#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
LOC220729	220729	broad.mit.edu	37	3	197348668	197348668	+	RNA	SNP	C	C	G	rs79940815	byFrequency	TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr3:197348668C>G	ENST00000418868.1	-	0	591					NR_003266.2																						ACTTGAGGCTCTGTCCACCAA	0.488													C|||	539	0.107628	0.0083	0.0692	5008	,	,		20710	0.1776		0.1074	False		,,,				2504	0.1973					ENST00000418868.1																			0																																																			0							g.chr3:197348668C>G																													3.37:g.197348668C>G								NR_003266.2						0	591	-									RNA	SNP	ENST00000418868.1	37																																																																																						0.488	AC024560.3-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000340283.1			4	190	0	0	0	1	0	4	190				
SETBP1	26040	broad.mit.edu	37	18	42281493	42281493	+	Missense_Mutation	SNP	A	A	T			TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr18:42281493A>T	ENST00000282030.5	+	2	478	c.182A>T	c.(181-183)gAt>gTt	p.D61V	SETBP1_ENST00000426838.4_Missense_Mutation_p.D61V	NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	61						nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		GAGGAGGAGGATGAACTAGGC	0.582									Schinzel-Giedion syndrome																													ENST00000282030.5																			0				NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104						c.(181-183)gAt>gTt		SET binding protein 1							79.0	67.0	71.0					18																	42281493		2203	4300	6503	SO:0001583	missense	26040	Schinzel-Giedion syndrome	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome		nucleus	DNA binding	g.chr18:42281493A>T	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217			15573	protein-coding gene	gene with protein product		611060				11231286	Standard	NM_015559		Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	ENST00000282030.5:c.182A>T	18.37:g.42281493A>T	ENSP00000282030:p.Asp61Val					SETBP1_ENST00000426838.4_Missense_Mutation_p.D61V	p.D61V	NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN		Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)	2	478	+			61					A6H8W5|Q6P6C3|Q9UEF3	Missense_Mutation	SNP	ENST00000282030.5	37	c.182A>T	CCDS11923.2	.	.	.	.	.	.	.	.	.	.	A	18.70	3.680110	0.68042	.	.	ENSG00000152217	ENST00000426838;ENST00000282030;ENST00000552979	T	0.71461	-0.57	5.7	5.7	0.88788	.	0.059261	0.64402	D	0.000003	T	0.78723	0.4328	L	0.44542	1.39	0.58432	D	0.999997	D;P	0.76494	0.999;0.936	D;P	0.66351	0.943;0.64	T	0.80917	-0.1168	10	0.87932	D	0	.	15.9644	0.79956	1.0:0.0:0.0:0.0	.	61;61	Q9Y6X0;Q9Y6X0-2	SETBP_HUMAN;.	V	61	ENSP00000282030:D61V	ENSP00000282030:D61V	D	+	2	0	SETBP1	40535491	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.636000	0.61339	2.170000	0.68504	0.482000	0.46254	GAT		0.582	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110		12	114	0	0	0	1	0	12	114				
ARHGAP30	257106	broad.mit.edu	37	1	161024210	161024210	+	Missense_Mutation	SNP	T	T	A			TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr1:161024210T>A	ENST00000368013.3	-	5	802	c.482A>T	c.(481-483)cAg>cTg	p.Q161L	ARHGAP30_ENST00000368015.1_Intron|ARHGAP30_ENST00000368016.3_Missense_Mutation_p.Q161L	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	161	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)			breast(2)|cervix(3)|endometrium(4)|kidney(2)|large_intestine(4)|lung(6)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			CATGTTGGTCTGGGCACTGAA	0.597																																						ENST00000368013.3																			0				breast(2)|cervix(3)|endometrium(4)|kidney(2)|large_intestine(4)|lung(6)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						c.(481-483)cAg>cTg		Rho GTPase activating protein 30							106.0	87.0	93.0					1																	161024210		2202	4300	6502	SO:0001583	missense	257106				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity	g.chr1:161024210T>A	AL832852	CCDS1215.1, CCDS30918.1, CCDS72958.1	1q23.3	2011-06-29			ENSG00000186517	ENSG00000186517		"""Rho GTPase activating proteins"""	27414	protein-coding gene	gene with protein product		614264					Standard	NM_001287602		Approved	FLJ00267	uc001fxl.3	Q7Z6I6	OTTHUMG00000031477	ENST00000368013.3:c.482A>T	1.37:g.161024210T>A	ENSP00000356992:p.Gln161Leu					ARHGAP30_ENST00000368016.3_Missense_Mutation_p.Q161L|ARHGAP30_ENST00000368015.1_Intron	p.Q161L	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	BRCA - Breast invasive adenocarcinoma(70;0.00122)		5	802	-	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		161			Rho-GAP.		Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	Missense_Mutation	SNP	ENST00000368013.3	37	c.482A>T	CCDS30918.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.189102	0.78789	.	.	ENSG00000186517	ENST00000368016;ENST00000368013;ENST00000368017	T;T	0.18016	2.24;2.24	5.47	5.47	0.80525	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.136109	0.49916	D	0.000136	T	0.07818	0.0196	N	0.12637	0.245	0.80722	D	1	P;B	0.37781	0.608;0.216	B;B	0.44224	0.444;0.234	T	0.17167	-1.0378	10	0.66056	D	0.02	.	13.5662	0.61819	0.0:0.0:0.0:1.0	.	161;161	Q7Z6I6;Q7Z6I6-2	RHG30_HUMAN;.	L	161;161;13	ENSP00000356995:Q161L;ENSP00000356992:Q161L	ENSP00000356992:Q161L	Q	-	2	0	ARHGAP30	159290834	0.981000	0.34729	0.998000	0.56505	0.993000	0.82548	1.585000	0.36600	2.081000	0.62600	0.524000	0.50904	CAG		0.597	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720		13	39	0	0	0	1	0	13	39				
TSSC2	650368	broad.mit.edu	37	11	3427845	3427845	+	RNA	SNP	C	C	T			TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr11:3427845C>T	ENST00000529482.1	+	0	962									tumor suppressing subtransferable candidate 2 pseudogene																		CTTCAAGTGGCAGGAGCAGAA	0.587																																						ENST00000529482.1																			0																																																			0							g.chr11:3427845C>T			11p15.4	2014-06-05	2008-06-30		ENSG00000223756	ENSG00000223756			12384	pseudogene	pseudogene	"""tumor-supressing STF cDNA 2"", ""asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase) (ALG1) pseudogene"""	608999	"""tumor suppressing subtransferable candidate 2"""			9403053	Standard	NR_024248		Approved				OTTHUMG00000011705		11.37:g.3427845C>T														0	962	+									RNA	SNP	ENST00000529482.1	37																																																																																						0.587	TSSC2-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000392020.1			6	75	0	0	0	1	0	6	75				
COL6A3	1293	broad.mit.edu	37	2	238280362	238280362	+	Intron	SNP	G	G	A	rs370194938|rs368338594		TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr2:238280362G>A	ENST00000295550.4	-	9	4738				COL6A3_ENST00000472056.1_Intron|COL6A3_ENST00000347401.3_Intron|COL6A3_ENST00000409809.1_Intron|COL6A3_ENST00000392003.2_Missense_Mutation_p.A1026V|COL6A3_ENST00000346358.4_Intron|COL6A3_ENST00000353578.4_Intron|COL6A3_ENST00000392004.3_Missense_Mutation_p.A1227V	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3						axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		AACCTCCGACGCCCCCATCTC	0.478																																						ENST00000392004.3																			0				breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217						c.(3679-3681)gCg>gTg		collagen, type VI, alpha 3		G	,VAL/ALA,VAL/ALA,,	0,4406		0,0,2203	71.0	79.0	76.0		,3077,3680,,	-3.3	0.0	2		76	1,8599	1.2+/-3.3	0,1,4299	no	intron,missense,missense,intron,intron	COL6A3	NM_004369.3,NM_057164.4,NM_057165.4,NM_057166.4,NM_057167.3	,64,64,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,,	,1026/1037,1227/1238,,	238280362	1,13005	2203	4300	6503	SO:0001627	intron_variant	1293				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity	g.chr2:238280362G>A	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.4285+12C>T	2.37:g.238280362G>A						COL6A3_ENST00000353578.4_Intron|COL6A3_ENST00000347401.3_Intron|COL6A3_ENST00000295550.4_Intron|COL6A3_ENST00000472056.1_Intron|COL6A3_ENST00000346358.4_Intron|COL6A3_ENST00000409809.1_Intron|COL6A3_ENST00000392003.2_Missense_Mutation_p.A1026V	p.A1227V	NM_057165.4	NP_476506.3	P12111	CO6A3_HUMAN		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)	8	3934	-		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)	1434			Nonhelical region.		A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	c.3680C>T	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	G	1.522	-0.546659	0.04024	0.0	1.16E-4	ENSG00000163359	ENST00000392004;ENST00000392003	T;T	0.61158	0.27;0.13	1.65	-3.29	0.05017	.	.	.	.	.	T	0.32285	0.0824	N	0.08118	0	0.09310	N	1	P;P	0.40578	0.718;0.722	B;B	0.39299	0.283;0.296	T	0.35895	-0.9770	9	0.54805	T	0.06	.	5.9709	0.19351	0.2324:0.2927:0.4749:0.0	.	1026;1227	A8MT30;E9PGQ9	.;.	V	1227;1026	ENSP00000375861:A1227V;ENSP00000375860:A1026V	ENSP00000375860:A1026V	A	-	2	0	COL6A3	237945101	.	.	0.000000	0.03702	0.000000	0.00434	.	.	-3.339000	0.00184	-3.258000	0.00049	GCG		0.478	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		5	246	0	0	0	1	0	5	246				
VPS13D	55187	broad.mit.edu	37	1	12416017	12416017	+	Missense_Mutation	SNP	C	C	G			TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr1:12416017C>G	ENST00000358136.3	+	48	9871	c.9741C>G	c.(9739-9741)aaC>aaG	p.N3247K	VPS13D_ENST00000356315.4_Missense_Mutation_p.N3222K	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		GAACCCAAAACTATATGGTGA	0.438																																						ENST00000358136.3																			0				NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130						c.(9739-9741)aaC>aaG		vacuolar protein sorting 13 homolog D (S. cerevisiae)							105.0	98.0	100.0					1																	12416017		2203	4300	6503	SO:0001583	missense	55187				protein localization			g.chr1:12416017C>G	AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"""vacuolar protein sorting 13D (yeast)"""				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.9741C>G	1.37:g.12416017C>G	ENSP00000350854:p.Asn3247Lys					VPS13D_ENST00000356315.4_Missense_Mutation_p.N3222K	p.N3247K	NM_015378.2	NP_056193.2	Q5THJ4	VP13D_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)	48	9871	+	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)	3246						Missense_Mutation	SNP	ENST00000358136.3	37	c.9741C>G	CCDS30588.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.0|24.0	4.481464|4.481464	0.84747|0.84747	.|.	.|.	ENSG00000048707|ENSG00000048707	ENST00000356315;ENST00000358136|ENST00000011700	T;T|.	0.53206|.	0.63;0.63|.	5.89|5.89	4.99|4.99	0.66335|0.66335	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.59018|0.59018	0.2163|0.2163	L|L	0.39898|0.39898	1.24|1.24	0.80722|0.80722	D|D	1|1	P;P|.	0.48834|.	0.916;0.863|.	P;B|.	0.46362|.	0.514;0.428|.	T|T	0.55927|0.55927	-0.8063|-0.8063	10|5	0.22109|.	T|.	0.4|.	.|.	15.0319|15.0319	0.71713|0.71713	0.0:0.932:0.0:0.068|0.0:0.932:0.0:0.068	.|.	3222;3246|.	Q5THJ4-2;Q5THJ4|.	.;VP13D_HUMAN|.	K|S	3222;3247|2069	ENSP00000348666:N3222K;ENSP00000350854:N3247K|.	ENSP00000348666:N3222K|.	N|T	+|+	3|2	2|0	VPS13D|VPS13D	12338604|12338604	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	5.754000|5.754000	0.68743|0.68743	1.505000|1.505000	0.48720|0.48720	0.655000|0.655000	0.94253|0.94253	AAC|ACT		0.438	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		5	125	0	0	0	1	0	5	125				
