#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	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
FRG1B	284802	broad.mit.edu	37	20	29628236	29628236	+	Missense_Mutation	SNP	G	G	C			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr20:29628236G>C	ENST00000278882.3	+	6	618	c.238G>C	c.(238-240)Gct>Cct	p.A80P	FRG1B_ENST00000358464.4_Missense_Mutation_p.A80P|FRG1B_ENST00000439954.2_Missense_Mutation_p.A85P			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	80								p.A80P(8)		endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						GGGGAAAATGGCTTTGTTGGC	0.363																																						ENST00000278882.3																			8	Substitution - Missense(8)	p.A80P(8)	prostate(4)|kidney(4)	endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						c.(238-240)Gct>Cct																																						SO:0001583	missense	0							g.chr20:29628236G>C			20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531			15792	other	unknown			"""chromosome 20 open reading frame 80"""	C20orf80			Standard	NR_003579		Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.238G>C	20.37:g.29628236G>C	ENSP00000278882:p.Ala80Pro					FRG1B_ENST00000439954.2_Missense_Mutation_p.A85P|FRG1B_ENST00000358464.4_Missense_Mutation_p.A80P	p.A80P							6	618	+								C4AME5	Missense_Mutation	SNP	ENST00000278882.3	37	c.238G>C		.	.	.	.	.	.	.	.	.	.	g	15.73	2.920277	0.52653	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	T	0.57595	0.39	2.08	2.08	0.27032	Actin cross-linking (1);	0.052409	0.85682	D	0.000000	T	0.68952	0.3057	.	.	.	0.80722	D	1	D;D	0.64830	0.994;0.988	D;D	0.85130	0.997;0.993	T	0.72766	-0.4194	9	0.87932	D	0	.	10.2211	0.43198	0.0:0.0:1.0:0.0	.	85;80	F5H5R5;Q9BZ01	.;FRG1B_HUMAN	P	80;85;80	ENSP00000408863:A85P	ENSP00000278882:A80P	A	+	1	0	FRG1B	28241897	1.000000	0.71417	1.000000	0.80357	0.334000	0.28698	8.494000	0.90477	1.475000	0.48197	0.423000	0.28283	GCT		0.363	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078494.2	NR_003579		4	98	0	0	0	1	0	4	98				
SSX5	6758	broad.mit.edu	37	X	48053626	48053626	+	Silent	SNP	A	A	G			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chrX:48053626A>G	ENST00000376923.1	-	3	218	c.219T>C	c.(217-219)aaT>aaC	p.N73N	SSX5_ENST00000347757.1_Silent_p.N73N|SSX5_ENST00000311798.1_Silent_p.N114N			O60225	SSX5_HUMAN	synovial sarcoma, X breakpoint 5	73	KRAB-related. {ECO:0000255|PROSITE- ProRule:PRU00120}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			endometrium(3)|kidney(1)|large_intestine(6)|lung(7)|skin(1)	18						CGACCCGTTTATTACGCATGA	0.483																																						ENST00000311798.1																			0				endometrium(3)|kidney(1)|large_intestine(6)|lung(7)|skin(1)	18						c.(340-342)aaT>aaC		synovial sarcoma, X breakpoint 5							151.0	133.0	139.0					X																	48053626		2203	4299	6502	SO:0001819	synonymous_variant	6758				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding	g.chrX:48053626A>G	BC016640	CCDS14288.1, CCDS14289.1	Xp11.23	2008-02-05			ENSG00000165583	ENSG00000165583			11339	protein-coding gene	gene with protein product		300327					Standard	NM_021015		Approved		uc004diz.1	O60225	OTTHUMG00000021471	ENST00000376923.1:c.219T>C	X.37:g.48053626A>G						SSX5_ENST00000347757.1_Silent_p.N73N|SSX5_ENST00000376923.1_Silent_p.N73N	p.N114N	NM_021015.3	NP_066295.3	O60225	SSX5_HUMAN			5	394	-			73					Q5JQ59|Q5JQ60|Q96AW3	Silent	SNP	ENST00000376923.1	37	c.342T>C	CCDS14289.1																																																																																				0.483	SSX5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056466.1	NM_021015		27	25	0	0	0	1	0	27	25				
TPR	7175	broad.mit.edu	37	1	186326600	186326600	+	Silent	SNP	T	T	C			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr1:186326600T>C	ENST00000367478.4	-	14	1949	c.1653A>G	c.(1651-1653)caA>caG	p.Q551Q	TPR_ENST00000474852.1_5'UTR	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	551					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		CTAAGAGACGTTGATTTTGTT	0.388			T	NTRK1	papillary thyroid																																	ENST00000367478.3				Dom	yes		1	1q25	7175	T	translocated promoter region			E	NTRK1		papillary thyroid		0				autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123						c.(1651-1653)caA>caG		translocated promoter region, nuclear basket protein							157.0	143.0	147.0					1																	186326600		1845	4088	5933	SO:0001819	synonymous_variant	7175				carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm	ATP binding|protein binding|serine-tRNA ligase activity	g.chr1:186326600T>C	U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"""translocated promoter region (to activated MET oncogene)"""			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.1653A>G	1.37:g.186326600T>C						TPR_ENST00000474852.1_5'UTR	p.Q551Q	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)	14	1949	-		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)	551					Q15655|Q5SWY0|Q99968	Silent	SNP	ENST00000367478.4	37	c.1653A>G	CCDS41446.1																																																																																				0.388	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292		11	46	0	0	0	1	0	11	46				
COL4A4	1286	broad.mit.edu	37	2	227924243	227924243	+	Missense_Mutation	SNP	C	C	T			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr2:227924243C>T	ENST00000396625.3	-	28	2468	c.2261G>A	c.(2260-2262)gGt>gAt	p.G754D	COL4A4_ENST00000329662.7_Missense_Mutation_p.G754D	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	754	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		TCCTTTCTGACCATTCACTCC	0.587																																						ENST00000396625.3																			0				breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98						c.(2260-2262)gGt>gAt		collagen, type IV, alpha 4							73.0	78.0	77.0					2																	227924243		1829	4076	5905	SO:0001583	missense	1286				axon guidance|glomerular basement membrane development	basal lamina|collagen type IV	extracellular matrix structural constituent|protein binding	g.chr2:227924243C>T		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"""Collagens"""	2206	protein-coding gene	gene with protein product	"""collagen of basement membrane, alpha-4 chain"""	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.2261G>A	2.37:g.227924243C>T	ENSP00000379866:p.Gly754Asp					COL4A4_ENST00000329662.7_Missense_Mutation_p.G754D	p.G754D	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)	28	2468	-		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)	754			Triple-helical region.		A8MTZ1|Q53RW9|Q53S42|Q53WR1	Missense_Mutation	SNP	ENST00000396625.3	37	c.2261G>A	CCDS42828.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.877527	0.91664	.	.	ENSG00000081052	ENST00000396625;ENST00000329662	D;D	0.99176	-5.52;-5.52	5.99	5.99	0.97316	.	.	.	.	.	D	0.99619	0.9861	H	0.98111	4.15	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97845	1.0271	9	0.87932	D	0	.	18.2507	0.90002	0.0:1.0:0.0:0.0	.	754	P53420	CO4A4_HUMAN	D	754	ENSP00000379866:G754D;ENSP00000328553:G754D	ENSP00000328553:G754D	G	-	2	0	COL4A4	227632487	1.000000	0.71417	0.981000	0.43875	0.969000	0.65631	5.446000	0.66600	2.840000	0.97914	0.655000	0.94253	GGT		0.587	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092		19	39	0	0	0	1	0	19	39				
TTLL1	25809	broad.mit.edu	37	22	43460261	43460261	+	Silent	SNP	G	G	A	rs553997208		TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr22:43460261G>A	ENST00000266254.7	-	6	813	c.573C>T	c.(571-573)ggC>ggT	p.G191G	TTLL1_ENST00000331018.7_Silent_p.G191G	NM_012263.4	NP_036395.1	O95922	TTLL1_HUMAN	tubulin tyrosine ligase-like family, member 1	191	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				axoneme assembly (GO:0035082)|epithelial cilium movement (GO:0003351)|protein polyglutamylation (GO:0018095)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	tubulin-glutamic acid ligase activity (GO:0070740)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(1)	23		Ovarian(80;0.0694)		BRCA - Breast invasive adenocarcinoma(115;0.00461)		ACTTCCTCCCGCCAATTAGTA	0.443													G|||	1	0.000199681	0.0	0.0014	5008	,	,		18567	0.0		0.0	False		,,,				2504	0.0					ENST00000331018.7																			0				breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(1)	23						c.(571-573)ggC>ggT		tubulin tyrosine ligase-like family, member 1							113.0	102.0	106.0					22																	43460261		2203	4300	6503	SO:0001819	synonymous_variant	25809				protein polyglutamylation	cytoplasm|microtubule	ATP binding|tubulin-glutamic acid ligase activity|tubulin-tyrosine ligase activity	g.chr22:43460261G>A	AL096886	CCDS14043.1	22q13.1	2013-02-14			ENSG00000100271	ENSG00000100271		"""Tubulin tyrosine ligase-like family"""	1312	protein-coding gene	gene with protein product		608955	"""tubulin tyrosine ligase-like 1"""	C22orf7		10591208, 11054573	Standard	NM_012263		Approved		uc003bdi.3	O95922	OTTHUMG00000150699	ENST00000266254.7:c.573C>T	22.37:g.43460261G>A						TTLL1_ENST00000266254.7_Silent_p.G191G	p.G191G			O95922	TTLL1_HUMAN		BRCA - Breast invasive adenocarcinoma(115;0.00461)	6	813	-		Ovarian(80;0.0694)	191			TTL.		B2RDS7|Q9BR27|Q9NRS9|Q9UMU0	Silent	SNP	ENST00000266254.7	37	c.573C>T	CCDS14043.1	.	.	.	.	.	.	.	.	.	.	G	5.471	0.271941	0.10349	.	.	ENSG00000100271	ENST00000495814	.	.	.	5.7	-2.69	0.06022	.	.	.	.	.	T	0.39118	0.1066	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.28459	-1.0043	4	.	.	.	.	1.7923	0.03054	0.382:0.2165:0.2908:0.1106	.	.	.	.	V	117	.	.	A	-	2	0	TTLL1	41790205	0.009000	0.17119	0.768000	0.31515	0.365000	0.29674	-1.156000	0.03160	-0.666000	0.05310	-0.373000	0.07131	GCG		0.443	TTLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319659.1	NM_012263		3	42	0	0	0	1	0	3	42				
TRIO	7204	broad.mit.edu	37	5	14488270	14488270	+	Silent	SNP	G	G	T	rs371334482		TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr5:14488270G>T	ENST00000344204.4	+	48	7557	c.7533G>T	c.(7531-7533)cgG>cgT	p.R2511R	TRIO_ENST00000537187.1_Intron|TRIO_ENST00000344135.5_5'Flank	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	2511					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					CCCTCCAGCGGCAGACACCCC	0.711																																						ENST00000344204.4																			0				NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118						c.(7531-7533)cgG>cgT		trio Rho guanine nucleotide exchange factor							8.0	10.0	9.0					5																	14488270		1896	3804	5700	SO:0001819	synonymous_variant	7204				apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity	g.chr5:14488270G>T	AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"""	12303	protein-coding gene	gene with protein product		601893	"""triple functional domain (PTPRF interacting)"""			8643598	Standard	NM_007118		Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.7533G>T	5.37:g.14488270G>T						TRIO_ENST00000537187.1_Intron	p.R2511R	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN			48	7557	+	Lung NSC(4;0.000742)		2511					D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Silent	SNP	ENST00000344204.4	37	c.7533G>T	CCDS3883.1																																																																																				0.711	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118		3	5	1	0	0.115264	1	0.115264	3	5				
GRIN2A	2903	broad.mit.edu	37	16	9857616	9857616	+	Missense_Mutation	SNP	G	G	C	rs587780351		TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr16:9857616G>C	ENST00000396573.2	-	14	4094	c.3785C>G	c.(3784-3786)aCc>aGc	p.T1262S	GRIN2A_ENST00000535259.1_Intron|GRIN2A_ENST00000404927.2_Intron|GRIN2A_ENST00000396575.2_Missense_Mutation_p.T1262S|GRIN2A_ENST00000330684.3_Missense_Mutation_p.T1262S|GRIN2A_ENST00000562109.1_Intron	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	1262					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CTGCTCCCCGGTGGCTGGGTT	0.522																																						ENST00000396573.2																			0				NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198						c.(3784-3786)aCc>aGc		glutamate receptor, ionotropic, N-methyl D-aspartate 2A	Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)						103.0	93.0	97.0					16																	9857616		2197	4300	6497	SO:0001583	missense	0				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding	g.chr16:9857616G>C		CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.3785C>G	16.37:g.9857616G>C	ENSP00000379818:p.Thr1262Ser					GRIN2A_ENST00000562109.1_Intron|GRIN2A_ENST00000396575.2_Missense_Mutation_p.T1262S|GRIN2A_ENST00000404927.2_Intron|GRIN2A_ENST00000330684.3_Missense_Mutation_p.T1262S|GRIN2A_ENST00000535259.1_Intron	p.T1262S	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN			14	4094	-			1262					O00669|Q17RZ6	Missense_Mutation	SNP	ENST00000396573.2	37	c.3785C>G	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	G	2.639	-0.284593	0.05605	.	.	ENSG00000183454	ENST00000396573;ENST00000330684;ENST00000396575	T;T;T	0.09911	2.93;2.93;2.93	5.11	1.55	0.23275	Glutamate [NMDA] receptor, epsilon subunit, C-terminal (1);	0.764422	0.13289	N	0.399108	T	0.05640	0.0148	N	0.22421	0.69	0.22280	N	0.999235	B	0.06786	0.001	B	0.09377	0.004	T	0.40440	-0.9563	9	.	.	.	.	1.996	0.03456	0.1799:0.1217:0.4535:0.2448	.	1262	Q12879	NMDE1_HUMAN	S	1262	ENSP00000379818:T1262S;ENSP00000332549:T1262S;ENSP00000379820:T1262S	.	T	-	2	0	GRIN2A	9765117	0.028000	0.19301	0.355000	0.25773	0.997000	0.91878	0.453000	0.21811	0.515000	0.28320	0.655000	0.94253	ACC		0.522	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			3	81	0	0	0	1	0	3	81				
BYSL	705	broad.mit.edu	37	6	41900430	41900430	+	Missense_Mutation	SNP	A	A	T	rs144306191		TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr6:41900430A>T	ENST00000230340.4	+	7	1675	c.1300A>T	c.(1300-1302)Atc>Ttc	p.I434F		NM_004053.3	NP_004044.3	Q13895	BYST_HUMAN	bystin-like	434					cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|female pregnancy (GO:0007565)|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)|trophectodermal cell differentiation (GO:0001829)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(5)|skin(1)	8	Colorectal(47;0.121)		STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000473)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			AGATGTTCCCATCACCGTGGA	0.557																																						ENST00000230340.4																			0				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(5)|skin(1)	8						c.(1300-1302)Atc>Ttc		bystin-like							51.0	50.0	50.0					6																	41900430		2203	4300	6503	SO:0001583	missense	705				cell adhesion|female pregnancy|ribosome biogenesis	cytoplasm|nucleolus		g.chr6:41900430A>T	L36720	CCDS34450.1	6p21.1	2008-08-29			ENSG00000112578	ENSG00000112578			1157	protein-coding gene	gene with protein product		603871				9925933, 17381424	Standard	NM_004053		Approved		uc003orl.3	Q13895	OTTHUMG00000014687	ENST00000230340.4:c.1300A>T	6.37:g.41900430A>T	ENSP00000230340:p.Ile434Phe						p.I434F	NM_004053.3	NP_004044.3	Q13895	BYST_HUMAN	STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000473)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)		7	1675	+	Colorectal(47;0.121)		434					Q6P5W4|Q86W44|Q96IP8	Missense_Mutation	SNP	ENST00000230340.4	37	c.1300A>T	CCDS34450.1	.	.	.	.	.	.	.	.	.	.	a	14.43	2.533796	0.45073	.	.	ENSG00000112578	ENST00000230340	T	0.32515	1.45	5.13	-4.96	0.03038	.	1.271460	0.05227	N	0.509666	T	0.05868	0.0153	N	0.22421	0.69	0.09310	N	1	B	0.13145	0.007	B	0.19148	0.024	T	0.28744	-1.0034	10	0.20519	T	0.43	-21.4271	8.82	0.35020	0.5654:0.1014:0.3333:0.0	.	434	Q13895	BYST_HUMAN	F	434	ENSP00000230340:I434F	ENSP00000230340:I434F	I	+	1	0	BYSL	42008408	0.000000	0.05858	0.000000	0.03702	0.095000	0.18619	0.101000	0.15251	-1.377000	0.02123	0.449000	0.29647	ATC		0.557	BYSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040535.2			8	15	0	0	0	1	0	8	15				
GLUD1P2	100381203	broad.mit.edu	37	10	48968566	48968566	+	RNA	SNP	A	A	G	rs201727873		TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr10:48968566A>G	ENST00000594520.1	+	0	723									glutamate dehydrogenase 1 pseudogene 2																		ACAGGATAACAAACTGGAAAA	0.318																																						ENST00000594520.1																			0																																																			0							g.chr10:48968566A>G	X66313, X66315, X66319		10q11.22	2013-02-15	2010-01-18	2010-01-18	ENSG00000227781				4337	pseudogene	pseudogene			"""glutamate dehydrogenase pseudogene 2"""	GLUDP2		8486350	Standard			Approved				OTTHUMG00000018156		10.37:g.48968566A>G														0	723	+									RNA	SNP	ENST00000594520.1	37																																																																																						0.318	GLUD1P2-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000461126.1	NG_016765		4	40	0	0	0	1	0	4	40				
DNAJB4	11080	broad.mit.edu	37	1	78478968	78478968	+	Missense_Mutation	SNP	G	G	T			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr1:78478968G>T	ENST00000370763.5	+	2	702	c.445G>T	c.(445-447)Gtg>Ttg	p.V149L	GIPC2_ENST00000476882.1_Intron|DNAJB4_ENST00000487931.1_3'UTR	NM_007034.3	NP_008965.2	Q9UDY4	DNJB4_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 4	149					protein folding (GO:0006457)|response to heat (GO:0009408)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chaperone binding (GO:0051087)|unfolded protein binding (GO:0051082)			endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	10						CAGGAATTCTGTGGGGCCATC	0.413																																						ENST00000370763.5																			0				endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	10						c.(445-447)Gtg>Ttg		DnaJ (Hsp40) homolog, subfamily B, member 4							123.0	123.0	123.0					1																	78478968		2203	4300	6503	SO:0001583	missense	11080				protein folding|response to heat|response to unfolded protein	cytoplasm|plasma membrane	heat shock protein binding|unfolded protein binding	g.chr1:78478968G>T	U40992	CCDS684.1	1p31.1	2011-09-02			ENSG00000162616	ENSG00000162616		"""Heat shock proteins / DNAJ (HSP40)"""	14886	protein-coding gene	gene with protein product		611327				9546042, 11147971	Standard	NM_007034		Approved	HLJ1	uc001dij.3	Q9UDY4	OTTHUMG00000040905	ENST00000370763.5:c.445G>T	1.37:g.78478968G>T	ENSP00000359799:p.Val149Leu					GIPC2_ENST00000476882.1_Intron|DNAJB4_ENST00000487931.1_3'UTR	p.V149L	NM_007034.3	NP_008965.2	Q9UDY4	DNJB4_HUMAN			2	702	+			149					B2R824|Q13431	Missense_Mutation	SNP	ENST00000370763.5	37	c.445G>T	CCDS684.1	.	.	.	.	.	.	.	.	.	.	G	13.53	2.264017	0.39995	.	.	ENSG00000162616	ENST00000426517;ENST00000370763	T;T	0.62941	-0.01;0.39	5.46	5.46	0.80206	.	0.622463	0.17026	N	0.189934	T	0.37999	0.1024	L	0.29908	0.895	0.80722	D	1	B	0.06786	0.001	B	0.08055	0.003	T	0.21245	-1.0251	10	0.19590	T	0.45	.	19.3687	0.94475	0.0:0.0:1.0:0.0	.	149	Q9UDY4	DNJB4_HUMAN	L	149	ENSP00000399494:V149L;ENSP00000359799:V149L	ENSP00000359799:V149L	V	+	1	0	DNAJB4	78251556	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.331000	0.79192	2.546000	0.85860	0.644000	0.83932	GTG		0.413	DNAJB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098248.3			20	68	1	0	5.35267e-07	1	5.83927e-07	20	68				
