#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_ACHILLES_Lineage_Results_Top_Genes	i_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	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_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	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_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	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_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	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
SPTA1	6708	broad.mit.edu	37	1	158592861	158592861	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr1:158592861G>A	ENST00000368147.4	-	43	6212	c.6032C>T	c.(6031-6033)gCc>gTc	p.A2011V		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2011					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.A2011V(6)		NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					CAGCAGAGCGGCATAACGCTC	0.483																																						uc001fst.1																			6	Substitution - Missense(6)		lung(4)|urinary_tract(1)|prostate(1)	ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8						c.(6031-6033)GCC>GTC		spectrin, alpha, erythrocytic 1							267.0	267.0	267.0					1																	158592861		1943	4143	6086	SO:0001583	missense	6708				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton	g.chr1:158592861G>A	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.6032C>T	1.37:g.158592861G>A	ENSP00000357129:p.Ala2011Val						p.A2011V	NM_003126	NP_003117	P02549	SPTA1_HUMAN			43	6231	-	all_hematologic(112;0.0378)		2011			Spectrin 19.		Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	c.6032C>T	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	G	9.476	1.096957	0.20552	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.51325	0.71;0.71	4.78	0.669	0.17918	.	.	.	.	.	T	0.22859	0.0552	M	0.68952	2.095	0.30521	N	0.768424	B	0.23990	0.095	B	0.29267	0.1	T	0.14531	-1.0469	9	0.33940	T	0.23	.	5.4632	0.16627	0.1562:0.0:0.5633:0.2805	.	2011	P02549	SPTA1_HUMAN	V	2011;2008	ENSP00000357130:A2011V;ENSP00000357129:A2008V	ENSP00000357129:A2008V	A	-	2	0	SPTA1	156859485	1.000000	0.71417	0.002000	0.10522	0.000000	0.00434	4.149000	0.58091	-0.029000	0.13827	-0.140000	0.14226	GCC		0.483	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
C1orf112	55732	broad.mit.edu	37	1	169772375	169772375	+	Silent	SNP	C	C	T			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr1:169772375C>T	ENST00000286031.6	+	5	937	c.237C>T	c.(235-237)tcC>tcT	p.S79S	C1orf112_ENST00000456684.1_Silent_p.S137S|C1orf112_ENST00000413811.2_Silent_p.S50S|C1orf112_ENST00000359326.4_Silent_p.S79S|C1orf112_ENST00000498289.1_3'UTR	NM_018186.2	NP_060656.2	Q9NSG2	CA112_HUMAN	chromosome 1 open reading frame 112	79										breast(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|stomach(1)	34	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					CACAGGAATCCATCATTTTGG	0.378																																						uc001ggp.2																			0					0						c.(235-237)TCC>TCT		hypothetical protein LOC55732							74.0	70.0	72.0					1																	169772375		2203	4300	6503	SO:0001819	synonymous_variant	55732							g.chr1:169772375C>T	AL354614	CCDS1285.1	1q24.2	2012-06-26			ENSG00000000460	ENSG00000000460			25565	protein-coding gene	gene with protein product						12477932	Standard	NM_018186		Approved	FLJ10706	uc001ggq.3	Q9NSG2	OTTHUMG00000035821	ENST00000286031.6:c.237C>T	1.37:g.169772375C>T						C1orf112_uc001ggj.2_RNA|C1orf112_uc001ggo.2_Silent_p.S79S|C1orf112_uc001ggq.2_Silent_p.S79S|C1orf112_uc009wvt.2_5'UTR|C1orf112_uc010plu.1_Silent_p.S50S|C1orf112_uc009wvu.1_Silent_p.S50S|C1orf112_uc001ggr.2_5'UTR|C1orf112_uc010plv.1_Silent_p.S21S	p.S79S	NM_018186	NP_060656	Q9NSG2	CA112_HUMAN			6	547	+	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)		79					A6NFP1|B3KU42|Q3KNQ1|Q9H8L5|Q9NVJ0	Silent	SNP	ENST00000286031.6	37	c.237C>T	CCDS1285.1																																																																																				0.378	C1orf112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087126.3	NM_018186	
DLG5	9231	broad.mit.edu	37	10	79566617	79566617	+	Silent	SNP	C	C	A			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr10:79566617C>A	ENST00000372391.2	-	26	4871	c.4866G>T	c.(4864-4866)gtG>gtT	p.V1622V	DLG5_ENST00000372388.2_Silent_p.V1282V|DLG5_ENST00000459739.1_5'UTR	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	1622	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				apical protein localization (GO:0045176)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|intracellular signal transduction (GO:0035556)|metanephric collecting duct development (GO:0072205)|midbrain development (GO:0030901)|negative regulation of cell proliferation (GO:0008285)|polarized epithelial cell differentiation (GO:0030859)|protein complex assembly (GO:0006461)|protein localization to adherens junction (GO:0071896)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|zonula adherens assembly (GO:0045186)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cytoskeletal protein binding (GO:0008092)|receptor signaling complex scaffold activity (GO:0030159)			breast(9)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(17)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	60	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)			AGGTGTCATCCACGTAGAGGA	0.572																																						uc001jzk.2																			0				ovary(5)|breast(3)	8						c.(4864-4866)GTG>GTT		discs large homolog 5							154.0	133.0	140.0					10																	79566617		2203	4300	6503	SO:0001819	synonymous_variant	9231				cell-cell adhesion|intracellular signal transduction|negative regulation of cell proliferation|regulation of apoptosis	cell junction|cytoplasm	beta-catenin binding|cytoskeletal protein binding|receptor signaling complex scaffold activity	g.chr10:79566617C>A	U61843	CCDS7353.2	10q23	2008-07-09	2001-11-28		ENSG00000151208	ENSG00000151208			2904	protein-coding gene	gene with protein product		604090	"""discs, large (Drosophila) homolog 5"""			9738934	Standard	XM_005270276		Approved	P-dlg, KIAA0583	uc001jzk.3	Q8TDM6	OTTHUMG00000018548	ENST00000372391.2:c.4866G>T	10.37:g.79566617C>A						DLG5_uc001jzi.2_Silent_p.V377V|DLG5_uc001jzj.2_Silent_p.V1037V|DLG5_uc009xru.1_RNA	p.V1622V	NM_004747	NP_004738	Q8TDM6	DLG5_HUMAN	Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)		26	4936	-	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		1622			SH3.		A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Silent	SNP	ENST00000372391.2	37	c.4866G>T	CCDS7353.2																																																																																				0.572	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2		
OR8H2	390151	broad.mit.edu	37	11	55873242	55873242	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr11:55873242G>A	ENST00000313503.1	+	1	724	c.724G>A	c.(724-726)Gtc>Atc	p.V242I		NM_001005200.1	NP_001005200.1	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H, member 2	242						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V242I(1)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(38)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	61	Esophageal squamous(21;0.00693)					CTCTACTTGCGTCTCTCATCT	0.383										HNSCC(53;0.14)																												uc010riy.1																			1	Substitution - Missense(1)		large_intestine(1)	ovary(1)|skin(1)	2						c.(724-726)GTC>ATC		olfactory receptor, family 8, subfamily H,							104.0	101.0	102.0					11																	55873242		2201	4296	6497	SO:0001583	missense	390151				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:55873242G>A	AB065657	CCDS31518.1	11q11	2012-08-09			ENSG00000181767	ENSG00000181767		"""GPCR / Class A : Olfactory receptors"""	15308	protein-coding gene	gene with protein product							Standard	NM_001005200		Approved		uc010riy.2	Q8N162	OTTHUMG00000166832	ENST00000313503.1:c.724G>A	11.37:g.55873242G>A	ENSP00000323982:p.Val242Ile	HNSCC(53;0.14)					p.V242I	NM_001005200	NP_001005200	Q8N162	OR8H2_HUMAN			1	724	+	Esophageal squamous(21;0.00693)		242			Helical; Name=6; (Potential).		Q6IFC1	Missense_Mutation	SNP	ENST00000313503.1	37	c.724G>A	CCDS31518.1	.	.	.	.	.	.	.	.	.	.	g	3.023	-0.201304	0.06219	.	.	ENSG00000181767	ENST00000313503	T	0.37584	1.19	3.35	1.37	0.22104	GPCR, rhodopsin-like superfamily (1);	0.382752	0.22692	N	0.056807	T	0.18882	0.0453	N	0.17838	0.53	0.09310	N	1	B	0.30526	0.283	B	0.29862	0.108	T	0.14952	-1.0454	10	0.72032	D	0.01	.	2.714	0.05182	0.1709:0.1414:0.5425:0.1452	.	242	Q8N162	OR8H2_HUMAN	I	242	ENSP00000323982:V242I	ENSP00000323982:V242I	V	+	1	0	OR8H2	55629818	0.000000	0.05858	0.341000	0.25589	0.081000	0.17604	-1.608000	0.02068	0.170000	0.19704	-0.908000	0.02827	GTC		0.383	OR8H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391540.1	NM_001005200	
GLYATL2	219970	broad.mit.edu	37	11	58602091	58602091	+	Silent	SNP	G	G	A			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr11:58602091G>A	ENST00000287275.1	-	6	1086	c.696C>T	c.(694-696)taC>taT	p.Y232Y	GLYATL2_ENST00000533636.1_5'Flank|GLYATL2_ENST00000532258.1_Silent_p.Y232Y	NM_145016.3	NP_659453.3	Q8WU03	GLYL2_HUMAN	glycine-N-acyltransferase-like 2	232						endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)			breast(1)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	23		Breast(21;0.0044)|all_epithelial(135;0.0216)			Glycine(DB00145)	CTTGGTGTCTGTATTTGGGGA	0.413																																						uc001nnd.3																			0				ovary(1)|skin(1)	2						c.(694-696)TAC>TAT		glycine-N-acyltransferase-like 2	Glycine(DB00145)						102.0	102.0	102.0					11																	58602091		2068	4216	6284	SO:0001819	synonymous_variant	219970					mitochondrion	glycine N-acyltransferase activity	g.chr11:58602091G>A	AF426250	CCDS41649.1	11q12.1	2008-02-05				ENSG00000156689			24178	protein-coding gene	gene with protein product		614762				12477932	Standard	NM_145016		Approved	BXMAS2-10, MGC24009	uc001nnd.4	Q8WU03		ENST00000287275.1:c.696C>T	11.37:g.58602091G>A						GLYATL2_uc009ymq.2_Silent_p.Y232Y	p.Y232Y	NM_145016	NP_659453	Q8WU03	GLYL2_HUMAN			6	827	-		Breast(21;0.0044)|all_epithelial(135;0.0216)	232					A5LGC7|Q86WC3|Q96AT2	Silent	SNP	ENST00000287275.1	37	c.696C>T	CCDS41649.1																																																																																				0.413	GLYATL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394599.1	NM_145016	
CTTN	2017	broad.mit.edu	37	11	70279266	70279266	+	Silent	SNP	G	G	A			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr11:70279266G>A	ENST00000301843.8	+	16	1532	c.1326G>A	c.(1324-1326)ccG>ccA	p.P442P	CTTN_ENST00000376561.3_Silent_p.P405P|CTTN_ENST00000346329.3_Silent_p.P405P|CTTN_ENST00000538675.1_Silent_p.P126P	NM_005231.3	NP_005222.2	Q14247	SRC8_HUMAN	cortactin	442					negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|mitotic spindle midzone (GO:1990023)|ruffle (GO:0001726)				breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	31			BRCA - Breast invasive adenocarcinoma(2;4.34e-41)|LUSC - Lung squamous cell carcinoma(11;1.51e-13)|STAD - Stomach adenocarcinoma(18;0.0513)	Lung(977;0.0234)|LUSC - Lung squamous cell carcinoma(976;0.133)		GGACGGAGCCGGAGCCCGTGT	0.652																																						uc001opv.3																			0				ovary(1)	1						c.(1324-1326)CCG>CCA		cortactin isoform a							48.0	50.0	49.0					11																	70279266		2200	4294	6494	SO:0001819	synonymous_variant	2017					cell cortex|cytoskeleton|lamellipodium|ruffle|soluble fraction	protein binding	g.chr11:70279266G>A	AJ288897	CCDS8197.1, CCDS41680.1, CCDS53676.1	11q13	2008-02-05	2004-06-08	2004-06-09	ENSG00000085733	ENSG00000085733			3338	protein-coding gene	gene with protein product		164765	"""ems1 sequence (mammary tumor and squamous cell carcinoma-associated (p80/85 src substrate)"""	EMS1		7685625	Standard	NM_005231		Approved		uc001opu.3	Q14247	OTTHUMG00000134307	ENST00000301843.8:c.1326G>A	11.37:g.70279266G>A						CTTN_uc001opu.2_Silent_p.P405P|CTTN_uc001opw.3_Silent_p.P405P|CTTN_uc010rqm.1_Silent_p.P126P|CTTN_uc001opx.2_Silent_p.P126P	p.P442P	NM_005231	NP_005222	Q14247	SRC8_HUMAN	BRCA - Breast invasive adenocarcinoma(2;4.34e-41)|LUSC - Lung squamous cell carcinoma(11;1.51e-13)|STAD - Stomach adenocarcinoma(18;0.0513)	Lung(977;0.0234)|LUSC - Lung squamous cell carcinoma(976;0.133)	16	1532	+			442					Q8N707|Q96H99	Silent	SNP	ENST00000301843.8	37	c.1326G>A	CCDS41680.1																																																																																				0.652	CTTN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259233.2	NM_138565	
