#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
HCLS1	3059	broad.mit.edu	37	3	121351231	121351231	+	Missense_Mutation	SNP	G	G	C			TCGA-FY-A3ON-01A-11D-A21Z-08	TCGA-FY-A3ON-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2b661b1c-472f-4911-83b6-ebf16248fe8f	f0119845-2a2b-4d0d-9f2e-24264ef9121c	g.chr3:121351231G>C	ENST00000314583.3	-	12	1279	c.1188C>G	c.(1186-1188)gaC>gaG	p.D396E	HCLS1_ENST00000428394.2_Missense_Mutation_p.D359E|HCLS1_ENST00000473883.1_5'UTR	NM_005335.4	NP_005326	P14317	HCLS1_HUMAN	hematopoietic cell-specific Lyn substrate 1	396					actin filament polymerization (GO:0030041)|cellular response to cytokine stimulus (GO:0071345)|erythrocyte differentiation (GO:0030218)|intracellular signal transduction (GO:0035556)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of cell proliferation (GO:0008284)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|regulation of actin filament polymerization (GO:0030833)|regulation of transcription, DNA-templated (GO:0006355)|response to hormone (GO:0009725)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	protein kinase binding (GO:0019901)|RNA polymerase II transcription factor binding (GO:0001085)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				GBM - Glioblastoma multiforme(114;0.0912)		CCTCCTCATAGTCCCCCTCTG	0.557																																						ENST00000314583.3																			0				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35						c.(1186-1188)gaC>gaG		hematopoietic cell-specific Lyn substrate 1							239.0	222.0	227.0					3																	121351231		2203	4300	6503	SO:0001583	missense	3059				erythrocyte differentiation|intracellular signal transduction|positive regulation of cell proliferation|positive regulation of tyrosine phosphorylation of STAT protein|response to hormone stimulus	mitochondrion|nucleus|plasma membrane	DNA binding|sequence-specific DNA binding transcription factor activity	g.chr3:121351231G>C		CCDS3003.1	3q13	2007-08-03			ENSG00000180353	ENSG00000180353			4844	protein-coding gene	gene with protein product	"""cortactin-like"""	601306				8978766, 15710041	Standard	NM_001292041		Approved	HS1, CTTNL	uc003eeh.4	P14317	OTTHUMG00000159409	ENST00000314583.3:c.1188C>G	3.37:g.121351231G>C	ENSP00000320176:p.Asp396Glu					HCLS1_ENST00000428394.2_Missense_Mutation_p.D359E|HCLS1_ENST00000473883.1_5'UTR	p.D396E	NM_005335.4	NP_005326.2	P14317	HCLS1_HUMAN		GBM - Glioblastoma multiforme(114;0.0912)	12	1279	-			396					B4DQ69|Q53Y93|Q6IBK9|Q9UDK0	Missense_Mutation	SNP	ENST00000314583.3	37	c.1188C>G	CCDS3003.1	.	.	.	.	.	.	.	.	.	.	G	2.757	-0.258643	0.05791	.	.	ENSG00000180353	ENST00000314583;ENST00000428394	T;T	0.19938	2.12;2.11	5.21	3.39	0.38822	.	0.780599	0.12384	N	0.473618	T	0.15739	0.0379	L	0.40543	1.245	0.42050	D	0.99111	P;P	0.46656	0.882;0.882	B;B	0.43701	0.428;0.428	T	0.09443	-1.0674	10	0.02654	T	1	-25.6477	8.1107	0.30914	0.1865:0.0:0.8135:0.0	.	359;396	E7EVW7;P14317	.;HCLS1_HUMAN	E	396;359	ENSP00000320176:D396E;ENSP00000387645:D359E	ENSP00000320176:D396E	D	-	3	2	HCLS1	122833921	1.000000	0.71417	1.000000	0.80357	0.218000	0.24690	1.109000	0.31135	1.441000	0.47550	-0.140000	0.14226	GAC		0.557	HCLS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355144.1	NM_005335		8	380	0	0	0	1	0	8	380				
PRDM9	56979	broad.mit.edu	37	5	23527606	23527606	+	Silent	SNP	C	C	A			TCGA-FY-A3ON-01A-11D-A21Z-08	TCGA-FY-A3ON-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2b661b1c-472f-4911-83b6-ebf16248fe8f	f0119845-2a2b-4d0d-9f2e-24264ef9121c	g.chr5:23527606C>A	ENST00000296682.3	+	11	2591	c.2409C>A	c.(2407-2409)ccC>ccA	p.P803P		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	803					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						GGGAGAAGCCCTATGTCTGCA	0.567										HNSCC(3;0.000094)																												ENST00000296682.3																			0				NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						c.(2407-2409)ccC>ccA		PR domain containing 9							63.0	66.0	65.0					5																	23527606		2182	4294	6476	SO:0001819	synonymous_variant	56979				meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleoplasm	histone-lysine N-methyltransferase activity|nucleic acid binding|zinc ion binding	g.chr5:23527606C>A	AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"""-"", ""Zinc fingers, C2H2-type"""	13994	protein-coding gene	gene with protein product	"""PR-domain containing protein 9"""	609760	"""minisatellite binding protein 3, 115kDa"", ""minisatellite binding protein 3 (115kD)"""	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.2409C>A	5.37:g.23527606C>A		HNSCC(3;0.000094)					p.P803P	NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN			11	2591	+			803					B4DX22|Q27Q50	Silent	SNP	ENST00000296682.3	37	c.2409C>A	CCDS43307.1																																																																																				0.567	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227		6	209	1	0	8.12818e-05	1	8.12818e-05	6	209				
POM121L9P	29774	broad.mit.edu	37	22	24659578	24659578	+	RNA	SNP	A	A	G			TCGA-FY-A3ON-01A-11D-A21Z-08	TCGA-FY-A3ON-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2b661b1c-472f-4911-83b6-ebf16248fe8f	f0119845-2a2b-4d0d-9f2e-24264ef9121c	g.chr22:24659578A>G	ENST00000414583.2	+	0	3103					NR_003714.1				POM121 transmembrane nucleoporin-like 9, pseudogene																		TGCGCAGGCCAACACTCACTG	0.617																																						ENST00000414583.2																			0																																																			0							g.chr22:24659578A>G	AL040062, AL117401		22q11.22	2012-03-13	2012-03-13		ENSG00000128262	ENSG00000128262			30080	pseudogene	pseudogene			"""POM121 membrane glycoprotein-like 9, pseudogene"""				Standard	NR_003714		Approved				OTTHUMG00000150763		22.37:g.24659578A>G								NR_003714.1						0	3103	+									RNA	SNP	ENST00000414583.2	37																																																																																						0.617	POM121L9P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000319991.1	NM_014549		4	39	0	0	0	1	0	4	39				