BAGE2	85319	broad.mit.edu	37	21	11058353	11058353	+	RNA	SNP	T	T	C	rs79433933		TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr21:11058353T>C	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		GAAATCTCTTTATAAAACCTT	0.343																																						ENST00000470054.1																			0													B melanoma antigen family, member 2							20.0	18.0	19.0					21																	11058353		692	1589	2281			85319							g.chr21:11058353T>C	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"""cancer/testis antigen family 2, member 2"""					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11058353T>C												Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)	0	324	-								A8K925|Q08ER0	RNA	SNP	ENST00000470054.1	37																																																																																						0.343	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482		13	176	0	0	0	1	0	13	176				
SH3BGR	6450	broad.mit.edu	37	21	40823936	40823936	+	Missense_Mutation	SNP	G	G	A			TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr21:40823936G>A	ENST00000333634.4	+	1	181	c.103G>A	c.(103-105)Gct>Act	p.A35T	SH3BGR_ENST00000380637.3_Intron|SH3BGR_ENST00000458295.1_Intron|SH3BGR_ENST00000380634.1_Intron|SH3BGR_ENST00000380631.1_Intron	NM_007341.2	NP_031367	P55822	SH3BG_HUMAN	SH3 domain binding glutamate-rich protein	35					positive regulation of signal transduction (GO:0009967)|protein complex assembly (GO:0006461)	cytosol (GO:0005829)	SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(2)	8		all_cancers(19;1.16e-23)|all_epithelial(19;1.22e-20)|Prostate(19;2.55e-06)|Breast(209;0.0133)		STAD - Stomach adenocarcinoma(101;0.00151)		CCTGGCACTTGCTTGCCTGTG	0.592																																						ENST00000333634.4																			0				NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(2)	8						c.(103-105)Gct>Act		SH3 domain binding glutamic acid-rich protein							101.0	99.0	100.0					21																	40823936		2203	4300	6503	SO:0001583	missense	6450				protein complex assembly	cytosol	SH3 domain binding|SH3/SH2 adaptor activity	g.chr21:40823936G>A		CCDS13666.1, CCDS33560.1	21q22.3	2014-02-19	2014-02-19		ENSG00000185437	ENSG00000185437			10822	protein-coding gene	gene with protein product	"""21-glutamic acid-rich protein"""	602230	"""SH3 domain binding glutamic acid-rich protein"""			9050928	Standard	NM_007341		Approved	21-GARP	uc002yya.3	P55822	OTTHUMG00000074113	ENST00000333634.4:c.103G>A	21.37:g.40823936G>A	ENSP00000332513:p.Ala35Thr					SH3BGR_ENST00000458295.1_Intron|SH3BGR_ENST00000380631.1_Intron|SH3BGR_ENST00000380634.1_Intron|SH3BGR_ENST00000380637.3_Intron	p.A35T	NM_007341.2	NP_031367.1	P55822	SH3BG_HUMAN		STAD - Stomach adenocarcinoma(101;0.00151)	1	181	+		all_cancers(19;1.16e-23)|all_epithelial(19;1.22e-20)|Prostate(19;2.55e-06)|Breast(209;0.0133)	35					A6ND59|D3DSI2|Q9BRB8	Missense_Mutation	SNP	ENST00000333634.4	37	c.103G>A	CCDS13666.1	.	.	.	.	.	.	.	.	.	.	G	14.20	2.465692	0.43839	.	.	ENSG00000185437	ENST00000333634	T	0.28255	1.62	4.22	2.29	0.28610	.	1.996380	0.02457	N	0.086146	T	0.19846	0.0477	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.10450	0.005	T	0.22730	-1.0208	10	0.72032	D	0.01	.	7.5132	0.27585	0.0932:0.1658:0.741:0.0	.	35	P55822	SH3BG_HUMAN	T	35	ENSP00000332513:A35T	ENSP00000332513:A35T	A	+	1	0	SH3BGR	39745806	0.000000	0.05858	0.005000	0.12908	0.300000	0.27592	0.483000	0.22292	1.013000	0.39391	0.655000	0.94253	GCT		0.592	SH3BGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157377.6	NM_007341		5	195	0	0	0	1	0	5	195				
SERF2	10169	broad.mit.edu	37	15	44085945	44085945	+	Missense_Mutation	SNP	A	A	T			TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr15:44085945A>T	ENST00000381359.1	+	5	1083	c.154A>T	c.(154-156)Aac>Tac	p.N52Y	MIR1282_ENST00000408865.1_RNA|SERF2_ENST00000249786.4_Missense_Mutation_p.N52Y|SERF2_ENST00000409291.1_Intron|HYPK_ENST00000406925.1_5'Flank|SERF2_ENST00000594896.1_Intron|SERF2_ENST00000409960.2_Missense_Mutation_p.Q96H|SERF2_ENST00000339624.5_Missense_Mutation_p.Q59H|SERF2_ENST00000402131.1_Missense_Mutation_p.N38Y|RP11-296A16.1_ENST00000417761.2_Intron|SERF2_ENST00000403425.1_Missense_Mutation_p.N38Y|SERF2_ENST00000409614.1_Missense_Mutation_p.N38Y|SERF2_ENST00000409646.1_Intron	NM_001199877.1	NP_001186806.1	P84101	SERF2_HUMAN	small EDRK-rich factor 2	52						cytosol (GO:0005829)|nucleus (GO:0005634)				lung(1)	1		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;7.81e-07)		GAAAAAGGCAAACGAGAAGAA	0.572																																						ENST00000381359.1																			0				lung(1)	1						c.(154-156)Aac>Tac		small EDRK-rich factor 2							215.0	176.0	189.0					15																	44085945		2198	4298	6496	SO:0001583	missense	10169					cytosol|nucleus		g.chr15:44085945A>T	AF073298	CCDS32218.1, CCDS55963.1, CCDS55964.1, CCDS55965.1	15q15.1	2008-01-18			ENSG00000140264	ENSG00000140264			10757	protein-coding gene	gene with protein product		605054				9731538	Standard	NM_001199876		Approved	H4F5rel, 4F5REL, FAM2C, HsT17089	uc010bdq.3	P84101	OTTHUMG00000059935	ENST00000381359.1:c.154A>T	15.37:g.44085945A>T	ENSP00000370764:p.Asn52Tyr					SERF2_ENST00000409291.1_Intron|SERF2_ENST00000402131.1_Missense_Mutation_p.N38Y|SERF2_ENST00000594896.1_Intron|SERF2_ENST00000409960.2_Missense_Mutation_p.Q96H|SERF2_ENST00000409614.1_Missense_Mutation_p.N38Y|SERF2_ENST00000409646.1_Intron|MIR1282_ENST00000408865.1_RNA|SERF2_ENST00000403425.1_Missense_Mutation_p.N38Y|SERF2_ENST00000339624.5_Missense_Mutation_p.Q59H|SERF2_ENST00000249786.4_Missense_Mutation_p.N52Y|RP11-296A16.1_ENST00000417761.2_Intron	p.N52Y	NM_001199877.1	NP_001186806.1	P84101	SERF2_HUMAN		GBM - Glioblastoma multiforme(94;7.81e-07)	5	1083	+		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)	52					A6NL45|B5MCG1|B9A026|O75918|O88891|Q9BZH7	Missense_Mutation	SNP	ENST00000381359.1	37	c.154A>T	CCDS32218.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.81|13.81	2.347824|2.347824	0.41599|0.41599	.|.	.|.	ENSG00000140264|ENSG00000140264	ENST00000381359;ENST00000249786;ENST00000402131;ENST00000403425;ENST00000409614|ENST00000409960;ENST00000339624	T;T;T;T;T|T;T	0.51817|0.55052	0.85;0.85;0.69;0.69;0.69|0.55;0.54	5.93|5.93	5.93|5.93	0.95920|0.95920	.|.	.|.	.|.	.|.	.|.	T|T	0.64594|0.64594	0.2612|0.2612	.|.	.|.	.|.	0.26907|0.26907	N|N	0.966983|0.966983	B|D;P	0.28026|0.61080	0.198|0.989;0.704	B|P;B	0.12837|0.56916	0.008|0.809;0.36	T|T	0.61019|0.61019	-0.7147|-0.7147	8|8	0.87932|0.51188	D|T	0|0.08	.|.	12.7757|12.7757	0.57445|0.57445	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	52|59;96	P84101|A6NL45;B9A026	SERF2_HUMAN|.;.	Y|H	52;52;38;38;38|96;59	ENSP00000370764:N52Y;ENSP00000249786:N52Y;ENSP00000386044:N38Y;ENSP00000384300:N38Y;ENSP00000386783:N38Y|ENSP00000387187:Q96H;ENSP00000339647:Q59H	ENSP00000249786:N52Y|ENSP00000339647:Q59H	N|Q	+|+	1|3	0|2	SERF2|SERF2	41873237|41873237	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	1.727000|1.727000	0.38095|0.38095	2.258000|2.258000	0.74832|0.74832	0.533000|0.533000	0.62120|0.62120	AAC|CAA		0.572	SERF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133233.2	NM_005770		5	189	0	0	0	1	0	5	189				
FRG1B	284802	broad.mit.edu	37	20	29625877	29625877	+	Missense_Mutation	SNP	G	G	A	rs7266938	byFrequency	TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr20:29625877G>A	ENST00000278882.3	+	5	501	c.121G>A	c.(121-123)Gcc>Acc	p.A41T	FRG1B_ENST00000439954.2_Missense_Mutation_p.A46T|FRG1B_ENST00000358464.4_Missense_Mutation_p.A41T			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	41								p.A41T(2)		endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						GTACAGAATCGCCCTGAAATC	0.358																																						ENST00000278882.3																			2	Substitution - Missense(2)	p.A41T(2)	urinary_tract(2)	endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						c.(121-123)Gcc>Acc																																						SO:0001583	missense	0							g.chr20:29625877G>A			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.121G>A	20.37:g.29625877G>A	ENSP00000278882:p.Ala41Thr					FRG1B_ENST00000439954.2_Missense_Mutation_p.A46T|FRG1B_ENST00000358464.4_Missense_Mutation_p.A41T	p.A41T							5	501	+								C4AME5	Missense_Mutation	SNP	ENST00000278882.3	37	c.121G>A		.	.	.	.	.	.	.	.	.	.	g	8.740	0.918766	0.17982	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	T	0.62498	0.02	1.68	1.68	0.24146	.	0.000000	0.85682	D	0.000000	T	0.48277	0.1491	.	.	.	0.52099	D	0.999942	B	0.24186	0.099	B	0.27715	0.082	T	0.43956	-0.9359	9	0.33940	T	0.23	.	9.3557	0.38164	0.0:0.0:1.0:0.0	rs7266938;rs7266938	46	F5H5R5	.	T	41;46;41	ENSP00000408863:A46T	ENSP00000278882:A41T	A	+	1	0	FRG1B	28239538	1.000000	0.71417	0.993000	0.49108	0.033000	0.12548	5.232000	0.65332	1.250000	0.43966	0.184000	0.17185	GCC		0.358	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078494.2	NR_003579		6	138	0	0	0	1	0	6	138				