CATSPERD	257062	broad.mit.edu	37	19	5751816	5751816	+	Silent	SNP	C	C	G			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr19:5751816C>G	ENST00000381624.3	+	12	1207	c.1146C>G	c.(1144-1146)ctC>ctG	p.L382L	CATSPERD_ENST00000381614.2_Silent_p.L40L	NM_152784.3	NP_689997.3	Q86XM0	CTSRD_HUMAN	catsper channel auxiliary subunit delta	382					multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)											ACCCTGAACTCCACGTTGGAA	0.468																																						ENST00000381624.3																			0											c.(1144-1146)ctC>ctG		catsper channel auxiliary subunit delta							68.0	63.0	64.0					19																	5751816		1919	4126	6045	SO:0001819	synonymous_variant	257062					integral to membrane		g.chr19:5751816C>G	BC043005	CCDS12149.2	19p13.3	2013-10-11	2012-02-22	2012-02-22	ENSG00000174898	ENSG00000174898			28598	protein-coding gene	gene with protein product			"""transmembrane protein 146"""	TMEM146		21224844	Standard	NM_152784		Approved	MGC39581	uc002mda.3	Q86XM0	OTTHUMG00000143036	ENST00000381624.3:c.1146C>G	19.37:g.5751816C>G						CATSPERD_ENST00000381614.2_Silent_p.L40L	p.L382L	NM_152784.3	NP_689997.3	Q86XM0	TM146_HUMAN			12	1207	+			382					Q6ZRP1	Silent	SNP	ENST00000381624.3	37	c.1146C>G	CCDS12149.2																																																																																				0.468	CATSPERD-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286953.2	NM_152784		9	57	0	0	0	1	0	9	57				
ZNF679	168417	broad.mit.edu	37	7	63709526	63709526	+	Nonsense_Mutation	SNP	C	C	T	rs191648017	byFrequency	TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr7:63709526C>T	ENST00000421025.1	+	2	300	c.31C>T	c.(31-33)Cga>Tga	p.R11*	ZNF679_ENST00000255746.4_Nonsense_Mutation_p.R11*	NM_001159524.1|NM_153363.2	NP_001152996.1|NP_699194.2	Q8IYX0	ZN679_HUMAN	zinc finger protein 679	11					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|skin(1)|stomach(1)	18						CCCTGGAAGCCGAGAAATGGT	0.572																																						ENST00000421025.1																			0				endometrium(2)|kidney(3)|lung(11)|skin(1)|stomach(1)	18						c.(31-33)Cga>Tga		zinc finger protein 679							47.0	39.0	42.0					7																	63709526		692	1591	2283	SO:0001587	stop_gained	168417				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr7:63709526C>T	BC033523	CCDS47592.1	7q11.21	2013-01-08			ENSG00000197123	ENSG00000197123		"""Zinc fingers, C2H2-type"", ""-"""	28650	protein-coding gene	gene with protein product	"""hypothetical protein MGC42415"""					12477932	Standard	NM_153363		Approved	MGC42415	uc003tsx.3	Q8IYX0	OTTHUMG00000156486	ENST00000421025.1:c.31C>T	7.37:g.63709526C>T	ENSP00000416809:p.Arg11*					ZNF679_ENST00000255746.4_Nonsense_Mutation_p.R11*	p.R11*	NM_001159524.1|NM_153363.2	NP_001152996.1|NP_699194.2	Q8IYX0	ZN679_HUMAN			2	300	+			11						Nonsense_Mutation	SNP	ENST00000421025.1	37	c.31C>T	CCDS47592.1	.	.	.	.	.	.	.	.	.	.	c	14.87	2.665496	0.47677	.	.	ENSG00000197123	ENST00000421025;ENST00000255746	.	.	.	0.421	0.421	0.16451	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13853	T	0.58	.	.	.	.	.	.	.	.	X	11	.	ENSP00000255746:R11X	R	+	1	2	ZNF679	63346961	0.009000	0.17119	0.004000	0.12327	0.004000	0.04260	0.420000	0.21263	0.452000	0.26830	0.455000	0.32223	CGA		0.572	ZNF679-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344317.2	NM_153363		7	34	0	0	0	1	0	7	34				
RGPD3	653489	broad.mit.edu	37	2	107049681	107049681	+	Missense_Mutation	SNP	T	T	C	rs369310197		TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr2:107049681T>C	ENST00000409886.3	-	16	2353	c.2266A>G	c.(2266-2268)Aac>Gac	p.N756D	RGPD3_ENST00000304514.7_Missense_Mutation_p.N756D	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	756					protein targeting to Golgi (GO:0000042)			p.N756D(6)		breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						TCACTATAGTTTTCGAGTTCC	0.373																																						ENST00000409886.3																			6	Substitution - Missense(6)	p.N756D(6)	endometrium(6)	breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						c.(2266-2268)Aac>Gac		RANBP2-like and GRIP domain containing 3							164.0	133.0	142.0					2																	107049681		692	1590	2282	SO:0001583	missense	653489				intracellular transport		binding	g.chr2:107049681T>C		CCDS46379.1	2q12.2	2013-01-10			ENSG00000153165	ENSG00000153165		"""Tetratricopeptide (TTC) repeat domain containing"""	32416	protein-coding gene	gene with protein product		612706				15710750, 15815621	Standard	NM_001144013		Approved	RGP3	uc010ywi.1	A6NKT7	OTTHUMG00000153182	ENST00000409886.3:c.2266A>G	2.37:g.107049681T>C	ENSP00000386588:p.Asn756Asp					RGPD3_ENST00000304514.7_Missense_Mutation_p.N756D	p.N756D	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN			16	2353	-			756					B8ZZM4	Missense_Mutation	SNP	ENST00000409886.3	37	c.2266A>G	CCDS46379.1	.	.	.	.	.	.	.	.	.	.	.	0.003	-2.481585	0.00163	.	.	ENSG00000153165	ENST00000409886;ENST00000452099;ENST00000304514	T;T	0.23754	1.89;1.89	2.34	2.34	0.29019	.	.	.	.	.	T	0.07638	0.0192	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.37979	-0.9682	9	0.02654	T	1	-2.2547	7.1228	0.25454	0.0:0.8499:0.0:0.1501	.	756	A6NKT7	RGPD3_HUMAN	D	756;514;756	ENSP00000386588:N756D;ENSP00000303659:N756D	ENSP00000303659:N756D	N	-	1	0	RGPD3	106416113	0.974000	0.33945	0.242000	0.24170	0.003000	0.03518	4.107000	0.57811	0.325000	0.23359	-1.206000	0.01644	AAC		0.373	RGPD3-002	KNOWN	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329975.1	XM_929931		4	296	0	0	0	1	0	4	296				
RUSC2	9853	broad.mit.edu	37	9	35548057	35548057	+	Silent	SNP	G	G	A			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr9:35548057G>A	ENST00000455600.1	+	2	2108	c.1539G>A	c.(1537-1539)tcG>tcA	p.S513S		NM_001135999.1	NP_001129471	Q8N2Y8	RUSC2_HUMAN	RUN and SH3 domain containing 2	513						cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)	Rab GTPase binding (GO:0017137)			NS(1)|breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(4)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32			Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)			GCCTGGGCTCGCTGGAACGTA	0.647																																						ENST00000455600.1																			0				NS(1)|breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(4)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						c.(1537-1539)tcG>tcA		RUN and SH3 domain containing 2							33.0	35.0	34.0					9																	35548057		2203	4300	6503	SO:0001819	synonymous_variant	9853					cytosol		g.chr9:35548057G>A	AB002373	CCDS35008.1	9p13.2	2003-12-02			ENSG00000198853	ENSG00000198853			23625	protein-coding gene	gene with protein product		611053				9205841	Standard	NM_001135999		Approved	KIAA0375	uc003zww.3	Q8N2Y8	OTTHUMG00000019861	ENST00000455600.1:c.1539G>A	9.37:g.35548057G>A							p.S513S	NM_001135999.1	NP_001129471.1	Q8N2Y8	RUSC2_HUMAN	Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)		2	2108	+			513					A2RU62|A7E2A9|O15080|Q5W134|Q641Q6|Q6P1W7	Silent	SNP	ENST00000455600.1	37	c.1539G>A	CCDS35008.1																																																																																				0.647	RUSC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052309.1	XM_048462		10	37	0	0	0	1	0	10	37				
TRERF1	55809	broad.mit.edu	37	6	42227383	42227383	+	Missense_Mutation	SNP	G	G	A	rs142184147		TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr6:42227383G>A	ENST00000372922.4	-	9	2525	c.1963C>T	c.(1963-1965)Cgg>Tgg	p.R655W	TRERF1_ENST00000541110.1_Missense_Mutation_p.R675W|TRERF1_ENST00000354325.2_Missense_Mutation_p.R572W|TRERF1_ENST00000340840.2_Missense_Mutation_p.R572W|TRERF1_ENST00000372917.4_Missense_Mutation_p.R572W	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	655	Interacts with CREBBP.|Pro-rich.				cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			GGCCGGTGCCGGAACTTTTTC	0.627																																						ENST00000541110.1																			0				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45						c.(2023-2025)Cgg>Tgg		transcriptional regulating factor 1		G	TRP/ARG	1,4405		0,1,2202	45.0	56.0	52.0		1963	4.4	1.0	6	dbSNP_134	52	0,8600		0,0,4300	no	missense	TRERF1	NM_033502.2	101	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	655/1201	42227383	1,13005	2203	4300	6503	SO:0001583	missense	55809				cholesterol catabolic process|homeostatic process|multicellular organismal development|positive regulation of transcription, DNA-dependent|regulation of hormone biosynthetic process|steroid biosynthetic process	nucleus	DNA bending activity|ligand-dependent nuclear receptor transcription coactivator activity|RNA polymerase II transcription cofactor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding	g.chr6:42227383G>A	AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496			18273	protein-coding gene	gene with protein product		610322	"""breast cancer anti-estrogen resistance 2"""	BCAR2		11349124	Standard	XM_005249223		Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.1963C>T	6.37:g.42227383G>A	ENSP00000362013:p.Arg655Trp					TRERF1_ENST00000372917.4_Missense_Mutation_p.R572W|TRERF1_ENST00000340840.2_Missense_Mutation_p.R572W|TRERF1_ENST00000372922.4_Missense_Mutation_p.R655W|TRERF1_ENST00000354325.2_Missense_Mutation_p.R572W	p.R675W			Q96PN7	TREF1_HUMAN	Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)		9	2591	-	Colorectal(47;0.196)		655			Interacts with CREBBP.|Pro-rich.		Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Missense_Mutation	SNP	ENST00000372922.4	37	c.2023C>T	CCDS4867.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.858002	0.91433	2.27E-4	0.0	ENSG00000124496	ENST00000541110;ENST00000372917;ENST00000372922;ENST00000340840;ENST00000354325	T;T;T;T;T	0.20881	2.08;2.34;2.04;2.34;2.34	5.32	4.45	0.53987	.	0.000000	0.53938	D	0.000049	T	0.36552	0.0971	M	0.75615	2.305	0.44562	D	0.997528	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.997	T	0.37888	-0.9686	10	0.87932	D	0	-16.6019	14.2029	0.65716	0.0722:0.0:0.9278:0.0	.	572;675;655;411;411	Q96PN7-4;Q05GC8;Q96PN7;Q96PN7-2;Q96PN7-3	.;.;TREF1_HUMAN;.;.	W	675;572;655;572;572	ENSP00000439689:R675W;ENSP00000362008:R572W;ENSP00000362013:R655W;ENSP00000339438:R572W;ENSP00000346285:R572W	ENSP00000339438:R572W	R	-	1	2	TRERF1	42335361	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.461000	0.97646	1.245000	0.43885	-0.119000	0.15052	CGG		0.627	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502		9	96	0	0	0	1	0	9	96				
NOL6	65083	broad.mit.edu	37	9	33468419	33468419	+	Splice_Site	SNP	G	G	A	rs201544071	byFrequency	TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr9:33468419G>A	ENST00000379471.2	-	10	1295	c.1208C>T	c.(1207-1209)cCg>cTg	p.P403L	NOL6_ENST00000455041.2_Splice_Site_p.P343L|NOL6_ENST00000464829.1_Intron			Q9H6R4	NOL6_HUMAN	nucleolar protein 6 (RNA-associated)	403					rRNA processing (GO:0006364)	condensed nuclear chromosome (GO:0000794)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|skin(2)	27			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.152)		AGCCAGGGCCGGCTTGGGGGG	0.577													G|||	3	0.000599042	0.0	0.0	5008	,	,		19071	0.003		0.0	False		,,,				2504	0.0					ENST00000379471.2																			0				endometrium(4)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|skin(2)	27						c.e10-1		nucleolar protein 6 (RNA-associated)		G	LEU/PRO,LEU/PRO	0,4406		0,0,2203	60.0	62.0	61.0		1208,1208	5.3	1.0	9		61	1,8599	1.2+/-3.3	0,1,4299	yes	missense-near-splice,missense-near-splice	NOL6	NM_022917.4,NM_139235.3	98,98	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	403/1147,403/700	33468419	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	65083				rRNA processing	condensed nuclear chromosome|nucleolus	RNA binding	g.chr9:33468419G>A	AF361079	CCDS6543.1, CCDS6544.1	9p12	2013-02-22	2013-02-22		ENSG00000165271	ENSG00000165271			19910	protein-coding gene	gene with protein product		611532	"""nucleolar protein family 6 (RNA-associated)"""			11895476, 15590835	Standard	NM_022917		Approved	bA311H10.1, Nrap, FLJ21959, MGC14896, MGC14921, MGC20838, UTP22	uc003zsz.3	Q9H6R4	OTTHUMG00000000394	ENST00000379471.2:c.1207-1C>T	9.37:g.33468419G>A						NOL6_ENST00000455041.2_Splice_Site_p.P343_splice|NOL6_ENST00000464829.1_Intron	p.P403_splice			Q9H6R4	NOL6_HUMAN	LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.152)	10	1295	-			403					Q5T5M3|Q5T5M4|Q7L4G6|Q8N6I0|Q8TEY9|Q8TEZ0|Q8TEZ1|Q9H675	Splice_Site	SNP	ENST00000379471.2	37	c.1206_splice		.	.	.	.	.	.	.	.	.	.	G	23.1	4.374148	0.82573	0.0	1.16E-4	ENSG00000165271	ENST00000353159;ENST00000297990;ENST00000379471;ENST00000325914;ENST00000455041	T;T;T;T	0.40756	1.02;1.02;1.02;1.02	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.65144	0.2663	M	0.71206	2.165	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;0.996;1.0	D;D;D;P;D	0.97110	0.999;0.999;0.997;0.781;1.0	T	0.63950	-0.6521	10	0.41790	T	0.15	.	18.6286	0.91350	0.0:0.0:1.0:0.0	.	343;400;403;403;403	B4DF80;Q9H6R4-4;Q9H6R4-2;Q9H6R4-3;Q9H6R4	.;.;.;.;NOL6_HUMAN	L	403;403;403;403;343	ENSP00000313978:P403L;ENSP00000297990:P403L;ENSP00000368784:P403L;ENSP00000395915:P343L	ENSP00000297990:P403L	P	-	2	0	NOL6	33458419	1.000000	0.71417	0.999000	0.59377	0.852000	0.48524	9.059000	0.93902	2.506000	0.84524	0.462000	0.41574	CCG		0.577	NOL6-005	NOVEL	non_canonical_TEC|basic	protein_coding	protein_coding	OTTHUMT00000001019.2	NM_022917	Missense_Mutation	6	17	0	0	0	1	0	6	17				
RAD21	5885	broad.mit.edu	37	8	117859877	117859877	+	Silent	SNP	T	T	G			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr8:117859877T>G	ENST00000297338.2	-	14	2045	c.1758A>C	c.(1756-1758)cgA>cgC	p.R586R	RAD21_ENST00000517749.1_Silent_p.R24R|UTP23_ENST00000520733.1_Intron|UTP23_ENST00000517820.1_Intron|RAD21_ENST00000523986.1_Silent_p.R90R|RAD21_ENST00000518055.1_Silent_p.R131R	NM_006265.2	NP_006256.1	O60216	RAD21_HUMAN	RAD21 homolog (S. pombe)	586					apoptotic process (GO:0006915)|chromosome segregation (GO:0007059)|DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|protein localization to chromatin (GO:0071168)|reciprocal meiotic recombination (GO:0007131)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(1)|stomach(1)	32	all_cancers(13;1.21e-21)|Lung NSC(37;0.000134)|Ovarian(258;0.0172)					TGTTCGTATTTCGACATAACT	0.388																																						ENST00000297338.2																			0				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(1)|stomach(1)	32						c.(1756-1758)cgA>cgC		RAD21 homolog (S. pombe)							88.0	81.0	83.0					8																	117859877		2203	4300	6503	SO:0001819	synonymous_variant	5885				apoptosis|cell division|chromosome segregation|double-strand break repair|mitotic metaphase/anaphase transition|mitotic prometaphase|protein localization to chromatin|reciprocal meiotic recombination|regulation of transcription from RNA polymerase II promoter	chromosome, centromeric region|cohesin complex|nuclear chromosome|nucleoplasm	protein binding	g.chr8:117859877T>G	BC050381	CCDS6321.1	8q24.11	2014-09-17	2001-11-28		ENSG00000164754	ENSG00000164754			9811	protein-coding gene	gene with protein product	"""sister chromatid cohesion 1"""	606462	"""RAD21 (S. pombe) homolog"""			8812457	Standard	NM_006265		Approved	KIAA0078, hHR21, SCC1	uc003yod.3	O60216	OTTHUMG00000164959	ENST00000297338.2:c.1758A>C	8.37:g.117859877T>G						RAD21_ENST00000518055.1_Silent_p.R131R|UTP23_ENST00000520733.1_Intron|RAD21_ENST00000517749.1_Silent_p.R24R|UTP23_ENST00000517820.1_Intron|RAD21_ENST00000523986.1_Silent_p.R90R	p.R586R	NM_006265.2	NP_006256.1	O60216	RAD21_HUMAN			14	2045	-	all_cancers(13;1.21e-21)|Lung NSC(37;0.000134)|Ovarian(258;0.0172)		586					A8K0E0|Q15001|Q99568	Silent	SNP	ENST00000297338.2	37	c.1758A>C	CCDS6321.1																																																																																				0.388	RAD21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381184.1	NM_006265		9	62	0	0	0	1	0	9	62				
