#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
LINC00264	645528	broad.mit.edu	37	10	26880266	26880266	+	lincRNA	SNP	G	G	A			TCGA-ET-A2N3-01B-21D-A23M-08	TCGA-ET-A2N3-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bcfcc7e4-b937-4f55-a703-e73a783d1fc1	27ec3857-71ae-4f7d-944d-112b47b0b97d	g.chr10:26880266G>A	ENST00000412114.1	+	0	501					NR_026793.1				long intergenic non-protein coding RNA 264																		ACCAAGCCCAGTGGACAGATG	0.443																																						ENST00000412114.1																			0																																																			0							g.chr10:26880266G>A			10p12.1	2012-10-12	2011-08-11	2011-08-11	ENSG00000233261	ENSG00000233261		"""Long non-coding RNAs"""	17776	non-coding RNA	RNA, long non-coding			"""chromosome 10 open reading frame 50"", ""non-protein coding RNA 264"""	C10orf50, NCRNA00264			Standard	NR_026793		Approved	bA128B16.2	uc001ist.3		OTTHUMG00000017839		10.37:g.26880266G>A								NR_026793.1						0	501	+									RNA	SNP	ENST00000412114.1	37																																																																																						0.443	LINC00264-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000047265.1	XR_040540		5	53	0	0	0	1	0	5	53				
SLC31A2	1318	broad.mit.edu	37	9	115923922	115923922	+	Missense_Mutation	SNP	G	G	C			TCGA-ET-A2N3-01B-21D-A23M-08	TCGA-ET-A2N3-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bcfcc7e4-b937-4f55-a703-e73a783d1fc1	27ec3857-71ae-4f7d-944d-112b47b0b97d	g.chr9:115923922G>C	ENST00000259392.3	+	3	340	c.207G>C	c.(205-207)gaG>gaC	p.E69D		NM_001860.2	NP_001851.1	O15432	COPT2_HUMAN	solute carrier family 31 (copper transporter), member 2	69					cellular copper ion homeostasis (GO:0006878)|copper ion transport (GO:0006825)|regulation of copper ion transmembrane transport (GO:1902311)	integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|recycling endosome (GO:0055037)	copper ion transmembrane transporter activity (GO:0005375)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	7					Carboplatin(DB00958)|Cisplatin(DB00515)	CCATCGCAGAGACAGACGGGG	0.552																																						ENST00000259392.3																			0				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	7						c.(205-207)gaG>gaC		solute carrier family 31 (copper transporter), member 2							102.0	103.0	103.0					9																	115923922		2087	4219	6306	SO:0001583	missense	1318					integral to plasma membrane	copper ion transmembrane transporter activity	g.chr9:115923922G>C		CCDS6788.1	9q32	2013-07-17	2013-07-17		ENSG00000136867	ENSG00000136867		"""Solute carriers"""	11017	protein-coding gene	gene with protein product	"""copper transporter 2"""	603088		COPT2		9207117	Standard	NM_001860		Approved	hCTR2, CTR2	uc004bgq.3	O15432	OTTHUMG00000021037	ENST00000259392.3:c.207G>C	9.37:g.115923922G>C	ENSP00000259392:p.Glu69Asp						p.E69D	NM_001860.2	NP_001851.1	O15432	COPT2_HUMAN			3	340	+			69						Missense_Mutation	SNP	ENST00000259392.3	37	c.207G>C	CCDS6788.1	.	.	.	.	.	.	.	.	.	.	G	1.883	-0.457409	0.04508	.	.	ENSG00000136867	ENST00000259392	T	0.76839	-1.05	5.46	-2.6	0.06190	.	1.244220	0.05253	N	0.514289	T	0.55065	0.1897	N	0.17872	0.535	0.09310	N	1	B;B	0.15719	0.014;0.007	B;B	0.14023	0.007;0.01	T	0.32161	-0.9917	10	0.13470	T	0.59	-0.8776	0.3488	0.00345	0.3534:0.1312:0.2224:0.293	.	69;69	B4DIE0;O15432	.;COPT2_HUMAN	D	69	ENSP00000259392:E69D	ENSP00000259392:E69D	E	+	3	2	SLC31A2	114963743	0.000000	0.05858	0.004000	0.12327	0.056000	0.15407	-0.249000	0.08842	-0.161000	0.10983	0.655000	0.94253	GAG		0.552	SLC31A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055509.2	NM_001860		34	64	0	0	0	1	0	34	64				
TSSC2	650368	broad.mit.edu	37	11	3427845	3427845	+	RNA	SNP	C	C	T			TCGA-ET-A2N3-01B-21D-A23M-08	TCGA-ET-A2N3-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bcfcc7e4-b937-4f55-a703-e73a783d1fc1	27ec3857-71ae-4f7d-944d-112b47b0b97d	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			4	57	0	0	0	1	0	4	57				
DNM1P47	100216544	broad.mit.edu	37	15	102292953	102292953	+	RNA	SNP	T	T	C			TCGA-ET-A2N3-01B-21D-A23M-08	TCGA-ET-A2N3-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bcfcc7e4-b937-4f55-a703-e73a783d1fc1	27ec3857-71ae-4f7d-944d-112b47b0b97d	g.chr15:102292953T>C	ENST00000561463.1	+	0	999									DNM1 pseudogene 47																		GGCACAGCGGTGCGACGAGAT	0.587																																						ENST00000561463.1																			0																																																			0							g.chr15:102292953T>C	AJ576276		15q26.3	2013-04-25			ENSG00000259660	ENSG00000259660			35200	pseudogene	pseudogene				DNM1DN14@			Standard	NG_009149		Approved	DNM1DN14-3			OTTHUMG00000172265		15.37:g.102292953T>C														0	999	+									RNA	SNP	ENST00000561463.1	37																																																																																						0.587	DNM1P47-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417589.1	NG_009149		3	13	0	0	0	1	0	3	13				
KLHL8	57563	broad.mit.edu	37	4	88106900	88106900	+	Missense_Mutation	SNP	G	G	A			TCGA-ET-A2N3-01B-21D-A23M-08	TCGA-ET-A2N3-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bcfcc7e4-b937-4f55-a703-e73a783d1fc1	27ec3857-71ae-4f7d-944d-112b47b0b97d	g.chr4:88106900G>A	ENST00000273963.5	-	3	609	c.268C>T	c.(268-270)Ccc>Tcc	p.P90S	KLHL8_ENST00000545252.1_Intron|KLHL8_ENST00000425278.2_Intron|KLHL8_ENST00000512111.1_Missense_Mutation_p.P90S|KLHL8_ENST00000498875.2_Intron	NM_020803.3	NP_065854.3	Q9P2G9	KLHL8_HUMAN	kelch-like family member 8	90	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	Cul3-RING ubiquitin ligase complex (GO:0031463)|nucleus (GO:0005634)				breast(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|stomach(1)|upper_aerodigestive_tract(1)	17		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)		CTAAAGTAGGGAATAACACAA	0.373																																						ENST00000273963.5																			0				breast(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|stomach(1)|upper_aerodigestive_tract(1)	17						c.