#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_Mutation_Status	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
CELSR2	1952	broad.mit.edu	37	1	109801499	109801499	+	Silent	SNP	C	C	T			TCGA-HC-A632-01A-11D-A29Q-08	TCGA-HC-A632-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62488eee-4473-454e-89d3-7102d7c34977	c00991ab-7597-4eaf-9574-ef30295beeb9	g.chr1:109801499C>T	ENST00000271332.3	+	2	3817	c.3756C>T	c.(3754-3756)tcC>tcT	p.S1252S		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	1252	EGF-like 1; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		TCGACTCCTCCGCGCCCTTCA	0.692																																					NSCLC(158;1285 2011 34800 34852 42084)	ENST00000271332.3																			0				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82						c.(3754-3756)tcC>tcT		cadherin, EGF LAG seven-pass G-type receptor 2							45.0	38.0	40.0					1																	109801499		2203	4300	6503	SO:0001819	synonymous_variant	1952				dendrite morphogenesis|homophilic cell adhesion|neural plate anterior/posterior regionalization|neuropeptide signaling pathway|regulation of cell-cell adhesion|regulation of transcription, DNA-dependent|Wnt receptor signaling pathway	cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding	g.chr1:109801499C>T	D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	3231	protein-coding gene	gene with protein product		604265	"""cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"""	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.3756C>T	1.37:g.109801499C>T			Somatic					p.S1252S	NM_001408.2	NP_001399.1	WXS	Illumina GAIIx	Phase_I	Q9HCU4	CELR2_HUMAN		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)	2	3817	+		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)	1252			EGF-like 1; calcium-binding.		Q5T2Y7|Q92566	Silent	SNP	ENST00000271332.3	37	c.3756C>T	CCDS796.1																																																																																				0.692	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408		7	29	7	29	---	---	---	---
CHI3L2	1117	broad.mit.edu	37	1	111783985	111783985	+	Missense_Mutation	SNP	C	C	T			TCGA-HC-A632-01A-11D-A29Q-08	TCGA-HC-A632-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62488eee-4473-454e-89d3-7102d7c34977	c00991ab-7597-4eaf-9574-ef30295beeb9	g.chr1:111783985C>T	ENST00000445067.2	+	11	1726	c.955C>T	c.(955-957)Ctc>Ttc	p.L319F	CHI3L2_ENST00000369744.2_Missense_Mutation_p.L309F|CHI3L2_ENST00000466741.1_Missense_Mutation_p.L240F|CHI3L2_ENST00000369748.4_Missense_Mutation_p.L319F|CHI3L2_ENST00000524472.1_Missense_Mutation_p.L240F|CHI3L2_ENST00000529459.1_3'UTR			Q15782	CH3L2_HUMAN	chitinase 3-like 2	319					carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)	extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(8)|prostate(1)	19		all_cancers(81;1.89e-05)|all_epithelial(167;7.36e-06)|all_lung(203;0.00018)|Lung NSC(277;0.000359)		Lung(183;0.0171)|Colorectal(144;0.0387)|all cancers(265;0.0464)|LUSC - Lung squamous cell carcinoma(189;0.0872)|Epithelial(280;0.0994)|COAD - Colon adenocarcinoma(174;0.141)		GATCACGCGGCTCCAGGATCA	0.537																																						ENST00000445067.2																			0				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(8)|prostate(1)	19						c.(955-957)Ctc>Ttc		chitinase 3-like 2							99.0	87.0	91.0					1																	111783985		2203	4300	6503	SO:0001583	missense	1117				chitin catabolic process	extracellular space	cation binding|chitinase activity	g.chr1:111783985C>T	U49835	CCDS30802.1, CCDS30803.1, CCDS41367.1	1p13.3	2008-02-05			ENSG00000064886	ENSG00000064886			1933	protein-coding gene	gene with protein product		601526				8702629	Standard	NM_001025197		Approved	YKL-39, YKL39	uc001eam.3	Q15782	OTTHUMG00000012174	ENST00000445067.2:c.955C>T	1.37:g.111783985C>T	ENSP00000437082:p.Leu319Phe		Somatic				CHI3L2_ENST00000524472.1_Missense_Mutation_p.L240F|CHI3L2_ENST00000529459.1_3'UTR|CHI3L2_ENST00000369744.2_Missense_Mutation_p.L309F|CHI3L2_ENST00000466741.1_Missense_Mutation_p.L240F|CHI3L2_ENST00000369748.4_Missense_Mutation_p.L319F	p.L319F			WXS	Illumina GAIIx	Phase_I	Q15782	CH3L2_HUMAN		Lung(183;0.0171)|Colorectal(144;0.0387)|all cancers(265;0.0464)|LUSC - Lung squamous cell carcinoma(189;0.0872)|Epithelial(280;0.0994)|COAD - Colon adenocarcinoma(174;0.141)	11	1726	+		all_cancers(81;1.89e-05)|all_epithelial(167;7.36e-06)|all_lung(203;0.00018)|Lung NSC(277;0.000359)	319					A6NNY3|B4DPR7|Q15749|Q15783|Q5VUV7|Q96F97	Missense_Mutation	SNP	ENST00000445067.2	37	c.955C>T	CCDS30802.1	.	.	.	.	.	.	.	.	.	.	C	6.324	0.427800	0.11987	.	.	ENSG00000064886	ENST00000445067;ENST00000369744;ENST00000369748;ENST00000466741;ENST00000524472;ENST00000497220;ENST00000472825	T;T;T;T;T;T;T	0.14391	3.43;3.43;3.43;3.43;3.43;3.52;2.51	3.59	-2.64	0.06114	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.289830	0.18617	U	0.136000	T	0.02610	0.0079	L	0.46819	1.47	0.09310	N	1	B;B	0.23990	0.095;0.095	B;B	0.28784	0.094;0.094	T	0.47182	-0.9137	10	0.09338	T	0.73	-2.2846	6.6071	0.22731	0.6286:0.2676:0.0:0.1039	.	309;319	A6NNY3;Q15782	.;CH3L2_HUMAN	F	319;309;319;240;240;112;15	ENSP00000437082:L319F;ENSP00000358759:L309F;ENSP00000358763:L319F;ENSP00000437086:L240F;ENSP00000432049:L240F;ENSP00000435250:L112F;ENSP00000435935:L15F	ENSP00000358759:L309F	L	+	1	0	CHI3L2	111585508	0.324000	0.24652	0.001000	0.08648	0.412000	0.31113	1.126000	0.31344	-0.454000	0.07066	0.655000	0.94253	CTC		0.537	CHI3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033669.4	NM_004000		34	69	34	69	---	---	---	---
ARHGEF2	9181	broad.mit.edu	37	1	155931554	155931554	+	Missense_Mutation	SNP	G	G	A			TCGA-HC-A632-01A-11D-A29Q-08	TCGA-HC-A632-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62488eee-4473-454e-89d3-7102d7c34977	c00991ab-7597-4eaf-9574-ef30295beeb9	g.chr1:155931554G>A	ENST00000361247.4	-	11	1465	c.1366C>T	c.(1366-1368)Cca>Tca	p.P456S	ARHGEF2_ENST00000477754.2_Intron|ARHGEF2_ENST00000313667.4_Missense_Mutation_p.P455S|ARHGEF2_ENST00000313695.7_Missense_Mutation_p.P428S|ARHGEF2_ENST00000462460.2_Missense_Mutation_p.P501S|ARHGEF2_ENST00000368315.4_Missense_Mutation_p.P457S|ARHGEF2_ENST00000368316.1_Missense_Mutation_p.P428S	NM_001162383.1|NM_001162384.1	NP_001155855.1|NP_001155856.1	Q92974	ARHG2_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 2	456					actin filament organization (GO:0007015)|apoptotic signaling pathway (GO:0097190)|cell morphogenesis (GO:0000902)|cellular hyperosmotic response (GO:0071474)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to tumor necrosis factor (GO:0071356)|establishment of mitotic spindle orientation (GO:0000132)|innate immune response (GO:0045087)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress (GO:1902219)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of necroptotic process (GO:0060546)|negative regulation of neurogenesis (GO:0050768)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cell proliferation (GO:0042127)|regulation of Rho protein signal transduction (GO:0035023)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|Rac GTPase binding (GO:0048365)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho GTPase binding (GO:0017048)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(4)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|skin(2)	40	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					CCAGGCACTGGGGTTTGGGCC	0.602																																					Melanoma(178;35 2768 6610 28839)	ENST00000462460.2																			0				breast(4)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|skin(2)	40						c.