G3BP2	9908	broad.mit.edu	37	4	76579226	76579226	+	Missense_Mutation	SNP	G	G	A			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr4:76579226G>A	ENST00000359707.4	-	8	1551	c.766C>T	c.(766-768)Cct>Tct	p.P256S	G3BP2_ENST00000502654.1_5'Flank|G3BP2_ENST00000395719.3_Missense_Mutation_p.P256S|G3BP2_ENST00000357854.3_Intron	NM_203505.2	NP_987101.1	Q9UN86	G3BP2_HUMAN	GTPase activating protein (SH3 domain) binding protein 2	256					cytoplasmic sequestering of NF-kappaB (GO:0007253)|mRNA transport (GO:0051028)|Ras protein signal transduction (GO:0007265)	cytoplasm (GO:0005737)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|receptor signaling complex scaffold activity (GO:0030159)			breast(3)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	27			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			GTACCACTAGGAGGCAGGTTT	0.443																																						ENST00000359707.4																			0				breast(3)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	27						c.(766-768)Cct>Tct		GTPase activating protein (SH3 domain) binding protein 2							86.0	84.0	85.0					4																	76579226		2203	4300	6503	SO:0001583	missense	9908				cytoplasmic sequestering of NF-kappaB|mRNA transport|Ras protein signal transduction|regulation of small GTPase mediated signal transduction	cytosol	GTPase activator activity|nucleotide binding|receptor signaling complex scaffold activity|RNA binding	g.chr4:76579226G>A	AB014560	CCDS3571.1, CCDS3572.1	4q21.1	2013-02-12	2006-11-01		ENSG00000138757	ENSG00000138757		"""RNA binding motif (RRM) containing"""	30291	protein-coding gene	gene with protein product	"""Ras-GTPase activating protein SH3 domain-binding protein 2"""					9734811, 9575347	Standard	NM_203504		Approved	KIAA0660	uc003his.3	Q9UN86	OTTHUMG00000130097	ENST00000359707.4:c.766C>T	4.37:g.76579226G>A	ENSP00000352738:p.Pro256Ser					G3BP2_ENST00000357854.3_Intron|G3BP2_ENST00000395719.3_Missense_Mutation_p.P256S	p.P256S	NM_203505.2	NP_987101.1	Q9UN86	G3BP2_HUMAN	Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)		8	1551	-			256					A8K6X1|O60606|O75149|Q9UPA1	Missense_Mutation	SNP	ENST00000359707.4	37	c.766C>T	CCDS3571.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.113928	0.77210	.	.	ENSG00000138757	ENST00000395719;ENST00000359707	T;T	0.78816	-1.21;-1.21	5.95	5.95	0.96441	.	0.047834	0.85682	D	0.000000	D	0.82600	0.5072	L	0.60455	1.87	0.80722	D	1	P	0.47910	0.902	P	0.53185	0.72	T	0.76572	-0.2910	10	0.17369	T	0.5	.	20.4024	0.99000	0.0:0.0:1.0:0.0	.	256	Q9UN86	G3BP2_HUMAN	S	256	ENSP00000379069:P256S;ENSP00000352738:P256S	ENSP00000352738:P256S	P	-	1	0	G3BP2	76798250	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.476000	0.97823	2.827000	0.97445	0.650000	0.86243	CCT		0.443	G3BP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252399.2	NM_012297		3	12	0	0	0	1	0	3	12				
TARS2	80222	broad.mit.edu	37	1	150468986	150468986	+	Missense_Mutation	SNP	G	G	T			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr1:150468986G>T	ENST00000369064.3	+	8	837	c.803G>T	c.(802-804)gGg>gTg	p.G268V	TARS2_ENST00000463555.1_Intron|TARS2_ENST00000438568.2_3'UTR|TARS2_ENST00000369054.2_Intron|TARS2_ENST00000606933.1_Intron	NM_025150.3	NP_079426.2	Q9BW92	SYTM_HUMAN	threonyl-tRNA synthetase 2, mitochondrial (putative)	268					gene expression (GO:0010467)|mitochondrial threonyl-tRNA aminoacylation (GO:0070159)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|threonine-tRNA ligase activity (GO:0004829)			cervix(1)|endometrium(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	35	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.51e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)		L-Threonine(DB00156)	AGGTCTTCAGGGGCCCCAGAG	0.517																																						ENST00000369064.3																			0				cervix(1)|endometrium(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	35						c.(802-804)gGg>gTg		threonyl-tRNA synthetase 2, mitochondrial (putative)	L-Threonine(DB00156)						115.0	110.0	112.0					1																	150468986		2203	4300	6503	SO:0001583	missense	80222				threonyl-tRNA aminoacylation	mitochondrial matrix	ATP binding|threonine-tRNA ligase activity	g.chr1:150468986G>T	BC007824	CCDS952.1, CCDS60251.1, CCDS60252.1	1q21.2	2012-10-26	2007-02-23	2007-02-23	ENSG00000143374	ENSG00000143374	6.1.1.3	"""Aminoacyl tRNA synthetases / Class II"""	30740	protein-coding gene	gene with protein product	"""threonine tRNA ligase 2, mitochondrial"""	612805	"""threonyl-tRNA synthetase-like 1"""	TARSL1			Standard	NM_001271895		Approved	FLJ12528	uc001euq.4	Q9BW92	OTTHUMG00000012809	ENST00000369064.3:c.803G>T	1.37:g.150468986G>T	ENSP00000358060:p.Gly268Val					TARS2_ENST00000606933.1_Intron|TARS2_ENST00000463555.1_Intron|TARS2_ENST00000438568.2_3'UTR|TARS2_ENST00000369054.2_Intron	p.G268V	NM_025150.3	NP_079426.2	Q9BW92	SYTM_HUMAN	UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.51e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)		8	837	+	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		268					Q53GW7|Q96I50|Q9H9V2	Missense_Mutation	SNP	ENST00000369064.3	37	c.803G>T	CCDS952.1	.	.	.	.	.	.	.	.	.	.	G	11.72	1.723472	0.30593	.	.	ENSG00000143374	ENST00000369064	.	.	.	5.02	0.831	0.18860	Threonyl/alanyl tRNA synthetase, SAD (2);Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain (1);	0.831895	0.11159	N	0.593226	T	0.04227	0.0117	N	0.05487	-0.04	0.09310	N	0.999992	B	0.34103	0.437	B	0.33846	0.171	T	0.32955	-0.9887	9	0.42905	T	0.14	-3.134	1.7989	0.03067	0.221:0.2524:0.3972:0.1295	.	268	Q9BW92	SYTM_HUMAN	V	268	.	ENSP00000358060:G268V	G	+	2	0	TARS2	148735610	0.668000	0.27493	0.000000	0.03702	0.947000	0.59692	1.230000	0.32612	-0.003000	0.14444	0.655000	0.94253	GGG		0.517	TARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035847.1	NM_025150		7	102	1	0	1.26484e-09	1	1.4319e-09	7	102				
EPM2A	7957	broad.mit.edu	37	6	145956563	145956563	+	Missense_Mutation	SNP	T	T	A			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr6:145956563T>A	ENST00000367519.3	-	3	1061	c.536A>T	c.(535-537)aAa>aTa	p.K179I	EPM2A_ENST00000496228.1_5'UTR	NM_005670.3	NP_005661.1	O95278	EPM2A_HUMAN	epilepsy, progressive myoclonus type 2A, Lafora disease (laforin)	179					autophagy (GO:0006914)|carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen metabolic process (GO:0005977)|habituation (GO:0046959)|inositol phosphate dephosphorylation (GO:0046855)|nervous system development (GO:0007399)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polysome (GO:0005844)	carbohydrate phosphatase activity (GO:0019203)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|starch binding (GO:2001070)			kidney(1)|large_intestine(2)|lung(2)|pancreas(1)|skin(1)	7		Ovarian(120;0.162)		OV - Ovarian serous cystadenocarcinoma(155;3.38e-07)|GBM - Glioblastoma multiforme(68;0.0203)		ATGCTTCAGTTTGATGGTTAC	0.438																																						ENST00000367519.3																			0				kidney(1)|large_intestine(2)|lung(2)|pancreas(1)|skin(1)	7						c.(535-537)aAa>aTa		epilepsy, progressive myoclonus type 2A, Lafora disease (laforin)							127.0	112.0	117.0					6																	145956563		2203	4300	6503	SO:0001583	missense	7957				glycogen metabolic process	cytosol|endoplasmic reticulum|nucleus|plasma membrane|polysome	carbohydrate binding|identical protein binding|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	g.chr6:145956563T>A	AF284580	CCDS5206.1	6q24	2011-06-09			ENSG00000112425	ENSG00000112425		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	3413	protein-coding gene	gene with protein product		607566	"""epilepsy, progressive myoclonus type 2, Lafora disease (laforin)"""			9222970, 7485240	Standard	XM_006715564		Approved	LDE, LD	uc003qkw.3	B3EWF7	OTTHUMG00000015747	ENST00000367519.3:c.536A>T	6.37:g.145956563T>A	ENSP00000356489:p.Lys179Ile					EPM2A_ENST00000496228.1_5'UTR	p.K179I	NM_005670.3	NP_005661.1	O95278	EPM2A_HUMAN		OV - Ovarian serous cystadenocarcinoma(155;3.38e-07)|GBM - Glioblastoma multiforme(68;0.0203)	3	1061	-		Ovarian(120;0.162)	179					B3KMU5|B4DRZ2|O95483|Q5T3F5|Q6IS15|Q8IU96|Q8IX24|Q8IX25|Q9BS66|Q9UEN2	Missense_Mutation	SNP	ENST00000367519.3	37	c.536A>T	CCDS5206.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.9|25.9	4.680428|4.680428	0.88542|0.88542	.|.	.|.	ENSG00000112425|ENSG00000112425	ENST00000535403;ENST00000367519;ENST00000392304;ENST00000324857|ENST00000450221;ENST00000435470	T|.	0.61274|.	0.12|.	5.91|5.91	4.76|4.76	0.60689|0.60689	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (1);|.	0.043038|.	0.85682|.	D|.	0.000000|.	T|T	0.47040|0.47040	0.1424|0.1424	L|L	0.49350|0.49350	1.555|1.555	0.58432|0.58432	D|D	0.999992|0.999992	D;D;D|.	0.71674|.	0.998;0.998;0.998|.	D;D;D|.	0.68943|.	0.961;0.929;0.942|.	T|T	0.45556|0.45556	-0.9253|-0.9253	10|5	0.59425|.	D|.	0.04|.	-20.7379|-20.7379	11.6928|11.6928	0.51525|0.51525	0.0:0.0687:0.0:0.9313|0.0:0.0687:0.0:0.9313	.|.	179;179;41|.	O95278;O95278-2;E1P599|.	EPM2A_HUMAN;.;.|.	I|Y	179|79;99	ENSP00000356489:K179I|.	ENSP00000320279:K179I|.	K|N	-|-	2|1	0|0	EPM2A|EPM2A	145998256|145998256	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	5.975000|5.975000	0.70475|0.70475	1.073000|1.073000	0.40885|0.40885	0.533000|0.533000	0.62120|0.62120	AAA|AAC		0.438	EPM2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042564.1			33	71	0	0	0	1	0	33	71				
SPARCL1	8404	broad.mit.edu	37	4	88401672	88401672	+	Splice_Site	SNP	C	C	T			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr4:88401672C>T	ENST00000282470.6	-	9	2139	c.1669G>A	c.(1669-1671)Gtc>Atc	p.V557I	SPARCL1_ENST00000503414.1_Splice_Site_p.V432I|SPARCL1_ENST00000418378.1_Splice_Site_p.V557I	NM_004684.4	NP_004675.3	Q14515	SPRL1_HUMAN	SPARC-like 1 (hevin)	557					signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(2)	21				OV - Ovarian serous cystadenocarcinoma(123;0.00118)		ATTTTCTTGACCTGGGATTAG	0.398																																						ENST00000418378.1																			0				breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(2)	21						c.e10-1		SPARC-like 1 (hevin)							84.0	85.0	85.0					4																	88401672		2203	4300	6503	SO:0001630	splice_region_variant	8404				signal transduction	extracellular space|proteinaceous extracellular matrix	calcium ion binding	g.chr4:88401672C>T	X86693	CCDS3622.1	4q22-q25	2013-01-10	2008-08-29		ENSG00000152583	ENSG00000152583		"""EF-hand domain containing"""	11220	protein-coding gene	gene with protein product		606041	"""SPARC-like 1 (mast9, hevin)"""			8488563, 7600298, 16844696	Standard	NM_001128310		Approved	MAST9	uc003hqs.4	Q14515	OTTHUMG00000130605	ENST00000282470.6:c.1669-1G>A	4.37:g.88401672C>T						SPARCL1_ENST00000282470.6_Splice_Site_p.V557_splice|SPARCL1_ENST00000503414.1_Splice_Site_p.V432_splice	p.V557_splice	NM_001128310.1	NP_001121782.1	Q14515	SPRL1_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;0.00118)	10	2240	-			557					B4E2Z0|E7ESU2|Q14800	Splice_Site	SNP	ENST00000282470.6	37	c.1668_splice	CCDS3622.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.789058	0.90367	.	.	ENSG00000152583	ENST00000282470;ENST00000418378;ENST00000438050;ENST00000503414	T;T;T	0.31769	2.04;2.04;1.48	4.92	4.92	0.64577	SPARC/Testican, calcium-binding domain (1);EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.62563	0.2438	M	0.87038	2.855	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.69669	-0.5083	10	0.87932	D	0	-12.3112	17.9858	0.89155	0.0:1.0:0.0:0.0	.	557	Q14515	SPRL1_HUMAN	I	557;557;432;432	ENSP00000282470:V557I;ENSP00000414856:V557I;ENSP00000422903:V432I	ENSP00000282470:V557I	V	-	1	0	SPARCL1	88620696	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	7.248000	0.78268	2.663000	0.90544	0.585000	0.79938	GTC		0.398	SPARCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253059.2		Missense_Mutation	20	49	0	0	0	1	0	20	49				
OTOF	9381	broad.mit.edu	37	2	26689990	26689990	+	Missense_Mutation	SNP	C	C	T	rs201493014		TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr2:26689990C>T	ENST00000272371.2	-	35	4465	c.4339G>A	c.(4339-4341)Gag>Aag	p.E1447K	OTOF_ENST00000402415.3_Missense_Mutation_p.E757K|OTOF_ENST00000339598.3_Missense_Mutation_p.E680K|OTOF_ENST00000403946.3_Missense_Mutation_p.E1447K|OTOF_ENST00000338581.6_Missense_Mutation_p.E680K	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	1447					membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ACAATGCGCTCCTCCTCGGTG	0.627													C|||	1	0.000199681	0.0	0.0014	5008	,	,		14388	0.0		0.0	False		,,,				2504	0.0				GBM(102;732 1451 20652 24062 31372)	ENST00000272371.2																			0				NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106						c.(4339-4341)Gag>Aag		otoferlin							58.0	53.0	54.0					2																	26689990		2203	4300	6503	SO:0001583	missense	9381				cellular membrane fusion|sensory perception of sound|synaptic vesicle exocytosis	basolateral plasma membrane|cell junction|cytosol|endoplasmic reticulum membrane|integral to membrane|membrane fraction|synaptic vesicle membrane	calcium ion binding	g.chr2:26689990C>T	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.4339G>A	2.37:g.26689990C>T	ENSP00000272371:p.Glu1447Lys					OTOF_ENST00000402415.3_Missense_Mutation_p.E757K|OTOF_ENST00000339598.3_Missense_Mutation_p.E680K|OTOF_ENST00000338581.6_Missense_Mutation_p.E680K|OTOF_ENST00000403946.3_Missense_Mutation_p.E1447K	p.E1447K	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN			35	4465	-	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)		1447					B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Missense_Mutation	SNP	ENST00000272371.2	37	c.4339G>A	CCDS1725.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	19.12	3.766700	0.69878	.	.	ENSG00000115155	ENST00000338581;ENST00000339598;ENST00000402415;ENST00000272371;ENST00000403946	T;T;T;T;T	0.79940	-1.06;-1.06;-1.06;-1.32;-1.32	4.42	4.42	0.53409	.	0.047076	0.85682	D	0.000000	T	0.74168	0.3681	L	0.47716	1.5	0.58432	D	0.999998	B;B;B;B	0.19073	0.017;0.014;0.029;0.033	B;B;B;B	0.26614	0.012;0.02;0.027;0.071	T	0.68368	-0.5427	10	0.06757	T	0.87	-33.9162	16.9753	0.86311	0.0:1.0:0.0:0.0	.	1447;680;757;680	Q9HC10;Q9HC10-2;Q9HC10-3;Q9HC10-4	OTOF_HUMAN;.;.;.	K	680;680;757;1447;1447	ENSP00000345137:E680K;ENSP00000344521:E680K;ENSP00000383906:E757K;ENSP00000272371:E1447K;ENSP00000385255:E1447K	ENSP00000272371:E1447K	E	-	1	0	OTOF	26543494	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.749000	0.85096	2.167000	0.68274	0.561000	0.74099	GAG		0.627	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3			9	29	0	0	0	1	0	9	29				
APC	324	broad.mit.edu	37	5	112174631	112174631	+	Nonsense_Mutation	SNP	C	C	T	rs121913331		TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr5:112174631C>T	ENST00000457016.1	+	16	3720	c.3340C>T	c.(3340-3342)Cga>Tga	p.R1114*	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Nonsense_Mutation_p.R1114*|APC_ENST00000508376.2_Nonsense_Mutation_p.R1114*			P25054	APC_HUMAN	adenomatous polyposis coli	1114	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R1114*(30)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AGAAACAAATCGAGTGGGTTC	0.403	R1114*(LOVO_LARGE_INTESTINE)|R1114*(SW948_LARGE_INTESTINE)	12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	ENST00000457016.1	R1114*(LOVO_LARGE_INTESTINE)|R1114*(SW948_LARGE_INTESTINE)	12	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	"""D, Mis, N, F, S"""	adenomatous polyposis of the colon gene			"""E, M, O"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""		31	Substitution - Nonsense(30)|Unknown(1)	p.R1114*(30)|p.?(1)	large_intestine(29)|ovary(1)|skin(1)	NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261	GRCh37	CM920048	APC	M	rs121913331	c.(3340-3342)Cga>Tga		adenomatous polyposis coli							90.0	82.0	85.0					5																	112174631		2202	4300	6502	SO:0001587	stop_gained	324	Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	canonical Wnt receptor signaling pathway|cell adhesion|cell cycle arrest|cell migration|cellular component disassembly involved in apoptosis|cytokinesis after mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cyclin-dependent protein kinase activity|negative regulation of microtubule depolymerization|positive regulation of apoptosis|positive regulation of cell migration|positive regulation of pseudopodium assembly|protein complex assembly|regulation of attachment of spindle microtubules to kinetochore|response to DNA damage stimulus|tight junction assembly	adherens junction|APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|centrosome|cytosol|kinetochore|lamellipodium|lateral plasma membrane|nucleus|ruffle membrane|tight junction	beta-catenin binding|gamma-catenin binding|microtubule plus-end binding|protein kinase binding|protein kinase regulator activity	g.chr5:112174631C>T	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3340C>T	5.37:g.112174631C>T	ENSP00000413133:p.Arg1114*	TSP Lung(16;0.13)				APC_ENST00000257430.4_Nonsense_Mutation_p.R1114*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.R1114*	p.R1114*			P25054	APC_HUMAN		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)	16	3720	+		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)	1114			Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.		D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	c.3340C>T	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	38	6.950292	0.97956	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.76	4.88	0.63580	.	0.190581	0.42172	D	0.000759	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.7869	14.0911	0.64990	0.3279:0.6721:0.0:0.0	.	.	.	.	X	1114;1096;1114;1114;1114	.	ENSP00000257430:R1114X	R	+	1	2	APC	112202530	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.208000	0.42797	1.423000	0.47198	0.655000	0.94253	CGA		0.403	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		17	30	0	0	0	1	0	17	30				
VGLL2	245806	broad.mit.edu	37	6	117589488	117589488	+	Silent	SNP	A	A	C			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr6:117589488A>C	ENST00000326274.5	+	2	415	c.225A>C	c.(223-225)ccA>ccC	p.P75P	VGLL2_ENST00000352536.3_Silent_p.P75P	NM_182645.3	NP_872586.1	Q8N8G2	VGLL2_HUMAN	vestigial-like family member 2	75					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			central_nervous_system(1)|kidney(1)|lung(3)	5				GBM - Glioblastoma multiforme(226;0.0254)|all cancers(137;0.0676)|OV - Ovarian serous cystadenocarcinoma(136;0.0757)		AAGAGCGCCCACCAGAGGCAG	0.577																																						ENST00000326274.5																			0				central_nervous_system(1)|kidney(1)|lung(3)	5						c.(223-225)ccA>ccC		vestigial like 2 (Drosophila)							103.0	118.0	113.0					6																	117589488		2203	4300	6503	SO:0001819	synonymous_variant	245806				transcription, DNA-dependent	nucleus		g.chr6:117589488A>C	AY056583	CCDS5114.1, CCDS5115.1	6q22.31	2014-03-03	2014-03-03		ENSG00000170162	ENSG00000170162			20232	protein-coding gene	gene with protein product		609979	"""vestigial like 2 (Drosophila)"""			12376544	Standard	NM_153453		Approved		uc003pxn.3	Q8N8G2	OTTHUMG00000015451	ENST00000326274.5:c.225A>C	6.37:g.117589488A>C						VGLL2_ENST00000352536.3_Silent_p.P75P	p.P75P	NM_182645.2	NP_872586.1	Q8N8G2	VGLL2_HUMAN		GBM - Glioblastoma multiforme(226;0.0254)|all cancers(137;0.0676)|OV - Ovarian serous cystadenocarcinoma(136;0.0757)	2	415	+			75					Q8WWX1	Silent	SNP	ENST00000326274.5	37	c.225A>C	CCDS5115.1																																																																																				0.577	VGLL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041975.2	NM_153453		13	102	0	0	0	1	0	13	102				