DYNC2H1	79659	broad.mit.edu	37	11	103014114	103014114	+	Nonsense_Mutation	SNP	C	C	T			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr11:103014114C>T	ENST00000375735.2	+	18	2836	c.2692C>T	c.(2692-2694)Cga>Tga	p.R898*	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Nonsense_Mutation_p.R898*	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	898	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)			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)		AGAAGTAGAACGACTTCCAAG	0.363																																						uc001pho.2																			0					0						c.(2692-2694)CGA>TGA		dynein, cytoplasmic 2, heavy chain 1							73.0	72.0	72.0					11																	103014114		1844	4086	5930	SO:0001587	stop_gained	79659				cell projection organization|Golgi organization|microtubule-based movement|multicellular organismal development	cilium axoneme|dynein complex|Golgi apparatus|microtubule|plasma membrane	ATP binding|ATPase activity|microtubule motor activity	g.chr11:103014114C>T	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.2692C>T	11.37:g.103014114C>T	ENSP00000364887:p.Arg898*					DYNC2H1_uc001phn.1_Nonsense_Mutation_p.R898*|DYNC2H1_uc009yxe.1_Intron	p.R898*	NM_001080463	NP_001073932	Q8NCM8	DYHC2_HUMAN		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)	18	2836	+		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)	898			Stem (By similarity).		O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Nonsense_Mutation	SNP	ENST00000375735.2	37	c.2692C>T	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	C	41	8.921098	0.99004	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	.	.	.	5.35	5.35	0.76521	.	0.599767	0.13264	U	0.401078	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07482	T	0.82	.	19.0679	0.93119	0.0:1.0:0.0:0.0	.	.	.	.	X	898	.	ENSP00000364887:R898X	R	+	1	2	DYNC2H1	102519324	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.540000	0.67205	2.525000	0.85131	0.460000	0.39030	CGA		0.363	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
BCL2L14	79370	broad.mit.edu	37	12	12232401	12232401	+	Silent	SNP	C	C	T			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr12:12232401C>T	ENST00000308721.5	+	2	368	c.162C>T	c.(160-162)tcC>tcT	p.S54S	BCL2L14_ENST00000586576.1_Silent_p.S87S|BCL2L14_ENST00000266434.4_Silent_p.S54S|BCL2L14_ENST00000396367.1_Silent_p.S54S|BCL2L14_ENST00000589718.1_Silent_p.S54S|BCL2L14_ENST00000396369.1_Silent_p.S54S	NM_138723.1	NP_620049.1	Q9BZR8	B2L14_HUMAN	BCL2-like 14 (apoptosis facilitator)	54					apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular organelle (GO:0043229)|membrane (GO:0016020)	protein kinase binding (GO:0019901)	p.S54S(1)		large_intestine(1)|lung(2)|skin(3)	6		Prostate(47;0.0872)		BRCA - Breast invasive adenocarcinoma(232;0.154)		GAAGTTTGTCCCAGAGGGGCC	0.488																																						uc001rac.2																			1	Substitution - coding silent(1)	p.S54S(1)	skin(1)	skin(1)	1						c.(160-162)TCC>TCT		BCL2-like 14 isoform 1							54.0	54.0	54.0					12																	12232401		2203	4300	6503	SO:0001819	synonymous_variant	79370				apoptosis|regulation of apoptosis	cytosol|endomembrane system|intracellular organelle|membrane	protein binding	g.chr12:12232401C>T	AF281254	CCDS8645.1, CCDS8646.1	12p13-p12	2014-03-07			ENSG00000121380	ENSG00000121380			16657	protein-coding gene	gene with protein product		606126				11054413	Standard	NM_030766		Approved	BCLG, BCL-G	uc001rac.3	Q9BZR8	OTTHUMG00000159528	ENST00000308721.5:c.162C>T	12.37:g.12232401C>T						ETV6_uc001raa.1_Intron|BCL2L14_uc001raf.1_RNA|BCL2L14_uc001rad.2_Silent_p.S54S|BCL2L14_uc001rae.2_Silent_p.S54S	p.S54S	NM_138723	NP_620049	Q9BZR8	B2L14_HUMAN		BRCA - Breast invasive adenocarcinoma(232;0.154)	2	363	+		Prostate(47;0.0872)	54					A8KAD0|Q96QR5|Q9BZR7	Silent	SNP	ENST00000308721.5	37	c.162C>T	CCDS8645.1																																																																																				0.488	BCL2L14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355994.3	NM_030766	
LIMA1	51474	broad.mit.edu	37	12	50575756	50575756	+	Missense_Mutation	SNP	C	C	T	rs200141288		TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr12:50575756C>T	ENST00000341247.4	-	10	1354	c.1205G>A	c.(1204-1206)cGt>cAt	p.R402H	LIMA1_ENST00000552491.1_Missense_Mutation_p.R99H|LIMA1_ENST00000552909.1_Missense_Mutation_p.R241H|LIMA1_ENST00000552783.1_Missense_Mutation_p.R243H|LIMA1_ENST00000394943.3_Missense_Mutation_p.R403H|LIMA1_ENST00000552823.1_Missense_Mutation_p.R242H|LIMA1_ENST00000547825.1_Missense_Mutation_p.R100H	NM_001113546.1|NM_016357.4	NP_001107018.1|NP_057441.1	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1	402	LIM zinc-binding. {ECO:0000255|PROSITE- ProRule:PRU00125}.				actin filament bundle assembly (GO:0051017)|negative regulation of actin filament depolymerization (GO:0030835)|ruffle organization (GO:0031529)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(2)	44						GGCCAAGAGACGCTCCATTGG	0.473																																						uc001rwj.3																			0				ovary(1)	1						c.(1204-1206)CGT>CAT		LIM domain and actin binding 1 isoform b		C	HIS/ARG,HIS/ARG,HIS/ARG	0,4406		0,0,2203	109.0	99.0	102.0		1208,728,1205	5.5	1.0	12		102	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense	LIMA1	NM_001113546.1,NM_001113547.1,NM_016357.4	29,29,29	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging,probably-damaging,probably-damaging	403/761,243/601,402/760	50575756	2,13004	2203	4300	6503	SO:0001583	missense	51474				actin filament bundle assembly|negative regulation of actin filament depolymerization|ruffle organization	cytoplasm|focal adhesion|stress fiber	actin filament binding|actin monomer binding|zinc ion binding	g.chr12:50575756C>T	AF198454	CCDS8802.1, CCDS44877.1, CCDS55826.1, CCDS58230.1	12q13.12	2006-04-12				ENSG00000050405			24636	protein-coding gene	gene with protein product	"""epithelial protein lost in neoplasm beta"""	608364				10806352, 10618726, 12566430	Standard	NM_016357		Approved	EPLIN	uc001rwk.4	Q9UHB6		ENST00000341247.4:c.1205G>A	12.37:g.50575756C>T	ENSP00000340184:p.Arg402His					LIMA1_uc001rwg.3_Missense_Mutation_p.R100H|LIMA1_uc001rwh.3_Missense_Mutation_p.R241H|LIMA1_uc001rwi.3_Missense_Mutation_p.R243H|LIMA1_uc001rwk.3_Missense_Mutation_p.R403H|LIMA1_uc010smr.1_RNA|LIMA1_uc010sms.1_RNA	p.R402H	NM_016357	NP_057441	Q9UHB6	LIMA1_HUMAN			10	1379	-			402			LIM zinc-binding.		B2RB09|Q2TAN7|Q59FE8|Q9BVF2|Q9H8J1|Q9HBN5|Q9NX96|Q9NXC3|Q9NXU6|Q9P0H8|Q9UHB5	Missense_Mutation	SNP	ENST00000341247.4	37	c.1205G>A	CCDS8802.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.004126	0.93287	0.0	2.33E-4	ENSG00000050405	ENST00000552491;ENST00000547825;ENST00000552823;ENST00000394943;ENST00000341247;ENST00000552783;ENST00000552909;ENST00000420992	D;D;D;D;D;D;D	0.87729	-2.29;-2.29;-2.29;-2.29;-2.29;-2.29;-2.29	5.49	5.49	0.81192	Zinc finger, LIM-type (5);	0.099034	0.64402	D	0.000002	D	0.94823	0.8328	M	0.88031	2.925	0.48236	D	0.999615	D;D;D	0.89917	0.989;1.0;0.976	P;D;P	0.91635	0.777;0.999;0.868	D	0.95082	0.8214	10	0.72032	D	0.01	.	19.7347	0.96198	0.0:1.0:0.0:0.0	.	412;402;241	Q59FE8;Q9UHB6;F8VQE1	.;LIMA1_HUMAN;.	H	99;100;242;403;402;243;241;321	ENSP00000448463:R99H;ENSP00000448706:R100H;ENSP00000450266:R242H;ENSP00000378400:R403H;ENSP00000340184:R402H;ENSP00000448779:R243H;ENSP00000450087:R241H	ENSP00000340184:R402H	R	-	2	0	LIMA1	48862023	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	3.716000	0.54904	2.746000	0.94184	0.655000	0.94253	CGT		0.473	LIMA1-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406235.2	NM_016357	
DGKA	1606	broad.mit.edu	37	12	56330335	56330335	+	Silent	SNP	G	G	A			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr12:56330335G>A	ENST00000331886.5	+	2	502	c.48G>A	c.(46-48)ctG>ctA	p.L16L	DGKA_ENST00000394147.1_Silent_p.L16L|DGKA_ENST00000551156.1_Silent_p.L16L	NM_001345.4	NP_001336.2	P23743	DGKA_HUMAN	diacylglycerol kinase, alpha 80kDa	16					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)|phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|large_intestine(1)|lung(11)|ovary(4)|pancreas(1)|skin(3)|urinary_tract(1)	25					Vitamin E(DB00163)	TTGCCCAGCTGCAAAAATACA	0.527																																						uc001sij.2																			0				ovary(3)|pancreas(1)	4						c.(46-48)CTG>CTA		diacylglycerol kinase, alpha 80kDa	Vitamin E(DB00163)						88.0	81.0	83.0					12																	56330335		2203	4300	6503	SO:0001819	synonymous_variant	1606				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity	g.chr12:56330335G>A	AF064767	CCDS8896.1	12q13.3	2013-01-10	2002-08-29			ENSG00000065357	2.7.1.107	"""EF-hand domain containing"""	2849	protein-coding gene	gene with protein product		125855	"""diacylglycerol kinase, alpha (80kD)"""	DAGK, DAGK1		8180475, 7959783	Standard	NM_001345		Approved	DGK-alpha	uc001sim.3	P23743		ENST00000331886.5:c.48G>A	12.37:g.56330335G>A						DGKA_uc009zoc.1_Silent_p.L16L|DGKA_uc001sih.1_5'UTR|DGKA_uc001sii.1_5'UTR|DGKA_uc009zod.1_Silent_p.L16L|DGKA_uc009zoe.1_Silent_p.L16L|DGKA_uc001sik.2_Silent_p.L16L|DGKA_uc001sil.2_Silent_p.L16L|DGKA_uc001sim.2_Silent_p.L16L|DGKA_uc001sin.2_Silent_p.L16L|DGKA_uc009zof.2_5'UTR|DGKA_uc001sio.2_5'UTR	p.L16L	NM_001345	NP_001336	P23743	DGKA_HUMAN			2	312	+			16					O75481|O75482|O75483|O95217|Q3ZE25|Q8IZ56|Q8N5Q2	Silent	SNP	ENST00000331886.5	37	c.48G>A	CCDS8896.1																																																																																				0.527	DGKA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407291.1		
FREM2	341640	broad.mit.edu	37	13	39266205	39266205	+	Missense_Mutation	SNP	T	T	G			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr13:39266205T>G	ENST00000280481.7	+	1	4940	c.4724T>G	c.(4723-4725)gTg>gGg	p.V1575G		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1575					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		ATCACCCAGGTGCCTATTCAT	0.418																																						uc001uwv.2																			0				ovary(7)|pancreas(1)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	11						c.(4723-4725)GTG>GGG		FRAS1-related extracellular matrix protein 2							105.0	104.0	105.0					13																	39266205		2203	4300	6503	SO:0001583	missense	341640				cell communication|homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding	g.chr13:39266205T>G	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.4724T>G	13.37:g.39266205T>G	ENSP00000280481:p.Val1575Gly						p.V1575G	NM_207361	NP_997244	Q5SZK8	FREM2_HUMAN		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)	1	5033	+		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)	1575			Extracellular (Potential).|CSPG 11.		Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	c.4724T>G	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	T	6.471	0.455065	0.12283	.	.	ENSG00000150893	ENST00000280481	T	0.29655	1.56	6.07	2.17	0.27698	.	0.484255	0.23644	N	0.046000	T	0.17365	0.0417	N	0.25060	0.705	0.80722	D	1	B	0.06786	0.001	B	0.10450	0.005	T	0.06409	-1.0828	10	0.27082	T	0.32	.	6.8638	0.24082	0.0:0.1324:0.1273:0.7403	.	1575	Q5SZK8	FREM2_HUMAN	G	1575	ENSP00000280481:V1575G	ENSP00000280481:V1575G	V	+	2	0	FREM2	38164205	1.000000	0.71417	0.946000	0.38457	0.958000	0.62258	3.473000	0.53122	0.542000	0.28846	0.528000	0.53228	GTG		0.418	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
