#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
POLRMT	5442	broad.mit.edu	37	19	620015	620015	+	Silent	SNP	G	G	C			TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	4f280fa7-808c-445d-b173-cb9c2d2f3a96	g.chr19:620015G>C	ENST00000588649.2	-	12	2913	c.2829C>G	c.(2827-2829)tcC>tcG	p.S943S	AC005559.2_ENST00000591847.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	943	Mediates interaction with TEFM.				gene expression (GO:0010467)|transcription from mitochondrial promoter (GO:0006390)|transcription initiation from mitochondrial promoter (GO:0006391)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(3)|large_intestine(1)|lung(9)|ovary(1)|pancreas(2)|prostate(1)|stomach(1)	20		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCAGGTTGACGGAGGCGGCGC	0.697																																						ENST00000588649.2																			0				cervix(2)|endometrium(3)|large_intestine(1)|lung(9)|ovary(1)|pancreas(2)|prostate(1)|stomach(1)	20						c.(2827-2829)tcC>tcG		polymerase (RNA) mitochondrial (DNA directed)							11.0	12.0	12.0					19																	620015		2166	4264	6430	SO:0001819	synonymous_variant	5442				transcription initiation from mitochondrial promoter	mitochondrial nucleoid	DNA binding|DNA-directed RNA polymerase activity|protein binding	g.chr19:620015G>C		CCDS12036.1	19p13.3	2010-10-22			ENSG00000099821	ENSG00000099821	2.7.7.6		9200	protein-coding gene	gene with protein product		601778				9097968	Standard	NM_005035		Approved	h-mtRPOL, APOLMT, MTRNAP, MTRPOL	uc002lpf.1	O00411		ENST00000588649.2:c.2829C>G	19.37:g.620015G>C							p.S943S	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	12	2913	-		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)	943			Mediates interaction with TEFM.		O60370	Silent	SNP	ENST00000588649.2	37	c.2829C>G	CCDS12036.1																																																																																				0.697	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035		3	10	0	0	0	1	0	3	10				
FUT3	2525	broad.mit.edu	37	19	5844400	5844400	+	Missense_Mutation	SNP	T	T	C	rs417341	byFrequency	TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	4f280fa7-808c-445d-b173-cb9c2d2f3a96	g.chr19:5844400T>C	ENST00000303225.6	-	3	1085	c.451A>G	c.(451-453)Aga>Gga	p.R151G	FUT3_ENST00000593144.1_5'Flank|FUT3_ENST00000458379.2_Missense_Mutation_p.R151G|FUT3_ENST00000589620.1_Missense_Mutation_p.R151G|FUT3_ENST00000589918.1_Missense_Mutation_p.R151G	NM_000149.3	NP_000140	P21217	FUT3_HUMAN	fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group)	151					cell-cell recognition (GO:0009988)|fucosylation (GO:0036065)|macromolecule glycosylation (GO:0043413)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(1)	14						TTGAAGTATCTGTCCAGGGCT	0.642													T|||	11	0.00219649	0.0061	0.0014	5008	,	,		14700	0.002		0.0	False		,,,				2504	0.0				Esophageal Squamous(82;745 1728 24593 44831)	ENST00000303225.6																			0				breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(1)	14						c.(451-453)Aga>Gga		fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group)		T	GLY/ARG,GLY/ARG,GLY/ARG,GLY/ARG	35,4371	40.0+/-72.8	0,35,2168	68.0	62.0	64.0		451,451,451,451	-0.1	0.1	19	dbSNP_80	64	0,8600		0,0,4300	yes	missense,missense,missense,missense	FUT3	NM_000149.3,NM_001097639.1,NM_001097640.1,NM_001097641.1	125,125,125,125	0,35,6468	CC,CT,TT		0.0,0.7944,0.2691	benign,benign,benign,benign	151/362,151/362,151/362,151/362	5844400	35,12971	2203	4300	6503	SO:0001583	missense	2525				protein glycosylation	Golgi cisterna membrane|integral to membrane|membrane fraction	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity	g.chr19:5844400T>C		CCDS12153.1	19p13.3	2014-07-19	2006-01-12		ENSG00000171124	ENSG00000171124	2.4.1.65	"""CD molecules"", ""Blood group antigens"", ""Fucosyltransferases"""	4014	protein-coding gene	gene with protein product		111100	"""fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group included)"""	LE		1977660, 1740457	Standard	NM_000149		Approved	CD174	uc002mdk.2	P21217	OTTHUMG00000180614	ENST00000303225.6:c.451A>G	19.37:g.5844400T>C	ENSP00000305603:p.Arg151Gly					FUT3_ENST00000589918.1_Missense_Mutation_p.R151G|FUT3_ENST00000589620.1_Missense_Mutation_p.R151G|FUT3_ENST00000458379.2_Missense_Mutation_p.R151G	p.R151G	NM_000149.3	NP_000140.1	P21217	FUT3_HUMAN			3	1085	-			151					B5U7U9|B5U7V0|Q32NE7|Q99448|Q99449	Missense_Mutation	SNP	ENST00000303225.6	37	c.451A>G	CCDS12153.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	0	0.0	T	0.001	-3.133225	0.00030	0.007944	0.0	ENSG00000171124	ENST00000303225;ENST00000458379	T;T	0.25579	1.79;1.79	2.24	-0.0815	0.13702	.	0.613784	0.14038	N	0.345642	T	0.02047	0.0064	N	0.00054	-2.38	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.42498	-0.9448	10	0.06625	T	0.88	.	4.5324	0.12011	0.0:0.4765:0.0:0.5235	rs417341;rs2561801;rs417341	151;151;151;151	B3W6H0;A8K737;B3GVC1;P21217	.;.;.;FUT3_HUMAN	G	151	ENSP00000305603:R151G;ENSP00000416443:R151G	ENSP00000305603:R151G	R	-	1	2	FUT3	5795400	0.000000	0.05858	0.072000	0.20136	0.088000	0.18126	-0.920000	0.04013	0.208000	0.20626	-1.216000	0.01612	AGA		0.642	FUT3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452204.1	NM_000149		14	56	0	0	0	1	0	14	56				
CCDC105	126402	broad.mit.edu	37	19	15132292	15132292	+	Silent	SNP	C	C	T			TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	4f280fa7-808c-445d-b173-cb9c2d2f3a96	g.chr19:15132292C>T	ENST00000292574.3	+	4	1084	c.1002C>T	c.(1000-1002)gcC>gcT	p.A334A		NM_173482.2	NP_775753.2	Q8IYK2	CC105_HUMAN	coiled-coil domain containing 105	334						extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(4)|skin(2)	23						GTGTGTGTGCCTCGCTGGCGC	0.622																																						ENST00000292574.3																			0				NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(4)|skin(2)	23						c.(1000-1002)gcC>gcT		coiled-coil domain containing 105							98.0	67.0	78.0					19																	15132292		2203	4300	6503	SO:0001819	synonymous_variant	126402				microtubule cytoskeleton organization	microtubule		g.chr19:15132292C>T	AK097684	CCDS12322.1	19p13.12	2008-02-05				ENSG00000160994			26866	protein-coding gene	gene with protein product						12477932	Standard	NM_173482		Approved	FLJ40365	uc002nae.2	Q8IYK2		ENST00000292574.3:c.1002C>T	19.37:g.15132292C>T							p.A334A	NM_173482.2	NP_775753.2	Q8IYK2	CC105_HUMAN			4	1084	+			334					Q8N7T5|Q8NDL5	Silent	SNP	ENST00000292574.3	37	c.1002C>T	CCDS12322.1																																																																																				0.622	CCDC105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466293.1	NM_173482		3	30	0	0	0	1	0	3	30				
GRAMD2	196996	broad.mit.edu	37	15	72454662	72454662	+	Missense_Mutation	SNP	T	T	C			TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	4f280fa7-808c-445d-b173-cb9c2d2f3a96	g.chr15:72454662T>C	ENST00000309731.7	-	11	1026	c.1013A>G	c.(1012-1014)gAg>gGg	p.E338G	GRAMD2_ENST00000564184.1_5'Flank	NM_001012642.2	NP_001012660.1	Q8IUY3	GRAM2_HUMAN	GRAM domain containing 2	338						integral component of membrane (GO:0016021)				cervix(2)|endometrium(1)|large_intestine(4)|lung(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	13						TAACTGCTGCTCTAGCCGAGA	0.488																																						ENST00000309731.7																			0				cervix(2)|endometrium(1)|large_intestine(4)|lung(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	13						c.(1012-1014)gAg>gGg		GRAM domain containing 2							87.0	80.0	83.0					15																	72454662		2199	4297	6496	SO:0001583	missense	196996					integral to membrane		g.chr15:72454662T>C	AK002016	CCDS32283.1	15q23	2006-11-29	2005-11-03	2005-11-03					27287	protein-coding gene	gene with protein product						12477932	Standard	NM_001012642		Approved		uc002atq.3	Q8IUY3		ENST00000309731.7:c.1013A>G	15.37:g.72454662T>C	ENSP00000311657:p.Glu338Gly						p.E338G	NM_001012642.2	NP_001012660.1	Q8IUY3	GRAM2_HUMAN			11	1026	-			338					B3KT68	Missense_Mutation	SNP	ENST00000309731.7	37	c.1013A>G	CCDS32283.1	.	.	.	.	.	.	.	.	.	.	T	19.65	3.866427	0.72065	.	.	ENSG00000175318	ENST00000309731	T	0.69040	-0.37	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.78710	0.4326	L	0.61218	1.895	0.51482	D	0.999923	D	0.89917	1.0	D	0.87578	0.998	T	0.80913	-0.1170	10	0.87932	D	0	.	12.5847	0.56410	0.0:0.0:0.0:1.0	.	338	Q8IUY3	GRAM2_HUMAN	G	338	ENSP00000311657:E338G	ENSP00000311657:E338G	E	-	2	0	GRAMD2	70241716	1.000000	0.71417	0.956000	0.39512	0.435000	0.31806	6.284000	0.72652	1.983000	0.57843	0.460000	0.39030	GAG		0.488	GRAMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420040.1	NM_001012642		11	33	0	0	0	1	0	11	33				
TG	7038	broad.mit.edu	37	8	133919035	133919035	+	Missense_Mutation	SNP	A	A	C			TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	4f280fa7-808c-445d-b173-cb9c2d2f3a96	g.chr8:133919035A>C	ENST00000220616.4	+	17	3777	c.3737A>C	c.(3736-3738)cAa>cCa	p.Q1246P	TG_ENST00000377869.1_Missense_Mutation_p.Q1246P	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1246					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		CAGCAGTGCCAATTGCTGTGC	0.632																																						ENST00000220616.4																			0				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168						c.(3736-3738)cAa>cCa		thyroglobulin							65.0	56.0	59.0					8																	133919035		2203	4300	6503	SO:0001583	missense	7038				hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity	g.chr8:133919035A>C	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.3737A>C	8.37:g.133919035A>C	ENSP00000220616:p.Gln1246Pro					TG_ENST00000377869.1_Missense_Mutation_p.Q1246P	p.Q1246P	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)	17	3777	+	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	1246					O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	c.3737A>C	CCDS34944.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.899|9.899	1.206274|1.206274	0.22205|0.22205	.|.	.|.	ENSG00000042832|ENSG00000042832	ENST00000518505|ENST00000377869;ENST00000543313;ENST00000220616	.|T;T	.|0.65549	.|-0.16;-0.15	5.48|5.48	-4.43|-4.43	0.03568|0.03568	.|.	.|0.542430	.|0.17260	.|N	.|0.180827	T|T	0.46964|0.46964	0.1420|0.1420	L|L	0.59436|0.59436	1.845|1.845	0.24681|0.24681	N|N	0.99337|0.99337	.|P	.|0.37955	.|0.612	.|B	.|0.34722	.|0.188	T|T	0.42464|0.42464	-0.9450|-0.9450	5|10	.|0.87932	.|D	.|0	.|.	4.713|4.713	0.12882|0.12882	0.3416:0.0:0.3927:0.2657|0.3416:0.0:0.3927:0.2657	.|.	.|1246	.|P01266	.|THYG_HUMAN	H|P	190|1246;52;1246	.|ENSP00000367100:Q1246P;ENSP00000220616:Q1246P	.|ENSP00000220616:Q1246P	N|Q	+|+	1|2	0|0	TG|TG	133988217|133988217	0.054000|0.054000	0.20591|0.20591	0.872000|0.872000	0.34217|0.34217	0.033000|0.033000	0.12548|0.12548	-0.627000|-0.627000	0.05521|0.05521	-0.851000|-0.851000	0.04147|0.04147	-1.054000|-1.054000	0.02325|0.02325	AAT|CAA		0.632	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		10	28	0	0	0	1	0	10	28				