TAAR2	9287	broad.mit.edu	37	6	132939259	132939259	+	Missense_Mutation	SNP	C	C	T			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr6:132939259C>T	ENST00000367931.1	-	2	85	c.86G>A	c.(85-87)gGa>gAa	p.G29E	TAAR2_ENST00000275191.2_5'UTR|TAAR2_ENST00000537809.1_5'UTR			Q9P1P5	TAAR2_HUMAN	trace amine associated receptor 2	29					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|trace-amine receptor activity (GO:0001594)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|skin(1)	23	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00608)|GBM - Glioblastoma multiforme(226;0.0151)		AGATCTATTTCCATATTCAGA	0.308																																						ENST00000367931.1																			0				breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|skin(1)	23						c.(85-87)gGa>gAa		trace amine associated receptor 2							57.0	60.0	59.0					6																	132939259		2201	4297	6498	SO:0001583	missense	9287					plasma membrane	G-protein coupled receptor activity	g.chr6:132939259C>T	AF112460	CCDS34541.1, CCDS5157.1	6q24	2012-08-08	2005-02-23	2005-02-24	ENSG00000146378	ENSG00000146378		"""GPCR / Class A : Trace amine associated receptors"""	4514	protein-coding gene	gene with protein product		604849	"""G protein-coupled receptor 58"""	GPR58		10684976, 15718104	Standard	NM_014626		Approved		uc003qdl.1	Q9P1P5	OTTHUMG00000015585	ENST00000367931.1:c.86G>A	6.37:g.132939259C>T	ENSP00000356908:p.Gly29Glu					TAAR2_ENST00000275191.2_5'UTR|TAAR2_ENST00000537809.1_5'UTR	p.G29E			Q9P1P5	TAAR2_HUMAN		OV - Ovarian serous cystadenocarcinoma(155;0.00608)|GBM - Glioblastoma multiforme(226;0.0151)	2	85	-	Breast(56;0.135)		29					Q5QD02|Q6NWS1|Q6NWS2|Q6NWS3	Missense_Mutation	SNP	ENST00000367931.1	37	c.86G>A	CCDS34541.1	.	.	.	.	.	.	.	.	.	.	C	15.27	2.784306	0.49997	.	.	ENSG00000146378	ENST00000367931	T	0.36520	1.25	5.5	5.5	0.81552	.	0.080740	0.49305	D	0.000141	T	0.35941	0.0949	N	0.20986	0.625	0.80722	D	1	D	0.89917	1.0	D	0.72982	0.979	T	0.17167	-1.0378	10	0.51188	T	0.08	-14.2529	14.5843	0.68312	0.1461:0.8539:0.0:0.0	.	29	Q9P1P5	TAAR2_HUMAN	E	29	ENSP00000356908:G29E	ENSP00000356908:G29E	G	-	2	0	TAAR2	132980952	0.033000	0.19621	1.000000	0.80357	0.992000	0.81027	0.182000	0.16900	2.740000	0.93945	0.650000	0.86243	GGA		0.308	TAAR2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390735.1	NM_014626		4	70	0	0	0	1	0	4	70				
CYP8B1	1582	broad.mit.edu	37	3	42916185	42916185	+	Missense_Mutation	SNP	A	A	T			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr3:42916185A>T	ENST00000316161.4	-	1	1448	c.1124T>A	c.(1123-1125)cTg>cAg	p.L375Q	KRBOX1_ENST00000426937.1_Intron|RP11-141M3.5_ENST00000471537.1_RNA|CYP8B1_ENST00000437102.1_Missense_Mutation_p.L375Q	NM_004391.2	NP_004382.2	Q9UNU6	CP8B1_HUMAN	cytochrome P450, family 8, subfamily B, polypeptide 1	375					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	7alpha-hydroxycholest-4-en-3-one 12alpha-hydroxylase activity (GO:0033778)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|sterol 12-alpha-hydroxylase activity (GO:0008397)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|prostate(2)|skin(5)	23				KIRC - Kidney renal clear cell carcinoma(284;0.213)|Kidney(284;0.249)		ATGGCGGAACAGATACTCCTG	0.582																																						ENST00000316161.4																			0				NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|prostate(2)|skin(5)	23						c.(1123-1125)cTg>cAg		cytochrome P450, family 8, subfamily B, polypeptide 1							91.0	89.0	89.0					3																	42916185		2203	4300	6503	SO:0001583	missense	1582				bile acid biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	7alpha-hydroxycholest-4-en-3-one 12alpha-hydroxylase activity|electron carrier activity|heme binding|oxygen binding|sterol 12-alpha-hydroxylase activity	g.chr3:42916185A>T	AF090318	CCDS2707.1	3p22.1	2004-02-27	2003-01-14		ENSG00000180432	ENSG00000180432		"""Cytochrome P450s"""	2653	protein-coding gene	gene with protein product		602172	"""cytochrome P450, subfamily VIIIB (sterol 12-alpha-hydroxylase), polypeptide 1"""			10051404	Standard	NM_004391		Approved	CYP12	uc003cmh.3	Q9UNU6	OTTHUMG00000133047	ENST00000316161.4:c.1124T>A	3.37:g.42916185A>T	ENSP00000318867:p.Leu375Gln					KRBOX1_ENST00000426937.1_Intron|CYP8B1_ENST00000437102.1_Missense_Mutation_p.L375Q|ACKR2_ENST00000471537.1_Intron	p.L375Q	NM_004391.2	NP_004382.2	Q9UNU6	CP8B1_HUMAN		KIRC - Kidney renal clear cell carcinoma(284;0.213)|Kidney(284;0.249)	1	1448	-			375					B2RCY3|O75958|Q6NWT2|Q6NWT3	Missense_Mutation	SNP	ENST00000316161.4	37	c.1124T>A	CCDS2707.1	.	.	.	.	.	.	.	.	.	.	A	0.008	-1.889784	0.00527	.	.	ENSG00000180432	ENST00000437102;ENST00000316161	T;T	0.01347	4.99;4.99	4.5	-3.15	0.05233	.	0.868719	0.10039	N	0.723678	T	0.00784	0.0026	N	0.16708	0.43	0.09310	N	1	B;B	0.19583	0.037;0.011	B;B	0.22152	0.038;0.023	T	0.48614	-0.9020	10	0.11182	T	0.66	-3.4574	0.9942	0.01463	0.3681:0.2559:0.2391:0.1369	.	375;375	C9JFR9;Q9UNU6	.;CP8B1_HUMAN	Q	375	ENSP00000404499:L375Q;ENSP00000318867:L375Q	ENSP00000318867:L375Q	L	-	2	0	CYP8B1	42891189	0.004000	0.15560	0.001000	0.08648	0.034000	0.12701	0.004000	0.13106	-0.406000	0.07588	0.459000	0.35465	CTG		0.582	CYP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256653.1	NM_004391		17	45	0	0	0	1	0	17	45				
PLCH1	23007	broad.mit.edu	37	3	155205833	155205833	+	Missense_Mutation	SNP	T	T	C			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr3:155205833T>C	ENST00000340059.7	-	20	2566	c.2567A>G	c.(2566-2568)aAt>aGt	p.N856S	PLCH1-AS2_ENST00000472913.1_RNA|PLCH1_ENST00000460012.1_Missense_Mutation_p.N838S|PLCH1_ENST00000447496.2_Missense_Mutation_p.N856S|PLCH1_ENST00000334686.6_Missense_Mutation_p.N838S|PLCH1_ENST00000494598.1_Missense_Mutation_p.N856S|PLCH1_ENST00000414191.1_Missense_Mutation_p.N838S	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	856					inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phosphatidylinositol-mediated signaling (GO:0048015)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase C activity (GO:0050429)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			NS(3)|breast(3)|endometrium(9)|kidney(4)|large_intestine(20)|lung(45)|ovary(2)|prostate(5)|skin(8)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	107			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			ATAGATTTCATTGATGGTTAT	0.338																																						ENST00000460012.1																			0				NS(3)|breast(3)|endometrium(9)|kidney(4)|large_intestine(20)|lung(45)|ovary(2)|prostate(5)|skin(8)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	107						c.(2512-2514)aAt>aGt		phospholipase C, eta 1							129.0	129.0	129.0					3																	155205833		2203	4300	6503	SO:0001583	missense	23007				lipid catabolic process|phosphatidylinositol-mediated signaling	membrane	calcium ion binding|calcium-dependent phospholipase C activity|phosphatidylinositol phospholipase C activity|signal transducer activity	g.chr3:155205833T>C	AB028992	CCDS33881.1, CCDS46939.1, CCDS46940.1	3q25	2013-01-10	2006-03-16	2006-03-16	ENSG00000114805	ENSG00000114805	3.1.4.11	"""EF-hand domain containing"""	29185	protein-coding gene	gene with protein product		612835	"""phospholipase C-like 3"""	PLCL3		15702972	Standard	NM_014996		Approved	KIAA1069, MGC117152, DKFZp434C1372, PLCeta1	uc021xge.1	Q4KWH8	OTTHUMG00000158477	ENST00000340059.7:c.2567A>G	3.37:g.155205833T>C	ENSP00000345988:p.Asn856Ser					PLCH1_ENST00000340059.7_Missense_Mutation_p.N856S|PLCH1_ENST00000414191.1_Missense_Mutation_p.N838S|PLCH1_ENST00000334686.6_Missense_Mutation_p.N838S|PLCH1_ENST00000494598.1_Missense_Mutation_p.N856S|PLCH1_ENST00000447496.2_Missense_Mutation_p.N856S	p.N838S			Q4KWH8	PLCH1_HUMAN	Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)		21	2870	-			856					Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	Missense_Mutation	SNP	ENST00000340059.7	37	c.2513A>G	CCDS46939.1	.	.	.	.	.	.	.	.	.	.	T	19.69	3.873844	0.72180	.	.	ENSG00000114805	ENST00000494598;ENST00000460012;ENST00000447496;ENST00000340059;ENST00000334686;ENST00000414191	T;T;T;T;T;T	0.29397	2.08;2.0;1.57;2.0;2.0;2.0	5.18	5.18	0.71444	C2 calcium/lipid-binding domain, CaLB (1);	0.642281	0.17446	N	0.173943	T	0.35770	0.0943	L	0.47190	1.495	0.54753	D	0.99998	P;B;B	0.40302	0.712;0.402;0.078	P;B;B	0.46718	0.525;0.171;0.053	T	0.03922	-1.0992	10	0.15499	T	0.54	.	15.0382	0.71767	0.0:0.0:0.0:1.0	.	838;856;856	Q4KWH8-2;Q4KWH8;Q4KWH8-3	.;PLCH1_HUMAN;.	S	856;838;856;856;838;838	ENSP00000419100:N856S;ENSP00000417502:N838S;ENSP00000402759:N856S;ENSP00000345988:N856S;ENSP00000335469:N838S;ENSP00000412977:N838S	ENSP00000335469:N838S	N	-	2	0	PLCH1	156688527	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.498000	0.81546	1.947000	0.56498	0.533000	0.62120	AAT		0.338	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1	NM_014996		14	25	0	0	0	1	0	14	25				
SIPA1L2	57568	broad.mit.edu	37	1	232649718	232649718	+	Silent	SNP	G	G	A			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr1:232649718G>A	ENST00000366630.1	-	2	1726	c.1368C>T	c.(1366-1368)tcC>tcT	p.S456S	SIPA1L2_ENST00000262861.4_Silent_p.S456S			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	456					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)	p.S456S(1)		NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				CTTCCAAGACGGAGACACCTG	0.493																																						ENST00000366630.1																			1	Substitution - coding silent(1)	p.S456S(1)	lung(1)	NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103						c.(1366-1368)tcC>tcT		signal-induced proliferation-associated 1 like 2							148.0	144.0	146.0					1																	232649718		1971	4164	6135	SO:0001819	synonymous_variant	57568				regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity	g.chr1:232649718G>A	AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.1368C>T	1.37:g.232649718G>A						SIPA1L2_ENST00000262861.4_Silent_p.S456S	p.S456S			Q9P2F8	SI1L2_HUMAN			2	1726	-		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)	456					Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Silent	SNP	ENST00000366630.1	37	c.1368C>T	CCDS41474.1																																																																																				0.493	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839		4	137	0	0	0	1	0	4	137				
MAGEC1	9947	broad.mit.edu	37	X	140994457	140994457	+	Missense_Mutation	SNP	A	A	C	rs199509682		TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chrX:140994457A>C	ENST00000285879.4	+	4	1553	c.1267A>C	c.(1267-1269)Att>Ctt	p.I423L	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	423										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					TTTATTGAGTATTTTACAGAG	0.463										HNSCC(15;0.026)																												ENST00000285879.4																			0				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127						c.(1267-1269)Att>Ctt		melanoma antigen family C, 1							101.0	112.0	108.0					X																	140994457		2193	4287	6480	SO:0001583	missense	9947						protein binding	g.chrX:140994457A>C	AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 1"""	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.1267A>C	X.37:g.140994457A>C	ENSP00000285879:p.Ile423Leu	HNSCC(15;0.026)				MAGEC1_ENST00000406005.2_Intron	p.I423L	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN			4	1553	+	Acute lymphoblastic leukemia(192;6.56e-05)		423					A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	37	c.1267A>C	CCDS35417.1	.	.	.	.	.	.	.	.	.	.	a	0.015	-1.558009	0.00910	.	.	ENSG00000155495	ENST00000285879	T	0.02498	4.27	.	.	.	.	.	.	.	.	T	0.01222	0.0040	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.42464	-0.9450	8	0.25106	T	0.35	.	3.6384	0.08158	0.249:0.5004:0.2507:0.0	.	423	O60732	MAGC1_HUMAN	L	423	ENSP00000285879:I423L	ENSP00000285879:I423L	I	+	1	0	MAGEC1	140822123	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-4.696000	0.00197	-3.581000	0.00137	-3.580000	0.00029	ATT		0.463	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462		54	41	0	0	0	1	0	54	41				
MUC16	94025	broad.mit.edu	37	19	9086501	9086501	+	Missense_Mutation	SNP	C	C	T			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr19:9086501C>T	ENST00000397910.4	-	1	5517	c.5314G>A	c.(5314-5316)Gag>Aag	p.E1772K		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1772	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTGGTGACCTCCTTGGTCCAA	0.493																																						ENST00000397910.4																			0				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						c.(5314-5316)Gag>Aag		mucin 16, cell surface associated							120.0	113.0	115.0					19																	9086501		1970	4143	6113	SO:0001583	missense	94025				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding	g.chr19:9086501C>T	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.5314G>A	19.37:g.9086501C>T	ENSP00000381008:p.Glu1772Lys						p.E1772K	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN			1	5517	-			1772			Ser-rich.|Thr-rich.		Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	c.5314G>A	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	4.903	0.167778	0.09339	.	.	ENSG00000181143	ENST00000397910	T	0.02682	4.2	1.32	-2.12	0.07165	.	.	.	.	.	T	0.01320	0.0043	N	0.08118	0	.	.	.	P	0.34977	0.478	B	0.23716	0.048	T	0.45056	-0.9287	8	0.87932	D	0	.	4.9511	0.14015	0.0:0.509:0.0:0.491	.	1772	B5ME49	.	K	1772	ENSP00000381008:E1772K	ENSP00000381008:E1772K	E	-	1	0	MUC16	8947501	0.000000	0.05858	0.000000	0.03702	0.075000	0.17131	-1.474000	0.02337	-0.700000	0.05070	0.305000	0.20034	GAG		0.493	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		25	57	0	0	0	1	0	25	57				
CCT6P3	643180	broad.mit.edu	37	7	64525465	64525465	+	RNA	SNP	T	T	G			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr7:64525465T>G	ENST00000426828.1	+	0	295				SNORA22_ENST00000384614.1_RNA	NR_033416.1				chaperonin containing TCP1, subunit 6 (zeta) pseudogene 3																		TCCAACGTCCTAATCATTGGA	0.398																																						ENST00000426828.1																			0																																																			0							g.chr7:64525465T>G			7q11.21	2010-06-29			ENSG00000234585	ENSG00000234585			35137	pseudogene	pseudogene							Standard	NR_033416		Approved		uc010kzt.1		OTTHUMG00000156630		7.37:g.64525465T>G								NR_033416.1						0	295	+									RNA	SNP	ENST00000426828.1	37																																																																																						0.398	CCT6P3-004	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000344862.1			39	80	0	0	0	1	0	39	80				
FGF7	2252	broad.mit.edu	37	15	49776572	49776572	+	Silent	SNP	A	A	C			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr15:49776572A>C	ENST00000267843.4	+	4	1067	c.456A>C	c.(454-456)gcA>gcC	p.A152A	FAM227B_ENST00000299338.6_Intron|FGF7_ENST00000560704.1_3'UTR|FAM227B_ENST00000561064.1_Intron	NM_002009.3	NP_002000.1	P21781	FGF7_HUMAN	fibroblast growth factor 7	152					actin cytoskeleton reorganization (GO:0031532)|branching involved in salivary gland morphogenesis (GO:0060445)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis development (GO:0008544)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle morphogenesis (GO:0031069)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|mesenchymal cell proliferation (GO:0010463)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein localization to cell surface (GO:0034394)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)|response to wounding (GO:0009611)|secretion by lung epithelial cell involved in lung growth (GO:0061033)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)	chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)	p.A152A(1)		kidney(1)|large_intestine(1)|lung(2)|prostate(1)	5		all_lung(180;0.00391)		all cancers(107;3.61e-08)|GBM - Glioblastoma multiforme(94;4.06e-05)		ACACATATGCATCAGCTAAAT	0.338																																						ENST00000267843.4																			1	Substitution - coding silent(1)	p.A152A(1)	kidney(1)	kidney(1)|large_intestine(1)|lung(2)|prostate(1)	5						c.(454-456)gcA>gcC		fibroblast growth factor 7	Palifermin(DB00039)						55.0	53.0	54.0					15																	49776572		2037	3875	5912	SO:0001819	synonymous_variant	2252				actin cytoskeleton reorganization|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|mesenchymal cell proliferation|positive regulation of cell division|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of keratinocyte migration|positive regulation of keratinocyte proliferation|positive regulation of peptidyl-tyrosine phosphorylation|protein localization at cell surface|secretion by lung epithelial cell involved in lung growth		chemoattractant activity|growth factor activity	g.chr15:49776572A>C	M60828	CCDS10131.1	15q21.2	2014-01-30	2010-08-18		ENSG00000140285	ENSG00000140285		"""Endogenous ligands"""	3685	protein-coding gene	gene with protein product	"""keratinocyte growth factor"""	148180	"""fibroblast growth factor 7 (keratinocyte growth factor)"""			7749227, 1409637	Standard	NM_002009		Approved	KGF	uc001zxn.3	P21781	OTTHUMG00000131517	ENST00000267843.4:c.456A>C	15.37:g.49776572A>C						FGF7_ENST00000560704.1_3'UTR|FAM227B_ENST00000299338.6_Intron|FAM227B_ENST00000561064.1_Intron	p.A152A	NM_002009.3	NP_002000.1	P21781	FGF7_HUMAN		all cancers(107;3.61e-08)|GBM - Glioblastoma multiforme(94;4.06e-05)	4	1067	+		all_lung(180;0.00391)	152					H0YNY5|Q6FGV5|Q96FG5	Silent	SNP	ENST00000267843.4	37	c.456A>C	CCDS10131.1																																																																																				0.338	FGF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254374.3	NM_002009		3	57	0	0	0	1	0	3	57				