(1501-1503)Cca>Tca		Rho/Rac guanine nucleotide exchange factor (GEF) 2							63.0	63.0	63.0					1																	155931554		2203	4300	6503	SO:0001583	missense	9181				actin filament organization|apoptosis|cell division|cell morphogenesis|induction of apoptosis by extracellular signals|intracellular protein transport|mitosis|negative regulation of microtubule depolymerization|nerve growth factor receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|regulation of cell proliferation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|Golgi apparatus|microtubule|ruffle membrane|spindle|tight junction	microtubule binding|Rac GTPase binding|Rac guanyl-nucleotide exchange factor activity|zinc ion binding	g.chr1:155931554G>A	AB014551	CCDS1125.1, CCDS53375.1, CCDS53376.1	1q21-q22	2013-01-10	2009-06-12		ENSG00000116584	ENSG00000116584		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	682	protein-coding gene	gene with protein product		607560	"""rho/rac guanine nucleotide exchange factor (GEF) 2"""			9857026, 9734811	Standard	NM_004723		Approved	LFP40, GEF-H1, KIAA0651, P40	uc001fmt.2	Q92974	OTTHUMG00000017464	ENST00000361247.4:c.1366C>T	1.37:g.155931554G>A	ENSP00000354837:p.Pro456Ser		Somatic				ARHGEF2_ENST00000368316.1_Missense_Mutation_p.P428S|ARHGEF2_ENST00000313695.7_Missense_Mutation_p.P428S|ARHGEF2_ENST00000361247.4_Missense_Mutation_p.P456S|ARHGEF2_ENST00000313667.4_Missense_Mutation_p.P455S|ARHGEF2_ENST00000368315.4_Missense_Mutation_p.P457S|ARHGEF2_ENST00000477754.2_Intron	p.P501S			WXS	Illumina GAIIx	Phase_I	Q92974	ARHG2_HUMAN			15	1755	-	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					PH.		D3DVA6|O75142|Q15079|Q5VY92|Q8TDA3|Q8WUG4|Q9H023	Missense_Mutation	SNP	ENST00000361247.4	37	c.1501C>T	CCDS53376.1	.	.	.	.	.	.	.	.	.	.	G	13.82	2.352360	0.41700	.	.	ENSG00000116584	ENST00000313695;ENST00000361247;ENST00000368315;ENST00000368316;ENST00000313667	T;T;T;T;T	0.62105	0.05;0.05;0.05;0.05;0.05	4.95	4.95	0.65309	Pleckstrin homology-type (1);	0.000000	0.46758	D	0.000263	T	0.30166	0.0756	L	0.44542	1.39	0.30675	N	0.752969	B;P;B	0.43231	0.245;0.801;0.359	B;B;B	0.35353	0.017;0.201;0.038	T	0.16482	-1.0401	10	0.14252	T	0.57	-23.6489	11.0118	0.47667	0.0:0.0:0.8142:0.1858	.	500;456;455	D3DVA5;Q92974;Q92974-2	.;ARHG2_HUMAN;.	S	428;456;457;428;455	ENSP00000315325:P428S;ENSP00000354837:P456S;ENSP00000357298:P457S;ENSP00000357299:P428S;ENSP00000314787:P455S	ENSP00000314787:P455S	P	-	1	0	ARHGEF2	154198178	0.549000	0.26481	0.998000	0.56505	0.997000	0.91878	0.714000	0.25808	2.724000	0.93272	0.655000	0.94253	CCA		0.602	ARHGEF2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046204.2	NM_004723		22	82	22	82	---	---	---	---
CD1C	911	broad.mit.edu	37	1	158260938	158260938	+	Missense_Mutation	SNP	G	G	A			TCGA-HC-A632-01A-11D-A29Q-08	TCGA-HC-A632-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62488eee-4473-454e-89d3-7102d7c34977	c00991ab-7597-4eaf-9574-ef30295beeb9	g.chr1:158260938G>A	ENST00000368170.3	+	2	355	c.76G>A	c.(76-78)Gtc>Atc	p.V26I		NM_001765.2	NP_001756.2	P29017	CD1C_HUMAN	CD1c molecule	26					antigen processing and presentation (GO:0019882)|T cell activation involved in immune response (GO:0002286)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	endogenous lipid antigen binding (GO:0030883)|exogenous lipid antigen binding (GO:0030884)|glycolipid binding (GO:0051861)|lipopeptide binding (GO:0071723)			NS(1)|endometrium(3)|large_intestine(4)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	39	all_hematologic(112;0.0378)					CCAGGAACACGTCTCCTTCCA	0.483																																						ENST00000368170.3																			0				NS(1)|endometrium(3)|large_intestine(4)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	39						c.(76-78)Gtc>Atc		CD1c molecule							70.0	60.0	64.0					1																	158260938		2203	4300	6503	SO:0001583	missense	911				antigen processing and presentation|T cell activation involved in immune response	endosome membrane|integral to plasma membrane	endogenous lipid antigen binding|exogenous lipid antigen binding|glycolipid binding|lipopeptide binding	g.chr1:158260938G>A	M28827	CCDS1175.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158481	ENSG00000158481		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1636	protein-coding gene	gene with protein product		188340	"""CD1C antigen, c polypeptide"", ""CD1c antigen"""	CD1		2447586	Standard	NM_001765		Approved		uc001fru.3	P29017	OTTHUMG00000017514	ENST00000368170.3:c.76G>A	1.37:g.158260938G>A	ENSP00000357152:p.Val26Ile		Somatic					p.V26I	NM_001765.2	NP_001756.2	WXS	Illumina GAIIx	Phase_I	P29017	CD1C_HUMAN			2	355	+	all_hematologic(112;0.0378)		26					Q5TDJ7|Q6IAS4|Q9UMM0|Q9UN96	Missense_Mutation	SNP	ENST00000368170.3	37	c.76G>A	CCDS1175.1	.	.	.	.	.	.	.	.	.	.	-	0.011	-1.714147	0.00706	.	.	ENSG00000158481	ENST00000368169;ENST00000368170	T	0.06142	3.34	3.32	-0.372	0.12520	MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	1.051030	0.07613	N	0.925743	T	0.00440	0.0014	N	0.01405	-0.89	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.46555	-0.9183	10	0.02654	T	1	.	3.3717	0.07223	0.4424:0.2865:0.2711:0.0	.	26	P29017	CD1C_HUMAN	I	26	ENSP00000357152:V26I	ENSP00000357151:V26I	V	+	1	0	CD1C	156527562	0.000000	0.05858	0.000000	0.03702	0.037000	0.13140	-1.950000	0.01530	-0.086000	0.12550	-0.312000	0.09012	GTC		0.483	CD1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046351.2	NM_001765		18	44	18	44	---	---	---	---
