#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
NRG2	9542	broad.mit.edu	37	5	139232068	139232068	+	Missense_Mutation	SNP	G	G	C	rs377110446		TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr5:139232068G>C	ENST00000361474.1	-	8	1717	c.1493C>G	c.(1492-1494)tCc>tGc	p.S498C	NRG2_ENST00000358522.3_Missense_Mutation_p.S500C|NRG2_ENST00000394770.1_3'UTR|NRG2_ENST00000289422.7_Missense_Mutation_p.S506C|NRG2_ENST00000545385.1_Missense_Mutation_p.S500C|NRG2_ENST00000541337.1_Missense_Mutation_p.S432C|CTB-35F21.4_ENST00000504413.1_RNA|NRG2_ENST00000289409.4_Missense_Mutation_p.S492C|NRG2_ENST00000340391.3_Missense_Mutation_p.S295C	NM_004883.2	NP_004874.1	O14511	NRG2_HUMAN	neuregulin 2	498					embryo development (GO:0009790)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	25			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGAGAACAGGAGTGGCTCCC	0.537																																						ENST00000541337.1																			0				breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	25						c.(1294-1296)tCc>tGc		neuregulin 2		G	CYS/SER,CYS/SER,CYS/SER,CYS/SER,CYS/SER	0,4406		0,0,2203	230.0	180.0	197.0		1295,1493,1475,1517,1499	5.2	1.0	5		197	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense	NRG2	NM_001184935.1,NM_004883.2,NM_013981.3,NM_013982.2,NM_013983.2	112,112,112,112,112	0,1,6502	CC,CG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	432/785,498/851,492/845,506/859,500/853	139232068	1,13005	2203	4300	6503	SO:0001583	missense	9542				embryo development	extracellular region|integral to membrane|plasma membrane	growth factor activity	g.chr5:139232068G>C		CCDS4217.1, CCDS54910.1	5q23-q33	2013-01-11			ENSG00000158458	ENSG00000158458		"""Immunoglobulin superfamily / I-set domain containing"""	7998	protein-coding gene	gene with protein product	"""neural- and thymus-derived activator for ErbB kinases"", ""divergent of neuregulin-1"""	603818				9168114, 9168115	Standard	NM_004883		Approved	Don-1, NTAK, HRG2	uc003lev.2	O14511	OTTHUMG00000129241	ENST00000361474.1:c.1493C>G	5.37:g.139232068G>C	ENSP00000354910:p.Ser498Cys					CTB-35F21.4_ENST00000504413.1_RNA|NRG2_ENST00000289422.7_Missense_Mutation_p.S506C|NRG2_ENST00000545385.1_Missense_Mutation_p.S500C|NRG2_ENST00000394770.1_3'UTR|NRG2_ENST00000361474.1_Missense_Mutation_p.S498C|NRG2_ENST00000340391.3_Missense_Mutation_p.S295C|NRG2_ENST00000358522.3_Missense_Mutation_p.S500C|NRG2_ENST00000289409.4_Missense_Mutation_p.S492C	p.S432C	NM_001184935.1	NP_001171864.1	O14511	NRG2_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		6	1524	-			498						Missense_Mutation	SNP	ENST00000361474.1	37	c.1295C>G	CCDS4217.1	.	.	.	.	.	.	.	.	.	.	G	16.21	3.059049	0.55325	0.0	1.16E-4	ENSG00000158458	ENST00000541337;ENST00000289422;ENST00000361474;ENST00000446269;ENST00000545385;ENST00000340391;ENST00000289409;ENST00000358522	T;T;T;T;T;T;T	0.54866	0.55;0.55;0.55;0.55;0.55;0.55;0.55	5.25	5.25	0.73442	Neuregulin 1-related, C-terminal (1);	0.145792	0.47852	D	0.000207	T	0.65312	0.2679	L	0.52364	1.645	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.72982	0.965;0.979;0.965;0.965	T	0.63466	-0.6631	10	0.40728	T	0.16	-22.7132	13.7792	0.63073	0.0:0.0:0.8465:0.1535	.	492;498;500;506	O14511-2;O14511;O14511-4;O14511-3	.;NRG2_HUMAN;.;.	C	432;506;498;506;500;295;492;500	ENSP00000444235:S432C;ENSP00000289422:S506C;ENSP00000354910:S498C;ENSP00000438753:S500C;ENSP00000342660:S295C;ENSP00000289409:S492C;ENSP00000351323:S500C	ENSP00000289409:S492C	S	-	2	0	NRG2	139212252	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.087000	0.41653	2.458000	0.83093	0.467000	0.42956	TCC		0.537	NRG2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251340.1	NM_013982		11	26	0	0	0	1	0	11	26				
POTEE	445582	broad.mit.edu	37	2	131976101	131976101	+	Silent	SNP	C	C	T	rs558466498		TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr2:131976101C>T	ENST00000356920.5	+	1	220	c.126C>T	c.(124-126)aaC>aaT	p.N42N	POTEE_ENST00000358087.5_Silent_p.N42N|PLEKHB2_ENST00000404460.1_Intron|PLEKHB2_ENST00000303908.3_Intron	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	42					retina homeostasis (GO:0001895)|substantia nigra development (GO:0021762)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)											GCAAGAGCAACGTGGGCACTT	0.592													c|||	1	0.000199681	0.0	0.0	5008	,	,		17826	0.0		0.0	False		,,,				2504	0.001					ENST00000356920.5																			0											c.(124-126)aaC>aaT		POTE ankyrin domain family, member E							131.0	151.0	144.0					2																	131976101		2194	4298	6492	SO:0001819	synonymous_variant	445582						ATP binding	g.chr2:131976101C>T	AY462868	CCDS46414.1	2q21.1	2014-04-10	2008-11-26	2008-11-26	ENSG00000188219	ENSG00000188219		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33895	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 2"""	608914	"""ANKRD26-like family C, member 1A"""	A26C1A			Standard	NM_001083538		Approved	POTE2, POTE-2, A26C1, POTE2gamma, CT104.2	uc002tsn.2	Q6S8J3	OTTHUMG00000186974	ENST00000356920.5:c.126C>T	2.37:g.131976101C>T						PLEKHB2_ENST00000303908.3_Intron|PLEKHB2_ENST00000404460.1_Intron|POTEE_ENST00000358087.5_Silent_p.N42N	p.N42N	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN			1	220	+			42					Q6S8J4|Q6S8J5|Q6S8J8	Silent	SNP	ENST00000356920.5	37	c.126C>T	CCDS46414.1																																																																																				0.592	POTEE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001083538		4	160	0	0	0	1	0	4	160				
SPOP	8405	broad.mit.edu	37	17	47696644	47696644	+	Missense_Mutation	SNP	A	A	C			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr17:47696644A>C	ENST00000393328.2	-	5	669	c.304T>G	c.(304-306)Ttc>Gtc	p.F102V	SPOP_ENST00000513080.1_5'Flank|SPOP_ENST00000504102.1_Missense_Mutation_p.F102V|SPOP_ENST00000347630.2_Missense_Mutation_p.F102V|SPOP_ENST00000503676.1_Missense_Mutation_p.F102V|SPOP_ENST00000393331.3_Missense_Mutation_p.F102V	NM_003563.3	NP_003554.1	O43791	SPOP_HUMAN	speckle-type POZ protein	102	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)			endometrium(18)|kidney(1)|large_intestine(3)|liver(1)|lung(4)|ovary(3)|prostate(33)	63						GAGAATTTGAATTTTGCCCGA	0.408										Prostate(2;0.17)																												ENST00000393331.3																			0				endometrium(18)|kidney(1)|large_intestine(3)|liver(1)|lung(4)|ovary(3)|prostate(33)	63						c.(304-306)Ttc>Gtc		speckle-type POZ protein							147.0	136.0	140.0					17																	47696644		2203	4300	6503	SO:0001583	missense	8405				mRNA processing	nucleus	protein binding	g.chr17:47696644A>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.304T>G	17.37:g.47696644A>C	ENSP00000377001:p.Phe102Val	Prostate(2;0.17)				SPOP_ENST00000347630.2_Missense_Mutation_p.F102V|SPOP_ENST00000393328.2_Missense_Mutation_p.F102V|SPOP_ENST00000504102.1_Missense_Mutation_p.F102V|SPOP_ENST00000503676.1_Missense_Mutation_p.F102V	p.F102V	NM_001007226.1|NM_001007227.1	NP_001007227.1|NP_001007228.1	O43791	SPOP_HUMAN			6	774	-			102			MATH.|Required for nuclear localization.		B2R6S3|D3DTW7|Q53HJ1	Missense_Mutation	SNP	ENST00000393328.2	37	c.304T>G	CCDS11551.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.465429	0.84425	.	.	ENSG00000121067	ENST00000393328;ENST00000393331;ENST00000347630;ENST00000504102;ENST00000503676;ENST00000513872;ENST00000509079;ENST00000505581;ENST00000507970;ENST00000514121;ENST00000515508	T;T;T;T;T;T;T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23;-0.23;-0.23;-0.23;-0.23;-0.23;-0.23	5.52	5.52	0.82312	TRAF-type (1);TRAF-like (1);MATH (3);	0.000000	0.85682	D	0.000000	T	0.77046	0.4073	L	0.48986	1.54	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.75869	-0.3165	10	0.39692	T	0.17	-11.8278	15.4649	0.75390	1.0:0.0:0.0:0.0	.	102	O43791	SPOP_HUMAN	V	102;102;102;102;102;55;102;102;102;102;102	ENSP00000377001:F102V;ENSP00000377004:F102V;ENSP00000240327:F102V;ENSP00000425905:F102V;ENSP00000420908:F102V;ENSP00000426986:F102V;ENSP00000420960:F102V;ENSP00000426262:F102V;ENSP00000424119:F102V;ENSP00000426537:F102V	ENSP00000240327:F102V	F	-	1	0	SPOP	45051643	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.135000	0.94478	2.317000	0.78254	0.460000	0.39030	TTC		0.408	SPOP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365154.2	NM_003563		23	62	0	0	0	1	0	23	62				
LRP12	29967	broad.mit.edu	37	8	105509398	105509398	+	Missense_Mutation	SNP	T	T	C			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr8:105509398T>C	ENST00000276654.5	-	5	1490	c.1382A>G	c.(1381-1383)aAt>aGt	p.N461S	LRP12_ENST00000424843.2_Missense_Mutation_p.N442S|LRP12_ENST00000518375.1_5'Flank	NM_013437.4	NP_038465.1	Q9Y561	LRP12_HUMAN	low density lipoprotein receptor-related protein 12	461	LDL-receptor class A 5. {ECO:0000255|PROSITE-ProRule:PRU00124}.				endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)			CACACAACGATTGTTTTTACA	0.423																																						ENST00000276654.5																			0				NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48						c.(1381-1383)aAt>aGt		low density lipoprotein receptor-related protein 12							115.0	105.0	108.0					8																	105509398		2203	4300	6503	SO:0001583	missense	29967				endocytosis|regulation of growth	coated pit|integral to plasma membrane	low-density lipoprotein receptor activity|protein binding	g.chr8:105509398T>C	AF166350	CCDS6303.1, CCDS47907.1	8q22.2	2013-02-27	2010-01-26		ENSG00000147650	ENSG00000147650		"""Low density lipoprotein receptors"""	31708	protein-coding gene	gene with protein product						12809483, 14676824	Standard	NM_013437		Approved	ST7, FLJ12929	uc003yma.3	Q9Y561	OTTHUMG00000164892	ENST00000276654.5:c.1382A>G	8.37:g.105509398T>C	ENSP00000276654:p.Asn461Ser					LRP12_ENST00000424843.2_Missense_Mutation_p.N442S	p.N461S	NM_013437.4	NP_038465.1	Q9Y561	LRP12_HUMAN	OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)		5	1490	-			461			LDL-receptor class A 5.		A8K137|B4DRQ2	Missense_Mutation	SNP	ENST00000276654.5	37	c.1382A>G	CCDS6303.1	.	.	.	.	.	.	.	.	.	.	T	17.25	3.343013	0.61073	.	.	ENSG00000147650	ENST00000424843;ENST00000276654;ENST00000523007	D;D;D	0.94966	-3.57;-3.57;-3.57	5.79	4.64	0.57946	.	0.000000	0.85682	D	0.000000	D	0.88640	0.6491	N	0.16201	0.385	0.80722	D	1	B;B	0.22746	0.06;0.074	B;B	0.27887	0.05;0.084	D	0.83873	0.0275	10	0.44086	T	0.13	-29.8765	11.8215	0.52240	0.0:0.0683:0.0:0.9317	.	442;461	Q9Y561-2;Q9Y561	.;LRP12_HUMAN	S	442;461;50	ENSP00000399148:N442S;ENSP00000276654:N461S;ENSP00000429305:N50S	ENSP00000276654:N461S	N	-	2	0	LRP12	105578574	1.000000	0.71417	0.989000	0.46669	0.985000	0.73830	8.040000	0.89188	1.030000	0.39839	0.455000	0.32223	AAT		0.423	LRP12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380821.1	NM_013437		13	44	0	0	0	1	0	13	44				
TCF12	6938	broad.mit.edu	37	15	57484403	57484403	+	Silent	SNP	A	A	G			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr15:57484403A>G	ENST00000267811.5	+	7	742	c.438A>G	c.(436-438)ctA>ctG	p.L146L	TCF12_ENST00000452095.2_Silent_p.L142L|TCF12_ENST00000557843.1_Silent_p.L146L|TCF12_ENST00000438423.2_Silent_p.L146L|TCF12_ENST00000333725.5_Silent_p.L146L	NM_003205.3|NM_207038.1	NP_003196.1|NP_996921.1	Q99081	HTF4_HUMAN	transcription factor 12	146					immune response (GO:0006955)|muscle organ development (GO:0007517)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)		TCF12/NR4A3(2)	breast(2)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	36		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		CAGCACAGCTATCTTCTTCAG	0.468			T	TEC	extraskeletal myxoid chondrosarcoma																																	ENST00000267811.5				Dom	yes		15	15q21	6938	T	"""transcription factor 12 (HTF4, helix-loop-helix transcription factors 4)"""			M	TEC		extraskeletal myxoid chondrosarcoma	TCF12/NR4A3(2)	0				breast(2)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	36						c.(436-438)ctA>ctG		transcription factor 12							92.0	94.0	94.0					15																	57484403		2192	4292	6484	SO:0001819	synonymous_variant	6938				immune response|muscle organ development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity	g.chr15:57484403A>G	BC050556	CCDS10159.1, CCDS10160.1, CCDS42042.1	15q21	2013-05-21	2008-07-31		ENSG00000140262	ENSG00000140262		"""Basic helix-loop-helix proteins"""	11623	protein-coding gene	gene with protein product	"""helix-loop-helix transcription factor 4"""	600480				1886779	Standard	NM_003205		Approved	HEB, HTF4, HsT17266, bHLHb20	uc002aeb.3	Q99081	OTTHUMG00000132047	ENST00000267811.5:c.438A>G	15.37:g.57484403A>G						TCF12_ENST00000557843.1_Silent_p.L146L|TCF12_ENST00000452095.2_Silent_p.L142L|TCF12_ENST00000438423.2_Silent_p.L146L|TCF12_ENST00000333725.5_Silent_p.L146L	p.L146L	NM_003205.3|NM_207038.1	NP_003196.1|NP_996921.1	Q99081	HTF4_HUMAN		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)	7	742	+		Colorectal(260;0.0907)	146					Q7Z3D9|Q86TC1|Q86VM2	Silent	SNP	ENST00000267811.5	37	c.438A>G	CCDS10159.1																																																																																				0.468	TCF12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255069.3	NM_003205		16	42	0	0	0	1	0	16	42				