(268-270)Ccc>Tcc		kelch-like family member 8							29.0	29.0	29.0					4																	88106900		2203	4297	6500	SO:0001583	missense	57563							g.chr4:88106900G>A	AB037799	CCDS3617.1, CCDS75163.1	4q21.3	2013-01-30	2013-01-30		ENSG00000145332	ENSG00000145332		"""Kelch-like"", ""BTB/POZ domain containing"""	18644	protein-coding gene	gene with protein product		611967	"""kelch-like 8 (Drosophila)"""				Standard	XM_005263153		Approved	KIAA1378	uc003hql.1	Q9P2G9	OTTHUMG00000130593	ENST00000273963.5:c.268C>T	4.37:g.88106900G>A	ENSP00000273963:p.Pro90Ser					KLHL8_ENST00000498875.2_Intron|KLHL8_ENST00000425278.2_Intron|KLHL8_ENST00000545252.1_Intron|KLHL8_ENST00000512111.1_Missense_Mutation_p.P90S	p.P90S	NM_020803.3	NP_065854.3	Q9P2G9	KLHL8_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;0.000603)	3	609	-		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)	90			BTB.		Q53XA3|Q6N018	Missense_Mutation	SNP	ENST00000273963.5	37	c.268C>T	CCDS3617.1	.	.	.	.	.	.	.	.	.	.	G	19.27	3.795615	0.70452	.	.	ENSG00000145332	ENST00000273963;ENST00000512111	T;T	0.71934	-0.61;-0.61	5.89	5.89	0.94794	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	T	0.78509	0.4294	L	0.55481	1.735	0.80722	D	1	P	0.51791	0.948	P	0.54499	0.754	T	0.76586	-0.2905	10	0.45353	T	0.12	.	20.2572	0.98426	0.0:0.0:1.0:0.0	.	90	Q9P2G9	KLHL8_HUMAN	S	90	ENSP00000273963:P90S;ENSP00000424131:P90S	ENSP00000273963:P90S	P	-	1	0	KLHL8	88325924	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	5.178000	0.65037	2.793000	0.96121	0.650000	0.86243	CCC		0.373	KLHL8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253040.1			7	24	0	0	0	1	0	7	24				
PLEKHA3	65977	broad.mit.edu	37	2	179360222	179360222	+	Splice_Site	SNP	G	G	C			TCGA-ET-A2N3-01B-21D-A23M-08	TCGA-ET-A2N3-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bcfcc7e4-b937-4f55-a703-e73a783d1fc1	27ec3857-71ae-4f7d-944d-112b47b0b97d	g.chr2:179360222G>C	ENST00000234453.5	+	5	852		c.e5-1			NM_019091.3	NP_061964.3	Q9HB20	PKHA3_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 3							Golgi apparatus (GO:0005794)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phospholipid binding (GO:0005543)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.0266)|all cancers(119;0.0865)			TAATTTTTCAGAACATGAATG	0.363																																						ENST00000234453.4																			0				endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11						c.e5-1		pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 3							91.0	84.0	86.0					2																	179360222		2203	4300	6503	SO:0001630	splice_region_variant	65977					cytoplasm|membrane		g.chr2:179360222G>C	AF286162	CCDS33336.1	2q31.2	2013-01-10	2002-01-14		ENSG00000116095	ENSG00000116095		"""Pleckstrin homology (PH) domain containing"""	14338	protein-coding gene	gene with protein product	"""four-phosphate-adaptor protein 1"""	607774	"""pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3"""			11001876, 15107860	Standard	NM_019091		Approved	FAPP1	uc002umn.3	Q9HB20	OTTHUMG00000154446	ENST00000234453.5:c.451-1G>C	2.37:g.179360222G>C								NM_019091.3	NP_061964.3	Q9HB20	PKHA3_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.0266)|all cancers(119;0.0865)		5	852	+								Q4ZG69|Q86TQ1|Q9NXT3	Splice_Site	SNP	ENST00000234453.5	37		CCDS33336.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.410541	0.83340	.	.	ENSG00000116095	ENST00000234453	.	.	.	5.95	5.95	0.96441	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.3747	0.98911	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PLEKHA3	179068468	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.213000	0.95133	2.817000	0.96982	0.563000	0.77884	.		0.363	PLEKHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335241.2	NM_019091	Intron	36	38	0	0	0	1	0	36	38				
ESYT2	57488	broad.mit.edu	37	7	158527136	158527136	+	Missense_Mutation	SNP	T	T	A			TCGA-ET-A2N3-01B-21D-A23M-08	TCGA-ET-A2N3-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bcfcc7e4-b937-4f55-a703-e73a783d1fc1	27ec3857-71ae-4f7d-944d-112b47b0b97d	g.chr7:158527136T>A	ENST00000251527.5	-	21	2678	c.2613A>T	c.(2611-2613)gaA>gaT	p.E871D	ESYT2_ENST00000435514.2_Missense_Mutation_p.E306D	NM_020728.2	NP_065779.1	A0FGR8	ESYT2_HUMAN	extended synaptotagmin-like protein 2	899	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.				endocytosis (GO:0006897)|lipid transport (GO:0006869)	extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|membrane (GO:0016020)|organelle membrane contact site (GO:0044232)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|identical protein binding (GO:0042802)|phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(16)|prostate(2)	32						CTTTGGCAAGTTCTTCAGATG	0.547																																						ENST00000251527.5																			0				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(16)|prostate(2)	32						c.(2611-2613)gaA>gaT		extended synaptotagmin-like protein 2							73.0	69.0	71.0					7																	158527136		2203	4300	6503	SO:0001583	missense	57488					integral to membrane|plasma membrane		g.chr7:158527136T>A	AB033054	CCDS34791.1	7q36.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000117868	ENSG00000117868		"""Synaptotagmins"""	22211	protein-coding gene	gene with protein product			"""family with sequence similarity 62 (C2 domain containing), member B"""	FAM62B		17672888	Standard	NM_020728		Approved	KIAA1228, CHR2SYT	uc003wob.1	A0FGR8	OTTHUMG00000151436	ENST00000251527.5:c.2613A>T	7.37:g.158527136T>A	ENSP00000251527:p.Glu871Asp					ESYT2_ENST00000435514.2_Missense_Mutation_p.E306D	p.E871D	NM_020728.2	NP_065779.1	A0FGR8	ESYT2_HUMAN			21	2678	-			899			C2 3.		A4D229|Q69YJ2|Q6UKI4|Q6ZTU0|Q6ZVU1|Q9BQS0|Q9NW47|Q9ULJ2	Missense_Mutation	SNP	ENST00000251527.5	37	c.2613A>T	CCDS34791.1	.	.	.	.	.	.	.	.	.	.	T	7.578	0.668137	0.14710	.	.	ENSG00000117868	ENST00000251527;ENST00000421679;ENST00000275418;ENST00000435514	T;T;T	0.06768	3.26;3.26;3.26	5.69	-10.4	0.00318	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.238434	0.43919	N	0.000505	T	0.01592	0.0051	N	0.03608	-0.345	0.25376	N	0.988659	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.35051	-0.9804	10	0.02654	T	1	-16.1671	4.8535	0.13549	0.0958:0.4081:0.0886:0.4075	.	871;899	A0FGR8-2;A0FGR8	.;ESYT2_HUMAN	D	871;920;862;306	ENSP00000251527:E871D;ENSP00000275418:E862D;ENSP00000411488:E306D	ENSP00000251527:E871D	E	-	3	2	ESYT2	158219897	0.198000	0.23374	0.610000	0.28997	0.993000	0.82548	-0.820000	0.04457	-1.367000	0.02152	0.482000	0.46254	GAA		0.547	ESYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322647.1	NM_020728		25	52	0	0	0	1	0	25	52				