SERF2	10169	broad.mit.edu	37	15	44085952	44085952	+	Missense_Mutation	SNP	A	A	T			TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr15:44085952A>T	ENST00000381359.1	+	5	1090	c.161A>T	c.(160-162)aAg>aTg	p.K54M	MIR1282_ENST00000408865.1_RNA|SERF2_ENST00000249786.4_Missense_Mutation_p.K54M|SERF2_ENST00000409291.1_Intron|HYPK_ENST00000406925.1_5'Flank|SERF2_ENST00000594896.1_Intron|SERF2_ENST00000409960.2_Nonsense_Mutation_p.R99*|SERF2_ENST00000339624.5_Nonsense_Mutation_p.R62*|SERF2_ENST00000402131.1_Missense_Mutation_p.K40M|RP11-296A16.1_ENST00000417761.2_Intron|SERF2_ENST00000403425.1_Missense_Mutation_p.K40M|SERF2_ENST00000409614.1_Missense_Mutation_p.K40M|SERF2_ENST00000409646.1_Intron	NM_001199877.1	NP_001186806.1	P84101	SERF2_HUMAN	small EDRK-rich factor 2	54						cytosol (GO:0005829)|nucleus (GO:0005634)				lung(1)	1		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;7.81e-07)		GCAAACGAGAAGAAGGAGGAA	0.562																																						ENST00000409960.2																			0				lung(1)	1						c.(295-297)Aga>Tga		small EDRK-rich factor 2							214.0	175.0	188.0					15																	44085952		2198	4298	6496	SO:0001583	missense	10169					cytosol|nucleus		g.chr15:44085952A>T	AF073298	CCDS32218.1, CCDS55963.1, CCDS55964.1, CCDS55965.1	15q15.1	2008-01-18			ENSG00000140264	ENSG00000140264			10757	protein-coding gene	gene with protein product		605054				9731538	Standard	NM_001199876		Approved	H4F5rel, 4F5REL, FAM2C, HsT17089	uc010bdq.3	P84101	OTTHUMG00000059935	ENST00000381359.1:c.161A>T	15.37:g.44085952A>T	ENSP00000370764:p.Lys54Met					SERF2_ENST00000409291.1_Intron|SERF2_ENST00000402131.1_Missense_Mutation_p.K40M|SERF2_ENST00000594896.1_Intron|SERF2_ENST00000409614.1_Missense_Mutation_p.K40M|SERF2_ENST00000381359.1_Missense_Mutation_p.K54M|SERF2_ENST00000409646.1_Intron|MIR1282_ENST00000408865.1_RNA|SERF2_ENST00000403425.1_Missense_Mutation_p.K40M|SERF2_ENST00000339624.5_Nonsense_Mutation_p.R62*|SERF2_ENST00000249786.4_Missense_Mutation_p.K54M|RP11-296A16.1_ENST00000417761.2_Intron	p.R99*	NM_001199875.1	NP_001186804.1	P84101	SERF2_HUMAN		GBM - Glioblastoma multiforme(94;7.81e-07)	3	342	+		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)	0					A6NL45|B5MCG1|B9A026|O75918|O88891|Q9BZH7	Nonsense_Mutation	SNP	ENST00000381359.1	37	c.295A>T	CCDS32218.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.7|24.7	4.556558|4.556558	0.86231|0.86231	.|.	.|.	ENSG00000140264|ENSG00000140264	ENST00000381359;ENST00000249786;ENST00000402131;ENST00000403425;ENST00000409614|ENST00000409960;ENST00000339624	T;T;T;T;T|.	0.58652|.	0.64;0.64;0.32;0.32;0.32|.	5.93|5.93	5.93|5.93	0.95920|0.95920	.|.	.|.	.|.	.|.	.|.	T|.	0.73156|.	0.3551|.	.|.	.|.	.|.	0.38867|0.38867	D|D	0.956615|0.956615	P|.	0.51240|.	0.943|.	P|.	0.55667|.	0.781|.	T|.	0.77653|.	-0.2507|.	8|.	0.72032|0.66056	D|D	0.01|0.02	.|.	12.7757|12.7757	0.57445|0.57445	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	54|.	P84101|.	SERF2_HUMAN|.	M|X	54;54;40;40;40|99;62	ENSP00000370764:K54M;ENSP00000249786:K54M;ENSP00000386044:K40M;ENSP00000384300:K40M;ENSP00000386783:K40M|.	ENSP00000249786:K54M|ENSP00000339647:R62X	K|R	+|+	2|1	0|2	SERF2|SERF2	41873244|41873244	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	3.957000|3.957000	0.56730|0.56730	2.258000|2.258000	0.74832|0.74832	0.533000|0.533000	0.62120|0.62120	AAG|AGA		0.562	SERF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133233.2	NM_005770		6	183	0	0	0	1	0	6	183				
ADAM15	8751	broad.mit.edu	37	1	155026852	155026852	+	Missense_Mutation	SNP	A	A	G			TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr1:155026852A>G	ENST00000356955.2	+	6	583	c.482A>G	c.(481-483)cAg>cGg	p.Q161R	ADAM15_ENST00000271836.6_Missense_Mutation_p.Q161R|ADAM15_ENST00000368410.2_Intron|ADAM15_ENST00000531455.1_Missense_Mutation_p.Q171R|ADAM15_ENST00000368413.1_Intron|ADAM15_ENST00000359280.4_Missense_Mutation_p.Q161R|ADAM15_ENST00000355956.2_Missense_Mutation_p.Q161R|ADAM15_ENST00000449910.2_Missense_Mutation_p.Q161R|ADAM15_ENST00000472434.1_3'UTR|ADAM15_ENST00000360674.4_Missense_Mutation_p.Q161R|ADAM15_ENST00000447332.3_Missense_Mutation_p.Q145R|ADAM15_ENST00000368412.3_Missense_Mutation_p.Q161R	NM_207197.2	NP_997080.1	Q13444	ADA15_HUMAN	ADAM metallopeptidase domain 15	161					angiogenesis (GO:0001525)|cardiac epithelial to mesenchymal transition (GO:0060317)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of receptor binding (GO:1900121)|protein kinase C signaling (GO:0070528)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(5)|urinary_tract(1)	39	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)			GGGGACCTTCAGGGTCCTCCC	0.547																																						ENST00000356955.2																			0				NS(1)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(5)|urinary_tract(1)	39						c.(481-483)cAg>cGg		ADAM metallopeptidase domain 15							53.0	60.0	58.0					1																	155026852		2203	4300	6503	SO:0001583	missense	8751				angiogenesis|cell-matrix adhesion|collagen catabolic process|proteolysis	acrosomal vesicle|adherens junction|endomembrane system|flagellum|integral to membrane	metalloendopeptidase activity|SH3 domain binding|zinc ion binding	g.chr1:155026852A>G	U46005	CCDS1084.1, CCDS1085.1, CCDS1086.1, CCDS1087.1, CCDS1088.1, CCDS44236.1, CCDS58031.1, CCDS58032.1, CCDS60282.1	1q21.3	2008-02-05	2007-06-04		ENSG00000143537	ENSG00000143537		"""ADAM metallopeptidase domain containing"""	193	protein-coding gene	gene with protein product	"""metargidin"""	605548	"""a disintegrin and metalloproteinase domain 15 (metargidin)"""			9516430	Standard	NM_003815		Approved	MDC15	uc001fgr.2	Q13444	OTTHUMG00000013898	ENST00000356955.2:c.482A>G	1.37:g.155026852A>G	ENSP00000349436:p.Gln161Arg					ADAM15_ENST00000355956.2_Missense_Mutation_p.Q161R|ADAM15_ENST00000447332.3_Missense_Mutation_p.Q145R|ADAM15_ENST00000360674.4_Missense_Mutation_p.Q161R|ADAM15_ENST00000271836.6_Missense_Mutation_p.Q161R|ADAM15_ENST00000368412.3_Missense_Mutation_p.Q161R|ADAM15_ENST00000531455.1_Missense_Mutation_p.Q171R|ADAM15_ENST00000368410.2_Intron|ADAM15_ENST00000359280.4_Missense_Mutation_p.Q161R|ADAM15_ENST00000368413.1_Intron|ADAM15_ENST00000449910.2_Missense_Mutation_p.Q161R|ADAM15_ENST00000472434.1_3'UTR	p.Q161R	NM_207197.2	NP_997080.1	Q13444	ADA15_HUMAN	BRCA - Breast invasive adenocarcinoma(34;0.000434)		6	583	+	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		161					B3KQU5|B4DLB5|B4DMH8|E9PN65|Q13493|Q53XQ0|Q5SR68|Q5SR69|Q6R267|Q71S61|Q71S62|Q71S63|Q71S64|Q71S65|Q71S66|Q71S67|Q71S68|Q71S69|Q96C78|U3KQL5	Missense_Mutation	SNP	ENST00000356955.2	37	c.482A>G	CCDS1087.1	.	.	.	.	.	.	.	.	.	.	A	1.097	-0.662136	0.03454	.	.	ENSG00000143537	ENST00000356955;ENST00000449910;ENST00000359280;ENST00000360674;ENST00000368412;ENST00000355956;ENST00000271836;ENST00000531455	T;T;T;T;T;T;T;T	0.00864	5.76;5.76;5.76;5.68;5.6;5.76;5.74;5.76	4.76	-1.8	0.07907	.	0.683951	0.12134	N	0.496540	T	0.00552	0.0018	L	0.45581	1.43	0.09310	N	0.999999	B;B;B;B;P;B;B;B;B;P	0.39551	0.018;0.018;0.006;0.399;0.628;0.014;0.014;0.014;0.399;0.678	B;B;B;B;B;B;B;B;P;P	0.48598	0.026;0.026;0.016;0.396;0.396;0.015;0.015;0.015;0.583;0.531	T	0.47328	-0.9126	10	0.33141	T	0.24	.	4.4022	0.11392	0.3939:0.3295:0.2766:0.0	.	171;178;145;161;161;161;161;161;161;161	E9PN65;B7Z390;B4DMH8;Q13444-10;Q13444-2;Q13444-4;Q13444-5;Q13444-3;Q13444-9;Q13444	.;.;.;.;.;.;.;.;.;ADA15_HUMAN	R	161;161;161;161;161;161;161;171	ENSP00000349436:Q161R;ENSP00000403843:Q161R;ENSP00000352226:Q161R;ENSP00000353892:Q161R;ENSP00000357397:Q161R;ENSP00000348227:Q161R;ENSP00000271836:Q161R;ENSP00000432927:Q171R	ENSP00000271836:Q161R	Q	+	2	0	ADAM15	153293476	0.000000	0.05858	0.002000	0.10522	0.140000	0.21249	-1.172000	0.03112	-0.173000	0.10761	-0.429000	0.05907	CAG		0.547	ADAM15-019	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387168.1	NM_003815		4	199	0	0	0	1	0	4	199				
LOC220729	220729	broad.mit.edu	37	3	197348646	197348646	+	RNA	SNP	T	T	C	rs377377382		TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr3:197348646T>C	ENST00000418868.1	-	0	613					NR_003266.2																						TGGGCCTGCCTGCCCTTTCCA	0.532																																						ENST00000418868.1																			0																																																			0							g.chr3:197348646T>C																													3.37:g.197348646T>C								NR_003266.2						0	613	-									RNA	SNP	ENST00000418868.1	37																																																																																						0.532	AC024560.3-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000340283.1			6	173	0	0	0	1	0	6	173				
NFX1	4799	broad.mit.edu	37	9	33294604	33294604	+	Missense_Mutation	SNP	A	A	G			TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr9:33294604A>G	ENST00000379540.3	+	2	274	c.212A>G	c.(211-213)cAt>cGt	p.H71R	NFX1_ENST00000318524.6_Missense_Mutation_p.H71R|NFX1_ENST00000379521.4_Missense_Mutation_p.H71R	NM_002504.4	NP_002495.2	Q12986	NFX1_HUMAN	nuclear transcription factor, X-box binding 1	71					inflammatory response (GO:0006954)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25			LUSC - Lung squamous cell carcinoma(29;0.00506)	GBM - Glioblastoma multiforme(74;0.224)		GTTCATCAGCATAGTTATCAT	0.453																																						ENST00000379540.3																			0				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25						c.(211-213)cAt>cGt		nuclear transcription factor, X-box binding 1							169.0	172.0	171.0					9																	33294604		2203	4300	6503	SO:0001583	missense	0				inflammatory response|interspecies interaction between organisms|negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|ligase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr9:33294604A>G	U19759	CCDS6538.1, CCDS6539.1, CCDS6540.1	9p12	2013-12-13			ENSG00000086102	ENSG00000086102			7803	protein-coding gene	gene with protein product		603255				7964459, 2511169	Standard	NM_002504		Approved	NFX2, MGC20369, Tex42, TEG-42	uc003zsq.3	Q12986	OTTHUMG00000019772	ENST00000379540.3:c.212A>G	9.37:g.33294604A>G	ENSP00000368856:p.His71Arg					NFX1_ENST00000318524.6_Missense_Mutation_p.H71R|NFX1_ENST00000379521.4_Missense_Mutation_p.H71R	p.H71R	NM_002504.4	NP_002495.2	Q12986	NFX1_HUMAN	LUSC - Lung squamous cell carcinoma(29;0.00506)	GBM - Glioblastoma multiforme(74;0.224)	2	274	+			71					A8K6H8|Q5VXW6|Q96EL5|Q9BXI1	Missense_Mutation	SNP	ENST00000379540.3	37	c.212A>G	CCDS6538.1	.	.	.	.	.	.	.	.	.	.	A	4.777	0.144520	0.09134	.	.	ENSG00000086102	ENST00000379540;ENST00000379521;ENST00000536210;ENST00000318524	T;T;T	0.21031	2.35;2.03;2.03	5.31	2.92	0.33932	.	0.474887	0.21097	N	0.080226	T	0.11281	0.0275	N	0.20986	0.625	0.09310	N	1	B;B;B;B	0.12013	0.001;0.0;0.0;0.005	B;B;B;B	0.09377	0.004;0.001;0.003;0.004	T	0.21621	-1.0240	10	0.66056	D	0.02	.	1.6876	0.02845	0.557:0.1793:0.0916:0.1721	.	71;71;71;71	F5GXD0;Q12986;Q12986-2;Q12986-3	.;NFX1_HUMAN;.;.	R	71	ENSP00000368856:H71R;ENSP00000368836:H71R;ENSP00000317695:H71R	ENSP00000317695:H71R	H	+	2	0	NFX1	33284604	0.001000	0.12720	0.828000	0.32881	0.601000	0.36947	0.285000	0.18883	0.810000	0.34279	0.450000	0.29827	CAT		0.453	NFX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052069.1			7	333	0	0	0	1	0	7	333				
