	LRP10_HUMAN	H	526	ENSP00000352601:R526H;ENSP00000447559:R526H	ENSP00000352601:R526H	R	+	2	0	LRP10	22416011	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.853000	0.75435	2.557000	0.86248	0.563000	0.77884	CGT		0.622	LRP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071663.3		
PSMB11	122706	broad.mit.edu	37	14	23511932	23511932	+	Silent	SNP	C	C	T	rs375580593		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:23511932C>T	ENST00000408907.2	+	1	557	c.498C>T	c.(496-498)gaC>gaT	p.D166D		NM_001099780.1	NP_001093250.1	A5LHX3	PSB11_HUMAN	proteasome (prosome, macropain) subunit, beta type, 11	166					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)	p.D166D(1)		endometrium(1)|kidney(2)|lung(4)	7	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.00643)		TCTATAGCGACGGCACCCGCC	0.617																																					p.D166D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C498T	14						.	C		3,4137		0,3,2067	42.0	46.0	45.0		498	-10.7	0.4	14		45	0,8374		0,0,4187	no	coding-synonymous	PSMB11	NM_001099780.1		0,3,6254	TT,TC,CC		0.0,0.0725,0.024		166/301	23511932	3,12511	2070	4187	6257	22581772	SO:0001819	synonymous_variant	122706	exon1				CCDS41923.1	14q11.2	2008-01-31				ENSG00000222028			31963	protein-coding gene	gene with protein product		611137				17540904	Standard	NM_001099780		Approved	beta5t	uc010ake.1	A5LHX3		ENST00000408907.2:c.498C>T	14.37:g.23511932C>T			22581772	NM_001099780		Silent	SNP	ENST00000408907.2	37	CCDS41923.1																																																																																				0.617	PSMB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408294.1	NM_001099780	
SLC7A8	23428	broad.mit.edu	37	14	23597361	23597361	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:23597361G>A	ENST00000316902.7	-	10	2033	c.1308C>T	c.(1306-1308)ttC>ttT	p.F436F	SLC7A8_ENST00000422941.2_Silent_p.F212F|SLC7A8_ENST00000453702.1_Silent_p.F233F|SLC7A8_ENST00000529705.2_Silent_p.F331F|SLC7A8_ENST00000469263.1_Intron	NM_012244.3	NP_036376.2	Q9UHI5	LAT2_HUMAN	solute carrier family 7 (amino acid transporter light chain, L system), member 8	436					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|metal ion homeostasis (GO:0055065)|neutral amino acid transport (GO:0015804)|organic cation transport (GO:0015695)|response to toxic substance (GO:0009636)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-amino acid transmembrane transporter activity (GO:0015179)|neutral amino acid transmembrane transporter activity (GO:0015175)|organic cation transmembrane transporter activity (GO:0015101)|peptide antigen binding (GO:0042605)|toxin transporter activity (GO:0019534)	p.F436F(1)		autonomic_ganglia(1)|endometrium(6)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|skin(1)	24	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.00809)	L-Alanine(DB00160)|L-DOPA(DB01235)|L-Glutamine(DB00130)|L-Phenylalanine(DB00120)	AGACCAGCAGGAAGGCCCAGA	0.577																																					p.F233F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C699T	14						.						155.0	131.0	139.0					14																	23597361		2203	4300	6503	22667201	SO:0001819	synonymous_variant	23428	exon8			Y18483	CCDS9590.1, CCDS41924.1, CCDS58304.1, CCDS58305.1	14q11.2	2013-05-22	2011-07-12		ENSG00000092068	ENSG00000092068		"""Solute carriers"""	11066	protein-coding gene	gene with protein product		604235				10080183, 10391915	Standard	NM_001267036		Approved	LPI-PC1, LAT2	uc001wiz.4	Q9UHI5	OTTHUMG00000028720	ENST00000316902.7:c.1308C>T	14.37:g.23597361G>A			22667201	NM_182728	B2R8Q4|B4DKT4|B4DTV6|D3DS46|F2Z2J4|Q86U05|Q9UKQ6|Q9UKQ7|Q9UKQ8|Q9Y445	Silent	SNP	ENST00000316902.7	37	CCDS9590.1																																																																																				0.577	SLC7A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071718.3		
DCAF11	80344	broad.mit.edu	37	14	24586588	24586588	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:24586588C>T	ENST00000446197.3	+	4	1124	c.397C>T	c.(397-399)Cga>Tga	p.R133*	DCAF11_ENST00000560171.1_Intron|DCAF11_ENST00000396936.1_Silent_p.L54L|DCAF11_ENST00000559115.1_Nonsense_Mutation_p.R133*|NRL_ENST00000561028.1_5'Flank|DCAF11_ENST00000396941.4_Nonsense_Mutation_p.R107*	NM_025230.4	NP_079506.3	Q8TEB1	DCA11_HUMAN	DDB1 and CUL4 associated factor 11	133					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)		p.R133*(1)									CAGCTTTCCTCGAATGTTGCA	0.592																																					p.R133X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C397T	14						.						38.0	42.0	41.0					14																	24586588		2203	4300	6503	23656428	SO:0001587	stop_gained	80344	exon4			AF130070	CCDS9610.1, CCDS41929.1	14q11.2	2013-01-09	2009-07-17	2009-07-17	ENSG00000100897	ENSG00000100897		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	20258	protein-coding gene	gene with protein product		613317	"""WD repeat domain 23"""	WDR23			Standard	NM_025230		Approved	PRO2389, GL014	uc001wlv.3	Q8TEB1	OTTHUMG00000028793	ENST00000446197.3:c.397C>T	14.37:g.24586588C>T	ENSP00000415556:p.Arg133*		23656428	NM_001163484	B3KQ83|D3DS56|Q5D039|Q86U00|Q86U39|Q8NDN2|Q9H2J0|Q9H3A3|Q9H5C9	Nonsense_Mutation	SNP	ENST00000446197.3	37	CCDS9610.1	.	.	.	.	.	.	.	.	.	.	c	36	5.650865	0.96714	.	.	ENSG00000100897	ENST00000326009;ENST00000446197;ENST00000396941	.	.	.	5.83	5.83	0.93111	.	0.297251	0.37304	N	0.002152	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.15499	T	0.54	-0.364	15.6375	0.76966	0.0:1.0:0.0:0.0	.	.	.	.	X	133;107;107	.	ENSP00000323680:R133X	R	+	1	2	DCAF11	23656428	0.865000	0.29922	0.999000	0.59377	0.992000	0.81027	2.796000	0.47869	2.763000	0.94921	0.563000	0.77884	CGA		0.592	DCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071907.4		
IPO4	79711	broad.mit.edu	37	14	24655969	24655969	+	Missense_Mutation	SNP	G	G	A	rs369050610		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:24655969G>A	ENST00000354464.6	-	9	961	c.785C>T	c.(784-786)gCg>gTg	p.A262V	RP11-468E2.2_ENST00000561419.1_3'UTR	NM_024658.3	NP_078934.3	Q8TEX9	IPO4_HUMAN	importin 4	262					DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)		p.A262V(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|stomach(2)|urinary_tract(1)	33				GBM - Glioblastoma multiforme(265;0.0087)		TATGCGTATCGCATTGCCCAG	0.512																																					p.A262V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C785T	14						.	G	VAL/ALA	3,4127		0,3,2062	95.0	99.0	97.0		785	4.1	0.1	14		97	0,8426		0,0,4213	no	missense	IPO4	NM_024658.3	64	0,3,6275	AA,AG,GG		0.0,0.0726,0.0239	benign	262/1082	24655969	3,12553	2065	4213	6278	23725809	SO:0001583	missense	79711	exon9			AF411122	CCDS9616.1	14q11.2	2003-03-10			ENSG00000196497	ENSG00000196497		"""Importins"""	19426	protein-coding gene	gene with protein product						11823430	Standard	NR_051979		Approved	Imp4, FLJ23338	uc001wmv.1	Q8TEX9	OTTHUMG00000028801	ENST00000354464.6:c.785C>T	14.37:g.24655969G>A	ENSP00000346453:p.Ala262Val		23725809	NM_024658	B2RN95|Q2NL96|Q86TZ9|Q8NCG8|Q96SJ3|Q9BTI4|Q9H5L0	Missense_Mutation	SNP	ENST00000354464.6	37	CCDS9616.1	.	.	.	.	.	.	.	.	.	.	G	7.363	0.625305	0.14257	7.26E-4	0.0	ENSG00000196497	ENST00000354464	T	0.04758	3.56	4.96	4.06	0.47325	Armadillo-like helical (1);Armadillo-type fold (1);	0.145704	0.47455	D	0.000224	T	0.04907	0.0132	L	0.38175	1.15	0.27139	N	0.9617	B	0.27882	0.192	B	0.31869	0.137	T	0.31223	-0.9951	10	0.30854	T	0.27	-5.8366	8.1597	0.31192	0.0:0.1529:0.5316:0.3155	.	262	Q8TEX9	IPO4_HUMAN	V	262	ENSP00000346453:A262V	ENSP00000346453:A262V	A	-	2	0	IPO4	23725809	1.000000	0.71417	0.068000	0.19968	0.145000	0.21501	4.300000	0.59079	1.429000	0.47314	0.655000	0.94253	GCG		0.512	IPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071931.4	NM_024658	
TSSK4	283629	broad.mit.edu	37	14	24675733	24675733	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:24675733C>T	ENST00000287913.6	+	2	412	c.244C>T	c.(244-246)Cac>Tac	p.H82Y	TM9SF1_ENST00000530611.1_Intron|TM9SF1_ENST00000556387.1_Intron|TSSK4_ENST00000556621.1_Missense_Mutation_p.H6Y|TSSK4_ENST00000428351.2_Intron|TSSK4_ENST00000339917.5_Missense_Mutation_p.H82Y			Q6SA08	TSSK4_HUMAN	testis-specific serine kinase 4	82	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|positive regulation of CREB transcription factor activity (GO:0032793)|protein phosphorylation (GO:0006468)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.H82Y(2)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)	8				GBM - Glioblastoma multiforme(265;0.018)		AGTCTTGCGGCACAAGTACCT	0.517																																					p.H82Y												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C244T	14						.						168.0	142.0	151.0					14																	24675733		2203	4300	6503	23745573	SO:0001583	missense	283629	exon2			AF542390	CCDS9618.1, CCDS53890.1	14q11.2	2006-03-31	2005-03-10	2005-03-12	ENSG00000139908	ENSG00000139908			19825	protein-coding gene	gene with protein product	"""chromosome 14 open reading frame 20"""	610711	"""serine/threonine kinase 22E"""	C14orf20, STK22E			Standard	NM_174944		Approved		uc001wnh.3	Q6SA08	OTTHUMG00000029323	ENST00000287913.6:c.244C>T	14.37:g.24675733C>T	ENSP00000287913:p.His82Tyr		23745573	NM_174944	Q2TA60|Q6ZNM2	Missense_Mutation	SNP	ENST00000287913.6	37	CCDS9618.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.99|16.99	3.274754|3.274754	0.59649|0.59649	.|.	.|.	ENSG00000139908|ENSG00000139908	ENST00000555092|ENST00000339917;ENST00000556621;ENST00000287913	.|T;T;T	.|0.78707	.|-1.2;-1.2;-1.2	4.97|4.97	4.97|4.97	0.65823|0.65823	.|Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.|0.235434	.|0.30235	.|N	.|0.010090	D|D	0.90463|0.90463	0.7013|0.7013	M|M	0.93062|0.93062	3.375|3.375	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|0.999;1.0	D|D	0.92460|0.92460	0.5977|0.5977	5|10	.|0.87932	.|D	.|0	.|.	15.2469|15.2469	0.73511|0.73511	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|82;82	.|Q6SA08-2;Q6SA08	.|.;TSSK4_HUMAN	V|Y	76|82;6;82	.|ENSP00000339179:H82Y;ENSP00000452054:H6Y;ENSP00000287913:H82Y	.|ENSP00000287913:H82Y	A|H	+|+	2|1	0|0	TSSK4|TSSK4	23745573|23745573	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	4.670000|4.670000	0.61583|0.61583	2.583000|2.583000	0.87209|0.87209	0.462000|0.462000	0.41574|0.41574	GCA|CAC		0.517	TSSK4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000073139.3	NM_174944	
NFATC4	4776	broad.mit.edu	37	14	24839226	24839226	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:24839226C>T	ENST00000250373.4	+	2	763	c.622C>T	c.(622-624)Cgc>Tgc	p.R208C	NFATC4_ENST00000413692.2_Missense_Mutation_p.R271C|NFATC4_ENST00000554473.1_5'Flank|NFATC4_ENST00000556759.1_5'Flank|NFATC4_ENST00000539237.2_Missense_Mutation_p.R240C|NFATC4_ENST00000553469.1_Missense_Mutation_p.R240C|NFATC4_ENST00000555453.1_Missense_Mutation_p.R196C|NFATC4_ENST00000554661.1_Missense_Mutation_p.R138C|NFATC4_ENST00000553879.1_Missense_Mutation_p.R138C|NFATC4_ENST00000555590.1_Missense_Mutation_p.R221C|NFATC4_ENST00000556279.1_Missense_Mutation_p.R240C|NFATC4_ENST00000554050.1_Missense_Mutation_p.R208C|NFATC4_ENST00000555167.1_5'Flank|NFATC4_ENST00000554591.1_Missense_Mutation_p.R271C|NFATC4_ENST00000553708.1_Missense_Mutation_p.R208C|NFATC4_ENST00000554344.1_Missense_Mutation_p.R138C|NFATC4_ENST00000422617.3_Missense_Mutation_p.R196C|NFATC4_ENST00000557451.1_Missense_Mutation_p.R138C|NFATC4_ENST00000424781.2_Missense_Mutation_p.R221C|NFATC4_ENST00000554966.1_Missense_Mutation_p.R221C|NFATC4_ENST00000556169.1_Missense_Mutation_p.R196C|NFATC4_ENST00000440487.2_3'UTR	NM_004554.4	NP_004545.2	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4	208	Pro-rich.				cellular respiration (GO:0045333)|cellular response to lithium ion (GO:0071285)|cellular response to UV (GO:0034644)|heart development (GO:0007507)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of synaptic plasticity (GO:0048167)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription coactivator activity (GO:0003713)	p.R208C(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(7)|liver(4)|lung(12)|ovary(1)|skin(2)	34				GBM - Glioblastoma multiforme(265;0.018)		GGCGGCCTCCCGCTTTGGCCT	0.682																																					p.R271C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C811T	14						.						21.0	23.0	22.0					14																	24839226		2194	4292	6486	23909066	SO:0001583	missense	4776	exon3			BC053855	CCDS9629.1, CCDS45089.1, CCDS55909.1, CCDS55910.1, CCDS55911.1, CCDS73625.1	14q11.2	2009-11-24			ENSG00000100968	ENSG00000100968		"""Nuclear factor of activated T-cells"""	7778	protein-coding gene	gene with protein product		602699				7749981	Standard	NM_004554		Approved	NFAT3	uc010tok.2	Q14934	OTTHUMG00000029351	ENST00000250373.4:c.622C>T	14.37:g.24839226C>T	ENSP00000250373:p.Arg208Cys		23909066	NM_001136022	B4DDG5|B4DY55|B5B2U7|B5B2U8|B5B2U9|B5B2V0|B5B2V1|B5B2V2|B5B2V3|B5B2V4|B5B2V5|B5B2V7|B5B2V8|B5B2V9|B5B2W0|B5B2W1|B5B2W2|B5B2W3|B5B2W4|B5B2W5|B5B2W6|B5B2W7|B5B2W8|B5B2W9|B5B2X0|Q7Z598|Q96H68	Missense_Mutation	SNP	ENST00000250373.4	37	CCDS9629.1	.	.	.	.	.	.	.	.	.	.	C	17.71	3.457911	0.63401	.	.	ENSG00000100968	ENST00000413692;ENST00000554591;ENST00000555590;ENST00000554966;ENST00000424781;ENST00000539237;ENST00000556279;ENST00000553469;ENST00000554050;ENST00000250373;ENST00000553708;ENST00000557674;ENST00000553879;ENST00000554344;ENST00000554661;ENST00000556169;ENST00000557451;ENST00000422617;ENST00000555453	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.15487	2.42;2.42;2.42;2.42;2.42;2.42;2.42;2.42;2.42;2.42;2.42;2.42;2.42;2.42;2.42;2.42;2.42;2.42;2.42	3.89	1.84	0.25277	.	0.234696	0.26669	N	0.023104	T	0.30510	0.0767	L	0.52573	1.65	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.998;0.998;1.0;0.998;1.0;1.0;0.998;0.998;0.998;0.998;1.0;0.999;1.0;1.0	P;P;D;P;D;D;P;P;P;P;D;P;D;D	0.91635	0.649;0.649;0.999;0.736;0.999;0.999;0.649;0.809;0.809;0.738;0.999;0.764;0.999;0.997	T	0.03130	-1.1069	10	0.87932	D	0	-1.8779	8.1215	0.30974	0.1756:0.6529:0.1715:0.0	.	196;196;240;240;221;221;221;271;271;196;240;185;271;208	Q14934-17;Q14934-9;Q14934-14;Q14934-4;Q14934-15;Q14934-6;Q14934-7;Q14934-2;Q14934-3;Q14934-10;Q14934-5;B4DU09;Q14934-11;Q14934	.;.;.;.;.;.;.;.;.;.;.;.;.;NFAC4_HUMAN	C	271;271;221;221;221;240;240;240;208;208;208;185;138;138;138;196;138;196;196	ENSP00000388910:R271C;ENSP00000452039:R271C;ENSP00000451224:R221C;ENSP00000450644:R221C;ENSP00000388668:R221C;ENSP00000439350:R240C;ENSP00000452270:R240C;ENSP00000451502:R240C;ENSP00000451151:R208C;ENSP00000250373:R208C;ENSP00000450590:R208C;ENSP00000452352:R185C;ENSP00000452349:R138C;ENSP00000450469:R138C;ENSP00000450733:R138C;ENSP00000451454:R196C;ENSP00000451284:R138C;ENSP00000396788:R196C;ENSP00000450686:R196C	ENSP00000250373:R208C	R	+	1	0	NFATC4	23909066	0.952000	0.32445	0.997000	0.53966	0.988000	0.76386	2.448000	0.44926	0.951000	0.37770	0.467000	0.42956	CGC		0.682	NFATC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073206.6	NM_004554	
KHNYN	23351	broad.mit.edu	37	14	24900924	24900924	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:24900924G>A	ENST00000251343.5	+	3	596	c.457G>A	c.(457-459)Gga>Aga	p.G153R	KHNYN_ENST00000556842.1_Missense_Mutation_p.G153R|KHNYN_ENST00000554268.1_5'Flank|KHNYN_ENST00000553935.1_Missense_Mutation_p.G153R|CBLN3_ENST00000267406.6_5'Flank|CBLN3_ENST00000555436.1_5'Flank			O15037	KHNYN_HUMAN	KH and NYN domain containing	153							RNA binding (GO:0003723)	p.G153R(1)		kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(3)	24						ACCATCTTCCGGAGCCTCTCA	0.602											OREG0022627	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G153R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G457A	14						.						55.0	63.0	60.0					14																	24900924		2203	4300	6503	23970764	SO:0001583	missense	23351	exon3			AB002321	CCDS32058.1	14q11.2	2010-11-23	2009-10-14	2009-10-14	ENSG00000100441	ENSG00000100441			20166	protein-coding gene	gene with protein product			"""KIAA0323"""	KIAA0323		17114934	Standard	NM_015299		Approved		uc001wph.4	O15037		ENST00000251343.5:c.457G>A	14.37:g.24900924G>A	ENSP00000251343:p.Gly153Arg	774	23970764	NM_015299	Q86TZ6|Q8IUQ2|Q96BA9	Missense_Mutation	SNP	ENST00000251343.5	37	CCDS32058.1	.	.	.	.	.	.	.	.	.	.	G	0.329	-0.957401	0.02267	.	.	ENSG00000100441	ENST00000251343;ENST00000556842;ENST00000553935	T;T;T	0.22539	1.95;1.95;1.95	4.86	3.02	0.34903	.	0.378304	0.14333	U	0.326211	T	0.12732	0.0309	L	0.31294	0.92	0.22521	N	0.999023	B;B	0.15719	0.014;0.008	B;B	0.10450	0.005;0.005	T	0.37596	-0.9699	10	0.09084	T	0.74	.	7.7683	0.28993	0.1972:0.0:0.8028:0.0	.	194;153	D3DS77;O15037	.;KHNYN_HUMAN	R	153	ENSP00000251343:G153R;ENSP00000451106:G153R;ENSP00000450799:G153R	ENSP00000251343:G153R	G	+	1	0	KHNYN	23970764	0.008000	0.16893	0.001000	0.08648	0.134000	0.20937	1.578000	0.36525	0.572000	0.29383	0.563000	0.77884	GGA		0.602	KHNYN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412928.1		
GZMH	2999	broad.mit.edu	37	14	25077579	25077579	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:25077579C>T	ENST00000216338.4	-	2	139	c.95G>A	c.(94-96)cGc>cAc	p.R32H	RP11-104E19.1_ENST00000555300.1_RNA|GZMH_ENST00000382548.4_Missense_Mutation_p.R32H|RP11-104E19.1_ENST00000557736.1_RNA|GZMH_ENST00000557220.2_Missense_Mutation_p.R32H	NM_033423.4	NP_219491.1	P20718	GRAH_HUMAN	granzyme H (cathepsin G-like 2, protein h-CCPX)	32	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				apoptotic process (GO:0006915)|cytolysis (GO:0019835)	membrane (GO:0016020)	serine-type endopeptidase activity (GO:0004252)	p.R32H(1)		central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)	12				GBM - Glioblastoma multiforme(265;0.0267)		CATGTAGGGGCGGGAGTGGGG	0.547																																					p.R32H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G95A	14						.						131.0	136.0	134.0					14																	25077579		2203	4300	6503	24147419	SO:0001583	missense	2999	exon2			M72150	CCDS9632.1, CCDS59243.1	14q11.2	2003-10-20			ENSG00000100450	ENSG00000100450			4710	protein-coding gene	gene with protein product		116831		CTSGL2		2049336	Standard	NM_033423		Approved	CGL-2, CCP-X, CTLA1, CSP-C	uc001wpr.2	P20718	OTTHUMG00000140185	ENST00000216338.4:c.95G>A	14.37:g.25077579C>T	ENSP00000216338:p.Arg32His		24147419	NM_033423	G3V2C5|Q6XGZ0|Q6XGZ1	Missense_Mutation	SNP	ENST00000216338.4	37	CCDS9632.1	.	.	.	.	.	.	.	.	.	.	c	17.51	3.408859	0.62399	.	.	ENSG00000100450	ENST00000216338;ENST00000382547;ENST00000557220;ENST00000382548	D;D	0.92752	-3.1;-2.41	4.49	-3.41	0.04839	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.84566	0.5500	N	0.21508	0.67	0.09310	N	1	B;P;P	0.40970	0.003;0.734;0.732	B;B;B	0.40134	0.005;0.32;0.199	T	0.75113	-0.3432	9	0.46703	T	0.11	.	10.4843	0.44713	0.0:0.4099:0.0:0.5901	.	32;32;32	G3V2C5;Q6XGZ1;P20718	.;.;GRAH_HUMAN	H	32	ENSP00000216338:R32H;ENSP00000371988:R32H	ENSP00000216338:R32H	R	-	2	0	GZMH	24147419	0.000000	0.05858	0.000000	0.03702	0.212000	0.24457	-2.437000	0.01018	-0.934000	0.03733	-0.254000	0.11334	CGC		0.547	GZMH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276538.2	NM_033423	
NOVA1	4857	broad.mit.edu	37	14	26917883	26917883	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:26917883C>A	ENST00000539517.2	-	5	1123	c.806G>T	c.(805-807)gGa>gTa	p.G269V	NOVA1_ENST00000465357.2_Missense_Mutation_p.G245V|NOVA1_ENST00000267422.7_Missense_Mutation_p.G147V	NM_002515.2	NP_002506.2	P51513	NOVA1_HUMAN	neuro-oncological ventral antigen 1	272					locomotory behavior (GO:0007626)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA metabolic process (GO:0051252)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.G269V(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(265;0.0135)		ATAAGGAGATCCGGTTGGATT	0.483																																					p.G269V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G806T	14						.						156.0	141.0	146.0					14																	26917883		2203	4300	6503	25987723	SO:0001583	missense	4857	exon5			U04840	CCDS9635.1, CCDS32060.1, CCDS32061.1	14q12	2006-06-09			ENSG00000139910	ENSG00000139910			7886	protein-coding gene	gene with protein product		602157				8558240	Standard	NM_006489		Approved		uc001wpy.3	P51513	OTTHUMG00000029385	ENST00000539517.2:c.806G>T	14.37:g.26917883C>A	ENSP00000438875:p.Gly269Val		25987723	NM_002515	A8K0S4|A8K4Q7|D3DS81|D3DS82|Q6B004	Missense_Mutation	SNP	ENST00000539517.2	37	CCDS32061.1	.	.	.	.	.	.	.	.	.	.	C	19.52	3.842355	0.71488	.	.	ENSG00000139910	ENST00000465357;ENST00000539517;ENST00000267422;ENST00000449198	T;T;T;T	0.44083	1.08;1.0;0.93;1.19	5.73	5.73	0.89815	.	0.000000	0.64402	D	0.000001	T	0.65790	0.2725	M	0.68952	2.095	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.994;0.998	T	0.65817	-0.6076	10	0.62326	D	0.03	-15.0239	19.8956	0.96956	0.0:1.0:0.0:0.0	.	272;245;269	P51513;D3DS81;P51513-4	NOVA1_HUMAN;.;.	V	245;269;147;228	ENSP00000447391:G245V;ENSP00000438875:G269V;ENSP00000267422:G147V;ENSP00000408914:G228V	ENSP00000267422:G147V	G	-	2	0	NOVA1	25987723	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.783000	0.85696	2.708000	0.92522	0.563000	0.77884	GGA		0.483	NOVA1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000073261.3	NM_006491	
HECTD1	25831	broad.mit.edu	37	14	31602603	31602603	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:31602603C>T	ENST00000399332.1	-	24	4251	c.3763G>A	c.(3763-3765)Gca>Aca	p.A1255T	HECTD1_ENST00000553700.1_Missense_Mutation_p.A1255T	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	1255					neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)	p.A1255T(1)		breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		TTAGCTTCTGCTTCTTTAGCT	0.398																																					p.A1255T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3763A	14						.						97.0	91.0	93.0					14																	31602603		1857	4109	5966	30672354	SO:0001583	missense	25831	exon24			AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"""Ankyrin repeat domain containing"""	20157	protein-coding gene	gene with protein product			"""HECT domain containing 1"""			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.3763G>A	14.37:g.31602603C>T	ENSP00000382269:p.Ala1255Thr		30672354	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Missense_Mutation	SNP	ENST00000399332.1	37	CCDS41939.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.8|25.8	4.675309|4.675309	0.88445|0.88445	.|.	.|.	ENSG00000092148|ENSG00000092148	ENST00000553700;ENST00000261312;ENST00000399332;ENST00000553957|ENST00000557369	T;T;T|.	0.43688|.	0.94;0.94;1.43|.	5.76|5.76	5.76|5.76	0.90799|0.90799	.|.	0.000000|.	0.64402|.	U|.	0.000001|.	T|T	0.75598|0.75598	0.3871|0.3871	M|M	0.65498|0.65498	2.005|2.005	0.80722|0.80722	D|D	1|1	D;P|.	0.60575|.	0.988;0.608|.	P;B|.	0.54759|.	0.76;0.173|.	T|T	0.72520|0.72520	-0.4268|-0.4268	10|5	0.59425|.	D|.	0.04|.	-14.2441|-14.2441	19.9719|19.9719	0.97287|0.97287	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1255;1255|.	D3DS86;Q9ULT8|.	.;HECD1_HUMAN|.	T|N	1255;1257;1255;729|85	ENSP00000450697:A1255T;ENSP00000382269:A1255T;ENSP00000451860:A729T|.	ENSP00000261312:A1257T|.	A|S	-|-	1|2	0|0	HECTD1|HECTD1	30672354|30672354	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	7.448000|7.448000	0.80631|0.80631	2.718000|2.718000	0.92993|0.92993	0.650000|0.650000	0.86243|0.86243	GCA|AGC		0.398	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1		
C14orf37	145407	broad.mit.edu	37	14	58604898	58604898	+	Silent	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:58604898A>G	ENST00000267485.7	-	2	1373	c.1179T>C	c.(1177-1179)acT>acC	p.T393T	C14orf37_ENST00000334342.5_5'UTR	NM_001001872.2	NP_001001872.2	Q86TY3	CN037_HUMAN	chromosome 14 open reading frame 37	393						integral component of membrane (GO:0016021)		p.T393T(1)		breast(7)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|skin(1)	33						AACTTTGATCAGTGAAAGCAG	0.522																																					p.T393T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1179C	14						.						109.0	103.0	105.0					14																	58604898		2203	4300	6503	57674651	SO:0001819	synonymous_variant	145407	exon2				CCDS32089.1	14q23.1	2012-09-03			ENSG00000139971	ENSG00000139971			19846	protein-coding gene	gene with protein product							Standard	NM_001001872		Approved		uc001xdc.3	Q86TY3	OTTHUMG00000171173	ENST00000267485.7:c.1179T>C	14.37:g.58604898A>G			57674651	NM_001001872	A8K8Z8|Q6P5Q1|Q86TY1	Silent	SNP	ENST00000267485.7	37	CCDS32089.1																																																																																				0.522	C14orf37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412059.1	NM_001001872	
RTN1	6252	broad.mit.edu	37	14	60193862	60193862	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:60193862G>A	ENST00000267484.5	-	3	1875	c.1540C>T	c.(1540-1542)Cgg>Tgg	p.R514W		NM_021136.2	NP_066959.1	Q16799	RTN1_HUMAN	reticulon 1	514					neuron differentiation (GO:0030182)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)		p.R514W(1)		central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(30)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(108;0.0968)		GCCAGGCCCCGCCGGCTTGGC	0.726																																					p.R514W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1540T	14						.						8.0	11.0	10.0					14																	60193862		2183	4264	6447	59263615	SO:0001583	missense	6252	exon3			L10333	CCDS9740.1, CCDS9741.1	14q21-q22	2008-08-29			ENSG00000139970	ENSG00000139970			10467	protein-coding gene	gene with protein product		600865	"""neuroendocrine-specific protein"""	NSP		8275708	Standard	NM_206852		Approved		uc001xen.1	Q16799	OTTHUMG00000028947	ENST00000267484.5:c.1540C>T	14.37:g.60193862G>A	ENSP00000267484:p.Arg514Trp		59263615	NM_021136	Q16800|Q16801|Q5BKZ4|Q9BQ59	Missense_Mutation	SNP	ENST00000267484.5	37	CCDS9740.1	.	.	.	.	.	.	.	.	.	.	G	15.89	2.966655	0.53507	.	.	ENSG00000139970	ENST00000432103;ENST00000267484;ENST00000433623	T	0.24151	1.87	5.02	4.11	0.48088	.	1.335100	0.04669	U	0.410340	T	0.26882	0.0658	L	0.36672	1.1	0.09310	N	1	D	0.63046	0.992	B	0.40534	0.332	T	0.45731	-0.9241	10	0.72032	D	0.01	.	14.1766	0.65546	0.0:0.4725:0.5275:0.0	.	514	Q16799	RTN1_HUMAN	W	94;514;440	ENSP00000267484:R514W	ENSP00000267484:R514W	R	-	1	2	RTN1	59263615	0.000000	0.05858	0.010000	0.14722	0.275000	0.26752	0.664000	0.25068	1.077000	0.40990	0.467000	0.42956	CGG		0.726	RTN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000072278.2		
PPM1A	5494	broad.mit.edu	37	14	60749845	60749845	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:60749845A>G	ENST00000395076.4	+	2	854	c.424A>G	c.(424-426)Att>Gtt	p.I142V	PPM1A_ENST00000325642.3_Missense_Mutation_p.I215V|PPM1A_ENST00000529574.1_Missense_Mutation_p.I142V|PPM1A_ENST00000325658.3_Missense_Mutation_p.I142V	NM_021003.4	NP_066283.1	P35813	PPM1A_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1A	142					cell cycle arrest (GO:0007050)|dephosphorylation (GO:0016311)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|N-terminal protein myristoylation (GO:0006499)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-threonine dephosphorylation (GO:0035970)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|protein dephosphorylation (GO:0006470)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|voltage-gated calcium channel complex (GO:0005891)	calmodulin-dependent protein phosphatase activity (GO:0033192)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine phosphatase activity (GO:0004722)|R-SMAD binding (GO:0070412)|signal transducer activity (GO:0004871)	p.I142V(1)		cervix(1)|endometrium(1)|large_intestine(8)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(108;0.046)		TACTTATTTCATTAACTGTGG	0.393																																					p.I142V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A424G	14						.						100.0	98.0	99.0					14																	60749845		2203	4300	6503	59819598	SO:0001583	missense	5494	exon2			S87759	CCDS9744.1, CCDS9745.1, CCDS45120.1	14q23.1	2013-01-24	2010-03-05		ENSG00000100614	ENSG00000100614	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	9275	protein-coding gene	gene with protein product	"""phosphatase 2C alpha"", ""protein phosphatase 2C, alpha isoform"""	606108	"""protein phosphatase 1A (formerly 2C), magnesium-dependent, alpha isoform"""			1311954	Standard	NM_177952		Approved	MGC9201, PP2Calpha, PP2CA	uc001xew.4	P35813	OTTHUMG00000140333	ENST00000395076.4:c.424A>G	14.37:g.60749845A>G	ENSP00000378514:p.Ile142Val		59819598	NM_021003	B5BU11|J3KNM0|O75551	Missense_Mutation	SNP	ENST00000395076.4	37	CCDS9744.1	.	.	.	.	.	.	.	.	.	.	A	12.10	1.836635	0.32421	.	.	ENSG00000100614	ENST00000325642;ENST00000529574;ENST00000395076;ENST00000325658;ENST00000525399;ENST00000531937	T;T;T;T;T;T	0.17054	2.3;2.3;2.3;2.3;2.3;2.3	5.89	5.89	0.94794	Protein phosphatase 2C-like (5);	0.043289	0.85682	D	0.000000	T	0.15609	0.0376	L	0.35593	1.075	0.80722	D	1	B;B;B	0.15719	0.005;0.003;0.014	B;B;B	0.20384	0.029;0.017;0.029	T	0.07673	-1.0760	9	.	.	.	-4.6722	16.2912	0.82752	1.0:0.0:0.0:0.0	.	142;142;142	P35813;P35813-2;B2R8E4	PPM1A_HUMAN;.;.	V	215;142;142;142;142;142	ENSP00000327255:I215V;ENSP00000432966:I142V;ENSP00000378514:I142V;ENSP00000314850:I142V;ENSP00000435398:I142V;ENSP00000435575:I142V	.	I	+	1	0	PPM1A	59819598	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.251000	0.74343	0.482000	0.46254	ATT		0.393	PPM1A-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276949.2	NM_021003	
SIX1	6495	broad.mit.edu	37	14	61113081	61113081	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:61113081C>T	ENST00000247182.6	-	2	1047	c.775G>A	c.(775-777)Ggc>Agc	p.G259S	SIX1_ENST00000554986.1_Missense_Mutation_p.G86S	NM_005982.3	NP_005973.1	Q15475	SIX1_HUMAN	SIX homeobox 1	259					aorta morphogenesis (GO:0035909)|apoptotic process (GO:0006915)|branching involved in ureteric bud morphogenesis (GO:0001658)|cochlea morphogenesis (GO:0090103)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic skeletal system morphogenesis (GO:0048704)|epithelial cell differentiation (GO:0030855)|facial nerve morphogenesis (GO:0021610)|generation of neurons (GO:0048699)|inner ear development (GO:0048839)|inner ear morphogenesis (GO:0042472)|kidney development (GO:0001822)|mesonephric tubule formation (GO:0072172)|metanephric mesenchyme development (GO:0072075)|middle ear morphogenesis (GO:0042474)|myoblast migration (GO:0051451)|negative regulation of branching involved in ureteric bud morphogenesis (GO:0090191)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron fate specification (GO:0048665)|organ induction (GO:0001759)|otic vesicle development (GO:0071599)|outflow tract morphogenesis (GO:0003151)|pattern specification process (GO:0007389)|pharyngeal system development (GO:0060037)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of mesenchymal cell proliferation involved in ureter development (GO:2000729)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ureteric bud formation (GO:0072107)|protein localization to nucleus (GO:0034504)|regulation of branch elongation involved in ureteric bud branching (GO:0072095)|regulation of neuron differentiation (GO:0045664)|regulation of protein localization (GO:0032880)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|skeletal muscle tissue development (GO:0007519)|thymus development (GO:0048538)|thyroid gland development (GO:0030878)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.G259S(1)		breast(2)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	13				OV - Ovarian serous cystadenocarcinoma(108;0.0201)		GTCTGCAGGCCGTGACTGGGC	0.622																																					p.G259S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G775A	14						.						65.0	67.0	66.0					14																	61113081		2203	4300	6503	60182834	SO:0001583	missense	6495	exon2			X91868	CCDS9748.1	14q23.1	2011-06-20	2007-07-13		ENSG00000126778	ENSG00000126778		"""Homeoboxes / SINE class"""	10887	protein-coding gene	gene with protein product		601205	"""sine oculis homeobox (Drosophila) homolog 1"", ""sine oculis homeobox homolog 1 (Drosophila)"", ""deafness, autosomal dominant 23"""	DFNA23		8617500, 15141091	Standard	NM_005982		Approved		uc001xfb.4	Q15475	OTTHUMG00000140334	ENST00000247182.6:c.775G>A	14.37:g.61113081C>T	ENSP00000247182:p.Gly259Ser		60182834	NM_005982	Q53Y16|Q96H64	Missense_Mutation	SNP	ENST00000247182.6	37	CCDS9748.1	.	.	.	.	.	.	.	.	.	.	C	13.87	2.367411	0.42003	.	.	ENSG00000126778	ENST00000247182;ENST00000555955;ENST00000553535	D;D;D	0.86769	-2.17;-2.08;-2.08	5.08	0.996	0.19844	.	0.262589	0.46758	N	0.000275	T	0.68742	0.3034	N	0.08118	0	0.46609	D	0.999126	B	0.02656	0.0	B	0.01281	0.0	T	0.55817	-0.8081	10	0.08179	T	0.78	-5.7459	10.3571	0.43972	0.0:0.6542:0.0:0.3458	.	259	Q15475	SIX1_HUMAN	S	259;75;75	ENSP00000247182:G259S;ENSP00000450952:G75S;ENSP00000450739:G75S	ENSP00000247182:G259S	G	-	1	0	SIX1	60182834	0.958000	0.32768	0.989000	0.46669	0.936000	0.57629	0.081000	0.14823	0.323000	0.23307	0.655000	0.94253	GGC		0.622	SIX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276951.3		
GPHN	10243	broad.mit.edu	37	14	67631930	67631930	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:67631930C>G	ENST00000315266.5	+	19	2984	c.1863C>G	c.(1861-1863)atC>atG	p.I621M	GPHN_ENST00000478722.1_Missense_Mutation_p.I654M|GPHN_ENST00000305960.9_Missense_Mutation_p.I590M|GPHN_ENST00000543237.1_Missense_Mutation_p.I667M|GPHN_ENST00000544752.2_3'UTR	NM_001024218.1	NP_001019389.1	Q9NQX3	GEPH_HUMAN	gephyrin	621	MPT adenylyltransferase.				establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycine receptor clustering (GO:0072579)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|molybdopterin adenylyltransferase activity (GO:0061598)|molybdopterin molybdotransferase activity (GO:0061599)|transferase activity (GO:0016740)	p.I654M(1)		large_intestine(8)|liver(1)|ovary(2)|stomach(1)	12		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		GAAAAATAATCTTTGCACTAC	0.333			T	MLL	AL																																p.I621M			Dom	yes		14	14q24	10243	gephyrin (GPH)		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1863G	14						.						136.0	130.0	132.0					14																	67631930		2203	4300	6503	66701683	SO:0001583	missense	10243	exon19			AB037806	CCDS9777.1, CCDS32103.1	14q23.3	2008-04-22			ENSG00000171723	ENSG00000171723			15465	protein-coding gene	gene with protein product		603930				1319186, 10325225, 18403029	Standard	XM_005267250		Approved	KIAA1385	uc001xix.3	Q9NQX3	OTTHUMG00000029785	ENST00000315266.5:c.1863C>G	14.37:g.67631930C>G	ENSP00000312771:p.Ile621Met		66701683	NM_001024218	Q9H4E9|Q9P2G2	Missense_Mutation	SNP	ENST00000315266.5	37	CCDS32103.1	.	.	.	.	.	.	.	.	.	.	C	12.77	2.036525	0.35893	.	.	ENSG00000171723	ENST00000315266;ENST00000478722;ENST00000543237;ENST00000305960;ENST00000555503	T;T;T;T;T	0.79940	-1.32;-1.32;-1.32;-1.32;-1.32	4.89	0.488	0.16848	Molybdenum cofactor synthesis (1);Molybdopterin binding (4);	0.095950	0.64402	D	0.000001	D	0.83147	0.5191	L	0.58969	1.84	0.50632	D	0.999889	B;P;P;B	0.38978	0.444;0.599;0.652;0.444	P;P;P;P	0.59703	0.784;0.707;0.862;0.733	T	0.77169	-0.2686	10	0.45353	T	0.12	-6.9132	4.8899	0.13722	0.5338:0.2792:0.0:0.187	.	590;667;621;654	F8W7D6;F5H039;Q9NQX3;Q9NQX3-2	.;.;GEPH_HUMAN;.	M	621;654;667;590;146	ENSP00000312771:I621M;ENSP00000417901:I654M;ENSP00000438404:I667M;ENSP00000303019:I590M;ENSP00000452009:I146M	ENSP00000303019:I590M	I	+	3	3	GPHN	66701683	1.000000	0.71417	0.997000	0.53966	0.977000	0.68977	1.223000	0.32527	-0.099000	0.12263	-0.314000	0.08810	ATC		0.333	GPHN-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000074299.2	NM_020806	
GALNT16	57452	broad.mit.edu	37	14	69787444	69787444	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:69787444C>T	ENST00000337827.4	+	2	521	c.194C>T	c.(193-195)tCg>tTg	p.S65L	GALNT16_ENST00000553669.1_Missense_Mutation_p.S65L|GALNT16_ENST00000448469.3_Missense_Mutation_p.S65L	NM_001168368.1|NM_020692.2	NP_001161840.1|NP_065743.2	Q8N428	GLT16_HUMAN	polypeptide N-acetylgalactosaminyltransferase 16	65					protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.S65L(1)									GGAACTCCCTCGAAAGGCTTT	0.592																																					p.S65L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C194T	14						.						100.0	99.0	99.0					14																	69787444		2203	4300	6503	68857197	SO:0001583	missense	57452	exon2			AB032956	CCDS32107.1	14q24.1	2014-03-13	2014-03-13	2013-01-25	ENSG00000100626	ENSG00000100626	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	23233	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 16"""	615132	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 1"", ""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 16"""	GALNTL1		10574461, 22186971	Standard	NM_020692		Approved	KIAA1130, GalNAc-T16	uc010aqu.2	Q8N428	OTTHUMG00000171231	ENST00000337827.4:c.194C>T	14.37:g.69787444C>T	ENSP00000336729:p.Ser65Leu		68857197	NM_020692	Q4KMG3|Q58A55|Q9ULT9	Missense_Mutation	SNP	ENST00000337827.4	37	CCDS32107.1	.	.	.	.	.	.	.	.	.	.	C	11.58	1.680050	0.29783	.	.	ENSG00000100626	ENST00000337827;ENST00000448469;ENST00000553669	T;T;T	0.55234	0.65;0.65;0.53	5.62	4.72	0.59763	.	2.186910	0.01753	N	0.030044	T	0.25606	0.0623	N	0.01576	-0.805	0.09310	N	1	B;B	0.12630	0.001;0.006	B;B	0.04013	0.001;0.001	T	0.44375	-0.9332	10	0.10636	T	0.68	.	5.7113	0.17937	0.0:0.6564:0.1882:0.1553	.	65;65	Q8N428;Q58A55	GLTL1_HUMAN;.	L	65	ENSP00000336729:S65L;ENSP00000402970:S65L;ENSP00000451200:S65L	ENSP00000336729:S65L	S	+	2	0	GALNTL1	68857197	0.071000	0.21146	0.868000	0.34077	0.949000	0.60115	1.107000	0.31110	2.660000	0.90430	0.650000	0.86243	TCG		0.592	GALNT16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412434.1	NM_001168368	
SIPA1L1	26037	broad.mit.edu	37	14	72054762	72054762	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:72054762G>A	ENST00000555818.1	+	2	521	c.173G>A	c.(172-174)cGa>cAa	p.R58Q	SIPA1L1_ENST00000358550.2_Missense_Mutation_p.R58Q|SIPA1L1_ENST00000381232.3_Missense_Mutation_p.R58Q	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	58					actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)	p.R58Q(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		GGACCCCCCCGAAGTGAAGGT	0.517																																					p.R58Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G173A	14						.						64.0	72.0	69.0					14																	72054762		2203	4300	6503	71124515	SO:0001583	missense	26037	exon2			AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.173G>A	14.37:g.72054762G>A	ENSP00000450832:p.Arg58Gln		71124515	NM_015556	J3KP19|O95321|Q9UDU4|Q9UNU4	Missense_Mutation	SNP	ENST00000555818.1	37	CCDS9807.1	.	.	.	.	.	.	.	.	.	.	G	14.09	2.431633	0.43122	.	.	ENSG00000197555	ENST00000381232;ENST00000555818;ENST00000358550	T;T;T	0.76448	-1.02;-1.02;-1.02	5.48	5.48	0.80851	.	0.150774	0.46442	D	0.000293	T	0.78780	0.4337	L	0.43152	1.355	0.80722	D	1	D;D;D	0.61697	0.99;0.973;0.99	P;P;P	0.50049	0.629;0.449;0.629	T	0.76282	-0.3016	10	0.32370	T	0.25	-8.9266	19.7112	0.96096	0.0:0.0:1.0:0.0	.	58;58;58	A6H8W6;O43166-2;O43166	.;.;SI1L1_HUMAN	Q	58	ENSP00000370630:R58Q;ENSP00000450832:R58Q;ENSP00000351352:R58Q	ENSP00000351352:R58Q	R	+	2	0	SIPA1L1	71124515	1.000000	0.71417	0.883000	0.34634	0.335000	0.28730	7.841000	0.86834	2.722000	0.93159	0.655000	0.94253	CGA		0.517	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556	
ABCD4	5826	broad.mit.edu	37	14	74753472	74753472	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:74753472G>A	ENST00000356924.4	-	18	1827	c.1684C>T	c.(1684-1686)Ctc>Ttc	p.L562F	AC005519.4_ENST00000554532.2_RNA|ABCD4_ENST00000298816.7_Missense_Mutation_p.L458F	NM_005050.3	NP_005041.1	O14678	ABCD4_HUMAN	ATP-binding cassette, sub-family D (ALD), member 4	562	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cobalamin metabolic process (GO:0009235)|transmembrane transport (GO:0055085)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)	p.L562F(1)		cervix(2)|endometrium(3)|kidney(3)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	27				BRCA - Breast invasive adenocarcinoma(234;0.00153)		ATGCGATAGAGCTCGCTCTCC	0.607																																					p.L562F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1684T	14						.						81.0	64.0	70.0					14																	74753472		2203	4300	6503	73823225	SO:0001583	missense	5826	exon18			AF009746	CCDS9828.1	14q24	2012-03-14			ENSG00000119688	ENSG00000119688		"""ATP binding cassette transporters / subfamily D"""	68	protein-coding gene	gene with protein product		603214		PXMP1L		9266848, 9302272	Standard	NR_003256		Approved	PMP69, P70R, EST352188	uc001xpr.2	O14678	OTTHUMG00000171207	ENST00000356924.4:c.1684C>T	14.37:g.74753472G>A	ENSP00000349396:p.Leu562Phe		73823225	NM_005050	A8K5L7|Q6IAQ0|Q96E75	Missense_Mutation	SNP	ENST00000356924.4	37	CCDS9828.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.114350	0.77210	.	.	ENSG00000119688	ENST00000356924;ENST00000298816	D;D	0.99874	-2.96;-7.39	5.18	4.29	0.51040	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.070653	0.64402	N	0.000016	D	0.99609	0.9858	L	0.54965	1.715	0.80722	D	1	D;D;P	0.57899	0.981;0.968;0.858	P;P;P	0.54401	0.751;0.708;0.6	D	0.97335	0.9953	10	0.72032	D	0.01	.	13.9895	0.64357	0.0725:0.0:0.9275:0.0	.	458;562;562	F8W7M4;A8K5L7;O14678	.;.;ABCD4_HUMAN	F	562;458	ENSP00000349396:L562F;ENSP00000298816:L458F	ENSP00000298816:L458F	L	-	1	0	ABCD4	73823225	1.000000	0.71417	1.000000	0.80357	0.869000	0.49853	6.047000	0.71038	1.426000	0.47256	-0.157000	0.13467	CTC		0.607	ABCD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314382.1	NM_005050	
ZC2HC1C	79696	broad.mit.edu	37	14	75538417	75538417	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:75538417G>A	ENST00000524913.1	+	2	1630	c.1141G>A	c.(1141-1143)Ggc>Agc	p.G381S	ACYP1_ENST00000555463.1_5'Flank|ZC2HC1C_ENST00000439583.2_Intron|ZC2HC1C_ENST00000238686.8_Missense_Mutation_p.G381S|ZC2HC1C_ENST00000526748.1_Intron	NM_024643.2	NP_078919.2	Q53FD0	ZC21C_HUMAN	zinc finger, C2HC-type containing 1C	381							metal ion binding (GO:0046872)	p.G381S(1)									AGGTTCCAGCGGCTCCATTGA	0.577																																					p.G381S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1141A	14						.						27.0	29.0	28.0					14																	75538417		1977	4158	6135	74608170	SO:0001583	missense	79696	exon2			AK026746	CCDS41972.1, CCDS45138.1	14q24.3	2013-01-10	2012-02-03	2012-02-03	ENSG00000119703	ENSG00000119703		"""Zinc fingers, C2HC-type containing"""	20354	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 140"", ""family with sequence similarity 164, member C"""	C14orf140, FAM164C			Standard	XM_005268062		Approved		uc001xrh.3	Q53FD0	OTTHUMG00000167439	ENST00000524913.1:c.1141G>A	14.37:g.75538417G>A	ENSP00000435550:p.Gly381Ser		74608170	NM_024643	E9PJQ0|Q9BTA8|Q9H5S9	Missense_Mutation	SNP	ENST00000524913.1	37	CCDS41972.1	.	.	.	.	.	.	.	.	.	.	G	5.925	0.354697	0.11239	.	.	ENSG00000119703	ENST00000524913;ENST00000238686	T	0.39592	1.07	5.33	-1.59	0.08453	.	0.994165	0.08163	N	0.988268	T	0.20047	0.0482	N	0.16368	0.405	0.23936	N	0.996416	B	0.16802	0.019	B	0.09377	0.004	T	0.21042	-1.0257	9	.	.	.	-1.0629	1.8109	0.03090	0.4567:0.0814:0.2314:0.2305	.	381	E9PJQ0	.	S	381	ENSP00000435550:G381S	.	G	+	1	0	FAM164C	74608170	0.045000	0.20229	0.087000	0.20705	0.609000	0.37215	0.056000	0.14256	-0.115000	0.11915	0.655000	0.94253	GGC		0.577	ZC2HC1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394616.4	NM_001042430	
PTPN21	11099	broad.mit.edu	37	14	88946606	88946606	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:88946606C>T	ENST00000556564.1	-	13	1453	c.1169G>A	c.(1168-1170)cGt>cAt	p.R390H	PTPN21_ENST00000328736.3_Missense_Mutation_p.R390H	NM_007039.3	NP_008970.2	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type 21	390					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein tyrosine phosphatase activity (GO:0004725)	p.R390H(2)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|liver(1)|lung(7)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						ACTGCCATTACGGATCCGACC	0.507																																					p.R390H												.	.	2	Substitution - Missense(2)	large_intestine(1)|skin(1)	c.G1169A	14						.						98.0	78.0	85.0					14																	88946606		2203	4300	6503	88016359	SO:0001583	missense	11099	exon13			X79510	CCDS9884.1	14q31	2011-06-09				ENSG00000070778		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9651	protein-coding gene	gene with protein product		603271				7519780	Standard	NM_007039		Approved	PTPD1, PTPRL10	uc001xwv.4	Q16825		ENST00000556564.1:c.1169G>A	14.37:g.88946606C>T	ENSP00000452414:p.Arg390His		88016359	NM_007039		Missense_Mutation	SNP	ENST00000556564.1	37	CCDS9884.1	.	.	.	.	.	.	.	.	.	.	C	16.87	3.242843	0.58995	.	.	ENSG00000070778	ENST00000328736;ENST00000556564	T;T	0.73152	-0.72;-0.72	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	D	0.84106	0.5399	M	0.71581	2.175	0.51482	D	0.999928	D	0.89917	1.0	D	0.83275	0.996	D	0.84247	0.0475	10	0.52906	T	0.07	.	19.3874	0.94563	0.0:1.0:0.0:0.0	.	390	Q16825	PTN21_HUMAN	H	390	ENSP00000330276:R390H;ENSP00000452414:R390H	ENSP00000330276:R390H	R	-	2	0	PTPN21	88016359	1.000000	0.71417	0.265000	0.24526	0.212000	0.24457	6.089000	0.71384	2.590000	0.87494	0.561000	0.74099	CGT		0.507	PTPN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410303.1		
KCNK13	56659	broad.mit.edu	37	14	90650709	90650709	+	Missense_Mutation	SNP	G	G	A	rs536825700		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:90650709G>A	ENST00000282146.4	+	2	1030	c.589G>A	c.(589-591)Gtc>Atc	p.V197I		NM_022054.2	NP_071337.2	Q9HB14	KCNKD_HUMAN	potassium channel, subfamily K, member 13	197					synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)	p.V197I(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(12)|prostate(1)|skin(4)	25		all_cancers(154;0.186)				CGTGTACTACGTCATGCTGAT	0.607													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19493	0.0		0.0	False		,,,				2504	0.0				p.V197I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G589A	14						.						151.0	127.0	135.0					14																	90650709		2203	4300	6503	89720462	SO:0001583	missense	56659	exon2			AF287303	CCDS9889.1	14q32.11	2012-03-07				ENSG00000152315		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6275	protein-coding gene	gene with protein product		607367				11060316, 16382106	Standard	NM_022054		Approved	K2p13.1, THIK-1, THIK1	uc001xye.1	Q9HB14		ENST00000282146.4:c.589G>A	14.37:g.90650709G>A	ENSP00000282146:p.Val197Ile		89720462	NM_022054	B5TJL8|Q96E79	Missense_Mutation	SNP	ENST00000282146.4	37	CCDS9889.1	.	.	.	.	.	.	.	.	.	.	G	17.72	3.458963	0.63401	.	.	ENSG00000152315	ENST00000282146	T	0.14893	2.47	5.31	5.31	0.75309	.	0.000000	0.37393	N	0.002109	T	0.39517	0.1081	M	0.62154	1.92	0.80722	D	1	D	0.76494	0.999	D	0.65140	0.932	T	0.06991	-1.0796	10	0.46703	T	0.11	.	18.9479	0.92628	0.0:0.0:1.0:0.0	.	197	Q9HB14	KCNKD_HUMAN	I	197	ENSP00000282146:V197I	ENSP00000282146:V197I	V	+	1	0	KCNK13	89720462	1.000000	0.71417	0.825000	0.32803	0.068000	0.16541	9.842000	0.99487	2.476000	0.83614	0.655000	0.94253	GTC		0.607	KCNK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411251.1	NM_022054	
TTC7B	145567	broad.mit.edu	37	14	91121401	91121401	+	Silent	SNP	C	C	T	rs117707187	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:91121401C>T	ENST00000328459.6	-	12	1516	c.1395G>A	c.(1393-1395)acG>acA	p.T465T	TTC7B_ENST00000357056.2_Silent_p.T465T	NM_001010854.1	NP_001010854.1	Q86TV6	TTC7B_HUMAN	tetratricopeptide repeat domain 7B	465								p.T465T(1)		NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	36		Melanoma(154;0.222)				TGAACTCTGACGTTTTCTCTC	0.493													C|||	4	0.000798722	0.0	0.0	5008	,	,		19463	0.001		0.003	False		,,,				2504	0.0				p.T465T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1395A	14						.	C		8,4398	14.3+/-33.2	0,8,2195	121.0	102.0	108.0		1395	-7.4	0.8	14	dbSNP_132	108	20,8580	15.3+/-51.7	0,20,4280	no	coding-synonymous	TTC7B	NM_001010854.1		0,28,6475	TT,TC,CC		0.2326,0.1816,0.2153		465/844	91121401	28,12978	2203	4300	6503	90191154	SO:0001819	synonymous_variant	145567	exon12			BC035865	CCDS32140.1	14q32.12	2013-01-11	2004-06-02	2004-06-04		ENSG00000165914		"""Tetratricopeptide (TTC) repeat domain containing"""	19858	protein-coding gene	gene with protein product			"""tetratricopeptide repeat domain 7 like 1"""	TTC7L1			Standard	XM_005267367		Approved		uc001xyp.3	Q86TV6		ENST00000328459.6:c.1395G>A	14.37:g.91121401C>T			90191154	NM_001010854	Q86U24|Q86VT3	Silent	SNP	ENST00000328459.6	37	CCDS32140.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	9.223	1.033865	0.19590	0.001816	0.002326	ENSG00000165914	ENST00000554462	.	.	.	5.75	-7.36	0.01417	.	.	.	.	.	T	0.46521	0.1397	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51403	-0.8710	4	.	.	.	-17.1517	6.8467	0.23992	0.0854:0.1305:0.1639:0.6202	.	.	.	.	I	135	.	.	V	-	1	0	TTC7B	90191154	0.000000	0.05858	0.811000	0.32455	0.973000	0.67179	-2.982000	0.00662	-1.050000	0.03230	-1.202000	0.01658	GTC		0.493	TTC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411364.2		
CATSPERB	79820	broad.mit.edu	37	14	92126207	92126207	+	Missense_Mutation	SNP	C	C	T	rs145060222		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:92126207C>T	ENST00000256343.3	-	15	1562	c.1406G>A	c.(1405-1407)cGt>cAt	p.R469H		NM_024764.2	NP_079040.2	Q9H7T0	CTSRB_HUMAN	catsper channel auxiliary subunit beta	469					cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|cilium (GO:0005929)|plasma membrane (GO:0005886)		p.R469H(1)		NS(1)|breast(4)|central_nervous_system(1)|kidney(3)|large_intestine(15)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(2)	54		all_cancers(154;0.0663)|all_epithelial(191;0.236)				AACCTTTCCACGTTGAGAAAC	0.363																																					p.R469H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1406A	14						.	C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	71.0	70.0	71.0		1406	1.2	0.2	14	dbSNP_134	71	0,8600		0,0,4300	no	missense	CATSPERB	NM_024764.2	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	469/1117	92126207	1,13005	2203	4300	6503	91195960	SO:0001583	missense	79820	exon15			AK024360	CCDS32142.1	14q32.12	2012-02-22	2012-02-22	2007-10-18	ENSG00000133962	ENSG00000133962			20500	protein-coding gene	gene with protein product		611169	"""chromosome 14 open reading frame 161"", ""cation channel, sperm-associated, beta"""	C14orf161		17478420	Standard	NM_024764		Approved	FLJ14298	uc001xzs.1	Q9H7T0	OTTHUMG00000171118	ENST00000256343.3:c.1406G>A	14.37:g.92126207C>T	ENSP00000256343:p.Arg469His		91195960	NM_024764	A0AV51	Missense_Mutation	SNP	ENST00000256343.3	37	CCDS32142.1	.	.	.	.	.	.	.	.	.	.	C	10.03	1.239223	0.22711	2.27E-4	0.0	ENSG00000133962	ENST00000256343	T	0.43688	0.94	4.76	1.25	0.21368	.	1.255810	0.05407	N	0.541778	T	0.27697	0.0681	N	0.22421	0.69	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.22836	-1.0205	10	0.41790	T	0.15	-2.0301	3.4961	0.07655	0.0:0.409:0.2905:0.3005	.	469	Q9H7T0	CTSRB_HUMAN	H	469	ENSP00000256343:R469H	ENSP00000256343:R469H	R	-	2	0	CATSPERB	91195960	0.000000	0.05858	0.169000	0.22859	0.098000	0.18820	-0.945000	0.03909	0.441000	0.26529	0.555000	0.69702	CGT		0.363	CATSPERB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411769.1	NM_024764	
ASB2	51676	broad.mit.edu	37	14	94405566	94405566	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:94405566C>T	ENST00000315988.4	-	6	1849	c.1361G>A	c.(1360-1362)gGc>gAc	p.G454D	RP11-131H24.4_ENST00000557646.1_5'Flank|ASB2_ENST00000555019.1_Missense_Mutation_p.G502D|ASB2_ENST00000556337.1_5'Flank	NM_016150.4	NP_057234.2	Q96Q27	ASB2_HUMAN	ankyrin repeat and SOCS box containing 2	454					intracellular signal transduction (GO:0035556)|myoblast differentiation (GO:0045445)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)	Cul5-RING ubiquitin ligase complex (GO:0031466)	ubiquitin-protein transferase activity (GO:0004842)	p.G454D(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1)|urinary_tract(1)	27		all_cancers(154;0.13)		COAD - Colon adenocarcinoma(157;0.217)|Epithelial(152;0.232)		GCAGGGCTCGCCGTCGCAGCC	0.687																																					p.G454D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1361A	14						.						29.0	29.0	29.0					14																	94405566		2201	4298	6499	93475319	SO:0001583	missense	51676	exon6			AF159164	CCDS9915.1, CCDS55940.1	14q31-q32	2013-01-10	2011-01-25					"""Ankyrin repeat domain containing"""	16012	protein-coding gene	gene with protein product		605759	"""ankyrin repeat and SOCS box-containing 2"""				Standard	NM_016150		Approved	ASB-2	uc001ycd.3	Q96Q27		ENST00000315988.4:c.1361G>A	14.37:g.94405566C>T	ENSP00000320675:p.Gly454Asp		93475319	NM_016150	B2RDP9|B4E166|Q9NSU5|Q9Y567	Missense_Mutation	SNP	ENST00000315988.4	37	CCDS9915.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.201233	0.79015	.	.	ENSG00000100628	ENST00000555019;ENST00000434324;ENST00000315988;ENST00000543546;ENST00000555507	T;T;T	0.67171	-0.25;-0.21;-0.18	5.07	5.07	0.68467	.	0.054069	0.64402	D	0.000001	T	0.57504	0.2058	N	0.04508	-0.205	0.45227	D	0.998231	D;D;D	0.62365	0.978;0.991;0.978	P;P;P	0.62089	0.88;0.898;0.88	T	0.55617	-0.8113	10	0.12103	T	0.63	.	13.232	0.59949	0.0:0.7034:0.2966:0.0	.	470;502;454	B3KPZ6;B4E166;Q96Q27	.;.;ASB2_HUMAN	D	502;470;454;400;400	ENSP00000451575:G502D;ENSP00000320675:G454D;ENSP00000450940:G400D	ENSP00000320675:G454D	G	-	2	0	ASB2	93475319	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.699000	0.61796	2.362000	0.80069	0.462000	0.41574	GGC		0.687	ASB2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412845.1		
ASB2	51676	broad.mit.edu	37	14	94405798	94405798	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:94405798A>G	ENST00000315988.4	-	6	1617	c.1129T>C	c.(1129-1131)Tac>Cac	p.Y377H	RP11-131H24.4_ENST00000557646.1_5'Flank|ASB2_ENST00000555019.1_Missense_Mutation_p.Y425H|ASB2_ENST00000556337.1_5'UTR	NM_016150.4	NP_057234.2	Q96Q27	ASB2_HUMAN	ankyrin repeat and SOCS box containing 2	377					intracellular signal transduction (GO:0035556)|myoblast differentiation (GO:0045445)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)	Cul5-RING ubiquitin ligase complex (GO:0031466)	ubiquitin-protein transferase activity (GO:0004842)	p.Y377H(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1)|urinary_tract(1)	27		all_cancers(154;0.13)		COAD - Colon adenocarcinoma(157;0.217)|Epithelial(152;0.232)		TCGGTGGCGTACACGTTGTTG	0.687																																					p.Y377H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1129C	14						.						37.0	30.0	32.0					14																	94405798		2200	4296	6496	93475551	SO:0001583	missense	51676	exon6			AF159164	CCDS9915.1, CCDS55940.1	14q31-q32	2013-01-10	2011-01-25					"""Ankyrin repeat domain containing"""	16012	protein-coding gene	gene with protein product		605759	"""ankyrin repeat and SOCS box-containing 2"""				Standard	NM_016150		Approved	ASB-2	uc001ycd.3	Q96Q27		ENST00000315988.4:c.1129T>C	14.37:g.94405798A>G	ENSP00000320675:p.Tyr377His		93475551	NM_016150	B2RDP9|B4E166|Q9NSU5|Q9Y567	Missense_Mutation	SNP	ENST00000315988.4	37	CCDS9915.1	.	.	.	.	.	.	.	.	.	.	A	9.558	1.117799	0.20877	.	.	ENSG00000100628	ENST00000555019;ENST00000434324;ENST00000315988;ENST00000543546;ENST00000555507	T;T;T	0.63580	-0.05;-0.05;-0.05	4.75	1.02	0.19986	Ankyrin repeat-containing domain (4);	0.660669	0.15679	N	0.249997	T	0.34454	0.0898	N	0.04787	-0.16	0.32108	N	0.589732	B;B;B	0.11235	0.0;0.004;0.001	B;B;B	0.12156	0.004;0.007;0.004	T	0.18147	-1.0346	10	0.45353	T	0.12	-24.5954	4.2345	0.10618	0.6305:0.0:0.2322:0.1373	.	393;425;377	B3KPZ6;B4E166;Q96Q27	.;.;ASB2_HUMAN	H	425;393;377;323;323	ENSP00000451575:Y425H;ENSP00000320675:Y377H;ENSP00000450940:Y323H	ENSP00000320675:Y377H	Y	-	1	0	ASB2	93475551	0.919000	0.31177	0.990000	0.47175	0.935000	0.57460	0.751000	0.26348	-0.067000	0.12976	0.379000	0.24179	TAC		0.687	ASB2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412845.1		
SERPINA4	5267	broad.mit.edu	37	14	95033476	95033476	+	Silent	SNP	C	C	T	rs148891129	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:95033476C>T	ENST00000557004.1	+	3	1240	c.819C>T	c.(817-819)gaC>gaT	p.D273D	SERPINA5_ENST00000553780.1_Intron|SERPINA4_ENST00000555095.1_Silent_p.D273D|SERPINA4_ENST00000298841.5_Silent_p.D273D			P29622	KAIN_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 4	273					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.D273D(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(9)|lung(28)|ovary(3)|skin(1)|urinary_tract(1)	46				COAD - Colon adenocarcinoma(157;0.211)		ACAAAGGAGACGCAACCGTGT	0.502													C|||	2	0.000399361	0.0015	0.0	5008	,	,		20647	0.0		0.0	False		,,,				2504	0.0				p.D273D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C819T	14						.	C		7,4399	11.4+/-27.6	0,7,2196	117.0	105.0	109.0		819	-6.9	0.0	14	dbSNP_134	109	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SERPINA4	NM_006215.2		0,8,6495	TT,TC,CC		0.0116,0.1589,0.0615		273/428	95033476	8,12998	2203	4300	6503	94103229	SO:0001819	synonymous_variant	5267	exon3			L19684	CCDS9927.1	14q32.13	2014-02-18	2005-08-18		ENSG00000100665	ENSG00000100665		"""Serine (or cysteine) peptidase inhibitors"""	8948	protein-coding gene	gene with protein product		147935	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 4"""	PI4		8227002, 24172014	Standard	NM_001289032		Approved	KST, KAL, KLST, kallistatin	uc001ydk.3	P29622	OTTHUMG00000170859	ENST00000557004.1:c.819C>T	14.37:g.95033476C>T			94103229	NM_006215	Q53XB5|Q86TR9|Q96BZ5	Silent	SNP	ENST00000557004.1	37	CCDS9927.1																																																																																				0.502	SERPINA4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410718.1	NM_006215	
CYP46A1	10858	broad.mit.edu	37	14	100166406	100166406	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:100166406G>A	ENST00000261835.3	+	5	515	c.411G>A	c.(409-411)caG>caA	p.Q137Q	CYP46A1_ENST00000423126.2_Silent_p.Q40Q	NM_006668.1	NP_006659.1	Q9Y6A2	CP46A_HUMAN	cytochrome P450, family 46, subfamily A, polypeptide 1	137					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cholesterol catabolic process (GO:0006707)|nervous system development (GO:0007399)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	cholesterol 24-hydroxylase activity (GO:0033781)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid hydroxylase activity (GO:0008395)	p.Q137Q(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|prostate(1)|skin(1)	25		Melanoma(154;0.0866)|all_epithelial(191;0.179)				GGCACAAGCAGCGGAGAGTCA	0.627																																					p.Q137Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G411A	14						.						76.0	64.0	68.0					14																	100166406		2203	4300	6503	99236159	SO:0001819	synonymous_variant	10858	exon5			AF094480	CCDS9954.1	14q32.2	2013-05-03	2003-02-14	2003-02-28	ENSG00000036530	ENSG00000036530		"""Cytochrome P450s"""	2641	protein-coding gene	gene with protein product		604087	"""cytochrome P450, subfamily 46 (cholesterol 24-hydroxylase)"""	CYP46		10377398	Standard	NM_006668		Approved		uc001ygo.3	Q9Y6A2	OTTHUMG00000171510	ENST00000261835.3:c.411G>A	14.37:g.100166406G>A			99236159	NM_006668	B4DHP8|E7EQG9|Q8N2B0	Silent	SNP	ENST00000261835.3	37	CCDS9954.1	.	.	.	.	.	.	.	.	.	.	G	9.718	1.159015	0.21454	.	.	ENSG00000036530	ENST00000380228	.	.	.	4.84	3.95	0.45737	.	.	.	.	.	T	0.59865	0.2225	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57441	-0.7811	4	.	.	.	.	9.8766	0.41207	0.0978:0.0:0.9022:0.0	.	.	.	.	T	124	.	.	A	+	1	0	CYP46A1	99236159	1.000000	0.71417	0.999000	0.59377	0.958000	0.62258	2.416000	0.44644	1.350000	0.45770	0.655000	0.94253	GCG		0.627	CYP46A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413814.1		
PPP1R13B	23368	broad.mit.edu	37	14	104202439	104202439	+	Silent	SNP	G	G	A	rs371359449		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:104202439G>A	ENST00000202556.9	-	16	3414	c.3132C>T	c.(3130-3132)gaC>gaT	p.D1044D	PPP1R13B_ENST00000555391.1_5'UTR|PPP1R13B_ENST00000423488.2_3'UTR	NM_015316.2	NP_056131.2	Q96KQ4	ASPP1_HUMAN	protein phosphatase 1, regulatory subunit 13B	1044	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				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.D1044D(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)				TGGTGAGGGCGTCCCCTTCGT	0.607													G|||	1	0.000199681	0.0	0.0	5008	,	,		20970	0.0		0.0	False		,,,				2504	0.001				p.D1044D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3132T	14						.	G		0,4260		0,0,2130	120.0	125.0	124.0		3132	-7.3	0.8	14		124	1,8449		0,1,4224	no	coding-synonymous	PPP1R13B	NM_015316.2		0,1,6354	AA,AG,GG		0.0118,0.0,0.0079		1044/1091	104202439	1,12709	2130	4225	6355	103272192	SO:0001819	synonymous_variant	23368	exon16			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.3132C>T	14.37:g.104202439G>A			103272192	NM_015316	B2RMX5|O94870	Silent	SNP	ENST00000202556.9	37	CCDS41997.1																																																																																				0.607	PPP1R13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414591.1	NM_015316	
PPP1R13B	23368	broad.mit.edu	37	14	104208418	104208418	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:104208418delG	ENST00000202556.9	-	11	1813	c.1531delC	c.(1531-1533)cagfs	p.Q511fs	PPP1R13B_ENST00000555391.1_5'UTR|PPP1R13B_ENST00000423488.2_5'UTR	NM_015316.2	NP_056131.2	Q96KQ4	ASPP1_HUMAN	protein phosphatase 1, regulatory subunit 13B	511	Pro-rich.				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.Q511fs*39(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)				GAGCCTGGCTGGGGGGTGCTG	0.647																																					p.Q511fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1531delC	14						.						67.0	77.0	74.0					14																	104208418		1952	4131	6083	103278171	SO:0001589	frameshift_variant	23368	exon11			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.1531delC	14.37:g.104208418delG	ENSP00000202556:p.Gln511fs		103278171	NM_015316	B2RMX5|O94870	Frame_Shift_Del	DEL	ENST00000202556.9	37	CCDS41997.1																																																																																				0.647	PPP1R13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414591.1	NM_015316	
ASPG	374569	broad.mit.edu	37	14	104571684	104571684	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:104571684delG	ENST00000551177.1	+	10	1162	c.1070delG	c.(1069-1071)cggfs	p.R357fs	ASPG_ENST00000549809.1_3'UTR|ASPG_ENST00000546892.2_Frame_Shift_Del_p.R357fs|ASPG_ENST00000455920.2_Frame_Shift_Del_p.R357fs	NM_001080464.2	NP_001073933.2	Q86U10	LPP60_HUMAN	asparaginase	357					asparagine metabolic process (GO:0006528)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)		1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)|asparaginase activity (GO:0004067)|lysophospholipase activity (GO:0004622)	p.E387fs*2(1)|p.E359fs*2(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	11						AAGGACCTTCGGGGGGAGATG	0.682																																					p.R357fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.1070delG	14						.						36.0	42.0	40.0					14																	104571684		2113	4232	6345	103641437	SO:0001589	frameshift_variant	374569	exon10				CCDS45170.1, CCDS45170.2	14q32.33	2014-03-14	2014-03-14	2008-11-06	ENSG00000166183	ENSG00000166183	3.1.1.5, 3.5.1.1	"""Ankyrin repeat domain containing"""	20123	protein-coding gene	gene with protein product	"""60-kDa-lysophospholipase"""		"""chromosome 14 open reading frame 76"", ""asparaginase homolog (S. cerevisiae)"""	C14orf76			Standard	NM_001080464		Approved		uc001yoq.2	Q86U10		ENST00000551177.1:c.1070delG	14.37:g.104571684delG	ENSP00000450040:p.Arg357fs		103641437	NM_001080464	B9EGQ2|Q8IV80	Frame_Shift_Del	DEL	ENST00000551177.1	37	CCDS45170.2																																																																																				0.682	ASPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407005.1	NM_001080464	
ACOT4	122970	broad.mit.edu	37	14	74060514	74060517	+	Frame_Shift_Del	DEL	CTTA	CTTA	-	rs74553611|rs562751690|rs77261428|rs77814755|rs375801976|rs77408762	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	CTTA	CTTA	CTTA	-	CTTA	-	Unknown	Valid	Germline	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr14:74060514_74060517delCTTA	ENST00000326303.4	+	2	820_823	c.566_569delCTTA	c.(565-570)gcttatfs	p.AY189fs		NM_152331.3	NP_689544.3	Q8N9L9	ACOT4_HUMAN	acyl-CoA thioesterase 4	189				ALAY -> DLQS (in Ref. 1; BAC04313). {ECO:0000305}.	acyl-CoA metabolic process (GO:0006637)|dicarboxylic acid catabolic process (GO:0043649)|dicarboxylic acid metabolic process (GO:0043648)|long-chain fatty acid metabolic process (GO:0001676)|saturated monocarboxylic acid metabolic process (GO:0032788)|short-chain fatty acid metabolic process (GO:0046459)|succinyl-CoA metabolic process (GO:0006104)|unsaturated monocarboxylic acid metabolic process (GO:0032789)|very long-chain fatty acid metabolic process (GO:0000038)	peroxisome (GO:0005777)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)|succinyl-CoA hydrolase activity (GO:0004778)	p.A189fs*32(2)		endometrium(1)|large_intestine(3)|lung(4)	8				BRCA - Breast invasive adenocarcinoma(234;0.00331)		TTGGCTCTAGCTTATTATAACTTT	0.495																																					p.189_190del												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.566_569del	14						.			103,4159		3,97,2031						4.3	1.0			126	861,7311		130,601,3355	no	frameshift	ACOT4	NM_152331.3		133,698,5386	A1A1,A1R,RR		10.536,2.4167,7.7529				964,11470				73130270	SO:0001589	frameshift_variant	122970	exon2			BC031799	CCDS9817.1	14q24.1	2011-02-16			ENSG00000177465	ENSG00000177465		"""Acyl CoA thioesterases"""	19748	protein-coding gene	gene with protein product		614314				16103133, 16940157	Standard	NM_152331		Approved	FLJ31235, PTE-Ib, PTE2B	uc001xoo.3	Q8N9L9	OTTHUMG00000169485	ENST00000326303.4:c.566_569delCTTA	14.37:g.74060514_74060517delCTTA	ENSP00000323071:p.Ala189fs		73130267	NM_152331	Q17RF4|Q5BKT6|Q86TX0|Q86TX1|Q96N88	Frame_Shift_Del	DEL	ENST00000326303.4	37	CCDS9817.1																																																																																				0.495	ACOT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404298.2	NM_152331	
TRPM1	4308	broad.mit.edu	37	15	31295081	31295081	+	Silent	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr15:31295081T>C	ENST00000256552.6	-	28	3969	c.3822A>G	c.(3820-3822)gaA>gaG	p.E1274E	TRPM1_ENST00000542188.1_Silent_p.E1291E|RP11-348B17.1_ENST00000561299.1_RNA|TRPM1_ENST00000397795.2_Silent_p.E1252E	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1									p.E1252E(1)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		TTGCCTCACATTCAGAAGAAG	0.453																																					p.E1252E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A3756G	15						.						95.0	96.0	96.0					15																	31295081		2074	4216	6290	29082373	SO:0001819	synonymous_variant	4308	exon27			AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	7146	protein-coding gene	gene with protein product		603576	"""melastatin 1"""	MLSN1		9806836, 9537257, 16382100	Standard	NM_001252020		Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.3822A>G	15.37:g.31295081T>C			29082373	NM_002420		Silent	SNP	ENST00000256552.6	37	CCDS58346.1																																																																																				0.453	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420	
GCHFR	2644	broad.mit.edu	37	15	41059477	41059477	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr15:41059477G>A	ENST00000260447.4	+	3	346	c.185G>A	c.(184-186)cGc>cAc	p.R62H	DNAJC17_ENST00000558727.1_5'Flank|GCHFR_ENST00000559445.1_Missense_Mutation_p.R51H|GCHFR_ENST00000559932.1_Missense_Mutation_p.R45H|GCHFR_ENST00000558670.1_3'UTR|C15orf62_ENST00000344320.6_5'Flank|GCHFR_ENST00000558467.1_Missense_Mutation_p.R45H	NM_005258.2	NP_005249.1	P30047	GFRP_HUMAN	GTP cyclohydrolase I feedback regulator	62					negative regulation of biosynthetic process (GO:0009890)|negative regulation of GTP cyclohydrolase I activity (GO:0043105)|neurotransmitter metabolic process (GO:0042133)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide metabolic process (GO:0046209)|protein heterooligomerization (GO:0051291)|regulation of nitric-oxide synthase activity (GO:0050999)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|melanosome (GO:0042470)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|protein complex (GO:0043234)	amino acid binding (GO:0016597)|enzyme inhibitor activity (GO:0004857)	p.R62H(3)		endometrium(2)|kidney(1)|large_intestine(1)|ovary(1)|prostate(1)	6		all_cancers(109;3.3e-18)|all_epithelial(112;2.33e-15)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;2.58e-05)|COAD - Colon adenocarcinoma(120;0.149)|BRCA - Breast invasive adenocarcinoma(123;0.163)		AAGCTGGAACGCAGGGGCTTC	0.597																																					p.R62H												.	.	3	Substitution - Missense(3)	large_intestine(1)|prostate(1)|endometrium(1)	c.G185A	15						.						119.0	110.0	113.0					15																	41059477		2203	4300	6503	38846769	SO:0001583	missense	2644	exon3			U78190	CCDS10064.1	15q15	2004-01-19	2004-05-20		ENSG00000137880	ENSG00000137880			4194	protein-coding gene	gene with protein product		602437	"""GTP cyclohydrolase I feedback regulatory protein"""			8702680, 1286669	Standard	NM_005258		Approved	GFRP, HsT16933	uc001zmr.1	P30047	OTTHUMG00000130069	ENST00000260447.4:c.185G>A	15.37:g.41059477G>A	ENSP00000260447:p.Arg62His		38846769	NM_005258	B2R4L6|B7ZLM8|Q2M1Q2|Q99749	Missense_Mutation	SNP	ENST00000260447.4	37	CCDS10064.1	.	.	.	.	.	.	.	.	.	.	G	14.21	2.467284	0.43839	.	.	ENSG00000137880	ENST00000260447	.	.	.	5.63	2.59	0.31030	.	0.430341	0.30593	N	0.009296	T	0.26268	0.0641	.	.	.	0.29342	N	0.86593	B;B	0.33266	0.209;0.404	B;B	0.30179	0.079;0.112	T	0.12604	-1.0541	8	0.39692	T	0.17	-5.2738	6.1139	0.20116	0.2853:0.1289:0.5857:0.0	.	51;62	B7ZLM8;P30047	.;GFRP_HUMAN	H	62	.	ENSP00000260447:R62H	R	+	2	0	GCHFR	38846769	0.944000	0.32072	0.998000	0.56505	0.989000	0.77384	1.650000	0.37292	0.852000	0.35287	-0.254000	0.11334	CGC		0.597	GCHFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252360.2	NM_005258	
JMJD7	100137047	broad.mit.edu	37	15	42127072	42127072	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr15:42127072T>C	ENST00000397299.4	+	2	239	c.199T>C	c.(199-201)Tgg>Cgg	p.W67R	PLA2G4B_ENST00000452633.1_5'Flank|PLA2G4B_ENST00000542534.2_Missense_Mutation_p.W67R|JMJD7-PLA2G4B_ENST00000382448.4_Missense_Mutation_p.W67R|JMJD7_ENST00000408047.1_Intron|JMJD7-PLA2G4B_ENST00000342159.4_Missense_Mutation_p.W67R	NM_001114632.1	NP_001108104.1	P0C870	JMJD7_HUMAN	jumonji domain containing 7	67								p.W67R(3)		NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)	8						CCTCCAGAAGTGGTCCCTCCC	0.612																																					p.W67R												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.T199C	15						.						71.0	71.0	71.0					15																	42127072		2203	4300	6503	39914364	SO:0001583	missense	8681	exon2				CCDS45240.1	15q15.1	2011-02-10			ENSG00000243789	ENSG00000243789			34397	protein-coding gene	gene with protein product							Standard	NM_001114632		Approved			P0C870	OTTHUMG00000156810	ENST00000397299.4:c.199T>C	15.37:g.42127072T>C	ENSP00000380467:p.Trp67Arg		39914364	NM_005090	A5D6V5|O95712|Q59GF9|Q8TB10|Q9UKV7	Missense_Mutation	SNP	ENST00000397299.4	37	CCDS45240.1	.	.	.	.	.	.	.	.	.	.	.	21.2	4.118356	0.77323	.	.	ENSG00000243789;ENSG00000168970;ENSG00000168970;ENSG00000168970	ENST00000397299;ENST00000542534;ENST00000382448;ENST00000342159	T;T;T;T	0.76448	-1.02;-1.02;-1.02;-1.02	4.77	3.64	0.41730	.	0.000000	0.49305	D	0.000144	D	0.89663	0.6780	H	0.94264	3.515	0.42288	D	0.992122	B;D;D	0.89917	0.202;1.0;0.999	B;D;D	0.79784	0.097;0.993;0.988	D	0.91188	0.4981	10	0.87932	D	0	-2.9801	9.7536	0.40490	0.0:0.0831:0.0:0.9169	.	67;67;67	P0C869-7;P0C869-6;P0C870	.;.;JMJD7_HUMAN	R	67	ENSP00000380467:W67R;ENSP00000441905:W67R;ENSP00000371886:W67R;ENSP00000342785:W67R	ENSP00000380467:W67R	W	+	1	0	JMJD7-PLA2G4B;JMJD7	39914364	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	4.832000	0.62759	1.919000	0.55581	0.533000	0.62120	TGG		0.612	JMJD7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326082.1	NM_001114632	
SPG11	80208	broad.mit.edu	37	15	44852471	44852471	+	IGR	SNP	T	T	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr15:44852471T>A	ENST00000261866.7	-	0	7774				EIF3J_ENST00000535391.1_Missense_Mutation_p.I145N|EIF3J_ENST00000261868.5_Missense_Mutation_p.I199N|EIF3J_ENST00000424492.3_Missense_Mutation_p.I150N|RP11-151N17.1_ENST00000558006.1_RNA	NM_025137.3	NP_079413.3	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)						cell death (GO:0008219)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)		p.I199N(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	72		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		TTGAAAAAAATTACCAATTCA	0.313																																					p.I199N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T596A	15						.						69.0	73.0	72.0					15																	44852471		2198	4298	6496	42639763	SO:0001628	intergenic_variant	8669	exon7				CCDS10112.1, CCDS53939.1	15q13-q15	2007-11-13			ENSG00000104133	ENSG00000104133			11226	protein-coding gene	gene with protein product	"""spatacsin"""	610844	"""KIAA1840"""	KIAA1840		10408536, 17322883	Standard	NM_001160227		Approved	FLJ21439	uc001ztx.3	Q96JI7	OTTHUMG00000131199		15.37:g.44852471T>A			42639763	NM_003758	A8KAX9|B9EK60|F5H3N6|Q4VC11|Q58G86|Q69YG6|Q6NW01|Q8N270|Q8TBU9|Q9H734	Missense_Mutation	SNP	ENST00000261866.7	37	CCDS10112.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.4|24.4	4.528801|4.528801	0.85706|0.85706	.|.	.|.	ENSG00000104131|ENSG00000104131	ENST00000261868;ENST00000535391;ENST00000424492|ENST00000536248	T;T;T|.	0.53857|.	0.6;0.6;0.6|.	5.33|5.33	5.33|5.33	0.75918|0.75918	Eukaryotic translation initiation factor 3-like domain (1);|.	0.156761|.	0.56097|.	D|.	0.000034|.	T|T	0.74928|0.74928	0.3781|0.3781	M|M	0.76727|0.76727	2.345|2.345	0.41923|0.41923	D|D	0.990527|0.990527	D;D;D|.	0.76494|.	0.995;0.999;0.998|.	D;D;D|.	0.70935|.	0.917;0.971;0.961|.	T|T	0.76356|0.76356	-0.2989|-0.2989	10|5	0.87932|.	D|.	0|.	.|.	15.5934|15.5934	0.76558|0.76558	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	145;150;199|.	B4DUI3;F5H425;O75822|.	.;.;EIF3J_HUMAN|.	N|K	199;145;150|77	ENSP00000261868:I199N;ENSP00000440221:I145N;ENSP00000414548:I150N|.	ENSP00000261868:I199N|.	I|N	+|+	2|3	0|2	EIF3J|EIF3J	42639763|42639763	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.983000|0.983000	0.72400|0.72400	7.320000|7.320000	0.79064|0.79064	2.140000|2.140000	0.66376|0.66376	0.368000|0.368000	0.22195|0.22195	ATT|AAT		0.313	SPG11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253927.1		
DUOX1	53905	broad.mit.edu	37	15	45427459	45427459	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr15:45427459C>T	ENST00000321429.4	+	6	872	c.465C>T	c.(463-465)acC>acT	p.T155T	DUOX1_ENST00000389037.3_Silent_p.T155T	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	155	Peroxidase-like; mediates peroxidase activity.				cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide biosynthetic process (GO:0050665)|hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|superoxide anion generation (GO:0042554)|thyroid hormone generation (GO:0006590)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|NADP binding (GO:0050661)|peroxidase activity (GO:0004601)	p.T155T(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|lung(16)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)	57		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		ACCCCGAGACCGGACGGAGTC	0.716																																					p.T155T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C465T	15						.						11.0	14.0	13.0					15																	45427459		2176	4278	6454	43214751	SO:0001819	synonymous_variant	53905	exon6			AF213465	CCDS32221.1	15q21	2013-01-10				ENSG00000137857		"""EF-hand domain containing"""	3062	protein-coding gene	gene with protein product	"""NADPH thyroid oxidase 1"", ""flavoprotein NADPH oxidase"", ""nicotinamide adenine dinucleotide phosphate oxidase"""	606758				10806195	Standard	XM_005254463		Approved	NOXEF1, THOX1, LNOX1	uc001zut.1	Q9NRD9		ENST00000321429.4:c.465C>T	15.37:g.45427459C>T			43214751	NM_017434	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Silent	SNP	ENST00000321429.4	37	CCDS32221.1																																																																																				0.716	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434	
SHF	90525	broad.mit.edu	37	15	45464459	45464459	+	Missense_Mutation	SNP	C	C	T	rs140713703		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr15:45464459C>T	ENST00000290894.8	-	6	1345	c.851G>A	c.(850-852)cGg>cAg	p.R284Q	SHF_ENST00000560734.1_Intron|SHF_ENST00000561091.1_5'Flank|SHF_ENST00000458022.2_Missense_Mutation_p.R100Q|SHF_ENST00000560540.1_Missense_Mutation_p.R302Q|SHF_ENST00000560471.1_Missense_Mutation_p.R349Q|SHF_ENST00000318390.6_Missense_Mutation_p.R294Q|RP11-519G16.2_ENST00000560034.1_RNA	NM_138356.2	NP_612365			Src homology 2 domain containing F									p.R284Q(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(2)	12		all_cancers(109;8.13e-11)|all_epithelial(112;6.29e-09)|Lung NSC(122;3.57e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;4.1e-16)|GBM - Glioblastoma multiforme(94;5.98e-06)		GGGAGGTAGCCGCCCCTTCTC	0.612																																					p.R284Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G851A	15						.	C	GLN/ARG	0,4396		0,0,2198	42.0	48.0	46.0		851	3.9	1.0	15	dbSNP_134	46	1,8595	1.2+/-3.3	0,1,4297	no	missense	SHF	NM_138356.2	43	0,1,6495	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	284/424	45464459	1,12991	2198	4298	6496	43251751	SO:0001583	missense	90525	exon6			BC007586	CCDS10120.2, CCDS73721.1	15q21.1	2013-02-14			ENSG00000138606	ENSG00000138606		"""SH2 domain containing"""	25116	protein-coding gene	gene with protein product						11095946	Standard	NM_138356		Approved		uc001zuy.3	Q7M4L6	OTTHUMG00000131353	ENST00000290894.8:c.851G>A	15.37:g.45464459C>T	ENSP00000290894:p.Arg284Gln		43251751	NM_138356		Missense_Mutation	SNP	ENST00000290894.8	37	CCDS10120.2	.	.	.	.	.	.	.	.	.	.	C	18.87	3.716063	0.68844	0.0	1.16E-4	ENSG00000138606	ENST00000290894;ENST00000361989;ENST00000318390;ENST00000458022;ENST00000413198	T;T;T	0.36340	1.26;1.26;1.26	3.91	3.91	0.45181	.	0.301738	0.34725	N	0.003730	T	0.44808	0.1311	L	0.43757	1.38	0.58432	D	0.999999	B;P;D;P	0.63880	0.236;0.899;0.993;0.627	B;B;P;B	0.55923	0.016;0.124;0.787;0.079	T	0.47169	-0.9138	10	0.66056	D	0.02	-15.1003	13.766	0.62995	0.0:1.0:0.0:0.0	.	147;227;294;284	Q8N9I8;E7EWB7;F8W6K9;Q7M4L6	.;.;.;SHF_HUMAN	Q	284;284;294;100;227	ENSP00000290894:R284Q;ENSP00000315978:R294Q;ENSP00000411530:R100Q	ENSP00000290894:R284Q	R	-	2	0	SHF	43251751	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	4.265000	0.58865	1.904000	0.55121	0.563000	0.77884	CGG		0.612	SHF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254141.2	NM_138356	
SLC24A5	283652	broad.mit.edu	37	15	48431190	48431190	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr15:48431190C>A	ENST00000341459.3	+	7	969	c.896C>A	c.(895-897)cCt>cAt	p.P299H	SLC24A5_ENST00000449382.2_Missense_Mutation_p.P239H	NM_205850.2	NP_995322.1	Q71RS6	NCKX5_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 5	299					ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|negative regulation of melanin biosynthetic process (GO:0048022)|response to stimulus (GO:0050896)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)	p.P299H(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(17)|skin(1)|upper_aerodigestive_tract(1)	27		all_lung(180;0.00217)		all cancers(107;3.29e-10)|GBM - Glioblastoma multiforme(94;7.32e-07)		TTCAACATGCCTGAAGCAGAC	0.308																																					p.P299H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C896A	15						.						57.0	59.0	59.0					15																	48431190		2198	4292	6490	46218482	SO:0001583	missense	283652	exon7			AF348468	CCDS10128.1	15q21.1	2014-01-28	2013-07-18		ENSG00000188467	ENSG00000188467		"""Solute carriers"""	20611	protein-coding gene	gene with protein product	"""oculocutaneous albinism 6 (autosomal recessive)"""	609802	"""solute carrier family 24, member 5"""			23364476	Standard	XM_005254308		Approved	JSX, OCA6	uc001zwe.3	Q71RS6	OTTHUMG00000131494	ENST00000341459.3:c.896C>A	15.37:g.48431190C>A	ENSP00000341550:p.Pro299His		46218482	NM_205850	A5X8Z8|A5X8Z9|Q14CT4|Q6DKH3	Missense_Mutation	SNP	ENST00000341459.3	37	CCDS10128.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.639280	0.87760	.	.	ENSG00000188467	ENST00000341459;ENST00000449382	T;T	0.77750	-1.1;-1.12	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	D	0.90885	0.7136	M	0.90252	3.1	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.91807	0.5456	10	0.72032	D	0.01	.	20.0417	0.97594	0.0:1.0:0.0:0.0	.	239;299	A5X8Z9;Q71RS6	.;NCKX5_HUMAN	H	299;239	ENSP00000341550:P299H;ENSP00000389966:P239H	ENSP00000341550:P299H	P	+	2	0	SLC24A5	46218482	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.281000	0.78621	2.736000	0.93811	0.655000	0.94253	CCT		0.308	SLC24A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254340.2	NM_205850	
SLC12A1	6557	broad.mit.edu	37	15	48541773	48541773	+	Splice_Site	SNP	G	G	A	rs199833808		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr15:48541773G>A	ENST00000558405.1	+	13	1700	c.1686G>A	c.(1684-1686)gcG>gcA	p.A562A	SLC12A1_ENST00000380993.3_Splice_Site_p.A562A|SLC12A1_ENST00000396577.3_Splice_Site_p.A562A			Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1	562					cell death (GO:0008219)|chemical homeostasis (GO:0048878)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|kidney development (GO:0001822)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:potassium:chloride symporter activity (GO:0008511)	p.A562A(3)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1)	59		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Potassium Chloride(DB00761)|Quinethazone(DB01325)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	CTTTTACAGCGGAACTGAACA	0.418													G|||	1	0.000199681	0.0	0.0	5008	,	,		19562	0.0		0.001	False		,,,				2504	0.0				p.A562A												.	.	3	Substitution - coding silent(3)	lung(2)|large_intestine(1)	c.G1686A	15						.						265.0	211.0	229.0					15																	48541773		2198	4297	6495	46329065	SO:0001630	splice_region_variant	6557	exon14				CCDS10129.2, CCDS53940.1	15q15-q21	2013-07-18	2013-07-18		ENSG00000074803	ENSG00000074803		"""Solute carriers"""	10910	protein-coding gene	gene with protein product		600839				8640224	Standard	NM_000338		Approved	NKCC2	uc010bem.3	Q13621	OTTHUMG00000131495	ENST00000558405.1:c.1685-1G>A	15.37:g.48541773G>A			46329065	NM_001184832	A8JYA2|E9PDW4	Silent	SNP	ENST00000558405.1	37	CCDS10129.2																																																																																				0.418	SLC12A1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417131.1		Silent
GALK2	2585	broad.mit.edu	37	15	49575902	49575902	+	Missense_Mutation	SNP	G	G	A	rs201091452		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr15:49575902G>A	ENST00000560031.1	+	7	1050	c.743G>A	c.(742-744)cGg>cAg	p.R248Q	GALK2_ENST00000327171.3_Missense_Mutation_p.R237Q|GALK2_ENST00000396509.2_Missense_Mutation_p.R224Q|GALK2_ENST00000543495.1_Missense_Mutation_p.R119Q|GALK2_ENST00000544523.1_Missense_Mutation_p.R224Q|GALK2_ENST00000559454.1_Missense_Mutation_p.R224Q|GALK2_ENST00000561014.1_3'UTR			Q01415	GALK2_HUMAN	galactokinase 2	248					carbohydrate metabolic process (GO:0005975)|galactose metabolic process (GO:0006012)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|galactokinase activity (GO:0004335)|N-acetylgalactosamine kinase activity (GO:0033858)	p.R237Q(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		all_lung(180;0.000325)		all cancers(107;3.71e-08)|GBM - Glioblastoma multiforme(94;7e-05)		ATGGAGTGTCGGCTGGCTGCG	0.428													G|||	1	0.000199681	0.0	0.0	5008	,	,		18083	0.0		0.001	False		,,,				2504	0.0				p.R248Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G743A	15						.						97.0	87.0	91.0					15																	49575902		2196	4295	6491	47363194	SO:0001583	missense	2585	exon7				CCDS32236.1, CCDS42034.1, CCDS73724.1	15q21.1-q21.2	2013-09-20			ENSG00000156958	ENSG00000156958	2.7.1.6		4119	protein-coding gene	gene with protein product		137028					Standard	XM_005254279		Approved	GK2	uc001zxj.1	Q01415	OTTHUMG00000172325	ENST00000560031.1:c.743G>A	15.37:g.49575902G>A	ENSP00000453129:p.Arg248Gln		47363194	NM_002044	Q7Z4Q4	Missense_Mutation	SNP	ENST00000560031.1	37	CCDS42034.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	37	6.047869	0.97236	.	.	ENSG00000156958	ENST00000327171;ENST00000396509;ENST00000543495;ENST00000544523	D;T;D	0.85773	-2.03;-0.55;-2.03	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	D	0.90393	0.6993	M	0.76574	2.34	0.80722	D	1	D;D	0.76494	0.999;0.999	P;P	0.54026	0.736;0.74	D	0.90030	0.4134	10	0.52906	T	0.07	1.2164	20.2935	0.98544	0.0:0.0:1.0:0.0	.	248;237	Q01415;Q7Z4Q4	GALK2_HUMAN;.	Q	237;248;119;224	ENSP00000316632:R237Q;ENSP00000443220:R119Q;ENSP00000440312:R224Q	ENSP00000316632:R237Q	R	+	2	0	GALK2	47363194	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.277000	0.95755	2.813000	0.96785	0.637000	0.83480	CGG		0.428	GALK2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417854.1		
CYP19A1	1588	broad.mit.edu	37	15	51503091	51503091	+	Missense_Mutation	SNP	C	C	T	rs577716822		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr15:51503091C>T	ENST00000396402.1	-	10	1579	c.1426G>A	c.(1426-1428)Gac>Aac	p.D476N	CYP19A1_ENST00000260433.2_Missense_Mutation_p.D476N|CYP19A1_ENST00000559878.1_Missense_Mutation_p.D476N|CYP19A1_ENST00000396404.4_Missense_Mutation_p.D476N|RP11-108K3.1_ENST00000559909.1_lincRNA	NM_000103.3	NP_000094.2	P11511	CP19A_HUMAN	cytochrome P450, family 19, subfamily A, polypeptide 1	476					androgen metabolic process (GO:0008209)|estrogen biosynthetic process (GO:0006703)|prostate gland growth (GO:0060736)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)	aromatase activity (GO:0070330)|electron carrier activity (GO:0009055)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)	p.D476N(1)		endometrium(1)|kidney(4)|large_intestine(9)|lung(11)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	33				all cancers(107;0.000372)|GBM - Glioblastoma multiforme(94;0.0128)	Aminoglutethimide(DB00357)|Anastrozole(DB01217)|Betamethasone(DB00443)|Bifonazole(DB04794)|Buserelin(DB06719)|Carbimazole(DB00389)|Chlorphenesin(DB00856)|Clomifene(DB00882)|Clotrimazole(DB00257)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Dexamethasone(DB01234)|Diethylstilbestrol(DB00255)|Dinoprostone(DB00917)|Drostanolone(DB00858)|Econazole(DB01127)|Edetic Acid(DB00974)|Etomidate(DB00292)|Exemestane(DB00990)|Ketoconazole(DB01026)|Letrozole(DB01006)|Levomethadyl Acetate(DB01227)|Levonorgestrel(DB00367)|Mefloquine(DB00358)|Melatonin(DB01065)|Methadone(DB00333)|Methyltestosterone(DB06710)|Miconazole(DB01110)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nicotine(DB00184)|Paclitaxel(DB01229)|Raloxifene(DB00481)|Sulfathiazole(DB06147)|Tamoxifen(DB00675)|Terbinafine(DB00857)|Testolactone(DB00894)|Testosterone(DB00624)|Tioconazole(DB01007)|Trastuzumab(DB00072)	AAGGACAAGTCGTGTATCTTC	0.468																																					p.D476N	Melanoma(142;1016 1807 39614 48966 51721)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1426A	15						.						261.0	213.0	230.0					15																	51503091		2196	4293	6489	49290383	SO:0001583	missense	1588	exon11			D14473	CCDS10139.1	15q21	2009-01-26	2003-02-14	2003-02-28	ENSG00000137869	ENSG00000137869		"""Cytochrome P450s"""	2594	protein-coding gene	gene with protein product		107910	"""cytochrome P450, subfamily XIX (aromatization of androgens)"""	CYP19		8477708	Standard	NM_031226		Approved	ARO, P-450AROM, CPV1, ARO1, CYAR, aromatase	uc001zza.4	P11511	OTTHUMG00000131747	ENST00000396402.1:c.1426G>A	15.37:g.51503091C>T	ENSP00000379683:p.Asp476Asn		49290383	NM_031226	Q16731|Q3B764|Q58FA0|Q8IYJ7	Missense_Mutation	SNP	ENST00000396402.1	37	CCDS10139.1	.	.	.	.	.	.	.	.	.	.	C	0.214	-1.034087	0.02029	.	.	ENSG00000137869	ENST00000396402;ENST00000260433;ENST00000396404	T;T;T	0.68624	-0.34;-0.34;-0.34	5.46	3.58	0.41010	.	0.125927	0.64402	N	0.000001	T	0.47078	0.1426	L	0.28192	0.835	0.45015	D	0.998031	B	0.19445	0.036	B	0.15870	0.014	T	0.37596	-0.9699	10	0.02654	T	1	-14.7692	12.1024	0.53792	0.0:0.8603:0.0:0.1397	.	476	P11511	CP19A_HUMAN	N	476	ENSP00000379683:D476N;ENSP00000260433:D476N;ENSP00000379685:D476N	ENSP00000260433:D476N	D	-	1	0	CYP19A1	49290383	1.000000	0.71417	0.135000	0.22099	0.011000	0.07611	2.198000	0.42705	0.792000	0.33850	0.655000	0.94253	GAC		0.468	CYP19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254669.1		
GNB5	10681	broad.mit.edu	37	15	52416741	52416741	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr15:52416741G>A	ENST00000261837.7	-	12	1170	c.1105C>T	c.(1105-1107)Cgc>Tgc	p.R369C	CTD-2184D3.6_ENST00000559825.1_lincRNA|GNB5_ENST00000358784.7_Missense_Mutation_p.R327C|GNB5_ENST00000396335.4_Missense_Mutation_p.R257C|GNB5_ENST00000559348.1_5'UTR|CTD-2184D3.7_ENST00000557898.1_RNA	NM_016194.3	NP_057278.2	O14775	GBB5_HUMAN	guanine nucleotide binding protein (G protein), beta 5	369					GTP catabolic process (GO:0006184)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	chaperone binding (GO:0051087)|G-protein gamma-subunit binding (GO:0031682)|GTPase activity (GO:0003924)|signal transducer activity (GO:0004871)	p.R369C(1)		large_intestine(1)|lung(1)	2				all cancers(107;0.0163)		GTGCTAACGCGGTTTTCATGT	0.493																																					p.R327C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C979T	15						.						116.0	114.0	115.0					15																	52416741		2195	4293	6488	50204033	SO:0001583	missense	10681	exon10			AF017656	CCDS10149.1, CCDS45261.1	15q21.1	2013-01-10			ENSG00000069966	ENSG00000069966		"""WD repeat domain containing"""	4401	protein-coding gene	gene with protein product		604447				9606987	Standard	NM_016194		Approved	GB5	uc031qrz.1	O14775	OTTHUMG00000131892	ENST00000261837.7:c.1105C>T	15.37:g.52416741G>A	ENSP00000261837:p.Arg369Cys		50204033	NM_006578	B2RBR5|Q9HAU9|Q9UFT3	Missense_Mutation	SNP	ENST00000261837.7	37	CCDS10149.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.210820	0.79240	.	.	ENSG00000069966	ENST00000261837;ENST00000396335;ENST00000544480;ENST00000358784	T	0.60548	0.18	5.88	4.89	0.63831	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.73337	0.3574	M	0.64567	1.98	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.75365	-0.3343	10	0.87932	D	0	-14.4654	15.8861	0.79251	0.0:0.0:0.7778:0.2222	.	369;257	O14775;O14775-3	GBB5_HUMAN;.	C	369;327;167;257	ENSP00000261837:R369C	ENSP00000261837:R369C	R	-	1	0	GNB5	50204033	1.000000	0.71417	0.999000	0.59377	0.708000	0.40852	3.788000	0.55446	2.806000	0.96561	0.644000	0.83932	CGC		0.493	GNB5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254842.1		
ONECUT1	3175	broad.mit.edu	37	15	53081839	53081839	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr15:53081839G>A	ENST00000305901.5	-	1	370	c.243C>T	c.(241-243)ggC>ggT	p.G81G	ONECUT1_ENST00000561401.2_Intron	NM_004498.2	NP_004489.1	Q9UBC0	HNF6_HUMAN	one cut homeobox 1	81					B cell differentiation (GO:0030183)|cell fate commitment (GO:0045165)|cilium assembly (GO:0042384)|endocrine pancreas development (GO:0031018)|endoderm development (GO:0007492)|epithelial cell development (GO:0002064)|glucose metabolic process (GO:0006006)|liver development (GO:0001889)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell-matrix adhesion (GO:0001952)|regulation of transcription, DNA-templated (GO:0006355)|spleen development (GO:0048536)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.G81G(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|prostate(2)|skin(1)	17				all cancers(107;0.0708)		GATGCAGGGGGCCGGCCAGGC	0.701																																					p.G81G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C243T	15						.						34.0	33.0	34.0					15																	53081839		2194	4292	6486	50869131	SO:0001819	synonymous_variant	3175	exon1			U77975	CCDS10150.1	15q21.3	2012-03-09	2007-07-16		ENSG00000169856	ENSG00000169856		"""Homeoboxes / CUT class"""	8138	protein-coding gene	gene with protein product		604164	"""one cut domain, family member 1"""	HNF6, HNF6A		8887657, 8790352	Standard	NM_004498		Approved	HNF-6	uc002aci.2	Q9UBC0	OTTHUMG00000131899	ENST00000305901.5:c.243C>T	15.37:g.53081839G>A			50869131	NM_004498	B2RTV4|Q99744|Q9UMR6	Silent	SNP	ENST00000305901.5	37	CCDS10150.1																																																																																				0.701	ONECUT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254849.2		
SLTM	79811	broad.mit.edu	37	15	59172302	59172302	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr15:59172302C>T	ENST00000380516.2	-	21	3088	c.3001G>A	c.(3001-3003)Gca>Aca	p.A1001T	SLTM_ENST00000536328.1_Missense_Mutation_p.A570T	NM_001013843.1|NM_024755.2	NP_001013865.1|NP_079031.2	Q9NWH9	SLTM_HUMAN	SAFB-like, transcription modulator	1001					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.A1001T(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						ATTGGGGATGCGTTACTGAAA	0.388																																					p.A1001T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3001A	15						.						47.0	47.0	47.0					15																	59172302		2192	4292	6484	56959594	SO:0001583	missense	79811	exon21			BC046119	CCDS10168.2	15q21.3	2013-02-12			ENSG00000137776	ENSG00000137776		"""RNA binding motif (RRM) containing"""	20709	protein-coding gene	gene with protein product							Standard	XR_243128		Approved	Met, FLJ13213	uc002afp.3	Q9NWH9	OTTHUMG00000074033	ENST00000380516.2:c.3001G>A	15.37:g.59172302C>T	ENSP00000369887:p.Ala1001Thr		56959594	NM_024755	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000380516.2	37	CCDS10168.2	.	.	.	.	.	.	.	.	.	.	C	15.50	2.851512	0.51270	.	.	ENSG00000137776	ENST00000380516;ENST00000432750;ENST00000536328	T	0.14391	2.51	5.66	2.39	0.29439	.	0.130623	0.34906	N	0.003599	T	0.14270	0.0345	N	0.22421	0.69	0.80722	D	1	D;D	0.63880	0.993;0.977	P;P	0.53649	0.731;0.508	T	0.02751	-1.1115	10	0.49607	T	0.09	.	9.1496	0.36955	0.5918:0.3015:0.1067:0.0	.	1001;570	Q9NWH9;A8K5V8	SLTM_HUMAN;.	T	1001;567;570	ENSP00000369887:A1001T	ENSP00000369887:A1001T	A	-	1	0	SLTM	56959594	1.000000	0.71417	0.253000	0.24343	0.711000	0.40976	3.407000	0.52644	0.694000	0.31654	0.563000	0.77884	GCA		0.388	SLTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157124.1	NM_024755	
FAM96A	84191	broad.mit.edu	37	15	64373324	64373324	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr15:64373324G>A	ENST00000300030.3	-	3	565	c.316C>T	c.(316-318)Cga>Tga	p.R106*	FAM96A_ENST00000380290.3_Intron|FAM96A_ENST00000557835.1_Intron|FAM96A_ENST00000559950.1_Nonsense_Mutation_p.R106*	NM_032231.4	NP_115607.1	Q9H5X1	FA96A_HUMAN	family with sequence similarity 96, member A	106					chromosome segregation (GO:0007059)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)	p.R106*(1)		kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	9						GGTAAACATCGCTGAAGTTTT	0.338																																					p.R106X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C316T	15						.						120.0	112.0	115.0					15																	64373324		2203	4300	6503	62160377	SO:0001587	stop_gained	84191	exon3				CCDS10189.1, CCDS45278.1	15q22.31	2014-01-16			ENSG00000166797	ENSG00000166797			26235	protein-coding gene	gene with protein product						23891004	Standard	NM_032231		Approved	FLJ22875	uc002amt.1	Q9H5X1	OTTHUMG00000132961	ENST00000300030.3:c.316C>T	15.37:g.64373324G>A	ENSP00000300030:p.Arg106*		62160377	NM_032231	A6NKS1|B2R5F8|B7Z8Z5	Nonsense_Mutation	SNP	ENST00000300030.3	37	CCDS10189.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.802775	0.90623	.	.	ENSG00000166797	ENST00000300030	.	.	.	5.99	3.94	0.45596	.	0.054206	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.92	10.6783	0.45799	0.0:0.0:0.5812:0.4188	.	.	.	.	X	106	.	ENSP00000300030:R106X	R	-	1	2	FAM96A	62160377	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.757000	0.55212	1.511000	0.48818	0.650000	0.86243	CGA		0.338	FAM96A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256520.1	NM_032231	
IGDCC4	57722	broad.mit.edu	37	15	65681724	65681724	+	Missense_Mutation	SNP	C	C	T	rs368140698		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr15:65681724C>T	ENST00000352385.2	-	14	2643	c.2434G>A	c.(2434-2436)Ggc>Agc	p.G812S		NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	812	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.G812S(1)		NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	44						GGCTTCAAGCCGCCAATGAGG	0.557																																					p.G812S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2434A	15						.	C	SER/GLY	1,4401	2.1+/-5.4	0,1,2200	132.0	100.0	111.0		2434	5.4	1.0	15		111	0,8598		0,0,4299	no	missense	IGDCC4	NM_020962.1	56	0,1,6499	TT,TC,CC		0.0,0.0227,0.0077	benign	812/1251	65681724	1,12999	2201	4299	6500	63468777	SO:0001583	missense	57722	exon14				CCDS10206.1	15q22.31	2013-02-11			ENSG00000103742	ENSG00000103742		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	13770	protein-coding gene	gene with protein product	"""likely ortholog of mouse neighbor of Punc E11"""						Standard	NM_020962		Approved	NOPE, LOC57722	uc002aou.1	Q8TDY8	OTTHUMG00000133136	ENST00000352385.2:c.2434G>A	15.37:g.65681724C>T	ENSP00000319623:p.Gly812Ser		63468777	NM_020962	Q9HCE4	Missense_Mutation	SNP	ENST00000352385.2	37	CCDS10206.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.462788	0.84425	2.27E-4	0.0	ENSG00000103742	ENST00000352385;ENST00000356152	T	0.58358	0.34	5.37	5.37	0.77165	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.118400	0.56097	D	0.000024	T	0.65302	0.2678	L	0.45285	1.41	0.36987	D	0.894614	D	0.69078	0.997	D	0.63703	0.917	T	0.69312	-0.5178	10	0.49607	T	0.09	-24.8806	19.1171	0.93346	0.0:1.0:0.0:0.0	.	812	Q8TDY8	IGDC4_HUMAN	S	812;541	ENSP00000319623:G812S	ENSP00000319623:G812S	G	-	1	0	IGDCC4	63468777	0.984000	0.35163	0.989000	0.46669	0.972000	0.66771	3.684000	0.54671	2.526000	0.85167	0.555000	0.69702	GGC		0.557	IGDCC4-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256825.2	NM_020962	
MYO9A	4649	broad.mit.edu	37	15	72144563	72144563	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr15:72144563C>T	ENST00000356056.5	-	36	6857	c.6385G>A	c.(6385-6387)Gtc>Atc	p.V2129I	MYO9A_ENST00000424560.1_Missense_Mutation_p.V2200I|MYO9A_ENST00000564571.1_Missense_Mutation_p.V2129I|MYO9A_ENST00000444904.1_Missense_Mutation_p.V2110I	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	2129	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.|Tail.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)	p.V2129I(1)		NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						CTTGCAATGACGTGTATGTTA	0.368																																					p.V2129I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G6385A	15						.						99.0	90.0	93.0					15																	72144563		2199	4297	6496	69931617	SO:0001583	missense	4649	exon36			AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"""Myosins / Myosin superfamily : Class IX"""	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.6385G>A	15.37:g.72144563C>T	ENSP00000348349:p.Val2129Ile		69931617	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	37	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.133509	0.77662	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904	T;T;T	0.20463	2.07;2.07;2.07	5.93	5.93	0.95920	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	.	.	.	.	T	0.47544	0.1451	M	0.64080	1.96	0.80722	D	1	B;D	0.89917	0.339;1.0	B;D	0.81914	0.064;0.995	T	0.29119	-1.0022	9	0.62326	D	0.03	.	20.3324	0.98724	0.0:1.0:0.0:0.0	.	2129;1893	B2RTY4;B2RTY4-5	MYO9A_HUMAN;.	I	2129;2200;2110	ENSP00000348349:V2129I;ENSP00000399162:V2200I;ENSP00000398250:V2110I	ENSP00000348349:V2129I	V	-	1	0	MYO9A	69931617	1.000000	0.71417	0.992000	0.48379	0.996000	0.88848	7.792000	0.85828	2.799000	0.96334	0.650000	0.86243	GTC		0.368	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901	
MAN2C1	4123	broad.mit.edu	37	15	75660857	75660857	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr15:75660857G>A	ENST00000267978.5	-	1	114	c.68C>T	c.(67-69)cCg>cTg	p.P23L	RP11-817O13.8_ENST00000563278.1_lincRNA|MAN2C1_ENST00000563539.1_5'UTR|MAN2C1_ENST00000569482.1_Missense_Mutation_p.P23L|MAN2C1_ENST00000563622.1_Missense_Mutation_p.P23L|MAN2C1_ENST00000565683.1_Missense_Mutation_p.P23L	NM_006715.3	NP_006706.2	Q9NTJ4	MA2C1_HUMAN	mannosidase, alpha, class 2C, member 1	23					mannose metabolic process (GO:0006013)		alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)	p.P23L(1)		central_nervous_system(4)|endometrium(4)|kidney(6)|large_intestine(6)|lung(20)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	44						AAAGTAGAGCGGCGACACGAA	0.692																																					p.P23L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C68T	15						.						22.0	22.0	22.0					15																	75660857		2138	4216	6354	73447910	SO:0001583	missense	4123	exon1			AF044414	CCDS32298.1, CCDS58389.1, CCDS58390.1, CCDS58391.1	15q24.2	2013-09-19			ENSG00000140400	ENSG00000140400	3.2.1.24		6827	protein-coding gene	gene with protein product		154580		MANA1, MANA		1757461, 752528	Standard	NM_006715		Approved		uc002bah.4	Q9NTJ4	OTTHUMG00000172698	ENST00000267978.5:c.68C>T	15.37:g.75660857G>A	ENSP00000267978:p.Pro23Leu		73447910	NM_006715	H3BMX2|H3BQY8|H3BUT6|Q13358|Q68EM8|Q9UL64	Missense_Mutation	SNP	ENST00000267978.5	37	CCDS32298.1	.	.	.	.	.	.	.	.	.	.	G	16.29	3.082656	0.55861	.	.	ENSG00000140400	ENST00000267978;ENST00000421803	T	0.16897	2.31	5.1	5.1	0.69264	.	0.614076	0.16702	N	0.203069	T	0.13157	0.0319	L	0.46157	1.445	0.21105	N	0.999784	P;P;P	0.44816	0.844;0.758;0.758	B;B;B	0.32864	0.154;0.074;0.074	T	0.22243	-1.0222	10	0.31617	T	0.26	-35.304	11.4476	0.50134	0.0:0.0:0.8197:0.1803	.	23;23;23	B4DH23;Q68EM8;Q9NTJ4	.;.;MA2C1_HUMAN	L	23	ENSP00000267978:P23L	ENSP00000267978:P23L	P	-	2	0	MAN2C1	73447910	0.254000	0.23992	0.948000	0.38648	0.895000	0.52256	1.514000	0.35834	2.516000	0.84829	0.591000	0.81541	CCG		0.692	MAN2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419965.1		
CSPG4	1464	broad.mit.edu	37	15	75968313	75968313	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr15:75968313G>A	ENST00000308508.5	-	10	6639	c.6547C>T	c.(6547-6549)Cgg>Tgg	p.R2183W	AC105020.1_ENST00000435356.1_5'Flank|CTD-2026K11.1_ENST00000569467.1_RNA	NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	2183	Cysteine-containing.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)	p.R2183W(1)		breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						GCTTCCGTCCGGGCGGCCTCG	0.697																																					p.R2183W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C6547T	15						.						22.0	24.0	23.0					15																	75968313		2195	4292	6487	73755368	SO:0001583	missense	1464	exon10			X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.6547C>T	15.37:g.75968313G>A	ENSP00000312506:p.Arg2183Trp		73755368	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	G	8.160	0.789350	0.16258	.	.	ENSG00000173546	ENST00000308508;ENST00000537176	T	0.20200	2.09	4.95	3.07	0.35406	.	1.539330	0.03726	N	0.252660	T	0.21718	0.0523	L	0.44542	1.39	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.26815	-1.0092	10	0.66056	D	0.02	.	6.6238	0.22818	0.3102:0.0:0.6898:0.0	.	2183	Q6UVK1	CSPG4_HUMAN	W	2183;215	ENSP00000312506:R2183W	ENSP00000312506:R2183W	R	-	1	2	CSPG4	73755368	0.006000	0.16342	0.001000	0.08648	0.302000	0.27658	0.924000	0.28777	0.506000	0.28125	0.511000	0.50034	CGG		0.697	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
HYKK	123688	broad.mit.edu	37	15	78825564	78825564	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr15:78825564G>A	ENST00000569878.1	+	4	674	c.674G>A	c.(673-675)gGa>gAa	p.G225E	HYKK_ENST00000388988.4_Missense_Mutation_p.G225E|HYKK_ENST00000408962.2_Intron|HYKK_ENST00000563233.1_Intron			A2RU49	HYKK_HUMAN	hydroxylysine kinase	225						cytoplasm (GO:0005737)	hydroxylysine kinase activity (GO:0047992)	p.G225E(1)									ATCAATCACGGAGATCTTAAT	0.358																																					p.G225E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G674A	15						.						57.0	50.0	52.0					15																	78825564		1827	4078	5905	76612619	SO:0001583	missense	123688	exon5			BC132753, BC144383, BM045979	CCDS42063.1, CCDS45318.1	15q25.1	2013-06-11	2013-06-11	2013-06-11	ENSG00000188266	ENSG00000188266	2.7.1.81		34403	protein-coding gene	gene with protein product	"""5-hydroxylysine kinase"""	614681	"""aminoglycoside phosphotransferase domain containing 1"""	AGPHD1		18780872, 22241472	Standard	NM_001013619		Approved	LOC123688	uc010unc.2	A2RU49		ENST00000569878.1:c.674G>A	15.37:g.78825564G>A	ENSP00000455459:p.Gly225Glu		76612619	NM_001013619	B7ZMA5|F8W6X5|Q6ZTN0	Missense_Mutation	SNP	ENST00000569878.1	37	CCDS42063.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.904991	0.92035	.	.	ENSG00000188266	ENST00000388988	T	0.47528	0.84	5.85	5.85	0.93711	Aminoglycoside phosphotransferase (1);Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.75642	0.3877	M	0.89287	3.02	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.77621	-0.2519	10	0.52906	T	0.07	.	20.1577	0.98120	0.0:0.0:1.0:0.0	.	225	A2RU49	AGPD1_HUMAN	E	225	ENSP00000373640:G225E	ENSP00000373640:G225E	G	+	2	0	AGPHD1	76612619	1.000000	0.71417	0.817000	0.32601	0.931000	0.56810	7.758000	0.85224	2.767000	0.95098	0.655000	0.94253	GGA		0.358	HYKK-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435834.1	NM_001013619	
RASGRF1	5923	broad.mit.edu	37	15	79284128	79284128	+	Silent	SNP	G	G	A	rs147869279	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr15:79284128G>A	ENST00000419573.3	-	22	3358	c.3084C>T	c.(3082-3084)ggC>ggT	p.G1028G	RASGRF1_ENST00000558480.2_Silent_p.G1012G|RASGRF1_ENST00000560334.1_5'UTR|RASGRF1_ENST00000394745.3_Silent_p.G244G	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	1028					activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.G1028G(1)		breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						CAGCCTTCACGCCTTCAGCCT	0.547													G|||	5	0.000998403	0.0038	0.0	5008	,	,		18401	0.0		0.0	False		,,,				2504	0.0				p.G1028G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3084T	15						.	G	,,	25,4367	31.7+/-61.6	0,25,2171	91.0	80.0	84.0		3036,3084,732	-2.1	1.0	15	dbSNP_134	84	0,8586		0,0,4293	no	coding-synonymous,coding-synonymous,coding-synonymous	RASGRF1	NM_001145648.1,NM_002891.4,NM_153815.2	,,	0,25,6464	AA,AG,GG		0.0,0.5692,0.1926	,,	1012/1258,1028/1274,244/490	79284128	25,12953	2196	4293	6489	77071183	SO:0001819	synonymous_variant	5923	exon22			M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.3084C>T	15.37:g.79284128G>A			77071183	NM_002891	F8VPA5|H0YKF2|J3KQP9|Q16027	Silent	SNP	ENST00000419573.3	37	CCDS10309.1																																																																																				0.547	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891	
ADAMTSL3	57188	broad.mit.edu	37	15	84566637	84566637	+	Missense_Mutation	SNP	C	C	T	rs267604348		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr15:84566637C>T	ENST00000286744.5	+	14	1719	c.1495C>T	c.(1495-1497)Cgg>Tgg	p.R499W	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.R499W	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	499	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R499W(1)		NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			CCGAGGGTTACGGTACCGGGT	0.443																																					p.R499W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1495T	15						.	C	TRP/ARG	0,4406		0,0,2203	117.0	97.0	104.0		1495	4.2	1.0	15		104	2,8598	2.2+/-6.3	0,2,4298	no	missense	ADAMTSL3	NM_207517.2	101	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	499/1692	84566637	2,13004	2203	4300	6503	82357641	SO:0001583	missense	57188	exon14			AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.1495C>T	15.37:g.84566637C>T	ENSP00000286744:p.Arg499Trp		82357641	NM_207517	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.305330	0.81247	0.0	2.33E-4	ENSG00000156218	ENST00000286744	T	0.58358	0.34	5.24	4.23	0.50019	.	0.000000	0.85682	D	0.000000	T	0.78104	0.4231	M	0.90870	3.155	0.53005	D	0.999965	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.84164	0.0430	10	0.87932	D	0	.	16.513	0.84292	0.1396:0.8604:0.0:0.0	.	499;499	P82987-2;P82987	.;ATL3_HUMAN	W	499	ENSP00000286744:R499W	ENSP00000286744:R499W	R	+	1	2	ADAMTSL3	82357641	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.820000	0.48057	2.440000	0.82611	0.655000	0.94253	CGG		0.443	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
NTRK3	4916	broad.mit.edu	37	15	88690572	88690572	+	Missense_Mutation	SNP	C	C	T	rs546426782		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr15:88690572C>T	ENST00000360948.2	-	5	619	c.458G>A	c.(457-459)cGg>cAg	p.R153Q	NTRK3_ENST00000558676.1_Missense_Mutation_p.R153Q|NTRK3_ENST00000317501.3_Missense_Mutation_p.R153Q|NTRK3_ENST00000542733.2_Missense_Mutation_p.R55Q|NTRK3_ENST00000357724.2_Missense_Mutation_p.R153Q|NTRK3_ENST00000394480.2_Missense_Mutation_p.R153Q|NTRK3_ENST00000557856.1_Missense_Mutation_p.R153Q|NTRK3_ENST00000540489.2_Missense_Mutation_p.R153Q|NTRK3_ENST00000355254.2_Missense_Mutation_p.R153Q	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	153					activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.R153Q(3)	ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			TTACAATTCCCGAAGACTCAG	0.478			T	ETV6	"""congenital fibrosarcoma, Secretory breast """					TSP Lung(13;0.10)			C|||	1	0.000199681	0.0008	0.0	5008	,	,		15425	0.0		0.0	False		,,,				2504	0.0				p.R153Q			Dom	yes		15	15q25	4916	"""neurotrophic tyrosine kinase, receptor, type 3"""		"""E, M"""	.	.	3	Substitution - Missense(3)	large_intestine(3)	c.G458A	15						.						88.0	71.0	77.0					15																	88690572		2201	4299	6500	86491576	SO:0001583	missense	4916	exon5			U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"""	8033	protein-coding gene	gene with protein product		191316				7806211	Standard	NM_001012338		Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000360948.2:c.458G>A	15.37:g.88690572C>T	ENSP00000354207:p.Arg153Gln		86491576	NM_001007156	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Missense_Mutation	SNP	ENST00000360948.2	37	CCDS32322.1	.	.	.	.	.	.	.	.	.	.	C	14.27	2.486062	0.44147	.	.	ENSG00000140538	ENST00000394480;ENST00000360948;ENST00000357724;ENST00000355254;ENST00000542733;ENST00000540489;ENST00000317501	T;T;T;T;T;T;T	0.58060	0.36;0.36;0.36;0.36;0.36;0.36;0.36	5.53	5.53	0.82687	.	0.499782	0.22098	N	0.064647	T	0.26048	0.0635	N	0.03930	-0.32	0.28422	N	0.917686	B;B;B;B;B;B	0.20261	0.002;0.002;0.0;0.043;0.003;0.0	B;B;B;B;B;B	0.09377	0.001;0.001;0.0;0.004;0.002;0.0	T	0.09292	-1.0681	10	0.08599	T	0.76	.	12.1388	0.53986	0.1825:0.8175:0.0:0.0	.	55;153;153;153;153;153	B7Z7U4;E9PG56;B7Z4C5;Q96CY4;Q16288-3;Q16288	.;.;.;.;.;NTRK3_HUMAN	Q	153;153;153;153;55;153;153	ENSP00000377990:R153Q;ENSP00000354207:R153Q;ENSP00000350356:R153Q;ENSP00000347397:R153Q;ENSP00000437773:R55Q;ENSP00000444673:R153Q;ENSP00000318328:R153Q	ENSP00000318328:R153Q	R	-	2	0	NTRK3	86491576	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.332000	0.33805	2.591000	0.87537	0.563000	0.77884	CGG		0.478	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding			
MRPS11	64963	broad.mit.edu	37	15	89018412	89018412	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr15:89018412G>A	ENST00000325844.4	+	4	618	c.353G>A	c.(352-354)cGg>cAg	p.R118Q	MRPS11_ENST00000353598.6_Missense_Mutation_p.R85Q|MRPS11_ENST00000557974.1_3'UTR	NM_022839.3	NP_073750.2	P82912	RT11_HUMAN	mitochondrial ribosomal protein S11	118					DNA damage response, detection of DNA damage (GO:0042769)|translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.R118Q(1)		large_intestine(3)	3	Lung NSC(78;0.203)		BRCA - Breast invasive adenocarcinoma(143;0.188)			GAGGGATTTCGGAATGCCAAG	0.522																																					p.R118Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G353A	15						.						124.0	105.0	112.0					15																	89018412		2201	4299	6500	86819416	SO:0001583	missense	64963	exon4			AB051349	CCDS10342.1, CCDS10343.1	15q25	2012-09-13			ENSG00000181991	ENSG00000181991		"""Mitochondrial ribosomal proteins / small subunits"""	14050	protein-coding gene	gene with protein product	"""cervical cancer proto-oncogene 2"""	611977				11402041	Standard	NM_022839		Approved	FLJ23406, HCC-2, FLJ22512	uc002bml.3	P82912	OTTHUMG00000148678	ENST00000325844.4:c.353G>A	15.37:g.89018412G>A	ENSP00000317376:p.Arg118Gln		86819416	NM_022839	B2RD52|Q969D7|Q96GI3|Q9BYC3	Missense_Mutation	SNP	ENST00000325844.4	37	CCDS10342.1	.	.	.	.	.	.	.	.	.	.	G	17.80	3.479255	0.63849	.	.	ENSG00000181991	ENST00000325844;ENST00000353598	T;T	0.35605	1.41;1.3	5.31	2.0	0.26442	.	0.113323	0.56097	D	0.000033	T	0.24890	0.0604	L	0.45470	1.425	0.35804	D	0.823398	P;D;P	0.53885	0.929;0.963;0.942	B;B;B	0.38500	0.118;0.275;0.188	T	0.31447	-0.9943	10	0.87932	D	0	-14.4484	5.3984	0.16283	0.5276:0.0:0.4724:0.0	.	117;85;118	P82912-2;P82912-3;P82912	.;.;RT11_HUMAN	Q	118;85	ENSP00000317376:R118Q;ENSP00000318054:R85Q	ENSP00000317376:R118Q	R	+	2	0	MRPS11	86819416	0.992000	0.36948	0.989000	0.46669	0.889000	0.51656	1.259000	0.32956	0.621000	0.30232	0.655000	0.94253	CGG		0.522	MRPS11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309067.2	NM_022839	
PGPEP1L	145814	broad.mit.edu	37	15	99514291	99514291	+	Missense_Mutation	SNP	C	C	T	rs200602348	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr15:99514291C>T	ENST00000378919.6	-	3	323	c.118G>A	c.(118-120)Gga>Aga	p.G40R	RP11-654A16.3_ENST00000559468.1_RNA|PGPEP1L_ENST00000535714.1_5'UTR	NM_001102612.2	NP_001096082.2	A6NFU8	PGPIL_HUMAN	pyroglutamyl-peptidase I-like	40							cysteine-type peptidase activity (GO:0008234)	p.G40R(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(2)|skin(1)|stomach(1)	14						TCCCAGATTCCGGTGACCCTC	0.607													C|||	2	0.000399361	0.0	0.0	5008	,	,		14734	0.002		0.0	False		,,,				2504	0.0				p.G40R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G118A	15						.						64.0	64.0	64.0					15																	99514291		2064	4216	6280	97331814	SO:0001583	missense	145814	exon3				CCDS53977.1, CCDS58400.1	15q26.3	2010-02-16			ENSG00000183571	ENSG00000183571			27080	protein-coding gene	gene with protein product							Standard	NM_001102612		Approved		uc002bum.3	A6NFU8		ENST00000378919.6:c.118G>A	15.37:g.99514291C>T	ENSP00000368199:p.Gly40Arg		97331814	NM_001102612	H0YF86	Missense_Mutation	SNP	ENST00000378919.6	37	CCDS53977.1	.	.	.	.	.	.	.	.	.	.	C	0.017	-1.492639	0.01009	.	.	ENSG00000183571	ENST00000378919;ENST00000535714	T	0.38560	1.13	4.34	-0.868	0.10652	.	.	.	.	.	T	0.13072	0.0317	N	0.01352	-0.895	0.09310	N	1	B	0.13594	0.008	B	0.10450	0.005	T	0.29458	-1.0011	9	0.19147	T	0.46	-17.6372	5.3353	0.15955	0.0:0.241:0.1387:0.6203	.	40	A6NFU8	PGPIL_HUMAN	R	40;33	ENSP00000368199:G40R	ENSP00000368199:G40R	G	-	1	0	PGPEP1L	97331814	0.124000	0.22315	0.025000	0.17156	0.012000	0.07955	0.250000	0.18235	-0.254000	0.09500	-1.078000	0.02229	GGA		0.607	PGPEP1L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415703.1	NM_001102612.2	
BAHD1	22893	broad.mit.edu	37	15	40751953	40751953	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr15:40751953delC	ENST00000416165.1	+	2	1361	c.1290delC	c.(1288-1290)cacfs	p.H430fs	BAHD1_ENST00000561234.1_Frame_Shift_Del_p.H430fs|BAHD1_ENST00000560846.1_Frame_Shift_Del_p.H430fs	NM_014952.3	NP_055767.3	Q8TBE0	BAHD1_HUMAN	bromo adjacent homology domain containing 1	430					heterochromatin assembly (GO:0031507)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|chromosome (GO:0005694)	chromatin binding (GO:0003682)	p.P431fs*16(1)|p.H430Q(1)		NS(1)|endometrium(6)|kidney(3)|large_intestine(3)|lung(10)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	28		all_cancers(109;8.28e-19)|all_epithelial(112;2.64e-15)|Lung NSC(122;5.14e-11)|all_lung(180;1.27e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.46e-06)|BRCA - Breast invasive adenocarcinoma(123;0.08)		CTTTCCAGCACCCTCCCTGGG	0.627																																					p.H430fs												.	.	2	Substitution - Missense(1)|Deletion - Frameshift(1)	large_intestine(1)|lung(1)	c.1290delC	15						.						51.0	49.0	50.0					15																	40751953		2203	4300	6503	38539245	SO:0001589	frameshift_variant	22893	exon2			AL833923	CCDS10058.1, CCDS73705.1	15q14	2005-11-10			ENSG00000140320	ENSG00000140320			29153	protein-coding gene	gene with protein product		613880				10231032	Standard	XM_005254229		Approved	KIAA0945	uc001zlu.2	Q8TBE0	OTTHUMG00000129982	ENST00000416165.1:c.1290delC	15.37:g.40751953delC	ENSP00000396976:p.His430fs		38539245	NM_014952	Q8NDF7|Q9Y2F4	Frame_Shift_Del	DEL	ENST00000416165.1	37	CCDS10058.1																																																																																				0.627	BAHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252248.1	NM_014952	
ADAMTS17	170691	broad.mit.edu	37	15	100516360	100516360	+	Missense_Mutation	SNP	C	C	T	rs147283866		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr15:100516360C>T	ENST00000268070.4	-	21	3122	c.3017G>A	c.(3016-3018)cGc>cAc	p.R1006H	CTD-3076O17.2_ENST00000559400.1_RNA|CTD-3076O17.1_ENST00000528696.3_RNA	NM_139057.2	NP_620688.2	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 17	1006	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R1006H(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)	50	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)		GCTGCCGTGGCGCCCTGTGAC	0.652																																					p.R1006H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3017A	15						.	C	HIS/ARG	2,4084		0,2,2041	53.0	41.0	45.0		3017	5.3	1.0	15	dbSNP_134	45	1,7869		0,1,3934	yes	missense	ADAMTS17	NM_139057.2	29	0,3,5975	TT,TC,CC		0.0127,0.0489,0.0251	probably-damaging	1006/1096	100516360	3,11953	2043	3935	5978	98333883	SO:0001583	missense	170691	exon21			AJ315735	CCDS10383.1	15q24	2014-01-28	2005-08-19		ENSG00000140470	ENSG00000140470		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17109	protein-coding gene	gene with protein product		607511	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 17"""			11867212	Standard	NM_139057		Approved	FLJ32769, FLJ16363	uc002bvv.1	Q8TE56	OTTHUMG00000149867	ENST00000268070.4:c.3017G>A	15.37:g.100516360C>T	ENSP00000268070:p.Arg1006His		98333883	NM_139057	Q2I7G4|Q6ZN75	Missense_Mutation	SNP	ENST00000268070.4	37	CCDS10383.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.577257	0.86645	4.89E-4	1.27E-4	ENSG00000140470	ENST00000268070	T	0.52057	0.68	5.28	5.28	0.74379	Zinc finger, C2H2 (1);	0.069376	0.56097	D	0.000035	T	0.49253	0.1546	L	0.39467	1.215	0.80722	D	1	D	0.56968	0.978	P	0.50314	0.637	T	0.29366	-1.0014	10	0.15499	T	0.54	.	19.2671	0.93993	0.0:1.0:0.0:0.0	.	1006	Q8TE56	ATS17_HUMAN	H	1006	ENSP00000268070:R1006H	ENSP00000268070:R1006H	R	-	2	0	ADAMTS17	98333883	1.000000	0.71417	1.000000	0.80357	0.739000	0.42172	5.576000	0.67437	2.615000	0.88500	0.563000	0.77884	CGC		0.652	ADAMTS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313595.1	NM_139057	
CLCN7	1186	broad.mit.edu	37	16	1515270	1515270	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:1515270G>A	ENST00000382745.4	-	2	816	c.211C>T	c.(211-213)Ccg>Tcg	p.P71S	LA16c-390E6.3_ENST00000563223.1_RNA|CLCN7_ENST00000448525.1_Intron|CLCN7_ENST00000262318.8_Intron|CLCN7_ENST00000566812.1_5'Flank	NM_001287.5	NP_001278.1	P51798	CLCN7_HUMAN	chloride channel, voltage-sensitive 7	71					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|response to pH (GO:0009268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)	p.P71S(1)		breast(2)|central_nervous_system(3)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|skin(2)	24		Hepatocellular(780;0.0893)				CAACTCACCGGGTCCAAAAGT	0.582																																					p.P71S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C211T	16						.						116.0	79.0	92.0					16																	1515270		2199	4300	6499	1455271	SO:0001583	missense	1186	exon2			Z67743	CCDS32361.1, CCDS45378.1	16p13	2012-09-26	2012-02-23		ENSG00000103249	ENSG00000103249		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ion channels / Chloride channels : Voltage-sensitive"""	2025	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 63"""	602727	"""chloride channel 7"""			8543009	Standard	NM_001114331		Approved	CLC-7, OPTA2, CLC7, ClC-7, PPP1R63	uc002clv.3	P51798	OTTHUMG00000044467	ENST00000382745.4:c.211C>T	16.37:g.1515270G>A	ENSP00000372193:p.Pro71Ser		1455271	NM_001287	A6NEJ7|A8K5T9|A8K7X1|B3KPN3|E9PDB9|Q9NYX5	Missense_Mutation	SNP	ENST00000382745.4	37	CCDS32361.1	.	.	.	.	.	.	.	.	.	.	G	11.94	1.790009	0.31685	.	.	ENSG00000103249	ENST00000262318;ENST00000382745;ENST00000428756	D	0.90955	-2.76	4.7	3.51	0.40186	.	0.669674	0.15319	N	0.268642	T	0.77478	0.4136	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.69636	-0.5092	10	0.07644	T	0.81	-36.7081	11.0856	0.48084	0.1107:0.0:0.8893:0.0	.	71	P51798	CLCN7_HUMAN	S	24;71;13	ENSP00000372193:P71S	ENSP00000262318:P24S	P	-	1	0	CLCN7	1455271	1.000000	0.71417	1.000000	0.80357	0.843000	0.47879	2.753000	0.47524	2.176000	0.68965	0.505000	0.49811	CCG		0.582	CLCN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103598.2	NM_001287	
ABCC1	4363	broad.mit.edu	37	16	16225674	16225674	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:16225674C>T	ENST00000399410.3	+	27	4023	c.3848C>T	c.(3847-3849)cCg>cTg	p.P1283L	ABCC1_ENST00000349029.5_Missense_Mutation_p.P1168L|ABCC1_ENST00000399408.2_Missense_Mutation_p.P1293L|ABCC1_ENST00000346370.5_Missense_Mutation_p.P1227L|ABCC1_ENST00000345148.5_Missense_Mutation_p.P1283L|ABCC1_ENST00000351154.5_Missense_Mutation_p.P1224L	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	1283					arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)	p.P1283L(1)		breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	GAGACAGCTCCGCCCAGCAGC	0.587																																					p.P1224L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3671T	16						.						41.0	44.0	43.0					16																	16225674		1979	4157	6136	16133175	SO:0001583	missense	4363	exon26			L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"""ATP binding cassette transporters / subfamily C"""	51	protein-coding gene	gene with protein product		158343	"""multidrug resistance associated protein 1"""	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.3848C>T	16.37:g.16225674C>T	ENSP00000382342:p.Pro1283Leu		16133175	NM_019862	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Missense_Mutation	SNP	ENST00000399410.3	37	CCDS42122.1	.	.	.	.	.	.	.	.	.	.	C	13.61	2.288804	0.40494	.	.	ENSG00000103222	ENST00000399410;ENST00000399408;ENST00000346370;ENST00000351154;ENST00000345148;ENST00000349029;ENST00000536381	D;D;D;D;D;D	0.84370	-1.84;-1.84;-1.84;-1.84;-1.84;-1.84	5.11	5.11	0.69529	.	0.133094	0.51477	D	0.000099	D	0.86477	0.5942	L	0.41027	1.25	0.49051	D	0.999745	B;B;B;D;B;B	0.64830	0.008;0.013;0.02;0.994;0.012;0.02	B;B;B;P;B;B	0.55087	0.008;0.017;0.018;0.768;0.008;0.018	D	0.85585	0.1242	10	0.35671	T	0.21	-24.0275	17.5407	0.87846	0.0:1.0:0.0:0.0	.	1168;1283;1227;1224;1283;1293	P33527-5;P33527-4;P33527-3;P33527-2;P33527;P33527-9	.;.;.;.;MRP1_HUMAN;.	L	1283;1293;1227;1224;1283;1168;967	ENSP00000382342:P1283L;ENSP00000382340:P1293L;ENSP00000263019:P1227L;ENSP00000263017:P1224L;ENSP00000263014:P1283L;ENSP00000263016:P1168L	ENSP00000263014:P1283L	P	+	2	0	ABCC1	16133175	0.528000	0.26314	0.078000	0.20375	0.002000	0.02628	3.150000	0.50662	2.387000	0.81309	0.655000	0.94253	CCG		0.587	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996	
TMC5	79838	broad.mit.edu	37	16	19483429	19483429	+	Missense_Mutation	SNP	G	G	A	rs141710338	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:19483429G>A	ENST00000396229.2	+	11	2551	c.1802G>A	c.(1801-1803)cGt>cAt	p.R601H	TMC5_ENST00000564959.1_Missense_Mutation_p.R284H|TMC5_ENST00000381414.4_Missense_Mutation_p.R601H|TMC5_ENST00000541464.1_Intron|TMC5_ENST00000219821.5_Missense_Mutation_p.R355H|TMC5_ENST00000561503.1_Missense_Mutation_p.R242H|TMC5_ENST00000542583.2_Missense_Mutation_p.R601H	NM_001105248.1	NP_001098718.1	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5	601					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.R601H(1)|p.R355H(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|liver(2)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						TCAGAGCTCCGTCAGGAGAAT	0.532													G|||	3	0.000599042	0.0	0.0	5008	,	,		18983	0.003		0.0	False		,,,				2504	0.0				p.R355H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1064A	16						.						118.0	109.0	112.0					16																	19483429		2197	4300	6497	19390930	SO:0001583	missense	79838	exon7			AY263164	CCDS10577.1, CCDS42126.1, CCDS45431.1	16p13.11	2008-02-05			ENSG00000103534	ENSG00000103534			22999	protein-coding gene	gene with protein product						12812529, 12906855	Standard	NM_024780		Approved	FLJ13593	uc010var.2	Q6UXY8	OTTHUMG00000131458	ENST00000396229.2:c.1802G>A	16.37:g.19483429G>A	ENSP00000379531:p.Arg601His		19390930	NM_024780	Q68DK8|Q8IY20|Q8NHV6|Q9H8I7	Missense_Mutation	SNP	ENST00000396229.2	37	CCDS45431.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	G	15.33	2.801960	0.50315	.	.	ENSG00000103534	ENST00000381414;ENST00000396229;ENST00000542583;ENST00000219821;ENST00000440743	T;T;T;T	0.58210	0.35;0.35;0.35;0.35	5.68	-1.85	0.07784	.	1.163500	0.06348	N	0.709285	T	0.58652	0.2137	L	0.51422	1.61	0.19575	N	0.999967	B;D;D;D;D	0.61080	0.075;0.989;0.98;0.98;0.989	B;P;B;B;P	0.50617	0.012;0.646;0.443;0.443;0.646	T	0.62821	-0.6773	10	0.40728	T	0.16	-0.0219	17.5855	0.87980	0.0:0.0:0.2504:0.7495	.	284;355;355;601;601	E7EU57;Q6UXY8-3;B3KUQ8;Q6UXY8;Q6UXY8-2	.;.;.;TMC5_HUMAN;.	H	601;601;601;355;284	ENSP00000370822:R601H;ENSP00000379531:R601H;ENSP00000446274:R601H;ENSP00000219821:R355H	ENSP00000219821:R355H	R	+	2	0	TMC5	19390930	0.000000	0.05858	0.552000	0.28243	0.951000	0.60555	-0.236000	0.09003	-0.204000	0.10235	0.561000	0.74099	CGT		0.532	TMC5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435888.1	NM_024780	
GPRC5B	51704	broad.mit.edu	37	16	19883887	19883887	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:19883887C>T	ENST00000300571.2	-	2	472	c.281G>A	c.(280-282)gGc>gAc	p.G94D	GPRC5B_ENST00000569847.1_Missense_Mutation_p.G94D|GPRC5B_ENST00000537135.1_Missense_Mutation_p.G120D|GPRC5B_ENST00000569479.1_Missense_Mutation_p.G94D|GPRC5B_ENST00000535671.1_Missense_Mutation_p.G94D	NM_016235.1	NP_057319.1	Q9NZH0	GPC5B_HUMAN	G protein-coupled receptor, class C, group 5, member B	94					glucose homeostasis (GO:0042593)|locomotory behavior (GO:0007626)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein tyrosine kinase activity (GO:0061098)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|G-protein coupled receptor binding (GO:0001664)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)	p.G94D(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25						AAAGTGGAGGCCCACAGGGCT	0.627																																					p.G94D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G281A	16						.						32.0	35.0	34.0					16																	19883887		2197	4300	6497	19791388	SO:0001583	missense	51704	exon2			AF202640	CCDS10581.1	16p12	2014-01-30	2014-01-30		ENSG00000167191	ENSG00000167191		"""GPCR / Class C : Orphans"""	13308	protein-coding gene	gene with protein product		605948	"""G protein-coupled receptor, family C, group 1, member B"", ""G protein-coupled receptor, family C, group 5, member B"""			10493829, 10783259	Standard	XM_005255357		Approved	RAIG-2	uc002dgt.3	Q9NZH0	OTTHUMG00000131460	ENST00000300571.2:c.281G>A	16.37:g.19883887C>T	ENSP00000300571:p.Gly94Asp		19791388	NM_016235	D2DFB0|O75205|Q8NBZ8	Missense_Mutation	SNP	ENST00000300571.2	37	CCDS10581.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.332020	0.81801	.	.	ENSG00000167191	ENST00000300571;ENST00000535671;ENST00000537135	D;D;D	0.88124	-2.34;-2.34;-2.34	5.8	5.8	0.92144	GPCR, family 3, C-terminal (1);	0.059655	0.64402	D	0.000002	D	0.92662	0.7668	M	0.71036	2.16	0.58432	D	0.999995	D;D	0.64830	0.994;0.99	D;P	0.64877	0.93;0.843	D	0.91748	0.5410	9	.	.	.	.	19.049	0.93034	0.0:1.0:0.0:0.0	.	120;94	B7Z831;Q9NZH0	.;GPC5B_HUMAN	D	94;94;120	ENSP00000300571:G94D;ENSP00000442858:G94D;ENSP00000441775:G120D	.	G	-	2	0	GPRC5B	19791388	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.981000	0.56902	2.755000	0.94549	0.655000	0.94253	GGC		0.627	GPRC5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254285.1		
LUC7L	55692	broad.mit.edu	37	16	258092	258092	+	Silent	SNP	C	C	T	rs371140629		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:258092C>T	ENST00000293872.8	-	4	461	c.351G>A	c.(349-351)gcG>gcA	p.A117A	LUC7L_ENST00000494366.1_5'Flank|LUC7L_ENST00000397780.1_Silent_p.A64A|LUC7L_ENST00000397783.1_Silent_p.A117A|LUC7L_ENST00000337351.4_Silent_p.A117A	NM_201412.1	NP_958815.1	Q9NQ29	LUC7L_HUMAN	LUC7-like (S. cerevisiae)	117					mRNA splice site selection (GO:0006376)|negative regulation of striated muscle tissue development (GO:0045843)	U1 snRNP (GO:0005685)	identical protein binding (GO:0042802)|mRNA binding (GO:0003729)	p.A117A(1)		NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	11		all_cancers(16;1.1e-06)|all_epithelial(16;2.71e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.0138)|all_lung(18;0.0306)				CAGAAACTTCCGCACTGATTT	0.468																																					p.A117A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G351A	16						.						152.0	135.0	141.0					16																	258092		2203	4300	6503	198093	SO:0001819	synonymous_variant	55692	exon4			AY005111	CCDS10401.1, CCDS32348.1	16p13.3	2010-01-25	2001-11-28		ENSG00000007392	ENSG00000007392			6723	protein-coding gene	gene with protein product		607782	"""LUC7 (S. cerevisiae)-like"""				Standard	NM_201412		Approved	LUC7B1, hLuc7B1, Luc7	uc002cgc.1	Q9NQ29	OTTHUMG00000060730	ENST00000293872.8:c.351G>A	16.37:g.258092C>T			198093	NM_201412	B8ZZ13|Q96S32|Q9NPH4	Silent	SNP	ENST00000293872.8	37	CCDS32348.1																																																																																				0.468	LUC7L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134239.1		
GPRC5B	51704	broad.mit.edu	37	16	19884093	19884093	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:19884093C>T	ENST00000300571.2	-	2	266	c.75G>A	c.(73-75)tcG>tcA	p.S25S	GPRC5B_ENST00000569847.1_Silent_p.S25S|GPRC5B_ENST00000537135.1_Silent_p.S51S|GPRC5B_ENST00000569479.1_Silent_p.S25S|GPRC5B_ENST00000535671.1_Silent_p.S25S	NM_016235.1	NP_057319.1	Q9NZH0	GPC5B_HUMAN	G protein-coupled receptor, class C, group 5, member B	25					glucose homeostasis (GO:0042593)|locomotory behavior (GO:0007626)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein tyrosine kinase activity (GO:0061098)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|G-protein coupled receptor binding (GO:0001664)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)	p.S25S(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25						CAGAGGCCACCGAGGTGATCA	0.577																																					p.S25S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G75A	16						.						54.0	53.0	54.0					16																	19884093		2197	4300	6497	19791594	SO:0001819	synonymous_variant	51704	exon2			AF202640	CCDS10581.1	16p12	2014-01-30	2014-01-30		ENSG00000167191	ENSG00000167191		"""GPCR / Class C : Orphans"""	13308	protein-coding gene	gene with protein product		605948	"""G protein-coupled receptor, family C, group 1, member B"", ""G protein-coupled receptor, family C, group 5, member B"""			10493829, 10783259	Standard	XM_005255357		Approved	RAIG-2	uc002dgt.3	Q9NZH0	OTTHUMG00000131460	ENST00000300571.2:c.75G>A	16.37:g.19884093C>T			19791594	NM_016235	D2DFB0|O75205|Q8NBZ8	Silent	SNP	ENST00000300571.2	37	CCDS10581.1																																																																																				0.577	GPRC5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254285.1		
DNAH3	55567	broad.mit.edu	37	16	20976249	20976249	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:20976249C>T	ENST00000261383.3	-	53	8956	c.8957G>A	c.(8956-8958)cGa>cAa	p.R2986Q	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	2986					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.R2986Q(2)		NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		CCCCAGCTGTCGGGCAGCTTC	0.527																																					p.R2986Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G8957A	16						.						108.0	107.0	107.0					16																	20976249		2201	4300	6501	20883750	SO:0001583	missense	55567	exon53			U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.8957G>A	16.37:g.20976249C>T	ENSP00000261383:p.Arg2986Gln		20883750	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	C	1.726	-0.495271	0.04291	.	.	ENSG00000158486	ENST00000261383	T	0.73363	-0.74	6.17	3.15	0.36227	Dynein heavy chain, coiled coil stalk (1);	0.251589	0.32175	N	0.006477	T	0.47563	0.1452	N	0.12443	0.215	0.80722	D	1	P	0.41624	0.757	B	0.30495	0.116	T	0.39563	-0.9608	10	0.12766	T	0.61	.	11.1276	0.48328	0.0:0.8049:0.0:0.1951	.	2986	Q8TD57	DYH3_HUMAN	Q	2986	ENSP00000261383:R2986Q	ENSP00000261383:R2986Q	R	-	2	0	DNAH3	20883750	0.933000	0.31639	0.677000	0.29947	0.013000	0.08279	2.550000	0.45811	0.457000	0.26962	-0.136000	0.14681	CGA		0.527	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
DNAH3	55567	broad.mit.edu	37	16	20976402	20976402	+	Missense_Mutation	SNP	C	C	T	rs369073466		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:20976402C>T	ENST00000261383.3	-	53	8803	c.8804G>A	c.(8803-8805)cGg>cAg	p.R2935Q	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	2935	Stalk. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.R2935Q(2)		NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		GGCCTGGAGCCGATCTACCAC	0.532																																					p.R2935Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G8804A	16						.	C	GLN/ARG	1,4401	2.1+/-5.4	0,1,2200	189.0	180.0	183.0		8804	2.9	0.0	16		183	0,8600		0,0,4300	no	missense	DNAH3	NM_017539.1	43	0,1,6500	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	2935/4117	20976402	1,13001	2201	4300	6501	20883903	SO:0001583	missense	55567	exon53			U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.8804G>A	16.37:g.20976402C>T	ENSP00000261383:p.Arg2935Gln		20883903	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	C	6.455	0.452051	0.12283	2.27E-4	0.0	ENSG00000158486	ENST00000261383	T	0.74106	-0.81	5.93	2.9	0.33743	Dynein heavy chain, coiled coil stalk (1);	0.153499	0.43260	D	0.000600	T	0.72645	0.3486	L	0.39020	1.185	0.80722	D	1	D	0.69078	0.997	P	0.55455	0.776	T	0.68081	-0.5503	10	0.34782	T	0.22	.	10.7918	0.46436	0.0:0.7909:0.0:0.2091	.	2935	Q8TD57	DYH3_HUMAN	Q	2935	ENSP00000261383:R2935Q	ENSP00000261383:R2935Q	R	-	2	0	DNAH3	20883903	1.000000	0.71417	0.023000	0.16930	0.000000	0.00434	4.922000	0.63404	0.395000	0.25257	-0.136000	0.14681	CGG		0.532	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
SCNN1G	6340	broad.mit.edu	37	16	23197640	23197640	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:23197640C>T	ENST00000300061.2	+	2	191	c.48C>T	c.(46-48)ccC>ccT	p.P16P		NM_001039.3	NP_001030.2	P51170	SCNNG_HUMAN	sodium channel, non-voltage-gated 1, gamma subunit	16					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|sodium channel activity (GO:0005272)|WW domain binding (GO:0050699)	p.P16P(1)		NS(2)|autonomic_ganglia(1)|breast(1)|cervix(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	34				GBM - Glioblastoma multiforme(48;0.0366)	Amiloride(DB00594)|Triamterene(DB00384)	AGAATCTGCCCGTGACGGGCC	0.617																																					p.P16P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C48T	16						.						52.0	56.0	55.0					16																	23197640		2197	4300	6497	23105141	SO:0001819	synonymous_variant	6340	exon2			U48937	CCDS10608.1	16p12	2012-02-28	2012-02-28		ENSG00000166828	ENSG00000166828		"""Ion channels / Sodium channel, nonvoltage-gated"", ""Sodium channels"""	10602	protein-coding gene	gene with protein product		600761	"""sodium channel, nonvoltage-gated 1, gamma"", ""sodium channel, non-voltage-gated 1, gamma"""			7490094	Standard	NM_001039		Approved	ENaCgamma, SCNEG	uc002dlm.1	P51170	OTTHUMG00000131609	ENST00000300061.2:c.48C>T	16.37:g.23197640C>T			23105141	NM_001039	P78437|Q6PCC2|Q93023|Q93024|Q93025|Q93026|Q93027|Q96TD2	Silent	SNP	ENST00000300061.2	37	CCDS10608.1																																																																																				0.617	SCNN1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254496.1	NM_001039	
GGA2	23062	broad.mit.edu	37	16	23494291	23494291	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:23494291G>A	ENST00000309859.4	-	9	915	c.833C>T	c.(832-834)aCg>aTg	p.T278M	GGA2_ENST00000569182.1_5'Flank|GGA2_ENST00000567468.1_Intron	NM_015044.4	NP_055859.1	Q9UJY4	GGA2_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 2	278	GAT. {ECO:0000255|PROSITE- ProRule:PRU00373}.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)	p.T278M(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(48;0.0386)		CCGGAACAGCGTGGGCCGCAG	0.577																																					p.T278M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C833T	16						.						150.0	109.0	123.0					16																	23494291		2197	4300	6497	23401792	SO:0001583	missense	23062	exon9			AF190863	CCDS10611.1	16p12	2010-02-12	2010-02-12		ENSG00000103365	ENSG00000103365			16064	protein-coding gene	gene with protein product		606005				10747088, 10749927	Standard	NM_015044		Approved	VEAR, KIAA1080	uc002dlq.3	Q9UJY4	OTTHUMG00000096957	ENST00000309859.4:c.833C>T	16.37:g.23494291G>A	ENSP00000311962:p.Thr278Met		23401792	NM_015044	D3DWF0|O14564|Q9NYN2|Q9UPS2	Missense_Mutation	SNP	ENST00000309859.4	37	CCDS10611.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.113989	0.77210	.	.	ENSG00000103365	ENST00000309859	T	0.50001	0.76	5.51	4.56	0.56223	GAT (2);	0.244990	0.41001	D	0.000968	T	0.50769	0.1635	L	0.46885	1.475	0.80722	D	1	D	0.56746	0.977	P	0.53593	0.73	T	0.49390	-0.8945	10	0.45353	T	0.12	-17.4058	10.2429	0.43324	0.0909:0.0:0.9091:0.0	.	278	Q9UJY4	GGA2_HUMAN	M	278	ENSP00000311962:T278M	ENSP00000311962:T278M	T	-	2	0	GGA2	23401792	1.000000	0.71417	0.994000	0.49952	0.945000	0.59286	3.386000	0.52492	1.316000	0.45131	0.655000	0.94253	ACG		0.577	GGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214019.1		
NDUFAB1	4706	broad.mit.edu	37	16	23598554	23598554	+	Silent	SNP	G	G	A	rs143906081		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:23598554G>A	ENST00000570319.1	-	2	255	c.255C>T	c.(253-255)taC>taT	p.Y85Y	NDUFAB1_ENST00000007516.3_Silent_p.Y85Y			O14561	ACPM_HUMAN	NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex, 1, 8kDa	85					cellular metabolic process (GO:0044237)|fatty acid biosynthetic process (GO:0006633)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|protein lipoylation (GO:0009249)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)	ACP phosphopantetheine attachment site binding involved in fatty acid biosynthetic process (GO:0000036)|calcium ion binding (GO:0005509)|fatty acid binding (GO:0005504)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)	p.Y85Y(1)		endometrium(1)|large_intestine(1)|lung(1)	3				GBM - Glioblastoma multiforme(48;0.0339)		GTTTCAATACGTAAAGAACAC	0.413													G|||	1	0.000199681	0.0	0.0	5008	,	,		18392	0.0		0.001	False		,,,				2504	0.0				p.Y85Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C255T	16						.	G		0,4394		0,0,2197	122.0	107.0	112.0		255	-5.0	0.9	16	dbSNP_134	112	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	NDUFAB1	NM_005003.2		0,2,6495	AA,AG,GG		0.0233,0.0,0.0154		85/157	23598554	2,12992	2197	4300	6497	23506055	SO:0001819	synonymous_variant	4706	exon2			AF087660	CCDS10614.1	16p12.3	2011-07-04	2002-08-29		ENSG00000004779	ENSG00000004779		"""Mitochondrial respiratory chain complex / Complex I"""	7694	protein-coding gene	gene with protein product	"""acyl carrier protein, mitochondrial"", ""complex I SDAP subunit"""	603836	"""NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex, 1 (8kD, SDAP)"""			9763677, 9878551	Standard	NM_005003		Approved	SDAP, FASN2A, ACP	uc002dlw.3	O14561	OTTHUMG00000096985	ENST00000570319.1:c.255C>T	16.37:g.23598554G>A			23506055	NM_005003	B2R4M1|Q9UNV1	Silent	SNP	ENST00000570319.1	37	CCDS10614.1																																																																																				0.413	NDUFAB1-005	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436917.1	NM_005003	
IL4R	3566	broad.mit.edu	37	16	27373886	27373886	+	Missense_Mutation	SNP	C	C	T	rs376032165		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:27373886C>T	ENST00000395762.2	+	11	1472	c.1213C>T	c.(1213-1215)Cgg>Tgg	p.R405W	IL4R_ENST00000543915.2_Missense_Mutation_p.R405W|IL4R_ENST00000380922.3_Missense_Mutation_p.R390W|IL4R_ENST00000170630.2_Missense_Mutation_p.R405W	NM_000418.3	NP_000409.1	P24394	IL4RA_HUMAN	interleukin 4 receptor	405					defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|ovulation (GO:0030728)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|production of molecular mediator involved in inflammatory response (GO:0002532)|regulation of cell proliferation (GO:0042127)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	interleukin-4 receptor activity (GO:0004913)|receptor signaling protein activity (GO:0005057)	p.R405W(1)		breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	33						CATTGTGGCCCGGCTAACAGA	0.587																																					p.R405W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1213T	16						.	C	TRP/ARG	0,4394		0,0,2197	67.0	69.0	68.0		1213	3.3	1.0	16		68	2,8598	2.2+/-6.3	0,2,4298	no	missense	IL4R	NM_000418.2	101	0,2,6495	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	405/826	27373886	2,12992	2197	4300	6497	27281387	SO:0001583	missense	3566	exon11			X52425	CCDS10629.1, CCDS58441.1	16p12.1-p11.2	2008-05-14			ENSG00000077238	ENSG00000077238		"""Interleukins and interleukin receptors"", ""CD molecules"""	6015	protein-coding gene	gene with protein product		147781				1679753	Standard	NM_000418		Approved	CD124	uc010bxy.4	P24394	OTTHUMG00000097015	ENST00000395762.2:c.1213C>T	16.37:g.27373886C>T	ENSP00000379111:p.Arg405Trp		27281387	NM_000418	B4E076|B9EKU8|H3BSY5|Q96P01|Q9H181|Q9H182|Q9H183|Q9H184|Q9H185|Q9H186|Q9H187|Q9H188	Missense_Mutation	SNP	ENST00000395762.2	37	CCDS10629.1	.	.	.	.	.	.	.	.	.	.	C	15.81	2.943449	0.53079	0.0	2.33E-4	ENSG00000077238	ENST00000395762;ENST00000543915;ENST00000380922;ENST00000170630	T;T;T;T	0.13089	2.62;2.62;2.62;2.62	5.42	3.3	0.37823	.	2.755460	0.00987	N	0.003472	T	0.38321	0.1036	M	0.64997	1.995	0.27482	N	0.952531	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.75484	0.986;0.986;0.986	T	0.05084	-1.0907	10	0.72032	D	0.01	-33.2675	9.8661	0.41145	0.4542:0.5457:0.0:0.0	.	390;405;405	B4E076;B9EGC0;P24394	.;.;IL4RA_HUMAN	W	405;405;390;405	ENSP00000379111:R405W;ENSP00000441667:R405W;ENSP00000370309:R390W;ENSP00000170630:R405W	ENSP00000170630:R405W	R	+	1	2	IL4R	27281387	0.974000	0.33945	0.990000	0.47175	0.317000	0.28152	0.336000	0.19823	1.255000	0.44051	0.655000	0.94253	CGG		0.587	IL4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214104.4		
QPRT	23475	broad.mit.edu	37	16	29690525	29690525	+	Missense_Mutation	SNP	G	G	A	rs370631780		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:29690525G>A	ENST00000395384.4	+	1	168	c.7G>A	c.(7-9)Gct>Act	p.A3T	QPRT_ENST00000219771.7_3'UTR|QPRT_ENST00000562473.1_Missense_Mutation_p.A3T	NM_014298.3	NP_055113.2	Q15274	NADC_HUMAN	quinolinate phosphoribosyltransferase	3					NAD biosynthetic process (GO:0009435)|NAD metabolic process (GO:0019674)|protein oligomerization (GO:0051259)|quinolinate catabolic process (GO:0034213)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	nicotinate-nucleotide diphosphorylase (carboxylating) activity (GO:0004514)|protein homodimerization activity (GO:0042803)	p.A3T(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)	9					Niacin(DB00627)	CACCATGGACGCTGAAGGTAA	0.647																																					p.A3T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G7A	16						.	G	THR/ALA	1,4393		0,1,2196	139.0	107.0	118.0		7	-2.8	0.8	16		118	0,8600		0,0,4300	no	missense	QPRT	NM_014298.3	58	0,1,6496	AA,AG,GG		0.0,0.0228,0.0077	benign	3/298	29690525	1,12993	2197	4300	6497	29598026	SO:0001583	missense	23475	exon1			D78177	CCDS10651.1	16p11.2	2008-07-31	2008-07-31		ENSG00000103485	ENSG00000103485	2.4.2.19		9755	protein-coding gene	gene with protein product	"""nicotinate-nucleotide pyrophosphorylase (carboxylating)"""	606248				9473669	Standard	NM_014298		Approved	QPRTase	uc002dto.3	Q15274	OTTHUMG00000097770	ENST00000395384.4:c.7G>A	16.37:g.29690525G>A	ENSP00000378782:p.Ala3Thr		29598026	NM_014298	Q53XW7|Q96G22|Q9BSG6	Missense_Mutation	SNP	ENST00000395384.4	37	CCDS10651.1	.	.	.	.	.	.	.	.	.	.	.	17.77	3.472297	0.63737	2.28E-4	0.0	ENSG00000103485	ENST00000449759;ENST00000395384	T	0.30714	1.52	2.63	-2.76	0.05896	.	1.999930	0.02952	N	0.141816	T	0.14313	0.0346	N	0.08118	0	0.21675	N	0.999596	B	0.02656	0.0	B	0.01281	0.0	T	0.13791	-1.0496	9	.	.	.	-10.9754	5.0959	0.14733	0.3324:0.4261:0.2415:0.0	.	3	Q15274	NADC_HUMAN	T	3	ENSP00000378782:A3T	.	A	+	1	0	QPRT	29598026	0.699000	0.27786	0.796000	0.32109	0.675000	0.39556	-0.693000	0.05121	-0.605000	0.05753	0.491000	0.48974	GCT		0.647	QPRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215011.2	NM_014298	
BCL7C	9274	broad.mit.edu	37	16	30900255	30900255	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:30900255T>C	ENST00000215115.4	-	5	1469	c.454A>G	c.(454-456)Ata>Gta	p.I152V	MIR4519_ENST00000570025.1_RNA|MIR4519_ENST00000564901.1_RNA|BCL7C_ENST00000380317.4_Missense_Mutation_p.I152V|AC106782.20_ENST00000572471.1_RNA|MIR4519_ENST00000565573.1_RNA	NM_004765.2	NP_004756.2	Q8WUZ0	BCL7C_HUMAN	B-cell CLL/lymphoma 7C	152	Pro-rich.				apoptotic process (GO:0006915)			p.I152V(1)		large_intestine(1)|lung(3)|prostate(1)|skin(1)	6			Colorectal(24;0.198)			CCAGCAGTTATGCCCCCGGGA	0.587																																					p.I152V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A454G	16						.						94.0	85.0	88.0					16																	30900255		2197	4300	6497	30807756	SO:0001583	missense	9274	exon5			AJ223980	CCDS10693.1, CCDS67012.1	16p11	2012-11-19			ENSG00000099385	ENSG00000099385			1006	protein-coding gene	gene with protein product		605847				9931421	Standard	NM_004765		Approved		uc002dzv.3	Q8WUZ0	OTTHUMG00000177719	ENST00000215115.4:c.454A>G	16.37:g.30900255T>C	ENSP00000215115:p.Ile152Val		30807756	NM_004765	O43770|Q6PD89	Missense_Mutation	SNP	ENST00000215115.4	37	CCDS10693.1	.	.	.	.	.	.	.	.	.	.	T	0.674	-0.800995	0.02841	.	.	ENSG00000099385	ENST00000380317;ENST00000215115	T;T	0.42131	0.98;1.02	5.27	1.67	0.24075	.	0.651220	0.13712	N	0.367989	T	0.12518	0.0304	N	0.00926	-1.1	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.19321	-1.0309	10	0.27785	T	0.31	-8.7582	3.569	0.07910	0.0:0.2003:0.1985:0.6012	.	152;152	Q8WUZ0;Q8WUZ0-2	BCL7C_HUMAN;.	V	152	ENSP00000369674:I152V;ENSP00000215115:I152V	ENSP00000215115:I152V	I	-	1	0	BCL7C	30807756	0.000000	0.05858	0.926000	0.36857	0.673000	0.39480	-0.500000	0.06405	0.962000	0.38057	0.459000	0.35465	ATA		0.587	BCL7C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255547.3	NM_004765	
FBXL19	54620	broad.mit.edu	37	16	30939843	30939843	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:30939843T>C	ENST00000380310.2	+	6	901	c.743T>C	c.(742-744)cTc>cCc	p.L248P	FBXL19_ENST00000562319.1_Missense_Mutation_p.L228P|FBXL19_ENST00000471231.2_5'UTR|FBXL19_ENST00000565690.1_Intron|FBXL19_ENST00000338343.4_Missense_Mutation_p.L228P	NM_001099784.2	NP_001093254.2	Q6PCT2	FXL19_HUMAN	F-box and leucine-rich repeat protein 19	248	Pro-rich.				proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)	SCF ubiquitin ligase complex (GO:0019005)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.L248P(1)		breast(2)|endometrium(3)|lung(5)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16						GCCTGCCTCCTCCGAGGATCG	0.647																																					p.L248P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T743C	16						.						23.0	27.0	26.0					16																	30939843		1898	4120	6018	30847344	SO:0001583	missense	54620	exon6			AK127701	CCDS45465.1, CCDS73873.1	16p11.2	2014-02-20			ENSG00000099364	ENSG00000099364		"""F-boxes / Leucine-rich repeats"""	25300	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1C"""	609085					Standard	NM_001099784		Approved	DKFZp434K0410, Fbl19, JHDM1C, CXXC11	uc002eab.2	Q6PCT2	OTTHUMG00000132403	ENST00000380310.2:c.743T>C	16.37:g.30939843T>C	ENSP00000369666:p.Leu248Pro		30847344	NM_001099784	A8MT10|Q8N789|Q9NT14	Missense_Mutation	SNP	ENST00000380310.2	37	CCDS45465.1	.	.	.	.	.	.	.	.	.	.	t	13.48	2.249690	0.39797	.	.	ENSG00000099364	ENST00000338343;ENST00000380310	T;T	0.23754	1.89;2.2	5.03	5.03	0.67393	.	0.452292	0.17297	U	0.179404	T	0.28267	0.0698	N	0.08118	0	0.51012	D	0.999908	D	0.58970	0.984	D	0.72982	0.979	T	0.11012	-1.0605	10	0.31617	T	0.26	-14.4912	11.1669	0.48547	0.0:0.0:0.0:1.0	.	248	Q6PCT2	FXL19_HUMAN	P	228;248	ENSP00000339712:L228P;ENSP00000369666:L248P	ENSP00000339712:L228P	L	+	2	0	FBXL19	30847344	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.693000	0.47027	1.900000	0.55004	0.392000	0.25879	CTC		0.647	FBXL19-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_019085	
CREBBP	1387	broad.mit.edu	37	16	3824575	3824575	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:3824575G>A	ENST00000262367.5	-	12	3087	c.2278C>T	c.(2278-2280)Cca>Tca	p.P760S	CREBBP_ENST00000382070.3_Missense_Mutation_p.P722S	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	760					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.P760S(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)		CTTACCCCTGGCACTGAGCCC	0.532			"""T, N, F, Mis, O"""	"""MLL, MORF, RUNXBP2"""	"""ALL, AML, DLBCL, B-NHL """		Rubinstein-Taybi syndrome																														p.P760S			Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2278T	16						.						170.0	134.0	146.0					16																	3824575		2197	4300	6497	3764576	SO:0001583	missense	1387	exon12			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.2278C>T	16.37:g.3824575G>A	ENSP00000262367:p.Pro760Ser		3764576	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	G	17.54	3.416282	0.62511	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070	D;D	0.83837	-1.77;-1.67	4.79	4.79	0.61399	.	0.156200	0.45361	D	0.000380	D	0.86213	0.5879	L	0.46157	1.445	0.80722	D	1	D;P	0.76494	0.999;0.904	D;P	0.64410	0.925;0.518	D	0.85133	0.0976	10	0.42905	T	0.14	-11.8381	12.8007	0.57584	0.0792:0.0:0.9208:0.0	.	790;760	Q4LE28;Q92793	.;CBP_HUMAN	S	760;790;722	ENSP00000262367:P760S;ENSP00000371502:P722S	ENSP00000262367:P760S	P	-	1	0	CREBBP	3764576	1.000000	0.71417	0.997000	0.53966	0.918000	0.54935	5.615000	0.67702	2.663000	0.90544	0.557000	0.71058	CCA		0.532	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380	
ADCY9	115	broad.mit.edu	37	16	4016010	4016010	+	Silent	SNP	G	G	A	rs199850891		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:4016010G>A	ENST00000294016.3	-	11	4366	c.3828C>T	c.(3826-3828)gaC>gaT	p.D1276D		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	1276					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)	p.D1276D(1)		breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						TGGCAATCTCGTCTGTGGGAG	0.592													G|||	1	0.000199681	0.0	0.0	5008	,	,		19154	0.001		0.0	False		,,,				2504	0.0				p.D1276D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3828T	16						.						119.0	100.0	106.0					16																	4016010		2197	4300	6497	3956011	SO:0001819	synonymous_variant	115	exon11			AF036927	CCDS32382.1	16p13.3	2013-02-04				ENSG00000162104	4.6.1.1	"""Adenylate cyclases"""	240	protein-coding gene	gene with protein product		603302				9628827	Standard	NM_001116		Approved	AC9	uc002cvx.3	O60503		ENST00000294016.3:c.3828C>T	16.37:g.4016010G>A			3956011	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Silent	SNP	ENST00000294016.3	37	CCDS32382.1																																																																																				0.592	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1		
ADCY9	115	broad.mit.edu	37	16	4027524	4027524	+	Silent	SNP	G	G	A	rs370804007		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:4027524G>A	ENST00000294016.3	-	9	3325	c.2787C>T	c.(2785-2787)gcC>gcT	p.A929A		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	929					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)	p.A929A(1)		breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						GCAGCGGCCCGGCCCCCACGA	0.672																																					p.A929A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2787T	16						.						32.0	26.0	28.0					16																	4027524		2180	4295	6475	3967525	SO:0001819	synonymous_variant	115	exon9			AF036927	CCDS32382.1	16p13.3	2013-02-04				ENSG00000162104	4.6.1.1	"""Adenylate cyclases"""	240	protein-coding gene	gene with protein product		603302				9628827	Standard	NM_001116		Approved	AC9	uc002cvx.3	O60503		ENST00000294016.3:c.2787C>T	16.37:g.4027524G>A			3967525	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Silent	SNP	ENST00000294016.3	37	CCDS32382.1																																																																																				0.672	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1		
SETD1A	9739	broad.mit.edu	37	16	30990501	30990501	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:30990501C>T	ENST00000262519.8	+	14	4080	c.3394C>T	c.(3394-3396)Cgt>Tgt	p.R1132C		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	1132	Pro-rich. {ECO:0000255}.				histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.R1132C(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(21)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	59						TGCGCCTCTGCGTCCCCCAGA	0.701																																					p.R1132C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3394T	16						.						8.0	10.0	9.0					16																	30990501		2135	4247	6382	30898002	SO:0001583	missense	9739	exon14			AB002337	CCDS32435.1	16p11.2	2013-02-12			ENSG00000099381	ENSG00000099381		"""Chromatin-modifying enzymes / K-methyltransferases"", ""RNA binding motif (RRM) containing"""	29010	protein-coding gene	gene with protein product		611052				9205841, 12670868	Standard	XM_005255723		Approved	KIAA0339, Set1, KMT2F	uc002ead.1	O15047	OTTHUMG00000150474	ENST00000262519.8:c.3394C>T	16.37:g.30990501C>T	ENSP00000262519:p.Arg1132Cys		30898002	NM_014712	A6NP62|Q6PIF3|Q8TAJ6	Missense_Mutation	SNP	ENST00000262519.8	37	CCDS32435.1	.	.	.	.	.	.	.	.	.	.	C	6.143	0.394545	0.11638	.	.	ENSG00000099381	ENST00000262519	D	0.94280	-3.39	5.03	5.03	0.67393	.	0.431580	0.21827	N	0.068522	D	0.87716	0.6247	L	0.27053	0.805	0.20307	N	0.999912	P	0.42010	0.768	B	0.32805	0.153	D	0.83379	0.0011	10	0.66056	D	0.02	.	17.1265	0.86715	0.0:1.0:0.0:0.0	.	1132	O15047	SET1A_HUMAN	C	1132	ENSP00000262519:R1132C	ENSP00000262519:R1132C	R	+	1	0	SETD1A	30898002	0.592000	0.26832	0.991000	0.47740	0.033000	0.12548	3.603000	0.54074	2.328000	0.79073	0.557000	0.71058	CGT		0.701	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318244.2	NM_014712	
ABCC11	85320	broad.mit.edu	37	16	48209185	48209185	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:48209185G>T	ENST00000394747.1	-	25	4031	c.3682C>A	c.(3682-3684)Ctc>Atc	p.L1228I	ABCC11_ENST00000394748.1_Missense_Mutation_p.L1228I|ABCC11_ENST00000356608.2_Missense_Mutation_p.L1228I|ABCC11_ENST00000565329.1_5'UTR|ABCC11_ENST00000353782.5_Missense_Mutation_p.L1228I	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	1228	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				organic anion transport (GO:0015711)|purine nucleotide transport (GO:0015865)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)|purine nucleotide transmembrane transporter activity (GO:0015216)	p.L1228I(1)		breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(3)|prostate(2)|skin(5)|urinary_tract(2)	83		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)			Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032)	GTTCCTGAGAGCAGCACTGGA	0.607																																					p.L1228I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3682A	16						.						77.0	60.0	66.0					16																	48209185		2201	4300	6501	46766686	SO:0001583	missense	85320	exon26			AF367202	CCDS10732.1, CCDS10733.1	16q12	2012-03-14			ENSG00000121270	ENSG00000121270		"""ATP binding cassette transporters / subfamily C"""	14639	protein-coding gene	gene with protein product		607040				11483364, 11435397	Standard	NM_033151		Approved	MRP8	uc002efg.1	Q96J66	OTTHUMG00000133146	ENST00000394747.1:c.3682C>A	16.37:g.48209185G>T	ENSP00000378230:p.Leu1228Ile		46766686	NM_145186	Q8TDJ0|Q96JA6|Q9BX80	Missense_Mutation	SNP	ENST00000394747.1	37	CCDS10732.1	.	.	.	.	.	.	.	.	.	.	G	8.967	0.972117	0.18736	.	.	ENSG00000121270	ENST00000353782;ENST00000356608;ENST00000394748;ENST00000394747	D;D;D;D	0.90732	-2.72;-2.72;-2.72;-2.72	4.69	-4.39	0.03611	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.278860	0.34268	N	0.004113	T	0.78597	0.4308	N	0.12611	0.24	0.80722	D	1	P;B	0.38827	0.649;0.149	B;B	0.37601	0.254;0.102	T	0.70633	-0.4818	10	0.87932	D	0	-7.4149	12.3075	0.54910	0.7254:0.0:0.2746:0.0	.	1228;1228	Q96J66-2;Q96J66	.;ABCCB_HUMAN	I	1228	ENSP00000311326:L1228I;ENSP00000349017:L1228I;ENSP00000378231:L1228I;ENSP00000378230:L1228I	ENSP00000311326:L1228I	L	-	1	0	ABCC11	46766686	0.154000	0.22792	0.068000	0.19968	0.019000	0.09904	0.590000	0.23954	-0.616000	0.05671	-0.216000	0.12614	CTC		0.607	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583	
CYLD	1540	broad.mit.edu	37	16	50815180	50815180	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:50815180G>A	ENST00000427738.3	+	9	1747	c.1542G>A	c.(1540-1542)acG>acA	p.T514T	CYLD_ENST00000398568.2_Silent_p.T511T|RP11-327F22.4_ENST00000575917.1_RNA|RP11-327F22.4_ENST00000564510.1_RNA|CYLD_ENST00000311559.9_Silent_p.T514T|CYLD_ENST00000568704.2_Intron|CYLD_ENST00000564326.1_Silent_p.T511T|CYLD_ENST00000566206.1_Silent_p.T511T|CYLD_ENST00000569418.1_Silent_p.T511T|CYLD_ENST00000540145.1_Silent_p.T514T			Q9NQC7	CYLD_HUMAN	cylindromatosis (turban tumor syndrome)	514	CAP-Gly 3. {ECO:0000255|PROSITE- ProRule:PRU00045}.|Interaction with IKBKG/NEMO.|Interaction with TRIP.				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.T514T(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)				CAGGCTGTACGGATGGAACCT	0.448			"""Mis, N, F, S"""		cylindroma	cylindroma			Multiple Trichoepithelioma, Familial;Familial Cylindromatosis																												p.T514T		yes	Rec	yes	Familial cylindromatosis	16	16q12-q13	1540	familial cylindromatosis gene		E	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1542A	16						.						108.0	104.0	105.0					16																	50815180		1942	4152	6094	49372681	SO:0001819	synonymous_variant	1540	exon11	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.1542G>A	16.37:g.50815180G>A			49372681	NM_015247	O94934|Q7L3N6|Q96EH0|Q9NZX9	Silent	SNP	ENST00000427738.3	37	CCDS45482.1																																																																																				0.448	CYLD-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422998.2		
FTO	79068	broad.mit.edu	37	16	53913790	53913790	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:53913790G>A	ENST00000471389.1	+	6	1232	c.1010G>A	c.(1009-1011)cGc>cAc	p.R337H	FTO_ENST00000394647.3_Missense_Mutation_p.R41H	NM_001080432.2	NP_001073901.1	Q9C0B1	FTO_HUMAN	fat mass and obesity associated	337					adipose tissue development (GO:0060612)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA demethylation (GO:0080111)|oxidative demethylation (GO:0070989)|oxidative single-stranded DNA demethylation (GO:0035552)|oxidative single-stranded RNA demethylation (GO:0035553)|regulation of lipid storage (GO:0010883)|regulation of multicellular organism growth (GO:0040014)|regulation of respiratory system process (GO:0044065)|regulation of white fat cell proliferation (GO:0070350)|RNA repair (GO:0042245)|temperature homeostasis (GO:0001659)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA-N1-methyladenine dioxygenase activity (GO:0043734)|ferrous iron binding (GO:0008198)|oxidative DNA demethylase activity (GO:0035516)|oxidative RNA demethylase activity (GO:0035515)	p.R337H(1)		endometrium(1)|kidney(2)|large_intestine(7)|lung(13)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	29						ATTTTACAACGCTGTCAGTTG	0.403																																					p.R337H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1010A	16						.						183.0	170.0	174.0					16																	53913790		2198	4300	6498	52471291	SO:0001583	missense	79068	exon6			BC003583	CCDS32448.1	16q12.2	2013-11-15			ENSG00000140718	ENSG00000140718		"""Alkylation repair homologs"""	24678	protein-coding gene	gene with protein product	"""AlkB homolog 9"", ""alpha-ketoglutarate-dependent dioxygenase"""	610966				17434869, 17991826, 22002720	Standard	NM_001080432		Approved	KIAA1752, MGC5149, ALKBH9	uc002ehr.3	Q9C0B1	OTTHUMG00000158780	ENST00000471389.1:c.1010G>A	16.37:g.53913790G>A	ENSP00000418823:p.Arg337His		52471291	NM_001080432	A2RUH1|B2RNS0|Q0P676|Q7Z785	Missense_Mutation	SNP	ENST00000471389.1	37	CCDS32448.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.007293	0.75046	.	.	ENSG00000140718	ENST00000471389;ENST00000394647	T;T	0.53640	0.61;0.61	5.83	3.54	0.40534	Alpha-ketoglutarate-dependent dioxygenase FTO, C-terminal (1);	0.311043	0.36374	N	0.002627	T	0.57242	0.2040	M	0.63843	1.955	0.43782	D	0.99631	D	0.69078	0.997	P	0.61070	0.883	T	0.60037	-0.7341	10	0.87932	D	0	-6.2093	7.391	0.26909	0.3082:0.0:0.6918:0.0	.	337	Q9C0B1	FTO_HUMAN	H	337;41	ENSP00000418823:R337H;ENSP00000378142:R41H	ENSP00000378142:R41H	R	+	2	0	FTO	52471291	0.998000	0.40836	0.997000	0.53966	0.948000	0.59901	1.461000	0.35255	1.466000	0.48025	0.650000	0.86243	CGC		0.403	FTO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352196.1	NM_001080432	
GPR97	222487	broad.mit.edu	37	16	57719789	57719789	+	Silent	SNP	G	G	A	rs150564489		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:57719789G>A	ENST00000333493.4	+	11	1652	c.1491G>A	c.(1489-1491)ccG>ccA	p.P497P	GPR97_ENST00000450388.3_Silent_p.P377P|RP11-405F3.4_ENST00000563062.1_RNA|GPR97_ENST00000327655.6_Silent_p.P287P	NM_170776.4	NP_740746.4	Q86Y34	GPR97_HUMAN	G protein-coupled receptor 97	497					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.P497P(1)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						TCTTCACCCCGTTGGGCCTCT	0.612													g|||	1	0.000199681	0.0	0.0	5008	,	,		19338	0.0		0.001	False		,,,				2504	0.0				p.P497P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1491A	16						.	G		1,4395	2.1+/-5.4	0,1,2197	109.0	95.0	100.0		1491	-11.2	0.1	16	dbSNP_134	100	0,8600		0,0,4300	no	coding-synonymous	GPR97	NM_170776.4		0,1,6497	AA,AG,GG		0.0,0.0227,0.0077		497/550	57719789	1,12995	2198	4300	6498	56277290	SO:0001819	synonymous_variant	222487	exon11			AY140959	CCDS10786.1	16q13	2014-08-08			ENSG00000182885	ENSG00000182885		"""-"", ""GPCR / Class B : Orphans"""	13728	protein-coding gene	gene with protein product						12435584, 222487	Standard	NM_170776		Approved	Pb99, PGR26	uc002emh.3	Q86Y34	OTTHUMG00000133458	ENST00000333493.4:c.1491G>A	16.37:g.57719789G>A			56277290	NM_170776	Q6ZMF4|Q86SL9|Q8IZF1	Silent	SNP	ENST00000333493.4	37	CCDS10786.1																																																																																				0.612	GPR97-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257333.2	NM_170776	
CNGB1	1258	broad.mit.edu	37	16	57992348	57992348	+	Missense_Mutation	SNP	G	G	A	rs369288085		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:57992348G>A	ENST00000251102.8	-	11	863	c.803C>T	c.(802-804)cCg>cTg	p.P268L	CNGB1_ENST00000564448.1_Missense_Mutation_p.P262L|CNGB1_ENST00000311183.4_Missense_Mutation_p.P268L	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	268					cation transport (GO:0006812)|cytosolic calcium ion homeostasis (GO:0051480)|detection of light stimulus involved in visual perception (GO:0050908)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|protein heterotetramerization (GO:0051290)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina homeostasis (GO:0001895)|rhodopsin mediated signaling pathway (GO:0016056)|sensory perception of smell (GO:0007608)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|intracellular cyclic nucleotide activated cation channel complex (GO:0017071)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)|transmembrane transporter complex (GO:1902495)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)	p.P268L(1)		breast(7)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(11)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	54						CACTGGCTGCGGCAAGGCCAT	0.612																																					p.P268L	Colon(156;1293 1853 16336 28962 38659)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C803T	16						.	G	LEU/PRO,LEU/PRO	0,4272		0,0,2136	74.0	89.0	84.0		803,803	4.1	1.0	16		84	1,8493		0,1,4246	no	missense,missense	CNGB1	NM_001135639.1,NM_001297.4	98,98	0,1,6382	AA,AG,GG		0.0118,0.0,0.0078	possibly-damaging,possibly-damaging	268/300,268/1252	57992348	1,12765	2136	4247	6383	56549849	SO:0001583	missense	1258	exon11			AF042498	CCDS42169.1, CCDS45495.1, CCDS67042.1	16q13	2013-02-14			ENSG00000070729	ENSG00000070729		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2151	protein-coding gene	gene with protein product	"""glutamic acid-rich protein"""	600724		CNCG2, CNCG3L		8766832, 7590744, 16382102	Standard	NM_001297		Approved	RCNC2, RCNCb, GARP, GAR1, CNGB1B, RP45	uc002emt.2	Q14028	OTTHUMG00000154810	ENST00000251102.8:c.803C>T	16.37:g.57992348G>A	ENSP00000251102:p.Pro268Leu		56549849	NM_001135639	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Missense_Mutation	SNP	ENST00000251102.8	37	CCDS42169.1	.	.	.	.	.	.	.	.	.	.	G	15.57	2.872799	0.51695	0.0	1.18E-4	ENSG00000070729	ENST00000251102;ENST00000311183	D;T	0.99804	-6.83;-0.99	4.14	4.14	0.48551	.	0.000000	0.39210	N	0.001424	D	0.99548	0.9838	L	0.55990	1.75	0.38716	D	0.953322	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	D	0.97385	0.9985	10	0.87932	D	0	.	12.2143	0.54398	0.0:0.0:1.0:0.0	.	268;268	Q14028-3;Q14028	.;CNGB1_HUMAN	L	268	ENSP00000251102:P268L;ENSP00000311670:P268L	ENSP00000251102:P268L	P	-	2	0	CNGB1	56549849	0.996000	0.38824	0.967000	0.41034	0.310000	0.27922	3.808000	0.55598	2.586000	0.87340	0.655000	0.94253	CCG		0.612	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297	
ELMO3	79767	broad.mit.edu	37	16	67237693	67237693	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:67237693C>T	ENST00000360833.1	+	19	2241	c.2184C>T	c.(2182-2184)aaC>aaT	p.N728N	MIR328_ENST00000385213.1_RNA|ELMO3_ENST00000393997.2_Silent_p.N745N|ELMO3_ENST00000477898.1_Silent_p.N579N			Q96BJ8	ELMO3_HUMAN	engulfment and cell motility 3	692					apoptotic process (GO:0006915)|phagocytosis (GO:0006909)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.N745N(1)		cervix(2)|kidney(4)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	18		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00067)|Epithelial(162;0.00442)|all cancers(182;0.0417)		AGCTGGAGAACGTGCCCATCC	0.642																																					p.N745N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2235T	16						.						31.0	37.0	35.0					16																	67237693		2098	4200	6298	65795194	SO:0001819	synonymous_variant	79767	exon20				CCDS10833.2	16q22.1	2010-03-18	2006-01-20		ENSG00000102890	ENSG00000102890		"""Engulfment and cell motility proteins"""	17289	protein-coding gene	gene with protein product		606422	"""engulfment and cell motility 3 (ced-12 homolog, C. elegans)"""			11595183	Standard	NM_024712		Approved	FLJ13824, CED12, ELMO-3, CED-12	uc002esa.3	Q96BJ8	OTTHUMG00000133570	ENST00000360833.1:c.2184C>T	16.37:g.67237693C>T			65795194	NM_024712	B4DV86|Q9H8A5	Silent	SNP	ENST00000360833.1	37																																																																																					0.642	ELMO3-001	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000257667.2	NM_024712	
ZDHHC1	29800	broad.mit.edu	37	16	67432126	67432126	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:67432126G>A	ENST00000348579.2	-	8	1257	c.916C>T	c.(916-918)Cgg>Tgg	p.R306W	ZDHHC1_ENST00000566075.1_5'Flank	NM_013304.2	NP_037436.1	Q8WTX9	ZDHC1_HUMAN	zinc finger, DHHC-type containing 1	306					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.R306W(1)		breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|urinary_tract(1)	10		Ovarian(137;0.223)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0178)|all cancers(182;5.71e-53)|Epithelial(162;4.73e-52)|OV - Ovarian serous cystadenocarcinoma(108;1.53e-29)|Kidney(780;4.37e-05)|BRCA - Breast invasive adenocarcinoma(181;5.8e-05)|GBM - Glioblastoma multiforme(240;0.0022)		TGAATGGGCCGCATCTTGGGA	0.627																																					p.R306W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C916T	16						.						113.0	102.0	106.0					16																	67432126		2198	4300	6498	65989627	SO:0001583	missense	29800	exon8			U90653	CCDS10836.1	16q22.1	2010-03-25	2003-01-27		ENSG00000159714	ENSG00000159714		"""Zinc fingers, DHHC-type"""	17916	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 1"""	C16orf1		10395086	Standard	NM_013304		Approved	HSU90653, ZNF377	uc010vjm.2	Q8WTX9	OTTHUMG00000137522	ENST00000348579.2:c.916C>T	16.37:g.67432126G>A	ENSP00000340299:p.Arg306Trp		65989627	NM_013304	O15461	Missense_Mutation	SNP	ENST00000348579.2	37	CCDS10836.1	.	.	.	.	.	.	.	.	.	.	G	18.48	3.632181	0.67015	.	.	ENSG00000159714	ENST00000348579	T	0.38240	1.15	5.46	5.46	0.80206	.	816.138000	0.00166	N	0.000000	T	0.40791	0.1131	L	0.29908	0.895	0.32700	N	0.513021	D	0.69078	0.997	P	0.47470	0.548	T	0.32903	-0.9889	10	0.59425	D	0.04	.	12.0005	0.53228	0.0:0.0:0.8155:0.1845	.	306	Q8WTX9	ZDHC1_HUMAN	W	306	ENSP00000340299:R306W	ENSP00000340299:R306W	R	-	1	2	ZDHHC1	65989627	0.999000	0.42202	0.996000	0.52242	0.490000	0.33462	3.463000	0.53050	2.563000	0.86464	0.407000	0.27541	CGG		0.627	ZDHHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268845.1	NM_013304	
ATP6V0D1	9114	broad.mit.edu	37	16	67472478	67472478	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:67472478C>T	ENST00000290949.3	-	8	1159	c.1009G>A	c.(1009-1011)Gcc>Acc	p.A337T	ATP6V0D1_ENST00000540149.1_Missense_Mutation_p.A378T|ATP6V0D1_ENST00000602876.1_Missense_Mutation_p.A260T|ATP6V0D1_ENST00000567694.1_5'UTR	NM_004691.4	NP_004682.2	P61421	VA0D1_HUMAN	ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d1	337					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP hydrolysis coupled proton transport (GO:0015991)|brain development (GO:0007420)|cellular iron ion homeostasis (GO:0006879)|cellular protein metabolic process (GO:0044267)|cilium assembly (GO:0042384)|endoplasmic reticulum unfolded protein response (GO:0030968)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|axon terminus (GO:0043679)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|proton-transporting V-type ATPase, V0 domain (GO:0033179)|synaptic vesicle (GO:0008021)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)	p.A337T(1)		large_intestine(3)|lung(3)|urinary_tract(2)	8		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0439)|Epithelial(162;0.101)		TGGCGCTGGGCGATACATTCA	0.527																																					p.A337T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1009A	16						.						148.0	123.0	132.0					16																	67472478		2198	4300	6498	66029979	SO:0001583	missense	9114	exon8			X71490	CCDS10838.1	16q22	2010-04-21	2006-01-20	2002-05-10	ENSG00000159720	ENSG00000159720		"""ATPases / V-type"""	13724	protein-coding gene	gene with protein product		607028	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump), member D"", ""ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d isoform 1"", ""ATPase, H+ transporting, lysosomal 38kDa, V0 subunit D1"""	ATP6D		8250920	Standard	NM_004691		Approved	ATP6DV, VATX, VPATPD, P39, Vma6	uc002ete.1	P61421	OTTHUMG00000137515	ENST00000290949.3:c.1009G>A	16.37:g.67472478C>T	ENSP00000290949:p.Ala337Thr		66029979	NM_004691	P12953|Q02547	Missense_Mutation	SNP	ENST00000290949.3	37	CCDS10838.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.519445	0.85495	.	.	ENSG00000159720	ENST00000290949;ENST00000426604;ENST00000540149	T;T	0.32272	1.46;1.46	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	T	0.61590	0.2359	M	0.86805	2.84	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.79108	0.992;0.989	T	0.67169	-0.5738	10	0.51188	T	0.08	-12.8015	17.1994	0.86902	0.0:1.0:0.0:0.0	.	378;337	F5GYQ1;P61421	.;VA0D1_HUMAN	T	337;260;378	ENSP00000290949:A337T;ENSP00000441282:A378T	ENSP00000290949:A337T	A	-	1	0	ATP6V0D1	66029979	1.000000	0.71417	0.998000	0.56505	0.981000	0.71138	4.083000	0.57643	2.397000	0.81536	0.650000	0.86243	GCC		0.527	ATP6V0D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268835.1	NM_004691	
ATP6V0D1	9114	broad.mit.edu	37	16	67472761	67472761	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:67472761G>A	ENST00000290949.3	-	7	979	c.829C>T	c.(829-831)Ctc>Ttc	p.L277F	ATP6V0D1_ENST00000540149.1_Missense_Mutation_p.L318F|ATP6V0D1_ENST00000602876.1_Missense_Mutation_p.L200F|ATP6V0D1_ENST00000567694.1_5'UTR	NM_004691.4	NP_004682.2	P61421	VA0D1_HUMAN	ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d1	277					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP hydrolysis coupled proton transport (GO:0015991)|brain development (GO:0007420)|cellular iron ion homeostasis (GO:0006879)|cellular protein metabolic process (GO:0044267)|cilium assembly (GO:0042384)|endoplasmic reticulum unfolded protein response (GO:0030968)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|axon terminus (GO:0043679)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|proton-transporting V-type ATPase, V0 domain (GO:0033179)|synaptic vesicle (GO:0008021)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)	p.L277F(1)		large_intestine(3)|lung(3)|urinary_tract(2)	8		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0439)|Epithelial(162;0.101)		CCCTCGAAGAGCAGCTTGTAC	0.612																																					p.L277F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C829T	16						.						99.0	97.0	98.0					16																	67472761		2198	4300	6498	66030262	SO:0001583	missense	9114	exon7			X71490	CCDS10838.1	16q22	2010-04-21	2006-01-20	2002-05-10	ENSG00000159720	ENSG00000159720		"""ATPases / V-type"""	13724	protein-coding gene	gene with protein product		607028	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump), member D"", ""ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d isoform 1"", ""ATPase, H+ transporting, lysosomal 38kDa, V0 subunit D1"""	ATP6D		8250920	Standard	NM_004691		Approved	ATP6DV, VATX, VPATPD, P39, Vma6	uc002ete.1	P61421	OTTHUMG00000137515	ENST00000290949.3:c.829C>T	16.37:g.67472761G>A	ENSP00000290949:p.Leu277Phe		66030262	NM_004691	P12953|Q02547	Missense_Mutation	SNP	ENST00000290949.3	37	CCDS10838.1	.	.	.	.	.	.	.	.	.	.	G	1.212	-0.629349	0.03610	.	.	ENSG00000159720	ENST00000290949;ENST00000426604;ENST00000540149	T;T	0.34859	1.34;1.34	5.21	4.26	0.50523	.	0.000000	0.85682	D	0.000000	T	0.50616	0.1626	L	0.54965	1.715	0.80722	D	1	D;D	0.76494	0.999;0.993	D;D	0.80764	0.994;0.992	T	0.41698	-0.9494	10	0.18710	T	0.47	-20.9512	12.5144	0.56024	0.0813:0.0:0.9187:0.0	.	318;277	F5GYQ1;P61421	.;VA0D1_HUMAN	F	277;200;318	ENSP00000290949:L277F;ENSP00000441282:L318F	ENSP00000290949:L277F	L	-	1	0	ATP6V0D1	66030262	1.000000	0.71417	0.975000	0.42487	0.014000	0.08584	5.793000	0.69060	1.207000	0.43291	-0.142000	0.14014	CTC		0.612	ATP6V0D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268835.1	NM_004691	
SLC7A6OS	84138	broad.mit.edu	37	16	68330407	68330407	+	IGR	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:68330407G>A	ENST00000263997.6	-	0	4189				SLC7A6_ENST00000566454.1_Silent_p.R420R|SLC7A6_ENST00000219343.6_Silent_p.R420R	NM_032178.2	NP_115554.2	Q96CW6	S7A6O_HUMAN	solute carrier family 7, member 6 opposite strand						hematopoietic progenitor cell differentiation (GO:0002244)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R420R(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)	10		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.034)|Epithelial(162;0.106)		AGCGGCCCCGGCCTCTCAAGG	0.572																																					p.R420R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1260A	16						.						97.0	99.0	98.0					16																	68330407		2198	4300	6498	66887908	SO:0001628	intergenic_variant	9057	exon9				CCDS10865.1	16q22.1	2010-03-11			ENSG00000103061	ENSG00000103061			25807	protein-coding gene	gene with protein product							Standard	NM_032178		Approved	FLJ13291	uc002evw.2	Q96CW6	OTTHUMG00000137558		16.37:g.68330407G>A			66887908	NM_003983	Q8TCZ3|Q9H8R8	Silent	SNP	ENST00000263997.6	37	CCDS10865.1																																																																																				0.572	SLC7A6OS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268894.3	NM_032178	
VPS4A	27183	broad.mit.edu	37	16	69354102	69354102	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:69354102G>A	ENST00000254950.11	+	7	835	c.679G>A	c.(679-681)Gat>Aat	p.D227N	COG8_ENST00000564419.1_5'UTR|RP11-343C2.11_ENST00000570054.2_Missense_Mutation_p.D251N	NM_013245.2	NP_037377.1			vacuolar protein sorting 4 homolog A (S. cerevisiae)									p.D227N(1)		NS(1)|central_nervous_system(1)|large_intestine(2)|lung(3)	7		Ovarian(137;0.101)				CATCTTCATCGATGAGGTGGA	0.562																																					p.D227N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G679A	16						.						55.0	62.0	60.0					16																	69354102		1959	4153	6112	67911603	SO:0001583	missense	27183	exon7			AF112215	CCDS45517.1	16q23.1	2010-04-21	2006-04-04		ENSG00000132612	ENSG00000132612		"""ATPases / AAA-type"""	13488	protein-coding gene	gene with protein product		609982	"""vacuolar protein sorting 4A (yeast homolog)"", ""vacuolar protein sorting 4A (yeast)"""			10637304, 11563910	Standard	NM_013245		Approved	VPS4, VPS4-1, FLJ22197, SKD2, SKD1, SKD1A	uc002eww.3	Q9UN37		ENST00000254950.11:c.679G>A	16.37:g.69354102G>A	ENSP00000254950:p.Asp227Asn		67911603	NM_013245		Missense_Mutation	SNP	ENST00000254950.11	37	CCDS45517.1	.	.	.	.	.	.	.	.	.	.	G	36	5.793421	0.96952	.	.	ENSG00000132612	ENST00000254950	D	0.99264	-5.65	6.07	6.07	0.98685	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.99718	0.9891	H	0.98005	4.125	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97532	1.0080	10	0.72032	D	0.01	-23.2675	20.239	0.98366	0.0:0.0:1.0:0.0	.	227	Q9UN37	VPS4A_HUMAN	N	227	ENSP00000254950:D227N	ENSP00000254950:D227N	D	+	1	0	VPS4A	67911603	1.000000	0.71417	0.996000	0.52242	0.829000	0.46940	9.864000	0.99589	2.884000	0.98904	0.655000	0.94253	GAT		0.562	VPS4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430563.3	NM_013245	
AARS	16	broad.mit.edu	37	16	70303575	70303575	+	Missense_Mutation	SNP	C	C	T	rs369366275		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:70303575C>T	ENST00000261772.8	-	7	1051	c.908G>A	c.(907-909)cGg>cAg	p.R303Q		NM_001605.2	NP_001596.2			alanyl-tRNA synthetase									p.R303Q(1)		breast(3)|cervix(2)|endometrium(5)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)	27		Ovarian(137;0.0365)		BRCA - Breast invasive adenocarcinoma(221;0.161)		AGTGATGGTCCGAGCGTGGTC	0.597																																					p.R303Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G908A	16						.	C	GLN/ARG	1,4395	2.1+/-5.4	0,1,2197	187.0	154.0	165.0		908	5.7	1.0	16		165	0,8600		0,0,4300	no	missense	AARS	NM_001605.2	43	0,1,6497	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	303/969	70303575	1,12995	2198	4300	6498	68861076	SO:0001583	missense	16	exon7			D32050	CCDS32474.1	16q22.1	2014-09-17			ENSG00000090861	ENSG00000090861	6.1.1.7	"""Aminoacyl tRNA synthetases / Class II"""	20	protein-coding gene	gene with protein product	"""alanine tRNA ligase 1, cytoplasmic"""	601065				8595897	Standard	NM_001605		Approved		uc002eyn.1	P49588	OTTHUMG00000177042	ENST00000261772.8:c.908G>A	16.37:g.70303575C>T	ENSP00000261772:p.Arg303Gln		68861076	NM_001605		Missense_Mutation	SNP	ENST00000261772.8	37	CCDS32474.1	.	.	.	.	.	.	.	.	.	.	C	36	5.904307	0.97087	2.27E-4	0.0	ENSG00000090861	ENST00000261772	T	0.74106	-0.81	5.67	5.67	0.87782	Alanyl-tRNA synthetase, class IIc, anti-codon-binding domain (1);Alanyl-tRNA synthetase, class IIc, core domain (1);Alanyl-tRNA synthetase, class IIc, N-terminal (1);	0.159627	0.56097	N	0.000029	D	0.92714	0.7684	H	0.99573	4.635	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95557	0.8626	10	0.87932	D	0	-15.9142	17.2644	0.87081	0.0:1.0:0.0:0.0	.	311;303	E7ETK8;P49588	.;SYAC_HUMAN	Q	303	ENSP00000261772:R303Q	ENSP00000261772:R303Q	R	-	2	0	AARS	68861076	1.000000	0.71417	0.999000	0.59377	0.974000	0.67602	7.818000	0.86416	2.697000	0.92050	0.655000	0.94253	CGG		0.597	AARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435021.2	NM_001605	
COG4	25839	broad.mit.edu	37	16	70530272	70530272	+	Missense_Mutation	SNP	C	C	T	rs376657474		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:70530272C>T	ENST00000323786.5	-	12	1565	c.1544G>A	c.(1543-1545)cGc>cAc	p.R515H		NM_001195139.1|NM_015386.2	NP_001182068.1|NP_056201.2	Q9H9E3	COG4_HUMAN	component of oligomeric golgi complex 4	511					Golgi organization (GO:0007030)|Golgi vesicle prefusion complex stabilization (GO:0048213)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)		p.R515H(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|pancreas(1)|prostate(2)	33		Ovarian(137;0.0694)				TGTCACCCCGCGCTGGATGTC	0.542																																					p.R515H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1544A	16						.	C	HIS/ARG,HIS/ARG	2,4394	4.2+/-10.8	0,2,2196	127.0	98.0	108.0		1544,1544	6.0	1.0	16		108	0,8600		0,0,4300	no	missense,missense	COG4	NM_001195139.1,NM_015386.2	29,29	0,2,6496	TT,TC,CC		0.0,0.0455,0.0154	probably-damaging,probably-damaging	515/769,515/790	70530272	2,12994	2198	4300	6498	69087773	SO:0001583	missense	25839	exon12			AL050101	CCDS10892.2, CCDS73909.1	16q22.1	2013-09-20			ENSG00000103051	ENSG00000103051		"""Components of oligomeric golgi complex"""	18620	protein-coding gene	gene with protein product		606976				11980916	Standard	NM_015386		Approved	COD1, DKFZP586E1519	uc002ezc.3	Q9H9E3	OTTHUMG00000128515	ENST00000323786.5:c.1544G>A	16.37:g.70530272C>T	ENSP00000315775:p.Arg515His		69087773	NM_015386	B4DMN8|C9JS23|Q96D40|Q9BRF0|Q9BVZ2|Q9H5Y4|Q9Y3W3	Missense_Mutation	SNP	ENST00000323786.5	37	CCDS10892.2	.	.	.	.	.	.	.	.	.	.	C	35	5.492919	0.96339	4.55E-4	0.0	ENSG00000103051	ENST00000323786;ENST00000338984;ENST00000539961	T	0.47177	0.85	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	T	0.66616	0.2807	L	0.54323	1.7	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	P;P;D	0.68621	0.902;0.902;0.959	T	0.65479	-0.6158	10	0.72032	D	0.01	-7.9769	20.5792	0.99380	0.0:1.0:0.0:0.0	.	421;510;511	Q8N8L9;Q6PIW8;Q9H9E3	.;.;COG4_HUMAN	H	515;511;173	ENSP00000315775:R515H	ENSP00000315775:R515H	R	-	2	0	COG4	69087773	1.000000	0.71417	0.998000	0.56505	0.871000	0.50021	7.629000	0.83207	2.873000	0.98535	0.561000	0.74099	CGC		0.542	COG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250326.3		
HYDIN	54768	broad.mit.edu	37	16	71012868	71012868	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:71012868G>A	ENST00000393567.2	-	30	4737	c.4587C>T	c.(4585-4587)ctC>ctT	p.L1529L		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	1529					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.L1528L(1)|p.L1480L(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				CAAAGTGATCGAGCATTTCAC	0.493																																					p.L1528L												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C4584T	16						.						130.0	113.0	119.0					16																	71012868		1917	4119	6036	69570369	SO:0001819	synonymous_variant	54768	exon30			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.4587C>T	16.37:g.71012868G>A			69570369	NM_032821	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Silent	SNP	ENST00000393567.2	37	CCDS59269.1																																																																																				0.493	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
HYDIN	54768	broad.mit.edu	37	16	71052111	71052111	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:71052111C>T	ENST00000393567.2	-	23	3715	c.3565G>A	c.(3565-3567)Gtt>Att	p.V1189I	HYDIN_ENST00000448089.2_Missense_Mutation_p.V1141I	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	1189					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.V1141I(1)|p.V1189I(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				GTGATGGTAACGTAGCGAATG	0.498																																					p.V1189I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G3565A	16						.						1.0	1.0	1.0					16																	71052111		206	529	735	69609612	SO:0001583	missense	54768	exon23			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.3565G>A	16.37:g.71052111C>T	ENSP00000377197:p.Val1189Ile		69609612	NM_032821	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	C	4.155	0.027205	0.08054	.	.	ENSG00000157423	ENST00000393567;ENST00000316490;ENST00000448089	T;T	0.04917	5.44;3.53	5.37	-2.44	0.06502	.	0.644972	0.11283	N	0.580141	T	0.04497	0.0123	L	0.31420	0.93	0.36463	D	0.86681	B	0.15473	0.013	B	0.08055	0.003	T	0.45293	-0.9271	10	0.14252	T	0.57	.	10.8538	0.46786	0.0:0.6343:0.135:0.2307	.	1189	F8WD23	.	I	1189;1189;1141	ENSP00000377197:V1189I;ENSP00000398544:V1141I	ENSP00000313052:V1189I	V	-	1	0	HYDIN	69609612	0.000000	0.05858	0.048000	0.18961	0.389000	0.30415	-2.575000	0.00910	-0.526000	0.06383	0.505000	0.49811	GTT		0.498	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
CMTR2	55783	broad.mit.edu	37	16	71317967	71317967	+	Silent	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:71317967A>G	ENST00000338099.5	-	3	2193	c.1857T>C	c.(1855-1857)gaT>gaC	p.D619D	CMTR2_ENST00000434935.2_Silent_p.D619D			Q8IYT2	CMTR2_HUMAN	cap methyltransferase 2	619					7-methylguanosine mRNA capping (GO:0006370)|cap2 mRNA methylation (GO:0097310)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)	p.D619D(1)									GGTAAGTTGGATCTCCATCAT	0.408																																					p.D619D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1857C	16						.						57.0	57.0	57.0					16																	71317967		2198	4300	6498	69875468	SO:0001819	synonymous_variant	55783	exon3			BC035005	CCDS10898.1	16q22.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000180917	ENSG00000180917			25635	protein-coding gene	gene with protein product	"""adrift homolog (Drosophila)"""		"""FtsJ methyltransferase domain containing 1"""	FTSJD1		21310715	Standard	NM_018348		Approved	FLJ11171, AFT, MTr2	uc010cga.3	Q8IYT2	OTTHUMG00000137587	ENST00000338099.5:c.1857T>C	16.37:g.71317967A>G			69875468	NM_018348	B2RCD5|D3DWS1|Q8NE77|Q8NFR5|Q9H8Z4|Q9NUS3|Q9NXF5	Silent	SNP	ENST00000338099.5	37	CCDS10898.1																																																																																				0.408	CMTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268984.2	NM_018348	
RBFOX1	54715	broad.mit.edu	37	16	7568327	7568327	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:7568327C>T	ENST00000550418.1	+	5	1194	c.206C>T	c.(205-207)gCc>gTc	p.A69V	RBFOX1_ENST00000535565.2_Missense_Mutation_p.A105V|RBFOX1_ENST00000552089.1_Missense_Mutation_p.A105V|RBFOX1_ENST00000547372.1_Missense_Mutation_p.A112V|RBFOX1_ENST00000355637.4_Missense_Mutation_p.A89V|RBFOX1_ENST00000553186.1_Missense_Mutation_p.A69V|RBFOX1_ENST00000547338.1_Missense_Mutation_p.A69V|RBFOX1_ENST00000340209.4_Missense_Mutation_p.A74V|RBFOX1_ENST00000311745.5_Missense_Mutation_p.A89V|RBFOX1_ENST00000436368.2_Missense_Mutation_p.A89V|RBFOX1_ENST00000422070.4_Missense_Mutation_p.A112V	NM_018723.3	NP_061193.2	Q9NWB1	RFOX1_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 1	69					mRNA processing (GO:0006397)|neuromuscular process controlling balance (GO:0050885)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|RNA transport (GO:0050658)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	nucleotide binding (GO:0000166)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)	p.A89V(2)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|lung(17)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)	55						TACCCTCCCGCCCAGACGCAC	0.642																																					p.A89V	Ovarian(157;934 2567 15163 39509)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C266T	16						.						114.0	108.0	110.0					16																	7568327		2197	4300	6497	7508328	SO:0001583	missense	54715	exon2			AF107203	CCDS10531.1, CCDS10532.1, CCDS45405.1, CCDS55983.1, CCDS55984.1	16p13.3	2013-02-12			ENSG00000078328	ENSG00000078328		"""RNA binding motif (RRM) containing"""	18222	protein-coding gene	gene with protein product	"""ataxin 2-binding protein 1"", ""hexaribonucleotide binding protein 1"""	605104				10814712, 16260614	Standard	NM_018723		Approved	A2BP1, FOX-1, HRNBP1	uc002cyy.2	Q9NWB1	OTTHUMG00000129551	ENST00000550418.1:c.206C>T	16.37:g.7568327C>T	ENSP00000450031:p.Ala69Val		7508328	NM_145893	Q7Z7I7|Q8TAE3|Q8TAF2|Q8WYB2|Q9NS20	Missense_Mutation	SNP	ENST00000550418.1	37	CCDS55983.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.343146	0.82022	.	.	ENSG00000078328	ENST00000547605;ENST00000550418;ENST00000553186;ENST00000547372;ENST00000422070;ENST00000535565;ENST00000552089;ENST00000551752;ENST00000547338;ENST00000436368;ENST00000311745;ENST00000355637;ENST00000352951;ENST00000340209	T;T;T;T;T;T;T;T;T;T;T	0.34472	1.81;1.38;1.72;1.62;1.63;1.79;1.38;1.47;1.68;1.63;1.36	4.67	4.67	0.58626	.	0.140569	0.47093	D	0.000258	T	0.38532	0.1044	L	0.44542	1.39	0.49299	D	0.99977	B;P;P;P;B;P;B;B;B	0.51933	0.383;0.949;0.722;0.743;0.142;0.57;0.039;0.023;0.215	B;P;B;P;B;B;B;B;B	0.45753	0.124;0.492;0.08;0.447;0.287;0.214;0.127;0.089;0.219	T	0.32613	-0.9900	10	0.51188	T	0.08	-4.6637	17.5929	0.88003	0.0:1.0:0.0:0.0	.	89;105;112;89;89;89;69;69;112	F8WAC5;F5H0M1;B7Z1U7;Q9NWB1-2;Q9NWB1-4;Q9NWB1-5;Q9NWB1-3;Q9NWB1;F8VZG9	.;.;.;.;.;.;.;RFOX1_HUMAN;.	V	69;69;69;112;112;105;105;69;69;89;89;89;89;74	ENSP00000450402:A69V;ENSP00000450031:A69V;ENSP00000447753:A69V;ENSP00000446842:A112V;ENSP00000391269:A112V;ENSP00000447281:A69V;ENSP00000447717:A69V;ENSP00000402745:A89V;ENSP00000309117:A89V;ENSP00000347855:A89V;ENSP00000344196:A74V	ENSP00000309117:A89V	A	+	2	0	RBFOX1	7508328	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.042000	0.76565	2.129000	0.65627	0.557000	0.71058	GCC		0.642	RBFOX1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409492.2	NM_145891	
FA2H	79152	broad.mit.edu	37	16	74773946	74773946	+	Missense_Mutation	SNP	C	C	T	rs147632811	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:74773946C>T	ENST00000219368.3	-	2	407	c.338G>A	c.(337-339)cGg>cAg	p.R113Q	FA2H_ENST00000544337.1_5'UTR	NM_024306.4	NP_077282.3	Q7L5A8	FA2H_HUMAN	fatty acid 2-hydroxylase	113					cell death (GO:0008219)|central nervous system myelin maintenance (GO:0032286)|fatty acid biosynthetic process (GO:0006633)|lipid modification (GO:0030258)|peripheral nervous system myelin maintenance (GO:0032287)|regulation of cell proliferation (GO:0042127)|regulation of hair cycle (GO:0042634)|sebaceous gland cell differentiation (GO:0001949)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	fatty acid alpha-hydroxylase activity (GO:0080132)|heme binding (GO:0020037)|iron ion binding (GO:0005506)	p.R113Q(1)		endometrium(2)|large_intestine(4)|lung(3)|skin(1)	10						CACTTTGAACCGTGGTTCCAT	0.537													C|||	2	0.000399361	0.0	0.0	5008	,	,		18815	0.0		0.001	False		,,,				2504	0.001				p.R113Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G338A	16						.	C	GLN/ARG	1,4395	2.1+/-5.4	0,1,2197	270.0	243.0	252.0		338	1.6	0.1	16	dbSNP_134	252	9,8591	7.1+/-27.0	0,9,4291	yes	missense	FA2H	NM_024306.4	43	0,10,6488	TT,TC,CC		0.1047,0.0227,0.0769	benign	113/373	74773946	10,12986	2198	4300	6498	73331447	SO:0001583	missense	79152	exon2			BC002679	CCDS10911.1	16q23	2013-03-04	2003-10-29	2003-10-31	ENSG00000103089	ENSG00000103089		"""Fatty acid hydroxylase domain containing"""	21197	protein-coding gene	gene with protein product	"""fatty acid hydroxylase"""	611026	"""fatty acid hydroxylase domain containing 1"", ""spastic paraplegia 35 (autosomal recessive)"""	FAXDC1, SPG35		20104589	Standard	NM_024306		Approved	FAAH, FLJ25287	uc002fde.2	Q7L5A8	OTTHUMG00000137603	ENST00000219368.3:c.338G>A	16.37:g.74773946C>T	ENSP00000219368:p.Arg113Gln		73331447	NM_024306	B7Z8T6|O75213|Q96DK1|Q9H1A5	Missense_Mutation	SNP	ENST00000219368.3	37	CCDS10911.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	c	12.93	2.085562	0.36758	2.27E-4	0.001047	ENSG00000103089	ENST00000219368	D	0.85702	-2.02	4.74	1.6	0.23607	.	0.580298	0.18201	N	0.148510	T	0.64260	0.2582	N	0.11201	0.11	0.46416	D	0.999035	B	0.20052	0.041	B	0.08055	0.003	T	0.46119	-0.9214	10	0.10902	T	0.67	-0.0465	5.3315	0.15936	0.0:0.5415:0.0:0.4585	.	113	Q7L5A8	FA2H_HUMAN	Q	113	ENSP00000219368:R113Q	ENSP00000219368:R113Q	R	-	2	0	FA2H	73331447	0.830000	0.29337	0.120000	0.21714	0.732000	0.41865	0.823000	0.27366	0.117000	0.18138	0.556000	0.70494	CGG		0.537	FA2H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269015.2	NM_024306	
CDYL2	124359	broad.mit.edu	37	16	80654678	80654678	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:80654678C>T	ENST00000570137.2	-	4	1144	c.989G>A	c.(988-990)cGg>cAg	p.R330Q	CDYL2_ENST00000562812.1_Missense_Mutation_p.R331Q|CDYL2_ENST00000566173.1_Missense_Mutation_p.R331Q|CDYL2_ENST00000563890.1_Missense_Mutation_p.R331Q	NM_152342.2	NP_689555.2	Q8N8U2	CDYL2_HUMAN	chromodomain protein, Y-like 2	330						nucleus (GO:0005634)	catalytic activity (GO:0003824)	p.R330Q(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	21						TTCTGCAATCCGAGTGCTCTC	0.547																																					p.R330Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G989A	16						.						54.0	61.0	59.0					16																	80654678		2203	4300	6503	79212179	SO:0001583	missense	124359	exon4			AK096185	CCDS32493.1	16q23.2	2008-02-05	2003-09-12			ENSG00000166446			23030	protein-coding gene	gene with protein product			"""chromodomain Y-like protein 2"""			12837688	Standard	NM_152342		Approved	FLJ38866	uc002ffs.3	Q8N8U2		ENST00000570137.2:c.989G>A	16.37:g.80654678C>T	ENSP00000476295:p.Arg330Gln		79212179	NM_152342	Q7Z5I8	Missense_Mutation	SNP	ENST00000570137.2	37	CCDS32493.1	.	.	.	.	.	.	.	.	.	.	C	32	5.151564	0.94645	.	.	ENSG00000166446	ENST00000299564	T	0.65178	-0.14	5.29	5.29	0.74685	Crotonase, core (1);	0.000000	0.85682	D	0.000000	T	0.59662	0.2210	L	0.41710	1.295	0.51233	D	0.999913	P	0.46512	0.879	B	0.43838	0.433	T	0.63950	-0.6521	10	0.59425	D	0.04	.	18.0955	0.89488	0.0:1.0:0.0:0.0	.	330	Q8N8U2	CDYL2_HUMAN	Q	330	ENSP00000299564:R330Q	ENSP00000299564:R330Q	R	-	2	0	CDYL2	79212179	1.000000	0.71417	0.970000	0.41538	0.992000	0.81027	5.895000	0.69814	2.741000	0.93983	0.655000	0.94253	CGG		0.547	CDYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434727.2	NM_152342	
HSDL1	83693	broad.mit.edu	37	16	84163250	84163250	+	Missense_Mutation	SNP	G	G	A	rs199812312		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:84163250G>A	ENST00000219439.4	-	5	973	c.797C>T	c.(796-798)tCg>tTg	p.S266L	HSDL1_ENST00000434463.3_Missense_Mutation_p.S211L	NM_001146051.1|NM_031463.4	NP_001139523.1|NP_113651.4	Q3SXM5	HSDL1_HUMAN	hydroxysteroid dehydrogenase like 1	266						mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)	p.S266L(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7						CACCAACCACGAGCACCTGTG	0.448																																					p.S266L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C797T	16						.						115.0	112.0	113.0					16																	84163250		2200	4300	6500	82720751	SO:0001583	missense	83693	exon5			AF237684	CCDS10942.1, CCDS54046.1	16q24	2011-09-20			ENSG00000103160	ENSG00000103160		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	16475	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 12C, member 3"""					12153137, 19027726	Standard	NM_031463		Approved	SDR12C3	uc002fhk.2	Q3SXM5	OTTHUMG00000137635	ENST00000219439.4:c.797C>T	16.37:g.84163250G>A	ENSP00000219439:p.Ser266Leu		82720751	NM_031463	B4DSL2|D3DUL4|Q3SXM4|Q8NC98|Q9BY22	Missense_Mutation	SNP	ENST00000219439.4	37	CCDS10942.1	.	.	.	.	.	.	.	.	.	.	G	7.968	0.748460	0.15710	.	.	ENSG00000103160	ENST00000434463;ENST00000219439	D;T	0.87256	-2.23;0.95	5.17	2.04	0.26737	NAD(P)-binding domain (1);	0.630649	0.17776	N	0.162431	D	0.86552	0.5960	M	0.87827	2.91	0.09310	N	1	B;B	0.20780	0.022;0.048	B;B	0.17098	0.003;0.017	T	0.79210	-0.1897	10	0.66056	D	0.02	0.0114	7.1057	0.25362	0.0668:0.3131:0.5074:0.1127	.	211;266	B4DSL2;Q3SXM5	.;HSDL1_HUMAN	L	211;266	ENSP00000407437:S211L;ENSP00000219439:S266L	ENSP00000219439:S266L	S	-	2	0	HSDL1	82720751	0.002000	0.14202	0.099000	0.21106	0.416000	0.31233	1.011000	0.29911	0.258000	0.21686	0.467000	0.42956	TCG		0.448	HSDL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269076.3	NM_031463	
CLEC18B	497190	broad.mit.edu	37	16	74451965	74451965	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:74451965delA	ENST00000339953.5	-	3	569	c.448delT	c.(448-450)tacfs	p.Y150fs		NM_001011880.2	NP_001011880.2	Q6UXF7	CL18B_HUMAN	C-type lectin domain family 18, member B	150	SCP.					extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)	p.Y150fs*26(1)		endometrium(3)|kidney(9)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						ACCTGCGTGTAGTGGGTGCAG	0.592																																					p.Y150fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.448delT	16						.						9.0	10.0	10.0					16																	74451965		1766	3604	5370	73009466	SO:0001589	frameshift_variant	497190	exon3			AY358373	CCDS32484.1	16q22.3	2010-04-27	2009-03-10	2009-03-10		ENSG00000140839		"""C-type lectin domain containing"""	33849	protein-coding gene	gene with protein product							Standard	NM_001011880		Approved		uc002fct.3	Q6UXF7		ENST00000339953.5:c.448delT	16.37:g.74451965delA	ENSP00000341051:p.Tyr150fs		73009466	NM_001011880	B4DF90	Frame_Shift_Del	DEL	ENST00000339953.5	37	CCDS32484.1																																																																																				0.592	CLEC18B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434697.1	NM_001011880	
USP10	9100	broad.mit.edu	37	16	84812561	84812561	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr16:84812561T>A	ENST00000219473.7	+	14	2383	c.2270T>A	c.(2269-2271)aTc>aAc	p.I757N	USP10_ENST00000570191.1_Missense_Mutation_p.I761N	NM_001272075.1|NM_005153.2	NP_001259004.1|NP_005144.2	Q14694	UBP10_HUMAN	ubiquitin specific peptidase 10	757	USP.				autophagy (GO:0006914)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA repair (GO:0006281)|protein deubiquitination (GO:0016579)|regulation of autophagy (GO:0010506)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.I757N(1)		endometrium(3)|kidney(1)|large_intestine(7)|lung(3)|prostate(1)|stomach(1)|urinary_tract(1)	17						GTCTTCCAGATCGGTCTGAAT	0.567																																					p.I757N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2270A	16						.						48.0	45.0	46.0					16																	84812561		2039	4182	6221	83370062	SO:0001583	missense	9100	exon14			D80012	CCDS45537.1, CCDS62004.1	16q	2008-03-25	2005-08-08			ENSG00000103194		"""Ubiquitin-specific peptidases"""	12608	protein-coding gene	gene with protein product		609818	"""ubiquitin specific protease 10"""			12838346	Standard	NM_005153		Approved	UBPO, KIAA0190	uc002fii.3	Q14694		ENST00000219473.7:c.2270T>A	16.37:g.84812561T>A	ENSP00000219473:p.Ile757Asn		83370062	NM_005153	B2RDJ8|B4DS84|Q9BWG7|Q9NSL7	Missense_Mutation	SNP	ENST00000219473.7	37	CCDS45537.1	.	.	.	.	.	.	.	.	.	.	T	14.65	2.597935	0.46318	.	.	ENSG00000103194	ENST00000219473	T	0.28069	1.63	5.08	5.08	0.68730	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.124637	0.64402	D	0.000019	T	0.39009	0.1062	N	0.20845	0.615	0.80722	D	1	D;D	0.89917	1.0;0.995	D;D	0.74674	0.984;0.978	T	0.23619	-1.0183	10	0.39692	T	0.17	-20.4543	14.0409	0.64674	0.0:0.0:0.0:1.0	.	761;757	Q14694-3;Q14694	.;UBP10_HUMAN	N	757	ENSP00000219473:I757N	ENSP00000219473:I757N	I	+	2	0	USP10	83370062	1.000000	0.71417	0.972000	0.41901	0.956000	0.61745	7.292000	0.78731	1.909000	0.55274	0.533000	0.62120	ATC		0.567	USP10-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433660.1		
COL1A1	1277	broad.mit.edu	37	17	48272099	48272100	+	Frame_Shift_Ins	INS	-	-	TA	rs72648344		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:48272099_48272100insTA	ENST00000225964.5	-	21	1561_1562	c.1443_1444insTA	c.(1441-1446)cccggafs	p.G482fs		NM_000088.3	NP_000079	P02452	CO1A1_HUMAN	collagen, type I, alpha 1	482	Triple-helical region.				blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|bone trabecula formation (GO:0060346)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to amino acid stimulus (GO:0071230)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal system development (GO:0048706)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|leukocyte migration (GO:0050900)|negative regulation of cell-substrate adhesion (GO:0010812)|osteoblast differentiation (GO:0001649)|platelet activation (GO:0030168)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterotrimerization (GO:0070208)|protein localization to nucleus (GO:0034504)|protein transport (GO:0015031)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to estradiol (GO:0032355)|response to hydrogen peroxide (GO:0042542)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|tooth mineralization (GO:0034505)|visual perception (GO:0007601)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)	p.G482fs*1(1)	COL1A1/PDGFB(429)	NS(1)|breast(3)|central_nervous_system(8)|endometrium(3)|kidney(4)|large_intestine(17)|liver(3)|lung(18)|ovary(1)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	71					Collagenase(DB00048)	CCAGGGGGTCCGGGCAGGCCAG	0.683			T	"""PDGFB, USP6"""	"""dermatofibrosarcoma protuberans, aneurysmal bone cyst """		Osteogenesis imperfecta																														p.G482_P483delinsX			Dom	yes		17	17q21.31-q22	1277	"""collagen, type I, alpha 1"""	yes	M	.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1444_1445insTA	17	GRCh37	CM070684	COL1A1	M	rs72648344	.																																			45627099	SO:0001589	frameshift_variant	1277	exon21			Z74615	CCDS11561.1	17q21.33	2014-09-17			ENSG00000108821	ENSG00000108821		"""Collagens"""	2197	protein-coding gene	gene with protein product		120150				3178743, 2857713	Standard	NM_000088		Approved	OI4	uc002iqm.3	P02452	OTTHUMG00000148674	ENST00000225964.5:c.1443_1444insTA	17.37:g.48272099_48272100insTA	ENSP00000225964:p.Gly482fs		45627098	NM_000088	O76045|P78441|Q13896|Q13902|Q13903|Q14037|Q14992|Q15176|Q15201|Q16050|Q59F64|Q7KZ30|Q7KZ34|Q8IVI5|Q8N473|Q9UML6|Q9UMM7	Frame_Shift_Ins	INS	ENST00000225964.5	37	CCDS11561.1																																																																																				0.683	COL1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309036.2		
RPS6KB1	6198	broad.mit.edu	37	17	58024089	58024090	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:58024089_58024090insA	ENST00000225577.4	+	15	1539_1540	c.1518_1519insA	c.(1519-1521)aaafs	p.K507fs	RPS6KB1_ENST00000443572.2_Frame_Shift_Ins_p.K484fs|RPS6KB1_ENST00000406116.3_Intron|RPS6KB1_ENST00000393021.3_Frame_Shift_Ins_p.K454fs|RP11-178C3.1_ENST00000591035.1_Intron	NM_001272042.1|NM_001272044.1|NM_001272060.1|NM_003161.2	NP_001258971.1|NP_001258973.1|NP_001258989.1|NP_003152.1	P23443	KS6B1_HUMAN	ribosomal protein S6 kinase, 70kDa, polypeptide 1	507	Autoinhibitory domain.				aging (GO:0007568)|apoptotic process (GO:0006915)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|G1/S transition of mitotic cell cycle (GO:0000082)|germ cell development (GO:0007281)|insulin receptor signaling pathway (GO:0008286)|long-term memory (GO:0007616)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of insulin receptor signaling pathway (GO:0046627)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of skeletal muscle tissue growth (GO:0048633)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of translation (GO:0045727)|positive regulation of translational initiation (GO:0045948)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|regulation of glucose import (GO:0046324)|response to drug (GO:0042493)|response to electrical stimulus involved in regulation of muscle adaptation (GO:0014878)|response to ethanol (GO:0045471)|response to glucagon (GO:0033762)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to leucine (GO:0043201)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|response to testosterone (GO:0033574)|response to toxic substance (GO:0009636)|response to tumor necrosis factor (GO:0034612)|response to wounding (GO:0009611)|signal transduction (GO:0007165)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|TOR signaling (GO:0031929)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	ATP binding (GO:0005524)|peptide binding (GO:0042277)|protein kinase activity (GO:0004672)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ribosomal protein S6 kinase activity (GO:0004711)	p.Q509fs*>18(1)		endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	14	all_cancers(5;1.63e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;3.57e-12)|all cancers(12;6.41e-11)			CTGGGCCATACAAAAAACAAGC	0.45																																					p.Y506fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1518_1519insA	17						.																																			55378872	SO:0001589	frameshift_variant	6198	exon15			M60724	CCDS11621.1, CCDS62271.1, CCDS62272.1, CCDS62273.1	17q23.1	2011-04-05	2002-08-29		ENSG00000108443	ENSG00000108443			10436	protein-coding gene	gene with protein product		608938	"""ribosomal protein S6 kinase, 70kD, polypeptide 1"""	STK14A		1922062	Standard	NM_003161		Approved	S6K1, p70(S6K)-alpha, PS6K	uc002ixy.4	P23443	OTTHUMG00000150642	ENST00000225577.4:c.1524dupA	17.37:g.58024095_58024095dupA	ENSP00000225577:p.Lys507fs		55378871	NM_003161	B2R779|B4DLT4|B4DTG1|E7ESB8|F6UYM1|Q7Z721	Frame_Shift_Ins	INS	ENST00000225577.4	37	CCDS11621.1																																																																																				0.450	RPS6KB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319324.1	NM_003161	
MYH4	4622	broad.mit.edu	37	17	10346761	10346761	+	Silent	SNP	A	A	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:10346761A>C	ENST00000255381.2	-	40	5861	c.5751T>G	c.(5749-5751)gcT>gcG	p.A1917A	RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	1917					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)	p.A1917A(1)		NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						CTTGGGACTCAGCAATGTCAG	0.473																																					p.A1917A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T5751G	17						.						167.0	152.0	157.0					17																	10346761		2203	4300	6503	10287486	SO:0001819	synonymous_variant	4622	exon40				CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"""Myosins / Myosin superfamily : Class II"""	7574	protein-coding gene	gene with protein product		160742	"""myosin, heavy polypeptide 4, skeletal muscle"""			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.5751T>G	17.37:g.10346761A>C			10287486	NM_017533		Silent	SNP	ENST00000255381.2	37	CCDS11154.1																																																																																				0.473	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533	
INPP5K	51763	broad.mit.edu	37	17	1401406	1401406	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:1401406G>A	ENST00000421807.2	-	8	1175	c.787C>T	c.(787-789)Cgc>Tgc	p.R263C	INPP5K_ENST00000542125.1_Missense_Mutation_p.R167C|INPP5K_ENST00000320345.6_Missense_Mutation_p.R187C|INPP5K_ENST00000406424.4_Missense_Mutation_p.R187C|INPP5K_ENST00000397335.3_Missense_Mutation_p.R171C	NM_016532.3	NP_057616.2	Q9BT40	INP5K_HUMAN	inositol polyphosphate-5-phosphatase K	263	Catalytic. {ECO:0000255}.				actin cytoskeleton organization (GO:0030036)|cellular response to cAMP (GO:0071320)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to hormone stimulus (GO:0032870)|cellular response to insulin stimulus (GO:0032869)|cellular response to tumor necrosis factor (GO:0071356)|dephosphorylation (GO:0016311)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inositol phosphate dephosphorylation (GO:0046855)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of dephosphorylation (GO:0035305)|negative regulation of glucose transport (GO:0010829)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of stress fiber assembly (GO:0051497)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of renal water transport (GO:2001153)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of urine volume (GO:0035810)|protein targeting to plasma membrane (GO:0072661)|regulation of glycogen biosynthetic process (GO:0005979)|ruffle assembly (GO:0097178)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	inositol bisphosphate phosphatase activity (GO:0016312)|inositol trisphosphate phosphatase activity (GO:0046030)|inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity (GO:0052659)|inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|inositol-polyphosphate 5-phosphatase activity (GO:0004445)|lipid phosphatase activity (GO:0042577)|phosphatidylinositol phosphate 5-phosphatase activity (GO:0034595)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:0034485)|vasopressin receptor activity (GO:0005000)	p.R263C(2)|p.R187C(2)		endometrium(1)|large_intestine(7)|lung(3)|skin(1)	12						GCAGGCTTGCGTTTTTTCTCA	0.577																																					p.R263C												.	.	4	Substitution - Missense(4)	large_intestine(4)	c.C787T	17						.						77.0	84.0	82.0					17																	1401406		2203	4300	6503	1348156	SO:0001583	missense	51763	exon8				CCDS11004.1, CCDS11005.1	17p13.3	2008-09-09			ENSG00000132376	ENSG00000132376			33882	protein-coding gene	gene with protein product	"""skeletal muscle and kidney enriched inositol phosphatase"""	607875				10753883, 12536145	Standard	NM_016532		Approved	SKIP	uc002fsr.3	Q9BT40	OTTHUMG00000150648	ENST00000421807.2:c.787C>T	17.37:g.1401406G>A	ENSP00000413937:p.Arg263Cys		1348156	NM_016532	B2R6I2|B2R750|D3DTH8|Q15733|Q9NPJ5|Q9P2R5	Missense_Mutation	SNP	ENST00000421807.2	37	CCDS11004.1	.	.	.	.	.	.	.	.	.	.	G	17.88	3.496271	0.64186	.	.	ENSG00000132376	ENST00000421807;ENST00000406424;ENST00000350761;ENST00000320345;ENST00000397335;ENST00000542125;ENST00000449479	D;D;D;D;D	0.97831	-4.56;-4.56;-4.56;-1.61;-4.56	5.53	4.55	0.56014	Endonuclease/exonuclease/phosphatase (2);Inositol polyphosphate-related phosphatase (1);	0.000000	0.85682	D	0.000000	D	0.99227	0.9731	H	0.98754	4.32	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98534	1.0629	10	0.87932	D	0	-11.3358	11.6844	0.51476	0.0:0.0:0.6792:0.3208	.	167;263	F5GXZ0;Q9BT40	.;INP5K_HUMAN	C	187;187;263;187;171;167;171	ENSP00000385177:R187C;ENSP00000318476:R187C;ENSP00000380496:R171C;ENSP00000440147:R167C;ENSP00000413259:R171C	ENSP00000318476:R187C	R	-	1	0	INPP5K	1348156	1.000000	0.71417	0.992000	0.48379	0.591000	0.36615	2.452000	0.44961	1.438000	0.47492	0.655000	0.94253	CGC		0.577	INPP5K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319381.4		
INPP5K	51763	broad.mit.edu	37	17	1417237	1417237	+	Silent	SNP	C	C	T	rs375141992		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:1417237C>T	ENST00000421807.2	-	2	469	c.81G>A	c.(79-81)gcG>gcA	p.A27A	INPP5K_ENST00000542125.1_Silent_p.A27A|INPP5K_ENST00000320345.6_5'UTR|PITPNA-AS1_ENST00000425081.2_RNA|INPP5K_ENST00000406424.4_5'UTR|INPP5K_ENST00000397335.3_Intron	NM_016532.3	NP_057616.2	Q9BT40	INP5K_HUMAN	inositol polyphosphate-5-phosphatase K	27	Catalytic. {ECO:0000255}.				actin cytoskeleton organization (GO:0030036)|cellular response to cAMP (GO:0071320)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to hormone stimulus (GO:0032870)|cellular response to insulin stimulus (GO:0032869)|cellular response to tumor necrosis factor (GO:0071356)|dephosphorylation (GO:0016311)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inositol phosphate dephosphorylation (GO:0046855)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of dephosphorylation (GO:0035305)|negative regulation of glucose transport (GO:0010829)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of stress fiber assembly (GO:0051497)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of renal water transport (GO:2001153)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of urine volume (GO:0035810)|protein targeting to plasma membrane (GO:0072661)|regulation of glycogen biosynthetic process (GO:0005979)|ruffle assembly (GO:0097178)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	inositol bisphosphate phosphatase activity (GO:0016312)|inositol trisphosphate phosphatase activity (GO:0046030)|inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity (GO:0052659)|inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|inositol-polyphosphate 5-phosphatase activity (GO:0004445)|lipid phosphatase activity (GO:0042577)|phosphatidylinositol phosphate 5-phosphatase activity (GO:0034595)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:0034485)|vasopressin receptor activity (GO:0005000)	p.A27A(1)		endometrium(1)|large_intestine(7)|lung(3)|skin(1)	12						CTAGAGGGGGCGCTGCCGAAG	0.542																																					p.A27A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G81A	17						.	C	,,	0,4406		0,0,2203	117.0	90.0	99.0		,81,	-1.3	1.0	17		99	1,8599	1.2+/-3.3	0,1,4299	no	utr-5,coding-synonymous,utr-5	INPP5K	NM_001135642.1,NM_016532.3,NM_130766.2	,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,	,27/449,	1417237	1,13005	2203	4300	6503	1363987	SO:0001819	synonymous_variant	51763	exon2				CCDS11004.1, CCDS11005.1	17p13.3	2008-09-09			ENSG00000132376	ENSG00000132376			33882	protein-coding gene	gene with protein product	"""skeletal muscle and kidney enriched inositol phosphatase"""	607875				10753883, 12536145	Standard	NM_016532		Approved	SKIP	uc002fsr.3	Q9BT40	OTTHUMG00000150648	ENST00000421807.2:c.81G>A	17.37:g.1417237C>T			1363987	NM_016532	B2R6I2|B2R750|D3DTH8|Q15733|Q9NPJ5|Q9P2R5	Silent	SNP	ENST00000421807.2	37	CCDS11004.1																																																																																				0.542	INPP5K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319381.4		
SLC43A2	124935	broad.mit.edu	37	17	1479979	1479979	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:1479979A>T	ENST00000301335.5	-	13	1548	c.1460T>A	c.(1459-1461)cTg>cAg	p.L487Q	SLC43A2_ENST00000412517.3_Missense_Mutation_p.L350Q|SLC43A2_ENST00000571650.1_Missense_Mutation_p.L491Q|SLC43A2_ENST00000382147.4_Missense_Mutation_p.L491Q	NM_001284498.1|NM_001284499.1	NP_001271427.1|NP_001271428.1	Q8N370	LAT4_HUMAN	solute carrier family 43 (amino acid system L transporter), member 2	487					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-amino acid transmembrane transporter activity (GO:0015179)	p.L487Q(1)		endometrium(4)|large_intestine(4)|liver(1)|lung(2)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (25;0.0883)		CAGAGACTGCAGTCCCGTGAG	0.637																																					p.L487Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1460A	17						.						47.0	46.0	46.0					17																	1479979		2203	4300	6503	1426729	SO:0001583	missense	124935	exon13			BC027923	CCDS11006.1, CCDS67107.1, CCDS67108.1	17p13.3	2013-07-17	2013-07-17		ENSG00000167703	ENSG00000167703		"""Solute carriers"""	23087	protein-coding gene	gene with protein product		610791				23268354	Standard	NM_001284498		Approved	MGC34680	uc002fsv.3	Q8N370	OTTHUMG00000090345	ENST00000301335.5:c.1460T>A	17.37:g.1479979A>T	ENSP00000301335:p.Leu487Gln		1426729	NM_152346	B7Z6X9|C9JNU8|D3DTH9|Q5CD75|Q6IPM1|Q8NBX1|Q8NC21|Q8WZ00	Missense_Mutation	SNP	ENST00000301335.5	37	CCDS11006.1	.	.	.	.	.	.	.	.	.	.	A	33	5.224279	0.95139	.	.	ENSG00000167703	ENST00000301335;ENST00000382147;ENST00000412517	D;D;D	0.83837	-1.77;-1.77;-1.77	6.07	6.07	0.98685	Major facilitator superfamily domain, general substrate transporter (1);	0.050411	0.85682	D	0.000000	D	0.91499	0.7316	M	0.83483	2.645	0.58432	D	0.999996	D;D	0.76494	0.988;0.999	P;D	0.71184	0.903;0.972	D	0.92534	0.6036	10	0.87932	D	0	-1.0025	16.2903	0.82747	1.0:0.0:0.0:0.0	.	487;491	Q8N370;Q8N370-3	LAT4_HUMAN;.	Q	487;491;350	ENSP00000301335:L487Q;ENSP00000371582:L491Q;ENSP00000408284:L350Q	ENSP00000301335:L487Q	L	-	2	0	SLC43A2	1426729	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	8.675000	0.91195	2.326000	0.78906	0.533000	0.62120	CTG		0.637	SLC43A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206717.4	NM_152346	
DNAH9	1770	broad.mit.edu	37	17	11797758	11797758	+	Missense_Mutation	SNP	C	C	T	rs147952506	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:11797758C>T	ENST00000262442.4	+	59	11419	c.11351C>T	c.(11350-11352)aCg>aTg	p.T3784M	DNAH9_ENST00000396001.2_3'UTR|DNAH9_ENST00000454412.2_Missense_Mutation_p.T3784M|DNAH9_ENST00000608377.1_Missense_Mutation_p.T96M	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	3784					cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.T3784M(1)		NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		CCAGTGCAGACGGGCACCGCC	0.512													C|||	4	0.000798722	0.0	0.0014	5008	,	,		19312	0.0		0.003	False		,,,				2504	0.0				p.T96M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C287T	17						.	C	MET/THR,MET/THR	1,4405	2.1+/-5.4	0,1,2202	91.0	90.0	90.0		11351,287	4.1	0.0	17	dbSNP_134	90	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense	DNAH9	NM_001372.3,NM_004662.2	81,81	0,7,6496	TT,TC,CC		0.0698,0.0227,0.0538	benign,benign	3784/4487,96/799	11797758	7,12999	2203	4300	6503	11738483	SO:0001583	missense	1770	exon5			U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.11351C>T	17.37:g.11797758C>T	ENSP00000262442:p.Thr3784Met		11738483	NM_004662	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	13.07	2.128436	0.37533	2.27E-4	6.98E-4	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703;ENST00000396001;ENST00000361801	T;T;T	0.27104	1.73;1.69;2.17	5.03	4.05	0.47172	.	0.291103	0.38548	N	0.001660	T	0.15782	0.0380	N	0.17474	0.49	0.29357	N	0.864914	B;B	0.26902	0.163;0.051	B;B	0.20184	0.028;0.017	T	0.08027	-1.0742	10	0.37606	T	0.19	.	12.6521	0.56768	0.3005:0.6995:0.0:0.0	.	137;3784	B7Z7H0;Q9NYC9	.;DYH9_HUMAN	M	3784;3784;2366;96;137	ENSP00000262442:T3784M;ENSP00000414874:T3784M;ENSP00000379323:T96M	ENSP00000262442:T3784M	T	+	2	0	DNAH9	11738483	0.137000	0.22531	0.025000	0.17156	0.943000	0.58893	3.774000	0.55341	1.086000	0.41228	0.655000	0.94253	ACG		0.512	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
PIGL	9487	broad.mit.edu	37	17	16216926	16216926	+	Silent	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:16216926G>T	ENST00000225609.5	+	4	509	c.492G>T	c.(490-492)gtG>gtT	p.V164V	PIGL_ENST00000581006.1_Intron|PIGL_ENST00000395844.4_Silent_p.V164V|PIGL_ENST00000498772.2_Silent_p.V164V	NM_004278.3	NP_004269.1	Q9Y2B2	PIGL_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class L	164					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	N-acetylglucosaminylphosphatidylinositol deacetylase activity (GO:0000225)	p.V164V(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|skin(1)	11				UCEC - Uterine corpus endometrioid carcinoma (92;0.0934)		ATGCAGCTGTGAGGTATGATT	0.468																																					p.V164V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G492T	17						.						225.0	195.0	205.0					17																	16216926		2203	4300	6503	16157651	SO:0001819	synonymous_variant	9487	exon4			AB017165	CCDS11176.1	17p12-p11.2	2013-02-26	2006-06-28		ENSG00000108474	ENSG00000108474	3.5.1.89	"""Phosphatidylinositol glycan anchor biosynthesis"""	8966	protein-coding gene	gene with protein product	"""N-acetylglucosaminylphosphatidylinositol deacetylase"""	605947	"""phosphatidylinositol glycan, class L"""			10085243	Standard	NM_004278		Approved		uc002gpv.3	Q9Y2B2	OTTHUMG00000059346	ENST00000225609.5:c.492G>T	17.37:g.16216926G>T			16157651	NM_004278	A8KA67|B4DYN4	Silent	SNP	ENST00000225609.5	37	CCDS11176.1																																																																																				0.468	PIGL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131881.1		
ZNF287	57336	broad.mit.edu	37	17	16455307	16455307	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:16455307T>C	ENST00000395824.1	-	6	2766	c.2149A>G	c.(2149-2151)Aca>Gca	p.T717A	ZNF287_ENST00000395825.3_Missense_Mutation_p.T717A			Q9HBT7	ZN287_HUMAN	zinc finger protein 287	710					positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T710A(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(5)|prostate(1)|urinary_tract(1)	20				UCEC - Uterine corpus endometrioid carcinoma (92;0.083)		ATAAGGCATGTTCTCTGGCTA	0.383																																					p.T717A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2149G	17						.						180.0	179.0	179.0					17																	16455307		2203	4300	6503	16396032	SO:0001583	missense	57336	exon6			AF217227	CCDS11179.2	17p11.2	2013-01-09			ENSG00000141040	ENSG00000141040		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13502	protein-coding gene	gene with protein product							Standard	NM_020653		Approved	ZKSCAN13, ZSCAN45	uc002gqi.2	Q9HBT7	OTTHUMG00000058993	ENST00000395824.1:c.2149A>G	17.37:g.16455307T>C	ENSP00000379168:p.Thr717Ala		16396032	NM_020653	Q6IAG1	Missense_Mutation	SNP	ENST00000395824.1	37	CCDS11179.2	.	.	.	.	.	.	.	.	.	.	T	8.168	0.791065	0.16258	.	.	ENSG00000141040	ENST00000395825;ENST00000395824	T;T	0.07216	3.21;3.21	4.89	2.5	0.30297	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.50627	D	0.000108	T	0.04182	0.0116	N	0.13299	0.325	0.24587	N	0.993842	B	0.15473	0.013	B	0.15870	0.014	T	0.33007	-0.9885	10	0.41790	T	0.15	.	3.6449	0.08181	0.3415:0.0924:0.0:0.5661	.	710	Q9HBT7	ZN287_HUMAN	A	717	ENSP00000379169:T717A;ENSP00000379168:T717A	ENSP00000379168:T717A	T	-	1	0	ZNF287	16396032	0.000000	0.05858	1.000000	0.80357	0.998000	0.95712	-0.665000	0.05286	0.973000	0.38340	0.454000	0.30748	ACA		0.383	ZNF287-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130504.1		
ZNF624	57547	broad.mit.edu	37	17	16527218	16527218	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:16527218C>A	ENST00000311331.7	-	6	1073	c.982G>T	c.(982-984)Gga>Tga	p.G328*		NM_020787.3	NP_065838.2	Q9P2J8	ZN624_HUMAN	zinc finger protein 624	328					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G328*(1)		breast(4)|endometrium(1)|kidney(1)|large_intestine(8)|lung(9)|ovary(1)|prostate(1)|skin(1)	26				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		GGTTTTTCTCCAGTGTGGATT	0.353																																					p.G328X	NSCLC(186;1023 2134 13330 38202 39800)											.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G982T	17						.						103.0	99.0	100.0					17																	16527218		2203	4300	6503	16467943	SO:0001587	stop_gained	57547	exon6			AB037770	CCDS11180.1	17p11.2	2013-01-08			ENSG00000197566	ENSG00000197566		"""Zinc fingers, C2H2-type"", ""-"""	29254	protein-coding gene	gene with protein product						10718198	Standard	NM_020787		Approved	KIAA1349	uc010cpi.2	Q9P2J8	OTTHUMG00000058996	ENST00000311331.7:c.982G>T	17.37:g.16527218C>A	ENSP00000310472:p.Gly328*		16467943	NM_020787	Q3SY62|Q3SY63|Q6ZN27	Nonsense_Mutation	SNP	ENST00000311331.7	37	CCDS11180.1	.	.	.	.	.	.	.	.	.	.	C	36	5.748648	0.96882	.	.	ENSG00000197566	ENST00000311331	.	.	.	2.79	2.79	0.32731	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	.	11.785	0.52037	0.0:1.0:0.0:0.0	.	.	.	.	X	328	.	ENSP00000310472:G328X	G	-	1	0	ZNF624	16467943	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	7.043000	0.76572	1.877000	0.54381	0.563000	0.77884	GGA		0.353	ZNF624-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130512.3	XM_047617	
RPA1	6117	broad.mit.edu	37	17	1792087	1792087	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:1792087A>G	ENST00000254719.5	+	14	1603	c.1493A>G	c.(1492-1494)tAc>tGc	p.Y498C		NM_002945.3	NP_002936.1	P27694	RFA1_HUMAN	replication protein A1, 70kDa	498					base-excision repair (GO:0006284)|DNA recombinase assembly (GO:0000730)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|G1/S transition of mitotic cell cycle (GO:0000082)|hemopoiesis (GO:0030097)|homeostasis of number of cells within a tissue (GO:0048873)|in utero embryonic development (GO:0001701)|meiotic nuclear division (GO:0007126)|mismatch repair (GO:0006298)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of cell proliferation (GO:0008284)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|DNA replication factor A complex (GO:0005662)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|metal ion binding (GO:0046872)|single-stranded DNA binding (GO:0003697)	p.Y498C(1)		breast(1)|endometrium(3)|large_intestine(2)|lung(2)|ovary(2)	10						AATGGATTGTACCGCTGTGAG	0.488								Nucleotide excision repair (NER)																													p.Y498C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1493G	17						.						146.0	119.0	128.0					17																	1792087		2203	4300	6503	1738837	SO:0001583	missense	6117	exon14			M63488	CCDS11014.1	17p13.3	2008-02-05	2002-08-29		ENSG00000132383	ENSG00000132383			10289	protein-coding gene	gene with protein product		179835	"""replication protein A1 (70kD)"""			8454588	Standard	NM_002945		Approved	REPA1, RPA70, HSSB, RF-A, RP-A	uc002fto.2	P27694	OTTHUMG00000090579	ENST00000254719.5:c.1493A>G	17.37:g.1792087A>G	ENSP00000254719:p.Tyr498Cys		1738837	NM_002945	A8K0Y9|Q59ES9	Missense_Mutation	SNP	ENST00000254719.5	37	CCDS11014.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.035096	0.75617	.	.	ENSG00000132383	ENST00000254719	T	0.54866	0.55	6.17	6.17	0.99709	Nucleic acid-binding, OB-fold-like (1);Replication factor A, C-terminal (1);Nucleic acid-binding, OB-fold (1);	0.051633	0.85682	D	0.000000	T	0.74981	0.3788	M	0.87971	2.92	0.58432	D	0.999999	D	0.89917	1.0	D	0.85130	0.997	T	0.79434	-0.1805	10	0.87932	D	0	-16.0473	11.8437	0.52371	0.8695:0.0:0.0:0.1305	.	498	P27694	RFA1_HUMAN	C	498	ENSP00000254719:Y498C	ENSP00000254719:Y498C	Y	+	2	0	RPA1	1738837	1.000000	0.71417	0.996000	0.52242	0.887000	0.51463	4.643000	0.61390	2.371000	0.80710	0.533000	0.62120	TAC		0.488	RPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207118.2	NM_002945	
FLCN	201163	broad.mit.edu	37	17	17125843	17125843	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:17125843A>T	ENST00000285071.4	-	7	1205	c.751T>A	c.(751-753)Tgg>Agg	p.W251R	FLCN_ENST00000389169.5_Missense_Mutation_p.W251R|RP11-45M22.4_ENST00000427497.3_Intron	NM_144997.5	NP_659434.2	Q8NFG4	FLCN_HUMAN	folliculin	251					cell-cell junction assembly (GO:0007043)|hemopoiesis (GO:0030097)|in utero embryonic development (GO:0001701)|negative regulation of ATP biosynthetic process (GO:2001170)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation involved in kidney development (GO:1901723)|negative regulation of energy homeostasis (GO:2000506)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of gene expression (GO:0010629)|negative regulation of mitochondrion organization (GO:0010823)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of gene expression (GO:0010628)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cytokinesis (GO:0032465)|regulation of histone acetylation (GO:0035065)|regulation of pro-B cell differentiation (GO:2000973)|regulation of protein phosphorylation (GO:0001932)|regulation of TOR signaling (GO:0032006)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)	p.W251R(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(11)|stomach(1)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						AGGCACGCCCACAGGTTGTCA	0.557									Familial Non-VHL Clear Cell Renal Cancer;Birt-Hogg-Dub syndrome																												p.W251R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T751A	17						.						127.0	97.0	107.0					17																	17125843		2203	4300	6503	17066568	SO:0001583	missense	201163	exon7	Familial Cancer Database	Familial Clear Cell Renal Cell Cancer, FcRCC, Familial Non-VHL Non-Papillary Clear Cell Renal Cancer;BHD, Fibrofolliculomas with Trichodiscomas and Acrochordons, incl.: Hornstein-Knickenberg syndrome, Perifollicular Fibromatosis	AF517523	CCDS32579.1, CCDS32580.1	17p11.2	2014-09-17			ENSG00000154803	ENSG00000154803			27310	protein-coding gene	gene with protein product		607273					Standard	NM_144997		Approved	BHD, MGC17998, MGC23445	uc002gra.4	Q8NFG4	OTTHUMG00000059275	ENST00000285071.4:c.751T>A	17.37:g.17125843A>T	ENSP00000285071:p.Trp251Arg		17066568	NM_144997	A6NJJ8|Q6ZRX1|Q96BD2|Q96BE4	Missense_Mutation	SNP	ENST00000285071.4	37	CCDS32579.1	.	.	.	.	.	.	.	.	.	.	A	28.7	4.946221	0.92593	.	.	ENSG00000154803	ENST00000285071;ENST00000389169	D;D	0.88664	-2.41;-2.41	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	D	0.91466	0.7306	L	0.34521	1.04	0.80722	D	1	D;D	0.89917	1.0;0.996	D;P	0.91635	0.999;0.877	D	0.92645	0.6128	10	0.87932	D	0	-10.1994	15.9707	0.80013	1.0:0.0:0.0:0.0	.	251;251	Q8NFG4-2;Q8NFG4	.;FLCN_HUMAN	R	251	ENSP00000285071:W251R;ENSP00000373821:W251R	ENSP00000285071:W251R	W	-	1	0	FLCN	17066568	1.000000	0.71417	0.998000	0.56505	0.878000	0.50629	8.395000	0.90188	2.180000	0.69256	0.379000	0.24179	TGG		0.557	FLCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131577.1	NM_144606	
MYO15A	51168	broad.mit.edu	37	17	18022120	18022120	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:18022120G>A	ENST00000205890.5	+	2	344	c.6G>A	c.(4-6)gcG>gcA	p.A2A		NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	2					inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.A2A(1)		breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					CCACCATggcgaaggaggaag	0.637																																					p.A2A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G6A	17						.						44.0	59.0	54.0					17																	18022120		1978	4138	6116	17962845	SO:0001819	synonymous_variant	51168	exon2			AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"""Myosins / Myosin superfamily : Class XV"""	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.6G>A	17.37:g.18022120G>A			17962845	NM_016239	B4DFC7	Silent	SNP	ENST00000205890.5	37	CCDS42271.1																																																																																				0.637	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239	
FAM83G	644815	broad.mit.edu	37	17	18907114	18907114	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:18907114G>T	ENST00000388995.6	-	2	464	c.241C>A	c.(241-243)Cct>Act	p.P81T	SLC5A10_ENST00000395647.2_Intron|SLC5A10_ENST00000395642.1_Intron|FAM83G_ENST00000345041.4_Missense_Mutation_p.P81T|SLC5A10_ENST00000417251.2_Intron|SLC5A10_ENST00000317977.6_Intron|SLC5A10_ENST00000395645.3_Intron|FAM83G_ENST00000585154.2_Missense_Mutation_p.P81T|SLC5A10_ENST00000395643.2_Intron			A6ND36	FA83G_HUMAN	family with sequence similarity 83, member G	81					BMP signaling pathway (GO:0030509)	cytosol (GO:0005829)|nucleus (GO:0005634)		p.P81T(1)		central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(3)|stomach(1)	22						GTGCCCCGAGGGTCCTCAGAG	0.692																																					p.P81T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C241A	17						.						17.0	20.0	19.0					17																	18907114		1865	4088	5953	18847839	SO:0001583	missense	644815	exon2			AK123558	CCDS42276.1	17p11.2	2014-05-01	2006-03-22		ENSG00000188522	ENSG00000188522			32554	protein-coding gene	gene with protein product	"""protein associated with SMAD1"""	615886				24554596	Standard	NM_001039999		Approved	FLJ41564, PAWS1	uc002guw.3	A6ND36	OTTHUMG00000059411	ENST00000388995.6:c.241C>A	17.37:g.18907114G>T	ENSP00000373647:p.Pro81Thr		18847839	NM_001039999	Q3KQZ4|Q6ZW60	Missense_Mutation	SNP	ENST00000388995.6	37	CCDS42276.1	.	.	.	.	.	.	.	.	.	.	G	13.37	2.217470	0.39201	.	.	ENSG00000188522	ENST00000388995;ENST00000345041;ENST00000399096	T;T	0.12255	2.7;2.7	5.01	4.01	0.46588	.	.	.	.	.	T	0.10981	0.0268	N	0.25485	0.75	0.33358	D	0.571958	B	0.30563	0.285	B	0.33846	0.171	T	0.14090	-1.0485	9	0.48119	T	0.1	-10.8091	8.8787	0.35360	0.0791:0.1511:0.7698:0.0	.	81	A6ND36	FA83G_HUMAN	T	81	ENSP00000373647:P81T;ENSP00000343279:P81T	ENSP00000343279:P81T	P	-	1	0	FAM83G	18847839	0.912000	0.30974	0.749000	0.31150	0.876000	0.50452	2.356000	0.44116	1.063000	0.40649	0.491000	0.48974	CCT		0.692	FAM83G-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253108.4		