CHD8	57680	broad.mit.edu	37	14	21871325	21871325	+	Nonsense_Mutation	SNP	G	G	A			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr14:21871325G>A	ENST00000557364.1	-	18	3828	c.3565C>T	c.(3565-3567)Cag>Tag	p.Q1189*	CHD8_ENST00000430710.3_Nonsense_Mutation_p.Q910*|CHD8_ENST00000399982.2_Nonsense_Mutation_p.Q1189*|CHD8_ENST00000555962.1_Intron			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	1189	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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)			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)		ATGGCAGCCTGTCGAAGGTTG	0.478																																						uc001was.1																			0				ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1)	10						c.(2728-2730)CAG>TAG		chromodomain helicase DNA binding protein 8							64.0	68.0	67.0					14																	21871325		2076	4223	6299	SO:0001587	stop_gained	57680				ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	MLL1 complex	ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding	g.chr14:21871325G>A	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.3565C>T	14.37:g.21871325G>A	ENSP00000451601:p.Gln1189*					CHD8_uc001war.1_Nonsense_Mutation_p.Q806*|CHD8_uc001wav.1_Nonsense_Mutation_p.Q352*	p.Q910*	NM_020920	NP_065971	Q9HCK8	CHD8_HUMAN	Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)	18	2822	-	all_cancers(95;0.00121)		1189			Helicase C-terminal.		Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Nonsense_Mutation	SNP	ENST00000557364.1	37	c.2728C>T	CCDS53885.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	34|34	5.409255|5.409255	0.96072|0.96072	.|.	.|.	ENSG00000100888|ENSG00000100888	ENST00000430710;ENST00000399982;ENST00000262707;ENST00000557364|ENST00000555935	.|.	.|.	.|.	5.32|5.32	5.32|5.32	0.75619|0.75619	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.74061	.|0.3667	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.72157	.|-0.4375	.|3	0.46703|.	T|.	0.11|.	-19.5637|-19.5637	17.9328|17.9328	0.89004|0.89004	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|I	910;1189;909;1189|414	.|.	ENSP00000262707:Q909X|.	Q|T	-|-	1|2	0|0	CHD8|CHD8	20941165|20941165	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	9.654000|9.654000	0.98509|0.98509	2.767000|2.767000	0.95098|0.95098	0.655000|0.655000	0.94253|0.94253	CAG|ACA		0.478	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920	
LRFN5	145581	broad.mit.edu	37	14	42360496	42360496	+	Missense_Mutation	SNP	G	G	C			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr14:42360496G>C	ENST00000298119.4	+	4	2618	c.1429G>C	c.(1429-1431)Gct>Cct	p.A477P	LRFN5_ENST00000554171.1_Intron|LRFN5_ENST00000554120.1_Intron	NM_152447.3	NP_689660.2	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III domain containing 5	477	Fibronectin type-III.					integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(67)|ovary(5)|pancreas(3)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(2)	120			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		CAATAATCTGGCTGCTGGAAC	0.403										HNSCC(30;0.082)																												uc001wvm.2																			0				ovary(5)|pancreas(2)|central_nervous_system(1)	8						c.(1429-1431)GCT>CCT		leucine rich repeat and fibronectin type III							161.0	128.0	139.0					14																	42360496		2203	4300	6503	SO:0001583	missense	145581					integral to membrane		g.chr14:42360496G>C	AK055365	CCDS9678.1	14q21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000165379	ENSG00000165379		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	20360	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 8"""	612811	"""chromosome 14 open reading frame 146"""	C14orf146		16828986	Standard	NM_152447		Approved	FIGLER8, SALM5	uc001wvm.3	Q96NI6	OTTHUMG00000140261	ENST00000298119.4:c.1429G>C	14.37:g.42360496G>C	ENSP00000298119:p.Ala477Pro	HNSCC(30;0.082)				LRFN5_uc010ana.2_Intron	p.A477P	NM_152447	NP_689660	Q96NI6	LRFN5_HUMAN	LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)	4	2627	+			477			Extracellular (Potential).|Fibronectin type-III.		B3KU78|Q86XL2	Missense_Mutation	SNP	ENST00000298119.4	37	c.1429G>C	CCDS9678.1	.	.	.	.	.	.	.	.	.	.	G	19.76	3.886881	0.72410	.	.	ENSG00000165379	ENST00000298119	T	0.69040	-0.37	5.88	5.88	0.94601	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.000000	0.53938	D	0.000046	T	0.79575	0.4469	M	0.62723	1.935	0.80722	D	1	D	0.69078	0.997	D	0.68943	0.961	T	0.77784	-0.2458	10	0.44086	T	0.13	.	17.7319	0.88380	0.0:0.0:1.0:0.0	.	477	Q96NI6	LRFN5_HUMAN	P	477	ENSP00000298119:A477P	ENSP00000298119:A477P	A	+	1	0	LRFN5	41430246	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.876000	0.87215	2.779000	0.95612	0.650000	0.86243	GCT		0.403	LRFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276786.1	NM_152447	
IL32	9235	broad.mit.edu	37	16	3119304	3119305	+	Frame_Shift_Ins	INS	-	-	G	rs398100042|rs2981599		TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr16:3119304_3119305insG	ENST00000534507.1	+	6	864_865	c.653_654insG	c.(652-657)gacaagfs	p.DK218fs	IL32_ENST00000444393.3_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000548652.1_Frame_Shift_Ins_p.DK163fs|IL32_ENST00000533097.2_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000552936.1_Frame_Shift_Ins_p.DK196fs|IL32_ENST00000548246.1_Frame_Shift_Ins_p.DK132fs|IL32_ENST00000440815.3_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000531965.1_Frame_Shift_Ins_p.DK162fs|IL32_ENST00000530890.1_Frame_Shift_Ins_p.DK152fs|IL32_ENST00000008180.9_Frame_Shift_Ins_p.DK152fs|RNU1-125P_ENST00000516752.1_RNA|IL32_ENST00000528163.2_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000526464.2_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000525643.2_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000325568.5_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000382213.3_Frame_Shift_Ins_p.DK163fs|IL32_ENST00000529699.1_Frame_Shift_Ins_p.DK152fs|IL32_ENST00000552356.1_Frame_Shift_Ins_p.DK152fs|IL32_ENST00000552664.1_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000530538.2_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000396887.3_Frame_Shift_Ins_p.DK115fs|IL32_ENST00000548476.1_Frame_Shift_Ins_p.DK218fs|IL32_ENST00000551513.1_Frame_Shift_Ins_p.DK209fs|IL32_ENST00000529550.1_Frame_Shift_Ins_p.DK172fs|IL32_ENST00000549213.1_Frame_Shift_Ins_p.DK115fs|IL32_ENST00000396890.2_Frame_Shift_Ins_p.DK218fs|IL32_ENST00000551122.1_Frame_Shift_Ins_p.DK115fs			P24001	IL32_HUMAN	interleukin 32	218					cell adhesion (GO:0007155)|defense response (GO:0006952)|immune response (GO:0006955)	extracellular space (GO:0005615)|membrane (GO:0016020)				breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	15						CCACGGGGGGACAAGGAGGAGC	0.574																																						uc002cto.2																			0				pancreas(1)	1						c.(652-654)GACfs		interleukin 32 isoform B																																				SO:0001589	frameshift_variant	9235				cell adhesion|defense response|immune response	extracellular space	cytokine activity	g.chr16:3119304_3119305insG	M59807	CCDS32377.1, CCDS32378.1, CCDS32379.1, CCDS45394.1	16p13.3	2011-07-21			ENSG00000008517	ENSG00000008517		"""Interleukins and interleukin receptors"""	16830	protein-coding gene	gene with protein product	"""natural killer cell transcript 4"""	606001				1729377, 9653642	Standard	XM_005255686		Approved	NK4, TAIF, TAIFb, TAIFd	uc002ctn.3	P24001	OTTHUMG00000167498	Exception_encountered	16.37:g.3119304_3119305insG	ENSP00000431775:p.Asp218fs					IL32_uc002ctk.2_Frame_Shift_Ins_p.D115fs|IL32_uc010uwp.1_Frame_Shift_Ins_p.D152fs|IL32_uc010btb.2_Frame_Shift_Ins_p.D162fs|IL32_uc002ctl.2_Frame_Shift_Ins_p.D172fs|IL32_uc002ctm.2_Frame_Shift_Ins_p.D172fs|IL32_uc002ctn.2_Frame_Shift_Ins_p.D172fs|IL32_uc002cts.3_Frame_Shift_Ins_p.D172fs|IL32_uc002ctp.2_Frame_Shift_Ins_p.D152fs|IL32_uc002ctq.2_Frame_Shift_Ins_p.D218fs|IL32_uc002ctr.2_Frame_Shift_Ins_p.D152fs|IL32_uc002ctt.2_Frame_Shift_Ins_p.D172fs|IL32_uc010uwr.1_Frame_Shift_Ins_p.D132fs|IL32_uc002ctu.2_Frame_Shift_Ins_p.D163fs	p.D218fs	NM_004221	NP_004212	P24001	IL32_HUMAN			6	864_865	+			218					A6NNM0|A8MPX0|B4DJM1|B8Q191|D3DUB0|D3DUB2|Q5VFH7|Q5VFH8|Q8WV38|Q96GK9	Frame_Shift_Ins	INS	ENST00000534507.1	37	c.653_654insG																																																																																					0.574	IL32-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000394812.2	NM_004221	
ZNF263	10127	broad.mit.edu	37	16	3339555	3339555	+	Missense_Mutation	SNP	A	A	G			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr16:3339555A>G	ENST00000219069.5	+	6	1925	c.1049A>G	c.(1048-1050)gAg>gGg	p.E350G	ZNF263_ENST00000574253.1_Missense_Mutation_p.R184G|ZNF263_ENST00000538765.1_5'UTR	NM_005741.4	NP_005732.2	O14978	ZN263_HUMAN	zinc finger protein 263	350					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)|skin(4)|urinary_tract(3)	20						CCTCCCCCAGAGGGTGGAATG	0.617																																						uc002cuq.2																			0				skin(3)|ovary(1)	4						c.(1048-1050)GAG>GGG		zinc finger protein 263							38.0	40.0	40.0					16																	3339555		2197	4300	6497	SO:0001583	missense	10127				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr16:3339555A>G	AC004232	CCDS10499.1	16p13.3	2013-01-09			ENSG00000006194	ENSG00000006194		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13056	protein-coding gene	gene with protein product		604191				9256059	Standard	NM_005741		Approved	FPM315, ZKSCAN12, ZSCAN44	uc002cuq.3	O14978	OTTHUMG00000129323	ENST00000219069.5:c.1049A>G	16.37:g.3339555A>G	ENSP00000219069:p.Glu350Gly					ZNF263_uc010uww.1_5'UTR|ZNF263_uc002cur.2_5'UTR	p.E350G	NM_005741	NP_005732	O14978	ZN263_HUMAN			6	1381	+			350					B2R634|O43387|Q96H95	Missense_Mutation	SNP	ENST00000219069.5	37	c.1049A>G	CCDS10499.1	.	.	.	.	.	.	.	.	.	.	A	9.047	0.991034	0.18966	.	.	ENSG00000006194	ENST00000219069	T	0.05382	3.45	5.49	5.49	0.81192	.	0.115595	0.39210	N	0.001430	T	0.03434	0.0099	N	0.08118	0	0.09310	N	1	P	0.39665	0.682	B	0.32864	0.154	T	0.48234	-0.9053	10	0.28530	T	0.3	.	13.5962	0.61991	1.0:0.0:0.0:0.0	.	350	O14978	ZN263_HUMAN	G	350	ENSP00000219069:E350G	ENSP00000219069:E350G	E	+	2	0	ZNF263	3279556	0.000000	0.05858	0.982000	0.44146	0.094000	0.18550	0.024000	0.13555	2.311000	0.77944	0.533000	0.62120	GAG		0.617	ZNF263-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251463.2		
ADCY9	115	broad.mit.edu	37	16	4016471	4016471	+	Missense_Mutation	SNP	C	C	T			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr16:4016471C>T	ENST00000294016.3	-	11	3905	c.3367G>A	c.(3367-3369)Gcg>Acg	p.A1123T		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	1123	Guanylate cyclase 2. {ECO:0000255|PROSITE-ProRule:PRU00099}.				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)			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						TGGGCCTGCGCGGTGTTCAGC	0.602																																						uc002cvx.2																			0				ovary(4)|large_intestine(1)|central_nervous_system(1)	6						c.(3367-3369)GCG>ACG		adenylate cyclase 9							83.0	71.0	75.0					16																	4016471		2197	4300	6497	SO:0001583	missense	115				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding	g.chr16:4016471C>T	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.3367G>A	16.37:g.4016471C>T	ENSP00000294016:p.Ala1123Thr						p.A1123T	NM_001116	NP_001107	O60503	ADCY9_HUMAN			11	3906	-			1123			Guanylate cyclase 2.|Cytoplasmic (Potential).		A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Missense_Mutation	SNP	ENST00000294016.3	37	c.3367G>A	CCDS32382.1	.	.	.	.	.	.	.	.	.	.	C	7.287	0.610271	0.14066	.	.	ENSG00000162104	ENST00000294016	T	0.30182	1.54	5.52	-1.4	0.08968	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.331667	0.37053	N	0.002268	T	0.09686	0.0238	N	0.10945	0.07	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.19160	-1.0314	10	0.09843	T	0.71	.	1.6337	0.02737	0.3895:0.3143:0.0975:0.1987	.	1123	O60503	ADCY9_HUMAN	T	1123	ENSP00000294016:A1123T	ENSP00000294016:A1123T	A	-	1	0	ADCY9	3956472	0.944000	0.32072	0.022000	0.16811	0.860000	0.49131	1.833000	0.39161	0.018000	0.15052	-0.181000	0.13052	GCG		0.602	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1		