PARP1	142	broad.mit.edu	37	1	226555255	226555255	+	Missense_Mutation	SNP	G	G	A			TCGA-HC-A632-01A-11D-A29Q-08	TCGA-HC-A632-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62488eee-4473-454e-89d3-7102d7c34977	c00991ab-7597-4eaf-9574-ef30295beeb9	g.chr1:226555255G>A	ENST00000366794.5	-	17	2475	c.2332C>T	c.(2332-2334)Ctc>Ttc	p.L778F	PARP1_ENST00000490921.1_5'UTR	NM_001618.3	NP_001609.2	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase 1	778	PARP alpha-helical. {ECO:0000255|PROSITE- ProRule:PRU00398}.				base-excision repair (GO:0006284)|cellular response to insulin stimulus (GO:0032869)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|gene expression (GO:0010467)|macrophage differentiation (GO:0030225)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein ADP-ribosylation (GO:0006471)|protein autoprocessing (GO:0016540)|protein poly-ADP-ribosylation (GO:0070212)|regulation of growth rate (GO:0040009)|signal transduction involved in regulation of gene expression (GO:0023019)|telomere maintenance (GO:0000723)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NAD binding (GO:0051287)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(4)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	44	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		CCTCCCCTGAGCAGACTGTAG	0.512								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA																														ENST00000366794.5																			0				breast(2)|endometrium(4)|kidney(4)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	44						c.(2332-2334)Ctc>Ttc	Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA	poly (ADP-ribose) polymerase 1							157.0	136.0	143.0					1																	226555255		2203	4300	6503	SO:0001583	missense	142				cellular response to insulin stimulus|protein ADP-ribosylation|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nuclear envelope|nucleolus|transcription factor complex	DNA binding|identical protein binding|NAD+ ADP-ribosyltransferase activity|protein N-terminus binding|transcription factor binding|zinc ion binding	g.chr1:226555255G>A	BC037545	CCDS1554.1	1q41-q42	2010-02-16	2008-07-28	2004-08-26	ENSG00000143799	ENSG00000143799	2.4.2.30	"""Poly (ADP-ribose) polymerases"""	270	protein-coding gene	gene with protein product		173870	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)"", ""poly (ADP-ribose) polymerase family, member 1"""	PPOL, ADPRT		10964595	Standard	NM_001618		Approved	PARP	uc001hqd.4	P09874	OTTHUMG00000037556	ENST00000366794.5:c.2332C>T	1.37:g.226555255G>A	ENSP00000355759:p.Leu778Phe		Somatic				PARP1_ENST00000490921.1_5'UTR	p.L778F	NM_001618.3	NP_001609.2	WXS	Illumina GAIIx	Phase_I	P09874	PARP1_HUMAN		GBM - Glioblastoma multiforme(131;0.0531)	17	2475	-	Breast(184;0.133)		778			PARP alpha-helical.		B1ANJ4|Q8IUZ9	Missense_Mutation	SNP	ENST00000366794.5	37	c.2332C>T	CCDS1554.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.697460	0.88830	.	.	ENSG00000143799	ENST00000366794	T	0.14022	2.54	5.56	5.56	0.83823	Poly(ADP-ribose) polymerase, regulatory domain (4);	0.000000	0.85682	D	0.000000	T	0.40862	0.1134	M	0.85041	2.73	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.34403	-0.9830	10	0.72032	D	0.01	.	12.8111	0.57639	0.0746:0.0:0.9254:0.0	.	778	P09874	PARP1_HUMAN	F	778	ENSP00000355759:L778F	ENSP00000355759:L778F	L	-	1	0	PARP1	224621878	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	6.411000	0.73298	2.626000	0.88956	0.655000	0.94253	CTC		0.512	PARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091519.1	NM_001618		38	71	38	71	---	---	---	---
FAHD2A	51011	broad.mit.edu	37	2	96072721	96072721	+	Missense_Mutation	SNP	G	G	A	rs373739961		TCGA-HC-A632-01A-11D-A29Q-08	TCGA-HC-A632-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62488eee-4473-454e-89d3-7102d7c34977	c00991ab-7597-4eaf-9574-ef30295beeb9	g.chr2:96072721G>A	ENST00000233379.4	+	3	431	c.278G>A	c.(277-279)cGg>cAg	p.R93Q	FAHD2A_ENST00000447036.1_Missense_Mutation_p.R93Q	NM_016044.2	NP_057128.2	Q96GK7	FAH2A_HUMAN	fumarylacetoacetate hydrolase domain containing 2A	93							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|lung(3)|ovary(1)	8						GTCCTACCACGGTCGGAGGTA	0.597																																						ENST00000233379.4																			0				breast(1)|cervix(1)|endometrium(1)|kidney(1)|lung(3)|ovary(1)	8						c.(277-279)cGg>cAg		fumarylacetoacetate hydrolase domain containing 2A		G	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	81.0	65.0	70.0		278	3.3	1.0	2		70	0,8600		0,0,4300	no	missense	FAHD2A	NM_016044.2	43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging	93/315	96072721	1,13005	2203	4300	6503	SO:0001583	missense	51011						hydrolase activity|metal ion binding	g.chr2:96072721G>A	AF151863	CCDS2014.1	2q11.2	2008-02-05			ENSG00000115042	ENSG00000115042			24252	protein-coding gene	gene with protein product							Standard	NM_016044		Approved	CGI-105	uc002sur.3	Q96GK7	OTTHUMG00000130397	ENST00000233379.4:c.278G>A	2.37:g.96072721G>A	ENSP00000233379:p.Arg93Gln		Somatic				FAHD2A_ENST00000447036.1_Missense_Mutation_p.R93Q	p.R93Q	NM_016044.2	NP_057128.2	WXS	Illumina GAIIx	Phase_I	Q96GK7	FAH2A_HUMAN			3	431	+			93					Q9Y3B0	Missense_Mutation	SNP	ENST00000233379.4	37	c.278G>A	CCDS2014.1	.	.	.	.	.	.	.	.	.	.	G	15.37	2.814323	0.50527	2.27E-4	0.0	ENSG00000115042	ENST00000447036;ENST00000233379;ENST00000418606	T;T	0.30714	1.52;1.52	3.35	3.35	0.38373	Fumarylacetoacetase, C-terminal-related (1);	0.069040	0.64402	D	0.000013	T	0.25419	0.0618	L	0.52206	1.635	0.40083	D	0.976157	B	0.20459	0.045	B	0.17722	0.019	T	0.07121	-1.0789	10	0.12430	T	0.62	.	12.5392	0.56158	0.0:0.0:1.0:0.0	.	93	Q96GK7	FAH2A_HUMAN	Q	93	ENSP00000406424:R93Q;ENSP00000233379:R93Q	ENSP00000233379:R93Q	R	+	2	0	FAHD2A	95436448	1.000000	0.71417	0.986000	0.45419	0.784000	0.44337	5.590000	0.67530	1.856000	0.53863	0.561000	0.74099	CGG		0.597	FAHD2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252778.1	NM_016044		16	36	16	36	---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	140990833	140990833	+	Missense_Mutation	SNP	G	G	T			TCGA-HC-A632-01A-11D-A29Q-08	TCGA-HC-A632-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62488eee-4473-454e-89d3-7102d7c34977	c00991ab-7597-4eaf-9574-ef30295beeb9	g.chr2:140990833G>T	ENST00000389484.3	-	91	14693	c.13722C>A	c.(13720-13722)aaC>aaA	p.N4574K		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	4574					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TTCCTAAGGAGTTTCGACAGT	0.323										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)	ENST00000389484.3																			0				NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606						c.(13720-13722)aaC>aaA		low density lipoprotein receptor-related protein 1B							100.0	99.0	99.0					2																	140990833		2202	4299	6501	SO:0001583	missense	53353				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding	g.chr2:140990833G>T	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.13722C>A	2.37:g.140990833G>T	ENSP00000374135:p.Asn4574Lys	TSP Lung(27;0.18)	Somatic					p.N4574K	NM_018557.2	NP_061027.2	WXS	Illumina GAIIx	Phase_I	Q9NZR2	LRP1B_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)	91	14693	-		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)	4574					Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	c.13722C>A	CCDS2182.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.435|8.435	0.849511|0.849511	0.17034|0.17034	.|.	.|.	ENSG00000168702|ENSG00000168702	ENST00000389484;ENST00000544579|ENST00000437977	T|.	0.43688|.	0.94|.	5.69|5.69	1.38|1.38	0.22167|0.22167	.|.	0.069032|.	0.56097|.	U|.	0.000030|.	T|T	0.30386|0.30386	0.0763|0.0763	N|N	0.19112|0.19112	0.55|0.55	0.29736|0.29736	N|N	0.837517|0.837517	B|.	0.12013|.	0.005|.	B|.	0.14023|.	0.01|.	T|T	0.28522|0.28522	-1.0041|-1.0041	10|5	0.28530|.	T|.	0.3|.	.|.	11.7752|11.7752	0.51981|0.51981	0.274:0.0:0.726:0.0|0.274:0.0:0.726:0.0	.|.	4574|.	Q9NZR2|.	LRP1B_HUMAN|.	K|N	4574;4512|773	ENSP00000374135:N4574K|.	ENSP00000374135:N4574K|.	N|T	-|-	3|2	2|0	LRP1B|LRP1B	140707303|140707303	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.343000|1.343000	0.33930|0.33930	0.350000|0.350000	0.24002|0.24002	0.585000|0.585000	0.79938|0.79938	AAC|ACT		0.323	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		9	14	9	14	---	---	---	---