SPECC1	92521	broad.mit.edu	37	17	20013740	20013740	+	Splice_Site	SNP	C	C	A			TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	4f280fa7-808c-445d-b173-cb9c2d2f3a96	g.chr17:20013740C>A	ENST00000261503.5	+	3	199	c.148C>A	c.(148-150)Ctc>Atc	p.L50I	SPECC1_ENST00000395527.4_Splice_Site_p.L50I|SPECC1_ENST00000395529.3_Splice_Site_p.L50I|SPECC1_ENST00000472876.1_Intron	NM_001033553.2	NP_001028725.1	Q5M775	CYTSB_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1	50					cell adhesion (GO:0007155)	nucleus (GO:0005634)				breast(1)|large_intestine(3)|ovary(4)	8				KIRC - Kidney renal clear cell carcinoma(2;0.166)|Kidney(2;0.196)		ACTCTCTCAGCTCAAGAGGGC	0.572																																						ENST00000395529.3																			0				breast(1)|large_intestine(3)|ovary(4)	8						c.e3-1		sperm antigen with calponin homology and coiled-coil domains 1							90.0	92.0	92.0					17																	20013740		2203	4300	6503	SO:0001630	splice_region_variant	92521					nucleus		g.chr17:20013740C>A	AY816329, AB041533	CCDS32590.1, CCDS42280.1, CCDS42281.1, CCDS45628.1, CCDS58531.1	17p11.2	2012-11-19	2010-09-17	2010-09-17	ENSG00000128487	ENSG00000128487			30615	protein-coding gene	gene with protein product	"""sperm antigen HCMOGT 1"", ""cytokinesis and spindle organization B"", ""cytospin B"""	608793				15602574, 18763323, 15087372	Standard	NM_001033553		Approved	HCMOGT-1, FLJ36955, NSP, CYTSB	uc002gwq.3	Q5M775	OTTHUMG00000179808	ENST00000261503.5:c.148-1C>A	17.37:g.20013740C>A						SPECC1_ENST00000261503.5_Splice_Site_p.L50_splice|SPECC1_ENST00000472876.1_Intron|SPECC1_ENST00000395527.4_Splice_Site_p.L50_splice	p.L50_splice	NM_152904.4	NP_690868.3	Q5M775	CYTSB_HUMAN		KIRC - Kidney renal clear cell carcinoma(2;0.166)|Kidney(2;0.196)	3	200	+			50					B4DHH0|B7WNS8|Q5IBP1|Q5IBP2|Q5IBP3|Q5IBP4|Q5M772|Q5M773|Q5M774|Q86XT8|Q8N4U4|Q8WU84|Q9HCQ3	Splice_Site	SNP	ENST00000261503.5	37	c.147_splice	CCDS32590.1	.	.	.	.	.	.	.	.	.	.	C	17.03	3.284741	0.59867	.	.	ENSG00000128487	ENST00000395530;ENST00000413167;ENST00000261503;ENST00000395529	T;T	0.65916	-0.18;2.8	5.29	5.29	0.74685	.	0.092570	0.44688	D	0.000425	T	0.72732	0.3497	L	0.43152	1.355	0.80722	D	1	D;P	0.71674	0.998;0.825	D;B	0.83275	0.996;0.299	T	0.70004	-0.4991	9	.	.	.	-12.3568	16.802	0.85617	0.0:1.0:0.0:0.0	.	50;50	Q5M775-2;Q5M775	.;CYTSB_HUMAN	I	50	ENSP00000261503:L50I;ENSP00000378900:L50I	.	L	+	1	0	SPECC1	19954332	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	4.763000	0.62257	2.647000	0.89833	0.655000	0.94253	CTC		0.572	SPECC1-018	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441206.1	NM_152904	Missense_Mutation	17	51	1	0	1.33834e-09	1	1.44129e-09	17	51				
FRG1B	284802	broad.mit.edu	37	20	29625955	29625955	+	Nonsense_Mutation	SNP	A	A	T			TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	4f280fa7-808c-445d-b173-cb9c2d2f3a96	g.chr20:29625955A>T	ENST00000278882.3	+	5	579	c.199A>T	c.(199-201)Aga>Tga	p.R67*	FRG1B_ENST00000358464.4_Nonsense_Mutation_p.R67*|FRG1B_ENST00000439954.2_Nonsense_Mutation_p.R72*			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	67										endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						AATTGGACCAAGAGAACAATG	0.338																																						ENST00000278882.3																			0				endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						c.(199-201)Aga>Tga																																						SO:0001587	stop_gained	0							g.chr20:29625955A>T			20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531			15792	other	unknown			"""chromosome 20 open reading frame 80"""	C20orf80			Standard	NR_003579		Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.199A>T	20.37:g.29625955A>T	ENSP00000278882:p.Arg67*					FRG1B_ENST00000358464.4_Nonsense_Mutation_p.R67*|FRG1B_ENST00000439954.2_Nonsense_Mutation_p.R72*	p.R67*							5	579	+								C4AME5	Nonsense_Mutation	SNP	ENST00000278882.3	37	c.199A>T		.	.	.	.	.	.	.	.	.	.	a	29.6	5.022161	0.93462	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	.	.	.	1.68	1.68	0.24146	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	.	7.3757	0.26827	1.0:0.0:0.0:0.0	.	.	.	.	X	67;72;67	.	ENSP00000278882:R67X	R	+	1	2	FRG1B	28239616	1.000000	0.71417	1.000000	0.80357	0.120000	0.20174	3.670000	0.54569	1.028000	0.39785	0.155000	0.16302	AGA		0.338	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078494.2	NR_003579		3	25	0	0	0	1	0	3	25				
NRAS	4893	broad.mit.edu	37	1	115256529	115256529	+	Missense_Mutation	SNP	T	T	C	rs11554290	byFrequency	TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	4f280fa7-808c-445d-b173-cb9c2d2f3a96	g.chr1:115256529T>C	ENST00000369535.4	-	3	435	c.182A>G	c.(181-183)cAa>cGa	p.Q61R		NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	61			Q -> K (in CMNS and NCMS; somatic mutation). {ECO:0000269|PubMed:23392294}.|Q -> R (in CMNS, NCMS and KNEN; also found in lung carcinoma cell and melanoma; dbSNP:rs11554290). {ECO:0000269|PubMed:18633438, ECO:0000269|PubMed:22499344, ECO:0000269|PubMed:23392294, ECO:0000269|PubMed:3276402}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.Q61R(817)|p.Q61L(175)|p.Q61P(23)|p.Q61K(1)		NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTACTCTTCTTGTCCAGCTGT	0.458	Q61L(C3A_LIVER)|Q61L(HEPG2_LIVER)|Q61L(HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(IPC298_SKIN)|Q61L(KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(MELJUSO_SKIN)|Q61L(MHHES1_BONE)|Q61L(MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61P(TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(HT1197_URINARY_TRACT)|Q61R(KMS27_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(KU1919_URINARY_TRACT)|Q61R(NCIH2347_LUNG)|Q61R(ONS76_CENTRAL_NERVOUS_SYSTEM)|Q61R(SKMEL2_SKIN)|Q61R(SW1271_LUNG)|Q61R(TT2609C02_THYROID)	50	Mis		"""melanoma, MM, AML, thyroid"""				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																												ENST00000369535.4	Q61L(C3A_LIVER)|Q61L(HEPG2_LIVER)|Q61L(HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(IPC298_SKIN)|Q61L(KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(MELJUSO_SKIN)|Q61L(MHHES1_BONE)|Q61L(MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61P(TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(HT1197_URINARY_TRACT)|Q61R(KMS27_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(KU1919_URINARY_TRACT)|Q61R(NCIH2347_LUNG)|Q61R(ONS76_CENTRAL_NERVOUS_SYSTEM)|Q61R(SKMEL2_SKIN)|Q61R(SW1271_LUNG)|Q61R(TT2609C02_THYROID)	50		Dom	yes		1	1p13.2	4893	Mis	neuroblastoma RAS viral (v-ras) oncogene homolog			"""L, E"""			"""melanoma, MM, AML, thyroid"""		1016	Substitution - Missense(1016)	p.Q61R(817)|p.Q61L(175)|p.Q61P(23)|p.Q61K(1)	skin(466)|thyroid(279)|haematopoietic_and_lymphoid_tissue(124)|NS(50)|large_intestine(27)|lung(17)|urinary_tract(11)|adrenal_gland(7)|liver(7)|breast(7)|soft_tissue(4)|testis(3)|endometrium(3)|ovary(3)|central_nervous_system(2)|pancreas(2)|eye(1)|prostate(1)|meninges(1)|autonomic_ganglia(1)	NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085						c.(181-183)cAa>cGa		neuroblastoma RAS viral (v-ras) oncogene homolog							180.0	156.0	164.0					1																	115256529		2203	4300	6503	SO:0001583	missense	4893	Noonan syndrome	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	Golgi membrane|plasma membrane	GTP binding|GTPase activity	g.chr1:115256529T>C	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.182A>G	1.37:g.115256529T>C	ENSP00000358548:p.Gln61Arg	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)					p.Q61R	NM_002524.4	NP_002515.1	P01111	RASN_HUMAN		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	3	435	-	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)	61		Q -> K (in neuroblastoma cell).|Q -> R (in lung carcinoma cell and melanoma; dbSNP:rs11554290).			Q14971|Q15104|Q15282	Missense_Mutation	SNP	ENST00000369535.4	37	c.182A>G	CCDS877.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.004139	0.74932	.	.	ENSG00000213281	ENST00000369535	D	0.83673	-1.75	5.08	5.08	0.68730	Small GTP-binding protein domain (1);	0.000000	0.53938	U	0.000043	D	0.86489	0.5945	M	0.92604	3.325	0.80722	D	1	B	0.28512	0.214	B	0.39590	0.304	D	0.88255	0.2919	10	0.66056	D	0.02	.	15.0132	0.71565	0.0:0.0:0.0:1.0	rs11554290;rs11554290	61	P01111	RASN_HUMAN	R	61	ENSP00000358548:Q61R	ENSP00000358548:Q61R	Q	-	2	0	NRAS	115058052	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.761000	0.85260	2.120000	0.65058	0.533000	0.62120	CAA		0.458	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033395.2	NM_002524		31	46	0	0	0	1	0	31	46				
PHLPP2	23035	broad.mit.edu	37	16	71682911	71682911	+	Missense_Mutation	SNP	T	T	C	rs149705576		TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	4f280fa7-808c-445d-b173-cb9c2d2f3a96	g.chr16:71682911T>C	ENST00000568954.1	-	19	4232	c.3854A>G	c.(3853-3855)cAt>cGt	p.H1285R	PHLPP2_ENST00000393524.2_Missense_Mutation_p.H1218R|PHLPP2_ENST00000567016.1_Missense_Mutation_p.H1320R|PHLPP2_ENST00000540628.1_Intron|PHLPP2_ENST00000360429.3_Intron|PHLPP2_ENST00000356272.3_Missense_Mutation_p.H1285R			Q6ZVD8	PHLP2_HUMAN	PH domain and leucine rich repeat protein phosphatase 2	1285					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)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment membrane (GO:0042622)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(7)|lung(15)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37						TTCCAGGTCATGAGGCACAAC	0.552																																						ENST00000393524.2																			0				central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(7)|lung(15)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37						c.(3652-3654)cAt>cGt		PH domain and leucine rich repeat protein phosphatase 2		T	ARG/HIS	0,4396		0,0,2198	106.0	96.0	99.0		3854	4.1	1.0	16	dbSNP_134	99	1,8599	1.2+/-3.3	0,1,4299	no	missense	PHLPP2	NM_015020.2	29	0,1,6497	CC,CT,TT		0.0116,0.0,0.0077	benign	1285/1324	71682911	1,12995	2198	4300	6498	SO:0001583	missense	23035					cytoplasm|membrane|nucleus	metal ion binding|phosphoprotein phosphatase activity	g.chr16:71682911T>C	BX647823	CCDS32479.1, CCDS73910.1	16q22.2	2013-01-11	2009-05-26	2009-05-26	ENSG00000040199	ENSG00000040199		"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"", ""Pleckstrin homology (PH) domain containing"""	29149	protein-coding gene	gene with protein product		611066	"""PH domain and leucine rich repeat protein phosphatase-like"""	PHLPPL		17386267	Standard	NM_001289003		Approved	KIAA0931	uc002fax.3	Q6ZVD8		ENST00000568954.1:c.3854A>G	16.37:g.71682911T>C	ENSP00000457991:p.His1285Arg					PHLPP2_ENST00000568954.1_Missense_Mutation_p.H1285R|PHLPP2_ENST00000567016.1_Missense_Mutation_p.H1320R|PHLPP2_ENST00000360429.3_Intron|PHLPP2_ENST00000356272.3_Missense_Mutation_p.H1285R|PHLPP2_ENST00000540628.1_Intron	p.H1218R			Q6ZVD8	PHLP2_HUMAN			17	4386	-			1285					A1L374|Q9NV17|Q9Y2E3	Missense_Mutation	SNP	ENST00000568954.1	37	c.3653A>G	CCDS32479.1	.	.	.	.	.	.	.	.	.	.	t	1.818	-0.473037	0.04445	0.0	1.16E-4	ENSG00000040199	ENST00000356272;ENST00000393524	T;T	0.39787	1.6;1.06	6.17	4.07	0.47477	.	0.203454	0.52532	N	0.000073	T	0.21062	0.0507	N	0.16478	0.41	0.22199	N	0.999296	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.13361	-1.0512	10	0.14656	T	0.56	-11.2858	5.0812	0.14656	0.0:0.491:0.3004:0.2086	.	1218;1285	Q6ZVD8-3;Q6ZVD8	.;PHLP2_HUMAN	R	1285;1218	ENSP00000348611:H1285R;ENSP00000377159:H1218R	ENSP00000348611:H1285R	H	-	2	0	PHLPP2	70240412	0.999000	0.42202	1.000000	0.80357	0.892000	0.51952	2.880000	0.48530	1.631000	0.50456	-0.140000	0.14226	CAT		0.552	PHLPP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000434139.1	NM_015020		5	51	0	0	0	1	0	5	51				