TPTE2P6	374491	broad.mit.edu	37	13	25168463	25168463	+	RNA	SNP	T	T	C	rs61946940	byFrequency	TCGA-FY-A3ON-01A-11D-A21Z-08	TCGA-FY-A3ON-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2b661b1c-472f-4911-83b6-ebf16248fe8f	f0119845-2a2b-4d0d-9f2e-24264ef9121c	g.chr13:25168463T>C	ENST00000453498.1	+	0	1135				TPTE2P6_ENST00000440905.1_RNA																							TGACAGTCCATCTCTGTACGA	0.363																																						ENST00000453498.1																			0																																																			0							g.chr13:25168463T>C																													13.37:g.25168463T>C														0	1135	+									RNA	SNP	ENST00000453498.1	37																																																																																						0.363	RP11-556N21.1-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000044193.1			3	51	0	0	0	1	0	3	51				
MAP1B	4131	broad.mit.edu	37	5	71490028	71490028	+	Missense_Mutation	SNP	G	G	C			TCGA-FY-A3ON-01A-11D-A21Z-08	TCGA-FY-A3ON-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2b661b1c-472f-4911-83b6-ebf16248fe8f	f0119845-2a2b-4d0d-9f2e-24264ef9121c	g.chr5:71490028G>C	ENST00000296755.7	+	5	1144	c.846G>C	c.(844-846)atG>atC	p.M282I		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	282					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		GTTTCAATATGCTCATCAATG	0.502																																					Melanoma(17;367 822 11631 31730 47712)	ENST00000296755.7																			0				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104						c.(844-846)atG>atC		microtubule-associated protein 1B							83.0	87.0	86.0					5																	71490028		2203	4300	6503	SO:0001583	missense	4131					microtubule|microtubule associated complex	structural molecule activity	g.chr5:71490028G>C	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 102"""	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.846G>C	5.37:g.71490028G>C	ENSP00000296755:p.Met282Ile						p.M282I	NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)	5	1144	+		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)	282					A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	37	c.846G>C	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	G	13.36	2.214244	0.39102	.	.	ENSG00000131711	ENST00000296755;ENST00000511641;ENST00000504492	T;T;T	0.12147	2.71;2.71;2.71	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.24044	0.0582	L	0.31207	0.915	0.80722	D	1	D;D	0.63880	0.993;0.993	D;D	0.70227	0.968;0.968	T	0.01024	-1.1477	10	0.02654	T	1	-22.0585	20.6525	0.99598	0.0:0.0:1.0:0.0	.	156;282	A2BDK6;P46821	.;MAP1B_HUMAN	I	282;299;156	ENSP00000296755:M282I;ENSP00000423444:M299I;ENSP00000423416:M156I	ENSP00000296755:M282I	M	+	3	0	MAP1B	71525784	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.765000	0.74965	2.890000	0.99128	0.585000	0.79938	ATG		0.502	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		12	121	0	0	0	1	0	12	121				
SUFU	51684	broad.mit.edu	37	10	104353429	104353429	+	Nonsense_Mutation	SNP	C	C	T			TCGA-FY-A3ON-01A-11D-A21Z-08	TCGA-FY-A3ON-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2b661b1c-472f-4911-83b6-ebf16248fe8f	f0119845-2a2b-4d0d-9f2e-24264ef9121c	g.chr10:104353429C>T	ENST00000369902.3	+	5	800	c.634C>T	c.(634-636)Cag>Tag	p.Q212*	SUFU_ENST00000369899.2_Nonsense_Mutation_p.Q212*|RNU6-43P_ENST00000384302.1_RNA|SUFU_ENST00000423559.2_Nonsense_Mutation_p.Q212*|SUFU_ENST00000471000.1_3'UTR	NM_016169.3	NP_057253.2	Q9UMX1	SUFU_HUMAN	suppressor of fused homolog (Drosophila)	212					cytoplasmic sequestering of transcription factor (GO:0042994)|heart looping (GO:0001947)|multicellular organismal development (GO:0007275)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|negative regulation of transcription factor import into nucleus (GO:0042992)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|skin development (GO:0043588)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|primary cilium (GO:0072372)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.Q212K(1)		breast(2)|central_nervous_system(7)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(2)	24		Colorectal(252;0.207)		Epithelial(162;1.36e-08)|all cancers(201;3.81e-07)|BRCA - Breast invasive adenocarcinoma(275;0.242)		ACACTCAGCCCAGCAGTGGAA	0.617			"""D, F, S"""		medulloblastoma	medulloblastoma			Medulloblastoma, associated with Germline SUFU Mutation																													ENST00000369902.3			yes	Rec	yes	Medulloblastoma predisposition	10	10q24.32	51684	"""D, F, S"""	suppressor of fused homolog (Drosophila)			O		medulloblastoma	medulloblastoma		1	Substitution - Missense(1)	p.Q212K(1)	lung(1)	breast(2)|central_nervous_system(7)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(2)	24						c.(634-636)Cag>Tag		suppressor of fused homolog (Drosophila)							95.0	81.0	85.0					10																	104353429		2203	4300	6503	SO:0001587	stop_gained	51684	Medulloblastoma, associated with Germline SUFU Mutation	Familial Cancer Database		negative regulation of transcription from RNA polymerase II promoter|proteolysis|skeletal system development	cytoplasm|nucleus	identical protein binding|protein binding|signal transducer activity|transcription corepressor activity|transcription factor binding	g.chr10:104353429C>T	AF175770	CCDS7537.1, CCDS53571.1	10q24.32	2014-09-17			ENSG00000107882	ENSG00000107882			16466	protein-coding gene	gene with protein product		607035				15367681	Standard	NM_016169		Approved	SUFUH, SUFUXL, PRO1280	uc001kvy.2	Q9UMX1	OTTHUMG00000018966	ENST00000369902.3:c.634C>T	10.37:g.104353429C>T	ENSP00000358918:p.Gln212*					SUFU_ENST00000423559.2_Nonsense_Mutation_p.Q212*|SUFU_ENST00000471000.1_3'UTR|SUFU_ENST00000369899.2_Nonsense_Mutation_p.Q212*	p.Q212*	NM_016169.3	NP_057253.2	Q9UMX1	SUFU_HUMAN		Epithelial(162;1.36e-08)|all cancers(201;3.81e-07)|BRCA - Breast invasive adenocarcinoma(275;0.242)	5	800	+		Colorectal(252;0.207)	212					Q7LCP7|Q9NT90|Q9NZ07|Q9UHK2|Q9UHM8|Q9UMY0	Nonsense_Mutation	SNP	ENST00000369902.3	37	c.634C>T	CCDS7537.1	.	