RRN3P1	730092	broad.mit.edu	37	16	21817457	21817457	+	RNA	SNP	G	G	A	rs202140854	byFrequency	TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr16:21817457G>A	ENST00000546471.1	-	0	1601							Q2M238	RN3P1_HUMAN	RNA polymerase I transcription factor homolog (S. cerevisiae) pseudogene 1																		CTTACATCCAGCTTGAGTAGT	0.259																																						uc010vbl.1																			0					0						c.(106-108)CTG>TTG		SubName: Full=Putative uncharacterized protein ENSP00000219758;																																						730092							g.chr16:21817457G>A			16p12.2	2012-10-16			ENSG00000248124	ENSG00000248124			30548	pseudogene	pseudogene						12477932	Standard	NR_003370		Approved		uc010vbl.1	Q2M238	OTTHUMG00000170417		16.37:g.21817457G>A						uc002diq.3_Intron	p.L36L	NR_003370						7	603	-								A8K6T4|B3KWX9|O75704	Silent	SNP	ENST00000546471.1	37	c.106C>T																																																																																					0.259	RRN3P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000409035.1	NR_003370	
TERF2IP	54386	broad.mit.edu	37	16	75690204	75690206	+	In_Frame_Del	DEL	GAA	GAA	-			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr16:75690204_75690206delGAA	ENST00000300086.4	+	3	992_994	c.895_897delGAA	c.(895-897)gaadel	p.E304del		NM_018975.3	NP_061848.2	Q9NYB0	TE2IP_HUMAN	telomeric repeat binding factor 2, interacting protein	304	Asp/Glu-rich (acidic).				negative regulation of DNA recombination at telomere (GO:0048239)|negative regulation of telomere maintenance (GO:0032205)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protection from non-homologous end joining at telomere (GO:0031848)|protein localization to chromosome, telomeric region (GO:0070198)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of transcription, DNA-templated (GO:0006355)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)|telomere maintenance via telomere lengthening (GO:0010833)|transcription, DNA-templated (GO:0006351)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear chromosome (GO:0000228)|nuclear chromosome, telomeric region (GO:0000784)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)	5						TGATgaggaggaagaagaagaag	0.424																																						uc002fet.1																			0				central_nervous_system(1)	1						c.(895-897)GAAdel		telomeric repeat binding factor 2, interacting				1,182,4081		0,0,1,0,182,1949						-3.9	1.0			71	0,377,7877		0,0,0,1,375,3751	no	codingComplex	TERF2IP	NM_018975.3		0,0,1,1,557,5700	A1A1,A1A2,A1R,A2A2,A2R,RR		4.5675,4.2917,4.4736				1,559,11958				SO:0001651	inframe_deletion	54386				negative regulation of DNA recombination at telomere|negative regulation of telomere maintenance|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|protection from non-homologous end joining at telomere|protein localization to chromosome, telomeric region|regulation of double-strand break repair via homologous recombination|telomere maintenance via telomerase|transcription, DNA-dependent	cytoplasm|nuclear telomere cap complex|nucleoplasm	DNA binding|protein binding	g.chr16:75690204_75690206delGAA	AK000669	CCDS32491.1	16q23.1	2012-10-03			ENSG00000166848	ENSG00000166848			19246	protein-coding gene	gene with protein product		605061				10850490	Standard	NM_018975		Approved	RAP1	uc002fet.2	Q9NYB0	OTTHUMG00000177136	ENST00000300086.4:c.895_897delGAA	16.37:g.75690213_75690215delGAA	ENSP00000300086:p.Glu304del						p.E304del	NM_018975	NP_061848	Q9NYB0	TE2IP_HUMAN			3	992_994	+			304			Asp/Glu-rich (acidic).		B4DQN4|Q4W4Y2|Q8WYZ3|Q9NWR2	In_Frame_Del	DEL	ENST00000300086.4	37	c.895_897delGAA	CCDS32491.1																																																																																				0.424	TERF2IP-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000435519.1	NM_018975	
NF1	4763	broad.mit.edu	37	17	29533304	29533304	+	Nonsense_Mutation	SNP	C	C	A			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr17:29533304C>A	ENST00000358273.4	+	12	1690	c.1307C>A	c.(1306-1308)tCg>tAg	p.S436*	NF1_ENST00000356175.3_Nonsense_Mutation_p.S436*|NF1_ENST00000431387.4_Nonsense_Mutation_p.S436*	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	436					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(6)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TATTGTCACTCGGTTGAACTT	0.413			"""D, Mis, N, F, S, O"""		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												uc002hgg.2			yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	D|Mis|N|F|S|O	neurofibromatosis type 1 gene			O		neurofibroma|glioma	neurofibroma|glioma		14	Whole gene deletion(8)|Unknown(6)	p.?(2)	soft_tissue(7)|autonomic_ganglia(3)|central_nervous_system(3)|lung(1)	soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330						c.(1306-1308)TCG>TAG		neurofibromin isoform 1							278.0	250.0	260.0					17																	29533304		2203	4300	6503	SO:0001587	stop_gained	4763	Neurofibromatosis_type_1	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	g.chr17:29533304C>A		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.1307C>A	17.37:g.29533304C>A	ENSP00000351015:p.Ser436*	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)				NF1_uc002hge.1_Nonsense_Mutation_p.S436*|NF1_uc002hgf.1_Nonsense_Mutation_p.S436*|NF1_uc002hgh.2_Nonsense_Mutation_p.S436*|NF1_uc010csn.1_Nonsense_Mutation_p.S296*	p.S436*	NM_001042492	NP_001035957	P21359	NF1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)	12	1640	+		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)	436					O00662|Q14284|Q14930|Q14931|Q9UMK3	Nonsense_Mutation	SNP	ENST00000358273.4	37	c.1307C>A	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	C	32	5.147742	0.94603	.	.	ENSG00000196712	ENST00000431387;ENST00000358273;ENST00000356175;ENST00000456735	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	.	.	.	X	436;436;436;102	.	ENSP00000348498:S436X	S	+	2	0	NF1	26557430	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	7.434000	0.80377	2.941000	0.99782	0.655000	0.94253	TCG		0.413	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267	
CYP4F11	57834	broad.mit.edu	37	19	16034748	16034748	+	De_novo_Start_OutOfFrame	SNP	G	G	A			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr19:16034748G>A	ENST00000591841.1	-	0	954				CYP4F11_ENST00000248041.8_Silent_p.H264H|CYP4F11_ENST00000402119.4_Silent_p.H264H|CYP4F11_ENST00000326742.8_Silent_p.H264H					cytochrome P450, family 4, subfamily F, polypeptide 11											NS(1)|breast(3)|endometrium(4)|large_intestine(2)|lung(11)|ovary(1)|skin(3)	25						CTGTGAAGTCGTGCACCAGGT	0.527																																						uc002nbu.2																			0				ovary(1)	1						c.(790-792)CAC>CAT		cytochrome P450 family 4 subfamily F polypeptide							110.0	106.0	108.0					19																	16034748		2203	4300	6503			57834				inflammatory response|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	aromatase activity|electron carrier activity|heme binding	g.chr19:16034748G>A	AF236085	CCDS12337.1	19p13.1	2011-07-29	2003-01-14		ENSG00000171903	ENSG00000171903		"""Cytochrome P450s"""	13265	protein-coding gene	gene with protein product		611517	"""cytochrome P450, subfamily IVF, polypeptide 11"""			10964514, 9068972	Standard	NM_021187		Approved		uc002nbu.2	Q9HBI6		ENST00000591841.1:c.-184C>T	19.37:g.16034748G>A						CYP4F11_uc010eab.1_Silent_p.H264H|CYP4F11_uc002nbt.2_Silent_p.H264H	p.H264H	NM_001128932	NP_001122404	Q9HBI6	CP4FB_HUMAN			7	828	-			264						Silent	SNP	ENST00000591841.1	37	c.792C>T																																																																																					0.527	CYP4F11-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460384.2	NM_021187	
USE1	55850	broad.mit.edu	37	19	17329200	17329200	+	Splice_Site	SNP	C	C	T			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr19:17329200C>T	ENST00000263897.5	+	6	469	c.422C>T	c.(421-423)aCt>aTt	p.T141I	USE1_ENST00000445667.2_Splice_Site_p.T141I|USE1_ENST00000379776.4_Splice_Site_p.T141I|USE1_ENST00000596136.1_Splice_Site_p.T141I|USE1_ENST00000595101.1_3'UTR	NM_018467.3	NP_060937	Q9NZ43	USE1_HUMAN	unconventional SNARE in the ER 1 homolog (S. cerevisiae)	141					endoplasmic reticulum tubular network organization (GO:0071786)|lysosomal transport (GO:0007041)|protein catabolic process (GO:0030163)|protein transport (GO:0015031)|regulation of ER to Golgi vesicle-mediated transport (GO:0060628)|secretion by cell (GO:0032940)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|lung(3)	6						AGGAAGAGAACGTGAGTGTCT	0.582																																						uc002nfo.2																			0					0						c.(421-423)ACT>ATT		unconventional SNARE in the ER 1 homolog							128.0	135.0	133.0					19																	17329200		2066	4198	6264	SO:0001630	splice_region_variant	55850				lysosomal transport|protein catabolic process|protein transport|secretion by cell|vesicle-mediated transport	endoplasmic reticulum membrane|integral to membrane	protein binding	g.chr19:17329200C>T	AF220052	CCDS46011.1	19p13.11	2007-08-20				ENSG00000053501			30882	protein-coding gene	gene with protein product	"""Q-SNARE"", ""SNARE-like tail-anchored protein 1 homolog (S. cerevisiae)"""	610675				16354670, 15029241	Standard	NM_018467		Approved	p31, SLT1, MDS032	uc002nfo.2	Q9NZ43		ENST00000263897.5:c.422+1C>T	19.37:g.17329200C>T						USE1_uc002nfn.2_3'UTR|USE1_uc010eal.1_Missense_Mutation_p.T141I	p.T141I	NM_018467	NP_060937	Q9NZ43	USE1_HUMAN			6	482	+			141			Cytoplasmic (Potential).		Q8NCK1|Q9BRT4	Missense_Mutation	SNP	ENST00000263897.5	37	c.422C>T	CCDS46011.1	.	.	.	.	.	.	.	.	.	.	C	14.17	2.455973	0.43634	.	.	ENSG00000053501	ENST00000263897;ENST00000445667;ENST00000379776	T;T	0.44083	0.93;0.93	2.58	-4.77	0.03219	.	0.656341	0.14815	N	0.296804	T	0.14013	0.0339	N	0.03608	-0.345	0.24989	N	0.991546	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.08351	-1.0726	10	0.37606	T	0.19	0.6364	4.2591	0.10732	0.0:0.3728:0.2683:0.3589	.	141;141	Q9NZ43-2;Q9NZ43	.;USE1_HUMAN	I	141	ENSP00000263897:T141I;ENSP00000390287:T141I	ENSP00000263897:T141I	T	+	2	0	USE1	17190200	0.176000	0.23096	0.898000	0.35279	0.558000	0.35554	-2.161000	0.01278	-0.948000	0.03668	0.313000	0.20887	ACT;ACT;ACA		0.582	USE1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463295.1	NM_018467	Missense_Mutation
PSG1	5669	broad.mit.edu	37	19	43382389	43382389	+	Missense_Mutation	SNP	C	C	T			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr19:43382389C>T	ENST00000436291.2	-	2	222	c.106G>A	c.(106-108)Gtc>Atc	p.V36I	PSG1_ENST00000244296.2_Missense_Mutation_p.V36I|PSG1_ENST00000601073.1_5'UTR|PSG1_ENST00000595356.1_Missense_Mutation_p.V36I|PSG1_ENST00000595124.1_Missense_Mutation_p.V36I|PSG1_ENST00000312439.6_Missense_Mutation_p.V36I|PSG1_ENST00000403380.3_Missense_Mutation_p.V36I	NM_001184825.1|NM_001184826.1	NP_001171754.1|NP_001171755.1	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	36	Ig-like V-type.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30		Prostate(69;0.00682)				TCAATCGTGACTTGGGCAGTG	0.463																																						uc002ovb.2																			0				ovary(2)	2						c.(106-108)GTC>ATC		pregnancy specific beta-1-glycoprotein 1							145.0	160.0	155.0					19																	43382389		2203	4299	6502	SO:0001583	missense	5669				female pregnancy	extracellular region		g.chr19:43382389C>T		CCDS12612.1, CCDS54275.1, CCDS59392.1, CCDS74380.1	19q13.2	2013-01-29			ENSG00000231924	ENSG00000231924		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9514	protein-coding gene	gene with protein product		176390		PSBG1			Standard	NM_006905		Approved	PSGGA, CD66f, PBG1		P11464	OTTHUMG00000151123	ENST00000436291.2:c.106G>A	19.37:g.43382389C>T	ENSP00000413041:p.Val36Ile					PSG3_uc002ouf.2_Intron|PSG1_uc002oug.1_Missense_Mutation_p.V36I|PSG11_uc002ouw.2_Intron|PSG7_uc002ous.1_Intron|PSG7_uc002out.1_Intron|PSG10_uc002ouv.1_Intron|PSG1_uc002oun.2_RNA|PSG1_uc002our.1_Missense_Mutation_p.V36I|PSG1_uc010eio.1_Missense_Mutation_p.V36I|PSG1_uc002oux.1_5'UTR|PSG1_uc002ouy.1_Missense_Mutation_p.V36I|PSG1_uc002ouz.1_Missense_Mutation_p.V36I|PSG1_uc002ova.1_Missense_Mutation_p.V36I|PSG1_uc002ovc.2_Missense_Mutation_p.V36I|PSG1_uc002ovd.1_Missense_Mutation_p.V36I	p.V36I	NM_006905	NP_008836	P11464	PSG1_HUMAN			2	244	-		Prostate(69;0.00682)	36			Ig-like V-type.		O75236|P11462|P11463|Q15231|Q15241|Q15243|Q16660|Q6ICR4|Q9P1W5|Q9UQ79	Missense_Mutation	SNP	ENST00000436291.2	37	c.106G>A	CCDS54275.1	.	.	.	.	.	.	.	.	.	.	N	10.98	1.505325	0.26949	.	.	ENSG00000231924	ENST00000270059;ENST00000436291;ENST00000403380;ENST00000312439;ENST00000244296	T;T;T;T	0.70749	-0.51;-0.51;-0.51;-0.51	1.64	-3.28	0.05033	Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.79975	0.4539	M	0.76727	2.345	0.09310	N	1	D;B;D;D;P;P;P;D;P	0.89917	1.0;0.328;0.989;0.998;0.869;0.508;0.62;0.994;0.832	D;B;P;D;P;B;B;P;P	0.91635	0.999;0.413;0.796;0.998;0.577;0.237;0.3;0.9;0.525	T	0.71623	-0.4537	9	0.72032	D	0.01	.	9.2011	0.37258	0.0:0.6856:0.3144:0.0	.	36;36;36;36;36;36;36;36;36	O75238;P11464-4;G5E9F7;P11464;Q8NBY8;P11464-3;Q9UPK8;O75237;P11464-2	.;.;.;PSG1_HUMAN;.;.;.;.;.	I	36	ENSP00000413041:V36I;ENSP00000385386:V36I;ENSP00000308970:V36I;ENSP00000244296:V36I	ENSP00000244296:V36I	V	-	1	0	PSG1	48074229	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.920000	0.04013	-0.759000	0.04684	0.184000	0.17185	GTC		0.463	PSG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321426.1		