ZNF814	730051	broad.mit.edu	37	19	58385762	58385762	+	Silent	SNP	C	C	G	rs199732634		TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	4f280fa7-808c-445d-b173-cb9c2d2f3a96	g.chr19:58385762C>G	ENST00000435989.2	-	3	1230	c.996G>C	c.(994-996)tcG>tcC	p.S332S	ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597832.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	332					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S332S(2)		NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						ATTTGCTAAACGATTTCCCAC	0.358																																						ENST00000435989.2																			2	Substitution - coding silent(2)	p.S332S(2)	kidney(2)	NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						c.(994-996)tcG>tcC		zinc finger protein 814							25.0	25.0	25.0					19																	58385762		692	1589	2281	SO:0001819	synonymous_variant	730051				regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding	g.chr19:58385762C>G		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"""Zinc fingers, C2H2-type"", ""-"""	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.996G>C	19.37:g.58385762C>G						ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597832.1_Intron	p.S332S	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN			3	1230	-			332					A6NF35	Silent	SNP	ENST00000435989.2	37	c.996G>C	CCDS46212.1																																																																																				0.358	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		2	1	0	0	0	1	0	2	1				
ZMIZ2	83637	broad.mit.edu	37	7	44801338	44801338	+	Missense_Mutation	SNP	G	G	A			TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	4f280fa7-808c-445d-b173-cb9c2d2f3a96	g.chr7:44801338G>A	ENST00000309315.4	+	11	1553	c.1430G>A	c.(1429-1431)cGg>cAg	p.R477Q	ZMIZ2_ENST00000265346.7_Missense_Mutation_p.R451Q|ZMIZ2_ENST00000413916.1_Missense_Mutation_p.R419Q|ZMIZ2_ENST00000441627.1_Missense_Mutation_p.R477Q|ZMIZ2_ENST00000433667.1_Missense_Mutation_p.R445Q	NM_031449.3	NP_113637.3	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2	477	Interaction with AR.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						CACGAGGACCGGCAGATGAAC	0.612																																					NSCLC(20;604 852 1948 16908 50522)	ENST00000309315.4																			0				breast(3)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						c.(1429-1431)cGg>cAg		zinc finger, MIZ-type containing 2							57.0	61.0	60.0					7																	44801338		2203	4300	6503	SO:0001583	missense	83637				positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear replication fork	ligand-dependent nuclear receptor transcription coactivator activity|protein binding|zinc ion binding	g.chr7:44801338G>A	AK090415	CCDS43576.1, CCDS43577.1, CCDS75591.1	7p13	2009-11-06			ENSG00000122515	ENSG00000122515		"""Zinc fingers, MIZ-type"""	22229	protein-coding gene	gene with protein product		611196					Standard	XM_005249866		Approved	KIAA1886, hZIMP7, ZIMP7, DKFZp761I2123, NET27	uc003tlr.3	Q8NF64	OTTHUMG00000155817	ENST00000309315.4:c.1430G>A	7.37:g.44801338G>A	ENSP00000311778:p.Arg477Gln					ZMIZ2_ENST00000441627.1_Missense_Mutation_p.R477Q|ZMIZ2_ENST00000433667.1_Missense_Mutation_p.R445Q|ZMIZ2_ENST00000413916.1_Missense_Mutation_p.R419Q|ZMIZ2_ENST00000265346.7_Missense_Mutation_p.R451Q	p.R477Q	NM_031449.3	NP_113637.3	Q8NF64	ZMIZ2_HUMAN			11	1553	+			477			Interaction with AR.		A4D2K7|D3DVL1|O94790|Q0VGB4|Q659A8|Q6JKL5|Q8WTX8|Q96Q01|Q9BQH7	Missense_Mutation	SNP	ENST00000309315.4	37	c.1430G>A	CCDS43576.1	.	.	.	.	.	.	.	.	.	.	G	37	6.209731	0.97380	.	.	ENSG00000122515	ENST00000413916;ENST00000309315;ENST00000441627;ENST00000433667;ENST00000265346;ENST00000414051	T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02	4.73	4.73	0.59995	.	0.000000	0.56097	D	0.000039	T	0.63954	0.2555	M	0.72894	2.215	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.76071	0.987;0.966;0.987	T	0.64659	-0.6355	10	0.44086	T	0.13	-16.8339	17.4928	0.87709	0.0:0.0:1.0:0.0	.	451;477;419	Q8NF64-2;Q8NF64;Q8NF64-3	.;ZMIZ2_HUMAN;.	Q	419;477;477;445;451;477	ENSP00000409648:R419Q;ENSP00000311778:R477Q;ENSP00000414723:R477Q;ENSP00000396601:R445Q;ENSP00000265346:R451Q	ENSP00000265346:R451Q	R	+	2	0	ZMIZ2	44767863	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.131000	0.94446	2.444000	0.82710	0.655000	0.94253	CGG		0.612	ZMIZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341790.1	NM_031449		16	17	0	0	0	1	0	16	17				
PCDHA6	56142	broad.mit.edu	37	5	140209392	140209392	+	Silent	SNP	T	T	C	rs146736705	byFrequency	TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	4f280fa7-808c-445d-b173-cb9c2d2f3a96	g.chr5:140209392T>C	ENST00000529310.1	+	1	1830	c.1716T>C	c.(1714-1716)ggT>ggC	p.G572G	PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	572					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGGTGGGTGGTACTGGTGGTG	0.687													.|||	9	0.00179712	0.0	0.0072	5008	,	,		16079	0.0		0.004	False		,,,				2504	0.0					ENST00000529310.1																			0				NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89						c.(1714-1716)ggT>ggC				T	,,,,,,,,	3,4403	8.1+/-20.4	0,3,2200	74.0	78.0	77.0		,,,,,1716,,1716,	-7.4	0.0	5	dbSNP_134	77	34,8564	23.4+/-69.3	0,34,4265	no	intron,intron,intron,intron,intron,coding-synonymous,intron,coding-synonymous,intron	PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_031411.1,NM_031848.1,NM_031849.1	,,,,,,,,	0,37,6465	CC,CT,TT		0.3954,0.0681,0.2845	,,,,,,,,	,,,,,572/951,,572/804,	140209392	37,12967	2203	4299	6502	SO:0001819	synonymous_variant	0							g.chr5:140209392T>C	AF152484	CCDS47281.1, CCDS47282.1	5q31	2010-11-26			ENSG00000081842	ENSG00000081842		"""Cadherins / Protocadherins : Clustered"""	8672	other	complex locus constituent	"""KIAA0345-like 8"""	606312		CNRS2		10380929, 10662547	Standard	NM_018909		Approved	CNR2, CRNR2, PCDH-ALPHA6		Q9UN73	OTTHUMG00000163353	ENST00000529310.1:c.1716T>C	5.37:g.140209392T>C						PCDHA1_ENST00000504120.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000512229.2_Intron	p.G572G	NM_018909.2|NM_031848.1|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		1	1830	+								O75283|Q9NRT8	Silent	SNP	ENST00000529310.1	37	c.1716T>C	CCDS47281.1																																																																																				0.687	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909		6	100	0	0	0	1	0	6	100				
SLC6A13	6540	broad.mit.edu	37	12	368928	368928	+	Intron	SNP	T	T	C	rs148217969	byFrequency	TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	4f280fa7-808c-445d-b173-cb9c2d2f3a96	g.chr12:368928T>C	ENST00000343164.4	-	2	255				RP11-283I3.4_ENST00000540868.1_RNA|SLC6A13_ENST00000436453.1_Silent_p.P97P|SLC6A13_ENST00000445055.2_Intron	NM_016615.4	NP_057699.2	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 13						neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(1)	28	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)			tatacatctatgGGACTCCCC	0.522													T|||	19	0.00379393	0.0113	0.0	5008	,	,		20126	0.0		0.004	False		,,,				2504	0.0					ENST00000436453.1																			0				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(1)	28						c.(289-291)ccA>ccG		solute carrier family 6 (neurotransmitter transporter), member 13																																				SO:0001627	intron_variant	6540				neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity	g.chr12:368928T>C	U76343	CCDS8502.1, CCDS53729.1, CCDS58198.1	12p13.33	2013-07-19	2013-07-19		ENSG00000010379	ENSG00000010379		"""Solute carriers"""	11046	protein-coding gene	gene with protein product	"""GABA transporter 2"""	615097	"""solute carrier family 6 (neurotransmitter transporter, GABA), member 13"""				Standard	NM_001243392		Approved	GAT2	uc001qic.2	Q9NSD5	OTTHUMG00000168053	ENST00000343164.4:c.202+88A>G	12.37:g.368928T>C						SLC6A13_ENST00000445055.2_Intron|SLC6A13_ENST00000343164.4_Intron	p.P97P	NM_001243392.1	NP_001230321.1	Q9NSD5	S6A13_HUMAN	OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)		2	343	-	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		0					B4DJL1|Q8TCC2|Q8WW56	Silent	SNP	ENST00000343164.4	37	c.291A>G	CCDS8502.1																																																																																				0.522	SLC6A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397801.1	NM_016615		3	16	0	0	0	1	0	3	16				
CD93	22918	broad.mit.edu	37	20	23065236	23065236	+	Missense_Mutation	SNP	G	G	C	rs372540092		TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	4f280fa7-808c-445d-b173-cb9c2d2f3a96	g.chr20:23065236G>C	ENST00000246006.4	-	1	1741	c.1594C>G	c.(1594-1596)Ctc>Gtc	p.L532V		NM_012072.3	NP_036204.2	Q9NPY3	C1QR1_HUMAN	CD93 molecule	532					macrophage activation (GO:0042116)|phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|complement component C1q binding (GO:0001849)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	39	Colorectal(13;0.0352)|Lung NSC(19;0.0542)|all_lung(19;0.118)					AGCATCTTGAGTGGGGCAGAT	0.662																																						ENST00000246006.4																			0				NS(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						c.(1594-1596)Ctc>Gtc		CD93 molecule							45.0	52.0	50.0					20																	23065236		2203	4300	6503	SO:0001583	missense	22918				cell-cell adhesion|interspecies interaction between organisms|macrophage activation|phagocytosis	plasma membrane	calcium ion binding|complement component C1q binding|receptor activity|sugar binding	g.chr20:23065236G>C	U94333	CCDS13149.1	20p11.21	2009-01-29	2006-03-28	2006-02-22	ENSG00000125810	ENSG00000125810		"""CD molecules"""	15855	protein-coding gene	gene with protein product		120577	"""matrix-remodelling associated 4"", ""complement component 1, q subcomponent, receptor 1"", ""CD93 antigen"""	MXRA4, C1QR1		9047234, 10648005	Standard	NM_012072		Approved	C1qRP, C1qR(P), dJ737E23.1, CDw93, ECSM3	uc002wsv.3	Q9NPY3	OTTHUMG00000032058	ENST00000246006.4:c.1594C>G	20.37:g.23065236G>C	ENSP00000246006:p.Leu532Val						p.L532V	NM_012072.3	NP_036204.2	Q9NPY3	C1QR1_HUMAN			1	1741	-	Colorectal(13;0.0352)|Lung NSC(19;0.0542)|all_lung(19;0.118)		532					O00274	Missense_Mutation	SNP	ENST00000246006.4	37	c.1594C>G	CCDS13149.1	.	.	.	.	.	.	.	.	.	.	G	3.681	-0.065621	0.07273	.	.	ENSG00000125810	ENST00000246006	T	0.80214	-1.35	5.59	1.36	0.22044	.	1.037860	0.07629	N	0.928371	T	0.66886	0.2835	L	0.34521	1.04	0.09310	N	1	B	0.20887	0.049	B	0.16722	0.016	T	0.48186	-0.9057	10	0.13853	T	0.58	-1.8619	4.7572	0.13090	0.2105:0.0:0.5355:0.2541	.	532	Q9NPY3	C1QR1_HUMAN	V	532	ENSP00000246006:L532V	ENSP00000246006:L532V	L	-	1	0	CD93	23013236	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.277000	0.18734	0.299000	0.22661	-0.137000	0.14449	CTC		0.662	CD93-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078312.2	NM_012072		21	59	0	0	0	1	0	21	59				