.	.	.	.	.	.	.	.	.	C	38	6.817597	0.97861	.	.	ENSG00000107882	ENST00000369902;ENST00000369899;ENST00000423559	.	.	.	6.08	6.08	0.98989	.	0.048329	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.28530	T	0.3	-20.855	20.2738	0.98482	0.0:1.0:0.0:0.0	.	.	.	.	X	212	.	ENSP00000358915:Q212X	Q	+	1	0	SUFU	104343419	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.487000	0.81328	2.894000	0.99253	0.655000	0.94253	CAG		0.617	SUFU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050089.1	NM_016169		18	80	0	0	0	1	0	18	80				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-FY-A3ON-01A-11D-A21Z-08	TCGA-FY-A3ON-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2b661b1c-472f-4911-83b6-ebf16248fe8f	f0119845-2a2b-4d0d-9f2e-24264ef9121c	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12068308}.|V -> E (in CRC; also found in sarcoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis; loss of regulation by PMRT5). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:12198537, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:23263490, ECO:0000269|PubMed:24455489}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	TCGAGATTTCACTGTAGCTAG	0.368	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												Colon(40;35 892 2973 5743 27438)	ENST00000288602.6	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61		Dom	yes		7	7q34	673	"""Mis, T, O"""	v-raf murine sarcoma viral oncogene homolog B1	yes	Cardio-facio-cutaneous syndrome	E	"""AKAP9, KIAA1549"""		"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	15808	Substitution - Missense(15790)|Complex - deletion inframe(17)|Insertion - In frame(1)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	thyroid(7476)|skin(3822)|large_intestine(3288)|NS(360)|haematopoietic_and_lymphoid_tissue(336)|ovary(211)|lung(58)|eye(57)|central_nervous_system(53)|soft_tissue(30)|biliary_tract(18)|liver(17)|prostate(13)|breast(10)|upper_aerodigestive_tract(9)|endometrium(8)|pancreas(8)|testis(7)|small_intestine(7)|genital_tract(4)|stomach(4)|bone(3)|autonomic_ganglia(2)|oesophagus(2)|urinary_tract(2)|adrenal_gland(2)|pituitary(1)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380						c.(1798-1800)gTg>gAg		v-raf murine sarcoma viral oncogene homolog B	Sorafenib(DB00398)						112.0	104.0	107.0					7																	140453136		2203	4300	6503	SO:0001583	missense	673	Cardiofaciocutaneous syndrome	Familial Cancer Database	CFC, CFCS	activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	g.chr7:140453136A>T	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1799T>A	7.37:g.140453136A>T	ENSP00000288602:p.Val600Glu						p.V600E	NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN			15	1859	-	Melanoma(164;0.00956)		600		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis).	Protein kinase.		A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	c.1799T>A	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.486113|4.486113	0.84854|0.84854	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.81739|.	-1.53|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.61565|.	0.2357|.	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	D|.	0.55385|.	0.971|.	D|.	0.66351|.	0.943|.	T|.	0.58160|.	-0.7685|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	600|.	P15056|.	BRAF_HUMAN|.	E|R	600|208	ENSP00000288602:V600E|.	ENSP00000288602:V600E|.	V|X	-|-	2|1	0|0	BRAF|BRAF	140099605|140099605	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.197000|9.197000	0.94985|0.94985	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	GTG|TGA		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		49	84	0	0	0	1	0	49	84				
ANKRD30BP3	338579	broad.mit.edu	37	10	45652269	45652269	+	RNA	SNP	G	G	A			TCGA-FY-A3ON-01A-11D-A21Z-08	TCGA-FY-A3ON-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2b661b1c-472f-4911-83b6-ebf16248fe8f	f0119845-2a2b-4d0d-9f2e-24264ef9121c	g.chr10:45652269G>A	ENST00000427229.2	+	0	1783																											CACCCTTGGCGGAAAGAACAC	0.473																																						ENST00000427229.2																			0																																																			0							g.chr10:45652269G>A																													10.37:g.45652269G>A														0	1783	+									RNA	SNP	ENST00000427229.2	37																																																																																						0.473	RP11-445N18.7-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000470688.1			3	43	0	0	0	1	0	3	43				
TUBB8P7	197331	broad.mit.edu	37	16	90161753	90161753	+	RNA	SNP	T	T	C	rs6500470	byFrequency	TCGA-FY-A3ON-01A-11D-A21Z-08	TCGA-FY-A3ON-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2b661b1c-472f-4911-83b6-ebf16248fe8f	f0119845-2a2b-4d0d-9f2e-24264ef9121c	g.chr16:90161753T>C	ENST00000564451.1	+	0	1106				TUBB8P7_ENST00000567960.1_RNA					tubulin, beta 8 class VIII pseudogene 7																		CAGACAGGATTATAAACACAT	0.562													.|||	1448	0.289137	0.6051	0.232	5008	,	,		18052	0.002		0.335	False		,,,				2504	0.1513					ENST00000564451.1																			0																																																			0							g.chr16:90161753T>C			16q24.3	2013-02-18			ENSG00000261812	ENSG00000261812			42345	pseudogene	pseudogene							Standard	NG_002334		Approved				OTTHUMG00000172847		16.37:g.90161753T>C						TUBB8P7_ENST00000567960.1_RNA								0	1106	+									RNA	SNP	ENST00000564451.1	37																																																																																						0.562	TUBB8P7-004	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000420856.1	NG_002334		4	116	0	0	0	1	0	4	116				