CACNG6	59285	broad.mit.edu	37	19	54503003	54503003	+	Silent	SNP	A	A	G			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr19:54503003A>G	ENST00000252729.2	+	3	1112	c.522A>G	c.(520-522)ggA>ggG	p.G174G	CACNG6_ENST00000346968.2_Intron|CACNG6_ENST00000352529.1_Intron	NM_145814.1	NP_665813.1	Q9BXT2	CCG6_HUMAN	calcium channel, voltage-dependent, gamma subunit 6	174					calcium ion transport (GO:0006816)	voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.168)		TCCGAGTTGGAGCCGTCTGCT	0.587																																						uc002qct.2																			0				ovary(2)	2						c.(520-522)GGA>GGG		voltage-dependent calcium channel gamma-6							174.0	147.0	156.0					19																	54503003		2203	4300	6503	SO:0001819	synonymous_variant	59285					voltage-gated calcium channel complex	voltage-gated calcium channel activity	g.chr19:54503003A>G	AF288386	CCDS12870.1, CCDS12871.1	19q13.4	2008-05-02			ENSG00000130433	ENSG00000130433		"""Calcium channel subunits"""	13625	protein-coding gene	gene with protein product		606898				11170751	Standard	NM_145814		Approved		uc002qct.3	Q9BXT2	OTTHUMG00000064907	ENST00000252729.2:c.522A>G	19.37:g.54503003A>G						CACNG6_uc002qcu.2_Intron|CACNG6_uc002qcv.2_Intron	p.G174G	NM_145814	NP_665813	Q9BXT2	CCG6_HUMAN		GBM - Glioblastoma multiforme(134;0.168)	3	1112	+	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)		174			Helical; (Potential).			Silent	SNP	ENST00000252729.2	37	c.522A>G	CCDS12870.1																																																																																				0.587	CACNG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139359.1		
LY75	4065	broad.mit.edu	37	2	160755280	160755280	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr2:160755280G>A	ENST00000263636.4	-	2	412	c.385C>T	c.(385-387)Cat>Tat	p.H129Y	LY75-CD302_ENST00000505052.1_Missense_Mutation_p.H129Y|LY75_ENST00000554112.1_Missense_Mutation_p.H129Y|LY75_ENST00000553424.1_Missense_Mutation_p.H129Y|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.H129Y	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	129	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		GCTGTGCCATGTCCATCCTTC	0.522																																						uc002ubc.3																			0					0						c.(385-387)CAT>TAT		lymphocyte antigen 75 precursor							90.0	82.0	84.0					2																	160755280		2203	4300	6503	SO:0001583	missense	4065				endocytosis|immune response|inflammatory response	integral to plasma membrane	receptor activity|sugar binding	g.chr2:160755280G>A	AF011333	CCDS2211.1	2q24	2011-08-30			ENSG00000054219	ENSG00000054219		"""CD molecules"", ""C-type lectin domain containing"""	6729	protein-coding gene	gene with protein product		604524				9553150	Standard	NM_002349		Approved	DEC-205, CLEC13B, CD205		O60449	OTTHUMG00000132025	ENST00000263636.4:c.385C>T	2.37:g.160755280G>A	ENSP00000263636:p.His129Tyr					LY75_uc002ubb.3_Missense_Mutation_p.H129Y|LY75_uc010fos.2_Missense_Mutation_p.H129Y|LY75_uc010fot.1_Missense_Mutation_p.H129Y	p.H129Y	NM_002349	NP_002340	O60449	LY75_HUMAN		COAD - Colon adenocarcinoma(177;0.132)	2	454	-			129			Extracellular (Potential).|Ricin B-type lectin.		O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	c.385C>T	CCDS2211.1	.	.	.	.	.	.	.	.	.	.	G	0.003	-2.450278	0.00175	.	.	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93	5.92	1.62	0.23740	Ricin B-related lectin (1);Ricin B lectin (1);	0.499688	0.15013	N	0.285447	T	0.14657	0.0354	N	0.11201	0.11	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.001	T	0.25222	-1.0138	10	0.02654	T	1	-6.0642	0.3453	0.00340	0.2326:0.2382:0.2775:0.2517	.	129;129;129	O60449-3;O60449;O60449-2	.;LY75_HUMAN;.	Y	129	ENSP00000451511:H129Y;ENSP00000451446:H129Y;ENSP00000263636:H129Y;ENSP00000423463:H129Y;ENSP00000421035:H129Y	ENSP00000423463:H129Y	H	-	1	0	LY75;LY75-CD302	160463526	0.000000	0.05858	0.292000	0.24919	0.008000	0.06430	0.149000	0.16243	0.309000	0.22966	0.655000	0.94253	CAT		0.522	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
SYN3	8224	broad.mit.edu	37	22	32937634	32937634	+	Silent	SNP	G	G	A	rs148217218		TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr22:32937634G>A	ENST00000358763.2	-	8	1082	c.840C>T	c.(838-840)taC>taT	p.Y280Y	SYN3_ENST00000332840.5_Silent_p.Y280Y	NM_001135774.1	NP_001129246.1	O14994	SYN3_HUMAN	synapsin III	280	C; actin-binding and synaptic-vesicle binding.				neurotransmitter secretion (GO:0007269)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33						CGGTGGTGGCGTAGGTTTTGG	0.552																																						uc003amx.2																			0				skin(1)	1						c.(838-840)TAC>TAT		synapsin III isoform IIIa		G	,,	1,4405	2.1+/-5.4	0,1,2202	230.0	171.0	191.0		837,840,840	-4.6	1.0	22	dbSNP_134	191	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	SYN3	NM_001135774.1,NM_003490.3,NM_133633.2	,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,	279/580,280/581,280/445	32937634	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	8224				neurotransmitter secretion	cell junction|synaptic vesicle membrane	ATP binding|ligase activity	g.chr22:32937634G>A	AF046873	CCDS13908.1	22q12.3	2008-05-14			ENSG00000185666	ENSG00000185666			11496	protein-coding gene	gene with protein product		602705				9539796	Standard	NM_003490		Approved		uc003amx.3	O14994	OTTHUMG00000031004	ENST00000358763.2:c.840C>T	22.37:g.32937634G>A						SYN3_uc003amy.2_Silent_p.Y280Y|SYN3_uc003amz.2_Silent_p.Y279Y	p.Y280Y	NM_003490	NP_003481	O14994	SYN3_HUMAN			7	999	-			280			C; actin-binding and synaptic-vesicle binding.		B1B1F9	Silent	SNP	ENST00000358763.2	37	c.840C>T	CCDS13908.1																																																																																				0.552	SYN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075892.4		
SI	6476	broad.mit.edu	37	3	164786544	164786544	+	Missense_Mutation	SNP	G	G	T			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr3:164786544G>T	ENST00000264382.3	-	5	511	c.449C>A	c.(448-450)aCt>aAt	p.T150N		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	150	Isomaltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)			NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	CTGATTTTGAGTTGTGAAGAG	0.393										HNSCC(35;0.089)																												uc003fei.2																			0				ovary(7)|upper_aerodigestive_tract(4)|skin(2)|pancreas(1)	14						c.(448-450)ACT>AAT		sucrase-isomaltase	Acarbose(DB00284)						132.0	135.0	134.0					3																	164786544		2203	4300	6503	SO:0001583	missense	6476				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity	g.chr3:164786544G>T	X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"""Oligosaccharide alpha-1,6-glucosidase"""	609845	"""sucrase-isomaltase"""			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.449C>A	3.37:g.164786544G>T	ENSP00000264382:p.Thr150Asn	HNSCC(35;0.089)					p.T150N	NM_001041	NP_001032	P14410	SUIS_HUMAN			5	511	-		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)	150			Lumenal.|Isomaltase.		A2RUC3|Q1JQ80|Q1RMC2	Missense_Mutation	SNP	ENST00000264382.3	37	c.449C>A	CCDS3196.1	.	.	.	.	.	.	.	.	.	.	G	14.49	2.551008	0.45383	.	.	ENSG00000090402	ENST00000264382	D	0.85339	-1.97	5.67	5.67	0.87782	Glycoside hydrolase-type carbohydrate-binding (1);	0.152091	0.56097	D	0.000023	D	0.90079	0.6901	M	0.82923	2.615	0.37880	D	0.93034	D	0.55605	0.972	P	0.51385	0.668	D	0.91713	0.5383	10	0.51188	T	0.08	.	17.0843	0.86606	0.0:0.1265:0.8735:0.0	.	150	P14410	SUIS_HUMAN	N	150	ENSP00000264382:T150N	ENSP00000264382:T150N	T	-	2	0	SI	166269238	1.000000	0.71417	0.966000	0.40874	0.040000	0.13550	3.870000	0.56070	2.835000	0.97688	0.591000	0.81541	ACT		0.393	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041	
PYDC2	152138	broad.mit.edu	37	3	191179074	191179074	+	Silent	SNP	C	C	T	rs141891926	byFrequency	TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr3:191179074C>T	ENST00000518817.1	+	1	123	c.123C>T	c.(121-123)acC>acT	p.T41T		NM_001083308.1	NP_001076777.1	Q56P42	PYDC2_HUMAN	pyrin domain containing 2	41	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	10						AGCTACAGACCGTCCCCCAGA	0.542													C|||	14	0.00279553	0.0098	0.0	5008	,	,		15104	0.001		0.0	False		,,,				2504	0.0					uc011bso.1																			0					0						c.(121-123)ACC>ACT		pyrin domain containing 2		C		33,4367	36.0+/-67.5	0,33,2167	77.0	85.0	82.0		123	-1.2	0.0	3	dbSNP_134	82	0,8600		0,0,4300	no	coding-synonymous	PYDC2	NM_001083308.1		0,33,6467	TT,TC,CC		0.0,0.75,0.2538		41/98	191179074	33,12967	2200	4300	6500	SO:0001819	synonymous_variant	152138					cytoplasm|nucleus		g.chr3:191179074C>T			3q28	2008-07-29				ENSG00000253548			33512	protein-coding gene	gene with protein product		615701				17178784	Standard	NM_001083308		Approved	POP2	uc011bso.2	Q56P42		ENST00000518817.1:c.123C>T	3.37:g.191179074C>T							p.T41T	NM_001083308	NP_001076777	Q56P42	PYDC2_HUMAN			1	123	+			41			DAPIN.			Silent	SNP	ENST00000518817.1	37	c.123C>T																																																																																					0.542	PYDC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000343231.2	NM_001083308	
KLHL5	51088	broad.mit.edu	37	4	39116788	39116788	+	Silent	SNP	C	C	G			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr4:39116788C>G	ENST00000504108.1	+	10	2332	c.2049C>G	c.(2047-2049)ccC>ccG	p.P683P	RP11-360F5.1_ENST00000509449.1_RNA|KLHL5_ENST00000261426.5_Silent_p.P622P|KLHL5_ENST00000508137.2_Silent_p.P496P|KLHL5_ENST00000359687.2_Silent_p.P683P|KLHL5_ENST00000381930.3_Silent_p.P683P|KLHL5_ENST00000261425.3_Silent_p.P637P	NM_015990.4	NP_057074.3	Q96PQ7	KLHL5_HUMAN	kelch-like family member 5	683						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(3)|kidney(1)|large_intestine(11)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	29						GATATGATCCCAAAACAGACA	0.383																																						uc003gts.2																			0				ovary(1)	1						c.(2047-2049)CCC>CCG		kelch-like 5 isoform 1							72.0	69.0	70.0					4																	39116788		2203	4300	6503	SO:0001819	synonymous_variant	51088					cytoplasm|cytoskeleton	actin binding	g.chr4:39116788C>G	AF272976	CCDS3449.1, CCDS33974.1, CCDS33975.1, CCDS54756.1	4p15.1	2013-01-30	2013-01-30		ENSG00000109790	ENSG00000109790		"""Kelch-like"", ""BTB/POZ domain containing"""	6356	protein-coding gene	gene with protein product		608064	"""kelch (Drosophila)-like 5"", ""kelch-like 5 (Drosophila)"""			11590829, 14672410	Standard	NM_001007075		Approved		uc003gtp.3	Q96PQ7	OTTHUMG00000097819	ENST00000504108.1:c.2049C>G	4.37:g.39116788C>G						KLHL5_uc003gtp.2_Silent_p.P637P|KLHL5_uc003gtq.2_Silent_p.P496P|KLHL5_uc003gtr.1_Silent_p.P683P|KLHL5_uc003gtt.2_Silent_p.P622P	p.P683P	NM_015990	NP_057074	Q96PQ7	KLHL5_HUMAN			10	2124	+			683			Kelch 5.		A8K170|B7WP68|E9PCF4|F8WAE7|G3XA92|Q6Y881|Q86XW0|Q9NUK3|Q9NV27|Q9NVA9|Q9Y2X2	Silent	SNP	ENST00000504108.1	37	c.2049C>G	CCDS33974.1	.	.	.	.	.	.	.	.	.	.	C	8.862	0.947253	0.18356	.	.	ENSG00000109790	ENST00000515612	.	.	.	6.06	-0.622	0.11560	.	.	.	.	.	T	0.43897	0.1268	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.27157	-1.0082	4	.	.	.	.	4.0483	0.09783	0.0976:0.475:0.0958:0.3316	.	.	.	.	E	195	.	.	Q	+	1	0	KLHL5	38793183	0.027000	0.19231	0.999000	0.59377	0.998000	0.95712	-0.832000	0.04400	0.111000	0.17947	0.655000	0.94253	CAA		0.383	KLHL5-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360604.1		