A1CF	29974	broad.mit.edu	37	10	52573721	52573721	+	Missense_Mutation	SNP	C	C	G			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr10:52573721C>G	ENST00000373993.1	-	8	1287	c.1243G>C	c.(1243-1245)Gga>Cga	p.G415R	A1CF_ENST00000373995.3_Missense_Mutation_p.G415R|A1CF_ENST00000395489.2_Missense_Mutation_p.G408R|ASAH2B_ENST00000483649.1_Intron|A1CF_ENST00000395495.1_Missense_Mutation_p.G360R|A1CF_ENST00000282641.2_Missense_Mutation_p.G415R|A1CF_ENST00000374001.2_Missense_Mutation_p.G407R|A1CF_ENST00000373997.3_Missense_Mutation_p.G407R|A1CF_ENST00000493415.1_5'UTR			Q9NQ94	A1CF_HUMAN	APOBEC1 complementation factor	415					cytidine to uridine editing (GO:0016554)|gene expression (GO:0010467)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|protein stabilization (GO:0050821)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			NS(1)|breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(14)|prostate(2)|skin(3)	29						CTTTTGTCTCCTTTGACCTGG	0.493																																						ENST00000395489.2																			0				NS(1)|breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(14)|prostate(2)|skin(3)	29						c.(1222-1224)Gga>Cga		APOBEC1 complementation factor							138.0	136.0	137.0					10																	52573721		2203	4300	6503	SO:0001583	missense	29974				cytidine to uridine editing|mRNA modification|mRNA processing|protein stabilization	apolipoprotein B mRNA editing enzyme complex|endoplasmic reticulum|nucleoplasm	nucleotide binding|protein binding|single-stranded RNA binding	g.chr10:52573721C>G	AF271790	CCDS7241.1, CCDS7242.1, CCDS7243.1, CCDS73133.1	10q21.1	2013-02-12			ENSG00000148584	ENSG00000148584		"""RNA binding motif (RRM) containing"""	24086	protein-coding gene	gene with protein product						11815617, 11072063	Standard	NM_014576		Approved	ACF, ASP, ACF64, ACF65, APOBEC1CF	uc001jjj.3	Q9NQ94	OTTHUMG00000018240	ENST00000373993.1:c.1243G>C	10.37:g.52573721C>G	ENSP00000363105:p.Gly415Arg					A1CF_ENST00000374001.1_Missense_Mutation_p.G407R|A1CF_ENST00000395495.1_Missense_Mutation_p.G360R|A1CF_ENST00000373995.3_Missense_Mutation_p.G415R|A1CF_ENST00000282641.2_Missense_Mutation_p.G415R|ASAH2B_ENST00000483649.1_Intron|A1CF_ENST00000373997.3_Missense_Mutation_p.G407R|A1CF_ENST00000493415.1_5'UTR|A1CF_ENST00000373993.1_Missense_Mutation_p.G415R	p.G408R	NM_001198819.1	NP_001185748.1	Q9NQ94	A1CF_HUMAN			12	1618	-			415			Required for nuclear localization.		A1L4F2|A8K7G7|B7ZM14|Q5SZQ0|Q9NQ93|Q9NQX8|Q9NQX9|Q9NXC9|Q9NZD3	Missense_Mutation	SNP	ENST00000373993.1	37	c.1222G>C	CCDS7242.1	.	.	.	.	.	.	.	.	.	.	C	14.08	2.428032	0.43122	.	.	ENSG00000148584	ENST00000374001;ENST00000373993;ENST00000373997;ENST00000373995;ENST00000282641;ENST00000395495;ENST00000395488;ENST00000395489	T;T;T;T;T;T;T	0.13538	2.74;2.76;2.74;2.73;2.76;2.58;2.76	5.87	5.87	0.94306	.	1.732920	0.03318	U	0.191521	T	0.25975	0.0633	L	0.33485	1.01	0.44181	D	0.996996	P;P;P;P	0.46277	0.875;0.779;0.859;0.683	B;B;P;P	0.51385	0.413;0.296;0.668;0.578	T	0.05683	-1.0870	10	0.25751	T	0.34	-11.3978	17.713	0.88327	0.0:1.0:0.0:0.0	.	408;415;407;415	F8W9F8;Q9NQ94;Q9NQ94-2;Q9NQ94-4	.;A1CF_HUMAN;.;.	R	407;415;407;415;415;360;390;408	ENSP00000363113:G407R;ENSP00000363105:G415R;ENSP00000363109:G407R;ENSP00000363107:G415R;ENSP00000282641:G415R;ENSP00000378873:G360R;ENSP00000378868:G408R	ENSP00000282641:G415R	G	-	1	0	A1CF	52243727	1.000000	0.71417	1.000000	0.80357	0.193000	0.23685	4.393000	0.59665	2.780000	0.95670	0.655000	0.94253	GGA		0.493	A1CF-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048086.2	NM_014576		17	39	0	0	0	1	0	17	39				
SDHAP1	255812	broad.mit.edu	37	3	195701278	195701278	+	RNA	SNP	C	C	T	rs200131790	byFrequency	TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr3:195701278C>T	ENST00000427841.1	-	0	1546					NR_003264.2				succinate dehydrogenase complex, subunit A, flavoprotein pseudogene 1																		CAGGCCTGCACGACTCTGCGA	0.537																																					Ovarian(67;1158 1227 12109 20189 43170)	ENST00000427841.1																			0																																																			0							g.chr3:195701278C>T	BC071730		3q29	2009-12-02	2006-11-21	2009-12-02	ENSG00000185485	ENSG00000185485			32455	pseudogene	pseudogene			"""succinate dehydrogenase complex, subunit A, flavoprotein-like 1"""	SDHAL1, SDHALP1			Standard	NR_003264		Approved		uc003fvy.3		OTTHUMG00000155716		3.37:g.195701278C>T								NR_003264.2						0	1546	-									RNA	SNP	ENST00000427841.1	37																																																																																						0.537	SDHAP1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000341367.1			6	30	0	0	0	1	0	6	30				
CLCN6	1185	broad.mit.edu	37	1	11889328	11889328	+	Silent	SNP	C	C	T			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr1:11889328C>T	ENST00000346436.6	+	13	1249	c.1197C>T	c.(1195-1197)tgC>tgT	p.C399C	CLCN6_ENST00000376492.3_3'UTR|CLCN6_ENST00000376496.3_Silent_p.C399C|CLCN6_ENST00000312413.6_Missense_Mutation_p.P344S|CLCN6_ENST00000376487.3_Silent_p.C377C	NM_001286.3	NP_001277	P51797	CLCN6_HUMAN	chloride channel, voltage-sensitive 6	399					cell volume homeostasis (GO:0006884)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|response to mechanical stimulus (GO:0009612)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|voltage-gated chloride channel activity (GO:0005247)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(4)	36	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		TAGGAGAATGCCGACAGATGT	0.512																																						ENST00000312413.6																			0				cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(4)	36						c.(1030-1032)Ccg>Tcg		chloride channel, voltage-sensitive 6							254.0	227.0	236.0					1																	11889328		2203	4300	6503	SO:0001819	synonymous_variant	1185				cell volume homeostasis|signal transduction	endosome membrane|integral to membrane	antiporter activity|ATP binding|voltage-gated chloride channel activity	g.chr1:11889328C>T	X83378	CCDS138.1, CCDS57972.1	1p36	2012-09-26	2012-02-23		ENSG00000011021	ENSG00000011021		"""Ion channels / Chloride channels : Voltage-sensitive"""	2024	protein-coding gene	gene with protein product		602726	"""chloride channel 6"""			8543009	Standard	NM_001286		Approved	CLC-6, KIAA0046, ClC-6	uc001ate.5	P51797	OTTHUMG00000002299	ENST00000346436.6:c.1197C>T	1.37:g.11889328C>T						CLCN6_ENST00000346436.6_Silent_p.C399C|CLCN6_ENST00000376496.3_Silent_p.C399C|CLCN6_ENST00000376492.3_3'UTR|CLCN6_ENST00000376487.3_Silent_p.C377C	p.P344S			P51797	CLCN6_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)	12	1143	+	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)	0					A8K1T4|B4DGT7|F8W9R3|O60818|O60819|O60820|O60821|P78520|P78521|Q17R81|Q5SNW2|Q5SNW3|Q5SNX1|Q5SNX2|Q5SNX3|Q99427|Q99428|Q99429	Missense_Mutation	SNP	ENST00000346436.6	37	c.1030C>T	CCDS138.1	.	.	.	.	.	.	.	.	.	.	C	14.55	2.570182	0.45798	.	.	ENSG00000011021	ENST00000312413;ENST00000376492	D	0.92149	-2.98	5.83	2.96	0.34315	.	.	.	.	.	D	0.85318	0.5669	.	.	.	0.26407	N	0.976323	B	0.14805	0.011	B	0.15484	0.013	T	0.73107	-0.4087	8	0.30078	T	0.28	-30.8747	8.0601	0.30627	0.0:0.6966:0.0:0.3034	.	344	P51797-3	.	S	344	ENSP00000308367:P344S	ENSP00000308367:P344S	P	+	1	0	CLCN6	11811915	1.000000	0.71417	1.000000	0.80357	0.622000	0.37654	1.380000	0.34351	0.811000	0.34303	-0.140000	0.14226	CCG		0.512	CLCN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006639.2	NM_001286		3	60	0	0	0	1	0	3	60				
GYS1	2997	broad.mit.edu	37	19	49490530	49490530	+	Missense_Mutation	SNP	T	T	C			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr19:49490530T>C	ENST00000323798.3	-	3	609	c.413A>G	c.(412-414)aAc>aGc	p.N138S	GYS1_ENST00000263276.6_Intron|GYS1_ENST00000544287.1_Intron|GYS1_ENST00000457974.1_5'UTR|GYS1_ENST00000541188.1_Missense_Mutation_p.N58S|GYS1_ENST00000540532.1_Missense_Mutation_p.N58S	NM_002103.4	NP_002094.2	P13807	GYS1_HUMAN	glycogen synthase 1 (muscle)	138					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|heart development (GO:0007507)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|inclusion body (GO:0016234)|membrane (GO:0016020)	glucose binding (GO:0005536)|glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000164)|all cancers(93;0.000226)|GBM - Glioblastoma multiforme(486;0.00561)|Epithelial(262;0.0286)		CACTCCGATGTTGCAGGTATC	0.637																																						ENST00000323798.3																			0				breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						c.(412-414)aAc>aGc		glycogen synthase 1 (muscle)							79.0	57.0	64.0					19																	49490530		2203	4300	6503	SO:0001583	missense	2997				glucose metabolic process|glycogen biosynthetic process	cytosol	glycogen (starch) synthase activity|protein binding	g.chr19:49490530T>C		CCDS12747.1, CCDS54292.1	19q13.3	2013-02-22			ENSG00000104812	ENSG00000104812	2.4.1.11	"""Glycosyltransferase group 1 domain containing"""	4706	protein-coding gene	gene with protein product		138570		GYS			Standard	NM_002103		Approved	GSY	uc002plp.3	P13807	OTTHUMG00000150723	ENST00000323798.3:c.413A>G	19.37:g.49490530T>C	ENSP00000317904:p.Asn138Ser					GYS1_ENST00000541188.1_Missense_Mutation_p.N58S|GYS1_ENST00000544287.1_Intron|GYS1_ENST00000263276.6_Intron|GYS1_ENST00000540532.1_Missense_Mutation_p.N58S|GYS1_ENST00000457974.1_5'UTR	p.N138S	NM_002103.4	NP_002094.2	P13807	GYS1_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.000164)|all cancers(93;0.000226)|GBM - Glioblastoma multiforme(486;0.00561)|Epithelial(262;0.0286)	3	609	-		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)	138					Q9BTT9	Missense_Mutation	SNP	ENST00000323798.3	37	c.413A>G	CCDS12747.1	.	.	.	.	.	.	.	.	.	.	T	9.550	1.115782	0.20795	.	.	ENSG00000104812	ENST00000323798;ENST00000541188;ENST00000540532;ENST00000457974	T;T;T	0.62364	0.03;0.03;0.03	3.82	1.72	0.24424	.	0.375071	0.31082	N	0.008299	T	0.35128	0.0921	N	0.11427	0.14	0.35386	D	0.790301	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.003	T	0.17684	-1.0361	10	0.22109	T	0.4	-20.8488	6.2651	0.20922	0.0:0.2247:0.0:0.7753	.	58;138	B7Z806;P13807	.;GYS1_HUMAN	S	138;58;58;137	ENSP00000317904:N138S;ENSP00000437922:N58S;ENSP00000445197:N58S	ENSP00000317904:N138S	N	-	2	0	GYS1	54182342	0.947000	0.32204	1.000000	0.80357	0.979000	0.70002	0.199000	0.17237	0.610000	0.30035	0.455000	0.32223	AAC		0.637	GYS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319791.1	NM_002103		3	5	0	0	0	1	0	3	5				
RP11-156P1.2	0	broad.mit.edu	37	17	45127107	45127107	+	IGR	SNP	C	C	G	rs374963948		TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr17:45127107C>G	ENST00000571841.1	+	0	889				LRRC37A17P_ENST00000570478.1_RNA|RP11-156P1.3_ENST00000575173.1_RNA																							CCTTCGTTCACCCAAGAGCAT	0.592																																						ENST00000575173.1																			0																																																	SO:0001628	intergenic_variant	0							g.chr17:45127107C>G																													17.37:g.45127107C>G														0	418	-									RNA	SNP	ENST00000571841.1	37																																																																																						0.592	RP11-156P1.2-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	protein_coding	OTTHUMT00000440447.1			4	46	0	0	0	1	0	4	46				
BAGE2	85319	broad.mit.edu	37	21	11058353	11058353	+	RNA	SNP	T	T	C	rs79433933		TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr21:11058353T>C	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		GAAATCTCTTTATAAAACCTT	0.343																																						ENST00000470054.1																			0													B melanoma antigen family, member 2							20.0	18.0	19.0					21																	11058353		692	1589	2281			85319							g.chr21:11058353T>C	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"""cancer/testis antigen family 2, member 2"""					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11058353T>C												Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)	0	324	-								A8K925|Q08ER0	RNA	SNP	ENST00000470054.1	37																																																																																						0.343	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482		3	91	0	0	0	1	0	3	91				
DDX24	57062	broad.mit.edu	37	14	94526642	94526642	+	Missense_Mutation	SNP	G	G	C			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr14:94526642G>C	ENST00000330836.5	-	5	1846	c.1715C>G	c.(1714-1716)aCt>aGt	p.T572S	DDX24_ENST00000555054.1_Missense_Mutation_p.T529S|DDX24_ENST00000544005.1_Missense_Mutation_p.T322S	NM_020414.3	NP_065147.1	Q9GZR7	DDX24_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 24	572					RNA metabolic process (GO:0016070)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			cervix(3)|endometrium(4)|kidney(4)|large_intestine(5)|lung(3)|ovary(2)|skin(1)|urinary_tract(1)	23		all_cancers(154;0.12)		Epithelial(152;0.114)|all cancers(159;0.19)|COAD - Colon adenocarcinoma(157;0.207)		TTTCTCATCAGTCTCACAATG	0.498																																						ENST00000330836.5																			0				cervix(3)|endometrium(4)|kidney(4)|large_intestine(5)|lung(3)|ovary(2)|skin(1)|urinary_tract(1)	23						c.(1714-1716)aCt>aGt		DEAD (Asp-Glu-Ala-Asp) box helicase 24							206.0	180.0	189.0					14																	94526642		2203	4300	6503	SO:0001583	missense	57062				RNA metabolic process	cytoplasm|nucleolus	ATP binding|ATP-dependent RNA helicase activity|protein binding|RNA binding	g.chr14:94526642G>C	AF214731	CCDS9918.1	14q32	2013-07-16	2013-07-16			ENSG00000089737		"""DEAD-boxes"""	13266	protein-coding gene	gene with protein product		606181	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 24"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 24"""			10936056, 18289627	Standard	NM_020414		Approved		uc001ycj.3	Q9GZR7		ENST00000330836.5:c.1715C>G	14.37:g.94526642G>C	ENSP00000328690:p.Thr572Ser					DDX24_ENST00000544005.1_Missense_Mutation_p.T322S|DDX24_ENST00000555054.1_Missense_Mutation_p.T529S	p.T572S	NM_020414.3	NP_065147.1	Q9GZR7	DDX24_HUMAN		Epithelial(152;0.114)|all cancers(159;0.19)|COAD - Colon adenocarcinoma(157;0.207)	5	1846	-		all_cancers(154;0.12)	572					E7EMJ4|Q4V9L5	Missense_Mutation	SNP	ENST00000330836.5	37	c.1715C>G	CCDS9918.1	.	.	.	.	.	.	.	.	.	.	G	12.44	1.937283	0.34189	.	.	ENSG00000089737	ENST00000330836;ENST00000544005;ENST00000440370;ENST00000543787;ENST00000555054;ENST00000542247	T;T;T	0.04654	3.58;3.58;3.58	5.74	3.8	0.43715	.	0.341205	0.36854	N	0.002361	T	0.04724	0.0128	L	0.31065	0.9	0.25906	N	0.983298	B	0.18310	0.027	B	0.17433	0.018	T	0.34675	-0.9819	10	0.18276	T	0.48	-2.7502	15.5826	0.76455	0.0:0.0:0.7508:0.2492	.	572	Q9GZR7	DDX24_HUMAN	S	572;322;517;198;529;529	ENSP00000328690:T572S;ENSP00000440623:T322S;ENSP00000452145:T529S	ENSP00000328690:T572S	T	-	2	0	DDX24	93596395	0.999000	0.42202	0.982000	0.44146	0.998000	0.95712	2.864000	0.48404	1.536000	0.49237	0.563000	0.77884	ACT		0.498	DDX24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412861.1	NM_020414		28	46	0	0	0	1	0	28	46				
KDM5D	8284	broad.mit.edu	37	Y	21868432	21868432	+	Missense_Mutation	SNP	C	C	A			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chrY:21868432C>A	ENST00000317961.4	-	26	4435	c.4164G>T	c.(4162-4164)atG>atT	p.M1388I	KDM5D_ENST00000541639.1_Missense_Mutation_p.M1419I|KDM5D_ENST00000382806.2_Missense_Mutation_p.M1331I	NM_004653.4	NP_004644.2	Q9BY66	KDM5D_HUMAN	lysine (K)-specific demethylase 5D	1388					histone H3-K4 demethylation (GO:0034720)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-K4 specific) (GO:0032453)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(9)|lung(6)|skin(1)	17					Vitamin C(DB00126)	GGTCCCCTTCCATCATGAGCT	0.607																																						ENST00000541639.1																			0				kidney(1)|large_intestine(9)|lung(6)|skin(1)	17						c.(4255-4257)atG>atT		lysine (K)-specific demethylase 5D	Vitamin C(DB00126)						35.0	32.0	32.0					Y																	21868432		580	1904	2484	SO:0001583	missense	8284				chromatin modification|spermatogenesis	nucleus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding	g.chrY:21868432C>A	U52191	CCDS14794.1, CCDS55554.1, CCDS55555.1	Yq11	2013-01-28	2009-04-06	2009-04-06	ENSG00000012817	ENSG00000012817		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	11115	protein-coding gene	gene with protein product		426000	"""Jumonji, AT rich interactive domain 1D (RBP2-like)"", ""Smcy homolog, Y-linked (mouse)"", ""jumonji, AT rich interactive domain 1D"""	HYA, HY, SMCY, JARID1D		795123, 8841177	Standard	NM_001146705		Approved	KIAA0234	uc011naz.2	Q9BY66	OTTHUMG00000036508	ENST00000317961.4:c.4164G>T	Y.37:g.21868432C>A	ENSP00000322408:p.Met1388Ile					KDM5D_ENST00000317961.4_Missense_Mutation_p.M1388I|KDM5D_ENST00000382806.2_Missense_Mutation_p.M1331I	p.M1419I	NM_001146705.1	NP_001140177.1	Q9BY66	KDM5D_HUMAN			27	4544	-			1388					A2RU19|A6H8V7|B7ZLX1|Q92509|Q92809|Q9HCU1	Missense_Mutation	SNP	ENST00000317961.4	37	c.4257G>T	CCDS14794.1																																																																																				0.607	KDM5D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088790.1	NM_004653		3	7	1	0	0.004672	1	0.00484189	3	7				