EEF1A1	1915	broad.mit.edu	37	6	74228523	74228523	+	Missense_Mutation	SNP	T	T	C			TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	4f280fa7-808c-445d-b173-cb9c2d2f3a96	g.chr6:74228523T>C	ENST00000316292.9	-	4	1661	c.670A>G	c.(670-672)Agt>Ggt	p.S224G	EEF1A1_ENST00000491404.1_Intron|EEF1A1_ENST00000331523.2_Missense_Mutation_p.S224G|EEF1A1_ENST00000309268.6_Missense_Mutation_p.S224G	NM_001402.5	NP_001393.1	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha 1	224	tr-type G.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation elongation factor activity (GO:0003746)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(6)|prostate(2)|skin(3)	18						GTGGTTCCACTGGCATTGCCA	0.517											OREG0003891|OREG0003895	type=REGULATORY REGION|Gene=D16891|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay|type=REGULATORY REGION|Gene=EEF1A1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																										ENST00000316292.9																			0				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(6)|prostate(2)|skin(3)	18						c.(670-672)Agt>Ggt		eukaryotic translation elongation factor 1 alpha 1							105.0	97.0	99.0					6																	74228523		2203	4297	6500	SO:0001583	missense	1915					cytosol|eukaryotic translation elongation factor 1 complex	GTP binding|GTPase activity|protein binding|translation elongation factor activity	g.chr6:74228523T>C	BC019669	CCDS4980.1	6q14.1	2010-06-30	2004-11-19		ENSG00000156508	ENSG00000156508			3189	protein-coding gene	gene with protein product		130590	"""leukocyte receptor cluster (LRC) member 7"""	EF1A, EEF1A, LENG7		8812466, 10941842	Standard	NM_001402		Approved	EE1A1	uc003phj.3	P68104	OTTHUMG00000015031	ENST00000316292.9:c.670A>G	6.37:g.74228523T>C	ENSP00000339063:p.Ser224Gly		OREG0003891|OREG0003895	type=REGULATORY REGION|Gene=D16891|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay|type=REGULATORY REGION|Gene=EEF1A1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	1151	EEF1A1_ENST00000309268.6_Missense_Mutation_p.S224G|EEF1A1_ENST00000331523.2_Missense_Mutation_p.S224G|EEF1A1_ENST00000491404.1_Intron	p.S224G	NM_001402.5	NP_001393.1	P68104	EF1A1_HUMAN			4	1661	-			224					P04719|P04720|Q6IQ15	Missense_Mutation	SNP	ENST00000316292.9	37	c.670A>G	CCDS4980.1	.	.	.	.	.	.	.	.	.	.	T	13.24	2.177470	0.38413	.	.	ENSG00000156508	ENST00000316292;ENST00000358190;ENST00000309268;ENST00000331523;ENST00000391977	T;T;T	0.46063	0.88;0.88;0.88	4.31	4.31	0.51392	Protein synthesis factor, GTP-binding (2);	0.264000	0.36374	U	0.002624	T	0.18964	0.0455	L	0.31664	0.95	0.53005	D	0.99996	B;B;B;B	0.09022	0.001;0.002;0.001;0.002	B;B;B;B	0.06405	0.001;0.001;0.001;0.002	T	0.09037	-1.0693	10	0.62326	D	0.03	.	13.8286	0.63366	0.0:0.0:0.0:1.0	.	224;224;224;224	P68104;Q53HR5;Q6IPS9;Q5VTE0	EF1A1_HUMAN;.;.;EF1A3_HUMAN	G	224;224;224;224;203	ENSP00000339063:S224G;ENSP00000339053:S224G;ENSP00000330054:S224G	ENSP00000339053:S224G	S	-	1	0	EEF1A1	74285244	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.725000	0.54970	1.719000	0.51432	0.449000	0.29647	AGT		0.517	EEF1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041210.2	NM_001402		17	24	0	0	0	1	0	17	24				
CD93	22918	broad.mit.edu	37	20	23065236	23065236	+	Missense_Mutation	SNP	G	G	C	rs372540092		TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-11A-21D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	3f734baf-71fe-415d-aad5-cb29b08cfe9c	g.chr20:23065236G>C	ENST00000246006.4	-	1	1741	c.1594C>G	c.(1594-1596)Ctc>Gtc	p.L532V		NM_012072.3	NP_036204.2	Q9NPY3	C1QR1_HUMAN	CD93 molecule	532					macrophage activation (GO:0042116)|phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|complement component C1q binding (GO:0001849)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	39	Colorectal(13;0.0352)|Lung NSC(19;0.0542)|all_lung(19;0.118)					AGCATCTTGAGTGGGGCAGAT	0.662																																						ENST00000246006.4																			0				NS(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						c.(1594-1596)Ctc>Gtc		CD93 molecule							45.0	52.0	50.0					20																	23065236		2203	4300	6503	SO:0001583	missense	22918				cell-cell adhesion|interspecies interaction between organisms|macrophage activation|phagocytosis	plasma membrane	calcium ion binding|complement component C1q binding|receptor activity|sugar binding	g.chr20:23065236G>C	U94333	CCDS13149.1	20p11.21	2009-01-29	2006-03-28	2006-02-22	ENSG00000125810	ENSG00000125810		"""CD molecules"""	15855	protein-coding gene	gene with protein product		120577	"""matrix-remodelling associated 4"", ""complement component 1, q subcomponent, receptor 1"", ""CD93 antigen"""	MXRA4, C1QR1		9047234, 10648005	Standard	NM_012072		Approved	C1qRP, C1qR(P), dJ737E23.1, CDw93, ECSM3	uc002wsv.3	Q9NPY3	OTTHUMG00000032058	ENST00000246006.4:c.1594C>G	20.37:g.23065236G>C	ENSP00000246006:p.Leu532Val						p.L532V	NM_012072.3	NP_036204.2	Q9NPY3	C1QR1_HUMAN			1	1741	-	Colorectal(13;0.0352)|Lung NSC(19;0.0542)|all_lung(19;0.118)		532					O00274	Missense_Mutation	SNP	ENST00000246006.4	37	c.1594C>G	CCDS13149.1	.	.	.	.	.	.	.	.	.	.	G	3.681	-0.065621	0.07273	.	.	ENSG00000125810	ENST00000246006	T	0.80214	-1.35	5.59	1.36	0.22044	.	1.037860	0.07629	N	0.928371	T	0.66886	0.2835	L	0.34521	1.04	0.09310	N	1	B	0.20887	0.049	B	0.16722	0.016	T	0.48186	-0.9057	10	0.13853	T	0.58	-1.8619	4.7572	0.13090	0.2105:0.0:0.5355:0.2541	.	532	Q9NPY3	C1QR1_HUMAN	V	532	ENSP00000246006:L532V	ENSP00000246006:L532V	L	-	1	0	CD93	23013236	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.277000	0.18734	0.299000	0.22661	-0.137000	0.14449	CTC		0.662	CD93-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078312.2	NM_012072		21	59	0	0	0	1	0	21	59				
FUT3	2525	broad.mit.edu	37	19	5844400	5844400	+	Missense_Mutation	SNP	T	T	C	rs417341	byFrequency	TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-11A-21D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	3f734baf-71fe-415d-aad5-cb29b08cfe9c	g.chr19:5844400T>C	ENST00000303225.6	-	3	1085	c.451A>G	c.(451-453)Aga>Gga	p.R151G	FUT3_ENST00000593144.1_5'Flank|FUT3_ENST00000458379.2_Missense_Mutation_p.R151G|FUT3_ENST00000589620.1_Missense_Mutation_p.R151G|FUT3_ENST00000589918.1_Missense_Mutation_p.R151G	NM_000149.3	NP_000140	P21217	FUT3_HUMAN	fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group)	151					cell-cell recognition (GO:0009988)|fucosylation (GO:0036065)|macromolecule glycosylation (GO:0043413)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(1)	14						TTGAAGTATCTGTCCAGGGCT	0.642													T|||	11	0.00219649	0.0061	0.0014	5008	,	,		14700	0.002		0.0	False		,,,				2504	0.0				Esophageal Squamous(82;745 1728 24593 44831)	ENST00000303225.6																			0				breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(1)	14						c.(451-453)Aga>Gga		fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group)		T	GLY/ARG,GLY/ARG,GLY/ARG,GLY/ARG	35,4371	40.0+/-72.8	0,35,2168	68.0	62.0	64.0		451,451,451,451	-0.1	0.1	19	dbSNP_80	64	0,8600		0,0,4300	yes	missense,missense,missense,missense	FUT3	NM_000149.3,NM_001097639.1,NM_001097640.1,NM_001097641.1	125,125,125,125	0,35,6468	CC,CT,TT		0.0,0.7944,0.2691	benign,benign,benign,benign	151/362,151/362,151/362,151/362	5844400	35,12971	2203	4300	6503	SO:0001583	missense	2525				protein glycosylation	Golgi cisterna membrane|integral to membrane|membrane fraction	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity	g.chr19:5844400T>C		CCDS12153.1	19p13.3	2014-07-19	2006-01-12		ENSG00000171124	ENSG00000171124	2.4.1.65	"""CD molecules"", ""Blood group antigens"", ""Fucosyltransferases"""	4014	protein-coding gene	gene with protein product		111100	"""fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group included)"""	LE		1977660, 1740457	Standard	NM_000149		Approved	CD174	uc002mdk.2	P21217	OTTHUMG00000180614	ENST00000303225.6:c.451A>G	19.37:g.5844400T>C	ENSP00000305603:p.Arg151Gly					FUT3_ENST00000458379.2_Missense_Mutation_p.R151G|FUT3_ENST00000589620.1_Missense_Mutation_p.R151G|FUT3_ENST00000589918.1_Missense_Mutation_p.R151G	p.R151G	NM_000149.3	NP_000140.1	P21217	FUT3_HUMAN			3	1085	-			151					B5U7U9|B5U7V0|Q32NE7|Q99448|Q99449	Missense_Mutation	SNP	ENST00000303225.6	37	c.451A>G	CCDS12153.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	0	0.0	T	0.001	-3.133225	0.00030	0.007944	0.0	ENSG00000171124	ENST00000303225;ENST00000458379	T;T	0.25579	1.79;1.79	2.24	-0.0815	0.13702	.	0.613784	0.14038	N	0.345642	T	0.02047	0.0064	N	0.00054	-2.38	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.42498	-0.9448	10	0.06625	T	0.88	.	4.5324	0.12011	0.0:0.4765:0.0:0.5235	rs417341;rs2561801;rs417341	151;151;151;151	B3W6H0;A8K737;B3GVC1;P21217	.;.;.;FUT3_HUMAN	G	151	ENSP00000305603:R151G;ENSP00000416443:R151G	ENSP00000305603:R151G	R	-	1	2	FUT3	5795400	0.000000	0.05858	0.072000	0.20136	0.088000	0.18126	-0.920000	0.04013	0.208000	0.20626	-1.216000	0.01612	AGA		0.642	FUT3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452204.1	NM_000149		14	56	0	0	0	1	0	14	56				
CCDC105	126402	broad.mit.edu	37	19	15132292	15132292	+	Silent	SNP	C	C	T			TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-11A-21D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	3f734baf-71fe-415d-aad5-cb29b08cfe9c	g.chr19:15132292C>T	ENST00000292574.3	+	4	1084	c.1002C>T	c.(1000-1002)gcC>gcT	p.A334A		NM_173482.2	NP_775753.2	Q8IYK2	CC105_HUMAN	coiled-coil domain containing 105	334						extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(4)|skin(2)	23						GTGTGTGTGCCTCGCTGGCGC	0.622																																						ENST00000292574.3																			0				NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(4)|skin(2)	23						c.(1000-1002)gcC>gcT		coiled-coil domain containing 105							98.0	67.0	78.0					19																	15132292		2203	4300	6503	SO:0001819	synonymous_variant	126402				microtubule cytoskeleton organization	microtubule		g.chr19:15132292C>T	AK097684	CCDS12322.1	19p13.12	2008-02-05				ENSG00000160994			26866	protein-coding gene	gene with protein product						12477932	Standard	NM_173482		Approved	FLJ40365	uc002nae.2	Q8IYK2		ENST00000292574.3:c.1002C>T	19.37:g.15132292C>T							p.A334A	NM_173482.2	NP_775753.2	Q8IYK2	CC105_HUMAN			4	1084	+			334					Q8N7T5|Q8NDL5	Silent	SNP	ENST00000292574.3	37	c.1002C>T	CCDS12322.1																																																																																				0.622	CCDC105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466293.1	NM_173482		3	30	0	0	0	1	0	3	30				
GRAMD2	196996	broad.mit.edu	37	15	72454662	72454662	+	Missense_Mutation	SNP	T	T	C			TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-11A-21D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	3f734baf-71fe-415d-aad5-cb29b08cfe9c	g.chr15:72454662T>C	ENST00000309731.7	-	11	1026	c.1013A>G	c.(1012-1014)gAg>gGg	p.E338G	GRAMD2_ENST00000564184.1_5'Flank	NM_001012642.2	NP_001012660.1	Q8IUY3	GRAM2_HUMAN	GRAM domain containing 2	338						integral component of membrane (GO:0016021)				cervix(2)|endometrium(1)|large_intestine(4)|lung(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	13						TAACTGCTGCTCTAGCCGAGA	0.488																																						ENST00000309731.7																			0				cervix(2)|endometrium(1)|large_intestine(4)|lung(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	13						c.(1012-1014)gAg>gGg		GRAM domain containing 2							87.0	80.0	83.0					15																	72454662		2199	4297	6496	SO:0001583	missense	196996					integral to membrane		g.chr15:72454662T>C	AK002016	CCDS32283.1	15q23	2006-11-29	2005-11-03	2005-11-03					27287	protein-coding gene	gene with protein product						12477932	Standard	NM_001012642		Approved		uc002atq.3	Q8IUY3		ENST00000309731.7:c.1013A>G	15.37:g.72454662T>C	ENSP00000311657:p.Glu338Gly						p.E338G	NM_001012642.2	NP_001012660.1	Q8IUY3	GRAM2_HUMAN			11	1026	-			338					B3KT68	Missense_Mutation	SNP	ENST00000309731.7	37	c.1013A>G	CCDS32283.1	.	.	.	.	.	.	.	.	.	.	T	19.65	3.866427	0.72065	.	.	ENSG00000175318	ENST00000309731	T	0.69040	-0.37	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.78710	0.4326	L	0.61218	1.895	0.51482	D	0.999923	D	0.89917	1.0	D	0.87578	0.998	T	0.80913	-0.1170	10	0.87932	D	0	.	12.5847	0.56410	0.0:0.0:0.0:1.0	.	338	Q8IUY3	GRAM2_HUMAN	G	338	ENSP00000311657:E338G	ENSP00000311657:E338G	E	-	2	0	GRAMD2	70241716	1.000000	0.71417	0.956000	0.39512	0.435000	0.31806	6.284000	0.72652	1.983000	0.57843	0.460000	0.39030	GAG		0.488	GRAMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420040.1	NM_001012642		11	33	0	0	0	1	0	11	33				