LAMC1	3915	broad.mit.edu	37	1	183111704	183111704	+	Missense_Mutation	SNP	G	G	A	rs79826197		TCGA-FY-A3ON-01A-11D-A21Z-08	TCGA-FY-A3ON-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2b661b1c-472f-4911-83b6-ebf16248fe8f	f0119845-2a2b-4d0d-9f2e-24264ef9121c	g.chr1:183111704G>A	ENST00000258341.4	+	28	4866	c.4609G>A	c.(4609-4611)Gag>Aag	p.E1537K	RP11-181K3.4_ENST00000457852.3_RNA	NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	1537	Domain II and I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						TAAGCTAAACGAGATTGAAGG	0.448													G|||	1	0.000199681	0.0	0.0	5008	,	,		23235	0.001		0.0	False		,,,				2504	0.0					ENST00000258341.4																			0				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						c.(4609-4611)Gag>Aag		laminin, gamma 1 (formerly LAMB2)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)						102.0	83.0	90.0					1																	183111704		2203	4300	6503	SO:0001583	missense	3915				axon guidance|cell migration|endoderm development|extracellular matrix disassembly|hemidesmosome assembly|positive regulation of epithelial cell proliferation|protein complex assembly|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	extracellular matrix structural constituent	g.chr1:183111704G>A	J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"""Laminins"""	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.4609G>A	1.37:g.183111704G>A	ENSP00000258341:p.Glu1537Lys						p.E1537K	NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN			28	4866	+			1537			Domain II and I.		Q5VYE7	Missense_Mutation	SNP	ENST00000258341.4	37	c.4609G>A	CCDS1351.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	14.36	2.510832	0.44660	.	.	ENSG00000135862	ENST00000258341	T	0.31510	1.49	5.57	5.57	0.84162	.	0.151272	0.64402	D	0.000018	T	0.31482	0.0798	M	0.72118	2.19	0.58432	D	0.999991	P	0.41131	0.739	B	0.30943	0.122	T	0.21042	-1.0257	10	0.17832	T	0.49	.	19.5381	0.95262	0.0:0.0:1.0:0.0	.	1537	P11047	LAMC1_HUMAN	K	1537	ENSP00000258341:E1537K	ENSP00000258341:E1537K	E	+	1	0	LAMC1	181378327	1.000000	0.71417	0.906000	0.35671	0.628000	0.37860	5.596000	0.67570	2.611000	0.88343	0.655000	0.94253	GAG		0.448	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293		3	66	0	0	0	1	0	3	66				
NCOA6	23054	broad.mit.edu	37	20	33345744	33345744	+	Silent	SNP	C	C	T			TCGA-FY-A3ON-01A-11D-A21Z-08	TCGA-FY-A3ON-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2b661b1c-472f-4911-83b6-ebf16248fe8f	f0119845-2a2b-4d0d-9f2e-24264ef9121c	g.chr20:33345744C>T	ENST00000374796.2	-	8	3377	c.807G>A	c.(805-807)caG>caA	p.Q269Q	NCOA6_ENST00000359003.2_Silent_p.Q269Q			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	269	CREBBP-binding region.|Gln-rich.|NCOA1-binding region.|TBP/GTF2A-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.Q269Q(15)		NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						gctgctgctgctgttgttgtt	0.537																																						ENST00000374796.2																			15	Substitution - coding silent(15)	p.Q269Q(15)	lung(5)|prostate(4)|endometrium(3)|central_nervous_system(1)|urinary_tract(1)|kidney(1)	NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						c.(805-807)caG>caA		nuclear receptor coactivator 6							64.0	52.0	56.0					20																	33345744		2203	4300	6503	SO:0001819	synonymous_variant	23054				brain development|cellular lipid metabolic process|DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|heart development|myeloid cell differentiation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|transcription initiation from RNA polymerase II promoter	transcription factor complex	chromatin binding|enzyme binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|retinoid X receptor binding|thyroid hormone receptor binding	g.chr20:33345744C>T	AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"""nuclear receptor coactivator RAP250"", ""activating signal cointegrator-2"", ""peroxisome proliferator-activated receptor interacting protein"""	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.807G>A	20.37:g.33345744C>T						NCOA6_ENST00000359003.2_Silent_p.Q269Q	p.Q269Q			Q14686	NCOA6_HUMAN			8	3377	-			269			CREBBP-binding region.|Gln-rich.|NCOA1-binding region.|TBP/GTF2A-binding region.		A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Silent	SNP	ENST00000374796.2	37	c.807G>A	CCDS13241.1																																																																																				0.537	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		3	26	0	0	0	1	0	3	26				
RETN	56729	broad.mit.edu	37	19	7734285	7734285	+	Missense_Mutation	SNP	G	G	A			TCGA-FY-A3ON-01A-11D-A21Z-08	TCGA-FY-A3ON-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2b661b1c-472f-4911-83b6-ebf16248fe8f	f0119845-2a2b-4d0d-9f2e-24264ef9121c	g.chr19:7734285G>A	ENST00000221515.2	+	2	161	c.73G>A	c.(73-75)Gaa>Aaa	p.E25K	RETN_ENST00000381324.2_Missense_Mutation_p.E25K	NM_001193374.1|NM_020415.3	NP_001180303.1|NP_065148.1	Q9HD89	RETN_HUMAN	resistin	25					aging (GO:0007568)|fat cell differentiation (GO:0045444)|negative regulation of feeding behavior (GO:2000252)|positive regulation of collagen metabolic process (GO:0010714)|positive regulation of progesterone secretion (GO:2000872)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of synaptic transmission (GO:0050806)|response to insulin (GO:0032868)|response to mechanical stimulus (GO:0009612)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				ovary(1)	1						GTGCTCCATGGAAGAAGCCAT	0.587																																						ENST00000221515.2																			0				ovary(1)	1						c.(73-75)Gaa>Aaa		resistin							161.0	144.0	150.0					19																	7734285		2203	4300	6503	SO:0001583	missense	56729						hormone activity	g.chr19:7734285G>A	AF205952	CCDS12182.1	19p13.2	2008-02-05				ENSG00000104918			20389	protein-coding gene	gene with protein product		605565				12050208	Standard	NM_020415		Approved	FIZZ3, ADSF, RETN1	uc002mhf.1	Q9HD89		ENST00000221515.2:c.73G>A	19.37:g.7734285G>A	ENSP00000221515:p.Glu25Lys					RETN_ENST00000381324.2_Missense_Mutation_p.E25K	p.E25K	NM_001193374.1|NM_020415.3	NP_001180303.1|NP_065148.1	Q9HD89	RETN_HUMAN			2	161	+			25					D6W649|Q540D9|Q76B53	Missense_Mutation	SNP	ENST00000221515.2	37	c.73G>A	CCDS12182.1	.	.	.	.	.	.	.	.	.	.	G	15.20	2.763448	0.49574	.	.	ENSG00000104918	ENST00000221515;ENST00000381324	T;T	0.48201	0.86;0.82	4.71	3.65	0.41850	.	0.549658	0.16095	N	0.229871	T	0.38026	0.1025	L	0.42245	1.32	0.09310	N	0.999993	P	0.36354	0.549	B	0.31946	0.138	T	0.28073	-1.0055	10	0.72032	D	0.01	-0.7237	10.7575	0.46245	0.0:0.1932:0.8068:0.0	.	25	Q9HD89	RETN_HUMAN	K	25	ENSP00000221515:E25K;ENSP00000370725:E25K	ENSP00000221515:E25K	E	+	1	0	RETN	7640285	0.956000	0.32656	0.011000	0.14972	0.013000	0.08279	2.702000	0.47102	0.959000	0.37980	0.462000	0.41574	GAA		0.587	RETN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461731.1	NM_020415		11	175	0	0	0	1	0	11	175				