POTEC	388468	broad.mit.edu	37	18	14513675	14513675	+	Missense_Mutation	SNP	T	T	C	rs371810308	byFrequency	TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr18:14513675T>C	ENST00000358970.5	-	10	1518	c.1519A>G	c.(1519-1521)Aaa>Gaa	p.K507E		NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	507								p.K507E(2)		NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						GAATTCATTTTCTTTTCAGCC	0.284													.|||	3	0.000599042	0.0	0.0	5008	,	,		16953	0.003		0.0	False		,,,				2504	0.0					ENST00000358970.5																			2	Substitution - Missense(2)	p.K507E(2)	urinary_tract(1)|prostate(1)	NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						c.(1519-1521)Aaa>Gaa		POTE ankyrin domain family, member C							164.0	115.0	130.0					18																	14513675		692	1590	2282	SO:0001583	missense	388468							g.chr18:14513675T>C	BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33894	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 6"""		"""ANKRD26-like family B, member 2"""	A26B2			Standard	NM_001137671		Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000358970.5:c.1519A>G	18.37:g.14513675T>C	ENSP00000351856:p.Lys507Glu						p.K507E	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN			10	1518	-			507						Missense_Mutation	SNP	ENST00000358970.5	37	c.1519A>G	CCDS45835.1	.	.	.	.	.	.	.	.	.	.	t	0.001	-3.812128	0.00004	.	.	ENSG00000183206	ENST00000358970	T	0.32753	1.44	1.53	-3.07	0.05363	.	.	.	.	.	T	0.10165	0.0249	N	0.11427	0.14	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31752	-0.9932	9	0.02654	T	1	.	3.0168	0.06063	0.0:0.3604:0.2511:0.3885	.	507	B2RU33	POTEC_HUMAN	E	507	ENSP00000351856:K507E	ENSP00000351856:K507E	K	-	1	0	POTEC	14503675	0.024000	0.19004	0.012000	0.15200	0.024000	0.10985	-0.021000	0.12504	-1.054000	0.03214	-3.018000	0.00074	AAA		0.284	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269		4	144	0	0	0	1	0	4	144				
FRG1B	284802	broad.mit.edu	37	20	29625941	29625941	+	Missense_Mutation	SNP	A	A	T	rs558255572		TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr20:29625941A>T	ENST00000278882.3	+	5	565	c.185A>T	c.(184-186)gAt>gTt	p.D62V	FRG1B_ENST00000439954.2_Missense_Mutation_p.D67V|FRG1B_ENST00000358464.4_Missense_Mutation_p.D62V			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	62								p.D62V(2)		endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						GGGCATTCAGATGCAATTGGA	0.333													.|||	1	0.000199681	0.0	0.0014	5008	,	,		30607	0.0		0.0	False		,,,				2504	0.0					ENST00000278882.3																			2	Substitution - Missense(2)	p.D62V(2)	urinary_tract(2)	endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						c.(184-186)gAt>gTt																																						SO:0001583	missense	0							g.chr20:29625941A>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.185A>T	20.37:g.29625941A>T	ENSP00000278882:p.Asp62Val					FRG1B_ENST00000439954.2_Missense_Mutation_p.D67V|FRG1B_ENST00000358464.4_Missense_Mutation_p.D62V	p.D62V							5	565	+								C4AME5	Missense_Mutation	SNP	ENST00000278882.3	37	c.185A>T		.	.	.	.	.	.	.	.	.	.	a	11.46	1.644922	0.29246	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	T	0.55930	0.49	1.68	1.68	0.24146	.	0.000000	0.85682	U	0.000000	T	0.67316	0.2880	.	.	.	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.68300	-0.5445	9	0.87932	D	0	.	7.3757	0.26827	1.0:0.0:0.0:0.0	.	67	F5H5R5	.	V	62;67;62	ENSP00000408863:D67V	ENSP00000278882:D62V	D	+	2	0	FRG1B	28239602	1.000000	0.71417	1.000000	0.80357	0.050000	0.14768	7.682000	0.84083	1.028000	0.39785	0.155000	0.16302	GAT		0.333	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078494.2	NR_003579		5	134	0	0	0	1	0	5	134				
TUBB8P7	197331	broad.mit.edu	37	16	90161602	90161602	+	RNA	SNP	T	T	C	rs368455696		TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr16:90161602T>C	ENST00000564451.1	+	0	955				TUBB8P7_ENST00000567960.1_RNA					tubulin, beta 8 class VIII pseudogene 7																		GCGGAGCTGATGGAGTCAGTG	0.612																																						ENST00000567960.1																			0																																																			0							g.chr16:90161602T>C			16q24.3	2013-02-18			ENSG00000261812	ENSG00000261812			42345	pseudogene	pseudogene							Standard	NG_002334		Approved				OTTHUMG00000172847		16.37:g.90161602T>C						TUBB8P7_ENST00000564451.1_RNA								0	338	+									RNA	SNP	ENST00000564451.1	37																																																																																						0.612	TUBB8P7-004	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000420856.1	NG_002334		3	25	0	0	0	1	0	3	25				
DACH2	117154	broad.mit.edu	37	X	86069820	86069820	+	Missense_Mutation	SNP	G	G	T			TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chrX:86069820G>T	ENST00000373125.4	+	10	1667	c.1667G>T	c.(1666-1668)gGc>gTc	p.G556V	DACH2_ENST00000373131.1_Missense_Mutation_p.G543V|DACH2_ENST00000510272.1_Missense_Mutation_p.G337V|DACH2_ENST00000508860.1_Missense_Mutation_p.G389V	NM_053281.3	NP_444511.1	Q96NX9	DACH2_HUMAN	dachshund family transcription factor 2	556					development of primary female sexual characteristics (GO:0046545)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.G556V(9)|p.G543V(9)		breast(2)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(14)|lung(28)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	71						AGTGACAGTGGCCTGAGGATG	0.398																																						ENST00000373131.1																			18	Substitution - Missense(18)	p.G556V(9)|p.G543V(9)	endometrium(8)|kidney(8)|lung(2)	breast(2)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(14)|lung(28)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	71						c.(1627-1629)gGc>gTc		dachshund homolog 2 (Drosophila)							57.0	48.0	51.0					X																	86069820		2203	4300	6503	SO:0001583	missense	117154				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|nucleotide binding	g.chrX:86069820G>T	AF428101	CCDS14455.1, CCDS48140.1, CCDS55457.1	Xq21.3	2014-02-03	2014-02-03		ENSG00000126733	ENSG00000126733			16814	protein-coding gene	gene with protein product		300608	"""dachshund homolog 2 (Drosophila)"""				Standard	NM_053281		Approved		uc004eew.2	Q96NX9	OTTHUMG00000021944	ENST00000373125.4:c.1667G>T	X.37:g.86069820G>T	ENSP00000362217:p.Gly556Val					DACH2_ENST00000508860.1_Missense_Mutation_p.G389V|DACH2_ENST00000477378.2_Intron|DACH2_ENST00000373125.4_Missense_Mutation_p.G556V|DACH2_ENST00000510272.1_Missense_Mutation_p.G337V	p.G543V	NM_001139514.1	NP_001132986.1	Q96NX9	DACH2_HUMAN			9	1791	+			556					B1AJV3|B4DQG3|Q8NAY3|Q8ND17|Q96N55	Missense_Mutation	SNP	ENST00000373125.4	37	c.1628G>T	CCDS14455.1	.	.	.	.	.	.	.	.	.	.	G	11.53	1.667616	0.29604	.	.	ENSG00000126733	ENST00000344497;ENST00000373131;ENST00000373125;ENST00000508860;ENST00000510272;ENST00000400297;ENST00000484479	D;D	0.82433	-1.57;-1.61	4.76	4.76	0.60689	.	0.153373	0.30410	N	0.009683	D	0.84451	0.5475	L	0.34521	1.04	0.80722	D	1	B;B;D;P	0.61697	0.172;0.085;0.99;0.793	B;B;P;B	0.60068	0.038;0.054;0.868;0.254	T	0.82857	-0.0250	10	0.27082	T	0.32	.	17.002	0.86383	0.0:0.0:1.0:0.0	.	422;556;543;556	Q1RMF5;A8K3I1;Q96NX9-2;Q96NX9	.;.;.;DACH2_HUMAN	V	556;543;556;389;337;389;221	ENSP00000362223:G543V;ENSP00000362217:G556V	ENSP00000345134:G556V	G	+	2	0	DACH2	85956476	0.999000	0.42202	0.958000	0.39756	0.913000	0.54294	3.863000	0.56016	1.932000	0.55993	0.415000	0.27848	GGC		0.398	DACH2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359266.1	NM_053281		6	31	1	0	5.9392e-07	1	6.22202e-07	6	31				
ADCK2	90956	broad.mit.edu	37	7	140374545	140374545	+	Silent	SNP	G	G	C			TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr7:140374545G>C	ENST00000072869.4	+	2	1246	c.1068G>C	c.(1066-1068)ctG>ctC	p.L356L	ADCK2_ENST00000476491.1_Silent_p.L356L	NM_052853.3	NP_443085.2	Q7Z695	ADCK2_HUMAN	aarF domain containing kinase 2	356	Protein kinase.					integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|kidney(2)|large_intestine(2)|lung(5)|prostate(1)|skin(4)	15	Melanoma(164;0.00956)					TTGAGAAGCTGATGGTCCAAC	0.458																																						ENST00000072869.4																			0				cervix(1)|kidney(2)|large_intestine(2)|lung(5)|prostate(1)|skin(4)	15						c.(1066-1068)ctG>ctC		aarF domain containing kinase 2							125.0	107.0	113.0					7																	140374545		2203	4300	6503	SO:0001819	synonymous_variant	90956					integral to membrane	ATP binding|protein serine/threonine kinase activity	g.chr7:140374545G>C	AF131745	CCDS5861.1	7q34	2003-07-21			ENSG00000133597	ENSG00000133597			19039	protein-coding gene	gene with protein product							Standard	NM_052853		Approved	MGC20727	uc003vvy.1	Q7Z695	OTTHUMG00000157409	ENST00000072869.4:c.1068G>C	7.37:g.140374545G>C						ADCK2_ENST00000476491.1_Silent_p.L356L	p.L356L	NM_052853.3	NP_443085.2	Q7Z695	ADCK2_HUMAN			2	1246	+	Melanoma(164;0.00956)		356			Protein kinase.		Q96CN6|Q9Y6T5	Silent	SNP	ENST00000072869.4	37	c.1068G>C	CCDS5861.1	.	.	.	.	.	.	.	.	.	.	G	9.643	1.139494	0.21205	.	.	ENSG00000133597	ENST00000483369	.	.	.	5.49	1.66	0.24008	.	.	.	.	.	T	0.54255	0.1847	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41928	-0.9481	4	.	.	.	-21.299	6.854	0.24030	0.0:0.4166:0.368:0.2153	.	.	.	.	H	194	.	.	D	+	1	0	ADCK2	140021014	0.996000	0.38824	0.999000	0.59377	0.989000	0.77384	0.466000	0.22019	0.097000	0.17492	-0.165000	0.13383	GAT		0.458	ADCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348734.1	NM_052853		16	27	0	0	0	1	0	16	27				
TUBB8P7	197331	broad.mit.edu	37	16	90161609	90161609	+	RNA	SNP	A	A	G	rs371305733		TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr16:90161609A>G	ENST00000564451.1	+	0	962				TUBB8P7_ENST00000567960.1_RNA					tubulin, beta 8 class VIII pseudogene 7																		TGATGGAGTCAGTGATGGACG	0.617																																						ENST00000567960.1																			0																																																			0							g.chr16:90161609A>G			16q24.3	2013-02-18			ENSG00000261812	ENSG00000261812			42345	pseudogene	pseudogene							Standard	NG_002334		Approved				OTTHUMG00000172847		16.37:g.90161609A>G						TUBB8P7_ENST00000564451.1_RNA								0	345	+									RNA	SNP	ENST00000564451.1	37																																																																																						0.617	TUBB8P7-004	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000420856.1	NG_002334		3	30	0	0	0	1	0	3	30				