LOC101927905	101927905	broad.mit.edu	37	12	8386955	8386955	+	lincRNA	SNP	T	T	C	rs75997195	byFrequency	TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-11A-21D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	3f734baf-71fe-415d-aad5-cb29b08cfe9c	g.chr12:8386955T>C	ENST00000304751.9	+	0	0				FAM86FP_ENST00000427893.2_RNA																							CTTGTGCTCCTGGCAGGCAGC	0.612													.|||	1	0.000199681	0.0008	0.0	5008	,	,		-128	0.0		0.0	False		,,,				2504	0.0					ENST00000427893.2																			0																																																			0							g.chr12:8386955T>C																													12.37:g.8386955T>C														0	811	-									RNA	SNP	ENST00000304751.9	37																																																																																						0.612	RP11-266K4.9-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000400464.1			5	44	0	0	0	1	0	5	44				
TG	7038	broad.mit.edu	37	8	133919035	133919035	+	Missense_Mutation	SNP	A	A	C			TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-11A-21D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	3f734baf-71fe-415d-aad5-cb29b08cfe9c	g.chr8:133919035A>C	ENST00000220616.4	+	17	3777	c.3737A>C	c.(3736-3738)cAa>cCa	p.Q1246P	TG_ENST00000377869.1_Missense_Mutation_p.Q1246P	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1246					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		CAGCAGTGCCAATTGCTGTGC	0.632																																						ENST00000220616.4																			0				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168						c.(3736-3738)cAa>cCa		thyroglobulin							65.0	56.0	59.0					8																	133919035		2203	4300	6503	SO:0001583	missense	7038				hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity	g.chr8:133919035A>C	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.3737A>C	8.37:g.133919035A>C	ENSP00000220616:p.Gln1246Pro					TG_ENST00000377869.1_Missense_Mutation_p.Q1246P	p.Q1246P	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)	17	3777	+	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	1246					O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	c.3737A>C	CCDS34944.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.899|9.899	1.206274|1.206274	0.22205|0.22205	.|.	.|.	ENSG00000042832|ENSG00000042832	ENST00000518505|ENST00000377869;ENST00000543313;ENST00000220616	.|T;T	.|0.65549	.|-0.16;-0.15	5.48|5.48	-4.43|-4.43	0.03568|0.03568	.|.	.|0.542430	.|0.17260	.|N	.|0.180827	T|T	0.46964|0.46964	0.1420|0.1420	L|L	0.59436|0.59436	1.845|1.845	0.24681|0.24681	N|N	0.99337|0.99337	.|P	.|0.37955	.|0.612	.|B	.|0.34722	.|0.188	T|T	0.42464|0.42464	-0.9450|-0.9450	5|10	.|0.87932	.|D	.|0	.|.	4.713|4.713	0.12882|0.12882	0.3416:0.0:0.3927:0.2657|0.3416:0.0:0.3927:0.2657	.|.	.|1246	.|P01266	.|THYG_HUMAN	H|P	190|1246;52;1246	.|ENSP00000367100:Q1246P;ENSP00000220616:Q1246P	.|ENSP00000220616:Q1246P	N|Q	+|+	1|2	0|0	TG|TG	133988217|133988217	0.054000|0.054000	0.20591|0.20591	0.872000|0.872000	0.34217|0.34217	0.033000|0.033000	0.12548|0.12548	-0.627000|-0.627000	0.05521|0.05521	-0.851000|-0.851000	0.04147|0.04147	-1.054000|-1.054000	0.02325|0.02325	AAT|CAA		0.632	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		10	28	0	0	0	1	0	10	28				
SPECC1	92521	broad.mit.edu	37	17	20013740	20013740	+	Splice_Site	SNP	C	C	A			TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-11A-21D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	3f734baf-71fe-415d-aad5-cb29b08cfe9c	g.chr17:20013740C>A	ENST00000261503.5	+	3	199	c.148C>A	c.(148-150)Ctc>Atc	p.L50I	SPECC1_ENST00000395527.4_Splice_Site_p.L50I|SPECC1_ENST00000395529.3_Splice_Site_p.L50I|SPECC1_ENST00000472876.1_Intron	NM_001033553.2	NP_001028725.1	Q5M775	CYTSB_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1	50					cell adhesion (GO:0007155)	nucleus (GO:0005634)				breast(1)|large_intestine(3)|ovary(4)	8				KIRC - Kidney renal clear cell carcinoma(2;0.166)|Kidney(2;0.196)		ACTCTCTCAGCTCAAGAGGGC	0.572																																						ENST00000395529.3																			0				breast(1)|large_intestine(3)|ovary(4)	8						c.e3-1		sperm antigen with calponin homology and coiled-coil domains 1							90.0	92.0	92.0					17																	20013740		2203	4300	6503	SO:0001630	splice_region_variant	92521					nucleus		g.chr17:20013740C>A	AY816329, AB041533	CCDS32590.1, CCDS42280.1, CCDS42281.1, CCDS45628.1, CCDS58531.1	17p11.2	2012-11-19	2010-09-17	2010-09-17	ENSG00000128487	ENSG00000128487			30615	protein-coding gene	gene with protein product	"""sperm antigen HCMOGT 1"", ""cytokinesis and spindle organization B"", ""cytospin B"""	608793				15602574, 18763323, 15087372	Standard	NM_001033553		Approved	HCMOGT-1, FLJ36955, NSP, CYTSB	uc002gwq.3	Q5M775	OTTHUMG00000179808	ENST00000261503.5:c.148-1C>A	17.37:g.20013740C>A						SPECC1_ENST00000472876.1_Intron|SPECC1_ENST00000261503.5_Splice_Site_p.L50_splice|SPECC1_ENST00000395527.4_Splice_Site_p.L50_splice	p.L50_splice	NM_152904.4	NP_690868.3	Q5M775	CYTSB_HUMAN		KIRC - Kidney renal clear cell carcinoma(2;0.166)|Kidney(2;0.196)	3	200	+			50					B4DHH0|B7WNS8|Q5IBP1|Q5IBP2|Q5IBP3|Q5IBP4|Q5M772|Q5M773|Q5M774|Q86XT8|Q8N4U4|Q8WU84|Q9HCQ3	Splice_Site	SNP	ENST00000261503.5	37	c.147_splice	CCDS32590.1	.	.	.	.	.	.	.	.	.	.	C	17.03	3.284741	0.59867	.	.	ENSG00000128487	ENST00000395530;ENST00000413167;ENST00000261503;ENST00000395529	T;T	0.65916	-0.18;2.8	5.29	5.29	0.74685	.	0.092570	0.44688	D	0.000425	T	0.72732	0.3497	L	0.43152	1.355	0.80722	D	1	D;P	0.71674	0.998;0.825	D;B	0.83275	0.996;0.299	T	0.70004	-0.4991	9	.	.	.	-12.3568	16.802	0.85617	0.0:1.0:0.0:0.0	.	50;50	Q5M775-2;Q5M775	.;CYTSB_HUMAN	I	50	ENSP00000261503:L50I;ENSP00000378900:L50I	.	L	+	1	0	SPECC1	19954332	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	4.763000	0.62257	2.647000	0.89833	0.655000	0.94253	CTC		0.572	SPECC1-018	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441206.1	NM_152904	Missense_Mutation	17	51	1	0	1.33834e-09	1	1.39187e-09	17	51				
NRAS	4893	broad.mit.edu	37	1	115256529	115256529	+	Missense_Mutation	SNP	T	T	C	rs11554290	byFrequency	TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-11A-21D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	3f734baf-71fe-415d-aad5-cb29b08cfe9c	g.chr1:115256529T>C	ENST00000369535.4	-	3	435	c.182A>G	c.(181-183)cAa>cGa	p.Q61R		NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	61			Q -> K (in CMNS and NCMS; somatic mutation). {ECO:0000269|PubMed:23392294}.|Q -> R (in CMNS, NCMS and KNEN; also found in lung carcinoma cell and melanoma; dbSNP:rs11554290). {ECO:0000269|PubMed:18633438, ECO:0000269|PubMed:22499344, ECO:0000269|PubMed:23392294, ECO:0000269|PubMed:3276402}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.Q61R(817)|p.Q61L(175)|p.Q61P(23)|p.Q61K(1)		NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTACTCTTCTTGTCCAGCTGT	0.458	Q61L(C3A_LIVER)|Q61L(HEPG2_LIVER)|Q61L(HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(IPC298_SKIN)|Q61L(KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(MELJUSO_SKIN)|Q61L(MHHES1_BONE)|Q61L(MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61P(TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(HT1197_URINARY_TRACT)|Q61R(KMS27_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(KU1919_URINARY_TRACT)|Q61R(NCIH2347_LUNG)|Q61R(ONS76_CENTRAL_NERVOUS_SYSTEM)|Q61R(SKMEL2_SKIN)|Q61R(SW1271_LUNG)|Q61R(TT2609C02_THYROID)	50	Mis		"""melanoma, MM, AML, thyroid"""				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																												ENST00000369535.4	Q61L(C3A_LIVER)|Q61L(HEPG2_LIVER)|Q61L(HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(IPC298_SKIN)|Q61L(KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(MELJUSO_SKIN)|Q61L(MHHES1_BONE)|Q61L(MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61P(TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(HT1197_URINARY_TRACT)|Q61R(KMS27_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(KU1919_URINARY_TRACT)|Q61R(NCIH2347_LUNG)|Q61R(ONS76_CENTRAL_NERVOUS_SYSTEM)|Q61R(SKMEL2_SKIN)|Q61R(SW1271_LUNG)|Q61R(TT2609C02_THYROID)	50		Dom	yes		1	1p13.2	4893	Mis	neuroblastoma RAS viral (v-ras) oncogene homolog			"""L, E"""			"""melanoma, MM, AML, thyroid"""		1016	Substitution - Missense(1016)	p.Q61R(817)|p.Q61L(175)|p.Q61P(23)|p.Q61K(1)	skin(466)|thyroid(279)|haematopoietic_and_lymphoid_tissue(124)|NS(50)|large_intestine(27)|lung(17)|urinary_tract(11)|adrenal_gland(7)|liver(7)|breast(7)|soft_tissue(4)|testis(3)|endometrium(3)|ovary(3)|central_nervous_system(2)|pancreas(2)|eye(1)|prostate(1)|meninges(1)|autonomic_ganglia(1)	NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085						c.(181-183)cAa>cGa		neuroblastoma RAS viral (v-ras) oncogene homolog							180.0	156.0	164.0					1																	115256529		2203	4300	6503	SO:0001583	missense	4893	Noonan syndrome	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	Golgi membrane|plasma membrane	GTP binding|GTPase activity	g.chr1:115256529T>C	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.182A>G	1.37:g.115256529T>C	ENSP00000358548:p.Gln61Arg	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)					p.Q61R	NM_002524.4	NP_002515.1	P01111	RASN_HUMAN		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	3	435	-	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)	61		Q -> K (in neuroblastoma cell).|Q -> R (in lung carcinoma cell and melanoma; dbSNP:rs11554290).			Q14971|Q15104|Q15282	Missense_Mutation	SNP	ENST00000369535.4	37	c.182A>G	CCDS877.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.004139	0.74932	.	.	ENSG00000213281	ENST00000369535	D	0.83673	-1.75	5.08	5.08	0.68730	Small GTP-binding protein domain (1);	0.000000	0.53938	U	0.000043	D	0.86489	0.5945	M	0.92604	3.325	0.80722	D	1	B	0.28512	0.214	B	0.39590	0.304	D	0.88255	0.2919	10	0.66056	D	0.02	.	15.0132	0.71565	0.0:0.0:0.0:1.0	rs11554290;rs11554290	61	P01111	RASN_HUMAN	R	61	ENSP00000358548:Q61R	ENSP00000358548:Q61R	Q	-	2	0	NRAS	115058052	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.761000	0.85260	2.120000	0.65058	0.533000	0.62120	CAA		0.458	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033395.2	NM_002524		31	46	0	0	0	1	0	31	46				