KIAA0907	22889	broad.mit.edu	37	1	155887393	155887393	+	Missense_Mutation	SNP	T	T	G			TCGA-ET-A2N3-01B-21D-A23M-08	TCGA-ET-A2N3-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bcfcc7e4-b937-4f55-a703-e73a783d1fc1	27ec3857-71ae-4f7d-944d-112b47b0b97d	g.chr1:155887393T>G	ENST00000368321.3	-	11	1360	c.1337A>C	c.(1336-1338)cAg>cCg	p.Q446P	KIAA0907_ENST00000368320.3_Missense_Mutation_p.Q446P|SNORA42_ENST00000384744.1_RNA	NM_014949.2	NP_055764.2	Q7Z7F0	K0907_HUMAN	KIAA0907	446	Pro-rich.						RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|urinary_tract(1)	21	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;8.82e-06)			gggctggggctggggctgggg	0.567																																						ENST00000368320.3																			0				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|urinary_tract(1)	21						c.(1336-1338)cAg>cCg		KIAA0907							14.0	18.0	16.0					1																	155887393		2157	4273	6430	SO:0001583	missense	22889							g.chr1:155887393T>G	BC062637	CCDS30885.1	1q22	2012-11-30			ENSG00000132680	ENSG00000132680			29145	protein-coding gene	gene with protein product						10048485	Standard	NM_014949		Approved	BLOM7	uc001fmi.1	Q7Z7F0	OTTHUMG00000014103	ENST00000368321.3:c.1337A>C	1.37:g.155887393T>G	ENSP00000357304:p.Gln446Pro					KIAA0907_ENST00000368321.3_Missense_Mutation_p.Q446P	p.Q446P			Q7Z7F0	K0907_HUMAN	OV - Ovarian serous cystadenocarcinoma(3;8.82e-06)		11	1362	-	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		446			Pro-rich.		O94981|Q7L7Q2|Q7Z7E9|Q8TBQ0	Missense_Mutation	SNP	ENST00000368321.3	37	c.1337A>C	CCDS30885.1	.	.	.	.	.	.	.	.	.	.	T	10.66	1.413076	0.25465	.	.	ENSG00000132680	ENST00000368321;ENST00000368320	T;T	0.32753	1.44;1.44	5.76	0.471	0.16752	.	0.977681	0.08344	N	0.960281	T	0.04003	0.0112	N	0.03608	-0.345	0.29419	N	0.860713	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43442	-0.9391	10	0.22706	T	0.39	.	8.2981	0.31997	0.1873:0.0:0.4136:0.3991	.	446;446	Q7Z7F0-2;Q7Z7F0	.;K0907_HUMAN	P	446	ENSP00000357304:Q446P;ENSP00000357303:Q446P	ENSP00000357303:Q446P	Q	-	2	0	KIAA0907	154154017	0.988000	0.35896	0.899000	0.35326	0.963000	0.63663	-0.615000	0.05597	-0.064000	0.13043	0.533000	0.62120	CAG		0.567	KIAA0907-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039583.1	NM_014949		10	43	0	0	0	1	0	10	43				
DSCAML1	57453	broad.mit.edu	37	11	117375679	117375679	+	Silent	SNP	G	G	A	rs139385882	byFrequency	TCGA-ET-A2N3-01B-21D-A23M-08	TCGA-ET-A2N3-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bcfcc7e4-b937-4f55-a703-e73a783d1fc1	27ec3857-71ae-4f7d-944d-112b47b0b97d	g.chr11:117375679G>A	ENST00000321322.6	-	10	2323	c.2322C>T	c.(2320-2322)gaC>gaT	p.D774D	DSCAML1_ENST00000527706.1_Silent_p.D504D	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	714	Ig-like C2-type 8.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		GGGGGTAGCCGTCCACCGAGC	0.597													g|||	2	0.000399361	0.0015	0.0	5008	,	,		17716	0.0		0.0	False		,,,				2504	0.0					ENST00000321322.6																			0				breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110						c.(2320-2322)gaC>gaT		Down syndrome cell adhesion molecule like 1		A		0,4402		0,0,2201	87.0	76.0	80.0		2322	-8.1	0.6	11	dbSNP_134	80	4,8588	3.7+/-12.6	0,4,4292	no	coding-synonymous	DSCAML1	NM_020693.2		0,4,6493	AA,AG,GG		0.0466,0.0,0.0308		774/2114	117375679	4,12990	2201	4296	6497	SO:0001819	synonymous_variant	57453				axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity	g.chr11:117375679G>A		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.2322C>T	11.37:g.117375679G>A						DSCAML1_ENST00000527706.1_Silent_p.D504D	p.D774D	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)	10	2323	-	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)	714			Ig-like C2-type 8.		Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Silent	SNP	ENST00000321322.6	37	c.2322C>T	CCDS8384.1																																																																																				0.597	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		29	49	0	0	0	1	0	29	49				
OR14C36	127066	broad.mit.edu	37	1	248512355	248512355	+	Silent	SNP	G	G	A	rs146830794		TCGA-ET-A2N3-01B-21D-A23M-08	TCGA-ET-A2N3-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bcfcc7e4-b937-4f55-a703-e73a783d1fc1	27ec3857-71ae-4f7d-944d-112b47b0b97d	g.chr1:248512355G>A	ENST00000317861.1	+	1	279	c.279G>A	c.(277-279)gcG>gcA	p.A93A		NM_001001918.1	NP_001001918.1	Q8NHC7	O14CZ_HUMAN	olfactory receptor, family 14, subfamily C, member 36	93						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A93A(1)		central_nervous_system(1)|endometrium(2)|large_intestine(4)|liver(2)|lung(20)|ovary(2)|prostate(3)|skin(7)|upper_aerodigestive_tract(2)	43						TTTCTAAGGCGGGATGTGTAG	0.478																																						ENST00000317861.1																			1	Substitution - coding silent(1)	p.A93A(1)	lung(1)	central_nervous_system(1)|endometrium(2)|large_intestine(4)|liver(2)|lung(20)|ovary(2)|prostate(3)|skin(7)|upper_aerodigestive_tract(2)	43						c.(277-279)gcG>gcA		olfactory receptor, family 14, subfamily C, member 36		G		1,4405	2.1+/-5.4	0,1,2202	103.0	90.0	94.0		279	-7.8	0.0	1	dbSNP_134	94	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	OR14C36	NM_001001918.1		0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231		93/313	248512355	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	127066				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr1:248512355G>A	BK004466	CCDS31112.1	1q44	2012-08-09	2008-04-02	2008-04-02	ENSG00000177174	ENSG00000177174		"""GPCR / Class A : Olfactory receptors"""	15026	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily BF, member 1"""	OR5BF1			Standard	NM_001001918		Approved		uc010pzl.2	Q8NHC7	OTTHUMG00000040463	ENST00000317861.1:c.279G>A	1.37:g.248512355G>A							p.A93A	NM_001001918.1	NP_001001918.1	Q8NHC7	O14CZ_HUMAN			1	279	+			93					Q6IEZ6	Silent	SNP	ENST00000317861.1	37	c.279G>A	CCDS31112.1																																																																																				0.478	OR14C36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097359.1	NM_001001918		5	71	0	0	0	1	0	5	71				