GPRIN3	285513	broad.mit.edu	37	4	90170302	90170302	+	Silent	SNP	C	C	T	rs145721148	byFrequency	TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr4:90170302C>T	ENST00000609438.1	-	2	1478	c.960G>A	c.(958-960)gcG>gcA	p.A320A	GPRIN3_ENST00000333209.4_Silent_p.A320A	NM_198281.2	NP_938022.2	Q6ZVF9	GRIN3_HUMAN	GPRIN family member 3	320										breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|prostate(2)|skin(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;5.67e-05)		CCTGCACCTCCGCATCTTGCC	0.537													C|||	3	0.000599042	0.0015	0.0014	5008	,	,		19868	0.0		0.0	False		,,,				2504	0.0					uc003hsm.1																			0				ovary(3)	3						c.(958-960)GCG>GCA		G protein-regulated inducer of neurite outgrowth		C		16,4390	23.3+/-48.9	0,16,2187	101.0	94.0	97.0		960	-11.3	0.0	4	dbSNP_134	97	0,8600		0,0,4300	no	coding-synonymous	GPRIN3	NM_198281.2		0,16,6487	TT,TC,CC		0.0,0.3631,0.123		320/777	90170302	16,12990	2203	4300	6503	SO:0001819	synonymous_variant	285513							g.chr4:90170302C>T	AK124616	CCDS34030.1	4q22.1	2006-08-24				ENSG00000185477			27733	protein-coding gene	gene with protein product		611241				15488195	Standard	NM_198281		Approved	GRIN3, FLJ42625	uc003hsm.1	Q6ZVF9		ENST00000609438.1:c.960G>A	4.37:g.90170302C>T							p.A320A	NM_198281	NP_938022	Q6ZVF9	GRIN3_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;5.67e-05)	2	1479	-		Hepatocellular(203;0.114)	320					Q8IVE4	Silent	SNP	ENST00000609438.1	37	c.960G>A	CCDS34030.1																																																																																				0.537	GPRIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363540.2	NM_198281	
MROH2B	133558	broad.mit.edu	37	5	41048449	41048449	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr5:41048449G>A	ENST00000399564.4	-	16	2111	c.1661C>T	c.(1660-1662)cCt>cTt	p.P554L	MROH2B_ENST00000506092.2_Missense_Mutation_p.P109L	NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	554																	CAGAAGCTCAGGTAAACGTGT	0.468																																						uc003jmj.3																			0				ovary(6)|central_nervous_system(2)	8						c.(1660-1662)CCT>CTT		HEAT repeat family member 7B2							135.0	128.0	130.0					5																	41048449		1890	4120	6010	SO:0001583	missense	133558						binding	g.chr5:41048449G>A		CCDS47202.1	5p13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000171495	ENSG00000171495		"""maestro heat-like repeat containing"""	26857	protein-coding gene	gene with protein product			"""HEAT repeat family member 7B2"""	HEATR7B2		12477932	Standard	NM_173489		Approved	DKFZp781F0822, FLJ40243	uc003jmj.4	Q7Z745	OTTHUMG00000162151	ENST00000399564.4:c.1661C>T	5.37:g.41048449G>A	ENSP00000382476:p.Pro554Leu					HEATR7B2_uc003jmi.3_Missense_Mutation_p.P109L	p.P554L	NM_173489	NP_775760	Q7Z745	HTRB2_HUMAN			16	2151	-			554			HEAT 6.		Q68DM1|Q7Z4U4|Q8N7X3	Missense_Mutation	SNP	ENST00000399564.4	37	c.1661C>T	CCDS47202.1	.	.	.	.	.	.	.	.	.	.	G	17.91	3.505305	0.64410	.	.	ENSG00000171495	ENST00000506092;ENST00000296803;ENST00000399564	T;T	0.10192	2.9;2.9	4.76	4.76	0.60689	Armadillo-type fold (1);	0.000000	0.53938	D	0.000042	T	0.28433	0.0703	L	0.60845	1.875	0.54753	D	0.999986	D	0.89917	1.0	D	0.87578	0.998	T	0.00373	-1.1781	10	0.62326	D	0.03	.	13.4769	0.61314	0.0:0.0:1.0:0.0	.	554	Q7Z745	HTRB2_HUMAN	L	109;258;554	ENSP00000441504:P109L;ENSP00000382476:P554L	ENSP00000296803:P258L	P	-	2	0	HEATR7B2	41084206	1.000000	0.71417	0.998000	0.56505	0.893000	0.52053	4.177000	0.58276	2.625000	0.88918	0.655000	0.94253	CCT		0.468	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489	
KCTD16	57528	broad.mit.edu	37	5	143853547	143853547	+	Missense_Mutation	SNP	A	A	C			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr5:143853547A>C	ENST00000507359.3	+	3	2248	c.1157A>C	c.(1156-1158)aAa>aCa	p.K386T	KCTD16_ENST00000512467.1_Missense_Mutation_p.K386T	NM_020768.3	NP_065819.1	Q68DU8	KCD16_HUMAN	potassium channel tetramerization domain containing 16	386					protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)				large_intestine(5)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	21		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)			AAAGCTGTTAAAGAAAAGCTC	0.443																																						uc003lnm.1																			0				large_intestine(2)|ovary(1)|skin(1)	4						c.(1156-1158)AAA>ACA		potassium channel tetramerisation domain							59.0	69.0	65.0					5																	143853547		2201	4300	6501	SO:0001583	missense	57528					cell junction|postsynaptic membrane|presynaptic membrane|voltage-gated potassium channel complex	voltage-gated potassium channel activity	g.chr5:143853547A>C	AB037738	CCDS34260.1	5q32	2013-06-20	2013-06-20		ENSG00000183775	ENSG00000183775			29244	protein-coding gene	gene with protein product		613423	"""potassium channel tetramerisation domain containing 16"""			10718198	Standard	NM_020768		Approved	KIAA1317	uc003lnm.1	Q68DU8	OTTHUMG00000163172	ENST00000507359.3:c.1157A>C	5.37:g.143853547A>C	ENSP00000426548:p.Lys386Thr					KCTD16_uc003lnn.1_Missense_Mutation_p.K386T	p.K386T	NM_020768	NP_065819	Q68DU8	KCD16_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)		4	1786	+		all_hematologic(541;0.118)	386					Q9P2M9	Missense_Mutation	SNP	ENST00000507359.3	37	c.1157A>C	CCDS34260.1	.	.	.	.	.	.	.	.	.	.	A	13.23	2.175100	0.38413	.	.	ENSG00000183775	ENST00000512467;ENST00000507359	T;T	0.45668	0.89;0.89	6.17	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.37073	0.0990	N	0.08118	0	0.49051	D	0.999745	D	0.61697	0.99	P	0.57101	0.813	T	0.28996	-1.0026	10	0.34782	T	0.22	.	12.919	0.58222	0.8782:0.0:0.0:0.1218	.	386	Q68DU8	KCD16_HUMAN	T	386	ENSP00000424151:K386T;ENSP00000426548:K386T	ENSP00000426548:K386T	K	+	2	0	KCTD16	143833740	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	8.855000	0.92236	1.134000	0.42165	0.533000	0.62120	AAA		0.443	KCTD16-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371898.3	XM_098368	
UNC5A	90249	broad.mit.edu	37	5	176301527	176301527	+	Silent	SNP	C	C	T			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr5:176301527C>T	ENST00000329542.4	+	8	1612	c.1338C>T	c.(1336-1338)acC>acT	p.T446T	UNC5A_ENST00000261961.3_Silent_p.T406T	NM_133369.2	NP_588610.2	Q6ZN44	UNC5A_HUMAN	unc-5 homolog A (C. elegans)	446	ZU5. {ECO:0000255|PROSITE- ProRule:PRU00485}.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(4)|kidney(3)|large_intestine(2)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	34	all_cancers(89;0.000119)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCTATGGGACCTTCAACTTCC	0.627																																						uc003mey.2																			0				skin(1)	1						c.(1336-1338)ACC>ACT		netrin receptor Unc5h1 precursor							90.0	100.0	96.0					5																	176301527		2203	4300	6503	SO:0001819	synonymous_variant	90249				apoptosis|axon guidance|regulation of apoptosis	integral to membrane|plasma membrane		g.chr5:176301527C>T	AB075856	CCDS34299.1	5q35.3	2013-01-11	2001-11-28		ENSG00000113763	ENSG00000113763		"""Immunoglobulin superfamily / I-set domain containing"""	12567	protein-coding gene	gene with protein product		607869	"""unc5 (C.elegans homolog) a"""				Standard	XM_006714927		Approved	KIAA1976, UNC5H1	uc003mey.3	Q6ZN44	OTTHUMG00000163225	ENST00000329542.4:c.1338C>T	5.37:g.176301527C>T						UNC5A_uc010jkg.1_Silent_p.T406T	p.T446T	NM_133369	NP_588610	Q6ZN44	UNC5A_HUMAN	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		8	1530	+	all_cancers(89;0.000119)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	446			ZU5.|Cytoplasmic (Potential).		B2RXE6|Q8TF26|Q96GP4	Silent	SNP	ENST00000329542.4	37	c.1338C>T	CCDS34299.1																																																																																				0.627	UNC5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372166.1	XM_030300	
GRM3	2913	broad.mit.edu	37	7	86469103	86469103	+	Missense_Mutation	SNP	C	C	T	rs141671463		TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr7:86469103C>T	ENST00000361669.2	+	4	3372	c.2273C>T	c.(2272-2274)aCg>aTg	p.T758M	GRM3_ENST00000394720.2_Intron|GRM3_ENST00000536043.1_Missense_Mutation_p.T630M|GRM3_ENST00000439827.1_Intron|GRM3_ENST00000546348.1_Missense_Mutation_p.T350M	NM_000840.2	NP_000831.2	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3	758					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.T758M(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)					GCCTTCAAAACGCGGAAGTGC	0.428																																					GBM(52;969 1098 3139 52280)	uc003uid.2																			1	Substitution - Missense(1)	p.T758M(1)	central_nervous_system(1)	lung(4)|ovary(3)|central_nervous_system(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|prostate(1)	13						c.(2272-2274)ACG>ATG		glutamate receptor, metabotropic 3 precursor	Acamprosate(DB00659)|Nicotine(DB00184)	C	MET/THR	0,4406		0,0,2203	117.0	102.0	107.0		2273	5.5	1.0	7	dbSNP_134	107	1,8599	1.2+/-3.3	0,1,4299	no	missense	GRM3	NM_000840.2	81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	758/880	86469103	1,13005	2203	4300	6503	SO:0001583	missense	2913				synaptic transmission	integral to plasma membrane		g.chr7:86469103C>T		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.2273C>T	7.37:g.86469103C>T	ENSP00000355316:p.Thr758Met					GRM3_uc010lef.2_Intron|GRM3_uc010leg.2_Missense_Mutation_p.T630M|GRM3_uc010leh.2_Missense_Mutation_p.T350M	p.T758M	NM_000840	NP_000831	Q14832	GRM3_HUMAN			4	3372	+	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)		758			Cytoplasmic (Potential).		Q2PNZ6|Q75MV4|Q75N17|Q86YG6|Q8TBH9	Missense_Mutation	SNP	ENST00000361669.2	37	c.2273C>T	CCDS5600.1	.	.	.	.	.	.	.	.	.	.	C	17.78	3.474192	0.63737	0.0	1.16E-4	ENSG00000198822	ENST00000361669;ENST00000546348;ENST00000536043	D;D;D	0.89485	-2.52;-2.52;-2.52	5.54	5.54	0.83059	GPCR, family 3, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.95984	0.8692	M	0.92784	3.345	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.96693	0.9512	10	0.87932	D	0	.	18.4662	0.90755	0.0:1.0:0.0:0.0	.	350;630;758	B7Z204;F5GYZ2;Q14832	.;.;GRM3_HUMAN	M	758;350;630	ENSP00000355316:T758M;ENSP00000444064:T350M;ENSP00000441407:T630M	ENSP00000355316:T758M	T	+	2	0	GRM3	86307039	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.920000	0.70017	2.603000	0.88011	0.563000	0.77884	ACG		0.428	GRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253362.2		