PLCB4	5332	broad.mit.edu	37	20	9388600	9388600	+	Missense_Mutation	SNP	G	G	T			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr20:9388600G>T	ENST00000378493.1	+	18	1663	c.1648G>T	c.(1648-1650)Gca>Tca	p.A550S	PLCB4_ENST00000278655.4_Missense_Mutation_p.A550S|PLCB4_ENST00000378501.2_Missense_Mutation_p.A550S|PLCB4_ENST00000334005.3_Missense_Mutation_p.A550S|PLCB4_ENST00000414679.2_Missense_Mutation_p.A562S|PLCB4_ENST00000378473.3_Missense_Mutation_p.A562S|PLCB4_ENST00000492632.1_3'UTR			Q15147	PLCB4_HUMAN	phospholipase C, beta 4	550					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|smooth endoplasmic reticulum (GO:0005790)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(2)|breast(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(11)|liver(4)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(19)|upper_aerodigestive_tract(1)	87						GGCGTGGATGGCATCTTATAA	0.448																																						ENST00000378501.2																			0				NS(2)|breast(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(11)|liver(4)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(19)|upper_aerodigestive_tract(1)	87						c.(1648-1650)Gca>Tca		phospholipase C, beta 4							168.0	153.0	158.0					20																	9388600		2203	4300	6503	SO:0001583	missense	5332				intracellular signal transduction|lipid catabolic process	cytosol	calcium ion binding|phosphatidylinositol phospholipase C activity|protein binding|signal transducer activity	g.chr20:9388600G>T		CCDS13104.1, CCDS13105.1, CCDS54447.1	20p12	2008-03-18			ENSG00000101333	ENSG00000101333	3.1.4.11		9059	protein-coding gene	gene with protein product		600810				8530101	Standard	NM_000933		Approved		uc021wam.1	Q15147	OTTHUMG00000031853	ENST00000378493.1:c.1648G>T	20.37:g.9388600G>T	ENSP00000367754:p.Ala550Ser					PLCB4_ENST00000378493.1_Missense_Mutation_p.A550S|PLCB4_ENST00000492632.1_3'UTR|PLCB4_ENST00000414679.2_Missense_Mutation_p.A562S|PLCB4_ENST00000378473.3_Missense_Mutation_p.A562S|PLCB4_ENST00000334005.3_Missense_Mutation_p.A550S|PLCB4_ENST00000278655.4_Missense_Mutation_p.A550S	p.A550S	NM_000933.3	NP_000924.3	Q15147	PLCB4_HUMAN			18	1663	+			550					B7ZLK6|E2QRH8|Q17R56|Q5JYS8|Q5JYS9|Q5JYT0|Q5JYT3|Q5JYT4|Q9BQW5|Q9BQW6|Q9BQW8|Q9UJQ2	Missense_Mutation	SNP	ENST00000378493.1	37	c.1648G>T	CCDS13105.1	.	.	.	.	.	.	.	.	.	.	G	18.37	3.609500	0.66558	.	.	ENSG00000101333	ENST00000334005;ENST00000378473;ENST00000278655;ENST00000378493;ENST00000378501;ENST00000414679	T;T;T;T;T;T	0.52983	0.64;0.64;0.64;0.64;0.64;0.64	5.56	5.56	0.83823	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (1);	0.121669	0.56097	D	0.000037	T	0.57095	0.2030	L	0.48642	1.525	0.80722	D	1	P;P;B;P	0.49358	0.923;0.481;0.141;0.716	P;B;B;B	0.54100	0.742;0.164;0.064;0.407	T	0.49485	-0.8935	10	0.32370	T	0.25	.	19.5275	0.95212	0.0:0.0:1.0:0.0	.	562;397;550;550	E2QRH8;Q15147-2;Q15147;Q15147-4	.;.;PLCB4_HUMAN;.	S	550;562;550;550;550;398	ENSP00000334105:A550S;ENSP00000367734:A562S;ENSP00000278655:A550S;ENSP00000367754:A550S;ENSP00000367762:A550S;ENSP00000390616:A398S	ENSP00000278655:A550S	A	+	1	0	PLCB4	9336600	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.486000	0.66856	2.616000	0.88540	0.563000	0.77884	GCA		0.448	PLCB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077948.2			26	96	1	0	9.57634e-11	1	1.10496e-10	26	96				
CCNA1	8900	broad.mit.edu	37	13	37014263	37014263	+	Silent	SNP	T	T	C			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr13:37014263T>C	ENST00000255465.4	+	6	1305	c.1041T>C	c.(1039-1041)ttT>ttC	p.F347F	CCNA1_ENST00000418263.1_Silent_p.F346F|CCNA1_ENST00000440264.1_Silent_p.F303F|CCNA1_ENST00000449823.1_Silent_p.F303F			P78396	CCNA1_HUMAN	cyclin A1	347					G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|male meiosis I (GO:0007141)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)				breast(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(2)|urinary_tract(1)	35		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.91e-07)|Epithelial(112;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0119)|GBM - Glioblastoma multiforme(144;0.0242)		CCAACCAGTTTCTCCTTCAGT	0.458																																						ENST00000418263.1																			0				breast(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(2)|urinary_tract(1)	35						c.(1036-1038)ttT>ttC		cyclin A1							158.0	156.0	157.0					13																	37014263		2203	4300	6503	SO:0001819	synonymous_variant	8900				cell division|G2/M transition of mitotic cell cycle|male meiosis I|mitosis|regulation of cyclin-dependent protein kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|spermatogenesis	cytosol|microtubule cytoskeleton|nucleoplasm	protein kinase binding	g.chr13:37014263T>C	U66838	CCDS9357.1, CCDS45031.1	13q12.3-q13	2014-01-21			ENSG00000133101	ENSG00000133101			1577	protein-coding gene	gene with protein product		604036				9041194	Standard	NM_003914		Approved	CT146	uc001uvr.4	P78396	OTTHUMG00000016733	ENST00000255465.4:c.1041T>C	13.37:g.37014263T>C						CCNA1_ENST00000255465.4_Silent_p.F347F|CCNA1_ENST00000440264.1_Silent_p.F303F|CCNA1_ENST00000449823.1_Silent_p.F303F	p.F346F	NM_001111045.1|NM_003914.3	NP_001104515.1|NP_003905.1	P78396	CCNA1_HUMAN	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.91e-07)|Epithelial(112;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0119)|GBM - Glioblastoma multiforme(144;0.0242)	6	1388	+		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	347					B7Z7E3|Q5T3V0|Q5U0G2|Q8IY91	Silent	SNP	ENST00000255465.4	37	c.1038T>C	CCDS9357.1																																																																																				0.458	CCNA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044514.2	NM_003914		28	86	0	0	0	1	0	28	86				
CLK2	1196	broad.mit.edu	37	1	155239353	155239353	+	Missense_Mutation	SNP	G	G	A	rs139555196		TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr1:155239353G>A	ENST00000368361.4	-	3	640	c.325C>T	c.(325-327)Cgc>Tgc	p.R109C	CLK2_ENST00000536801.1_Missense_Mutation_p.R109C|CLK2_ENST00000355560.4_Missense_Mutation_p.R108C|CLK2_ENST00000361168.5_Missense_Mutation_p.R109C|CLK2_ENST00000497188.1_5'Flank			P49760	CLK2_HUMAN	CDC-like kinase 2	109					negative regulation of gluconeogenesis (GO:0045721)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of RNA splicing (GO:0043484)|response to ionizing radiation (GO:0010212)|response to retinoic acid (GO:0032526)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)	p.R109S(1)		endometrium(4)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	22	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			CGCTGGCTGCGGTAACTGCTG	0.592								Other conserved DNA damage response genes																														ENST00000368361.4																			1	Substitution - Missense(1)	p.R109S(1)	lung(1)	endometrium(4)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	22						c.(325-327)Cgc>Tgc	Other conserved DNA damage response genes	CDC-like kinase 2		G	CYS/ARG	1,4405		0,1,2202	111.0	103.0	106.0		325	4.6	1.0	1	dbSNP_134	106	0,8600		0,0,4300	no	missense	CLK2	NM_003993.2	180	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	109/499	155239353	1,13005	2203	4300	6503	SO:0001583	missense	1196					nucleus	ATP binding|protein serine/threonine kinase activity|protein tyrosine kinase activity	g.chr1:155239353G>A	L29218	CCDS1107.1, CCDS72939.1	1q21	2008-05-02			ENSG00000176444	ENSG00000176444		"""CDC-like kinases"""	2069	protein-coding gene	gene with protein product		602989				7990150, 9856501	Standard	XM_005244876		Approved	clk2	uc001fjw.3	P49760	OTTHUMG00000035873	ENST00000368361.4:c.325C>T	1.37:g.155239353G>A	ENSP00000357345:p.Arg109Cys					CLK2_ENST00000361168.5_Missense_Mutation_p.R109C|CLK2_ENST00000355560.4_Missense_Mutation_p.R108C|CLK2_ENST00000536801.1_Missense_Mutation_p.R109C	p.R109C			P49760	CLK2_HUMAN	Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)		3	640	-	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		109					B1AVS9|B5MBX6|Q96CQ0	Missense_Mutation	SNP	ENST00000368361.4	37	c.325C>T		.	.	.	.	.	.	.	.	.	.	.	14.81	2.645084	0.47258	2.27E-4	0.0	ENSG00000176444	ENST00000361168;ENST00000368361;ENST00000355560;ENST00000536801	T;T;T;T	0.56776	0.47;0.46;0.44;0.46	4.63	4.63	0.57726	.	0.000000	0.85682	D	0.000000	T	0.50548	0.1622	M	0.70595	2.14	0.58432	D	0.999997	D;D	0.71674	0.997;0.998	B;P	0.50754	0.446;0.649	T	0.59016	-0.7533	10	0.72032	D	0.01	.	11.5254	0.50576	0.0:0.0:0.8209:0.1791	.	109;109	P49760;P49760-3	CLK2_HUMAN;.	C	109;109;108;109	ENSP00000354856:R109C;ENSP00000357345:R109C;ENSP00000347759:R108C;ENSP00000441023:R109C	ENSP00000347759:R108C	R	-	1	0	CLK2	153505977	1.000000	0.71417	1.000000	0.80357	0.617000	0.37484	4.893000	0.63199	2.424000	0.82194	0.650000	0.86243	CGC		0.592	CLK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000087391.1	NM_003993		4	103	0	0	0	1	0	4	103				
TRMT61A	115708	broad.mit.edu	37	14	104000981	104000981	+	Silent	SNP	G	G	A			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr14:104000981G>A	ENST00000389749.4	+	4	800	c.693G>A	c.(691-693)ctG>ctA	p.L231L		NM_152307.2	NP_689520.2	Q96FX7	TRM61_HUMAN	tRNA methyltransferase 61 homolog A (S. cerevisiae)	231						nucleus (GO:0005634)|tRNA (m1A) methyltransferase complex (GO:0031515)	tRNA (adenine-N1-)-methyltransferase activity (GO:0016429)			skin(1)	1						TGAGCACCCTGGAGGTGCTGC	0.682																																						ENST00000389749.4																			0				skin(1)	1						c.(691-693)ctG>ctA		tRNA methyltransferase 61 homolog A (S. cerevisiae)							16.0	22.0	20.0					14																	104000981		2102	4197	6299	SO:0001819	synonymous_variant	115708					nucleus	protein binding|tRNA (adenine-N1-)-methyltransferase activity	g.chr14:104000981G>A	AK097771	CCDS41994.1	14q32	2009-01-09	2009-01-09	2009-01-09		ENSG00000166166			23790	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 172"""	C14orf172		16043508	Standard	NM_152307		Approved	FLJ40452, GCD14, Gcd14p, hTRM61	uc010aws.3	Q96FX7		ENST00000389749.4:c.693G>A	14.37:g.104000981G>A							p.L231L	NM_152307.2	NP_689520.2	Q96FX7	TRM61_HUMAN			4	800	+			231					A6NN78|Q8N7Q9	Silent	SNP	ENST00000389749.4	37	c.693G>A	CCDS41994.1	.	.	.	.	.	.	.	.	.	.	G	4.554	0.102945	0.08731	.	.	ENSG00000166166	ENST00000299202	.	.	.	4.67	3.7	0.42460	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-27.1472	7.9809	0.30183	0.0857:0.1624:0.752:0.0	.	.	.	.	X	133	.	.	W	+	2	0	TRMT61A	103070734	1.000000	0.71417	1.000000	0.80357	0.388000	0.30384	3.304000	0.51866	2.140000	0.66376	0.313000	0.20887	TGG		0.682	TRMT61A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414988.1	NM_152307		13	11	0	0	0	1	0	13	11				
HSD3B1	3283	broad.mit.edu	37	1	120056908	120056908	+	Nonsense_Mutation	SNP	C	C	A			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr1:120056908C>A	ENST00000369413.3	+	4	907	c.762C>A	c.(760-762)taC>taA	p.Y254*	HSD3B1_ENST00000528909.1_Nonsense_Mutation_p.Y254*|HSD3B1_ENST00000235547.6_Nonsense_Mutation_p.Y256*			P14060	3BHS1_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	254					androgen biosynthetic process (GO:0006702)|estrogen biosynthetic process (GO:0006703)|glucocorticoid biosynthetic process (GO:0006704)|mineralocorticoid biosynthetic process (GO:0006705)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|smooth endoplasmic reticulum membrane (GO:0030868)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|steroid delta-isomerase activity (GO:0004769)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(18)|ovary(2)|prostate(1)|skin(1)	32	all_neural(166;0.219)	all_lung(203;3.16e-06)|Lung NSC(69;2.19e-05)|all_epithelial(167;0.000624)		Lung(183;0.0106)|LUSC - Lung squamous cell carcinoma(189;0.0554)	Trilostane(DB01108)	GACAGTTCTACTATATCTCAG	0.522																																						ENST00000235547.6																			0				central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(18)|ovary(2)|prostate(1)|skin(1)	32						c.(766-768)taC>taA		hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	NADH(DB00157)|Trilostane(DB01108)						69.0	73.0	72.0					1																	120056908		2203	4300	6503	SO:0001587	stop_gained	3283				androgen biosynthetic process|estrogen biosynthetic process|glucocorticoid biosynthetic process|mineralocorticoid biosynthetic process	integral to membrane|microsome|mitochondrial inner membrane|mitochondrial intermembrane space|smooth endoplasmic reticulum membrane	3-beta-hydroxy-delta5-steroid dehydrogenase activity|binding|steroid delta-isomerase activity	g.chr1:120056908C>A	S45679	CCDS903.1	1p12	2014-06-03			ENSG00000203857	ENSG00000203857	1.1.1.145, 5.3.3.1	"""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	5217	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 11E, member 1"""	109715		HSDB3, HSD3B		2779585, 19027726	Standard	NM_000862		Approved	SDR11E1	uc001ehv.1	P14060	OTTHUMG00000012525	ENST00000369413.3:c.762C>A	1.37:g.120056908C>A	ENSP00000358421:p.Tyr254*					HSD3B1_ENST00000369413.3_Nonsense_Mutation_p.Y254*|HSD3B1_ENST00000528909.1_Nonsense_Mutation_p.Y254*	p.Y256*	NM_000862.2	NP_000853.1	P14060	3BHS1_HUMAN		Lung(183;0.0106)|LUSC - Lung squamous cell carcinoma(189;0.0554)	4	907	+	all_neural(166;0.219)	all_lung(203;3.16e-06)|Lung NSC(69;2.19e-05)|all_epithelial(167;0.000624)	254					A8K691|Q14545|Q8IV65	Nonsense_Mutation	SNP	ENST00000369413.3	37	c.768C>A	CCDS903.1	.	.	.	.	.	.	.	.	.	.	C	15.05	2.716840	0.48622	.	.	ENSG00000203857	ENST00000369413;ENST00000235547;ENST00000528909	.	.	.	3.26	-2.17	0.07059	.	0.059560	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.1299	8.547	0.33429	0.0:0.3017:0.0:0.6983	.	.	.	.	X	254;256;254	.	ENSP00000235547:Y256X	Y	+	3	2	HSD3B1	119858431	0.987000	0.35691	0.990000	0.47175	0.312000	0.27988	0.266000	0.18534	-0.371000	0.08004	-0.657000	0.03884	TAC		0.522	HSD3B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034993.3	NM_000862		18	62	1	0	1.67942e-08	1	1.86602e-08	18	62				
LRP1B	53353	broad.mit.edu	37	2	141115581	141115581	+	Missense_Mutation	SNP	C	C	T	rs199649226		TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr2:141115581C>T	ENST00000389484.3	-	74	12333	c.11362G>A	c.(11362-11364)Gga>Aga	p.G3788R		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	3788	LDL-receptor class A 32. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		GAACCATCTCCGCAGTCATCA	0.418										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)	ENST00000389484.3																			0				NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606						c.(11362-11364)Gga>Aga		low density lipoprotein receptor-related protein 1B							151.0	140.0	144.0					2																	141115581		2203	4299	6502	SO:0001583	missense	53353				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding	g.chr2:141115581C>T	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.11362G>A	2.37:g.141115581C>T	ENSP00000374135:p.Gly3788Arg	TSP Lung(27;0.18)					p.G3788R	NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)	74	12333	-		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)	3788			LDL-receptor class A 32.		Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	c.11362G>A	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	33	5.214571	0.95104	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.95307	-3.67	5.82	5.82	0.92795	Low-density lipoprotein (LDL) receptor class A, conserved site (1);Growth factor, receptor (1);	0.000000	0.85682	D	0.000000	D	0.96269	0.8783	L	0.53249	1.67	0.58432	D	0.999999	D	0.76494	0.999	D	0.68483	0.958	D	0.94488	0.7699	10	0.27785	T	0.31	.	20.0966	0.97849	0.0:1.0:0.0:0.0	.	3788	Q9NZR2	LRP1B_HUMAN	R	3788;3726	ENSP00000374135:G3788R	ENSP00000374135:G3788R	G	-	1	0	LRP1B	140832051	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.487000	0.81328	2.751000	0.94390	0.650000	0.86243	GGA		0.418	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		20	43	0	0	0	1	0	20	43				
HIVEP1	3096	broad.mit.edu	37	6	12162077	12162077	+	Missense_Mutation	SNP	C	C	T	rs267600787		TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr6:12162077C>T	ENST00000379388.2	+	8	7225	c.6893C>T	c.(6892-6894)cCg>cTg	p.P2298L	HIVEP1_ENST00000541134.1_Missense_Mutation_p.P163L	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	2298					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				TCCAGGTCCCCGTGTCATCAG	0.488																																						ENST00000379388.2																			0				NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90						c.(6892-6894)cCg>cTg		human immunodeficiency virus type I enhancer binding protein 1							93.0	93.0	93.0					6																	12162077		2016	4189	6205	SO:0001583	missense	3096				transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding	g.chr6:12162077C>T	J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"""Zinc fingers, C2H2-type"""	4920	protein-coding gene	gene with protein product		194540	"""human immunodeficiency virus type I enhancer-binding protein 1"", ""zinc finger protein 40"""	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.6893C>T	6.37:g.12162077C>T	ENSP00000368698:p.Pro2298Leu					HIVEP1_ENST00000541134.1_Missense_Mutation_p.P163L	p.P2298L	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN			8	7225	+	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)	2298					B2RTU3|Q14122|Q5MPB1|Q5VW60	Missense_Mutation	SNP	ENST00000379388.2	37	c.6893C>T	CCDS43426.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.212070	0.79240	.	.	ENSG00000095951	ENST00000379388;ENST00000442081;ENST00000541134;ENST00000542327	T;T	0.51817	2.65;0.69	5.96	5.09	0.68999	.	0.000000	0.35936	N	0.002892	T	0.43500	0.1250	M	0.79805	2.47	0.80722	D	1	D	0.69078	0.997	P	0.48571	0.582	T	0.48703	-0.9012	10	0.35671	T	0.21	-15.8137	11.0902	0.48110	0.0:0.8597:0.0:0.1403	.	2298	P15822	ZEP1_HUMAN	L	2298;225;163;280	ENSP00000368698:P2298L;ENSP00000445617:P163L	ENSP00000368698:P2298L	P	+	2	0	HIVEP1	12270063	0.989000	0.36119	0.650000	0.29550	0.857000	0.48899	3.609000	0.54117	1.538000	0.49270	0.655000	0.94253	CCG		0.488	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114		3	78	0	0	0	1	0	3	78				