LOC101927209	101927209	broad.mit.edu	37	1	142713773	142713773	+	lincRNA	SNP	C	C	G	rs199933143		TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr1:142713773C>G	ENST00000610091.1	-	0	1885																											TCTTTTTCCACATTGTCATTT	0.284																																						ENST00000369381.2																			0																																																			0							g.chr1:142713773C>G																													1.37:g.142713773C>G														0	832	-									RNA	SNP	ENST00000610091.1	37																																																																																						0.284	RP11-417J8.6-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000037265.2			3	37	0	0	0	1	0	3	37				
TBP	6908	broad.mit.edu	37	6	170871046	170871046	+	Silent	SNP	A	A	G	rs369312237|rs62430309	byFrequency	TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr6:170871046A>G	ENST00000392092.2	+	3	501	c.222A>G	c.(220-222)caA>caG	p.Q74Q	TBP_ENST00000230354.6_Silent_p.Q74Q|TBP_ENST00000540980.1_Silent_p.Q54Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	74	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		agcaacagcaacagcagcagc	0.567																																						ENST00000392092.2																			0				breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26						c.(220-222)caA>caG		TATA box binding protein							16.0	21.0	19.0					6																	170871046		1983	3871	5854	SO:0001819	synonymous_variant	6908				cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction	transcription factor TFIIA complex|transcription factor TFIID complex	repressing transcription factor binding|transcription regulatory region DNA binding	g.chr6:170871046A>G	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"""General transcription factors"""	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.222A>G	6.37:g.170871046A>G						TBP_ENST00000230354.6_Silent_p.Q74Q|TBP_ENST00000540980.1_Silent_p.Q54Q	p.Q74Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)	3	501	+		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)	74			Poly-Gln.		B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	37	c.222A>G	CCDS5315.1																																																																																				0.567	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194		3	27	0	0	0	1	0	3	27				
PCDHGA8	9708	broad.mit.edu	37	5	140772818	140772818	+	Silent	SNP	G	G	A			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr5:140772818G>A	ENST00000398604.2	+	1	438	c.438G>A	c.(436-438)gcG>gcA	p.A146A	PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron	NM_032088.1	NP_114477.1	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8	146	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(6)|kidney(6)|large_intestine(6)|lung(30)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGAAATCGCGGTTCCTGGAG	0.453																																						ENST00000398604.2																			0				endometrium(6)|kidney(6)|large_intestine(6)|lung(30)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	51						c.(436-438)gcG>gcA									52.0	57.0	55.0					5																	140772818		1945	4156	6101	SO:0001819	synonymous_variant	0							g.chr5:140772818G>A	AF152515	CCDS47291.1, CCDS75338.1	5q31	2010-01-26			ENSG00000253767	ENSG00000253767		"""Cadherins / Protocadherins : Clustered"""	8706	other	protocadherin		606295				10380929	Standard	NM_014004		Approved	KIAA0327, PCDH-GAMMA-A8		Q9Y5G5	OTTHUMG00000164053	ENST00000398604.2:c.438G>A	5.37:g.140772818G>A						PCDHGB3_ENST00000576222.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron	p.A146A	NM_032088.1	NP_114477.1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		1	438	+								A7MCZ4|O15039	Silent	SNP	ENST00000398604.2	37	c.438G>A	CCDS47291.1																																																																																				0.453	PCDHGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376972.1	NM_032088		26	39	0	0	0	1	0	26	39				
LRP4	4038	broad.mit.edu	37	11	46924428	46924428	+	Silent	SNP	T	T	G			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr11:46924428T>G	ENST00000378623.1	-	2	347	c.105A>C	c.(103-105)gcA>gcC	p.A35A		NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	35	LDL-receptor class A 1. {ECO:0000255|PROSITE-ProRule:PRU00124}.				dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		GAGCACTCACTGCACATGTGA	0.587																																						ENST00000378623.1																			0				breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70						c.(103-105)gcA>gcC		low density lipoprotein receptor-related protein 4							81.0	71.0	74.0					11																	46924428		2201	4299	6500	SO:0001819	synonymous_variant	4038				endocytosis|negative regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	integral to membrane	calcium ion binding|receptor activity	g.chr11:46924428T>G	AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"""Low density lipoprotein receptors"""	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.105A>C	11.37:g.46924428T>G							p.A35A	NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN		Lung(87;0.159)	2	347	-			35			LDL-receptor class A 1.		B2RN39|Q4AC85|Q5KTZ5	Silent	SNP	ENST00000378623.1	37	c.105A>C	CCDS31478.1																																																																																				0.587	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334		11	22	0	0	0	1	0	11	22				
KRTAP4-4	84616	broad.mit.edu	37	17	39316834	39316834	+	Missense_Mutation	SNP	C	C	T	rs201735937		TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr17:39316834C>T	ENST00000390661.3	-	1	149	c.110G>A	c.(109-111)cGc>cAc	p.R37H		NM_032524.1	NP_115913.1	Q9BYR3	KRA44_HUMAN	keratin associated protein 4-4	37	26 X 5 AA repeats of C-C-[GRQVCH]-[SPT]- [VSTQR].					keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(5)	7		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			GCAGCTGGGGCGGCAGCAGGT	0.652																																						ENST00000390661.3																			0				kidney(1)|large_intestine(1)|lung(5)	7						c.(109-111)cGc>cAc		keratin associated protein 4-4							38.0	51.0	47.0					17																	39316834		2182	4289	6471	SO:0001583	missense	84616					keratin filament		g.chr17:39316834C>T	AJ406936	CCDS11383.1	17q21.2	2013-06-25			ENSG00000171396	ENSG00000171396		"""Keratin associated proteins"""	16928	protein-coding gene	gene with protein product			"""keratin associated protein 4-13"""	KRTAP4-13		11279113	Standard	NM_032524		Approved	KAP4.4, KAP4.13	uc002hwc.3	Q9BYR3	OTTHUMG00000133428	ENST00000390661.3:c.110G>A	17.37:g.39316834C>T	ENSP00000375076:p.Arg37His						p.R37H	NM_032524.1	NP_115913.1	Q9BYR3	KRA44_HUMAN	STAD - Stomach adenocarcinoma(17;0.000449)		1	149	-		Breast(137;0.000496)	37			26 X 5 AA repeats of C-C-[GRQVCH]-[SPT]- [VSTQR].		Q9BYU7	Missense_Mutation	SNP	ENST00000390661.3	37	c.110G>A	CCDS11383.1	.	.	.	.	.	.	.	.	.	.	.	14.74	2.626581	0.46840	.	.	ENSG00000171396	ENST00000390661	T	0.01495	4.83	5.25	0.674	0.17946	.	0.575390	0.11899	N	0.518835	T	0.04497	0.0123	H	0.94542	3.55	0.09310	N	1	B	0.30236	0.274	B	0.23275	0.045	T	0.18209	-1.0344	10	0.59425	D	0.04	.	5.1247	0.14878	0.3927:0.4434:0.0:0.1638	.	37	Q9BYR3	KRA44_HUMAN	H	37	ENSP00000375076:R37H	ENSP00000375076:R37H	R	-	2	0	KRTAP4-4	36570360	0.000000	0.05858	0.943000	0.38184	0.985000	0.73830	-2.118000	0.01325	0.580000	0.29522	-0.234000	0.12200	CGC		0.652	KRTAP4-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257291.1			26	55	0	0	0	1	0	26	55				
TFCP2L1	29842	broad.mit.edu	37	2	122007205	122007205	+	Missense_Mutation	SNP	C	C	T			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr2:122007205C>T	ENST00000263707.5	-	3	330	c.233G>A	c.(232-234)cGa>cAa	p.R78Q		NM_014553.2	NP_055368.1	Q9NZI6	TF2L1_HUMAN	transcription factor CP2-like 1	78					cell morphogenesis (GO:0000902)|cytoplasm organization (GO:0007028)|determination of adult lifespan (GO:0008340)|epithelial cell maturation (GO:0002070)|female pregnancy (GO:0007565)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of growth (GO:0045927)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|salivary gland development (GO:0007431)|steroid biosynthetic process (GO:0006694)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(4)|large_intestine(5)|lung(7)|ovary(1)|pancreas(2)|skin(1)|stomach(1)	22	Renal(3;0.01)					CTCCAGTAGTCGGATTTCATA	0.458																																						ENST00000263707.5																			0				cervix(1)|endometrium(4)|large_intestine(5)|lung(7)|ovary(1)|pancreas(2)|skin(1)|stomach(1)	22						c.(232-234)cGa>cAa		transcription factor CP2-like 1							110.0	116.0	114.0					2																	122007205		2203	4300	6503	SO:0001583	missense	29842				female pregnancy|steroid biosynthetic process	mitochondrion|nucleolus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity	g.chr2:122007205C>T	AF198488	CCDS2134.1	2q14	2008-02-05			ENSG00000115112	ENSG00000115112			17925	protein-coding gene	gene with protein product		609785				10644752, 11073954	Standard	NM_014553		Approved	LBP-9, CRTR1	uc002tmx.3	Q9NZI6	OTTHUMG00000131443	ENST00000263707.5:c.233G>A	2.37:g.122007205C>T	ENSP00000263707:p.Arg78Gln						p.R78Q	NM_014553.2	NP_055368.1	Q9NZI6	TF2L1_HUMAN			3	330	-	Renal(3;0.01)		78					Q4ZG43	Missense_Mutation	SNP	ENST00000263707.5	37	c.233G>A	CCDS2134.1	.	.	.	.	.	.	.	.	.	.	C	34	5.315284	0.95655	.	.	ENSG00000115112	ENST00000263707	T	0.17213	2.29	5.76	5.76	0.90799	CP2 transcription factor (1);	0.129573	0.53938	D	0.000053	T	0.28566	0.0707	L	0.52126	1.63	0.80722	D	1	B;P	0.50156	0.193;0.932	B;P	0.49953	0.148;0.627	T	0.00191	-1.1936	10	0.34782	T	0.22	.	19.9857	0.97347	0.0:1.0:0.0:0.0	.	78;78	Q5JV87;Q9NZI6	.;TF2L1_HUMAN	Q	78	ENSP00000263707:R78Q	ENSP00000263707:R78Q	R	-	2	0	TFCP2L1	121723675	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	6.010000	0.70753	2.706000	0.92434	0.655000	0.94253	CGA		0.458	TFCP2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338539.1	NM_014553		24	45	0	0	0	1	0	24	45				
LAMB1	3912	broad.mit.edu	37	7	107626753	107626753	+	Missense_Mutation	SNP	C	C	A			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr7:107626753C>A	ENST00000222399.6	-	6	709	c.479G>T	c.(478-480)tGg>tTg	p.W160L	LAMB1_ENST00000393561.1_Missense_Mutation_p.W184L|LAMB1_ENST00000393560.1_Missense_Mutation_p.W160L	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	160	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|neuron projection development (GO:0031175)|neuronal-glial interaction involved in cerebral cortex radial glia guided migration (GO:0021812)|odontogenesis (GO:0042476)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell proliferation (GO:0050679)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-2 complex (GO:0005607)|laminin-8 complex (GO:0043257)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)|structural molecule activity (GO:0005198)			NS(3)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(37)|ovary(6)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)	82						ATACACACCCCAGGTTTTCCC	0.438																																						ENST00000393561.1																			0				NS(3)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(37)|ovary(6)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)	82						c.(550-552)tGg>tTg		laminin, beta 1	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)						92.0	91.0	91.0					7																	107626753		2203	4300	6503	SO:0001583	missense	3912				axon guidance|odontogenesis|positive regulation of cell migration|positive regulation of epithelial cell proliferation|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-2 complex|laminin-8 complex|perinuclear region of cytoplasm	extracellular matrix structural constituent	g.chr7:107626753C>A	M61916	CCDS5750.1	7q22	2013-03-01			ENSG00000091136	ENSG00000091136		"""Laminins"""	6486	protein-coding gene	gene with protein product		150240	"""cutis laxa with marfanoid phenotype"""	CLM		2563160, 2704655, 1864606	Standard	NM_002291		Approved		uc003vew.2	P07942	OTTHUMG00000149966	ENST00000222399.6:c.479G>T	7.37:g.107626753C>A	ENSP00000222399:p.Trp160Leu					LAMB1_ENST00000222399.6_Missense_Mutation_p.W160L|LAMB1_ENST00000393560.1_Missense_Mutation_p.W160L	p.W184L			P07942	LAMB1_HUMAN			4	735	-			160			Laminin N-terminal.		Q14D91	Missense_Mutation	SNP	ENST00000222399.6	37	c.551G>T	CCDS5750.1	.	.	.	.	.	.	.	.	.	.	C	34	5.356967	0.95854	.	.	ENSG00000091136	ENST00000393561;ENST00000222399;ENST00000393560	T;T;T	0.79033	-1.23;-1.23;-1.23	5.86	5.86	0.93980	Laminin, N-terminal (3);	.	.	.	.	D	0.92061	0.7484	H	0.94345	3.525	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	D	0.93404	0.6763	9	0.87932	D	0	.	20.1916	0.98230	0.0:1.0:0.0:0.0	.	160;160;184	E7EPA6;P07942;G3XAI2	.;LAMB1_HUMAN;.	L	184;160;160	ENSP00000377191:W184L;ENSP00000222399:W160L;ENSP00000377190:W160L	ENSP00000222399:W160L	W	-	2	0	LAMB1	107413989	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	7.818000	0.86416	2.770000	0.95276	0.655000	0.94253	TGG		0.438	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291		15	40	1	0	2.61681e-11	1	2.98317e-11	15	40				