WHAMMP3	339005	broad.mit.edu	37	15	23191911	23191911	+	RNA	SNP	C	C	T	rs147199465		TCGA-ET-A2N3-01B-21D-A23M-08	TCGA-ET-A2N3-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bcfcc7e4-b937-4f55-a703-e73a783d1fc1	27ec3857-71ae-4f7d-944d-112b47b0b97d	g.chr15:23191911C>T	ENST00000400153.2	-	0	1785					NR_003521.1		Q1A5X7	WHAL1_HUMAN	WAS protein homolog associated with actin, golgi membranes and microtubules pseudogene 3																		TGATTTTCTTCGCACTGATCC	0.408																																						ENST00000400153.2																			0																																																			0							g.chr15:23191911C>T	BC048987		15q11.2	2014-03-20	2011-06-24	2011-06-24	ENSG00000187667	ENSG00000276141			27892	pseudogene	pseudogene			"""WAS protein homology region 2 domain containing 1-like 1"", ""WAS protein homolog associated with actin, golgi membranes and microtubules-like 1"", ""WAS protein homolog associated with actin, golgi membranes and microtubules-like 1 (pseudogene)"""	WHDC1L1, WHAMML1		18226259	Standard	NR_003521		Approved		uc001yvg.3	Q1A5X7	OTTHUMG00000171921		15.37:g.23191911C>T								NR_003521.1						0	1785	-								Q1A5X8|Q52M16|Q52M18	RNA	SNP	ENST00000400153.2	37																																																																																						0.408	WHAMMP3-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000415907.1	NR_003521		5	42	0	0	0	1	0	5	42				
BMS1P20	96610	broad.mit.edu	37	22	22664606	22664606	+	RNA	SNP	A	A	G	rs187344612		TCGA-ET-A2N3-01B-21D-A23M-08	TCGA-ET-A2N3-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bcfcc7e4-b937-4f55-a703-e73a783d1fc1	27ec3857-71ae-4f7d-944d-112b47b0b97d	g.chr22:22664606A>G	ENST00000426066.1	+	0	787					NR_027293.1				BMS1 pseudogene 20																		GTCTTCATGCAAACTTGGTAT	0.398																																						ENST00000426066.1																			0																																																			0							g.chr22:22664606A>G			22q11.22	2013-09-20			ENSG00000236850	ENSG00000236850			49153	pseudogene	pseudogene							Standard	XR_430414		Approved				OTTHUMG00000151046		22.37:g.22664606A>G								NR_027293.1						0	787	+									RNA	SNP	ENST00000426066.1	37																																																																																						0.398	BMS1P20-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000473090.1			3	31	0	0	0	1	0	3	31				
DCAF4L2	138009	broad.mit.edu	37	8	88886182	88886182	+	Silent	SNP	C	C	T			TCGA-ET-A2N3-01B-21D-A23M-08	TCGA-ET-A2N3-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bcfcc7e4-b937-4f55-a703-e73a783d1fc1	27ec3857-71ae-4f7d-944d-112b47b0b97d	g.chr8:88886182C>T	ENST00000319675.3	-	1	114	c.18G>A	c.(16-18)ccG>ccA	p.P6P		NM_152418.3	NP_689631.1	Q8NA75	DC4L2_HUMAN	DDB1 and CUL4 associated factor 4-like 2	6										breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|liver(2)|lung(40)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	83						CGAGCAGTCGCGGTCTTTTGC	0.517																																						ENST00000319675.3																			0				breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|liver(2)|lung(40)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	83						c.(16-18)ccG>ccA		DDB1 and CUL4 associated factor 4-like 2							45.0	45.0	45.0					8																	88886182		2203	4300	6503	SO:0001819	synonymous_variant	138009							g.chr8:88886182C>T	AL833507	CCDS6245.1	8q21.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000176566		"""WD repeat domain containing"""	26657	protein-coding gene	gene with protein product			"""WD repeat domain 21C"""	WDR21C		14702039	Standard	NM_152418		Approved		uc003ydz.3	Q8NA75		ENST00000319675.3:c.18G>A	8.37:g.88886182C>T							p.P6P	NM_152418.3	NP_689631.1	Q8NA75	DC4L2_HUMAN			1	114	-			6						Silent	SNP	ENST00000319675.3	37	c.18G>A	CCDS6245.1																																																																																				0.517	DCAF4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375302.1	NM_152418		24	25	0	0	0	1	0	24	25				
CSAG4	100130935	broad.mit.edu	37	X	151896231	151896231	+	RNA	SNP	A	A	G			TCGA-ET-A2N3-01B-21D-A23M-08	TCGA-ET-A2N3-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bcfcc7e4-b937-4f55-a703-e73a783d1fc1	27ec3857-71ae-4f7d-944d-112b47b0b97d	g.chrX:151896231A>G	ENST00000361201.4	-	0	499					NR_073432.1				CSAG family, member 4 (pseudogene)											endometrium(2)|kidney(2)|lung(1)	5						GAGTGGCTGGATAGTGTTGGC	0.517																																						ENST00000361201.4																			0				endometrium(2)|kidney(2)|lung(1)	5																																														0							g.chrX:151896231A>G	BC013171		Xq28	2014-01-21	2012-04-19		ENSG00000242599	ENSG00000242599			20923	pseudogene	pseudogene			"""CSAG family, member 4"""				Standard	NR_073432		Approved				OTTHUMG00000022646		X.37:g.151896231A>G								NR_073432.1						0	499	-									RNA	SNP	ENST00000361201.4	37																																																																																						0.517	CSAG4-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000058758.2			8	27	0	0	0	1	0	8	27				
OLFM1	10439	broad.mit.edu	37	9	137982159	137982159	+	Missense_Mutation	SNP	G	G	A			TCGA-ET-A2N3-01B-21D-A23M-08	TCGA-ET-A2N3-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bcfcc7e4-b937-4f55-a703-e73a783d1fc1	27ec3857-71ae-4f7d-944d-112b47b0b97d	g.chr9:137982159G>A	ENST00000371793.3	+	2	520	c.269G>A	c.(268-270)cGc>cAc	p.R90H	OLFM1_ENST00000277415.11_Missense_Mutation_p.R72H|OLFM1_ENST00000392991.4_Missense_Mutation_p.R90H|OLFM1_ENST00000371796.3_Missense_Mutation_p.R63H|OLFM1_ENST00000252854.4_Missense_Mutation_p.R72H	NM_001282611.1	NP_001269540.1	Q99784	NOE1_HUMAN	olfactomedin 1	90					negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of neuron migration (GO:2001223)|nervous system development (GO:0007399)|protein oligomerization (GO:0051259)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(2)	21		Myeloproliferative disorder(178;0.0333)		Epithelial(140;5.49e-08)|OV - Ovarian serous cystadenocarcinoma(145;9.68e-08)|all cancers(34;1.88e-07)		CGGGATGCCCGCACAAAACAG	0.557																																						ENST00000252854.4																			0				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(2)	21						c.