SPOP	8405	broad.mit.edu	37	17	47696432	47696432	+	Missense_Mutation	SNP	A	A	C			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr17:47696432A>C	ENST00000393328.2	-	6	756	c.391T>G	c.(391-393)Tgg>Ggg	p.W131G	SPOP_ENST00000504102.1_Missense_Mutation_p.W131G|SPOP_ENST00000347630.2_Missense_Mutation_p.W131G|SPOP_ENST00000503676.1_Missense_Mutation_p.W131G|SPOP_ENST00000513080.1_5'Flank|SPOP_ENST00000393331.3_Missense_Mutation_p.W131G	NM_003563.3	NP_003554.1	O43791	SPOP_HUMAN	speckle-type POZ protein	131	Important for binding substrate proteins.|MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.|Required for nuclear localization.				glucose homeostasis (GO:0042593)|positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902237)|positive regulation of type B pancreatic cell apoptotic process (GO:2000676)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	Cul3-RING ubiquitin ligase complex (GO:0031463)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	ubiquitin protein ligase binding (GO:0031625)	p.W131G(2)|p.W131R(1)		endometrium(18)|kidney(1)|large_intestine(3)|liver(1)|lung(4)|ovary(3)|prostate(33)	63						TTGAATCCCCAGTCTTTGCCT	0.458										Prostate(2;0.17)																												ENST00000393331.3																			3	Substitution - Missense(3)	p.W131G(2)|p.W131R(1)	prostate(3)	endometrium(18)|kidney(1)|large_intestine(3)|liver(1)|lung(4)|ovary(3)|prostate(33)	63						c.(391-393)Tgg>Ggg		speckle-type POZ protein							121.0	124.0	123.0					17																	47696432		2203	4300	6503	SO:0001583	missense	8405				mRNA processing	nucleus	protein binding	g.chr17:47696432A>C	AJ000644	CCDS11551.1	17q21.33	2013-01-09			ENSG00000121067	ENSG00000121067		"""BTB/POZ domain containing"""	11254	protein-coding gene	gene with protein product		602650				9414087	Standard	NM_001007227		Approved	TEF2, BTBD32	uc002ipg.3	O43791	OTTHUMG00000161496	ENST00000393328.2:c.391T>G	17.37:g.47696432A>C	ENSP00000377001:p.Trp131Gly	Prostate(2;0.17)				SPOP_ENST00000504102.1_Missense_Mutation_p.W131G|SPOP_ENST00000393328.2_Missense_Mutation_p.W131G|SPOP_ENST00000347630.2_Missense_Mutation_p.W131G|SPOP_ENST00000503676.1_Missense_Mutation_p.W131G	p.W131G	NM_001007226.1|NM_001007227.1	NP_001007227.1|NP_001007228.1	O43791	SPOP_HUMAN			7	861	-			131			MATH.|Required for nuclear localization.		B2R6S3|D3DTW7|Q53HJ1	Missense_Mutation	SNP	ENST00000393328.2	37	c.391T>G	CCDS11551.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.058244	0.76074	.	.	ENSG00000121067	ENST00000393328;ENST00000393331;ENST00000347630;ENST00000504102;ENST00000503536;ENST00000503676;ENST00000513872;ENST00000509079;ENST00000505581;ENST00000507970;ENST00000514121	T;T;T;T;T;T;T;T;T	0.70045	-0.45;-0.45;-0.45;-0.45;-0.45;-0.45;-0.45;-0.45;-0.45	5.41	5.41	0.78517	TRAF-type (1);TRAF-like (1);MATH (3);	0.000000	0.85682	D	0.000000	T	0.81851	0.4910	H	0.95402	3.665	0.80722	D	1	P	0.43024	0.798	P	0.47786	0.557	D	0.87031	0.2135	10	0.72032	D	0.01	0.1404	15.258	0.73599	1.0:0.0:0.0:0.0	.	131	O43791	SPOP_HUMAN	G	131;131;131;131;15;131;84;131;131;131;131	ENSP00000377001:W131G;ENSP00000377004:W131G;ENSP00000240327:W131G;ENSP00000425905:W131G;ENSP00000420908:W131G;ENSP00000426986:W131G;ENSP00000420960:W131G;ENSP00000426262:W131G;ENSP00000424119:W131G	ENSP00000240327:W131G	W	-	1	0	SPOP	45051431	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.056000	0.93881	2.261000	0.74972	0.460000	0.39030	TGG		0.458	SPOP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365154.2	NM_003563		39	85	0	0	0	1	0	39	85				
IGHG2	3501	broad.mit.edu	37	14	106110960	106110960	+	RNA	SNP	G	G	A			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr14:106110960G>A	ENST00000390545.2	-	0	167							P01859	IGHG2_HUMAN	immunoglobulin heavy constant gamma 2 (G2m marker)						complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	antigen binding (GO:0003823)										AGGACTGTAGGACAGCCGGGA	0.632																																						ENST00000390545.2																			0																				63.0	69.0	67.0					14																	106110960		2106	4236	6342			0							g.chr14:106110960G>A	J00230		14q32.33	2012-10-02			ENSG00000211893	ENSG00000211893		"""Immunoglobulins / IGH locus"""	5526	other	immunoglobulin gene		147110					Standard	NG_001019		Approved			P01859	OTTHUMG00000152482		14.37:g.106110960G>A														0	167	-								A6NE66	RNA	SNP	ENST00000390545.2	37																																																																																						0.632	IGHG2-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	IG_C_gene	IG_C_gene	OTTHUMT00000326391.1	NG_001019		11	45	0	0	0	1	0	11	45				
MSH3	4437	broad.mit.edu	37	5	79968166	79968166	+	Missense_Mutation	SNP	C	C	T			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr5:79968166C>T	ENST00000265081.6	+	5	976	c.896C>T	c.(895-897)gCa>gTa	p.A299V		NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	299					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		CGCCTGGTGGCAAAAGGATAT	0.448								Mismatch excision repair (MMR)																													Melanoma(88;1010 1399 13793 26548 36275)	ENST00000265081.6																			0				NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						c.(895-897)gCa>gTa	Mismatch excision repair (MMR)	mutS homolog 3							96.0	92.0	93.0					5																	79968166		2203	4300	6503	SO:0001583	missense	4437				maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments	MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding	g.chr5:79968166C>T	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"""Divergent upstream protein"", ""Mismatch repair protein 1"""	600887	"""mutS (E. coli) homolog 3"", ""mutS homolog 3 (E. coli)"""				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.896C>T	5.37:g.79968166C>T	ENSP00000265081:p.Ala299Val						p.A299V	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)	5	976	+		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)	299					A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Missense_Mutation	SNP	ENST00000265081.6	37	c.896C>T	CCDS34195.1	.	.	.	.	.	.	.	.	.	.	C	33	5.223189	0.95139	.	.	ENSG00000113318	ENST00000265081;ENST00000535995	D	0.86366	-2.11	5.69	5.69	0.88448	DNA mismatch repair protein MutS, N-terminal (2);DNA mismatch repair protein MutS-like, N-terminal (1);	0.058541	0.64402	D	0.000002	D	0.94225	0.8146	M	0.84511	2.7	0.54753	D	0.999983	D	0.71674	0.998	D	0.72338	0.977	D	0.93953	0.7233	9	.	.	.	-16.607	19.4293	0.94758	0.0:1.0:0.0:0.0	.	299	P20585	MSH3_HUMAN	V	299;290	ENSP00000265081:A299V	.	A	+	2	0	MSH3	80003922	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.384000	0.79751	2.697000	0.92050	0.650000	0.86243	GCA		0.448	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		13	41	0	0	0	1	0	13	41				
SIPA1L3	23094	broad.mit.edu	37	19	38610375	38610375	+	Silent	SNP	G	G	A			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr19:38610375G>A	ENST00000222345.6	+	9	3230	c.2721G>A	c.(2719-2721)gtG>gtA	p.V907V		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	907					hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CCAAGGAGGTGGTGTTCAACT	0.542																																						ENST00000222345.6																			0				NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59						c.(2719-2721)gtG>gtA		signal-induced proliferation-associated 1 like 3							111.0	123.0	119.0					19																	38610375		2202	4300	6502	SO:0001819	synonymous_variant	23094				regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity	g.chr19:38610375G>A	AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738			23801	protein-coding gene	gene with protein product							Standard	XM_005258671		Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.2721G>A	19.37:g.38610375G>A							p.V907V	NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)		9	3230	+			907					Q2TV87	Silent	SNP	ENST00000222345.6	37	c.2721G>A	CCDS33007.1																																																																																				0.542	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278		6	98	0	0	0	1	0	6	98				
CLEC4C	170482	broad.mit.edu	37	12	7882195	7882195	+	Missense_Mutation	SNP	T	T	C	rs147980423		TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr12:7882195T>C	ENST00000542353.1	-	7	1129	c.639A>G	c.(637-639)atA>atG	p.I213M	CLEC4C_ENST00000360345.3_Missense_Mutation_p.I213M|CLEC4C_ENST00000354629.5_Missense_Mutation_p.I182M|CLEC4C_ENST00000540085.1_Missense_Mutation_p.I182M	NM_130441.2	NP_569708.1	Q8WTT0	CLC4C_HUMAN	C-type lectin domain family 4, member C	213					innate immune response (GO:0045087)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.I213M(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				Kidney(36;0.0915)		ATTTCATTTATATGTAGATCT	0.353																																						ENST00000542353.1																			1	Substitution - Missense(1)	p.I213M(1)	lung(1)	autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						c.(637-639)atA>atG		C-type lectin domain family 4, member C		T	MET/ILE,MET/ILE	1,4405	2.1+/-5.4	0,1,2202	102.0	95.0	97.0		639,546	0.4	0.8	12	dbSNP_134	97	0,8600		0,0,4300	no	missense,missense	CLEC4C	NM_130441.2,NM_203503.1	10,10	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	213/214,182/183	7882195	1,13005	2203	4300	6503	SO:0001583	missense	170482				innate immune response	integral to membrane	sugar binding	g.chr12:7882195T>C	AF325460	CCDS8583.1, CCDS8584.1	12p13.2-p12.3	2008-02-05	2004-02-13	2005-02-11	ENSG00000198178	ENSG00000198178		"""C-type lectin domain containing"", ""CD molecules"""	13258	protein-coding gene	gene with protein product		606677	"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 7"""	CLECSF11, CLECSF7		11031109, 11536172	Standard	NM_130441		Approved	HECL, DLEC, BDCA2, CD303	uc001qth.1	Q8WTT0	OTTHUMG00000168441	ENST00000542353.1:c.639A>G	12.37:g.7882195T>C	ENSP00000440428:p.Ile213Met					CLEC4C_ENST00000360345.3_Missense_Mutation_p.I213M|CLEC4C_ENST00000354629.5_Missense_Mutation_p.I182M|CLEC4C_ENST00000540085.1_Missense_Mutation_p.I182M	p.I213M	NM_130441.2	NP_569708.1	Q8WTT0	CLC4C_HUMAN		Kidney(36;0.0915)	7	1129	-			213					D3DUU3|Q3T1C3|Q6UXS8|Q8WXX8	Missense_Mutation	SNP	ENST00000542353.1	37	c.639A>G	CCDS8583.1	.	.	.	.	.	.	.	.	.	.	T	8.930	0.963293	0.18583	2.27E-4	0.0	ENSG00000198178	ENST00000542353;ENST00000354629;ENST00000540085;ENST00000360345	T;T;T;T	0.02579	4.31;4.24;4.24;4.31	1.66	0.398	0.16319	.	.	.	.	.	T	0.03178	0.0093	N	0.22421	0.69	0.20074	N	0.999931	B;D	0.53312	0.399;0.959	B;P	0.49301	0.057;0.606	T	0.45934	-0.9227	9	0.72032	D	0.01	.	4.4536	0.11633	0.0:0.0:0.3502:0.6498	.	182;213	Q8WTT0-2;Q8WTT0	.;CLC4C_HUMAN	M	213;182;182;213	ENSP00000440428:I213M;ENSP00000346648:I182M;ENSP00000445338:I182M;ENSP00000353500:I213M	ENSP00000346648:I182M	I	-	3	3	CLEC4C	7773462	0.182000	0.23173	0.766000	0.31476	0.049000	0.14656	-0.112000	0.10791	0.101000	0.17610	0.418000	0.28097	ATA		0.353	CLEC4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399750.1	NM_203503		5	38	0	0	0	1	0	5	38				
KIR3DL1	3811	broad.mit.edu	37	19	55294987	55294987	+	Intron	SNP	C	C	T	rs2736416		TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr19:55294987C>T	ENST00000538269.1	+	2	61				KIR2DL1_ENST00000291633.7_Silent_p.S315S|KIR2DL4_ENST00000396284.2_Intron|KIR3DL1_ENST00000402254.2_Intron|KIR3DL1_ENST00000541392.1_Intron|KIR2DL3_ENST00000434419.2_Silent_p.S289S|CTB-61M7.1_ENST00000400864.3_RNA|KIR2DL1_ENST00000336077.6_Silent_p.S289S			P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1						immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		CAGCGAATAGCGAGGTAGGTA	0.532																																						ENST00000336077.6																			0				breast(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	17						c.(865-867)agC>agT		killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 1							153.0	156.0	155.0					19																	55294987		2170	4188	6358	SO:0001627	intron_variant	3802				immune response|natural killer cell inhibitory signaling pathway	integral to plasma membrane	protein binding|receptor activity	g.chr19:55294987C>T	L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000538269.1:c.35-34002C>T	19.37:g.55294987C>T						KIR3DL1_ENST00000538269.1_Intron|KIR2DL3_ENST00000434419.2_Silent_p.S289S|CTB-61M7.1_ENST00000400864.3_RNA|KIR3DL1_ENST00000402254.2_Intron|KIR2DL4_ENST00000396284.2_Intron|KIR2DL1_ENST00000291633.7_Silent_p.S315S|KIR3DL1_ENST00000541392.1_Intron	p.S289S	NM_014218.2	NP_055033.2	P43626	KI2L1_HUMAN		GBM - Glioblastoma multiforme(193;0.0192)	7	907	+			289					O43473|Q14946|Q16541	Silent	SNP	ENST00000538269.1	37	c.867C>T																																																																																					0.532	KIR3DL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_013289		8	83	0	0	0	1	0	8	83				
DNAH2	146754	broad.mit.edu	37	17	7680790	7680790	+	Missense_Mutation	SNP	A	A	C			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr17:7680790A>C	ENST00000572933.1	+	33	6545	c.5085A>C	c.(5083-5085)gaA>gaC	p.E1695D	DNAH2_ENST00000389173.2_Missense_Mutation_p.E1695D			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	1695	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				AGTATTCAGAAGCCATCAGGG	0.498																																						ENST00000572933.1																			0				NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189						c.(5083-5085)gaA>gaC		dynein, axonemal, heavy chain 2							273.0	270.0	271.0					17																	7680790		2203	4300	6503	SO:0001583	missense	146754				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity	g.chr17:7680790A>C	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"""Axonemal dyneins"""	2948	protein-coding gene	gene with protein product		603333	"""dynein, axonemal, heavy polypeptide 2"", ""dynein heavy chain domain 3"""	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.5085A>C	17.37:g.7680790A>C	ENSP00000458355:p.Glu1695Asp					DNAH2_ENST00000389173.2_Missense_Mutation_p.E1695D	p.E1695D			Q9P225	DYH2_HUMAN			33	6545	+		all_cancers(10;4.66e-07)|Prostate(122;0.081)	1695			Stem (By similarity).		A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	37	c.5085A>C	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	A	12.12	1.843483	0.32606	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.22336	1.96	5.51	0.222	0.15288	.	0.126125	0.52532	D	0.000080	T	0.11153	0.0272	L	0.31120	0.905	0.80722	D	1	B	0.14805	0.011	B	0.17979	0.02	T	0.21930	-1.0231	10	0.11485	T	0.65	.	6.4479	0.21887	0.5362:0.1288:0.335:0.0	.	1695	Q9P225	DYH2_HUMAN	D	1695	ENSP00000373825:E1695D	ENSP00000353818:E1695D	E	+	3	2	DNAH2	7621515	0.987000	0.35691	0.998000	0.56505	0.982000	0.71751	0.257000	0.18369	0.073000	0.16731	0.477000	0.44152	GAA		0.498	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		18	322	0	0	0	1	0	18	322				
ZNF836	162962	broad.mit.edu	37	19	52658800	52658800	+	Silent	SNP	A	A	G			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr19:52658800A>G	ENST00000322146.8	-	5	2657	c.2136T>C	c.(2134-2136)taT>taC	p.Y712Y	ZNF836_ENST00000597252.1_Silent_p.Y712Y|CTC-471J1.8_ENST00000594362.1_RNA	NM_001102657.1	NP_001096127.1	Q6ZNA1	ZN836_HUMAN	zinc finger protein 836	712					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						GATTTCTGTGATATCTTGCAA	0.398																																						ENST00000322146.8																			0				endometrium(2)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						c.(2134-2136)taT>taC		zinc finger protein 836							67.0	67.0	67.0					19																	52658800		1976	4174	6150	SO:0001819	synonymous_variant	162962				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:52658800A>G	BC011784	CCDS46162.1	19q13.33	2013-01-08			ENSG00000196267	ENSG00000196267		"""Zinc fingers, C2H2-type"", ""-"""	34333	protein-coding gene	gene with protein product							Standard	NM_001102657		Approved	FLJ16287	uc010ydj.2	Q6ZNA1		ENST00000322146.8:c.2136T>C	19.37:g.52658800A>G						ZNF836_ENST00000597252.1_Silent_p.Y712Y|CTC-471J1.8_ENST00000594362.1_RNA	p.Y712Y	NM_001102657.1	NP_001096127.1	Q6ZNA1	ZN836_HUMAN			5	2657	-			712						Silent	SNP	ENST00000322146.8	37	c.2136T>C	CCDS46162.1																																																																																				0.398	ZNF836-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462456.1	NM_001102657		7	56	0	0	0	1	0	7	56				
TLK1	9874	broad.mit.edu	37	2	171902685	171902685	+	Splice_Site	SNP	G	G	C			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr2:171902685G>C	ENST00000431350.2	-	11	1572	c.1168C>G	c.(1168-1170)Ctg>Gtg	p.L390V	TLK1_ENST00000360843.3_Splice_Site_p.L411V|TLK1_ENST00000442919.2_Splice_Site_p.L342V|TLK1_ENST00000434911.2_Splice_Site_p.L294V|TLK1_ENST00000521943.1_Splice_Site_p.L342V			Q9UKI8	TLK1_HUMAN	tousled-like kinase 1	390					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|liver(3)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	33						GAGGCTTACAGTTGTGGTAAA	0.333																																						ENST00000442919.2																			0				breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|liver(3)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	33						c.e11+1		tousled-like kinase 1							159.0	152.0	154.0					2																	171902685		2203	4300	6503	SO:0001630	splice_region_variant	9874				cell cycle|chromatin modification|intracellular protein transport|intracellular signal transduction|regulation of chromatin assembly or disassembly|response to DNA damage stimulus	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity	g.chr2:171902685G>C	AB004885	CCDS2241.1, CCDS46447.1, CCDS46448.1	2q31.1	2010-04-19			ENSG00000198586	ENSG00000198586			11841	protein-coding gene	gene with protein product		608438				9427565, 12660173	Standard	NM_012290		Approved	KIAA0137, PKU-BETA	uc002ugp.2	Q9UKI8	OTTHUMG00000132243	ENST00000431350.2:c.1169+1C>G	2.37:g.171902685G>C						TLK1_ENST00000521943.1_Splice_Site_p.L342_splice|TLK1_ENST00000431350.2_Splice_Site_p.L390_splice|TLK1_ENST00000360843.3_Splice_Site_p.L411_splice|TLK1_ENST00000434911.2_Splice_Site_p.L294_splice	p.L342_splice	NM_012290.4	NP_036422.3	Q9UKI8	TLK1_HUMAN			11	1639	-			390					B3KR15|B4DX87|Q14150|Q8N591|Q9NYH2|Q9Y4F6	Splice_Site	SNP	ENST00000431350.2	37	c.1025_splice	CCDS2241.1	.	.	.	.	.	.	.	.	.	.	G	8.327	0.825545	0.16749	.	.	ENSG00000198586	ENST00000442919;ENST00000431350;ENST00000360843;ENST00000521943;ENST00000434911	T;T;T;T;T	0.62639	0.03;0.01;0.01;0.03;0.02	5.13	3.29	0.37713	.	0.000000	0.64402	D	0.000001	T	0.60907	0.2305	L	0.41236	1.265	0.50313	D	0.999861	B;D;B	0.62365	0.218;0.991;0.167	B;P;B	0.56751	0.05;0.805;0.024	T	0.55405	-0.8146	10	0.21014	T	0.42	-9.3847	8.9395	0.35720	0.2942:0.0:0.7058:0.0	.	294;411;390	B4DX87;Q9UKI8-2;Q9UKI8	.;.;TLK1_HUMAN	V	342;390;411;342;294	ENSP00000402165:L342V;ENSP00000411099:L390V;ENSP00000354089:L411V;ENSP00000428113:L342V;ENSP00000409222:L294V	ENSP00000354089:L411V	L	-	1	2	TLK1	171610931	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	2.027000	0.41078	1.295000	0.44724	-0.229000	0.12294	CTG		0.333	TLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255314.1	NM_012290	Missense_Mutation	4	78	0	0	0	1	0	4	78				