OR2M7	391196	broad.mit.edu	37	1	248487356	248487356	+	Missense_Mutation	SNP	C	C	A	rs145948434		TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr1:248487356C>A	ENST00000317965.2	-	1	543	c.515G>T	c.(514-516)cGg>cTg	p.R172L		NM_001004691.1	NP_001004691.1	Q8NG81	OR2M7_HUMAN	olfactory receptor, family 2, subfamily M, member 7	172						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R172L(1)|p.R172Q(1)		breast(1)|endometrium(6)|large_intestine(3)|lung(29)|skin(3)	42	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GGCTATTTCCCGAGACCCACA	0.433																																						ENST00000317965.2																			2	Substitution - Missense(2)	p.R172L(1)|p.R172Q(1)	lung(1)|skin(1)	breast(1)|endometrium(6)|large_intestine(3)|lung(29)|skin(3)	42						c.(514-516)cGg>cTg		olfactory receptor, family 2, subfamily M, member 7							178.0	185.0	183.0					1																	248487356		2203	4298	6501	SO:0001583	missense	391196				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr1:248487356C>A	BK004486	CCDS31111.1	1q44	2012-08-09			ENSG00000177186	ENSG00000177186		"""GPCR / Class A : Olfactory receptors"""	19594	protein-coding gene	gene with protein product							Standard	NM_001004691		Approved		uc010pzk.2	Q8NG81	OTTHUMG00000040461	ENST00000317965.2:c.515G>T	1.37:g.248487356C>A	ENSP00000324557:p.Arg172Leu						p.R172L	NM_001004691.1	NP_001004691.1	Q8NG81	OR2M7_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.0265)		1	543	-	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		172					B2RNL0|Q6IEX6	Missense_Mutation	SNP	ENST00000317965.2	37	c.515G>T	CCDS31111.1	.	.	.	.	.	.	.	.	.	.	C	7.321	0.616938	0.14129	.	.	ENSG00000177186	ENST00000317965	T	0.00115	8.71	1.54	0.552	0.17230	GPCR, rhodopsin-like superfamily (1);	0.295108	0.18339	U	0.144258	T	0.00144	0.0004	L	0.56199	1.76	0.09310	N	1	B	0.17268	0.021	B	0.24394	0.053	T	0.39313	-0.9620	10	0.59425	D	0.04	.	3.5068	0.07693	0.0:0.4143:0.0:0.5857	.	172	Q8NG81	OR2M7_HUMAN	L	172	ENSP00000324557:R172L	ENSP00000324557:R172L	R	-	2	0	OR2M7	246553979	0.002000	0.14202	0.390000	0.26220	0.131000	0.20780	0.708000	0.25719	0.845000	0.35118	0.184000	0.17185	CGG		0.433	OR2M7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097357.1	NM_001004691		4	159	1	0	0.00909568	1	0.00909568	4	159				
HGF	3082	broad.mit.edu	37	7	81359092	81359092	+	Missense_Mutation	SNP	T	T	C			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr7:81359092T>C	ENST00000222390.5	-	8	1095	c.869A>G	c.(868-870)gAc>gGc	p.D290G	HGF_ENST00000457544.2_Missense_Mutation_p.D285G	NM_000601.4	NP_000592.3	P14210	HGF_HUMAN	hepatocyte growth factor (hepapoietin A; scatter factor)	290					activation of MAPK activity (GO:0000187)|blood coagulation (GO:0007596)|cell chemotaxis (GO:0060326)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epithelial to mesenchymal transition (GO:0001837)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|hyaluronan metabolic process (GO:0030212)|liver development (GO:0001889)|mitotic nuclear division (GO:0007067)|myoblast proliferation (GO:0051450)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of hydrogen peroxide-mediated programmed cell death (GO:1901299)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|organ regeneration (GO:0031100)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of cell migration (GO:0030335)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	catalytic activity (GO:0003824)|chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|identical protein binding (GO:0042802)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(41)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	75						CATAGTATTGTCAGCTATTGG	0.358																																						ENST00000222390.5																			0				NS(2)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(41)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	75						c.(868-870)gAc>gGc		hepatocyte growth factor (hepapoietin A; scatter factor)							102.0	97.0	99.0					7																	81359092		2203	4300	6503	SO:0001583	missense	3082				epithelial to mesenchymal transition|mitosis|platelet activation|platelet degranulation|proteolysis|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling	platelet alpha granule lumen	growth factor activity|serine-type endopeptidase activity	g.chr7:81359092T>C		CCDS5597.1, CCDS47626.1, CCDS47627.1, CCDS47628.1, CCDS47629.1	7q21.1	2009-09-11			ENSG00000019991	ENSG00000019991			4893	protein-coding gene	gene with protein product	"""hepatopoietin A"", ""fibroblast-derived tumor cytotoxic factor"", ""scatter factor"", ""lung fibroblast-derived mitogen"""	142409	"""deafness, autosomal recessive 39"""	DFNB39		1837206, 19576567	Standard	XM_006715956		Approved	SF, F-TCF, HGFB, HPTA	uc003uhl.3	P14210	OTTHUMG00000023804	ENST00000222390.5:c.869A>G	7.37:g.81359092T>C	ENSP00000222390:p.Asp290Gly					HGF_ENST00000457544.2_Missense_Mutation_p.D285G	p.D290G	NM_000601.4	NP_000592.3	P14210	HGF_HUMAN			8	1095	-			290					A1L3U6|Q02935|Q13494|Q14519|Q3KRB2|Q8TCE2|Q9BYL9|Q9BYM0|Q9UDU6	Missense_Mutation	SNP	ENST00000222390.5	37	c.869A>G	CCDS5597.1	.	.	.	.	.	.	.	.	.	.	T	6.167	0.398911	0.11696	.	.	ENSG00000019991	ENST00000222390;ENST00000457544	T;T	0.62105	0.05;0.05	5.61	5.61	0.85477	Kringle (2);Kringle-like fold (1);	0.447497	0.27518	N	0.019006	T	0.46698	0.1406	N	0.24115	0.695	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.0	T	0.38265	-0.9669	10	0.27082	T	0.32	.	11.6784	0.51442	0.1324:0.0:0.0:0.8676	.	285;290	P14210-3;P14210	.;HGF_HUMAN	G	290;285	ENSP00000222390:D290G;ENSP00000391238:D285G	ENSP00000222390:D290G	D	-	2	0	HGF	81197028	0.977000	0.34250	1.000000	0.80357	0.117000	0.20001	2.304000	0.43655	2.254000	0.74563	0.533000	0.62120	GAC		0.358	HGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253315.2	NM_000601		21	42	0	0	0	1	0	21	42				
DNM1P47	100216544	broad.mit.edu	37	15	102304747	102304747	+	RNA	SNP	A	A	C	rs201867308		TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr15:102304747A>C	ENST00000561463.1	+	0	12793									DNM1 pseudogene 47																		CTCGTGGAGGAGTCGGCAGAG	0.607																																						ENST00000561463.1																			0																																																			0							g.chr15:102304747A>C	AJ576276		15q26.3	2013-04-25			ENSG00000259660	ENSG00000259660			35200	pseudogene	pseudogene				DNM1DN14@			Standard	NG_009149		Approved	DNM1DN14-3			OTTHUMG00000172265		15.37:g.102304747A>C														0	12793	+									RNA	SNP	ENST00000561463.1	37																																																																																						0.607	DNM1P47-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417589.1	NG_009149		3	19	0	0	0	1	0	3	19				
L1CAM	3897	broad.mit.edu	37	X	153137798	153137798	+	Missense_Mutation	SNP	G	G	A			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chrX:153137798G>A	ENST00000370060.1	-	5	398	c.209C>T	c.(208-210)aCg>aTg	p.T70M	L1CAM_ENST00000370057.3_Missense_Mutation_p.T70M|L1CAM_ENST00000538883.1_Missense_Mutation_p.T72M|L1CAM_ENST00000361981.3_Missense_Mutation_p.T65M|L1CAM_ENST00000543994.1_Missense_Mutation_p.T72M|L1CAM_ENST00000370055.1_Missense_Mutation_p.T65M|L1CAM_ENST00000361699.4_Missense_Mutation_p.T70M	NM_001278116.1	NP_001265045.1	P32004	L1CAM_HUMAN	L1 cell adhesion molecule	70	Ig-like C2-type 1.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cell-cell adhesion mediated by integrin (GO:0033631)|chemotaxis (GO:0006935)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|homotypic cell-cell adhesion (GO:0034109)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|nervous system development (GO:0007399)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	sialic acid binding (GO:0033691)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|liver(1)|lung(31)|ovary(13)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	81	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					ACCATCCCTCGTCCAGCGGAA	0.627																																						ENST00000370060.1																			0				NS(1)|breast(4)|central_nervous_system(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|liver(1)|lung(31)|ovary(13)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	81						c.(208-210)aCg>aTg		L1 cell adhesion molecule							70.0	60.0	64.0					X																	153137798		2203	4300	6503	SO:0001583	missense	3897				axon guidance|blood coagulation|cell death|leukocyte migration	integral to membrane		g.chrX:153137798G>A	M74387	CCDS14733.1, CCDS14734.1, CCDS48192.1	Xq28	2014-09-17	2003-04-07		ENSG00000198910	ENSG00000198910		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	6470	protein-coding gene	gene with protein product		308840	"""antigen identified by monoclonal antibody R1"""	HSAS1, SPG1, HSAS, MASA, MIC5, S10			Standard	NM_001278116		Approved	CD171	uc031tks.1	P32004	OTTHUMG00000024221	ENST00000370060.1:c.209C>T	X.37:g.153137798G>A	ENSP00000359077:p.Thr70Met					L1CAM_ENST00000361981.3_Missense_Mutation_p.T65M|L1CAM_ENST00000361699.4_Missense_Mutation_p.T70M|L1CAM_ENST00000543994.1_Missense_Mutation_p.T72M|L1CAM_ENST00000538883.1_Missense_Mutation_p.T72M|L1CAM_ENST00000370055.1_Missense_Mutation_p.T65M|L1CAM_ENST00000370057.3_Missense_Mutation_p.T70M	p.T70M	NM_001278116.1	NP_001265045.1	P32004	L1CAM_HUMAN			5	398	-	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)		70			Ig-like C2-type 1.		A0AV65|A4ZYW4|B2RMU7|G3XAF4|Q8TA87	Missense_Mutation	SNP	ENST00000370060.1	37	c.209C>T	CCDS14733.1	.	.	.	.	.	.	.	.	.	.	G	11.97	1.797191	0.31777	.	.	ENSG00000198910	ENST00000370060;ENST00000543994;ENST00000370057;ENST00000538883;ENST00000361981;ENST00000370055;ENST00000361699;ENST00000439496;ENST00000407935;ENST00000420165;ENST00000458029	T;T;T;T;T;T;T;T;T;T;T	0.14391	2.51;2.51;2.51;2.51;2.51;2.51;2.51;2.51;2.51;2.51;2.51	4.87	0.984	0.19773	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.562925	0.16722	N	0.202236	T	0.12944	0.0314	L	0.56396	1.775	0.26843	N	0.968337	P;B;P	0.43857	0.784;0.077;0.819	B;B;B	0.43536	0.298;0.033;0.423	T	0.13282	-1.0515	10	0.40728	T	0.16	.	2.1838	0.03881	0.1688:0.2758:0.4118:0.1436	.	65;70;70	G3XAF4;P32004-2;P32004	.;.;L1CAM_HUMAN	M	70;72;70;72;65;65;70;70;65;65;70	ENSP00000359077:T70M;ENSP00000438430:T72M;ENSP00000359074:T70M;ENSP00000439645:T72M;ENSP00000354712:T65M;ENSP00000359072:T65M;ENSP00000355380:T70M;ENSP00000402407:T70M;ENSP00000384902:T65M;ENSP00000392524:T65M;ENSP00000396079:T70M	ENSP00000355380:T70M	T	-	2	0	L1CAM	152790992	1.000000	0.71417	0.064000	0.19789	0.804000	0.45430	3.204000	0.51082	-0.115000	0.11915	-0.344000	0.07964	ACG		0.627	L1CAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061094.2	NM_024003		6	11	0	0	0	1	0	6	11				
IGKV1-6	28943	broad.mit.edu	37	2	89265896	89265896	+	RNA	SNP	C	C	T			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr2:89265896C>T	ENST00000464162.1	-	0	264									immunoglobulin kappa variable 1-6																		TGATGGGACCCCACTTTGTAA	0.488																																						ENST00000464162.1																			0																				163.0	152.0	155.0					2																	89265896		1870	4092	5962			0							g.chr2:89265896C>T	M64858		2p11.2	2012-02-10			ENSG00000239855	ENSG00000239855		"""Immunoglobulins / IGK locus"""	5742	other	immunoglobulin gene							Standard	NG_000834		Approved				OTTHUMG00000151559		2.37:g.89265896C>T														0	264	-									RNA	SNP	ENST00000464162.1	37																																																																																						0.488	IGKV1-6-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene	OTTHUMT00000323134.2	NG_000834		37	120	0	0	0	1	0	37	120				
PLPPR5	163404	broad.mit.edu	37	1	99380467	99380467	+	Missense_Mutation	SNP	C	C	T			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr1:99380467C>T	ENST00000263177.4	-	5	1029	c.808G>A	c.(808-810)Gtg>Atg	p.V270M	LPPR5_ENST00000370188.3_Missense_Mutation_p.V270M	NM_001037317.1	NP_001032394.1	Q32ZL2	LPPR5_HUMAN		270						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)										TTATTCACCACGCACACAACC	0.393																																						ENST00000370188.3																			0											c.(808-810)Gtg>Atg									158.0	152.0	154.0					1																	99380467		2203	4300	6503	SO:0001583	missense	0					integral to membrane	hydrolase activity	g.chr1:99380467C>T																												ENST00000263177.4:c.808G>A	1.37:g.99380467C>T	ENSP00000263177:p.Val270Met					LPPR5_ENST00000263177.4_Missense_Mutation_p.V270M	p.V270M	NM_001010861.2	NP_001010861.1	Q32ZL2	LPPR5_HUMAN			5	1168	-			270					A8MPX4|B7UCH3|Q32ZD0|Q3ZCU7	Missense_Mutation	SNP	ENST00000263177.4	37	c.808G>A	CCDS30778.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.672630	0.88348	.	.	ENSG00000117598	ENST00000370188;ENST00000263177	T;T	0.75477	-0.94;-0.94	5.98	5.98	0.97165	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.063249	0.64402	D	0.000006	D	0.88355	0.6414	M	0.89840	3.065	0.58432	D	0.999994	D;D	0.89917	1.0;1.0	D;D	0.83275	0.993;0.996	D	0.89456	0.3733	10	0.87932	D	0	.	19.4463	0.94849	0.0:1.0:0.0:0.0	.	270;270	Q32ZL2-2;Q32ZL2	.;LPPR5_HUMAN	M	270	ENSP00000359207:V270M;ENSP00000263177:V270M	ENSP00000263177:V270M	V	-	1	0	AL161744.1	99153055	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	6.698000	0.74608	2.835000	0.97688	0.650000	0.86243	GTG		0.393	LPPR5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393221.1			4	99	0	0	0	1	0	4	99				
C6orf89	221477	broad.mit.edu	37	6	36891198	36891198	+	Missense_Mutation	SNP	C	C	A			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr6:36891198C>A	ENST00000480824.2	+	9	1319	c.1025C>A	c.(1024-1026)aCc>aAc	p.T342N	C6orf89_ENST00000355190.3_Missense_Mutation_p.T349N|C6orf89_ENST00000359359.2_Missense_Mutation_p.T236N|C6orf89_ENST00000510325.2_Missense_Mutation_p.T236N|C6orf89_ENST00000373685.1_Missense_Mutation_p.T342N			Q6UWU4	CF089_HUMAN	chromosome 6 open reading frame 89	342					epithelial cell proliferation (GO:0050673)|positive regulation of cell cycle (GO:0045787)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(2)	15						TGCGATGGAACCGCTTTCTCA	0.473																																						ENST00000480824.2																			0				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(2)	15						c.(1024-1026)aCc>aAc		chromosome 6 open reading frame 89							87.0	72.0	77.0					6																	36891198		2203	4300	6503	SO:0001583	missense	221477					integral to membrane		g.chr6:36891198C>A	AK058086	CCDS4827.1, CCDS69100.1, CCDS75444.1	6p21.31	2013-03-14			ENSG00000198663	ENSG00000198663			21114	protein-coding gene	gene with protein product	"""bombesin receptor activated protein"""					21857995, 23460338	Standard	NM_152734		Approved	FLJ25357, BRAP	uc003omw.3	Q6UWU4	OTTHUMG00000014613	ENST00000480824.2:c.1025C>A	6.37:g.36891198C>A	ENSP00000475947:p.Thr342Asn					C6orf89_ENST00000373685.1_Missense_Mutation_p.T342N|C6orf89_ENST00000359359.2_Missense_Mutation_p.T236N|C6orf89_ENST00000510325.2_Missense_Mutation_p.T236N|C6orf89_ENST00000355190.3_Missense_Mutation_p.T349N	p.T342N			Q6UWU4	CF089_HUMAN			9	1319	+			342					B4DTT1|F4NAR0|F4NAR1|Q6ZMG5|Q7Z356|Q8IZ35	Missense_Mutation	SNP	ENST00000480824.2	37	c.1025C>A		.	.	.	.	.	.	.	.	.	.	C	17.82	3.482801	0.63962	.	.	ENSG00000198663	ENST00000359359;ENST00000510325;ENST00000355190;ENST00000373685	.	.	.	5.56	5.56	0.83823	.	0.114234	0.64402	D	0.000008	T	0.65544	0.2701	M	0.62723	1.935	0.38208	D	0.94037	D;D	0.76494	0.999;0.999	D;D	0.64237	0.923;0.923	T	0.69235	-0.5198	9	0.66056	D	0.02	-0.4644	15.0388	0.71770	0.0:1.0:0.0:0.0	.	342;349	Q6UWU4;Q6UWU4-2	CF089_HUMAN;.	N	236;236;349;342	.	ENSP00000347322:T349N	T	+	2	0	C6orf89	36999176	1.000000	0.71417	1.000000	0.80357	0.450000	0.32258	3.818000	0.55678	2.634000	0.89283	0.561000	0.74099	ACC		0.473	C6orf89-004	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000040387.2	NM_152734		12	40	1	0	6.31663e-08	1	6.92399e-08	12	40				