(214-216)cGc>cAc		olfactomedin 1							107.0	80.0	89.0					9																	137982159		2203	4300	6503	SO:0001583	missense	10439				nervous system development	endoplasmic reticulum lumen	protein binding	g.chr9:137982159G>A	AF035301	CCDS6986.1, CCDS6987.1, CCDS65183.1, CCDS65184.1	9q34.3	2014-01-20			ENSG00000130558	ENSG00000130558			17187	protein-coding gene	gene with protein product	"""pancortin"""	605366				9039501	Standard	NM_006334		Approved	NOE1, OlfA, AMY, NOELIN	uc004cfl.4	Q99784	OTTHUMG00000020897	ENST00000371793.3:c.269G>A	9.37:g.137982159G>A	ENSP00000360858:p.Arg90His					OLFM1_ENST00000392991.4_Missense_Mutation_p.R90H|OLFM1_ENST00000371793.3_Missense_Mutation_p.R90H|OLFM1_ENST00000371796.3_Missense_Mutation_p.R63H|OLFM1_ENST00000277415.11_Missense_Mutation_p.R72H	p.R72H	NM_014279.4	NP_055094.1	Q99784	NOE1_HUMAN		Epithelial(140;5.49e-08)|OV - Ovarian serous cystadenocarcinoma(145;9.68e-08)|all cancers(34;1.88e-07)	2	402	+		Myeloproliferative disorder(178;0.0333)	90					Q53XZ8|Q6IMJ4|Q6IMJ5|Q8N8R0|Q969S7|Q99452	Missense_Mutation	SNP	ENST00000371793.3	37	c.215G>A		.	.	.	.	.	.	.	.	.	.	G	20.7	4.040594	0.75732	.	.	ENSG00000130558	ENST00000277415;ENST00000252854;ENST00000339720;ENST00000371796;ENST00000539529;ENST00000392991;ENST00000371793	T;T;T;T;T;T;T	0.56103	0.48;0.48;0.48;0.48;0.48;0.48;0.48	4.75	4.75	0.60458	.	0.048862	0.64402	N	0.000001	T	0.45558	0.1348	L	0.41824	1.3	0.80722	D	1	B;P;B;B	0.34892	0.094;0.474;0.067;0.385	B;B;B;B	0.29524	0.037;0.075;0.103;0.101	T	0.53676	-0.8405	10	0.87932	D	0	.	18.1101	0.89533	0.0:0.0:1.0:0.0	.	90;90;72;72	Q99784;Q99784-2;Q6IMJ8;Q6IMJ7	NOE1_HUMAN;.;.;.	H	72;72;79;63;7;90;90	ENSP00000277415:R72H;ENSP00000252854:R72H;ENSP00000340318:R79H;ENSP00000360861:R63H;ENSP00000444296:R7H;ENSP00000376717:R90H;ENSP00000360858:R90H	ENSP00000252854:R72H	R	+	2	0	OLFM1	137121980	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.691000	0.84191	2.309000	0.77851	0.655000	0.94253	CGC		0.557	OLFM1-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000054974.1	NM_014279		20	29	0	0	0	1	0	20	29				
ADPRH	141	broad.mit.edu	37	3	119305355	119305355	+	Silent	SNP	G	G	A			TCGA-ET-A2N3-01B-21D-A23M-08	TCGA-ET-A2N3-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bcfcc7e4-b937-4f55-a703-e73a783d1fc1	27ec3857-71ae-4f7d-944d-112b47b0b97d	g.chr3:119305355G>A	ENST00000478399.1	+	3	1927	c.522G>A	c.(520-522)gcG>gcA	p.A174A	ADPRH_ENST00000465513.1_Silent_p.A174A|ADPRH_ENST00000478927.1_Silent_p.A174A|ADPRH_ENST00000357003.3_Silent_p.A174A|ADPRH_ENST00000471850.1_3'UTR			P54922	ADPRH_HUMAN	ADP-ribosylarginine hydrolase	174					cellular protein modification process (GO:0006464)|protein de-ADP-ribosylation (GO:0051725)		ADP-ribosylarginine hydrolase activity (GO:0003875)|magnesium ion binding (GO:0000287)			breast(1)|kidney(1)|lung(10)|ovary(1)	13		Lung NSC(201;0.0977)		GBM - Glioblastoma multiforme(114;0.23)		GGGCCCTTGCGTCTGCTCTTT	0.537																																					GBM(133;579 1804 5989 9967 40052)	ENST00000478399.1																			0				breast(1)|kidney(1)|lung(10)|ovary(1)	13						c.(520-522)gcG>gcA		ADP-ribosylarginine hydrolase							124.0	127.0	126.0					3																	119305355		2203	4300	6503	SO:0001819	synonymous_variant	141				protein de-ADP-ribosylation		ADP-ribosylarginine hydrolase activity|magnesium ion binding	g.chr3:119305355G>A	L13291	CCDS2990.1	3q13.31-q13.33	2004-02-27			ENSG00000144843	ENSG00000144843			269	protein-coding gene	gene with protein product		603081				8349667, 12070318	Standard	NM_001125		Approved	ARH1	uc003ecs.3	P54922	OTTHUMG00000159420	ENST00000478399.1:c.522G>A	3.37:g.119305355G>A						ADPRH_ENST00000478927.1_Silent_p.A174A|ADPRH_ENST00000465513.1_Silent_p.A174A|ADPRH_ENST00000357003.3_Silent_p.A174A|ADPRH_ENST00000471850.1_3'UTR	p.A174A			P54922	ADPRH_HUMAN		GBM - Glioblastoma multiforme(114;0.23)	3	1927	+		Lung NSC(201;0.0977)	174					B2R8H1|D3DN83	Silent	SNP	ENST00000478399.1	37	c.522G>A	CCDS2990.1																																																																																				0.537	ADPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355199.1	NM_001125		26	218	0	0	0	1	0	26	218				
RP11-206L10.10	0	broad.mit.edu	37	1	745643	745643	+	RNA	DEL	C	C	-	rs200097270	byFrequency	TCGA-ET-A2N3-01B-21D-A23M-08	TCGA-ET-A2N3-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bcfcc7e4-b937-4f55-a703-e73a783d1fc1	27ec3857-71ae-4f7d-944d-112b47b0b97d	g.chr1:745643delC	ENST00000435300.1	-	0	340				RP11-206L10.8_ENST00000447500.1_RNA																							TTCAAAGTGACAGACTGTGGG	0.299													|||unknown(NO_COVERAGE)	135	0.0269569	0.0234	0.0288	5008	,	,		20667	0.0		0.0417	False		,,,				2504	0.0429					ENST00000435300.1																			0																																																			0							g.chr1:745643delC																													1.37:g.745643delC														0	340	-									RNA	DEL	ENST00000435300.1	37																																																																																						0.299	RP11-206L10.10-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000007014.1			7	7						7	7	---	---	---	---
GRM6	2916	broad.mit.edu	37	5	178418554	178418555	+	Frame_Shift_Ins	INS	-	-	C	rs17078894|rs281865186	byFrequency	TCGA-ET-A2N3-01B-21D-A23M-08	TCGA-ET-A2N3-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bcfcc7e4-b937-4f55-a703-e73a783d1fc1	27ec3857-71ae-4f7d-944d-112b47b0b97d	g.chr5:178418554_178418555insC	ENST00000517717.1	-	4	765_766	c.727_728insG	c.(727-729)gtcfs	p.V243fs	RP11-281O15.4_ENST00000519491.1_RNA|GRM6_ENST00000231188.5_Frame_Shift_Ins_p.V243fs			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6	243					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|detection of light stimulus involved in visual perception (GO:0050908)|detection of visible light (GO:0009584)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|locomotory behavior (GO:0007626)|positive regulation of calcium ion import (GO:0090280)|regulation of synaptic transmission, glutamatergic (GO:0051966)|retina development in camera-type eye (GO:0060041)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|new growing cell tip (GO:0035841)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|endometrium(9)|large_intestine(12)|lung(21)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	55	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.245)		GGCAATACAGACCCCCCCTGGG	0.624																																						ENST00000231188.5																			0				NS(2)|breast(4)|endometrium(9)|large_intestine(12)|lung(21)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	55	GRCh37	CI054463	GRM6	I		c.