KSR1	8844	broad.mit.edu	37	17	25909716	25909716	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:25909716C>T	ENST00000319524.6	+	4	565	c.565C>T	c.(565-567)Cgg>Tgg	p.R189W	KSR1_ENST00000509603.2_Missense_Mutation_p.R189W|KSR1_ENST00000398988.3_Missense_Mutation_p.R52W|KSR1_ENST00000268763.6_Missense_Mutation_p.R52W			Q8IVT5	KSR1_HUMAN	kinase suppressor of ras 1	189					Ras protein signal transduction (GO:0007265)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R189W(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(12)|prostate(2)|urinary_tract(1)	28	Lung NSC(42;0.00836)		BRCA - Breast invasive adenocarcinoma(3;0.00122)	UCEC - Uterine corpus endometrioid carcinoma (53;0.168)		ATTGGATGCGCGGCGGGAAAG	0.642																																					p.R52W	Esophageal Squamous(88;1120 1336 6324 10502 16832)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C154T	17						.						43.0	47.0	46.0					17																	25909716		2010	4199	6209	22933843	SO:0001583	missense	8844	exon5			U43586	CCDS58532.1	17q11.2	2012-05-23	2005-12-14	2005-12-14	ENSG00000141068	ENSG00000141068			6465	protein-coding gene	gene with protein product		601132	"""kinase suppressor of ras"""	KSR		8521512	Standard	XM_006722151		Approved	RSU2	uc031qzj.1	Q8IVT5	OTTHUMG00000132051	ENST00000319524.6:c.565C>T	17.37:g.25909716C>T	ENSP00000323178:p.Arg189Trp		22933843	NM_014238	F8WEA9|H7BYU0|Q13476	Missense_Mutation	SNP	ENST00000319524.6	37		.	.	.	.	.	.	.	.	.	.	C	15.58	2.876600	0.51801	.	.	ENSG00000141068	ENST00000319524;ENST00000509603;ENST00000268763;ENST00000398982	T;T;T	0.00475	7.17;7.17;7.17	5.7	5.7	0.88788	.	0.322591	0.34156	N	0.004218	T	0.00967	0.0032	M	0.65975	2.015	0.51012	D	0.9999	D	0.76494	0.999	P	0.56434	0.798	T	0.73199	-0.4058	10	0.66056	D	0.02	.	13.3818	0.60770	0.1575:0.8425:0.0:0.0	.	187	Q8IVT5	KSR1_HUMAN	W	189;189;52;52	ENSP00000323178:R189W;ENSP00000438795:R189W;ENSP00000268763:R52W	ENSP00000268763:R52W	R	+	1	2	KSR1	22933843	0.095000	0.21747	0.966000	0.40874	0.064000	0.16182	0.682000	0.25335	2.695000	0.91970	0.455000	0.32223	CGG		0.642	KSR1-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_014238	
SDF2	6388	broad.mit.edu	37	17	26976290	26976290	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:26976290A>G	ENST00000247020.4	-	3	651	c.353T>C	c.(352-354)gTg>gCg	p.V118A	SDF2_ENST00000592250.1_5'UTR	NM_006923.3	NP_008854.2	Q99470	SDF2_HUMAN	stromal cell-derived factor 2	118	MIR 2. {ECO:0000255|PROSITE- ProRule:PRU00131}.				protein glycosylation (GO:0006486)|protein O-linked mannosylation (GO:0035269)	extracellular space (GO:0005615)|membrane (GO:0016020)	dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169)	p.V118A(1)		endometrium(1)|large_intestine(2)|lung(2)|prostate(2)	7	Lung NSC(42;0.00431)					AAAAGCACTCACTTCCTAGAA	0.478																																					p.V118A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T353C	17						.						78.0	74.0	75.0					17																	26976290		2203	4300	6503	24000417	SO:0001583	missense	6388	exon3			BC001406	CCDS11238.1	17q11.2	2004-02-16			ENSG00000132581	ENSG00000132581			10675	protein-coding gene	gene with protein product		602934				8918255	Standard	NR_045585		Approved		uc002hbw.3	Q99470	OTTHUMG00000132681	ENST00000247020.4:c.353T>C	17.37:g.26976290A>G	ENSP00000247020:p.Val118Ala		24000417	NM_006923	Q9BQ79	Missense_Mutation	SNP	ENST00000247020.4	37	CCDS11238.1	.	.	.	.	.	.	.	.	.	.	A	27.8	4.866935	0.91511	.	.	ENSG00000132581	ENST00000247020	D	0.87334	-2.24	5.65	5.65	0.86999	MIR motif (2);MIR (2);	0.056190	0.64402	D	0.000001	D	0.94653	0.8276	M	0.90483	3.12	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.95499	0.8576	10	0.72032	D	0.01	-15.009	16.2321	0.82352	1.0:0.0:0.0:0.0	.	118	Q99470	SDF2_HUMAN	A	118	ENSP00000247020:V118A	ENSP00000247020:V118A	V	-	2	0	SDF2	24000417	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.897000	0.92532	2.288000	0.76882	0.529000	0.55759	GTG		0.478	SDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255965.2	NM_006923	
SLFN11	91607	broad.mit.edu	37	17	33680077	33680077	+	Silent	SNP	G	G	A	rs377115038		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:33680077G>A	ENST00000394566.1	-	7	2276	c.2004C>T	c.(2002-2004)gaC>gaT	p.D668D	SLFN11_ENST00000308377.4_Silent_p.D668D	NM_001104587.1|NM_001104588.1|NM_001104589.1|NM_001104590.1	NP_001098057.1|NP_001098058.1|NP_001098059.1|NP_001098060.1	Q7Z7L1	SLN11_HUMAN	schlafen family member 11	668					defense response to virus (GO:0051607)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|tRNA binding (GO:0000049)	p.D668D(1)		autonomic_ganglia(1)|breast(1)|kidney(3)|large_intestine(14)|lung(17)|ovary(1)|prostate(4)|skin(2)|stomach(5)|upper_aerodigestive_tract(2)	50		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TCTGAGCTTCGTCAATGACGA	0.433																																					p.D668D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2004T	17						.	G	,,,,	0,4406		0,0,2203	130.0	128.0	129.0		2004,2004,2004,2004,2004	0.2	0.8	17		129	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLFN11	NM_001104587.1,NM_001104588.1,NM_001104589.1,NM_001104590.1,NM_152270.3	,,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,,	668/902,668/902,668/902,668/902,668/902	33680077	1,13005	2203	4300	6503	30704190	SO:0001819	synonymous_variant	91607	exon6			AK074184	CCDS11294.1	17q12	2006-04-05			ENSG00000172716	ENSG00000172716			26633	protein-coding gene	gene with protein product		614953				12477932	Standard	NM_001104587		Approved	FLJ34922	uc010ctr.3	Q7Z7L1	OTTHUMG00000132948	ENST00000394566.1:c.2004C>T	17.37:g.33680077G>A			30704190	NM_001104589	E1P643|Q8N3S8|Q8N762|Q8TEE0	Silent	SNP	ENST00000394566.1	37	CCDS11294.1																																																																																				0.433	SLFN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256480.1	NM_152270	
TRPV3	162514	broad.mit.edu	37	17	3458053	3458053	+	Missense_Mutation	SNP	G	G	A	rs146728389		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:3458053G>A	ENST00000576742.1	-	2	413	c.92C>T	c.(91-93)cCg>cTg	p.P31L	TRPV3_ENST00000301365.4_Missense_Mutation_p.P31L|TRPV3_ENST00000572519.1_Missense_Mutation_p.P31L	NM_001258205.1|NM_145068.3	NP_001245134.1|NP_659505.1	Q8NET8	TRPV3_HUMAN	transient receptor potential cation channel, subfamily V, member 3	31					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|negative regulation of hair cycle (GO:0042636)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium channel activity (GO:0005262)	p.P31L(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(12)|ovary(5)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	35					Menthol(DB00825)	GATCTCCGCCGGCCTCTTCTC	0.642																																					p.P31L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C92T	17						.	G	LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	39.0	41.0	41.0		92	2.8	0.2	17	dbSNP_134	41	0,8600		0,0,4300	no	missense	TRPV3	NM_145068.2	98	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	31/791	3458053	1,13005	2203	4300	6503	3404803	SO:0001583	missense	162514	exon2			AF514998	CCDS11029.1, CCDS58500.1	17p13.3	2013-01-10			ENSG00000167723	ENSG00000167723		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	18084	protein-coding gene	gene with protein product		607066				12016205, 12077606, 16382100	Standard	NM_001258205		Approved	VRL3	uc002fvr.3	Q8NET8	OTTHUMG00000090695	ENST00000576742.1:c.92C>T	17.37:g.3458053G>A	ENSP00000461518:p.Pro31Leu		3404803	NM_145068	Q8NDW7|Q8NET9|Q8NFH2	Missense_Mutation	SNP	ENST00000576742.1	37	CCDS11029.1	.	.	.	.	.	.	.	.	.	.	G	7.540	0.660422	0.14645	2.27E-4	0.0	ENSG00000167723	ENST00000381913;ENST00000301365	T	0.41400	1.0	4.79	2.78	0.32641	.	0.104424	0.42821	D	0.000653	T	0.25344	0.0616	N	0.19112	0.55	0.33242	D	0.557416	B;B;B	0.24483	0.003;0.063;0.104	B;B;B	0.18263	0.001;0.009;0.021	T	0.22277	-1.0221	10	0.54805	T	0.06	-1.713	8.2076	0.31465	0.1907:0.0:0.8093:0.0	.	31;31;31	Q8NET8-3;Q8NET8;Q8NET8-2	.;TRPV3_HUMAN;.	L	31	ENSP00000301365:P31L	ENSP00000301365:P31L	P	-	2	0	TRPV3	3404803	0.949000	0.32298	0.217000	0.23759	0.012000	0.07955	2.711000	0.47177	0.565000	0.29255	-0.448000	0.05591	CCG		0.642	TRPV3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207379.2	NM_145068	
HEATR9	256957	broad.mit.edu	37	17	34182334	34182334	+	Silent	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:34182334A>G	ENST00000311880.2	-	15	1594	c.1446T>C	c.(1444-1446)taT>taC	p.Y482Y	C17orf66_ENST00000592980.1_Silent_p.Y442Y	NM_152781.2	NP_689994.2	A2RTY3	HEAT9_HUMAN		482					hematopoietic progenitor cell differentiation (GO:0002244)			p.Y482Y(1)		breast(3)|central_nervous_system(1)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(6)|lung(11)|skin(2)|stomach(4)	38		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0184)		TAGGTGCCTCATATACAGAGA	0.433																																					p.Y482Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1446C	17						.						95.0	92.0	93.0					17																	34182334		2203	4300	6503	31206447	SO:0001819	synonymous_variant	256957	exon15																														ENST00000311880.2:c.1446T>C	17.37:g.34182334A>G			31206447	NM_152781	B4DX21|B4DXA4|B4DXF0|Q8N4R4|Q96M46	Silent	SNP	ENST00000311880.2	37	CCDS11299.1																																																																																				0.433	C17orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256487.1		
RPL23	9349	broad.mit.edu	37	17	37006676	37006676	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:37006676G>A	ENST00000479035.2	-	4	411	c.279C>T	c.(277-279)ggC>ggT	p.G93G	RPL23_ENST00000394332.1_Silent_p.G93G|RPL23_ENST00000577407.1_Silent_p.G93G|SNORA21_ENST00000362423.1_RNA|RPL23_ENST00000245857.5_Silent_p.G34G|SNORA21_ENST00000516890.1_RNA|RPL23_ENST00000394333.1_Intron	NM_000978.3	NP_000969.1	P62829	RL23_HUMAN	ribosomal protein L23	93					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosomal protein import into nucleus (GO:0006610)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.G93G(1)		endometrium(2)|large_intestine(1)	3						AAAGAAACACGCCATCTTTTC	0.423																																					p.G93G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C279T	17						.						164.0	146.0	152.0					17																	37006676		2203	4300	6503	34260202	SO:0001819	synonymous_variant	9349	exon4			X52839	CCDS11330.1	17q12	2011-04-06			ENSG00000125691	ENSG00000125691		"""L ribosomal proteins"""	10316	protein-coding gene	gene with protein product		603662				1861993	Standard	NM_000978		Approved	rpL17, L23	uc002hqx.1	P62829	OTTHUMG00000133118	ENST00000479035.2:c.279C>T	17.37:g.37006676G>A			34260202	NM_000978	P23131|P24048|Q29246|Q3SWV7|Q6P5S1	Silent	SNP	ENST00000479035.2	37	CCDS11330.1																																																																																				0.423	RPL23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256785.3	NM_000978	
KRT24	192666	broad.mit.edu	37	17	38857463	38857463	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:38857463G>A	ENST00000264651.2	-	3	840	c.784C>T	c.(784-786)Cgc>Tgc	p.R262C		NM_019016.2	NP_061889.2	Q2M2I5	K1C24_HUMAN	keratin 24	262	Coil 1B.|Rod.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	structural molecule activity (GO:0005198)	p.R262C(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00526)				AGGTCAGAGCGGGTCATAGTC	0.532																																					p.R262C	GBM(61;380 1051 14702 23642 31441)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C784T	17						.						123.0	106.0	112.0					17																	38857463		2203	4300	6503	36110989	SO:0001583	missense	192666	exon3				CCDS11372.1	17q21.2	2013-06-25			ENSG00000167916	ENSG00000167916		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	18527	protein-coding gene	gene with protein product		607742				16831889	Standard	NM_019016		Approved	FLJ20261, MGC138169, MGC138173	uc002hvd.3	Q2M2I5	OTTHUMG00000133372	ENST00000264651.2:c.784C>T	17.37:g.38857463G>A	ENSP00000264651:p.Arg262Cys		36110989	NM_019016	Q9NXG7	Missense_Mutation	SNP	ENST00000264651.2	37	CCDS11372.1	.	.	.	.	.	.	.	.	.	.	G	13.61	2.289046	0.40494	.	.	ENSG00000167916	ENST00000264651	D	0.91740	-2.9	5.82	3.74	0.42951	Prefoldin (1);Filament (1);	.	.	.	.	D	0.92430	0.7597	M	0.89353	3.025	0.24118	N	0.995811	B	0.30236	0.274	B	0.28465	0.09	D	0.87838	0.2649	9	0.87932	D	0	.	10.8044	0.46509	0.0758:0.0:0.7089:0.2153	.	262	Q2M2I5	K1C24_HUMAN	C	262	ENSP00000264651:R262C	ENSP00000264651:R262C	R	-	1	0	KRT24	36110989	0.007000	0.16637	0.310000	0.25168	0.257000	0.26127	1.742000	0.38248	1.486000	0.48398	-0.259000	0.10710	CGC		0.532	KRT24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257217.1	NM_019016	
KRTAP9-4	85280	broad.mit.edu	37	17	39406161	39406161	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:39406161G>A	ENST00000334109.2	+	1	223	c.189G>A	c.(187-189)caG>caA	p.Q63Q		NM_033191.2	NP_149461.2	Q9BYQ2	KRA94_HUMAN	keratin associated protein 9-4	63	15 X 5 AA repeats of C-C-[RQVGE]-[SPTN]- [TASPF].					keratin filament (GO:0045095)		p.Q63Q(1)		breast(1)|large_intestine(1)|lung(11)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			CCTGCTGCCAGCCCACCTGTG	0.647																																					p.Q63Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G189A	17						.						75.0	68.0	70.0					17																	39406161		2203	4300	6503	36659687	SO:0001819	synonymous_variant	85280	exon1			AJ406948	CCDS11386.1	17q21.2	2013-06-25			ENSG00000241595	ENSG00000241595		"""Keratin associated proteins"""	18902	protein-coding gene	gene with protein product						11279113	Standard	NM_033191		Approved	KAP9.4	uc002hwi.3	Q9BYQ2	OTTHUMG00000133438	ENST00000334109.2:c.189G>A	17.37:g.39406161G>A			36659687	NM_033191	Q0VAE3	Silent	SNP	ENST00000334109.2	37	CCDS11386.1																																																																																				0.647	KRTAP9-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257306.1		
KRT13	3860	broad.mit.edu	37	17	39659270	39659270	+	Silent	SNP	G	G	A	rs375082810		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:39659270G>A	ENST00000246635.3	-	4	862	c.816C>T	c.(814-816)cgC>cgT	p.R272R	KRT13_ENST00000587544.1_Silent_p.R272R|AC019349.5_ENST00000411759.1_RNA|KRT13_ENST00000336861.3_Silent_p.R272R|KRT13_ENST00000587118.1_5'Flank	NM_153490.2	NP_705694	P13646	K1C13_HUMAN	keratin 13	272	Linker 12.|Rod.				cellular response to retinoic acid (GO:0071300)|cytoskeleton organization (GO:0007010)|response to radiation (GO:0009314)|tongue morphogenesis (GO:0043587)	extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)	p.R272R(1)		NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	33		Breast(137;0.000286)				CTGCCAGCACGCGGGTCAGGT	0.607																																					p.R272R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C816T	17						.	G	,	2,4404	4.2+/-10.8	0,2,2201	221.0	210.0	214.0		816,816	-8.6	0.5	17		214	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	KRT13	NM_002274.3,NM_153490.2	,	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	,	272/421,272/459	39659270	2,13004	2203	4300	6503	36912796	SO:0001819	synonymous_variant	3860	exon4				CCDS11396.1, CCDS11397.1	17q21.2	2013-06-20			ENSG00000171401	ENSG00000171401		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6415	protein-coding gene	gene with protein product	"""keratin, type I cytoskeletal 13"", ""cytokeratin 13"""	148065				16831889	Standard	NM_153490		Approved	K13, CK13, MGC3781, MGC161462	uc002hwu.1	P13646	OTTHUMG00000133434	ENST00000246635.3:c.816C>T	17.37:g.39659270G>A			36912796	NM_153490	Q53G54|Q6AZK5|Q8N240	Silent	SNP	ENST00000246635.3	37	CCDS11396.1																																																																																				0.607	KRT13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257297.1	NM_153490	
ZZEF1	23140	broad.mit.edu	37	17	3917396	3917396	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:3917396G>A	ENST00000381638.2	-	51	8525	c.8401C>T	c.(8401-8403)Cgg>Tgg	p.R2801W		NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	2801							calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)	p.R2801W(1)		central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						GTCTGGAACCGCCCCAGGTGT	0.577																																					p.R2801W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C8401T	17						.						78.0	66.0	70.0					17																	3917396		2203	4300	6503	3864145	SO:0001583	missense	23140	exon51			BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"""Zinc fingers, ZZ-type"", ""EF-hand domain containing"""	29027	protein-coding gene	gene with protein product			"""zinc finger, ZZ-type with EF hand domain 1"""			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.8401C>T	17.37:g.3917396G>A	ENSP00000371051:p.Arg2801Trp		3864145	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Missense_Mutation	SNP	ENST00000381638.2	37	CCDS11043.1	.	.	.	.	.	.	.	.	.	.	G	19.57	3.852779	0.71719	.	.	ENSG00000074755	ENST00000381638	T	0.29397	1.57	5.56	4.54	0.55810	.	0.061904	0.64402	D	0.000012	T	0.41994	0.1183	N	0.20986	0.625	0.52099	D	0.999943	D	0.89917	1.0	D	0.91635	0.999	T	0.41963	-0.9479	10	0.87932	D	0	-14.6833	15.5459	0.76101	0.0:0.0:0.8156:0.1844	.	2801	O43149	ZZEF1_HUMAN	W	2801	ENSP00000371051:R2801W	ENSP00000371051:R2801W	R	-	1	2	ZZEF1	3864145	0.999000	0.42202	0.959000	0.39883	0.894000	0.52154	3.008000	0.49544	2.605000	0.88082	0.563000	0.77884	CGG		0.577	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113	
WNK4	65266	broad.mit.edu	37	17	40935972	40935972	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:40935972G>A	ENST00000246914.5	+	3	830	c.809G>A	c.(808-810)cGg>cAg	p.R270Q		NM_032387.4	NP_115763.2	Q96J92	WNK4_HUMAN	WNK lysine deficient protein kinase 4	270	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				chloride transport (GO:0006821)|distal tubule morphogenesis (GO:0072156)|intracellular signal transduction (GO:0035556)|ion homeostasis (GO:0050801)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)|renal sodium ion absorption (GO:0070294)	cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein serine/threonine kinase activity (GO:0004674)	p.R258R(1)|p.R270Q(1)		NS(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|prostate(1)|skin(5)|stomach(1)	35		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		AGGCGGTTCCGGGAGATGAAG	0.667																																					p.R270Q	Esophageal Squamous(6;201 374 4964 23855 42828)											.	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(2)	c.G809A	17						.						24.0	25.0	25.0					17																	40935972		2203	4300	6503	38189498	SO:0001583	missense	65266	exon3			AJ309861	CCDS11439.1	17q21-q22	2005-01-19	2005-01-19	2005-01-19		ENSG00000126562			14544	protein-coding gene	gene with protein product		601844	"""protein kinase, lysine deficient 4"""	PRKWNK4			Standard	NM_032387		Approved		uc002ibj.3	Q96J92		ENST00000246914.5:c.809G>A	17.37:g.40935972G>A	ENSP00000246914:p.Arg270Gln		38189498	NM_032387	B0LPI0|Q8N8X3|Q8N8Z2|Q96DT8|Q9BYS5	Missense_Mutation	SNP	ENST00000246914.5	37	CCDS11439.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.078317	0.76528	.	.	ENSG00000126562	ENST00000246914;ENST00000316085	T	0.25085	1.82	4.09	4.09	0.47781	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.42964	D	0.000631	T	0.28632	0.0709	L	0.31578	0.945	0.37836	D	0.928908	D;D	0.65815	0.995;0.995	P;P	0.59825	0.864;0.864	T	0.17623	-1.0363	10	0.87932	D	0	-8.6006	4.8659	0.13607	0.2771:0.0:0.7229:0.0	.	270;270	B0LPI0;Q96J92	.;WNK4_HUMAN	Q	270;42	ENSP00000246914:R270Q	ENSP00000246914:R270Q	R	+	2	0	WNK4	38189498	1.000000	0.71417	0.914000	0.36105	0.980000	0.70556	7.443000	0.80521	2.095000	0.63458	0.563000	0.77884	CGG		0.667	WNK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452389.1		
TMEM101	84336	broad.mit.edu	37	17	42089386	42089386	+	Silent	SNP	C	C	T	rs556952458		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:42089386C>T	ENST00000589334.1	-	5	999	c.684G>A	c.(682-684)acG>acA	p.T228T	TMEM101_ENST00000206380.3_Silent_p.T228T|TMEM101_ENST00000542039.1_Silent_p.T170T			Q96IK0	TM101_HUMAN	transmembrane protein 101	228					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	signal transducer activity (GO:0004871)	p.T228T(1)		central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		Breast(137;0.0264)|Prostate(33;0.0861)		BRCA - Breast invasive adenocarcinoma(366;0.113)		CAACACGCCGCGTGTTGTGCC	0.552													C|||	1	0.000199681	0.0	0.0014	5008	,	,		20916	0.0		0.0	False		,,,				2504	0.0				p.T228T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G684A	17						.						108.0	88.0	95.0					17																	42089386		2203	4300	6503	39444912	SO:0001819	synonymous_variant	84336	exon4			AK172826	CCDS11474.1	17q21.31	2005-12-16							28653	protein-coding gene	gene with protein product						12761501	Standard	NM_032376		Approved	MGC4251, FLJ23987	uc002ieu.3	Q96IK0		ENST00000589334.1:c.684G>A	17.37:g.42089386C>T			39444912	NM_032376	B2R9N6	Silent	SNP	ENST00000589334.1	37	CCDS11474.1																																																																																				0.552	TMEM101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457665.1	NM_032376	
ANKFY1	51479	broad.mit.edu	37	17	4083080	4083080	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:4083080G>A	ENST00000341657.4	-	17	2368	c.2333C>T	c.(2332-2334)gCc>gTc	p.A778V	ANKFY1_ENST00000574367.1_Missense_Mutation_p.A779V|ANKFY1_ENST00000570535.1_Missense_Mutation_p.A820V|CYB5D2_ENST00000573984.1_Intron	NM_016376.3	NP_057460.3	Q9P2R3	ANFY1_HUMAN	ankyrin repeat and FYVE domain containing 1	778					endosomal vesicle fusion (GO:0034058)|endosome localization (GO:0032439)|Golgi to lysosome transport (GO:0090160)|positive regulation of pinocytosis (GO:0048549)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|macropinosome (GO:0044354)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol phosphate binding (GO:1901981)|Rab GTPase binding (GO:0017137)	p.A779V(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|liver(1)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						CCCCCAAGAGGCTGCCAAATG	0.552																																					p.A779V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2336T	17						.						178.0	187.0	184.0					17																	4083080		1958	4154	6112	4029829	SO:0001583	missense	51479	exon17			AB033081	CCDS42236.1, CCDS58502.1	17p13.3	2013-01-10			ENSG00000185722	ENSG00000185722		"""Zinc fingers, FYVE domain containing"", ""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	20763	protein-coding gene	gene with protein product		607927				10940552, 17273843	Standard	NM_016376		Approved	ANKHZN, KIAA1255, ZFYVE14, BTBD23	uc002fxn.3	Q9P2R3	OTTHUMG00000177727	ENST00000341657.4:c.2333C>T	17.37:g.4083080G>A	ENSP00000343362:p.Ala778Val		4029829	NM_016376	A8KA65|Q5RKV4|Q9ULG5	Missense_Mutation	SNP	ENST00000341657.4	37		.	.	.	.	.	.	.	.	.	.	G	21.9	4.221048	0.79464	.	.	ENSG00000185722	ENST00000341657;ENST00000535427	.	.	.	5.35	5.35	0.76521	Ankyrin repeat-containing domain (4);	0.110341	0.64402	D	0.000007	T	0.57021	0.2025	L	0.28014	0.82	0.80722	D	1	P;P;P;P	0.48503	0.911;0.722;0.675;0.868	P;B;B;P	0.50490	0.642;0.423;0.298;0.526	T	0.58008	-0.7712	9	0.49607	T	0.09	-17.2875	18.2323	0.89937	0.0:0.0:1.0:0.0	.	720;778;779;820	F5H754;Q9P2R3;Q9P2R3-2;Q9P2R3-4	.;ANFY1_HUMAN;.;.	V	779;720	.	ENSP00000343362:A779V	A	-	2	0	ANKFY1	4029829	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.665000	0.68052	2.790000	0.95986	0.591000	0.81541	GCC		0.552	ANKFY1-008	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000438702.1	NM_016376	
GRN	2896	broad.mit.edu	37	17	42428090	42428090	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:42428090C>T	ENST00000053867.3	+	7	692	c.630C>T	c.(628-630)gaC>gaT	p.D210D	GRN_ENST00000589265.1_Intron	NM_002087.2	NP_002078.1	P28799	GRN_HUMAN	granulin	210					blastocyst hatching (GO:0001835)|cell death (GO:0008219)|embryo implantation (GO:0007566)|positive regulation of epithelial cell proliferation (GO:0050679)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)	growth factor activity (GO:0008083)|poly(A) RNA binding (GO:0044822)	p.D210D(1)		central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.189)		TGTGTCCGGACGCACGGTCCC	0.592											OREG0024459	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D210D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C630T	17						.						109.0	88.0	95.0					17																	42428090		2203	4300	6503	39783616	SO:0001819	synonymous_variant	2896	exon7			M75161	CCDS11483.1	17q21.32	2014-09-17				ENSG00000030582			4601	protein-coding gene	gene with protein product	"""progranulin"""	138945				1417868, 9826678	Standard	XM_005257253		Approved	PCDGF, PGRN, CLN11	uc002igp.1	P28799		ENST00000053867.3:c.630C>T	17.37:g.42428090C>T		908	39783616	NM_002087	D3DX55|P23781|P23782|P23783|P23784|Q53HQ8|Q53Y88|Q540U8|Q9BWE7|Q9H8S1|Q9UCH0	Silent	SNP	ENST00000053867.3	37	CCDS11483.1																																																																																				0.592	GRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457766.1	NM_002087	
ARHGAP27	201176	broad.mit.edu	37	17	43472874	43472874	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:43472874T>G	ENST00000428638.1	-	17	2617	c.2618A>C	c.(2617-2619)cAg>cCg	p.Q873P	ARHGAP27_ENST00000528384.1_Missense_Mutation_p.Q505P|ARHGAP27_ENST00000582826.1_5'Flank|ARHGAP27_ENST00000442348.1_Missense_Mutation_p.Q846P|ARHGAP27_ENST00000532038.1_Missense_Mutation_p.Q651P|CTB-39G8.3_ENST00000592389.1_RNA|ARHGAP27_ENST00000376922.2_Missense_Mutation_p.Q532P|ARHGAP27_ENST00000455881.1_Missense_Mutation_p.Q532P|ARHGAP27_ENST00000532891.2_Missense_Mutation_p.Q851P			Q6ZUM4	RHG27_HUMAN	Rho GTPase activating protein 27	873	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of Rac GTPase activity (GO:0032855)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|SH3 domain binding (GO:0017124)	p.Q532P(1)		endometrium(4)|large_intestine(9)|lung(3)|skin(1)	17	Renal(3;0.0405)					CTCCACCACCTGGTTCTGGAA	0.662											OREG0024481	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q532P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1595C	17						.						43.0	33.0	36.0					17																	43472874		2202	4298	6500	40828657	SO:0001583	missense	201176	exon17			AK125535	CCDS11498.1, CCDS74082.1	17q21.31	2013-01-10			ENSG00000159314	ENSG00000159314		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	31813	protein-coding gene	gene with protein product		610591	"""SH3 domain containing 20"""	SH3D20		15147912	Standard	NM_199282		Approved	CAMGAP1, FLJ43547, SH3P20	uc002iix.3	Q6ZUM4	OTTHUMG00000166982	ENST00000428638.1:c.2618A>C	17.37:g.43472874T>G	ENSP00000403323:p.Gln873Pro	916	40828657	NM_199282	A4FU35|A8K3N5|C9JTF3|Q494U0|Q6NWZ8|Q8WY58	Missense_Mutation	SNP	ENST00000428638.1	37		.	.	.	.	.	.	.	.	.	.	T	28.2	4.897943	0.91962	.	.	ENSG00000159314	ENST00000532038;ENST00000376922;ENST00000528384;ENST00000532891;ENST00000428638;ENST00000442348;ENST00000455881	T;T;T;T;T;T;T	0.11712	2.75;2.75;2.75;2.75;2.75;2.75;2.75	4.45	4.45	0.53987	Rho GTPase-activating protein domain (3);Rho GTPase activation protein (1);	0.135000	0.51477	D	0.000095	T	0.32315	0.0825	M	0.79614	2.46	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.994	T	0.07520	-1.0768	10	0.87932	D	0	.	11.7041	0.51587	0.0:0.0:0.0:1.0	.	846;873	F8WBX1;Q6ZUM4	.;RHG27_HUMAN	P	651;532;505;851;873;846;532	ENSP00000432762:Q651P;ENSP00000366121:Q532P;ENSP00000431591:Q505P;ENSP00000433942:Q851P;ENSP00000403323:Q873P;ENSP00000409330:Q846P;ENSP00000408235:Q532P	ENSP00000366121:Q532P	Q	-	2	0	ARHGAP27	40828657	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.047000	0.71038	1.877000	0.54381	0.443000	0.29094	CAG		0.662	ARHGAP27-202	KNOWN	basic	protein_coding	protein_coding		NM_199282	
HOXB3	3213	broad.mit.edu	37	17	46629580	46629580	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:46629580G>A	ENST00000470495.1	-	1	1704	c.257C>T	c.(256-258)cCg>cTg	p.P86L	HOXB3_ENST00000490677.1_Intron|HOXB3_ENST00000476342.1_Missense_Mutation_p.P86L|HOXB3_ENST00000311626.4_Missense_Mutation_p.P86L|HOXB-AS1_ENST00000435312.1_RNA|HOXB-AS1_ENST00000508688.1_RNA|HOXB-AS1_ENST00000502764.2_RNA|HOXB3_ENST00000498678.1_Missense_Mutation_p.P86L|HOXB3_ENST00000460160.1_Intron|HOXB3_ENST00000485909.2_Intron|HOXB-AS3_ENST00000465846.2_RNA|HOXB3_ENST00000489475.1_Missense_Mutation_p.P13L|HOXB3_ENST00000472863.1_Missense_Mutation_p.P13L			P14651	HXB3_HUMAN	homeobox B3	86					angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|cartilage development (GO:0051216)|definitive hemopoiesis (GO:0060216)|embryonic skeletal system morphogenesis (GO:0048704)|face development (GO:0060324)|glossopharyngeal nerve morphogenesis (GO:0021615)|hematopoietic progenitor cell differentiation (GO:0002244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of neurogenesis (GO:0050767)|rhombomere development (GO:0021546)|thyroid gland development (GO:0030878)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P86L(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(2)|lung(16)|prostate(4)|upper_aerodigestive_tract(1)	30						TGAGCCAGGCGGGGCCGACAG	0.687																																					p.P86L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C257T	17						.						38.0	48.0	45.0					17																	46629580		2203	4298	6501	43984579	SO:0001583	missense	3213	exon3				CCDS11528.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120093	ENSG00000120093		"""Homeoboxes / ANTP class : HOXL subclass"""	5114	protein-coding gene	gene with protein product		142966	"""homeo box B3"""	HOX2, HOX2G		1973146, 1358459	Standard	XM_006721854		Approved		uc002ino.3	P14651	OTTHUMG00000159922	ENST00000470495.1:c.257C>T	17.37:g.46629580G>A	ENSP00000417207:p.Pro86Leu		43984579	NM_002146	A8K567|B7Z5N8|B7Z5P8|B7ZAD0|D3DTV3|O95615|P17484	Missense_Mutation	SNP	ENST00000470495.1	37	CCDS11528.1	.	.	.	.	.	.	.	.	.	.	G	7.583	0.669147	0.14776	.	.	ENSG00000120093	ENST00000470495;ENST00000472863;ENST00000311626;ENST00000498678;ENST00000489475;ENST00000476342;ENST00000471459	D;D;D;D;D;D;T	0.91792	-2.91;-2.81;-2.91;-2.91;-2.81;-2.91;1.39	3.9	2.92	0.33932	.	0.483471	0.20787	U	0.085698	D	0.89784	0.6815	M	0.75085	2.285	0.80722	D	1	B	0.12013	0.005	B	0.06405	0.002	D	0.86216	0.1628	10	0.48119	T	0.1	.	8.5248	0.33298	0.1808:0.0:0.8192:0.0	.	86	P14651	HXB3_HUMAN	L	86;13;86;86;13;86;13	ENSP00000417207:P86L;ENSP00000419676:P13L;ENSP00000308252:P86L;ENSP00000420595:P86L;ENSP00000418729:P13L;ENSP00000418892:P86L;ENSP00000417400:P13L	ENSP00000308252:P86L	P	-	2	0	HOXB3	43984579	1.000000	0.71417	0.999000	0.59377	0.126000	0.20510	7.217000	0.77982	0.982000	0.38575	-0.291000	0.09656	CCG		0.687	HOXB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358261.1		
SPOP	8405	broad.mit.edu	37	17	47684619	47684619	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:47684619G>A	ENST00000393328.2	-	9	1195	c.830C>T	c.(829-831)gCt>gTt	p.A277V	SPOP_ENST00000393331.3_Missense_Mutation_p.A277V|SPOP_ENST00000347630.2_Missense_Mutation_p.A277V|SPOP_ENST00000503676.1_Missense_Mutation_p.A277V|SPOP_ENST00000504102.1_Missense_Mutation_p.A277V	NM_003563.3	NP_003554.1	O43791	SPOP_HUMAN	speckle-type POZ protein	277	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				glucose homeostasis (GO:0042593)|positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902237)|positive regulation of type B pancreatic cell apoptotic process (GO:2000676)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	Cul3-RING ubiquitin ligase complex (GO:0031463)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	ubiquitin protein ligase binding (GO:0031625)	p.A277V(1)		endometrium(18)|kidney(1)|large_intestine(3)|liver(1)|lung(4)|ovary(3)|prostate(33)	63						TACCTTGTCAGCAGCTGCCAG	0.393										Prostate(2;0.17)																											p.A277V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C830T	17						.						146.0	133.0	137.0					17																	47684619		2203	4300	6503	45039618	SO:0001583	missense	8405	exon9			AJ000644	CCDS11551.1	17q21.33	2013-01-09			ENSG00000121067	ENSG00000121067		"""BTB/POZ domain containing"""	11254	protein-coding gene	gene with protein product		602650				9414087	Standard	NM_001007227		Approved	TEF2, BTBD32	uc002ipg.3	O43791	OTTHUMG00000161496	ENST00000393328.2:c.830C>T	17.37:g.47684619G>A	ENSP00000377001:p.Ala277Val		45039618	NM_001007229	B2R6S3|D3DTW7|Q53HJ1	Missense_Mutation	SNP	ENST00000393328.2	37	CCDS11551.1	.	.	.	.	.	.	.	.	.	.	G	36	5.728252	0.96856	.	.	ENSG00000121067	ENST00000393328;ENST00000393331;ENST00000347630;ENST00000504102;ENST00000503536;ENST00000503676;ENST00000513872	D;D;D;D;D	0.87650	-2.28;-2.28;-2.28;-2.28;-2.28	5.33	5.33	0.75918	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.94820	0.8327	H	0.96269	3.795	0.80722	D	1	D	0.69078	0.997	P	0.55824	0.785	D	0.96136	0.9096	10	0.87932	D	0	-10.4837	18.8133	0.92068	0.0:0.0:1.0:0.0	.	277	O43791	SPOP_HUMAN	V	277;277;277;277;161;277;230	ENSP00000377001:A277V;ENSP00000377004:A277V;ENSP00000240327:A277V;ENSP00000425905:A277V;ENSP00000420908:A277V	ENSP00000240327:A277V	A	-	2	0	SPOP	45039618	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.657000	0.98554	2.777000	0.95525	0.591000	0.81541	GCT		0.393	SPOP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365154.2	NM_003563	
EME1	146956	broad.mit.edu	37	17	48453445	48453445	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:48453445G>A	ENST00000338165.4	+	3	876	c.794G>A	c.(793-795)gGt>gAt	p.G265D	MRPL27_ENST00000225969.4_5'Flank|EME1_ENST00000393271.2_Missense_Mutation_p.G265D|MRPL27_ENST00000442592.3_5'Flank|EME1_ENST00000511648.2_Missense_Mutation_p.G265D|MRPL27_ENST00000503633.1_5'Flank	NM_152463.2	NP_689676.2	Q96AY2	EME1_HUMAN	essential meiotic structure-specific endonuclease 1	265					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cytoplasm (GO:0005737)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)	p.G265D(1)		endometrium(4)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	19	Breast(11;5.62e-19)		BRCA - Breast invasive adenocarcinoma(22;2.43e-08)			CAGATGGAAGGTGGGGGCCAG	0.572								Direct reversal of damage;Homologous recombination																													p.G265D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G794A	17						.						89.0	76.0	80.0					17																	48453445		2203	4300	6503	45808444	SO:0001583	missense	146956	exon3			BC016470	CCDS11565.1, CCDS54141.1	17q21.33	2013-07-03	2013-07-03			ENSG00000154920			24965	protein-coding gene	gene with protein product	"""SLX2 structure-specific endonuclease subunit homolog A (S. cerevisiae)"""	610885	"""essential meiotic endonuclease 1 homolog 1 (S. pombe)"""			12721304	Standard	NM_001166131		Approved	FLJ31364, MMS4L, SLX2A	uc010dbp.2	Q96AY2		ENST00000338165.4:c.794G>A	17.37:g.48453445G>A	ENSP00000339897:p.Gly265Asp		45808444	NM_001166131	Q96N62	Missense_Mutation	SNP	ENST00000338165.4	37	CCDS11565.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.857235	0.91433	.	.	ENSG00000154920	ENST00000338165;ENST00000393271;ENST00000511519;ENST00000511648	T;T;T;T	0.37752	1.78;1.78;1.18;1.78	5.25	5.25	0.73442	ERCC4 domain (2);	0.000000	0.85682	D	0.000000	T	0.65565	0.2703	M	0.83953	2.67	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.70901	-0.4746	10	0.72032	D	0.01	-22.5914	18.8577	0.92259	0.0:0.0:1.0:0.0	.	265;265	Q96AY2-2;Q96AY2	.;EME1_HUMAN	D	265;265;108;265	ENSP00000339897:G265D;ENSP00000376952:G265D;ENSP00000423029:G108D;ENSP00000421700:G265D	ENSP00000339897:G265D	G	+	2	0	EME1	45808444	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.967000	0.93402	2.453000	0.82957	0.650000	0.86243	GGT		0.572	EME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367118.3	NM_152463	
EPN3	55040	broad.mit.edu	37	17	48614290	48614290	+	Missense_Mutation	SNP	G	G	A	rs141972412		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:48614290G>A	ENST00000268933.3	+	2	952	c.373G>A	c.(373-375)Gag>Aag	p.E125K	EPN3_ENST00000541226.1_Missense_Mutation_p.E69K|RP11-94C24.8_ENST00000513017.1_RNA|EPN3_ENST00000537145.1_Missense_Mutation_p.E180K	NM_017957.2	NP_060427.2	Q9H201	EPN3_HUMAN	epsin 3	125	ENTH. {ECO:0000255|PROSITE- ProRule:PRU00243}.					clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	lipid binding (GO:0008289)	p.E125K(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;2.88e-09)			CAACGTGCGCGAGAAGGTCAA	0.637																																					p.E125K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G373A	17						.	G	LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	83.0	60.0	68.0		373	5.5	1.0	17	dbSNP_134	68	0,8600		0,0,4300	yes	missense	EPN3	NM_017957.2	56	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	125/633	48614290	1,13005	2203	4300	6503	45969289	SO:0001583	missense	55040	exon2			AF324241	CCDS11570.1	17q21.33	2008-07-18				ENSG00000049283			18235	protein-coding gene	gene with protein product		607264				10951261, 11359770	Standard	NM_017957		Approved	FLJ20778, MGC129899	uc002ira.4	Q9H201		ENST00000268933.3:c.373G>A	17.37:g.48614290G>A	ENSP00000268933:p.Glu125Lys		45969289	NM_017957	A8K6J3|A8KAB2|Q9BVN6|Q9NWK2	Missense_Mutation	SNP	ENST00000268933.3	37	CCDS11570.1	.	.	.	.	.	.	.	.	.	.	G	37	6.010800	0.97200	2.27E-4	0.0	ENSG00000049283	ENST00000268933;ENST00000503246;ENST00000442715;ENST00000537145;ENST00000541226;ENST00000507467;ENST00000411703	T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02	5.47	5.47	0.80525	Epsin domain, N-terminal (1);ENTH/VHS (2);Epsin-like, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.61438	0.2347	L	0.58669	1.825	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.53906	-0.8372	10	0.24483	T	0.36	-26.9203	18.9294	0.92558	0.0:0.0:1.0:0.0	.	180;180;125	B4DK18;F6QWW5;Q9H201	.;.;EPN3_HUMAN	K	125;125;180;180;69;125;125	ENSP00000268933:E125K;ENSP00000426762:E125K;ENSP00000439512:E180K;ENSP00000440540:E69K;ENSP00000421515:E125K	ENSP00000268933:E125K	E	+	1	0	EPN3	45969289	1.000000	0.71417	0.997000	0.53966	0.928000	0.56348	9.838000	0.99474	2.571000	0.86741	0.561000	0.74099	GAG		0.637	EPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367573.1	NM_017957	
TM4SF5	9032	broad.mit.edu	37	17	4684107	4684107	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:4684107C>T	ENST00000270560.3	+	2	232	c.201C>T	c.(199-201)gcC>gcT	p.A67A		NM_003963.2	NP_003954.2	O14894	T4S5_HUMAN	transmembrane 4 L six family member 5	67						integral component of plasma membrane (GO:0005887)		p.A67A(1)		large_intestine(2)|lung(3)|ovary(1)	6						GGATTGCAGCCGTTCGGGCAG	0.582																																					p.A67A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C201T	17						.						66.0	62.0	63.0					17																	4684107		2203	4300	6503	4630856	SO:0001819	synonymous_variant	9032	exon2			AF027204	CCDS11054.1	17p13.3	2007-01-06	2005-03-21		ENSG00000142484	ENSG00000142484			11857	protein-coding gene	gene with protein product		604657	"""transmembrane 4 superfamily member 5"""			9479038	Standard	NM_003963		Approved		uc002fyw.1	O14894	OTTHUMG00000090776	ENST00000270560.3:c.201C>T	17.37:g.4684107C>T			4630856	NM_003963	Q17RW9|Q6IB79	Silent	SNP	ENST00000270560.3	37	CCDS11054.1																																																																																				0.582	TM4SF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207558.2		
VMO1	284013	broad.mit.edu	37	17	4688713	4688713	+	Missense_Mutation	SNP	C	C	A	rs377200420		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:4688713C>A	ENST00000328739.5	-	3	632	c.553G>T	c.(553-555)Ggc>Tgc	p.G185C	VMO1_ENST00000354194.4_3'UTR|VMO1_ENST00000416307.2_3'UTR|VMO1_ENST00000441199.2_3'UTR	NM_182566.2	NP_872372.1	Q7Z5L0	VMO1_HUMAN	vitelline membrane outer layer 1 homolog (chicken)	185						extracellular vesicular exosome (GO:0070062)		p.G185C(1)		kidney(2)|large_intestine(3)|liver(1)|lung(3)|ovary(1)|pancreas(1)	11						TCGCCGAGGCCTCTAGGTCCC	0.672																																					p.G185C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G553T	17						.						54.0	52.0	52.0					17																	4688713		2203	4300	6503	4635453	SO:0001583	missense	284013	exon3			AF521892	CCDS11055.1, CCDS45585.1, CCDS45586.1, CCDS45587.1	17p13.2	2013-03-07	2005-11-14						30387	protein-coding gene	gene with protein product						22025569	Standard	NM_182566		Approved		uc002fyx.3	Q7Z5L0		ENST00000328739.5:c.553G>T	17.37:g.4688713C>A	ENSP00000328397:p.Gly185Cys		4635453	NM_182566	C9JQ15|E9PAU9|E9PGP4|Q3SXP1|Q8IUY1	Missense_Mutation	SNP	ENST00000328739.5	37	CCDS11055.1	.	.	.	.	.	.	.	.	.	.	C	11.79	1.744610	0.30865	.	.	ENSG00000182853	ENST00000328739	T	0.53423	0.62	4.77	4.77	0.60923	.	0.254416	0.40385	N	0.001101	T	0.71542	0.3352	M	0.85777	2.775	0.24919	N	0.991995	D	0.89917	1.0	D	0.91635	0.999	T	0.66760	-0.5842	10	0.87932	D	0	-29.602	15.333	0.74229	0.0:1.0:0.0:0.0	.	185	Q7Z5L0	VMO1_HUMAN	C	185	ENSP00000328397:G185C	ENSP00000328397:G185C	G	-	1	0	VMO1	4635453	0.083000	0.21467	0.122000	0.21767	0.021000	0.10359	2.271000	0.43364	2.491000	0.84063	0.561000	0.74099	GGC		0.672	VMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439587.1	NM_182566	
NUP88	4927	broad.mit.edu	37	17	5290411	5290411	+	Missense_Mutation	SNP	T	T	G	rs577225211	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:5290411T>G	ENST00000573584.1	-	15	2445	c.1936A>C	c.(1936-1938)Agt>Cgt	p.S646R	NUP88_ENST00000573169.1_5'Flank	NM_002532.4	NP_002523.2	Q99567	NUP88_HUMAN	nucleoporin 88kDa	646					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	transporter activity (GO:0005215)	p.S646R(1)		endometrium(4)|kidney(4)|large_intestine(4)|lung(3)	15						GAGTGAAAACTGTGAAGTAGT	0.378																																					p.S646R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1936C	17						.						83.0	82.0	83.0					17																	5290411		2203	4300	6503	5231135	SO:0001583	missense	4927	exon15			Y08612	CCDS11070.1	17p13	2004-02-18	2002-08-29		ENSG00000108559	ENSG00000108559			8067	protein-coding gene	gene with protein product		602552	"""nucleoporin 88kD"""			9049309	Standard	NM_002532		Approved	MGC8530	uc002gbo.2	Q99567	OTTHUMG00000099453	ENST00000573584.1:c.1936A>C	17.37:g.5290411T>G	ENSP00000458954:p.Ser646Arg		5231135	NM_002532	D3DTM2|Q9BWE5	Missense_Mutation	SNP	ENST00000573584.1	37	CCDS11070.1	.	.	.	.	.	.	.	.	.	.	T	12.00	1.806932	0.31961	.	.	ENSG00000108559	ENST00000225696;ENST00000543132	.	.	.	4.63	3.54	0.40534	.	0.089581	0.85682	N	0.000000	T	0.29321	0.0730	N	0.16066	0.365	0.44587	D	0.997559	B;B	0.16603	0.0;0.018	B;B	0.19391	0.001;0.025	T	0.05115	-1.0905	9	0.12766	T	0.61	-6.0682	6.5349	0.22348	0.1554:0.0:0.1622:0.6824	.	531;646	B4DP20;Q99567	.;NUP88_HUMAN	R	646;531	.	ENSP00000225696:S646R	S	-	1	0	NUP88	5231135	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.500000	0.45381	0.899000	0.36444	0.455000	0.32223	AGT		0.378	NUP88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216918.3	NM_002532	
CACNA1G	8913	broad.mit.edu	37	17	48681634	48681634	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:48681634G>A	ENST00000359106.5	+	22	4288	c.4288G>A	c.(4288-4290)Ggg>Agg	p.G1430R	CACNA1G_ENST00000507609.1_Missense_Mutation_p.G1430R|CACNA1G_ENST00000514079.1_Missense_Mutation_p.G1430R|CACNA1G_ENST00000429973.2_Missense_Mutation_p.G1430R|CACNA1G_ENST00000352832.5_Missense_Mutation_p.G1407R|CACNA1G_ENST00000513689.2_Missense_Mutation_p.G1430R|CACNA1G_ENST00000507336.1_Missense_Mutation_p.G1430R|CACNA1G_ENST00000514717.1_Missense_Mutation_p.G1407R|CACNA1G_ENST00000442258.2_Missense_Mutation_p.G1407R|CACNA1G_ENST00000360761.4_Missense_Mutation_p.G1407R|CACNA1G_ENST00000502264.1_Missense_Mutation_p.G1407R|CACNA1G_ENST00000507896.1_Missense_Mutation_p.G1430R|CACNA1G_ENST00000515765.1_Missense_Mutation_p.G1430R|CACNA1G_ENST00000358244.5_Missense_Mutation_p.G1407R|CACNA1G_ENST00000513964.1_Missense_Mutation_p.G1430R|CACNA1G_ENST00000514181.1_Missense_Mutation_p.G1430R|CACNA1G_ENST00000512389.1_Missense_Mutation_p.G1430R|CACNA1G_ENST00000416767.4_Missense_Mutation_p.G1430R|CACNA1G_ENST00000503485.1_Missense_Mutation_p.G1430R|CACNA1G_ENST00000505165.1_Missense_Mutation_p.G1430R|CACNA1G_ENST00000515411.1_Missense_Mutation_p.G1430R|CACNA1G_ENST00000515165.1_Missense_Mutation_p.G1430R|CACNA1G_ENST00000510115.1_Missense_Mutation_p.G1407R|CACNA1G_ENST00000507510.2_Missense_Mutation_p.G1430R|CACNA1G_ENST00000510366.1_Missense_Mutation_p.G1430R|CACNA1G_ENST00000354983.4_Missense_Mutation_p.G1407R	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	1430					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)	p.G1430R(2)|p.G1407R(1)		breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	CGGCATCTTGGGGGTGCAGGT	0.587																																					p.G1407R												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.G4219A	17						.						119.0	127.0	124.0					17																	48681634		2107	4219	6326	46036633	SO:0001583	missense	8913	exon21			AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.4288G>A	17.37:g.48681634G>A	ENSP00000352011:p.Gly1430Arg		46036633	NM_198382	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Missense_Mutation	SNP	ENST00000359106.5	37	CCDS45730.1	.	.	.	.	.	.	.	.	.	.	g	22.6	4.308029	0.81247	.	.	ENSG00000006283	ENST00000360761;ENST00000352832;ENST00000416767;ENST00000354983;ENST00000442258;ENST00000502264;ENST00000512389;ENST00000513964;ENST00000514717;ENST00000510366;ENST00000503485;ENST00000507510;ENST00000507336;ENST00000513689;ENST00000507609;ENST00000510115;ENST00000515165;ENST00000514181;ENST00000515765;ENST00000514079;ENST00000358244;ENST00000359106;ENST00000429973;ENST00000515411;ENST00000505165;ENST00000507896;ENST00000506520	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97665	-4.48;-4.48;-4.48;-4.48;-4.48;-4.48;-4.48;-4.48;-4.48;-4.48;-4.48;-4.48;-4.48;-4.48;-4.48;-4.48;-4.48;-4.48;-4.48;-4.48;-4.48;-4.48;-4.48;-4.48;-4.48;-4.48;-4.48	4.82	3.83	0.44106	Ion transport (1);	0.123056	0.56097	D	0.000035	D	0.99217	0.9728	H	0.99682	4.7	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	0.999;1.0;1.0;0.998;1.0;0.999;1.0;1.0;0.997;1.0;0.999;0.997;0.999;0.998;0.998;1.0;1.0;1.0;1.0;0.998;0.999;1.0;0.999;0.997;0.999;0.999;1.0	D	0.98360	1.0548	10	0.87932	D	0	.	14.2871	0.66254	0.0:0.0:0.85:0.15	.	460;1407;1430;1430;1430;1430;1430;1430;1430;1430;1430;1430;1407;1430;1430;1430;1430;1430;1407;1430;1407;1407;1407;1407;1430;1407;1430	B4DKD3;Q19QZ5;Q19QZ1;Q19QZ4;Q19R07;Q19QY8;Q19R10;Q19QZ6;Q19QZ3;Q19R06;Q19R00;Q19R04;O43497-10;Q19QZ9;Q19QZ7;Q19R08;Q19QZ8;Q19R03;O43497-4;Q19R02;Q19R12;Q19R17;Q19R11;Q2TAC4;O43497;Q19R13;O43497-11	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;CAC1G_HUMAN;.;.	R	1407;1407;1430;1407;1407;1407;1430;1430;1407;1430;1430;1430;1430;1430;1430;1407;1430;1430;1430;1430;1407;1430;1430;1430;1430;1430;245	ENSP00000353990:G1407R;ENSP00000339302:G1407R;ENSP00000392390:G1430R;ENSP00000347078:G1407R;ENSP00000409759:G1407R;ENSP00000425522:G1407R;ENSP00000426261:G1430R;ENSP00000425451:G1430R;ENSP00000422407:G1407R;ENSP00000426814:G1430R;ENSP00000427238:G1430R;ENSP00000423112:G1430R;ENSP00000420918:G1430R;ENSP00000426172:G1430R;ENSP00000423045:G1430R;ENSP00000427173:G1407R;ENSP00000426098:G1430R;ENSP00000425698:G1430R;ENSP00000426232:G1430R;ENSP00000423317:G1430R;ENSP00000350979:G1407R;ENSP00000352011:G1430R;ENSP00000414388:G1430R;ENSP00000423155:G1430R;ENSP00000422268:G1430R;ENSP00000421518:G1430R;ENSP00000427697:G245R	ENSP00000339302:G1407R	G	+	1	0	CACNA1G	46036633	1.000000	0.71417	0.994000	0.49952	0.881000	0.50899	9.869000	0.99810	0.995000	0.38917	0.563000	0.77884	GGG		0.587	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896	
MRPS23	51649	broad.mit.edu	37	17	55918609	55918609	+	Silent	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:55918609T>C	ENST00000313608.8	-	3	273	c.228A>G	c.(226-228)tcA>tcG	p.S76S	MRPS23_ENST00000578444.1_Silent_p.S76S	NM_016070.3	NP_057154.2	Q9Y3D9	RT23_HUMAN	mitochondrial ribosomal protein S23	76					translation (GO:0006412)	intermediate filament cytoskeleton (GO:0045111)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.S76S(1)		endometrium(2)|large_intestine(1)|lung(2)	5	Breast(9;8.75e-08)					ACCCATACACTGAATAAAACT	0.338																																					p.S76S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A228G	17						.						99.0	101.0	100.0					17																	55918609		2203	4300	6503	53273608	SO:0001819	synonymous_variant	51649	exon3			AB061206	CCDS11598.1	17q22-q23	2012-09-13				ENSG00000181610		"""Mitochondrial ribosomal proteins / small subunits"""	14509	protein-coding gene	gene with protein product		611985				11279123	Standard	NM_016070		Approved	MRP-S23, CGI-138, HSPC329	uc002ivc.3	Q9Y3D9		ENST00000313608.8:c.228A>G	17.37:g.55918609T>C			53273608	NM_016070	B2R6V3|Q96Q24|Q9BWH8|Q9P053	Silent	SNP	ENST00000313608.8	37	CCDS11598.1																																																																																				0.338	MRPS23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443301.1	NM_016070	
MPO	4353	broad.mit.edu	37	17	56350895	56350895	+	Missense_Mutation	SNP	C	C	T	rs119469013		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:56350895C>T	ENST00000225275.3	-	9	1677	c.1501G>A	c.(1501-1503)Ggc>Agc	p.G501S	MPO_ENST00000340482.3_Missense_Mutation_p.G533S|MPO_ENST00000578493.1_5'Flank	NM_000250.1	NP_000241.1	P05164	PERM_HUMAN	myeloperoxidase	501					aging (GO:0007568)|defense response (GO:0006952)|defense response to fungus (GO:0050832)|hydrogen peroxide catabolic process (GO:0042744)|hypochlorous acid biosynthetic process (GO:0002149)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of apoptotic process (GO:0043066)|negative regulation of growth of symbiont in host (GO:0044130)|oxidation-reduction process (GO:0055114)|removal of superoxide radicals (GO:0019430)|respiratory burst involved in defense response (GO:0002679)|response to food (GO:0032094)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|response to oxidative stress (GO:0006979)|response to yeast (GO:0001878)	azurophil granule (GO:0042582)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|secretory granule (GO:0030141)	chromatin binding (GO:0003682)|heme binding (GO:0020037)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.G501S(1)		breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(13)|ovary(2)|pancreas(1)|skin(4)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	46					Aminosalicylic Acid(DB00233)|Bivalirudin(DB00006)|Calcipotriol(DB02300)|Carboplatin(DB00958)|Cefaclor(DB00833)|Cefdinir(DB00535)|Cisplatin(DB00515)|Cysteamine(DB00847)|Dapsone(DB00250)|Enoxaparin(DB01225)|Human Serum Albumin(DB00062)|L-Carnitine(DB00583)|Melatonin(DB01065)|Mesalazine(DB00244)|Nabumetone(DB00461)|Octreotide(DB00104)|Oxaliplatin(DB00526)|Propylthiouracil(DB00550)|Ticlopidine(DB00208)|Tolmetin(DB00500)	AGGGTGTGGCCGTAGCGGAAG	0.597																																					p.G501S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1501A	17	GRCh37	CM044668	MPO	M	rs119469013	.						262.0	213.0	230.0					17																	56350895		2203	4300	6503	53705894	SO:0001583	missense	4353	exon9				CCDS11604.1	17q21.3-q23	2014-09-17				ENSG00000005381	1.11.1.7		7218	protein-coding gene	gene with protein product		606989					Standard	NM_000250		Approved		uc002ivu.1	P05164		ENST00000225275.3:c.1501G>A	17.37:g.56350895C>T	ENSP00000225275:p.Gly501Ser		53705894	NM_000250	A1L4B8|Q14862|Q4PJH5|Q9UCL7	Missense_Mutation	SNP	ENST00000225275.3	37	CCDS11604.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.984047	0.93044	.	.	ENSG00000005381	ENST00000340482;ENST00000225275	T;T	0.77489	-1.1;-1.1	4.27	4.27	0.50696	.	0.112755	0.64402	D	0.000014	D	0.89560	0.6750	M	0.91300	3.195	0.46499	A	0.999071	D	0.89917	1.0	D	0.65773	0.938	D	0.92837	0.6285	9	0.87932	D	0	-16.606	15.8812	0.79207	0.0:1.0:0.0:0.0	.	501	P05164	PERM_HUMAN	S	533;501	ENSP00000344419:G533S;ENSP00000225275:G501S	ENSP00000225275:G501S	G	-	1	0	MPO	53705894	1.000000	0.71417	0.969000	0.41365	0.852000	0.48524	7.627000	0.83176	2.207000	0.71202	0.561000	0.74099	GGC		0.597	MPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443971.1		
BZRAP1	9256	broad.mit.edu	37	17	56386099	56386099	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:56386099C>T	ENST00000343736.4	-	22	4697	c.4534G>A	c.(4534-4536)Ggg>Agg	p.G1512R	BZRAP1_ENST00000268893.6_Missense_Mutation_p.G1452R|BZRAP1_ENST00000355701.3_Missense_Mutation_p.G1512R			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	1512						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)	p.G1512R(2)		cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CTGATGCCCCCGCTGCCCGCC	0.637																																					p.G1512R												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G4534A	17						.						18.0	20.0	19.0					17																	56386099		2192	4287	6479	53741098	SO:0001583	missense	9256	exon22			AB014512	CCDS11605.1, CCDS45742.1	17q22-q23	2014-01-09	2014-01-09						16831	protein-coding gene	gene with protein product		610764				9734811, 9915832	Standard	NM_004758		Approved	PRAX-1, KIAA0612, RIM-BP1, RIMBP1	uc002ivx.5	O95153		ENST00000343736.4:c.4534G>A	17.37:g.56386099C>T	ENSP00000345824:p.Gly1512Arg		53741098	NM_004758	O75111|Q8N5W3	Missense_Mutation	SNP	ENST00000343736.4	37	CCDS11605.1	.	.	.	.	.	.	.	.	.	.	C	10.75	1.437532	0.25900	.	.	ENSG00000005379	ENST00000355701;ENST00000343736;ENST00000268893	T;T;T	0.04275	3.66;3.66;3.68	5.42	1.76	0.24704	.	0.971136	0.08515	N	0.934281	T	0.07908	0.0198	L	0.29908	0.895	0.09310	N	0.999998	B;P;D	0.76494	0.013;0.816;0.999	B;B;P	0.61328	0.003;0.208;0.887	T	0.35500	-0.9786	10	0.11485	T	0.65	.	5.6651	0.17690	0.0:0.6275:0.1687:0.2038	.	1512;1452;1512	B7ZVZ7;O95153-2;O95153	.;.;RIMB1_HUMAN	R	1512;1512;1452	ENSP00000347929:G1512R;ENSP00000345824:G1512R;ENSP00000268893:G1452R	ENSP00000268893:G1452R	G	-	1	0	BZRAP1	53741098	0.498000	0.26075	0.963000	0.40424	0.958000	0.62258	1.412000	0.34714	0.635000	0.30488	0.462000	0.41574	GGG		0.637	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758	
TEX14	56155	broad.mit.edu	37	17	56649391	56649391	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:56649391T>C	ENST00000240361.8	-	25	3831	c.3746A>G	c.(3745-3747)gAa>gGa	p.E1249G	TEX14_ENST00000349033.5_Missense_Mutation_p.E1203G|TEX14_ENST00000389934.3_Missense_Mutation_p.E1243G			Q8IWB6	TEX14_HUMAN	testis expressed 14	1249					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)	p.E1203G(1)|p.E1249G(1)		breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TTGAATAAATTCTTGACTGTT	0.423																																					p.E1243G												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A3728G	17						.						100.0	99.0	100.0					17																	56649391		2203	4300	6503	54004390	SO:0001583	missense	56155	exon25			AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"""cancer/testis antigen 113"""	605792	"""testis expressed sequence 14"""			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.3746A>G	17.37:g.56649391T>C	ENSP00000240361:p.Glu1249Gly		54004390	NM_198393	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Missense_Mutation	SNP	ENST00000240361.8	37	CCDS56042.1	.	.	.	.	.	.	.	.	.	.	T	15.13	2.742434	0.49151	.	.	ENSG00000121101	ENST00000240361;ENST00000389934;ENST00000349033	T;T;T	0.23754	1.89;1.89;1.89	4.83	4.83	0.62350	.	0.090887	0.47455	D	0.000221	T	0.41259	0.1151	M	0.63843	1.955	0.23903	N	0.99651	D;D;D	0.59357	0.985;0.961;0.982	P;P;P	0.58331	0.691;0.691;0.837	T	0.28996	-1.0026	10	0.87932	D	0	-11.8968	10.7272	0.46074	0.0:0.0:0.0:1.0	.	1249;1203;1243	Q8IWB6;Q8IWB6-3;Q8IWB6-2	TEX14_HUMAN;.;.	G	1249;1243;1203	ENSP00000240361:E1249G;ENSP00000374584:E1243G;ENSP00000268910:E1203G	ENSP00000240361:E1249G	E	-	2	0	TEX14	54004390	0.984000	0.35163	0.641000	0.29422	0.357000	0.29423	3.619000	0.54196	2.039000	0.60335	0.459000	0.35465	GAA		0.423	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1		
CLTC	1213	broad.mit.edu	37	17	57733219	57733219	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:57733219G>A	ENST00000269122.3	+	6	1074	c.800G>A	c.(799-801)aGt>aAt	p.S267N	CLTC_ENST00000393043.1_Missense_Mutation_p.S267N|CLTC_ENST00000579456.1_Intron	NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	267	Globular terminal domain.|WD40-like repeat 6.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)	p.S267N(1)	CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					CTGTAGATCAGTGAAAAGCAT	0.323			T	"""ALK, TFE3"""	"""ALCL, renal """																																p.S267N			Dom	yes		17	17q11-qter	1213	"""clathrin, heavy polypeptide (Hc)"""		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G800A	17						.						111.0	104.0	106.0					17																	57733219		2203	4300	6503	55088001	SO:0001583	missense	1213	exon6			X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367			2092	protein-coding gene	gene with protein product		118955	"""clathrin, heavy polypeptide (Hc)"", ""clathrin, heavy chain"", ""clathrin, heavy polypeptide-like 2"""	CLTCL2		1765375, 7584026	Standard	NM_004859		Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.800G>A	17.37:g.57733219G>A	ENSP00000269122:p.Ser267Asn		55088001	NM_004859	D3DU00|Q6N0A0|Q86TF2	Missense_Mutation	SNP	ENST00000269122.3	37	CCDS32696.1	.	.	.	.	.	.	.	.	.	.	G	19.81	3.896947	0.72639	.	.	ENSG00000141367	ENST00000269122;ENST00000393043	T;T	0.26223	1.75;1.75	5.57	5.57	0.84162	Clathrin, heavy chain, propeller, N-terminal (1);Clathrin, heavy chain, linker/propeller domain (1);	0.000000	0.85682	D	0.000000	T	0.46908	0.1417	M	0.85373	2.75	0.80722	D	1	B;B	0.20459	0.015;0.045	B;B	0.37304	0.029;0.246	T	0.49360	-0.8948	10	0.59425	D	0.04	.	19.5594	0.95366	0.0:0.0:1.0:0.0	.	267;267	Q00610;Q00610-2	CLH1_HUMAN;.	N	267	ENSP00000269122:S267N;ENSP00000376763:S267N	ENSP00000269122:S267N	S	+	2	0	CLTC	55088001	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.869000	0.99810	2.613000	0.88420	0.585000	0.79938	AGT		0.323	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258859.1	NM_004859	
VMP1	81671	broad.mit.edu	37	17	57851133	57851133	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:57851133G>A	ENST00000262291.4	+	7	911	c.601G>A	c.(601-603)Gga>Aga	p.G201R	VMP1_ENST00000537567.1_Missense_Mutation_p.G67R|VMP1_ENST00000545362.1_Missense_Mutation_p.G145R|VMP1_ENST00000536180.1_Missense_Mutation_p.G104R|VMP1_ENST00000539763.1_Missense_Mutation_p.G9R	NM_030938.3	NP_112200.2	Q96GC9	VMP1_HUMAN	vacuole membrane protein 1	201					autophagy (GO:0006914)|cell junction assembly (GO:0034329)|embryo implantation (GO:0007566)|regulation of autophagy (GO:0010506)|single organismal cell-cell adhesion (GO:0016337)	autophagic vacuole membrane (GO:0000421)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|pre-autophagosomal structure (GO:0000407)		p.G201R(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|skin(2)	16						TACAGCAATCGGAGAGCTGCC	0.433																																					p.G201R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G601A	17						.						82.0	77.0	79.0					17																	57851133		2203	4300	6503	55205915	SO:0001583	missense	81671	exon7				CCDS11619.1	17q23.1	2014-05-20	2011-03-02	2011-03-02	ENSG00000062716	ENSG00000062716			29559	protein-coding gene	gene with protein product	"""ectopic P-granules autophagy protein 3 homolog (C. elegans)"", ""transport and golgi organization 5 homolog (Drosophila)"""	611753	"""transmembrane protein 49"""	TMEM49		11230166, 11785947	Standard	NM_030938		Approved	EPG3, TANGO5	uc002ixu.4	Q96GC9	OTTHUMG00000179882	ENST00000262291.4:c.601G>A	17.37:g.57851133G>A	ENSP00000262291:p.Gly201Arg		55205915	NM_030938	B4DVV9|Q9H0P4|Q9P089	Missense_Mutation	SNP	ENST00000262291.4	37	CCDS11619.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.164039	0.78339	.	.	ENSG00000062716	ENST00000262291;ENST00000537567;ENST00000539763;ENST00000536180;ENST00000545362	T;T;T	0.43688	0.94;0.94;0.94	6.04	5.08	0.68730	.	0.049251	0.85682	N	0.000000	T	0.73249	0.3563	M	0.93594	3.435	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.81747	-0.0791	10	0.87932	D	0	-8.1764	15.3322	0.74223	0.0665:0.0:0.9335:0.0	.	67;104;145;201	B4DED7;B4DGZ7;F5H2J3;Q96GC9	.;.;.;VMP1_HUMAN	R	201;67;9;104;145	ENSP00000262291:G201R;ENSP00000445130:G67R;ENSP00000444969:G104R	ENSP00000262291:G201R	G	+	1	0	VMP1	55205915	1.000000	0.71417	0.909000	0.35828	0.560000	0.35617	9.869000	0.99810	1.578000	0.49821	-0.253000	0.11424	GGA		0.433	VMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448793.1	NM_030938	
TBX4	9496	broad.mit.edu	37	17	59560350	59560350	+	Missense_Mutation	SNP	C	C	A	rs199727670		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:59560350C>A	ENST00000240335.1	+	8	1156	c.1111C>A	c.(1111-1113)Cct>Act	p.P371T	TBX4_ENST00000589449.1_3'UTR|TBX4_ENST00000393853.4_Missense_Mutation_p.P372T	NM_018488.2	NP_060958.2	P57082	TBX4_HUMAN	T-box 4	371					angiogenesis (GO:0001525)|embryonic limb morphogenesis (GO:0030326)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P371T(1)|p.P371S(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(15)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						CCGTTCCCCCCCTCCCTACGA	0.587																																					p.P371T												.	.	2	Substitution - Missense(2)	large_intestine(1)|skin(1)	c.C1111A	17						.																																			56915132	SO:0001583	missense	9496	exon8			AF188703	CCDS11629.1	17q21-q22	2005-10-11				ENSG00000121075		"""T-boxes"""	11603	protein-coding gene	gene with protein product		601719				10945475	Standard	NM_018488		Approved		uc002izi.3	P57082		ENST00000240335.1:c.1111C>A	17.37:g.59560350C>A	ENSP00000240335:p.Pro371Thr		56915132	NM_018488	A5PKU7|B2RMT1|B7ZLV3	Missense_Mutation	SNP	ENST00000240335.1	37	CCDS11629.1	.	.	.	.	.	.	.	.	.	.	C	17.14	3.314164	0.60414	.	.	ENSG00000121075	ENST00000393853;ENST00000240335	T;T	0.44881	0.91;0.91	5.51	5.51	0.81932	.	0.201931	0.33057	N	0.005336	T	0.48314	0.1493	N	0.14661	0.345	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.80764	0.994;0.994	T	0.45585	-0.9251	9	.	.	.	.	18.4117	0.90554	0.0:1.0:0.0:0.0	.	372;371	A5PKU7;P57082	.;TBX4_HUMAN	T	372;371	ENSP00000377435:P372T;ENSP00000240335:P371T	.	P	+	1	0	TBX4	56915132	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.621000	0.67743	2.590000	0.87494	0.655000	0.94253	CCT		0.587	TBX4-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449649.1	NM_018488	
INTS2	57508	broad.mit.edu	37	17	59974893	59974893	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:59974893C>T	ENST00000444766.3	-	11	1530	c.1455G>A	c.(1453-1455)atG>atA	p.M485I	INTS2_ENST00000251334.6_Missense_Mutation_p.M477I	NM_020748.2	NP_065799	Q9H0H0	INT2_HUMAN	integrator complex subunit 2	485					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|intracellular (GO:0005622)|membrane (GO:0016020)		p.M485I(1)		NS(1)|breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	38						TGTGAAAGTACATAGCCACCA	0.358																																					p.M485I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1455A	17						.						55.0	49.0	51.0					17																	59974893		1867	4105	5972	57329675	SO:0001583	missense	57508	exon11			AB033113	CCDS45750.1	17q23.2	2006-04-26	2006-03-15	2006-03-15		ENSG00000108506			29241	protein-coding gene	gene with protein product		611346	"""KIAA1287"""	KIAA1287		16239144	Standard	NR_026641		Approved	INT2	uc002izn.3	Q9H0H0		ENST00000444766.3:c.1455G>A	17.37:g.59974893C>T	ENSP00000414237:p.Met485Ile		57329675	NM_020748	Q9ULD3	Missense_Mutation	SNP	ENST00000444766.3	37	CCDS45750.1	.	.	.	.	.	.	.	.	.	.	C	9.956	1.221594	0.22457	.	.	ENSG00000108506	ENST00000444766;ENST00000251334	T	0.26957	1.7	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.24353	0.0590	N	0.03154	-0.405	0.80722	D	1	P	0.39044	0.656	P	0.51777	0.679	T	0.24083	-1.0170	9	.	.	.	-20.2342	20.3754	0.98918	0.0:1.0:0.0:0.0	.	485	Q9H0H0	INT2_HUMAN	I	485;484	ENSP00000414237:M485I	.	M	-	3	0	INTS2	57329675	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.294000	0.78760	2.894000	0.99253	0.591000	0.81541	ATG		0.358	INTS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000445368.1	NM_020748	
MED13	9969	broad.mit.edu	37	17	60140626	60140626	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:60140626A>G	ENST00000397786.2	-	2	179	c.103T>C	c.(103-105)Tgg>Cgg	p.W35R		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	35					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.W35R(1)		breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						GGGCCTTGCCATACATATTTT	0.398																																					p.W35R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T103C	17						.						113.0	113.0	113.0					17																	60140626		1857	4091	5948	57495408	SO:0001583	missense	9969	exon2			AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"""thyroid hormone receptor associated protein 1"""	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.103T>C	17.37:g.60140626A>G	ENSP00000380888:p.Trp35Arg		57495408	NM_005121	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	37	CCDS42366.1	.	.	.	.	.	.	.	.	.	.	A	16.50	3.141674	0.57044	.	.	ENSG00000108510	ENST00000397786;ENST00000262436	T	0.76448	-1.02	5.67	5.67	0.87782	Mediator complex, subunit Med13, N-terminal, metazoa/fungi (1);	0.000000	0.85682	D	0.000000	D	0.86522	0.5953	M	0.63428	1.95	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.87610	0.2503	10	0.66056	D	0.02	-12.9543	15.9024	0.79392	1.0:0.0:0.0:0.0	.	35	Q9UHV7	MED13_HUMAN	R	35	ENSP00000380888:W35R	ENSP00000262436:W35R	W	-	1	0	MED13	57495408	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.339000	0.96797	2.146000	0.66826	0.533000	0.62120	TGG		0.398	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121	
ACE	1636	broad.mit.edu	37	17	61574339	61574339	+	Silent	SNP	G	G	A	rs201117207	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:61574339G>A	ENST00000290866.4	+	24	3708	c.3684G>A	c.(3682-3684)ccG>ccA	p.P1228P	ACE_ENST00000577647.1_Silent_p.P654P|ACE_ENST00000290863.6_Silent_p.P654P|ACE_ENST00000413513.3_Silent_p.P613P|ACE_ENST00000421982.2_Silent_p.P433P|ACE_ENST00000490216.2_Silent_p.P654P|ACE_ENST00000428043.1_Intron	NM_000789.3	NP_000780.1	P12821	ACE_HUMAN	angiotensin I converting enzyme	1228	Peptidase M2 2.		P -> L (no effect on activity; increases secretion; rate of solubilization is 2.5- fold higher than wild-type). {ECO:0000269|PubMed:11551873, ECO:0000269|PubMed:14694062}.		angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|arachidonic acid secretion (GO:0050482)|blood vessel remodeling (GO:0001974)|cellular protein metabolic process (GO:0044267)|hematopoietic stem cell differentiation (GO:0060218)|hormone catabolic process (GO:0042447)|kidney development (GO:0001822)|mononuclear cell proliferation (GO:0032943)|peptide catabolic process (GO:0043171)|regulation of blood pressure (GO:0008217)|regulation of renal output by angiotensin (GO:0002019)|regulation of smooth muscle cell migration (GO:0014910)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|bradykinin receptor binding (GO:0031711)|carboxypeptidase activity (GO:0004180)|chloride ion binding (GO:0031404)|drug binding (GO:0008144)|endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|peptidyl-dipeptidase activity (GO:0008241)|zinc ion binding (GO:0008270)	p.P1228P(1)		autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(3)|lung(22)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	51					Benazepril(DB00542)|Candoxatril(DB00616)|Captopril(DB01197)|Cilazapril(DB01340)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)	ACTGGACGCCGAACTCCGGTA	0.677													g|||	12	0.00239617	0.0	0.0	5008	,	,		13975	0.001		0.0	False		,,,				2504	0.0112				p.P613P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1839A	17						.						25.0	26.0	26.0					17																	61574339		2202	4295	6497	58928071	SO:0001819	synonymous_variant	1636	exon12			J04144	CCDS11637.1, CCDS45755.1, CCDS54155.1	17q23.3	2013-06-12	2013-06-12		ENSG00000159640	ENSG00000159640	3.4.15.1	"""CD molecules"""	2707	protein-coding gene	gene with protein product	"""peptidyl-dipeptidase A"""	106180	"""angiotensin I converting enzyme (peptidyl-dipeptidase A) 1"""	DCP1		2554286, 10319862	Standard	NM_001178057		Approved	ACE1, CD143	uc002jau.2	P12821	OTTHUMG00000154927	ENST00000290866.4:c.3684G>A	17.37:g.61574339G>A			58928071	NM_001178057	B0LPF0|B4DXI3|E7EU16|P22966|Q53YX9|Q59GY8|Q7M4L4	Silent	SNP	ENST00000290866.4	37	CCDS11637.1																																																																																				0.677	ACE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337675.2		
POLG2	11232	broad.mit.edu	37	17	62493051	62493051	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:62493051C>A	ENST00000539111.2	-	1	103	c.36G>T	c.(34-36)aaG>aaT	p.K12N		NM_007215.3	NP_009146.2	Q9UHN1	DPOG2_HUMAN	polymerase (DNA directed), gamma 2, accessory subunit	12					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)	extracellular vesicular exosome (GO:0070062)|mitochondrial chromosome (GO:0000262)|mitochondrial nucleoid (GO:0042645)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)	p.K12N(1)		central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(4)|skin(2)|stomach(1)|urinary_tract(1)	15	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;4.97e-11)			ACCTGCAGACCTTATGGCAGG	0.577																																					p.K12N	Colon(3;18 21 435 17652 48887)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G36T	17						.						59.0	58.0	59.0					17																	62493051		2203	4300	6503	59923513	SO:0001583	missense	11232	exon1			U94703	CCDS32706.1	17q23.3	2012-05-18			ENSG00000256525	ENSG00000256525		"""DNA polymerases"""	9180	protein-coding gene	gene with protein product		604983				9153213	Standard	NM_007215		Approved	MTPOLB, HP55	uc002jei.3	Q9UHN1		ENST00000539111.2:c.36G>T	17.37:g.62493051C>A	ENSP00000442563:p.Lys12Asn		59923513	NM_007215	O00419|Q0IJ81|Q96GW2|Q9UK35|Q9UK94	Missense_Mutation	SNP	ENST00000539111.2	37	CCDS32706.1	.	.	.	.	.	.	.	.	.	.	C	17.58	3.425551	0.62733	.	.	ENSG00000256525	ENST00000539111	D	0.88818	-2.43	4.45	-1.18	0.09617	.	0.542075	0.17169	N	0.184364	T	0.80042	0.4551	L	0.34521	1.04	0.09310	N	1	B;B	0.26400	0.148;0.089	B;B	0.24155	0.051;0.038	T	0.69917	-0.5015	10	0.72032	D	0.01	-8.6659	7.9153	0.29814	0.0:0.6089:0.1668:0.2243	.	12;12	E5KS15;Q9UHN1	.;DPOG2_HUMAN	N	12	ENSP00000442563:K12N	ENSP00000442563:K12N	K	-	3	2	POLG2	59923513	0.000000	0.05858	0.021000	0.16686	0.813000	0.45954	-0.510000	0.06328	-0.099000	0.12263	-0.367000	0.07326	AAG		0.577	POLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443820.1	NM_007215	
ALOX12	239	broad.mit.edu	37	17	6899444	6899444	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:6899444G>T	ENST00000251535.6	+	1	61	c.8G>T	c.(7-9)cGc>cTc	p.R3L	RP11-589P10.7_ENST00000572547.1_RNA|AC027763.2_ENST00000399541.2_Intron|RP11-589P10.5_ENST00000573222.1_lincRNA	NM_000697.2	NP_000688.2	P18054	LOX12_HUMAN	arachidonate 12-lipoxygenase	3	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				aging (GO:0007568)|arachidonic acid metabolic process (GO:0019369)|cellular component movement (GO:0006928)|cellular response to lipid (GO:0071396)|establishment of skin barrier (GO:0061436)|fatty acid oxidation (GO:0019395)|hepoxilin biosynthetic process (GO:0051122)|hepoxilin metabolic process (GO:0051121)|leukotriene A4 metabolic process (GO:1901751)|linoleic acid metabolic process (GO:0043651)|lipoxin A4 biosynthetic process (GO:2001303)|lipoxin B4 biosynthetic process (GO:2001306)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of platelet aggregation (GO:0090331)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of gene expression (GO:0010628)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of vasodilation (GO:0045909)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|superoxide anion generation (GO:0042554)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|sarcolemma (GO:0042383)	arachidonate 12-lipoxygenase activity (GO:0004052)|hepoxilin A3 synthase activity (GO:0051120)|hepoxilin-epoxide hydrolase activity (GO:0047977)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)	p.R3L(1)		breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(4)|ovary(1)|prostate(3)|urinary_tract(1)	19						GCCATGGGCCGCTACCGCATC	0.741																																					p.R3L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G8T	17						.						3.0	4.0	3.0					17																	6899444		1604	3112	4716	6840168	SO:0001583	missense	239	exon1			M35418	CCDS11084.1	17p13.1	2010-01-14			ENSG00000108839	ENSG00000108839	1.13.11.31	"""Arachidonate lipoxygenases"""	429	protein-coding gene	gene with protein product	"""platelet 12-LOX"""	152391				1570320	Standard	NM_000697		Approved	12S-LOX	uc002gdx.4	P18054	OTTHUMG00000102088	ENST00000251535.6:c.8G>T	17.37:g.6899444G>T	ENSP00000251535:p.Arg3Leu		6840168	NM_000697	O95569|Q6ISF8|Q9UQM4	Missense_Mutation	SNP	ENST00000251535.6	37	CCDS11084.1	.	.	.	.	.	.	.	.	.	.	G	16.21	3.057408	0.55325	.	.	ENSG00000108839	ENST00000251535	T	0.70045	-0.45	4.89	4.89	0.63831	Lipoxygenase, LH2 (4);Lipase/lipooxygenase, PLAT/LH2 (1);	0.482173	0.21032	N	0.081323	T	0.50377	0.1612	N	0.20685	0.6	0.40685	D	0.982348	B	0.02656	0.0	B	0.04013	0.001	T	0.43653	-0.9378	10	0.22706	T	0.39	-16.0961	13.7403	0.62845	0.0:0.0:1.0:0.0	.	3	P18054	LOX12_HUMAN	L	3	ENSP00000251535:R3L	ENSP00000251535:R3L	R	+	2	0	ALOX12	6840168	0.978000	0.34361	1.000000	0.80357	0.946000	0.59487	0.628000	0.24522	2.709000	0.92574	0.591000	0.81541	CGC		0.741	ALOX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219922.2		
ASGR1	432	broad.mit.edu	37	17	7077519	7077519	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:7077519C>T	ENST00000269299.3	-	7	931	c.532G>A	c.(532-534)Gcc>Acc	p.A178T	ASGR1_ENST00000380920.4_Missense_Mutation_p.A77T|ASGR1_ENST00000572879.1_Missense_Mutation_p.A38T|ASGR1_ENST00000574388.1_Missense_Mutation_p.A139T	NM_001197216.2|NM_001671.4	NP_001184145.1|NP_001662.1	P07306	ASGR1_HUMAN	asialoglycoprotein receptor 1	178	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cellular response to extracellular stimulus (GO:0031668)|receptor-mediated endocytosis (GO:0006898)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	asialoglycoprotein receptor activity (GO:0004873)|carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)	p.A178T(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|skin(1)|urinary_tract(1)	10						TAGTTGTCGGCGTCAGCCCAG	0.682																																					p.A139T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G415A	17						.						85.0	85.0	85.0					17																	7077519		2203	4300	6503	7018243	SO:0001583	missense	432	exon6				CCDS11089.1, CCDS56017.1	17p13-p11	2011-08-30			ENSG00000141505	ENSG00000141505		"""C-type lectin domain containing"""	742	protein-coding gene	gene with protein product		108360					Standard	NM_001671		Approved	CLEC4H1	uc002ges.4	P07306	OTTHUMG00000102159	ENST00000269299.3:c.532G>A	17.37:g.7077519C>T	ENSP00000269299:p.Ala178Thr		7018243	NM_001197216	I3L1X1	Missense_Mutation	SNP	ENST00000269299.3	37	CCDS11089.1	.	.	.	.	.	.	.	.	.	.	C	17.28	3.348406	0.61183	.	.	ENSG00000141505	ENST00000269299;ENST00000380920	T	0.53857	0.6	4.69	4.69	0.59074	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.000000	0.53938	D	0.000054	D	0.84817	0.5556	H	0.99697	4.71	0.39812	D	0.972727	D	0.89917	1.0	D	0.97110	1.0	D	0.91867	0.5504	10	0.87932	D	0	.	15.4907	0.75602	0.0:1.0:0.0:0.0	.	178	P07306	ASGR1_HUMAN	T	178;139	ENSP00000269299:A178T	ENSP00000269299:A178T	A	-	1	0	ASGR1	7018243	0.964000	0.33143	0.644000	0.29465	0.003000	0.03518	1.900000	0.39828	2.602000	0.87976	0.205000	0.17691	GCC		0.682	ASGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220004.3	NM_001671	
ABCA8	10351	broad.mit.edu	37	17	66873753	66873753	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:66873753G>A	ENST00000269080.2	-	31	4123	c.3986C>T	c.(3985-3987)gCg>gTg	p.A1329V	ABCA8_ENST00000430352.2_Missense_Mutation_p.A1369V|ABCA8_ENST00000586539.1_Missense_Mutation_p.A1369V	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	1329	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)	p.A1329V(1)		breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					GGGCCACAGCGCGTTCTCCTG	0.597																																					p.A1329V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3986T	17						.						140.0	119.0	126.0					17																	66873753		2203	4300	6503	64385348	SO:0001583	missense	10351	exon31			AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"""ATP binding cassette transporters / subfamily A"""	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.3986C>T	17.37:g.66873753G>A	ENSP00000269080:p.Ala1329Val		64385348	NM_007168	A1L3U3|C9JQE6|Q86WW0	Missense_Mutation	SNP	ENST00000269080.2	37	CCDS11680.1	.	.	.	.	.	.	.	.	.	.	G	9.177	1.022563	0.19433	.	.	ENSG00000141338	ENST00000269080;ENST00000430352	D;D	0.93763	-3.28;-3.28	4.34	-0.109	0.13584	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.455820	0.18056	N	0.153094	D	0.85004	0.5598	N	0.17723	0.515	0.25438	N	0.988124	B;B;B	0.14805	0.011;0.004;0.011	B;B;B	0.14023	0.01;0.004;0.006	T	0.73707	-0.3898	10	0.41790	T	0.15	.	8.385	0.32494	0.3401:0.0:0.6599:0.0	.	1369;1369;1329	A1L3U3;C9JQE6;O94911	.;.;ABCA8_HUMAN	V	1329;1369	ENSP00000269080:A1329V;ENSP00000402814:A1369V	ENSP00000269080:A1329V	A	-	2	0	ABCA8	64385348	0.064000	0.20934	0.007000	0.13788	0.521000	0.34408	1.858000	0.39408	-0.051000	0.13334	0.637000	0.83480	GCG		0.597	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168	
DVL2	1856	broad.mit.edu	37	17	7132748	7132748	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:7132748C>T	ENST00000005340.5	-	7	1048	c.766G>A	c.(766-768)Gtc>Atc	p.V256I	DVL2_ENST00000574642.1_5'UTR|DVL2_ENST00000575458.1_Missense_Mutation_p.V250I	NM_004422.2	NP_004413.1	O14641	DVL2_HUMAN	dishevelled segment polarity protein 2	256					canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration in hindbrain (GO:0021535)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|convergent extension involved in neural plate elongation (GO:0022007)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hippo signaling (GO:0035329)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|segment specification (GO:0007379)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|clathrin-coated endocytic vesicle (GO:0045334)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|identical protein binding (GO:0042802)	p.V256I(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(7)|skin(1)	25						GAATCTGTGACGCTGCTGAAG	0.582																																					p.V256I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G766A	17						.						150.0	140.0	144.0					17																	7132748		2203	4300	6503	7073472	SO:0001583	missense	1856	exon7			BC014844	CCDS11091.1	17p13.1	2013-05-22	2013-05-22		ENSG00000004975	ENSG00000004975		"""Dishevelled homologs"""	3086	protein-coding gene	gene with protein product		602151	"""dishevelled 2 (homologous to Drosophila dsh)"", ""dishevelled, dsh homolog 2 (Drosophila)"""			8662242	Standard	NM_004422		Approved		uc002gez.1	O14641	OTTHUMG00000102155	ENST00000005340.5:c.766G>A	17.37:g.7132748C>T	ENSP00000005340:p.Val256Ile		7073472	NM_004422	D3DTN3|Q53XM0	Missense_Mutation	SNP	ENST00000005340.5	37	CCDS11091.1	.	.	.	.	.	.	.	.	.	.	C	0.023	-1.403625	0.01165	.	.	ENSG00000004975	ENST00000005340	T	0.17213	2.29	5.07	5.07	0.68467	PDZ/DHR/GLGF (1);	0.062552	0.64402	D	0.000008	T	0.04634	0.0126	N	0.00504	-1.425	0.47094	D	0.999312	B;B	0.23316	0.083;0.083	B;B	0.17979	0.02;0.02	T	0.34054	-0.9844	10	0.02654	T	1	-21.0413	15.9192	0.79547	0.0:1.0:0.0:0.0	.	250;256	B4DLQ0;O14641	.;DVL2_HUMAN	I	256	ENSP00000005340:V256I	ENSP00000005340:V256I	V	-	1	0	DVL2	7073472	0.875000	0.30112	0.968000	0.41197	0.026000	0.11368	1.749000	0.38319	2.368000	0.80403	0.462000	0.41574	GTC		0.582	DVL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219999.2	NM_004422	
HID1	283987	broad.mit.edu	37	17	72949111	72949111	+	Missense_Mutation	SNP	G	G	A	rs115082567		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:72949111G>A	ENST00000425042.2	-	16	2119	c.2042C>T	c.(2041-2043)aCg>aTg	p.T681M		NM_030630.2	NP_085133.1	Q8IV36	HID1_HUMAN	HID1 domain containing	681					intracellular protein transport (GO:0006886)|response to brefeldin A (GO:0031001)	cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi medial cisterna (GO:0005797)|Golgi trans cisterna (GO:0000138)		p.T681M(1)									CCACTCTGGCGTTGGGCTCCA	0.692													G|||	1	0.000199681	0.0008	0.0	5008	,	,		14547	0.0		0.0	False		,,,				2504	0.0				p.T681M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2042T	17						.						25.0	22.0	23.0					17																	72949111		2202	4295	6497	70460706	SO:0001583	missense	283987	exon16				CCDS32726.1	17q25.1	2012-10-10	2012-10-10	2012-10-10	ENSG00000167861	ENSG00000167861			15736	protein-coding gene	gene with protein product	"""downregulated in multiple cancer 1"""	605752	"""chromosome 17 open reading frame 28"""	C17orf28		11281419, 21337012	Standard	NM_030630		Approved	DMC1, HID-1	uc002jmj.4	Q8IV36	OTTHUMG00000166490	ENST00000425042.2:c.2042C>T	17.37:g.72949111G>A	ENSP00000413520:p.Thr681Met		70460706	NM_030630	Q8N5L6|Q8TE83|Q9NT34	Missense_Mutation	SNP	ENST00000425042.2	37	CCDS32726.1	.	.	.	.	.	.	.	.	.	.	G	14.13	2.443168	0.43429	.	.	ENSG00000167861	ENST00000525426;ENST00000425042;ENST00000318565	.	.	.	5.09	5.09	0.68999	.	0.111406	0.64402	D	0.000012	D	0.84042	0.5385	M	0.86268	2.805	0.51233	D	0.999915	D	0.89917	1.0	D	0.80764	0.994	D	0.86973	0.2099	9	0.87932	D	0	-4.0576	18.4895	0.90842	0.0:0.0:1.0:0.0	.	681	Q8IV36	CQ028_HUMAN	M	453;681;453	.	ENSP00000317795:T453M	T	-	2	0	C17orf28	70460706	1.000000	0.71417	0.428000	0.26697	0.075000	0.17131	4.678000	0.61641	2.372000	0.80975	0.561000	0.74099	ACG		0.692	HID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390011.2	NM_030630	
GGA3	23163	broad.mit.edu	37	17	73235525	73235525	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:73235525C>A	ENST00000245541.6	-	14	1927	c.1711G>T	c.(1711-1713)Ggc>Tgc	p.G571C	GGA3_ENST00000538886.1_Missense_Mutation_p.G449C|GGA3_ENST00000351904.7_Missense_Mutation_p.G538C|GGA3_ENST00000578348.1_Missense_Mutation_p.G449C|GGA3_ENST00000582717.1_Missense_Mutation_p.G499C|GGA3_ENST00000582486.1_Missense_Mutation_p.G499C	NM_138619.2	NP_619525.1	Q9NZ52	GGA3_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 3	571	Unstructured hinge.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|endosome (GO:0005768)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)	p.G571C(1)		breast(2)|endometrium(3)|large_intestine(4)|liver(1)|lung(4)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	20			all cancers(21;2.39e-06)|Epithelial(20;2.38e-05)			GGGGGGCTGCCCTGGGACTGG	0.677											OREG0024729	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G538C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1612T	17						.						19.0	22.0	21.0					17																	73235525		2203	4300	6503	70747120	SO:0001583	missense	23163	exon13			AF190864	CCDS11716.1, CCDS11717.1, CCDS54164.1, CCDS58597.1	17q25	2010-02-12	2010-02-12			ENSG00000125447			17079	protein-coding gene	gene with protein product		606006				10747089, 10749927	Standard	NR_033345		Approved	KIAA0154	uc002jni.2	Q9NZ52		ENST00000245541.6:c.1711G>T	17.37:g.73235525C>A	ENSP00000245541:p.Gly571Cys	1143	70747120	NM_014001	B7Z7E2|B7Z7M9|J3KRN0|Q15017|Q6IS16|Q9UJY3	Missense_Mutation	SNP	ENST00000245541.6	37	CCDS11717.1	.	.	.	.	.	.	.	.	.	.	C	10.73	1.431457	0.25813	.	.	ENSG00000125447	ENST00000245541;ENST00000351904;ENST00000537584;ENST00000538886	T;T	0.48836	2.13;0.8	5.32	4.35	0.52113	.	0.160296	0.56097	D	0.000025	T	0.39886	0.1095	M	0.61703	1.905	0.80722	D	1	P;B;B	0.42357	0.777;0.246;0.062	B;B;B	0.30646	0.118;0.051;0.023	T	0.44574	-0.9319	10	0.51188	T	0.08	-19.2967	12.1502	0.54046	0.0:0.9216:0.0:0.0784	.	449;538;571	B7Z7E2;Q9NZ52-2;Q9NZ52	.;.;GGA3_HUMAN	C	571;538;499;449	ENSP00000245541:G571C;ENSP00000326575:G538C	ENSP00000245541:G571C	G	-	1	0	GGA3	70747120	0.465000	0.25815	0.998000	0.56505	0.716000	0.41182	0.872000	0.28037	1.482000	0.48325	0.563000	0.77884	GGC		0.677	GGA3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446645.1	NM_138619	
RECQL5	9400	broad.mit.edu	37	17	73626357	73626357	+	Splice_Site	SNP	T	T	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:73626357T>G	ENST00000317905.5	-	14	1878	c.1719A>C	c.(1717-1719)gaA>gaC	p.E573D	RECQL5_ENST00000423245.2_Splice_Site_p.E546D|RECQL5_ENST00000443199.2_5'UTR	NM_004259.6	NP_004250.4	O94762	RECQ5_HUMAN	RecQ protein-like 5	573	Interaction with POLR2A.				chromosome separation (GO:0051304)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|mitotic nuclear division (GO:0007067)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA helicase activity (GO:0003678)|nucleic acid binding (GO:0003676)|RNA polymerase II core binding (GO:0000993)	p.E546D(1)		breast(1)|cervix(3)|endometrium(3)|kidney(7)|large_intestine(7)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	36	all_cancers(13;2.73e-08)|Breast(9;6.04e-09)|all_epithelial(9;6.79e-09)		all cancers(21;1.15e-06)|Epithelial(20;2.19e-06)|Lung(188;0.101)|LUSC - Lung squamous cell carcinoma(166;0.112)			GGAGGTCAGCTCTGTGGGTGC	0.632								Other identified genes with known or suspected DNA repair function																													p.E573D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1719C	17						.						34.0	36.0	35.0					17																	73626357		2122	4237	6359	71137952	SO:0001630	splice_region_variant	9400	exon14			AB006533	CCDS32735.1, CCDS42380.1, CCDS45777.1	17q25	2014-03-07	2014-03-07	2014-03-07	ENSG00000108469	ENSG00000108469			9950	protein-coding gene	gene with protein product	"""RecQ protein 5"""	603781				9878247	Standard	NM_004259		Approved	RecQ5, FLJ90603	uc010dgl.3	O94762		ENST00000317905.5:c.1719-1A>C	17.37:g.73626357T>G			71137952	NM_004259	Q9H0B1|Q9P1W7|Q9UNC8	Missense_Mutation	SNP	ENST00000317905.5	37	CCDS42380.1	.	.	.	.	.	.	.	.	.	.	T	13.03	2.116704	0.37339	.	.	ENSG00000108469	ENST00000443199;ENST00000423245;ENST00000317905	T	0.57436	0.4	5.39	1.43	0.22495	.	0.778654	0.12257	N	0.485044	T	0.25158	0.0611	N	0.08118	0	0.80722	D	1	B;B	0.17038	0.008;0.02	B;B	0.17433	0.011;0.018	T	0.09773	-1.0659	10	0.11794	T	0.64	.	4.1894	0.10414	0.0:0.2424:0.1789:0.5787	.	573;546	O94762;Q6P4G0	RECQ5_HUMAN;.	D	168;573;573	ENSP00000317636:E573D	ENSP00000317636:E573D	E	-	3	2	RECQL5	71137952	1.000000	0.71417	0.846000	0.33378	0.930000	0.56654	1.824000	0.39072	0.336000	0.23639	-0.290000	0.09829	GAA		0.632	RECQL5-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448207.1	NM_004259	Missense_Mutation
GALK1	2584	broad.mit.edu	37	17	73760039	73760039	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:73760039C>T	ENST00000588479.1	-	2	868	c.294G>A	c.(292-294)tcG>tcA	p.S98S	GALK1_ENST00000437911.1_Silent_p.S128S|GALK1_ENST00000225614.2_Silent_p.S98S			P51570	GALK1_HUMAN	galactokinase 1	98					carbohydrate metabolic process (GO:0005975)|galactitol metabolic process (GO:0019402)|galactose catabolic process (GO:0019388)|galactose metabolic process (GO:0006012)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)|galactokinase activity (GO:0004335)|galactose binding (GO:0005534)	p.S98S(1)		endometrium(2)|large_intestine(1)|lung(1)|prostate(1)	5	all_cancers(13;1.5e-07)		all cancers(21;1.03e-06)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			CAGGCTCCAGCGAGCGCTGGG	0.632																																					p.S98S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G294A	17						.						37.0	33.0	34.0					17																	73760039		2203	4300	6503	71271634	SO:0001819	synonymous_variant	2584	exon2				CCDS11728.1	17q25.1	2013-09-19			ENSG00000108479	ENSG00000108479	2.7.1.6		4118	protein-coding gene	gene with protein product		604313		GALK		7670469	Standard	NM_000154		Approved		uc002jpk.3	P51570	OTTHUMG00000179832	ENST00000588479.1:c.294G>A	17.37:g.73760039C>T			71271634	NM_000154	B2RC07|B4E1G6	Silent	SNP	ENST00000588479.1	37	CCDS11728.1																																																																																				0.632	GALK1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448430.1		
UNC13D	201294	broad.mit.edu	37	17	73836307	73836307	+	Splice_Site	SNP	C	C	T	rs139155193		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:73836307C>T	ENST00000207549.4	-	10	1236	c.857G>A	c.(856-858)cGg>cAg	p.R286Q	UNC13D_ENST00000412096.2_Splice_Site_p.R286Q|UNC13D_ENST00000587504.1_5'UTR	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	286	Interaction with RAB27A.				defense response to virus (GO:0051607)|germinal center formation (GO:0002467)|granuloma formation (GO:0002432)|natural killer cell degranulation (GO:0043320)|phagocytosis (GO:0006909)|positive regulation of exocytosis (GO:0045921)|regulation of mast cell degranulation (GO:0043304)	endosome (GO:0005768)|exocytic vesicle (GO:0070382)|lysosome (GO:0005764)|membrane (GO:0016020)		p.R286Q(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)			CCGACCTACCCGCTTATGGAT	0.657									Familial Hemophagocytic Lymphohistiocytosis																												p.R286Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G857A	17						.	C	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	49.0	44.0	46.0		857	3.6	1.0	17	dbSNP_134	46	0,8600		0,0,4300	no	missense-near-splice	UNC13D	NM_199242.2	43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	286/1091	73836307	1,13005	2203	4300	6503	71347902	SO:0001630	splice_region_variant	201294	exon10	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	AK024474	CCDS11730.1	17q25.3	2014-09-17				ENSG00000092929			23147	protein-coding gene	gene with protein product		608897					Standard	NM_199242		Approved	Munc13-4	uc002jpp.3	Q70J99		ENST00000207549.4:c.858+1G>A	17.37:g.73836307C>T			71347902	NM_199242	B4DWG9|Q9H7K5	Missense_Mutation	SNP	ENST00000207549.4	37	CCDS11730.1	.	.	.	.	.	.	.	.	.	.	C	2.738	-0.262869	0.05754	2.27E-4	0.0	ENSG00000092929	ENST00000207549;ENST00000412096;ENST00000448606	T;T	0.68624	-0.33;-0.34	4.56	3.59	0.41128	.	0.398279	0.23861	N	0.043852	T	0.31857	0.0810	N	0.03324	-0.35	0.31068	N	0.713379	P;P	0.51351	0.944;0.743	B;B	0.37451	0.25;0.033	T	0.30909	-0.9962	10	0.12766	T	0.61	-0.0617	5.2099	0.15310	0.0:0.6402:0.0:0.3598	.	286;286	B4DTQ6;Q70J99	.;UN13D_HUMAN	Q	286	ENSP00000207549:R286Q;ENSP00000388093:R286Q	ENSP00000207549:R286Q	R	-	2	0	UNC13D	71347902	0.977000	0.34250	1.000000	0.80357	0.439000	0.31926	0.864000	0.27926	1.134000	0.42165	0.563000	0.77884	CGG		0.657	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950	Missense_Mutation
FBF1	85302	broad.mit.edu	37	17	73914246	73914246	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:73914246G>A	ENST00000586717.1	-	20	2474	c.2201C>T	c.(2200-2202)aCg>aTg	p.T734M	FBF1_ENST00000389570.4_Missense_Mutation_p.T734M|FBF1_ENST00000319129.5_Missense_Mutation_p.T733M			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	734					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)		p.T734M(1)		large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	4						CACATACCGCGTGTGGGAGGT	0.652																																					p.T733M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2198T	17						.						33.0	41.0	38.0					17																	73914246		2098	4222	6320	71425841	SO:0001583	missense	85302	exon20			AK074045	CCDS45779.1	17q25.3	2011-04-21			ENSG00000188878	ENSG00000188878			24674	protein-coding gene	gene with protein product	"""albatross"""					11347906	Standard	NM_001080542		Approved	FLJ00103, FBF-1, KIAA1863, ALB	uc002jqc.3	Q8TES7		ENST00000586717.1:c.2201C>T	17.37:g.73914246G>A	ENSP00000465132:p.Thr734Met		71425841	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000586717.1	37		.	.	.	.	.	.	.	.	.	.	G	19.18	3.776826	0.70107	.	.	ENSG00000188878	ENST00000337792;ENST00000389570;ENST00000319129;ENST00000427433	T;T	0.23950	1.88;1.88	5.19	5.19	0.71726	.	.	.	.	.	T	0.53530	0.1802	M	0.74258	2.255	0.58432	D	0.999994	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.999	T	0.57271	-0.7840	9	0.66056	D	0.02	.	18.304	0.90174	0.0:0.0:1.0:0.0	.	748;734;733	Q8TES7-6;Q8TES7;A6NLR5	.;FBF1_HUMAN;.	M	734;734;733;747	ENSP00000374221:T734M;ENSP00000324292:T733M	ENSP00000324292:T733M	T	-	2	0	FBF1	71425841	1.000000	0.71417	0.892000	0.35008	0.110000	0.19582	8.866000	0.92307	2.415000	0.81967	0.563000	0.77884	ACG		0.652	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542	
MPDU1	9526	broad.mit.edu	37	17	7487223	7487223	+	Missense_Mutation	SNP	C	C	T	rs148935720	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:7487223C>T	ENST00000250124.6	+	1	259	c.43C>T	c.(43-45)Ccg>Tcg	p.P15S	MPDU1_ENST00000396501.4_Missense_Mutation_p.P15S|MPDU1_ENST00000423172.2_Missense_Mutation_p.P15S|AC113189.5_ENST00000573187.1_RNA|AC113189.5_ENST00000572046.1_RNA|AC113189.5_ENST00000417897.1_RNA|MPDU1_ENST00000582151.1_Missense_Mutation_p.P15S|AC113189.5_ENST00000415124.1_RNA	NM_004870.3	NP_004861.2	O75352	MPU1_HUMAN	mannose-P-dolichol utilization defect 1	15					dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|oligosaccharide biosynthetic process (GO:0009312)|protein folding (GO:0006457)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)		p.P15S(1)		central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(1)|lung(1)	7						GCTGCTCGTGCCGATTCTTTT	0.532													C|||	11	0.00219649	0.0083	0.0	5008	,	,		15403	0.0		0.0	False		,,,				2504	0.0				p.P15S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C43T	17						.	C	SER/PRO	19,4387	27.2+/-55.0	0,19,2184	145.0	149.0	147.0		43	5.2	1.0	17	dbSNP_134	147	0,8600		0,0,4300	yes	missense	MPDU1	NM_004870.3	74	0,19,6484	TT,TC,CC		0.0,0.4312,0.1461	benign	15/248	7487223	19,12987	2203	4300	6503	7427947	SO:0001583	missense	9526	exon1			AF038961	CCDS11115.1	17p13.1-p12	2008-07-03			ENSG00000129255	ENSG00000129255			7207	protein-coding gene	gene with protein product		604041				8663248, 9653160, 11733564	Standard	NM_004870		Approved	SL15, Lec35, PQLC5, CDGIf	uc002ghw.3	O75352	OTTHUMG00000108147	ENST00000250124.6:c.43C>T	17.37:g.7487223C>T	ENSP00000250124:p.Pro15Ser		7427947	NM_004870	B3KQP1|B4DT74|Q9BUU8	Missense_Mutation	SNP	ENST00000250124.6	37	CCDS11115.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	14.20	2.464332	0.43736	0.004312	0.0	ENSG00000129255	ENST00000250124;ENST00000396501;ENST00000301597;ENST00000423172;ENST00000359822	T;D;D;T	0.88124	-0.66;-2.34;-2.02;-1.0	5.25	5.25	0.73442	.	0.298622	0.36034	N	0.002823	T	0.81322	0.4798	L	0.39898	1.24	0.32584	N	0.528021	D;B;B	0.56968	0.978;0.158;0.012	P;B;B	0.50537	0.643;0.046;0.003	T	0.82514	-0.0419	10	0.19590	T	0.45	-31.2751	14.5347	0.67953	0.0:1.0:0.0:0.0	.	15;15;15	B4DT74;B4DLH7;O75352	.;.;MPU1_HUMAN	S	15	ENSP00000250124:P15S;ENSP00000379758:P15S;ENSP00000414071:P15S;ENSP00000352876:P15S	ENSP00000250124:P15S	P	+	1	0	MPDU1	7427947	0.976000	0.34144	1.000000	0.80357	0.911000	0.54048	2.771000	0.47670	2.894000	0.99253	0.655000	0.94253	CCG		0.532	MPDU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226950.4		
FXR2	9513	broad.mit.edu	37	17	7496122	7496122	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:7496122delG	ENST00000250113.7	-	14	1953	c.1619delC	c.(1618-1620)ccafs	p.P540fs	SOX15_ENST00000538513.2_5'Flank|SOX15_ENST00000250055.2_5'Flank|SOX15_ENST00000570788.1_5'Flank|FXR2_ENST00000573057.1_5'Flank	NM_004860.3	NP_004851.2	P51116	FXR2_HUMAN	fragile X mental retardation, autosomal homolog 2	540						cytoplasm (GO:0005737)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.P540fs*32(1)|p.A541fs*14(1)		NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)	26				READ - Rectum adenocarcinoma(115;0.17)		GGCACTTGCTGGGGGGGGTTC	0.612																																					p.P540fs												.	.	2	Deletion - Frameshift(1)|Insertion - Frameshift(1)	large_intestine(2)	c.1619delC	17						.			40,24,3406		1,0,38,3,18,1675	20.0	22.0	21.0			4.5	1.0	17		21	44,58,7634		1,0,42,4,50,3771	no	codingComplex	FXR2	NM_004860.3		2,0,80,7,68,5446	A1A1,A1A2,A1R,A2A2,A2R,RR		1.3185,1.8444,1.4813			7496122	84,82,11040	1812	4065	5877	7436847	SO:0001589	frameshift_variant	9513	exon14			U31501	CCDS45604.1	17p13.3	2014-09-17				ENSG00000129245			4024	protein-coding gene	gene with protein product		605339		FMR1L2		7489725, 9259278	Standard	NM_004860		Approved		uc002gia.2	P51116		ENST00000250113.7:c.1619delC	17.37:g.7496122delG	ENSP00000250113:p.Pro540fs		7436847	NM_004860	B2R9M2|D3DTQ1|Q86V09|Q8WUM2	Frame_Shift_Del	DEL	ENST00000250113.7	37	CCDS45604.1																																																																																				0.612	FXR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441084.1		
UBB	7314	broad.mit.edu	37	17	16285785	16285785	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:16285785delC	ENST00000395837.1	+	2	745	c.564delC	c.(562-564)atcfs	p.I188fs	UBB_ENST00000395839.1_Frame_Shift_Del_p.I188fs|UBB_ENST00000535788.1_Frame_Shift_Del_p.I112fs|UBB_ENST00000578649.1_3'UTR|UBB_ENST00000302182.3_Frame_Shift_Del_p.I188fs|RP11-138I1.4_ENST00000583934.1_RNA	NM_001281718.1|NM_001281720.1	NP_001268647.1|NP_001268649.1	P0CG47	UBB_HUMAN	ubiquitin B	188	Ubiquitin-like 3. {ECO:0000255|PROSITE- ProRule:PRU00214}.		GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFV KTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA GKQLEDGRTLSDYNIQKESTLHLVLRLRGGC -> YADLRE DPDRQDHHPGSGAQ (in UBB(+1); loss of polyubiquitination; impairs the ubiquitin-proteasome pathway; refractory to disassembly by DUBs; slow degradation by UCHL3).		activation of MAPK activity (GO:0000187)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)		p.D191fs*35(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		AAGAAGGCATCCCCCCCGACC	0.547																																					p.I188fs	Melanoma(163;1126 3406 34901)											.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.564delC	17						.																																			16226510	SO:0001589	frameshift_variant	7314	exon2				CCDS11177.1	17p12-p11.2	2010-11-25			ENSG00000170315	ENSG00000170315			12463	protein-coding gene	gene with protein product	"""polyubiquitin B"""	191339				2154095	Standard	NM_018955		Approved	MGC8385, FLJ25987	uc002gpx.3	P0CG47	OTTHUMG00000058987	ENST00000395837.1:c.564delC	17.37:g.16285785delC	ENSP00000379178:p.Ile188fs		16226510	NM_018955	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Frame_Shift_Del	DEL	ENST00000395837.1	37	CCDS11177.1																																																																																				0.547	UBB-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130459.1	NM_018955	
EXOC7	23265	broad.mit.edu	37	17	74097830	74097830	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr17:74097830G>A	ENST00000335146.7	-	3	294	c.241C>T	c.(241-243)Ctg>Ttg	p.L81L	EXOC7_ENST00000589210.1_Silent_p.L81L|EXOC7_ENST00000406660.3_Silent_p.L81L|EXOC7_ENST00000607838.1_Silent_p.L81L|EXOC7_ENST00000411744.2_Silent_p.L81L|EXOC7_ENST00000332065.5_Silent_p.L81L|EXOC7_ENST00000467929.2_Silent_p.L40L|EXOC7_ENST00000405575.4_Silent_p.L81L			Q9UPT5	EXOC7_HUMAN	exocyst complex component 7	81					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)		p.L81L(1)		NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	14			LUSC - Lung squamous cell carcinoma(166;0.187)			AGGCAGGACAGCGTCTTCTCA	0.537																																					p.L81L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C241T	17						.						132.0	111.0	118.0					17																	74097830		2203	4300	6503	71609425	SO:0001819	synonymous_variant	23265	exon3			BC029432	CCDS11741.1, CCDS32738.1, CCDS45781.1, CCDS45782.1, CCDS45784.1, CCDS74164.1	17q25.3	2013-01-22			ENSG00000182473	ENSG00000182473			23214	protein-coding gene	gene with protein product		608163				12477932	Standard	NM_001013839		Approved	EXO70, KIAA1067, YJL085W, Exo70p	uc010wsw.2	Q9UPT5	OTTHUMG00000150720	ENST00000335146.7:c.241C>T	17.37:g.74097830G>A			71609425	NM_001145299	B5MC69|B8XXP2|Q8ND93|Q8WV91|Q96FF0|Q9H8C3|Q9H9X3|Q9HA32	Silent	SNP	ENST00000335146.7	37	CCDS45782.1																																																																																				0.537	EXOC7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000319768.2	NM_015219	
CEP192	55125	broad.mit.edu	37	18	13049590	13049590	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr18:13049590C>T	ENST00000325971.8	+	14	2605	c.1012C>T	c.(1012-1014)Cag>Tag	p.Q338*	CEP192_ENST00000430049.2_Nonsense_Mutation_p.Q459*|CEP192_ENST00000506447.1_Nonsense_Mutation_p.Q934*			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	338					centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)	p.Q338*(1)|p.Q934*(1)		NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						CAGAGAAAATCAGAGGCAAAA	0.383																																					p.Q934X												.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C2800T	18						.						114.0	118.0	117.0					18																	13049590		2200	4297	6497	13039590	SO:0001587	stop_gained	55125	exon16			AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.1012C>T	18.37:g.13049590C>T	ENSP00000317156:p.Gln338*		13039590	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Nonsense_Mutation	SNP	ENST00000325971.8	37		.	.	.	.	.	.	.	.	.	.	C	17.08	3.296929	0.60086	.	.	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049	.	.	.	5.52	3.7	0.42460	.	0.144768	0.32287	N	0.006312	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05436	T	0.98	-1.8042	8.3629	0.32369	0.0:0.5837:0.3327:0.0836	.	.	.	.	X	934;338;338;459	.	ENSP00000317156:Q338X	Q	+	1	0	CEP192	13039590	0.000000	0.05858	0.003000	0.11579	0.013000	0.08279	0.057000	0.14279	0.786000	0.33708	0.650000	0.86243	CAG		0.383	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
CEP192	55125	broad.mit.edu	37	18	13116476	13116476	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr18:13116476C>T	ENST00000325971.8	+	41	7195	c.5602C>T	c.(5602-5604)Cga>Tga	p.R1868*	CEP192_ENST00000430049.2_Nonsense_Mutation_p.R1989*|CEP192_ENST00000540847.2_3'UTR|CEP192_ENST00000506447.1_Nonsense_Mutation_p.R2464*			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	1868					centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)	p.R1868*(1)|p.R2464*(1)		NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						AGTCAATCTGCGAAATAATTC	0.413																																					p.R2464X												.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C7390T	18						.						87.0	81.0	83.0					18																	13116476		2203	4300	6503	13106476	SO:0001587	stop_gained	55125	exon43			AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.5602C>T	18.37:g.13116476C>T	ENSP00000317156:p.Arg1868*		13106476	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Nonsense_Mutation	SNP	ENST00000325971.8	37		.	.	.	.	.	.	.	.	.	.	C	54	21.944488	0.99944	.	.	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049;ENST00000540847	.	.	.	4.98	0.745	0.18359	.	0.065221	0.64402	D	0.000010	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.3063	15.1127	0.72372	0.5855:0.4145:0.0:0.0	.	.	.	.	X	2464;1868;1868;1989;468	.	ENSP00000317156:R1868X	R	+	1	2	CEP192	13106476	1.000000	0.71417	0.974000	0.42286	0.652000	0.38707	0.826000	0.27407	-0.082000	0.12640	0.467000	0.42956	CGA		0.413	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
DSG3	1830	broad.mit.edu	37	18	29055985	29055985	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr18:29055985C>A	ENST00000257189.4	+	16	2845	c.2762C>A	c.(2761-2763)tCc>tAc	p.S921Y		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	921					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S921Y(1)		breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(28)|ovary(4)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			CCAGCTGTTTCCATCCCTGAC	0.502																																					p.S921Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2762A	18						.						136.0	126.0	130.0					18																	29055985		2203	4300	6503	27309983	SO:0001583	missense	1830	exon16			M76482	CCDS11898.1	18q12.1	2010-06-24	2010-06-24		ENSG00000134757	ENSG00000134757		"""Cadherins / Major cadherins"""	3050	protein-coding gene	gene with protein product	"""pemphigus vulgaris antigen"""	169615	"""desmoglein 3 (pemphigus vulgaris antigen)"""			1601426	Standard	NM_001944		Approved	CDHF6	uc002kws.3	P32926	OTTHUMG00000131985	ENST00000257189.4:c.2762C>A	18.37:g.29055985C>A	ENSP00000257189:p.Ser921Tyr		27309983	NM_001944	A8K2V2	Missense_Mutation	SNP	ENST00000257189.4	37	CCDS11898.1	.	.	.	.	.	.	.	.	.	.	C	16.03	3.006023	0.54361	.	.	ENSG00000134757	ENST00000257189	T	0.77229	-1.08	5.54	4.66	0.58398	.	0.564359	0.16009	N	0.233914	T	0.76492	0.3995	L	0.44542	1.39	0.27630	N	0.948051	P	0.51351	0.944	P	0.45753	0.492	T	0.72184	-0.4367	10	0.87932	D	0	.	16.6974	0.85339	0.0:0.8703:0.1297:0.0	.	921	P32926	DSG3_HUMAN	Y	921	ENSP00000257189:S921Y	ENSP00000257189:S921Y	S	+	2	0	DSG3	27309983	0.566000	0.26618	0.926000	0.36857	0.532000	0.34746	2.570000	0.45981	1.459000	0.47892	0.655000	0.94253	TCC		0.502	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944	
KLHL14	57565	broad.mit.edu	37	18	30321953	30321953	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr18:30321953C>T	ENST00000359358.4	-	3	1445	c.1007G>A	c.(1006-1008)cGg>cAg	p.R336Q	KLHL14_ENST00000358095.4_Missense_Mutation_p.R336Q	NM_020805.1	NP_065856.1	Q9P2G3	KLH14_HUMAN	kelch-like family member 14	336						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)		p.R336Q(1)		breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(20)|ovary(2)	31						GCTGGGGAGCCGGTCCGGTCC	0.403																																					p.R336Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1007A	18						.						82.0	78.0	79.0					18																	30321953		2203	4300	6503	28575951	SO:0001583	missense	57565	exon3			AB037805	CCDS32813.1	18q12.1	2013-10-15	2013-01-30		ENSG00000197705	ENSG00000197705		"""Kelch-like"", ""BTB/POZ domain containing"""	29266	protein-coding gene	gene with protein product	"""printor"""	613772	"""kelch-like 14 (Drosophila)"""			10718198, 19535332	Standard	NM_020805		Approved	KIAA1384	uc002kxm.1	Q9P2G3	OTTHUMG00000179819	ENST00000359358.4:c.1007G>A	18.37:g.30321953C>T	ENSP00000352314:p.Arg336Gln		28575951	NM_020805	A6NNW1|B4DHA0|Q8WU41	Missense_Mutation	SNP	ENST00000359358.4	37	CCDS32813.1	.	.	.	.	.	.	.	.	.	.	C	16.22	3.061621	0.55432	.	.	ENSG00000197705	ENST00000359358;ENST00000358095	T;T	0.77229	-0.85;-1.08	5.9	5.9	0.94986	Galactose oxidase, beta-propeller (1);	0.053328	0.85682	D	0.000000	T	0.74772	0.3760	N	0.03608	-0.345	0.80722	D	1	D	0.64830	0.994	D	0.64042	0.921	T	0.77525	-0.2555	10	0.30854	T	0.27	.	20.274	0.98482	0.0:1.0:0.0:0.0	.	336	Q9P2G3	KLH14_HUMAN	Q	336	ENSP00000352314:R336Q;ENSP00000350808:R336Q	ENSP00000350808:R336Q	R	-	2	0	KLHL14	28575951	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	7.298000	0.78815	2.797000	0.96272	0.650000	0.86243	CGG		0.403	KLHL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448376.1		
EPG5	57724	broad.mit.edu	37	18	43481065	43481065	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr18:43481065C>T	ENST00000282041.5	-	26	4576	c.4542G>A	c.(4540-4542)ccG>ccA	p.P1514P	EPG5_ENST00000585906.1_5'UTR	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	1514					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)			p.P1514P(1)		NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						GAGGCTTCGTCGGGTGCAGAG	0.498																																					p.P1514P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G4542A	18						.						65.0	73.0	70.0					18																	43481065		2037	4173	6210	41735063	SO:0001819	synonymous_variant	57724	exon26			AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"""KIAA1632"""	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.4542G>A	18.37:g.43481065C>T			41735063	NM_020964	A2BDF3|Q9H8C8	Silent	SNP	ENST00000282041.5	37	CCDS11926.2																																																																																				0.498	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964	
MAPK4	5596	broad.mit.edu	37	18	48255652	48255652	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr18:48255652C>T	ENST00000400384.2	+	6	2228	c.1192C>T	c.(1192-1194)Cgc>Tgc	p.R398C	MAPK4_ENST00000540640.1_Missense_Mutation_p.R187C|MAPK4_ENST00000592595.1_3'UTR	NM_002747.3	NP_002738.2	P31152	MK04_HUMAN	mitogen-activated protein kinase 4	398					cell cycle (GO:0007049)|MAPK cascade (GO:0000165)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)	p.R398C(1)		lung(4)|skin(3)|upper_aerodigestive_tract(1)	8		Colorectal(6;0.0297)		Colorectal(21;0.156)		GGTGGACCCGCGCAAGGACTC	0.701																																					p.R398C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1192T	18						.						15.0	18.0	17.0					18																	48255652		2083	4194	6277	46509650	SO:0001583	missense	5596	exon6			X59727	CCDS42437.1	18q21.1	2012-10-02			ENSG00000141639	ENSG00000141639		"""Mitogen-activated protein kinase cascade / Kinases"""	6878	protein-coding gene	gene with protein product		176949		PRKM4		8290275	Standard	XM_005258299		Approved	Erk3-related, Erk4	uc002lev.3	P31152	OTTHUMG00000179853	ENST00000400384.2:c.1192C>T	18.37:g.48255652C>T	ENSP00000383234:p.Arg398Cys		46509650	NM_002747	A1A4C4|Q0VG04	Missense_Mutation	SNP	ENST00000400384.2	37	CCDS42437.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.412600	0.83340	.	.	ENSG00000141639	ENST00000400384;ENST00000540640	T;T	0.76578	-1.03;0.98	5.51	4.64	0.57946	.	0.000000	0.64402	D	0.000018	T	0.78240	0.4252	L	0.34521	1.04	0.80722	D	1	D	0.71674	0.998	P	0.56042	0.79	T	0.80688	-0.1271	10	0.87932	D	0	-25.978	13.3571	0.60633	0.0:0.9226:0.0:0.0774	.	398	P31152	MK04_HUMAN	C	398;187	ENSP00000383234:R398C;ENSP00000439231:R187C	ENSP00000383234:R398C	R	+	1	0	MAPK4	46509650	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	5.584000	0.67490	1.318000	0.45170	0.561000	0.74099	CGC		0.701	MAPK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448631.2	NM_002747	
MBD2	8932	broad.mit.edu	37	18	51731394	51731394	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr18:51731394G>A	ENST00000256429.3	-	2	904	c.676C>T	c.(676-678)Cga>Tga	p.R226*	MBD2_ENST00000583046.1_Nonsense_Mutation_p.R226*|MBD2_ENST00000398398.2_Nonsense_Mutation_p.R226*	NM_003927.4	NP_003918.1	Q9UBB5	MBD2_HUMAN	methyl-CpG binding domain protein 2	226					ATP-dependent chromatin remodeling (GO:0043044)|cellular protein complex assembly (GO:0043623)|maternal behavior (GO:0042711)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|histone deacetylase complex (GO:0000118)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	C2H2 zinc finger domain binding (GO:0070742)|chromatin binding (GO:0003682)|methyl-CpG binding (GO:0008327)|mRNA binding (GO:0003729)|protein domain specific binding (GO:0019904)|satellite DNA binding (GO:0003696)|siRNA binding (GO:0035197)	p.R226*(1)		breast(1)|large_intestine(3)|lung(2)|prostate(1)|urinary_tract(1)	8				Colorectal(16;0.0212)|READ - Rectum adenocarcinoma(32;0.188)		GGATCGTTTCGCAGTCTCTGT	0.368																																					p.R226X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C676T	18						.						292.0	273.0	280.0					18																	51731394		2203	4300	6503	49985392	SO:0001587	stop_gained	8932	exon2			AF072242	CCDS11953.1, CCDS45871.1	18q21	2008-08-01			ENSG00000134046	ENSG00000134046			6917	protein-coding gene	gene with protein product		603547				9774669, 10441743	Standard	NM_003927		Approved		uc002lfg.2	Q9UBB5	OTTHUMG00000132705	ENST00000256429.3:c.676C>T	18.37:g.51731394G>A	ENSP00000256429:p.Arg226*		49985392	NM_015832	O95242|Q9UIS8	Nonsense_Mutation	SNP	ENST00000256429.3	37	CCDS11953.1	.	.	.	.	.	.	.	.	.	.	G	38	6.919315	0.97936	.	.	ENSG00000134046	ENST00000256429;ENST00000398398	.	.	.	5.78	4.86	0.63082	.	0.000000	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.5094	11.6469	0.51265	0.0:0.0:0.6809:0.3191	.	.	.	.	X	226	.	ENSP00000256429:R226X	R	-	1	2	MBD2	49985392	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.237000	0.51344	2.739000	0.93911	0.643000	0.83706	CGA		0.368	MBD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256003.2	NM_003927	
EPB41L3	23136	broad.mit.edu	37	18	5423422	5423422	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr18:5423422G>A	ENST00000341928.2	-	11	1634	c.1294C>T	c.(1294-1296)Cgc>Tgc	p.R432C	EPB41L3_ENST00000400111.3_Missense_Mutation_p.R432C|EPB41L3_ENST00000342933.3_Missense_Mutation_p.R432C|EPB41L3_ENST00000540638.2_Missense_Mutation_p.R432C|EPB41L3_ENST00000544123.1_Missense_Mutation_p.R432C|EPB41L3_ENST00000542652.2_5'UTR	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	432	Hydrophilic.				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)	p.R432C(2)		breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						CTGGATGAGCGTTCAAAGTAA	0.483																																					p.R432C												.	.	2	Substitution - Missense(2)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	c.C1294T	18						.						194.0	148.0	164.0					18																	5423422		2203	4300	6503	5413422	SO:0001583	missense	23136	exon11			AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.1294C>T	18.37:g.5423422G>A	ENSP00000343158:p.Arg432Cys		5413422	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	De_novo_Start_OutOfFrame	SNP	ENST00000341928.2	37	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.747670	0.89663	.	.	ENSG00000082397	ENST00000341928;ENST00000540638;ENST00000544123;ENST00000545076;ENST00000342933;ENST00000400111	D;D;D;D	0.96619	-4.07;-4.07;-4.07;-4.07	6.08	6.08	0.98989	FERM adjacent (FA) (1);	0.000000	0.85682	D	0.000000	D	0.98814	0.9600	H	0.94886	3.595	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.997;0.999;0.998;1.0	D	0.98997	1.0810	10	0.87932	D	0	.	20.6721	0.99693	0.0:0.0:1.0:0.0	.	432;323;432;432	F5GX05;A8K968;Q9Y2J2-2;Q9Y2J2	.;.;.;E41L3_HUMAN	C	432;323;432;323;432;432	ENSP00000343158:R432C;ENSP00000441174:R432C;ENSP00000341138:R432C;ENSP00000382981:R432C	ENSP00000343158:R432C	R	-	1	0	EPB41L3	5413422	1.000000	0.71417	0.998000	0.56505	0.460000	0.32559	7.837000	0.86796	2.894000	0.99253	0.591000	0.81541	CGC		0.483	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307	
EPB41L3	23136	broad.mit.edu	37	18	5433483	5433483	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr18:5433483A>T	ENST00000341928.2	-	8	1237	c.897T>A	c.(895-897)gaT>gaA	p.D299E	EPB41L3_ENST00000400111.3_Missense_Mutation_p.D299E|EPB41L3_ENST00000342933.3_Missense_Mutation_p.D299E|EPB41L3_ENST00000540638.2_Missense_Mutation_p.D299E|EPB41L3_ENST00000544123.1_Missense_Mutation_p.D299E|EPB41L3_ENST00000542652.2_5'UTR	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	299	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)	p.D299E(1)		breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						CATGATGTAAATCTACCCCAT	0.318																																					p.D299E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T897A	18						.						170.0	161.0	164.0					18																	5433483		2203	4299	6502	5423483	SO:0001583	missense	23136	exon8			AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.897T>A	18.37:g.5433483A>T	ENSP00000343158:p.Asp299Glu		5423483	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	37	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	A	19.69	3.874202	0.72180	.	.	ENSG00000082397	ENST00000341928;ENST00000540638;ENST00000544123;ENST00000545076;ENST00000342933;ENST00000400111	T;T;T;T	0.81415	-1.49;-1.49;-1.49;-1.49	5.9	2.34	0.29019	Band 4.1 domain (1);FERM central domain (1);FERM domain (1);Pleckstrin homology-type (1);FERM conserved site (1);	0.042714	0.85682	D	0.000000	D	0.84924	0.5580	L	0.58302	1.8	0.80722	D	1	D;P;D;D;B	0.76494	0.993;0.467;0.999;0.998;0.375	D;B;D;D;B	0.76575	0.966;0.269;0.988;0.979;0.23	T	0.82615	-0.0370	10	0.51188	T	0.08	.	8.6948	0.34289	0.7098:0.0:0.2902:0.0	.	299;299;190;299;299	F5GX05;Q9Y2J2-3;A8K968;Q9Y2J2-2;Q9Y2J2	.;.;.;.;E41L3_HUMAN	E	299;190;299;190;299;299	ENSP00000343158:D299E;ENSP00000441174:D299E;ENSP00000341138:D299E;ENSP00000382981:D299E	ENSP00000343158:D299E	D	-	3	2	EPB41L3	5423483	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	2.673000	0.46858	0.509000	0.28195	0.533000	0.62120	GAT		0.318	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307	
ATP8B1	5205	broad.mit.edu	37	18	55315881	55315881	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr18:55315881G>A	ENST00000283684.4	-	27	3594	c.3595C>T	c.(3595-3597)Cgc>Tgc	p.R1199C	RP11-35G9.5_ENST00000588925.1_RNA|RP11-35G9.3_ENST00000592201.1_RNA|RP11-35G9.3_ENST00000591854.1_RNA|ATP8B1_ENST00000536015.1_Missense_Mutation_p.R1199C|RP11-35G9.3_ENST00000599199.1_RNA			O43520	AT8B1_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 1	1199					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|drug transmembrane transport (GO:0006855)|inner ear receptor cell development (GO:0060119)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|phospholipid translocation (GO:0045332)|regulation of microvillus assembly (GO:0032534)|sensory perception of sound (GO:0007605)|transmembrane transport (GO:0055085)|vestibulocochlear nerve formation (GO:0021650)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|cardiolipin binding (GO:1901612)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.R1199C(1)		breast(6)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(19)|ovary(3)|prostate(1)	53		Colorectal(73;0.229)				ACGCCCCGGCGGAACACCTGC	0.652																																					p.R1199C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3595T	18						.																																			53466879	SO:0001583	missense	5205	exon28			AF038007	CCDS11965.1	18q21	2010-04-28	2010-04-28		ENSG00000081923	ENSG00000081923		"""ATPases / P-type"""	3706	protein-coding gene	gene with protein product		602397	"""ATPase, Class I, type 8B, member 1"", ""ATPase, class I, type 8B, member 1"""	FIC1, BRIC, PFIC1		9500542, 7655458	Standard	NM_005603		Approved	ATPIC, PFIC	uc002lgw.3	O43520	OTTHUMG00000132739	ENST00000283684.4:c.3595C>T	18.37:g.55315881G>A	ENSP00000283684:p.Arg1199Cys		53466879	NM_005603	Q9BTP8	Missense_Mutation	SNP	ENST00000283684.4	37	CCDS11965.1	.	.	.	.	.	.	.	.	.	.	G	17.57	3.423429	0.62733	.	.	ENSG00000081923	ENST00000283684;ENST00000536015	T;T	0.39592	1.07;1.07	5.27	4.4	0.53042	.	0.308515	0.37348	N	0.002136	T	0.48995	0.1531	M	0.69823	2.125	0.58432	D	0.999999	D	0.60575	0.988	P	0.46975	0.533	T	0.55798	-0.8084	10	0.56958	D	0.05	.	14.1764	0.65544	0.0:0.2852:0.7148:0.0	.	1199	O43520	AT8B1_HUMAN	C	1199	ENSP00000283684:R1199C;ENSP00000445359:R1199C	ENSP00000283684:R1199C	R	-	1	0	ATP8B1	53466879	1.000000	0.71417	1.000000	0.80357	0.469000	0.32828	3.969000	0.56816	1.212000	0.43366	-0.264000	0.10439	CGC		0.652	ATP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256097.1	NM_005603	
MALT1	10892	broad.mit.edu	37	18	56401613	56401613	+	Splice_Site	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr18:56401613C>T	ENST00000348428.3	+	12	1733	c.1475C>T	c.(1474-1476)aCg>aTg	p.T492M	RP11-126O1.4_ENST00000588835.1_RNA|MALT1_ENST00000345724.3_Splice_Site_p.T481M	NM_006785.2|NM_173844.1	NP_006776.1|NP_776216.1	Q9UDY8	MALT1_HUMAN	mucosa associated lymphoid tissue lymphoma translocation gene 1	492	Caspase-like.				activation of NF-kappaB-inducing kinase activity (GO:0007250)|B-1 B cell differentiation (GO:0001923)|defense response (GO:0006952)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|nuclear export (GO:0051168)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|protein oligomerization (GO:0051259)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of T cell receptor signaling pathway (GO:0050856)|response to fungus (GO:0009620)|response to molecule of bacterial origin (GO:0002237)|T cell proliferation (GO:0042098)|T cell receptor signaling pathway (GO:0050852)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)|protein self-association (GO:0043621)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)	p.T481M(1)		central_nervous_system(1)|large_intestine(7)|lung(1)|ovary(2)|skin(1)	12						GGATATGCCACGTAAGAACAT	0.408			T	BIRC3	MALT																																p.T481M			Dom	yes		18	18q21	10892	mucosa associated lymphoid tissue lymphoma translocation gene 1		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1442T	18						.						135.0	114.0	121.0					18																	56401613		2203	4300	6503	54552593	SO:0001630	splice_region_variant	10892	exon11				CCDS11967.1, CCDS11968.1	18q21	2013-01-11			ENSG00000172175	ENSG00000172175		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6819	protein-coding gene	gene with protein product	"""paracaspase"""	604860		MLT		10339464, 10406266, 10523859	Standard	NM_006785		Approved		uc002lhm.1	Q9UDY8	OTTHUMG00000132761	ENST00000348428.3:c.1475+1C>T	18.37:g.56401613C>T			54552593	NM_173844	Q9NTB7|Q9ULX4	Missense_Mutation	SNP	ENST00000348428.3	37	CCDS11967.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.348500	0.82132	.	.	ENSG00000172175	ENST00000348428;ENST00000345724	T;T	0.55234	0.53;0.53	5.88	5.01	0.66863	Peptidase C14, caspase catalytic (1);	0.043150	0.85682	N	0.000000	T	0.76884	0.4050	M	0.90309	3.105	0.58432	D	0.999992	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.82196	-0.0577	10	0.87932	D	0	.	13.7132	0.62680	0.0:0.9253:0.0:0.0747	.	481;492	Q9UDY8-2;Q9UDY8	.;MALT1_HUMAN	M	492;481	ENSP00000319279:T492M;ENSP00000304161:T481M	ENSP00000304161:T481M	T	+	2	0	MALT1	54552593	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.487000	0.81328	1.491000	0.48482	0.650000	0.86243	ACG		0.408	MALT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256132.2		Missense_Mutation
MALT1	10892	broad.mit.edu	37	18	56414733	56414733	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr18:56414733A>G	ENST00000348428.3	+	17	2392	c.2134A>G	c.(2134-2136)Att>Gtt	p.I712V	RP11-126O1.4_ENST00000588835.1_RNA|MALT1_ENST00000345724.3_Missense_Mutation_p.I701V	NM_006785.2|NM_173844.1	NP_006776.1|NP_776216.1	Q9UDY8	MALT1_HUMAN	mucosa associated lymphoid tissue lymphoma translocation gene 1	712					activation of NF-kappaB-inducing kinase activity (GO:0007250)|B-1 B cell differentiation (GO:0001923)|defense response (GO:0006952)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|nuclear export (GO:0051168)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|protein oligomerization (GO:0051259)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of T cell receptor signaling pathway (GO:0050856)|response to fungus (GO:0009620)|response to molecule of bacterial origin (GO:0002237)|T cell proliferation (GO:0042098)|T cell receptor signaling pathway (GO:0050852)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)|protein self-association (GO:0043621)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)	p.I701V(1)		central_nervous_system(1)|large_intestine(7)|lung(1)|ovary(2)|skin(1)	12						GAAACCTCTCATTGCTAAATT	0.423			T	BIRC3	MALT																																p.I701V			Dom	yes		18	18q21	10892	mucosa associated lymphoid tissue lymphoma translocation gene 1		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2101G	18						.						156.0	156.0	156.0					18																	56414733		2203	4300	6503	54565713	SO:0001583	missense	10892	exon16				CCDS11967.1, CCDS11968.1	18q21	2013-01-11			ENSG00000172175	ENSG00000172175		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6819	protein-coding gene	gene with protein product	"""paracaspase"""	604860		MLT		10339464, 10406266, 10523859	Standard	NM_006785		Approved		uc002lhm.1	Q9UDY8	OTTHUMG00000132761	ENST00000348428.3:c.2134A>G	18.37:g.56414733A>G	ENSP00000319279:p.Ile712Val		54565713	NM_173844	Q9NTB7|Q9ULX4	Missense_Mutation	SNP	ENST00000348428.3	37	CCDS11967.1	.	.	.	.	.	.	.	.	.	.	A	17.20	3.330059	0.60743	.	.	ENSG00000172175	ENST00000348428;ENST00000345724	T;T	0.12879	2.64;2.65	5.64	5.64	0.86602	.	0.148189	0.64402	D	0.000013	T	0.16085	0.0387	L	0.41236	1.265	0.37846	D	0.929232	B;B	0.27117	0.168;0.047	B;B	0.34722	0.188;0.092	T	0.11203	-1.0597	10	0.29301	T	0.29	.	15.5301	0.75952	1.0:0.0:0.0:0.0	.	701;712	Q9UDY8-2;Q9UDY8	.;MALT1_HUMAN	V	712;701	ENSP00000319279:I712V;ENSP00000304161:I701V	ENSP00000304161:I701V	I	+	1	0	MALT1	54565713	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.582000	0.60957	2.152000	0.67230	0.528000	0.53228	ATT		0.423	MALT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256132.2		
EPB41L3	23136	broad.mit.edu	37	18	5489118	5489118	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr18:5489118G>A	ENST00000341928.2	-	2	405	c.65C>T	c.(64-66)gCg>gTg	p.A22V	EPB41L3_ENST00000400111.3_Missense_Mutation_p.A22V|EPB41L3_ENST00000342933.3_Missense_Mutation_p.A22V|EPB41L3_ENST00000540638.2_Missense_Mutation_p.A22V|EPB41L3_ENST00000544123.1_Missense_Mutation_p.A22V	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	22					apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)	p.A22V(1)		breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						cgcccccgccgccTCCTGGGG	0.687																																					p.A22V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C65T	18						.						20.0	22.0	22.0					18																	5489118		2147	4173	6320	5479118	SO:0001583	missense	23136	exon2			AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.65C>T	18.37:g.5489118G>A	ENSP00000343158:p.Ala22Val		5479118	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	37	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	G	9.226	1.034639	0.19590	.	.	ENSG00000082397	ENST00000341928;ENST00000544123;ENST00000342933;ENST00000400111;ENST00000542652	T;D;T;D	0.82803	-1.48;-1.61;-1.48;-1.65	5.58	3.76	0.43208	.	0.666605	0.15145	N	0.278024	D	0.88676	0.6501	M	0.63428	1.95	0.22081	N	0.999371	D;B;B;B	0.89917	1.0;0.021;0.072;0.063	D;B;B;B	0.76071	0.987;0.024;0.024;0.024	T	0.79478	-0.1787	10	0.35671	T	0.21	.	12.6536	0.56776	0.0:0.0:0.4918:0.5082	.	22;22;22;22	F5GX05;Q9Y2J2-3;Q9Y2J2-2;Q9Y2J2	.;.;.;E41L3_HUMAN	V	22;22;22;22;103	ENSP00000343158:A22V;ENSP00000441174:A22V;ENSP00000341138:A22V;ENSP00000382981:A22V	ENSP00000343158:A22V	A	-	2	0	EPB41L3	5479118	0.987000	0.35691	0.633000	0.29310	0.036000	0.12997	2.784000	0.47774	0.691000	0.31592	-0.224000	0.12420	GCG		0.687	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307	
ZNF532	55205	broad.mit.edu	37	18	56586956	56586956	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr18:56586956G>A	ENST00000336078.4	+	4	2213	c.1437G>A	c.(1435-1437)acG>acA	p.T479T	ZNF532_ENST00000591083.1_Silent_p.T479T|ZNF532_ENST00000591230.1_Silent_p.T479T|ZNF532_ENST00000589288.1_Silent_p.T479T|ZNF532_ENST00000591808.1_Silent_p.T479T	NM_018181.4	NP_060651.2	Q9HCE3	ZN532_HUMAN	zinc finger protein 532	479					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T479T(1)		breast(5)|central_nervous_system(1)|cervix(2)|endometrium(14)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(4)|urinary_tract(1)	52						TGAAAGCCACGGTCATATCTG	0.557																																					p.T479T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1437A	18						.						33.0	29.0	30.0					18																	56586956		2203	4300	6503	54737936	SO:0001819	synonymous_variant	55205	exon4			AB046849	CCDS11969.1	18q21.32	2005-08-22			ENSG00000074657	ENSG00000074657		"""Zinc fingers, C2H2-type"""	30940	protein-coding gene	gene with protein product						10997877	Standard	XM_005266723		Approved	FLJ10697	uc002lho.3	Q9HCE3	OTTHUMG00000132759	ENST00000336078.4:c.1437G>A	18.37:g.56586956G>A			54737936	NM_018181	Q4G0V6|Q7L7Z7|Q96QR7|Q9NVJ6	Silent	SNP	ENST00000336078.4	37	CCDS11969.1																																																																																				0.557	ZNF532-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256130.1	NM_018181	
CLUL1	27098	broad.mit.edu	37	18	618060	618060	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr18:618060C>T	ENST00000400606.2	+	2	205	c.60C>T	c.(58-60)tgC>tgT	p.C20C	CLUL1_ENST00000338387.7_Silent_p.C20C|CLUL1_ENST00000581619.1_Silent_p.C45C|CLUL1_ENST00000580436.1_3'UTR|CLUL1_ENST00000540035.1_Silent_p.C72C|CLUL1_ENST00000579494.1_Silent_p.C20C	NM_014410.4	NP_055225.1	Q15846	CLUL1_HUMAN	clusterin-like 1 (retinal)	20					cell death (GO:0008219)	extracellular region (GO:0005576)		p.C20C(1)		NS(1)|breast(1)|endometrium(5)|large_intestine(5)|liver(2)|lung(7)|ovary(2)|skin(1)	24						ACAGTCACTGCGCACCCACTT	0.463																																					p.C20C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C60T	18						.						129.0	133.0	132.0					18																	618060		2016	4185	6201	608060	SO:0001819	synonymous_variant	27098	exon2			D63813	CCDS42405.1, CCDS74187.1	18p11.32	2008-07-28				ENSG00000079101			2096	protein-coding gene	gene with protein product						10675623, 14507903	Standard	NM_199167		Approved		uc002kkq.3	Q15846		ENST00000400606.2:c.60C>T	18.37:g.618060C>T			608060	NM_014410	A0FDN7	Silent	SNP	ENST00000400606.2	37	CCDS42405.1																																																																																				0.463	CLUL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441183.1		
RNF152	220441	broad.mit.edu	37	18	59483391	59483391	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr18:59483391C>T	ENST00000312828.3	-	2	1405	c.306G>A	c.(304-306)ctG>ctA	p.L102L		NM_173557.2	NP_775828.1	Q8N8N0	RN152_HUMAN	ring finger protein 152	102					apoptotic process (GO:0006915)|protein K48-linked ubiquitination (GO:0070936)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.L102L(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(10)|skin(1)	17		Colorectal(73;0.186)				TGGGCAGGGGCAGCATGTAGC	0.642																																					p.L102L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G306A	18						.						76.0	84.0	81.0					18																	59483391		2203	4300	6503	57634371	SO:0001819	synonymous_variant	220441	exon2			AK096495	CCDS11978.1	18q21.33	2013-01-09			ENSG00000176641	ENSG00000176641		"""RING-type (C3HC4) zinc fingers"""	26811	protein-coding gene	gene with protein product							Standard	XM_005266650		Approved	FLJ39176	uc002lih.1	Q8N8N0	OTTHUMG00000132774	ENST00000312828.3:c.306G>A	18.37:g.59483391C>T			57634371	NM_173557	B3KV99|Q52LA4	Silent	SNP	ENST00000312828.3	37	CCDS11978.1																																																																																				0.642	RNF152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256180.1	NM_173557	
TSHZ1	10194	broad.mit.edu	37	18	72998703	72998703	+	Silent	SNP	G	G	A	rs202060462		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr18:72998703G>A	ENST00000580243.1	+	2	1689	c.1341G>A	c.(1339-1341)tcG>tcA	p.S447S	TSHZ1_ENST00000322038.5_Silent_p.S402S			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	447					anterior/posterior pattern specification (GO:0009952)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|soft palate development (GO:0060023)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S402S(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(11)|liver(1)|lung(14)|ovary(1)|skin(6)|upper_aerodigestive_tract(2)	42		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		TGACCACCTCGGCTTCTAAGA	0.612													G|||	1	0.000199681	0.0	0.0	5008	,	,		16437	0.001		0.0	False		,,,				2504	0.0				p.S402S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1206A	18						.						41.0	43.0	43.0					18																	72998703		2203	4300	6503	71127691	SO:0001819	synonymous_variant	10194	exon2			AF039698	CCDS12009.1	18q22.3	2013-11-20	2007-07-16	2006-03-14	ENSG00000179981	ENSG00000179981		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	10669	protein-coding gene	gene with protein product		614427	"""serologically defined colon cancer antigen 33"", ""teashirt zinc finger 1"", ""teashirt family zinc finger 1"""	SDCCAG33		17586487	Standard	NM_005786		Approved	NY-CO-33, TSH1	uc002lly.4	Q6ZSZ6	OTTHUMG00000132859	ENST00000580243.1:c.1341G>A	18.37:g.72998703G>A			71127691	NM_005786	O60534|Q4LE29|Q53EU4	Silent	SNP	ENST00000580243.1	37																																																																																					0.612	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786	
TSHZ1	10194	broad.mit.edu	37	18	73000139	73000139	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr18:73000139G>T	ENST00000580243.1	+	2	3125	c.2777G>T	c.(2776-2778)aGg>aTg	p.R926M	TSHZ1_ENST00000322038.5_Missense_Mutation_p.R881M			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	926					anterior/posterior pattern specification (GO:0009952)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|soft palate development (GO:0060023)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R881M(2)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(11)|liver(1)|lung(14)|ovary(1)|skin(6)|upper_aerodigestive_tract(2)	42		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		CCGCAGGAGAGGGTGCACATC	0.582																																					p.R881M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2642T	18						.						62.0	57.0	59.0					18																	73000139		2203	4300	6503	71129127	SO:0001583	missense	10194	exon2			AF039698	CCDS12009.1	18q22.3	2013-11-20	2007-07-16	2006-03-14	ENSG00000179981	ENSG00000179981		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	10669	protein-coding gene	gene with protein product		614427	"""serologically defined colon cancer antigen 33"", ""teashirt zinc finger 1"", ""teashirt family zinc finger 1"""	SDCCAG33		17586487	Standard	NM_005786		Approved	NY-CO-33, TSH1	uc002lly.4	Q6ZSZ6	OTTHUMG00000132859	ENST00000580243.1:c.2777G>T	18.37:g.73000139G>T	ENSP00000464391:p.Arg926Met		71129127	NM_005786	O60534|Q4LE29|Q53EU4	Missense_Mutation	SNP	ENST00000580243.1	37		.	.	.	.	.	.	.	.	.	.	G	10.76	1.440136	0.25900	.	.	ENSG00000179981	ENST00000322038	T	0.26373	1.74	4.57	4.57	0.56435	Homeobox (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	T	0.52996	0.1769	M	0.70275	2.135	0.47123	D	0.999323	D	0.89917	1.0	D	0.83275	0.996	T	0.50389	-0.8834	10	0.87932	D	0	-39.7336	17.9077	0.88925	0.0:0.0:1.0:0.0	.	926	Q6ZSZ6	TSH1_HUMAN	M	881	ENSP00000323584:R881M	ENSP00000323584:R881M	R	+	2	0	TSHZ1	71129127	1.000000	0.71417	0.992000	0.48379	0.982000	0.71751	9.208000	0.95075	-0.339000	0.08401	-0.182000	0.12963	AGG		0.582	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786	
ZNF516	9658	broad.mit.edu	37	18	74091126	74091126	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr18:74091126G>A	ENST00000443185.2	-	4	3261	c.2944C>T	c.(2944-2946)Cct>Tct	p.P982S	RP11-504I13.3_ENST00000583287.1_RNA|ZNF516_ENST00000524431.2_5'UTR	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	982					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P982S(1)		central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Prostate(75;0.0869)|Esophageal squamous(42;0.129)		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)		GGACCCTGAGGCTGAGCACTG	0.657																																					p.P982S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2944T	18						.						23.0	27.0	26.0					18																	74091126		1960	4074	6034	72220114	SO:0001583	missense	9658	exon4			D86975	CCDS74234.1	18q23	2013-01-08				ENSG00000101493		"""Zinc fingers, C2H2-type"""	28990	protein-coding gene	gene with protein product		615114				9039502	Standard	NM_014643		Approved	HsT287, KIAA0222	uc021ulp.1	Q92618		ENST00000443185.2:c.2944C>T	18.37:g.74091126G>A	ENSP00000394757:p.Pro982Ser		72220114	NM_014643		Missense_Mutation	SNP	ENST00000443185.2	37		.	.	.	.	.	.	.	.	.	.	G	10.76	1.441607	0.25900	.	.	ENSG00000101493	ENST00000443185	T	0.10763	2.84	3.83	2.01	0.26516	.	0.760060	0.12527	N	0.461151	T	0.08891	0.0220	.	.	.	0.44136	D	0.996927	B	0.24721	0.11	B	0.16722	0.016	T	0.13124	-1.0521	9	0.46703	T	0.11	-15.8774	8.2017	0.31428	0.1888:0.0:0.8112:0.0	.	982	Q92618	ZN516_HUMAN	S	982	ENSP00000394757:P982S	ENSP00000394757:P982S	P	-	1	0	ZNF516	72220114	1.000000	0.71417	0.996000	0.52242	0.698000	0.40448	1.693000	0.37742	0.409000	0.25649	0.491000	0.48974	CCT		0.657	ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643	
TSHZ1	10194	broad.mit.edu	37	18	72998443	72998443	+	Frame_Shift_Del	DEL	C	C	-	rs372094271		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr18:72998443delC	ENST00000580243.1	+	2	1429	c.1081delC	c.(1081-1083)cccfs	p.P362fs	TSHZ1_ENST00000322038.5_Frame_Shift_Del_p.P317fs			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	362					anterior/posterior pattern specification (GO:0009952)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|soft palate development (GO:0060023)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.C318fs*14(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(11)|liver(1)|lung(14)|ovary(1)|skin(6)|upper_aerodigestive_tract(2)	42		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		GGACCTGGCGCCCCCCTGCTC	0.597																																					p.P316fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.946delC	18						.						68.0	73.0	71.0					18																	72998443		2203	4300	6503	71127431	SO:0001589	frameshift_variant	10194	exon2			AF039698	CCDS12009.1	18q22.3	2013-11-20	2007-07-16	2006-03-14	ENSG00000179981	ENSG00000179981		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	10669	protein-coding gene	gene with protein product		614427	"""serologically defined colon cancer antigen 33"", ""teashirt zinc finger 1"", ""teashirt family zinc finger 1"""	SDCCAG33		17586487	Standard	NM_005786		Approved	NY-CO-33, TSH1	uc002lly.4	Q6ZSZ6	OTTHUMG00000132859	ENST00000580243.1:c.1081delC	18.37:g.72998443delC	ENSP00000464391:p.Pro362fs		71127431	NM_005786	O60534|Q4LE29|Q53EU4	Frame_Shift_Del	DEL	ENST00000580243.1	37																																																																																					0.597	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786	
ZNF516	9658	broad.mit.edu	37	18	74153391	74153391	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr18:74153391C>T	ENST00000443185.2	-	3	1937	c.1620G>A	c.(1618-1620)gcG>gcA	p.A540A	ZNF516_ENST00000524431.2_5'UTR	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	540					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A540A(1)		central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Prostate(75;0.0869)|Esophageal squamous(42;0.129)		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)		TCTCGCGGCGCGCGCGGCGAT	0.697																																					p.A540A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1620A	18						.						10.0	13.0	12.0					18																	74153391		2041	4128	6169	72282379	SO:0001819	synonymous_variant	9658	exon3			D86975	CCDS74234.1	18q23	2013-01-08				ENSG00000101493		"""Zinc fingers, C2H2-type"""	28990	protein-coding gene	gene with protein product		615114				9039502	Standard	NM_014643		Approved	HsT287, KIAA0222	uc021ulp.1	Q92618		ENST00000443185.2:c.1620G>A	18.37:g.74153391C>T			72282379	NM_014643		Silent	SNP	ENST00000443185.2	37																																																																																					0.697	ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643	
LMNB2	84823	broad.mit.edu	37	19	2431861	2431862	+	Frame_Shift_Ins	INS	-	-	G	rs149126950	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:2431861_2431862insG	ENST00000582871.1	-	10	1655_1656	c.1569_1570insC	c.(1567-1572)ccctcgfs	p.S524fs	LMNB2_ENST00000325327.3_Frame_Shift_Ins_p.S544fs|LMNB2_ENST00000475819.1_5'Flank	NM_032737.3	NP_116126.3	Q03252	LMNB2_HUMAN	lamin B2	524	LTD.|Tail.					lamin filament (GO:0005638)|nuclear inner membrane (GO:0005637)	structural molecule activity (GO:0005198)	p.S524fs*23(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACCAGCGTCGAGGGGGGGCTGT	0.678																																					p.S524fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1570_1571insC	19						.																																			2382862	SO:0001589	frameshift_variant	84823	exon10			M94362	CCDS12090.1, CCDS12090.2	19p13.3	2013-01-16			ENSG00000176619	ENSG00000176619		"""Intermediate filaments type V, lamins"""	6638	protein-coding gene	gene with protein product		150341		LMN2		1630457	Standard	NM_032737		Approved		uc002lvy.4	Q03252	OTTHUMG00000150626	ENST00000582871.1:c.1570dupC	19.37:g.2431868_2431868dupG	ENSP00000462730:p.Ser524fs		2382861	NM_032737	O75292|Q14734|Q96DF6	Frame_Shift_Ins	INS	ENST00000582871.1	37																																																																																					0.678	LMNB2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_032737	
DNMT1	1786	broad.mit.edu	37	19	10265386	10265386	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:10265386C>G	ENST00000340748.4	-	20	1895	c.1660G>C	c.(1660-1662)Gcg>Ccg	p.A554P	DNMT1_ENST00000359526.4_Missense_Mutation_p.A570P|DNMT1_ENST00000540357.1_Missense_Mutation_p.A554P			P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1	554	Interaction with the PRC2/EED-EZH2 complex. {ECO:0000250}.		A -> V (in ADCADN). {ECO:0000269|PubMed:22328086}.		cellular response to amino acid stimulus (GO:0071230)|chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|gene silencing (GO:0016458)|maintenance of DNA methylation (GO:0010216)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methyl-CpG binding (GO:0008327)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.A554P(1)|p.A554T(1)		breast(5)|endometrium(8)|kidney(5)|large_intestine(21)|lung(11)|ovary(2)|pancreas(1)|prostate(10)|skin(5)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Procainamide(DB01035)	ACAAACTGCGCGTGTCGCAGG	0.557																																					p.A570P												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1708C	19						.						52.0	46.0	48.0					19																	10265386		2203	4300	6503	10126386	SO:0001583	missense	1786	exon21			X63692	CCDS12228.1, CCDS45958.1	19p13.2	2014-09-17				ENSG00000130816	2.1.1.37		2976	protein-coding gene	gene with protein product		126375		DNMT		1594447	Standard	NM_001379		Approved	MCMT, CXXC9	uc010xlc.2	P26358		ENST00000340748.4:c.1660G>C	19.37:g.10265386C>G	ENSP00000345739:p.Ala554Pro		10126386	NM_001130823	A0AV63|B7ZLW6|Q9UHG5|Q9ULA2|Q9UMZ6	Missense_Mutation	SNP	ENST00000340748.4	37	CCDS12228.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.198999	0.79015	.	.	ENSG00000130816	ENST00000359526;ENST00000540357;ENST00000340748;ENST00000541266	T;T;T	0.36157	1.27;1.27;1.27	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.63908	0.2551	M	0.78049	2.395	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.66204	-0.5982	10	0.87932	D	0	.	18.77	0.91888	0.0:1.0:0.0:0.0	.	554;570;554	F5GX68;P26358-2;P26358	.;.;DNMT1_HUMAN	P	570;554;554;422	ENSP00000352516:A570P;ENSP00000440457:A554P;ENSP00000345739:A554P	ENSP00000345739:A554P	A	-	1	0	DNMT1	10126386	1.000000	0.71417	0.922000	0.36590	0.143000	0.21401	7.617000	0.83032	2.813000	0.96785	0.655000	0.94253	GCG		0.557	DNMT1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451166.1	NM_001379	
DNM2	1785	broad.mit.edu	37	19	10939809	10939809	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:10939809G>A	ENST00000355667.6	+	19	2236	c.2156G>A	c.(2155-2157)cGg>cAg	p.R719Q	DNM2_ENST00000359692.6_Missense_Mutation_p.R715Q|DNM2_ENST00000408974.4_Missense_Mutation_p.R715Q|DNM2_ENST00000389253.4_Missense_Mutation_p.R719Q|DNM2_ENST00000585892.1_Missense_Mutation_p.R719Q|DNM2_ENST00000314646.5_Missense_Mutation_p.R719Q	NM_001005360.2|NM_001190716.1	NP_001005360.1|NP_001177645.1	P50570	DYN2_HUMAN	dynamin 2	719	GED. {ECO:0000255|PROSITE- ProRule:PRU00720}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|endocytosis (GO:0006897)|G2/M transition of mitotic cell cycle (GO:0000086)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|nitric oxide metabolic process (GO:0046209)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic vesicle transport (GO:0048489)|transferrin transport (GO:0033572)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	enzyme binding (GO:0019899)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|microtubule binding (GO:0008017)	p.R715Q(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	42			Epithelial(33;4.17e-05)|all cancers(31;8.48e-05)			GCACAGCGGCGGGACGACATG	0.622			"""F, N, Splice, Mis, O"""		ETP ALL																																p.R719Q			Rec	yes		19	19p13.2	1785	dynamin 2		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2156A	19						.						52.0	39.0	44.0					19																	10939809		2203	4300	6503	10800809	SO:0001583	missense	1785	exon19				CCDS32907.1, CCDS32908.1, CCDS45968.1, CCDS45969.1, CCDS59351.1	19p	2014-09-17						"""Pleckstrin homology (PH) domain containing"""	2974	protein-coding gene	gene with protein product	"""dynamin II"", ""cytoskeletal protein"""	602378				7590285, 9143510	Standard	NM_001190716		Approved	DYNII, DYN2, CMTDIB, CMTDI1, DI-CMTB	uc002mps.2	P50570		ENST00000355667.6:c.2156G>A	19.37:g.10939809G>A	ENSP00000347890:p.Arg719Gln		10800809	NM_001190716	A8K1B6|E7EV30|E9PEQ4|K7ESI9|Q5I0Y0|Q7Z5S3|Q9UPH4	Missense_Mutation	SNP	ENST00000355667.6	37	CCDS45968.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.219124	0.79464	.	.	ENSG00000079805	ENST00000408974;ENST00000355667;ENST00000359692;ENST00000389253;ENST00000314646;ENST00000545324	T;T;T	0.74737	-0.87;-0.87;-0.87	5.06	5.06	0.68205	GTPase effector domain, GED (1);Dynamin GTPase effector (2);	0.000000	0.64402	D	0.000001	D	0.90710	0.7085	H	0.96518	3.835	0.80722	D	1	D;D;D;P;D;D;D	0.89917	1.0;1.0;1.0;0.931;1.0;1.0;1.0	D;D;D;P;D;D;D	0.91635	0.998;0.995;0.991;0.846;0.999;0.997;0.996	D	0.93728	0.7039	10	0.87932	D	0	.	17.1888	0.86873	0.0:0.0:1.0:0.0	.	313;719;448;715;715;719;719	Q8N1K8;F5H4R9;B4DJ53;A8K1B6;P50570-2;P50570;E9PEQ4	.;.;.;.;.;DYN2_HUMAN;.	Q	715;715;719;719;719;326	ENSP00000386192:R715Q;ENSP00000373905:R719Q;ENSP00000313164:R719Q	ENSP00000313164:R719Q	R	+	2	0	DNM2	10800809	1.000000	0.71417	0.998000	0.56505	0.049000	0.14656	9.625000	0.98406	2.353000	0.79882	0.467000	0.42956	CGG		0.622	DNM2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452592.1	NM_004945	
ZNF433	163059	broad.mit.edu	37	19	12127301	12127301	+	Silent	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:12127301A>G	ENST00000344980.6	-	4	551	c.381T>C	c.(379-381)acT>acC	p.T127T	ZNF433_ENST00000419886.2_Silent_p.T92T|CTD-2006C1.2_ENST00000476474.1_RNA|CTD-2006C1.2_ENST00000495324.1_RNA|CTD-2006C1.2_ENST00000406892.2_RNA	NM_001080411.1	NP_001073880.1	Q8N7K0	ZN433_HUMAN	zinc finger protein 433	127					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T127T(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(1)|prostate(1)|skin(1)	14						CCTTGTGTCCAGTGTCATCTC	0.383																																					p.T127T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T381C	19						.						110.0	113.0	112.0					19																	12127301		2184	4289	6473	11988301	SO:0001819	synonymous_variant	163059	exon4			AK098300	CCDS45983.1	19p13.13	2013-01-08			ENSG00000197647	ENSG00000197647		"""Zinc fingers, C2H2-type"", ""-"""	20811	protein-coding gene	gene with protein product							Standard	NM_001080411		Approved	FLJ40981	uc002msy.1	Q8N7K0	OTTHUMG00000156427	ENST00000344980.6:c.381T>C	19.37:g.12127301A>G			11988301	NM_001080411	Q86VX3	Silent	SNP	ENST00000344980.6	37	CCDS45983.1																																																																																				0.383	ZNF433-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403716.1	NM_152602	
ZNF443	10224	broad.mit.edu	37	19	12541611	12541611	+	Missense_Mutation	SNP	G	G	A	rs143414951		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:12541611G>A	ENST00000301547.5	-	4	1572	c.1375C>T	c.(1375-1377)Cgt>Tgt	p.R459C	CTD-3105H18.16_ENST00000595562.1_Intron	NM_005815.4	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	459					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R459C(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|pancreas(1)|prostate(1)	28						CTGGAAATACGGTAGGCTTTG	0.403																																					p.R459C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1375T	19						.	G	CYS/ARG	4,4402	8.1+/-20.4	0,4,2199	107.0	108.0	108.0		1375	-1.1	0.0	19	dbSNP_134	108	0,8600		0,0,4300	no	missense	ZNF443	NM_005815.4	180	0,4,6499	AA,AG,GG		0.0,0.0908,0.0308	probably-damaging	459/672	12541611	4,13002	2203	4300	6503	12402611	SO:0001583	missense	10224	exon4			AB011414	CCDS32918.1	19p13.13	2013-01-08			ENSG00000180855	ENSG00000180855		"""Zinc fingers, C2H2-type"", ""-"""	20878	protein-coding gene	gene with protein product		606697				9731181	Standard	NM_005815		Approved	ZK1	uc002mtu.3	Q9Y2A4	OTTHUMG00000156404	ENST00000301547.5:c.1375C>T	19.37:g.12541611G>A	ENSP00000301547:p.Arg459Cys		12402611	NM_005815		Missense_Mutation	SNP	ENST00000301547.5	37	CCDS32918.1	.	.	.	.	.	.	.	.	.	.	G	6.887	0.533192	0.13188	9.08E-4	0.0	ENSG00000180855	ENST00000301547;ENST00000411622	T	0.07444	3.19	1.37	-1.12	0.09808	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06962	0.0177	L	0.52126	1.63	0.09310	N	1	B	0.18610	0.029	B	0.15484	0.013	T	0.40831	-0.9542	9	0.56958	D	0.05	.	1.1147	0.01711	0.1824:0.1601:0.4053:0.2522	.	459	Q9Y2A4	ZN443_HUMAN	C	459	ENSP00000301547:R459C	ENSP00000301547:R459C	R	-	1	0	ZNF443	12402611	0.000000	0.05858	0.000000	0.03702	0.296000	0.27459	-1.440000	0.02412	-0.380000	0.07894	-0.534000	0.04291	CGT		0.403	ZNF443-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344084.1	NM_005815	
ZNF791	163049	broad.mit.edu	37	19	12738861	12738861	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:12738861A>G	ENST00000343325.4	+	4	680	c.518A>G	c.(517-519)cAg>cGg	p.Q173R	ZNF490_ENST00000465656.1_Intron|ZNF791_ENST00000458122.3_Missense_Mutation_p.Q141R|ZNF791_ENST00000446165.1_3'UTR|ZNF791_ENST00000540038.1_Missense_Mutation_p.Q64R|AC010422.1_ENST00000408416.1_RNA	NM_153358.2	NP_699189.2	Q3KP31	ZN791_HUMAN	zinc finger protein 791	173					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.Q173R(1)		endometrium(3)|large_intestine(5)|lung(6)|ovary(2)|prostate(3)	19						ATATATCACCAGCCCTTTCAA	0.388																																					p.Q173R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A518G	19						.						58.0	59.0	59.0					19																	12738861		2203	4300	6503	12599861	SO:0001583	missense	163049	exon4			AK074877	CCDS12273.1	19p13.2-p13.13	2013-01-08			ENSG00000173875	ENSG00000173875		"""Zinc fingers, C2H2-type"", ""-"""	26895	protein-coding gene	gene with protein product							Standard	NM_153358		Approved	FLJ90396	uc002mua.2	Q3KP31	OTTHUMG00000156426	ENST00000343325.4:c.518A>G	19.37:g.12738861A>G	ENSP00000342974:p.Gln173Arg		12599861	NM_153358	B7Z586|Q8NC99	Missense_Mutation	SNP	ENST00000343325.4	37	CCDS12273.1	.	.	.	.	.	.	.	.	.	.	A	5.868	0.344248	0.11126	.	.	ENSG00000173875	ENST00000343325;ENST00000393303;ENST00000458122;ENST00000540038	T;T;T	0.07216	3.21;3.21;3.21	1.83	1.83	0.25207	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03695	0.0105	N	0.10782	0.045	0.09310	N	1	P	0.43701	0.815	B	0.32762	0.152	T	0.38866	-0.9641	9	0.62326	D	0.03	.	7.2856	0.26337	1.0:0.0:0.0:0.0	.	173	Q3KP31	ZN791_HUMAN	R	173;155;141;64	ENSP00000342974:Q173R;ENSP00000441761:Q141R;ENSP00000441038:Q64R	ENSP00000342974:Q173R	Q	+	2	0	ZNF791	12599861	0.000000	0.05858	0.341000	0.25589	0.739000	0.42172	-1.919000	0.01572	0.834000	0.34852	0.402000	0.26972	CAG		0.388	ZNF791-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344140.1	NM_153358	
BEST2	54831	broad.mit.edu	37	19	12867087	12867087	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:12867087C>A	ENST00000549706.1	+	9	1405	c.1081C>A	c.(1081-1083)Cag>Aag	p.Q361K	BEST2_ENST00000553030.1_Missense_Mutation_p.Q361K|BEST2_ENST00000042931.1_Missense_Mutation_p.Q361K			Q8NFU1	BEST2_HUMAN	bestrophin 2	361					chloride transmembrane transport (GO:1902476)|membrane depolarization (GO:0051899)|sensory perception of smell (GO:0007608)	chloride channel complex (GO:0034707)|cilium (GO:0005929)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)	p.Q361K(1)		breast(3)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|pancreas(1)	12						GCCTTCCTTCCAGGGCTCCAC	0.612																																					p.Q361K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1081A	19						.						102.0	104.0	103.0					19																	12867087		2032	4185	6217	12728087	SO:0001583	missense	54831	exon8			AF440756	CCDS42506.1	19p13.13	2014-08-12	2006-10-18	2006-10-18	ENSG00000039987	ENSG00000039987		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	17107	protein-coding gene	gene with protein product		607335	"""vitelliform macular dystrophy 2-like 1"""	VMD2L1		12032738, 16912113	Standard	NM_017682		Approved	FLJ20132	uc002mux.3	Q8NFU1	OTTHUMG00000169293	ENST00000549706.1:c.1081C>A	19.37:g.12867087C>A	ENSP00000448310:p.Gln361Lys		12728087	NM_017682	Q53YQ8|Q9NXP0	Missense_Mutation	SNP	ENST00000549706.1	37	CCDS42506.1	.	.	.	.	.	.	.	.	.	.	C	7.135	0.580662	0.13686	.	.	ENSG00000039987	ENST00000549706;ENST00000553030;ENST00000042931	D;D;D	0.97791	-4.54;-4.54;-4.54	4.03	4.03	0.46877	.	0.000000	0.64402	D	0.000002	D	0.93710	0.7990	L	0.31926	0.97	0.54753	D	0.999987	B	0.22909	0.077	B	0.20955	0.032	D	0.90164	0.4230	10	0.02654	T	1	-19.029	15.0879	0.72170	0.0:1.0:0.0:0.0	.	361	Q8NFU1	BEST2_HUMAN	K	361	ENSP00000448310:Q361K;ENSP00000447203:Q361K;ENSP00000042931:Q361K	ENSP00000042931:Q361K	Q	+	1	0	BEST2	12728087	1.000000	0.71417	1.000000	0.80357	0.744000	0.42396	4.624000	0.61254	2.086000	0.62901	0.491000	0.48974	CAG		0.612	BEST2-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403343.1	NM_017682	
MUM1	84939	broad.mit.edu	37	19	1360183	1360183	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:1360183G>C	ENST00000415183.3	+	4	292	c.266G>C	c.(265-267)aGa>aCa	p.R89T	MUM1_ENST00000591806.1_Missense_Mutation_p.R89T|MUM1_ENST00000311401.5_Missense_Mutation_p.R20T|MUM1_ENST00000344663.3_Missense_Mutation_p.R89T			Q2TAK8	MUM1_HUMAN	melanoma associated antigen (mutated) 1	88					chromatin organization (GO:0006325)|DNA repair (GO:0006281)	nucleus (GO:0005634)	nucleosome binding (GO:0031491)	p.R89T(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTGGCCTACAGACGGTCGCTT	0.587											OREG0025088	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R89T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G266C	19						.						69.0	66.0	67.0					19																	1360183		2203	4300	6503	1311183	SO:0001583	missense	84939	exon5			AK075241	CCDS12062.1	19p13.3	2008-02-05				ENSG00000160953			29641	protein-coding gene	gene with protein product						11042152, 7644523	Standard	NM_032853		Approved	MUM-1	uc002lrz.2	Q2TAK8		ENST00000415183.3:c.266G>C	19.37:g.1360183G>C	ENSP00000394925:p.Arg89Thr	595	1311183	NM_032853	A1L489|B5ME02|B7ZLY8|J3KQD6|Q13109|Q5XKB9|Q8N2I4|Q96A67	Missense_Mutation	SNP	ENST00000415183.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.88|13.88	2.369783|2.369783	0.42003|0.42003	.|.	.|.	ENSG00000160953|ENSG00000160953	ENST00000542512|ENST00000344663;ENST00000311401;ENST00000415183	.|T;T;T	.|0.54675	.|0.56;0.56;0.56	4.7|4.7	4.7|4.7	0.59300|0.59300	.|.	.|0.000000	.|0.64402	.|D	.|0.000014	T|T	0.69396|0.69396	0.3106|0.3106	M|M	0.70595|0.70595	2.14|2.14	0.34039|0.34039	D|D	0.654812|0.654812	.|D;D;P;D	.|0.89917	.|1.0;1.0;0.865;1.0	.|D;D;P;D	.|0.83275	.|0.996;0.996;0.519;0.946	T|T	0.77397|0.77397	-0.2603|-0.2603	6|10	0.87932|0.45353	D|T	0|0.12	.|.	13.0197|13.0197	0.58779|0.58779	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|89;89;20;88	.|B7ZLY8;D6W5Y8;Q2TAK8-2;Q2TAK8	.|.;.;.;MUM1_HUMAN	H|T	20|89;20;89	.|ENSP00000345789:R89T;ENSP00000309135:R20T;ENSP00000394925:R89T	ENSP00000439335:D20H|ENSP00000309135:R20T	D|R	+|+	1|2	0|0	MUM1|MUM1	1311183|1311183	0.561000|0.561000	0.26578|0.26578	0.542000|0.542000	0.28115|0.28115	0.107000|0.107000	0.19398|0.19398	4.173000|4.173000	0.58249|0.58249	2.427000|2.427000	0.82271|0.82271	0.655000|0.655000	0.94253|0.94253	GAC|AGA		0.587	MUM1-016	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000449510.1	NM_032853	
NACC1	112939	broad.mit.edu	37	19	13246460	13246460	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:13246460G>A	ENST00000292431.4	+	2	565	c.439G>A	c.(439-441)Gtg>Atg	p.V147M		NM_052876.3	NP_443108.1	Q96RE7	NACC1_HUMAN	nucleus accumbens associated 1, BEN and BTB (POZ) domain containing	147					negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|protein homooligomerization (GO:0051260)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear body (GO:0016604)|nucleus (GO:0005634)		p.V147M(1)		endometrium(3)|large_intestine(2)|lung(3)|skin(1)	9						CCAGAGCCCCGTGGCGCAGAC	0.692																																					p.V147M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G439A	19						.						7.0	8.0	8.0					19																	13246460		2176	4254	6430	13107460	SO:0001583	missense	112939	exon2			AF395817	CCDS12294.1	19p13.13	2013-01-09	2008-10-03	2008-10-03		ENSG00000160877		"""BEN domain containing"", ""BTB/POZ domain containing"""	20967	protein-coding gene	gene with protein product	"""nucleus accumbens associated 1"", ""BEN domain containing 8"""	610672	"""BTB (POZ) domain containing 14B"""	BTBD14B		12477932	Standard	NM_052876		Approved	NAC1, NAC-1, BEND8, BTBD30	uc002mwm.4	Q96RE7		ENST00000292431.4:c.439G>A	19.37:g.13246460G>A	ENSP00000292431:p.Val147Met		13107460	NM_052876		Missense_Mutation	SNP	ENST00000292431.4	37	CCDS12294.1	.	.	.	.	.	.	.	.	.	.	G	14.72	2.620542	0.46736	.	.	ENSG00000160877	ENST00000292431	T	0.55930	0.49	5.08	4.03	0.46877	.	0.070230	0.56097	D	0.000026	T	0.50326	0.1609	L	0.46157	1.445	0.36816	D	0.886159	D	0.57571	0.98	P	0.47981	0.563	T	0.55698	-0.8100	10	0.30078	T	0.28	.	12.7043	0.57051	0.0:0.0:0.834:0.166	.	147	Q96RE7	NACC1_HUMAN	M	147	ENSP00000292431:V147M	ENSP00000292431:V147M	V	+	1	0	NACC1	13107460	1.000000	0.71417	0.894000	0.35097	0.335000	0.28730	5.012000	0.64017	1.125000	0.41998	-0.324000	0.08512	GTG		0.692	NACC1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452879.1	NM_052876	
MRI1	84245	broad.mit.edu	37	19	13879216	13879216	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:13879216C>T	ENST00000319545.8	+	3	472	c.415C>T	c.(415-417)Cag>Tag	p.Q139*	MRI1_ENST00000040663.6_Intron	NM_032285.2	NP_115661.1			methylthioribose-1-phosphate isomerase 1									p.Q139*(1)		breast(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)	6						gcataccaggcagagggaact	0.557																																					p.Q139X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C415T	19						.						40.0	36.0	37.0					19																	13879216		2120	4112	6232	13740216	SO:0001587	stop_gained	84245	exon3				CCDS12297.1, CCDS32923.1	19p13.13	2013-05-29	2013-05-29			ENSG00000037757	5.3.1.23		28469	protein-coding gene	gene with protein product	"""mediator of RhoA-dependent invasion"", ""S-methyl-5-thioribose-1-phosphate isomerase 1"""	615105	"""methylthioribose-1-phosphate isomerase homolog (S. cerevisiae)"""			15215245, 19620624, 23124037	Standard	XR_244089		Approved	MGC3207, Ypr118w, mtnA, MRDI	uc002mxe.3	Q9BV20		ENST00000319545.8:c.415C>T	19.37:g.13879216C>T	ENSP00000314871:p.Gln139*		13740216	NM_032285		Nonsense_Mutation	SNP	ENST00000319545.8	37	CCDS12297.1	.	.	.	.	.	.	.	.	.	.	C	15.00	2.703589	0.48412	.	.	ENSG00000037757	ENST00000319545	.	.	.	1.78	1.78	0.24846	.	.	.	.	.	.	.	.	.	.	.	0.19575	N	0.999968	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	7.0668	0.25157	0.0:1.0:0.0:0.0	.	.	.	.	X	139	.	ENSP00000314871:Q139X	Q	+	1	0	MRI1	13740216	0.019000	0.18553	0.027000	0.17364	0.056000	0.15407	0.787000	0.26858	1.328000	0.45358	0.436000	0.28706	CAG		0.557	MRI1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000453422.1	NM_032285	
ADAMTSL5	339366	broad.mit.edu	37	19	1507271	1507271	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:1507271G>A	ENST00000413997.2	-	9	851	c.852C>T	c.(850-852)gcC>gcT	p.A284A	ADAMTSL5_ENST00000330475.4_Silent_p.A274A|CTB-25B13.9_ENST00000590252.1_RNA|ADAMTSL5_ENST00000590562.1_5'UTR|ADAMTSL5_ENST00000395467.2_Silent_p.A43A			Q6ZMM2	ATL5_HUMAN	ADAMTS-like 5	284						extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.A274A(1)		cervix(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	10		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGGTGGGCCCGGCTGCTTGCA	0.677																																					p.A274A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C822T	19						.						89.0	83.0	85.0					19																	1507271		2203	4300	6503	1458271	SO:0001819	synonymous_variant	339366	exon9			BC040620	CCDS12071.1	19p13.3	2008-02-05	2006-02-07	2006-02-07		ENSG00000185761			27912	protein-coding gene	gene with protein product			"""thrombospondin, type I, domain containing 6"""	THSD6			Standard	NM_213604		Approved		uc002ltd.2	Q6ZMM2		ENST00000413997.2:c.852C>T	19.37:g.1507271G>A			1458271	NM_213604	B4DXK7|Q8IW95	Silent	SNP	ENST00000413997.2	37																																																																																					0.677	ADAMTSL5-202	KNOWN	basic	protein_coding	protein_coding		XM_294919	
CC2D1A	54862	broad.mit.edu	37	19	14041080	14041080	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:14041080G>T	ENST00000318003.7	+	28	3054	c.2813G>T	c.(2812-2814)aGg>aTg	p.R938M	CC2D1A_ENST00000589606.1_Missense_Mutation_p.R937M	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	938					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|signal transducer activity (GO:0004871)	p.R938M(1)		NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	27			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			GCGCTCTATAGGCGGAATCTG	0.637																																					p.R938M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2813T	19						.						155.0	173.0	167.0					19																	14041080		2045	4180	6225	13902080	SO:0001583	missense	54862	exon28			AF536205	CCDS42512.1	19p13.12	2007-01-08				ENSG00000132024			30237	protein-coding gene	gene with protein product	"""mental retardation, nonsyndromic, autosomal recessive, 3"""	610055				12761501, 16033914	Standard	NM_017721		Approved	FLJ20241, MRT3	uc002mxo.2	Q6P1N0		ENST00000318003.7:c.2813G>T	19.37:g.14041080G>T	ENSP00000313601:p.Arg938Met		13902080	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Missense_Mutation	SNP	ENST00000318003.7	37	CCDS42512.1	.	.	.	.	.	.	.	.	.	.	G	16.03	3.005975	0.54361	.	.	ENSG00000132024	ENST00000318003;ENST00000254346	T	0.32988	1.43	4.36	3.24	0.37175	.	0.151774	0.42548	D	0.000684	T	0.34919	0.0914	L	0.42245	1.32	0.37912	D	0.931399	D;D;D	0.71674	0.998;0.986;0.998	P;P;P	0.59288	0.832;0.855;0.844	T	0.36768	-0.9734	10	0.87932	D	0	-10.4946	3.4678	0.07555	0.4091:0.0:0.5909:0.0	.	559;937;938	Q9NX28;Q6P1N0-2;Q6P1N0	.;.;C2D1A_HUMAN	M	938;560	ENSP00000313601:R938M	ENSP00000254346:R560M	R	+	2	0	CC2D1A	13902080	1.000000	0.71417	0.883000	0.34634	0.480000	0.33159	4.149000	0.58091	1.984000	0.57885	0.462000	0.41574	AGG		0.637	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721	
CCDC105	126402	broad.mit.edu	37	19	15121859	15121859	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:15121859C>T	ENST00000292574.3	+	1	304	c.222C>T	c.(220-222)cgC>cgT	p.R74R	SLC1A6_ENST00000430939.2_5'Flank	NM_173482.2	NP_775753.2	Q8IYK2	CC105_HUMAN	coiled-coil domain containing 105	74						extracellular vesicular exosome (GO:0070062)		p.R74R(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(4)|skin(2)	23						GGCGCTTCCGCGTGGAGATGA	0.697																																					p.R74R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C222T	19						.						10.0	10.0	10.0					19																	15121859		2150	4258	6408	14982859	SO:0001819	synonymous_variant	126402	exon1			AK097684	CCDS12322.1	19p13.12	2008-02-05				ENSG00000160994			26866	protein-coding gene	gene with protein product						12477932	Standard	NM_173482		Approved	FLJ40365	uc002nae.2	Q8IYK2		ENST00000292574.3:c.222C>T	19.37:g.15121859C>T			14982859	NM_173482	Q8N7T5|Q8NDL5	Silent	SNP	ENST00000292574.3	37	CCDS12322.1																																																																																				0.697	CCDC105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466293.1	NM_173482	
SYDE1	85360	broad.mit.edu	37	19	15220792	15220792	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:15220792G>A	ENST00000342784.2	+	3	739	c.708G>A	c.(706-708)ccG>ccA	p.P236P	SYDE1_ENST00000600440.1_Silent_p.P169P|SYDE1_ENST00000600252.1_5'UTR	NM_033025.4	NP_149014.3	Q6ZW31	SYDE1_HUMAN	synapse defective 1, Rho GTPase, homolog 1 (C. elegans)	236					activation of Rho GTPase activity (GO:0032862)|positive regulation of synaptic transmission (GO:0050806)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptonemal complex assembly (GO:0007130)	cerebellar mossy fiber (GO:0044300)|cytosol (GO:0005829)|synaptic membrane (GO:0097060)	Rho GTPase activator activity (GO:0005100)	p.P236P(1)		endometrium(4)|kidney(1)|large_intestine(7)|lung(2)|ovary(1)|pancreas(1)|skin(1)	17						GGGACTCACCGGAGCGCCCAG	0.776																																					p.P236P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G708A	19						.						2.0	3.0	3.0					19																	15220792		1259	2352	3611	15081792	SO:0001819	synonymous_variant	85360	exon3			BC029926	CCDS12324.1, CCDS74299.1	19p13.12	2008-02-05				ENSG00000105137			25824	protein-coding gene	gene with protein product						12477932	Standard	XM_005260126		Approved	7h3, FLJ13511	uc002nah.1	Q6ZW31		ENST00000342784.2:c.708G>A	19.37:g.15220792G>A			15081792	NM_033025	Q7L2I8|Q8N6J2|Q9H8K4	Silent	SNP	ENST00000342784.2	37	CCDS12324.1																																																																																				0.776	SYDE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465666.1	NM_033025	
RASAL3	64926	broad.mit.edu	37	19	15565692	15565692	+	Silent	SNP	C	C	T	rs180738895	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:15565692C>T	ENST00000343625.7	-	12	1819	c.1734G>A	c.(1732-1734)gcG>gcA	p.A578A	RASAL3_ENST00000608577.1_5'Flank	NM_022904.1	NP_075055.1	Q86YV0	RASL3_HUMAN	RAS protein activator like 3	578	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)	Ras GTPase activator activity (GO:0005099)	p.A578A(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|skin(1)	18						TGCCCAGCTCCGCAGGGAACC	0.582													C|||	3	0.000599042	0.0008	0.0	5008	,	,		19949	0.002		0.0	False		,,,				2504	0.0				p.A578A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1734A	19						.	C		0,4174		0,0,2087	21.0	25.0	24.0		1734	-4.6	0.9	19		24	1,8419		0,1,4209	no	coding-synonymous	RASAL3	NM_022904.1		0,1,6296	TT,TC,CC		0.0119,0.0,0.0079		578/1012	15565692	1,12593	2087	4210	6297	15426692	SO:0001819	synonymous_variant	64926	exon12				CCDS46006.1	19p13.12	2008-12-18			ENSG00000105122	ENSG00000105122			26129	protein-coding gene	gene with protein product						12477932	Standard	NM_022904		Approved	FLJ21438	uc002nbe.2	Q86YV0		ENST00000343625.7:c.1734G>A	19.37:g.15565692C>T			15426692	NM_022904	Q8N2T9|Q9H735	Silent	SNP	ENST00000343625.7	37	CCDS46006.1																																																																																				0.582	RASAL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461331.3	NM_022904	
OR10H1	26539	broad.mit.edu	37	19	15918475	15918475	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:15918475C>T	ENST00000334920.2	-	1	461	c.373G>A	c.(373-375)Gcc>Acc	p.A125T		NM_013940.2	NP_039228.1	Q9Y4A9	O10H1_HUMAN	olfactory receptor, family 10, subfamily H, member 1	125						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A125T(1)		cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|skin(2)|urinary_tract(1)	29						TGGCAGATGGCCACGTAGCGG	0.642																																					p.A125T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G373A	19						.						51.0	42.0	45.0					19																	15918475		2202	4298	6500	15779475	SO:0001583	missense	26539	exon1			AC004510	CCDS12335.1	19p13.1	2012-08-09				ENSG00000186723		"""GPCR / Class A : Olfactory receptors"""	8172	protein-coding gene	gene with protein product							Standard	NM_013940		Approved		uc002nbq.2	Q9Y4A9		ENST00000334920.2:c.373G>A	19.37:g.15918475C>T	ENSP00000335596:p.Ala125Thr		15779475	NM_013940	Q6IFQ2|Q96R59	Missense_Mutation	SNP	ENST00000334920.2	37	CCDS12335.1	.	.	.	.	.	.	.	.	.	.	.	18.34	3.602029	0.66445	.	.	ENSG00000186723	ENST00000334920	T	0.01947	4.54	4.71	4.71	0.59529	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49305	D	0.000141	T	0.09949	0.0244	H	0.94264	3.515	0.44485	D	0.997426	P	0.48911	0.917	P	0.44447	0.45	T	0.05852	-1.0860	10	0.87932	D	0	.	15.1534	0.72720	0.0:1.0:0.0:0.0	.	125	Q9Y4A9	O10H1_HUMAN	T	125	ENSP00000335596:A125T	ENSP00000335596:A125T	A	-	1	0	OR10H1	15779475	0.999000	0.42202	0.993000	0.49108	0.185000	0.23345	3.525000	0.53502	2.169000	0.68431	0.643000	0.83706	GCC		0.642	OR10H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460364.1		
HSH2D	84941	broad.mit.edu	37	19	16268144	16268144	+	Missense_Mutation	SNP	G	G	A	rs531173054		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:16268144G>A	ENST00000253680.6	+	8	1130	c.599G>A	c.(598-600)cGc>cAc	p.R200H	HSH2D_ENST00000397372.4_Missense_Mutation_p.R111H|HSH2D_ENST00000588246.1_Missense_Mutation_p.R200H|HSH2D_ENST00000593154.2_Missense_Mutation_p.R200H			Q96JZ2	HSH2D_HUMAN	hematopoietic SH2 domain containing	200					negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of mitochondrial depolarization (GO:0051902)|positive regulation of signal transduction (GO:0009967)|T cell activation (GO:0042110)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.R200H(1)		central_nervous_system(1)|kidney(1)|large_intestine(2)	4						GGAGAGACCCGCCAGAAACTC	0.552													G|||	1	0.000199681	0.0	0.0014	5008	,	,		15454	0.0		0.0	False		,,,				2504	0.0				p.R200H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G599A	19						.						43.0	50.0	48.0					19																	16268144		1838	4080	5918	16129144	SO:0001583	missense	84941	exon8			AK027792	CCDS74304.1	19p13.12	2013-02-14				ENSG00000196684		"""SH2 domain containing"""	24920	protein-coding gene	gene with protein product		608349				11700021	Standard	NM_032855		Approved	ALX, HSH2, FLJ14886	uc002ndp.4	Q96JZ2		ENST00000253680.6:c.599G>A	19.37:g.16268144G>A	ENSP00000253680:p.Arg200His		16129144	NM_032855	B5ME72|Q6ZNG7	Missense_Mutation	SNP	ENST00000253680.6	37		.	.	.	.	.	.	.	.	.	.	G	16.04	3.011352	0.54361	.	.	ENSG00000196684	ENST00000397372;ENST00000253680	T	0.46063	0.88	3.81	3.81	0.43845	.	0.952299	0.08563	N	0.927184	T	0.50240	0.1604	L	0.46157	1.445	0.09310	N	1	D;D	0.76494	0.999;0.999	P;P	0.54924	0.764;0.683	T	0.35992	-0.9766	10	0.45353	T	0.12	.	11.493	0.50391	0.0:0.0:1.0:0.0	.	143;200	Q96JZ2-2;Q96JZ2	.;HSH2D_HUMAN	H	111;200	ENSP00000253680:R200H	ENSP00000253680:R200H	R	+	2	0	HSH2D	16129144	0.005000	0.15991	0.017000	0.16124	0.032000	0.12392	1.442000	0.35046	2.412000	0.81896	0.561000	0.74099	CGC		0.552	HSH2D-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_032855	
CHERP	10523	broad.mit.edu	37	19	16643558	16643558	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:16643558G>A	ENST00000198939.6	-	5	561	c.525C>T	c.(523-525)gcC>gcT	p.A175A	CHERP_ENST00000546361.2_Silent_p.A175A|CTD-3222D19.2_ENST00000409035.1_Intron					calcium homeostasis endoplasmic reticulum protein									p.A175A(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|stomach(1)|urinary_tract(3)	24						AGTTCTTCCCGGCCTGCAACA	0.647																																					p.A175A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C525T	19						.						44.0	53.0	50.0					19																	16643558		2112	4227	6339	16504558	SO:0001819	synonymous_variant	10523	exon5			U94836	CCDS42518.1	19p13.1	2013-01-28				ENSG00000085872		"""G patch domain containing"""	16930	protein-coding gene	gene with protein product						8896557, 10794731	Standard	NM_006387		Approved	ERPROT213-21, DAN16	uc002nei.1	Q8IWX8	OTTHUMG00000169304	ENST00000198939.6:c.525C>T	19.37:g.16643558G>A			16504558	NM_006387		Silent	SNP	ENST00000198939.6	37																																																																																					0.647	CHERP-003	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000403372.1	NM_006387	
NWD1	284434	broad.mit.edu	37	19	16860311	16860311	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:16860311G>A	ENST00000552788.1	+	4	858	c.858G>A	c.(856-858)acG>acA	p.T286T	NWD1_ENST00000549814.1_Silent_p.T286T|NWD1_ENST00000523826.1_Silent_p.T80T|NWD1_ENST00000379808.3_Silent_p.T286T|NWD1_ENST00000339803.6_Silent_p.T151T|NWD1_ENST00000524140.2_Silent_p.T286T			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	286							ATP binding (GO:0005524)	p.T151T(1)		NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						AGCTGGATACGGCCGGACAGG	0.602																																					p.T286T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G858A	19						.																																			16721311	SO:0001819	synonymous_variant	284434	exon6			BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"""WD repeat domain containing"""	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.858G>A	19.37:g.16860311G>A			16721311	NM_001007525	C9J021|Q68CT3	Silent	SNP	ENST00000552788.1	37																																																																																					0.602	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525	
GTPBP3	84705	broad.mit.edu	37	19	17450378	17450378	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:17450378A>T	ENST00000324894.8	+	7	1012	c.944A>T	c.(943-945)gAg>gTg	p.E315V	GTPBP3_ENST00000600625.1_Missense_Mutation_p.E315V|GTPBP3_ENST00000358792.7_Missense_Mutation_p.E347V|GTPBP3_ENST00000361619.5_Missense_Mutation_p.E337V|GTPBP3_ENST00000598038.1_3'UTR	NM_032620.3|NM_133644.3	NP_116009.2|NP_598399.2	Q969Y2	GTPB3_HUMAN	GTP binding protein 3 (mitochondrial)	315	TrmE-type G.				tRNA modification (GO:0006400)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.E347V(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|skin(2)|upper_aerodigestive_tract(1)	18						GGGCCCGTGGAGCAGGAGGGC	0.697																																					p.E315V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A944T	19						.						21.0	21.0	21.0					19																	17450378		2197	4295	6492	17311378	SO:0001583	missense	84705	exon7			AF360742	CCDS32950.1, CCDS32951.1, CCDS56088.1, CCDS59364.1	19p13.2	2008-02-05				ENSG00000130299			14880	protein-coding gene	gene with protein product		608536				1290633	Standard	NM_001128855		Approved	MSS1, THDF1, GTPBG3, MTGP1, FLJ14700	uc010xpo.2	Q969Y2		ENST00000324894.8:c.944A>T	19.37:g.17450378A>T	ENSP00000313818:p.Glu315Val		17311378	NM_032620	A6NFH1|A6NIG5|A6NKR4|A8K7B4|B7Z4V8|Q8TCY6|Q8WUW9|Q969G4|Q9BX61	Missense_Mutation	SNP	ENST00000324894.8	37	CCDS32951.1	.	.	.	.	.	.	.	.	.	.	a	25.4	4.635774	0.87760	.	.	ENSG00000130299	ENST00000361619;ENST00000324894;ENST00000358792	T;T;T	0.18174	2.23;2.23;2.23	4.95	4.95	0.65309	Small GTP-binding protein domain (1);GTP-binding domain, HSR1-related (1);	0.102643	0.64402	D	0.000005	T	0.54334	0.1852	H	0.95850	3.73	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.91635	0.997;0.999;0.995;0.985	T	0.69101	-0.5234	10	0.87932	D	0	-33.7411	12.857	0.57890	1.0:0.0:0.0:0.0	.	337;315;315;347	A6NIG5;Q969Y2;Q969Y2-3;Q969Y2-2	.;GTPB3_HUMAN;.;.	V	337;315;347	ENSP00000354598:E337V;ENSP00000313818:E315V;ENSP00000351644:E347V	ENSP00000313818:E315V	E	+	2	0	GTPBP3	17311378	1.000000	0.71417	1.000000	0.80357	0.757000	0.42996	7.951000	0.87819	1.990000	0.58119	0.402000	0.26972	GAG		0.697	GTPBP3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463624.1	NM_032620	
FAM129C	199786	broad.mit.edu	37	19	17657584	17657584	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:17657584C>T	ENST00000335393.4	+	14	1875	c.1737C>T	c.(1735-1737)tgC>tgT	p.C579C	FAM129C_ENST00000332386.5_Silent_p.C579C|FAM129C_ENST00000601861.1_Silent_p.C548C|FAM129C_ENST00000599124.1_Silent_p.C512C|FAM129C_ENST00000595684.1_Silent_p.C579C|FAM129C_ENST00000600871.1_Silent_p.C525C|FAM129C_ENST00000352727.3_Silent_p.C543C|FAM129C_ENST00000449408.2_Silent_p.C305C|FAM129C_ENST00000599164.1_Silent_p.C548C	NM_173544.4	NP_775815	Q86XR2	NIBL2_HUMAN	family with sequence similarity 129, member C	579								p.C579C(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|liver(2)|lung(14)|ovary(1)|skin(3)|stomach(1)	33						TCCGGGGGTGCTTGCTGCAGA	0.632																																					p.C579C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1737T	19						.						67.0	45.0	53.0					19																	17657584		2203	4299	6502	17518584	SO:0001819	synonymous_variant	199786	exon14			AY254198	CCDS12362.1, CCDS42521.1	19p13.11	2008-02-05				ENSG00000167483			24130	protein-coding gene	gene with protein product	B cell novel protein 1	609967				12886250	Standard	NM_173544		Approved	FLJ39802, BCNP1	uc021uqj.1	Q86XR2		ENST00000335393.4:c.1737C>T	19.37:g.17657584C>T			17518584	NM_173544	B4DNU3|B4DVN7|Q7Z6H6|Q86XR3|Q86XR4|Q8TEQ3	Silent	SNP	ENST00000335393.4	37	CCDS12362.1																																																																																				0.632	FAM129C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464206.1	NM_173544	
UNC13A	23025	broad.mit.edu	37	19	17759346	17759346	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:17759346G>A	ENST00000519716.2	-	16	1709	c.1710C>T	c.(1708-1710)tgC>tgT	p.C570C	UNC13A_ENST00000252773.7_Silent_p.C570C|UNC13A_ENST00000552293.1_Silent_p.C570C|UNC13A_ENST00000551649.1_Silent_p.C570C|UNC13A_ENST00000550896.1_Silent_p.C568C|UNC13A_ENST00000428389.2_Silent_p.C658C	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	570					beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)	p.C570C(1)		breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						GCAGCCCCTCGCACTCGTAGC	0.627																																					p.C570C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1710T	19						.						101.0	111.0	107.0					19																	17759346		2199	4299	6498	17620346	SO:0001819	synonymous_variant	23025	exon15			AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.1710C>T	19.37:g.17759346G>A			17620346	NM_001080421	E5RHY9	Silent	SNP	ENST00000519716.2	37	CCDS46013.2																																																																																				0.627	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604	
MAP1S	55201	broad.mit.edu	37	19	17844226	17844226	+	Missense_Mutation	SNP	C	C	T	rs373990918		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:17844226C>T	ENST00000324096.4	+	6	3164	c.3013C>T	c.(3013-3015)Cgt>Tgt	p.R1005C	CTD-3149D2.4_ENST00000595363.1_RNA|MAP1S_ENST00000544059.2_Missense_Mutation_p.R979C	NM_018174.4	NP_060644.4	Q66K74	MAP1S_HUMAN	microtubule-associated protein 1S	1005	Necessary for association with actin. {ECO:0000250}.|Necessary for interaction with RASSF1 isoform A and isoform C.				apoptotic DNA fragmentation (GO:0006309)|brain development (GO:0007420)|execution phase of apoptosis (GO:0097194)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|nervous system development (GO:0007399)|neuron projection morphogenesis (GO:0048812)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	actin filament binding (GO:0051015)|beta-tubulin binding (GO:0048487)|DNA binding (GO:0003677)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)	p.R1005C(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	25						GCATTGGGACCGTGACCTGCA	0.617																																					p.R1005C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3013T	19						.	C	CYS/ARG	0,4404		0,0,2202	34.0	25.0	28.0		3013	-1.0	0.3	19		28	1,8597	1.2+/-3.3	0,1,4298	no	missense	MAP1S	NM_018174.4	180	0,1,6500	TT,TC,CC		0.0116,0.0,0.0077	benign	1005/1060	17844226	1,13001	2202	4299	6501	17705226	SO:0001583	missense	55201	exon6			BC067115	CCDS32954.1	19p13.12	2008-02-05	2006-07-04	2006-07-04		ENSG00000130479			15715	protein-coding gene	gene with protein product		607573	"""chromosome 19 open reading frame 5"", ""VCY2 interacting protein 1"", ""BPY2 interacting protein 1"""	C19orf5, VCY2IP1, BPY2IP1		11827465, 15528209, 16297881, 14627543	Standard	NM_018174		Approved	FLJ10669, MAP8	uc002nhe.1	Q66K74		ENST00000324096.4:c.3013C>T	19.37:g.17844226C>T	ENSP00000325313:p.Arg1005Cys		17705226	NM_018174	B4DH53|Q27QB1|Q6NXF1|Q8N3L8|Q8N3W5|Q8NI88|Q96H94|Q96IT4|Q96SP8|Q9BRC6|Q9H928|Q9NVK7	Missense_Mutation	SNP	ENST00000324096.4	37	CCDS32954.1	.	.	.	.	.	.	.	.	.	.	C	3.563	-0.089148	0.07097	0.0	1.16E-4	ENSG00000130479	ENST00000324096;ENST00000544059	T;T	0.18810	2.19;2.19	4.29	-0.957	0.10350	.	0.645748	0.13467	N	0.385729	T	0.12646	0.0307	L	0.36672	1.1	0.09310	N	1	B;B	0.21821	0.041;0.061	B;B	0.10450	0.005;0.004	T	0.22661	-1.0210	10	0.56958	D	0.05	-5.557	2.9117	0.05739	0.2779:0.4661:0.1534:0.1026	.	979;1005	B4DH53;Q66K74	.;MAP1S_HUMAN	C	1005;979	ENSP00000325313:R1005C;ENSP00000439243:R979C	ENSP00000325313:R1005C	R	+	1	0	MAP1S	17705226	0.000000	0.05858	0.345000	0.25642	0.001000	0.01503	0.019000	0.13444	0.241000	0.21283	-0.282000	0.10007	CGT		0.617	MAP1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466027.1	NM_018174	
JAK3	3718	broad.mit.edu	37	19	17945419	17945419	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:17945419G>A	ENST00000527670.1	-	16	2340	c.2311C>T	c.(2311-2313)Cga>Tga	p.R771*	JAK3_ENST00000534444.1_Nonsense_Mutation_p.R771*|JAK3_ENST00000458235.1_Nonsense_Mutation_p.R771*			P52333	JAK3_HUMAN	Janus kinase 3	771	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell differentiation (GO:0030183)|enzyme linked receptor protein signaling pathway (GO:0007167)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of dendritic cell cytokine production (GO:0002731)|negative regulation of FasL biosynthetic process (GO:0045221)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of T cell activation (GO:0050868)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of thymocyte apoptotic process (GO:0070244)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of T cell apoptotic process (GO:0070232)|response to interleukin-15 (GO:0070672)|response to interleukin-2 (GO:0070669)|response to interleukin-4 (GO:0070670)|response to interleukin-9 (GO:0071104)|STAT protein import into nucleus (GO:0007262)|T cell homeostasis (GO:0043029)|tyrosine phosphorylation of STAT protein (GO:0007260)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)	p.R771*(1)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(85)|kidney(4)|large_intestine(11)|lung(22)|ovary(3)|prostate(5)|skin(1)|stomach(2)|upper_aerodigestive_tract(5)	147					Tofacitinib(DB08895)	ATGACGGCTCGGAAGGAGGGC	0.617		2	Mis		"""acute megakaryocytic leukemia, ETP ALL"""																																p.R771X			Dom	yes		19	19p13.1	3718	Janus kinase 3		L	.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2311T	19	GRCh37	CM012988	JAK3	M		.						48.0	50.0	49.0					19																	17945419		2203	4300	6503	17806419	SO:0001587	stop_gained	3718	exon17			U31601	CCDS12366.1	19p13-p12	2014-09-17	2009-04-23		ENSG00000105639	ENSG00000105639	2.7.10.1		6193	protein-coding gene	gene with protein product	"""tyrosine-protein kinase JAK3"", ""leukocyte Janus kinase"""	600173				8921370, 9226382	Standard	NM_000215		Approved	L-JAK, JAKL, LJAK, JAK3_HUMAN, JAK-3	uc002nhn.4	P52333	OTTHUMG00000165648	ENST00000527670.1:c.2311C>T	19.37:g.17945419G>A	ENSP00000432511:p.Arg771*		17806419	NM_000215	Q13259|Q13260|Q13611|Q8N1E8|Q99699|Q9Y6S2	Nonsense_Mutation	SNP	ENST00000527670.1	37	CCDS12366.1	.	.	.	.	.	.	.	.	.	.	G	40	8.237922	0.98719	.	.	ENSG00000105639	ENST00000458235;ENST00000527670;ENST00000534444	.	.	.	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.6397	15.3385	0.74277	0.0:0.0:1.0:0.0	.	.	.	.	X	771	.	ENSP00000391676:R771X	R	-	1	2	JAK3	17806419	1.000000	0.71417	0.993000	0.49108	0.739000	0.42172	3.280000	0.51677	2.207000	0.71202	0.484000	0.47621	CGA		0.617	JAK3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385549.1	NM_000215	
JAK3	3718	broad.mit.edu	37	19	17947985	17947985	+	Missense_Mutation	SNP	G	G	A	rs587778414		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:17947985G>A	ENST00000527670.1	-	12	1768	c.1739C>T	c.(1738-1740)tCg>tTg	p.S580L	JAK3_ENST00000534444.1_Missense_Mutation_p.S580L|JAK3_ENST00000526008.1_5'Flank|JAK3_ENST00000458235.1_Missense_Mutation_p.S580L			P52333	JAK3_HUMAN	Janus kinase 3	580	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell differentiation (GO:0030183)|enzyme linked receptor protein signaling pathway (GO:0007167)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of dendritic cell cytokine production (GO:0002731)|negative regulation of FasL biosynthetic process (GO:0045221)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of T cell activation (GO:0050868)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of thymocyte apoptotic process (GO:0070244)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of T cell apoptotic process (GO:0070232)|response to interleukin-15 (GO:0070672)|response to interleukin-2 (GO:0070669)|response to interleukin-4 (GO:0070670)|response to interleukin-9 (GO:0071104)|STAT protein import into nucleus (GO:0007262)|T cell homeostasis (GO:0043029)|tyrosine phosphorylation of STAT protein (GO:0007260)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)	p.S580L(1)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(85)|kidney(4)|large_intestine(11)|lung(22)|ovary(3)|prostate(5)|skin(1)|stomach(2)|upper_aerodigestive_tract(5)	147					Tofacitinib(DB08895)	ATGCCGGTACGACACTTGGCT	0.587		2	Mis		"""acute megakaryocytic leukemia, ETP ALL"""																																p.S580L			Dom	yes		19	19p13.1	3718	Janus kinase 3		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1739T	19						.						47.0	34.0	39.0					19																	17947985		2200	4290	6490	17808985	SO:0001583	missense	3718	exon13			U31601	CCDS12366.1	19p13-p12	2014-09-17	2009-04-23		ENSG00000105639	ENSG00000105639	2.7.10.1		6193	protein-coding gene	gene with protein product	"""tyrosine-protein kinase JAK3"", ""leukocyte Janus kinase"""	600173				8921370, 9226382	Standard	NM_000215		Approved	L-JAK, JAKL, LJAK, JAK3_HUMAN, JAK-3	uc002nhn.4	P52333	OTTHUMG00000165648	ENST00000527670.1:c.1739C>T	19.37:g.17947985G>A	ENSP00000432511:p.Ser580Leu		17808985	NM_000215	Q13259|Q13260|Q13611|Q8N1E8|Q99699|Q9Y6S2	Missense_Mutation	SNP	ENST00000527670.1	37	CCDS12366.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.701556	0.88924	.	.	ENSG00000105639	ENST00000458235;ENST00000428406;ENST00000527670;ENST00000534444	T;T;T	0.63744	-0.06;-0.06;-0.06	4.17	4.17	0.49024	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000001	D	0.82715	0.5097	M	0.92970	3.365	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76071	0.983;0.987	D	0.87222	0.2254	10	0.87932	D	0	-24.0981	14.3465	0.66668	0.0:0.0:1.0:0.0	.	580;580	P52333-2;P52333	.;JAK3_HUMAN	L	580	ENSP00000391676:S580L;ENSP00000432511:S580L;ENSP00000436421:S580L	ENSP00000413248:S580L	S	-	2	0	JAK3	17808985	1.000000	0.71417	0.776000	0.31678	0.931000	0.56810	7.168000	0.77570	2.316000	0.78162	0.484000	0.47621	TCG		0.587	JAK3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385549.1	NM_000215	
PIK3R2	5296	broad.mit.edu	37	19	18273019	18273019	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:18273019G>A	ENST00000593731.1	+	8	1469	c.909G>A	c.(907-909)ccG>ccA	p.P303P	PIK3R2_ENST00000222254.8_Silent_p.P303P			O00459	P85B_HUMAN	phosphoinositide-3-kinase, regulatory subunit 2 (beta)	303					blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)	phosphatidylinositol 3-kinase regulator activity (GO:0035014)|receptor tyrosine kinase binding (GO:0030971)	p.P303P(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(3)|pancreas(1)|stomach(1)	24					Isoprenaline(DB01064)	CAGCGCTGCCGCCTAAACCCC	0.612																																					p.P303P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G909A	19						.						24.0	23.0	23.0					19																	18273019		2201	4297	6498	18134019	SO:0001819	synonymous_variant	5296	exon8				CCDS12371.1	19p13.11	2013-03-28	2008-02-04		ENSG00000105647	ENSG00000105647		"""SH2 domain containing"""	8980	protein-coding gene	gene with protein product		603157				1314371	Standard	NM_005027		Approved	P85B, p85	uc002nia.2	O00459	OTTHUMG00000183383	ENST00000593731.1:c.909G>A	19.37:g.18273019G>A			18134019	NM_005027	Q5EAT5|Q9UPH9	Silent	SNP	ENST00000593731.1	37	CCDS12371.1																																																																																				0.612	PIK3R2-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000466386.2	NM_005027	
CILP2	148113	broad.mit.edu	37	19	19654875	19654875	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:19654875C>T	ENST00000291495.5	+	8	1606	c.1521C>T	c.(1519-1521)ggC>ggT	p.G507G	CILP2_ENST00000586018.1_Silent_p.G513G	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	507						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)		p.G507G(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	32						CCTACCAGGGCGACTTTACCA	0.647																																					p.G507G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1521T	19						.						24.0	28.0	27.0					19																	19654875		2203	4300	6503	19515875	SO:0001819	synonymous_variant	148113	exon8			AF542080	CCDS12405.1	19p13.11	2013-01-14				ENSG00000160161		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	24213	protein-coding gene	gene with protein product		612419				12477932	Standard	NM_153221		Approved	MGC45771	uc002nmv.4	Q8IUL8		ENST00000291495.5:c.1521C>T	19.37:g.19654875C>T			19515875	NM_153221	Q6NV88|Q8N4A6|Q8WV21	Silent	SNP	ENST00000291495.5	37	CCDS12405.1																																																																																				0.647	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221	
ZNF57	126295	broad.mit.edu	37	19	2917536	2917536	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:2917536A>C	ENST00000306908.5	+	4	1065	c.917A>C	c.(916-918)aAg>aCg	p.K306T	AC006277.2_ENST00000520090.2_RNA|ZNF57_ENST00000523428.1_Missense_Mutation_p.K274T	NM_173480.2	NP_775751.1	Q68EA5	ZNF57_HUMAN	zinc finger protein 57	306					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K306T(1)		endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|GBM - Glioblastoma multiforme(1328;0.00161)|STAD - Stomach adenocarcinoma(1328;0.18)		ACGGGAGAGAAGCCCTATGAA	0.478																																					p.K306T	NSCLC(150;910 1964 4303 10464 26498)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A917C	19						.						73.0	76.0	75.0					19																	2917536		2203	4300	6503	2868536	SO:0001583	missense	126295	exon4			M88368	CCDS12098.1	19p13.3	2013-01-08			ENSG00000171970	ENSG00000171970		"""Zinc fingers, C2H2-type"", ""-"""	13125	protein-coding gene	gene with protein product			"""zinc finger protein 424"""	ZNF424		1505991	Standard	NM_173480		Approved		uc002lwr.3	Q68EA5	OTTHUMG00000164485	ENST00000306908.5:c.917A>C	19.37:g.2917536A>C	ENSP00000303696:p.Lys306Thr		2868536	NM_173480	Q8N6R9	Missense_Mutation	SNP	ENST00000306908.5	37	CCDS12098.1	.	.	.	.	.	.	.	.	.	.	A	16.00	2.998111	0.54147	.	.	ENSG00000171970	ENST00000306908;ENST00000395204;ENST00000523428	T;T	0.24908	1.83;1.83	2.25	2.25	0.28309	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.49745	0.1575	M	0.85099	2.735	0.25801	N	0.984506	D	0.76494	0.999	D	0.68943	0.961	T	0.30001	-0.9993	9	0.87932	D	0	.	8.0503	0.30575	1.0:0.0:0.0:0.0	.	306	Q68EA5	ZNF57_HUMAN	T	306;308;274	ENSP00000303696:K306T;ENSP00000430223:K274T	ENSP00000303696:K306T	K	+	2	0	ZNF57	2868536	0.007000	0.16637	0.005000	0.12908	0.107000	0.19398	0.524000	0.22940	1.038000	0.40049	0.418000	0.28097	AAG		0.478	ZNF57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378969.1	NM_173480	
NFIC	4782	broad.mit.edu	37	19	3381842	3381842	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:3381842C>T	ENST00000443272.2	+	2	214	c.163C>T	c.(163-165)Cgt>Tgt	p.R55C	NFIC_ENST00000341919.3_Missense_Mutation_p.R55C|NFIC_ENST00000395111.3_Missense_Mutation_p.R46C|NFIC_ENST00000586919.1_Missense_Mutation_p.R46C|NFIC_ENST00000589123.1_Missense_Mutation_p.R46C|NFIC_ENST00000346156.5_Missense_Mutation_p.R46C|NFIC_ENST00000590282.1_Missense_Mutation_p.R55C	NM_001245002.1	NP_001231931.1	P08651	NFIC_HUMAN	nuclear factor I/C (CCAAT-binding transcription factor)	55					DNA replication (GO:0006260)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleolus (GO:0005730)|nucleus (GO:0005634)	core promoter proximal region DNA binding (GO:0001159)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R46C(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.8e-05)|Epithelial(107;2.94e-108)|BRCA - Breast invasive adenocarcinoma(158;0.00154)|STAD - Stomach adenocarcinoma(1328;0.191)		GGACGAGGAGCGTGCGGTCAA	0.647																																					p.R55C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C163T	19						.						107.0	110.0	109.0					19																	3381842		2203	4300	6503	3332842	SO:0001583	missense	4782	exon2			X12492	CCDS12107.1, CCDS45914.1, CCDS58640.1, CCDS59330.1, CCDS59331.1	19p13.3	2008-02-05				ENSG00000141905			7786	protein-coding gene	gene with protein product		600729		NFI		3398920, 7590749	Standard	NM_205843		Approved	CTF, NF-I, CTF5	uc010xhi.2	P08651		ENST00000443272.2:c.163C>T	19.37:g.3381842C>T	ENSP00000396843:p.Arg55Cys		3332842	NM_005597	A8K1H0|B7Z4U5|B7Z9C3|K7EMU1|P08652|Q14932|Q9UPJ3|Q9UPJ9|Q9UPK0|Q9UPK1	Missense_Mutation	SNP	ENST00000443272.2	37	CCDS59330.1	.	.	.	.	.	.	.	.	.	.	C	12.80	2.047827	0.36085	.	.	ENSG00000141905	ENST00000443272;ENST00000395111;ENST00000346156;ENST00000341919;ENST00000343825;ENST00000269778	T;T;T	0.55052	0.54;0.65;0.54	3.77	3.77	0.43336	CTF transcription factor/nuclear factor 1, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.66877	0.2834	M	0.64997	1.995	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.85130	0.993;0.993;0.997;0.997;0.995	T	0.70029	-0.4984	10	0.87932	D	0	.	10.8428	0.46726	0.1892:0.8108:0.0:0.0	.	55;55;46;55;46	B7Z4U5;P08651;P08651-3;P08651-5;P08651-2	.;NFIC_HUMAN;.;.;.	C	46;46;46;55;55;55	ENSP00000378543:R46C;ENSP00000301935:R46C;ENSP00000342194:R55C	ENSP00000269778:R55C	R	+	1	0	NFIC	3332842	1.000000	0.71417	1.000000	0.80357	0.121000	0.20230	1.972000	0.40540	1.805000	0.52779	0.467000	0.42956	CGT		0.647	NFIC-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452834.1	NM_005597	
ZNF98	148198	broad.mit.edu	37	19	22574469	22574469	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:22574469C>T	ENST00000357774.5	-	4	1689	c.1568G>A	c.(1567-1569)tGc>tAc	p.C523Y		NM_001098626.1	NP_001092096.1	A6NK75	ZNF98_HUMAN	zinc finger protein 98	523					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.C523Y(1)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)				GGCTTTGCCGCATTCTTCACA	0.383																																					p.C523Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1568A	19						.						74.0	63.0	67.0					19																	22574469		2177	4275	6452	22366309	SO:0001583	missense	148198	exon4				CCDS46031.1	19p12	2014-02-14	2010-04-20	2008-06-12	ENSG00000197360	ENSG00000197360		"""Zinc fingers, C2H2-type"", ""-"""	13174	protein-coding gene	gene with protein product	"""zinc finger protein 739"""	603980					Standard	NM_001098626		Approved	ZNF739, F7175	uc002nqt.2	A6NK75	OTTHUMG00000182940	ENST00000357774.5:c.1568G>A	19.37:g.22574469C>T	ENSP00000350418:p.Cys523Tyr		22366309	NM_001098626		Missense_Mutation	SNP	ENST00000357774.5	37	CCDS46031.1	.	.	.	.	.	.	.	.	.	.	.	11.19	1.564778	0.27915	.	.	ENSG00000197360	ENST00000357774	D	0.85861	-2.04	1.26	1.26	0.21427	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.92987	0.7768	H	0.95187	3.635	0.33535	D	0.594108	D	0.89917	1.0	D	0.85130	0.997	D	0.91502	0.5220	9	0.62326	D	0.03	.	6.3254	0.21240	0.2919:0.7081:0.0:0.0	.	523	A6NK75	ZNF98_HUMAN	Y	523	ENSP00000350418:C523Y	ENSP00000350418:C523Y	C	-	2	0	ZNF98	22366309	0.944000	0.32072	0.004000	0.12327	0.189000	0.23516	2.563000	0.45922	0.665000	0.31066	0.289000	0.19496	TGC		0.383	ZNF98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464398.1	NM_001098626	
CCNE1	898	broad.mit.edu	37	19	30314671	30314671	+	Missense_Mutation	SNP	C	C	T	rs147896943		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:30314671C>T	ENST00000262643.3	+	12	1499	c.1220C>T	c.(1219-1221)cCg>cTg	p.P407L	CCNE1_ENST00000444983.2_Missense_Mutation_p.P392L|CCNE1_ENST00000357943.5_Missense_Mutation_p.P364L	NM_001238.2	NP_001229.1	P24864	CCNE1_HUMAN	cyclin E1	407					androgen receptor signaling pathway (GO:0030521)|cell division (GO:0051301)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|Wnt signaling pathway (GO:0016055)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)|kinase activity (GO:0016301)|transcription coactivator activity (GO:0003713)	p.P407L(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(12)|skin(1)	20	all_cancers(1;2.19e-31)|all_epithelial(1;1.49e-30)|all_lung(1;1.37e-11)|Lung NSC(1;2.35e-11)|Ovarian(5;0.000902)|Breast(6;0.0203)|Esophageal squamous(110;0.195)		UCEC - Uterine corpus endometrioid carcinoma (4;2.65e-06)|Epithelial(1;6.85e-98)|all cancers(1;1.38e-94)|OV - Ovarian serous cystadenocarcinoma(1;1.38e-90)|STAD - Stomach adenocarcinoma(5;5.8e-07)|GBM - Glioblastoma multiforme(4;0.0394)|Lung(7;0.092)|LUAD - Lung adenocarcinoma(5;0.115)|BRCA - Breast invasive adenocarcinoma(6;0.183)|COAD - Colon adenocarcinoma(1;0.188)|Colorectal(1;0.202)			AGCAGCGGGCCGGAAATGGCG	0.577			A		serous ovarian																																p.P392L			Dom	yes		19	19q12	898	cyclin E1		E	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1175T	19						.	C	LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	76.0	75.0	75.0		1220	0.1	0.0	19	dbSNP_134	75	0,8600		0,0,4300	no	missense	CCNE1	NM_001238.2	98	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	407/411	30314671	1,13005	2203	4300	6503	35006511	SO:0001583	missense	898	exon10			M73812	CCDS12419.1	19q12	2014-07-03			ENSG00000105173	ENSG00000105173			1589	protein-coding gene	gene with protein product	"""cyclin Es"", ""cyclin Et"""	123837		CCNE		1833066	Standard	NM_001238		Approved		uc002nsn.3	P24864	OTTHUMG00000177626	ENST00000262643.3:c.1220C>T	19.37:g.30314671C>T	ENSP00000262643:p.Pro407Leu		35006511	NM_057182	A8K684|Q14091|Q8NFG1|Q92501|Q9UD21	Missense_Mutation	SNP	ENST00000262643.3	37	CCDS12419.1	.	.	.	.	.	.	.	.	.	.	C	7.238	0.600749	0.13939	2.27E-4	0.0	ENSG00000105173	ENST00000262643;ENST00000357943;ENST00000444983	T;T;T	0.46451	1.88;0.87;1.88	5.98	0.0616	0.14341	.	0.920061	0.09453	N	0.800132	T	0.15262	0.0368	N	0.02011	-0.69	0.09310	N	0.999994	B	0.02656	0.0	B	0.01281	0.0	T	0.18209	-1.0344	10	0.54805	T	0.06	.	2.5026	0.04637	0.2827:0.3844:0.0741:0.2587	.	407	P24864	CCNE1_HUMAN	L	407;364;392	ENSP00000262643:P407L;ENSP00000350625:P364L;ENSP00000410179:P392L	ENSP00000262643:P407L	P	+	2	0	CCNE1	35006511	0.858000	0.29795	0.012000	0.15200	0.001000	0.01503	0.300000	0.19156	-0.112000	0.11979	-0.271000	0.10264	CCG		0.577	CCNE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438138.1	NM_001238	
EEF2	1938	broad.mit.edu	37	19	3979966	3979966	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:3979966G>A	ENST00000309311.6	-	10	1533	c.1445C>T	c.(1444-1446)aCg>aTg	p.T482M	SNORD37_ENST00000384048.1_RNA	NM_001961.3	NP_001952.1	P13639	EF2_HUMAN	eukaryotic translation elongation factor 2	482					cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|hematopoietic progenitor cell differentiation (GO:0002244)|positive regulation of gene expression (GO:0010628)|positive regulation of translation (GO:0045727)|translation (GO:0006412)|translational elongation (GO:0006414)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation activator activity (GO:0008494)|translation elongation factor activity (GO:0003746)	p.T482M(1)		endometrium(4)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|GBM - Glioblastoma multiforme(1328;0.0223)|STAD - Stomach adenocarcinoma(1328;0.18)		GATGGTGCCCGTCTTCACCAG	0.597																																					p.T482M	Colon(165;1804 1908 4071 6587 18799)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1445T	19						.						69.0	56.0	61.0					19																	3979966		2203	4300	6503	3930966	SO:0001583	missense	1938	exon10			Z11692	CCDS12117.1	19p13.3	2012-09-20			ENSG00000167658	ENSG00000167658			3214	protein-coding gene	gene with protein product	"""polypeptidyl-tRNA translocase"""	130610		EF2		2610926, 6427766	Standard	NM_001961		Approved	EEF-2	uc002lze.3	P13639		ENST00000309311.6:c.1445C>T	19.37:g.3979966G>A	ENSP00000307940:p.Thr482Met		3930966	NM_001961	B2RMP5|D6W618|Q58J86	Missense_Mutation	SNP	ENST00000309311.6	37	CCDS12117.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.857706	0.91433	.	.	ENSG00000167658	ENST00000543343;ENST00000309311	T	0.81078	-1.45	5.45	5.45	0.79879	Translation elongation factor EFTu/EF1A, domain 2 (1);Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.049591	0.85682	D	0.000000	D	0.93739	0.7999	H	0.97564	4.03	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.95733	0.8776	10	0.87932	D	0	-44.5585	18.2479	0.89993	0.0:0.0:1.0:0.0	.	482	P13639	EF2_HUMAN	M	482	ENSP00000307940:T482M	ENSP00000307940:T482M	T	-	2	0	EEF2	3930966	1.000000	0.71417	0.945000	0.38365	0.972000	0.66771	9.808000	0.99193	2.555000	0.86185	0.561000	0.74099	ACG		0.597	EEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457615.2	NM_001961	
ZBTB7A	51341	broad.mit.edu	37	19	4047941	4047941	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:4047941C>T	ENST00000322357.4	-	3	1842	c.1564G>A	c.(1564-1566)Gcc>Acc	p.A522T	ZBTB7A_ENST00000601588.1_Missense_Mutation_p.A522T	NM_015898.2	NP_056982.1	O95365	ZBT7A_HUMAN	zinc finger and BTB domain containing 7A	522					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone acetyltransferase binding (GO:0035035)|metal ion binding (GO:0046872)	p.A522T(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	14		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.014)|STAD - Stomach adenocarcinoma(1328;0.18)		CTGGGCTgggcgggggcgccg	0.801																																					p.A522T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1564A	19						.						4.0	4.0	4.0					19																	4047941		1948	3627	5575	3998941	SO:0001583	missense	51341	exon3			AF000561	CCDS12119.1	19p13.3	2013-01-08		2005-04-07		ENSG00000178951		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	18078	protein-coding gene	gene with protein product	"""zinc finger and BTB domain containing 7A, HIV-1 inducer of short transcripts binding protein"", ""lymphoma related factor"""	605878	"""zinc finger and BTB domain containing 7"""	ZBTB7		9973611, 9927193	Standard	NM_015898		Approved	FBI-1, LRF, DKFZp547O146, pokemon, ZNF857A	uc002lzi.3	O95365		ENST00000322357.4:c.1564G>A	19.37:g.4047941C>T	ENSP00000323670:p.Ala522Thr		3998941	NM_015898	D6W619|O00456|Q14D41|Q5XG86	Missense_Mutation	SNP	ENST00000322357.4	37	CCDS12119.1	.	.	.	.	.	.	.	.	.	.	C	13.99	2.401097	0.42613	.	.	ENSG00000178951	ENST00000322357	T	0.12672	2.66	3.68	1.12	0.20585	.	0.707193	0.12246	U	0.486099	T	0.05410	0.0143	N	0.14661	0.345	0.09310	N	1	P	0.39782	0.688	B	0.24541	0.054	T	0.34925	-0.9809	10	0.13853	T	0.58	.	10.6089	0.45410	0.0:0.6238:0.3762:0.0	.	522	O95365	ZBT7A_HUMAN	T	522	ENSP00000323670:A522T	ENSP00000323670:A522T	A	-	1	0	ZBTB7A	3998941	0.000000	0.05858	0.369000	0.25952	0.711000	0.40976	-0.016000	0.12613	0.615000	0.30124	0.549000	0.68633	GCC		0.801	ZBTB7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457621.2	NM_015898	
ANKRD27	84079	broad.mit.edu	37	19	33131228	33131228	+	Missense_Mutation	SNP	G	G	A	rs377510221		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:33131228G>A	ENST00000306065.4	-	11	1126	c.968C>T	c.(967-969)aCg>aTg	p.T323M	ANKRD27_ENST00000587352.1_Missense_Mutation_p.T323M	NM_032139.2	NP_115515.2	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	323	VPS9. {ECO:0000255|PROSITE- ProRule:PRU00550}.				early endosome to late endosome transport (GO:0045022)|positive regulation of GTPase activity (GO:0043547)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|lysosome (GO:0005764)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)	p.T323M(1)		breast(3)|endometrium(7)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	42	Esophageal squamous(110;0.137)					AGGGATCTCCGTTTTCACAAG	0.458																																					p.T323M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C968T	19						.	G	MET/THR	0,4406		0,0,2203	117.0	109.0	112.0		968	5.0	1.0	19		112	1,8599	1.2+/-3.3	0,1,4299	no	missense	ANKRD27	NM_032139.2	81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	323/1051	33131228	1,13005	2203	4300	6503	37823068	SO:0001583	missense	84079	exon11			AK054561	CCDS32986.1	19q13.12	2013-01-10				ENSG00000105186		"""Ankyrin repeat domain containing"""	25310	protein-coding gene	gene with protein product	"""Vps9 domain and ankyrin-repeat-containing protein"""					11230166, 16525121	Standard	NM_032139		Approved	FLJ00040, DKFZp434L0718, VARP	uc002ntn.1	Q96NW4		ENST00000306065.4:c.968C>T	19.37:g.33131228G>A	ENSP00000304292:p.Thr323Met		37823068	NM_032139	Q71MF5|Q86UC3|Q8ND80|Q9H0I4	Missense_Mutation	SNP	ENST00000306065.4	37	CCDS32986.1	.	.	.	.	.	.	.	.	.	.	G	19.79	3.892426	0.72524	0.0	1.16E-4	ENSG00000105186	ENST00000306065	T	0.31769	1.48	4.97	4.97	0.65823	Vacuolar sorting protein 9, subgroup (1);Vacuolar sorting protein 9 (2);	0.000000	0.56097	D	0.000036	T	0.51770	0.1694	L	0.49126	1.545	0.53688	D	0.999978	D	0.89917	1.0	D	0.75484	0.986	T	0.53662	-0.8407	10	0.72032	D	0.01	-20.5798	18.6142	0.91296	0.0:0.0:1.0:0.0	.	323	Q96NW4	ANR27_HUMAN	M	323	ENSP00000304292:T323M	ENSP00000304292:T323M	T	-	2	0	ANKRD27	37823068	1.000000	0.71417	1.000000	0.80357	0.708000	0.40852	8.288000	0.89921	2.466000	0.83321	0.557000	0.71058	ACG		0.458	ANKRD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450329.1	NM_032139	
APLP1	333	broad.mit.edu	37	19	36365649	36365649	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:36365649C>T	ENST00000221891.4	+	10	1414	c.1222C>T	c.(1222-1224)Cgt>Tgt	p.R408C	APLP1_ENST00000537454.2_Missense_Mutation_p.R369C|APLP1_ENST00000586861.1_Missense_Mutation_p.R402C|APLP1_ENST00000589298.2_3'UTR	NM_001024807.1|NM_005166.3	NP_001019978.1|NP_005157.1	P51693	APLP1_HUMAN	amyloid beta (A4) precursor-like protein 1	408					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular response to norepinephrine stimulus (GO:0071874)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|mRNA polyadenylation (GO:0006378)|negative regulation of cAMP biosynthetic process (GO:0030818)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|regulation of translation (GO:0006417)	basement membrane (GO:0005604)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|alpha-2B adrenergic receptor binding (GO:0031695)|alpha-2C adrenergic receptor binding (GO:0031696)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|transition metal ion binding (GO:0046914)	p.R408C(1)		breast(4)|endometrium(2)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	33	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			ACAGGCGGAGCGTGTCCTGTT	0.677																																					p.R408C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1222T	19						.						56.0	40.0	45.0					19																	36365649		2203	4298	6501	41057489	SO:0001583	missense	333	exon10			U48437	CCDS32997.1	19q	2008-07-15							597	protein-coding gene	gene with protein product	"""amyloid-like protein 1"", ""amyloid precursor-like protein 1"""	104775				8432545	Standard	NM_001024807		Approved	APLP	uc002ocf.3	P51693		ENST00000221891.4:c.1222C>T	19.37:g.36365649C>T	ENSP00000221891:p.Arg408Cys		41057489	NM_001024807	O00113|Q96A92	Missense_Mutation	SNP	ENST00000221891.4	37	CCDS32997.1	.	.	.	.	.	.	.	.	.	.	C	18.27	3.586109	0.66105	.	.	ENSG00000105290	ENST00000537454;ENST00000221891	T;T	0.51574	0.7;0.7	4.27	1.85	0.25348	Amyloidogenic glycoprotein, E2 domain (2);	0.153019	0.30771	N	0.008908	T	0.63651	0.2529	M	0.74881	2.28	0.54753	D	0.999988	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	P;P;D;D	0.71870	0.853;0.87;0.958;0.975	T	0.67047	-0.5769	10	0.87932	D	0	-8.9873	10.5329	0.44988	0.345:0.655:0.0:0.0	.	402;369;408;408	B7Z4G8;F5GZ08;P51693-2;P51693	.;.;.;APLP1_HUMAN	C	369;408	ENSP00000441501:R369C;ENSP00000221891:R408C	ENSP00000221891:R408C	R	+	1	0	APLP1	41057489	1.000000	0.71417	0.982000	0.44146	0.810000	0.45777	1.918000	0.40006	0.888000	0.36160	0.555000	0.69702	CGT		0.677	APLP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452564.1	NM_001024807	
LRFN3	79414	broad.mit.edu	37	19	36431584	36431584	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:36431584G>T	ENST00000588831.1	+	3	2311	c.1257G>T	c.(1255-1257)aaG>aaT	p.K419N	LRFN3_ENST00000246529.3_Missense_Mutation_p.K419N			Q9BTN0	LRFN3_HUMAN	leucine rich repeat and fibronectin type III domain containing 3	419					cell adhesion (GO:0007155)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)		p.K419N(1)		cervix(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(2)|upper_aerodigestive_tract(1)	12	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			CTTCTGCCAAGGTGGCCGACA	0.682																																					p.K419N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1257T	19						.						47.0	49.0	48.0					19																	36431584		2203	4299	6502	41123424	SO:0001583	missense	79414	exon2			BC003578	CCDS12483.1	19q13.13	2013-02-11				ENSG00000126243		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	28370	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 1"""	612809				12975309, 16495444, 16828986	Standard	NM_024509		Approved	MGC2656, SALM4, FIGLER1	uc002oco.3	Q9BTN0		ENST00000588831.1:c.1257G>T	19.37:g.36431584G>T	ENSP00000466989:p.Lys419Asn		41123424	NM_024509	Q6UY10	Missense_Mutation	SNP	ENST00000588831.1	37	CCDS12483.1	.	.	.	.	.	.	.	.	.	.	G	1.120	-0.655604	0.03480	.	.	ENSG00000126243	ENST00000246529	T	0.54866	0.55	5.07	1.71	0.24356	.	0.000000	0.38164	N	0.001782	T	0.25791	0.0628	N	0.08118	0	0.25618	N	0.986434	B	0.09022	0.002	B	0.09377	0.004	T	0.14952	-1.0454	10	0.18276	T	0.48	.	7.2387	0.26084	0.3823:0.0:0.6177:0.0	.	419	Q9BTN0	LRFN3_HUMAN	N	419	ENSP00000246529:K419N	ENSP00000246529:K419N	K	+	3	2	LRFN3	41123424	0.009000	0.17119	0.980000	0.43619	0.291000	0.27294	0.179000	0.16840	0.524000	0.28502	-0.218000	0.12543	AAG		0.682	LRFN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457403.2	NM_024509	
FSD1	79187	broad.mit.edu	37	19	4306202	4306202	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:4306202C>T	ENST00000221856.6	+	3	266	c.119C>T	c.(118-120)tCg>tTg	p.S40L	FSD1_ENST00000597590.1_Missense_Mutation_p.S40L	NM_024333.2	NP_077309.1	Q9BTV5	FSD1_HUMAN	fibronectin type III and SPRY domain containing 1	40					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)		p.S40L(1)		breast(2)|cervix(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.034)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGGCGAACTCGGCGAAGGTG	0.562																																					p.S40L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C119T	19						.						107.0	108.0	108.0					19																	4306202		2203	4300	6503	4257202	SO:0001583	missense	79187	exon3			AF316829	CCDS12127.1	19p13.3	2013-02-11	2005-03-01			ENSG00000105255		"""Fibronectin type III domain containing"""	13745	protein-coding gene	gene with protein product		609828	"""fibronectin type 3 and SPRY domain containing 1"""			11267680	Standard	NM_024333		Approved	MGC3213, MIR1	uc002lzy.2	Q9BTV5		ENST00000221856.6:c.119C>T	19.37:g.4306202C>T	ENSP00000221856:p.Ser40Leu		4257202	NM_024333	B2RDT0|Q9BXN0|Q9HAG4	Missense_Mutation	SNP	ENST00000221856.6	37	CCDS12127.1	.	.	.	.	.	.	.	.	.	.	C	17.58	3.425319	0.62733	.	.	ENSG00000105255	ENST00000221856	T	0.49432	0.78	4.15	4.15	0.48705	B-box, C-terminal (1);	0.073583	0.56097	D	0.000032	T	0.61763	0.2373	M	0.76574	2.34	0.47276	D	0.999375	D;D	0.69078	0.997;0.997	P;P	0.57152	0.814;0.716	T	0.65817	-0.6076	10	0.46703	T	0.11	.	13.9351	0.64021	0.0:1.0:0.0:0.0	.	27;40	B4DIC5;Q9BTV5	.;FSD1_HUMAN	L	40	ENSP00000221856:S40L	ENSP00000221856:S40L	S	+	2	0	FSD1	4257202	1.000000	0.71417	0.700000	0.30305	0.153000	0.21895	6.908000	0.75730	1.882000	0.54519	0.313000	0.20887	TCG		0.562	FSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458091.1	NM_024333	
ZNF382	84911	broad.mit.edu	37	19	37117812	37117812	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:37117812C>T	ENST00000292928.2	+	5	1126	c.1013C>T	c.(1012-1014)gCc>gTc	p.A338V	ZNF382_ENST00000423582.1_Missense_Mutation_p.A289V|ZNF382_ENST00000435416.1_Missense_Mutation_p.A337V|ZNF382_ENST00000439428.1_Missense_Mutation_p.A337V|CTD-3234P18.2_ENST00000585467.1_lincRNA	NM_001256838.1|NM_032825.4	NP_001243767.1|NP_116214.2	Q96SR6	ZN382_HUMAN	zinc finger protein 382	338	Required for transcriptional repression activity; probably mediates sequence- specific DNA-binding. {ECO:0000250}.				negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A338V(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	34	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			CAGAAGACAGCCCTCACCCTT	0.448																																					p.A338V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1013T	19						.						75.0	74.0	74.0					19																	37117812		2203	4300	6503	41809652	SO:0001583	missense	84911	exon5			AF513816	CCDS33004.1, CCDS58659.1	19q13.13	2013-01-08			ENSG00000161298	ENSG00000161298		"""Zinc fingers, C2H2-type"", ""-"""	17409	protein-coding gene	gene with protein product		609516					Standard	NM_032825		Approved	FLJ14686, KS1	uc010efb.4	Q96SR6	OTTHUMG00000048153	ENST00000292928.2:c.1013C>T	19.37:g.37117812C>T	ENSP00000292928:p.Ala338Val		41809652	NM_032825	A3KMP6|A8MT55|C9K0V5|Q53ZY8|Q5JPJ2	Missense_Mutation	SNP	ENST00000292928.2	37	CCDS33004.1	.	.	.	.	.	.	.	.	.	.	C	15.12	2.740342	0.49045	.	.	ENSG00000161298	ENST00000423582;ENST00000292928;ENST00000439428;ENST00000435416	T;T;T;T	0.08282	3.11;3.11;3.11;3.11	4.47	3.34	0.38264	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.41938	D	0.000791	T	0.07188	0.0182	L	0.35414	1.06	0.24743	N	0.993022	B;B;B	0.24823	0.112;0.112;0.068	B;B;B	0.26416	0.069;0.069;0.031	T	0.26503	-1.0101	10	0.28530	T	0.3	.	11.6192	0.51108	0.1782:0.8218:0.0:0.0	.	337;337;338	Q96SR6-2;Q96SR6-3;Q96SR6	.;.;ZN382_HUMAN	V	289;338;337;337	ENSP00000389722:A289V;ENSP00000292928:A338V;ENSP00000407593:A337V;ENSP00000410113:A337V	ENSP00000292928:A338V	A	+	2	0	ZNF382	41809652	0.000000	0.05858	1.000000	0.80357	0.997000	0.91878	-1.340000	0.02650	2.481000	0.83766	0.591000	0.81541	GCC		0.448	ZNF382-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109562.2	NM_032825	
RYR1	6261	broad.mit.edu	37	19	39075661	39075661	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:39075661G>A	ENST00000359596.3	+	102	14725	c.14725G>A	c.(14725-14727)Gaa>Aaa	p.E4909K	RYR1_ENST00000360985.3_Missense_Mutation_p.E4904K|RYR1_ENST00000355481.4_Missense_Mutation_p.E4904K			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	4909					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.E4909K(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CGCGGGTGACGAATACGAGCT	0.592																																					p.E4904K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G14710A	19						.						267.0	200.0	223.0					19																	39075661		2203	4300	6503	43767501	SO:0001583	missense	6261	exon101			J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.14725G>A	19.37:g.39075661G>A	ENSP00000352608:p.Glu4909Lys		43767501	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	G	15.17	2.754502	0.49362	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.98455	-4.94;-4.94;-4.94	5.08	5.08	0.68730	Ion transport (1);	0.000000	0.64402	U	0.000002	D	0.98538	0.9512	M	0.82056	2.57	0.43010	D	0.994547	D;D	0.71674	0.998;0.998	P;P	0.58391	0.749;0.838	D	0.98953	1.0795	10	0.56958	D	0.05	.	15.0756	0.72074	0.0:0.1424:0.8576:0.0	.	4904;4909	P21817-2;P21817	.;RYR1_HUMAN	K	4909;4904;4904	ENSP00000352608:E4909K;ENSP00000347667:E4904K;ENSP00000354254:E4904K	ENSP00000347667:E4904K	E	+	1	0	RYR1	43767501	0.951000	0.32395	0.993000	0.49108	0.813000	0.45954	3.120000	0.50430	2.658000	0.90341	0.449000	0.29647	GAA		0.592	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
FCGBP	8857	broad.mit.edu	37	19	40366425	40366425	+	Silent	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:40366425C>A	ENST00000221347.6	-	30	13816	c.13809G>T	c.(13807-13809)gcG>gcT	p.A4603A		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4603	VWFD 11. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)		p.A4603A(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			CCGCGTACGCCGCCGGCACGC	0.677																																					p.A4603A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G13809T	19						.						47.0	54.0	52.0					19																	40366425		2203	4298	6501	45058265	SO:0001819	synonymous_variant	8857	exon30			D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.13809G>T	19.37:g.40366425C>A			45058265	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																				0.677	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
FCGBP	8857	broad.mit.edu	37	19	40368478	40368478	+	Silent	SNP	G	G	A	rs77170940		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	A	Unknown	Valid	Germline	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:40368478G>A	ENST00000221347.6	-	28	12877	c.12870C>T	c.(12868-12870)ccC>ccT	p.P4290P		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4290	VWFD 10. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)		p.P4290P(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			AGGTGGTGAAGGGGCCCCCTG	0.617																																					p.P4290P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C12870T	19						.						105.0	100.0	102.0					19																	40368478		2203	4298	6501	45060318	SO:0001819	synonymous_variant	8857	exon28			D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.12870C>T	19.37:g.40368478G>A			45060318	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																				0.617	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
SPTBN4	57731	broad.mit.edu	37	19	41071391	41071391	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:41071391C>T	ENST00000352632.3	+	28	6064	c.5978C>T	c.(5977-5979)gCg>gTg	p.A1993V	SPTBN4_ENST00000338932.3_Missense_Mutation_p.A1993V|SPTBN4_ENST00000392025.1_Missense_Mutation_p.A736V|SPTBN4_ENST00000598249.1_Missense_Mutation_p.A1993V			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	1993					actin filament capping (GO:0051693)|adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cardiac conduction (GO:0061337)|central nervous system projection neuron axonogenesis (GO:0021952)|clustering of voltage-gated sodium channels (GO:0045162)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization to plasma membrane (GO:0090002)|fertilization (GO:0009566)|negative regulation of heart rate (GO:0010459)|positive regulation of multicellular organism growth (GO:0040018)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of sodium ion transport (GO:0002028)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|nuclear matrix (GO:0016363)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|PML body (GO:0016605)|spectrin (GO:0008091)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phosphatase binding (GO:0019902)|phospholipid binding (GO:0005543)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.A1993V(1)		breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	73			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GAGCTGGAGGCGCGGGTGCCT	0.637																																					p.A1993V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5978T	19						.						63.0	64.0	64.0					19																	41071391		2203	4300	6503	45763231	SO:0001583	missense	57731	exon28			AF082075	CCDS12559.1, CCDS42569.1	19q13.13	2013-01-10				ENSG00000160460		"""Pleckstrin homology (PH) domain containing"""	14896	protein-coding gene	gene with protein product		606214				11086001	Standard	NM_020971		Approved	SPTBN3, KIAA1642	uc002onz.3	Q9H254		ENST00000352632.3:c.5978C>T	19.37:g.41071391C>T	ENSP00000263373:p.Ala1993Val		45763231	NM_020971	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Missense_Mutation	SNP	ENST00000352632.3	37	CCDS12559.1	.	.	.	.	.	.	.	.	.	.	C	19.36	3.813176	0.70912	.	.	ENSG00000160460	ENST00000428507;ENST00000352632;ENST00000338932;ENST00000392025	T;T;T	0.55234	0.53;0.53;0.53	4.54	4.54	0.55810	.	0.199731	0.30830	U	0.008782	T	0.50616	0.1626	M	0.74467	2.265	0.80722	D	1	P;P	0.51351	0.915;0.944	B;B	0.35727	0.148;0.209	T	0.63778	-0.6560	10	0.54805	T	0.06	.	16.2652	0.82574	0.0:1.0:0.0:0.0	.	736;1993	C9JY79;Q9H254	.;SPTN4_HUMAN	V	1993;1993;1993;736	ENSP00000263373:A1993V;ENSP00000340345:A1993V;ENSP00000375879:A736V	ENSP00000340345:A1993V	A	+	2	0	SPTBN4	45763231	1.000000	0.71417	0.846000	0.33378	0.788000	0.44548	5.821000	0.69257	2.385000	0.81259	0.549000	0.68633	GCG		0.637	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2		
ADCK4	79934	broad.mit.edu	37	19	41198068	41198068	+	Nonsense_Mutation	SNP	G	G	A	rs368669658		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:41198068G>A	ENST00000324464.3	-	15	1808	c.1507C>T	c.(1507-1509)Cga>Tga	p.R503*	NUMBL_ENST00000598779.1_5'Flank|NUMBL_ENST00000540131.1_5'Flank|ADCK4_ENST00000243583.6_Nonsense_Mutation_p.R462*|NUMBL_ENST00000252891.4_5'Flank|ADCK4_ENST00000450541.1_Nonsense_Mutation_p.R462*|NUMBL_ENST00000599594.1_5'Flank	NM_024876.3	NP_079152.3	Q96D53	ADCK4_HUMAN	aarF domain containing kinase 4	503						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	protein serine/threonine kinase activity (GO:0004674)	p.R503*(2)		NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(6)|stomach(2)|urinary_tract(1)	17			Lung(22;9.49e-05)|LUSC - Lung squamous cell carcinoma(20;0.000219)			ATGTGGGCTCGGAGGTGGGCA	0.692																																					p.R503X												.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C1507T	19						.						32.0	31.0	32.0					19																	41198068		2197	4297	6494	45889908	SO:0001587	stop_gained	79934	exon15			AK022291	CCDS12562.1, CCDS46081.1	19q13.2	2008-02-05				ENSG00000123815			19041	protein-coding gene	gene with protein product		615567					Standard	NM_024876		Approved	FLJ12229, COQ8	uc002oor.2	Q96D53		ENST00000324464.3:c.1507C>T	19.37:g.41198068G>A	ENSP00000315118:p.Arg503*		45889908	NM_024876	Q8TAJ1|Q9HA52	Nonsense_Mutation	SNP	ENST00000324464.3	37	CCDS12562.1	.	.	.	.	.	.	.	.	.	.	G	36	5.768083	0.96914	.	.	ENSG00000123815	ENST00000324464;ENST00000450541;ENST00000243583	.	.	.	5.43	-1.77	0.07982	.	0.686977	0.15303	N	0.269515	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	0.6725	8.025	0.30431	0.074:0.4866:0.3411:0.0982	.	.	.	.	X	503;462;462	.	ENSP00000243583:R462X	R	-	1	2	ADCK4	45889908	0.000000	0.05858	0.063000	0.19743	0.497000	0.33675	-0.335000	0.07873	-0.005000	0.14395	0.561000	0.74099	CGA		0.692	ADCK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462731.1	NM_024876	
CCDC97	90324	broad.mit.edu	37	19	41822573	41822573	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:41822573T>G	ENST00000269967.3	+	2	453	c.331T>G	c.(331-333)Ttc>Gtc	p.F111V		NM_052848.1	NP_443080.1	Q96F63	CCD97_HUMAN	coiled-coil domain containing 97	111								p.F111V(1)		biliary_tract(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)	17						CCTGGAGCGCTTCCGCACAGG	0.632																																					p.F111V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T331G	19						.						54.0	49.0	51.0					19																	41822573		2203	4300	6503	46514413	SO:0001583	missense	90324	exon2			BC011577	CCDS12578.1	19q13.2	2008-02-05							28289	protein-coding gene	gene with protein product						12477932	Standard	NM_052848		Approved	FLJ40267, MGC20255	uc002oqg.3	Q96F63		ENST00000269967.3:c.331T>G	19.37:g.41822573T>G	ENSP00000269967:p.Phe111Val		46514413	NM_052848	Q658N6|Q96IF3	Missense_Mutation	SNP	ENST00000269967.3	37	CCDS12578.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.548365	0.86127	.	.	ENSG00000142039	ENST00000269967	.	.	.	4.66	4.66	0.58398	.	0.072119	0.56097	D	0.000030	T	0.67107	0.2858	M	0.68317	2.08	0.52501	D	0.999955	D	0.55172	0.97	P	0.54346	0.749	T	0.71790	-0.4486	9	0.72032	D	0.01	-5.5766	13.0731	0.59072	0.0:0.0:0.0:1.0	.	111	Q96F63	CCD97_HUMAN	V	111	.	ENSP00000269967:F111V	F	+	1	0	CCDC97	46514413	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.880000	0.75578	1.742000	0.51746	0.455000	0.32223	TTC		0.632	CCDC97-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463293.1	NM_052848	
CEACAM5	1048	broad.mit.edu	37	19	42225008	42225008	+	Silent	SNP	G	G	A	rs144920263		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:42225008G>A	ENST00000221992.6	+	8	2052	c.1938G>A	c.(1936-1938)acG>acA	p.T646T	CEACAM5_ENST00000405816.1_Silent_p.T646T|CEACAM5_ENST00000398599.4_Silent_p.T645T|CEA_ENST00000598976.1_Intron	NM_004363.2	NP_004354.2	P06731	CEAM5_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 5	646	Ig-like 7.			T -> Q (in Ref. 3; AAA62835). {ECO:0000305}.	homotypic cell-cell adhesion (GO:0034109)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of myotube differentiation (GO:0010832)	anchored component of membrane (GO:0031225)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of external side of plasma membrane (GO:0071575)|integral component of plasma membrane (GO:0005887)	GPI anchor binding (GO:0034235)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)	p.T646T(1)		breast(1)|endometrium(3)|kidney(5)|large_intestine(4)|lung(10)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	34				OV - Ovarian serous cystadenocarcinoma(3;0.00278)|all cancers(3;0.00625)|Epithelial(262;0.0379)|GBM - Glioblastoma multiforme(1328;0.142)		CCAAAATCACGCCAAATAATA	0.488																																					p.T646T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1938A	19						.	G		0,4406		0,0,2203	194.0	155.0	168.0		1938	-1.3	0.0	19	dbSNP_134	168	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CEACAM5	NM_004363.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		646/703	42225008	1,13005	2203	4300	6503	46916848	SO:0001819	synonymous_variant	1048	exon8			M17303	CCDS12584.1	19q13.1-q13.2	2013-01-29			ENSG00000105388	ENSG00000105388		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1817	protein-coding gene	gene with protein product		114890		CEA			Standard	XM_005258413		Approved	CD66e	uc002orl.3	P06731	OTTHUMG00000151061	ENST00000221992.6:c.1938G>A	19.37:g.42225008G>A			46916848	NM_004363	H9KVA7	Silent	SNP	ENST00000221992.6	37	CCDS12584.1	.	.	.	.	.	.	.	.	.	.	G	0.857	-0.736738	0.03111	0.0	1.16E-4	ENSG00000105388	ENST00000398599	T	0.11930	2.73	2.44	-1.29	0.09288	.	.	.	.	.	T	0.08447	0.0210	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.39643	-0.9604	5	.	.	.	.	4.0895	0.09963	0.2044:0.0:0.426:0.3696	.	.	.	.	T	642	ENSP00000381600:A642T	.	A	+	1	0	CEACAM5	46916848	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.304000	0.08199	-0.396000	0.07703	-2.104000	0.00359	GCC		0.488	CEACAM5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321132.2	NM_004363	
ERF	2077	broad.mit.edu	37	19	42753762	42753762	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:42753762A>G	ENST00000222329.4	-	4	659	c.502T>C	c.(502-504)Tct>Cct	p.S168P	ERF_ENST00000440177.2_Missense_Mutation_p.S93P|AC006486.9_ENST00000594664.1_Intron|ERF_ENST00000595941.1_5'Flank	NM_006494.2	NP_006485.2	P50548	ERF_HUMAN	Ets2 repressor factor	168	Poly-Ser.				cell cycle (GO:0007049)|cell differentiation (GO:0030154)|chorio-allantoic fusion (GO:0060710)|ectodermal cell differentiation (GO:0010668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)|trophoblast giant cell differentiation (GO:0060707)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription corepressor activity (GO:0003714)	p.S168P(1)		central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(1)	17		Prostate(69;0.00682)				GAAGATGAAGATGAAGAGCAG	0.657																																					p.S168P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T502C	19						.						39.0	43.0	42.0					19																	42753762		2203	4300	6503	47445602	SO:0001583	missense	2077	exon4			U58535	CCDS12600.1	19q13	2008-07-16				ENSG00000105722			3444	protein-coding gene	gene with protein product	"""Ets2 repressor factor"""	611888				7588608, 9192842	Standard	XM_005258644		Approved	PE-2, PE2	uc002ote.4	P50548		ENST00000222329.4:c.502T>C	19.37:g.42753762A>G	ENSP00000222329:p.Ser168Pro		47445602	NM_006494	B2RAP1|B7Z4R0|Q59G38|Q9UPI7	Missense_Mutation	SNP	ENST00000222329.4	37	CCDS12600.1	.	.	.	.	.	.	.	.	.	.	A	12.53	1.966579	0.34659	.	.	ENSG00000105722	ENST00000222329;ENST00000440177	T;T	0.19532	3.15;2.14	4.74	4.74	0.60224	.	0.521709	0.19771	N	0.106433	T	0.19005	0.0456	N	0.08118	0	0.27430	N	0.954033	D	0.65815	0.995	P	0.54889	0.763	T	0.04811	-1.0925	10	0.66056	D	0.02	.	10.8199	0.46599	1.0:0.0:0.0:0.0	.	168	P50548	ERF_HUMAN	P	168;93	ENSP00000222329:S168P;ENSP00000388173:S93P	ENSP00000222329:S168P	S	-	1	0	ERF	47445602	0.023000	0.18921	0.175000	0.22980	0.598000	0.36846	1.293000	0.33353	2.134000	0.65973	0.533000	0.62120	TCT		0.657	ERF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463684.1	NM_006494	
CIC	23152	broad.mit.edu	37	19	42796844	42796844	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:42796844C>T	ENST00000575354.2	+	14	3342	c.3302C>T	c.(3301-3303)gCa>gTa	p.A1101V	CIC_ENST00000572681.2_Missense_Mutation_p.A2009V|CIC_ENST00000160740.3_Missense_Mutation_p.A1100V	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	1101	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.A1101V(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				GGCAGCCCTGCACCCACCTCC	0.662			"""Mis, F, S"""		oligodendroglioma																																p.A1101V			Rec	yes		19	19q13.2	23152	capicua homolog		O	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3302T	19						.						57.0	63.0	61.0					19																	42796844		2203	4300	6503	47488684	SO:0001583	missense	23152	exon14			AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.3302C>T	19.37:g.42796844C>T	ENSP00000458663:p.Ala1101Val		47488684	NM_015125	Q7LGI1|Q9UEG5|Q9Y6T1	Missense_Mutation	SNP	ENST00000575354.2	37	CCDS12601.1	.	.	.	.	.	.	.	.	.	.	C	13.96	2.393185	0.42410	.	.	ENSG00000079432	ENST00000160740	.	.	.	5.05	-2.83	0.05769	.	.	.	.	.	T	0.16128	0.0388	N	0.08118	0	0.20307	N	0.999913	B	0.02656	0.0	B	0.01281	0.0	T	0.24297	-1.0164	8	0.87932	D	0	0.681	5.1763	0.15137	0.0:0.3416:0.1665:0.4919	.	1101	Q96RK0	CIC_HUMAN	V	1101	.	ENSP00000160740:A1101V	A	+	2	0	CIC	47488684	0.010000	0.17322	0.951000	0.38953	0.807000	0.45602	-0.199000	0.09491	-0.157000	0.11059	-0.339000	0.08088	GCA		0.662	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2		
MEGF8	1954	broad.mit.edu	37	19	42840322	42840323	+	Missense_Mutation	DNP	CG	CG	TA			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	CG	CG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:42840322_42840323CG>TA	ENST00000251268.6	+	6	1068_1069	c.1068_1069CG>TA	c.(1066-1071)caCGac>caTAac	p.D357N	MEGF8_ENST00000334370.4_Missense_Mutation_p.D357N	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	357					BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)	p.H356>?(2)		breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				GCACCCCGCACGACCTCTTCTC	0.678																																					.												.	.	2	Complex(2)	large_intestine(2)	c.1068_1069TA	19						.																																			47532163	SO:0001583	missense	1954	exon6			AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"""HBV pre s2 binding protein 1"""	604267	"""EGF-like-domain, multiple 4"", ""chromosome 19 open reading frame 49"""	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	Exception_encountered	19.37:g.42840322_42840323delinsTA	ENSP00000251268:p.Asp357Asn		47532162	NM_001410	A8KAY0|O75097	Missense_Mutation	DNP	ENST00000251268.6	37																																																																																					0.678	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410	