OR5L2	26338	broad.mit.edu	37	11	55594965	55594965	+	Missense_Mutation	SNP	G	G	A			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr11:55594965G>A	ENST00000378397.1	+	1	271	c.271G>A	c.(271-273)Gcc>Acc	p.A91T		NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L, member 2	91						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A91T(1)		breast(2)|kidney(1)|large_intestine(1)|lung(42)|ovary(1)|prostate(3)|skin(1)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	59		all_epithelial(135;0.208)				CAAGGACAAAGCCATCTCCTT	0.463										HNSCC(27;0.073)																												ENST00000378397.1																			1	Substitution - Missense(1)	p.A91T(1)	lung(1)	breast(2)|kidney(1)|large_intestine(1)|lung(42)|ovary(1)|prostate(3)|skin(1)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	59						c.(271-273)Gcc>Acc		olfactory receptor, family 5, subfamily L, member 2							202.0	190.0	194.0					11																	55594965		2200	4296	6496	SO:0001583	missense	26338				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:55594965G>A	AB065782	CCDS31511.1	11q11	2012-08-09			ENSG00000205030	ENSG00000205030		"""GPCR / Class A : Olfactory receptors"""	8351	protein-coding gene	gene with protein product						1370859	Standard	NM_001004739		Approved	HTPCRX16, HSHTPCRX16	uc001nhy.1	Q8NGL0	OTTHUMG00000166812	ENST00000378397.1:c.271G>A	11.37:g.55594965G>A	ENSP00000367650:p.Ala91Thr	HNSCC(27;0.073)					p.A91T	NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN			1	271	+		all_epithelial(135;0.208)	91					Q6IF66|Q96RB2	Missense_Mutation	SNP	ENST00000378397.1	37	c.271G>A	CCDS31511.1	.	.	.	.	.	.	.	.	.	.	.	0.150	-1.092451	0.01858	.	.	ENSG00000205030	ENST00000378397	T	0.01113	5.32	5.21	-4.85	0.03142	GPCR, rhodopsin-like superfamily (1);	1.280730	0.05354	N	0.532408	T	0.00384	0.0012	N	0.00483	-1.445	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.46541	-0.9184	10	0.02654	T	1	-1.6022	5.4008	0.16295	0.473:0.0:0.2951:0.2319	.	91	Q8NGL0	OR5L2_HUMAN	T	91	ENSP00000367650:A91T	ENSP00000367650:A91T	A	+	1	0	OR5L2	55351541	0.000000	0.05858	0.048000	0.18961	0.609000	0.37215	-2.846000	0.00735	-0.880000	0.03997	-0.333000	0.08304	GCC		0.463	OR5L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391516.1	NM_001004739		5	132	0	0	0	1	0	5	132				
TAAR8	83551	broad.mit.edu	37	6	132874616	132874616	+	Missense_Mutation	SNP	C	C	T	rs553376051		TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr6:132874616C>T	ENST00000275200.1	+	1	785	c.785C>T	c.(784-786)aCg>aTg	p.T262M		NM_053278.1	NP_444508.1	Q969N4	TAAR8_HUMAN	trace amine associated receptor 8	262					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)			endometrium(3)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22	Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.00412)|GBM - Glioblastoma multiforme(226;0.00792)		CTGGGGGTCACGGTACTAGCA	0.393													C|||	1	0.000199681	0.0	0.0	5008	,	,		16853	0.0		0.0	False		,,,				2504	0.001					ENST00000275200.1																			0				endometrium(3)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22						c.(784-786)aCg>aTg		trace amine associated receptor 8							135.0	142.0	140.0					6																	132874616		2203	4300	6503	SO:0001583	missense	83551					plasma membrane	G-protein coupled receptor activity	g.chr6:132874616C>T	AF380193	CCDS5154.1	6q23.2	2014-05-14	2005-02-23	2005-02-24	ENSG00000146385	ENSG00000146385		"""GPCR / Class A : Trace amine associated receptors"""	14964	protein-coding gene	gene with protein product		606927	"""trace amine receptor 5"""	GPR102, TRAR5		11574155, 15718104	Standard	NM_053278		Approved	TA5, TAR5	uc011ecj.2	Q969N4	OTTHUMG00000015586	ENST00000275200.1:c.785C>T	6.37:g.132874616C>T	ENSP00000275200:p.Thr262Met						p.T262M	NM_053278.1	NP_444508.1	Q969N4	TAAR8_HUMAN		OV - Ovarian serous cystadenocarcinoma(155;0.00412)|GBM - Glioblastoma multiforme(226;0.00792)	1	785	+	Breast(56;0.112)		262					Q5VUQ0	Missense_Mutation	SNP	ENST00000275200.1	37	c.785C>T	CCDS5154.1	.	.	.	.	.	.	.	.	.	.	C	9.504	1.103876	0.20632	.	.	ENSG00000146385	ENST00000275200	T	0.36340	1.26	4.72	0.192	0.15134	GPCR, rhodopsin-like superfamily (1);	0.241133	0.28577	N	0.014844	T	0.25269	0.0614	L	0.45228	1.405	0.09310	N	1	D	0.54601	0.967	P	0.57425	0.82	T	0.13229	-1.0517	10	0.59425	D	0.04	-14.1077	9.1451	0.36928	0.0:0.4997:0.0:0.5003	.	262	Q969N4	TAAR8_HUMAN	M	262	ENSP00000275200:T262M	ENSP00000275200:T262M	T	+	2	0	TAAR8	132916309	0.007000	0.16637	0.003000	0.11579	0.140000	0.21249	1.990000	0.40717	-0.026000	0.13895	-1.170000	0.01741	ACG		0.393	TAAR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042262.1	NM_053278		25	50	0	0	0	1	0	25	50				
PNLIPRP1	5407	broad.mit.edu	37	10	118352048	118352048	+	Missense_Mutation	SNP	T	T	A			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr10:118352048T>A	ENST00000528052.1	+	4	396	c.325T>A	c.(325-327)Tgc>Agc	p.C109S	PNLIPRP1_ENST00000358834.4_Missense_Mutation_p.C109S|PNLIPRP1_ENST00000442761.1_Missense_Mutation_p.C109S|PNLIPRP1_ENST00000534537.1_Missense_Mutation_p.C109S|PNLIPRP1_ENST00000480870.2_3'UTR			P54315	LIPR1_HUMAN	pancreatic lipase-related protein 1	109					lipid metabolic process (GO:0006629)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|triglyceride lipase activity (GO:0004806)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	38				all cancers(201;0.0161)		GACAGACATGTGCAAGGTAGG	0.448																																						ENST00000528052.1																			0				breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	38						c.(325-327)Tgc>Agc		pancreatic lipase-related protein 1							83.0	81.0	82.0					10																	118352048		2203	4300	6503	SO:0001583	missense	5407				lipid metabolic process		calcium ion binding|triglyceride lipase activity	g.chr10:118352048T>A	BC025784	CCDS7595.1	10q26.12	2006-07-04			ENSG00000187021	ENSG00000187021			9156	protein-coding gene	gene with protein product		604422				1379598	Standard	NM_006229		Approved	PLRP1	uc001lco.1	P54315	OTTHUMG00000019109	ENST00000528052.1:c.325T>A	10.37:g.118352048T>A	ENSP00000433933:p.Cys109Ser					PNLIPRP1_ENST00000480870.2_3'UTR|PNLIPRP1_ENST00000534537.1_Missense_Mutation_p.C109S|PNLIPRP1_ENST00000358834.4_Missense_Mutation_p.C109S|PNLIPRP1_ENST00000442761.1_Missense_Mutation_p.C109S	p.C109S			P54315	LIPR1_HUMAN		all cancers(201;0.0161)	4	396	+			109					Q68D83|Q68DR6|Q8TAU2|Q9BS82	Missense_Mutation	SNP	ENST00000528052.1	37	c.325T>A	CCDS7595.1	.	.	.	.	.	.	.	.	.	.	T	15.78	2.933653	0.52866	.	.	ENSG00000187021	ENST00000531984;ENST00000358834;ENST00000528052;ENST00000442761;ENST00000530319;ENST00000527980;ENST00000471549;ENST00000534537	D;D;D;D;D;D;D;D	0.90788	-2.73;-2.73;-2.73;-2.73;-2.73;-2.73;-2.73;-2.73	5.21	5.21	0.72293	Lipase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.94955	0.8368	M	0.77820	2.39	0.58432	D	0.999999	D;D	0.89917	1.0;0.985	D;D	0.97110	1.0;0.943	D	0.95501	0.8577	10	0.87932	D	0	-10.1575	14.3502	0.66697	0.0:0.0:0.0:1.0	.	109;109	P54315;P54315-2	LIPR1_HUMAN;.	S	109	ENSP00000436123:C109S;ENSP00000351695:C109S;ENSP00000433933:C109S;ENSP00000400963:C109S;ENSP00000437263:C109S;ENSP00000433785:C109S;ENSP00000431207:C109S;ENSP00000434159:C109S	ENSP00000351695:C109S	C	+	1	0	PNLIPRP1	118342038	1.000000	0.71417	1.000000	0.80357	0.322000	0.28314	6.212000	0.72188	2.088000	0.63022	0.533000	0.62120	TGC		0.448	PNLIPRP1-011	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384633.1	NM_006229		12	28	0	0	0	1	0	12	28				
SV2A	9900	broad.mit.edu	37	1	149883419	149883419	+	Missense_Mutation	SNP	C	C	T	rs200101517		TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr1:149883419C>T	ENST00000369146.3	-	3	1226	c.736G>A	c.(736-738)Gcc>Acc	p.A246T	SV2A_ENST00000369145.1_Missense_Mutation_p.A246T	NM_001278719.1|NM_014849.3	NP_001265648.1|NP_055664.3	Q7L0J3	SV2A_HUMAN	synaptic vesicle glycoprotein 2A	246					cellular calcium ion homeostasis (GO:0006874)|neurotransmitter transport (GO:0006836)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	protein kinase binding (GO:0019901)|receptor activity (GO:0004872)|transmembrane transporter activity (GO:0022857)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(16)|ovary(6)|pancreas(1)|prostate(8)|skin(2)|urinary_tract(2)	55	Breast(34;0.00769)|all_hematologic(923;0.127)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)		Levetiracetam(DB01202)	GAGAAGAAGGCGAAGACGCTG	0.577																																						ENST00000369146.3																			0				breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(16)|ovary(6)|pancreas(1)|prostate(8)|skin(2)|urinary_tract(2)	55						c.(736-738)Gcc>Acc		synaptic vesicle glycoprotein 2A	Levetiracetam(DB01202)						129.0	94.0	106.0					1																	149883419		2203	4300	6503	SO:0001583	missense	0				neurotransmitter transport	cell junction|endoplasmic reticulum|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity	g.chr1:149883419C>T	AB018279	CCDS940.1	1q21.2	2008-02-05			ENSG00000159164	ENSG00000159164			20566	protein-coding gene	gene with protein product		185860				7681585, 10611374	Standard	NM_014849		Approved	SV2, KIAA0736	uc001etg.3	Q7L0J3	OTTHUMG00000012209	ENST00000369146.3:c.736G>A	1.37:g.149883419C>T	ENSP00000358142:p.Ala246Thr					SV2A_ENST00000369145.1_Missense_Mutation_p.A246T	p.A246T	NM_014849.3	NP_055664.3	Q7L0J3	SV2A_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)		3	1226	-	Breast(34;0.00769)|all_hematologic(923;0.127)|Colorectal(459;0.171)		246					D3DUZ7|O94841|Q5QNX8|Q7Z3L6|Q8NBJ6|Q9BVZ9	Missense_Mutation	SNP	ENST00000369146.3	37	c.736G>A	CCDS940.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.922107	0.92319	.	.	ENSG00000159164	ENST00000369146;ENST00000369145	T;T	0.56776	0.44;0.44	5.2	5.2	0.72013	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.121063	0.56097	D	0.000036	T	0.49457	0.1558	L	0.49126	1.545	0.58432	D	0.999999	D	0.67145	0.996	D	0.62955	0.909	T	0.45279	-0.9272	10	0.07030	T	0.85	-19.2459	16.2778	0.82654	0.0:1.0:0.0:0.0	.	246	Q7L0J3	SV2A_HUMAN	T	246	ENSP00000358142:A246T;ENSP00000358141:A246T	ENSP00000358141:A246T	A	-	1	0	SV2A	148150043	0.996000	0.38824	0.999000	0.59377	0.974000	0.67602	2.965000	0.49200	2.711000	0.92665	0.655000	0.94253	GCC		0.577	SV2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033754.1			4	9	0	0	0	1	0	4	9				
MOV10L1	54456	broad.mit.edu	37	22	50582666	50582666	+	Silent	SNP	C	C	T	rs139092160		TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr22:50582666C>T	ENST00000262794.5	+	18	2582	c.2499C>T	c.(2497-2499)ttC>ttT	p.F833F	MOV10L1_ENST00000395858.3_Silent_p.F833F|MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000545383.1_Silent_p.F833F|MOV10L1_ENST00000395852.1_5'Flank|MOV10L1_ENST00000540615.1_Silent_p.F813F	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	833					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)	p.F833F(1)		breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		CCTGCAGGTTCGAGGAGGTGA	0.642																																						ENST00000262794.5																			1	Substitution - coding silent(1)	p.F833F(1)	skin(1)	breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67						c.(2497-2499)ttC>ttT		Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)							59.0	53.0	55.0					22																	50582666		2203	4300	6503	SO:0001819	synonymous_variant	54456				germ cell development|multicellular organismal development|spermatogenesis		ATP binding|ATP-dependent RNA helicase activity|magnesium ion binding|RNA binding	g.chr22:50582666C>T	AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"""cardiac helicase activated by MEF2C protein"""	605794	"""Mov10 (mouse)-like 1"", ""Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"""			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.2499C>T	22.37:g.50582666C>T						MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000395858.3_Silent_p.F833F|MOV10L1_ENST00000540615.1_Silent_p.F813F|MOV10L1_ENST00000545383.1_Silent_p.F833F	p.F833F	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)	18	2582	+		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)	833					A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Silent	SNP	ENST00000262794.5	37	c.2499C>T	CCDS14084.1																																																																																				0.642	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995		14	24	0	0	0	1	0	14	24				
MARCO	8685	broad.mit.edu	37	2	119726816	119726816	+	Missense_Mutation	SNP	G	G	A	rs535947483	byFrequency	TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr2:119726816G>A	ENST00000327097.4	+	2	313	c.178G>A	c.(178-180)Gct>Act	p.A60T	MARCO_ENST00000541757.1_De_novo_Start_OutOfFrame	NM_006770.3	NP_006761.1	Q9UEW3	MARCO_HUMAN	macrophage receptor with collagenous structure	60					apoptotic cell clearance (GO:0043277)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(12)|lung(37)|ovary(4)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	70						CACCGCTGGCGCTGGGCTGCT	0.597																																					GBM(8;18 374 7467 11269 32796)	ENST00000541757.1																			0				breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(12)|lung(37)|ovary(4)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	70								macrophage receptor with collagenous structure							111.0	101.0	104.0					2																	119726816		2203	4300	6503	SO:0001583	missense	8685				cell surface receptor linked signaling pathway|innate immune response	collagen|integral to plasma membrane	pattern recognition receptor activity|scavenger receptor activity	g.chr2:119726816G>A	AF035819	CCDS2124.1	2q14.2	2011-10-11			ENSG00000019169	ENSG00000019169			6895	protein-coding gene	gene with protein product	"""scavenger receptor class A, member 2"""	604870				9468508, 7867067, 10331948	Standard	NM_006770		Approved	SCARA2	uc002tln.1	Q9UEW3	OTTHUMG00000131400	ENST00000327097.4:c.178G>A	2.37:g.119726816G>A	ENSP00000318916:p.Ala60Thr					MARCO_ENST00000327097.4_Missense_Mutation_p.A60T				Q9UEW3	MARCO_HUMAN			0	324	+								B4DW79|Q9Y5S3	Translation_Start_Site	SNP	ENST00000327097.4	37		CCDS2124.1	.	.	.	.	.	.	.	.	.	.	G	9.535	1.111800	0.20714	.	.	ENSG00000019169	ENST00000327097;ENST00000410021	D	0.89617	-2.54	4.54	1.73	0.24493	.	1.724340	0.03251	N	0.181929	T	0.78039	0.4221	N	0.11201	0.11	0.09310	N	0.999998	B	0.21147	0.052	B	0.10450	0.005	T	0.64415	-0.6413	9	.	.	.	.	5.9794	0.19399	0.3356:0.0:0.6644:0.0	.	60	Q9UEW3	MARCO_HUMAN	T	60	ENSP00000318916:A60T	.	A	+	1	0	MARCO	119443286	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.296000	0.08287	0.164000	0.19529	0.655000	0.94253	GCT		0.597	MARCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254190.2	NM_006770		17	45	0	0	0	1	0	17	45				