PHLPP2	23035	broad.mit.edu	37	16	71682911	71682911	+	Missense_Mutation	SNP	T	T	C	rs149705576		TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-11A-21D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	3f734baf-71fe-415d-aad5-cb29b08cfe9c	g.chr16:71682911T>C	ENST00000568954.1	-	19	4232	c.3854A>G	c.(3853-3855)cAt>cGt	p.H1285R	PHLPP2_ENST00000393524.2_Missense_Mutation_p.H1218R|PHLPP2_ENST00000567016.1_Missense_Mutation_p.H1320R|PHLPP2_ENST00000540628.1_Intron|PHLPP2_ENST00000360429.3_Intron|PHLPP2_ENST00000356272.3_Missense_Mutation_p.H1285R			Q6ZVD8	PHLP2_HUMAN	PH domain and leucine rich repeat protein phosphatase 2	1285					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)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment membrane (GO:0042622)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(7)|lung(15)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37						TTCCAGGTCATGAGGCACAAC	0.552																																						ENST00000393524.2																			0				central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(7)|lung(15)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37						c.(3652-3654)cAt>cGt		PH domain and leucine rich repeat protein phosphatase 2		T	ARG/HIS	0,4396		0,0,2198	106.0	96.0	99.0		3854	4.1	1.0	16	dbSNP_134	99	1,8599	1.2+/-3.3	0,1,4299	no	missense	PHLPP2	NM_015020.2	29	0,1,6497	CC,CT,TT		0.0116,0.0,0.0077	benign	1285/1324	71682911	1,12995	2198	4300	6498	SO:0001583	missense	23035					cytoplasm|membrane|nucleus	metal ion binding|phosphoprotein phosphatase activity	g.chr16:71682911T>C	BX647823	CCDS32479.1, CCDS73910.1	16q22.2	2013-01-11	2009-05-26	2009-05-26	ENSG00000040199	ENSG00000040199		"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"", ""Pleckstrin homology (PH) domain containing"""	29149	protein-coding gene	gene with protein product		611066	"""PH domain and leucine rich repeat protein phosphatase-like"""	PHLPPL		17386267	Standard	NM_001289003		Approved	KIAA0931	uc002fax.3	Q6ZVD8		ENST00000568954.1:c.3854A>G	16.37:g.71682911T>C	ENSP00000457991:p.His1285Arg					PHLPP2_ENST00000540628.1_Intron|PHLPP2_ENST00000360429.3_Intron|PHLPP2_ENST00000356272.3_Missense_Mutation_p.H1285R|PHLPP2_ENST00000568954.1_Missense_Mutation_p.H1285R|PHLPP2_ENST00000567016.1_Missense_Mutation_p.H1320R	p.H1218R			Q6ZVD8	PHLP2_HUMAN			17	4386	-			1285					A1L374|Q9NV17|Q9Y2E3	Missense_Mutation	SNP	ENST00000568954.1	37	c.3653A>G	CCDS32479.1	.	.	.	.	.	.	.	.	.	.	t	1.818	-0.473037	0.04445	0.0	1.16E-4	ENSG00000040199	ENST00000356272;ENST00000393524	T;T	0.39787	1.6;1.06	6.17	4.07	0.47477	.	0.203454	0.52532	N	0.000073	T	0.21062	0.0507	N	0.16478	0.41	0.22199	N	0.999296	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.13361	-1.0512	10	0.14656	T	0.56	-11.2858	5.0812	0.14656	0.0:0.491:0.3004:0.2086	.	1218;1285	Q6ZVD8-3;Q6ZVD8	.;PHLP2_HUMAN	R	1285;1218	ENSP00000348611:H1285R;ENSP00000377159:H1218R	ENSP00000348611:H1285R	H	-	2	0	PHLPP2	70240412	0.999000	0.42202	1.000000	0.80357	0.892000	0.51952	2.880000	0.48530	1.631000	0.50456	-0.140000	0.14226	CAT		0.552	PHLPP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000434139.1	NM_015020		5	51	0	0	0	1	0	5	51				
GGT3P	2679	broad.mit.edu	37	22	18769203	18769203	+	RNA	SNP	G	G	A	rs111245818	byFrequency	TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-11A-21D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	3f734baf-71fe-415d-aad5-cb29b08cfe9c	g.chr22:18769203G>A	ENST00000412448.1	-	0	1083							A6NGU5	GGT3_HUMAN	gamma-glutamyltransferase 3 pseudogene						glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)										AGCCAGCCGCGGCAGGGTCAG	0.637													g|||	253	0.0505192	0.0068	0.0908	5008	,	,		47818	0.0079		0.1213	False		,,,				2504	0.0521					ENST00000412448.1																			0																																																			0							g.chr22:18769203G>A			22q11.21	2008-08-05	2008-03-10	2008-03-10	ENSG00000197421	ENSG00000197421		"""Gamma-glutamyltransferases"""	4252	pseudogene	pseudogene			"""gamma-glutamyltransferase 3"""	GGT3		8104871, 18357469	Standard	NR_003267		Approved		uc002zob.1	A6NGU5	OTTHUMG00000150161		22.37:g.18769203G>A														0	1083	-									RNA	SNP	ENST00000412448.1	37																																																																																						0.637	GGT3P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000341281.1	NR_003267		5	40	0	0	0	1	0	5	40				
ZMIZ2	83637	broad.mit.edu	37	7	44801338	44801338	+	Missense_Mutation	SNP	G	G	A			TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-11A-21D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	3f734baf-71fe-415d-aad5-cb29b08cfe9c	g.chr7:44801338G>A	ENST00000309315.4	+	11	1553	c.1430G>A	c.(1429-1431)cGg>cAg	p.R477Q	ZMIZ2_ENST00000265346.7_Missense_Mutation_p.R451Q|ZMIZ2_ENST00000413916.1_Missense_Mutation_p.R419Q|ZMIZ2_ENST00000441627.1_Missense_Mutation_p.R477Q|ZMIZ2_ENST00000433667.1_Missense_Mutation_p.R445Q	NM_031449.3	NP_113637.3	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2	477	Interaction with AR.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						CACGAGGACCGGCAGATGAAC	0.612																																					NSCLC(20;604 852 1948 16908 50522)	ENST00000309315.4																			0				breast(3)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						c.(1429-1431)cGg>cAg		zinc finger, MIZ-type containing 2							57.0	61.0	60.0					7																	44801338		2203	4300	6503	SO:0001583	missense	83637				positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear replication fork	ligand-dependent nuclear receptor transcription coactivator activity|protein binding|zinc ion binding	g.chr7:44801338G>A	AK090415	CCDS43576.1, CCDS43577.1, CCDS75591.1	7p13	2009-11-06			ENSG00000122515	ENSG00000122515		"""Zinc fingers, MIZ-type"""	22229	protein-coding gene	gene with protein product		611196					Standard	XM_005249866		Approved	KIAA1886, hZIMP7, ZIMP7, DKFZp761I2123, NET27	uc003tlr.3	Q8NF64	OTTHUMG00000155817	ENST00000309315.4:c.1430G>A	7.37:g.44801338G>A	ENSP00000311778:p.Arg477Gln					ZMIZ2_ENST00000413916.1_Missense_Mutation_p.R419Q|ZMIZ2_ENST00000441627.1_Missense_Mutation_p.R477Q|ZMIZ2_ENST00000433667.1_Missense_Mutation_p.R445Q|ZMIZ2_ENST00000265346.7_Missense_Mutation_p.R451Q	p.R477Q	NM_031449.3	NP_113637.3	Q8NF64	ZMIZ2_HUMAN			11	1553	+			477			Interaction with AR.		A4D2K7|D3DVL1|O94790|Q0VGB4|Q659A8|Q6JKL5|Q8WTX8|Q96Q01|Q9BQH7	Missense_Mutation	SNP	ENST00000309315.4	37	c.1430G>A	CCDS43576.1	.	.	.	.	.	.	.	.	.	.	G	37	6.209731	0.97380	.	.	ENSG00000122515	ENST00000413916;ENST00000309315;ENST00000441627;ENST00000433667;ENST00000265346;ENST00000414051	T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02	4.73	4.73	0.59995	.	0.000000	0.56097	D	0.000039	T	0.63954	0.2555	M	0.72894	2.215	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.76071	0.987;0.966;0.987	T	0.64659	-0.6355	10	0.44086	T	0.13	-16.8339	17.4928	0.87709	0.0:0.0:1.0:0.0	.	451;477;419	Q8NF64-2;Q8NF64;Q8NF64-3	.;ZMIZ2_HUMAN;.	Q	419;477;477;445;451;477	ENSP00000409648:R419Q;ENSP00000311778:R477Q;ENSP00000414723:R477Q;ENSP00000396601:R445Q;ENSP00000265346:R451Q	ENSP00000265346:R451Q	R	+	2	0	ZMIZ2	44767863	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.131000	0.94446	2.444000	0.82710	0.655000	0.94253	CGG		0.612	ZMIZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341790.1	NM_031449		16	17	0	0	0	1	0	16	17				
BCRP7	100133163	broad.mit.edu	37	22	18844763	18844763	+	3'UTR	SNP	T	T	C	rs1064849		TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-11A-21D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	3f734baf-71fe-415d-aad5-cb29b08cfe9c	g.chr22:18844763T>C	ENST00000412938.1	+	0	3013																											TCACAGCCTCTGAGGGCAGCA	0.562																																						ENST00000412938.1																			0																																																	SO:0001624	3_prime_UTR_variant	0							g.chr22:18844763T>C																												ENST00000412938.1:c.*3010T>C	22.37:g.18844763T>C														0	3013	+									RNA	SNP	ENST00000412938.1	37																																																																																						0.562	AC008132.13-002	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000471615.1			4	10	0	0	0	1	0	4	10				
PCDHA6	56142	broad.mit.edu	37	5	140209392	140209392	+	Silent	SNP	T	T	C	rs146736705	byFrequency	TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-11A-21D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	3f734baf-71fe-415d-aad5-cb29b08cfe9c	g.chr5:140209392T>C	ENST00000529310.1	+	1	1830	c.1716T>C	c.(1714-1716)ggT>ggC	p.G572G	PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	572					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGGTGGGTGGTACTGGTGGTG	0.687													.|||	9	0.00179712	0.0	0.0072	5008	,	,		16079	0.0		0.004	False		,,,				2504	0.0					ENST00000529310.1																			0				NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89						c.(1714-1716)ggT>ggC				T	,,,,,,,,	3,4403	8.1+/-20.4	0,3,2200	74.0	78.0	77.0		,,,,,1716,,1716,	-7.4	0.0	5	dbSNP_134	77	34,8564	23.4+/-69.3	0,34,4265	no	intron,intron,intron,intron,intron,coding-synonymous,intron,coding-synonymous,intron	PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_031411.1,NM_031848.1,NM_031849.1	,,,,,,,,	0,37,6465	CC,CT,TT		0.3954,0.0681,0.2845	,,,,,,,,	,,,,,572/951,,572/804,	140209392	37,12967	2203	4299	6502	SO:0001819	synonymous_variant	0							g.chr5:140209392T>C	AF152484	CCDS47281.1, CCDS47282.1	5q31	2010-11-26			ENSG00000081842	ENSG00000081842		"""Cadherins / Protocadherins : Clustered"""	8672	other	complex locus constituent	"""KIAA0345-like 8"""	606312		CNRS2		10380929, 10662547	Standard	NM_018909		Approved	CNR2, CRNR2, PCDH-ALPHA6		Q9UN73	OTTHUMG00000163353	ENST00000529310.1:c.1716T>C	5.37:g.140209392T>C						PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron	p.G572G	NM_018909.2|NM_031848.1|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		1	1830	+								O75283|Q9NRT8	Silent	SNP	ENST00000529310.1	37	c.1716T>C	CCDS47281.1																																																																																				0.687	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909		6	100	0	0	0	1	0	6	100				
SLC6A13	6540	broad.mit.edu	37	12	368928	368928	+	Intron	SNP	T	T	C	rs148217969	byFrequency	TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-11A-21D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	3f734baf-71fe-415d-aad5-cb29b08cfe9c	g.chr12:368928T>C	ENST00000343164.4	-	2	255				RP11-283I3.4_ENST00000540868.1_RNA|SLC6A13_ENST00000436453.1_Silent_p.P97P|SLC6A13_ENST00000445055.2_Intron	NM_016615.4	NP_057699.2	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 13						neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(1)	28	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)			tatacatctatgGGACTCCCC	0.522													T|||	19	0.00379393	0.0113	0.0	5008	,	,		20126	0.0		0.004	False		,,,				2504	0.0					ENST00000436453.1																			0				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(1)	28						c.(289-291)ccA>ccG		solute carrier family 6 (neurotransmitter transporter), member 13																																				SO:0001627	intron_variant	6540				neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity	g.chr12:368928T>C	U76343	CCDS8502.1, CCDS53729.1, CCDS58198.1	12p13.33	2013-07-19	2013-07-19		ENSG00000010379	ENSG00000010379		"""Solute carriers"""	11046	protein-coding gene	gene with protein product	"""GABA transporter 2"""	615097	"""solute carrier family 6 (neurotransmitter transporter, GABA), member 13"""				Standard	NM_001243392		Approved	GAT2	uc001qic.2	Q9NSD5	OTTHUMG00000168053	ENST00000343164.4:c.202+88A>G	12.37:g.368928T>C						SLC6A13_ENST00000343164.4_Intron|SLC6A13_ENST00000445055.2_Intron	p.P97P	NM_001243392.1	NP_001230321.1	Q9NSD5	S6A13_HUMAN	OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)		2	343	-	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		0					B4DJL1|Q8TCC2|Q8WW56	Silent	SNP	ENST00000343164.4	37	c.291A>G	CCDS8502.1																																																																																				0.522	SLC6A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397801.1	NM_016615		3	16	0	0	0	1	0	3	16				