LIPE	3991	broad.mit.edu	37	19	42914540	42914540	+	Silent	SNP	G	G	A	rs370746342		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:42914540G>A	ENST00000244289.4	-	2	1614	c.1338C>T	c.(1336-1338)gaC>gaT	p.D446D	LIPE_ENST00000602000.1_Intron|LIPE-AS1_ENST00000593491.2_RNA|LIPE-AS1_ENST00000599276.1_RNA|LIPE-AS1_ENST00000597203.1_RNA|LIPE-AS1_ENST00000594624.2_RNA	NM_005357.2	NP_005348.2	Q05469	LIPS_HUMAN	lipase, hormone-sensitive	446					cholesterol metabolic process (GO:0008203)|diacylglycerol catabolic process (GO:0046340)|lipid catabolic process (GO:0016042)|long-chain fatty acid catabolic process (GO:0042758)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)	hormone-sensitive lipase activity (GO:0033878)|triglyceride lipase activity (GO:0004806)	p.D446D(1)		breast(2)|endometrium(4)|kidney(7)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		Prostate(69;0.00682)				TGAGCCCCTCGTCGCCCTCAA	0.657																																					p.D446D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1338T	19						.	G		0,4406		0,0,2203	33.0	34.0	33.0		1338	-6.3	0.1	19		33	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	LIPE	NM_005357.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		446/1077	42914540	1,13005	2203	4300	6503	47606380	SO:0001819	synonymous_variant	3991	exon2			L11706	CCDS12607.1	19q13.1-q13.2	2014-03-14			ENSG00000079435	ENSG00000079435	3.1.1.3		6621	protein-coding gene	gene with protein product		151750				8506334	Standard	NM_005357		Approved	HSL	uc002otr.3	Q05469	OTTHUMG00000182814	ENST00000244289.4:c.1338C>T	19.37:g.42914540G>A			47606380	NM_005357	Q3LRT2|Q6NSL7	Silent	SNP	ENST00000244289.4	37	CCDS12607.1																																																																																				0.657	LIPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463861.1	NM_005357	
PSG3	5671	broad.mit.edu	37	19	43237119	43237119	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:43237119C>T	ENST00000327495.5	-	3	710	c.526G>A	c.(526-528)Gca>Aca	p.A176T	PSG3_ENST00000595140.1_Missense_Mutation_p.A176T|PSG3_ENST00000490592.1_5'Flank	NM_021016.3	NP_066296.2	Q16557	PSG3_HUMAN	pregnancy specific beta-1-glycoprotein 3	176	Ig-like C2-type 1.				defense response (GO:0006952)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.A176T(1)		central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	36		Prostate(69;0.00682)				AGGTAGCTTGCGTCCGGAGTC	0.517																																					p.A176T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G526A	19						.						209.0	207.0	208.0					19																	43237119		2203	4298	6501	47928959	SO:0001583	missense	5671	exon3				CCDS12611.1	19q13.2	2013-01-29			ENSG00000221826	ENSG00000221826		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9520	protein-coding gene	gene with protein product		176392				2341148	Standard	NM_021016		Approved		uc002oue.3	Q16557	OTTHUMG00000151120	ENST00000327495.5:c.526G>A	19.37:g.43237119C>T	ENSP00000332215:p.Ala176Thr		47928959	NM_021016	Q08265|Q9BRW2|Q9UPL4|Q9UQ77	Missense_Mutation	SNP	ENST00000327495.5	37	CCDS12611.1	.	.	.	.	.	.	.	.	.	.	-	0.010	-1.783341	0.00628	.	.	ENSG00000221826	ENST00000327495	T	0.12465	2.68	1.59	-1.61	0.08399	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.04048	0.0113	N	0.04724	-0.175	0.09310	N	1	B;B	0.19073	0.033;0.013	B;B	0.20955	0.032;0.022	T	0.42103	-0.9471	9	0.05620	T	0.96	.	2.1773	0.03865	0.0:0.2463:0.3237:0.43	.	154;176	Q08266;Q16557	.;PSG3_HUMAN	T	176	ENSP00000332215:A176T	ENSP00000332215:A176T	A	-	1	0	PSG3	47928959	0.000000	0.05858	0.005000	0.12908	0.005000	0.04900	-1.357000	0.02607	-0.070000	0.12908	-0.515000	0.04445	GCA		0.517	PSG3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321423.2	NM_021016	
ZNF283	284349	broad.mit.edu	37	19	44352520	44352520	+	Silent	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:44352520T>C	ENST00000324461.7	+	7	2064	c.1767T>C	c.(1765-1767)caT>caC	p.H589H	ZNF283_ENST00000588797.1_Silent_p.H450H	NM_181845.1	NP_862828.1	Q8N7M2	ZN283_HUMAN	zinc finger protein 283	589					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H589H(1)		endometrium(1)|large_intestine(3)|lung(4)	8		Prostate(69;0.0352)				TAGTTAAGCATGAGAGAGTCC	0.408																																					p.H589H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1767C	19						.						87.0	97.0	93.0					19																	44352520		2175	4289	6464	49044360	SO:0001819	synonymous_variant	284349	exon7			AK098175	CCDS46097.1, CCDS74387.1	19q13.31	2013-01-08			ENSG00000167637	ENSG00000167637		"""Zinc fingers, C2H2-type"", ""-"""	13077	protein-coding gene	gene with protein product						12743021	Standard	NM_181845		Approved		uc002oxr.4	Q8N7M2		ENST00000324461.7:c.1767T>C	19.37:g.44352520T>C			49044360	NM_181845	B4DGZ5|B7WP04|Q6RFR9|Q86WM6	Silent	SNP	ENST00000324461.7	37	CCDS46097.1																																																																																				0.408	ZNF283-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459909.1	NM_181845	
ZNF233	353355	broad.mit.edu	37	19	44771075	44771075	+	Missense_Mutation	SNP	C	C	T	rs372189870		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:44771075C>T	ENST00000391958.2	+	4	326	c.199C>T	c.(199-201)Cgg>Tgg	p.R67W	ZNF235_ENST00000589799.1_Intron|ZNF233_ENST00000592581.1_Missense_Mutation_p.R67W|ZNF233_ENST00000589522.1_Missense_Mutation_p.R67W|ZNF233_ENST00000334152.1_Missense_Mutation_p.S184L	NM_181756.2	NP_861421.2	A6NK53	ZN233_HUMAN	zinc finger protein 233	67	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R67W(1)		breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(4)|skin(3)|urinary_tract(1)	20		Prostate(69;0.0435)|all_neural(266;0.226)				AGACAAGCTTCGGATGATGGA	0.438																																					p.R67W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C199T	19						.	C	TRP/ARG,TRP/ARG	0,4406		0,0,2203	98.0	96.0	97.0		199,199	-2.8	0.0	19		97	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ZNF233	NM_001207005.1,NM_181756.2	101,101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	67/671,67/671	44771075	1,13005	2203	4300	6503	49462915	SO:0001583	missense	353355	exon4			AY166792	CCDS33047.1	19q13.31	2013-01-08				ENSG00000159915		"""Zinc fingers, C2H2-type"", ""-"""	30946	protein-coding gene	gene with protein product						12743021	Standard	NM_001207005		Approved	FLJ38032	uc021uvi.1	A6NK53		ENST00000391958.2:c.199C>T	19.37:g.44771075C>T	ENSP00000375820:p.Arg67Trp		49462915	NM_181756	B2RN78|B2RN79|Q86WL8	Missense_Mutation	SNP	ENST00000391958.2	37	CCDS33047.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	5.963|5.963	0.361590|0.361590	0.11296|0.11296	0.0|0.0	1.16E-4|1.16E-4	ENSG00000159915|ENSG00000159915	ENST00000391958|ENST00000334152	T|T	0.03920|0.05649	3.76|3.41	3.85|3.85	-2.82|-2.82	0.05787|0.05787	Krueppel-associated box (2);|.	.|.	.|.	.|.	.|.	T|T	0.01189|0.01189	0.0039|0.0039	N|N	0.00074|0.00074	-2.255|-2.255	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.47911|0.47911	-0.9080|-0.9080	9|7	0.02654|0.87932	T|D	1|0	-0.6143|-0.6143	5.6596|5.6596	0.17662|0.17662	0.0:0.464:0.1729:0.363|0.0:0.464:0.1729:0.363	.|.	67|.	A6NK53|.	ZN233_HUMAN|.	W|L	67|184	ENSP00000375820:R67W|ENSP00000334957:S184L	ENSP00000375820:R67W|ENSP00000334957:S184L	R|S	+|+	1|2	2|0	ZNF233|ZNF233	49462915|49462915	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.006000|0.006000	0.05464|0.05464	-0.217000|-0.217000	0.09253|0.09253	-0.868000|-0.868000	0.04058|0.04058	-0.518000|-0.518000	0.04402|0.04402	CGG|TCG		0.438	ZNF233-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000460737.1	NM_181756	
ZNF112	7771	broad.mit.edu	37	19	44832605	44832605	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:44832605G>T	ENST00000337401.4	-	5	1811	c.1723C>A	c.(1723-1725)Cac>Aac	p.H575N	ZNF112_ENST00000536500.1_Missense_Mutation_p.H592N|ZNF112_ENST00000354340.4_Missense_Mutation_p.H569N	NM_001083335.1	NP_001076804.1	Q9UJU3	ZN112_HUMAN	zinc finger protein 112	575					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.H569N(1)									TCTCCAGTGTGGACTCTCTGA	0.438																																					p.H569N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1705A	19						.						151.0	154.0	153.0					19																	44832605		2203	4300	6503	49524445	SO:0001583	missense	7771	exon4			AF198358		19q13.2	2014-02-06	2012-11-27		ENSG00000062370	ENSG00000062370		"""Zinc fingers, C2H2-type"""	12892	protein-coding gene	gene with protein product		603994	"""zinc finger protein 112 homolog (mouse)"", ""zinc finger protein 228"""	ZFP112, ZNF228			Standard	NM_013380		Approved			Q9UJU3	OTTHUMG00000182357	ENST00000337401.4:c.1723C>A	19.37:g.44832605G>T	ENSP00000337081:p.His575Asn		49524445	NM_013380	A4FU53|Q9HCA7	Missense_Mutation	SNP	ENST00000337401.4	37	CCDS54276.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.130626	0.77549	.	.	ENSG00000062370	ENST00000337401;ENST00000412927;ENST00000354340;ENST00000536500;ENST00000253426	T;T;T	0.67345	-0.26;-0.26;-0.26	5.1	5.1	0.69264	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.35903	N	0.002906	D	0.87034	0.6077	H	0.94183	3.505	0.51482	D	0.999929	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.87578	0.998;0.997;0.998	D	0.90657	0.4587	10	0.87932	D	0	-5.3094	17.6533	0.88171	0.0:0.0:1.0:0.0	.	574;592;575	B4DYT4;F5GWS7;Q9UJU3	.;.;ZF112_HUMAN	N	575;575;569;592;574	ENSP00000337081:H575N;ENSP00000346305:H569N;ENSP00000441990:H592N	ENSP00000253426:H574N	H	-	1	0	ZNF285	49524445	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.324000	0.96373	2.541000	0.85698	0.655000	0.94253	CAC		0.438	ZNF112-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460744.1	NM_013380	
CEACAM20	125931	broad.mit.edu	37	19	45024581	45024581	+	RNA	SNP	C	C	T	rs12982449	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:45024581C>T	ENST00000454753.1	-	0	1235							Q6UY09	CEA20_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 20							integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)	15		Prostate(69;0.0352)				CATAGGGCCCCGTGTCATTCC	0.627																																					p.T319T												.	.	0			c.G957A	19						.						58.0	57.0	57.0					19																	45024581		1951	4150	6101	49716421			125931	exon5			AY358129	CCDS74390.1, CCDS74391.1, CCDS74392.1, CCDS74393.1	19q13.31	2013-01-30			ENSG00000176395	ENSG00000273777		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Immunoglobulin superfamily / I-set domain containing"""	24879	protein-coding gene	gene with protein product						12975309	Standard	NM_001102600		Approved	UNQ9366	uc010ejo.1	Q6UY09	OTTHUMG00000151532		19.37:g.45024581C>T			49716421	NM_001102597		Silent	SNP	ENST00000454753.1	37																																																																																					0.627	CEACAM20-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000323032.1	NM_198444	
CKM	1158	broad.mit.edu	37	19	45821217	45821217	+	Missense_Mutation	SNP	C	C	T	rs1803285		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:45821217C>T	ENST00000221476.3	-	3	388	c.214G>A	c.(214-216)Gtg>Atg	p.V72M		NM_001824.4	NP_001815.2	P06732	KCRM_HUMAN	creatine kinase, muscle	72	Phosphagen kinase N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00842}.				cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|phosphocreatine biosynthetic process (GO:0046314)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|creatine kinase activity (GO:0004111)	p.V72M(1)		cervix(1)|endometrium(1)|large_intestine(8)|lung(3)|prostate(2)|skin(2)	17		Ovarian(192;0.0336)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;2.29e-44)|Epithelial(262;1.05e-38)|GBM - Glioblastoma multiforme(486;3.56e-07)	Creatine(DB00148)	ACGCAGCCCACGGTCATGATG	0.592																																					p.V72M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G214A	19						.						64.0	54.0	57.0					19																	45821217		2203	4300	6503	50513057	SO:0001583	missense	1158	exon3			M14780	CCDS12659.1	19q13.32	2012-10-02			ENSG00000104879	ENSG00000104879	2.7.3.2		1994	protein-coding gene	gene with protein product		123310		CKMM			Standard	NM_001824		Approved		uc002pbd.4	P06732		ENST00000221476.3:c.214G>A	19.37:g.45821217C>T	ENSP00000221476:p.Val72Met		50513057	NM_001824	Q96QL9	Missense_Mutation	SNP	ENST00000221476.3	37	CCDS12659.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.649634	0.87958	.	.	ENSG00000104879	ENST00000221476	T	0.70399	-0.48	4.62	4.62	0.57501	ATP:guanido phosphotransferase, N-terminal (4);	0.070689	0.56097	D	0.000026	T	0.78078	0.4227	M	0.86097	2.795	0.58432	D	0.999999	D	0.54772	0.968	P	0.47626	0.552	D	0.83635	0.0147	10	0.87932	D	0	-32.9684	15.0581	0.71930	0.0:1.0:0.0:0.0	rs1803285	72	P06732	KCRM_HUMAN	M	72	ENSP00000221476:V72M	ENSP00000221476:V72M	V	-	1	0	CKM	50513057	1.000000	0.71417	0.995000	0.50966	0.986000	0.74619	7.283000	0.78640	2.418000	0.82041	0.650000	0.86243	GTG		0.592	CKM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457569.1		
DMPK	1760	broad.mit.edu	37	19	46280657	46280657	+	Silent	SNP	G	G	A	rs369938946		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:46280657G>A	ENST00000291270.4	-	8	1199	c.1074C>T	c.(1072-1074)ttC>ttT	p.F358F	DMPK_ENST00000458663.2_Silent_p.F358F|DMPK_ENST00000343373.4_Silent_p.F368F|DMPK_ENST00000595361.1_5'Flank|DMPK_ENST00000354227.5_Silent_p.F358F|DMPK_ENST00000600757.1_Silent_p.F368F|DMPK_ENST00000447742.2_Silent_p.F358F	NM_004409.3	NP_004400.4	Q09013	DMPK_HUMAN	dystrophia myotonica-protein kinase	358	AGC-kinase C-terminal.				cellular calcium ion homeostasis (GO:0006874)|muscle cell apoptotic process (GO:0010657)|nuclear envelope organization (GO:0006998)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|regulation of excitatory postsynaptic membrane potential involved in skeletal muscle contraction (GO:0014853)|regulation of heart contraction (GO:0008016)|regulation of myotube differentiation (GO:0010830)|regulation of skeletal muscle contraction by calcium ion signaling (GO:0014722)|regulation of sodium ion transport (GO:0002028)|regulation of synapse structural plasticity (GO:0051823)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of mitochondrial outer membrane (GO:0031307)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|myosin phosphatase regulator activity (GO:0017020)|protein serine/threonine kinase activity (GO:0004674)	p.F358F(1)|p.F368F(1)		endometrium(5)|kidney(1)|large_intestine(1)|lung(6)|stomach(1)|urinary_tract(2)	16		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00616)|GBM - Glioblastoma multiforme(486;0.0825)|Epithelial(262;0.24)		TGGCACCTTCGAAATCCGGTG	0.647													G|||	1	0.000199681	0.0	0.0	5008	,	,		19300	0.0		0.0	False		,,,				2504	0.001				p.F368F	Esophageal Squamous(35;307 869 9153 24033 28903)											.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1104T	19						.						53.0	44.0	47.0					19																	46280657		2203	4300	6503	50972497	SO:0001819	synonymous_variant	1760	exon7			L19268	CCDS12674.1, CCDS46117.1, CCDS46118.1, CCDS46119.1, CCDS74400.1	19q13.3	2014-02-05					2.7.11.1		2933	protein-coding gene	gene with protein product	"""dystrophia myotonica 1"", ""DM protein kinase"", ""myotonin protein kinase A"", ""myotonic dystrophy associated protein kinase"", ""thymopoietin homolog"""	605377	"""dystrophia myotonica 1 (includes dystrophia myotonia protein kinase)"""	DM1, DM		1546325, 1546326	Standard	NM_001288765		Approved	DMK, DM1PK, MDPK, MT-PK	uc002pdf.1	Q09013		ENST00000291270.4:c.1074C>T	19.37:g.46280657G>A			50972497	NM_001081563	E5KR08|Q16205|Q6P5Z6	Silent	SNP	ENST00000291270.4	37	CCDS12674.1																																																																																				0.647	DMPK-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460572.1	NM_004409	
HIF3A	64344	broad.mit.edu	37	19	46825048	46825048	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:46825048G>A	ENST00000377670.4	+	10	1191	c.1160G>A	c.(1159-1161)cGg>cAg	p.R387Q	AC007193.10_ENST00000596807.1_RNA|HIF3A_ENST00000339613.2_Missense_Mutation_p.R331Q|HIF3A_ENST00000244303.6_Missense_Mutation_p.R318Q|HIF3A_ENST00000300862.3_Missense_Mutation_p.R385Q|HIF3A_ENST00000420102.2_Missense_Mutation_p.R336Q|HIF3A_ENST00000600383.1_Missense_Mutation_p.R318Q|HIF3A_ENST00000472815.1_Missense_Mutation_p.R318Q	NM_152795.3	NP_690008.2	Q9Y2N7	HIF3A_HUMAN	hypoxia inducible factor 3, alpha subunit	387					cellular response to hypoxia (GO:0071456)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|transcription from RNA polymerase II promoter (GO:0006366)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.R385Q(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(14)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	33		Ovarian(192;0.00965)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00204)|all cancers(93;0.0107)|GBM - Glioblastoma multiforme(486;0.0489)|Epithelial(262;0.136)		CCTGGCCCCCGGATCCTTGCC	0.687																																					p.R387Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1160A	19						.						55.0	67.0	63.0					19																	46825048		2203	4300	6503	51516888	SO:0001583	missense	64344	exon10			AK027725	CCDS12681.2, CCDS12682.1, CCDS42580.1, CCDS42580.2	19q13	2013-05-21			ENSG00000124440	ENSG00000124440		"""Basic helix-loop-helix proteins"""	15825	protein-coding gene	gene with protein product		609976				11573933, 11734856	Standard	NM_152794		Approved	IPAS, MOP7, PASD7, bHLHe17	uc002peh.3	Q9Y2N7	OTTHUMG00000141296	ENST00000377670.4:c.1160G>A	19.37:g.46825048G>A	ENSP00000366898:p.Arg387Gln		51516888	NM_152795	B0M185|B4DNA2|Q58A43|Q66K72|Q8WXA1|Q96K34|Q9H7Z9|Q9HAI2	Missense_Mutation	SNP	ENST00000377670.4	37	CCDS12681.2	.	.	.	.	.	.	.	.	.	.	G	7.051	0.564395	0.13498	.	.	ENSG00000124440	ENST00000244302;ENST00000377670;ENST00000244303;ENST00000339613;ENST00000291300;ENST00000300862;ENST00000420102	T;T;T;T;T	0.65364	0.58;-0.15;0.46;0.58;-0.15	4.43	2.21	0.28008	.	1.992350	0.02375	N	0.078257	T	0.47563	0.1452	N	0.24115	0.695	0.26147	N	0.980193	B;B;B;B;B;B;B	0.24533	0.06;0.105;0.008;0.052;0.005;0.005;0.034	B;B;B;B;B;B;B	0.13407	0.009;0.007;0.003;0.006;0.001;0.001;0.003	T	0.27434	-1.0074	10	0.22706	T	0.39	.	6.6904	0.23167	0.2301:0.0:0.7699:0.0	.	336;318;385;336;331;387;387	F5H884;B4DNA2;Q9Y2N7-2;B4DSD9;A8MPQ1;Q9Y2N7;B0M185	.;.;.;.;.;HIF3A_HUMAN;.	Q	387;387;318;331;331;385;336	ENSP00000366898:R387Q;ENSP00000244303:R318Q;ENSP00000341877:R331Q;ENSP00000300862:R385Q;ENSP00000407771:R336Q	ENSP00000244302:R387Q	R	+	2	0	HIF3A	51516888	0.896000	0.30565	1.000000	0.80357	0.313000	0.28021	0.432000	0.21461	0.599000	0.29845	-0.126000	0.14955	CGG		0.687	HIF3A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280556.3		
C5AR1	728	broad.mit.edu	37	19	47823356	47823356	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:47823356G>A	ENST00000355085.3	+	2	344	c.322G>A	c.(322-324)Gcc>Acc	p.A108T		NM_001736.3	NP_001727.1	P21730	C5AR1_HUMAN	complement component 5a receptor 1	108					activation of MAPK activity (GO:0000187)|activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|cell proliferation in hindbrain (GO:0021534)|cellular defense response (GO:0006968)|chemotaxis (GO:0006935)|complement component C5a signaling pathway (GO:0038178)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|inflammatory response (GO:0006954)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of neuron apoptotic process (GO:0043524)|neutrophil chemotaxis (GO:0030593)|organ regeneration (GO:0031100)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|response to lipopolysaccharide (GO:0032496)|response to peptidoglycan (GO:0032494)|sensory perception of chemical stimulus (GO:0007606)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C5a anaphylatoxin receptor activity (GO:0004944)|complement component C5a receptor activity (GO:0004878)	p.A108T(1)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(11)|ovary(2)|prostate(1)|skin(1)	20		all_cancers(25;2e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;0.000267)|OV - Ovarian serous cystadenocarcinoma(262;0.000618)|Epithelial(262;0.0142)|GBM - Glioblastoma multiforme(486;0.0242)		TGGCGGGGCCGCCTGCAGCAT	0.607																																					p.P107P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G321A	19						.						74.0	67.0	69.0					19																	47823356		2203	4300	6503	52515196	SO:0001583	missense	728	exon2				CCDS33063.1	19q13.3-q13.4	2012-08-10	2006-02-09	2006-02-09		ENSG00000197405		"""CD molecules"", ""Complement system"", ""GPCR / Class A : Complement component receptors"""	1338	protein-coding gene	gene with protein product		113995	"""complement component 5 receptor 1 (C5a ligand)"""	C5R1		1612600	Standard	NM_001736		Approved	C5A, C5AR, CD88	uc002pgj.1	P21730		ENST00000355085.3:c.322G>A	19.37:g.47823356G>A	ENSP00000347197:p.Ala108Thr		52515196	NM_001736		Missense_Mutation	SNP	ENST00000355085.3	37	CCDS33063.1	.	.	.	.	.	.	.	.	.	.	G	18.22	3.576846	0.65878	.	.	ENSG00000197405	ENST00000355085	T	0.38240	1.15	4.67	3.58	0.41010	GPCR, rhodopsin-like superfamily (1);	0.142652	0.45867	U	0.000323	T	0.40886	0.1135	M	0.68952	2.095	0.36780	D	0.884319	P	0.50272	0.933	P	0.50490	0.642	T	0.44421	-0.9329	10	0.31617	T	0.26	.	6.9602	0.24593	0.0912:0.0:0.735:0.1739	.	108	P21730	C5AR_HUMAN	T	108	ENSP00000347197:A108T	ENSP00000347197:A108T	A	+	1	0	C5AR1	52515196	0.000000	0.05858	0.479000	0.27329	0.034000	0.12701	-0.119000	0.10676	2.128000	0.65567	0.478000	0.44815	GCC		0.607	C5AR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466925.1	NM_001736	
LIG1	3978	broad.mit.edu	37	19	48634423	48634423	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:48634423G>A	ENST00000263274.7	-	19	2150	c.1731C>T	c.(1729-1731)caC>caT	p.H577H	LIG1_ENST00000427526.2_Silent_p.H546H|LIG1_ENST00000536218.1_Silent_p.H509H	NM_000234.1	NP_000225.1	P18858	DNLI1_HUMAN	ligase I, DNA, ATP-dependent	577					anatomical structure morphogenesis (GO:0009653)|base-excision repair (GO:0006284)|cell division (GO:0051301)|DNA biosynthetic process (GO:0071897)|DNA ligation involved in DNA repair (GO:0051103)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|response to hydrogen peroxide (GO:0042542)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|metal ion binding (GO:0046872)	p.H577H(1)		breast(1)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(22)|prostate(2)|skin(1)	44		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	CTTCCAGGGCGTGGATCTGTC	0.572								Nucleotide excision repair (NER)																													p.H577H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1731T	19						.						142.0	95.0	111.0					19																	48634423		2203	4300	6503	53326235	SO:0001819	synonymous_variant	3978	exon19				CCDS12711.1, CCDS74409.1, CCDS74410.1	19q13.2-q13.3	2014-09-17				ENSG00000105486	6.5.1.1		6598	protein-coding gene	gene with protein product		126391					Standard	XM_005258934		Approved		uc002pia.1	P18858		ENST00000263274.7:c.1731C>T	19.37:g.48634423G>A			53326235	NM_000234	B2RAI8|Q2TB12|Q32P23	Silent	SNP	ENST00000263274.7	37	CCDS12711.1																																																																																				0.572	LIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465575.1	NM_000234	
SYNGR4	23546	broad.mit.edu	37	19	48869127	48869127	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:48869127C>T	ENST00000344846.2	+	2	278	c.28C>T	c.(28-30)Ctg>Ttg	p.L10L	TMEM143_ENST00000435956.3_5'Flank|TMEM143_ENST00000293261.3_5'Flank|TMEM143_ENST00000377431.2_5'Flank|TMEM143_ENST00000436660.2_5'Flank|TMEM143_ENST00000598012.1_5'Flank|TMEM143_ENST00000541566.1_5'Flank	NM_012451.3	NP_036583.2	O95473	SNG4_HUMAN	synaptogyrin 4	10						integral component of membrane (GO:0016021)		p.L10L(1)		breast(1)|endometrium(2)|large_intestine(4)|lung(2)|skin(1)	10		all_epithelial(76;5.08e-07)|all_lung(116;5.76e-06)|Lung NSC(112;1.18e-05)|Prostate(7;0.0143)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000138)|all cancers(93;0.00017)|Epithelial(262;0.0138)|GBM - Glioblastoma multiforme(486;0.0146)		CCTCCAGGAGCTGGCCAACAG	0.657																																					p.L10L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C28T	19						.						101.0	99.0	100.0					19																	48869127		2203	4300	6503	53560939	SO:0001819	synonymous_variant	23546	exon2			AJ011733	CCDS12717.1	19q13.3	2008-07-04				ENSG00000105467			11502	protein-coding gene	gene with protein product		608373					Standard	NM_012451		Approved		uc002piz.3	O95473		ENST00000344846.2:c.28C>T	19.37:g.48869127C>T			53560939	NM_012451	Q3KP58	Silent	SNP	ENST00000344846.2	37	CCDS12717.1																																																																																				0.657	SYNGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465704.1		
GRIN2D	2906	broad.mit.edu	37	19	48925182	48925182	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:48925182G>A	ENST00000263269.3	+	10	2320	c.2232G>A	c.(2230-2232)gcG>gcA	p.A744A		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	744					adult locomotory behavior (GO:0008344)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|regulation of sensory perception of pain (GO:0051930)|signal transduction (GO:0007165)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)	p.A744A(1)		autonomic_ganglia(1)|breast(6)|endometrium(2)|large_intestine(9)|lung(12)|ovary(5)|pancreas(1)|prostate(1)	37		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	TAGAGGAAGCGCTCACTCAGC	0.642																																					p.A744A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2232A	19						.						66.0	62.0	63.0					19																	48925182		2203	4300	6503	53616994	SO:0001819	synonymous_variant	2906	exon10			U77783	CCDS12719.1	19q13.33	2012-08-29			ENSG00000105464	ENSG00000105464		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4588	protein-coding gene	gene with protein product	"""N-methyl-d-aspartate receptor subunit 2D"""	602717		NMDAR2D		9480759, 9418891	Standard	NM_000836		Approved	GluN2D, EB11, NR2D	uc002pjc.4	O15399		ENST00000263269.3:c.2232G>A	19.37:g.48925182G>A			53616994	NM_000836		Silent	SNP	ENST00000263269.3	37	CCDS12719.1																																																																																				0.642	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1		
HSD17B14	51171	broad.mit.edu	37	19	49334994	49334994	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:49334994C>A	ENST00000263278.4	-	5	566	c.300G>T	c.(298-300)gaG>gaT	p.E100D	HSD17B14_ENST00000599157.1_Intron	NM_016246.2	NP_057330.2	Q9BPX1	DHB14_HUMAN	hydroxysteroid (17-beta) dehydrogenase 14	100					steroid catabolic process (GO:0006706)	cytosol (GO:0005829)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)	p.E100D(1)		large_intestine(3)|lung(1)|skin(1)	5		all_epithelial(76;7e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000341)|all cancers(93;0.000764)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.0346)		CAGAGGTCTCCTCAGGCCTCT	0.632																																					p.E100D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G300T	19						.						49.0	52.0	51.0					19																	49334994		2203	4300	6503	54026806	SO:0001583	missense	51171	exon5			AF126781	CCDS12736.1	19q13.33	2011-09-14	2006-11-22	2006-11-22		ENSG00000087076		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	23238	protein-coding gene	gene with protein product	"""retinal short-chain dehydrogenase/reductase 3"", ""short chain dehydrogenase/reductase family 47C, member 1"""	612832	"""dehydrogenase/reductase (SDR family) member 10"""	DHRS10		10800688, 17067289, 19027726	Standard	XM_005258969		Approved	retSDR3, SDR47C1	uc002pkv.1	Q9BPX1		ENST00000263278.4:c.300G>T	19.37:g.49334994C>A	ENSP00000263278:p.Glu100Asp		54026806	NM_016246	Q9UKU3	Missense_Mutation	SNP	ENST00000263278.4	37	CCDS12736.1	.	.	.	.	.	.	.	.	.	.	C	0.127	-1.118233	0.01785	.	.	ENSG00000087076	ENST00000263278	D	0.87887	-2.31	4.26	2.09	0.27110	NAD(P)-binding domain (1);	0.271871	0.33477	N	0.004873	T	0.76234	0.3959	L	0.37561	1.115	0.29912	N	0.823461	B	0.02656	0.0	B	0.08055	0.003	T	0.62196	-0.6905	10	0.17369	T	0.5	.	6.4383	0.21835	0.0:0.7788:0.0:0.2212	.	100	Q9BPX1	DHB14_HUMAN	D	100	ENSP00000263278:E100D	ENSP00000263278:E100D	E	-	3	2	HSD17B14	54026806	0.997000	0.39634	0.967000	0.41034	0.019000	0.09904	0.352000	0.20113	1.140000	0.42260	0.558000	0.71614	GAG		0.632	HSD17B14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466212.1	NM_016246	
PPP1R15A	23645	broad.mit.edu	37	19	49377339	49377339	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:49377339A>T	ENST00000200453.5	+	2	1118	c.849A>T	c.(847-849)gaA>gaT	p.E283D		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	283	Glu-rich.				apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)	p.E283D(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		GGAAAGGAGAAGCTGCCCCAG	0.607																																					p.E283D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A849T	19						.						59.0	75.0	70.0					19																	49377339		2203	4300	6503	54069151	SO:0001583	missense	23645	exon2			U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14375	protein-coding gene	gene with protein product	"""growth arrest and DNA-damage-inducible 34"""	611048	"""protein phosphatase 1, regulatory (inhibitor) subunit 15A"""			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.849A>T	19.37:g.49377339A>T	ENSP00000200453:p.Glu283Asp		54069151	NM_014330	B4DKQ3|Q6IA96|Q9NVU6	Missense_Mutation	SNP	ENST00000200453.5	37	CCDS12738.1	.	.	.	.	.	.	.	.	.	.	A	10.01	1.234347	0.22626	.	.	ENSG00000087074	ENST00000200453;ENST00000540695;ENST00000544084	T	0.06142	3.34	3.85	-0.0501	0.13832	.	2.815450	0.01559	N	0.020036	T	0.04497	0.0123	L	0.27053	0.805	0.09310	N	1	B	0.12013	0.005	B	0.08055	0.003	T	0.35599	-0.9782	10	0.14252	T	0.57	-1.3759	1.1155	0.01713	0.4219:0.2958:0.1156:0.1667	.	283	O75807	PR15A_HUMAN	D	283;123;241	ENSP00000200453:E283D	ENSP00000200453:E283D	E	+	3	2	PPP1R15A	54069151	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-2.208000	0.01229	-0.320000	0.08640	0.528000	0.53228	GAA		0.607	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330	
TBC1D17	79735	broad.mit.edu	37	19	50387731	50387731	+	Missense_Mutation	SNP	T	T	C	rs202133410		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:50387731T>C	ENST00000221543.5	+	12	1558	c.1259T>C	c.(1258-1260)aTg>aCg	p.M420T	TBC1D17_ENST00000535102.2_Missense_Mutation_p.M387T	NM_024682.2	NP_078958	Q9HA65	TBC17_HUMAN	TBC1 domain family, member 17	420	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				autophagy (GO:0006914)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	Rab GTPase activator activity (GO:0005097)	p.M420T(1)		NS(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15		all_lung(116;0.000338)|Lung NSC(112;0.000446)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.017)		GTCCAGGGCATGAGTGATCTT	0.637																																					p.M387T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1160C	19						.						179.0	169.0	172.0					19																	50387731		2203	4300	6503	55079543	SO:0001583	missense	79735	exon11			AK090606	CCDS12785.1, CCDS54294.1	19q13.33	2013-07-09				ENSG00000104946			25699	protein-coding gene	gene with protein product						22854040	Standard	NM_024682		Approved	FLJ12168	uc002pqo.3	Q9HA65		ENST00000221543.5:c.1259T>C	19.37:g.50387731T>C	ENSP00000221543:p.Met420Thr		55079543	NM_001168222	B4DT12|B9A6L8|F5H1W7	Missense_Mutation	SNP	ENST00000221543.5	37	CCDS12785.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.061004	0.76074	.	.	ENSG00000104946	ENST00000221543;ENST00000535102	T;T	0.18657	2.2;2.2	5.22	5.22	0.72569	Rab-GAP/TBC domain (4);	0.000000	0.85682	D	0.000000	T	0.64864	0.2637	H	0.99238	4.48	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.79799	-0.1651	10	0.87932	D	0	-36.2632	13.0289	0.58831	0.0:0.0:0.0:1.0	.	387;420	F5H1W7;Q9HA65	.;TBC17_HUMAN	T	420;387	ENSP00000221543:M420T;ENSP00000446323:M387T	ENSP00000221543:M420T	M	+	2	0	TBC1D17	55079543	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.441000	0.80485	1.962000	0.57031	0.459000	0.35465	ATG		0.637	TBC1D17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466404.1	NM_024682	
MYH14	79784	broad.mit.edu	37	19	50775222	50775222	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:50775222C>T	ENST00000596571.1	+	23	3165	c.3165C>T	c.(3163-3165)gaC>gaT	p.D1055D	MYH14_ENST00000425460.1_Silent_p.D1063D|MYH14_ENST00000376970.2_Silent_p.D1088D|MYH14_ENST00000601313.1_Silent_p.D1096D|MYH14_ENST00000262269.8_Silent_p.D1096D|MYH14_ENST00000440075.2_Silent_p.D1096D|MYH14_ENST00000598205.1_Silent_p.D1063D			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1055					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.D1096D(1)|p.T1055I(1)		central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		CAATCGCAGACATGGAGGGTG	0.582																																					p.D1063D												.	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(2)	c.C3189T	19						.						32.0	34.0	33.0					19																	50775222		2048	4181	6229	55467034	SO:0001819	synonymous_variant	79784	exon25			AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"""Myosins / Myosin superfamily : Class II"""	23212	protein-coding gene	gene with protein product		608568	"""myosin, heavy polypeptide 14"", ""myosin, heavy chain 14"""	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.3165C>T	19.37:g.50775222C>T			55467034	NM_001077186	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Silent	SNP	ENST00000596571.1	37	CCDS59411.1	.	.	.	.	.	.	.	.	.	.	C	6.341	0.431000	0.12045	.	.	ENSG00000105357	ENST00000301415;ENST00000376965	.	.	.	3.17	3.17	0.36434	.	.	.	.	.	T	0.72061	0.3414	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.76605	-0.2898	5	0.87932	D	0	.	12.625	0.56623	0.0:1.0:0.0:0.0	.	.	.	.	I	1055	.	ENSP00000301415:T1055I	T	+	2	0	MYH14	55467034	1.000000	0.71417	0.999000	0.59377	0.721000	0.41392	1.174000	0.31932	2.071000	0.62044	0.655000	0.94253	ACA		0.582	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	
SYT3	84258	broad.mit.edu	37	19	51135707	51135707	+	Silent	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:51135707A>G	ENST00000338916.4	-	2	1143	c.510T>C	c.(508-510)gcT>gcC	p.A170A	SYT3_ENST00000544769.1_Silent_p.A170A|SYT3_ENST00000593901.1_Silent_p.A170A|SYT3_ENST00000600079.1_Silent_p.A170A	NM_032298.2	NP_115674.1	Q9BQG1	SYT3_HUMAN	synaptotagmin III	170					calcium ion-dependent exocytosis (GO:0017156)|positive regulation of vesicle fusion (GO:0031340)|response to calcium ion (GO:0051592)	cell junction (GO:0030054)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|metal ion binding (GO:0046872)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)	p.A170A(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(2)|skin(3)|urinary_tract(2)	35		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00462)|GBM - Glioblastoma multiforme(134;0.0188)		CTGCTGCTGCAGCCTCTGGAT	0.652																																					p.A170A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T510C	19						.						26.0	27.0	27.0					19																	51135707		2196	4287	6483	55827519	SO:0001819	synonymous_variant	84258	exon2			AL136594	CCDS12798.1	19q13.33	2014-07-02			ENSG00000213023	ENSG00000213023		"""Synaptotagmins"""	11511	protein-coding gene	gene with protein product		600327				7749232	Standard	NM_032298		Approved		uc002psv.3	Q9BQG1	OTTHUMG00000183064	ENST00000338916.4:c.510T>C	19.37:g.51135707A>G			55827519	NM_032298	Q8N5Z1|Q8N640	Silent	SNP	ENST00000338916.4	37	CCDS12798.1																																																																																				0.652	SYT3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464910.1	NM_032298	
RPL36	25873	broad.mit.edu	37	19	5692167	5692167	+	IGR	SNP	T	T	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:5692167T>A	ENST00000577222.1	+	0	874				LONP1_ENST00000590729.1_Missense_Mutation_p.D789V|LONP1_ENST00000593119.1_Missense_Mutation_p.D855V|LONP1_ENST00000585374.1_Missense_Mutation_p.D805V|LONP1_ENST00000540670.2_Missense_Mutation_p.D723V|LONP1_ENST00000360614.3_Missense_Mutation_p.D919V			Q9Y3U8	RL36_HUMAN	ribosomal protein L36						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.D919V(1)		breast(1)|upper_aerodigestive_tract(1)	2						GTCGTAGAAGTCCTTCTTGTT	0.647																																					p.D919V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2756T	19						.						180.0	151.0	160.0					19																	5692167		2203	4300	6503	5643167	SO:0001628	intergenic_variant	9361	exon18				CCDS12147.1	19p13.2	2011-04-06				ENSG00000130255		"""L ribosomal proteins"""	13631	protein-coding gene	gene with protein product							Standard	NM_033643		Approved	DKFZp566B023, L36	uc002mcv.3	Q9Y3U8			19.37:g.5692167T>A			5643167	NM_004793	B2R4Y1|D6W634|Q6FIG1|Q9UQF6	Missense_Mutation	SNP	ENST00000577222.1	37	CCDS12147.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.663613	0.88251	.	.	ENSG00000196365	ENST00000360614;ENST00000358403;ENST00000540670	T;T	0.38077	1.16;1.16	4.43	4.43	0.53597	Ribosomal protein S5 domain 2-type fold (1);Peptidase S16, Lon C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.73063	0.3539	H	0.98612	4.28	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.996;0.998	T	0.82550	-0.0401	10	0.87932	D	0	-49.0937	11.6876	0.51497	0.0:0.0:0.0:1.0	.	919;855;919	E5KMH8;Q8N8K8;P36776	.;.;LONM_HUMAN	V	919;883;723	ENSP00000353826:D919V;ENSP00000441523:D723V	ENSP00000351177:D883V	D	-	2	0	LONP1	5643167	1.000000	0.71417	0.993000	0.49108	0.919000	0.55068	7.309000	0.78937	1.627000	0.50400	0.374000	0.22700	GAC		0.647	RPL36-001	KNOWN	alternative_5_UTR|overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442561.1	NM_015414	
SIGLEC9	27180	broad.mit.edu	37	19	51629046	51629046	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:51629046A>G	ENST00000250360.3	+	2	681	c.614A>G	c.(613-615)cAg>cGg	p.Q205R	SIGLEC9_ENST00000440804.3_Missense_Mutation_p.Q205R	NM_014441.2	NP_055256.1	Q9Y336	SIGL9_HUMAN	sialic acid binding Ig-like lectin 9	205	Ig-like C2-type 1.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)	p.Q205R(1)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(3)|lung(25)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	45		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.000826)|OV - Ovarian serous cystadenocarcinoma(262;0.00295)		CCACAGCCCCAGGACCATGGC	0.652																																					p.Q205R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A614G	19						.						71.0	68.0	69.0					19																	51629046		2203	4300	6503	56320858	SO:0001583	missense	27180	exon2			AF135027	CCDS12825.1, CCDS56100.1	19q13.3-q13.4	2013-01-29			ENSG00000129450	ENSG00000129450		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10878	protein-coding gene	gene with protein product		605640				10903842	Standard	NM_014441		Approved	CD329	uc002pvu.3	Q9Y336		ENST00000250360.3:c.614A>G	19.37:g.51629046A>G	ENSP00000250360:p.Gln205Arg		56320858	NM_001198558	Q6GTU4|Q9BYI9	Missense_Mutation	SNP	ENST00000250360.3	37	CCDS12825.1	.	.	.	.	.	.	.	.	.	.	.	15.36	2.811459	0.50527	.	.	ENSG00000129450	ENST00000440804;ENST00000250360	T;T	0.03065	4.06;4.06	2.88	2.88	0.33553	Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.195257	0.25258	N	0.031973	T	0.10035	0.0246	L	0.58925	1.835	0.23440	N	0.997673	D	0.57257	0.979	P	0.61070	0.883	T	0.03887	-1.0995	10	0.59425	D	0.04	.	7.2031	0.25891	1.0:0.0:0.0:0.0	.	205	Q9Y336	SIGL9_HUMAN	R	205	ENSP00000413861:Q205R;ENSP00000250360:Q205R	ENSP00000250360:Q205R	Q	+	2	0	SIGLEC9	56320858	0.007000	0.16637	0.622000	0.29159	0.901000	0.52897	0.260000	0.18424	1.170000	0.42753	0.421000	0.28195	CAG		0.652	SIGLEC9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464224.1	NM_014441	
CLDND2	125875	broad.mit.edu	37	19	51871734	51871734	+	Missense_Mutation	SNP	C	C	T	rs199591571		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:51871734C>T	ENST00000291715.1	-	1	523	c.98G>A	c.(97-99)cGc>cAc	p.R33H	ETFB_ENST00000309244.4_5'Flank|CTD-2616J11.10_ENST00000595500.1_RNA|CTD-2616J11.11_ENST00000600067.1_5'Flank|CLDND2_ENST00000601435.1_Missense_Mutation_p.R33H	NM_152353.2	NP_689566.1	Q8NHS1	CLDN2_HUMAN	claudin domain containing 2	33						integral component of membrane (GO:0016021)		p.R33H(1)		endometrium(1)|kidney(1)|large_intestine(2)	4		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000211)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		CTCTTGTTGGCGGGTCCAGTA	0.647																																					p.R33H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G98A	19						.						97.0	86.0	89.0					19																	51871734		2203	4300	6503	56563546	SO:0001583	missense	125875	exon1			BC029518	CCDS12829.1	19q13.41	2008-02-05				ENSG00000160318			28511	protein-coding gene	gene with protein product						12477932	Standard	NM_152353		Approved	MGC33839	uc002pwi.1	Q8NHS1		ENST00000291715.1:c.98G>A	19.37:g.51871734C>T	ENSP00000291715:p.Arg33His		56563546	NM_152353		Missense_Mutation	SNP	ENST00000291715.1	37	CCDS12829.1	.	.	.	.	.	.	.	.	.	.	C	13.92	2.379582	0.42207	.	.	ENSG00000160318	ENST00000291715	D	0.88586	-2.4	4.26	-0.592	0.11671	.	0.599027	0.14794	N	0.298044	T	0.79015	0.4375	L	0.42245	1.32	0.09310	N	1	B	0.18310	0.027	B	0.10450	0.005	T	0.59910	-0.7365	10	0.15499	T	0.54	-14.7456	3.6896	0.08340	0.1713:0.538:0.0:0.2907	.	33	Q8NHS1	CLDN2_HUMAN	H	33	ENSP00000291715:R33H	ENSP00000291715:R33H	R	-	2	0	CLDND2	56563546	0.000000	0.05858	0.003000	0.11579	0.950000	0.60333	-0.094000	0.11094	-0.197000	0.10350	0.561000	0.74099	CGC		0.647	CLDND2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464268.1	NM_152353	
OSCAR	126014	broad.mit.edu	37	19	54599075	54599075	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:54599075C>T	ENST00000284648.6	-	5	914	c.717G>A	c.(715-717)ccG>ccA	p.P239P	OSCAR_ENST00000356532.3_Intron|OSCAR_ENST00000391761.1_Silent_p.P228P|OSCAR_ENST00000391760.1_3'UTR|OSCAR_ENST00000359649.4_Silent_p.P243P|OSCAR_ENST00000358375.4_Intron|OSCAR_ENST00000351806.4_Intron			Q8IYS5	OSCAR_HUMAN	osteoclast associated, immunoglobulin-like receptor	239						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.P243P(1)		large_intestine(1)|skin(1)	2	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)					ggtctgagggcggaggtcctg	0.701																																					p.P243P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G729A	19						.						6.0	7.0	7.0					19																	54599075		1981	3805	5786	59290887	SO:0001819	synonymous_variant	126014	exon5			AK130199	CCDS12873.1, CCDS12874.1, CCDS12875.1, CCDS12876.1, CCDS62789.1, CCDS74444.1	19q13.42	2013-01-29			ENSG00000170909	ENSG00000170909		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29960	protein-coding gene	gene with protein product		606862				11805147	Standard	NM_206818		Approved		uc002qda.3	Q8IYS5	OTTHUMG00000064966	ENST00000284648.6:c.717G>A	19.37:g.54599075C>T			59290887	NM_206818	B7WNS2|Q5GRG5|Q8N763|Q8NHL4|Q8WXQ0|Q8WXQ1|Q8WXQ2	Silent	SNP	ENST00000284648.6	37																																																																																					0.701	OSCAR-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000139493.4	NM_133169	
TFPT	29844	broad.mit.edu	37	19	54611369	54611369	+	Silent	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:54611369T>C	ENST00000391759.1	-	5	1011	c.606A>G	c.(604-606)gcA>gcG	p.A202A	NDUFA3_ENST00000391764.3_Intron|TFPT_ENST00000391757.1_Missense_Mutation_p.Q190R|TFPT_ENST00000391758.1_Silent_p.A193A	NM_013342.3	NP_037474.1	P0C1Z6	TFPT_HUMAN	TCF3 (E2A) fusion partner (in childhood Leukemia)	202					apoptotic signaling pathway (GO:0097190)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin filament (GO:0005884)|cytoplasm (GO:0005737)|Ino80 complex (GO:0031011)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.A202A(1)		large_intestine(2)|lung(2)	4	all_cancers(19;0.004)|all_epithelial(19;0.00195)|all_lung(19;0.0193)|Lung NSC(19;0.0358)|Breast(117;0.137)|Ovarian(34;0.19)					GCGCATTTCCTGCTCGGCGTC	0.701			T	TCF3	pre-B ALL																																p.A202A			Dom	yes		19	19q13	29844	TCF3 (E2A) fusion partner (in childhood Leukemia)		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A606G	19						.						51.0	55.0	54.0					19																	54611369		2203	4300	6503	59303181	SO:0001819	synonymous_variant	29844	exon5			AF052052	CCDS12878.1	19q13	2011-07-06			ENSG00000105619	ENSG00000105619		"""INO80 complex subunits"""	13630	protein-coding gene	gene with protein product	"""amida, partner of the E2A"", ""INO80 complex subunit F"""	609519				10644725, 16230350	Standard	NM_013342		Approved	FB1, amida, INO80F	uc010yej.1	P0C1Z6	OTTHUMG00000065906	ENST00000391759.1:c.606A>G	19.37:g.54611369T>C			59303181	NM_013342		Silent	SNP	ENST00000391759.1	37	CCDS12878.1	.	.	.	.	.	.	.	.	.	.	T	10.38	1.333651	0.24167	.	.	ENSG00000105619	ENST00000391757	.	.	.	5.04	-9.32	0.00643	.	.	.	.	.	T	0.31040	0.0784	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.47058	-0.9146	5	0.87932	D	0	-1.5994	4.3251	0.11036	0.1553:0.4449:0.1731:0.2268	.	.	.	.	R	190	.	ENSP00000375637:Q190R	Q	-	2	0	TFPT	59303181	0.000000	0.05858	0.000000	0.03702	0.135000	0.20990	-1.927000	0.01561	-1.941000	0.01042	-1.003000	0.02500	CAG		0.701	TFPT-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141215.4	NM_013342	
LENG8	114823	broad.mit.edu	37	19	54967409	54967409	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:54967409G>A	ENST00000326764.5	+	9	1768	c.1289G>A	c.(1288-1290)cGc>cAc	p.R430H	LENG8_ENST00000376514.2_Intron	NM_052925.2	NP_443157.1	Q96PV6	LENG8_HUMAN	leukocyte receptor cluster (LRC) member 8	393								p.R430H(1)		breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.139)		TCCCCGACGCGCCACTTCCGC	0.617																																					p.R430H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1289A	19						.						95.0	113.0	107.0					19																	54967409		2203	4296	6499	59659221	SO:0001583	missense	114823	exon9			AF211975	CCDS12894.1	19q13.4	2008-02-05			ENSG00000167615	ENSG00000167615			15500	protein-coding gene	gene with protein product						10941842	Standard	XM_005278248		Approved	KIAA1932, MGC40108, pp13842	uc002qfw.2	Q96PV6	OTTHUMG00000065548	ENST00000326764.5:c.1289G>A	19.37:g.54967409G>A	ENSP00000318374:p.Arg430His		59659221	NM_052925	B0VJY9|Q8IZ27|Q8NCX6	Missense_Mutation	SNP	ENST00000326764.5	37	CCDS12894.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.133730	0.77662	.	.	ENSG00000167615	ENST00000326764;ENST00000301196;ENST00000376526;ENST00000431846	T;T;T	0.36699	1.29;1.28;1.24	4.73	4.73	0.59995	.	0.063133	0.64402	D	0.000016	T	0.41949	0.1181	N	0.24115	0.695	0.80722	D	1	D;D	0.76494	0.998;0.999	P;D	0.67231	0.747;0.95	T	0.11792	-1.0573	10	0.15066	T	0.55	-12.3824	15.6504	0.77088	0.0:0.0:1.0:0.0	.	430;393	Q96PV6-2;F8W9Q9	.;.	H	430;393;393;430	ENSP00000318374:R430H;ENSP00000365709:R393H;ENSP00000388053:R430H	ENSP00000301196:R393H	R	+	2	0	LENG8	59659221	1.000000	0.71417	0.974000	0.42286	0.741000	0.42261	3.917000	0.56424	2.363000	0.80096	0.555000	0.69702	CGC		0.617	LENG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140523.2	NM_052925	
KIR3DL1	3811	broad.mit.edu	37	19	55286660	55286660	+	Intron	SNP	G	G	A	rs142372160	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:55286660G>A	ENST00000538269.1	+	2	61				KIR3DL1_ENST00000541392.1_Intron|CTB-61M7.1_ENST00000400864.3_RNA|KIR2DL3_ENST00000434419.2_Intron|KIR2DL1_ENST00000291633.7_Silent_p.T138T|KIR2DL1_ENST00000336077.6_Silent_p.T138T|KIR2DL4_ENST00000396284.2_Intron|KIR3DL1_ENST00000402254.2_Intron			P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1						immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)	p.T138T(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		TGGGCCCCACGGTTCTGGCAG	0.557													.|||	4	0.000798722	0.003	0.0	5008	,	,		12757	0.0		0.0	False		,,,				2504	0.0				p.T138T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G414A	19						.	G		19,3969		5,9,1980	71.0	61.0	64.0		414	-0.2	0.0	19	dbSNP_134	64	0,7952		0,0,3976	no	coding-synonymous	KIR2DL1	NM_014218.2		5,9,5956	AA,AG,GG		0.0,0.4764,0.1591		138/349	55286660	19,11921	1994	3976	5970	59978472	SO:0001627	intron_variant	3802	exon4			L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000538269.1:c.35-42329G>A	19.37:g.55286660G>A			59978472	NM_014218	O43473|Q14946|Q16541	Silent	SNP	ENST00000538269.1	37																																																																																					0.557	KIR3DL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_013289	
NLRP2	55655	broad.mit.edu	37	19	55494668	55494668	+	Silent	SNP	C	C	T	rs144234287		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:55494668C>T	ENST00000543010.1	+	6	1745	c.1602C>T	c.(1600-1602)gaC>gaT	p.D534D	NLRP2_ENST00000339757.7_Silent_p.D512D|NLRP2_ENST00000263437.6_Silent_p.D531D|NLRP2_ENST00000391721.4_Silent_p.D510D|NLRP2_ENST00000537859.1_Silent_p.D512D|NLRP2_ENST00000538819.1_Silent_p.D510D|NLRP2_ENST00000448584.2_Silent_p.D534D|NLRP2_ENST00000427260.2_Silent_p.D511D	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	534					positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)	p.D534D(2)		large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		ACATTGGGGACGTACAGAAGC	0.557																																					p.D511D												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1533T	19						.	C	,,,	1,4405	2.1+/-5.4	0,1,2202	90.0	82.0	85.0		1602,1536,1533,1602	-2.6	0.0	19	dbSNP_134	85	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NLRP2	NM_001174081.1,NM_001174082.1,NM_001174083.1,NM_017852.3	,,,	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	,,,	534/1063,512/1041,511/1040,534/1063	55494668	3,13003	2203	4300	6503	60186480	SO:0001819	synonymous_variant	55655	exon7			AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"""Nucleotide-binding domain and leucine rich repeat containing"""	22948	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"""	609364	"""NACHT, leucine rich repeat and PYD containing 2"""	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.1602C>T	19.37:g.55494668C>T			60186480	NM_001174083	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Silent	SNP	ENST00000543010.1	37	CCDS12913.1																																																																																				0.557	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852	
SYT5	6861	broad.mit.edu	37	19	55687156	55687156	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:55687156G>A	ENST00000354308.3	-	5	830	c.461C>T	c.(460-462)cCg>cTg	p.P154L	CTD-2587H24.5_ENST00000591665.1_RNA|SYT5_ENST00000592935.1_5'Flank|SYT5_ENST00000590851.1_Missense_Mutation_p.P151L|SYT5_ENST00000537500.1_Missense_Mutation_p.P154L	NM_003180.2	NP_003171.2	O00445	SYT5_HUMAN	synaptotagmin V	154	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium ion-dependent exocytosis (GO:0017156)|energy reserve metabolic process (GO:0006112)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|dense core granule (GO:0031045)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|metal ion binding (GO:0046872)|transporter activity (GO:0005215)	p.P154L(2)		kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	18			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0452)		CCGTTTGTCCGGCAGCAGGTA	0.617																																					p.P154L												.	.	2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	c.C461T	19						.						102.0	99.0	100.0					19																	55687156		2203	4300	6503	60378968	SO:0001583	missense	6861	exon5			X96783	CCDS12919.1, CCDS74455.1	19q13.42	2014-07-02			ENSG00000129990	ENSG00000129990		"""Synaptotagmins"""	11513	protein-coding gene	gene with protein product	"""synaptotagmin 5"""	600782				9177789	Standard	XM_006723338		Approved		uc002qjn.1	O00445	OTTHUMG00000180669	ENST00000354308.3:c.461C>T	19.37:g.55687156G>A	ENSP00000346265:p.Pro154Leu		60378968	NM_003180	B3KWJ8|B7Z300|Q86X72	Missense_Mutation	SNP	ENST00000354308.3	37	CCDS12919.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.734265	0.89482	.	.	ENSG00000129990	ENST00000537500;ENST00000354308;ENST00000543844	T;T	0.70516	-0.49;-0.49	4.54	3.49	0.39957	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.86151	0.5864	M	0.92026	3.265	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79108	0.973;0.99;0.992	D	0.89215	0.3567	10	0.87932	D	0	.	13.6042	0.62037	0.0:0.0:0.843:0.157	.	151;154;154	B7Z300;Q4FD32;O00445	.;.;SYT5_HUMAN	L	154;154;151	ENSP00000442896:P154L;ENSP00000346265:P154L	ENSP00000346265:P154L	P	-	2	0	SYT5	60378968	1.000000	0.71417	0.998000	0.56505	0.769000	0.43574	9.744000	0.98853	1.223000	0.43536	0.555000	0.69702	CCG		0.617	SYT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452501.1	NM_003180	
NAT14	57106	broad.mit.edu	37	19	55997947	55997947	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:55997947G>A	ENST00000205194.4	+	3	548	c.245G>A	c.(244-246)cGg>cAg	p.R82Q	NAT14_ENST00000592719.1_Intron|NAT14_ENST00000587400.1_Intron|SSC5D_ENST00000389623.6_5'Flank|NAT14_ENST00000591590.1_3'UTR|SSC5D_ENST00000587166.1_5'Flank	NM_020378.3	NP_065111.1	Q8WUY8	NAT14_HUMAN	N-acetyltransferase 14 (GCN5-related, putative)	82	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				DNA-templated transcription, initiation (GO:0006352)|positive regulation of transcription, DNA-templated (GO:0045893)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|N-acetyltransferase activity (GO:0008080)	p.R82Q(1)		central_nervous_system(1)|large_intestine(1)|ovary(1)|pancreas(1)	4	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0527)		CTGGGCCTGCGGGCCCGATGG	0.761																																					p.R82Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G245A	19						.						5.0	7.0	6.0					19																	55997947		2079	4039	6118	60689759	SO:0001583	missense	57106	exon3			AB055059	CCDS12926.1	19q13.42	2011-11-25	2008-09-24		ENSG00000090971	ENSG00000090971			28918	protein-coding gene	gene with protein product	"""K562 cells-derived leucine zipper-like protein 1"""		"""N-acetyltransferase 14"""			10873651	Standard	NM_020378		Approved	KLP1	uc002qle.2	Q8WUY8		ENST00000205194.4:c.245G>A	19.37:g.55997947G>A	ENSP00000205194:p.Arg82Gln		60689759	NM_020378	Q8TDY7|Q9NS72	Missense_Mutation	SNP	ENST00000205194.4	37	CCDS12926.1	.	.	.	.	.	.	.	.	.	.	.	15.30	2.791411	0.50102	.	.	ENSG00000090971	ENST00000205194	.	.	.	3.25	3.25	0.37280	GCN5-related N-acetyltransferase (GNAT) domain (1);Acyl-CoA N-acyltransferase (1);	0.000000	0.56097	D	0.000024	T	0.28764	0.0713	N	0.24115	0.695	0.32126	N	0.587377	B	0.21381	0.055	B	0.12156	0.007	T	0.24404	-1.0161	9	0.22109	T	0.4	-34.5275	8.6281	0.33901	0.0:0.2367:0.7633:0.0	.	82	Q8WUY8	NAT14_HUMAN	Q	82	.	ENSP00000205194:R82Q	R	+	2	0	NAT14	60689759	0.304000	0.24472	0.998000	0.56505	0.803000	0.45373	1.219000	0.32479	1.840000	0.53500	0.313000	0.20887	CGG		0.761	NAT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453339.1	NM_020378	
NLRP13	126204	broad.mit.edu	37	19	56423396	56423396	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:56423396A>G	ENST00000342929.3	-	5	1786	c.1787T>C	c.(1786-1788)aTa>aCa	p.I596T	NLRP13_ENST00000588751.1_Missense_Mutation_p.I596T	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	596							ATP binding (GO:0005524)	p.I596T(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(58)|ovary(4)|pancreas(2)|prostate(2)|skin(13)|stomach(2)|urinary_tract(1)	109		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		TTCTCTTGCTATGTTTTTATT	0.403																																					p.I596T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1787C	19						.						82.0	86.0	85.0					19																	56423396		2203	4300	6503	61115208	SO:0001583	missense	126204	exon5			AY154468	CCDS33119.1	19q13.43	2008-02-05	2006-12-08	2006-12-08	ENSG00000173572	ENSG00000173572		"""Nucleotide-binding domain and leucine rich repeat containing"""	22937	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 13"""	609660	"""NACHT, leucine rich repeat and PYD containing 13"""	NALP13		12563287	Standard	NM_176810		Approved	NOD14, PAN13, CLR19.7	uc010ygg.2	Q86W25	OTTHUMG00000167839	ENST00000342929.3:c.1787T>C	19.37:g.56423396A>G	ENSP00000343891:p.Ile596Thr		61115208	NM_176810	Q7RTR5	Missense_Mutation	SNP	ENST00000342929.3	37	CCDS33119.1	.	.	.	.	.	.	.	.	.	.	A	0.028	-1.353760	0.01256	.	.	ENSG00000173572	ENST00000342929	D	0.88431	-2.38	1.82	0.792	0.18625	.	.	.	.	.	T	0.71745	0.3376	N	0.10809	0.05	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.56208	-0.8017	9	0.09843	T	0.71	.	3.7371	0.08515	0.7998:0.0:0.2002:0.0	.	596	Q86W25	NAL13_HUMAN	T	596	ENSP00000343891:I596T	ENSP00000343891:I596T	I	-	2	0	NLRP13	61115208	0.000000	0.05858	0.001000	0.08648	0.047000	0.14425	-0.344000	0.07780	0.192000	0.20272	-0.408000	0.06270	ATA		0.403	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810	
NLRP8	126205	broad.mit.edu	37	19	56467229	56467229	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:56467229C>T	ENST00000291971.3	+	3	1876	c.1805C>T	c.(1804-1806)cCg>cTg	p.P602L	NLRP8_ENST00000590542.1_Missense_Mutation_p.P602L	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	602					neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)	p.P602L(2)		breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		CCACCTTCTCCGGGCAGTGGG	0.468																																					p.P602L												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1805T	19						.						53.0	50.0	51.0					19																	56467229		2203	4300	6503	61159041	SO:0001583	missense	126205	exon3			AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"""Nucleotide-binding domain and leucine rich repeat containing"""	22940	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"""	609659	"""NACHT, leucine rich repeat and PYD containing 8"""	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.1805C>T	19.37:g.56467229C>T	ENSP00000291971:p.Pro602Leu		61159041	NM_176811	Q7RTR4	Missense_Mutation	SNP	ENST00000291971.3	37	CCDS12937.1	.	.	.	.	.	.	.	.	.	.	C	3.111	-0.182585	0.06340	.	.	ENSG00000179709	ENST00000291971	D	0.84370	-1.84	2.03	-4.06	0.03986	.	.	.	.	.	T	0.58250	0.2109	N	0.02315	-0.6	0.09310	N	1	B;B	0.16166	0.016;0.003	B;B	0.08055	0.002;0.003	T	0.46162	-0.9211	9	0.25751	T	0.34	.	3.5751	0.07932	0.1944:0.2457:0.0:0.5598	.	602;602	Q86W28-2;Q86W28	.;NALP8_HUMAN	L	602	ENSP00000291971:P602L	ENSP00000291971:P602L	P	+	2	0	NLRP8	61159041	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.530000	0.02221	-1.228000	0.02568	-0.357000	0.07601	CCG		0.468	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811	
ZNF835	90485	broad.mit.edu	37	19	57174972	57174972	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:57174972C>T	ENST00000537055.2	-	2	1826	c.1595G>A	c.(1594-1596)cGt>cAt	p.R532H		NM_001005850.2	NP_001005850.2	Q9Y2P0	ZN835_HUMAN	zinc finger protein 835	532					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R554H(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(22)|pancreas(3)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	47						TGCTGGTCCACGCGGGTTTCT	0.582																																					p.R554H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1661A	19						.						50.0	53.0	52.0					19																	57174972		2051	4208	6259	61866784	SO:0001583	missense	90485	exon2			AK023017	CCDS56105.1	19q13.43	2013-01-08			ENSG00000127903	ENSG00000127903		"""Zinc fingers, C2H2-type"""	34332	protein-coding gene	gene with protein product							Standard	NM_001005850		Approved	BC37295_3	uc010ygn.2	Q9Y2P0		ENST00000537055.2:c.1595G>A	19.37:g.57174972C>T	ENSP00000444747:p.Arg532His		61866784	NM_001005850	B7Z5Y0|G3V1S0	Missense_Mutation	SNP	ENST00000537055.2	37	CCDS56105.1	.	.	.	.	.	.	.	.	.	.	C	1.834	-0.469165	0.04445	.	.	ENSG00000127903	ENST00000342088;ENST00000537055	T	0.06933	3.24	1.83	-3.66	0.04489	.	.	.	.	.	T	0.03434	0.0099	N	0.03608	-0.345	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.40869	-0.9540	9	0.66056	D	0.02	.	7.2836	0.26324	0.0:0.1772:0.5802:0.2426	.	554	Q9Y2P0	ZN835_HUMAN	H	554;532	ENSP00000444747:R532H	ENSP00000341756:R554H	R	-	2	0	ZNF835	61866784	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.834000	0.04391	-2.824000	0.00342	-1.474000	0.01003	CGT		0.582	ZNF835-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459800.1	NM_001005850	
ZNF304	57343	broad.mit.edu	37	19	57868579	57868579	+	Missense_Mutation	SNP	G	G	A	rs146642030		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:57868579G>A	ENST00000282286.5	+	3	1515	c.1342G>A	c.(1342-1344)Gtg>Atg	p.V448M	ZNF304_ENST00000598744.1_Missense_Mutation_p.V406M|ZNF304_ENST00000391705.3_Missense_Mutation_p.V448M|ZNF304_ENST00000443917.2_Missense_Mutation_p.V495M			Q9HCX3	ZN304_HUMAN	zinc finger protein 304	448					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.V448M(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)	26		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)		AAGATCCTACGTGTGCAGCAA	0.478																																					p.V448M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1342A	19						.						72.0	71.0	71.0					19																	57868579		2203	4300	6503	62560391	SO:0001583	missense	57343	exon3			AJ276316	CCDS12950.1, CCDS74462.1	19q13.4	2013-01-08				ENSG00000131845		"""Zinc fingers, C2H2-type"", ""-"""	13505	protein-coding gene	gene with protein product		613840					Standard	XM_005259090		Approved		uc010ygw.2	Q9HCX3		ENST00000282286.5:c.1342G>A	19.37:g.57868579G>A	ENSP00000282286:p.Val448Met		62560391	NM_020657		Missense_Mutation	SNP	ENST00000282286.5	37	CCDS12950.1	.	.	.	.	.	.	.	.	.	.	G	13.00	2.106594	0.37145	.	.	ENSG00000131845	ENST00000282286;ENST00000391705;ENST00000443917	T;T;T	0.07688	3.17;3.17;3.17	3.77	2.73	0.32206	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.17619	0.0423	L	0.42686	1.345	0.09310	N	1	D;D	0.76494	0.999;0.998	D;P	0.68765	0.96;0.858	T	0.05370	-1.0889	9	0.59425	D	0.04	.	7.9462	0.29987	0.206:0.0:0.794:0.0	.	448;495	Q9HCX3;E7EQD3	ZN304_HUMAN;.	M	448;448;495	ENSP00000282286:V448M;ENSP00000375586:V448M;ENSP00000401642:V495M	ENSP00000282286:V448M	V	+	1	0	ZNF304	62560391	0.000000	0.05858	0.050000	0.19076	0.860000	0.49131	-0.998000	0.03701	1.167000	0.42706	0.650000	0.86243	GTG		0.478	ZNF304-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465785.1		
SLC25A23	79085	broad.mit.edu	37	19	6454624	6454624	+	Silent	SNP	A	A	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:6454624A>C	ENST00000301454.4	-	5	694	c.588T>G	c.(586-588)ggT>ggG	p.G196G	SLC25A23_ENST00000334510.5_Silent_p.G196G|SLC25A23_ENST00000414491.2_Silent_p.G13G	NM_024103.2	NP_077008.2	Q9BV35	SCMC3_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 23	196					adenine nucleotide transport (GO:0051503)|cellular response to calcium ion (GO:0071277)|regulation of cellular respiration (GO:0043457)|regulation of oxidative phosphorylation (GO:0002082)|regulation of sequestering of calcium ion (GO:0051282)|transmembrane transport (GO:0055085)|urea homeostasis (GO:0097274)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)	p.G196G(1)		endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|pancreas(1)|skin(1)	17						GTGACACGGCACCTGCCACTG	0.647																																					p.G196G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T588G	19						.																																			6405624	SO:0001819	synonymous_variant	79085	exon5			AJ619962	CCDS32882.1	19p13.1	2014-02-06			ENSG00000125648	ENSG00000125648		"""Solute carriers"", ""EF-hand domain containing"""	19375	protein-coding gene	gene with protein product		608746				15123600	Standard	NM_024103		Approved	FLJ30339, MGC2615, APC2	uc002mex.1	Q9BV35	OTTHUMG00000180852	ENST00000301454.4:c.588T>G	19.37:g.6454624A>C			6405624	NM_024103	B4DGB6|Q4LBC2|Q705K3|Q86Y43|Q8N2N4|Q96NQ4	Silent	SNP	ENST00000301454.4	37	CCDS32882.1																																																																																				0.647	SLC25A23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453325.1	NM_024103	
C3	718	broad.mit.edu	37	19	6710725	6710725	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:6710725C>T	ENST00000245907.6	-	13	1703	c.1611G>A	c.(1609-1611)ctG>ctA	p.L537L		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	537					complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)	p.L537L(1)		breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	TGGCACCGATCAGCGTGTAGT	0.677																																					p.L537L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1611A	19						.						56.0	51.0	52.0					19																	6710725		2203	4299	6502	6661725	SO:0001819	synonymous_variant	718	exon13			J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"""Complement system"", ""Endogenous ligands"""	1318	protein-coding gene	gene with protein product	"""C3a anaphylatoxin"", ""complement component C3a"", ""complement component C3b"", ""prepro-C3"""	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.1611G>A	19.37:g.6710725C>T			6661725	NM_000064	A7E236	Silent	SNP	ENST00000245907.6	37	CCDS32883.1																																																																																				0.677	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064	
EMR1	2015	broad.mit.edu	37	19	6897511	6897511	+	Missense_Mutation	SNP	G	G	A	rs375715052		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	None	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:6897511G>A	ENST00000312053.4	+	5	504	c.467G>A	c.(466-468)aGt>aAt	p.S156N	EMR1_ENST00000450315.3_Intron|AC020895.1_ENST00000580648.1_RNA|EMR1_ENST00000250572.8_Missense_Mutation_p.S156N|EMR1_ENST00000601198.1_3'UTR|EMR1_ENST00000381407.5_Intron|EMR1_ENST00000381404.4_Missense_Mutation_p.S104N	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 1	156	EGF-like 3; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(8)	62	all_hematologic(4;0.166)					GGAAGCTACAGTTGCAGCTGT	0.453																																					p.S156N												.	.	0			c.G467A	19						.	G	ASN/SER	0,4406		0,0,2203	102.0	87.0	92.0		467	-8.2	0.0	19		92	1,8599	1.2+/-3.3	0,1,4299	no	missense	EMR1	NM_001974.3	46	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	156/887	6897511	1,13005	2203	4300	6503	6848511	SO:0001583	missense	2015	exon5			X81479	CCDS12175.1, CCDS58643.1, CCDS58644.1, CCDS58645.1, CCDS58646.1	19p13.3	2014-08-08	2003-11-26					"""-"", ""GPCR / Class B : Orphans"""	3336	protein-coding gene	gene with protein product		600493	"""egf-like module containing, mucin-like, hormone receptor-like sequence 1"""	TM7LN3		7601460, 9500513	Standard	NM_001974		Approved		uc002mfw.4	Q14246		ENST00000312053.4:c.467G>A	19.37:g.6897511G>A	ENSP00000311545:p.Ser156Asn		6848511	NM_001974	A6NHV2|B7Z486|B7Z489|E7EPX9|E9PD45|H9KV79|Q2I7G5|Q6ZMN0|Q8NGA7	Missense_Mutation	SNP	ENST00000312053.4	37	CCDS12175.1	.	.	.	.	.	.	.	.	.	.	G	2.107	-0.404630	0.04832	0.0	1.16E-4	ENSG00000174837	ENST00000543519;ENST00000312053;ENST00000381404;ENST00000250572	D;D;D	0.92149	-2.26;-2.98;-2.26	4.12	-8.24	0.01029	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	.	.	.	.	T	0.81370	0.4808	L	0.35414	1.06	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.13407	0.002;0.009;0.006	T	0.65763	-0.6089	9	0.26408	T	0.33	.	2.6623	0.05030	0.4622:0.1169:0.3025:0.1183	.	156;104;156	Q14246-2;E9PD45;Q14246	.;.;EMR1_HUMAN	N	156;156;104;156	ENSP00000311545:S156N;ENSP00000370811:S104N;ENSP00000250572:S156N	ENSP00000250572:S156N	S	+	2	0	EMR1	6848511	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-4.332000	0.00251	-1.215000	0.02610	-2.772000	0.00119	AGT		0.453	EMR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458485.1		
ACTL9	284382	broad.mit.edu	37	19	8807853	8807853	+	Missense_Mutation	SNP	C	C	T	rs112957538		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:8807853C>T	ENST00000324436.3	-	1	1319	c.1199G>A	c.(1198-1200)cGg>cAg	p.R400Q		NM_178525.3	NP_848620.3	Q8TC94	ACTL9_HUMAN	actin-like 9	400						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.R400Q(1)		NS(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(15)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	36						GTACTGCTCCCGCAGGACCCA	0.632													C|||	1	0.000199681	0.0008	0.0	5008	,	,		16042	0.0		0.0	False		,,,				2504	0.0				p.R400Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1199A	19						.	C	GLN/ARG	2,4404		0,2,2201	45.0	46.0	45.0		1199	3.5	0.1	19	dbSNP_132	45	3,8597		0,3,4297	yes	missense	ACTL9	NM_178525.3	43	0,5,6498	TT,TC,CC		0.0349,0.0454,0.0384	probably-damaging	400/417	8807853	5,13001	2203	4300	6503	8668853	SO:0001583	missense	284382	exon1				CCDS12207.1	19p13.2	2014-08-08			ENSG00000181786	ENSG00000181786			28494	protein-coding gene	gene with protein product							Standard	NM_178525		Approved	MGC33407	uc002mkl.2	Q8TC94	OTTHUMG00000182194	ENST00000324436.3:c.1199G>A	19.37:g.8807853C>T	ENSP00000316674:p.Arg400Gln		8668853	NM_178525	A8K893|Q6X960	Missense_Mutation	SNP	ENST00000324436.3	37	CCDS12207.1	.	.	.	.	.	.	.	.	.	.	c	16.39	3.109296	0.56398	4.54E-4	3.49E-4	ENSG00000181786	ENST00000324436	D	0.95412	-3.7	4.51	3.47	0.39725	.	0.167469	0.28098	U	0.016602	D	0.94525	0.8237	M	0.71581	2.175	0.28929	N	0.891688	D	0.59357	0.985	P	0.47864	0.559	D	0.90913	0.4777	10	0.87932	D	0	.	8.0568	0.30610	0.0:0.8115:0.0:0.1885	.	400	Q8TC94	ACTL9_HUMAN	Q	400	ENSP00000316674:R400Q	ENSP00000316674:R400Q	R	-	2	0	ACTL9	8668853	1.000000	0.71417	0.070000	0.20053	0.289000	0.27227	3.503000	0.53340	1.249000	0.43950	0.457000	0.33378	CGG		0.632	ACTL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459953.1	NM_178525	
MUC16	94025	broad.mit.edu	37	19	9089904	9089904	+	Silent	SNP	G	G	A	rs374207045		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:9089904G>A	ENST00000397910.4	-	1	2114	c.1911C>T	c.(1909-1911)tcC>tcT	p.S637S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	637	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.S637S(2)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TCAAATCTGCGGATGTCTCAG	0.582																																					p.S637S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1911T	19						.	G		1,4373		0,1,2186	113.0	117.0	115.0		1911	-3.1	0.0	19		115	0,8566		0,0,4283	no	coding-synonymous	MUC16	NM_024690.2		0,1,6469	AA,AG,GG		0.0,0.0229,0.0077		637/14508	9089904	1,12939	2187	4283	6470	8950904	SO:0001819	synonymous_variant	94025	exon1			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.1911C>T	19.37:g.9089904G>A			8950904	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																				0.582	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
IGFLR1	79713	broad.mit.edu	37	19	36231924	36231924	+	Splice_Site	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:36231924C>A	ENST00000592537.1	-	2	258		c.e2+1		IGFLR1_ENST00000246532.1_Splice_Site|IGFLR1_ENST00000587101.1_5'Flank|IGFLR1_ENST00000592889.1_Splice_Site|IGFLR1_ENST00000344990.3_Splice_Site|AD000671.6_ENST00000589807.1_Splice_Site|IGFLR1_ENST00000588992.1_Splice_Site|KMT2B_ENST00000607650.1_RNA			Q9H665	IGFR1_HUMAN	IGF-like family receptor 1							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.?(1)		endometrium(2)|kidney(3)|large_intestine(1)|lung(8)|prostate(1)	15						CGGATTCTCACCCGGGCAGGG	0.652																																					.												.	.	1	Unknown(1)	large_intestine(1)	.	19						.						18.0	25.0	23.0					19																	36231924		2201	4298	6499	40923764	SO:0001630	splice_region_variant	79713	.			AK026226	CCDS12472.1	19q13.12	2012-10-02	2011-04-04	2011-04-04	ENSG00000126246	ENSG00000126246			23620	protein-coding gene	gene with protein product		614143	"""U2(RNU2) small nuclear RNA auxiliary factor 1-like 4"", ""transmembrane protein 149"""	U2AF1L4, TMEM149		21454693	Standard	NM_024660		Approved	FLJ22573	uc002obd.4	Q9H665		ENST00000592537.1:c.157+1G>T	19.37:g.36231924C>A			40923764	.	Q8N5X0	Splice_Site	SNP	ENST00000592537.1	37	CCDS12472.1	.	.	.	.	.	.	.	.	.	.	C	13.00	2.107460	0.37145	.	.	ENSG00000126246	ENST00000246532;ENST00000344990	.	.	.	4.93	4.93	0.64822	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.4962	0.61428	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	IGFLR1	40923764	0.968000	0.33430	0.995000	0.50966	0.103000	0.19146	0.940000	0.28992	2.564000	0.86499	0.561000	0.74099	.		0.652	IGFLR1-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459077.1	NM_024660	Intron
ZNF419	79744	broad.mit.edu	37	19	58002859	58002859	+	Silent	SNP	T	T	C	rs62126198	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	T	T	C	Unknown	Valid	LOH	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr19:58002859T>C	ENST00000221735.7	+	3	279	c.93T>C	c.(91-93)gaT>gaC	p.D31D	ZNF419_ENST00000520540.1_Silent_p.D19D|ZNF419_ENST00000415379.2_Silent_p.D18D|ZNF419_ENST00000442920.2_Silent_p.D18D|AC003005.4_ENST00000601674.1_Silent_p.D18D|ZNF419_ENST00000424930.2_Silent_p.D32D|ZNF419_ENST00000347466.6_Silent_p.D32D|ZNF419_ENST00000518999.1_Silent_p.D32D|ZNF419_ENST00000354197.4_Silent_p.D19D|ZNF419_ENST00000426954.2_Silent_p.D19D			Q96HQ0	ZN419_HUMAN	zinc finger protein 419	31	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D32D(1)|p.D11D(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0252)|Lung(386;0.171)		CCTTTGAGGATGTGGCTGTCT	0.498																																					p.D32D												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T96C	19						.						174.0	165.0	168.0					19																	58002859		2203	4300	6503	62694671	SO:0001819	synonymous_variant	79744	exon3			AK026886	CCDS42637.1, CCDS46211.1, CCDS54325.1, CCDS54326.1, CCDS54327.1, CCDS54328.1	19q13.43	2013-01-08	2006-12-15	2006-12-15	ENSG00000105136	ENSG00000105136		"""Zinc fingers, C2H2-type"", ""-"""	20648	protein-coding gene	gene with protein product			"""zinc finger protein 419A"""	ZNF419A			Standard	NM_001098492		Approved		uc010ety.1	Q96HQ0	OTTHUMG00000037073	ENST00000221735.7:c.93T>C	19.37:g.58002859T>C			62694671	NM_001098494	B4DXU7|B4E348|B7ZA41|E9PCP4|E9PED0|E9PET3|E9PFX9|Q9H5P0	Silent	SNP	ENST00000221735.7	37	CCDS54326.1																																																																																				0.498	ZNF419-006	KNOWN	NAGNAG_splice_site|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378506.1	NM_024691	
KIF1B	23095	broad.mit.edu	37	1	10394645	10394645	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:10394645G>C	ENST00000377086.1	+	28	3194	c.2992G>C	c.(2992-2994)Gag>Cag	p.E998Q	KIF1B_ENST00000377081.1_Missense_Mutation_p.E998Q|KIF1B_ENST00000263934.6_Missense_Mutation_p.E952Q			O60333	KIF1B_HUMAN	kinesin family member 1B	998					anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)	p.E952Q(1)		breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		CATCGTCAGTGAGAAAGGTGA	0.507																																					p.E952Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2854C	1						.						221.0	199.0	207.0					1																	10394645		2203	4300	6503	10317232	SO:0001583	missense	23095	exon26			AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.2992G>C	1.37:g.10394645G>C	ENSP00000366290:p.Glu998Gln		10317232	NM_015074	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Missense_Mutation	SNP	ENST00000377086.1	37		.	.	.	.	.	.	.	.	.	.	G	35	5.453376	0.96223	.	.	ENSG00000054523	ENST00000355249;ENST00000263934;ENST00000377086;ENST00000377081	T;T;T	0.76578	-1.03;-1.03;-1.03	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	D	0.84955	0.5587	L	0.39514	1.22	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.997;0.999;0.989	D;D;D;D;D;D	0.87578	0.998;0.987;0.997;0.995;0.915;0.979	D	0.84963	0.0878	10	0.62326	D	0.03	.	20.2699	0.98469	0.0:0.0:1.0:0.0	.	984;958;998;972;998;952	Q4R9M9;Q4R9M7;Q4VXC4;Q4R9M8;O60333;O60333-2	.;.;.;.;KIF1B_HUMAN;.	Q	998;952;998;998	ENSP00000263934:E952Q;ENSP00000366290:E998Q;ENSP00000366284:E998Q	ENSP00000263934:E952Q	E	+	1	0	KIF1B	10317232	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.798000	0.99111	2.854000	0.98071	0.655000	0.94253	GAG		0.507	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1		
KIF1B	23095	broad.mit.edu	37	1	10435089	10435089	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:10435089G>A	ENST00000377086.1	+	47	5476	c.5274G>A	c.(5272-5274)caG>caA	p.Q1758Q	KIF1B_ENST00000377081.1_Silent_p.Q1758Q|KIF1B_ENST00000263934.6_Silent_p.Q1712Q			O60333	KIF1B_HUMAN	kinesin family member 1B	1758	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)	p.Q1712Q(1)		breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		GTGAGGACCAGCAGGCCATGG	0.507																																					p.Q1712Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G5136A	1						.						101.0	78.0	86.0					1																	10435089		2203	4300	6503	10357676	SO:0001819	synonymous_variant	23095	exon45			AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.5274G>A	1.37:g.10435089G>A			10357676	NM_015074	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Silent	SNP	ENST00000377086.1	37																																																																																					0.507	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1		
CASZ1	54897	broad.mit.edu	37	1	10725412	10725412	+	Missense_Mutation	SNP	C	C	T	rs376050510		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:10725412C>T	ENST00000377022.3	-	5	550	c.233G>A	c.(232-234)cGc>cAc	p.R78H	CASZ1_ENST00000478728.2_5'UTR|CASZ1_ENST00000344008.5_Missense_Mutation_p.R78H	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	78					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R78H(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		TTCCTCGCTGCGGGGGGCCCG	0.701																																					p.R78H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G233A	1						.	C	HIS/ARG,HIS/ARG	0,4246		0,0,2123	43.0	53.0	49.0		233,233	4.4	1.0	1		49	2,8434		0,2,4216	no	missense,missense	CASZ1	NM_001079843.1,NM_017766.3	29,29	0,2,6339	TT,TC,CC		0.0237,0.0,0.0158	possibly-damaging,possibly-damaging	78/1760,78/1167	10725412	2,12680	2123	4218	6341	10647999	SO:0001583	missense	54897	exon5			AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"""Zinc fingers, C2H2-type"""	26002	protein-coding gene	gene with protein product	"""zinc finger protein 693"", ""survival related gene"""	609895	"""castor homolog 1, zinc finger (Drosophila)"""			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.233G>A	1.37:g.10725412C>T	ENSP00000366221:p.Arg78His		10647999	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Missense_Mutation	SNP	ENST00000377022.3	37	CCDS41246.1	.	.	.	.	.	.	.	.	.	.	C	18.23	3.578237	0.65878	0.0	2.37E-4	ENSG00000130940	ENST00000377022;ENST00000344008	.	.	.	4.42	4.42	0.53409	.	0.203933	0.32314	N	0.006272	T	0.31009	0.0783	N	0.14661	0.345	0.28487	N	0.914679	D;P;D	0.64830	0.983;0.771;0.994	B;B;P	0.47744	0.401;0.289;0.556	T	0.22034	-1.0228	9	0.59425	D	0.04	-17.2461	17.4322	0.87542	0.0:1.0:0.0:0.0	.	102;78;78	B7Z1S3;Q86V15-2;Q86V15	.;.;CASZ1_HUMAN	H	78	.	ENSP00000339445:R78H	R	-	2	0	CASZ1	10647999	0.750000	0.28316	0.996000	0.52242	0.941000	0.58515	0.655000	0.24933	2.191000	0.70037	0.511000	0.50034	CGC		0.701	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766	
SLC35A3	23443	broad.mit.edu	37	1	100459241	100459241	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:100459241T>C	ENST00000370155.3	+	2	523	c.131T>C	c.(130-132)gTt>gCt	p.V44A	SLC35A3_ENST00000370156.3_3'UTR|SLC35A3_ENST00000370153.1_Missense_Mutation_p.V86A|SLC35A3_ENST00000427993.2_Missense_Mutation_p.V44A|SLC35A3_ENST00000465289.1_Missense_Mutation_p.V44A	NM_012243.1	NP_036375.1	Q9Y2D2	S35A3_HUMAN	solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member A3	44					transmembrane transport (GO:0055085)|UDP-N-acetylglucosamine metabolic process (GO:0006047)|UDP-N-acetylglucosamine transport (GO:0015788)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	sugar:proton symporter activity (GO:0005351)|UDP-N-acetylglucosamine transmembrane transporter activity (GO:0005462)	p.V44A(1)		biliary_tract(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	11		all_epithelial(167;0.000686)|all_lung(203;0.0154)|Lung NSC(277;0.0155)		Epithelial(280;0.124)|all cancers(265;0.198)|Lung(183;0.199)		ACAGCAGTGGTTGTTGCTGAA	0.348																																					p.V44A	Ovarian(7;298 356 944 2149 6911)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T131C	1						.						146.0	152.0	150.0					1																	100459241		2203	4300	6503	100231829	SO:0001583	missense	23443	exon2			AB021981	CCDS762.1, CCDS60204.1, CCDS60205.1	1p21	2013-05-22			ENSG00000117620	ENSG00000117620		"""Solute carriers"""	11023	protein-coding gene	gene with protein product		605632	"""solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member 3"""			10393322	Standard	NM_001271685		Approved		uc001dsr.2	Q9Y2D2	OTTHUMG00000010805	ENST00000370155.3:c.131T>C	1.37:g.100459241T>C	ENSP00000359174:p.Val44Ala		100231829	NM_012243	A8K3F8|D3DT54|Q68CR2|Q9BSB7	Missense_Mutation	SNP	ENST00000370155.3	37	CCDS762.1	.	.	.	.	.	.	.	.	.	.	T	18.78	3.697660	0.68386	.	.	ENSG00000117620	ENST00000370155;ENST00000465289;ENST00000427993;ENST00000532693;ENST00000370153;ENST00000422078	T;T;T;T;T	0.48201	0.82;0.85;0.82;0.82;0.84	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.43897	0.1268	M	0.66506	2.035	0.80722	D	1	B;P;B	0.36768	0.188;0.569;0.019	B;B;B	0.42282	0.074;0.382;0.074	T	0.52139	-0.8615	10	0.72032	D	0.01	-10.1995	16.0624	0.80847	0.0:0.0:0.0:1.0	.	44;85;44	Q9BSB7;Q9Y2D2-2;Q9Y2D2	.;.;S35A3_HUMAN	A	44;44;44;44;86;44	ENSP00000359174:V44A;ENSP00000418527:V44A;ENSP00000414947:V44A;ENSP00000359172:V86A;ENSP00000401679:V44A	ENSP00000359172:V86A	V	+	2	0	SLC35A3	100231829	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.592000	0.82676	2.250000	0.74265	0.455000	0.32223	GTT		0.348	SLC35A3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000029783.1	NM_012243	
MASP2	10747	broad.mit.edu	37	1	11087552	11087552	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:11087552G>A	ENST00000400897.3	-	11	1466	c.1451C>T	c.(1450-1452)gCc>gTc	p.A484V	RP4-635E18.8_ENST00000607145.1_RNA	NM_006610.3	NP_006601.2	O00187	MASP2_HUMAN	mannan-binding lectin serine peptidase 2	484	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|complement component C4b binding (GO:0001855)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)	p.A484V(1)		biliary_tract(1)|endometrium(2)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	Ovarian(185;0.249)	Lung NSC(185;1.04e-05)|all_lung(284;1.31e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.071)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.12e-07)|COAD - Colon adenocarcinoma(227;7.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|READ - Rectum adenocarcinoma(331;0.0487)|STAD - Stomach adenocarcinoma(313;0.192)		CTCATAGACGGCATGAGCAGC	0.473																																					p.A484V	GBM(35;611 746 20780 22741 36496)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1451T	1						.						166.0	158.0	161.0					1																	11087552		2203	4300	6503	11010139	SO:0001583	missense	10747	exon11			X98400	CCDS123.1, CCDS124.1	1p36.3-p36.2	2014-09-17	2005-08-17		ENSG00000009724	ENSG00000009724			6902	protein-coding gene	gene with protein product		605102	"""mannan-binding lectin serine protease 2"", ""mannan-binding lectin serine peptidase 1 pseudogene 1"", ""mannan-binding lectin serine protease 1 pseudogene 1"""	MASP1P1		9087411, 9777418	Standard	NM_006610		Approved		uc001aru.3	O00187	OTTHUMG00000002121	ENST00000400897.3:c.1451C>T	1.37:g.11087552G>A	ENSP00000383690:p.Ala484Val		11010139	NM_006610	A8K458|A8MWJ2|O75754|Q5TEQ5|Q5TER0|Q96QG4|Q9BZH0|Q9H498|Q9H499|Q9UBP3|Q9UC48|Q9ULC7|Q9UMV3|Q9Y270	Missense_Mutation	SNP	ENST00000400897.3	37	CCDS123.1	.	.	.	.	.	.	.	.	.	.	G	0.006	-2.046600	0.00398	.	.	ENSG00000009724	ENST00000400897	D	0.92805	-3.11	5.27	0.117	0.14652	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.148628	0.43747	N	0.000528	T	0.63698	0.2533	N	0.00392	-1.555	0.22903	N	0.998583	B	0.09022	0.002	B	0.08055	0.003	T	0.65294	-0.6203	10	0.02654	T	1	.	3.5051	0.07688	0.4161:0.0:0.3045:0.2793	.	484	O00187	MASP2_HUMAN	V	484	ENSP00000383690:A484V	ENSP00000383690:A484V	A	-	2	0	MASP2	11010139	0.003000	0.15002	0.001000	0.08648	0.033000	0.12548	0.517000	0.22832	0.219000	0.20840	-0.244000	0.11960	GCC		0.473	MASP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006072.1	NM_006610	
KIAA1324	57535	broad.mit.edu	37	1	109743447	109743447	+	Silent	SNP	C	C	T	rs529832723		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:109743447C>T	ENST00000369939.3	+	21	3081	c.2898C>T	c.(2896-2898)ggC>ggT	p.G966G	KIAA1324_ENST00000369938.1_3'UTR|KIAA1324_ENST00000529753.1_Silent_p.G879G	NM_020775.4	NP_065826	Q6UXG2	K1324_HUMAN	KIAA1324	966					cellular response to starvation (GO:0009267)|macroautophagy (GO:0016236)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|positive regulation of autophagic vacuole assembly (GO:2000786)|positive regulation of vacuole organization (GO:0044090)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	poly(A) RNA binding (GO:0044822)	p.G966G(1)		NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34		all_epithelial(167;0.000102)|all_lung(203;0.000323)|Lung NSC(277;0.00063)		Colorectal(144;0.0188)|Lung(183;0.0527)|COAD - Colon adenocarcinoma(174;0.14)|Epithelial(280;0.21)|all cancers(265;0.249)		TCATGGAAGGCGAGGATGTAG	0.493											OREG0013630	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1	0.000199681	0.0	0.0	5008	,	,		23794	0.001		0.0	False		,,,				2504	0.0				p.G966G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2898T	1						.						110.0	97.0	101.0					1																	109743447		2203	4300	6503	109544970	SO:0001819	synonymous_variant	57535	exon21			AK057647	CCDS794.1, CCDS58015.1	1p13.3	2008-09-18			ENSG00000116299	ENSG00000116299			29618	protein-coding gene	gene with protein product	"""estrogen induced gene 121"""	611298				10718198, 16322283	Standard	NM_020775		Approved	maba1, EIG121	uc021orb.1	Q6UXG2	OTTHUMG00000011725	ENST00000369939.3:c.2898C>T	1.37:g.109743447C>T		1422	109544970	NM_020775	Q08AE6|Q5T5C9|Q5T5D0|Q5T5D1|Q9P2M2	Silent	SNP	ENST00000369939.3	37	CCDS794.1																																																																																				0.493	KIAA1324-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032389.2	NM_020775	
RBM15	64783	broad.mit.edu	37	1	110884690	110884690	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:110884690T>A	ENST00000369784.3	+	1	3563	c.2663T>A	c.(2662-2664)cTt>cAt	p.L888H	RP5-1074L1.1_ENST00000449169.1_RNA|RBM15_ENST00000602849.1_Missense_Mutation_p.L888H|RBM15_ENST00000487146.2_Missense_Mutation_p.L888H	NM_022768.4	NP_073605.4	Q96T37	RBM15_HUMAN	RNA binding motif protein 15	888	SPOC. {ECO:0000255|PROSITE- ProRule:PRU00249}.				negative regulation of myeloid cell differentiation (GO:0045638)|patterning of blood vessels (GO:0001569)|placenta blood vessel development (GO:0060674)|positive regulation of transcription of Notch receptor target (GO:0007221)|spleen development (GO:0048536)|ventricular septum morphogenesis (GO:0060412)|viral process (GO:0016032)	membrane (GO:0016020)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.L888H(1)		ovary(3)	3		all_cancers(81;2.89e-06)|all_epithelial(167;2.96e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Breast(1374;0.0634)		BRCA - Breast invasive adenocarcinoma(282;0.000224)|Epithelial(280;0.000476)|Kidney(133;0.000539)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|all cancers(265;0.00144)|Lung(183;0.0238)|Colorectal(144;0.103)|LUSC - Lung squamous cell carcinoma(189;0.135)		CAGAGGCCACTTAGGAACCTT	0.527			T	MKL1	acute megakaryocytic leukemia																																p.L888H			Dom	yes		1	1p13	64783	RNA binding motif protein 15		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2663A	1						.						79.0	85.0	83.0					1																	110884690		2203	4300	6503	110686213	SO:0001583	missense	64783	exon1			AF368063	CCDS822.1, CCDS59198.1	1p13	2013-02-12			ENSG00000162775	ENSG00000162775		"""RNA binding motif (RRM) containing"""	14959	protein-coding gene	gene with protein product	"""one twenty-two"""	606077				11431691, 11344311	Standard	NM_001201545		Approved	OTT, OTT1	uc001dzl.1	Q96T37	OTTHUMG00000011284	ENST00000369784.3:c.2663T>A	1.37:g.110884690T>A	ENSP00000358799:p.Leu888His		110686213	NM_022768	A1A693|Q3ZB86|Q4V760|Q5D058|Q5T613|Q86VW9|Q96PE4|Q96SC5|Q96SC6|Q96SC9|Q96SD0|Q96T38|Q9BRA5|Q9H6R8|Q9H9Y0	Missense_Mutation	SNP	ENST00000369784.3	37	CCDS822.1	.	.	.	.	.	.	.	.	.	.	T	18.51	3.639288	0.67244	.	.	ENSG00000162775	ENST00000369784	T	0.25579	1.79	5.25	5.25	0.73442	Spen Paralogue and Orthologue SPOC, C-terminal-like (2);Spen paralogue/orthologue C-terminal, metazoa (1);Spen paralogue and orthologue SPOC, C-terminal (1);	0.000000	0.42172	D	0.000760	T	0.45756	0.1358	M	0.81497	2.545	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.54002	-0.8358	10	0.87932	D	0	-8.3469	15.1284	0.72500	0.0:0.0:0.0:1.0	.	888;888	Q96T37-3;Q96T37	.;RBM15_HUMAN	H	888	ENSP00000358799:L888H	ENSP00000358799:L888H	L	+	2	0	RBM15	110686213	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.977000	0.88081	1.982000	0.57802	0.533000	0.62120	CTT		0.527	RBM15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000031114.2	NM_022768	
KCNA10	3744	broad.mit.edu	37	1	111061151	111061151	+	Missense_Mutation	SNP	G	G	A	rs200254580		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:111061151G>A	ENST00000369771.2	-	1	646	c.259C>T	c.(259-261)Cgg>Tgg	p.R87W		NM_005549.2	NP_005540.1	Q16322	KCA10_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 10	87					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)|intracellular cyclic nucleotide activated cation channel activity (GO:0005221)	p.R87W(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(3)|skin(1)|urinary_tract(1)	35		all_cancers(81;4.57e-06)|all_epithelial(167;1.52e-05)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0238)|all cancers(265;0.0874)|Colorectal(144;0.103)|Epithelial(280;0.116)|LUSC - Lung squamous cell carcinoma(189;0.134)	Dalfampridine(DB06637)	ATGATCACCCGCTGGTTTCCT	0.552																																					p.R87W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C259T	1						.						84.0	87.0	86.0					1																	111061151		2203	4300	6503	110862674	SO:0001583	missense	3744	exon1			U96110	CCDS826.1	1p13.1	2012-07-05			ENSG00000143105	ENSG00000143105		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6219	protein-coding gene	gene with protein product		602420				16382104	Standard	NM_005549		Approved	Kv1.8	uc001dzt.1	Q16322	OTTHUMG00000022785	ENST00000369771.2:c.259C>T	1.37:g.111061151G>A	ENSP00000358786:p.Arg87Trp		110862674	NM_005549		Missense_Mutation	SNP	ENST00000369771.2	37	CCDS826.1	.	.	.	.	.	.	.	.	.	.	G	16.12	3.032158	0.54790	.	.	ENSG00000143105	ENST00000369771	T	0.77489	-1.1	5.86	-0.262	0.12958	BTB/POZ-like (1);BTB/POZ fold (2);	0.052302	0.64402	D	0.000001	T	0.78572	0.4304	L	0.60455	1.87	0.43255	D	0.995189	D	0.89917	1.0	P	0.61397	0.888	T	0.82526	-0.0413	10	0.87932	D	0	.	16.1736	0.81836	0.0:0.0:0.2988:0.7012	.	87	Q16322	KCA10_HUMAN	W	87	ENSP00000358786:R87W	ENSP00000358786:R87W	R	-	1	2	KCNA10	110862674	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.726000	0.47302	0.276000	0.22118	-0.274000	0.10170	CGG		0.552	KCNA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059081.1	NM_005549	
KCNA2	3737	broad.mit.edu	37	1	111146221	111146221	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:111146221G>A	ENST00000485317.1	-	3	1857	c.1184C>T	c.(1183-1185)gCg>gTg	p.A395V	KCNA2_ENST00000440270.1_Missense_Mutation_p.A395V|KCNA2_ENST00000369770.3_Intron|KCNA2_ENST00000316361.4_Missense_Mutation_p.A395V|KCNA2_ENST00000525120.1_5'Flank			P16389	KCNA2_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 2	395					optic nerve structural organization (GO:0021633)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	juxtaparanode region of axon (GO:0044224)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)	p.A395V(1)		endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		all_cancers(81;5.55e-06)|all_epithelial(167;1.87e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Colorectal(144;0.00878)|Lung(183;0.0234)|all cancers(265;0.0492)|Epithelial(280;0.0529)|COAD - Colon adenocarcinoma(174;0.131)|LUSC - Lung squamous cell carcinoma(189;0.133)|READ - Rectum adenocarcinoma(129;0.191)	Dalfampridine(DB06637)	ACCTGCAATCGCACATAGGGA	0.517																																					p.A395V	Pancreas(18;568 735 10587 23710 36357)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1184T	1						.						96.0	96.0	96.0					1																	111146221		2203	4300	6503	110947744	SO:0001583	missense	3737	exon2			L02752	CCDS827.1, CCDS55625.1	1p13	2012-07-05			ENSG00000177301	ENSG00000177301		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6220	protein-coding gene	gene with protein product		176262				16382104	Standard	NM_004974		Approved	Kv1.2, HK4	uc009wfw.3	P16389	OTTHUMG00000011567	ENST00000485317.1:c.1184C>T	1.37:g.111146221G>A	ENSP00000433109:p.Ala395Val		110947744	NM_004974	Q86XG6	Missense_Mutation	SNP	ENST00000485317.1	37	CCDS827.1	.	.	.	.	.	.	.	.	.	.	G	18.99	3.740388	0.69304	.	.	ENSG00000177301	ENST00000485317;ENST00000440270;ENST00000316361	D;D;D	0.98192	-4.78;-4.78;-4.78	5.4	5.4	0.78164	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98651	0.9548	M	0.64170	1.965	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99899	1.1157	10	0.72032	D	0.01	.	19.1701	0.93574	0.0:0.0:1.0:0.0	.	395	P16389	KCNA2_HUMAN	V	395	ENSP00000433109:A395V;ENSP00000415257:A395V;ENSP00000314520:A395V	ENSP00000314520:A395V	A	-	2	0	KCNA2	110947744	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	9.802000	0.99131	2.518000	0.84900	0.655000	0.94253	GCG		0.517	KCNA2-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128001.2	NM_004974	
ADORA3	140	broad.mit.edu	37	1	112031414	112031414	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:112031414C>T	ENST00000369716.4	-	3	823	c.690G>A	c.(688-690)acG>acA	p.T230T	ADORA3_ENST00000369717.4_Silent_p.T149T|RNU6-792P_ENST00000363490.1_RNA	NM_020683.6	NP_065734.5	P33765	AA3R_HUMAN	adenosine A3 receptor	0					activation of adenylate cyclase activity (GO:0007190)|histamine secretion by mast cell (GO:0002553)|inflammatory response (GO:0006954)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of mucus secretion (GO:0070257)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of heart contraction (GO:0008016)|response to wounding (GO:0009611)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	G-protein coupled adenosine receptor activity (GO:0001609)	p.T230T(2)|p.T149T(1)		NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)|skin(1)	12		all_cancers(81;1.63e-06)|all_epithelial(167;5.01e-06)|all_lung(203;8.02e-05)|Lung NSC(277;0.000156)		all cancers(265;0.0185)|Colorectal(144;0.0186)|Lung(183;0.0238)|COAD - Colon adenocarcinoma(174;0.0644)|Epithelial(280;0.0872)|LUSC - Lung squamous cell carcinoma(189;0.134)	Adenosine(DB00640)|Aminophylline(DB01223)|Enprofylline(DB00824)	AGTACCAGCCCGTGTCCTCTT	0.532																																					p.T149T												.	.	3	Substitution - coding silent(3)	endometrium(2)|large_intestine(1)	c.G447A	1						.						123.0	106.0	111.0					1																	112031414		2203	4300	6503	111832937	SO:0001819	synonymous_variant	140	exon3			BC029831	CCDS838.1, CCDS839.1, CCDS41369.1	1p13.2	2014-09-17			ENSG00000121933	ENSG00000121933		"""GPCR / Class A : Adenosine receptors"", ""Immunoglobulin superfamily / V-set domain containing"""	268	protein-coding gene	gene with protein product		600445				7607699	Standard	NM_020683		Approved	AD026	uc001ebf.3	P33765	OTTHUMG00000011957	ENST00000369716.4:c.690G>A	1.37:g.112031414C>T			111832937	NM_001081976	A2A3P4|Q6UWU0|Q9BYZ1	Silent	SNP	ENST00000369716.4	37	CCDS838.1	.	.	.	.	.	.	.	.	.	.	C	6.172	0.399948	0.11696	.	.	ENSG00000121933	ENST00000414219;ENST00000442484	.	.	.	5.25	-8.72	0.00845	.	.	.	.	.	T	0.14485	0.0350	.	.	.	0.33321	D	0.567366	.	.	.	.	.	.	T	0.09596	-1.0667	4	.	.	.	-3.7626	5.7031	0.17893	0.1069:0.1583:0.1055:0.6293	.	.	.	.	Q	90;43	.	.	R	-	2	0	ADORA3	111832937	0.000000	0.05858	0.014000	0.15608	0.734000	0.41952	-3.578000	0.00425	-1.446000	0.01945	-0.448000	0.05591	CGG		0.532	ADORA3-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000157679.1	NM_000677, NM_020683	
MTOR	2475	broad.mit.edu	37	1	11319309	11319309	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:11319309C>T	ENST00000361445.4	-	2	234	c.158G>A	c.(157-159)cGa>cAa	p.R53Q		NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	53	Interaction with NBN.				cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)	p.R53Q(1)		breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	AAGCACCTCTCGGAGTTCCAT	0.512																																					p.R53Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G158A	1						.						98.0	96.0	97.0					1																	11319309		2203	4300	6503	11241896	SO:0001583	missense	2475	exon2			L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"""FK506 binding protein 12-rapamycin associated protein 2"", ""rapamycin target protein"", ""FKBP12-rapamycin complex-associated protein 1"", ""FKBP-rapamycin associated protein"", ""rapamycin associated protein FRAP2"", ""dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)"", ""rapamycin and FKBP12 target 1"", ""mammalian target of rapamycin"""	601231	"""FK506 binding protein 12-rapamycin associated protein 1"""	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.158G>A	1.37:g.11319309C>T	ENSP00000354558:p.Arg53Gln		11241896	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	ENST00000361445.4	37	CCDS127.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.276348	0.80580	.	.	ENSG00000198793	ENST00000361445;ENST00000539766	T	0.65549	-0.16	5.7	5.7	0.88788	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.59959	0.2232	M	0.76574	2.34	0.80722	D	1	P	0.47106	0.89	B	0.30716	0.119	T	0.68356	-0.5430	10	0.48119	T	0.1	.	19.4425	0.94827	0.0:1.0:0.0:0.0	.	53	P42345	MTOR_HUMAN	Q	53	ENSP00000354558:R53Q	ENSP00000354558:R53Q	R	-	2	0	MTOR	11241896	1.000000	0.71417	0.998000	0.56505	0.862000	0.49288	7.444000	0.80532	2.685000	0.91497	0.655000	0.94253	CGA		0.512	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958	
KCND3	3752	broad.mit.edu	37	1	112524273	112524273	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:112524273C>T	ENST00000315987.2	-	2	1555	c.1076G>A	c.(1075-1077)tGg>tAg	p.W359*	KCND3_ENST00000369697.1_Nonsense_Mutation_p.W359*|KCND3_ENST00000302127.4_Nonsense_Mutation_p.W359*	NM_004980.4	NP_004971.2	Q9UK17	KCND3_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 3	359					cell death (GO:0008219)|membrane repolarization (GO:0086009)|potassium ion export (GO:0071435)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)	p.W359*(1)		NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	49		all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05)		all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231)	Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	AATGGTGTACCAAAACGAGGC	0.542																																					p.W359X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G1076A	1						.						105.0	88.0	94.0					1																	112524273		2203	4300	6503	112325796	SO:0001587	stop_gained	3752	exon2			AF048713	CCDS843.1, CCDS844.1	1p13.2	2014-09-17			ENSG00000171385	ENSG00000171385		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6239	protein-coding gene	gene with protein product		605411	"""spinocerebellar ataxia 22"", ""spinocerebellar ataxia 19"""	SCA22, SCA19		10942109, 16382104, 23280837	Standard	NM_172198		Approved	Kv4.3, KSHIVB	uc001ebu.1	Q9UK17	OTTHUMG00000011989	ENST00000315987.2:c.1076G>A	1.37:g.112524273C>T	ENSP00000319591:p.Trp359*		112325796	NM_004980	O60576|O60577|Q14D71|Q5T0M0|Q9UH85|Q9UH86|Q9UK16	Nonsense_Mutation	SNP	ENST00000315987.2	37	CCDS843.1	.	.	.	.	.	.	.	.	.	.	C	39	7.367133	0.98238	.	.	ENSG00000171385	ENST00000369697;ENST00000315987;ENST00000302127	.	.	.	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.1956	0.93686	0.0:1.0:0.0:0.0	.	.	.	.	X	359	.	ENSP00000306923:W359X	W	-	2	0	KCND3	112325796	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	7.818000	0.86416	2.636000	0.89361	0.655000	0.94253	TGG		0.542	KCND3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000033144.1	NM_172198	
BCL2L15	440603	broad.mit.edu	37	1	114429940	114429940	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:114429940T>C	ENST00000393316.3	-	1	229	c.58A>G	c.(58-60)Atg>Gtg	p.M20V	BCL2L15_ENST00000393320.3_Missense_Mutation_p.M20V|BCL2L15_ENST00000471267.1_Missense_Mutation_p.M20V|AP4B1-AS1_ENST00000419536.1_RNA|BCL2L15_ENST00000488450.1_5'Flank	NM_001010922.2	NP_001010922.1	Q5TBC7	B2L15_HUMAN	BCL2-like 15	20					apoptotic process (GO:0006915)	cytosol (GO:0005829)|nucleus (GO:0005634)		p.M20V(1)		breast(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(3)|ovary(1)	9	Lung SC(450;0.184)	all_cancers(81;3.95e-08)|all_epithelial(167;9.95e-08)|all_lung(203;1.31e-05)|Lung NSC(69;2.46e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AAGAAGTCCATGAGTAGAGTG	0.458																																					p.M20V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A58G	1						.						228.0	202.0	210.0					1																	114429940		2203	4300	6503	114231463	SO:0001583	missense	440603	exon1				CCDS30809.1	1p13.2	2014-03-07			ENSG00000188761	ENSG00000188761			33624	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 178"""	C1orf178		12700646, 15961081, 16690252, 17412810	Standard	NM_001010922		Approved	Bfk, FLJ22588	uc001edw.3	Q5TBC7	OTTHUMG00000011940	ENST00000393316.3:c.58A>G	1.37:g.114429940T>C	ENSP00000376992:p.Met20Val		114231463	NM_001010922	A0PJY6|A8K074|I6LA82	Missense_Mutation	SNP	ENST00000393316.3	37	CCDS30809.1	.	.	.	.	.	.	.	.	.	.	T	10.21	1.286948	0.23478	.	.	ENSG00000188761	ENST00000393316;ENST00000393320;ENST00000471267	T;T	0.03889	3.77;3.77	5.65	-11.1	0.00147	.	2.427000	0.01010	N	0.003810	T	0.00906	0.0030	L	0.29908	0.895	0.09310	N	1	B;B	0.12013	0.005;0.005	B;B	0.13407	0.006;0.009	T	0.43147	-0.9409	10	0.38643	T	0.18	.	4.0848	0.09942	0.3073:0.4315:0.0962:0.165	.	20;20	Q68DJ4;Q5TBC7	.;B2L15_HUMAN	V	20	ENSP00000376992:M20V;ENSP00000417458:M20V	ENSP00000376992:M20V	M	-	1	0	BCL2L15	114231463	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.188000	0.00277	-1.541000	0.01727	-1.119000	0.02030	ATG		0.458	BCL2L15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033026.2	NM_001010922	
CLCN6	1185	broad.mit.edu	37	1	11896131	11896131	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:11896131C>T	ENST00000346436.6	+	18	1953	c.1901C>T	c.(1900-1902)cCg>cTg	p.P634L	CLCN6_ENST00000376487.3_Missense_Mutation_p.P612L|CLCN6_ENST00000312413.6_3'UTR|CLCN6_ENST00000376496.3_Missense_Mutation_p.P634L	NM_001286.3	NP_001277	P51797	CLCN6_HUMAN	chloride channel, voltage-sensitive 6	634	CBS 1. {ECO:0000255|PROSITE- ProRule:PRU00703}.				cell volume homeostasis (GO:0006884)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|response to mechanical stimulus (GO:0009612)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|voltage-gated chloride channel activity (GO:0005247)	p.P634L(1)		cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(4)	36	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		CATGCCTTCCCGGTGGTCACA	0.562																																					p.P634L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1901T	1						.						131.0	100.0	110.0					1																	11896131		2203	4300	6503	11818718	SO:0001583	missense	1185	exon18			X83378	CCDS138.1, CCDS57972.1	1p36	2012-09-26	2012-02-23		ENSG00000011021	ENSG00000011021		"""Ion channels / Chloride channels : Voltage-sensitive"""	2024	protein-coding gene	gene with protein product		602726	"""chloride channel 6"""			8543009	Standard	NM_001286		Approved	CLC-6, KIAA0046, ClC-6	uc001ate.5	P51797	OTTHUMG00000002299	ENST00000346436.6:c.1901C>T	1.37:g.11896131C>T	ENSP00000234488:p.Pro634Leu		11818718	NM_001286	A8K1T4|B4DGT7|F8W9R3|O60818|O60819|O60820|O60821|P78520|P78521|Q17R81|Q5SNW2|Q5SNW3|Q5SNX1|Q5SNX2|Q5SNX3|Q99427|Q99428|Q99429	Missense_Mutation	SNP	ENST00000346436.6	37	CCDS138.1	.	.	.	.	.	.	.	.	.	.	C	32	5.192629	0.94960	.	.	ENSG00000011021	ENST00000346436;ENST00000376487;ENST00000376496	D;D;D	0.92858	-3.12;-3.12;-3.12	5.71	5.71	0.89125	Cystathionine beta-synthase, core (3);	0.196194	0.56097	D	0.000038	D	0.93671	0.7978	L	0.29908	0.895	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.74348	0.957;0.983	D	0.94398	0.7620	10	0.87932	D	0	-26.8311	18.8314	0.92141	0.0:1.0:0.0:0.0	.	612;634	F8W9R3;P51797	.;CLCN6_HUMAN	L	634;612;634	ENSP00000234488:P634L;ENSP00000365670:P612L;ENSP00000365679:P634L	ENSP00000234488:P634L	P	+	2	0	CLCN6	11818718	1.000000	0.71417	0.985000	0.45067	0.989000	0.77384	7.487000	0.81328	2.700000	0.92200	0.462000	0.41574	CCG		0.562	CLCN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006639.2	NM_001286	
NPPB	4879	broad.mit.edu	37	1	11918407	11918407	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:11918407G>A	ENST00000376468.3	-	2	349	c.252C>T	c.(250-252)acC>acT	p.T84T		NM_002521.2	NP_002512.1	P16860	ANFB_HUMAN	natriuretic peptide B	84					body fluid secretion (GO:0007589)|cell surface receptor signaling pathway (GO:0007166)|cGMP biosynthetic process (GO:0006182)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|regulation of blood vessel size (GO:0050880)|regulation of vascular permeability (GO:0043114)|regulation of vasodilation (GO:0042312)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|protein complex (GO:0043234)	diuretic hormone activity (GO:0008613)|hormone activity (GO:0005179)|receptor binding (GO:0005102)	p.T84T(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	11	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.88e-06)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)	Carvedilol(DB01136)	GGATGCCCTCGGTGGCTACCT	0.642																																					p.T84T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C252T	1						.						40.0	40.0	40.0					1																	11918407		2203	4300	6503	11840994	SO:0001819	synonymous_variant	4879	exon2			BC025785	CCDS140.1	1p36.2	2014-01-30	2010-11-09		ENSG00000120937	ENSG00000120937		"""Endogenous ligands"""	7940	protein-coding gene	gene with protein product		600295	"""natriuretic peptide precursor B"""			2597152	Standard	NM_002521		Approved		uc001atj.3	P16860	OTTHUMG00000002389	ENST00000376468.3:c.252C>T	1.37:g.11918407G>A			11840994	NM_002521	B0ZBE9|Q6FGY0|Q9P2Q7	Silent	SNP	ENST00000376468.3	37	CCDS140.1																																																																																				0.642	NPPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006854.1	NM_002521	
CD101	9398	broad.mit.edu	37	1	117561169	117561169	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:117561169C>T	ENST00000256652.4	+	6	2062	c.2004C>T	c.(2002-2004)gcC>gcT	p.A668A	CD101_ENST00000369470.1_Silent_p.A668A	NM_001256106.1|NM_001256109.1|NM_001256111.1|NM_004258.4	NP_001243035.1|NP_001243038.1|NP_001243040.1|NP_004249.2	Q93033	IGSF2_HUMAN	CD101 molecule	668	Ig-like C2-type 6.				cell surface receptor signaling pathway (GO:0007166)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)	p.A668A(1)		NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(14)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						TGAGGATAGCCGTCACTTTAC	0.408																																					p.A668A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2004T	1						.						48.0	50.0	50.0					1																	117561169		2203	4300	6503	117362692	SO:0001819	synonymous_variant	9398	exon6			Z33642	CCDS891.1	1p13	2013-01-29	2009-10-27	2009-10-27	ENSG00000134256	ENSG00000134256		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5949	protein-coding gene	gene with protein product		604516	"""immunoglobulin superfamily, member 2"""	IGSF2		7722300	Standard	NM_004258		Approved	V7	uc010oxb.2	Q93033	OTTHUMG00000012029	ENST00000256652.4:c.2004C>T	1.37:g.117561169C>T			117362692	NM_004258	Q15856	Silent	SNP	ENST00000256652.4	37	CCDS891.1																																																																																				0.408	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258	
ADAM30	11085	broad.mit.edu	37	1	120436621	120436621	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:120436621G>A	ENST00000369400.1	-	1	2497	c.2339C>T	c.(2338-2340)cCc>cTc	p.P780L		NM_021794.3	NP_068566.2	Q9UKF2	ADA30_HUMAN	ADAM metallopeptidase domain 30	780					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.P780L(1)		NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(16)|ovary(2)|skin(2)	38	all_cancers(5;7.07e-10)|all_epithelial(5;1.62e-10)|all_neural(166;0.153)|Breast(55;0.234)	all_lung(203;1.55e-06)|Lung NSC(69;1.04e-05)|all_epithelial(167;0.00138)		Lung(183;0.0204)|LUSC - Lung squamous cell carcinoma(189;0.117)		CTTTGCTTTGGGTCGTTTACT	0.363																																					p.P780L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2339T	1						.						310.0	321.0	318.0					1																	120436621		2203	4300	6503	120238144	SO:0001583	missense	11085	exon1			AF171932	CCDS907.1	1p12	2012-05-16	2005-08-18		ENSG00000134249	ENSG00000134249		"""ADAM metallopeptidase domain containing"""	208	protein-coding gene	gene with protein product		604779	"""a disintegrin and metalloproteinase domain 30"""				Standard	NM_021794		Approved	svph4	uc001eij.3	Q9UKF2	OTTHUMG00000012176	ENST00000369400.1:c.2339C>T	1.37:g.120436621G>A	ENSP00000358407:p.Pro780Leu		120238144	NM_021794	A8K8W8|Q5T3X6|Q9UKF1	Missense_Mutation	SNP	ENST00000369400.1	37	CCDS907.1	.	.	.	.	.	.	.	.	.	.	G	10.87	1.471581	0.26423	.	.	ENSG00000134249	ENST00000369400;ENST00000543066	T	0.01178	5.22	4.04	-0.537	0.11872	.	.	.	.	.	T	0.00271	0.0008	N	0.14661	0.345	0.09310	N	1	B	0.19706	0.038	B	0.14578	0.011	T	0.40720	-0.9548	9	0.52906	T	0.07	.	3.7246	0.08470	0.2072:0.0:0.3177:0.4751	.	780	Q9UKF2	ADA30_HUMAN	L	780;771	ENSP00000358407:P780L	ENSP00000358407:P780L	P	-	2	0	ADAM30	120238144	0.002000	0.14202	0.001000	0.08648	0.190000	0.23558	0.293000	0.19029	-0.192000	0.10432	0.655000	0.94253	CCC		0.363	ADAM30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033678.1	NM_021794	
NOTCH2	4853	broad.mit.edu	37	1	120506201	120506201	+	Silent	SNP	C	C	T	rs369028361		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:120506201C>T	ENST00000256646.2	-	11	2130	c.1911G>A	c.(1909-1911)acG>acA	p.T637T		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	637	EGF-like 16; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)	p.T637T(1)		breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		GCTTACCTGACGTGCCTGGCT	0.483			"""N, F, Mis"""		"""marginal zone lymphoma, DLBCL"""				Alagille Syndrome																												p.T637T			Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1911A	1						.	C	,	0,4406		0,0,2203	204.0	177.0	186.0		1911,1911	-11.1	0.0	1		186	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	NOTCH2	NM_001200001.1,NM_024408.3	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	637/1236,637/2472	120506201	1,13005	2203	4300	6503	120307724	SO:0001819	synonymous_variant	4853	exon11	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"""Ankyrin repeat domain containing"""	7882	protein-coding gene	gene with protein product		600275	"""Notch (Drosophila) homolog 2"", ""Notch homolog 2 (Drosophila)"""			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.1911G>A	1.37:g.120506201C>T			120307724	NM_024408	Q5T3X7|Q99734|Q9H240	Silent	SNP	ENST00000256646.2	37	CCDS908.1																																																																																				0.483	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408	
GABPB2	126626	broad.mit.edu	37	1	151079545	151079545	+	Missense_Mutation	SNP	G	G	A	rs370629015		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:151079545G>A	ENST00000368918.3	+	7	1100	c.769G>A	c.(769-771)Gtt>Att	p.V257I	GABPB2_ENST00000368917.1_Missense_Mutation_p.V219I|GABPB2_ENST00000467551.1_3'UTR|GABPB2_ENST00000368916.1_Missense_Mutation_p.V219I	NM_144618.2	NP_653219.1	Q8TAK5	GABP2_HUMAN	GA binding protein transcription factor, beta subunit 2	257					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|transcription regulatory region DNA binding (GO:0044212)	p.V257I(1)		breast(1)|endometrium(2)|large_intestine(3)|liver(2)|lung(7)	15				all cancers(107;7.17e-05)|GBM - Glioblastoma multiforme(94;0.000662)		AGGAAATTCCGTTGACTCATC	0.398																																					p.V257I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G769A	1						.	G	ILE/VAL	0,4406		0,0,2203	70.0	70.0	70.0		769	3.5	1.0	1		70	1,8599	1.2+/-3.3	0,1,4299	no	missense	GABPB2	NM_144618.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	257/449	151079545	1,13005	2203	4300	6503	149346169	SO:0001583	missense	126626	exon7				CCDS983.1	1q21.2	2013-01-10			ENSG00000143458	ENSG00000143458		"""Ankyrin repeat domain containing"""	28441	protein-coding gene	gene with protein product						7958862	Standard	NM_144618		Approved	MGC29891	uc001ewr.2	Q8TAK5	OTTHUMG00000012193	ENST00000368918.3:c.769G>A	1.37:g.151079545G>A	ENSP00000357914:p.Val257Ile		149346169	NM_144618	B1AVJ8|D3DV14|Q8NAR5	Missense_Mutation	SNP	ENST00000368918.3	37	CCDS983.1	.	.	.	.	.	.	.	.	.	.	G	12.96	2.095270	0.36952	0.0	1.16E-4	ENSG00000143458	ENST00000368918;ENST00000368917;ENST00000368916	T;T;T	0.61510	0.1;0.14;0.14	5.41	3.52	0.40303	.	0.381437	0.26532	N	0.023842	T	0.27278	0.0669	L	0.50333	1.59	0.29719	N	0.838813	B;B;B	0.18741	0.002;0.03;0.005	B;B;B	0.16289	0.001;0.015;0.002	T	0.13442	-1.0509	10	0.20519	T	0.43	-1.4981	9.8001	0.40759	0.0775:0.1458:0.7766:0.0	.	219;257;257	Q5SZG2;B2R924;Q8TAK5	.;.;GABP2_HUMAN	I	257;219;219	ENSP00000357914:V257I;ENSP00000357913:V219I;ENSP00000357912:V219I	ENSP00000357912:V219I	V	+	1	0	GABPB2	149346169	1.000000	0.71417	1.000000	0.80357	0.677000	0.39632	2.191000	0.42640	0.824000	0.34613	0.557000	0.71058	GTT		0.398	GABPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033700.2	NM_144618	
SCNM1	79005	broad.mit.edu	37	1	151141517	151141517	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:151141517T>C	ENST00000368905.4	+	7	760	c.649T>C	c.(649-651)Ttt>Ctt	p.F217L		NM_001204856.1|NM_024041.3	NP_001191785.1|NP_076946.1	Q9BWG6	SCNM1_HUMAN	sodium channel modifier 1	217	Required for interaction with LUC7L2. {ECO:0000250}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)	p.F217L(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	17	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			AAATGTTGAGTTTGACTCTGA	0.428																																					p.F217L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T649C	1						.						270.0	224.0	240.0					1																	151141517		2203	4300	6503	149408141	SO:0001583	missense	79005	exon7			BC000264	CCDS987.1, CCDS55636.1	1q21.3	2012-03-13			ENSG00000163156	ENSG00000163156			23136	protein-coding gene	gene with protein product		608095				12920299	Standard	NM_024041		Approved	MGC3180	uc001ewz.3	Q9BWG6	OTTHUMG00000012258	ENST00000368905.4:c.649T>C	1.37:g.151141517T>C	ENSP00000357901:p.Phe217Leu		149408141	NM_024041	B4DWR1|Q5JR74	Missense_Mutation	SNP	ENST00000368905.4	37	CCDS987.1	.	.	.	.	.	.	.	.	.	.	T	33	5.223138	0.95139	.	.	ENSG00000163156	ENST00000368905;ENST00000368902	.	.	.	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.72653	0.3487	M	0.75264	2.295	0.50171	D	0.999857	D	0.71674	0.998	D	0.80764	0.994	T	0.77362	-0.2616	9	0.87932	D	0	-10.3274	13.0938	0.59180	0.0:0.0:0.0:1.0	.	217	Q9BWG6	SCNM1_HUMAN	L	217;182	.	ENSP00000357898:F182L	F	+	1	0	SCNM1	149408141	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.057000	0.76669	2.173000	0.68751	0.454000	0.30748	TTT		0.428	SCNM1-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034064.2	NM_024041	
THEM4	117145	broad.mit.edu	37	1	151867594	151867594	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:151867594A>C	ENST00000368814.3	-	2	525	c.176T>G	c.(175-177)cTg>cGg	p.L59R	THEM4_ENST00000489410.1_Missense_Mutation_p.L59R	NM_053055.4	NP_444283.2	Q5T1C6	THEM4_HUMAN	thioesterase superfamily member 4	59					epidermal growth factor receptor signaling pathway (GO:0007173)|fatty acid metabolic process (GO:0006631)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|protein kinase B signaling (GO:0043491)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)	cell projection (GO:0042995)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	palmitoyl-CoA hydrolase activity (GO:0016290)	p.L59R(1)		endometrium(1)|large_intestine(4)|lung(3)|urinary_tract(1)	9	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			GTCAAAGAGCAGTCTTAGGTC	0.413																																					p.L59R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T176G	1						.						81.0	79.0	80.0					1																	151867594		2203	4300	6503	150134218	SO:0001583	missense	117145	exon2			AJ313515	CCDS1006.1	1q21.3	2008-02-05			ENSG00000159445	ENSG00000159445			17947	protein-coding gene	gene with protein product	"""C-terminal modulator protein"""	606388				11598301	Standard	NM_053055		Approved	CTMP	uc001ezj.2	Q5T1C6	OTTHUMG00000013049	ENST00000368814.3:c.176T>G	1.37:g.151867594A>C	ENSP00000357804:p.Leu59Arg		150134218	NM_053055	B2RBX2|Q96KR2	Missense_Mutation	SNP	ENST00000368814.3	37	CCDS1006.1	.	.	.	.	.	.	.	.	.	.	A	14.58	2.577416	0.45902	.	.	ENSG00000159445	ENST00000368814;ENST00000489410	T;T	0.25414	2.1;1.8	4.16	3.02	0.34903	.	0.302870	0.29028	N	0.013374	T	0.06554	0.0168	L	0.43757	1.38	0.09310	N	1	B	0.17852	0.024	B	0.18561	0.022	T	0.35425	-0.9789	10	0.15952	T	0.53	-3.3511	7.0398	0.25013	0.7988:0.0:0.0:0.2012	.	59	Q5T1C6	THEM4_HUMAN	R	59	ENSP00000357804:L59R;ENSP00000433304:L59R	ENSP00000357804:L59R	L	-	2	0	THEM4	150134218	0.030000	0.19436	0.022000	0.16811	0.751000	0.42716	1.398000	0.34554	0.908000	0.36671	0.528000	0.53228	CTG		0.413	THEM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036615.1	NM_053055	
FLG	2312	broad.mit.edu	37	1	152278031	152278031	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:152278031G>A	ENST00000368799.1	-	3	9366	c.9331C>T	c.(9331-9333)Cgt>Tgt	p.R3111C	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3111	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.R3111C(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GGGTGTCCACGAATGGTGTCC	0.597									Ichthyosis																												p.R3111C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C9331T	1						.						157.0	214.0	195.0					1																	152278031		2057	4237	6294	150544655	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.9331C>T	1.37:g.152278031G>A	ENSP00000357789:p.Arg3111Cys		150544655	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	G	7.742	0.701582	0.15172	.	.	ENSG00000143631	ENST00000368799	T	0.02197	4.4	2.27	-3.48	0.04739	.	.	.	.	.	T	0.00906	0.0030	M	0.66939	2.045	0.09310	N	1	P	0.46952	0.887	B	0.37387	0.248	T	0.32455	-0.9906	9	0.56958	D	0.05	.	6.2481	0.20830	0.1378:0.5742:0.288:0.0	.	3111	P20930	FILA_HUMAN	C	3111	ENSP00000357789:R3111C	ENSP00000357789:R3111C	R	-	1	0	FLG	150544655	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.055000	0.14229	-1.091000	0.03065	-0.507000	0.04495	CGT		0.597	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
FLG2	388698	broad.mit.edu	37	1	152327413	152327413	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:152327413T>C	ENST00000388718.5	-	3	2921	c.2849A>G	c.(2848-2850)cAa>cGa	p.Q950R	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	950	Ser-rich.				establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.Q950R(1)		NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGACCTGTGTTGTCCAAATCC	0.498																																					p.Q950R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2849G	1						.						296.0	296.0	296.0					1																	152327413		2203	4300	6503	150594037	SO:0001583	missense	388698	exon3			AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"""EF-hand domain containing"""	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.2849A>G	1.37:g.152327413T>C	ENSP00000373370:p.Gln950Arg		150594037	NM_001014342	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	37	CCDS30861.1	.	.	.	.	.	.	.	.	.	.	T	8.996	0.978958	0.18812	.	.	ENSG00000143520	ENST00000388718	T	0.22336	1.96	3.95	2.82	0.32997	.	.	.	.	.	T	0.03348	0.0097	N	0.05031	-0.125	0.09310	N	1	P	0.51791	0.948	P	0.46362	0.514	T	0.16778	-1.0391	9	0.14252	T	0.57	.	5.8533	0.18707	0.0:0.123:0.0:0.877	.	950	Q5D862	FILA2_HUMAN	R	950	ENSP00000373370:Q950R	ENSP00000373370:Q950R	Q	-	2	0	FLG2	150594037	0.001000	0.12720	0.002000	0.10522	0.071000	0.16799	0.468000	0.22051	0.583000	0.29574	0.533000	0.62120	CAA		0.498	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342	
KPRP	448834	broad.mit.edu	37	1	152733156	152733156	+	Silent	SNP	C	C	T	rs371632676		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:152733156C>T	ENST00000606109.1	+	1	1120	c.1092C>T	c.(1090-1092)ggC>ggT	p.G364G	KPRP_ENST00000368773.1_Silent_p.G364G			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	364	Pro-rich.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)		p.G364G(2)		NS(1)|breast(1)|endometrium(9)|kidney(1)|large_intestine(10)|lung(21)|ovary(6)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCTCCTGGGGCGCCTCCTGCC	0.662																																					p.G364G												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1092T	1						.	C		0,4406		0,0,2203	56.0	59.0	58.0		1092	-7.5	0.0	1		58	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	KPRP	NM_001025231.1		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		364/580	152733156	2,13004	2203	4300	6503	150999780	SO:0001819	synonymous_variant	448834	exon2			AY960854	CCDS30862.1	1q21.3	2008-02-05	2007-02-02	2006-12-07	ENSG00000203786	ENSG00000203786			31823	protein-coding gene	gene with protein product		613260	"""chromosome 1 open reading frame 45"""	C1orf45		16297201	Standard	NM_001025231		Approved		uc001fal.1	Q5T749	OTTHUMG00000012402	ENST00000606109.1:c.1092C>T	1.37:g.152733156C>T			150999780	NM_001025231		Silent	SNP	ENST00000606109.1	37	CCDS30862.1																																																																																				0.662	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231	
IVL	3713	broad.mit.edu	37	1	152883532	152883532	+	Missense_Mutation	SNP	T	T	G	rs201506560		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	G	T	G	Unknown	Valid	Germline	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:152883532T>G	ENST00000368764.3	+	2	1323	c.1259T>G	c.(1258-1260)gTg>gGg	p.V420G	IVL_ENST00000392667.2_Missense_Mutation_p.V274G			P07476	INVO_HUMAN	involucrin	420	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].				isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			gagaggcaggtggagcacctg	0.647																																					p.V420G												.	.	0			c.T1259G	1						.						16.0	15.0	15.0					1																	152883532		2083	4116	6199	151150156	SO:0001583	missense	3713	exon2			BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.1259T>G	1.37:g.152883532T>G	ENSP00000357753:p.Val420Gly		151150156	NM_005547	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	37	CCDS1030.1	.	.	.	.	.	.	.	.	.	.	T	8.226	0.803580	0.16467	.	.	ENSG00000163207	ENST00000368764;ENST00000392667	T;T	0.13420	3.0;2.59	3.76	-3.15	0.05233	.	.	.	.	.	T	0.01870	0.0059	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.46470	-0.9189	9	0.23891	T	0.37	.	4.6214	0.12450	0.5475:0.0:0.1669:0.2857	.	420	P07476	INVO_HUMAN	G	420;274	ENSP00000357753:V420G;ENSP00000376435:V274G	ENSP00000357753:V420G	V	+	2	0	IVL	151150156	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.069000	0.03444	-0.925000	0.03775	-4.545000	0.00004	GTG		0.647	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547	
HAX1	10456	broad.mit.edu	37	1	154248123	154248123	+	Silent	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:154248123T>C	ENST00000328703.7	+	7	999	c.786T>C	c.(784-786)gaT>gaC	p.D262D	HAX1_ENST00000532105.1_Silent_p.D134D|HAX1_ENST00000483970.2_Silent_p.D270D|HAX1_ENST00000457918.2_Silent_p.D214D	NM_006118.3	NP_006109.2	O00165	HAX1_HUMAN	HCLS1 associated protein X-1	262	Involved in HCLS1 binding.|Involved in PKD2 binding.|Required for localization in sarcoplasmic reticulum. {ECO:0000250}.				cellular response to cytokine stimulus (GO:0071345)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of actin filament polymerization (GO:0030833)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrion degradation (GO:1903146)|regulation of protein targeting to mitochondrion (GO:1903214)	actin cytoskeleton (GO:0015629)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|lamellipodium (GO:0030027)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|sarcoplasmic reticulum (GO:0016529)|transcription factor complex (GO:0005667)	interleukin-1 binding (GO:0019966)|protein N-terminus binding (GO:0047485)	p.D262D(1)		cervix(1)|endometrium(2)|large_intestine(2)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	15	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			CAGCCCTGGATGATGCCTTTT	0.498									Kostmann syndrome																												p.D214D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T642C	1						.						128.0	103.0	111.0					1																	154248123		2203	4300	6503	152514747	SO:0001819	synonymous_variant	10456	exon7	Familial Cancer Database	Kostmann Infantile Agranulocytosis, Severe Congenital Neutropenia, Congenital Agranulocytosis	U68566	CCDS1064.1, CCDS44230.1	1q21.3	2014-09-17			ENSG00000143575	ENSG00000143575			16915	protein-coding gene	gene with protein product	"""HCLS1 (and PKD2) associated protein"""	605998				9058808, 10760273	Standard	NM_006118		Approved	HS1BP1, HCLSBP1	uc001fes.3	O00165	OTTHUMG00000035978	ENST00000328703.7:c.786T>C	1.37:g.154248123T>C			152514747	NM_001018837	A8W4W9|A8W4X0|B4DUJ7|Q5VYD5|Q5VYD7|Q96AU4|Q9BS80	Silent	SNP	ENST00000328703.7	37	CCDS1064.1																																																																																				0.498	HAX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087650.1	NM_006118	
ADAR	103	broad.mit.edu	37	1	154574443	154574443	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:154574443C>T	ENST00000368474.4	-	2	874	c.675G>A	c.(673-675)ccG>ccA	p.P225P	ADAR_ENST00000368471.3_5'UTR|ADAR_ENST00000471068.1_5'Flank|ADAR_ENST00000292205.5_Silent_p.P268P	NM_001111.4|NM_015840.3|NM_015841.3	NP_001102|NP_056655.2|NP_056656.2	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific	225					adenosine to inosine editing (GO:0006382)|base conversion or substitution editing (GO:0016553)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|miRNA loading onto RISC involved in gene silencing by miRNA (GO:0035280)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|pre-miRNA processing (GO:0031054)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.P225P(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(4)|prostate(2)|skin(2)	51	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)		GTTCCAAACTCGGGTCTGAGT	0.537																																					p.P225P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G675A	1						.						81.0	85.0	84.0					1																	154574443		2203	4300	6503	152841067	SO:0001819	synonymous_variant	103	exon2			BC038227	CCDS1071.1, CCDS30879.1	1q21.3	2012-03-22			ENSG00000160710	ENSG00000160710	3.5.4.-		225	protein-coding gene	gene with protein product		146920	"""interferon-induced protein 4"""	IFI4, G1P1		7972084	Standard	NM_001111		Approved	ADAR1	uc001ffh.3	P55265	OTTHUMG00000037261	ENST00000368474.4:c.675G>A	1.37:g.154574443C>T			152841067	NM_015841	B1AQQ9|B1AQR0|D3DV76|O15223|O43859|O43860|Q9BYM3|Q9BYM4	Silent	SNP	ENST00000368474.4	37	CCDS1071.1																																																																																				0.537	ADAR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090691.2	NM_001111	
RUSC1	23623	broad.mit.edu	37	1	155291234	155291234	+	Intron	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:155291234C>T	ENST00000368352.5	+	2	65				RUSC1-AS1_ENST00000443642.1_RNA|RUSC1_ENST00000368347.4_5'Flank|RUSC1-AS1_ENST00000543656.1_RNA|RUSC1-AS1_ENST00000450199.1_RNA|RUSC1_ENST00000368354.3_Intron|RUSC1-AS1_ENST00000446880.1_RNA	NM_001105203.1	NP_001098673.1	Q9BVN2	RUSC1_HUMAN	RUN and SH3 domain containing 1						positive regulation of signal transduction (GO:0009967)|protein polyubiquitination (GO:0000209)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(2)|skin(1)|urinary_tract(1)	21	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;1.55e-10)|all cancers(21;4.15e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)			CGCCCCCCTTCGGAGATCCAG	0.637																																					p.E16K												.	.	0			c.G46A	1						.						10.0	11.0	11.0					1																	155291234		1825	4070	5895	153557858	SO:0001627	intron_variant	284618	exon2			AB026894	CCDS1112.1, CCDS41410.1, CCDS41411.1, CCDS41412.1	1q21-q22	2011-04-28			ENSG00000160753	ENSG00000160753			17153	protein-coding gene	gene with protein product						10760598	Standard	NM_001105203		Approved	NESCA	uc001fkj.2	Q9BVN2	OTTHUMG00000013910	ENST00000368352.5:c.-86-245C>T	1.37:g.155291234C>T			153557858	NM_001039517	B3KWM9|Q5T9U9|Q5T9V0|Q5T9V1|Q5T9V2|Q9UPY4|Q9Y4T5	Missense_Mutation	SNP	ENST00000368352.5	37	CCDS41410.1																																																																																				0.637	RUSC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039071.1		
GON4L	54856	broad.mit.edu	37	1	155736398	155736398	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:155736398G>T	ENST00000368331.1	-	21	2914	c.2866C>A	c.(2866-2868)Cta>Ata	p.L956I	GON4L_ENST00000361040.5_Missense_Mutation_p.L956I|GON4L_ENST00000471341.1_5'UTR|GON4L_ENST00000437809.1_Missense_Mutation_p.L956I|GON4L_ENST00000271883.5_Missense_Mutation_p.L956I	NM_001282858.1|NM_001282860.1	NP_001269787.1|NP_001269789.1	Q3T8J9	GON4L_HUMAN	gon-4-like (C. elegans)	956					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.L956I(1)		NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	45	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					TCTTTTTCTAGGCTTCGATCT	0.502																																					p.L956I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2866A	1						.						140.0	131.0	134.0					1																	155736398		2203	4300	6503	154003022	SO:0001583	missense	54856	exon21			AB046826	CCDS1121.1, CCDS44242.1, CCDS60296.1	1q22	2013-10-31	2006-11-08	2006-02-16	ENSG00000116580	ENSG00000116580			25973	protein-coding gene	gene with protein product		610393	"""gon-4 homolog (C.elegans)"""	GON4		16545939, 21454521	Standard	XM_005245283		Approved	FLJ20203, GON-4	uc001fly.1	Q3T8J9	OTTHUMG00000014106	ENST00000368331.1:c.2866C>A	1.37:g.155736398G>T	ENSP00000357315:p.Leu956Ile		154003022	NM_032292	B7ZBL4|Q14C93|Q3T8J8|Q5VYZ5|Q5W0D5|Q6AWA6|Q6P1Q6|Q7Z3L3|Q8IY79|Q9BQI1|Q9HCG6	Missense_Mutation	SNP	ENST00000368331.1	37		.	.	.	.	.	.	.	.	.	.	G	4.794	0.147580	0.09134	.	.	ENSG00000116580	ENST00000437809;ENST00000368331;ENST00000271883;ENST00000361040	T;T;T;T	0.61627	0.09;0.09;0.09;0.09	4.84	1.8	0.24995	.	0.643972	0.13657	N	0.371851	T	0.20373	0.0490	L	0.56769	1.78	0.09310	N	1	P;P;B;B	0.40211	0.707;0.563;0.132;0.208	B;B;B;B	0.29716	0.106;0.098;0.049;0.106	T	0.09684	-1.0663	10	0.18710	T	0.47	.	4.1904	0.10417	0.0856:0.292:0.4724:0.15	.	956;152;956;956	Q3T8J9-2;Q1ED43;Q3T8J9;Q3T8J9-3	.;.;GON4L_HUMAN;.	I	956	ENSP00000396117:L956I;ENSP00000357315:L956I;ENSP00000271883:L956I;ENSP00000354322:L956I	ENSP00000271883:L956I	L	-	1	2	GON4L	154003022	0.002000	0.14202	0.001000	0.08648	0.044000	0.14063	0.808000	0.27154	0.208000	0.20626	0.558000	0.71614	CTA		0.502	GON4L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_032292	
CASP9	842	broad.mit.edu	37	1	15833446	15833446	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:15833446C>T	ENST00000333868.5	-	4	672	c.578G>A	c.(577-579)cGc>cAc	p.R193H	CASP9_ENST00000546424.1_Missense_Mutation_p.R193H|CASP9_ENST00000375890.4_Missense_Mutation_p.R110H|CASP9_ENST00000348549.5_Intron	NM_001229.3	NP_001220.2	P55211	CASP9_HUMAN	caspase 9, apoptosis-related cysteine peptidase	193					activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|aging (GO:0007568)|apoptotic process (GO:0006915)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell apoptotic process (GO:0034349)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of apoptotic process (GO:0042981)|regulation of response to DNA damage stimulus (GO:2001020)|response to antibiotic (GO:0046677)|response to cobalt ion (GO:0032025)|response to estradiol (GO:0032355)|response to lipopolysaccharide (GO:0032496)|signal transduction in response to DNA damage (GO:0042770)	apoptosome (GO:0043293)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|enzyme activator activity (GO:0008047)|peptidase activity (GO:0008233)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)	p.R193H(1)		central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|stomach(1)	18		Breast(348;0.000207)|all_lung(284;0.000211)|Colorectal(325;0.000259)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;8.49e-07)|COAD - Colon adenocarcinoma(227;4.36e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00013)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00763)|READ - Rectum adenocarcinoma(331;0.0655)		CGAGGAGAAGCGACGCCGCAA	0.592																																					p.R110H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G329A	1						.						102.0	99.0	100.0					1																	15833446		2203	4300	6503	15706033	SO:0001583	missense	842	exon4			U60521	CCDS158.1, CCDS159.1, CCDS159.2, CCDS59995.1	1p36.21	2012-04-17	2005-08-17		ENSG00000132906	ENSG00000132906		"""Caspases"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1511	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 56"""	602234	"""caspase 9, apoptosis-related cysteine protease"""			8663294, 9390557	Standard	NM_001229		Approved	MCH6, ICE-LAP6, APAF-3, PPP1R56	uc001awn.4	P55211	OTTHUMG00000002256	ENST00000333868.5:c.578G>A	1.37:g.15833446C>T	ENSP00000330237:p.Arg193His		15706033	NM_032996	B4E1A3|O95348|Q53Y70|Q5JRU9|Q5UGI1|Q92852|Q9BQ62|Q9UEQ3|Q9UIJ8	Missense_Mutation	SNP	ENST00000333868.5	37	CCDS158.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.964638	0.74131	.	.	ENSG00000132906	ENST00000546424;ENST00000333868;ENST00000375874;ENST00000375890;ENST00000447522;ENST00000440484	T;T;T;T;T	0.20881	2.04;2.04;2.04;2.04;4.02	5.78	5.78	0.91487	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase precursor p45, core (2);Peptidase C14, ICE, catalytic subunit p20 (1);	0.046702	0.85682	D	0.000000	T	0.53367	0.1792	M	0.89030	3	0.58432	D	0.999994	D;D	0.89917	1.0;1.0	D;D	0.76575	0.988;0.979	T	0.59658	-0.7413	10	0.66056	D	0.02	.	15.508	0.75757	0.0:1.0:0.0:0.0	.	193;193	P55211;F8VVS7	CASP9_HUMAN;.	H	193;193;37;110;110;193	ENSP00000449584:R193H;ENSP00000330237:R193H;ENSP00000365051:R110H;ENSP00000396540:R110H;ENSP00000411304:R193H	ENSP00000330237:R193H	R	-	2	0	CASP9	15706033	1.000000	0.71417	0.957000	0.39632	0.049000	0.14656	6.612000	0.74187	2.726000	0.93360	0.561000	0.74099	CGC		0.592	CASP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006438.1	NM_032996	
ARHGEF2	9181	broad.mit.edu	37	1	155920255	155920255	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:155920255G>A	ENST00000361247.4	-	21	2821	c.2722C>T	c.(2722-2724)Cgc>Tgc	p.R908C	ARHGEF2_ENST00000477754.2_Intron|ARHGEF2_ENST00000368316.1_Missense_Mutation_p.R880C|ARHGEF2_ENST00000368315.4_Missense_Mutation_p.R909C|ARHGEF2_ENST00000462460.2_Missense_Mutation_p.R953C|ARHGEF2_ENST00000313695.7_Missense_Mutation_p.R880C|ARHGEF2_ENST00000313667.4_Missense_Mutation_p.R907C	NM_001162383.1|NM_001162384.1	NP_001155855.1|NP_001155856.1	Q92974	ARHG2_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 2	908					actin filament organization (GO:0007015)|apoptotic signaling pathway (GO:0097190)|cell morphogenesis (GO:0000902)|cellular hyperosmotic response (GO:0071474)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to tumor necrosis factor (GO:0071356)|establishment of mitotic spindle orientation (GO:0000132)|innate immune response (GO:0045087)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress (GO:1902219)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of necroptotic process (GO:0060546)|negative regulation of neurogenesis (GO:0050768)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cell proliferation (GO:0042127)|regulation of Rho protein signal transduction (GO:0035023)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|Rac GTPase binding (GO:0048365)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho GTPase binding (GO:0017048)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.R880C(1)		breast(4)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|skin(2)	40	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					AGATCCAGGCGGTCAGTGCCT	0.587																																					p.R908C	Melanoma(178;35 2768 6610 28839)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2722T	1						.						68.0	61.0	64.0					1																	155920255		2203	4300	6503	154186879	SO:0001583	missense	9181	exon21			AB014551	CCDS1125.1, CCDS53375.1, CCDS53376.1	1q21-q22	2013-01-10	2009-06-12		ENSG00000116584	ENSG00000116584		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	682	protein-coding gene	gene with protein product		607560	"""rho/rac guanine nucleotide exchange factor (GEF) 2"""			9857026, 9734811	Standard	NM_004723		Approved	LFP40, GEF-H1, KIAA0651, P40	uc001fmt.2	Q92974	OTTHUMG00000017464	ENST00000361247.4:c.2722C>T	1.37:g.155920255G>A	ENSP00000354837:p.Arg908Cys		154186879	NM_001162383	D3DVA6|O75142|Q15079|Q5VY92|Q8TDA3|Q8WUG4|Q9H023	Missense_Mutation	SNP	ENST00000361247.4	37	CCDS53376.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.219869	0.79464	.	.	ENSG00000116584	ENST00000313695;ENST00000361247;ENST00000368315;ENST00000368316;ENST00000313667	T;T;T;T;T	0.66815	-0.23;-0.11;-0.11;-0.23;-0.23	5.45	5.45	0.79879	.	0.000000	0.46442	D	0.000284	T	0.65015	0.2651	N	0.24115	0.695	0.48185	D	0.999604	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.77557	0.982;0.973;0.988;0.99	T	0.68880	-0.5292	10	0.59425	D	0.04	-22.3154	14.657	0.68841	0.0:0.0:1.0:0.0	.	952;908;907;909	D3DVA5;Q92974;Q92974-2;Q5VY93	.;ARHG2_HUMAN;.;.	C	880;908;909;880;907	ENSP00000315325:R880C;ENSP00000354837:R908C;ENSP00000357298:R909C;ENSP00000357299:R880C;ENSP00000314787:R907C	ENSP00000314787:R907C	R	-	1	0	ARHGEF2	154186879	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.501000	0.60393	2.838000	0.97847	0.655000	0.94253	CGC		0.587	ARHGEF2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046204.2	NM_004723	
OR10J1	26476	broad.mit.edu	37	1	159410420	159410420	+	Missense_Mutation	SNP	T	T	C	rs201898028		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:159410420T>C	ENST00000423932.3	+	1	909	c.872T>C	c.(871-873)aTc>aCc	p.I291T	RP11-550P17.5_ENST00000431862.1_RNA	NM_012351.2	NP_036483.2	P30954	O10J1_HUMAN	olfactory receptor, family 10, subfamily J, member 1	291					G-protein coupled receptor signaling pathway (GO:0007186)|sensory perception of chemical stimulus (GO:0007606)|single fertilization (GO:0007338)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I291T(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|skin(2)|stomach(1)	25	all_hematologic(112;0.0429)					TACACTGTCATCACTCCCCTA	0.507																																					p.I291T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T872C	1						.						152.0	125.0	134.0					1																	159410420		2203	4300	6503	157677044	SO:0001583	missense	26476	exon1			X64995	CCDS1185.1	1q23.2	2012-08-09			ENSG00000196184	ENSG00000196184		"""GPCR / Class A : Olfactory receptors"""	8175	protein-coding gene	gene with protein product						1370859	Standard	NM_012351		Approved	HGMP07J, HSHGMP07J	uc010piv.2	P30954	OTTHUMG00000022737	ENST00000423932.3:c.872T>C	1.37:g.159410420T>C	ENSP00000399078:p.Ile291Thr		157677044	NM_012351	Q2M1M8|Q5VSV1|Q6IET5|Q96R56	Missense_Mutation	SNP	ENST00000423932.3	37	CCDS1185.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	T	16.36	3.100955	0.56183	.	.	ENSG00000196184	ENST00000423932	T	0.00202	8.56	4.42	4.42	0.53409	GPCR, rhodopsin-like superfamily (1);	0.819468	0.10147	N	0.710135	T	0.00271	0.0008	M	0.84948	2.725	0.24451	N	0.994488	P	0.46512	0.879	P	0.55260	0.772	T	0.33292	-0.9874	10	0.87932	D	0	.	11.9432	0.52913	0.0:0.0:0.0:1.0	.	291	P30954	O10J1_HUMAN	T	291	ENSP00000399078:I291T	ENSP00000399078:I291T	I	+	2	0	OR10J1	157677044	0.824000	0.29247	0.976000	0.42696	0.970000	0.65996	3.088000	0.50175	1.962000	0.57031	0.528000	0.53228	ATC		0.507	OR10J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059020.1	NM_012351	
PVRL4	81607	broad.mit.edu	37	1	161047365	161047365	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:161047365G>A	ENST00000368012.3	-	3	910	c.608C>T	c.(607-609)gCc>gTc	p.A203V	PVRL4_ENST00000453926.2_5'Flank	NM_030916.2	NP_112178.2	Q96NY8	PVRL4_HUMAN	poliovirus receptor-related 4	203	Ig-like C2-type 1.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|viral process (GO:0016032)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A203V(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|urinary_tract(1)	20	all_cancers(52;8.9e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			TGAGGTGACGGCAGCAGAGCG	0.622																																					p.A203V	NSCLC(76;1160 1387 14476 16172 29359)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C608T	1						.						99.0	85.0	90.0					1																	161047365		2203	4300	6503	159313989	SO:0001583	missense	81607	exon3			AF426163	CCDS1216.1	1q22-q23.2	2013-01-14			ENSG00000143217	ENSG00000143217		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	19688	protein-coding gene	gene with protein product		609607				11544254	Standard	NM_030916		Approved	nectin-4, PRR4, LNIR	uc001fxo.2	Q96NY8	OTTHUMG00000031475	ENST00000368012.3:c.608C>T	1.37:g.161047365G>A	ENSP00000356991:p.Ala203Val		159313989	NM_030916	B4DQW3|Q96K15	Missense_Mutation	SNP	ENST00000368012.3	37	CCDS1216.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.018954	0.75275	.	.	ENSG00000143217	ENST00000368012	T	0.75938	-0.98	5.65	5.65	0.86999	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.106962	0.41500	D	0.000874	T	0.53142	0.1778	N	0.11427	0.14	0.80722	D	1	P	0.43938	0.822	P	0.45377	0.478	T	0.60772	-0.7197	10	0.38643	T	0.18	.	17.214	0.86938	0.0:0.0:1.0:0.0	.	203	Q96NY8	PVRL4_HUMAN	V	203	ENSP00000356991:A203V	ENSP00000356991:A203V	A	-	2	0	PVRL4	159313989	0.999000	0.42202	0.795000	0.32087	0.683000	0.39861	6.667000	0.74451	2.660000	0.90430	0.555000	0.69702	GCC		0.622	PVRL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077074.1	NM_030916	
B4GALT3	8703	broad.mit.edu	37	1	161143694	161143694	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:161143694C>T	ENST00000319769.5	-	5	857	c.635G>A	c.(634-636)cGg>cAg	p.R212Q	PPOX_ENST00000535223.1_Intron|PPOX_ENST00000495483.1_Intron|PPOX_ENST00000432542.2_Intron|B4GALT3_ENST00000470882.1_5'UTR|B4GALT3_ENST00000367998.1_Missense_Mutation_p.R212Q	NM_001199873.1|NM_003779.3	NP_001186802.1|NP_003770.1	O60512	B4GT3_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 3	212					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|galactosyltransferase activity (GO:0008378)|metal ion binding (GO:0046872)|N-acetyllactosamine synthase activity (GO:0003945)	p.R212Q(1)		cervix(1)|endometrium(5)|large_intestine(6)|lung(6)	18	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		N-Acetyl-D-glucosamine(DB00141)	GCGGGGTCCCCGGGGGTCACA	0.547																																					p.R212Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G635A	1						.						89.0	85.0	86.0					1																	161143694		2203	4300	6503	159410318	SO:0001583	missense	8703	exon5			BC006099	CCDS1222.1	1q21-q23	2013-02-19			ENSG00000158850	ENSG00000158850		"""Beta 4-glycosyltransferases"""	926	protein-coding gene	gene with protein product		604014				9405390, 9597550	Standard	NM_001199873		Approved	beta4Gal-T3	uc001fys.2	O60512	OTTHUMG00000034348	ENST00000319769.5:c.635G>A	1.37:g.161143694C>T	ENSP00000320965:p.Arg212Gln		159410318	NM_001199874	D3DVG3|O60910|Q9BPZ4|Q9H8T2	Missense_Mutation	SNP	ENST00000319769.5	37	CCDS1222.1	.	.	.	.	.	.	.	.	.	.	C	9.614	1.131990	0.21041	.	.	ENSG00000158850	ENST00000319769;ENST00000407555;ENST00000541560;ENST00000367998;ENST00000367997	T;T	0.22743	1.94;1.94	4.99	4.99	0.66335	.	0.454073	0.25708	N	0.028821	T	0.00967	0.0032	N	0.00050	-2.405	0.34669	D	0.723553	B;B	0.11235	0.002;0.004	B;B	0.08055	0.003;0.001	T	0.47328	-0.9126	10	0.02654	T	1	.	10.749	0.46198	0.0:0.9123:0.0:0.0877	.	212;212	B3KPV4;O60512	.;B4GT3_HUMAN	Q	212;189;212;212;212	ENSP00000320965:R212Q;ENSP00000356977:R212Q	ENSP00000320965:R212Q	R	-	2	0	B4GALT3	159410318	0.453000	0.25721	1.000000	0.80357	0.998000	0.95712	0.945000	0.29056	2.586000	0.87340	0.655000	0.94253	CGG		0.547	B4GALT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083054.1	NM_003779	
DDR2	4921	broad.mit.edu	37	1	162724476	162724476	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	T	T	T	Unknown	Wildtype	None	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:162724476T>G	ENST00000367922.3	+	6	686	c.248T>G	c.(247-249)cTg>cGg	p.L83R	DDR2_ENST00000367921.3_Missense_Mutation_p.L83R	NM_001014796.1	NP_001014796.1	Q16832	DDR2_HUMAN	discoidin domain receptor tyrosine kinase 2	83	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|chondrocyte proliferation (GO:0035988)|collagen fibril organization (GO:0030199)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|endochondral bone growth (GO:0003416)|extracellular matrix organization (GO:0030198)|ossification (GO:0001503)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of extracellular matrix disassembly (GO:0090091)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autophosphorylation (GO:0046777)|regulation of bone mineralization (GO:0030500)|regulation of extracellular matrix disassembly (GO:0010715)|signal transduction (GO:0007165)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(2)|kidney(1)|lung(2)|ovary(1)|skin(1)	7	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.113)		Regorafenib(DB08896)	CCTGATGACCTGAAGGAGTTT	0.572																																					p.L83R	NSCLC(161;314 2006 8283 19651 23192)											.	.	0			c.T248G	1						.						113.0	113.0	113.0					1																	162724476		2203	4300	6503	160991100	SO:0001583	missense	4921	exon6			AK095975	CCDS1241.1	1q12-q23	2009-07-10	2008-01-23		ENSG00000162733	ENSG00000162733	2.7.10.1		2731	protein-coding gene	gene with protein product		191311	"""discoidin domain receptor family, member 2"""	TYRO10, NTRKR3		9659899	Standard	XM_005245221		Approved	TKT	uc001gcg.3	Q16832	OTTHUMG00000034423	ENST00000367922.3:c.248T>G	1.37:g.162724476T>G	ENSP00000356899:p.Leu83Arg		160991100	NM_001014796	Q7Z730	Missense_Mutation	SNP	ENST00000367922.3	37	CCDS1241.1	.	.	.	.	.	.	.	.	.	.	T	15.33	2.801423	0.50315	.	.	ENSG00000162733	ENST00000446985;ENST00000415555;ENST00000542391;ENST00000367922;ENST00000367921	D;D;D;D	0.98178	-4.77;-4.77;-4.77;-4.77	5.37	5.37	0.77165	Coagulation factor 5/8 C-terminal type domain (4);Galactose-binding domain-like (1);	0.079486	0.52532	D	0.000074	D	0.94175	0.8131	N	0.19112	0.55	0.44555	D	0.997512	P	0.44734	0.842	P	0.44732	0.459	D	0.94879	0.8037	9	0.42905	T	0.14	.	14.1948	0.65662	0.0:0.0:0.0:1.0	.	83	Q16832	DDR2_HUMAN	R	83	ENSP00000400309:L83R;ENSP00000391310:L83R;ENSP00000356899:L83R;ENSP00000356898:L83R	ENSP00000356898:L83R	L	+	2	0	DDR2	160991100	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.786000	0.62425	2.023000	0.59567	0.528000	0.53228	CTG		0.572	DDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083213.2	NM_006182	
POU2F1	5451	broad.mit.edu	37	1	167385014	167385014	+	Silent	SNP	G	G	A	rs373597853		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:167385014G>A	ENST00000541643.3	+	17	2361	c.2199G>A	c.(2197-2199)gcG>gcA	p.A733A	POU2F1_ENST00000367866.2_Silent_p.A756A|POU2F1_ENST00000429375.2_Silent_p.A693A|POU2F1_ENST00000420254.3_Intron|POU2F1_ENST00000367862.5_Silent_p.A745A|POU2F1_ENST00000367865.1_3'UTR			P14859	PO2F1_HUMAN	POU class 2 homeobox 1	733					gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A733A(1)		breast(2)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	30						GCGGGGCTGCGTCCACCACCA	0.612													g|||	1	0.000199681	0.0	0.0	5008	,	,		14422	0.0		0.001	False		,,,				2504	0.0				p.A756A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2268A	1						.						82.0	86.0	84.0					1																	167385014		2203	4300	6503	165651638	SO:0001819	synonymous_variant	5451	exon16			BC001664	CCDS1259.1, CCDS1259.2, CCDS55655.1, CCDS55656.1	1q24.2	2011-06-20	2007-07-13		ENSG00000143190	ENSG00000143190		"""Homeoboxes / POU class"""	9212	protein-coding gene	gene with protein product		164175	"""POU domain class 2, transcription factor 1"""	OTF1		1887216	Standard	NM_002697		Approved	OCT1	uc001gee.3	P14859	OTTHUMG00000034436	ENST00000541643.3:c.2199G>A	1.37:g.167385014G>A			165651638	NM_002697	B1AL91|B1AL93|B4E029|J3KP77|Q5TBT7|Q6PK46|Q8NEU9|Q9BPV1	Silent	SNP	ENST00000541643.3	37																																																																																					0.612	POU2F1-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_002697	
F5	2153	broad.mit.edu	37	1	169510018	169510018	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:169510018G>A	ENST00000367797.3	-	13	4511	c.4310C>T	c.(4309-4311)aCt>aTt	p.T1437I	F5_ENST00000367796.3_Missense_Mutation_p.T1442I	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	1437	35 X 9 AA approximate tandem repeats of [TNP]-L-S-P-D-L-S-Q-T.|B.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)	p.T1437I(1)		NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	TGGAGAGAGAGTCACCTGGCT	0.512																																					p.T1437I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4310T	1						.						70.0	74.0	72.0					1																	169510018		2203	4300	6503	167776642	SO:0001583	missense	2153	exon13			M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.4310C>T	1.37:g.169510018G>A	ENSP00000356771:p.Thr1437Ile		167776642	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	.	.	.	.	.	.	.	.	.	.	g	16.95	3.263636	0.59431	.	.	ENSG00000198734	ENST00000367797;ENST00000367796	T;T	0.38401	1.14;1.14	5.32	2.68	0.31781	.	0.636106	0.16642	N	0.205619	T	0.18383	0.0441	L	0.59436	1.845	0.25629	N	0.986321	P	0.38922	0.651	B	0.38428	0.273	T	0.12760	-1.0535	9	0.66056	D	0.02	-7.4852	5.5902	0.17297	0.0978:0.0:0.5397:0.3625	.	1437	P12259	FA5_HUMAN	I	1437;1442	ENSP00000356771:T1437I;ENSP00000356770:T1442I	ENSP00000356770:T1442I	T	-	2	0	F5	167776642	0.000000	0.05858	0.643000	0.29450	0.089000	0.18198	0.297000	0.19101	2.484000	0.83849	0.591000	0.81541	ACT		0.512	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
MYOC	4653	broad.mit.edu	37	1	171605667	171605667	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:171605667T>C	ENST00000037502.6	-	3	984	c.913A>G	c.(913-915)Agc>Ggc	p.S305G		NM_000261.1	NP_000252.1	Q99972	MYOC_HUMAN	myocilin, trabecular meshwork inducible glucocorticoid response	305	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				bone development (GO:0060348)|clustering of voltage-gated sodium channels (GO:0045162)|ERBB2-ERBB3 signaling pathway (GO:0038133)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neuron projection development (GO:0031175)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|osteoblast differentiation (GO:0001649)|positive regulation of cell migration (GO:0030335)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of MAPK cascade (GO:0043408)|skeletal muscle hypertrophy (GO:0014734)	cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|node of Ranvier (GO:0033268)|proteinaceous extracellular matrix (GO:0005578)	fibronectin binding (GO:0001968)|frizzled binding (GO:0005109)|myosin light chain binding (GO:0032027)	p.S305G(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|prostate(1)|urinary_tract(2)	28	all_cancers(6;5.47e-10)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					ATAAACTGGCTGATGAGGTCA	0.567																																					p.S305G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A913G	1						.						84.0	73.0	77.0					1																	171605667		2203	4300	6503	169872290	SO:0001583	missense	4653	exon3			BC029261	CCDS1297.1	1q23-q24	2008-02-05			ENSG00000034971	ENSG00000034971			7610	protein-coding gene	gene with protein product		601652		GLC1A		9169133, 9005853	Standard	NM_000261		Approved	TIGR, JOAG1	uc001ghu.3	Q99972	OTTHUMG00000034789	ENST00000037502.6:c.913A>G	1.37:g.171605667T>C	ENSP00000037502:p.Ser305Gly		169872290	NM_000261	B2RD84|O00620|Q7Z6Q9	Missense_Mutation	SNP	ENST00000037502.6	37	CCDS1297.1	.	.	.	.	.	.	.	.	.	.	T	4.458	0.084863	0.08583	.	.	ENSG00000034971	ENST00000037502;ENST00000357746;ENST00000536591;ENST00000537133	D	0.89196	-2.48	5.76	2.04	0.26737	Olfactomedin-like (3);	0.403084	0.33813	N	0.004521	T	0.67998	0.2953	L	0.34521	1.04	0.30039	N	0.812767	B;B	0.32128	0.202;0.357	B;B	0.37731	0.129;0.257	T	0.57015	-0.7883	10	0.20519	T	0.43	.	5.0265	0.14387	0.0:0.2843:0.1484:0.5673	.	247;305	B4DV44;Q99972	.;MYOC_HUMAN	G	305;258;238;305	ENSP00000037502:S305G	ENSP00000037502:S305G	S	-	1	0	MYOC	169872290	0.073000	0.21202	0.755000	0.31263	0.009000	0.06853	0.551000	0.23361	0.418000	0.25898	-0.451000	0.05528	AGC		0.567	MYOC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084178.2	NM_000261	
METTL13	51603	broad.mit.edu	37	1	171765763	171765763	+	Missense_Mutation	SNP	C	C	T	rs199878964		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:171765763C>T	ENST00000361735.3	+	8	2233	c.1967C>T	c.(1966-1968)cCt>cTt	p.P656L	METTL13_ENST00000466643.1_3'UTR|METTL13_ENST00000367737.5_Missense_Mutation_p.P500L|METTL13_ENST00000362019.3_Missense_Mutation_p.P570L|METTL13_ENST00000458517.1_Missense_Mutation_p.P655L	NM_015935.4	NP_057019.3	Q8N6R0	MET13_HUMAN	methyltransferase like 13	656							methyltransferase activity (GO:0008168)	p.P656L(1)		breast(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(8)|lung(17)|stomach(3)	41						CAGCTGCACCCTGAGCAAAAA	0.552																																					p.P570L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1709T	1						.						117.0	110.0	113.0					1																	171765763		2203	4300	6503	170032386	SO:0001583	missense	51603	exon8			AF132936	CCDS1299.1, CCDS1300.1, CCDS30936.1	1q24-q25.3	2009-02-23	2009-02-23	2009-02-23	ENSG00000010165	ENSG00000010165			24248	protein-coding gene	gene with protein product			"""KIAA0859"""	KIAA0859		10810093, 10048485	Standard	NM_001007239		Approved	CGI-01	uc001ghz.3	Q8N6R0	OTTHUMG00000034912	ENST00000361735.3:c.1967C>T	1.37:g.171765763C>T	ENSP00000354920:p.Pro656Leu		170032386	NM_014955	A6NFK0|A8K6S5|O94940|Q53EZ6|Q5TGP9|Q5TGQ0|Q8N2P8|Q96J11|Q96SQ0|Q9Y2Z1|Q9Y3M6	Missense_Mutation	SNP	ENST00000361735.3	37	CCDS1299.1	.	.	.	.	.	.	.	.	.	.	C	15.82	2.946717	0.53186	.	.	ENSG00000010165	ENST00000458517;ENST00000362019;ENST00000367737;ENST00000361735;ENST00000367736;ENST00000341850	T;T;T;T;T	0.79247	-1.25;-1.25;-1.25;-1.25;-1.25	5.79	5.79	0.91817	.	0.459579	0.26742	N	0.022725	T	0.66548	0.2800	L	0.36672	1.1	0.28180	N	0.928192	B;P;B	0.38767	0.008;0.646;0.0	B;B;B	0.41571	0.011;0.36;0.005	T	0.68800	-0.5313	10	0.72032	D	0.01	-0.688	19.635	0.95728	0.0:1.0:0.0:0.0	.	655;500;656	B4E2X3;Q8N6R0-1;Q8N6R0	.;.;MTL13_HUMAN	L	655;570;500;656;356;353	ENSP00000401955:P655L;ENSP00000355393:P570L;ENSP00000356711:P500L;ENSP00000354920:P656L;ENSP00000356710:P356L	ENSP00000341732:P353L	P	+	2	0	METTL13	170032386	0.034000	0.19679	0.412000	0.26496	0.966000	0.64601	3.279000	0.51670	2.733000	0.93635	0.655000	0.94253	CCT		0.552	METTL13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084528.5	NM_014955	
TNN	63923	broad.mit.edu	37	1	175067535	175067535	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:175067535C>A	ENST00000239462.4	+	9	2036	c.1923C>A	c.(1921-1923)gaC>gaA	p.D641E		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	641	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)		p.D641E(1)		NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		TCTCCTGGGACCCGGTGCAGG	0.567																																					p.D641E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1923A	1						.						68.0	75.0	73.0					1																	175067535		2203	4300	6503	173334158	SO:0001583	missense	63923	exon9			AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.1923C>A	1.37:g.175067535C>A	ENSP00000239462:p.Asp641Glu		173334158	NM_022093	B9EGP3|Q5R360	Missense_Mutation	SNP	ENST00000239462.4	37	CCDS30943.1	.	.	.	.	.	.	.	.	.	.	C	12.46	1.944252	0.34283	.	.	ENSG00000120332	ENST00000239462	T	0.55413	0.52	5.14	0.76	0.18442	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.247775	0.46442	N	0.000286	T	0.54447	0.1859	M	0.64676	1.99	0.23758	N	0.996926	B;P	0.43024	0.033;0.798	B;P	0.54270	0.158;0.747	T	0.51340	-0.8718	10	0.02654	T	1	.	10.7869	0.46411	0.0:0.3981:0.5272:0.0748	.	641;641	B3KXB6;Q9UQP3	.;TENN_HUMAN	E	641	ENSP00000239462:D641E	ENSP00000239462:D641E	D	+	3	2	TNN	173334158	0.001000	0.12720	0.970000	0.41538	0.469000	0.32828	-0.163000	0.09997	-0.038000	0.13624	0.460000	0.39030	GAC		0.567	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527	
RFWD2	64326	broad.mit.edu	37	1	176012866	176012866	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:176012866G>A	ENST00000367669.3	-	13	2024	c.1510C>T	c.(1510-1512)Cag>Tag	p.Q504*	RFWD2_ENST00000308769.8_Nonsense_Mutation_p.Q480*	NM_022457.5	NP_071902.2	Q8NHY2	RFWD2_HUMAN	ring finger and WD repeat domain 2, E3 ubiquitin protein ligase	504					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin protein ligase activity (GO:0061630)|zinc ion binding (GO:0008270)	p.Q504*(1)		endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						TTTGACCTCTGTCCTGTGAAT	0.348																																					p.Q504X	Ovarian(134;1413 1765 5706 35534 51541)											.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1510T	1						.						188.0	191.0	190.0					1																	176012866		2203	4300	6503	174279489	SO:0001587	stop_gained	64326	exon13			AK001278	CCDS30944.1, CCDS44279.1	1q25.1-q25.2	2013-01-09	2012-02-23		ENSG00000143207	ENSG00000143207		"""WD repeat domain containing"", ""RING-type (C3HC4) zinc fingers"""	17440	protein-coding gene	gene with protein product		608067	"""ring finger and WD repeat domain 2"""			10395541	Standard	XM_005245447		Approved	FLJ10416, COP1, RNF200	uc001gku.1	Q8NHY2	OTTHUMG00000034986	ENST00000367669.3:c.1510C>T	1.37:g.176012866G>A	ENSP00000356641:p.Gln504*		174279489	NM_022457	E9PKI0|Q504W6|Q6H103|Q9H6L7|X5D9B4	Nonsense_Mutation	SNP	ENST00000367669.3	37	CCDS30944.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.795234	0.90453	.	.	ENSG00000143207	ENST00000367665;ENST00000367669;ENST00000367666;ENST00000308769	.	.	.	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	-0.2584	19.5392	0.95267	0.0:0.0:1.0:0.0	.	.	.	.	X	279;504;339;480	.	ENSP00000310943:Q480X	Q	-	1	0	RFWD2	174279489	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	9.419000	0.97397	2.718000	0.92993	0.563000	0.77884	CAG		0.348	RFWD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084672.2	NM_022457	
BRINP2	57795	broad.mit.edu	37	1	177250436	177250436	+	Silent	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:177250436T>C	ENST00000361539.4	+	8	2436	c.2124T>C	c.(2122-2124)taT>taC	p.Y708Y	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	708					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	extracellular region (GO:0005576)		p.Y708Y(1)									ACTACCCATATACTCAAGGTT	0.502																																					p.Y708Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T2124C	1						.						109.0	111.0	110.0					1																	177250436		2203	4300	6503	175517059	SO:0001819	synonymous_variant	57795	exon8				CCDS1320.1	1q24	2013-08-06	2013-08-06	2013-07-31	ENSG00000198797	ENSG00000198797			13746	protein-coding gene	gene with protein product			"""family with sequence similarity 5, member B"""	FAM5B		15193423	Standard	NM_021165		Approved	DBCCR1L2	uc001glf.3	Q9C0B6	OTTHUMG00000034953	ENST00000361539.4:c.2124T>C	1.37:g.177250436T>C			175517059	NM_021165	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Silent	SNP	ENST00000361539.4	37	CCDS1320.1																																																																																				0.502	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165	
PQLC2	54896	broad.mit.edu	37	1	19644277	19644277	+	Missense_Mutation	SNP	G	G	A	rs546350739		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:19644277G>A	ENST00000375153.3	+	2	746	c.106G>A	c.(106-108)Gag>Aag	p.E36K	RN7SL85P_ENST00000583604.1_RNA|PQLC2_ENST00000400548.2_Intron|PQLC2_ENST00000375155.3_Missense_Mutation_p.E36K	NM_001040125.1	NP_001035214.1	Q6ZP29	LAAT1_HUMAN	PQ loop repeat containing 2	36	PQ-loop 1.				amino acid homeostasis (GO:0080144)|arginine transport (GO:0015809)|lysine transport (GO:0015819)	integral component of organelle membrane (GO:0031301)|lysosomal membrane (GO:0005765)	arginine transmembrane transporter activity (GO:0015181)|basic amino acid transmembrane transporter activity (GO:0015174)|L-lysine transmembrane transporter activity (GO:0015189)	p.E36K(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(1)	10		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;1.89e-05)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.00124)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		CGGCTGGGACGAGGCCAGCGT	0.607																																					p.E36K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G106A	1						.						288.0	282.0	284.0					1																	19644277		2203	4300	6503	19516864	SO:0001583	missense	54896	exon3			BC015324	CCDS195.2, CCDS30618.1	1p36.13	2013-10-11			ENSG00000040487	ENSG00000040487			26001	protein-coding gene	gene with protein product		614760				23169667	Standard	XM_005245915		Approved	FLJ20320	uc001bby.3	Q6ZP29	OTTHUMG00000002521	ENST00000375153.3:c.106G>A	1.37:g.19644277G>A	ENSP00000364295:p.Glu36Lys		19516864	NM_017765	B3KWQ5|Q6ZMJ3|Q6ZP27|Q9NXC7	Missense_Mutation	SNP	ENST00000375153.3	37	CCDS195.2	.	.	.	.	.	.	.	.	.	.	G	12.98	2.099473	0.37048	.	.	ENSG00000040487	ENST00000375155;ENST00000375153	T;T	0.42513	0.97;0.97	5.5	0.347	0.16022	.	0.374216	0.28371	N	0.015587	T	0.24160	0.0585	L	0.38692	1.165	0.23406	N	0.997742	B	0.09022	0.002	B	0.06405	0.002	T	0.07328	-1.0778	10	0.22706	T	0.39	-21.9005	3.3615	0.07188	0.2041:0.1281:0.537:0.1307	.	36	Q6ZP29	PQLC2_HUMAN	K	36	ENSP00000364297:E36K;ENSP00000364295:E36K	ENSP00000364295:E36K	E	+	1	0	PQLC2	19516864	0.000000	0.05858	0.909000	0.35828	0.898000	0.52572	-0.144000	0.10280	0.586000	0.29626	0.478000	0.44815	GAG		0.607	PQLC2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007255.1	NM_017765	
FAM163A	148753	broad.mit.edu	37	1	179782924	179782924	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:179782924G>A	ENST00000341785.4	+	5	500	c.104G>A	c.(103-105)tGc>tAc	p.C35Y	RP11-12M5.3_ENST00000415218.1_RNA|RP11-12M5.3_ENST00000453051.1_RNA	NM_173509.2	NP_775780.1	Q96GL9	F163A_HUMAN	family with sequence similarity 163, member A	35						integral component of membrane (GO:0016021)		p.C35Y(1)		endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(1)	15						TATTACTGCTGCAAGAAGAGC	0.627																																					p.C35Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G104A	1						.						39.0	37.0	37.0					1																	179782924		2203	4300	6503	178049547	SO:0001583	missense	148753	exon5			BC009382	CCDS1333.1	1q25.2	2008-06-05	2008-06-05	2008-06-05	ENSG00000143340	ENSG00000143340			28274	protein-coding gene	gene with protein product		611727	"""chromosome 1 open reading frame 76"""	C1orf76		12477932	Standard	NM_173509		Approved	MGC16664	uc001gnj.3	Q96GL9	OTTHUMG00000035262	ENST00000341785.4:c.104G>A	1.37:g.179782924G>A	ENSP00000354891:p.Cys35Tyr		178049547	NM_173509	A8K8R7	Missense_Mutation	SNP	ENST00000341785.4	37	CCDS1333.1	.	.	.	.	.	.	.	.	.	.	G	19.38	3.815586	0.70912	.	.	ENSG00000143340	ENST00000341785	.	.	.	4.63	4.63	0.57726	.	0.000000	0.85682	D	0.000000	T	0.78027	0.4219	M	0.68593	2.085	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.81200	-0.1041	9	0.87932	D	0	-18.1671	17.4521	0.87595	0.0:0.0:1.0:0.0	.	35	Q96GL9	F163A_HUMAN	Y	35	.	ENSP00000354891:C35Y	C	+	2	0	FAM163A	178049547	1.000000	0.71417	1.000000	0.80357	0.634000	0.38068	8.869000	0.92326	2.293000	0.77203	0.462000	0.41574	TGC		0.627	FAM163A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085300.1	NM_173509	
PTPRC	5788	broad.mit.edu	37	1	198697577	198697577	+	Splice_Site	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:198697577G>A	ENST00000367376.2	+	16	1994	c.1823G>A	c.(1822-1824)tGc>tAc	p.C608Y	PTPRC_ENST00000352140.3_Splice_Site_p.C560Y|PTPRC_ENST00000348564.6_Splice_Site_p.C449Y|PTPRC_ENST00000442510.2_Splice_Site_p.C610Y|PTPRC_ENST00000594404.1_Splice_Site_p.C447Y	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	608					axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.C608Y(1)		breast(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(22)|lung(41)|ovary(4)|pancreas(2)|prostate(1)|skin(13)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	111						AAAAGATCCTGGTAAGAGTTG	0.328																																					p.C447Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1340A	1						.						66.0	70.0	69.0					1																	198697577		2203	4295	6498	196964200	SO:0001630	splice_region_variant	5788	exon13			Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237		"""CD molecules"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9666	protein-coding gene	gene with protein product		151460		CD45		2169617	Standard	NM_001267798		Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000367376.2:c.1823+1G>A	1.37:g.198697577G>A			196964200	NM_080921	A8K7W6|Q16614|Q9H0Y6	Missense_Mutation	SNP	ENST00000367376.2	37		.	.	.	.	.	.	.	.	.	.	G	14.43	2.532285	0.45073	.	.	ENSG00000081237	ENST00000367376;ENST00000367366;ENST00000352140;ENST00000535566;ENST00000530727;ENST00000442510;ENST00000367367;ENST00000348564	T	0.02525	4.26	5.47	5.47	0.80525	.	0.339310	0.25442	N	0.030648	T	0.02418	0.0074	N	0.08118	0	0.42923	D	0.994299	P;P;B;B;B	0.36249	0.461;0.545;0.175;0.175;0.175	B;B;B;B;B	0.33960	0.092;0.173;0.087;0.087;0.087	T	0.63296	-0.6669	10	0.62326	D	0.03	.	17.5151	0.87771	0.0:0.0:1.0:0.0	.	544;544;449;560;608	F5GXZ3;B4DSZ5;B1ALS3;E9PC28;P08575	.;.;.;.;PTPRC_HUMAN	Y	610;544;560;560;494;608;542;447	ENSP00000193532:C560Y	ENSP00000306782:C447Y	C	+	2	0	PTPRC	196964200	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.865000	0.69583	2.547000	0.85894	0.603000	0.83216	TGC		0.328	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding			Missense_Mutation
CAMSAP2	23271	broad.mit.edu	37	1	200816394	200816394	+	Missense_Mutation	SNP	G	G	A	rs373510531		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:200816394G>A	ENST00000236925.4	+	10	1248	c.1199G>A	c.(1198-1200)cGt>cAt	p.R400H	CAMSAP2_ENST00000358823.2_Missense_Mutation_p.R389H|CAMSAP2_ENST00000413307.2_Missense_Mutation_p.R373H			Q08AD1	CAMP2_HUMAN	calmodulin regulated spectrin-associated protein family, member 2	400					microtubule cytoskeleton organization (GO:0000226)|regulation of organelle organization (GO:0033043)	cytoplasm (GO:0005737)|microtubule minus-end (GO:0036449)	microtubule minus-end binding (GO:0051011)	p.R389H(1)									AGGTATTCACGTCCCCAGGCT	0.348													G|||	1	0.000199681	0.0	0.0	5008	,	,		16230	0.0		0.001	False		,,,				2504	0.0				p.R389H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1166A	1						.	G	HIS/ARG	0,4406		0,0,2203	108.0	103.0	105.0		1166	-1.1	0.0	1		105	1,8599	1.2+/-3.3	0,1,4299	no	missense	CAMSAP2	NM_203459.1	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	389/1479	200816394	1,13005	2203	4300	6503	199083017	SO:0001583	missense	23271	exon9			AB029001	CCDS1404.1, CCDS72998.1, CCDS72999.1	1q32	2011-08-18	2011-08-18	2011-08-18	ENSG00000118200	ENSG00000118200			29188	protein-coding gene	gene with protein product		613775	"""calmodulin regulated spectrin-associated protein 1-like 1"""	CAMSAP1L1		15897902, 19508979	Standard	XM_005245040		Approved	KIAA1078	uc001gvk.3	Q08AD1	OTTHUMG00000035740	ENST00000236925.4:c.1199G>A	1.37:g.200816394G>A	ENSP00000236925:p.Arg400His		199083017	NM_203459	B1APG6|Q08AD2|Q6PGN8|Q96FB3|Q9UG20|Q9UPS4	Missense_Mutation	SNP	ENST00000236925.4	37		.	.	.	.	.	.	.	.	.	.	G	12.09	1.834182	0.32421	0.0	1.16E-4	ENSG00000118200	ENST00000358823;ENST00000413307;ENST00000236925	T;T;T	0.15256	2.46;2.44;2.46	5.2	-1.15	0.09709	.	1.016080	0.07830	N	0.961142	T	0.07863	0.0197	N	0.19112	0.55	0.09310	N	1	P;P;P	0.48350	0.608;0.909;0.872	B;B;B	0.35353	0.102;0.151;0.201	T	0.32428	-0.9907	10	0.13108	T	0.6	-2.8047	8.6131	0.33815	0.5261:0.0:0.4739:0.0	.	373;400;389	Q08AD1-2;Q08AD1;Q08AD1-3	.;CAMP2_HUMAN;.	H	389;373;400	ENSP00000351684:R389H;ENSP00000416800:R373H;ENSP00000236925:R400H	ENSP00000236925:R400H	R	+	2	0	CAMSAP1L1	199083017	0.000000	0.05858	0.036000	0.18154	0.953000	0.61014	0.150000	0.16263	-0.022000	0.13986	-0.251000	0.11542	CGT		0.348	CAMSAP2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086956.2	NM_203459	
CACNA1S	779	broad.mit.edu	37	1	201061232	201061232	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:201061232C>T	ENST00000362061.3	-	4	635	c.409G>A	c.(409-411)Gtg>Atg	p.V137M	CACNA1S_ENST00000367338.3_Missense_Mutation_p.V137M	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	137					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.V137M(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TCCAGAATCACGGTGAAGACC	0.572																																					p.V137M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G409A	1						.						82.0	80.0	81.0					1																	201061232		2203	4300	6503	199327855	SO:0001583	missense	779	exon4			L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.409G>A	1.37:g.201061232C>T	ENSP00000355192:p.Val137Met		199327855	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	37	CCDS1407.1	.	.	.	.	.	.	.	.	.	.	C	12.32	1.901774	0.33535	.	.	ENSG00000081248	ENST00000362061;ENST00000367338	D;D	0.98617	-5.03;-5.03	4.48	4.48	0.54585	Ion transport (1);	0.261523	0.31167	U	0.008121	D	0.96331	0.8803	L	0.31065	0.9	0.34374	D	0.692331	B	0.21309	0.054	B	0.20767	0.031	D	0.97564	1.0100	10	0.45353	T	0.12	.	16.2806	0.82678	0.0:1.0:0.0:0.0	.	137	Q13698	CAC1S_HUMAN	M	137	ENSP00000355192:V137M;ENSP00000356307:V137M	ENSP00000355192:V137M	V	-	1	0	CACNA1S	199327855	0.000000	0.05858	0.927000	0.36925	0.938000	0.57974	0.165000	0.16564	2.198000	0.70561	0.655000	0.94253	GTG		0.572	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069	
ARL8A	127829	broad.mit.edu	37	1	202107528	202107528	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:202107528G>A	ENST00000272217.2	-	2	340	c.172C>T	c.(172-174)Cgc>Tgc	p.R58C	ARL8A_ENST00000486225.1_5'Flank	NM_001256129.1|NM_138795.3	NP_001243058.1|NP_620150.1	Q96BM9	ARL8A_HUMAN	ADP-ribosylation factor-like 8A	58					chromosome segregation (GO:0007059)|GTP catabolic process (GO:0006184)|mitotic nuclear division (GO:0007067)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|midbody (GO:0030496)|spindle midzone (GO:0051233)	alpha-tubulin binding (GO:0043014)|beta-tubulin binding (GO:0048487)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.R58C(1)		large_intestine(1)|lung(2)|ovary(2)|skin(1)	6						GTGATTTTGCGCATGTTGAAA	0.502																																					p.R58C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C172T	1						.						191.0	156.0	168.0					1																	202107528		2203	4300	6503	200374151	SO:0001583	missense	127829	exon2			BC015408	CCDS1421.1, CCDS73004.1	1q32.1	2014-05-09	2005-11-03	2005-11-03	ENSG00000143862	ENSG00000143862		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	25192	protein-coding gene	gene with protein product			"""ADP-ribosylation factor-like 10B"""	ARL10B		8889548	Standard	NM_001256129		Approved	FLJ45195, Gie2	uc001gxk.2	Q96BM9	OTTHUMG00000035923	ENST00000272217.2:c.172C>T	1.37:g.202107528G>A	ENSP00000272217:p.Arg58Cys		200374151	NM_138795	B3KXD0	Missense_Mutation	SNP	ENST00000272217.2	37	CCDS1421.1	.	.	.	.	.	.	.	.	.	.	G	18.44	3.624168	0.66901	.	.	ENSG00000143862	ENST00000272217	T	0.64085	-0.08	4.8	3.87	0.44632	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.79233	0.4411	M	0.84156	2.68	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.81797	-0.0768	10	0.87932	D	0	0.0206	12.5379	0.56152	0.0:0.0:0.6326:0.3674	.	58	Q96BM9	ARL8A_HUMAN	C	58	ENSP00000272217:R58C	ENSP00000272217:R58C	R	-	1	0	ARL8A	200374151	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.496000	0.45346	0.980000	0.38523	0.591000	0.81541	CGC		0.502	ARL8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087493.1	NM_138795	
KDM5B	10765	broad.mit.edu	37	1	202702680	202702680	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:202702680C>T	ENST00000367265.3	-	23	4922	c.3758G>A	c.(3757-3759)cGa>cAa	p.R1253Q	KDM5B_ENST00000367264.2_Missense_Mutation_p.R1289Q	NM_006618.3	NP_006609.3	Q9UGL1	KDM5B_HUMAN	lysine (K)-specific demethylase 5B	1253					histone H3-K4 demethylation (GO:0034720)|histone H3-K4 demethylation, trimethyl-H3-K4-specific (GO:0034721)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-trimethyl-K4 specific) (GO:0034647)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.R1253Q(1)		breast(2)|ovary(2)|skin(1)|urinary_tract(1)	6						AATCATATATCGAAGTGCATC	0.507																																					p.R1253Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3758A	1						.						98.0	97.0	97.0					1																	202702680		2203	4300	6503	200969303	SO:0001583	missense	10765	exon23			AJ243706	CCDS30974.1	1q32.1	2014-06-12	2009-04-06	2009-04-06	ENSG00000117139	ENSG00000117139		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	18039	protein-coding gene	gene with protein product	"""cancer/testis antigen 31"", ""protein phosphatase 1, regulatory subunit 98"""	605393	"""Jumonji, AT rich interactive domain 1B (RBP2-like)"", ""jumonji, AT rich interactive domain 1B"""	JARID1B		11483573, 11478881	Standard	NM_006618		Approved	RBBP2H1A, PLU-1, CT31, PPP1R98	uc001gyf.3	Q9UGL1	OTTHUMG00000041401	ENST00000367265.3:c.3758G>A	1.37:g.202702680C>T	ENSP00000356234:p.Arg1253Gln		200969303	NM_006618	O95811|Q15752|Q9Y3Q5	Missense_Mutation	SNP	ENST00000367265.3	37	CCDS30974.1	.	.	.	.	.	.	.	.	.	.	C	14.21	2.467295	0.43839	.	.	ENSG00000117139	ENST00000367265;ENST00000538292;ENST00000367264;ENST00000235790	T;T;T	0.00864	5.6;5.6;5.6	6.09	6.09	0.99107	.	0.267618	0.39341	N	0.001400	T	0.01905	0.0060	N	0.16743	0.435	0.54753	D	0.999989	D;B	0.89917	1.0;0.111	P;B	0.62885	0.908;0.02	T	0.66520	-0.5903	10	0.02654	T	1	-16.4572	20.6935	0.99705	0.0:1.0:0.0:0.0	.	1289;1253	Q9UGL1-2;Q9UGL1	.;KDM5B_HUMAN	Q	1253;1095;1289;1095	ENSP00000356234:R1253Q;ENSP00000356233:R1289Q;ENSP00000235790:R1095Q	ENSP00000235790:R1095Q	R	-	2	0	KDM5B	200969303	1.000000	0.71417	0.969000	0.41365	0.999000	0.98932	4.515000	0.60489	2.897000	0.99335	0.643000	0.83706	CGA		0.507	KDM5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099184.2	NM_006618	
PPFIA4	8497	broad.mit.edu	37	1	203029509	203029509	+	Silent	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:203029509A>G	ENST00000447715.2	+	27	3123	c.2682A>G	c.(2680-2682)tcA>tcG	p.S894S	PPFIA4_ENST00000272198.6_Silent_p.S410S|PPFIA4_ENST00000367240.2_Silent_p.S895S|PPFIA4_ENST00000599966.1_Silent_p.S410S|PPFIA4_ENST00000414050.2_Silent_p.S623S|PPFIA4_ENST00000295706.4_Silent_p.S410S			O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4	894	SAM 1. {ECO:0000255|PROSITE- ProRule:PRU00184}.				cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)		p.S1049S(1)		NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(20)|ovary(4)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	50						AGATGGTGTCATTGACCAGCC	0.592																																					p.S410S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1230G	1						.						71.0	81.0	78.0					1																	203029509		2203	4300	6503	201296132	SO:0001819	synonymous_variant	8497	exon9			AF034801	CCDS44296.1	1q32.1	2013-01-10			ENSG00000143847	ENSG00000143847		"""Sterile alpha motif (SAM) domain containing"""	9248	protein-coding gene	gene with protein product	"""Liprin-alpha4"""	603145				9624153	Standard	XM_005245553		Approved		uc009xaj.3	O75335	OTTHUMG00000042123	ENST00000447715.2:c.2682A>G	1.37:g.203029509A>G			201296132	NM_015053	A2RUJ5|B1APN8|B1N949|B7ZM43|O94971	Silent	SNP	ENST00000447715.2	37																																																																																					0.592	PPFIA4-005	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000462949.1	NM_015053	
CHI3L1	1116	broad.mit.edu	37	1	203149763	203149763	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:203149763G>A	ENST00000255409.3	-	8	854	c.729C>T	c.(727-729)taC>taT	p.Y243Y		NM_001276.2	NP_001267.2	P36222	CH3L1_HUMAN	chitinase 3-like 1 (cartilage glycoprotein-39)	243					activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cellular response to tumor necrosis factor (GO:0071356)|chitin catabolic process (GO:0006032)|inflammatory response (GO:0006954)|interleukin-8 secretion (GO:0072606)|lung development (GO:0030324)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase B signaling (GO:0051897)|response to interleukin-1 (GO:0070555)|response to interleukin-6 (GO:0070741)|response to mechanical stimulus (GO:0009612)|response to tumor necrosis factor (GO:0034612)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|extracellular matrix structural constituent (GO:0005201)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)	p.Y243Y(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|skin(1)	18						GCCTCAACATGTACCCCACAG	0.572																																					p.Y243Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C729T	1						.						22.0	22.0	22.0					1																	203149763		2203	4300	6503	201416386	SO:0001819	synonymous_variant	1116	exon8			BC008568	CCDS1435.1	1q32.1	2008-02-05			ENSG00000133048	ENSG00000133048			1932	protein-coding gene	gene with protein product		601525				8245017, 9244440	Standard	NM_001276		Approved	GP39, YKL40	uc001gzi.2	P36222	OTTHUMG00000042122	ENST00000255409.3:c.729C>T	1.37:g.203149763G>A			201416386	NM_001276	B2R7B0|P30923|Q8IVA4|Q96HI7	Silent	SNP	ENST00000255409.3	37	CCDS1435.1																																																																																				0.572	CHI3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100265.1	NM_001276	
NUAK2	81788	broad.mit.edu	37	1	205272760	205272760	+	Missense_Mutation	SNP	G	G	A	rs561905076		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:205272760G>A	ENST00000367157.3	-	7	1831	c.1705C>T	c.(1705-1707)Cgg>Tgg	p.R569W		NM_030952.1	NP_112214.1			NUAK family, SNF1-like kinase, 2									p.R569W(1)		breast(3)|kidney(3)|large_intestine(4)|lung(4)|ovary(3)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23	Breast(84;0.186)		BRCA - Breast invasive adenocarcinoma(75;0.117)			ACACAGCCCCGCAGTGGGGGC	0.667													G|||	1	0.000199681	0.0	0.0	5008	,	,		16143	0.001		0.0	False		,,,				2504	0.0				p.R569W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1705T	1						.						26.0	32.0	30.0					1																	205272760		2200	4293	6493	203539383	SO:0001583	missense	81788	exon7			AK074830	CCDS1453.1	1q32.1	2008-02-05			ENSG00000163545	ENSG00000163545			29558	protein-coding gene	gene with protein product	"""SNF1/AMP activated protein kinase"""	608131				11230166	Standard	NM_030952		Approved	SNARK, FLJ90349	uc001hce.3	Q9H093	OTTHUMG00000037196	ENST00000367157.3:c.1705C>T	1.37:g.205272760G>A	ENSP00000356125:p.Arg569Trp		203539383	NM_030952		Missense_Mutation	SNP	ENST00000367157.3	37	CCDS1453.1	.	.	.	.	.	.	.	.	.	.	G	17.11	3.304897	0.60305	.	.	ENSG00000163545	ENST00000367157	D	0.85773	-2.03	4.82	1.6	0.23607	.	0.000000	0.40908	D	0.000994	D	0.90549	0.7038	M	0.72894	2.215	0.50813	D	0.999891	D	0.89917	1.0	D	0.91635	0.999	D	0.89683	0.3892	10	0.87932	D	0	.	12.9973	0.58654	0.0:0.0:0.5903:0.4097	.	569	Q9H093	NUAK2_HUMAN	W	569	ENSP00000356125:R569W	ENSP00000356125:R569W	R	-	1	2	NUAK2	203539383	1.000000	0.71417	0.908000	0.35775	0.880000	0.50808	2.097000	0.41748	0.032000	0.15435	0.393000	0.25936	CGG		0.667	NUAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090390.1	NM_030952	
RAB29	8934	broad.mit.edu	37	1	205740743	205740743	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:205740743G>A	ENST00000367139.3	-	4	538	c.235C>T	c.(235-237)Cgg>Tgg	p.R79W	RAB7L1_ENST00000414729.1_Missense_Mutation_p.R79W|RAB7L1_ENST00000446390.2_Missense_Mutation_p.R55W|RAB7L1_ENST00000468887.1_Intron|RAB7L1_ENST00000437324.2_Missense_Mutation_p.R7W|RAB7L1_ENST00000235932.4_Missense_Mutation_p.R79W	NM_003929.2	NP_003920.1	O14966	RAB7L_HUMAN		79					cell differentiation (GO:0030154)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|positive regulation of intracellular protein transport (GO:0090316)|protein transport (GO:0015031)|retrograde transport, plasma membrane to Golgi (GO:0035526)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|vacuole (GO:0005773)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.R79W(2)		endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|urinary_tract(1)	10	Breast(84;0.0799)		BRCA - Breast invasive adenocarcinoma(75;0.0194)			GAGGCATCCCGATAATACAAT	0.522																																					p.R79W	Pancreas(25;658 872 27763 34889 38531)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C235T	1						.						162.0	144.0	150.0					1																	205740743		2203	4300	6503	204007366	SO:0001583	missense	8934	exon4																														ENST00000367139.3:c.235C>T	1.37:g.205740743G>A	ENSP00000356107:p.Arg79Trp		204007366	NM_001135662	B4E1K3|C9JE77	Missense_Mutation	SNP	ENST00000367139.3	37	CCDS1459.1	.	.	.	.	.	.	.	.	.	.	G	18.40	3.615555	0.66672	.	.	ENSG00000117280	ENST00000367139;ENST00000235932;ENST00000437324;ENST00000446390;ENST00000414729	D;D;T;D;D	0.82526	-1.62;-1.62;-0.71;-1.62;-1.62	5.27	4.33	0.51752	Small GTP-binding protein domain (1);	0.068633	0.56097	D	0.000037	D	0.93242	0.7847	H	0.96518	3.835	0.37089	D	0.899368	D;D	0.89917	0.999;1.0	D;D	0.83275	0.96;0.996	D	0.95394	0.8484	10	0.87932	D	0	-15.5917	11.2968	0.49282	0.0:0.0:0.6007:0.3993	.	55;79	B4E1K3;O14966	.;RAB7L_HUMAN	W	79;79;7;55;79	ENSP00000356107:R79W;ENSP00000235932:R79W;ENSP00000416613:R7W;ENSP00000389899:R55W;ENSP00000402910:R79W	ENSP00000235932:R79W	R	-	1	2	RAB7L1	204007366	1.000000	0.71417	1.000000	0.80357	0.724000	0.41520	2.898000	0.48672	1.146000	0.42352	0.305000	0.20034	CGG		0.522	RAB7L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087732.1		
PM20D1	148811	broad.mit.edu	37	1	205812819	205812819	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:205812819C>T	ENST00000367136.4	-	6	847	c.803G>A	c.(802-804)gGc>gAc	p.G268D	PM20D1_ENST00000460624.1_5'UTR	NM_152491.4	NP_689704.4	Q6GTS8	P20D1_HUMAN	peptidase M20 domain containing 1	268					negative regulation of neuron death (GO:1901215)|regulation of defense response to virus by host (GO:0050691)|regulation of viral process (GO:0050792)	extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|peptidase activity (GO:0008233)	p.G268D(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)	28	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0252)			TGCAAGGATGCCAATGCTTGT	0.512																																					p.G268D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G803A	1						.						99.0	93.0	95.0					1																	205812819		2203	4300	6503	204079442	SO:0001583	missense	148811	exon6				CCDS1460.1	1q32.1	2008-02-05			ENSG00000162877	ENSG00000162877			26518	protein-coding gene	gene with protein product							Standard	NM_152491		Approved	FLJ32569, Cps1	uc001hdj.3	Q6GTS8	OTTHUMG00000035999	ENST00000367136.4:c.803G>A	1.37:g.205812819C>T	ENSP00000356104:p.Gly268Asp		204079442	NM_152491	Q6P4E3|Q96DM4	Missense_Mutation	SNP	ENST00000367136.4	37	CCDS1460.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.959732	0.92791	.	.	ENSG00000162877	ENST00000367136	T	0.57436	0.4	6.06	6.06	0.98353	Peptidase M20, dimerisation (2);	0.000000	0.85682	D	0.000000	T	0.70736	0.3258	M	0.83012	2.62	0.80722	D	1	D	0.55385	0.971	P	0.52672	0.706	T	0.74309	-0.3707	10	0.87932	D	0	.	20.2159	0.98296	0.0:1.0:0.0:0.0	.	268	Q6GTS8	P20D1_HUMAN	D	268	ENSP00000356104:G268D	ENSP00000356104:G268D	G	-	2	0	PM20D1	204079442	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	6.717000	0.74707	2.882000	0.98803	0.655000	0.94253	GGC		0.512	PM20D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087736.1	NM_152491	
DYRK3	8444	broad.mit.edu	37	1	206821802	206821802	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:206821802G>A	ENST00000367109.2	+	3	1427	c.1259G>A	c.(1258-1260)tGc>tAc	p.C420Y	DYRK3_ENST00000367108.3_Missense_Mutation_p.C400Y|DYRK3_ENST00000367106.1_Missense_Mutation_p.C400Y|DYRK3_ENST00000489878.1_Intron	NM_003582.2	NP_003573.2	O43781	DYRK3_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3	420	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				erythrocyte differentiation (GO:0030218)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)	p.C385Y(1)|p.C420Y(1)		central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(9)|lung(8)|skin(1)|stomach(2)	25	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)			CAGTTGGCCTGCATGATGGAG	0.488																																					p.C420Y	Melanoma(164;427 2622 26826 51707)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1259A	1						.						128.0	137.0	134.0					1																	206821802		2203	4300	6503	204888425	SO:0001583	missense	8444	exon3			Y12735	CCDS30999.1, CCDS31000.1	1q32	2008-07-18			ENSG00000143479	ENSG00000143479	2.7.12.1		3094	protein-coding gene	gene with protein product	"""regulatory erythroid kinase"", ""dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 5"", ""protein kinase Dyrk3"""	603497				9748265	Standard	NM_003582		Approved	RED, REDK, hYAK3-2	uc001hej.3	O43781	OTTHUMG00000036339	ENST00000367109.2:c.1259G>A	1.37:g.206821802G>A	ENSP00000356076:p.Cys420Tyr		204888425	NM_003582	D3DT79|Q7Z752|Q9HBY6|Q9HBY7	Missense_Mutation	SNP	ENST00000367109.2	37	CCDS30999.1	.	.	.	.	.	.	.	.	.	.	G	19.01	3.743574	0.69418	.	.	ENSG00000143479	ENST00000367109;ENST00000367108;ENST00000367106	T;T;T	0.64991	-0.13;-0.13;-0.13	5.31	5.31	0.75309	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.69396	0.3106	N	0.25890	0.77	0.80722	D	1	D;D	0.71674	0.996;0.998	D;D	0.70227	0.968;0.928	T	0.71364	-0.4615	10	0.56958	D	0.05	.	18.1352	0.89617	0.0:0.0:1.0:0.0	.	420;400	O43781;O43781-2	DYRK3_HUMAN;.	Y	420;400;400	ENSP00000356076:C420Y;ENSP00000356075:C400Y;ENSP00000356073:C400Y	ENSP00000356073:C400Y	C	+	2	0	DYRK3	204888425	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.657000	0.98554	2.765000	0.95021	0.555000	0.69702	TGC		0.488	DYRK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088458.1	NM_003582	
MAPKAPK2	9261	broad.mit.edu	37	1	206902135	206902135	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:206902135C>T	ENST00000367103.3	+	2	553	c.360C>T	c.(358-360)atC>atT	p.I120I	MAPKAPK2_ENST00000294981.4_Silent_p.I120I	NM_004759.4|NM_032960.3	NP_004750.1|NP_116584.2	P49137	MAPK2_HUMAN	mitogen-activated protein kinase-activated protein kinase 2	120	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|activation of MAPK activity (GO:0000187)|arachidonic acid metabolic process (GO:0019369)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|G2 DNA damage checkpoint (GO:0031572)|gene expression (GO:0010467)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|leukotriene metabolic process (GO:0006691)|macropinocytosis (GO:0044351)|MAPK cascade (GO:0000165)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of interleukin-6 production (GO:0032675)|regulation of tumor necrosis factor production (GO:0032680)|response to cytokine (GO:0034097)|response to lipopolysaccharide (GO:0032496)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)	p.I120I(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	19	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.211)			TCGTACGGATCGTGGATGTGT	0.602																																					p.I120I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C360T	1						.						48.0	54.0	52.0					1																	206902135		2203	4300	6503	204968758	SO:0001819	synonymous_variant	9261	exon2			U12779	CCDS1466.1, CCDS31001.1	1q32	2008-02-05			ENSG00000162889	ENSG00000162889			6887	protein-coding gene	gene with protein product		602006				8179591, 8280084	Standard	NM_004759		Approved		uc001hem.2	P49137	OTTHUMG00000036342	ENST00000367103.3:c.360C>T	1.37:g.206902135C>T			204968758	NM_032960	Q5SY30|Q5SY41|Q8IYD6	Silent	SNP	ENST00000367103.3	37	CCDS31001.1																																																																																				0.602	MAPKAPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088465.1	NM_004759	
DDOST	1650	broad.mit.edu	37	1	20978911	20978911	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:20978911G>A	ENST00000375048.3	-	11	1437	c.1332C>T	c.(1330-1332)atC>atT	p.I444I	DDOST_ENST00000415136.2_Silent_p.I407I|DDOST_ENST00000602624.2_Silent_p.I427I|PINK1-AS_ENST00000451424.1_RNA	NM_005216.4	NP_005207	P39656	OST48_HUMAN	dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit (non-catalytic)	444					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|innate immune response (GO:0045087)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|response to cytokine (GO:0034097)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|T cell activation (GO:0042110)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)|protein complex (GO:0043234)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)	p.I444I(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)|skin(1)	13		all_lung(284;2.98e-05)|Lung NSC(340;3.25e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.17e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000141)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.00046)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GCAAGAAGACGATGCTGAAGA	0.592																																					p.I444I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1332T	1						.						47.0	46.0	46.0					1																	20978911		2203	4300	6503	20851498	SO:0001819	synonymous_variant	1650	exon11			D29643	CCDS212.1	1p36.1	2013-03-06	2013-03-06		ENSG00000244038	ENSG00000244038	2.4.1.119		2728	protein-coding gene	gene with protein product	"""oligosaccharyltransferase subunit 48"""	602202	"""dolichyl-diphosphooligosaccharide-protein glycosyltransferase"", ""dolichyl-diphosphooligosaccharide--protein glycosyltransferase"""			9367678	Standard	NM_005216		Approved	OST, KIAA0115, OST48, WBP1	uc001bdo.1	P39656	OTTHUMG00000002844	ENST00000375048.3:c.1332C>T	1.37:g.20978911G>A			20851498	NM_005216	B2RDQ4|B4DJE3|B4DLI2|O43244|Q5VWA5|Q8NI93|Q9BUI2	Silent	SNP	ENST00000375048.3	37	CCDS212.1																																																																																				0.592	DDOST-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007961.2	NM_005216	
CD55	1604	broad.mit.edu	37	1	207504495	207504495	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:207504495T>A	ENST00000367064.3	+	6	965	c.707T>A	c.(706-708)aTt>aAt	p.I236N	CD55_ENST00000314754.8_Missense_Mutation_p.I236N|CD55_ENST00000465534.1_3'UTR|CD55_ENST00000367063.2_Missense_Mutation_p.I236N|CD55_ENST00000367065.5_Missense_Mutation_p.I236N|CD55_ENST00000367062.4_Missense_Mutation_p.I236N|CD55_ENST00000391921.4_Missense_Mutation_p.I172N|CD55_ENST00000367067.4_3'UTR|CD55_ENST00000391920.4_Missense_Mutation_p.I236N	NM_000574.3	NP_000565.1	P08174	DAF_HUMAN	CD55 molecule, decay accelerating factor for complement (Cromer blood group)	236	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				CD4-positive, alpha-beta T cell cytokine production (GO:0035743)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|maternal process involved in parturition (GO:0060137)|negative regulation of complement activation (GO:0045916)|positive regulation of CD4-positive, alpha-beta T cell activation (GO:2000516)|positive regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000563)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of complement activation (GO:0030449)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|respiratory burst (GO:0045730)|response to peptide hormone (GO:0043434)|response to virus (GO:0009615)|spermatogenesis (GO:0007283)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	enzyme inhibitor activity (GO:0004857)|lipid binding (GO:0008289)|virus receptor activity (GO:0001618)	p.I236N(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	16					Chloramphenicol(DB00446)	AATGGAATAATTCAAGGGGAA	0.313																																					p.I236N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T707A	1						.						127.0	117.0	121.0					1																	207504495		2203	4300	6503	205571118	SO:0001583	missense	1604	exon6			BC001288	CCDS31006.1, CCDS44307.1, CCDS73022.1	1q32	2014-09-17	2006-03-28	2006-02-23	ENSG00000196352	ENSG00000196352		"""CD molecules"", ""Blood group antigens"""	2665	protein-coding gene	gene with protein product		125240	"""decay accelerating factor for complement (CD55, Cromer blood group system)"""	DAF			Standard	XM_005273077		Approved	CR, TC, CROM	uc001hfr.4	P08174	OTTHUMG00000036255	ENST00000367064.3:c.707T>A	1.37:g.207504495T>A	ENSP00000356031:p.Ile236Asn		205571118	NM_000574	B1AP14|D3DT83|D3DT84|E7ER69|P09679|P78361|Q14UF2|Q14UF3|Q14UF4|Q14UF5|Q14UF6	Missense_Mutation	SNP	ENST00000367064.3	37	CCDS31006.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.62|13.62	2.290860|2.290860	0.40494|0.40494	.|.	.|.	ENSG00000196352|ENSG00000196352	ENST00000343420|ENST00000367064;ENST00000367063;ENST00000391921;ENST00000536840;ENST00000314754;ENST00000367065;ENST00000391920;ENST00000367062	.|T;T;T;T;T;T;T	.|0.67523	.|-0.27;-0.27;-0.27;-0.27;-0.27;-0.27;-0.27	5.13|5.13	2.59|2.59	0.31030|0.31030	.|Complement control module (2);Sushi/SCR/CCP (3);	.|0.411675	.|0.24615	.|N	.|0.037008	T|T	0.79335|0.79335	0.4428|0.4428	M|M	0.87900|0.87900	2.915|2.915	0.22989|0.22989	N|N	0.998469|0.998469	.|D;D;D;D;D	.|0.89917	.|0.998;1.0;1.0;1.0;1.0	.|D;D;D;D;D	.|0.91635	.|0.989;0.999;0.995;0.999;0.997	T|T	0.66304|0.66304	-0.5957|-0.5957	5|10	.|0.39692	.|T	.|0.17	.|.	5.4921|5.4921	0.16781|0.16781	0.1737:0.0:0.181:0.6453|0.1737:0.0:0.181:0.6453	.|.	.|172;236;236;236;236	.|B1AP15;Q14UF4;P08174-2;P08174;B1AP13	.|.;.;.;DAF_HUMAN;.	I|N	246|236;236;172;172;236;236;236;236	.|ENSP00000356031:I236N;ENSP00000356030:I236N;ENSP00000375788:I172N;ENSP00000316333:I236N;ENSP00000356032:I236N;ENSP00000375787:I236N;ENSP00000356029:I236N	.|ENSP00000316333:I236N	F|I	+|+	1|2	0|0	CD55|CD55	205571118|205571118	0.264000|0.264000	0.24093|0.24093	0.010000|0.010000	0.14722|0.14722	0.004000|0.004000	0.04260|0.04260	1.695000|1.695000	0.37763|0.37763	0.881000|0.881000	0.35993|0.35993	-0.321000|-0.321000	0.08615|0.08615	TTC|ATT		0.313	CD55-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000088208.2	NM_000574	
RCOR3	55758	broad.mit.edu	37	1	211486788	211486788	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:211486788G>A	ENST00000367005.4	+	11	1307	c.1166G>A	c.(1165-1167)cGg>cAg	p.R389Q	RCOR3_ENST00000526255.1_3'UTR|RCOR3_ENST00000419091.2_Missense_Mutation_p.R447Q|RCOR3_ENST00000367006.4_Silent_p.S366S	NM_018254.3	NP_060724.1	Q9P2K3	RCOR3_HUMAN	REST corepressor 3	389	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.R389Q(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.00961)|all cancers(67;0.0999)|Epithelial(68;0.171)		CAGGCTCCTCGGACACTGGGT	0.502																																					p.R447Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1340A	1						.						108.0	87.0	94.0					1																	211486788		2203	4300	6503	209553411	SO:0001583	missense	55758	exon12			AK001738	CCDS31016.1, CCDS44312.1, CCDS44313.1, CCDS44314.1	1q32.3	2008-02-05			ENSG00000117625	ENSG00000117625			25594	protein-coding gene	gene with protein product						10718198	Standard	NM_018254		Approved	FLJ10876	uc010psw.2	Q9P2K3	OTTHUMG00000036996	ENST00000367005.4:c.1166G>A	1.37:g.211486788G>A	ENSP00000355972:p.Arg389Gln		209553411	NM_001136223	B3KYA2|B4DYY7|Q5VT47|Q7L9I5|Q8N5U3|Q9NV83	Missense_Mutation	SNP	ENST00000367005.4	37	CCDS31016.1	.	.	.	.	.	.	.	.	.	.	G	9.696	1.153253	0.21371	.	.	ENSG00000117625	ENST00000419091;ENST00000367005;ENST00000529763	T;T	0.43688	0.94;0.94	4.87	3.73	0.42828	.	0.652992	0.15024	N	0.284825	T	0.21761	0.0524	.	.	.	0.23933	N	0.996428	B;B	0.12013	0.005;0.0	B;B	0.04013	0.001;0.0	T	0.09818	-1.0657	9	0.18276	T	0.48	-11.2798	4.8674	0.13615	0.174:0.2262:0.5998:0.0	.	447;389	Q9P2K3-3;Q9P2K3	.;RCOR3_HUMAN	Q	447;389;165	ENSP00000413929:R447Q;ENSP00000355972:R389Q	ENSP00000355972:R389Q	R	+	2	0	RCOR3	209553411	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.439000	0.44846	2.251000	0.74343	0.650000	0.86243	CGG		0.502	RCOR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089821.1	NM_018254	
CENPF	1063	broad.mit.edu	37	1	214828673	214828673	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:214828673G>A	ENST00000366955.3	+	17	8580	c.8412G>A	c.(8410-8412)caG>caA	p.Q2804Q		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2900	Sufficient for centromere localization.|Sufficient for self-association.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)	p.Q2804Q(1)		NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		CCTGTAAACAGCTGGAAGAGG	0.403																																					p.Q2804Q	Colon(80;575 1284 11000 14801 43496)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G8412A	1						.						89.0	90.0	90.0					1																	214828673		2203	4300	6503	212895296	SO:0001819	synonymous_variant	1063	exon17			U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"""mitosin"""	600236	"""centromere protein F, 350/400kDa (mitosin)"""			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.8412G>A	1.37:g.214828673G>A			212895296	NM_016343	Q13171|Q13246|Q5VVM7	Silent	SNP	ENST00000366955.3	37	CCDS31023.1																																																																																				0.403	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
USH2A	7399	broad.mit.edu	37	1	216108090	216108090	+	Missense_Mutation	SNP	C	C	T	rs376983577		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:216108090C>T	ENST00000307340.3	-	38	7554	c.7168G>A	c.(7168-7170)Gga>Aga	p.G2390R	USH2A_ENST00000366943.2_Missense_Mutation_p.G2390R	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	2390	Fibronectin type-III 10. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.G2390R(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		GTCTCTTCTCCGCTGTACATG	0.343										HNSCC(13;0.011)			C|||	1	0.000199681	0.0	0.0	5008	,	,		15245	0.0		0.0	False		,,,				2504	0.001				p.G2390R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G7168A	1						.	C	ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	107.0	101.0	103.0		7168	1.8	0.0	1		103	0,8596		0,0,4298	no	missense	USH2A	NM_206933.2	125	0,1,6500	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	2390/5203	216108090	1,13001	2203	4298	6501	214174713	SO:0001583	missense	7399	exon38			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.7168G>A	1.37:g.216108090C>T	ENSP00000305941:p.Gly2390Arg		214174713	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	13.80	2.345769	0.41599	2.27E-4	0.0	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.15372	2.45;2.43	5.57	1.84	0.25277	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.791048	0.10314	N	0.689575	T	0.11324	0.0276	L	0.51422	1.61	0.09310	N	1	P	0.44309	0.832	B	0.34180	0.177	T	0.23619	-1.0183	10	0.16896	T	0.51	.	4.3753	0.11267	0.0:0.2207:0.1626:0.6167	.	2390	O75445	USH2A_HUMAN	R	2390	ENSP00000305941:G2390R;ENSP00000355910:G2390R	ENSP00000305941:G2390R	G	-	1	0	USH2A	214174713	0.042000	0.20092	0.000000	0.03702	0.440000	0.31957	0.850000	0.27737	0.073000	0.16731	-0.345000	0.07892	GGA		0.343	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
HSPG2	3339	broad.mit.edu	37	1	22179420	22179420	+	Missense_Mutation	SNP	G	G	A	rs566319401		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:22179420G>A	ENST00000374695.3	-	51	6662	c.6583C>T	c.(6583-6585)Cgg>Tgg	p.R2195W	HSPG2_ENST00000430507.1_Missense_Mutation_p.R141W	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2195	Ig-like C2-type 7.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)	p.R2195W(1)		breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	ACCTGGTGCCGGGCAGGGAGG	0.692													G|||	1	0.000199681	0.0	0.0	5008	,	,		14016	0.0		0.0	False		,,,				2504	0.001				p.R2195W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C6583T	1						.						29.0	31.0	31.0					1																	22179420		2201	4295	6496	22052007	SO:0001583	missense	3339	exon51			M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.6583C>T	1.37:g.22179420G>A	ENSP00000363827:p.Arg2195Trp		22052007	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	37	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	G	19.88	3.909280	0.72868	.	.	ENSG00000142798	ENST00000374695;ENST00000430507	T;T	0.21734	2.41;1.99	5.97	4.07	0.47477	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.30227	N	0.010105	T	0.55465	0.1922	H	0.94698	3.57	0.31762	N	0.633267	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.981	T	0.70178	-0.4943	10	0.59425	D	0.04	.	11.3768	0.49733	0.0:0.1371:0.7203:0.1426	.	135;2195	Q59EG0;P98160	.;PGBM_HUMAN	W	2195;141	ENSP00000363827:R2195W;ENSP00000416385:R141W	ENSP00000363827:R2195W	R	-	1	2	HSPG2	22052007	0.000000	0.05858	0.984000	0.44739	0.738000	0.42128	0.144000	0.16135	0.829000	0.34733	0.655000	0.94253	CGG		0.692	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
HSPG2	3339	broad.mit.edu	37	1	22202846	22202846	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:22202846C>T	ENST00000374695.3	-	23	2958	c.2879G>A	c.(2878-2880)aGc>aAc	p.S960N		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	960	Laminin IV type A 2. {ECO:0000255|PROSITE-ProRule:PRU00458}.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)	p.S960N(1)		breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GGTGTGGGTGCTTGCGGCGTT	0.632																																					p.S960N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2879A	1						.						59.0	53.0	55.0					1																	22202846		2203	4300	6503	22075433	SO:0001583	missense	3339	exon23			M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.2879G>A	1.37:g.22202846C>T	ENSP00000363827:p.Ser960Asn		22075433	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	37	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	C	0.038	-1.298973	0.01364	.	.	ENSG00000142798	ENST00000374695	T	0.75154	-0.91	4.92	3.05	0.35203	Laminin B type IV (1);	0.185564	0.26166	N	0.025949	T	0.45337	0.1337	N	0.03115	-0.41	0.23802	N	0.996808	B	0.02656	0.0	B	0.01281	0.0	T	0.27054	-1.0085	10	0.07813	T	0.8	.	9.2828	0.37737	0.0:0.8221:0.0:0.1779	.	960	P98160	PGBM_HUMAN	N	960	ENSP00000363827:S960N	ENSP00000363827:S960N	S	-	2	0	HSPG2	22075433	0.991000	0.36638	0.695000	0.30226	0.022000	0.10575	1.462000	0.35266	0.501000	0.28013	-0.254000	0.11334	AGC		0.632	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
USH2A	7399	broad.mit.edu	37	1	216595383	216595383	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:216595383G>A	ENST00000307340.3	-	2	682	c.296C>T	c.(295-297)gCc>gTc	p.A99V	USH2A_ENST00000366942.3_Missense_Mutation_p.A99V|USH2A_ENST00000366943.2_Missense_Mutation_p.A99V	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	99					hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.A99V(2)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TGAGAAAAGGGCAGTGTAGGT	0.453										HNSCC(13;0.011)																											p.A99V												.	.	2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	c.C296T	1						.						117.0	109.0	112.0					1																	216595383		2203	4300	6503	214662006	SO:0001583	missense	7399	exon2			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.296C>T	1.37:g.216595383G>A	ENSP00000305941:p.Ala99Val		214662006	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	G	17.00	3.276410	0.59649	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.19806	2.58;2.58;2.12	5.42	3.49	0.39957	.	1.106060	0.07114	U	0.842689	T	0.22589	0.0545	L	0.59436	1.845	0.23962	N	0.996335	P;B	0.34724	0.465;0.099	B;B	0.31101	0.124;0.082	T	0.22661	-1.0210	10	0.32370	T	0.25	.	10.1323	0.42687	0.0:0.1341:0.5879:0.278	.	99;99	O75445-2;O75445	.;USH2A_HUMAN	V	99	ENSP00000305941:A99V;ENSP00000355910:A99V;ENSP00000355909:A99V	ENSP00000305941:A99V	A	-	2	0	USH2A	214662006	0.015000	0.18098	0.323000	0.25347	0.797000	0.45037	0.422000	0.21296	0.619000	0.30197	0.591000	0.81541	GCC		0.453	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
WDR26	80232	broad.mit.edu	37	1	224592229	224592229	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:224592229G>A	ENST00000414423.2	-	8	1395	c.1202C>T	c.(1201-1203)gCt>gTt	p.A401V	WDR26_ENST00000295024.6_Missense_Mutation_p.A254V|WDR26_ENST00000366852.2_3'UTR	NM_001115113.2|NM_025160.6	NP_001108585.2|NP_079436.4	Q9H7D7	WDR26_HUMAN	WD repeat domain 26	401						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.A254V(1)|p.A401V(1)		biliary_tract(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)	18				GBM - Glioblastoma multiforme(131;0.0104)		AACGCCATAAGCATGTCCTTC	0.413																																					p.A401V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1202T	1						.						123.0	114.0	117.0					1																	224592229		2203	4300	6503	222658852	SO:0001583	missense	80232	exon8			AK024669	CCDS31037.1, CCDS31037.2	1q42.13	2013-01-09			ENSG00000162923	ENSG00000162923		"""WD repeat domain containing"""	21208	protein-coding gene	gene with protein product	"""GID complex subunit 7 homolog (S. cerevisiae)"""						Standard	NM_001115113		Approved	FLJ21016, GID7	uc001hop.4	Q9H7D7	OTTHUMG00000037636	ENST00000414423.2:c.1202C>T	1.37:g.224592229G>A	ENSP00000408108:p.Ala401Val		222658852	NM_025160	A0MNN3|Q4G100|Q59EC4|Q5GLZ9|Q86UY4|Q9H3C2	Missense_Mutation	SNP	ENST00000414423.2	37	CCDS31037.2	.	.	.	.	.	.	.	.	.	.	G	31	5.087994	0.94100	.	.	ENSG00000162923	ENST00000414423;ENST00000295024	T;T	0.60171	0.21;0.21	4.65	4.65	0.58169	.	0.000000	0.85682	D	0.000000	T	0.57607	0.2065	L	0.41236	1.265	0.80722	D	1	D	0.53151	0.958	P	0.48921	0.595	T	0.57906	-0.7730	10	0.37606	T	0.19	.	17.7113	0.88322	0.0:0.0:1.0:0.0	.	385	Q9H7D7-2	.	V	401;254	ENSP00000408108:A401V;ENSP00000295024:A254V	ENSP00000295024:A254V	A	-	2	0	WDR26	222658852	1.000000	0.71417	0.999000	0.59377	0.983000	0.72400	9.657000	0.98554	2.430000	0.82344	0.484000	0.47621	GCT		0.413	WDR26-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000091760.2	NM_025160	
ACBD3	64746	broad.mit.edu	37	1	226353656	226353656	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:226353656T>C	ENST00000366812.5	-	2	386	c.332A>G	c.(331-333)aAg>aGg	p.K111R		NM_022735.3	NP_073572.2	Q9H3P7	GCP60_HUMAN	acyl-CoA binding domain containing 3	111	ACB. {ECO:0000255|PROSITE- ProRule:PRU00573}.				steroid biosynthetic process (GO:0006694)|transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)	fatty-acyl-CoA binding (GO:0000062)	p.K111R(1)		breast(2)|endometrium(3)|large_intestine(5)|lung(7)|skin(1)|urinary_tract(2)	20	Breast(184;0.158)			GBM - Glioblastoma multiforme(131;0.121)		TGCCACAAGCTTCAATTTTTC	0.363																																					p.K111R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A332G	1						.						109.0	104.0	106.0					1																	226353656		2203	4300	6503	224420279	SO:0001583	missense	64746	exon2			AB043587	CCDS1551.1	1q41	2013-10-16	2010-04-30	2003-11-12	ENSG00000182827	ENSG00000182827		"""A-kinase anchor proteins"""	15453	protein-coding gene	gene with protein product	"""PBR- and PKA-associated protein 7"""	606809	"""golgi complex associated protein 1, 60kDa"", ""acyl-Coenzyme A binding domain containing 3"""	GOLPH1, GOCAP1		12692076, 20150326	Standard	NM_022735		Approved	GCP60, PAP7	uc001hpy.3	Q9H3P7	OTTHUMG00000037560	ENST00000366812.5:c.332A>G	1.37:g.226353656T>C	ENSP00000355777:p.Lys111Arg		224420279	NM_022735	B2RB29|Q5VTJ0|Q6P9F1|Q8IZC5|Q8N4D6|Q9H6U3	Missense_Mutation	SNP	ENST00000366812.5	37	CCDS1551.1	.	.	.	.	.	.	.	.	.	.	T	13.11	2.139766	0.37728	.	.	ENSG00000182827	ENST00000366812	T	0.22539	1.95	5.78	5.78	0.91487	FERM/acyl-CoA-binding protein, 3-helical bundle (1);Acyl-CoA-binding protein, ACBP, conserved site (1);Acyl-CoA-binding protein, ACBP (3);	0.045250	0.85682	D	0.000000	T	0.11367	0.0277	N	0.10945	0.07	0.40443	D	0.980062	B	0.14805	0.011	B	0.19946	0.027	T	0.16778	-1.0391	10	0.34782	T	0.22	-33.969	8.149	0.31130	0.0:0.1881:0.0:0.8119	.	111	Q9H3P7	GCP60_HUMAN	R	111	ENSP00000355777:K111R	ENSP00000355777:K111R	K	-	2	0	ACBD3	224420279	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	2.463000	0.45058	2.205000	0.71048	0.533000	0.62120	AAG		0.363	ACBD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091528.1	NM_022735	
AGT	183	broad.mit.edu	37	1	230846290	230846290	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:230846290C>T	ENST00000366667.4	-	2	521	c.307G>A	c.(307-309)Gcc>Acc	p.A103T	RP11-99J16__A.2_ENST00000412344.1_RNA	NM_000029.3	NP_000020.1	P01019	ANGT_HUMAN	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	103					activation of NF-kappaB-inducing kinase activity (GO:0007250)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|angiotensin maturation (GO:0002003)|angiotensin mediated vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001998)|angiotensin-mediated drinking behavior (GO:0003051)|artery smooth muscle contraction (GO:0014824)|astrocyte activation (GO:0048143)|blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|branching involved in ureteric bud morphogenesis (GO:0001658)|catenin import into nucleus (GO:0035411)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|cellular lipid metabolic process (GO:0044255)|cellular protein metabolic process (GO:0044267)|cellular response to mechanical stimulus (GO:0071260)|cellular sodium ion homeostasis (GO:0006883)|cytokine secretion (GO:0050663)|ERK1 and ERK2 cascade (GO:0070371)|establishment of blood-nerve barrier (GO:0008065)|excretion (GO:0007588)|extracellular matrix organization (GO:0030198)|fibroblast proliferation (GO:0048144)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|kidney development (GO:0001822)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of tissue remodeling (GO:0034104)|nitric oxide mediated signal transduction (GO:0007263)|ovarian follicle rupture (GO:0001543)|peristalsis (GO:0030432)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of cytokine production (GO:0001819)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of extracellular matrix constituent secretion (GO:0003331)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of NAD(P)H oxidase activity (GO:0033864)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of organ growth (GO:0046622)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of blood volume by renin-angiotensin (GO:0002016)|regulation of calcium ion transport (GO:0051924)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of norepinephrine secretion (GO:0014061)|regulation of proteolysis (GO:0030162)|regulation of renal output by angiotensin (GO:0002019)|regulation of renal sodium excretion (GO:0035813)|regulation of vasoconstriction (GO:0019229)|renal response to blood flow involved in circulatory renin-angiotensin regulation of systemic arterial blood pressure (GO:0001999)|renal system process (GO:0003014)|renin-angiotensin regulation of aldosterone production (GO:0002018)|response to cold (GO:0009409)|response to muscle activity involved in regulation of muscle adaptation (GO:0014873)|response to salt stress (GO:0009651)|small molecule metabolic process (GO:0044281)|smooth muscle cell differentiation (GO:0051145)|smooth muscle cell proliferation (GO:0048659)|stress-activated MAPK cascade (GO:0051403)|uterine smooth muscle contraction (GO:0070471)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	growth factor activity (GO:0008083)|hormone activity (GO:0005179)|serine-type endopeptidase inhibitor activity (GO:0004867)|superoxide-generating NADPH oxidase activator activity (GO:0016176)|type 1 angiotensin receptor binding (GO:0031702)|type 2 angiotensin receptor binding (GO:0031703)	p.A103T(1)		endometrium(5)|kidney(1)|large_intestine(6)|lung(7)|pancreas(1)|prostate(5)	25	Breast(184;0.0735)|Ovarian(103;0.183)	all_cancers(173;4.64e-23)|all_epithelial(177;3.61e-18)|Breast(1374;0.00093)|all_neural(198;0.0604)|Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;4.4e-06)|Colorectal(1306;5.46e-06)|COAD - Colon adenocarcinoma(196;0.000256)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		ACCATTGCGGCCCTCAACTTG	0.572																																					p.A103T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G307A	1						.						88.0	87.0	88.0					1																	230846290		2203	4300	6503	228912913	SO:0001583	missense	183	exon2			K02215	CCDS1585.1	1q42.2	2014-02-18	2005-08-18	2001-06-29	ENSG00000135744	ENSG00000135744		"""Serine (or cysteine) peptidase inhibitors"", ""Endogenous ligands"""	333	protein-coding gene	gene with protein product	"""alpha-1 antiproteinase, antitrypsin"""	106150		SERPINA8		6089875, 24172014	Standard	NM_000029		Approved		uc001hty.4	P01019	OTTHUMG00000037757	ENST00000366667.4:c.307G>A	1.37:g.230846290C>T	ENSP00000355627:p.Ala103Thr		228912913	NM_000029	Q16358|Q16359|Q96F91	Missense_Mutation	SNP	ENST00000366667.4	37	CCDS1585.1	.	.	.	.	.	.	.	.	.	.	C	7.837	0.721063	0.15372	.	.	ENSG00000135744	ENST00000366667;ENST00000430091	D	0.87809	-2.3	5.09	5.09	0.68999	Serpin domain (1);	0.239066	0.42294	D	0.000725	T	0.79930	0.4531	L	0.55103	1.725	0.09310	N	1	D;P;D	0.53312	0.959;0.543;0.959	B;B;B	0.35770	0.21;0.042;0.21	T	0.74662	-0.3590	10	0.32370	T	0.25	.	9.6197	0.39714	0.0:0.7647:0.155:0.0802	.	103;103;103	B0ZBE2;B2R5S1;P01019	.;.;ANGT_HUMAN	T	103	ENSP00000355627:A103T	ENSP00000355627:A103T	A	-	1	0	AGT	228912913	0.276000	0.24211	0.233000	0.24025	0.024000	0.10985	2.236000	0.43052	2.526000	0.85167	0.491000	0.48974	GCC		0.572	AGT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092102.1	NM_000029	
DISC1	27185	broad.mit.edu	37	1	232172563	232172563	+	Missense_Mutation	SNP	G	G	A	rs376617666		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:232172563G>A	ENST00000439617.2	+	13	2604	c.2551G>A	c.(2551-2553)Gaa>Aaa	p.E851K	DISC1_ENST00000366637.3_Missense_Mutation_p.E161K	NM_001164537.1|NM_001164540.1|NM_018662.2	NP_001158009.1|NP_001158012.1|NP_061132.2	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1	851	Interaction with ATF4 and ATF5.|Interaction with PAFAH1B1.|Necessary and sufficient for interaction with PCNT and localization at the centrosome.				canonical Wnt signaling pathway (GO:0060070)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cerebral cortex radially oriented cell migration (GO:0021799)|microtubule cytoskeleton organization (GO:0000226)|mitochondrial calcium ion homeostasis (GO:0051560)|neuron migration (GO:0001764)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neuron projection development (GO:0010975)|regulation of synapse maturation (GO:0090128)|TOR signaling (GO:0031929)	cell junction (GO:0030054)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|postsynaptic membrane (GO:0045211)		p.E883K(1)		breast(1)|cervix(1)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	15		all_cancers(173;0.0208)|Prostate(94;0.0975)				TGGTGTCCACGAAGCACAAGC	0.617																																					p.E729K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2185A	1						.	G	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	0,4002		0,0,2001	25.0	29.0	28.0		2485,2647,2185,2551	2.3	0.0	1		28	1,8325		0,1,4162	no	missense,missense,missense,missense	DISC1	NM_001012957.1,NM_001164537.1,NM_001164540.1,NM_018662.2	56,56,56,56	0,1,6163	AA,AG,GG		0.012,0.0,0.0081	probably-damaging,probably-damaging,probably-damaging,probably-damaging	829/833,883/887,729/733,851/855	232172563	1,12327	2001	4163	6164	230239186	SO:0001583	missense	27185	exon11			AF222980	CCDS31055.1, CCDS31056.1, CCDS53482.1, CCDS53483.1, CCDS53484.1, CCDS59205.1, CCDS59206.1, CCDS59207.1	1q42.1	2008-02-05			ENSG00000162946	ENSG00000162946			2888	protein-coding gene	gene with protein product		605210				10814723	Standard	NM_001164550		Approved		uc010pxh.2	Q9NRI5	OTTHUMG00000037835	ENST00000439617.2:c.2551G>A	1.37:g.232172563G>A	ENSP00000403888:p.Glu851Lys		230239186	NM_001164540	A6NLH2|C4P091|C4P095|C4P0A1|C4P0A3|C4P0B3|C4P0B6|C4P0C1|C9J6D0|O75045|Q5VT44|Q5VT45|Q8IXJ0|Q8IXJ1|Q9BX19|Q9NRI3|Q9NRI4	Missense_Mutation	SNP	ENST00000439617.2	37		.	.	.	.	.	.	.	.	.	.	G	15.53	2.861920	0.51482	0.0	1.2E-4	ENSG00000162946	ENST00000439617;ENST00000366637;ENST00000366638;ENST00000532576	T	0.12361	2.69	5.3	2.26	0.28386	.	0.460210	0.22500	N	0.059257	T	0.08802	0.0218	N	0.24115	0.695	0.09310	N	0.999999	P;P	0.49559	0.925;0.925	B;B	0.39935	0.314;0.314	T	0.17776	-1.0358	10	0.87932	D	0	-12.4481	9.6702	0.40008	0.2484:0.0:0.7516:0.0	.	829;851	Q9NRI5-2;Q9NRI5	.;DISC1_HUMAN	K	851;829;883;729	ENSP00000403888:E851K	ENSP00000355597:E829K	E	+	1	0	DISC1	230239186	1.000000	0.71417	0.002000	0.10522	0.366000	0.29705	3.360000	0.52299	0.833000	0.34828	0.650000	0.86243	GAA		0.617	DISC1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000092351.2	NM_018662	
COA6	388753	broad.mit.edu	37	1	234510069	234510069	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:234510069C>T	ENST00000366613.1	+	2	252	c.216C>T	c.(214-216)aaC>aaT	p.N72N	RP5-827C21.4_ENST00000451795.1_RNA|COA6_ENST00000366612.1_Silent_p.N26N|RP5-827C21.6_ENST00000610233.1_RNA|COA6_ENST00000366615.4_Silent_p.N102N	NM_001012985.2	NP_001013003.1	Q5JTJ3	COA6_HUMAN	cytochrome c oxidase assembly factor 6 homolog (S. cerevisiae)	72						mitochondrion (GO:0005739)	cytochrome-c oxidase activity (GO:0004129)|poly(A) RNA binding (GO:0044822)	p.N72N(1)									TAGATGAGAACTTAGAGGATG	0.478																																					p.N72N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C216T	1						.						97.0	99.0	98.0					1																	234510069		2203	4300	6503	232576692	SO:0001819	synonymous_variant	388753	exon2				CCDS31059.1, CCDS55690.1	1q42.2	2012-10-15	2012-10-15	2012-10-15	ENSG00000168275	ENSG00000168275		"""Mitochondrial respiratory chain complex assembly factors"""	18025	protein-coding gene	gene with protein product		614772	"""chromosome 1 open reading frame 31"""	C1orf31		22984289	Standard	NM_001012985		Approved		uc001hwc.3	Q5JTJ3	OTTHUMG00000037945	ENST00000366613.1:c.216C>T	1.37:g.234510069C>T			232576692	NM_001012985	Q5JTJ2|Q5JTJ4|Q8TA88	Silent	SNP	ENST00000366613.1	37	CCDS31059.1																																																																																				0.478	COA6-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000092613.1	NM_001012985	
LYST	1130	broad.mit.edu	37	1	235950518	235950518	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:235950518A>G	ENST00000389794.3	-	14	5018	c.4844T>C	c.(4843-4845)aTa>aCa	p.I1615T	LYST_ENST00000389793.2_Missense_Mutation_p.I1615T|LYST_ENST00000536965.1_3'UTR			Q99698	LYST_HUMAN	lysosomal trafficking regulator	1615					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)		p.I1615T(1)		NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			AGAGACCCATATGGAGATTTT	0.398																																					p.I1615T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T4844C	1						.						142.0	145.0	144.0					1																	235950518		2203	4300	6503	234017141	SO:0001583	missense	1130	exon14			U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"""WD repeat domain containing"""	1968	protein-coding gene	gene with protein product		606897	"""Chediak-Higashi syndrome 1"""	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.4844T>C	1.37:g.235950518A>G	ENSP00000374444:p.Ile1615Thr		234017141	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Missense_Mutation	SNP	ENST00000389794.3	37	CCDS31062.1	.	.	.	.	.	.	.	.	.	.	A	14.86	2.661496	0.47572	.	.	ENSG00000143669	ENST00000389794;ENST00000389793	T;T	0.63255	-0.03;-0.03	5.71	3.39	0.38822	.	0.470181	0.26279	N	0.025290	T	0.50922	0.1644	L	0.36672	1.1	0.80722	D	1	B	0.28552	0.215	B	0.29524	0.103	T	0.48080	-0.9066	10	0.72032	D	0.01	.	9.9524	0.41647	0.8622:0.0:0.1378:0.0	.	1615	Q99698	LYST_HUMAN	T	1615	ENSP00000374444:I1615T;ENSP00000374443:I1615T	ENSP00000374443:I1615T	I	-	2	0	LYST	234017141	0.991000	0.36638	0.989000	0.46669	0.987000	0.75469	4.652000	0.61454	0.439000	0.26476	0.477000	0.44152	ATA		0.398	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5		
KMO	8564	broad.mit.edu	37	1	241725495	241725495	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:241725495T>C	ENST00000366559.4	+	7	789	c.478T>C	c.(478-480)Tgt>Cgt	p.C160R	KMO_ENST00000366558.3_Missense_Mutation_p.C160R|KMO_ENST00000366557.4_Missense_Mutation_p.C160R|KMO_ENST00000484628.1_3'UTR	NM_003679.4	NP_003670.2			kynurenine 3-monooxygenase (kynurenine 3-hydroxylase)									p.C160R(1)		NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)	33	Ovarian(103;0.103)|all_lung(81;0.23)		OV - Ovarian serous cystadenocarcinoma(106;0.0176)			AGATGTCACTTGTGACCTCAT	0.393																																					p.C160R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T478C	1						.						159.0	134.0	142.0					1																	241725495		2203	4300	6503	239792118	SO:0001583	missense	8564	exon7			AF056032	CCDS1618.1	1q42-q44	2010-11-23			ENSG00000117009	ENSG00000117009	1.14.13.9		6381	protein-coding gene	gene with protein product		603538				9237672	Standard	NM_003679		Approved		uc009xgp.3	O15229	OTTHUMG00000039635	ENST00000366559.4:c.478T>C	1.37:g.241725495T>C	ENSP00000355517:p.Cys160Arg		239792118	NM_003679		Missense_Mutation	SNP	ENST00000366559.4	37	CCDS1618.1	.	.	.	.	.	.	.	.	.	.	T	7.732	0.699505	0.15106	.	.	ENSG00000117009	ENST00000366559;ENST00000366558;ENST00000366557	T;T;T	0.57107	0.42;0.42;0.42	5.83	5.83	0.93111	Monooxygenase, FAD-binding (1);Aromatic-ring hydroxylase-like (1);	0.539779	0.22163	N	0.063759	T	0.51466	0.1676	M	0.65498	2.005	0.09310	N	0.999995	P;P;P	0.40476	0.642;0.642;0.718	B;B;B	0.39258	0.295;0.295;0.195	T	0.52859	-0.8519	10	0.33940	T	0.23	.	12.5932	0.56454	0.0:0.0:0.0:1.0	.	160;160;160	O15229;A8K693;O15229-2	KMO_HUMAN;.;.	R	160	ENSP00000355517:C160R;ENSP00000355516:C160R;ENSP00000355515:C160R	ENSP00000355515:C160R	C	+	1	0	KMO	239792118	0.573000	0.26676	0.014000	0.15608	0.280000	0.26924	5.072000	0.64389	2.227000	0.72691	0.459000	0.35465	TGT		0.393	KMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095612.1	NM_003679	
LYPLA2	11313	broad.mit.edu	37	1	24124706	24124706	+	IGR	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:24124706C>T	ENST00000374514.3	+	0	1810				GALE_ENST00000374497.3_Silent_p.A84A|GALE_ENST00000470383.1_5'Flank	NM_007260.2	NP_009191.1	O95372	LYPA2_HUMAN	lysophospholipase II						fatty acid metabolic process (GO:0006631)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	hydrolase activity (GO:0016787)	p.A84A(1)		endometrium(3)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;1.79e-24)|Colorectal(126;4.8e-08)|COAD - Colon adenocarcinoma(152;2.83e-06)|GBM - Glioblastoma multiforme(114;4.22e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000946)|KIRC - Kidney renal clear cell carcinoma(1967;0.00314)|STAD - Stomach adenocarcinoma(196;0.0123)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0827)|LUSC - Lung squamous cell carcinoma(448;0.184)		AGTGGATGACCGCCATAAAGC	0.562																																					p.A84A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G252A	1						.						33.0	35.0	34.0					1																	24124706		2202	4300	6502	23997293	SO:0001628	intergenic_variant	2582	exon5			AF098668	CCDS241.1	1p36.11	2008-08-08			ENSG00000011009	ENSG00000011009	3.1.1.5		6738	protein-coding gene	gene with protein product							Standard	NM_007260		Approved	APT-2	uc001bht.3	O95372	OTTHUMG00000002961		1.37:g.24124706C>T			23997293	NM_000403	Q7Z4Z2	Silent	SNP	ENST00000374514.3	37	CCDS241.1																																																																																				0.562	LYPLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008245.1		
SRSF10	10772	broad.mit.edu	37	1	24301554	24301554	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:24301554G>A	ENST00000492112.2	-	3	247	c.184C>T	c.(184-186)Cgt>Tgt	p.R62C	SRSF10_ENST00000374453.3_Missense_Mutation_p.R62C|SRSF10_ENST00000343255.5_Missense_Mutation_p.R62C|SRSF10_ENST00000453840.3_Missense_Mutation_p.R62C|SRSF10_ENST00000344989.6_Missense_Mutation_p.R62C|SRSF10_ENST00000484146.2_Missense_Mutation_p.R62C|SRSF10_ENST00000341154.6_Intron|SRSF10_ENST00000374452.5_Missense_Mutation_p.R62C			O75494	SRS10_HUMAN	serine/arginine-rich splicing factor 10	62	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cytoplasmic transport (GO:0016482)|mRNA export from nucleus (GO:0006406)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing, via transesterification reactions (GO:0000375)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RS domain binding (GO:0050733)|unfolded protein binding (GO:0051082)	p.R62C(1)									TCAGCATCACGAACATCCTCA	0.408																																					p.R62C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C184T	1						.						4.0	2.0	3.0					1																	24301554		1686	2531	4217	24174141	SO:0001583	missense	10772	exon3			AF047448	CCDS30629.1, CCDS30630.1, CCDS53280.1, CCDS53281.1, CCDS53282.1, CCDS53283.1, CCDS72728.1	1p36.11	2014-06-13	2010-06-22	2010-06-22	ENSG00000188529	ENSG00000188529		"""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	16713	protein-coding gene	gene with protein product	"""splicing factor, arginine/serine-rich 13"", ""SR splicing factor 10"", ""protein phosphatase 1, regulatory subunit 149"""	605221	"""FUS-interacting protein (serine-arginine rich) 2"", ""FUS interacting protein (serine/arginine-rich) 1"", ""splicing factor, arginine/serine-rich 13A"", ""neural-salient SR protein"""	FUSIP2, FUSIP1, SFRS13A		11891055, 20516191	Standard	XM_006710298		Approved	TASR1, TASR2, SRp38, SRrp40, SFRS13, PPP1R149	uc021oir.1	O75494	OTTHUMG00000013893	ENST00000492112.2:c.184C>T	1.37:g.24301554G>A	ENSP00000420195:p.Arg62Cys		24174141	NM_001191007	A6NFM6|A6NI42|A6NIU7|B4DJP9|O60572|Q5JRH9|Q5JRI0|Q5JRI2|Q5JRI3|Q5JRI4|Q96G09|Q96P17	Missense_Mutation	SNP	ENST00000492112.2	37	CCDS30630.1	.	.	.	.	.	.	.	.	.	.	G	17.11	3.305955	0.60305	.	.	ENSG00000188529	ENST00000344989;ENST00000484146;ENST00000453840;ENST00000374452;ENST00000374453;ENST00000492112;ENST00000343255	T;T;T;T;T;T;T	0.74947	2.25;2.25;2.25;2.25;-0.89;2.25;2.25	3.82	3.82	0.43975	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.64402	U	0.000001	T	0.80188	0.4577	L	0.60845	1.875	0.80722	D	1	D;B	0.54964	0.969;0.224	P;B	0.55055	0.767;0.071	D	0.83829	0.0251	10	0.87932	D	0	.	16.263	0.82557	0.0:0.0:1.0:0.0	.	62;62	O75494;O75494-3	SRS10_HUMAN;.	C	62	ENSP00000342913:R62C;ENSP00000419813:R62C;ENSP00000388991:R62C;ENSP00000363576:R62C;ENSP00000363577:R62C;ENSP00000420195:R62C;ENSP00000344149:R62C	ENSP00000344149:R62C	R	-	1	0	SRSF10	24174141	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.356000	0.79445	2.143000	0.66587	0.650000	0.86243	CGT		0.408	SRSF10-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038950.2	NM_006625	
OPN3	23596	broad.mit.edu	37	1	241767829	241767829	+	Silent	SNP	G	G	A	rs570915682		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:241767829G>A	ENST00000366554.2	-	2	532	c.426C>T	c.(424-426)cgC>cgT	p.R142R	OPN3_ENST00000469376.1_5'UTR|OPN3_ENST00000331838.5_Intron	NM_014322.2	NP_055137.2	Q9H1Y3	OPN3_HUMAN	opsin 3	142					detection of light stimulus (GO:0009583)|detection of visible light (GO:0009584)|G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	G-protein coupled photoreceptor activity (GO:0008020)|G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)	p.R142R(1)		endometrium(1)|large_intestine(5)|lung(5)	11	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)			CATGGACCACGCGAATGTAAC	0.532													G|||	1	0.000199681	0.0	0.0	5008	,	,		19895	0.0		0.0	False		,,,				2504	0.001				p.R142R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C426T	1						.						77.0	74.0	75.0					1																	241767829		2203	4300	6503	239834452	SO:0001819	synonymous_variant	23596	exon2			AF140242	CCDS31072.1	1q43	2014-06-13	2008-04-16		ENSG00000054277	ENSG00000054277		"""GPCR / Class A : Opsin receptors"""	14007	protein-coding gene	gene with protein product	"""panopsin"", ""protein phosphatase 1, regulatory subunit 116"""	606695	"""encephalopsin"""	ECPN		10234000, 11401433	Standard	NM_014322		Approved	ERO, NMO-1, encephalopsin, PPP1R116	uc001hza.3	Q9H1Y3	OTTHUMG00000039691	ENST00000366554.2:c.426C>T	1.37:g.241767829G>A			239834452	NM_014322	Q8IX08|Q9Y344	Silent	SNP	ENST00000366554.2	37	CCDS31072.1																																																																																				0.532	OPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095713.1	NM_014322	
ZBTB18	10472	broad.mit.edu	37	1	244217563	244217563	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:244217563G>A	ENST00000358704.4	+	2	636	c.487G>A	c.(487-489)Gat>Aat	p.D163N		NM_001278196.1|NM_006352.4|NM_205768.2	NP_001265125.1|NP_006343.2|NP_991331.1	Q99592	ZBT18_HUMAN	zinc finger and BTB domain containing 18	154					cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron development (GO:0048666)|regulation of cell division (GO:0051302)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D154N(1)									CATAGCAGGCGATTTGCCCAG	0.517																																					p.D154N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G460A	1						.						58.0	57.0	58.0					1																	244217563		2203	4300	6503	242284186	SO:0001583	missense	10472	exon1			U38896	CCDS1622.1	1q44	2013-09-19	2013-01-09	2013-01-09	ENSG00000179456	ENSG00000179456		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	13030	protein-coding gene	gene with protein product		608433	"""zinc finger protein 238"""	ZNF238		9568537, 9013868	Standard	NM_205768		Approved	C2H2-171, TAZ-1, RP58	uc031psv.1	Q99592	OTTHUMG00000040013	ENST00000358704.4:c.487G>A	1.37:g.244217563G>A	ENSP00000351539:p.Asp163Asn		242284186	NM_006352	A8K5U3|Q13397|Q5VU40|Q8N463|Q9UD99	Missense_Mutation	SNP	ENST00000358704.4	37	CCDS1622.1	.	.	.	.	.	.	.	.	.	.	G	13.99	2.402982	0.42613	.	.	ENSG00000179456	ENST00000366538;ENST00000358704	T	0.11495	2.77	5.28	5.28	0.74379	.	0.000000	0.64402	D	0.000001	T	0.09113	0.0225	L	0.29908	0.895	0.80722	D	1	D;D;P	0.53745	0.962;0.962;0.951	B;B;B	0.38880	0.269;0.269;0.284	T	0.35574	-0.9783	10	0.18276	T	0.48	.	18.9107	0.92483	0.0:0.0:1.0:0.0	.	163;154;163	B4DF20;Q99592;Q99592-2	.;ZN238_HUMAN;.	N	163	ENSP00000351539:D163N	ENSP00000351539:D163N	D	+	1	0	ZNF238	242284186	1.000000	0.71417	0.981000	0.43875	0.991000	0.79684	9.185000	0.94900	2.475000	0.83589	0.650000	0.86243	GAT		0.517	ZBTB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096513.2	NM_205768	
ZBTB18	10472	broad.mit.edu	37	1	244218199	244218199	+	Missense_Mutation	SNP	G	G	A	rs371575631		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:244218199G>A	ENST00000358704.4	+	2	1272	c.1123G>A	c.(1123-1125)Gcg>Acg	p.A375T		NM_001278196.1|NM_006352.4|NM_205768.2	NP_001265125.1|NP_006343.2|NP_991331.1	Q99592	ZBT18_HUMAN	zinc finger and BTB domain containing 18	366	Interaction with DNMT3A.				cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron development (GO:0048666)|regulation of cell division (GO:0051302)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A366T(1)									CCTGAGCCCCGCGGGCCAGAT	0.617																																					p.A366T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1096A	1						.	G	THR/ALA,THR/ALA	0,4406		0,0,2203	57.0	52.0	54.0		1123,1096	5.8	1.0	1		54	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ZNF238	NM_205768.2,NM_006352.3	58,58	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	375/532,366/523	244218199	1,13005	2203	4300	6503	242284822	SO:0001583	missense	10472	exon1			U38896	CCDS1622.1	1q44	2013-09-19	2013-01-09	2013-01-09	ENSG00000179456	ENSG00000179456		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	13030	protein-coding gene	gene with protein product		608433	"""zinc finger protein 238"""	ZNF238		9568537, 9013868	Standard	NM_205768		Approved	C2H2-171, TAZ-1, RP58	uc031psv.1	Q99592	OTTHUMG00000040013	ENST00000358704.4:c.1123G>A	1.37:g.244218199G>A	ENSP00000351539:p.Ala375Thr		242284822	NM_006352	A8K5U3|Q13397|Q5VU40|Q8N463|Q9UD99	Missense_Mutation	SNP	ENST00000358704.4	37	CCDS1622.1	.	.	.	.	.	.	.	.	.	.	G	8.958	0.969948	0.18659	0.0	1.16E-4	ENSG00000179456	ENST00000366538;ENST00000358704	T	0.12039	2.72	5.83	5.83	0.93111	.	0.115591	0.64402	D	0.000014	T	0.09686	0.0238	N	0.19112	0.55	0.49915	D	0.99983	B;B	0.27117	0.038;0.168	B;B	0.15484	0.006;0.013	T	0.15983	-1.0418	10	0.07482	T	0.82	.	20.1184	0.97949	0.0:0.0:1.0:0.0	.	366;375	Q99592;Q99592-2	ZN238_HUMAN;.	T	375	ENSP00000351539:A375T	ENSP00000351539:A375T	A	+	1	0	ZNF238	242284822	0.991000	0.36638	0.996000	0.52242	0.979000	0.70002	2.700000	0.47085	2.775000	0.95449	0.650000	0.86243	GCG		0.617	ZBTB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096513.2	NM_205768	