RAB33B	83452	broad.mit.edu	37	4	140393995	140393995	+	Silent	SNP	T	T	C			TCGA-HC-A632-01A-11D-A29Q-08	TCGA-HC-A632-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62488eee-4473-454e-89d3-7102d7c34977	c00991ab-7597-4eaf-9574-ef30295beeb9	g.chr4:140393995T>C	ENST00000305626.5	+	2	794	c.405T>C	c.(403-405)caT>caC	p.H135H		NM_031296.1	NP_112586.1	Q9H082	RB33B_HUMAN	RAB33B, member RAS oncogene family	135					autophagy (GO:0006914)|GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|regulation of autophagic vacuole assembly (GO:2000785)|regulation of retrograde vesicle-mediated transport, Golgi to ER (GO:2000156)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	4	all_hematologic(180;0.162)					GCAAACAACATTTGCTAGCCA	0.393																																						ENST00000305626.5																			0				large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	4						c.(403-405)caT>caC		RAB33B, member RAS oncogene family							131.0	125.0	127.0					4																	140393995		2203	4300	6503	SO:0001819	synonymous_variant	83452				protein transport|small GTPase mediated signal transduction	Golgi membrane	GTP binding	g.chr4:140393995T>C	AF350420	CCDS3747.1	4q28	2008-02-05			ENSG00000172007	ENSG00000172007		"""RAB, member RAS oncogene"""	16075	protein-coding gene	gene with protein product		605950					Standard	NM_031296		Approved	DKFZP434G099	uc003ihv.3	Q9H082	OTTHUMG00000133384	ENST00000305626.5:c.405T>C	4.37:g.140393995T>C			Somatic					p.H135H	NM_031296.1	NP_112586.1	WXS	Illumina GAIIx	Phase_I	Q9H082	RB33B_HUMAN			2	794	+	all_hematologic(180;0.162)		135					B2R987|Q4W5B0	Silent	SNP	ENST00000305626.5	37	c.405T>C	CCDS3747.1																																																																																				0.393	RAB33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257235.2	NM_031296		53	75	53	75	---	---	---	---
ZNF827	152485	broad.mit.edu	37	4	146824152	146824152	+	Missense_Mutation	SNP	C	C	A			TCGA-HC-A632-01A-11D-A29Q-08	TCGA-HC-A632-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62488eee-4473-454e-89d3-7102d7c34977	c00991ab-7597-4eaf-9574-ef30295beeb9	g.chr4:146824152C>A	ENST00000508784.1	-	2	486	c.259G>T	c.(259-261)Gac>Tac	p.D87Y	ZNF827_ENST00000379448.4_Missense_Mutation_p.D87Y|ZNF827_ENST00000513320.1_Intron			Q17R98	ZN827_HUMAN	zinc finger protein 827	87					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	all_hematologic(180;0.151)					ACCTCACTGTCCAGTGCCACC	0.602																																						ENST00000508784.1																			0				NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						c.(259-261)Gac>Tac		zinc finger protein 827							72.0	63.0	66.0					4																	146824152		2203	4300	6503	SO:0001583	missense	152485				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr4:146824152C>A	AK091130	CCDS34072.1	4q31.22	2013-01-08			ENSG00000151612	ENSG00000151612		"""Zinc fingers, C2H2-type"""	27193	protein-coding gene	gene with protein product						12477932	Standard	NM_178835		Approved		uc003ikm.3	Q17R98	OTTHUMG00000161362	ENST00000508784.1:c.259G>T	4.37:g.146824152C>A	ENSP00000421863:p.Asp87Tyr		Somatic				ZNF827_ENST00000513320.1_Intron|ZNF827_ENST00000379448.4_Missense_Mutation_p.D87Y	p.D87Y			WXS	Illumina GAIIx	Phase_I	Q17R98	ZN827_HUMAN			2	486	-	all_hematologic(180;0.151)		87					B7ZL52|Q7Z4S7|Q8N279	Missense_Mutation	SNP	ENST00000508784.1	37	c.259G>T		.	.	.	.	.	.	.	.	.	.	C	11.61	1.690427	0.29962	.	.	ENSG00000151612	ENST00000508784;ENST00000379448;ENST00000281318	T;T	0.11385	2.78;2.82	5.93	5.09	0.68999	.	0.086220	0.85682	D	0.000000	T	0.15696	0.0378	N	0.19112	0.55	0.53688	D	0.999979	P;P	0.51537	0.911;0.946	P;P	0.55161	0.594;0.77	T	0.02885	-1.1098	10	0.87932	D	0	-26.0842	15.1601	0.72778	0.0:0.9325:0.0:0.0675	.	87;87	Q17R98;Q17R98-2	ZN827_HUMAN;.	Y	87;87;86	ENSP00000421863:D87Y;ENSP00000368761:D87Y	ENSP00000281318:D86Y	D	-	1	0	ZNF827	147043602	1.000000	0.71417	0.051000	0.19133	0.328000	0.28507	7.416000	0.80143	1.524000	0.49035	-0.258000	0.10820	GAC		0.602	ZNF827-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000364654.2	NM_178835		27	40	27	40	---	---	---	---
GCNT2	2651	broad.mit.edu	37	6	10529594	10529594	+	Silent	SNP	T	T	A			TCGA-HC-A632-01A-11D-A29Q-08	TCGA-HC-A632-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62488eee-4473-454e-89d3-7102d7c34977	c00991ab-7597-4eaf-9574-ef30295beeb9	g.chr6:10529594T>A	ENST00000379597.3	+	1	1006	c.450T>A	c.(448-450)gcT>gcA	p.A150A	GCNT2_ENST00000410107.1_Intron|GCNT2_ENST00000495262.1_Silent_p.A150A|GCNT2_ENST00000397423.2_Intron			Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group)	150					maintenance of lens transparency (GO:0036438)|negative regulation of cell-substrate adhesion (GO:0010812)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of protein kinase B signaling (GO:0051897)|posttranscriptional regulation of gene expression (GO:0010608)|protein glycosylation (GO:0006486)|transforming growth factor beta receptor signaling pathway (GO:0007179)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)			endometrium(2)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)	12	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)		TCCCAAATGCTTTTCTGGCTT	0.512																																						ENST00000379597.3																			0				endometrium(2)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)	12						c.