EEF1A1	1915	broad.mit.edu	37	6	74228523	74228523	+	Missense_Mutation	SNP	T	T	C			TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-11A-21D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	3f734baf-71fe-415d-aad5-cb29b08cfe9c	g.chr6:74228523T>C	ENST00000316292.9	-	4	1661	c.670A>G	c.(670-672)Agt>Ggt	p.S224G	EEF1A1_ENST00000491404.1_Intron|EEF1A1_ENST00000331523.2_Missense_Mutation_p.S224G|EEF1A1_ENST00000309268.6_Missense_Mutation_p.S224G	NM_001402.5	NP_001393.1	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha 1	224	tr-type G.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation elongation factor activity (GO:0003746)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(6)|prostate(2)|skin(3)	18						GTGGTTCCACTGGCATTGCCA	0.517											OREG0003891|OREG0003895	type=REGULATORY REGION|Gene=D16891|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay|type=REGULATORY REGION|Gene=EEF1A1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																										ENST00000316292.9																			0				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(6)|prostate(2)|skin(3)	18						c.(670-672)Agt>Ggt		eukaryotic translation elongation factor 1 alpha 1							105.0	97.0	99.0					6																	74228523		2203	4297	6500	SO:0001583	missense	1915					cytosol|eukaryotic translation elongation factor 1 complex	GTP binding|GTPase activity|protein binding|translation elongation factor activity	g.chr6:74228523T>C	BC019669	CCDS4980.1	6q14.1	2010-06-30	2004-11-19		ENSG00000156508	ENSG00000156508			3189	protein-coding gene	gene with protein product		130590	"""leukocyte receptor cluster (LRC) member 7"""	EF1A, EEF1A, LENG7		8812466, 10941842	Standard	NM_001402		Approved	EE1A1	uc003phj.3	P68104	OTTHUMG00000015031	ENST00000316292.9:c.670A>G	6.37:g.74228523T>C	ENSP00000339063:p.Ser224Gly		OREG0003891|OREG0003895	type=REGULATORY REGION|Gene=D16891|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay|type=REGULATORY REGION|Gene=EEF1A1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	1151	EEF1A1_ENST00000331523.2_Missense_Mutation_p.S224G|EEF1A1_ENST00000491404.1_Intron|EEF1A1_ENST00000309268.6_Missense_Mutation_p.S224G	p.S224G	NM_001402.5	NP_001393.1	P68104	EF1A1_HUMAN			4	1661	-			224					P04719|P04720|Q6IQ15	Missense_Mutation	SNP	ENST00000316292.9	37	c.670A>G	CCDS4980.1	.	.	.	.	.	.	.	.	.	.	T	13.24	2.177470	0.38413	.	.	ENSG00000156508	ENST00000316292;ENST00000358190;ENST00000309268;ENST00000331523;ENST00000391977	T;T;T	0.46063	0.88;0.88;0.88	4.31	4.31	0.51392	Protein synthesis factor, GTP-binding (2);	0.264000	0.36374	U	0.002624	T	0.18964	0.0455	L	0.31664	0.95	0.53005	D	0.99996	B;B;B;B	0.09022	0.001;0.002;0.001;0.002	B;B;B;B	0.06405	0.001;0.001;0.001;0.002	T	0.09037	-1.0693	10	0.62326	D	0.03	.	13.8286	0.63366	0.0:0.0:0.0:1.0	.	224;224;224;224	P68104;Q53HR5;Q6IPS9;Q5VTE0	EF1A1_HUMAN;.;.;EF1A3_HUMAN	G	224;224;224;224;203	ENSP00000339063:S224G;ENSP00000339053:S224G;ENSP00000330054:S224G	ENSP00000339053:S224G	S	-	1	0	EEF1A1	74285244	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.725000	0.54970	1.719000	0.51432	0.449000	0.29647	AGT		0.517	EEF1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041210.2	NM_001402		17	24	0	0	0	1	0	17	24				
CACNA2D1	781	broad.mit.edu	37	7	81596976	81596977	+	Frame_Shift_Del	DEL	AC	AC	-			TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	4f280fa7-808c-445d-b173-cb9c2d2f3a96	g.chr7:81596976_81596977delAC	ENST00000356253.5	-	30	2689_2690	c.2434_2435delGT	c.(2434-2436)gttfs	p.V812fs	CACNA2D1_ENST00000356860.3_Frame_Shift_Del_p.V800fs|CACNA2D1_ENST00000535308.1_Frame_Shift_Del_p.V12fs			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	812					calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	TTTAATTCCAACAACTGAAAAA	0.262																																						ENST00000356860.3																			0				breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81						c.(2398-2400)tfs		calcium channel, voltage-dependent, alpha 2/delta subunit 1	Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)																																			SO:0001589	frameshift_variant	781					voltage-gated calcium channel complex	metal ion binding	g.chr7:81596976_81596977delAC	M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"""Calcium channel subunits"""	1399	protein-coding gene	gene with protein product		114204	"""long intergenic non-protein coding RNA 1112"""	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.2434_2435delGT	7.37:g.81596976_81596977delAC	ENSP00000348589:p.Val812fs					CACNA2D1_ENST00000535308.1_Frame_Shift_Del_p.V12fs|CACNA2D1_ENST00000356253.5_Frame_Shift_Del_p.V812fs	p.V800fs	NM_000722.2	NP_000713.2	P54289	CA2D1_HUMAN			30	2736_2737	-			812					Q17R45|Q9UD80|Q9UD81|Q9UD82	Frame_Shift_Del	DEL	ENST00000356253.5	37	c.2398_2399delGT																																																																																					0.262	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding				2	4						2	4	---	---	---	---
MICALCL	84953	broad.mit.edu	37	11	12316384	12316389	+	In_Frame_Del	DEL	CTCCTA	CTCCTA	-	rs3812754|rs542581403|rs199786165	byFrequency	TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	4f280fa7-808c-445d-b173-cb9c2d2f3a96	g.chr11:12316384_12316389delCTCCTA	ENST00000256186.2	+	3	1697_1702	c.1406_1411delCTCCTA	c.(1405-1413)cctcctaca>cca	p.PT470del		NM_032867.2	NP_116256.2	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	470	Poly-Pro.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	mitogen-activated protein kinase binding (GO:0051019)	p.T471delT(2)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(5)|lung(5)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	30				Epithelial(150;0.00177)		cctcctcctcctcctACAGCGGGAGG	0.573																																						ENST00000256186.2																			2	Deletion - In frame(2)	p.T471delT(2)	upper_aerodigestive_tract(1)|skin(1)	breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(5)|lung(5)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	30						c.(1405-1413)cca>c		MICAL C-terminal like				494,2594		71,352,1121						-0.7	0.0		dbSNP_107	5	1955,4965		272,1411,1777	no	coding	MICALCL	NM_032867.2		343,1763,2898	A1A1,A1R,RR		28.2514,15.9974,24.4704				2449,7559				SO:0001651	inframe_deletion	84953				cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm	mitogen-activated protein kinase binding	g.chr11:12316384_12316389delCTCCTA	BK000463	CCDS41620.1	11p15.3	2005-11-01			ENSG00000133808	ENSG00000133808			25933	protein-coding gene	gene with protein product		612355				12110185	Standard	NM_032867		Approved	FLJ14966	uc001mkg.1	Q6ZW33	OTTHUMG00000165777	ENST00000256186.2:c.1406_1411delCTCCTA	11.37:g.12316384_12316389delCTCCTA	ENSP00000256186:p.Pro470_Thr471del						p.PPT469del	NM_032867.2	NP_116256.2	Q6ZW33	MICLK_HUMAN		Epithelial(150;0.00177)	3	1697_1702	+			469			Poly-Pro.		Q7RTP7|Q96JU6	In_Frame_Del	DEL	ENST00000256186.2	37	c.1406_1411delCTCCTA	CCDS41620.1																																																																																				0.573	MICALCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386164.1	NM_032867		4	7						4	7	---	---	---	---
EMG1	10436	broad.mit.edu	37	12	7080212	7080213	+	Splice_Site	INS	-	-	C	rs11428482|rs374779752|rs17857448		TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	4f280fa7-808c-445d-b173-cb9c2d2f3a96	g.chr12:7080212_7080213insC	ENST00000261406.6	+	2	267_268	c.124_125insC	c.(124-126)ttt>tCtt	p.F42fs	PHB2_ENST00000542912.1_5'Flank|PHB2_ENST00000440277.1_5'Flank|PHB2_ENST00000535923.1_5'Flank|PHB2_ENST00000546111.1_5'Flank|PHB2_ENST00000544134.1_5'Flank|EMG1_ENST00000546220.1_3'UTR|PHB2_ENST00000399433.2_5'Flank	NM_006331.7	NP_006322.4			EMG1 N1-specific pseudouridine methyltransferase																		GAGGCCGTAGTTTATTGTGGTG	0.569																																						ENST00000546220.1																			0													EMG1 N1-specific pseudouridine methyltransferase				3746,4		1873,0,2						5.4	1.0		dbSNP_120	28	7902,2		3951,0,1	no	frameshift	EMG1	NM_006331.7		5824,0,3	A1A1,A1R,RR		0.0253,0.1067,0.0515				11648,6				SO:0001630	splice_region_variant	10436				ribosomal small subunit biogenesis	cytoplasm|nucleolus	rRNA (pseudouridine) methyltransferase activity|rRNA binding	g.chr12:7080212_7080213insC	U72514	CCDS73430.1	12p13	2013-05-22	2013-05-22			ENSG00000126749			16912	protein-coding gene	gene with protein product		611531	"""EMG1 nucleolar protein homolog (S. cerevisiae)"""			9074930, 11935223, 19463982	Standard	NM_006331		Approved	C2F, NEP1, Grcc2f	uc001qsh.4	Q92979		ENST00000261406.6:c.124-1->C	12.37:g.7080212_7080213insC						U47924.28_ENST00000261406.6_lincRNA|U47924.19_ENST00000564245.1_RNA				Q92979	NEP1_HUMAN			0	157_158	+									RNA	INS	ENST00000261406.6	37																																																																																						0.569	EMG1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_006331	Frame_Shift_Ins	9	2						9	2	---	---	---	---
RP11-439I14.2	0	broad.mit.edu	37	16	64770704	64770705	+	lincRNA	INS	-	-	CCAGTGATGGTCACCT	rs200421189|rs71143515|rs377231404|rs145408521|rs140029302	byFrequency	TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	4f280fa7-808c-445d-b173-cb9c2d2f3a96	g.chr16:64770704_64770705insCCAGTGATGGTCACCT	ENST00000564293.1	+	0	453_454																											TGTCACCACTGCCACCTTGTTC	0.371														3288	0.65655	0.8434	0.5144	5008	,	,		21531	0.6052		0.5537	False		,,,				2504	0.6636					ENST00000564293.1																			0																																																			0							g.chr16:64770704_64770705insCCAGTGATGGTCACCT																													16.37:g.64770704_64770705insCCAGTGATGGTCACCT														0	453_454	+									RNA	INS	ENST00000564293.1	37																																																																																						0.371	RP11-439I14.2-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000422725.1			3	3						3	3	---	---	---	---
BAGE2	85319	broad.mit.edu	37	21	11085837	11085838	+	RNA	INS	-	-	TAC	rs199904990		TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-10A-01D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	4f280fa7-808c-445d-b173-cb9c2d2f3a96	g.chr21:11085837_11085838insTAC	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)		accatcaccatcaccaccacca	0.584																																						ENST00000470054.1																			0													B melanoma antigen family, member 2																																						85319							g.chr21:11085837_11085838insTAC	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.11085837_11085838insTAC												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	INS	ENST00000470054.1	37																																																																																						0.584	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482		2	4						2	4	---	---	---	---