TRIM58	25893	broad.mit.edu	37	1	248039484	248039484	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:248039484G>T	ENST00000366481.3	+	6	1202	c.1154G>T	c.(1153-1155)tGg>tTg	p.W385L	OR2W3_ENST00000537741.1_Intron	NM_015431.3	NP_056246.3	Q8NG06	TRI58_HUMAN	tripartite motif containing 58	385	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.W385L(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(39)|ovary(4)|pancreas(1)|skin(7)|stomach(1)	63	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0286)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			TGGGCCCTGTGGCTGCTGAAA	0.542																																					p.W385L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1154T	1						.						118.0	120.0	119.0					1																	248039484		2203	4300	6503	246106107	SO:0001583	missense	25893	exon6			AF327057	CCDS1636.1	1q44	2013-01-09	2011-01-25		ENSG00000162722	ENSG00000162722		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	24150	protein-coding gene	gene with protein product			"""tripartite motif-containing 58"""				Standard	NM_015431		Approved	BIA2	uc001ido.3	Q8NG06	OTTHUMG00000040203	ENST00000366481.3:c.1154G>T	1.37:g.248039484G>T	ENSP00000355437:p.Trp385Leu		246106107	NM_015431	Q6B0H9	Missense_Mutation	SNP	ENST00000366481.3	37	CCDS1636.1	.	.	.	.	.	.	.	.	.	.	G	17.08	3.297083	0.60086	.	.	ENSG00000162722	ENST00000366481	T	0.68903	-0.36	4.05	4.05	0.47172	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.53938	D	0.000056	T	0.69333	0.3099	L	0.35593	1.075	0.80722	D	1	D	0.58620	0.983	P	0.60117	0.869	T	0.68996	-0.5262	10	0.41790	T	0.15	.	14.5446	0.68020	0.0:0.0:1.0:0.0	.	385	Q8NG06	TRI58_HUMAN	L	385	ENSP00000355437:W385L	ENSP00000355437:W385L	W	+	2	0	TRIM58	246106107	0.016000	0.18221	0.998000	0.56505	0.898000	0.52572	0.665000	0.25083	2.559000	0.86315	0.650000	0.86243	TGG		0.542	TRIM58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096860.1	NM_015431	
OR2M5	127059	broad.mit.edu	37	1	248308976	248308976	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:248308976A>G	ENST00000366476.1	+	1	527	c.527A>G	c.(526-528)cAc>cGc	p.H176R		NM_001004690.1	NP_001004690.1	A3KFT3	OR2M5_HUMAN	olfactory receptor, family 2, subfamily M, member 5	176						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H176R(1)		NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	49	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0388)			GAAATAGCCCACTTCTTCTGT	0.423																																					p.H176R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A527G	1						.						295.0	277.0	283.0					1																	248308976		2203	4298	6501	246375599	SO:0001583	missense	127059	exon1				CCDS31105.1	1q44	2012-08-09		2004-03-10	ENSG00000162727	ENSG00000162727		"""GPCR / Class A : Olfactory receptors"""	19576	protein-coding gene	gene with protein product				OR2M5P			Standard	NM_001004690		Approved		uc010pze.2	A3KFT3	OTTHUMG00000040447	ENST00000366476.1:c.527A>G	1.37:g.248308976A>G	ENSP00000355432:p.His176Arg		246375599	NM_001004690		Missense_Mutation	SNP	ENST00000366476.1	37	CCDS31105.1	.	.	.	.	.	.	.	.	.	.	a	16.94	3.260572	0.59431	.	.	ENSG00000162727	ENST00000366476	T	0.00174	8.62	3.13	3.13	0.36017	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33253	U	0.005106	T	0.00637	0.0021	H	0.96239	3.79	0.09310	N	1	P	0.49783	0.928	P	0.55260	0.772	T	0.08680	-1.0710	10	0.87932	D	0	.	11.279	0.49184	1.0:0.0:0.0:0.0	.	176	A3KFT3	OR2M5_HUMAN	R	176	ENSP00000355432:H176R	ENSP00000355432:H176R	H	+	2	0	OR2M5	246375599	0.003000	0.15002	0.021000	0.16686	0.818000	0.46254	1.732000	0.38146	1.190000	0.43042	0.403000	0.27427	CAC		0.423	OR2M5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097343.1	NM_001004690	
ACOT7	11332	broad.mit.edu	37	1	6341230	6341230	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:6341230C>T	ENST00000377855.2	-	8	1122	c.976G>A	c.(976-978)Gcc>Acc	p.A326T	ACOT7_ENST00000377845.3_Missense_Mutation_p.A296T|ACOT7_ENST00000608083.1_Missense_Mutation_p.A284T|ACOT7_ENST00000545482.1_Missense_Mutation_p.A211T|ACOT7_ENST00000377842.3_Missense_Mutation_p.A275T|ACOT7_ENST00000361521.4_Missense_Mutation_p.A316T	NM_181864.2	NP_863654.1	O00154	BACH_HUMAN	acyl-CoA thioesterase 7	326					coenzyme A biosynthetic process (GO:0015937)|fatty acid catabolic process (GO:0009062)|long-chain fatty-acyl-CoA catabolic process (GO:0036116)|medium-chain fatty acid biosynthetic process (GO:0051792)|medium-chain fatty-acyl-CoA catabolic process (GO:0036114)|palmitic acid biosynthetic process (GO:1900535)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)	carboxylic ester hydrolase activity (GO:0052689)|fatty-acyl-CoA binding (GO:0000062)|long-chain fatty acyl-CoA binding (GO:0036042)|palmitoyl-CoA hydrolase activity (GO:0016290)|protein homodimerization activity (GO:0042803)	p.A316T(1)		kidney(1)|large_intestine(3)|lung(10)|pancreas(1)|prostate(1)	16	Ovarian(185;0.0634)|all_lung(157;0.175)	all_cancers(23;1.42e-38)|all_epithelial(116;3.96e-23)|all_lung(118;3.69e-08)|Lung NSC(185;8.52e-07)|all_hematologic(16;6.92e-06)|Colorectal(325;4.53e-05)|Acute lymphoblastic leukemia(12;5e-05)|all_neural(13;0.000164)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)		Epithelial(90;9.16e-37)|GBM - Glioblastoma multiforme(13;5.89e-29)|OV - Ovarian serous cystadenocarcinoma(86;7.63e-19)|Colorectal(212;1.27e-07)|COAD - Colon adenocarcinoma(227;2.06e-05)|Kidney(185;7.74e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00129)|BRCA - Breast invasive adenocarcinoma(365;0.00132)|STAD - Stomach adenocarcinoma(132;0.00195)|READ - Rectum adenocarcinoma(331;0.0481)		AAGGCACTGGCGGCCCGGTAG	0.632											OREG0013034	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A326T	GBM(74;673 1226 4974 11850 13190)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G976A	1						.						65.0	58.0	61.0					1																	6341230		2203	4300	6503	6263817	SO:0001583	missense	11332	exon8			AB074417	CCDS65.1, CCDS66.1, CCDS67.1, CCDS30573.1	1p36	2008-08-14			ENSG00000097021	ENSG00000097021		"""Acyl CoA thioesterases"""	24157	protein-coding gene	gene with protein product	"""brain acyl CoA hydrolase"""	602587				10578051, 16103133, 16940157	Standard	XM_005263427		Approved	BACH, ACH1, ACT, CTE-II, LACH1, MGC1126, hBACH	uc001amt.3	O00154	OTTHUMG00000001295	ENST00000377855.2:c.976G>A	1.37:g.6341230C>T	ENSP00000367086:p.Ala326Thr	633	6263817	NM_181864	A8K0K7|A8K232|A8K6B8|A8K837|B3KQ12|O43703|Q53Y78|Q5JYL2|Q5JYL3|Q5JYL4|Q5JYL5|Q5JYL6|Q5TGR4|Q9UJM9|Q9Y539|Q9Y540	Missense_Mutation	SNP	ENST00000377855.2	37	CCDS65.1	.	.	.	.	.	.	.	.	.	.	C	18.57	3.652579	0.67472	.	.	ENSG00000097021	ENST00000377855;ENST00000377845;ENST00000377842;ENST00000361521;ENST00000545482	T;T;T;T;T	0.54866	0.55;0.55;0.55;0.55;0.55	4.56	4.56	0.56223	.	0.072810	0.56097	D	0.000027	T	0.32255	0.0823	N	0.22421	0.69	0.80722	D	1	P;P;D;B	0.54964	0.581;0.753;0.969;0.419	B;B;B;B	0.37989	0.055;0.123;0.262;0.034	T	0.37888	-0.9686	10	0.02654	T	1	.	16.3206	0.82950	0.0:1.0:0.0:0.0	.	316;326;296;275	B3KQ12;O00154;O00154-5;O00154-6	.;BACH_HUMAN;.;.	T	326;296;275;316;211	ENSP00000367086:A326T;ENSP00000367076:A296T;ENSP00000367073:A275T;ENSP00000354615:A316T;ENSP00000439218:A211T	ENSP00000354615:A316T	A	-	1	0	ACOT7	6263817	1.000000	0.71417	0.982000	0.44146	0.913000	0.54294	7.403000	0.79983	2.076000	0.62316	0.462000	0.41574	GCC		0.632	ACOT7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003773.1	NM_007274	
ZBTB48	3104	broad.mit.edu	37	1	6646807	6646807	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:6646807G>A	ENST00000377674.4	+	5	1255	c.1097G>A	c.(1096-1098)cGg>cAg	p.R366Q		NM_001278647.1|NM_001278648.1|NM_005341.2	NP_001265576.1|NP_001265577.1|NP_005332.1	P10074	ZBT48_HUMAN	zinc finger and BTB domain containing 48	366					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R366Q(1)		central_nervous_system(1)|kidney(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	11	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;1.35e-07)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(304;0.00109)|STAD - Stomach adenocarcinoma(132;0.017)|READ - Rectum adenocarcinoma(331;0.0642)		ATGGAGCTGCGGGTGCACATG	0.647																																					p.R366Q	Esophageal Squamous(125;1449 1657 4031 29866 49542)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1097A	1						.						92.0	68.0	76.0					1																	6646807		2203	4300	6503	6569394	SO:0001583	missense	3104	exon5			BC013573	CCDS84.1	1p36.3	2013-01-08	2006-09-20	2006-09-20	ENSG00000204859	ENSG00000204859		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	4930	protein-coding gene	gene with protein product		165270	"""GLI-Kruppel family member HKR3"""	HKR3		2850480, 8661141	Standard	NM_001278647		Approved	ZNF855	uc001anx.3	P10074	OTTHUMG00000001438	ENST00000377674.4:c.1097G>A	1.37:g.6646807G>A	ENSP00000366902:p.Arg366Gln		6569394	NM_005341	Q5SY19	Missense_Mutation	SNP	ENST00000377674.4	37	CCDS84.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.966382	0.92855	.	.	ENSG00000204859	ENST00000377674;ENST00000545645	T	0.20598	2.06	5.62	5.62	0.85841	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.048315	0.85682	D	0.000000	T	0.36771	0.0979	L	0.39147	1.195	0.54753	D	0.999989	D	0.89917	1.0	D	0.76575	0.988	T	0.01757	-1.1280	10	0.12430	T	0.62	-30.8515	19.0188	0.92905	0.0:0.0:1.0:0.0	.	366	P10074	ZBT48_HUMAN	Q	366;4	ENSP00000366902:R366Q	ENSP00000366902:R366Q	R	+	2	0	ZBTB48	6569394	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.539000	0.73856	2.826000	0.97356	0.561000	0.74099	CGG		0.647	ZBTB48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004193.1	NM_005341	
H6PD	9563	broad.mit.edu	37	1	9322156	9322156	+	Missense_Mutation	SNP	G	G	A	rs149081812		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:9322156G>A	ENST00000377403.2	+	4	1086	c.784G>A	c.(784-786)Gac>Aac	p.D262N	H6PD_ENST00000602477.1_Missense_Mutation_p.D273N	NM_001282587.1|NM_004285.3	NP_001269516.1|NP_004276.2	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	262	Glucose 1-dehydrogenase.				pentose-phosphate shunt (GO:0006098)|response to alcohol (GO:0097305)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	6-phosphogluconolactonase activity (GO:0017057)|carbohydrate binding (GO:0030246)|glucose 1-dehydrogenase [NAD(P)] activity (GO:0047936)|glucose-6-phosphate dehydrogenase activity (GO:0004345)|NADP binding (GO:0050661)	p.D262N(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	all_lung(157;0.23)	all_epithelial(116;1.28e-19)|all_lung(118;5.22e-06)|Lung NSC(185;1.98e-05)|Renal(390;0.000147)|Breast(348;0.00109)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.88e-07)|COAD - Colon adenocarcinoma(227;7.47e-05)|Kidney(185;0.000244)|KIRC - Kidney renal clear cell carcinoma(229;0.000905)|STAD - Stomach adenocarcinoma(132;0.00176)|BRCA - Breast invasive adenocarcinoma(304;0.00183)|READ - Rectum adenocarcinoma(331;0.0419)		TGTCATTCGCGACGTCCTCCA	0.597																																					p.D262N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G784A	1						.	G	ASN/ASP	1,4405	2.1+/-5.4	0,1,2202	77.0	70.0	72.0		784	5.2	0.1	1	dbSNP_134	72	0,8600		0,0,4300	no	missense	H6PD	NM_004285.3	23	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	262/792	9322156	1,13005	2203	4300	6503	9244743	SO:0001583	missense	9563	exon4			AJ012590	CCDS101.1, CCDS72697.1	1p36	2008-02-05	2003-10-10		ENSG00000049239	ENSG00000049239	1.1.1.47		4795	protein-coding gene	gene with protein product		138090	"""glucose dehyrogenase"""	GDH		10349511	Standard	NM_001282587		Approved		uc001apt.3	O95479	OTTHUMG00000001768	ENST00000377403.2:c.784G>A	1.37:g.9322156G>A	ENSP00000366620:p.Asp262Asn		9244743	NM_004285	Q4TT33|Q66I35|Q68DT3	Missense_Mutation	SNP	ENST00000377403.2	37	CCDS101.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.743685	0.89663	2.27E-4	0.0	ENSG00000049239	ENST00000377403	D	0.99809	-6.86	5.25	5.25	0.73442	Glucose-6-phosphate dehydrogenase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.99896	0.9950	H	0.99090	4.425	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96102	0.9070	10	0.87932	D	0	-46.4464	17.8292	0.88676	0.0:0.0:1.0:0.0	.	262	O95479	G6PE_HUMAN	N	262	ENSP00000366620:D262N	ENSP00000366620:D262N	D	+	1	0	H6PD	9244743	1.000000	0.71417	0.148000	0.22405	0.580000	0.36256	9.405000	0.97313	2.460000	0.83146	0.561000	0.74099	GAC		0.597	H6PD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004928.2	NM_004285	
CLSTN1	22883	broad.mit.edu	37	1	9809959	9809959	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:9809959delT	ENST00000377298.4	-	6	1454	c.662delA	c.(661-663)aacfs	p.N221fs	CLSTN1_ENST00000377288.3_Frame_Shift_Del_p.N221fs|CLSTN1_ENST00000361311.4_Frame_Shift_Del_p.N211fs	NM_001009566.1	NP_001009566.1	O94985	CSTN1_HUMAN	calsyntenin 1	221	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	beta-amyloid binding (GO:0001540)|calcium ion binding (GO:0005509)|kinesin binding (GO:0019894)|X11-like protein binding (GO:0042988)	p.N221fs*5(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(9)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	36	all_lung(157;0.222)	all_lung(284;4.03e-05)|Lung NSC(185;6.93e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;8.36e-08)|COAD - Colon adenocarcinoma(227;1.93e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419)		TTTCTCTGTGTTTTTTATATA	0.408																																					p.N211fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.632delA	1						.						124.0	110.0	115.0					1																	9809959		2203	4300	6503	9732546	SO:0001589	frameshift_variant	22883	exon5			AB020718	CCDS105.1, CCDS30580.1	1p36.22	2011-07-01			ENSG00000171603	ENSG00000171603		"""Cadherins / Cadherin-related"""	17447	protein-coding gene	gene with protein product	"""cadherin-related family member 12"""	611321				10048485	Standard	XM_005263432		Approved	CSTN1, KIAA0911, CDHR12	uc001aqh.3	O94985	OTTHUMG00000001451	ENST00000377298.4:c.662delA	1.37:g.9809959delT	ENSP00000366513:p.Asn221fs		9732546	NM_014944	A8K183|Q5SR52|Q5UE58|Q71MN0|Q8N4K9	Frame_Shift_Del	DEL	ENST00000377298.4	37	CCDS30580.1																																																																																				0.408	CLSTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004239.1		
NIPAL3	57185	broad.mit.edu	37	1	24795492	24795492	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:24795492C>T	ENST00000374399.4	+	12	1406	c.1038C>T	c.(1036-1038)caC>caT	p.H346H	NIPAL3_ENST00000003912.3_Silent_p.H264H	NM_020448.4	NP_065181.1	Q6P499	NPAL3_HUMAN	NIPA-like domain containing 3	346						integral component of membrane (GO:0016021)	magnesium ion transmembrane transporter activity (GO:0015095)	p.H346H(1)		endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|skin(1)	14						AGAACATGCACGATAAAGGGA	0.483																																					p.H346H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1038T	1						.						132.0	129.0	130.0					1																	24795492		2203	4300	6503	24668079	SO:0001819	synonymous_variant	57185	exon12			BX640883	CCDS30631.1	1p36.12-p35.1	2009-03-24		2009-03-24	ENSG00000001461	ENSG00000001461			25233	protein-coding gene	gene with protein product				NPAL3		8619474, 9110174	Standard	NM_020448		Approved	DJ462O23.2	uc001bjh.3	Q6P499	OTTHUMG00000003299	ENST00000374399.4:c.1038C>T	1.37:g.24795492C>T			24668079	NM_020448	A2A298|Q6MZT9|Q9BVE6	Silent	SNP	ENST00000374399.4	37	CCDS30631.1																																																																																				0.483	NIPAL3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276996.1	NM_020448	
SRRM1	10250	broad.mit.edu	37	1	24977931	24977931	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:24977931C>T	ENST00000323848.9	+	6	868	c.553C>T	c.(553-555)Cga>Tga	p.R185*	SRRM1_ENST00000537199.1_Intron|SRRM1_ENST00000447431.2_Nonsense_Mutation_p.R185*|SRRM1_ENST00000479034.1_3'UTR|SRRM1_ENST00000374389.4_Nonsense_Mutation_p.R185*	NM_005839.3	NP_005830.2	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	185	Arg-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.R185*(1)		breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	36		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		CCCTAGAAGACGATCTTCCCC	0.468																																					p.R185X	Ovarian(68;897 1494 3282 17478)											.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C553T	1						.						52.0	54.0	53.0					1																	24977931		2203	4300	6503	24850518	SO:0001587	stop_gained	10250	exon6			AF048977	CCDS255.1	1p36	2010-04-22			ENSG00000133226	ENSG00000133226			16638	protein-coding gene	gene with protein product	"""Ser/Arg-related nuclear matrix protein"", ""plenty of prolines 101-like"""	605975				9531537	Standard	NM_005839		Approved	SRM160, POP101, MGC39488	uc001bjm.3	Q8IYB3	OTTHUMG00000003320	ENST00000323848.9:c.553C>T	1.37:g.24977931C>T	ENSP00000326261:p.Arg185*		24850518	NM_005839	O60585|Q5VVN4	Nonsense_Mutation	SNP	ENST00000323848.9	37	CCDS255.1	.	.	.	.	.	.	.	.	.	.	C	39	7.328000	0.98214	.	.	ENSG00000133226	ENST00000323848;ENST00000447431;ENST00000374389	.	.	.	5.7	5.7	0.88788	.	0.000000	0.49916	D	0.000135	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.9683	16.1539	0.81644	0.1339:0.8661:0.0:0.0	.	.	.	.	X	185	.	ENSP00000326261:R185X	R	+	1	2	SRRM1	24850518	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.876000	0.39588	2.677000	0.91161	0.650000	0.86243	CGA		0.468	SRRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009292.2	NM_005839	
RHCE	6006	broad.mit.edu	37	1	25712264	25712264	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:25712264C>T	ENST00000294413.7	-	7	1069	c.1011G>A	c.(1009-1011)ctG>ctA	p.L337L	RHCE_ENST00000425135.1_Intron|RHCE_ENST00000243186.6_Silent_p.L337L|RHCE_ENST00000374352.2_Silent_p.L321L|RHCE_ENST00000455194.1_Silent_p.L232L|RHCE_ENST00000413854.1_Silent_p.L337L|RHCE_ENST00000349438.4_Intron|RHCE_ENST00000349320.3_Silent_p.L321L|RHCE_ENST00000346452.4_Silent_p.L186L|RHCE_ENST00000340849.4_Silent_p.L232L	NM_020485.4	NP_065231	P18577	RHCE_HUMAN	Rh blood group, CcEe antigens	337						integral component of plasma membrane (GO:0005887)	ammonium transmembrane transporter activity (GO:0008519)	p.L337L(1)		endometrium(8)|large_intestine(6)|lung(3)	17		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0426)|OV - Ovarian serous cystadenocarcinoma(117;2.12e-27)|Colorectal(126;3.16e-08)|COAD - Colon adenocarcinoma(152;1.72e-06)|STAD - Stomach adenocarcinoma(196;0.00035)|KIRC - Kidney renal clear cell carcinoma(1967;0.000769)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|GBM - Glioblastoma multiforme(114;0.00458)|READ - Rectum adenocarcinoma(331;0.0649)		TCTCTCCAAGCAGACCCAGCA	0.512																																					p.L232L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G696A	1						.						281.0	221.0	241.0					1																	25712264		2203	4300	6503	25584851	SO:0001819	synonymous_variant	6006	exon5			BC075081	CCDS30634.1, CCDS30635.1, CCDS30636.1, CCDS30637.1	1p36.11	2014-09-17	2006-02-23		ENSG00000188672	ENSG00000188672		"""CD molecules"", ""Blood group antigens"""	10008	protein-coding gene	gene with protein product		111700	"""Rhesus blood group, CcEe antigens"""	RH		8220426	Standard	NM_138618		Approved	CD240CE	uc001bkf.3	P18577	OTTHUMG00000007650	ENST00000294413.7:c.1011G>A	1.37:g.25712264C>T			25584851	NM_138617	A7DW68|B7UDF3|B7UDF4|B7UDF5|B7UDF6|B7UDF7|B7UDF8|B7UDF9|B7UDG0|B7UDG1|B7UDG2|B7UDG3|Q02163|Q02164|Q02165|Q16160|Q2MJW0|Q2VC86|Q3LTM6|Q6AZX5|Q6J2U3|Q7RU06|Q8IZT2|Q8IZT3|Q8IZT4|Q8IZT5|Q9UD13|Q9UD14|Q9UD15|Q9UD16|Q9UD73|Q9UD74|Q9UEC2|Q9UEC3|Q9UPN0	Silent	SNP	ENST00000294413.7	37	CCDS30635.1	.	.	.	.	.	.	.	.	.	.	c	3.841	-0.033884	0.07543	.	.	ENSG00000188672	ENST00000447203	.	.	.	4.91	-2.14	0.07123	.	.	.	.	.	T	0.49304	0.1549	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40627	-0.9553	5	0.35671	T	0.21	-17.5537	4.3355	0.11083	0.2247:0.312:0.3857:0.0776	.	.	.	.	T	337	.	ENSP00000388555:A337T	A	-	1	0	RHCE	25584851	0.996000	0.38824	0.717000	0.30585	0.365000	0.29674	0.145000	0.16157	-0.631000	0.05560	0.555000	0.69702	GCT		0.512	RHCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020312.2	NM_020485	
UBXN11	91544	broad.mit.edu	37	1	26608890	26608891	+	Frame_Shift_Del	DEL	CC	CC	-	rs376181141		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	CC	CC	CC	-	CC	-	Unknown	Valid	Germline	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:26608890_26608891delCC	ENST00000374222.1	-	16	1926_1927	c.1462_1463delGG	c.(1462-1464)ggtfs	p.G488fs	UBXN11_ENST00000374221.3_Frame_Shift_Del_p.G488fs|UBXN11_ENST00000314675.7_Frame_Shift_Del_p.G368fs|UBXN11_ENST00000357089.4_Frame_Shift_Del_p.G455fs|UBXN11_ENST00000374223.1_Frame_Shift_Del_p.G245fs|UBXN11_ENST00000374217.2_Frame_Shift_Del_p.G455fs			Q5T124	UBX11_HUMAN	UBX domain protein 11	488	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.		Missing.|Missing. {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						gggaccgggaccgggacaggga	0.713																																					p.368_368del												.	.	0			c.1102_1103del	1						.																																			26481478	SO:0001589	frameshift_variant	91544	exon11			AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"""UBX domain containing"""	30600	protein-coding gene	gene with protein product	"""socius"""	609151	"""UBX domain containing 5"""	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1462_1463delGG	1.37:g.26608890_26608891delCC	ENSP00000363339:p.Gly488fs		26481477	NM_001077262	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Frame_Shift_Del	DEL	ENST00000374222.1	37	CCDS41288.1																																																																																				0.713	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
UBXN11	91544	broad.mit.edu	37	1	26608893	26608896	+	Frame_Shift_Del	DEL	GGAC	GGAC	-	rs72872911|rs367932248|rs534102934	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	GGAC	GGAC	GGAC	-	GGAC	-	Unknown	Valid	Germline	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:26608893_26608896delGGAC	ENST00000374222.1	-	16	1921_1924	c.1457_1460delGTCC	c.(1456-1461)tgtcccfs	p.CP486fs	UBXN11_ENST00000374221.3_Frame_Shift_Del_p.CP486fs|UBXN11_ENST00000314675.7_Frame_Shift_Del_p.CP366fs|UBXN11_ENST00000357089.4_Frame_Shift_Del_p.CP453fs|UBXN11_ENST00000374223.1_Frame_Shift_Del_p.CP243fs|UBXN11_ENST00000374217.2_Frame_Shift_Del_p.CP453fs			Q5T124	UBX11_HUMAN	UBX domain protein 11	486	Pro-rich.		C -> CPGPGPGPS. {ECO:0000269|PubMed:15498874}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						accgggaccgggacagggaccagg	0.716																																					p.366_367del												.	.	0			c.1097_1100del	1						.																																			26481483	SO:0001589	frameshift_variant	91544	exon11			AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"""UBX domain containing"""	30600	protein-coding gene	gene with protein product	"""socius"""	609151	"""UBX domain containing 5"""	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1457_1460delGTCC	1.37:g.26608893_26608896delGGAC	ENSP00000363339:p.Cys486fs		26481480	NM_001077262	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Frame_Shift_Del	DEL	ENST00000374222.1	37	CCDS41288.1																																																																																				0.716	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
KDF1	126695	broad.mit.edu	37	1	27277924	27277924	+	Silent	SNP	C	C	T	rs374737581		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:27277924C>T	ENST00000320567.5	-	2	1036	c.948G>A	c.(946-948)tcG>tcA	p.S316S		NM_152365.2	NP_689578.2	Q8NAX2	KDF1_HUMAN		316					developmental growth (GO:0048589)|establishment of skin barrier (GO:0061436)|keratinocyte development (GO:0003334)|limb epidermis development (GO:0060887)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of stem cell proliferation (GO:2000647)|positive regulation of epidermal cell differentiation (GO:0045606)|regulation of epidermal cell division (GO:0010482)	cell cortex (GO:0005938)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)		p.S316S(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;3.37e-51)|OV - Ovarian serous cystadenocarcinoma(117;2.22e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)		AACGACCCTCCGAGGTCTGTG	0.637													C|||	1	0.000199681	0.0	0.0	5008	,	,		17652	0.001		0.0	False		,,,				2504	0.0				p.S316S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G948A	1						.	C		0,4406		0,0,2203	36.0	38.0	37.0		948	-10.0	0.3	1		37	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	C1orf172	NM_152365.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		316/399	27277924	1,13005	2203	4300	6503	27150511	SO:0001819	synonymous_variant	126695	exon2																														ENST00000320567.5:c.948G>A	1.37:g.27277924C>T			27150511	NM_152365	Q5QP32|Q8N0S7	Silent	SNP	ENST00000320567.5	37	CCDS293.1																																																																																				0.637	C1orf172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012340.1		
MAP3K6	9064	broad.mit.edu	37	1	27684808	27684808	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:27684808C>T	ENST00000493901.1	-	22	3018	c.2779G>A	c.(2779-2781)Gcc>Acc	p.A927T	MAP3K6_ENST00000357582.2_Missense_Mutation_p.A927T|MAP3K6_ENST00000374040.3_Missense_Mutation_p.A919T	NM_004672.3	NP_004663.3	O95382	M3K6_HUMAN	mitogen-activated protein kinase kinase kinase 6	927					activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)	p.A919T(1)		breast(4)|central_nervous_system(2)|lung(3)|ovary(1)	10		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.69e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00132)|KIRC - Kidney renal clear cell carcinoma(1967;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		GCAGAAGGGGCATCTGAGGGA	0.642											OREG0013282	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A927T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2779A	1						.						79.0	90.0	86.0					1																	27684808		2203	4300	6503	27557395	SO:0001583	missense	9064	exon21			AF100318	CCDS299.1, CCDS72738.1	1p36.11	2011-06-09			ENSG00000142733	ENSG00000142733		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6858	protein-coding gene	gene with protein product	"""apoptosis signal regulating kinase 2"""	604468				9875215	Standard	XM_005246029		Approved	MAPKKK6, ASK2, MEKK6	uc001bny.1	O95382	OTTHUMG00000004631	ENST00000493901.1:c.2779G>A	1.37:g.27684808C>T	ENSP00000419591:p.Ala927Thr	796	27557395	NM_004672	A2ACE8|A2VDG4|A2VDG5|Q59HF4|Q5SSD4|Q75PK3|Q96B75	Missense_Mutation	SNP	ENST00000493901.1	37	CCDS299.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	7.190|7.190	0.591270|0.591270	0.13812|0.13812	.|.	.|.	ENSG00000142733|ENSG00000142733	ENST00000374040;ENST00000493901;ENST00000545447;ENST00000357582|ENST00000472410	T;T;T|.	0.24350|.	1.86;1.86;1.86|.	4.82|4.82	-0.528|-0.528	0.11905|0.11905	Protein kinase-like domain (1);|.	.|.	.|.	.|.	.|.	T|T	0.16727|0.16727	0.0402|0.0402	N|N	0.12182|0.12182	0.205|0.205	0.09310|0.09310	N|N	1|1	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.04013|.	0.001;0.0|.	T|T	0.27157|0.27157	-1.0082|-1.0082	9|5	0.09084|.	T|.	0.74|.	.|.	4.2395|4.2395	0.10642|0.10642	0.0:0.4522:0.1657:0.3821|0.0:0.4522:0.1657:0.3821	.|.	919;927|.	O95382-3;O95382|.	.;M3K6_HUMAN|.	T|I	919;927;650;927|650	ENSP00000363152:A919T;ENSP00000419591:A927T;ENSP00000350195:A927T|.	ENSP00000350195:A927T|.	A|M	-|-	1|3	0|0	MAP3K6|MAP3K6	27557395|27557395	0.005000|0.005000	0.15991|0.15991	0.030000|0.030000	0.17652|0.17652	0.558000|0.558000	0.35554|0.35554	-0.272000|-0.272000	0.08560|0.08560	0.254000|0.254000	0.21573|0.21573	0.650000|0.650000	0.86243|0.86243	GCC|ATG		0.642	MAP3K6-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013469.2	NM_004672	
EYA3	2140	broad.mit.edu	37	1	28365415	28365415	+	Splice_Site	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:28365415A>G	ENST00000373871.3	-	5	399	c.159T>C	c.(157-159)atT>atC	p.I53I	EYA3_ENST00000373863.3_Splice_Site_p.I53I|EYA3_ENST00000373864.1_5'UTR|EYA3_ENST00000471498.1_5'UTR|EYA3_ENST00000545175.1_5'UTR|EYA3_ENST00000540618.1_Splice_Site_p.I53I|EYA3_ENST00000436342.2_5'UTR	NM_001282561.1|NM_001282562.1	NP_001269490.1|NP_001269491.1	Q99504	EYA3_HUMAN	EYA transcriptional coactivator and phosphatase 3	53					anatomical structure morphogenesis (GO:0009653)|double-strand break repair (GO:0006302)|histone dephosphorylation (GO:0016576)|multicellular organismal development (GO:0007275)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of DNA repair (GO:0045739)|regulation of transcription, DNA-templated (GO:0006355)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.I53I(1)		breast(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	15		Colorectal(325;3.46e-05)|all_lung(284;0.000414)|Lung NSC(340;0.000432)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0484)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;2.8e-06)|STAD - Stomach adenocarcinoma(196;0.00364)|KIRC - Kidney renal clear cell carcinoma(1967;0.00378)|BRCA - Breast invasive adenocarcinoma(304;0.00718)|READ - Rectum adenocarcinoma(331;0.0642)		TGCATGTCATAACTGAAAGAA	0.328																																					p.I53I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T159C	1						.						94.0	93.0	93.0					1																	28365415		2203	4300	6503	28238002	SO:0001630	splice_region_variant	2140	exon5			U81602	CCDS316.1, CCDS60050.1, CCDS60051.1, CCDS60052.1	1p36	2014-06-19	2014-06-19		ENSG00000158161	ENSG00000158161		"""Protein tyrosine phosphatases / Asp-based PTPs"""	3521	protein-coding gene	gene with protein product		601655	"""eyes absent (Drosophila) homolog 3"", ""eyes absent homolog 3 (Drosophila)"""			9020840	Standard	NM_001990		Approved	DKFZp686C132	uc001bpi.2	Q99504	OTTHUMG00000003916	ENST00000373871.3:c.158-1T>C	1.37:g.28365415A>G			28238002	NM_001990	A8K190|B4DIR7|B4DNZ7|O95463|Q8IVX7|Q99813	Silent	SNP	ENST00000373871.3	37	CCDS316.1																																																																																				0.328	EYA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011184.1	NM_001990	Silent
SERINC2	347735	broad.mit.edu	37	1	31897608	31897608	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:31897608T>C	ENST00000373709.3	+	3	430	c.280T>C	c.(280-282)Tac>Cac	p.Y94H	SERINC2_ENST00000491976.1_3'UTR|SERINC2_ENST00000373710.1_Missense_Mutation_p.Y103H|SERINC2_ENST00000536859.1_Missense_Mutation_p.Y98H|SERINC2_ENST00000536384.1_Missense_Mutation_p.Y98H	NM_178865.4	NP_849196.2	Q96SA4	SERC2_HUMAN	serine incorporator 2	94					phosphatidylserine metabolic process (GO:0006658)|positive regulation of transferase activity (GO:0051347)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	L-serine transmembrane transporter activity (GO:0015194)	p.Y94H(1)		cervix(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)	12		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0629)|Breast(348;0.0707)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0541)|READ - Rectum adenocarcinoma(331;0.151)		CCTGCTTGGCTACCGCGCTGT	0.662																																					p.Y39H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T115C	1						.						36.0	34.0	35.0					1																	31897608		2203	4299	6502	31670195	SO:0001583	missense	347735	exon4			AY094595	CCDS30662.1, CCDS55583.1, CCDS55584.1, CCDS55585.1	1p35.1	2008-02-05	2005-11-01	2005-11-01	ENSG00000168528	ENSG00000168528			23231	protein-coding gene	gene with protein product		614549	"""tumor differentially expressed 2-like"""	TDE2L		12949800	Standard	NM_178865		Approved	FKSG84, PRO0899, TDE2	uc010ogh.2	Q96SA4	OTTHUMG00000003796	ENST00000373709.3:c.280T>C	1.37:g.31897608T>C	ENSP00000362813:p.Tyr94His		31670195	NM_001199039	A0AVB4|B4DJK5|B7Z567|B7ZAP2|E7EUZ9|Q86Y23	Missense_Mutation	SNP	ENST00000373709.3	37	CCDS30662.1	.	.	.	.	.	.	.	.	.	.	T	14.30	2.495413	0.44352	.	.	ENSG00000168528	ENST00000373710;ENST00000536859;ENST00000373709;ENST00000536384	T;T;T;T	0.15487	2.42;2.42;2.42;2.42	4.3	-1.56	0.08532	.	0.531078	0.20656	N	0.088107	T	0.13756	0.0333	N	0.25332	0.735	0.35589	D	0.806888	B;B;B;B	0.26041	0.14;0.056;0.056;0.028	B;B;B;B	0.37451	0.169;0.25;0.25;0.068	T	0.17289	-1.0374	10	0.48119	T	0.1	-13.284	10.6074	0.45402	0.0:0.7291:0.0:0.2709	.	98;103;98;94	B4DJK5;E7EUZ9;B7Z567;Q96SA4	.;.;.;SERC2_HUMAN	H	103;98;94;98	ENSP00000362814:Y103H;ENSP00000444307:Y98H;ENSP00000362813:Y94H;ENSP00000439048:Y98H	ENSP00000362813:Y94H	Y	+	1	0	SERINC2	31670195	0.973000	0.33851	0.899000	0.35326	0.992000	0.81027	1.346000	0.33964	-0.265000	0.09352	0.533000	0.62120	TAC		0.662	SERINC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010680.1	NM_018565	
TRIM62	55223	broad.mit.edu	37	1	33613287	33613287	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:33613287G>A	ENST00000291416.5	-	5	1152	c.919C>T	c.(919-921)Cgc>Tgc	p.R307C	TRIM62_ENST00000543586.1_Missense_Mutation_p.R186C	NM_018207.2	NP_060677.2	Q9BVG3	TRI62_HUMAN	tripartite motif containing 62	307	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				innate immune response (GO:0045087)|negative regulation of viral transcription (GO:0032897)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral entry into host cell (GO:0046596)|regulation of viral release from host cell (GO:1902186)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.R307C(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0393)				AGGATCAGGCGCTGGTGGGCT	0.632																																					p.R307C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C919T	1						.						48.0	55.0	52.0					1																	33613287		2201	4299	6500	33385874	SO:0001583	missense	55223	exon5			BC007999	CCDS376.1	1p35.1	2013-10-11	2011-01-25		ENSG00000116525	ENSG00000116525		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	25574	protein-coding gene	gene with protein product	"""ductal epithelium-associated RING Chromosome 1"""		"""tripartite motif-containing 62"""			19536326	Standard	NM_018207		Approved	FLJ10759, DEAR1	uc001bxb.3	Q9BVG3	OTTHUMG00000004132	ENST00000291416.5:c.919C>T	1.37:g.33613287G>A	ENSP00000291416:p.Arg307Cys		33385874	NM_018207	B3KVH5|B4DTE4|D3DPR1|Q9NVG0	Missense_Mutation	SNP	ENST00000291416.5	37	CCDS376.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.962971	0.74016	.	.	ENSG00000116525	ENST00000291416;ENST00000373432;ENST00000373430;ENST00000543586	T;T	0.11063	2.81;2.81	5.74	4.81	0.61882	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	0.000000	0.85682	D	0.000000	T	0.15262	0.0368	N	0.10760	0.04	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.28776	-1.0033	10	0.39692	T	0.17	.	13.7557	0.62935	0.0:0.0:0.8452:0.1548	.	307	Q9BVG3	TRI62_HUMAN	C	307;307;307;186	ENSP00000291416:R307C;ENSP00000441173:R186C	ENSP00000291416:R307C	R	-	1	0	TRIM62	33385874	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.290000	0.51755	1.386000	0.46466	0.491000	0.48974	CGC		0.632	TRIM62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011890.1	NM_018207	
SFPQ	6421	broad.mit.edu	37	1	35654934	35654934	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:35654934C>T	ENST00000357214.5	-	5	1563	c.1465G>A	c.(1465-1467)Gaa>Aaa	p.E489K		NM_005066.2	NP_005057.1	P23246	SFPQ_HUMAN	splicing factor proline/glutamine-rich	489					alternative mRNA splicing, via spliceosome (GO:0000380)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H3 deacetylation (GO:0070932)|mRNA processing (GO:0006397)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902177)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|histone deacetylase binding (GO:0042826)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.E489K(1)	SFPQ/TFE3(6)	NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(4)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	25		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.196)				TGAGAATATTCGTACTCAAAC	0.388			T	TFE3	papillary renal cell																																p.E489K			Dom	yes		1	1p34.3	6421	splicing factor proline/glutamine rich(polypyrimidine tract binding protein associated)		E	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1465A	1						.						93.0	79.0	84.0					1																	35654934		2203	4300	6503	35427521	SO:0001583	missense	6421	exon5			X70944	CCDS388.1	1p34.3	2014-06-13	2010-05-04		ENSG00000116560	ENSG00000116560		"""RNA binding motif (RRM) containing"""	10774	protein-coding gene	gene with protein product	"""polypyrimidine tract binding protein associated"", ""protein phosphatase 1, regulatory subunit 140"""	605199	"""splicing factor proline/glutamine rich (polypyrimidine tract-binding protein-associated)"""			8449401	Standard	NM_005066		Approved	PSF, PPP1R140	uc001bys.3	P23246	OTTHUMG00000004157	ENST00000357214.5:c.1465G>A	1.37:g.35654934C>T	ENSP00000349748:p.Glu489Lys		35427521	NM_005066	P30808|Q5SZ71	Missense_Mutation	SNP	ENST00000357214.5	37	CCDS388.1	.	.	.	.	.	.	.	.	.	.	C	37	6.026624	0.97216	.	.	ENSG00000116560	ENST00000357214	T	0.39406	1.08	5.84	5.84	0.93424	NOPS (1);	0.000000	0.85682	D	0.000000	T	0.68339	0.2990	M	0.79258	2.445	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.70249	-0.4924	10	0.87932	D	0	-23.5096	20.1346	0.98019	0.0:1.0:0.0:0.0	.	489	P23246	SFPQ_HUMAN	K	489	ENSP00000349748:E489K	ENSP00000349748:E489K	E	-	1	0	SFPQ	35427521	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	7.770000	0.85390	2.765000	0.95021	0.655000	0.94253	GAA		0.388	SFPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011984.4	NM_005066	
KIAA0319L	79932	broad.mit.edu	37	1	35916002	35916002	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:35916002A>G	ENST00000325722.3	-	14	2405	c.2171T>C	c.(2170-2172)gTc>gCc	p.V724A	KIAA0319L_ENST00000485551.1_5'UTR|KIAA0319L_ENST00000373266.4_Missense_Mutation_p.V161A	NM_024874.4	NP_079150.3	Q8IZA0	K319L_HUMAN	KIAA0319-like	724	PKD 5. {ECO:0000255|PROSITE- ProRule:PRU00151}.					cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.V724A(2)		breast(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(12)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	34		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				GAGGTAGCTGACTATTCCCTT	0.557																																					p.V724A												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T2171C	1						.						131.0	116.0	121.0					1																	35916002		2203	4300	6503	35688589	SO:0001583	missense	79932	exon14			AY163234	CCDS390.1	1p34.3	2008-10-24			ENSG00000142687	ENSG00000142687			30071	protein-coding gene	gene with protein product		613535				11347906	Standard	NM_024874		Approved	KIAA1837	uc001byx.3	Q8IZA0	OTTHUMG00000004370	ENST00000325722.3:c.2171T>C	1.37:g.35916002A>G	ENSP00000318406:p.Val724Ala		35688589	NM_024874	B1AN13|D3DPR8|O95010|Q6PJJ7|Q7L1C9|Q8N2B3|Q8NDA0|Q8WY39|Q8WYZ5|Q96IC3|Q96JJ0|Q9BUW6|Q9H7V0	Missense_Mutation	SNP	ENST00000325722.3	37	CCDS390.1	.	.	.	.	.	.	.	.	.	.	A	19.84	3.902645	0.72754	.	.	ENSG00000142687	ENST00000325722;ENST00000373266;ENST00000426982	T;T;T	0.69685	2.45;-0.42;2.45	5.87	5.87	0.94306	PKD/Chitinase domain (1);Fibronectin, type III (1);PKD/REJ-like protein (1);PKD domain (2);	0.319384	0.34133	N	0.004224	T	0.58104	0.2099	L	0.31752	0.955	0.80722	D	1	P;P;B	0.38745	0.592;0.645;0.085	B;B;B	0.38683	0.183;0.279;0.066	T	0.62205	-0.6903	10	0.54805	T	0.06	-4.9732	15.4585	0.75336	1.0:0.0:0.0:0.0	.	724;724;166	Q8IZA0-2;Q8IZA0;Q8IZA0-3	.;K319L_HUMAN;.	A	724;161;724	ENSP00000318406:V724A;ENSP00000362363:V161A;ENSP00000395883:V724A	ENSP00000318406:V724A	V	-	2	0	KIAA0319L	35688589	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.860000	0.75473	2.247000	0.74100	0.482000	0.46254	GTC		0.557	KIAA0319L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012684.2	NM_024874	
SCMH1	22955	broad.mit.edu	37	1	41494305	41494305	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:41494305C>T	ENST00000326197.7	-	14	2107	c.1808G>A	c.(1807-1809)cGg>cAg	p.R603Q	SCMH1_ENST00000372596.1_Missense_Mutation_p.R520Q|SCMH1_ENST00000361191.5_Missense_Mutation_p.R520Q|SCMH1_ENST00000397174.2_Missense_Mutation_p.R561Q|SCMH1_ENST00000397171.2_Missense_Mutation_p.R520Q|SCMH1_ENST00000337495.5_Missense_Mutation_p.R591Q|SCMH1_ENST00000372595.1_Missense_Mutation_p.R542Q|SCMH1_ENST00000361705.3_Missense_Mutation_p.R534Q|SCMH1_ENST00000456518.2_Missense_Mutation_p.R423Q|SCMH1_ENST00000402904.2_Missense_Mutation_p.R603Q|SCMH1_ENST00000372597.1_Missense_Mutation_p.R534Q|SCMH1_ENST00000472037.1_5'UTR					sex comb on midleg homolog 1 (Drosophila)									p.R534Q(1)|p.R591Q(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(2)|pancreas(2)|upper_aerodigestive_tract(1)	15	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)|Breast(333;0.162)	Myeloproliferative disorder(586;0.0393)				ATCAGCTTCCCGGACAAACTG	0.607																																					p.R520Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1559A	1						.						130.0	109.0	116.0					1																	41494305		2203	4300	6503	41266892	SO:0001583	missense	22955	exon15			AF149045	CCDS461.1, CCDS30688.1, CCDS53301.1, CCDS53302.1, CCDS53303.1, CCDS53304.1	1p34	2013-01-10			ENSG00000010803	ENSG00000010803		"""Sterile alpha motif (SAM) domain containing"""	19003	protein-coding gene	gene with protein product						10524249	Standard	NM_012236		Approved	Scml3	uc001cgs.3	Q96GD3	OTTHUMG00000005720	ENST00000326197.7:c.1808G>A	1.37:g.41494305C>T	ENSP00000318094:p.Arg603Gln		41266892	NM_001172218		Missense_Mutation	SNP	ENST00000326197.7	37	CCDS30688.1	.	.	.	.	.	.	.	.	.	.	C	16.89	3.246901	0.59103	.	.	ENSG00000010803	ENST00000361705;ENST00000456518;ENST00000402904;ENST00000397174;ENST00000397171;ENST00000361191;ENST00000372597;ENST00000372596;ENST00000337495;ENST00000372595;ENST00000326197	T;T;T;T;T;T;T;T;T;T;T	0.50277	0.75;0.75;0.75;0.75;0.75;0.75;0.75;0.75;0.75;0.75;0.75	4.71	3.79	0.43588	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.064498	0.64402	N	0.000018	T	0.51381	0.1671	N	0.17901	0.54	0.32862	D	0.508098	B;P;D;P	0.71674	0.001;0.772;0.998;0.776	B;B;D;B	0.75484	0.004;0.089;0.986;0.36	T	0.58405	-0.7642	10	0.22109	T	0.4	.	15.1181	0.72419	0.0:0.9221:0.0:0.0779	.	423;591;534;603	B4DRQ8;Q96GD3-2;Q96GD3-4;Q96GD3	.;.;.;SCMH1_HUMAN	Q	534;423;603;561;520;520;534;520;591;542;603	ENSP00000354996:R534Q;ENSP00000403974:R423Q;ENSP00000386079:R603Q;ENSP00000380359:R561Q;ENSP00000380356:R520Q;ENSP00000354656:R520Q;ENSP00000361678:R534Q;ENSP00000361677:R520Q;ENSP00000337352:R591Q;ENSP00000361676:R542Q;ENSP00000318094:R603Q	ENSP00000318094:R603Q	R	-	2	0	SCMH1	41266892	0.209000	0.23505	1.000000	0.80357	0.569000	0.35902	2.218000	0.42889	0.706000	0.31912	-1.119000	0.02030	CGG		0.607	SCMH1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015656.1		
HIVEP3	59269	broad.mit.edu	37	1	41990544	41990544	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:41990544G>A	ENST00000372583.1	-	6	6130	c.5245C>T	c.(5245-5247)Cgc>Tgc	p.R1749C	HIVEP3_ENST00000429157.2_Missense_Mutation_p.R1749C|HIVEP3_ENST00000460604.1_Intron|HIVEP3_ENST00000372584.1_Missense_Mutation_p.R1749C|HIVEP3_ENST00000247584.5_Missense_Mutation_p.R1749C	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	1749					positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R1749C(1)		NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				CCTCGGCCGCGGCCTCGCACA	0.507																																					p.R1749C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5245T	1						.						132.0	113.0	119.0					1																	41990544		2203	4300	6503	41763131	SO:0001583	missense	59269	exon6			AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"""Zinc fingers, C2H2-type"""	13561	protein-coding gene	gene with protein product	"""kappabinding protein-1"""	606649	"""human immunodeficiency virus type I enhancer-binding protein 3"""			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.5245C>T	1.37:g.41990544G>A	ENSP00000361664:p.Arg1749Cys		41763131	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Missense_Mutation	SNP	ENST00000372583.1	37	CCDS463.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.403450	0.83230	.	.	ENSG00000127124	ENST00000372584;ENST00000372583;ENST00000247584;ENST00000429157	T;T;T;T	0.11712	2.76;2.75;2.75;2.76	4.85	4.85	0.62838	.	0.000000	0.50627	D	0.000105	T	0.37156	0.0993	M	0.80183	2.485	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.27226	-1.0080	10	0.87932	D	0	-19.7098	17.7486	0.88428	0.0:0.0:1.0:0.0	.	1749;1749	Q5T1R4-2;Q5T1R4	.;ZEP3_HUMAN	C	1749	ENSP00000361665:R1749C;ENSP00000361664:R1749C;ENSP00000247584:R1749C;ENSP00000410828:R1749C	ENSP00000247584:R1749C	R	-	1	0	HIVEP3	41763131	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.439000	0.80444	2.520000	0.84964	0.561000	0.74099	CGC		0.507	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503	
FAM183A	440585	broad.mit.edu	37	1	43613700	43613700	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:43613700G>T	ENST00000335282.4	+	1	78	c.78G>T	c.(76-78)aaG>aaT	p.K26N	FAM183A_ENST00000409337.1_3'UTR|FAM183A_ENST00000410048.1_Intron	NM_001101376.2	NP_001094846.2	A6NL82	F183A_HUMAN	family with sequence similarity 183, member A	26								p.K26N(1)		kidney(1)|large_intestine(1)|lung(2)|ovary(3)	7						TGTACCTCAAGGAGCTACGAA	0.607																																					p.K26N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G78T	1						.						84.0	87.0	86.0					1																	43613700		2025	4174	6199	43386287	SO:0001583	missense	440585	exon1			AI192630, AI375550, AL139138	CCDS44126.1	1p34.2	2008-08-11			ENSG00000186973	ENSG00000186973			34347	protein-coding gene	gene with protein product						11181995	Standard	NM_001101376		Approved	LOC440585, hCG23177	uc009vwo.3	A6NL82	OTTHUMG00000007286	ENST00000335282.4:c.78G>T	1.37:g.43613700G>T	ENSP00000334415:p.Lys26Asn		43386287	NM_001101376	B7ZBL8	Missense_Mutation	SNP	ENST00000335282.4	37	CCDS44126.1	.	.	.	.	.	.	.	.	.	.	G	13.35	2.209893	0.39003	.	.	ENSG00000186973	ENST00000409706;ENST00000409396;ENST00000335282	.	.	.	4.66	-5.87	0.02297	.	0.000000	0.64402	D	0.000003	T	0.75049	0.3797	M	0.83953	2.67	0.35447	D	0.795377	D	0.89917	1.0	D	0.85130	0.997	T	0.79978	-0.1575	9	0.87932	D	0	.	13.7914	0.63143	0.2382:0.0:0.7618:0.0	.	26	A6NL82	F183A_HUMAN	N	26	.	ENSP00000334415:K26N	K	+	3	2	FAM183A	43386287	0.989000	0.36119	0.154000	0.22540	0.015000	0.08874	-0.053000	0.11846	-0.991000	0.03476	-0.242000	0.12053	AAG		0.607	FAM183A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019024.3	NM_001101376	
MED8	112950	broad.mit.edu	37	1	43851779	43851779	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:43851779C>A	ENST00000372457.4	-	6	655	c.612G>T	c.(610-612)caG>caT	p.Q204H	RP1-92O14.6_ENST00000436713.1_RNA|MED8_ENST00000372455.4_Missense_Mutation_p.Q115H|MED8_ENST00000290663.6_Missense_Mutation_p.Q204H	NM_001001653.2|NM_201542.3	NP_001001653.1|NP_963836.2	Q96G25	MED8_HUMAN	mediator complex subunit 8	204					gene expression (GO:0010467)|protein ubiquitination (GO:0016567)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.Q115H(1)		endometrium(2)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)	9	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GCTGGCCTGCCTGGCCAGGAC	0.562																																					p.Q204H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G612T	1						.						148.0	147.0	147.0					1																	43851779		2203	4300	6503	43624366	SO:0001583	missense	112950	exon6			AF521562, BC010543	CCDS486.2, CCDS487.2, CCDS60108.1	1p34.1	2008-02-05	2007-07-30		ENSG00000159479	ENSG00000159479			19971	protein-coding gene	gene with protein product		607956	"""mediator of RNA polymerase II transcription, subunit 8 homolog (S. cerevisiae)"""			12149480, 9671713	Standard	NM_052877		Approved	MGC17544, MGC19641, ARC32	uc001cje.2	Q96G25	OTTHUMG00000007421	ENST00000372457.4:c.612G>T	1.37:g.43851779C>A	ENSP00000361535:p.Gln204His		43624366	NM_052877	A9IZ91|A9IZ92|Q5JUY8|Q96FQ4	Missense_Mutation	SNP	ENST00000372457.4	37	CCDS487.2	.	.	.	.	.	.	.	.	.	.	C	9.454	1.091426	0.20471	.	.	ENSG00000159479	ENST00000290663;ENST00000372457;ENST00000372455	.	.	.	5.9	3.69	0.42338	.	0.128926	0.50627	D	0.000102	T	0.25158	0.0611	N	0.04880	-0.145	0.36532	D	0.870783	B;B	0.11235	0.001;0.004	B;B	0.11329	0.001;0.006	T	0.14559	-1.0468	9	0.12430	T	0.62	-19.1708	6.5926	0.22656	0.1389:0.6429:0.0:0.2181	.	204;204	Q96G25;Q96G25-2	MED8_HUMAN;.	H	204;204;115	.	ENSP00000290663:Q204H	Q	-	3	2	MED8	43624366	0.773000	0.28580	1.000000	0.80357	0.995000	0.86356	-0.117000	0.10708	1.474000	0.48178	0.650000	0.86243	CAG		0.562	MED8-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318959.1	NM_052877	
SZT2	23334	broad.mit.edu	37	1	43903090	43903090	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:43903090G>A	ENST00000562955.1	+	43	6030	c.6030G>A	c.(6028-6030)ctG>ctA	p.L2010L	SZT2_ENST00000372442.1_Silent_p.L1168L	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	2067					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)		p.L1168L(2)		NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						TCCAGGCCCTGCGCTCTGTGC	0.527																																					p.L1168L												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G3504A	1						.						143.0	132.0	135.0					1																	43903090		2203	4300	6503	43675677	SO:0001819	synonymous_variant	23334	exon29			AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"""seizure threshold 2 homolog A (mouse)"", ""seizure threshold 2 homolog B (mouse)"""	615463	"""chromosome 1 open reading frame 84"", ""KIAA0467"""	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.6030G>A	1.37:g.43903090G>A			43675677	NM_015284	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Silent	SNP	ENST00000562955.1	37	CCDS30694.2																																																																																				0.527	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284	
PTPRF	5792	broad.mit.edu	37	1	44064425	44064425	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:44064425G>T	ENST00000359947.4	+	13	2494	c.2154G>T	c.(2152-2154)gaG>gaT	p.E718D	PTPRF_ENST00000496447.1_3'UTR|PTPRF_ENST00000438120.1_Missense_Mutation_p.E718D|PTPRF_ENST00000422171.2_Missense_Mutation_p.E75D|PTPRF_ENST00000372413.3_Missense_Mutation_p.E718D|PTPRF_ENST00000372414.3_Missense_Mutation_p.E718D	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	718	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|negative regulation of receptor binding (GO:1900121)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.E708D(1)		NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)	72	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				TGGAGGTGGAGCCACTGAACT	0.637																																					p.E718D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2154T	1						.						63.0	60.0	61.0					1																	44064425		2203	4300	6503	43837012	SO:0001583	missense	5792	exon13			Y00815	CCDS489.2, CCDS490.2	1p34	2013-02-11			ENSG00000142949	ENSG00000142949		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9670	protein-coding gene	gene with protein product		179590		LAR		7558042	Standard	NM_130440		Approved		uc001cjr.3	P10586	OTTHUMG00000007501	ENST00000359947.4:c.2154G>T	1.37:g.44064425G>T	ENSP00000353030:p.Glu718Asp		43837012	NM_130440	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Missense_Mutation	SNP	ENST00000359947.4	37	CCDS489.2	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	10.16|10.16|10.16	1.274055|1.274055|1.274055	0.23221|0.23221|0.23221	.|.|.	.|.|.	ENSG00000142949|ENSG00000142949|ENSG00000142949	ENST00000412568;ENST00000414879|ENST00000359947;ENST00000438120;ENST00000372414;ENST00000372413;ENST00000422171|ENST00000429895	.|T;T;T;T;T|.	.|0.57595|.	.|0.39;0.39;0.39;0.39;0.39|.	4.35|4.35|4.35	0.0817|0.0817|0.0817	0.14425|0.14425|0.14425	.|Fibronectin, type III (4);Immunoglobulin-like fold (1);|.	.|0.000000|.	.|0.34580|.	.|N|.	.|0.003856|.	T|T|T	0.41696|0.41696|0.41696	0.1170|0.1170|0.1170	L|L|L	0.35793|0.35793|0.35793	1.09|1.09|1.09	0.52099|0.52099|0.52099	D|D|D	0.999949|0.999949|0.999949	.|B;B;B;B;B|.	.|0.14805|.	.|0.002;0.0;0.011;0.0;0.0|.	.|B;B;B;B;B|.	.|0.24006|.	.|0.013;0.004;0.05;0.0;0.012|.	T|T|T	0.12293|0.12293|0.12293	-1.0553|-1.0553|-1.0553	5|10|5	.|0.25106|.	.|T|.	.|0.35|.	.|.|.	5.1902|5.1902|5.1902	0.15205|0.15205|0.15205	0.4346:0.142:0.4234:0.0|0.4346:0.142:0.4234:0.0|0.4346:0.142:0.4234:0.0	.|.|.	.|374;75;477;718;718|.	.|Q59FI2;F2Z3B8;Q5W9G3;P10586-2;P10586|.	.|.;.;.;.;PTPRF_HUMAN|.	S|D|I	284;141|718;718;718;718;75|375	.|ENSP00000353030:E718D;ENSP00000398822:E718D;ENSP00000361491:E718D;ENSP00000361490:E718D;ENSP00000387885:E75D|.	.|ENSP00000353030:E718D|.	A|E|S	+|+|+	1|3|2	0|2|0	PTPRF|PTPRF|PTPRF	43837012|43837012|43837012	0.544000|0.544000|0.544000	0.26441|0.26441|0.26441	0.938000|0.938000|0.938000	0.37757|0.37757|0.37757	0.953000|0.953000|0.953000	0.61014|0.61014|0.61014	0.023000|0.023000|0.023000	0.13533|0.13533|0.13533	-0.191000|-0.191000|-0.191000	0.10448|0.10448|0.10448	0.449000|0.449000|0.449000	0.29647|0.29647|0.29647	GCC|GAG|AGC		0.637	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1		
KDM4A	9682	broad.mit.edu	37	1	44163576	44163576	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:44163576C>T	ENST00000372396.3	+	19	2867	c.2733C>T	c.(2731-2733)aaC>aaT	p.N911N	KDM4A-AS1_ENST00000398804.3_RNA|KDM4A-AS1_ENST00000439057.1_RNA	NM_014663.2	NP_055478.2	O75164	KDM4A_HUMAN	lysine (K)-specific demethylase 4A	911	Tudor 1.				cardiac muscle hypertrophy in response to stress (GO:0014898)|histone demethylation (GO:0016577)|histone H3-K36 demethylation (GO:0070544)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K36 specific) (GO:0051864)|methylated histone binding (GO:0035064)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.N911N(1)		breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(13)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	37						AGCATAAGAACGGGCGCTTCT	0.502																																					p.N911N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2733T	1						.						115.0	112.0	113.0					1																	44163576		2203	4300	6503	43936163	SO:0001819	synonymous_variant	9682	exon19			AB014577	CCDS491.1	1p34.1	2013-01-23	2009-04-06	2009-04-06	ENSG00000066135	ENSG00000066135		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	22978	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 3A"", ""tudor domain containing 14A"""	609764	"""jumonji domain containing 2"", ""jumonji domain containing 2A"""	JMJD2, JMJD2A		9734811, 15138608	Standard	XM_005271354		Approved	KIAA0677, JHDM3A, TDRD14A	uc001cjx.3	O75164	OTTHUMG00000007560	ENST00000372396.3:c.2733C>T	1.37:g.44163576C>T			43936163	NM_014663	Q5VVB1	Silent	SNP	ENST00000372396.3	37	CCDS491.1																																																																																				0.502	KDM4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019960.1	NM_014663	
HECTD3	79654	broad.mit.edu	37	1	45469565	45469565	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:45469565G>A	ENST00000372172.4	-	19	2462	c.2391C>T	c.(2389-2391)cgC>cgT	p.R797R	HECTD3_ENST00000372168.3_Silent_p.R407R|HECTD3_ENST00000486132.1_5'UTR	NM_024602.5	NP_078878.3	Q5T447	HECD3_HUMAN	HECT domain containing E3 ubiquitin protein ligase 3	797	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.R797R(1)|p.R407R(1)|p.R513R(1)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|stomach(1)	28	Acute lymphoblastic leukemia(166;0.155)					GTGCTGGCAGGCGACTGCGGC	0.622																																					p.R797R												.	.	3	Substitution - coding silent(3)	large_intestine(3)	c.C2391T	1						.						41.0	49.0	46.0					1																	45469565		2062	4182	6244	45242152	SO:0001819	synonymous_variant	79654	exon19			BC019105	CCDS41318.1	1p34.1	2012-02-23	2012-02-23		ENSG00000126107	ENSG00000126107			26117	protein-coding gene	gene with protein product			"""HECT domain containing 3"""			12477932	Standard	NM_024602		Approved	FLJ21156	uc009vxk.3	Q5T447	OTTHUMG00000008587	ENST00000372172.4:c.2391C>T	1.37:g.45469565G>A			45242152	NM_024602	B3KPV7|B3KRH4|Q5T448|Q9H783	Silent	SNP	ENST00000372172.4	37	CCDS41318.1																																																																																				0.622	HECTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023734.1	NM_024602	
TESK2	10420	broad.mit.edu	37	1	45923268	45923268	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:45923268delT	ENST00000372086.3	-	2	590	c.190delA	c.(190-192)atafs	p.I64fs	TESK2_ENST00000451835.2_Frame_Shift_Del_p.I64fs|TESK2_ENST00000372084.1_Frame_Shift_Del_p.I64fs|TESK2_ENST00000341771.6_Frame_Shift_Del_p.I64fs|TESK2_ENST00000486676.1_5'UTR|TESK2_ENST00000538496.1_Intron	NM_007170.2	NP_009101.2	Q96S53	TESK2_HUMAN	testis-specific kinase 2	64	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|focal adhesion assembly (GO:0048041)|protein phosphorylation (GO:0006468)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)	p.I64fs*1(1)		breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(9)|ovary(2)|pancreas(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	32	Acute lymphoblastic leukemia(166;0.155)					CCAGACCCTATTTTTTCACAG	0.433																																					p.I64X												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.190delA	1						.						106.0	101.0	103.0					1																	45923268		1873	4103	5976	45695855	SO:0001589	frameshift_variant	10420	exon2			AJ132545	CCDS41323.1	1p32	2010-04-27			ENSG00000070759	ENSG00000070759	2.7.12.1		11732	protein-coding gene	gene with protein product		604746				10512679	Standard	NM_007170		Approved		uc001cns.1	Q96S53	OTTHUMG00000007680	ENST00000372086.3:c.190delA	1.37:g.45923268delT	ENSP00000361158:p.Ile64fs		45695855	NM_007170	Q5T422|Q5T423|Q8N520|Q9Y3Q6	Frame_Shift_Del	DEL	ENST00000372086.3	37	CCDS41323.1																																																																																				0.433	TESK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020523.1	NM_007170	
POMGNT1	55624	broad.mit.edu	37	1	46660030	46660030	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:46660030G>A	ENST00000371984.3	-	9	952	c.795C>T	c.(793-795)cgC>cgT	p.R265R	POMGNT1_ENST00000485714.1_5'Flank|POMGNT1_ENST00000371992.1_Silent_p.R265R|POMGNT1_ENST00000535522.1_Silent_p.R243R|POMGNT1_ENST00000396420.3_3'UTR|POMGNT1_ENST00000371986.3_Silent_p.R265R	NM_017739.3	NP_060209	Q8WZA1	PMGT1_HUMAN	protein O-linked mannose N-acetylglucosaminyltransferase 1 (beta 1,2-)	265	Poly-Arg.		R -> H (in MDDGA3; found on the same allele as Q-311; unknown pathological significance). {ECO:0000269|PubMed:15236414}.		protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity (GO:0047223)	p.R265R(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	20	Acute lymphoblastic leukemia(166;0.155)					AGAAGCGCCGGCGGCGACGGT	0.602																																					p.R265R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C795T	1						.						83.0	83.0	83.0					1																	46660030		2203	4300	6503	46432617	SO:0001819	synonymous_variant	55624	exon9				CCDS531.1, CCDS57995.1	1p34.1	2014-09-17	2013-07-31		ENSG00000085998	ENSG00000085998	2.4.1.-	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	19139	protein-coding gene	gene with protein product	"""protein O-mannose beta-1,2-N-acetylglucosaminyltransferase"""	606822	"""muscle-eye-brain disease"", ""protein O-linked mannose beta1,2-N-acetylglucosaminyltransferase"""	MEB		11742540, 12788071	Standard	NM_017739		Approved	FLJ20277, MGAT1.2, LGMD2O	uc001cpg.3	Q8WZA1	OTTHUMG00000007604	ENST00000371984.3:c.795C>T	1.37:g.46660030G>A			46432617	NM_017739	D3DQ16|Q5VST2|Q5VST3|Q9BV55|Q9H9L8|Q9NXF9|Q9NYF7	Silent	SNP	ENST00000371984.3	37	CCDS531.1																																																																																				0.602	POMGNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020146.1	NM_017739	
PGM1	5236	broad.mit.edu	37	1	64095186	64095186	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:64095186A>G	ENST00000371084.3	+	2	550	c.337A>G	c.(337-339)Att>Gtt	p.I113V	PGM1_ENST00000371083.4_Missense_Mutation_p.I131V|PGM1_ENST00000540265.1_5'UTR	NM_002633.2	NP_002624.2	P36871	PGM1_HUMAN	phosphoglucomutase 1	113					carbohydrate metabolic process (GO:0005975)|galactose catabolic process (GO:0019388)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	magnesium ion binding (GO:0000287)|phosphoglucomutase activity (GO:0004614)	p.I113V(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20						TGGTGGGATCATTCTGACAGC	0.463																																					p.I131V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A391G	1						.						112.0	123.0	119.0					1																	64095186		2203	4300	6503	63867774	SO:0001583	missense	5236	exon2			BC019920	CCDS625.1, CCDS53323.1, CCDS53324.1	1p22.1	2012-10-02			ENSG00000079739	ENSG00000079739	5.4.2.2		8905	protein-coding gene	gene with protein product		171900				4517931, 1530890	Standard	NM_002633		Approved		uc010ooz.2	P36871	OTTHUMG00000008968	ENST00000371084.3:c.337A>G	1.37:g.64095186A>G	ENSP00000360125:p.Ile113Val		63867774	NM_001172818	B2R5N9|B4DPV0|Q16105|Q16106|Q5BKZ9|Q6NW22|Q86U74|Q96J40|Q9NTY4	Missense_Mutation	SNP	ENST00000371084.3	37	CCDS625.1	.	.	.	.	.	.	.	.	.	.	A	18.73	3.685885	0.68157	.	.	ENSG00000079739	ENST00000538673;ENST00000371084;ENST00000371083	T;T	0.62941	-0.01;-0.01	5.48	5.48	0.80851	Alpha-D-phosphohexomutase, alpha/beta/alpha domain I (1);Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III (2);Alpha-D-phosphohexomutase, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.31544	0.0800	N	0.16266	0.395	0.80722	D	1	P;B	0.38473	0.633;0.063	B;B	0.35655	0.207;0.086	T	0.25363	-1.0134	10	0.26408	T	0.33	-16.5709	15.8924	0.79309	1.0:0.0:0.0:0.0	.	131;113	P36871-2;P36871	.;PGM1_HUMAN	V	89;113;131	ENSP00000360125:I113V;ENSP00000360124:I131V	ENSP00000360124:I131V	I	+	1	0	PGM1	63867774	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.210000	0.95106	2.210000	0.71456	0.533000	0.62120	ATT		0.463	PGM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024868.1	NM_002633	
ASB17	127247	broad.mit.edu	37	1	76397587	76397587	+	Silent	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:76397587T>C	ENST00000284142.6	-	1	529	c.390A>G	c.(388-390)gcA>gcG	p.A130A		NM_080868.2	NP_543144.1	Q8WXJ9	ASB17_HUMAN	ankyrin repeat and SOCS box containing 17	130					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)			p.A130A(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(11)|ovary(2)|urinary_tract(1)	21						TCCATATCAGTGCCAGGTTAC	0.338																																					p.A130A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A390G	1						.						49.0	48.0	48.0					1																	76397587		2203	4299	6502	76170175	SO:0001819	synonymous_variant	127247	exon1			AF403035	CCDS671.1	1p22.3	2013-01-11	2011-01-25		ENSG00000154007	ENSG00000154007		"""Ankyrin repeat domain containing"""	19769	protein-coding gene	gene with protein product			"""ankyrin repeat and SOCS box-containing 17"""			12076535	Standard	NM_080868		Approved		uc001dhe.2	Q8WXJ9	OTTHUMG00000009787	ENST00000284142.6:c.390A>G	1.37:g.76397587T>C			76170175	NM_080868	B1APB8|Q8N0X5	Silent	SNP	ENST00000284142.6	37	CCDS671.1																																																																																				0.338	ASB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026982.1	NM_080868	
ELTD1	64123	broad.mit.edu	37	1	79357326	79357326	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:79357326C>A	ENST00000370742.3	-	14	1956	c.1893G>T	c.(1891-1893)tgG>tgT	p.W631C		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	631					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.W631C(1)		NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		CCCCAAAGATCCAGGTGGTGC	0.468																																					p.W631C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1893T	1						.						65.0	65.0	65.0					1																	79357326		1969	4142	6111	79129914	SO:0001583	missense	64123	exon14			AF192403	CCDS41352.1	1p33-p32	2014-08-08			ENSG00000162618	ENSG00000162618		"""-"", ""GPCR / Class B : Orphans"""	20822	protein-coding gene	gene with protein product						11050079	Standard	NM_022159		Approved	ETL	uc001diq.4	Q9HBW9	OTTHUMG00000009738	ENST00000370742.3:c.1893G>T	1.37:g.79357326C>A	ENSP00000359778:p.Trp631Cys		79129914	NM_022159	B1AR71|Q5KU34	Missense_Mutation	SNP	ENST00000370742.3	37	CCDS41352.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.301679	0.81136	.	.	ENSG00000162618	ENST00000370742;ENST00000401034	T;T	0.59224	0.28;0.28	5.59	5.59	0.84812	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	D	0.84534	0.5493	H	0.98178	4.165	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90055	0.4152	9	.	.	.	.	19.5833	0.95478	0.0:1.0:0.0:0.0	.	631	Q9HBW9	ELTD1_HUMAN	C	631;89	ENSP00000359778:W631C;ENSP00000383813:W89C	.	W	-	3	0	ELTD1	79129914	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.792000	0.85828	2.612000	0.88384	0.655000	0.94253	TGG		0.468	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159	
GTF2B	2959	broad.mit.edu	37	1	89323159	89323159	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:89323159C>T	ENST00000370500.5	-	6	665	c.547G>A	c.(547-549)Gta>Ata	p.V183I	GTF2B_ENST00000494819.1_5'UTR	NM_001514.5	NP_001505.1	Q00403	TF2B_HUMAN	general transcription factor IIB	183					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	nucleoplasm (GO:0005654)	core promoter binding (GO:0001047)|thyroid hormone receptor binding (GO:0046966)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.V183I(1)		endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	10		Lung NSC(277;0.123)		all cancers(265;0.0131)|Epithelial(280;0.0255)		ATTCGTGATACGGCACATATT	0.289																																					p.V183I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G547A	1						.						27.0	28.0	28.0					1																	89323159		2203	4299	6502	89095747	SO:0001583	missense	2959	exon6			M76766	CCDS715.1	1p22-p21	2010-03-23			ENSG00000137947	ENSG00000137947		"""General transcription factors"""	4648	protein-coding gene	gene with protein product		189963				1876184, 8162052	Standard	NM_001514		Approved	TFIIB	uc001dmo.4	Q00403	OTTHUMG00000010611	ENST00000370500.5:c.547G>A	1.37:g.89323159C>T	ENSP00000359531:p.Val183Ile		89095747	NM_001514	A8K1A7|Q5JS30	Missense_Mutation	SNP	ENST00000370500.5	37	CCDS715.1	.	.	.	.	.	.	.	.	.	.	C	16.23	3.065152	0.55432	.	.	ENSG00000137947	ENST00000370500;ENST00000448623;ENST00000418217	T;T;T	0.52526	0.75;0.66;0.72	5.53	4.61	0.57282	Transcription factor TFIIB, cyclin-related (1);Cyclin-like (3);	0.000000	0.85682	D	0.000000	T	0.24392	0.0591	L	0.37466	1.105	0.80722	D	1	B	0.22909	0.077	B	0.23716	0.048	T	0.07597	-1.0764	10	0.38643	T	0.18	-41.1916	14.4108	0.67113	0.0:0.9291:0.0:0.0709	.	183	Q00403	TF2B_HUMAN	I	183;182;178	ENSP00000359531:V183I;ENSP00000415741:V182I;ENSP00000402345:V178I	ENSP00000359531:V183I	V	-	1	0	GTF2B	89095747	1.000000	0.71417	0.900000	0.35374	0.990000	0.78478	7.361000	0.79497	1.467000	0.48044	0.561000	0.74099	GTA		0.289	GTF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029279.1	NM_001514	
DNTTIP2	30836	broad.mit.edu	37	1	94343217	94343217	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:94343217A>G	ENST00000436063.2	-	2	331	c.274T>C	c.(274-276)Tca>Cca	p.S92P	DNTTIP2_ENST00000460191.1_5'UTR	NM_014597.4	NP_055412.2	Q5QJE6	TDIF2_HUMAN	deoxynucleotidyltransferase, terminal, interacting protein 2	92					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.S92P(1)		NS(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	38		all_lung(203;0.0111)|Lung NSC(277;0.0347)		all cancers(265;0.00679)|GBM - Glioblastoma multiforme(16;0.0278)|Epithelial(280;0.128)		GAATAATTTGACTCTGCCTCA	0.453																																					p.S92P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T274C	1						.						102.0	96.0	98.0					1																	94343217		1917	4123	6040	94115805	SO:0001583	missense	30836	exon2			AY394925	CCDS44174.1	1p22.1	2008-02-05			ENSG00000067334	ENSG00000067334			24013	protein-coding gene	gene with protein product	"""acidic 82 kDa protein mRNA"""	611199				15047147	Standard	NM_014597		Approved	HSU15552, ERBP, TdIF2	uc001dqf.3	Q5QJE6	OTTHUMG00000010268	ENST00000436063.2:c.274T>C	1.37:g.94343217A>G	ENSP00000411010:p.Ser92Pro		94115805	NM_014597	Q12987|Q53H59|Q5TFJ4|Q6TLI0|Q76MJ8|Q86WX9	Missense_Mutation	SNP	ENST00000436063.2	37	CCDS44174.1	.	.	.	.	.	.	.	.	.	.	A	15.55	2.867273	0.51588	.	.	ENSG00000067334	ENST00000436063;ENST00000528680	T	0.37584	1.19	4.91	3.77	0.43336	.	0.136590	0.33854	N	0.004483	T	0.39384	0.1076	M	0.71581	2.175	0.37034	D	0.896815	D	0.58268	0.982	P	0.58172	0.834	T	0.45086	-0.9285	10	0.87932	D	0	.	9.8491	0.41046	0.8475:0.0:0.0:0.1525	.	92	Q5QJE6	TDIF2_HUMAN	P	92;99	ENSP00000411010:S92P	ENSP00000352137:S92P	S	-	1	0	DNTTIP2	94115805	1.000000	0.71417	0.952000	0.39060	0.685000	0.39939	5.842000	0.69417	0.889000	0.36185	-0.349000	0.07799	TCA		0.453	DNTTIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028317.2	NM_014597	
PLPPR4	9890	broad.mit.edu	37	1	99730225	99730225	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:99730225G>A	ENST00000370185.3	+	1	717	c.220G>A	c.(220-222)Gag>Aag	p.E74K	LPPR4_ENST00000457765.1_Missense_Mutation_p.E74K	NM_014839.4	NP_055654.2	Q7Z2D5	LPPR4_HUMAN		74					axonogenesis (GO:0007409)|inner ear development (GO:0048839)|phospholipid dephosphorylation (GO:0046839)	integral component of plasma membrane (GO:0005887)	lipid phosphatase activity (GO:0042577)|phosphatidate phosphatase activity (GO:0008195)	p.E74K(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(39)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	72		all_epithelial(167;3.54e-06)|all_lung(203;0.00139)|Lung NSC(277;0.00202)		Epithelial(280;0.0736)|all cancers(265;0.0975)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)|Colorectal(170;0.22)		TTATTTCGTCGAGGTGAGTTG	0.597																																					p.E74K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G220A	1						.						25.0	9.0	15.0					1																	99730225		1779	3452	5231	99502813	SO:0001583	missense	9890	exon1																														ENST00000370185.3:c.220G>A	1.37:g.99730225G>A	ENSP00000359204:p.Glu74Lys		99502813	NM_014839	E7EPS1|O75043|Q5T9R9|Q86XQ5|Q8N3F1|Q96MP0	Missense_Mutation	SNP	ENST00000370185.3	37	CCDS757.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.252485	0.80135	.	.	ENSG00000117600	ENST00000370185;ENST00000457765;ENST00000263178	T;T	0.48201	0.82;0.82	4.9	4.9	0.64082	.	0.518300	0.20720	N	0.086921	T	0.50854	0.1640	M	0.62723	1.935	0.54753	D	0.999987	P;P	0.50443	0.912;0.935	B;P	0.52343	0.192;0.696	T	0.56092	-0.8036	10	0.72032	D	0.01	-26.9932	17.0125	0.86410	0.0:0.0:1.0:0.0	.	74;74	E7EPS1;Q7Z2D5	.;LPPR4_HUMAN	K	74	ENSP00000359204:E74K;ENSP00000394913:E74K	ENSP00000263178:E74K	E	+	1	0	RP4-788L13.1	99502813	1.000000	0.71417	0.976000	0.42696	0.930000	0.56654	7.276000	0.78559	2.551000	0.86045	0.561000	0.74099	GAG		0.597	LPPR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029670.2		
CEPT1	10390	broad.mit.edu	37	1	111703836	111703836	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:111703836delT	ENST00000545121.1	+	4	755	c.547delT	c.(547-549)tttfs	p.F184fs	CEPT1_ENST00000357172.4_Frame_Shift_Del_p.F184fs	NM_001007794.1	NP_001007795.1	Q9Y6K0	CEPT1_HUMAN	choline/ethanolamine phosphotransferase 1	184					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	diacylglycerol cholinephosphotransferase activity (GO:0004142)|ethanolaminephosphotransferase activity (GO:0004307)|metal ion binding (GO:0046872)	p.C185fs*26(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)	8		all_cancers(81;2.27e-05)|all_epithelial(167;7.36e-06)|all_lung(203;0.00018)|Lung NSC(277;0.000359)		Lung(183;0.0173)|Colorectal(144;0.0375)|all cancers(265;0.0701)|LUSC - Lung squamous cell carcinoma(189;0.0888)|Epithelial(280;0.103)|COAD - Colon adenocarcinoma(174;0.141)	Choline(DB00122)	TGATTGGATGTTTTTTTGTTG	0.383																																					p.F183fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.547delT	1						.						234.0	234.0	234.0					1																	111703836		2203	4300	6503	111505359	SO:0001589	frameshift_variant	10390	exon4			AF068302	CCDS830.1	1p13	2010-07-08			ENSG00000134255	ENSG00000134255	2.7.8.1, 2.7.8.2		24289	protein-coding gene	gene with protein product						10191259, 12216837	Standard	XM_005270353		Approved		uc001eah.1	Q9Y6K0	OTTHUMG00000012357	ENST00000545121.1:c.547delT	1.37:g.111703836delT	ENSP00000441980:p.Phe184fs		111505359	NM_006090	Q69YJ9|Q9P0Y8	Frame_Shift_Del	DEL	ENST00000545121.1	37	CCDS830.1																																																																																				0.383	CEPT1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034462.2	NM_006090	
PPP1R12B	4660	broad.mit.edu	37	1	202407190	202407190	+	Intron	DEL	T	T	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:202407190delT	ENST00000608999.1	+	10	1611				PPP1R12B_ENST00000356764.2_3'UTR|PPP1R12B_ENST00000336894.4_Intron|RP11-175B9.2_ENST00000602961.1_RNA|PPP1R12B_ENST00000480184.1_Frame_Shift_Del_p.V499fs	NM_001197131.1|NM_002481.3	NP_001184060.1|NP_002472.2	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory subunit 12B						G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of catalytic activity (GO:0043085)|regulation of muscle contraction (GO:0006937)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	enzyme activator activity (GO:0008047)			central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(17)|ovary(4)|skin(3)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(75;0.166)			TCCAAGGCAGTTTTTTTTTTC	0.388																																					p.V499fs												.	.	0			c.1496delT	1						.		,,	92,128,3982		2,0,88,2,124,1885	28.0	30.0	30.0		,,	1.9	0.0	1		31	174,230,7838		0,1,173,13,203,3731	no	intron,utr-3,codingComplex	PPP1R12B	NM_002481.3,NM_001167858.1,NM_001167857.1	,,	2,1,261,15,327,5616	A1A1,A1A2,A1R,A2A2,A2R,RR		4.9017,5.2356,5.0145	,,	,,	202407190	266,358,11820	2202	4300	6502	200673813	SO:0001627	intron_variant	4660	exon10			AB003062	CCDS1426.1, CCDS44294.1, CCDS44295.1, CCDS53458.1, CCDS53459.1, CCDS73005.1	1q32.1	2013-01-10	2011-10-04	2001-08-10	ENSG00000077157	ENSG00000077157		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	7619	protein-coding gene	gene with protein product	"""myosin phosphatase regulatory subunit"", ""myosin phosphatase, target subunit 2"""	603768	"""protein phosphatase 1, regulatory (inhibitor) subunit 12B"""	MYPT2		9570949	Standard	NM_002481		Approved	MGC87886, MGC131980, PP1bp55	uc001gya.2	O60237	OTTHUMG00000041393	ENST00000608999.1:c.1458+38T>-	1.37:g.202407190delT			200673813	NM_001167857	A8MYF5|B7ZMN6|Q2TAI8|Q5T506|Q5VUK2|Q8N179|Q9HCB7|Q9HCB8	Frame_Shift_Del	DEL	ENST00000608999.1	37	CCDS1426.1																																																																																				0.388	PPP1R12B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000099166.3	NM_032105	
OR2T6	254879	broad.mit.edu	37	1	248551360	248551360	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr1:248551360G>A	ENST00000355728.2	+	1	451	c.451G>A	c.(451-453)Ggt>Agt	p.G151S		NM_001005471.1	NP_001005471.1	Q8NHC8	OR2T6_HUMAN	olfactory receptor, family 2, subfamily T, member 6	151						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G151S(1)		endometrium(3)|large_intestine(5)|lung(38)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CTCTTGGTTCGGTGGGGCTTT	0.557																																					p.G151S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G451A	1						.						85.0	80.0	82.0					1																	248551360		2203	4300	6503	246617983	SO:0001583	missense	254879	exon1			AF399481	CCDS31114.1	1q44	2012-08-09		2004-03-10	ENSG00000198104	ENSG00000198104		"""GPCR / Class A : Olfactory receptors"""	15018	protein-coding gene	gene with protein product				OR2T6P, OR2T9			Standard	NM_001005471		Approved	OST703	uc001iei.1	Q8NHC8	OTTHUMG00000040448	ENST00000355728.2:c.451G>A	1.37:g.248551360G>A	ENSP00000347965:p.Gly151Ser		246617983	NM_001005471	A6NE36	Missense_Mutation	SNP	ENST00000355728.2	37	CCDS31114.1	.	.	.	.	.	.	.	.	.	.	G	12.48	1.951623	0.34471	.	.	ENSG00000198104	ENST00000355728	T	0.37058	1.22	4.19	3.27	0.37495	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46442	D	0.000298	T	0.44726	0.1307	L	0.41710	1.295	0.09310	N	1	D	0.76494	0.999	D	0.70935	0.971	T	0.10474	-1.0628	10	0.56958	D	0.05	.	8.15	0.31134	0.1722:0.0:0.8278:0.0	.	151	Q8NHC8	OR2T6_HUMAN	S	151	ENSP00000347965:G151S	ENSP00000347965:G151S	G	+	1	0	OR2T6	246617983	0.000000	0.05858	0.860000	0.33809	0.070000	0.16714	-0.012000	0.12699	2.320000	0.78422	0.643000	0.83706	GGT		0.557	OR2T6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097344.1	NM_001005471	
ZNF831	128611	broad.mit.edu	37	20	57769139	57769140	+	Frame_Shift_Ins	INS	-	-	G	rs55786258	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr20:57769139_57769140insG	ENST00000371030.2	+	1	3065_3066	c.3065_3066insG	c.(3064-3069)ttggggfs	p.LG1022fs		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	1022							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.D1025fs*9(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					GGGGCACAGTTGGGGGGGGACA	0.678																																					p.L1022fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.3065_3066insG	20						.																																			57202535	SO:0001589	frameshift_variant	128611	exon1			AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 174"""	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.3073dupG	20.37:g.57769147_57769147dupG	ENSP00000360069:p.Leu1022fs		57202534	NM_178457	Q5TDR4|Q8TCP0	Frame_Shift_Ins	INS	ENST00000371030.2	37	CCDS42894.1																																																																																				0.678	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457	
JAG1	182	broad.mit.edu	37	20	10621802	10621802	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr20:10621802C>T	ENST00000254958.5	-	24	3522	c.3007G>A	c.(3007-3009)Gag>Aag	p.E1003K	JAG1_ENST00000423891.2_Missense_Mutation_p.E844K	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	1003					angiogenesis (GO:0001525)|aorta morphogenesis (GO:0035909)|auditory receptor cell differentiation (GO:0042491)|blood vessel remodeling (GO:0001974)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cell fate determination (GO:0001709)|ciliary body morphogenesis (GO:0061073)|distal tubule development (GO:0072017)|endocardial cushion cell development (GO:0061444)|endothelial cell differentiation (GO:0045446)|hemopoiesis (GO:0030097)|keratinocyte differentiation (GO:0030216)|loop of Henle development (GO:0072070)|morphogenesis of an epithelial sheet (GO:0002011)|myoblast differentiation (GO:0045445)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of stem cell differentiation (GO:2000737)|nervous system development (GO:0007399)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|response to muramyl dipeptide (GO:0032495)|T cell mediated immunity (GO:0002456)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)|structural molecule activity (GO:0005198)	p.E1003K(2)		biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|urinary_tract(1)	44						GGGGAAGGCTCGCAAGCGATG	0.413									Alagille Syndrome																												p.E1003K												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G3007A	20	GRCh37	CM993759	JAG1	M		.						132.0	120.0	124.0					20																	10621802		2203	4300	6503	10569802	SO:0001583	missense	182	exon24	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	U61276	CCDS13112.1	20p12.1-p11.23	2011-05-12	2010-06-24		ENSG00000101384	ENSG00000101384		"""CD molecules"""	6188	protein-coding gene	gene with protein product		601920	"""Alagille syndrome"""	AGS, JAGL1		7697721, 9207788	Standard	NM_000214		Approved	AHD, AWS, HJ1, CD339	uc002wnw.2	P78504	OTTHUMG00000031872	ENST00000254958.5:c.3007G>A	20.37:g.10621802C>T	ENSP00000254958:p.Glu1003Lys		10569802	NM_000214	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Missense_Mutation	SNP	ENST00000254958.5	37	CCDS13112.1	.	.	.	.	.	.	.	.	.	.	C	31	5.075638	0.94000	.	.	ENSG00000101384	ENST00000254958;ENST00000423891	D;D	0.86230	-2.06;-2.09	6.07	6.07	0.98685	.	0.045665	0.85682	D	0.000000	D	0.84638	0.5516	L	0.45581	1.43	0.80722	D	1	P	0.51351	0.944	B	0.38755	0.281	D	0.86378	0.1727	10	0.72032	D	0.01	.	20.6439	0.99570	0.0:1.0:0.0:0.0	.	1003	P78504	JAG1_HUMAN	K	1003;844	ENSP00000254958:E1003K;ENSP00000389519:E844K	ENSP00000254958:E1003K	E	-	1	0	JAG1	10569802	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.294000	0.78760	2.884000	0.98904	0.655000	0.94253	GAG		0.413	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214	
VPS16	64601	broad.mit.edu	37	20	2845025	2845025	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr20:2845025C>T	ENST00000380445.3	+	18	1807	c.1735C>T	c.(1735-1737)Ctg>Ttg	p.L579L	VPS16_ENST00000380443.3_Silent_p.L265L|PTPRA_ENST00000380393.3_5'UTR|VPS16_ENST00000380469.3_Silent_p.L435L	NM_022575.2	NP_072097.2	Q9H269	VPS16_HUMAN	vacuolar protein sorting 16 homolog (S. cerevisiae)	579					intracellular protein transport (GO:0006886)|viral entry into host cell (GO:0046718)	actin filament (GO:0005884)|axon (GO:0030424)|early endosome (GO:0005769)|HOPS complex (GO:0030897)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|recycling endosome (GO:0055037)		p.L579L(1)		NS(3)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	37						CACGGTGTTGCTGCACCTGAA	0.582																																					p.L435L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1303T	20						.						90.0	84.0	86.0					20																	2845025		2203	4300	6503	2793025	SO:0001819	synonymous_variant	64601	exon14			AF308801	CCDS13036.1, CCDS13037.1	20p13	2009-07-07	2009-07-07	2009-07-07	ENSG00000215305	ENSG00000215305			14584	protein-coding gene	gene with protein product		608550					Standard	NM_022575		Approved		uc002whe.3	Q9H269	OTTHUMG00000031714	ENST00000380445.3:c.1735C>T	20.37:g.2845025C>T			2793025	NM_080413	Q5JUB1|Q8WU31|Q96EE7|Q96N92|Q9H1Q4|Q9H1Q5	Silent	SNP	ENST00000380445.3	37	CCDS13036.1																																																																																				0.582	VPS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077658.2	NM_022575	
UBOX5	22888	broad.mit.edu	37	20	3102420	3102420	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr20:3102420G>A	ENST00000217173.2	-	3	1336	c.865C>T	c.(865-867)Ctg>Ttg	p.L289L	UBOX5_ENST00000348031.2_Silent_p.L289L|UBOX5-AS1_ENST00000446537.1_RNA	NM_001267584.1|NM_014948.3	NP_001254513.1|NP_055763.1			U-box domain containing 5									p.L289L(1)		endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	20						CACTTCTCCAGTGTGCTCTGG	0.592																																					p.L289L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C865T	20						.						52.0	47.0	48.0					20																	3102420		2203	4300	6503	3050420	SO:0001819	synonymous_variant	22888	exon3			AB020667	CCDS13046.1, CCDS13047.1	20p13	2013-01-28			ENSG00000185019	ENSG00000185019		"""RING-type (C3HC4) zinc fingers"", ""U-box domain containing"""	17777	protein-coding gene	gene with protein product						11274149	Standard	NM_014948		Approved	UIP5, KIAA0860, Ubce7ip5, RNF37	uc002whw.4	O94941	OTTHUMG00000031731	ENST00000217173.2:c.865C>T	20.37:g.3102420G>A			3050420	NM_014948		Silent	SNP	ENST00000217173.2	37	CCDS13046.1																																																																																				0.592	UBOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077706.2	NM_014948	
JAG1	182	broad.mit.edu	37	20	10625566	10625566	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr20:10625566G>A	ENST00000254958.5	-	18	2804	c.2289C>T	c.(2287-2289)ggC>ggT	p.G763G	JAG1_ENST00000488480.1_RNA|JAG1_ENST00000423891.2_Silent_p.G604G	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	763	EGF-like 14. {ECO:0000255|PROSITE- ProRule:PRU00076}.				angiogenesis (GO:0001525)|aorta morphogenesis (GO:0035909)|auditory receptor cell differentiation (GO:0042491)|blood vessel remodeling (GO:0001974)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cell fate determination (GO:0001709)|ciliary body morphogenesis (GO:0061073)|distal tubule development (GO:0072017)|endocardial cushion cell development (GO:0061444)|endothelial cell differentiation (GO:0045446)|hemopoiesis (GO:0030097)|keratinocyte differentiation (GO:0030216)|loop of Henle development (GO:0072070)|morphogenesis of an epithelial sheet (GO:0002011)|myoblast differentiation (GO:0045445)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of stem cell differentiation (GO:2000737)|nervous system development (GO:0007399)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|response to muramyl dipeptide (GO:0032495)|T cell mediated immunity (GO:0002456)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)|structural molecule activity (GO:0005198)	p.G763G(2)		biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|urinary_tract(1)	44						TAAAGGACTCGCCGTTGACCA	0.592									Alagille Syndrome																												p.G763G												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C2289T	20						.						178.0	181.0	180.0					20																	10625566		2203	4300	6503	10573566	SO:0001819	synonymous_variant	182	exon18	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	U61276	CCDS13112.1	20p12.1-p11.23	2011-05-12	2010-06-24		ENSG00000101384	ENSG00000101384		"""CD molecules"""	6188	protein-coding gene	gene with protein product		601920	"""Alagille syndrome"""	AGS, JAGL1		7697721, 9207788	Standard	NM_000214		Approved	AHD, AWS, HJ1, CD339	uc002wnw.2	P78504	OTTHUMG00000031872	ENST00000254958.5:c.2289C>T	20.37:g.10625566G>A			10573566	NM_000214	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Silent	SNP	ENST00000254958.5	37	CCDS13112.1																																																																																				0.592	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214	
DNMT3B	1789	broad.mit.edu	37	20	31375164	31375164	+	Silent	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr20:31375164C>A	ENST00000328111.2	+	6	882	c.561C>A	c.(559-561)ccC>ccA	p.P187P	DNMT3B_ENST00000375623.4_Silent_p.P145P|DNMT3B_ENST00000348286.2_Silent_p.P187P|DNMT3B_ENST00000353855.2_Silent_p.P187P|DNMT3B_ENST00000344505.4_Silent_p.P187P|DNMT3B_ENST00000443239.3_Silent_p.P145P|DNMT3B_ENST00000456297.2_Silent_p.P111P|DNMT3B_ENST00000201963.3_Silent_p.P199P	NM_006892.3	NP_008823.1	Q9UBC3	DNM3B_HUMAN	DNA (cytosine-5-)-methyltransferase 3 beta	187	Interaction with DNMT1 and DNMT3A.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation on cytosine within a CG sequence (GO:0010424)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of neuron differentiation (GO:0045666)|protein complex localization (GO:0031503)|regulation of gene expression by genetic imprinting (GO:0006349)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA-methyltransferase activity (GO:0009008)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)|unmethylated CpG binding (GO:0045322)	p.P199P(1)|p.P187P(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(16)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GCAGTACCCCCTACGCCCGCC	0.627																																					p.P187P												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C561A	20						.						78.0	71.0	74.0					20																	31375164		2203	4299	6502	30838825	SO:0001819	synonymous_variant	1789	exon6				CCDS13204.1, CCDS13205.1, CCDS13206.1, CCDS13207.1, CCDS56183.1, CCDS56184.1	20q11.2	2014-09-17			ENSG00000088305	ENSG00000088305			2979	protein-coding gene	gene with protein product		602900				9662389, 10433969	Standard	NM_006892		Approved		uc002wyc.3	Q9UBC3	OTTHUMG00000032226	ENST00000328111.2:c.561C>A	20.37:g.31375164C>A			30838825	NM_175848	A2A2E2|B4DSM8|B4DSU1|E1P5M6|E1P5M7|E7EN63|E9PBF2|Q9UBD4|Q9UJQ5|Q9UKA6|Q9UNE5|Q9Y5R9|Q9Y5S0	Silent	SNP	ENST00000328111.2	37	CCDS13205.1																																																																																				0.627	DNMT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078643.2	NM_006892	
NECAB3	63941	broad.mit.edu	37	20	32247494	32247494	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr20:32247494G>A	ENST00000246190.6	-	8	743	c.688C>T	c.(688-690)Cgc>Tgc	p.R230C	NECAB3_ENST00000375238.4_Missense_Mutation_p.R230C|RP1-63M2.6_ENST00000607224.1_RNA|NECAB3_ENST00000606525.1_5'UTR|C20orf144_ENST00000375222.3_5'Flank	NM_031232.3	NP_112509.3	Q96P71	NECA3_HUMAN	N-terminal EF-hand calcium binding protein 3	230					protein metabolic process (GO:0019538)|protein secretion (GO:0009306)|regulation of amyloid precursor protein biosynthetic process (GO:0042984)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|Golgi cis cisterna (GO:0000137)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.R230C(1)		large_intestine(3)|lung(5)|skin(2)	10						TCCTGGAGGCGGTTCACCTGG	0.697																																					p.R230C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C688T	20						.						9.0	11.0	11.0					20																	32247494		1967	4140	6107	31711155	SO:0001583	missense	63941	exon8			AB039947	CCDS42866.1, CCDS42867.1	20q11.21	2013-01-10	2007-12-06	2007-12-06	ENSG00000125967	ENSG00000125967		"""N-terminal EF-hand calcium binding proteins"", ""EF-hand domain containing"""	15851	protein-coding gene	gene with protein product	"""EF-hand calcium binding protein 3"""	612478	"""amyloid beta (A4) precursor protein-binding, family A, member 2 binding protein"""	SYTIP2, APBA2BP		10833507	Standard	NM_031232		Approved	XB51, dJ63M2.4, NIP1, dJ63M2.5, EFCBP3	uc002wzn.4	Q96P71	OTTHUMG00000032264	ENST00000246190.6:c.688C>T	20.37:g.32247494G>A	ENSP00000246190:p.Arg230Cys		31711155	NM_031232	A8K780|E1P5N2|Q5JWF5|Q5JWF6|Q5JWF7|Q86VV1|Q9H433|Q9H8G8|Q9HBW7|Q9HCQ9	Missense_Mutation	SNP	ENST00000246190.6	37	CCDS42866.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.994999	0.74703	.	.	ENSG00000125967	ENST00000375238;ENST00000246190;ENST00000439478	T;T;T	0.34472	1.36;1.63;1.61	5.1	4.13	0.48395	.	0.069252	0.56097	D	0.000033	T	0.61677	0.2366	M	0.83223	2.63	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	T	0.67173	-0.5737	10	0.87932	D	0	-0.4573	12.5236	0.56073	0.0:0.0:0.832:0.168	.	107;230;230	E1P5N3;Q96P71;Q96P71-2	.;NECA3_HUMAN;.	C	230	ENSP00000364386:R230C;ENSP00000246190:R230C;ENSP00000392064:R230C	ENSP00000246190:R230C	R	-	1	0	NECAB3	31711155	1.000000	0.71417	0.998000	0.56505	0.807000	0.45602	1.146000	0.31589	1.092000	0.41356	0.462000	0.41574	CGC		0.697	NECAB3-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078724.2		
ITCH	83737	broad.mit.edu	37	20	32996556	32996556	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr20:32996556G>A	ENST00000262650.6	+	4	306	c.170G>A	c.(169-171)tGc>tAc	p.C57Y	ITCH_ENST00000535650.1_Intron|ITCH_ENST00000374864.4_Missense_Mutation_p.C57Y			Q96J02	ITCH_HUMAN	itchy E3 ubiquitin protein ligase	57	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				apoptotic process (GO:0006915)|defense response to virus (GO:0051607)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of defense response to virus (GO:0050687)|negative regulation of JNK cascade (GO:0046329)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|protein K29-linked ubiquitination (GO:0035519)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of cell growth (GO:0001558)|regulation of protein deubiquitination (GO:0090085)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	CXCR chemokine receptor binding (GO:0045236)|ligase activity (GO:0016874)|ribonucleoprotein complex binding (GO:0043021)|ubiquitin-protein transferase activity (GO:0004842)	p.C57Y(1)		NS(1)|breast(9)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(13)|skin(1)|upper_aerodigestive_tract(1)	36						ACAGAAAAATGCAACAACACA	0.378																																					p.C57Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G170A	20						.						136.0	122.0	127.0					20																	32996556		2203	4300	6503	32460217	SO:0001583	missense	83737	exon4			AF095745	CCDS13234.1, CCDS58768.1, CCDS58769.1	20q11.22	2014-09-17	2012-02-23		ENSG00000078747	ENSG00000078747			13890	protein-coding gene	gene with protein product		606409	"""itchy (mouse homolog) E3 ubiquitin protein ligase"", ""itchy E3 ubiquitin protein ligase homolog (mouse)"""			11318614	Standard	NM_001257137		Approved	AIP4	uc010geu.2	Q96J02	OTTHUMG00000032300	ENST00000262650.6:c.170G>A	20.37:g.32996556G>A	ENSP00000262650:p.Cys57Tyr		32460217	NM_031483	A6NEW4|B4E234|E1P5P3|F5H217|O43584|Q5QP37|Q5TEL0|Q96F66|Q9BY75|Q9H451|Q9H4U5	Missense_Mutation	SNP	ENST00000262650.6	37	CCDS58768.1	.	.	.	.	.	.	.	.	.	.	G	19.24	3.789124	0.70337	.	.	ENSG00000078747	ENST00000374864;ENST00000262650	T;T	0.68765	-0.35;-0.35	5.35	5.35	0.76521	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.229945	0.50627	D	0.000119	T	0.73156	0.3551	L	0.41492	1.28	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.76575	0.988;0.932	T	0.71817	-0.4478	10	0.40728	T	0.16	.	12.0823	0.53677	0.0794:0.0:0.9206:0.0	.	57;57	Q96J02;Q5QP37	ITCH_HUMAN;.	Y	57	ENSP00000363998:C57Y;ENSP00000262650:C57Y	ENSP00000262650:C57Y	C	+	2	0	ITCH	32460217	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.603000	0.82811	2.522000	0.85027	0.655000	0.94253	TGC		0.378	ITCH-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078783.2		
ATRN	8455	broad.mit.edu	37	20	3575147	3575147	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr20:3575147C>T	ENST00000262919.5	+	20	3412	c.3344C>T	c.(3343-3345)gCg>gTg	p.A1115V	ATRN_ENST00000446916.2_Missense_Mutation_p.A1115V	NM_139321.2	NP_647537.1	O75882	ATRN_HUMAN	attractin	1115	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cerebellum development (GO:0021549)|inflammatory response (GO:0006954)|myelination (GO:0042552)|pigmentation (GO:0043473)|regulation of multicellular organism growth (GO:0040014)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)	p.A1115V(1)		breast(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	59						AATGGGCACGCGTCTCTGTGC	0.512																																					p.A1115V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3344T	20						.						81.0	66.0	71.0					20																	3575147		2203	4300	6503	3523147	SO:0001583	missense	8455	exon20			AF034957	CCDS13053.1, CCDS13054.1	20p13	2008-07-02			ENSG00000088812	ENSG00000088812			885	protein-coding gene	gene with protein product	"""mahogany protein"""	603130				9736737, 8596018	Standard	NM_139321		Approved	DPPT-L, MGCA	uc002wim.2	O75882	OTTHUMG00000031746	ENST00000262919.5:c.3344C>T	20.37:g.3575147C>T	ENSP00000262919:p.Ala1115Val		3523147	NM_139322	A8KAE5|O60295|O95414|Q3MIT3|Q5TDA2|Q5TDA4|Q5VYW3|Q9NTQ3|Q9NTQ4|Q9NU01|Q9NZ57|Q9NZ58|Q9UC75|Q9UDF5	Missense_Mutation	SNP	ENST00000262919.5	37	CCDS13053.1	.	.	.	.	.	.	.	.	.	.	C	34	5.327710	0.95733	.	.	ENSG00000088812	ENST00000262919;ENST00000446916;ENST00000340500	T;T	0.06294	3.32;3.38	6.06	6.06	0.98353	EGF-like, laminin (1);	0.047923	0.85682	D	0.000000	T	0.36468	0.0968	M	0.92026	3.265	0.80722	D	1	D;D	0.89917	0.999;1.0	P;D	0.85130	0.89;0.997	T	0.28713	-1.0035	10	0.72032	D	0.01	-12.7972	20.2157	0.98296	0.0:1.0:0.0:0.0	.	1115;1115	O75882;O75882-2	ATRN_HUMAN;.	V	1115;1115;1041	ENSP00000262919:A1115V;ENSP00000416587:A1115V	ENSP00000262919:A1115V	A	+	2	0	ATRN	3523147	1.000000	0.71417	0.496000	0.27539	0.778000	0.44026	7.703000	0.84585	2.881000	0.98747	0.650000	0.86243	GCG		0.512	ATRN-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077740.2	NM_139321	
MAP1LC3A	84557	broad.mit.edu	37	20	33147624	33147624	+	Silent	SNP	G	G	A	rs550144245		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr20:33147624G>A	ENST00000360668.3	+	4	1049	c.288G>A	c.(286-288)gcG>gcA	p.A96A	MAP1LC3A_ENST00000397709.1_Silent_p.A96A|MAP1LC3A_ENST00000476428.1_3'UTR|MAP1LC3A_ENST00000374837.3_Silent_p.A100A			Q9H492	MLP3A_HUMAN	microtubule-associated protein 1 light chain 3 alpha	96					autophagic vacuole assembly (GO:0000045)|mitochondrion degradation (GO:0000422)	autophagic vacuole (GO:0005776)|autophagic vacuole membrane (GO:0000421)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|late endosome (GO:0005770)|microtubule (GO:0005874)|organelle membrane (GO:0031090)	phosphatidylethanolamine binding (GO:0008429)|phospholipid binding (GO:0005543)	p.A100A(1)		cervix(1)|kidney(1)|large_intestine(1)|upper_aerodigestive_tract(2)	5						CGCCCATCGCGGACATCTACG	0.637													G|||	1	0.000199681	0.0	0.0	5008	,	,		15084	0.0		0.0	False		,,,				2504	0.001				p.A100A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G300A	20						.						52.0	57.0	55.0					20																	33147624		2203	4300	6503	32611285	SO:0001819	synonymous_variant	84557	exon5				CCDS13237.1, CCDS13238.1	20q11.22	2014-02-12			ENSG00000101460	ENSG00000101460			6838	protein-coding gene	gene with protein product		601242				8833088, 17580304	Standard	NM_032514		Approved	MAP1BLC3, MAP1ALC3, LC3, LC3A, ATG8E	uc002xaq.2	Q9H492	OTTHUMG00000032306	ENST00000360668.3:c.288G>A	20.37:g.33147624G>A			32611285	NM_181509	E1P5P4|E1P5P5|Q9BXW5	Silent	SNP	ENST00000360668.3	37	CCDS13238.1																																																																																				0.637	MAP1LC3A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078801.2	NM_181509	
ZHX3	23051	broad.mit.edu	37	20	39831215	39831215	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr20:39831215T>C	ENST00000309060.3	-	4	2757	c.2342A>G	c.(2341-2343)cAg>cGg	p.Q781R	ZHX3_ENST00000558993.1_Intron|ZHX3_ENST00000544979.2_Missense_Mutation_p.Q781R|ZHX3_ENST00000557816.1_Intron|ZHX3_ENST00000559234.1_Missense_Mutation_p.Q781R|ZHX3_ENST00000540170.1_Missense_Mutation_p.Q781R|ZHX3_ENST00000432768.2_Missense_Mutation_p.Q781R|ZHX3_ENST00000560361.1_Missense_Mutation_p.Q781R			Q9H4I2	ZHX3_HUMAN	zinc fingers and homeoboxes 3	781					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of osteoblast differentiation (GO:0045669)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.Q781R(1)		endometrium(2)|kidney(5)|large_intestine(8)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		Myeloproliferative disorder(115;0.00425)				GACAAAGAGCTGCCGCAGCAA	0.582																																					p.Q781R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2342G	20						.						79.0	85.0	83.0					20																	39831215		2203	4300	6503	39264629	SO:0001583	missense	23051	exon3			AB007855	CCDS13315.1	20q12	2012-03-09	2004-01-29	2004-01-30	ENSG00000174306	ENSG00000174306		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	15935	protein-coding gene	gene with protein product		609598	"""triple homeobox 1"""	TIX1		9455477	Standard	XM_005260343		Approved	KIAA0395	uc002xjs.1	Q9H4I2	OTTHUMG00000032481	ENST00000309060.3:c.2342A>G	20.37:g.39831215T>C	ENSP00000312222:p.Gln781Arg		39264629	NM_015035	E1P5W5|F5H820|O43145|Q6NUJ7	Missense_Mutation	SNP	ENST00000309060.3	37	CCDS13315.1	.	.	.	.	.	.	.	.	.	.	T	15.10	2.734074	0.48939	.	.	ENSG00000174306	ENST00000309060;ENST00000373263;ENST00000540170;ENST00000544979;ENST00000373262	D;D;D	0.91577	-2.87;-2.87;-2.87	6.07	6.07	0.98685	Homeodomain-related (1);Homeobox (2);Homeodomain-like (1);	0.054060	0.85682	D	0.000000	D	0.92596	0.7648	L	0.60455	1.87	0.45979	D	0.998793	P;P;P	0.51933	0.893;0.949;0.55	P;P;B	0.54759	0.601;0.76;0.254	D	0.91779	0.5434	10	0.38643	T	0.18	-20.5346	16.6288	0.85011	0.0:0.0:0.0:1.0	.	781;781;781	A8K8Q0;Q9H4I2;F5H820	.;ZHX3_HUMAN;.	R	781;781;781;781;559	ENSP00000362360:Q781R;ENSP00000442290:Q781R;ENSP00000443783:Q781R	ENSP00000312222:Q781R	Q	-	2	0	ZHX3	39264629	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.164000	0.58190	2.326000	0.78906	0.533000	0.62120	CAG		0.582	ZHX3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079262.3	NM_015035	
TTPAL	79183	broad.mit.edu	37	20	43108858	43108858	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr20:43108858C>T	ENST00000372904.3	+	3	362	c.219C>T	c.(217-219)agC>agT	p.S73S	TTPAL_ENST00000262605.4_Silent_p.S73S|TTPAL_ENST00000372906.2_Silent_p.S73S	NM_024331.4	NP_077307.2	Q9BTX7	TTPAL_HUMAN	tocopherol (alpha) transfer protein-like	73						intracellular (GO:0005622)|membrane (GO:0016020)	transporter activity (GO:0005215)	p.S73S(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|ovary(2)|skin(5)	18						CCAACCTGAGCACATCCCTCG	0.587																																					p.S73S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C219T	20						.						117.0	75.0	89.0					20																	43108858		2203	4300	6503	42542272	SO:0001819	synonymous_variant	79183	exon2			BC003071	CCDS13332.2	20q13.12	2008-06-23	2008-06-23	2008-06-23	ENSG00000124120	ENSG00000124120			16114	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 121"""	C20orf121			Standard	NM_024331		Approved	dJ179M20.3	uc002xmd.2	Q9BTX7	OTTHUMG00000032536	ENST00000372904.3:c.219C>T	20.37:g.43108858C>T			42542272	NM_001039199	E1P5X3|Q5QPC1|Q9H1G2|Q9NQG8	Silent	SNP	ENST00000372904.3	37	CCDS13332.2																																																																																				0.587	TTPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106886.2	NM_024331	
RIMS4	140730	broad.mit.edu	37	20	43384935	43384935	+	Missense_Mutation	SNP	C	C	G	rs199569233		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr20:43384935C>G	ENST00000372851.3	-	6	716	c.650G>C	c.(649-651)cGc>cCc	p.R217P	RIMS4_ENST00000541604.2_Missense_Mutation_p.R218P	NM_001205317.1|NM_182970.3	NP_001192246.1|NP_892015.1	Q9H426	RIMS4_HUMAN	regulating synaptic membrane exocytosis 4	217	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|neurotransmitter transport (GO:0006836)|regulation of membrane potential (GO:0042391)	cell junction (GO:0030054)|presynaptic active zone (GO:0048786)|synaptic membrane (GO:0097060)		p.R217P(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(11)|ovary(5)|urinary_tract(1)	29		Myeloproliferative disorder(115;0.0122)				CAGCAGCACGCGAGCCACACC	0.637																																					p.R217P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G650C	20						.						55.0	48.0	51.0					20																	43384935		2203	4300	6503	42818349	SO:0001583	missense	140730	exon6				CCDS13338.1, CCDS56191.1	20q13.12	2005-02-03	2003-06-18	2003-06-20	ENSG00000101098	ENSG00000101098			16183	protein-coding gene	gene with protein product		611601	"""chromosome 20 open reading frame 190"""	C20orf190		12620390	Standard	NM_182970		Approved	dJ781B1.3	uc010ggu.3	Q9H426	OTTHUMG00000032546	ENST00000372851.3:c.650G>C	20.37:g.43384935C>G	ENSP00000361942:p.Arg217Pro		42818349	NM_182970	A4FU94|E1P613|Q3MI44|Q5JWT7	Missense_Mutation	SNP	ENST00000372851.3	37	CCDS13338.1	.	.	.	.	.	.	.	.	.	.	C	18.09	3.546798	0.65198	.	.	ENSG00000101098	ENST00000372851;ENST00000541604	T;T	0.79653	-1.29;-1.29	5.07	5.07	0.68467	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.81536	0.4843	L	0.55990	1.75	0.58432	D	0.999998	P;P	0.42375	0.778;0.778	P;P	0.48488	0.579;0.579	D	0.83484	0.0066	10	0.87932	D	0	.	11.9083	0.52725	0.0:0.9205:0.0:0.0795	.	218;217	E1P613;Q9H426	.;RIMS4_HUMAN	P	217;218	ENSP00000361942:R217P;ENSP00000439287:R218P	ENSP00000361942:R217P	R	-	2	0	RIMS4	42818349	1.000000	0.71417	0.997000	0.53966	0.977000	0.68977	3.229000	0.51278	2.355000	0.79922	0.655000	0.94253	CGC		0.637	RIMS4-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000101027.2	NM_182970	
ZNF335	63925	broad.mit.edu	37	20	44596438	44596438	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr20:44596438C>T	ENST00000322927.2	-	5	849	c.749G>A	c.(748-750)tGc>tAc	p.C250Y	ZNF335_ENST00000426788.1_Missense_Mutation_p.C95Y|ZNF335_ENST00000494955.1_5'UTR	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	250					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.C250Y(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)				CCGGTACTGGCACATCTTGCA	0.632																																					p.C250Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G749A	20						.						68.0	65.0	66.0					20																	44596438		2203	4300	6503	44029845	SO:0001583	missense	63925	exon5			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.749G>A	20.37:g.44596438C>T	ENSP00000325326:p.Cys250Tyr		44029845	NM_022095	B4DLG7|Q548D0|Q9H684	Missense_Mutation	SNP	ENST00000322927.2	37	CCDS13389.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.550029	0.86127	.	.	ENSG00000198026	ENST00000322927;ENST00000426788	T;T	0.57752	0.38;0.38	4.78	4.78	0.61160	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.000000	0.85682	D	0.000000	T	0.62744	0.2453	L	0.29908	0.895	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.67217	-0.5726	10	0.87932	D	0	-24.5775	16.9733	0.86306	0.0:1.0:0.0:0.0	.	95;250	Q9H4Z2-2;Q9H4Z2	.;ZN335_HUMAN	Y	250;95	ENSP00000325326:C250Y;ENSP00000397098:C95Y	ENSP00000325326:C250Y	C	-	2	0	ZNF335	44029845	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.130000	0.77235	2.469000	0.83416	0.561000	0.74099	TGC		0.632	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1	NM_022095	
SLC12A5	57468	broad.mit.edu	37	20	44680470	44680470	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr20:44680470C>T	ENST00000454036.2	+	18	2456	c.2407C>T	c.(2407-2409)Cgc>Tgc	p.R803C	SLC12A5_ENST00000243964.3_Missense_Mutation_p.R780C	NM_001134771.1	NP_001128243.1	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 5	803					cellular ion homeostasis (GO:0006873)|chloride transmembrane transport (GO:1902476)|ion transport (GO:0006811)|learning (GO:0007612)|multicellular organism growth (GO:0035264)|potassium ion transport (GO:0006813)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|thermosensory behavior (GO:0040040)|transmembrane transport (GO:0055085)|transport (GO:0006810)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)	p.R780C(2)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(1)|lung(38)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	80		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)	CCGCAACTGGCGCCAGAAGGA	0.622																																					p.R780C												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.C2338T	20						.						57.0	59.0	58.0					20																	44680470		2203	4300	6503	44113877	SO:0001583	missense	57468	exon18			AB033002	CCDS13391.1, CCDS46610.1	20q13.12	2013-05-22	2010-04-20		ENSG00000124140	ENSG00000124140		"""Solute carriers"""	13818	protein-coding gene	gene with protein product		606726					Standard	NM_020708		Approved	KIAA1176, KCC2	uc010zxl.1	Q9H2X9	OTTHUMG00000032638	ENST00000454036.2:c.2407C>T	20.37:g.44680470C>T	ENSP00000387694:p.Arg803Cys		44113877	NM_020708	A2RTX2|Q5VZ41|Q9H4Z0|Q9ULP4	Missense_Mutation	SNP	ENST00000454036.2	37	CCDS46610.1	.	.	.	.	.	.	.	.	.	.	C	17.39	3.378090	0.61735	.	.	ENSG00000124140	ENST00000454036;ENST00000243964	D;D	0.85955	-2.05;-2.05	4.02	0.702	0.18110	.	0.293334	0.32175	N	0.006475	D	0.90642	0.7065	M	0.83774	2.66	0.80722	D	1	D;D	0.89917	0.999;1.0	P;D	0.64042	0.836;0.921	D	0.90193	0.4251	10	0.87932	D	0	.	12.0918	0.53730	0.5948:0.4052:0.0:0.0	.	803;780	Q9H2X9;Q9H2X9-2	S12A5_HUMAN;.	C	803;780	ENSP00000387694:R803C;ENSP00000243964:R780C	ENSP00000243964:R780C	R	+	1	0	SLC12A5	44113877	0.991000	0.36638	0.997000	0.53966	0.978000	0.69477	0.333000	0.19768	0.058000	0.16222	0.462000	0.41574	CGC		0.622	SLC12A5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471538.1		
NCOA5	57727	broad.mit.edu	37	20	44695716	44695716	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr20:44695716T>C	ENST00000290231.6	-	5	771	c.607A>G	c.(607-609)Att>Gtt	p.I203V		NM_020967.2	NP_066018.1	Q9HCD5	NCOA5_HUMAN	nuclear receptor coactivator 5	203					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|extracellular space (GO:0005615)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.I203V(1)		central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|skin(2)|urinary_tract(1)	21		Myeloproliferative disorder(115;0.0122)				TTGACCACAATCACAGAACAA	0.433																																					p.I203V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A607G	20						.						104.0	100.0	101.0					20																	44695716		2203	4300	6503	44129123	SO:0001583	missense	57727	exon5				CCDS13392.1	20q12-q13.12	2008-07-02			ENSG00000124160	ENSG00000124160			15909	protein-coding gene	gene with protein product	"""coactivator independent of AF-2"""					11780052, 11113208	Standard	XM_005260474		Approved	bA465L10.6, CIA	uc002xre.3	Q9HCD5	OTTHUMG00000032639	ENST00000290231.6:c.607A>G	20.37:g.44695716T>C	ENSP00000290231:p.Ile203Val		44129123	NM_020967	B2RTV9|E1P5R0|Q6HA99|Q9H1F2|Q9H2T2|Q9H4Y9	Missense_Mutation	SNP	ENST00000290231.6	37	CCDS13392.1	.	.	.	.	.	.	.	.	.	.	T	14.78	2.638995	0.47153	.	.	ENSG00000124160	ENST00000290231;ENST00000372291	T	0.57107	0.42	5.4	5.4	0.78164	Anticodon-binding (2);	0.092278	0.64402	D	0.000001	T	0.41581	0.1165	L	0.38838	1.175	0.58432	D	0.999992	B;B	0.15930	0.004;0.015	B;B	0.17722	0.019;0.013	T	0.31888	-0.9927	10	0.42905	T	0.14	-11.089	9.2537	0.37571	0.0:0.0794:0.0:0.9206	.	203;98	Q9HCD5;Q5JY17	NCOA5_HUMAN;.	V	203;98	ENSP00000290231:I203V	ENSP00000290231:I203V	I	-	1	0	NCOA5	44129123	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	5.016000	0.64041	2.263000	0.75096	0.533000	0.62120	ATT		0.433	NCOA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079559.1	NM_020967	
ZNFX1	57169	broad.mit.edu	37	20	47863850	47863850	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr20:47863850G>A	ENST00000396105.1	-	14	5957	c.5711C>T	c.(5710-5712)aCg>aTg	p.T1904M	ZNFX1_ENST00000469991.1_5'Flank|ZNFX1_ENST00000371754.4_Intron|ZNFX1_ENST00000371752.1_Missense_Mutation_p.T1904M	NM_021035.2	NP_066363.1	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	1904							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.T1904M(2)		cervix(2)|endometrium(8)|kidney(7)|large_intestine(15)|liver(1)|lung(17)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	60			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			GTTGTTGGCCGTGTCAGACCA	0.517																																					p.T1904M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C5711T	20						.						135.0	118.0	124.0					20																	47863850		2203	4300	6503	47297257	SO:0001583	missense	57169	exon14			AK022641	CCDS13417.1	20q13.13	2014-02-12			ENSG00000124201	ENSG00000124201			29271	protein-coding gene	gene with protein product						10718198	Standard	NM_021035		Approved	KIAA1404, FLJ11277	uc002xui.3	Q9P2E3	OTTHUMG00000032696	ENST00000396105.1:c.5711C>T	20.37:g.47863850G>A	ENSP00000379412:p.Thr1904Met		47297257	NM_021035	Q9BQM7|Q9BQM8|Q9H8C1|Q9H9S2|Q9NUM1|Q9NWW1	Missense_Mutation	SNP	ENST00000396105.1	37	CCDS13417.1	.	.	.	.	.	.	.	.	.	.	G	8.767	0.925067	0.18056	.	.	ENSG00000124201	ENST00000371752;ENST00000396105	D;D	0.86769	-2.17;-2.17	5.54	3.62	0.41486	.	0.282842	0.30695	N	0.009073	T	0.79782	0.4505	L	0.45581	1.43	0.09310	N	0.999999	P	0.43662	0.814	B	0.35859	0.212	T	0.69495	-0.5130	10	0.38643	T	0.18	-3.9845	9.6987	0.40173	0.1615:0.0:0.8385:0.0	.	1904	Q9P2E3	ZNFX1_HUMAN	M	1904	ENSP00000360817:T1904M;ENSP00000379412:T1904M	ENSP00000360817:T1904M	T	-	2	0	ZNFX1	47297257	0.443000	0.25641	0.003000	0.11579	0.539000	0.34962	2.606000	0.46291	0.743000	0.32719	-0.222000	0.12452	ACG		0.517	ZNFX1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079647.2	NM_021035	
NFATC2	4773	broad.mit.edu	37	20	50140350	50140350	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr20:50140350C>T	ENST00000396009.3	-	2	649	c.430G>A	c.(430-432)Ggg>Agg	p.G144R	NFATC2_ENST00000609943.1_Missense_Mutation_p.G124R|NFATC2_ENST00000371564.3_Missense_Mutation_p.G144R|NFATC2_ENST00000609507.1_Intron|NFATC2_ENST00000610033.1_Intron|NFATC2_ENST00000414705.1_Missense_Mutation_p.G124R	NM_001258297.1|NM_173091.3	NP_001245226.1|NP_775114.1	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	144	Trans-activation domain A (TAD-A).				B cell receptor signaling pathway (GO:0050853)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear transcription factor complex (GO:0044798)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G144R(1)	EWSR1/NFATC2(9)	breast(2)|endometrium(7)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	53	Hepatocellular(150;0.248)					GCGGCCACCCCGGCCAGGGGC	0.716																																					p.G144R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G430A	20						.						8.0	11.0	10.0					20																	50140350		2176	4218	6394	49573757	SO:0001583	missense	4773	exon2			U43342, U43341	CCDS13437.1, CCDS33488.1, CCDS46614.1, CCDS68156.1, CCDS68157.1	20q13.2	2009-11-24			ENSG00000101096	ENSG00000101096		"""Nuclear factor of activated T-cells"""	7776	protein-coding gene	gene with protein product		600490				8202141	Standard	NM_012340		Approved	NF-ATP, NFATp, NFAT1	uc002xwd.4	Q13469	OTTHUMG00000032747	ENST00000396009.3:c.430G>A	20.37:g.50140350C>T	ENSP00000379330:p.Gly144Arg		49573757	NM_012340	B5B2N8|B5B2N9|B5B2P0|B5B2P2|B5B2P3|Q13468|Q5TFW7|Q5TFW8|Q9NPX6|Q9NQH3|Q9UJR2	Missense_Mutation	SNP	ENST00000396009.3	37	CCDS13437.1	.	.	.	.	.	.	.	.	.	.	C	11.78	1.740428	0.30865	.	.	ENSG00000101096	ENST00000371564;ENST00000396009;ENST00000414705	T;T;T	0.70749	-0.51;-0.51;-0.51	5.25	5.25	0.73442	.	0.458058	0.25358	N	0.031244	T	0.54775	0.1879	N	0.22421	0.69	0.33233	D	0.556135	P;P;P;P	0.47962	0.814;0.903;0.606;0.607	B;B;B;B	0.34489	0.151;0.183;0.184;0.062	T	0.64960	-0.6284	10	0.27785	T	0.31	-18.5356	18.8428	0.92190	0.0:1.0:0.0:0.0	.	124;124;144;144	B5B2N9;B5B2P2;Q13469;B5B2N8	.;.;NFAC2_HUMAN;.	R	144;144;124	ENSP00000360619:G144R;ENSP00000379330:G144R;ENSP00000396471:G124R	ENSP00000360619:G144R	G	-	1	0	NFATC2	49573757	0.068000	0.21057	0.122000	0.21767	0.028000	0.11728	1.400000	0.34577	2.452000	0.82932	0.462000	0.41574	GGG		0.716	NFATC2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079730.2	NM_012340	
LRRN4	164312	broad.mit.edu	37	20	6022424	6022424	+	Silent	SNP	C	C	T	rs368584881|rs115443528	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr20:6022424C>T	ENST00000378858.4	-	5	1691	c.1467G>A	c.(1465-1467)tcG>tcA	p.S489S		NM_152611.4	NP_689824.2	Q8WUT4	LRRN4_HUMAN	leucine rich repeat neuronal 4	489					long-term memory (GO:0007616)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)		p.S489S(1)		breast(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(2)	27						TGCGGTCCCACGAGGTAGGGA	0.642													C|||	21	0.00419329	0.0151	0.0014	5008	,	,		16819	0.0		0.0	False		,,,				2504	0.0				p.S489S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1467A	20						.	C		28,4378	33.5+/-64.1	0,28,2175	102.0	109.0	107.0		1467	-7.5	0.0	20	dbSNP_132	107	0,8600		0,0,4300	no	coding-synonymous	LRRN4	NM_152611.3		0,28,6475	TT,TC,CC		0.0,0.6355,0.2153		489/741	6022424	28,12978	2203	4300	6503	5970424	SO:0001819	synonymous_variant	164312	exon5			AL118505	CCDS13097.1	20p12.3	2013-02-11	2008-05-20	2008-05-20	ENSG00000125872	ENSG00000125872		"""Fibronectin type III domain containing"""	16208	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 75"""	C20orf75		15870286	Standard	NM_152611		Approved	dJ1056H1.1, NLRR4	uc002wmo.3	Q8WUT4	OTTHUMG00000031825	ENST00000378858.4:c.1467G>A	20.37:g.6022424C>T			5970424	NM_152611	A8K258|Q5JWV6|Q9H419	Silent	SNP	ENST00000378858.4	37	CCDS13097.1																																																																																				0.642	LRRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077907.2	NM_152611	
ZNF217	7764	broad.mit.edu	37	20	52198379	52198379	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr20:52198379G>A	ENST00000371471.2	-	2	1412	c.987C>T	c.(985-987)tcC>tcT	p.S329S	ZNF217_ENST00000540425.1_5'Flank|ZNF217_ENST00000302342.3_Silent_p.S329S			O75362	ZN217_HUMAN	zinc finger protein 217	329					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.S329S(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			GCTCCTTCTCGGAACTCGAAT	0.547																																					p.S329S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C987T	20						.						132.0	130.0	131.0					20																	52198379		2203	4300	6503	51631786	SO:0001819	synonymous_variant	7764	exon1			AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"""Zinc fingers, C2H2-type"""	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.987C>T	20.37:g.52198379G>A			51631786	NM_006526	E1P5Y6|Q14DB8	Silent	SNP	ENST00000371471.2	37	CCDS13443.1																																																																																				0.547	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526	
DIDO1	11083	broad.mit.edu	37	20	61538704	61538704	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr20:61538704T>G	ENST00000266070.4	-	5	1494	c.1169A>C	c.(1168-1170)gAg>gCg	p.E390A	DIDO1_ENST00000370366.1_Missense_Mutation_p.E390A|DIDO1_ENST00000370368.1_Missense_Mutation_p.E390A|DIDO1_ENST00000370371.4_Missense_Mutation_p.E390A|DIDO1_ENST00000395335.2_Missense_Mutation_p.E390A|DIDO1_ENST00000395340.1_Missense_Mutation_p.E390A|DIDO1_ENST00000266071.5_Missense_Mutation_p.E390A|DIDO1_ENST00000395343.1_Missense_Mutation_p.E390A|DIDO1_ENST00000354665.4_Missense_Mutation_p.E390A	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	390					apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.E390A(1)		NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					ACCAGGCGCCTCTATCACCTG	0.468																																					p.E390A	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1169C	20						.						67.0	74.0	71.0					20																	61538704		2203	4300	6503	61009149	SO:0001583	missense	11083	exon5			AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"""Zinc fingers, PHD-type"""	2680	protein-coding gene	gene with protein product		604140	"""chromosome 20 open reading frame 158"", ""death associated transcription factor 1"""	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.1169A>C	20.37:g.61538704T>G	ENSP00000266070:p.Glu390Ala		61009149	NM_022105	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Missense_Mutation	SNP	ENST00000266070.4	37	CCDS33506.1	.	.	.	.	.	.	.	.	.	.	T	13.71	2.317271	0.40996	.	.	ENSG00000101191	ENST00000266070;ENST00000395343;ENST00000395340;ENST00000395335;ENST00000370371;ENST00000370368;ENST00000354665;ENST00000370366;ENST00000266071	T;T;T;T;T;T;T;T;T	0.20200	2.96;2.96;2.6;2.6;2.09;2.09;2.09;2.09;2.09	4.96	4.96	0.65561	.	0.000000	0.43579	D	0.000552	T	0.42063	0.1186	M	0.62016	1.91	0.47308	D	0.999381	D;P;D;D	0.69078	0.981;0.95;0.997;0.991	P;P;D;P	0.65233	0.886;0.828;0.933;0.664	T	0.36286	-0.9754	10	0.72032	D	0.01	-33.048	14.9327	0.70929	0.0:0.0:0.0:1.0	.	390;390;390;390	Q9BTC0-2;Q9BTC0-3;Q9BTC0-1;Q9BTC0	.;.;.;DIDO1_HUMAN	A	390	ENSP00000266070:E390A;ENSP00000378752:E390A;ENSP00000378749:E390A;ENSP00000378744:E390A;ENSP00000359397:E390A;ENSP00000359394:E390A;ENSP00000346692:E390A;ENSP00000359391:E390A;ENSP00000266071:E390A	ENSP00000266070:E390A	E	-	2	0	DIDO1	61009149	1.000000	0.71417	0.228000	0.23943	0.044000	0.14063	7.182000	0.77689	2.001000	0.58596	0.459000	0.35465	GAG		0.468	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796	
KCNQ2	3785	broad.mit.edu	37	20	62051006	62051006	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr20:62051006C>A	ENST00000359125.2	-	12	1441	c.1267G>T	c.(1267-1269)Ggg>Tgg	p.G423W	KCNQ2_ENST00000360480.3_Intron|KCNQ2_ENST00000344462.4_Intron|KCNQ2_ENST00000359689.1_Missense_Mutation_p.G423W|KCNQ2_ENST00000354587.3_Intron|KCNQ2_ENST00000370224.1_Intron|KCNQ2_ENST00000357249.2_Intron	NM_172107.2	NP_742105.1	O43526	KCNQ2_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 2	423					axon guidance (GO:0007411)|nervous system development (GO:0007399)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ankyrin binding (GO:0030506)|delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)	p.G423W(1)		biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|liver(1)|lung(30)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	CACAGGGGCCCTCTGCACGGG	0.652																																					p.G423W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1267T	20						.						38.0	36.0	37.0					20																	62051006		2203	4299	6502	61521450	SO:0001583	missense	3785	exon12			AF033348	CCDS13518.1, CCDS13519.1, CCDS13520.1, CCDS13521.1, CCDS46629.1	20q13.33	2012-07-05			ENSG00000075043	ENSG00000075043		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6296	protein-coding gene	gene with protein product		602235		EBN, EBN1		9425895, 16382104	Standard	NM_172107		Approved	Kv7.2, ENB1, BFNC, KCNA11, HNSPC	uc002yex.3	O43526	OTTHUMG00000033049	ENST00000359125.2:c.1267G>T	20.37:g.62051006C>A	ENSP00000352035:p.Gly423Trp		61521450	NM_172107	O43796|O75580|O95845|Q4VXP4|Q4VXR6|Q5VYT8|Q96J59|Q99454	Missense_Mutation	SNP	ENST00000359125.2	37	CCDS13520.1	.	.	.	.	.	.	.	.	.	.	C	15.47	2.843188	0.51057	.	.	ENSG00000075043	ENST00000359125;ENST00000359689	D;D	0.99060	-5.38;-5.38	4.83	3.88	0.44766	.	.	.	.	.	D	0.94892	0.8349	N	0.08118	0	0.80722	D	1	P	0.39831	0.69	B	0.35971	0.215	D	0.93879	0.7169	9	0.72032	D	0.01	.	9.0779	0.36534	0.0:0.8302:0.0:0.1698	.	423	O43526	KCNQ2_HUMAN	W	423	ENSP00000352035:G423W;ENSP00000352718:G423W	ENSP00000352035:G423W	G	-	1	0	KCNQ2	61521450	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.672000	0.54583	1.026000	0.39733	0.655000	0.94253	GGG		0.652	KCNQ2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080353.1	NM_172109	
RTEL1	51750	broad.mit.edu	37	20	62290785	62290785	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr20:62290785C>T	ENST00000360203.5	+	2	355	c.30C>T	c.(28-30)acC>acT	p.T10T	RTEL1_ENST00000318100.4_Silent_p.T10T|RTEL1-TNFRSF6B_ENST00000482936.1_Silent_p.T10T|RTEL1_ENST00000508582.2_Silent_p.T10T|RTEL1_ENST00000488316.1_3'UTR|RTEL1_ENST00000370018.3_Silent_p.T10T					regulator of telomere elongation helicase 1									p.T10T(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(38;6.47e-12)|all_epithelial(29;3.75e-13)		Epithelial(9;1.25e-09)|all cancers(9;5.13e-09)|BRCA - Breast invasive adenocarcinoma(10;7.26e-05)|OV - Ovarian serous cystadenocarcinoma(5;0.00223)|Colorectal(105;0.107)			ATGGTGTGACCGTAGACTTCC	0.542																																					p.T10T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C30T	20						.						154.0	126.0	135.0					20																	62290785		2203	4300	6503	61761229	SO:0001819	synonymous_variant	51750	exon2			AB029011	CCDS13530.2, CCDS13531.1, CCDS13530.3, CCDS63331.1, CCDS74751.1	20q13.3	2012-06-27	2004-10-29	2004-10-29	ENSG00000258366	ENSG00000258366			15888	protein-coding gene	gene with protein product		608833	"""chromosome 20 open reading frame 41"""	C20orf41		10655513, 15210109	Standard	NM_016434		Approved	bK3184A7.3, NHL, DKFZP434C013, KIAA1088, RTEL	uc011abd.2	Q9NZ71	OTTHUMG00000032992	ENST00000360203.5:c.30C>T	20.37:g.62290785C>T			61761229	NM_016434		Silent	SNP	ENST00000360203.5	37																																																																																					0.542	RTEL1-011	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000289781.1	NM_032957	
SAMD10	140700	broad.mit.edu	37	20	62608360	62608360	+	Missense_Mutation	SNP	C	C	T	rs200217276		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr20:62608360C>T	ENST00000369886.3	-	3	583	c.409G>A	c.(409-411)Gtc>Atc	p.V137I	ZNF512B_ENST00000217130.3_Intron|SAMD10_ENST00000498830.1_5'UTR|ZNF512B_ENST00000450537.1_Intron	NM_080621.4	NP_542188.1	Q9BYL1	SAM10_HUMAN	sterile alpha motif domain containing 10	137	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.							p.V137I(1)		kidney(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|prostate(1)	7	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					TCCACGTAGACGAGGTAGTTG	0.632													C|||	1	0.000199681	0.0	0.0	5008	,	,		15940	0.0		0.001	False		,,,				2504	0.0				p.V137I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G409A	20						.						113.0	100.0	104.0					20																	62608360		2203	4300	6503	62078804	SO:0001583	missense	140700	exon3				CCDS13549.1	20q13.33	2013-01-10	2004-07-15	2004-07-16	ENSG00000130590	ENSG00000130590		"""Sterile alpha motif (SAM) domain containing"""	16129	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 136"""	C20orf136			Standard	NM_080621		Approved		uc002yhm.2	Q9BYL1	OTTHUMG00000033011	ENST00000369886.3:c.409G>A	20.37:g.62608360C>T	ENSP00000358902:p.Val137Ile		62078804	NM_080621		Missense_Mutation	SNP	ENST00000369886.3	37	CCDS13549.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	10.71	1.427973	0.25726	.	.	ENSG00000130590	ENST00000369886	D	0.84873	-1.91	4.86	1.42	0.22433	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 2 (1);	0.389123	0.25938	N	0.027340	T	0.60353	0.2262	N	0.01705	-0.755	0.26873	N	0.967706	B	0.06786	0.001	B	0.06405	0.002	T	0.52646	-0.8548	10	0.27785	T	0.31	-14.9007	7.0284	0.24952	0.0:0.6189:0.0:0.3811	.	137	Q9BYL1	SAM10_HUMAN	I	137	ENSP00000358902:V137I	ENSP00000358902:V137I	V	-	1	0	SAMD10	62078804	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	0.906000	0.28517	0.482000	0.27582	0.460000	0.39030	GTC		0.632	SAMD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080255.1	NM_080621	
DDX27	55661	broad.mit.edu	37	20	47858504	47858504	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr20:47858504delA	ENST00000371764.4	+	17	2074	c.2065delA	c.(2065-2067)aaafs	p.K691fs	ZNFX1_ENST00000469991.1_Intron|ZNFX1_ENST00000371754.4_Intron|DDX27_ENST00000484427.1_3'UTR	NM_017895.7	NP_060365.7	Q96GQ7	DDX27_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	691						nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)	p.K691fs*4(3)		NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	45			BRCA - Breast invasive adenocarcinoma(12;0.000899)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			GAAGGATGCCAAAAAAAAGGG	0.488																																					p.K689fs												.	.	3	Deletion - Frameshift(3)	large_intestine(2)|ovary(1)	c.2065delA	20						.						67.0	72.0	70.0					20																	47858504		2203	4300	6503	47291911	SO:0001589	frameshift_variant	55661	exon17			AL049766	CCDS13416.1	20q13.13	2010-07-06	2003-06-13		ENSG00000124228	ENSG00000124228		"""DEAD-boxes"""	15837	protein-coding gene	gene with protein product			"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 27"""				Standard	NM_017895		Approved	dJ686N3.1, DRS1	uc002xuh.3	Q96GQ7	OTTHUMG00000033072	ENST00000371764.4:c.2065delA	20.37:g.47858504delA	ENSP00000360828:p.Lys691fs		47291911	NM_017895	A0AVB6|B7ZLY1|Q5VXM7|Q8WYG4|Q969N7|Q96F57|Q96L97|Q9BWY9|Q9BXF0|Q9H990|Q9NWU3|Q9P0C2|Q9UGD6	Frame_Shift_Del	DEL	ENST00000371764.4	37	CCDS13416.1																																																																																				0.488	DDX27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080485.1		
TCEA2	6919	broad.mit.edu	37	20	62697850	62697850	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr20:62697850C>T	ENST00000343484.5	+	2	263	c.94C>T	c.(94-96)Cgg>Tgg	p.R32W	TCEA2_ENST00000465111.1_3'UTR|TCEA2_ENST00000395053.3_Missense_Mutation_p.R32W|TCEA2_ENST00000361317.2_Missense_Mutation_p.R5W	NM_003195.4	NP_003186.1	Q15560	TCEA2_HUMAN	transcription elongation factor A (SII), 2	32	TFIIS N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00649}.				DNA-templated transcription, elongation (GO:0006354)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription, elongation (GO:0032784)	centrosome (GO:0005813)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R32W(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)	12	all_cancers(38;3.45e-11)|all_epithelial(29;9.12e-13)|Lung NSC(23;2e-09)|all_lung(23;6.77e-09)					GGATTTGCTGCGGGAGCTGAA	0.582																																					p.R5W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C13T	20						.						100.0	99.0	99.0					20																	62697850		2203	4300	6503	62168294	SO:0001583	missense	6919	exon3			U86749	CCDS13553.1, CCDS13554.1	20q13.33	2011-01-25			ENSG00000171703	ENSG00000171703			11614	protein-coding gene	gene with protein product		604784				9441762, 8566795	Standard	NM_003195		Approved	TFIIS	uc021wgq.1	Q15560	OTTHUMG00000033026	ENST00000343484.5:c.94C>T	20.37:g.62697850C>T	ENSP00000343515:p.Arg32Trp		62168294	NM_198723	B3KNM1|Q8TD37|Q8TD38	Missense_Mutation	SNP	ENST00000343484.5	37	CCDS13553.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.093172	0.76756	.	.	ENSG00000171703	ENST00000361317;ENST00000343484;ENST00000395053;ENST00000339217;ENST00000415602;ENST00000440819;ENST00000458442	.	.	.	4.75	-2.37	0.06643	Transcription factor IIS, N-terminal (4);Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type (1);	0.361885	0.27917	N	0.017329	T	0.71281	0.3321	M	0.82630	2.6	0.37097	D	0.89972	D;D;D;D;D	0.89917	0.995;0.995;0.997;0.999;1.0	D;D;P;D;D	0.76575	0.952;0.952;0.901;0.979;0.988	T	0.74954	-0.3488	9	0.87932	D	0	-23.5336	9.582	0.39493	0.7187:0.1974:0.0:0.0838	.	32;32;5;5;32	Q15560;Q6IB64;Q5JRI7;B3KNM1;Q86VL0	TCEA2_HUMAN;.;.;.;.	W	5;32;32;5;5;5;5	.	ENSP00000339432:R5W	R	+	1	2	TCEA2	62168294	0.995000	0.38212	0.992000	0.48379	0.938000	0.57974	1.427000	0.34881	-0.092000	0.12417	0.563000	0.77884	CGG		0.582	TCEA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080277.2	NM_198723	
ADAMTS1	9510	broad.mit.edu	37	21	28216684	28216684	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr21:28216684G>A	ENST00000284984.3	-	1	1044	c.590C>T	c.(589-591)aCg>aTg	p.T197M		NM_006988.3	NP_008919.3	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 1	197					heart trabecula formation (GO:0060347)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|negative regulation of cell proliferation (GO:0008285)|ovulation from ovarian follicle (GO:0001542)	basement membrane (GO:0005604)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)	heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.T197M(1)		central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(20)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	42		Breast(209;0.000962)		Lung(58;0.215)		GACCCCGCACGTGCCGCCGAC	0.721											OREG0026151	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T197M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C590T	21						.						10.0	9.0	9.0					21																	28216684		2106	4146	6252	27138555	SO:0001583	missense	9510	exon1			AF060152	CCDS33524.1	21q21.3	2008-05-14	2005-08-19		ENSG00000154734	ENSG00000154734		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	217	protein-coding gene	gene with protein product		605174	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 1"""			10438512	Standard	NM_006988		Approved	C3-C5, METH1, KIAA1346	uc002ymf.3	Q9UHI8	OTTHUMG00000078688	ENST00000284984.3:c.590C>T	21.37:g.28216684G>A	ENSP00000284984:p.Thr197Met	800	27138555	NM_006988	D3DSD5|Q9NSJ8|Q9P2K0|Q9UH83|Q9UP80	Missense_Mutation	SNP	ENST00000284984.3	37	CCDS33524.1	.	.	.	.	.	.	.	.	.	.	G	11.75	1.730448	0.30684	.	.	ENSG00000154734	ENST00000284984	T	0.62364	0.03	3.85	1.44	0.22558	.	.	.	.	.	T	0.37156	0.0993	N	0.08118	0	0.25331	N	0.989031	B	0.10296	0.003	B	0.01281	0.0	T	0.19582	-1.0301	9	0.33940	T	0.23	.	6.2908	0.21059	0.0:0.0893:0.1676:0.7431	.	197	Q9UHI8	ATS1_HUMAN	M	197	ENSP00000284984:T197M	ENSP00000284984:T197M	T	-	2	0	ADAMTS1	27138555	1.000000	0.71417	0.987000	0.45799	0.499000	0.33736	0.731000	0.26058	0.114000	0.18032	-0.521000	0.04368	ACG		0.721	ADAMTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171650.2		
ADAMTS5	11096	broad.mit.edu	37	21	28338027	28338027	+	Silent	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr21:28338027C>A	ENST00000284987.5	-	1	805	c.684G>T	c.(682-684)ccG>ccT	p.P228P		NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	228					defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.P228P(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	72						CGCGTCCGCTCGGGTTGCTGT	0.746																																					p.P228P	Esophageal Squamous(53;683 1080 10100 14424 45938)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G684T	21						.						8.0	11.0	10.0					21																	28338027		2171	4199	6370	27259898	SO:0001819	synonymous_variant	11096	exon1			AF142099	CCDS13579.1	21q21.3	2008-07-31	2008-07-31		ENSG00000154736	ENSG00000154736		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	221	protein-coding gene	gene with protein product	"""aggrecanase-2"""	605007	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"""			10438522	Standard	NM_007038		Approved	ADMP-2, ADAMTS11	uc002ymg.3	Q9UNA0	OTTHUMG00000078686	ENST00000284987.5:c.684G>T	21.37:g.28338027C>A			27259898	NM_007038	Q52LV4|Q9UKP2	Silent	SNP	ENST00000284987.5	37	CCDS13579.1																																																																																				0.746	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1		
USP16	10600	broad.mit.edu	37	21	30422428	30422428	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr21:30422428C>T	ENST00000334352.4	+	17	2353	c.2122C>T	c.(2122-2124)Cgc>Tgc	p.R708C	USP16_ENST00000399975.3_Missense_Mutation_p.R707C|USP16_ENST00000535828.1_Missense_Mutation_p.R337C|USP16_ENST00000399976.2_Missense_Mutation_p.R708C	NM_001032410.1	NP_001027582.1			ubiquitin specific peptidase 16									p.R708C(1)		breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(2)	34						TTTTAACCTACGCAAAGTTAA	0.383																																					p.R707C	Melanoma(92;625 1444 27493 34101 44971)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2119T	21						.						82.0	79.0	80.0					21																	30422428		2202	4300	6502	29344299	SO:0001583	missense	10600	exon16			AF126736	CCDS13583.1, CCDS42912.1	21q21	2008-04-11	2005-08-08		ENSG00000156256	ENSG00000156256		"""Ubiquitin-specific peptidases"""	12614	protein-coding gene	gene with protein product		604735	"""ubiquitin specific protease 16"""			12838346	Standard	NM_006447		Approved	Ubp-M	uc002ymy.3	Q9Y5T5	OTTHUMG00000078802	ENST00000334352.4:c.2122C>T	21.37:g.30422428C>T	ENSP00000334808:p.Arg708Cys		29344299	NM_001001992		Missense_Mutation	SNP	ENST00000334352.4	37	CCDS13583.1	.	.	.	.	.	.	.	.	.	.	C	14.79	2.639723	0.47153	.	.	ENSG00000156256	ENST00000399975;ENST00000399976;ENST00000334352;ENST00000535828	T;T;T;T	0.31769	1.48;1.48;1.48;1.48	5.83	4.77	0.60923	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.107337	0.64402	D	0.000003	T	0.30448	0.0765	L	0.48260	1.515	0.54753	D	0.99998	B;B;B;B	0.28820	0.224;0.066;0.021;0.003	B;B;B;B	0.30572	0.117;0.017;0.008;0.009	T	0.05666	-1.0871	10	0.39692	T	0.17	.	15.8192	0.78626	0.0:0.9244:0.0:0.0756	.	337;693;707;708	B4DUS4;Q9Y5T5-3;Q9Y5T5-2;Q9Y5T5	.;.;.;UBP16_HUMAN	C	707;708;708;337	ENSP00000382857:R707C;ENSP00000382858:R708C;ENSP00000334808:R708C;ENSP00000442855:R337C	ENSP00000334808:R708C	R	+	1	0	USP16	29344299	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	4.082000	0.57635	2.758000	0.94735	0.655000	0.94253	CGC		0.383	USP16-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171847.1		
SCAF4	57466	broad.mit.edu	37	21	33044520	33044520	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr21:33044520C>T	ENST00000286835.7	-	20	3018	c.2636G>A	c.(2635-2637)cGt>cAt	p.R879H	SCAF4_ENST00000434667.3_Missense_Mutation_p.R864H|SCAF4_ENST00000399804.1_Missense_Mutation_p.R857H	NM_020706.2	NP_065757.1	O95104	SFR15_HUMAN	SR-related CTD-associated factor 4	879						nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R879H(1)		NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(11)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						TGGCATGGGACGGGGCGGCAT	0.637																																					p.R864H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2591A	21						.						66.0	65.0	65.0					21																	33044520		2203	4300	6503	31966391	SO:0001583	missense	57466	exon19			AB032998	CCDS33537.1, CCDS46644.1, CCDS54482.1	21q22.1	2013-02-12	2011-01-10	2011-01-10	ENSG00000156304	ENSG00000156304		"""RNA binding motif (RRM) containing"""	19304	protein-coding gene	gene with protein product			"""splicing factor, arginine/serine-rich 15"""	SFRS15		10574461	Standard	NM_020706		Approved	KIAA1172, DKFZp434E098, SRA4	uc002ypd.2	O95104	OTTHUMG00000084903	ENST00000286835.7:c.2636G>A	21.37:g.33044520C>T	ENSP00000286835:p.Arg879His		31966391	NM_001145444	C9JLZ0|Q0P5W8|Q6P1M5|Q8N3I8|Q9UFM1|Q9ULP8	Missense_Mutation	SNP	ENST00000286835.7	37	CCDS33537.1	.	.	.	.	.	.	.	.	.	.	C	9.985	1.229082	0.22542	.	.	ENSG00000156304	ENST00000434667;ENST00000286835;ENST00000399804	T;T;T	0.51325	0.8;0.79;0.71	5.13	5.13	0.70059	.	0.000000	0.64402	D	0.000003	T	0.37812	0.1017	L	0.27053	0.805	0.47153	D	0.999331	B;B;B	0.32800	0.266;0.385;0.266	B;B;B	0.29598	0.048;0.104;0.048	T	0.27606	-1.0069	10	0.48119	T	0.1	-12.4702	18.7778	0.91918	0.0:1.0:0.0:0.0	.	864;857;879	C9JLZ0;O95104-2;O95104	.;.;SFR15_HUMAN	H	864;879;857	ENSP00000402377:R864H;ENSP00000286835:R879H;ENSP00000382703:R857H	ENSP00000286835:R879H	R	-	2	0	SCAF4	31966391	0.995000	0.38212	0.664000	0.29753	0.175000	0.22909	3.205000	0.51090	2.671000	0.90904	0.555000	0.69702	CGT		0.637	SCAF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000192659.1	XM_047889	
PRDM15	63977	broad.mit.edu	37	21	43241454	43241454	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr21:43241454G>A	ENST00000269844.3	-	23	3237	c.3127C>T	c.(3127-3129)Cgt>Tgt	p.R1043C	PRDM15_ENST00000422911.1_Missense_Mutation_p.R734C|PRDM15_ENST00000447207.2_Missense_Mutation_p.R677C|PRDM15_ENST00000398548.1_Missense_Mutation_p.R714C|PRDM15_ENST00000538201.1_Missense_Mutation_p.R697C	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	1043					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)	p.R1043C(2)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(3)|skin(2)|stomach(2)|urinary_tract(1)	43						AGGTTTTCACGGTGGATGACC	0.602																																					p.R1043C												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.C3127T	21						.						157.0	138.0	144.0					21																	43241454		2203	4300	6503	42114523	SO:0001583	missense	63977	exon23			AF276513	CCDS13676.1, CCDS42932.1, CCDS63370.1	21q22.3	2013-01-08	2002-07-31		ENSG00000141956	ENSG00000141956		"""Zinc fingers, C2H2-type"""	13999	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 83"""	ZNF298, C21orf83		12036297, 12036298	Standard	NM_022115		Approved		uc002yzq.1	P57071	OTTHUMG00000086781	ENST00000269844.3:c.3127C>T	21.37:g.43241454G>A	ENSP00000269844:p.Arg1043Cys		42114523	NM_022115	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Missense_Mutation	SNP	ENST00000269844.3	37	CCDS13676.1	.	.	.	.	.	.	.	.	.	.	g	21.1	4.102361	0.76983	.	.	ENSG00000141956	ENST00000422911;ENST00000398548;ENST00000538201;ENST00000447207;ENST00000269844	T;T;T;T;T	0.09817	2.98;2.98;2.98;2.98;2.94	4.55	4.55	0.56014	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.21227	0.0511	L	0.31804	0.96	0.80722	D	1	D;D;P	0.89917	1.0;1.0;0.877	D;D;B	0.83275	0.996;0.996;0.307	T	0.01175	-1.1428	9	0.66056	D	0.02	-34.7344	13.3588	0.60644	0.0:0.0:0.842:0.1579	.	1043;734;714	P57071;E9PDJ6;E9PF37	PRD15_HUMAN;.;.	C	734;714;697;677;1043	ENSP00000408592:R734C;ENSP00000381556:R714C;ENSP00000444044:R697C;ENSP00000390245:R677C;ENSP00000269844:R1043C	ENSP00000269844:R1043C	R	-	1	0	PRDM15	42114523	1.000000	0.71417	0.999000	0.59377	0.972000	0.66771	3.375000	0.52410	2.244000	0.73946	0.556000	0.70494	CGT		0.602	PRDM15-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022115	
WDR4	10785	broad.mit.edu	37	21	44293771	44293771	+	Silent	SNP	A	A	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr21:44293771A>T	ENST00000398208.2	-	3	245	c.186T>A	c.(184-186)ggT>ggA	p.G62G	WDR4_ENST00000330317.2_Silent_p.G62G|WDR4_ENST00000492742.1_5'UTR	NM_001260474.1|NM_001260475.1|NM_001260476.1|NM_018669.5	NP_001247403.1|NP_001247404.1|NP_001247405.1|NP_061139.2			WD repeat domain 4									p.G62G(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|ovary(2)	11				Colorectal(79;0.0165)|Lung(125;0.0484)|STAD - Stomach adenocarcinoma(101;0.0624)|COAD - Colon adenocarcinoma(84;0.128)|LUSC - Lung squamous cell carcinoma(216;0.244)		CCAGAATCGCACCGCTCCCCT	0.522																																					p.G62G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T186A	21						.						105.0	92.0	96.0					21																	44293771		2203	4300	6503	43166840	SO:0001819	synonymous_variant	10785	exon3			AJ243912	CCDS13691.1	21q22.3	2013-01-09			ENSG00000160193	ENSG00000160193		"""WD repeat domain containing"""	12756	protein-coding gene	gene with protein product	"""TRM82 tRNA methyltransferase 82 homolog (S. cerevisiae)"""	605924				12403464	Standard	NM_018669		Approved	TRM82, TRMT82	uc002zci.4	P57081	OTTHUMG00000086826	ENST00000398208.2:c.186T>A	21.37:g.44293771A>T			43166840	NM_033661		Silent	SNP	ENST00000398208.2	37	CCDS13691.1																																																																																				0.522	WDR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195479.1		
CRYAA	1409	broad.mit.edu	37	21	44592189	44592189	+	Silent	SNP	C	C	T	rs145514574		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr21:44592189C>T	ENST00000291554.2	+	3	413	c.321C>T	c.(319-321)caC>caT	p.H107H	CRYAA_ENST00000482775.1_3'UTR|CRYAA_ENST00000398133.1_Silent_p.H87H|CRYAA_ENST00000398132.1_Silent_p.H70H	NM_000394.2	NP_000385.1	P02489	CRYAA_HUMAN	crystallin, alpha A	107					negative regulation of apoptotic process (GO:0043066)|negative regulation of intracellular transport (GO:0032387)|protein homooligomerization (GO:0051260)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural constituent of eye lens (GO:0005212)|unfolded protein binding (GO:0051082)	p.H107H(1)		NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)	11						AGGACGACCACGGCTACATTT	0.677																																					p.H107H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C321T	21						.	C		1,4405	2.1+/-5.4	0,1,2202	68.0	58.0	61.0		321	-3.4	1.0	21	dbSNP_134	61	0,8600		0,0,4300	no	coding-synonymous	CRYAA	NM_000394.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		107/174	44592189	1,13005	2203	4300	6503	43465258	SO:0001819	synonymous_variant	1409	exon3				CCDS13695.1	21q22.3	2011-09-05			ENSG00000160202	ENSG00000160202		"""Heat shock proteins / HSPB"""	2388	protein-coding gene	gene with protein product		123580		CRYA1			Standard	XM_005261093		Approved	HSPB4	uc002zdd.1	P02489	OTTHUMG00000086842	ENST00000291554.2:c.321C>T	21.37:g.44592189C>T			43465258	NM_000394	Q53X53	Silent	SNP	ENST00000291554.2	37	CCDS13695.1																																																																																				0.677	CRYAA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195562.1		
SIK1	150094	broad.mit.edu	37	21	44841645	44841645	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr21:44841645G>A	ENST00000270162.6	-	5	504	c.372C>T	c.(370-372)aaC>aaT	p.N124N		NM_173354.3	NP_775490.2	P57059	SIK1_HUMAN	salt-inducible kinase 1	124	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac muscle cell differentiation (GO:0055007)|cell cycle (GO:0007049)|entrainment of circadian clock by photoperiod (GO:0043153)|intracellular signal transduction (GO:0035556)|negative regulation of CREB transcription factor activity (GO:0032792)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of triglyceride biosynthetic process (GO:0010868)|positive regulation of anoikis (GO:2000210)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell differentiation (GO:0045595)|regulation of mitotic cell cycle (GO:0007346)|regulation of myotube differentiation (GO:0010830)|regulation of sodium ion transport (GO:0002028)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|cAMP response element binding protein binding (GO:0008140)|magnesium ion binding (GO:0000287)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)	p.N124N(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|testis(2)|urinary_tract(1)	21					Dabrafenib(DB08912)	TCCGCGCCTCGTTCTCACTCA	0.582																																					p.N124N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C372T	21						.						58.0	53.0	55.0					21																	44841645		2203	4300	6503	43666073	SO:0001819	synonymous_variant	150094	exon5			BC038504	CCDS33575.1	21q22.3	2008-12-23	2008-12-23	2008-12-23	ENSG00000142178	ENSG00000142178			11142	protein-coding gene	gene with protein product	"""myocardial SNF1-like kinase"""	605705	"""SNF1-like kinase"""	SNF1LK		7893599	Standard	NM_173354		Approved	msk	uc002zdf.2	P57059	OTTHUMG00000086874	ENST00000270162.6:c.372C>T	21.37:g.44841645G>A			43666073	NM_173354	A6NC84|Q5R2V5|Q6ZNL8|Q86YJ2	Silent	SNP	ENST00000270162.6	37	CCDS33575.1																																																																																				0.582	SIK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195654.1	NM_173354	
AGPAT3	56894	broad.mit.edu	37	21	45390556	45390556	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr21:45390556C>T	ENST00000398063.2	+	5	1025	c.533C>T	c.(532-534)aCg>aTg	p.T178M	AGPAT3_ENST00000327505.2_Missense_Mutation_p.T178M|AGPAT3_ENST00000398061.1_Missense_Mutation_p.T178M|AGPAT3_ENST00000398058.1_Missense_Mutation_p.T178M|AGPAT3_ENST00000291572.8_Missense_Mutation_p.T178M|AGPAT3_ENST00000546158.1_Missense_Mutation_p.T178M|AGPAT3_ENST00000479117.1_3'UTR	NM_001037553.1	NP_001032642.1	Q9NRZ7	PLCC_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 3	178					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)	p.T178M(1)		large_intestine(4)|lung(5)|ovary(1)|prostate(1)	11				STAD - Stomach adenocarcinoma(101;0.18)|Colorectal(79;0.24)		TGCGAGGGGACGCGCTTCACG	0.627																																					p.T178M	Pancreas(60;623 1650 5574 52796)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C533T	21						.						68.0	55.0	60.0					21																	45390556		2203	4300	6503	44214984	SO:0001583	missense	56894	exon6			AF156774	CCDS13703.1	21q22.3	2013-02-05			ENSG00000160216	ENSG00000160216	2.3.1.51	"""1-acylglycerol-3-phosphate O-acyltransferases"""	326	protein-coding gene	gene with protein product		614794					Standard	XM_005261159		Approved	LPAAT-gamma	uc002zdw.3	Q9NRZ7	OTTHUMG00000086892	ENST00000398063.2:c.533C>T	21.37:g.45390556C>T	ENSP00000381140:p.Thr178Met		44214984	NM_020132	D3DSL2|Q3ZCU2|Q6UWP6|Q6ZUC6|Q8N3Q7|Q9NRZ6	Missense_Mutation	SNP	ENST00000398063.2	37	CCDS13703.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.235422	0.79800	.	.	ENSG00000160216	ENST00000291572;ENST00000398061;ENST00000327505;ENST00000398063;ENST00000438598;ENST00000398058;ENST00000457068;ENST00000422850;ENST00000546158	D;D;D;D;D;D;D;D	0.97688	-4.49;-4.49;-4.49;-4.49;-4.49;-4.49;-4.49;-4.49	4.48	4.48	0.54585	Phospholipid/glycerol acyltransferase (2);	0.000000	0.85682	D	0.000000	D	0.99121	0.9697	H	0.95114	3.625	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	D	0.99264	1.0891	10	0.87932	D	0	-18.8622	17.1642	0.86811	0.0:1.0:0.0:0.0	.	198;178	Q9NRZ7-3;Q9NRZ7	.;PLCC_HUMAN	M	178	ENSP00000291572:T178M;ENSP00000381138:T178M;ENSP00000332989:T178M;ENSP00000381140:T178M;ENSP00000381135:T178M;ENSP00000413906:T178M;ENSP00000414440:T178M;ENSP00000443510:T178M	ENSP00000291572:T178M	T	+	2	0	AGPAT3	44214984	1.000000	0.71417	0.996000	0.52242	0.657000	0.38888	7.258000	0.78371	2.049000	0.60858	0.313000	0.20887	ACG		0.627	AGPAT3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195722.1	NM_020132	
TRPM2	7226	broad.mit.edu	37	21	45855046	45855046	+	Missense_Mutation	SNP	G	G	A	rs550041022		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr21:45855046G>A	ENST00000397928.1	+	28	4452	c.4007G>A	c.(4006-4008)cGc>cAc	p.R1336H	TRPM2_ENST00000300481.9_Missense_Mutation_p.R1282H|snoZ6_ENST00000581669.1_RNA|TRPM2_ENST00000300482.5_Missense_Mutation_p.R1336H|TRPM2_ENST00000397932.2_Missense_Mutation_p.R1386H|TRPM2_ENST00000498430.1_3'UTR	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	1336					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)	p.R1336H(1)		breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						CTGCGTGGGCGCGGGAGCCTC	0.667													G|||	1	0.000199681	0.0008	0.0	5008	,	,		15646	0.0		0.0	False		,,,				2504	0.0				p.R1336H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4007A	21						.						89.0	82.0	84.0					21																	45855046		2203	4300	6503	44679474	SO:0001583	missense	7226	exon28			AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Nudix motif containing"""	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.4007G>A	21.37:g.45855046G>A	ENSP00000381023:p.Arg1336His		44679474	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Missense_Mutation	SNP	ENST00000397928.1	37	CCDS13710.1	.	.	.	.	.	.	.	.	.	.	G	18.11	3.551389	0.65311	.	.	ENSG00000142185	ENST00000300482;ENST00000397928;ENST00000300481;ENST00000397932;ENST00000540347	T;T;T;T	0.79033	-1.23;-1.23;2.42;-1.23	4.86	4.86	0.63082	NUDIX hydrolase domain-like (1);	0.000000	0.64402	D	0.000003	D	0.88526	0.6460	M	0.91459	3.21	0.20074	N	0.999936	D;D;D;D	0.71674	0.998;0.99;0.998;0.966	D;P;P;P	0.63703	0.917;0.72;0.751;0.635	T	0.82448	-0.0452	10	0.87932	D	0	-4.4048	11.4611	0.50211	0.0897:0.0:0.9103:0.0	.	17;1386;1122;1336	B4DVI8;E9PGK7;Q5KTC1;O94759	.;.;.;TRPM2_HUMAN	H	1336;1336;1282;1386;80	ENSP00000300482:R1336H;ENSP00000381023:R1336H;ENSP00000300481:R1282H;ENSP00000381026:R1386H	ENSP00000300481:R1282H	R	+	2	0	TRPM2	44679474	0.850000	0.29656	0.224000	0.23877	0.653000	0.38743	3.901000	0.56303	2.420000	0.82092	0.543000	0.68304	CGC		0.667	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307	
ITGB2	3689	broad.mit.edu	37	21	46321585	46321585	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr21:46321585C>T	ENST00000397850.2	-	7	1015	c.563G>A	c.(562-564)cGa>cAa	p.R188Q	ITGB2_ENST00000355153.4_Missense_Mutation_p.R188Q|ITGB2_ENST00000397854.3_Missense_Mutation_p.R131Q|ITGB2_ENST00000397857.1_Missense_Mutation_p.R188Q|ITGB2_ENST00000397852.1_Missense_Mutation_p.R188Q|ITGB2_ENST00000302347.5_Missense_Mutation_p.R188Q			P05107	ITB2_HUMAN	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)	188	VWFA.				apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|receptor clustering (GO:0043113)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|glycoprotein binding (GO:0001948)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)	p.N181fs*20(1)|p.R188Q(1)|p.V180fs*21(1)		breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(4)|skin(3)	35				Colorectal(79;0.0669)	Simvastatin(DB00641)	GCATGGGTTTCGCAGCTTATC	0.607																																					p.R188Q												.	.	3	Deletion - Frameshift(2)|Substitution - Missense(1)	breast(2)|large_intestine(1)	c.G563A	21						.						145.0	129.0	135.0					21																	46321585		2203	4300	6503	45146013	SO:0001583	missense	3689	exon6			AK222505	CCDS13716.1	21q22.3	2014-09-17	2006-03-02		ENSG00000160255	ENSG00000160255		"""CD molecules"", ""Complement system"", ""Integrins"""	6155	protein-coding gene	gene with protein product		600065	"""integrin, beta 2 (antigen CD18 (p95), lymphocyte function-associated antigen 1; macrophage antigen 1 (mac-1) beta subunit)"""	CD18, MFI7			Standard	NM_000211		Approved	LFA-1, MAC-1	uc002zgf.3	P05107	OTTHUMG00000090257	ENST00000397850.2:c.563G>A	21.37:g.46321585C>T	ENSP00000380948:p.Arg188Gln		45146013	NM_001127491	B3KTS8|D3DSM1|Q16418|Q53HS5|Q9UD72	Missense_Mutation	SNP	ENST00000397850.2	37	CCDS13716.1	.	.	.	.	.	.	.	.	.	.	C	7.102	0.574353	0.13623	.	.	ENSG00000160255	ENST00000397852;ENST00000397857;ENST00000397854;ENST00000355153;ENST00000397850;ENST00000302347;ENST00000545414;ENST00000320216	D;D;D;D;D;D;D	0.92299	-3.01;-3.01;-3.01;-3.01;-3.01;-3.01;-3.01	4.14	-1.16	0.09678	Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);	.	.	.	.	D	0.86188	0.5873	L	0.42245	1.32	0.09310	N	1	B;B	0.27416	0.178;0.018	B;B	0.21917	0.037;0.007	T	0.73733	-0.3890	9	0.42905	T	0.14	.	8.5444	0.33413	0.0:0.2696:0.0:0.7304	.	131;188	A8MYE6;P05107	.;ITB2_HUMAN	Q	188;188;131;188;188;188;131;179	ENSP00000380950:R188Q;ENSP00000380955:R188Q;ENSP00000380952:R131Q;ENSP00000347279:R188Q;ENSP00000380948:R188Q;ENSP00000303242:R188Q;ENSP00000317697:R179Q	ENSP00000303242:R188Q	R	-	2	0	ITGB2	45146013	0.000000	0.05858	0.169000	0.22859	0.035000	0.12851	-0.006000	0.12833	-0.223000	0.09943	0.555000	0.69702	CGA		0.607	ITGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206566.2	NM_000211	
ADARB1	104	broad.mit.edu	37	21	46595934	46595934	+	Silent	SNP	G	G	A	rs201356458		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr21:46595934G>A	ENST00000360697.3	+	2	333	c.318G>A	c.(316-318)gcG>gcA	p.A106A	ADARB1_ENST00000348831.4_Silent_p.A106A|ADARB1_ENST00000539173.1_Silent_p.A106A|ADARB1_ENST00000437626.1_Intron|ADARB1_ENST00000389863.4_Silent_p.A106A			P78563	RED1_HUMAN	adenosine deaminase, RNA-specific, B1	106	DRBM 1. {ECO:0000255|PROSITE- ProRule:PRU00266}.				adenosine to inosine editing (GO:0006382)|base conversion or substitution editing (GO:0016553)|defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|positive regulation of viral genome replication (GO:0045070)|regulation of cell cycle (GO:0051726)|RNA processing (GO:0006396)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|double-stranded RNA adenosine deaminase activity (GO:0003726)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.A106A(2)		endometrium(4)|kidney(1)|large_intestine(3)|lung(8)|skin(1)	17				Colorectal(79;0.115)		CCGTGCACGCGCCTTTGTTTG	0.557																																					p.A106A												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G318A	21						.						113.0	118.0	116.0					21																	46595934		2203	4300	6503	45420362	SO:0001819	synonymous_variant	104	exon4			U76420	CCDS33589.1, CCDS33590.1, CCDS42970.1	21q22.3	2012-03-22	2010-06-24		ENSG00000197381	ENSG00000197381	3.5.-.-		226	protein-coding gene	gene with protein product	"""RED1 homolog (rat)"""	601218	"""adenosine deaminase, RNA-specific, B1 (homolog of rat RED1)"""			9143496, 14759252	Standard	NR_027672		Approved	ADAR2, DRADA2, ADAR2g, DRABA2, RED1, hRED1, ADAR2a-L1, ADAR2a-L2, ADAR2a-L3, ADAR2a, ADAR2b, ADAR2c, ADAR2d	uc002zgy.2	P78563	OTTHUMG00000090295	ENST00000360697.3:c.318G>A	21.37:g.46595934G>A			45420362	NM_015834	A6NFK8|A6NJ84|C3TTQ1|C3TTQ2|C9JUP4|G5E9B4|O00395|O00465|O00691|O00692|P78555|Q4AE79|Q6P0M9|Q8NFD1	Silent	SNP	ENST00000360697.3	37	CCDS33589.1																																																																																				0.557	ADARB1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206648.2	NM_015833	
NCAM2	4685	broad.mit.edu	37	21	22710732	22710732	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr21:22710732delA	ENST00000400546.1	+	8	1171	c.922delA	c.(922-924)aaafs	p.K308fs	NCAM2_ENST00000535285.1_Frame_Shift_Del_p.K333fs|NCAM2_ENST00000284894.7_Frame_Shift_Del_p.K166fs	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	308	Ig-like C2-type 4.				axonal fasciculation (GO:0007413)|neuron cell-cell adhesion (GO:0007158)|sensory perception of smell (GO:0007608)	axon (GO:0030424)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.N309fs*62(1)		breast(4)|cervix(2)|endometrium(8)|kidney(6)|large_intestine(22)|liver(4)|lung(49)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	108		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		AATACAGCTTAAAAATGAAAC	0.383																																					p.K308fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.922delA	21						.						59.0	57.0	58.0					21																	22710732		1855	4086	5941	21632603	SO:0001589	frameshift_variant	4685	exon8				CCDS42910.1	21q21	2013-02-11			ENSG00000154654	ENSG00000154654		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7657	protein-coding gene	gene with protein product		602040				9226371	Standard	NM_004540		Approved	NCAM21, MGC51008	uc002yld.2	O15394	OTTHUMG00000078121	ENST00000400546.1:c.922delA	21.37:g.22710732delA	ENSP00000383392:p.Lys308fs		21632603	NM_004540	A8MQ06|B7Z841|Q7Z7F2	Frame_Shift_Del	DEL	ENST00000400546.1	37	CCDS42910.1																																																																																				0.383	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540	
SLC19A1	6573	broad.mit.edu	37	21	46951414	46951414	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr21:46951414C>T	ENST00000311124.4	-	3	990	c.838G>A	c.(838-840)Ggc>Agc	p.G280S	SLC19A1_ENST00000380010.4_Missense_Mutation_p.G280S|SLC19A1_ENST00000485649.2_Missense_Mutation_p.G240S|SLC19A1_ENST00000567670.1_Missense_Mutation_p.G280S	NM_194255.2	NP_919231.1	P41440	S19A1_HUMAN	solute carrier family 19 (folate transporter), member 1	280					folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|methotrexate transporter activity (GO:0015350)	p.G280S(1)		endometrium(4)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	10				Colorectal(79;0.0569)|READ - Rectum adenocarcinoma(84;0.172)	Methotrexate(DB00563)|Pralatrexate(DB06813)	AGGTAGTAGCCGGCCGAGTTG	0.672																																					p.G280S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G838A	21						.						57.0	67.0	64.0					21																	46951414		2203	4300	6503	45775842	SO:0001583	missense	6573	exon3			U15939	CCDS13725.1, CCDS56217.1, CCDS56218.1	21q22.3	2013-05-22			ENSG00000173638	ENSG00000173638		"""Solute carriers"""	10937	protein-coding gene	gene with protein product		600424				9570943	Standard	NM_194255		Approved	FOLT	uc002zhl.2	P41440	OTTHUMG00000090397	ENST00000311124.4:c.838G>A	21.37:g.46951414C>T	ENSP00000308895:p.Gly280Ser		45775842	NM_194255	B2R7U8|B7Z8C3|E9PFY4|O00553|O60227|Q13026|Q9BTX8	Missense_Mutation	SNP	ENST00000311124.4	37	CCDS13725.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.818805	0.90873	.	.	ENSG00000173638	ENST00000380014;ENST00000311124;ENST00000380010;ENST00000485649	D;D;D	0.90504	-2.68;-2.68;-2.68	4.09	4.09	0.47781	Major facilitator superfamily domain, general substrate transporter (1);	0.055638	0.64402	D	0.000001	D	0.95968	0.8687	M	0.91196	3.185	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.73380	0.98;0.98;0.966;0.98	D	0.96949	0.9693	10	0.72032	D	0.01	-28.3551	15.2444	0.73497	0.0:1.0:0.0:0.0	.	240;302;280;280	B7Z8C3;D3DSM6;E9PFY4;P41440	.;.;.;S19A1_HUMAN	S	27;280;280;240	ENSP00000308895:G280S;ENSP00000369347:G280S;ENSP00000441772:G240S	ENSP00000308895:G280S	G	-	1	0	SLC19A1	45775842	1.000000	0.71417	0.920000	0.36463	0.803000	0.45373	6.974000	0.76122	2.018000	0.59344	0.313000	0.20887	GGC		0.672	SLC19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206796.1		
GAB4	128954	broad.mit.edu	37	22	17473038	17473038	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:17473038C>T	ENST00000400588.1	-	2	310	c.203G>A	c.(202-204)cGg>cAg	p.R68Q	GAB4_ENST00000523144.1_5'UTR	NM_001037814.1	NP_001032903.1	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member 4	68	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.							p.R68Q(1)|p.R68L(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(24)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44		all_epithelial(15;0.112)|Lung NSC(13;0.248)				CTGGCCCCTCCGCAGGATAAA	0.498																																					p.R68Q												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G203A	22						.						132.0	140.0	137.0					22																	17473038		2188	4298	6486	15853038	SO:0001583	missense	128954	exon2			AK057252	CCDS42976.1	22q11.2	2013-01-10			ENSG00000215568	ENSG00000215568		"""Pleckstrin homology (PH) domain containing"""	18325	protein-coding gene	gene with protein product							Standard	NM_001037814		Approved		uc002zlw.3	Q2WGN9	OTTHUMG00000149992	ENST00000400588.1:c.203G>A	22.37:g.17473038C>T	ENSP00000383431:p.Arg68Gln		15853038	NM_001037814		Missense_Mutation	SNP	ENST00000400588.1	37	CCDS42976.1	.	.	.	.	.	.	.	.	.	.	C	10.87	1.472798	0.26423	.	.	ENSG00000215568	ENST00000400588	T	0.76448	-1.02	1.81	-1.75	0.08031	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	U	0.000000	T	0.73257	0.3564	M	0.73598	2.24	0.36738	D	0.882052	P	0.51537	0.946	P	0.45167	0.472	T	0.72494	-0.4276	10	0.66056	D	0.02	.	6.3963	0.21614	0.0:0.5727:0.0:0.4273	.	68	Q2WGN9	GAB4_HUMAN	Q	68	ENSP00000383431:R68Q	ENSP00000383431:R68Q	R	-	2	0	GAB4	15853038	1.000000	0.71417	0.760000	0.31359	0.006000	0.05464	4.177000	0.58276	-0.407000	0.07576	-1.860000	0.00561	CGG		0.498	GAB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315426.1	XM_372882	
CECR2	27443	broad.mit.edu	37	22	18031734	18031734	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:18031734C>T	ENST00000400585.2	+	18	4242	c.3804C>T	c.(3802-3804)gtC>gtT	p.V1268V	CECR2_ENST00000400573.5_Silent_p.V1410V|CECR2_ENST00000262608.8_Silent_p.V1411V			Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2	1452					apoptotic DNA fragmentation (GO:0006309)|ATP-dependent chromatin remodeling (GO:0043044)|cytokinesis (GO:0000910)|cytoskeleton organization (GO:0007010)|execution phase of apoptosis (GO:0097194)|neural tube development (GO:0021915)|vesicle-mediated transport (GO:0016192)	CERF complex (GO:0090537)|nucleus (GO:0005634)		p.V1410V(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	59		all_epithelial(15;0.139)		Lung(27;0.146)		TGCACCCGGTCCAGTCGCAGG	0.522																																					p.S1411F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4232T	22						.						68.0	73.0	71.0					22																	18031734		2080	4208	6288	16411734	SO:0001819	synonymous_variant	27443	exon17			AF336133		22q11.2	2012-04-19			ENSG00000099954	ENSG00000099954			1840	protein-coding gene	gene with protein product		607576				11381032	Standard	XM_006724077		Approved	KIAA1740	uc002zml.2	Q9BXF3	OTTHUMG00000150072	ENST00000400585.2:c.3804C>T	22.37:g.18031734C>T			16411734	NM_031413	A8MS90|A8MX16|Q658Z4|Q96P58|Q9C0C3	Silent	SNP	ENST00000400585.2	37																																																																																					0.522	CECR2-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000316226.2	NM_031413	
GSC2	2928	broad.mit.edu	37	22	19136533	19136533	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:19136533C>T	ENST00000086933.2	-	3	588	c.589G>A	c.(589-591)Gtc>Atc	p.V197I		NM_005315.1	NP_005306.1	O15499	GSC2_HUMAN	goosecoid homeobox 2	197					anatomical structure morphogenesis (GO:0009653)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.V197I(1)		central_nervous_system(1)|large_intestine(1)|lung(2)	4	Colorectal(54;0.0993)					GACTTCTTGACGCCGGGCAGG	0.637																																					p.V197I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G589A	22						.						8.0	9.0	9.0					22																	19136533		2179	4263	6442	17516533	SO:0001583	missense	2928	exon3				CCDS13757.1	22q11.21	2011-06-20	2007-08-28	2007-08-28	ENSG00000063515	ENSG00000063515		"""Homeoboxes / PRD class"""	4613	protein-coding gene	gene with protein product		601845	"""goosecoid-like"""	GSCL		9150167	Standard	NM_005315		Approved		uc011ags.2	O15499	OTTHUMG00000150122	ENST00000086933.2:c.589G>A	22.37:g.19136533C>T	ENSP00000086933:p.Val197Ile		17516533	NM_005315		Missense_Mutation	SNP	ENST00000086933.2	37	CCDS13757.1	.	.	.	.	.	.	.	.	.	.	C	11.65	1.702487	0.30232	.	.	ENSG00000063515	ENST00000086933	D	0.90620	-2.7	4.45	-3.86	0.04230	.	0.665589	0.14345	N	0.325499	T	0.76779	0.4035	L	0.27053	0.805	0.09310	N	1	B	0.25048	0.117	B	0.15052	0.012	T	0.62973	-0.6740	10	0.33940	T	0.23	-1.8577	1.8819	0.03230	0.214:0.3371:0.2935:0.1553	.	197	O15499	GSC2_HUMAN	I	197	ENSP00000086933:V197I	ENSP00000086933:V197I	V	-	1	0	GSC2	17516533	0.003000	0.15002	0.001000	0.08648	0.074000	0.17049	-0.447000	0.06828	-0.160000	0.11002	0.455000	0.32223	GTC		0.637	GSC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316440.2	NM_005315	
CLTCL1	8218	broad.mit.edu	37	22	19210287	19210287	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:19210287G>A	ENST00000263200.10	-	15	2410	c.2338C>T	c.(2338-2340)Cgt>Tgt	p.R780C	CLTCL1_ENST00000427926.1_Missense_Mutation_p.R780C|CLTCL1_ENST00000353891.5_Missense_Mutation_p.R780C	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	780	Heavy chain arm.|Proximal segment.				anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)	p.R780C(1)		breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					AAGCCAAAACGATCACACACG	0.502			T	?	ALCL																																p.R780C			Dom	yes		22	22q11.21	8218	"""clathrin, heavy polypeptide-like 1"""		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2338T	22						.						107.0	110.0	109.0					22																	19210287		2109	4225	6334	17590287	SO:0001583	missense	8218	exon15				CCDS46662.1, CCDS54497.1, CCDS46662.2, CCDS54497.2	22q11.2	2008-06-10	2006-09-29		ENSG00000070371	ENSG00000070371			2093	protein-coding gene	gene with protein product		601273	"""clathrin, heavy polypeptide-like 1"""	CLTCL		8844170, 15133132	Standard	NM_007098		Approved	CLTD, CLH22, CHC22	uc021wle.1	P53675	OTTHUMG00000150109	ENST00000263200.10:c.2338C>T	22.37:g.19210287G>A	ENSP00000445677:p.Arg780Cys		17590287	NM_001835	B7Z7U5|Q14017|Q15808|Q15809	Missense_Mutation	SNP	ENST00000263200.10	37	CCDS46662.1	.	.	.	.	.	.	.	.	.	.	G	12.28	1.890648	0.33348	.	.	ENSG00000070371	ENST00000353891;ENST00000263200;ENST00000427926	T;T;T	0.15487	2.42;2.42;2.42	4.17	-1.34	0.09143	Tetratricopeptide-like helical (1);	0.071181	0.56097	D	0.000033	T	0.43500	0.1250	M	0.91818	3.245	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.75484	0.985;0.986	T	0.52343	-0.8588	10	0.87932	D	0	-15.2981	10.2953	0.43620	0.0:0.1046:0.4596:0.4357	.	780;780	P53675-2;P53675	.;CLH2_HUMAN	C	780	ENSP00000439662:R780C;ENSP00000445677:R780C;ENSP00000441158:R780C	ENSP00000445677:R780C	R	-	1	0	CLTCL1	17590287	1.000000	0.71417	0.153000	0.22517	0.032000	0.12392	1.773000	0.38563	0.029000	0.15352	-0.314000	0.08810	CGT		0.502	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098	
SNAP29	9342	broad.mit.edu	37	22	21213406	21213406	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:21213406C>T	ENST00000215730.7	+	1	136	c.8C>T	c.(7-9)gCt>gTt	p.A3V	PI4KA_ENST00000572273.1_5'Flank|PI4KA_ENST00000255882.6_5'Flank	NM_004782.3	NP_004773.1	O95721	SNP29_HUMAN	synaptosomal-associated protein, 29kDa	3					autophagic vacuole fusion (GO:0000046)|exocytosis (GO:0006887)|membrane fusion (GO:0061025)|protein transport (GO:0015031)|vesicle targeting (GO:0006903)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|SNARE complex (GO:0031201)|synapse (GO:0045202)	SNAP receptor activity (GO:0005484)	p.A3V(1)		breast(1)|endometrium(1)|large_intestine(5)|lung(1)|upper_aerodigestive_tract(1)	9	all_cancers(11;2.77e-25)|all_epithelial(7;8.92e-24)|Lung NSC(8;1.49e-15)|all_lung(8;2.54e-14)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000592)|Lung(15;0.0117)			ACCATGTCAGCTTACCCTAAA	0.726																																					p.A3V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C8T	22						.						10.0	12.0	11.0					22																	21213406		2181	4263	6444	19543406	SO:0001583	missense	9342	exon1			AF115436	CCDS13784.1	22q11.21	2008-06-10	2002-08-29		ENSG00000099940	ENSG00000099940			11133	protein-coding gene	gene with protein product	"""soluble 29 kDa NSF attachment protein"""	604202	"""synaptosomal-associated protein, 29kD"""			9852078, 10591208	Standard	NM_004782		Approved	SNAP-29, CEDNIK	uc011ahw.2	O95721	OTTHUMG00000150765	ENST00000215730.7:c.8C>T	22.37:g.21213406C>T	ENSP00000215730:p.Ala3Val		19543406	NM_004782		Missense_Mutation	SNP	ENST00000215730.7	37	CCDS13784.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.364909	0.82463	.	.	ENSG00000099940	ENST00000215730	.	.	.	5.49	4.45	0.53987	.	0.055224	0.64402	D	0.000001	T	0.62998	0.2474	L	0.52573	1.65	0.47994	D	0.999566	D	0.56746	0.977	P	0.52793	0.709	T	0.66528	-0.5901	9	0.62326	D	0.03	-5.3519	14.2908	0.66275	0.0:0.8459:0.1541:0.0	.	3	O95721	SNP29_HUMAN	V	3	.	ENSP00000215730:A3V	A	+	2	0	SNAP29	19543406	0.956000	0.32656	0.849000	0.33467	0.132000	0.20833	2.009000	0.40903	1.266000	0.44231	0.585000	0.79938	GCT		0.726	SNAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320000.4	NM_004782	
CRKL	1399	broad.mit.edu	37	22	21304066	21304066	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:21304066G>A	ENST00000354336.3	+	3	1354	c.845G>A	c.(844-846)cGc>cAc	p.R282H		NM_005207.3	NP_005198.1	P46109	CRKL_HUMAN	v-crk avian sarcoma virus CT10 oncogene homolog-like	282	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.				activation of MAPKK activity (GO:0000186)|anterior/posterior pattern specification (GO:0009952)|blood vessel development (GO:0001568)|heart development (GO:0007507)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|parathyroid gland development (GO:0060017)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|thymus development (GO:0048538)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)	poly(A) RNA binding (GO:0044822)|SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)	p.R282H(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)	14	all_cancers(11;1.16e-25)|all_epithelial(7;3.37e-24)|Lung NSC(8;7.25e-16)|all_lung(8;1.37e-14)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.176)			GTGAACGGGCGCAAAGGGCTT	0.458																																					p.R282H	Pancreas(85;3 1441 23889 42519 42763)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G845A	22						.						203.0	192.0	196.0					22																	21304066		2203	4300	6503	19634066	SO:0001583	missense	1399	exon3				CCDS13785.1	22q11.21	2013-07-09	2013-07-09		ENSG00000099942	ENSG00000099942		"""SH2 domain containing"""	2363	protein-coding gene	gene with protein product		602007				8361759, 8798523	Standard	NM_005207		Approved		uc002ztf.2	P46109	OTTHUMG00000150807	ENST00000354336.3:c.845G>A	22.37:g.21304066G>A	ENSP00000346300:p.Arg282His		19634066	NM_005207	A8KA44|D3DX35	Missense_Mutation	SNP	ENST00000354336.3	37	CCDS13785.1	.	.	.	.	.	.	.	.	.	.	G	35	5.570661	0.96540	.	.	ENSG00000099942	ENST00000354336	T	0.10192	2.9	5.31	5.31	0.75309	Src homology-3 domain (2);Variant SH3 (1);	0.051635	0.85682	D	0.000000	T	0.31451	0.0797	L	0.61036	1.89	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.01367	-1.1373	10	0.87932	D	0	.	16.4745	0.84128	0.0:0.0:1.0:0.0	.	282	P46109	CRKL_HUMAN	H	282	ENSP00000346300:R282H	ENSP00000346300:R282H	R	+	2	0	CRKL	19634066	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	9.869000	0.99810	2.485000	0.83878	0.591000	0.81541	CGC		0.458	CRKL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320158.1	NM_005207	
PRAME	23532	broad.mit.edu	37	22	22890514	22890514	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:22890514A>C	ENST00000398741.1	-	6	1811	c.1505T>G	c.(1504-1506)cTg>cGg	p.L502R	PRAME_ENST00000539862.1_Missense_Mutation_p.L486R|PRAME_ENST00000402697.1_Missense_Mutation_p.L502R|PRAME_ENST00000405655.3_Missense_Mutation_p.L502R|PRAME_ENST00000424204.2_Missense_Mutation_p.L486R|PRAME_ENST00000543184.1_Missense_Mutation_p.L502R|PRAME_ENST00000398743.2_Missense_Mutation_p.L502R|PRAME_ENST00000485532.1_5'Flank	NM_206955.1	NP_996838.1	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma	502	Mediates interaction with RARA.				apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	retinoic acid receptor binding (GO:0042974)	p.L502R(1)		autonomic_ganglia(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)		READ - Rectum adenocarcinoma(21;0.0649)		ACAGGGGCACAGGATGGGCTC	0.532																																					p.L502R	Melanoma(73;1707 1838 15168 27201)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1505G	22						.						165.0	159.0	161.0					22																	22890514		2203	4300	6503	21220514	SO:0001583	missense	23532	exon6			U65011	CCDS13801.1	22q11.22	2013-01-17			ENSG00000185686	ENSG00000185686		"""-"""	9336	protein-coding gene	gene with protein product	"""cancer/testis antigen 130"""	606021		MAPE		9047241, 10591208	Standard	XM_006725402		Approved	CT130	uc002zwj.3	P78395	OTTHUMG00000151172	ENST00000398741.1:c.1505T>G	22.37:g.22890514A>C	ENSP00000381726:p.Leu502Arg		21220514	NM_206955	B2R6Y7|O43481|Q8IXN8	Missense_Mutation	SNP	ENST00000398741.1	37	CCDS13801.1	.	.	.	.	.	.	.	.	.	.	A	10.32	1.317109	0.23908	.	.	ENSG00000185686	ENST00000398743;ENST00000543184;ENST00000398741;ENST00000405655;ENST00000539862;ENST00000402697;ENST00000424204	T;T;T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74;0.74;0.74	3.67	1.49	0.22878	.	0.460218	0.18100	N	0.151715	T	0.54175	0.1842	L	0.61387	1.9	0.09310	N	1	D	0.56746	0.977	P	0.62089	0.898	T	0.41342	-0.9514	10	0.49607	T	0.09	.	3.0452	0.06151	0.6722:0.0:0.1172:0.2105	.	502	P78395	PRAME_HUMAN	R	502;502;502;502;486;502;486	ENSP00000381728:L502R;ENSP00000445675:L502R;ENSP00000381726:L502R;ENSP00000384343:L502R;ENSP00000445097:L486R;ENSP00000385198:L502R;ENSP00000407342:L486R	ENSP00000381726:L502R	L	-	2	0	PRAME	21220514	0.890000	0.30428	0.124000	0.21820	0.040000	0.13550	0.605000	0.24179	0.255000	0.21593	-0.350000	0.07774	CTG		0.532	PRAME-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321644.1	NM_206953	
PIWIL3	440822	broad.mit.edu	37	22	25120896	25120896	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:25120896G>A	ENST00000332271.5	-	18	2632	c.2216C>T	c.(2215-2217)gCg>gTg	p.A739V	PIWIL3_ENST00000532537.2_5'UTR|PIWIL3_ENST00000533313.1_Missense_Mutation_p.A621V|PIWIL3_ENST00000527701.1_Missense_Mutation_p.A621V	NM_001008496.3|NM_001255975.1	NP_001008496.2|NP_001242904.1	Q7Z3Z3	PIWL3_HUMAN	piwi-like RNA-mediated gene silencing 3	739	Piwi. {ECO:0000255|PROSITE- ProRule:PRU00150}.				cell differentiation (GO:0030154)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	RNA binding (GO:0003723)	p.A739V(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(15)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						CATCTTTTTCGCTTCATGGTC	0.418																																					p.A739V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2216T	22						.						158.0	126.0	137.0					22																	25120896		2203	4300	6503	23450896	SO:0001583	missense	440822	exon18			AB079368	CCDS33623.1	22q11.23	2013-02-15	2013-02-15		ENSG00000184571	ENSG00000184571		"""Argonaute/PIWI family"""	18443	protein-coding gene	gene with protein product		610314	"""piwi-like 3 (Drosophila)"""			12906857	Standard	NM_001008496		Approved	HIWI3	uc003abd.2	Q7Z3Z3	OTTHUMG00000150788	ENST00000332271.5:c.2216C>T	22.37:g.25120896G>A	ENSP00000330031:p.Ala739Val		23450896	NM_001008496		Missense_Mutation	SNP	ENST00000332271.5	37	CCDS33623.1	.	.	.	.	.	.	.	.	.	.	G	0.022	-1.413573	0.01145	.	.	ENSG00000184571	ENST00000332271;ENST00000533313;ENST00000527701	T;T;T	0.22336	1.96;1.96;1.96	2.84	1.78	0.24846	Stem cell self-renewal protein Piwi (3);Ribonuclease H-like (1);	0.591182	0.16680	N	0.203973	T	0.01800	0.0057	N	0.00009	-3.08	0.09310	N	1	B;B;B	0.20780	0.012;0.011;0.048	B;B;B	0.08055	0.0;0.0;0.003	T	0.40608	-0.9554	10	0.02654	T	1	-4.0519	4.2377	0.10634	0.8195:0.0:0.1805:0.0	.	621;730;739	E9PIP6;B4DYF7;Q7Z3Z3	.;.;PIWL3_HUMAN	V	739;621;621	ENSP00000330031:A739V;ENSP00000431843:A621V;ENSP00000435718:A621V	ENSP00000330031:A739V	A	-	2	0	PIWIL3	23450896	0.985000	0.35326	0.000000	0.03702	0.001000	0.01503	4.291000	0.59025	0.343000	0.23821	-0.378000	0.06908	GCG		0.418	PIWIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320084.2	NM_001008496	
SGSM1	129049	broad.mit.edu	37	22	25308689	25308689	+	Silent	SNP	G	G	A	rs527822776		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:25308689G>A	ENST00000400359.4	+	23	3070	c.3063G>A	c.(3061-3063)acG>acA	p.T1021T	SGSM1_ENST00000400358.4_Silent_p.T966T	NM_001039948.2|NM_133454.2	NP_001035037.1|NP_597711.1	Q2NKQ1	SGSM1_HUMAN	small G protein signaling modulator 1	1021	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.					Golgi apparatus (GO:0005794)	Rab GTPase activator activity (GO:0005097)	p.T966T(1)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(14)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	41						CCATGGACACGCACTTTGCAA	0.498													G|||	1	0.000199681	0.0	0.0	5008	,	,		18843	0.001		0.0	False		,,,				2504	0.0				p.T966T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2898A	22						.						90.0	90.0	90.0					22																	25308689		2155	4274	6429	23638689	SO:0001819	synonymous_variant	129049	exon22			AB075821	CCDS46674.1, CCDS46675.1, CCDS74834.1	22q11.23	2013-07-09	2007-08-14	2007-08-14	ENSG00000167037	ENSG00000167037		"""Small G protein signaling modulators"""	29410	protein-coding gene	gene with protein product		611417	"""RUN and TBC1 domain containing 2"""	RUTBC2		11853319, 17509819, 22637480	Standard	NM_133454		Approved	KIAA1941	uc003abg.2	Q2NKQ1	OTTHUMG00000150837	ENST00000400359.4:c.3063G>A	22.37:g.25308689G>A			23638689	NM_001098497	A5LGW1|A8MUT4|B0QYW0|B0QYW1|B5MEG1|B9A6J4|Q5TFL3|Q8TF60	Silent	SNP	ENST00000400359.4	37	CCDS46674.1																																																																																				0.498	SGSM1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320282.1	XM_059318	
CRYBB1	1414	broad.mit.edu	37	22	27003954	27003954	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:27003954C>T	ENST00000215939.2	-	4	461	c.331G>A	c.(331-333)Ggg>Agg	p.G111R		NM_001887.3	NP_001878.1	P53674	CRBB1_HUMAN	crystallin, beta B1	111	Beta/gamma crystallin 'Greek key' 2. {ECO:0000255|PROSITE-ProRule:PRU00028}.				visual perception (GO:0007601)		structural constituent of eye lens (GO:0005212)	p.G111R(1)		breast(1)|endometrium(4)|large_intestine(8)|lung(8)|ovary(1)|prostate(3)|skin(2)|urinary_tract(4)	31						AACATCTCCCCGCGGAAGTTG	0.557																																					p.G111R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G331A	22						.						92.0	74.0	80.0					22																	27003954		2203	4300	6503	25333954	SO:0001583	missense	1414	exon4				CCDS13840.1	22q12.1	2008-06-10			ENSG00000100122	ENSG00000100122			2397	protein-coding gene	gene with protein product		600929				8575764, 12360425	Standard	NM_001887		Approved		uc003acy.1	P53674	OTTHUMG00000150980	ENST00000215939.2:c.331G>A	22.37:g.27003954C>T	ENSP00000215939:p.Gly111Arg		25333954	NM_001887		Missense_Mutation	SNP	ENST00000215939.2	37	CCDS13840.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.993638	0.93167	.	.	ENSG00000100122	ENST00000215939	D	0.93133	-3.17	4.64	4.64	0.57946	Beta/gamma crystallin (5);Gamma-crystallin-related (1);	0.000000	0.85682	D	0.000000	D	0.97971	0.9332	H	0.97365	3.99	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99486	1.0949	10	0.87932	D	0	.	16.6379	0.85064	0.0:1.0:0.0:0.0	.	111	P53674	CRBB1_HUMAN	R	111	ENSP00000215939:G111R	ENSP00000215939:G111R	G	-	1	0	CRYBB1	25333954	1.000000	0.71417	0.961000	0.40146	0.962000	0.63368	5.522000	0.67092	2.401000	0.81631	0.585000	0.79938	GGG		0.557	CRYBB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320767.1	NM_001887	
CRYBB1	1414	broad.mit.edu	37	22	27008105	27008105	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:27008105G>A	ENST00000215939.2	-	3	360	c.230C>T	c.(229-231)tCg>tTg	p.S77L		NM_001887.3	NP_001878.1	P53674	CRBB1_HUMAN	crystallin, beta B1	77	Beta/gamma crystallin 'Greek key' 1. {ECO:0000255|PROSITE-ProRule:PRU00028}.				visual perception (GO:0007601)		structural constituent of eye lens (GO:0005212)	p.S77L(1)		breast(1)|endometrium(4)|large_intestine(8)|lung(8)|ovary(1)|prostate(3)|skin(2)|urinary_tract(4)	31						GCACTCCCCCGAGAATTCTGC	0.612																																					p.S77L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C230T	22						.						88.0	78.0	81.0					22																	27008105		2203	4300	6503	25338105	SO:0001583	missense	1414	exon3				CCDS13840.1	22q12.1	2008-06-10			ENSG00000100122	ENSG00000100122			2397	protein-coding gene	gene with protein product		600929				8575764, 12360425	Standard	NM_001887		Approved		uc003acy.1	P53674	OTTHUMG00000150980	ENST00000215939.2:c.230C>T	22.37:g.27008105G>A	ENSP00000215939:p.Ser77Leu		25338105	NM_001887		Missense_Mutation	SNP	ENST00000215939.2	37	CCDS13840.1	.	.	.	.	.	.	.	.	.	.	G	10.30	1.312232	0.23908	.	.	ENSG00000100122	ENST00000215939	T	0.77489	-1.1	3.85	3.85	0.44370	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.811995	0.11262	N	0.582484	T	0.71213	0.3313	L	0.54863	1.705	0.33899	D	0.638222	B	0.31209	0.313	B	0.27887	0.084	T	0.76088	-0.3087	10	0.51188	T	0.08	.	8.8646	0.35278	0.1045:0.0:0.8955:0.0	.	77	P53674	CRBB1_HUMAN	L	77	ENSP00000215939:S77L	ENSP00000215939:S77L	S	-	2	0	CRYBB1	25338105	0.935000	0.31712	0.999000	0.59377	0.438000	0.31896	1.500000	0.35682	1.961000	0.56991	0.491000	0.48974	TCG		0.612	CRYBB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320767.1	NM_001887	
CRYBA4	1413	broad.mit.edu	37	22	27021570	27021570	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:27021570G>A	ENST00000354760.3	+	4	319	c.284G>A	c.(283-285)cGg>cAg	p.R95Q	CRYBA4_ENST00000466315.1_3'UTR	NM_001886.2	NP_001877.1	P53673	CRBA4_HUMAN	crystallin, beta A4	95	Beta/gamma crystallin 'Greek key' 2. {ECO:0000255|PROSITE-ProRule:PRU00028}.				camera-type eye development (GO:0043010)|visual perception (GO:0007601)		structural constituent of eye lens (GO:0005212)	p.R95Q(1)		large_intestine(6)|liver(1)|lung(6)|skin(3)|urinary_tract(2)	18						ACCTCCTTCCGGCCTGCGGCC	0.597																																					p.R95Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G284A	22						.						91.0	95.0	94.0					22																	27021570		2203	4300	6503	25351570	SO:0001583	missense	1413	exon4				CCDS13841.1	22q12.1	2008-06-10			ENSG00000196431	ENSG00000196431			2396	protein-coding gene	gene with protein product		123631				8999933, 960806	Standard	NM_001886		Approved		uc003acz.4	P53673	OTTHUMG00000150983	ENST00000354760.3:c.284G>A	22.37:g.27021570G>A	ENSP00000346805:p.Arg95Gln		25351570	NM_001886	Q4VB22|Q6ICE4	Missense_Mutation	SNP	ENST00000354760.3	37	CCDS13841.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.886542	0.91814	.	.	ENSG00000196431	ENST00000354760	D	0.82344	-1.6	4.43	4.43	0.53597	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.061993	0.64402	D	0.000005	D	0.90242	0.6949	M	0.87269	2.87	0.80722	D	1	D	0.89917	1.0	P	0.59012	0.85	D	0.91644	0.5329	10	0.56958	D	0.05	.	14.5934	0.68386	0.0:0.0:1.0:0.0	.	95	P53673	CRBA4_HUMAN	Q	95	ENSP00000346805:R95Q	ENSP00000346805:R95Q	R	+	2	0	CRYBA4	25351570	1.000000	0.71417	0.999000	0.59377	0.710000	0.40934	8.309000	0.89969	2.304000	0.77564	0.561000	0.74099	CGG		0.597	CRYBA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320793.1	NM_001886	
ASCC2	84164	broad.mit.edu	37	22	30221101	30221101	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:30221101C>T	ENST00000397771.2	-	5	563	c.386G>A	c.(385-387)cGc>cAc	p.R129H	ASCC2_ENST00000542393.1_Missense_Mutation_p.R76H|ASCC2_ENST00000307790.3_Missense_Mutation_p.R129H			Q9H1I8	ASCC2_HUMAN	activating signal cointegrator 1 complex subunit 2	129					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)			p.R129H(1)		endometrium(3)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(5;0.000103)|Epithelial(10;0.0169)|all cancers(5;0.0259)			AGTGGACATGCGGAGGAAGGT	0.572																																					p.R129H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G386A	22						.						151.0	142.0	145.0					22																	30221101		2203	4300	6503	28551101	SO:0001583	missense	84164	exon4			AY013289	CCDS13869.1, CCDS56226.1	22q12.1	2004-07-27			ENSG00000100325	ENSG00000100325			24103	protein-coding gene	gene with protein product	"""ASC 1 complex subunit P100"""	614216				12077347, 9847074	Standard	NM_032204		Approved	ASC1p100, FLJ21588, DKFZp586O0223	uc003agr.3	Q9H1I8	OTTHUMG00000067658	ENST00000397771.2:c.386G>A	22.37:g.30221101C>T	ENSP00000380877:p.Arg129His		28551101	NM_032204	B7Z8E0|F5H6J9|Q4TT54|Q8TAZ0|Q9H711|Q9H9D6	Missense_Mutation	SNP	ENST00000397771.2	37	CCDS13869.1	.	.	.	.	.	.	.	.	.	.	C	33	5.194605	0.94960	.	.	ENSG00000100325	ENST00000307790;ENST00000397771;ENST00000542393;ENST00000431535;ENST00000412689	T;T;T;T;T	0.36340	1.26;1.26;1.26;1.26;1.26	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.66906	0.2837	M	0.85041	2.73	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.993;0.999	T	0.70718	-0.4795	10	0.87932	D	0	-16.435	19.1613	0.93533	0.0:1.0:0.0:0.0	.	76;129	F5H6J9;Q9H1I8	.;ASCC2_HUMAN	H	129;129;76;129;129	ENSP00000305502:R129H;ENSP00000380877:R129H;ENSP00000437570:R76H;ENSP00000412382:R129H;ENSP00000417032:R129H	ENSP00000305502:R129H	R	-	2	0	ASCC2	28551101	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.469000	0.80959	2.768000	0.95171	0.655000	0.94253	CGC		0.572	ASCC2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322127.1	NM_032204	
RFPL3	10738	broad.mit.edu	37	22	32756704	32756704	+	Missense_Mutation	SNP	G	G	A	rs140074264		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:32756704G>A	ENST00000249007.4	+	2	1044	c.839G>A	c.(838-840)cGc>cAc	p.R280H	RFPL3S_ENST00000400234.1_3'UTR|RFPL3_ENST00000397468.1_Missense_Mutation_p.R251H|RFPL3_ENST00000382088.3_Missense_Mutation_p.R251H|RFPL3S_ENST00000461833.1_5'UTR|RFPL3S_ENST00000382084.4_3'UTR	NM_001098535.1	NP_001092005.1	O75679	RFPL3_HUMAN	ret finger protein-like 3	280	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.						zinc ion binding (GO:0008270)	p.R280H(1)|p.R251H(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|stomach(1)	15						GAGCCACTGCGCCCATTTTTG	0.473																																					p.R251H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G752A	22						.	G	HIS/ARG,HIS/ARG	0,4406		0,0,2203	128.0	106.0	113.0		839,752	0.5	0.2	22	dbSNP_134	113	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	RFPL3	NM_001098535.1,NM_006604.2	29,29	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	possibly-damaging,possibly-damaging	280/318,251/289	32756704	2,13004	2203	4300	6503	31086704	SO:0001583	missense	10738	exon3			AJ010232	CCDS13904.1, CCDS43011.1	22q12	2006-04-25			ENSG00000128276	ENSG00000128276			9980	protein-coding gene	gene with protein product		605970				10508838	Standard	NM_006604		Approved		uc010gwn.3	O75679	OTTHUMG00000030290	ENST00000249007.4:c.839G>A	22.37:g.32756704G>A	ENSP00000249007:p.Arg280His		31086704	NM_006604	A2A279|Q6IC03|Q6IC04|Q6NSX3|Q8N5R4	Missense_Mutation	SNP	ENST00000249007.4	37	CCDS43011.1	.	.	.	.	.	.	.	.	.	.	G	9.110	1.006366	0.19199	0.0	2.33E-4	ENSG00000128276	ENST00000397468;ENST00000249007;ENST00000382088	T;T;T	0.69435	-0.4;-0.4;-0.4	0.475	0.475	0.16774	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	.	.	.	.	T	0.66742	0.2820	M	0.66560	2.04	0.09310	N	1	P	0.47762	0.9	P	0.50378	0.639	T	0.56269	-0.8007	9	0.49607	T	0.09	.	4.19	0.10416	0.0:0.4466:0.5533:1.0E-4	.	280	O75679	RFPL3_HUMAN	H	251;280;251	ENSP00000380609:R251H;ENSP00000249007:R280H;ENSP00000371520:R251H	ENSP00000249007:R280H	R	+	2	0	RFPL3	31086704	0.000000	0.05858	0.151000	0.22473	0.075000	0.17131	-0.991000	0.03728	0.473000	0.27368	0.205000	0.17691	CGC		0.473	RFPL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075172.3	NM_006604	
LARGE	9215	broad.mit.edu	37	22	33700318	33700318	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:33700318C>T	ENST00000354992.2	-	13	2198	c.1627G>A	c.(1627-1629)Gtg>Atg	p.V543M	LARGE_ENST00000437602.2_Missense_Mutation_p.V543M|LARGE_ENST00000337431.2_Missense_Mutation_p.V491M|LARGE_ENST00000397394.2_Missense_Mutation_p.V543M|LARGE_ENST00000452586.2_Missense_Mutation_p.V342M|LARGE_ENST00000402320.1_Missense_Mutation_p.V491M	NM_004737.4	NP_004728.1	O95461	LARGE_HUMAN	like-glycosyltransferase	543					glycoprotein biosynthetic process (GO:0009101)|glycosphingolipid biosynthetic process (GO:0006688)|muscle cell cellular homeostasis (GO:0046716)|N-acetylglucosamine metabolic process (GO:0006044)|protein glycosylation (GO:0006486)	integral component of Golgi membrane (GO:0030173)	acetylglucosaminyltransferase activity (GO:0008375)|transferase activity, transferring glycosyl groups (GO:0016757)	p.V543M(2)|p.V543L(1)		breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(1;0.219)				AGCAGGTTCACGGGGTAGAAC	0.572																																					p.V543M	Colon(70;397 1175 4573 19089 45288)											.	.	3	Substitution - Missense(3)	lung(2)|large_intestine(1)	c.G1627A	22						.						177.0	138.0	151.0					22																	33700318		2203	4300	6503	32030318	SO:0001583	missense	9215	exon12			AJ007583	CCDS13912.1	22q12.3	2013-02-22			ENSG00000133424	ENSG00000133424		"""Glycosyltransferase family 8 domain containing"""	6511	protein-coding gene	gene with protein product		603590				9892679, 10591208, 12966029	Standard	NM_004737		Approved	KIAA0609	uc003ane.4	O95461	OTTHUMG00000150914	ENST00000354992.2:c.1627G>A	22.37:g.33700318C>T	ENSP00000347088:p.Val543Met		32030318	NM_133642	B0QXZ7|O60348|Q17R80|Q9UGD1|Q9UGE7|Q9UGG3|Q9UGZ8|Q9UH22	Missense_Mutation	SNP	ENST00000354992.2	37	CCDS13912.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.973646	0.74246	.	.	ENSG00000133424	ENST00000443693;ENST00000429788;ENST00000354992;ENST00000337431;ENST00000397394;ENST00000402320;ENST00000452586;ENST00000437602	T;T;T;T;T;T	0.58210	1.84;1.84;1.84;1.84;1.84;0.35	5.33	4.31	0.51392	.	0.000000	0.85682	D	0.000000	T	0.76399	0.3982	M	0.90425	3.115	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.77004	0.989;0.939;0.973;0.989	T	0.81865	-0.0736	10	0.72032	D	0.01	-16.1227	13.9395	0.64046	0.0:0.9271:0.0:0.0729	.	543;342;491;543	B7Z2I9;E9PH73;O95461-2;O95461	.;.;.;LARGE_HUMAN	M	220;220;543;491;543;491;342;543	ENSP00000347088:V543M;ENSP00000336636:V491M;ENSP00000380549:V543M;ENSP00000385223:V491M;ENSP00000407917:V342M;ENSP00000388544:V543M	ENSP00000336636:V491M	V	-	1	0	LARGE	32030318	1.000000	0.71417	0.960000	0.40013	0.884000	0.51177	5.565000	0.67365	1.260000	0.44134	-0.251000	0.11542	GTG		0.572	LARGE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320515.2	NM_133642	
LARGE	9215	broad.mit.edu	37	22	34046575	34046575	+	Silent	SNP	G	G	A	rs535793068		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:34046575G>A	ENST00000354992.2	-	4	757	c.186C>T	c.(184-186)cgC>cgT	p.R62R	LARGE_ENST00000437602.2_Silent_p.R62R|LARGE_ENST00000337431.2_Silent_p.R62R|LARGE_ENST00000397394.2_Silent_p.R62R|LARGE_ENST00000402320.1_Silent_p.R62R	NM_004737.4	NP_004728.1	O95461	LARGE_HUMAN	like-glycosyltransferase	62					glycoprotein biosynthetic process (GO:0009101)|glycosphingolipid biosynthetic process (GO:0006688)|muscle cell cellular homeostasis (GO:0046716)|N-acetylglucosamine metabolic process (GO:0006044)|protein glycosylation (GO:0006486)	integral component of Golgi membrane (GO:0030173)	acetylglucosaminyltransferase activity (GO:0008375)|transferase activity, transferring glycosyl groups (GO:0016757)	p.R62R(1)		breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(1;0.219)				CCAGGCTCTCGCGCTCCCGCT	0.701													G|||	1	0.000199681	0.0	0.0	5008	,	,		16273	0.0		0.0	False		,,,				2504	0.001				p.R62R	Colon(70;397 1175 4573 19089 45288)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C186T	22						.						32.0	32.0	32.0					22																	34046575		2201	4297	6498	32376575	SO:0001819	synonymous_variant	9215	exon3			AJ007583	CCDS13912.1	22q12.3	2013-02-22			ENSG00000133424	ENSG00000133424		"""Glycosyltransferase family 8 domain containing"""	6511	protein-coding gene	gene with protein product		603590				9892679, 10591208, 12966029	Standard	NM_004737		Approved	KIAA0609	uc003ane.4	O95461	OTTHUMG00000150914	ENST00000354992.2:c.186C>T	22.37:g.34046575G>A			32376575	NM_133642	B0QXZ7|O60348|Q17R80|Q9UGD1|Q9UGE7|Q9UGG3|Q9UGZ8|Q9UH22	Silent	SNP	ENST00000354992.2	37	CCDS13912.1																																																																																				0.701	LARGE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320515.2	NM_133642	
HMOX1	3162	broad.mit.edu	37	22	35782824	35782824	+	Silent	SNP	C	C	T	rs201495169	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:35782824C>T	ENST00000216117.8	+	3	630	c.291C>T	c.(289-291)taC>taT	p.Y97Y		NM_002133.2	NP_002124.1	P09601	HMOX1_HUMAN	heme oxygenase (decycling) 1	97					angiogenesis (GO:0001525)|cell death (GO:0008219)|cellular iron ion homeostasis (GO:0006879)|cellular response to arsenic-containing substance (GO:0071243)|cellular response to cadmium ion (GO:0071276)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient (GO:0031670)|endothelial cell proliferation (GO:0001935)|erythrocyte homeostasis (GO:0034101)|excretion (GO:0007588)|heme catabolic process (GO:0042167)|heme oxidation (GO:0006788)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|iron ion homeostasis (GO:0055072)|low-density lipoprotein particle clearance (GO:0034383)|negative regulation of DNA binding (GO:0043392)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of mast cell cytokine production (GO:0032764)|negative regulation of mast cell degranulation (GO:0043305)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smooth muscle cell proliferation (GO:0048662)|porphyrin-containing compound metabolic process (GO:0006778)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of vasodilation (GO:0045909)|protein homooligomerization (GO:0051260)|regulation of angiogenesis (GO:0045765)|regulation of blood pressure (GO:0008217)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to estrogen (GO:0043627)|response to hydrogen peroxide (GO:0042542)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|smooth muscle hyperplasia (GO:0014806)|transmembrane transport (GO:0055085)|wound healing involved in inflammatory response (GO:0002246)	caveola (GO:0005901)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|heme binding (GO:0020037)|heme oxygenase (decyclizing) activity (GO:0004392)|metal ion binding (GO:0046872)|phospholipase D activity (GO:0004630)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)	p.Y97Y(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	16					Vitamin E(DB00163)	CCTTCTGGTACGGGCCCCGCT	0.647													C|||	12	0.00239617	0.0008	0.0	5008	,	,		17597	0.0		0.0	False		,,,				2504	0.0112				p.Y97Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C291T	22						.	C		0,4406		0,0,2203	49.0	52.0	51.0		291	-0.0	1.0	22		51	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	HMOX1	NM_002133.2		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		97/289	35782824	2,13004	2203	4300	6503	34112824	SO:0001819	synonymous_variant	3162	exon3				CCDS13914.1	22q12	2003-10-13			ENSG00000100292	ENSG00000100292	1.14.99.3		5013	protein-coding gene	gene with protein product		141250				10591208	Standard	NM_002133		Approved	bK286B10, HO-1	uc003ant.2	P09601	OTTHUMG00000150960	ENST00000216117.8:c.291C>T	22.37:g.35782824C>T			34112824	NM_002133		Silent	SNP	ENST00000216117.8	37	CCDS13914.1																																																																																				0.647	HMOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320657.1		
RBFOX2	23543	broad.mit.edu	37	22	36140246	36140246	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:36140246G>A	ENST00000405409.2	-	12	1468	c.1100C>T	c.(1099-1101)aCg>aTg	p.T367M	RBFOX2_ENST00000414461.2_Missense_Mutation_p.T370M|RBFOX2_ENST00000416721.2_3'UTR|RBFOX2_ENST00000262829.7_3'UTR|RBFOX2_ENST00000359369.4_Missense_Mutation_p.T370M|RBFOX2_ENST00000397303.2_3'UTR|RBFOX2_ENST00000449924.2_3'UTR	NM_001031695.2|NM_001082576.1|NM_001082577.1|NM_014309.2	NP_001026865.1|NP_001076045.1|NP_001076046.1|NP_055124.1	O43251	RFOX2_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 2	0	Ala-rich.				dendrite morphogenesis (GO:0048813)|intracellular estrogen receptor signaling pathway (GO:0030520)|mRNA processing (GO:0006397)|negative regulation of transcription, DNA-templated (GO:0045892)|neuromuscular process controlling balance (GO:0050885)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of cell proliferation (GO:0042127)|regulation of definitive erythrocyte differentiation (GO:0010724)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.T367M(1)		endometrium(4)|large_intestine(7)|lung(7)	18						GGGGTCTCACGTCACTTCAGT	0.443																																					p.T367M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1100T	22						.						37.0	38.0	38.0					22																	36140246		2203	4300	6503	34470192	SO:0001583	missense	23543	exon12			AL009266	CCDS13921.1, CCDS43013.1, CCDS46699.1, CCDS46700.1, CCDS46701.1	22q12-q13	2013-02-12	2010-09-10	2010-09-10	ENSG00000100320	ENSG00000100320		"""RNA binding motif (RRM) containing"""	9906	protein-coding gene	gene with protein product	"""hexaribonucleotide binding protein 2"""	612149	"""RNA binding motif protein 9"""	RBM9			Standard	NM_014309		Approved	HNRBP2, FOX-2, HRNBP2	uc003aon.4	O43251	OTTHUMG00000150585	ENST00000405409.2:c.1100C>T	22.37:g.36140246G>A	ENSP00000384944:p.Thr367Met		34470192	NM_014309	A4F5G8|A8K5Z5|B0QYY8|B0QYY9|Q0PRL5|Q0VH35|Q5TF71|Q6IC09|Q8TD00|Q8WYB1|Q96DZ6|Q96NL7|Q9UGW4|Q9UH33	Missense_Mutation	SNP	ENST00000405409.2	37	CCDS13921.1	.	.	.	.	.	.	.	.	.	.	G	19.31	3.803790	0.70682	.	.	ENSG00000100320	ENST00000405409;ENST00000338644;ENST00000414461;ENST00000359369	T;T;T	0.37915	1.4;1.2;1.17	5.93	5.93	0.95920	.	.	.	.	.	T	0.65616	0.2708	.	.	.	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.985;0.994;0.994	T	0.67554	-0.5641	8	0.87932	D	0	.	20.3409	0.98764	0.0:0.0:1.0:0.0	.	370;367;370	B0QYY4;O43251-9;O43251-4	.;.;.	M	367;400;370;370	ENSP00000384944:T367M;ENSP00000407855:T370M;ENSP00000352328:T370M	ENSP00000342831:T400M	T	-	2	0	RBFOX2	34470192	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.957000	0.63652	2.814000	0.96858	0.655000	0.94253	ACG		0.443	RBFOX2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318976.3		
RBFOX2	23543	broad.mit.edu	37	22	36156026	36156026	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:36156026C>T	ENST00000438146.2	-	10	1017	c.1018G>A	c.(1018-1020)Gct>Act	p.A340T	RBFOX2_ENST00000414461.2_Missense_Mutation_p.A269T|RBFOX2_ENST00000416721.2_Missense_Mutation_p.A265T|RBFOX2_ENST00000262829.7_Missense_Mutation_p.A247T|RBFOX2_ENST00000359369.4_Missense_Mutation_p.A245T|RBFOX2_ENST00000397303.2_Missense_Mutation_p.A246T|RBFOX2_ENST00000405409.2_Missense_Mutation_p.A266T|RBFOX2_ENST00000449924.2_Missense_Mutation_p.A269T	NM_001082578.1|NM_001082579.1	NP_001076047|NP_001076048.1	O43251	RFOX2_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 2	279	Ala-rich.				dendrite morphogenesis (GO:0048813)|intracellular estrogen receptor signaling pathway (GO:0030520)|mRNA processing (GO:0006397)|negative regulation of transcription, DNA-templated (GO:0045892)|neuromuscular process controlling balance (GO:0050885)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of cell proliferation (GO:0042127)|regulation of definitive erythrocyte differentiation (GO:0010724)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.A266T(3)		endometrium(4)|large_intestine(7)|lung(7)	18						CCTCTGAAAGCGGCTGCCGTG	0.537																																					p.A339T												.	.	3	Substitution - Missense(3)	large_intestine(2)|endometrium(1)	c.G1015A	22						.						61.0	62.0	62.0					22																	36156026		2203	4300	6503	34485972	SO:0001583	missense	23543	exon10			AL009266	CCDS13921.1, CCDS43013.1, CCDS46699.1, CCDS46700.1, CCDS46701.1	22q12-q13	2013-02-12	2010-09-10	2010-09-10	ENSG00000100320	ENSG00000100320		"""RNA binding motif (RRM) containing"""	9906	protein-coding gene	gene with protein product	"""hexaribonucleotide binding protein 2"""	612149	"""RNA binding motif protein 9"""	RBM9			Standard	NM_014309		Approved	HNRBP2, FOX-2, HRNBP2	uc003aon.4	O43251	OTTHUMG00000150585	ENST00000438146.2:c.1018G>A	22.37:g.36156026C>T	ENSP00000413035:p.Ala340Thr		34485972	NM_001082579	A4F5G8|A8K5Z5|B0QYY8|B0QYY9|Q0PRL5|Q0VH35|Q5TF71|Q6IC09|Q8TD00|Q8WYB1|Q96DZ6|Q96NL7|Q9UGW4|Q9UH33	Missense_Mutation	SNP	ENST00000438146.2	37	CCDS43013.1	.	.	.	.	.	.	.	.	.	.	C	18.77	3.695825	0.68386	.	.	ENSG00000100320	ENST00000405409;ENST00000338644;ENST00000414461;ENST00000449924;ENST00000262829;ENST00000397303;ENST00000359369;ENST00000416721;ENST00000438146	T;T;T;T;T;T;T	0.56776	1.23;0.94;0.52;0.74;1.24;0.73;0.44	5.48	5.48	0.80851	.	0.049338	0.85682	D	0.000000	T	0.69593	0.3128	L	0.49350	1.555	0.48901	D	0.999728	D;P;P;P;P;D;D;D;D	0.89917	0.961;0.939;0.939;0.858;0.939;0.994;0.983;1.0;0.961	B;B;B;B;B;P;P;D;P	0.91635	0.304;0.154;0.154;0.109;0.154;0.842;0.566;0.999;0.692	T	0.71457	-0.4587	10	0.87932	D	0	.	19.3581	0.94422	0.0:1.0:0.0:0.0	.	245;339;340;247;265;266;269;269;246	B0QYY4;O43251-6;O43251-8;O43251-3;O43251-5;O43251-9;O43251-10;O43251-4;B0QYV1	.;.;.;.;.;.;.;.;.	T	266;275;269;269;247;246;245;265;340	ENSP00000384944:A266T;ENSP00000407855:A269T;ENSP00000391670:A269T;ENSP00000380470:A246T;ENSP00000352328:A245T;ENSP00000405651:A265T;ENSP00000413035:A340T	ENSP00000262829:A247T	A	-	1	0	RBFOX2	34485972	0.997000	0.39634	0.999000	0.59377	0.990000	0.78478	3.400000	0.52594	2.581000	0.87130	0.563000	0.77884	GCT		0.537	RBFOX2-005	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319299.3		
MYH9	4627	broad.mit.edu	37	22	36688070	36688070	+	Missense_Mutation	SNP	C	C	T	rs373912645		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:36688070C>T	ENST00000216181.5	-	31	4536	c.4306G>A	c.(4306-4308)Gcg>Acg	p.A1436T		NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	1436					actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)	p.A1436T(1)		NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						AGGTTGCACGCGCTCTGGCGC	0.592			T	ALK	ALCL		"""Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"""		Hereditary Macrothrombocytopenia, MYH9-associated																												p.A1436T			Dom	yes		22	22q13.1	4627	"""myosin, heavy polypeptide 9, non-muscle"""	yes	L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4306A	22						.	C	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	76.0	66.0	69.0		4306	4.8	1.0	22		69	0,8600		0,0,4300	no	missense	MYH9	NM_002473.4	58	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	1436/1961	36688070	1,13005	2203	4300	6503	35018016	SO:0001583	missense	4627	exon31	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA		CCDS13927.1	22q13.1	2014-09-17	2006-09-29		ENSG00000100345	ENSG00000100345		"""Myosins / Myosin superfamily : Class II"""	7579	protein-coding gene	gene with protein product	"""nonmuscle myosin heavy chain II-A"""	160775	"""myosin, heavy polypeptide 9, non-muscle"""	DFNA17		1860190, 11023810	Standard	NM_002473		Approved	NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS	uc003apg.3	P35579	OTTHUMG00000030429	ENST00000216181.5:c.4306G>A	22.37:g.36688070C>T	ENSP00000216181:p.Ala1436Thr		35018016	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Missense_Mutation	SNP	ENST00000216181.5	37	CCDS13927.1	.	.	.	.	.	.	.	.	.	.	C	14.40	2.523004	0.44866	2.27E-4	0.0	ENSG00000100345	ENST00000337818;ENST00000216181	D	0.82984	-1.67	4.8	4.8	0.61643	Myosin tail (1);	0.191379	0.44483	D	0.000441	T	0.78578	0.4305	L	0.37697	1.125	0.80722	D	1	B	0.21225	0.053	B	0.20955	0.032	T	0.76350	-0.2991	10	0.72032	D	0.01	.	18.2076	0.89859	0.0:1.0:0.0:0.0	.	1436	P35579	MYH9_HUMAN	T	858;1436	ENSP00000216181:A1436T	ENSP00000216181:A1436T	A	-	1	0	MYH9	35018016	1.000000	0.71417	0.960000	0.40013	0.022000	0.10575	7.771000	0.85420	2.352000	0.79861	0.462000	0.41574	GCG		0.592	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473	
EIF3D	8664	broad.mit.edu	37	22	36920017	36920017	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:36920017C>T	ENST00000216190.8	-	5	687	c.317G>A	c.(316-318)cGc>cAc	p.R106H	EIF3D_ENST00000541106.1_Missense_Mutation_p.R57H|EIF3D_ENST00000405442.1_Missense_Mutation_p.R106H	NM_003753.3	NP_003744.1			eukaryotic translation initiation factor 3, subunit D									p.R106H(1)		cervix(1)|endometrium(2)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	15						TTTGTCTCTGCGGAGGTTCCT	0.453																																					p.R106H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G317A	22						.						161.0	149.0	153.0					22																	36920017		2203	4300	6503	35249963	SO:0001583	missense	8664	exon5			U54558	CCDS13930.1	22q13.1	2007-07-27	2007-07-27	2007-07-27	ENSG00000100353	ENSG00000100353			3278	protein-coding gene	gene with protein product		603915	"""eukaryotic translation initiation factor 3, subunit 7 zeta, 66/67kDa"""	EIF3S7		9341143	Standard	NM_003753		Approved	eIF3-p66, eIF3-zeta, eIF3d	uc003apr.3	O15371	OTTHUMG00000150599	ENST00000216190.8:c.317G>A	22.37:g.36920017C>T	ENSP00000216190:p.Arg106His		35249963	NM_003753		Missense_Mutation	SNP	ENST00000216190.8	37	CCDS13930.1	.	.	.	.	.	.	.	.	.	.	C	19.40	3.820157	0.71028	.	.	ENSG00000100353	ENST00000216190;ENST00000397177;ENST00000541106;ENST00000405442;ENST00000455547;ENST00000457241;ENST00000432675;ENST00000402116	.	.	.	5.35	4.33	0.51752	.	0.000000	0.85682	D	0.000000	T	0.64371	0.2592	L	0.45285	1.41	0.80722	D	1	D;D	0.61697	0.99;0.989	P;D	0.63957	0.75;0.92	T	0.59408	-0.7460	9	0.19590	T	0.45	-4.4581	14.0474	0.64712	0.0:0.9276:0.0:0.0724	.	57;106	B4DVY1;O15371	.;EIF3D_HUMAN	H	106;106;57;106;106;106;106;106	.	ENSP00000216190:R106H	R	-	2	0	EIF3D	35249963	1.000000	0.71417	1.000000	0.80357	0.513000	0.34164	7.500000	0.81588	1.260000	0.44134	-0.258000	0.10820	CGC		0.453	EIF3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319026.1		
MCHR1	2847	broad.mit.edu	37	22	41077177	41077177	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:41077177C>T	ENST00000249016.4	+	2	1210	c.514C>T	c.(514-516)Ctc>Ttc	p.L172F	MCHR1_ENST00000381433.2_Intron|MCHR1_ENST00000498400.1_3'UTR	NM_005297.3	NP_005288.3	Q99705	MCHR1_HUMAN	melanin-concentrating hormone receptor 1	172					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)|generation of precursor metabolites and energy (GO:0006091)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	integral component of plasma membrane (GO:0005887)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|hormone binding (GO:0042562)|melanin-concentrating hormone receptor activity (GO:0030273)|neuropeptide receptor activity (GO:0008188)	p.L172F(1)		endometrium(5)|large_intestine(7)|lung(6)|pancreas(1)|urinary_tract(1)	20						GATCCACCAGCTCATGGGCAA	0.552																																					p.L172F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C514T	22						.						170.0	159.0	163.0					22																	41077177		2203	4300	6503	39407123	SO:0001583	missense	2847	exon2				CCDS14004.1	22q13.3	2014-06-05	2006-02-15	2006-02-15	ENSG00000128285	ENSG00000128285		"""GPCR / Class A : MCH receptors"""	4479	protein-coding gene	gene with protein product		601751	"""G protein-coupled receptor 24"""	GPR24			Standard	XM_005261581		Approved	SLC1, MCH1R	uc003ayz.3	Q99705	OTTHUMG00000150256	ENST00000249016.4:c.514C>T	22.37:g.41077177C>T	ENSP00000249016:p.Leu172Phe		39407123	NM_005297	B2RBX6|Q5R3J1|Q96S47|Q9BV08	Missense_Mutation	SNP	ENST00000249016.4	37	CCDS14004.1	.	.	.	.	.	.	.	.	.	.	C	18.00	3.525944	0.64860	.	.	ENSG00000128285	ENST00000249016	T	0.25579	1.79	4.95	4.95	0.65309	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.36386	0.0965	N	0.26042	0.785	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.05225	-1.0898	10	0.15066	T	0.55	.	17.1367	0.86742	0.0:1.0:0.0:0.0	.	172	Q99705	MCHR1_HUMAN	F	172	ENSP00000249016:L172F	ENSP00000249016:L172F	L	+	1	0	MCHR1	39407123	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.858000	0.62947	2.459000	0.83118	0.563000	0.77884	CTC		0.552	MCHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317142.1	NM_005297	
MCHR1	2847	broad.mit.edu	37	22	41077820	41077820	+	Missense_Mutation	SNP	C	C	T	rs200156668		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:41077820C>T	ENST00000249016.4	+	2	1853	c.1157C>T	c.(1156-1158)aCg>aTg	p.T386M	MCHR1_ENST00000381433.2_Missense_Mutation_p.T260M|MCHR1_ENST00000498400.1_3'UTR	NM_005297.3	NP_005288.3	Q99705	MCHR1_HUMAN	melanin-concentrating hormone receptor 1	386					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)|generation of precursor metabolites and energy (GO:0006091)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	integral component of plasma membrane (GO:0005887)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|hormone binding (GO:0042562)|melanin-concentrating hormone receptor activity (GO:0030273)|neuropeptide receptor activity (GO:0008188)	p.T386M(1)		endometrium(5)|large_intestine(7)|lung(6)|pancreas(1)|urinary_tract(1)	20						CTCTGTGAGACGTTCCGCAAA	0.587																																					p.T386M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1157T	22						.						120.0	95.0	104.0					22																	41077820		2203	4300	6503	39407766	SO:0001583	missense	2847	exon2				CCDS14004.1	22q13.3	2014-06-05	2006-02-15	2006-02-15	ENSG00000128285	ENSG00000128285		"""GPCR / Class A : MCH receptors"""	4479	protein-coding gene	gene with protein product		601751	"""G protein-coupled receptor 24"""	GPR24			Standard	XM_005261581		Approved	SLC1, MCH1R	uc003ayz.3	Q99705	OTTHUMG00000150256	ENST00000249016.4:c.1157C>T	22.37:g.41077820C>T	ENSP00000249016:p.Thr386Met		39407766	NM_005297	B2RBX6|Q5R3J1|Q96S47|Q9BV08	Missense_Mutation	SNP	ENST00000249016.4	37	CCDS14004.1	.	.	.	.	.	.	.	.	.	.	C	19.13	3.768587	0.69878	.	.	ENSG00000128285	ENST00000249016;ENST00000381433	T;T	0.38077	1.16;1.16	5.4	4.39	0.52855	.	0.088038	0.85682	D	0.000000	T	0.42404	0.1201	N	0.19112	0.55	0.44862	D	0.99787	D	0.89917	1.0	D	0.68621	0.959	T	0.44452	-0.9327	10	0.87932	D	0	.	12.0112	0.53289	0.0:0.9156:0.0:0.0844	.	386	Q99705	MCHR1_HUMAN	M	386;260	ENSP00000249016:T386M;ENSP00000370841:T260M	ENSP00000249016:T386M	T	+	2	0	MCHR1	39407766	0.835000	0.29415	0.881000	0.34555	0.942000	0.58702	1.705000	0.37867	1.419000	0.47118	0.655000	0.94253	ACG		0.587	MCHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317142.1	NM_005297	
EP300	2033	broad.mit.edu	37	22	41556708	41556708	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:41556708A>G	ENST00000263253.7	+	20	4872	c.3653A>G	c.(3652-3654)gAc>gGc	p.D1218G		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	1218					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)	p.Y1198_L1243del(1)|p.D1218G(1)		NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						TTGGGGGATGACCCTTCCCAG	0.423			"""T,  N, F, Mis, O"""	"""MLL, RUNXBP2"""	"""colorectal, breast, pancreatic, AML, ALL, DLBCL"""				Rubinstein-Taybi syndrome																												p.D1218G			Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"""L, E"""	.	.	2	Substitution - Missense(1)|Deletion - In frame(1)	large_intestine(1)|breast(1)	c.A3653G	22						.						132.0	106.0	115.0					22																	41556708		2203	4300	6503	39886654	SO:0001583	missense	2033	exon20	Familial Cancer Database	Broad Thumb-Hallux syndrome	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"""Chromatin-modifying enzymes / K-acetyltransferases"""	3373	protein-coding gene	gene with protein product	"""histone acetyltransferase p300"""	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.3653A>G	22.37:g.41556708A>G	ENSP00000263253:p.Asp1218Gly		39886654	NM_001429	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	37	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	A	18.54	3.645371	0.67358	.	.	ENSG00000100393	ENST00000263253	D	0.85411	-1.98	5.51	5.51	0.81932	.	0.000000	0.50627	D	0.000105	D	0.93311	0.7868	M	0.88105	2.93	0.58432	D	0.999993	D	0.89917	1.0	D	0.80764	0.994	D	0.94360	0.7587	10	0.66056	D	0.02	-11.0906	15.6322	0.76920	1.0:0.0:0.0:0.0	.	1218	Q09472	EP300_HUMAN	G	1218	ENSP00000263253:D1218G	ENSP00000263253:D1218G	D	+	2	0	EP300	39886654	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.097000	0.63578	0.455000	0.32223	GAC		0.423	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429	
PNPLA5	150379	broad.mit.edu	37	22	44283515	44283515	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:44283515C>G	ENST00000597664.1	-	5	848	c.719G>C	c.(718-720)tGc>tCc	p.C240S	PNPLA5_ENST00000593866.1_Missense_Mutation_p.C126S|PNPLA5_ENST00000381198.2_Missense_Mutation_p.C126S|PNPLA5_ENST00000216177.4_Missense_Mutation_p.C240S			Q7Z6Z6	PLPL5_HUMAN	patatin-like phospholipase domain containing 5	240					lipid catabolic process (GO:0016042)		hydrolase activity (GO:0016787)	p.C240S(1)		endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	16		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				GCCTTGTCTGCAGTTGTCGGC	0.592																																					p.C240S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G719C	22						.						121.0	74.0	90.0					22																	44283515		2203	4300	6503	42614848	SO:0001583	missense	150379	exon5			Z97055	CCDS14053.1, CCDS54537.1	22q13.31	2009-01-12			ENSG00000100341	ENSG00000100341		"""Patatin-like phospholipase domain containing"""	24888	protein-coding gene	gene with protein product		611589				16799181, 19029121	Standard	NM_138814		Approved	dJ388M5.4, GS2L	uc003beg.3	Q7Z6Z6	OTTHUMG00000030779	ENST00000597664.1:c.719G>C	22.37:g.44283515C>G	ENSP00000471069:p.Cys240Ser		42614848	NM_138814	B1AHL8|B3KPR1|Q6ZST0	Missense_Mutation	SNP	ENST00000597664.1	37		.	.	.	.	.	.	.	.	.	.	C	14.79	2.641035	0.47153	.	.	ENSG00000100341	ENST00000216177;ENST00000381198;ENST00000438734	T;T;T	0.76578	-1.03;0.48;0.06	4.53	3.48	0.39840	Acyl transferase/acyl hydrolase/lysophospholipase (1);	0.067296	0.64402	N	0.000017	D	0.84383	0.5460	M	0.90309	3.105	0.58432	D	0.999998	P;P;B	0.42518	0.659;0.782;0.132	P;B;B	0.47705	0.555;0.187;0.051	D	0.85916	0.1443	10	0.59425	D	0.04	-43.3358	11.7236	0.51696	0.0:0.821:0.179:0.0	.	148;126;240	E9PGS4;Q7Z6Z6-2;Q7Z6Z6	.;.;PLPL5_HUMAN	S	240;126;148	ENSP00000216177:C240S;ENSP00000370595:C126S;ENSP00000405732:C148S	ENSP00000216177:C240S	C	-	2	0	PNPLA5	42614848	1.000000	0.71417	0.964000	0.40570	0.847000	0.48162	3.017000	0.49615	0.993000	0.38866	0.313000	0.20887	TGC		0.592	PNPLA5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000075667.4	NM_138814	
PARVB	29780	broad.mit.edu	37	22	44532359	44532359	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:44532359A>G	ENST00000338758.7	+	7	716	c.653A>G	c.(652-654)cAt>cGt	p.H218R	PARVB_ENST00000406477.3_Missense_Mutation_p.H251R|PARVB_ENST00000404989.1_Missense_Mutation_p.H181R	NM_013327.4	NP_037459.2	Q9HBI1	PARVB_HUMAN	parvin, beta	218					actin cytoskeleton reorganization (GO:0031532)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell projection assembly (GO:0030031)|establishment or maintenance of cell polarity regulating cell shape (GO:0071963)|lamellipodium assembly (GO:0030032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)		p.H251R(1)		NS(1)|breast(1)|endometrium(3)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Ovarian(80;0.0246)|all_neural(38;0.0423)				GGCCTGCTGCATTCCAGCCAC	0.557																																					p.H251R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A752G	22						.						91.0	78.0	83.0					22																	44532359		2203	4300	6503	42863692	SO:0001583	missense	29780	exon8			AF151814	CCDS14056.1, CCDS46724.1, CCDS58808.1, CCDS74874.1	22q13.2-q13.33	2013-01-24			ENSG00000188677	ENSG00000188677		"""Parvins"""	14653	protein-coding gene	gene with protein product	"""affixin"""	608121				10810093, 11171322	Standard	NM_001003828		Approved	CGI-56	uc003ben.3	Q9HBI1	OTTHUMG00000150665	ENST00000338758.7:c.653A>G	22.37:g.44532359A>G	ENSP00000342492:p.His218Arg		42863692	NM_001003828	B0QYM8|B0QYN1|B2R9X6|Q5TGJ5|Q86X93|Q96PN1|Q9NSP7|Q9UGT3|Q9Y368|Q9Y3L6|Q9Y3L7	Missense_Mutation	SNP	ENST00000338758.7	37	CCDS14056.1	.	.	.	.	.	.	.	.	.	.	A	13.58	2.278386	0.40294	.	.	ENSG00000188677	ENST00000406477;ENST00000338758;ENST00000404989	T;T;T	0.29142	1.58;1.62;1.62	4.63	4.63	0.57726	Calponin homology domain (1);	0.110943	0.64402	D	0.000007	T	0.28067	0.0692	L	0.46157	1.445	0.80722	D	1	B;B;B;B	0.13594	0.005;0.001;0.001;0.008	B;B;B;B	0.18561	0.002;0.001;0.002;0.022	T	0.05131	-1.0904	10	0.33141	T	0.24	-16.5926	12.8988	0.58113	1.0:0.0:0.0:0.0	.	218;181;218;251	A6NG58;B0QYM8;Q9HBI1;Q9HBI1-2	.;.;PARVB_HUMAN;.	R	251;218;181	ENSP00000384515:H251R;ENSP00000342492:H218R;ENSP00000384353:H181R	ENSP00000342492:H218R	H	+	2	0	PARVB	42863692	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.131000	0.89601	1.737000	0.51674	0.533000	0.62120	CAT		0.557	PARVB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319518.2	NM_001003828	
FBLN1	2192	broad.mit.edu	37	22	45946483	45946483	+	Missense_Mutation	SNP	G	G	A	rs146772136	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:45946483G>A	ENST00000327858.6	+	14	1780	c.1685G>A	c.(1684-1686)cGc>cAc	p.R562H	FBLN1_ENST00000476366.1_3'UTR|FBLN1_ENST00000348697.2_Missense_Mutation_p.R562H|FBLN1_ENST00000442170.2_Missense_Mutation_p.R562H|FBLN1_ENST00000262722.7_Missense_Mutation_p.R562H|FBLN1_ENST00000402984.3_Missense_Mutation_p.R600H|FBLN1_ENST00000340923.5_Missense_Mutation_p.R562H	NM_006486.2	NP_006477	P23142	FBLN1_HUMAN	fibulin 1	562	EGF-like 9; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|viral process (GO:0016032)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)|peptidase activator activity (GO:0016504)	p.R562H(1)		biliary_tract(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)	30		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		AACTACCGCCGCTCCGCAGCC	0.607																																					p.R562H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1685A	22						.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	6,4400	11.4+/-27.6	0,6,2197	84.0	75.0	78.0		1685,1685,1685,1685	4.8	1.0	22	dbSNP_134	78	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense,missense,missense	FBLN1	NM_001996.3,NM_006485.3,NM_006486.2,NM_006487.2	29,29,29,29	0,8,6495	AA,AG,GG		0.0233,0.1362,0.0615	probably-damaging,probably-damaging,probably-damaging,probably-damaging	562/684,562/602,562/704,562/567	45946483	8,12998	2203	4300	6503	44325147	SO:0001583	missense	2192	exon14				CCDS14067.1, CCDS14068.1, CCDS14069.1, CCDS43028.1	22q13.31	2010-06-15			ENSG00000077942	ENSG00000077942		"""Fibulins"""	3600	protein-coding gene	gene with protein product		135820				2269669, 1400330	Standard	NM_006485		Approved	FBLN	uc003bgj.1	P23142	OTTHUMG00000151340	ENST00000327858.6:c.1685G>A	22.37:g.45946483G>A	ENSP00000331544:p.Arg562His		44325147	NM_006487	B0QY42|B1AHL4|P23143|P23144|P37888|Q5TIC4|Q8TBH8|Q9HBQ5|Q9UC21|Q9UGR4|Q9UH41	Missense_Mutation	SNP	ENST00000327858.6	37	CCDS14067.1	.	.	.	.	.	.	.	.	.	.	G	18.50	3.637005	0.67130	0.001362	2.33E-4	ENSG00000077942	ENST00000348697;ENST00000402984;ENST00000262722;ENST00000327858;ENST00000442170;ENST00000340923	D;D;D;D;D;D	0.93763	-1.56;-2.26;-2.98;-3.28;-1.56;-2.26	4.78	4.78	0.61160	Epidermal growth factor-like (1);EGF-like calcium-binding (1);	0.138096	0.46145	D	0.000317	D	0.95220	0.8450	M	0.78285	2.405	0.35072	D	0.762611	D;D;P;D	0.89917	0.999;0.999;0.524;1.0	P;D;B;P	0.67900	0.885;0.954;0.096;0.868	D	0.95998	0.8991	10	0.45353	T	0.12	.	6.613	0.22761	0.2337:0.0:0.7663:0.0	.	600;562;562;562	B1AHL2;P23142;B1AHL4;P23142-4	.;FBLN1_HUMAN;.;.	H	562;600;562;562;562;562	ENSP00000262723:R562H;ENSP00000385521:R600H;ENSP00000262722:R562H;ENSP00000331544:R562H;ENSP00000393812:R562H;ENSP00000342212:R562H	ENSP00000262722:R562H	R	+	2	0	FBLN1	44325147	0.995000	0.38212	1.000000	0.80357	0.779000	0.44077	3.779000	0.55379	2.205000	0.71048	0.462000	0.41574	CGC		0.607	FBLN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322287.1	NM_006486	
GTSE1	51512	broad.mit.edu	37	22	46724615	46724615	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:46724615G>A	ENST00000454366.1	+	10	1967	c.1755G>A	c.(1753-1755)aaG>aaA	p.K585K		NM_016426.6	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	566					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|microtubule-based process (GO:0007017)	cytoplasmic microtubule (GO:0005881)|membrane (GO:0016020)		p.K566K(1)		NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	27		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)		GCAACAGAAAGACAGATTCCA	0.478																																					p.K585K	GBM(153;542 1915 12487 29016 50495)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1755A	22						.						103.0	100.0	101.0					22																	46724615		2203	4300	6503	45103279	SO:0001819	synonymous_variant	51512	exon10			AF223408	CCDS14074.2	22q13.2-q13.3	2008-06-10			ENSG00000075218	ENSG00000075218			13698	protein-coding gene	gene with protein product		607477				10974554, 10984615, 12750368	Standard	NM_016426		Approved	GTSE-1, B99	uc011aqy.2	Q9NYZ3	OTTHUMG00000150486	ENST00000454366.1:c.1755G>A	22.37:g.46724615G>A			45103279	NM_016426	B0QYM3|Q20WK2|Q53GX5|Q5R3I6|Q6DHX4|Q9BRE0|Q9UGZ9|Q9Y557	Silent	SNP	ENST00000454366.1	37	CCDS14074.2																																																																																				0.478	GTSE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318360.2	NM_016426	
TBC1D22A	25771	broad.mit.edu	37	22	47307999	47307999	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:47307999G>A	ENST00000337137.4	+	8	1096	c.930G>A	c.(928-930)gcG>gcA	p.A310A	TBC1D22A_ENST00000380995.1_Silent_p.A263A|TBC1D22A_ENST00000406733.1_Silent_p.A263A|TBC1D22A_ENST00000355704.3_Silent_p.A232A|TBC1D22A_ENST00000407381.3_Silent_p.A251A	NM_001284304.1|NM_001284305.1|NM_014346.2	NP_001271233.1|NP_001271234.1|NP_055161.1	Q8WUA7	TB22A_HUMAN	TBC1 domain family, member 22A	310	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						protein homodimerization activity (GO:0042803)|Rab GTPase activator activity (GO:0005097)	p.A310A(1)		breast(1)|endometrium(3)|large_intestine(10)|lung(5)|ovary(2)|prostate(1)	22		all_cancers(38;4.44e-05)|all_epithelial(38;0.000507)|Breast(42;0.0488)|all_lung(38;0.0682)|Ovarian(80;0.0731)|all_neural(38;0.0966)|Glioma(61;0.222)|Lung SC(80;0.236)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0347)|BRCA - Breast invasive adenocarcinoma(115;0.231)		TCATATGGGCGATCCGCCACC	0.383																																					p.A310A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G930A	22						.						196.0	173.0	181.0					22																	47307999		2203	4300	6503	45686663	SO:0001819	synonymous_variant	25771	exon8			AK125705	CCDS14078.1, CCDS63511.1, CCDS63512.1, CCDS74877.1	22q13	2008-01-22	2005-01-05	2005-01-05	ENSG00000054611	ENSG00000054611			1309	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 4"""	C22orf4			Standard	XM_005261496		Approved		uc003bib.3	Q8WUA7	OTTHUMG00000150332	ENST00000337137.4:c.930G>A	22.37:g.47307999G>A			45686663	NM_014346	B0QYI2|B0QYI3|B9A6M3|Q5TE47|Q6ZUH2|Q92680|Q9BVD6|Q9UGG0|Q9UGT2|Q9UGU6|Q9UH25|Q9Y4W5	Silent	SNP	ENST00000337137.4	37	CCDS14078.1																																																																																				0.383	TBC1D22A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317600.3	NM_014346	
SBF1	6305	broad.mit.edu	37	22	50885653	50885653	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:50885653C>T	ENST00000390679.3	-	40	5706	c.5522G>A	c.(5521-5523)cGc>cAc	p.R1841H	SBF1_ENST00000348911.6_Missense_Mutation_p.R1842H|SBF1_ENST00000380817.3_Missense_Mutation_p.R1867H			O95248	MTMR5_HUMAN	SET binding factor 1	1841	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cell death (GO:0008219)|positive regulation of Rab GTPase activity (GO:0032851)|protein dephosphorylation (GO:0006470)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.R1841H(1)		breast(1)|central_nervous_system(2)|endometrium(6)|kidney(8)|large_intestine(3)|lung(18)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	43		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)		GTTGTAAACGCGACGCGTTGT	0.687																																					p.R1867H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5600A	22						.						43.0	52.0	49.0					22																	50885653		2089	4196	6285	49232519	SO:0001583	missense	6305	exon41			U93181	CCDS14091.1, CCDS14091.2	22q13.33	2013-01-10			ENSG00000100241	ENSG00000100241		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"", ""DENN/MADD domain containing"", ""Pleckstrin homology (PH) domain containing"""	10542	protein-coding gene	gene with protein product	"""myotubularin related 5"", ""DENN/MADD domain containing 7A"""	603560				9537414, 9736772	Standard	NM_002972		Approved	MTMR5, DENND7A	uc003blh.3	O95248	OTTHUMG00000150204	ENST00000390679.3:c.5522G>A	22.37:g.50885653C>T	ENSP00000375097:p.Arg1841His		49232519	NM_002972	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Missense_Mutation	SNP	ENST00000390679.3	37		.	.	.	.	.	.	.	.	.	.	C	24.9	4.582224	0.86748	.	.	ENSG00000100241	ENST00000380817;ENST00000348911;ENST00000337034;ENST00000390679	T;T;T	0.17691	2.26;2.26;2.26	3.51	3.51	0.40186	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.073236	0.56097	N	0.000037	T	0.53658	0.1810	H	0.95679	3.705	0.58432	D	0.999999	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.999;0.993;0.995	T	0.71401	-0.4604	10	0.87932	D	0	.	15.1872	0.73012	0.0:1.0:0.0:0.0	.	1841;1867;388	O95248;O95248-4;A6PVG7	MTMR5_HUMAN;.;.	H	1867;1842;1877;1841	ENSP00000370196:R1867H;ENSP00000252027:R1842H;ENSP00000375097:R1841H	ENSP00000336522:R1877H	R	-	2	0	SBF1	49232519	1.000000	0.71417	0.981000	0.43875	0.903000	0.53119	7.331000	0.79192	1.989000	0.58080	0.462000	0.41574	CGC		0.687	SBF1-201	KNOWN	basic	protein_coding	protein_coding			
APOBEC3D	140564	broad.mit.edu	37	22	39421185	39421185	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:39421185delC	ENST00000216099.8	+	3	728	c.321delC	c.(319-321)aacfs	p.N107fs	APOBEC3D_ENST00000427494.2_Intron|APOBEC3D_ENST00000381568.4_Frame_Shift_Del_p.N107fs	NM_152426.3	NP_689639.2	Q96AK3	ABC3D_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3D	107	CMP/dCMP deaminase zinc-binding 1.				defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines (GO:0016814)|zinc ion binding (GO:0008270)	p.C109fs*6(2)		breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)	11	Melanoma(58;0.04)					TATCATGGAACCCCTGCCTGC	0.542																																					p.N107fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.321delC	22						.						115.0	115.0	115.0					22																	39421185		2203	4300	6503	37751131	SO:0001589	frameshift_variant	140564	exon3			BF832090	CCDS46709.1	22q13.1	2012-10-19	2008-05-01		ENSG00000243811	ENSG00000243811		"""Apolipoprotein B mRNA editing enzymes"""	17354	protein-coding gene	gene with protein product		609900	"""apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3D (putative)"", ""apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3E pseudogene"""	APOBEC3E		11863358	Standard	NM_152426		Approved	ARP6, APOBEC3DE	uc003awt.4	Q96AK3	OTTHUMG00000151084	ENST00000216099.8:c.321delC	22.37:g.39421185delC	ENSP00000216099:p.Asn107fs		37751131	NM_152426	Q5JZ91|Q7Z2N2|Q7Z2N5|Q7Z2N6	Frame_Shift_Del	DEL	ENST00000216099.8	37	CCDS46709.1																																																																																				0.542	APOBEC3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321232.2	NM_152426	
CELSR1	9620	broad.mit.edu	37	22	46931196	46931196	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:46931196delG	ENST00000262738.3	-	1	1871	c.1872delC	c.(1870-1872)cccfs	p.P624fs	CELSR1_ENST00000395964.1_Frame_Shift_Del_p.P624fs|CELSR1_ENST00000497509.1_5'Flank	NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	624	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)	p.T625fs*43(1)		breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		AGTCAGGGGTGGGGGCAGGAT	0.652																																					p.P624fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1872delC	22						.						25.0	28.0	27.0					22																	46931196		2202	4296	6498	45309860	SO:0001589	frameshift_variant	9620	exon1			AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	1850	protein-coding gene	gene with protein product	"""flamingo homolog 2 (Drosophila)"""	604523	"""cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"""			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.1872delC	22.37:g.46931196delG	ENSP00000262738:p.Pro624fs		45309860	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Frame_Shift_Del	DEL	ENST00000262738.3	37	CCDS14076.1																																																																																				0.652	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
MIOX	55586	broad.mit.edu	37	22	50925838	50925838	+	Nonsense_Mutation	SNP	C	C	T	rs564759857	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr22:50925838C>T	ENST00000216075.6	+	2	114	c.40C>T	c.(40-42)Cga>Tga	p.R14*	MIOX_ENST00000395732.3_Nonsense_Mutation_p.R14*|MIOX_ENST00000395733.3_Nonsense_Mutation_p.R14*	NM_017584.5	NP_060054.4	Q9UGB7	MIOX_HUMAN	myo-inositol oxygenase	14					inositol catabolic process (GO:0019310)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)	aldo-keto reductase (NADP) activity (GO:0004033)|ferric iron binding (GO:0008199)|inositol oxygenase activity (GO:0050113)|NADP binding (GO:0050661)|oxidoreductase activity, acting on NAD(P)H (GO:0016651)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen (GO:0016701)	p.R14*(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	13		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CCTGGTCTACCGACCTGATGT	0.597																																					p.R14X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C40T	22						.						101.0	86.0	91.0					22																	50925838		2203	4300	6503	49272704	SO:0001587	stop_gained	55586	exon2			AF197129	CCDS14092.1	22q13.3	2008-06-11	2005-06-15	2005-06-15	ENSG00000100253	ENSG00000100253			14522	protein-coding gene	gene with protein product	"""kidney-specific protein 32"""	606774	"""aldehyde reductase (aldose reductase) like 6"""	ALDRL6		10944187, 11716759	Standard	NM_017584		Approved		uc003bll.1	Q9UGB7	OTTHUMG00000150207	ENST00000216075.6:c.40C>T	22.37:g.50925838C>T	ENSP00000216075:p.Arg14*		49272704	NM_017584	Q05DJ6|Q5S8C9|Q9BZZ1|Q9UHB8	Nonsense_Mutation	SNP	ENST00000216075.6	37	CCDS14092.1	.	.	.	.	.	.	.	.	.	.	C	36	5.683939	0.96774	.	.	ENSG00000100253	ENST00000395733;ENST00000216075;ENST00000395732;ENST00000451761	.	.	.	4.65	2.48	0.30137	.	0.153235	0.44483	D	0.000456	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.2765	9.5834	0.39501	0.3824:0.6176:0.0:0.0	.	.	.	.	X	14;14;14;9	.	ENSP00000216075:R14X	R	+	1	2	MIOX	49272704	0.956000	0.32656	0.397000	0.26308	0.977000	0.68977	0.638000	0.24674	0.519000	0.28406	-0.500000	0.04577	CGA		0.597	MIOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316835.1	NM_017584	
KLF11	8462	broad.mit.edu	37	2	10192489	10192489	+	Missense_Mutation	SNP	G	G	A	rs142970758		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:10192489G>A	ENST00000305883.1	+	4	1556	c.1394G>A	c.(1393-1395)cGc>cAc	p.R465H	KLF11_ENST00000535335.1_Missense_Mutation_p.R448H|KLF11_ENST00000540845.1_Missense_Mutation_p.R448H|RP11-254F7.3_ENST00000607181.1_RNA	NM_003597.4	NP_003588.1	O14901	KLF11_HUMAN	Kruppel-like factor 11	465					apoptotic process (GO:0006915)|cellular response to peptide (GO:1901653)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.R465H(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.133)|OV - Ovarian serous cystadenocarcinoma(76;0.228)		CGTTTCATGCGCAGTGACCAC	0.567																																					p.R448H	Melanoma(56;431 1507 23687 50789)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1343A	2						.	G	HIS/ARG,HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	98.0	91.0	93.0		1343,1343,1394	6.1	1.0	2	dbSNP_134	93	0,8600		0,0,4300	no	missense,missense,missense	KLF11	NM_001177716.1,NM_001177718.1,NM_003597.4	29,29,29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging	448/496,448/496,465/513	10192489	1,13005	2203	4300	6503	10109940	SO:0001583	missense	8462	exon4			AF028008	CCDS1668.1, CCDS54333.1	2p25	2013-01-08	2004-11-29	2004-12-01	ENSG00000172059	ENSG00000172059		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	11811	protein-coding gene	gene with protein product		603301	"""TGFB inducible early growth response 2"""	TIEG2		9748269, 11087666	Standard	NM_001177716		Approved	Tieg3, MODY7	uc002raf.1	O14901	OTTHUMG00000119004	ENST00000305883.1:c.1394G>A	2.37:g.10192489G>A	ENSP00000307023:p.Arg465His		10109940	NM_001177718	B4DZE7|Q9EPF4	Missense_Mutation	SNP	ENST00000305883.1	37	CCDS1668.1	.	.	.	.	.	.	.	.	.	.	G	36	5.783317	0.96937	2.27E-4	0.0	ENSG00000172059	ENST00000305883;ENST00000540845;ENST00000535335	T;T;T	0.35973	1.28;1.28;1.28	6.08	6.08	0.98989	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.66963	0.2843	M	0.83118	2.625	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.68678	-0.5345	10	0.87932	D	0	.	20.6721	0.99693	0.0:0.0:1.0:0.0	.	465	O14901	KLF11_HUMAN	H	465;448;448	ENSP00000307023:R465H;ENSP00000444690:R448H;ENSP00000442722:R448H	ENSP00000307023:R465H	R	+	2	0	KLF11	10109940	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.835000	0.99442	2.894000	0.99253	0.591000	0.81541	CGC		0.567	KLF11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000239202.3	NM_003597	