(448-450)gcT>gcA		glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group)							67.0	62.0	63.0					6																	10529594		2203	4300	6503	SO:0001819	synonymous_variant	2651					Golgi membrane|integral to membrane	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity	g.chr6:10529594T>A	L41605	CCDS4512.1, CCDS4513.1, CCDS34338.1	6p24.2	2014-07-18	2006-02-23		ENSG00000111846	ENSG00000111846	2.4.1.150	"""Blood group antigens"", ""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	4204	protein-coding gene	gene with protein product	"""Ii blood group"", ""unassigned linkage group 3"""	600429	"""glucosaminyl (N-acetyl) transferase 5"", ""glucosaminyl (N-acetyl) transferase 2, I-branching enzyme"", ""glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (Ii blood group)"", ""cataract, congenital"""	NACGT1, II, GCNT5, CCAT		8449405, 9915862	Standard	NM_145649		Approved	IGNT, NAGCT1, bA421M1.1, bA360O19.2, ULG3	uc003mze.3	Q06430	OTTHUMG00000014244	ENST00000379597.3:c.450T>A	6.37:g.10529594T>A			Somatic				GCNT2_ENST00000397423.2_Intron|GCNT2_ENST00000410107.1_Intron|GCNT2_ENST00000495262.1_Silent_p.A150A	p.A150A			WXS	Illumina GAIIx	Phase_I	Q8N0V5	GNT2A_HUMAN		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)	1	1006	+	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)	150						Silent	SNP	ENST00000379597.3	37	c.450T>A	CCDS34338.1																																																																																				0.512	GCNT2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327912.3	NM_145649		39	56	39	56	---	---	---	---
POLR3A	11128	broad.mit.edu	37	10	79742556	79742556	+	Missense_Mutation	SNP	C	C	T	rs371116845		TCGA-HC-A632-01A-11D-A29Q-08	TCGA-HC-A632-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62488eee-4473-454e-89d3-7102d7c34977	c00991ab-7597-4eaf-9574-ef30295beeb9	g.chr10:79742556C>T	ENST00000372371.3	-	27	3586	c.3449G>A	c.(3448-3450)aGa>aAa	p.R1150K		NM_007055.3	NP_008986.2	O14802	RPC1_HUMAN	polymerase (RNA) III (DNA directed) polypeptide A, 155kDa	1150					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|ribonucleoside binding (GO:0032549)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	all_cancers(46;0.0356)|all_epithelial(25;0.00102)|Breast(12;0.00124)|Prostate(51;0.0095)		Epithelial(14;0.00161)|OV - Ovarian serous cystadenocarcinoma(4;0.00323)|all cancers(16;0.00646)			GATGGAATATCTCACTGTCTC	0.507																																						ENST00000372371.3																			0				breast(1)|endometrium(7)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59						c.(3448-3450)aGa>aAa		polymerase (RNA) III (DNA directed) polypeptide A, 155kDa		C	LYS/ARG	0,4406		0,0,2203	128.0	102.0	111.0		3449	5.0	0.7	10		111	1,8599	1.2+/-3.3	0,1,4299	no	missense	POLR3A	NM_007055.3	26	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	1150/1391	79742556	1,13005	2203	4300	6503	SO:0001583	missense	11128				innate immune response|positive regulation of interferon-beta production|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	DNA-directed RNA polymerase III complex	DNA binding|DNA-directed RNA polymerase activity|ribonucleoside binding|zinc ion binding	g.chr10:79742556C>T	AF021351	CCDS7354.1	10q22-q23	2013-01-21			ENSG00000148606	ENSG00000148606		"""RNA polymerase subunits"""	30074	protein-coding gene	gene with protein product		614258				9331371, 12391170	Standard	NM_007055		Approved	RPC1, RPC155, hRPC155	uc001jzn.3	O14802	OTTHUMG00000018550	ENST00000372371.3:c.3449G>A	10.37:g.79742556C>T	ENSP00000361446:p.Arg1150Lys		Somatic					p.R1150K	NM_007055.3	NP_008986.2	WXS	Illumina GAIIx	Phase_I	O14802	RPC1_HUMAN	Epithelial(14;0.00161)|OV - Ovarian serous cystadenocarcinoma(4;0.00323)|all cancers(16;0.00646)		27	3586	-	all_cancers(46;0.0356)|all_epithelial(25;0.00102)|Breast(12;0.00124)|Prostate(51;0.0095)		1150					Q8IW34|Q8TCW5	Missense_Mutation	SNP	ENST00000372371.3	37	c.3449G>A	CCDS7354.1	.	.	.	.	.	.	.	.	.	.	C	4.783	0.145565	0.09134	0.0	1.16E-4	ENSG00000148606	ENST00000372371;ENST00000540842	T	0.67171	-0.25	5.92	5.01	0.66863	RNA polymerase Rpb1, domain 5 (1);	0.000000	0.85682	D	0.000000	T	0.50154	0.1599	N	0.13272	0.32	0.54753	D	0.999988	B	0.18741	0.03	B	0.17098	0.017	T	0.41610	-0.9499	9	.	.	.	-24.2459	16.698	0.85341	0.1302:0.8698:0.0:0.0	.	1150	O14802	RPC1_HUMAN	K	1150;1129	ENSP00000361446:R1150K	.	R	-	2	0	POLR3A	79412562	1.000000	0.71417	0.692000	0.30179	0.061000	0.15899	5.542000	0.67218	1.483000	0.48342	0.655000	0.94253	AGA		0.507	POLR3A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048923.1	NM_007055		5	58	5	58	---	---	---	---
OR4A16	81327	broad.mit.edu	37	11	55111605	55111605	+	Missense_Mutation	SNP	G	G	A			TCGA-HC-A632-01A-11D-A29Q-08	TCGA-HC-A632-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62488eee-4473-454e-89d3-7102d7c34977	c00991ab-7597-4eaf-9574-ef30295beeb9	g.chr11:55111605G>A	ENST00000314721.2	+	1	979	c.929G>A	c.(928-930)aGa>aAa	p.R310K		NM_001005274.1	NP_001005274.1	Q8NH70	O4A16_HUMAN	olfactory receptor, family 4, subfamily A, member 16	310						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(28)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	51						GTTAGAAAAAGAGTATCTCCC	0.348																																						ENST00000314721.2																			0				NS(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(28)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	51						c.(928-930)aGa>aAa		olfactory receptor, family 4, subfamily A, member 16							31.0	32.0	32.0					11																	55111605		2201	4293	6494	SO:0001583	missense	81327				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:55111605G>A	AB065519	CCDS31499.1	11q11	2012-08-09			ENSG00000181961	ENSG00000181961		"""GPCR / Class A : Olfactory receptors"""	15153	protein-coding gene	gene with protein product							Standard	NM_001005274		Approved	OR4A16Q	uc010rie.2	Q8NH70	OTTHUMG00000166710	ENST00000314721.2:c.929G>A	11.37:g.55111605G>A	ENSP00000325128:p.Arg310Lys		Somatic					p.R310K	NM_001005274.1	NP_001005274.1	WXS	Illumina GAIIx	Phase_I	Q8NH70	O4A16_HUMAN			1	979	+			310					Q6IFL3	Missense_Mutation	SNP	ENST00000314721.2	37	c.929G>A	CCDS31499.1	.	.	.	.	.	.	.	.	.	.	g	8.185	0.794773	0.16327	.	.	ENSG00000181961	ENST00000314721	T	0.38077	1.16	3.02	-0.365	0.12549	.	.	.	.	.	T	0.14874	0.0359	N	0.08118	0	0.09310	N	1	B	0.14012	0.009	B	0.15484	0.013	T	0.27536	-1.0071	9	0.21014	T	0.42	.	3.838	0.08902	0.2306:0.4546:0.3147:0.0	.	310	Q8NH70	O4A16_HUMAN	K	310	ENSP00000325128:R310K	ENSP00000325128:R310K	R	+	2	0	OR4A16	54868181	0.000000	0.05858	0.015000	0.15790	0.034000	0.12701	-0.048000	0.11944	0.074000	0.16767	0.423000	0.28283	AGA		0.348	OR4A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391160.1	NM_001005274		7	36	7	36	---	---	---	---