USH2A	7399	broad.mit.edu	37	1	216251673	216251673	+	Missense_Mutation	SNP	C	C	T	rs541275063	byFrequency	TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr1:216251673C>T	ENST00000307340.3	-	27	5716	c.5330G>A	c.(5329-5331)cGg>cAg	p.R1777Q	RP11-22M7.2_ENST00000446411.1_RNA|RP11-22M7.2_ENST00000445619.1_RNA|USH2A_ENST00000366943.2_Missense_Mutation_p.R1777Q|RP11-22M7.2_ENST00000442606.1_RNA|RP11-22M7.2_ENST00000430890.1_RNA	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	1777	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		GGTATTTAACCGGAAGGTCAA	0.373										HNSCC(13;0.011)			C|||	2	0.000399361	0.0015	0.0	5008	,	,		18311	0.0		0.0	False		,,,				2504	0.0					ENST00000366943.2																			0				NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527						c.(5329-5331)cGg>cAg		Usher syndrome 2A (autosomal recessive, mild)							204.0	224.0	217.0					1																	216251673		2203	4300	6503	SO:0001583	missense	7399				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding	g.chr1:216251673C>T	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.5330G>A	1.37:g.216251673C>T	ENSP00000305941:p.Arg1777Gln	HNSCC(13;0.011)				RP11-22M7.2_ENST00000430890.1_RNA|RP11-22M7.2_ENST00000445619.1_RNA|RP11-22M7.2_ENST00000446411.1_RNA|USH2A_ENST00000307340.3_Missense_Mutation_p.R1777Q	p.R1777Q			O75445	USH2A_HUMAN		OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)	27	5716	-			1777			Laminin G-like 2.		Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	c.5330G>A	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	12.17	1.857576	0.32791	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.78246	-1.16;-1.16	5.58	-2.94	0.05581	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Fibronectin, type III (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	1.073040	0.07458	N	0.900087	T	0.56455	0.1986	N	0.20807	0.61	0.09310	N	1	B	0.22346	0.068	B	0.13407	0.009	T	0.35574	-0.9783	10	0.16896	T	0.51	.	5.5354	0.17007	0.3139:0.3219:0.0:0.3642	.	1777	O75445	USH2A_HUMAN	Q	1777	ENSP00000305941:R1777Q;ENSP00000355910:R1777Q	ENSP00000305941:R1777Q	R	-	2	0	USH2A	214318296	0.953000	0.32496	0.031000	0.17742	0.987000	0.75469	0.152000	0.16302	-0.352000	0.08237	-0.142000	0.14014	CGG		0.373	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		5	712	0	0	0	1	0	5	712				
KCNH7	90134	broad.mit.edu	37	2	163236410	163236410	+	Silent	SNP	G	G	A			TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr2:163236410G>A	ENST00000332142.5	-	14	3183	c.3084C>T	c.(3082-3084)taC>taT	p.Y1028Y		NM_033272.3	NP_150375.2	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 7	1028					circadian rhythm (GO:0007623)|potassium ion transmembrane transport (GO:0071805)|protein heterooligomerization (GO:0051291)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)|signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(22)|lung(53)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	108					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	CCACTTCCCCGTAGGTGAGGT	0.512																																					GBM(196;1492 2208 17507 24132 45496)	ENST00000332142.5																			0				NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(22)|lung(53)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	108						c.(3082-3084)taC>taT		potassium voltage-gated channel, subfamily H (eag-related), member 7	Ibutilide(DB00308)						181.0	171.0	174.0					2																	163236410		2203	4300	6503	SO:0001819	synonymous_variant	90134				regulation of transcription, DNA-dependent	integral to membrane	protein binding|signal transducer activity	g.chr2:163236410G>A	AF032897	CCDS2219.1, CCDS2220.1	2q24.3	2012-07-05			ENSG00000184611	ENSG00000184611		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18863	protein-coding gene	gene with protein product		608169				16382104	Standard	NM_173162		Approved	Kv11.3, HERG3, erg3	uc002uch.2	Q9NS40	OTTHUMG00000132069	ENST00000332142.5:c.3084C>T	2.37:g.163236410G>A							p.Y1028Y	NM_033272.3	NP_150375.2	Q9NS40	KCNH7_HUMAN			14	3183	-			1028					Q53QU4|Q53TB7|Q53TP9|Q8IV15	Silent	SNP	ENST00000332142.5	37	c.3084C>T	CCDS2219.1																																																																																				0.512	KCNH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255093.1	NM_033272		5	311	0	0	0	1	0	5	311				
CARHSP1	23589	broad.mit.edu	37	16	8952307	8952307	+	Missense_Mutation	SNP	G	G	A			TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr16:8952307G>A	ENST00000396593.2	-	3	540	c.181C>T	c.(181-183)Ccc>Tcc	p.P61S	RP11-77H9.2_ENST00000565934.1_RNA|CARHSP1_ENST00000561530.1_Missense_Mutation_p.P61S|CARHSP1_ENST00000567554.1_Missense_Mutation_p.P61S|CARHSP1_ENST00000311052.5_Missense_Mutation_p.P61S|CARHSP1_ENST00000567626.1_5'Flank|CARHSP1_ENST00000562843.1_Missense_Mutation_p.P61S	NM_001042476.1|NM_001278260.1|NM_001278261.1|NM_001278262.1|NM_001278263.1|NM_001278264.1|NM_001278265.1|NM_001278266.1|NM_014316.3	NP_001035941.1|NP_001265189.1|NP_001265190.1|NP_001265191.1|NP_001265192.1|NP_001265193.1|NP_001265194.1|NP_001265195.1|NP_055131.2	Q9Y2V2	CHSP1_HUMAN	calcium regulated heat stable protein 1, 24kDa	61					intracellular signal transduction (GO:0035556)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasmic exosome (RNase complex) (GO:0000177)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|P granule (GO:0043186)	DNA binding (GO:0003677)|mRNA 3'-UTR binding (GO:0003730)|phosphatase binding (GO:0019902)			endometrium(2)|lung(1)	3						TTGTAGACGGGGCCCTGTGAA	0.607																																						ENST00000396593.2																			0				endometrium(2)|lung(1)	3						c.(181-183)Ccc>Tcc		calcium regulated heat stable protein 1, 24kDa							55.0	61.0	59.0					16																	8952307		2197	4300	6497	SO:0001583	missense	23589				intracellular signal transduction|regulation of mRNA stability|regulation of transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|P granule	DNA binding|mRNA 3'-UTR binding|phosphatase binding	g.chr16:8952307G>A	AF115345	CCDS10537.1	16p13.2	2008-02-05	2002-08-29		ENSG00000153048	ENSG00000153048			17150	protein-coding gene	gene with protein product			"""calcium regulated heat stable protein 1 (24kD)"""			9712905	Standard	NM_014316		Approved	CRHSP-24, CSDC1	uc031quz.1	Q9Y2V2	OTTHUMG00000129695	ENST00000396593.2:c.181C>T	16.37:g.8952307G>A	ENSP00000379838:p.Pro61Ser					CARHSP1_ENST00000562843.1_Missense_Mutation_p.P61S|CARHSP1_ENST00000311052.5_Missense_Mutation_p.P61S|RP11-77H9.2_ENST00000565934.1_RNA|CARHSP1_ENST00000567554.1_Missense_Mutation_p.P61S|CARHSP1_ENST00000561530.1_Missense_Mutation_p.P61S	p.P61S	NM_001042476.1|NM_001278260.1|NM_001278261.1|NM_001278262.1|NM_001278263.1|NM_001278264.1|NM_001278265.1|NM_001278266.1|NM_014316.3	NP_001035941.1|NP_001265189.1|NP_001265190.1|NP_001265191.1|NP_001265192.1|NP_001265193.1|NP_001265194.1|NP_001265195.1|NP_055131.2	Q9Y2V2	CHSP1_HUMAN			3	540	-			61					B2R4C3|D3DUF5|Q2YDX5|Q9BQ53	Missense_Mutation	SNP	ENST00000396593.2	37	c.181C>T	CCDS10537.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.551441	0.86127	.	.	ENSG00000153048	ENST00000396593;ENST00000311052	.	.	.	5.37	3.32	0.38043	Nucleic acid-binding, OB-fold-like (1);	0.000000	0.85682	D	0.000000	T	0.69637	0.3133	M	0.84846	2.72	0.80722	D	1	P	0.48407	0.91	P	0.45998	0.5	T	0.74990	-0.3475	9	0.87932	D	0	1.8599	13.1807	0.59653	0.0:0.0:0.7102:0.2898	.	61	Q9Y2V2	CHSP1_HUMAN	S	61	.	ENSP00000311847:P61S	P	-	1	0	CARHSP1	8859808	1.000000	0.71417	0.848000	0.33437	0.927000	0.56198	7.797000	0.85911	0.576000	0.29452	0.561000	0.74099	CCC		0.607	CARHSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251902.1	NM_014316		6	81	0	0	0	1	0	6	81				
ANKRD30BP2	149992	broad.mit.edu	37	21	14414844	14414844	+	RNA	SNP	T	T	C	rs372981463		TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr21:14414844T>C	ENST00000507941.1	+	0	95									ankyrin repeat domain 30B pseudogene 2																		ACTGGGCCTGTGCCAATGGCC	0.433																																						ENST00000507941.1																			0																																																			0							g.chr21:14414844T>C	AF427490		21q11.2	2010-06-14	2010-06-14	2010-06-14	ENSG00000224309	ENSG00000224309			16620	pseudogene	pseudogene	"""cancer/testis antigen 85"""		"""chromosome 21 open reading frame 99"""	C21orf99		12036297, 17114284	Standard	NR_026916		Approved	CT85, CTSP-1	uc002yja.4		OTTHUMG00000074164		21.37:g.14414844T>C														0	95	+									RNA	SNP	ENST00000507941.1	37																																																																																						0.433	ANKRD30BP2-004	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000372094.1	NR_026916		4	110	0	0	0	1	0	4	110				
SBSN	374897	broad.mit.edu	37	19	36018407	36018407	+	Silent	SNP	T	T	C			TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr19:36018407T>C	ENST00000452271.2	-	1	805	c.777A>G	c.(775-777)agA>agG	p.R259R	SBSN_ENST00000518157.1_Intron	NM_001166034.1	NP_001159506.1	Q6UWP8	SBSN_HUMAN	suprabasin	259	Ala/Gly/His-rich.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				large_intestine(5)|lung(6)|ovary(1)|prostate(2)	14	all_lung(56;1.62e-08)|Lung NSC(56;2.47e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			CCTGGCCAAATCTCCCTGCCT	0.627																																						ENST00000452271.2																			0				large_intestine(5)|lung(6)|ovary(1)|prostate(2)	14						c.(775-777)agA>agG		suprabasin							56.0	57.0	57.0					19																	36018407		692	1591	2283	SO:0001819	synonymous_variant	374897					extracellular region		g.chr19:36018407T>C	AY358701	CCDS12464.1, CCDS54253.1	19q13.13	2008-02-05							24950	protein-coding gene	gene with protein product		609969				12228223	Standard	NM_198538		Approved	UNQ698, HLAR698	uc002oad.2	Q6UWP8		ENST00000452271.2:c.777A>G	19.37:g.36018407T>C						SBSN_ENST00000518157.1_Intron	p.R259R	NM_001166034.1	NP_001159506.1	Q6UWP8	SBSN_HUMAN	LUSC - Lung squamous cell carcinoma(66;0.0724)		1	805	-	all_lung(56;1.62e-08)|Lung NSC(56;2.47e-08)|Esophageal squamous(110;0.162)		132					A8K5J0|E9PBV3	Silent	SNP	ENST00000452271.2	37	c.777A>G	CCDS54253.1																																																																																				0.627	SBSN-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109463.3	NM_198538		4	18	0	0	0	1	0	4	18				