CYP3A5	1577	broad.mit.edu	37	7	99262902	99262902	+	Missense_Mutation	SNP	C	C	G			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr7:99262902C>G	ENST00000222982.4	-	7	656	c.557G>C	c.(556-558)gGc>gCc	p.G186A	CYP3A5_ENST00000343703.5_Missense_Mutation_p.G176A|CYP3A5_ENST00000480723.1_5'Flank|CYP3A5_ENST00000339843.2_3'UTR	NM_000777.3	NP_000768.1	P20815	CP3A5_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 5	186					alkaloid catabolic process (GO:0009822)|drug catabolic process (GO:0042737)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxygen binding (GO:0019825)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_epithelial(64;2.77e-08)|Lung NSC(181;0.00396)|all_lung(186;0.00659)|Esophageal squamous(72;0.0166)				ado-trastuzumab emtansine(DB05773)|Alfentanil(DB00802)|Alprazolam(DB00404)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Apixaban(DB06605)|Aprepitant(DB00673)|Argatroban(DB00278)|Aripiprazole(DB01238)|Artemether(DB06697)|Astemizole(DB00637)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Beclomethasone(DB00394)|Boceprevir(DB08873)|Brentuximab vedotin(DB08870)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Carbamazepine(DB00564)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Cilostazol(DB01166)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clonidine(DB00575)|Clopidogrel(DB00758)|Cocaine(DB00907)|Codeine(DB00318)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diltiazem(DB00343)|Disulfiram(DB00822)|Docetaxel(DB01248)|Dolutegravir(DB08930)|Domperidone(DB01184)|Dutasteride(DB01126)|Enzalutamide(DB08899)|Eplerenone(DB00700)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estrone(DB00655)|Ethosuximide(DB00593)|Etoposide(DB00773)|Felodipine(DB01023)|Fentanyl(DB00813)|Finasteride(DB01216)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flutamide(DB00499)|Fluticasone Propionate(DB00588)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gestodene(DB06730)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Indinavir(DB00224)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Levomethadyl Acetate(DB01227)|Lidocaine(DB00281)|Losartan(DB00678)|Lovastatin(DB00227)|Methadone(DB00333)|Midazolam(DB00683)|Mifepristone(DB00834)|Modafinil(DB00745)|Mycophenolate mofetil(DB00688)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ondansetron(DB00904)|Oxazepam(DB00842)|Oxcarbazepine(DB00776)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Pentamidine(DB00738)|Perampanel(DB08883)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Progesterone(DB00396)|Propranolol(DB00571)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinine(DB00468)|Ranitidine(DB00863)|Reserpine(DB00206)|Rifampicin(DB01045)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Rosuvastatin(DB01098)|Salmeterol(DB00938)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Teniposide(DB00444)|Testosterone(DB00624)|Thalidomide(DB01041)|Trazodone(DB00656)|Tretinoin(DB00755)|Triazolam(DB00897)|Troleandomycin(DB01361)|Udenafil(DB06267)|Valproic Acid(DB00313)|Vardenafil(DB00862)|Verapamil(DB00661)|Vincristine(DB00541)|Voriconazole(DB00582)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Ziprasidone(DB00246)|Zolpidem(DB00425)	AAATGATGTGCCAGTAATCAC	0.418																																						uc003urq.2																			0					0						c.(556-558)GGC>GCC		cytochrome P450, family 3, subfamily A,	Alfentanil(DB00802)|Clopidogrel(DB00758)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Indinavir(DB00224)|Irinotecan(DB00762)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Mephenytoin(DB00532)|Midazolam(DB00683)|Mifepristone(DB00834)|Phenytoin(DB00252)|Quinine(DB00468)|Saquinavir(DB01232)|Tacrolimus(DB00864)|Troleandomycin(DB01361)|Verapamil(DB00661)|Vincristine(DB00541)						168.0	146.0	154.0					7																	99262902		2203	4300	6503	SO:0001583	missense	1577				alkaloid catabolic process|drug catabolic process|oxidative demethylation|steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding	g.chr7:99262902C>G	L26985	CCDS5672.1, CCDS55134.1	7q21.1	2007-12-14	2003-01-14		ENSG00000106258	ENSG00000106258		"""Cytochrome P450s"""	2638	protein-coding gene	gene with protein product		605325	"""cytochrome P450, subfamily IIIA (niphedipine oxidase), polypeptide 5"""				Standard	NR_033808		Approved	PCN3, P450PCN3, CP35		P20815	OTTHUMG00000156724	ENST00000222982.4:c.557G>C	7.37:g.99262902C>G	ENSP00000222982:p.Gly186Ala					ZNF498_uc003urn.2_Intron|CYP3A5_uc003urp.2_Missense_Mutation_p.G6A|CYP3A5_uc003urr.2_Missense_Mutation_p.G73A|CYP3A5_uc011kiy.1_Missense_Mutation_p.G176A|CYP3A5_uc003urs.2_Intron|CYP3A5_uc010lgg.2_Intron	p.G186A	NM_000777	NP_000768	P20815	CP3A5_HUMAN			7	644	-	all_epithelial(64;2.77e-08)|Lung NSC(181;0.00396)|all_lung(186;0.00659)|Esophageal squamous(72;0.0166)		186					A4D289|B7Z5I7|Q53WY8|Q75MV0|Q9HB56	Missense_Mutation	SNP	ENST00000222982.4	37	c.557G>C	CCDS5672.1	.	.	.	.	.	.	.	.	.	.	C	9.618	1.133091	0.21041	.	.	ENSG00000106258	ENST00000222982;ENST00000343703	T;T	0.66995	-0.24;-0.24	3.83	1.85	0.25348	.	0.118586	0.85682	N	0.000000	T	0.44498	0.1296	N	0.10645	0.015	0.80722	D	1	B;B	0.09022	0.002;0.002	B;B	0.12156	0.007;0.007	T	0.24083	-1.0170	10	0.51188	T	0.08	.	11.2806	0.49192	0.0:0.6429:0.3571:0.0	.	176;186	F5H4S0;P20815	.;CP3A5_HUMAN	A	186;176	ENSP00000222982:G186A;ENSP00000342969:G176A	ENSP00000222982:G186A	G	-	2	0	CYP3A5	99100838	0.997000	0.39634	0.222000	0.23844	0.394000	0.30568	3.559000	0.53756	0.172000	0.19760	-0.181000	0.13052	GGC		0.418	CYP3A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345469.1		
PIP	5304	broad.mit.edu	37	7	142836647	142836647	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr7:142836647G>A	ENST00000291009.3	+	4	393	c.353G>A	c.(352-354)cGg>cAg	p.R118Q		NM_002652.2	NP_002643.1	P12273	PIP_HUMAN	prolactin-induced protein	118					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of T cell apoptotic process (GO:0070233)|positive regulation of gene expression (GO:0010628)|proteolysis (GO:0006508)|regulation of immune system process (GO:0002682)|retina homeostasis (GO:0001895)	apical plasma membrane (GO:0016324)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	actin binding (GO:0003779)|aspartic-type endopeptidase activity (GO:0004190)|glycoprotein binding (GO:0001948)|IgG binding (GO:0019864)|protein dimerization activity (GO:0046983)	p.R118L(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|skin(1)	18	Melanoma(164;0.059)	Ovarian(593;2.82e-05)|Breast(660;0.012)		BRCA - Breast invasive adenocarcinoma(188;0.0026)|LUSC - Lung squamous cell carcinoma(290;0.0733)|Lung(243;0.08)		GATGTTATTCGGGAATTAGGC	0.453																																						uc003wcf.1																			1	Substitution - Missense(1)		lung(1)	ovary(1)	1						c.(352-354)CGG>CAG		prolactin-induced protein precursor							165.0	157.0	159.0					7																	142836647		2203	4299	6502	SO:0001583	missense	5304					extracellular region	actin binding	g.chr7:142836647G>A		CCDS34768.1	7q34	2013-09-19			ENSG00000159763	ENSG00000159763			8993	protein-coding gene	gene with protein product	"""prolactin-inducible protein"""	176720				2727805, 1955075	Standard	NM_002652		Approved	GCDFP-15, GCDFP15, GPIP4	uc003wcf.1	P12273	OTTHUMG00000152635	ENST00000291009.3:c.353G>A	7.37:g.142836647G>A	ENSP00000291009:p.Arg118Gln						p.R118Q	NM_002652	NP_002643	P12273	PIP_HUMAN		BRCA - Breast invasive adenocarcinoma(188;0.0026)|LUSC - Lung squamous cell carcinoma(290;0.0733)|Lung(243;0.08)	4	389	+	Melanoma(164;0.059)	Ovarian(593;2.82e-05)|Breast(660;0.012)	118					A0A963|A0A9C3|A0A9F3|A4D2I1	Missense_Mutation	SNP	ENST00000291009.3	37	c.353G>A	CCDS34768.1	.	.	.	.	.	.	.	.	.	.	g	11.86	1.763881	0.31228	.	.	ENSG00000159763	ENST00000291009	T	0.14022	2.54	4.78	-4.48	0.03515	.	1.221410	0.05988	N	0.645521	T	0.08492	0.0211	M	0.65975	2.015	0.09310	N	1	P	0.48089	0.905	B	0.24974	0.057	T	0.33420	-0.9869	10	0.25106	T	0.35	.	3.3187	0.07043	0.5027:0.1128:0.2699:0.1146	.	118	P12273	PIP_HUMAN	Q	118	ENSP00000291009:R118Q	ENSP00000291009:R118Q	R	+	2	0	PIP	142546769	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.459000	0.01000	-1.283000	0.02393	-1.746000	0.00682	CGG		0.453	PIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327089.1	NM_002652	
DMRT3	58524	broad.mit.edu	37	9	990484	990484	+	Missense_Mutation	SNP	G	G	A	rs569551719		TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chr9:990484G>A	ENST00000190165.2	+	2	936	c.898G>A	c.(898-900)Gca>Aca	p.A300T		NM_021240.2	NP_067063.1	Q9NQL9	DMRT3_HUMAN	doublesex and mab-3 related transcription factor 3	300					adult walking behavior (GO:0007628)|male sex differentiation (GO:0046661)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|sex differentiation (GO:0007548)|transcription, DNA-templated (GO:0006351)|transmission of nerve impulse (GO:0019226)|ventral spinal cord interneuron specification (GO:0021521)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	26		all_lung(10;1.39e-08)|Lung NSC(10;1.42e-08)		Lung(218;0.0196)		GCGAACTTCCGCAGAACCTGA	0.582													G|||	1	0.000199681	0.0	0.0	5008	,	,		17348	0.0		0.0	False		,,,				2504	0.001					uc003zgw.1																			0				ovary(2)|central_nervous_system(1)	3						c.(898-900)GCA>ACA		doublesex and mab-3 related transcription factor							112.0	99.0	103.0					9																	990484		2203	4300	6503	SO:0001583	missense	58524				cell differentiation|multicellular organismal development|sex differentiation	nucleus	DNA binding|metal ion binding|sequence-specific DNA binding transcription factor activity	g.chr9:990484G>A	AJ301581	CCDS6443.1	9p24.3	2008-07-21	2001-12-17	2001-12-07	ENSG00000064218	ENSG00000064218			13909	protein-coding gene	gene with protein product	"""testis-specific protein"""	614754	"""DMRT-like family A3"""	DMRTA3		11543627, 10729223	Standard	NM_021240		Approved		uc003zgw.2	Q9NQL9	OTTHUMG00000019436	ENST00000190165.2:c.898G>A	9.37:g.990484G>A	ENSP00000190165:p.Ala300Thr						p.A300T	NM_021240	NP_067063	Q9NQL9	DMRT3_HUMAN		Lung(218;0.0196)	2	936	+		all_lung(10;1.39e-08)|Lung NSC(10;1.42e-08)	300					Q7LA03|Q7LCH8|Q96SC7|Q9NRQ9	Missense_Mutation	SNP	ENST00000190165.2	37	c.898G>A	CCDS6443.1	.	.	.	.	.	.	.	.	.	.	G	0.259	-1.001105	0.02128	.	.	ENSG00000064218	ENST00000190165	T	0.22945	1.93	4.82	-0.683	0.11335	.	0.563471	0.18677	N	0.134271	T	0.08179	0.0204	N	0.08118	0	0.09310	N	0.999999	B	0.13145	0.007	B	0.04013	0.001	T	0.25467	-1.0131	10	0.13853	T	0.58	-5.7403	1.3835	0.02235	0.2056:0.1081:0.3604:0.3258	.	300	Q9NQL9	DMRT3_HUMAN	T	300	ENSP00000190165:A300T	ENSP00000190165:A300T	A	+	1	0	DMRT3	980484	0.042000	0.20092	0.001000	0.08648	0.005000	0.04900	0.306000	0.19279	-0.113000	0.11958	-0.384000	0.06662	GCA		0.582	DMRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051490.1	NM_021240	
ZBED1	9189	broad.mit.edu	37	X	2407462	2407462	+	Silent	SNP	C	C	T			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chrX:2407462C>T	ENST00000381223.4	-	2	1502	c.1299G>A	c.(1297-1299)acG>acA	p.T433T	ZBED1_ENST00000381222.2_Silent_p.T433T|ZBED1_ENST00000515319.1_5'Flank|ZBED1_ENST00000381218.3_Silent_p.T433T|DHRSX_ENST00000334651.5_Intron	NM_001171135.1|NM_001171136.1|NM_004729.3	NP_001164606.1|NP_001164607.1|NP_004720.1	O96006	ZBED1_HUMAN	zinc finger, BED-type containing 1	433					metabolic process (GO:0008152)	nuclear chromosome (GO:0000228)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transposase activity (GO:0004803)	p.T433T(1)		endometrium(8)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|upper_aerodigestive_tract(1)	25		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				TGATGTTGAGCGTGGTGTTCA	0.597																																						uc004cqg.2																			1	Substitution - coding silent(1)		endometrium(1)		0						c.(1297-1299)ACG>ACA		zinc finger, BED-type containing 1							174.0	151.0	158.0					X																	2407462		2203	4296	6499	SO:0001819	synonymous_variant	9189					nuclear chromosome	DNA binding|metal ion binding|protein dimerization activity|transposase activity	g.chrX:2407462C>T	AB018328	CCDS14118.1	Xp22.33 and Yp11	2013-05-03	2004-01-14	2004-01-16	ENSG00000214717	ENSG00000214717		"""Pseudoautosomal regions / PAR1"", ""Zinc fingers, BED-type"""	447	protein-coding gene	gene with protein product		300178	"""Ac-like transposable element"""	ALTE		9872452, 9887332, 23533661	Standard	NM_001171135		Approved	TRAMP, KIAA0785, DREF, hDREF	uc004cqh.2	O96006	OTTHUMG00000021069	ENST00000381223.4:c.1299G>A	X.37:g.2407462C>T						DHRSX_uc004cqf.3_Intron|ZBED1_uc004cqh.1_Silent_p.T433T	p.T433T	NM_004729	NP_004720	O96006	ZBED1_HUMAN			2	1500	-		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)	433					Q96BY4	Silent	SNP	ENST00000381223.4	37	c.1299G>A	CCDS14118.1																																																																																				0.597	ZBED1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144310.3	NM_004729	