LTBR	4055	broad.mit.edu	37	12	6494476	6494476	+	Missense_Mutation	SNP	T	T	G			TCGA-HC-A632-01A-11D-A29Q-08	TCGA-HC-A632-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62488eee-4473-454e-89d3-7102d7c34977	c00991ab-7597-4eaf-9574-ef30295beeb9	g.chr12:6494476T>G	ENST00000228918.4	+	4	729	c.403T>G	c.(403-405)Tgg>Ggg	p.W135G	LTBR_ENST00000543190.1_Missense_Mutation_p.W28G|LTBR_ENST00000541102.1_Missense_Mutation_p.W28G|LTBR_ENST00000539925.1_Missense_Mutation_p.W116G	NM_002342.2	NP_002333.1	P36941	TNR3_HUMAN	lymphotoxin beta receptor (TNFR superfamily, member 3)	135					apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of JNK cascade (GO:0046330)|signal transduction (GO:0007165)|viral process (GO:0016032)	integral component of membrane (GO:0016021)	identical protein binding (GO:0042802)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|cervix(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)	15						CTGTGCTGCCTGGGCCCTCGA	0.622																																						ENST00000228918.4																			0				breast(1)|cervix(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)	15						c.(403-405)Tgg>Ggg		lymphotoxin beta receptor (TNFR superfamily, member 3)							53.0	56.0	55.0					12																	6494476		2203	4300	6503	SO:0001583	missense	4055				apoptosis|cellular response to mechanical stimulus|interspecies interaction between organisms|positive regulation of I-kappaB kinase/NF-kappaB cascade	integral to membrane	protein binding|receptor activity	g.chr12:6494476T>G	L04270	CCDS8544.1, CCDS59233.1	12p13	2013-05-22				ENSG00000111321		"""Tumor necrosis factor receptor superfamily"""	6718	protein-coding gene	gene with protein product		600979		D12S370		8171323, 8486360	Standard	NM_002342		Approved	TNFCR, TNFR-RP, TNFR2-RP, TNF-R-III, TNFRSF3	uc001qny.2	P36941		ENST00000228918.4:c.403T>G	12.37:g.6494476T>G	ENSP00000228918:p.Trp135Gly		Somatic				LTBR_ENST00000543190.1_Missense_Mutation_p.W28G|LTBR_ENST00000539925.1_Missense_Mutation_p.W116G|LTBR_ENST00000541102.1_Missense_Mutation_p.W28G	p.W135G	NM_002342.2	NP_002333.1	WXS	Illumina GAIIx	Phase_I	P36941	TNR3_HUMAN			4	729	+			135					B7Z1D2|D3DUR2|F5GXE7	Missense_Mutation	SNP	ENST00000228918.4	37	c.403T>G	CCDS8544.1	.	.	.	.	.	.	.	.	.	.	T	0.012	-1.663508	0.00772	.	.	ENSG00000111321	ENST00000539925;ENST00000228918;ENST00000540343;ENST00000536876;ENST00000543190;ENST00000541102	T;T;T;T;T	0.71461	1.08;1.08;1.08;-0.57;-0.57	4.26	-8.52	0.00920	TNFR/CD27/30/40/95 cysteine-rich region (1);	1.278260	0.05851	N	0.621226	T	0.46092	0.1375	L	0.28054	0.825	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.001	T	0.22103	-1.0226	9	.	.	.	0.0011	1.9926	0.03449	0.1987:0.4097:0.2006:0.1909	.	116;116;135	F5GXE7;B7Z1D2;P36941	.;.;TNR3_HUMAN	G	116;135;28;130;28;28	ENSP00000440875:W116G;ENSP00000228918:W135G;ENSP00000437647:W130G;ENSP00000438955:W28G;ENSP00000438605:W28G	.	W	+	1	0	LTBR	6364737	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-5.926000	0.00090	-1.952000	0.01027	-1.840000	0.00586	TGG		0.622	LTBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399422.1			29	65	29	65	---	---	---	---
USP15	9958	broad.mit.edu	37	12	62777656	62777656	+	Silent	SNP	A	A	G			TCGA-HC-A632-01A-11D-A29Q-08	TCGA-HC-A632-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62488eee-4473-454e-89d3-7102d7c34977	c00991ab-7597-4eaf-9574-ef30295beeb9	g.chr12:62777656A>G	ENST00000280377.5	+	10	1183	c.1125A>G	c.(1123-1125)ggA>ggG	p.G375G	USP15_ENST00000353364.3_Silent_p.G346G|USP15_ENST00000393654.3_Silent_p.G350G	NM_001252078.1	NP_001239007.1	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	375	USP.				BMP signaling pathway (GO:0030509)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|protein deubiquitination (GO:0016579)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|identical protein binding (GO:0042802)|SMAD binding (GO:0046332)|transforming growth factor beta receptor binding (GO:0005160)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(15)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	37			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		AGTTCTCTGGATATCAGCAGC	0.348																																					Melanoma(181;615 2041 39364 49691 50001)	ENST00000280377.5																			0				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(15)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	37						c.(1123-1125)ggA>ggG		ubiquitin specific peptidase 15							109.0	104.0	105.0					12																	62777656		2203	4299	6502	SO:0001819	synonymous_variant	9958				protein deubiquitination|ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity	g.chr12:62777656A>G	AB011101	CCDS8963.1, CCDS58250.1, CCDS58251.1	12q14	2006-07-18	2005-08-08					"""Ubiquitin-specific peptidases"""	12613	protein-coding gene	gene with protein product		604731	"""ubiquitin specific protease 15"""			12838346	Standard	NM_001252078		Approved	KIAA0529, UNPH4	uc001src.2	Q9Y4E8	OTTHUMG00000170186	ENST00000280377.5:c.1125A>G	12.37:g.62777656A>G			Somatic				USP15_ENST00000393654.3_Silent_p.G350G|USP15_ENST00000353364.3_Silent_p.G346G	p.G375G	NM_001252078.1	NP_001239007.1	WXS	Illumina GAIIx	Phase_I	Q9Y4E8	UBP15_HUMAN	GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)	10	1183	+			375					Q08AL5|Q9H8G9|Q9HCA6|Q9UNP0|Q9Y5B5	Silent	SNP	ENST00000280377.5	37	c.1125A>G	CCDS58251.1																																																																																				0.348	USP15-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407831.2	NM_006313		24	42	24	42	---	---	---	---
NR2E3	10002	broad.mit.edu	37	15	72105883	72105883	+	RNA	SNP	G	G	T	rs375364175		TCGA-HC-A632-01A-11D-A29Q-08	TCGA-HC-A632-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62488eee-4473-454e-89d3-7102d7c34977	c00991ab-7597-4eaf-9574-ef30295beeb9	g.chr15:72105883G>T	ENST00000398840.2	+	0	1092							Q9Y5X4	NR2E3_HUMAN	nuclear receptor subfamily 2, group E, member 3						eye photoreceptor cell development (GO:0042462)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phototransduction (GO:0007602)|positive regulation of rhodopsin gene expression (GO:0045872)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|lung(1)	3						ATGGAGACGCGTGTCCTGCAG	0.647																																						ENST00000398840.2																			0				breast(1)|endometrium(1)|lung(1)	3								nuclear receptor subfamily 2, group E, member 3							49.0	53.0	51.0					15																	72105883		1990	4161	6151			10002				phototransduction|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription from RNA polymerase II promoter|visual perception	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding	g.chr15:72105883G>T		CCDS73750.1, CCDS73751.1	15q23	2013-01-16			ENSG00000031544	ENSG00000278570		"""Nuclear hormone receptors"""	7974	protein-coding gene	gene with protein product		604485				10220376	Standard	NM_016346		Approved	PNR, rd7, RP37	uc002ath.1	Q9Y5X4	OTTHUMG00000172841		15.37:g.72105883G>T			Somatic								WXS	Illumina GAIIx	Phase_I	Q9Y5X4	NR2E3_HUMAN			0	1092	+								B6ZGU0|Q9UHM4	RNA	SNP	ENST00000398840.2	37			.	.	.	.	.	.	.	.	.	.	G	11.34	1.610350	0.28712	.	.	ENSG00000031544	ENST00000326995;ENST00000398840	.	.	.	5.36	3.01	0.34805	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.082780	0.47455	U	0.000239	T	0.75384	0.3842	M	0.90252	3.1	0.58432	D	0.999997	P	0.41041	0.736	P	0.50049	0.629	D	0.85001	0.0900	8	0.87932	D	0	.	11.5782	0.50877	0.1733:0.0:0.8267:0.0	.	301	Q9Y5X4	NR2E3_HUMAN	L	213;301	.	ENSP00000317199:R213L	R	+	2	0	NR2E3	69892937	1.000000	0.71417	0.023000	0.16930	0.649000	0.38597	5.609000	0.67661	1.162000	0.42619	0.561000	0.74099	CGT		0.647	NR2E3-202	KNOWN	basic	processed_transcript	processed_transcript		NM_014249		3	37	3	37	---	---	---	---