IL18R1	8809	broad.mit.edu	37	2	102992454	102992454	+	Missense_Mutation	SNP	G	G	A	rs35292939	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:102992454G>A	ENST00000409599.1	+	6	912	c.556G>A	c.(556-558)Gtg>Atg	p.V186M	IL18R1_ENST00000233957.1_Missense_Mutation_p.V186M			Q13478	IL18R_HUMAN	interleukin 18 receptor 1	186	Ig-like C2-type 2.				immune response (GO:0006955)|natural killer cell activation (GO:0030101)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|signal transduction (GO:0007165)|T-helper 1 cell differentiation (GO:0045063)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-18 receptor activity (GO:0042008)|receptor activity (GO:0004872)	p.V186M(1)		breast(1)|endometrium(3)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34						TTACTCCTGCGTGCATTTCCT	0.343																																					p.V186M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G556A	2						.	G	MET/VAL	2,4404	4.2+/-10.8	0,2,2201	63.0	64.0	64.0		556	0.8	0.1	2	dbSNP_126	64	1,8599	1.2+/-3.3	0,1,4299	no	missense	IL18R1	NM_003855.2	21	0,3,6500	AA,AG,GG		0.0116,0.0454,0.0231	probably-damaging	186/542	102992454	3,13003	2203	4300	6503	102358886	SO:0001583	missense	8809	exon4			U43672	CCDS2060.1	2q12	2013-01-29			ENSG00000115604	ENSG00000115604		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5988	protein-coding gene	gene with protein product		604494				8626725, 10191101	Standard	NM_003855		Approved	IL1RRP, IL-1Rrp, CD218a	uc010fiy.3	Q13478	OTTHUMG00000130780	ENST00000409599.1:c.556G>A	2.37:g.102992454G>A	ENSP00000387211:p.Val186Met		102358886	NM_003855	B2R9Y5|Q52LC9	Missense_Mutation	SNP	ENST00000409599.1	37	CCDS2060.1	.	.	.	.	.	.	.	.	.	.	G	6.649	0.488232	0.12641	4.54E-4	1.16E-4	ENSG00000115604	ENST00000410040;ENST00000409599;ENST00000233957	T;T;T	0.12672	2.66;2.66;2.66	4.9	0.749	0.18381	.	0.464333	0.19164	N	0.121110	T	0.09686	0.0238	L	0.55990	1.75	0.21445	N	0.999684	D;D	0.54397	0.966;0.966	B;B	0.38842	0.283;0.283	T	0.25363	-1.0134	10	0.48119	T	0.1	.	3.113	0.06365	0.3087:0.0:0.5015:0.1898	rs35292939	186;186	B7ZKV7;Q13478	.;IL18R_HUMAN	M	186	ENSP00000386663:V186M;ENSP00000387211:V186M;ENSP00000233957:V186M	ENSP00000233957:V186M	V	+	1	0	IL18R1	102358886	0.000000	0.05858	0.089000	0.20774	0.086000	0.17979	-0.373000	0.07494	0.563000	0.29222	0.655000	0.94253	GTG		0.343	IL18R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253294.2	NM_003855	
ANAPC1	64682	broad.mit.edu	37	2	112545811	112545811	+	Splice_Site	SNP	C	C	T	rs371127987		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:112545811C>T	ENST00000341068.3	-	39	5571	c.4799G>A	c.(4798-4800)cGg>cAg	p.R1600Q		NM_022662.3	NP_073153.1	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1	1600					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)		p.R1600Q(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(7)|lung(16)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	49						CTAGACTCACCGGTTGTCAGT	0.408																																					p.R1600Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4799A	2						.	C	GLN/ARG	0,4386		0,0,2193	13.0	12.0	13.0		4799	4.6	1.0	2		13	1,8529		0,1,4264	no	missense-near-splice	ANAPC1	NM_022662.2	43	0,1,6457	TT,TC,CC		0.0117,0.0,0.0077	probably-damaging	1600/1945	112545811	1,12915	2193	4265	6458	112262282	SO:0001630	splice_region_variant	64682	exon39			AJ278357	CCDS2093.1	2q12.1	2011-06-15			ENSG00000153107	ENSG00000153107		"""Anaphase promoting complex subunits"""	19988	protein-coding gene	gene with protein product		608473				11179667	Standard	NM_022662		Approved	MCPR, TSG24, APC1	uc002ssh.3	Q9H1A4	OTTHUMG00000131277	ENST00000341068.3:c.4799+1G>A	2.37:g.112545811C>T			112262282	NM_022662	Q2M3H8|Q9BSE6|Q9H8D0	Missense_Mutation	SNP	ENST00000341068.3	37	CCDS2093.1	.	.	.	.	.	.	.	.	.	.	C	33	5.260444	0.95368	0.0	1.17E-4	ENSG00000153107	ENST00000341068	T	0.26373	1.74	4.55	4.55	0.56014	.	0.000000	0.42821	D	0.000651	T	0.26011	0.0634	M	0.64404	1.975	0.80722	D	1	P	0.47910	0.902	B	0.35470	0.203	T	0.18650	-1.0330	9	.	.	.	-10.5534	17.7013	0.88295	0.0:1.0:0.0:0.0	.	1600	Q9H1A4	APC1_HUMAN	Q	1600	ENSP00000339109:R1600Q	.	R	-	2	0	ANAPC1	112262282	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.554000	0.82212	2.242000	0.73789	0.650000	0.86243	CGG		0.408	ANAPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254045.2	NM_022662	Missense_Mutation
STEAP3	55240	broad.mit.edu	37	2	120005330	120005330	+	Missense_Mutation	SNP	G	G	A	rs201076547		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:120005330G>A	ENST00000354888.5	+	4	1072	c.568G>A	c.(568-570)Gtg>Atg	p.V190M	STEAP3_ENST00000393107.2_Missense_Mutation_p.V190M|STEAP3_ENST00000393106.2_Missense_Mutation_p.V190M|STEAP3_ENST00000425223.2_Missense_Mutation_p.V190M|STEAP3-AS1_ENST00000454260.1_RNA|STEAP3_ENST00000450943.2_Missense_Mutation_p.V190M|STEAP3_ENST00000393108.2_Missense_Mutation_p.V190M|STEAP3_ENST00000409811.1_Missense_Mutation_p.V190M|STEAP3_ENST00000393110.2_Missense_Mutation_p.V200M	NM_182915.2	NP_878919.2	Q658P3	STEA3_HUMAN	STEAP family member 3, metalloreductase	190					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cellular iron ion homeostasis (GO:0006879)|copper ion import (GO:0015677)|exosomal secretion (GO:1990182)|ferric iron import into cell (GO:0097461)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902167)|protein secretion (GO:0009306)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)	cupric reductase activity (GO:0008823)|ferric-chelate reductase (NADPH) activity (GO:0052851)|ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)	p.V190M(1)		breast(1)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	17						CTTCATGCCCGTGGACATGGG	0.677													G|||	1	0.000199681	0.0	0.0	5008	,	,		19086	0.0		0.0	False		,,,				2504	0.001				p.V200M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G598A	2						.	G	MET/VAL,MET/VAL,MET/VAL	0,4406		0,0,2203	41.0	41.0	41.0		568,568,598	-0.9	0.1	2		41	1,8599		0,1,4299	yes	missense,missense,missense	STEAP3	NM_001008410.1,NM_018234.2,NM_182915.2	21,21,21	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign	190/489,190/489,200/499	120005330	1,13005	2203	4300	6503	119721800	SO:0001583	missense	55240	exon4			AY029585	CCDS2125.1, CCDS42738.1	2q14.2	2011-09-30	2011-09-30		ENSG00000115107	ENSG00000115107			24592	protein-coding gene	gene with protein product		609671				12606722	Standard	NM_182915		Approved	TSAP6, dudlin-2, STMP3	uc002tlr.3	Q658P3	OTTHUMG00000131402	ENST00000354888.5:c.568G>A	2.37:g.120005330G>A	ENSP00000346961:p.Val190Met		119721800	NM_182915	A8K6E3|Q4VBR2|Q4ZG36|Q53SQ8|Q7Z389|Q86SF6|Q8NEW6|Q8TDP3|Q8TF03|Q9NVB5	Missense_Mutation	SNP	ENST00000354888.5	37	CCDS2125.1	.	.	.	.	.	.	.	.	.	.	G	11.58	1.681825	0.29872	0.0	1.16E-4	ENSG00000115107	ENST00000393108;ENST00000354888;ENST00000450943;ENST00000393110;ENST00000393106;ENST00000409811;ENST00000393107;ENST00000425223	T;T;T;T;T;T;T;T	0.20069	2.1;2.1;2.1;2.1;2.1;2.1;2.1;2.1	4.68	-0.901	0.10540	NAD(P)-binding domain (1);	0.445427	0.21640	N	0.071359	T	0.12732	0.0309	M	0.62723	1.935	0.28556	N	0.911368	P;B;B	0.35844	0.524;0.127;0.078	B;B;B	0.22152	0.028;0.038;0.017	T	0.11203	-1.0597	9	.	.	.	-6.889	2.0488	0.03566	0.2513:0.1346:0.484:0.1302	.	190;200;190	B8ZZX6;Q658P3-2;Q658P3	.;.;STEA3_HUMAN	M	190;190;190;200;190;190;190;190	ENSP00000376820:V190M;ENSP00000346961:V190M;ENSP00000396873:V190M;ENSP00000376822:V200M;ENSP00000376818:V190M;ENSP00000386510:V190M;ENSP00000376819:V190M;ENSP00000396214:V190M	.	V	+	1	0	STEAP3	119721800	0.973000	0.33851	0.081000	0.20488	0.861000	0.49209	1.672000	0.37523	-0.097000	0.12307	0.558000	0.71614	GTG		0.677	STEAP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254193.1	NM_018234	
CNTNAP5	129684	broad.mit.edu	37	2	125262114	125262114	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:125262114C>T	ENST00000431078.1	+	8	1669	c.1305C>T	c.(1303-1305)cgC>cgT	p.R435R		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	435	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)		p.R435R(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		TGACAGAACGCGTAGCTGAAA	0.502																																					p.R435R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1305T	2						.						57.0	60.0	59.0					2																	125262114		1960	4158	6118	124978584	SO:0001819	synonymous_variant	129684	exon8			AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.1305C>T	2.37:g.125262114C>T			124978584	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Silent	SNP	ENST00000431078.1	37	CCDS46401.1																																																																																				0.502	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3		
IWS1	55677	broad.mit.edu	37	2	128253619	128253619	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:128253619G>A	ENST00000295321.4	-	7	1930	c.1671C>T	c.(1669-1671)gaC>gaT	p.D557D	IWS1_ENST00000455721.2_3'UTR|AC010976.2_ENST00000599001.1_RNA	NM_017969.2	NP_060439.2	Q96ST2	IWS1_HUMAN	IWS1 homolog (S. cerevisiae)	557	Interaction with SUPT6H and ALYREF.				mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|regulation of histone H3-K36 trimethylation (GO:2001253)|regulation of histone H4 acetylation (GO:0090239)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.D557D(1)		cervix(1)|endometrium(2)|kidney(6)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0735)		TCACGACGTCGTCTGCATCAC	0.483																																					p.D557D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1671T	2						.						252.0	232.0	239.0					2																	128253619		2203	4300	6503	127970089	SO:0001819	synonymous_variant	55677	exon7			AK000868	CCDS2146.1	2q14.3	2006-03-17			ENSG00000163166	ENSG00000163166			25467	protein-coding gene	gene with protein product							Standard	NM_017969		Approved	DKFZp761G0123, FLJ10006, FLJ14655, FLJ32319	uc002ton.2	Q96ST2	OTTHUMG00000131527	ENST00000295321.4:c.1671C>T	2.37:g.128253619G>A			127970089	NM_017969	Q2TB65|Q6P157|Q8N3E8|Q96MI7|Q9NV97|Q9NWH8	Silent	SNP	ENST00000295321.4	37	CCDS2146.1																																																																																				0.483	IWS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254384.2	NM_017969	
UGGT1	56886	broad.mit.edu	37	2	128937438	128937438	+	Silent	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:128937438A>G	ENST00000259253.6	+	35	3941	c.3894A>G	c.(3892-3894)acA>acG	p.T1298T	UGGT1_ENST00000375990.3_Silent_p.T1274T	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	1298	Glucosyltransferase. {ECO:0000250}.				'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)|unfolded protein binding (GO:0051082)	p.T1298T(1)		NS(1)|breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(14)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						TGTCCCCCACATTTAAGGTTT	0.338																																					p.T1298T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A3894G	2						.						126.0	128.0	127.0					2																	128937438		2203	4300	6503	128653908	SO:0001819	synonymous_variant	56886	exon35			AF227905	CCDS2154.1	2q14.3	2009-07-23	2009-07-23	2009-07-23	ENSG00000136731	ENSG00000136731			15663	protein-coding gene	gene with protein product		605897	"""UDP-glucose ceramide glucosyltransferase-like 1"""	UGCGL1		10694380	Standard	NM_020120		Approved	HUGT1	uc002tps.3	Q9NYU2	OTTHUMG00000131570	ENST00000259253.6:c.3894A>G	2.37:g.128937438A>G			128653908	NM_020120	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	Silent	SNP	ENST00000259253.6	37	CCDS2154.1	.	.	.	.	.	.	.	.	.	.	A	10.67	1.416382	0.25552	.	.	ENSG00000136731	ENST00000418197	.	.	.	5.72	-5.25	0.02781	.	.	.	.	.	T	0.39410	0.1077	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.36163	-0.9759	4	.	.	.	.	3.9243	0.09257	0.3714:0.1145:0.4034:0.1107	.	.	.	.	V	27	.	.	I	+	1	0	UGGT1	128653908	0.155000	0.22806	0.894000	0.35097	0.977000	0.68977	-0.298000	0.08265	-1.224000	0.02581	0.533000	0.62120	ATT		0.338	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254435.2	NM_020120	
TPO	7173	broad.mit.edu	37	2	1520659	1520659	+	Silent	SNP	C	C	T	rs367751257		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:1520659C>T	ENST00000345913.4	+	15	2614	c.2523C>T	c.(2521-2523)tcC>tcT	p.S841S	TPO_ENST00000337415.3_Silent_p.S841S|TPO_ENST00000349624.3_Silent_p.S668S|TPO_ENST00000329066.4_Silent_p.S841S|TPO_ENST00000382201.3_Silent_p.S784S|TPO_ENST00000497517.2_3'UTR|TPO_ENST00000382198.1_Silent_p.S668S|TPO_ENST00000346956.3_Silent_p.S797S	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	841					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)	p.S841S(1)		breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	CCCCAGACTCCGGGAGGCTCC	0.617																																					p.S797S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2391T	2						.	C	,,,,,	0,4406		0,0,2203	59.0	64.0	62.0		2523,2523,2352,2352,2391,2004	-4.7	0.8	2		62	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TPO	NM_000547.5,NM_001206744.1,NM_001206745.1,NM_175719.3,NM_175721.3,NM_175722.3	,,,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,,,,	841/934,841/934,784/877,784/877,797/890,668/761	1520659	1,13005	2203	4300	6503	1499666	SO:0001819	synonymous_variant	7173	exon13				CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.2523C>T	2.37:g.1520659C>T			1499666	NM_175721	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Silent	SNP	ENST00000345913.4	37	CCDS1643.1	.	.	.	.	.	.	.	.	.	.	C	1.081	-0.667012	0.03428	0.0	1.16E-4	ENSG00000115705	ENST00000446278	.	.	.	5.39	-4.7	0.03288	.	.	.	.	.	T	0.64616	0.2614	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63998	-0.6510	4	.	.	.	-30.6172	15.2063	0.73180	0.0:0.1275:0.0:0.8725	.	.	.	.	L	316	.	.	P	+	2	0	TPO	1499666	0.261000	0.24063	0.802000	0.32245	0.050000	0.14768	-1.712000	0.01885	-1.229000	0.02564	-1.008000	0.02478	CCG		0.617	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547	
FAM84A	151354	broad.mit.edu	37	2	14774312	14774312	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:14774312G>A	ENST00000295092.2	+	2	497	c.209G>A	c.(208-210)cGc>cAc	p.R70H	AC011897.1_ENST00000581929.1_5'Flank|FAM84A_ENST00000331243.4_Missense_Mutation_p.R70H	NM_145175.2	NP_660158.2	Q96KN4	FA84A_HUMAN	family with sequence similarity 84, member A	70								p.R70H(2)		endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|upper_aerodigestive_tract(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)		GBM - Glioblastoma multiforme(1;0.00969)			AGCCCCAGCCGCCACCACCAC	0.637																																					p.R70H												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.G209A	2						.						17.0	21.0	20.0					2																	14774312		2200	4293	6493	14691763	SO:0001583	missense	151354	exon2			AJ417080, BC026346	CCDS1684.1	2p24.3	2005-08-09			ENSG00000162981	ENSG00000162981			20743	protein-coding gene	gene with protein product	"""neurological/sensory 1"""	611234				14702039	Standard	NM_145175		Approved	NSE1, FLJ35392	uc002rbz.2	Q96KN4	OTTHUMG00000119093	ENST00000295092.2:c.209G>A	2.37:g.14774312G>A	ENSP00000295092:p.Arg70His		14691763	NM_145175	A6NP76|Q86UZ2|Q8NAH7|Q8TAM5	Missense_Mutation	SNP	ENST00000295092.2	37	CCDS1684.1	.	.	.	.	.	.	.	.	.	.	G	9.652	1.141823	0.21205	.	.	ENSG00000162981	ENST00000295092;ENST00000331243;ENST00000359969	T;T	0.03717	3.83;3.83	4.96	2.11	0.27256	.	0.303544	0.23682	N	0.045618	T	0.02012	0.0063	N	0.08118	0	0.29839	N	0.829353	B	0.02656	0.0	B	0.01281	0.0	T	0.33599	-0.9862	10	0.36615	T	0.2	-21.7059	7.1006	0.25336	0.3782:0.0:0.6217:0.0	.	70	Q96KN4	FA84A_HUMAN	H	70	ENSP00000295092:R70H;ENSP00000330681:R70H	ENSP00000295092:R70H	R	+	2	0	FAM84A	14691763	1.000000	0.71417	0.992000	0.48379	0.988000	0.76386	0.825000	0.27393	0.585000	0.29608	0.655000	0.94253	CGC		0.637	FAM84A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239308.2	NM_145175	
CCNT2	905	broad.mit.edu	37	2	135710902	135710902	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:135710902A>G	ENST00000264157.5	+	9	907	c.877A>G	c.(877-879)Act>Gct	p.T293A	CCNT2_ENST00000295238.6_Missense_Mutation_p.T293A|CCNT2_ENST00000537343.1_Missense_Mutation_p.T118A	NM_001241.3|NM_058241.2	NP_001232.1|NP_490595.1	O60583	CCNT2_HUMAN	cyclin T2	293					cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.T293A(1)		endometrium(2)|kidney(3)|large_intestine(10)|lung(6)|ovary(2)|prostate(1)|skin(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.107)		agatagtgtcactggtgtgcc	0.423																																					p.T293A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A877G	2						.						89.0	82.0	85.0					2																	135710902		2203	4300	6503	135427372	SO:0001583	missense	905	exon9			AF048731	CCDS2174.1, CCDS2175.1	2q21.3	2010-11-15			ENSG00000082258	ENSG00000082258			1600	protein-coding gene	gene with protein product		603862				9499409, 10465067	Standard	NM_001241		Approved		uc002tuc.2	O60583	OTTHUMG00000131712	ENST00000264157.5:c.877A>G	2.37:g.135710902A>G	ENSP00000264157:p.Thr293Ala		135427372	NM_058241	A8KA48|D3DP73|D3DP74|O60582|Q29R66|Q53SR4|Q5I1Y0	Missense_Mutation	SNP	ENST00000264157.5	37	CCDS2174.1	.	.	.	.	.	.	.	.	.	.	A	10.33	1.319983	0.23994	.	.	ENSG00000082258	ENST00000537343;ENST00000295238;ENST00000264157	T;T	0.22945	1.93;1.97	5.83	3.5	0.40072	.	0.369488	0.32719	N	0.005739	T	0.13157	0.0319	N	0.19112	0.55	0.34666	D	0.723171	B;B;B	0.12013	0.0;0.001;0.005	B;B;B	0.10450	0.001;0.002;0.005	T	0.13442	-1.0509	10	0.25751	T	0.34	.	4.3134	0.10981	0.651:0.0:0.2103:0.1387	.	118;293;293	B4DH21;O60583;O60583-2	.;CCNT2_HUMAN;.	A	118;293;293	ENSP00000295238:T293A;ENSP00000264157:T293A	ENSP00000264157:T293A	T	+	1	0	CCNT2	135427372	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	0.717000	0.25851	1.046000	0.40249	0.477000	0.44152	ACT		0.423	CCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254629.1	NM_058241	
NEB	4703	broad.mit.edu	37	2	152383462	152383462	+	Silent	SNP	G	G	A	rs373945534		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:152383462G>A	ENST00000172853.10	-	120	16959	c.16812C>T	c.(16810-16812)ctC>ctT	p.L5604L	NEB_ENST00000427231.2_Silent_p.L7305L|NEB_ENST00000397345.3_Silent_p.L7305L|NEB_ENST00000409198.1_Silent_p.L5604L|NEB_ENST00000604864.1_Silent_p.L7305L|NEB_ENST00000603639.1_Silent_p.L7305L			P20929	NEBU_HUMAN	nebulin	5604					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.L5604L(1)		NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TCCTGAGGGCGAGCACCGTGT	0.463																																					p.L7305L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C21915T	2						.	G	,,	1,3843		0,1,1921	110.0	114.0	113.0		21915,21915,16812	5.1	1.0	2		113	0,8246		0,0,4123	no	coding-synonymous,coding-synonymous,coding-synonymous	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	,,	0,1,6044	AA,AG,GG		0.0,0.026,0.0083	,,	7305/8526,7305/8526,5604/6670	152383462	1,12089	1922	4123	6045	152091708	SO:0001819	synonymous_variant	4703	exon148			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.16812C>T	2.37:g.152383462G>A			152091708	NM_001164507	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																					0.463	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
STAM2	10254	broad.mit.edu	37	2	152977247	152977247	+	Silent	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:152977247A>G	ENST00000263904.4	-	14	1768	c.1419T>C	c.(1417-1419)ggT>ggC	p.G473G		NM_005843.4	NP_005834.4	O75886	STAM2_HUMAN	signal transducing adaptor molecule (SH3 domain and ITAM motif) 2	473					endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)		p.G473G(1)		endometrium(3)|large_intestine(4)|lung(8)|ovary(1)	16				BRCA - Breast invasive adenocarcinoma(221;0.22)		AAGCAGTTGTACCAGTAGCTG	0.408																																					p.G473G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1419C	2						.						173.0	154.0	160.0					2																	152977247		2203	4300	6503	152685493	SO:0001819	synonymous_variant	10254	exon14			AF042274	CCDS2196.1	2q23.3	2009-04-29			ENSG00000115145	ENSG00000115145			11358	protein-coding gene	gene with protein product	"""HSE1 homolog (S. cerevisiae)"""	606244				10899310, 10993906	Standard	NM_005843		Approved	Hbp	uc002tyc.4	O75886	OTTHUMG00000131885	ENST00000263904.4:c.1419T>C	2.37:g.152977247A>G			152685493	NM_005843	A8K8A0|D3DPA1|Q7LDQ0|Q9UF58	Silent	SNP	ENST00000263904.4	37	CCDS2196.1																																																																																				0.408	STAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254835.2	NM_005843	
TANC1	85461	broad.mit.edu	37	2	160043535	160043535	+	Splice_Site	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:160043535G>A	ENST00000263635.6	+	16	2979	c.2742G>A	c.(2740-2742)aaG>aaA	p.K914K	TANC1_ENST00000454300.1_Splice_Site_p.K808K	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	914					dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)		p.K914K(1)		breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						CCAACGTGAAGGTGAGCAACC	0.622																																					p.K914K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2742A	2						.						33.0	33.0	33.0					2																	160043535		1928	4139	6067	159751781	SO:0001630	splice_region_variant	85461	exon16			AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29364	protein-coding gene	gene with protein product	"""rolling pebbles homolog B (Drosophila)"""	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.2742+1G>A	2.37:g.160043535G>A			159751781	NM_033394	C9JD88|Q49AI8	Silent	SNP	ENST00000263635.6	37	CCDS42766.1																																																																																				0.622	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1		Silent
PXDN	7837	broad.mit.edu	37	2	1652071	1652071	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:1652071G>A	ENST00000252804.4	-	17	3531	c.3481C>T	c.(3481-3483)Cgg>Tgg	p.R1161W		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	1161					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.R1161W(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)		TCCCGGCCCCGCTGGATGTTG	0.592																																					p.R1161W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3481T	2						.						70.0	81.0	78.0					2																	1652071		2041	4217	6258	1631078	SO:0001583	missense	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.3481C>T	2.37:g.1652071G>A	ENSP00000252804:p.Arg1161Trp		1631078	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Missense_Mutation	SNP	ENST00000252804.4	37	CCDS46221.1	.	.	.	.	.	.	.	.	.	.	G	17.83	3.484681	0.63962	.	.	ENSG00000130508	ENST00000252804	D	0.84516	-1.86	5.59	3.58	0.41010	.	0.000000	0.85682	D	0.000000	D	0.95101	0.8413	H	0.98577	4.27	0.54753	D	0.999989	D	0.89917	1.0	D	0.97110	1.0	D	0.96246	0.9179	10	0.87932	D	0	-37.3055	12.9876	0.58599	0.0:0.0:0.4409:0.5591	.	1161	Q92626	PXDN_HUMAN	W	1161	ENSP00000252804:R1161W	ENSP00000252804:R1161W	R	-	1	2	PXDN	1631078	1.000000	0.71417	0.992000	0.48379	0.983000	0.72400	1.986000	0.40677	1.314000	0.45095	0.650000	0.86243	CGG		0.592	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455	
MARCH7	64844	broad.mit.edu	37	2	160599647	160599647	+	Missense_Mutation	SNP	C	C	T	rs139916486		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:160599647C>T	ENST00000259050.4	+	3	351	c.229C>T	c.(229-231)Cgc>Tgc	p.R77C	MARCH7_ENST00000409591.1_Missense_Mutation_p.R39C|MARCH7_ENST00000539065.1_Missense_Mutation_p.R77C|MARCH7_ENST00000473749.1_3'UTR|MARCH7_ENST00000409175.1_Missense_Mutation_p.R77C	NM_001282805.1|NM_001282807.1|NM_022826.2	NP_001269734.1|NP_001269736.1|NP_073737.1	Q9H992	MARH7_HUMAN	membrane-associated ring finger (C3HC4) 7, E3 ubiquitin protein ligase	77	Ser-rich.				protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.R77C(1)		breast(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(2)	18						TCAGGGAGCACGCTCAAGATC	0.413																																					p.R77C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C229T	2						.	C	CYS/ARG	0,4406		0,0,2203	125.0	121.0	122.0		229	3.7	1.0	2	dbSNP_134	122	1,8599	1.2+/-3.3	0,1,4299	no	missense	MARCH7	NM_022826.2	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	77/705	160599647	1,13005	2203	4300	6503	160307893	SO:0001583	missense	64844	exon3			AK022973	CCDS2210.1, CCDS63038.1, CCDS63039.1	2q24.2	2013-01-09	2012-02-23	2005-01-27	ENSG00000136536	ENSG00000136536		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	17393	protein-coding gene	gene with protein product		613334	"""axotrophin"", ""membrane-associated ring finger (C3HC4) 7"""	AXOT		14722266	Standard	XM_005246773		Approved	MARCH-VII, RNF177	uc002uax.3	Q9H992	OTTHUMG00000132029	ENST00000259050.4:c.229C>T	2.37:g.160599647C>T	ENSP00000259050:p.Arg77Cys		160307893	NM_022826	A8K9X1|B7Z7P5|D3DPB0|Q53GQ1|Q9BTR9	Missense_Mutation	SNP	ENST00000259050.4	37	CCDS2210.1	.	.	.	.	.	.	.	.	.	.	C	12.52	1.961234	0.34565	0.0	1.16E-4	ENSG00000136536	ENST00000409175;ENST00000539065;ENST00000259050;ENST00000421037;ENST00000409591	T;T;T;T;T	0.45668	2.61;2.69;2.61;0.89;2.6	5.54	3.72	0.42706	.	0.603491	0.19244	N	0.119081	T	0.23611	0.0571	N	0.16478	0.41	0.41849	D	0.990169	B;B;B	0.15719	0.007;0.014;0.014	B;B;B	0.08055	0.003;0.002;0.001	T	0.09862	-1.0655	10	0.40728	T	0.16	-1.1016	6.2791	0.20997	0.0:0.7617:0.0:0.2383	.	77;39;77	F5H6W4;B7Z7P5;Q9H992	.;.;MARH7_HUMAN	C	77;77;77;77;39	ENSP00000386830:R77C;ENSP00000442992:R77C;ENSP00000259050:R77C;ENSP00000392862:R77C;ENSP00000387238:R39C	ENSP00000259050:R77C	R	+	1	0	MARCH7	160307893	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.150000	0.50662	2.607000	0.88179	0.650000	0.86243	CGC		0.413	MARCH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255040.3	NM_022826	
SCN3A	6328	broad.mit.edu	37	2	165948808	165948808	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:165948808C>G	ENST00000360093.3	-	27	5254	c.4763G>C	c.(4762-4764)gGc>gCc	p.G1588A	SCN3A_ENST00000409101.3_Missense_Mutation_p.G1539A|SCN3A_ENST00000540861.1_Missense_Mutation_p.G71A|SCN3A_ENST00000465043.1_5'UTR|AC013463.2_ENST00000431341.1_RNA|SCN3A_ENST00000283254.7_Missense_Mutation_p.G1588A	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	1588					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.G1588A(1)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GATGTTCCAGCCTATAGTGAA	0.438																																					p.G1588A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4763C	2						.						127.0	117.0	120.0					2																	165948808		2203	4300	6503	165657054	SO:0001583	missense	6328	exon27			AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10590	protein-coding gene	gene with protein product		182391	"""sodium channel, voltage-gated, type III, alpha polypeptide"""			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.4763G>C	2.37:g.165948808C>G	ENSP00000353206:p.Gly1588Ala		165657054	NM_006922	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Missense_Mutation	SNP	ENST00000360093.3	37		.	.	.	.	.	.	.	.	.	.	C	29.5	5.011838	0.93346	.	.	ENSG00000153253	ENST00000360093;ENST00000283254;ENST00000409101;ENST00000540861	D;D;D;D	0.98329	-4.87;-4.87;-4.87;-4.87	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	D	0.98579	0.9525	L	0.55481	1.735	0.80722	D	1	D;D;D	0.89917	0.999;0.996;1.0	D;D;D	0.87578	0.998;0.96;0.977	D	0.98786	1.0734	10	0.42905	T	0.14	.	19.9348	0.97133	0.0:1.0:0.0:0.0	.	1539;1539;1588	Q9NY46-2;Q9NY46-4;Q9NY46-3	.;.;.	A	1588;1588;1539;71	ENSP00000353206:G1588A;ENSP00000283254:G1588A;ENSP00000386726:G1539A;ENSP00000439920:G71A	ENSP00000283254:G1588A	G	-	2	0	SCN3A	165657054	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.776000	0.85560	2.789000	0.95967	0.591000	0.81541	GGC		0.438	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922	
SCN3A	6328	broad.mit.edu	37	2	165997318	165997318	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:165997318C>T	ENST00000360093.3	-	13	2353	c.1862G>A	c.(1861-1863)cGc>cAc	p.R621H	SCN3A_ENST00000409101.3_Missense_Mutation_p.R621H|SCN3A_ENST00000283254.7_Missense_Mutation_p.R621H	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	621					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.R621H(1)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GTTACTGTTGCGTCGCTCTCC	0.498																																					p.R621H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1862A	2						.						249.0	180.0	204.0					2																	165997318		2203	4300	6503	165705564	SO:0001583	missense	6328	exon13			AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10590	protein-coding gene	gene with protein product		182391	"""sodium channel, voltage-gated, type III, alpha polypeptide"""			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.1862G>A	2.37:g.165997318C>T	ENSP00000353206:p.Arg621His		165705564	NM_006922	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Missense_Mutation	SNP	ENST00000360093.3	37		.	.	.	.	.	.	.	.	.	.	C	20.7	4.033327	0.75504	.	.	ENSG00000153253	ENST00000360093;ENST00000283254;ENST00000409101;ENST00000440431	D;D;D;D	0.93426	-3.22;-3.22;-3.22;-3.22	6.07	6.07	0.98685	Domain of unknown function DUF3451 (1);	0.000000	0.64402	D	0.000006	D	0.96917	0.8993	M	0.83223	2.63	0.80722	D	1	D;D;D;D;D	0.89917	0.999;1.0;0.993;0.993;1.0	D;D;P;P;D	0.78314	0.956;0.991;0.698;0.698;0.99	D	0.95040	0.8177	10	0.29301	T	0.29	.	20.6593	0.99626	0.0:1.0:0.0:0.0	.	621;621;621;621;621	Q9NY46;E7EUE6;Q9NY46-2;Q9NY46-4;Q9NY46-3	SCN3A_HUMAN;.;.;.;.	H	621	ENSP00000353206:R621H;ENSP00000283254:R621H;ENSP00000386726:R621H;ENSP00000403348:R621H	ENSP00000283254:R621H	R	-	2	0	SCN3A	165705564	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.030000	0.70903	2.885000	0.99019	0.655000	0.94253	CGC		0.498	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922	
SCN2A	6326	broad.mit.edu	37	2	166245766	166245766	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:166245766A>G	ENST00000375437.2	+	27	5740	c.5450A>G	c.(5449-5451)aAa>aGa	p.K1817R	SCN2A_ENST00000375427.2_Missense_Mutation_p.K1817R|SCN2A_ENST00000283256.6_Missense_Mutation_p.K1817R|SCN2A_ENST00000357398.3_Missense_Mutation_p.K1817R	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	1817					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.K1817R(1)		NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GAGTTTGCCAAACTTTCTGAT	0.473																																					p.K1817R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A5450G	2						.						138.0	139.0	139.0					2																	166245766		2203	4300	6503	165954012	SO:0001583	missense	6326	exon26			AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10588	protein-coding gene	gene with protein product		182390	"""sodium channel, voltage-gated, type II, alpha 2 polypeptide"", ""sodium channel, voltage-gated, type II, alpha 1 polypeptide"""	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.5450A>G	2.37:g.166245766A>G	ENSP00000364586:p.Lys1817Arg		165954012	NM_001040143	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Missense_Mutation	SNP	ENST00000375437.2	37	CCDS33314.1	.	.	.	.	.	.	.	.	.	.	A	11.37	1.618104	0.28801	.	.	ENSG00000136531	ENST00000375437;ENST00000357398;ENST00000283256;ENST00000375427	D;D;D;D	0.96168	-3.93;-3.93;-3.93;-3.93	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	D	0.96160	0.8748	L	0.58969	1.84	0.45097	D	0.998111	B;P	0.38978	0.028;0.652	B;P	0.50617	0.036;0.646	D	0.96214	0.9155	10	0.56958	D	0.05	.	16.1723	0.81825	1.0:0.0:0.0:0.0	.	1817;1817	Q99250-2;Q99250	.;SCN2A_HUMAN	R	1817	ENSP00000364586:K1817R;ENSP00000349973:K1817R;ENSP00000283256:K1817R;ENSP00000364576:K1817R	ENSP00000283256:K1817R	K	+	2	0	SCN2A	165954012	1.000000	0.71417	1.000000	0.80357	0.671000	0.39405	4.446000	0.60014	2.281000	0.76405	0.524000	0.50904	AAA		0.473	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007	
TTC21B	79809	broad.mit.edu	37	2	166786686	166786686	+	Silent	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:166786686T>C	ENST00000243344.7	-	9	1220	c.1083A>G	c.(1081-1083)ctA>ctG	p.L361L		NM_024753.4	NP_079029.3	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B	361					forebrain dorsal/ventral pattern formation (GO:0021798)|intraciliary retrograde transport (GO:0035721)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|protein localization to cilium (GO:0061512)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|nuclear chromatin (GO:0000790)		p.L361L(1)		breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(9)|lung(28)|ovary(2)|pancreas(2)|skin(2)|urinary_tract(1)	58						TCATACCAACTAGGGCAGACA	0.358																																					p.L361L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1083G	2						.						107.0	107.0	107.0					2																	166786686		2203	4300	6503	166494932	SO:0001819	synonymous_variant	79809	exon9			AB082523	CCDS33315.1	2q24.3	2014-09-04			ENSG00000123607	ENSG00000123607		"""Tetratricopeptide (TTC) repeat domain containing"", ""Intraflagellar transport homologs"""	25660	protein-coding gene	gene with protein product		612014				12056414, 21258341	Standard	NM_024753		Approved	FLJ11457, JBTS11, NPHP12, IFT139, THM1	uc002udk.3	Q7Z4L5	OTTHUMG00000154083	ENST00000243344.7:c.1083A>G	2.37:g.166786686T>C			166494932	NM_024753	A8MUZ3|Q3LIE4|Q53T84|Q6P4A1|Q6PIF5|Q8NCN3|Q96MA4|Q9HAK8	Silent	SNP	ENST00000243344.7	37	CCDS33315.1																																																																																				0.358	TTC21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333770.1	NM_024753	
SCN1A	6323	broad.mit.edu	37	2	166892600	166892600	+	Silent	SNP	C	C	T	rs375953445		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:166892600C>T	ENST00000303395.4	-	16	3386	c.3387G>A	c.(3385-3387)acG>acA	p.T1129T	SCN1A_ENST00000375405.3_Silent_p.T1118T|SCN1A_ENST00000409050.1_Silent_p.T1101T|AC010127.3_ENST00000599041.1_RNA|SCN1A_ENST00000423058.2_Silent_p.T1129T|AC010127.3_ENST00000597623.1_RNA|AC010127.3_ENST00000595268.1_RNA|AC010127.3_ENST00000595647.1_RNA			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1129					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)	p.T1118T(1)		NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TAAAGTCTTCCGTGTTTAAAT	0.348																																					p.T1101T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3303A	2						.	C	,,,	0,4406		0,0,2203	154.0	158.0	157.0		3387,3303,3387,3354	-2.5	1.0	2		157	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SCN1A	NM_001165963.1,NM_001165964.1,NM_001202435.1,NM_006920.4	,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,,	1129/2010,1101/1982,1129/2010,1118/1999	166892600	1,13005	2203	4300	6503	166600846	SO:0001819	synonymous_variant	6323	exon16			AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10585	protein-coding gene	gene with protein product		182389	"""febrile convulsions 3"""	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.3387G>A	2.37:g.166892600C>T			166600846	NM_001165964	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Silent	SNP	ENST00000303395.4	37	CCDS54413.1																																																																																				0.348	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920	
XIRP2	129446	broad.mit.edu	37	2	168103037	168103037	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:168103037A>G	ENST00000409195.1	+	9	5224	c.5135A>G	c.(5134-5136)gAt>gGt	p.D1712G	XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.D1490G|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.D1712G|XIRP2_ENST00000409605.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1537					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)		p.D1712G(1)		NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						ATAGGTGGTGATGTCAAACGT	0.338																																					p.D1490G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A4469G	2						.						143.0	136.0	138.0					2																	168103037		1879	4103	5982	167811283	SO:0001583	missense	129446	exon7			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.5135A>G	2.37:g.168103037A>G	ENSP00000386840:p.Asp1712Gly		167811283	NM_001199144	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	A	17.52	3.410528	0.62399	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.04917	3.54;3.54;3.53	5.59	5.59	0.84812	.	0.047711	0.85682	D	0.000000	T	0.26340	0.0643	M	0.77313	2.365	0.50813	D	0.999892	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.87578	0.996;0.998;0.974	T	0.00904	-1.1520	10	0.66056	D	0.02	-22.737	14.7546	0.69554	1.0:0.0:0.0:0.0	.	1537;1537;1490	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	G	1712;1712;1490	ENSP00000386840:D1712G;ENSP00000295237:D1712G;ENSP00000387255:D1490G	ENSP00000295237:D1712G	D	+	2	0	XIRP2	167811283	1.000000	0.71417	1.000000	0.80357	0.842000	0.47809	8.962000	0.93254	2.134000	0.65973	0.528000	0.53228	GAT		0.338	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
ABCB11	8647	broad.mit.edu	37	2	169830285	169830285	+	Silent	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:169830285T>C	ENST00000263817.6	-	13	1498	c.1374A>G	c.(1372-1374)ggA>ggG	p.G458G		NM_003742.2	NP_003733.2	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 11	458	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|canalicular bile acid transport (GO:0015722)|small molecule metabolic process (GO:0044281)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|bile acid-exporting ATPase activity (GO:0015432)|canalicular bile acid transmembrane transporter activity (GO:0015126)|sodium-exporting ATPase activity, phosphorylative mechanism (GO:0008554)|transporter activity (GO:0005215)	p.G458G(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(16)|lung(26)|ovary(3)|stomach(1)	57					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Chlorpromazine(DB00477)|Cimetidine(DB00501)|Clofazimine(DB00845)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Digoxin(DB00390)|Doxorubicin(DB00997)|Ethinyl Estradiol(DB00977)|Fluorescein(DB00693)|Fusidic Acid(DB02703)|Glyburide(DB01016)|Ketoconazole(DB01026)|Novobiocin(DB01051)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Ponatinib(DB08901)|Pravastatin(DB00175)|Progesterone(DB00396)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Tamoxifen(DB00675)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	TTTTTCCAGCTCCACTGGGTC	0.453																																					p.G458G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1374G	2						.						181.0	171.0	174.0					2																	169830285		1900	4115	6015	169538531	SO:0001819	synonymous_variant	8647	exon13			AF091582	CCDS46444.1	2q24	2012-03-14			ENSG00000073734	ENSG00000073734		"""ATP binding cassette transporters / subfamily B"""	42	protein-coding gene	gene with protein product	"""ABC member 16, MDR/TAP subfamily"""	603201	"""progressive familial intrahepatic cholestasis 2"", ""bile salt export pump"""	BSEP, PFIC2		9806540	Standard	NM_003742		Approved	ABC16, SPGP, PFIC-2, PGY4	uc002ueo.1	O95342	OTTHUMG00000154039	ENST00000263817.6:c.1374A>G	2.37:g.169830285T>C			169538531	NM_003742	Q53TL2|Q9UNB2	Silent	SNP	ENST00000263817.6	37	CCDS46444.1																																																																																				0.453	ABCB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333616.2	NM_003742	
ABCB11	8647	broad.mit.edu	37	2	169853219	169853219	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:169853219C>T	ENST00000263817.6	-	6	527	c.403G>A	c.(403-405)Gag>Aag	p.E135K		NM_003742.2	NP_003733.2	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 11	135	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|canalicular bile acid transport (GO:0015722)|small molecule metabolic process (GO:0044281)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|bile acid-exporting ATPase activity (GO:0015432)|canalicular bile acid transmembrane transporter activity (GO:0015126)|sodium-exporting ATPase activity, phosphorylative mechanism (GO:0008554)|transporter activity (GO:0005215)	p.E135K(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(16)|lung(26)|ovary(3)|stomach(1)	57					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Chlorpromazine(DB00477)|Cimetidine(DB00501)|Clofazimine(DB00845)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Digoxin(DB00390)|Doxorubicin(DB00997)|Ethinyl Estradiol(DB00977)|Fluorescein(DB00693)|Fusidic Acid(DB02703)|Glyburide(DB01016)|Ketoconazole(DB01026)|Novobiocin(DB01051)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Ponatinib(DB08901)|Pravastatin(DB00175)|Progesterone(DB00396)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Tamoxifen(DB00675)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	ATTTCGCTCTCGATGTTCAGC	0.378																																					p.E135K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G403A	2						.						61.0	59.0	60.0					2																	169853219		1872	4105	5977	169561465	SO:0001583	missense	8647	exon6			AF091582	CCDS46444.1	2q24	2012-03-14			ENSG00000073734	ENSG00000073734		"""ATP binding cassette transporters / subfamily B"""	42	protein-coding gene	gene with protein product	"""ABC member 16, MDR/TAP subfamily"""	603201	"""progressive familial intrahepatic cholestasis 2"", ""bile salt export pump"""	BSEP, PFIC2		9806540	Standard	NM_003742		Approved	ABC16, SPGP, PFIC-2, PGY4	uc002ueo.1	O95342	OTTHUMG00000154039	ENST00000263817.6:c.403G>A	2.37:g.169853219C>T	ENSP00000263817:p.Glu135Lys		169561465	NM_003742	Q53TL2|Q9UNB2	Missense_Mutation	SNP	ENST00000263817.6	37	CCDS46444.1	.	.	.	.	.	.	.	.	.	.	C	17.51	3.407011	0.62399	.	.	ENSG00000073734	ENST00000263817	D	0.86769	-2.17	5.03	4.14	0.48551	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.809444	0.11715	N	0.536491	D	0.88912	0.6566	L	0.41356	1.27	0.58432	D	0.999999	D	0.65815	0.995	P	0.58130	0.833	D	0.85431	0.1149	10	0.41790	T	0.15	-0.2788	14.1611	0.65448	0.0:0.9255:0.0:0.0745	.	135	O95342	ABCBB_HUMAN	K	135	ENSP00000263817:E135K	ENSP00000263817:E135K	E	-	1	0	ABCB11	169561465	1.000000	0.71417	0.900000	0.35374	0.035000	0.12851	5.525000	0.67110	1.206000	0.43276	0.650000	0.86243	GAG		0.378	ABCB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333616.2	NM_003742	
LRP2	4036	broad.mit.edu	37	2	170097634	170097634	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:170097634C>A	ENST00000263816.3	-	25	4194	c.3909G>T	c.(3907-3909)aaG>aaT	p.K1303N	LRP2_ENST00000443831.1_Missense_Mutation_p.K1166N	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1303	LDL-receptor class A 14. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.K1303N(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)"""	TAGGGCAGTCCTTCTCATCAC	0.502																																					p.K1303N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3909T	2						.						210.0	157.0	175.0					2																	170097634		2203	4300	6503	169805880	SO:0001583	missense	4036	exon25				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.3909G>T	2.37:g.170097634C>A	ENSP00000263816:p.Lys1303Asn		169805880	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	C	9.285	1.049217	0.19827	.	.	ENSG00000081479	ENST00000263816;ENST00000443831	D;D	0.95821	-3.82;-3.82	5.92	2.11	0.27256	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.258719	0.46442	N	0.000297	D	0.93070	0.7794	L	0.42487	1.325	0.31741	N	0.635763	P;P	0.48998	0.88;0.918	P;P	0.57009	0.811;0.543	D	0.87786	0.2615	10	0.19590	T	0.45	.	0.9493	0.01372	0.1523:0.3601:0.1483:0.3393	.	1166;1303	E9PC35;P98164	.;LRP2_HUMAN	N	1303;1166	ENSP00000263816:K1303N;ENSP00000409813:K1166N	ENSP00000263816:K1303N	K	-	3	2	LRP2	169805880	0.950000	0.32346	0.998000	0.56505	0.050000	0.14768	0.038000	0.13862	0.391000	0.25143	-0.769000	0.03391	AAG		0.502	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
TLK1	9874	broad.mit.edu	37	2	172016851	172016851	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:172016851C>T	ENST00000431350.2	-	1	492	c.88G>A	c.(88-90)Gcg>Acg	p.A30T	TLK1_ENST00000521943.1_Intron|TLK1_ENST00000360843.3_Missense_Mutation_p.A30T|TLK1_ENST00000442919.2_5'UTR			Q9UKI8	TLK1_HUMAN	tousled-like kinase 1	30					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.A30T(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|liver(3)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	33						GACCTGGCCGCCGCCGCCGAG	0.687																																					p.A30T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G88A	2						.						27.0	35.0	33.0					2																	172016851		2202	4299	6501	171725097	SO:0001583	missense	9874	exon1			AB004885	CCDS2241.1, CCDS46447.1, CCDS46448.1	2q31.1	2010-04-19			ENSG00000198586	ENSG00000198586			11841	protein-coding gene	gene with protein product		608438				9427565, 12660173	Standard	NM_012290		Approved	KIAA0137, PKU-BETA	uc002ugp.2	Q9UKI8	OTTHUMG00000132243	ENST00000431350.2:c.88G>A	2.37:g.172016851C>T	ENSP00000411099:p.Ala30Thr		171725097	NM_012290	B3KR15|B4DX87|Q14150|Q8N591|Q9NYH2|Q9Y4F6	Missense_Mutation	SNP	ENST00000431350.2	37	CCDS2241.1	.	.	.	.	.	.	.	.	.	.	C	14.76	2.631938	0.46944	.	.	ENSG00000198586	ENST00000431350;ENST00000360843	T;T	0.70631	-0.5;-0.5	3.46	3.46	0.39613	.	0.719069	0.10204	U	0.702962	T	0.45637	0.1352	N	0.08118	0	0.80722	D	1	B;P	0.47604	0.001;0.898	B;B	0.31869	0.0;0.137	T	0.50857	-0.8778	10	0.66056	D	0.02	.	10.3406	0.43875	0.0:1.0:0.0:0.0	.	30;30	Q9UKI8-2;Q9UKI8	.;TLK1_HUMAN	T	30	ENSP00000411099:A30T;ENSP00000354089:A30T	ENSP00000352810:A30T	A	-	1	0	TLK1	171725097	1.000000	0.71417	1.000000	0.80357	0.777000	0.43975	1.999000	0.40806	1.781000	0.52344	0.545000	0.68477	GCG		0.687	TLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255314.1	NM_012290	
DYNC1I2	1781	broad.mit.edu	37	2	172604355	172604355	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:172604355C>T	ENST00000397119.3	+	18	2040	c.1873C>T	c.(1873-1875)Cga>Tga	p.R625*	DYNC1I2_ENST00000358002.6_Nonsense_Mutation_p.R617*|DYNC1I2_ENST00000508530.1_Nonsense_Mutation_p.R598*|DYNC1I2_ENST00000409453.1_Nonsense_Mutation_p.R624*|DYNC1I2_ENST00000410079.3_Nonsense_Mutation_p.R617*|DYNC1I2_ENST00000263811.4_Nonsense_Mutation_p.R619*|DYNC1I2_ENST00000340296.4_Nonsense_Mutation_p.R599*|DYNC1I2_ENST00000409773.1_Nonsense_Mutation_p.R625*|DYNC1I2_ENST00000409317.1_Nonsense_Mutation_p.R619*|DYNC1I2_ENST00000409197.1_Nonsense_Mutation_p.R599*|DYNC1I2_ENST00000534253.2_Nonsense_Mutation_p.R625*	NM_001378.1	NP_001369.1	Q13409	DC1I2_HUMAN	dynein, cytoplasmic 1, intermediate chain 2	625					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|G2/M transition of mitotic cell cycle (GO:0000086)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|transport (GO:0006810)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|microtubule (GO:0005874)|vesicle (GO:0031982)	microtubule motor activity (GO:0003777)	p.R625*(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)	15			OV - Ovarian serous cystadenocarcinoma(117;0.198)			TAATGCAAACCGAGCTGATGC	0.438																																					p.R625X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1873T	2						.						59.0	55.0	56.0					2																	172604355		1873	4103	5976	172312601	SO:0001587	stop_gained	1781	exon18			AK055491	CCDS46450.1, CCDS63054.1, CCDS63056.1, CCDS63057.1	2q31.1	2013-01-10	2005-11-24	2005-11-24	ENSG00000077380	ENSG00000077380		"""Cytoplasmic dyneins"", ""WD repeat domain containing"""	2964	protein-coding gene	gene with protein product		603331	"""dynein, cytoplasmic, intermediate polypeptide 2"""	DNCI2		10049579, 16260502	Standard	NM_001378		Approved		uc002uha.2	Q13409	OTTHUMG00000154061	ENST00000397119.3:c.1873C>T	2.37:g.172604355C>T	ENSP00000380308:p.Arg625*		172312601	NM_001378	B7ZA04|D3DPD4|D3DPD5|D3DPD6|Q32LY9|Q53S84|Q5BJF8|Q7Z4X1|Q96NG7|Q96S87|Q9BXZ5|Q9NT58	Nonsense_Mutation	SNP	ENST00000397119.3	37	CCDS46450.1	.	.	.	.	.	.	.	.	.	.	C	36	5.819453	0.96982	.	.	ENSG00000077380	ENST00000340296;ENST00000534253;ENST00000263811;ENST00000397119;ENST00000410079;ENST00000508530;ENST00000409197;ENST00000409317;ENST00000409773;ENST00000409453;ENST00000358002	.	.	.	5.75	3.84	0.44239	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.2044	12.6623	0.56822	0.5156:0.4844:0.0:0.0	.	.	.	.	X	599;625;619;625;617;598;599;619;625;624;617	.	ENSP00000263811:R619X	R	+	1	2	DYNC1I2	172312601	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	1.149000	0.31626	1.419000	0.47118	0.591000	0.81541	CGA		0.438	DYNC1I2-001	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333683.2	NM_001378	
SLC25A12	8604	broad.mit.edu	37	2	172666181	172666181	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:172666181G>A	ENST00000422440.2	-	13	1277	c.1240C>T	c.(1240-1242)Cgg>Tgg	p.R414W	SLC25A12_ENST00000392592.4_Missense_Mutation_p.R307W	NM_003705.4	NP_003696.2	O75746	CMC1_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 12	414					aspartate transport (GO:0015810)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)	p.R414W(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|upper_aerodigestive_tract(1)	23			OV - Ovarian serous cystadenocarcinoma(117;0.216)		L-Aspartic Acid(DB00128)	AATTTGTCCCGAACAAAATCA	0.393																																					p.R414W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1240T	2						.						100.0	103.0	102.0					2																	172666181		2203	4300	6503	172374427	SO:0001583	missense	8604	exon13			Y14494	CCDS33327.1	2q24	2013-05-22	2012-03-29		ENSG00000115840	ENSG00000115840		"""Solute carriers"", ""EF-hand domain containing"""	10982	protein-coding gene	gene with protein product		603667	"""solute carrier family 25 (mitochondrial carrier, Aralar), member 12"""			9722566, 10702666, 11566871	Standard	NM_003705		Approved	Aralar	uc002uhh.3	O75746	OTTHUMG00000134290	ENST00000422440.2:c.1240C>T	2.37:g.172666181G>A	ENSP00000388658:p.Arg414Trp		172374427	NM_003705	B3KR64|Q96AM8	Missense_Mutation	SNP	ENST00000422440.2	37	CCDS33327.1	.	.	.	.	.	.	.	.	.	.	g	19.90	3.912275	0.72983	.	.	ENSG00000115840	ENST00000422440;ENST00000392592	T;T	0.80123	-1.34;-1.34	5.47	5.47	0.80525	Mitochondrial carrier domain (2);	0.101693	0.64402	D	0.000003	D	0.91078	0.7192	M	0.90309	3.105	0.58432	D	0.999994	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.92521	0.6025	10	0.87932	D	0	-10.7845	14.0993	0.65044	0.0:0.0:0.8124:0.1876	.	307;414	B3KR64;O75746	.;CMC1_HUMAN	W	414;307	ENSP00000388658:R414W;ENSP00000376371:R307W	ENSP00000376371:R307W	R	-	1	2	SLC25A12	172374427	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.600000	0.61083	2.555000	0.86185	0.650000	0.86243	CGG		0.393	SLC25A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259010.2	NM_003705	
OLA1	29789	broad.mit.edu	37	2	174943734	174943734	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:174943734C>T	ENST00000409546.1	-	10	1741	c.1111G>A	c.(1111-1113)Gaa>Aaa	p.E371K	OLA1_ENST00000284719.3_Missense_Mutation_p.E351K|OLA1_ENST00000344357.5_Missense_Mutation_p.E193K|OLA1_ENST00000392560.2_5'UTR|OLA1_ENST00000428402.2_Intron					Obg-like ATPase 1									p.E351K(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	11						TTAAAATCTTCGTATTTCATT	0.353																																					p.E193K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G577A	2						.						72.0	67.0	69.0					2																	174943734		2203	4300	6503	174651980	SO:0001583	missense	29789	exon9				CCDS2255.1, CCDS42779.1	2q31.1	2014-06-24	2007-07-27	2007-07-27	ENSG00000138430	ENSG00000138430			28833	protein-coding gene	gene with protein product		611175	"""GTP-binding protein 9 (putative)"""	GTPBP9		17430889, 24486488	Standard	NM_013341		Approved	PTD004	uc002uih.3	Q9NTK5	OTTHUMG00000132335	ENST00000409546.1:c.1111G>A	2.37:g.174943734C>T	ENSP00000386350:p.Glu371Lys		174651980	NM_001011708		Missense_Mutation	SNP	ENST00000409546.1	37		.	.	.	.	.	.	.	.	.	.	C	14.93	2.682395	0.47991	.	.	ENSG00000138430	ENST00000284719;ENST00000344357;ENST00000409546	T;T	0.44083	0.93;0.93	6.17	6.17	0.99709	Domain of unknown function DUF933 (1);TGS-like (1);Beta-grasp fold, ferredoxin-type (1);	0.335148	0.35838	N	0.002952	T	0.47673	0.1458	M	0.69823	2.125	0.52501	D	0.999955	B;B;B	0.27791	0.008;0.189;0.008	B;B;B	0.19391	0.025;0.018;0.025	T	0.38134	-0.9675	10	0.48119	T	0.1	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	351;193;351	D7EHM2;Q9NTK5-2;Q9NTK5	.;.;OLA1_HUMAN	K	351;193;371	ENSP00000284719:E351K;ENSP00000386350:E371K	ENSP00000284719:E351K	E	-	1	0	OLA1	174651980	1.000000	0.71417	0.985000	0.45067	0.961000	0.63080	3.939000	0.56591	2.941000	0.99782	0.655000	0.94253	GAA		0.353	OLA1-003	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000333877.1	NM_013341	
HOXD10	3236	broad.mit.edu	37	2	176981726	176981726	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:176981726G>A	ENST00000249501.4	+	1	420	c.165G>A	c.(163-165)ccG>ccA	p.P55P	HOXD10_ENST00000490088.2_Intron	NM_002148.3	NP_002139.2	P28358	HXD10_HUMAN	homeobox D10	55					adult locomotory behavior (GO:0008344)|anterior/posterior pattern specification (GO:0009952)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|neuromuscular process (GO:0050905)|peripheral nervous system neuron development (GO:0048935)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal muscle tissue development (GO:0007519)|spinal cord motor neuron cell fate specification (GO:0021520)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P55P(2)		endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	17			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0226)|READ - Rectum adenocarcinoma(9;0.0556)		GACTGCTCCCGTCTCTGGCCA	0.488																																					p.P55P												.	.	2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	c.G165A	2						.						109.0	109.0	109.0					2																	176981726		2203	4300	6503	176689972	SO:0001819	synonymous_variant	3236	exon1				CCDS2266.1	2q31.1	2014-09-17	2005-12-22		ENSG00000128710	ENSG00000128710		"""Homeoboxes / ANTP class : HOXL subclass"""	5133	protein-coding gene	gene with protein product		142984	"""homeo box D10"""	HOX4, HOX4D		1973146, 1358459	Standard	NM_002148		Approved		uc002ukj.3	P28358	OTTHUMG00000132511	ENST00000249501.4:c.165G>A	2.37:g.176981726G>A			176689972	NM_002148	Q6NT10	Silent	SNP	ENST00000249501.4	37	CCDS2266.1																																																																																				0.488	HOXD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255692.2		
TTN	7273	broad.mit.edu	37	2	179404854	179404854	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:179404854G>A	ENST00000591111.1	-	301	93340	c.93116C>T	c.(93115-93117)gCt>gTt	p.A31039V	TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.A23740V|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000415561.1_RNA|TTN-AS1_ENST00000592600.1_RNA|RP11-65L3.4_ENST00000604692.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.A23807V|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.A32680V|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.A30112V|TTN-AS1_ENST00000591867.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.A23615V|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000588716.1_RNA			Q8WZ42	TITIN_HUMAN	titin	31039	Fibronectin type-III 126. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.A23807V(1)|p.A23615V(1)|p.A30110V(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGGTCCACCAGCATTACAAGC	0.468																																					p.L23615L												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.C70843T	2						.						234.0	235.0	235.0					2																	179404854		1995	4168	6163	179113100	SO:0001583	missense	7273	exon179			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.93116C>T	2.37:g.179404854G>A	ENSP00000465570:p.Ala31039Val		179113100	NM_003319	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	19.31	3.803597	0.70682	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57907	0.37;0.37;0.37;0.37	5.96	5.96	0.96718	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.67487	0.2898	L	0.51422	1.61	0.53005	D	0.999965	D;D;D;D	0.63046	0.984;0.984;0.984;0.992	P;P;P;P	0.61070	0.802;0.802;0.802;0.883	T	0.67526	-0.5648	9	0.87932	D	0	.	20.422	0.99049	0.0:0.0:1.0:0.0	.	23615;23740;23807;31039	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	V	30112;23615;23807;23740;23612	ENSP00000343764:A30112V;ENSP00000434586:A23615V;ENSP00000340554:A23807V;ENSP00000352154:A23740V	ENSP00000340554:A23807V	A	-	2	0	TTN	179113100	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	8.062000	0.89475	2.832000	0.97577	0.655000	0.94253	GCT		0.468	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	broad.mit.edu	37	2	179412414	179412414	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:179412414G>A	ENST00000591111.1	-	289	89240	c.89016C>T	c.(89014-89016)acC>acT	p.T29672T	TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Silent_p.T22373T|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Silent_p.T22440T|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000589042.1_Silent_p.T31313T|TTN-AS1_ENST00000592630.1_RNA|RP11-65L3.2_ENST00000603415.1_RNA|TTN_ENST00000342992.6_Silent_p.T28745T|TTN_ENST00000460472.2_Silent_p.T22248T			Q8WZ42	TITIN_HUMAN	titin	29672	Fibronectin type-III 116. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.T28743T(1)|p.T22248T(1)|p.T22440T(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CAATGGGGCCGGTTACTGGAC	0.468																																					p.P22248L												.	.	3	Substitution - coding silent(3)	large_intestine(3)	c.C66743T	2						.						134.0	129.0	131.0					2																	179412414		1942	4140	6082	179120660	SO:0001819	synonymous_variant	7273	exon167			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.89016C>T	2.37:g.179412414G>A			179120660	NM_003319	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.468	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	broad.mit.edu	37	2	179479261	179479261	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:179479261C>T	ENST00000591111.1	-	211	44281	c.44057G>A	c.(44056-44058)gGc>gAc	p.G14686D	TTN_ENST00000359218.5_Missense_Mutation_p.G7387D|RP11-171I2.4_ENST00000605334.1_lincRNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.G7454D|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.G16327D|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.G13759D|TTN_ENST00000460472.2_Missense_Mutation_p.G7262D|TTN-AS1_ENST00000589234.1_RNA			Q8WZ42	TITIN_HUMAN	titin	14686	Ig-like 96.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.G7454D(1)|p.G7262D(1)|p.G13759D(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GATATATGTGCCAGTGTCACT	0.418																																					p.G7262D												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.G21785A	2						.						105.0	99.0	101.0					2																	179479261		1973	4140	6113	179187506	SO:0001583	missense	7273	exon89			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.44057G>A	2.37:g.179479261C>T	ENSP00000465570:p.Gly14686Asp		179187506	NM_003319	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	11.92	1.783520	0.31593	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.77489	-1.1;-1.1;-1.1;-1.1	5.77	5.77	0.91146	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.92237	0.7538	H	0.96970	3.915	0.48185	D	0.999602	D;D;D;D	0.64830	0.994;0.994;0.994;0.994	D;D;D;D	0.63793	0.918;0.918;0.918;0.918	D	0.93961	0.7240	9	0.87932	D	0	.	20.3627	0.98863	0.0:1.0:0.0:0.0	.	7262;7387;7454;14686	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	D	13759;7262;7454;7387;7262	ENSP00000343764:G13759D;ENSP00000434586:G7262D;ENSP00000340554:G7454D;ENSP00000352154:G7387D	ENSP00000340554:G7454D	G	-	2	0	TTN	179187506	1.000000	0.71417	0.952000	0.39060	0.692000	0.40212	6.062000	0.71155	2.885000	0.99019	0.655000	0.94253	GGC		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	broad.mit.edu	37	2	179494150	179494150	+	Silent	SNP	T	T	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:179494150T>G	ENST00000591111.1	-	190	39603	c.39379A>C	c.(39379-39381)Agg>Cgg	p.R13127R	TTN_ENST00000359218.5_Silent_p.R5828R|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342175.6_Silent_p.R5895R|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000589042.1_Silent_p.R14768R|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000342992.6_Silent_p.R12200R|TTN_ENST00000460472.2_Silent_p.R5703R			Q8WZ42	TITIN_HUMAN	titin	13127	Ig-like 87.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R12200R(1)|p.R5895R(1)|p.R5703R(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTTAAAGGCCTCAGAAGACCA	0.438																																					p.R5703R												.	.	3	Substitution - coding silent(3)	large_intestine(3)	c.A17107C	2						.						99.0	98.0	98.0					2																	179494150		1948	4159	6107	179202395	SO:0001819	synonymous_variant	7273	exon68			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.39379A>C	2.37:g.179494150T>G			179202395	NM_003319	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	broad.mit.edu	37	2	179497757	179497757	+	Silent	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:179497757A>G	ENST00000591111.1	-	184	38402	c.38178T>C	c.(38176-38178)atT>atC	p.I12726I	TTN_ENST00000359218.5_Silent_p.I5427I|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342175.6_Silent_p.I5494I|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000589042.1_Silent_p.I14367I|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000342992.6_Silent_p.I11799I|TTN_ENST00000460472.2_Silent_p.I5302I			Q8WZ42	TITIN_HUMAN	titin	12726					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.I11799I(1)|p.I5494I(1)|p.I5302I(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTCCATCCTCAATGATTTCAC	0.388																																					p.I5302I												.	.	3	Substitution - coding silent(3)	large_intestine(3)	c.T15906C	2						.						91.0	86.0	87.0					2																	179497757		1859	4106	5965	179206002	SO:0001819	synonymous_variant	7273	exon62			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.38178T>C	2.37:g.179497757A>G			179206002	NM_003319	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	broad.mit.edu	37	2	179616722	179616722	+	Intron	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:179616722G>A	ENST00000591111.1	-	45	10585				TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000360870.5_Missense_Mutation_p.R3469C|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Intron|TTN_ENST00000342992.6_Intron|TTN_ENST00000460472.2_Intron			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.R3469C(2)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AAGGCGTCACGTGTATCCCTT	0.353																																					p.R3469C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C10405T	2						.						132.0	147.0	142.0					2																	179616722		2203	4298	6501	179324967	SO:0001627	intron_variant	7273	exon46			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10360+1128C>T	2.37:g.179616722G>A			179324967	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	2.768	-0.256412	0.05829	.	.	ENSG00000155657	ENST00000360870;ENST00000446208	T	0.61627	0.09	5.86	3.86	0.44501	.	.	.	.	.	T	0.41903	0.1179	L	0.29908	0.895	0.37181	D	0.903512	P	0.42735	0.788	B	0.33042	0.157	T	0.51880	-0.8649	9	0.38643	T	0.18	.	14.6187	0.68569	0.0:0.0:0.7269:0.2731	.	3469	Q8WZ42-6	.	C	3469;74	ENSP00000354117:R3469C	ENSP00000354117:R3469C	R	-	1	0	TTN	179324967	0.004000	0.15560	0.065000	0.19835	0.033000	0.12548	1.182000	0.32029	1.459000	0.47892	0.655000	0.94253	CGT		0.353	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
COL5A2	1290	broad.mit.edu	37	2	189898884	189898884	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:189898884C>T	ENST00000374866.3	-	54	4686	c.4412G>A	c.(4411-4413)cGc>cAc	p.R1471H		NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2	1471	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				axon guidance (GO:0007411)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|negative regulation of endodermal cell differentiation (GO:1903225)|skeletal system development (GO:0001501)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)	p.R1471H(1)		NS(3)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(53)|ovary(3)|prostate(2)|skin(6)|urinary_tract(3)	95			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			GATGGGCAAGCGTGCCACATT	0.423																																					p.R1471H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4412A	2						.						137.0	112.0	121.0					2																	189898884		2203	4300	6503	189607129	SO:0001583	missense	1290	exon54			Y14690	CCDS33350.1	2q14-q32	2014-09-17			ENSG00000204262	ENSG00000204262		"""Collagens"""	2210	protein-coding gene	gene with protein product	"""AB collagen"""	120190				1572660	Standard	NM_000393		Approved		uc002uqk.3	P05997	OTTHUMG00000149842	ENST00000374866.3:c.4412G>A	2.37:g.189898884C>T	ENSP00000364000:p.Arg1471His		189607129	NM_000393	P78440|Q13908|Q53WR4|Q59GR4|Q6LDJ5|Q7KZ55|Q86XF6|Q96QB0|Q96QB3	Missense_Mutation	SNP	ENST00000374866.3	37	CCDS33350.1	.	.	.	.	.	.	.	.	.	.	C	16.80	3.224327	0.58668	.	.	ENSG00000204262	ENST00000374866;ENST00000452536	T	0.76060	-0.99	5.1	4.23	0.50019	Fibrillar collagen, C-terminal (4);	0.000000	0.50627	D	0.000107	D	0.85013	0.5600	M	0.87682	2.9	0.80722	D	1	D;D	0.63880	0.993;0.993	P;P	0.58266	0.787;0.836	D	0.87778	0.2610	10	0.72032	D	0.01	.	13.527	0.61601	0.0:0.9252:0.0:0.0748	.	1111;1471	Q5PR22;P05997	.;CO5A2_HUMAN	H	1471;1111	ENSP00000364000:R1471H	ENSP00000364000:R1471H	R	-	2	0	COL5A2	189607129	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.648000	0.83479	1.381000	0.46364	0.650000	0.86243	CGC		0.423	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313523.1	NM_000393	
CCDC150	284992	broad.mit.edu	37	2	197511212	197511212	+	Missense_Mutation	SNP	G	G	A	rs369159032		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:197511212G>A	ENST00000389175.4	+	2	295	c.160G>A	c.(160-162)Gat>Aat	p.D54N	CCDC150_ENST00000272831.7_5'UTR|CCDC150_ENST00000423093.2_5'UTR|CCDC150_ENST00000472405.2_Intron	NM_001080539.1	NP_001074008.1	Q8NCX0	CC150_HUMAN	coiled-coil domain containing 150	54								p.D54N(1)		breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(14)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	33						AATAATGTTGGATTTTGGTGA	0.383																																					p.D54N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G160A	2						.						96.0	88.0	90.0					2																	197511212		1866	4107	5973	197219457	SO:0001583	missense	284992	exon2				CCDS46478.1	2q33.1	2008-04-10			ENSG00000144395	ENSG00000144395			26834	protein-coding gene	gene with protein product							Standard	NM_001080539		Approved	FLJ39660	uc002utp.1	Q8NCX0	OTTHUMG00000154475	ENST00000389175.4:c.160G>A	2.37:g.197511212G>A	ENSP00000373827:p.Asp54Asn		197219457	NM_001080539	Q6P5U6|Q6P663|Q8N8V5	Missense_Mutation	SNP	ENST00000389175.4	37	CCDS46478.1	.	.	.	.	.	.	.	.	.	.	G	1.805	-0.476227	0.04414	.	.	ENSG00000144395	ENST00000389175;ENST00000536389	T	0.30448	1.53	4.32	1.55	0.23275	.	0.238888	0.32231	N	0.006399	T	0.24547	0.0595	L	0.51422	1.61	0.09310	N	0.999996	B;P	0.41848	0.13;0.763	B;B	0.39840	0.047;0.311	T	0.09773	-1.0659	10	0.48119	T	0.1	.	6.5388	0.22369	0.3081:0.0:0.6919:0.0	.	54;54	Q8NCX0;F5H6M2	CC150_HUMAN;.	N	54	ENSP00000373827:D54N	ENSP00000373827:D54N	D	+	1	0	CCDC150	197219457	0.976000	0.34144	0.014000	0.15608	0.009000	0.06853	1.497000	0.35649	0.220000	0.20860	-0.742000	0.03525	GAT		0.383	CCDC150-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335377.2	NM_001080539	
AOX1	316	broad.mit.edu	37	2	201485474	201485474	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:201485474C>T	ENST00000374700.2	+	17	2047	c.1806C>T	c.(1804-1806)gaC>gaT	p.D602D	AOX1_ENST00000485106.1_Intron	NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	602					inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)	p.D602D(1)		breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	ACTGTGATGACATGCCTCTGG	0.473																																					p.D602D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1806T	2						.						150.0	129.0	136.0					2																	201485474		2203	4300	6503	201193719	SO:0001819	synonymous_variant	316	exon17			AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.1806C>T	2.37:g.201485474C>T			201193719	NM_001159	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Silent	SNP	ENST00000374700.2	37	CCDS33360.1																																																																																				0.473	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159	
AOX1	316	broad.mit.edu	37	2	201505907	201505907	+	Splice_Site	SNP	C	C	T	rs200451350	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:201505907C>T	ENST00000374700.2	+	24	2896	c.2655C>T	c.(2653-2655)ttC>ttT	p.F885F	AOX1_ENST00000485106.1_3'UTR	NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	885					inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)	p.F885F(1)		breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	AATCATTATTCGTAAGTGTTT	0.383													c|||	3	0.000599042	0.0	0.0	5008	,	,		18738	0.003		0.0	False		,,,				2504	0.0				p.F885F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2655T	2						.	G		0,4406		0,0,2203	89.0	88.0	89.0		2655	-8.6	0.0	2		89	1,8599	1.2+/-3.3	0,1,4299	yes	coding-synonymous-near-splice	AOX1	NM_001159.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		885/1339	201505907	1,13005	2203	4300	6503	201214152	SO:0001630	splice_region_variant	316	exon24			AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.2655+1C>T	2.37:g.201505907C>T			201214152	NM_001159	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Silent	SNP	ENST00000374700.2	37	CCDS33360.1																																																																																				0.383	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159	Silent
CASP10	843	broad.mit.edu	37	2	202060635	202060635	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:202060635C>T	ENST00000272879.5	+	5	832	c.648C>T	c.(646-648)tcC>tcT	p.S216S	CASP10_ENST00000286186.6_Silent_p.S216S|CASP10_ENST00000313728.7_Silent_p.S216S|CASP10_ENST00000492363.1_3'UTR|CASP10_ENST00000448480.1_Silent_p.S216S|CASP10_ENST00000346817.5_Silent_p.S216S|CASP10_ENST00000374650.3_Silent_p.S216S|CASP10_ENST00000360132.3_Silent_p.S216S	NM_032974.4	NP_116756.2	Q92851	CASPA_HUMAN	caspase 10, apoptosis-related cysteine peptidase	216					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|innate immune response (GO:0045087)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of apoptotic process (GO:0042981)	CD95 death-inducing signaling complex (GO:0031265)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097199)|death effector domain binding (GO:0035877)|ubiquitin protein ligase binding (GO:0031625)	p.S216S(1)		breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	27						AACTAGTTTCCCAAACAGATG	0.463																																					p.S216S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C648T	2						.						220.0	204.0	209.0					2																	202060635		2203	4300	6503	201768880	SO:0001819	synonymous_variant	843	exon5			U60519	CCDS2338.1, CCDS2339.1, CCDS2340.1, CCDS56159.1, CCDS56160.1	2q33-q34	2014-09-17	2005-08-17		ENSG00000003400	ENSG00000003400	3.4.22.63	"""Caspases"""	1500	protein-coding gene	gene with protein product		601762	"""caspase 10, apoptosis-related cysteine protease"""			8755496	Standard	NM_032974		Approved	MCH4	uc002uxj.1	Q92851	OTTHUMG00000132818	ENST00000272879.5:c.648C>T	2.37:g.202060635C>T			201768880	NM_032974	Q68HC0|Q6KF62|Q6KF63|Q8IUP5|Q8WYQ8|Q99845|Q9Y2U6|Q9Y2U7	Silent	SNP	ENST00000272879.5	37	CCDS2338.1																																																																																				0.463	CASP10-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256273.1	NM_032977	
NDUFS1	4719	broad.mit.edu	37	2	207009680	207009680	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:207009680C>T	ENST00000233190.6	-	9	1074	c.808G>A	c.(808-810)Gtg>Atg	p.V270M	NDUFS1_ENST00000449699.1_Missense_Mutation_p.V270M|NDUFS1_ENST00000423725.1_Missense_Mutation_p.V213M|NDUFS1_ENST00000455934.2_Missense_Mutation_p.V284M|NDUFS1_ENST00000457011.1_Missense_Mutation_p.V154M|NDUFS1_ENST00000440274.1_Missense_Mutation_p.V234M|NDUFS1_ENST00000432169.1_Missense_Mutation_p.V159M	NM_005006.6	NP_004997.4	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1, 75kDa (NADH-coenzyme Q reductase)	270	4Fe-4S Mo/W bis-MGD-type. {ECO:0000255|PROSITE-ProRule:PRU01004}.				apoptotic mitochondrial changes (GO:0008637)|ATP metabolic process (GO:0046034)|cellular metabolic process (GO:0044237)|cellular respiration (GO:0045333)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|regulation of mitochondrial membrane potential (GO:0051881)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial respiratory chain complex I (GO:0005747)	2 iron, 2 sulfur cluster binding (GO:0051537)|4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)	p.V270M(1)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(15)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						ATCCTCATCACTTCTCCAGTT	0.378																																					p.V270M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G808A	2						.						195.0	162.0	174.0					2																	207009680		2203	4300	6503	206717925	SO:0001583	missense	4719	exon9				CCDS2366.1, CCDS56162.1, CCDS56163.1, CCDS56164.1, CCDS56165.1	2q33-q34	2011-07-04	2002-08-29		ENSG00000023228	ENSG00000023228	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7707	protein-coding gene	gene with protein product	"""complex I 75kDa subunit"", ""NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial"""	157655	"""NADH dehydrogenase (ubiquinone) Fe-S protein 1 (75kD) (NADH-coenzyme Q reductase)"""			1935949	Standard	NM_005006		Approved	CI-75k	uc010ziq.2	P28331	OTTHUMG00000132892	ENST00000233190.6:c.808G>A	2.37:g.207009680C>T	ENSP00000233190:p.Val270Met		206717925	NM_005006	B4DIN9|B4DJA0|B4DPG1|B4DUC1|E7ENF3|Q53TR8|Q8N1C4|Q8TCC9	Missense_Mutation	SNP	ENST00000233190.6	37	CCDS2366.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.507823	0.85282	.	.	ENSG00000023228	ENST00000233190;ENST00000423725;ENST00000457011;ENST00000440274;ENST00000455934;ENST00000449699;ENST00000432169	D;D;D;D;D;D;D	0.86694	-2.16;-2.16;-2.16;-2.16;-2.16;-2.16;-2.16	5.47	4.6	0.57074	.	0.000000	0.85682	D	0.000000	D	0.94066	0.8098	M	0.88241	2.94	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;0.999;0.999	D;D;D;D	0.77004	0.989;0.963;0.973;0.963	D	0.94932	0.8083	10	0.87932	D	0	-21.6891	14.342	0.66633	0.0:0.9285:0.0:0.0715	.	159;234;284;270	B4DPG1;E7ENF3;B4DJA0;P28331	.;.;.;NDUS1_HUMAN	M	270;213;154;234;284;270;159	ENSP00000233190:V270M;ENSP00000397760:V213M;ENSP00000400976:V154M;ENSP00000409766:V234M;ENSP00000392709:V284M;ENSP00000399912:V270M;ENSP00000409689:V159M	ENSP00000233190:V270M	V	-	1	0	NDUFS1	206717925	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.757000	0.85209	1.307000	0.44944	0.655000	0.94253	GTG		0.378	NDUFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256391.4	NM_005006	
CRYGB	1419	broad.mit.edu	37	2	209010656	209010656	+	Missense_Mutation	SNP	G	G	A	rs545870578		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:209010656G>A	ENST00000260988.4	-	2	141	c.94C>T	c.(94-96)Cgc>Tgc	p.R32C		NM_005210.3	NP_005201.2	P07316	CRGB_HUMAN	crystallin, gamma B	32	Beta/gamma crystallin 'Greek key' 1. {ECO:0000255|PROSITE-ProRule:PRU00028}.				lens fiber cell morphogenesis (GO:0070309)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	structural constituent of eye lens (GO:0005212)	p.R32C(2)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|stomach(1)	14				Epithelial(149;0.0641)|LUSC - Lung squamous cell carcinoma(261;0.0703)|Lung(261;0.132)		GAGTTGCAGCGGCTGAAATAG	0.577																																					p.R32C												.	.	2	Substitution - Missense(2)	large_intestine(1)|stomach(1)	c.C94T	2						.						61.0	59.0	59.0					2																	209010656		2203	4300	6503	208718901	SO:0001583	missense	1419	exon2				CCDS2380.1	2q34	2013-02-14			ENSG00000182187	ENSG00000182187			2409	protein-coding gene	gene with protein product		123670	"""crystallin, gamma 1-2"""	CRYG2			Standard	NM_005210		Approved		uc002vcp.4	P07316	OTTHUMG00000132941	ENST00000260988.4:c.94C>T	2.37:g.209010656G>A	ENSP00000260988:p.Arg32Cys		208718901	NM_005210	Q17RB5|Q53ST2	Missense_Mutation	SNP	ENST00000260988.4	37	CCDS2380.1	.	.	.	.	.	.	.	.	.	.	G	13.77	2.335088	0.41398	.	.	ENSG00000182187	ENST00000260988	T	0.77750	-1.12	4.73	4.73	0.59995	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.000000	0.85682	D	0.000000	T	0.77798	0.4184	M	0.88775	2.98	0.58432	D	0.999999	P	0.35542	0.508	B	0.29077	0.098	T	0.80910	-0.1171	10	0.59425	D	0.04	.	10.6021	0.45373	0.0:0.0:0.8081:0.1919	.	32	P07316	CRGB_HUMAN	C	32	ENSP00000260988:R32C	ENSP00000260988:R32C	R	-	1	0	CRYGB	208718901	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	3.759000	0.55227	2.614000	0.88457	0.561000	0.74099	CGC		0.577	CRYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256473.2	NM_005210	
C2orf80	389073	broad.mit.edu	37	2	209045520	209045520	+	Silent	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:209045520T>C	ENST00000341287.4	-	6	510	c.315A>G	c.(313-315)gaA>gaG	p.E105E	C2orf80_ENST00000453017.1_Silent_p.E105E|C2orf80_ENST00000451346.1_Silent_p.E86E	NM_001099334.2	NP_001092804	Q0P641	CB080_HUMAN	chromosome 2 open reading frame 80	105								p.E105E(1)		endometrium(2)|large_intestine(3)|lung(6)|skin(2)	13						TTTTAAAGACTTCCTCAATCG	0.353																																					p.E105E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A315G	2						.						106.0	100.0	102.0					2																	209045520		1800	4082	5882	208753765	SO:0001819	synonymous_variant	389073	exon6			AC016697, AW136505, BC035737	CCDS42809.1	2q33.3	2013-10-31			ENSG00000188674	ENSG00000188674			34352	protein-coding gene	gene with protein product	"""gonad development associated 1"""	615536				22080834, 24055526	Standard	NM_001099334		Approved	LOC389073, GONDA1	uc002vcr.3	Q0P641	OTTHUMG00000154751	ENST00000341287.4:c.315A>G	2.37:g.209045520T>C			208753765	NM_001099334	A6NKZ3	Silent	SNP	ENST00000341287.4	37	CCDS42809.1	.	.	.	.	.	.	.	.	.	.	T	8.529	0.870483	0.17322	.	.	ENSG00000188674	ENST00000428015	.	.	.	4.67	2.26	0.28386	.	.	.	.	.	T	0.54175	0.1842	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43845	-0.9366	4	.	.	.	-25.0117	6.2852	0.21029	0.0:0.192:0.0:0.808	.	.	.	.	G	57	.	.	S	-	1	0	C2orf80	208753765	1.000000	0.71417	1.000000	0.80357	0.859000	0.49053	0.413000	0.21148	0.395000	0.25257	0.455000	0.32223	AGT		0.353	C2orf80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336931.1	NM_001099334	
SMARCAL1	50485	broad.mit.edu	37	2	217279870	217279870	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:217279870C>A	ENST00000357276.4	+	3	773	c.443C>A	c.(442-444)gCt>gAt	p.A148D	AC098820.2_ENST00000457694.1_RNA|SMARCAL1_ENST00000358207.5_Missense_Mutation_p.A148D	NM_014140.3	NP_054859.2	Q9NZC9	SMAL1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1	148					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA metabolic process (GO:0006259)|DNA strand renaturation (GO:0000733)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|replication fork processing (GO:0031297)	nucleus (GO:0005634)|site of double-strand break (GO:0035861)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)	p.A148D(1)		NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(15)|ovary(3)|prostate(1)|skin(1)	42		Renal(323;0.0458)		Epithelial(149;9.48e-06)|all cancers(144;0.000621)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0111)		CAAGGTCATGCTCAGGCTTCA	0.493									Schimke Immuno-Osseous Dysplasia																												p.A148D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C443A	2						.						129.0	118.0	122.0					2																	217279870		2203	4300	6503	216988115	SO:0001583	missense	50485	exon3	Familial Cancer Database	SIOD	AF210833	CCDS2403.1	2q35	2014-09-17			ENSG00000138375	ENSG00000138375			11102	protein-coding gene	gene with protein product	"""HepA-related protein"", ""ATP-driven annealing helicase"""	606622				10713074, 10857751, 18974355	Standard	NM_014140		Approved	HHARP, HARP	uc002vgd.4	Q9NZC9	OTTHUMG00000133055	ENST00000357276.4:c.443C>A	2.37:g.217279870C>A	ENSP00000349823:p.Ala148Asp		216988115	NM_014140	A6NEH0|Q53R00|Q96AY1|Q9NXQ5|Q9UFH3|Q9UI93	Missense_Mutation	SNP	ENST00000357276.4	37	CCDS2403.1	.	.	.	.	.	.	.	.	.	.	C	10.96	1.497377	0.26861	.	.	ENSG00000138375	ENST00000357276;ENST00000358207;ENST00000427645;ENST00000392128	T;T;T;D	0.86297	1.87;1.87;1.44;-2.1	4.8	1.06	0.20224	.	1.111760	0.06822	N	0.792468	T	0.75317	0.3833	N	0.14661	0.345	0.09310	N	1	B	0.31125	0.309	B	0.22386	0.039	T	0.61720	-0.7005	10	0.48119	T	0.1	1.2333	8.7365	0.34532	0.0:0.6813:0.0:0.3187	.	148	Q9NZC9	SMAL1_HUMAN	D	148;148;47;12	ENSP00000349823:A148D;ENSP00000350940:A148D;ENSP00000392997:A47D;ENSP00000375974:A12D	ENSP00000349823:A148D	A	+	2	0	SMARCAL1	216988115	0.000000	0.05858	0.001000	0.08648	0.025000	0.11179	-0.900000	0.04097	0.014000	0.14944	0.655000	0.94253	GCT		0.493	SMARCAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256671.2		
CDK5R2	8941	broad.mit.edu	37	2	219825322	219825322	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:219825322C>T	ENST00000302625.4	+	1	946	c.780C>T	c.(778-780)gcC>gcT	p.A260A	AC097468.7_ENST00000429343.1_RNA	NM_003936.4	NP_003927.1	Q13319	CD5R2_HUMAN	cyclin-dependent kinase 5, regulatory subunit 2 (p39)	260					cerebellum development (GO:0021549)|hippocampus development (GO:0021766)|layer formation in cerebral cortex (GO:0021819)|neuron migration (GO:0001764)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|superior olivary nucleus maturation (GO:0021722)	cyclin-dependent protein kinase 5 holoenzyme complex (GO:0016533)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	cyclin-dependent protein kinase 5 activator activity (GO:0016534)|lipid binding (GO:0008289)	p.A260A(1)		central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(1)|ovary(1)	8		Renal(207;0.0474)		Epithelial(149;9.77e-07)|all cancers(144;0.000167)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGCTGCAGGCCGCCTTCCTCA	0.637																																					p.A260A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C780T	2						.						94.0	95.0	95.0					2																	219825322		2203	4300	6503	219533566	SO:0001819	synonymous_variant	8941	exon1			U34051	CCDS2427.1	2q35	2008-05-22			ENSG00000171450	ENSG00000171450			1776	protein-coding gene	gene with protein product	"""neuronal CDK5 activator isoform"""	603764				7592934	Standard	NM_003936		Approved	p39nck5ai, P39, NCK5AI	uc002vjf.4	Q13319	OTTHUMG00000133083	ENST00000302625.4:c.780C>T	2.37:g.219825322C>T			219533566	NM_003936	Q4ZFW6	Silent	SNP	ENST00000302625.4	37	CCDS2427.1																																																																																				0.637	CDK5R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256728.1	NM_003936	
CCDC108	255101	broad.mit.edu	37	2	219888813	219888813	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:219888813C>T	ENST00000341552.5	-	15	2602	c.2519G>A	c.(2518-2520)tGc>tAc	p.C840Y	CCDC108_ENST00000441968.1_Missense_Mutation_p.C840Y|CCDC108_ENST00000453220.1_Missense_Mutation_p.C840Y	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	840						integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)	p.C840Y(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(1)|lung(34)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGGGTAGGTGCAGATGAGGAT	0.617																																					p.C840Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2519A	2						.						65.0	73.0	70.0					2																	219888813		2203	4300	6503	219597057	SO:0001583	missense	255101	exon15			NM_194302, AL833882, AK127189	CCDS2430.2, CCDS2431.2, CCDS63125.1, CCDS63126.1	2q35	2008-02-05			ENSG00000181378	ENSG00000181378			25325	protein-coding gene	gene with protein product		614270				12477932	Standard	NM_194302		Approved	DKFZp434O0527, MGC35338	uc002vjl.2	Q6ZU64	OTTHUMG00000133013	ENST00000341552.5:c.2519G>A	2.37:g.219888813C>T	ENSP00000340776:p.Cys840Tyr		219597057	NM_194302	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Missense_Mutation	SNP	ENST00000341552.5	37	CCDS2430.2	.	.	.	.	.	.	.	.	.	.	C	9.175	1.022021	0.19433	.	.	ENSG00000181378	ENST00000341552;ENST00000441968;ENST00000453220	T;T;T	0.40225	1.04;1.04;1.04	5.84	0.636	0.17729	.	1.046920	0.07560	N	0.916817	T	0.32763	0.0840	N	0.22421	0.69	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.36792	-0.9733	10	0.59425	D	0.04	-1.3169	13.9987	0.64419	0.0:0.3757:0.553:0.0713	.	840	Q6ZU64	CC108_HUMAN	Y	840	ENSP00000340776:C840Y;ENSP00000413377:C840Y;ENSP00000409117:C840Y	ENSP00000340776:C840Y	C	-	2	0	CCDC108	219597057	0.950000	0.32346	0.012000	0.15200	0.720000	0.41350	0.704000	0.25661	0.090000	0.17273	-0.304000	0.09214	TGC		0.617	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302	
MOGAT1	116255	broad.mit.edu	37	2	223553240	223553240	+	Splice_Site	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:223553240A>G	ENST00000446656.3	+	2	272	c.272A>G	c.(271-273)cAt>cGt	p.H91R		NM_058165.2	NP_477513.2	Q96PD6	MOGT1_HUMAN	monoacylglycerol O-acyltransferase 1	91					diacylglycerol biosynthetic process (GO:0006651)|glycerol metabolic process (GO:0006071)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	2-acylglycerol O-acyltransferase activity (GO:0003846)|diacylglycerol O-acyltransferase activity (GO:0004144)	p.H91R(1)		breast(1)|cervix(1)|endometrium(1)|lung(5)|urinary_tract(1)	9		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;2.06e-07)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0105)		TTTCCAATTCATGTGAGTACA	0.373																																					p.H91R	Ovarian(93;205 1446 2385 11581 25911)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A272G	2						.						72.0	65.0	67.0					2																	223553240		1820	4081	5901	223261484	SO:0001630	splice_region_variant	116255	exon2			AF384163	CCDS46524.1	2q36.2	2006-10-06	2004-05-28	2004-05-28	ENSG00000124003	ENSG00000124003			18210	protein-coding gene	gene with protein product		610268	"""diacylglycerol O-acyltransferase 2 like 1"""	DGAT2L1		14970677	Standard	NM_058165		Approved	DGAT2L, MGAT1	uc010fws.1	Q96PD6	OTTHUMG00000153394	ENST00000446656.3:c.273+1A>G	2.37:g.223553240A>G			223261484	NM_058165	Q6IEE5	Missense_Mutation	SNP	ENST00000446656.3	37	CCDS46524.1	.	.	.	.	.	.	.	.	.	.	A	6.178	0.400955	0.11696	.	.	ENSG00000124003	ENST00000446656	T	0.12255	2.7	4.64	3.42	0.39159	.	0.362178	0.26975	N	0.021557	T	0.05227	0.0139	N	0.03608	-0.345	0.26024	N	0.981821	B	0.02656	0.0	B	0.09377	0.004	T	0.40098	-0.9581	10	0.16896	T	0.51	-4.5191	8.176	0.31283	0.8406:0.0:0.1594:0.0	.	91	Q96PD6	MOGT1_HUMAN	R	91	ENSP00000406674:H91R	ENSP00000406674:H91R	H	+	2	0	MOGAT1	223261484	0.022000	0.18835	0.992000	0.48379	0.807000	0.45602	1.094000	0.30951	0.859000	0.35456	0.533000	0.62120	CAT		0.373	MOGAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331010.3	NM_058165	Missense_Mutation
TRIP12	9320	broad.mit.edu	37	2	230701593	230701593	+	Missense_Mutation	SNP	C	C	T	rs75723349		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:230701593C>T	ENST00000283943.5	-	5	1293	c.1115G>A	c.(1114-1116)cGg>cAg	p.R372Q	TRIP12_ENST00000543084.1_Intron|TRIP12_ENST00000389044.4_Missense_Mutation_p.R414Q|TRIP12_ENST00000409677.1_Missense_Mutation_p.R414Q|TRIP12_ENST00000389045.3_Missense_Mutation_p.R69Q	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	372					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)	p.R372Q(1)		breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		TTCATCTGTCCGAGCAGCTGA	0.507																																					p.R372Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1115A	2						.						78.0	80.0	80.0					2																	230701593		2203	4300	6503	230409837	SO:0001583	missense	9320	exon5			L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.1115G>A	2.37:g.230701593C>T	ENSP00000283943:p.Arg372Gln		230409837	NM_004238	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Missense_Mutation	SNP	ENST00000283943.5	37	CCDS33391.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.217595	0.79352	.	.	ENSG00000153827	ENST00000283943;ENST00000389045;ENST00000389044;ENST00000409677;ENST00000453485	T;T;T	0.45276	0.9;1.32;0.93	5.75	5.75	0.90469	Armadillo-like helical (1);	0.000000	0.85682	D	0.000000	T	0.48978	0.1530	N	0.24115	0.695	0.80722	D	1	D;D;D;D	0.64830	0.994;0.994;0.994;0.994	D;D;D;D	0.64042	0.921;0.921;0.921;0.921	T	0.20371	-1.0277	10	0.14656	T	0.56	.	20.3046	0.98621	0.0:1.0:0.0:0.0	.	372;69;414;372	D4HL82;Q14CF1;Q14CA3;Q14669	.;.;.;TRIPC_HUMAN	Q	372;69;414;414;213	ENSP00000283943:R372Q;ENSP00000373697:R69Q;ENSP00000373696:R414Q	ENSP00000283943:R372Q	R	-	2	0	TRIP12	230409837	1.000000	0.71417	0.966000	0.40874	0.980000	0.70556	7.332000	0.79203	2.878000	0.98634	0.650000	0.86243	CGG		0.507	TRIP12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331861.3	NM_004238	
SP110	3431	broad.mit.edu	37	2	231036875	231036875	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:231036875G>A	ENST00000358662.4	-	16	1800	c.1722C>T	c.(1720-1722)tgC>tgT	p.C574C	AC009950.2_ENST00000594622.1_RNA|SP110_ENST00000258381.6_Silent_p.C574C|AC009950.2_ENST00000595586.2_RNA|AC009950.2_ENST00000609120.1_RNA|AC009950.2_ENST00000600787.1_RNA|AC009950.2_ENST00000454058.1_RNA	NM_004509.3	NP_004500	Q9HB58	SP110_HUMAN	SP110 nuclear body protein	574					regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)	p.C574C(1)		breast(4)|endometrium(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Renal(207;0.0112)|all_lung(227;0.0223)|Lung NSC(271;0.0983)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.169)		Epithelial(121;2.61e-12)|all cancers(144;6.39e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.0097)		TGCAGAAGGTGCAACTCCACA	0.557																																					p.C574C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1722T	2						.						126.0	116.0	119.0					2																	231036875		2203	4300	6503	230745119	SO:0001819	synonymous_variant	3431	exon16			L22343	CCDS2474.1, CCDS2475.1, CCDS2476.1, CCDS54435.1	2q37.1	2014-09-17	2001-12-19	2001-12-20	ENSG00000135899	ENSG00000135899			5401	protein-coding gene	gene with protein product		604457	"""interferon-induced protein 41, 30kD"""	IFI41, IFI75		7693701, 10388521	Standard	NM_080424		Approved		uc002vqg.3	Q9HB58	OTTHUMG00000133204	ENST00000358662.4:c.1722C>T	2.37:g.231036875G>A			230745119	NM_080424	B4DVI4|F5H1M1|Q14976|Q14977|Q53TG2|Q8WUZ6|Q9HCT8	Silent	SNP	ENST00000358662.4	37	CCDS2474.1																																																																																				0.557	SP110-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000332414.1	NM_080424	
ALPP	250	broad.mit.edu	37	2	233244618	233244618	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:233244618C>T	ENST00000392027.2	+	5	898	c.629C>T	c.(628-630)aCg>aTg	p.T210M	AC068134.8_ENST00000439072.1_RNA|AC068134.8_ENST00000441266.1_RNA	NM_001632.3	NP_001623.3	P05187	PPB1_HUMAN	alkaline phosphatase, placental	210					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|zinc ion binding (GO:0008270)	p.T210M(1)		NS(1)|biliary_tract(1)|endometrium(1)|kidney(4)|large_intestine(2)|liver(1)|lung(10)|ovary(2)	22		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)		GACATCGCTACGCAGCTCATC	0.677																																					p.T210M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C629T	2						.						70.0	71.0	71.0					2																	233244618		2203	4299	6502	232952862	SO:0001583	missense	250	exon5			M14169	CCDS2490.1	2q37.1	2010-06-24	2010-06-24		ENSG00000163283	ENSG00000163283	3.1.3.1		439	protein-coding gene	gene with protein product	"""Regan isozyme"""	171800	"""alkaline phosphatase, placental (Regan isozyme)"""			3001717, 3461452	Standard	XM_005246439		Approved		uc002vsq.3	P05187	OTTHUMG00000133255	ENST00000392027.2:c.629C>T	2.37:g.233244618C>T	ENSP00000375881:p.Thr210Met		232952862	NM_001632	P05188|P06861|Q53S78|Q96DB7	Missense_Mutation	SNP	ENST00000392027.2	37	CCDS2490.1	.	.	.	.	.	.	.	.	.	.	.	6.201	0.405192	0.11754	.	.	ENSG00000163283	ENST00000392027	D	0.96830	-4.14	2.31	0.138	0.14793	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	1.049910	0.07399	N	0.890517	D	0.95984	0.8692	L	0.58510	1.815	0.09310	N	1	D	0.67145	0.996	P	0.59357	0.856	D	0.87768	0.2603	10	0.34782	T	0.22	.	3.6095	0.08055	0.4832:0.2837:0.0:0.2331	.	210	P05187	PPB1_HUMAN	M	210	ENSP00000375881:T210M	ENSP00000375881:T210M	T	+	2	0	ALPP	232952862	0.000000	0.05858	0.017000	0.16124	0.018000	0.09664	-1.487000	0.02310	-0.133000	0.11537	0.298000	0.19748	ACG		0.677	ALPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257032.3	NM_001632	
CHRND	1144	broad.mit.edu	37	2	233399868	233399868	+	Missense_Mutation	SNP	G	G	A	rs148939701	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:233399868G>A	ENST00000258385.3	+	12	1432	c.1400G>A	c.(1399-1401)cGc>cAc	p.R467H	CHRND_ENST00000457943.2_Missense_Mutation_p.R273H|CHRND_ENST00000543200.1_Missense_Mutation_p.R452H	NM_000751.2	NP_000742.1	Q07001	ACHD_HUMAN	cholinergic receptor, nicotinic, delta (muscle)	467					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|muscle contraction (GO:0006936)|musculoskeletal movement (GO:0050881)|neuromuscular process (GO:0050905)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|skeletal muscle tissue growth (GO:0048630)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)	p.R467H(1)		breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)	34		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;1.89e-16)|BRCA - Breast invasive adenocarcinoma(100;0.00078)|Lung(119;0.00579)|LUSC - Lung squamous cell carcinoma(224;0.00754)	Galantamine(DB00674)	CGAGTGGCCCGCACAGTGGAC	0.642													G|||	11	0.00219649	0.0	0.0058	5008	,	,		18152	0.0		0.005	False		,,,				2504	0.002				p.R467H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1400A	2						.	G	HIS/ARG	2,4404	4.2+/-10.8	0,2,2201	94.0	98.0	97.0		1400	5.1	1.0	2	dbSNP_134	97	17,8583	12.6+/-44.7	0,17,4283	yes	missense	CHRND	NM_000751.1	29	0,19,6484	AA,AG,GG		0.1977,0.0454,0.1461	probably-damaging	467/518	233399868	19,12987	2203	4300	6503	233108112	SO:0001583	missense	1144	exon12			X55019	CCDS2494.1, CCDS58754.1	2q37.1	2012-02-11	2012-02-07		ENSG00000135902	ENSG00000135902		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1965	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, delta (muscle)"""	100720	"""cholinergic receptor, nicotinic, delta"""	ACHRD			Standard	NM_000751		Approved		uc002vsw.4	Q07001	OTTHUMG00000133261	ENST00000258385.3:c.1400G>A	2.37:g.233399868G>A	ENSP00000258385:p.Arg467His		233108112	NM_000751	A8K661|B4DT92|Q52LH4	Missense_Mutation	SNP	ENST00000258385.3	37	CCDS2494.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	19.85	3.903400	0.72754	4.54E-4	0.001977	ENSG00000135902	ENST00000543200;ENST00000258385;ENST00000457943	D;D;D	0.85702	-2.02;-2.02;-2.02	5.13	5.13	0.70059	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.054551	0.64402	D	0.000002	D	0.90369	0.6986	M	0.74258	2.255	0.46185	D	0.998915	D;D;D;D	0.89917	1.0;0.998;0.998;0.998	D;D;D;D	0.77004	0.989;0.946;0.946;0.946	D	0.90554	0.4511	10	0.72032	D	0.01	.	8.1029	0.30868	0.0795:0.0:0.7623:0.1582	.	273;452;467;467	B4E3W4;B4DT92;A8K661;Q07001	.;.;.;ACHD_HUMAN	H	452;467;273	ENSP00000438380:R452H;ENSP00000258385:R467H;ENSP00000391055:R273H	ENSP00000258385:R467H	R	+	2	0	CHRND	233108112	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.878000	0.56130	2.389000	0.81357	0.655000	0.94253	CGC		0.642	CHRND-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257038.2		
GIGYF2	26058	broad.mit.edu	37	2	233710491	233710491	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:233710491G>A	ENST00000409547.1	+	28	3666	c.3355G>A	c.(3355-3357)Gaa>Aaa	p.E1119K	GIGYF2_ENST00000409451.3_Missense_Mutation_p.E1140K|GIGYF2_ENST00000373563.4_Missense_Mutation_p.E1119K|GIGYF2_ENST00000409196.3_Missense_Mutation_p.E1113K|GIGYF2_ENST00000373566.3_Missense_Mutation_p.E1141K|GIGYF2_ENST00000409480.1_Missense_Mutation_p.E1141K	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	1119					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.E1119K(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		AGAAGAAGAAGAAAAGTTGCT	0.373																																					p.E1113K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3337A	2						.						109.0	112.0	111.0					2																	233710491		2203	4300	6503	233418735	SO:0001583	missense	26058	exon25			U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"""Trinucleotide (CAG) repeat containing"""	11960	protein-coding gene	gene with protein product	"""GYF domain containing 2"""	612003	"""PERQ amino acid rich, with GYF domain 2"", ""PERQ amino acid rich, with GYF domain 3"", ""trinucleotide repeat containing 15"", ""Parkinson disease (autosomal recessive, early onset) 11"""	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.3355G>A	2.37:g.233710491G>A	ENSP00000386537:p.Glu1119Lys		233418735	NM_001103148	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Missense_Mutation	SNP	ENST00000409547.1	37	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.043390	0.93685	.	.	ENSG00000204120	ENST00000373566;ENST00000373563;ENST00000409480;ENST00000409547;ENST00000409196;ENST00000409451;ENST00000426102	T;T;T;T;T;T	0.77358	-1.08;-1.09;-1.08;-1.09;-1.08;-1.08	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	D	0.87116	0.6097	M	0.72353	2.195	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.63793	0.918;0.918;0.918	D	0.86507	0.1807	10	0.49607	T	0.09	-20.0543	19.843	0.96697	0.0:0.0:1.0:0.0	.	1140;1119;1113	A6H8W4;Q6Y7W6;E9PBB0	.;PERQ2_HUMAN;.	K	1141;1119;1141;1119;1113;1140;148	ENSP00000362667:E1141K;ENSP00000362664:E1119K;ENSP00000386765:E1141K;ENSP00000386537:E1119K;ENSP00000387070:E1113K;ENSP00000387170:E1140K	ENSP00000362664:E1119K	E	+	1	0	GIGYF2	233418735	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.679000	0.91253	0.655000	0.94253	GAA		0.373	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146	
SAG	6295	broad.mit.edu	37	2	234229326	234229326	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:234229326G>A	ENST00000409110.1	+	5	462	c.232G>A	c.(232-234)Gtg>Atg	p.V78M	SAG_ENST00000449594.2_5'UTR|SAG_ENST00000461532.1_3'UTR	NM_000541.4	NP_000532.2	P10523	ARRS_HUMAN	S-antigen; retina and pineal gland (arrestin)	78					cell surface receptor signaling pathway (GO:0007166)|negative regulation of catalytic activity (GO:0043086)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	cytosol (GO:0005829)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	protein phosphatase inhibitor activity (GO:0004864)	p.V78M(1)		cervix(1)|kidney(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	9		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.018)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.054)		Epithelial(121;2.86e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00608)|Lung(119;0.00714)|GBM - Glioblastoma multiforme(43;0.207)		GGACATTGACGTGATCGGCTT	0.617																																					p.V78M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G232A	2						.						35.0	38.0	37.0					2																	234229326		2113	4261	6374	233894065	SO:0001583	missense	6295	exon5				CCDS46545.1	2q37.1	2013-02-14			ENSG00000130561	ENSG00000130561			10521	protein-coding gene	gene with protein product	"""arrestin 1"""	181031				2249983	Standard	NM_000541		Approved	ARRESTIN, RP47	uc002vuh.2	P10523	OTTHUMG00000153213	ENST00000409110.1:c.232G>A	2.37:g.234229326G>A	ENSP00000386444:p.Val78Met		233894065	NM_000541	A0FDN6|Q53SV3|Q99858	Missense_Mutation	SNP	ENST00000409110.1	37	CCDS46545.1	.	.	.	.	.	.	.	.	.	.	G	15.76	2.928706	0.52759	.	.	ENSG00000130561	ENST00000252857;ENST00000447536;ENST00000409110	T;T	0.52057	0.68;0.68	4.46	3.58	0.41010	Arrestin, N-terminal (1);Immunoglobulin E-set (1);Arrestin-like, N-terminal (1);Arrestin, conserved site (1);	0.129974	0.52532	D	0.000075	T	0.66665	0.2812	M	0.85710	2.77	0.80722	D	1	D	0.76494	0.999	D	0.65140	0.932	T	0.70121	-0.4959	10	0.56958	D	0.05	-20.3991	10.102	0.42511	0.1633:0.0:0.8367:0.0	.	78	P10523	ARRS_HUMAN	M	78	ENSP00000408937:V78M;ENSP00000386444:V78M	ENSP00000252857:V78M	V	+	1	0	SAG	233894065	1.000000	0.71417	0.948000	0.38648	0.257000	0.26127	3.631000	0.54280	1.224000	0.43551	0.655000	0.94253	GTG		0.617	SAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330126.1	NM_000541	
SCLY	51540	broad.mit.edu	37	2	239006920	239006920	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:239006920G>A	ENST00000555827.1	+	12	1326	c.1262G>A	c.(1261-1263)aGc>aAc	p.S421N	ESPNL_ENST00000409169.1_5'Flank|ESPNL_ENST00000343063.3_5'Flank|SCLY_ENST00000422984.2_Missense_Mutation_p.S327N|SCLY_ENST00000254663.6_Missense_Mutation_p.S429N|SCLY_ENST00000429612.2_Missense_Mutation_p.S215N			Q96I15	SCLY_HUMAN	selenocysteine lyase	421					cellular amino acid metabolic process (GO:0006520)	cytosol (GO:0005829)	pyridoxal phosphate binding (GO:0030170)|selenocysteine lyase activity (GO:0009000)|transferase activity (GO:0016740)	p.S421N(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	22		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285)		GTGGGCCGCAGCACCACCAGG	0.721																																					p.S421N	Melanoma(24;424 891 11947 32582 36034)|Ovarian(46;648 1065 26199 32764 45893)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1262A	2						.						30.0	29.0	29.0					2																	239006920		2202	4296	6498	238671659	SO:0001583	missense	51540	exon12			AF175767	CCDS2524.1, CCDS2524.2	2q37.3	2008-02-05			ENSG00000132330	ENSG00000132330			18161	protein-coding gene	gene with protein product	"""putative selenocysteine lyase"""	611056				10692412	Standard	NM_016510		Approved	SCL	uc010fyv.4	Q96I15	OTTHUMG00000133336	ENST00000555827.1:c.1262G>A	2.37:g.239006920G>A	ENSP00000450613:p.Ser421Asn		238671659	NM_016510	B9A068|J3KN06|Q53SN1|Q53SN8|Q7L670|Q9NVT7|Q9NZR7	Missense_Mutation	SNP	ENST00000555827.1	37		.	.	.	.	.	.	.	.	.	.	G	11.94	1.787527	0.31593	.	.	ENSG00000132330	ENST00000254663;ENST00000555827;ENST00000422984;ENST00000429612	D;D;D;T	0.86432	-2.12;-2.12;-2.12;0.93	4.77	1.71	0.24356	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.624610	0.17464	N	0.173354	T	0.69771	0.3148	N	0.13168	0.305	0.22728	N	0.998805	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.06405	0.002;0.0;0.002	T	0.51888	-0.8648	10	0.15066	T	0.55	-14.8338	3.8887	0.09110	0.0923:0.1632:0.5762:0.1683	.	327;215;421	E7ESG3;E7ESH3;Q96I15	.;.;SCLY_HUMAN	N	429;421;327;215	ENSP00000254663:S429N;ENSP00000450613:S421N;ENSP00000416865:S327N;ENSP00000393694:S215N	ENSP00000254663:S421N	S	+	2	0	SCLY	238671659	0.000000	0.05858	0.998000	0.56505	0.855000	0.48748	-0.082000	0.11304	0.961000	0.38030	0.603000	0.83216	AGC		0.721	SCLY-204	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_016510	
ANKMY1	51281	broad.mit.edu	37	2	241468581	241468581	+	Missense_Mutation	SNP	G	G	A	rs150953451		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:241468581G>A	ENST00000272972.3	-	4	773	c.559C>T	c.(559-561)Cgc>Tgc	p.R187C	ANKMY1_ENST00000462004.1_Intron|ANKMY1_ENST00000391987.1_Missense_Mutation_p.R187C|ANKMY1_ENST00000405523.3_Intron|ANKMY1_ENST00000361678.4_Intron|ANKMY1_ENST00000536462.1_Intron|ANKMY1_ENST00000373318.2_Intron|ANKMY1_ENST00000405002.1_Intron|ANKMY1_ENST00000406958.1_Intron|ANKMY1_ENST00000373320.4_Intron|ANKMY1_ENST00000403283.1_Intron|ANKMY1_ENST00000401804.1_Missense_Mutation_p.R276C	NM_016552.2	NP_057636.2	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1	187							metal ion binding (GO:0046872)	p.R187C(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)		AGCTCTTTGCGGAAAGAGCTT	0.478													G|||	1	0.000199681	0.0008	0.0	5008	,	,		21296	0.0		0.0	False		,,,				2504	0.0				p.R187C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C559T	2						.						149.0	147.0	147.0					2																	241468581		2203	4300	6503	241117254	SO:0001583	missense	51281	exon4			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.559C>T	2.37:g.241468581G>A	ENSP00000272972:p.Arg187Cys		241117254	NM_016552	B2RB78|Q4ZFV3|Q8IYX5|Q8NDK5|Q9H0V8|Q9NX10	Missense_Mutation	SNP	ENST00000272972.3	37	CCDS2536.1	1|1	4.578754578754579E-4|4.578754578754579E-4	1|1	0.0020325203252032522|0.0020325203252032522	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	7.806|7.806	0.714596|0.714596	0.15306|0.15306	.|.	.|.	ENSG00000144504|ENSG00000144504	ENST00000443318|ENST00000272972;ENST00000391987;ENST00000401804;ENST00000539830;ENST00000418708	.|T;T;T;T	.|0.46819	.|0.86;0.86;0.86;0.86	4.79|4.79	1.7|1.7	0.24286|0.24286	.|.	.|0.258312	.|0.28595	.|N	.|0.014781	T|T	0.38026|0.38026	0.1025|0.1025	M|M	0.75447|0.75447	2.3|2.3	0.09310|0.09310	N|N	1|1	.|P;P	.|0.36959	.|0.575;0.575	.|B;B	.|0.24974	.|0.057;0.057	T|T	0.40117|0.40117	-0.9580|-0.9580	5|10	.|0.72032	.|D	.|0.01	-16.9551|-16.9551	5.5897|5.5897	0.17293|0.17293	0.085:0.1374:0.6368:0.1408|0.085:0.1374:0.6368:0.1408	.|.	.|187;187	.|Q4ZFV3;Q9P2S6	.|.;ANKY1_HUMAN	L|C	131|187;187;276;187;187	.|ENSP00000272972:R187C;ENSP00000375847:R187C;ENSP00000385887:R276C;ENSP00000407015:R187C	.|ENSP00000272972:R187C	P|R	-|-	2|1	0|0	ANKMY1|ANKMY1	241117254|241117254	0.944000|0.944000	0.32072|0.32072	0.055000|0.055000	0.19348|0.19348	0.095000|0.095000	0.18619|0.18619	1.470000|1.470000	0.35354|0.35354	0.520000|0.520000	0.28426|0.28426	0.655000|0.655000	0.94253|0.94253	CCG|CGC		0.478	ANKMY1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257187.2	NM_017844	
TRAPPC12	51112	broad.mit.edu	37	2	3391482	3391482	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:3391482C>T	ENST00000324266.5	+	2	283	c.88C>T	c.(88-90)Ctc>Ttc	p.L30F	TRAPPC12_ENST00000382110.2_Missense_Mutation_p.L30F	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	30					vesicle-mediated transport (GO:0016192)			p.L30F(1)									GCAGGGGTTGCTCTTCCAGGA	0.652																																					p.L30F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C88T	2						.						33.0	30.0	31.0					2																	3391482		2203	4299	6502	3370489	SO:0001583	missense	51112	exon2			BC017475	CCDS1652.1	2p25.3	2013-01-10	2011-12-12	2011-12-12	ENSG00000171853	ENSG00000171853		"""Trafficking protein particle complex"", ""Tetratricopeptide (TTC) repeat domain containing"""	24284	protein-coding gene	gene with protein product		614139	"""tetratricopeptide repeat domain 15"""	TTC15		10810093, 21525244, 20562859	Standard	NM_016030		Approved	CGI-87, TTC-15	uc002qxm.1	Q8WVT3	OTTHUMG00000090328	ENST00000324266.5:c.88C>T	2.37:g.3391482C>T	ENSP00000324318:p.Leu30Phe		3370489	NM_016030	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Missense_Mutation	SNP	ENST00000324266.5	37	CCDS1652.1	.	.	.	.	.	.	.	.	.	.	C	18.27	3.586624	0.66105	.	.	ENSG00000171853	ENST00000382110;ENST00000304601;ENST00000324266	T;T	0.66280	-0.2;-0.2	5.11	4.22	0.49857	.	0.079888	0.51477	D	0.000097	T	0.71879	0.3392	L	0.52573	1.65	0.09310	N	0.999995	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.78314	0.946;0.991;0.988	T	0.63386	-0.6649	10	0.56958	D	0.05	.	11.524	0.50569	0.0:0.916:0.0:0.084	.	13;30;30	E7ENL7;Q8WVT3;Q53S18	.;TPC12_HUMAN;.	F	30;13;30	ENSP00000371544:L30F;ENSP00000324318:L30F	ENSP00000303612:L13F	L	+	1	0	TTC15	3370489	0.021000	0.18746	0.019000	0.16419	0.002000	0.02628	0.662000	0.25038	1.346000	0.45694	0.563000	0.77884	CTC		0.652	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030	
ASAP2	8853	broad.mit.edu	37	2	9514980	9514980	+	Silent	SNP	C	C	T	rs373037678		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:9514980C>T	ENST00000281419.3	+	17	1993	c.1653C>T	c.(1651-1653)tgC>tgT	p.C551C	ASAP2_ENST00000315273.4_Silent_p.C551C	NM_003887.2	NP_003878.1	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	551					positive regulation of catalytic activity (GO:0043085)|regulation of ARF GTPase activity (GO:0032312)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|enzyme activator activity (GO:0008047)|zinc ion binding (GO:0008270)	p.C551C(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	36						ACAGTCTTTGCGAGGCCGTCA	0.483													C|||	1	0.000199681	0.0	0.0	5008	,	,		17019	0.0		0.0	False		,,,				2504	0.001				p.C551C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1653T	2						.	C	,	2,4404	4.2+/-10.8	0,2,2201	117.0	112.0	114.0		1653,1653	-3.2	0.9	2		114	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ASAP2	NM_001135191.1,NM_003887.2	,	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	,	551/962,551/1007	9514980	2,13004	2203	4300	6503	9432431	SO:0001819	synonymous_variant	8853	exon17			AB007860	CCDS1661.1, CCDS46224.1	2p24	2013-01-10	2008-09-22	2008-09-22	ENSG00000151693	ENSG00000151693		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	2721	protein-coding gene	gene with protein product	"""centaurin, beta 3"""	603817	"""development and differentiation enhancing factor 2"""	DDEF2		10022920, 9455477	Standard	NM_003887		Approved	KIAA0400, PAP, SHAG1, CENTB3	uc002qzh.2	O43150	OTTHUMG00000117485	ENST00000281419.3:c.1653C>T	2.37:g.9514980C>T			9432431	NM_001135191	D6W4Y8	Silent	SNP	ENST00000281419.3	37	CCDS1661.1																																																																																				0.483	ASAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000237522.1	NM_003887	
CENPO	79172	broad.mit.edu	37	2	25037308	25037308	+	Silent	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:25037308T>C	ENST00000380834.2	+	4	705	c.280T>C	c.(280-282)Ttg>Ctg	p.L94L	CENPO_ENST00000260662.1_Silent_p.L94L|CENPO_ENST00000473706.1_Silent_p.L88L			Q9BU64	CENPO_HUMAN	centromere protein O	94					CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.L94L(1)		breast(2)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					GCAAGAAGCATTGGAAGAGAA	0.383																																					p.L88L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T262C	2						.						209.0	206.0	207.0					2																	25037308		2203	4300	6503	24890812	SO:0001819	synonymous_variant	79172	exon3			AK027859	CCDS1714.1, CCDS56113.1	2p23.3	2013-11-05			ENSG00000138092	ENSG00000138092			28152	protein-coding gene	gene with protein product		611504				16622420, 16622419	Standard	NM_024322		Approved	MGC11266, CENP-O	uc002rfp.2	Q9BU64	OTTHUMG00000125525	ENST00000380834.2:c.280T>C	2.37:g.25037308T>C			24890812	NM_001199803	B2RDC0|D6W536|Q53T55|Q96JV3	Silent	SNP	ENST00000380834.2	37	CCDS1714.1																																																																																				0.383	CENPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246856.2	NM_024322	
GPR113	165082	broad.mit.edu	37	2	26536714	26536714	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:26536714G>A	ENST00000311519.1	-	8	1189	c.1190C>T	c.(1189-1191)cCg>cTg	p.P397L	GPR113_ENST00000333478.6_Missense_Mutation_p.P198L|GPR113_ENST00000541401.1_5'UTR|GPR113_ENST00000459892.1_5'UTR|GPR113_ENST00000421160.2_Missense_Mutation_p.P328L	NM_001145168.1	NP_001138640.1	Q8IZF5	GP113_HUMAN	G protein-coupled receptor 113	397					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.P198L(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(4)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GTCAGCCATCGGGCAGCGCTG	0.597																																					p.P328L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C983T	2						.						99.0	95.0	96.0					2																	26536714		2203	4300	6503	26390218	SO:0001583	missense	165082	exon7			AB083619	CCDS33159.2, CCDS46238.1, CCDS46239.1	2p24.1	2014-08-08			ENSG00000173567	ENSG00000173567		"""-"", ""GPCR / Class B : Orphans"""	18989	protein-coding gene	gene with protein product						12435584	Standard	NM_153835		Approved	hGPCR37, PGR23	uc002rhe.4	Q8IZF5	OTTHUMG00000150225	ENST00000311519.1:c.1190C>T	2.37:g.26536714G>A	ENSP00000307831:p.Pro397Leu		26390218	NM_001145169	B4DF15|E9PEV1|Q53TA5|Q6UXT7|Q6UXX3|Q86SL7|Q8IXD8|Q8TDT3	Missense_Mutation	SNP	ENST00000311519.1	37	CCDS46239.1	.	.	.	.	.	.	.	.	.	.	G	37	6.513339	0.97629	.	.	ENSG00000173567	ENST00000333478;ENST00000421160;ENST00000311519	T;T;T	0.07908	3.15;3.15;3.15	5.8	5.8	0.92144	.	.	.	.	.	T	0.14960	0.0361	L	0.61218	1.895	0.80722	D	1	B;P;B	0.50617	0.04;0.937;0.002	B;P;B	0.45506	0.017;0.483;0.004	T	0.00197	-1.1930	9	0.54805	T	0.06	-25.3472	15.561	0.76244	0.0:0.0:1.0:0.0	.	328;198;397	E9PEV1;Q8IZF5-2;Q8IZF5	.;.;GP113_HUMAN	L	198;328;397	ENSP00000327396:P198L;ENSP00000388537:P328L;ENSP00000307831:P397L	ENSP00000307831:P397L	P	-	2	0	GPR113	26390218	0.997000	0.39634	0.966000	0.40874	0.015000	0.08874	3.155000	0.50700	2.755000	0.94549	0.655000	0.94253	CCG		0.597	GPR113-004	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316892.1	NM_153835	
SLC30A3	7781	broad.mit.edu	37	2	27479255	27479255	+	Splice_Site	SNP	G	G	A	rs140122355	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:27479255G>A	ENST00000233535.4	-	7	1369	c.1017C>T	c.(1015-1017)atC>atT	p.I339I	SLC30A3_ENST00000447008.2_Splice_Site_p.I334I	NM_003459.4	NP_003450.2	Q99726	ZNT3_HUMAN	solute carrier family 30 (zinc transporter), member 3	339					positive regulation of transport (GO:0051050)|regulation of sequestering of zinc ion (GO:0061088)|transmembrane transport (GO:0055085)|transport (GO:0006810)|zinc ion transmembrane transport (GO:0071577)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	zinc transporting ATPase activity (GO:0015633)	p.I339I(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(11)|pancreas(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GTGACTCACCGATGGCCAGGT	0.547																																					p.I339I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1017T	2						.						64.0	60.0	61.0					2																	27479255		2203	4300	6503	27332759	SO:0001630	splice_region_variant	7781	exon7			U76010	CCDS1743.1	2p23.3	2013-05-22			ENSG00000115194	ENSG00000115194		"""Solute carriers"""	11014	protein-coding gene	gene with protein product		602878		ZNT3		8962159	Standard	NM_003459		Approved		uc002rjj.3	Q99726	OTTHUMG00000128409	ENST00000233535.4:c.1018+1C>T	2.37:g.27479255G>A			27332759	NM_003459	Q8TC03	Missense_Mutation	SNP	ENST00000233535.4	37	CCDS1743.1																																																																																				0.547	SLC30A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250189.2		Silent
NRXN1	9378	broad.mit.edu	37	2	50149313	50149313	+	Silent	SNP	C	C	T	rs369748793		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:50149313C>T	ENST00000406316.2	-	22	5679	c.4203G>A	c.(4201-4203)acG>acA	p.T1401T	NRXN1_ENST00000406859.3_Silent_p.T1401T|NRXN1_ENST00000405472.3_Silent_p.T1423T|NRXN1_ENST00000342183.5_Silent_p.T366T|NRXN1_ENST00000401710.1_Silent_p.T419T|NRXN1_ENST00000402717.3_Silent_p.T1423T|NRXN1_ENST00000404971.1_Silent_p.T1471T|NRXN1_ENST00000401669.2_Silent_p.T1431T	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	1401					adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)	p.T366T(2)|p.T1401T(1)|p.T1472T(1)|p.T1471T(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			CGACCATACCCGTGGTGCTGC	0.552																																					p.T366T												.	.	5	Substitution - coding silent(5)	lung(4)|large_intestine(1)	c.G1098A	2						.	C	,,	0,4406		0,0,2203	93.0	76.0	82.0		4413,4203,1098	-4.1	1.0	2		82	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	NRXN1	NM_001135659.1,NM_004801.4,NM_138735.2	,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,	1471/1548,1401/1478,366/443	50149313	1,13005	2203	4300	6503	50002817	SO:0001819	synonymous_variant	9378	exon6			AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.4203G>A	2.37:g.50149313C>T			50002817	NM_138735	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Silent	SNP	ENST00000406316.2	37	CCDS54360.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	3.696|3.696	-0.062624|-0.062624	0.07273|0.07273	0.0|0.0	1.16E-4|1.16E-4	ENSG00000179915|ENSG00000179915	ENST00000378262|ENST00000412315	.|.	.|.	.|.	5.97|5.97	-4.09|-4.09	0.03951|0.03951	.|.	.|.	.|.	.|.	.|.	T|T	0.38134|0.38134	0.1029|0.1029	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.35992|0.35992	-0.9766|-0.9766	4|4	.|.	.|.	.|.	.|.	1.7802|1.7802	0.03030|0.03030	0.3857:0.2624:0.0796:0.2723|0.3857:0.2624:0.0796:0.2723	.|.	.|.	.|.	.|.	R|Q	68|134	.|.	.|.	G|R	-|-	1|2	0|0	NRXN1|NRXN1	50002817|50002817	0.001000|0.001000	0.12720|0.12720	0.952000|0.952000	0.39060|0.39060	0.954000|0.954000	0.61252|0.61252	-1.296000|-1.296000	0.02762|0.02762	-0.692000|-0.692000	0.05128|0.05128	-0.989000|-0.989000	0.02550|0.02550	GGG|CGG		0.552	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2		
OTX1	5013	broad.mit.edu	37	2	63282689	63282689	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:63282689C>T	ENST00000282549.2	+	5	579	c.303C>T	c.(301-303)agC>agT	p.S101S	OTX1_ENST00000366671.3_Silent_p.S101S	NM_014562.3	NP_055377.1	P32242	OTX1_HUMAN	orthodenticle homeobox 1	101					anterior/posterior pattern specification (GO:0009952)|diencephalon morphogenesis (GO:0048852)|inner ear morphogenesis (GO:0042472)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.S101S(1)		endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|pancreas(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	20	Lung NSC(7;0.121)|all_lung(7;0.211)					AGAGCGGGAGCGGAACCAAGA	0.647																																					p.S101S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C303T	2						.						27.0	30.0	29.0					2																	63282689		2203	4300	6503	63136193	SO:0001819	synonymous_variant	5013	exon5				CCDS1873.1	2p15	2011-06-20	2007-02-15		ENSG00000115507	ENSG00000115507		"""Homeoboxes / PRD class"""	8521	protein-coding gene	gene with protein product		600036	"""orthodenticle (Drosophila) homolog 1"", ""orthodenticle homolog 1 (Drosophila)"""			7959790	Standard	NM_001199770		Approved		uc002scd.3	P32242	OTTHUMG00000129454	ENST00000282549.2:c.303C>T	2.37:g.63282689C>T			63136193	NM_001199770	A6NHA2|B3KTJ4|Q53TG6	Silent	SNP	ENST00000282549.2	37	CCDS1873.1																																																																																				0.647	OTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251617.1		
ADD2	119	broad.mit.edu	37	2	70890806	70890806	+	Silent	SNP	C	C	T	rs115476558		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:70890806C>T	ENST00000264436.4	-	16	2376	c.1932G>A	c.(1930-1932)ccG>ccA	p.P644P	ADD2_ENST00000407644.2_Silent_p.P644P|ADD2_ENST00000355733.3_3'UTR	NM_001617.3	NP_001608.1	P35612	ADDB_HUMAN	adducin 2 (beta)	644					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|barbed-end actin filament capping (GO:0051016)|hemopoiesis (GO:0030097)|positive regulation of protein binding (GO:0032092)|protein complex assembly (GO:0006461)	cytoplasmic membrane-bounded vesicle (GO:0016023)|F-actin capping protein complex (GO:0008290)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|spectrin binding (GO:0030507)|structural molecule activity (GO:0005198)	p.P644P(1)		autonomic_ganglia(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(11)|lung(13)|ovary(3)|pancreas(1)|skin(2)	36						CCACCCCTTCCGGCTGGGTTG	0.517													C|||	1	0.000199681	0.0	0.0	5008	,	,		18094	0.0		0.001	False		,,,				2504	0.0				p.P644P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1932A	2						.						98.0	89.0	92.0					2																	70890806		2203	4300	6503	70744314	SO:0001819	synonymous_variant	119	exon16			X58199	CCDS1906.1, CCDS1909.1, CCDS46318.1, CCDS54365.1	2p13.3	2008-02-05			ENSG00000075340	ENSG00000075340			244	protein-coding gene	gene with protein product		102681				1840603	Standard	NM_001617		Approved	ADDB	uc021vjc.1	P35612	OTTHUMG00000129710	ENST00000264436.4:c.1932G>A	2.37:g.70890806C>T			70744314	NM_001185054	A8K4P2|B4DM17|D6W5G7|D6W5G8|Q13482|Q16412|Q59G82|Q5U5P4|Q6P0P2|Q6PGQ4|Q7Z688|Q7Z689|Q7Z690|Q7Z691	Silent	SNP	ENST00000264436.4	37	CCDS1906.1																																																																																				0.517	ADD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251918.4	NM_001617	
ATP6V1B1	525	broad.mit.edu	37	2	71163197	71163197	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:71163197G>A	ENST00000234396.4	+	1	186	c.113G>A	c.(112-114)cGt>cAt	p.R38H	ATP6V1B1_ENST00000412314.1_Missense_Mutation_p.R38H	NM_001692.3	NP_001683.2	P15313	VATB1_HUMAN	ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B1	38					ATP hydrolysis coupled proton transport (GO:0015991)|ATP metabolic process (GO:0046034)|calcium ion homeostasis (GO:0055074)|cellular iron ion homeostasis (GO:0006879)|excretion (GO:0007588)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|ossification (GO:0001503)|pH reduction (GO:0045851)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|regulation of pH (GO:0006885)|sensory perception of sound (GO:0007605)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lateral plasma membrane (GO:0016328)|microvillus (GO:0005902)|proton-transporting V-type ATPase, V1 domain (GO:0033180)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	ATP binding (GO:0005524)|hydrogen ion transmembrane transporter activity (GO:0015078)|hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances (GO:0016820)	p.R38H(1)		endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|prostate(1)|skin(1)	19						ACCCACCCCCGTGTCAGTGAG	0.652																																					p.R38H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G113A	2						.						53.0	57.0	56.0					2																	71163197		2203	4300	6503	71016705	SO:0001583	missense	525	exon1			AF107466	CCDS1912.1	2p13	2010-04-21	2008-07-31	2002-05-10	ENSG00000116039	ENSG00000116039	3.6.3.14	"""ATPases / V-type"""	853	protein-coding gene	gene with protein product	"""Renal tubular acidosis with deafness"""	192132	"""vacuolar proton pump 3"""	VPP3, ATP6B1		9916796, 2527371	Standard	XM_005264368		Approved	VATB, RTA1B, Vma2	uc002shj.3	P15313	OTTHUMG00000129711	ENST00000234396.4:c.113G>A	2.37:g.71163197G>A	ENSP00000234396:p.Arg38His		71016705	NM_001692	Q53FY0|Q6P4H6	Missense_Mutation	SNP	ENST00000234396.4	37	CCDS1912.1	.	.	.	.	.	.	.	.	.	.	G	17.42	3.386014	0.61956	.	.	ENSG00000116039	ENST00000234396;ENST00000483246;ENST00000412314	D;D	0.84070	-1.8;-1.8	4.89	4.89	0.63831	.	0.000000	0.44097	D	0.000497	T	0.80984	0.4729	L	0.29908	0.895	0.58432	D	0.999994	B;P	0.46859	0.039;0.885	B;P	0.49361	0.022;0.608	T	0.82975	-0.0190	10	0.54805	T	0.06	-9.6208	15.5589	0.76223	0.0:0.0:1.0:0.0	.	38;38	C9JL73;P15313	.;VATB1_HUMAN	H	38;13;38	ENSP00000234396:R38H;ENSP00000388353:R38H	ENSP00000234396:R38H	R	+	2	0	ATP6V1B1	71016705	1.000000	0.71417	0.921000	0.36526	0.930000	0.56654	6.055000	0.71103	2.256000	0.74724	0.467000	0.42956	CGT		0.652	ATP6V1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251920.2	NM_001692	
PAIP2B	400961	broad.mit.edu	37	2	71429613	71429613	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:71429613C>A	ENST00000244221.8	-	2	273	c.107G>T	c.(106-108)tGg>tTg	p.W36L		NM_020459.1	NP_065192.1	Q9ULR5	PAI2B_HUMAN	poly(A) binding protein interacting protein 2B	36					negative regulation of translational initiation (GO:0045947)	cytoplasm (GO:0005737)	translation repressor activity, nucleic acid binding (GO:0000900)	p.W36L(1)		large_intestine(1)|lung(1)	2						ATTCTCCATCCACATGTACTC	0.398																																					p.W36L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G107T	2						.						198.0	196.0	197.0					2																	71429613		1983	4205	6188	71283121	SO:0001583	missense	400961	exon2				CCDS46322.1	2p13.3	2007-07-16			ENSG00000124374	ENSG00000124374			29200	protein-coding gene	gene with protein product		611018				16804161	Standard	NM_020459		Approved	KIAA1155	uc002shu.2	Q9ULR5	OTTHUMG00000153284	ENST00000244221.8:c.107G>T	2.37:g.71429613C>A	ENSP00000244221:p.Trp36Leu		71283121	NM_020459		Missense_Mutation	SNP	ENST00000244221.8	37	CCDS46322.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.565207	0.86439	.	.	ENSG00000124374	ENST00000244221	.	.	.	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	D	0.83142	0.5190	M	0.84326	2.69	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.85416	0.1140	9	0.87932	D	0	-4.6266	16.9623	0.86275	0.0:1.0:0.0:0.0	.	36	Q9ULR5	PAI2B_HUMAN	L	36	.	ENSP00000244221:W36L	W	-	2	0	PAIP2B	71283121	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.630000	0.67805	2.680000	0.91292	0.563000	0.77884	TGG		0.398	PAIP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330547.2	XM_376062	
DYSF	8291	broad.mit.edu	37	2	71825770	71825770	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:71825770G>T	ENST00000258104.3	+	33	3874	c.3597G>T	c.(3595-3597)tgG>tgT	p.W1199C	DYSF_ENST00000409744.1_Missense_Mutation_p.W1186C|DYSF_ENST00000410020.3_Missense_Mutation_p.W1217C|DYSF_ENST00000409762.1_Missense_Mutation_p.W1216C|DYSF_ENST00000409651.1_Missense_Mutation_p.W1231C|DYSF_ENST00000409366.1_Missense_Mutation_p.W1200C|DYSF_ENST00000413539.2_Missense_Mutation_p.W1230C|DYSF_ENST00000479049.2_3'UTR|DYSF_ENST00000409582.3_Missense_Mutation_p.W1216C|DYSF_ENST00000410041.1_Missense_Mutation_p.W1217C|DYSF_ENST00000429174.2_Missense_Mutation_p.W1199C|DYSF_ENST00000394120.2_Missense_Mutation_p.W1200C	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1199	C2 4. {ECO:0000255|PROSITE- ProRule:PRU00041}.				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.W1199C(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						ACCCCACCTGGGACCAGACGC	0.592																																					p.W1231C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3693T	2						.						100.0	91.0	94.0					2																	71825770		2203	4300	6503	71679278	SO:0001583	missense	8291	exon34			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.3597G>T	2.37:g.71825770G>T	ENSP00000258104:p.Trp1199Cys		71679278	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Missense_Mutation	SNP	ENST00000258104.3	37	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.679435	0.88542	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	D;D;D;D;D;D;D;D;D;D;D	0.84298	-1.83;-1.83;-1.83;-1.83;-1.83;-1.83;-1.83;-1.83;-1.83;-1.83;-1.83	5.66	5.66	0.87406	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	D	0.96185	0.8756	H	0.99525	4.61	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;0.998;0.998;0.998;1.0;1.0;1.0;1.0;0.998;1.0;1.0	D	0.97933	1.0321	10	0.87932	D	0	-15.0448	17.2321	0.86987	0.0:0.0:1.0:0.0	.	1231;1217;1200;1186;1217;1186;1216;1185;1230;1216;1199;1185;1200;1199	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	C	1230;1216;1216;1199;1199;1231;1200;1186;1200;1217;1217	ENSP00000407046:W1230C;ENSP00000387137:W1216C;ENSP00000386547:W1216C;ENSP00000398305:W1199C;ENSP00000258104:W1199C;ENSP00000386683:W1231C;ENSP00000377678:W1200C;ENSP00000386285:W1186C;ENSP00000386512:W1200C;ENSP00000386881:W1217C;ENSP00000386617:W1217C	ENSP00000258104:W1199C	W	+	3	0	DYSF	71679278	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.598000	0.98277	2.675000	0.91044	0.655000	0.94253	TGG		0.592	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494	
ALMS1	7840	broad.mit.edu	37	2	73716868	73716868	+	Silent	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:73716868T>C	ENST00000264448.6	+	10	7890	c.7779T>C	c.(7777-7779)caT>caC	p.H2593H	AC096546.1_ENST00000408160.1_RNA|ALMS1_ENST00000409009.1_Silent_p.H2551H	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2593					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.H2593H(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CTTCTGAACATCCACAACTAG	0.478																																					p.H2593H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T7779C	2						.						102.0	99.0	100.0					2																	73716868		1938	4124	6062	73570376	SO:0001819	synonymous_variant	7840	exon10			AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.7779T>C	2.37:g.73716868T>C			73570376	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	37	CCDS42697.1																																																																																				0.478	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
ALMS1	7840	broad.mit.edu	37	2	73828377	73828377	+	Silent	SNP	C	C	T	rs571782143		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:73828377C>T	ENST00000264448.6	+	19	12036	c.11925C>T	c.(11923-11925)aaC>aaT	p.N3975N	ALMS1_ENST00000464408.2_3'UTR|ALMS1_ENST00000409009.1_Silent_p.N3933N	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	3975					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.N3975N(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						AGAAGGAAAACGTGCCTAACA	0.478													c|||	1	0.000199681	0.0008	0.0	5008	,	,		21483	0.0		0.0	False		,,,				2504	0.0				p.N3975N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C11925T	2						.						113.0	124.0	120.0					2																	73828377		2186	4296	6482	73681885	SO:0001819	synonymous_variant	7840	exon19			AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.11925C>T	2.37:g.73828377C>T			73681885	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	37	CCDS42697.1																																																																																				0.478	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
SLC4A5	57835	broad.mit.edu	37	2	74469129	74469129	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:74469129C>T	ENST00000377634.4	-	20	2509	c.2110G>A	c.(2110-2112)Gct>Act	p.A704T	SLC4A5_ENST00000377632.1_Missense_Mutation_p.A704T|SLC4A5_ENST00000346834.4_Missense_Mutation_p.A704T|SLC4A5_ENST00000359484.4_Missense_Mutation_p.A640T|SLC4A5_ENST00000423644.1_Missense_Mutation_p.A704T|SLC4A5_ENST00000358683.4_Missense_Mutation_p.A640T|RP11-287D1.3_ENST00000451608.2_3'UTR|SLC4A5_ENST00000357822.5_Missense_Mutation_p.A704T|SLC4A5_ENST00000483195.1_5'UTR|SLC4A5_ENST00000394019.2_Missense_Mutation_p.A704T					solute carrier family 4 (sodium bicarbonate cotransporter), member 5									p.A704T(1)		breast(5)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(13)|ovary(5)|pancreas(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48						ACCAGAGAAGCGTTGGTGTCT	0.493																																					p.A704T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2110A	2						.						151.0	136.0	141.0					2																	74469129		2203	4300	6503	74322637	SO:0001583	missense	57835	exon15			AF243499	CCDS1936.1, CCDS1937.1	2p13.1	2013-07-19	2013-07-19		ENSG00000188687	ENSG00000188687		"""Solute carriers"""	18168	protein-coding gene	gene with protein product		606757	"""solute carrier family 4, sodium bicarbonate cotransporter, member 5"""			10978526, 11087115	Standard	NM_133478		Approved	NBC4	uc002sko.1	Q9BY07	OTTHUMG00000090263	ENST00000377634.4:c.2110G>A	2.37:g.74469129C>T	ENSP00000366861:p.Ala704Thr		74322637	NM_021196		Missense_Mutation	SNP	ENST00000377634.4	37	CCDS1936.1	.	.	.	.	.	.	.	.	.	.	C	6.875	0.530913	0.13127	.	.	ENSG00000188687	ENST00000394019;ENST00000451608;ENST00000346834;ENST00000359484;ENST00000423644;ENST00000358683;ENST00000357822;ENST00000377632;ENST00000377634;ENST00000425249	T;T;T;T;T;T;T;T;T	0.76709	-1.04;-0.86;-0.99;-0.47;-0.99;-1.04;-0.86;-1.04;-0.1	5.4	-4.48	0.03515	Bicarbonate transporter, C-terminal (1);	1.186260	0.06270	N	0.695480	T	0.55955	0.1953	N	0.14661	0.345	0.09310	N	1	B;B;B;B;B	0.15141	0.001;0.012;0.0;0.001;0.0	B;B;B;B;B	0.08055	0.001;0.003;0.001;0.001;0.002	T	0.41161	-0.9524	10	0.13470	T	0.59	.	8.5178	0.33257	0.1158:0.1929:0.0:0.6913	.	704;704;640;704;704	Q9BY07-4;E7EQT3;Q9BY07-7;Q9BY07;Q9BY07-3	.;.;.;S4A5_HUMAN;.	T	704;704;704;640;704;640;704;704;704;704	ENSP00000377587:A704T;ENSP00000251768:A704T;ENSP00000352461:A640T;ENSP00000395804:A704T;ENSP00000351513:A640T;ENSP00000350475:A704T;ENSP00000366859:A704T;ENSP00000366861:A704T;ENSP00000405678:A704T	ENSP00000251768:A704T	A	-	1	0	SLC4A5	74322637	0.000000	0.05858	0.032000	0.17829	0.811000	0.45836	-0.723000	0.04952	-0.762000	0.04664	0.655000	0.94253	GCT		0.493	SLC4A5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206583.3		
LOXL3	84695	broad.mit.edu	37	2	74763995	74763995	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:74763995C>T	ENST00000264094.3	-	5	824	c.753G>A	c.(751-753)acG>acA	p.T251T	LOXL3_ENST00000484369.1_5'Flank|LOXL3_ENST00000409249.1_Silent_p.T251T|LOXL3_ENST00000409986.1_Intron|LOXL3_ENST00000393937.2_Intron|LOXL3_ENST00000409549.1_Silent_p.T251T	NM_032603.2	NP_115992.1	P58215	LOXL3_HUMAN	lysyl oxidase-like 3	251	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.				epithelial to mesenchymal transition (GO:0001837)|negative regulation of transcription, DNA-templated (GO:0045892)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)	p.T251T(1)		endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30						GGTGGGCCTCCGTGCCCACGC	0.637																																					p.T251T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G753A	2						.						47.0	51.0	50.0					2																	74763995		2203	4300	6503	74617503	SO:0001819	synonymous_variant	84695	exon5			AF282619	CCDS1953.1, CCDS74527.1	2p13	2008-05-23			ENSG00000115318	ENSG00000115318			13869	protein-coding gene	gene with protein product		607163				11386757	Standard	NM_032603		Approved		uc002smp.1	P58215	OTTHUMG00000129953	ENST00000264094.3:c.753G>A	2.37:g.74763995C>T			74617503	NM_032603	D6W5J1|Q2EHP2|Q6IPL7|Q96RS1	Silent	SNP	ENST00000264094.3	37	CCDS1953.1																																																																																				0.637	LOXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252215.1	NM_032603	
GCFC2	6936	broad.mit.edu	37	2	75921498	75921498	+	Missense_Mutation	SNP	C	C	T	rs373951174		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:75921498C>T	ENST00000321027.3	-	6	1022	c.889G>A	c.(889-891)Gta>Ata	p.V297I	GCFC2_ENST00000541687.1_3'UTR|GCFC2_ENST00000409857.3_Missense_Mutation_p.V259I	NM_001201334.1|NM_003203.4	NP_001188263.1|NP_003194.3	P16383	GCFC2_HUMAN	GC-rich sequence DNA-binding factor 2	297					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)|U2-type post-mRNA release spliceosomal complex (GO:0071008)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)	p.V297I(1)									ACATCTTGTACGTATTTTTCA	0.294																																					p.V297I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G889A	2						.						171.0	179.0	176.0					2																	75921498		2203	4300	6503	75775006	SO:0001583	missense	6936	exon6			AB026911	CCDS1961.1, CCDS62943.1	2p12	2014-01-17	2011-11-24	2011-11-24	ENSG00000005436	ENSG00000005436			1317	protein-coding gene	gene with protein product	"""GC binding factor"""	189901	"""transcription factor 9 (binds GC-rich sequences)"", ""chromosome 2 open reading frame 3"""	TCF9, C2orf3		1370479, 2556218, 17309879, 24304693	Standard	NM_003203		Approved	DNABF, GCF	uc002sno.3	P16383	OTTHUMG00000129989	ENST00000321027.3:c.889G>A	2.37:g.75921498C>T	ENSP00000318690:p.Val297Ile		75775006	NM_003203	A4UHQ8|O95032|Q53TY0|Q6P2F2	Missense_Mutation	SNP	ENST00000321027.3	37	CCDS1961.1	.	.	.	.	.	.	.	.	.	.	C	0.250	-1.006997	0.02112	.	.	ENSG00000005436	ENST00000321027;ENST00000409857	T;T	0.14640	2.49;2.5	5.29	-6.56	0.01848	.	1.322790	0.04729	N	0.420869	T	0.04998	0.0134	N	0.01874	-0.695	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.42916	-0.9423	10	0.35671	T	0.21	-0.009	10.5735	0.45214	0.0:0.5793:0.2687:0.152	.	297	P16383	GCF_HUMAN	I	297;259	ENSP00000318690:V297I;ENSP00000386552:V259I	ENSP00000318690:V297I	V	-	1	0	C2orf3	75775006	0.000000	0.05858	0.000000	0.03702	0.032000	0.12392	-0.854000	0.04299	-0.651000	0.05415	-0.302000	0.09304	GTA		0.294	GCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252255.2	NM_003203	
CTNNA2	1496	broad.mit.edu	37	2	80136821	80136821	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:80136821C>T	ENST00000402739.4	+	6	959	c.954C>T	c.(952-954)gcC>gcT	p.A318A	CTNNA2_ENST00000361291.4_Silent_p.A352A|CTNNA2_ENST00000541047.1_Silent_p.A318A|CTNNA2_ENST00000540488.1_Silent_p.A318A|CTNNA2_ENST00000496558.1_Silent_p.A318A|CTNNA2_ENST00000466387.1_Silent_p.A318A	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	318					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)	p.A318A(2)		breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						CGCTGATGGCCGACTCCTCCT	0.642																																					p.A319A												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C957T	2						.						51.0	57.0	55.0					2																	80136821		2043	4203	6246	79990332	SO:0001819	synonymous_variant	1496	exon7				CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"""cadherin-associated protein, related"", ""cancer/testis antigen 114"""	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.954C>T	2.37:g.80136821C>T			79990332	NM_004389	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Silent	SNP	ENST00000402739.4	37																																																																																					0.642	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389	
RETSAT	54884	broad.mit.edu	37	2	85573110	85573110	+	Missense_Mutation	SNP	G	G	A	rs146678348	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:85573110G>A	ENST00000295802.4	-	6	1217	c.1105C>T	c.(1105-1107)Cgc>Tgc	p.R369C	RETSAT_ENST00000263854.6_Missense_Mutation_p.R369C|RETSAT_ENST00000475624.2_5'UTR|RETSAT_ENST00000457495.2_Missense_Mutation_p.R308C	NM_017750.3	NP_060220.3	Q6NUM9	RETST_HUMAN	retinol saturase (all-trans-retinol 13,14-reductase)	369					oxidation-reduction process (GO:0055114)|retinol metabolic process (GO:0042572)	endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nuclear outer membrane (GO:0005640)	all-trans-retinol 13,14-reductase activity (GO:0051786)|oxidoreductase activity (GO:0016491)	p.R369S(1)|p.R369C(1)		NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	30					Vitamin A(DB00162)	GGCAGGCAGCGGGCGTTCCCC	0.582																																					p.R369C												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.C1105T	2						.	G	CYS/ARG	7,4399	12.9+/-30.5	0,7,2196	112.0	100.0	104.0		1105	5.7	1.0	2	dbSNP_134	104	0,8600		0,0,4300	yes	missense	RETSAT	NM_017750.3	180	0,7,6496	AA,AG,GG		0.0,0.1589,0.0538	probably-damaging	369/611	85573110	7,12999	2203	4300	6503	85426621	SO:0001583	missense	54884	exon6			AK075261	CCDS1972.1	2p11.2	2008-02-05			ENSG00000042445	ENSG00000042445	1.3.99.23		25991	protein-coding gene	gene with protein product						12975309, 15358783	Standard	NM_017750		Approved	FLJ20296	uc002spd.3	Q6NUM9	OTTHUMG00000154611	ENST00000295802.4:c.1105C>T	2.37:g.85573110G>A	ENSP00000295802:p.Arg369Cys		85426621	NM_017750	A6NIK3|Q53R95|Q53SA9|Q6UX05|Q8N2H5|Q96FA4|Q9NXE5	Missense_Mutation	SNP	ENST00000295802.4	37	CCDS1972.1	.	.	.	.	.	.	.	.	.	.	G	16.37	3.103799	0.56291	0.001589	0.0	ENSG00000042445	ENST00000295802;ENST00000263854;ENST00000457495	T;T	0.27557	1.66;1.72	5.66	5.66	0.87406	.	0.173355	0.52532	D	0.000077	T	0.56804	0.2010	M	0.77103	2.36	0.49130	D	0.999754	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.65987	0.94;0.94;0.917	T	0.59156	-0.7507	10	0.62326	D	0.03	-19.3083	17.2509	0.87042	0.0:0.0:1.0:0.0	.	308;308;369	G5E9N3;B4DKE1;Q6NUM9	.;.;RETST_HUMAN	C	369;369;308	ENSP00000295802:R369C;ENSP00000405040:R308C	ENSP00000263854:R369C	R	-	1	0	RETSAT	85426621	0.912000	0.30974	0.995000	0.50966	0.073000	0.16967	3.515000	0.53429	2.672000	0.90937	0.467000	0.42956	CGC		0.582	RETSAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252489.1	NM_017750	
TEKT4	150483	broad.mit.edu	37	2	95539280	95539280	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:95539280C>T	ENST00000295201.4	+	2	651	c.514C>T	c.(514-516)Cgg>Tgg	p.R172W	AC097374.2_ENST00000568768.1_RNA	NM_144705.2	NP_653306.1	Q8WW24	TEKT4_HUMAN	tektin 4	172					cell projection organization (GO:0030030)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)|nucleus (GO:0005634)		p.R172W(1)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	28						CGAGCTCATCCGGAACATTCA	0.607																																					p.R172W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C514T	2						.						74.0	67.0	69.0					2																	95539280		2203	4300	6503	94903007	SO:0001583	missense	150483	exon2			AK097438	CCDS2005.1	2q11.2	2008-02-05			ENSG00000163060	ENSG00000163060			31012	protein-coding gene	gene with protein product							Standard	XM_005263876		Approved	MGC27019	uc002stw.1	Q8WW24	OTTHUMG00000130396	ENST00000295201.4:c.514C>T	2.37:g.95539280C>T	ENSP00000295201:p.Arg172Trp		94903007	NM_144705		Missense_Mutation	SNP	ENST00000295201.4	37	CCDS2005.1	.	.	.	.	.	.	.	.	.	.	.	15.21	2.766285	0.49574	.	.	ENSG00000163060	ENST00000295201	T	0.02763	4.17	1.71	0.625	0.17665	.	0.059263	0.64402	D	0.000005	T	0.10165	0.0249	M	0.84846	2.72	0.80722	D	1	D	0.76494	0.999	P	0.60173	0.87	T	0.01608	-1.1313	10	0.72032	D	0.01	-8.1561	4.823	0.13400	0.3613:0.6387:0.0:0.0	.	172	Q8WW24	TEKT4_HUMAN	W	172	ENSP00000295201:R172W	ENSP00000295201:R172W	R	+	1	2	TEKT4	94903007	1.000000	0.71417	0.978000	0.43139	0.861000	0.49209	0.230000	0.17852	-0.005000	0.14395	0.306000	0.20318	CGG		0.607	TEKT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252777.1	NM_144705	
B3GALT1	8708	broad.mit.edu	37	2	168725851	168725851	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:168725851delG	ENST00000392690.3	+	1	394	c.302delG	c.(301-303)tggfs	p.W101fs	AC016723.4_ENST00000430546.1_RNA|AC016723.4_ENST00000436982.2_RNA|B3GALT1_ENST00000305861.1_Frame_Shift_Del_p.W101fs			Q9Y5Z6	B3GT1_HUMAN	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 1	101					oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)	p.D103fs*10(1)		cervix(1)|endometrium(1)|large_intestine(1)|lung(9)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	18						AGAGAGACGTGGGGGGATGAG	0.473																																					p.W101fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.302delG	2						.						63.0	63.0	63.0					2																	168725851		2203	4300	6503	168434097	SO:0001589	frameshift_variant	8708	exon2			E07739	CCDS2227.1	2q24.3	2013-02-19			ENSG00000172318	ENSG00000172318		"""Beta 3-glycosyltransferases"""	916	protein-coding gene	gene with protein product		603093				9582303	Standard	NM_020981		Approved	beta3Gal-T1	uc002udz.1	Q9Y5Z6	OTTHUMG00000132163	ENST00000392690.3:c.302delG	2.37:g.168725851delG	ENSP00000376456:p.Trp101fs		168434097	NM_020981	D3DPB8|Q53SS2	Frame_Shift_Del	DEL	ENST00000392690.3	37	CCDS2227.1																																																																																				0.473	B3GALT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255211.2	NM_020981	
SGOL2	151246	broad.mit.edu	37	2	201436992	201436992	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:201436992delA	ENST00000357799.4	+	7	2021	c.1923delA	c.(1921-1923)ctafs	p.L641fs		NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN	shugoshin-like 2 (S. pombe)	641					meiotic sister chromatid cohesion, centromeric (GO:0051754)|mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)		p.G644fs*18(1)		NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						TGCATGGCCTAAAAAAAGGTA	0.333																																					p.L641fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1923delA	2						.						76.0	79.0	78.0					2																	201436992		1786	3980	5766	201145237	SO:0001589	frameshift_variant	151246	exon7			AY094614	CCDS42796.1	2q33.2	2008-02-05			ENSG00000163535	ENSG00000163535			30812	protein-coding gene	gene with protein product		612425					Standard	NM_001160046		Approved	TRIPIN, FLJ25211	uc002uvw.2	Q562F6	OTTHUMG00000154535	ENST00000357799.4:c.1923delA	2.37:g.201436992delA	ENSP00000350447:p.Leu641fs		201145237	NM_001160046	Q53RR9|Q53T20|Q86XY4|Q8IWK2|Q8IZK1|Q8N1Q5|Q96LQ3	Frame_Shift_Del	DEL	ENST00000357799.4	37	CCDS42796.1																																																																																				0.333	SGOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335834.1	NM_152524	
VIL1	7429	broad.mit.edu	37	2	219301848	219301850	+	Splice_Site	DEL	TCT	TCT	-	rs370515062		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	TCT	TCT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:219301848_219301850delTCT	ENST00000248444.5	+	17	2061_2063	c.1973_1975delTCT	c.(1972-1977)gtcttc>gtc	p.F660del	VIL1_ENST00000392114.2_Splice_Site_p.F349del	NM_007127.2	NP_009058.2	P09327	VILI_HUMAN	villin 1	660	Core.				actin filament capping (GO:0051693)|actin filament depolymerization (GO:0030042)|actin filament polymerization (GO:0030041)|actin filament severing (GO:0051014)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cytoplasmic actin-based contraction involved in cell motility (GO:0060327)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell differentiation (GO:0030855)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell migration (GO:0010634)|protein complex assembly (GO:0006461)|regulation of actin nucleation (GO:0051125)|regulation of cell shape (GO:0008360)|regulation of lamellipodium morphogenesis (GO:2000392)|regulation of wound healing (GO:0061041)|response to bacterium (GO:0009617)	actin filament bundle (GO:0032432)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|microvillus (GO:0005902)|ruffle (GO:0001726)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|identical protein binding (GO:0042802)|lysophosphatidic acid binding (GO:0035727)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)	p.F660delF(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(20)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Renal(207;0.0474)		Epithelial(149;6.88e-07)|all cancers(144;0.00013)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCTCAATAGGTCTTCTTCTGGAT	0.567																																					p.658_659del												.	.	1	Deletion - In frame(1)	large_intestine(1)	c.1973_1975del	2						.																																			219010094	SO:0001630	splice_region_variant	7429	exon17			X12901	CCDS2417.1	2q35	2012-10-02			ENSG00000127831	ENSG00000127831			12690	protein-coding gene	gene with protein product		193040		VIL		2846586	Standard	NM_007127		Approved	D2S1471	uc002via.3	P09327	OTTHUMG00000133112	ENST00000248444.5:c.1972-1TCT>-	2.37:g.219301854_219301856delTCT			219010092	NM_007127	B2R9A7|Q53S11|Q96AC8	In_Frame_Del	DEL	ENST00000248444.5	37	CCDS2417.1																																																																																				0.567	VIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256778.3	NM_007127	In_Frame_Del
PPP1R7	5510	broad.mit.edu	37	2	242102705	242102705	+	Silent	SNP	C	C	T	rs545930743		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr2:242102705C>T	ENST00000234038.6	+	7	1077	c.603C>T	c.(601-603)atC>atT	p.I201I	PPP1R7_ENST00000407025.1_Silent_p.I201I|PPP1R7_ENST00000404405.3_Silent_p.I195I|PPP1R7_ENST00000401987.1_Silent_p.I158I|PPP1R7_ENST00000402734.1_Silent_p.I142I|PPP1R7_ENST00000406106.3_Silent_p.I201I|PPP1R7_ENST00000485630.1_3'UTR|PPP1R7_ENST00000272983.8_Silent_p.I158I	NM_001282412.1|NM_001282413.1|NM_002712.1	NP_001269341.1|NP_001269342.1|NP_002703.1	Q15435	PP1R7_HUMAN	protein phosphatase 1, regulatory subunit 7	201					positive regulation of protein dephosphorylation (GO:0035307)|regulation of catalytic activity (GO:0050790)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	enzyme regulator activity (GO:0030234)|protein phosphatase type 1 regulator activity (GO:0008599)	p.I201I(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|ovary(3)	23		all_cancers(19;6.1e-33)|all_epithelial(40;1.07e-13)|Breast(86;0.000141)|Renal(207;0.00528)|all_lung(227;0.0446)|Ovarian(221;0.104)|Lung NSC(271;0.115)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.92e-32)|all cancers(36;5.35e-29)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-14)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.24e-08)|BRCA - Breast invasive adenocarcinoma(100;3.56e-06)|Lung(119;0.000588)|LUSC - Lung squamous cell carcinoma(224;0.0048)|Colorectal(34;0.0137)|COAD - Colon adenocarcinoma(134;0.096)		CACAGGCAATCGAAAATATCG	0.507													C|||	1	0.000199681	0.0	0.0014	5008	,	,		18757	0.0		0.0	False		,,,				2504	0.0				p.I201I	NSCLC(62;446 1299 5417 11238 27640)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C603T	2						.						177.0	187.0	184.0					2																	242102705		2203	4300	6503	241751378	SO:0001819	synonymous_variant	5510	exon7			AF067136	CCDS2546.1, CCDS63190.1, CCDS63192.1, CCDS63193.1, CCDS63194.1	2q37.3	2012-04-17	2011-10-04		ENSG00000115685	ENSG00000115685		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9295	protein-coding gene	gene with protein product		602877	"""protein phosphatase 1, regulatory (inhibitor) subunit 7"""			7498485, 7670491, 10231361	Standard	NM_001282413		Approved	sds22	uc002wat.1	Q15435	OTTHUMG00000133390	ENST00000234038.6:c.603C>T	2.37:g.242102705C>T			241751378	NM_002712	B4DFD4|B5MCY6|Q9UQE5|Q9UQE6|Q9Y6K4	Silent	SNP	ENST00000234038.6	37	CCDS2546.1	.	.	.	.	.	.	.	.	.	.	C	4.894	0.166124	0.09339	.	.	ENSG00000115685	ENST00000450367	.	.	.	5.03	-0.532	0.11890	.	.	.	.	.	T	0.49813	0.1579	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.34825	-0.9813	4	.	.	.	-15.4131	4.7303	0.12961	0.1275:0.2416:0.0:0.6309	.	.	.	.	L	176	.	.	S	+	2	0	PPP1R7	241751378	0.913000	0.31002	0.967000	0.41034	0.470000	0.32858	-0.084000	0.11268	-0.242000	0.09667	-0.238000	0.12139	TCG		0.507	PPP1R7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257244.4	NM_002712	
ZBED2	79413	broad.mit.edu	37	3	111312734	111312734	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:111312734C>T	ENST00000317012.4	-	2	1323	c.315G>A	c.(313-315)atG>atA	p.M105I	CD96_ENST00000438817.2_Intron|CD96_ENST00000283285.5_Intron|CD96_ENST00000352690.4_Intron	NM_024508.4	NP_078784.2	Q9BTP6	ZBED2_HUMAN	zinc finger, BED-type containing 2	105							DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.M105I(1)		large_intestine(3)|lung(1)|skin(2)	6						CCTCTCTGTGCATGCTTTTCA	0.637																																					p.M105I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G315A	3						.						50.0	48.0	49.0					3																	111312734		2203	4300	6503	112795424	SO:0001583	missense	79413	exon2			BC003536	CCDS2960.2	3p13-q13.2	2013-05-03			ENSG00000177494	ENSG00000177494		"""Zinc fingers, BED-type"""	20710	protein-coding gene	gene with protein product		615246				23533661	Standard	NM_024508		Approved	MGC10796	uc003dxy.3	Q9BTP6	OTTHUMG00000074061	ENST00000317012.4:c.315G>A	3.37:g.111312734C>T	ENSP00000321370:p.Met105Ile		112795424	NM_024508	D3DN62	Missense_Mutation	SNP	ENST00000317012.4	37	CCDS2960.2	.	.	.	.	.	.	.	.	.	.	C	15.65	2.895194	0.52121	.	.	ENSG00000177494	ENST00000317012	.	.	.	4.66	3.76	0.43208	Zinc finger, BED-type predicted (3);	0.000000	0.51477	U	0.000093	T	0.27169	0.0666	N	0.14661	0.345	0.21020	N	0.999802	P	0.51791	0.948	P	0.49421	0.61	T	0.05733	-1.0867	9	0.33940	T	0.23	-17.4135	9.5993	0.39593	0.2181:0.7819:0.0:0.0	.	105	Q9BTP6	ZBED2_HUMAN	I	105	.	ENSP00000321370:M105I	M	-	3	0	ZBED2	112795424	1.000000	0.71417	0.848000	0.33437	0.858000	0.48976	0.743000	0.26231	1.107000	0.41642	0.467000	0.42956	ATG		0.637	ZBED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157228.2	NM_024508	
SYN2	6854	broad.mit.edu	37	3	12228986	12228986	+	RNA	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:12228986C>T	ENST00000432424.2	+	0	7794							Q92777	SYN2_HUMAN	synapsin II						neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)	p.S427L(1)		breast(5)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)	18						tcctcctcctcGGCTCCTCAG	0.692																																					p.S495L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1484T	3						.						8.0	11.0	10.0					3																	12228986		1931	4011	5942	12203986			6854	exon13				CCDS74900.1, CCDS74901.1	3p25.2	2013-09-20			ENSG00000157152	ENSG00000157152			11495	protein-coding gene	gene with protein product		600755				8530057	Standard	XM_006713311		Approved	SYNII, SYNIIa, SYNIIb	uc003bwm.3	Q92777	OTTHUMG00000155335		3.37:g.12228986C>T			12203986	NM_133625	A8MY98	Missense_Mutation	SNP	ENST00000432424.2	37		.	.	.	.	.	.	.	.	.	.	C	12.17	1.856725	0.32791	.	.	ENSG00000157152	ENST00000540660	.	.	.	4.53	3.65	0.41850	.	0.681381	0.12175	N	0.492651	T	0.31544	0.0800	L	0.29908	0.895	0.21697	N	0.999585	B	0.17852	0.024	B	0.12156	0.007	T	0.26121	-1.0112	9	0.87932	D	0	-0.0152	8.7247	0.34463	0.1422:0.4667:0.3911:0.0	.	496	Q92777	SYN2_HUMAN	L	428	.	ENSP00000442512:S428L	S	+	2	0	SYN2	12203986	1.000000	0.71417	0.998000	0.56505	0.786000	0.44442	1.200000	0.32247	1.089000	0.41292	-0.175000	0.13238	TCG		0.692	SYN2-002	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000339528.3	NM_133625	
C3orf52	79669	broad.mit.edu	37	3	111831892	111831892	+	Silent	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:111831892T>C	ENST00000264848.5	+	5	608	c.549T>C	c.(547-549)agT>agC	p.S183S	C3orf52_ENST00000431717.2_Intron|C3orf52_ENST00000430855.1_Intron|C3orf52_ENST00000467942.2_3'UTR|MIR567_ENST00000385205.1_RNA	NM_024616.2	NP_078892	Q5BVD1	TTMP_HUMAN	chromosome 3 open reading frame 52	183						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.S183S(1)		endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4						ATATGATGAGTGAGGAGTTGG	0.438																																					p.S183S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T549C	3						.						147.0	136.0	140.0					3																	111831892		1972	4171	6143	113314582	SO:0001819	synonymous_variant	79669	exon5			AY830714	CCDS46887.1, CCDS54620.1	3q13.2	2006-01-30			ENSG00000114529	ENSG00000114529			26255	protein-coding gene	gene with protein product	"""TPA induced trans-membrane protein"""	611956				15737651	Standard	NM_024616		Approved	FLJ23186, TTMP	uc011bhs.2	Q5BVD1	OTTHUMG00000159230	ENST00000264848.5:c.549T>C	3.37:g.111831892T>C			113314582	NM_024616	B4DNV2|B4E0Z2|Q96AJ4|Q9H5Q1	Silent	SNP	ENST00000264848.5	37	CCDS46887.1																																																																																				0.438	C3orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353961.1	NM_024616	
STXBP5L	9515	broad.mit.edu	37	3	121001127	121001127	+	Missense_Mutation	SNP	C	C	T	rs77475405	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:121001127C>T	ENST00000273666.6	+	20	2396	c.2125C>T	c.(2125-2127)Cgt>Tgt	p.R709C	STXBP5L_ENST00000472879.1_Intron|STXBP5L_ENST00000492541.1_Missense_Mutation_p.R709C|STXBP5L_ENST00000471454.1_Intron|STXBP5L_ENST00000497029.1_Missense_Mutation_p.R709C	NM_014980.2	NP_055795.1	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	709					exocytosis (GO:0006887)|glucose homeostasis (GO:0042593)|negative regulation of insulin secretion (GO:0046676)|positive regulation of protein secretion (GO:0050714)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R709C(1)		NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(12)|lung(28)|ovary(7)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				GBM - Glioblastoma multiforme(114;0.0694)		CTTTTGCATGCGTGGCCTGTC	0.388													C|||	5	0.000998403	0.0	0.0	5008	,	,		13563	0.0		0.005	False		,,,				2504	0.0				p.R709C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2125T	3						.	C	CYS/ARG	1,3921		0,1,1960	105.0	94.0	97.0		2125	5.8	1.0	3	dbSNP_131	97	10,8326		0,10,4158	yes	missense	STXBP5L	NM_014980.2	180	0,11,6118	TT,TC,CC		0.12,0.0255,0.0897	benign	709/1187	121001127	11,12247	1961	4168	6129	122483817	SO:0001583	missense	9515	exon20			AB023223	CCDS43137.1	3q13.33-q21.1	2013-01-10			ENSG00000145087	ENSG00000145087		"""WD repeat domain containing"""	30757	protein-coding gene	gene with protein product		609381				10231032, 14767561	Standard	NM_014980		Approved	KIAA1006, LLGL4	uc003eec.4	Q9Y2K9	OTTHUMG00000159426	ENST00000273666.6:c.2125C>T	3.37:g.121001127C>T	ENSP00000273666:p.Arg709Cys		122483817	NM_014980	Q4G1B4|Q6PIC3	Missense_Mutation	SNP	ENST00000273666.6	37	CCDS43137.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	C	20.2	3.957053	0.73902	2.55E-4	0.0012	ENSG00000145087	ENST00000273666;ENST00000497029;ENST00000492541;ENST00000471262	T;T;T;T	0.38240	1.7;1.15;1.48;1.72	5.75	5.75	0.90469	.	0.722627	0.14706	N	0.303242	T	0.33411	0.0862	N	0.03608	-0.345	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.58160	-0.7685	10	0.62326	D	0.03	-12.692	19.9381	0.97149	0.0:1.0:0.0:0.0	.	709	Q9Y2K9	STB5L_HUMAN	C	709	ENSP00000273666:R709C;ENSP00000420287:R709C;ENSP00000420666:R709C;ENSP00000420167:R709C	ENSP00000273666:R709C	R	+	1	0	STXBP5L	122483817	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.540000	0.67205	2.701000	0.92244	0.585000	0.79938	CGT		0.388	STXBP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355256.3		
ADCY5	111	broad.mit.edu	37	3	123044275	123044275	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:123044275C>T	ENST00000462833.1	-	8	3194	c.1982G>A	c.(1981-1983)cGc>cAc	p.R661H	ADCY5_ENST00000309879.5_Missense_Mutation_p.R311H|ADCY5_ENST00000491190.1_Missense_Mutation_p.R294H	NM_183357.2	NP_899200.1	O95622	ADCY5_HUMAN	adenylate cyclase 5	661					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenosine receptor signaling pathway (GO:0001973)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)	p.R661H(2)		breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(22)|ovary(5)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(114;0.0342)		GGTTCTCTGGCGGTTCATCTT	0.592																																					p.R661H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1982A	3						.						174.0	178.0	177.0					3																	123044275		2203	4300	6503	124526965	SO:0001583	missense	111	exon8			U65473	CCDS3022.1, CCDS56274.1	3q21.1	2013-02-04			ENSG00000173175	ENSG00000173175	4.6.1.1	"""Adenylate cyclases"""	236	protein-coding gene	gene with protein product		600293				10481931	Standard	NM_183357		Approved	AC5	uc003egh.2	O95622	OTTHUMG00000159517	ENST00000462833.1:c.1982G>A	3.37:g.123044275C>T	ENSP00000419361:p.Arg661His		124526965	NM_183357	B7Z8A6|Q7RTV7|Q8NFM3	Missense_Mutation	SNP	ENST00000462833.1	37	CCDS3022.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.991873	0.74703	.	.	ENSG00000173175	ENST00000462833;ENST00000491190;ENST00000309879;ENST00000466617	T;D;D;T	0.82344	-1.19;-1.6;-1.59;-1.44	5.23	4.34	0.51931	.	0.000000	0.64402	D	0.000001	T	0.80182	0.4576	M	0.79258	2.445	0.80722	D	1	P;B	0.43542	0.81;0.218	B;B	0.31191	0.125;0.049	T	0.81750	-0.0790	10	0.41790	T	0.15	.	15.7407	0.77894	0.0:0.8631:0.1369:0.0	.	661;294	O95622;B3KWA8	ADCY5_HUMAN;.	H	661;294;311;220	ENSP00000419361:R661H;ENSP00000418537:R294H;ENSP00000308685:R311H;ENSP00000420082:R220H	ENSP00000308685:R311H	R	-	2	0	ADCY5	124526965	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.320000	0.79064	1.403000	0.46800	0.655000	0.94253	CGC		0.592	ADCY5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355889.4	XM_171048	
TXNRD3NB	645840	broad.mit.edu	37	3	126291319	126291319	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:126291319T>G	ENST00000404489.2	-	1	160	c.68A>C	c.(67-69)gAg>gCg	p.E23A	TXNRD3NB_ENST00000383572.2_Missense_Mutation_p.E23A			Q6F5E7	TR3N_HUMAN	thioredoxin reductase 3 neighbor	23								p.E23A(1)		endometrium(1)|large_intestine(2)|skin(2)	5						CCTCACAGGCTCCAGTGGCAT	0.602																																					p.E23A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A68C	3						.						45.0	43.0	44.0					3																	126291319		2203	4300	6503	127774009	SO:0001583	missense	645840	exon3			BC130546	CCDS33846.1	3q21.3	2011-04-13	2011-04-13	2011-04-13	ENSG00000206483	ENSG00000206483			33870	protein-coding gene	gene with protein product	"""thioredoxin reductase 3 new transcript 1"""		"""thioredoxin reductase 3 intronic transcript 1"""	TXNRD3IT1		15674732	Standard	NM_001039783		Approved	TR2IT1, TXNRD3NT1	uc003ejc.3	Q6F5E7	OTTHUMG00000162732	ENST00000404489.2:c.68A>C	3.37:g.126291319T>G	ENSP00000384071:p.Glu23Ala		127774009	NM_001039783		Missense_Mutation	SNP	ENST00000404489.2	37	CCDS33846.1	.	.	.	.	.	.	.	.	.	.	T	1.194	-0.634419	0.03584	.	.	ENSG00000206483	ENST00000383572;ENST00000404489	.	.	.	0.661	-0.769	0.11009	.	.	.	.	.	T	0.12178	0.0296	N	0.08118	0	0.09310	N	1	P	0.35481	0.504	B	0.29598	0.104	T	0.15607	-1.0431	7	0.87932	D	0	.	.	.	.	.	23	Q6F5E7	TR3N_HUMAN	A	23	.	ENSP00000373066:E23A	E	-	2	0	TXNRD3NB	127774009	0.001000	0.12720	0.002000	0.10522	0.002000	0.02628	-0.514000	0.06298	-0.310000	0.08766	-0.456000	0.05471	GAG		0.602	TXNRD3NB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370233.2	NM_001039783	
CNTN6	27255	broad.mit.edu	37	3	1371596	1371596	+	Silent	SNP	G	G	A	rs184379443		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:1371596G>A	ENST00000446702.2	+	11	1968	c.1341G>A	c.(1339-1341)acG>acA	p.T447T	CNTN6_ENST00000350110.2_Silent_p.T447T|CNTN6_ENST00000539053.1_Silent_p.T375T			Q9UQ52	CNTN6_HUMAN	contactin 6	447	Ig-like C2-type 5.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.T447T(1)		breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		AAAGAGGAACGGAGACCCTTA	0.333													G|||	1	0.000199681	0.0	0.0014	5008	,	,		14962	0.0		0.0	False		,,,				2504	0.0				p.T447T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1341A	3						.	G		1,4401	2.1+/-5.4	0,1,2200	51.0	52.0	52.0		1341	-11.4	0.0	3		52	0,8594		0,0,4297	no	coding-synonymous	CNTN6	NM_014461.2		0,1,6497	AA,AG,GG		0.0,0.0227,0.0077		447/1029	1371596	1,12995	2201	4297	6498	1346596	SO:0001819	synonymous_variant	27255	exon11			AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	2176	protein-coding gene	gene with protein product	"""neural adhesion molecule"""	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.1341G>A	3.37:g.1371596G>A			1346596	NM_014461	Q2KHM2	Silent	SNP	ENST00000446702.2	37	CCDS2557.1																																																																																				0.333	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461	
PLXND1	23129	broad.mit.edu	37	3	129275481	129275481	+	Silent	SNP	G	G	A	rs542768361		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:129275481G>A	ENST00000324093.4	-	35	5818	c.5640C>T	c.(5638-5640)taC>taT	p.Y1880Y	PLXND1_ENST00000504689.1_Silent_p.Y36Y|PLXND1_ENST00000393239.1_3'UTR	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1880					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)	p.Y1880Y(1)	PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						ACCTCTTGGCGTACTTATAAA	0.552																																					p.Y1880Y	Ovarian(97;366 1484 3738 22084 39045)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C5640T	3						.						150.0	135.0	140.0					3																	129275481		2203	4300	6503	130758171	SO:0001819	synonymous_variant	23129	exon35			AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"""Plexins"""	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.5640C>T	3.37:g.129275481G>A			130758171	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Silent	SNP	ENST00000324093.4	37	CCDS33854.1	.	.	.	.	.	.	.	.	.	.	G	8.297	0.819115	0.16607	.	.	ENSG00000004399	ENST00000506979	.	.	.	4.93	-6.7	0.01766	.	.	.	.	.	T	0.64659	0.2618	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.67864	-0.5560	4	.	.	.	.	16.6509	0.85189	0.6493:0.0:0.3507:0.0	.	.	.	.	C	224	.	.	R	-	1	0	PLXND1	130758171	0.000000	0.05858	0.869000	0.34112	0.909000	0.53808	-2.886000	0.00712	-1.421000	0.02007	-0.379000	0.06801	CGC		0.552	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103	
CEP63	80254	broad.mit.edu	37	3	134266208	134266208	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:134266208T>C	ENST00000337090.3	+	9	1134	c.961T>C	c.(961-963)Tac>Cac	p.Y321H	CEP63_ENST00000332047.5_Intron|CEP63_ENST00000513612.2_Missense_Mutation_p.Y321H|CEP63_ENST00000606977.1_Missense_Mutation_p.Y321H|CEP63_ENST00000354446.3_Intron|CEP63_ENST00000383229.3_Missense_Mutation_p.Y321H			Q96MT8	CEP63_HUMAN	centrosomal protein 63kDa	321					centriole replication (GO:0007099)|DNA damage checkpoint (GO:0000077)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|signal transduction in response to DNA damage (GO:0042770)|spindle assembly (GO:0051225)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|spindle pole (GO:0000922)		p.Y321H(1)		kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						AGAAAAGAAGTACACCTCTCA	0.453																																					p.Y321H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T961C	3						.						119.0	115.0	116.0					3																	134266208		2203	4300	6503	135748898	SO:0001583	missense	80254	exon10			AK056465	CCDS3086.1, CCDS43152.1, CCDS43153.1, CCDS43154.1	3q22.1	2014-02-20			ENSG00000182923	ENSG00000182923			25815	protein-coding gene	gene with protein product		614724				14654843, 24240477	Standard	NM_001042383		Approved	FLJ13386	uc003eqo.1	Q96MT8	OTTHUMG00000159725	ENST00000337090.3:c.961T>C	3.37:g.134266208T>C	ENSP00000336524:p.Tyr321His		135748898	NM_025180	D3DND8|D3DND9|D3DNE0|Q96CR0|Q9H8F5|Q9H8N0	Missense_Mutation	SNP	ENST00000337090.3	37	CCDS3086.1	.	.	.	.	.	.	.	.	.	.	T	6.847	0.525587	0.13066	.	.	ENSG00000182923	ENST00000337090;ENST00000383229;ENST00000513612	T;T;T	0.29655	2.29;1.56;2.29	4.98	1.13	0.20643	.	0.936960	0.09074	N	0.852375	T	0.24122	0.0584	L	0.51422	1.61	0.09310	N	1	B;P	0.38711	0.001;0.643	B;B	0.38056	0.002;0.264	T	0.23904	-1.0175	10	0.45353	T	0.12	4.9168	1.3137	0.02102	0.1396:0.1604:0.1675:0.5324	.	321;321	Q96MT8;Q96MT8-2	CEP63_HUMAN;.	H	321	ENSP00000336524:Y321H;ENSP00000372716:Y321H;ENSP00000426129:Y321H	ENSP00000336524:Y321H	Y	+	1	0	CEP63	135748898	0.000000	0.05858	0.027000	0.17364	0.079000	0.17450	-0.205000	0.09411	0.100000	0.17581	0.533000	0.62120	TAC		0.453	CEP63-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000470139.1	NM_025180	
CNTN6	27255	broad.mit.edu	37	3	1424991	1424991	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:1424991C>T	ENST00000446702.2	+	19	3043	c.2416C>T	c.(2416-2418)Cca>Tca	p.P806S	CNTN6_ENST00000350110.2_Missense_Mutation_p.P806S|CNTN6_ENST00000539053.1_Missense_Mutation_p.P734S			Q9UQ52	CNTN6_HUMAN	contactin 6	806	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.P806S(1)		breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		TCAACTGGCCCCAAGGGGAAC	0.438																																					p.P806S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2416T	3						.						186.0	194.0	191.0					3																	1424991		2203	4300	6503	1399991	SO:0001583	missense	27255	exon19			AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	2176	protein-coding gene	gene with protein product	"""neural adhesion molecule"""	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.2416C>T	3.37:g.1424991C>T	ENSP00000407822:p.Pro806Ser		1399991	NM_014461	Q2KHM2	Missense_Mutation	SNP	ENST00000446702.2	37	CCDS2557.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.237993	0.79800	.	.	ENSG00000134115	ENST00000446702;ENST00000539053;ENST00000350110	T;T;T	0.79749	-1.3;-1.3;-1.3	5.36	5.36	0.76844	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.56097	D	0.000021	D	0.93363	0.7884	H	0.96662	3.86	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95386	0.8477	10	0.87932	D	0	.	17.2576	0.87062	0.0:1.0:0.0:0.0	.	806	Q9UQ52	CNTN6_HUMAN	S	806;734;806	ENSP00000407822:P806S;ENSP00000442791:P734S;ENSP00000341882:P806S	ENSP00000341882:P806S	P	+	1	0	CNTN6	1399991	1.000000	0.71417	0.786000	0.31890	0.731000	0.41821	6.885000	0.75606	2.532000	0.85374	0.591000	0.81541	CCA		0.438	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461	
PPP2R3A	5523	broad.mit.edu	37	3	135797265	135797265	+	Silent	SNP	G	G	A	rs141556100	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:135797265G>A	ENST00000264977.3	+	7	3218	c.2601G>A	c.(2599-2601)tcG>tcA	p.S867S	PPP2R3A_ENST00000492624.2_Silent_p.S131S|PPP2R3A_ENST00000490467.1_Silent_p.S131S|PPP2R3A_ENST00000334546.2_Silent_p.S246S	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	867					eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)	p.S867S(1)		breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						AAATTACTTCGACAGAGATAA	0.279																																					p.S246S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G738A	3						.	G	,,	0,4406		0,0,2203	65.0	65.0	65.0		393,2601,738	-6.3	0.7	3	dbSNP_134	65	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	PPP2R3A	NM_001190447.1,NM_002718.4,NM_181897.2	,,	0,1,6500	AA,AG,GG		0.0116,0.0,0.0077	,,	131/415,867/1151,246/530	135797265	1,13001	2203	4298	6501	137279955	SO:0001819	synonymous_variant	5523	exon6			L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""EF-hand domain containing"""	9307	protein-coding gene	gene with protein product		604944	"""protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha"""	PPP2R3		8392071	Standard	NM_002718		Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.2601G>A	3.37:g.135797265G>A			137279955	NM_181897	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Silent	SNP	ENST00000264977.3	37	CCDS3087.1																																																																																				0.279	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718	
CLSTN2	64084	broad.mit.edu	37	3	140167446	140167446	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:140167446C>T	ENST00000458420.3	+	6	1063	c.873C>T	c.(871-873)gcC>gcT	p.A291A	RP11-68L1.2_ENST00000509191.1_RNA|RP11-68L1.2_ENST00000502712.1_RNA	NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	291					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)	p.A291A(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						GCGATGGAGCCGTGTCTTCCC	0.532										HNSCC(16;0.037)																											p.A291A	GBM(45;858 913 3709 36904 37282)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C873T	3						.						143.0	138.0	140.0					3																	140167446		2203	4300	6503	141650136	SO:0001819	synonymous_variant	64084	exon6			AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"""Cadherins / Cadherin-related"""	17448	protein-coding gene	gene with protein product	"""cadherin-related family member 13"""	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.873C>T	3.37:g.140167446C>T			141650136	NM_022131	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Silent	SNP	ENST00000458420.3	37	CCDS3112.1																																																																																				0.532	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131	
FGD5	152273	broad.mit.edu	37	3	14905701	14905701	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:14905701G>A	ENST00000285046.5	+	2	2702	c.2592G>A	c.(2590-2592)tcG>tcA	p.S864S	FGD5_ENST00000543601.1_Silent_p.S623S	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	864					actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)	p.S623S(1)		NS(2)|breast(2)|endometrium(3)|kidney(5)|large_intestine(10)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(1)	54						ACCTTACGTCGGATGAAGAGC	0.587																																					p.S864S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2592A	3						.						86.0	90.0	89.0					3																	14905701		1980	4159	6139	14880705	SO:0001819	synonymous_variant	152273	exon2			AK097276	CCDS46767.1	3p25.1	2013-01-10			ENSG00000154783	ENSG00000154783		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	19117	protein-coding gene	gene with protein product		614788					Standard	NM_152536		Approved	ZFYVE23, FLJ39957, FLJ00274	uc003bzc.3	Q6ZNL6	OTTHUMG00000155556	ENST00000285046.5:c.2592G>A	3.37:g.14905701G>A			14880705	NM_152536	B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Silent	SNP	ENST00000285046.5	37	CCDS46767.1	.	.	.	.	.	.	.	.	.	.	G	7.125	0.578692	0.13686	.	.	ENSG00000154783	ENST00000457774	.	.	.	4.37	-7.89	0.01174	.	.	.	.	.	T	0.44286	0.1286	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49133	-0.8971	4	.	.	.	-10.9797	5.856	0.18720	0.4727:0.0:0.2566:0.2707	.	.	.	.	R	78	.	.	G	+	1	0	FGD5	14880705	0.004000	0.15560	0.501000	0.27601	0.671000	0.39405	-2.467000	0.00993	-1.359000	0.02174	-1.232000	0.01568	GGA		0.587	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536	
TRPC1	7220	broad.mit.edu	37	3	142455286	142455286	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:142455286G>A	ENST00000476941.1	+	2	724	c.238G>A	c.(238-240)Gta>Ata	p.V80I	TRPC1_ENST00000273482.6_Missense_Mutation_p.V80I	NM_001251845.1	NP_001238774.1	P48995	TRPC1_HUMAN	transient receptor potential cation channel, subfamily C, member 1	80					axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to calcium ion (GO:0051592)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|sarcomere (GO:0030017)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|inositol 1,4,5 trisphosphate binding (GO:0070679)|ion channel binding (GO:0044325)|store-operated calcium channel activity (GO:0015279)	p.V80I(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(2)|stomach(3)|urinary_tract(1)	37						CATAAATTGCGTAGATGTGCT	0.343																																					p.V80I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G238A	3						.						154.0	155.0	155.0					3																	142455286		2203	4300	6503	143937976	SO:0001583	missense	7220	exon2			X89066	CCDS3126.1, CCDS58856.1	3q23	2011-12-14			ENSG00000144935	ENSG00000144935		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12333	protein-coding gene	gene with protein product		602343				7568191, 16382100	Standard	NM_001251845		Approved	HTRP-1	uc003evc.3	P48995	OTTHUMG00000159301	ENST00000476941.1:c.238G>A	3.37:g.142455286G>A	ENSP00000419313:p.Val80Ile		143937976	NM_003304	Q14CE4	Missense_Mutation	SNP	ENST00000476941.1	37	CCDS58856.1	.	.	.	.	.	.	.	.	.	.	G	14.95	2.688585	0.48097	.	.	ENSG00000144935	ENST00000476941;ENST00000273482	T;T	0.53423	0.62;0.62	5.75	5.75	0.90469	Ankyrin repeat-containing domain (3);	0.056070	0.64402	D	0.000001	T	0.44052	0.1275	L	0.46157	1.445	0.80722	D	1	P;P	0.47962	0.54;0.903	B;B	0.39068	0.081;0.289	T	0.32348	-0.9910	10	0.30854	T	0.27	0.2544	19.9376	0.97146	0.0:0.0:1.0:0.0	.	80;80	P48995;P48995-2	TRPC1_HUMAN;.	I	80	ENSP00000419313:V80I;ENSP00000273482:V80I	ENSP00000273482:V80I	V	+	1	0	TRPC1	143937976	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.238000	0.72350	2.711000	0.92665	0.655000	0.94253	GTA		0.343	TRPC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354520.1	NM_003304	
SERP1	27230	broad.mit.edu	37	3	150262252	150262252	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:150262252C>A	ENST00000479209.1	-	4	1466	c.194G>T	c.(193-195)gGc>gTc	p.G65V	EIF2A_ENST00000487799.1_5'Flank|SERP1_ENST00000239944.2_Missense_Mutation_p.G65V|EIF2A_ENST00000406576.3_5'Flank|SERP1_ENST00000487153.1_Missense_Mutation_p.A40S|EIF2A_ENST00000460851.1_5'Flank|EIF2A_ENST00000273435.5_5'Flank			Q9Y6X1	SERP1_HUMAN	stress-associated endoplasmic reticulum protein 1	65					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|endoplasmic reticulum unfolded protein response (GO:0030968)|glucose metabolic process (GO:0006006)|multicellular organismal aging (GO:0010259)|muscle organ morphogenesis (GO:0048644)|plasma membrane organization (GO:0007009)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of insulin secretion (GO:0032024)|positive regulation of organ growth (GO:0046622)|positive regulation of translation (GO:0045727)|post-embryonic development (GO:0009791)|protein glycosylation (GO:0006486)|protein transport (GO:0015031)|response to stress (GO:0006950)|skeletal system development (GO:0001501)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|ribosome (GO:0005840)		p.G65V(1)		large_intestine(1)|lung(3)	4			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			ACTTCACATGCCCATCCTGAT	0.323																																					p.G65V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G194T	3						.						99.0	103.0	102.0					3																	150262252		2203	4300	6503	151744942	SO:0001583	missense	27230	exon3			AK125413	CCDS3150.1	3q25.1	2007-12-07	2007-12-07		ENSG00000120742	ENSG00000120742			10759	protein-coding gene	gene with protein product	"""ribosome associated membrane protein 4"""					10601334, 11230166	Standard	NM_014445		Approved	RAMP4, FLJ43424	uc003exy.3	Q9Y6X1	OTTHUMG00000159769	ENST00000479209.1:c.194G>T	3.37:g.150262252C>A	ENSP00000420076:p.Gly65Val		151744942	NM_014445	D3DNI6	Missense_Mutation	SNP	ENST00000479209.1	37	CCDS3150.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.43|13.43	2.234937|2.234937	0.39498|0.39498	.|.	.|.	ENSG00000120742|ENSG00000120742	ENST00000487153|ENST00000239944;ENST00000479209	.|.	.|.	.|.	5.7|5.7	5.7|5.7	0.88788|0.88788	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.83524|0.83524	0.5273|0.5273	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.87578	.|0.998	D|D	0.84714|0.84714	0.0736|0.0736	5|8	0.87932|0.87932	D|D	0|0	-7.3118|-7.3118	19.049|19.049	0.93034|0.93034	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|65	.|Q9Y6X1	.|SERP1_HUMAN	S|V	40|65	.|.	ENSP00000420002:A40S|ENSP00000239944:G65V	A|G	-|-	1|2	0|0	SERP1|SERP1	151744942|151744942	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	6.803000|6.803000	0.75180|0.75180	2.869000|2.869000	0.98440|0.98440	0.558000|0.558000	0.71614|0.71614	GCA|GGC		0.323	SERP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357239.1	NM_014445	
SIAH2	6478	broad.mit.edu	37	3	150460020	150460020	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:150460020C>T	ENST00000312960.3	-	2	1410	c.883G>A	c.(883-885)Gac>Aac	p.D295N		NM_005067.5	NP_005058.3	O43255	SIAH2_HUMAN	siah E3 ubiquitin protein ligase 2	295	SBD.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|cellular protein catabolic process (GO:0044257)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|regulation of protein ubiquitination (GO:0031396)|regulation of RNA biosynthetic process (GO:2001141)|small GTPase mediated signal transduction (GO:0007264)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	ligase activity (GO:0016874)|transcription corepressor activity (GO:0003714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.D295N(1)		endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|pancreas(1)	16			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			ACAAGGCAGTCGCTGTTCATG	0.498																																					p.D295N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G883A	3						.						91.0	80.0	84.0					3																	150460020		2203	4300	6503	151942710	SO:0001583	missense	6478	exon2			U76248	CCDS3152.1	3q25	2012-02-23	2012-02-23		ENSG00000181788	ENSG00000181788	6.3.2.1		10858	protein-coding gene	gene with protein product		602213	"""seven in absentia (Drosophila) homolog 2"", ""seven in absentia homolog 2 (Drosophila)"""			9334332	Standard	NM_005067		Approved		uc003eyi.3	O43255	OTTHUMG00000159847	ENST00000312960.3:c.883G>A	3.37:g.150460020C>T	ENSP00000322457:p.Asp295Asn		151942710	NM_005067	O43270	Missense_Mutation	SNP	ENST00000312960.3	37	CCDS3152.1	.	.	.	.	.	.	.	.	.	.	C	33	5.230324	0.95207	.	.	ENSG00000181788	ENST00000312960	T	0.28069	1.63	5.81	5.81	0.92471	TRAF-type (1);Seven-in-absentia protein, TRAF-like domain (1);TRAF-like (1);	0.000000	0.85682	D	0.000000	T	0.65842	0.2730	M	0.93808	3.46	0.58432	D	0.999997	D	0.89917	1.0	D	0.97110	1.0	T	0.73170	-0.4067	10	0.56958	D	0.05	.	15.1984	0.73116	0.0:0.9312:0.0:0.0688	.	295	O43255	SIAH2_HUMAN	N	295	ENSP00000322457:D295N	ENSP00000322457:D295N	D	-	1	0	SIAH2	151942710	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	6.080000	0.71299	2.746000	0.94184	0.591000	0.81541	GAC		0.498	SIAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357697.1	NM_005067	
MED12L	116931	broad.mit.edu	37	3	150804740	150804740	+	Silent	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:150804740T>C	ENST00000474524.1	+	1	65	c.27T>C	c.(25-27)taT>taC	p.Y9Y	MED12L_ENST00000273432.4_Silent_p.Y9Y|MED12L_ENST00000422248.2_Silent_p.Y9Y|MED12L_ENST00000309237.4_Silent_p.Y9Y	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	9						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.Y9Y(1)		NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TTCTCAGCTATGAGCAGAGAC	0.652																																					p.Y9Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T27C	3						.						8.0	11.0	10.0					3																	150804740		2170	4281	6451	152287430	SO:0001819	synonymous_variant	116931	exon1			AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"""			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.27T>C	3.37:g.150804740T>C			152287430	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Silent	SNP	ENST00000474524.1	37	CCDS33876.1																																																																																				0.652	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002	
LXN	56925	broad.mit.edu	37	3	158383162	158383162	+	IGR	SNP	T	T	G	rs202136453		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	G	T	G	Unknown	Valid	Germline	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:158383162T>G	ENST00000264265.3	-	0	1116				GFM1_ENST00000486715.1_Missense_Mutation_p.F473V|GFM1_ENST00000490261.1_3'UTR|GFM1_ENST00000264263.5_Missense_Mutation_p.F492V|GFM1_ENST00000478576.1_Missense_Mutation_p.F473V	NM_020169.3	NP_064554.3	Q9BS40	LXN_HUMAN	latexin						detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|inflammatory response (GO:0006954)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	heparin binding (GO:0008201)|metalloendopeptidase inhibitor activity (GO:0008191)			breast(2)|endometrium(1)|kidney(2)	5			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)			TATTGGCAGGTTTACAAGAGA	0.338																																					p.F473V												.	.	0			c.T1417G	3						.						45.0	48.0	47.0					3																	158383162		2203	4297	6500	159865856	SO:0001628	intergenic_variant	85476	exon12			AF087851	CCDS3183.1	3q25.32	2004-05-10			ENSG00000079257	ENSG00000079257			13347	protein-coding gene	gene with protein product		609305					Standard	NM_020169		Approved		uc003fch.3	Q9BS40	OTTHUMG00000158807		3.37:g.158383162T>G			159865856	NM_024996	Q96PN2|Q9NQS6	Missense_Mutation	SNP	ENST00000264265.3	37	CCDS3183.1	.	.	.	.	.	.	.	.	.	.	T	30	5.051216	0.93740	.	.	ENSG00000168827	ENST00000486715;ENST00000478576;ENST00000264263	T;T;T	0.71341	-0.56;-0.56;-0.56	6.17	6.17	0.99709	Elongation factor G/III/V (1);	0.000000	0.85682	D	0.000000	T	0.81889	0.4918	L	0.56199	1.76	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.83188	-0.0085	10	0.87932	D	0	-16.9522	16.8222	0.85835	0.0:0.0:0.0:1.0	.	492;473;473	Q96RP9-2;Q96RP9;C9IZ01	.;EFGM_HUMAN;.	V	473;473;492	ENSP00000419038:F473V;ENSP00000418755:F473V;ENSP00000264263:F492V	ENSP00000264263:F492V	F	+	1	0	GFM1	159865856	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.730000	0.68546	2.371000	0.80710	0.533000	0.62120	TTT		0.338	LXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352284.1	NM_020169	
IQCJ-SCHIP1	100505385	broad.mit.edu	37	3	159605541	159605541	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:159605541G>T	ENST00000460298.1	+	5	1162	c.921G>T	c.(919-921)gaG>gaT	p.E307D	IQCJ-SCHIP1_ENST00000337808.6_Missense_Mutation_p.E347D|IQCJ-SCHIP1_ENST00000412423.2_Missense_Mutation_p.E334D|IQCJ-SCHIP1_ENST00000476809.1_Missense_Mutation_p.E396D|IQCJ-SCHIP1_ENST00000527095.1_Missense_Mutation_p.E115D|SCHIP1_ENST00000482804.1_Missense_Mutation_p.E120D|IQCJ-SCHIP1_ENST00000485419.1_Missense_Mutation_p.E423D|SCHIP1_ENST00000445224.2_Missense_Mutation_p.E104D					IQCJ-SCHIP1 readthrough									p.E347D(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(7)	12						CTACTGAAGAGGAGTCTGAAT	0.468																																					p.E115D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G345T	3						.						179.0	187.0	184.0					3																	159605541		2203	4300	6503	161088235	SO:0001583	missense	29970	exon4				CCDS56289.1, CCDS56291.1	3q25.33	2011-03-24			ENSG00000250588	ENSG00000250588			38842	other	readthrough							Standard	NM_001197113		Approved		uc003fcq.2		OTTHUMG00000162426	ENST00000460298.1:c.921G>T	3.37:g.159605541G>T	ENSP00000417305:p.Glu307Asp		161088235	NM_001197108		Missense_Mutation	SNP	ENST00000460298.1	37		.	.	.	.	.	.	.	.	.	.	G	11.34	1.609487	0.28623	.	.	ENSG00000250588;ENSG00000250588;ENSG00000250588;ENSG00000250588;ENSG00000250588;ENSG00000250588;ENSG00000151967;ENSG00000151967	ENST00000476809;ENST00000485419;ENST00000337808;ENST00000412423;ENST00000527095;ENST00000460298;ENST00000445224;ENST00000482804	T;T;T;T;T;T;T;T	0.55413	0.52;0.52;0.52;0.52;0.52;0.52;0.52;0.52	5.29	1.54	0.23209	.	0.090843	0.85682	D	0.000000	T	0.35278	0.0926	N	0.25647	0.755	0.29441	N	0.859147	B;B;B;B;B;B	0.20368	0.02;0.001;0.0;0.006;0.008;0.044	B;B;B;B;B;B	0.22601	0.04;0.006;0.001;0.016;0.028;0.019	T	0.21109	-1.0255	10	0.27785	T	0.31	.	9.1147	0.36750	0.3348:0.0:0.6652:0.0	.	307;120;104;334;347;423	C9J366;C9JWG6;Q9P0W5-4;Q9P0W5-2;Q9P0W5;Q9P0W5-5	.;.;.;.;SCHI1_HUMAN;.	D	396;423;347;334;115;307;104;120	ENSP00000418692:E396D;ENSP00000420182:E423D;ENSP00000337239:E347D;ENSP00000400942:E334D;ENSP00000436076:E115D;ENSP00000417305:E307D;ENSP00000404860:E104D;ENSP00000419230:E120D	ENSP00000337239:E347D	E	+	3	2	SCHIP1;IQCJ-SCHIP1	161088235	0.983000	0.35010	0.975000	0.42487	0.596000	0.36781	0.096000	0.15147	0.066000	0.16515	0.650000	0.86243	GAG		0.468	IQCJ-SCHIP1-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000352558.2	NM_001197113	
SMC4	10051	broad.mit.edu	37	3	160141307	160141307	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:160141307G>A	ENST00000357388.3	+	14	2565	c.2114G>A	c.(2113-2115)cGc>cAc	p.R705H	SMC4_ENST00000462787.1_Missense_Mutation_p.R705H|SMC4_ENST00000344722.5_Missense_Mutation_p.R705H|SMC4_ENST00000469762.1_Missense_Mutation_p.R680H|RP11-432B6.3_ENST00000483754.1_Intron|SMC4_ENST00000360111.2_Missense_Mutation_p.R705H	NM_001002800.1	NP_001002800.1	Q9NTJ3	SMC4_HUMAN	structural maintenance of chromosomes 4	705	Flexible hinge.				kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)|mitotic sister chromatid segregation (GO:0000070)	condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)	p.R705H(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(15)|lung(20)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			GAGAAAATTCGCCAAGCTTTT	0.353																																					p.R705H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2114A	3						.						97.0	109.0	105.0					3																	160141307		2202	4300	6502	161624001	SO:0001583	missense	10051	exon14			AF092564	CCDS3189.1, CCDS75046.1	3q26.1	2006-07-06	2006-07-06	2006-07-06	ENSG00000113810	ENSG00000113810		"""Structural maintenance of chromosomes proteins"""	14013	protein-coding gene	gene with protein product		605575	"""SMC4 (structural maintenance of chromosomes 4, yeast)-like 1"", ""SMC4 structural maintenance of chromosomes 4-like 1 (yeast)"""	SMC4L1		9789013, 10319587	Standard	NM_005496		Approved	hCAP-C, CAP-C	uc003fdh.3	Q9NTJ3	OTTHUMG00000159006	ENST00000357388.3:c.2114G>A	3.37:g.160141307G>A	ENSP00000349961:p.Arg705His		161624001	NM_001002800	A6NLT9|D3DNL8|O95752|Q8NDL4|Q9UNT9	Missense_Mutation	SNP	ENST00000357388.3	37	CCDS3189.1	.	.	.	.	.	.	.	.	.	.	G	18.26	3.585052	0.66105	.	.	ENSG00000113810	ENST00000357388;ENST00000360111;ENST00000469762;ENST00000462787;ENST00000344722;ENST00000545277	D;D;D;D;D	0.86562	-2.14;-2.14;-2.14;-2.14;-2.14	5.96	4.18	0.49190	SMCs flexible hinge (3);RecF/RecN/SMC (1);	0.099662	0.64402	D	0.000002	D	0.87605	0.6219	M	0.79693	2.465	0.58432	D	0.999995	P;P;P;P	0.52170	0.807;0.734;0.951;0.903	B;B;P;B	0.45881	0.151;0.272;0.496;0.168	D	0.86195	0.1615	10	0.54805	T	0.06	-1.4422	8.3075	0.32051	0.0631:0.1154:0.7016:0.1199	.	705;680;680;705	Q9NTJ3-2;B3KXX5;E9PD53;Q9NTJ3	.;.;.;SMC4_HUMAN	H	705;705;680;705;705;299	ENSP00000349961:R705H;ENSP00000353225:R705H;ENSP00000417964:R680H;ENSP00000420734:R705H;ENSP00000341382:R705H	ENSP00000341382:R705H	R	+	2	0	SMC4	161624001	1.000000	0.71417	0.989000	0.46669	0.915000	0.54546	3.975000	0.56859	0.862000	0.35528	0.650000	0.86243	CGC		0.353	SMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352862.1		
SLITRK3	22865	broad.mit.edu	37	3	164907221	164907221	+	Silent	SNP	G	G	A	rs140074591		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:164907221G>A	ENST00000475390.1	-	2	1841	c.1398C>T	c.(1396-1398)aaC>aaT	p.N466N	SLITRK3_ENST00000241274.3_Silent_p.N466N			O94933	SLIK3_HUMAN	SLIT and NTRK-like family, member 3	466					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)		p.N466N(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(66)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(5)	119						TCTCTATATCGTTGCCATTAA	0.473										HNSCC(40;0.11)			G|||	1	0.000199681	0.0	0.0	5008	,	,		17925	0.001		0.0	False		,,,				2504	0.0				p.N466N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1398T	3						.						57.0	59.0	58.0					3																	164907221		2203	4300	6503	166389915	SO:0001819	synonymous_variant	22865	exon2			AB020655	CCDS3197.1	3q26.1	2004-07-28			ENSG00000121871	ENSG00000121871			23501	protein-coding gene	gene with protein product		609679				10048485, 14557068	Standard	NM_014926		Approved	KIAA0848	uc003fek.3	O94933	OTTHUMG00000158072	ENST00000475390.1:c.1398C>T	3.37:g.164907221G>A			166389915	NM_014926	Q1RMY6	Silent	SNP	ENST00000475390.1	37	CCDS3197.1																																																																																				0.473	SLITRK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350126.1	NM_014926	
NCEH1	57552	broad.mit.edu	37	3	172351525	172351525	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:172351525G>A	ENST00000475381.1	-	5	1200	c.967C>T	c.(967-969)Cgc>Tgc	p.R323C	NCEH1_ENST00000543711.1_Missense_Mutation_p.R190C|NCEH1_ENST00000273512.3_Missense_Mutation_p.R355C|NCEH1_ENST00000538775.1_Missense_Mutation_p.R363C			Q6PIU2	NCEH1_HUMAN	neutral cholesterol ester hydrolase 1	323					lipid catabolic process (GO:0016042)|protein dephosphorylation (GO:0006470)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carboxylic ester hydrolase activity (GO:0052689)|phosphate ion binding (GO:0042301)|serine hydrolase activity (GO:0017171)	p.R355C(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|prostate(1)|skin(1)	15						GGGGCGGAGCGGGCATCCAGC	0.542																																					p.R363C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1087T	3						.						86.0	82.0	83.0					3																	172351525		2203	4300	6503	173834219	SO:0001583	missense	57552	exon5			AB037784	CCDS54681.1, CCDS54682.1	3q26.31	2009-07-23	2009-07-23	2009-07-23	ENSG00000144959	ENSG00000144959			29260	protein-coding gene	gene with protein product		613234	"""arylacetamide deacetylase-like 1"""	AADACL1		10718198	Standard	NM_001146276		Approved	KIAA1363, NCEH	uc011bpx.2	Q6PIU2	OTTHUMG00000156872	ENST00000475381.1:c.967C>T	3.37:g.172351525G>A	ENSP00000418571:p.Arg323Cys		173834219	NM_001146276	B7Z2K4|B7Z3A1|B7Z5U2|B7Z906|B7ZAW6|F5H7K4|Q86WZ1|Q9P2I4	Missense_Mutation	SNP	ENST00000475381.1	37		.	.	.	.	.	.	.	.	.	.	G	15.22	2.767775	0.49574	.	.	ENSG00000144959	ENST00000475381;ENST00000538775;ENST00000273512;ENST00000543711	T;T;T;T	0.12465	2.68;2.68;2.68;2.68	5.57	4.68	0.58851	Alpha/beta hydrolase fold-3 (1);	0.107874	0.64402	D	0.000011	T	0.42449	0.1203	M	0.90650	3.135	0.53688	D	0.999973	D;D	0.76494	0.999;0.999	P;P	0.61070	0.819;0.883	T	0.57021	-0.7882	10	0.87932	D	0	-4.7198	16.0715	0.80940	0.0:0.1389:0.861:0.0	.	363;323	F5H7K4;Q6PIU2	.;NCEH1_HUMAN	C	323;363;355;190	ENSP00000418571:R323C;ENSP00000442464:R363C;ENSP00000273512:R355C;ENSP00000443227:R190C	ENSP00000273512:R355C	R	-	1	0	NCEH1	173834219	0.908000	0.30866	0.632000	0.29296	0.351000	0.29236	1.662000	0.37418	1.306000	0.44926	0.491000	0.48974	CGC		0.542	NCEH1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000346367.3	NM_020792	
TBL1XR1	79718	broad.mit.edu	37	3	176767912	176767912	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:176767912G>A	ENST00000430069.1	-	7	834	c.575C>T	c.(574-576)aCa>aTa	p.T192I	TBL1XR1_ENST00000457928.2_Missense_Mutation_p.T192I|TBL1XR1-AS1_ENST00000454723.2_RNA			Q9BZK7	TBL1R_HUMAN	transducin (beta)-like 1 X-linked receptor 1	192					canonical Wnt signaling pathway (GO:0060070)|cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|histone binding (GO:0042393)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)	p.T192I(1)		breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(7)|liver(1)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31	all_cancers(143;1.44e-17)|Ovarian(172;0.00163)|Breast(254;0.214)	Acute lymphoblastic leukemia(1;0.00599)|all_hematologic(1;0.0632)|Prostate(884;0.215)	OV - Ovarian serous cystadenocarcinoma(80;9.83e-31)			TATTCTTGCTGTTGAGTCTCC	0.373																																					p.T192I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C575T	3						.						169.0	162.0	164.0					3																	176767912		1937	4134	6071	178250606	SO:0001583	missense	79718	exon7			AK022956	CCDS46961.1	3q26.33	2013-01-10	2008-01-17		ENSG00000177565	ENSG00000177565		"""WD repeat domain containing"""	29529	protein-coding gene	gene with protein product		608628	"""transducin (beta)-like 1X-linked receptor 1"""			11063877, 11931768	Standard	NM_024665		Approved	IRA1, FLJ12894, TBLR1, C21, DC42	uc003fix.4	Q9BZK7	OTTHUMG00000157140	ENST00000430069.1:c.575C>T	3.37:g.176767912G>A	ENSP00000405574:p.Thr192Ile		178250606	NM_024665	D3DNQ9|Q14DC3|Q9H2I1|Q9H9A1	Missense_Mutation	SNP	ENST00000430069.1	37	CCDS46961.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.977966	0.92982	.	.	ENSG00000177565	ENST00000430069;ENST00000457928	T;T	0.69306	-0.39;-0.39	5.23	5.23	0.72850	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.82176	0.4980	M	0.79011	2.435	0.80722	D	1	D	0.65815	0.995	D	0.70016	0.967	D	0.83816	0.0244	10	0.62326	D	0.03	-23.5005	18.1806	0.89776	0.0:0.0:1.0:0.0	.	192	Q9BZK7	TBL1R_HUMAN	I	192	ENSP00000405574:T192I;ENSP00000413251:T192I	ENSP00000405574:T192I	T	-	2	0	TBL1XR1	178250606	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.692000	0.98682	2.596000	0.87737	0.655000	0.94253	ACA		0.373	TBL1XR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347587.3	NM_024665	
PIK3CA	5290	broad.mit.edu	37	3	178952085	178952085	+	Missense_Mutation	SNP	A	A	G	rs121913279		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:178952085A>G	ENST00000263967.3	+	21	3297	c.3140A>G	c.(3139-3141)cAt>cGt	p.H1047R	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1047	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		H -> L (in BC; unknown pathological significance). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16353168}.|H -> R (in CLOVE, KERSEB, CRC, BC and OC; also found in an endometrial carcinoma sample; shows an increase in lipid kinase activity; oncogenic in vivo; requires binding to p85 regulatory subunit to induce cellular transformation but not interaction with RAS; may mimic the conformatitonal change triggered by the interaction with RAS; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells; increases lipid kinase activity; may alter the interaction of the PI3K/ PI4K kinase domain with the cell membrane). {ECO:0000269|PubMed:15016963, ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16114017, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|H -> Y (in MCAP; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.H1047R(1387)|p.H1047L(194)|p.H1047P(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AATGATGCACATCATGGTGGC	0.378	H1047L(EFM19_BREAST)|H1047R(BT20_BREAST)|H1047R(CAL29_URINARY_TRACT)|H1047R(CAL33_UPPER_AERODIGESTIVE_TRACT)|H1047R(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|H1047R(HCC1954_BREAST)|H1047R(HCT116_LARGE_INTESTINE)|H1047R(HSC2_UPPER_AERODIGESTIVE_TRACT)|H1047R(LS180_LARGE_INTESTINE)|H1047R(MCAS_OVARY)|H1047R(MDAMB453_BREAST)|H1047R(NCIH1048_LUNG)|H1047R(RKO_LARGE_INTESTINE)|H1047R(SKOV3_OVARY)|H1047R(T47D_BREAST)	57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											p.H1047R	Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	PIK3CA,breast,NS,Substitution - Missense,0 	.	1582	Substitution - Missense(1582)	breast(961)|large_intestine(245)|endometrium(114)|ovary(77)|urinary_tract(36)|upper_aerodigestive_tract(26)|lung(19)|central_nervous_system(19)|stomach(19)|haematopoietic_and_lymphoid_tissue(11)|thyroid(10)|NS(9)|liver(7)|kidney(6)|soft_tissue(6)|skin(4)|prostate(4)|pituitary(3)|pancreas(3)|meninges(1)|cervix(1)|bone(1)	c.A3140G	3						.						99.0	89.0	92.0					3																	178952085		1912	4130	6042	180434779	SO:0001583	missense	5290	exon21				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3140A>G	3.37:g.178952085A>G	ENSP00000263967:p.His1047Arg		180434779	NM_006218	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	14.34	2.506328	0.44558	.	.	ENSG00000121879	ENST00000263967	T	0.80214	-1.35	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	T	0.62466	0.2430	N	0.08118	0	0.80722	D	1	P	0.38597	0.639	B	0.28011	0.085	T	0.67526	-0.5648	10	0.40728	T	0.16	-21.2893	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1047	P42336	PK3CA_HUMAN	R	1047	ENSP00000263967:H1047R	ENSP00000263967:H1047R	H	+	2	0	PIK3CA	180434779	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	8.859000	0.92264	2.333000	0.79357	0.482000	0.46254	CAT		0.378	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2		
CCDC39	339829	broad.mit.edu	37	3	180364957	180364957	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:180364957C>T	ENST00000442201.2	-	11	1556	c.1437G>A	c.(1435-1437)gcG>gcA	p.A479A	CCDC39_ENST00000273654.4_Silent_p.A563A	NM_181426.1	NP_852091.1	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	479					axonemal dynein complex assembly (GO:0070286)|cilium-dependent cell motility (GO:0060285)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)		p.A563A(1)|p.A479A(1)		NS(1)|breast(1)|endometrium(4)|large_intestine(9)|lung(22)|ovary(6)|prostate(2)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			TTGCTTCAAGCGCTTGTTTTT	0.348																																					p.A479A												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G1437A	3						.						125.0	111.0	116.0					3																	180364957		1786	4055	5841	181847651	SO:0001819	synonymous_variant	339829	exon11			BC047103	CCDS46964.1	3q26.33	2012-07-27			ENSG00000145075	ENSG00000145075			25244	protein-coding gene	gene with protein product		613798				21131972	Standard	NM_181426		Approved	DKFZp434A128, CILD14, FAP59	uc010hxe.3	Q9UFE4	OTTHUMG00000157857	ENST00000442201.2:c.1437G>A	3.37:g.180364957C>T			181847651	NM_181426	B4E2H1	Silent	SNP	ENST00000442201.2	37	CCDS46964.1																																																																																				0.348	CCDC39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349783.3	XM_291028	
MCCC1	56922	broad.mit.edu	37	3	182740294	182740294	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:182740294C>A	ENST00000265594.4	-	16	1926	c.1780G>T	c.(1780-1782)Gac>Tac	p.D594Y	MCCC1_ENST00000489909.1_5'UTR|MCCC1_ENST00000539926.1_3'UTR|MCCC1_ENST00000492597.1_Missense_Mutation_p.D485Y	NM_020166.3	NP_064551.3	Q96RQ3	MCCA_HUMAN	methylcrotonoyl-CoA carboxylase 1 (alpha)	594					biotin metabolic process (GO:0006768)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)|methylcrotonoyl-CoA carboxylase activity (GO:0004485)	p.D594Y(1)		central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(17)|ovary(1)|pancreas(2)|prostate(1)|skin(2)	40	all_cancers(143;1.84e-14)|Ovarian(172;0.0355)		all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21)		Biotin(DB00121)	TAAGTGCAGTCTCCCTCGCTG	0.328																																					p.D594Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1780T	3						.						82.0	80.0	81.0					3																	182740294		2203	4300	6503	184222988	SO:0001583	missense	56922	exon16			AF310972	CCDS3241.1	3q27.1	2010-04-30	2010-04-30		ENSG00000078070	ENSG00000078070	6.4.1.4		6936	protein-coding gene	gene with protein product		609010	"""methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)"""			11170888	Standard	XR_241502		Approved	MCCA	uc003fle.3	Q96RQ3	OTTHUMG00000158355	ENST00000265594.4:c.1780G>T	3.37:g.182740294C>A	ENSP00000265594:p.Asp594Tyr		184222988	NM_020166	Q59ES4|Q9H959|Q9NS97	Missense_Mutation	SNP	ENST00000265594.4	37	CCDS3241.1	.	.	.	.	.	.	.	.	.	.	C	12.63	1.995064	0.35226	.	.	ENSG00000078070	ENST00000265594;ENST00000492597;ENST00000392616;ENST00000476176	D;D;D	0.95821	-3.82;-3.75;-3.55	5.67	4.81	0.61882	.	0.236397	0.41001	D	0.000980	D	0.94506	0.8231	L	0.40543	1.245	0.80722	D	1	D;P;P	0.58970	0.984;0.895;0.715	P;P;B	0.50617	0.646;0.646;0.438	D	0.94915	0.8068	10	0.87932	D	0	.	14.8719	0.70465	0.0:0.9304:0.0:0.0696	.	547;485;594	E9PG35;E9PHF7;Q96RQ3	.;.;MCCA_HUMAN	Y	594;485;444;547	ENSP00000265594:D594Y;ENSP00000419898:D485Y;ENSP00000420433:D547Y	ENSP00000265594:D594Y	D	-	1	0	MCCC1	184222988	0.905000	0.30787	0.896000	0.35187	0.203000	0.24098	3.432000	0.52824	1.554000	0.49487	-0.119000	0.15052	GAC		0.328	MCCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350775.1	NM_020166	
MCF2L2	23101	broad.mit.edu	37	3	182910845	182910845	+	Silent	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:182910845A>G	ENST00000328913.3	-	27	3255	c.2958T>C	c.(2956-2958)aaT>aaC	p.N986N	MCF2L2_ENST00000468976.1_5'UTR|MCF2L2_ENST00000473233.1_Silent_p.N986N	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2	986							Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.N986N(1)		breast(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(25)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			CTCTTTCCATATTTTTAATCC	0.507																																					p.N986N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T2958C	3						.						225.0	196.0	206.0					3																	182910845		2203	4300	6503	184393539	SO:0001819	synonymous_variant	23101	exon27			AB020668	CCDS3243.1	3q27	2012-07-24			ENSG00000053524	ENSG00000053524		"""Rho guanine nucleotide exchange factors"""	30319	protein-coding gene	gene with protein product							Standard	NM_015078		Approved	KIAA0861, ARHGEF22	uc003fli.1	Q86YR7	OTTHUMG00000158388	ENST00000328913.3:c.2958T>C	3.37:g.182910845A>G			184393539	NM_015078	O94942|Q6P2B8|Q6ZVJ5|Q8N318	Silent	SNP	ENST00000328913.3	37	CCDS3243.1																																																																																				0.507	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	NM_015078	
ABCC5	10057	broad.mit.edu	37	3	183669277	183669277	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:183669277T>C	ENST00000334444.6	-	20	3136	c.2896A>G	c.(2896-2898)Acc>Gcc	p.T966A	ABCC5_ENST00000265586.6_Missense_Mutation_p.T966A	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	966	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)	p.T966A(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cisplatin(DB00515)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Glutathione(DB00143)|Mercaptopurine(DB01033)|Probenecid(DB01032)|Rifampicin(DB01045)|Sildenafil(DB00203)|Sulfinpyrazone(DB01138)|Zidovudine(DB00495)	CCTGTGGGGGTCGTGTCAAAA	0.507																																					p.T966A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2896G	3						.						75.0	78.0	77.0					3																	183669277		1913	4150	6063	185151971	SO:0001583	missense	10057	exon20			AF104942	CCDS33898.1, CCDS43176.1	3q27	2012-03-14			ENSG00000114770	ENSG00000114770		"""ATP binding cassette transporters / subfamily C"""	56	protein-coding gene	gene with protein product		605251				8894702, 9827529	Standard	XM_005247058		Approved	MRP5, SMRP, EST277145, MOAT-C	uc003fmg.3	O15440	OTTHUMG00000156871	ENST00000334444.6:c.2896A>G	3.37:g.183669277T>C	ENSP00000333926:p.Thr966Ala		185151971	NM_005688	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Missense_Mutation	SNP	ENST00000334444.6	37	CCDS43176.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.098927	0.76870	.	.	ENSG00000114770	ENST00000334444;ENST00000265586	D;D	0.89939	-2.59;-2.59	6.11	4.93	0.64822	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.093893	0.64402	D	0.000001	D	0.96473	0.8849	H	0.97806	4.08	0.58432	D	0.999998	D;D	0.89917	1.0;0.998	D;D	0.85130	0.997;0.977	D	0.96872	0.9640	10	0.72032	D	0.01	-33.6669	12.6858	0.56946	0.1238:0.0:0.0:0.8762	.	966;966	Q86UX3;O15440	.;MRP5_HUMAN	A	966	ENSP00000333926:T966A;ENSP00000265586:T966A	ENSP00000265586:T966A	T	-	1	0	ABCC5	185151971	1.000000	0.71417	0.816000	0.32577	0.640000	0.38277	7.825000	0.86693	1.096000	0.41439	0.533000	0.62120	ACC		0.507	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688	
AP2M1	1173	broad.mit.edu	37	3	183898757	183898757	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:183898757C>T	ENST00000292807.5	+	6	698	c.550C>T	c.(550-552)Ctc>Ttc	p.L184F	EIF2B5_ENST00000444495.1_Intron|AP2M1_ENST00000382456.3_Missense_Mutation_p.L182F|AP2M1_ENST00000411763.2_Missense_Mutation_p.L209F|AP2M1_ENST00000461733.1_3'UTR|AP2M1_ENST00000439647.1_Missense_Mutation_p.L182F	NM_004068.3	NP_004059.2	Q96CW1	AP2M1_HUMAN	adaptor-related protein complex 2, mu 1 subunit	184	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of protein localization to plasma membrane (GO:1903077)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|transporter activity (GO:0005215)	p.L184F(1)		endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(1)	18	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.92e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TGTGAACCTGCTCATGTCCCC	0.592																																					p.L182F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C544T	3						.						135.0	144.0	141.0					3																	183898757		2059	4195	6254	185381451	SO:0001583	missense	1173	exon5			U36188	CCDS43177.1, CCDS43178.1	3q28	2008-07-18			ENSG00000161203	ENSG00000161203			564	protein-coding gene	gene with protein product	"""clathrin-associated/assembly/adaptor protein, medium 1"", ""plasma membrane adaptor AP-2 50kDA protein"", ""clathrin coat adaptor protein AP50"", ""clathrin adaptor complex AP2, mu subunit"", ""HA2 50 kDA subunit"", ""clathrin assembly protein complex 2 medium chain"", ""AP-2 mu 2 chain"""	601024		CLAPM1		8595912	Standard	NM_004068		Approved	AP50, mu2	uc003fmw.3	Q96CW1	OTTHUMG00000156822	ENST00000292807.5:c.550C>T	3.37:g.183898757C>T	ENSP00000292807:p.Leu184Phe		185381451	NM_001025205	A6NE12|D3DNT1|P20172|P53679	Missense_Mutation	SNP	ENST00000292807.5	37	CCDS43177.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.344947	0.82022	.	.	ENSG00000161203	ENST00000382456;ENST00000411763;ENST00000292807;ENST00000540821;ENST00000539646;ENST00000439647	T;T;T;T	0.22336	1.96;1.96;1.96;1.96	6.07	6.07	0.98685	Clathrin adaptor, mu subunit, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.57213	0.2038	M	0.93978	3.48	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.997;1.0;0.999	T	0.66496	-0.5909	10	0.87932	D	0	.	14.2055	0.65732	0.0:0.9239:0.0:0.0761	.	54;184;182	B4DTI4;Q96CW1;Q96CW1-2	.;AP2M1_HUMAN;.	F	182;209;184;124;169;182	ENSP00000371894:L182F;ENSP00000403362:L209F;ENSP00000292807:L184F;ENSP00000409081:L182F	ENSP00000292807:L184F	L	+	1	0	AP2M1	185381451	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.679000	0.68160	2.884000	0.98904	0.655000	0.94253	CTC		0.592	AP2M1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346013.1	NM_004068	
LSG1	55341	broad.mit.edu	37	3	194386286	194386286	+	Splice_Site	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:194386286C>A	ENST00000265245.5	-	5	835	c.521G>T	c.(520-522)aGt>aTt	p.S174I	AC046143.1_ENST00000408791.1_RNA	NM_018385.2	NP_060855.2	Q9H089	LSG1_HUMAN	large 60S subunit nuclear export GTPase 1	174	CP-type G. {ECO:0000255|PROSITE- ProRule:PRU01058}.				GTP catabolic process (GO:0006184)|nuclear export (GO:0051168)|protein transport (GO:0015031)|ribosome biogenesis (GO:0042254)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.S174I(1)		breast(2)|endometrium(3)|large_intestine(2)|lung(9)	16	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;4.34e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;7.55e-06)		GATAATTCACCTTCTCTCAAT	0.373																																					p.S174I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G521T	3						.						95.0	90.0	92.0					3																	194386286		2203	4300	6503	195867575	SO:0001630	splice_region_variant	55341	exon5				CCDS33922.1	3q29	2013-08-21	2013-08-21		ENSG00000041802	ENSG00000041802			25652	protein-coding gene	gene with protein product		610780	"""large subunit GTPase 1 homolog (S. cerevisiae)"""			11230166	Standard	NM_018385		Approved	FLJ11301	uc003fui.3	Q9H089	OTTHUMG00000156021	ENST00000265245.5:c.521+1G>T	3.37:g.194386286C>A			195867575	NM_018385	A0JLT4|A0PJK3|A6NI18|Q7L9H8|Q9NUK8	Missense_Mutation	SNP	ENST00000265245.5	37	CCDS33922.1	.	.	.	.	.	.	.	.	.	.	C	30	5.054764	0.93793	.	.	ENSG00000041802	ENST00000265245	T	0.61040	0.14	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	D	0.84288	0.5439	H	0.95224	3.64	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87861	0.2664	9	.	.	.	.	19.4154	0.94694	0.0:1.0:0.0:0.0	.	174	Q9H089	LSG1_HUMAN	I	174	ENSP00000265245:S174I	.	S	-	2	0	LSG1	195867575	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	7.414000	0.80117	2.884000	0.98904	0.655000	0.94253	AGT		0.373	LSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342740.1	NM_018385	Missense_Mutation
CRBN	51185	broad.mit.edu	37	3	3216859	3216859	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:3216859C>T	ENST00000231948.4	-	2	184	c.162G>A	c.(160-162)ccG>ccA	p.P54P	CRBN_ENST00000432408.2_Silent_p.P53P	NM_016302.3	NP_057386.2	Q96SW2	CRBN_HUMAN	cereblon	54					negative regulation of ion transmembrane transport (GO:0034766)|negative regulation of protein homooligomerization (GO:0032463)|positive regulation of protein homodimerization activity (GO:0090073)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP-dependent peptidase activity (GO:0004176)	p.P54P(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	11				Epithelial(13;0.00244)|OV - Ovarian serous cystadenocarcinoma(96;0.00617)|all cancers(10;0.0079)	Lenalidomide(DB00480)|Pomalidomide(DB08910)|Thalidomide(DB01041)	TATGTGATGTCGGCAGACTGG	0.308																																					p.P53P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G159A	3						.						234.0	226.0	229.0					3																	3216859		2203	4300	6503	3191859	SO:0001819	synonymous_variant	51185	exon2			BC017419	CCDS2562.1, CCDS54547.1	3p26.3	2014-05-27			ENSG00000113851	ENSG00000113851			30185	protein-coding gene	gene with protein product		609262	"""mental retardation, non-syndromic, autosomal recessive, 2A"""	MRT2A		15557513	Standard	NM_016302		Approved	MRT2	uc003bpq.3	Q96SW2	OTTHUMG00000090261	ENST00000231948.4:c.162G>A	3.37:g.3216859C>T			3191859	NM_001173482	B2R6H4|C9IZA9|C9JAH6|Q6AI62|Q6NVZ0|Q9UHW4	Silent	SNP	ENST00000231948.4	37	CCDS2562.1	.	.	.	.	.	.	.	.	.	.	C	9.287	1.049569	0.19827	.	.	ENSG00000113851	ENST00000424814;ENST00000450014	.	.	.	5.05	-0.286	0.12862	.	.	.	.	.	T	0.51652	0.1687	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40384	-0.9566	4	.	.	.	-15.8212	6.2246	0.20701	0.0:0.2986:0.1233:0.5782	.	.	.	.	Q	50	.	.	R	-	2	0	CRBN	3191859	0.881000	0.30235	0.999000	0.59377	0.988000	0.76386	-0.164000	0.09983	0.013000	0.14918	-0.351000	0.07748	CGA		0.308	CRBN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206579.3	NM_016302	
RARB	5915	broad.mit.edu	37	3	25622055	25622055	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:25622055C>T	ENST00000404969.1	+	5	649	c.649C>T	c.(649-651)Cga>Tga	p.R217*	RARB_ENST00000458646.1_Nonsense_Mutation_p.R98*|RARB_ENST00000437042.2_Nonsense_Mutation_p.R98*|RARB_ENST00000462272.1_3'UTR|RARB_ENST00000330688.4_Nonsense_Mutation_p.R210*			P10826	RARB_HUMAN	retinoic acid receptor, beta	217	Ligand-binding.				embryonic digestive tract development (GO:0048566)|embryonic eye morphogenesis (GO:0048048)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|glandular epithelial cell development (GO:0002068)|growth plate cartilage development (GO:0003417)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of myelination (GO:0031641)|retinal pigment epithelium development (GO:0003406)|signal transduction (GO:0007165)|striatum development (GO:0021756)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ureteric bud development (GO:0001657)|ventricular cardiac muscle cell differentiation (GO:0055012)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|drug binding (GO:0008144)|retinoic acid receptor activity (GO:0003708)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.R210*(1)		breast(3)|kidney(1)|large_intestine(10)|lung(11)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	28					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Tamibarotene(DB04942)|Tazarotene(DB00799)	TGCTGACCATCGAGTCCGACT	0.468																																					p.R210X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C628T	3						.						96.0	89.0	91.0					3																	25622055		2203	4300	6503	25597059	SO:0001587	stop_gained	5915	exon5			Y00291	CCDS2642.1, CCDS46775.1	3p24	2013-01-16			ENSG00000077092	ENSG00000077092		"""Nuclear hormone receptors"""	9865	protein-coding gene	gene with protein product		180220					Standard	NM_016152		Approved	HAP, NR1B2, RRB2	uc003cdh.3	P10826	OTTHUMG00000130480	ENST00000404969.1:c.649C>T	3.37:g.25622055C>T	ENSP00000385865:p.Arg217*		25597059	NM_000965	P12891|Q00989|Q15298|Q9UN48	Nonsense_Mutation	SNP	ENST00000404969.1	37		.	.	.	.	.	.	.	.	.	.	C	40	8.484011	0.98832	.	.	ENSG00000077092	ENST00000383772;ENST00000404969;ENST00000538226;ENST00000437042;ENST00000330688;ENST00000458646	.	.	.	5.2	4.32	0.51571	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.5985	0.62004	0.2826:0.7174:0.0:0.0	.	.	.	.	X	217;217;217;98;210;98	.	ENSP00000332296:R210X	R	+	1	2	RARB	25597059	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.859000	0.55987	1.186000	0.42985	0.491000	0.48974	CGA		0.468	RARB-201	KNOWN	basic	protein_coding	protein_coding		NM_000965, NM_016152	
ZCWPW2	152098	broad.mit.edu	37	3	28476697	28476697	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:28476697C>T	ENST00000383768.2	+	4	617	c.429C>T	c.(427-429)ggC>ggT	p.G143G	ZCWPW2_ENST00000421010.1_Silent_p.G143G			Q504Y3	ZCPW2_HUMAN	zinc finger, CW type with PWWP domain 2	143	PWWP. {ECO:0000255|PROSITE- ProRule:PRU00162}.						zinc ion binding (GO:0008270)	p.G143G(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(6)|ovary(2)	17						AATTCCTGGGCGATCCCCATT	0.378																																					p.G143G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C429T	3						.						110.0	113.0	112.0					3																	28476697		2203	4300	6503	28451701	SO:0001819	synonymous_variant	152098	exon3			BC065764	CCDS33723.1	3p23	2005-08-22			ENSG00000206559	ENSG00000206559			23574	protein-coding gene	gene with protein product						14607086	Standard	XM_005264892		Approved	ZCW2	uc003cei.3	Q504Y3	OTTHUMG00000155705	ENST00000383768.2:c.429C>T	3.37:g.28476697C>T			28451701	NM_001040432		Silent	SNP	ENST00000383768.2	37	CCDS33723.1	.	.	.	.	.	.	.	.	.	.	C	10.16	1.274439	0.23307	.	.	ENSG00000206559	ENST00000428875	.	.	.	6.06	-6.29	0.02013	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-21.7995	1.1994	0.01881	0.2214:0.143:0.3513:0.2843	.	.	.	.	X	127	.	.	R	+	1	2	ZCWPW2	28451701	0.967000	0.33354	0.961000	0.40146	0.964000	0.63967	-0.228000	0.09114	-0.777000	0.04572	-1.358000	0.01219	CGA		0.378	ZCWPW2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341318.1	XM_087384	
OSBPL10	114884	broad.mit.edu	37	3	31921213	31921213	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:31921213G>A	ENST00000396556.2	-	2	513	c.391C>T	c.(391-393)Ctg>Ttg	p.L131L	OSBPL10_ENST00000438237.2_Silent_p.L131L	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	131	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				lipid transport (GO:0006869)		cholesterol binding (GO:0015485)	p.L131L(2)		breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	34				STAD - Stomach adenocarcinoma(1;0.00406)		TCATCGCTCAGGGACACTATG	0.493																																					p.L131L												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C391T	3						.						106.0	99.0	101.0					3																	31921213		2203	4300	6503	31896217	SO:0001819	synonymous_variant	114884	exon2			AF392451	CCDS2651.1, CCDS54559.1	3p23	2013-01-10			ENSG00000144645	ENSG00000144645		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16395	protein-coding gene	gene with protein product		606738					Standard	NM_001174060		Approved		uc021wuu.1	Q9BXB5	OTTHUMG00000130672	ENST00000396556.2:c.391C>T	3.37:g.31921213G>A			31896217	NM_017784	B4E212|Q9BTU5	Silent	SNP	ENST00000396556.2	37	CCDS2651.1																																																																																				0.493	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2		
GLB1	2720	broad.mit.edu	37	3	33099692	33099692	+	Missense_Mutation	SNP	G	G	A	rs72555366	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:33099692G>A	ENST00000399402.3	-	6	663	c.532C>T	c.(532-534)Cgc>Tgc	p.R178C	GLB1_ENST00000445488.2_Missense_Mutation_p.R256C|GLB1_ENST00000307363.5_Missense_Mutation_p.R208C|GLB1_ENST00000307377.8_Intron	NM_001079811.1	NP_001073279	P16278	BGAL_HUMAN	galactosidase, beta 1	208					carbohydrate metabolic process (GO:0005975)|galactose catabolic process (GO:0019388)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|glycosphingolipid metabolic process (GO:0006687)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)	beta-galactosidase activity (GO:0004565)|galactoside binding (GO:0016936)	p.R208C(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	21		Melanoma(143;0.104)				AGATGGTGGCGAAAGCGCTTC	0.488													G|||	2	0.000399361	0.0	0.0029	5008	,	,		18386	0.0		0.0	False		,,,				2504	0.0				p.R208C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C622T	3	GRCh37	CM930342	GLB1	M	rs72555366	.						40.0	42.0	42.0					3																	33099692		1861	4106	5967	33074696	SO:0001583	missense	2720	exon6			M22590	CCDS43061.1, CCDS43062.1, CCDS46785.1	3p22.3	2012-10-02			ENSG00000170266	ENSG00000170266	3.2.1.23		4298	protein-coding gene	gene with protein product		611458	"""elastin receptor 1, 67kDa"", ""elastin receptor 1 (67kD)"""	ELNR1		110522, 3143362	Standard	NM_000404		Approved	EBP	uc003cfi.1	P16278	OTTHUMG00000155781	ENST00000399402.3:c.532C>T	3.37:g.33099692G>A	ENSP00000382333:p.Arg178Cys		33074696	NM_000404	B2R7H8|B7Z6B0|P16279	Missense_Mutation	SNP	ENST00000399402.3	37	CCDS43062.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	16.81	3.225238	0.58668	.	.	ENSG00000170266	ENST00000399402;ENST00000307363;ENST00000445488;ENST00000415454;ENST00000440656	D;D;D;D;D	0.98531	-4.98;-4.98;-4.98;-4.98;-4.98	5.57	4.67	0.58626	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.275466	0.40064	N	0.001193	D	0.99214	0.9727	M	0.94142	3.5	0.80722	A	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.80764	0.984;0.984;0.994	D	0.98979	1.0804	9	0.87932	D	0	-1.0692	15.5242	0.75890	0.0:0.0:0.8606:0.1394	.	208;208;256	Q53G40;P16278;B7Z6Q5	.;BGAL_HUMAN;.	C	178;208;256;49;77	ENSP00000382333:R178C;ENSP00000306920:R208C;ENSP00000393377:R256C;ENSP00000411813:R49C;ENSP00000411769:R77C	ENSP00000306920:R208C	R	-	1	0	GLB1	33074696	1.000000	0.71417	0.649000	0.29536	0.038000	0.13279	5.013000	0.64023	1.424000	0.47217	0.655000	0.94253	CGC		0.488	GLB1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000341570.2	NM_000404	
PDCD6IP	10015	broad.mit.edu	37	3	33906776	33906776	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:33906776G>A	ENST00000307296.3	+	17	2663	c.2286G>A	c.(2284-2286)gtG>gtA	p.V762V	PDCD6IP_ENST00000457054.2_Silent_p.V767V			Q8WUM4	PDC6I_HUMAN	programmed cell death 6 interacting protein	762	Interaction with EIAV p9.|Pro-rich.|Self-association.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell division (GO:0051301)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)	p.V762V(1)		central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|skin(1)|stomach(1)	23						CACCACCTGTGCTTCCAGCAA	0.522																																					p.V767V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2301A	3						.						44.0	46.0	45.0					3																	33906776		2203	4300	6503	33881780	SO:0001819	synonymous_variant	10015	exon17			BC020066	CCDS2660.1, CCDS54561.1	3p22.3	2012-08-30	2001-11-29		ENSG00000170248	ENSG00000170248			8766	protein-coding gene	gene with protein product	"""ALG-2 interacting protein X"""	608074	"""programmed cell death 6-interacting protein"""			9880530	Standard	NM_001162429		Approved	Alix, AIP1, Hp95	uc003cfy.4	Q8WUM4	OTTHUMG00000130751	ENST00000307296.3:c.2286G>A	3.37:g.33906776G>A			33881780	NM_001162429	C5MQH7|E9PFU1|Q6NUS1|Q9BX86|Q9NUN0|Q9P2H2|Q9UKL5	Silent	SNP	ENST00000307296.3	37	CCDS2660.1																																																																																				0.522	PDCD6IP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253251.2		
TRANK1	9881	broad.mit.edu	37	3	36871100	36871100	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:36871100C>T	ENST00000429976.2	-	22	8879	c.8632G>A	c.(8632-8634)Gca>Aca	p.A2878T	TRANK1_ENST00000301807.6_Missense_Mutation_p.A2328T|TRANK1_ENST00000428977.2_Missense_Mutation_p.A2328T	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	2878							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)	p.A2328T(1)|p.A2878T(1)|p.A2321T(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						CAGTCTCGTGCATCCCTGACT	0.488																																					p.A2878T												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.G8632A	3						.						113.0	114.0	114.0					3																	36871100		2048	4195	6243	36846104	SO:0001583	missense	9881	exon22			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.8632G>A	3.37:g.36871100C>T	ENSP00000416168:p.Ala2878Thr		36846104	NM_014831	Q8N8K0	Missense_Mutation	SNP	ENST00000429976.2	37	CCDS46789.2	.	.	.	.	.	.	.	.	.	.	C	17.77	3.470353	0.63625	.	.	ENSG00000168016	ENST00000428977;ENST00000429976;ENST00000301807	T;T;T	0.35789	1.29;1.71;1.29	5.17	5.17	0.71159	.	0.000000	0.40469	U	0.001086	T	0.50701	0.1631	L	0.36672	1.1	0.37072	D	0.898561	D	0.89917	1.0	D	0.83275	0.996	T	0.56685	-0.7938	10	0.59425	D	0.04	.	15.7786	0.78243	0.0:1.0:0.0:0.0	.	2878	O15050	TRNK1_HUMAN	T	2328;2878;2328	ENSP00000416826:A2328T;ENSP00000416168:A2878T;ENSP00000301807:A2328T	ENSP00000301807:A2328T	A	-	1	0	TRANK1	36846104	0.958000	0.32768	0.366000	0.25914	0.140000	0.21249	3.682000	0.54656	2.596000	0.87737	0.561000	0.74099	GCA		0.488	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831	
EPM2AIP1	9852	broad.mit.edu	37	3	37033489	37033489	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:37033489C>T	ENST00000322716.5	-	1	1306	c.1080G>A	c.(1078-1080)gcG>gcA	p.A360A	MLH1_ENST00000536378.1_5'Flank|MLH1_ENST00000458205.2_5'Flank|MLH1_ENST00000455445.2_5'Flank|MLH1_ENST00000231790.2_5'Flank|MLH1_ENST00000435176.1_5'Flank|MLH1_ENST00000539477.1_5'Flank	NM_014805.3	NP_055620.1	Q7L775	EPMIP_HUMAN	EPM2A (laforin) interacting protein 1	360			A -> S (in dbSNP:rs4647201).		positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of glycogen biosynthetic process (GO:0045725)|response to insulin (GO:0032868)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)		p.A360A(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|liver(1)|lung(12)|ovary(2)	27						AAACCAAGAACGCTTCCATTT	0.418																																					p.A360A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1080A	3						.						185.0	187.0	186.0					3																	37033489		1867	4107	5974	37008493	SO:0001819	synonymous_variant	9852	exon1			AB018309	CCDS46790.1	3p22.1	2003-03-26							19735	protein-coding gene	gene with protein product		607911					Standard	NM_014805		Approved	KIAA0766, FLJ11207	uc003cgk.3	Q7L775		ENST00000322716.5:c.1080G>A	3.37:g.37033489C>T			37008493	NM_014805	O94866|Q9H3L3	Silent	SNP	ENST00000322716.5	37	CCDS46790.1																																																																																				0.418	EPM2AIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000470593.1	NM_014805	
EPM2AIP1	9852	broad.mit.edu	37	3	37034067	37034067	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:37034067G>A	ENST00000322716.5	-	1	728	c.502C>T	c.(502-504)Cga>Tga	p.R168*	MLH1_ENST00000536378.1_5'Flank|MLH1_ENST00000458205.2_5'Flank|MLH1_ENST00000455445.2_5'Flank|MLH1_ENST00000231790.2_5'Flank|MLH1_ENST00000435176.1_5'Flank|MLH1_ENST00000539477.1_5'Flank	NM_014805.3	NP_055620.1	Q7L775	EPMIP_HUMAN	EPM2A (laforin) interacting protein 1	168					positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of glycogen biosynthetic process (GO:0045725)|response to insulin (GO:0032868)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)		p.R168*(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|liver(1)|lung(12)|ovary(2)	27						TCCCTGGCTCGGTTAAAAAGC	0.507																																					p.R168X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C502T	3						.						104.0	104.0	104.0					3																	37034067		1967	4157	6124	37009071	SO:0001587	stop_gained	9852	exon1			AB018309	CCDS46790.1	3p22.1	2003-03-26							19735	protein-coding gene	gene with protein product		607911					Standard	NM_014805		Approved	KIAA0766, FLJ11207	uc003cgk.3	Q7L775		ENST00000322716.5:c.502C>T	3.37:g.37034067G>A	ENSP00000406027:p.Arg168*		37009071	NM_014805	O94866|Q9H3L3	Nonsense_Mutation	SNP	ENST00000322716.5	37	CCDS46790.1	.	.	.	.	.	.	.	.	.	.	G	37	5.984705	0.97173	.	.	ENSG00000178567	ENST00000322716	.	.	.	5.26	4.39	0.52855	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07644	T	0.81	-0.8473	13.0999	0.59214	0.0:0.0:0.8387:0.1613	.	.	.	.	X	168	.	ENSP00000406027:R168X	R	-	1	2	EPM2AIP1	37009071	0.262000	0.24073	0.555000	0.28281	0.978000	0.69477	2.750000	0.47500	1.432000	0.47375	0.563000	0.77884	CGA		0.507	EPM2AIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000470593.1	NM_014805	
GOLGA4	2803	broad.mit.edu	37	3	37323570	37323570	+	Missense_Mutation	SNP	G	G	A	rs372845682		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:37323570G>A	ENST00000361924.2	+	3	658	c.284G>A	c.(283-285)cGa>cAa	p.R95Q	GOLGA4_ENST00000435830.2_Intron|GOLGA4_ENST00000444882.1_Missense_Mutation_p.R95Q|GOLGA4_ENST00000356847.4_Missense_Mutation_p.R117Q	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	95					Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)	p.R95Q(1)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						TCTTTGGTACGAACATCTTCC	0.488																																					p.R117Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G350A	3						.	G	GLN/ARG,GLN/ARG	0,4406		0,0,2203	100.0	99.0	99.0		350,284	5.8	1.0	3		99	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	GOLGA4	NM_001172713.1,NM_002078.4	43,43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	117/2244,95/2231	37323570	1,13005	2203	4300	6503	37298574	SO:0001583	missense	2803	exon4			U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"""golgin 245"""	602509	"""golgi autoantigen, golgin subfamily a, 4"""			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.284G>A	3.37:g.37323570G>A	ENSP00000354486:p.Arg95Gln		37298574	NM_001172713	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	ENST00000361924.2	37	CCDS2666.1	.	.	.	.	.	.	.	.	.	.	G	37	6.001799	0.97189	0.0	1.16E-4	ENSG00000144674	ENST00000361924;ENST00000444882;ENST00000356847;ENST00000450863	T;T	0.34072	1.57;1.38	5.8	5.8	0.92144	.	0.000000	0.30565	N	0.009342	T	0.59004	0.2162	L	0.54323	1.7	0.58432	D	0.999997	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.996;0.996;0.996;0.998	T	0.57653	-0.7774	10	0.66056	D	0.02	.	20.0706	0.97721	0.0:0.0:1.0:0.0	.	95;117;95;117	Q86W71;F8W8Q7;Q13439;E7EVX2	.;.;GOGA4_HUMAN;.	Q	95;95;117;117	ENSP00000354486:R95Q;ENSP00000349305:R117Q	ENSP00000349305:R117Q	R	+	2	0	GOLGA4	37298574	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	9.320000	0.96346	2.744000	0.94065	0.655000	0.94253	CGA		0.488	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078	
SLC22A14	9389	broad.mit.edu	37	3	38349170	38349170	+	Missense_Mutation	SNP	C	C	T	rs1078846		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:38349170C>T	ENST00000273173.4	+	3	825	c.734C>T	c.(733-735)tCg>tTg	p.S245L	SLC22A14_ENST00000448498.1_Missense_Mutation_p.S245L	NM_004803.3	NP_004794.2	Q9Y267	S22AE_HUMAN	solute carrier family 22, member 14	245			S -> L (in dbSNP:rs1078846).		organic cation transport (GO:0015695)	integral component of plasma membrane (GO:0005887)	organic cation transmembrane transporter activity (GO:0015101)	p.S245L(1)		central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(5)|prostate(2)|skin(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0554)|Kidney(284;0.0696)		TTTGGCATCTCGCAGTCAGTG	0.577																																					p.S245L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C734T	3						.						188.0	179.0	182.0					3																	38349170		2203	4300	6503	38324174	SO:0001583	missense	9389	exon3			AB011082	CCDS2677.1	3p21.3	2013-05-22	2008-01-11	2003-10-15	ENSG00000144671	ENSG00000144671		"""Solute carriers"""	8495	protein-coding gene	gene with protein product		604048	"""organic cationic transporter-like 4"", ""solute carrier family 22 (organic cation transporter), member 14"""	ORCTL4		10072596	Standard	NM_004803		Approved	OCTL2	uc003cib.2	Q9Y267	OTTHUMG00000131082	ENST00000273173.4:c.734C>T	3.37:g.38349170C>T	ENSP00000273173:p.Ser245Leu		38324174	NM_004803	A0AVS9|A1L4H6|B2RCX3|Q6DJT3	Missense_Mutation	SNP	ENST00000273173.4	37	CCDS2677.1	.	.	.	.	.	.	.	.	.	.	C	11.62	1.694104	0.30052	.	.	ENSG00000144671	ENST00000466887;ENST00000448498;ENST00000423219;ENST00000273173	T;T;T	0.74315	-0.23;-0.83;-0.83	5.0	-0.945	0.10388	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.368237	0.29233	N	0.012744	T	0.55970	0.1954	L	0.31294	0.92	0.09310	N	1	B	0.18166	0.026	B	0.16289	0.015	T	0.49716	-0.8910	10	0.87932	D	0	.	5.8782	0.18840	0.0:0.3028:0.4183:0.2789	rs1078846;rs1078846	245	Q9Y267	S22AE_HUMAN	L	113;245;245;245	ENSP00000442528:S113L;ENSP00000396283:S245L;ENSP00000273173:S245L	ENSP00000273173:S245L	S	+	2	0	SLC22A14	38324174	0.000000	0.05858	0.006000	0.13384	0.001000	0.01503	-0.046000	0.11983	-0.017000	0.14103	-0.137000	0.14449	TCG		0.577	SLC22A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253742.3	NM_004803	
ZNF619	285267	broad.mit.edu	37	3	40529660	40529660	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:40529660delT	ENST00000314686.5	+	6	2016	c.1611delT	c.(1609-1611)catfs	p.H537fs	ZNF619_ENST00000520737.1_3'UTR|ZNF619_ENST00000456778.1_Frame_Shift_Del_p.H509fs|ZNF619_ENST00000522736.1_Frame_Shift_Del_p.H544fs|ZNF619_ENST00000429348.2_Frame_Shift_Del_p.H553fs|ZNF619_ENST00000521353.1_Frame_Shift_Del_p.H593fs|ZNF619_ENST00000432264.2_Frame_Shift_Del_p.H553fs|ZNF619_ENST00000447116.2_Frame_Shift_Del_p.H593fs			Q8N2I2	ZN619_HUMAN	zinc finger protein 619	537					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.Q540fs*>21(1)		breast(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		AAATAGCACATTTTTTTCAGG	0.488																																					p.H509fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1527delT	3						.						118.0	116.0	116.0					3																	40529660		2203	4300	6503	40504664	SO:0001589	frameshift_variant	285267	exon4			AK075245	CCDS46801.1, CCDS46802.1, CCDS46803.1	3p21.33	2013-01-08			ENSG00000177873	ENSG00000177873		"""Zinc fingers, C2H2-type"", ""-"""	26910	protein-coding gene	gene with protein product							Standard	NM_001145083		Approved	FLJ90764	uc011azb.2	Q8N2I2	OTTHUMG00000131391	ENST00000314686.5:c.1611delT	3.37:g.40529660delT	ENSP00000322529:p.His537fs		40504664	NM_001145083	B4E271|C9JRN5|D4PHA2|E9PCD9	Frame_Shift_Del	DEL	ENST00000314686.5	37																																																																																					0.488	ZNF619-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000254180.2	NM_173656	
VIPR1	7433	broad.mit.edu	37	3	42560743	42560743	+	Silent	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:42560743C>A	ENST00000325123.4	+	3	326	c.213C>A	c.(211-213)acC>acA	p.T71T	VIPR1_ENST00000473575.1_3'UTR|VIPR1_ENST00000433647.1_Silent_p.T30T|VIPR1_ENST00000438259.2_5'UTR|VIPR1-AS1_ENST00000593621.1_RNA|VIPR1-AS1_ENST00000602176.1_RNA|VIPR1-AS1_ENST00000452639.3_RNA|VIPR1_ENST00000543411.1_Silent_p.T24T|VIPR1-AS1_ENST00000596630.1_RNA|VIPR1-AS1_ENST00000600342.1_RNA|VIPR1-AS1_ENST00000593611.1_RNA|VIPR1-AS1_ENST00000601312.1_RNA|VIPR1-AS1_ENST00000598837.1_RNA	NM_001251885.1|NM_004624.3	NP_001238814.1|NP_004615.2	P32241	VIPR1_HUMAN	vasoactive intestinal peptide receptor 1	71					digestion (GO:0007586)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|muscle contraction (GO:0006936)|positive regulation of cell proliferation (GO:0008284)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	vasoactive intestinal polypeptide receptor activity (GO:0004999)	p.T71T(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|ovary(2)|skin(1)|urinary_tract(3)	18				KIRC - Kidney renal clear cell carcinoma(284;0.241)		ACAACCTCACCTGCTGGCCAG	0.597																																					p.T71T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C213A	3						.						100.0	83.0	89.0					3																	42560743		2203	4300	6503	42535747	SO:0001819	synonymous_variant	7433	exon3			AH005329	CCDS2698.1, CCDS58827.1, CCDS58828.1, CCDS58829.1	3p22	2012-08-10			ENSG00000114812	ENSG00000114812		"""GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"""	12694	protein-coding gene	gene with protein product	"""VIP and PACAP receptor 1"""	192321				7708752	Standard	NM_004624		Approved	VPAC1, RDC1, HVR1, VPAC1R	uc003clf.2	P32241	OTTHUMG00000131792	ENST00000325123.4:c.213C>A	3.37:g.42560743C>A			42535747	NM_004624	A5JUT9|B3KPV1|B4DEB5|B4DGI4|F5H1F5|G3V0I1|Q15871|Q6P2M6	Silent	SNP	ENST00000325123.4	37	CCDS2698.1																																																																																				0.597	VIPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254728.4	NM_004624	