(727-729)ctgfs		glutamate receptor, metabotropic 6				0,4262		0,0,2131				http://www.ncbi.nlm.nih.gov/sites/varvu?gene		5.3	1.0		dbSNP_129	140	2,8252		0,2,4125	no	frameshift	GRM6	NM_000843.3		0,2,6256	A1A1,A1R,RR		0.0242,0.0,0.016				2,12514				SO:0001589	frameshift_variant	2916				detection of visible light|visual perception	integral to plasma membrane		g.chr5:178418554_178418555insC	U82083	CCDS4442.1	5q35	2014-01-28						"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4598	protein-coding gene	gene with protein product		604096				9215706	Standard	NM_000843		Approved	GPRC1F, mGlu6, MGLUR6, CSNB1B	uc003mjr.3	O15303	OTTHUMG00000130889	ENST00000517717.1:c.728dupG	5.37:g.178418561_178418561dupC	ENSP00000430767:p.Val243fs					GRM6_ENST00000517717.1_Frame_Shift_Ins_p.L243fs	p.L243fs	NM_000843.3	NP_000834.2	O15303	GRM6_HUMAN	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.245)	3	905_906	-	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	243						Frame_Shift_Ins	INS	ENST00000517717.1	37	c.727_728insG	CCDS4442.1																																																																																				0.624	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2			75	156						75	156	---	---	---	---
ECM2	1842	broad.mit.edu	37	9	95277146	95277148	+	In_Frame_Del	DEL	TCC	TCC	-	rs137929518	byFrequency	TCGA-ET-A2N3-01B-21D-A23M-08	TCGA-ET-A2N3-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bcfcc7e4-b937-4f55-a703-e73a783d1fc1	27ec3857-71ae-4f7d-944d-112b47b0b97d	g.chr9:95277146_95277148delTCC	ENST00000344604.5	-	4	968_970	c.819_821delGGA	c.(817-822)gaggat>gat	p.E273del	CENPP_ENST00000375587.3_Intron|ECM2_ENST00000444490.2_In_Frame_Del_p.E251del	NM_001197295.1|NM_001393.3	NP_001184224.1|NP_001384.1	O94769	ECM2_HUMAN	extracellular matrix protein 2, female organ and adipocyte specific	273	Poly-Glu.				cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27						ctcctcctcatcctcctcctcct	0.606																																						ENST00000344604.5																			0				breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27						c.(817-822)gat>ga		extracellular matrix protein 2, female organ and adipocyte specific																																				SO:0001651	inframe_deletion	1842				cell-matrix adhesion		integrin binding	g.chr9:95277146_95277148delTCC	AB011792	CCDS6698.1, CCDS56578.1	9q22.3	2008-07-21			ENSG00000106823	ENSG00000106823			3154	protein-coding gene	gene with protein product	"""matrix glycoprotein SC1/ECM2"""	603479				9790758	Standard	NM_001393		Approved		uc011lty.2	O94769	OTTHUMG00000020226	ENST00000344604.5:c.819_821delGGA	9.37:g.95277155_95277157delTCC	ENSP00000344758:p.Glu273del					ECM2_ENST00000444490.2_In_Frame_Del_p.ED251del|CENPP_ENST00000375587.3_Intron	p.ED273del	NM_001197295.1|NM_001393.3	NP_001184224.1|NP_001384.1	O94769	ECM2_HUMAN			4	968_970	-			273			Poly-Glu.		B2R730|E2PU11|Q5T9F2|Q7Z3D0	In_Frame_Del	DEL	ENST00000344604.5	37	c.819_821delGGA	CCDS6698.1																																																																																				0.606	ECM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053091.1	NM_001393		7	186						7	186	---	---	---	---
MICALCL	84953	broad.mit.edu	37	11	12316387	12316389	+	In_Frame_Del	DEL	CTA	CTA	-	rs3812754|rs542581403|rs199786165	byFrequency	TCGA-ET-A2N3-01B-21D-A23M-08	TCGA-ET-A2N3-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bcfcc7e4-b937-4f55-a703-e73a783d1fc1	27ec3857-71ae-4f7d-944d-112b47b0b97d	g.chr11:12316387_12316389delCTA	ENST00000256186.2	+	3	1700_1702	c.1409_1411delCTA	c.(1408-1413)cctaca>cca	p.T471del		NM_032867.2	NP_116256.2	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	471			T -> P (in dbSNP:rs3812754).		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	mitogen-activated protein kinase binding (GO:0051019)	p.T471delT(2)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(5)|lung(5)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	30				Epithelial(150;0.00177)		cctcctcctcctACAGCGGGAGG	0.576																																						ENST00000256186.2																			2	Deletion - In frame(2)	p.T471delT(2)	upper_aerodigestive_tract(1)|skin(1)	breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(5)|lung(5)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	30						c.(1408-1413)cca>c		MICAL C-terminal like				571,2409		136,299,1055						0.4	0.0		dbSNP_107	5	2322,4470		556,1210,1630	no	coding	MICALCL	NM_032867.2		692,1509,2685	A1A1,A1R,RR		34.1873,19.1611,29.605				2893,6879				SO:0001651	inframe_deletion	84953				cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm	mitogen-activated protein kinase binding	g.chr11:12316387_12316389delCTA	BK000463	CCDS41620.1	11p15.3	2005-11-01			ENSG00000133808	ENSG00000133808			25933	protein-coding gene	gene with protein product		612355				12110185	Standard	NM_032867		Approved	FLJ14966	uc001mkg.1	Q6ZW33	OTTHUMG00000165777	ENST00000256186.2:c.1409_1411delCTA	11.37:g.12316387_12316389delCTA	ENSP00000256186:p.Thr471del						p.PT470del	NM_032867.2	NP_116256.2	Q6ZW33	MICLK_HUMAN		Epithelial(150;0.00177)	3	1700_1702	+			470			Poly-Pro.		Q7RTP7|Q96JU6	In_Frame_Del	DEL	ENST00000256186.2	37	c.1409_1411delCTA	CCDS41620.1																																																																																				0.576	MICALCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386164.1	NM_032867		5	5						5	5	---	---	---	---
BCL9L	283149	broad.mit.edu	37	11	118774003	118774014	+	In_Frame_Del	DEL	CGCCCCCGCCCC	CGCCCCCGCCCC	-	rs561163109|rs537366265|rs559945924	byFrequency	TCGA-ET-A2N3-01B-21D-A23M-08	TCGA-ET-A2N3-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bcfcc7e4-b937-4f55-a703-e73a783d1fc1	27ec3857-71ae-4f7d-944d-112b47b0b97d	g.chr11:118774003_118774014delCGCCCCCGCCCC	ENST00000334801.3	-	4	1644_1655	c.680_691delGGGGCGGGGGCG	c.(679-693)gggggcgggggcgtc>gtc	p.GGGG227del	BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	227					canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)			NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		TTTCCGGGGAcgcccccgcccccgcccccgcc	0.693														11	0.00219649	0.0015	0.0101	5008	,	,		12847	0.002		0.0	False		,,,				2504	0.0					ENST00000334801.3																			0				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56						c.