GOLGA2	2801	broad.mit.edu	37	9	131027885	131027885	+	Silent	SNP	C	C	T			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr9:131027885C>T	ENST00000421699.2	-	11	843	c.831G>A	c.(829-831)acG>acA	p.T277T	GOLGA2_ENST00000609374.1_Silent_p.T265T	NM_004486.4	NP_004477.3	Q08379	GOGA2_HUMAN	golgin A2	277					mitotic cell cycle (GO:0000278)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)				NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34						TCTTCTGCTGCGTGGAGACAG	0.612																																						ENST00000421699.2																			0				NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34						c.(829-831)acG>acA		golgin A2							26.0	25.0	25.0					9																	131027885		2203	4300	6503	SO:0001819	synonymous_variant	2801					Golgi cisterna membrane	protein binding	g.chr9:131027885C>T	L06147	CCDS6896.2	9q34.13	2010-06-28	2010-02-12		ENSG00000167110	ENSG00000167110			4425	protein-coding gene	gene with protein product	"""Golgi matrix protein GM130"", ""SY11 protein"""	602580	"""golgi autoantigen, golgin subfamily a, 2"""			8315394	Standard	NM_004486		Approved	GM130, golgin-95	uc011maw.2	Q08379	OTTHUMG00000020732	ENST00000421699.2:c.831G>A	9.37:g.131027885C>T							p.T277T	NM_004486.4	NP_004477.3	Q08379	GOGA2_HUMAN			11	843	-			277					Q6GRM9|Q9BRB0|Q9NYF9	Silent	SNP	ENST00000421699.2	37	c.831G>A	CCDS6896.2	.	.	.	.	.	.	.	.	.	.	c	0.132	-1.112798	0.01799	.	.	ENSG00000167110	ENST00000458730	.	.	.	5.72	-11.4	0.00090	.	.	.	.	.	T	0.40297	0.1111	.	.	.	0.40691	D	0.982395	.	.	.	.	.	.	T	0.50250	-0.8850	4	.	.	.	.	4.5879	0.12291	0.0723:0.2299:0.2727:0.4251	.	.	.	.	T	210	.	.	A	-	1	0	GOLGA2	130067706	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-2.197000	0.01240	-3.307000	0.00191	-1.054000	0.02325	GCA		0.612	GOLGA2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054358.2	NM_004486		5	15	0	0	0	1	0	5	15				
GOT1L1	137362	broad.mit.edu	37	8	37794525	37794525	+	Missense_Mutation	SNP	C	C	A			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr8:37794525C>A	ENST00000307599.4	-	5	669	c.570G>T	c.(568-570)aaG>aaT	p.K190N	GOT1L1_ENST00000518826.1_5'Flank	NM_152413.2	NP_689626.2	Q8NHS2	AATC2_HUMAN	glutamic-oxaloacetic transaminase 1-like 1	190					biosynthetic process (GO:0009058)|cellular amino acid metabolic process (GO:0006520)	cytoplasm (GO:0005737)	pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)			central_nervous_system(1)|endometrium(3)|lung(8)|ovary(1)|prostate(1)	14	Colorectal(12;0.00627)	Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;1.37e-11)			TTGGTGTCAACTTGCAGTCGA	0.537																																						ENST00000307599.4																			0				central_nervous_system(1)|endometrium(3)|lung(8)|ovary(1)|prostate(1)	14						c.(568-570)aaG>aaT		glutamic-oxaloacetic transaminase 1-like 1							142.0	156.0	151.0					8																	37794525		2049	4201	6250	SO:0001583	missense	137362				biosynthetic process|cellular amino acid metabolic process	cytoplasm	pyridoxal phosphate binding|transaminase activity	g.chr8:37794525C>A	BC029504	CCDS47839.1	8p12	2005-09-22			ENSG00000169154	ENSG00000169154			28487	protein-coding gene	gene with protein product						12477932	Standard	NM_152413		Approved	MGC33309	uc011lbj.1	Q8NHS2	OTTHUMG00000164027	ENST00000307599.4:c.570G>T	8.37:g.37794525C>A	ENSP00000303077:p.Lys190Asn						p.K190N	NM_152413.2	NP_689626.2	Q8NHS2	AATC2_HUMAN	LUSC - Lung squamous cell carcinoma(8;1.37e-11)		5	669	-	Colorectal(12;0.00627)	Lung NSC(58;0.118)|all_lung(54;0.195)	190					A8MWL4	Missense_Mutation	SNP	ENST00000307599.4	37	c.570G>T	CCDS47839.1	.	.	.	.	.	.	.	.	.	.	C	7.259	0.604839	0.14002	.	.	ENSG00000169154	ENST00000307599	D	0.90444	-2.67	4.66	-0.921	0.10472	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	1.178000	0.06441	N	0.725898	T	0.80829	0.4698	N	0.22421	0.69	0.09310	N	1	B	0.30973	0.302	B	0.28385	0.089	T	0.70128	-0.4957	10	0.72032	D	0.01	-6.7023	1.5989	0.02669	0.2677:0.4185:0.1329:0.1809	.	190	Q8NHS2	AATC2_HUMAN	N	190	ENSP00000303077:K190N	ENSP00000303077:K190N	K	-	3	2	GOT1L1	37913682	0.000000	0.05858	0.004000	0.12327	0.179000	0.23085	-0.734000	0.04893	0.072000	0.16694	0.484000	0.47621	AAG		0.537	GOT1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376823.1	NM_152413		14	29	1	0	4.3838e-07	1	4.71465e-07	14	29				
LOC645752	645752	broad.mit.edu	37	15	78208916	78208916	+	lincRNA	SNP	C	C	G	rs56290535	byFrequency	TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr15:78208916C>G	ENST00000565869.1	+	0	53				RN7SL214P_ENST00000487317.2_RNA|RP11-114H24.2_ENST00000567226.1_RNA																							TCCAGATGTTCTCCTCCATCT	0.627													C|||	476	0.0950479	0.0998	0.1023	5008	,	,		17114	0.0675		0.1054	False		,,,				2504	0.1012					ENST00000565869.1																			0																																																			0							g.chr15:78208916C>G																													15.37:g.78208916C>G														0	53	+									RNA	SNP	ENST00000565869.1	37																																																																																						0.627	RP11-114H24.7-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000421587.1			4	36	0	0	0	1	0	4	36				
ZSCAN2	54993	broad.mit.edu	37	15	85164527	85164527	+	Silent	SNP	C	C	T	rs199585522	byFrequency	TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr15:85164527C>T	ENST00000448803.2	+	3	1393	c.1101C>T	c.(1099-1101)tgC>tgT	p.C367C	ZSCAN2_ENST00000327179.6_Silent_p.C366C|ZSCAN2_ENST00000538076.1_Intron|ZSCAN2_ENST00000541040.1_Intron|ZSCAN2_ENST00000546148.1_Silent_p.C367C|ZSCAN2_ENST00000358472.3_Silent_p.C217C|ZSCAN2_ENST00000485222.2_Intron	NM_181877.3	NP_870992.2	Q7Z7L9	ZSCA2_HUMAN	zinc finger and SCAN domain containing 2	367					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.C367C(1)		breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(7)|liver(2)|lung(4)|ovary(1)|pancreas(1)	19				UCEC - Uterine corpus endometrioid carcinoma (272;0.168)|all cancers(203;5.43e-22)		GTAAAGAATGCGGCGAAAGCT	0.502													C|||	13	0.00259585	0.0	0.0	5008	,	,		18127	0.0099		0.0	False		,,,				2504	0.0031					ENST00000448803.2																			1	Substitution - coding silent(1)	p.C367C(1)	kidney(1)	breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(7)|liver(2)|lung(4)|ovary(1)|pancreas(1)	19						c.(1099-1101)tgC>tgT		zinc finger and SCAN domain containing 2		C		2,4404	4.2+/-10.8	0,2,2201	133.0	138.0	136.0		1101	-3.2	0.8	15		136	3,8595	3.0+/-9.4	0,3,4296	no	coding-synonymous	ZSCAN2	NM_181877.3		0,5,6497	TT,TC,CC		0.0349,0.0454,0.0384		367/615	85164527	5,12999	2203	4299	6502	SO:0001819	synonymous_variant	54993				cell differentiation|multicellular organismal development|spermatogenesis|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr15:85164527C>T	BC041620	CCDS10329.2, CCDS32315.1, CCDS32316.1	15q25.2	2013-01-08	2004-11-01	2004-11-02	ENSG00000176371	ENSG00000176371		"""-"", ""Zinc fingers, C2H2-type"""	20994	protein-coding gene	gene with protein product			"""zinc finger protein 29"""	ZFP29		1937051	Standard	NM_017894		Approved	FLJ20595, ZNF854	uc002bkr.3	Q7Z7L9	OTTHUMG00000074027	ENST00000448803.2:c.1101C>T	15.37:g.85164527C>T						ZSCAN2_ENST00000485222.2_Intron|ZSCAN2_ENST00000358472.3_Silent_p.C217C|ZSCAN2_ENST00000538076.1_Intron|ZSCAN2_ENST00000327179.6_Silent_p.C366C|ZSCAN2_ENST00000546148.1_Silent_p.C367C|ZSCAN2_ENST00000541040.1_Intron	p.C367C	NM_181877.3	NP_870992.2	Q7Z7L9	ZSCA2_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (272;0.168)|all cancers(203;5.43e-22)	3	1393	+			367					A6NG83|B2RMQ9|Q6ZQY9|Q9NWU4	Silent	SNP	ENST00000448803.2	37	c.1101C>T	CCDS10329.2																																																																																				0.502	ZSCAN2-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396956.1	NM_017894		4	112	0	0	0	1	0	4	112				
AHNAK2	113146	broad.mit.edu	37	14	105414154	105414154	+	Missense_Mutation	SNP	C	C	T	rs374320063		TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr14:105414154C>T	ENST00000333244.5	-	7	7753	c.7634G>A	c.(7633-7635)gGc>gAc	p.G2545D	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2545						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GTCCACTTGGCCAGCCTGGAC	0.642																																						ENST00000333244.5																			0				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33						c.(7633-7635)gGc>gAc		AHNAK nucleoprotein 2							106.0	118.0	114.0					14																	105414154		1897	4111	6008	SO:0001583	missense	113146					nucleus		g.chr14:105414154C>T	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.7634G>A	14.37:g.105414154C>T	ENSP00000353114:p.Gly2545Asp					AHNAK2_ENST00000557457.1_Intron	p.G2545D	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)		7	7753	-		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	2545					Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	c.7634G>A	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	c	11.37	1.618337	0.28801	.	.	ENSG00000185567	ENST00000333244	T	0.00730	5.77	3.7	-7.39	0.01402	.	.	.	.	.	T	0.01156	0.0038	M	0.68952	2.095	0.09310	N	1	P	0.50528	0.936	P	0.47603	0.551	T	0.00212	-1.1914	9	0.44086	T	0.13	.	4.1089	0.10050	0.301:0.4751:0.1225:0.1013	.	2545	Q8IVF2	AHNK2_HUMAN	D	2545	ENSP00000353114:G2545D	ENSP00000353114:G2545D	G	-	2	0	AHNAK2	104485199	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	-2.143000	0.01297	-2.347000	0.00620	-1.231000	0.01572	GGC		0.642	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		4	157	0	0	0	1	0	4	157				
LRRTM3	347731	broad.mit.edu	37	10	68687766	68687766	+	Missense_Mutation	SNP	T	T	G			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr10:68687766T>G	ENST00000361320.4	+	2	1670	c.1092T>G	c.(1090-1092)agT>agG	p.S364R	CTNNA3_ENST00000373744.4_Intron|CTNNA3_ENST00000433211.2_Intron	NM_178011.3	NP_821079.3	Q86VH5	LRRT3_HUMAN	leucine rich repeat transmembrane neuronal 3	364					positive regulation of beta-amyloid formation (GO:1902004)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	41						GTGGCAAAAGTACTACAGAGA	0.512																																						ENST00000361320.4																			0				breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	41						c.(1090-1092)agT>agG		leucine rich repeat transmembrane neuronal 3							65.0	66.0	66.0					10																	68687766		2203	4300	6503	SO:0001583	missense	347731					integral to membrane		g.chr10:68687766T>G	BX640611	CCDS7270.1	10q22.1	2007-01-22				ENSG00000198739			19410	protein-coding gene	gene with protein product		610869				12676565	Standard	XR_247527		Approved		uc001jmz.1	Q86VH5		ENST00000361320.4:c.1092T>G	10.37:g.68687766T>G	ENSP00000355187:p.Ser364Arg					CTNNA3_ENST00000494580.1_Intron|CTNNA3_ENST00000373744.4_Intron|CTNNA3_ENST00000433211.1_Intron	p.S364R	NM_178011.3	NP_821079.3	Q86VH5	LRRT3_HUMAN			2	1670	+			364					A8K2A3|Q2NKX7|Q6N0A3	Missense_Mutation	SNP	ENST00000361320.4	37	c.1092T>G	CCDS7270.1	.	.	.	.	.	.	.	.	.	.	T	1.535	-0.543444	0.04053	.	.	ENSG00000198739	ENST00000361320;ENST00000373722	T	0.44881	0.91	5.94	3.62	0.41486	.	0.000000	0.85682	D	0.000000	T	0.26376	0.0644	L	0.29908	0.895	0.37848	D	0.929273	B;B	0.18310	0.016;0.027	B;B	0.18263	0.009;0.021	T	0.10245	-1.0638	10	0.12103	T	0.63	.	8.2537	0.31741	0.0:0.2214:0.0:0.7786	.	364;364	Q86VH5;Q86VH5-2	LRRT3_HUMAN;.	R	364	ENSP00000355187:S364R	ENSP00000355187:S364R	S	+	3	2	LRRTM3	68357772	0.990000	0.36364	1.000000	0.80357	0.994000	0.84299	0.161000	0.16481	0.500000	0.27991	0.528000	0.53228	AGT		0.512	LRRTM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048277.2	NM_178011		4	36	0	0	0	1	0	4	36				
THTPA	79178	broad.mit.edu	37	14	24026130	24026130	+	Missense_Mutation	SNP	G	G	A			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr14:24026130G>A	ENST00000288014.6	+	1	900	c.164G>A	c.(163-165)cGa>cAa	p.R55Q	RP11-66N24.4_ENST00000555446.1_RNA|THTPA_ENST00000554970.1_Missense_Mutation_p.R55Q|RP11-66N24.4_ENST00000556354.1_RNA|THTPA_ENST00000554789.1_Missense_Mutation_p.R55Q|RP11-66N24.4_ENST00000553985.1_RNA|THTPA_ENST00000556015.1_Missense_Mutation_p.R55Q|THTPA_ENST00000404535.3_Missense_Mutation_p.R55Q			Q9BU02	THTPA_HUMAN	thiamine triphosphatase	55	CYTH. {ECO:0000255|PROSITE- ProRule:PRU01044}.				dephosphorylation (GO:0016311)|generation of precursor metabolites and energy (GO:0006091)|small molecule metabolic process (GO:0044281)|thiamine diphosphate metabolic process (GO:0042357)|thiamine metabolic process (GO:0006772)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)	hydrolase activity (GO:0016787)|magnesium ion binding (GO:0000287)|thiamin-triphosphatase activity (GO:0050333)			large_intestine(1)|prostate(2)	3	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00643)		CACTGGCTGCGACGACGAGAG	0.577																																						ENST00000288014.6																			0				large_intestine(1)|prostate(2)	3						c.(163-165)cGa>cAa		thiamine triphosphatase	Thiamine(DB00152)						66.0	53.0	57.0					14																	24026130		2203	4300	6503	SO:0001583	missense	0				dephosphorylation|generation of precursor metabolites and energy|thiamine metabolic process	cytosol|nucleolus|soluble fraction	thiamin-triphosphatase activity	g.chr14:24026130G>A	AF432862	CCDS32053.1, CCDS58306.1, CCDS58307.1	14q11.2	2011-04-28					3.6.1.28		18987	protein-coding gene	gene with protein product		611612				11827967	Standard	NR_046051		Approved	THTPASE	uc001wkh.5	Q9BU02		ENST00000288014.6:c.164G>A	14.37:g.24026130G>A	ENSP00000288014:p.Arg55Gln					THTPA_ENST00000556015.1_Missense_Mutation_p.R55Q|RP11-66N24.4_ENST00000555446.1_RNA|THTPA_ENST00000554970.1_Missense_Mutation_p.R55Q|THTPA_ENST00000554789.1_Missense_Mutation_p.R55Q|RP11-66N24.4_ENST00000553985.1_RNA|RP11-66N24.4_ENST00000556354.1_RNA|THTPA_ENST00000404535.3_Missense_Mutation_p.R55Q	p.R55Q			Q9BU02	THTPA_HUMAN		GBM - Glioblastoma multiforme(265;0.00643)	1	900	+	all_cancers(95;0.000251)		55					D3DS50|G3V4J3	Missense_Mutation	SNP	ENST00000288014.6	37	c.164G>A	CCDS32053.1	.	.	.	.	.	.	.	.	.	.	G	35	5.510741	0.96386	.	.	ENSG00000157306	ENST00000404535;ENST00000288014;ENST00000557630;ENST00000556015;ENST00000554970;ENST00000554789	T;T;T;T;T;T	0.79247	-1.25;-1.25;-1.25;-1.25;-1.25;-1.25	5.91	5.91	0.95273	CYTH domain (2);CYTH-like domain (1);	0.000000	0.85682	D	0.000000	D	0.90807	0.7113	M	0.91561	3.22	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.92164	0.5738	10	0.87932	D	0	-7.5265	17.7923	0.88558	0.0:0.0:1.0:0.0	.	55;55	G3V4J3;Q9BU02	.;THTPA_HUMAN	Q	55	ENSP00000384580:R55Q;ENSP00000288014:R55Q;ENSP00000452281:R55Q;ENSP00000451835:R55Q;ENSP00000452465:R55Q;ENSP00000450459:R55Q	ENSP00000288014:R55Q	R	+	2	0	THTPA	23095970	1.000000	0.71417	0.991000	0.47740	0.936000	0.57629	6.831000	0.75324	2.793000	0.96121	0.655000	0.94253	CGA		0.577	THTPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413800.2			4	10	0	0	0	1	0	4	10				