PAWR	5074	broad.mit.edu	37	12	79990400	79990400	+	Missense_Mutation	SNP	T	T	C			TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr12:79990400T>C	ENST00000328827.4	-	5	1094	c.722A>G	c.(721-723)tAt>tGt	p.Y241C		NM_002583.2	NP_002574.2	Q96IZ0	PAWR_HUMAN	PRKC, apoptosis, WT1, regulator	241					actin filament bundle assembly (GO:0051017)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|interleukin-2 biosynthetic process (GO:0042094)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of amyloid precursor protein biosynthetic process (GO:0042986)|positive regulation of apoptotic process (GO:0043065)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|enzyme binding (GO:0019899)|leucine zipper domain binding (GO:0043522)|transcription corepressor activity (GO:0003714)			NS(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	8						TGTTCGAGAATATCTACTTGA	0.358																																						ENST00000328827.4																			0				NS(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	8						c.(721-723)tAt>tGt		PRKC, apoptosis, WT1, regulator							102.0	97.0	99.0					12																	79990400		2203	4300	6503	SO:0001583	missense	5074				actin filament bundle assembly|apoptosis|induction of apoptosis|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	actin binding|enzyme binding|leucine zipper domain binding|transcription corepressor activity	g.chr12:79990400T>C	U63809	CCDS31863.1	12q21.2	2013-03-07			ENSG00000177425	ENSG00000177425			8614	protein-coding gene	gene with protein product	"""prostate apoptosis response-4"""	601936				8943350, 9790775	Standard	NM_002583		Approved	par-4, PAR4	uc001syx.3	Q96IZ0	OTTHUMG00000170080	ENST00000328827.4:c.722A>G	12.37:g.79990400T>C	ENSP00000328088:p.Tyr241Cys						p.Y241C	NM_002583.2	NP_002574.2	Q96IZ0	PAWR_HUMAN			5	1094	-			241					O75796|Q6FHY9|Q8N700	Missense_Mutation	SNP	ENST00000328827.4	37	c.722A>G	CCDS31863.1	.	.	.	.	.	.	.	.	.	.	T	16.09	3.023211	0.54683	.	.	ENSG00000177425	ENST00000328827	T	0.18960	2.18	5.51	-0.0393	0.13876	.	0.734850	0.12666	N	0.449235	T	0.28300	0.0699	L	0.43152	1.355	0.35779	D	0.821481	D	0.63046	0.992	P	0.55999	0.789	T	0.26883	-1.0090	9	.	.	.	-0.0346	11.2479	0.49008	0.4913:0.0:0.0:0.5087	.	241	Q96IZ0	PAWR_HUMAN	C	241	ENSP00000328088:Y241C	.	Y	-	2	0	PAWR	78514531	1.000000	0.71417	0.844000	0.33320	0.796000	0.44982	1.731000	0.38135	-0.247000	0.09597	-0.481000	0.04817	TAT		0.358	PAWR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407175.1	NM_002583		46	76	0	0	0	1	0	46	76				
C2CD3	26005	broad.mit.edu	37	11	73879565	73879565	+	Nonsense_Mutation	SNP	C	C	T			TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr11:73879565C>T	ENST00000334126.7	-	2	375	c.149G>A	c.(148-150)tGg>tAg	p.W50*	PPME1_ENST00000328257.8_5'Flank|PPME1_ENST00000398427.4_5'Flank|C2CD3_ENST00000539061.1_Nonsense_Mutation_p.W50*|C2CD3_ENST00000313663.7_Nonsense_Mutation_p.W50*			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	50					brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					TGCAATCTTCCATATGACTCT	0.458																																						ENST00000334126.7																			0				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64						c.(148-150)tGg>tAg		C2 calcium-dependent domain containing 3							166.0	161.0	162.0					11																	73879565		2200	4293	6493	SO:0001587	stop_gained	26005					centrosome		g.chr11:73879565C>T	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.149G>A	11.37:g.73879565C>T	ENSP00000334379:p.Trp50*					C2CD3_ENST00000313663.7_Nonsense_Mutation_p.W50*|C2CD3_ENST00000539061.1_Nonsense_Mutation_p.W50*	p.W50*			Q4AC94	C2CD3_HUMAN			2	375	-	Breast(11;4.16e-06)		50					C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Nonsense_Mutation	SNP	ENST00000334126.7	37	c.149G>A		.	.	.	.	.	.	.	.	.	.	C	34	5.394499	0.96009	.	.	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681;ENST00000289350;ENST00000539061;ENST00000535954	.	.	.	5.57	4.66	0.58398	.	0.000000	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.8029	12.332	0.55046	0.0:0.9176:0.0:0.0824	.	.	.	.	X	50;50;50;50;50;92	.	ENSP00000289350:W50X	W	-	2	0	C2CD3	73557213	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.944000	0.75940	1.355000	0.45865	0.655000	0.94253	TGG		0.458	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531		7	256	0	0	0	1	0	7	256				
SOX5	6660	broad.mit.edu	37	12	23696258	23696258	+	Missense_Mutation	SNP	T	T	C			TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr12:23696258T>C	ENST00000451604.2	-	13	1759	c.1658A>G	c.(1657-1659)gAa>gGa	p.E553G	SOX5_ENST00000381381.2_Missense_Mutation_p.E432G|SOX5_ENST00000545921.1_Missense_Mutation_p.E543G|SOX5_ENST00000541536.1_Missense_Mutation_p.E432G|SOX5_ENST00000546136.1_Missense_Mutation_p.E540G|SOX5_ENST00000537393.1_Missense_Mutation_p.E518G|SOX5_ENST00000309359.1_Missense_Mutation_p.E540G|SOX5_ENST00000396007.2_Missense_Mutation_p.E167G			P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5	553					cartilage development (GO:0051216)|cell fate commitment (GO:0045165)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system neuron differentiation (GO:0021953)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|oligodendrocyte differentiation (GO:0048709)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of timing of neuron differentiation (GO:0060164)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear transcription factor complex (GO:0044798)	sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(25)|ovary(5)|skin(2)|upper_aerodigestive_tract(3)	57						TATGTGGGGTTCATTGCTACC	0.458																																						ENST00000546136.1																			0				NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(25)|ovary(5)|skin(2)|upper_aerodigestive_tract(3)	57						c.(1618-1620)gAa>gGa		SRY (sex determining region Y)-box 5							182.0	161.0	168.0					12																	23696258		2203	4300	6503	SO:0001583	missense	6660				transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity	g.chr12:23696258T>C	AB081589	CCDS8699.1, CCDS41761.1, CCDS44844.1, CCDS58216.1, CCDS58217.1	12p12.1	2010-04-20			ENSG00000134532	ENSG00000134532		"""SRY (sex determining region Y)-boxes"""	11201	protein-coding gene	gene with protein product		604975				8812465	Standard	NM_006940		Approved	L-SOX5, MGC35153	uc001rfw.3	P35711	OTTHUMG00000169026	ENST00000451604.2:c.1658A>G	12.37:g.23696258T>C	ENSP00000398273:p.Glu553Gly					SOX5_ENST00000545921.1_Missense_Mutation_p.E543G|SOX5_ENST00000309359.1_Missense_Mutation_p.E540G|SOX5_ENST00000396007.2_Missense_Mutation_p.E167G|SOX5_ENST00000451604.2_Missense_Mutation_p.E553G|SOX5_ENST00000537393.1_Missense_Mutation_p.E518G|SOX5_ENST00000381381.2_Missense_Mutation_p.E432G|SOX5_ENST00000541536.1_Missense_Mutation_p.E432G	p.E540G			P35711	SOX5_HUMAN			12	1621	-			553					B7Z8V0|F5H5B0|Q86UK8|Q8J017|Q8J018|Q8J019|Q8J020|Q8N1D9|Q8N7E0|Q8TEA4	Missense_Mutation	SNP	ENST00000451604.2	37	c.1619A>G	CCDS8699.1	.	.	.	.	.	.	.	.	.	.	T	28.9	4.958616	0.92726	.	.	ENSG00000134532	ENST00000546136;ENST00000309359;ENST00000381381;ENST00000451604;ENST00000435266;ENST00000537393;ENST00000541536;ENST00000396007;ENST00000545921	D;D;D;D;D;D;D;D	0.97455	-4.38;-4.38;-4.31;-4.39;-4.38;-4.31;-4.36;-4.39	6.17	6.17	0.99709	High mobility group, superfamily (1);	0.000000	0.85682	D	0.000000	D	0.98166	0.9394	M	0.71036	2.16	0.51012	D	0.999902	D;D;D;D	0.76494	0.999;0.989;0.999;0.998	D;D;D;D	0.81914	0.995;0.969;0.989;0.957	D	0.98655	1.0681	10	0.52906	T	0.07	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	518;432;553;167	F5H0I3;P35711-4;P35711;P35711-3	.;.;SOX5_HUMAN;.	G	540;540;432;553;505;518;432;167;543	ENSP00000437487:E540G;ENSP00000308927:E540G;ENSP00000370788:E432G;ENSP00000398273:E553G;ENSP00000439832:E518G;ENSP00000441973:E432G;ENSP00000379328:E167G;ENSP00000443520:E543G	ENSP00000308927:E540G	E	-	2	0	SOX5	23587525	1.000000	0.71417	0.998000	0.56505	0.948000	0.59901	8.026000	0.88783	2.371000	0.80710	0.533000	0.62120	GAA		0.458	SOX5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402006.2	NM_006940		5	210	0	0	0	1	0	5	210				
MED12L	116931	broad.mit.edu	37	3	151148114	151148116	+	In_Frame_Del	DEL	CAG	CAG	-	rs147600909		TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr3:151148114_151148116delCAG	ENST00000474524.1	+	42	6369_6371	c.6331_6333delCAG	c.(6331-6333)cagdel	p.Q2115del	MED12L_ENST00000273432.4_In_Frame_Del_p.Q1779del	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	2115	Gln-rich.					mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.Q2111E(1)		NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			GCAGCAGACCCAGCAGCAGCAGC	0.527																																						ENST00000474524.1																			1	Substitution - Missense(1)	p.Q2111E(1)	lung(1)	NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128						c.(6331-6333)del		mediator complex subunit 12-like																																				SO:0001651	inframe_deletion	116931				regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex		g.chr3:151148114_151148116delCAG	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"""			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.6331_6333delCAG	3.37:g.151148123_151148125delCAG	ENSP00000417235:p.Gln2115del					MED12L_ENST00000273432.4_In_Frame_Del_p.Q1779del	p.Q2115del	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)		42	6369_6371	+			2115			Gln-rich.		Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	In_Frame_Del	DEL	ENST00000474524.1	37	c.6331_6333delCAG	CCDS33876.1																																																																																				0.527	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		7	159						7	159	---	---	---	---