(679-693)gtc>g		B-cell CLL/lymphoma 9-like				17,22,3805		5,0,7,9,4,1897						3.8	0.8			15	25,37,7438		5,0,15,12,13,3705	no	codingComplex	BCL9L	NM_182557.2		10,0,22,21,17,5602	A1A1,A1A2,A1R,A2A2,A2R,RR		0.8267,1.0146,0.8903				42,59,11243				SO:0001651	inframe_deletion	283149				negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		transcription coactivator activity	g.chr11:118774003_118774014delCGCCCCCGCCCC	AB094091	CCDS8403.1	11q23.3	2012-06-06				ENSG00000186174			23688	protein-coding gene	gene with protein product		609004				12964048	Standard	NM_182557		Approved	DLNB11	uc001pug.3	Q86UU0		ENST00000334801.3:c.680_691delGGGGCGGGGGCG	11.37:g.118774003_118774014delCGCCCCCGCCCC	ENSP00000335320:p.Gly227_Gly230del					BCL9L_ENST00000526143.1_5'UTR	p.GGGGV227del	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)	4	1644_1655	-	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)	227					A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	In_Frame_Del	DEL	ENST00000334801.3	37	c.680_691delGGGGCGGGGGCG	CCDS8403.1																																																																																				0.693	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557		4	5						4	5	---	---	---	---
CLIP1	6249	broad.mit.edu	37	12	122812690	122812691	+	Frame_Shift_Ins	INS	-	-	T			TCGA-ET-A2N3-01B-21D-A23M-08	TCGA-ET-A2N3-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bcfcc7e4-b937-4f55-a703-e73a783d1fc1	27ec3857-71ae-4f7d-944d-112b47b0b97d	g.chr12:122812690_122812691insT	ENST00000540338.1	-	16	3093_3094	c.3052_3053insA	c.(3052-3054)agcfs	p.S1018fs	CLIP1_ENST00000361654.4_Frame_Shift_Ins_p.S896fs|CLIP1_ENST00000545889.1_Frame_Shift_Ins_p.S593fs|CLIP1_ENST00000537178.1_Frame_Shift_Ins_p.S972fs|CLIP1_ENST00000302528.7_Frame_Shift_Ins_p.S1007fs|CLIP1_ENST00000358808.2_Frame_Shift_Ins_p.S1007fs			P30622	CLIP1_HUMAN	CAP-GLY domain containing linker protein 1	1018					microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|positive regulation of microtubule polymerization (GO:0031116)|transport (GO:0006810)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|intermediate filament (GO:0005882)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	metal ion binding (GO:0046872)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|nucleic acid binding (GO:0003676)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|endometrium(4)|kidney(5)|large_intestine(16)|liver(1)|lung(21)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)		CTGGTTGTGGCTTGTTTCCATT	0.505																																						ENST00000358808.2																			0				NS(1)|breast(5)|endometrium(4)|kidney(5)|large_intestine(16)|liver(1)|lung(21)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						c.(3019-3021)ccafs		CAP-GLY domain containing linker protein 1																																				SO:0001589	frameshift_variant	6249				mitotic prometaphase|positive regulation of microtubule polymerization	centrosome|cytosol|endosome|intermediate filament|kinetochore	nucleic acid binding|protein homodimerization activity|zinc ion binding	g.chr12:122812690_122812691insT		CCDS9232.1, CCDS9233.1, CCDS58285.1	12q24.3	2013-01-17	2007-01-05	2007-01-05	ENSG00000130779	ENSG00000130779			10461	protein-coding gene	gene with protein product	"""restin"""	179838	"""restin (Reed-Steinberg cell-expressed intermediate filament-associated protein)"""	RSN		8222754	Standard	NM_001247997		Approved	CYLN1, CLIP170, CLIP, CLIP-170	uc001ucg.2	P30622	OTTHUMG00000168922	ENST00000540338.1:c.3053dupA	12.37:g.122812692_122812692dupT	ENSP00000439093:p.Ser1018fs					CLIP1_ENST00000361654.4_Frame_Shift_Ins_p.P896fs|CLIP1_ENST00000540338.1_Frame_Shift_Ins_p.P1018fs|CLIP1_ENST00000537178.1_Frame_Shift_Ins_p.P972fs|CLIP1_ENST00000545889.1_Frame_Shift_Ins_p.P593fs|CLIP1_ENST00000302528.7_Frame_Shift_Ins_p.P1007fs	p.P1007fs	NM_001247997.1|NM_002956.2	NP_001234926.1|NP_002947.1	P30622	CLIP1_HUMAN		OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)	16	3173_3174	-	all_neural(191;0.0837)|Medulloblastoma(191;0.163)		1018					A0AVD3|Q17RS4|Q29RG0	Frame_Shift_Ins	INS	ENST00000540338.1	37	c.3019_3020insA	CCDS58285.1																																																																																				0.505	CLIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401625.1	NM_002956		8	199						8	199	---	---	---	---
OR4N2	390429	broad.mit.edu	37	14	20296055	20296056	+	Frame_Shift_Ins	INS	-	-	T	rs149523724		TCGA-ET-A2N3-01B-21D-A23M-08	TCGA-ET-A2N3-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bcfcc7e4-b937-4f55-a703-e73a783d1fc1	27ec3857-71ae-4f7d-944d-112b47b0b97d	g.chr14:20296055_20296056insT	ENST00000315947.1	+	1	448_449	c.448_449insT	c.(448-450)cttfs	p.L150fs	OR4N2_ENST00000568211.1_Frame_Shift_Ins_p.L150fs	NM_001004723.1	NP_001004723.1	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N, member 2	150						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(1)|lung(32)|ovary(2)|prostate(1)|skin(2)|stomach(2)	52	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		GGCTCTGTGGCTTGGGGGTTTT	0.53																																						ENST00000568211.1																			0				breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(1)|lung(32)|ovary(2)|prostate(1)|skin(2)|stomach(2)	52						c.(448-450)tggfs		olfactory receptor, family 4, subfamily N, member 2																																				SO:0001589	frameshift_variant	390429				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr14:20296055_20296056insT		CCDS32022.1	14q11.2	2013-09-23				ENSG00000176294		"""GPCR / Class A : Olfactory receptors"""	14742	protein-coding gene	gene with protein product							Standard	NM_001004723		Approved		uc010tkv.2	Q8NGD1		ENST00000315947.1:c.450dupT	14.37:g.20296057_20296057dupT	ENSP00000319601:p.Leu150fs					OR4N2_ENST00000315947.1_Frame_Shift_Ins_p.W150fs	p.W150fs			Q8NGD1	OR4N2_HUMAN	Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)	1	448_449	+	all_cancers(95;0.00108)		150					Q6IEY9|Q6IFA2	Frame_Shift_Ins	INS	ENST00000315947.1	37	c.448_449insT	CCDS32022.1																																																																																				0.530	OR4N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409821.2			43	331						43	331	---	---	---	---