TBCD	6904	broad.mit.edu	37	17	80847559	80847559	+	Missense_Mutation	SNP	A	A	G			TCGA-HC-A632-01A-11D-A29Q-08	TCGA-HC-A632-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62488eee-4473-454e-89d3-7102d7c34977	c00991ab-7597-4eaf-9574-ef30295beeb9	g.chr17:80847559A>G	ENST00000355528.4	+	16	1679	c.1549A>G	c.(1549-1551)Aat>Gat	p.N517D	TBCD_ENST00000539345.2_Missense_Mutation_p.N517D|TBCD_ENST00000397466.2_Missense_Mutation_p.N131D	NM_005993.4	NP_005984.3	Q9BTW9	TBCD_HUMAN	tubulin folding cofactor D	517					'de novo' posttranslational protein folding (GO:0051084)|adherens junction assembly (GO:0034333)|cellular protein metabolic process (GO:0044267)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of microtubule polymerization (GO:0031115)|positive regulation of GTPase activity (GO:0043547)|post-chaperonin tubulin folding pathway (GO:0007023)|protein folding (GO:0006457)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|tight junction (GO:0005923)	beta-tubulin binding (GO:0048487)|chaperone binding (GO:0051087)|GTPase activator activity (GO:0005096)					Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)			CTTCCAGGAGAATGTGGGGAG	0.502																																						ENST00000355528.4																			0											c.(1549-1551)Aat>Gat		tubulin folding cofactor D							103.0	102.0	103.0					17																	80847559		1974	4159	6133	SO:0001583	missense	6904				'de novo' posttranslational protein folding|adherens junction assembly|negative regulation of cell-substrate adhesion|negative regulation of microtubule polymerization|post-chaperonin tubulin folding pathway|tight junction assembly	adherens junction|cytoplasm|lateral plasma membrane|microtubule|tight junction	beta-tubulin binding|chaperone binding|GTPase activator activity	g.chr17:80847559A>G	BC003094	CCDS45818.1	17q25.3	2006-11-21	2006-11-21			ENSG00000141556			11581	protein-coding gene	gene with protein product		604649	"""tubulin-specific chaperone d"""				Standard	NM_005993		Approved		uc002kfz.3	Q9BTW9		ENST00000355528.4:c.1549A>G	17.37:g.80847559A>G	ENSP00000347719:p.Asn517Asp		Somatic				TBCD_ENST00000539345.2_Missense_Mutation_p.N517D|TBCD_ENST00000397466.2_Missense_Mutation_p.N131D	p.N517D	NM_005993.4	NP_005984.3	WXS	Illumina GAIIx	Phase_I	Q9BTW9	TBCD_HUMAN	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)		16	1679	+	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	517					O95458|Q7L8K1|Q8IXP6|Q8NAX0|Q8WYH4|Q96E74|Q9UF82|Q9UG46|Q9Y2J3	Missense_Mutation	SNP	ENST00000355528.4	37	c.1549A>G	CCDS45818.1	.	.	.	.	.	.	.	.	.	.	a	21.9	4.210295	0.79240	.	.	ENSG00000141556	ENST00000355528;ENST00000334614;ENST00000397466;ENST00000536182	T;T	0.67865	-0.29;-0.29	4.7	4.7	0.59300	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.84570	0.5501	M	0.91300	3.195	0.45318	D	0.998312	D;D;P	0.89917	1.0;1.0;0.877	D;D;P	0.91635	0.998;0.999;0.66	D	0.88066	0.2797	9	.	.	.	.	13.637	0.62227	1.0:0.0:0.0:0.0	.	517;517;517	Q9BTW9;Q9BTW9-4;F5H8C7	TBCD_HUMAN;.;.	D	517;268;131;517	ENSP00000347719:N517D;ENSP00000380608:N131D	.	N	+	1	0	TBCD	78440848	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.545000	0.73883	1.884000	0.54569	0.392000	0.25879	AAT		0.502	TBCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439415.1	NM_005993		6	34	6	34	---	---	---	---
CFAP53	220136	broad.mit.edu	37	18	47753887	47753887	+	Missense_Mutation	SNP	C	C	T	rs147186159		TCGA-HC-A632-01A-11D-A29Q-08	TCGA-HC-A632-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62488eee-4473-454e-89d3-7102d7c34977	c00991ab-7597-4eaf-9574-ef30295beeb9	g.chr18:47753887C>T	ENST00000398545.4	-	8	1526	c.1409G>A	c.(1408-1410)cGc>cAc	p.R470H		NM_145020.3	NP_659457.2														endometrium(1)|kidney(4)|large_intestine(6)|lung(6)|ovary(1)|pancreas(1)|skin(1)	20				STAD - Stomach adenocarcinoma(97;2.66e-05)|Colorectal(21;7.57e-05)|Lung(128;0.00932)|READ - Rectum adenocarcinoma(32;0.164)		AAACTCTCGGCGTTTCTCTTC	0.502																																						ENST00000398545.4																			0				endometrium(1)|kidney(4)|large_intestine(6)|lung(6)|ovary(1)|pancreas(1)|skin(1)	20						c.(1408-1410)cGc>cAc		coiled-coil domain containing 11							241.0	239.0	240.0					18																	47753887		2009	4174	6183	SO:0001583	missense	220136							g.chr18:47753887C>T																												ENST00000398545.4:c.1409G>A	18.37:g.47753887C>T	ENSP00000381553:p.Arg470His		Somatic					p.R470H	NM_145020.3	NP_659457.2	WXS	Illumina GAIIx	Phase_I	Q96M91	CCD11_HUMAN		STAD - Stomach adenocarcinoma(97;2.66e-05)|Colorectal(21;7.57e-05)|Lung(128;0.00932)|READ - Rectum adenocarcinoma(32;0.164)	8	1526	-			470						Missense_Mutation	SNP	ENST00000398545.4	37	c.1409G>A	CCDS11940.2	.	.	.	.	.	.	.	.	.	.	C	16.41	3.116355	0.56505	.	.	ENSG00000172361	ENST00000398545	T	0.10477	2.87	5.38	5.38	0.77491	.	0.129638	0.51477	D	0.000092	T	0.24967	0.0606	L	0.50333	1.59	0.36085	D	0.843068	D	0.89917	1.0	D	0.91635	0.999	T	0.07083	-1.0791	10	0.15066	T	0.55	-5.2134	14.9816	0.71316	0.0:1.0:0.0:0.0	.	470	Q96M91	CCD11_HUMAN	H	470	ENSP00000381553:R470H	ENSP00000381553:R470H	R	-	2	0	CCDC11	46007885	0.846000	0.29590	0.960000	0.40013	0.968000	0.65278	0.563000	0.23547	2.688000	0.91661	0.650000	0.86243	CGC		0.502	CCDC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255922.3			28	157	28	157	---	---	---	---