FAM86JP	100125556	broad.mit.edu	37	3	125642556	125642557	+	RNA	INS	-	-	C	rs373923595|rs112362688|rs60014637	byFrequency	TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-11A-21D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	3f734baf-71fe-415d-aad5-cb29b08cfe9c	g.chr3:125642556_125642557insC	ENST00000485843.1	+	0	332					NR_024251.1				family with sequence similarity 86, member J, pseudogene																		ATCATCTCCCAGGCATCACAGG	0.579													|||unknown(NO_COVERAGE)	1259	0.251398	0.5719	0.1686	5008	,	,		19581	0.0982		0.1471	False		,,,				2504	0.1421					ENST00000485843.1																			0																																																			0							g.chr3:125642556_125642557insC			3q21.2	2012-06-28			ENSG00000171084	ENSG00000171084			44097	pseudogene	pseudogene							Standard	NR_024250		Approved		uc003eif.4		OTTHUMG00000159586		3.37:g.125642556_125642557insC								NR_024251.1						0	332	+									RNA	INS	ENST00000485843.1	37																																																																																						0.579	FAM86JP-004	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000356339.1	NR_024251		5	11						5	11	---	---	---	---
MSH3	4437	broad.mit.edu	37	5	79950742	79950750	+	In_Frame_Del	DEL	CCCCCAGCT	CCCCCAGCT	-	rs144629981|rs3045983|rs557874766|rs1047489	byFrequency	TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-11A-21D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	3f734baf-71fe-415d-aad5-cb29b08cfe9c	g.chr5:79950742_79950750delCCCCCAGCT	ENST00000265081.6	+	1	276_284	c.196_204delCCCCCAGCT	c.(196-204)cccccagctdel	p.PPA66del	DHFR_ENST00000505337.1_5'Flank|DHFR_ENST00000513048.1_5'Flank|DHFR_ENST00000504396.1_5'Flank|DHFR_ENST00000439211.2_5'UTR|DHFR_ENST00000511032.1_5'Flank	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	66					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		gCCCCCAGCGCCCCCAGCTCCCGCCTTCC	0.732								Mismatch excision repair (MMR)						1174	0.234425	0.2874	0.2061	5008	,	,		7173	0.0565		0.2535	False		,,,				2504	0.3466				Melanoma(88;1010 1399 13793 26548 36275)	ENST00000265081.6																			0				NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						c.(196-204)del	Mismatch excision repair (MMR)	mutS homolog 3			,	1105,2179		342,421,879					,	4.0	1.0		dbSNP_102	4	1941,4615		567,807,1904	no	coding,utr-5	DHFR,MSH3	NM_002439.3,NM_000791.3	,	909,1228,2783	A1A1,A1R,RR		29.6065,33.648,30.9553	,	,		3046,6794				SO:0001651	inframe_deletion	4437				maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments	MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding	g.chr5:79950742_79950750delCCCCCAGCT	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"""Divergent upstream protein"", ""Mismatch repair protein 1"""	600887	"""mutS (E. coli) homolog 3"", ""mutS homolog 3 (E. coli)"""				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.196_204delCCCCCAGCT	5.37:g.79950742_79950750delCCCCCAGCT	ENSP00000265081:p.Pro66_Ala68del					DHFR_ENST00000439211.2_5'UTR	p.PPA66del	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)	1	276_284	+		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)	66					A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	In_Frame_Del	DEL	ENST00000265081.6	37	c.196_204delCCCCCAGCT	CCDS34195.1																																																																																				0.732	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		4	5						4	5	---	---	---	---
CACNA2D1	781	broad.mit.edu	37	7	81596976	81596977	+	Frame_Shift_Del	DEL	AC	AC	-			TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-11A-21D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	3f734baf-71fe-415d-aad5-cb29b08cfe9c	g.chr7:81596976_81596977delAC	ENST00000356253.5	-	30	2689_2690	c.2434_2435delGT	c.(2434-2436)gttfs	p.V812fs	CACNA2D1_ENST00000356860.3_Frame_Shift_Del_p.V800fs|CACNA2D1_ENST00000535308.1_Frame_Shift_Del_p.V12fs			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	812					calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	TTTAATTCCAACAACTGAAAAA	0.262																																						ENST00000356860.3																			0				breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81						c.(2398-2400)tfs		calcium channel, voltage-dependent, alpha 2/delta subunit 1	Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)																																			SO:0001589	frameshift_variant	781					voltage-gated calcium channel complex	metal ion binding	g.chr7:81596976_81596977delAC	M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"""Calcium channel subunits"""	1399	protein-coding gene	gene with protein product		114204	"""long intergenic non-protein coding RNA 1112"""	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.2434_2435delGT	7.37:g.81596976_81596977delAC	ENSP00000348589:p.Val812fs					CACNA2D1_ENST00000535308.1_Frame_Shift_Del_p.V12fs|CACNA2D1_ENST00000356253.5_Frame_Shift_Del_p.V812fs	p.V800fs	NM_000722.2	NP_000713.2	P54289	CA2D1_HUMAN			30	2736_2737	-			812					Q17R45|Q9UD80|Q9UD81|Q9UD82	Frame_Shift_Del	DEL	ENST00000356253.5	37	c.2398_2399delGT																																																																																					0.262	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding				2	4						2	4	---	---	---	---
SSPO	23145	broad.mit.edu	37	7	149499116	149499117	+	RNA	DEL	AT	AT	-	rs61047652	byFrequency	TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-11A-21D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	3f734baf-71fe-415d-aad5-cb29b08cfe9c	g.chr7:149499116_149499117delAT	ENST00000378016.2	+	0	7495							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CCCGGCCCCCATGCCCCTGCAG	0.703														853	0.170327	0.0242	0.2262	5008	,	,		13338	0.1726		0.2674	False		,,,				2504	0.226					ENST00000378016.2																			0													SCO-spondin				151,3337		13,125,1606						-6.4	0.0		dbSNP_129	6	1814,5686		323,1168,2259	no	intron	SSPO	NM_198455.2		336,1293,3865	A1A1,A1R,RR		24.1867,4.3291,17.8831				1965,9023						23145				cell adhesion	extracellular space	peptidase inhibitor activity	g.chr7:149499116_149499117delAT	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149499116_149499117delAT										A2VEC9	SSPO_HUMAN	OV - Ovarian serous cystadenocarcinoma(82;0.00625)		0	7495	+	Melanoma(164;0.165)|Ovarian(565;0.177)							Q76B61	RNA	DEL	ENST00000378016.2	37																																																																																						0.703	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				4	8						4	8	---	---	---	---
RP11-439I14.2	0	broad.mit.edu	37	16	64770704	64770705	+	lincRNA	INS	-	-	CCAGTGATGGTCACCT	rs200421189|rs71143515|rs377231404|rs145408521|rs140029302	byFrequency	TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-11A-21D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	3f734baf-71fe-415d-aad5-cb29b08cfe9c	g.chr16:64770704_64770705insCCAGTGATGGTCACCT	ENST00000564293.1	+	0	453_454																											TGTCACCACTGCCACCTTGTTC	0.371														3288	0.65655	0.8434	0.5144	5008	,	,		21531	0.6052		0.5537	False		,,,				2504	0.6636					ENST00000564293.1																			0																																																			0							g.chr16:64770704_64770705insCCAGTGATGGTCACCT																													16.37:g.64770704_64770705insCCAGTGATGGTCACCT														0	453_454	+									RNA	INS	ENST00000564293.1	37																																																																																						0.371	RP11-439I14.2-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000422725.1			3	3						3	3	---	---	---	---
KRT10	3858	broad.mit.edu	37	17	38978766	38978768	+	In_Frame_Del	DEL	TCC	TCC	-	rs148510452|rs556262610	byFrequency	TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-11A-21D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	3f734baf-71fe-415d-aad5-cb29b08cfe9c	g.chr17:38978766_38978768delTCC	ENST00000269576.5	-	1	79_81	c.70_72delGGA	c.(70-72)ggadel	p.G24del	TMEM99_ENST00000301665.3_Intron|TMEM99_ENST00000496847.1_Intron	NM_000421.3	NP_000412	P13645	K1C10_HUMAN	keratin 10	24	Gly-rich.|Head.			Missing (in Ref. 1; AAA60544). {ECO:0000305}.	cellular response to calcium ion (GO:0071277)|keratinocyte differentiation (GO:0030216)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of epidermis (GO:0030280)			NS(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	11		Breast(137;0.000301)				ctcctccacatcctcctcctcct	0.547																																						ENST00000269576.5																			0				NS(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	11						c.(70-72)del		keratin 10			,,,	689,7,3556		198,0,293,0,7,1628					,,,	3.0	0.1		dbSNP_134	51	1494,8,6750		368,0,758,0,8,2992	no	intron,intron,intron,codingComplex	KRT10,TMEM99	NM_145274.3,NM_001195387.1,NM_001195386.1,NM_000421.3	,,,	566,0,1051,0,15,4620	A1A1,A1A2,A1R,A2A2,A2R,RR		18.2016,16.3688,17.5784	,,,	,,,		2183,15,10306				SO:0001651	inframe_deletion	3858				epidermis development		protein binding|structural constituent of epidermis	g.chr17:38978766_38978768delTCC	J04029	CCDS11377.1	17q21.2	2013-06-20	2008-08-01		ENSG00000186395	ENSG00000186395		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6413	protein-coding gene	gene with protein product	"""cytokeratin 10"", ""epidermolytic hyperkeratosis"""	148080	"""keratosis palmaris et plantaris"""	KPP		2461420, 16831889	Standard	NM_000421		Approved	K10, CK10	uc002hvi.3	P13645	OTTHUMG00000133368	ENST00000269576.5:c.70_72delGGA	17.37:g.38978775_38978777delTCC	ENSP00000269576:p.Gly24del					TMEM99_ENST00000301665.3_Intron|TMEM99_ENST00000496847.1_Intron	p.G24del	NM_000421.3	NP_000412.3	P13645	K1C10_HUMAN			1	79_81	-		Breast(137;0.000301)	24	Missing (in Ref. 1; AAA60544).		Gly-rich.|Head.		Q14664|Q8N175	In_Frame_Del	DEL	ENST00000269576.5	37	c.70_72delGGA	CCDS11377.1																																																																																				0.547	KRT10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257875.1	NM_000421		8	28						8	28	---	---	---	---
BAGE2	85319	broad.mit.edu	37	21	11085837	11085838	+	RNA	INS	-	-	TAC	rs199904990		TCGA-BJ-A45F-01A-12D-A23U-08	TCGA-BJ-A45F-11A-21D-A23U-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6ce7fe03-659a-4e69-a365-9096354276e4	3f734baf-71fe-415d-aad5-cb29b08cfe9c	g.chr21:11085837_11085838insTAC	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)		accatcaccatcaccaccacca	0.584																																						ENST00000470054.1																			0													B melanoma antigen family, member 2																																						85319							g.chr21:11085837_11085838insTAC	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.11085837_11085838insTAC												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	INS	ENST00000470054.1	37																																																																																						0.584	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482		2	4						2	4	---	---	---	---