ACTG1	71	broad.mit.edu	37	17	79478956	79478956	+	Silent	SNP	G	G	A	rs532725688		TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr17:79478956G>A	ENST00000575842.1	-	2	762	c.336C>T	c.(334-336)ccC>ccT	p.P112P	RP13-766D20.2_ENST00000430912.1_RNA|ACTG1_ENST00000573283.1_Silent_p.P112P|ACTG1_ENST00000331925.2_Silent_p.P112P|ACTG1_ENST00000575087.1_Silent_p.P112P|AC139149.1_ENST00000584254.1_RNA			P63261	ACTG_HUMAN	actin, gamma 1	112					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|platelet aggregation (GO:0070527)|retina homeostasis (GO:0001895)|sarcomere organization (GO:0045214)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|membrane (GO:0016020)|myofibril (GO:0030016)|nucleus (GO:0005634)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|lung(8)|ovary(2)|prostate(5)|urinary_tract(1)	29	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0547)			TGTTGGCCTTGGGGTTCAGGG	0.622																																						ENST00000575842.1																			0				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|lung(8)|ovary(2)|prostate(5)|urinary_tract(1)	29						c.(334-336)ccC>ccT		actin, gamma 1							44.0	55.0	51.0					17																	79478956		2203	4298	6501	SO:0001819	synonymous_variant	71				adherens junction organization|axon guidance|blood coagulation|cell junction assembly|cellular component movement	cytoskeleton|cytosol	ATP binding|identical protein binding	g.chr17:79478956G>A		CCDS11782.1	17q25	2010-04-23	2004-05-19		ENSG00000184009	ENSG00000184009			144	protein-coding gene	gene with protein product		102560	"""deafness, autosomal dominant 20; deafness, autosomal dominant 26"""	ACTG, DFNA20, DFNA26		14684684	Standard	NM_001614		Approved		uc002kal.2	P63261		ENST00000575842.1:c.336C>T	17.37:g.79478956G>A						ACTG1_ENST00000331925.2_Silent_p.P112P|ACTG1_ENST00000573283.1_Silent_p.P112P|ACTG1_ENST00000575087.1_Silent_p.P112P	p.P112P			P63261	ACTG_HUMAN	BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0547)		2	762	-	all_neural(118;0.0878)|Melanoma(429;0.242)		112					A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Silent	SNP	ENST00000575842.1	37	c.336C>T	CCDS11782.1																																																																																				0.622	ACTG1-012	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439935.2	NM_001614		19	38	0	0	0	1	0	19	38				
ELAVL4	1996	broad.mit.edu	37	1	50661330	50661330	+	Silent	SNP	G	G	A	rs116732512		TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr1:50661330G>A	ENST00000371823.4	+	5	830	c.606G>A	c.(604-606)acG>acA	p.T202T	ELAVL4_ENST00000371821.1_Silent_p.T207T|ELAVL4_ENST00000371824.1_Silent_p.T202T|ELAVL4_ENST00000357083.4_Silent_p.T219T|ELAVL4_ENST00000371819.1_Silent_p.T207T|ELAVL4_ENST00000371827.1_Silent_p.T202T|ELAVL4_ENST00000448907.2_Silent_p.T205T	NM_001144774.1|NM_021952.3	NP_001138246.1|NP_068771.2	P26378	ELAV4_HUMAN	ELAV like neuron-specific RNA binding protein 4	202	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|RNA processing (GO:0006396)		AU-rich element binding (GO:0017091)|mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.T202T(1)|p.T219T(1)		NS(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(2)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	32						GCGGTGCTACGGAACCGATTA	0.582													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18269	0.0		0.0	False		,,,				2504	0.0					ENST00000371824.1																			2	Substitution - coding silent(2)	p.T202T(1)|p.T219T(1)	skin(2)	NS(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(2)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	32						c.(604-606)acG>acA		ELAV like neuron-specific RNA binding protein 4		G	,,,,	4,4402	8.1+/-20.4	0,4,2199	111.0	112.0	111.0		606,657,606,615,606	-7.9	0.8	1	dbSNP_132	111	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ELAVL4	NM_001144774.1,NM_001144775.1,NM_001144776.1,NM_001144777.1,NM_021952.3	,,,,	0,4,6499	AA,AG,GG		0.0,0.0908,0.0308	,,,,	202/367,219/384,202/367,205/370,202/381	50661330	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	1996				mRNA processing		AU-rich element binding|mRNA 3'-UTR binding|nucleotide binding	g.chr1:50661330G>A	AY033998	CCDS553.1, CCDS44138.1, CCDS44139.1, CCDS44140.1, CCDS53315.1, CCDS72788.1	1p34	2013-10-03	2013-10-03		ENSG00000162374	ENSG00000162374		"""RNA binding motif (RRM) containing"""	3315	protein-coding gene	gene with protein product	"""Hu antigen D"""	168360	"""ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4 (Hu antigen D)"", ""ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4"""	HUD		8222755	Standard	XM_005270581		Approved	PNEM	uc001csb.2	P26378	OTTHUMG00000007877	ENST00000371823.4:c.606G>A	1.37:g.50661330G>A						ELAVL4_ENST00000371821.1_Silent_p.T207T|ELAVL4_ENST00000357083.4_Silent_p.T219T|ELAVL4_ENST00000448907.2_Silent_p.T205T|ELAVL4_ENST00000371827.1_Silent_p.T202T|ELAVL4_ENST00000371819.1_Silent_p.T207T|ELAVL4_ENST00000371823.4_Silent_p.T202T	p.T202T			P26378	ELAV4_HUMAN			5	863	+			202			RRM 2.		B1APY6|B1APY7|B7Z4G7|Q8IYD4|Q96J74|Q96J75|Q9UD24	Silent	SNP	ENST00000371823.4	37	c.606G>A	CCDS553.1																																																																																				0.582	ELAVL4-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000021712.1	NM_021952		5	67	0	0	0	1	0	5	67				
OR1D2	4991	broad.mit.edu	37	17	2995484	2995484	+	Missense_Mutation	SNP	C	C	A			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr17:2995484C>A	ENST00000331459.1	-	1	806	c.807G>T	c.(805-807)aaG>aaT	p.K269N		NM_002548.2	NP_002539.2	P34982	OR1D2_HUMAN	olfactory receptor, family 1, subfamily D, member 2	269					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|G-protein coupled receptor signaling pathway (GO:0007186)|protein import into nucleus, translocation (GO:0000060)|sensory perception of smell (GO:0007608)|single fertilization (GO:0007338)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(2)|large_intestine(2)|lung(10)|ovary(1)	15						CTACTGAGTCCTTCACAGAGT	0.512																																						ENST00000331459.1																			0				kidney(2)|large_intestine(2)|lung(10)|ovary(1)	15						c.(805-807)aaG>aaT		olfactory receptor, family 1, subfamily D, member 2							110.0	104.0	106.0					17																	2995484		2203	4300	6503	SO:0001583	missense	4991				cellular component movement|chemotaxis|protein import into nucleus, translocation|sensory perception of smell|single fertilization	integral to plasma membrane	olfactory receptor activity	g.chr17:2995484C>A	U04678	CCDS11019.1	17p13.3	2012-08-09			ENSG00000184166	ENSG00000184166		"""GPCR / Class A : Olfactory receptors"""	8183	protein-coding gene	gene with protein product		164342		OLFR1		1370859, 1840504	Standard	NM_002548		Approved	OR17-4	uc010vrb.2	P34982	OTTHUMG00000090619	ENST00000331459.1:c.807G>T	17.37:g.2995484C>A	ENSP00000327585:p.Lys269Asn						p.K269N	NM_002548.2	NP_002539.2	P34982	OR1D2_HUMAN			1	806	-			269					Q6IFL8|Q96RA4|Q9UM78	Missense_Mutation	SNP	ENST00000331459.1	37	c.807G>T	CCDS11019.1	.	.	.	.	.	.	.	.	.	.	c	12.81	2.049341	0.36181	.	.	ENSG00000184166	ENST00000331459	T	0.00107	8.72	3.21	-0.214	0.13161	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00178	0.0005	L	0.46885	1.475	0.09310	N	0.999999	P	0.46912	0.886	P	0.49361	0.608	T	0.39722	-0.9600	9	0.66056	D	0.02	.	3.4795	0.07597	0.1745:0.4799:0.0:0.3456	.	269	P34982	OR1D2_HUMAN	N	269	ENSP00000327585:K269N	ENSP00000327585:K269N	K	-	3	2	OR1D2	2942234	0.000000	0.05858	0.959000	0.39883	0.721000	0.41392	-1.650000	0.01991	0.077000	0.16863	0.543000	0.68304	AAG		0.512	OR1D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207207.1	NM_002548		4	62	1	0	3.59834e-05	1	3.85536e-05	4	62				
ATP7A	538	broad.mit.edu	37	X	77264645	77264645	+	Missense_Mutation	SNP	G	G	A			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chrX:77264645G>A	ENST00000341514.6	+	7	1909	c.1754G>A	c.(1753-1755)aGt>aAt	p.S585N	ATP7A_ENST00000343533.5_Missense_Mutation_p.S585N|ATP7A_ENST00000350425.4_Intron	NM_000052.5	NP_000043.4	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide	585	HMA 6. {ECO:0000255|PROSITE- ProRule:PRU00280}.				blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|cartilage development (GO:0051216)|catecholamine metabolic process (GO:0006584)|cellular copper ion homeostasis (GO:0006878)|central nervous system neuron development (GO:0021954)|cerebellar Purkinje cell differentiation (GO:0021702)|collagen fibril organization (GO:0030199)|copper ion export (GO:0060003)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detoxification of copper ion (GO:0010273)|dopamine metabolic process (GO:0042417)|elastic fiber assembly (GO:0048251)|elastin biosynthetic process (GO:0051542)|epinephrine metabolic process (GO:0042414)|extracellular matrix organization (GO:0030198)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|lung alveolus development (GO:0048286)|mitochondrion organization (GO:0007005)|negative regulation of metalloenzyme activity (GO:0048553)|negative regulation of neuron apoptotic process (GO:0043524)|neuron projection morphogenesis (GO:0048812)|norepinephrine biosynthetic process (GO:0042421)|norepinephrine metabolic process (GO:0042415)|peptidyl-lysine modification (GO:0018205)|pigmentation (GO:0043473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of oxidoreductase activity (GO:0051353)|pyramidal neuron development (GO:0021860)|regulation of gene expression (GO:0010468)|regulation of oxidative phosphorylation (GO:0002082)|release of cytochrome c from mitochondria (GO:0001836)|removal of superoxide radicals (GO:0019430)|response to iron(III) ion (GO:0010041)|response to zinc ion (GO:0010043)|serotonin metabolic process (GO:0042428)|skin development (GO:0043588)|T-helper cell differentiation (GO:0042093)|transmembrane transport (GO:0055085)|tryptophan metabolic process (GO:0006568)|tyrosine metabolic process (GO:0006570)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|copper-dependent protein binding (GO:0032767)|copper-exporting ATPase activity (GO:0004008)|superoxide dismutase copper chaperone activity (GO:0016532)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(26)|pancreas(1)|prostate(1)|urinary_tract(1)	53					Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	ATAGAGTCTAGTCTCACAAAA	0.408																																						ENST00000341514.6																			0				breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(26)|pancreas(1)|prostate(1)|urinary_tract(1)	53						c.(1753-1755)aGt>aAt		ATPase, Cu++ transporting, alpha polypeptide							208.0	204.0	205.0					X																	77264645		2203	4296	6499	SO:0001583	missense	538				ATP biosynthetic process|blood vessel development|blood vessel remodeling|cartilage development|cellular copper ion homeostasis|cerebellar Purkinje cell differentiation|collagen fibril organization|copper ion import|detoxification of copper ion|dopamine metabolic process|elastic fiber assembly|elastin biosynthetic process|epinephrine metabolic process|hair follicle morphogenesis|locomotory behavior|lung alveolus development|negative regulation of metalloenzyme activity|neuroprotection|peptidyl-lysine modification|pigmentation|positive regulation of metalloenzyme activity|positive regulation of oxidoreductase activity|pyramidal neuron development|regulation of oxidative phosphorylation|removal of superoxide radicals|serotonin metabolic process|skin development|T-helper cell differentiation|tryptophan metabolic process	basolateral plasma membrane|cytosol|endoplasmic reticulum|integral to membrane|late endosome|neuron projection|neuronal cell body|perinuclear region of cytoplasm|trans-Golgi network|trans-Golgi network transport vesicle	ATP binding|copper-dependent protein binding|copper-exporting ATPase activity|superoxide dismutase copper chaperone activity	g.chrX:77264645G>A	L06133	CCDS35339.1, CCDS75997.1	Xq21.1	2012-10-22	2008-07-31		ENSG00000165240	ENSG00000165240	3.6.3.4	"""ATPases / P-type"""	869	protein-coding gene	gene with protein product	"""copper pump 1"", ""copper-transporting ATPase 1"""	300011	"""Menkes syndrome"""	MNK		10079817	Standard	NM_000052		Approved		uc004ecx.4	Q04656	OTTHUMG00000021885	ENST00000341514.6:c.1754G>A	X.37:g.77264645G>A	ENSP00000345728:p.Ser585Asn					ATP7A_ENST00000350425.4_Intron|ATP7A_ENST00000343533.5_Missense_Mutation_p.S585N	p.S585N	NM_000052.5	NP_000043.3	Q04656	ATP7A_HUMAN			7	1909	+			585			HMA 6.		B1AT72|O00227|O00745|Q9BYY8	Missense_Mutation	SNP	ENST00000341514.6	37	c.1754G>A	CCDS35339.1	.	.	.	.	.	.	.	.	.	.	G	0.209	-1.038069	0.02013	.	.	ENSG00000165240	ENST00000343533;ENST00000341514;ENST00000355691	D;D	0.86164	-2.08;-2.08	5.1	2.27	0.28462	Heavy metal-associated domain, HMA (3);Heavy metal-associated domain, copper ion-binding (1);Heavy-metal-associated, conserved site (1);	0.247613	0.39615	N	0.001310	T	0.68366	0.2993	N	0.05510	-0.035	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.15052	0.001;0.012	T	0.49418	-0.8942	10	0.16896	T	0.51	-3.37	4.7722	0.13162	0.1393:0.5084:0.2721:0.0801	.	585;595	Q04656;Q59HD1	ATP7A_HUMAN;.	N	585;585;595	ENSP00000343026:S585N;ENSP00000345728:S585N	ENSP00000345728:S585N	S	+	2	0	ATP7A	77151301	0.338000	0.24775	0.716000	0.30569	0.032000	0.12392	0.419000	0.21247	0.053000	0.16036	-2.164000	0.00325	AGT		0.408	ATP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057306.1	NM_000052		5	142	0	0	0	1	0	5	142				
AEBP1	165	broad.mit.edu	37	7	44152662	44152662	+	Missense_Mutation	SNP	C	C	A			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr7:44152662C>A	ENST00000223357.3	+	19	2947	c.2642C>A	c.(2641-2643)cCt>cAt	p.P881H	MIR4649_ENST00000582839.1_RNA|AEBP1_ENST00000450684.2_Missense_Mutation_p.P456H	NM_001129.3	NP_001120.3	Q8IUX7	AEBP1_HUMAN	AE binding protein 1	881	Interaction with PTEN. {ECO:0000250}.				cell adhesion (GO:0007155)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(13)|upper_aerodigestive_tract(2)	33						GACAAGTTCCCTCATGAGAGT	0.577																																						ENST00000223357.3																			0				NS(1)|breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(13)|upper_aerodigestive_tract(2)	33						c.(2641-2643)cCt>cAt		AE binding protein 1							139.0	150.0	147.0					7																	44152662		2203	4300	6503	SO:0001583	missense	165				cell adhesion|muscle organ development|proteolysis|skeletal system development	cytoplasm|extracellular space|nucleus	DNA binding|metallocarboxypeptidase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr7:44152662C>A	D86479	CCDS5476.1	7p	2008-07-18	2001-11-28		ENSG00000106624	ENSG00000106624			303	protein-coding gene	gene with protein product	"""aortic carboxypeptidase-like protein"", ""adipocyte enhancer binding protein 1"""	602981	"""AE-binding protein 1"""			8920928	Standard	NM_001129		Approved	ACLP	uc003tkb.4	Q8IUX7	OTTHUMG00000023362	ENST00000223357.3:c.2642C>A	7.37:g.44152662C>A	ENSP00000223357:p.Pro881His					AEBP1_ENST00000450684.2_Missense_Mutation_p.P456H	p.P881H	NM_001129.3	NP_001120.3	Q8IUX7	AEBP1_HUMAN			19	2947	+			881			Interaction with PTEN (By similarity).		Q14113|Q59ER7|Q6ZSC7|Q7KZ79	Missense_Mutation	SNP	ENST00000223357.3	37	c.2642C>A	CCDS5476.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.897975	0.91962	.	.	ENSG00000106624	ENST00000223357;ENST00000450684	T;T	0.14516	2.5;2.5	5.27	5.27	0.74061	Peptidase M14, carboxypeptidase A (2);	0.000000	0.85682	D	0.000000	T	0.50616	0.1626	M	0.93150	3.385	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.64153	-0.6474	10	0.87932	D	0	-17.9528	18.8544	0.92246	0.0:1.0:0.0:0.0	.	456;881	Q8IUX7-2;Q8IUX7	.;AEBP1_HUMAN	H	881;456	ENSP00000223357:P881H;ENSP00000398878:P456H	ENSP00000223357:P881H	P	+	2	0	AEBP1	44119187	1.000000	0.71417	0.969000	0.41365	0.997000	0.91878	7.725000	0.84808	2.621000	0.88768	0.591000	0.81541	CCT		0.577	AEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250993.2	NM_001129		6	238	1	0	0.0293803	1	0.0298783	6	238				