FRG1B	284802	broad.mit.edu	37	20	29623222	29623222	+	Missense_Mutation	SNP	G	G	A			TCGA-FY-A3ON-01A-11D-A21Z-08	TCGA-FY-A3ON-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2b661b1c-472f-4911-83b6-ebf16248fe8f	f0119845-2a2b-4d0d-9f2e-24264ef9121c	g.chr20:29623222G>A	ENST00000278882.3	+	3	414	c.34G>A	c.(34-36)Gtc>Atc	p.V12I	FRG1B_ENST00000439954.2_Missense_Mutation_p.G13D|FRG1B_ENST00000358464.4_Missense_Mutation_p.V12I			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	12										endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						CTCGACAATGGTCTTTTTACC	0.413																																						ENST00000278882.3																			0				endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						c.(34-36)Gtc>Atc																																						SO:0001583	missense	0							g.chr20:29623222G>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.34G>A	20.37:g.29623222G>A	ENSP00000278882:p.Val12Ile					FRG1B_ENST00000439954.2_Missense_Mutation_p.G13D|FRG1B_ENST00000358464.4_Missense_Mutation_p.V12I	p.V12I							3	414	+								C4AME5	Missense_Mutation	SNP	ENST00000278882.3	37	c.34G>A		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	9.540|9.540	1.113211|1.113211	0.20795|0.20795	.|.	.|.	ENSG00000149531|ENSG00000149531	ENST00000439954|ENST00000278882;ENST00000358464	T|.	0.80480|.	-1.38|.	1.93|1.93	1.93|1.93	0.25924|0.25924	.|.	.|0.176961	.|0.36591	.|U	.|0.002516	T|T	0.41073|0.41073	0.1143|0.1143	.|.	.|.	.|.	0.23848|0.23848	N|N	0.996674|0.996674	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.27971|0.27971	-1.0058|-1.0058	6|6	0.87932|0.48119	D|T	0|0.1	.|.	9.8943|9.8943	0.41309|0.41309	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	D|I	13|12	ENSP00000408863:G13D|.	ENSP00000408863:G13D|ENSP00000278882:V12I	G|V	+|+	2|1	0|0	FRG1B|FRG1B	28236883|28236883	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.102000|0.102000	0.19082|0.19082	8.270000|8.270000	0.89880|0.89880	1.399000|1.399000	0.46721|0.46721	0.423000|0.423000	0.28283|0.28283	GGT|GTC		0.413	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078494.2	NR_003579		31	813	0	0	0	1	0	31	813				
MTR	4548	broad.mit.edu	37	1	237024474	237024474	+	Frame_Shift_Del	DEL	A	A	-			TCGA-FY-A3ON-01A-11D-A21Z-08	TCGA-FY-A3ON-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2b661b1c-472f-4911-83b6-ebf16248fe8f	f0119845-2a2b-4d0d-9f2e-24264ef9121c	g.chr1:237024474delA	ENST00000366577.5	+	20	2487	c.2093delA	c.(2092-2094)caafs	p.Q698fs	MTR_ENST00000535889.1_Intron	NM_000254.2	NP_000245.2	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase	698	B12-binding N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00666}.				cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|methylation (GO:0032259)|nervous system development (GO:0007399)|pteridine-containing compound metabolic process (GO:0042558)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	cobalamin binding (GO:0031419)|methionine synthase activity (GO:0008705)|S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	67	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)	AGGTTAAACCAAAAAAAATAT	0.308																																						ENST00000366577.5																			0				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	67						c.(2092-2094)cafs		5-methyltetrahydrofolate-homocysteine methyltransferase	Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)			61,4205		23,15,2095	67.0	69.0	68.0			3.8	1.0	1		69	81,8173		35,11,4081	no	frameshift	MTR	NM_000254.2		58,26,6176	A1A1,A1R,RR		0.9813,1.4299,1.1342			237024474	142,12378	2203	4300	6503	SO:0001589	frameshift_variant	4548				nervous system development|xenobiotic metabolic process	cytosol	cobalamin binding|homocysteine S-methyltransferase activity|methionine synthase activity|protein binding|zinc ion binding	g.chr1:237024474delA	U73338	CCDS1614.1, CCDS73054.1	1q43	2011-05-12			ENSG00000116984	ENSG00000116984	2.1.1.13		7468	protein-coding gene	gene with protein product		156570				8968735	Standard	NM_000254		Approved	cblG	uc001hyi.4	Q99707	OTTHUMG00000040060	ENST00000366577.5:c.2093delA	1.37:g.237024474delA	ENSP00000355536:p.Gln698fs					MTR_ENST00000535889.1_Intron	p.Q698fs	NM_000254.2	NP_000245.2	Q99707	METH_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	20	2487	+	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	698			B12-binding N-terminal.		A1L4N8|A9Z1W4|B9EGF7|Q99713|Q99723	Frame_Shift_Del	DEL	ENST00000366577.5	37	c.2093delA	CCDS1614.1																																																																																				0.308	MTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096632.2	NM_000254		8	99						8	99	---	---	---	---