LOC101243545	101243545	broad.mit.edu	37	3	161146872	161146873	+	lincRNA	DEL	AT	AT	-	rs139058677		TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr3:161146872_161146873delAT	ENST00000473595.1	+	0	1231				RP11-3P17.5_ENST00000602890.1_lincRNA	NR_102265.1																						TGGTGAAAAGATATATATATAT	0.342																																						ENST00000473595.1																			0																																																			0							g.chr3:161146872_161146873delAT																													3.37:g.161146882_161146883delAT								NR_102265.1						0	1231	+									RNA	DEL	ENST00000473595.1	37																																																																																						0.342	RP11-3P17.4-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000353185.1			7	26						7	26	---	---	---	---
BTN2A3P	54718	broad.mit.edu	37	6	26422388	26422390	+	RNA	DEL	CCT	CCT	-	rs113134648	byFrequency	TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr6:26422388_26422390delCCT	ENST00000466808.2	+	0	42_44							Q96KV6	BT2A3_HUMAN	butyrophilin, subfamily 2, member A3, pseudogene							integral component of membrane (GO:0016021)											GGCCAGCCTCCCTCCTCCTCCTC	0.586																																						ENST00000466808.2																			0																	383,304,2,3575		10,8,0,355,12,0,272,0,2,1473						0.4	0.0		dbSNP_134	150	684,576,1,6991		22,7,0,633,28,0,513,0,1,2922	no	intergenic				32,15,0,988,40,0,785,0,3,4395	A1A1,A1A2,A1A3,A1R,A2A2,A2A3,A2R,A3A3,A3R,RR		15.2811,16.1585,15.5801				1067,880,3,10566						0							g.chr6:26422388_26422390delCCT	AL021917		6p22.1	2014-01-14	2011-09-06	2011-09-06	ENSG00000124549	ENSG00000124549		"""Butyrophilins"""	13229	pseudogene	pseudogene		613592	"""butyrophilin, subfamily 2, member A3"""	BTN2A3			Standard	NR_027795		Approved	BTN2.3	uc011dkl.1	Q96KV6	OTTHUMG00000014453		6.37:g.26422397_26422399delCCT														0	42_44	+								A6NEF4	RNA	DEL	ENST00000466808.2	37																																																																																						0.586	BTN2A3P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000040118.4	NR_027795		7	233						7	233	---	---	---	---
TYW1B	441250	broad.mit.edu	37	7	72159821	72159821	+	RNA	DEL	T	T	-			TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr7:72159821delT	ENST00000435769.2	-	0	1494				TYW1B_ENST00000343721.5_RNA|TYW1B_ENST00000438125.1_RNA			Q6NUM6	TYW1B_HUMAN	tRNA-yW synthesizing protein 1 homolog B (S. cerevisiae)						tRNA processing (GO:0008033)		4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity (GO:0016491)										TCCTTAGTAATTTTTTTTTTT	0.388																																						ENST00000438125.1																			0													tRNA-yW synthesizing protein 1 homolog B (S. cerevisiae)							44.0	37.0	39.0					7																	72159821		692	1591	2283			441250				tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity	g.chr7:72159821delT	BC068520	CCDS69309.1	7q11.23	2011-08-11	2009-07-28		ENSG00000254184	ENSG00000277149			33908	protein-coding gene	gene with protein product	"""radical S-adenosyl methionine and flavodoxin domains 1"", ""non-protein coding RNA 69"", ""long intergenic non-protein coding RNA 69"""		"""tRNA-yW synthesizing protein 1 homolog B (non-protein coding)"""				Standard	NM_001145440		Approved	RSAFD2, MGC87315, NCRNA00069, LINC00069	uc011kej.2	Q6NUM6	OTTHUMG00000157067		7.37:g.72159821delT										Q6NUM6	TYW1B_HUMAN			0	984	-								A6NG09|B4DFY2|Q3KQX2	RNA	DEL	ENST00000435769.2	37																																																																																						0.388	TYW1B-001	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347346.2	NM_001145440		9	93						9	93	---	---	---	---
PTPLAD2	401494	broad.mit.edu	37	9	21007045	21007046	+	Frame_Shift_Ins	INS	-	-	T			TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr9:21007045_21007046insT	ENST00000495827.2	-	7	734_735	c.689_690insA	c.(688-690)aagfs	p.K230fs	PTPLAD2_ENST00000513293.2_Frame_Shift_Ins_p.K230fs	NM_001010915.3	NP_001010915.2	Q5VWC8	HACD4_HUMAN	protein tyrosine phosphatase-like A domain containing 2	230	Poly-Lys.				fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	lyase activity (GO:0016829)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)	10				Lung(24;6.02e-14)|LUSC - Lung squamous cell carcinoma(38;1.29e-10)		TTCACATCTTCTTTTTTTTAAT	0.371																																						ENST00000495827.1																			0				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)	10						c.(688-690)aaafs		protein tyrosine phosphatase-like A domain containing 2																																				SO:0001589	frameshift_variant	401494				fatty acid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	lyase activity	g.chr9:21007045_21007046insT		CCDS43791.1	9p21.3	2008-02-05			ENSG00000188921	ENSG00000188921			20920	protein-coding gene	gene with protein product		615941					Standard	NM_001010915		Approved	Em:AL662879.1, OTTHUMG00000021016	uc010mir.1	Q5VWC8	OTTHUMG00000021016	ENST00000495827.2:c.690dupA	9.37:g.21007053_21007053dupT	ENSP00000419503:p.Lys230fs					PTPLAD2_ENST00000513293.2_Frame_Shift_Ins_p.K230fs	p.K230fs	NM_001010915.3	NP_001010915.2	Q5VWC8	HACD4_HUMAN		Lung(24;6.02e-14)|LUSC - Lung squamous cell carcinoma(38;1.29e-10)	7	734_735	-			230			Poly-Lys.		Q7Z385	Frame_Shift_Ins	INS	ENST00000495827.2	37	c.689_690insA	CCDS43791.1																																																																																				0.371	PTPLAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055434.3	NM_001010915		7	198						7	198	---	---	---	---
TFAM	7019	broad.mit.edu	37	10	60148570	60148570	+	Frame_Shift_Del	DEL	A	A	-	rs544132101|rs78912196		TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr10:60148570delA	ENST00000487519.1	+	4	958	c.432delA	c.(430-432)acafs	p.T144fs	TFAM_ENST00000373899.3_3'UTR|TFAM_ENST00000373895.3_Frame_Shift_Del_p.T144fs	NM_001270782.1|NM_003201.2	NP_001257711.1|NP_003192.1	Q00059	TFAM_HUMAN	transcription factor A, mitochondrial	144					DNA-dependent DNA replication (GO:0006261)|gene expression (GO:0010467)|mitochondrial respiratory chain complex assembly (GO:0033108)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|transcription from mitochondrial promoter (GO:0006390)|transcription initiation from mitochondrial promoter (GO:0006391)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|mitochondrial light strand promoter sense binding (GO:0070363)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(1)|lung(4)|prostate(1)	7						AAGCTATGACAAAAAAAAAAG	0.269																																						ENST00000487519.1																			0				kidney(1)|large_intestine(1)|lung(4)|prostate(1)	7						c.(430-432)acfs		transcription factor A, mitochondrial							39.0	47.0	44.0					10																	60148570		2195	4296	6491	SO:0001589	frameshift_variant	7019				DNA-dependent DNA replication|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase I promoter|transcription initiation from mitochondrial promoter	mitochondrial nucleoid	mitochondrial light strand promoter sense binding|protein binding|sequence-specific DNA binding transcription factor activity	g.chr10:60148570delA	BC018628	CCDS7253.1, CCDS59217.1	10q21	2010-09-24			ENSG00000108064	ENSG00000108064			11741	protein-coding gene	gene with protein product		600438		TCF6, TCF6L2		7789991	Standard	NM_003201		Approved		uc001jkf.4	Q00059	OTTHUMG00000018270	ENST00000487519.1:c.432delA	10.37:g.60148570delA	ENSP00000420588:p.Thr144fs					TFAM_ENST00000373899.3_3'UTR|TFAM_ENST00000373895.3_Frame_Shift_Del_p.T144fs	p.T144fs	NM_003201.1	NP_003192.1	Q00059	TFAM_HUMAN			4	958	+			144					A8MRB2|A9QXC6|B5BU05|Q5U0C6	Frame_Shift_Del	DEL	ENST00000487519.1	37	c.432delA	CCDS7253.1																																																																																				0.269	TFAM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048146.1	NM_003201		13	161						13	161	---	---	---	---
TMBIM4	51643	broad.mit.edu	37	12	66531936	66531937	+	Frame_Shift_Ins	INS	-	-	A	rs199863727	byFrequency	TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr12:66531936_66531937insA	ENST00000358230.3	-	7	640_641	c.520_521insT	c.(520-522)tatfs	p.Y174fs	TMBIM4_ENST00000544599.1_5'UTR|TMBIM4_ENST00000556010.1_Intron|TMBIM4_ENST00000539652.1_Intron|TMBIM4_ENST00000542724.1_Frame_Shift_Ins_p.Y143fs|TMBIM4_ENST00000398033.4_Frame_Shift_Ins_p.I159fs|TMBIM4_ENST00000286424.7_Frame_Shift_Ins_p.Y221fs	NM_016056.2	NP_057140.2	Q9HC24	LFG4_HUMAN	transmembrane BAX inhibitor motif containing 4	174					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|regulation of calcium-mediated signaling (GO:0050848)	Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(4)|ovary(1)|prostate(2)	9				GBM - Glioblastoma multiforme(28;0.0745)		TATCTCACTATAAAAAAAAAAC	0.351																																						ENST00000358230.3																			0				central_nervous_system(1)|endometrium(1)|large_intestine(4)|ovary(1)|prostate(2)	9						c.(520-522)tagfs		transmembrane BAX inhibitor motif containing 4																																				SO:0001589	frameshift_variant	51643					integral to membrane	protein binding	g.chr12:66531936_66531937insA	AF113127	CCDS41805.1, CCDS61187.1, CCDS73493.1	12q14.3	2014-05-09			ENSG00000155957	ENSG00000155957			24257	protein-coding gene	gene with protein product						11042152, 10810093	Standard	NM_001282609		Approved	CGI-119, S1R, ZPRO, LFG4, GAAP	uc001stc.3	Q9HC24	OTTHUMG00000168973	ENST00000358230.3:c.521dupT	12.37:g.66531946_66531946dupA	ENSP00000350965:p.Tyr174fs					TMBIM4_ENST00000544599.1_5'UTR|TMBIM4_ENST00000556010.1_Intron|TMBIM4_ENST00000398033.4_Frame_Shift_Ins_p.S159fs|TMBIM4_ENST00000286424.7_Frame_Shift_Ins_p.*221fs|TMBIM4_ENST00000539652.1_Intron|TMBIM4_ENST00000542724.1_Frame_Shift_Ins_p.*143fs	p.*174fs	NM_016056.2	NP_057140.2	Q9HC24	TMBI4_HUMAN		GBM - Glioblastoma multiforme(28;0.0745)	7	640_641	-			174					Q542Z6|Q9UHY5|Q9Y3C2	Frame_Shift_Ins	INS	ENST00000358230.3	37	c.520_521insT	CCDS41805.1																																																																																				0.351	TMBIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401832.2	NM_016056		7	104						7	104	---	---	---	---
TPTE2P6	374491	broad.mit.edu	37	13	25157747	25157748	+	RNA	INS	-	-	T	rs74332804		TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr13:25157747_25157748insT	ENST00000453498.1	+	0	554				TPTE2P6_ENST00000440905.1_RNA																							AAAATGGGAGGTTTTTTTAGGG	0.411																																						ENST00000453498.1																			0																																																			0							g.chr13:25157747_25157748insT																													13.37:g.25157754_25157754dupT														0	554	+									RNA	INS	ENST00000453498.1	37																																																																																						0.411	RP11-556N21.1-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000044193.1			4	9						4	9	---	---	---	---