POMGNT2	84892	broad.mit.edu	37	3	43121653	43121653	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:43121653C>T	ENST00000344697.2	-	2	1616	c.1271G>A	c.(1270-1272)cGt>cAt	p.R424H	POMGNT2_ENST00000441964.1_Missense_Mutation_p.R424H	NM_032806.5	NP_116195.2	Q8NAT1	PMGT2_HUMAN	protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-)	424					protein O-linked glycosylation (GO:0006493)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein O-GlcNAc transferase activity (GO:0097363)	p.R424H(1)									TTGCAGGATACGGGCTTGCTC	0.622																																					p.R424H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1271A	3						.						41.0	40.0	40.0					3																	43121653		2203	4300	6503	43096657	SO:0001583	missense	84892	exon2			AK092147	CCDS2709.1	3p22.1	2014-07-15	2013-08-22	2013-08-22	ENSG00000144647	ENSG00000144647			25902	protein-coding gene	gene with protein product		614828	"""chromosome 3 open reading frame 39"", ""glycosyltransferase-like domain containing 2"""	C3orf39, GTDC2		12477932	Standard	NM_032806		Approved	FLJ14566, AGO61	uc003cmr.2	Q8NAT1	OTTHUMG00000133038	ENST00000344697.2:c.1271G>A	3.37:g.43121653C>T	ENSP00000344125:p.Arg424His		43096657	NM_032806	B3KWC3|Q96SY3	Missense_Mutation	SNP	ENST00000344697.2	37	CCDS2709.1	.	.	.	.	.	.	.	.	.	.	C	18.11	3.551883	0.65311	.	.	ENSG00000144647	ENST00000441964;ENST00000344697	T;T	0.78246	-1.16;-1.16	5.23	5.23	0.72850	.	0.054192	0.85682	D	0.000000	D	0.83216	0.5206	L	0.61387	1.9	0.80722	D	1	D	0.62365	0.991	P	0.54965	0.765	T	0.81703	-0.0812	10	0.33940	T	0.23	-12.0407	18.2115	0.89872	0.0:1.0:0.0:0.0	.	424	Q8NAT1	AGO61_HUMAN	H	424	ENSP00000408992:R424H;ENSP00000344125:R424H	ENSP00000344125:R424H	R	-	2	0	C3orf39	43096657	1.000000	0.71417	0.945000	0.38365	0.635000	0.38103	4.859000	0.62954	2.614000	0.88457	0.650000	0.86243	CGT		0.622	POMGNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256643.1	NM_032806	
CCR9	10803	broad.mit.edu	37	3	45943177	45943177	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:45943177C>T	ENST00000357632.2	+	3	1077	c.897C>T	c.(895-897)ttC>ttT	p.F299F	CCR9_ENST00000422395.1_3'UTR|Y_RNA_ENST00000364765.1_RNA|CCR9_ENST00000355983.2_Silent_p.F287F|LZTFL1_ENST00000539217.1_Intron|LZTFL1_ENST00000536047.1_Intron|CCR9_ENST00000395963.2_Silent_p.F287F	NM_001256369.1|NM_031200.2	NP_001243298.1|NP_112477.1	P51686	CCR9_HUMAN	chemokine (C-C motif) receptor 9	299					cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)	p.F299F(1)		breast(1)|endometrium(4)|large_intestine(8)|lung(2)|ovary(2)|prostate(2)|skin(1)	20				BRCA - Breast invasive adenocarcinoma(193;0.00118)|KIRC - Kidney renal clear cell carcinoma(197;0.0182)|Kidney(197;0.0214)		ACATCTGCTTCCAGGTCACCC	0.502																																					p.F287F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C861T	3						.						165.0	145.0	152.0					3																	45943177		2203	4300	6503	45918181	SO:0001819	synonymous_variant	10803	exon2			AJ132337	CCDS2732.1, CCDS2733.1	3p21.31	2012-09-20			ENSG00000173585	ENSG00000173585		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1610	protein-coding gene	gene with protein product		604738		GPR28		10229797	Standard	NM_006641		Approved	GPR-9-6, CDw199	uc003coz.2	P51686	OTTHUMG00000133450	ENST00000357632.2:c.897C>T	3.37:g.45943177C>T			45918181	NM_006641	Q4VBM3|Q549E0|Q9UQQ6	Silent	SNP	ENST00000357632.2	37	CCDS2732.1																																																																																				0.502	CCR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257323.2		
PRSS50	29122	broad.mit.edu	37	3	46783880	46783880	+	Intron	SNP	A	A	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:46783880A>T	ENST00000460241.1	-	4	1129				PRSS45_ENST00000442359.2_Missense_Mutation_p.L216Q			Q9UI38	TSP50_HUMAN	protease, serine, 50						proteolysis (GO:0006508)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)	serine-type endopeptidase activity (GO:0004252)|threonine-type endopeptidase activity (GO:0004298)	p.L216Q(1)		endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11						GCACAGGAACAGGAGGCAGGC	0.562																																					p.L216Q	Pancreas(41;915 1239 11561 17469)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T647A	3						.						196.0	252.0	233.0					3																	46783880		2124	4253	6377	46758884	SO:0001627	intron_variant	377047	exon4			AF100707	CCDS2745.1	3p21.31	2011-05-24			ENSG00000206549	ENSG00000206549		"""Serine peptidases / Serine peptidases"""	17910	protein-coding gene	gene with protein product	"""cancer/testis antigen 20"", ""testes specific protease 50"""	607950				10397268	Standard	NM_013270		Approved	TSP50, CT20	uc003cqe.1	Q9UI38	OTTHUMG00000164067	ENST00000460241.1:c.541+6234T>A	3.37:g.46783880A>T			46758884	NM_199183		Missense_Mutation	SNP	ENST00000460241.1	37	CCDS2745.1	.	.	.	.	.	.	.	.	.	.	A	12.95	2.091500	0.36952	.	.	ENSG00000188086	ENST00000331814;ENST00000442359	D	0.90004	-2.6	5.35	2.97	0.34412	.	0.304500	0.23876	N	0.043697	D	0.83926	0.5360	.	.	.	0.09310	N	1	P	0.51147	0.942	P	0.45610	0.487	T	0.77600	-0.2527	9	0.72032	D	0.01	.	1.8967	0.03259	0.5718:0.1742:0.0875:0.1665	.	216	Q7RTY3-2	.	Q	248;216	ENSP00000401932:L216Q	ENSP00000330940:L248Q	L	-	2	0	PRSS45	46758884	0.075000	0.21258	0.359000	0.25824	0.305000	0.27757	0.747000	0.26290	1.113000	0.41760	0.533000	0.62120	CTG		0.562	PRSS50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354544.1		
NBEAL2	23218	broad.mit.edu	37	3	47048602	47048602	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:47048602G>A	ENST00000450053.3	+	46	7360	c.7181G>A	c.(7180-7182)cGg>cAg	p.R2394Q	NBEAL2_ENST00000383740.2_Intron|NBEAL2_ENST00000292309.5_Missense_Mutation_p.R2210Q	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	2394					blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)		p.R1771Q(1)|p.R2394Q(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		GTCCCCCACCGGCAGCCCCAC	0.592																																					p.R2394Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G7181A	3						.						48.0	55.0	53.0					3																	47048602		2026	4173	6199	47023606	SO:0001583	missense	23218	exon46			AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"""WD repeat domain containing"""	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.7181G>A	3.37:g.47048602G>A	ENSP00000415034:p.Arg2394Gln		47023606	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Missense_Mutation	SNP	ENST00000450053.3	37	CCDS46817.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.30|12.30	1.895280|1.895280	0.33442|0.33442	.|.	.|.	ENSG00000160796|ENSG00000160796	ENST00000416683|ENST00000292309;ENST00000450053;ENST00000445550	.|T;T	.|0.43688	.|0.94;0.94	4.62|4.62	4.62|4.62	0.57501|0.57501	.|.	.|0.324544	.|0.31020	.|N	.|0.008415	T|T	0.30823|0.30823	0.0777|0.0777	L|L	0.44542|0.44542	1.39|1.39	0.80722|0.80722	D|D	1|1	.|B	.|0.15473	.|0.013	.|B	.|0.14578	.|0.011	T|T	0.13522|0.13522	-1.0506|-1.0506	5|10	.|0.27785	.|T	.|0.31	.|.	6.4881|6.4881	0.22099|0.22099	0.0961:0.1857:0.7182:0.0|0.0961:0.1857:0.7182:0.0	.|.	.|2394	.|Q6ZNJ1	.|NBEL2_HUMAN	S|Q	1682|2210;2394;337	.|ENSP00000292309:R2210Q;ENSP00000415034:R2394Q	.|ENSP00000292309:R2210Q	G|R	+|+	1|2	0|0	NBEAL2|NBEAL2	47023606|47023606	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.970000|0.970000	0.65996|0.65996	1.906000|1.906000	0.39887|0.39887	2.393000|2.393000	0.81446|0.81446	0.655000|0.655000	0.94253|0.94253	GGC|CGG		0.592	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064	
CDC25A	993	broad.mit.edu	37	3	48209414	48209414	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:48209414G>A	ENST00000302506.3	-	10	1359	c.951C>T	c.(949-951)tcC>tcT	p.S317S	CDC25A_ENST00000351231.3_Silent_p.S277S|CDC25A_ENST00000459900.1_5'UTR	NM_001789.2	NP_001780.2	P30304	MPIP1_HUMAN	cell division cycle 25A	317					cell proliferation (GO:0008283)|cellular response to UV (GO:0034644)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|response to radiation (GO:0009314)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)	p.S317S(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(9)|prostate(1)|skin(1)	20				BRCA - Breast invasive adenocarcinoma(193;0.000685)|KIRC - Kidney renal clear cell carcinoma(197;0.00596)|Kidney(197;0.00684)		AAGATGCCAGGGATAAAGACT	0.443																																					p.S317S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C951T	3						.						80.0	75.0	77.0					3																	48209414		2203	4300	6503	48184418	SO:0001819	synonymous_variant	993	exon10			M81933	CCDS2760.1, CCDS2761.1	3p21	2013-01-17	2013-01-17		ENSG00000164045	ENSG00000164045		"""Protein tyrosine phosphatases / Class III Cys-based PTPs"""	1725	protein-coding gene	gene with protein product		116947	"""cell division cycle 25A"", ""cell division cycle 25 homolog A (S. cerevisiae)"", ""cell division cycle 25 homolog A (S. pombe)"""			1836978	Standard	NM_001789		Approved		uc003csh.1	P30304	OTTHUMG00000133535	ENST00000302506.3:c.951C>T	3.37:g.48209414G>A			48184418	NM_001789	Q8IZH5|Q96IL3|Q9H2F2	Silent	SNP	ENST00000302506.3	37	CCDS2760.1																																																																																				0.443	CDC25A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257512.2	NM_001789	
COL7A1	1294	broad.mit.edu	37	3	48627098	48627098	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:48627098C>T	ENST00000328333.8	-	16	2211	c.2104G>A	c.(2104-2106)Gtc>Atc	p.V702I	COL7A1_ENST00000454817.1_Missense_Mutation_p.V702I	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	702	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Nonhelical region (NC1).				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.V702I(1)		NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GTAATGGTGACAGATGAGCTG	0.627																																					p.V702I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2104A	3						.						90.0	90.0	90.0					3																	48627098		2203	4300	6503	48602102	SO:0001583	missense	1294	exon16			L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"""Collagens"", ""Fibronectin type III domain containing"""	2214	protein-coding gene	gene with protein product	"""collagen VII, alpha-1 polypeptide"", ""LC collagen"""	120120	"""epidermolysis bullosa, dystrophic, dominant and recessive"""	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.2104G>A	3.37:g.48627098C>T	ENSP00000332371:p.Val702Ile		48602102	NM_000094	Q14054|Q16507	Missense_Mutation	SNP	ENST00000328333.8	37	CCDS2773.1	.	.	.	.	.	.	.	.	.	.	C	12.19	1.862357	0.32884	.	.	ENSG00000114270	ENST00000328333;ENST00000454817	T;T	0.57907	0.37;0.37	5.26	2.51	0.30379	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.337476	0.20861	N	0.084354	T	0.26846	0.0657	N	0.05124	-0.11	0.27273	N	0.958327	B	0.06786	0.001	B	0.14023	0.01	T	0.16247	-1.0409	10	0.22706	T	0.39	.	7.7257	0.28759	0.0:0.7353:0.0:0.2647	.	702	Q02388	CO7A1_HUMAN	I	702	ENSP00000332371:V702I;ENSP00000412569:V702I	ENSP00000332371:V702I	V	-	1	0	COL7A1	48602102	1.000000	0.71417	0.999000	0.59377	0.955000	0.61496	1.531000	0.36018	0.330000	0.23485	0.561000	0.74099	GTC		0.627	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094	
COL7A1	1294	broad.mit.edu	37	3	48630587	48630587	+	Silent	SNP	G	G	A	rs117857033	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:48630587G>A	ENST00000328333.8	-	5	737	c.630C>T	c.(628-630)ctC>ctT	p.L210L	COL7A1_ENST00000454817.1_Silent_p.L210L	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	210	Nonhelical region (NC1).|VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.L210L(1)		NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		TCCGGGAAACGAGGGGCAGTA	0.592													g|||	5	0.000998403	0.0	0.0	5008	,	,		20618	0.005		0.0	False		,,,				2504	0.0				p.L210L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C630T	3						.						109.0	85.0	93.0					3																	48630587		2203	4300	6503	48605591	SO:0001819	synonymous_variant	1294	exon5			L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"""Collagens"", ""Fibronectin type III domain containing"""	2214	protein-coding gene	gene with protein product	"""collagen VII, alpha-1 polypeptide"", ""LC collagen"""	120120	"""epidermolysis bullosa, dystrophic, dominant and recessive"""	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.630C>T	3.37:g.48630587G>A			48605591	NM_000094	Q14054|Q16507	Silent	SNP	ENST00000328333.8	37	CCDS2773.1																																																																																				0.592	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094	
DAG1	1605	broad.mit.edu	37	3	49569652	49569652	+	Missense_Mutation	SNP	G	G	A	rs370669533		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:49569652G>A	ENST00000539901.1	+	3	2266	c.1708G>A	c.(1708-1710)Gtg>Atg	p.V570M	DAG1_ENST00000515359.2_Missense_Mutation_p.V570M|DAG1_ENST00000308775.2_Missense_Mutation_p.V570M|DAG1_ENST00000541308.1_Missense_Mutation_p.V570M|DAG1_ENST00000545947.1_Missense_Mutation_p.V570M|DAG1_ENST00000538711.1_Missense_Mutation_p.V570M	NM_001177644.2	NP_001171115	Q14118	DAG1_HUMAN	dystroglycan 1 (dystrophin-associated glycoprotein 1)	570					basement membrane organization (GO:0071711)|branching involved in salivary gland morphogenesis (GO:0060445)|calcium-dependent cell-matrix adhesion (GO:0016340)|commissural neuron axon guidance (GO:0071679)|cytoskeletal anchoring at plasma membrane (GO:0007016)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|extracellular matrix organization (GO:0030198)|membrane protein ectodomain proteolysis (GO:0006509)|microtubule anchoring (GO:0034453)|modulation by virus of host morphology or physiology (GO:0019048)|morphogenesis of an epithelial sheet (GO:0002011)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell migration (GO:0030336)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase B signaling (GO:0051898)|nerve maturation (GO:0021682)|NLS-bearing protein import into nucleus (GO:0006607)|response to peptide hormone (GO:0043434)	basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell outer membrane (GO:0009279)|cell-cell adherens junction (GO:0005913)|contractile ring (GO:0070938)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystroglycan complex (GO:0016011)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|node of Ranvier (GO:0033268)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|alpha-actinin binding (GO:0051393)|calcium ion binding (GO:0005509)|laminin-1 binding (GO:0043237)|SH2 domain binding (GO:0042169)|structural constituent of muscle (GO:0008307)|tubulin binding (GO:0015631)|vinculin binding (GO:0017166)|virus receptor activity (GO:0001618)	p.V570M(1)		NS(1)|autonomic_ganglia(2)|breast(2)|endometrium(1)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	23				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.00241)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		CAGCAGCCACGTGGGCAAACA	0.602																																					p.V570M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1708A	3						.						61.0	58.0	59.0					3																	49569652		2203	4300	6503	49544656	SO:0001583	missense	1605	exon3			L19711	CCDS2799.1	3p21	2014-09-17			ENSG00000173402	ENSG00000173402			2666	protein-coding gene	gene with protein product	"""alpha-dystroglycan"", ""dystrophin-associated glycoprotein-1"", ""beta-dystroglycan"""	128239				7774920, 1741056	Standard	NM_001177643		Approved	A3a, 156DAG, AGRNR, DAG	uc021wyd.1	Q14118	OTTHUMG00000156869	ENST00000539901.1:c.1708G>A	3.37:g.49569652G>A	ENSP00000439334:p.Val570Met		49544656	NM_004393	A8K6M7|Q969J9	Missense_Mutation	SNP	ENST00000539901.1	37	CCDS2799.1	.	.	.	.	.	.	.	.	.	.	G	14.52	2.560028	0.45590	.	.	ENSG00000173402	ENST00000515359;ENST00000308775;ENST00000545947;ENST00000541308;ENST00000539901;ENST00000538711	D;D;D;D;D;D	0.98822	-5.16;-5.16;-5.16;-5.16;-5.16;-5.16	5.97	5.06	0.68205	Dystroglycan-type cadherin-like (1);Cadherin-like (1);Immunoglobulin-like fold (1);	0.232840	0.43747	D	0.000528	D	0.96377	0.8818	L	0.54323	1.7	0.39362	D	0.965947	D	0.67145	0.996	B	0.42282	0.382	D	0.94076	0.7340	9	.	.	.	-20.2153	6.0558	0.19811	0.0794:0.1411:0.649:0.1305	.	570	Q14118	DAG1_HUMAN	M	570	ENSP00000440705:V570M;ENSP00000312435:V570M;ENSP00000442600:V570M;ENSP00000440590:V570M;ENSP00000439334:V570M;ENSP00000438421:V570M	.	V	+	1	0	DAG1	49544656	0.924000	0.31332	0.999000	0.59377	0.851000	0.48451	1.467000	0.35321	2.837000	0.97791	0.655000	0.94253	GTG		0.602	DAG1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346326.1		
RNF123	63891	broad.mit.edu	37	3	49735919	49735919	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:49735919G>A	ENST00000327697.6	+	8	674	c.530G>A	c.(529-531)cGc>cAc	p.R177H	RNF123_ENST00000432042.1_Missense_Mutation_p.R31H	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	177	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.R177H(1)		NS(1)|breast(4)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;4.71e-05)|Kidney(197;0.00227)|KIRC - Kidney renal clear cell carcinoma(197;0.00255)		GATGGCAACCGCGTGCGCAAG	0.557																																					p.R177H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G530A	3						.						85.0	76.0	79.0					3																	49735919		2203	4300	6503	49710923	SO:0001583	missense	63891	exon8			AK022627	CCDS33758.1	3p24.3	2008-02-05			ENSG00000164068	ENSG00000164068		"""RING-type (C3HC4) zinc fingers"""	21148	protein-coding gene	gene with protein product		614472					Standard	NM_022064		Approved	FLJ12565	uc003cxh.4	Q5XPI4	OTTHUMG00000156891	ENST00000327697.6:c.530G>A	3.37:g.49735919G>A	ENSP00000328287:p.Arg177His		49710923	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Missense_Mutation	SNP	ENST00000327697.6	37	CCDS33758.1	.	.	.	.	.	.	.	.	.	.	G	33	5.251129	0.95305	.	.	ENSG00000164068	ENST00000327697;ENST00000389066;ENST00000432042	T;T	0.61627	0.09;0.09	4.96	4.96	0.65561	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.305497	0.35349	N	0.003274	T	0.79191	0.4404	M	0.85945	2.785	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.82489	-0.0432	10	0.87932	D	0	-29.0934	17.731	0.88377	0.0:0.0:1.0:0.0	.	177	Q5XPI4	RN123_HUMAN	H	177;177;31	ENSP00000328287:R177H;ENSP00000392443:R31H	ENSP00000328287:R177H	R	+	2	0	RNF123	49710923	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	8.786000	0.91826	2.735000	0.93741	0.561000	0.74099	CGC		0.557	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064	
IQCF3	401067	broad.mit.edu	37	3	51864500	51864500	+	Missense_Mutation	SNP	C	C	T	rs371775341		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:51864500C>T	ENST00000456080.1	+	8	1313	c.148C>T	c.(148-150)Cgc>Tgc	p.R50C	IQCF3_ENST00000440739.2_Missense_Mutation_p.R50C|IQCF3_ENST00000437810.2_Missense_Mutation_p.R50C|IQCF3_ENST00000462079.1_3'UTR|IQCF3_ENST00000444293.1_Intron|IQCF3_ENST00000446775.1_Missense_Mutation_p.R50C			P0C7M6	IQCF3_HUMAN	IQ motif containing F3	50								p.R50C(1)		endometrium(1)|large_intestine(2)|lung(2)|ovary(1)	6				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		GGTCCTGGTGCGCAGGACCCT	0.617																																					p.R50C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C148T	3						.	C	CYS/ARG,CYS/ARG	0,4366		0,0,2183	56.0	65.0	62.0		148,148	3.8	0.8	3		62	1,8579		0,1,4289	no	missense,missense	IQCF3	NM_001085479.2,NM_001207023.1	180,180	0,1,6472	TT,TC,CC		0.0117,0.0,0.0077	probably-damaging,probably-damaging	50/155,50/155	51864500	1,12945	2183	4290	6473	51839540	SO:0001583	missense	401067	exon5			AK057432	CCDS46837.1	3p21.31	2008-06-12			ENSG00000229972	ENSG00000229972			31816	protein-coding gene	gene with protein product							Standard	NM_001085479		Approved		uc021wyz.1	P0C7M6	OTTHUMG00000156910	ENST00000456080.1:c.148C>T	3.37:g.51864500C>T	ENSP00000415609:p.Arg50Cys		51839540	NM_001085479	B2RUV0	Missense_Mutation	SNP	ENST00000456080.1	37	CCDS46837.1	.	.	.	.	.	.	.	.	.	.	C	18.90	3.721897	0.68959	0.0	1.17E-4	ENSG00000229972	ENST00000456080;ENST00000437810;ENST00000446775;ENST00000440739	T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17	4.72	3.82	0.43975	.	.	.	.	.	T	0.73791	0.3632	L	0.61036	1.89	0.39616	D	0.969963	D	0.89917	1.0	D	0.97110	1.0	T	0.76591	-0.2903	9	0.87932	D	0	.	9.9353	0.41548	0.2116:0.7884:0.0:0.0	.	50	P0C7M6	IQCF3_HUMAN	C	50	ENSP00000415609:R50C;ENSP00000409373:R50C;ENSP00000401767:R50C;ENSP00000402012:R50C	ENSP00000409373:R50C	R	+	1	0	IQCF3	51839540	0.966000	0.33281	0.764000	0.31436	0.907000	0.53573	2.078000	0.41567	1.291000	0.44653	0.655000	0.94253	CGC		0.617	IQCF3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346579.2	NM_001085479	
TLR9	54106	broad.mit.edu	37	3	52255659	52255659	+	Silent	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:52255659A>G	ENST00000360658.2	-	2	3306	c.2673T>C	c.(2671-2673)ctT>ctC	p.L891L	TLR9_ENST00000494383.1_Missense_Mutation_p.S1045P|TLR9_ENST00000597542.1_Silent_p.L915L	NM_017442.3	NP_059138.1	Q9NR96	TLR9_HUMAN	toll-like receptor 9	891	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|maintenance of gastrointestinal epithelium (GO:0030277)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of chemokine production (GO:0032722)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to molecule of bacterial origin (GO:0002237)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|early phagosome (GO:0032009)|endolysosome membrane (GO:0036020)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|siRNA binding (GO:0035197)|transmembrane signaling receptor activity (GO:0004888)	p.L891L(1)		endometrium(4)|large_intestine(11)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(193;2.41e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Chloroquine(DB00608)|Hydroxychloroquine(DB01611)	GCTGCCCCCGAAGCTCGTTGT	0.637																																					p.L891L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T2673C	3						.						76.0	80.0	79.0					3																	52255659		2203	4299	6502	52230699	SO:0001819	synonymous_variant	54106	exon2			AF259262	CCDS2848.1	3p21.3	2006-02-23			ENSG00000239732	ENSG00000239732		"""CD molecules"""	15633	protein-coding gene	gene with protein product		605474				11022119	Standard	NM_017442		Approved	CD289	uc003ddb.3	Q9NR96	OTTHUMG00000158106	ENST00000360658.2:c.2673T>C	3.37:g.52255659A>G			52230699	NM_017442	B3Y661|D1CS56|Q6UVZ2|Q9HD68|Q9HD69|Q9HD70|Q9NYC2|Q9NYC3	Silent	SNP	ENST00000360658.2	37	CCDS2848.1	.	.	.	.	.	.	.	.	.	.	A	1.839	-0.467855	0.04476	.	.	ENSG00000173366	ENST00000494383	.	.	.	5.22	1.26	0.21427	.	.	.	.	.	T	0.50582	0.1624	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33189	-0.9878	4	.	.	.	.	4.2757	0.10808	0.2924:0.4973:0.1314:0.0789	.	.	.	.	P	1045	.	.	S	-	1	0	RP11-330H6.5	52230699	0.104000	0.21937	0.745000	0.31077	0.342000	0.28953	0.552000	0.23376	-0.055000	0.13244	-0.213000	0.12676	TCG		0.637	TLR9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000350203.1		
DNAH1	25981	broad.mit.edu	37	3	52388995	52388995	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:52388995A>C	ENST00000420323.2	+	21	3878	c.3617A>C	c.(3616-3618)aAt>aCt	p.N1206T		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	1206	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.N1206T(1)		cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		ATGACCCAGAATATGTCATTT	0.557																																					p.N1206T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3617C	3						.						129.0	131.0	130.0					3																	52388995		2075	4205	6280	52364035	SO:0001583	missense	25981	exon21			U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"""Axonemal dyneins"""	2940	protein-coding gene	gene with protein product		603332	"""dynein, axonemal, heavy polypeptide 1"""			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.3617A>C	3.37:g.52388995A>C	ENSP00000401514:p.Asn1206Thr		52364035	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	37	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	G	12.98	2.099962	0.37048	.	.	ENSG00000114841	ENST00000420323	T	0.59906	0.23	5.29	5.29	0.74685	.	0.000000	0.64402	D	0.000016	T	0.23171	0.0560	N	0.00742	-1.23	0.19300	N	0.999973	B	0.06786	0.001	B	0.06405	0.002	T	0.16660	-1.0395	10	0.02654	T	1	.	14.1402	0.65316	0.0728:0.0:0.9272:0.0	.	1206	C9JXH6	.	T	1206	ENSP00000401514:N1206T	ENSP00000401514:N1206T	N	+	2	0	DNAH1	52364035	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	2.856000	0.48341	1.252000	0.44001	-0.355000	0.07637	AAT		0.557	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512	
CHDH	55349	broad.mit.edu	37	3	53851888	53851888	+	Silent	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:53851888T>C	ENST00000315251.6	-	9	2138	c.1701A>G	c.(1699-1701)gcA>gcG	p.A567A		NM_018397.4	NP_060867.2	Q8NE62	CHDH_HUMAN	choline dehydrogenase	567					glycine betaine biosynthetic process from choline (GO:0019285)	mitochondrial inner membrane (GO:0005743)	choline dehydrogenase activity (GO:0008812)|flavin adenine dinucleotide binding (GO:0050660)	p.A567A(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	17		Hepatocellular(537;0.152)		BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)	Choline(DB00122)	TAATGTCAGCTGCCTTCTCTG	0.582																																					p.A567A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1701G	3						.						94.0	73.0	80.0					3																	53851888		2203	4300	6503	53826928	SO:0001819	synonymous_variant	55349	exon9			AJ272267	CCDS2873.1	3p21	2004-11-24			ENSG00000016391	ENSG00000016391	1.1.99.1		24288	protein-coding gene	gene with protein product							Standard	NM_018397		Approved		uc003dgz.3	Q8NE62	OTTHUMG00000158281	ENST00000315251.6:c.1701A>G	3.37:g.53851888T>C			53826928	NM_018397	Q9NY17	Silent	SNP	ENST00000315251.6	37	CCDS2873.1																																																																																				0.582	CHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350567.2	NM_018397	
CCDC66	285331	broad.mit.edu	37	3	56597803	56597803	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:56597803delA	ENST00000394672.3	+	4	264	c.194delA	c.(193-195)gaafs	p.E65fs	CCDC66_ENST00000442522.2_3'UTR|CCDC66_ENST00000538560.1_Frame_Shift_Del_p.E65fs|CCDC66_ENST00000326595.7_Frame_Shift_Del_p.E31fs|CCDC66_ENST00000436465.2_Frame_Shift_Del_p.E65fs	NM_001012506.4|NM_001141947.1	NP_001012524.4|NP_001135419.1	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66	65					post-embryonic retina morphogenesis in camera-type eye (GO:0060060)|retinal rod cell development (GO:0046548)			p.K66fs*22(1)		breast(1)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(2)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)		ATTGGGAGTGAAAAACTTTTG	0.338																																					p.E65fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.194delA	3						.						85.0	70.0	75.0					3																	56597803		692	1591	2283	56572843	SO:0001589	frameshift_variant	285331	exon4			AL832692	CCDS33770.2, CCDS46852.1	3p14.3	2006-03-27			ENSG00000180376	ENSG00000180376			27709	protein-coding gene	gene with protein product						14702039	Standard	NR_024460		Approved	DKFZp686C0433	uc003dhz.3	A2RUB6	OTTHUMG00000155748	ENST00000394672.3:c.194delA	3.37:g.56597803delA	ENSP00000378167:p.Glu65fs		56572843	NM_001141947	B3KWL8|Q4VC34|Q8N949	Frame_Shift_Del	DEL	ENST00000394672.3	37	CCDS46852.1																																																																																				0.338	CCDC66-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341473.1	NM_001012506	
DNAH12	201625	broad.mit.edu	37	3	57488097	57488097	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:57488097G>A	ENST00000351747.2	-	10	1376	c.1196C>T	c.(1195-1197)gCa>gTa	p.A399V	DNAH12_ENST00000389536.4_Missense_Mutation_p.A399V|DNAH12_ENST00000311202.6_Missense_Mutation_p.A399V	NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	399	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.A399V(2)		breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						CCGATGTACTGCTGCCTTCAG	0.398																																					p.A399V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1196T	3						.						277.0	242.0	254.0					3																	57488097		2203	4300	6503	57463137	SO:0001583	missense	201625	exon10			U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844		"""Axonemal dyneins"""	2943	protein-coding gene	gene with protein product		603340	"""dynein, axonemal, heavy polypeptide 12"", ""dynein heavy chain domain 2"", ""dynein heavy domain 2"", ""dynein, axonemal, heavy chain 12-like"", ""dynein, axonemal, heavy chain 7-like"""	DNHD2, DNAH12L, DNAH7L		8812413, 8666668	Standard	NM_198564		Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.1196C>T	3.37:g.57488097G>A	ENSP00000295937:p.Ala399Val		57463137	NM_178504	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Missense_Mutation	SNP	ENST00000351747.2	37		.	.	.	.	.	.	.	.	.	.	G	0.669	-0.802687	0.02841	.	.	ENSG00000174844	ENST00000351747;ENST00000495027;ENST00000389536;ENST00000311202	T;T;T;T	0.21191	2.17;2.02;3.69;3.22	5.34	3.46	0.39613	.	0.244679	0.33854	N	0.004496	T	0.17365	0.0417	L	0.54908	1.71	0.39659	D	0.970586	B;B	0.32467	0.372;0.006	B;B	0.34489	0.184;0.007	T	0.04495	-1.0947	10	0.08837	T	0.75	.	8.1966	0.31400	0.0734:0.0:0.6492:0.2774	.	399;399	Q6ZR08-4;Q6ZR08	.;DYH12_HUMAN	V	399	ENSP00000295937:A399V;ENSP00000418137:A399V;ENSP00000374187:A399V;ENSP00000312554:A399V	ENSP00000312554:A399V	A	-	2	0	DNAH12	57463137	0.963000	0.33076	0.012000	0.15200	0.051000	0.14879	4.276000	0.58933	0.658000	0.30925	0.655000	0.94253	GCA		0.398	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504	
DENND6A	201627	broad.mit.edu	37	3	57619032	57619032	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:57619032C>T	ENST00000311128.5	-	15	1383	c.1313G>A	c.(1312-1314)cGc>cAc	p.R438H	RP11-755B10.2_ENST00000470427.1_RNA	NM_152678.2	NP_689891.1	Q8IWF6	DEN6A_HUMAN	DENN/MADD domain containing 6A	438					positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of Rab GTPase activity (GO:0032851)	cytoplasm (GO:0005737)|recycling endosome (GO:0055037)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.R438H(1)									CAAAAAATAGCGTCGAAGAAT	0.303																																					p.R438H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1313A	3						.						81.0	84.0	83.0					3																	57619032		2203	4298	6501	57594072	SO:0001583	missense	201627	exon15			AK074156	CCDS33773.1	3p14.3	2013-10-11	2012-10-03	2012-10-03	ENSG00000174839	ENSG00000174839		"""DENN/MADD domain containing"""	26635	protein-coding gene	gene with protein product			"""family with sequence similarity 116, member A"""	FAM116A		21330364	Standard	NM_152678		Approved	FLJ34969, AFI1A	uc003dja.3	Q8IWF6	OTTHUMG00000158639	ENST00000311128.5:c.1313G>A	3.37:g.57619032C>T	ENSP00000311401:p.Arg438His		57594072	NM_152678	Q7Z5T4|Q8N235|Q8TEG8	Missense_Mutation	SNP	ENST00000311128.5	37	CCDS33773.1	.	.	.	.	.	.	.	.	.	.	C	34	5.323079	0.95708	.	.	ENSG00000174839	ENST00000311128	.	.	.	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	D	0.85864	0.5796	M	0.90369	3.11	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.88151	0.2851	9	0.87932	D	0	-17.6848	19.7457	0.96251	0.0:1.0:0.0:0.0	.	438	Q8IWF6	F116A_HUMAN	H	438	.	ENSP00000311401:R438H	R	-	2	0	FAM116A	57594072	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.363000	0.79516	2.725000	0.93324	0.557000	0.71058	CGC		0.303	DENND6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351594.1	NM_152678	
SLMAP	7871	broad.mit.edu	37	3	57817166	57817166	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:57817166G>A	ENST00000428312.1	+	2	349	c.255G>A	c.(253-255)ttG>ttA	p.L85L	SLMAP_ENST00000416870.1_5'UTR|SLMAP_ENST00000295952.3_Silent_p.L85L|SLMAP_ENST00000383718.3_Silent_p.L85L|SLMAP_ENST00000449503.2_Silent_p.L85L|SLMAP_ENST00000295951.3_Silent_p.L85L			Q14BN4	SLMAP_HUMAN	sarcolemma associated protein	85	FHA. {ECO:0000255|PROSITE- ProRule:PRU00086}.|Necessary for targeting to centrosomes. {ECO:0000250}.				muscle contraction (GO:0006936)	cytoskeleton (GO:0005856)|integral component of plasma membrane (GO:0005887)|smooth endoplasmic reticulum (GO:0005790)		p.L85L(1)		endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|urinary_tract(2)	18				BRCA - Breast invasive adenocarcinoma(55;0.000271)|KIRC - Kidney renal clear cell carcinoma(284;0.0602)|Kidney(284;0.0754)|OV - Ovarian serous cystadenocarcinoma(275;0.182)		GCCAGAGATTGAGTCGAGGCT	0.363																																					p.L85L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G255A	3						.						69.0	71.0	70.0					3																	57817166		2203	4300	6503	57792206	SO:0001819	synonymous_variant	7871	exon2			AF100750	CCDS33774.1	3p21.2-p14.3	2008-07-18			ENSG00000163681	ENSG00000163681			16643	protein-coding gene	gene with protein product	"""Sarcolemmal-associated protein"""	602701				9405447, 11042152	Standard	NM_007159		Approved	SLAP, KIAA1601	uc003djd.1	Q14BN4	OTTHUMG00000133764	ENST00000428312.1:c.255G>A	3.37:g.57817166G>A			57792206	NM_007159	Q14C95|Q6AI54|Q6UXC9|Q6ZVQ8|Q8NCW9|Q9H297|Q9HCH1|Q9Y681	Silent	SNP	ENST00000428312.1	37																																																																																					0.363	SLMAP-013	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351584.1	NM_007159	
FLNB	2317	broad.mit.edu	37	3	58092501	58092501	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:58092501C>T	ENST00000295956.4	+	12	2007	c.1842C>T	c.(1840-1842)ggC>ggT	p.G614G	FLNB_ENST00000429972.2_Silent_p.G614G|FLNB_ENST00000348383.5_Silent_p.G614G|FLNB_ENST00000419752.2_Silent_p.G445G|FLNB_ENST00000490882.1_Silent_p.G614G|FLNB_ENST00000493452.1_Silent_p.G445G|FLNB_ENST00000358537.3_Silent_p.G614G|FLNB_ENST00000357272.4_Silent_p.G614G	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	614					actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)	p.G614G(2)		NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		AGGAGCCTGGCGAATATGCTG	0.532																																					p.G614G												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1842T	3						.						140.0	111.0	121.0					3																	58092501		2203	4300	6503	58067541	SO:0001819	synonymous_variant	2317	exon12			AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"""actin binding protein 278"""	603381	"""filamin B, beta (actin binding protein 278)"", ""Larsen syndrome 1 (autosomal dominant)"""	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.1842C>T	3.37:g.58092501C>T			58067541	NM_001164317	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Silent	SNP	ENST00000295956.4	37	CCDS2885.1																																																																																				0.532	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457	
FLNB	2317	broad.mit.edu	37	3	58112417	58112417	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:58112417A>G	ENST00000295956.4	+	24	4315	c.4150A>G	c.(4150-4152)Agt>Ggt	p.S1384G	FLNB_ENST00000429972.2_Missense_Mutation_p.S1384G|FLNB_ENST00000348383.5_Missense_Mutation_p.S1384G|FLNB_ENST00000419752.2_Missense_Mutation_p.S1215G|FLNB_ENST00000490882.1_Missense_Mutation_p.S1384G|FLNB_ENST00000493452.1_Missense_Mutation_p.S1215G|FLNB_ENST00000358537.3_Missense_Mutation_p.S1384G|FLNB_ENST00000357272.4_Missense_Mutation_p.S1384G	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	1384	Interaction with FBLP1.				actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)	p.S1384G(1)		NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		TGGCAGCTGCAGTGCTGAGTA	0.517																																					p.S1384G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A4150G	3						.						116.0	115.0	115.0					3																	58112417		2203	4300	6503	58087457	SO:0001583	missense	2317	exon24			AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"""actin binding protein 278"""	603381	"""filamin B, beta (actin binding protein 278)"", ""Larsen syndrome 1 (autosomal dominant)"""	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.4150A>G	3.37:g.58112417A>G	ENSP00000295956:p.Ser1384Gly		58087457	NM_001164317	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Missense_Mutation	SNP	ENST00000295956.4	37	CCDS2885.1	.	.	.	.	.	.	.	.	.	.	A	19.28	3.796987	0.70567	.	.	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272;ENST00000493452;ENST00000419752	D;D;D;D;D;D;D;D	0.84944	-1.92;-1.92;-1.92;-1.92;-1.92;-1.92;-1.92;-1.92	5.95	5.95	0.96441	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.075293	0.85682	D	0.000000	D	0.91116	0.7203	M	0.62209	1.925	0.52099	D	0.999945	D;D;D;D;D;D	0.69078	0.987;0.974;0.997;0.994;0.995;0.995	P;P;D;D;D;D	0.83275	0.882;0.731;0.996;0.95;0.996;0.996	D	0.90741	0.4650	10	0.45353	T	0.12	.	16.4237	0.83790	1.0:0.0:0.0:0.0	.	1384;1384;1215;1215;1384;1384	O75369-2;B2ZZ83;E7EN95;O75369-7;Q60FE7;O75369	.;.;.;.;.;FLNB_HUMAN	G	1384;1384;1384;1384;1384;1384;1215;1215	ENSP00000295956:S1384G;ENSP00000420213:S1384G;ENSP00000351339:S1384G;ENSP00000415599:S1384G;ENSP00000232447:S1384G;ENSP00000349819:S1384G;ENSP00000418510:S1215G;ENSP00000414532:S1215G	ENSP00000295956:S1384G	S	+	1	0	FLNB	58087457	1.000000	0.71417	0.996000	0.52242	0.618000	0.37518	4.873000	0.63057	2.279000	0.76181	0.533000	0.62120	AGT		0.517	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457	
DNASE1L3	1776	broad.mit.edu	37	3	58190537	58190537	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:58190537G>T	ENST00000394549.2	-	4	708	c.392C>A	c.(391-393)tCc>tAc	p.S131Y	DNASE1L3_ENST00000486455.1_Missense_Mutation_p.S101Y|DNASE1L3_ENST00000318316.3_Missense_Mutation_p.S131Y|DNASE1L3_ENST00000483681.1_Missense_Mutation_p.S131Y	NM_004944.3	NP_004935.1	Q13609	DNSL3_HUMAN	deoxyribonuclease I-like 3	131					apoptotic DNA fragmentation (GO:0006309)|developmental programmed cell death (GO:0010623)|DNA metabolic process (GO:0006259)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)|deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)	p.S131Y(1)		breast(2)|large_intestine(4)|lung(6)	12				BRCA - Breast invasive adenocarcinoma(55;0.00021)|KIRC - Kidney renal clear cell carcinoma(284;0.0445)|Kidney(284;0.0556)|OV - Ovarian serous cystadenocarcinoma(275;0.202)		GGGCTCCCTGGAAAACACATC	0.527																																					p.S131Y	Esophageal Squamous(96;1069 1424 4841 43466 52325)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C392A	3						.						127.0	114.0	118.0					3																	58190537		2203	4300	6503	58165577	SO:0001583	missense	1776	exon6			AF047354	CCDS2886.1, CCDS58836.1	3p14.3	2008-05-15			ENSG00000163687	ENSG00000163687			2959	protein-coding gene	gene with protein product	"""DNase gamma"""	602244				9205125, 9714828, 14646506	Standard	NM_004944		Approved	DNAS1L3, LSD	uc003djo.2	Q13609	OTTHUMG00000159153	ENST00000394549.2:c.392C>A	3.37:g.58190537G>T	ENSP00000378053:p.Ser131Tyr		58165577	NM_004944	B2R8B1|B7Z707|O75803	Missense_Mutation	SNP	ENST00000394549.2	37	CCDS2886.1	.	.	.	.	.	.	.	.	.	.	G	18.78	3.696955	0.68386	.	.	ENSG00000163687	ENST00000486455;ENST00000450710;ENST00000318316;ENST00000483681;ENST00000477209;ENST00000394549;ENST00000461914	T;T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79;0.79	5.81	5.81	0.92471	Endonuclease/exonuclease/phosphatase (2);	0.000000	0.64402	D	0.000001	T	0.76608	0.4011	M	0.90650	3.135	0.51767	D	0.999938	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.80630	-0.1297	10	0.87932	D	0	.	20.0628	0.97684	0.0:0.0:1.0:0.0	.	101;131;131	B7Z707;E9PES0;Q13609	.;.;DNSL3_HUMAN	Y	101;131;131;131;5;131;131	ENSP00000419052:S101Y;ENSP00000316193:S131Y;ENSP00000417047:S131Y;ENSP00000417976:S5Y;ENSP00000378053:S131Y;ENSP00000418113:S131Y	ENSP00000316193:S131Y	S	-	2	0	DNASE1L3	58165577	1.000000	0.71417	1.000000	0.80357	0.472000	0.32918	6.402000	0.73260	2.745000	0.94114	0.655000	0.94253	TCC		0.527	DNASE1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353533.1	NM_004944	
C3orf67	200844	broad.mit.edu	37	3	58849555	58849556	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	AG	AG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:58849555_58849556delAG	ENST00000482387.1	-	8	1042_1043	c.946_947delCT	c.(946-948)ctafs	p.L318fs	RP11-147N17.1_ENST00000463703.1_RNA|RP11-147N17.1_ENST00000493123.1_RNA|C3orf67_ENST00000472469.1_Frame_Shift_Del_p.L225fs|C3orf67_ENST00000295966.7_Frame_Shift_Del_p.L318fs|RP11-147N17.1_ENST00000492031.1_RNA|RP11-147N17.1_ENST00000482372.1_RNA			Q6ZVT6	CC067_HUMAN	chromosome 3 open reading frame 67	318								p.L316fs*4(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(3)|prostate(2)|skin(1)	19		all_cancers(2;0.000156)|all_epithelial(2;0.000493)|Breast(2;0.00446)|all_lung(2;0.074)|Lung NSC(2;0.248)		BRCA - Breast invasive adenocarcinoma(55;5.93e-06)|Kidney(10;0.00155)|KIRC - Kidney renal clear cell carcinoma(10;0.00172)|OV - Ovarian serous cystadenocarcinoma(275;0.23)		ACCCAGAAGTAGAGACTGTCTG	0.465																																					p.316_316del												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.946_947del	3						.																																			58824596	SO:0001589	frameshift_variant	200844	exon12			AK124920	CCDS33776.1	3p14.2	2011-01-25			ENSG00000163689	ENSG00000163689			24763	protein-coding gene	gene with protein product							Standard	NM_198463		Approved	FLJ42117, FLJ42930	uc003dkt.1	Q6ZVT6	OTTHUMG00000159151	ENST00000482387.1:c.946_947delCT	3.37:g.58849557_58849558delAG	ENSP00000417122:p.Leu318fs		58824595	NM_198463	B9EKV6|Q6ZV69	Frame_Shift_Del	DEL	ENST00000482387.1	37																																																																																					0.465	C3orf67-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000353803.1	NM_198463	
ARL13B	200894	broad.mit.edu	37	3	93755447	93755447	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:93755447delA	ENST00000394222.3	+	5	813	c.538delA	c.(538-540)aaafs	p.K181fs	ARL13B_ENST00000539730.1_5'UTR|ARL13B_ENST00000303097.7_Frame_Shift_Del_p.K74fs|ARL13B_ENST00000535334.1_Frame_Shift_Del_p.K78fs|ARL13B_ENST00000471138.1_Frame_Shift_Del_p.K181fs|ARL13B_ENST00000486562.1_3'UTR	NM_001174150.1	NP_001167621.1	Q3SXY8	AR13B_HUMAN	ADP-ribosylation factor-like 13B	181					cilium assembly (GO:0042384)|dorsal/ventral pattern formation (GO:0009953)|formation of radial glial scaffolds (GO:0021943)|heart looping (GO:0001947)|interneuron migration from the subpallium to the cortex (GO:0021830)|left/right axis specification (GO:0070986)|neural tube patterning (GO:0021532)|nonmotile primary cilium assembly (GO:0035058)|small GTPase mediated signal transduction (GO:0007264)|smoothened signaling pathway (GO:0007224)	ciliary membrane (GO:0060170)|cilium (GO:0005929)|intracellular (GO:0005622)|primary cilium (GO:0072372)	GTP binding (GO:0005525)	p.G75fs*16(1)|p.G182fs*16(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|urinary_tract(2)	10						CAAGTCCATTAAAAAAGGCCT	0.378																																					p.K180fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.538delA	3						.						67.0	69.0	69.0					3																	93755447		2203	4300	6503	95238137	SO:0001589	frameshift_variant	200894	exon5			AL713789	CCDS2924.1, CCDS2925.1, CCDS54615.1	3q11	2014-05-09	2005-11-18	2005-11-18	ENSG00000169379	ENSG00000169379		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	25419	protein-coding gene	gene with protein product		608922	"""ADP-ribosylation factor-like 2-like 1"""	ARL2L1		15314642, 18674751	Standard	NR_033427		Approved	DKFZp761H079, JBTS8	uc003drf.3	Q3SXY8	OTTHUMG00000159012	ENST00000394222.3:c.538delA	3.37:g.93755447delA	ENSP00000377769:p.Lys181fs		95238137	NM_001174150	D3DN29|G3V1S8|Q504W8|Q8TCL5	Frame_Shift_Del	DEL	ENST00000394222.3	37	CCDS2925.1																																																																																				0.378	ARL13B-005	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352904.1	NM_182896	
OR5H14	403273	broad.mit.edu	37	3	97868537	97868537	+	Missense_Mutation	SNP	C	C	T	rs370923244		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:97868537C>T	ENST00000437310.1	+	1	368	c.308C>T	c.(307-309)tCg>tTg	p.S103L	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005514.1	NP_001005514.1	A6NHG9	O5H14_HUMAN	olfactory receptor, family 5, subfamily H, member 14	103						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S103L(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	31						CAGTTGTTTTCGTTTGCAATC	0.393																																					p.S103L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C308T	3						.	C	LEU/SER	1,4395	2.1+/-5.4	0,1,2197	198.0	204.0	202.0		308	0.9	0.0	3		202	0,8598		0,0,4299	no	missense	OR5H14	NM_001005514.1	145	0,1,6496	TT,TC,CC		0.0,0.0227,0.0077	benign	103/311	97868537	1,12993	2198	4299	6497	99351227	SO:0001583	missense	403273	exon1				CCDS33798.1	3q11.2	2013-09-23			ENSG00000236032	ENSG00000236032		"""GPCR / Class A : Olfactory receptors"""	31286	protein-coding gene	gene with protein product							Standard	NM_001005514		Approved		uc003dsg.1	A6NHG9	OTTHUMG00000160079	ENST00000437310.1:c.308C>T	3.37:g.97868537C>T	ENSP00000401706:p.Ser103Leu		99351227	NM_001005514	B9EH15	Missense_Mutation	SNP	ENST00000437310.1	37	CCDS33798.1	.	.	.	.	.	.	.	.	.	.	C	5.956	0.360362	0.11296	2.27E-4	0.0	ENSG00000236032	ENST00000437310	T	0.00382	7.61	2.49	0.873	0.19118	GPCR, rhodopsin-like superfamily (1);	0.149335	0.31566	N	0.007432	T	0.00109	0.0003	N	0.00760	-1.21	0.09310	N	1	B	0.24317	0.101	B	0.17098	0.017	T	0.30679	-0.9970	10	0.39692	T	0.17	.	4.1872	0.10404	0.0:0.5102:0.0:0.4897	.	103	A6NHG9	O5H14_HUMAN	L	103	ENSP00000401706:S103L	ENSP00000401706:S103L	S	+	2	0	OR5H14	99351227	0.000000	0.05858	0.016000	0.15963	0.006000	0.05464	-0.106000	0.10890	0.365000	0.24400	0.195000	0.17529	TCG		0.393	OR5H14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359112.1		
NR1I2	8856	broad.mit.edu	37	3	119531660	119531660	+	Frame_Shift_Del	DEL	G	G	-	rs377500972		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:119531660delG	ENST00000337940.4	+	5	812	c.764delG	c.(763-765)cggfs	p.R255fs	NR1I2_ENST00000466380.1_Frame_Shift_Del_p.R179fs|NR1I2_ENST00000393716.2_Frame_Shift_Del_p.R216fs	NM_022002.2	NP_071285.1	O75469	NR1I2_HUMAN	nuclear receptor subfamily 1, group I, member 2	216	Ligand-binding.				drug export (GO:0046618)|exogenous drug catabolic process (GO:0042738)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|steroid metabolic process (GO:0008202)|transcription initiation from RNA polymerase II promoter (GO:0006367)|xenobiotic metabolic process (GO:0006805)|xenobiotic transport (GO:0042908)	nucleoplasm (GO:0005654)	drug binding (GO:0008144)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.E257fs*59(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(2)|prostate(2)|skin(3)	23				GBM - Glioblastoma multiforme(114;0.175)	Docetaxel(DB01248)|Erlotinib(DB00530)|Estradiol(DB00783)|Ethinyl Estradiol(DB00977)|Paclitaxel(DB01229)|Rifampicin(DB01045)|Rifaximin(DB01220)|Rilpivirine(DB08864)|Vitamin E(DB00163)	CTGCAGCTGCGGGGGGAGGAT	0.587																																					p.R216fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.647delG	3						.						77.0	77.0	77.0					3																	119531660		2203	4300	6503	121014350	SO:0001589	frameshift_variant	8856	exon5			AF061056	CCDS2995.1, CCDS43136.1, CCDS54627.1	3q12-q13.3	2013-03-25			ENSG00000144852	ENSG00000144852		"""Nuclear hormone receptors"""	7968	protein-coding gene	gene with protein product	"""pregnane X receptor"", ""orphan nuclear receptor PXR"""	603065				9727070, 9770465	Standard	NM_003889		Approved	ONR1, PXR, BXR, SXR, PAR2	uc003edk.3	O75469	OTTHUMG00000159400	ENST00000337940.4:c.764delG	3.37:g.119531660delG	ENSP00000336528:p.Arg255fs		121014350	NM_003889	Q006P5|Q008C8|Q96AC7|Q9UJ22|Q9UJ23|Q9UJ24|Q9UJ25|Q9UJ26|Q9UJ27|Q9UNW4	Frame_Shift_Del	DEL	ENST00000337940.4	37	CCDS2995.1																																																																																				0.587	NR1I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355126.1		
MECOM	2122	broad.mit.edu	37	3	168833257	168833257	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:168833257delT	ENST00000464456.1	-	7	3039	c.1839delA	c.(1837-1839)aaafs	p.K613fs	MECOM_ENST00000468789.1_Frame_Shift_Del_p.K613fs|MECOM_ENST00000460814.1_Frame_Shift_Del_p.K613fs|MECOM_ENST00000264674.3_Frame_Shift_Del_p.K678fs|MECOM_ENST00000392736.3_Frame_Shift_Del_p.K613fs|MECOM_ENST00000494292.1_Frame_Shift_Del_p.K801fs|MECOM_ENST00000472280.1_Frame_Shift_Del_p.K614fs|MECOM_ENST00000433243.2_Frame_Shift_Del_p.K614fs	NM_001164000.1	NP_001157472.1	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus	22					regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G614fs*30(2)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	85						CGTTGCTTCCTTTTTTTCCCC	0.498																																					p.K678fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.2034delA	3						.						121.0	110.0	114.0					3																	168833257		2203	4300	6503	170315951	SO:0001589	frameshift_variant	2122	exon8			S82592, AF164154	CCDS3205.1, CCDS54669.1, CCDS54670.1	3q26.2	2013-01-08	2009-08-07	2009-08-07	ENSG00000085276	ENSG00000085276		"""Zinc fingers, C2H2-type"""	3498	protein-coding gene	gene with protein product		165215	"""myelodysplasia syndrome 1"", ""ecotropic viral integration site 1"""	MDS1, EVI1		2115646, 8171026, 8643684	Standard	NM_001105077		Approved	MDS1-EVI1, PRDM3	uc011bpj.1	Q03112	OTTHUMG00000158596	ENST00000464456.1:c.1839delA	3.37:g.168833257delT	ENSP00000419770:p.Lys613fs		170315951	NM_001105077	Q13466|Q6FH90	Frame_Shift_Del	DEL	ENST00000464456.1	37	CCDS54669.1																																																																																				0.498	MECOM-020	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351519.1	NM_005241, NM_004991	
MUC4	4585	broad.mit.edu	37	3	195515747	195515747	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr3:195515747C>T	ENST00000463781.3	-	2	3163	c.2704G>A	c.(2704-2706)Gcc>Acc	p.A902T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A902T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	907	Ser-rich.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.A902T(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAAATGGCGGCTGTCTCCTGA	0.607																																					p.A902T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2704A	3						.						83.0	87.0	86.0					3																	195515747		2070	4186	6256	197000142	SO:0001583	missense	4585	exon2			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.2704G>A	3.37:g.195515747C>T	ENSP00000417498:p.Ala902Thr		197000142	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	c	6.828	0.521956	0.13005	.	.	ENSG00000145113	ENST00000463781;ENST00000475231;ENST00000392409	T;T	0.49139	0.79;0.8	2.78	-5.56	0.02529	.	1.962100	0.02835	N	0.127184	T	0.21186	0.0510	N	0.14661	0.345	0.09310	N	1	B;B	0.22346	0.068;0.035	B;B	0.20767	0.031;0.004	T	0.19031	-1.0318	10	0.06494	T	0.89	0.8101	1.2495	0.01979	0.1729:0.2887:0.1181:0.4203	.	902;907	E7ESK3;Q99102	.;MUC4_HUMAN	T	902;902;876	ENSP00000417498:A902T;ENSP00000420243:A902T	ENSP00000376209:A876T	A	-	1	0	MUC4	197000142	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.741000	0.04855	-1.266000	0.02446	-0.414000	0.06135	GCC		0.607	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
C4orf45	152940	broad.mit.edu	37	4	159956188	159956189	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr4:159956188_159956189insA	ENST00000434826.2	-	1	144_145	c.60_61insT	c.(58-63)tttacafs	p.T21fs	C4orf45_ENST00000508011.1_Intron	NM_152543.2	NP_689756.2	Q96LM5	CD045_HUMAN	chromosome 4 open reading frame 45	21								p.T21fs*43(1)		large_intestine(2)|lung(3)	5						TATTTACCTGTAAAAATCATTT	0.332																																					p.T21fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.61_62insT	4						.																																			160175639	SO:0001589	frameshift_variant	152940	exon1				CCDS47156.1	4q32.1	2012-03-02			ENSG00000164123	ENSG00000164123			26342	protein-coding gene	gene with protein product							Standard	NM_152543		Approved	FLJ25371	uc003iqf.1	Q96LM5	OTTHUMG00000161988	ENST00000434826.2:c.61dupT	4.37:g.159956193_159956193dupA	ENSP00000412215:p.Thr21fs		160175638	NM_152543	A8MPU3|C9J0T8	Frame_Shift_Ins	INS	ENST00000434826.2	37	CCDS47156.1																																																																																				0.332	C4orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366636.1	NM_152543	
CFI	3426	broad.mit.edu	37	4	110663747	110663747	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr4:110663747G>A	ENST00000394634.2	-	12	1641	c.1434C>T	c.(1432-1434)aaC>aaT	p.N478N	CFI_ENST00000394635.3_Silent_p.N486N|CFI_ENST00000512148.1_Silent_p.N471N	NM_000204.3	NP_000195	P05156	CFAI_HUMAN	complement factor I	478	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.N478N(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|skin(2)|stomach(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000331)		AGACTCTTTCGTTATCTAAAC	0.333																																					p.N478N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1434T	4						.						73.0	72.0	72.0					4																	110663747		2203	4299	6502	110883196	SO:0001819	synonymous_variant	3426	exon12			J02770	CCDS34049.1	4q25	2014-09-17	2006-02-10	2006-02-10		ENSG00000205403	3.4.21.45	"""Complement system"""	5394	protein-coding gene	gene with protein product	"""Konglutinogen-activating factor"", ""C3b-inactivator"""	217030	"""I factor (complement)"""	IF		2956252	Standard	NM_000204		Approved	FI, C3b-INA, KAF	uc003hzr.4	P05156		ENST00000394634.2:c.1434C>T	4.37:g.110663747G>A			110883196	NM_000204	O60442	Silent	SNP	ENST00000394634.2	37	CCDS34049.1																																																																																				0.333	CFI-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_000204	
ANK2	287	broad.mit.edu	37	4	114278303	114278303	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr4:114278303C>A	ENST00000357077.4	+	38	8582	c.8529C>A	c.(8527-8529)agC>agA	p.S2843R	ANK2_ENST00000264366.6_Missense_Mutation_p.S2810R|ANK2_ENST00000506722.1_Intron|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000394537.3_Intron|ANK2_ENST00000510275.2_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	2843					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.S2843R(1)		NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		CCAGTGAAAGCTTTTCATCTT	0.403																																					p.S2843R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C8529A	4						.						111.0	110.0	111.0					4																	114278303		2203	4300	6503	114497752	SO:0001583	missense	287	exon38			M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"""Ankyrin repeat domain containing"""	493	protein-coding gene	gene with protein product		106410	"""long (electrocardiographic) QT syndrome 4"""	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.8529C>A	4.37:g.114278303C>A	ENSP00000349588:p.Ser2843Arg		114497752	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	37	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	C	0.268	-0.994969	0.02145	.	.	ENSG00000145362	ENST00000357077;ENST00000264366	T;T	0.66638	-0.2;-0.22	5.75	2.02	0.26589	.	1.366100	0.04438	N	0.370319	T	0.57373	0.2049	L	0.47716	1.5	0.09310	N	1	B;B	0.28178	0.201;0.202	B;B	0.21360	0.024;0.034	T	0.36696	-0.9737	9	.	.	.	.	5.7431	0.18104	0.0:0.588:0.1288:0.2832	.	2810;2843	Q01484;Q01484-4	ANK2_HUMAN;.	R	2843;2810	ENSP00000349588:S2843R;ENSP00000264366:S2810R	.	S	+	3	2	ANK2	114497752	0.000000	0.05858	0.002000	0.10522	0.009000	0.06853	-0.118000	0.10692	0.368000	0.24481	-0.145000	0.13849	AGC		0.403	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148	
SETD7	80854	broad.mit.edu	37	4	140454347	140454347	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr4:140454347C>T	ENST00000274031.3	-	3	980	c.344G>A	c.(343-345)cGt>cAt	p.R115H	SETD7_ENST00000406354.1_3'UTR|SETD7_ENST00000506866.2_Missense_Mutation_p.R115H|SETD7_ENST00000404104.3_Missense_Mutation_p.R115H	NM_030648.2	NP_085151.1	Q8WTS6	SETD7_HUMAN	SET domain containing (lysine methyltransferase) 7	115					chromatin modification (GO:0016568)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)	p.R115H(1)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	8	all_hematologic(180;0.156)					CACTCCATGACGAATGTTATC	0.458																																					p.R115H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G344A	4						.						177.0	152.0	160.0					4																	140454347		2203	4300	6503	140673797	SO:0001583	missense	80854	exon3			AB051504	CCDS3748.1	4q31.1	2011-07-01			ENSG00000145391	ENSG00000145391		"""Chromatin-modifying enzymes / K-methyltransferases"""	30412	protein-coding gene	gene with protein product		606594				11850410, 11779497	Standard	NM_030648		Approved	KIAA1717, SET7, SET7/9, Set9, KMT7	uc003ihw.3	Q8WTS6	OTTHUMG00000133385	ENST00000274031.3:c.344G>A	4.37:g.140454347C>T	ENSP00000274031:p.Arg115His		140673797	NM_030648	B5WWL3|Q0VAH3|Q4W5A9|Q9C0E6	Missense_Mutation	SNP	ENST00000274031.3	37	CCDS3748.1	.	.	.	.	.	.	.	.	.	.	C	34	5.370884	0.95923	.	.	ENSG00000145391	ENST00000506866;ENST00000274031;ENST00000404104	T;T;T	0.60040	0.22;0.22;0.78	5.84	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.76162	0.3949	M	0.76838	2.35	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.79704	-0.1692	10	0.72032	D	0.01	-21.9116	14.6848	0.69042	0.0:0.9308:0.0:0.0692	.	115;115	B5MCZ8;Q8WTS6	.;SETD7_HUMAN	H	115	ENSP00000427300:R115H;ENSP00000274031:R115H;ENSP00000385913:R115H	ENSP00000274031:R115H	R	-	2	0	SETD7	140673797	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	7.304000	0.78882	1.479000	0.48272	0.655000	0.94253	CGT		0.458	SETD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257236.1	NM_030648	
UCP1	7350	broad.mit.edu	37	4	141489827	141489827	+	Silent	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr4:141489827T>C	ENST00000262999.3	-	1	132	c.57A>G	c.(55-57)tcA>tcG	p.S19S		NM_021833.4	NP_068605.1	P25874	UCP1_HUMAN	uncoupling protein 1 (mitochondrial, proton carrier)	19					brown fat cell differentiation (GO:0050873)|cellular metabolic process (GO:0044237)|mitochondrial transport (GO:0006839)|proton transport (GO:0015992)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	oxidative phosphorylation uncoupler activity (GO:0017077)	p.S19S(1)		NS(1)|breast(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(1)|stomach(1)	16	all_hematologic(180;0.162)					CTATTCCAGCTGAGAAGAGCT	0.627																																					p.S19S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A57G	4						.						47.0	40.0	42.0					4																	141489827		2203	4300	6503	141709277	SO:0001819	synonymous_variant	7350	exon1			X51955	CCDS3753.1	4q28-q31	2013-05-22			ENSG00000109424	ENSG00000109424		"""Solute carriers"""	12517	protein-coding gene	gene with protein product		113730		UCP		2380264	Standard	NM_021833		Approved	SLC25A7	uc011chj.2	P25874	OTTHUMG00000133415	ENST00000262999.3:c.57A>G	4.37:g.141489827T>C			141709277	NM_021833	Q13218|Q4KMZ3|Q68G66	Silent	SNP	ENST00000262999.3	37	CCDS3753.1																																																																																				0.627	UCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257273.1		
RNF150	57484	broad.mit.edu	37	4	142053667	142053667	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr4:142053667C>T	ENST00000515673.2	-	1	329	c.296G>A	c.(295-297)cGc>cAc	p.R99H	RNF150_ENST00000420921.2_Intron|RNF150_ENST00000306799.3_Missense_Mutation_p.R99H|RNF150_ENST00000507500.1_Missense_Mutation_p.R99H			Q9ULK6	RN150_HUMAN	ring finger protein 150	99	PA.					integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.R99H(1)|p.R8H(1)		breast(1)|large_intestine(10)|lung(7)|ovary(1)	19	all_hematologic(180;0.162)					GCAGGCCAGGCGGTCGTGGGC	0.672																																					p.R99H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G296A	4						.						24.0	24.0	24.0					4																	142053667		2198	4294	6492	142273117	SO:0001583	missense	57484	exon1			AB033040	CCDS34065.1	4q31.1	2013-01-09			ENSG00000170153	ENSG00000170153		"""RING-type (C3HC4) zinc fingers"""	23138	protein-coding gene	gene with protein product						10574462	Standard	XM_005263150		Approved	KIAA1214	uc003iio.1	Q9ULK6	OTTHUMG00000161380	ENST00000515673.2:c.296G>A	4.37:g.142053667C>T	ENSP00000425840:p.Arg99His		142273117	NM_020724	Q3T1D0|Q6ZNW6	Missense_Mutation	SNP	ENST00000515673.2	37	CCDS34065.1	.	.	.	.	.	.	.	.	.	.	C	16.76	3.213003	0.58452	.	.	ENSG00000170153	ENST00000306799;ENST00000515673;ENST00000507500	T;T;T	0.06371	3.31;3.31;3.31	4.06	4.06	0.47325	Protease-associated domain, PA (1);	0.294750	0.29638	N	0.011587	T	0.06645	0.0170	L	0.41236	1.265	0.80722	D	1	P;P;P	0.45672	0.5;0.864;0.555	B;B;B	0.39590	0.179;0.304;0.17	T	0.48969	-0.8987	10	0.14656	T	0.56	.	16.6376	0.85063	0.0:1.0:0.0:0.0	.	99;99;99	Q9ULK6-2;Q9ULK6-3;Q9ULK6	.;.;RN150_HUMAN	H	99	ENSP00000304321:R99H;ENSP00000425840:R99H;ENSP00000425568:R99H	ENSP00000304321:R99H	R	-	2	0	RNF150	142273117	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.694000	0.61760	1.991000	0.58162	0.455000	0.32223	CGC		0.672	RNF150-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364739.2	XM_291090	
FAM198B	51313	broad.mit.edu	37	4	159091962	159091962	+	Missense_Mutation	SNP	C	C	T	rs376041501		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr4:159091962C>T	ENST00000296530.8	-	2	1187	c.566G>A	c.(565-567)cGa>cAa	p.R189Q	RP11-597D13.9_ENST00000509463.1_RNA|RP11-597D13.9_ENST00000514381.1_RNA|RP11-597D13.9_ENST00000505532.1_RNA|FAM198B_ENST00000393807.5_Missense_Mutation_p.R189Q|FAM198B_ENST00000585682.1_Missense_Mutation_p.R189Q|RP11-597D13.9_ENST00000503611.1_RNA|FAM198B_ENST00000589306.1_Intron|FAM198B_ENST00000592057.1_Missense_Mutation_p.R189Q	NM_016613.6	NP_057697.2	Q6UWH4	F198B_HUMAN	family with sequence similarity 198, member B	189						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.R189Q(2)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(14)|skin(2)|urinary_tract(1)	26						GCCCCCGGCTCGCACTCCCGG	0.617											OREG0016378	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R189Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G566A	4						.	C	GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	39.0	44.0	42.0		566,566,566	-2.9	0.0	4		42	3,8597	3.0+/-9.4	0,3,4297	no	missense,missense,missense	FAM198B	NM_001031700.2,NM_001128424.1,NM_016613.6	43,43,43	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	benign,benign,benign	189/528,189/520,189/520	159091962	3,13003	2203	4300	6503	159311412	SO:0001583	missense	51313	exon2				CCDS3798.1, CCDS34087.1	4q32.1	2012-11-29	2009-10-19	2009-10-19	ENSG00000164125	ENSG00000164125			25312	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 18"""	C4orf18		12975309	Standard	NM_001031700		Approved	FLJ38155, DKFZp434L142	uc003ipr.4	Q6UWH4	OTTHUMG00000161537	ENST00000296530.8:c.566G>A	4.37:g.159091962C>T	ENSP00000296530:p.Arg189Gln	1798	159311412	NM_001128424	Q498Z3|Q6IAF9|Q6ZMF2|Q86XL0	Missense_Mutation	SNP	ENST00000296530.8	37	CCDS3798.1	.	.	.	.	.	.	.	.	.	.	C	6.863	0.528552	0.13127	0.0	3.49E-4	ENSG00000164125	ENST00000337222;ENST00000296530;ENST00000393807;ENST00000417442	T;T	0.30448	1.54;1.53	3.82	-2.92	0.05615	.	1.300400	0.05171	N	0.499509	T	0.22126	0.0533	L	0.50333	1.59	0.09310	N	1	B;B;B	0.18968	0.013;0.032;0.032	B;B;B	0.08055	0.002;0.003;0.002	T	0.20075	-1.0286	10	0.33141	T	0.24	.	0.7124	0.00926	0.3251:0.1559:0.2957:0.2233	.	189;189;189	Q6UWH4-3;Q6UWH4-2;Q6UWH4	.;.;F198B_HUMAN	Q	189	ENSP00000296530:R189Q;ENSP00000377396:R189Q	ENSP00000296530:R189Q	R	-	2	0	FAM198B	159311412	0.000000	0.05858	0.000000	0.03702	0.364000	0.29643	-0.939000	0.03933	-0.720000	0.04935	0.655000	0.94253	CGA		0.617	FAM198B-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365230.1	NM_001031700, NM_016613	
NEK1	4750	broad.mit.edu	37	4	170345785	170345785	+	Silent	SNP	C	C	T	rs190807750		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr4:170345785C>T	ENST00000439128.2	-	29	3697	c.3057G>A	c.(3055-3057)tcG>tcA	p.S1019S	NEK1_ENST00000507142.1_Silent_p.S1047S|NEK1_ENST00000510533.1_Silent_p.S975S|NEK1_ENST00000512193.1_Silent_p.S950S|NEK1_ENST00000511633.1_Silent_p.S1003S	NM_012224.2	NP_036356.1	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1	1019					cellular response to DNA damage stimulus (GO:0006974)|cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.S1047S(1)		NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|stomach(1)	45		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)		GTGGTAAATGCGAGTGAGATC	0.393													C|||	1	0.000199681	0.0	0.0	5008	,	,		19210	0.0		0.001	False		,,,				2504	0.0				p.S975S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2925A	4						.						97.0	93.0	94.0					4																	170345785		1862	4090	5952	170582360	SO:0001819	synonymous_variant	4750	exon28			AB067488	CCDS47162.1, CCDS56348.1, CCDS56349.1, CCDS56350.1, CCDS56351.1	4q32.3	2012-11-15	2012-11-15		ENSG00000137601	ENSG00000137601			7744	protein-coding gene	gene with protein product		604588	"""NIMA (never in mitosis gene a)-related kinase 1"""			1382974, 8274451	Standard	NM_012224		Approved	NY-REN-55, KIAA1901	uc003isd.2	Q96PY6	OTTHUMG00000160963	ENST00000439128.2:c.3057G>A	4.37:g.170345785C>T			170582360	NM_001199400	G5E9Z3|Q05DG5|Q14CB7|Q5H9T1|Q6PIB8|Q96SS2|Q9H6P7|Q9Y594	Silent	SNP	ENST00000439128.2	37	CCDS47162.1																																																																																				0.393	NEK1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000363157.3		
ADAM29	11086	broad.mit.edu	37	4	175897874	175897874	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr4:175897874T>A	ENST00000359240.3	+	5	1868	c.1198T>A	c.(1198-1200)Tgt>Agt	p.C400S	RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000514159.1_Missense_Mutation_p.C400S|ADAM29_ENST00000445694.1_Missense_Mutation_p.C400S|ADAM29_ENST00000404450.4_Missense_Mutation_p.C400S	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	400	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.C400S(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		TGTGAAGCGCTGTGGGAATGG	0.408																																					p.C400S	Ovarian(140;1727 1835 21805 25838 41440)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1198A	4						.						229.0	223.0	225.0					4																	175897874		2203	4300	6503	176134449	SO:0001583	missense	11086	exon3			AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"""ADAM metallopeptidase domain containing"""	207	protein-coding gene	gene with protein product	"""cancer/testis antigen 73"""	604778	"""a disintegrin and metalloproteinase domain 29"""			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.1198T>A	4.37:g.175897874T>A	ENSP00000352177:p.Cys400Ser		176134449	NM_001130705	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Missense_Mutation	SNP	ENST00000359240.3	37	CCDS3823.1	.	.	.	.	.	.	.	.	.	.	T	13.30	2.196591	0.38806	.	.	ENSG00000168594	ENST00000359240;ENST00000445694;ENST00000404450;ENST00000514159	T;T;T;T	0.08008	3.14;3.14;3.14;3.14	3.6	3.6	0.41247	Blood coagulation inhibitor, Disintegrin (1);	0.000000	0.37906	U	0.001895	T	0.32194	0.0821	M	0.89601	3.045	0.32443	N	0.546413	D	0.89917	1.0	D	0.77004	0.989	T	0.51841	-0.8654	9	.	.	.	.	10.78	0.46371	0.0:0.0:0.0:1.0	.	400	Q9UKF5	ADA29_HUMAN	S	400	ENSP00000352177:C400S;ENSP00000414544:C400S;ENSP00000384229:C400S;ENSP00000423517:C400S	.	C	+	1	0	ADAM29	176134449	1.000000	0.71417	0.950000	0.38849	0.012000	0.07955	5.589000	0.67523	1.866000	0.54105	0.472000	0.43445	TGT		0.408	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding			
DCTD	1635	broad.mit.edu	37	4	183836080	183836080	+	Silent	SNP	C	C	T	rs371179209		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr4:183836080C>T	ENST00000438320.2	-	3	530	c.240G>A	c.(238-240)ccG>ccA	p.P80P	DCTD_ENST00000513383.1_5'UTR|DCTD_ENST00000510370.1_Silent_p.P80P|DCTD_ENST00000357067.3_Silent_p.P91P	NM_001921.2	NP_001912.2	P32321	DCTD_HUMAN	dCMP deaminase	80					nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide biosynthetic process (GO:0009165)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside biosynthetic process (GO:0046134)|pyrimidine nucleotide metabolic process (GO:0006220)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	dCMP deaminase activity (GO:0004132)|zinc ion binding (GO:0008270)	p.P80P(1)		endometrium(4)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|urinary_tract(1)	18		all_lung(41;5.16e-14)|Lung NSC(41;1.33e-13)|Colorectal(36;0.00666)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.202)		all cancers(43;1.65e-24)|Epithelial(43;3.44e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.39e-10)|Colorectal(24;4.69e-07)|COAD - Colon adenocarcinoma(29;7.07e-05)|STAD - Stomach adenocarcinoma(60;0.000118)|GBM - Glioblastoma multiforme(59;0.000472)|LUSC - Lung squamous cell carcinoma(40;0.00984)|READ - Rectum adenocarcinoma(43;0.0419)	Cytarabine(DB00987)	CCCTACCGTACGGGTATTTGG	0.473																																					p.P80P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G240A	4						.	C	,	0,4406		0,0,2203	231.0	160.0	184.0		273,240	-10.3	0.2	4		184	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	DCTD	NM_001012732.1,NM_001921.2	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	91/190,80/179	183836080	1,13005	2203	4300	6503	184073074	SO:0001819	synonymous_variant	1635	exon3			L12136	CCDS3831.1, CCDS34108.1	4q35.1	2008-08-01			ENSG00000129187	ENSG00000129187	3.5.4.12		2710	protein-coding gene	gene with protein product		607638					Standard	XM_005262778		Approved		uc003ivg.3	P32321	OTTHUMG00000160685	ENST00000438320.2:c.240G>A	4.37:g.183836080C>T			184073074	NM_001921	B2R836|D3DP49|D3DP50|Q5M7Z8|Q9BVD8	Silent	SNP	ENST00000438320.2	37	CCDS3831.1																																																																																				0.473	DCTD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361743.2		
SORBS2	8470	broad.mit.edu	37	4	186545077	186545077	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr4:186545077C>T	ENST00000284776.7	-	13	2003	c.1494G>A	c.(1492-1494)acG>acA	p.T498T	SORBS2_ENST00000437304.2_Intron|SORBS2_ENST00000448662.2_Intron|SORBS2_ENST00000498125.1_Intron|SORBS2_ENST00000418609.1_Silent_p.T402T|SORBS2_ENST00000449407.2_Intron|SORBS2_ENST00000393528.3_Intron|SORBS2_ENST00000319471.9_Intron|SORBS2_ENST00000355634.5_Silent_p.T598T|SORBS2_ENST00000431808.1_Silent_p.T498T	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	498					actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)	p.T498T(1)		endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		GCACCTCCTCCGTGGAGCACT	0.572																																					p.T498T	Esophageal Squamous(153;41 2433 9491 36028)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1494A	4						.						89.0	82.0	84.0					4																	186545077		2203	4300	6503	186782071	SO:0001819	synonymous_variant	8470	exon13				CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"""Arg/Abl interacting protein"""					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.1494G>A	4.37:g.186545077C>T			186782071	NM_021069	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Silent	SNP	ENST00000284776.7	37	CCDS3845.1																																																																																				0.572	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603	
SORBS2	8470	broad.mit.edu	37	4	186578601	186578601	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr4:186578601C>T	ENST00000284776.7	-	6	753	c.244G>A	c.(244-246)Gga>Aga	p.G82R	SORBS2_ENST00000437304.2_Missense_Mutation_p.G261R|SORBS2_ENST00000448662.2_Missense_Mutation_p.G151R|SORBS2_ENST00000498125.1_5'Flank|SORBS2_ENST00000418609.1_5'Flank|SORBS2_ENST00000449407.2_Missense_Mutation_p.G168R|SORBS2_ENST00000393528.3_Missense_Mutation_p.G128R|SORBS2_ENST00000319471.9_Missense_Mutation_p.G168R|SORBS2_ENST00000355634.5_Missense_Mutation_p.G182R|SORBS2_ENST00000431808.1_Missense_Mutation_p.G82R	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	82	SoHo. {ECO:0000255|PROSITE- ProRule:PRU00195}.				actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)	p.G82R(1)|p.G151R(1)		endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		GTGGGGATTCCGGATTCATCC	0.562																																					p.G151R	Esophageal Squamous(153;41 2433 9491 36028)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G451A	4						.						95.0	93.0	93.0					4																	186578601		2203	4300	6503	186815595	SO:0001583	missense	8470	exon6				CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"""Arg/Abl interacting protein"""					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.244G>A	4.37:g.186578601C>T	ENSP00000284776:p.Gly82Arg		186815595	NM_001145672	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Missense_Mutation	SNP	ENST00000284776.7	37	CCDS3845.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	34|34	5.305198|5.305198	0.95601|0.95601	.|.	.|.	ENSG00000154556|ENSG00000154556	ENST00000284776;ENST00000448662;ENST00000431808;ENST00000437304;ENST00000319471;ENST00000449407;ENST00000355634;ENST00000393528;ENST00000319454;ENST00000445343;ENST00000439914;ENST00000444771|ENST00000438278	T;T;T;T;T;T;T;T;T;T;T;T|.	0.39229|.	1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09;1.09|.	4.88|4.88	4.88|4.88	0.63580|0.63580	Sorbin-like (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.67258|0.67258	0.2874|0.2874	L|L	0.42529|0.42529	1.33|1.33	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D;D;D;D;D;D|.	0.89917|.	0.998;0.988;1.0;0.994;1.0;1.0;1.0;1.0;1.0;1.0;0.983;1.0|.	P;P;D;P;D;D;D;D;D;D;P;D|.	0.97110|.	0.895;0.757;1.0;0.891;1.0;1.0;1.0;1.0;0.997;1.0;0.83;1.0|.	T|T	0.62914|0.62914	-0.6753|-0.6753	10|5	0.87932|.	D|.	0|.	-30.881|-30.881	18.5848|18.5848	0.91185|0.91185	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	145;128;151;128;182;82;168;261;151;128;82;128|.	B7Z3D7;G3XAI0;C9JKV9;O94875-4;B3KPQ7;O94875;E9PAS5;E9PAW4;B7Z1G5;O94875-5;O94875-3;O94875-2|.	.;.;.;.;.;SRBS2_HUMAN;.;.;.;.;.;.|.	R|Q	82;151;82;261;168;168;182;128;128;82;82;82|25	ENSP00000284776:G82R;ENSP00000409158:G151R;ENSP00000411764:G82R;ENSP00000396008:G261R;ENSP00000322182:G168R;ENSP00000397262:G168R;ENSP00000347852:G182R;ENSP00000377162:G128R;ENSP00000321983:G128R;ENSP00000399048:G82R;ENSP00000408909:G82R;ENSP00000410483:G82R|.	ENSP00000284776:G82R|.	G|R	-|-	1|2	0|0	SORBS2|SORBS2	186815595|186815595	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.998000|0.998000	0.95712|0.95712	7.085000|7.085000	0.76875|0.76875	2.697000|2.697000	0.92050|0.92050	0.563000|0.563000	0.77884|0.77884	GGA|CGG		0.562	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603	
POLN	353497	broad.mit.edu	37	4	2172415	2172415	+	Silent	SNP	T	T	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr4:2172415T>A	ENST00000511885.2	-	13	1898	c.1545A>T	c.(1543-1545)tcA>tcT	p.S515S	POLN_ENST00000382865.1_Silent_p.S515S|POLN_ENST00000515357.1_5'UTR			Q7Z5Q5	DPOLN_HUMAN	polymerase (DNA directed) nu	515					double-strand break repair via homologous recombination (GO:0000724)|interstrand cross-link repair (GO:0036297)|translesion synthesis (GO:0019985)	nucleus (GO:0005634)	cyclin binding (GO:0030332)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)	p.S515S(1)		kidney(6)|large_intestine(5)|liver(1)|lung(8)|ovary(2)|skin(4)|urinary_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(23;0.0955)			CCACTGCTTCTGATGTAGACG	0.463								DNA polymerases (catalytic subunits)																													p.S515S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1545T	4						.						145.0	136.0	139.0					4																	2172415		2203	4300	6503	2142213	SO:0001819	synonymous_variant	353497	exon11			AF044578	CCDS3360.1	4p16.3	2012-05-18			ENSG00000130997	ENSG00000130997		"""DNA polymerases"""	18870	protein-coding gene	gene with protein product		610887				12794064	Standard	NM_181808		Approved		uc003ger.2	Q7Z5Q5	OTTHUMG00000090081	ENST00000511885.2:c.1545A>T	4.37:g.2172415T>A			2142213	NM_181808	A2A336|B4E158|Q4TTW4|Q6ZNF4	Silent	SNP	ENST00000511885.2	37	CCDS3360.1	.	.	.	.	.	.	.	.	.	.	T	0.569	-0.841905	0.02671	.	.	ENSG00000130997	ENST00000511098	.	.	.	5.65	-6.61	0.01818	.	.	.	.	.	T	0.27697	0.0681	.	.	.	0.33556	D	0.596743	.	.	.	.	.	.	T	0.33343	-0.9872	4	.	.	.	-16.241	2.0335	0.03534	0.2508:0.3879:0.1338:0.2275	.	.	.	.	L	149	.	.	Q	-	2	0	POLN	2142213	0.013000	0.17824	0.020000	0.16555	0.005000	0.04900	-2.773000	0.00778	-1.412000	0.02030	-0.256000	0.11100	CAG		0.463	POLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000205684.2	NM_181808	
GRK4	2868	broad.mit.edu	37	4	3015555	3015558	+	Splice_Site	DEL	AGTA	AGTA	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	AGTA	AGTA					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr4:3015555_3015558delAGTA	ENST00000398052.4	+	8	1084	c.741delAGTA	c.(739-741)gta>gt	p.V248fs	GRK4_ENST00000398051.4_Splice_Site_p.V216fs|GRK4_ENST00000345167.6_Splice_Site_p.V216fs|GRK4_ENST00000504933.1_Splice_Site_p.V248fs	NM_182982.2	NP_892027.2	P32298	GRK4_HUMAN	G protein-coupled receptor kinase 4	248	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				G-protein coupled receptor internalization (GO:0002031)|receptor internalization (GO:0031623)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|rhodopsin kinase activity (GO:0050254)	p.?(1)		lung(1)|upper_aerodigestive_tract(1)	2				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		GTAGATTCGTAGTAAGTGTCTCCT	0.417																																					p.247_247del												.	.	1	Unknown(1)	large_intestine(1)	c.741_741del	4						.																																			2985356	SO:0001630	splice_region_variant	2868	exon8				CCDS33946.1, CCDS33947.1, CCDS47002.1, CCDS68656.1	4p16.3	2008-02-05	2004-02-04	2004-02-06	ENSG00000125388	ENSG00000125388			4543	protein-coding gene	gene with protein product		137026	"""G protein-coupled receptor kinase 2-like (Drosophila)"""	GPRK2L		1338872	Standard	NM_182982		Approved	GPRK4	uc003ggn.1	P32298	OTTHUMG00000159914	ENST00000398052.4:c.741+1AGTA>-	4.37:g.3015555_3015558delAGTA			2985353	NM_182982	O00641|O00642|Q13293|Q13294|Q13295|Q14453|Q14725|Q15313|Q15314|Q15315|Q15316|Q17RH6|Q53EQ8	Splice_Site	DEL	ENST00000398052.4	37	CCDS33946.1																																																																																				0.417	GRK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358176.2	NM_005307	Frame_Shift_Del
EVC	2121	broad.mit.edu	37	4	5721019	5721019	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr4:5721019G>A	ENST00000264956.6	+	2	403	c.219G>A	c.(217-219)gcG>gcA	p.A73A	EVC_ENST00000509451.1_Silent_p.A73A|EVC_ENST00000382674.2_Silent_p.A73A	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	73					cartilage development (GO:0051216)|endochondral bone growth (GO:0003416)|muscle organ development (GO:0007517)|positive regulation of smoothened signaling pathway (GO:0045880)|skeletal system development (GO:0001501)|smoothened signaling pathway (GO:0007224)	ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A73A(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|stomach(1)	28		Myeloproliferative disorder(84;0.117)				AGTCTAATGCGCAGACCCCCT	0.483																																					p.A73A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G219A	4						.						196.0	196.0	196.0					4																	5721019		2203	4300	6503	5771920	SO:0001819	synonymous_variant	2121	exon2			AF216184	CCDS3383.1	4p16	2008-07-03			ENSG00000072840	ENSG00000072840			3497	protein-coding gene	gene with protein product		604831				10700184	Standard	NM_153717		Approved	DWF-1	uc003gil.1	P57679	OTTHUMG00000090427	ENST00000264956.6:c.219G>A	4.37:g.5721019G>A			5771920	NM_153717		Silent	SNP	ENST00000264956.6	37	CCDS3383.1																																																																																				0.483	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1		
JAKMIP1	152789	broad.mit.edu	37	4	6086661	6086661	+	Missense_Mutation	SNP	C	C	T	rs371853673		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr4:6086661C>T	ENST00000282924.5	-	5	1351	c.866G>A	c.(865-867)cGa>cAa	p.R289Q	JAKMIP1_ENST00000409831.1_Missense_Mutation_p.R289Q|JAKMIP1_ENST00000409371.3_Missense_Mutation_p.R124Q|JAKMIP1_ENST00000409021.3_Missense_Mutation_p.R289Q|JAKMIP1_ENST00000457227.2_5'UTR|JAKMIP1_ENST00000410077.2_Missense_Mutation_p.R124Q	NM_144720.3	NP_653321.1	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein 1	289	Mediates association with microtubules.				cognition (GO:0050890)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|microtubule (GO:0005874)|ribonucleoprotein complex (GO:0030529)	GABA receptor binding (GO:0050811)|RNA binding (GO:0003723)	p.R289Q(2)		NS(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						TAGTTGAAATCGCCTCACATC	0.383																																					p.R289Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G866A	4						.	C	GLN/ARG,GLN/ARG	0,4406		0,0,2203	207.0	196.0	200.0		866,866	4.8	1.0	4		200	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	JAKMIP1	NM_001099433.1,NM_144720.3	43,43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	289/832,289/627	6086661	1,13005	2203	4300	6503	6137562	SO:0001583	missense	152789	exon5			AK056126	CCDS3385.1, CCDS47005.1	4p16.1	2013-10-11	2009-08-13		ENSG00000152969	ENSG00000152969			26460	protein-coding gene	gene with protein product		611195				18941173	Standard	NM_144720		Approved	MARLIN1, JAMIP1, Gababrbp, FLJ31564	uc010idb.1	Q96N16	OTTHUMG00000125491	ENST00000282924.5:c.866G>A	4.37:g.6086661C>T	ENSP00000282924:p.Arg289Gln		6137562	NM_144720	A6H2J2|A6H2J3|A6H2J4|A6H2J5|A8MTK6|B4DHZ8|B8ZZR7|D3DVT0|Q86Y69|Q8N7G3	Missense_Mutation	SNP	ENST00000282924.5	37	CCDS3385.1	.	.	.	.	.	.	.	.	.	.	C	32	5.169452	0.94768	0.0	1.16E-4	ENSG00000152969	ENST00000409021;ENST00000409371;ENST00000418227;ENST00000425341;ENST00000429819;ENST00000282924;ENST00000409831;ENST00000410077	T;T;T;T;T	0.41400	1.41;1.14;1.41;1.41;1.0	4.79	4.79	0.61399	.	0.117591	0.37669	N	0.001986	T	0.65186	0.2667	M	0.77313	2.365	0.45946	D	0.998774	D;D;D;D;D	0.71674	0.998;0.974;0.998;0.998;0.974	D;P;D;D;P	0.75484	0.986;0.455;0.986;0.986;0.455	T	0.70630	-0.4819	10	0.87932	D	0	.	15.0225	0.71640	0.0:1.0:0.0:0.0	.	124;289;124;289;289	B4DHZ8;F2Z2K5;Q96N16-5;Q96N16-2;Q96N16	.;.;.;.;JKIP1_HUMAN	Q	289;124;289;289;181;289;289;124	ENSP00000386711:R289Q;ENSP00000387042:R124Q;ENSP00000282924:R289Q;ENSP00000386925:R289Q;ENSP00000386745:R124Q	ENSP00000282924:R289Q	R	-	2	0	JAKMIP1	6137562	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	7.396000	0.79891	2.203000	0.70933	0.591000	0.81541	CGA		0.383	JAKMIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246816.2	NM_144720	
TBC1D14	57533	broad.mit.edu	37	4	6996029	6996029	+	Splice_Site	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr4:6996029C>T	ENST00000409757.4	+	4	1086	c.962C>T	c.(961-963)gCa>gTa	p.A321V	AC097382.5_ENST00000441093.1_RNA|RN7SKP292_ENST00000365522.1_RNA|TBC1D14_ENST00000410031.1_Splice_Site_p.A93V|TBC1D14_ENST00000448507.1_Splice_Site_p.A321V|TBC1D14_ENST00000451522.2_Splice_Site_p.A41V	NM_020773.2	NP_065824.2	Q9P2M4	TBC14_HUMAN	TBC1 domain family, member 14	321					negative regulation of autophagy (GO:0010507)|recycling endosome to Golgi transport (GO:0071955)|regulation of autophagic vacuole assembly (GO:2000785)	autophagic vacuole (GO:0005776)|Golgi apparatus (GO:0005794)|recycling endosome (GO:0055037)	protein kinase binding (GO:0019901)|Rab GTPase activator activity (GO:0005097)	p.A306V(1)		breast(1)|endometrium(5)|large_intestine(4)|lung(9)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	22						GACAGACCAGCGTGAGTTTAA	0.448																																					p.A321V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C962T	4						.						139.0	132.0	135.0					4																	6996029		2203	4300	6503	7046930	SO:0001630	splice_region_variant	57533	exon4			AL833868	CCDS3394.2, CCDS47006.1, CCDS75104.1	4p16.1	2008-01-22			ENSG00000132405	ENSG00000132405			29246	protein-coding gene	gene with protein product		614855				10718198	Standard	NM_020773		Approved	KIAA1322	uc003gjs.4	Q9P2M4	OTTHUMG00000090493	ENST00000409757.4:c.962+1C>T	4.37:g.6996029C>T			7046930	NM_001113361	B9A6L5|D3DVT4|E9PAZ6|Q8IW15|Q8NDK3	Missense_Mutation	SNP	ENST00000409757.4	37	CCDS3394.2	.	.	.	.	.	.	.	.	.	.	C	23.5	4.427888	0.83667	.	.	ENSG00000132405	ENST00000448507;ENST00000409757;ENST00000410031;ENST00000451522	T;T;T;T	0.58940	0.3;0.3;0.3;0.3	5.33	5.33	0.75918	.	0.049288	0.85682	D	0.000000	T	0.60025	0.2237	M	0.76328	2.33	0.80722	D	1	P;P	0.52692	0.887;0.955	B;B	0.41332	0.3;0.354	T	0.67925	-0.5544	10	0.59425	D	0.04	-17.5466	16.5604	0.84551	0.0:1.0:0.0:0.0	.	41;321	Q9P2M4-2;Q9P2M4	.;TBC14_HUMAN	V	321;321;93;41	ENSP00000404041:A321V;ENSP00000386921:A321V;ENSP00000386343:A93V;ENSP00000388886:A41V	ENSP00000386921:A321V	A	+	2	0	TBC1D14	7046930	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.017000	0.76399	2.778000	0.95560	0.655000	0.94253	GCA		0.448	TBC1D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206981.3	NM_020773	Missense_Mutation
SORCS2	57537	broad.mit.edu	37	4	7730156	7730156	+	Silent	SNP	C	C	T	rs551349051		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr4:7730156C>T	ENST00000507866.2	+	22	3058	c.2949C>T	c.(2947-2949)gaC>gaT	p.D983D	SORCS2_ENST00000329016.9_Silent_p.D811D	NM_020777.2	NP_065828.2	Q96PQ0	SORC2_HUMAN	sortilin-related VPS10 domain containing receptor 2	983					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)	p.D833D(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(8)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	42						GGAGGGAAGACGTGGGCCTGG	0.602													C|||	1	0.000199681	0.0	0.0	5008	,	,		17746	0.0		0.0	False		,,,				2504	0.001				p.D983D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2949T	4						.						55.0	61.0	59.0					4																	7730156		1938	4140	6078	7781056	SO:0001819	synonymous_variant	57537	exon22			AB037750	CCDS47008.1	4p16.1	2008-02-05			ENSG00000184985	ENSG00000184985			16698	protein-coding gene	gene with protein product		606284				11499680	Standard	NM_020777		Approved	KIAA1329	uc003gkb.4	Q96PQ0	OTTHUMG00000159981	ENST00000507866.2:c.2949C>T	4.37:g.7730156C>T			7781056	NM_020777	Q9P2L7	Silent	SNP	ENST00000507866.2	37	CCDS47008.1																																																																																				0.602	SORCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358685.4	NM_020777	
ZCCHC4	29063	broad.mit.edu	37	4	25366746	25366746	+	Missense_Mutation	SNP	G	G	A	rs140336886		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr4:25366746G>A	ENST00000302874.4	+	12	1388	c.1364G>A	c.(1363-1365)cGc>cAc	p.R455H		NM_024936.2	NP_079212.2	Q9H5U6	ZCHC4_HUMAN	zinc finger, CCHC domain containing 4	455							methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.R455H(1)		endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|pancreas(1)	9		Breast(46;0.0503)				GATCATAAACGCAGTACTTGT	0.403													G|||	1	0.000199681	0.0	0.0	5008	,	,		19809	0.0		0.001	False		,,,				2504	0.0				p.R455H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1364A	4						.						139.0	125.0	129.0					4																	25366746		1917	4125	6042	24975844	SO:0001583	missense	29063	exon12			AF161537	CCDS43218.1	4p15.31	2014-02-18			ENSG00000168228	ENSG00000168228		"""Zinc fingers, CCHC domain containing"""	22917	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 4"""	611792				11042152	Standard	NM_024936		Approved	HSPC052, FLJ23024, ZGRF4	uc003grl.4	Q9H5U6	OTTHUMG00000160563	ENST00000302874.4:c.1364G>A	4.37:g.25366746G>A	ENSP00000303468:p.Arg455His		24975844	NM_024936	B2RXF6|B4DRD8|B7ZW20|Q5IW78|Q96AN7	Missense_Mutation	SNP	ENST00000302874.4	37	CCDS43218.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	15.36	2.810778	0.50421	.	.	ENSG00000168228	ENST00000302874	T	0.37058	1.22	5.73	5.73	0.89815	Zinc finger, CCHC-type (1);	0.198703	0.53938	D	0.000042	T	0.31575	0.0801	L	0.52759	1.655	0.40440	D	0.98003	P	0.39094	0.659	B	0.24541	0.054	T	0.20140	-1.0284	10	0.46703	T	0.11	-19.288	18.6595	0.91468	0.0:0.0:1.0:0.0	.	455	Q9H5U6	ZCHC4_HUMAN	H	455	ENSP00000303468:R455H	ENSP00000303468:R455H	R	+	2	0	ZCCHC4	24975844	1.000000	0.71417	0.994000	0.49952	0.663000	0.39108	5.146000	0.64845	2.720000	0.93068	0.591000	0.81541	CGC		0.403	ZCCHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361151.1		
GABRA2	2555	broad.mit.edu	37	4	46252503	46252503	+	Missense_Mutation	SNP	G	G	A	rs200801680		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr4:46252503G>A	ENST00000510861.1	-	10	1351	c.1178C>T	c.(1177-1179)aCg>aTg	p.T393M	GABRA2_ENST00000540012.1_Missense_Mutation_p.T398M|GABRA2_ENST00000507069.1_Missense_Mutation_p.T453M|GABRA2_ENST00000356504.1_Missense_Mutation_p.T393M|GABRA2_ENST00000514090.1_Missense_Mutation_p.T393M|GABRA2_ENST00000381620.4_Missense_Mutation_p.T393M			P47869	GBRA2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 2	393					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|neurotransmitter transport (GO:0006836)|regulation of neurotransmitter levels (GO:0001505)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of synaptic vesicle membrane (GO:0030285)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.T393M(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(9)|lung(33)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	56					Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zolpidem(DB00425)|Zopiclone(DB01198)	GGGTTCTGGCGTGGTTGCACT	0.428																																					p.T393M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1178T	4						.						189.0	190.0	190.0					4																	46252503		2203	4299	6502	45947260	SO:0001583	missense	2555	exon10				CCDS3471.1	4p12	2012-06-22			ENSG00000151834	ENSG00000151834		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4076	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 2"""	137140					Standard	NM_000807		Approved		uc010igc.2	P47869	OTTHUMG00000044266	ENST00000510861.1:c.1178C>T	4.37:g.46252503G>A	ENSP00000421828:p.Thr393Met		45947260	NM_000807	A8K0U7|B7Z1H8|Q59G14	Missense_Mutation	SNP	ENST00000510861.1	37	CCDS3471.1	.	.	.	.	.	.	.	.	.	.	G	16.47	3.133103	0.56828	.	.	ENSG00000151834	ENST00000510861;ENST00000514090;ENST00000381620;ENST00000356504;ENST00000540012;ENST00000507069	D;D;D;D;D;T	0.85556	-2.0;-2.0;-2.0;-2.0;-2.0;-0.54	5.96	5.07	0.68467	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.449819	0.27214	N	0.020396	D	0.87176	0.6112	L	0.34521	1.04	0.37020	D	0.896158	D;D	0.71674	0.998;0.991	D;P	0.65573	0.936;0.714	D	0.88736	0.3240	10	0.54805	T	0.06	.	14.1321	0.65260	0.0:0.1496:0.8504:0.0	.	398;393	B7Z1H8;P47869	.;GBRA2_HUMAN	M	393;393;393;393;398;453	ENSP00000421828:T393M;ENSP00000421300:T393M;ENSP00000371033:T393M;ENSP00000348897:T393M;ENSP00000444409:T398M;ENSP00000427603:T453M	ENSP00000348897:T393M	T	-	2	0	GABRA2	45947260	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.877000	0.48506	2.827000	0.97445	0.655000	0.94253	ACG		0.428	GABRA2-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360848.2		
ZAR1	326340	broad.mit.edu	37	4	48492311	48492311	+	Start_Codon_SNP	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr4:48492311G>A	ENST00000327939.4	+	1	43	c.3G>A	c.(1-3)atG>atA	p.M1I		NM_175619.1	NP_783318.1	Q86SH2	ZAR1_HUMAN	zygote arrest 1	1					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)		p.M1I(1)		endometrium(1)|large_intestine(4)	5						GTGCGCCCATGGCGGCCCTGG	0.751																																					p.M1I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3A	4						.						2.0	3.0	3.0					4																	48492311		1505	3391	4896	48187068	SO:0001582	initiator_codon_variant	326340	exon1			AY193890	CCDS3483.1	4p11	2014-02-20			ENSG00000182223	ENSG00000182223			20436	protein-coding gene	gene with protein product	"""zinc finger, 3CxxC-type 6"""	607520				12539046	Standard	NM_175619		Approved	Z3CXXC6	uc003gyd.3	Q86SH2	OTTHUMG00000102093	ENST00000327939.4:c.3G>A	4.37:g.48492311G>A	ENSP00000329803:p.Met1Ile		48187068	NM_175619		Missense_Mutation	SNP	ENST00000327939.4	37	CCDS3483.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.525375	0.85600	.	.	ENSG00000182223	ENST00000327939	.	.	.	4.31	3.46	0.39613	.	0.000000	0.85682	U	0.000000	T	0.42675	0.1213	.	.	.	0.80722	D	1	P	0.39551	0.678	B	0.36885	0.235	T	0.49818	-0.8899	8	0.87932	D	0	-14.978	9.1888	0.37187	0.1088:0.0:0.8912:0.0	.	1	Q86SH2	ZAR1_HUMAN	I	1	.	ENSP00000329803:M1I	M	+	3	0	ZAR1	48187068	1.000000	0.71417	0.523000	0.27875	0.769000	0.43574	4.701000	0.61810	1.933000	0.56026	0.305000	0.20034	ATG		0.751	ZAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219927.3		Missense_Mutation
PPAT	5471	broad.mit.edu	37	4	57269471	57269471	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr4:57269471G>T	ENST00000264220.2	-	4	636	c.499C>A	c.(499-501)Cca>Aca	p.P167T	PPAT_ENST00000507648.1_5'UTR	NM_002703.4	NP_002694.3	Q06203	PUR1_HUMAN	phosphoribosyl pyrophosphate amidotransferase	167	Glutamine amidotransferase type-2. {ECO:0000255|PROSITE-ProRule:PRU00609}.				'de novo' IMP biosynthetic process (GO:0006189)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|G1/S transition of mitotic cell cycle (GO:0000082)|glutamine catabolic process (GO:0006543)|kidney development (GO:0001822)|lactation (GO:0007595)|maternal process involved in female pregnancy (GO:0060135)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|organ regeneration (GO:0031100)|protein homotetramerization (GO:0051289)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|amidophosphoribosyltransferase activity (GO:0004044)|metal ion binding (GO:0046872)	p.P167T(1)		cervix(1)|endometrium(2)|large_intestine(6)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	20	Glioma(25;0.08)|all_neural(26;0.101)				Fluorouracil(DB00544)|L-Glutamine(DB00130)|Mercaptopurine(DB01033)	ACCCAGTCTGGGGTGTCATCT	0.428																																					p.P167T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C499A	4						.						84.0	78.0	80.0					4																	57269471		2203	4300	6503	56964228	SO:0001583	missense	5471	exon4				CCDS3505.1	4q12	2012-10-02			ENSG00000128059	ENSG00000128059	2.4.2.14		9238	protein-coding gene	gene with protein product		172450					Standard	NM_002703		Approved	GPAT, PRAT	uc003hbr.3	Q06203	OTTHUMG00000128842	ENST00000264220.2:c.499C>A	4.37:g.57269471G>T	ENSP00000264220:p.Pro167Thr		56964228	NM_002703		Missense_Mutation	SNP	ENST00000264220.2	37	CCDS3505.1	.	.	.	.	.	.	.	.	.	.	G	15.60	2.880795	0.51801	.	.	ENSG00000128059	ENST00000264220	T	0.76186	-1.0	5.51	5.51	0.81932	Glutamine amidotransferase, type II (1);Glutamine amidotransferase, class-II (1);	0.098406	0.64402	D	0.000001	T	0.66636	0.2809	L	0.33137	0.985	0.58432	D	0.999994	B	0.33549	0.417	B	0.35899	0.213	T	0.66536	-0.5899	10	0.41790	T	0.15	-12.4695	14.8817	0.70537	0.0:0.2541:0.7459:0.0	.	167	Q06203	PUR1_HUMAN	T	167	ENSP00000264220:P167T	ENSP00000264220:P167T	P	-	1	0	PPAT	56964228	1.000000	0.71417	0.999000	0.59377	0.966000	0.64601	5.874000	0.69652	2.593000	0.87608	0.655000	0.94253	CCA		0.428	PPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250781.2	NM_002703	
UGT2B11	10720	broad.mit.edu	37	4	70078408	70078408	+	Silent	SNP	T	T	C	rs546752504	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr4:70078408T>C	ENST00000446444.1	-	2	761	c.753A>G	c.(751-753)ggA>ggG	p.G251G	RP11-704M14.1_ENST00000505646.1_RNA|RP11-704M14.1_ENST00000504301.1_RNA	NM_001073.1	NP_001064.1	O75310	UDB11_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B11	251					estrogen metabolic process (GO:0008210)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)	p.G251G(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	42						TGTCAGCTTTTCCCATTGTCT	0.373													.|||	2	0.000399361	0.0015	0.0	5008	,	,		13896	0.0		0.0	False		,,,				2504	0.0				p.G251G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A753G	4						.						135.0	139.0	138.0					4																	70078408		2203	4299	6502	70112997	SO:0001819	synonymous_variant	10720	exon2			AF016492	CCDS3527.1	4q13.3	2008-02-05	2005-07-20		ENSG00000213759	ENSG00000213759		"""UDP glucuronosyltransferases"""	12545	protein-coding gene	gene with protein product		603064	"""UDP glycosyltransferase 2 family, polypeptide B11"""			9675083	Standard	NM_001073		Approved		uc003heh.3	O75310	OTTHUMG00000129395	ENST00000446444.1:c.753A>G	4.37:g.70078408T>C			70112997	NM_001073	Q3KNV9	Silent	SNP	ENST00000446444.1	37	CCDS3527.1																																																																																				0.373	UGT2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251551.2	NM_001073	
ADAMTS3	9508	broad.mit.edu	37	4	73205333	73205333	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr4:73205333G>A	ENST00000286657.4	-	5	775	c.739C>T	c.(739-741)Cgc>Tgc	p.R247C		NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	247	Poly-Arg.				collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|protein processing (GO:0016485)|vascular endothelial growth factor production (GO:0010573)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R247C(1)		NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(33)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	76			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TGTCTGCGGCGTCTCATTGTT	0.483																																					p.R247C	NSCLC(168;1941 2048 2918 13048 43078)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C739T	4						.						244.0	235.0	238.0					4																	73205333		2203	4300	6503	73424197	SO:0001583	missense	9508	exon5			AB002364	CCDS3553.1	4q21	2008-07-29	2005-08-19		ENSG00000156140	ENSG00000156140	3.4.24.-	"""ADAM metallopeptidases with thrombospondin type 1 motif"""	219	protein-coding gene	gene with protein product		605011	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3"""			10094461	Standard	NM_014243		Approved	KIAA0366, ADAMTS-4	uc003hgk.2	O15072	OTTHUMG00000129912	ENST00000286657.4:c.739C>T	4.37:g.73205333G>A	ENSP00000286657:p.Arg247Cys		73424197	NM_014243	A1L3U9|Q9BXZ8	Missense_Mutation	SNP	ENST00000286657.4	37	CCDS3553.1	.	.	.	.	.	.	.	.	.	.	G	13.95	2.389077	0.42410	.	.	ENSG00000156140	ENST00000286657	T	0.63913	-0.07	5.31	5.31	0.75309	.	0.215894	0.35838	N	0.002943	T	0.71962	0.3402	M	0.66939	2.045	0.50039	D	0.999845	D	0.61080	0.989	P	0.51701	0.677	T	0.75465	-0.3308	10	0.72032	D	0.01	.	19.1722	0.93583	0.0:0.0:1.0:0.0	.	247	O15072	ATS3_HUMAN	C	247	ENSP00000286657:R247C	ENSP00000286657:R247C	R	-	1	0	ADAMTS3	73424197	0.691000	0.27709	0.337000	0.25536	0.022000	0.10575	4.078000	0.57606	2.763000	0.94921	0.563000	0.77884	CGC		0.483	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2		
ANKRD17	26057	broad.mit.edu	37	4	73957885	73957885	+	Silent	SNP	T	T	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr4:73957885T>G	ENST00000358602.4	-	29	5576	c.5460A>C	c.(5458-5460)tcA>tcC	p.S1820S	ANKRD17_ENST00000330838.6_Silent_p.S1569S|ANKRD17_ENST00000509867.2_Silent_p.S1707S	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	1820					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.S1820S(1)		NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TAGGTGCTGATGACCCTATTT	0.393																																					p.S1569S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A4707C	4						.						179.0	174.0	176.0					4																	73957885		2203	4300	6503	74176749	SO:0001819	synonymous_variant	26057	exon28			AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"""Ankyrin repeat domain containing"""	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.5460A>C	4.37:g.73957885T>G			74176749	NM_198889	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Silent	SNP	ENST00000358602.4	37	CCDS34004.1																																																																																				0.393	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217	
CXCL11	6373	broad.mit.edu	37	4	76957119	76957119	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr4:76957119T>C	ENST00000503860.1	-	2	400	c.22A>G	c.(22-24)Ata>Gta	p.I8V	ART3_ENST00000341029.5_Intron|CXCL11_ENST00000306621.3_Missense_Mutation_p.I8V			O14625	CXL11_HUMAN	chemokine (C-X-C motif) ligand 11	8					cell-cell signaling (GO:0007267)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of cAMP metabolic process (GO:0030816)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|regulation of cell proliferation (GO:0042127)|signal transduction (GO:0007165)|T cell chemotaxis (GO:0010818)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)|CXCR3 chemokine receptor binding (GO:0048248)|heparin binding (GO:0008201)	p.I8V(1)		kidney(1)|large_intestine(3)|lung(1)|skin(1)	6			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			GCCAAGGCTATAGCCATGCCC	0.403																																					p.I8V	Pancreas(31;57 931 1690 18027 37686)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A22G	4						.						187.0	151.0	164.0					4																	76957119		2203	4300	6503	77176143	SO:0001583	missense	6373	exon1			U66096	CCDS3574.1	4q21	2013-02-25	2002-08-22	2002-08-23	ENSG00000169248	ENSG00000169248		"""Endogenous ligands"""	10638	protein-coding gene	gene with protein product		604852	"""small inducible cytokine subfamily B (Cys-X-Cys), member 11"""	SCYB9B, SCYB11		9730616	Standard	NM_005409		Approved	H174, b-R1, I-TAC, IP-9	uc003hjm.3	O14625	OTTHUMG00000130101	ENST00000503860.1:c.22A>G	4.37:g.76957119T>C	ENSP00000425819:p.Ile8Val		77176143	NM_005409	Q53YA3|Q92840	Missense_Mutation	SNP	ENST00000503860.1	37	CCDS3574.1	.	.	.	.	.	.	.	.	.	.	T	0.080	-1.185102	0.01620	.	.	ENSG00000169248	ENST00000306621;ENST00000503860	T;T	0.44482	0.92;0.92	4.38	-5.35	0.02697	.	0.807437	0.10899	N	0.621808	T	0.13114	0.0318	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.29852	-0.9998	9	0.07175	T	0.84	-7.4378	1.8389	0.03146	0.1386:0.3458:0.1428:0.3728	.	8	O14625	CXL11_HUMAN	V	8	ENSP00000306884:I8V;ENSP00000425819:I8V	ENSP00000306884:I8V	I	-	1	0	CXCL11	77176143	0.003000	0.15002	0.000000	0.03702	0.002000	0.02628	-0.491000	0.06474	-1.071000	0.03145	-2.075000	0.00382	ATA		0.403	CXCL11-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000362816.1		
THAP9	79725	broad.mit.edu	37	4	83826049	83826049	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr4:83826049delA	ENST00000302236.5	+	2	292	c.241delA	c.(241-243)aaafs	p.K82fs		NM_024672.4	NP_078948.3	Q9H5L6	THAP9_HUMAN	THAP domain containing 9	82					DNA integration (GO:0015074)|DNA recombination (GO:0006310)|transposition, DNA-mediated (GO:0006313)		metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transferase activity (GO:0016740)|transposase activity (GO:0004803)	p.G83fs*26(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(13)|lung(5)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(3)	33		Hepatocellular(203;0.114)				AAGAAAGCTGAAAAAAGGAGC	0.353																																					p.K81fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.241delA	4						.						75.0	77.0	76.0					4																	83826049		2203	4300	6503	84045073	SO:0001589	frameshift_variant	79725	exon2			AK091412	CCDS3598.1	4q21.3	2013-01-25			ENSG00000168152	ENSG00000168152		"""THAP (C2CH-type zinc finger) domain containing"""	23192	protein-coding gene	gene with protein product		612537				12575992	Standard	NM_024672		Approved	FLJ34093	uc003hnt.2	Q9H5L6	OTTHUMG00000130291	ENST00000302236.5:c.241delA	4.37:g.83826049delA	ENSP00000305533:p.Lys82fs		84045073	NM_024672	B3KRE2|Q59AC9	Frame_Shift_Del	DEL	ENST00000302236.5	37	CCDS3598.1																																																																																				0.353	THAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252633.1	NM_024672	
HELQ	113510	broad.mit.edu	37	4	84374994	84374994	+	Silent	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr4:84374994A>G	ENST00000295488.3	-	2	564	c.402T>C	c.(400-402)ccT>ccC	p.P134P	MRPS18C_ENST00000295491.4_5'Flank|MRPS18C_ENST00000507019.1_5'Flank|HELQ_ENST00000440639.2_5'UTR|MRPS18C_ENST00000507349.1_5'Flank|HELQ_ENST00000510985.1_Silent_p.P134P	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	134					double-strand break repair via homologous recombination (GO:0000724)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.P134P(1)		breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(17)|ovary(2)|skin(2)	38						TCTTATGTTCAGGGAGTTGCA	0.378								Other identified genes with known or suspected DNA repair function																													p.P134P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T402C	4						.						207.0	213.0	211.0					4																	84374994		2203	4300	6503	84594018	SO:0001819	synonymous_variant	113510	exon2			AF436845	CCDS3603.1, CCDS75158.1	4q21.23	2009-02-26			ENSG00000163312	ENSG00000163312			18536	protein-coding gene	gene with protein product		606769				11751861	Standard	XM_005262711		Approved	Hel308	uc003hom.3	Q8TDG4	OTTHUMG00000130423	ENST00000295488.3:c.402T>C	4.37:g.84374994A>G			84594018	NM_133636	Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Silent	SNP	ENST00000295488.3	37	CCDS3603.1																																																																																				0.378	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1	NM_133636	
ZNF330	27309	broad.mit.edu	37	4	142143532	142143532	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr4:142143532delA	ENST00000262990.4	+	2	235	c.7delA	c.(7-9)aaafs	p.K5fs	ZNF330_ENST00000421169.2_5'UTR	NM_014487.4	NP_055302.1	Q9Y3S2	ZN330_HUMAN	zinc finger protein 330	5						chromosome, centromeric region (GO:0000775)|midbody (GO:0030496)|nucleolus (GO:0005730)	metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)	p.K5fs*18(1)		kidney(1)|large_intestine(4)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	14	all_hematologic(180;0.162)					GAAAATGCCTAAAAAAAAGAC	0.353																																					p.K3fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.7delA	4						.						73.0	78.0	76.0					4																	142143532		2203	4300	6503	142362982	SO:0001589	frameshift_variant	27309	exon2			AJ006591	CCDS3754.1	4q31.21	2008-05-15			ENSG00000109445	ENSG00000109445		"""Zinc fingers, C2H2-type"""	15462	protein-coding gene	gene with protein product		609550				11528117, 10593942	Standard	NM_001292002		Approved	NOA36, HSA6591	uc003iiq.4	Q9Y3S2	OTTHUMG00000133413	ENST00000262990.4:c.7delA	4.37:g.142143532delA	ENSP00000262990:p.Lys5fs		142362982	NM_014487	B2RDA3	Frame_Shift_Del	DEL	ENST00000262990.4	37	CCDS3754.1																																																																																				0.353	ZNF330-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257271.2	NM_014487	
CYP4V2	285440	broad.mit.edu	37	4	187130360	187130360	+	Missense_Mutation	SNP	G	G	A	rs200623218	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr4:187130360G>A	ENST00000378802.4	+	10	1643	c.1339G>A	c.(1339-1341)Gag>Aag	p.E447K	CYP4V2_ENST00000502665.1_3'UTR	NM_207352.3	NP_997235.3	Q6ZWL3	CP4V2_HUMAN	cytochrome P450, family 4, subfamily V, polypeptide 2	447					fatty acid omega-oxidation (GO:0010430)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)	p.E447K(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|skin(1)|stomach(2)	20		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.33e-10)|BRCA - Breast invasive adenocarcinoma(30;3.84e-05)|GBM - Glioblastoma multiforme(59;0.000132)|STAD - Stomach adenocarcinoma(60;0.000293)|LUSC - Lung squamous cell carcinoma(40;0.00242)|READ - Rectum adenocarcinoma(43;0.17)		GTTCTTCCCCGAGAATGCACA	0.522													g|||	2	0.000399361	0.0	0.0	5008	,	,		17599	0.0		0.001	False		,,,				2504	0.001				p.E447K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1339A	4						.	A	LYS/GLU	0,4406		0,0,2203	118.0	105.0	109.0		1339	4.6	1.0	4		109	1,8599	1.2+/-3.3	0,1,4299	yes	missense	CYP4V2	NM_207352.3	56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	447/526	187130360	1,13005	2203	4300	6503	187367354	SO:0001583	missense	285440	exon10			AK022114	CCDS34119.1	4q35.2	2004-07-05			ENSG00000145476	ENSG00000145476		"""Cytochrome P450s"""	23198	protein-coding gene	gene with protein product		608614				15042513	Standard	NM_207352		Approved	CYP4AH1	uc003iyw.4	Q6ZWL3	OTTHUMG00000160379	ENST00000378802.4:c.1339G>A	4.37:g.187130360G>A	ENSP00000368079:p.Glu447Lys		187367354	NM_207352	B7U6W2|Q6ZTM4	Missense_Mutation	SNP	ENST00000378802.4	37	CCDS34119.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	g	22.3	4.269494	0.80469	0.0	1.16E-4	ENSG00000145476	ENST00000378802;ENST00000274118	T	0.80994	-1.44	5.39	4.55	0.56014	.	0.049581	0.85682	N	0.000000	D	0.88716	0.6512	M	0.80183	2.485	0.80722	D	1	D	0.76494	0.999	D	0.65010	0.931	D	0.89887	0.4034	10	0.56958	D	0.05	.	14.4893	0.67639	0.0701:0.0:0.9299:0.0	.	447	Q6ZWL3	CP4V2_HUMAN	K	447;425	ENSP00000368079:E447K	ENSP00000274118:E425K	E	+	1	0	CYP4V2	187367354	1.000000	0.71417	0.967000	0.41034	0.472000	0.32918	7.036000	0.76524	1.530000	0.49136	-0.119000	0.15052	GAG		0.522	CYP4V2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360398.1	XM_209612	
CTNND2	1501	broad.mit.edu	37	5	11385070	11385070	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:11385070G>A	ENST00000304623.8	-	7	1073	c.884C>T	c.(883-885)cCg>cTg	p.P295L	CTNND2_ENST00000495388.2_5'Flank|CTNND2_ENST00000359640.2_Missense_Mutation_p.P295L|CTNND2_ENST00000503622.1_Intron|CTNND2_ENST00000458100.2_Intron|CTNND2_ENST00000511377.1_Missense_Mutation_p.P204L	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	295					cell adhesion (GO:0007155)|learning (GO:0007612)|morphogenesis of a branching structure (GO:0001763)|multicellular organismal development (GO:0007275)|regulation of synaptic plasticity (GO:0048167)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.P295L(1)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(29)|liver(1)|lung(71)|ovary(4)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	136						ggagccgcgcggcgcggcgta	0.781																																					p.P295L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C884T	5						.						23.0	29.0	27.0					5																	11385070		2150	4210	6360	11438070	SO:0001583	missense	1501	exon7			U52828	CCDS3881.1, CCDS75227.1, CCDS75228.1	5p15.2	2013-02-14	2012-08-15		ENSG00000169862	ENSG00000169862		"""Armadillo repeat containing"""	2516	protein-coding gene	gene with protein product	"""neural plakophilin-related arm-repeat protein"""	604275	"""catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)"""			9342840, 9223106	Standard	XM_005248251		Approved	NPRAP, GT24	uc003jfa.1	Q9UQB3	OTTHUMG00000090511	ENST00000304623.8:c.884C>T	5.37:g.11385070G>A	ENSP00000307134:p.Pro295Leu		11438070	NM_001332	B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	Missense_Mutation	SNP	ENST00000304623.8	37	CCDS3881.1	.	.	.	.	.	.	.	.	.	.	G	14.63	2.592117	0.46214	.	.	ENSG00000169862	ENST00000304623;ENST00000359640;ENST00000511377	T;T;T	0.76578	-0.95;-1.03;-0.97	3.22	2.16	0.27623	.	3.044690	0.03894	U	0.279144	T	0.49677	0.1571	N	0.02011	-0.69	0.80722	D	1	P	0.36483	0.555	B	0.19666	0.026	T	0.49173	-0.8967	10	0.39692	T	0.17	-8.5733	7.8303	0.29338	0.0:0.0:0.3987:0.6013	.	295	Q9UQB3	CTND2_HUMAN	L	295;295;204	ENSP00000307134:P295L;ENSP00000352661:P295L;ENSP00000426510:P204L	ENSP00000307134:P295L	P	-	2	0	CTNND2	11438070	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.369000	0.52365	1.313000	0.45069	0.462000	0.41574	CCG		0.781	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206999.1	NM_001332	
KCNN2	3781	broad.mit.edu	37	5	113699683	113699683	+	Silent	SNP	C	C	T	rs144098012	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:113699683C>T	ENST00000512097.3	+	3	1585	c.567C>T	c.(565-567)caC>caT	p.H189H	KCNN2_ENST00000264773.3_Silent_p.H189H|KCNN2_ENST00000507750.1_3'UTR			Q9H2S1	KCNN2_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	189					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transport (GO:1901379)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|protein homodimerization activity (GO:0042803)|small conductance calcium-activated potassium channel activity (GO:0016286)	p.H189H(2)		breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(21)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(142;2.86e-05)|all_epithelial(76;9.33e-06)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Breast(839;0.159)|Lung NSC(810;0.174)|all_lung(232;0.206)		OV - Ovarian serous cystadenocarcinoma(64;1.89e-08)|Epithelial(69;2.04e-08)|all cancers(49;3.74e-06)|COAD - Colon adenocarcinoma(37;0.142)|Colorectal(14;0.195)	Miconazole(DB01110)|Procaine(DB00721)	TCGTGTACCACGCCAGGGAAA	0.493																																					p.H189H												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C567T	5						.	C		3,4401	6.2+/-15.9	0,3,2199	203.0	170.0	181.0		567	4.1	1.0	5	dbSNP_134	181	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous	KCNN2	NM_021614.2		0,14,6488	TT,TC,CC		0.1279,0.0681,0.1077		189/580	113699683	14,12990	2202	4300	6502	113727582	SO:0001819	synonymous_variant	3781	exon2			AF239613	CCDS4114.1, CCDS43352.1	5q22.3	2012-07-05			ENSG00000080709	ENSG00000080709		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6291	protein-coding gene	gene with protein product		605879				16382103	Standard	NM_001278204		Approved	KCa2.2, hSK2	uc003kqo.3	Q9H2S1	OTTHUMG00000128836	ENST00000512097.3:c.567C>T	5.37:g.113699683C>T			113727582	NM_021614	A6NF94|Q0VFZ4|Q6PJI0|Q6X2Y2	Silent	SNP	ENST00000512097.3	37	CCDS4114.1																																																																																				0.493	KCNN2-001	KNOWN	not_organism_supported|upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250775.2	NM_021614	
ALDH7A1	501	broad.mit.edu	37	5	125895025	125895025	+	Splice_Site	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:125895025G>T	ENST00000409134.3	-	11	1134	c.915C>A	c.(913-915)gcC>gcA	p.A305A	ALDH7A1_ENST00000447989.2_Splice_Site_p.A332A|ALDH7A1_ENST00000553117.1_Splice_Site_p.A305A	NM_001182.4|NM_001201377.1	NP_001173.2|NP_001188306.1	P49419	AL7A1_HUMAN	aldehyde dehydrogenase 7 family, member A1	305					cellular aldehyde metabolic process (GO:0006081)|cellular nitrogen compound metabolic process (GO:0034641)|glycine betaine biosynthetic process from choline (GO:0019285)|lysine catabolic process (GO:0006554)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|betaine-aldehyde dehydrogenase activity (GO:0008802)|L-aminoadipate-semialdehyde dehydrogenase activity (GO:0004043)	p.A277A(1)		endometrium(1)|kidney(4)|large_intestine(4)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	16		all_cancers(142;0.24)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0417)|OV - Ovarian serous cystadenocarcinoma(64;0.068)|all cancers(49;0.109)		CATCTTCAAAGGCTTAGGAAA	0.453																																					p.A305A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C915A	5						.						85.0	70.0	75.0					5																	125895025		2203	4300	6503	125922924	SO:0001630	splice_region_variant	501	exon11			S74728	CCDS4137.2, CCDS56380.1	5q31	2013-06-03			ENSG00000164904	ENSG00000164904	1.2.1.31	"""Aldehyde dehydrogenases"""	877	protein-coding gene	gene with protein product	"""antiquitin 1"", ""26g turgor protein homolog"", ""alpha-aminoadipic semialdehyde dehydrogenase"", ""alpha-AASA dehydrogenase"", ""delta1-piperideine-6-carboxylate dehydrogenease"", ""P6c dehydrogenase"""	107323		ATQ1		9417906	Standard	NM_001182		Approved	EPD, PDE	uc003ktx.3	P49419	OTTHUMG00000128942	ENST00000409134.3:c.914-1C>A	5.37:g.125895025G>T			125922924	NM_001182	B2R669|B4DIC7|B4DMA0|E7EPT3|O14619|Q6IPU8|Q9BUL4	Silent	SNP	ENST00000409134.3	37	CCDS4137.2																																																																																				0.453	ALDH7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250921.2	NM_001182	Silent
MEGF10	84466	broad.mit.edu	37	5	126783332	126783332	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:126783332A>C	ENST00000274473.6	+	22	3079	c.2812A>C	c.(2812-2814)Aca>Cca	p.T938P	MEGF10_ENST00000503335.2_Missense_Mutation_p.T938P|MEGF10_ENST00000510828.1_3'UTR	NM_032446.2	NP_115822.1	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10	938					homotypic cell-cell adhesion (GO:0034109)|muscle cell development (GO:0055001)|recognition of apoptotic cell (GO:0043654)|regulation of muscle cell differentiation (GO:0051147)|regulation of skeletal muscle tissue development (GO:0048641)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell differentiation (GO:0014816)|skeletal muscle satellite cell proliferation (GO:0014841)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)		p.T938P(1)		breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(28)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	68		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)		CCAGTGTGCCACATCCCCTCA	0.532																																					p.T938P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2812C	5						.						136.0	114.0	121.0					5																	126783332		2203	4300	6503	126811231	SO:0001583	missense	84466	exon22			AK021631	CCDS4142.1	5q33	2008-02-05			ENSG00000145794	ENSG00000145794			29634	protein-coding gene	gene with protein product		612453				11347906	Standard	NM_032446		Approved	KIAA1780	uc003kui.4	Q96KG7	OTTHUMG00000128984	ENST00000274473.6:c.2812A>C	5.37:g.126783332A>C	ENSP00000274473:p.Thr938Pro		126811231	NM_032446	Q68DE5|Q8WUL3	Missense_Mutation	SNP	ENST00000274473.6	37	CCDS4142.1	.	.	.	.	.	.	.	.	.	.	A	10.23	1.293888	0.23564	.	.	ENSG00000145794	ENST00000503335;ENST00000274473	T;T	0.76578	-1.03;-1.03	5.93	-2.78	0.05859	.	0.408988	0.24256	N	0.040134	T	0.57403	0.2051	L	0.27053	0.805	0.26864	N	0.967889	B	0.02656	0.0	B	0.01281	0.0	T	0.40813	-0.9543	10	0.30078	T	0.28	-0.0115	7.2064	0.25909	0.5878:0.1098:0.3024:0.0	.	938	Q96KG7	MEG10_HUMAN	P	938	ENSP00000423354:T938P;ENSP00000274473:T938P	ENSP00000274473:T938P	T	+	1	0	MEGF10	126811231	0.642000	0.27260	0.548000	0.28192	0.910000	0.53928	1.216000	0.32443	-0.344000	0.08338	-0.290000	0.09829	ACA		0.532	MEGF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250973.2	NM_032446	
P4HA2	8974	broad.mit.edu	37	5	131546131	131546131	+	Silent	SNP	C	C	T	rs200709337		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:131546131C>T	ENST00000401867.1	-	7	1123	c.555G>A	c.(553-555)acG>acA	p.T185T	P4HA2_ENST00000379100.2_Silent_p.T185T|P4HA2_ENST00000379086.1_Silent_p.T185T|P4HA2_ENST00000379104.2_Silent_p.T185T|P4HA2_ENST00000360568.3_Silent_p.T185T|P4HA2_ENST00000166534.4_Silent_p.T185T			O15460	P4HA2_HUMAN	prolyl 4-hydroxylase, alpha polypeptide II	185					peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|procollagen-proline 4-dioxygenase complex (GO:0016222)	electron carrier activity (GO:0009055)|iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)|procollagen-proline 4-dioxygenase activity (GO:0004656)	p.T185T(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24		all_cancers(142;0.103)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		L-Proline(DB00172)|Succinic acid(DB00139)	TCCACAACACCGTATGATAAT	0.552																																					p.T185T	Esophageal Squamous(68;117 1135 17362 19256 34242)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G555A	5						.	C	,,,,	0,4406		0,0,2203	261.0	249.0	253.0		555,555,555,555,555	-11.8	0.0	5		253	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	P4HA2	NM_001017973.1,NM_001017974.1,NM_001142598.1,NM_001142599.1,NM_004199.2	,,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,,,	185/534,185/534,185/534,185/536,185/536	131546131	1,13005	2203	4300	6503	131574030	SO:0001819	synonymous_variant	8974	exon6			U90441	CCDS4151.1, CCDS34230.1	5q31	2008-12-09	2008-12-09		ENSG00000072682	ENSG00000072682	1.14.11.2		8547	protein-coding gene	gene with protein product	"""4-PH alpha 2"", ""collagen prolyl 4-hydroxylase alpha(II)"""	600608	"""procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide II"""			9211872, 9149945	Standard	NM_001142598		Approved	C-P4Halpha(II)	uc003kwl.3	O15460	OTTHUMG00000059647	ENST00000401867.1:c.555G>A	5.37:g.131546131C>T			131574030	NM_001017974	D3DQ85|D3DQ86|Q8WWN0	Silent	SNP	ENST00000401867.1	37	CCDS4151.1																																																																																				0.552	P4HA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000132653.4	NM_004199	
HSPA4	3308	broad.mit.edu	37	5	132425263	132425263	+	Silent	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:132425263A>G	ENST00000304858.2	+	11	1543	c.1254A>G	c.(1252-1254)gaA>gaG	p.E418E		NM_002154.3	NP_002145.3	P34932	HSP74_HUMAN	heat shock 70kDa protein 4	418					chaperone-mediated protein complex assembly (GO:0051131)|protein import into mitochondrial outer membrane (GO:0045040)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)	p.E418E(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|stomach(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GTGACTGTGAAGTCTTTTCCA	0.363																																					p.E418E	Colon(114;1299 1588 6063 12302 48757)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1254G	5						.						130.0	124.0	126.0					5																	132425263		2203	4300	6503	132453162	SO:0001819	synonymous_variant	3308	exon11			AB023420	CCDS4166.1	5q31.1	2011-09-07	2002-08-29		ENSG00000170606	ENSG00000170606		"""Heat shock proteins / HSP70"""	5237	protein-coding gene	gene with protein product	"""hsp70 RY"""	601113	"""heat shock 70kD protein 4"""			8335910	Standard	NM_002154		Approved	HS24/P52, HSPH2	uc003kyj.3	P34932	OTTHUMG00000129012	ENST00000304858.2:c.1254A>G	5.37:g.132425263A>G			132453162	NM_002154	O95756|Q2TAL4|Q9BUK9	Silent	SNP	ENST00000304858.2	37	CCDS4166.1																																																																																				0.363	HSPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251011.1	NM_002154, NM_198431	
SKP1	6500	broad.mit.edu	37	5	133494191	133494191	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:133494191C>A	ENST00000353411.6	-	5	594	c.411G>T	c.(409-411)aaG>aaT	p.K137N	SKP1_ENST00000522855.1_Missense_Mutation_p.K137N|SKP1_ENST00000521216.1_Missense_Mutation_p.K137N|SKP1_ENST00000517625.1_Missense_Mutation_p.K137N|SKP1_ENST00000522552.1_Missense_Mutation_p.K137N	NM_170679.2	NP_733779.1	P63208	SKP1_HUMAN	S-phase kinase-associated protein 1	137	Interaction with the F-box domain of F- box proteins. {ECO:0000250}.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|histone H2A monoubiquitination (GO:0035518)|mitotic cell cycle (GO:0000278)|Notch signaling pathway (GO:0007219)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|viral process (GO:0016032)	Cul7-RING ubiquitin ligase complex (GO:0031467)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|SCF ubiquitin ligase complex (GO:0019005)	ubiquitin-protein transferase activity (GO:0004842)	p.K137N(1)		large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TATTGAAGGTCTTGCGAATCT	0.413																																					p.K137N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G411T	5						.						165.0	160.0	162.0					5																	133494191		2203	4300	6503	133522090	SO:0001583	missense	6500	exon5			U33760	CCDS4171.1, CCDS4172.1	5q31	2011-11-18	2007-11-13	2007-11-13	ENSG00000113558	ENSG00000113558			10899	protein-coding gene	gene with protein product		601434	"""S-phase kinase-associated protein 1A (p19A)"""	SKP1A		7553852, 8646875	Standard	NM_006930		Approved	EMC19, OCP2, TCEB1L, MGC34403, OCP-II, p19A	uc003kzc.4	P63208	OTTHUMG00000129117	ENST00000353411.6:c.411G>T	5.37:g.133494191C>A	ENSP00000231487:p.Lys137Asn		133522090	NM_170679	D3DQ97|D3DQ98|P34991|Q8TAY2	Missense_Mutation	SNP	ENST00000353411.6	37	CCDS4171.1	.	.	.	.	.	.	.	.	.	.	C	15.67	2.901089	0.52227	.	.	ENSG00000113558	ENST00000353411;ENST00000522552;ENST00000521216;ENST00000517625;ENST00000522855;ENST00000328392;ENST00000519321	T;T;T;T;T;T;T	0.50001	0.77;0.76;0.77;0.77;0.77;0.76;0.77	5.06	2.22	0.28083	SKP1 component, dimerisation (2);BTB/POZ fold (1);	0.000000	0.85682	U	0.000000	T	0.50752	0.1634	M	0.83118	2.625	0.80722	D	1	B;B;B	0.26902	0.007;0.019;0.163	B;B;B	0.29785	0.025;0.026;0.107	T	0.55244	-0.8171	10	0.62326	D	0.03	-3.0874	10.7727	0.46332	0.0:0.7898:0.0:0.2102	.	137;137;137	E5RJR5;P63208-2;P63208	.;.;SKP1_HUMAN	N	137	ENSP00000231487:K137N;ENSP00000429472:K137N;ENSP00000431067:K137N;ENSP00000429961:K137N;ENSP00000429686:K137N;ENSP00000331708:K137N;ENSP00000429415:K137N	ENSP00000331708:K137N	K	-	3	2	SKP1	133522090	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.259000	0.51515	0.635000	0.30488	0.563000	0.77884	AAG		0.413	SKP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251162.2	NM_170679	
JADE2	23338	broad.mit.edu	37	5	133896569	133896569	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:133896569C>T	ENST00000402835.1	+	6	861	c.606C>T	c.(604-606)tgC>tgT	p.C202C	PHF15_ENST00000395003.1_Silent_p.C202C|PHF15_ENST00000282605.4_Silent_p.C202C|PHF15_ENST00000361895.2_Silent_p.C202C														p.C202C(1)		NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	22			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			ATGTTGTCTGCGACGTGTGTC	0.607																																					p.C202C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C606T	5						.						238.0	183.0	201.0					5																	133896569		2203	4300	6503	133924468	SO:0001819	synonymous_variant	23338	exon6																														ENST00000402835.1:c.606C>T	5.37:g.133896569C>T			133924468	NM_015288		Silent	SNP	ENST00000402835.1	37																																																																																					0.607	PHF15-007	PUTATIVE	alternative_5_UTR|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000318543.1		
SPOCK1	6695	broad.mit.edu	37	5	136476300	136476300	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:136476300G>T	ENST00000394945.1	-	4	485	c.316C>A	c.(316-318)Ctg>Atg	p.L106M	SPOCK1_ENST00000282223.7_Missense_Mutation_p.L106M	NM_004598.3	NP_004589.1	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1	106					cell adhesion (GO:0007155)|central nervous system neuron differentiation (GO:0021953)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron projection development (GO:0010977)|nervous system development (GO:0007399)|neurogenesis (GO:0022008)|neuron migration (GO:0001764)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|postsynaptic density (GO:0014069)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasm (GO:0016528)	calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.L106M(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(2)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CTGACACACAGGGCGGTCTGG	0.607																																					p.L106M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C316A	5						.						63.0	52.0	56.0					5																	136476300		2203	4300	6503	136504199	SO:0001583	missense	6695	exon4			AF231124	CCDS4191.1	5q31.2	2008-02-05	2005-11-04	2005-11-04	ENSG00000152377	ENSG00000152377			11251	protein-coding gene	gene with protein product		602264	"""sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican)"""	TIC1, SPOCK		9545645	Standard	NM_004598		Approved	testican-1	uc003lbp.3	Q08629	OTTHUMG00000129157	ENST00000394945.1:c.316C>A	5.37:g.136476300G>T	ENSP00000378401:p.Leu106Met		136504199	NM_004598	B3KSW3|Q59EW0|Q8N630|Q9UCL8	Missense_Mutation	SNP	ENST00000394945.1	37	CCDS4191.1	.	.	.	.	.	.	.	.	.	.	G	9.521	1.108410	0.20714	.	.	ENSG00000152377	ENST00000394945;ENST00000282223;ENST00000505690	T;T;T	0.45668	0.89;0.89;0.91	5.74	2.89	0.33648	.	0.505227	0.19686	N	0.108394	T	0.15089	0.0364	N	0.02247	-0.625	0.26545	N	0.974015	B	0.13145	0.007	B	0.09377	0.004	T	0.21177	-1.0253	10	0.13108	T	0.6	.	7.6194	0.28177	0.0:0.3136:0.4305:0.256	.	106	Q08629	TICN1_HUMAN	M	106	ENSP00000378401:L106M;ENSP00000282223:L106M;ENSP00000424517:L106M	ENSP00000282223:L106M	L	-	1	2	SPOCK1	136504199	0.766000	0.28496	0.992000	0.48379	0.990000	0.78478	1.647000	0.37260	1.409000	0.46915	0.650000	0.86243	CTG		0.607	SPOCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251222.1	NM_004598	
HNRNPA0	10949	broad.mit.edu	37	5	137088931	137088931	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:137088931G>A	ENST00000314940.4	-	1	1108	c.825C>T	c.(823-825)ggC>ggT	p.G275G		NM_006805.3	NP_006796.1	Q13151	ROA0_HUMAN	heterogeneous nuclear ribonucleoprotein A0	275	Gly-rich.				3'-UTR-mediated mRNA stabilization (GO:0070935)|gene expression (GO:0010467)|inflammatory response (GO:0006954)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|response to lipopolysaccharide (GO:0032496)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|RNA binding (GO:0003723)	p.G275G(1)		large_intestine(1)|lung(2)|skin(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			Tgcctccaccgccgccgccgc	0.632																																					p.G275G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C825T	5						.						9.0	13.0	11.0					5																	137088931		1925	3891	5816	137116830	SO:0001819	synonymous_variant	10949	exon1			U23803	CCDS4193.1	5q31	2013-02-12		2007-08-16	ENSG00000177733	ENSG00000177733		"""RNA binding motif (RRM) containing"""	5030	protein-coding gene	gene with protein product		609409		HNRPA0		7585247	Standard	NM_006805		Approved	hnRNPA0	uc003lbt.3	Q13151	OTTHUMG00000129156	ENST00000314940.4:c.825C>T	5.37:g.137088931G>A			137116830	NM_006805	Q6IB18	Silent	SNP	ENST00000314940.4	37	CCDS4193.1																																																																																				0.632	HNRNPA0-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251221.1	NM_006805	
EGR1	1958	broad.mit.edu	37	5	137802588	137802588	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:137802588G>A	ENST00000239938.4	+	2	722	c.450G>A	c.(448-450)tgG>tgA	p.W150*		NM_001964.2	NP_001955.1	P18146	EGR1_HUMAN	early growth response 1	150					BMP signaling pathway (GO:0030509)|cellular response to antibiotic (GO:0071236)|cellular response to cAMP (GO:0071320)|cellular response to drug (GO:0035690)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to gamma radiation (GO:0071480)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heparin (GO:0071504)|cellular response to hyperoxia (GO:0071455)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|cellular response to isoquinoline alkaloid (GO:0071317)|cellular response to mechanical stimulus (GO:0071260)|cellular response to mycophenolic acid (GO:0071506)|cellular response to steroid hormone stimulus (GO:0071383)|circadian rhythm (GO:0007623)|cytokine-mediated signaling pathway (GO:0019221)|glomerular mesangial cell proliferation (GO:0072110)|interleukin-1-mediated signaling pathway (GO:0070498)|learning or memory (GO:0007611)|long-term synaptic potentiation (GO:0060291)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oligodendrocyte differentiation (GO:0048709)|positive regulation of glomerular metanephric mesangial cell proliferation (GO:0072303)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of protein sumoylation (GO:0033233)|response to amphetamine (GO:0001975)|response to carbon monoxide (GO:0034465)|response to cocaine (GO:0042220)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to norepinephrine (GO:0071873)|response to nutrient levels (GO:0031667)|skeletal muscle cell differentiation (GO:0035914)|T cell differentiation (GO:0030217)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|histone acetyltransferase binding (GO:0035035)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.W150*(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|ovary(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			ACACCTTGTGGCCCGAGCCCC	0.632																																					p.W150X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G450A	5						.						94.0	99.0	97.0					5																	137802588		2203	4300	6503	137830487	SO:0001587	stop_gained	1958	exon2			M62829	CCDS4206.1	5q23-q31	2013-01-08			ENSG00000120738	ENSG00000120738		"""Zinc fingers, C2H2-type"""	3238	protein-coding gene	gene with protein product	"""nerve growth factor-induced protein A"", ""transcription factor ETR103"", ""zinc finger protein 225"", ""early growth response protein 1"""	128990				3127059	Standard	NM_001964		Approved	TIS8, G0S30, NGFI-A, KROX-24, ZIF-268, AT225, ZNF225	uc003ldb.1	P18146	OTTHUMG00000129197	ENST00000239938.4:c.450G>A	5.37:g.137802588G>A	ENSP00000239938:p.Trp150*		137830487	NM_001964		Nonsense_Mutation	SNP	ENST00000239938.4	37	CCDS4206.1	.	.	.	.	.	.	.	.	.	.	G	37	6.291485	0.97449	.	.	ENSG00000120738	ENST00000535792;ENST00000239938	.	.	.	4.89	4.89	0.63831	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.869	18.0413	0.89319	0.0:0.0:1.0:0.0	.	.	.	.	X	150	.	ENSP00000239938:W150X	W	+	3	0	EGR1	137830487	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	7.876000	0.87215	2.251000	0.74343	0.462000	0.41574	TGG		0.632	EGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251274.1	NM_001964	
HSPA9	3313	broad.mit.edu	37	5	137895675	137895675	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:137895675C>T	ENST00000297185.3	-	11	1413	c.1288G>A	c.(1288-1290)Ggc>Agc	p.G430S	HSPA9_ENST00000501917.2_Intron|SNORD63_ENST00000411005.1_RNA|SNORD63_ENST00000384262.1_RNA	NM_004134.6	NP_004125.3	P38646	GRP75_HUMAN	heat shock 70kDa protein 9 (mortalin)	430					cellular protein metabolic process (GO:0044267)|negative regulation of apoptotic process (GO:0043066)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein targeting to mitochondrion (GO:0006626)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)	p.G430S(1)		breast(2)|endometrium(1)|kidney(4)|large_intestine(8)|lung(12)|upper_aerodigestive_tract(1)	28			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			GTGACATCGCCGGCCAACACA	0.502																																					p.G430S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1288A	5						.						69.0	65.0	67.0					5																	137895675		2203	4300	6503	137923574	SO:0001583	missense	3313	exon11			L11066	CCDS4208.1	5q31.1	2011-09-02	2006-10-31	2006-10-31	ENSG00000113013	ENSG00000113013		"""Heat shock proteins / HSP70"""	5244	protein-coding gene	gene with protein product		600548	"""heat shock 70kDa protein 9B (mortalin-2)"""	HSPA9B		7684501	Standard	NM_004134		Approved	GRP75, PBP74, mot-2, mthsp75	uc003ldf.3	P38646	OTTHUMG00000129206	ENST00000297185.3:c.1288G>A	5.37:g.137895675C>T	ENSP00000297185:p.Gly430Ser		137923574	NM_004134	B2RCM1|P30036|P31932|Q1HB43|Q53H23|Q6GU03|Q9BWB7|Q9UC56	Missense_Mutation	SNP	ENST00000297185.3	37	CCDS4208.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.190997	0.78789	.	.	ENSG00000113013	ENST00000297185;ENST00000541333;ENST00000540484	T	0.01323	5.01	5.48	5.48	0.80851	.	0.043355	0.85682	D	0.000000	T	0.17874	0.0429	H	0.97758	4.07	0.80722	D	1	D;D	0.76494	0.995;0.999	D;D	0.85130	0.961;0.997	T	0.18871	-1.0323	10	0.87932	D	0	-8.9524	19.3107	0.94186	0.0:1.0:0.0:0.0	.	361;430	B7Z1V7;P38646	.;GRP75_HUMAN	S	430;383;416	ENSP00000297185:G430S	ENSP00000297185:G430S	G	-	1	0	HSPA9	137923574	1.000000	0.71417	1.000000	0.80357	0.008000	0.06430	7.743000	0.85020	2.749000	0.94314	0.655000	0.94253	GGC		0.502	HSPA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251285.1	NM_004134	
PCDHB3	56132	broad.mit.edu	37	5	140480771	140480771	+	Missense_Mutation	SNP	G	G	A	rs374259978		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:140480771G>A	ENST00000231130.2	+	1	538	c.538G>A	c.(538-540)Gta>Ata	p.V180I	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	180	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.V180I(1)		NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCACTTCCACGTACTCACTCG	0.517																																					p.V180I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G538A	5						.						87.0	86.0	87.0					5																	140480771		2203	4300	6503	140460955	SO:0001583	missense	56132	exon1			AF152496	CCDS4245.1	5q31	2010-01-26			ENSG00000113205	ENSG00000113205		"""Cadherins / Protocadherins : Clustered"""	8688	other	protocadherin		606329				10380929	Standard	NM_018937		Approved	PCDH-BETA3	uc003lio.3	Q9Y5E6	OTTHUMG00000129622	ENST00000231130.2:c.538G>A	5.37:g.140480771G>A	ENSP00000231130:p.Val180Ile		140460955	NM_018937	B2R8P2	Missense_Mutation	SNP	ENST00000231130.2	37	CCDS4245.1	.	.	.	.	.	.	.	.	.	.	G	9.261	1.043333	0.19748	.	.	ENSG00000113205	ENST00000231130	T	0.39056	1.1	5.08	3.27	0.37495	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.19485	0.0468	N	0.05177	-0.1	0.09310	N	1	P	0.36222	0.544	B	0.37780	0.258	T	0.08785	-1.0705	9	0.21014	T	0.42	.	3.7904	0.08718	0.1544:0.1306:0.581:0.134	.	180	Q9Y5E6	PCDB3_HUMAN	I	180	ENSP00000231130:V180I	ENSP00000231130:V180I	V	+	1	0	PCDHB3	140460955	0.000000	0.05858	0.799000	0.32177	0.827000	0.46813	-0.395000	0.07287	1.266000	0.44231	0.655000	0.94253	GTA		0.517	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2	NM_018937	
PCDHB4	56131	broad.mit.edu	37	5	140503211	140503211	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:140503211C>T	ENST00000194152.1	+	1	1631	c.1631C>T	c.(1630-1632)gCg>gTg	p.A544V	AC005754.8_ENST00000606030.1_lincRNA	NM_018938.2	NP_061761.1	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4	544	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A544V(1)		autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|lung(35)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	67			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AGCAGCGAGGCGCTGGTGCGC	0.687																																					p.A544V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1631T	5						.						40.0	45.0	43.0					5																	140503211		2202	4294	6496	140483395	SO:0001583	missense	56131	exon1			AF152497	CCDS4246.1	5q31	2010-01-26			ENSG00000081818	ENSG00000081818		"""Cadherins / Protocadherins : Clustered"""	8689	other	protocadherin		606330				10380929	Standard	NM_018938		Approved	PCDH-BETA4	uc003lip.1	Q9Y5E5	OTTHUMG00000129617	ENST00000194152.1:c.1631C>T	5.37:g.140503211C>T	ENSP00000194152:p.Ala544Val		140483395	NM_018938	Q4V761	Missense_Mutation	SNP	ENST00000194152.1	37	CCDS4246.1	.	.	.	.	.	.	.	.	.	.	C	12.55	1.972665	0.34848	.	.	ENSG00000081818	ENST00000194152	T	0.01787	4.64	3.88	3.88	0.44766	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.01489	0.0048	N	0.20685	0.6	0.39162	D	0.962431	P	0.45078	0.85	P	0.45232	0.474	T	0.66300	-0.5958	9	0.13853	T	0.58	.	5.2581	0.15558	0.0:0.733:0.0:0.267	.	544	Q9Y5E5	PCDB4_HUMAN	V	544	ENSP00000194152:A544V	ENSP00000194152:A544V	A	+	2	0	PCDHB4	140483395	0.049000	0.20398	1.000000	0.80357	0.989000	0.77384	0.401000	0.20948	2.189000	0.69895	0.485000	0.47835	GCG		0.687	PCDHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251812.2	NM_018938	
PCDHB12	56124	broad.mit.edu	37	5	140588662	140588662	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:140588662G>A	ENST00000239450.2	+	1	372	c.183G>A	c.(181-183)tcG>tcA	p.S61S	PCDHB12_ENST00000541609.1_Intron	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	61	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.S61S(1)		NS(1)|breast(3)|endometrium(10)|large_intestine(17)|lung(38)|ovary(3)|pancreas(1)|prostate(2)|skin(7)|stomach(1)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AGCTGTCTTCGCGGGGGGCTC	0.512																																					p.S61S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G183A	5						.						83.0	94.0	90.0					5																	140588662		2203	4300	6503	140568846	SO:0001819	synonymous_variant	56124	exon1			AF152491	CCDS4254.1	5q31	2010-01-26			ENSG00000120328	ENSG00000120328		"""Cadherins / Protocadherins : Clustered"""	8683	other	protocadherin		606338				10380929	Standard	NM_018932		Approved	PCDH-BETA12	uc003liz.3	Q9Y5F1	OTTHUMG00000129620	ENST00000239450.2:c.183G>A	5.37:g.140588662G>A			140568846	NM_018932	B4DDU1	Silent	SNP	ENST00000239450.2	37	CCDS4254.1																																																																																				0.512	PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251815.2	NM_018932	
PCDHB12	56124	broad.mit.edu	37	5	140590109	140590109	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:140590109G>A	ENST00000239450.2	+	1	1819	c.1630G>A	c.(1630-1632)Gag>Aag	p.E544K	PCDHB12_ENST00000541609.1_Missense_Mutation_p.E207K	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	544	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.E544K(1)		NS(1)|breast(3)|endometrium(10)|large_intestine(17)|lung(38)|ovary(3)|pancreas(1)|prostate(2)|skin(7)|stomach(1)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TTTGAGCAGCGAGGCGCTGGT	0.697																																					p.E544K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1630A	5						.						38.0	43.0	41.0					5																	140590109		2203	4299	6502	140570293	SO:0001583	missense	56124	exon1			AF152491	CCDS4254.1	5q31	2010-01-26			ENSG00000120328	ENSG00000120328		"""Cadherins / Protocadherins : Clustered"""	8683	other	protocadherin		606338				10380929	Standard	NM_018932		Approved	PCDH-BETA12	uc003liz.3	Q9Y5F1	OTTHUMG00000129620	ENST00000239450.2:c.1630G>A	5.37:g.140590109G>A	ENSP00000239450:p.Glu544Lys		140570293	NM_018932	B4DDU1	Missense_Mutation	SNP	ENST00000239450.2	37	CCDS4254.1	.	.	.	.	.	.	.	.	.	.	G	14.68	2.608053	0.46527	.	.	ENSG00000120328	ENST00000541609;ENST00000239450;ENST00000507840	T;T	0.01705	4.68;4.68	3.41	-1.73	0.08081	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.01695	0.0054	N	0.10837	0.055	0.23743	N	0.996964	P	0.49253	0.921	P	0.49421	0.61	T	0.51100	-0.8748	9	0.72032	D	0.01	.	7.059	0.25115	0.2621:0.3285:0.4093:0.0	.	544	Q9Y5F1	PCDBC_HUMAN	K	207;544;164	ENSP00000440199:E207K;ENSP00000239450:E544K	ENSP00000239450:E544K	E	+	1	0	PCDHB12	140570293	0.000000	0.05858	0.850000	0.33497	0.972000	0.66771	0.076000	0.14712	-0.321000	0.08627	0.485000	0.47835	GAG		0.697	PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251815.2	NM_018932	
PCDHGA9	56107	broad.mit.edu	37	5	140784429	140784429	+	Missense_Mutation	SNP	C	C	T	rs377687399		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:140784429C>T	ENST00000573521.1	+	1	1910	c.1910C>T	c.(1909-1911)gCg>gTg	p.A637V	PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB4_ENST00000519479.1_Intron	NM_018921.2|NM_032089.1	NP_061744.1|NP_114478.1	Q9Y5G4	PCDG9_HUMAN	protocadherin gamma subfamily A, 9	637	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GATAGAGATGCGCTCAAACAG	0.607																																					p.A637V												.	.	0			c.C1910T	5						.	C	,,,,,,,,VAL/ALA,,,,,,VAL/ALA	2,4370		0,2,2184	39.0	47.0	44.0		,,,,,,,,1910,,,,,,1910	2.5	0.0	5		44	0,8592		0,0,4296	no	intron,intron,intron,intron,intron,intron,intron,intron,missense,intron,intron,intron,intron,intron,missense	PCDHGB4,PCDHGA8,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_032088.1,NM_032089.1	,,,,,,,,64,,,,,,64	0,2,6480	TT,TC,CC		0.0,0.0457,0.0154	,,,,,,,,,,,,,,	,,,,,,,,637/933,,,,,,637/829	140784429	2,12962	2186	4296	6482	140764613	SO:0001583	missense	56107	exon1			AF152516	CCDS58981.1, CCDS75341.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8707	other	protocadherin		606296				10380929	Standard	NM_018921		Approved	PCDH-GAMMA-A9		Q9Y5G4		ENST00000573521.1:c.1910C>T	5.37:g.140784429C>T	ENSP00000460274:p.Ala637Val		140764613	NM_018921	A2RU65|Q9Y5C9	Missense_Mutation	SNP	ENST00000573521.1	37	CCDS58981.1																																																																																				0.607	PCDHGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437105.1	NM_018921	
PCDHGC4	56098	broad.mit.edu	37	5	140865426	140865426	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:140865426G>A	ENST00000306593.1	+	1	686	c.686G>A	c.(685-687)cGg>cAg	p.R229Q	PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB4_ENST00000519479.1_Intron	NM_018928.2|NM_032406.1	NP_061751.1|NP_115782.1	Q9Y5F7	PCDGL_HUMAN	protocadherin gamma subfamily C, 4	229	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R229Q(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(13)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	42			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCAGAGCTCCGGGTATCCGTG	0.597																																					p.R229Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G686A	5						.						34.0	38.0	37.0					5																	140865426		2203	4300	6503	140845610	SO:0001583	missense	56098	exon1			AF152525	CCDS4262.1, CCDS75349.1	5q31	2010-01-26			ENSG00000242419	ENSG00000242419		"""Cadherins / Protocadherins : Clustered"""	8717	other	protocadherin		606305				10380929	Standard	NM_018928		Approved	PCDH-GAMMA-C4		Q9Y5F7	OTTHUMG00000129625	ENST00000306593.1:c.686G>A	5.37:g.140865426G>A	ENSP00000306918:p.Arg229Gln		140845610	NM_032406	Q495T2|Q9Y5C3	Missense_Mutation	SNP	ENST00000306593.1	37	CCDS4262.1	.	.	.	.	.	.	.	.	.	.	G	2.108	-0.404354	0.04832	.	.	ENSG00000242419	ENST00000306593	T	0.01725	4.67	5.0	3.05	0.35203	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.00754	0.0025	N	0.12422	0.21	0.09310	N	0.999999	P;B	0.41313	0.745;0.007	B;B	0.27500	0.08;0.01	T	0.31110	-0.9955	9	0.10902	T	0.67	.	0.7718	0.01025	0.2648:0.1692:0.3912:0.1748	.	229;229	Q9Y5F7-2;Q9Y5F7	.;PCDGL_HUMAN	Q	229	ENSP00000306918:R229Q	ENSP00000306918:R229Q	R	+	2	0	PCDHGC4	140845610	0.000000	0.05858	1.000000	0.80357	0.948000	0.59901	0.313000	0.19415	1.327000	0.45338	0.561000	0.74099	CGG		0.597	PCDHGC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251820.1	NM_018928	
PCDH12	51294	broad.mit.edu	37	5	141325326	141325326	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:141325326C>A	ENST00000231484.3	-	4	4385	c.3175G>T	c.(3175-3177)Gcg>Tcg	p.A1059S		NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	1059					calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A1059S(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGAGTCTCGCCATCCAGGCC	0.667																																					p.A1059S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3175T	5						.						44.0	47.0	46.0					5																	141325326		2203	4300	6503	141305510	SO:0001583	missense	51294	exon4			AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"""Cadherins / Protocadherins : Non-clustered"""	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.3175G>T	5.37:g.141325326C>A	ENSP00000231484:p.Ala1059Ser		141305510	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	37	CCDS4269.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.806883	0.90623	.	.	ENSG00000113555	ENST00000231484	T	0.58940	0.3	5.46	5.46	0.80206	.	0.123573	0.53938	D	0.000049	T	0.73442	0.3587	M	0.64997	1.995	0.54753	D	0.999981	D	0.76494	0.999	D	0.80764	0.994	T	0.73069	-0.4099	10	0.46703	T	0.11	.	16.7873	0.85577	0.0:1.0:0.0:0.0	.	1059	Q9NPG4	PCD12_HUMAN	S	1059	ENSP00000231484:A1059S	ENSP00000231484:A1059S	A	-	1	0	PCDH12	141305510	1.000000	0.71417	1.000000	0.80357	0.825000	0.46686	3.913000	0.56394	2.572000	0.86782	0.591000	0.81541	GCG		0.667	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580	
PCDH12	51294	broad.mit.edu	37	5	141335533	141335533	+	Silent	SNP	C	C	T	rs547886985		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:141335533C>T	ENST00000231484.3	-	1	3094	c.1884G>A	c.(1882-1884)tcG>tcA	p.S628S	PCDH12_ENST00000512221.1_5'Flank|AC005740.6_ENST00000607378.1_RNA	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	628	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S628S(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CATTTGCCCCCGAGTCTGCAT	0.577													C|||	1	0.000199681	0.0	0.0	5008	,	,		19328	0.0		0.001	False		,,,				2504	0.0				p.S628S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1884A	5						.						73.0	67.0	69.0					5																	141335533		2203	4300	6503	141315717	SO:0001819	synonymous_variant	51294	exon1			AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"""Cadherins / Protocadherins : Non-clustered"""	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.1884G>A	5.37:g.141335533C>T			141315717	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Silent	SNP	ENST00000231484.3	37	CCDS4269.1																																																																																				0.577	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580	
RNF14	9604	broad.mit.edu	37	5	141353245	141353245	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:141353245T>C	ENST00000394520.2	+	3	401	c.92T>C	c.(91-93)gTc>gCc	p.V31A	RNF14_ENST00000356143.1_Missense_Mutation_p.V31A|RNF14_ENST00000394514.2_5'UTR|RNF14_ENST00000502341.1_3'UTR|RNF14_ENST00000347642.3_Missense_Mutation_p.V31A|RNF14_ENST00000394515.3_Missense_Mutation_p.V31A|AC005740.5_ENST00000520882.1_RNA|RNF14_ENST00000394519.1_Missense_Mutation_p.V31A|RNF14_ENST00000540015.1_Missense_Mutation_p.V31A	NM_001201365.1|NM_004290.4	NP_001188294.1|NP_004281.1	Q9UBS8	RNF14_HUMAN	ring finger protein 14	31	RWD. {ECO:0000255|PROSITE- ProRule:PRU00179}.				androgen receptor signaling pathway (GO:0030521)|positive regulation of transcription, DNA-templated (GO:0045893)|protein ubiquitination (GO:0016567)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|small conjugating protein ligase activity (GO:0019787)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.V31A(1)		cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15		all_hematologic(541;0.0536)|Ovarian(839;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.0407)		GCAGAGTCTGTCCAAGGTGGA	0.388																																					p.V31A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T92C	5						.						85.0	87.0	86.0					5																	141353245		2203	4300	6503	141333429	SO:0001583	missense	9604	exon3			AF060544	CCDS4270.1, CCDS4271.1	5q23.3-q31.1	2008-02-05			ENSG00000013561	ENSG00000013561		"""RING-type (C3HC4) zinc fingers"""	10058	protein-coding gene	gene with protein product		605675				10085091, 10320776	Standard	NM_183399		Approved	ARA54, HFB30, TRIAD2	uc003lmc.3	Q9UBS8	OTTHUMG00000129660	ENST00000394520.2:c.92T>C	5.37:g.141353245T>C	ENSP00000378028:p.Val31Ala		141333429	NM_183401	A0AV26|A6NMR2|A8MTW5|B3KN72|B7ZLV2|D3DQE4|O94793|Q6IBV0	Missense_Mutation	SNP	ENST00000394520.2	37	CCDS4270.1	.	.	.	.	.	.	.	.	.	.	T	4.840	0.156132	0.09236	.	.	ENSG00000013561	ENST00000511961;ENST00000506822;ENST00000513019;ENST00000356143;ENST00000394520;ENST00000347642;ENST00000540015;ENST00000506938;ENST00000512565;ENST00000394515;ENST00000507163;ENST00000394519;ENST00000507291	T;T;T;T;T;T;D;T;D;T;T;T;T	0.90444	2.01;2.01;2.01;2.01;2.01;2.01;-2.67;2.01;-2.67;2.01;2.01;2.01;1.97	5.91	3.49	0.39957	Ubiquitin-conjugating enzyme/RWD-like (2);RWD domain (3);	0.408220	0.28119	N	0.016536	T	0.63379	0.2506	N	0.00453	-1.485	0.30812	N	0.738762	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.001	T	0.60732	-0.7205	10	0.08381	T	0.77	.	4.0624	0.09844	0.0:0.174:0.3891:0.4369	.	31;31;31	B7Z3J5;B7Z229;Q9UBS8	.;.;RNF14_HUMAN	A	31	ENSP00000423420:V31A;ENSP00000423273:V31A;ENSP00000421780:V31A;ENSP00000348462:V31A;ENSP00000378028:V31A;ENSP00000324956:V31A;ENSP00000442490:V31A;ENSP00000420837:V31A;ENSP00000426832:V31A;ENSP00000378023:V31A;ENSP00000422527:V31A;ENSP00000378027:V31A;ENSP00000423294:V31A	ENSP00000324956:V31A	V	+	2	0	RNF14	141333429	0.882000	0.30256	1.000000	0.80357	0.997000	0.91878	1.466000	0.35310	1.015000	0.39444	0.377000	0.23210	GTC		0.388	RNF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251860.2	NM_004290	
SPRY4	81848	broad.mit.edu	37	5	141694439	141694439	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:141694439C>T	ENST00000434127.2	-	2	478	c.235G>A	c.(235-237)Gcc>Acc	p.A79T	SPRY4_ENST00000344120.4_Missense_Mutation_p.A102T|SPRY4_ENST00000503582.1_5'Flank	NM_001127496.1	NP_001120968.1	Q9C004	SPY4_HUMAN	sprouty homolog 4 (Drosophila)	79					multicellular organismal development (GO:0007275)|negative regulation of MAP kinase activity (GO:0043407)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)		p.A102T(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(1)	18		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCACAGCGGGCGGGCGTCGGG	0.657									Testicular Cancer, Familial Clustering of																												p.A102T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G304A	5						.						27.0	34.0	32.0					5																	141694439		2200	4297	6497	141674623	SO:0001583	missense	81848	exon3	Familial Cancer Database		AF227516	CCDS4274.1, CCDS47296.1	5q31.3	2010-08-05			ENSG00000187678	ENSG00000187678			15533	protein-coding gene	gene with protein product		607984				16465403	Standard	NM_030964		Approved		uc010jgi.1	Q9C004	OTTHUMG00000129663	ENST00000434127.2:c.235G>A	5.37:g.141694439C>T	ENSP00000399468:p.Ala79Thr		141674623	NM_030964	A4FVB2|A4FVB3|Q6QIX2|Q9C003	Missense_Mutation	SNP	ENST00000434127.2	37	CCDS47296.1	.	.	.	.	.	.	.	.	.	.	C	5.663	0.306885	0.10733	.	.	ENSG00000187678	ENST00000344120;ENST00000434127;ENST00000359661	T;T	0.63580	-0.05;-0.04	5.77	1.58	0.23477	.	0.687272	0.14744	N	0.301020	T	0.31575	0.0801	N	0.08118	0	0.21105	N	0.999789	B;B	0.22003	0.063;0.006	B;B	0.12156	0.007;0.002	T	0.16928	-1.0386	10	0.09590	T	0.72	-17.321	4.2449	0.10667	0.2178:0.4614:0.2244:0.0964	.	79;79	Q9C004-2;Q9C004	.;SPY4_HUMAN	T	102;79;79	ENSP00000344967:A102T;ENSP00000399468:A79T	ENSP00000344967:A102T	A	-	1	0	SPRY4	141674623	0.001000	0.12720	0.452000	0.26994	0.562000	0.35680	-0.102000	0.10956	0.740000	0.32651	-0.314000	0.08810	GCC		0.657	SPRY4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370652.1		
FBXL7	23194	broad.mit.edu	37	5	15936591	15936591	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:15936591C>T	ENST00000504595.1	+	4	1253	c.772C>T	c.(772-774)Cgg>Tgg	p.R258W	MIR887_ENST00000401258.1_RNA|FBXL7_ENST00000510662.1_Missense_Mutation_p.R211W|FBXL7_ENST00000329673.7_Missense_Mutation_p.R246W	NM_001278317.1|NM_012304.3	NP_001265246.1|NP_036436.1	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	258					cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)	p.R258W(2)		cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(13)|lung(33)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	60						CAGCTTGACCCGGGAGGCCTC	0.582																																					p.R258W												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.C772T	5						.						51.0	51.0	51.0					5																	15936591		2101	4220	6321	15989591	SO:0001583	missense	23194	exon4			AB020647	CCDS54833.1, CCDS64129.1	5p15.1	2011-06-09				ENSG00000183580		"""F-boxes / Leucine-rich repeats"""	13604	protein-coding gene	gene with protein product		605656				10048485, 10531035	Standard	NM_012304		Approved	KIAA0840, FBL7, FBL6	uc003jfn.1	Q9UJT9		ENST00000504595.1:c.772C>T	5.37:g.15936591C>T	ENSP00000423630:p.Arg258Trp		15989591	NM_012304	B9EGF1|D6RDY7|O94926	Missense_Mutation	SNP	ENST00000504595.1	37	CCDS54833.1	.	.	.	.	.	.	.	.	.	.	C	17.42	3.386340	0.61956	.	.	ENSG00000183580	ENST00000504595;ENST00000510662;ENST00000329673	T;T;T	0.53857	0.6;0.6;0.6	5.31	5.31	0.75309	.	0.053169	0.85682	D	0.000000	T	0.65217	0.2670	L	0.61036	1.89	0.80722	D	1	D	0.71674	0.998	P	0.54174	0.744	T	0.69146	-0.5222	10	0.72032	D	0.01	.	18.9742	0.92728	0.0:1.0:0.0:0.0	.	258	Q9UJT9	FBXL7_HUMAN	W	258;211;246	ENSP00000423630:R258W;ENSP00000425184:R211W;ENSP00000329632:R246W	ENSP00000329632:R246W	R	+	1	2	FBXL7	15989591	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.940000	0.70187	2.495000	0.84180	0.655000	0.94253	CGG		0.582	FBXL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366117.1	NM_012304	
MYO10	4651	broad.mit.edu	37	5	16699596	16699596	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:16699596G>A	ENST00000513610.1	-	26	3973	c.3519C>T	c.(3517-3519)gtC>gtT	p.V1173V	MYO10_ENST00000274203.9_Silent_p.V530V|MYO10_ENST00000505695.1_Silent_p.V512V|MYO10_ENST00000515803.1_Silent_p.V512V|MYO10_ENST00000427430.2_Silent_p.V530V	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	1173					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)	p.V1173V(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						ACGGCAGAGTGACACAGCTGT	0.498																																					p.V1173V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3519T	5						.						65.0	65.0	65.0					5																	16699596		2011	4176	6187	16752596	SO:0001819	synonymous_variant	4651	exon26			AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"""Myosins / Myosin superfamily : Class X"", ""Pleckstrin homology (PH) domain containing"""	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.3519C>T	5.37:g.16699596G>A			16752596	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	37	CCDS54834.1																																																																																				0.498	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334	
PPP2R2B	5521	broad.mit.edu	37	5	145980003	145980003	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:145980003G>A	ENST00000394413.3	-	7	1381	c.811C>T	c.(811-813)Cca>Tca	p.P271S	PPP2R2B_ENST00000530902.1_5'UTR|PPP2R2B_ENST00000394409.3_Missense_Mutation_p.P329S|PPP2R2B_ENST00000394414.1_Missense_Mutation_p.P337S|PPP2R2B_ENST00000394411.4_Missense_Mutation_p.P271S|PPP2R2B_ENST00000336640.6_Missense_Mutation_p.P274S|PPP2R2B_ENST00000504198.1_Missense_Mutation_p.P277S|PPP2R2B_ENST00000394410.2_Missense_Mutation_p.P260S|PPP2R2B_ENST00000453001.1_Missense_Mutation_p.P271S|CTB-99A3.1_ENST00000512730.1_RNA|PPP2R2B_ENST00000508545.2_Missense_Mutation_p.P260S|PPP2R2B_ENST00000356826.3_Missense_Mutation_p.P271S			Q00005	2ABB_HUMAN	protein phosphatase 2, regulatory subunit B, beta	271					apoptotic process (GO:0006915)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	cytoskeleton (GO:0005856)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)	p.P274S(1)		endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(9)|ovary(1)|prostate(4)|skin(3)	32			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTGTTGCTTGGATCTTCCGGC	0.413																																					p.P271S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C811T	5						.						69.0	68.0	68.0					5																	145980003		2203	4300	6503	145960196	SO:0001583	missense	5521	exon8			M64930	CCDS4283.1, CCDS4284.1, CCDS43380.1, CCDS4284.2, CCDS64282.1	5q32	2013-01-10	2010-04-14		ENSG00000156475	ENSG00000156475	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""WD repeat domain containing"""	9305	protein-coding gene	gene with protein product	"""PP2A subunit B isoform beta"""	604325	"""spinocerebellar ataxia 12"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B, beta isoform"""	SCA12		1849734, 10581021	Standard	NM_181674		Approved	PR55-BETA, PR52B	uc003log.5	Q00005	OTTHUMG00000163381	ENST00000394413.3:c.811C>T	5.37:g.145980003G>A	ENSP00000377935:p.Pro271Ser		145960196	NM_001127381	A6NEJ2|A8K102|B3KPD0|B7Z2F2|B7Z304|D3DQF7|D3DQF8|G3V149	Missense_Mutation	SNP	ENST00000394413.3	37	CCDS4284.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.864538	0.91511	.	.	ENSG00000156475	ENST00000394413;ENST00000508545;ENST00000394414;ENST00000394411;ENST00000356826;ENST00000453001;ENST00000394410;ENST00000336640;ENST00000504198;ENST00000394409	T;T;T;T;T;T;T;T;T;T	0.74947	-0.89;-0.89;1.4;-0.89;-0.89;-0.89;-0.89;-0.89;-0.89;1.4	5.8	5.8	0.92144	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.83866	0.5347	M	0.85859	2.78	0.80722	D	1	P;P;P;B;P;P	0.48162	0.799;0.906;0.906;0.313;0.861;0.906	P;P;P;B;B;P	0.49332	0.607;0.477;0.477;0.267;0.328;0.477	D	0.85734	0.1333	10	0.62326	D	0.03	-10.9741	20.0467	0.97609	0.0:0.0:1.0:0.0	.	329;277;260;337;274;271	Q00005-4;Q00005-3;G3V149;Q00005-5;Q00005-2;Q00005	.;.;.;.;.;2ABB_HUMAN	S	271;260;337;271;271;271;260;274;277;329	ENSP00000377935:P271S;ENSP00000431320:P260S;ENSP00000377936:P337S;ENSP00000377933:P271S;ENSP00000349283:P271S;ENSP00000398779:P271S;ENSP00000377932:P260S;ENSP00000336591:P274S;ENSP00000421396:P277S;ENSP00000377931:P329S	ENSP00000336591:P274S	P	-	1	0	AC011357.1	145960196	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.749000	0.94314	0.655000	0.94253	CCA		0.413	PPP2R2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251893.2	NM_181678	
TENM2	57451	broad.mit.edu	37	5	167645725	167645725	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:167645725C>T	ENST00000518659.1	+	23	4868	c.4829C>T	c.(4828-4830)aCa>aTa	p.T1610I	TENM2_ENST00000519204.1_Missense_Mutation_p.T1489I|TENM2_ENST00000545108.1_Missense_Mutation_p.T1609I|TENM2_ENST00000403607.2_Missense_Mutation_p.T1434I|TENM2_ENST00000520394.1_Missense_Mutation_p.T1371I	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	1610					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.T1443I(1)									AGCCTGGTGACAGGGGAGTAC	0.458																																					p.T1601I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4802T	5						.						106.0	104.0	105.0					5																	167645725		2010	4181	6191	167578303	SO:0001583	missense	57451	exon23			AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"""odz, odd Oz/ten-m homolog 2 (Drosophila)"""	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.4829C>T	5.37:g.167645725C>T	ENSP00000429430:p.Thr1610Ile		167578303	NM_001122679	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	37		.	.	.	.	.	.	.	.	.	.	C	18.93	3.726864	0.69074	.	.	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	T;T;T;T;T	0.54071	1.53;0.59;1.53;1.53;1.53	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.78168	0.4241	M	0.87097	2.86	0.58432	D	0.999994	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.80764	0.994;0.987;0.994	T	0.80821	-0.1211	10	0.87932	D	0	.	20.1577	0.98120	0.0:1.0:0.0:0.0	.	1609;1610;1371	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	I	1610;1609;1489;1371;1434	ENSP00000429430:T1610I;ENSP00000438635:T1609I;ENSP00000428964:T1489I;ENSP00000427874:T1371I;ENSP00000384905:T1434I	ENSP00000384905:T1434I	T	+	2	0	ODZ2	167578303	1.000000	0.71417	0.977000	0.42913	0.992000	0.81027	4.811000	0.62606	2.767000	0.95098	0.655000	0.94253	ACA		0.458	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679	
TENM2	57451	broad.mit.edu	37	5	167653158	167653158	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:167653158G>A	ENST00000518659.1	+	24	5213	c.5174G>A	c.(5173-5175)cGg>cAg	p.R1725Q	TENM2_ENST00000519204.1_Missense_Mutation_p.R1604Q|TENM2_ENST00000545108.1_Missense_Mutation_p.R1724Q|TENM2_ENST00000403607.2_Missense_Mutation_p.R1549Q|TENM2_ENST00000520394.1_Missense_Mutation_p.R1486Q	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	1725					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R1558Q(1)									AGTCTGCACCGGGAAATGGAG	0.522																																					p.R1716Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5147A	5						.						52.0	56.0	54.0					5																	167653158		1986	4149	6135	167585736	SO:0001583	missense	57451	exon24			AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"""odz, odd Oz/ten-m homolog 2 (Drosophila)"""	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.5174G>A	5.37:g.167653158G>A	ENSP00000429430:p.Arg1725Gln		167585736	NM_001122679	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	37		.	.	.	.	.	.	.	.	.	.	G	23.0	4.362496	0.82353	.	.	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	D;D;D;D;D	0.89485	-2.05;-2.04;-2.15;-2.52;-2.52	5.08	5.08	0.68730	.	0.103719	0.64402	D	0.000004	D	0.92097	0.7495	L	0.53249	1.67	0.48975	D	0.99973	D;D;D	0.76494	0.987;0.962;0.999	P;B;D	0.71870	0.733;0.347;0.975	D	0.88517	0.3093	10	0.11485	T	0.65	.	18.8316	0.92143	0.0:0.0:1.0:0.0	.	1724;1725;1486	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	Q	1725;1724;1604;1486;1549	ENSP00000429430:R1725Q;ENSP00000438635:R1724Q;ENSP00000428964:R1604Q;ENSP00000427874:R1486Q;ENSP00000384905:R1549Q	ENSP00000384905:R1549Q	R	+	2	0	ODZ2	167585736	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.499000	0.73683	2.543000	0.85770	0.555000	0.69702	CGG		0.522	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679	
RANBP17	64901	broad.mit.edu	37	5	170336709	170336709	+	Silent	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:170336709C>A	ENST00000523189.1	+	6	698	c.534C>A	c.(532-534)acC>acA	p.T178T		NM_022897.3	NP_075048.1	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	178					mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)	GTP binding (GO:0005525)	p.T178T(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	50	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			AAATAGCTACCTCATTTCGTG	0.313			T	TRD@	ALL																																p.T178T			Dom	yes		5	5q34	64901	RAN binding protein 17		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C534A	5						.						84.0	82.0	82.0					5																	170336709		2202	4294	6496	170269287	SO:0001819	synonymous_variant	64901	exon6			AF222747	CCDS34287.1	5q34	2009-01-12			ENSG00000204764	ENSG00000204764			14428	protein-coding gene	gene with protein product		606141				11024021	Standard	NM_022897		Approved		uc003mba.3	Q9H2T7	OTTHUMG00000163203	ENST00000523189.1:c.534C>A	5.37:g.170336709C>A			170269287	NM_022897	Q8IU74	Silent	SNP	ENST00000523189.1	37	CCDS34287.1																																																																																				0.313	RANBP17-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372036.1	NM_022897	
UBTD2	92181	broad.mit.edu	37	5	171639165	171639165	+	Missense_Mutation	SNP	G	G	A	rs144720396		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:171639165G>A	ENST00000393792.2	-	3	779	c.374C>T	c.(373-375)cCg>cTg	p.P125L		NM_152277.2	NP_689490.2	Q8WUN7	UBTD2_HUMAN	ubiquitin domain containing 2	125						cytoplasm (GO:0005737)		p.P125L(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(1)|prostate(1)|skin(1)	10	Renal(175;0.000159)|Lung NSC(126;0.00976)|all_lung(126;0.0156)	Medulloblastoma(196;0.00853)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			GTTGATTGGCGGTGCCAAGCA	0.438																																					p.P125L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C374T	5						.	G	LEU/PRO	1,4405		0,1,2202	126.0	117.0	120.0		374	6.0	1.0	5	dbSNP_134	120	0,8600		0,0,4300	no	missense	UBTD2	NM_152277.2	98	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging	125/235	171639165	1,13005	2203	4300	6503	171571770	SO:0001583	missense	92181	exon3			AF251700	CCDS4379.2	5q35.1	2008-10-30			ENSG00000168246	ENSG00000168246			24463	protein-coding gene	gene with protein product	"""dendritic cell derived ubiquitin like protein"""	610174				12507522	Standard	NM_152277		Approved	DC-UbP, MGC30022	uc003mbp.1	Q8WUN7	OTTHUMG00000130519	ENST00000393792.2:c.374C>T	5.37:g.171639165G>A	ENSP00000377381:p.Pro125Leu		171571770	NM_152277	Q8TDQ3	Missense_Mutation	SNP	ENST00000393792.2	37	CCDS4379.2	.	.	.	.	.	.	.	.	.	.	G	20.6	4.014332	0.75161	2.27E-4	0.0	ENSG00000168246	ENST00000393792	T	0.30981	1.51	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.52789	0.1756	L	0.55990	1.75	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.42515	-0.9447	10	0.49607	T	0.09	.	17.9158	0.88950	0.0:0.0:1.0:0.0	.	125	Q8WUN7	UBTD2_HUMAN	L	125	ENSP00000377381:P125L	ENSP00000377381:P125L	P	-	2	0	UBTD2	171571770	1.000000	0.71417	0.984000	0.44739	0.936000	0.57629	9.611000	0.98342	2.832000	0.97577	0.655000	0.94253	CCG		0.438	UBTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252936.1	NM_152277	
NSD1	64324	broad.mit.edu	37	5	176638222	176638222	+	Missense_Mutation	SNP	G	G	A	rs189716582		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:176638222G>A	ENST00000439151.2	+	5	2867	c.2822G>A	c.(2821-2823)cGt>cAt	p.R941H	NSD1_ENST00000361032.4_Missense_Mutation_p.R838H|NSD1_ENST00000354179.4_Missense_Mutation_p.R672H|NSD1_ENST00000347982.4_Missense_Mutation_p.R672H	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	941					gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.R941H(2)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		AGTCCTGGTCGTGGGGACTGT	0.458			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)			G|||	1	0.000199681	0.0	0.0	5008	,	,		20013	0.001		0.0	False		,,,				2504	0.0				p.R941H			Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2822A	5						.						69.0	67.0	68.0					5																	176638222		2203	4300	6503	176570828	SO:0001583	missense	64324	exon5	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	14234	protein-coding gene	gene with protein product		606681	"""Sotos syndrome"""	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.2822G>A	5.37:g.176638222G>A	ENSP00000395929:p.Arg941His		176570828	NM_022455	Q96PD8|Q96RN7	Missense_Mutation	SNP	ENST00000439151.2	37	CCDS4412.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	11.39	1.625248	0.28889	.	.	ENSG00000165671	ENST00000354179;ENST00000439151;ENST00000347982;ENST00000361032	D;D;D;D	0.93076	-3.05;-3.05;-3.05;-3.16	5.16	-0.569	0.11756	.	0.862835	0.10178	N	0.706203	D	0.82563	0.5064	N	0.14661	0.345	0.09310	N	1	P;P;P	0.49447	0.924;0.924;0.876	B;B;B	0.40782	0.34;0.34;0.118	T	0.75494	-0.3298	9	.	.	.	.	2.2969	0.04153	0.1735:0.2387:0.4155:0.1723	.	672;838;941	Q96L73-2;Q96L73-3;Q96L73	.;.;NSD1_HUMAN	H	672;941;672;838	ENSP00000346111:R672H;ENSP00000395929:R941H;ENSP00000343209:R672H;ENSP00000354310:R838H	.	R	+	2	0	NSD1	176570828	0.027000	0.19231	0.013000	0.15412	0.969000	0.65631	0.270000	0.18607	-0.173000	0.10761	-0.137000	0.14449	CGT		0.458	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349	
RGS14	10636	broad.mit.edu	37	5	176794503	176794503	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:176794503G>A	ENST00000408923.3	+	6	760	c.572G>A	c.(571-573)cGc>cAc	p.R191H		NM_006480.4	NP_006471.2	O43566	RGS14_HUMAN	regulator of G-protein signaling 14	191					cell division (GO:0051301)|chromosome segregation (GO:0007059)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mitotic nuclear division (GO:0007067)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of synaptic plasticity (GO:0031914)|nucleocytoplasmic transport (GO:0006913)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of GTPase activity (GO:0043547)|positive regulation of neurogenesis (GO:0050769)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|response to oxidative stress (GO:0006979)|spindle organization (GO:0007051)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual learning (GO:0008542)|zygote asymmetric cell division (GO:0010070)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|microtubule (GO:0005874)|nuclear body (GO:0016604)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|spindle (GO:0005819)|spindle pole (GO:0000922)	GDP-dissociation inhibitor activity (GO:0005092)|GTPase activator activity (GO:0005096)|microtubule binding (GO:0008017)|receptor signaling complex scaffold activity (GO:0030159)|receptor signaling protein activity (GO:0005057)	p.R191H(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|skin(3)|upper_aerodigestive_tract(1)	12	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCCGAGGGACGCCCTCTGCGG	0.677																																					p.R191H	NSCLC(47;353 1896 28036)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G572A	5						.						21.0	22.0	22.0					5																	176794503		2025	4175	6200	176727109	SO:0001583	missense	10636	exon6			AF037195	CCDS43405.1	5q35.3	2008-02-05	2007-08-14		ENSG00000169220	ENSG00000169220		"""Regulators of G-protein signaling"""	9996	protein-coding gene	gene with protein product		602513	"""regulator of G-protein signalling 14"""				Standard	NM_006480		Approved		uc003mgf.3	O43566	OTTHUMG00000163324	ENST00000408923.3:c.572G>A	5.37:g.176794503G>A	ENSP00000386229:p.Arg191His		176727109	NM_006480	O43565|Q506M1|Q6ZWA4|Q8TD62	Missense_Mutation	SNP	ENST00000408923.3	37	CCDS43405.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.8|23.8	4.463462|4.463462	0.84425|0.84425	.|.	.|.	ENSG00000169220|ENSG00000169220	ENST00000511890|ENST00000408923	.|T	.|0.40225	.|1.04	4.5|4.5	4.5|4.5	0.54988|0.54988	.|.	.|0.000000	.|0.64402	.|D	.|0.000001	T|T	0.52757|0.52757	0.1754|0.1754	L|L	0.59436|0.59436	1.845|1.845	0.37356|0.37356	D|D	0.911006|0.911006	.|D;D;P	.|0.76494	.|0.999;0.999;0.597	.|D;D;B	.|0.68765	.|0.96;0.928;0.219	T|T	0.57682|0.57682	-0.7769|-0.7769	5|10	.|0.40728	.|T	.|0.16	-20.4278|-20.4278	6.0913|6.0913	0.19995|0.19995	0.1309:0.0:0.692:0.177|0.1309:0.0:0.692:0.177	.|.	.|38;38;191	.|O43566-5;O43566-4;O43566	.|.;.;RGS14_HUMAN	T|H	61|191	.|ENSP00000386229:R191H	.|ENSP00000386229:R191H	A|R	+|+	1|2	0|0	RGS14|RGS14	176727109|176727109	0.978000|0.978000	0.34361|0.34361	0.996000|0.996000	0.52242|0.52242	0.820000|0.820000	0.46376|0.46376	2.153000|2.153000	0.42282|0.42282	2.344000|2.344000	0.79699|0.79699	0.313000|0.313000	0.20887|0.20887	GCC|CGC		0.677	RGS14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372676.1	NM_006480	
ZNF354C	30832	broad.mit.edu	37	5	178505727	178505727	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:178505727G>T	ENST00000315475.6	+	5	600	c.294G>T	c.(292-294)caG>caT	p.Q98H		NM_014594.1	NP_055409.1	Q86Y25	Z354C_HUMAN	zinc finger protein 354C	98					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q98H(1)		endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|urinary_tract(3)	30	all_cancers(89;0.00065)|all_epithelial(37;0.000153)|Renal(175;0.000159)|Lung NSC(126;0.00175)|all_lung(126;0.00309)	all_cancers(40;0.19)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.247)		CTCATAGACAGGACATTTTTA	0.373																																					p.Q98H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G294T	5						.						62.0	64.0	63.0					5																	178505727		2203	4300	6503	178438333	SO:0001583	missense	30832	exon5				CCDS4443.1	5q35	2013-01-08			ENSG00000177932	ENSG00000177932		"""Zinc fingers, C2H2-type"", ""-"""	16736	protein-coding gene	gene with protein product						10786630	Standard	NM_014594		Approved	KID3	uc003mju.3	Q86Y25	OTTHUMG00000130888	ENST00000315475.6:c.294G>T	5.37:g.178505727G>T	ENSP00000324064:p.Gln98His		178438333	NM_014594	Q6P4P9|Q8NFX1	Missense_Mutation	SNP	ENST00000315475.6	37	CCDS4443.1	.	.	.	.	.	.	.	.	.	.	G	11.96	1.795150	0.31777	.	.	ENSG00000177932	ENST00000315475	T	0.06142	3.34	4.09	0.0464	0.14233	.	.	.	.	.	T	0.05273	0.0140	L	0.39898	1.24	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.39165	-0.9627	9	0.44086	T	0.13	-6.5778	3.9638	0.09423	0.4525:0.1837:0.3638:0.0	.	98	Q86Y25	Z354C_HUMAN	H	98	ENSP00000324064:Q98H	ENSP00000324064:Q98H	Q	+	3	2	ZNF354C	178438333	0.000000	0.05858	0.003000	0.11579	0.008000	0.06430	-0.636000	0.05465	-0.121000	0.11787	0.591000	0.81541	CAG		0.373	ZNF354C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253473.2		
BRD9	65980	broad.mit.edu	37	5	881237	881237	+	Missense_Mutation	SNP	C	C	T	rs144680205		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:881237C>T	ENST00000467963.1	-	9	1193	c.1027G>A	c.(1027-1029)Gag>Aag	p.E343K	BRD9_ENST00000388890.4_Missense_Mutation_p.E227K|BRD9_ENST00000483173.1_Missense_Mutation_p.E290K|BRD9_ENST00000435709.2_Intron|BRD9_ENST00000323510.4_Missense_Mutation_p.E247K|BRD9_ENST00000494422.1_Intron	NM_023924.4	NP_076413.3	Q9H8M2	BRD9_HUMAN	bromodomain containing 9	343					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		lysine-acetylated histone binding (GO:0070577)|nucleic acid binding (GO:0003676)	p.E247K(1)|p.E343K(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(3)	29			Epithelial(17;0.00202)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00815)|Lung(60;0.185)			GCGTCCGGCTCGGCCGTGTTG	0.587																																					p.E343K												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1027A	5						.	C	LYS/GLU,LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	73.0	63.0	66.0		868,1027	4.2	0.7	5	dbSNP_134	66	0,8600		0,0,4300	no	missense,missense	BRD9	NM_001009877.2,NM_023924.4	56,56	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign	290/545,343/598	881237	1,13005	2203	4300	6503	934237	SO:0001583	missense	65980	exon9			AK023503	CCDS34127.1, CCDS34128.1, CCDS34127.2, CCDS34128.2	5p15.33	2008-02-05			ENSG00000028310	ENSG00000028310			25818	protein-coding gene	gene with protein product						12477932	Standard	NM_023924		Approved	FLJ13441	uc003jbq.3	Q9H8M2	OTTHUMG00000159258	ENST00000467963.1:c.1027G>A	5.37:g.881237C>T	ENSP00000419765:p.Glu343Lys		934237	NM_023924	A6NFY8|B4DMQ2|B4DR93|Q2XUS1|Q6UWU9|Q8IUS4|Q9H5Q5|Q9H7R9	Missense_Mutation	SNP	ENST00000467963.1	37	CCDS34127.2	.	.	.	.	.	.	.	.	.	.	C	18.12	3.552341	0.65311	2.27E-4	0.0	ENSG00000028310	ENST00000323510;ENST00000388890;ENST00000483173;ENST00000467963	T;T;T;T	0.47528	0.84;0.84;0.84;0.84	5.05	4.18	0.49190	.	0.093796	0.64402	D	0.000001	T	0.41351	0.1155	L	0.29908	0.895	0.80722	D	1	D;P;D;P	0.58970	0.984;0.579;0.964;0.938	P;B;B;B	0.47162	0.54;0.241;0.315;0.245	T	0.38564	-0.9655	10	0.72032	D	0.01	-27.8089	11.439	0.50086	0.0:0.9152:0.0:0.0848	.	290;343;247;227	B4DMQ2;Q9H8M2;Q9H8M2-1;Q9H8M2-3	.;BRD9_HUMAN;.;.	K	247;227;290;343	ENSP00000323557:E247K;ENSP00000373542:E227K;ENSP00000419845:E290K;ENSP00000419765:E343K	ENSP00000323557:E247K	E	-	1	0	BRD9	934237	0.999000	0.42202	0.719000	0.30619	0.990000	0.78478	5.146000	0.64845	1.123000	0.41961	0.550000	0.68814	GAG		0.587	BRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354113.1	NM_023924	
CDH6	1004	broad.mit.edu	37	5	31323064	31323064	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:31323064C>T	ENST00000265071.2	+	12	2287	c.2022C>T	c.(2020-2022)atC>atT	p.I674I		NM_004932.3	NP_004923.1	P55285	CADH6_HUMAN	cadherin 6, type 2, K-cadherin (fetal kidney)	674					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.I674I(1)		NS(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(42)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CTTTTGATATCGGCACCCTGA	0.498																																					p.I674I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2022T	5						.						84.0	79.0	81.0					5																	31323064		2203	4300	6503	31358821	SO:0001819	synonymous_variant	1004	exon12			D31784	CCDS3894.1	5p13.3	2010-01-26			ENSG00000113361	ENSG00000113361		"""Cadherins / Major cadherins"""	1765	protein-coding gene	gene with protein product	"""K-Cadherin"""	603007				7743525, 10191097	Standard	NM_004932		Approved		uc003jhe.2	P55285	OTTHUMG00000090673	ENST00000265071.2:c.2022C>T	5.37:g.31323064C>T			31358821	NM_004932	A8K5H5|Q9BWS0	Silent	SNP	ENST00000265071.2	37	CCDS3894.1																																																																																				0.498	CDH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207355.2	NM_004932	
ADAMTS12	81792	broad.mit.edu	37	5	33576443	33576443	+	Missense_Mutation	SNP	C	C	T	rs375250179		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:33576443C>T	ENST00000504830.1	-	19	4023	c.3688G>A	c.(3688-3690)Gaa>Aaa	p.E1230K	ADAMTS12_ENST00000352040.3_Missense_Mutation_p.E1145K|ADAMTS12_ENST00000504582.1_5'Flank	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	1230	Spacer 2.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.E1230K(1)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						GTCCCAGTTTCGGAAGTAGTG	0.572										HNSCC(64;0.19)																											p.E1230K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3688A	5						.	C	LYS/GLU	0,4406		0,0,2203	124.0	122.0	123.0		3688	-3.8	0.0	5		123	1,8599	1.2+/-3.3	0,1,4299	no	missense	ADAMTS12	NM_030955.2	56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	1230/1595	33576443	1,13005	2203	4300	6503	33612200	SO:0001583	missense	81792	exon19			AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14605	protein-coding gene	gene with protein product		606184	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"""			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.3688G>A	5.37:g.33576443C>T	ENSP00000422554:p.Glu1230Lys		33612200	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	37	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	c	0.011	-1.732625	0.00687	0.0	1.16E-4	ENSG00000151388	ENST00000504830;ENST00000352040	T;T	0.57752	0.38;0.39	5.47	-3.81	0.04294	.	1.567560	0.02893	N	0.134478	T	0.20495	0.0493	N	0.01352	-0.895	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.36335	-0.9752	10	0.07030	T	0.85	.	8.7989	0.34896	0.0:0.1517:0.5354:0.3129	.	1145;1230	P58397-3;P58397	.;ATS12_HUMAN	K	1230;1145	ENSP00000422554:E1230K;ENSP00000344847:E1145K	ENSP00000344847:E1145K	E	-	1	0	ADAMTS12	33612200	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-0.059000	0.11731	-0.177000	0.10690	-1.254000	0.01491	GAA		0.572	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955	
ADAMTS12	81792	broad.mit.edu	37	5	33881301	33881301	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:33881301G>T	ENST00000504830.1	-	2	747	c.412C>A	c.(412-414)Ctc>Atc	p.L138I	ADAMTS12_ENST00000352040.3_Missense_Mutation_p.L138I|ADAMTS12_ENST00000515401.1_Missense_Mutation_p.L138I	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	138					cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.L138I(2)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						AGATGGCAGAGGGGGGCAGAG	0.537										HNSCC(64;0.19)																											p.L138I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C412A	5						.						66.0	65.0	65.0					5																	33881301		2203	4300	6503	33917058	SO:0001583	missense	81792	exon2			AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14605	protein-coding gene	gene with protein product		606184	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"""			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.412C>A	5.37:g.33881301G>T	ENSP00000422554:p.Leu138Ile		33917058	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	37	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	G	4.945	0.175557	0.09391	.	.	ENSG00000151388	ENST00000504830;ENST00000352040;ENST00000515401	T;T;T	0.05925	3.37;3.37;3.37	5.65	4.67	0.58626	Peptidase M12B, propeptide (1);	0.617071	0.16836	N	0.197539	T	0.04318	0.0119	N	0.24115	0.695	0.09310	N	1	B;B;B	0.31383	0.09;0.321;0.096	B;B;B	0.36808	0.093;0.15;0.233	T	0.41466	-0.9507	10	0.22109	T	0.4	.	1.3998	0.02268	0.1487:0.2121:0.4197:0.2195	.	138;138;138	P58397-3;D6REX0;P58397	.;.;ATS12_HUMAN	I	138	ENSP00000422554:L138I;ENSP00000344847:L138I;ENSP00000421638:L138I	ENSP00000344847:L138I	L	-	1	0	ADAMTS12	33917058	0.009000	0.17119	0.027000	0.17364	0.043000	0.13939	1.561000	0.36342	2.670000	0.90874	0.467000	0.42956	CTC		0.537	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955	
RAI14	26064	broad.mit.edu	37	5	34811201	34811201	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:34811201A>G	ENST00000265109.3	+	8	822	c.535A>G	c.(535-537)Aat>Gat	p.N179D	RAI14_ENST00000512629.1_Missense_Mutation_p.N179D|RAI14_ENST00000397449.1_Missense_Mutation_p.N172D|RAI14_ENST00000428746.2_Missense_Mutation_p.N179D|RAI14_ENST00000503673.1_Missense_Mutation_p.N179D|RAI14_ENST00000515799.1_Missense_Mutation_p.N182D|RAI14_ENST00000506376.1_Missense_Mutation_p.N171D	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	179						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.N179D(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(19)|lung(22)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(31;0.000191)					AGCAGATGTCAATTCCAGGAA	0.413																																					p.N179D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A535G	5						.						190.0	182.0	185.0					5																	34811201		2203	4300	6503	34846958	SO:0001583	missense	26064	exon8			AB037755	CCDS34142.1, CCDS54837.1, CCDS54838.1, CCDS54839.1	5p13.3-p13.2	2013-01-10			ENSG00000039560	ENSG00000039560		"""Ankyrin repeat domain containing"""	14873	protein-coding gene	gene with protein product	"""novel retinal pigment epithelial"""	606586				11042181	Standard	NM_015577		Approved	NORPEG, KIAA1334, RAI13, DKFZp564G013	uc011coj.2	Q9P0K7	OTTHUMG00000162019	ENST00000265109.3:c.535A>G	5.37:g.34811201A>G	ENSP00000265109:p.Asn179Asp		34846958	NM_001145522	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Missense_Mutation	SNP	ENST00000265109.3	37	CCDS34142.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.528895	0.85706	.	.	ENSG00000039560	ENST00000265109;ENST00000512629;ENST00000428746;ENST00000503673;ENST00000515799;ENST00000506376;ENST00000397449	T;T;T;T;T;T;T	0.74002	-0.8;-0.8;-0.8;-0.8;0.17;-0.8;-0.8	5.68	5.68	0.88126	Ankyrin repeat-containing domain (4);	.	.	.	.	T	0.78805	0.4341	N	0.21240	0.645	0.53688	D	0.99997	D;D;D;D	0.89917	0.998;0.999;1.0;0.999	D;D;D;D	0.85130	0.994;0.996;0.997;0.996	T	0.81716	-0.0806	9	0.66056	D	0.02	-29.0901	15.9191	0.79547	1.0:0.0:0.0:0.0	.	171;179;182;179	Q9P0K7-3;E9PED3;Q9P0K7-2;Q9P0K7	.;.;.;RAI14_HUMAN	D	179;179;179;179;182;171;172	ENSP00000265109:N179D;ENSP00000422377:N179D;ENSP00000388725:N179D;ENSP00000422942:N179D;ENSP00000427123:N182D;ENSP00000423854:N171D;ENSP00000380591:N172D	ENSP00000265109:N179D	N	+	1	0	RAI14	34846958	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.648000	0.74359	2.156000	0.67533	0.477000	0.44152	AAT		0.413	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577	
RAD1	5810	broad.mit.edu	37	5	34914808	34914808	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	A	A	A	Unknown	Wildtype	None	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:34914808A>G	ENST00000382038.2	-	2	1609	c.190T>C	c.(190-192)Ttt>Ctt	p.F64L	BRIX1_ENST00000336767.5_5'Flank|RAD1_ENST00000341754.4_Missense_Mutation_p.F64L	NM_002853.3	NP_002844.1	O60671	RAD1_HUMAN	RAD1 checkpoint DNA exonuclease	64					cellular response to DNA damage stimulus (GO:0006974)|cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|meiotic recombination checkpoint (GO:0051598)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|substantia nigra development (GO:0021762)	chromosome (GO:0005694)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|damaged DNA binding (GO:0003684)|exodeoxyribonuclease III activity (GO:0008853)			endometrium(3)|large_intestine(1)|lung(5)|urinary_tract(1)	10	all_lung(31;0.000107)	Lung NSC(810;5.19e-05)|Ovarian(839;0.0448)|Breast(839;0.198)	COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)			ACCTGAATAAAAGCATTTGCT	0.363								Other conserved DNA damage response genes																													p.F64L												.	.	0			c.T190C	5						.						165.0	150.0	155.0					5																	34914808		2203	4300	6503	34950565	SO:0001583	missense	5810	exon2			AF074717	CCDS3905.1	5p13	2014-08-08	2014-08-08		ENSG00000113456	ENSG00000113456	3.1.11.2		9806	protein-coding gene	gene with protein product	"""exonuclease homolog RAD1"", ""checkpoint control protein HRAD1"", ""cell cycle checkpoint protein Hrad1"", ""Rad1-like DNA damage checkpoint"", ""DNA repair exonuclease REC1"""	603153	"""RAD1 (S. pombe) homolog"", ""RAD1 homolog (S. pombe)"""			9716408, 9828137	Standard	NR_026591		Approved	HRAD1, REC1	uc003jix.3	O60671	OTTHUMG00000090783	ENST00000382038.2:c.190T>C	5.37:g.34914808A>G	ENSP00000371469:p.Phe64Leu		34950565	NM_002853	O75572|O95304|Q1W161|Q5KSM0|Q5KSM1|Q9UEP1	Missense_Mutation	SNP	ENST00000382038.2	37	CCDS3905.1	.	.	.	.	.	.	.	.	.	.	A	34	5.293593	0.95546	.	.	ENSG00000113456	ENST00000382038;ENST00000341754;ENST00000542494	T;T	0.18016	2.24;2.24	5.73	4.57	0.56435	.	0.000000	0.85682	D	0.000000	T	0.46678	0.1405	M	0.91300	3.195	0.80722	D	1	D	0.67145	0.996	D	0.65323	0.934	T	0.55835	-0.8078	10	0.72032	D	0.01	.	11.7122	0.51630	0.931:0.0:0.069:0.0	.	64	O60671	RAD1_HUMAN	L	64	ENSP00000371469:F64L;ENSP00000340879:F64L	ENSP00000313467:F64L	F	-	1	0	RAD1	34950565	1.000000	0.71417	0.995000	0.50966	0.989000	0.77384	6.782000	0.75073	0.999000	0.39023	0.533000	0.62120	TTT		0.363	RAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207567.1	NM_002853	
LMBRD2	92255	broad.mit.edu	37	5	36104182	36104182	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:36104182G>A	ENST00000296603.4	-	18	2516	c.2054C>T	c.(2053-2055)tCg>tTg	p.S685L		NM_001007527.1	NP_001007528.1	Q68DH5	LMBD2_HUMAN	LMBR1 domain containing 2	685						integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.S685L(1)		breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_lung(31;0.000146)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			GCGAGACATCGAGAGATATCG	0.368																																					p.S685L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2054T	5						.						97.0	87.0	90.0					5																	36104182		2203	4300	6503	36139939	SO:0001583	missense	92255	exon18				CCDS34145.1	5p13.2	2008-02-05			ENSG00000164187	ENSG00000164187			25287	protein-coding gene	gene with protein product							Standard	NM_001007527		Approved	DKFZp434H2226	uc003jkb.1	Q68DH5	OTTHUMG00000162150	ENST00000296603.4:c.2054C>T	5.37:g.36104182G>A	ENSP00000296603:p.Ser685Leu		36139939	NM_001007527	B3KRB6|Q9NTC7	Missense_Mutation	SNP	ENST00000296603.4	37	CCDS34145.1	.	.	.	.	.	.	.	.	.	.	G	17.58	3.424944	0.62733	.	.	ENSG00000164187	ENST00000296603;ENST00000546130	.	.	.	5.42	5.42	0.78866	.	0.000000	0.64402	D	0.000001	T	0.53899	0.1825	M	0.62723	1.935	0.50171	D	0.999853	P	0.44006	0.824	B	0.34779	0.189	T	0.62091	-0.6927	9	0.54805	T	0.06	-10.7096	16.9782	0.86320	0.0:0.0:1.0:0.0	.	685	Q68DH5	LMBD2_HUMAN	L	685;579	.	ENSP00000296603:S685L	S	-	2	0	LMBRD2	36139939	1.000000	0.71417	0.993000	0.49108	0.808000	0.45660	6.313000	0.72844	2.536000	0.85505	0.491000	0.48974	TCG		0.368	LMBRD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367552.1	NM_001007527	
NIPBL	25836	broad.mit.edu	37	5	37063967	37063967	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:37063967C>T	ENST00000282516.8	+	46	8435	c.7936C>T	c.(7936-7938)Cgg>Tgg	p.R2646W	NIPBL_ENST00000448238.2_Missense_Mutation_p.R2646W	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	2646					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)	p.R2646W(2)		autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			CACAAATGCTCGGAACAAAGC	0.433																																					p.R2646W												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C7936T	5						.						82.0	78.0	79.0					5																	37063967		2203	4300	6503	37099724	SO:0001583	missense	25836	exon46			AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"""sister chromatid cohesion 2 homolog (yeast)"""	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.7936C>T	5.37:g.37063967C>T	ENSP00000282516:p.Arg2646Trp		37099724	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Missense_Mutation	SNP	ENST00000282516.8	37	CCDS3920.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.548329	0.86127	.	.	ENSG00000164190	ENST00000282516;ENST00000448238	D;D	0.94330	-3.38;-3.4	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	D	0.95890	0.8662	M	0.65975	2.015	0.58432	D	0.999997	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.988;0.988;0.995	D	0.95961	0.8962	10	0.72032	D	0.01	-6.6721	14.2603	0.66080	0.149:0.851:0.0:0.0	.	2646;2646;2646	Q6IEH8;Q6KC79;Q6KC79-2	.;NIPBL_HUMAN;.	W	2646	ENSP00000282516:R2646W;ENSP00000406266:R2646W	ENSP00000282516:R2646W	R	+	1	2	NIPBL	37099724	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.599000	0.54045	2.583000	0.87209	0.591000	0.81541	CGG		0.433	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384	
PRKAA1	5562	broad.mit.edu	37	5	40765078	40765078	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:40765078G>T	ENST00000397128.2	-	7	1092	c.1084C>A	c.(1084-1086)Ctt>Att	p.L362I	PRKAA1_ENST00000354209.3_Missense_Mutation_p.L377I	NM_006251.5|NM_206907.3	NP_006242.5|NP_996790.3	Q13131	AAPK1_HUMAN	protein kinase, AMP-activated, alpha 1 catalytic subunit	362	AIS.				activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|cell cycle arrest (GO:0007050)|cellular response to ethanol (GO:0071361)|cellular response to glucose starvation (GO:0042149)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|cholesterol biosynthetic process (GO:0006695)|cold acclimation (GO:0009631)|fatty acid biosynthetic process (GO:0006633)|fatty acid homeostasis (GO:0055089)|fatty acid oxidation (GO:0019395)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glucose import in response to insulin stimulus (GO:2001274)|negative regulation of glucosylceramide biosynthetic process (GO:0046318)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of gene expression (GO:0010628)|positive regulation of glycolytic process (GO:0045821)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|regulation of energy homeostasis (GO:2000505)|regulation of transcription, DNA-templated (GO:0006355)|regulation of vesicle-mediated transport (GO:0060627)|response to activity (GO:0014823)|response to caffeine (GO:0031000)|response to camptothecin (GO:1901563)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	AMP-activated protein kinase complex (GO:0031588)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)	[acetyl-CoA carboxylase] kinase activity (GO:0050405)|[hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity (GO:0047322)|AMP-activated protein kinase activity (GO:0004679)|ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|chromatin binding (GO:0003682)|histone serine kinase activity (GO:0035174)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|tau-protein kinase activity (GO:0050321)	p.L377I(1)		breast(1)	1					Acetylsalicylic acid(DB00945)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Phenformin(DB00914)	TGATCATCAAGAAAAGAATCA	0.438																																					p.L362I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1084A	5						.						93.0	92.0	92.0					5																	40765078		1992	4162	6154	40800835	SO:0001583	missense	5562	exon7				CCDS3932.2, CCDS3933.2	5p13.1	2012-10-03			ENSG00000132356	ENSG00000132356			9376	protein-coding gene	gene with protein product	"""AMPK, alpha, 1"""	602739				8557660	Standard	XM_006714481		Approved	AMPKa1	uc003jmb.3	Q13131	OTTHUMG00000162269	ENST00000397128.2:c.1084C>A	5.37:g.40765078G>T	ENSP00000380317:p.Leu362Ile		40800835	NM_006251	A8MTQ6|B2R7E1|O00286|Q5D0E1|Q86VS1|Q9UNQ4	Missense_Mutation	SNP	ENST00000397128.2	37	CCDS3932.2	.	.	.	.	.	.	.	.	.	.	G	10.31	1.314373	0.23908	.	.	ENSG00000132356	ENST00000397128;ENST00000354209	T;T	0.07114	3.22;3.22	6.16	3.01	0.34805	.	0.125033	0.53938	D	0.000045	T	0.04907	0.0132	N	0.19112	0.55	0.80722	D	1	B;B	0.12013	0.001;0.005	B;B	0.13407	0.002;0.009	T	0.40175	-0.9577	10	0.18276	T	0.48	-12.3058	7.609	0.28118	0.1373:0.0:0.6261:0.2365	.	362;377	Q13131;Q13131-2	AAPK1_HUMAN;.	I	362;377	ENSP00000380317:L362I;ENSP00000346148:L377I	ENSP00000346148:L377I	L	-	1	0	AC008810.1	40800835	1.000000	0.71417	0.904000	0.35570	0.974000	0.67602	3.140000	0.50585	0.929000	0.37192	0.650000	0.86243	CTT		0.438	PRKAA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253833.2	NM_006251	
C7	730	broad.mit.edu	37	5	40981584	40981584	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:40981584C>T	ENST00000313164.9	+	18	2800	c.2441C>T	c.(2440-2442)aCg>aTg	p.T814M		NM_000587.2	NP_000578.2	P10643	CO7_HUMAN	complement component 7	814	Factor I module (FIM) 2.				cellular sodium ion homeostasis (GO:0006883)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)		p.T814M(1)					Ovarian(839;0.0112)				AAGGAGCAGACGATGTCTGAG	0.552																																					p.T814M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2441T	5						.						68.0	71.0	70.0					5																	40981584		2132	4244	6376	41017341	SO:0001583	missense	730	exon18			J03507	CCDS47201.1	5p13.1	2014-09-17			ENSG00000112936	ENSG00000112936		"""Complement system"""	1346	protein-coding gene	gene with protein product		217070					Standard	NM_000587		Approved		uc003jmh.3	P10643	OTTHUMG00000150340	ENST00000313164.9:c.2441C>T	5.37:g.40981584C>T	ENSP00000322061:p.Thr814Met		41017341	NM_000587	Q6P3T5|Q92489	Missense_Mutation	SNP	ENST00000313164.9	37	CCDS47201.1	.	.	.	.	.	.	.	.	.	.	C	14.37	2.515047	0.44763	.	.	ENSG00000112936	ENST00000313164	T	0.68765	-0.35	5.83	5.83	0.93111	Factor I / membrane attack complex (1);	0.113950	0.64402	D	0.000017	T	0.81706	0.4879	M	0.68952	2.095	0.58432	D	0.999994	D	0.89917	1.0	D	0.91635	0.999	T	0.81315	-0.0988	10	0.56958	D	0.05	-12.4769	19.7325	0.96188	0.0:1.0:0.0:0.0	.	814	P10643	CO7_HUMAN	M	814	ENSP00000322061:T814M	ENSP00000322061:T814M	T	+	2	0	C7	41017341	0.996000	0.38824	0.128000	0.21923	0.307000	0.27823	3.700000	0.54786	2.763000	0.94921	0.563000	0.77884	ACG		0.552	C7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317680.1		
NIM1K	167359	broad.mit.edu	37	5	43277354	43277354	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:43277354G>T	ENST00000512796.1	+	3	1987	c.488G>T	c.(487-489)aGc>aTc	p.S163I	NIM1_ENST00000326035.2_Missense_Mutation_p.S163I			Q8IY84	NIM1_HUMAN		163	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein phosphorylation (GO:0006468)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.S163I(1)									GGAAAAATTAGCACTGAGGGG	0.532																																					p.S163I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G488T	5						.						110.0	99.0	103.0					5																	43277354		2203	4300	6503	43313111	SO:0001583	missense	167359	exon3																														ENST00000512796.1:c.488G>T	5.37:g.43277354G>T	ENSP00000420849:p.Ser163Ile		43313111	NM_153361	B3KVM1	Missense_Mutation	SNP	ENST00000512796.1	37	CCDS3943.1	.	.	.	.	.	.	.	.	.	.	G	19.11	3.764459	0.69878	.	.	ENSG00000177453	ENST00000326035;ENST00000512796	T;T	0.66995	-0.24;-0.24	5.91	4.13	0.48395	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.171635	0.51477	D	0.000097	T	0.49729	0.1574	N	0.16166	0.38	0.43841	D	0.996422	B	0.25235	0.121	B	0.32980	0.156	T	0.47548	-0.9109	10	0.66056	D	0.02	.	6.9911	0.24755	0.2022:0.1249:0.6729:0.0	.	163	Q8IY84	NIM1_HUMAN	I	163	ENSP00000313572:S163I;ENSP00000420849:S163I	ENSP00000313572:S163I	S	+	2	0	AC114947.1	43313111	1.000000	0.71417	0.983000	0.44433	0.970000	0.65996	1.426000	0.34870	0.843000	0.35070	0.650000	0.86243	AGC		0.532	NIM1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368017.1		
MAP3K1	4214	broad.mit.edu	37	5	56178351	56178351	+	Silent	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:56178351T>C	ENST00000399503.3	+	14	3324	c.3324T>C	c.(3322-3324)agT>agC	p.S1108S		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	1108					activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)	p.S945S(1)		NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		TTATACCCAGTGACGAGACAG	0.423																																					p.S1108S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T3324C	5						.						116.0	111.0	113.0					5																	56178351		1987	4174	6161	56214108	SO:0001819	synonymous_variant	4214	exon14			U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6848	protein-coding gene	gene with protein product		600982	"""mitogen-activated protein kinase kinase kinase 1"""	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.3324T>C	5.37:g.56178351T>C			56214108	NM_005921		Silent	SNP	ENST00000399503.3	37	CCDS43318.1																																																																																				0.423	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066	
ACTBL2	345651	broad.mit.edu	37	5	56778142	56778142	+	Silent	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:56778142T>C	ENST00000423391.1	-	1	494	c.393A>G	c.(391-393)ccA>ccG	p.P131P	CTD-2023N9.1_ENST00000506106.1_RNA|AC025470.1_ENST00000584598.1_RNA	NM_001017992.3	NP_001017992.1	Q562R1	ACTBL_HUMAN	actin, beta-like 2	131						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)	p.P131P(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(3)|pancreas(1)|prostate(2)	28		Lung NSC(810;0.000135)|Prostate(74;0.055)|Breast(144;0.0707)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;4.24e-37)		CATACATGGCTGGTGTGTTGA	0.562																																					p.P131P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A393G	5						.						119.0	100.0	106.0					5																	56778142		2203	4300	6503	56813899	SO:0001819	synonymous_variant	345651	exon1				CCDS34163.1	5q11.2	2014-08-08			ENSG00000169067	ENSG00000169067			17780	protein-coding gene	gene with protein product		614835					Standard	NM_001017992		Approved	DKFZp686D0972	uc003jrm.3	Q562R1	OTTHUMG00000162330	ENST00000423391.1:c.393A>G	5.37:g.56778142T>C			56813899	NM_001017992	B2RPJ1|Q562R2|Q562S9|Q562X8	Silent	SNP	ENST00000423391.1	37	CCDS34163.1																																																																																				0.562	ACTBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368579.1	NM_001017992	
IPO11	51194	broad.mit.edu	37	5	61811235	61811235	+	Silent	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:61811235T>C	ENST00000325324.6	+	20	1972	c.1803T>C	c.(1801-1803)tgT>tgC	p.C601C	CKS1B_ENST00000600888.1_5'Flank|KIF2A_ENST00000509663.2_3'UTR|IPO11_ENST00000409296.3_Silent_p.C641C	NM_016338.4	NP_057422.3	Q9UI26	IPO11_HUMAN	importin 11	601					ribosomal protein import into nucleus (GO:0006610)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)	p.C601C(1)		endometrium(2)|kidney(3)|large_intestine(5)|lung(14)|skin(4)|stomach(2)	30		Lung NSC(810;8.99e-06)|Prostate(74;0.0235)|Ovarian(174;0.0511)|Breast(144;0.077)		Lung(70;0.0613)		ATGTGGGATGTTTGGTACAAT	0.343																																					p.C641C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1923C	5						.						182.0	162.0	169.0					5																	61811235		2203	4300	6503	61846992	SO:0001819	synonymous_variant	51194	exon20			AF111109	CCDS34167.1, CCDS47217.1	5q12.1	2008-09-19			ENSG00000086200	ENSG00000086200		"""Importins"""	20628	protein-coding gene	gene with protein product		610889					Standard	NM_016338		Approved	RanBP11	uc011cqr.2	Q9UI26	OTTHUMG00000154400	ENST00000325324.6:c.1803T>C	5.37:g.61811235T>C			61846992	NM_001134779	A6NGJ5|B4DZ73|D3DW98|Q8N5R2|Q9NSJ6|Q9NVB1	Silent	SNP	ENST00000325324.6	37	CCDS34167.1																																																																																				0.343	IPO11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335062.1	NM_016338	
MAST4	375449	broad.mit.edu	37	5	66396393	66396393	+	Missense_Mutation	SNP	C	C	T	rs202115078		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:66396393C>T	ENST00000403625.2	+	8	1338	c.1043C>T	c.(1042-1044)cCg>cTg	p.P348L	MAST4_ENST00000261569.7_Missense_Mutation_p.P154L|MAST4_ENST00000404260.3_Missense_Mutation_p.P351L|MAST4_ENST00000403666.1_Missense_Mutation_p.P159L|MAST4_ENST00000490016.2_Missense_Mutation_p.P159L|MAST4_ENST00000405643.1_Missense_Mutation_p.P169L	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	351						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.P351L(1)		breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		AGGAACACGCCGATGCGCCCC	0.473																																					p.P159L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C476T	5						.						84.0	85.0	85.0					5																	66396393		2076	4206	6282	66432149	SO:0001583	missense	375449	exon7			AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.1043C>T	5.37:g.66396393C>T	ENSP00000385727:p.Pro348Leu		66432149	NM_015183	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	37	CCDS54861.1	.	.	.	.	.	.	.	.	.	.	C	16.80	3.224152	0.58668	.	.	ENSG00000069020	ENST00000404260;ENST00000403625;ENST00000490016;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569;ENST00000436277;ENST00000432399	T;T;T;T;T;T;T	0.27557	1.66;1.66;1.66;1.66;1.66;1.66;1.66	6.17	6.17	0.99709	Microtubule-associated serine/threonine-protein kinase, domain (1);	0.204155	0.30134	U	0.010335	T	0.35770	0.0943	L	0.58810	1.83	0.24800	N	0.992706	P;P;P;B;B	0.52061	0.95;0.918;0.899;0.287;0.205	B;B;B;B;B	0.43508	0.422;0.34;0.23;0.068;0.047	T	0.38178	-0.9673	10	0.46703	T	0.11	-13.8956	16.376	0.83392	0.1323:0.8677:0.0:0.0	.	169;351;154;159;159	E7EWQ5;O15021;O15021-2;O15021-3;D6RAK1	.;MAST4_HUMAN;.;.;.	L	351;348;159;159;169;169;154;154;154	ENSP00000385048:P351L;ENSP00000385727:P348L;ENSP00000421739:P159L;ENSP00000384313:P159L;ENSP00000384099:P169L;ENSP00000261569:P154L;ENSP00000392478:P154L	ENSP00000261569:P154L	P	+	2	0	MAST4	66432149	0.909000	0.30893	0.391000	0.26233	0.953000	0.61014	3.676000	0.54612	2.941000	0.99782	0.655000	0.94253	CCG		0.473	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2		
RASGRF2	5924	broad.mit.edu	37	5	80476080	80476080	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:80476080T>C	ENST00000265080.4	+	18	2840	c.2773T>C	c.(2773-2775)Tgg>Cgg	p.W925R		NM_006909.2	NP_008840.1	O14827	RGRF2_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 2	925					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.W925R(1)		biliary_tract(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(28)|ovary(5)|prostate(3)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75		Lung NSC(167;0.00498)|all_lung(232;0.00531)|Ovarian(174;0.0357)		OV - Ovarian serous cystadenocarcinoma(54;4.22e-42)|Epithelial(54;4.04e-35)|all cancers(79;2.52e-29)		CCTCCGTCACTGGGTCTCAAA	0.398																																					p.W925R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2773C	5						.						126.0	118.0	121.0					5																	80476080		2203	4300	6503	80511836	SO:0001583	missense	5924	exon18			AF023130	CCDS4052.1	5q13	2013-01-10			ENSG00000113319	ENSG00000113319		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	9876	protein-coding gene	gene with protein product		606614					Standard	NM_006909		Approved	GRF2, Ras-GRF2	uc003kha.2	O14827	OTTHUMG00000119015	ENST00000265080.4:c.2773T>C	5.37:g.80476080T>C	ENSP00000265080:p.Trp925Arg		80511836	NM_006909	B9EG89|Q9UK56	Missense_Mutation	SNP	ENST00000265080.4	37	CCDS4052.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.173781	0.78452	.	.	ENSG00000113319	ENST00000265080	T	0.62364	0.03	5.43	5.43	0.79202	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.79828	0.4513	M	0.80982	2.52	0.58432	D	0.999998	D	0.76494	0.999	D	0.85130	0.997	T	0.82932	-0.0212	10	0.87932	D	0	.	14.4608	0.67448	0.0:0.0:0.0:1.0	.	925	O14827	RGRF2_HUMAN	R	925	ENSP00000265080:W925R	ENSP00000265080:W925R	W	+	1	0	RASGRF2	80511836	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.338000	0.79269	2.069000	0.61940	0.379000	0.24179	TGG		0.398	RASGRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239215.2	NM_006909	
GPR98	84059	broad.mit.edu	37	5	89948308	89948308	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:89948308A>G	ENST00000405460.2	+	19	3658	c.3562A>G	c.(3562-3564)Att>Gtt	p.I1188V		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	1188	Calx-beta 9. {ECO:0000305|PubMed:11606593}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.I1188V(1)		NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		AAAACCAATCATTCTCCATGC	0.358																																					p.I1188V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3562G	5						.						97.0	89.0	91.0					5																	89948308		1882	4121	6003	89984064	SO:0001583	missense	84059	exon19			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.3562A>G	5.37:g.89948308A>G	ENSP00000384582:p.Ile1188Val		89984064	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	5.128|5.128	0.209310|0.209310	0.09757|0.09757	.|.	.|.	ENSG00000164199|ENSG00000164199	ENST00000504142|ENST00000405460;ENST00000296619;ENST00000399043	.|T	.|0.26518	.|1.73	6.07|6.07	4.91|4.91	0.64330|0.64330	.|.	.|0.389825	.|0.31734	.|N	.|0.007155	T|T	0.14830|0.14830	0.0358|0.0358	N|N	0.14661|0.14661	0.345|0.345	0.43913|0.43913	D|D	0.996553|0.996553	.|B	.|0.06786	.|0.001	.|B	.|0.06405	.|0.002	T|T	0.06607|0.06607	-1.0817|-1.0817	5|10	.|0.32370	.|T	.|0.25	.|.	9.8185|9.8185	0.40867|0.40867	0.8517:0.0:0.1483:0.0|0.8517:0.0:0.1483:0.0	.|.	.|1188	.|Q8WXG9	.|GPR98_HUMAN	R|V	776|1188	.|ENSP00000384582:I1188V	.|ENSP00000296619:I1188V	H|I	+|+	2|1	0|0	GPR98|GPR98	89984064|89984064	0.930000|0.930000	0.31532|0.31532	0.722000|0.722000	0.30670|0.30670	0.462000|0.462000	0.32619|0.32619	1.610000|1.610000	0.36869|0.36869	1.108000|1.108000	0.41662|0.41662	0.477000|0.477000	0.44152|0.44152	CAT|ATT		0.358	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
ANKRD32	84250	broad.mit.edu	37	5	94014612	94014612	+	Nonsense_Mutation	SNP	C	C	T	rs370026748		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:94014612C>T	ENST00000265140.5	+	15	2346	c.1927C>T	c.(1927-1929)Cga>Tga	p.R643*		NM_032290.3	NP_115666.2	Q9BQI6	ANR32_HUMAN	ankyrin repeat domain 32	643						centrosome (GO:0005813)|nucleus (GO:0005634)		p.R7*(1)|p.R643*(1)		NS(1)|breast(2)|endometrium(2)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|skin(1)	13		all_cancers(142;1.51e-09)|all_epithelial(76;4.68e-12)|all_lung(232;5.94e-05)|Ovarian(174;0.000953)|Lung NSC(167;0.00105)|Colorectal(57;0.122)|Lung SC(612;0.152)		all cancers(79;3.88e-18)		AAATGTGATGCGACACATGTC	0.368																																					p.R643X												.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C1927T	5						.						276.0	247.0	257.0					5																	94014612		2203	4300	6503	94040368	SO:0001587	stop_gained	84250	exon15			AL136560	CCDS4071.2	5q15	2013-01-10			ENSG00000133302	ENSG00000133302		"""Ankyrin repeat domain containing"""	25408	protein-coding gene	gene with protein product			"""BRCT domain containing 1"""	BRCTD1			Standard	NM_032290		Approved	DKFZp761C121, DKFZp564C0469	uc003kkr.4	Q9BQI6	OTTHUMG00000121133	ENST00000265140.5:c.1927C>T	5.37:g.94014612C>T	ENSP00000265140:p.Arg643*		94040368	NM_032290	B4DMG4|Q3B7K4|Q6NSA5|Q6PHW9|Q9Y402	Nonsense_Mutation	SNP	ENST00000265140.5	37	CCDS4071.2	.	.	.	.	.	.	.	.	.	.	C	44	10.803972	0.99470	.	.	ENSG00000133302	ENST00000265140	.	.	.	5.71	4.83	0.62350	.	0.246709	0.29348	N	0.012407	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.448	0.38710	0.1444:0.7847:0.0:0.0709	.	.	.	.	X	643	.	ENSP00000265140:R643X	R	+	1	2	ANKRD32	94040368	0.998000	0.40836	1.000000	0.80357	0.993000	0.82548	1.459000	0.35234	1.378000	0.46305	0.557000	0.71058	CGA		0.368	ANKRD32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241610.1	NM_032290	
MGAT1	4245	broad.mit.edu	37	5	180219052	180219052	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr5:180219052T>G	ENST00000446023.2	-	3	1670	c.920A>C	c.(919-921)gAg>gCg	p.E307A	MGAT1_ENST00000333055.3_Missense_Mutation_p.E307A|MGAT1_ENST00000427865.2_Missense_Mutation_p.E307A|MGAT1_ENST00000393340.3_Missense_Mutation_p.E307A|MGAT1_ENST00000307826.4_Missense_Mutation_p.E307A	NM_001114617.1|NM_001114618.1	NP_001108089.1|NP_001108090.1	P26572	MGAT1_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,2-N-acetylglucosaminyltransferase	307					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine catabolic process (GO:0006049)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	acetylglucosaminyltransferase activity (GO:0008375)|alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity (GO:0003827)|metal ion binding (GO:0046872)	p.E307A(1)		endometrium(1)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	13	all_cancers(89;1.11e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.0027)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00356)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TCTTGAGATCTCAGGGCGTAT	0.612																																					p.E307A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A920C	5						.						42.0	45.0	44.0					5																	180219052		2203	4300	6503	180151658	SO:0001583	missense	4245	exon2			M61829	CCDS4458.1	5q35.3	2013-02-25			ENSG00000131446	ENSG00000131446	2.4.1.101	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	7044	protein-coding gene	gene with protein product		160995		MGAT, GLYT1		1827260	Standard	NM_002406		Approved	GNT-1, GLCNAC-TI	uc003mmg.4	P26572	OTTHUMG00000130937	ENST00000446023.2:c.920A>C	5.37:g.180219052T>G	ENSP00000404718:p.Glu307Ala		180151658	NM_002406	A8K404|B3KRU8|D3DWR1|Q6IBE3	Missense_Mutation	SNP	ENST00000446023.2	37	CCDS4458.1	.	.	.	.	.	.	.	.	.	.	T	14.64	2.596714	0.46318	.	.	ENSG00000131446	ENST00000333055;ENST00000307826;ENST00000446023;ENST00000393340;ENST00000452920;ENST00000427865	D;D;D;D;D	0.87887	-2.31;-2.31;-2.31;-2.31;-2.31	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	D	0.93360	0.7883	M	0.84082	2.675	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94186	0.7436	10	0.87932	D	0	-15.2626	13.3162	0.60409	0.0:0.0:0.0:1.0	.	307	P26572	MGAT1_HUMAN	A	307;307;307;307;164;307	ENSP00000332073:E307A;ENSP00000311888:E307A;ENSP00000404718:E307A;ENSP00000377010:E307A;ENSP00000402838:E307A	ENSP00000311888:E307A	E	-	2	0	MGAT1	180151658	1.000000	0.71417	0.545000	0.28153	0.009000	0.06853	7.255000	0.78338	2.090000	0.63153	0.533000	0.62120	GAG		0.612	MGAT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368189.1	NM_001114618	
TFAP2A	7020	broad.mit.edu	37	6	10400781	10400781	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:10400781C>T	ENST00000482890.1	-	7	1277	c.925G>A	c.(925-927)Gaa>Aaa	p.E309K	TFAP2A_ENST00000379608.3_Missense_Mutation_p.E303K|TFAP2A_ENST00000497266.1_5'UTR|TFAP2A_ENST00000379613.3_Missense_Mutation_p.E311K|TFAP2A_ENST00000379604.2_Missense_Mutation_p.E309K|TFAP2A_ENST00000319516.4_Missense_Mutation_p.E305K			P05549	AP2A_HUMAN	transcription factor AP-2 alpha (activating enhancer binding protein 2 alpha)	309	H-S-H (helix-span-helix), dimerization.				anterior neuropore closure (GO:0021506)|basement membrane organization (GO:0071711)|bone morphogenesis (GO:0060349)|cellular response to iron ion (GO:0071281)|cornea development in camera-type eye (GO:0061303)|embryonic body morphogenesis (GO:0010172)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|embryonic pattern specification (GO:0009880)|epidermis morphogenesis (GO:0048730)|eyelid development in camera-type eye (GO:0061029)|face morphogenesis (GO:0060325)|forebrain neuron development (GO:0021884)|inner ear morphogenesis (GO:0042472)|keratinocyte development (GO:0003334)|kidney development (GO:0001822)|lens induction in camera-type eye (GO:0060235)|metanephric nephron development (GO:0072210)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell development (GO:0014032)|oculomotor nerve formation (GO:0021623)|optic cup structural organization (GO:0003409)|optic vesicle morphogenesis (GO:0003404)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cell migration (GO:0030335)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of tooth mineralization (GO:0070172)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell differentiation (GO:0045595)|regulation of neuron differentiation (GO:0045664)|retina layer formation (GO:0010842)|sensory perception of sound (GO:0007605)|sympathetic nervous system development (GO:0048485)|transcription from RNA polymerase II promoter (GO:0006366)|trigeminal nerve development (GO:0021559)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.E309K(1)|p.E303K(1)		breast(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)	13	Breast(50;0.0427)|Ovarian(93;0.0991)	all_hematologic(90;0.107)				AATTCGGTTTCGCACACGTAC	0.507																																					p.E309K												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G925A	6						.						135.0	120.0	125.0					6																	10400781		2203	4300	6503	10508767	SO:0001583	missense	7020	exon6			X52611	CCDS4510.1, CCDS34337.1, CCDS43422.1	6p24.3	2013-09-19	2001-11-28		ENSG00000137203	ENSG00000137203			11742	protein-coding gene	gene with protein product		107580	"""transcription factor AP-2 alpha (activating enhancer-binding protein 2 alpha)"""	TFAP2, AP2TF		1916817, 3063603	Standard	NM_001032280		Approved	AP-2	uc003myr.3	P05549	OTTHUMG00000014235	ENST00000482890.1:c.925G>A	6.37:g.10400781C>T	ENSP00000418541:p.Glu309Lys		10508767	NM_003220	Q13777|Q5TAV5|Q8N1C6	Missense_Mutation	SNP	ENST00000482890.1	37	CCDS4510.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.073736	0.76415	.	.	ENSG00000137203	ENST00000379613;ENST00000379604;ENST00000319516;ENST00000379608;ENST00000482890	D;D;D;D;D	0.97575	-4.44;-4.44;-4.44;-4.44;-4.44	5.29	5.29	0.74685	Transcription factor AP-2, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98178	0.9398	M	0.82323	2.585	0.80722	D	1	P;B;D	0.69078	0.952;0.142;0.997	B;B;P	0.60473	0.348;0.058;0.875	D	0.98928	1.0786	10	0.87932	D	0	-10.4915	18.9454	0.92620	0.0:1.0:0.0:0.0	.	305;309;303	Q5TAV5;P05549;Q8N1C6	.;AP2A_HUMAN;.	K	311;309;305;303;309	ENSP00000368933:E311K;ENSP00000368924:E309K;ENSP00000316516:E305K;ENSP00000368928:E303K;ENSP00000418541:E309K	ENSP00000316516:E305K	E	-	1	0	TFAP2A	10508767	1.000000	0.71417	0.998000	0.56505	0.932000	0.56968	7.818000	0.86416	2.463000	0.83235	0.655000	0.94253	GAA		0.507	TFAP2A-007	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353619.2	NM_003220	
POPDC3	64208	broad.mit.edu	37	6	105609452	105609452	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:105609452C>T	ENST00000254765.3	-	2	611	c.333G>A	c.(331-333)ttG>ttA	p.L111L	BVES-AS1_ENST00000580511.1_RNA|BVES-AS1_ENST00000580854.1_RNA|POPDC3_ENST00000474760.1_Intron|BVES-AS1_ENST00000369120.2_RNA|BVES-AS1_ENST00000369122.3_RNA	NM_022361.4	NP_071756.2	Q9HBV1	POPD3_HUMAN	popeye domain containing 3	111					regulation of membrane potential (GO:0042391)	integral component of membrane (GO:0016021)		p.L111L(1)		NS(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|skin(3)|urinary_tract(1)	26		all_cancers(87;4.87e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0157)|Colorectal(196;0.202)|Lung NSC(302;0.238)				GGGAGCTGTACAACACTTGGA	0.428																																					p.L111L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G333A	6						.						153.0	164.0	160.0					6																	105609452		2203	4300	6503	105716145	SO:0001819	synonymous_variant	64208	exon2			BC022323	CCDS5052.1	6q21	2003-06-12			ENSG00000132429	ENSG00000132429			17649	protein-coding gene	gene with protein product		605824				10882522	Standard	NM_022361		Approved	POP3, MGC22671, bA355M14.1	uc003prb.3	Q9HBV1	OTTHUMG00000015293	ENST00000254765.3:c.333G>A	6.37:g.105609452C>T			105716145	NM_022361	B2RA98|Q5T3Y8|Q8TBW6	Silent	SNP	ENST00000254765.3	37	CCDS5052.1																																																																																				0.428	POPDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041651.1	NM_022361	
GCNT2	2651	broad.mit.edu	37	6	10586562	10586562	+	Intron	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:10586562T>C	ENST00000379597.3	+	2	1481				GCNT2_ENST00000397423.2_Intron|GCNT2_ENST00000495262.1_Intron|GCNT2_ENST00000265012.4_Missense_Mutation_p.F114L|GCNT2_ENST00000410107.1_Intron|GCNT2_ENST00000316170.3_Intron			Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group)						maintenance of lens transparency (GO:0036438)|negative regulation of cell-substrate adhesion (GO:0010812)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of protein kinase B signaling (GO:0051897)|posttranscriptional regulation of gene expression (GO:0010608)|protein glycosylation (GO:0006486)|transforming growth factor beta receptor signaling pathway (GO:0007179)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)	p.F114L(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)	12	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)		TGAAAGGCTCTTTAGGGCTAT	0.463																																					p.F114L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T340C	6						.						86.0	79.0	81.0					6																	10586562		2203	4300	6503	10694548	SO:0001627	intron_variant	2651	exon1			L41605	CCDS4512.1, CCDS4513.1, CCDS34338.1	6p24.2	2014-07-18	2006-02-23		ENSG00000111846	ENSG00000111846	2.4.1.150	"""Blood group antigens"", ""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	4204	protein-coding gene	gene with protein product	"""Ii blood group"", ""unassigned linkage group 3"""	600429	"""glucosaminyl (N-acetyl) transferase 5"", ""glucosaminyl (N-acetyl) transferase 2, I-branching enzyme"", ""glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (Ii blood group)"", ""cataract, congenital"""	NACGT1, II, GCNT5, CCAT		8449405, 9915862	Standard	NM_145649		Approved	IGNT, NAGCT1, bA421M1.1, bA360O19.2, ULG3	uc003mze.3	Q06430	OTTHUMG00000014244	ENST00000379597.3:c.926-35022T>C	6.37:g.10586562T>C			10694548	NM_145655		Missense_Mutation	SNP	ENST00000379597.3	37	CCDS34338.1	.	.	.	.	.	.	.	.	.	.	T	11.60	1.685877	0.29962	.	.	ENSG00000111846	ENST00000265012	T	0.08634	3.07	5.58	5.58	0.84498	.	.	.	.	.	T	0.01870	0.0059	N	0.16602	0.42	0.80722	D	1	B	0.06786	0.001	B	0.17979	0.02	T	0.24012	-1.0172	9	0.02654	T	1	.	15.7616	0.78087	0.0:0.0:0.0:1.0	.	114	Q8NFS9	GNT2C_HUMAN	L	114	ENSP00000265012:F114L	ENSP00000265012:F114L	F	+	1	0	GCNT2	10694548	1.000000	0.71417	1.000000	0.80357	0.819000	0.46315	4.764000	0.62264	2.121000	0.65114	0.533000	0.62120	TTT		0.463	GCNT2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327912.3	NM_145649	
PREP	5550	broad.mit.edu	37	6	105726112	105726112	+	Silent	SNP	G	G	A	rs116581811	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:105726112G>A	ENST00000369110.3	-	15	2232	c.2040C>T	c.(2038-2040)caC>caT	p.H680H	RP3-355L5.4_ENST00000452363.1_RNA	NM_002726.4	NP_002717.3	P48147	PPCE_HUMAN	prolyl endopeptidase	680					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.H680H(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)	TCCCCGCCCCGTGGCCCGCCT	0.562													G|||	35	0.00698882	0.0265	0.0	5008	,	,		19566	0.0		0.0	False		,,,				2504	0.0				p.H680H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2040T	6						.	G		98,4308	77.8+/-116.1	1,96,2106	95.0	86.0	89.0		2040	-1.3	1.0	6	dbSNP_132	89	0,8600		0,0,4300	no	coding-synonymous	PREP	NM_002726.4		1,96,6406	AA,AG,GG		0.0,2.2242,0.7535		680/711	105726112	98,12908	2203	4300	6503	105832805	SO:0001819	synonymous_variant	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.2040C>T	6.37:g.105726112G>A			105832805	NM_002726	Q8N6D4	Silent	SNP	ENST00000369110.3	37	CCDS5053.1																																																																																				0.562	PREP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041658.1		
SCML4	256380	broad.mit.edu	37	6	108042074	108042074	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:108042074C>T	ENST00000369020.3	-	6	1051	c.806G>A	c.(805-807)tGc>tAc	p.C269Y	SCML4_ENST00000479803.1_5'UTR|SCML4_ENST00000369021.3_Missense_Mutation_p.C240Y|SCML4_ENST00000369022.2_Missense_Mutation_p.C211Y|SCML4_ENST00000369025.2_Missense_Mutation_p.C27Y	NM_198081.3	NP_932347.2	Q8N228	SCML4_HUMAN	sex comb on midleg-like 4 (Drosophila)	269					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.C240Y(1)		endometrium(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(1)	25		all_cancers(87;3.26e-06)|Acute lymphoblastic leukemia(125;3.08e-08)|all_hematologic(75;1.15e-06)|all_epithelial(87;0.00142)|Colorectal(196;0.0316)		BRCA - Breast invasive adenocarcinoma(108;0.01)|Epithelial(106;0.0509)|all cancers(137;0.0586)|OV - Ovarian serous cystadenocarcinoma(136;0.0758)		CTGCCTCTTGCAGTACAGCGA	0.637																																					p.C269Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G806A	6						.						52.0	57.0	55.0					6																	108042074		2203	4300	6503	108148767	SO:0001583	missense	256380	exon6				CCDS5060.2, CCDS69163.1, CCDS75500.1	6q21	2013-01-10			ENSG00000146285	ENSG00000146285		"""Sterile alpha motif (SAM) domain containing"""	21397	protein-coding gene	gene with protein product							Standard	NM_001286409		Approved	dJ47M23.1	uc010kdf.3	Q8N228	OTTHUMG00000015313	ENST00000369020.3:c.806G>A	6.37:g.108042074C>T	ENSP00000358016:p.Cys269Tyr		108148767	NM_198081	B0QZ10|B0QZ11|B7ZBX3|Q5JXD0|Q5T0T6|Q8IYY6	Missense_Mutation	SNP	ENST00000369020.3	37	CCDS5060.2	.	.	.	.	.	.	.	.	.	.	C	8.582	0.882501	0.17467	.	.	ENSG00000146285	ENST00000369022;ENST00000369025;ENST00000369020;ENST00000369021	T;T;T	0.42900	1.0;0.99;0.96	5.11	0.906	0.19314	.	0.507616	0.21731	N	0.069979	T	0.09598	0.0236	N	0.22421	0.69	0.22851	N	0.998653	B;B;B	0.10296	0.001;0.0;0.003	B;B;B	0.08055	0.003;0.002;0.003	T	0.22277	-1.0221	10	0.56958	D	0.05	.	4.1673	0.10313	0.1315:0.3465:0.4282:0.0938	.	269;269;240	B4E0X3;Q8N228;Q8N228-3	.;SCML4_HUMAN;.	Y	211;27;269;240	ENSP00000358018:C211Y;ENSP00000358016:C269Y;ENSP00000358017:C240Y	ENSP00000358016:C269Y	C	-	2	0	SCML4	108148767	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	1.098000	0.31000	0.271000	0.22005	0.650000	0.86243	TGC		0.637	SCML4-005	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000041700.3	XM_171128	
SEC63	11231	broad.mit.edu	37	6	108230131	108230131	+	Splice_Site	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:108230131G>A	ENST00000369002.4	-	8	912	c.733C>T	c.(733-735)Cgt>Tgt	p.R245C		NM_007214.4	NP_009145.1	Q9UGP8	SEC63_HUMAN	SEC63 homolog (S. cerevisiae)	245	SEC63 1.				liver development (GO:0001889)|multicellular organismal aging (GO:0010259)|nitrogen compound metabolic process (GO:0006807)|posttranslational protein targeting to membrane (GO:0006620)|posttranslational protein targeting to membrane, translocation (GO:0031204)|protein targeting to membrane (GO:0006612)|renal system development (GO:0072001)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)	p.R245C(1)		endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		all_cancers(87;5.35e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00225)|Colorectal(196;0.0294)		BRCA - Breast invasive adenocarcinoma(108;0.0079)|Epithelial(106;0.0356)|all cancers(137;0.0525)|OV - Ovarian serous cystadenocarcinoma(136;0.054)		GTTTACTTACGTTTCATATCC	0.323																																					p.R245C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C733T	6						.						92.0	85.0	87.0					6																	108230131		2203	4300	6503	108336824	SO:0001630	splice_region_variant	11231	exon8			BC048287	CCDS5061.1	6q21	2011-09-05	2006-09-12		ENSG00000025796	ENSG00000025796		"""Heat shock proteins / DNAJ (HSP40)"""	21082	protein-coding gene	gene with protein product		608648	"""SEC63-like (S. cerevisiae)"""			10219736, 10543453	Standard	NM_007214		Approved	SEC63L, PRO2507, ERdj2, DNAJC23	uc003psc.4	Q9UGP8	OTTHUMG00000015316	ENST00000369002.4:c.733+1C>T	6.37:g.108230131G>A			108336824	NM_007214	O95380|Q5THN4|Q86VS9|Q8IWL0|Q9NTE0	Missense_Mutation	SNP	ENST00000369002.4	37	CCDS5061.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.434311	0.83776	.	.	ENSG00000025796	ENST00000369002;ENST00000423697	T	0.60672	0.17	4.97	4.97	0.65823	Sec63 domain (3);	0.000000	0.85682	D	0.000000	T	0.70996	0.3288	M	0.81802	2.56	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.995	T	0.74293	-0.3712	9	.	.	.	-7.1167	14.0174	0.64531	0.0:0.0:0.8482:0.1518	.	245;245	Q9UGP8;B3KQF0	SEC63_HUMAN;.	C	245;105	ENSP00000357998:R245C	.	R	-	1	0	SEC63	108336824	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.472000	0.80996	2.298000	0.77334	0.557000	0.71058	CGT		0.323	SEC63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041705.4	NM_007214	Missense_Mutation
NEDD9	4739	broad.mit.edu	37	6	11191156	11191156	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:11191156C>T	ENST00000379446.5	-	5	1112	c.946G>A	c.(946-948)Gca>Aca	p.A316T	NEDD9_ENST00000504387.1_Missense_Mutation_p.A316T|RP3-510L9.1_ENST00000500636.2_RNA	NM_001271033.1|NM_006403.3	NP_001257962.1|NP_006394.1	Q14511	CASL_HUMAN	neural precursor cell expressed, developmentally down-regulated 9	316					actin filament bundle assembly (GO:0051017)|cell adhesion (GO:0007155)|cytoskeleton organization (GO:0007010)|integrin-mediated signaling pathway (GO:0007229)|mitotic nuclear division (GO:0007067)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle pole (GO:0000922)		p.A316T(4)		endometrium(3)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	Breast(50;0.0768)|Ovarian(93;0.152)	all_hematologic(90;0.135)	Epithelial(50;0.0647)|all cancers(50;0.179)			ACATCATATGCGTCGTTCTGA	0.572																																					p.A316T												.	.	4	Substitution - Missense(4)	large_intestine(4)	c.G946A	6						.						71.0	74.0	73.0					6																	11191156		2203	4300	6503	11299142	SO:0001583	missense	4739	exon5			L43821	CCDS4520.1, CCDS34340.1, CCDS47373.1, CCDS75400.1	6p25-p24	2011-04-13			ENSG00000111859	ENSG00000111859		"""Cas scaffolding proteins"""	7733	protein-coding gene	gene with protein product	"""Cas scaffolding protein family member 2"", ""Cas-like"""	602265					Standard	NM_182966		Approved	HEF1, CAS-L, CASS2	uc003mzv.2	Q14511	OTTHUMG00000014255	ENST00000379446.5:c.946G>A	6.37:g.11191156C>T	ENSP00000368759:p.Ala316Thr		11299142	NM_006403	A8K9G7|A8MSJ9|G5E9Y9|Q5T9R4|Q5XKI0	Missense_Mutation	SNP	ENST00000379446.5	37	CCDS4520.1	.	.	.	.	.	.	.	.	.	.	C	14.75	2.627474	0.46944	.	.	ENSG00000111859	ENST00000379446;ENST00000504387	T;T	0.39592	1.07;1.19	5.94	5.94	0.96194	.	0.290933	0.37577	N	0.002028	T	0.23094	0.0558	L	0.57536	1.79	0.80722	D	1	P;P;P	0.52577	0.81;0.825;0.954	B;B;B	0.35039	0.194;0.145;0.163	T	0.19353	-1.0308	10	0.10377	T	0.69	-23.9187	20.3633	0.98874	0.0:1.0:0.0:0.0	.	316;316;316	G5E9Y9;A8K9G7;Q14511	.;.;CASL_HUMAN	T	316	ENSP00000368759:A316T;ENSP00000422871:A316T	ENSP00000368759:A316T	A	-	1	0	NEDD9	11299142	0.998000	0.40836	0.239000	0.24122	0.059000	0.15707	3.460000	0.53028	2.826000	0.97356	0.561000	0.74099	GCA		0.572	NEDD9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039853.2	NM_006403	
REV3L	5980	broad.mit.edu	37	6	111634569	111634569	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:111634569G>T	ENST00000358835.3	-	29	9044	c.8590C>A	c.(8590-8592)Cct>Act	p.P2864T	REV3L_ENST00000368805.1_Missense_Mutation_p.P2864T|RP5-1112D6.8_ENST00000607434.1_RNA|REV3L_ENST00000462119.1_5'UTR|REV3L_ENST00000368802.3_Missense_Mutation_p.P2864T|REV3L_ENST00000435970.1_Missense_Mutation_p.P2786T			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	2864					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)	p.P2786T(1)		NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		GAAACAGCAGGGCAGGAATCT	0.378								DNA polymerases (catalytic subunits)																													p.P2864T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C8590A	6						.						115.0	109.0	111.0					6																	111634569		2203	4300	6503	111741262	SO:0001583	missense	5980	exon28			AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"""DNA polymerases"""	9968	protein-coding gene	gene with protein product	"""polymerase, DNA, zeta"""	602776	"""REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta"", ""REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"""			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.8590C>A	6.37:g.111634569G>T	ENSP00000351697:p.Pro2864Thr		111741262	NM_002912	O43214|Q5TC33	Missense_Mutation	SNP	ENST00000358835.3	37	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	G	27.7	4.855222	0.91355	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970	T;T;T;T	0.17370	2.28;2.28;2.28;2.28	5.78	5.78	0.91487	DNA polymerase, palm domain (1);DNA-directed DNA polymerase, family B, multifunctional domain (1);	0.059454	0.64402	D	0.000002	T	0.46210	0.1381	M	0.89785	3.06	0.80722	D	1	D	0.67145	0.996	D	0.74023	0.982	T	0.55667	-0.8105	10	0.87932	D	0	.	20.0026	0.97425	0.0:0.0:1.0:0.0	.	2864	O60673	DPOLZ_HUMAN	T	2864;2864;2864;2786	ENSP00000357792:P2864T;ENSP00000357795:P2864T;ENSP00000351697:P2864T;ENSP00000402003:P2786T	ENSP00000351697:P2864T	P	-	1	0	REV3L	111741262	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.827000	0.99397	2.722000	0.93159	0.650000	0.86243	CCT		0.378	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912	
SOGA3	387104	broad.mit.edu	37	6	127797149	127797149	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:127797149C>T	ENST00000525778.1	-	6	2767	c.2022G>A	c.(2020-2022)acG>acA	p.T674T	SOGA3_ENST00000465909.2_Silent_p.T674T|SOGA3_ENST00000474293.2_5'Flank|SOGA3_ENST00000481848.2_Silent_p.T674T|SOGA3_ENST00000368268.2_Silent_p.T674T|SOGA3_ENST00000556132.1_Silent_p.T674T			Q5TF21	SOGA3_HUMAN	SOGA family member 3	674					regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)		p.T674T(1)									TGAGCTCCGCCGTGATGCGCT	0.662																																					p.T674T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2022A	6						.						63.0	67.0	66.0					6																	127797149		2191	4295	6486	127838842	SO:0001819	synonymous_variant	387104	exon6			AK096490	CCDS43505.1	6q22.33	2013-03-28	2012-02-27	2012-02-27	ENSG00000214338	ENSG00000214338			21494	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 174"""	C6orf174			Standard	NM_001012279		Approved	dJ403A15.3	uc003qbd.3	Q5TF21	OTTHUMG00000166438	ENST00000525778.1:c.2022G>A	6.37:g.127797149C>T			127838842	NM_001012279		Silent	SNP	ENST00000525778.1	37	CCDS43505.1																																																																																				0.662	SOGA3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388246.1	NM_001012279	