DNMT3A	1788	broad.mit.edu	37	2	25463196	25463197	+	Frame_Shift_Del	DEL	TT	TT	-			TCGA-FY-A3ON-01A-11D-A21Z-08	TCGA-FY-A3ON-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2b661b1c-472f-4911-83b6-ebf16248fe8f	f0119845-2a2b-4d0d-9f2e-24264ef9121c	g.chr2:25463196_25463197delTT	ENST00000264709.3	-	19	2633_2634	c.2296_2297delAA	c.(2296-2298)aagfs	p.K766fs	DNMT3A_ENST00000402667.1_Frame_Shift_Del_p.K543fs|DNMT3A_ENST00000380746.4_Frame_Shift_Del_p.K577fs|DNMT3A_ENST00000474887.1_5'UTR|DNMT3A_ENST00000321117.5_Frame_Shift_Del_p.K766fs	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	766	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GATGTCCCTCTTGTCACTAACG	0.545			"""Mis, F, N, S"""		AML																																	ENST00000264709.3				Rec	yes		2	2p23	1788	"""Mis, F, N, S"""	DNA (cytosine-5-)-methyltransferase 3 alpha			L			AML		0				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021						c.(2296-2298)gfs		DNA (cytosine-5-)-methyltransferase 3 alpha																																				SO:0001589	frameshift_variant	1788				regulation of gene expression by genetic imprinting	cytoplasm|euchromatin|nuclear matrix	DNA (cytosine-5-)-methyltransferase activity|DNA binding|metal ion binding|protein binding	g.chr2:25463196_25463197delTT		CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.2296_2297delAA	2.37:g.25463196_25463197delTT	ENSP00000264709:p.Lys766fs					DNMT3A_ENST00000321117.5_Frame_Shift_Del_p.K766fs|DNMT3A_ENST00000474887.1_5'UTR|DNMT3A_ENST00000402667.1_Frame_Shift_Del_p.K543fs|DNMT3A_ENST00000380746.4_Frame_Shift_Del_p.K577fs	p.K766fs	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN			19	2633_2634	-	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)		766					E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Frame_Shift_Del	DEL	ENST00000264709.3	37	c.2296_2297delAA	CCDS33157.1																																																																																				0.545	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552		37	218						37	218	---	---	---	---
ANKRD36BP2	645784	broad.mit.edu	37	2	89083951	89083951	+	RNA	DEL	A	A	-	rs111608027		TCGA-FY-A3ON-01A-11D-A21Z-08	TCGA-FY-A3ON-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2b661b1c-472f-4911-83b6-ebf16248fe8f	f0119845-2a2b-4d0d-9f2e-24264ef9121c	g.chr2:89083951delA	ENST00000393525.3	+	0	576									ankyrin repeat domain 36B pseudogene 2																		CTTTTTTTTCAGTGTATTTCT	0.348																																						ENST00000393525.3																			0																																																			0							g.chr2:89083951delA			2q11.2	2010-09-30			ENSG00000230006	ENSG00000230006			33607	pseudogene	pseudogene							Standard	NR_015424		Approved		uc010fhg.4		OTTHUMG00000151690		2.37:g.89083951delA														0	576	+									RNA	DEL	ENST00000393525.3	37																																																																																						0.348	ANKRD36BP2-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000323523.1			2	4						2	4	---	---	---	---
DLX2	1746	broad.mit.edu	37	2	172967128	172967129	+	In_Frame_Ins	INS	-	-	GCT	rs201510837|rs376692475	byFrequency	TCGA-FY-A3ON-01A-11D-A21Z-08	TCGA-FY-A3ON-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2b661b1c-472f-4911-83b6-ebf16248fe8f	f0119845-2a2b-4d0d-9f2e-24264ef9121c	g.chr2:172967128_172967129insGCT	ENST00000234198.4	-	1	499_500	c.138_139insAGC	c.(136-141)agcctc>agcAGCctc	p.46_47insS	DLX2_ENST00000466293.2_In_Frame_Ins_p.46_47insS|AC104801.1_ENST00000448117.1_lincRNA	NM_004405.3	NP_004396.1	Q07687	DLX2_HUMAN	distal-less homeobox 2	46	Poly-Ser.				brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|cartilage development (GO:0051216)|cerebral cortex GABAergic interneuron fate commitment (GO:0021893)|embryonic cranial skeleton morphogenesis (GO:0048701)|hippocampus development (GO:0021766)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|olfactory bulb development (GO:0021772)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|subpallium development (GO:0021544)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded RNA binding (GO:0003727)			endometrium(1)|large_intestine(1)|lung(6)|ovary(2)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.216)			GGCTTGTGGAGgctgctgctgc	0.738														113	0.0225639	0.0008	0.0865	5008	,	,		12199	0.0387		0.0109	False		,,,				2504	0.002				GBM(188;775 2993 11256 23072)	ENST00000234198.4																			0				endometrium(1)|large_intestine(1)|lung(6)|ovary(2)|urinary_tract(1)	11						c.(136-141)agtcca>agAGCtcca		distal-less homeobox 2																																				SO:0001652	inframe_insertion	1746					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr2:172967128_172967129insGCT	U51003	CCDS2248.1	2q31.1	2011-06-20	2005-12-22		ENSG00000115844	ENSG00000115844		"""Homeoboxes / ANTP class : NKL subclass"""	2915	protein-coding gene	gene with protein product		126255	"""distal-less homeo box 2"""			1354641	Standard	NM_004405		Approved	TES-1	uc002uhn.3	Q07687	OTTHUMG00000132276	ENST00000234198.4:c.136_138dupAGC	2.37:g.172967135_172967137dupGCT	ENSP00000234198:p.Ser46_Ser46dup					DLX2_ENST00000466293.2_In_Frame_Ins_p.46_46S>RA	p.46_46S>RA	NM_004405.3	NP_004396.1	Q07687	DLX2_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.216)		1	499_500	-			46			Poly-Ser.		B4DMK4|B7ZA14	In_Frame_Ins	INS	ENST00000234198.4	37	c.138_139insAGC	CCDS2248.1																																																																																				0.738	DLX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255368.3			3	6						3	6	---	---	---	---