TCF25	22980	broad.mit.edu	37	16	89951019	89951020	+	Frame_Shift_Ins	INS	-	-	A			TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr16:89951019_89951020insA	ENST00000263346.8	+	3	440_441	c.384_385insA	c.(385-387)aaafs	p.K129fs	TCF25_ENST00000563406.1_3'UTR|TCF25_ENST00000263347.7_5'Flank	NM_014972.2	NP_055787.1	Q9BQ70	TCF25_HUMAN	transcription factor 25 (basic helix-loop-helix)	129					heart development (GO:0007507)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|large_intestine(1)|lung(8)|ovary(3)|skin(1)|urinary_tract(2)	18		all_cancers(9;4.71e-08)|Lung NSC(15;0.000192)|all_lung(18;0.000319)|all_neural(9;0.0122)|all_hematologic(23;0.027)		BRCA - Breast invasive adenocarcinoma(80;0.0288)		TCCGGAAGAAGAAAAAAAAACA	0.446																																						ENST00000263346.8																			0				breast(1)|endometrium(2)|large_intestine(1)|lung(8)|ovary(3)|skin(1)|urinary_tract(2)	18						c.(382-387)aaaaaafs		transcription factor 25 (basic helix-loop-helix)																																				SO:0001589	frameshift_variant	22980				heart development|negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity	g.chr16:89951019_89951020insA	AF322111	CCDS10987.1	16q24.3	2008-02-05			ENSG00000141002	ENSG00000141002			29181	protein-coding gene	gene with protein product		612326				12107429, 16574069	Standard	NM_014972		Approved	Nulp1, KIAA1049	uc002fpb.2	Q9BQ70	OTTHUMG00000138986	ENST00000263346.8:c.393dupA	16.37:g.89951028_89951028dupA	ENSP00000263346:p.Lys129fs					TCF25_ENST00000563406.1_3'UTR	p.KK128fs	NM_014972.2	NP_055787.1	Q9BQ70	TCF25_HUMAN		BRCA - Breast invasive adenocarcinoma(80;0.0288)	3	440_441	+		all_cancers(9;4.71e-08)|Lung NSC(15;0.000192)|all_lung(18;0.000319)|all_neural(9;0.0122)|all_hematologic(23;0.027)	128					Q2MK75|Q9UPV3	Frame_Shift_Ins	INS	ENST00000263346.8	37	c.384_385insA	CCDS10987.1																																																																																				0.446	TCF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272875.2	NM_014972		7	90						7	90	---	---	---	---
LYPD3	27076	broad.mit.edu	37	19	43969653	43969655	+	In_Frame_Del	DEL	AGC	AGC	-	rs141441894	byFrequency	TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr19:43969653_43969655delAGC	ENST00000244333.3	-	1	157_159	c.69_71delGCT	c.(67-72)ctgctt>ctt	p.23_24LL>L		NM_014400.2	NP_055215.2	O95274	LYPD3_HUMAN	LY6/PLAUR domain containing 3	23					cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|pancreas(1)|upper_aerodigestive_tract(2)	11		Prostate(69;0.0153)				ACCTCCGCGAAGCAGCAGCAGCA	0.675																																						ENST00000244333.3																			0				cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|pancreas(1)|upper_aerodigestive_tract(2)	11						c.(67-72)ctt>ct		LY6/PLAUR domain containing 3																																				SO:0001651	inframe_deletion	27076					anchored to plasma membrane		g.chr19:43969653_43969655delAGC	AF082889	CCDS12620.1	19q13.31	2008-02-05				ENSG00000124466			24880	protein-coding gene	gene with protein product		609484				11179665, 11245483	Standard	NM_014400		Approved	C4.4A	uc002owl.1	O95274		ENST00000244333.3:c.69_71delGCT	19.37:g.43969662_43969664delAGC	ENSP00000244333:p.Leu24del						p.LL23del	NM_014400.2	NP_055215.2	O95274	LYPD3_HUMAN			1	157_159	-		Prostate(69;0.0153)	23					Q9UJ74	In_Frame_Del	DEL	ENST00000244333.3	37	c.69_71delGCT	CCDS12620.1																																																																																				0.675	LYPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463177.1	NM_014400		9	270						9	270	---	---	---	---
CCDC155	147872	broad.mit.edu	37	19	49920666	49920668	+	In_Frame_Del	DEL	CTG	CTG	-	rs139882972		TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr19:49920666_49920668delCTG	ENST00000447857.3	+	20	1793_1795	c.1588_1590delCTG	c.(1588-1590)ctgdel	p.L536del		NM_144688.4	NP_653289.3	Q8N6L0	KASH5_HUMAN	coiled-coil domain containing 155	536	Poly-Leu.					chromosome, telomeric region (GO:0000781)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(10)|ovary(1)|stomach(1)	22						TGTCCTGGGCctgctgctgctgc	0.65																																						ENST00000447857.3																			0				NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(10)|ovary(1)|stomach(1)	22						c.(1588-1590)del		coiled-coil domain containing 155				2,210,3744		1,0,0,70,70,1837						-4.5	0.9		dbSNP_134	52	8,291,7573		1,0,6,67,157,3705	no	codingComplex	CCDC155	NM_144688.4		2,0,6,137,227,5542	A1A1,A1A2,A1R,A2A2,A2R,RR		3.7983,5.3589,4.3203				10,501,11317				SO:0001651	inframe_deletion	147872					integral to membrane	calcium ion binding	g.chr19:49920666_49920668delCTG		CCDS46140.1	19q13.33	2014-01-21			ENSG00000161609	ENSG00000161609			26520	protein-coding gene	gene with protein product							Standard	NM_144688		Approved	FLJ32658, KASH5	uc002pnm.2	Q8N6L0	OTTHUMG00000183170	ENST00000447857.3:c.1588_1590delCTG	19.37:g.49920675_49920677delCTG	ENSP00000404220:p.Leu536del						p.L536del	NM_144688.4	NP_653289.3	Q8N6L0	CC155_HUMAN			20	1793_1795	+			536			Poly-Leu.		Q96MC3	In_Frame_Del	DEL	ENST00000447857.3	37	c.1588_1590delCTG	CCDS46140.1																																																																																				0.650	CCDC155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465436.2	NM_144688		3	4						3	4	---	---	---	---
GFRA4	64096	broad.mit.edu	37	20	3641263	3641264	+	Frame_Shift_Del	DEL	CG	CG	-			TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr20:3641263_3641264delCG	ENST00000319242.3	-	3	635_636	c.636_637delCG	c.(634-639)cgcgtgfs	p.V213fs	GFRA4_ENST00000290417.2_Frame_Shift_Del_p.V183fs			Q9GZZ7	GFRA4_HUMAN	GDNF family receptor alpha 4	213					negative regulation of ossification (GO:0030279)	anchored component of membrane (GO:0031225)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	glial cell-derived neurotrophic factor receptor activity (GO:0016167)			large_intestine(1)|lung(2)	3						CAGGGCGCCACGCGCGCGCTCA	0.698																																						ENST00000290417.2																			0				large_intestine(1)|lung(2)	3						c.(544-549)cgtgfs		GDNF family receptor alpha 4																																				SO:0001589	frameshift_variant	64096					anchored to membrane|extracellular region|plasma membrane	receptor activity	g.chr20:3641263_3641264delCG	AF253318	CCDS13055.1, CCDS13056.1	20p13-p12	2008-07-16			ENSG00000125861	ENSG00000125861			13821	protein-coding gene	gene with protein product	"""persephin receptor"""					10958791, 15225646	Standard	XM_005260793		Approved		uc002win.3	Q9GZZ7	OTTHUMG00000031748	ENST00000319242.3:c.636_637delCG	20.37:g.3641269_3641270delCG	ENSP00000313423:p.Val213fs					GFRA4_ENST00000319242.3_Frame_Shift_Del_p.RV212fs	p.RV182fs	NM_022139.3|NM_145762.2	NP_071422.1|NP_665705.1	Q9GZZ7	GFRA4_HUMAN			4	545_546	-			212					Q5JT74|Q9H191|Q9H192	Frame_Shift_Del	DEL	ENST00000319242.3	37	c.546_547delCG	CCDS13056.1																																																																																				0.698	GFRA4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077744.1	NM_145762		2	4						2	4	---	---	---	---
MED15	51586	broad.mit.edu	37	22	20920814	20920816	+	In_Frame_Del	DEL	CAG	CAG	-	rs67182670|rs535773989	byFrequency	TCGA-DJ-A2PO-01A-21D-A19J-08	TCGA-DJ-A2PO-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b5ffc76d-2cea-418a-bc0d-806af868c101	b8861657-0dcc-433c-bfa6-3c83eaddddb5	g.chr22:20920814_20920816delCAG	ENST00000263205.7	+	7	820_822	c.751_753delCAG	c.(751-753)cagdel	p.Q262del	MED15_ENST00000406969.1_In_Frame_Del_p.Q236del|MED15_ENST00000382974.2_In_Frame_Del_p.Q191del|MED15_ENST00000292733.7_In_Frame_Del_p.Q262del|MED15_ENST00000425759.2_In_Frame_Del_p.Q151del|MED15_ENST00000478831.1_3'UTR|MED15_ENST00000542773.1_In_Frame_Del_p.Q67del|MED15_ENST00000541476.1_In_Frame_Del_p.Q236del	NM_001003891.1	NP_001003891.1	Q96RN5	MED15_HUMAN	mediator complex subunit 15	262	Poly-Gln.		Missing.	Missing (in Ref. 3; BAB85034). {ECO:0000305}.	gene expression (GO:0010467)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.Q250_Q251insQ(4)		central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	25	all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209)			acaacagcaacagcagcagcagc	0.591																																						ENST00000263205.7																			4	Insertion - In frame(4)	p.Q250_Q251insQ(4)	ovary(2)|large_intestine(2)	central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	25						c.(751-753)del		mediator complex subunit 15																																				SO:0001651	inframe_deletion	51586				regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|mediator complex	protein binding	g.chr22:20920814_20920816delCAG	AF056191	CCDS13781.1, CCDS33602.1, CCDS74824.1	22q11.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000099917	ENSG00000099917			14248	protein-coding gene	gene with protein product		607372	"""trinucleotide repeat containing 7"", ""PC2 (positive cofactor 2, multiprotein complex) glutamine/Q-rich-associated protein"""	TNRC7, PCQAP		11024300, 11414760, 15175163	Standard	XM_005261632		Approved	TIG-1, CAG7A, Arc105	uc002zsp.3	Q96RN5	OTTHUMG00000150810	ENST00000263205.7:c.751_753delCAG	22.37:g.20920823_20920825delCAG	ENSP00000263205:p.Gln262del					MED15_ENST00000478831.1_3'UTR|MED15_ENST00000382974.2_In_Frame_Del_p.Q191del|MED15_ENST00000541476.1_In_Frame_Del_p.Q236del|MED15_ENST00000425759.2_In_Frame_Del_p.Q151del|MED15_ENST00000292733.7_In_Frame_Del_p.Q262del|MED15_ENST00000406969.1_In_Frame_Del_p.Q236del|MED15_ENST00000542773.1_In_Frame_Del_p.Q67del	p.Q262del	NM_001003891.1	NP_001003891.1	Q96RN5	MED15_HUMAN	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209)		7	820_822	+	all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	262	Missing (in Ref. 3; BAB85034).	Missing.	Poly-Gln.		D3DX31|D3DX32|O15413|Q6IC31|Q8NF16|Q96CT0|Q96IH7|Q9P1T3	In_Frame_Del	DEL	ENST00000263205.7	37	c.751_753delCAG	CCDS33602.1																																																																																				0.591	MED15-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320177.2	NM_015889		12	119						12	119	---	---	---	---