ULK4P2	100288380	broad.mit.edu	37	15	32716934	32716934	+	RNA	DEL	C	C	-			TCGA-ET-A2N3-01B-21D-A23M-08	TCGA-ET-A2N3-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bcfcc7e4-b937-4f55-a703-e73a783d1fc1	27ec3857-71ae-4f7d-944d-112b47b0b97d	g.chr15:32716934delC	ENST00000562108.1	-	0	277				ULK4P1_ENST00000565949.1_RNA|U8_ENST00000384260.1_RNA																							AAAAAAAAAACTTTTGAGGCA	0.289																																						ENST00000562108.1																			0																																																			0							g.chr15:32716934delC																													15.37:g.32716934delC						ULK4P1_ENST00000565949.1_RNA								0	277	-									RNA	DEL	ENST00000562108.1	37																																																																																						0.289	RP13-395E19.3-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000429843.1			8	25						8	25	---	---	---	---
DNM1P47	100216544	broad.mit.edu	37	15	102293062	102293064	+	RNA	DEL	CTC	CTC	-	rs4965539|rs62026972	byFrequency	TCGA-ET-A2N3-01B-21D-A23M-08	TCGA-ET-A2N3-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bcfcc7e4-b937-4f55-a703-e73a783d1fc1	27ec3857-71ae-4f7d-944d-112b47b0b97d	g.chr15:102293062_102293064delCTC	ENST00000561463.1	+	0	1108_1110									DNM1 pseudogene 47																		AGTTCATCTTCTCAGAGCTGCTG	0.576																																						ENST00000561463.1																			0																																																			0							g.chr15:102293062_102293064delCTC	AJ576276		15q26.3	2013-04-25			ENSG00000259660	ENSG00000259660			35200	pseudogene	pseudogene				DNM1DN14@			Standard	NG_009149		Approved	DNM1DN14-3			OTTHUMG00000172265		15.37:g.102293062_102293064delCTC														0	1108_1110	+									RNA	DEL	ENST00000561463.1	37																																																																																						0.576	DNM1P47-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417589.1	NG_009149		2	4						2	4	---	---	---	---
CTC-513N18.6	0	broad.mit.edu	37	19	20634038	20634039	+	lincRNA	DEL	TG	TG	-	rs144024329		TCGA-ET-A2N3-01B-21D-A23M-08	TCGA-ET-A2N3-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bcfcc7e4-b937-4f55-a703-e73a783d1fc1	27ec3857-71ae-4f7d-944d-112b47b0b97d	g.chr19:20634038_20634039delTG	ENST00000598131.1	+	0	160																											TTAGTAAAAATGTGTGTGTGTG	0.401																																						ENST00000598131.1																			0																																																			0							g.chr19:20634038_20634039delTG																													19.37:g.20634048_20634049delTG														0	160	+									RNA	DEL	ENST00000598131.1	37																																																																																						0.401	CTC-513N18.6-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000463072.1			10	70						10	70	---	---	---	---
GCAT	23464	broad.mit.edu	37	22	38211250	38211251	+	Frame_Shift_Ins	INS	-	-	A			TCGA-ET-A2N3-01B-21D-A23M-08	TCGA-ET-A2N3-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bcfcc7e4-b937-4f55-a703-e73a783d1fc1	27ec3857-71ae-4f7d-944d-112b47b0b97d	g.chr22:38211250_38211251insA	ENST00000248924.6	+	5	750_751	c.694_695insA	c.(694-696)gaafs	p.E232fs	GCAT_ENST00000323205.6_Frame_Shift_Ins_p.E258fs	NM_014291.3	NP_055106.1	O75600	KBL_HUMAN	glycine C-acetyltransferase	232					biosynthetic process (GO:0009058)|cellular amino acid metabolic process (GO:0006520)|L-threonine catabolic process to glycine (GO:0019518)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	glycine C-acetyltransferase activity (GO:0008890)|pyridoxal phosphate binding (GO:0030170)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|skin(1)	12	Melanoma(58;0.045)				Glycine(DB00145)	CTTCATGGATGAATGCCATGCC	0.629																																						ENST00000323205.6																			0				haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|skin(1)	12						c.(772-774)atgfs		glycine C-acetyltransferase	Glycine(DB00145)|Pyridoxal Phosphate(DB00114)																																			SO:0001589	frameshift_variant	23464				biosynthetic process|cellular amino acid metabolic process		glycine C-acetyltransferase activity|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups	g.chr22:38211250_38211251insA	AF077740	CCDS13957.1, CCDS54527.1	22q13.1	2010-01-19	2010-01-19		ENSG00000100116	ENSG00000100116	2.3.1.29		4188	protein-coding gene	gene with protein product	"""2-amino-3-ketobutyrate coenzyme A ligase"""	607422	"""glycine C-acetyltransferase (2-amino-3-ketobutyrate coenzyme A ligase)"""				Standard	NM_014291		Approved	KBL	uc003aua.2	O75600	OTTHUMG00000150664	ENST00000248924.6:c.696dupA	22.37:g.38211252_38211252dupA	ENSP00000248924:p.Glu232fs					GCAT_ENST00000248924.6_Frame_Shift_Ins_p.M232fs	p.M258fs	NM_001171690.1	NP_001165161.1	O75600	KBL_HUMAN			5	835_836	+	Melanoma(58;0.045)		232					E2QC23|Q6ZWF1|Q96CA9	Frame_Shift_Ins	INS	ENST00000248924.6	37	c.772_773insA	CCDS13957.1																																																																																				0.629	GCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319506.1	NM_014291.2		21	15						21	15	---	---	---	---
FTX	100302692	broad.mit.edu	37	X	73506653	73506654	+	lincRNA	INS	-	-	A	rs397771084|rs58093396		TCGA-ET-A2N3-01B-21D-A23M-08	TCGA-ET-A2N3-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bcfcc7e4-b937-4f55-a703-e73a783d1fc1	27ec3857-71ae-4f7d-944d-112b47b0b97d	g.chrX:73506653_73506654insA	ENST00000429124.1	-	0	174				MIR374A_ENST00000362298.1_RNA|MIR545_ENST00000385085.1_RNA					FTX transcript, XIST regulator (non-protein coding)																		acctgtcccttaaaaaaaaaaa	0.455													|||unknown(HR)	2504	0.663311	0.4841	0.4856	3775	,	,		12960	0.5714		0.5	False		,,,				2504	0.4581					ENST00000429124.1																			0																																																			0							g.chrX:73506653_73506654insA	AK057701		Xq13.2	2013-12-18	2011-04-21	2011-04-21	ENSG00000230590	ENSG00000230590		"""Long non-coding RNAs"", ""-"""	37190	non-coding RNA	RNA, long non-coding	"""five prime to XIST"""		"""non-protein coding RNA 182"", ""mir-374a-545 cluster host gene (non-protein coding)"""	NCRNA00182, MIR374AHG		12045143, 21254562, 21118898	Standard	NR_028379		Approved	LINC00182, FLJ33139	uc010nlq.1		OTTHUMG00000021850		X.37:g.73506664_73506664dupA														0	174	-									RNA	INS	ENST00000429124.1	37																																																																																						0.455	FTX-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000057255.2	NR_028379		3	4						3	4	---	---	---	---