SOGA3	387104	broad.mit.edu	37	6	127836184	127836184	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:127836184G>A	ENST00000525778.1	-	3	1855	c.1110C>T	c.(1108-1110)atC>atT	p.I370I	SOGA3_ENST00000465909.2_Silent_p.I370I|SOGA3_ENST00000481848.2_Silent_p.I370I|SOGA3_ENST00000368268.2_Silent_p.I370I|SOGA3_ENST00000556132.1_Silent_p.I370I			Q5TF21	SOGA3_HUMAN	SOGA family member 3	370					regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)		p.I370I(1)									TCAGCTCATCGATCTCGTTCT	0.537																																					p.I370I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1110T	6						.						131.0	131.0	131.0					6																	127836184		2102	4216	6318	127877877	SO:0001819	synonymous_variant	387104	exon3			AK096490	CCDS43505.1	6q22.33	2013-03-28	2012-02-27	2012-02-27	ENSG00000214338	ENSG00000214338			21494	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 174"""	C6orf174			Standard	NM_001012279		Approved	dJ403A15.3	uc003qbd.3	Q5TF21	OTTHUMG00000166438	ENST00000525778.1:c.1110C>T	6.37:g.127836184G>A			127877877	NM_001012279		Silent	SNP	ENST00000525778.1	37	CCDS43505.1																																																																																				0.537	SOGA3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388246.1	NM_001012279	
THEMIS	387357	broad.mit.edu	37	6	128040959	128040959	+	Missense_Mutation	SNP	C	C	T	rs555567289		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:128040959C>T	ENST00000368248.2	-	5	1916	c.1768G>A	c.(1768-1770)Gta>Ata	p.V590I	THEMIS_ENST00000537166.1_Missense_Mutation_p.V555I|THEMIS_ENST00000543064.1_Missense_Mutation_p.V629I|THEMIS_ENST00000368250.1_Missense_Mutation_p.V511I	NM_001010923.2	NP_001010923.1	Q8N1K5	THMS1_HUMAN	thymocyte selection associated	590					negative T cell selection (GO:0043383)|positive T cell selection (GO:0043368)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.V590I(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(3)	60						GTTATGTCTACGTGATGACGC	0.373																																					p.V590I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1768A	6						.						171.0	151.0	158.0					6																	128040959		2203	4300	6503	128082652	SO:0001583	missense	387357	exon5			AK094863	CCDS34534.1, CCDS55055.1	6q22.33	2012-02-08	2009-06-25	2009-06-25	ENSG00000172673	ENSG00000172673			21569	protein-coding gene	gene with protein product	"""thymocyte expressed molecule involved in selection"""	613607	"""chromosome 6 open reading frame 207"", ""chromosome 6 open reading frame 190"", ""thymocyte selection pathway associated"""	C6orf207, C6orf190, TSEPA		19597499, 19597498, 19597497	Standard	NM_001010923		Approved	bA325O24.4, FLJ40584, bA325O24.3	uc011ebt.2	Q8N1K5	OTTHUMG00000015534	ENST00000368248.2:c.1768G>A	6.37:g.128040959C>T	ENSP00000357231:p.Val590Ile		128082652	NM_001010923	A1L4F0|A8K7N1|B3KT31|B3KW32|B3KY07|F5H1J9|Q5T3C4|Q5T3C5|Q6MZT7	Missense_Mutation	SNP	ENST00000368248.2	37	CCDS34534.1	.	.	.	.	.	.	.	.	.	.	C	10.63	1.403371	0.25291	.	.	ENSG00000172673	ENST00000368250;ENST00000543064;ENST00000368248;ENST00000537166	T;T;T;T	0.27104	2.16;1.69;2.17;2.16	6.05	1.24	0.21308	.	1.650000	0.03148	N	0.167598	T	0.09905	0.0243	L	0.51422	1.61	0.09310	N	1	B;B	0.21821	0.061;0.021	B;B	0.13407	0.009;0.004	T	0.25916	-1.0118	10	0.38643	T	0.18	-0.6224	7.8048	0.29195	0.0:0.5865:0.0:0.4135	.	629;590	F5H1J9;Q8N1K5	.;THMS1_HUMAN	I	511;629;590;555	ENSP00000357233:V511I;ENSP00000439594:V629I;ENSP00000357231:V590I;ENSP00000439863:V555I	ENSP00000357231:V590I	V	-	1	0	THEMIS	128082652	0.032000	0.19561	0.001000	0.08648	0.836000	0.47400	0.103000	0.15292	0.135000	0.18707	0.650000	0.86243	GTA		0.373	THEMIS-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_001010923	
ARHGAP18	93663	broad.mit.edu	37	6	129929118	129929118	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:129929118C>T	ENST00000368149.2	-	9	1290	c.1202G>A	c.(1201-1203)aGc>aAc	p.S401N		NM_033515.2	NP_277050.2			Rho GTPase activating protein 18									p.S401N(1)		NS(2)|endometrium(1)|large_intestine(4)|lung(4)|ovary(2)|prostate(2)|skin(3)	18				OV - Ovarian serous cystadenocarcinoma(136;0.0621)|GBM - Glioblastoma multiforme(226;0.0638)|all cancers(137;0.074)		CTTCAGCAGGCTGGCGGCATC	0.458																																					p.S401N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1202A	6						.						95.0	93.0	94.0					6																	129929118		2203	4300	6503	129970811	SO:0001583	missense	93663	exon9			AB053293	CCDS34535.1	6q23.1	2011-06-29			ENSG00000146376	ENSG00000146376		"""Rho GTPase activating proteins"""	21035	protein-coding gene	gene with protein product		613351					Standard	NM_033515		Approved	MacGAP, bA307O14.2	uc003qbr.3	Q8N392	OTTHUMG00000015547	ENST00000368149.2:c.1202G>A	6.37:g.129929118C>T	ENSP00000357131:p.Ser401Asn		129970811	NM_033515		Missense_Mutation	SNP	ENST00000368149.2	37	CCDS34535.1	.	.	.	.	.	.	.	.	.	.	C	31	5.102697	0.94245	.	.	ENSG00000146376	ENST00000368149;ENST00000275189	.	.	.	6.03	6.03	0.97812	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.73273	0.3566	L	0.59436	1.845	0.80722	D	1	D;D	0.89917	1.0;0.992	D;D	0.79784	0.993;0.937	T	0.68405	-0.5417	8	.	.	.	.	20.5568	0.99304	0.0:1.0:0.0:0.0	.	401;401	A9UK01;Q8N392	.;RHG18_HUMAN	N	356;401	.	.	S	-	2	0	ARHGAP18	129970811	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.985000	0.70556	2.861000	0.98227	0.655000	0.94253	AGC		0.458	ARHGAP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042185.2	NM_033515	
SLC18B1	116843	broad.mit.edu	37	6	133091423	133091423	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:133091423G>A	ENST00000275227.4	-	14	1453	c.1357C>T	c.(1357-1359)Cct>Tct	p.P453S		NM_052831.2	NP_439896.1	Q6NT16	S18B1_HUMAN	solute carrier family 18, subfamily B, member 1	453					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)		p.P453S(1)									GTTTCATTAGGCAAGAGAGTA	0.388																																					p.P453S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1357T	6						.						214.0	186.0	196.0					6																	133091423		2203	4300	6503	133133116	SO:0001583	missense	116843	exon14			AK124442	CCDS5163.1	6q22.3-q23.3	2013-05-22	2012-03-09	2012-03-09	ENSG00000146409	ENSG00000146409		"""Solute carriers"""	21573	protein-coding gene	gene with protein product		613361	"""chromosome 6 open reading frame 192"""	C6orf192		19697161	Standard	XM_006715328		Approved	dJ55C23.6	uc003qdw.1	Q6NT16	OTTHUMG00000015595	ENST00000275227.4:c.1357C>T	6.37:g.133091423G>A	ENSP00000275227:p.Pro453Ser		133133116	NM_052831	A8K1K3|B3KW77|Q6ISF2	Missense_Mutation	SNP	ENST00000275227.4	37	CCDS5163.1	.	.	.	.	.	.	.	.	.	.	G	8.361	0.833140	0.16820	.	.	ENSG00000146409	ENST00000275227	T	0.04015	3.73	5.2	-2.02	0.07388	.	0.646374	0.16190	N	0.225440	T	0.00967	0.0032	L	0.38838	1.175	0.24915	N	0.992013	B	0.13594	0.008	B	0.12837	0.008	T	0.46830	-0.9163	10	0.09338	T	0.73	-0.6496	9.916	0.41434	0.5781:0.0:0.4219:0.0	.	453	Q6NT16	CF192_HUMAN	S	453	ENSP00000275227:P453S	ENSP00000275227:P453S	P	-	1	0	C6orf192	133133116	0.096000	0.21769	0.006000	0.13384	0.412000	0.31113	0.237000	0.17985	-0.737000	0.04824	0.655000	0.94253	CCT		0.388	SLC18B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042273.1	NM_052831	
MTFR2	113115	broad.mit.edu	37	6	136560604	136560604	+	Splice_Site	SNP	C	C	T	rs369622195		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:136560604C>T	ENST00000420702.1	-	6	1258	c.869G>A	c.(868-870)cGg>cAg	p.R290Q	MTFR2_ENST00000451457.2_Splice_Site_p.R290Q	NM_001099286.1	NP_001092756.1	Q6P444	MTFR2_HUMAN	mitochondrial fission regulator 2	290					aerobic respiration (GO:0009060)|mitochondrial fission (GO:0000266)|mitochondrion organization (GO:0007005)	mitochondrion (GO:0005739)		p.R290Q(1)									AACAACATACCGCTCAATTGC	0.264																																					p.R290Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G869A	6						.	C	GLN/ARG,GLN/ARG	0,4406		0,0,2203	86.0	82.0	84.0		869,869	5.3	1.0	6		84	1,8599	1.2+/-3.3	0,1,4299	no	missense-near-splice,missense-near-splice	FAM54A	NM_001099286.1,NM_138419.3	43,43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	290/386,290/386	136560604	1,13005	2203	4300	6503	136602297	SO:0001630	splice_region_variant	113115	exon6			BC011716	CCDS5176.1	6q23.2	2012-11-30	2012-11-29	2012-11-29	ENSG00000146410	ENSG00000146410			21115	protein-coding gene	gene with protein product			"""DUF729 domain containing 1"", ""family with sequence similarity 54, member A"""	DUFD1, FAM54A			Standard	NM_138419		Approved		uc003qgt.1	Q6P444	OTTHUMG00000015643	ENST00000420702.1:c.869+1G>A	6.37:g.136560604C>T			136602297	NM_138419	A8K8D8|E1P585|Q5JWR7|Q6ZUE8|Q7L3U6|Q9BZ39	Missense_Mutation	SNP	ENST00000420702.1	37	CCDS5176.1	.	.	.	.	.	.	.	.	.	.	C	18.30	3.593305	0.66219	0.0	1.16E-4	ENSG00000146410	ENST00000451457;ENST00000420702	T;T	0.60171	0.21;0.21	5.31	5.31	0.75309	.	0.101955	0.64402	D	0.000004	T	0.66268	0.2772	L	0.59436	1.845	0.51767	D	0.999938	D	0.89917	1.0	D	0.87578	0.998	T	0.65166	-0.6234	9	.	.	.	-15.5654	15.8921	0.79305	0.0:1.0:0.0:0.0	.	290	Q6P444	FA54A_HUMAN	Q	290	ENSP00000407010:R290Q;ENSP00000395232:R290Q	.	R	-	2	0	FAM54A	136602297	1.000000	0.71417	0.965000	0.40720	0.099000	0.18886	2.627000	0.46469	2.482000	0.83794	0.557000	0.71058	CGG		0.264	MTFR2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042378.2	NM_138419	Missense_Mutation
IFNGR1	3459	broad.mit.edu	37	6	137519517	137519517	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:137519517A>C	ENST00000367739.4	-	7	1242	c.1121T>G	c.(1120-1122)aTa>aGa	p.I374R	IFNGR1_ENST00000543628.1_Missense_Mutation_p.I346R	NM_000416.2	NP_000407.1	P15260	INGR1_HUMAN	interferon gamma receptor 1	374					cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to virus (GO:0009615)|signal transduction (GO:0007165)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|vesicle (GO:0031982)	interferon-gamma receptor activity (GO:0004906)	p.I374R(1)		central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	18	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000829)|OV - Ovarian serous cystadenocarcinoma(155;0.00389)	Interferon gamma-1b(DB00033)	CTCTCTCTCTATTGGAGTCAG	0.433																																					p.I374R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1121G	6						.						119.0	120.0	120.0					6																	137519517		2203	4300	6503	137561210	SO:0001583	missense	3459	exon7				CCDS5185.1	6q23-q24	2014-09-17			ENSG00000027697	ENSG00000027697		"""Interferons"", ""CD molecules"""	5439	protein-coding gene	gene with protein product		107470		IFNGR			Standard	NM_000416		Approved	CD119	uc003qho.2	P15260	OTTHUMG00000015656	ENST00000367739.4:c.1121T>G	6.37:g.137519517A>C	ENSP00000356713:p.Ile374Arg		137561210	NM_000416	B4DFT7|E1P587|Q53Y96	Missense_Mutation	SNP	ENST00000367739.4	37	CCDS5185.1	.	.	.	.	.	.	.	.	.	.	A	11.83	1.756877	0.31137	.	.	ENSG00000027697	ENST00000367739;ENST00000543628	T;T	0.73152	-0.72;-0.57	5.39	-7.0	0.01599	.	3.263400	0.00718	N	0.000876	T	0.25344	0.0616	N	0.22421	0.69	0.09310	N	1	P;B	0.35077	0.483;0.351	B;B	0.28139	0.086;0.04	T	0.20174	-1.0283	10	0.66056	D	0.02	1.1632	1.1355	0.01754	0.2195:0.3707:0.1676:0.2423	.	346;374	F5H5M7;P15260	.;INGR1_HUMAN	R	374;346	ENSP00000356713:I374R;ENSP00000443282:I346R	ENSP00000356713:I374R	I	-	2	0	IFNGR1	137561210	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-0.476000	0.06591	-1.075000	0.03129	0.533000	0.62120	ATA		0.433	IFNGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042401.1		
HECA	51696	broad.mit.edu	37	6	139488273	139488273	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:139488273G>A	ENST00000367658.2	+	2	1409	c.1124G>A	c.(1123-1125)gGc>gAc	p.G375D	RP1-225E12.2_ENST00000586229.1_RNA|RP1-225E12.2_ENST00000588529.1_RNA|RP1-225E12.2_ENST00000589192.1_RNA|RP1-225E12.2_ENST00000587577.1_RNA|RP1-225E12.2_ENST00000586266.1_RNA|RP1-225E12.2_ENST00000415194.2_RNA|RP1-225E12.2_ENST00000590679.1_RNA|RP1-225E12.2_ENST00000585447.1_RNA|RP1-225E12.3_ENST00000585874.1_RNA|RP1-225E12.2_ENST00000588638.1_RNA|RP1-225E12.2_ENST00000591102.1_RNA	NM_016217.2	NP_057301.1	Q9UBI9	HDC_HUMAN	headcase homolog (Drosophila)	375					respiratory tube development (GO:0030323)	membrane (GO:0016020)		p.G375D(1)		endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)	15				GBM - Glioblastoma multiforme(68;0.000252)|OV - Ovarian serous cystadenocarcinoma(155;0.000387)		GCCCAAGTGGGCCAGGGGGAA	0.607																																					p.G375D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1124A	6						.						54.0	48.0	50.0					6																	139488273		2203	4300	6503	139529966	SO:0001583	missense	51696	exon2			AB033492	CCDS5194.1	6q23-q24	2010-11-25			ENSG00000112406	ENSG00000112406			21041	protein-coding gene	gene with protein product		607977				11696983, 19643820	Standard	NM_016217		Approved	HDCL, hHDC, HDC, dJ225E12.1	uc003qin.3	Q9UBI9	OTTHUMG00000015686	ENST00000367658.2:c.1124G>A	6.37:g.139488273G>A	ENSP00000356630:p.Gly375Asp		139529966	NM_016217		Missense_Mutation	SNP	ENST00000367658.2	37	CCDS5194.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.502270	0.85176	.	.	ENSG00000112406	ENST00000367658	.	.	.	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	T	0.62636	0.2444	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.66976	-0.5787	9	0.87932	D	0	.	18.6449	0.91407	0.0:0.0:1.0:0.0	.	375	Q9UBI9	HDC_HUMAN	D	375	.	ENSP00000356630:G375D	G	+	2	0	HECA	139529966	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.211000	0.95120	2.642000	0.89623	0.563000	0.77884	GGC		0.607	HECA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042456.1	NM_016217	
HIVEP2	3097	broad.mit.edu	37	6	143095278	143095278	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:143095278T>C	ENST00000367604.1	-	4	1237	c.598A>G	c.(598-600)Aaa>Gaa	p.K200E	HIVEP2_ENST00000012134.2_Missense_Mutation_p.K200E|HIVEP2_ENST00000367603.2_Missense_Mutation_p.K200E			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	200					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K200E(1)		NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		ACACTAGGTTTGGCACACGCT	0.453																																					p.K200E	Esophageal Squamous(107;843 1510 13293 16805 42198)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A598G	6						.						139.0	133.0	135.0					6																	143095278		1904	4126	6030	143136971	SO:0001583	missense	3097	exon5			M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"""Zinc fingers, C2H2-type"""	4921	protein-coding gene	gene with protein product	"""c-myc intron binding protein 1"""	143054	"""human immunodeficiency virus type I enhancer-binding protein 2"""			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.598A>G	6.37:g.143095278T>C	ENSP00000356576:p.Lys200Glu		143136971	NM_006734	Q02646|Q5THT5|Q9NS05	Missense_Mutation	SNP	ENST00000367604.1	37	CCDS43510.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.126351	0.77549	.	.	ENSG00000010818	ENST00000367604;ENST00000367603;ENST00000012134	T;T;T	0.28255	1.62;1.62;1.62	5.79	5.79	0.91817	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.044914	0.85682	D	0.000000	T	0.46927	0.1418	M	0.68952	2.095	0.52501	D	0.999957	D	0.89917	1.0	D	0.80764	0.994	T	0.51084	-0.8750	10	0.87932	D	0	-23.0063	16.1343	0.81471	0.0:0.0:0.0:1.0	.	200	P31629	ZEP2_HUMAN	E	200	ENSP00000356576:K200E;ENSP00000356575:K200E;ENSP00000012134:K200E	ENSP00000012134:K200E	K	-	1	0	HIVEP2	143136971	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.997000	0.88414	2.209000	0.71365	0.533000	0.62120	AAA		0.453	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1		
UTRN	7402	broad.mit.edu	37	6	144743072	144743072	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:144743072T>C	ENST00000367545.3	+	3	200	c.200T>C	c.(199-201)tTg>tCg	p.L67S		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	67	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.L67S(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		AGGAAGCTATTGGATCTTCTA	0.428																																					p.L67S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T200C	6						.						108.0	94.0	98.0					6																	144743072		2203	4300	6503	144784765	SO:0001583	missense	7402	exon3			AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"""utrophin (homologous to dystrophin)"""	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.200T>C	6.37:g.144743072T>C	ENSP00000356515:p.Leu67Ser		144784765	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	37	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.819464	0.90873	.	.	ENSG00000152818	ENST00000367529;ENST00000367545;ENST00000421035	D;D	0.95554	-3.74;-3.74	6.03	6.03	0.97812	Calponin homology domain (5);	0.000000	0.41396	D	0.000891	D	0.97904	0.9311	M	0.88640	2.97	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98869	1.0765	10	0.87932	D	0	.	16.5582	0.84512	0.0:0.0:0.0:1.0	.	67	P46939	UTRO_HUMAN	S	67;67;72	ENSP00000356515:L67S;ENSP00000396276:L72S	ENSP00000356499:L67S	L	+	2	0	UTRN	144784765	1.000000	0.71417	0.937000	0.37676	0.979000	0.70002	7.274000	0.78538	2.308000	0.77769	0.533000	0.62120	TTG		0.428	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1		
LATS1	9113	broad.mit.edu	37	6	150001474	150001474	+	Silent	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:150001474T>C	ENST00000543571.1	-	5	2677	c.2130A>G	c.(2128-2130)acA>acG	p.T710T	LATS1_ENST00000253339.5_Silent_p.T710T|LATS1_ENST00000542747.1_5'UTR	NM_004690.3	NP_004681.1			large tumor suppressor kinase 1									p.T710T(1)		central_nervous_system(1)|lung(5)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)		CTATTCCTAGTGTCTTTATCT	0.363																																					p.T710T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A2130G	6						.						94.0	100.0	98.0					6																	150001474		2203	4300	6503	150043167	SO:0001819	synonymous_variant	9113	exon5			AF104413	CCDS34551.1, CCDS59040.1	6q25.1	2013-04-25	2013-04-25		ENSG00000131023	ENSG00000131023			6514	protein-coding gene	gene with protein product		603473	"""LATS (large tumor suppressor, Drosophila) homolog 1"", ""LATS, large tumor suppressor, homolog 1 (Drosophila)"""			9988268, 15122335	Standard	NM_004690		Approved	WARTS	uc003qmu.2	O95835	OTTHUMG00000016437	ENST00000543571.1:c.2130A>G	6.37:g.150001474T>C			150043167	NM_004690		Silent	SNP	ENST00000543571.1	37	CCDS34551.1																																																																																				0.363	LATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043923.4	NM_004690	
FNDC1	84624	broad.mit.edu	37	6	159655349	159655349	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:159655349G>A	ENST00000297267.9	+	11	4005	c.3805G>A	c.(3805-3807)Gtg>Atg	p.V1269M	FNDC1_ENST00000340366.6_Missense_Mutation_p.V1206M	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1269					cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.V1269M(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		CGCTGCCACCGTGAGCCCCGT	0.721																																					p.V1269M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3805A	6						.						11.0	14.0	13.0					6																	159655349		2000	4121	6121	159575339	SO:0001583	missense	84624	exon11			AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"""Fibronectin type III domain containing"""	21184	protein-coding gene	gene with protein product		609991	"""fibronectin type III domain containing 2"""	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.3805G>A	6.37:g.159655349G>A	ENSP00000297267:p.Val1269Met		159575339	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.68|11.68	1.711916|1.711916	0.30322|0.30322	.|.	.|.	ENSG00000164694|ENSG00000164694	ENST00000329629|ENST00000297267;ENST00000340366	.|T;T	.|0.07021	.|3.23;4.04	4.78|4.78	-0.556|-0.556	0.11803|0.11803	.|.	.|1.932380	.|0.02608	.|N	.|0.101774	T|T	0.01661|0.01661	0.0053|0.0053	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B;B	.|0.14805	.|0.011;0.007	.|B;B	.|0.12837	.|0.003;0.008	T|T	0.47222|0.47222	-0.9134|-0.9134	5|10	.|0.54805	.|T	.|0.06	0.7402|0.7402	11.2002|11.2002	0.48736|0.48736	0.0:0.3123:0.6058:0.0819|0.0:0.3123:0.6058:0.0819	.|.	.|1206;1269	.|Q4ZHG4-2;Q4ZHG4	.|.;FNDC1_HUMAN	H|M	1164|1269;1206	.|ENSP00000297267:V1269M;ENSP00000342460:V1206M	.|ENSP00000297267:V1269M	R|V	+|+	2|1	0|0	FNDC1|FNDC1	159575339|159575339	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	0.050000|0.050000	0.14120|0.14120	-0.512000|-0.512000	0.06505|0.06505	-0.188000|-0.188000	0.12872|0.12872	CGT|GTG		0.721	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532	
ATXN1	6310	broad.mit.edu	37	6	16327992	16327992	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:16327992T>C	ENST00000244769.4	-	8	1486	c.550A>G	c.(550-552)Atg>Gtg	p.M184V	ATXN1_ENST00000436367.1_Missense_Mutation_p.M184V	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	184					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)	p.M184V(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				AGACTGCCCATGTTGGCCAGC	0.657																																					p.M184V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A550G	6						.						24.0	28.0	26.0					6																	16327992		2190	4282	6472	16435971	SO:0001583	missense	6310	exon8			X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"""Ataxins"""	10548	protein-coding gene	gene with protein product		601556	"""spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"""	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.550A>G	6.37:g.16327992T>C	ENSP00000244769:p.Met184Val		16435971	NM_000332	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	37	CCDS34342.1	.	.	.	.	.	.	.	.	.	.	T	10.56	1.383471	0.25031	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.25579	1.79;1.79	5.26	1.69	0.24217	.	0.269109	0.42294	D	0.000726	T	0.07548	0.0190	L	0.39633	1.23	0.25688	N	0.985729	B	0.09022	0.002	B	0.08055	0.003	T	0.30446	-0.9978	10	0.36615	T	0.2	-22.2223	9.219	0.37364	0.0:0.2051:0.0:0.7949	.	184	P54253	ATX1_HUMAN	V	184	ENSP00000244769:M184V;ENSP00000416360:M184V	ENSP00000244769:M184V	M	-	1	0	ATXN1	16435971	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	2.192000	0.42649	0.845000	0.35118	0.383000	0.25322	ATG		0.657	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332	
SLC22A3	6581	broad.mit.edu	37	6	160872075	160872075	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:160872075G>A	ENST00000275300.2	+	11	1810	c.1658G>A	c.(1657-1659)cGc>cAc	p.R553H	SLC22A3_ENST00000392145.1_Missense_Mutation_p.R554H	NM_021977.3	NP_068812.1	O75751	S22A3_HUMAN	solute carrier family 22 (organic cation transporter), member 3	553					dopamine transport (GO:0015872)|drug transmembrane transport (GO:0006855)|histamine uptake (GO:0051615)|organic cation transport (GO:0015695)|quaternary ammonium group transport (GO:0015697)|regulation of appetite (GO:0032098)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dopamine transmembrane transporter activity (GO:0005329)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|toxin transporter activity (GO:0019534)	p.R553H(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		Breast(66;0.00028)|Ovarian(120;0.0308)|Prostate(117;0.218)		OV - Ovarian serous cystadenocarcinoma(65;9.47e-17)|BRCA - Breast invasive adenocarcinoma(81;9.75e-06)	Adefovir Dipivoxil(DB00718)|Amphetamine(DB00182)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Colchicine(DB01394)|Desipramine(DB01151)|Dopamine(DB00988)|Estradiol(DB00783)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imipramine(DB00458)|Irinotecan(DB00762)|Lamivudine(DB00709)|Melphalan(DB01042)|Metformin(DB00331)|Methamphetamine(DB01577)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Phenoxybenzamine(DB00925)|Prazosin(DB00457)|Procainamide(DB01035)|Progesterone(DB00396)|Testosterone(DB00624)|Vincristine(DB00541)	CCAGTTTCCCGCTCTCACCTT	0.453																																					p.R553H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1658A	6						.						44.0	39.0	41.0					6																	160872075		2203	4300	6503	160792065	SO:0001583	missense	6581	exon11			AF078749	CCDS5277.1	6q25.3	2013-07-18	2013-07-18		ENSG00000146477	ENSG00000146477		"""Solute carriers"""	10967	protein-coding gene	gene with protein product		604842	"""solute carrier family 22 (extraneuronal monoamine transporter), member 3"""			9632645, 9933568	Standard	NM_021977		Approved	OCT3, EMT	uc003qti.4	O75751	OTTHUMG00000015953	ENST00000275300.2:c.1658G>A	6.37:g.160872075G>A	ENSP00000275300:p.Arg553His		160792065	NM_021977	Q5SYN6|Q9UP02	Missense_Mutation	SNP	ENST00000275300.2	37	CCDS5277.1	.	.	.	.	.	.	.	.	.	.	g	5.669	0.308120	0.10733	.	.	ENSG00000146477	ENST00000275300;ENST00000392145	T;T	0.74842	-0.88;-0.88	4.59	-0.39	0.12450	.	0.789302	0.11836	N	0.524785	T	0.26882	0.0658	N	0.14661	0.345	0.09310	N	1	P	0.34892	0.474	B	0.22386	0.039	T	0.06935	-1.0799	10	0.46703	T	0.11	.	4.4747	0.11729	0.3787:0.166:0.4553:0.0	.	553	O75751	S22A3_HUMAN	H	553;554	ENSP00000275300:R553H;ENSP00000375989:R554H	ENSP00000275300:R553H	R	+	2	0	SLC22A3	160792065	0.004000	0.15560	0.285000	0.24819	0.080000	0.17528	0.090000	0.15025	-0.201000	0.10284	-1.036000	0.02392	CGC		0.453	SLC22A3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042953.1	NM_021977	
UNC93A	54346	broad.mit.edu	37	6	167721364	167721364	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:167721364C>T	ENST00000230256.3	+	7	1249	c.1074C>T	c.(1072-1074)ggC>ggT	p.G358G	UNC93A_ENST00000366829.2_Silent_p.G316G	NM_018974.3	NP_061847.2	Q86WB7	UN93A_HUMAN	unc-93 homolog A (C. elegans)	358						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.G358G(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	40		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		GCCTGTGGGGCGTGGCAGATG	0.622																																					p.G316G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C948T	6						.						116.0	84.0	95.0					6																	167721364		2203	4300	6503	167641354	SO:0001819	synonymous_variant	54346	exon6			AJ508812	CCDS5300.1, CCDS47515.1	6q27	2014-05-16	2001-11-28		ENSG00000112494	ENSG00000112494			12570	protein-coding gene	gene with protein product		607995	"""unc93 (C.elegans) homolog A"""			12381271	Standard	NM_001143947		Approved	dJ366N23.2, dJ366N23.1	uc003qvq.3	Q86WB7	OTTHUMG00000016021	ENST00000230256.3:c.1074C>T	6.37:g.167721364C>T			167641354	NM_001143947	B3KRP5|Q4QQJ4|Q5JZD6	Silent	SNP	ENST00000230256.3	37	CCDS5300.1																																																																																				0.622	UNC93A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043125.2	NM_018974	
BPHL	670	broad.mit.edu	37	6	3137600	3137600	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:3137600C>T	ENST00000380379.5	+	5	586	c.537C>T	c.(535-537)atC>atT	p.I179I	BPHL_ENST00000380375.3_Silent_p.I162I|BPHL_ENST00000434640.1_Silent_p.I162I|BPHL_ENST00000380368.2_Silent_p.I162I|RP1-40E16.11_ENST00000447644.1_RNA	NM_004332.2	NP_004323.2	Q86WA6	BPHL_HUMAN	biphenyl hydrolase-like (serine hydrolase)	179					cellular amino acid metabolic process (GO:0006520)|response to toxic substance (GO:0009636)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)	p.I162I(1)		endometrium(4)|kidney(1)|large_intestine(2)|lung(6)	13	Ovarian(93;0.0386)	all_hematologic(90;0.108)				TTTCAGGCATCCGAGATGTTT	0.438																																					p.I179I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C537T	6						.						138.0	144.0	142.0					6																	3137600		2203	4300	6503	3082599	SO:0001819	synonymous_variant	670	exon5			X81372	CCDS4483.2	6p25	2008-08-29	2008-08-29		ENSG00000137274	ENSG00000137274			1094	protein-coding gene	gene with protein product	"""breast epithelial mucin-associated antigen"""	603156		MCNAA		7759552, 9721218, 15832508	Standard	NM_004332		Approved	Bph-rp	uc003mva.3	Q86WA6	OTTHUMG00000014140	ENST00000380379.5:c.537C>T	6.37:g.3137600C>T			3082599	NM_004332	Q00306|Q13855|Q3KP51	Silent	SNP	ENST00000380379.5	37	CCDS4483.2																																																																																				0.438	BPHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039670.5		
SSR1	6745	broad.mit.edu	37	6	7310176	7310176	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:7310176C>G	ENST00000244763.4	-	2	252	c.166G>C	c.(166-168)Gta>Cta	p.V56L	SSR1_ENST00000474597.1_Missense_Mutation_p.V56L|SSR1_ENST00000397511.2_Missense_Mutation_p.V56L|SSR1_ENST00000534851.1_Missense_Mutation_p.V56L|SSR1_ENST00000462112.1_Missense_Mutation_p.V56L|SSR1_ENST00000479365.1_Missense_Mutation_p.V56L|SSR1_ENST00000488834.1_5'UTR|SSR1_ENST00000489567.1_Missense_Mutation_p.V56L	NM_003144.3	NP_003135.2	P43307	SSRA_HUMAN	signal sequence receptor, alpha	56					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|endoplasmic reticulum unfolded protein response (GO:0030968)|gene expression (GO:0010467)|positive regulation of cell proliferation (GO:0008284)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)		p.V56L(1)		NS(1)|endometrium(2)|large_intestine(3)|lung(2)|prostate(1)	9	Ovarian(93;0.0398)					TCTTCTTCTACCTCGGCTTCA	0.333																																					p.V56L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G166C	6						.						174.0	168.0	170.0					6																	7310176		2203	4300	6503	7255175	SO:0001583	missense	6745	exon2				CCDS4499.1	6p24.3	2010-11-24	2008-08-26		ENSG00000124783	ENSG00000124783			11323	protein-coding gene	gene with protein product	"""translocon-associated protein alpha"""	600868					Standard	NM_001292008		Approved	TRAPA	uc003mxf.4	P43307	OTTHUMG00000014202	ENST00000244763.4:c.166G>C	6.37:g.7310176C>G	ENSP00000244763:p.Val56Leu		7255175	NM_003144	A8K685|Q53GX2|Q53H19|Q5TAM3|Q6IB43|Q8NBH9|Q96IA2|Q9TNQ8|Q9UN49	Missense_Mutation	SNP	ENST00000244763.4	37	CCDS4499.1	.	.	.	.	.	.	.	.	.	.	C	16.43	3.121262	0.56613	.	.	ENSG00000124783	ENST00000474597;ENST00000244763;ENST00000397511;ENST00000534851;ENST00000489567;ENST00000479365;ENST00000462112	T;T;T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82;0.82;0.82	4.71	3.84	0.44239	.	0.132413	0.49916	D	0.000133	T	0.57710	0.2072	M	0.82823	2.61	0.58432	D	0.999997	B;P;B	0.49185	0.036;0.92;0.014	B;D;B	0.65443	0.081;0.935;0.035	T	0.54964	-0.8214	10	0.19147	T	0.46	.	12.9065	0.58156	0.0:0.9168:0.0:0.0832	.	56;56;56	C9J5W0;C9JBX5;P43307	.;.;SSRA_HUMAN	L	56	ENSP00000418617:V56L;ENSP00000244763:V56L;ENSP00000380647:V56L;ENSP00000443020:V56L;ENSP00000420730:V56L;ENSP00000417911:V56L;ENSP00000417290:V56L	ENSP00000244763:V56L	V	-	1	0	SSR1	7255175	1.000000	0.71417	0.999000	0.59377	0.983000	0.72400	4.698000	0.61789	2.600000	0.87896	0.655000	0.94253	GTA		0.333	SSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039775.2		
CDKAL1	54901	broad.mit.edu	37	6	20546689	20546689	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:20546689G>A	ENST00000378610.1	+	1	118	c.108G>A	c.(106-108)ccG>ccA	p.P36P	CDKAL1_ENST00000378624.4_Missense_Mutation_p.R4Q|CDKAL1_ENST00000274695.4_Silent_p.P36P			Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein 1-like 1	36					maintenance of translational fidelity (GO:1990145)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|N6-threonylcarbomyladenosine methylthiotransferase activity (GO:0035598)	p.P36P(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|stomach(1)	29	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)			ATGTTGTCCCGAAGGTACGAA	0.388																																					p.P36P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G108A	6						.						114.0	105.0	108.0					6																	20546689		2203	4300	6503	20654668	SO:0001819	synonymous_variant	54901	exon3			AK000349	CCDS4546.1	6p22.2	2008-02-05			ENSG00000145996	ENSG00000145996			21050	protein-coding gene	gene with protein product		611259					Standard	NM_017774		Approved	FLJ20342	uc003ndd.2	Q5VV42	OTTHUMG00000014340	ENST00000378610.1:c.108G>A	6.37:g.20546689G>A			20654668	NM_017774	A8K6S0|Q6P385|Q6ZR27|Q9NXB3	Missense_Mutation	SNP	ENST00000378610.1	37	CCDS4546.1	.	.	.	.	.	.	.	.	.	.	G	16.14	3.039487	0.55003	.	.	ENSG00000145996	ENST00000378624	T	0.43294	0.95	5.35	1.33	0.21861	.	.	.	.	.	T	0.11367	0.0277	.	.	.	0.22156	N	0.999329	B	0.02656	0.0	B	0.01281	0.0	T	0.30475	-0.9977	8	0.87932	D	0	.	2.4846	0.04595	0.3809:0.3231:0.0706:0.2254	.	4	Q5VV42-2	.	Q	4	ENSP00000367889:R4Q	ENSP00000367889:R4Q	R	+	2	0	CDKAL1	20654668	0.998000	0.40836	1.000000	0.80357	0.886000	0.51366	0.455000	0.21843	0.109000	0.17891	-0.290000	0.09829	CGA		0.388	CDKAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039986.1	NM_017774	
NRSN1	140767	broad.mit.edu	37	6	24134688	24134688	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:24134688G>T	ENST00000378491.4	+	3	434	c.133G>T	c.(133-135)Gag>Tag	p.E45*	NRSN1_ENST00000378478.1_Nonsense_Mutation_p.E45*|NRSN1_ENST00000378475.1_Nonsense_Mutation_p.E45*	NM_080723.4	NP_542454.3			neurensin 1									p.E45*(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	22						TTGGGAGTATGAGGATGATTT	0.478																																					p.E45X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G133T	6						.						130.0	114.0	119.0					6																	24134688		2203	4300	6503	24242667	SO:0001587	stop_gained	140767	exon3			AF418980	CCDS4549.1	6p22.1	2008-02-05	2006-07-04	2006-07-04	ENSG00000152954	ENSG00000152954			17881	protein-coding gene	gene with protein product			"""vesicular membrane protein p24"""	VMP		12463420	Standard	NM_080723		Approved	p24	uc010jpq.1	Q8IZ57	OTTHUMG00000016406	ENST00000378491.4:c.133G>T	6.37:g.24134688G>T	ENSP00000367752:p.Glu45*		24242667	NM_080723		Nonsense_Mutation	SNP	ENST00000378491.4	37	CCDS4549.1	.	.	.	.	.	.	.	.	.	.	G	38	6.714175	0.97784	.	.	ENSG00000152954	ENST00000378491;ENST00000378478;ENST00000378477;ENST00000378475	.	.	.	5.74	5.74	0.90152	.	0.049126	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-21.4328	19.9279	0.97110	0.0:0.0:1.0:0.0	.	.	.	.	X	45	.	ENSP00000367736:E45X	E	+	1	0	NRSN1	24242667	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.441000	0.97557	2.715000	0.92844	0.655000	0.94253	GAG		0.478	NRSN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043866.1	NM_080723	
SLC17A4	10050	broad.mit.edu	37	6	25762243	25762243	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:25762243G>A	ENST00000377905.4	+	2	172	c.53G>A	c.(52-54)gGc>gAc	p.G18D	SLC17A4_ENST00000397076.2_5'UTR|SLC17A4_ENST00000439485.2_Missense_Mutation_p.G18D	NM_005495.2	NP_005486.1	Q9Y2C5	S17A4_HUMAN	solute carrier family 17, member 4	18					phosphate ion transmembrane transport (GO:0035435)|phosphate-containing compound metabolic process (GO:0006796)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	sodium:phosphate symporter activity (GO:0005436)	p.G18D(1)		breast(4)|endometrium(1)|kidney(4)|large_intestine(3)|lung(21)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						TCCAGTGATGGCAATTTAAAC	0.418																																					p.G18D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G53A	6						.						83.0	76.0	79.0					6																	25762243		2203	4300	6503	25870222	SO:0001583	missense	10050	exon2			AB020527	CCDS4564.1, CCDS75411.1	6p22.2	2013-07-18	2013-07-18		ENSG00000146039	ENSG00000146039		"""Solute carriers"""	10932	protein-coding gene	gene with protein product		604216	"""solute carrier family 17 (sodium phosphate), member 4"""			10319585	Standard	NM_005495		Approved	KIAA2138	uc003nfe.3	Q9Y2C5	OTTHUMG00000014410	ENST00000377905.4:c.53G>A	6.37:g.25762243G>A	ENSP00000367137:p.Gly18Asp		25870222	NM_005495	B4DDV9|E7EPE8|E7EU17|Q32MB7|Q32MB8	Missense_Mutation	SNP	ENST00000377905.4	37	CCDS4564.1	.	.	.	.	.	.	.	.	.	.	G	8.496	0.863118	0.17250	.	.	ENSG00000146039	ENST00000377905;ENST00000439485	T;T	0.74209	-0.06;-0.82	4.15	-0.852	0.10713	Major facilitator superfamily domain, general substrate transporter (1);	2.313570	0.01865	N	0.036852	T	0.27559	0.0677	N	0.08118	0	0.09310	N	0.999999	B;B	0.26081	0.141;0.002	B;B	0.22753	0.041;0.003	T	0.14643	-1.0465	10	0.12103	T	0.63	.	7.5399	0.27731	0.5058:0.0:0.4942:0.0	.	18;18	E7EPE8;Q9Y2C5	.;S17A4_HUMAN	D	18	ENSP00000367137:G18D;ENSP00000391345:G18D	ENSP00000367137:G18D	G	+	2	0	SLC17A4	25870222	0.000000	0.05858	0.000000	0.03702	0.218000	0.24690	-0.350000	0.07721	-0.188000	0.10499	0.557000	0.71058	GGC		0.418	SLC17A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040068.1		
SLC17A3	10786	broad.mit.edu	37	6	25845699	25845699	+	Missense_Mutation	SNP	C	C	T	rs114720409		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:25845699C>T	ENST00000360657.3	-	11	1459	c.1174G>A	c.(1174-1176)Gtt>Att	p.V392I	SLC17A3_ENST00000397060.4_Missense_Mutation_p.V470I|SLC17A3_ENST00000361703.6_Missense_Mutation_p.V392I			O00476	NPT4_HUMAN	solute carrier family 17 (organic anion transporter), member 3	392					drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|glucose-6-phosphate transport (GO:0015760)|ion transmembrane transport (GO:0034220)|organic acid transport (GO:0015849)|organic anion transport (GO:0015711)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|regulation of anion transport (GO:0044070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|efflux transmembrane transporter activity (GO:0015562)|organic anion transmembrane transporter activity (GO:0008514)|sodium:phosphate symporter activity (GO:0005436)|toxin transporter activity (GO:0019534)|urate transmembrane transporter activity (GO:0015143)|voltage-gated anion channel activity (GO:0008308)	p.V392I(2)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)	20						AACAGGTTAACGGCAAACAGC	0.413													c|||	1	0.000199681	0.0	0.0	5008	,	,		17398	0.001		0.0	False		,,,				2504	0.0				p.V470I												.	.	2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	c.G1408A	6						.	T	ILE/VAL,ILE/VAL	0,4406		0,0,2203	153.0	140.0	144.0		1408,1174	-1.0	0.2	6	dbSNP_132	144	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	SLC17A3	NM_001098486.1,NM_006632.3	29,29	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign,benign	470/499,392/421	25845699	2,13004	2203	4300	6503	25953678	SO:0001583	missense	10786	exon12			U90545	CCDS4566.2, CCDS47385.1	6p22.2	2013-07-18	2013-07-18		ENSG00000124564	ENSG00000124564		"""Solute carriers"""	10931	protein-coding gene	gene with protein product		611034	"""solute carrier family 17 (sodium phosphate), member 3"""			9149941	Standard	NM_006632		Approved	NPT4	uc003nfk.4	O00476	OTTHUMG00000014412	ENST00000360657.3:c.1174G>A	6.37:g.25845699C>T	ENSP00000353873:p.Val392Ile		25953678	NM_001098486	B7WNJ5|B7Z511|Q8WWC7|Q9H533	Missense_Mutation	SNP	ENST00000360657.3	37	CCDS4566.2	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	c	0.689	-0.795199	0.02862	0.0	2.33E-4	ENSG00000124564	ENST00000505420;ENST00000397060;ENST00000360657;ENST00000361703	T;T;T;T	0.58358	0.37;0.34;0.34;0.34	4.78	-0.986	0.10252	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.286281	0.24476	N	0.038196	T	0.05960	0.0155	N	0.02854	-0.475	0.09310	N	0.999991	B;B	0.06786	0.0;0.001	B;B	0.06405	0.002;0.001	T	0.41413	-0.9510	10	0.02654	T	1	.	9.0827	0.36561	0.0:0.2541:0.0:0.7459	.	470;392	B7Z511;O00476	.;NPT4_HUMAN	I	23;470;392;392	ENSP00000424027:V23I;ENSP00000380250:V470I;ENSP00000353873:V392I;ENSP00000355307:V392I	ENSP00000353873:V392I	V	-	1	0	SLC17A3	25953678	0.003000	0.15002	0.167000	0.22817	0.012000	0.07955	-0.783000	0.04638	-0.328000	0.08539	-1.158000	0.01797	GTT		0.413	SLC17A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040070.2		
HIST1H4G	8369	broad.mit.edu	37	6	26247163	26247163	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:26247163C>T	ENST00000244537.4	-	1	96	c.43G>A	c.(43-45)Ggt>Agt	p.G15S		NM_003547.2	NP_003538.1	Q99525	H4G_HUMAN	histone cluster 1, H4g	15						nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.G15S(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	7		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)				CACTTGGCACCGCCTTTCCCA	0.517																																					p.G15S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G43A	6						.						50.0	46.0	47.0					6																	26247163		2203	4300	6503	26355142	SO:0001583	missense	8369	exon1			Z80788	CCDS4599.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000124578	ENSG00000275663		"""Histones / Replication-dependent"""	4792	protein-coding gene	gene with protein product		602832	"""H4 histone family, member L"", ""histone 1, H4g"""	H4FL		9119399, 12408966	Standard	NM_003547		Approved	H4/l	uc003nhf.3	Q99525	OTTHUMG00000014444	ENST00000244537.4:c.43G>A	6.37:g.26247163C>T	ENSP00000244537:p.Gly15Ser		26355142	NM_003547		Missense_Mutation	SNP	ENST00000244537.4	37	CCDS4599.1	.	.	.	.	.	.	.	.	.	.	.	13.67	2.305481	0.40795	.	.	ENSG00000124578	ENST00000244537	.	.	.	3.19	3.19	0.36642	Histone-fold (2);	.	.	.	.	T	0.72771	0.3502	.	.	.	0.44454	D	0.997384	D	0.89917	1.0	D	0.78314	0.991	T	0.77013	-0.2745	7	0.56958	D	0.05	.	14.349	0.66688	0.0:1.0:0.0:0.0	.	15	Q99525	H4G_HUMAN	S	15	.	ENSP00000244537:G15S	G	-	1	0	HIST1H4G	26355142	1.000000	0.71417	0.743000	0.31040	0.008000	0.06430	6.999000	0.76283	1.754000	0.51921	0.501000	0.49751	GGT		0.517	HIST1H4G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040107.1	NM_003547	
OR2J3	442186	broad.mit.edu	37	6	29080339	29080339	+	Silent	SNP	C	C	T	rs533563712		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:29080339C>T	ENST00000377169.1	+	1	672	c.672C>T	c.(670-672)atC>atT	p.I224I		NM_001005216.2	NP_001005216.2	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J, member 3	224						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I224I(1)		endometrium(2)|large_intestine(5)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24						ATGGTGCCATCGTCCGAGCTA	0.458													C|||	1	0.000199681	0.0008	0.0	5008	,	,		22591	0.0		0.0	False		,,,				2504	0.0				p.I224I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C672T	6						.						109.0	118.0	115.0					6																	29080339		1301	2573	3874	29188318	SO:0001819	synonymous_variant	442186	exon1				CCDS43433.1	6p22.2-p21.31	2012-08-09			ENSG00000204701	ENSG00000204701		"""GPCR / Class A : Olfactory receptors"""	8261	protein-coding gene	gene with protein product		615016					Standard	NM_001005216		Approved	OR6-6	uc011dll.2	O76001	OTTHUMG00000031092	ENST00000377169.1:c.672C>T	6.37:g.29080339C>T			29188318	NM_001005216	B0UY52|B9EH11|Q5SUJ7|Q6IF25|Q96R15|Q9GZK5|Q9GZL4|Q9GZL5	Silent	SNP	ENST00000377169.1	37	CCDS43433.1																																																																																				0.458	OR2J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076132.2		
GABBR1	2550	broad.mit.edu	37	6	29571438	29571438	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:29571438C>T	ENST00000377034.4	-	23	3103	c.2768G>A	c.(2767-2769)cGc>cAc	p.R923H	GABBR1_ENST00000377016.4_Missense_Mutation_p.R861H|GABBR1_ENST00000355973.3_Missense_Mutation_p.R806H|GABBR1_ENST00000376977.3_3'UTR|GABBR1_ENST00000377012.4_Missense_Mutation_p.R806H	NM_001470.2	NP_001461.1	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 1	923				Missing (in Ref. 7; CAA09031). {ECO:0000305}.	adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	G-protein coupled GABA receptor activity (GO:0004965)	p.R923H(1)		endometrium(3)|kidney(1)|large_intestine(13)|liver(1)|lung(16)|ovary(5)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47					Baclofen(DB00181)|Progabide(DB00837)|Vigabatrin(DB01080)	GCGCCGGGAGCGGAGCTGCTG	0.637																																					p.R861H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2582A	6						.						15.0	15.0	15.0					6																	29571438		1509	2707	4216	29679417	SO:0001583	missense	2550	exon22			Y11044	CCDS4663.1, CCDS4664.1, CCDS4665.1	6p21.3	2012-08-29			ENSG00000204681	ENSG00000204681		"""GABA receptors"", ""GPCR / Class C : GABA(B) receptors"""	4070	protein-coding gene	gene with protein product	"""GABA-B receptor"""	603540				9753614, 9798068	Standard	NM_001470		Approved	hGB1a, GPRC3A	uc003nmt.4	Q9UBS5	OTTHUMG00000031095	ENST00000377034.4:c.2768G>A	6.37:g.29571438C>T	ENSP00000366233:p.Arg923His		29679417	NM_021904	B0UXY7|O95375|O95468|O95975|O96022|Q5STL4|Q5SUJ8|Q5SUL3|Q71SG6|Q86W60|Q9UQQ0	Missense_Mutation	SNP	ENST00000377034.4	37	CCDS4663.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.076621	0.76415	.	.	ENSG00000204681	ENST00000355973;ENST00000377016;ENST00000377012;ENST00000377034	D;D;D;T	0.83591	-1.74;-1.66;-1.74;-0.53	3.58	3.58	0.41010	.	0.000000	0.85682	D	0.000000	T	0.78898	0.4356	N	0.24115	0.695	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.998	D;D;D	0.80764	0.994;0.98;0.964	T	0.80652	-0.1287	10	0.48119	T	0.1	-11.5491	10.8844	0.46957	0.0:1.0:0.0:0.0	.	861;923;806	Q9UBS5-3;Q9UBS5;Q5SUJ9	.;GABR1_HUMAN;.	H	806;861;806;923	ENSP00000348248:R806H;ENSP00000366215:R861H;ENSP00000366211:R806H;ENSP00000366233:R923H	ENSP00000348248:R806H	R	-	2	0	GABBR1	29679417	1.000000	0.71417	0.994000	0.49952	0.967000	0.64934	4.347000	0.59373	1.994000	0.58287	0.591000	0.81541	CGC		0.637	GABBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076141.3		
HLA-F	3134	broad.mit.edu	37	6	29692199	29692199	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:29692199A>G	ENST00000376861.1	+	4	968	c.584A>G	c.(583-585)aAt>aGt	p.N195S	HLA-F_ENST00000334668.4_Missense_Mutation_p.N195S|HLA-F_ENST00000434407.2_Missense_Mutation_p.N195S|HLA-F_ENST00000440587.2_Missense_Mutation_p.N77S|HLA-F_ENST00000259951.7_Missense_Mutation_p.N195S			P30511	HLAF_HUMAN	major histocompatibility complex, class I, F	195	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)	p.N195S(1)		cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8						TACTTGGAGAATGGGAAGGAG	0.582																																					p.N195S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A584G	6						.						47.0	49.0	48.0					6																	29692199		1510	2706	4216	29800178	SO:0001583	missense	3134	exon3			AY253269	CCDS43437.1, CCDS43438.1, CCDS43439.1	6p21.3	2013-01-11			ENSG00000204642	ENSG00000204642		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4963	protein-coding gene	gene with protein product		143110				1688605	Standard	NM_018950		Approved		uc003nno.4	P30511	OTTHUMG00000031156	ENST00000376861.1:c.584A>G	6.37:g.29692199A>G	ENSP00000366057:p.Asn195Ser		29800178	NM_018950	Q5JQI8|Q5JQJ1|Q5SPT5|Q860R0|Q8MGQ1|Q8WLP5|Q95HC0|Q9TP68	Missense_Mutation	SNP	ENST00000376861.1	37	CCDS43438.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	15.26|15.26	2.780588|2.780588	0.49891|0.49891	.|.	.|.	ENSG00000204642|ENSG00000204642	ENST00000429294|ENST00000376861;ENST00000449921;ENST00000334668;ENST00000259951;ENST00000399258;ENST00000440587;ENST00000434407	.|T;T;T;T;T	.|0.00009	.|9.51;9.51;9.51;9.51;9.51	1.63|1.63	-3.26|-3.26	0.05064|0.05064	.|MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.|2.815270	.|0.01930	.|U	.|0.041154	T|T	0.00178|0.00178	0.0005|0.0005	H|H	0.98818|0.98818	4.34|4.34	0.19575|0.19575	N|N	0.999969|0.999969	.|D;P;P;P	.|0.71674	.|0.998;0.838;0.806;0.806	.|D;P;B;P	.|0.79784	.|0.993;0.57;0.434;0.796	T|T	0.50338|0.50338	-0.8840|-0.8840	5|10	.|0.87932	.|D	.|0	.|.	2.011|2.011	0.03488|0.03488	0.3183:0.0:0.2069:0.4748|0.3183:0.0:0.2069:0.4748	.|.	.|195;195;195;195	.|A8MVU7;P30511;P30511-3;P30511-2	.|.;HLAF_HUMAN;.;.	V|S	74|195;172;195;195;109;77;195	.|ENSP00000366057:N195S;ENSP00000334263:N195S;ENSP00000259951:N195S;ENSP00000404130:N77S;ENSP00000397376:N195S	.|ENSP00000259951:N195S	M|N	+|+	1|2	0|0	HLA-F|HLA-F	29800178|29800178	0.001000|0.001000	0.12720|0.12720	0.889000|0.889000	0.34880|0.34880	0.706000|0.706000	0.40770|0.40770	0.114000|0.114000	0.15520|0.15520	-0.758000|-0.758000	0.04690|0.04690	0.358000|0.358000	0.22013|0.22013	ATG|AAT		0.582	HLA-F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195083.1	NM_018950	
TRIM40	135644	broad.mit.edu	37	6	30115548	30115548	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:30115548G>A	ENST00000396581.1	+	6	1122	c.736G>A	c.(736-738)Gga>Aga	p.G246R	TRIM40_ENST00000307859.4_Missense_Mutation_p.G217R|TRIM40_ENST00000376724.2_Missense_Mutation_p.G246R			Q6P9F5	TRI40_HUMAN	tripartite motif containing 40	246					negative regulation of cell growth (GO:0030308)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein localization to nucleus (GO:1900181)|protein neddylation (GO:0045116)	IkappaB kinase complex (GO:0008385)	zinc ion binding (GO:0008270)	p.G217R(1)		ovary(1)	1						GTTGGAGAAAGGAGTCAGTGA	0.448																																					p.G217R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G649A	6						.						104.0	109.0	108.0					6																	30115548		2203	4300	6503	30223527	SO:0001583	missense	135644	exon5			AF489517	CCDS4675.1, CCDS69069.1	6p21.31	2013-01-09	2011-01-25		ENSG00000204614	ENSG00000204614		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	18736	protein-coding gene	gene with protein product			"""tripartite motif-containing 40"""				Standard	NM_138700		Approved	RNF35	uc003npm.2	Q6P9F5	OTTHUMG00000031083	ENST00000396581.1:c.736G>A	6.37:g.30115548G>A	ENSP00000379826:p.Gly246Arg		30223527	NM_138700	Q5SRJ6|Q5SS36|Q8TD96	Missense_Mutation	SNP	ENST00000396581.1	37		.	.	.	.	.	.	.	.	.	.	G	1.179	-0.638780	0.03557	.	.	ENSG00000204614	ENST00000396581;ENST00000376724;ENST00000307859	T;T;T	0.64803	0.01;0.01;-0.12	3.09	0.672	0.17935	.	1.873640	0.02730	N	0.115031	T	0.07458	0.0188	N	0.00538	-1.39	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.26395	-1.0104	10	0.06494	T	0.89	.	4.8752	0.13653	0.7277:0.0:0.2723:0.0	.	217;246	Q5SRJ6;Q6P9F5	.;TRI40_HUMAN	R	246;246;217	ENSP00000379826:G246R;ENSP00000365914:G246R;ENSP00000308310:G217R	ENSP00000308310:G217R	G	+	1	0	TRIM40	30223527	0.048000	0.20356	0.004000	0.12327	0.011000	0.07611	0.710000	0.25748	0.137000	0.18759	-1.216000	0.01612	GGA		0.448	TRIM40-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000076117.2		
TRIM15	89870	broad.mit.edu	37	6	30139754	30139754	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:30139754G>A	ENST00000376694.4	+	7	1495	c.1026G>A	c.(1024-1026)ccG>ccA	p.P342P	TRIM15_ENST00000376688.1_Intron	NM_033229.2	NP_150232.2	Q9C019	TRI15_HUMAN	tripartite motif containing 15	342	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				innate immune response (GO:0045087)|mesodermal cell fate determination (GO:0007500)|negative regulation of intracellular transport of viral material (GO:1901253)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of RIG-I signaling pathway (GO:1900246)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of type I interferon production (GO:0032481)	intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.P342P(1)		large_intestine(2)|lung(8)|prostate(2)|skin(1)|urinary_tract(1)	14						TGGGCTTCCCGGGCTTCTCCT	0.706																																					p.P342P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1026A	6						.						6.0	6.0	6.0					6																	30139754		1491	2660	4151	30247733	SO:0001819	synonymous_variant	89870	exon7			AF220132, U34249	CCDS4677.1	6p21.33	2013-01-09	2011-01-25		ENSG00000204610	ENSG00000204610		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16284	protein-coding gene	gene with protein product			"""zinc finger protein 178"", ""tripartite motif-containing 15"""	ZNF178		11331580, 8304341, 8812418	Standard	NM_033229		Approved	ZNFB7, RNF93	uc010jrx.3	Q9C019	OTTHUMG00000031031	ENST00000376694.4:c.1026G>A	6.37:g.30139754G>A			30247733	NM_033229	A2BEC9|O95604|Q8IUX9|Q9C018	Silent	SNP	ENST00000376694.4	37	CCDS4677.1																																																																																				0.706	TRIM15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076026.2	NM_033229	
TRIM39	56658	broad.mit.edu	37	6	30297398	30297398	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:30297398C>T	ENST00000396547.1	+	2	464	c.304C>T	c.(304-306)Cgg>Tgg	p.R102W	TRIM39_ENST00000376659.5_Missense_Mutation_p.R102W|TRIM39_ENST00000376656.4_Missense_Mutation_p.R102W|HCG18_ENST00000413358.2_RNA|TRIM39_ENST00000396551.3_Missense_Mutation_p.R102W|TRIM39_ENST00000540416.1_Missense_Mutation_p.R102W|TRIM39-RPP21_ENST00000513556.1_Missense_Mutation_p.R14W|HCG18_ENST00000426882.1_RNA|TRIM39_ENST00000396548.1_Missense_Mutation_p.R102W|HCG18_ENST00000412685.2_RNA			Q9HCM9	TRI39_HUMAN	tripartite motif containing 39	102					apoptotic process (GO:0006915)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|positive regulation of apoptotic signaling pathway (GO:2001235)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.R102W(1)		ovary(3)	3						GCGGAAGATCCGGGATGAGAG	0.552																																					p.R102W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C304T	6						.						53.0	51.0	52.0					6																	30297398		1510	2707	4217	30405377	SO:0001583	missense	56658	exon1			BC034985	CCDS34377.1, CCDS34378.1	6p22.1	2013-01-09	2011-01-25	2002-06-07	ENSG00000204599	ENSG00000204599		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10065	protein-coding gene	gene with protein product		605700	"""ring finger protein 23"", ""tripartite motif-containing 39"""	RNF23		11006080	Standard	NM_021253		Approved			Q9HCM9	OTTHUMG00000031066	ENST00000396547.1:c.304C>T	6.37:g.30297398C>T	ENSP00000379796:p.Arg102Trp		30405377	NM_001199119	Q5STG3|Q5STG4|Q76BL3|Q8IYT9|Q96IB6	Missense_Mutation	SNP	ENST00000396547.1	37	CCDS34377.1	.	.	.	.	.	.	.	.	.	.	C	17.15	3.315565	0.60524	.	.	ENSG00000204599;ENSG00000204599;ENSG00000204599;ENSG00000204599;ENSG00000204599;ENSG00000204599;ENSG00000204599;ENSG00000204599;ENSG00000204599;ENSG00000204599;ENSG00000204599;ENSG00000248167	ENST00000458516;ENST00000396551;ENST00000376656;ENST00000545104;ENST00000540416;ENST00000449040;ENST00000412529;ENST00000428728;ENST00000396548;ENST00000376659;ENST00000396547;ENST00000513556	T;T;T;T;T;T;T;T;T	0.57752	0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38	5.23	1.37	0.22104	Zinc finger, B-box (2);	0.000000	0.43260	D	0.000582	T	0.28962	0.0719	N	0.08118	0	0.09310	N	1	B;D;P	0.89917	0.005;1.0;0.902	B;D;B	0.74348	0.002;0.983;0.118	T	0.14924	-1.0455	10	0.72032	D	0.01	.	5.3433	0.15996	0.2917:0.5506:0.0:0.1577	.	16;102;102	F5H2V3;Q9HCM9;Q9HCM9-2	.;TRI39_HUMAN;.	W	102;102;102;102;102;102;16;102;102;102;102;14	ENSP00000405928:R102W;ENSP00000379800:R102W;ENSP00000365844:R102W;ENSP00000439400:R102W;ENSP00000406019:R102W;ENSP00000379797:R102W;ENSP00000365847:R102W;ENSP00000379796:R102W;ENSP00000424048:R14W	ENSP00000365844:R102W	R	+	1	2	TRIM39-RPP21;TRIM39	30405377	1.000000	0.71417	0.735000	0.30896	0.933000	0.57130	1.011000	0.29911	0.055000	0.16094	0.555000	0.69702	CGG		0.552	TRIM39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076086.2	NM_172016	
C6orf15	29113	broad.mit.edu	37	6	31079267	31079267	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:31079267delG	ENST00000259870.3	-	2	872	c.869delC	c.(868-870)ccafs	p.P290fs		NM_014070.2	NP_054789.2	Q6UXA7	CF015_HUMAN	chromosome 6 open reading frame 15	290	Pro-rich.				extracellular matrix organization (GO:0030198)	interstitial matrix (GO:0005614)	heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)	p.P290fs*>36(1)		endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|stomach(1)	17						ATTGATACCTGGGTATAGATG	0.532																																					p.P290fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.869delC	6						.						56.0	58.0	57.0					6																	31079267		1779	3528	5307	31187246	SO:0001589	frameshift_variant	29113	exon2			AB031481	CCDS4693.1	6p21	2011-12-12			ENSG00000204542	ENSG00000204542			13927	protein-coding gene	gene with protein product		611401					Standard	NM_014070		Approved	STG	uc003nsk.1	Q6UXA7	OTTHUMG00000031111	ENST00000259870.3:c.869delC	6.37:g.31079267delG	ENSP00000259870:p.Pro290fs		31187246	NM_014070	B0S7V8|Q0EFA6|Q2L6G7|Q5SQ81|Q86Z05|Q9UIG3	Frame_Shift_Del	DEL	ENST00000259870.3	37	CCDS4693.1																																																																																				0.532	C6orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076184.2	NM_014070	
POU5F1	5460	broad.mit.edu	37	6	31138323	31138323	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:31138323C>T	ENST00000259915.8	-	1	147	c.75G>A	c.(73-75)ccG>ccA	p.P25P	POU5F1_ENST00000441888.3_Intron	NM_002701.4	NP_002692.2	Q01860	PO5F1_HUMAN	POU class 5 homeobox 1	25					anatomical structure morphogenesis (GO:0009653)|blastocyst development (GO:0001824)|BMP signaling pathway involved in heart induction (GO:0003130)|cardiac cell fate determination (GO:0060913)|cell fate commitment involved in formation of primary germ layer (GO:0060795)|endodermal cell fate specification (GO:0001714)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of gene silencing by miRNA (GO:0060965)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of asymmetric cell division (GO:0009786)|regulation of gene expression (GO:0010468)|regulation of heart induction by regulation of canonical Wnt signaling pathway (GO:0090081)|regulation of methylation-dependent chromatin silencing (GO:0090308)|regulation of transcription, DNA-templated (GO:0006355)|response to wounding (GO:0009611)|somatic stem cell maintenance (GO:0035019)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)	p.P25P(1)	EWSR1/POU5F1(10)	breast(1)|large_intestine(2)|lung(3)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	13					Dopamine(DB00988)|Norepinephrine(DB00368)	AGCCCGGCTCCGGCCCCCCTG	0.701			T	EWSR1	sarcoma																																p.P25P			Dom	yes		6	6p21.31	5460	"""POU domain, class 5, transcription factor 1"""		M	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G75A	6						.						4.0	4.0	4.0					6																	31138323		1369	2486	3855	31246302	SO:0001819	synonymous_variant	5460	exon1			Z11898	CCDS34391.1, CCDS47398.1, CCDS47398.2, CCDS75420.1	6p21.33	2011-06-20	2007-07-13		ENSG00000204531	ENSG00000204531		"""Homeoboxes / POU class"""	9221	protein-coding gene	gene with protein product		164177	"""POU domain class 5, transcription factor 1"""	OTF3		1408763	Standard	NM_002701		Approved	OCT3, Oct4, MGC22487	uc003nsv.3	Q01860	OTTHUMG00000031206	ENST00000259915.8:c.75G>A	6.37:g.31138323C>T			31246302	NM_002701	A6NCS1|A6NLL8|D2IYK4|P31359|Q15167|Q15168|Q16422|Q5STF3|Q5STF4	Silent	SNP	ENST00000259915.8	37	CCDS34391.1																																																																																				0.701	POU5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076413.4	NM_002701	
TNXB	7148	broad.mit.edu	37	6	32017322	32017322	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:32017322G>A	ENST00000375244.3	-	28	9683	c.9482C>T	c.(9481-9483)cCg>cTg	p.P3161L	TNXB_ENST00000375247.2_Missense_Mutation_p.P3159L			P22105	TENX_HUMAN	tenascin XB	3206	Fibronectin type-III 23. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)	p.P3226L(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						AGGGGCCTCCGGGGCCTCAGT	0.657																																					p.P3159L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C9476T	6						.						38.0	42.0	41.0					6																	32017322		1158	2496	3654	32125300	SO:0001583	missense	7148	exon28			X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.9482C>T	6.37:g.32017322G>A	ENSP00000364393:p.Pro3161Leu		32125300	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		.	.	.	.	.	.	.	.	.	.	G	14.06	2.421733	0.43020	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.59638	0.42;0.25	3.87	3.87	0.44632	.	0.000000	0.46758	D	0.000279	T	0.62454	0.2429	M	0.69823	2.125	0.32882	D	0.510649	D	0.71674	0.998	D	0.64321	0.924	T	0.66606	-0.5881	10	0.72032	D	0.01	.	11.246	0.48998	0.0:0.0:1.0:0.0	.	3159	P22105-3	.	L	3161;3159	ENSP00000364393:P3161L;ENSP00000364396:P3159L	ENSP00000364393:P3161L	P	-	2	0	TNXB	32125300	0.988000	0.35896	0.992000	0.48379	0.080000	0.17528	3.815000	0.55651	2.006000	0.58801	0.306000	0.20318	CCG		0.657	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
TAP2	6891	broad.mit.edu	37	6	32798079	32798079	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:32798079T>C	ENST00000452392.2	-	9	1773	c.1600A>G	c.(1600-1602)Atc>Gtc	p.I534V	TAP2_ENST00000485701.1_5'Flank|TAP2_ENST00000374899.4_Missense_Mutation_p.I534V|TAP2_ENST00000374897.2_Missense_Mutation_p.I534V			Q9UDX4	S14L3_HUMAN	transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)	0						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)	p.I534V(1)								Vitamin E(DB00163)	TACTGTGAGATGGGCTTTTCA	0.587																																					p.I534V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1600G	6						.						142.0	133.0	136.0					6																	32798079		1511	2708	4219	32906057	SO:0001583	missense	6891	exon9			M74447	CCDS4755.1	6p21.3	2014-09-17			ENSG00000204267	ENSG00000204267		"""ATP binding cassette transporters / subfamily B"""	44	protein-coding gene	gene with protein product		170261		ABCB3		1529427, 1946428, 16395595	Standard	NM_001290043		Approved	PSF2, RING11, D6S217E	uc003ocd.3	Q03519	OTTHUMG00000031068	ENST00000452392.2:c.1600A>G	6.37:g.32798079T>C	ENSP00000391806:p.Ile534Val		32906057	NM_018833	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Missense_Mutation	SNP	ENST00000452392.2	37		.	.	.	.	.	.	.	.	.	.	T	1.513	-0.549048	0.04024	.	.	ENSG00000204267;ENSG00000204267;ENSG00000204267;ENSG00000250264	ENST00000556934;ENST00000374899;ENST00000374897;ENST00000452392	D;D;D	0.93953	-3.32;-3.32;-3.32	5.4	-10.8	0.00216	ATPase, AAA+ type, core (1);ABC transporter-like (2);	1.303810	0.05563	N	0.569658	T	0.70894	0.3276	N	0.24115	0.695	0.19775	N	0.999958	B;B;B;B	0.20368	0.044;0.001;0.001;0.001	B;B;B;B	0.22601	0.04;0.017;0.017;0.017	T	0.66779	-0.5837	9	0.33940	T	0.23	-30.6347	10.7598	0.46258	0.06:0.2799:0.5106:0.1495	.	534;535;534;534	E7ENX8;Q59H06;Q03519;Q9UP03	.;.;TAP2_HUMAN;.	V	534	ENSP00000364034:I534V;ENSP00000364032:I534V;ENSP00000391806:I534V	ENSP00000364032:I534V	I	-	1	0	XXbac-BPG246D15.9;TAP2	32906057	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-6.126000	0.00079	-5.162000	0.00020	-2.063000	0.00397	ATC		0.587	TAP2-001	NOVEL	mRNA_end_NF|cds_end_NF|basic|appris_principal|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000361828.1	NM_000544	
PSMB9	5698	broad.mit.edu	37	6	32825078	32825078	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:32825078C>T	ENST00000374859.2	+	3	236	c.167C>T	c.(166-168)cCg>cTg	p.P56L	PSMB9_ENST00000395330.1_Missense_Mutation_p.P33L|PSMB9_ENST00000453265.2_Intron	NM_002800.4	NP_002791.1	P28065	PSB9_HUMAN	proteasome (prosome, macropain) subunit, beta type, 9	56					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|spermatoproteasome complex (GO:1990111)	threonine-type endopeptidase activity (GO:0004298)	p.P56L(1)		large_intestine(4)|lung(4)|skin(1)	9					Carfilzomib(DB08889)	AAGCTGTCCCCGCTGCACGAG	0.522																																					p.P56L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C167T	6						.						116.0	106.0	110.0					6																	32825078		1511	2708	4219	32933056	SO:0001583	missense	5698	exon3				CCDS4759.1	6p21.3	2013-03-27	2013-03-27		ENSG00000240065	ENSG00000240065		"""Proteasome (prosome, macropain) subunits"""	9546	protein-coding gene	gene with protein product		177045	"""proteasome (prosome, macropain) subunit, beta type, 9 (large multifunctional protease 2)"", ""large multifunctional peptidase 2"""	LMP2		1922385, 1529427	Standard	NM_002800		Approved	RING12, beta1i, PSMB6i	uc003sga.3	P28065	OTTHUMG00000031287	ENST00000374859.2:c.167C>T	6.37:g.32825078C>T	ENSP00000363993:p.Pro56Leu		32933056	NM_002800	B0V0T1|Q16523|Q5JNW4	Missense_Mutation	SNP	ENST00000374859.2	37	CCDS4759.1	.	.	.	.	.	.	.	.	.	.	C	13.21	2.168793	0.38315	.	.	ENSG00000240065	ENST00000395330;ENST00000414474;ENST00000374859	T;T;T	0.21932	1.98;1.98;1.98	5.57	4.65	0.58169	Proteasome, beta-type subunit, conserved site (1);	0.111770	0.64402	D	0.000008	T	0.12178	0.0296	L	0.55481	1.735	0.80722	D	1	B	0.27971	0.196	B	0.29176	0.099	T	0.02533	-1.1145	10	0.35671	T	0.21	-23.6606	13.6202	0.62132	0.0:0.8433:0.1567:0.0	.	56	P28065	PSB9_HUMAN	L	33;33;56	ENSP00000378739:P33L;ENSP00000394363:P33L;ENSP00000363993:P56L	ENSP00000363993:P56L	P	+	2	0	PSMB9	32933056	0.999000	0.42202	0.848000	0.33437	0.572000	0.35998	4.858000	0.62947	2.622000	0.88805	0.637000	0.83480	CCG		0.522	PSMB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076624.5	NM_002800	
VPS52	6293	broad.mit.edu	37	6	33218698	33218698	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:33218698G>A	ENST00000445902.2	-	20	2310	c.2092C>T	c.(2092-2094)Cga>Tga	p.R698*	HCG25_ENST00000450514.1_RNA|HCG25_ENST00000422366.1_RNA|VPS52_ENST00000482399.1_3'UTR|HCG25_ENST00000427196.1_RNA|VPS52_ENST00000478934.1_5'UTR|HCG25_ENST00000442228.1_RNA|VPS52_ENST00000436044.2_Nonsense_Mutation_p.R573*	NM_022553.4	NP_072047.4	Q8N1B4	VPS52_HUMAN	vacuolar protein sorting 52 homolog (S. cerevisiae)	698					ectodermal cell differentiation (GO:0010668)|embryonic ectodermal digestive tract development (GO:0048611)|protein transport (GO:0015031)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)		p.R698*(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(8)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	28						GGGAGGGCTCGGAGCTGCGGC	0.572																																					p.R698X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2092T	6						.						85.0	82.0	83.0					6																	33218698		1510	2708	4218	33326676	SO:0001587	stop_gained	6293	exon20			AJ223319	CCDS4770.2	6p21.3	2010-02-17	2006-12-19	2003-09-05	ENSG00000223501	ENSG00000223501			10518	protein-coding gene	gene with protein product		603443	"""SAC2 suppressor of actin mutations 2-like (yeast)"", ""vacuolar protein sorting 52 (yeast)"""	SACM2L		9790748	Standard	NM_022553		Approved	ARE1	uc003odm.1	Q8N1B4	OTTHUMG00000031276	ENST00000445902.2:c.2092C>T	6.37:g.33218698G>A	ENSP00000409952:p.Arg698*		33326676	NM_022553	A2BF38|B0UZZ4|B4DNI9|Q53GR4|Q5JPA0|Q5SQW1|Q8IUN6|Q9NPT5	Nonsense_Mutation	SNP	ENST00000445902.2	37	CCDS4770.2	.	.	.	.	.	.	.	.	.	.	G	41	8.647580	0.98899	.	.	ENSG00000223501	ENST00000445902;ENST00000418054;ENST00000436044	.	.	.	4.82	4.82	0.62117	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	-7.4444	11.2767	0.49172	0.0:0.0:0.817:0.183	.	.	.	.	X	698;676;573	.	ENSP00000414785:R676X	R	-	1	2	VPS52	33326676	1.000000	0.71417	0.997000	0.53966	0.926000	0.56050	4.192000	0.58378	2.612000	0.88384	0.551000	0.68910	CGA		0.572	VPS52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076598.2	NM_022553	
PPARD	5467	broad.mit.edu	37	6	35393613	35393613	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:35393613G>A	ENST00000311565.4	+	9	1432	c.1083G>A	c.(1081-1083)cgG>cgA	p.R361R	PPARD_ENST00000540939.1_Silent_p.R258R|PPARD_ENST00000448077.2_Silent_p.R322R|PPARD_ENST00000418635.2_Silent_p.R263R|PPARD_ENST00000360694.3_Silent_p.R361R	NM_001171818.1	NP_001165289.1	Q03181	PPARD_HUMAN	peroxisome proliferator-activated receptor delta	361	Ligand-binding.				adipose tissue development (GO:0060612)|anagen (GO:0042640)|apoptotic signaling pathway (GO:0097190)|axon ensheathment (GO:0008366)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cell-substrate adhesion (GO:0031589)|cellular response to hypoxia (GO:0071456)|cholesterol metabolic process (GO:0008203)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|fatty acid beta-oxidation (GO:0006635)|fatty acid catabolic process (GO:0009062)|fatty acid transport (GO:0015908)|gene expression (GO:0010467)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|heart development (GO:0007507)|intracellular receptor signaling pathway (GO:0030522)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)|lipid metabolic process (GO:0006629)|mRNA transcription (GO:0009299)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of inflammatory response (GO:0050728)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|phospholipid biosynthetic process (GO:0008654)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epidermis development (GO:0045684)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of insulin secretion (GO:0032024)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasodilation (GO:0045909)|proteoglycan metabolic process (GO:0006029)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to activity (GO:0014823)|response to glucose (GO:0009749)|response to vitamin A (GO:0033189)|transcription initiation from RNA polymerase II promoter (GO:0006367)|vitamin A metabolic process (GO:0006776)|wound healing (GO:0042060)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|drug binding (GO:0008144)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|linoleic acid binding (GO:0070539)|lipid binding (GO:0008289)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.R361R(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|large_intestine(4)|liver(2)|lung(9)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23					Bezafibrate(DB01393)|Icosapent(DB00159)|Sulindac(DB00605)|Treprostinil(DB00374)	CCACAGACCGGCCAGGCCTCA	0.647																																					p.R361R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1083A	6						.						87.0	79.0	82.0					6																	35393613		2203	4300	6503	35501591	SO:0001819	synonymous_variant	5467	exon9			L07592	CCDS4803.1, CCDS4804.1, CCDS54994.1, CCDS54995.1	6p21.2	2013-01-16	2006-10-17		ENSG00000112033	ENSG00000112033		"""Nuclear hormone receptors"""	9235	protein-coding gene	gene with protein product		600409	"""peroxisome proliferative activated receptor, delta"""			1333051	Standard	NM_177435		Approved	NUC1, NUCII, FAAR, NR1C2	uc003okm.3	Q03181	OTTHUMG00000014567	ENST00000311565.4:c.1083G>A	6.37:g.35393613G>A			35501591	NM_001171818	A8K6J6|B4E3V3|B6ZGS1|B7Z3W1|E9PE18|Q5D1P0|Q7Z5K0|Q9BUD4	Silent	SNP	ENST00000311565.4	37	CCDS4803.1																																																																																				0.647	PPARD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040288.1	NM_006238	
ZFAND3	60685	broad.mit.edu	37	6	38029400	38029400	+	Silent	SNP	C	C	T	rs567905352		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:38029400C>T	ENST00000287218.4	+	3	591	c.144C>T	c.(142-144)tcC>tcT	p.S48S	ZFAND3_ENST00000373391.2_Silent_p.S48S	NM_021943.2	NP_068762.1	Q9H8U3	ZFAN3_HUMAN	zinc finger, AN1-type domain 3	48							DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.S48S(1)		endometrium(2)|large_intestine(4)|lung(2)|ovary(1)	9						ACGATGATTCCGCTCCAAGTA	0.413													C|||	1	0.000199681	0.0	0.0	5008	,	,		19413	0.0		0.0	False		,,,				2504	0.001				p.S48S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C144T	6						.						104.0	99.0	101.0					6																	38029400		2203	4300	6503	38137378	SO:0001819	synonymous_variant	60685	exon3			AK023284	CCDS4836.1	6p21.2	2013-09-19	2005-12-15	2005-12-15	ENSG00000156639	ENSG00000156639		"""Zinc fingers, AN1-type domain containing"""	18019	protein-coding gene	gene with protein product		607455	"""testis expressed sequence 27"""	TEX27			Standard	NM_021943		Approved	FLJ13222	uc003onx.3	Q9H8U3	OTTHUMG00000014629	ENST00000287218.4:c.144C>T	6.37:g.38029400C>T			38137378	NM_021943	Q5SZZ0|Q5SZZ1	Silent	SNP	ENST00000287218.4	37	CCDS4836.1	.	.	.	.	.	.	.	.	.	.	C	9.959	1.222408	0.22457	.	.	ENSG00000156639	ENST00000373389	.	.	.	5.56	1.81	0.25067	.	.	.	.	.	T	0.39226	0.1070	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.23833	-1.0177	4	.	.	.	-6.967	6.4276	0.21778	0.1156:0.5682:0.0:0.3162	.	.	.	.	C	25	.	.	R	+	1	0	ZFAND3	38137378	0.001000	0.12720	0.976000	0.42696	0.997000	0.91878	-0.368000	0.07543	0.402000	0.25451	0.563000	0.77884	CGC		0.413	ZFAND3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040424.3	NM_021943	
GLP1R	2740	broad.mit.edu	37	6	39024237	39024237	+	Missense_Mutation	SNP	G	G	A	rs150253529	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:39024237G>A	ENST00000373256.4	+	2	186	c.143G>A	c.(142-144)cGc>cAc	p.R48H		NM_002062.3	NP_002053.3	P43220	GLP1R_HUMAN	glucagon-like peptide 1 receptor	48					activation of adenylate cyclase activity (GO:0007190)|cAMP-mediated signaling (GO:0019933)|energy reserve metabolic process (GO:0006112)|learning or memory (GO:0007611)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of heart contraction (GO:0008016)|regulation of insulin secretion (GO:0050796)|response to stress (GO:0006950)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glucagon receptor activity (GO:0004967)|transmembrane signaling receptor activity (GO:0004888)	p.R48H(1)		breast(5)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	31					Exenatide(DB01276)|Glucagon recombinant(DB00040)|Liraglutide(DB06655)	CAGTGCCAGCGCTCCCTGACT	0.597													G|||	3	0.000599042	0.0015	0.0014	5008	,	,		15670	0.0		0.0	False		,,,				2504	0.0				p.R48H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G143A	6						.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	67.0	57.0	60.0		143	-0.1	0.9	6	dbSNP_134	60	0,8600		0,0,4300	no	missense	GLP1R	NM_002062.3	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	48/464	39024237	1,13005	2203	4300	6503	39132215	SO:0001583	missense	2740	exon2				CCDS4839.1	6p21	2012-08-10			ENSG00000112164	ENSG00000112164		"""GPCR / Class B : Glucagon receptors"""	4324	protein-coding gene	gene with protein product		138032					Standard	NM_002062		Approved		uc003ooj.4	P43220	OTTHUMG00000014638	ENST00000373256.4:c.143G>A	6.37:g.39024237G>A	ENSP00000362353:p.Arg48His		39132215	NM_002062	Q2M229|Q99669	Missense_Mutation	SNP	ENST00000373256.4	37	CCDS4839.1	.	.	.	.	.	.	.	.	.	.	G	7.644	0.681430	0.14907	2.27E-4	0.0	ENSG00000112164	ENST00000373256	T	0.54071	0.59	5.53	-0.0514	0.13827	GPCR, family 2, extracellular hormone receptor domain (1);	0.667290	0.14086	N	0.342378	T	0.11580	0.0282	N	0.25890	0.77	0.09310	N	0.999999	B	0.06786	0.001	B	0.04013	0.001	T	0.29397	-1.0013	10	0.15066	T	0.55	.	3.3445	0.07131	0.295:0.0:0.4126:0.2924	.	48	P43220	GLP1R_HUMAN	H	48	ENSP00000362353:R48H	ENSP00000362353:R48H	R	+	2	0	GLP1R	39132215	0.014000	0.17966	0.918000	0.36340	0.347000	0.29111	-0.050000	0.11904	-0.078000	0.12730	-0.182000	0.12963	CGC		0.597	GLP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040443.1		
LRFN2	57497	broad.mit.edu	37	6	40399677	40399677	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:40399677delG	ENST00000338305.6	-	2	1718	c.1176delC	c.(1174-1176)cccfs	p.P392fs		NM_020737.1	NP_065788.1	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III domain containing 2	392						cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)		p.K393fs*39(1)|p.P392P(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	58	Ovarian(28;0.0418)|Colorectal(47;0.196)					GGCGGGACTTGGGGGGTGCAG	0.672																																					p.P392fs												.	.	2	Deletion - Frameshift(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	c.1176delC	6						.						48.0	46.0	47.0					6																	40399677		2202	4300	6502	40507655	SO:0001589	frameshift_variant	57497	exon2			AB033072	CCDS34443.1	6p21.2-p21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000156564	ENSG00000156564		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	21226	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 2"""	612808	"""KIAA1246"""	KIAA1246, SALM1		16495444, 16828986	Standard	NM_020737		Approved	FIGLER2	uc003oph.1	Q9ULH4	OTTHUMG00000014662	ENST00000338305.6:c.1176delC	6.37:g.40399677delG	ENSP00000345985:p.Pro392fs		40507655	NM_020737	A5PKU3|Q5SYP9	Frame_Shift_Del	DEL	ENST00000338305.6	37	CCDS34443.1																																																																																				0.672	LRFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040488.1	XM_166372	
PRICKLE4	29964	broad.mit.edu	37	6	41754789	41754789	+	Silent	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:41754789T>C	ENST00000394260.1	+	5	957	c.957T>C	c.(955-957)ctT>ctC	p.L319L	PRICKLE4_ENST00000458694.1_Silent_p.L359L|TOMM6_ENST00000398884.3_5'Flank|TOMM6_ENST00000398881.3_5'Flank|PRICKLE4_ENST00000394263.1_Silent_p.L359L			Q2TBC4	PRIC4_HUMAN	prickle homolog 4 (Drosophila)	319						nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.L359L(2)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	13	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			GCGAGCGCCTTCCCCAGTCCT	0.592											OREG0017435	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L359L												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T1077C	6						.						80.0	94.0	89.0					6																	41754789		2203	4300	6503	41862767	SO:0001819	synonymous_variant	29964	exon8			AF216754	CCDS34449.1	6p21.1	2010-08-05	2007-09-18	2007-09-18	ENSG00000124593	ENSG00000124593			16805	protein-coding gene	gene with protein product		611389	"""chromosome 6 open reading frame 49"""	C6orf49		15702247	Standard	NM_013397		Approved	OEBT, DKFZp761H221	uc011duf.1	Q2TBC4	OTTHUMG00000014685	ENST00000394260.1:c.957T>C	6.37:g.41754789T>C		903	41862767	NM_013397	A2A3M0|A6PVU1|B3KQ15|Q5T3D4|Q9NSV1	Silent	SNP	ENST00000394260.1	37																																																																																					0.592	PRICKLE4-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000303948.1	NM_013397	
SLC22A7	10864	broad.mit.edu	37	6	43269339	43269339	+	Missense_Mutation	SNP	G	G	A	rs202177785		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:43269339G>A	ENST00000372585.5	+	7	1065	c.970G>A	c.(970-972)Gcc>Acc	p.A324T	SLC22A7_ENST00000372589.3_Missense_Mutation_p.A322T|SLC22A7_ENST00000487175.1_3'UTR|SLC22A7_ENST00000372574.3_Missense_Mutation_p.A322T	NM_153320.2	NP_696961.2	Q9Y694	S22A7_HUMAN	solute carrier family 22 (organic anion transporter), member 7	324					organic anion transport (GO:0015711)|response to stilbenoid (GO:0035634)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)	p.A324T(1)		NS(2)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(3)	26			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)		Acetylsalicylic acid(DB00945)|Allopurinol(DB00437)|Aminohippurate(DB00345)|Bumetanide(DB00887)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Cimetidine(DB00501)|Clarithromycin(DB01211)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Docetaxel(DB01248)|Enalapril(DB00584)|Erythromycin(DB00199)|Fluorouracil(DB00544)|Ganciclovir(DB01004)|Glyburide(DB01016)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Methotrexate(DB00563)|Minocycline(DB01017)|Oxtriphylline(DB01303)|Oxytetracycline(DB00595)|Pravastatin(DB00175)|Probenecid(DB01032)|Rifampicin(DB01045)|Salicylic acid(DB00936)|Testosterone(DB00624)|Tetracycline(DB00759)|Theophylline(DB00277)|Valproic Acid(DB00313)|Zalcitabine(DB00943)|Zidovudine(DB00495)	CAAAGTGGCCGCCGGGGAACG	0.587																																					p.A322T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G964A	6						.	G	THR/ALA,THR/ALA	0,4406		0,0,2203	68.0	54.0	59.0		964,970	3.8	0.0	6		59	1,8599		0,1,4299	no	missense,missense	SLC22A7	NM_006672.3,NM_153320.2	58,58	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	322/547,324/549	43269339	1,13005	2203	4300	6503	43377317	SO:0001583	missense	10864	exon6			AF097518	CCDS4892.1, CCDS4893.2	6p21.1	2013-05-22			ENSG00000137204	ENSG00000137204		"""Solute carriers"""	10971	protein-coding gene	gene with protein product		604995				9650585, 10773670	Standard	XM_006714970		Approved	NLT, OAT2	uc003out.3	Q9Y694	OTTHUMG00000014726	ENST00000372585.5:c.970G>A	6.37:g.43269339G>A	ENSP00000361666:p.Ala324Thr		43377317	NM_006672	B2CZX6|Q5T046|Q5T048|Q5T050|Q9H2W5	Missense_Mutation	SNP	ENST00000372585.5	37	CCDS4893.2	.	.	.	.	.	.	.	.	.	.	G	6.097	0.386154	0.11524	0.0	1.16E-4	ENSG00000137204	ENST00000372589;ENST00000372585;ENST00000372574;ENST00000436107	T;T;T;T	0.59638	0.25;0.25;0.25;0.25	5.56	3.76	0.43208	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.141460	0.06628	N	0.758635	T	0.12987	0.0315	N	0.03608	-0.345	0.19575	N	0.999967	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.002;0.001;0.002	T	0.26815	-1.0092	10	0.13470	T	0.59	.	9.0902	0.36605	0.1761:0.0:0.8239:0.0	.	324;322;322	Q9Y694;Q9Y694-2;Q9Y694-3	S22A7_HUMAN;.;.	T	322;324;322;17	ENSP00000361670:A322T;ENSP00000361666:A324T;ENSP00000361655:A322T;ENSP00000393836:A17T	ENSP00000361655:A322T	A	+	1	0	SLC22A7	43377317	0.001000	0.12720	0.001000	0.08648	0.056000	0.15407	0.760000	0.26475	0.693000	0.31634	0.462000	0.41574	GCC		0.587	SLC22A7-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040588.1		
CAPN11	11131	broad.mit.edu	37	6	44144729	44144729	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:44144729C>A	ENST00000398776.1	+	11	1269	c.1231C>A	c.(1231-1233)Cac>Aac	p.H411N	CAPN11_ENST00000542245.1_Missense_Mutation_p.H411N	NM_007058.3	NP_008989.2	Q9UMQ6	CAN11_HUMAN	calpain 11	411	Domain III.				proteolysis (GO:0006508)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|peptidase activity (GO:0008233)	p.H411N(1)		breast(3)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	36	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CTGCAGGAACCACCCTGGTGG	0.652																																					p.H411N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1231A	6						.						61.0	68.0	65.0					6																	44144729		2178	4283	6461	44252707	SO:0001583	missense	11131	exon11			AJ242832	CCDS47436.1	6p12	2013-01-10			ENSG00000137225	ENSG00000137225		"""EF-hand domain containing"""	1478	protein-coding gene	gene with protein product		604822				10409436	Standard	NM_007058		Approved		uc003owt.1	Q9UMQ6	OTTHUMG00000014758	ENST00000398776.1:c.1231C>A	6.37:g.44144729C>A	ENSP00000381758:p.His411Asn		44252707	NM_007058	B2RA64|Q5T3G1|Q8N4R5	Missense_Mutation	SNP	ENST00000398776.1	37	CCDS47436.1	.	.	.	.	.	.	.	.	.	.	C	8.837	0.941213	0.18281	.	.	ENSG00000137225	ENST00000398776;ENST00000542245	D;D	0.86956	-2.19;-2.19	4.38	-8.76	0.00830	Peptidase C2, calpain, large subunit, domain III (2);Peptidase C2, calpain, domain III (1);	1.269220	0.05568	N	0.570620	T	0.55909	0.1950	L	0.28458	0.855	0.09310	N	0.999997	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.49862	-0.8894	10	0.35671	T	0.21	.	6.2626	0.20910	0.4216:0.1905:0.0:0.3879	.	65;411	B4DT90;Q9UMQ6	.;CAN11_HUMAN	N	411	ENSP00000381758:H411N;ENSP00000441078:H411N	ENSP00000381758:H411N	H	+	1	0	CAPN11	44252707	0.000000	0.05858	0.171000	0.22900	0.828000	0.46876	-3.304000	0.00519	-2.207000	0.00740	0.561000	0.74099	CAC		0.652	CAPN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040714.3		
SLC35B2	347734	broad.mit.edu	37	6	44223046	44223046	+	Silent	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:44223046C>A	ENST00000393812.3	-	4	839	c.696G>T	c.(694-696)cgG>cgT	p.R232R	MIR4647_ENST00000583964.1_RNA|SLC35B2_ENST00000537814.1_Silent_p.R99R|SLC35B2_ENST00000393810.1_3'UTR|SLC35B2_ENST00000495706.1_5'UTR|SLC35B2_ENST00000538577.1_Silent_p.R139R	NM_178148.2	NP_835361.1	Q8TB61	S35B2_HUMAN	solute carrier family 35 (adenosine 3'-phospho 5'-phosphosulfate transporter), member B2	232					3'-phospho-5'-adenylyl sulfate transmembrane transport (GO:1902559)|3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|3'-phosphoadenosine 5'-phosphosulfate transport (GO:0046963)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate transmembrane transporter activity (GO:0046964)|signal transducer activity (GO:0004871)	p.R232R(1)		breast(1)|central_nervous_system(2)|kidney(3)|large_intestine(2)|lung(4)|ovary(2)|urinary_tract(1)	15	all_cancers(18;2e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CGTAGCTGCGCCGAGACACAA	0.582																																					p.R232R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G696T	6						.						85.0	83.0	83.0					6																	44223046		2203	4300	6503	44331024	SO:0001819	synonymous_variant	347734	exon4			AK075456	CCDS34462.1, CCDS69127.1, CCDS75462.1, CCDS75463.1	6p12.1-p11.21	2013-07-17	2013-07-17		ENSG00000157593	ENSG00000157593		"""Solute carriers"""	16872	protein-coding gene	gene with protein product		610788	"""solute carrier family 35, member B2"""				Standard	NM_001286517		Approved	UGTrel4	uc003oxd.3	Q8TB61	OTTHUMG00000014760	ENST00000393812.3:c.696G>T	6.37:g.44223046C>A			44331024	NM_178148	B4DDU9|F5H7Y9|Q2VY06|Q53GA3|Q5T9W1|Q5T9W2|Q7Z2G3|Q8NBK6|Q96AR6	Silent	SNP	ENST00000393812.3	37	CCDS34462.1																																																																																				0.582	SLC35B2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040724.2		
GCLC	2729	broad.mit.edu	37	6	53374047	53374047	+	Splice_Site	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:53374047A>G	ENST00000229416.6	-	7	1238	c.755T>C	c.(754-756)gTg>gCg	p.V252A	RP1-27K12.4_ENST00000508884.1_RNA	NM_001197115.1|NM_001498.3	NP_001184044.1|NP_001489.1	P48506	GSH1_HUMAN	glutamate-cysteine ligase, catalytic subunit	252					apoptotic mitochondrial changes (GO:0008637)|cell redox homeostasis (GO:0045454)|cellular nitrogen compound metabolic process (GO:0034641)|cysteine metabolic process (GO:0006534)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|L-ascorbic acid metabolic process (GO:0019852)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|regulation of blood vessel size (GO:0050880)|regulation of mitochondrial depolarization (GO:0051900)|response to arsenic-containing substance (GO:0046685)|response to heat (GO:0009408)|response to hormone (GO:0009725)|response to nitrosative stress (GO:0051409)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|glutamate-cysteine ligase complex (GO:0017109)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|coenzyme binding (GO:0050662)|glutamate binding (GO:0016595)|glutamate-cysteine ligase activity (GO:0004357)|magnesium ion binding (GO:0000287)	p.V252A(1)		breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22	Lung NSC(77;0.0137)				L-Cysteine(DB00151)|Vitamin E(DB00163)	TTGGAATGTCACCTGTTTAAG	0.418																																					p.V252A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T755C	6						.						90.0	85.0	87.0					6																	53374047		2203	4300	6503	53482006	SO:0001630	splice_region_variant	2729	exon7			M90656	CCDS4952.1, CCDS75471.1	6p12	2008-02-05				ENSG00000001084	6.3.2.2		4311	protein-coding gene	gene with protein product		606857		GLCLC, GLCL		1350904	Standard	NM_001498		Approved	GCS	uc003pbw.2	P48506		ENST00000229416.6:c.754-1T>C	6.37:g.53374047A>G			53482006	NM_001498	Q14399	Missense_Mutation	SNP	ENST00000229416.6	37	CCDS4952.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.349513	0.82132	.	.	ENSG00000001084	ENST00000229416	T	0.77750	-1.12	5.42	5.42	0.78866	.	0.053129	0.85682	D	0.000000	T	0.64983	0.2648	L	0.43646	1.37	0.80722	D	1	B	0.33841	0.428	B	0.36719	0.231	T	0.70757	-0.4785	10	0.54805	T	0.06	.	15.7507	0.77983	1.0:0.0:0.0:0.0	.	252	P48506	GSH1_HUMAN	A	252	ENSP00000229416:V252A	ENSP00000229416:V252A	V	-	2	0	GCLC	53482006	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	9.287000	0.95975	2.179000	0.69175	0.460000	0.39030	GTG		0.418	GCLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359710.2		Missense_Mutation
COL12A1	1303	broad.mit.edu	37	6	75855893	75855893	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:75855893C>T	ENST00000322507.8	-	24	4794	c.4485G>A	c.(4483-4485)caG>caA	p.Q1495Q	COL12A1_ENST00000483888.2_Silent_p.Q1495Q|COL12A1_ENST00000345356.6_Silent_p.Q331Q|COL12A1_ENST00000416123.2_Silent_p.Q1495Q	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1495	Fibronectin type-III 10. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)	p.Q1495Q(1)		breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						CTCCCACAGGCTGCCACTGCA	0.463																																					p.Q1495Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G4485A	6						.						83.0	84.0	83.0					6																	75855893		1997	4193	6190	75912613	SO:0001819	synonymous_variant	1303	exon24			U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"", ""Fibronectin type III domain containing"""	2188	protein-coding gene	gene with protein product	"""collagen type XII proteoglycan"""	120320	"""collagen, type XII, alpha 1-like"""	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.4485G>A	6.37:g.75855893C>T			75912613	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Silent	SNP	ENST00000322507.8	37	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	C	9.522	1.108525	0.20714	.	.	ENSG00000111799	ENST00000419671	.	.	.	5.19	1.37	0.22104	.	.	.	.	.	T	0.40067	0.1102	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.27297	-1.0078	4	.	.	.	.	7.0389	0.25008	0.0:0.4761:0.0:0.5239	.	.	.	.	T	237	.	.	A	-	1	0	COL12A1	75912613	0.968000	0.33430	1.000000	0.80357	0.991000	0.79684	0.094000	0.15107	0.581000	0.29539	0.655000	0.94253	GCC		0.463	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370	
MYO6	4646	broad.mit.edu	37	6	76538312	76538312	+	Silent	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:76538312T>C	ENST00000369977.3	+	4	382	c.243T>C	c.(241-243)taT>taC	p.Y81Y	MYO6_ENST00000369975.1_Silent_p.Y81Y|MYO6_ENST00000369985.4_Silent_p.Y81Y|MYO6_ENST00000369981.3_Silent_p.Y81Y	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	81	Myosin motor.				actin filament-based movement (GO:0030048)|auditory receptor cell differentiation (GO:0042491)|cellular response to electrical stimulus (GO:0071257)|dendrite development (GO:0016358)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|endocytosis (GO:0006897)|glutamate secretion (GO:0014047)|inner ear morphogenesis (GO:0042472)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein targeting (GO:0006605)|regulation of secretion (GO:0051046)|regulation of synaptic plasticity (GO:0048167)|response to drug (GO:0042493)|sensory perception of sound (GO:0007605)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell cortex (GO:0005938)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microvillus (GO:0005902)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|unconventional myosin complex (GO:0016461)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|minus-end directed microfilament motor activity (GO:0060001)|motor activity (GO:0003774)	p.Y81Y(1)		breast(2)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(16)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	58		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		AAGTTCGATATAGTAAAGACA	0.284																																					p.Y81Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T243C	6						.						91.0	100.0	97.0					6																	76538312		2203	4298	6501	76595032	SO:0001819	synonymous_variant	4646	exon4			U90236, AB002387	CCDS34487.1, CCDS75481.1	6q14.1	2014-09-17	2004-05-19		ENSG00000196586	ENSG00000196586		"""Myosins / Myosin superfamily : Class VI"""	7605	protein-coding gene	gene with protein product		600970	"""deafness, autosomal recessive 37"""	DFNA22, DFNB37		9259267, 11468689	Standard	XM_005248719		Approved	KIAA0389	uc003pih.1	Q9UM54	OTTHUMG00000015061	ENST00000369977.3:c.243T>C	6.37:g.76538312T>C			76595032	NM_004999	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Silent	SNP	ENST00000369977.3	37	CCDS34487.1																																																																																				0.284	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2	NM_004999	
CYB5R4	51167	broad.mit.edu	37	6	84650287	84650287	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:84650287G>A	ENST00000369681.5	+	14	1453	c.1313G>A	c.(1312-1314)aGc>aAc	p.S438N	CYB5R4_ENST00000479164.1_3'UTR	NM_016230.3	NP_057314.2	Q7L1T6	NB5R4_HUMAN	cytochrome b5 reductase 4	438					cell development (GO:0048468)|detection of oxygen (GO:0003032)|generation of precursor metabolites and energy (GO:0006091)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|NADP metabolic process (GO:0006739)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|superoxide metabolic process (GO:0006801)	endoplasmic reticulum (GO:0005783)|perinuclear region of cytoplasm (GO:0048471)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|NAD(P)H oxidase activity (GO:0016174)|NADPH-hemoprotein reductase activity (GO:0003958)|oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor (GO:0016653)	p.S438N(1)		breast(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	23		all_cancers(76;7e-07)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00128)		BRCA - Breast invasive adenocarcinoma(397;0.0871)		ATTTGGAGAAGCCAATTGGAG	0.279																																					p.S438N	Esophageal Squamous(86;1289 1332 25971 40349 52675)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1313A	6						.						54.0	58.0	56.0					6																	84650287		2203	4300	6503	84707006	SO:0001583	missense	51167	exon14			AF169803	CCDS5000.2	6q14.2	2012-09-19		2005-07-13	ENSG00000065615	ENSG00000065615	1.6.2.2		20147	protein-coding gene	gene with protein product		608343	"""NADPH cytochrome B5 oxidoreductase"""	NCB5OR		10611283	Standard	NM_016230		Approved	b5+b5R, dJ676J13.1	uc003pkf.3	Q7L1T6	OTTHUMG00000015118	ENST00000369681.5:c.1313G>A	6.37:g.84650287G>A	ENSP00000358695:p.Ser438Asn		84707006	NM_016230	B1AEM2|Q5TGI9|Q9NUE4|Q9UHI9	Missense_Mutation	SNP	ENST00000369681.5	37	CCDS5000.2	.	.	.	.	.	.	.	.	.	.	G	1.562	-0.536457	0.04082	.	.	ENSG00000065615	ENST00000369681	D	0.94650	-3.48	5.81	-0.744	0.11101	Oxidoreductase FAD/NAD(P)-binding (1);	0.722759	0.14954	N	0.288722	T	0.75354	0.3838	N	0.12611	0.24	0.29640	N	0.844761	B	0.02656	0.0	B	0.09377	0.004	T	0.60576	-0.7236	10	0.19147	T	0.46	.	11.7835	0.52028	0.5536:0.0:0.4464:0.0	.	438	Q7L1T6	NB5R4_HUMAN	N	438	ENSP00000358695:S438N	ENSP00000358695:S438N	S	+	2	0	CYB5R4	84707006	0.995000	0.38212	0.875000	0.34327	0.958000	0.62258	1.355000	0.34068	-0.082000	0.12640	-0.136000	0.14681	AGC		0.279	CYB5R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041362.4	NM_016230	
TBX18	9096	broad.mit.edu	37	6	85457710	85457710	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:85457710G>A	ENST00000369663.5	-	5	1204	c.867C>T	c.(865-867)tcC>tcT	p.S289S	TBX18_ENST00000606521.1_5'UTR|TBX18_ENST00000606784.1_Silent_p.S131S	NM_001080508.1	NP_001073977.1	O95935	TBX18_HUMAN	T-box 18	289					anterior/posterior axis specification (GO:0009948)|cochlea morphogenesis (GO:0090103)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060829)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation involved in ureter development (GO:2000729)|sensory perception of sound (GO:0007605)|sinoatrial node development (GO:0003163)|smooth muscle cell differentiation (GO:0051145)|somitogenesis (GO:0001756)|ureter development (GO:0072189)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.S289S(1)		NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(9)|liver(1)|lung(31)|ovary(2)|pancreas(3)|prostate(6)|skin(3)	61		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)		CTCCCTCCCCGGATGGAACAG	0.448																																					p.S289S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C867T	6						.						104.0	90.0	95.0					6																	85457710		2203	4300	6503	85514429	SO:0001819	synonymous_variant	9096	exon5			AJ010278	CCDS34495.1	6q14.1-q15	2012-12-19			ENSG00000112837	ENSG00000112837		"""T-boxes"""	11595	protein-coding gene	gene with protein product		604613				9888994, 16688725, 23242162	Standard	NM_001080508		Approved		uc003pkl.2	O95935	OTTHUMG00000015129	ENST00000369663.5:c.867C>T	6.37:g.85457710G>A			85514429	NM_001080508	A2RU13|Q7Z6U4|Q9UJI6	Silent	SNP	ENST00000369663.5	37	CCDS34495.1																																																																																				0.448	TBX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041378.2	NM_001080508	
ZNF292	23036	broad.mit.edu	37	6	87964929	87964929	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:87964929G>T	ENST00000369577.3	+	8	1625	c.1582G>T	c.(1582-1584)Gga>Tga	p.G528*	ZNF292_ENST00000339907.4_Nonsense_Mutation_p.G523*	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	528						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.G383*(1)|p.G528*(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		AAGAGAGAGGGGATTTATATC	0.418																																					p.G528X												.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.G1582T	6						.						118.0	109.0	112.0					6																	87964929		1871	4098	5969	88021648	SO:0001587	stop_gained	23036	exon8			AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"""Zinc fingers, C2H2-type"""	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.1582G>T	6.37:g.87964929G>T	ENSP00000358590:p.Gly528*		88021648	NM_015021	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Nonsense_Mutation	SNP	ENST00000369577.3	37	CCDS47457.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.044163	0.93685	.	.	ENSG00000188994	ENST00000369577;ENST00000339907	.	.	.	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	20.1991	0.98252	0.0:0.0:1.0:0.0	.	.	.	.	X	528;523	.	ENSP00000342847:G523X	G	+	1	0	ZNF292	88021648	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	7.876000	0.87215	2.775000	0.95449	0.650000	0.86243	GGA		0.418	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021	
MDN1	23195	broad.mit.edu	37	6	90387403	90387403	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:90387403C>T	ENST00000369393.3	-	76	12540	c.12425G>A	c.(12424-12426)cGc>cAc	p.R4142H	RP1-122O8.7_ENST00000438877.1_RNA|MDN1_ENST00000428876.1_Missense_Mutation_p.R4142H			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	4142					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)	p.R4142H(1)		NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		AAGACCTTTGCGATACGACAA	0.468																																					p.R4142H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G12425A	6						.						140.0	133.0	135.0					6																	90387403		2203	4300	6503	90444124	SO:0001583	missense	23195	exon76			AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.12425G>A	6.37:g.90387403C>T	ENSP00000358400:p.Arg4142His		90444124	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	C	18.86	3.712639	0.68730	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.04156	3.69;3.69	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.15739	0.0379	M	0.77820	2.39	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.01767	-1.1278	10	0.36615	T	0.2	.	18.9378	0.92592	0.0:1.0:0.0:0.0	.	4142	Q9NU22	MDN1_HUMAN	H	4142	ENSP00000358400:R4142H;ENSP00000413970:R4142H	ENSP00000358400:R4142H	R	-	2	0	MDN1	90444124	1.000000	0.71417	1.000000	0.80357	0.609000	0.37215	7.481000	0.81124	2.460000	0.83146	0.561000	0.74099	CGC		0.468	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
MDN1	23195	broad.mit.edu	37	6	90463873	90463873	+	Missense_Mutation	SNP	G	G	A	rs201577289		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:90463873G>A	ENST00000369393.3	-	21	3008	c.2893C>T	c.(2893-2895)Cgg>Tgg	p.R965W	MDN1_ENST00000428876.1_Missense_Mutation_p.R965W			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	965					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)	p.R965W(1)		NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CACAGAGTCCGAAGGCTGTAG	0.507																																					p.R965W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2893T	6						.	G	TRP/ARG	0,4406		0,0,2203	85.0	86.0	86.0		2893	5.5	1.0	6		86	1,8599	1.2+/-3.3	0,1,4299	yes	missense	MDN1	NM_014611.1	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	965/5597	90463873	1,13005	2203	4300	6503	90520594	SO:0001583	missense	23195	exon21			AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.2893C>T	6.37:g.90463873G>A	ENSP00000358400:p.Arg965Trp		90520594	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.265563	0.80358	0.0	1.16E-4	ENSG00000112159	ENST00000369393;ENST00000428876;ENST00000439638	T;T;T	0.68025	-0.3;-0.3;-0.3	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	D	0.86197	0.5875	H	0.94542	3.55	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.89580	0.3820	10	0.87932	D	0	.	19.4868	0.95032	0.0:0.0:1.0:0.0	.	892;965	Q5T795;Q9NU22	.;MDN1_HUMAN	W	965;965;892	ENSP00000358400:R965W;ENSP00000413970:R965W;ENSP00000409664:R892W	ENSP00000358400:R965W	R	-	1	2	MDN1	90520594	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.591000	0.82666	2.598000	0.87819	0.563000	0.77884	CGG		0.507	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
TTLL2	83887	broad.mit.edu	37	6	167753996	167753996	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr6:167753996G>A	ENST00000239587.5	+	3	696	c.608G>A	c.(607-609)gGc>gAc	p.G203D		NM_031949.4	NP_114155.4	Q9BWV7	TTLL2_HUMAN	tubulin tyrosine ligase-like family, member 2	203	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)		ligase activity (GO:0016874)	p.G203D(1)		central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(66;7.8e-06)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		CAGATGCTGGGCACCAAGCAT	0.463																																					p.G203D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G608A	6						.						96.0	93.0	94.0					6																	167753996		2203	4300	6503	167673986	SO:0001583	missense	83887	exon3			AK093039	CCDS5301.1	6q27	2013-02-14		2004-01-14	ENSG00000120440	ENSG00000120440		"""Tubulin tyrosine ligase-like family"""	21211	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 104"""	C6orf104		11054573	Standard	XM_006715572		Approved	NYD-TSPG, dJ366N23.3	uc003qvs.1	Q9BWV7	OTTHUMG00000016023	ENST00000239587.5:c.608G>A	6.37:g.167753996G>A	ENSP00000239587:p.Gly203Asp		167673986	NM_031949	B2RB11|B3KS77|Q7Z6R8|Q86X22	Missense_Mutation	SNP	ENST00000239587.5	37	CCDS5301.1	.	.	.	.	.	.	.	.	.	.	G	0.584	-0.836025	0.02713	.	.	ENSG00000120440	ENST00000239587;ENST00000540954	T	0.07908	3.15	3.52	0.691	0.18045	.	0.674638	0.12906	N	0.429379	T	0.01627	0.0052	N	0.25094	0.71	0.09310	N	1	B	0.19331	0.035	B	0.22152	0.038	T	0.46775	-0.9167	10	0.33940	T	0.23	.	6.8783	0.24158	0.4005:0.0:0.5995:0.0	.	203	Q9BWV7	TTLL2_HUMAN	D	203;130	ENSP00000239587:G203D	ENSP00000239587:G203D	G	+	2	0	TTLL2	167673986	0.766000	0.28496	0.000000	0.03702	0.011000	0.07611	1.248000	0.32827	0.008000	0.14787	0.484000	0.47621	GGC		0.463	TTLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043127.3	NM_031949	
ACTL6B	51412	broad.mit.edu	37	7	100252642	100252642	+	Splice_Site	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:100252642C>T	ENST00000160382.5	-	4	475	c.369G>A	c.(367-369)ccG>ccA	p.P123P		NM_016188.4	NP_057272.1	O94805	ACL6B_HUMAN	actin-like 6B	123					chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|nervous system development (GO:0007399)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	structural constituent of cytoskeleton (GO:0005200)|transcription coactivator activity (GO:0003713)	p.P123P(1)		endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|skin(1)	13	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)					AGGCACTCACCGGAGCCTCGG	0.592																																					p.P123P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G369A	7						.						197.0	140.0	160.0					7																	100252642		2203	4300	6503	100090578	SO:0001630	splice_region_variant	51412	exon4			AB015906	CCDS5702.1	7q22	2008-02-01	2004-07-12	2004-07-14	ENSG00000077080	ENSG00000077080			160	protein-coding gene	gene with protein product		612458	"""actin-like 6"""	ACTL6		9799793	Standard	NM_016188		Approved	BAF53B	uc003uvy.3	O94805	OTTHUMG00000159661	ENST00000160382.5:c.369+1G>A	7.37:g.100252642C>T			100090578	NM_016188	A4D2D0|O75421	Silent	SNP	ENST00000160382.5	37	CCDS5702.1																																																																																				0.592	ACTL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356745.1	NM_016188	Silent
EPHB4	2050	broad.mit.edu	37	7	100417218	100417218	+	Missense_Mutation	SNP	C	C	T	rs61735975		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:100417218C>T	ENST00000358173.3	-	6	1726	c.1258G>A	c.(1258-1260)Gtc>Atc	p.V420I	EPHB4_ENST00000477446.1_5'UTR|RN7SL750P_ENST00000582814.1_RNA|EPHB4_ENST00000360620.3_Missense_Mutation_p.V420I	NM_004444.4	NP_004435.3	P54760	EPHB4_HUMAN	EPH receptor B4	420	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|ephrin receptor signaling pathway (GO:0048013)|heart morphogenesis (GO:0003007)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.V420I(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(3)	47	Lung NSC(181;0.041)|all_lung(186;0.0581)					TCAAATGGGACGGGCCCCGTG	0.612													C|||	1	0.000199681	0.0008	0.0	5008	,	,		15965	0.0		0.0	False		,,,				2504	0.0				p.V420I	GBM(200;2113 3072 25865 52728)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1258A	7						.	C	ILE/VAL	3,4403	6.2+/-15.9	0,3,2200	91.0	87.0	88.0		1258	1.2	0.0	7	dbSNP_129	88	1,8599	1.2+/-3.3	0,1,4299	yes	missense	EPHB4	NM_004444.4	29	0,4,6499	TT,TC,CC		0.0116,0.0681,0.0308	benign	420/988	100417218	4,13002	2203	4300	6503	100255154	SO:0001583	missense	2050	exon6			AY056047	CCDS5706.1	7q22	2013-02-11	2004-10-28		ENSG00000196411	ENSG00000196411		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3395	protein-coding gene	gene with protein product		600011	"""EphB4"""	HTK		8188704	Standard	NM_004444		Approved	Tyro11	uc003uwn.1	P54760	OTTHUMG00000157040	ENST00000358173.3:c.1258G>A	7.37:g.100417218C>T	ENSP00000350896:p.Val420Ile		100255154	NM_004444	B5A970|B5A971|B5A972|Q7Z635|Q9BTA5|Q9BXP0	Missense_Mutation	SNP	ENST00000358173.3	37	CCDS5706.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	12.41	1.929234	0.34096	6.81E-4	1.16E-4	ENSG00000196411	ENST00000360620;ENST00000358173	T;T	0.54071	0.59;0.59	5.46	1.2	0.21068	Fibronectin, type III (2);	0.813262	0.10268	N	0.695167	T	0.41743	0.1172	L	0.43152	1.355	0.09310	N	1	B;B;B	0.12013	0.004;0.002;0.005	B;B;B	0.04013	0.001;0.0;0.001	T	0.34527	-0.9825	10	0.46703	T	0.11	.	6.9927	0.24763	0.0:0.5748:0.2663:0.1589	.	420;420;420	B5A970;Q96L35;P54760	.;.;EPHB4_HUMAN	I	420	ENSP00000353833:V420I;ENSP00000350896:V420I	ENSP00000350896:V420I	V	-	1	0	EPHB4	100255154	0.003000	0.15002	0.001000	0.08648	0.779000	0.44077	0.705000	0.25675	0.645000	0.30675	-0.119000	0.15052	GTC		0.612	EPHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347222.1	NM_004444	
KMT2E	55904	broad.mit.edu	37	7	104702672	104702672	+	Silent	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:104702672T>C	ENST00000311117.3	+	4	678	c.133T>C	c.(133-135)Tta>Cta	p.L45L	KMT2E_ENST00000476671.1_Silent_p.L45L|KMT2E_ENST00000334877.4_Silent_p.L45L|KMT2E_ENST00000257745.4_Silent_p.L45L|KMT2E_ENST00000334914.7_5'UTR	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	45					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.L45L(1)									TCCCCACCAGTTATATACCAG	0.393																																					p.L45L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T133C	7						.						169.0	159.0	162.0					7																	104702672		2203	4300	6503	104489908	SO:0001819	synonymous_variant	55904	exon4			AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	18541	protein-coding gene	gene with protein product		608444	"""myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"""	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.133T>C	7.37:g.104702672T>C			104489908	NM_182931	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Silent	SNP	ENST00000311117.3	37	CCDS34723.1																																																																																				0.393	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1		
PIK3CG	5294	broad.mit.edu	37	7	106508826	106508826	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:106508826G>A	ENST00000359195.3	+	2	1130	c.820G>A	c.(820-822)Gtc>Atc	p.V274I	PIK3CG_ENST00000496166.1_Missense_Mutation_p.V274I|PIK3CG_ENST00000440650.2_Missense_Mutation_p.V274I	NM_001282427.1|NM_002649.2	NP_001269356.1|NP_002640.2	P48736	PK3CG_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	274	PI3K-RBD. {ECO:0000255|PROSITE- ProRule:PRU00879}.				adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cytokine production (GO:0001816)|dendritic cell chemotaxis (GO:0002407)|endocytosis (GO:0006897)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte apoptotic process (GO:0097284)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|natural killer cell chemotaxis (GO:0035747)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of triglyceride catabolic process (GO:0010897)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion mediated by integrin (GO:0033628)|respiratory burst involved in defense response (GO:0002679)|secretory granule localization (GO:0032252)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell proliferation (GO:0042098)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V274I(1)		breast(7)|central_nervous_system(9)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(16)|liver(4)|lung(59)|ovary(4)|pancreas(4)|prostate(3)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	132						TGTGCTGCGCGTCTGTGGCCG	0.542																																					p.V274I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G820A	7						.						54.0	51.0	52.0					7																	106508826		2203	4300	6503	106296062	SO:0001583	missense	5294	exon2				CCDS5739.1	7q22	2012-07-13	2012-07-13		ENSG00000105851	ENSG00000105851	2.7.1.153		8978	protein-coding gene	gene with protein product		601232	"""phosphoinositide-3-kinase, catalytic, gamma polypeptide"""				Standard	XM_005250443		Approved		uc003vdw.3	P48736	OTTHUMG00000157641	ENST00000359195.3:c.820G>A	7.37:g.106508826G>A	ENSP00000352121:p.Val274Ile		106296062	NM_002649	A4D0Q6|Q8IV23|Q9BZC8	Missense_Mutation	SNP	ENST00000359195.3	37	CCDS5739.1	.	.	.	.	.	.	.	.	.	.	G	15.86	2.957818	0.53400	.	.	ENSG00000105851	ENST00000440650;ENST00000496166;ENST00000359195	T;T;T	0.79749	-1.3;-1.3;-1.3	5.99	5.99	0.97316	Phosphoinositide 3-kinase, ras-binding (2);	0.053681	0.64402	D	0.000001	T	0.74921	0.3780	L	0.48642	1.525	0.80722	D	1	B	0.29909	0.261	B	0.28916	0.096	T	0.70368	-0.4891	10	0.30854	T	0.27	-35.1478	14.0585	0.64786	0.0769:0.0:0.9231:0.0	.	274	P48736	PK3CG_HUMAN	I	274	ENSP00000392258:V274I;ENSP00000419260:V274I;ENSP00000352121:V274I	ENSP00000352121:V274I	V	+	1	0	PIK3CG	106296062	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	6.694000	0.74587	2.840000	0.97914	0.655000	0.94253	GTC		0.542	PIK3CG-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349294.1		
LAMB4	22798	broad.mit.edu	37	7	107688493	107688493	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:107688493C>A	ENST00000388781.3	-	28	4269	c.4186G>T	c.(4186-4188)Ggc>Tgc	p.G1396C	LAMB4_ENST00000388780.3_Missense_Mutation_p.G1396C|LAMB4_ENST00000205386.4_Missense_Mutation_p.G1396C	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	1396	Domain alpha.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)		p.G1396C(1)		NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						CCCTTCCGGCCCGTGCAGAGA	0.547																																					p.G1396C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4186T	7						.						71.0	76.0	74.0					7																	107688493		2203	4300	6503	107475729	SO:0001583	missense	22798	exon28			AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"""Laminins"""	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.4186G>T	7.37:g.107688493C>A	ENSP00000373433:p.Gly1396Cys		107475729	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Missense_Mutation	SNP	ENST00000388781.3	37	CCDS34732.1	.	.	.	.	.	.	.	.	.	.	C	13.85	2.360395	0.41801	.	.	ENSG00000091128	ENST00000205386;ENST00000388781;ENST00000422975;ENST00000388780	T;T;T;T	0.33216	1.42;1.42;1.81;1.45	3.24	2.31	0.28768	.	.	.	.	.	T	0.35913	0.0948	N	0.19112	0.55	0.21290	N	0.999739	D;B	0.65815	0.995;0.005	D;B	0.63703	0.917;0.002	T	0.20605	-1.0270	9	0.62326	D	0.03	.	10.9537	0.47345	0.1893:0.8107:0.0:0.0	.	1396;1396	A4D0S4-3;A4D0S4	.;LAMB4_HUMAN	C	1396;1396;422;1396	ENSP00000205386:G1396C;ENSP00000373433:G1396C;ENSP00000416562:G422C;ENSP00000373432:G1396C	ENSP00000205386:G1396C	G	-	1	0	LAMB4	107475729	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.076000	0.14712	0.495000	0.27882	0.467000	0.42956	GGC		0.547	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857	
IMMP2L	83943	broad.mit.edu	37	7	110303686	110303686	+	Missense_Mutation	SNP	C	C	T	rs200952795		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:110303686C>T	ENST00000405709.2	-	6	942	c.500G>A	c.(499-501)cGc>cAc	p.R167H	IMMP2L_ENST00000450877.1_Missense_Mutation_p.R149H|IMMP2L_ENST00000489381.1_5'UTR|IMMP2L_ENST00000331762.3_Missense_Mutation_p.R167H|IMMP2L_ENST00000452895.1_Missense_Mutation_p.R167H|IMMP2L_ENST00000415362.1_Missense_Mutation_p.R167H	NM_032549.3	NP_115938.1	Q96T52	IMP2L_HUMAN	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	167					ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|protein processing involved in protein targeting to mitochondrion (GO:0006627)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|mitochondrial inner membrane peptidase complex (GO:0042720)	peptidase activity (GO:0008233)|serine-type peptidase activity (GO:0008236)	p.R167H(1)		endometrium(3)|large_intestine(6)|lung(5)	14				UCEC - Uterine corpus endometrioid carcinoma (4;0.053)|Epithelial(3;2.27e-07)|all cancers(3;1.36e-05)|STAD - Stomach adenocarcinoma(3;0.00148)|KIRC - Kidney renal clear cell carcinoma(11;0.0339)|Lung(3;0.0375)|Kidney(11;0.0415)|LUSC - Lung squamous cell carcinoma(290;0.173)		TACTGGTAAGCGCTCTGGAGG	0.498													C|||	1	0.000199681	0.0	0.0	5008	,	,		14096	0.001		0.0	False		,,,				2504	0.0				p.R167H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G500A	7						.						80.0	79.0	80.0					7																	110303686		2203	4300	6503	110090922	SO:0001583	missense	83943	exon6			AF359563	CCDS5753.1	7q31	2014-01-06	2005-08-17		ENSG00000184903	ENSG00000184903			14598	protein-coding gene	gene with protein product		605977	"""IMP2 inner mitochondrial membrane protease-like (S. cerevisiae)"", ""IMMP2L intronic transcript 1 (non-protein coding)"""	IMMP2L-IT1		11254443	Standard	NM_032549		Approved	IMP2	uc010ljr.2	Q96T52	OTTHUMG00000155023	ENST00000405709.2:c.500G>A	7.37:g.110303686C>T	ENSP00000384966:p.Arg167His		110090922	NM_032549	Q75MF1|Q75MN9|Q75MP0|Q75MS5|Q75MS8|Q96HJ2	Missense_Mutation	SNP	ENST00000405709.2	37	CCDS5753.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	27.2	4.809274	0.90707	.	.	ENSG00000184903	ENST00000405709;ENST00000331762;ENST00000452895;ENST00000450877;ENST00000415362	.	.	.	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.70116	0.3187	M	0.87971	2.92	0.80722	D	1	B	0.18310	0.027	B	0.10450	0.005	T	0.70139	-0.4954	9	0.59425	D	0.04	-9.17	11.9696	0.53055	0.0:0.9193:0.0:0.0807	.	167	Q96T52	IMP2L_HUMAN	H	167;167;167;149;167	.	ENSP00000329553:R167H	R	-	2	0	IMMP2L	110090922	0.976000	0.34144	0.968000	0.41197	0.909000	0.53808	2.370000	0.44240	2.756000	0.94617	0.563000	0.77884	CGC		0.498	IMMP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338109.4	NM_032549	
IMMP2L	83943	broad.mit.edu	37	7	110603598	110603598	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:110603598T>G	ENST00000405709.2	-	4	705	c.263A>C	c.(262-264)aAg>aCg	p.K88T	IMMP2L_ENST00000450877.1_Missense_Mutation_p.K70T|IMMP2L_ENST00000489381.1_5'UTR|IMMP2L_ENST00000331762.3_Missense_Mutation_p.K88T|IMMP2L_ENST00000452895.1_Missense_Mutation_p.K88T|IMMP2L_ENST00000415362.1_Missense_Mutation_p.K88T|IMMP2L_ENST00000447215.1_Missense_Mutation_p.K88T|IMMP2L_ENST00000437687.1_Missense_Mutation_p.K88T	NM_032549.3	NP_115938.1	Q96T52	IMP2L_HUMAN	IMP2 inner mitochondrial membrane peptidase-like (S. cerevisiae)	88					ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|protein processing involved in protein targeting to mitochondrion (GO:0006627)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|mitochondrial inner membrane peptidase complex (GO:0042720)	peptidase activity (GO:0008233)|serine-type peptidase activity (GO:0008236)	p.K88T(1)		endometrium(3)|large_intestine(6)|lung(5)	14				UCEC - Uterine corpus endometrioid carcinoma (4;0.053)|Epithelial(3;2.27e-07)|all cancers(3;1.36e-05)|STAD - Stomach adenocarcinoma(3;0.00148)|KIRC - Kidney renal clear cell carcinoma(11;0.0339)|Lung(3;0.0375)|Kidney(11;0.0415)|LUSC - Lung squamous cell carcinoma(290;0.173)		CTTAATGATCTTCTGTTCTGG	0.313																																					p.K88T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A263C	7						.						82.0	79.0	80.0					7																	110603598		2202	4298	6500	110390834	SO:0001583	missense	83943	exon4			AF359563	CCDS5753.1	7q31	2014-01-06	2005-08-17		ENSG00000184903	ENSG00000184903			14598	protein-coding gene	gene with protein product		605977	"""IMP2 inner mitochondrial membrane protease-like (S. cerevisiae)"", ""IMMP2L intronic transcript 1 (non-protein coding)"""	IMMP2L-IT1		11254443	Standard	NM_032549		Approved	IMP2	uc010ljr.2	Q96T52	OTTHUMG00000155023	ENST00000405709.2:c.263A>C	7.37:g.110603598T>G	ENSP00000384966:p.Lys88Thr		110390834	NM_032549	Q75MF1|Q75MN9|Q75MP0|Q75MS5|Q75MS8|Q96HJ2	Missense_Mutation	SNP	ENST00000405709.2	37	CCDS5753.1	.	.	.	.	.	.	.	.	.	.	T	12.87	2.068490	0.36470	.	.	ENSG00000184903	ENST00000405709;ENST00000331762;ENST00000452895;ENST00000450877;ENST00000415362;ENST00000447215;ENST00000437687	.	.	.	5.7	5.7	0.88788	Peptidase S24/S26A/S26B/S26C (1);Peptidase S24/S26A/S26B/S26C, beta-ribbon domain (1);Peptidase S24/S26A/S26B (1);	0.000000	0.85682	D	0.000000	T	0.59514	0.2199	N	0.13198	0.31	0.49299	D	0.999773	D;D	0.89917	0.999;1.0	D;D	0.80764	0.994;0.979	T	0.58092	-0.7697	9	0.21014	T	0.42	-4.4327	15.6151	0.76760	0.0:0.0:0.0:1.0	.	88;88	Q96T52-2;Q96T52	.;IMP2L_HUMAN	T	88;88;88;70;88;88;88	.	ENSP00000329553:K88T	K	-	2	0	IMMP2L	110390834	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.057000	0.71119	2.177000	0.69029	0.477000	0.44152	AAG		0.313	IMMP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338109.4	NM_032549	
GPR85	54329	broad.mit.edu	37	7	112723788	112723788	+	Missense_Mutation	SNP	G	G	A	rs372071765		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:112723788G>A	ENST00000297146.3	-	3	1592	c.989C>T	c.(988-990)gCc>gTc	p.A330V	GPR85_ENST00000487573.1_5'Flank|GPR85_ENST00000424100.1_Missense_Mutation_p.A330V|GPR85_ENST00000501255.2_Missense_Mutation_p.A330V|GPR85_ENST00000449591.1_Missense_Mutation_p.A330V	NM_001146266.1	NP_001139738.1	P60893	GPR85_HUMAN	G protein-coupled receptor 85	330					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.A330V(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	17						TCCTGCTTGGGCAAAACTCAT	0.493																																					p.A330V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C989T	7						.	G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	0,4406		0,0,2203	54.0	56.0	55.0		989,989,989,989	4.9	1.0	7		55	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	GPR85	NM_001146265.1,NM_001146266.1,NM_001146267.1,NM_018970.6	64,64,64,64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	330/371,330/371,330/371,330/371	112723788	1,13005	2203	4300	6503	112511024	SO:0001583	missense	54329	exon3			AF250237	CCDS5758.1	7q31	2012-08-21			ENSG00000164604	ENSG00000164604		"""GPCR / Class A : Orphans"""	4536	protein-coding gene	gene with protein product		605188				10978537, 10833454	Standard	NM_018970		Approved	SREB2	uc003vgp.1	P60893	OTTHUMG00000156933	ENST00000297146.3:c.989C>T	7.37:g.112723788G>A	ENSP00000297146:p.Ala330Val		112511024	NM_001146267	Q9JHI6|Q9NPD1	Missense_Mutation	SNP	ENST00000297146.3	37	CCDS5758.1	.	.	.	.	.	.	.	.	.	.	G	11.20	1.570084	0.28003	0.0	1.16E-4	ENSG00000164604	ENST00000501255;ENST00000297146;ENST00000424100;ENST00000449591	T;T;T;T	0.35605	1.3;1.3;1.3;1.3	4.91	4.91	0.64330	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.46073	0.1374	M	0.68952	2.095	0.80722	D	1	P	0.35033	0.481	P	0.46389	0.515	T	0.33954	-0.9848	10	0.02654	T	1	.	18.6417	0.91398	0.0:0.0:1.0:0.0	.	330	P60893	GPR85_HUMAN	V	330	ENSP00000445808:A330V;ENSP00000297146:A330V;ENSP00000396763:A330V;ENSP00000401178:A330V	ENSP00000297146:A330V	A	-	2	0	GPR85	112511024	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.601000	0.98297	2.718000	0.92993	0.585000	0.79938	GCC		0.493	GPR85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346650.2		
CADPS2	93664	broad.mit.edu	37	7	122303526	122303526	+	Missense_Mutation	SNP	C	C	T	rs372484743		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:122303526C>T	ENST00000449022.2	-	3	570	c.551G>A	c.(550-552)cGt>cAt	p.R184H	CADPS2_ENST00000412584.2_Missense_Mutation_p.R184H|CADPS2_ENST00000334010.7_Missense_Mutation_p.R184H|CADPS2_ENST00000313070.7_Missense_Mutation_p.R184H	NM_017954.10	NP_060424.9	Q86UW7	CAPS2_HUMAN	Ca++-dependent secretion activator 2	184					cellular response to starvation (GO:0009267)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasmic membrane-bounded vesicle (GO:0016023)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)	p.R184H(1)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(2)	43						ACTCCGCACACGTTTTTCTAT	0.428																																					p.R184H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G551A	7						.	C	HIS/ARG,HIS/ARG,HIS/ARG	0,3728		0,0,1864	98.0	87.0	91.0		551,551,551	5.3	1.0	7		91	1,8247		0,1,4123	no	missense,missense,missense	CADPS2	NM_001009571.3,NM_001167940.1,NM_017954.10	29,29,29	0,1,5987	TT,TC,CC		0.0121,0.0,0.0084	probably-damaging,probably-damaging,probably-damaging	184/1256,184/1301,184/1297	122303526	1,11975	1864	4124	5988	122090762	SO:0001583	missense	93664	exon3				CCDS47691.1, CCDS55158.1	7q31.32	2013-01-10	2008-08-28		ENSG00000081803	ENSG00000081803		"""Pleckstrin homology (PH) domain containing"""	16018	protein-coding gene	gene with protein product		609978	"""Ca++-dependent activator protein for secretion 2"""				Standard	NM_017954		Approved		uc010lkq.3	Q86UW7	OTTHUMG00000157093	ENST00000449022.2:c.551G>A	7.37:g.122303526C>T	ENSP00000398481:p.Arg184His		122090762	NM_001167940	A4D0X3|B7ZM56|Q658Q2|Q7Z5T7|Q8IZW9|Q8N7M4|Q9H6P4|Q9HCI1|Q9NWK8	Missense_Mutation	SNP	ENST00000449022.2	37	CCDS55158.1	.	.	.	.	.	.	.	.	.	.	C	33	5.234824	0.95207	0.0	1.21E-4	ENSG00000081803	ENST00000313070;ENST00000334010;ENST00000420900;ENST00000545465;ENST00000412584;ENST00000449022	D;D;D;D	0.90324	-2.65;-2.65;-2.65;-2.65	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	D	0.95762	0.8621	M	0.82323	2.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.991	D	0.96206	0.9149	10	0.87932	D	0	-8.917	18.8783	0.92347	0.0:1.0:0.0:0.0	.	184;184	Q86UW7-2;Q86UW7	.;CAPS2_HUMAN	H	184;184;184;151;184;184	ENSP00000325581:R184H;ENSP00000333940:R184H;ENSP00000400401:R184H;ENSP00000398481:R184H	ENSP00000325581:R184H	R	-	2	0	CADPS2	122090762	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.792000	0.85828	2.468000	0.83385	0.650000	0.86243	CGT		0.428	CADPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347414.2	NM_017954	
FSCN3	29999	broad.mit.edu	37	7	127236393	127236393	+	Missense_Mutation	SNP	C	C	T	rs148605578		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:127236393C>T	ENST00000265825.5	+	3	1072	c.853C>T	c.(853-855)Cgt>Tgt	p.R285C	GCC1_ENST00000497650.1_5'Flank|FSCN3_ENST00000420086.2_Missense_Mutation_p.R151C	NM_020369.2	NP_065102.1	Q9NQT6	FSCN3_HUMAN	fascin actin-bundling protein 3, testicular	285						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.R285C(2)		endometrium(2)|large_intestine(3)|liver(2)|lung(17)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30						TGGTGAGGTGCGTGCTGCTTC	0.552																																					p.R285C												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.C853T	7						.	C	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	242.0	209.0	220.0		853	2.7	0.2	7	dbSNP_134	220	0,8600		0,0,4300	no	missense	FSCN3	NM_020369.2	180	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	285/499	127236393	1,13005	2203	4300	6503	127023629	SO:0001583	missense	29999	exon3				CCDS34746.1	7q31.3	2014-02-03	2014-02-03		ENSG00000106328	ENSG00000106328		"""Fascins"""	3961	protein-coding gene	gene with protein product		615800	"""fascin (Strongylocentrotus purpuratus) homolog 3 (actin-bundling protein, testicular)"", ""fascin homolog 3, actin-bundling protein, testicular (Strongylocentrotus purpuratus)"""			11925108	Standard	NM_020369		Approved		uc003vmd.2	Q9NQT6	OTTHUMG00000022935	ENST00000265825.5:c.853C>T	7.37:g.127236393C>T	ENSP00000265825:p.Arg285Cys		127023629	NM_020369	A4D0Z2|A6NLL7|B2RA62|B4DU68	Missense_Mutation	SNP	ENST00000265825.5	37	CCDS34746.1	.	.	.	.	.	.	.	.	.	.	C	2.163	-0.391742	0.04932	2.27E-4	0.0	ENSG00000106328	ENST00000265825;ENST00000420086	T;T	0.43688	1.54;0.94	5.46	2.7	0.31948	Fascin domain (1);Actin cross-linking (1);	0.606401	0.16719	N	0.202340	T	0.11495	0.0280	N	0.00308	-1.67	0.09310	N	0.999999	B;B	0.14012	0.009;0.0	B;B	0.12156	0.007;0.0	T	0.27468	-1.0073	10	0.27785	T	0.31	-34.8419	7.4384	0.27169	0.0:0.1632:0.0:0.8368	.	151;285	B4DU68;Q9NQT6	.;FSCN3_HUMAN	C	285;151	ENSP00000265825:R285C;ENSP00000412243:R151C	ENSP00000265825:R285C	R	+	1	0	FSCN3	127023629	0.002000	0.14202	0.162000	0.22713	0.027000	0.11550	0.424000	0.21330	0.399000	0.25367	-0.794000	0.03295	CGT		0.552	FSCN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059256.2	NM_020369	
SND1	27044	broad.mit.edu	37	7	127343284	127343284	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:127343284A>T	ENST00000354725.3	+	7	941	c.747A>T	c.(745-747)aaA>aaT	p.K249N		NM_014390.2	NP_055205.2	Q7KZF4	SND1_HUMAN	staphylococcal nuclease and tudor domain containing 1	249	TNase-like 2. {ECO:0000255|PROSITE- ProRule:PRU00272}.				gene silencing by RNA (GO:0031047)|osteoblast differentiation (GO:0001649)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|dense body (GO:0097433)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|RISC complex (GO:0016442)	nuclease activity (GO:0004518)|poly(A) RNA binding (GO:0044822)|transcription cofactor activity (GO:0003712)	p.K249N(1)		central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	41						CAGAAGCCAAATTTTTCACTG	0.493																																					p.K249N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A747T	7						.						122.0	110.0	114.0					7																	127343284		2203	4300	6503	127130520	SO:0001583	missense	27044	exon7				CCDS34747.1	7q31.3	2014-03-24			ENSG00000197157	ENSG00000197157		"""Tudor domain containing"""	30646	protein-coding gene	gene with protein product	"""p100 EBNA2 co-activator"", ""Tudor-SN"""	602181				7651391, 9003410, 12819296	Standard	NM_014390		Approved	TDRD11, p100	uc003vmi.3	Q7KZF4	OTTHUMG00000157560	ENST00000354725.3:c.747A>T	7.37:g.127343284A>T	ENSP00000346762:p.Lys249Asn		127130520	NM_014390	Q13122|Q96AG0	Missense_Mutation	SNP	ENST00000354725.3	37	CCDS34747.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.640646	0.87859	.	.	ENSG00000197157	ENST00000354725;ENST00000438400	T	0.34072	1.38	6.07	2.21	0.28008	Staphylococcal nuclease (SNase-like) (4);Staphylococcal nuclease (SNase-like), OB-fold (1);	0.000000	0.85682	D	0.000000	T	0.61375	0.2342	M	0.91038	3.17	0.58432	D	0.999992	D	0.59767	0.986	D	0.70227	0.968	T	0.62478	-0.6846	10	0.72032	D	0.01	-14.0995	7.3526	0.26700	0.6262:0.0:0.3738:0.0	.	249	Q7KZF4	SND1_HUMAN	N	249;239	ENSP00000346762:K249N	ENSP00000346762:K249N	K	+	3	2	SND1	127130520	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.272000	0.43373	0.456000	0.26937	0.533000	0.62120	AAA		0.493	SND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349148.1	NM_014390	
HILPDA	29923	broad.mit.edu	37	7	128097427	128097427	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:128097427G>A	ENST00000257696.4	+	2	306	c.105G>A	c.(103-105)tcG>tcA	p.S35S	HILPDA_ENST00000435296.2_Silent_p.S35S|HILPDA_ENST00000481454.1_Intron|RP11-212P7.3_ENST00000462662.1_RNA|RP11-155G14.6_ENST00000493710.1_RNA	NM_001098786.1|NM_013332.3	NP_001092256.1|NP_037464.1	Q9Y5L2	HLPDA_HUMAN	hypoxia inducible lipid droplet-associated	35	Required for targeting to lipid droplets.				autocrine signaling (GO:0035425)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokine production (GO:0001819)|positive regulation of lipid storage (GO:0010884)|response to stress (GO:0006950)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|secretory granule (GO:0030141)	receptor binding (GO:0005102)	p.S35S(1)									AGAGCCCATCGCCTGGGACCT	0.537																																					p.S35S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G105A	7						.						116.0	107.0	110.0					7																	128097427		2203	4300	6503	127884663	SO:0001819	synonymous_variant	29923	exon2			AF144755	CCDS5802.1	7q32.1	2011-11-02	2011-11-02	2011-11-02	ENSG00000135245	ENSG00000135245			28859	protein-coding gene	gene with protein product	"""hypoxia inducible gene 2"""		"""chromosome 7 open reading frame 68"""	C7orf68		10690527, 15930302	Standard	NM_001098786		Approved	FLJ21076, HIG-2, HIG2	uc010lli.3	Q9Y5L2	OTTHUMG00000157712	ENST00000257696.4:c.105G>A	7.37:g.128097427G>A			127884663	NM_001098786	A4D0Z5|Q52LY5|Q53HJ7	Silent	SNP	ENST00000257696.4	37	CCDS5802.1																																																																																				0.537	HILPDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349450.1	NM_013332	
SMO	6608	broad.mit.edu	37	7	128848637	128848637	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:128848637C>T	ENST00000249373.3	+	7	1582	c.1302C>T	c.(1300-1302)ccC>ccT	p.P434P	RP11-286H14.8_ENST00000466717.1_RNA	NM_005631.4	NP_005622.1	Q99835	SMO_HUMAN	smoothened, frizzled class receptor	434					adenohypophysis development (GO:0021984)|anterior/posterior pattern specification (GO:0009952)|atrial septum morphogenesis (GO:0060413)|axon extension involved in axon guidance (GO:0048846)|canonical Wnt signaling pathway (GO:0060070)|cardioblast differentiation (GO:0010002)|cell fate specification (GO:0001708)|cellular response to cholesterol (GO:0071397)|central nervous system neuron differentiation (GO:0021953)|cerebellar cortex morphogenesis (GO:0021696)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|detection of cell density by contact stimulus involved in contact inhibition (GO:0060248)|determination of left/right asymmetry in lateral mesoderm (GO:0003140)|determination of left/right symmetry (GO:0007368)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic neurocranium morphogenesis (GO:0048702)|embryonic viscerocranium morphogenesis (GO:0048703)|epithelial-mesenchymal cell signaling (GO:0060684)|exocrine pancreas development (GO:0031017)|facial nerve development (GO:0021561)|floor plate formation (GO:0021508)|forebrain morphogenesis (GO:0048853)|gonad development (GO:0008406)|hair follicle morphogenesis (GO:0031069)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|mammary gland epithelial cell differentiation (GO:0060644)|mesenchymal to epithelial transition involved in metanephric renal vesicle formation (GO:0072285)|midgut development (GO:0007494)|multicellular organism growth (GO:0035264)|muscle cell fate commitment (GO:0042693)|myoblast migration (GO:0051451)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA binding (GO:0043392)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of gene expression (GO:0010629)|negative regulation of hair follicle development (GO:0051799)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neuron fate commitment (GO:0048663)|neuron projection regeneration (GO:0031102)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|otolith morphogenesis (GO:0032474)|pancreas morphogenesis (GO:0061113)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gene expression (GO:0010628)|positive regulation of hh target transcription factor activity (GO:0007228)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to nucleus (GO:0034504)|protein stabilization (GO:0050821)|regulation of heart morphogenesis (GO:2000826)|regulation of stem cell maintenance (GO:2000036)|renal system development (GO:0072001)|semicircular canal morphogenesis (GO:0048752)|skeletal muscle fiber development (GO:0048741)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021910)|somite development (GO:0061053)|spermatogenesis (GO:0007283)|thalamus development (GO:0021794)|type B pancreatic cell development (GO:0003323)|vasculogenesis (GO:0001570)|ventral midline determination (GO:0007371)	ciliary membrane (GO:0060170)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	drug binding (GO:0008144)|G-protein coupled receptor activity (GO:0004930)|patched binding (GO:0005113)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.P434P(1)		biliary_tract(1)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(14)|liver(1)|lung(11)|pancreas(2)|prostate(1)|skin(20)|upper_aerodigestive_tract(3)|urinary_tract(1)	64					Fluocinonide(DB01047)|Vismodegib(DB08828)	GCAACCACCCCGGGCTGCTGA	0.617			Mis		skin basal cell																																p.P434P			Dom	yes		7	7q31-q32	6608	smoothened homolog (Drosophila)		E	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1302T	7						.						53.0	45.0	48.0					7																	128848637		2203	4300	6503	128635873	SO:0001819	synonymous_variant	6608	exon7			U84401	CCDS5811.1	7q32.1	2014-01-29	2014-01-29	2003-01-17	ENSG00000128602	ENSG00000128602		"""GPCR / Class F : Frizzled receptors"""	11119	protein-coding gene	gene with protein product	"""frizzled family member 11"""	601500	"""smoothened (Drosophila) homolog"", ""smoothened homolog (Drosophila)"", ""smoothened, seven transmembrane spanning receptor"", ""smoothened, frizzled family receptor"""	SMOH		9628830	Standard	NM_005631		Approved	FZD11	uc003vor.3	Q99835	OTTHUMG00000158421	ENST00000249373.3:c.1302C>T	7.37:g.128848637C>T			128635873	NM_005631	A4D1K5	Silent	SNP	ENST00000249373.3	37	CCDS5811.1																																																																																				0.617	SMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350986.1	NM_005631	
CPA4	51200	broad.mit.edu	37	7	129948157	129948157	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:129948157G>A	ENST00000222482.4	+	8	741	c.713G>A	c.(712-714)tGg>tAg	p.W238*	CPA4_ENST00000445470.2_Nonsense_Mutation_p.W205*|CPA4_ENST00000493259.1_Nonsense_Mutation_p.W134*	NM_016352.3	NP_057436.2	Q9UI42	CBPA4_HUMAN	carboxypeptidase A4	238					histone acetylation (GO:0016573)	extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.W238*(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Melanoma(18;0.0435)					AACCGATTATGGAGGAAGACG	0.547																																					p.W205X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G614A	7						.						88.0	83.0	85.0					7																	129948157		2203	4300	6503	129735393	SO:0001587	stop_gained	51200	exon7			AF095719	CCDS5818.1, CCDS55163.1	7q32	2008-07-18			ENSG00000128510	ENSG00000128510			15740	protein-coding gene	gene with protein product	"""carboxypeptidase A3"""	607635				10383164, 10860668	Standard	NM_016352		Approved	CPA3	uc003vpr.3	Q9UI42	OTTHUMG00000157825	ENST00000222482.4:c.713G>A	7.37:g.129948157G>A	ENSP00000222482:p.Trp238*		129735393	NM_001163446	B7Z576|Q86UY9	Nonsense_Mutation	SNP	ENST00000222482.4	37	CCDS5818.1	.	.	.	.	.	.	.	.	.	.	G	38	6.780567	0.97833	.	.	ENSG00000128510	ENST00000445470;ENST00000222482;ENST00000538687;ENST00000493259	.	.	.	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	17.5655	0.87918	0.0:0.0:1.0:0.0	.	.	.	.	X	205;238;43;134	.	ENSP00000222482:W238X	W	+	2	0	CPA4	129735393	1.000000	0.71417	0.998000	0.56505	0.924000	0.55760	9.230000	0.95299	2.741000	0.93983	0.585000	0.79938	TGG		0.547	CPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349725.1	NM_016352	
TBXAS1	6916	broad.mit.edu	37	7	139529205	139529205	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:139529205T>C	ENST00000455353.1	+	1	153	c.16T>C	c.(16-18)Ttt>Ctt	p.F6L	TBXAS1_ENST00000436047.2_Missense_Mutation_p.F7L|TBXAS1_ENST00000416849.2_Missense_Mutation_p.F7L|TBXAS1_ENST00000462275.1_3'UTR|TBXAS1_ENST00000263552.6_Missense_Mutation_p.F7L|TBXAS1_ENST00000336425.5_Missense_Mutation_p.F6L|TBXAS1_ENST00000448866.1_Missense_Mutation_p.F6L|TBXAS1_ENST00000458722.1_Missense_Mutation_p.F6L|TBXAS1_ENST00000414508.2_Missense_Mutation_p.F7L|TBXAS1_ENST00000411653.1_Missense_Mutation_p.F6L|TBXAS1_ENST00000425687.1_Intron|TBXAS1_ENST00000539806.1_Missense_Mutation_p.F7L			P24557	THAS_HUMAN	thromboxane A synthase 1 (platelet)	6					arachidonic acid metabolic process (GO:0019369)|cellular chloride ion homeostasis (GO:0030644)|cyclooxygenase pathway (GO:0019371)|icosanoid metabolic process (GO:0006690)|positive regulation of vasoconstriction (GO:0045907)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	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)|thromboxane-A synthase activity (GO:0004796)	p.F7L(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	28	Melanoma(164;0.0142)				Ridogrel(DB01207)|Sulfasalazine(DB00795)	AGCCTTGGGGTTTCTAAAATT	0.567																																					p.F7L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T19C	7						.						70.0	64.0	66.0					7																	139529205		2203	4300	6503	139175674	SO:0001583	missense	6916	exon1			L36085	CCDS5855.1, CCDS5856.1, CCDS55174.1, CCDS55175.1	7q34-q35	2014-09-17	2008-07-31		ENSG00000059377	ENSG00000059377	5.3.99.5	"""Cytochrome P450s"""	11609	protein-coding gene	gene with protein product	"""cytochrome P450, family 5, subfamily A, polypeptide 1"""	274180	"""thromboxane A synthase 1 (platelet, cytochrome P450, subfamily V)"""			1714723, 8964509	Standard	NM_001061		Approved	CYP5, CYP5A1, THAS, TXS, TXAS, TS	uc011kqv.2	P24557	OTTHUMG00000157302	ENST00000455353.1:c.16T>C	7.37:g.139529205T>C	ENSP00000391567:p.Phe6Leu		139175674	NM_001061	B4DJG6|E7EMU9|E7EP08|E7ESB5|O14987|Q16843|Q16844|Q8IUN1|Q96CN2|Q9GZW4|Q9HD77|Q9HD78|Q9HD79|Q9HD80|Q9HD81|Q9HD82|Q9HD83|Q9HD84	Missense_Mutation	SNP	ENST00000455353.1	37		.	.	.	.	.	.	.	.	.	.	T	6.833	0.522955	0.13066	.	.	ENSG00000059377	ENST00000263552;ENST00000438104;ENST00000336425;ENST00000416849;ENST00000436047;ENST00000414508;ENST00000448866;ENST00000455353;ENST00000458722;ENST00000411653;ENST00000539806	T;T;T;T;T;T;T;T;T;T;T	0.28454	1.61;1.61;1.61;1.61;1.61;1.61;1.61;1.61;1.61;1.61;1.61	5.17	-2.95	0.05564	.	1.027400	0.07686	N	0.937888	T	0.10852	0.0265	N	0.03608	-0.345	0.09310	N	1	B;B;B;B;B;B	0.09022	0.001;0.002;0.001;0.0;0.0;0.0	B;B;B;B;B;B	0.06405	0.002;0.001;0.001;0.0;0.0;0.0	T	0.36163	-0.9759	10	0.10377	T	0.69	.	7.0274	0.24948	0.0:0.502:0.1559:0.3421	.	7;7;7;7;7;6	B7Z6W1;E7EP08;B4E0M5;E7EMU9;Q53F23;P24557	.;.;.;.;.;THAS_HUMAN	L	7;6;6;7;7;7;6;6;6;6;7	ENSP00000263552:F7L;ENSP00000388612:F6L;ENSP00000338087:F6L;ENSP00000389414:F7L;ENSP00000392361:F7L;ENSP00000392702:F7L;ENSP00000402536:F6L;ENSP00000391567:F6L;ENSP00000411274:F6L;ENSP00000411326:F6L;ENSP00000444626:F7L	ENSP00000263552:F7L	F	+	1	0	TBXAS1	139175674	0.000000	0.05858	0.000000	0.03702	0.210000	0.24377	-0.881000	0.04179	-0.388000	0.07797	0.528000	0.53228	TTT		0.567	TBXAS1-008	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000348380.1		
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12068308}.|V -> E (in CRC; also found in sarcoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis; loss of regulation by PMRT5). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:12198537, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:23263490, ECO:0000269|PubMed:24455489}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	TCGAGATTTCACTGTAGCTAG	0.368	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												p.V600E	Colon(40;35 892 2973 5743 27438)		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	BRAF,pituitary,NS,Substitution - Missense,0 	.	15808	Substitution - Missense(15790)|Complex - deletion inframe(17)|Insertion - In frame(1)	thyroid(7476)|skin(3822)|large_intestine(3288)|NS(360)|haematopoietic_and_lymphoid_tissue(336)|ovary(211)|lung(58)|eye(57)|central_nervous_system(53)|soft_tissue(30)|biliary_tract(18)|liver(17)|prostate(13)|breast(10)|upper_aerodigestive_tract(9)|endometrium(8)|pancreas(8)|testis(7)|small_intestine(7)|genital_tract(4)|stomach(4)|bone(3)|autonomic_ganglia(2)|oesophagus(2)|urinary_tract(2)|adrenal_gland(2)|pituitary(1)	c.T1799A	7						.						112.0	104.0	107.0					7																	140453136		2203	4300	6503	140099605	SO:0001583	missense	673	exon15	Familial Cancer Database	CFC, CFCS	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1799T>A	7.37:g.140453136A>T	ENSP00000288602:p.Val600Glu		140099605	NM_004333	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.486113|4.486113	0.84854|0.84854	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.81739|.	-1.53|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.61565|.	0.2357|.	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	D|.	0.55385|.	0.971|.	D|.	0.66351|.	0.943|.	T|.	0.58160|.	-0.7685|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	600|.	P15056|.	BRAF_HUMAN|.	E|R	600|208	ENSP00000288602:V600E|.	ENSP00000288602:V600E|.	V|X	-|-	2|1	0|0	BRAF|BRAF	140099605|140099605	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.197000|9.197000	0.94985|0.94985	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	GTG|TGA		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333	
PRSS1	5644	broad.mit.edu	37	7	142459799	142459799	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:142459799C>T	ENST00000311737.7	+	3	381	c.375C>T	c.(373-375)acC>acT	p.T125T	PRSS1_ENST00000486171.1_Silent_p.T139T	NM_002769.4	NP_002760.1	P07477	TRY1_HUMAN	protease, serine, 1 (trypsin 1)	125	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cobalamin metabolic process (GO:0009235)|digestion (GO:0007586)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.T125T(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(24)|prostate(2)	38	Melanoma(164;0.047)	all_cancers(3;2.14e-49)|Acute lymphoblastic leukemia(3;7.3e-185)|all_hematologic(3;1.1e-165)	all cancers(2;0.000126)|Colorectal(2;0.000157)|Epithelial(2;0.000191)|COAD - Colon adenocarcinoma(2;0.00189)		Aprotinin(DB06692)	GCGTGTCCACCATCTCTCTGC	0.577																																					p.T125T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C375T	7						.						120.0	115.0	117.0					7																	142459799		2203	4300	6503	142139373	SO:0001819	synonymous_variant	5644	exon3			M22612	CCDS5872.1	7q34	2012-10-02			ENSG00000204983	ENSG00000204983	3.4.21.4	"""Serine peptidases / Serine peptidases"""	9475	protein-coding gene	gene with protein product		276000		TRY1			Standard	NM_002769		Approved		uc003wak.2	P07477	OTTHUMG00000158923	ENST00000311737.7:c.375C>T	7.37:g.142459799C>T			142139373	NM_002769	A1A509|A6NJ71|B2R5I5|Q5NV57|Q7M4N3|Q7M4N4|Q92955|Q9HAN4|Q9HAN5|Q9HAN6|Q9HAN7	Silent	SNP	ENST00000311737.7	37	CCDS5872.1																																																																																				0.577	PRSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352538.2		
EPHB6	2051	broad.mit.edu	37	7	142563811	142563811	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:142563811A>G	ENST00000392957.2	+	9	1986	c.1199A>G	c.(1198-1200)gAc>gGc	p.D400G	EPHB6_ENST00000442129.1_Missense_Mutation_p.D400G|EPHB6_ENST00000411471.2_Missense_Mutation_p.D123G	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	400	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|receptor activity (GO:0004872)	p.D385G(1)		NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87	Melanoma(164;0.059)					GGTCGAGGGGACCTGCTCTTC	0.637																																					p.D400G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1199G	7						.						33.0	29.0	30.0					7																	142563811		2203	4300	6503	142273933	SO:0001583	missense	2051	exon9			D83492	CCDS5873.2, CCDS75672.1	7q33-q35	2013-02-11	2004-10-28		ENSG00000106123	ENSG00000106123		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3396	protein-coding gene	gene with protein product		602757	"""EphB6"""				Standard	XM_006715881		Approved	HEP	uc011kst.2	O15197	OTTHUMG00000155707	ENST00000392957.2:c.1199A>G	7.37:g.142563811A>G	ENSP00000376684:p.Asp400Gly		142273933	NM_004445	A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Missense_Mutation	SNP	ENST00000392957.2	37	CCDS5873.2	.	.	.	.	.	.	.	.	.	.	A	24.6	4.548686	0.86127	.	.	ENSG00000106123	ENST00000392957;ENST00000442129;ENST00000411471	T;T;T	0.57907	0.37;0.37;0.37	4.96	4.96	0.65561	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.44097	D	0.000499	T	0.75191	0.3816	M	0.89095	3.005	0.80722	D	1	D	0.67145	0.996	D	0.69479	0.964	T	0.81017	-0.1123	10	0.87932	D	0	.	13.829	0.63368	1.0:0.0:0.0:0.0	.	400	O15197	EPHB6_HUMAN	G	400;400;123	ENSP00000376684:D400G;ENSP00000410789:D400G;ENSP00000409061:D123G	ENSP00000376684:D400G	D	+	2	0	EPHB6	142273933	1.000000	0.71417	0.995000	0.50966	0.927000	0.56198	9.283000	0.95860	1.856000	0.53863	0.379000	0.24179	GAC		0.637	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1		
OR2F2	135948	broad.mit.edu	37	7	143632554	143632554	+	Missense_Mutation	SNP	G	G	A	rs371292578		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:143632554G>A	ENST00000408955.2	+	1	296	c.229G>A	c.(229-231)Gta>Ata	p.V77I		NM_001004685.1	NP_001004685.1	O95006	OR2F2_HUMAN	olfactory receptor, family 2, subfamily F, member 2	77						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V77I(2)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(19)|ovary(3)|skin(2)|stomach(1)|urinary_tract(1)	32	Melanoma(164;0.0903)					TGCCACAAGCGTAGTCCCCCA	0.512																																					p.V77I												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.G229A	7						.	A	ILE/VAL	0,4406		0,0,2203	234.0	227.0	229.0		229	3.5	1.0	7		229	1,8599	819.2+/-406.8	0,1,4299	no	missense	OR2F2	NM_001004685.1	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	77/318	143632554	1,13005	2203	4300	6503	143263487	SO:0001583	missense	135948	exon1				CCDS43666.1	7q33-q35	2012-08-09			ENSG00000221910	ENSG00000221910		"""GPCR / Class A : Olfactory receptors"""	8247	protein-coding gene	gene with protein product							Standard	NM_001004685		Approved	OR7-1	uc011ktv.2	O95006	OTTHUMG00000157768	ENST00000408955.2:c.229G>A	7.37:g.143632554G>A	ENSP00000386222:p.Val77Ile		143263487	NM_001004685	A4D2G0|Q6IFP8	Missense_Mutation	SNP	ENST00000408955.2	37	CCDS43666.1	.	.	.	.	.	.	.	.	.	.	A	0	-2.610724	0.00121	0.0	1.16E-4	ENSG00000221910	ENST00000408955	T	0.01406	4.93	3.49	3.49	0.39957	GPCR, rhodopsin-like superfamily (1);	0.112829	0.38720	N	0.001581	T	0.00695	0.0023	N	0.04116	-0.275	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.48779	-0.9005	10	0.02654	T	1	-21.3021	7.1257	0.25471	0.8867:0.0:0.1133:0.0	.	77	O95006	OR2F2_HUMAN	I	77	ENSP00000386222:V77I	ENSP00000386222:V77I	V	+	1	0	OR2F2	143263487	0.000000	0.05858	0.961000	0.40146	0.011000	0.07611	1.138000	0.31491	0.524000	0.28502	-0.490000	0.04691	GTA		0.512	OR2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349570.1		
ZNF786	136051	broad.mit.edu	37	7	148767658	148767658	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:148767658C>T	ENST00000491431.1	-	4	2270	c.2206G>A	c.(2206-2208)Gat>Aat	p.D736N	ZNF786_ENST00000451334.3_Missense_Mutation_p.D699N|ZNF786_ENST00000316286.9_Missense_Mutation_p.D650N	NM_152411.3	NP_689624.2	Q8N393	ZN786_HUMAN	zinc finger protein 786	736					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D735N(1)		breast(4)|cervix(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(2)|skin(2)|soft_tissue(1)|urinary_tract(2)	26	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			TTCCCACAATCGCCACAGGCA	0.522																																					p.D736N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2206A	7						.						147.0	149.0	148.0					7																	148767658		2031	4208	6239	148398591	SO:0001583	missense	136051	exon4			AK095701, AL834510	CCDS47738.1	7q36.1	2013-01-08			ENSG00000197362	ENSG00000197362		"""Zinc fingers, C2H2-type"", ""-"""	21806	protein-coding gene	gene with protein product							Standard	NM_152411		Approved	DKFZp762I137	uc003wfh.2	Q8N393	OTTHUMG00000158975	ENST00000491431.1:c.2206G>A	7.37:g.148767658C>T	ENSP00000417470:p.Asp736Asn		148398591	NM_152411	A1A568|B4DMI1	Missense_Mutation	SNP	ENST00000491431.1	37	CCDS47738.1	.	.	.	.	.	.	.	.	.	.	C	16.62	3.172755	0.57584	.	.	ENSG00000197362	ENST00000316286;ENST00000491431;ENST00000451334	T;T;T	0.17528	2.27;2.27;2.27	4.45	4.45	0.53987	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.39020	N	0.001481	T	0.29716	0.0742	L	0.41079	1.255	0.22424	N	0.999114	D	0.76494	0.999	D	0.66196	0.942	T	0.02901	-1.1096	10	0.72032	D	0.01	-36.2922	12.492	0.55905	0.0:1.0:0.0:0.0	.	736	Q8N393	ZN786_HUMAN	N	650;736;699	ENSP00000313516:D650N;ENSP00000417470:D736N;ENSP00000404984:D699N	ENSP00000313516:D650N	D	-	1	0	ZNF786	148398591	0.000000	0.05858	0.821000	0.32701	0.664000	0.39144	-0.292000	0.08332	2.325000	0.78763	0.467000	0.42956	GAT		0.522	ZNF786-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352751.1	NM_152411	
GIMAP8	155038	broad.mit.edu	37	7	150164078	150164078	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:150164078C>T	ENST00000307271.3	+	2	866	c.292C>T	c.(292-294)Ctc>Ttc	p.L98F		NM_175571.2	NP_783161.1	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	98	AIG1-type G 1.					cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)	p.L98F(1)		breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(26)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)		CCATGCTCTGCTCTTGGTAAT	0.512																																					p.L98F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C292T	7						.						129.0	122.0	124.0					7																	150164078		2203	4300	6503	149795011	SO:0001583	missense	155038	exon2			AL834361	CCDS34777.1	7q36.1	2014-04-04			ENSG00000171115	ENSG00000171115		"""GTPases, IMAP"""	21792	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 9"""					15474311	Standard	XM_005249951		Approved	DKFZp667I133, hIAN6, IAN9	uc003whj.3	Q8ND71	OTTHUMG00000158327	ENST00000307271.3:c.292C>T	7.37:g.150164078C>T	ENSP00000305107:p.Leu98Phe		149795011	NM_175571		Missense_Mutation	SNP	ENST00000307271.3	37	CCDS34777.1	.	.	.	.	.	.	.	.	.	.	C	20.0	3.930856	0.73327	.	.	ENSG00000171115	ENST00000307271	T	0.14266	2.52	4.48	4.48	0.54585	AIG1 (1);	0.000000	0.42294	D	0.000734	T	0.49167	0.1541	H	0.96301	3.8	0.37406	D	0.91304	D	0.89917	1.0	D	0.91635	0.999	T	0.68224	-0.5465	10	0.72032	D	0.01	.	12.5139	0.56021	0.0:1.0:0.0:0.0	.	98	Q8ND71	GIMA8_HUMAN	F	98	ENSP00000305107:L98F	ENSP00000305107:L98F	L	+	1	0	GIMAP8	149795011	1.000000	0.71417	0.829000	0.32907	0.105000	0.19272	2.098000	0.41757	2.343000	0.79666	0.655000	0.94253	CTC		0.512	GIMAP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350701.1	NM_175571	
NOS3	4846	broad.mit.edu	37	7	150710862	150710862	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:150710862C>T	ENST00000297494.3	+	26	3663	c.3306C>T	c.(3304-3306)cgC>cgT	p.R1102R	ATG9B_ENST00000605938.1_3'UTR|ATG9B_ENST00000377974.2_3'UTR|ATG9B_ENST00000444312.1_3'UTR|NOS3_ENST00000477227.1_3'UTR|ATG9B_ENST00000494791.1_5'UTR|NOS3_ENST00000461406.1_Silent_p.R896R	NM_000603.4	NP_000594.2	P60323	NANO3_HUMAN	nitric oxide synthase 3 (endothelial cell)	0					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|oogenesis (GO:0048477)|regulation of cell cycle (GO:0051726)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.R1102R(1)		NS(3)|breast(3)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(11)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	50	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		AGGTGCACCGCGTGCTGTGCC	0.706																																					p.R1102R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3306T	7						.						41.0	31.0	35.0					7																	150710862		2200	4299	6499	150341795	SO:0001819	synonymous_variant	4846	exon26				CCDS5912.1, CCDS55182.1, CCDS55183.1	7q36	2007-02-15			ENSG00000164867	ENSG00000164867	1.14.13.39		7876	protein-coding gene	gene with protein product	"""endothelial nitric oxide synthase"""	163729				1379542	Standard	NM_000603		Approved	ECNOS, eNOS	uc003wif.3	P29474	OTTHUMG00000158343	ENST00000297494.3:c.3306C>T	7.37:g.150710862C>T			150341795	NM_000603	Q495E5	Silent	SNP	ENST00000297494.3	37	CCDS5912.1																																																																																				0.706	NOS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350750.2	NM_000603	
PAXIP1	22976	broad.mit.edu	37	7	154752642	154752642	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:154752642G>A	ENST00000404141.1	-	12	2549	c.2395C>T	c.(2395-2397)Cca>Tca	p.P799S	PAXIP1_ENST00000473219.1_5'UTR|PAXIP1_ENST00000397192.1_Missense_Mutation_p.P799S			Q6ZW49	PAXI1_HUMAN	PAX interacting (with transcription-activation domain) protein 1	799	Interaction with TP53BP1.				adipose tissue development (GO:0060612)|chorion development (GO:0060717)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|endothelial cell migration (GO:0043542)|histone H3-K4 methylation (GO:0051568)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K36 methylation (GO:0000416)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of isotype switching (GO:0045830)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)		p.P765S(1)		NS(1)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	33	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)		GGGGCAAATGGATCCTGCAGA	0.418																																					p.P799S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2395T	7						.						63.0	63.0	63.0					7																	154752642		1929	4133	6062	154383575	SO:0001583	missense	22976	exon12			U80735	CCDS47753.1	7q36	2007-07-06	2005-04-05	2005-04-05	ENSG00000157212	ENSG00000157212			8624	protein-coding gene	gene with protein product		608254	"""PAX transcription activation domain interacting protein 1 like"""	PAXIP1L		9225980	Standard	XM_005249539		Approved	CAGF29, CAGF28, TNRC2, PTIP	uc022aqf.1	Q6ZW49	OTTHUMG00000151322	ENST00000404141.1:c.2395C>T	7.37:g.154752642G>A	ENSP00000384048:p.Pro799Ser		154383575	NM_007349	O15404|Q6N099|Q6ZWH9|Q7Z315|Q86UN0|Q8N4P9|Q96HP2	Missense_Mutation	SNP	ENST00000404141.1	37	CCDS47753.1	.	.	.	.	.	.	.	.	.	.	G	12.34	1.908201	0.33721	.	.	ENSG00000157212	ENST00000404141;ENST00000397192;ENST00000357094;ENST00000323199	T;T	0.34667	1.35;1.35	5.51	5.51	0.81932	.	0.000000	0.56097	U	0.000036	T	0.42337	0.1198	M	0.71581	2.175	0.58432	D	0.999999	P;P;P	0.48503	0.533;0.607;0.911	B;B;B	0.39840	0.149;0.187;0.311	T	0.49331	-0.8951	10	0.52906	T	0.07	-27.3302	19.4545	0.94882	0.0:0.0:1.0:0.0	.	752;765;799	B4DEQ6;Q6ZW49-1;Q6ZW49	.;.;PAXI1_HUMAN	S	799;799;623;752	ENSP00000384048:P799S;ENSP00000380376:P799S	ENSP00000319149:P752S	P	-	1	0	PAXIP1	154383575	1.000000	0.71417	0.592000	0.28758	0.011000	0.07611	7.554000	0.82212	2.590000	0.87494	0.650000	0.86243	CCA		0.418	PAXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322223.1	NM_007349	
SUN1	23353	broad.mit.edu	37	7	905656	905656	+	Silent	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:905656T>C	ENST00000405266.1	+	17	2067	c.2043T>C	c.(2041-2043)ttT>ttC	p.F681F	SUN1_ENST00000401592.1_Silent_p.F644F|SUN1_ENST00000413514.2_Silent_p.F442F|SUN1_ENST00000425407.2_Silent_p.F561F|SUN1_ENST00000452783.2_Silent_p.F541F|SUN1_ENST00000456758.2_Silent_p.F833F|SUN1_ENST00000389574.3_Silent_p.F561F			O94901	SUN1_HUMAN	Sad1 and UNC84 domain containing 1	671	SUN. {ECO:0000255|PROSITE- ProRule:PRU00802}.				cytoskeletal anchoring at nuclear membrane (GO:0090286)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)	acrosomal membrane (GO:0002080)|integral component of nuclear inner membrane (GO:0005639)|nuclear envelope (GO:0005635)|SUN-KASH complex (GO:0034993)		p.F561F(1)		NS(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						TGAGTCTGTTTGGGATCCCGC	0.562																																					p.F644F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1932C	7						.						103.0	107.0	105.0					7																	905656		2064	4205	6269	872182	SO:0001819	synonymous_variant	23353	exon16			AF202724	CCDS43533.1, CCDS47525.1, CCDS55078.1, CCDS55079.1, CCDS55080.1	7p22.3	2010-01-27	2010-01-27	2010-01-27	ENSG00000164828	ENSG00000164828			18587	protein-coding gene	gene with protein product	"""Sad1 unc-84 domain protein 1"""	607723	"""unc-84 homolog A (C. elegans)"""	UNC84A		11593002	Standard	NM_001130965		Approved	KIAA0810, FLJ12407	uc021zym.1	O94901	OTTHUMG00000151426	ENST00000405266.1:c.2043T>C	7.37:g.905656T>C			872182	NM_001130965	A5PL20|B3KMV7|B4DZF7|B7WNY4|B7WP53|E9PDU4|E9PF23|F8WD13|Q96CZ7|Q9HA14|Q9UH98	Silent	SNP	ENST00000405266.1	37		.	.	.	.	.	.	.	.	.	.	T	11.83	1.755633	0.31046	.	.	ENSG00000164828	ENST00000433212	.	.	.	4.94	-2.07	0.07276	.	.	.	.	.	T	0.55321	0.1913	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52230	-0.8603	4	.	.	.	-32.7979	10.4136	0.44307	0.0:0.3228:0.0:0.6772	.	.	.	.	R	493	.	.	W	+	1	0	SUN1	872182	0.954000	0.32549	0.938000	0.37757	0.956000	0.61745	0.012000	0.13287	-0.300000	0.08895	0.533000	0.62120	TGG		0.562	SUN1-001	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000322566.1	NM_025154	
SDK1	221935	broad.mit.edu	37	7	4169604	4169604	+	Missense_Mutation	SNP	C	C	T	rs140791078		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:4169604C>T	ENST00000404826.2	+	27	4143	c.4004C>T	c.(4003-4005)aCg>aTg	p.T1335M	SDK1_ENST00000389531.3_Missense_Mutation_p.T1335M	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1335	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.T1335M(1)		NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		GGGAACCACACGCAGTCGGCC	0.652																																					p.T1335M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4004T	7						.	C	MET/THR	1,4405	2.1+/-5.4	0,1,2202	59.0	55.0	57.0		4004	5.7	1.0	7	dbSNP_134	57	0,8598		0,0,4299	no	missense	SDK1	NM_152744.3	81	0,1,6501	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	1335/2214	4169604	1,13003	2203	4299	6502	4136130	SO:0001583	missense	221935	exon27			AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19307	protein-coding gene	gene with protein product		607216	"""sidekick homolog 1 (chicken)"", ""sidekick homolog 1, cell adhesion molecule (chicken)"""			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.4004C>T	7.37:g.4169604C>T	ENSP00000385899:p.Thr1335Met		4136130	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	37	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	C	18.46	3.629391	0.67015	2.27E-4	0.0	ENSG00000146555	ENST00000404826;ENST00000389531	T;T	0.59502	0.26;0.26	5.73	5.73	0.89815	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.069462	0.56097	D	0.000032	T	0.75852	0.3906	M	0.72479	2.2	0.58432	D	0.999991	D;D	0.89917	0.999;1.0	D;D	0.66351	0.91;0.943	T	0.77354	-0.2619	10	0.87932	D	0	.	19.9025	0.96993	0.0:1.0:0.0:0.0	.	1335;1335	F8W6X9;Q7Z5N4	.;SDK1_HUMAN	M	1335	ENSP00000385899:T1335M;ENSP00000374182:T1335M	ENSP00000374182:T1335M	T	+	2	0	SDK1	4136130	0.987000	0.35691	0.975000	0.42487	0.639000	0.38242	3.462000	0.53042	2.722000	0.93159	0.655000	0.94253	ACG		0.652	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744	
SDK1	221935	broad.mit.edu	37	7	4198172	4198172	+	Missense_Mutation	SNP	C	C	T	rs150578081		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:4198172C>T	ENST00000404826.2	+	31	4857	c.4718C>T	c.(4717-4719)aCg>aTg	p.T1573M	SDK1_ENST00000389531.3_Missense_Mutation_p.T1573M	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1573	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.T1573M(1)		NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		GCGGTGACCACGCTGCAGGAT	0.602																																					p.T1573M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4718T	7						.	C	MET/THR	0,4406		0,0,2203	85.0	76.0	79.0		4718	4.8	0.9	7	dbSNP_134	79	1,8599	1.2+/-3.3	0,1,4299	no	missense	SDK1	NM_152744.3	81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	1573/2214	4198172	1,13005	2203	4300	6503	4164698	SO:0001583	missense	221935	exon31			AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19307	protein-coding gene	gene with protein product		607216	"""sidekick homolog 1 (chicken)"", ""sidekick homolog 1, cell adhesion molecule (chicken)"""			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.4718C>T	7.37:g.4198172C>T	ENSP00000385899:p.Thr1573Met		4164698	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	37	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.599896	0.87055	0.0	1.16E-4	ENSG00000146555	ENST00000404826;ENST00000389531	T;T	0.64991	-0.13;-0.13	4.81	4.81	0.61882	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000002	D	0.83704	0.5312	M	0.91612	3.225	0.58432	D	0.999999	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.83275	0.996;0.962;0.982	D	0.88156	0.2854	10	0.87932	D	0	.	17.8759	0.88825	0.0:1.0:0.0:0.0	.	1573;60;1573	F8W6X9;F2Z3E9;Q7Z5N4	.;.;SDK1_HUMAN	M	1573	ENSP00000385899:T1573M;ENSP00000374182:T1573M	ENSP00000374182:T1573M	T	+	2	0	SDK1	4164698	1.000000	0.71417	0.939000	0.37840	0.962000	0.63368	7.717000	0.84732	2.210000	0.71456	0.563000	0.77884	ACG		0.602	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744	
SDK1	221935	broad.mit.edu	37	7	4260968	4260968	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:4260968G>A	ENST00000404826.2	+	40	5938	c.5799G>A	c.(5797-5799)acG>acA	p.T1933T	SDK1_ENST00000389531.3_Silent_p.T1913T	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1933	Fibronectin type-III 13. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.T1933T(1)		NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		CACCTACCACGGGCTATGTGA	0.647																																					p.T1933T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G5799A	7						.						49.0	38.0	42.0					7																	4260968		2203	4300	6503	4227494	SO:0001819	synonymous_variant	221935	exon40			AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19307	protein-coding gene	gene with protein product		607216	"""sidekick homolog 1 (chicken)"", ""sidekick homolog 1, cell adhesion molecule (chicken)"""			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.5799G>A	7.37:g.4260968G>A			4227494	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Silent	SNP	ENST00000404826.2	37	CCDS34590.1																																																																																				0.647	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744	
MMD2	221938	broad.mit.edu	37	7	4955678	4955678	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:4955678C>T	ENST00000404774.3	-	4	517	c.323G>A	c.(322-324)cGg>cAg	p.R108Q	MMD2_ENST00000401401.3_Missense_Mutation_p.R108Q|MMD2_ENST00000406755.1_Missense_Mutation_p.R108Q	NM_001100600.1	NP_001094070.1	Q8IY49	PAQRA_HUMAN	monocyte to macrophage differentiation-associated 2	108						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)		p.R108Q(2)		central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(11)	14		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.097)|OV - Ovarian serous cystadenocarcinoma(56;3.4e-14)		GATGACCATCCGGTCGAACAT	0.587																																					p.R108Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G323A	7						.						43.0	46.0	45.0					7																	4955678		1916	4123	6039	4922204	SO:0001583	missense	221938	exon4			BC037881	CCDS47529.1, CCDS47530.1, CCDS59047.1	7p22	2004-06-23			ENSG00000136297	ENSG00000136297			30133	protein-coding gene	gene with protein product		614581				12477932	Standard	NM_198403		Approved	PAQR10	uc003sno.4	Q8IY49	OTTHUMG00000151844	ENST00000404774.3:c.323G>A	7.37:g.4955678C>T	ENSP00000384690:p.Arg108Gln		4922204	NM_198403	B5MBW4|Q6NVU5|Q6TCH0	Missense_Mutation	SNP	ENST00000404774.3	37	CCDS47529.1	.	.	.	.	.	.	.	.	.	.	C	35	5.479753	0.96307	.	.	ENSG00000136297	ENST00000404774;ENST00000406755;ENST00000401401	T;T;T	0.30448	1.53;1.53;1.53	4.58	4.58	0.56647	.	0.000000	0.64402	D	0.000001	T	0.63402	0.2508	M	0.89904	3.07	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.998	T	0.72766	-0.4194	10	0.72032	D	0.01	-32.1146	16.5463	0.84446	0.0:1.0:0.0:0.0	.	108;108;108	B5MBW4;Q8IY49;Q8IY49-2	.;PAQRA_HUMAN;.	Q	108	ENSP00000384690:R108Q;ENSP00000385963:R108Q;ENSP00000384141:R108Q	ENSP00000384141:R108Q	R	-	2	0	MMD2	4922204	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	7.174000	0.77620	2.381000	0.81170	0.591000	0.81541	CGG		0.587	MMD2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324136.1	NM_198403	
RNF216	54476	broad.mit.edu	37	7	5780791	5780791	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	None	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:5780791C>G	ENST00000425013.2	-	4	910	c.686G>C	c.(685-687)gGc>gCc	p.G229A	RNF216_ENST00000389902.3_Missense_Mutation_p.G286A	NM_207111.3|NM_207116.2	NP_996994.1|NP_996999.1	Q9NWF9	RN216_HUMAN	ring finger protein 216	229					apoptotic process (GO:0006915)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|regulation of defense response to virus by host (GO:0050691)|regulation of interferon-beta production (GO:0032648)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)		FBXL18/RNF216(2)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)|skin(1)|urinary_tract(4)	33		Ovarian(82;0.07)		UCEC - Uterine corpus endometrioid carcinoma (126;0.135)|OV - Ovarian serous cystadenocarcinoma(56;2.69e-13)		AGAAGAGGGGCCTGAAATCCC	0.552																																					p.G229A												.	.	0			c.G686C	7						.						74.0	75.0	75.0					7																	5780791		2203	4300	6503	5747317	SO:0001583	missense	54476	exon4			AY062174	CCDS34594.1, CCDS34595.1	7p22.1	2014-02-12	2007-08-20		ENSG00000011275	ENSG00000011275		"""RING-type (C3HC4) zinc fingers"""	21698	protein-coding gene	gene with protein product		609948					Standard	NM_207111		Approved	TRIAD3, UBCE7IP1, ZIN	uc003sox.2	Q9NWF9	OTTHUMG00000155500	ENST00000425013.2:c.686G>C	7.37:g.5780791C>G	ENSP00000404602:p.Gly229Ala		5747317	NM_207116	Q6Y691|Q75ML7|Q7Z2H7|Q7Z7C1|Q8NHW7|Q9NYT1	Missense_Mutation	SNP	ENST00000425013.2	37	CCDS34595.1	.	.	.	.	.	.	.	.	.	.	C	15.78	2.934649	0.52866	.	.	ENSG00000011275	ENST00000425013;ENST00000389902	T;T	0.58060	0.52;0.36	5.97	4.14	0.48551	.	0.282691	0.35320	N	0.003290	T	0.44244	0.1284	L	0.39898	1.24	0.40586	D	0.981443	P;P	0.40534	0.72;0.669	B;B	0.39840	0.311;0.221	T	0.40098	-0.9581	10	0.49607	T	0.09	-4.9688	11.066	0.47976	0.0:0.8013:0.1292:0.0694	.	229;286	Q9NWF9;Q9NWF9-1	RN216_HUMAN;.	A	229;286	ENSP00000404602:G229A;ENSP00000374552:G286A	ENSP00000374550:G229A	G	-	2	0	RNF216	5747317	0.994000	0.37717	0.954000	0.39281	0.969000	0.65631	1.881000	0.39638	0.831000	0.34780	0.561000	0.74099	GGC		0.552	RNF216-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000340374.1	NM_207111	
PMS2	5395	broad.mit.edu	37	7	6029582	6029582	+	Silent	SNP	G	G	A	rs186577215		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:6029582G>A	ENST00000265849.7	-	10	1098	c.993C>T	c.(991-993)tgC>tgT	p.C331C	PMS2_ENST00000441476.2_Silent_p.C225C|PMS2_ENST00000406569.3_Silent_p.C331C|PMS2_ENST00000469652.1_Intron|PMS2_ENST00000382321.4_Intron	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	331					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|single base insertion or deletion binding (GO:0032138)	p.C331C(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(11)|lung(13)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)		TGATATCAACGCATTCTAAGG	0.294			"""Mis, N, F"""			"""colorectal, endometrial, ovarian, medulloblastoma, glioma"""		Direct reversal of damage;Mismatch excision repair (MMR)	Turcot syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				A|||	1	0.000199681	0.0008	0.0	5008	,	,		16265	0.0		0.0	False		,,,				2504	0.0				p.C331C		yes	Rec		"""Hereditary non-polyposis colorectal cancer, Turcot syndrome"""	7	7p22	5395	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)		E	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C993T	7						.	A		1,4401	2.1+/-5.4	0,1,2200	66.0	61.0	63.0		993	5.6	1.0	7		63	0,8600		0,0,4300	no	coding-synonymous	PMS2	NM_000535.5		0,1,6500	AA,AG,GG		0.0,0.0227,0.0077		331/863	6029582	1,13001	2201	4300	6501	5996108	SO:0001819	synonymous_variant	5395	exon10	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III		CCDS5343.1	7p22.1	2014-09-17	2001-11-28		ENSG00000122512	ENSG00000122512			9122	protein-coding gene	gene with protein product		600259	"""postmeiotic segregation increased (S. cerevisiae) 2"""	PMSL2		8072530	Standard	NM_000535		Approved	H_DJ0042M02.9, HNPCC4	uc003spl.3	P54278	OTTHUMG00000023135	ENST00000265849.7:c.993C>T	7.37:g.6029582G>A			5996108	NM_000535	B2R610|Q52LH6|Q5FBW9|Q5FBX1|Q5FBX2|Q75MR2	Silent	SNP	ENST00000265849.7	37	CCDS5343.1																																																																																				0.294	PMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207353.3	NM_000535	
USP42	84132	broad.mit.edu	37	7	6196564	6196564	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:6196564A>G	ENST00000306177.5	+	16	3979	c.3821A>G	c.(3820-3822)cAg>cGg	p.Q1274R		NM_032172.2	NP_115548.1	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	1274					cell differentiation (GO:0030154)|protein deubiquitination (GO:0016579)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)	p.Q1374R(1)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(2)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	35		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)		CGGAGAGCCCAGGGTGGCTTT	0.527																																					p.R1274G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3820G	7						.						34.0	38.0	37.0					7																	6196564		1881	4108	5989	6163089	SO:0001583	missense	84132	exon16			AK022759	CCDS47535.1	7p22.2	2005-08-08	2005-08-08		ENSG00000106346	ENSG00000106346		"""Ubiquitin-specific peptidases"""	20068	protein-coding gene	gene with protein product			"""ubiquitin specific protease 42"""			12838346	Standard	NM_032172		Approved	FLJ12697	uc011jwp.2	Q9H9J4	OTTHUMG00000151888	ENST00000306177.5:c.3821A>G	7.37:g.6196564A>G	ENSP00000301962:p.Gln1274Arg		6163089	NM_032172	A2RUE3|B5MDA5|Q0VIN8|Q3C166|Q6P9B4	Missense_Mutation	SNP	ENST00000306177.5	37	CCDS47535.1	.	.	.	.	.	.	.	.	.	.	A	13.45	2.240897	0.39598	.	.	ENSG00000106346	ENST00000306177	T	0.13901	2.55	5.78	2.02	0.26589	.	0.586891	0.16130	N	0.228240	T	0.06645	0.0170	N	0.08118	0	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.32402	-0.9908	10	0.52906	T	0.07	.	6.9495	0.24538	0.642:0.284:0.0739:0.0	.	1170;1274;1274	A4D2N7;Q9H9J4-2;Q9H9J4	.;.;UBP42_HUMAN	R	1274	ENSP00000301962:Q1274R	ENSP00000301962:Q1274R	Q	+	2	0	USP42	6163089	0.969000	0.33509	0.039000	0.18376	0.034000	0.12701	2.930000	0.48924	0.107000	0.17824	0.533000	0.62120	CAG		0.527	USP42-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324262.3	XM_166526	
OSBPL3	26031	broad.mit.edu	37	7	24844019	24844019	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:24844019G>A	ENST00000313367.2	-	22	2933	c.2482C>T	c.(2482-2484)Caa>Taa	p.Q828*	OSBPL3_ENST00000487020.1_5'UTR|OSBPL3_ENST00000396431.1_Nonsense_Mutation_p.Q797*|OSBPL3_ENST00000431825.2_Nonsense_Mutation_p.Q761*|OSBPL3_ENST00000352860.1_Nonsense_Mutation_p.Q797*|OSBPL3_ENST00000396429.1_Nonsense_Mutation_p.Q792*|OSBPL3_ENST00000353930.1_Nonsense_Mutation_p.Q792*|OSBPL3_ENST00000409069.1_Nonsense_Mutation_p.Q761*	NM_015550.2	NP_056365.1	Q9H4L5	OSBL3_HUMAN	oxysterol binding protein-like 3	828					lipid transport (GO:0006869)	cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)	p.Q828*(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(19)|prostate(1)|skin(3)|urinary_tract(1)	43						CTCTGCTTTTGTATTTCAGCT	0.413																																					p.Q792X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2374T	7						.						147.0	126.0	133.0					7																	24844019		2203	4300	6503	24810544	SO:0001587	stop_gained	26031	exon21			AB014604	CCDS5390.1, CCDS5391.1, CCDS5392.1, CCDS47564.1	7p15.3	2013-01-10			ENSG00000070882	ENSG00000070882		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16370	protein-coding gene	gene with protein product		606732		OSBP3		9734811	Standard	XM_005249698		Approved	ORP-3, ORP3, KIAA0704	uc003sxf.3	Q9H4L5	OTTHUMG00000023277	ENST00000313367.2:c.2482C>T	7.37:g.24844019G>A	ENSP00000315410:p.Gln828*		24810544	NM_145321	A4D167|A4D168|A4D169|A4D170|A4D171|A4D172|B8ZZ79|B8ZZP0|O14591|O43357|O43358|Q8N702|Q8N703|Q8N704|Q8NFH0|Q8NFH1|Q8NI12|Q8NI13|Q9BZF4|Q9UED6	Nonsense_Mutation	SNP	ENST00000313367.2	37	CCDS5390.1	.	.	.	.	.	.	.	.	.	.	G	44	10.704371	0.99453	.	.	ENSG00000070882	ENST00000313367;ENST00000352860;ENST00000353930;ENST00000431825;ENST00000396431;ENST00000396429;ENST00000409069	.	.	.	5.73	5.73	0.89815	.	0.054531	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	-21.9633	19.8966	0.96963	0.0:0.0:1.0:0.0	.	.	.	.	X	828;797;792;761;797;792;761	.	ENSP00000315410:Q828X	Q	-	1	0	OSBPL3	24810544	1.000000	0.71417	0.738000	0.30950	0.896000	0.52359	8.818000	0.91991	2.700000	0.92200	0.655000	0.94253	CAA		0.413	OSBPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214085.2		
HOXA7	3204	broad.mit.edu	37	7	27194742	27194742	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:27194742C>T	ENST00000242159.3	-	2	612	c.479G>A	c.(478-480)cGc>cAc	p.R160H	HOXA-AS3_ENST00000518947.2_RNA|HOXA-AS3_ENST00000521231.1_RNA|HOXA-AS3_ENST00000524304.1_RNA|RP1-170O19.22_ENST00000467897.2_RNA|HOXA7_ENST00000523796.2_5'UTR|HOXA-AS3_ENST00000518848.1_RNA|RP1-170O19.23_ENST00000498652.1_RNA|HOXA-AS3_ENST00000521197.1_RNA	NM_006896.3	NP_008827.2	P31268	HXA7_HUMAN	homeobox A7	160	Poly-Arg.				angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of monocyte differentiation (GO:0045656)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.R160H(1)		endometrium(3)|large_intestine(1)|lung(10)|prostate(1)|urinary_tract(1)	16						GATTTCAATGCGGCGGCGCCG	0.607																																					p.R160H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G479A	7						.						94.0	100.0	98.0					7																	27194742		2203	4300	6503	27161267	SO:0001583	missense	3204	exon2				CCDS5408.1	7p15.2	2011-06-20	2005-12-22		ENSG00000122592	ENSG00000122592		"""Homeoboxes / ANTP class : HOXL subclass"""	5108	protein-coding gene	gene with protein product		142950	"""homeo box A7"""	HOX1A, HOX1		1973146, 1358459	Standard	NM_006896		Approved		uc003sys.3	P31268	OTTHUMG00000023217	ENST00000242159.3:c.479G>A	7.37:g.27194742C>T	ENSP00000242159:p.Arg160His		27161267	NM_006896	A4D191|O43368|O43486|O95655|Q9NSC8|Q9UDM1	Missense_Mutation	SNP	ENST00000242159.3	37	CCDS5408.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.953305	0.92660	.	.	ENSG00000122592	ENST00000242159	D	0.97505	-4.41	4.96	4.96	0.65561	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99140	0.9703	H	0.98155	4.16	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99038	1.0823	10	0.87932	D	0	.	18.2675	0.90056	0.0:1.0:0.0:0.0	.	160	P31268	HXA7_HUMAN	H	160	ENSP00000242159:R160H	ENSP00000242159:R160H	R	-	2	0	HOXA7	27161267	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.679000	0.84048	2.324000	0.78689	0.456000	0.33151	CGC		0.607	HOXA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358695.1		
AC005013.5	0	broad.mit.edu	37	7	28997342	28997342	+	lincRNA	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:28997342C>T	ENST00000436594.1	+	0	60				TRIL_ENST00000322982.3_RNA																							CTTCCAGCCGCGAGAGCTTCT	0.652																																					p.S107S												.	.	0			c.G321A	7						.						36.0	38.0	37.0					7																	28997342		1918	4141	6059	28963867			9865	exon1																															7.37:g.28997342C>T			28963867	NM_014817		Silent	SNP	ENST00000436594.1	37																																																																																					0.652	AC005013.5-001	KNOWN	basic|exp_conf	lincRNA	lincRNA	OTTHUMT00000327953.3		
RP9	6100	broad.mit.edu	37	7	33138949	33138949	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:33138949G>A	ENST00000297157.3	-	3	300	c.283C>T	c.(283-285)Cca>Tca	p.P95S		NM_203288.1	NP_976033.1	Q8TA86	RP9_HUMAN	retinitis pigmentosa 9 (autosomal dominant)	95	PIM1-binding. {ECO:0000250}.				cognition (GO:0050890)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|signal recognition particle receptor complex (GO:0005785)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.P95S(1)		large_intestine(3)|lung(3)|urinary_tract(1)	7			GBM - Glioblastoma multiforme(11;0.0403)			TTCCCCAGTGGCATCCAAAGT	0.443																																					p.P95S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C283T	7						.						167.0	147.0	154.0					7																	33138949		2203	4300	6503	33105474	SO:0001583	missense	6100	exon3			AX016710	CCDS5440.1	7p14.3	2014-01-28			ENSG00000164610	ENSG00000164610			10288	protein-coding gene	gene with protein product	"""Pim-1 kinase associated protein"""	607331				8513323	Standard	NM_203288		Approved	PAP-1	uc003tdm.3	Q8TA86	OTTHUMG00000152988	ENST00000297157.3:c.283C>T	7.37:g.33138949G>A	ENSP00000297157:p.Pro95Ser		33105474	NM_203288		Missense_Mutation	SNP	ENST00000297157.3	37	CCDS5440.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.478431	0.84747	.	.	ENSG00000164610	ENST00000297157;ENST00000448915	D;D	0.85258	-1.96;-1.96	3.43	3.43	0.39272	.	0.000000	0.85682	U	0.000000	D	0.90048	0.6892	L	0.56199	1.76	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.91442	0.5174	10	0.72032	D	0.01	-19.084	15.7391	0.77870	0.0:0.0:1.0:0.0	.	95	Q8TA86	RP9_HUMAN	S	95;61	ENSP00000297157:P95S;ENSP00000411577:P61S	ENSP00000297157:P95S	P	-	1	0	RP9	33105474	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.918000	0.92759	1.862000	0.54008	0.563000	0.77884	CCA		0.443	RP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328914.1	NM_203288	
GPR141	353345	broad.mit.edu	37	7	37780693	37780693	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:37780693T>C	ENST00000447769.1	+	4	987	c.698T>C	c.(697-699)gTc>gCc	p.V233A	EPDR1_ENST00000476620.1_Intron|GPR141_ENST00000461610.1_Intron|GPR141_ENST00000334425.1_Missense_Mutation_p.V233A			Q7Z602	GP141_HUMAN	G protein-coupled receptor 141	233						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.V233A(1)		NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(13)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TTTATAGGGGTCATCCTTGTT	0.418																																					p.V233A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T698C	7						.						163.0	163.0	163.0					7																	37780693		2203	4300	6503	37747218	SO:0001583	missense	353345	exon1			AY288420	CCDS5451.1	7p14.1	2012-08-21			ENSG00000187037	ENSG00000187037		"""GPCR / Class A : Orphans"""	19997	protein-coding gene	gene with protein product		609045				12679517, 14623098	Standard	NM_181791		Approved	PGR13	uc003tfm.1	Q7Z602	OTTHUMG00000102105	ENST00000447769.1:c.698T>C	7.37:g.37780693T>C	ENSP00000390410:p.Val233Ala		37747218	NM_181791	A4D1X7|Q0VAR5|Q86SP3	Missense_Mutation	SNP	ENST00000447769.1	37	CCDS5451.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.375179	0.82682	.	.	ENSG00000187037	ENST00000447769;ENST00000334425	T;T	0.74315	-0.83;-0.83	5.2	5.2	0.72013	GPCR, rhodopsin-like superfamily (1);	0.198107	0.43579	D	0.000551	T	0.78717	0.4327	M	0.66939	2.045	0.80722	D	1	P	0.45715	0.865	P	0.49829	0.623	T	0.78605	-0.2139	10	0.39692	T	0.17	-18.5361	14.4964	0.67691	0.0:0.0:0.0:1.0	.	233	Q7Z602	GP141_HUMAN	A	233	ENSP00000390410:V233A;ENSP00000334540:V233A	ENSP00000334540:V233A	V	+	2	0	GPR141	37747218	1.000000	0.71417	0.867000	0.34043	0.982000	0.71751	7.493000	0.81493	2.324000	0.78689	0.533000	0.62120	GTC		0.418	GPR141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219943.2	NM_181791	
SFRP4	6424	broad.mit.edu	37	7	37956092	37956092	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:37956092C>T	ENST00000436072.2	-	1	425	c.48G>A	c.(46-48)gcG>gcA	p.A16A	EPDR1_ENST00000476620.1_Intron	NM_003014.3	NP_003005.2	Q6FHJ7	SFRP4_HUMAN	secreted frizzled-related protein 4	16					brain development (GO:0007420)|cell differentiation (GO:0030154)|decidualization (GO:0046697)|epithelium development (GO:0060429)|gonad development (GO:0008406)|mammary gland involution (GO:0060056)|menstrual cycle phase (GO:0022601)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of JNK cascade (GO:0046329)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of sodium-dependent phosphate transport (GO:2000119)|phosphate ion homeostasis (GO:0055062)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epidermal cell differentiation (GO:0045606)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte apoptotic process (GO:1902174)|positive regulation of receptor internalization (GO:0002092)|response to hormone (GO:0009725)|vasculature development (GO:0001944)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.A16A(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	29						GCACGCCCAGCGCCAGGTGCA	0.677																																					p.A16A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G48A	7						.						39.0	36.0	37.0					7																	37956092		2201	4298	6499	37922617	SO:0001819	synonymous_variant	6424	exon1			AF026692	CCDS5453.1	7p14.1	2008-07-18			ENSG00000106483	ENSG00000106483		"""Secreted frizzled-related proteins"""	10778	protein-coding gene	gene with protein product		606570				10211996	Standard	NM_003014		Approved	frpHE, FRP-4, FRPHE	uc003tfo.4	Q6FHJ7	OTTHUMG00000023026	ENST00000436072.2:c.48G>A	7.37:g.37956092C>T			37922617	NM_003014	B4DYC1|O14877|Q05BG7|Q1ZYW2|Q4G124|Q6FHM0|Q6PD64	Silent	SNP	ENST00000436072.2	37	CCDS5453.1																																																																																				0.677	SFRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220017.2	NM_003014	
HECW1	23072	broad.mit.edu	37	7	43590187	43590187	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:43590187C>T	ENST00000395891.2	+	27	4997	c.4392C>T	c.(4390-4392)taC>taT	p.Y1464Y	HECW1_ENST00000453890.1_Silent_p.Y1430Y	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	1464	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.Y1443Y(1)		NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						GCGGCTTCTACGAGGTGAGGC	0.652																																					p.Y1464Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4392T	7						.						32.0	37.0	35.0					7																	43590187		2136	4251	6387	43556712	SO:0001819	synonymous_variant	23072	exon27			AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.4392C>T	7.37:g.43590187C>T			43556712	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Silent	SNP	ENST00000395891.2	37	CCDS5469.2																																																																																				0.652	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052	
COA1	55744	broad.mit.edu	37	7	43687204	43687204	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:43687204C>T	ENST00000395879.1	-	2	1726	c.45G>A	c.(43-45)ctG>ctA	p.L15L	COA1_ENST00000310564.6_Silent_p.L15L|COA1_ENST00000223336.6_Silent_p.L15L|COA1_ENST00000395880.3_Silent_p.L15L			Q9GZY4	COA1_HUMAN	cytochrome c oxidase assembly factor 1 homolog (S. cerevisiae)	15					mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrial respiratory chain complex IV assembly (GO:0033617)	cytoplasm (GO:0005737)|integral component of mitochondrial inner membrane (GO:0031305)|mitochondrion (GO:0005739)		p.L15L(1)									TCCTTGCTCCCAGAGGCATTG	0.488																																					p.L15L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G45A	7						.						68.0	69.0	68.0					7																	43687204		2203	4300	6503	43653729	SO:0001819	synonymous_variant	55744	exon3			AK001665	CCDS5471.1	7p13	2012-12-05	2012-10-15	2012-06-25	ENSG00000106603	ENSG00000106603		"""Mitochondrial respiratory chain complex assembly factors"""	21868	protein-coding gene	gene with protein product		614769	"""chromosome 7 open reading frame 44"""	C7orf44		22356826	Standard	NM_018224		Approved	FLJ10803, MITRAC15	uc003tin.2	Q9GZY4	OTTHUMG00000128949	ENST00000395879.1:c.45G>A	7.37:g.43687204C>T			43653729	NM_018224	A6NJU8|A8KAH8|Q9HAB7|Q9NVD2	Silent	SNP	ENST00000395879.1	37	CCDS5471.1																																																																																				0.488	COA1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313664.1	NM_018224	
NPC1L1	29881	broad.mit.edu	37	7	44579111	44579111	+	Silent	SNP	G	G	A	rs200674464		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:44579111G>A	ENST00000289547.4	-	2	940	c.885C>T	c.(883-885)ttC>ttT	p.F295F	NPC1L1_ENST00000381160.3_Silent_p.F295F|NPC1L1_ENST00000423141.1_Silent_p.F295F|NPC1L1_ENST00000546276.1_Silent_p.F295F	NM_013389.2	NP_037521.2	Q9UHC9	NPCL1_HUMAN	NPC1-like 1	295					cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intestinal cholesterol absorption (GO:0030299)|lipoprotein metabolic process (GO:0042157)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)	brush border membrane (GO:0031526)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hedgehog receptor activity (GO:0008158)|myosin V binding (GO:0031489)|Rab GTPase binding (GO:0017137)	p.F295F(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(7)|lung(27)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	57					Ezetimibe(DB00973)	TGACCACAGCGAAGACAGAGC	0.622													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19127	0.0		0.0	False		,,,				2504	0.0				p.F295F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C885T	7						.	G	,	2,4404	4.2+/-10.8	0,2,2201	81.0	86.0	84.0		885,885	-10.1	0.0	7	dbSNP_134	84	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	NPC1L1	NM_001101648.1,NM_013389.2	,	0,4,6499	AA,AG,GG		0.0233,0.0454,0.0308	,	295/1333,295/1360	44579111	4,13002	2203	4300	6503	44545636	SO:0001819	synonymous_variant	29881	exon2				CCDS5491.1, CCDS43575.1, CCDS75587.1	7p13	2012-11-15	2012-11-15		ENSG00000015520	ENSG00000015520			7898	protein-coding gene	gene with protein product		608010	"""NPC1 (Niemann-Pick disease, type C1, gene)-like 1"""			10783261	Standard	NM_013389		Approved		uc003tlb.3	Q9UHC9	OTTHUMG00000023691	ENST00000289547.4:c.885C>T	7.37:g.44579111G>A			44545636	NM_013389	A4D2J7|B7ZLE6|D3DVK9|Q17RV5|Q6R3Q4|Q9UHC8	Silent	SNP	ENST00000289547.4	37	CCDS5491.1																																																																																				0.622	NPC1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251256.1	NM_013389	
TBRG4	9238	broad.mit.edu	37	7	45145306	45145306	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:45145306C>A	ENST00000258770.3	-	3	590	c.469G>T	c.(469-471)Ggc>Tgc	p.G157C	TBRG4_ENST00000494076.1_Missense_Mutation_p.G157C|SNORA5C_ENST00000364902.1_RNA|TBRG4_ENST00000395655.4_Missense_Mutation_p.G157C|TBRG4_ENST00000471142.1_5'Flank|TBRG4_ENST00000361278.3_Missense_Mutation_p.G157C|SNORA5B_ENST00000363786.1_RNA|SNORA5A_ENST00000384111.1_RNA	NM_004749.3	NP_004740.2	Q969Z0	TBRG4_HUMAN	transforming growth factor beta regulator 4	157					cell cycle arrest (GO:0007050)|cellular respiration (GO:0045333)|positive regulation of cell proliferation (GO:0008284)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)	p.G157C(1)		cervix(1)|endometrium(3)|large_intestine(2)|lung(8)|skin(1)|stomach(2)	17						TTGGGGATGCCCAGAGCATAC	0.592																																					p.G157C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G469T	7						.						65.0	62.0	63.0					7																	45145306		2203	4300	6503	45111831	SO:0001583	missense	9238	exon3			AB023165	CCDS5501.1, CCDS5502.1	7p13	2006-07-07			ENSG00000136270	ENSG00000136270			17443	protein-coding gene	gene with protein product	"""FAST kinase domains 4"", ""cell cycle progression 2 protein"""	611325				9383053	Standard	NM_004749		Approved	Cpr2, KIAA0948, H_TD2522F11.8, FASTKD4	uc011kcd.3	Q969Z0	OTTHUMG00000129247	ENST00000258770.3:c.469G>T	7.37:g.45145306C>A	ENSP00000258770:p.Gly157Cys		45111831	NM_199122	A4D2L2|A4D2L3|D3DVL5|D3DVL6|O14710|Q53GI8|Q8NDM4|Q9BUC6|Q9Y2F6	Missense_Mutation	SNP	ENST00000258770.3	37	CCDS5501.1	.	.	.	.	.	.	.	.	.	.	C	7.273	0.607544	0.14002	.	.	ENSG00000136270	ENST00000258770;ENST00000361278;ENST00000395655;ENST00000494076;ENST00000478532;ENST00000461363	T;T;T;T;T;T	0.41400	1.0;1.0;1.0;1.0;1.0;1.0	5.76	1.67	0.24075	.	0.959523	0.08682	N	0.909375	T	0.53578	0.1805	L	0.58101	1.795	0.09310	N	1	D;D;D	0.69078	0.997;0.989;0.994	P;P;P	0.57204	0.815;0.639;0.778	T	0.43572	-0.9383	10	0.56958	D	0.05	.	10.4558	0.44550	0.0:0.4755:0.4433:0.0811	.	168;157;157	B4DU42;Q969Z0-2;Q969Z0	.;.;TBRG4_HUMAN	C	157;157;157;157;122;103	ENSP00000258770:G157C;ENSP00000354992:G157C;ENSP00000379016:G157C;ENSP00000420597:G157C;ENSP00000418631:G122C;ENSP00000417743:G103C	ENSP00000258770:G157C	G	-	1	0	TBRG4	45111831	0.001000	0.12720	0.010000	0.14722	0.012000	0.07955	0.358000	0.20216	0.319000	0.23209	-0.175000	0.13238	GGC		0.592	TBRG4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251351.1	NM_030900	
ZNF273	10793	broad.mit.edu	37	7	64378017	64378017	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:64378017T>C	ENST00000476120.1	+	2	232	c.161T>C	c.(160-162)cTg>cCg	p.L54P	ZNF273_ENST00000527278.1_3'UTR|ZNF273_ENST00000545510.1_Missense_Mutation_p.L21P|ZNF273_ENST00000319636.5_5'UTR	NM_021148.2	NP_066971.2	Q14593	ZN273_HUMAN	zinc finger protein 273	54					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L54P(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Lung NSC(55;0.0295)|all_lung(88;0.0691)				TGGCAATGCCTGGACACTTCA	0.393																																					p.L54P	Ovarian(154;605 895 6696 7659 15316 19321 21716 23848 32322 36932)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T161C	7						.						142.0	148.0	146.0					7																	64378017		2203	4300	6503	64015452	SO:0001583	missense	10793	exon2			X78932	CCDS5528.2	7q11.21	2013-01-08				ENSG00000198039		"""Zinc fingers, C2H2-type"", ""-"""	13067	protein-coding gene	gene with protein product		604756				7865130	Standard	NR_003099		Approved	HZF9	uc003tto.3	Q14593		ENST00000476120.1:c.161T>C	7.37:g.64378017T>C	ENSP00000418719:p.Leu54Pro		64015452	NM_021148	B3KQZ5|Q6P3V4	Missense_Mutation	SNP	ENST00000476120.1	37	CCDS5528.2	.	.	.	.	.	.	.	.	.	.	.	14.39	2.521085	0.44866	.	.	ENSG00000198039	ENST00000476120;ENST00000545510	T;T	0.19250	2.16;2.16	0.118	0.118	0.14667	Krueppel-associated box (4);	.	.	.	.	T	0.51907	0.1702	H	0.97540	4.025	0.51482	D	0.999925	D	0.56287	0.975	P	0.58130	0.833	T	0.64728	-0.6339	8	0.87932	D	0	.	.	.	.	.	54	Q14593	ZN273_HUMAN	P	54;21	ENSP00000418719:L54P;ENSP00000440725:L21P	ENSP00000418719:L54P	L	+	2	0	ZNF273	64015452	0.265000	0.24102	0.790000	0.31976	0.795000	0.44927	1.788000	0.38714	0.165000	0.19558	0.163000	0.16589	CTG		0.393	ZNF273-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313502.1		
AUTS2	26053	broad.mit.edu	37	7	69064845	69064845	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:69064845G>A	ENST00000342771.4	+	1	527	c.206G>A	c.(205-207)cGg>cAg	p.R69Q	AUTS2_ENST00000403018.2_Missense_Mutation_p.R69Q|AUTS2_ENST00000406775.2_Missense_Mutation_p.R69Q|RP5-942I16.1_ENST00000436600.2_lincRNA	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	69								p.R69Q(1)		breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		GCCCCGTCCCGGCCCAGACCC	0.667																																					p.R69Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G206A	7						.						17.0	19.0	19.0					7																	69064845		2146	4143	6289	68702781	SO:0001583	missense	26053	exon1			AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.206G>A	7.37:g.69064845G>A	ENSP00000344087:p.Arg69Gln		68702781	NM_015570	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Missense_Mutation	SNP	ENST00000342771.4	37	CCDS5539.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.447004	0.84101	.	.	ENSG00000158321	ENST00000406775;ENST00000342771;ENST00000403018	T;T	0.39406	1.1;1.08	4.11	3.2	0.36748	.	0.000000	0.39475	N	0.001355	T	0.49423	0.1556	L	0.34521	1.04	0.26326	N	0.977598	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.992;0.992;0.996	T	0.29027	-1.0025	9	.	.	.	.	11.634	0.51192	0.0981:0.0:0.9019:0.0	.	69;69;69	Q8WXX7-2;Q8WXX7;Q6PJU5	.;AUTS2_HUMAN;.	Q	69	ENSP00000385263:R69Q;ENSP00000344087:R69Q	.	R	+	2	0	AUTS2	68702781	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.252000	0.65445	1.996000	0.58369	0.655000	0.94253	CGG		0.667	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2		
AUTS2	26053	broad.mit.edu	37	7	70255094	70255094	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:70255094G>A	ENST00000342771.4	+	19	3213	c.2892G>A	c.(2890-2892)ccG>ccA	p.P964P	AUTS2_ENST00000406775.2_Silent_p.P940P	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	964								p.P964P(1)		breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		AGGCCGAGCCGCGCAAGGGTG	0.682																																					p.P964P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2892A	7						.						14.0	13.0	13.0					7																	70255094		2152	4254	6406	69893030	SO:0001819	synonymous_variant	26053	exon19			AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.2892G>A	7.37:g.70255094G>A			69893030	NM_015570	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Silent	SNP	ENST00000342771.4	37	CCDS5539.1																																																																																				0.682	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2		
ABHD11	83451	broad.mit.edu	37	7	73150967	73150967	+	Silent	SNP	C	C	T	rs199981712		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:73150967C>T	ENST00000222800.3	-	6	939	c.870G>A	c.(868-870)acG>acA	p.T290T	LINC00035_ENST00000427153.1_RNA|ABHD11_ENST00000395147.4_Silent_p.T233T|ABHD11_ENST00000437775.2_Silent_p.T283T|ABHD11_ENST00000468998.1_5'Flank|ABHD11_ENST00000458339.1_3'UTR	NM_148912.2	NP_683710.1	Q8NFV4	ABHDB_HUMAN	abhydrolase domain containing 11	290						mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)	p.T290T(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(1)	4		Lung NSC(55;0.0908)|all_lung(88;0.198)				CGTTCGGCACCGTCTGCATCT	0.602																																					p.T290T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G870A	7						.						101.0	95.0	97.0					7																	73150967		2203	4300	6503	72788903	SO:0001819	synonymous_variant	83451	exon6			AF217971	CCDS5558.1, CCDS47607.1, CCDS47608.1, CCDS75615.1	7q11.23	2010-08-05	2005-01-24	2005-01-27	ENSG00000106077	ENSG00000106077		"""Abhydrolase domain containing"""	16407	protein-coding gene	gene with protein product			"""Williams Beuren syndrome chromosome region 21"""	WBSCR21		12073013	Standard	NR_026910		Approved	PP1226	uc003tzb.3	Q8NFV4	OTTHUMG00000130029	ENST00000222800.3:c.870G>A	7.37:g.73150967C>T			72788903	NM_148912	H7BYM8|Q6PJU0|Q8N722|Q8N723|Q8NFV2|Q8NFV3|Q9HBS8	Silent	SNP	ENST00000222800.3	37	CCDS5558.1																																																																																				0.602	ABHD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252306.1		
LIMK1	3984	broad.mit.edu	37	7	73513396	73513396	+	Missense_Mutation	SNP	G	G	A	rs544200500		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:73513396G>A	ENST00000336180.2	+	5	487	c.436G>A	c.(436-438)Gtc>Atc	p.V146I	LIMK1_ENST00000538333.3_Missense_Mutation_p.V112I|LIMK1_ENST00000418310.1_Missense_Mutation_p.V176I|LIMK1_ENST00000491052.1_3'UTR	NM_002314.3	NP_002305.1	P53667	LIMK1_HUMAN	LIM domain kinase 1	146					actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|nervous system development (GO:0007399)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of axon extension (GO:0045773)|positive regulation of stress fiber assembly (GO:0051496)|protein phosphorylation (GO:0006468)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)	ATP binding (GO:0005524)|heat shock protein binding (GO:0031072)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)	p.V146I(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	21		Lung NSC(55;0.137)			Dabrafenib(DB08912)	GGTGACCCCCGTCATCGAGCA	0.602													G|||	1	0.000199681	0.0008	0.0	5008	,	,		14101	0.0		0.0	False		,,,				2504	0.0				p.V146I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G436A	7						.						149.0	130.0	137.0					7																	73513396		2203	4300	6503	73151332	SO:0001583	missense	3984	exon5			D26309	CCDS5563.1, CCDS56491.1	7q11.23	2005-01-21			ENSG00000106683	ENSG00000106683			6613	protein-coding gene	gene with protein product		601329				8673124, 8812460	Standard	NM_002314		Approved	LIMK	uc003uaa.2	P53667	OTTHUMG00000023448	ENST00000336180.2:c.436G>A	7.37:g.73513396G>A	ENSP00000336740:p.Val146Ile		73151332	NM_002314	B7Z6I8|D3DXF4|D3DXF5|O15283|Q15820|Q15821|Q75MU3|Q9Y5Q1	Missense_Mutation	SNP	ENST00000336180.2	37	CCDS5563.1	.	.	.	.	.	.	.	.	.	.	G	16.48	3.134156	0.56828	.	.	ENSG00000106683	ENST00000418310;ENST00000419043;ENST00000336180;ENST00000423685;ENST00000538333	T;T;T;T	0.75477	-0.89;-0.89;0.57;-0.94	5.41	5.41	0.78517	.	0.140169	0.45867	D	0.000331	T	0.68650	0.3024	L	0.47716	1.5	0.47905	D	0.999546	B;B	0.23185	0.006;0.081	B;B	0.09377	0.003;0.004	T	0.64521	-0.6388	10	0.38643	T	0.18	-40.0786	16.7569	0.85502	0.0:0.0:1.0:0.0	.	112;146	B7Z6I8;P53667	.;LIMK1_HUMAN	I	176;146;146;112;112	ENSP00000409717:V176I;ENSP00000336740:V146I;ENSP00000396480:V112I;ENSP00000444452:V112I	ENSP00000336740:V146I	V	+	1	0	LIMK1	73151332	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.369000	0.59511	2.571000	0.86741	0.603000	0.83216	GTC		0.602	LIMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252335.2	NM_002314	
ZP3	7784	broad.mit.edu	37	7	76062947	76062947	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:76062947C>T	ENST00000394857.3	+	4	754	c.696C>T	c.(694-696)acC>acT	p.T232T	ZP3_ENST00000336517.4_Silent_p.T181T|ZP3_ENST00000416245.1_Silent_p.T56T	NM_001110354.1	NP_001103824.1	P21754	ZP3_HUMAN	zona pellucida glycoprotein 3 (sperm receptor)	232	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				binding of sperm to zona pellucida (GO:0007339)|blastocyst formation (GO:0001825)|calcium ion transmembrane transport (GO:0070588)|egg coat formation (GO:0035803)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|negative regulation of transcription, DNA-templated (GO:0045892)|oocyte development (GO:0048599)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of acrosomal vesicle exocytosis (GO:2000368)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of antral ovarian follicle growth (GO:2000388)|positive regulation of calcium ion import (GO:0090280)|positive regulation of humoral immune response (GO:0002922)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of ovarian follicle development (GO:2000386)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type IV hypersensitivity (GO:0001809)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|outer acrosomal membrane (GO:0002081)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|carbohydrate binding (GO:0030246)|manganese ion transmembrane transporter activity (GO:0005384)|signal transducer activity (GO:0004871)|store-operated calcium channel activity (GO:0015279)	p.T181T(1)		endometrium(1)|large_intestine(3)|lung(2)|skin(1)	7						CTTATCACACCATCGTGGACT	0.552																																					p.T181T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C543T	7						.						125.0	104.0	111.0					7																	76062947		2203	4300	6503	75900883	SO:0001819	synonymous_variant	7784	exon5			M60504	CCDS5586.1, CCDS47618.1	7q11.23	2014-07-04	2002-09-17	2002-09-20	ENSG00000188372	ENSG00000188372		"""Zona pellucida glycoproteins"""	13189	protein-coding gene	gene with protein product		182889	"""zona pellucida glycoprotein 3A (sperm receptor)"""	ZP3A, ZP3B		1478648	Standard	NM_007155		Approved	ZP3-424, ZP3-372, ZPC	uc003ufd.4	P21754	OTTHUMG00000130575	ENST00000394857.3:c.696C>T	7.37:g.76062947C>T			75900883	NM_007155	Q06633|Q29RW0	Silent	SNP	ENST00000394857.3	37	CCDS47618.1	.	.	.	.	.	.	.	.	.	.	C	9.037	0.988808	0.18966	.	.	ENSG00000188372	ENST00000394860	.	.	.	5.52	2.32	0.28847	.	.	.	.	.	T	0.44973	0.1319	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	T	0.35847	-0.9772	4	.	.	.	-17.277	3.0826	0.06267	0.1677:0.4288:0.3061:0.0974	.	.	.	.	L	54	.	.	P	+	2	0	ZP3	75900883	0.129000	0.22400	1.000000	0.80357	0.946000	0.59487	0.558000	0.23469	1.310000	0.45006	0.655000	0.94253	CCA		0.552	ZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253004.1		
GRM3	2913	broad.mit.edu	37	7	86468859	86468859	+	Missense_Mutation	SNP	G	G	A	rs563221454		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:86468859G>A	ENST00000361669.2	+	4	3128	c.2029G>A	c.(2029-2031)Gct>Act	p.A677T	GRM3_ENST00000439827.1_Intron|GRM3_ENST00000394720.2_Intron|GRM3_ENST00000546348.1_Missense_Mutation_p.A269T|GRM3_ENST00000536043.1_Missense_Mutation_p.A549T	NM_000840.2	NP_000831.2	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3	677					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|axon (GO:0030424)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)	p.A677T(1)		NS(2)|breast(6)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(43)|ovary(3)|pancreas(2)|prostate(4)|skin(25)|upper_aerodigestive_tract(5)	109	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)					CAAGAATGGCGCTCAGAGGCC	0.547													G|||	1	0.000199681	0.0	0.0	5008	,	,		19950	0.0		0.0	False		,,,				2504	0.001				p.A677T	GBM(52;969 1098 3139 52280)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2029A	7						.						84.0	81.0	82.0					7																	86468859		2203	4300	6503	86306795	SO:0001583	missense	2913	exon4				CCDS5600.1	7q21.1-q21.2	2012-08-29			ENSG00000198822	ENSG00000198822		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4595	protein-coding gene	gene with protein product		601115				8824806	Standard	NM_000840		Approved	GPRC1C, mGlu3, MGLUR3	uc003uid.3	Q14832	OTTHUMG00000022884	ENST00000361669.2:c.2029G>A	7.37:g.86468859G>A	ENSP00000355316:p.Ala677Thr		86306795	NM_000840	Q2PNZ6|Q75MV4|Q75N17|Q86YG6|Q8TBH9	Missense_Mutation	SNP	ENST00000361669.2	37	CCDS5600.1	.	.	.	.	.	.	.	.	.	.	G	16.12	3.032724	0.54790	.	.	ENSG00000198822	ENST00000361669;ENST00000546348;ENST00000536043	D;D;D	0.88354	-2.37;-2.37;-2.37	5.69	4.81	0.61882	GPCR, family 3, C-terminal (2);	0.093168	0.64402	D	0.000001	D	0.87458	0.6182	N	0.20401	0.57	0.80722	D	1	D;D;P	0.58620	0.966;0.983;0.789	P;P;P	0.58077	0.74;0.832;0.538	D	0.86350	0.1710	10	0.32370	T	0.25	.	13.7075	0.62648	0.0739:0.0:0.9261:0.0	.	269;549;677	B7Z204;F5GYZ2;Q14832	.;.;GRM3_HUMAN	T	677;269;549	ENSP00000355316:A677T;ENSP00000444064:A269T;ENSP00000441407:A549T	ENSP00000355316:A677T	A	+	1	0	GRM3	86306795	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.609000	0.98334	1.413000	0.46997	0.563000	0.77884	GCT		0.547	GRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253362.2		
CFAP69	79846	broad.mit.edu	37	7	89917577	89917577	+	Silent	SNP	C	C	T	rs188534119	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:89917577C>T	ENST00000389297.4	+	15	1937	c.1686C>T	c.(1684-1686)atC>atT	p.I562I	C7orf63_ENST00000497910.1_Silent_p.I544I|C7orf63_ENST00000316089.8_Silent_p.I562I	NM_001039706.2|NM_001160138.1	NP_001034795.2|NP_001153610.1	A5D8W1	CG063_HUMAN		562								p.I562I(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|prostate(3)	37						GAGTAGATATCGTTCTTCATG	0.338													A|||	32	0.00638978	0.0227	0.0029	5008	,	,		17386	0.0		0.0	False		,,,				2504	0.0				p.I544I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1632T	7						.	A	,	94,3560		1,92,1734	122.0	113.0	116.0		1686,1632	3.0	1.0	7		116	0,8164		0,0,4082	no	coding-synonymous,coding-synonymous	C7orf63	NM_001039706.2,NM_001160138.1	,	1,92,5816	TT,TC,CC		0.0,2.5725,0.7954	,	562/942,544/924	89917577	94,11724	1827	4082	5909	89755513	SO:0001819	synonymous_variant	79846	exon15																														ENST00000389297.4:c.1686C>T	7.37:g.89917577C>T			89755513	NM_001160138	A3KMP9|B4DYW6|B4DZP7|B9EIM7|Q6V705|Q8IY89|Q9H7C2	Silent	SNP	ENST00000389297.4	37	CCDS43613.2																																																																																				0.338	C7orf63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139891.4		
AKAP9	10142	broad.mit.edu	37	7	91708453	91708453	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:91708453A>G	ENST00000359028.2	+	32	7267	c.7042A>G	c.(7042-7044)Agt>Ggt	p.S2348G	AKAP9_ENST00000356239.3_Missense_Mutation_p.S2336G|AKAP9_ENST00000358100.2_Missense_Mutation_p.S2348G			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	2348	Glu-rich.				G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)	p.S2336G(1)|p.S2348G(1)		NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			ATGTTTGATGAGTGATCAAGA	0.299			T	BRAF	papillary thyroid																																p.S2328G			Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A6982G	7						.						46.0	45.0	45.0					7																	91708453		2203	4300	6503	91546389	SO:0001583	missense	10142	exon31			AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.7042A>G	7.37:g.91708453A>G	ENSP00000351922:p.Ser2348Gly		91546389	NM_147185	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	37		.	.	.	.	.	.	.	.	.	.	A	15.09	2.728741	0.48833	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394534	T;T;T;T	0.04015	3.82;3.83;3.82;3.73	5.22	5.22	0.72569	.	0.000000	0.40222	N	0.001144	T	0.17916	0.0430	M	0.66506	2.035	0.42923	D	0.994296	P;D;P;P	0.67145	0.946;0.996;0.884;0.884	P;D;P;P	0.70227	0.585;0.968;0.585;0.585	T	0.02837	-1.1104	10	0.26408	T	0.33	.	15.3939	0.74774	1.0:0.0:0.0:0.0	.	2340;2348;2336;2328	Q99996-6;Q99996;Q99996-2;Q99996-3	.;AKAP9_HUMAN;.;.	G	2336;2348;2348;2340;182	ENSP00000348573:S2336G;ENSP00000351922:S2348G;ENSP00000350813:S2348G;ENSP00000378042:S182G	ENSP00000348573:S2336G	S	+	1	0	AKAP9	91546389	1.000000	0.71417	0.997000	0.53966	0.986000	0.74619	4.597000	0.61062	2.088000	0.63022	0.477000	0.44152	AGT		0.299	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
CYP51A1	1595	broad.mit.edu	37	7	91761173	91761173	+	De_novo_Start_OutOfFrame	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:91761173T>C	ENST00000450723.1	-	0	151				CYP51A1_ENST00000003100.8_Missense_Mutation_p.Y69C|CTB-161K23.1_ENST00000453068.1_RNA|LRRD1_ENST00000422722.1_5'UTR	NM_001146152.1	NP_001139624.1	Q16850	CP51A_HUMAN	cytochrome P450, family 51, subfamily A, polypeptide 1						cholesterol biosynthetic process (GO:0006695)|cholesterol biosynthetic process via 24,25-dihydrolanosterol (GO:0033488)|demethylation (GO:0070988)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|sterol 14-demethylase activity (GO:0008398)	p.Y69C(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|skin(1)	10	all_cancers(62;2.16e-09)|all_epithelial(64;3.86e-08)|Breast(17;0.00206)|all_lung(186;0.169)|all_hematologic(106;0.215)|Lung NSC(181;0.227)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)		Itraconazole(DB01167)|Ketoconazole(DB01026)|Sertaconazole(DB01153)|Tioconazole(DB01007)	GGAGAAAATGTATGGAGGACT	0.343																																					p.Y69C	GBM(70;1100 1190 11592 25836 51397)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A206G	7						.						42.0	44.0	43.0					7																	91761173		2203	4297	6500	91599109			1595	exon2			U51685	CCDS5623.1, CCDS55123.1	7q21.2	2012-10-10	2003-02-14	2003-02-28	ENSG00000001630	ENSG00000001630		"""Cytochrome P450s"""	2649	protein-coding gene	gene with protein product		601637	"""cytochrome P450, 51 (lanosterol 14-alpha-demethylase)"""	CYP51		8975714	Standard	NM_000786		Approved	CP51, CYPL1, P450L1, LDM, P450-14DM	uc003ulm.4	Q16850	OTTHUMG00000131131	ENST00000450723.1:c.-110A>G	7.37:g.91761173T>C			91599109	NM_000786	A4D1F8|B2RAI4|B4DJ55|O00770|O00772|Q16784|Q8N1A8|Q99868	Missense_Mutation	SNP	ENST00000450723.1	37	CCDS55123.1	.	.	.	.	.	.	.	.	.	.	T	15.91	2.971042	0.53614	.	.	ENSG00000001630	ENST00000003100;ENST00000496998;ENST00000435873	D	0.85088	-1.94	5.22	5.22	0.72569	.	0.416475	0.29328	N	0.012476	T	0.74816	0.3766	N	0.22421	0.69	0.80722	D	1	B;B	0.16802	0.002;0.019	B;B	0.12156	0.005;0.007	T	0.70468	-0.4863	10	0.41790	T	0.15	.	9.8883	0.41274	0.264:0.0:0.0:0.736	.	9;63	B3KRC6;Q16850	.;CP51A_HUMAN	C	69;9;13	ENSP00000003100:Y69C	ENSP00000003100:Y69C	Y	-	2	0	CYP51A1	91599109	0.991000	0.36638	0.999000	0.59377	0.989000	0.77384	4.416000	0.59815	2.089000	0.63090	0.528000	0.53228	TAC		0.343	CYP51A1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000342054.2		
COL1A2	1278	broad.mit.edu	37	7	94024363	94024363	+	Missense_Mutation	SNP	C	C	T	rs543810166		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:94024363C>T	ENST00000297268.6	+	1	491	c.20C>T	c.(19-21)aCg>aTg	p.T7M		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	7					blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)	p.T7M(1)	COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	TTTGTGGATACGCGGACTTTG	0.557										HNSCC(75;0.22)	OREG0018169	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1	0.000199681	0.0	0.0	5008	,	,		17202	0.0		0.0	False		,,,				2504	0.001				p.T7M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C20T	7						.						195.0	165.0	175.0					7																	94024363		2203	4300	6503	93862299	SO:0001583	missense	1278	exon1			Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"""Collagens"""	2198	protein-coding gene	gene with protein product	"""alpha 2(I)-collagen"", ""alpha-2 collagen type I"", ""type I procollagen"", ""collagen I, alpha-2 polypeptide"", ""collagen of skin, tendon and bone, alpha-2 chain"""	120160	"""osteogenesis imperfecta type IV"""	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.20C>T	7.37:g.94024363C>T	ENSP00000297268:p.Thr7Met	1302	93862299	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Missense_Mutation	SNP	ENST00000297268.6	37	CCDS34682.1	.	.	.	.	.	.	.	.	.	.	C	13.50	2.254608	0.39896	.	.	ENSG00000164692	ENST00000297268;ENST00000545487	D	0.89617	-2.54	5.2	4.33	0.51752	.	0.110120	0.64402	N	0.000009	D	0.82838	0.5124	L	0.50333	1.59	0.36628	D	0.876133	B;B	0.32071	0.355;0.101	B;B	0.20955	0.032;0.014	D	0.83921	0.0301	10	0.48119	T	0.1	.	9.3742	0.38272	0.0:0.8399:0.0:0.1601	.	7;7	B4DTF5;P08123	.;CO1A2_HUMAN	M	7	ENSP00000297268:T7M	ENSP00000297268:T7M	T	+	2	0	COL1A2	93862299	1.000000	0.71417	1.000000	0.80357	0.778000	0.44026	2.819000	0.48049	1.579000	0.49836	0.655000	0.94253	ACG		0.557	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089	
DYNC1I1	1780	broad.mit.edu	37	7	95657561	95657561	+	Silent	SNP	T	T	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:95657561T>A	ENST00000324972.6	+	11	1288	c.1095T>A	c.(1093-1095)atT>atA	p.I365I	DYNC1I1_ENST00000359388.4_Silent_p.I328I|DYNC1I1_ENST00000457059.1_Silent_p.I348I|DYNC1I1_ENST00000437599.1_Silent_p.I345I|DYNC1I1_ENST00000537881.1_Silent_p.I328I|DYNC1I1_ENST00000447467.2_Silent_p.I348I	NM_004411.4	NP_004402.1	O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1	365					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|metabolic process (GO:0008152)|vesicle transport along microtubule (GO:0047496)	cytoplasmic dynein complex (GO:0005868)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|kinetochore (GO:0000776)|microtubule (GO:0005874)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)|spectrin binding (GO:0030507)	p.I365I(1)		NS(2)|autonomic_ganglia(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(27)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	54	all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191)		STAD - Stomach adenocarcinoma(171;0.0957)			CGGGCCAGATTGTCCTCTGGG	0.532																																					p.I365I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1095A	7						.						205.0	177.0	186.0					7																	95657561		2203	4300	6503	95495497	SO:0001819	synonymous_variant	1780	exon11			AF063228	CCDS5644.1, CCDS47645.1, CCDS47646.1, CCDS64718.1	7q21.3-q22.1	2013-01-18	2005-11-24	2005-11-24	ENSG00000158560	ENSG00000158560		"""Cytoplasmic dyneins"", ""WD repeat domain containing"""	2963	protein-coding gene	gene with protein product		603772	"""dynein, cytoplasmic, intermediate polypeptide 1"""	DNCI1		10049579, 16260502	Standard	NM_004411		Approved	DNCIC1	uc003uoc.4	O14576	OTTHUMG00000153983	ENST00000324972.6:c.1095T>A	7.37:g.95657561T>A			95495497	NM_004411	B4DME3|F5H050|G5E9K1|Q8TBF7|Q9Y2X1	Silent	SNP	ENST00000324972.6	37	CCDS5644.1																																																																																				0.532	DYNC1I1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333432.1	NM_004411	
ZNF394	84124	broad.mit.edu	37	7	99096340	99096340	+	Splice_Site	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:99096340C>T	ENST00000337673.6	-	2	785	c.582G>A	c.(580-582)ccG>ccA	p.P194P	ZNF789_ENST00000494186.1_Intron|ZNF789_ENST00000493485.1_Intron|ZNF394_ENST00000426306.2_Intron|ZNF394_ENST00000394177.3_5'UTR	NM_032164.2	NP_115540.2	Q53GI3	ZN394_HUMAN	zinc finger protein 394	194	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P194P(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(5)|stomach(1)|urinary_tract(1)	16	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					AGCACTCACTCGGCGGAACTG	0.582																																					p.P194P	Ovarian(24;589 697 9939 12704 40742)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G582A	7						.						113.0	82.0	93.0					7																	99096340		2203	4300	6503	98934276	SO:0001630	splice_region_variant	84124	exon2			BC025241	CCDS5666.1	7q22.1	2014-01-28			ENSG00000160908	ENSG00000160908		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	18832	protein-coding gene	gene with protein product							Standard	NM_032164		Approved	ZKSCAN14, FLJ12298, ZSCAN46	uc003uqs.3	Q53GI3	OTTHUMG00000154660	ENST00000337673.6:c.583+1G>A	7.37:g.99096340C>T			98934276	NM_032164	A4D281|Q05DA6|Q6P5X9|Q8TB27|Q9HA37|Q9UD51	Silent	SNP	ENST00000337673.6	37	CCDS5666.1																																																																																				0.582	ZNF394-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336498.1	NM_032164	Silent
STAG3	10734	broad.mit.edu	37	7	99799945	99799945	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:99799945C>T	ENST00000426455.1	+	24	2952	c.2545C>T	c.(2545-2547)Ccg>Tcg	p.P849S	GATS_ENST00000436886.2_3'UTR|STAG3_ENST00000394018.2_Missense_Mutation_p.P791S|STAG3_ENST00000317296.5_Missense_Mutation_p.P849S|STAG3_ENST00000440830.1_3'UTR|GATS_ENST00000543273.1_RNA	NM_001282716.1	NP_001269645.1	Q9UJ98	STAG3_HUMAN	stromal antigen 3	849					chromosome segregation (GO:0007059)|synaptonemal complex assembly (GO:0007130)	chromosome, centromeric region (GO:0000775)|extracellular space (GO:0005615)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)|nucleolus (GO:0005730)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)|transverse filament (GO:0000802)		p.P849S(1)		breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(11)|lung(30)|ovary(5)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	66	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CTTCATCCAGCCGGGAGACCT	0.542																																					p.P849S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2545T	7						.						74.0	76.0	75.0					7																	99799945		2203	4300	6503	99637881	SO:0001583	missense	10734	exon24			AJ007798	CCDS34703.1, CCDS64730.1, CCDS75642.1	7q22	2008-02-01			ENSG00000066923	ENSG00000066923			11356	protein-coding gene	gene with protein product		608489				10698974	Standard	XM_005250116		Approved		uc003utx.1	Q9UJ98	OTTHUMG00000155183	ENST00000426455.1:c.2545C>T	7.37:g.99799945C>T	ENSP00000400359:p.Pro849Ser		99637881	NM_012447	A6H8Z1|B4DZ10|D6W5U8|H7BYK9|Q8NDP3	Missense_Mutation	SNP	ENST00000426455.1	37	CCDS34703.1	.	.	.	.	.	.	.	.	.	.	.	4.879	0.163369	0.09287	.	.	ENSG00000066923	ENST00000426455;ENST00000394018;ENST00000317296	T;T;T	0.22539	1.95;1.96;1.95	5.56	2.63	0.31362	.	0.280729	0.25555	N	0.029870	T	0.15305	0.0369	L	0.40543	1.245	0.38320	D	0.943505	B;B;B	0.15473	0.002;0.013;0.005	B;B;B	0.11329	0.005;0.003;0.006	T	0.07558	-1.0766	10	0.54805	T	0.06	-2.2314	5.6436	0.17577	0.0:0.5626:0.2716:0.1658	.	791;849;849	B4DZ10;D6W5U7;Q9UJ98	.;.;STAG3_HUMAN	S	849;791;849	ENSP00000400359:P849S;ENSP00000377586:P791S;ENSP00000319318:P849S	ENSP00000319318:P849S	P	+	1	0	STAG3	99637881	0.001000	0.12720	0.994000	0.49952	0.089000	0.18198	0.531000	0.23052	0.723000	0.32274	0.563000	0.77884	CCG		0.542	STAG3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338734.2	NM_012447	
HTR5A	3361	broad.mit.edu	37	7	154863063	154863063	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr7:154863063C>T	ENST00000287907.2	+	1	1030	c.454C>T	c.(454-456)Cgc>Tgc	p.R152C	HTR5A-AS1_ENST00000543018.1_5'UTR|HTR5A-AS1_ENST00000395731.2_5'UTR|HTR5A-AS1_ENST00000493904.1_5'UTR	NM_024012.3	NP_076917.1	P47898	5HT5A_HUMAN	5-hydroxytryptamine (serotonin) receptor 5A, G protein-coupled	152					cAMP-mediated signaling (GO:0019933)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|hippocampus development (GO:0021766)|response to estradiol (GO:0032355)|serotonin receptor signaling pathway (GO:0007210)	dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	serotonin receptor activity (GO:0004993)	p.R152C(2)		NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(22)|ovary(2)|prostate(3)|stomach(1)	48	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0238)	UCEC - Uterine corpus endometrioid carcinoma (81;0.171)	Asenapine(DB06216)|Loxapine(DB00408)|Olanzapine(DB00334)	ATACACGCTCCGCACCCGCAA	0.627																																					p.R152C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C454T	7						.						97.0	71.0	80.0					7																	154863063		2203	4300	6503	154493996	SO:0001583	missense	3361	exon1				CCDS5936.1	7q36.1	2012-08-08	2012-02-03		ENSG00000157219	ENSG00000157219		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5300	protein-coding gene	gene with protein product		601305	"""5-hydroxytryptamine (serotonin) receptor 5A"""			7988681	Standard	NM_024012		Approved	5-HT5A	uc003wlu.2	P47898	OTTHUMG00000151327	ENST00000287907.2:c.454C>T	7.37:g.154863063C>T	ENSP00000287907:p.Arg152Cys		154493996	NM_024012	Q2M2D2	Missense_Mutation	SNP	ENST00000287907.2	37	CCDS5936.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.183618	0.78677	.	.	ENSG00000157219	ENST00000287907	T	0.73469	-0.75	4.75	3.86	0.44501	GPCR, rhodopsin-like superfamily (1);	0.124687	0.56097	D	0.000034	D	0.86969	0.6061	M	0.94142	3.5	0.53688	D	0.99997	D	0.62365	0.991	P	0.60012	0.867	D	0.88615	0.3159	10	0.66056	D	0.02	.	10.0952	0.42471	0.1551:0.6954:0.1494:0.0	.	152	P47898	5HT5A_HUMAN	C	152	ENSP00000287907:R152C	ENSP00000287907:R152C	R	+	1	0	HTR5A	154493996	1.000000	0.71417	0.800000	0.32199	0.948000	0.59901	3.890000	0.56220	1.187000	0.43000	0.655000	0.94253	CGC		0.627	HTR5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322240.1	NM_024012	
ADAM7	8756	broad.mit.edu	37	8	24349417	24349418	+	Splice_Site	INS	-	-	A	rs3736281	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr8:24349417_24349418insA	ENST00000175238.6	+	14	1441_1442	c.1358_1359insA	c.(1357-1362)ataaaa>atAaaaa	p.IK453fs	ADAM7_ENST00000520720.1_Splice_Site_p.IK225fs|RP11-561E1.1_ENST00000519364.1_RNA|ADAM7_ENST00000380789.1_Splice_Site_p.IK453fs|RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA	NM_003817.3	NP_003808.2	Q9H2U9	ADAM7_HUMAN	ADAM metallopeptidase domain 7	453	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.		I -> T (in dbSNP:rs3736281).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.A456fs*11(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)		CCTCAACAGATAAAAAAAGCAG	0.436																																					p.I453fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1358_1359insA	8						.																																			24405308	SO:0001630	splice_region_variant	8756	exon14			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.1357-1->A	8.37:g.24349424_24349424dupA			24405307	NM_003817	A8K8X7|O75959|Q6PEJ6	Frame_Shift_Ins	INS	ENST00000175238.6	37	CCDS6045.1																																																																																				0.436	ADAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215150.1	NM_003817	Frame_Shift_Ins
PKHD1L1	93035	broad.mit.edu	37	8	110534466	110534466	+	Missense_Mutation	SNP	C	C	T	rs181620735	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr8:110534466C>T	ENST00000378402.5	+	74	12187	c.12083C>T	c.(12082-12084)gCt>gTt	p.A4028V		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	4028					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.A4032V(1)		NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			CTTGGACAAGCTGTAATTTTA	0.388										HNSCC(38;0.096)																											p.A4028V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C12083T	8						.						80.0	78.0	78.0					8																	110534466		1855	4094	5949	110603642	SO:0001583	missense	93035	exon74			AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.12083C>T	8.37:g.110534466C>T	ENSP00000367655:p.Ala4028Val		110603642	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.352842	0.82132	.	.	ENSG00000205038	ENST00000378402;ENST00000526472	D;D	0.87103	-2.21;-2.03	5.93	5.05	0.67936	.	0.055722	0.64402	D	0.000001	D	0.90779	0.7105	M	0.80183	2.485	0.36213	D	0.851471	D	0.59357	0.985	P	0.51385	0.668	D	0.93900	0.7187	10	0.59425	D	0.04	.	14.9846	0.71336	0.0:0.8568:0.1432:0.0	.	4028	Q86WI1	PKHL1_HUMAN	V	4028;956	ENSP00000367655:A4028V;ENSP00000437376:A956V	ENSP00000367655:A4028V	A	+	2	0	PKHD1L1	110603642	1.000000	0.71417	1.000000	0.80357	0.751000	0.42716	3.361000	0.52306	1.513000	0.48852	0.655000	0.94253	GCT		0.388	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
TRPS1	7227	broad.mit.edu	37	8	116599477	116599477	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr8:116599477C>T	ENST00000220888.5	-	4	2571	c.2412G>A	c.(2410-2412)ccG>ccA	p.P804P	TRPS1_ENST00000520276.1_Silent_p.P808P|TRPS1_ENST00000395715.3_Silent_p.P817P|TRPS1_ENST00000519076.1_Silent_p.P558P|TRPS1_ENST00000519674.1_Silent_p.P804P			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	804	Mediates interaction with GLI3.				chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.P804P(1)		autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			GGGTGTATGACGGACTCCCCC	0.567									Langer-Giedion syndrome																												p.P817P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2451A	8						.						153.0	159.0	157.0					8																	116599477		1969	4135	6104	116668652	SO:0001819	synonymous_variant	7227	exon5	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"""GATA zinc finger domain containing"", ""Zinc fingers, C2H2-type"""	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.2412G>A	8.37:g.116599477C>T			116668652	NM_014112	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Silent	SNP	ENST00000220888.5	37																																																																																					0.567	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112	
ENPP2	5168	broad.mit.edu	37	8	120613656	120613656	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr8:120613656T>C	ENST00000075322.6	-	10	938	c.880A>G	c.(880-882)Acc>Gcc	p.T294A	ENPP2_ENST00000259486.6_Missense_Mutation_p.T294A|ENPP2_ENST00000522826.1_Missense_Mutation_p.T294A|ENPP2_ENST00000427067.2_Missense_Mutation_p.T290A	NM_001040092.2	NP_001035181.1	Q13822	ENPP2_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 2	294					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylcholine catabolic process (GO:0034638)|phospholipid catabolic process (GO:0009395)|regulation of cell migration (GO:0030334)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alkylglycerophosphoethanolamine phosphodiesterase activity (GO:0047391)|calcium ion binding (GO:0005509)|hydrolase activity (GO:0016787)|lysophospholipase activity (GO:0004622)|nucleic acid binding (GO:0003676)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.T294A(1)		breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(30)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)	69	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			TCTGGCAGGGTGAGCCACTGC	0.403																																					p.T294A	Melanoma(20;305 879 2501 4818 31020)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A880G	8						.						140.0	131.0	134.0					8																	120613656		2203	4300	6503	120682837	SO:0001583	missense	5168	exon10			D45421	CCDS6329.1, CCDS34936.1, CCDS47914.1	8q24.12	2014-04-09	2008-08-01		ENSG00000136960	ENSG00000136960	3.1.4.1, 3.6.1.9		3357	protein-coding gene	gene with protein product	"""autotaxin"""	601060		PDNP2		8586446	Standard	NM_001040092		Approved	ATX, PD-IALPHA	uc003yos.2	Q13822	OTTHUMG00000164995	ENST00000075322.6:c.880A>G	8.37:g.120613656T>C	ENSP00000075322:p.Thr294Ala		120682837	NM_001130863	A8UHA1|E9PHP7|Q13827|Q14555|Q15117|Q9UCQ8|Q9UCR0|Q9UCR1|Q9UCR2|Q9UCR3|Q9UCR4	Missense_Mutation	SNP	ENST00000075322.6	37	CCDS34936.1	.	.	.	.	.	.	.	.	.	.	T	12.09	1.832405	0.32421	.	.	ENSG00000136960	ENST00000259486;ENST00000427067;ENST00000522826;ENST00000075322	T;T;T;T	0.72051	-0.62;-0.62;-0.62;-0.62	5.96	3.48	0.39840	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.421963	0.27535	N	0.018924	T	0.63498	0.2516	L	0.52573	1.65	0.24352	N	0.994915	B;B;B	0.15930	0.0;0.015;0.004	B;B;B	0.20384	0.003;0.029;0.009	T	0.55885	-0.8070	10	0.49607	T	0.09	.	10.1044	0.42524	0.2605:0.0:0.0:0.7395	.	294;294;294	E9PHP7;Q13822;Q13822-2	.;ENPP2_HUMAN;.	A	294;290;294;294	ENSP00000259486:T294A;ENSP00000403315:T290A;ENSP00000428291:T294A;ENSP00000075322:T294A	ENSP00000075322:T294A	T	-	1	0	ENPP2	120682837	1.000000	0.71417	0.908000	0.35775	0.708000	0.40852	1.950000	0.40323	0.441000	0.26529	0.533000	0.62120	ACC		0.403	ENPP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000381390.1		
TAF2	6873	broad.mit.edu	37	8	120795758	120795758	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr8:120795758C>T	ENST00000378164.2	-	16	2273	c.1975G>A	c.(1975-1977)Gtt>Att	p.V659I		NM_003184.3	NP_003175	Q6P1X5	TAF2_HUMAN	TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa	659					G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to organic cyclic compound (GO:0014070)|transcription initiation from RNA polymerase II promoter (GO:0006367)	transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	metallopeptidase activity (GO:0008237)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.V659I(2)		NS(2)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(21)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	49	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			TGTGCAACAACATCTCTCTCA	0.428																																					p.V659I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1975A	8						.						115.0	109.0	111.0					8																	120795758		2203	4300	6503	120864939	SO:0001583	missense	6873	exon16			AF040701	CCDS34937.1	8q24	2012-07-18	2002-08-29	2001-12-07	ENSG00000064313	ENSG00000064313			11536	protein-coding gene	gene with protein product		604912	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, B, 150kD"""	TAF2B		9774672, 9418870	Standard	NM_003184		Approved	TAFII150, CIF150	uc003you.3	Q6P1X5	OTTHUMG00000165009	ENST00000378164.2:c.1975G>A	8.37:g.120795758C>T	ENSP00000367406:p.Val659Ile		120864939	NM_003184	B2RE82|O43487|O43604|O60668|Q86WW7|Q8IWK4	Missense_Mutation	SNP	ENST00000378164.2	37	CCDS34937.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.155796	0.78114	.	.	ENSG00000064313	ENST00000378164	T	0.52983	0.64	6.07	6.07	0.98685	.	0.060702	0.64402	D	0.000003	T	0.44932	0.1317	L	0.39566	1.225	0.80722	D	1	P	0.40144	0.704	B	0.38683	0.279	T	0.21109	-1.0255	10	0.33940	T	0.23	-16.4676	20.6593	0.99626	0.0:1.0:0.0:0.0	.	659	Q6P1X5	TAF2_HUMAN	I	659	ENSP00000367406:V659I	ENSP00000367406:V659I	V	-	1	0	TAF2	120864939	1.000000	0.71417	0.975000	0.42487	0.977000	0.68977	7.794000	0.85869	2.885000	0.99019	0.655000	0.94253	GTT		0.428	TAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381436.1	NM_003184	
PTK2	5747	broad.mit.edu	37	8	141669578	141669578	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr8:141669578G>A	ENST00000522684.1	-	32	3375	c.3146C>T	c.(3145-3147)aCg>aTg	p.T1049M	PTK2_ENST00000517887.1_Missense_Mutation_p.T1093M|PTK2_ENST00000430260.2_Missense_Mutation_p.T359M|PTK2_ENST00000519465.1_Missense_Mutation_p.T677M|PTK2_ENST00000340930.3_Missense_Mutation_p.T1062M|PTK2_ENST00000535192.1_Missense_Mutation_p.T1003M|PTK2_ENST00000521059.1_Missense_Mutation_p.T1049M|PTK2_ENST00000519419.1_Missense_Mutation_p.T1093M|PTK2_ENST00000538769.1_Missense_Mutation_p.T717M|PTK2_ENST00000517712.1_Missense_Mutation_p.T112M|PTK2_ENST00000395218.2_Missense_Mutation_p.T1062M	NM_153831.3	NP_722560.1	Q05397	FAK1_HUMAN	protein tyrosine kinase 2	1049	Interaction with ARHGEF28. {ECO:0000250}.|Interaction with TGFB1I1.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell motility (GO:0048870)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|central nervous system neuron axonogenesis (GO:0021955)|embryo development (GO:0009790)|endothelial cell migration (GO:0043542)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|establishment of nucleus localization (GO:0040023)|extracellular matrix organization (GO:0030198)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|growth hormone receptor signaling pathway (GO:0060396)|heart morphogenesis (GO:0003007)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of organ growth (GO:0046621)|negative regulation of synapse assembly (GO:0051964)|netrin-activated signaling pathway (GO:0038007)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|placenta development (GO:0001890)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|regulation of endothelial cell migration (GO:0010594)|regulation of focal adhesion assembly (GO:0051893)|regulation of osteoblast differentiation (GO:0045667)|regulation of Rho GTPase activity (GO:0032319)|signal complex assembly (GO:0007172)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)	apical plasma membrane (GO:0016324)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|stress fiber (GO:0001725)	actin binding (GO:0003779)|ATP binding (GO:0005524)|JUN kinase binding (GO:0008432)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)	p.T1062M(1)|p.T1071M(1)|p.T1004M(1)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(6)|lung(23)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	48	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)			GTGTGGTCTCGTCTGCCCAAG	0.507																																					p.T1062M												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.C3185T	8						.						155.0	107.0	123.0					8																	141669578		2203	4300	6503	141738760	SO:0001583	missense	5747	exon33			L13616	CCDS6381.1, CCDS56557.1	8q24.3	2013-02-18	2013-02-18		ENSG00000169398	ENSG00000169398	2.7.10.1	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9611	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 71"""	600758	"""PTK2 protein tyrosine kinase 2"""			8422239	Standard	NM_153831		Approved	FAK, FADK, FAK1, PPP1R71	uc003yvt.3	Q05397	OTTHUMG00000067438	ENST00000522684.1:c.3146C>T	8.37:g.141669578G>A	ENSP00000429911:p.Thr1049Met		141738760	NM_001199649	B4E2N6|F5H4S4|Q14291|Q9UD85	Missense_Mutation	SNP	ENST00000522684.1	37	CCDS6381.1	.	.	.	.	.	.	.	.	.	.	G	18.80	3.701740	0.68501	.	.	ENSG00000169398	ENST00000522684;ENST00000535192;ENST00000519465;ENST00000517887;ENST00000521059;ENST00000395214;ENST00000395218;ENST00000354438;ENST00000395221;ENST00000517712;ENST00000523539;ENST00000340930;ENST00000538769;ENST00000519419;ENST00000430260;ENST00000521986	T;T;T;T;T;T;T;T;T;T;T;T;T	0.30981	1.51;1.51;1.51;1.51;1.51;1.51;1.51;1.51;1.51;1.51;1.51;1.51;1.51	5.85	5.85	0.93711	Focal adhesion kinase, targeting (FAT) domain (3);	0.600804	0.18454	N	0.140749	T	0.33177	0.0854	N	0.14661	0.345	0.32661	N	0.518151	P;P;P;P;P;P;P;P;P;P	0.50528	0.936;0.786;0.916;0.841;0.841;0.841;0.879;0.616;0.75;0.75	P;P;P;P;P;B;P;P;B;P	0.50934	0.654;0.654;0.572;0.467;0.467;0.379;0.555;0.489;0.408;0.549	T	0.38735	-0.9647	10	0.87932	D	0	.	20.1577	0.98120	0.0:0.0:1.0:0.0	.	1062;747;972;1049;1071;1003;1004;876;717;677	B4E2N6;B4DH13;Q59GN8;Q05397;Q658W2;Q8IYN9;Q59GM6;Q05397-2;Q8N9D7;E9PEI4	.;.;.;FAK1_HUMAN;.;.;.;.;.;.	M	1049;1003;677;1093;1049;1004;1062;973;747;112;721;1062;717;1093;359;750	ENSP00000429911:T1049M;ENSP00000438009:T1003M;ENSP00000429170:T677M;ENSP00000429082:T1093M;ENSP00000429474:T1049M;ENSP00000378644:T1062M;ENSP00000430916:T112M;ENSP00000428492:T721M;ENSP00000341189:T1062M;ENSP00000445742:T717M;ENSP00000429129:T1093M;ENSP00000403416:T359M;ENSP00000430603:T750M	ENSP00000341189:T1062M	T	-	2	0	PTK2	141738760	1.000000	0.71417	0.331000	0.25455	0.978000	0.69477	7.070000	0.76763	2.767000	0.95098	0.655000	0.94253	ACG		0.507	PTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378054.5	NM_005607	