KAT6A	7994	broad.mit.edu	37	8	41798420	41798422	+	In_Frame_Del	DEL	CTC	CTC	-	rs139076845		TCGA-FY-A3ON-01A-11D-A21Z-08	TCGA-FY-A3ON-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2b661b1c-472f-4911-83b6-ebf16248fe8f	f0119845-2a2b-4d0d-9f2e-24264ef9121c	g.chr8:41798420_41798422delCTC	ENST00000396930.3	-	16	3520_3522	c.2977_2979delGAG	c.(2977-2979)gagdel	p.E993del	KAT6A_ENST00000406337.1_In_Frame_Del_p.E993del|KAT6A_ENST00000265713.2_In_Frame_Del_p.E993del	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	993	Poly-Glu.				aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										GGCTTTCCGGCTCCTCCTCCTCC	0.567																																						ENST00000396930.3																			0											c.(2977-2979)del		K(lysine) acetyltransferase 6A																																				SO:0001651	inframe_deletion	7994				histone H3 acetylation|myeloid cell differentiation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription coactivator activity|transcription factor binding|zinc ion binding	g.chr8:41798420_41798422delCTC	U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"", ""Zinc fingers, PHD-type"""	13013	protein-coding gene	gene with protein product	"""Monocytic leukemia zinc finger protein"""	601408	"""runt-related transcription factor binding protein 2"", ""MYST histone acetyltransferase (monocytic leukemia) 3"""	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.2977_2979delGAG	8.37:g.41798429_41798431delCTC	ENSP00000380136:p.Glu993del					KAT6A_ENST00000406337.1_In_Frame_Del_p.E993del|KAT6A_ENST00000265713.2_In_Frame_Del_p.E993del	p.E993del	NM_001099412.1	NP_001092882.1	Q92794	MYST3_HUMAN			16	3520_3522	-			993			Poly-Glu.		Q76L81	In_Frame_Del	DEL	ENST00000396930.3	37	c.2977_2979delGAG	CCDS6124.1																																																																																				0.567	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766		7	205						7	205	---	---	---	---
SCUBE2	57758	broad.mit.edu	37	11	9113009	9113011	+	In_Frame_Del	DEL	GCA	GCA	-	rs142900716|rs59844091		TCGA-FY-A3ON-01A-11D-A21Z-08	TCGA-FY-A3ON-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2b661b1c-472f-4911-83b6-ebf16248fe8f	f0119845-2a2b-4d0d-9f2e-24264ef9121c	g.chr11:9113009_9113011delGCA	ENST00000309263.3	-	1	137_139	c.65_67delTGC	c.(64-69)ctgccg>ccg	p.L22del	SCUBE2_ENST00000450649.2_In_Frame_Del_p.L22del|MIR5691_ENST00000579525.1_RNA|SCUBE2_ENST00000457346.2_In_Frame_Del_p.L22del|SCUBE2_ENST00000520467.1_In_Frame_Del_p.L22del|SCUBE2_ENST00000534295.1_Intron			Q9NQ36	SCUB2_HUMAN	signal peptide, CUB domain, EGF-like 2	22						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			breast(1)|endometrium(5)|kidney(3)|large_intestine(15)|liver(1)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42				all cancers(16;8.57e-09)|Epithelial(150;4.42e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0116)		agcagtggcggcagcagcagcag	0.788																																						ENST00000457346.2																			0				breast(1)|endometrium(5)|kidney(3)|large_intestine(15)|liver(1)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42						c.(64-69)ccg>c		signal peptide, CUB domain, EGF-like 2			,	125,51		61,3,24					,		0.2		dbSNP_134	1	181,401		88,5,198	no	coding,coding	SCUBE2	NM_020974.2,NM_001170690.1	,	149,8,222	A1A1,A1R,RR		31.0997,28.9773,40.3694	,	,		306,452				SO:0001651	inframe_deletion	57758					extracellular region	calcium ion binding	g.chr11:9113009_9113011delGCA	AK131552	CCDS7797.1, CCDS7797.2, CCDS53599.1	11p15.4	2014-09-04			ENSG00000175356	ENSG00000175356			30425	protein-coding gene	gene with protein product		611747				12270931, 11528127	Standard	NM_020974		Approved	Cegf1, Cegb1, FLJ16792	uc001mhi.2	Q9NQ36	OTTHUMG00000163880	ENST00000309263.3:c.65_67delTGC	11.37:g.9113018_9113020delGCA	ENSP00000310658:p.Leu22del					SCUBE2_ENST00000309263.3_In_Frame_Del_p.LP22del|SCUBE2_ENST00000450649.2_In_Frame_Del_p.LP22del|SCUBE2_ENST00000534295.1_Intron|SCUBE2_ENST00000520467.1_In_Frame_Del_p.LP22del	p.LP22del			Q9NQ36	SCUB2_HUMAN		all cancers(16;8.57e-09)|Epithelial(150;4.42e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0116)	1	139_141	-			22					Q2NKQ8|Q6ZWI1	In_Frame_Del	DEL	ENST00000309263.3	37	c.65_67delTGC																																																																																					0.788	SCUBE2-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000385812.2	NM_020974		2	4						2	4	---	---	---	---
SF3B2	10992	broad.mit.edu	37	11	65836145	65836146	+	Splice_Site	INS	-	-	A			TCGA-FY-A3ON-01A-11D-A21Z-08	TCGA-FY-A3ON-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2b661b1c-472f-4911-83b6-ebf16248fe8f	f0119845-2a2b-4d0d-9f2e-24264ef9121c	g.chr11:65836145_65836146insA	ENST00000322535.6	+	22	2666_2667	c.2617_2618insA	c.(2617-2619)caa>cAaa	p.Q873fs	SF3B2_ENST00000528302.1_Splice_Site_p.Q856fs|PACS1_ENST00000320580.4_5'Flank|RP11-1167A19.2_ENST00000529036.1_Intron	NM_006842.2	NP_006833.2	Q13435	SF3B2_HUMAN	splicing factor 3b, subunit 2, 145kDa	873					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	41						CCCTATACAGCAAAAAAAACGG	0.515											OREG0021094	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000528302.1																			0				breast(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	41						c.e21-1		splicing factor 3b, subunit 2, 145kDa				4,4260		0,4,2128						5.6	1.0			80	1,8253		0,1,4126	no	frameshift-near-splice	SF3B2	NM_006842.2		0,5,6254	A1A1,A1R,RR		0.0121,0.0938,0.0399				5,12513				SO:0001630	splice_region_variant	10992				interspecies interaction between organisms	catalytic step 2 spliceosome|nucleoplasm|U12-type spliceosomal complex	nucleic acid binding|protein binding	g.chr11:65836145_65836146insA	U41371	CCDS31612.1	11q13	2010-07-21	2002-08-29		ENSG00000087365	ENSG00000087365			10769	protein-coding gene	gene with protein product		605591	"""splicing factor 3b, subunit 2, 145kD"""			8566756	Standard	XM_005273726		Approved	SAP145, SF3b1, Cus1, SF3b145	uc001ogy.1	Q13435	OTTHUMG00000166751	ENST00000322535.6:c.2617-1->A	11.37:g.65836153_65836153dupA			OREG0021094	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1087	RP11-1167A19.2_ENST00000529036.1_Intron|SF3B2_ENST00000322535.6_Splice_Site_p.K873_splice	p.K856_splice			Q13435	SF3B2_HUMAN			21	2620_2621	+			873					A8K485|B4DT19|Q7L4T5|Q7Z627|Q969K1|Q96CM6|Q9BWD2	Splice_Site	INS	ENST00000322535.6	37	c.2565_splice	CCDS31612.1																																																																																				0.515	SF3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391352.2		Frame_Shift_Ins	8	94						8	94	---	---	---	---