RAI2	10742	broad.mit.edu	37	X	17818684	17818684	+	Missense_Mutation	SNP	G	G	C			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chrX:17818684G>C	ENST00000545871.1	-	3	1907	c.1447C>G	c.(1447-1449)Caa>Gaa	p.Q483E	RAI2_ENST00000451717.1_Missense_Mutation_p.Q483E|RAI2_ENST00000331511.1_Missense_Mutation_p.Q483E|RAI2_ENST00000415486.3_Missense_Mutation_p.Q433E|RAI2_ENST00000360011.1_Missense_Mutation_p.Q483E	NM_001172739.1|NM_001172743.1	NP_001166210|NP_001166214	Q9Y5P3	RAI2_HUMAN	retinoic acid induced 2	483					embryo development (GO:0009790)					breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|prostate(1)	22	Hepatocellular(33;0.183)					TCTTCCCCTTGGCTGTTGATG	0.468																																						uc004cyf.2																			0				ovary(1)|breast(1)	2						c.(1447-1449)CAA>GAA		retinoic acid induced 2							256.0	264.0	261.0					X																	17818684		2203	4300	6503	SO:0001583	missense	10742				embryo development			g.chrX:17818684G>C	Z93242	CCDS14183.1, CCDS55374.1	Xp22	2008-02-05			ENSG00000131831	ENSG00000131831			9835	protein-coding gene	gene with protein product		300217				10049581, 10394933	Standard	NR_033348		Approved		uc010nfa.3	Q9Y5P3	OTTHUMG00000021209	ENST00000545871.1:c.1447C>G	X.37:g.17818684G>C	ENSP00000444210:p.Gln483Glu					RAI2_uc004cyg.2_Missense_Mutation_p.Q483E|RAI2_uc010nfa.2_Missense_Mutation_p.Q483E|RAI2_uc004cyh.3_Missense_Mutation_p.Q483E|RAI2_uc011miy.1_Missense_Mutation_p.Q433E	p.Q483E	NM_021785	NP_068557	Q9Y5P3	RAI2_HUMAN			3	2017	-	Hepatocellular(33;0.183)		483					B1B1K2|B4DQM9|E7EMN4|Q8N6X7	Missense_Mutation	SNP	ENST00000545871.1	37	c.1447C>G	CCDS14183.1	.	.	.	.	.	.	.	.	.	.	G	12.42	1.931247	0.34096	.	.	ENSG00000131831	ENST00000331511;ENST00000360011;ENST00000545871;ENST00000451717;ENST00000415486	T;T;T;T;T	0.32272	1.47;1.47;1.47;1.47;1.46	5.12	5.12	0.69794	.	0.477878	0.21357	N	0.075870	T	0.28797	0.0714	L	0.29908	0.895	0.37528	D	0.917826	B;B	0.21606	0.058;0.058	B;B	0.27076	0.076;0.076	T	0.17289	-1.0374	10	0.54805	T	0.06	-1.4961	17.7433	0.88413	0.0:0.0:1.0:0.0	.	433;483	E7EMN4;Q9Y5P3	.;RAI2_HUMAN	E	483;483;483;483;433	ENSP00000333456:Q483E;ENSP00000353106:Q483E;ENSP00000444210:Q483E;ENSP00000401323:Q483E;ENSP00000392578:Q433E	ENSP00000333456:Q483E	Q	-	1	0	RAI2	17728605	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.932000	0.63476	2.378000	0.81104	0.600000	0.82982	CAA		0.468	RAI2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055937.1	NM_021785	
EIF2S3	1968	broad.mit.edu	37	X	24073154	24073154	+	Splice_Site	SNP	G	G	A			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chrX:24073154G>A	ENST00000253039.4	+	1	322	c.69G>A	c.(67-69)ttG>ttA	p.L23L		NM_001415.3	NP_001406.1	P41091	IF2G_HUMAN	eukaryotic translation initiation factor 2, subunit 3 gamma, 52kDa	23					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			breast(1)|cervix(1)|endometrium(4)|large_intestine(1)|lung(4)|ovary(1)	12						TCACCACCTTGGTGAGGTTTT	0.587											OREG0019714	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										uc004dbc.2																			0				lung(1)	1						c.(67-69)TTG>TTA		eukaryotic translation initiation factor 2,							75.0	62.0	67.0					X																	24073154		2203	4300	6503	SO:0001630	splice_region_variant	1968					cytosol	GTP binding|GTPase activity|protein binding|translation initiation factor activity	g.chrX:24073154G>A	L19161	CCDS14210.1	Xp22.2-p22.1	2008-07-31	2002-08-29		ENSG00000130741	ENSG00000130741			3267	protein-coding gene	gene with protein product	"""eukaryotic translation initiation factor 2G"""	300161	"""eukaryotic translation initiation factor 2, subunit 3 (gamma, 52kD)"""	EIF2G		8106381, 9736774	Standard	NM_001415		Approved	EIF2gamma, EIF2	uc004dbc.3	P41091	OTTHUMG00000021262	ENST00000253039.4:c.69+1G>A	X.37:g.24073154G>A			OREG0019714	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	768		p.L23L	NM_001415	NP_001406	P41091	IF2G_HUMAN			1	90	+			23					B5BTZ4	Silent	SNP	ENST00000253039.4	37	c.69G>A	CCDS14210.1	.	.	.	.	.	.	.	.	.	.	G	13.48	2.249807	0.39797	.	.	ENSG00000130741	ENST00000423068	.	.	.	5.21	5.21	0.72293	.	.	.	.	.	T	0.74122	0.3675	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.73209	-0.4055	4	.	.	.	.	17.8958	0.88887	0.0:0.0:1.0:0.0	.	.	.	.	R	23	.	.	G	+	1	0	EIF2S3	23983075	1.000000	0.71417	0.997000	0.53966	0.510000	0.34073	5.359000	0.66074	2.416000	0.81992	0.600000	0.82982	GGA		0.587	EIF2S3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056079.1	NM_001415	Silent
PORCN	64840	broad.mit.edu	37	X	48368320	48368320	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chrX:48368320G>A	ENST00000326194.6	+	1	155	c.112G>A	c.(112-114)Gcc>Acc	p.A38T	PORCN_ENST00000486272.1_3'UTR|PORCN_ENST00000537758.1_Missense_Mutation_p.A38T|PORCN_ENST00000355961.4_Missense_Mutation_p.A38T|PORCN_ENST00000355092.3_Missense_Mutation_p.A38T|PORCN_ENST00000361988.3_Missense_Mutation_p.A38T|PORCN_ENST00000359882.4_Missense_Mutation_p.A38T|AF196972.9_ENST00000445586.1_RNA|PORCN_ENST00000367574.4_5'UTR	NM_203475.1	NP_982301.1	Q9H237	PORCN_HUMAN	porcupine homolog (Drosophila)	38	Leu-rich.				glycoprotein metabolic process (GO:0009100)|Wnt signaling pathway (GO:0016055)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|integral component of endoplasmic reticulum membrane (GO:0030176)	transferase activity, transferring acyl groups (GO:0016746)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						CATCTGCCTCGCCTGCCGCCT	0.597																																						uc010nie.1																			0				ovary(2)|central_nervous_system(1)	3						c.(112-114)GCC>ACC		porcupine isoform D							46.0	41.0	43.0					X																	48368320		2203	4300	6503	SO:0001583	missense	64840				Wnt receptor signaling pathway	endoplasmic reticulum membrane|integral to membrane	acyltransferase activity	g.chrX:48368320G>A	AF317058	CCDS14296.1, CCDS14297.1, CCDS14298.1, CCDS14299.1	Xp11.23	2014-02-05			ENSG00000102312	ENSG00000102312			17652	protein-coding gene	gene with protein product		300651	"""dermal hypoplasia, focal"""	DHOF		10866835, 12034504, 17546030	Standard	NM_203474		Approved	MG61, PORC, PPN, por	uc004djv.1	Q9H237	OTTHUMG00000024116	ENST00000326194.6:c.112G>A	X.37:g.48368320G>A	ENSP00000322304:p.Ala38Thr					PORCN_uc004djq.1_Missense_Mutation_p.A151T|PORCN_uc004djr.1_Missense_Mutation_p.A38T|PORCN_uc004djs.1_Missense_Mutation_p.A38T|PORCN_uc004djt.1_5'UTR|PORCN_uc011mlx.1_5'UTR|PORCN_uc004dju.1_5'UTR|PORCN_uc004djv.1_Missense_Mutation_p.A38T|PORCN_uc004djw.1_Missense_Mutation_p.A38T	p.A38T	NM_203475	NP_982301	Q9H237	PORCN_HUMAN			2	270	+			38			Helical; (Potential).|Leu-rich.		B2RBN8|B7ZAR3|Q14829|Q9H234|Q9H235|Q9H236|Q9UJU7	Missense_Mutation	SNP	ENST00000326194.6	37	c.112G>A	CCDS14299.1	.	.	.	.	.	.	.	.	.	.	G	13.78	2.338188	0.41398	.	.	ENSG00000102312	ENST00000359882;ENST00000537758;ENST00000355961;ENST00000489940;ENST00000361988;ENST00000326194;ENST00000355092	D;D;D;D;D;D;D	0.97688	-3.49;-4.49;-3.49;-2.38;-3.49;-4.49;-3.49	5.44	2.25	0.28309	.	0.486738	0.21687	N	0.070625	D	0.90988	0.7166	N	0.12746	0.255	0.80722	D	1	B;B;B;B;B	0.31817	0.004;0.005;0.004;0.004;0.341	B;B;B;B;B	0.19148	0.007;0.003;0.004;0.007;0.024	D	0.85912	0.1441	10	0.23891	T	0.37	-4.0195	9.0523	0.36383	0.3054:0.0:0.6946:0.0	.	38;38;38;38;38	Q9H237-3;Q9H237;Q9H237-4;Q9H237-2;C9JWI5	.;PORCN_HUMAN;.;.;.	T	38	ENSP00000352946:A38T;ENSP00000446401:A38T;ENSP00000348233:A38T;ENSP00000419212:A38T;ENSP00000354978:A38T;ENSP00000322304:A38T;ENSP00000347207:A38T	ENSP00000322304:A38T	A	+	1	0	PORCN	48253264	1.000000	0.71417	0.999000	0.59377	0.986000	0.74619	1.505000	0.35736	0.497000	0.27926	0.529000	0.55759	GCC		0.597	PORCN-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000356990.1	NM_022825	
WNK3	65267	broad.mit.edu	37	X	54276526	54276526	+	Nonsense_Mutation	SNP	G	G	A			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chrX:54276526G>A	ENST00000375159.2	-	15	2613	c.2614C>T	c.(2614-2616)Cga>Tga	p.R872*	WNK3_ENST00000375169.3_Nonsense_Mutation_p.R872*|WNK3_ENST00000354646.2_Nonsense_Mutation_p.R872*			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	872					intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of ion transmembrane transporter activity (GO:0032414)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of rubidium ion transmembrane transporter activity (GO:2000688)|positive regulation of rubidium ion transport (GO:2000682)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(24)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						ATACAGAATCGCCACCGACCA	0.423																																						uc004dtd.1																			0				lung(4)|ovary(3)|kidney(2)|central_nervous_system(2)	11						c.(2614-2616)CGA>TGA		WNK lysine deficient protein kinase 3 isoform 2							47.0	40.0	42.0					X																	54276526		2203	4300	6503	SO:0001587	stop_gained	65267				intracellular protein kinase cascade|positive regulation of establishment of protein localization in plasma membrane|positive regulation of peptidyl-threonine phosphorylation|positive regulation of rubidium ion transmembrane transporter activity|positive regulation of rubidium ion transport|positive regulation of sodium ion transmembrane transporter activity|positive regulation of sodium ion transport|protein autophosphorylation	adherens junction|tight junction	ATP binding|protein binding|protein serine/threonine kinase activity|rubidium ion transmembrane transporter activity|sodium ion transmembrane transporter activity	g.chrX:54276526G>A	AJ409088	CCDS14357.1, CCDS35302.1	Xp11.22	2008-05-14	2005-01-19	2005-01-22	ENSG00000196632	ENSG00000196632			14543	protein-coding gene	gene with protein product		300358	"""protein kinase, lysine deficient 3"""	PRKWNK3			Standard	NM_020922		Approved		uc004dtc.2	Q9BYP7	OTTHUMG00000021626	ENST00000375159.2:c.2614C>T	X.37:g.54276526G>A	ENSP00000364301:p.Arg872*					WNK3_uc004dtc.1_Nonsense_Mutation_p.R872*	p.R872*	NM_001002838	NP_001002838	Q9BYP7	WNK3_HUMAN			16	3053	-			872					B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Nonsense_Mutation	SNP	ENST00000375159.2	37	c.2614C>T	CCDS14357.1	.	.	.	.	.	.	.	.	.	.	G	40	8.203670	0.98704	.	.	ENSG00000196632	ENST00000375169;ENST00000354646;ENST00000375159	.	.	.	5.5	3.51	0.40186	.	0.000000	0.48286	D	0.000184	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.145	10.596	0.45338	0.0:0.0:0.3882:0.6118	.	.	.	.	X	872	.	ENSP00000346667:R872X	R	-	1	2	WNK3	54293251	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	1.218000	0.32467	1.062000	0.40625	0.506000	0.49869	CGA		0.423	WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2	NM_020922	
IL1RAPL2	26280	broad.mit.edu	37	X	105011568	105011568	+	Silent	SNP	C	C	T			TCGA-06-5410-01A-01D-1696-08	TCGA-06-5410-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	67244284-dc40-46cb-a2ac-3f4a38f7bbe4	2df41e20-041f-4e1e-86d9-3c38e36c9b33	g.chrX:105011568C>T	ENST00000372582.1	+	11	2731	c.1975C>T	c.(1975-1977)Ctg>Ttg	p.L659L	IL1RAPL2_ENST00000344799.4_Silent_p.L659L	NM_017416.1	NP_059112.1	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2	659					central nervous system development (GO:0007417)|cytokine-mediated signaling pathway (GO:0019221)	integral component of membrane (GO:0016021)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)			breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(23)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						TAATAACACCCTGAAAGATAC	0.448																																						uc004elz.1																			0				breast(2)|ovary(1)	3						c.(1975-1977)CTG>TTG		interleukin 1 receptor accessory protein-like 2							128.0	129.0	128.0					X																	105011568		2203	4300	6503	SO:0001819	synonymous_variant	26280				central nervous system development|innate immune response	integral to membrane	interleukin-1, Type II, blocking receptor activity	g.chrX:105011568C>T	AF181285	CCDS14517.1	Xq22	2013-01-11			ENSG00000189108	ENSG00000189108		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5997	protein-coding gene	gene with protein product		300277				10757639	Standard	NM_017416		Approved	IL-1R9, TIGIRR-1, IL1RAPL-2, IL1R9	uc004elz.1	Q9NP60	OTTHUMG00000022141	ENST00000372582.1:c.1975C>T	X.37:g.105011568C>T							p.L659L	NM_017416	NP_059112	Q9NP60	IRPL2_HUMAN			11	2731	+			659			Cytoplasmic (Potential).		Q2M3U3|Q9NZN0	Silent	SNP	ENST00000372582.1	37	c.1975C>T	CCDS14517.1																																																																																				0.448	IL1RAPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057785.1	NM_017416	