TBX3	6926	broad.mit.edu	37	12	115118775	115118775	+	Missense_Mutation	SNP	T	T	A			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr12:115118775T>A	ENST00000257566.3	-	2	955	c.566A>T	c.(565-567)gAc>gTc	p.D189V	TBX3_ENST00000349155.2_Missense_Mutation_p.D189V	NM_016569.3	NP_057653.3	O15119	TBX3_HUMAN	T-box 3	189					anterior/posterior axis specification, embryo (GO:0008595)|atrioventricular bundle cell differentiation (GO:0003167)|blood vessel development (GO:0001568)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cardiac muscle cell fate commitment (GO:0060923)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|female genitalia development (GO:0030540)|follicle-stimulating hormone secretion (GO:0046884)|forelimb morphogenesis (GO:0035136)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|limbic system development (GO:0021761)|luteinizing hormone secretion (GO:0032275)|male genitalia development (GO:0030539)|mammary gland development (GO:0030879)|mammary placode formation (GO:0060596)|mesoderm morphogenesis (GO:0048332)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sinoatrial node cell development (GO:0060931)|skeletal system development (GO:0001501)|specification of organ position (GO:0010159)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum morphogenesis (GO:0060412)	nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(1)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		AGCGGGGCTGTCCGGGTGAAT	0.468																																						ENST00000349155.2																			0				breast(5)|endometrium(1)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						c.(565-567)gAc>gTc		T-box 3							112.0	106.0	108.0					12																	115118775		2203	4300	6503	SO:0001583	missense	6926				anterior/posterior axis specification, embryo|anti-apoptosis|cell aging|embryonic arm morphogenesis|embryonic digit morphogenesis|female genitalia development|follicle-stimulating hormone secretion|luteinizing hormone secretion|male genitalia development|mesoderm morphogenesis|negative regulation of myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle|positive regulation of cell proliferation|regulation of transcription from RNA polymerase II promoter|skeletal system development	nucleus	sequence-specific DNA binding	g.chr12:115118775T>A	BC025258	CCDS9175.1, CCDS9176.1	12q24.21	2013-09-05	2008-07-31		ENSG00000135111	ENSG00000135111		"""T-boxes"""	11602	protein-coding gene	gene with protein product		601621	"""ulnar mammary syndrome"""	UMS		8988164	Standard	NM_005996		Approved	TBX3-ISO, XHL	uc001tvt.1	O15119	OTTHUMG00000169586	ENST00000257566.3:c.566A>T	12.37:g.115118775T>A	ENSP00000257566:p.Asp189Val					TBX3_ENST00000257566.3_Missense_Mutation_p.D189V	p.D189V	NM_005996.3	NP_005987.3	O15119	TBX3_HUMAN		BRCA - Breast invasive adenocarcinoma(302;0.0574)	2	1529	-	Medulloblastoma(191;0.163)|all_neural(191;0.178)		189					Q8TB20|Q9UKF8	Missense_Mutation	SNP	ENST00000257566.3	37	c.566A>T	CCDS9176.1	.	.	.	.	.	.	.	.	.	.	T	30	5.052814	0.93793	.	.	ENSG00000135111	ENST00000349155;ENST00000257566;ENST00000361100	D;D	0.91464	-2.85;-2.85	5.81	5.81	0.92471	Transcription factor, T-box, conserved site (1);p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.97445	0.9164	H	0.98866	4.355	0.80722	D	1	D;D;D	0.89917	0.996;1.0;0.998	D;D;D	0.97110	0.994;1.0;0.997	D	0.99016	1.0816	10	0.87932	D	0	.	15.352	0.74396	0.0:0.0:0.0:1.0	.	189;189;189	B4E3A6;O15119-2;O15119	.;.;TBX3_HUMAN	V	189	ENSP00000257567:D189V;ENSP00000257566:D189V	ENSP00000257566:D189V	D	-	2	0	TBX3	113603158	1.000000	0.71417	0.997000	0.53966	0.938000	0.57974	7.698000	0.84413	2.225000	0.72522	0.533000	0.62120	GAC		0.468	TBX3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404947.2	NM_016569, NM_005996		5	58	0	0	0	1	0	5	58				
C10orf54	64115	broad.mit.edu	37	10	73521465	73521465	+	Missense_Mutation	SNP	C	C	T	rs200235042	byFrequency	TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr10:73521465C>T	ENST00000394957.3	-	2	459	c.401G>A	c.(400-402)cGc>cAc	p.R134H	C10orf54_ENST00000481568.2_5'UTR|CDH23_ENST00000224721.6_Intron	NM_022153.1	NP_071436.1	Q9H7M9	GI24_HUMAN	chromosome 10 open reading frame 54	134	Ig-like.				BMP signaling pathway (GO:0030509)|negative regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000562)|negative regulation of T cell cytokine production (GO:0002725)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of stem cell differentiation (GO:2000738)|stem cell differentiation (GO:0048863)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|endometrium(1)|lung(1)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	9						GGTCAGGTTGCGCATGGTGAT	0.647													C|||	2	0.000399361	0.0	0.0	5008	,	,		22472	0.002		0.0	False		,,,				2504	0.0					ENST00000394957.3																			0				breast(1)|central_nervous_system(2)|endometrium(1)|lung(1)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	9						c.(400-402)cGc>cAc		chromosome 10 open reading frame 54							73.0	69.0	71.0					10																	73521465		2203	4300	6503	SO:0001583	missense	64115					integral to membrane	receptor activity	g.chr10:73521465C>T	AF193048	CCDS31218.1	10q22.1	2013-11-28			ENSG00000107738	ENSG00000107738		"""Immunoglobulin superfamily / V-set domain containing"""	30085	protein-coding gene	gene with protein product	"""stress induced secreted protein 1"""	615608				12975309	Standard	NM_022153		Approved	SISP1, GI24, B7-H5, B7H5	uc001jsd.3	Q9H7M9	OTTHUMG00000018426	ENST00000394957.3:c.401G>A	10.37:g.73521465C>T	ENSP00000378409:p.Arg134His					CDH23_ENST00000224721.6_Intron|C10orf54_ENST00000481568.1_5'UTR	p.R134H	NM_022153.1	NP_071436.1	Q9H7M9	GI24_HUMAN			2	459	-			134			Ig-like.		A1L0X9|A4ZYV1|A8MVH5|Q6UXF3|Q8WUG3|Q8WYZ8	Missense_Mutation	SNP	ENST00000394957.3	37	c.401G>A	CCDS31218.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	14.53	2.562276	0.45694	.	.	ENSG00000107738	ENST00000394957;ENST00000263569	T	0.66280	-0.2	5.75	-6.8	0.01709	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.040480	0.07437	N	0.896600	T	0.35128	0.0921	N	0.17674	0.51	0.19300	N	0.999974	B;B	0.18013	0.025;0.002	B;B	0.09377	0.004;0.003	T	0.18461	-1.0336	10	0.48119	T	0.1	-0.7654	0.3776	0.00390	0.3311:0.2135:0.1402:0.3152	.	130;134	Q2TA85;Q9H7M9	.;GI24_HUMAN	H	134;130	ENSP00000378409:R134H	ENSP00000263569:R130H	R	-	2	0	C10orf54	73191471	0.000000	0.05858	0.542000	0.28115	0.970000	0.65996	-1.375000	0.02563	-1.017000	0.03367	0.655000	0.94253	CGC		0.647	C10orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048548.1	NM_022153		3	17	0	0	0	1	0	3	17				
USH2A	7399	broad.mit.edu	37	1	216246603	216246603	+	Missense_Mutation	SNP	C	C	T	rs140895792	byFrequency	TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr1:216246603C>T	ENST00000307340.3	-	28	5998	c.5612G>A	c.(5611-5613)gGt>gAt	p.G1871D	RP11-22M7.2_ENST00000430890.1_RNA|RP11-22M7.2_ENST00000445619.1_RNA|USH2A_ENST00000366943.2_Missense_Mutation_p.G1871D|RP11-22M7.2_ENST00000446411.1_RNA	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	1871	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		AACGACAGCACCCCGTGTAAA	0.443										HNSCC(13;0.011)			C|||	8	0.00159744	0.0061	0.0	5008	,	,		18422	0.0		0.0	False		,,,				2504	0.0					ENST00000366943.2																			0				NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527						c.(5611-5613)gGt>gAt		Usher syndrome 2A (autosomal recessive, mild)		C	ASP/GLY	13,4393	20.2+/-43.8	0,13,2190	78.0	64.0	69.0		5612	5.9	1.0	1	dbSNP_134	69	1,8599	1.2+/-3.3	0,1,4299	yes	missense	USH2A	NM_206933.2	94	0,14,6489	TT,TC,CC		0.0116,0.2951,0.1076	probably-damaging	1871/5203	216246603	14,12992	2203	4300	6503	SO:0001583	missense	7399				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding	g.chr1:216246603C>T	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.5612G>A	1.37:g.216246603C>T	ENSP00000305941:p.Gly1871Asp	HNSCC(13;0.011)				RP11-22M7.2_ENST00000445619.1_RNA|RP11-22M7.2_ENST00000430890.1_RNA|USH2A_ENST00000307340.3_Missense_Mutation_p.G1871D|RP11-22M7.2_ENST00000446411.1_RNA	p.G1871D			O75445	USH2A_HUMAN		OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)	28	5998	-			1871			Fibronectin type-III 5.|Laminin G-like 2.		Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	c.5612G>A	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.359386	0.82353	0.002951	1.16E-4	ENSG00000042781	ENST00000307340;ENST00000366943	D;D	0.82081	-1.57;-1.57	5.93	5.93	0.95920	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Fibronectin, type III (3);Laminin G domain (2);	0.000000	0.45867	D	0.000322	D	0.91805	0.7407	M	0.81239	2.535	0.43133	D	0.99487	D	0.89917	1.0	D	0.81914	0.995	D	0.90759	0.4663	10	0.45353	T	0.12	.	20.3507	0.98813	0.0:1.0:0.0:0.0	.	1871	O75445	USH2A_HUMAN	D	1871	ENSP00000305941:G1871D;ENSP00000355910:G1871D	ENSP00000305941:G1871D	G	-	2	0	USH2A	214313226	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.754000	0.62191	2.808000	0.96608	0.655000	0.94253	GGT		0.443	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		10	6	0	0	0	1	0	10	6				
URAD	646625	broad.mit.edu	37	13	28562733	28562733	+	Silent	SNP	G	G	A	rs267603794		TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr13:28562733G>A	ENST00000332715.5	-	1	58	c.42C>T	c.(40-42)ttC>ttT	p.F14F	RN7SL272P_ENST00000487762.2_RNA	NM_001105577.1	NP_001099047.1	A6NGE7	URAD_HUMAN	ureidoimidazoline (2-oxo-4-hydroxy-4-carboxy-5-) decarboxylase	14					allantoin biosynthetic process (GO:0019428)|purine nucleobase metabolic process (GO:0006144)|urate catabolic process (GO:0019628)	peroxisome (GO:0005777)	carboxy-lyase activity (GO:0016831)										ACACATCCACGAATTCTCCAA	0.512																																						ENST00000332715.4																			0											c.(40-42)ttC>ttT		ureidoimidazoline (2-oxo-4-hydroxy-4-carboxy-5-) decarboxylase							103.0	109.0	107.0					13																	28562733		2101	4222	6323	SO:0001819	synonymous_variant	646625							g.chr13:28562733G>A		CCDS45020.1	13q12.2	2014-04-09	2013-06-18	2013-06-18	ENSG00000183463	ENSG00000183463	4.1.1.n1		17785	protein-coding gene	gene with protein product	"""OHCU decarboxylase"""	615804	"""parahox cluster neighbor"""	PRHOXNB		16462750	Standard	NM_001105577		Approved		uc010aan.1	A6NGE7	OTTHUMG00000186217	ENST00000332715.5:c.42C>T	13.37:g.28562733G>A							p.F14F	NM_001105577.1	NP_001099047.1					1	41	-									Silent	SNP	ENST00000332715.5	37	c.42C>T	CCDS45020.1																																																																																				0.512	URAD-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472432.1			11	38	0	0	0	1	0	11	38				
ALMS1	7840	broad.mit.edu	37	2	73717897	73717897	+	Nonsense_Mutation	SNP	T	T	G	rs541559170	byFrequency	TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr2:73717897T>G	ENST00000264448.6	+	10	8919	c.8808T>G	c.(8806-8808)taT>taG	p.Y2936*	ALMS1_ENST00000409009.1_Nonsense_Mutation_p.Y2894*|AC096546.1_ENST00000408160.1_RNA	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2936					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						AAGCCCCATATGTAGATCATC	0.428																																						ENST00000264448.6																			0				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						c.(8806-8808)taT>taG		Alstrom syndrome 1							199.0	184.0	189.0					2																	73717897		1886	4109	5995	SO:0001587	stop_gained	7840				G2/M transition of mitotic cell cycle	centrosome|cilium|cytosol|microtubule basal body|spindle pole		g.chr2:73717897T>G	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.8808T>G	2.37:g.73717897T>G	ENSP00000264448:p.Tyr2936*					ALMS1_ENST00000409009.1_Nonsense_Mutation_p.Y2894*	p.Y2936*	NM_015120.4	NP_055935.4	Q8TCU4	ALMS1_HUMAN			10	8919	+			2936					Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Nonsense_Mutation	SNP	ENST00000264448.6	37	c.8808T>G	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	t	47	13.098870	0.99719	.	.	ENSG00000116127	ENST00000409009;ENST00000264448	.	.	.	4.78	1.04	0.20106	.	0.694941	0.13228	N	0.403881	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.18276	T	0.48	.	5.4028	0.16305	0.0:0.09:0.3465:0.5635	.	.	.	.	X	2894;2936	.	ENSP00000264448:Y2936X	Y	+	3	2	ALMS1	73571405	0.076000	0.21285	0.016000	0.15963	0.021000	0.10359	0.421000	0.21280	0.177000	0.19895	-0.299000	0.09455	TAT		0.428	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		5	136	0	0	0	1	0	5	136				
FBN3	84467	broad.mit.edu	37	19	8190851	8190851	+	Missense_Mutation	SNP	C	C	T			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr19:8190851C>T	ENST00000600128.1	-	22	3070	c.2656G>A	c.(2656-2658)Gtc>Atc	p.V886I	FBN3_ENST00000270509.2_Missense_Mutation_p.V886I|FBN3_ENST00000601739.1_Missense_Mutation_p.V886I			Q75N90	FBN3_HUMAN	fibrillin 3	886	EGF-like 11; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						GCAGTGTTGACGCAACGCCCG	0.637																																						ENST00000600128.1																			0				NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						c.(2656-2658)Gtc>Atc		fibrillin 3							68.0	58.0	61.0					19																	8190851		2203	4300	6503	SO:0001583	missense	84467					proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent	g.chr19:8190851C>T		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.2656G>A	19.37:g.8190851C>T	ENSP00000470498:p.Val886Ile					FBN3_ENST00000270509.2_Missense_Mutation_p.V886I|FBN3_ENST00000601739.1_Missense_Mutation_p.V886I	p.V886I			Q75N90	FBN3_HUMAN			22	3070	-			886			EGF-like 11; calcium-binding.		Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	c.2656G>A	CCDS12196.1	.	.	.	.	.	.	.	.	.	.	c	5.198	0.221976	0.09863	.	.	ENSG00000142449	ENST00000270509	D	0.90324	-2.65	4.0	-3.64	0.04515	Matrix fibril-associated (1);EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.309128	0.28694	N	0.014452	T	0.77123	0.4084	N	0.12961	0.28	0.29881	N	0.826019	B	0.09022	0.002	B	0.04013	0.001	T	0.61247	-0.7101	10	0.30078	T	0.28	.	8.8603	0.35253	0.0:0.4287:0.1847:0.3866	.	886	Q75N90	FBN3_HUMAN	I	886	ENSP00000270509:V886I	ENSP00000270509:V886I	V	-	1	0	FBN3	8096851	0.433000	0.25562	0.079000	0.20413	0.001000	0.01503	-0.127000	0.10547	-1.022000	0.03346	-2.349000	0.00243	GTC		0.637	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		7	28	0	0	0	1	0	7	28				