LRP1	4035	broad.mit.edu	37	12	57605740	57605742	+	In_Frame_Del	DEL	TGC	TGC	-			TCGA-FY-A3ON-01A-11D-A21Z-08	TCGA-FY-A3ON-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2b661b1c-472f-4911-83b6-ebf16248fe8f	f0119845-2a2b-4d0d-9f2e-24264ef9121c	g.chr12:57605740_57605742delTGC	ENST00000243077.3	+	87	13755_13757	c.13289_13291delTGC	c.(13288-13293)ttgctg>ttg	p.4430_4431LL>L		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	4430					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	CCTCTGCTGTTGCTGCTGCTGCT	0.557																																						ENST00000243077.3																			0				NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184						c.(13288-13293)ttg>t		low density lipoprotein receptor-related protein 1	Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)																																			SO:0001651	inframe_deletion	4035				aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity	g.chr12:57605740_57605742delTGC	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.13289_13291delTGC	12.37:g.57605749_57605751delTGC	ENSP00000243077:p.Leu4434del						p.LL4432del	NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN		BRCA - Breast invasive adenocarcinoma(357;0.0103)	87	13755_13757	+			4432					Q2PP12|Q86SW0|Q8IVG8	In_Frame_Del	DEL	ENST00000243077.3	37	c.13289_13291delTGC	CCDS8932.1																																																																																				0.557	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		7	212						7	212	---	---	---	---
MEG3	55384	broad.mit.edu	37	14	101302257	101302258	+	RNA	INS	-	-	A			TCGA-FY-A3ON-01A-11D-A21Z-08	TCGA-FY-A3ON-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2b661b1c-472f-4911-83b6-ebf16248fe8f	f0119845-2a2b-4d0d-9f2e-24264ef9121c	g.chr14:101302257_101302258insA	ENST00000554041.1	-	0	143																											CGCCGTGGCCCTGAGAGTCCTG	0.658																																						ENST00000554041.1																			0																																																			0							g.chr14:101302257_101302258insA																													14.37:g.101302257_101302258insA														0	143	-									RNA	INS	ENST00000554041.1	37																																																																																						0.658	RP11-123M6.2-001	KNOWN	basic	antisense	antisense	OTTHUMT00000414687.1			2	4						2	4	---	---	---	---
IGHV3-21	28444	broad.mit.edu	37	14	106691799	106691801	+	RNA	DEL	ACT	ACT	-	rs553767931|rs571911882	byFrequency	TCGA-FY-A3ON-01A-11D-A21Z-08	TCGA-FY-A3ON-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2b661b1c-472f-4911-83b6-ebf16248fe8f	f0119845-2a2b-4d0d-9f2e-24264ef9121c	g.chr14:106691799_106691801delACT	ENST00000390607.2	-	0	301_303									immunoglobulin heavy variable 3-21																		AGTATATGTAACTACTACTACTA	0.517																																						ENST00000390607.2																			0																																																			0							g.chr14:106691799_106691801delACT	Z14073		14q32.33	2012-02-08			ENSG00000211947	ENSG00000211947		"""Immunoglobulins / IGH locus"""	5586	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000152279		14.37:g.106691808_106691810delACT														0	301_303	-									RNA	DEL	ENST00000390607.2	37																																																																																						0.517	IGHV3-21-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene	OTTHUMT00000325667.1	NG_001019		7	457						7	457	---	---	---	---
RRN3P1	730092	broad.mit.edu	37	16	21817398	21817399	+	RNA	INS	-	-	A	rs371932459|rs144931984|rs149686515		TCGA-FY-A3ON-01A-11D-A21Z-08	TCGA-FY-A3ON-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2b661b1c-472f-4911-83b6-ebf16248fe8f	f0119845-2a2b-4d0d-9f2e-24264ef9121c	g.chr16:21817398_21817399insA	ENST00000546471.1	-	0	1607							Q2M238	RN3P1_HUMAN	RNA polymerase I transcription factor homolog (S. cerevisiae) pseudogene 1																		TAAATGaaaataaaaaaataaa	0.302																																						ENST00000546471.1																			0																																																			0							g.chr16:21817398_21817399insA			16p12.2	2012-10-16			ENSG00000248124	ENSG00000248124			30548	pseudogene	pseudogene						12477932	Standard	NR_003370		Approved		uc010vbl.1	Q2M238	OTTHUMG00000170417		16.37:g.21817405_21817405dupA														0	1607	-								A8K6T4|B3KWX9|O75704	RNA	INS	ENST00000546471.1	37																																																																																						0.302	RRN3P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000409035.1	NR_003370		5	6						5	6	---	---	---	---
CCDC57	284001	broad.mit.edu	37	17	80173535	80173535	+	5'Flank	DEL	C	C	-	rs61581716	byFrequency	TCGA-FY-A3ON-01A-11D-A21Z-08	TCGA-FY-A3ON-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2b661b1c-472f-4911-83b6-ebf16248fe8f	f0119845-2a2b-4d0d-9f2e-24264ef9121c	g.chr17:80173535delC	ENST00000389641.4	-	0	0				CCDC57_ENST00000392343.3_5'Flank|RP13-516M14.2_ENST00000581303.1_RNA|CCDC57_ENST00000392347.1_5'Flank			Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57											endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	16	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)			tccttccctgccccccacact	0.701													|||unknown(LONG_INSERTION)	2565	0.512181	0.5688	0.5375	5008	,	,		10887	0.5258		0.4235	False		,,,				2504	0.4949					ENST00000581303.1																			0																																																	SO:0001631	upstream_gene_variant	0							g.chr17:80173535delC	BC040264		17q25.3	2006-03-08			ENSG00000176155	ENSG00000176155			27564	protein-coding gene	gene with protein product						12477932	Standard	XM_006722279		Approved	FLJ00130, FLJ23754	uc002kdx.1	Q2TAC2	OTTHUMG00000140396		17.37:g.80173535delC	Exception_encountered													0	1371	+								A6NP51|A8MQC7|Q8IWG2|Q8TER3	RNA	DEL	ENST00000389641.4	37																																																																																						0.701	CCDC57-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000277182.3	NM_198082		2	4						2	4	---	---	---	---