PTK2	5747	broad.mit.edu	37	8	141711018	141711018	+	Missense_Mutation	SNP	C	C	T	rs200596356		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr8:141711018C>T	ENST00000522684.1	-	26	2700	c.2471G>A	c.(2470-2472)cGc>cAc	p.R824H	PTK2_ENST00000517887.1_Missense_Mutation_p.R868H|PTK2_ENST00000430260.2_Missense_Mutation_p.R134H|PTK2_ENST00000519465.1_Missense_Mutation_p.R452H|PTK2_ENST00000340930.3_Missense_Mutation_p.R824H|PTK2_ENST00000535192.1_Missense_Mutation_p.R778H|PTK2_ENST00000521059.1_Missense_Mutation_p.R824H|PTK2_ENST00000519419.1_Missense_Mutation_p.R868H|PTK2_ENST00000538769.1_Missense_Mutation_p.R492H|PTK2_ENST00000395218.2_Missense_Mutation_p.R824H	NM_153831.3	NP_722560.1	Q05397	FAK1_HUMAN	protein tyrosine kinase 2	824	Interaction with TGFB1I1.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell motility (GO:0048870)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|central nervous system neuron axonogenesis (GO:0021955)|embryo development (GO:0009790)|endothelial cell migration (GO:0043542)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|establishment of nucleus localization (GO:0040023)|extracellular matrix organization (GO:0030198)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|growth hormone receptor signaling pathway (GO:0060396)|heart morphogenesis (GO:0003007)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of organ growth (GO:0046621)|negative regulation of synapse assembly (GO:0051964)|netrin-activated signaling pathway (GO:0038007)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|placenta development (GO:0001890)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|regulation of endothelial cell migration (GO:0010594)|regulation of focal adhesion assembly (GO:0051893)|regulation of osteoblast differentiation (GO:0045667)|regulation of Rho GTPase activity (GO:0032319)|signal complex assembly (GO:0007172)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)	apical plasma membrane (GO:0016324)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|stress fiber (GO:0001725)	actin binding (GO:0003779)|ATP binding (GO:0005524)|JUN kinase binding (GO:0008432)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)	p.R846H(1)|p.R824H(1)|p.R776H(1)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(6)|lung(23)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	48	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)			TTCCAGCCAGCGCTGATCTTC	0.433													C|||	1	0.000199681	0.0	0.0	5008	,	,		19722	0.001		0.0	False		,,,				2504	0.0				p.R824H												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.G2471A	8						.						121.0	119.0	120.0					8																	141711018		2203	4300	6503	141780200	SO:0001583	missense	5747	exon26			L13616	CCDS6381.1, CCDS56557.1	8q24.3	2013-02-18	2013-02-18		ENSG00000169398	ENSG00000169398	2.7.10.1	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9611	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 71"""	600758	"""PTK2 protein tyrosine kinase 2"""			8422239	Standard	NM_153831		Approved	FAK, FADK, FAK1, PPP1R71	uc003yvt.3	Q05397	OTTHUMG00000067438	ENST00000522684.1:c.2471G>A	8.37:g.141711018C>T	ENSP00000429911:p.Arg824His		141780200	NM_001199649	B4E2N6|F5H4S4|Q14291|Q9UD85	Missense_Mutation	SNP	ENST00000522684.1	37	CCDS6381.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	35	5.494761	0.96339	.	.	ENSG00000169398	ENST00000522684;ENST00000535192;ENST00000519465;ENST00000517887;ENST00000521059;ENST00000395214;ENST00000395218;ENST00000354438;ENST00000395221;ENST00000523539;ENST00000340930;ENST00000538769;ENST00000519419;ENST00000430260;ENST00000521986	T;T;T;T;T;T;T;T;T;T;T;T	0.77358	-1.07;-1.06;-1.07;-1.09;-1.07;-1.05;-1.05;-1.07;-1.05;-1.09;1.19;-1.05	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	D	0.87935	0.6303	M	0.68952	2.095	0.58432	D	0.999999	D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0;1.0;1.0;1.0;0.999;0.999	D;D;P;D;P;D;D;D;P;P	0.91635	0.996;0.999;0.904;0.994;0.904;0.994;0.925;0.966;0.904;0.904	D	0.87803	0.2626	10	0.72032	D	0.01	.	19.9157	0.97061	0.0:1.0:0.0:0.0	.	824;519;744;824;846;778;776;672;492;452	B4E2N6;B4DH13;Q59GN8;Q05397;Q658W2;Q8IYN9;Q59GM6;Q05397-2;Q8N9D7;E9PEI4	.;.;.;FAK1_HUMAN;.;.;.;.;.;.	H	824;778;452;868;824;776;824;745;519;496;824;492;868;134;522	ENSP00000429911:R824H;ENSP00000438009:R778H;ENSP00000429170:R452H;ENSP00000429082:R868H;ENSP00000429474:R824H;ENSP00000378644:R824H;ENSP00000428492:R496H;ENSP00000341189:R824H;ENSP00000445742:R492H;ENSP00000429129:R868H;ENSP00000403416:R134H;ENSP00000430603:R522H	ENSP00000341189:R824H	R	-	2	0	PTK2	141780200	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.321000	0.72881	2.808000	0.96608	0.655000	0.94253	CGC		0.433	PTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378054.5	NM_005607	
SLC45A4	57210	broad.mit.edu	37	8	142238331	142238331	+	Missense_Mutation	SNP	C	C	T	rs142818740		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr8:142238331C>T	ENST00000024061.3	-	1	342	c.35G>A	c.(34-36)cGt>cAt	p.R12H	SLC45A4_ENST00000433583.2_Intron|SLC45A4_ENST00000517878.1_Intron|SLC45A4_ENST00000519067.1_Missense_Mutation_p.R12H	NM_001080431.1	NP_001073900.1	Q5BKX6	S45A4_HUMAN	solute carrier family 45, member 4						transport (GO:0006810)	integral component of membrane (GO:0016021)		p.R12H(1)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31	all_cancers(97;1.52e-15)|all_epithelial(106;2.92e-14)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)			GGTCTTTGGACGGGACAGCCC	0.557																																					p.R12H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G35A	8						.		HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	176.0	165.0	168.0		35	-2.8	0.0	8	dbSNP_134	168	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SLC45A4	NM_001080431.1	29	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	benign	12/799	142238331	2,13004	2203	4300	6503	142307513	SO:0001583	missense	57210	exon1			AB032952	CCDS34948.1, CCDS69550.1, CCDS75795.1	8q24.3	2013-05-22						"""Solute carriers"""	29196	protein-coding gene	gene with protein product							Standard	NM_001080431		Approved	KIAA1126	uc003ywd.1	Q5BKX6		ENST00000024061.3:c.35G>A	8.37:g.142238331C>T	ENSP00000024061:p.Arg12His		142307513	NM_001080431	Q6ZRI2|Q9ULU3	Missense_Mutation	SNP	ENST00000024061.3	37	CCDS34948.1	.	.	.	.	.	.	.	.	.	.	c	4.960	0.178387	0.09443	2.27E-4	1.16E-4	ENSG00000022567	ENST00000519067;ENST00000024061	T;T	0.14893	2.53;2.47	1.43	-2.85	0.05734	.	1.774100	0.04212	U	0.331991	T	0.12263	0.0298	N	0.22421	0.69	0.18873	N	0.999989	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.35226	-0.9797	10	0.72032	D	0.01	.	7.4325	0.27137	0.0:0.5035:0.0:0.4965	.	12;12	Q5BKX6-3;Q5BKX6-2	.;.	H	12	ENSP00000429059:R12H;ENSP00000024061:R12H	ENSP00000024061:R12H	R	-	2	0	SLC45A4	142307513	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.198000	0.01239	-1.751000	0.01326	-1.730000	0.00700	CGT		0.557	SLC45A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378571.3	XM_050325	
LY6E	4061	broad.mit.edu	37	8	144103202	144103202	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr8:144103202C>A	ENST00000520466.1	+	5	795	c.392C>A	c.(391-393)cCc>cAc	p.P131H	LY6E_ENST00000522024.1_Missense_Mutation_p.P131H|LY6E_ENST00000522971.1_Missense_Mutation_p.P131H|LY6E_ENST00000519546.1_3'UTR|LY6E_ENST00000523847.1_Intron|LY6E_ENST00000522528.1_3'UTR|LY6E_ENST00000292494.6_Missense_Mutation_p.P131H|LY6E_ENST00000429120.2_Missense_Mutation_p.P131H|LY6E_ENST00000521182.1_3'UTR|LY6E_ENST00000521003.1_Missense_Mutation_p.P131H|LY6E_ENST00000521699.1_Missense_Mutation_p.P131H|LY6E_ENST00000519611.1_3'UTR|LY6E_ENST00000517503.1_3'UTR			Q16553	LY6E_HUMAN	lymphocyte antigen 6 complex, locus E	131					adrenal gland development (GO:0030325)|cell surface receptor signaling pathway (GO:0007166)|epinephrine secretion (GO:0048242)|in utero embryonic development (GO:0001701)|norepinephrine metabolic process (GO:0042415)|organ growth (GO:0035265)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)		p.P131H(1)		endometrium(1)|kidney(3)|large_intestine(2)|lung(1)	7	all_cancers(97;1.94e-10)|all_epithelial(106;1.22e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					CGGTTTGGCCCCTGACCGCCC	0.677																																					p.P131H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C392A	8						.						21.0	24.0	23.0					8																	144103202		2199	4294	6493	144174577	SO:0001583	missense	4061	exon4			U42376	CCDS6394.1	8q24	2008-08-07				ENSG00000160932			6727	protein-coding gene	gene with protein product	"""retinoic acid induced gene E"""	601384				8757598, 8650192	Standard	NM_001127213		Approved	TSA-1, RIG-E, SCA-2	uc003yxm.2	Q16553		ENST00000520466.1:c.392C>A	8.37:g.144103202C>A	ENSP00000428572:p.Pro131His		144174577	NM_002346	B2R4X5|D3DWJ2|Q0VDE5	Missense_Mutation	SNP	ENST00000520466.1	37	CCDS6394.1	.	.	.	.	.	.	.	.	.	.	c	15.25	2.776976	0.49786	.	.	ENSG00000160932	ENST00000292494;ENST00000429120;ENST00000521699;ENST00000520466;ENST00000521003;ENST00000522971;ENST00000522024	D;D;D;D;D;D;D	0.83673	-1.75;-1.75;-1.75;-1.75;-1.75;-1.75;-1.75	3.32	1.43	0.22495	.	0.533478	0.16140	N	0.227795	D	0.82435	0.5036	L	0.51422	1.61	0.27101	N	0.962628	D	0.67145	0.996	P	0.54372	0.75	T	0.73544	-0.3949	10	0.87932	D	0	-5.9231	7.1513	0.25612	0.0:0.7488:0.0:0.2512	.	131	Q16553	LY6E_HUMAN	H	131	ENSP00000292494:P131H;ENSP00000414307:P131H;ENSP00000427915:P131H;ENSP00000428572:P131H;ENSP00000428169:P131H;ENSP00000428159:P131H;ENSP00000428442:P131H	ENSP00000292494:P131H	P	+	2	0	LY6E	144174577	0.922000	0.31269	0.993000	0.49108	0.682000	0.39822	0.393000	0.20817	0.392000	0.25172	0.655000	0.94253	CCC		0.677	LY6E-016	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380125.1	NM_001127213	
MYOM2	9172	broad.mit.edu	37	8	2046803	2046803	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr8:2046803G>A	ENST00000262113.4	+	19	2571	c.2430G>A	c.(2428-2430)atG>atA	p.M810I	MYOM2_ENST00000523438.1_Missense_Mutation_p.M235I	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	810	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)	p.M810I(1)		autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		CCTGGACCATGCCGGAGCCCG	0.657																																					p.M810I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2430A	8						.						29.0	27.0	27.0					8																	2046803		2203	4300	6503	2034210	SO:0001583	missense	9172	exon19				CCDS5957.1	8p23.3	2014-06-06	2012-10-17		ENSG00000036448	ENSG00000036448		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7614	protein-coding gene	gene with protein product		603509	"""myomesin (M-protein) 2 (165kD)"", ""myomesin (M-protein) 2, 165kDa"""				Standard	XM_006716237		Approved		uc003wpx.4	P54296	OTTHUMG00000129175	ENST00000262113.4:c.2430G>A	8.37:g.2046803G>A	ENSP00000262113:p.Met810Ile		2034210	NM_003970	Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	37	CCDS5957.1	.	.	.	.	.	.	.	.	.	.	G	7.330	0.618753	0.14129	.	.	ENSG00000036448	ENST00000262113;ENST00000523438	T;T	0.51574	0.7;0.7	5.14	-1.47	0.08772	.	0.338008	0.35805	N	0.002980	T	0.14657	0.0354	N	0.04387	-0.21	0.26323	N	0.977632	B	0.29835	0.258	B	0.24006	0.05	T	0.26430	-1.0103	10	0.08381	T	0.77	.	3.0506	0.06168	0.127:0.1127:0.4124:0.3479	.	810	P54296	MYOM2_HUMAN	I	810;235	ENSP00000262113:M810I;ENSP00000428396:M235I	ENSP00000262113:M810I	M	+	3	0	MYOM2	2034210	0.997000	0.39634	0.001000	0.08648	0.711000	0.40976	0.345000	0.19979	-0.701000	0.05063	0.561000	0.74099	ATG		0.657	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970	
SGK223	157285	broad.mit.edu	37	8	8233781	8233781	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr8:8233781G>T	ENST00000520004.1	-	3	2402	c.2138C>A	c.(2137-2139)cCt>cAt	p.P713H	SGK223_ENST00000330777.4_Missense_Mutation_p.P713H			Q86YV5	SG223_HUMAN		715	Poly-Pro.						ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)	p.P713H(1)									TGGAGGCGGAGGAGGAGGTGA	0.537																																					p.P713H	GBM(34;731 755 10259 33573 33867)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2138A	8						.						100.0	111.0	108.0					8																	8233781		1961	4160	6121	8271191	SO:0001583	missense	157285	exon2																														ENST00000520004.1:c.2138C>A	8.37:g.8233781G>T	ENSP00000428054:p.Pro713His		8271191	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	37	CCDS43706.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.975080	0.74360	.	.	ENSG00000182319	ENST00000330777;ENST00000520004	D;D	0.82984	-1.67;-1.67	5.42	5.42	0.78866	.	0.657623	0.14323	N	0.326914	D	0.87838	0.6278	L	0.32530	0.975	0.53688	D	0.999974	D	0.89917	1.0	D	0.87578	0.998	D	0.87839	0.2650	10	0.72032	D	0.01	.	18.1973	0.89826	0.0:0.0:1.0:0.0	.	713	Q86YV5	SG223_HUMAN	H	713	ENSP00000330930:P713H;ENSP00000428054:P713H	ENSP00000330930:P713H	P	-	2	0	AC068353.1	8271191	1.000000	0.71417	0.729000	0.30791	0.859000	0.49053	6.973000	0.76116	2.725000	0.93324	0.655000	0.94253	CCT		0.537	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
SLC18A1	6570	broad.mit.edu	37	8	20036640	20036640	+	Silent	SNP	G	G	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr8:20036640G>C	ENST00000276373.5	-	3	746	c.480C>G	c.(478-480)ctC>ctG	p.L160L	SLC18A1_ENST00000440926.1_Silent_p.L160L|SLC18A1_ENST00000437980.1_Silent_p.L160L|SLC18A1_ENST00000265808.7_Silent_p.L160L|SLC18A1_ENST00000381608.4_Silent_p.L160L|SLC18A1_ENST00000519026.1_Silent_p.L160L	NM_003053.3	NP_003044.1	P54219	VMAT1_HUMAN	solute carrier family 18 (vesicular monoamine transporter), member 1	160					monoamine transport (GO:0015844)|neurotransmitter transport (GO:0006836)|transmembrane transport (GO:0055085)	clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	drug transmembrane transporter activity (GO:0015238)|monoamine transmembrane transporter activity (GO:0008504)	p.L160L(1)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	29				Colorectal(74;0.0747)	Ephedra(DB01363)|Methamphetamine(DB01577)|Norepinephrine(DB00368)|Reserpine(DB00206)	ACCTGTTGGTGAGAGGGCCCA	0.512																																					p.L160L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C480G	8						.						54.0	55.0	55.0					8																	20036640		2203	4300	6503	20080920	SO:0001819	synonymous_variant	6570	exon3				CCDS6013.1, CCDS47814.1, CCDS47815.1	8p21.3	2013-07-18	2013-07-18		ENSG00000036565	ENSG00000036565		"""Solute carriers"""	10934	protein-coding gene	gene with protein product		193002		VMAT1, VAT1			Standard	NM_003053		Approved	CGAT	uc003wzm.3	P54219	OTTHUMG00000097017	ENST00000276373.5:c.480C>G	8.37:g.20036640G>C			20080920	NM_003053	E9PDJ5|Q9BRE4	Silent	SNP	ENST00000276373.5	37	CCDS6013.1																																																																																				0.512	SLC18A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214106.1		
EGR3	1960	broad.mit.edu	37	8	22548693	22548693	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr8:22548693G>T	ENST00000317216.2	-	2	814	c.457C>A	c.(457-459)Ctc>Atc	p.L153I	EGR3_ENST00000519492.1_3'UTR|EGR3_ENST00000524088.1_5'UTR|RP11-459E5.1_ENST00000523627.1_RNA|EGR3_ENST00000522910.1_Missense_Mutation_p.L115I	NM_001199881.1|NM_004430.2	NP_001186810.1|NP_004421.2	Q06889	EGR3_HUMAN	early growth response 3	153					cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|circadian rhythm (GO:0007623)|endothelial cell chemotaxis (GO:0035767)|muscle organ development (GO:0007517)|negative regulation of apoptotic process (GO:0043066)|neuromuscular synaptic transmission (GO:0007274)|peripheral nervous system development (GO:0007422)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of T cell differentiation in thymus (GO:0033089)|regulation of gamma-delta T cell differentiation (GO:0045586)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L153I(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	10		Prostate(55;0.0421)|Breast(100;0.102)		Colorectal(74;0.0145)|BRCA - Breast invasive adenocarcinoma(99;0.053)|COAD - Colon adenocarcinoma(73;0.0608)		TCTGAGTAGAGGTCGCCGCAG	0.652																																					p.L153I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C457A	8						.						28.0	31.0	30.0					8																	22548693		2203	4300	6503	22604638	SO:0001583	missense	1960	exon2			X63741	CCDS6033.1, CCDS56528.1	8p23-p21	2013-01-08			ENSG00000179388	ENSG00000179388		"""Zinc fingers, C2H2-type"""	3240	protein-coding gene	gene with protein product	"""zinc finger protein pilot"""	602419				1906159, 11909874	Standard	NM_004430		Approved	PILOT	uc003xcm.1	Q06889	OTTHUMG00000097825	ENST00000317216.2:c.457C>A	8.37:g.22548693G>T	ENSP00000318057:p.Leu153Ile		22604638	NM_004430	A8K8U9|B4DHJ5|E7EW38|Q2M3W2	Missense_Mutation	SNP	ENST00000317216.2	37	CCDS6033.1	.	.	.	.	.	.	.	.	.	.	G	0.014	-1.582479	0.00879	.	.	ENSG00000179388	ENST00000317216;ENST00000522910	T;T	0.19806	2.12;2.12	5.39	4.51	0.55191	.	0.149916	0.45126	N	0.000385	T	0.12050	0.0293	N	0.12961	0.28	0.80722	D	1	B;B	0.28713	0.106;0.22	B;B	0.33392	0.163;0.163	T	0.04440	-1.0951	10	0.02654	T	1	-21.8734	13.221	0.59887	0.0:0.0:0.8395:0.1605	.	115;153	E7EW38;Q06889	.;EGR3_HUMAN	I	153;115	ENSP00000318057:L153I;ENSP00000430310:L115I	ENSP00000318057:L153I	L	-	1	0	EGR3	22604638	1.000000	0.71417	0.998000	0.56505	0.480000	0.33159	2.946000	0.49050	1.249000	0.43950	-0.521000	0.04368	CTC		0.652	EGR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215098.1	NM_004430	
STC1	6781	broad.mit.edu	37	8	23702424	23702424	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr8:23702424G>T	ENST00000290271.2	-	4	886	c.603C>A	c.(601-603)caC>caA	p.H201Q	STC1_ENST00000524323.1_Missense_Mutation_p.H132Q	NM_003155.2	NP_003146.1	P52823	STC1_HUMAN	stanniocalcin 1	201					bone development (GO:0060348)|cellular calcium ion homeostasis (GO:0006874)|cellular response to cAMP (GO:0071320)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to hypoxia (GO:0071456)|chondrocyte proliferation (GO:0035988)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|endothelial cell morphogenesis (GO:0001886)|growth plate cartilage axis specification (GO:0003421)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of renal phosphate excretion (GO:1903403)|ossification (GO:0001503)|positive regulation of calcium ion import (GO:0090280)|regulation of anion transport (GO:0044070)|regulation of cardiac muscle cell contraction (GO:0086004)|response to vitamin D (GO:0033280)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)		p.H201Q(1)		breast(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	26		Prostate(55;0.055)|Breast(100;0.116)		Colorectal(74;0.0155)|COAD - Colon adenocarcinoma(73;0.0632)		TTTGGGCACAGTGGTCTGTCT	0.537																																					p.H201Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C603A	8						.						192.0	164.0	174.0					8																	23702424		2203	4300	6503	23758369	SO:0001583	missense	6781	exon4				CCDS6043.1	8p22-p12	2008-06-23			ENSG00000159167	ENSG00000159167			11373	protein-coding gene	gene with protein product		601185		STC		9480753	Standard	NM_003155		Approved		uc003xdw.1	P52823	OTTHUMG00000097853	ENST00000290271.2:c.603C>A	8.37:g.23702424G>T	ENSP00000290271:p.His201Gln		23758369	NM_003155	B4DN22|Q71UE5	Missense_Mutation	SNP	ENST00000290271.2	37	CCDS6043.1	.	.	.	.	.	.	.	.	.	.	G	11.16	1.557324	0.27827	.	.	ENSG00000159167	ENST00000290271;ENST00000540277;ENST00000524323	.	.	.	6.16	6.16	0.99307	.	0.184216	0.64402	D	0.000013	T	0.46229	0.1382	L	0.29908	0.895	0.42268	D	0.992046	B	0.27286	0.174	B	0.28709	0.093	T	0.33599	-0.9862	9	0.18710	T	0.47	-17.9215	14.9655	0.71188	0.0:0.1423:0.8577:0.0	.	201	P52823	STC1_HUMAN	Q	201;132;132	.	ENSP00000290271:H201Q	H	-	3	2	STC1	23758369	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.727000	0.61993	2.937000	0.99478	0.650000	0.86243	CAC		0.537	STC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215143.1		
ADAM28	10863	broad.mit.edu	37	8	24199150	24199150	+	Silent	SNP	G	G	A	rs145453785	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr8:24199150G>A	ENST00000265769.4	+	16	1820	c.1710G>A	c.(1708-1710)tcG>tcA	p.S570S	RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|ADAM28_ENST00000397649.3_Silent_p.S317S|RP11-624C23.1_ENST00000518988.1_RNA|RP11-624C23.1_ENST00000523700.1_RNA	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	570	Cys-rich.				spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.S570S(1)		central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		AAGGTGGGTCGGATAATTTGC	0.413													G|||	3	0.000599042	0.0023	0.0	5008	,	,		21334	0.0		0.0	False		,,,				2504	0.0				p.S570S	NSCLC(193;488 2149 22258 34798 40734)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1710A	8						.	G		3,4403	6.2+/-15.9	0,3,2200	263.0	251.0	255.0		1710	-1.3	0.2	8	dbSNP_134	255	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	ADAM28	NM_014265.4		0,9,6494	AA,AG,GG		0.0698,0.0681,0.0692		570/776	24199150	9,12997	2203	4300	6503	24255095	SO:0001819	synonymous_variant	10863	exon16			AJ242015	CCDS34865.1, CCDS47830.1	8p21.2	2005-11-29	2005-08-18		ENSG00000042980	ENSG00000042980		"""ADAM metallopeptidase domain containing"""	206	protein-coding gene	gene with protein product		606188	"""a disintegrin and metalloproteinase domain 28"""				Standard	XM_005273378		Approved	eMDCII, MDC-Lm, MDC-Ls, ADAM23	uc003xdy.3	Q9UKQ2	OTTHUMG00000163780	ENST00000265769.4:c.1710G>A	8.37:g.24199150G>A			24255095	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	Silent	SNP	ENST00000265769.4	37	CCDS34865.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	0.066	-1.212798	0.01555	6.81E-4	6.98E-4	ENSG00000042980	ENST00000521629	.	.	.	5.84	-1.3	0.09259	.	.	.	.	.	T	0.20618	0.0496	.	.	.	0.22142	N	0.999336	.	.	.	.	.	.	T	0.24764	-1.0151	4	.	.	.	.	2.6844	0.05103	0.6138:0.1127:0.152:0.1216	.	.	.	.	R	203	.	.	G	+	1	0	ADAM28	24255095	0.005000	0.15991	0.213000	0.23690	0.003000	0.03518	1.195000	0.32186	-0.393000	0.07739	-2.289000	0.00267	GGA		0.413	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778	
DOCK5	80005	broad.mit.edu	37	8	25265542	25265542	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr8:25265542G>A	ENST00000276440.7	+	49	5181	c.5137G>A	c.(5137-5139)Gcc>Acc	p.A1713T		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	1713					positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.A1713T(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		CTCGTCAGGTGCCAGAGTTGA	0.483																																					p.A1713T	Pancreas(145;34 1887 3271 10937 30165)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5137A	8						.						57.0	50.0	52.0					8																	25265542		2203	4300	6503	25321459	SO:0001583	missense	80005	exon49				CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.5137G>A	8.37:g.25265542G>A	ENSP00000276440:p.Ala1713Thr		25321459	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Missense_Mutation	SNP	ENST00000276440.7	37	CCDS6047.1	.	.	.	.	.	.	.	.	.	.	G	14.85	2.659785	0.47572	.	.	ENSG00000147459	ENST00000276440	T	0.03920	3.76	5.92	5.0	0.66597	.	0.531595	0.18879	N	0.128618	T	0.04724	0.0128	N	0.24115	0.695	0.34663	D	0.722862	B	0.22800	0.075	B	0.27500	0.08	T	0.29488	-1.0010	10	0.40728	T	0.16	.	11.9977	0.53212	0.0:0.0:0.7359:0.2641	.	1713	Q9H7D0	DOCK5_HUMAN	T	1713	ENSP00000276440:A1713T	ENSP00000276440:A1713T	A	+	1	0	DOCK5	25321459	0.998000	0.40836	1.000000	0.80357	0.873000	0.50193	3.007000	0.49536	2.804000	0.96469	0.655000	0.94253	GCC		0.483	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940	
DPYSL2	1808	broad.mit.edu	37	8	26492407	26492407	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr8:26492407C>T	ENST00000311151.5	+	8	1214	c.802C>T	c.(802-804)Cgg>Tgg	p.R268W	DPYSL2_ENST00000523027.1_Missense_Mutation_p.R232W|DPYSL2_ENST00000521983.1_3'UTR|DPYSL2_ENST00000521913.1_Missense_Mutation_p.R232W	NM_001386.5	NP_001377.1	Q16555	DPYL2_HUMAN	dihydropyrimidinase-like 2	268					axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|endocytosis (GO:0006897)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|olfactory bulb development (GO:0021772)|positive regulation of glutamate secretion (GO:0014049)|pyrimidine nucleobase catabolic process (GO:0006208)|regulation of neuron differentiation (GO:0045664)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|spinal cord development (GO:0021510)|synaptic vesicle transport (GO:0048489)	axon (GO:0030424)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	dihydropyrimidinase activity (GO:0004157)	p.R268W(1)		breast(1)|endometrium(5)|large_intestine(8)|lung(3)|prostate(1)|skin(1)|stomach(1)	20		all_cancers(63;0.121)|Ovarian(32;2.68e-05)|all_epithelial(46;0.116)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;3.33e-10)|Colorectal(74;0.183)		CGCCCAGGCACGGAAGAAGGG	0.607																																					p.R268W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C802T	8						.						82.0	70.0	74.0					8																	26492407		2203	4300	6503	26548324	SO:0001583	missense	1808	exon8			D78013	CCDS6051.1, CCDS59096.1	8p22-p21	2011-09-28			ENSG00000092964	ENSG00000092964			3014	protein-coding gene	gene with protein product		602463				8973361	Standard	NM_001197293		Approved	DRP-2, DHPRP2, CRMP2, DRP2	uc003xfa.3	Q16555	OTTHUMG00000099439	ENST00000311151.5:c.802C>T	8.37:g.26492407C>T	ENSP00000309539:p.Arg268Trp		26548324	NM_001386	A8K5H2|B4DR31|D3DSS7|O00424	Missense_Mutation	SNP	ENST00000311151.5	37	CCDS6051.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.479557	0.84747	.	.	ENSG00000092964	ENST00000521913;ENST00000311151;ENST00000522745;ENST00000523027	D;D;D;D	0.91686	-2.89;-2.89;-2.89;-2.89	5.8	2.63	0.31362	Amidohydrolase 1 (1);	0.000000	0.85682	D	0.000000	D	0.96713	0.8927	M	0.94101	3.495	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;P;D	0.87578	0.998;0.904;0.968	D	0.97117	0.9808	10	0.87932	D	0	-23.4218	13.5282	0.61607	0.6902:0.3098:0.0:0.0	.	268;268;324	Q53ET2;Q16555;Q59GB4	.;DPYL2_HUMAN;.	W	232;268;268;232	ENSP00000427985:R232W;ENSP00000309539:R268W;ENSP00000428909:R268W;ENSP00000431117:R232W	ENSP00000309539:R268W	R	+	1	2	DPYSL2	26548324	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	2.460000	0.45031	0.741000	0.32674	0.561000	0.74099	CGG		0.607	DPYSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216904.3	NM_001386	
CHRNA2	1135	broad.mit.edu	37	8	27320707	27320707	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr8:27320707T>A	ENST00000520933.2	-	5	1406	c.1253A>T	c.(1252-1254)gAg>gTg	p.E418V	CHRNA2_ENST00000407991.1_Missense_Mutation_p.E418V|CHRNA2_ENST00000240132.2_Missense_Mutation_p.E403V			Q15822	ACHA2_HUMAN	cholinergic receptor, nicotinic, alpha 2 (neuronal)	418					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transport (GO:0006811)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|drug binding (GO:0008144)	p.E418V(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	23		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0208)|Epithelial(17;2.77e-10)|Colorectal(74;0.136)	Atracurium(DB00732)|Biperiden(DB00810)|Carbachol(DB00411)|Cisatracurium Besylate(DB00565)|Decamethonium(DB01245)|Dextromethorphan(DB00514)|Doxacurium chloride(DB01135)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Mecamylamine(DB00657)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicotine(DB00184)|Pancuronium(DB01337)|Pipecuronium(DB01338)|Procaine(DB00721)|Rocuronium(DB00728)|Tubocurarine(DB01199)|Vecuronium(DB01339)	GTCCTCCTCCTCCACCACCAC	0.657																																					p.E418V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1253T	8						.						113.0	97.0	102.0					8																	27320707		2203	4300	6503	27376624	SO:0001583	missense	1135	exon6			U62431	CCDS6059.1, CCDS64856.1	8p21	2012-02-11	2006-02-01		ENSG00000120903	ENSG00000120903		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1956	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 2 (neuronal)"""	118502	"""cholinergic receptor, nicotinic, alpha polypeptide 2 (neuronal)"""			1505988	Standard	NM_000742		Approved		uc010lur.3	Q15822	OTTHUMG00000102083	ENST00000520933.2:c.1253A>T	8.37:g.27320707T>A	ENSP00000429616:p.Glu418Val		27376624	NM_000742	A8KAX3|B4DK19|J3KMY9|Q9HAQ3	Missense_Mutation	SNP	ENST00000520933.2	37	CCDS6059.1	.	.	.	.	.	.	.	.	.	.	T	2.257	-0.370164	0.05069	.	.	ENSG00000120903	ENST00000407991;ENST00000520933;ENST00000240132	T;T;T	0.72725	-0.68;-0.68;-0.68	4.62	3.45	0.39498	Neurotransmitter-gated ion-channel transmembrane domain (2);	1.917620	0.03050	N	0.154447	T	0.60392	0.2265	N	0.22421	0.69	0.25868	N	0.983749	B;B	0.02656	0.0;0.0	B;B	0.12837	0.008;0.004	T	0.45848	-0.9233	10	0.33940	T	0.23	.	8.7642	0.34694	0.1693:0.0:0.0:0.8307	.	403;418	B4DK19;Q15822	.;ACHA2_HUMAN	V	418;418;403	ENSP00000385026:E418V;ENSP00000429616:E418V;ENSP00000240132:E403V	ENSP00000240132:E403V	E	-	2	0	CHRNA2	27376624	0.003000	0.15002	0.082000	0.20525	0.019000	0.09904	0.584000	0.23864	0.783000	0.33636	-0.695000	0.03696	GAG		0.657	CHRNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376125.4		
TEX15	56154	broad.mit.edu	37	8	30700952	30700952	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr8:30700952A>G	ENST00000256246.2	-	1	5656	c.5582T>C	c.(5581-5583)aTg>aCg	p.M1861T		NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	1861					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)			p.M1861T(1)		NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		TGAGGAGATCATTTCTATGAT	0.333																																					p.M1861T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T5582C	8						.						88.0	91.0	90.0					8																	30700952		2203	4299	6502	30820494	SO:0001583	missense	56154	exon1			AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"""cancer/testis antigen 42"""	605795	"""testis expressed sequence 15"""			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.5582T>C	8.37:g.30700952A>G	ENSP00000256246:p.Met1861Thr		30820494	NM_031271		Missense_Mutation	SNP	ENST00000256246.2	37	CCDS6080.1	.	.	.	.	.	.	.	.	.	.	A	13.06	2.123340	0.37436	.	.	ENSG00000133863	ENST00000256246	T	0.10860	2.83	5.82	5.82	0.92795	.	0.305250	0.29253	N	0.012690	T	0.15912	0.0383	L	0.51422	1.61	0.29578	N	0.849351	P	0.39480	0.675	B	0.41988	0.372	T	0.03103	-1.1072	10	0.87932	D	0	.	15.1792	0.72941	1.0:0.0:0.0:0.0	.	1861	Q9BXT5	TEX15_HUMAN	T	1861	ENSP00000256246:M1861T	ENSP00000256246:M1861T	M	-	2	0	TEX15	30820494	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.281000	0.72632	2.232000	0.73038	0.528000	0.53228	ATG		0.333	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1		
KCNU1	157855	broad.mit.edu	37	8	36644850	36644850	+	Silent	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr8:36644850T>C	ENST00000399881.3	+	2	259	c.222T>C	c.(220-222)gcT>gcC	p.A74A		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	74					multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)	p.A74A(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		GTACCATCGCTAGGAGCCATG	0.428																																					p.A74A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T222C	8						.						84.0	81.0	82.0					8																	36644850		1925	4116	6041	36764008	SO:0001819	synonymous_variant	157855	exon2			BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.222T>C	8.37:g.36644850T>C			36764008	NM_001031836		Silent	SNP	ENST00000399881.3	37	CCDS55220.1																																																																																				0.428	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836	
SFRP1	6422	broad.mit.edu	37	8	41166262	41166262	+	Silent	SNP	C	C	T	rs558728015		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr8:41166262C>T	ENST00000220772.3	-	1	754	c.417G>A	c.(415-417)tcG>tcA	p.S139S	SFRP1_ENST00000379845.3_5'Flank	NM_003012.4	NP_003003.3	Q8N474	SFRP1_HUMAN	secreted frizzled-related protein 1	139	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				bone trabecula formation (GO:0060346)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cellular response to BMP stimulus (GO:0071773)|cellular response to estradiol stimulus (GO:0071392)|cellular response to estrogen stimulus (GO:0071391)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heparin (GO:0071504)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to prostaglandin E stimulus (GO:0071380)|cellular response to starvation (GO:0009267)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vitamin D (GO:0071305)|cellular response to X-ray (GO:0071481)|convergent extension involved in somitogenesis (GO:0090246)|digestive tract morphogenesis (GO:0048546)|dorsal/ventral axis specification (GO:0009950)|female gonad development (GO:0008585)|gonad development (GO:0008406)|hematopoietic progenitor cell differentiation (GO:0002244)|hematopoietic stem cell differentiation (GO:0060218)|male gonad development (GO:0008584)|menstrual cycle phase (GO:0022601)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of bone remodeling (GO:0046851)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of canonical Wnt signaling pathway involved in controlling type B pancreatic cell proliferation (GO:2000080)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of planar cell polarity pathway involved in axis elongation (GO:2000041)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|negative regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000054)|neural crest cell fate commitment (GO:0014034)|neural tube closure (GO:0001843)|osteoblast differentiation (GO:0001649)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of non-canonical Wnt signaling pathway (GO:2000052)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|proteolysis (GO:0006508)|regulation of angiogenesis (GO:0045765)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell cycle process (GO:0010564)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|somatic stem cell maintenance (GO:0035019)|stromal-epithelial cell signaling involved in prostate gland development (GO:0044345)|ureteric bud development (GO:0001657)|vasculature development (GO:0001944)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	cysteine-type endopeptidase activity (GO:0004197)|drug binding (GO:0008144)|frizzled binding (GO:0005109)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.S139S(1)		breast(1)|central_nervous_system(1)|large_intestine(2)|liver(1)|lung(1)|skin(1)	7	Breast(1;9.19e-13)|Ovarian(28;0.00769)|Colorectal(14;0.0305)|Lung SC(25;0.211)	all_lung(54;0.0034)|Lung NSC(58;0.0134)|Hepatocellular(245;0.023)|Esophageal squamous(32;0.0559)	BRCA - Breast invasive adenocarcinoma(1;1.11e-10)|LUSC - Lung squamous cell carcinoma(45;0.00894)|COAD - Colon adenocarcinoma(11;0.0174)			CCGGCTCGCACGAGTCGCGCA	0.662																																					p.S139S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G417A	8						.						25.0	30.0	28.0					8																	41166262		2203	4300	6503	41285419	SO:0001819	synonymous_variant	6422	exon1			AF017987	CCDS34886.1	8p11.21	2006-12-15			ENSG00000104332	ENSG00000104332		"""Secreted frizzled-related proteins"""	10776	protein-coding gene	gene with protein product		604156				9391078, 9192640	Standard	NM_003012		Approved	SARP2, FRP, FRP-1	uc003xnt.3	Q8N474	OTTHUMG00000164074	ENST00000220772.3:c.417G>A	8.37:g.41166262C>T			41285419	NM_003012	O00546|O14779	Silent	SNP	ENST00000220772.3	37	CCDS34886.1																																																																																				0.662	SFRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377132.1	NM_003012	
PRKDC	5591	broad.mit.edu	37	8	48739274	48739274	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr8:48739274C>T	ENST00000314191.2	-	64	8779	c.8723G>A	c.(8722-8724)cGa>cAa	p.R2908Q	PRKDC_ENST00000338368.3_Missense_Mutation_p.R2908Q|PRKDC_ENST00000523565.1_5'UTR	NM_006904.6	NP_008835.5	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide	2909	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.|KIP-binding.				B cell lineage commitment (GO:0002326)|brain development (GO:0007420)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|ectopic germ cell programmed cell death (GO:0035234)|heart development (GO:0007507)|immunoglobulin V(D)J recombination (GO:0033152)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of protein phosphorylation (GO:0001933)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|pro-B cell differentiation (GO:0002328)|protein destabilization (GO:0031648)|regulation of circadian rhythm (GO:0042752)|response to gamma radiation (GO:0010332)|rhythmic process (GO:0048511)|signal transduction involved in mitotic G1 DNA damage checkpoint (GO:0072431)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell receptor V(D)J recombination (GO:0033153)|telomere maintenance (GO:0000723)	cytosol (GO:0005829)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)	p.R2909Q(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(9)|cervix(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(30)|lung(56)|ovary(6)|pancreas(1)|prostate(8)|skin(7)	147		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)			Caffeine(DB00201)	CCCACGGACTCGCTTGGCAGG	0.627								Non-homologous end-joining																													p.E2909K	Esophageal Squamous(79;1091 1253 12329 31680 40677)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G8725A	8						.						25.0	28.0	27.0					8																	48739274		2053	4200	6253	48901827	SO:0001583	missense	5591	exon63				CCDS75734.1, CCDS75735.1	8q11	2014-09-17				ENSG00000253729	2.7.11.1		9413	protein-coding gene	gene with protein product		600899		HYRC, HYRC1		7638222	Standard	NM_001081640		Approved	DNPK1, p350, DNAPK, XRCC7, DNA-PKcs	uc003xqi.3	P78527		ENST00000314191.2:c.8723G>A	8.37:g.48739274C>T	ENSP00000313420:p.Arg2908Gln		48901827	NM_001081640	P78528|Q13327|Q13337|Q14175|Q59H99|Q7Z611|Q96SE6|Q9UME3	Missense_Mutation	SNP	ENST00000314191.2	37		.	.	.	.	.	.	.	.	.	.	C	13.82	2.349747	0.41599	.	.	ENSG00000253729	ENST00000314191;ENST00000338368	T;T	0.02916	4.18;4.11	5.7	3.9	0.45041	PIK-related kinase (1);	0.076347	0.53938	N	0.000058	T	0.02929	0.0087	L	0.48362	1.52	0.40459	D	0.980228	P;B	0.36909	0.573;0.261	B;B	0.29716	0.106;0.044	T	0.55444	-0.8140	10	0.39692	T	0.17	.	9.2458	0.37525	0.0:0.7841:0.0:0.2159	.	2908;2909	E7EUY0;P78527	.;PRKDC_HUMAN	Q	2908	ENSP00000313420:R2908Q;ENSP00000345182:R2908Q	ENSP00000313420:R2908Q	R	-	2	0	PRKDC	48901827	0.916000	0.31088	0.836000	0.33094	0.203000	0.24098	3.039000	0.49791	1.407000	0.46875	0.655000	0.94253	CGA		0.627	PRKDC-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001081640	
PXDNL	137902	broad.mit.edu	37	8	52321417	52321417	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr8:52321417C>G	ENST00000356297.4	-	17	2867	c.2767G>C	c.(2767-2769)Ggc>Cgc	p.G923R	PXDNL_ENST00000543296.1_Missense_Mutation_p.G923R	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	923					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.G122R(1)		NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				CAAGGAAAGCCTGTCTTCAGG	0.617																																					p.G923R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2767C	8						.						25.0	29.0	28.0					8																	52321417		1946	4141	6087	52483970	SO:0001583	missense	137902	exon17				CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"""Immunoglobulin superfamily / I-set domain containing"""	26359	protein-coding gene	gene with protein product	"""polysomal ribonuclease 1 homolog (Xenopus)"""	615904	"""peroxidasin homolog-like (Drosophila)"""			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.2767G>C	8.37:g.52321417C>G	ENSP00000348645:p.Gly923Arg		52483970	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.26|14.26	2.481795|2.481795	0.44147|0.44147	.|.	.|.	ENSG00000147485|ENSG00000147485	ENST00000356297;ENST00000543296|ENST00000522933	T;T|.	0.74526|.	-0.85;-0.85|.	3.66|3.66	3.66|3.66	0.41972|0.41972	.|.	0.000000|.	0.52532|.	D|.	0.000076|.	T|T	0.74283|0.74283	0.3696|0.3696	M|M	0.80422|0.80422	2.495|2.495	0.43608|0.43608	D|D	0.995978|0.995978	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	T|T	0.76653|0.76653	-0.2880|-0.2880	10|5	0.87932|.	D|.	0|.	.|.	12.8212|12.8212	0.57694|0.57694	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	923|.	A1KZ92|.	PXDNL_HUMAN|.	R|H	923|41	ENSP00000348645:G923R;ENSP00000444865:G923R|.	ENSP00000348645:G923R|.	G|Q	-|-	1|3	0|2	PXDNL|PXDNL	52483970|52483970	0.996000|0.996000	0.38824|0.38824	0.005000|0.005000	0.12908|0.12908	0.040000|0.040000	0.13550|0.13550	3.833000|3.833000	0.55790|0.55790	1.581000|1.581000	0.49865|0.49865	0.561000|0.561000	0.74099|0.74099	GGC|CAG		0.617	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	
RGS20	8601	broad.mit.edu	37	8	54791853	54791853	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr8:54791853C>T	ENST00000297313.3	+	2	293	c.201C>T	c.(199-201)gcC>gcT	p.A67A	RP11-1070A24.2_ENST00000606037.1_RNA|RGS20_ENST00000344277.6_Intron|RGS20_ENST00000522225.1_5'Flank|RGS20_ENST00000276500.4_5'Flank	NM_170587.2	NP_733466.1	O76081	RGS20_HUMAN	regulator of G-protein signaling 20	67					positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.A67A(1)		breast(2)|endometrium(1)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(7;1.37e-06)|Epithelial(17;0.000126)|all cancers(17;0.0009)			ACTCGCCCGCCGCCCCGAAGC	0.647																																					p.A67A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C201T	8						.						95.0	120.0	112.0					8																	54791853		2203	4300	6503	54954406	SO:0001819	synonymous_variant	8601	exon2			AF074979	CCDS6155.1, CCDS6156.1, CCDS69482.1	8q11.23	2008-07-25	2007-08-14		ENSG00000147509	ENSG00000147509		"""Regulators of G-protein signaling"""	14600	protein-coding gene	gene with protein product		607193	"""regulator of G-protein signalling 20"""			9748279, 9748280	Standard	NM_003702		Approved	RGSZ1, ZGAP1	uc003xrp.3	O76081	OTTHUMG00000164750	ENST00000297313.3:c.201C>T	8.37:g.54791853C>T			54954406	NM_170587	Q96BG9	Silent	SNP	ENST00000297313.3	37	CCDS6155.1																																																																																				0.647	RGS20-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000380058.1		
RP1	6101	broad.mit.edu	37	8	55540770	55540770	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr8:55540770G>A	ENST00000220676.1	+	4	4476	c.4328G>A	c.(4327-4329)cGg>cAg	p.R1443Q		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	1443					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)	p.R1443Q(1)		NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			GAAGAACCACGGACTTCTGAA	0.343																																					p.R1443Q	Colon(91;1014 1389 7634 14542 40420)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4328A	8						.						55.0	58.0	57.0					8																	55540770		2202	4299	6501	55703323	SO:0001583	missense	6101	exon4			AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.4328G>A	8.37:g.55540770G>A	ENSP00000220676:p.Arg1443Gln		55703323	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	G	14.36	2.512880	0.44660	.	.	ENSG00000104237	ENST00000220676	T	0.66460	-0.21	5.48	2.34	0.29019	.	0.101948	0.43260	D	0.000589	T	0.39358	0.1075	L	0.27053	0.805	0.24758	N	0.99295	D	0.56035	0.974	B	0.34452	0.183	T	0.51180	-0.8738	10	0.87932	D	0	-3.4877	0.3721	0.00381	0.3128:0.1908:0.3043:0.1922	.	1443	P56715	RP1_HUMAN	Q	1443	ENSP00000220676:R1443Q	ENSP00000220676:R1443Q	R	+	2	0	RP1	55703323	0.998000	0.40836	0.991000	0.47740	0.875000	0.50365	1.133000	0.31430	0.141000	0.18875	0.655000	0.94253	CGG		0.343	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269	
CHD7	55636	broad.mit.edu	37	8	61655122	61655122	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr8:61655122C>T	ENST00000423902.2	+	2	1610	c.1131C>T	c.(1129-1131)aaC>aaT	p.N377N	CHD7_ENST00000525508.1_Silent_p.N377N|CHD7_ENST00000524602.1_Silent_p.N377N	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	377					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.N377N(1)		NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			ACCAAATGAACACACAAACTA	0.502																																					p.N377N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1131T	8						.						90.0	90.0	90.0					8																	61655122		2128	4242	6370	61817676	SO:0001819	synonymous_variant	55636	exon2			AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"""CHARGE association"""	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.1131C>T	8.37:g.61655122C>T			61817676	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Silent	SNP	ENST00000423902.2	37	CCDS47865.1																																																																																				0.502	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762	
GPAA1	8733	broad.mit.edu	37	8	145139713	145139713	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr8:145139713C>T	ENST00000355091.4	+	8	1220	c.1099C>T	c.(1099-1101)Cgc>Tgc	p.R367C	GPAA1_ENST00000361036.6_Missense_Mutation_p.R307C	NM_003801.3	NP_003792.1	O43292	GPAA1_HUMAN	glycosylphosphatidylinositol anchor attachment 1	367					attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein complex assembly (GO:0006461)|protein retention in ER lumen (GO:0006621)	endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|membrane (GO:0016020)	tubulin binding (GO:0015631)	p.R367C(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|upper_aerodigestive_tract(2)	19	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.02e-40)|all cancers(56;2.11e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CGGCCTCTCCCGCTTCGTCTC	0.602																																					p.R367C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1099T	8						.						103.0	112.0	109.0					8																	145139713		2011	4180	6191	145211701	SO:0001583	missense	8733	exon8			AB006969	CCDS43776.1	8q24.3	2012-12-10	2012-12-10		ENSG00000197858	ENSG00000197858			4446	protein-coding gene	gene with protein product	"""GPI transamidase subunit"""	603048	"""anchor attachment protein 1 (Gaa1p, yeast) homolog"", ""GPAA1P anchor attachment protein 1 homolog (yeast)"", ""glycosylphosphatidylinositol anchor attachment protein 1 homolog (yeast)"""			9828142	Standard	NM_003801		Approved	GAA1, hGAA1	uc003zax.3	O43292	OTTHUMG00000165438	ENST00000355091.4:c.1099C>T	8.37:g.145139713C>T	ENSP00000347206:p.Arg367Cys		145211701	NM_003801	Q9NSS0|Q9UQ31	Missense_Mutation	SNP	ENST00000355091.4	37	CCDS43776.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.470390	0.84533	.	.	ENSG00000197858	ENST00000355091;ENST00000361036	.	.	.	5.29	4.38	0.52667	.	0.179403	0.49916	D	0.000124	T	0.77425	0.4128	M	0.86953	2.85	0.80722	D	1	D;D	0.76494	0.995;0.999	P;P	0.57283	0.636;0.817	T	0.81629	-0.0846	9	0.66056	D	0.02	-17.0405	13.3536	0.60615	0.0:0.8401:0.1599:0.0	.	367;307	O43292;O43292-2	GPAA1_HUMAN;.	C	367;307	.	ENSP00000347206:R367C	R	+	1	0	GPAA1	145211701	1.000000	0.71417	0.971000	0.41717	0.978000	0.69477	6.998000	0.76277	1.161000	0.42604	0.561000	0.74099	CGC		0.602	GPAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384070.1	NM_003801	
ZNF462	58499	broad.mit.edu	37	9	109691732	109691732	+	Missense_Mutation	SNP	C	C	T	rs377746677		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:109691732C>T	ENST00000277225.5	+	3	5828	c.5539C>T	c.(5539-5541)Cgc>Tgc	p.R1847C	ZNF462_ENST00000441147.2_Missense_Mutation_p.R692C|ZNF462_ENST00000457913.1_Missense_Mutation_p.R1847C			Q96JM2	ZN462_HUMAN	zinc finger protein 462	1847					chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R1847C(1)		NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						GCTCCCATTCCGCTGCATCAA	0.517																																					p.R1847C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5539T	9						.	C	CYS/ARG	1,4405		0,1,2202	101.0	74.0	83.0		5539	5.9	1.0	9		83	0,8600		0,0,4300	no	missense	ZNF462	NM_021224.4	180	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	1847/2507	109691732	1,13005	2203	4300	6503	108731553	SO:0001583	missense	58499	exon3			AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"""Zinc fingers, C2H2-type"""	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.5539C>T	9.37:g.109691732C>T	ENSP00000277225:p.Arg1847Cys		108731553	NM_021224	Q5T0T4|Q8N408	Missense_Mutation	SNP	ENST00000277225.5	37	CCDS35096.1	.	.	.	.	.	.	.	.	.	.	C	11.91	1.781110	0.31502	2.27E-4	0.0	ENSG00000148143	ENST00000277225;ENST00000457913;ENST00000374686;ENST00000441147	T;T;T;T	0.05996	3.36;3.78;3.92;3.89	5.92	5.92	0.95590	Zinc finger, C2H2-like (1);	0.048788	0.85682	D	0.000000	T	0.12092	0.0294	N	0.14661	0.345	0.80722	D	1	P;D	0.89917	0.822;1.0	B;D	0.69654	0.143;0.965	T	0.07616	-1.0763	10	0.87932	D	0	.	14.1727	0.65519	0.2486:0.7514:0.0:0.0	.	1847;1847	Q96JM2-3;Q96JM2	.;ZN462_HUMAN	C	1847;1847;730;692	ENSP00000277225:R1847C;ENSP00000414570:R1847C;ENSP00000363818:R730C;ENSP00000397306:R692C	ENSP00000277225:R1847C	R	+	1	0	ZNF462	108731553	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.146000	0.58072	2.813000	0.96785	0.561000	0.74099	CGC		0.517	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224	
FRRS1L	23732	broad.mit.edu	37	9	111903825	111903825	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:111903825C>A	ENST00000561981.2	-	4	659	c.660G>T	c.(658-660)agG>agT	p.R220S		NM_014334.2	NP_055149.2	Q9P0K9	FRS1L_HUMAN	ferric-chelate reductase 1-like	220	DOMON. {ECO:0000255|PROSITE- ProRule:PRU00246}.					cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)		p.R220S(1)									GTATGCGGACCCTGCCATTGT	0.443																																					p.R220S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G660T	9						.						91.0	88.0	89.0					9																	111903825		2203	4300	6503	110943646	SO:0001583	missense	23732	exon4			AF155065	CCDS35098.1	9q31.3	2014-07-16	2012-03-06	2012-03-06	ENSG00000260230	ENSG00000260230			1362	protein-coding gene	gene with protein product		604574	"""chromosome 9 open reading frame 4"""	C9orf4		10603000	Standard	NM_014334		Approved	CG-6	uc004bdw.1	Q9P0K9	OTTHUMG00000020468	ENST00000561981.2:c.660G>T	9.37:g.111903825C>A	ENSP00000477141:p.Arg220Ser		110943646	NM_014334	Q5T4G4	Missense_Mutation	SNP	ENST00000561981.2	37	CCDS35098.1	.	.	.	.	.	.	.	.	.	.	C	13.62	2.290945	0.40494	.	.	ENSG00000136805	ENST00000374581	T	0.77489	-1.1	5.52	-0.744	0.11101	DOMON domain (3);	0.000000	0.85682	D	0.000000	T	0.77651	0.4162	L	0.34521	1.04	0.58432	D	0.999999	D	0.69078	0.997	D	0.80764	0.994	T	0.72377	-0.4312	10	0.33940	T	0.23	-5.2926	10.3263	0.43796	0.0:0.4393:0.0:0.5607	.	220	Q9P0K9	CI004_HUMAN	S	220	ENSP00000363709:R220S	ENSP00000363709:R220S	R	-	3	2	C9orf4	110943646	0.391000	0.25221	0.998000	0.56505	0.999000	0.98932	-0.266000	0.08631	0.030000	0.15379	0.591000	0.81541	AGG		0.443	FRRS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053586.2	NM_014334	
MUSK	4593	broad.mit.edu	37	9	113530241	113530241	+	Silent	SNP	G	G	A	rs139945437	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:113530241G>A	ENST00000374448.4	+	9	1196	c.1062G>A	c.(1060-1062)acG>acA	p.T354T	MUSK_ENST00000416899.2_Silent_p.T354T|MUSK_ENST00000189978.5_Silent_p.T354T	NM_001166281.1|NM_005592.3	NP_001159753.1|NP_005583.1	O15146	MUSK_HUMAN	muscle, skeletal, receptor tyrosine kinase	354	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|memory (GO:0007613)|multicellular organismal development (GO:0007275)|neuromuscular junction development (GO:0007528)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein geranylgeranylation (GO:2000541)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.T354T(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(23)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	49						TGGTCCACACGGCCTGGAATG	0.547													G|||	21	0.00419329	0.0136	0.0029	5008	,	,		16207	0.0		0.0	False		,,,				2504	0.001				p.T354T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1062A	9						.	G	,,	19,3887		0,19,1934	73.0	75.0	74.0		,,1062	-10.2	0.0	9	dbSNP_134	74	0,8296		0,0,4148	no	intron,intron,coding-synonymous	MUSK	NM_001166280.1,NM_001166281.1,NM_005592.3	,,	0,19,6082	AA,AG,GG		0.0,0.4864,0.1557	,,	,,354/870	113530241	19,12183	1953	4148	6101	112570062	SO:0001819	synonymous_variant	4593	exon8			AF006464	CCDS48005.1, CCDS75874.1	9q31.3-q32	2013-01-29			ENSG00000030304	ENSG00000030304		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7525	protein-coding gene	gene with protein product		601296				7546737	Standard	NM_005592		Approved		uc022blv.1	O15146	OTTHUMG00000020485	ENST00000374448.4:c.1062G>A	9.37:g.113530241G>A			112570062	NM_005592	Q32MJ8|Q32MJ9|Q5VZW7|Q5VZW8	Silent	SNP	ENST00000374448.4	37	CCDS48005.1																																																																																				0.547	MUSK-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
SUSD1	64420	broad.mit.edu	37	9	114840904	114840904	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:114840904A>G	ENST00000374270.3	-	12	1839	c.1667T>C	c.(1666-1668)cTa>cCa	p.L556P	SUSD1_ENST00000374264.2_Missense_Mutation_p.L556P|SUSD1_ENST00000374263.3_Missense_Mutation_p.L556P	NM_022486.3	NP_071931.2	Q6UWL2	SUSD1_HUMAN	sushi domain containing 1	556						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)	p.L556P(1)	SUSD1/ROD1(2)	central_nervous_system(1)|endometrium(4)|large_intestine(8)|lung(11)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						ACCCGGACGTAGGTCCAAGCA	0.493																																					p.L556P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1667C	9						.						150.0	144.0	146.0					9																	114840904		2203	4300	6503	113880725	SO:0001583	missense	64420	exon12			AL137432	CCDS6783.1, CCDS65105.1, CCDS65106.1	9q31.3-q33.1	2008-02-05			ENSG00000106868	ENSG00000106868			25413	protein-coding gene	gene with protein product						12975309	Standard	NM_022486		Approved	DKFZP761E1824	uc004bfu.3	Q6UWL2	OTTHUMG00000020499	ENST00000374270.3:c.1667T>C	9.37:g.114840904A>G	ENSP00000363388:p.Leu556Pro		113880725	NM_022486	A1A4C5|A8KA03|Q5T8V6|Q5T8V7|Q6P9G7|Q8WU83|Q96DM9|Q9H6V2|Q9NTA7	Missense_Mutation	SNP	ENST00000374270.3	37	CCDS6783.1	.	.	.	.	.	.	.	.	.	.	a	11.63	1.696382	0.30142	.	.	ENSG00000106868	ENST00000374270;ENST00000374263;ENST00000374264	T;D;T	0.81659	1.1;-1.52;1.1	4.96	3.77	0.43336	.	0.000000	0.37348	N	0.002128	D	0.89705	0.6792	M	0.89968	3.075	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.998	D	0.88959	0.3392	9	.	.	.	-6.8608	7.9641	0.30089	0.9035:0.0:0.0965:0.0	.	556;556;556	F8WAQ1;Q6UWL2-2;Q6UWL2	.;.;SUSD1_HUMAN	P	556	ENSP00000363388:L556P;ENSP00000363381:L556P;ENSP00000363382:L556P	.	L	-	2	0	SUSD1	113880725	0.992000	0.36948	0.560000	0.28344	0.030000	0.12068	3.450000	0.52957	0.799000	0.34018	0.524000	0.50904	CTA		0.493	SUSD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053668.3	NM_022486	
PRPF4	9128	broad.mit.edu	37	9	116053261	116053261	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:116053261C>T	ENST00000374198.4	+	13	1442	c.1340C>T	c.(1339-1341)gCt>gTt	p.A447V	PRPF4_ENST00000374199.4_Missense_Mutation_p.A446V	NM_001244926.1|NM_004697.4	NP_001231855.1|NP_004688.2	O43172	PRP4_HUMAN	pre-mRNA processing factor 4	447				A -> P (in Ref. 1; AAB87640). {ECO:0000305}.	gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U4/U6 snRNP (GO:0071001)		p.A447V(1)		NS(1)|breast(2)|endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|prostate(2)	23						ACCATCCCTGCTCATCAGAAC	0.493																																					p.A447V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1340T	9						.						210.0	171.0	184.0					9																	116053261		2203	4300	6503	115093082	SO:0001583	missense	9128	exon13			AF001687	CCDS6791.1, CCDS59142.1	9q31-q33	2013-10-03	2013-10-03		ENSG00000136875	ENSG00000136875		"""WD repeat domain containing"""	17349	protein-coding gene	gene with protein product	"""PRP4/STK/WD splicing factor"", ""U4/U6 small nuclear ribonucleoprotein Prp4"""	607795	"""PRP4 pre-mRNA processing factor 4 homolog (yeast)"""			9257651, 9404889	Standard	NM_004697		Approved	Prp4p, HPRP4, HPRP4P, PRP4, SNRNP60	uc004bgx.3	O43172	OTTHUMG00000020517	ENST00000374198.4:c.1340C>T	9.37:g.116053261C>T	ENSP00000363313:p.Ala447Val		115093082	NM_004697	O43445|O43864|Q5T1M8|Q96DG2|Q96IK4	Missense_Mutation	SNP	ENST00000374198.4	37	CCDS6791.1	.	.	.	.	.	.	.	.	.	.	C	32	5.176140	0.94846	.	.	ENSG00000136875	ENST00000374199;ENST00000374198	T;T	0.62498	0.02;0.02	5.82	5.82	0.92795	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.212696	0.48286	D	0.000197	D	0.83161	0.5194	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.76071	0.987;0.983	D	0.86083	0.1545	10	0.87932	D	0	.	17.255	0.87053	0.0:1.0:0.0:0.0	.	462;447	Q59EL4;O43172	.;PRP4_HUMAN	V	446;447	ENSP00000363315:A446V;ENSP00000363313:A447V	ENSP00000363313:A447V	A	+	2	0	PRPF4	115093082	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.109000	0.77062	2.752000	0.94435	0.655000	0.94253	GCT		0.493	PRPF4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053708.2	NM_004697	
TNC	3371	broad.mit.edu	37	9	117838829	117838829	+	Silent	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:117838829T>C	ENST00000350763.4	-	8	3111	c.2700A>G	c.(2698-2700)cgA>cgG	p.R900R	TNC_ENST00000345230.3_Silent_p.R900R|TNC_ENST00000423613.2_Silent_p.R900R|TNC_ENST00000535648.1_Silent_p.R900R|TNC_ENST00000346706.3_Silent_p.R900R|TNC_ENST00000542877.1_Silent_p.R900R|TNC_ENST00000341037.4_Silent_p.R900R|TNC_ENST00000340094.3_Silent_p.R900R|TNC_ENST00000537320.1_Silent_p.R900R	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	900	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)	p.R900R(1)		NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						GGGAAACACGTCGAAGATTCC	0.478																																					p.R900R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A2700G	9						.						294.0	269.0	277.0					9																	117838829		2203	4300	6503	116878650	SO:0001819	synonymous_variant	3371	exon8				CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	5318	protein-coding gene	gene with protein product	"""hexabrachion (tenascin)"""	187380	"""hexabrachion (tenascin C, cytotactin)"", ""deafness, autosomal dominant 56"""	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.2700A>G	9.37:g.117838829T>C			116878650	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Silent	SNP	ENST00000350763.4	37	CCDS6811.1																																																																																				0.478	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
ASTN2	23245	broad.mit.edu	37	9	119802165	119802165	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:119802165G>A	ENST00000313400.4	-	6	1456	c.1356C>T	c.(1354-1356)ggC>ggT	p.G452G	ASTN2_ENST00000361209.2_Silent_p.G401G|ASTN2_ENST00000361477.3_5'UTR|ASTN2_ENST00000373996.3_Silent_p.G452G			O75129	ASTN2_HUMAN	astrotactin 2	452					negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)		p.G401G(1)		breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						ACATCTGGCTGCCACACACCA	0.522																																					p.G401G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1203T	9						.						113.0	91.0	99.0					9																	119802165		2203	4300	6503	118841986	SO:0001819	synonymous_variant	23245	exon5			AF116574	CCDS6814.1, CCDS6815.1, CCDS48009.1, CCDS48009.2, CCDS55334.1	9q33	2008-02-05			ENSG00000148219	ENSG00000148219			17021	protein-coding gene	gene with protein product		612856				9734811	Standard	NM_014010		Approved	KIAA0634	uc004bjt.2	O75129	OTTHUMG00000021013	ENST00000313400.4:c.1356C>T	9.37:g.119802165G>A			118841986	NM_014010	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Silent	SNP	ENST00000313400.4	37																																																																																					0.522	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010	
CDK5RAP2	55755	broad.mit.edu	37	9	123199787	123199787	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:123199787C>T	ENST00000349780.4	-	25	3920	c.3741G>A	c.(3739-3741)caG>caA	p.Q1247Q	CDK5RAP2_ENST00000359309.3_Silent_p.Q1206Q|CDK5RAP2_ENST00000360822.3_Silent_p.Q1215Q|CDK5RAP2_ENST00000360190.4_Silent_p.Q1247Q	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	1247					brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)	p.Q1247Q(1)		breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						TGGCTTGGGACTGAACTAATG	0.413																																					p.Q1247Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3741A	9						.						118.0	109.0	112.0					9																	123199787		2203	4300	6503	122239608	SO:0001819	synonymous_variant	55755	exon25			BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"""centrosomin"""	608201	"""microcephaly, primary autosomal recessive 3"""	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.3741G>A	9.37:g.123199787C>T			122239608	NM_018249	Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Silent	SNP	ENST00000349780.4	37	CCDS6823.1																																																																																				0.413	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055535.1	NM_018249	
C5	727	broad.mit.edu	37	9	123783948	123783948	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:123783948G>A	ENST00000223642.1	-	11	1170	c.1141C>T	c.(1141-1143)Cag>Tag	p.Q381*		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	381					activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cell surface receptor signaling pathway (GO:0007166)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukocyte migration involved in inflammatory response (GO:0002523)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of macrophage chemotaxis (GO:0010760)|negative regulation of norepinephrine secretion (GO:0010700)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of chemotaxis (GO:0050921)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|response to stress (GO:0006950)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)	chemokine activity (GO:0008009)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)	p.Q381*(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(14)|lung(5)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(323;4.98e-53)|GBM - Glioblastoma multiforme(294;0.0242)	Eculizumab(DB01257)|Intravenous Immunoglobulin(DB00028)	CCTACCAACTGGTCAAGCGAA	0.378																																					p.Q381X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1141T	9						.						169.0	162.0	164.0					9																	123783948		2203	4300	6503	122823769	SO:0001587	stop_gained	727	exon11			M57729	CCDS6826.1	9q33-q34	2014-09-17			ENSG00000106804	ENSG00000106804		"""Complement system"", ""Endogenous ligands"""	1331	protein-coding gene	gene with protein product	"""prepro-C5"", ""C5a anaphylatoxin"""	120900					Standard	NM_001735		Approved	CPAMD4, C5a, C5b	uc004bkv.3	P01031	OTTHUMG00000020579	ENST00000223642.1:c.1141C>T	9.37:g.123783948G>A	ENSP00000223642:p.Gln381*		122823769	NM_001735	Q14CJ0|Q27I61	Nonsense_Mutation	SNP	ENST00000223642.1	37	CCDS6826.1	.	.	.	.	.	.	.	.	.	.	G	36	5.845996	0.97016	.	.	ENSG00000106804	ENST00000223642;ENST00000430906	.	.	.	5.97	4.12	0.48240	.	0.782162	0.12739	N	0.443220	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11485	T	0.65	.	10.9611	0.47385	0.0:0.2871:0.5815:0.1314	.	.	.	.	X	381;452	.	ENSP00000223642:Q381X	Q	-	1	0	C5	122823769	1.000000	0.71417	0.850000	0.33497	0.981000	0.71138	1.790000	0.38734	0.827000	0.34685	0.655000	0.94253	CAG		0.378	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735	
OR1L3	26735	broad.mit.edu	37	9	125438017	125438017	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:125438017G>A	ENST00000304820.2	+	1	703	c.609G>A	c.(607-609)ggG>ggA	p.G203G		NM_001005234.1	NP_001005234.1	Q8NH93	OR1L3_HUMAN	olfactory receptor, family 1, subfamily L, member 3	203						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G203G(1)		breast(1)|kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	16						TGACAGAAGGGCTGGCCTCTG	0.433																																					p.G203G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G609A	9						.						163.0	156.0	159.0					9																	125438017		2203	4300	6503	124477838	SO:0001819	synonymous_variant	26735	exon1				CCDS35128.1	9q33.2	2013-09-20			ENSG00000171481	ENSG00000171481		"""GPCR / Class A : Olfactory receptors"""	8215	protein-coding gene	gene with protein product							Standard	NM_001005234		Approved	OR9-D	uc011lzb.2	Q8NH93	OTTHUMG00000020619	ENST00000304820.2:c.609G>A	9.37:g.125438017G>A			124477838	NM_001005234	B2RNF4|Q6IFN1	Silent	SNP	ENST00000304820.2	37	CCDS35128.1																																																																																				0.433	OR1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053950.1		
GOLGA1	2800	broad.mit.edu	37	9	127674275	127674275	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:127674275C>T	ENST00000373555.4	-	11	1207	c.874G>A	c.(874-876)Gtt>Att	p.V292I		NM_002077.3	NP_002068	Q92805	GOGA1_HUMAN	golgin A1	292					protein targeting to Golgi (GO:0000042)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)		p.V292I(1)		NS(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)	20						TGTGTGATAACGTCTTCTTTC	0.443																																					p.V292I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G874A	9						.						205.0	184.0	191.0					9																	127674275		2203	4300	6503	126714096	SO:0001583	missense	2800	exon11			U51587	CCDS6860.1	9q34.11	2010-02-12	2010-02-12		ENSG00000136935	ENSG00000136935			4424	protein-coding gene	gene with protein product		602502	"""golgi autoantigen, golgin subfamily a, 1"""			9324025	Standard	NM_002077		Approved	golgin-97, MGC33154	uc004bpc.3	Q92805	OTTHUMG00000020665	ENST00000373555.4:c.874G>A	9.37:g.127674275C>T	ENSP00000362656:p.Val292Ile		126714096	NM_002077	Q5T164|Q8IYZ9	Missense_Mutation	SNP	ENST00000373555.4	37	CCDS6860.1	.	.	.	.	.	.	.	.	.	.	C	0.011	-1.706135	0.00719	.	.	ENSG00000136935	ENST00000373555	T	0.76839	-1.05	5.84	-0.601	0.11638	.	0.187899	0.25503	U	0.030222	T	0.56543	0.1992	N	0.19112	0.55	0.09310	N	1	B;B	0.10296	0.003;0.002	B;B	0.08055	0.003;0.0	T	0.35400	-0.9790	10	0.33940	T	0.23	1.5149	5.6101	0.17400	0.1359:0.4923:0.2678:0.104	.	191;292	Q59HA1;Q92805	.;GOGA1_HUMAN	I	292	ENSP00000362656:V292I	ENSP00000362656:V292I	V	-	1	0	GOLGA1	126714096	0.968000	0.33430	0.000000	0.03702	0.005000	0.04900	-0.118000	0.10692	-0.688000	0.05155	-0.829000	0.03081	GTT		0.443	GOLGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054049.1	NM_002077	
CIZ1	25792	broad.mit.edu	37	9	130939951	130939951	+	Missense_Mutation	SNP	C	C	T	rs370598569		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:130939951C>T	ENST00000393608.1	-	10	1914	c.1712G>A	c.(1711-1713)cGc>cAc	p.R571H	CIZ1_ENST00000538431.1_Missense_Mutation_p.R571H|CIZ1_ENST00000476727.2_Intron|CIZ1_ENST00000357558.5_Missense_Mutation_p.R543H|CIZ1_ENST00000372948.3_Missense_Mutation_p.R515H|CIZ1_ENST00000372938.5_Missense_Mutation_p.R571H|CIZ1_ENST00000541172.1_Missense_Mutation_p.R470H|CIZ1_ENST00000372954.1_Missense_Mutation_p.R491H|CIZ1_ENST00000325721.8_Missense_Mutation_p.R542H|CIZ1_ENST00000277465.4_Missense_Mutation_p.R543H	NM_012127.2	NP_036259.2	Q9ULV3	CIZ1_HUMAN	CDKN1A interacting zinc finger protein 1	571					maintenance of protein location in nucleus (GO:0051457)|positive regulation of DNA-dependent DNA replication initiation (GO:0032298)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.R571H(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|liver(1)|lung(9)|ovary(3)|prostate(2)|urinary_tract(2)	35						GTCACTGGGGCGGGGGACAGG	0.642																																					p.R515H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1544A	9						.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	1,4397		0,1,2198	22.0	21.0	22.0		1544,1712,1529,1472,1712	5.5	0.0	9		22	1,8593		0,1,4296	no	missense,missense,missense,missense,missense	CIZ1	NM_001131015.1,NM_001131016.1,NM_001131017.1,NM_001131018.1,NM_012127.2	29,29,29,29,29	0,2,6494	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	515/843,571/899,510/838,491/819,571/899	130939951	2,12990	2199	4297	6496	129979772	SO:0001583	missense	25792	exon11			AB030835	CCDS6894.1, CCDS48033.1, CCDS48034.1, CCDS75910.1	9q34.1	2012-10-05			ENSG00000148337	ENSG00000148337			16744	protein-coding gene	gene with protein product		611420				10529385	Standard	NM_001131015		Approved	LSFR1, ZNF356	uc011mas.2	Q9ULV3	OTTHUMG00000020735	ENST00000393608.1:c.1712G>A	9.37:g.130939951C>T	ENSP00000377232:p.Arg571His		129979772	NM_001131015	A8K9J8|B4E131|B7ZAS8|Q5SYW3|Q5SYW5|Q8WU72|Q9H868|Q9NYM8|Q9UHK4|Q9Y3F9|Q9Y3G0	Missense_Mutation	SNP	ENST00000393608.1	37	CCDS6894.1	.	.	.	.	.	.	.	.	.	.	C	18.92	3.726164	0.69074	2.27E-4	1.16E-4	ENSG00000148337	ENST00000372954;ENST00000393608;ENST00000538431;ENST00000357558;ENST00000325721;ENST00000537314;ENST00000541172;ENST00000277465;ENST00000372948;ENST00000372938;ENST00000415526	T;T;T;T;T;T;T;T;T;T	0.38722	1.12;1.29;1.27;1.44;1.29;1.71;1.44;1.12;1.29;1.88	5.48	5.48	0.80851	.	0.000000	0.50627	D	0.000108	T	0.57095	0.2030	L	0.46157	1.445	0.09310	N	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;0.999;1.0	D;D;D;D;D;D;D	0.76071	0.954;0.912;0.967;0.987;0.949;0.932;0.927	T	0.51826	-0.8656	10	0.59425	D	0.04	-7.5708	14.2147	0.65786	0.1493:0.8506:0.0:0.0	.	571;510;515;491;571;542;543	B7Z3U7;B4E0A3;Q9ULV3-4;Q9ULV3-3;Q9ULV3;Q9ULV3-2;Q5SYW2	.;.;.;.;CIZ1_HUMAN;.;.	H	491;571;571;543;542;510;470;543;515;571;493	ENSP00000362045:R491H;ENSP00000377232:R571H;ENSP00000439244:R571H;ENSP00000350169:R543H;ENSP00000320374:R542H;ENSP00000445057:R470H;ENSP00000277465:R543H;ENSP00000362039:R515H;ENSP00000362029:R571H;ENSP00000398011:R493H	ENSP00000277465:R543H	R	-	2	0	CIZ1	129979772	0.819000	0.29175	0.042000	0.18584	0.006000	0.05464	3.448000	0.52943	2.577000	0.86979	0.462000	0.41574	CGC		0.642	CIZ1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054399.1	NM_012127	
TOR1A	1861	broad.mit.edu	37	9	132576259	132576259	+	Missense_Mutation	SNP	C	C	T	rs147805267		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:132576259C>T	ENST00000351698.4	-	5	1039	c.991G>A	c.(991-993)Gat>Aat	p.D331N		NM_000113.2	NP_000104.1	O14656	TOR1A_HUMAN	torsin family 1, member A (torsin A)	331	Interaction with KLC1.|Interaction with SYNE3.				ATP catabolic process (GO:0006200)|cell adhesion (GO:0007155)|chaperone mediated protein folding requiring cofactor (GO:0051085)|chaperone-mediated protein folding (GO:0061077)|chaperone-mediated protein transport (GO:0072321)|ER-associated misfolded protein catabolic process (GO:0071712)|intermediate filament cytoskeleton organization (GO:0045104)|neuron projection development (GO:0031175)|nuclear envelope organization (GO:0006998)|nuclear membrane organization (GO:0071763)|organelle organization (GO:0006996)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|protein deneddylation (GO:0000338)|protein homooligomerization (GO:0051260)|protein localization to nucleus (GO:0034504)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of protein localization to cell surface (GO:2000008)|response to oxidative stress (GO:0006979)|synaptic vesicle transport (GO:0048489)|wound healing, spreading of cells (GO:0044319)	cell junction (GO:0030054)|cytoplasmic vesicle membrane (GO:0030659)|cytoskeleton (GO:0005856)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|secretory granule (GO:0030141)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cytoskeletal protein binding (GO:0008092)|kinesin binding (GO:0019894)|unfolded protein binding (GO:0051082)	p.D331N(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(5)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	20		Ovarian(14;0.00556)				TGTCAATCATCGTAGTAATAA	0.473													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18935	0.0		0.0	False		,,,				2504	0.0				p.D331N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G991A	9						.	C	ASN/ASP	2,4404	4.2+/-10.8	0,2,2201	121.0	115.0	117.0		991	4.7	0.9	9	dbSNP_134	117	0,8600		0,0,4300	no	missense	TOR1A	NM_000113.2	23	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging	331/333	132576259	2,13004	2203	4300	6503	131616080	SO:0001583	missense	1861	exon5			AF007871	CCDS6930.1	9q32-q34	2008-07-21	2004-11-24	2004-11-26	ENSG00000136827	ENSG00000136827			3098	protein-coding gene	gene with protein product		605204	"""dystonia 1, torsion (autosomal dominant; torsin A)"""	DYT1		10644435	Standard	NM_000113		Approved	DQ2	uc004byl.3	O14656	OTTHUMG00000020794	ENST00000351698.4:c.991G>A	9.37:g.132576259C>T	ENSP00000345719:p.Asp331Asn		131616080	NM_000113	B2RB58|Q53Y64|Q96CA0	Missense_Mutation	SNP	ENST00000351698.4	37	CCDS6930.1	.	.	.	.	.	.	.	.	.	.	C	18.65	3.669221	0.67814	4.54E-4	0.0	ENSG00000136827	ENST00000427355;ENST00000351698	T	0.55930	0.49	4.71	4.71	0.59529	.	0.111882	0.38436	N	0.001689	T	0.41534	0.1163	L	0.28274	0.84	0.29490	N	0.855709	D	0.57257	0.979	P	0.44623	0.455	T	0.46555	-0.9183	10	0.59425	D	0.04	-3.1391	10.4662	0.44609	0.1942:0.8058:0.0:0.0	.	331	O14656	TOR1A_HUMAN	N	300;331	ENSP00000345719:D331N	ENSP00000345719:D331N	D	-	1	0	TOR1A	131616080	0.995000	0.38212	0.894000	0.35097	0.876000	0.50452	3.597000	0.54031	2.159000	0.67721	0.491000	0.48974	GAT		0.473	TOR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054611.1	NM_000113	
PRDM12	59335	broad.mit.edu	37	9	133543670	133543670	+	Silent	SNP	C	C	T	rs145300834	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:133543670C>T	ENST00000253008.2	+	3	600	c.540C>T	c.(538-540)atC>atT	p.I180I		NM_021619.2	NP_067632.2	Q9H4Q4	PRD12_HUMAN	PR domain containing 12	180	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				neurogenesis (GO:0022008)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)	p.I180I(1)		kidney(2)|large_intestine(3)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	11		all_hematologic(13;0.0433)|Acute lymphoblastic leukemia(5;0.0534)		OV - Ovarian serous cystadenocarcinoma(145;0.000344)		TGGTCCAGATCGGCACCAGCA	0.587													C|||	3	0.000599042	0.0023	0.0	5008	,	,		20285	0.0		0.0	False		,,,				2504	0.0				p.I180I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C540T	9						.	C		6,4400	11.4+/-27.6	0,6,2197	213.0	159.0	177.0		540	-10.4	0.9	9	dbSNP_134	177	0,8600		0,0,4300	no	coding-synonymous	PRDM12	NM_021619.2		0,6,6497	TT,TC,CC		0.0,0.1362,0.0461		180/368	133543670	6,13000	2203	4300	6503	132533491	SO:0001819	synonymous_variant	59335	exon3			AY004252	CCDS6934.1	9q33-q34	2013-01-08			ENSG00000130711	ENSG00000130711		"""Zinc fingers, C2H2-type"""	13997	protein-coding gene	gene with protein product	"""PR-domain containing protein 12"", ""PR-domain zinc finger protein 12"""					14523459	Standard	NM_021619		Approved		uc004bzt.1	Q9H4Q4	OTTHUMG00000020808	ENST00000253008.2:c.540C>T	9.37:g.133543670C>T			132533491	NM_021619	A3KFK9	Silent	SNP	ENST00000253008.2	37	CCDS6934.1																																																																																				0.587	PRDM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054664.1	NM_021619	
SETX	23064	broad.mit.edu	37	9	135205332	135205332	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:135205332C>T	ENST00000224140.5	-	10	1835	c.1653G>A	c.(1651-1653)caG>caA	p.Q551Q	SETX_ENST00000372169.2_Silent_p.Q551Q|SETX_ENST00000393220.1_Silent_p.Q551Q	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	551					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)	p.Q551Q(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		AAAGAGACTGCTGCCCAAGCT	0.423																																					p.Q551Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1653A	9						.						90.0	95.0	93.0					9																	135205332		2203	4299	6502	134195153	SO:0001819	synonymous_variant	23064	exon10			AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"""amyotrophic lateral sclerosis 4"", ""spinocerebellar ataxia, recessive, non-Friedreich type 1"""	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.1653G>A	9.37:g.135205332C>T			134195153	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Silent	SNP	ENST00000224140.5	37	CCDS6947.1																																																																																				0.423	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046	
REXO4	57109	broad.mit.edu	37	9	136277474	136277474	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:136277474G>A	ENST00000371942.3	-	4	1054	c.855C>T	c.(853-855)ccC>ccT	p.P285P	REXO4_ENST00000478037.1_5'UTR|REXO4_ENST00000371935.2_Intron	NM_020385.2	NP_065118.2	Q9GZR2	REXO4_HUMAN	REX4, RNA exonuclease 4 homolog (S. cerevisiae)	285	Exonuclease.				regulation of transcription, DNA-templated (GO:0006355)	nucleolus (GO:0005730)|nucleus (GO:0005634)	exonuclease activity (GO:0004527)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P285P(2)		kidney(1)|large_intestine(4)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	15				OV - Ovarian serous cystadenocarcinoma(145;8.58e-08)|Epithelial(140;9.55e-07)|all cancers(34;1.05e-05)		AGTCCGTCACGGGCTCAGTTG	0.547																																					p.P285P												.	.	2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	c.C855T	9						.						239.0	223.0	228.0					9																	136277474		2203	4300	6503	135267295	SO:0001819	synonymous_variant	57109	exon4			AF273304	CCDS6969.1, CCDS65179.1	9q34	2008-02-05	2005-08-22	2005-08-22	ENSG00000148300	ENSG00000148300			12820	protein-coding gene	gene with protein product		602930	"""Xenopus prevents mitotic catatrophe 2 homolog"", ""XPMC2 prevents mitotic catastrophe 2 homolog (Xenopus laevis)"""	XPMC2H		9325058	Standard	NM_020385		Approved		uc004cdm.3	Q9GZR2	OTTHUMG00000020870	ENST00000371942.3:c.855C>T	9.37:g.136277474G>A			135267295	NM_020385	B2RAT2|Q5T8S4|Q5T8S5|Q5T8S6|Q9GZW3	Silent	SNP	ENST00000371942.3	37	CCDS6969.1																																																																																				0.547	REXO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054899.1		
TMEM8C	389827	broad.mit.edu	37	9	136384136	136384136	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:136384136C>T	ENST00000339996.3	-	3	360	c.259G>A	c.(259-261)Gac>Aac	p.D87N	TMEM8C_ENST00000413714.1_5'UTR	NM_001080483.2	NP_001073952.1	A6NI61	TMM8C_HUMAN	transmembrane protein 8C	87					muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|plasma membrane fusion (GO:0045026)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.D87N(1)		NS(1)|autonomic_ganglia(1)|large_intestine(2)|lung(4)	8						TCGTCGAAGTCGGCCAGTGCT	0.632																																					p.D87N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G259A	9						.						102.0	88.0	93.0					9																	136384136		2203	4300	6503	135373957	SO:0001583	missense	389827	exon3			BX324209	CCDS35170.1	9q34.2	2009-06-19		2009-06-19	ENSG00000187616	ENSG00000187616			33778	protein-coding gene	gene with protein product	"""transmembrane protein 226"""	615345					Standard	NM_001080483		Approved	TMEM226	uc011mdk.2	A6NI61	OTTHUMG00000131685	ENST00000339996.3:c.259G>A	9.37:g.136384136C>T	ENSP00000419712:p.Asp87Asn		135373957	NM_001080483		Missense_Mutation	SNP	ENST00000339996.3	37	CCDS35170.1	.	.	.	.	.	.	.	.	.	.	C	17.19	3.326038	0.60743	.	.	ENSG00000187616	ENST00000339996	T	0.43294	0.95	5.09	5.09	0.68999	.	0.120272	0.53938	D	0.000044	T	0.51092	0.1654	M	0.67953	2.075	0.80722	D	1	D	0.54397	0.966	P	0.51355	0.667	T	0.46803	-0.9165	10	0.13853	T	0.58	-47.5793	17.0532	0.86525	0.0:1.0:0.0:0.0	.	87	A6NI61	TMM8C_HUMAN	N	87	ENSP00000419712:D87N	ENSP00000419712:D87N	D	-	1	0	TMEM8C	135373957	1.000000	0.71417	0.999000	0.59377	0.517000	0.34286	7.246000	0.78247	2.346000	0.79739	0.313000	0.20887	GAC		0.632	TMEM8C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356200.2	NM_001080483	
COL5A1	1289	broad.mit.edu	37	9	137704336	137704336	+	Silent	SNP	C	C	T	rs377422775		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:137704336C>T	ENST00000371817.3	+	47	4146	c.3732C>T	c.(3730-3732)gaC>gaT	p.D1244D		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1244	Triple-helical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)	p.D1244D(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		AGACAGGAGACGTGGGCCAGA	0.532																																					p.D1244D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3732T	9						.	C		0,4406		0,0,2203	123.0	92.0	102.0		3732	-3.1	0.9	9		102	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	COL5A1	NM_000093.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		1244/1839	137704336	1,13005	2203	4300	6503	136844157	SO:0001819	synonymous_variant	1289	exon47			D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.3732C>T	9.37:g.137704336C>T			136844157	NM_000093	Q15094|Q5SUX4	Silent	SNP	ENST00000371817.3	37	CCDS6982.1																																																																																				0.532	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	
CARD9	64170	broad.mit.edu	37	9	139264209	139264209	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:139264209C>T	ENST00000371732.5	-	7	1235	c.1070G>A	c.(1069-1071)cGg>cAg	p.R357Q	CARD9_ENST00000315908.7_Missense_Mutation_p.R357Q|CARD9_ENST00000460290.1_5'Flank|CARD9_ENST00000371734.3_Missense_Mutation_p.R357Q	NM_052813.4	NP_434700.2	Q9H257	CARD9_HUMAN	caspase recruitment domain family, member 9	357					defense response to Gram-positive bacterium (GO:0050830)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of apoptotic process (GO:0042981)|regulation of interleukin-2 biosynthetic process (GO:0045076)|regulation of interleukin-6 biosynthetic process (GO:0045408)|regulation of tumor necrosis factor biosynthetic process (GO:0042534)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to fungus (GO:0009620)|response to muramyl dipeptide (GO:0032495)|response to peptidoglycan (GO:0032494)	cytoplasm (GO:0005737)	CARD domain binding (GO:0050700)|protein homodimerization activity (GO:0042803)	p.R357Q(1)		endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)|prostate(3)|skin(1)	15		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;4.58e-06)|Epithelial(140;5.65e-06)		CACCTGGTCCCGCTCAATGGC	0.607																																					p.R357Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1070A	9						.						95.0	64.0	75.0					9																	139264209		2194	4297	6491	138384030	SO:0001583	missense	64170	exon7			AF311287	CCDS6997.1, CCDS48057.1	9q34	2014-09-17			ENSG00000187796	ENSG00000187796			16391	protein-coding gene	gene with protein product		607212				11053425	Standard	NM_052813		Approved		uc004chg.3	Q9H257	OTTHUMG00000020925	ENST00000371732.5:c.1070G>A	9.37:g.139264209C>T	ENSP00000360797:p.Arg357Gln		138384030	NM_052813	Q5SXM5|Q5SXM6|Q9H854	Missense_Mutation	SNP	ENST00000371732.5	37	CCDS6997.1	.	.	.	.	.	.	.	.	.	.	C	20.0	3.930866	0.73327	.	.	ENSG00000187796	ENST00000371734;ENST00000371732;ENST00000315908	T;T;T	0.36157	1.27;1.27;1.27	3.9	3.9	0.45041	.	0.000000	0.64402	D	0.000001	T	0.59729	0.2215	M	0.76727	2.345	0.53688	D	0.99997	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.997;0.997;0.998	T	0.66333	-0.5950	10	0.72032	D	0.01	-45.4341	15.0355	0.71744	0.0:1.0:0.0:0.0	.	253;357;357	B4DIK5;Q9H257-2;Q9H257	.;.;CARD9_HUMAN	Q	357	ENSP00000360799:R357Q;ENSP00000360797:R357Q;ENSP00000323719:R357Q	ENSP00000323719:R357Q	R	-	2	0	CARD9	138384030	1.000000	0.71417	0.922000	0.36590	0.233000	0.25261	7.297000	0.78799	2.011000	0.59026	0.462000	0.41574	CGG		0.607	CARD9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055053.1	NM_052813	
DMRT1	1761	broad.mit.edu	37	9	916764	916764	+	Splice_Site	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	T	T	T	Unknown	Wildtype	None	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:916764T>C	ENST00000382276.3	+	4	973	c.824T>C	c.(823-825)aTg>aCg	p.M275T	DMRT1_ENST00000569227.1_Splice_Site_p.M117T	NM_021951.2	NP_068770.2	Q9Y5R6	DMRT1_HUMAN	doublesex and mab-3 related transcription factor 1	275					cell morphogenesis (GO:0000902)|germ cell migration (GO:0008354)|intracellular signal transduction (GO:0035556)|male germ cell proliferation (GO:0002176)|male sex determination (GO:0030238)|male sex differentiation (GO:0046661)|negative regulation of meiosis (GO:0045835)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oocyte development (GO:0048599)|positive regulation of male gonad development (GO:2000020)|positive regulation of meiosis I (GO:0060903)|positive regulation of mitosis (GO:0045840)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of nodal signaling pathway (GO:1900107)|Sertoli cell development (GO:0060009)|Sertoli cell differentiation (GO:0060008)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(2)|lung(10)|ovary(1)	13		all_lung(10;2.66e-10)|Lung NSC(10;2.82e-10)|Breast(48;0.232)		Lung(218;0.037)		CTTAAGCAGATGAAGAACATG	0.443																																					p.M275T												.	.	0			c.T824C	9						.						121.0	111.0	114.0					9																	916764		2203	4300	6503	906764	SO:0001630	splice_region_variant	1761	exon4			AF130728	CCDS6442.1	9p24.3	2014-01-21			ENSG00000137090	ENSG00000137090			2934	protein-coding gene	gene with protein product	"""DM domain expressed in testis 1"""	602424				9490411, 10332030	Standard	XM_006716732		Approved	DMT1, CT154	uc003zgv.3	Q9Y5R6	OTTHUMG00000019435	ENST00000382276.3:c.823-1T>C	9.37:g.916764T>C			906764	NM_021951	B2R913|Q6T1H8|Q6T1H9|Q8IW77	Missense_Mutation	SNP	ENST00000382276.3	37	CCDS6442.1	.	.	.	.	.	.	.	.	.	.	T	14.85	2.657192	0.47467	.	.	ENSG00000137090	ENST00000382276	T	0.19532	2.14	5.44	5.44	0.79542	.	0.000000	0.64402	D	0.000001	T	0.28632	0.0709	M	0.79926	2.475	0.43259	D	0.995197	P	0.47762	0.9	B	0.40940	0.344	T	0.13845	-1.0494	10	0.29301	T	0.29	.	14.3746	0.66865	0.0:0.0:0.0:1.0	.	275	Q9Y5R6	DMRT1_HUMAN	T	275	ENSP00000371711:M275T	ENSP00000371711:M275T	M	+	2	0	DMRT1	906764	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	4.966000	0.63715	2.193000	0.70182	0.533000	0.62120	ATG		0.443	DMRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051489.2	NM_021951	Missense_Mutation
FREM1	158326	broad.mit.edu	37	9	14842415	14842415	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:14842415C>A	ENST00000380880.3	-	9	2420	c.1637G>T	c.(1636-1638)cGa>cTa	p.R546L	FREM1_ENST00000380881.4_Missense_Mutation_p.R547L|FREM1_ENST00000422223.2_Missense_Mutation_p.R546L			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	546					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)	p.R547L(1)		breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		ATCTGAAGCTCGCAGCATGGA	0.512																																					p.R546L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1637T	9						.						134.0	133.0	133.0					9																	14842415		2032	4189	6221	14832415	SO:0001583	missense	158326	exon10			AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"""chromosome 9 open reading frame 154"""	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.1637G>T	9.37:g.14842415C>A	ENSP00000370262:p.Arg546Leu		14832415	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	.	.	.	.	.	.	.	.	.	.	C	7.807	0.714907	0.15306	.	.	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.51071	0.72;0.72;0.72	5.93	3.9	0.45041	.	0.304152	0.37955	N	0.001873	T	0.23766	0.0575	N	0.08118	0	0.38169	D	0.939289	B	0.11235	0.004	B	0.09377	0.004	T	0.09250	-1.0683	10	0.29301	T	0.29	-15.6786	6.7728	0.23602	0.0:0.7027:0.0:0.2973	.	546	Q5H8C1	FREM1_HUMAN	L	547;546;546	ENSP00000370263:R547L;ENSP00000412940:R546L;ENSP00000370262:R546L	ENSP00000370257:R549L	R	-	2	0	FREM1	14832415	1.000000	0.71417	1.000000	0.80357	0.011000	0.07611	3.209000	0.51122	1.546000	0.49388	-0.119000	0.15052	CGA		0.512	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
ADAMTSL1	92949	broad.mit.edu	37	9	18533267	18533267	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:18533267C>T	ENST00000380548.4	+	3	553	c.214C>T	c.(214-216)Cga>Tga	p.R72*	ADAMTSL1_ENST00000380570.4_Nonsense_Mutation_p.R72*|ADAMTSL1_ENST00000431052.2_Nonsense_Mutation_p.R72*|ADAMTSL1_ENST00000327883.7_Nonsense_Mutation_p.R72*|ADAMTSL1_ENST00000276935.6_Nonsense_Mutation_p.R72*|ADAMTSL1_ENST00000380566.4_Nonsense_Mutation_p.R72*	NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	72	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R72*(2)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(2)|lung(17)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(50;1.29e-17)		AAGAAATATCCGATACAGAAC	0.303																																					p.R72X												.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C214T	9						.						119.0	120.0	120.0					9																	18533267		2203	4299	6502	18523267	SO:0001587	stop_gained	92949	exon3			AF176313	CCDS6485.1, CCDS47954.1	9p21.3	2013-01-11			ENSG00000178031	ENSG00000178031		"""Immunoglobulin superfamily / I-set domain containing"""	14632	protein-coding gene	gene with protein product	"""punctin"""	609198	"""chromosome 9 open reading frame 94"""	C9orf94		9628581, 11805097	Standard	NM_001040272		Approved	ADAMTSR1, FLJ35283	uc003zne.4	Q8N6G6	OTTHUMG00000019604	ENST00000380548.4:c.214C>T	9.37:g.18533267C>T	ENSP00000369921:p.Arg72*		18523267	NM_052866	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Nonsense_Mutation	SNP	ENST00000380548.4	37	CCDS47954.1	.	.	.	.	.	.	.	.	.	.	C	35	5.483150	0.96307	.	.	ENSG00000178031	ENST00000380548;ENST00000327883;ENST00000431052;ENST00000380570;ENST00000380566;ENST00000276935	.	.	.	5.2	3.26	0.37387	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.5407	0.45031	0.3524:0.6476:0.0:0.0	.	.	.	.	X	72	.	ENSP00000276935:R72X	R	+	1	2	ADAMTSL1	18523267	0.760000	0.28428	0.995000	0.50966	0.986000	0.74619	0.178000	0.16820	0.623000	0.30267	0.542000	0.68232	CGA		0.303	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1		
CCL21	6366	broad.mit.edu	37	9	34709818	34709818	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:34709818G>A	ENST00000259607.2	-	2	201	c.144C>T	c.(142-144)taC>taT	p.Y48Y	CCL21_ENST00000378792.1_Silent_p.Y48Y	NM_002989.2	NP_002980.1	O00585	CCL21_HUMAN	chemokine (C-C motif) ligand 21	48					activation of Rho GTPase activity (GO:0032862)|cell chemotaxis (GO:0060326)|cell maturation (GO:0048469)|cell-cell signaling (GO:0007267)|dendritic cell chemotaxis (GO:0002407)|dendritic cell dendrite assembly (GO:0097026)|establishment of T cell polarity (GO:0001768)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|immunological synapse formation (GO:0001771)|inflammatory response (GO:0006954)|mesangial cell-matrix adhesion (GO:0035759)|negative regulation of dendritic cell dendrite assembly (GO:2000548)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative regulation of leukocyte tethering or rolling (GO:1903237)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell motility (GO:2000147)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of chemotaxis (GO:0050921)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of glycoprotein biosynthetic process (GO:0010560)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myeloid dendritic cell chemotaxis (GO:2000529)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of T cell migration (GO:2000406)|release of sequestered calcium ion into cytosol (GO:0051209)|response to prostaglandin E (GO:0034695)|ruffle organization (GO:0031529)|T cell costimulation (GO:0031295)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	CCR7 chemokine receptor binding (GO:0031732)|chemokine activity (GO:0008009)|chemokine receptor binding (GO:0042379)	p.Y48Y(1)		large_intestine(4)	4	all_epithelial(49;0.0899)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.173)		CCTGCTTCCGGTAGCTGCGGA	0.597																																					p.Y48Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C144T	9						.						96.0	82.0	87.0					9																	34709818		2203	4300	6503	34699818	SO:0001819	synonymous_variant	6366	exon2			AB002409	CCDS6571.1	9p13	2014-05-16	2002-08-22	2002-08-23	ENSG00000137077	ENSG00000137077		"""Chemokine ligands"", ""Endogenous ligands"""	10620	protein-coding gene	gene with protein product	"""beta chemokine exodus-2"", ""secondary lymphoid tissue chemokine"", ""Efficient Chemoattractant for Lymphocytes"""	602737	"""small inducible cytokine subfamily A (Cys-Cys), member 21"""	SCYA21		9235955	Standard	NM_002989		Approved	SLC, exodus-2, TCA4, CKb9, 6Ckine, ECL	uc003zvo.4	O00585	OTTHUMG00000019838	ENST00000259607.2:c.144C>T	9.37:g.34709818G>A			34699818	NM_002989		Silent	SNP	ENST00000259607.2	37	CCDS6571.1																																																																																				0.597	CCL21-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052245.1	NM_002989	
NPR2	4882	broad.mit.edu	37	9	35806091	35806091	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:35806091C>T	ENST00000342694.2	+	15	2488	c.2233C>T	c.(2233-2235)Cgg>Tgg	p.R745W		NM_003995.3	NP_003986.2	P20594	ANPRB_HUMAN	natriuretic peptide receptor 2	745	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				bone development (GO:0060348)|cell surface receptor signaling pathway (GO:0007166)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cGMP biosynthetic process (GO:0006182)|intracellular signal transduction (GO:0035556)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of oocyte maturation (GO:1900194)|ossification (GO:0001503)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|signal transduction (GO:0007165)|single organism reproductive process (GO:0044702)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.R745W(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(2)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)		Erythrityl Tetranitrate(DB01613)|Nesiritide(DB04899)	AAATGGTCAGCGGCCATATTT	0.527																																					p.R745W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2233T	9						.						62.0	64.0	63.0					9																	35806091		2203	4300	6503	35796091	SO:0001583	missense	4882	exon15			AJ005282	CCDS6590.1	9p21-p12	2014-03-03	2014-03-03		ENSG00000159899	ENSG00000159899			7944	protein-coding gene	gene with protein product	"""guanylate cyclase B"""	108961	"""acromesomelic dysplasia, Maroteaux type"", ""atrionatriuretic peptide receptor B"", ""natriuretic peptide receptor B"""	ANPRB, NPRB, AMDM		9634515, 15146390	Standard	XM_005251478		Approved	GUCY2B, ANPb	uc003zyd.3	P20594	OTTHUMG00000019871	ENST00000342694.2:c.2233C>T	9.37:g.35806091C>T	ENSP00000341083:p.Arg745Trp		35796091	NM_003995	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Missense_Mutation	SNP	ENST00000342694.2	37	CCDS6590.1	.	.	.	.	.	.	.	.	.	.	C	9.738	1.163998	0.21538	.	.	ENSG00000159899	ENST00000342694;ENST00000447210	D;D	0.85629	-2.01;-2.01	5.82	4.9	0.64082	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.40385	N	0.001116	T	0.81317	0.4797	L	0.50919	1.6	0.40077	D	0.976089	B;B	0.18863	0.031;0.031	B;B	0.15484	0.013;0.005	T	0.77699	-0.2490	10	0.44086	T	0.13	.	13.2317	0.59947	0.2969:0.7031:0.0:0.0	.	745;745	P20594-2;P20594	.;ANPRB_HUMAN	W	745;4	ENSP00000341083:R745W;ENSP00000393029:R4W	ENSP00000341083:R745W	R	+	1	2	NPR2	35796091	0.850000	0.29656	1.000000	0.80357	0.996000	0.88848	-0.083000	0.11286	1.405000	0.46838	0.563000	0.77884	CGG		0.527	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1		
FBXO10	26267	broad.mit.edu	37	9	37522822	37522822	+	Splice_Site	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:37522822C>T	ENST00000432825.2	-	7	1978	c.1930G>A	c.(1930-1932)Gct>Act	p.A644T	RP11-613M10.8_ENST00000544475.1_5'UTR|FBXO10_ENST00000541829.1_Splice_Site_p.A169T|FBXO10_ENST00000543968.1_5'UTR	NM_012166.2	NP_036298.2	Q9UK96	FBX10_HUMAN	F-box protein 10	644					apoptotic process (GO:0006915)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)	p.A644T(1)		breast(1)|endometrium(5)|large_intestine(11)|lung(15)|prostate(1)|upper_aerodigestive_tract(1)	34				GBM - Glioblastoma multiforme(29;0.0107)		AGCTCCTCACCGTAGATGGTA	0.552																																					p.A644T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1930A	9						.						74.0	83.0	80.0					9																	37522822		1885	3959	5844	37512822	SO:0001630	splice_region_variant	26267	exon7			AF174598	CCDS47966.1	9p13.1	2014-01-29	2004-06-15		ENSG00000147912	ENSG00000147912		"""F-boxes /  ""other"""""	13589	protein-coding gene	gene with protein product		609092	"""F-box only protein 10"""			10531035, 10531037, 19300908	Standard	NM_012166		Approved	FBX10	uc004aab.3	Q9UK96	OTTHUMG00000019926	ENST00000432825.2:c.1930+1G>A	9.37:g.37522822C>T			37512822	NM_012166	Q08AL3|Q08AL4|Q5JRT8|Q9UKC3	Missense_Mutation	SNP	ENST00000432825.2	37	CCDS47966.1	.	.	.	.	.	.	.	.	.	.	C	16.94	3.261241	0.59431	.	.	ENSG00000147912	ENST00000432825;ENST00000541829	T;T	0.79454	-1.27;0.97	4.72	4.72	0.59763	Pectin lyase fold/virulence factor (1);Carbohydrate-binding/sugar hydrolysis domain (1);	0.590917	0.17099	N	0.187080	T	0.62986	0.2473	N	0.14661	0.345	0.45295	D	0.998297	B;B;P	0.51653	0.064;0.038;0.947	B;B;B	0.40009	0.021;0.025;0.316	T	0.64601	-0.6369	9	.	.	.	-1.7974	16.6157	0.84915	0.0:1.0:0.0:0.0	.	523;169;644	Q59F51;Q08AL4;Q9UK96	.;.;FBX10_HUMAN	T	644;169	ENSP00000403802:A644T;ENSP00000441307:A169T	.	A	-	1	0	FBXO10	37512822	1.000000	0.71417	1.000000	0.80357	0.576000	0.36127	2.583000	0.46094	2.443000	0.82685	0.650000	0.86243	GCT		0.552	FBXO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052472.3		Missense_Mutation
SLC25A51	92014	broad.mit.edu	37	9	37888004	37888004	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:37888004G>A	ENST00000377716.2	-	3	1287	c.544C>T	c.(544-546)Cgg>Tgg	p.R182W	SLC25A51_ENST00000242275.6_Missense_Mutation_p.R182W|SLC25A51_ENST00000380590.3_Missense_Mutation_p.R182W|SLC25A51_ENST00000496760.1_Intron|RP11-613M10.9_ENST00000540557.1_Intron			Q9H1U9	S2551_HUMAN	solute carrier family 25, member 51	182					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)		p.R182W(1)									AGTCCATTCCGGAAAAGAATG	0.458																																					p.R182W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C544T	9						.						90.0	86.0	88.0					9																	37888004		2203	4297	6500	37878004	SO:0001583	missense	92014	exon3			BC008500	CCDS6614.1	9p13.3-p12	2013-05-22	2012-03-29	2012-03-29	ENSG00000122696	ENSG00000122696		"""Solute carriers"""	23323	protein-coding gene	gene with protein product			"""mitochondrial carrier triple repeat 1"""	MCART1		12477932	Standard	NM_033412		Approved	MGC14836, CG7943	uc004aav.2	Q9H1U9	OTTHUMG00000019935	ENST00000377716.2:c.544C>T	9.37:g.37888004G>A	ENSP00000366945:p.Arg182Trp		37878004	NM_033412		Missense_Mutation	SNP	ENST00000377716.2	37	CCDS6614.1	.	.	.	.	.	.	.	.	.	.	.	19.70	3.876204	0.72180	.	.	ENSG00000122696	ENST00000380590;ENST00000377716;ENST00000242275	D;D;D	0.82526	-1.62;-1.62;-1.62	4.64	4.64	0.57946	Mitochondrial carrier domain (2);	0.144460	0.43919	D	0.000510	D	0.92358	0.7575	M	0.90650	3.135	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.93936	0.7219	10	0.87932	D	0	.	15.3749	0.74596	0.0:0.0:1.0:0.0	.	182	Q9H1U9	MCAR1_HUMAN	W	182	ENSP00000369964:R182W;ENSP00000366945:R182W;ENSP00000242275:R182W	ENSP00000242275:R182W	R	-	1	2	MCART1	37878004	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	5.062000	0.64326	2.303000	0.77524	0.585000	0.79938	CGG		0.458	SLC25A51-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313746.1	NM_033412	
SMC5	23137	broad.mit.edu	37	9	72895763	72895763	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:72895763G>A	ENST00000361138.5	+	6	825	c.767G>A	c.(766-768)cGg>cAg	p.R256Q		NM_015110.3	NP_055925.2	Q8IY18	SMC5_HUMAN	structural maintenance of chromosomes 5	256					cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|mitotic nuclear division (GO:0007067)|positive regulation of maintenance of mitotic sister chromatid cohesion (GO:0034184)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|telomere maintenance via recombination (GO:0000722)	cell junction (GO:0030054)|chromosome, telomeric region (GO:0000781)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)	p.R256Q(1)		breast(1)|central_nervous_system(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(4)	35						TTCTATGAACGGAAGCGACAT	0.358																																					p.R256Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G767A	9						.						154.0	163.0	160.0					9																	72895763		2203	4300	6503	72085583	SO:0001583	missense	23137	exon6			AB011166	CCDS6632.1	9q21.11	2008-02-05	2006-07-06	2006-07-06	ENSG00000198887	ENSG00000198887		"""Structural maintenance of chromosomes proteins"""	20465	protein-coding gene	gene with protein product		609386	"""SMC5 structural maintenance of chromosomes 5-like 1 (yeast)"""	SMC5L1		9628581	Standard	NM_015110		Approved	KIAA0594	uc004ahr.2	Q8IY18	OTTHUMG00000019992	ENST00000361138.5:c.767G>A	9.37:g.72895763G>A	ENSP00000354957:p.Arg256Gln		72085583	NM_015110	A6NM81|O60335|Q05D92|Q5VZ60|Q96SB9	Missense_Mutation	SNP	ENST00000361138.5	37	CCDS6632.1	.	.	.	.	.	.	.	.	.	.	G	12.45	1.942207	0.34283	.	.	ENSG00000198887	ENST00000361138	T	0.80653	-1.4	5.19	4.29	0.51040	RecF/RecN/SMC (1);	0.345212	0.30723	N	0.009012	T	0.64125	0.2570	L	0.35644	1.08	0.28538	N	0.912249	P	0.35745	0.518	B	0.20767	0.031	T	0.58907	-0.7553	10	0.27785	T	0.31	-7.5728	8.0086	0.30340	0.232:0.0:0.768:0.0	.	256	Q8IY18	SMC5_HUMAN	Q	256	ENSP00000354957:R256Q	ENSP00000354957:R256Q	R	+	2	0	SMC5	72085583	1.000000	0.71417	0.949000	0.38748	0.651000	0.38670	4.507000	0.60434	2.436000	0.82500	0.585000	0.79938	CGG		0.358	SMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052603.1	NM_015110	
TMEM2	23670	broad.mit.edu	37	9	74349810	74349810	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:74349810G>A	ENST00000377044.4	-	6	1844	c.1305C>T	c.(1303-1305)gtC>gtT	p.V435V	TMEM2_ENST00000377066.5_Intron	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	435					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.V435V(1)		central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		CTGTGCTTGCGACCACAATCT	0.443																																					p.V435V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1305T	9						.						206.0	193.0	197.0					9																	74349810		2203	4300	6503	73539630	SO:0001819	synonymous_variant	23670	exon6				CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.1305C>T	9.37:g.74349810G>A			73539630	NM_013390	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Silent	SNP	ENST00000377044.4	37	CCDS6638.1																																																																																				0.443	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390	
NMRK1	54981	broad.mit.edu	37	9	77676483	77676483	+	Splice_Site	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:77676483C>T	ENST00000361092.4	-	9	817	c.581G>A	c.(580-582)tGt>tAt	p.C194Y	NMRK1_ENST00000482537.1_5'UTR|NMRK1_ENST00000376808.4_Splice_Site_p.C170Y|NMRK1_ENST00000376811.1_Splice_Site_p.C198Y	NM_017881.2	NP_060351.1	Q9NWW6	NRK1_HUMAN	nicotinamide riboside kinase 1	194					NAD biosynthetic process (GO:0009435)		ATP binding (GO:0005524)|metal ion binding (GO:0046872)|ribosylnicotinamide kinase activity (GO:0050262)	p.C194Y(1)									CACTTGCAAACCTTGGGAATA	0.313																																					p.C194Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G581A	9						.						112.0	106.0	108.0					9																	77676483		2202	4300	6502	76866303	SO:0001630	splice_region_variant	54981	exon9			AK097144	CCDS6650.1, CCDS47981.1	9q21.31	2012-03-30	2012-03-30	2012-03-30	ENSG00000106733	ENSG00000106733			26057	protein-coding gene	gene with protein product		608704	"""chromosome 9 open reading frame 95"""	C9orf95		15137942	Standard	NM_017881		Approved	FLJ20559, NRK1, bA235O14.2	uc004ajr.4	Q9NWW6	OTTHUMG00000020034	ENST00000361092.4:c.581-1G>A	9.37:g.77676483C>T			76866303	NM_017881	Q5W124|Q8N430	Missense_Mutation	SNP	ENST00000361092.4	37	CCDS6650.1	.	.	.	.	.	.	.	.	.	.	C	8.386	0.838724	0.16891	.	.	ENSG00000106733	ENST00000376811;ENST00000361092;ENST00000376808	T;T;T	0.46063	0.88;0.92;0.89	3.82	1.95	0.26073	.	.	.	.	.	T	0.24005	0.0581	L	0.38175	1.15	0.31146	N	0.706001	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.06405	0.001;0.001;0.002	T	0.34725	-0.9817	9	0.02654	T	1	.	4.7338	0.12977	0.2128:0.6753:0.0:0.1119	.	170;198;194	Q9NWW6-2;Q5W125;Q9NWW6	.;.;NRK1_HUMAN	Y	198;194;170	ENSP00000366007:C198Y;ENSP00000354387:C194Y;ENSP00000366004:C170Y	ENSP00000354387:C194Y	C	-	2	0	C9orf95	76866303	0.983000	0.35010	0.988000	0.46212	0.573000	0.36030	0.087000	0.14958	0.579000	0.29504	0.462000	0.41574	TGT		0.313	NMRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052705.1	NM_017881	Missense_Mutation
VPS13A	23230	broad.mit.edu	37	9	79933458	79933458	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:79933458G>A	ENST00000360280.3	+	41	5524	c.5264G>A	c.(5263-5265)gGc>gAc	p.G1755D	VPS13A_ENST00000376634.4_Missense_Mutation_p.G1755D|VPS13A_ENST00000423463.2_3'UTR|VPS13A_ENST00000357409.5_Missense_Mutation_p.G1755D|VPS13A_ENST00000376636.3_Missense_Mutation_p.G1716D	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	1755					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)		p.G1755D(2)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						TCAGGGGAAGGCAAAAACTGG	0.348																																					p.G1716D												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G5147A	9						.						57.0	58.0	58.0					9																	79933458		2203	4298	6501	79123278	SO:0001583	missense	23230	exon40			AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"""chorein"""	605978	"""chorea acanthocytosis"", ""vacuolar protein sorting 13A (yeast)"""	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.5264G>A	9.37:g.79933458G>A	ENSP00000353422:p.Gly1755Asp		79123278	NM_001018037	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	37	CCDS6655.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.73|15.73	2.918844|2.918844	0.52546|0.52546	.|.	.|.	ENSG00000197969|ENSG00000197969	ENST00000419472|ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409	.|T;T;T;T	.|0.13089	.|2.62;2.62;2.62;2.62	5.4|5.4	3.37|3.37	0.38596|0.38596	.|.	.|0.290247	.|0.32785	.|N	.|0.005641	T|T	0.14356|0.14356	0.0347|0.0347	L|L	0.44542|0.44542	1.39|1.39	0.80722|0.80722	D|D	1|1	.|P;B;P;P;P	.|0.48089	.|0.905;0.288;0.846;0.905;0.905	.|P;B;B;B;B	.|0.46452	.|0.517;0.142;0.319;0.413;0.413	T|T	0.02037|0.02037	-1.1225|-1.1225	5|10	.|0.45353	.|T	.|0.12	.|.	7.936|7.936	0.29931|0.29931	0.0:0.2374:0.4745:0.2881|0.0:0.2374:0.4745:0.2881	.|.	.|7;1716;1755;1755;1755	.|B1ALW4;Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4	.|.;.;VP13A_HUMAN;.;.	T|D	8|1755;1716;1755;1755	.|ENSP00000365821:G1755D;ENSP00000365823:G1716D;ENSP00000353422:G1755D;ENSP00000349985:G1755D	.|ENSP00000349985:G1755D	A|G	+|+	1|2	0|0	VPS13A|VPS13A	79123278|79123278	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	4.269000|4.269000	0.58890|0.58890	1.350000|1.350000	0.45770|0.45770	0.460000|0.460000	0.39030|0.39030	GCA|GGC		0.348	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186	
GNA14	9630	broad.mit.edu	37	9	80046301	80046301	+	Missense_Mutation	SNP	G	G	A	rs545966792		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:80046301G>A	ENST00000341700.6	-	4	1042	c.529C>T	c.(529-531)Cgc>Tgc	p.R177C	GNA14_ENST00000464095.1_5'UTR	NM_004297.3	NP_004288.1	O95837	GNA14_HUMAN	guanine nucleotide binding protein (G protein), alpha 14	177					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)	p.R177C(1)		endometrium(3)|kidney(1)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	24						ACTCGGACGCGAAGCACATCT	0.473													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19965	0.0		0.0	False		,,,				2504	0.0				p.R177C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C529T	9						.						205.0	163.0	177.0					9																	80046301		2203	4300	6503	79236121	SO:0001583	missense	9630	exon4			AF105201	CCDS6657.1	9q21	2008-05-23			ENSG00000156049	ENSG00000156049			4382	protein-coding gene	gene with protein product		604397				10191087, 17620339	Standard	NM_004297		Approved		uc004aku.3	O95837	OTTHUMG00000020058	ENST00000341700.6:c.529C>T	9.37:g.80046301G>A	ENSP00000365807:p.Arg177Cys		79236121	NM_004297	B1ALW3	Missense_Mutation	SNP	ENST00000341700.6	37	CCDS6657.1	.	.	.	.	.	.	.	.	.	.	G	17.39	3.377287	0.61735	.	.	ENSG00000156049	ENST00000341700	D	0.89939	-2.59	5.42	5.42	0.78866	G protein alpha subunit, helical insertion (1);	0.094954	0.64402	D	0.000002	D	0.94518	0.8235	H	0.95151	3.63	0.58432	D	0.999999	D	0.55605	0.972	P	0.54026	0.74	D	0.95401	0.8490	10	0.87932	D	0	.	12.5108	0.56005	0.0:0.0:0.7272:0.2728	.	177	O95837	GNA14_HUMAN	C	177	ENSP00000365807:R177C	ENSP00000365807:R177C	R	-	1	0	GNA14	79236121	0.606000	0.26949	0.910000	0.35882	0.518000	0.34316	0.858000	0.27845	2.705000	0.92388	0.655000	0.94253	CGC		0.473	GNA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052759.1		
C9orf64	84267	broad.mit.edu	37	9	86571107	86571107	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:86571107G>A	ENST00000376344.3	-	1	525	c.309C>T	c.(307-309)tgC>tgT	p.C103C	C9orf64_ENST00000314700.1_5'UTR|C9orf64_ENST00000376340.2_5'UTR	NM_032307.3	NP_115683.3	Q5T6V5	CI064_HUMAN	chromosome 9 open reading frame 64	103								p.C103C(1)		central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	15						TGACGGCGGCGCACAGGGACC	0.552																																					p.C103C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C309T	9						.						131.0	129.0	130.0					9																	86571107		2074	4202	6276	85760927	SO:0001819	synonymous_variant	84267	exon1			AK090882	CCDS6666.2	9q22.1	2014-06-11			ENSG00000165118	ENSG00000165118			28144	protein-coding gene	gene with protein product		611342				24911101	Standard	NM_032307		Approved	MGC10999	uc004anb.3	Q5T6V5	OTTHUMG00000020111	ENST00000376344.3:c.309C>T	9.37:g.86571107G>A			85760927	NM_032307	B2RPI6|Q8N2B1|Q9BT18	Silent	SNP	ENST00000376344.3	37	CCDS6666.2																																																																																				0.552	C9orf64-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052865.1	NM_032307	
C9orf170	401535	broad.mit.edu	37	9	89763654	89763654	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:89763654C>T	ENST00000375941.2	+	1	96	c.9C>T	c.(7-9)agC>agT	p.S3S		NM_001001709.2	NP_001001709.1	A2RU37	CI170_HUMAN	chromosome 9 open reading frame 170	3								p.S3S(1)		large_intestine(3)|lung(2)|prostate(1)	6						GAATGTGGAGCAGGCGCGGCC	0.706																																					p.S3S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C9T	9						.						10.0	11.0	11.0					9																	89763654		2185	4289	6474	88953474	SO:0001819	synonymous_variant	401535	exon1			AK127445	CCDS35058.1	9q21.33	2009-02-11			ENSG00000204446	ENSG00000204446			33817	protein-coding gene	gene with protein product							Standard	NM_001001709		Approved	FLJ45537	uc004apa.1	A2RU37	OTTHUMG00000159587	ENST00000375941.2:c.9C>T	9.37:g.89763654C>T			88953474	NM_001001709		Silent	SNP	ENST00000375941.2	37	CCDS35058.1																																																																																				0.706	C9orf170-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356346.1	NM_001001709	
SPATA31E1	286234	broad.mit.edu	37	9	90500977	90500977	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:90500977C>T	ENST00000325643.5	+	4	1641	c.1575C>T	c.(1573-1575)gcC>gcT	p.A525A		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	525					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)		p.A525A(1)									agacccaggcccacctctcac	0.647																																					p.A525A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1575T	9						.						45.0	48.0	47.0					9																	90500977		2203	4299	6502	89690797	SO:0001819	synonymous_variant	286234	exon4			AK093185	CCDS6676.1	9q22.1-q22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000177992	ENSG00000177992			26672	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 79"", ""family with sequence similarity 75, member E1"""	C9orf79, FAM75E1			Standard	NM_178828		Approved	FLJ35866	uc004app.4	Q6ZUB1	OTTHUMG00000020157	ENST00000325643.5:c.1575C>T	9.37:g.90500977C>T			89690797	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Silent	SNP	ENST00000325643.5	37	CCDS6676.1																																																																																				0.647	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828	
SECISBP2	79048	broad.mit.edu	37	9	91934686	91934686	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:91934686G>A	ENST00000375807.3	+	2	227	c.156G>A	c.(154-156)ccG>ccA	p.P52P	SECISBP2_ENST00000339901.4_Missense_Mutation_p.V20I|SECISBP2_ENST00000534113.2_5'UTR	NM_001282688.1|NM_001282690.1|NM_024077.3	NP_001269617.1|NP_001269619.1|NP_076982.3	Q96T21	SEBP2_HUMAN	SECIS binding protein 2	52					translation (GO:0006412)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|ribonucleoprotein complex binding (GO:0043021)|selenocysteine insertion sequence binding (GO:0035368)	p.P52P(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(3)|skin(2)	32						CATACTATCCGTTTGTTCAGG	0.438																																					p.P52P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G156A	9						.						141.0	142.0	142.0					9																	91934686		2203	4300	6503	91124506	SO:0001819	synonymous_variant	79048	exon2			AF380995	CCDS6683.1, CCDS65076.1, CCDS65077.1	9q22	2008-02-05			ENSG00000187742	ENSG00000187742			30972	protein-coding gene	gene with protein product		607693				11230166	Standard	XM_005252193		Approved		uc004aqj.1	Q96T21	OTTHUMG00000020182	ENST00000375807.3:c.156G>A	9.37:g.91934686G>A			91124506	NM_024077	F8W892|Q5HYY1|Q8IYC0|Q9H0A1	Missense_Mutation	SNP	ENST00000375807.3	37	CCDS6683.1	.	.	.	.	.	.	.	.	.	.	G	12.38	1.922108	0.33908	.	.	ENSG00000187742	ENST00000339901	T	0.72394	-0.65	4.61	-9.23	0.00672	.	.	.	.	.	T	0.39937	0.1097	.	.	.	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.39961	-0.9588	8	0.11485	T	0.65	-5.8881	2.2054	0.03934	0.1682:0.1012:0.2344:0.4962	.	20	Q96T21-2	.	I	20	ENSP00000364959:V20I	ENSP00000364959:V20I	V	+	1	0	SECISBP2	91124506	0.673000	0.27539	0.013000	0.15412	0.949000	0.60115	-0.224000	0.09164	-3.773000	0.00109	-0.831000	0.03077	GTT		0.438	SECISBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052990.3	NM_024077	
SEMA4D	10507	broad.mit.edu	37	9	92006198	92006198	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:92006198C>T	ENST00000450295.1	-	9	1531	c.755G>A	c.(754-756)cGg>cAg	p.R252Q	SEMA4D_ENST00000422704.2_Missense_Mutation_p.R252Q|SEMA4D_ENST00000420987.1_Missense_Mutation_p.R252Q|SEMA4D_ENST00000343780.4_Missense_Mutation_p.R252Q|SEMA4D_ENST00000455551.2_Missense_Mutation_p.R252Q|SEMA4D_ENST00000356444.2_Missense_Mutation_p.R252Q|SEMA4D_ENST00000438547.2_Missense_Mutation_p.R252Q|SEMA4D_ENST00000339861.4_Missense_Mutation_p.R252Q			Q92854	SEM4D_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	252	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|immune response (GO:0006955)|leukocyte aggregation (GO:0070486)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ossification involved in bone maturation (GO:0043931)|positive regulation of cell migration (GO:0030335)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell projection organization (GO:0031344)|regulation of cell shape (GO:0008360)|regulation of dendrite morphogenesis (GO:0048814)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)	p.R252Q(2)		NS(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(8)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	34						TCTTGCTATCCGTGGGATCAG	0.572																																					p.R252Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G755A	9						.						183.0	131.0	149.0					9																	92006198		2203	4300	6503	91196018	SO:0001583	missense	10507	exon11			U60800	CCDS6685.1, CCDS47991.1	9q22-q31	2013-01-11			ENSG00000187764	ENSG00000187764		"""Semaphorins"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10732	protein-coding gene	gene with protein product	"""M-sema G"""	601866	"""chromosome 9 open reading frame 164"""	SEMAJ, C9orf164		8876214, 8969198	Standard	NM_006378		Approved	CD100, coll-4, FLJ39737	uc004aqo.1	Q92854	OTTHUMG00000020185	ENST00000450295.1:c.755G>A	9.37:g.92006198C>T	ENSP00000416523:p.Arg252Gln		91196018	NM_001142287	B2RPM6|Q7Z5S4|Q8N8B0	Missense_Mutation	SNP	ENST00000450295.1	37	CCDS6685.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.634428	0.87660	.	.	ENSG00000187764	ENST00000339861;ENST00000420987;ENST00000455551;ENST00000343780;ENST00000450295;ENST00000438547;ENST00000356444;ENST00000422704	T;T;T;T;T;T;T;T	0.31769	1.48;1.48;1.48;1.48;1.48;1.48;1.48;1.48	5.16	5.16	0.70880	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.71617	0.3361	H	0.97611	4.04	0.51012	D	0.9999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.82639	-0.0358	10	0.87932	D	0	.	18.8335	0.92151	0.0:1.0:0.0:0.0	.	252;252	Q92854-2;Q92854	.;SEM4D_HUMAN	Q	252	ENSP00000344923:R252Q;ENSP00000391733:R252Q;ENSP00000411981:R252Q;ENSP00000343418:R252Q;ENSP00000416523:R252Q;ENSP00000405102:R252Q;ENSP00000348822:R252Q;ENSP00000388768:R252Q	ENSP00000344923:R252Q	R	-	2	0	SEMA4D	91196018	0.831000	0.29352	0.011000	0.14972	0.705000	0.40729	7.226000	0.78060	2.696000	0.92011	0.555000	0.69702	CGG		0.572	SEMA4D-018	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342411.1	NM_006378	
FAM120A	23196	broad.mit.edu	37	9	96291778	96291778	+	Silent	SNP	C	C	T	rs150866667	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:96291778C>T	ENST00000277165.6	+	9	1844	c.1650C>T	c.(1648-1650)ccC>ccT	p.P550P	FAM120A_ENST00000375389.3_Silent_p.P550P|FAM120A_ENST00000475933.1_3'UTR|FAM120A_ENST00000340893.4_Silent_p.P550P|FAM120A_ENST00000333936.5_Silent_p.P578P	NM_014612.3	NP_055427.2	Q9NZB2	F120A_HUMAN	family with sequence similarity 120A	550						cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)	p.P550P(1)		endometrium(5)|kidney(3)|large_intestine(8)|lung(12)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						CCCTGCCCCCCGTCGCACCTG	0.597													c|||	2	0.000399361	0.0	0.0	5008	,	,		17699	0.0		0.0	False		,,,				2504	0.002				p.P550P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1650T	9						.	T		0,4406		0,0,2203	79.0	70.0	73.0		1650	-11.0	0.0	9	dbSNP_134	73	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	FAM120A	NM_014612.3		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		550/1119	96291778	2,13004	2203	4300	6503	95331599	SO:0001819	synonymous_variant	23196	exon9			AF214737	CCDS6706.1, CCDS75859.1	9q22.31	2013-03-08	2006-07-04	2006-07-04	ENSG00000048828	ENSG00000048828			13247	protein-coding gene	gene with protein product	"""DNA polymerase-transactivated protein 1"", ""oxidative stess-associated Src activator"""	612265	"""chromosome 9 open reading frame 10"""	C9orf10		14585507	Standard	NM_001286722		Approved	KIAA0183, DNAPTP1, OSSA	uc004atw.3	Q9NZB2	OTTHUMG00000020252	ENST00000277165.6:c.1650C>T	9.37:g.96291778C>T			95331599	NM_014612	A6NGU0|C4AMC6|O60649|Q14688|Q4VXF4|Q4VXF5|Q4VXG2|Q86V69|Q96I21|Q9NZB1	Silent	SNP	ENST00000277165.6	37	CCDS6706.1	.	.	.	.	.	.	.	.	.	.	c	0.390	-0.923857	0.02377	0.0	2.33E-4	ENSG00000048828	ENST00000446420	.	.	.	5.51	-11.0	0.00169	.	0.085405	0.51477	D	0.000100	T	0.43277	0.1240	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.66897	-0.5807	6	0.44086	T	0.13	-12.0011	1.428	0.02327	0.1981:0.3159:0.2147:0.2713	.	.	.	.	L	393	.	ENSP00000396534:P393L	P	+	2	0	FAM120A	95331599	0.000000	0.05858	0.003000	0.11579	0.137000	0.21094	-2.625000	0.00875	-4.131000	0.00071	-1.594000	0.00841	CCG		0.597	FAM120A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053160.2	NM_014612	
TRIM14	9830	broad.mit.edu	37	9	100854209	100854209	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:100854209G>A	ENST00000341469.2	-	5	784	c.775C>T	c.(775-777)Cga>Tga	p.R259*	TRIM14_ENST00000342043.3_Nonsense_Mutation_p.R259*|TRIM14_ENST00000375098.3_Nonsense_Mutation_p.R259*|TRIM14_ENST00000538344.1_Nonsense_Mutation_p.R40*	NM_014788.2	NP_055603.2	Q14142	TRI14_HUMAN	tripartite motif containing 14	259	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				innate immune response (GO:0045087)|negative regulation of viral transcription (GO:0032897)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	cytoplasm (GO:0005737)|intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.R259*(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	9		Acute lymphoblastic leukemia(62;0.0559)				AATAGCGATCGCTCTGGTGAG	0.537																																					p.R259X	Colon(14;460 597 13826 51781)											.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C775T	9						.						135.0	138.0	137.0					9																	100854209		2203	4300	6503	99894030	SO:0001587	stop_gained	9830	exon5			AF220130	CCDS6734.1	9q31.1	2011-04-20	2011-01-25		ENSG00000106785	ENSG00000106785		"""Tripartite motif containing / Tripartite motif containing"""	16283	protein-coding gene	gene with protein product		606556	"""tripartite motif-containing 14"""			11331580	Standard	XM_005252320		Approved	KIAA0129	uc004ayd.2	Q14142	OTTHUMG00000020339	ENST00000341469.2:c.775C>T	9.37:g.100854209G>A	ENSP00000344208:p.Arg259*		99894030	NM_014788	A8K9W0|E7EQC4|F8W956|Q548W9|Q5TBQ8|Q6ZWL7|Q9BRD8|Q9C020	Nonsense_Mutation	SNP	ENST00000341469.2	37	CCDS6734.1	.	.	.	.	.	.	.	.	.	.	G	33	5.206616	0.95033	.	.	ENSG00000106785	ENST00000375098;ENST00000311688;ENST00000341469;ENST00000342043;ENST00000375084;ENST00000538344	.	.	.	5.54	2.46	0.29980	.	0.095709	0.42420	D	0.000701	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.5818	0.50896	0.0:0.0:0.3828:0.6172	.	.	.	.	X	259;102;259;259;259;40	.	ENSP00000307909:R102X	R	-	1	2	TRIM14	99894030	0.992000	0.36948	0.979000	0.43373	0.566000	0.35808	0.732000	0.26072	0.190000	0.20209	0.555000	0.69702	CGA		0.537	TRIM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053350.1	NM_014788	
SEC16A	9919	broad.mit.edu	37	9	139370177	139370177	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chr9:139370177C>T	ENST00000371706.3	-	1	1390	c.1357G>A	c.(1357-1359)Gtg>Atg	p.V453M	SEC16A_ENST00000431893.2_Missense_Mutation_p.V453M|SEC16A_ENST00000313050.7_Missense_Mutation_p.V631M|SEC16A_ENST00000290037.6_Missense_Mutation_p.V453M			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	453					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|protein transport (GO:0015031)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)		p.V631M(1)		breast(1)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(15)|lung(14)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)		TCACCAACCACGTTGGCGCGA	0.527																																					p.V631M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1891A	9						.						36.0	40.0	39.0					9																	139370177		2127	4226	6353	138489998	SO:0001583	missense	9919	exon3			AK074565	CCDS55351.1, CCDS75936.1	9q34.3	2007-06-20	2007-06-20	2007-06-20	ENSG00000148396	ENSG00000148396			29006	protein-coding gene	gene with protein product		612854	"""KIAA0310"""	KIAA0310		9205841	Standard	NM_014866		Approved	p250	uc004chx.3	O15027	OTTHUMG00000020932	ENST00000371706.3:c.1357G>A	9.37:g.139370177C>T	ENSP00000360771:p.Val453Met		138489998	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Missense_Mutation	SNP	ENST00000371706.3	37		.	.	.	.	.	.	.	.	.	.	C	0.008	-1.902131	0.00517	.	.	ENSG00000148396	ENST00000313050;ENST00000371706;ENST00000290037;ENST00000431893;ENST00000404925	T;T;T;T	0.17054	2.3;2.3;2.31;2.3	5.49	-2.09	0.07232	.	0.340132	0.31358	N	0.007787	T	0.06781	0.0173	N	0.20986	0.625	0.53005	D	0.999968	B;B;B;P	0.34743	0.269;0.388;0.388;0.466	B;B;B;B	0.23018	0.019;0.043;0.043;0.019	T	0.42447	-0.9451	10	0.19147	T	0.46	-5.0082	7.3434	0.26650	0.1208:0.2668:0.0:0.6124	.	631;453;453;258	F1T0I1;O15027-5;O15027-4;A4QN19	.;.;.;.	M	631;453;453;453;258	ENSP00000325827:V631M;ENSP00000360771:V453M;ENSP00000290037:V453M;ENSP00000387583:V453M	ENSP00000290037:V453M	V	-	1	0	SEC16A	138489998	0.006000	0.16342	0.018000	0.16275	0.008000	0.06430	0.076000	0.14712	-0.618000	0.05656	-0.188000	0.12872	GTG		0.527	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459	
WWC3	55841	broad.mit.edu	37	X	10106864	10106864	+	Missense_Mutation	SNP	G	G	A	rs200633994		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:10106864G>A	ENST00000380861.4	+	21	3363	c.2972G>A	c.(2971-2973)cGt>cAt	p.R991H	WWC3_ENST00000454666.1_Missense_Mutation_p.R991H	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	991					negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)	p.R991H(1)		NS(1)|breast(3)|endometrium(10)|kidney(1)|large_intestine(11)|lung(17)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	52						TGCGCCCTCCGTGAGCTGCGG	0.687																																					p.R991H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2972A	X						.						29.0	24.0	26.0					X																	10106864		2202	4297	6499	10066864	SO:0001583	missense	55841	exon21			AK091936	CCDS14136.1	Xp22.32	2008-02-05			ENSG00000047644	ENSG00000047644		"""WW, C2 and coiled-coil domain containing"""	29237	protein-coding gene	gene with protein product						10574462	Standard	NM_015691		Approved	KIAA1280, BM042	uc004csx.4	Q9ULE0	OTTHUMG00000021123	ENST00000380861.4:c.2972G>A	X.37:g.10106864G>A	ENSP00000370242:p.Arg991His		10066864	NM_015691	A8KA96|Q659C1|Q9BTQ1	Missense_Mutation	SNP	ENST00000380861.4	37	CCDS14136.1	.	.	.	.	.	.	.	.	.	.	G	19.83	3.901049	0.72754	.	.	ENSG00000047644	ENST00000380861;ENST00000454666;ENST00000543412	T;T	0.42900	0.96;0.96	5.32	4.46	0.54185	.	0.000000	0.85682	D	0.000000	T	0.66086	0.2754	M	0.82323	2.585	0.37998	D	0.934126	D	0.89917	1.0	D	0.83275	0.996	T	0.73341	-0.4013	9	.	.	.	-16.9653	13.4351	0.61079	0.0784:0.0:0.9216:0.0	.	991	Q9ULE0	WWC3_HUMAN	H	991;991;486	ENSP00000370242:R991H;ENSP00000399584:R991H	.	R	+	2	0	WWC3	10066864	1.000000	0.71417	0.003000	0.11579	0.447000	0.32167	9.495000	0.97964	1.149000	0.42402	0.529000	0.55759	CGT		0.687	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691	
ZMAT1	84460	broad.mit.edu	37	X	101141680	101141680	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:101141680A>G	ENST00000372782.3	-	6	576	c.529T>C	c.(529-531)Tgc>Cgc	p.C177R	ZMAT1_ENST00000540921.1_Missense_Mutation_p.C177R|ZMAT1_ENST00000494068.1_5'UTR|ZMAT1_ENST00000458570.1_Missense_Mutation_p.C6R	NM_001011657.3	NP_001011657	Q5H9K5	ZMAT1_HUMAN	zinc finger, matrin-type 1	177						nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.C6R(1)		endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	22						CAAATATGGCAAACATAGGTT	0.313																																					p.C177R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T529C	X						.						106.0	90.0	95.0					X																	101141680		2202	4300	6502	101028336	SO:0001583	missense	84460	exon6			Z69304	CCDS35348.1	Xq21	2012-10-05	2010-09-15		ENSG00000166432	ENSG00000166432		"""Zinc fingers, matrin-type"""	29377	protein-coding gene	gene with protein product							Standard	NM_001011657		Approved	KIAA1789	uc011mrl.2	Q5H9K5	OTTHUMG00000022044	ENST00000372782.3:c.529T>C	X.37:g.101141680A>G	ENSP00000361868:p.Cys177Arg		101028336	NM_001011657	Q8NDS3|Q96JN6	Missense_Mutation	SNP	ENST00000372782.3	37	CCDS35348.1	.	.	.	.	.	.	.	.	.	.	A	19.34	3.808928	0.70797	.	.	ENSG00000166432	ENST00000372782;ENST00000540921;ENST00000458570	D;D;D	0.98947	-5.26;-5.26;-5.26	4.94	4.94	0.65067	Zinc finger, C2H2-like (1);Zinc finger, U1-type (1);Zinc finger, C2H2 (1);	0.000000	0.49916	D	0.000137	D	0.98745	0.9578	M	0.69358	2.11	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.99601	1.0978	10	0.87932	D	0	-9.9466	11.6009	0.51001	1.0:0.0:0.0:0.0	.	177	Q5H9K5	ZMAT1_HUMAN	R	177;177;6	ENSP00000361868:C177R;ENSP00000437529:C177R;ENSP00000413044:C6R	ENSP00000361868:C177R	C	-	1	0	ZMAT1	101028336	1.000000	0.71417	0.724000	0.30704	0.982000	0.71751	6.828000	0.75308	1.941000	0.56285	0.481000	0.45027	TGC		0.313	ZMAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057598.1		
FAM199X	139231	broad.mit.edu	37	X	103411571	103411571	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:103411571C>T	ENST00000493442.1	+	1	271	c.105C>T	c.(103-105)agC>agT	p.S35S		NM_207318.3	NP_997201.1	Q6PEV8	F199X_HUMAN	family with sequence similarity 199, X-linked	35								p.S35S(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(1)	11						CCTGCCCGAGCGAGGAGCCGG	0.667																																					p.S35S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C105T	X						.						27.0	24.0	25.0					X																	103411571		2203	4297	6500	103298227	SO:0001819	synonymous_variant	139231	exon1			BC016683	CCDS35364.1	Xq22	2010-02-11	2010-02-11	2010-02-11	ENSG00000123575	ENSG00000123575			25195	protein-coding gene	gene with protein product			"""chromosome X open reading frame 39"""	CXorf39			Standard	NM_207318		Approved		uc004elw.3	Q6PEV8	OTTHUMG00000022126	ENST00000493442.1:c.105C>T	X.37:g.103411571C>T			103298227	NM_207318	Q8WVP6|Q96AV3	Silent	SNP	ENST00000493442.1	37	CCDS35364.1																																																																																				0.667	FAM199X-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057764.1	NM_207318	
FAM199X	139231	broad.mit.edu	37	X	103430795	103430795	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:103430795A>G	ENST00000493442.1	+	3	632	c.466A>G	c.(466-468)Ata>Gta	p.I156V		NM_207318.3	NP_997201.1	Q6PEV8	F199X_HUMAN	family with sequence similarity 199, X-linked	156								p.I156V(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(1)	11						TTCTGATGTCATACCCAGTAT	0.418																																					p.I156V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A466G	X						.						146.0	135.0	139.0					X																	103430795		2203	4300	6503	103317451	SO:0001583	missense	139231	exon3			BC016683	CCDS35364.1	Xq22	2010-02-11	2010-02-11	2010-02-11	ENSG00000123575	ENSG00000123575			25195	protein-coding gene	gene with protein product			"""chromosome X open reading frame 39"""	CXorf39			Standard	NM_207318		Approved		uc004elw.3	Q6PEV8	OTTHUMG00000022126	ENST00000493442.1:c.466A>G	X.37:g.103430795A>G	ENSP00000417581:p.Ile156Val		103317451	NM_207318	Q8WVP6|Q96AV3	Missense_Mutation	SNP	ENST00000493442.1	37	CCDS35364.1	.	.	.	.	.	.	.	.	.	.	A	17.41	3.383742	0.61845	.	.	ENSG00000123575	ENST00000493442	.	.	.	5.07	3.92	0.45320	.	0.039718	0.85682	N	0.000000	T	0.54046	0.1834	L	0.60455	1.87	0.54753	D	0.999987	B	0.02656	0.0	B	0.04013	0.001	T	0.45745	-0.9240	8	.	.	.	-4.7858	9.056	0.36405	0.9119:0.0:0.0881:0.0	.	156	Q6PEV8	F199X_HUMAN	V	156	.	.	I	+	1	0	FAM199X	103317451	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.274000	0.72587	0.703000	0.31848	0.486000	0.48141	ATA		0.418	FAM199X-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057764.1	NM_207318	
ESX1	80712	broad.mit.edu	37	X	103495447	103495447	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:103495447G>A	ENST00000372588.4	-	4	766	c.683C>T	c.(682-684)gCt>gTt	p.A228V		NM_153448.3	NP_703149.1	Q8N693	ESX1_HUMAN	ESX homeobox 1	228					labyrinthine layer blood vessel development (GO:0060716)|labyrinthine layer morphogenesis (GO:0060713)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)	p.A228V(1)		endometrium(2)|large_intestine(10)|lung(12)|ovary(1)|skin(2)	27						AGGATCCAGAGCAGGAGCAGC	0.542																																					p.A228V	Pancreas(200;1705 2227 25194 28471 45274)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C683T	X						.						196.0	151.0	166.0					X																	103495447		2203	4300	6503	103382103	SO:0001583	missense	80712	exon4			AL049631	CCDS14516.1	Xq22.2	2011-06-20	2007-07-11	2006-02-08	ENSG00000123576	ENSG00000123576		"""Homeoboxes / PRD class"""	14865	protein-coding gene	gene with protein product		300154	"""extraembryonic, spermatogenesis, homeobox 1 homolog (mouse)"""	ESX1L		11374906, 17242862	Standard	NM_153448		Approved	ESXR1	uc004ely.3	Q8N693	OTTHUMG00000022125	ENST00000372588.4:c.683C>T	X.37:g.103495447G>A	ENSP00000361669:p.Ala228Val		103382103	NM_153448	B0QYU3|Q7Z6K7	Missense_Mutation	SNP	ENST00000372588.4	37	CCDS14516.1	.	.	.	.	.	.	.	.	.	.	G	7.801	0.713562	0.15306	.	.	ENSG00000123576	ENST00000372588	T	0.71698	-0.59	4.46	1.75	0.24633	.	.	.	.	.	T	0.48804	0.1520	N	0.16567	0.415	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.30937	-0.9961	9	0.35671	T	0.21	0.0469	3.5009	0.07673	0.636:0.0:0.1952:0.1687	.	228	Q8N693	ESX1_HUMAN	V	228	ENSP00000361669:A228V	ENSP00000361669:A228V	A	-	2	0	ESX1	103382103	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-0.105000	0.10907	0.148000	0.19059	-1.434000	0.01081	GCT		0.542	ESX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057763.2	NM_153448	
GUCY2F	2986	broad.mit.edu	37	X	108652307	108652307	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:108652307G>A	ENST00000218006.2	-	9	2173	c.1882C>T	c.(1882-1884)Cga>Tga	p.R628*		NM_001522.2	NP_001513.2	P51841	GUC2F_HUMAN	guanylate cyclase 2F, retinal	628	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> Q (in dbSNP:rs7883913). {ECO:0000269|PubMed:17344846}.		intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)	p.R628*(1)		breast(3)|central_nervous_system(2)|endometrium(5)|kidney(6)|large_intestine(14)|lung(33)|prostate(3)|skin(1)	67						AGGCTCCCTCGGGAACAGAAT	0.403																																					p.R628X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1882T	X						.						158.0	136.0	144.0					X																	108652307		2203	4300	6503	108538963	SO:0001587	stop_gained	2986	exon9			L37378	CCDS14545.1	Xq22	2008-08-01			ENSG00000101890	ENSG00000101890			4691	protein-coding gene	gene with protein product	"""guanylate cyclase 2D-like, membrane (retina-specific)"""	300041				8838319, 7777544	Standard	NM_001522		Approved	GUC2DL, GC-F, RetGC-2, ROS-GC2, CYGF	uc004eod.4	P51841	OTTHUMG00000022184	ENST00000218006.2:c.1882C>T	X.37:g.108652307G>A	ENSP00000218006:p.Arg628*		108538963	NM_001522	Q9UJF1	Nonsense_Mutation	SNP	ENST00000218006.2	37	CCDS14545.1	.	.	.	.	.	.	.	.	.	.	G	41	8.908864	0.98998	.	.	ENSG00000101890	ENST00000218006	.	.	.	5.05	3.05	0.35203	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.0422	0.47838	0.0:0.0:0.3554:0.6446	.	.	.	.	X	628	.	ENSP00000218006:R628X	R	-	1	2	GUCY2F	108538963	0.103000	0.21917	0.916000	0.36221	0.976000	0.68499	0.031000	0.13710	0.438000	0.26450	0.600000	0.82982	CGA		0.403	GUCY2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057884.1	NM_001522	
KIAA1210	57481	broad.mit.edu	37	X	118223411	118223411	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:118223411C>A	ENST00000402510.2	-	11	1781	c.1782G>T	c.(1780-1782)atG>atT	p.M594I		NM_020721.1	NP_065772.1	Q9ULL0	K1210_HUMAN	KIAA1210	594								p.M594I(1)|p.M418I(1)		breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(31)|ovary(4)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	64						TAGGCTGCTCCATGTTGTCCT	0.493																																					p.M594I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1782T	X						.						105.0	92.0	96.0					X																	118223411		1964	4140	6104	118107439	SO:0001583	missense	57481	exon11			AB033036	CCDS48156.1	Xq24	2012-10-04			ENSG00000250423	ENSG00000250423			29218	protein-coding gene	gene with protein product						10574462	Standard	NM_020721		Approved		uc004era.4	Q9ULL0	OTTHUMG00000162980	ENST00000402510.2:c.1782G>T	X.37:g.118223411C>A	ENSP00000384670:p.Met594Ile		118107439	NM_020721	B7ZCI8|Q5JPN4	Missense_Mutation	SNP	ENST00000402510.2	37	CCDS48156.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.56|10.56	1.385231|1.385231	0.25031|0.25031	.|.	.|.	ENSG00000248857|ENSG00000250423	ENST00000440399|ENST00000402510	.|T	.|0.09073	.|3.02	5.34|5.34	-2.32|-2.32	0.06745|0.06745	.|.	.|.	.|.	.|.	.|.	.|T	.|0.03564	.|0.0102	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B	.|0.24823	.|0.112	.|B	.|0.27076	.|0.076	.|T	.|0.47837	.|-0.9086	.|9	.|0.19147	.|T	.|0.46	.|.	5.4802|5.4802	0.16719|0.16719	0.1473:0.3058:0.0:0.547|0.1473:0.3058:0.0:0.547	.|.	.|594	.|Q9ULL0	.|K1210_HUMAN	X|I	1|594	.|ENSP00000384670:M594I	.|ENSP00000384670:M594I	G|M	-|-	1|3	0|0	KIAA1210|RP13-347D8.6	118107439|118107439	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.016000|0.016000	0.09150|0.09150	-1.010000|-1.010000	0.03656|0.03656	-0.450000|-0.450000	0.07107|0.07107	0.594000|0.594000	0.82650|0.82650	GGA|ATG		0.493	KIAA1210-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371251.2	NM_020721	
C1GALT1C1	29071	broad.mit.edu	37	X	119760129	119760129	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:119760129G>A	ENST00000304661.5	-	2	1131	c.893C>T	c.(892-894)gCa>gTa	p.A298V	C1GALT1C1_ENST00000371313.2_Missense_Mutation_p.A298V	NM_001011551.2	NP_001011551.1	Q96EU7	C1GLC_HUMAN	C1GALT1-specific chaperone 1	298					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.A298V(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	11						ATGCCCAAATGCCCTAAGGCG	0.398																																					p.A298V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C893T	X						.						137.0	112.0	120.0					X																	119760129		2203	4300	6503	119644157	SO:0001583	missense	29071	exon3			AJ238398	CCDS14602.1	Xq24	2008-02-05			ENSG00000171155	ENSG00000171155			24338	protein-coding gene	gene with protein product		300611				11042152, 12361956	Standard	NM_152692		Approved	COSMC, C1GALT2	uc004esz.3	Q96EU7	OTTHUMG00000022305	ENST00000304661.5:c.893C>T	X.37:g.119760129G>A	ENSP00000304364:p.Ala298Val		119644157	NM_152692	A8K246|Q8WWS3|Q9NZX1	Missense_Mutation	SNP	ENST00000304661.5	37	CCDS14602.1	.	.	.	.	.	.	.	.	.	.	G	16.35	3.099138	0.56183	.	.	ENSG00000171155	ENST00000304661;ENST00000371313	T;T	0.39997	1.05;1.05	5.46	5.46	0.80206	.	0.118098	0.56097	D	0.000021	T	0.36771	0.0979	L	0.39633	1.23	0.48571	D	0.999678	B	0.16396	0.017	B	0.17098	0.017	T	0.11251	-1.0595	9	.	.	.	-9.0354	17.3879	0.87422	0.0:0.0:1.0:0.0	.	298	Q96EU7	C1GLC_HUMAN	V	298	ENSP00000304364:A298V;ENSP00000360363:A298V	.	A	-	2	0	C1GALT1C1	119644157	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.585000	0.82584	2.406000	0.81754	0.544000	0.68410	GCA		0.398	C1GALT1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058117.1	NM_152692	
GLUD2	2747	broad.mit.edu	37	X	120182804	120182804	+	Silent	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:120182804T>C	ENST00000328078.1	+	1	1343	c.1266T>C	c.(1264-1266)atT>atC	p.I422I		NM_012084.3	NP_036216.2	P49448	DHE4_HUMAN	glutamate dehydrogenase 2	422					glutamate biosynthetic process (GO:0006537)|glutamate catabolic process (GO:0006538)|glutamate metabolic process (GO:0006536)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	ADP binding (GO:0043531)|glutamate dehydrogenase (NAD+) activity (GO:0004352)|glutamate dehydrogenase [NAD(P)+] activity (GO:0004353)|GTP binding (GO:0005525)|leucine binding (GO:0070728)	p.I422I(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|urinary_tract(1)	38						AGAGAAACATTTTGGTTATTC	0.448																																					p.I422I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1266C	X						.						178.0	166.0	170.0					X																	120182804		2203	4300	6503	120010485	SO:0001819	synonymous_variant	2747	exon1			U08997	CCDS14603.1	Xq24-q25	2008-02-05	2003-02-24	2003-02-28	ENSG00000182890	ENSG00000182890			4336	protein-coding gene	gene with protein product		300144	"""glutamate dehydrogenase pseudogene 1"""	GLUDP1		8207021, 9109504	Standard	NM_012084		Approved		uc004eto.3	P49448	OTTHUMG00000022320	ENST00000328078.1:c.1266T>C	X.37:g.120182804T>C			120010485	NM_012084	B2R8G0|Q9UDQ4	Silent	SNP	ENST00000328078.1	37	CCDS14603.1																																																																																				0.448	GLUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058133.1	NM_012084	
THOC2	57187	broad.mit.edu	37	X	122747914	122747914	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:122747914C>G	ENST00000245838.8	-	34	4469	c.4438G>C	c.(4438-4440)Gag>Cag	p.E1480Q	THOC2_ENST00000355725.4_Missense_Mutation_p.E1480Q|THOC2_ENST00000497887.1_5'UTR|THOC2_ENST00000491737.1_Missense_Mutation_p.E1365Q	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN	THO complex 2	1480	Lys-rich.				mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)	p.E1480Q(1)|p.E1401Q(1)		breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						CTTTTCCGCTCTTTCCTGTCC	0.348																																					p.E1480Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G4438C	X						.						115.0	103.0	107.0					X																	122747914		1819	4070	5889	122575595	SO:0001583	missense	57187	exon34			AF441770	CCDS43988.1	Xq25-q26.3	2013-02-11	2004-08-09		ENSG00000125676	ENSG00000125676		"""THO complex subunits"""	19073	protein-coding gene	gene with protein product		300395	"""chromosome X open reading frame 3"""	CXorf3		11979277	Standard	NM_001081550		Approved	THO2, dJ506G2.1	uc004etu.3	Q8NI27	OTTHUMG00000022334	ENST00000245838.8:c.4438G>C	X.37:g.122747914C>G	ENSP00000245838:p.Glu1480Gln		122575595	NM_001081550	A6NM50|Q5JZ12|Q6IN92|Q9H8I6	Missense_Mutation	SNP	ENST00000245838.8	37	CCDS43988.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.06|16.06	3.016624|3.016624	0.54468|0.54468	.|.	.|.	ENSG00000125676|ENSG00000125676	ENST00000245838;ENST00000355725;ENST00000416618;ENST00000491737|ENST00000448128;ENST00000441692	.|.	.|.	.|.	6.06|6.06	6.06|6.06	0.98353|0.98353	.|.	0.164319|.	0.40554|.	N|.	0.001079|.	T|T	0.62307|0.62307	0.2417|0.2417	L|L	0.29908|0.29908	0.895|0.895	0.54753|0.54753	D|D	0.999988|0.999988	P|.	0.36048|.	0.534|.	B|.	0.29785|.	0.107|.	T|T	0.63292|0.63292	-0.6670|-0.6670	9|6	0.16420|0.62326	T|D	0.52|0.03	-8.4744|-8.4744	19.5104|19.5104	0.95139|0.95139	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1480|.	Q8NI27|.	THOC2_HUMAN|.	Q|N	1480;1480;69;1365|75;274	.|.	ENSP00000245838:E1480Q|ENSP00000415211:K274N	E|K	-|-	1|3	0|2	THOC2|THOC2	122575595|122575595	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.993000|0.993000	0.82548|0.82548	6.459000|6.459000	0.73513|0.73513	2.562000|2.562000	0.86427|0.86427	0.600000|0.600000	0.82982|0.82982	GAG|AAG		0.348	THOC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058153.3		
XPNPEP2	7512	broad.mit.edu	37	X	128879237	128879237	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:128879237C>T	ENST00000371106.3	+	4	485	c.293C>T	c.(292-294)tCt>tTt	p.S98F	XPNPEP2_ENST00000371105.3_Missense_Mutation_p.S98F	NM_003399.5	NP_003390.4	O43895	XPP2_HUMAN	X-prolyl aminopeptidase (aminopeptidase P) 2, membrane-bound	98						anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)	p.S98F(1)		endometrium(3)|kidney(3)|large_intestine(5)|liver(1)|lung(20)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	37						TTTACAGGGTCTGCAGGTGAC	0.498																																					p.S98F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C293T	X						.						332.0	201.0	245.0					X																	128879237		2203	4300	6503	128706918	SO:0001583	missense	7512	exon4			U90724	CCDS14613.1	Xq25	2008-02-05			ENSG00000122121	ENSG00000122121	3.4.11.9		12823	protein-coding gene	gene with protein product		300145				9375790, 9628831	Standard	NM_003399		Approved		uc004eut.1	O43895	OTTHUMG00000022373	ENST00000371106.3:c.293C>T	X.37:g.128879237C>T	ENSP00000360147:p.Ser98Phe		128706918	NM_003399	A0AV16|O75994	Missense_Mutation	SNP	ENST00000371106.3	37	CCDS14613.1	.	.	.	.	.	.	.	.	.	.	C	18.79	3.698707	0.68501	.	.	ENSG00000122121	ENST00000371105;ENST00000371106	T	0.81415	-1.49	5.67	3.87	0.44632	Creatinase (1);	0.261280	0.45867	D	0.000340	D	0.93638	0.7968	H	0.99130	4.44	0.40855	D	0.983781	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.983	D	0.94239	0.7483	10	0.87932	D	0	-0.454	11.7956	0.52098	0.0:0.669:0.331:0.0	.	98;98	B4DV70;O43895	.;XPP2_HUMAN	F	98	ENSP00000360147:S98F	ENSP00000360146:S98F	S	+	2	0	XPNPEP2	128706918	1.000000	0.71417	0.964000	0.40570	0.725000	0.41563	4.938000	0.63519	0.543000	0.28864	-0.217000	0.12591	TCT		0.498	XPNPEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058210.1	NM_003399	
USP26	83844	broad.mit.edu	37	X	132160053	132160053	+	Silent	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:132160053G>A	ENST00000511190.1	-	6	2665	c.2196C>T	c.(2194-2196)ttC>ttT	p.F732F	USP26_ENST00000370832.1_Silent_p.F732F|USP26_ENST00000406273.1_Silent_p.F732F	NM_031907.1	NP_114113.1	Q9BXU7	UBP26_HUMAN	ubiquitin specific peptidase 26	732	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)	p.F732F(1)		breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	60	Acute lymphoblastic leukemia(192;0.000127)					ACACTTTTTGGAATCTTTCTG	0.398																																					p.F732F	NSCLC(104;342 1621 36940 47097 52632)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2196T	X						.						70.0	72.0	71.0					X																	132160053		2195	4289	6484	131987719	SO:0001819	synonymous_variant	83844	exon1			AF285593	CCDS14635.1	Xq26.2	2012-07-13	2005-08-08		ENSG00000134588	ENSG00000134588	3.4.19.12	"""Ubiquitin-specific peptidases"""	13485	protein-coding gene	gene with protein product		300309	"""ubiquitin specific protease 26"""			12838346	Standard	NM_031907		Approved		uc011mvf.2	Q9BXU7	OTTHUMG00000022429	ENST00000511190.1:c.2196C>T	X.37:g.132160053G>A			131987719	NM_031907	B9WRT6|Q5H9H4	Silent	SNP	ENST00000511190.1	37	CCDS14635.1																																																																																				0.398	USP26-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359441.1	NM_031907	
GPC4	2239	broad.mit.edu	37	X	132440090	132440090	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:132440090T>C	ENST00000370828.3	-	5	1494	c.970A>G	c.(970-972)Atg>Gtg	p.M324V	GPC4_ENST00000535467.1_Missense_Mutation_p.M254V	NM_001448.2	NP_001439.2	O75487	GPC4_HUMAN	glypican 4	324					anatomical structure morphogenesis (GO:0009653)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.M324V(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|skin(1)|upper_aerodigestive_tract(1)	28	Acute lymphoblastic leukemia(192;0.000127)					TGCATGTTCATAATAGCATCA	0.498																																					p.M324V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A970G	X						.						155.0	136.0	143.0					X																	132440090		2203	4300	6503	132267756	SO:0001583	missense	2239	exon5			AF030186	CCDS14637.1	Xq26.1	2008-02-05			ENSG00000076716	ENSG00000076716		"""Proteoglycans / Cell Surface : Glypicans"""	4452	protein-coding gene	gene with protein product	"""glypican proteoglycan 4"""	300168				9787072	Standard	NM_001448		Approved	K-glypican	uc004exc.1	O75487	OTTHUMG00000022434	ENST00000370828.3:c.970A>G	X.37:g.132440090T>C	ENSP00000359864:p.Met324Val		132267756	NM_001448	B2R6J7|B4E2C0|Q6ZMA6|Q96L43|Q9NU08|Q9UJN1|Q9UPD9	Missense_Mutation	SNP	ENST00000370828.3	37	CCDS14637.1	.	.	.	.	.	.	.	.	.	.	t	14.78	2.637377	0.47049	.	.	ENSG00000076716	ENST00000370828;ENST00000536418;ENST00000535467	T;T	0.52295	0.67;0.67	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.57519	0.2059	M	0.82517	2.595	0.80722	D	1	P	0.40066	0.701	P	0.45406	0.479	T	0.57602	-0.7783	10	0.18710	T	0.47	-0.5346	14.1785	0.65559	0.0:0.0:0.0:1.0	.	324	O75487	GPC4_HUMAN	V	324;318;254	ENSP00000359864:M324V;ENSP00000444959:M254V	ENSP00000359864:M324V	M	-	1	0	GPC4	132267756	1.000000	0.71417	0.990000	0.47175	0.994000	0.84299	7.698000	0.84413	1.946000	0.56461	0.483000	0.47432	ATG		0.498	GPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058338.1	NM_001448	
FAM127A	8933	broad.mit.edu	37	X	134166697	134166697	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:134166697G>A	ENST00000257013.7	+	1	365	c.284G>A	c.(283-285)cGg>cAg	p.R95Q	FAM127A_ENST00000464369.1_Intron	NM_001078171.1	NP_001071639.1	O15255	CXX1_HUMAN	family with sequence similarity 127, member A	0						plasma membrane (GO:0005886)				endometrium(3)|urinary_tract(1)	4	Acute lymphoblastic leukemia(192;0.000127)					AATGATTACCGGGGCTTTCTG	0.642																																					p.R95Q												.	.	0			c.G284A	X						.						41.0	43.0	42.0					X																	134166697		2192	4291	6483	133994363	SO:0001583	missense	8933	exon1			Y13374	CCDS43997.1	Xq26	2014-05-16	2006-11-16	2006-11-16	ENSG00000134590	ENSG00000134590			2569	protein-coding gene	gene with protein product		300213	"""CAAX box 1"""	CXX1		9403077, 15716091, 16093683	Standard	NM_001078171		Approved	Mart8, Mar8, MAR8C	uc004eyd.3	A6ZKI3	OTTHUMG00000022465	ENST00000257013.7:c.284G>A	X.37:g.134166697G>A	ENSP00000257013:p.Arg95Gln		133994363	NM_001078171	Q6IBF1	Missense_Mutation	SNP	ENST00000257013.7	37	CCDS43997.1	.	.	.	.	.	.	.	.	.	.	g	9.204	1.029249	0.19512	.	.	ENSG00000134590	ENST00000257013	T	0.27557	1.66	3.56	1.65	0.23941	.	.	.	.	.	T	0.12561	0.0305	N	0.04880	-0.145	0.21675	N	0.999598	B	0.02656	0.0	B	0.04013	0.001	T	0.32877	-0.9890	9	0.19147	T	0.46	.	5.2923	0.15733	0.0:0.2258:0.5377:0.2365	.	95	A6ZKI3	F127A_HUMAN	Q	95	ENSP00000257013:R95Q	ENSP00000257013:R95Q	R	+	2	0	FAM127A	133994363	1.000000	0.71417	0.996000	0.52242	0.920000	0.55202	1.076000	0.30729	0.297000	0.22615	-0.330000	0.08379	CGG		0.642	FAM127A-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058391.2	NM_001078171	
SAGE1	55511	broad.mit.edu	37	X	134988609	134988609	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:134988609A>G	ENST00000370709.3	+	6	635	c.635A>G	c.(634-636)gAa>gGa	p.E212G	SAGE1_ENST00000535938.1_Missense_Mutation_p.E212G|SAGE1_ENST00000324447.3_Missense_Mutation_p.E212G|SAGE1_ENST00000537770.1_Intron			Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	212						nucleus (GO:0005634)		p.E212G(1)		breast(5)|endometrium(5)|large_intestine(10)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	55	Acute lymphoblastic leukemia(192;0.000127)					CAGAAGATGGAAAATGTCCAA	0.448																																					p.E212G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A635G	X						.						192.0	160.0	171.0					X																	134988609		2203	4300	6503	134816275	SO:0001583	missense	55511	exon7			AJ278111	CCDS14652.1	Xq26	2009-03-25			ENSG00000181433	ENSG00000181433			30369	protein-coding gene	gene with protein product	"""cancer/testis antigen 14"""	300359				10919659	Standard	NM_018666		Approved	SAGE, CT14	uc004ezh.3	Q9NXZ1	OTTHUMG00000022496	ENST00000370709.3:c.635A>G	X.37:g.134988609A>G	ENSP00000359743:p.Glu212Gly		134816275	NM_018666	Q5JNW0	Missense_Mutation	SNP	ENST00000370709.3	37	CCDS14652.1	.	.	.	.	.	.	.	.	.	.	A	2.105	-0.405091	0.04832	.	.	ENSG00000181433	ENST00000324447;ENST00000535938;ENST00000370709	T;T;T	0.35236	1.32;1.32;1.32	1.34	1.34	0.21922	.	0.508177	0.18613	N	0.136112	T	0.18882	0.0453	N	0.24115	0.695	0.31719	N	0.638587	B	0.02656	0.0	B	0.01281	0.0	T	0.11060	-1.0603	10	0.25106	T	0.35	.	4.4322	0.11533	1.0:0.0:0.0:0.0	.	212	Q9NXZ1	SAGE1_HUMAN	G	212	ENSP00000323191:E212G;ENSP00000445959:E212G;ENSP00000359743:E212G	ENSP00000323191:E212G	E	+	2	0	SAGE1	134816275	1.000000	0.71417	0.566000	0.28421	0.079000	0.17450	1.420000	0.34804	0.786000	0.33708	0.151000	0.16131	GAA		0.448	SAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058448.1	NM_018666	
ZIC3	7547	broad.mit.edu	37	X	136648918	136648918	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:136648918G>A	ENST00000287538.5	+	1	618	c.68G>A	c.(67-69)cGc>cAc	p.R23H	RP1-137H15.2_ENST00000456631.1_RNA|ZIC3_ENST00000370606.3_Missense_Mutation_p.R23H|RP1-137H15.2_ENST00000442841.1_RNA	NM_003413.3	NP_003404.1	O60481	ZIC3_HUMAN	Zic family member 3	23					anterior/posterior pattern specification (GO:0009952)|cell differentiation (GO:0030154)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of left/right asymmetry in nervous system (GO:0035545)|determination of left/right symmetry (GO:0007368)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|heart looping (GO:0001947)|lung development (GO:0030324)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R23H(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|large_intestine(3)|liver(1)|lung(18)|ovary(3)|soft_tissue(2)|urinary_tract(1)	37	Acute lymphoblastic leukemia(192;0.000127)					GGCGCGCCGCGCCACCACGAG	0.731																																					p.R23H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G68A	X						.						10.0	10.0	10.0					X																	136648918		2177	4268	6445	136476584	SO:0001583	missense	7547	exon1			AF028706	CCDS14663.1	Xq24-q27.1	2013-01-08	2011-05-19		ENSG00000156925	ENSG00000156925		"""Zinc fingers, C2H2-type"""	12874	protein-coding gene	gene with protein product		300265	"""heterotaxy 1"", ""Zic family member 3 (odd-paired homolog, Drosophila)"""	HTX1		8298651, 7747776	Standard	NM_003413		Approved	HTX, ZNF203	uc004fak.3	O60481	OTTHUMG00000022525	ENST00000287538.5:c.68G>A	X.37:g.136648918G>A	ENSP00000287538:p.Arg23His		136476584	NM_003413	B2CNW4|Q14DE5|Q5JY75	Missense_Mutation	SNP	ENST00000287538.5	37	CCDS14663.1	.	.	.	.	.	.	.	.	.	.	g	11.87	1.767764	0.31320	.	.	ENSG00000156925	ENST00000287538;ENST00000370606	T;T	0.12255	2.7;2.76	4.12	4.12	0.48240	.	0.000000	0.85682	D	0.000000	T	0.13798	0.0334	L	0.57536	1.79	0.58432	D	0.999998	B	0.12630	0.006	B	0.04013	0.001	T	0.05632	-1.0873	10	0.12103	T	0.63	.	12.9894	0.58610	0.0:0.0:1.0:0.0	.	23	O60481	ZIC3_HUMAN	H	23	ENSP00000287538:R23H;ENSP00000359638:R23H	ENSP00000287538:R23H	R	+	2	0	ZIC3	136476584	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	7.365000	0.79537	1.917000	0.55516	0.525000	0.51046	CGC		0.731	ZIC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058526.1		
IDS	3423	broad.mit.edu	37	X	148579832	148579832	+	Nonsense_Mutation	SNP	G	G	A	rs104894860		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:148579832G>A	ENST00000340855.6	-	5	723	c.514C>T	c.(514-516)Cga>Tga	p.R172*	IDS_ENST00000422081.2_5'UTR|IDS_ENST00000541269.1_5'UTR|IDS_ENST00000370441.4_Nonsense_Mutation_p.R172*|IDS_ENST00000370443.4_Nonsense_Mutation_p.R172*|IDS_ENST00000490775.1_5'UTR	NM_000202.5|NM_001166550.1	NP_000193.1|NP_001160022.1	P22304	IDS_HUMAN	iduronate 2-sulfatase	172					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	lysosomal lumen (GO:0043202)	iduronate-2-sulfatase activity (GO:0004423)|metal ion binding (GO:0046872)	p.R172*(1)		NS(1)|breast(3)|endometrium(5)|large_intestine(2)|lung(8)|prostate(1)	20	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					TCTGGCCCTCGACATGTCTTT	0.453																																					p.R172X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C514T	X	GRCh37	CM920366	IDS	M	rs104894860	.						63.0	49.0	54.0					X																	148579832		2203	4300	6503	148387737	SO:0001587	stop_gained	3423	exon5			M58342	CCDS14685.1, CCDS14686.1	Xq27.3-q28	2012-10-02	2008-08-01		ENSG00000010404	ENSG00000010404	3.1.6.13		5389	protein-coding gene	gene with protein product	"""Hunter syndrome"""	300823		SIDS			Standard	NM_006123		Approved		uc011mxe.2	P22304	OTTHUMG00000022615	ENST00000340855.6:c.514C>T	X.37:g.148579832G>A	ENSP00000339801:p.Arg172*		148387737	NM_006123	D3DWT4|Q14604|Q9BRM3	Nonsense_Mutation	SNP	ENST00000340855.6	37	CCDS14685.1	.	.	.	.	.	.	.	.	.	.	G	36	5.875166	0.97055	.	.	ENSG00000010404	ENST00000340855;ENST00000370441;ENST00000370443	.	.	.	4.89	3.76	0.43208	.	0.259269	0.45606	D	0.000351	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13853	T	0.58	.	10.8228	0.46614	0.0:0.0:0.1761:0.8239	.	.	.	.	X	172	.	ENSP00000339801:R172X	R	-	1	2	IDS	148387737	1.000000	0.71417	0.828000	0.32881	0.480000	0.33159	4.645000	0.61404	0.586000	0.29626	0.523000	0.50628	CGA		0.453	IDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058677.3		
GABRQ	55879	broad.mit.edu	37	X	151820154	151820154	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:151820154G>A	ENST00000370306.2	+	8	1087	c.1067G>A	c.(1066-1068)cGa>cAa	p.R356Q		NM_018558.2	NP_061028.3	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) A receptor, theta	356					neurotransmitter transport (GO:0006836)|signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|neurotransmitter transporter activity (GO:0005326)|transmembrane signaling receptor activity (GO:0004888)	p.R356Q(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(9)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	52	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TTCTACAGTCGAGGACCTCGG	0.507																																					p.R356Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1067A	X						.						214.0	173.0	187.0					X																	151820154		2203	4300	6503	151570810	SO:0001583	missense	55879	exon8			U47334	CCDS14707.1	Xq28	2012-06-22	2012-02-03		ENSG00000147402	ENSG00000268089		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	14454	protein-coding gene	gene with protein product	"""GABA(A) receptor, theta"""	300349	"""gamma-aminobutyric acid (GABA) receptor, theta"""			10804200, 10449790	Standard	NM_018558		Approved	THETA	uc004ffp.1	Q9UN88	OTTHUMG00000022649	ENST00000370306.2:c.1067G>A	X.37:g.151820154G>A	ENSP00000359329:p.Arg356Gln		151570810	NM_018558	A6NFN1|Q32MB4|Q9NZK8	Missense_Mutation	SNP	ENST00000370306.2	37	CCDS14707.1	.	.	.	.	.	.	.	.	.	.	G	10.10	1.256510	0.22965	.	.	ENSG00000147402	ENST00000370306	D	0.87966	-2.32	5.88	3.98	0.46160	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.454404	0.17307	N	0.179007	T	0.70245	0.3202	N	0.20574	0.59	0.28237	N	0.92587	P	0.37573	0.6	B	0.27608	0.081	T	0.59888	-0.7369	10	0.12103	T	0.63	.	6.5242	0.22293	0.1114:0.1817:0.7069:0.0	.	356	Q9UN88	GBRT_HUMAN	Q	356	ENSP00000359329:R356Q	ENSP00000359329:R356Q	R	+	2	0	GABRQ	151570810	1.000000	0.71417	0.006000	0.13384	0.162000	0.22319	5.637000	0.67854	0.533000	0.28675	-0.218000	0.12543	CGA		0.507	GABRQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058763.2	NM_018558	
GABRQ	55879	broad.mit.edu	37	X	151821371	151821371	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:151821371G>A	ENST00000370306.2	+	9	1546	c.1526G>A	c.(1525-1527)cGc>cAc	p.R509H		NM_018558.2	NP_061028.3	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) A receptor, theta	509					neurotransmitter transport (GO:0006836)|signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|neurotransmitter transporter activity (GO:0005326)|transmembrane signaling receptor activity (GO:0004888)	p.R509H(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(9)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	52	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TCGGATGAGCGCCATGGCCAT	0.542																																					p.R509H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1526A	X						.						79.0	68.0	71.0					X																	151821371		2203	4300	6503	151572027	SO:0001583	missense	55879	exon9			U47334	CCDS14707.1	Xq28	2012-06-22	2012-02-03		ENSG00000147402	ENSG00000268089		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	14454	protein-coding gene	gene with protein product	"""GABA(A) receptor, theta"""	300349	"""gamma-aminobutyric acid (GABA) receptor, theta"""			10804200, 10449790	Standard	NM_018558		Approved	THETA	uc004ffp.1	Q9UN88	OTTHUMG00000022649	ENST00000370306.2:c.1526G>A	X.37:g.151821371G>A	ENSP00000359329:p.Arg509His		151572027	NM_018558	A6NFN1|Q32MB4|Q9NZK8	Missense_Mutation	SNP	ENST00000370306.2	37	CCDS14707.1	.	.	.	.	.	.	.	.	.	.	G	9.142	1.013975	0.19277	.	.	ENSG00000147402	ENST00000370306	T	0.78707	-1.2	4.4	-0.308	0.12773	Neurotransmitter-gated ion-channel transmembrane domain (2);	4.416530	0.00424	N	0.000073	T	0.61173	0.2326	N	0.08118	0	0.09310	N	1	B	0.17038	0.02	B	0.09377	0.004	T	0.51585	-0.8687	10	0.44086	T	0.13	.	8.3332	0.32200	0.4021:0.0:0.5979:0.0	.	509	Q9UN88	GBRT_HUMAN	H	509	ENSP00000359329:R509H	ENSP00000359329:R509H	R	+	2	0	GABRQ	151572027	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.804000	0.01738	-0.229000	0.09854	-1.016000	0.02456	CGC		0.542	GABRQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058763.2	NM_018558	
NSDHL	50814	broad.mit.edu	37	X	152037427	152037427	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:152037427T>G	ENST00000370274.3	+	8	1083	c.889T>G	c.(889-891)Tac>Gac	p.Y297D	NSDHL_ENST00000440023.1_Missense_Mutation_p.Y297D	NM_015922.2	NP_057006.1	Q15738	NSDHL_HUMAN	NAD(P) dependent steroid dehydrogenase-like	297					cholesterol biosynthetic process (GO:0006695)|hair follicle development (GO:0001942)|labyrinthine layer blood vessel development (GO:0060716)|small molecule metabolic process (GO:0044281)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|sterol-4-alpha-carboxylate 3-dehydrogenase (decarboxylating) activity (GO:0047012)	p.Y297D(1)		NS(1)|breast(1)|cervix(1)|endometrium(4)|large_intestine(3)|lung(5)	15	Acute lymphoblastic leukemia(192;6.56e-05)					CCACATCCCCTACTGGGTGGC	0.572																																					p.Y297D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T889G	X						.						123.0	108.0	113.0					X																	152037427		2203	4300	6503	151788083	SO:0001583	missense	50814	exon9			X96621	CCDS14717.1	Xq28	2011-09-14			ENSG00000147383	ENSG00000147383	1.1.1.170	"""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	13398	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 31E, member 1"""	300275				10710235, 12837764, 19027726	Standard	NM_015922		Approved	XAP104, H105e3, SDR31E1	uc004fgs.1	Q15738	OTTHUMG00000024185	ENST00000370274.3:c.889T>G	X.37:g.152037427T>G	ENSP00000359297:p.Tyr297Asp		151788083	NM_001129765	D3DWT6|O00344	Missense_Mutation	SNP	ENST00000370274.3	37	CCDS14717.1	.	.	.	.	.	.	.	.	.	.	T	18.92	3.726085	0.69074	.	.	ENSG00000147383	ENST00000370274;ENST00000440023	D;D	0.87334	-2.24;-2.24	4.12	4.12	0.48240	.	0.000000	0.85682	D	0.000000	D	0.92038	0.7477	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	D	0.91367	0.5116	10	0.42905	T	0.14	-34.9486	10.7061	0.45956	0.0:0.0:0.0:1.0	.	297	Q15738	NSDHL_HUMAN	D	297	ENSP00000359297:Y297D;ENSP00000391854:Y297D	ENSP00000359297:Y297D	Y	+	1	0	NSDHL	151788083	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	7.939000	0.87685	1.598000	0.50083	0.441000	0.28932	TAC		0.572	NSDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060927.1	NM_015922	
ZNF275	10838	broad.mit.edu	37	X	152612539	152612539	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:152612539C>T	ENST00000421401.3	+	4	573	c.396C>T	c.(394-396)ggC>ggT	p.G132G	ZNF275_ENST00000370249.2_Silent_p.G79G|ZNF275_ENST00000440091.1_Silent_p.G162G|ZNF275_ENST00000370251.3_Silent_p.G132G			Q9NSD4	ZN275_HUMAN	zinc finger protein 275	132					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G79G(1)		endometrium(5)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	16	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GGGAATGTGGCGACTGCGGGA	0.577																																					p.G132G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C396T	X						.						50.0	53.0	52.0					X																	152612539		2112	4202	6314	152265733	SO:0001819	synonymous_variant	10838	exon4			BC041602		Xq28	2013-01-08			ENSG00000063587	ENSG00000063587		"""Zinc fingers, C2H2-type"", ""-"""	13069	protein-coding gene	gene with protein product							Standard	NM_001080485		Approved		uc004fhg.2	Q9NSD4	OTTHUMG00000067450	ENST00000421401.3:c.396C>T	X.37:g.152612539C>T			152265733	NM_001080485	A6NE92	Silent	SNP	ENST00000421401.3	37																																																																																					0.577	ZNF275-201	KNOWN	basic	protein_coding	protein_coding		NM_001080485	
ZNF275	10838	broad.mit.edu	37	X	152612702	152612702	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:152612702G>A	ENST00000421401.3	+	4	736	c.559G>A	c.(559-561)Gga>Aga	p.G187R	ZNF275_ENST00000370249.2_Missense_Mutation_p.G134R|ZNF275_ENST00000440091.1_Missense_Mutation_p.G217R|ZNF275_ENST00000370251.3_Missense_Mutation_p.G187R			Q9NSD4	ZN275_HUMAN	zinc finger protein 275	187					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G134R(1)		endometrium(5)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	16	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CGAGGAGTGCGGAAAACGGTT	0.602																																					p.G187R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G559A	X						.						88.0	93.0	91.0					X																	152612702		2197	4287	6484	152265896	SO:0001583	missense	10838	exon4			BC041602		Xq28	2013-01-08			ENSG00000063587	ENSG00000063587		"""Zinc fingers, C2H2-type"", ""-"""	13069	protein-coding gene	gene with protein product							Standard	NM_001080485		Approved		uc004fhg.2	Q9NSD4	OTTHUMG00000067450	ENST00000421401.3:c.559G>A	X.37:g.152612702G>A	ENSP00000398977:p.Gly187Arg		152265896	NM_001080485	A6NE92	Missense_Mutation	SNP	ENST00000421401.3	37		.	.	.	.	.	.	.	.	.	.	G	16.73	3.204493	0.58234	.	.	ENSG00000063587	ENST00000370251;ENST00000421401;ENST00000440091;ENST00000370249	T;T;T;T	0.35789	1.29;1.29;4.31;1.29	4.84	4.84	0.62591	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.44483	D	0.000448	T	0.59945	0.2231	M	0.73962	2.25	0.36738	D	0.882072	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.69851	-0.5033	10	0.72032	D	0.01	-53.0828	14.4763	0.67548	0.0:0.0:1.0:0.0	.	187;187	Q9NSD4;A6NFS0	ZN275_HUMAN;.	R	187;187;217;134	ENSP00000359271:G187R;ENSP00000398977:G187R;ENSP00000411097:G217R;ENSP00000359269:G134R	ENSP00000359269:G134R	G	+	1	0	ZNF275	152265896	1.000000	0.71417	0.913000	0.36048	0.580000	0.36256	5.493000	0.66899	2.386000	0.81285	0.513000	0.50165	GGA		0.602	ZNF275-201	KNOWN	basic	protein_coding	protein_coding		NM_001080485	
ATP2B3	492	broad.mit.edu	37	X	152826336	152826336	+	Silent	SNP	C	C	T	rs181539158		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:152826336C>T	ENST00000349466.2	+	18	3368	c.3042C>T	c.(3040-3042)ttC>ttT	p.F1014F	ATP2B3_ENST00000393842.1_Silent_p.F1000F|ATP2B3_ENST00000359149.3_Silent_p.F1014F|ATP2B3_ENST00000263519.4_Silent_p.F1014F|ATP2B3_ENST00000370186.1_Silent_p.F1000F|ATP2B3_ENST00000370181.2_Silent_p.F1000F			Q16720	AT2B3_HUMAN	ATPase, Ca++ transporting, plasma membrane 3	1014					blood coagulation (GO:0007596)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)	p.F1014F(5)|p.F1014L(3)|p.F1000F(2)|p.F1000L(1)		NS(2)|breast(5)|endometrium(7)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|skin(3)	50	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TGGGCACTTTCGGGATTCAGG	0.572													C|||	1	0.000264901	0.0008	0.0	3775	,	,		13946	0.0		0.0	False		,,,				2504	0.0				p.F1014F												.	.	11	Substitution - coding silent(7)|Substitution - Missense(4)	lung(4)|breast(4)|large_intestine(3)	c.C3042T	X						.						194.0	141.0	159.0					X																	152826336		2203	4300	6503	152479530	SO:0001819	synonymous_variant	492	exon17			U60414	CCDS14722.1, CCDS35440.1	Xq28	2014-07-18			ENSG00000067842	ENSG00000067842	3.6.3.8	"""ATPases / P-type"""	816	protein-coding gene	gene with protein product	"""plasma membrane calcium-transporting ATPase 3"", ""cilia and flagella associated protein 39"""	300014	"""spinocerebellar ataxia, X-linked 1"", ""cerebellar ataxia 2 (X-linked)"""	SCAX1, CLA2		8187550, 22912398	Standard	NM_021949		Approved	PMCA3, CFAP39	uc004fht.1	Q16720	OTTHUMG00000024202	ENST00000349466.2:c.3042C>T	X.37:g.152826336C>T			152479530	NM_021949	B7WNR8|B7WNY5|Q12995|Q16858	Silent	SNP	ENST00000349466.2	37	CCDS35440.1																																																																																				0.572	ATP2B3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060957.1	NM_021949	
ATP2B3	492	broad.mit.edu	37	X	152830477	152830477	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:152830477C>T	ENST00000349466.2	+	20	3584	c.3258C>T	c.(3256-3258)ggC>ggT	p.G1086G	ATP2B3_ENST00000393842.1_Silent_p.G1072G|ATP2B3_ENST00000359149.3_Silent_p.G1086G|ATP2B3_ENST00000263519.4_Silent_p.G1086G|ATP2B3_ENST00000370186.1_Silent_p.G1072G|ATP2B3_ENST00000370181.2_Silent_p.G1072G			Q16720	AT2B3_HUMAN	ATPase, Ca++ transporting, plasma membrane 3	1086					blood coagulation (GO:0007596)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)	p.G1086G(2)|p.G1072G(1)		NS(2)|breast(5)|endometrium(7)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|skin(3)	50	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TGGCCGAAGGCGAGGAAGAGA	0.662																																					p.G1086G												.	.	3	Substitution - coding silent(3)	large_intestine(3)	c.C3258T	X						.						28.0	26.0	27.0					X																	152830477		2199	4293	6492	152483671	SO:0001819	synonymous_variant	492	exon19			U60414	CCDS14722.1, CCDS35440.1	Xq28	2014-07-18			ENSG00000067842	ENSG00000067842	3.6.3.8	"""ATPases / P-type"""	816	protein-coding gene	gene with protein product	"""plasma membrane calcium-transporting ATPase 3"", ""cilia and flagella associated protein 39"""	300014	"""spinocerebellar ataxia, X-linked 1"", ""cerebellar ataxia 2 (X-linked)"""	SCAX1, CLA2		8187550, 22912398	Standard	NM_021949		Approved	PMCA3, CFAP39	uc004fht.1	Q16720	OTTHUMG00000024202	ENST00000349466.2:c.3258C>T	X.37:g.152830477C>T			152483671	NM_021949	B7WNR8|B7WNY5|Q12995|Q16858	Silent	SNP	ENST00000349466.2	37	CCDS35440.1																																																																																				0.662	ATP2B3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060957.1	NM_021949	
BCAP31	10134	broad.mit.edu	37	X	152969519	152969519	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:152969519C>T	ENST00000345046.6	-	5	779	c.372G>A	c.(370-372)tcG>tcA	p.S124S	BCAP31_ENST00000458587.2_Silent_p.S191S|BCAP31_ENST00000441714.1_Silent_p.S124S	NM_001256447.1	NP_001243376.1	P51572	BAP31_HUMAN	B-cell receptor-associated protein 31	124					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|protein localization to endoplasmic reticulum exit site (GO:0070973)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lipid particle (GO:0005811)|membrane (GO:0016020)		p.S124S(1)		endometrium(2)|large_intestine(2)|lung(2)|prostate(1)	7	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TGGCCTGCTGCGAAATGAGAG	0.522																																					p.S191S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G573A	X						.						67.0	54.0	59.0					X																	152969519		2203	4300	6503	152622713	SO:0001819	synonymous_variant	10134	exon5			X81109	CCDS14727.1, CCDS48191.1	Xq28	2005-10-11			ENSG00000185825	ENSG00000185825			16695	protein-coding gene	gene with protein product		300398					Standard	NM_001139441		Approved	DXS1357E, BAP31, 6C6-Ag, CDM	uc011mza.1	P51572	OTTHUMG00000024218	ENST00000345046.6:c.372G>A	X.37:g.152969519C>T			152622713	NM_001139457	B3KQ79|D3DWV5|Q13836|Q96CF0	Silent	SNP	ENST00000345046.6	37	CCDS14727.1																																																																																				0.522	BCAP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061071.1	NM_005745	
ABCD1	215	broad.mit.edu	37	X	153005591	153005591	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:153005591G>A	ENST00000218104.3	+	6	1933	c.1534G>A	c.(1534-1536)Ggc>Agc	p.G512S	U52111.14_ENST00000434284.1_RNA	NM_000033.3	NP_000024.2	P33897	ABCD1_HUMAN	ATP-binding cassette, sub-family D (ALD), member 1	512	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.		G -> S (in ALD; CALD and AS-types; reduced ATPase activity).		alpha-linolenic acid metabolic process (GO:0036109)|ATP catabolic process (GO:0006200)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|linoleic acid metabolic process (GO:0043651)|long-chain fatty acid catabolic process (GO:0042758)|peroxisomal long-chain fatty acid import (GO:0015910)|peroxisomal membrane transport (GO:0015919)|peroxisome organization (GO:0007031)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid catabolic process (GO:0042760)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|peroxisomal fatty-acyl-CoA transporter activity (GO:0005325)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)	p.G512S(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|urinary_tract(2)	18	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CAATGGCTGCGGCAAGAGCTC	0.647																																					p.G512S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1534A	X	GRCh37	CM014158|CM950050	ABCD1	M		.						107.0	93.0	98.0					X																	153005591		2203	4300	6503	152658785	SO:0001583	missense	215	exon6			Z21876	CCDS14728.1	Xq28	2012-03-14			ENSG00000101986	ENSG00000101986		"""ATP binding cassette transporters / subfamily D"""	61	protein-coding gene	gene with protein product		300371		ALD		8441467, 6795626	Standard	NM_000033		Approved	AMN, ALDP, adrenoleukodystrophy	uc004fif.2	P33897	OTTHUMG00000024215	ENST00000218104.3:c.1534G>A	X.37:g.153005591G>A	ENSP00000218104:p.Gly512Ser		152658785	NM_000033	Q6GTZ2	Missense_Mutation	SNP	ENST00000218104.3	37	CCDS14728.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.748025	0.89663	.	.	ENSG00000101986	ENST00000218104	D	0.99863	-7.27	4.93	4.93	0.64822	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.059325	0.64402	D	0.000003	D	0.99914	0.9959	H	0.98612	4.28	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.96081	0.9054	10	0.87932	D	0	-21.7921	14.4412	0.67318	0.0:0.0:1.0:0.0	.	512	P33897	ABCD1_HUMAN	S	512	ENSP00000218104:G512S	ENSP00000218104:G512S	G	+	1	0	ABCD1	152658785	1.000000	0.71417	0.982000	0.44146	0.666000	0.39218	9.186000	0.94906	2.283000	0.76528	0.429000	0.28392	GGC		0.647	ABCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061041.1	NM_000033	
IDH3G	3421	broad.mit.edu	37	X	153052970	153052970	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:153052970G>A	ENST00000217901.5	-	8	819	c.623C>T	c.(622-624)gCg>gTg	p.A208V	IDH3G_ENST00000497043.1_5'UTR|IDH3G_ENST00000370093.1_Missense_Mutation_p.A208V|IDH3G_ENST00000370092.3_Missense_Mutation_p.A208V|IDH3G_ENST00000427365.2_Missense_Mutation_p.A150V	NM_004135.3	NP_004126.1	P51553	IDH3G_HUMAN	isocitrate dehydrogenase 3 (NAD+) gamma	208					carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|isocitrate dehydrogenase (NAD+) activity (GO:0004449)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)	p.A208V(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|prostate(1)	17	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					GCTCTCCTGCGCCAGCTTGAA	0.607																																					p.A208V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C623T	X						.						69.0	61.0	64.0					X																	153052970		2203	4300	6503	152706164	SO:0001583	missense	3421	exon8				CCDS14730.1, CCDS44019.1	Xq28	2008-02-05			ENSG00000067829	ENSG00000067829	1.1.1.41		5386	protein-coding gene	gene with protein product		300089				9286695	Standard	NM_004135		Approved		uc004fip.4	P51553	OTTHUMG00000024219	ENST00000217901.5:c.623C>T	X.37:g.153052970G>A	ENSP00000217901:p.Ala208Val		152706164	NM_004135	E9PDD5|Q9BUU5	Missense_Mutation	SNP	ENST00000217901.5	37	CCDS14730.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	36|36	5.724447|5.724447	0.96847|0.96847	.|.	.|.	ENSG00000067829|ENSG00000067829	ENST00000370092;ENST00000217901;ENST00000370093;ENST00000427365;ENST00000393771;ENST00000444450;ENST00000444338|ENST00000424541	T;T;T;T;T;D|.	0.82619|.	-1.18;-1.18;-1.18;-1.18;-1.18;-1.63|.	5.84|5.84	5.84|5.84	0.93424|0.93424	Isopropylmalate dehydrogenase-like domain (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.88078|0.88078	0.6340|0.6340	H|H	0.96333|0.96333	3.805|3.805	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;0.999|.	D;P|.	0.63488|.	0.915;0.824|.	D|D	0.91638|0.91638	0.5324|0.5324	10|5	0.87932|.	D|.	0|.	.|.	17.7311|17.7311	0.88378|0.88378	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	208;208|.	E9PDD5;P51553|.	.;IDH3G_HUMAN|.	V|C	208;208;208;150;104;185;148|19	ENSP00000359110:A208V;ENSP00000217901:A208V;ENSP00000359111:A208V;ENSP00000408529:A150V;ENSP00000401862:A185V;ENSP00000402747:A148V|.	ENSP00000217901:A208V|.	A|R	-|-	2|1	0|0	IDH3G|IDH3G	152706164|152706164	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.934000|0.934000	0.57294|0.57294	9.754000|9.754000	0.98908|0.98908	2.460000|2.460000	0.83146|0.83146	0.596000|0.596000	0.82720|0.82720	GCG|CGC		0.607	IDH3G-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061084.27		
STS	412	broad.mit.edu	37	X	7177531	7177531	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:7177531C>T	ENST00000217961.4	+	5	759	c.539C>T	c.(538-540)aCg>aTg	p.T180M		NM_000351.4	NP_000342.2	P08842	STS_HUMAN	steroid sulfatase (microsomal), isozyme S	180					cellular protein metabolic process (GO:0044267)|epidermis development (GO:0008544)|female pregnancy (GO:0007565)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|steroid catabolic process (GO:0006706)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|steryl-sulfatase activity (GO:0004773)|sulfuric ester hydrolase activity (GO:0008484)	p.T180M(1)		NS(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|prostate(2)|skin(1)	27		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)			Norelgestromin(DB06713)	GTCTTCACCACGGGCTTCAAG	0.542									Ichthyosis																												p.T180M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C539T	X						.						95.0	73.0	80.0					X																	7177531		2203	4299	6502	7187531	SO:0001583	missense	412	exon5	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	M16505	CCDS14127.1	Xp22.32	2013-06-10	2007-07-19		ENSG00000101846	ENSG00000101846	3.1.6.2	"""Arylsulfatase family"""	11425	protein-coding gene	gene with protein product	"""arylsulfatase C"""	300747	"""steroid sulfatase (microsomal), arylsulfatase C, isozyme S"""	ARSC1			Standard	NM_000351		Approved	ARSC	uc004cry.4	P08842	OTTHUMG00000021102	ENST00000217961.4:c.539C>T	X.37:g.7177531C>T	ENSP00000217961:p.Thr180Met		7187531	NM_000351	B2RA47	Missense_Mutation	SNP	ENST00000217961.4	37	CCDS14127.1	.	.	.	.	.	.	.	.	.	.	C	12.00	1.806397	0.31961	.	.	ENSG00000101846	ENST00000217961	D	0.98617	-5.03	3.85	-3.9	0.04181	Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	2.322600	0.02116	N	0.055214	D	0.95500	0.8538	L	0.28400	0.85	0.09310	N	1	B	0.16802	0.019	B	0.20577	0.03	D	0.90142	0.4214	10	0.45353	T	0.12	.	3.3178	0.07039	0.3165:0.2544:0.3455:0.0836	.	180	P08842	STS_HUMAN	M	180	ENSP00000217961:T180M	ENSP00000217961:T180M	T	+	2	0	STS	7187531	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.334000	0.07883	-1.188000	0.02705	-1.134000	0.01955	ACG		0.542	STS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055686.1	NM_000351	
GPR143	4935	broad.mit.edu	37	X	9728808	9728808	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:9728808C>T	ENST00000467482.1	-	2	455	c.309G>A	c.(307-309)tcG>tcA	p.S103S	GPR143_ENST00000380929.2_Silent_p.S123S			P51810	GP143_HUMAN	G protein-coupled receptor 143	103					calcium-mediated signaling using intracellular calcium source (GO:0035584)|eye pigment biosynthetic process (GO:0006726)|G-protein coupled receptor signaling pathway (GO:0007186)|melanosome localization (GO:0032400)|melanosome organization (GO:0032438)|melanosome transport (GO:0032402)|neuropeptide signaling pathway (GO:0007218)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of calcium-mediated signaling (GO:0050848)|signal transduction (GO:0007165)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|melanosome membrane (GO:0033162)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|G-protein coupled receptor activity (GO:0004930)|L-DOPA binding (GO:0072544)|L-DOPA receptor activity (GO:0035643)|tyrosine binding (GO:0072545)	p.S123S(1)		endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	15		Hepatocellular(5;0.000888)				GGTTCATATCCGAGACGCTGT	0.498																																					p.S103S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G309A	X						.						90.0	65.0	74.0					X																	9728808		2203	4299	6502	9688808	SO:0001819	synonymous_variant	4935	exon2			Z48804	CCDS14134.1, CCDS14134.2	Xp22.3	2013-09-27	2003-12-01		ENSG00000101850	ENSG00000101850		"""GPCR / Unclassified : 7TM orphan receptors"""	20145	protein-coding gene	gene with protein product	"""ocular albinism 1"""	300808	"""ocular albinism 1 (Nettleship-Falls)"""	OA1		7647783, 10471510	Standard	NM_000273		Approved		uc004cst.2	P51810	OTTHUMG00000021118	ENST00000467482.1:c.309G>A	X.37:g.9728808C>T			9688808	NM_000273	Q6NTI7	Silent	SNP	ENST00000467482.1	37	CCDS14134.2	.	.	.	.	.	.	.	.	.	.	C	3.054	-0.194762	0.06259	.	.	ENSG00000101850	ENST00000447366	.	.	.	4.47	-8.93	0.00771	.	.	.	.	.	T	0.34337	0.0894	.	.	.	0.52501	D	0.999956	.	.	.	.	.	.	T	0.57051	-0.7877	4	.	.	.	-12.4809	1.9083	0.03281	0.1803:0.2208:0.134:0.4649	.	.	.	.	R	39	.	.	G	-	1	0	GPR143	9688808	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-4.588000	0.00212	-5.074000	0.00022	-1.893000	0.00533	GGA		0.498	GPR143-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055714.2	NM_000273	
BEND2	139105	broad.mit.edu	37	X	18213475	18213475	+	Missense_Mutation	SNP	G	G	A	rs546359357		TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:18213475G>A	ENST00000380033.4	-	7	1253	c.1121C>T	c.(1120-1122)tCg>tTg	p.S374L	BEND2_ENST00000380030.3_Intron	NM_153346.4	NP_699177.2	Q8NDZ0	BEND2_HUMAN	BEN domain containing 2	374								p.S374L(1)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(11)|liver(1)|lung(21)|ovary(3)|prostate(1)	49						CGTATTTCCCGATAAAGCTGG	0.398																																					p.S374L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1121T	X						.						179.0	150.0	160.0					X																	18213475		2203	4300	6503	18123396	SO:0001583	missense	139105	exon7			AK128155	CCDS14184.1, CCDS55375.1	Xp22.22	2012-11-22	2008-10-03	2008-10-03	ENSG00000177324	ENSG00000177324		"""BEN domain containing"""	28509	protein-coding gene	gene with protein product			"""chromosome X open reading frame 20"""	CXorf20		12477932	Standard	NM_153346		Approved	MGC33653	uc004cyj.4	Q8NDZ0	OTTHUMG00000021211	ENST00000380033.4:c.1121C>T	X.37:g.18213475G>A	ENSP00000369372:p.Ser374Leu		18123396	NM_153346	E9PFY2|Q4V9S2|Q5JXE5	Missense_Mutation	SNP	ENST00000380033.4	37	CCDS14184.1	.	.	.	.	.	.	.	.	.	.	G	3.849	-0.032224	0.07543	.	.	ENSG00000177324	ENST00000380033	T	0.20463	2.07	3.21	-0.891	0.10573	.	.	.	.	.	T	0.07458	0.0188	N	0.05124	-0.11	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41124	-0.9526	9	0.07175	T	0.84	.	6.5021	0.22174	0.7407:0.0:0.2593:0.0	.	374	Q8NDZ0	BEND2_HUMAN	L	374	ENSP00000369372:S374L	ENSP00000369372:S374L	S	-	2	0	BEND2	18123396	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.014000	0.12656	-0.252000	0.09528	-1.212000	0.01626	TCG		0.398	BEND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055940.1	NM_153346	
SH3KBP1	30011	broad.mit.edu	37	X	19606773	19606773	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:19606773A>G	ENST00000397821.3	-	12	1576	c.1286T>C	c.(1285-1287)cTg>cCg	p.L429P	SH3KBP1_ENST00000541422.1_Missense_Mutation_p.L168P|SH3KBP1_ENST00000379697.3_Missense_Mutation_p.L473P|SH3KBP1_ENST00000379698.4_Missense_Mutation_p.L392P|SH3KBP1_ENST00000379716.1_Missense_Mutation_p.L191P	NM_031892.2	NP_114098.1	Q96B97	SH3K1_HUMAN	SH3-domain kinase binding protein 1	429					apoptotic process (GO:0006915)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|cytoskeleton organization (GO:0007010)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|regulation of cell shape (GO:0008360)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)		p.L429P(1)		breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|skin(4)	29						GGTGTGTGTCAGCGGACCCAC	0.627																																					p.L392P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1175C	X						.						110.0	104.0	106.0					X																	19606773		2203	4300	6503	19516694	SO:0001583	missense	30011	exon11			AF230904	CCDS14193.1, CCDS35213.1, CCDS55383.1	Xp22.1-p21.3	2008-02-05			ENSG00000147010	ENSG00000147010			13867	protein-coding gene	gene with protein product		300374				8889549, 7566098	Standard	NM_031892		Approved	CIN85	uc004czm.3	Q96B97	OTTHUMG00000021227	ENST00000397821.3:c.1286T>C	X.37:g.19606773A>G	ENSP00000380921:p.Leu429Pro		19516694	NM_001024666	B7Z1D5|Q5JPT4|Q5JPT5|Q8IWX6|Q8IX98|Q96RN4|Q9NYR0	Missense_Mutation	SNP	ENST00000397821.3	37	CCDS14193.1	.	.	.	.	.	.	.	.	.	.	A	14.99	2.699587	0.48307	.	.	ENSG00000147010	ENST00000379702;ENST00000397821;ENST00000379716;ENST00000379698;ENST00000541422;ENST00000379726;ENST00000379697	T;T;T;T;T;T	0.38560	1.55;1.55;1.55;1.55;1.55;1.13	5.84	5.84	0.93424	.	1.180670	0.05971	N	0.642430	T	0.34542	0.0901	N	0.22421	0.69	0.58432	D	0.999999	B;B;P	0.43169	0.026;0.003;0.8	B;B;B	0.38562	0.009;0.002;0.276	T	0.03784	-1.1004	10	0.54805	T	0.06	-3.9728	11.1231	0.48302	0.9255:0.0:0.0745:0.0	.	191;429;392	Q5JPT4;Q96B97;Q5JPT5	.;SH3K1_HUMAN;.	P	414;429;191;392;168;409;473	ENSP00000380921:L429P;ENSP00000369039:L191P;ENSP00000369020:L392P;ENSP00000442499:L168P;ENSP00000369049:L409P;ENSP00000369019:L473P	ENSP00000369019:L473P	L	-	2	0	SH3KBP1	19516694	1.000000	0.71417	0.980000	0.43619	0.380000	0.30137	3.737000	0.55060	1.961000	0.56991	0.481000	0.45027	CTG		0.627	SH3KBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055992.1	NM_031892	
RPS6KA3	6197	broad.mit.edu	37	X	20181083	20181083	+	Splice_Site	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:20181083C>T	ENST00000379565.3	-	19	2047	c.1840G>A	c.(1840-1842)Ggt>Agt	p.G614S	RPS6KA3_ENST00000479809.1_5'UTR|RPS6KA3_ENST00000540702.1_Splice_Site_p.G585S|RPS6KA3_ENST00000379548.4_Splice_Site_p.G584S|RPS6KA3_ENST00000544447.1_Splice_Site_p.G586S	NM_004586.2	NP_004577.1	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 3	614	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|central nervous system development (GO:0007417)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.G614S(1)		breast(4)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(14)|lung(7)|ovary(1)|stomach(1)	41					Acetylsalicylic acid(DB00945)	TACACTCACCCGGTAAGCATT	0.343																																					p.G614S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1840A	X						.						153.0	131.0	138.0					X																	20181083		2203	4300	6503	20091004	SO:0001630	splice_region_variant	6197	exon19			U08316	CCDS14197.1	Xp22.2-p22.1	2013-06-03	2002-08-29		ENSG00000177189	ENSG00000177189			10432	protein-coding gene	gene with protein product		300075	"""ribosomal protein S6 kinase, 90kD, polypeptide 3"", ""mental retardation, X-linked 19"", ""Coffin-Lowry syndrome"""	MRX19, CLS		8141249, 11896450, 16879200	Standard	XM_005274573		Approved	RSK, RSK2, HU-3	uc004czu.3	P51812	OTTHUMG00000021231	ENST00000379565.3:c.1841+1G>A	X.37:g.20181083C>T			20091004	NM_004586	B2R9V4|Q4VAP3|Q59H26|Q5JPK8|Q7Z3Z7	Missense_Mutation	SNP	ENST00000379565.3	37	CCDS14197.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.784084	0.90282	.	.	ENSG00000177189	ENST00000379565;ENST00000544447;ENST00000379548;ENST00000540702	T;T;T;T	0.58210	0.35;0.35;0.35;0.35	5.04	5.04	0.67666	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.79046	0.4380	M	0.91768	3.24	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.998;0.996;1.0;0.999	D	0.84869	0.0824	10	0.87932	D	0	.	17.5875	0.87986	0.0:1.0:0.0:0.0	.	585;584;586;614	B4DG22;F5GYC4;B7ZB17;P51812	.;.;.;KS6A3_HUMAN	S	614;586;584;585	ENSP00000368884:G614S;ENSP00000440220:G586S;ENSP00000368865:G584S;ENSP00000444837:G585S	ENSP00000368865:G584S	G	-	1	0	RPS6KA3	20091004	1.000000	0.71417	1.000000	0.80357	0.790000	0.44656	7.818000	0.86416	2.080000	0.62538	0.415000	0.27848	GGT		0.343	RPS6KA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056011.3	NM_004586	Missense_Mutation
PTCHD1	139411	broad.mit.edu	37	X	23411304	23411304	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:23411304G>T	ENST00000379361.4	+	3	2529	c.1669G>T	c.(1669-1671)Ggg>Tgg	p.G557W		NM_173495.2	NP_775766.2	Q96NR3	PTHD1_HUMAN	patched domain containing 1	557					cognition (GO:0050890)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hedgehog receptor activity (GO:0008158)	p.G452W(1)		NS(1)|breast(4)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(4)|skin(2)|urinary_tract(2)	42						TCCTGTGATTGGGTTTTACAT	0.428																																					p.G557W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1669T	X						.						98.0	91.0	93.0					X																	23411304		2203	4300	6503	23321225	SO:0001583	missense	139411	exon3			AK054858	CCDS35215.2	Xp22.13	2008-02-05			ENSG00000165186	ENSG00000165186			26392	protein-coding gene	gene with protein product		300828					Standard	NM_173495		Approved	FLJ30296	uc004dal.4	Q96NR3	OTTHUMG00000021251	ENST00000379361.4:c.1669G>T	X.37:g.23411304G>T	ENSP00000368666:p.Gly557Trp		23321225	NM_173495	B4DQH0|Q0IJ60|Q6P6B8	Missense_Mutation	SNP	ENST00000379361.4	37	CCDS35215.2	.	.	.	.	.	.	.	.	.	.	G	17.55	3.418413	0.62622	.	.	ENSG00000165186	ENST00000379361	D	0.85556	-2.0	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.88526	0.6460	L	0.54323	1.7	0.58432	D	0.999999	P	0.34997	0.479	P	0.48304	0.573	D	0.86585	0.1856	10	0.38643	T	0.18	.	18.7851	0.91951	0.0:0.0:1.0:0.0	.	557	Q96NR3	PTHD1_HUMAN	W	557	ENSP00000368666:G557W	ENSP00000368666:G557W	G	+	1	0	PTCHD1	23321225	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.476000	0.97823	2.381000	0.81170	0.600000	0.82982	GGG		0.428	PTCHD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056047.2	NM_173495	
CASK	8573	broad.mit.edu	37	X	41428944	41428944	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:41428944T>C	ENST00000378163.1	-	16	2033	c.1559A>G	c.(1558-1560)cAt>cGt	p.H520R	CASK_ENST00000378154.1_Missense_Mutation_p.H520R|CASK_ENST00000361962.4_Missense_Mutation_p.H520R|CASK_ENST00000442742.2_Missense_Mutation_p.H520R|CASK_ENST00000318588.9_Missense_Mutation_p.H520R|CASK_ENST00000378166.4_Missense_Mutation_p.H520R|CASK_ENST00000378158.1_Missense_Mutation_p.H520R|RNU6-1321P_ENST00000390905.1_RNA|CASK_ENST00000421587.2_Missense_Mutation_p.H514R|CASK_ENST00000472704.1_5'UTR			O14936	CSKP_HUMAN	calcium/calmodulin-dependent serine protein kinase (MAGUK family)	520	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				calcium ion import (GO:0070509)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of wound healing (GO:0061045)|nucleotide phosphorylation (GO:0046939)|positive regulation of calcium ion import (GO:0090280)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	actin cytoskeleton (GO:0015629)|basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell-cell junction (GO:0005911)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nuclear lamina (GO:0005652)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	ATP binding (GO:0005524)|guanylate kinase activity (GO:0004385)|protein serine/threonine kinase activity (GO:0004674)	p.H520R(1)		breast(3)|endometrium(5)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|ovary(3)|prostate(1)|stomach(1)	32						CATGCCCCCATGCATAATTCT	0.294																																					p.H520R	NSCLC(42;104 1086 3090 27189 35040)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1559G	X						.						109.0	106.0	107.0					X																	41428944		2202	4300	6502	41313888	SO:0001583	missense	8573	exon16			AF035582	CCDS14257.1, CCDS48094.1, CCDS48095.1	Xp11.4	2010-02-09			ENSG00000147044	ENSG00000147044			1497	protein-coding gene	gene with protein product		300172	"""trinucleotide repeat containing 8"""	TNRC8		9722958	Standard	NM_003688		Approved	LIN2, CAGH39, FGS4	uc004dfl.4	O14936	OTTHUMG00000021378	ENST00000378163.1:c.1559A>G	X.37:g.41428944T>C	ENSP00000367405:p.His520Arg		41313888	NM_001126054	A6NES1|B7ZKY0|O43215|Q17RI4|Q59HA0|Q5VT16|Q5VT17|Q5VT18|Q5VT19|Q66T42|Q9BYH6|Q9NYB2|Q9NYB3	Missense_Mutation	SNP	ENST00000378163.1	37		.	.	.	.	.	.	.	.	.	.	T	17.09	3.299863	0.60195	.	.	ENSG00000147044	ENST00000421587;ENST00000318588;ENST00000361962;ENST00000378163;ENST00000378179;ENST00000378158;ENST00000378166;ENST00000442742;ENST00000378154	T;T;T;T;T;T;T;T;T	0.25579	1.79;1.79;1.79;1.79;1.79;1.79;1.79;1.79;1.79	5.06	5.06	0.68205	PDZ/DHR/GLGF (4);	0.000000	0.42420	D	0.000706	T	0.48822	0.1521	M	0.65975	2.015	0.80722	D	1	P;P;B;D;D	0.89917	0.702;0.597;0.096;0.958;1.0	B;P;B;P;D	0.81914	0.421;0.774;0.089;0.828;0.995	T	0.51252	-0.8729	10	0.66056	D	0.02	.	13.9485	0.64101	0.0:0.0:0.0:1.0	.	514;520;520;520;135	O14936-3;O14936-4;O14936-2;O14936;Q5JS72	.;.;.;CSKP_HUMAN;.	R	514;520;520;520;135;520;520;520;520	ENSP00000400526:H514R;ENSP00000322727:H520R;ENSP00000354641:H520R;ENSP00000367405:H520R;ENSP00000367421:H135R;ENSP00000367400:H520R;ENSP00000367408:H520R;ENSP00000398007:H520R;ENSP00000367396:H520R	ENSP00000322727:H520R	H	-	2	0	CASK	41313888	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.308000	0.78929	1.669000	0.50854	0.437000	0.28790	CAT		0.294	CASK-007	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000056285.1	NM_003688	
EFHC2	80258	broad.mit.edu	37	X	44120518	44120518	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:44120518T>A	ENST00000420999.1	-	4	492	c.409A>T	c.(409-411)Act>Tct	p.T137S		NM_025184.3	NP_079460.2	Q5JST6	EFHC2_HUMAN	EF-hand domain (C-terminal) containing 2	137	DM10 1. {ECO:0000255|PROSITE- ProRule:PRU00665}.						calcium ion binding (GO:0005509)	p.T137S(1)		NS(1)|breast(7)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	29						GGCGGAAGAGTAATCCGATGA	0.408																																					p.T137S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A409T	X						.						56.0	49.0	51.0					X																	44120518		1856	4089	5945	44005462	SO:0001583	missense	80258	exon4			AK026254	CCDS55405.1	Xp11	2014-01-31			ENSG00000183690	ENSG00000183690		"""EF-hand domain containing"""	26233	protein-coding gene	gene with protein product		300817	"""mental retardation, X-linked 74"""	MRX74		17221867	Standard	NM_025184		Approved	FLJ22843	uc004dgb.4	Q5JST6	OTTHUMG00000021393	ENST00000420999.1:c.409A>T	X.37:g.44120518T>A	ENSP00000404232:p.Thr137Ser		44005462	NM_025184	Q5JST8|Q68DK4|Q8NEI0|Q9H653	Missense_Mutation	SNP	ENST00000420999.1	37	CCDS55405.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.74|14.74	2.626008|2.626008	0.46840|0.46840	.|.	.|.	ENSG00000183690|ENSG00000183690	ENST00000333807;ENST00000420999|ENST00000441230	T;T|.	0.66460|.	-0.21;-0.21|.	5.83|5.83	-7.42|-7.42	0.01388|0.01388	Uncharacterised domain DM10 (2);|.	0.595355|.	0.17362|.	N|.	0.177011|.	T|T	0.10766|0.10766	0.0263|0.0263	N|N	0.02916|0.02916	-0.46|-0.46	0.19300|0.19300	N|N	0.999973|0.999973	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.27971|0.27971	-1.0058|-1.0058	10|5	0.48119|.	T|.	0.1|.	0.91|0.91	6.1799|6.1799	0.20465|0.20465	0.1251:0.1613:0.628:0.0856|0.1251:0.1613:0.628:0.0856	.|.	137|.	Q5JST6|.	EFHC2_HUMAN|.	S|F	137;165|117	ENSP00000333823:T137S;ENSP00000404232:T165S|.	ENSP00000333823:T137S|.	T|Y	-|-	1|2	0|0	EFHC2|EFHC2	44005462|44005462	0.997000|0.997000	0.39634|0.39634	0.014000|0.014000	0.15608|0.15608	0.934000|0.934000	0.57294|0.57294	0.320000|0.320000	0.19540|0.19540	-1.769000|-1.769000	0.01297|0.01297	-0.269000|-0.269000	0.10298|0.10298	ACT|TAC		0.408	EFHC2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056312.2	NM_025184	
CFP	5199	broad.mit.edu	37	X	47486558	47486558	+	Missense_Mutation	SNP	C	C	T	rs8177077	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:47486558C>T	ENST00000396992.3	-	5	868	c.748G>A	c.(748-750)Ggc>Agc	p.G250S	CFP_ENST00000247153.3_Missense_Mutation_p.G250S|CFP_ENST00000377005.2_Missense_Mutation_p.G250S|CFP_ENST00000480317.1_5'Flank	NM_001145252.1	NP_001138724.1	P27918	PROP_HUMAN	complement factor properdin	250	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.		G -> S (in dbSNP:rs8177077). {ECO:0000269|Ref.5}.		complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|defense response to bacterium (GO:0042742)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)		p.G250S(1)		breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	18						GGTGGCAGGCCGGTGCACCTC	0.607													C|||	13	0.00344371	0.0091	0.0	3775	,	,		13282	0.0		0.001	False		,,,				2504	0.0				p.G250S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G748A	X						.	C	SER/GLY,SER/GLY	41,3794		0,31,10,1601,561	31.0	33.0	32.0		748,748	5.4	0.9	X	dbSNP_117	32	1,6726		0,1,0,2427,1871	yes	missense,missense	CFP	NM_001145252.1,NM_002621.2	56,56	0,32,10,4028,2432	TT,TC,T,CC,C		0.0149,1.0691,0.3977	benign,benign	250/470,250/470	47486558	42,10520	2203	4299	6502	47371502	SO:0001583	missense	5199	exon6			M83652	CCDS14282.1	Xp11.4	2014-09-17	2006-03-02	2006-03-02	ENSG00000126759	ENSG00000126759		"""Complement system"""	8864	protein-coding gene	gene with protein product		300383	"""properdin P factor, complement"""	PFC		1783405	Standard	NM_001145252		Approved		uc004dih.3	P27918	OTTHUMG00000021451	ENST00000396992.3:c.748G>A	X.37:g.47486558C>T	ENSP00000380189:p.Gly250Ser		47371502	NM_002621	O15134|O15135|O15136|O75826	Missense_Mutation	SNP	ENST00000396992.3	37	CCDS14282.1	5	0.0030138637733574444	2	0.00411522633744856	0	0.0	0	0.0	0	0.0	C	9.910	1.209223	0.22205	0.010691	1.49E-4	ENSG00000126759	ENST00000396992;ENST00000247153;ENST00000377005;ENST00000469388	T;T;T;T	0.50548	0.74;0.74;0.74;0.74	5.43	5.43	0.79202	.	0.483859	0.23904	N	0.043415	T	0.45637	0.1352	L	0.33339	1.005	0.40184	D	0.977326	P;D	0.89917	0.892;1.0	P;D	0.79108	0.516;0.992	T	0.38802	-0.9644	10	0.10377	T	0.69	.	13.7904	0.63135	0.0:1.0:0.0:0.0	rs8177077	186;250	B3KVK6;P27918	.;PROP_HUMAN	S	250;250;250;115	ENSP00000380189:G250S;ENSP00000247153:G250S;ENSP00000366204:G250S;ENSP00000418258:G115S	ENSP00000247153:G250S	G	-	1	0	CFP	47371502	0.021000	0.18746	0.903000	0.35520	0.018000	0.09664	0.245000	0.18142	2.415000	0.81967	0.596000	0.82720	GGC		0.607	CFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056435.2	NM_002621	
EBP	10682	broad.mit.edu	37	X	48386663	48386663	+	Missense_Mutation	SNP	C	C	T	rs141925556	byFrequency	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:48386663C>T	ENST00000495186.1	+	5	1334	c.511C>T	c.(511-513)Cgc>Tgc	p.R171C	EBP_ENST00000276096.6_3'UTR	NM_006579.2	NP_006570.1	Q15125	EBP_HUMAN	emopamil binding protein (sterol isomerase)	171					cholesterol biosynthetic process (GO:0006695)|cholesterol metabolic process (GO:0008203)|drug transmembrane transport (GO:0006855)|hemopoiesis (GO:0030097)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)	C-8 sterol isomerase activity (GO:0000247)|cholestenol delta-isomerase activity (GO:0047750)|drug transmembrane transporter activity (GO:0015238)|steroid delta-isomerase activity (GO:0004769)|transmembrane signaling receptor activity (GO:0004888)	p.R171S(1)|p.R171C(1)		NS(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|stomach(1)	11					Tamoxifen(DB00675)	GACAGAGCACCGCGACGGATT	0.572													C|||	1	0.000264901	0.0	0.0	3775	,	,		14261	0.0		0.001	False		,,,				2504	0.0				p.R171C	Ovarian(41;550 1000 33077 33474 52335)											.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.C511T	X						.		CYS/ARG	0,3835		0,0,0,1632,571	124.0	84.0	97.0		511	2.8	0.0	X	dbSNP_134	97	7,6721		0,4,3,2424,1869	yes	missense	EBP	NM_006579.2	180	0,4,3,4056,2440	TT,TC,T,CC,C		0.104,0.0,0.0663	probably-damaging	171/231	48386663	7,10556	2203	4300	6503	48271607	SO:0001583	missense	10682	exon5			Z37986	CCDS14300.1	Xp11.23-p11.22	2013-05-22	2001-11-28		ENSG00000147155	ENSG00000147155			3133	protein-coding gene	gene with protein product	"""3-beta-hydroxysteroid-delta-8,delta-7-isomerase"", ""Chondrodysplasia punctata-2, X-linked dominant (Happle syndrome)"", ""sterol 8-isomerase"""	300205	"""emopamil-binding protein (sterol isomerase)"""	CDPX2		7706302, 8938429	Standard	NM_006579		Approved	CPX, CPXD, CHO2	uc004djx.4	Q15125	OTTHUMG00000034482	ENST00000495186.1:c.511C>T	X.37:g.48386663C>T	ENSP00000417052:p.Arg171Cys		48271607	NM_006579	Q6FGL3|Q6IBI9	Missense_Mutation	SNP	ENST00000495186.1	37	CCDS14300.1	1	6.027727546714888E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	11.09	1.536167	0.27475	0.0	0.00104	ENSG00000147155	ENST00000495186	D	0.97941	-4.62	5.57	2.76	0.32466	.	0.497349	0.21659	N	0.071058	D	0.97942	0.9323	M	0.78049	2.395	0.09310	N	0.999995	D	0.89917	1.0	D	0.64595	0.927	D	0.93656	0.6977	9	.	.	.	-0.2063	7.076	0.25205	0.3041:0.6119:0.0:0.084	.	171	Q15125	EBP_HUMAN	C	171	ENSP00000417052:R171C	.	R	+	1	0	EBP	48271607	0.854000	0.29725	0.000000	0.03702	0.016000	0.09150	2.435000	0.44811	0.142000	0.18901	-0.360000	0.07572	CGC		0.572	EBP-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083372.1	NM_006579	
WAS	7454	broad.mit.edu	37	X	48544178	48544178	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:48544178C>T	ENST00000376701.4	+	4	491	c.416C>T	c.(415-417)gCc>gTc	p.A139V	WAS_ENST00000483750.1_3'UTR	NM_000377.2	NP_000368.1	P42768	WASP_HUMAN	Wiskott-Aldrich syndrome	139	WH1. {ECO:0000255|PROSITE- ProRule:PRU00410}.				actin filament polymerization (GO:0030041)|actin filament-based movement (GO:0030048)|actin polymerization or depolymerization (GO:0008154)|blood coagulation (GO:0007596)|defense response (GO:0006952)|endosomal transport (GO:0016197)|epidermis development (GO:0008544)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|protein complex assembly (GO:0006461)|regulation of catalytic activity (GO:0050790)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|vesicle membrane (GO:0012506)	identical protein binding (GO:0042802)|phospholipase binding (GO:0043274)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)|small GTPase regulator activity (GO:0005083)	p.A139V(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	28		all_lung(315;1.27e-10)				GCCTTCCGGGCCCTCGTGCAG	0.607			"""Mis, N, F, S"""			lymphoma																															p.A139V			X-linked recessive		Wiskott-Aldrich syndrome	X	Xp11.23-p11.22	7454	Wiskott-Aldrich syndrome		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C416T	X						.						33.0	29.0	30.0					X																	48544178		2199	4283	6482	48429122	SO:0001583	missense	7454	exon4			AF115548	CCDS14303.1	Xp11.4-p11.21	2014-09-17	2012-07-12		ENSG00000015285	ENSG00000015285			12731	protein-coding gene	gene with protein product	"""eczema-thrombocytopenia"""	300392	"""thrombocytopenia 1 (X-linked)"", ""Wiskott-Aldrich syndrome (eczema-thrombocytopenia)"""	IMD2, THC		7795648	Standard	NM_000377		Approved	WASP	uc004dkm.4	P42768	OTTHUMG00000034483	ENST00000376701.4:c.416C>T	X.37:g.48544178C>T	ENSP00000365891:p.Ala139Val		48429122	NM_000377	Q9BU11|Q9UNJ9	Missense_Mutation	SNP	ENST00000376701.4	37	CCDS14303.1	.	.	.	.	.	.	.	.	.	.	C	12.62	1.993102	0.35131	.	.	ENSG00000015285	ENST00000450772;ENST00000376701	D;D	0.99488	-6.0;-6.0	5.16	5.16	0.70880	EVH1 (3);Pleckstrin homology-type (1);	0.186284	0.46145	D	0.000307	D	0.97673	0.9237	L	0.27053	0.805	0.09310	N	1	B	0.30236	0.274	B	0.34346	0.18	D	0.94056	0.7322	10	0.28530	T	0.3	-6.6287	13.1148	0.59294	0.0:1.0:0.0:0.0	.	139	P42768	WASP_HUMAN	V	139	ENSP00000410537:A139V;ENSP00000365891:A139V	ENSP00000365891:A139V	A	+	2	0	WAS	48429122	0.000000	0.05858	0.985000	0.45067	0.911000	0.54048	0.525000	0.22956	2.156000	0.67533	0.464000	0.42555	GCC		0.607	WAS-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083379.1	NM_000377	
GRIPAP1	56850	broad.mit.edu	37	X	48855685	48855685	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:48855685C>T	ENST00000376441.1	-	3	170	c.136G>A	c.(136-138)Gcc>Acc	p.A46T	GRIPAP1_ENST00000376423.4_Missense_Mutation_p.A46T|GRIPAP1_ENST00000376444.3_Missense_Mutation_p.A46T|GRIPAP1_ENST00000376425.3_Missense_Mutation_p.A46T	NM_020137.3	NP_064522.3	Q4V328	GRAP1_HUMAN	GRIP1 associated protein 1	46						blood microparticle (GO:0072562)|endosome (GO:0005768)		p.A46T(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(2)	10						TCCAAGTAGGCGACCTTCTGT	0.542																																					p.A46T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G136A	X						.						133.0	95.0	108.0					X																	48855685		2203	4300	6503	48740629	SO:0001583	missense	56850	exon3			AB032993	CCDS35248.1	Xp11.23	2008-02-05			ENSG00000068400	ENSG00000068400			18706	protein-coding gene	gene with protein product		300408				10896157	Standard	NM_020137		Approved	GRASP-1, GRASP1, KIAA1167, MPMGp800B12492Q3, DKFZp434P0630	uc004dly.1	Q4V328	OTTHUMG00000033192	ENST00000376441.1:c.136G>A	X.37:g.48855685C>T	ENSP00000365624:p.Ala46Thr		48740629	NM_020137	A6NL78|Q3MJ75|Q4V327|Q4V330|Q5HYG1|Q6N046|Q96DH8|Q9NQ43|Q9ULQ3	Missense_Mutation	SNP	ENST00000376441.1	37	CCDS35248.1	.	.	.	.	.	.	.	.	.	.	c	15.67	2.902576	0.52227	.	.	ENSG00000068400	ENST00000376425;ENST00000376444;ENST00000376441;ENST00000537291;ENST00000376423	T;T;T;T	0.26957	1.7;1.7;1.7;1.7	5.13	4.27	0.50696	.	0.324915	0.28712	N	0.014396	T	0.14743	0.0356	L	0.29908	0.895	0.23192	N	0.998149	B;B	0.31817	0.341;0.098	B;B	0.19148	0.024;0.021	T	0.17198	-1.0377	10	0.18276	T	0.48	-7.3992	9.9499	0.41631	0.0:0.9029:0.0:0.0971	.	46;46	Q4V328-2;Q4V328	.;GRAP1_HUMAN	T	46	ENSP00000365608:A46T;ENSP00000365627:A46T;ENSP00000365624:A46T;ENSP00000365606:A46T	ENSP00000365606:A46T	A	-	1	0	GRIPAP1	48740629	0.022000	0.18835	0.998000	0.56505	0.988000	0.76386	0.388000	0.20735	1.167000	0.42706	0.521000	0.50471	GCC		0.542	GRIPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080970.2	NM_207672	
PRAF2	11230	broad.mit.edu	37	X	48930138	48930138	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:48930138C>T	ENST00000376390.4	-	2	434	c.351G>A	c.(349-351)gcG>gcA	p.A117A	PRAF2_ENST00000376386.3_Silent_p.A117A|PRAF2_ENST00000491199.1_Intron|AF196779.12_ENST00000376358.3_Silent_p.A231A|WDR45_ENST00000553851.1_Silent_p.A231A	NM_007213.1	NP_009144.1	O60831	PRAF2_HUMAN	PRA1 domain family, member 2	117					L-glutamate transport (GO:0015813)|protein transport (GO:0015031)	endosome (GO:0005768)|integral component of membrane (GO:0016021)		p.A117A(1)		endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	8						AAGCGCCGCCCGCGACCCAGA	0.687																																					p.A117A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G351A	X						.						6.0	7.0	7.0					X																	48930138		2134	4191	6325	48817082	SO:0001819	synonymous_variant	11230	exon2			BC021213	CCDS14317.1	Xp11.23	2008-02-05	2004-11-15		ENSG00000243279	ENSG00000243279			28911	protein-coding gene	gene with protein product		300840	"""PRA1 domain family 2"""			16481131	Standard	NM_007213		Approved	JM4		O60831	OTTHUMG00000034499	ENST00000376390.4:c.351G>A	X.37:g.48930138C>T			48817082	NM_007213	B2RD20	Silent	SNP	ENST00000376390.4	37	CCDS14317.1																																																																																				0.687	PRAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083415.2	NM_007213	
CCDC22	28952	broad.mit.edu	37	X	49098488	49098488	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:49098488G>A	ENST00000376227.3	+	3	405	c.235G>A	c.(235-237)Ggc>Agc	p.G79S	CCDC22_ENST00000496651.1_Intron	NM_014008.3	NP_054727.1	O60826	CCD22_HUMAN	coiled-coil domain containing 22	79								p.G79S(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(2)|skin(1)	18						TCAGGACCTGGGCTATCCCTT	0.597																																					p.G79S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G235A	X						.						76.0	53.0	61.0					X																	49098488		2203	4300	6503	48985432	SO:0001583	missense	28952	exon3			BC000972	CCDS14322.1	Xp11.23	2008-02-05	2005-07-24	2005-07-24	ENSG00000101997	ENSG00000101997			28909	protein-coding gene	gene with protein product		300859	"""chromosome X open reading frame 37"""	CXorf37		12477932	Standard	NM_014008		Approved	JM1	uc004dnd.2	O60826	OTTHUMG00000024141	ENST00000376227.3:c.235G>A	X.37:g.49098488G>A	ENSP00000365401:p.Gly79Ser		48985432	NM_014008	A8K7G1	Missense_Mutation	SNP	ENST00000376227.3	37	CCDS14322.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.609272	0.87258	.	.	ENSG00000101997	ENST00000376227;ENST00000538876	.	.	.	5.08	4.22	0.49857	.	0.000000	0.85682	D	0.000000	T	0.78534	0.4298	M	0.82823	2.61	0.47511	D	0.99944	D;D	0.76494	0.996;0.999	D;D	0.73708	0.965;0.981	T	0.80872	-0.1188	9	0.72032	D	0.01	-19.5026	11.5249	0.50573	0.0899:0.0:0.91:0.0	.	79;79	B4DLA4;O60826	.;CCD22_HUMAN	S	79	.	ENSP00000365401:G79S	G	+	1	0	CCDC22	48985432	1.000000	0.71417	1.000000	0.80357	0.476000	0.33039	6.027000	0.70881	1.128000	0.42052	0.597000	0.82753	GGC		0.597	CCDC22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060822.1	NM_014008	
CLCN5	1184	broad.mit.edu	37	X	49855519	49855519	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:49855519G>A	ENST00000307367.2	+	11	2417	c.2126G>A	c.(2125-2127)cGg>cAg	p.R709Q	CLCN5_ENST00000376088.3_Missense_Mutation_p.R779Q|CLCN5_ENST00000376108.3_Missense_Mutation_p.R709Q|CLCN5_ENST00000376091.3_Missense_Mutation_p.R779Q			P51795	CLCN5_HUMAN	chloride channel, voltage-sensitive 5	709	CBS 2. {ECO:0000255|PROSITE- ProRule:PRU00703}.				chloride transmembrane transport (GO:1902476)|endocytosis (GO:0006897)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)	p.R709Q(1)		central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(8)|ovary(2)|skin(1)	30	Ovarian(276;0.236)					CTGGGACTGCGGCAGTGCCTG	0.458																																					p.R779Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2336A	X						.						103.0	83.0	90.0					X																	49855519		2203	4300	6503	49742259	SO:0001583	missense	1184	exon14			X91906	CCDS14328.1, CCDS48115.1, CCDS69763.1	Xp11.23-p11.22	2012-09-26	2012-02-23		ENSG00000171365	ENSG00000171365		"""Ion channels / Chloride channels : Voltage-sensitive"""	2023	protein-coding gene	gene with protein product	"""Dent disease"""	300008	"""nephrolithiasis 2, X-linked"", ""nephrolithiasis 1 (X-linked)"", ""chloride channel 5"""	NPHL2, NPHL1		7874126, 8111383, 8099916, 8559248, 9602200	Standard	NM_001272102		Approved	DENTS, XLRH, hClC-K2, hCIC-K2, CLC5, XRN, ClC-5	uc004doq.1	P51795	OTTHUMG00000021514	ENST00000307367.2:c.2126G>A	X.37:g.49855519G>A	ENSP00000304257:p.Arg709Gln		49742259	NM_001127899	A1L475|B3KPN6|Q5JQD5|Q7RTN8	Missense_Mutation	SNP	ENST00000307367.2	37	CCDS14328.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.971039	0.92919	.	.	ENSG00000171365	ENST00000376088;ENST00000450422;ENST00000376091;ENST00000376108;ENST00000307367	D;D;D;D	0.93859	-3.3;-3.3;-3.3;-3.3	5.13	5.13	0.70059	Cystathionine beta-synthase, core (3);	0.048966	0.85682	D	0.000000	D	0.97504	0.9183	M	0.93375	3.41	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.72982	0.979;0.975	D	0.98674	1.0689	10	0.87932	D	0	-6.2354	16.6583	0.85234	0.0:0.0:1.0:0.0	.	709;779	P51795;P51795-2	CLCN5_HUMAN;.	Q	779;611;779;709;709	ENSP00000365256:R779Q;ENSP00000365259:R779Q;ENSP00000365276:R709Q;ENSP00000304257:R709Q	ENSP00000304257:R709Q	R	+	2	0	CLCN5	49742259	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	9.705000	0.98719	2.280000	0.76307	0.600000	0.82982	CGG		0.458	CLCN5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056544.1		
SHROOM4	57477	broad.mit.edu	37	X	50377303	50377303	+	Silent	SNP	G	G	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:50377303G>T	ENST00000289292.7	-	4	2053	c.1770C>A	c.(1768-1770)acC>acA	p.T590T	SHROOM4_ENST00000376020.2_Silent_p.T590T|SHROOM4_ENST00000460112.3_Silent_p.T474T			Q9ULL8	SHRM4_HUMAN	shroom family member 4	590					actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)	p.T590T(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					TACGCAGATTGGTAGCAAAAC	0.582																																					p.T590T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1770A	X						.						42.0	41.0	41.0					X																	50377303		2203	4300	6503	50394043	SO:0001819	synonymous_variant	57477	exon4			AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.1770C>A	X.37:g.50377303G>T			50394043	NM_020717	A7E2X9|D6RFW0|Q96LA0	Silent	SNP	ENST00000289292.7	37	CCDS35277.1																																																																																				0.582	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717	
GPR173	54328	broad.mit.edu	37	X	53106713	53106713	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:53106713G>A	ENST00000332582.4	+	2	1401	c.910G>A	c.(910-912)Gtg>Atg	p.V304M		NM_018969.5	NP_061842.1	Q9NS66	GP173_HUMAN	G protein-coupled receptor 173	304					negative regulation of neuron migration (GO:2001223)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|gonadotropin-releasing hormone receptor activity (GO:0004968)	p.V304M(2)		breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)	16						ACCCTACATCGTGGCCTGCTA	0.602																																					p.V304M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G910A	X						.						114.0	70.0	85.0					X																	53106713		2203	4300	6503	53123438	SO:0001583	missense	54328	exon2			AB040801	CCDS14349.1	Xp11	2012-08-21	2006-02-15		ENSG00000184194	ENSG00000184194		"""GPCR / Class A : Orphans"""	18186	protein-coding gene	gene with protein product		300253	"""G-protein coupled receptor 173"", ""G protein coupled receptor 173"""			10833454	Standard	NM_018969		Approved	SREB3	uc004dru.3	Q9NS66	OTTHUMG00000021596	ENST00000332582.4:c.910G>A	X.37:g.53106713G>A	ENSP00000331600:p.Val304Met		53123438	NM_018969	B1B0A5	Missense_Mutation	SNP	ENST00000332582.4	37	CCDS14349.1	.	.	.	.	.	.	.	.	.	.	G	16.40	3.111492	0.56398	.	.	ENSG00000184194	ENST00000332582	T	0.74106	-0.81	5.03	5.03	0.67393	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.82664	0.5086	L	0.57536	1.79	0.58432	D	0.999998	D	0.67145	0.996	D	0.65874	0.939	D	0.84685	0.0719	10	0.72032	D	0.01	-11.3712	14.8667	0.70422	0.0:0.0:1.0:0.0	.	304	Q9NS66	GP173_HUMAN	M	304	ENSP00000331600:V304M	ENSP00000331600:V304M	V	+	1	0	GPR173	53123438	1.000000	0.71417	0.958000	0.39756	0.959000	0.62525	7.971000	0.88012	2.094000	0.63399	0.529000	0.55759	GTG		0.602	GPR173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056717.2	NM_018969	
IQSEC2	23096	broad.mit.edu	37	X	53272650	53272650	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:53272650A>G	ENST00000375368.5	-	8	2923	c.2723T>C	c.(2722-2724)gTt>gCt	p.V908A	IQSEC2_ENST00000396435.3_Missense_Mutation_p.V918A|IQSEC2_ENST00000375365.2_Missense_Mutation_p.V713A			Q5JU85	IQEC2_HUMAN	IQ motif and Sec7 domain 2	908	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)	p.V915A(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(10)|ovary(4)|skin(1)	29						ACCATTGTCAACCCCTGGGGG	0.602																																					p.V918A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2753C	X						.						45.0	28.0	34.0					X																	53272650		2197	4283	6480	53289375	SO:0001583	missense	23096	exon9			AB011094	CCDS35298.1, CCDS48130.1	Xp11.23	2014-01-31			ENSG00000124313	ENSG00000124313			29059	protein-coding gene	gene with protein product		300522	"""mental retardation, X-linked 1 (non-dysmorphic)"""	MRX1		9628581, 20473311	Standard	NM_001243197		Approved	KIAA0522	uc004dsd.3	Q5JU85	OTTHUMG00000021608	ENST00000375368.5:c.2723T>C	X.37:g.53272650A>G	ENSP00000364517:p.Val908Ala		53289375	NM_001111125	B3KT97|C7SDG1|O60275|Q5JUX1	Missense_Mutation	SNP	ENST00000375368.5	37		.	.	.	.	.	.	.	.	.	.	A	25.6	4.655472	0.88056	.	.	ENSG00000124313	ENST00000396435;ENST00000375368;ENST00000375365	T;T;T	0.55234	0.53;0.53;0.53	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.67249	0.2873	L	0.53729	1.69	0.80722	D	1	D;D	0.67145	0.987;0.996	D;D	0.76071	0.937;0.987	T	0.70479	-0.4860	10	0.87932	D	0	.	13.424	0.61015	1.0:0.0:0.0:0.0	.	918;713	Q5JU85-2;Q5JU85-3	.;.	A	918;908;713	ENSP00000379712:V918A;ENSP00000364517:V908A;ENSP00000364514:V713A	ENSP00000364514:V713A	V	-	2	0	IQSEC2	53289375	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.279000	0.95777	1.882000	0.54519	0.477000	0.44152	GTT		0.602	IQSEC2-201	KNOWN	basic	protein_coding	protein_coding		XM_291345	
SMC1A	8243	broad.mit.edu	37	X	53432063	53432063	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:53432063G>A	ENST00000322213.4	-	13	2204	c.2077C>T	c.(2077-2079)Cgg>Tgg	p.R693W	SMC1A_ENST00000375340.6_Missense_Mutation_p.R459W	NM_006306.2	NP_006297.2	Q14683	SMC1A_HUMAN	structural maintenance of chromosomes 1A	693			R -> G (in CDLS2). {ECO:0000269|PubMed:19701948}.		DNA repair (GO:0006281)|gene expression (GO:0010467)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic sister chromatid cohesion (GO:0007064)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA endoreduplication (GO:0032876)|response to radiation (GO:0009314)|RNA splicing (GO:0008380)|signal transduction in response to DNA damage (GO:0042770)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin core heterodimer (GO:0008280)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|meiotic cohesin complex (GO:0030893)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)	p.R693W(1)		NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(8)|ovary(5)|upper_aerodigestive_tract(2)	49						GCCTCTTTCCGTTTTGCCTTC	0.537																																					p.R693W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2077T	X						.						95.0	69.0	78.0					X																	53432063		2203	4300	6503	53448788	SO:0001583	missense	8243	exon13			S78271	CCDS14352.1, CCDS75985.1	Xp11.22-p11.21	2014-09-17	2006-07-06	2006-07-06	ENSG00000072501	ENSG00000072501		"""Structural maintenance of chromosomes proteins"""	11111	protein-coding gene	gene with protein product		300040	"""SMC1 (structural maintenance of chromosomes 1, yeast)-like 1"", ""SMC1 structural maintenance of chromosomes 1-like 1 (yeast)"""	SMC1L1		7757074	Standard	NM_006306		Approved	DXS423E, KIAA0178, SB1.8, Smcb	uc004dsg.3	Q14683	OTTHUMG00000021614	ENST00000322213.4:c.2077C>T	X.37:g.53432063G>A	ENSP00000323421:p.Arg693Trp		53448788	NM_006306	O14995|Q16351|Q2M228	Missense_Mutation	SNP	ENST00000322213.4	37	CCDS14352.1	.	.	.	.	.	.	.	.	.	.	G	17.81	3.480469	0.63849	.	.	ENSG00000072501	ENST00000322213;ENST00000375340	T;D	0.86366	-1.29;-2.11	5.28	3.42	0.39159	RecF/RecN/SMC (1);	0.000000	0.85682	D	0.000000	D	0.94221	0.8145	M	0.91920	3.255	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.973;0.999;0.999	D	0.94189	0.7439	10	0.87932	D	0	.	12.7916	0.57537	0.0:0.0:0.7185:0.2815	.	459;671;693	B7Z709;Q6MZR8;Q14683	.;.;SMC1A_HUMAN	W	693;459	ENSP00000323421:R693W;ENSP00000364489:R459W	ENSP00000323421:R693W	R	-	1	2	SMC1A	53448788	0.967000	0.33354	0.993000	0.49108	0.997000	0.91878	1.337000	0.33862	0.492000	0.27815	0.600000	0.82982	CGG		0.537	SMC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056756.2	NM_006306	
TRO	7216	broad.mit.edu	37	X	54956374	54956374	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:54956374G>A	ENST00000173898.7	+	12	3329	c.3217G>A	c.(3217-3219)Gtc>Atc	p.V1073I	TRO_ENST00000375022.4_Intron|SNORA11_ENST00000408823.1_RNA|TRO_ENST00000375041.2_Missense_Mutation_p.V676I|TRO_ENST00000319167.8_Intron|TRO_ENST00000399736.1_Intron|TRO_ENST00000420798.2_Missense_Mutation_p.V604I	NM_001039705.2	NP_001034794.1	Q12816	TROP_HUMAN	trophinin	1073	62 X 10 AA approximate tandem repeats.				embryo implantation (GO:0007566)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.V1073I(1)		breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|skin(2)|urinary_tract(1)	37						TGGCTGTGCCGTCAGCACCAG	0.572																																					p.V1073I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3217A	X						.						28.0	27.0	27.0					X																	54956374		2035	4165	6200	54973099	SO:0001583	missense	7216	exon12			U04811	CCDS43958.1, CCDS43959.1, CCDS59527.1, CCDS59528.1, CCDS59529.1	Xp11.22-p11.21	2008-02-05			ENSG00000067445	ENSG00000067445			12326	protein-coding gene	gene with protein product		300132				9533028, 11454705	Standard	NM_001039705		Approved	MAGE-D3, KIAA1114, MAGED3	uc004dtq.4	Q12816	OTTHUMG00000021640	ENST00000173898.7:c.3217G>A	X.37:g.54956374G>A	ENSP00000173898:p.Val1073Ile		54973099	NM_001039705	B1AKE9|B1AKF1|F5GY27|Q96SX2|Q9NU89|Q9UPN8	Missense_Mutation	SNP	ENST00000173898.7	37	CCDS43959.1	.	.	.	.	.	.	.	.	.	.	G	0.241	-1.013447	0.02095	.	.	ENSG00000067445	ENST00000173898;ENST00000420798;ENST00000375041	T;T;T	0.09445	2.99;2.99;2.98	2.94	-5.88	0.02290	.	.	.	.	.	T	0.01489	0.0048	N	0.01109	-1.01	0.09310	N	1	P;B	0.35401	0.499;0.307	B;B	0.18561	0.022;0.022	T	0.33033	-0.9884	9	0.02654	T	1	.	1.4874	0.02450	0.235:0.2404:0.3477:0.1769	.	676;1073	B1AKE9;Q12816	.;TROP_HUMAN	I	1073;604;676	ENSP00000173898:V1073I;ENSP00000405126:V604I;ENSP00000364181:V676I	ENSP00000173898:V1073I	V	+	1	0	TRO	54973099	.	.	0.000000	0.03702	0.001000	0.01503	.	.	-2.042000	0.00914	-1.644000	0.00765	GTC		0.572	TRO-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056837.3	NM_016157	
SLC16A2	6567	broad.mit.edu	37	X	73744270	73744270	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:73744270G>A	ENST00000587091.1	+	3	829	c.652G>A	c.(652-654)Gtc>Atc	p.V218I	SLC16A2_ENST00000276033.5_Missense_Mutation_p.V292I	NM_006517.4	NP_006508.2	P36021	MOT8_HUMAN	solute carrier family 16, member 2 (thyroid hormone transporter)	218					monocarboxylic acid transport (GO:0015718)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)|transporter activity (GO:0005215)	p.V292I(1)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|skin(2)	21					L-Leucine(DB00149)|L-Tryptophan(DB00150)|L-Tyrosine(DB00135)|Levothyroxine(DB00451)|Liotrix(DB01583)|Pyruvic acid(DB00119)	GCCATCCCTCGTCATCCTGGG	0.552																																					p.V292I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G874A	X						.						119.0	93.0	102.0					X																	73744270		2203	4300	6503	73660995	SO:0001583	missense	6567	exon3				CCDS14426.1, CCDS14426.2	Xq13.2	2013-05-22	2012-03-20		ENSG00000147100	ENSG00000147100		"""Solute carriers"""	10923	protein-coding gene	gene with protein product		300095	"""solute carrier family 16 (monocarboxylic acid transporters), member 2 (putative transporter)"", ""Allan-Herndon-Dudley syndrome"", ""solute carrier family 16 (monocarboxylic acid transporters), member 2"", ""mental retardation, X-linked 22"", ""solute carrier family 16, member 2 (monocarboxylic acid transporter 8)"""	DXS128, AHDS, MRX22		7981683, 12871948, 15889350	Standard	NM_006517		Approved	XPCT, MCT8, MCT7	uc031tjy.1	P36021	OTTHUMG00000021857	ENST00000587091.1:c.652G>A	X.37:g.73744270G>A	ENSP00000465734:p.Val218Ile		73660995	NM_006517	Q7Z797	Missense_Mutation	SNP	ENST00000587091.1	37	CCDS14426.2	.	.	.	.	.	.	.	.	.	.	G	18.42	3.620631	0.66787	.	.	ENSG00000147100	ENST00000276033	T	0.37235	1.21	5.75	5.75	0.90469	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	T	0.46870	0.1415	L	0.49640	1.575	0.58432	D	0.999998	B	0.33739	0.422	P	0.44732	0.459	T	0.32161	-0.9917	10	0.39692	T	0.17	.	18.939	0.92598	0.0:0.0:1.0:0.0	.	218	P36021	MOT8_HUMAN	I	292	ENSP00000276033:V292I	ENSP00000276033:V292I	V	+	1	0	SLC16A2	73660995	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.472000	0.97709	2.420000	0.82092	0.597000	0.82753	GTC		0.552	SLC16A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057266.3		
KIAA2022	340533	broad.mit.edu	37	X	73961286	73961286	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:73961286T>C	ENST00000055682.6	-	3	3717	c.3106A>G	c.(3106-3108)Atc>Gtc	p.I1036V		NM_001008537.2	NP_001008537.1	Q5QGS0	K2022_HUMAN	KIAA2022	1036					base-excision repair, gap-filling (GO:0006287)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|nervous system development (GO:0007399)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)	delta DNA polymerase complex (GO:0043625)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|DNA-directed DNA polymerase activity (GO:0003887)	p.I1036V(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(23)|liver(1)|lung(41)|ovary(7)|pancreas(2)|prostate(4)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	109						CTTTGCTGGATCACCAGCTTA	0.468																																					p.I1036V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3106G	X						.						82.0	76.0	78.0					X																	73961286		2203	4300	6503	73878011	SO:0001583	missense	340533	exon3				CCDS35337.1	Xq13.3	2014-02-19			ENSG00000050030	ENSG00000050030			29433	protein-coding gene	gene with protein product	"""XLMR-related protein, neurite extension"""	300524				15466006, 23615299	Standard	NM_001008537		Approved	XPN, MRX98	uc004eby.3	Q5QGS0	OTTHUMG00000021860	ENST00000055682.6:c.3106A>G	X.37:g.73961286T>C	ENSP00000055682:p.Ile1036Val		73878011	NM_001008537	A7YY87|Q5JUX9|Q8IVE9	Missense_Mutation	SNP	ENST00000055682.6	37	CCDS35337.1	.	.	.	.	.	.	.	.	.	.	T	19.18	3.777180	0.70107	.	.	ENSG00000050030	ENST00000373468;ENST00000055682	T;T	0.38560	1.13;1.13	5.48	5.48	0.80851	.	0.047434	0.85682	D	0.000000	T	0.57858	0.2082	L	0.47716	1.5	0.58432	D	0.999998	D	0.67145	0.996	D	0.80764	0.994	T	0.60459	-0.7259	10	0.66056	D	0.02	-10.2115	14.6114	0.68519	0.0:0.0:0.0:1.0	.	1036	Q5QGS0	K2022_HUMAN	V	1036	ENSP00000362567:I1036V;ENSP00000055682:I1036V	ENSP00000055682:I1036V	I	-	1	0	KIAA2022	73878011	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.698000	0.84413	1.830000	0.53286	0.486000	0.48141	ATC		0.468	KIAA2022-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057270.2	NM_001008537	
TBX22	50945	broad.mit.edu	37	X	79282244	79282244	+	Silent	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:79282244C>T	ENST00000373294.5	+	5	703	c.675C>T	c.(673-675)caC>caT	p.H225H	TBX22_ENST00000373291.1_Silent_p.H105H|TBX22_ENST00000442340.1_Silent_p.H105H|TBX22_ENST00000373296.3_Silent_p.H225H	NM_016954.2	NP_058650.1	Q9Y458	TBX22_HUMAN	T-box 22	225					multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H225H(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(13)|lung(38)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						CCCGAGTGCACGTGATAGAGC	0.453																																					p.H225H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C675T	X						.						169.0	134.0	146.0					X																	79282244		2203	4300	6503	79168900	SO:0001819	synonymous_variant	50945	exon6			AL031000	CCDS14445.1, CCDS43975.1	Xq21.1	2011-02-11			ENSG00000122145	ENSG00000122145		"""T-boxes"""	11600	protein-coding gene	gene with protein product		300307	"""cleft palate and/or ankyloglossia"""	CPX, CLPA		11559848, 14729838	Standard	NM_001109878		Approved		uc004edj.1	Q9Y458	OTTHUMG00000021901	ENST00000373294.5:c.675C>T	X.37:g.79282244C>T			79168900	NM_001109878	Q5JZ06|Q96LC0|Q9HBF1	Silent	SNP	ENST00000373294.5	37	CCDS14445.1																																																																																				0.453	TBX22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057334.1	NM_016954	
PCDH11X	27328	broad.mit.edu	37	X	91090594	91090594	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	Illumina			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:91090594C>T	ENST00000373094.1	+	1	936	c.91C>T	c.(91-93)Cga>Tga	p.R31*	PCDH11X_ENST00000504220.2_Nonsense_Mutation_p.R31*|PCDH11X_ENST00000361655.2_Nonsense_Mutation_p.R31*|PCDH11X_ENST00000406881.1_Nonsense_Mutation_p.R31*|PCDH11X_ENST00000298274.8_Nonsense_Mutation_p.R31*|PCDH11X_ENST00000361724.1_Nonsense_Mutation_p.R31*|PCDH11X_ENST00000373097.1_Nonsense_Mutation_p.R31*|PCDH11X_ENST00000395337.2_Nonsense_Mutation_p.R31*|PCDH11X_ENST00000373088.1_Nonsense_Mutation_p.R31*	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	31	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R31*(2)		NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						CTACACCATCCGAGAAGAAAT	0.488																																					p.R31X	NSCLC(38;925 1092 2571 38200 45895)											.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C91T	X						.						138.0	104.0	116.0					X																	91090594		2203	4300	6503	90977250	SO:0001587	stop_gained	27328	exon1			AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290		"""Cadherins / Protocadherins : Non-clustered"""	8656	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 119"""	300246	"""protocadherin 11"""	PCDH11		10644456	Standard	NM_001168360		Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.91C>T	X.37:g.91090594C>T	ENSP00000362186:p.Arg31*		90977250	NM_032968	A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Nonsense_Mutation	SNP	ENST00000373094.1	37	CCDS14461.1	.	.	.	.	.	.	.	.	.	.	C	35	5.533906	0.96460	.	.	ENSG00000102290	ENST00000395337;ENST00000373094;ENST00000373097;ENST00000361724;ENST00000373088;ENST00000504220;ENST00000361655;ENST00000406881;ENST00000356934;ENST00000298274	.	.	.	3.93	3.03	0.35002	.	0.257973	0.31936	N	0.006833	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.1697	0.48565	0.1941:0.8058:0.0:0.0	.	.	.	.	X	31	.	ENSP00000298274:R31X	R	+	1	2	PCDH11X	90977250	0.376000	0.25098	0.607000	0.28956	0.913000	0.54294	0.709000	0.25734	0.748000	0.32831	0.415000	0.27848	CGA		0.488	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969	
RENBP	5973	broad.mit.edu	37	X	153209824	153209824	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:153209824A>G	ENST00000393700.3	-	2	154	c.74T>C	c.(73-75)gTg>gCg	p.V25A	RENBP_ENST00000462086.1_5'Flank|RENBP_ENST00000369997.3_Missense_Mutation_p.V25A|RENBP_ENST00000412763.1_Missense_Mutation_p.V25A	NM_002910.5	NP_002901.2	P51606	RENBP_HUMAN	renin binding protein	25					N-acetylglucosamine metabolic process (GO:0006044)|N-acetylmannosamine metabolic process (GO:0006051)|N-acetylneuraminate catabolic process (GO:0019262)|regulation of blood pressure (GO:0008217)	extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|endopeptidase inhibitor activity (GO:0004866)|N-acylglucosamine 2-epimerase activity (GO:0050121)	p.V15A(1)|p.V25A(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	20	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)				N-Acetyl-D-glucosamine(DB00141)	CTCCTGCCCCACGCGCTCCTT	0.642																																					p.V25A												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T74C	X						.						115.0	105.0	109.0					X																	153209824		2203	4300	6503	152863018	SO:0001583	missense	5973	exon2				CCDS14738.2	Xq28	2013-09-23	2001-11-28		ENSG00000102032	ENSG00000102032			9959	protein-coding gene	gene with protein product	"""N-acylglucosamine 2-epimerase"", ""GlcNAc 2-epimerase"", ""N-acetyl-D-glucosamine 2-epimerase"""	312420	"""renin-binding protein"""			1618798	Standard	NM_002910		Approved	RNBP, RBP	uc004fjo.2	P51606	OTTHUMG00000024224	ENST00000393700.3:c.74T>C	X.37:g.153209824A>G	ENSP00000377303:p.Val25Ala		152863018	NM_002910	B4DNZ3|Q96BI6	Missense_Mutation	SNP	ENST00000393700.3	37	CCDS14738.2	.	.	.	.	.	.	.	.	.	.	A	18.52	3.642096	0.67244	.	.	ENSG00000102032	ENST00000393700;ENST00000412763;ENST00000369997	T;T;T	0.28666	1.63;1.6;1.63	4.29	4.29	0.51040	Six-hairpin glycosidase (1);Six-hairpin glycosidase-like (1);	0.229755	0.37304	N	0.002146	T	0.41949	0.1181	M	0.63428	1.95	0.09310	N	0.999998	D;P	0.53745	0.962;0.935	P;B	0.52598	0.703;0.431	T	0.32402	-0.9908	10	0.66056	D	0.02	-12.8376	11.6977	0.51553	1.0:0.0:0.0:0.0	.	25;25	P51606-2;P51606	.;RENBP_HUMAN	A	25	ENSP00000377303:V25A;ENSP00000387811:V25A;ENSP00000359014:V25A	ENSP00000359014:V25A	V	-	2	0	RENBP	152863018	0.266000	0.24112	0.083000	0.20561	0.522000	0.34438	3.633000	0.54295	1.598000	0.50083	0.356000	0.21956	GTG		0.642	RENBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061103.3	NM_002910	
FLNA	2316	broad.mit.edu	37	X	153593592	153593592	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	TCGA-AA-3877-01A-01W-0995-10	TCGA-AA-3877-10A-01W-0995-10	g.chrX:153593592delC	ENST00000369850.3	-	11	1839	c.1603delG	c.(1603-1605)gatfs	p.D535fs	FLNA_ENST00000422373.1_Frame_Shift_Del_p.D535fs|FLNA_ENST00000360319.4_Frame_Shift_Del_p.D535fs|FLNA_ENST00000344736.4_Frame_Shift_Del_p.D535fs	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	535					actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|cilium assembly (GO:0042384)|cytoplasmic sequestering of protein (GO:0051220)|early endosome to late endosome transport (GO:0045022)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization (GO:0045184)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription factor import into nucleus (GO:0042993)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|receptor clustering (GO:0043113)|spindle assembly involved in mitosis (GO:0090307)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical dendrite (GO:0097440)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|Myb complex (GO:0031523)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|Fc-gamma receptor I complex binding (GO:0034988)|glycoprotein binding (GO:0001948)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)|Rho GTPase binding (GO:0017048)|signal transducer activity (GO:0004871)|small GTPase binding (GO:0031267)|transcription factor binding (GO:0008134)	p.D535fs*34(1)		breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TACACGCCATCCCCCAGGTCC	0.637																																					p.D535fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1603delG	X						.						96.0	101.0	99.0					X																	153593592		2067	4166	6233	153246786	SO:0001589	frameshift_variant	2316	exon11			X70082	CCDS44021.1, CCDS48194.1	Xq28	2009-07-23	2009-07-23		ENSG00000196924	ENSG00000196924			3754	protein-coding gene	gene with protein product	"""actin binding protein 280"""	300017	"""filamin A, alpha (actin binding protein 280)"""	FLN1, FLN, OPD2, OPD1		8406501, 12612583	Standard	NM_001456		Approved	ABP-280	uc004fkk.2	P21333	OTTHUMG00000022712	ENST00000369850.3:c.1603delG	X.37:g.153593592delC	ENSP00000358866:p.Asp535fs		153246786	NM_001456	E9KL45|Q5HY53|Q5HY55|Q8NF52	Frame_Shift_Del	DEL	ENST00000369850.3	37	CCDS48194.1																																																																																				0.637	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3		