GPR112	139378	broad.mit.edu	37	X	135426829	135426829	+	Missense_Mutation	SNP	T	T	A			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chrX:135426829T>A	ENST00000394143.1	+	6	1255	c.964T>A	c.(964-966)Tca>Aca	p.S322T	GPR112_ENST00000370652.1_Missense_Mutation_p.S322T|GPR112_ENST00000412101.1_Missense_Mutation_p.S117T|GPR112_ENST00000287534.4_Missense_Mutation_p.S259T|GPR112_ENST00000394141.1_Missense_Mutation_p.S117T	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	322					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					ATCAACTTCATCAGCCATCTC	0.383																																						ENST00000394143.1																			0				NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199						c.(964-966)Tca>Aca		G protein-coupled receptor 112							122.0	104.0	111.0					X																	135426829		2203	4300	6503	SO:0001583	missense	139378				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity	g.chrX:135426829T>A	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.964T>A	X.37:g.135426829T>A	ENSP00000377699:p.Ser322Thr					GPR112_ENST00000370652.1_Missense_Mutation_p.S322T|GPR112_ENST00000394141.1_Missense_Mutation_p.S117T|GPR112_ENST00000287534.4_Missense_Mutation_p.S259T|GPR112_ENST00000412101.1_Missense_Mutation_p.S117T	p.S322T	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN			6	1255	+	Acute lymphoblastic leukemia(192;0.000127)		322					A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	c.964T>A	CCDS35409.1	.	.	.	.	.	.	.	.	.	.	t	0.157	-1.085486	0.01873	.	.	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.27720	1.69;1.69;1.65;1.81;1.65	4.27	1.9	0.25705	.	.	.	.	.	T	0.08891	0.0220	N	0.02539	-0.55	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.36625	-0.9740	9	0.02654	T	1	.	3.8811	0.09079	0.1734:0.0:0.6081:0.2185	.	259;117;322	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	T	322;322;117;259;117	ENSP00000377699:S322T;ENSP00000359686:S322T;ENSP00000416526:S117T;ENSP00000287534:S259T;ENSP00000377697:S117T	ENSP00000287534:S259T	S	+	1	0	GPR112	135254495	0.856000	0.29760	0.078000	0.20375	0.010000	0.07245	0.342000	0.19926	0.168000	0.19655	-0.365000	0.07479	TCA		0.383	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			23	22	0	0	0	1	0	23	22				
ZNF318	24149	broad.mit.edu	37	6	43323502	43323502	+	Frame_Shift_Del	DEL	T	T	-			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr6:43323502delT	ENST00000361428.2	-	4	1647	c.1570delA	c.(1570-1572)aggfs	p.R526fs	ZNF318_ENST00000318149.3_Frame_Shift_Del_p.R526fs	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	526					meiotic nuclear division (GO:0007126)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(21)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	61			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)			CTACGTCGCCTTTTTTCCTGT	0.493																																						ENST00000361428.2																			0				autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(21)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	61						c.(1570-1572)ggfs		zinc finger protein 318							215.0	222.0	219.0					6																	43323502		2203	4300	6503	SO:0001589	frameshift_variant	24149				meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	nucleic acid binding|zinc ion binding	g.chr6:43323502delT	AF090114	CCDS4895.2	6p21.1	2013-09-19			ENSG00000171467	ENSG00000171467		"""Zinc fingers, C2H2-type"""	13578	protein-coding gene	gene with protein product						10873617	Standard	NM_014345		Approved	HRIHFB2436, ZFP318	uc003oux.3	Q5VUA4	OTTHUMG00000014732	ENST00000361428.2:c.1570delA	6.37:g.43323502delT	ENSP00000354964:p.Arg526fs					ZNF318_ENST00000318149.3_Frame_Shift_Del_p.R526fs	p.R526fs	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)		4	1647	-			526					O94796|Q4G0E4|Q8NEM6|Q9UNU8|Q9Y2W9	Frame_Shift_Del	DEL	ENST00000361428.2	37	c.1570delA	CCDS4895.2																																																																																				0.493	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	NM_014345		8	573						8	573	---	---	---	---
ZAN	7455	broad.mit.edu	37	7	100371476	100371477	+	RNA	INS	-	-	G	rs148800656|rs200325383|rs372381708	byFrequency	TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr7:100371476_100371477insG	ENST00000348028.3	+	0	5932_5933				ZAN_ENST00000538115.1_RNA|ZAN_ENST00000546292.1_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000542585.1_RNA|ZAN_ENST00000349350.6_RNA|ZAN_ENST00000443370.1_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000449052.1_RNA			Q9Y493	ZAN_HUMAN	zonadhesin (gene/pseudogene)						binding of sperm to zona pellucida (GO:0007339)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.?(1)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)	139	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			GCTGCTCCGTTTCGGGCCTCAG	0.624													G|-|G|deletion	2230	0.445288	0.2133	0.5418	5008	,	,		17915	0.7867		0.3419	False		,,,				2504	0.4448					ENST00000542585.1																			1	Unknown(1)	p.?(1)	upper_aerodigestive_tract(1)	NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)	139								zonadhesin (gene/pseudogene)			,	906,2950		139,628,1161					,	4.6	0.9		dbSNP_134	33	2934,5018		557,1820,1599	no	frameshift,frameshift	ZAN	NM_173059.1,NM_003386.1	,	696,2448,2760	A1A1,A1R,RR		36.8964,23.4959,32.5203	,	,		3840,7968						7455				binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane		g.chr7:100371476_100371477insG	U83191		7q22.1	2013-10-10	2013-10-10		ENSG00000146839	ENSG00000146839			12857	protein-coding gene	gene with protein product		602372	"""zonadhesin"""			9799793, 17033959	Standard	NM_003386		Approved		uc003uwk.3	Q9Y493	OTTHUMG00000157037		7.37:g.100371476_100371477insG						ZAN_ENST00000449052.1_RNA|ZAN_ENST00000546292.1_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000538115.1_RNA|ZAN_ENST00000349350.6_RNA|ZAN_ENST00000443370.1_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000348028.3_RNA		NM_003386.1	NP_003377.1	Q9Y493	ZAN_HUMAN	STAD - Stomach adenocarcinoma(171;0.19)		0	5914	+	Lung NSC(181;0.041)|all_lung(186;0.0581)							A0FKC8|D6W5W4|O00218|Q96L85|Q96L86|Q96L87|Q96L88|Q96L89|Q96L90|Q9BXN9|Q9BZ83|Q9BZ84|Q9BZ85|Q9BZ86|Q9BZ87|Q9BZ88	RNA	INS	ENST00000348028.3	37																																																																																						0.624	ZAN-006	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347214.1	NM_003386		6	8						6	8	---	---	---	---
C7orf55-LUC7L2	100996928	broad.mit.edu	37	7	139094365	139094366	+	Frame_Shift_Del	DEL	AG	AG	-	rs368249579	byFrequency	TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr7:139094365_139094366delAG	ENST00000354926.4	+	7	1098_1099	c.744_745delAG	c.(742-747)gaagagfs	p.EE248fs	LUC7L2_ENST00000541515.3_Frame_Shift_Del_p.EE314fs|C7orf55-LUC7L2_ENST00000263545.6_Frame_Shift_Del_p.EE247fs|C7orf55-LUC7L2_ENST00000541170.3_Frame_Shift_Del_p.EE245fs	NM_001270643.1|NM_016019.4	NP_001257572.1|NP_057103.2			C7orf55-LUC7L2 readthrough																		AACGAAGAGAAGAGAGAGAGAG	0.391														64	0.0127796	0.028	0.0014	5008	,	,		16418	0.004		0.002	False		,,,				2504	0.0204					ENST00000354926.4																			0											c.(742-747)gaagfs						136,3410		1,134,1638						5.1	1.0			34	290,7544		0,290,3627	no	frameshift	LUC7L2	NM_016019.3		1,424,5265	A1A1,A1R,RR		3.7018,3.8353,3.7434				426,10954				SO:0001589	frameshift_variant	0							g.chr7:139094365_139094366delAG		CCDS59084.1	7q34	2013-02-14			ENSG00000146963	ENSG00000146963			44671	other	readthrough							Standard	NM_001244584		Approved		uc011kqt.3		OTTHUMG00000151717	ENST00000354926.4:c.744_745delAG	7.37:g.139094375_139094376delAG	ENSP00000347005:p.Glu248fs					C7orf55-LUC7L2_ENST00000541170.3_Frame_Shift_Del_p.EE245fs|C7orf55-LUC7L2_ENST00000263545.6_Frame_Shift_Del_p.EE247fs|LUC7L2_ENST00000541515.3_Frame_Shift_Del_p.EE314fs	p.EE248fs	NM_016019.3	NP_057103.2					7	1098_1099	+									Frame_Shift_Del	DEL	ENST00000354926.4	37	c.744_745delAG	CCDS43656.1																																																																																				0.391	C7orf55-LUC7L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323618.2			3	4						3	4	---	---	---	---
BHLHE22	27319	broad.mit.edu	37	8	65494021	65494023	+	In_Frame_Del	DEL	GCA	GCA	-	rs62519837		TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr8:65494021_65494023delGCA	ENST00000321870.1	+	1	1208_1210	c.674_676delGCA	c.(673-678)ggcagc>ggc	p.S234del	RP11-21C4.1_ENST00000517909.1_RNA	NM_152414.4	NP_689627.1	Q8NFJ8	BHE22_HUMAN	basic helix-loop-helix family, member e22	234	Ser-rich.				anterior commissure morphogenesis (GO:0021960)|cerebral cortex regionalization (GO:0021796)|corpus callosum morphogenesis (GO:0021540)|corticospinal tract morphogenesis (GO:0021957)|negative regulation of transcription, DNA-templated (GO:0045892)|retinal bipolar neuron differentiation (GO:0060040)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.S234delS(1)|p.S226G(1)		NS(1)|central_nervous_system(1)|lung(1)|prostate(1)|skin(1)	5						ggcagcggcggcagcagcagcag	0.709																																					Colon(113;104 1586 2865 9855 18065)	ENST00000321870.1																			2	Substitution - Missense(1)|Deletion - In frame(1)	p.S234delS(1)|p.S226G(1)	central_nervous_system(1)|skin(1)	NS(1)|central_nervous_system(1)|lung(1)|prostate(1)|skin(1)	5						c.(673-678)ggc>g		basic helix-loop-helix family, member e22																																				SO:0001651	inframe_deletion	27319				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus		g.chr8:65494021_65494023delGCA	U80755	CCDS6179.1	8q12.1	2009-01-12	2009-01-12	2009-01-12		ENSG00000180828		"""Basic helix-loop-helix proteins"""	11963	protein-coding gene	gene with protein product		613483	"""trinucleotide repeat containing 20"", ""basic helix-loop-helix domain containing, class B, 5"""	TNRC20, BHLHB5		9225980, 12213201, 18557763	Standard	NM_152414		Approved	CAGL85, Beta3, bHLHe22	uc003xvi.3	Q8NFJ8		ENST00000321870.1:c.674_676delGCA	8.37:g.65494030_65494032delGCA	ENSP00000318799:p.Ser234del					RP11-21C4.1_ENST00000517909.1_RNA	p.GS225del	NM_152414.4	NP_689627.1	Q8NFJ8	BHE22_HUMAN			1	1208_1210	+			225			Gly-rich.|Ser-rich.			In_Frame_Del	DEL	ENST00000321870.1	37	c.674_676delGCA	CCDS6179.1																																																																																				0.709	BHLHE22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378549.1	NM_152414		2	4						2	4	---	---	---	---
ABCA1	19	broad.mit.edu	37	9	107556793	107556794	+	Splice_Site	INS	-	-	AA	rs397938228|rs77663187|rs377469216		TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr9:107556793_107556794insAA	ENST00000374736.3	-	40	5777		c.e40-2			NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1						apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)	p.?(2)		NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	ATTCAGCTTCTAAAAAAAAAAA	0.406																																						ENST00000374736.3																			2	Unknown(2)	p.?(2)	lung(1)|kidney(1)	NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115						c.e40-2		ATP-binding cassette, sub-family A (ABC1), member 1	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)																																			SO:0001630	splice_region_variant	19				Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol transporter activity|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding	g.chr9:107556793_107556794insAA	AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"""ATP binding cassette transporters / subfamily A"""	29	protein-coding gene	gene with protein product	"""Tangier disease"""	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.5383-2->TT	9.37:g.107556802_107556803dupAA								NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN		OV - Ovarian serous cystadenocarcinoma(323;0.023)	40	5777	-								Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Splice_Site	INS	ENST00000374736.3	37		CCDS6762.1																																																																																				0.406	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502	Intron	11	25						11	25	---	---	---	---
ANK3	288	broad.mit.edu	37	10	61834099	61834099	+	Frame_Shift_Del	DEL	A	A	-			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr10:61834099delA	ENST00000280772.2	-	37	6731	c.6540delT	c.(6538-6540)gctfs	p.A2180fs	ANK3_ENST00000503366.1_Intron|ANK3_ENST00000373827.2_Intron|ANK3_ENST00000355288.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	2180					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						GAACATCCCCAGCTGAGGGAT	0.463																																						ENST00000280772.1																			0				NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						c.(6538-6540)gcfs		ankyrin 3, node of Ranvier (ankyrin G)							110.0	109.0	109.0					10																	61834099		2203	4300	6503	SO:0001589	frameshift_variant	288				establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding	g.chr10:61834099delA	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"""Ankyrin repeat domain containing"""	494	protein-coding gene	gene with protein product	"""ankyrin-3, node of Ranvier"", ""ankyrin-G"""	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.6540delT	10.37:g.61834099delA	ENSP00000280772:p.Ala2180fs					ANK3_ENST00000355288.2_Intron|ANK3_ENST00000373827.2_Intron|ANK3_ENST00000503366.1_Intron	p.A2180fs	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN			37	6731	-			2180					B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Frame_Shift_Del	DEL	ENST00000280772.2	37	c.6540delT	CCDS7258.1																																																																																				0.463	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		10	134						10	134	---	---	---	---
KMT2A	4297	broad.mit.edu	37	11	118374348	118374348	+	Frame_Shift_Del	DEL	A	A	-			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr11:118374348delA	ENST00000389506.5	+	27	7732	c.7732delA	c.(7732-7734)accfs	p.T2578fs	KMT2A_ENST00000534358.1_Frame_Shift_Del_p.T2581fs|KMT2A_ENST00000354520.4_Frame_Shift_Del_p.T2540fs			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	2578					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										CCCCAATAATACCTCATGCCA	0.478																																						ENST00000534358.1																			0											c.(7741-7743)ccfs		lysine (K)-specific methyltransferase 2A							62.0	63.0	63.0					11																	118374348		2200	4296	6496	SO:0001589	frameshift_variant	4297							g.chr11:118374348delA	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7132	protein-coding gene	gene with protein product		159555	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)"", ""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"""	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.7732delA	11.37:g.118374348delA	ENSP00000374157:p.Thr2578fs					KMT2A_ENST00000389506.5_Frame_Shift_Del_p.T2578fs|KMT2A_ENST00000354520.4_Frame_Shift_Del_p.T2540fs	p.T2581fs	NM_001197104.1|NM_005933.3	NP_001184033.1|NP_005924.2					27	7764	+								E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Frame_Shift_Del	DEL	ENST00000389506.5	37	c.7741delA	CCDS31686.1																																																																																				0.478	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		11	35						11	35	---	---	---	---
GOLGA8EP	390535	broad.mit.edu	37	15	23438975	23438976	+	RNA	INS	-	-	C			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr15:23438975_23438976insC	ENST00000526079.1	+	0	558_559					NR_027407.1|NR_033350.1				golgin A8 family, member E, pseudogene																		AAGAAGGCTAACCCCCCAGAGT	0.629																																						ENST00000526079.1																			0																																																			0							g.chr15:23438975_23438976insC			15q11.2	2014-03-21	2012-10-05	2012-10-05	ENSG00000175676	ENSG00000175676			32377	pseudogene	pseudogene			"""golgi autoantigen, golgin subfamily a, 8E"", ""golgin A8 family, member E"""	GOLGA8E		12477932	Standard	NR_033350		Approved		uc001yvu.3		OTTHUMG00000167132		15.37:g.23438981_23438981dupC								NR_027407.1|NR_033350.1						0	558_559	+									RNA	INS	ENST00000526079.1	37																																																																																						0.629	GOLGA8EP-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000393312.1	NR_033350.1		2	4						2	4	---	---	---	---
SMG1P4	100507526	broad.mit.edu	37	16	21893165	21893166	+	RNA	INS	-	-	T			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr16:21893165_21893166insT	ENST00000540706.1	-	0	1816_1817																											GTACCTACCTATTTTTTCTTTT	0.317																																						ENST00000540706.1																			0																																																			0							g.chr16:21893165_21893166insT																													16.37:g.21893171_21893171dupT														0	1816_1817	-									RNA	INS	ENST00000540706.1	37																																																																																						0.317	RP11-645C24.2-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000402428.1			2	4						2	4	---	---	---	---
CWC25	54883	broad.mit.edu	37	17	36981421	36981421	+	Frame_Shift_Del	DEL	G	G	-			TCGA-YL-A8SO-01B-31D-A377-08	TCGA-YL-A8SO-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b01429d0-5689-4988-9b04-c5c9173cc5a5	ce7b01a1-f923-4ed8-a350-eaf02a60ac73	g.chr17:36981421delG	ENST00000225428.5	-	1	313	c.16delC	c.(16-18)ctgfs	p.L6fs	MIR4727_ENST00000584037.1_RNA|CWC25_ENST00000536127.1_5'UTR	NM_017748.3	NP_060218.1	Q9NXE8	CWC25_HUMAN	CWC25 spliceosome-associated protein homolog (S. cerevisiae)	6										central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)	14						CCACTCACCAGGTCTCCGCCC	0.597																																						ENST00000225428.4																			0				central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)	14						c.(16-18)tgfs		CWC25 spliceosome-associated protein homolog (S. cerevisiae)							35.0	35.0	35.0					17																	36981421		1857	4086	5943	SO:0001589	frameshift_variant	54883							g.chr17:36981421delG	AK000298	CCDS45663.1	17q12	2010-01-26	2010-01-26	2010-01-26		ENSG00000273559			25989	protein-coding gene	gene with protein product			"""coiled-coil domain containing 49"""	CCDC49		19941820	Standard	NM_017748		Approved	FLJ20291	uc002hqu.4	Q9NXE8		ENST00000225428.5:c.16delC	17.37:g.36981421delG	ENSP00000225428:p.Leu6fs					CWC25_ENST00000536127.1_5'UTR	p.L6fs	NM_017748.3	NP_060218.1	Q9NXE8	CWC25_HUMAN			1	313	-			6					A0JLM3|Q68DK5	Frame_Shift_Del	DEL	ENST00000225428.5	37	c.16delC	CCDS45663.1																																																																																				0.597	CWC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442186.6	NM_017748		2	4						2	4	---	---	---	---