DNAJC28	54943	broad.mit.edu	37	21	34861298	34861298	+	Missense_Mutation	SNP	G	G	A			TCGA-HC-A632-01A-11D-A29Q-08	TCGA-HC-A632-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62488eee-4473-454e-89d3-7102d7c34977	c00991ab-7597-4eaf-9574-ef30295beeb9	g.chr21:34861298G>A	ENST00000314399.3	-	2	841	c.403C>T	c.(403-405)Cat>Tat	p.H135Y	DNAJC28_ENST00000381947.3_Missense_Mutation_p.H135Y|DNAJC28_ENST00000402202.1_Missense_Mutation_p.H135Y	NM_017833.3	NP_060303.2	Q9NX36	DJC28_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 28	135										endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(5)|skin(1)|urinary_tract(1)	18						CTTAAATAATGTCGGTGTTGG	0.403																																						ENST00000314399.3																			0				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(5)|skin(1)|urinary_tract(1)	18						c.(403-405)Cat>Tat		DnaJ (Hsp40) homolog, subfamily C, member 28							109.0	96.0	101.0					21																	34861298		2203	4300	6503	SO:0001583	missense	54943						heat shock protein binding	g.chr21:34861298G>A	AK000468	CCDS13626.1	21q22.11	2011-09-02	2008-06-17	2008-06-17	ENSG00000177692	ENSG00000177692		"""Heat shock proteins / DNAJ (HSP40)"""	1297	protein-coding gene	gene with protein product	"""Orf28"""		"""chromosome 21 open reading frame 55"""	C21orf55			Standard	NM_017833		Approved	C21orf78	uc002yrw.3	Q9NX36	OTTHUMG00000065531	ENST00000314399.3:c.403C>T	21.37:g.34861298G>A	ENSP00000320303:p.His135Tyr		Somatic				DNAJC28_ENST00000381947.3_Missense_Mutation_p.H135Y|DNAJC28_ENST00000402202.1_Missense_Mutation_p.H135Y	p.H135Y	NM_017833.3	NP_060303.2	WXS	Illumina GAIIx	Phase_I	Q9NX36	DJC28_HUMAN			2	841	-			135					D3DSF2	Missense_Mutation	SNP	ENST00000314399.3	37	c.403C>T	CCDS13626.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.976890	0.74360	.	.	ENSG00000177692	ENST00000381947;ENST00000314399;ENST00000402202	T;T;T	0.54866	0.55;0.55;0.55	5.38	5.38	0.77491	.	0.048758	0.85682	D	0.000000	T	0.73583	0.3605	M	0.83692	2.655	0.47183	D	0.999344	D	0.89917	1.0	D	0.66716	0.946	T	0.73078	-0.4096	10	0.33141	T	0.24	-13.9707	17.9044	0.88914	0.0:0.0:1.0:0.0	.	135	Q9NX36	DJC28_HUMAN	Y	135	ENSP00000371373:H135Y;ENSP00000320303:H135Y;ENSP00000385777:H135Y	ENSP00000320303:H135Y	H	-	1	0	DNAJC28	33783168	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.181000	0.94874	2.530000	0.85305	0.655000	0.94253	CAT		0.403	DNAJC28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140454.3			16	48	16	48	---	---	---	---
GGA1	26088	broad.mit.edu	37	22	38028487	38028487	+	Missense_Mutation	SNP	A	A	G			TCGA-HC-A632-01A-11D-A29Q-08	TCGA-HC-A632-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62488eee-4473-454e-89d3-7102d7c34977	c00991ab-7597-4eaf-9574-ef30295beeb9	g.chr22:38028487A>G	ENST00000343632.4	+	16	2160	c.1774A>G	c.(1774-1776)Atc>Gtc	p.I592V	GGA1_ENST00000406772.1_Missense_Mutation_p.I519V|GGA1_ENST00000325180.8_Missense_Mutation_p.I505V|GGA1_ENST00000381756.5_Missense_Mutation_p.I609V|GGA1_ENST00000337437.4_Missense_Mutation_p.I559V	NM_001172687.1|NM_013365.4	NP_001166158.1|NP_037497.1	Q9UJY5	GGA1_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 1	592	GAE. {ECO:0000255|PROSITE- ProRule:PRU00093}.				intracellular protein transport (GO:0006886)|positive regulation of protein catabolic process (GO:0045732)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|urinary_tract(1)	10	Melanoma(58;0.0574)					CCCCTCAGCAATCACCCAGGT	0.637																																						ENST00000406772.1																			0				breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|urinary_tract(1)	10						c.(1555-1557)Atc>Gtc		golgi-associated, gamma adaptin ear containing, ARF binding protein 1							125.0	113.0	117.0					22																	38028487		2203	4300	6503	SO:0001583	missense	26088				intracellular protein transport|vesicle-mediated transport	clathrin adaptor complex|endosome membrane|Golgi apparatus part	protein binding	g.chr22:38028487A>G	AF190862	CCDS13951.1, CCDS33643.1, CCDS54526.1	22q13.31	2010-02-12	2010-02-12		ENSG00000100083	ENSG00000100083			17842	protein-coding gene	gene with protein product		606004				10747088, 10747089, 16407204	Standard	NM_013365		Approved		uc003atc.3	Q9UJY5	OTTHUMG00000030985	ENST00000343632.4:c.1774A>G	22.37:g.38028487A>G	ENSP00000341344:p.Ile592Val		Somatic				GGA1_ENST00000337437.4_Missense_Mutation_p.I559V|GGA1_ENST00000343632.4_Missense_Mutation_p.I592V|GGA1_ENST00000325180.8_Missense_Mutation_p.I505V|GGA1_ENST00000381756.5_Missense_Mutation_p.I609V	p.I519V	NM_001172688.1	NP_001166159.1	WXS	Illumina GAIIx	Phase_I	Q9UJY5	GGA1_HUMAN			17	2207	+	Melanoma(58;0.0574)		592			GAE.		A8K3D3|B0QYR7|Q5TG07|Q86YA9|Q8NCS6|Q9BW94|Q9UG00|Q9UGW0|Q9UGW1	Missense_Mutation	SNP	ENST00000343632.4	37	c.1555A>G	CCDS13951.1	.	.	.	.	.	.	.	.	.	.	A	7.518	0.656092	0.14580	.	.	ENSG00000100083	ENST00000343632;ENST00000381756;ENST00000325180;ENST00000337437;ENST00000406772	T;T;T;T;T	0.45276	0.9;0.9;0.9;0.9;0.9	5.3	4.24	0.50183	Coatomer/clathrin adaptor appendage, Ig-like subdomain (1);Clathrin adaptor, gamma-adaptin, appendage (2);Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain (2);	0.114666	0.64402	D	0.000014	T	0.48978	0.1530	L	0.31157	0.91	0.80722	D	1	B;P;B	0.46656	0.025;0.882;0.025	B;D;B	0.68765	0.034;0.96;0.034	T	0.29427	-1.0012	10	0.22109	T	0.4	-30.363	12.151	0.54050	0.8566:0.1434:0.0:0.0	.	609;505;592	Q6IC75;Q86YA9;Q9UJY5	.;.;GGA1_HUMAN	V	592;609;505;559;519	ENSP00000341344:I592V;ENSP00000371175:I609V;ENSP00000321288:I505V;ENSP00000338647:I559V;ENSP00000385287:I519V	ENSP00000321288:I505V	I	+	1	0	GGA1	36358433	0.946000	0.32159	0.647000	0.29507	0.217000	0.24651	2.128000	0.42045	0.816000	0.34421	0.459000	0.35465	ATC		0.637	GGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075873.3	NM_013365		16	162	16	162	---	---	---	---
XG	7499	broad.mit.edu	37	X	2726251	2726251	+	Silent	SNP	C	C	T			TCGA-HC-A632-01A-11D-A29Q-08	TCGA-HC-A632-10A-01D-A29Q-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	62488eee-4473-454e-89d3-7102d7c34977	c00991ab-7597-4eaf-9574-ef30295beeb9	g.chrX:2726251C>T	ENST00000381174.5	+	8	624	c.399C>T	c.(397-399)ggC>ggT	p.G133G	XG_ENST00000419513.2_Silent_p.G148G|XG_ENST00000426774.1_Silent_p.G134G			P55808	XG_HUMAN	Xg blood group	133						integral component of plasma membrane (GO:0005887)				endometrium(1)|large_intestine(3)|lung(3)|ovary(1)	8		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				CAACGTATGGCAATCCAGAAG	0.493																																						ENST00000426774.1																			0				endometrium(1)|large_intestine(3)|lung(3)|ovary(1)	8						c.(400-402)ggC>ggT		Xg blood group							120.0	86.0	97.0					X																	2726251		2203	4298	6501	SO:0001819	synonymous_variant	7499					integral to membrane|plasma membrane		g.chrX:2726251C>T	AF380356	CCDS14120.1, CCDS48073.1	Xp22.32	2014-07-19	2006-01-12		ENSG00000124343	ENSG00000124343		"""Blood group antigens"", ""Pseudoautosomal regions / PAR1"""	12806	protein-coding gene	gene with protein product		300879	"""Xg blood group (pseudoautosomal boundary-divided on the X chromosome)"""	PBDX		8054981	Standard	NM_175569		Approved		uc004cqp.3	P55808	OTTHUMG00000021075	ENST00000381174.5:c.399C>T	X.37:g.2726251C>T			Somatic				XG_ENST00000419513.2_Silent_p.G148G|XG_ENST00000381174.5_Silent_p.G133G	p.G134G	NM_001141920.1|NM_175569.2	NP_001135392.1|NP_780778.1	WXS	Illumina GAIIx	Phase_I	P55808	XG_HUMAN			8	625	+		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)	133					E9PCH1|Q496N8|Q496N9|Q496P0|Q71BZ5	Silent	SNP	ENST00000381174.5	37	c.402C>T	CCDS14120.1																																																																																				0.493	XG-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055633.2	NM_175569		3	22	3	22	---	---	---	---