BCAM	4059	broad.mit.edu	37	19	45316773	45316773	+	Missense_Mutation	SNP	G	G	A			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr19:45316773G>A	ENST00000270233.6	+	6	702	c.680G>A	c.(679-681)cGc>cAc	p.R227H	BCAM_ENST00000589651.1_Missense_Mutation_p.R227H	NM_001013257.2|NM_005581.4	NP_001013275.1|NP_005572.2	P50895	BCAM_HUMAN	basal cell adhesion molecule (Lutheran blood group)	227	Ig-like V-type 2.				cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	laminin binding (GO:0043236)|laminin receptor activity (GO:0005055)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)				CTGCGGCTCCGCAAGGATGAC	0.706																																						ENST00000391955.1																			0				central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22						c.(679-681)cGc>cAc		basal cell adhesion molecule (Lutheran blood group)							41.0	45.0	43.0					19																	45316773		2200	4295	6495	SO:0001583	missense	4059				cell-matrix adhesion	integral to plasma membrane	laminin binding|laminin receptor activity	g.chr19:45316773G>A	X83425	CCDS12644.1, CCDS42575.1	19q12-q13	2014-07-18	2006-02-23	2006-01-12		ENSG00000187244		"""CD molecules"", ""Blood group antigens"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6722	protein-coding gene	gene with protein product		612773	"""Lutheran blood group (Auberger b antigen included)"", ""basal cell adhesion molecule (Lu and Au blood groups)"""	LU			Standard	NM_005581		Approved	CD239	uc002ozu.4	P50895		ENST00000270233.6:c.680G>A	19.37:g.45316773G>A	ENSP00000270233:p.Arg227His					BCAM_ENST00000270233.6_Missense_Mutation_p.R227H	p.R227H			P50895	BCAM_HUMAN			6	724	+	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)	227			Ig-like V-type 2.		A8MYF9|A9YWT5|A9YWT6|Q86VC7	Missense_Mutation	SNP	ENST00000270233.6	37	c.680G>A	CCDS12644.1	.	.	.	.	.	.	.	.	.	.	.	7.126	0.578928	0.13686	.	.	ENSG00000187244	ENST00000270233;ENST00000391955	T;T	0.76060	-0.99;-0.99	4.15	-8.31	0.01001	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.46718	0.1407	N	0.05441	-0.05	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.34750	-0.9816	9	0.22706	T	0.39	-5.8484	9.5003	0.39013	0.7786:0.0935:0.1279:0.0	.	227	P50895	BCAM_HUMAN	H	227	ENSP00000270233:R227H;ENSP00000375817:R227H	ENSP00000270233:R227H	R	+	2	0	BCAM	50008613	0.000000	0.05858	0.022000	0.16811	0.207000	0.24258	-2.249000	0.01188	-1.804000	0.01241	-1.244000	0.01528	CGC		0.706	BCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453220.1	NM_005581		3	43	0	0	0	1	0	3	43				
NCOA3	8202	broad.mit.edu	37	20	46267838	46267838	+	Missense_Mutation	SNP	A	A	G			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr20:46267838A>G	ENST00000371998.3	+	14	2790	c.2599A>G	c.(2599-2601)Agt>Ggt	p.S867G	NCOA3_ENST00000371997.3_Missense_Mutation_p.S877G|NCOA3_ENST00000341724.6_Intron|NCOA3_ENST00000372004.3_Missense_Mutation_p.S867G			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	867					androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						TGTTGGCTCAAGTCCTCCAGT	0.438																																						ENST00000372004.3																			0				breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						c.(2599-2601)Agt>Ggt		nuclear receptor coactivator 3							132.0	125.0	127.0					20																	46267838		2203	4300	6503	SO:0001583	missense	8202				androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleoplasm	androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding	g.chr20:46267838A>G	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7670	protein-coding gene	gene with protein product	"""receptor-associated coactivator 3"", ""thyroid hormone receptor activator molecule 1"""	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.2599A>G	20.37:g.46267838A>G	ENSP00000361066:p.Ser867Gly					NCOA3_ENST00000371997.3_Missense_Mutation_p.S877G|NCOA3_ENST00000371998.3_Missense_Mutation_p.S867G|NCOA3_ENST00000341724.6_Intron	p.S867G	NM_001174087.1|NM_001174088.1|NM_006534.3|NM_181659.2	NP_001167558.1|NP_001167559.1|NP_006525.2|NP_858045.1	Q9Y6Q9	NCOA3_HUMAN			14	2815	+			867					A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Missense_Mutation	SNP	ENST00000371998.3	37	c.2599A>G	CCDS13407.1	.	.	.	.	.	.	.	.	.	.	A	0.478	-0.881188	0.02530	.	.	ENSG00000124151	ENST00000340189;ENST00000372004;ENST00000371998;ENST00000371997	T;T;T	0.02032	4.69;4.66;4.49	5.48	1.94	0.25998	.	0.419679	0.26620	N	0.023379	T	0.01387	0.0045	N	0.14661	0.345	0.20074	N	0.999931	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.06405	0.001;0.002;0.001;0.0;0.001;0.001	T	0.48969	-0.8987	10	0.25106	T	0.35	-2.4782	5.5729	0.17206	0.6259:0.1358:0.2383:0.0	.	867;877;871;867;867;867	A8K0W8;Q9Y6Q9-3;Q59EE8;Q0IIN7;Q9Y6Q9-5;Q9Y6Q9	.;.;.;.;.;NCOA3_HUMAN	G	867;867;867;877	ENSP00000361073:S867G;ENSP00000361066:S867G;ENSP00000361065:S877G	ENSP00000345671:S867G	S	+	1	0	NCOA3	45701245	0.301000	0.24444	0.046000	0.18839	0.101000	0.19017	0.839000	0.27586	0.059000	0.16252	-0.472000	0.04984	AGT		0.438	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534		25	56	0	0	0	1	0	25	56				
THOC5	8563	broad.mit.edu	37	22	29904508	29904508	+	Splice_Site	SNP	C	C	A			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr22:29904508C>A	ENST00000490103.1	-	20	2112	c.1990G>T	c.(1990-1992)Ggt>Tgt	p.G664C	THOC5_ENST00000397871.1_Splice_Site_p.G664C|THOC5_ENST00000397873.2_Splice_Site_p.G664C|THOC5_ENST00000397872.1_Splice_Site_p.G664C	NM_003678.4	NP_003669.4	Q13769	THOC5_HUMAN	THO complex 5	664					blastocyst development (GO:0001824)|cell morphogenesis (GO:0000902)|monocyte differentiation (GO:0030224)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of DNA damage checkpoint (GO:2000002)|negative regulation of macrophage differentiation (GO:0045650)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|primitive hemopoiesis (GO:0060215)|regulation of mRNA export from nucleus (GO:0010793)|regulation of stem cell division (GO:2000035)|RNA splicing (GO:0008380)|stem cell division (GO:0017145)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	mRNA binding (GO:0003729)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(4)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						CTGCTAGGACCCCTAGAGAAA	0.458																																						ENST00000490103.1																			0				NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(4)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						c.e20-1		THO complex 5							86.0	78.0	81.0					22																	29904508		2203	4300	6503	SO:0001630	splice_region_variant	8563				intronless viral mRNA export from host nucleus|monocyte differentiation|mRNA processing|primitive hemopoiesis|RNA splicing	cytoplasm|intermediate filament cytoskeleton|THO complex part of transcription export complex	protein binding|RNA binding	g.chr22:29904508C>A	AB023200	CCDS13859.1	22q12	2013-02-11			ENSG00000100296	ENSG00000100296		"""THO complex subunits"""	19074	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 79"""	612733	"""chromosome 22 open reading frame 19"""	C22orf19		11979277, 8242058, 10231032, 19015024, 18373705	Standard	NM_003678		Approved	PK1.3, KIAA0983, Fmip, fSAP79	uc003afs.3	Q13769	OTTHUMG00000151291	ENST00000490103.1:c.1989-1G>T	22.37:g.29904508C>A						THOC5_ENST00000397871.1_Splice_Site_p.G664_splice|THOC5_ENST00000397872.1_Splice_Site_p.G664_splice|THOC5_ENST00000397873.2_Splice_Site_p.G664_splice	p.G664_splice	NM_003678.4	NP_003669.4	Q13769	THOC5_HUMAN			20	2112	-			664					O60839|Q9UPZ5	Splice_Site	SNP	ENST00000490103.1	37	c.1988_splice	CCDS13859.1	.	.	.	.	.	.	.	.	.	.	C	30	5.054326	0.93793	.	.	ENSG00000100296	ENST00000490103;ENST00000397872;ENST00000397871;ENST00000397873	T;T;T;T	0.24151	1.87;1.87;1.87;1.87	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.55146	0.1902	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.55016	-0.8206	10	0.87932	D	0	-33.6037	19.9372	0.97144	0.0:1.0:0.0:0.0	.	664	Q13769	THOC5_HUMAN	C	664	ENSP00000420306:G664C;ENSP00000380970:G664C;ENSP00000380969:G664C;ENSP00000380971:G664C	ENSP00000380969:G664C	G	-	1	0	THOC5	28234508	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	7.317000	0.79018	2.810000	0.96702	0.655000	0.94253	GGT		0.458	THOC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322097.1	NM_003678	Missense_Mutation	3	14	1	0	0.004672	1	0.00484189	3	14				
ITGA2	3673	broad.mit.edu	37	5	52344214	52344214	+	Missense_Mutation	SNP	C	C	A			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr5:52344214C>A	ENST00000296585.5	+	5	552	c.409C>A	c.(409-411)Cag>Aag	p.Q137K		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	137					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular response to hormone stimulus (GO:0032870)|collagen-activated signaling pathway (GO:0038065)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|hepatocyte differentiation (GO:0070365)|hypotonic response (GO:0006971)|integrin-mediated signaling pathway (GO:0007229)|mammary gland development (GO:0030879)|mesodermal cell differentiation (GO:0048333)|organ morphogenesis (GO:0009887)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell projection organization (GO:0031346)|positive regulation of collagen binding (GO:0033343)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|response to amine (GO:0014075)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to muscle activity (GO:0014850)|response to organic cyclic compound (GO:0014070)|skin morphogenesis (GO:0043589)|substrate-dependent cell migration (GO:0006929)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	axon terminus (GO:0043679)|basal part of cell (GO:0045178)|cell outer membrane (GO:0009279)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin alpha2-beta1 complex (GO:0034666)|integrin complex (GO:0008305)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(1)|lung(18)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	47		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)				TCTGTGGGCACAGCAATGTGG	0.438																																						ENST00000296585.5																			0				breast(3)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(1)|lung(18)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	47						c.(409-411)Cag>Aag		integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)							150.0	144.0	146.0					5																	52344214		2203	4300	6503	SO:0001583	missense	3673				axon guidance|blood coagulation|cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|organ morphogenesis	integrin complex	collagen binding|identical protein binding|receptor activity	g.chr5:52344214C>A		CCDS3957.1	5q11.2	2010-03-23			ENSG00000164171	ENSG00000164171		"""CD molecules"", ""Integrins"""	6137	protein-coding gene	gene with protein product		192974		CD49B			Standard	NM_002203		Approved	CD49b	uc003joy.3	P17301	OTTHUMG00000131165	ENST00000296585.5:c.409C>A	5.37:g.52344214C>A	ENSP00000296585:p.Gln137Lys						p.Q137K	NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN			5	552	+		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)	137					Q14595	Missense_Mutation	SNP	ENST00000296585.5	37	c.409C>A	CCDS3957.1	.	.	.	.	.	.	.	.	.	.	C	13.81	2.346923	0.41599	.	.	ENSG00000164171	ENST00000296585	D	0.91894	-2.93	5.34	5.34	0.76211	.	0.259371	0.39909	N	0.001235	D	0.90933	0.7150	M	0.64170	1.965	0.80722	D	1	B;B	0.20052	0.006;0.041	B;B	0.19391	0.02;0.025	D	0.87244	0.2268	10	0.27082	T	0.32	.	19.0411	0.92999	0.0:1.0:0.0:0.0	.	137;137	E7ESP4;P17301	.;ITA2_HUMAN	K	137	ENSP00000296585:Q137K	ENSP00000296585:Q137K	Q	+	1	0	ITGA2	52379971	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.753000	0.68736	2.482000	0.83794	0.557000	0.71058	CAG		0.438	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203		13	6	1	0	1.5842e-08	1	1.77058e-08	13	6				
ATM	472	broad.mit.edu	37	11	108180935	108180935	+	Frame_Shift_Del	DEL	T	T	-			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr11:108180935delT	ENST00000452508.2	+	40	6000	c.5811delT	c.(5809-5811)aatfs	p.N1937fs	C11orf65_ENST00000525729.1_Intron|ATM_ENST00000278616.4_Frame_Shift_Del_p.N1937fs			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1937					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TGGATTTAAATTATCTAGAAG	0.328			"""D, Mis, N, F, S"""		T-PLL	"""leukemia, lymphoma, medulloblastoma, glioma"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												ENST00000278616.4			yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	"""D, Mis, N, F, S"""	ataxia telangiectasia mutated			"""L, O"""		"""leukemia, lymphoma, medulloblastoma, glioma"""	T-PLL		0				NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448						c.(5809-5811)aafs	Genes defective in diseases associated with sensitivity to DNA damaging agents	ataxia telangiectasia mutated							71.0	75.0	74.0					11																	108180935		2201	4297	6498	SO:0001589	frameshift_variant	472	Ataxia Telangiectasia	Familial Cancer Database	AT, Louis-Bar syndrome	cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding	g.chr11:108180935delT	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"""TEL1, telomere maintenance 1, homolog (S. cerevisiae)"""	607585	"""ataxia telangiectasia mutated (includes complementation groups A, C and D)"", ""ataxia telangiectasia mutated"""	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.5811delT	11.37:g.108180935delT	ENSP00000388058:p.Asn1937fs	TSP Lung(14;0.12)				C11orf65_ENST00000525729.1_Intron|ATM_ENST00000452508.2_Frame_Shift_Del_p.N1937fs	p.N1937fs	NM_000051.3	NP_000042.3	Q13315	ATM_HUMAN		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	39	6196	+		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)	1937					B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Frame_Shift_Del	DEL	ENST00000452508.2	37	c.5811delT	CCDS31669.1																																																																																				0.328	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		12	34						12	34	---	---	---	---
RP11-377D9.3	0	broad.mit.edu	37	12	13174142	13174144	+	lincRNA	DEL	AAC	AAC	-			TCGA-YL-A8SH-01B-11D-A377-08	TCGA-YL-A8SH-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	340cfd1e-1582-4ee4-99b3-49e6249c4fa2	521257bd-e4e2-4c76-8154-e87abb022203	g.chr12:13174142_13174144delAAC	ENST00000543321.1	+	0	1025																											ctgtctcaaaaacaacaacaaca	0.552																																						ENST00000543321.1																			0																																																			0							g.chr12:13174142_13174144delAAC																													12.37:g.13174151_13174153delAAC														0	1025	+									RNA	DEL	ENST00000543321.1	37																																																																																						0.552	RP11-377D9.3-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000401005.1			3	4						3	4	---	---	---	---
