#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
CD44	960	broad.mit.edu	37	11	35232956	35232956	+	Silent	SNP	T	T	C			TCGA-DJ-A13P-01A-11D-A10S-08	TCGA-DJ-A13P-10A-01D-A10S-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d67fb1e-4411-4aca-8d9a-f76dad5e03fb	541aed7f-ed74-4214-b7d3-85c7dc551738	g.chr11:35232956T>C	ENST00000428726.2	+	14	1893	c.1770T>C	c.(1768-1770)acT>acC	p.T590T	RP1-68D18.2_ENST00000510619.2_RNA|CD44_ENST00000360158.4_Intron|CD44_ENST00000278386.6_Intron|CD44_ENST00000437706.2_Intron|CD44_ENST00000434472.2_Silent_p.T277T|CD44_ENST00000433354.2_Silent_p.T562T|CD44_ENST00000263398.6_Intron|CD44_ENST00000449691.2_Silent_p.T547T|CD44_ENST00000352818.4_Intron|RP1-68D18.4_ENST00000528869.1_RNA|CD44_ENST00000433892.2_Silent_p.T341T|CD44_ENST00000415148.2_Silent_p.T547T|CD44_ENST00000526669.2_Intron	NM_000610.3	NP_000601.3	P16070	CD44_HUMAN	CD44 molecule (Indian blood group)	590	Stem.				blood coagulation (GO:0007596)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in ureteric bud morphogenesis (GO:0001658)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cell-matrix adhesion (GO:0007160)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|monocyte aggregation (GO:0070487)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of monocyte aggregation (GO:1900625)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|Wnt signaling pathway (GO:0016055)|wound healing involved in inflammatory response (GO:0002246)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|skin(1)	23	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.00731)		Hyaluronan(DB08818)	CTGCAGTTACTGTTGGAGATT	0.398																																						ENST00000428726.2																			0				cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|skin(1)	23						c.(1768-1770)acT>acC		CD44 molecule (Indian blood group)	Hyaluronidase(DB00070)						215.0	197.0	203.0					11																	35232956		2202	4298	6500	SO:0001819	synonymous_variant	960				cell-cell adhesion|cell-matrix adhesion|interferon-gamma-mediated signaling pathway|negative regulation of apoptosis|negative regulation of DNA damage response, signal transduction by p53 class mediator|positive regulation of ERK1 and ERK2 cascade|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-tyrosine phosphorylation	cell surface|Golgi apparatus|integral to plasma membrane	collagen binding|hyaluronic acid binding|receptor activity	g.chr11:35232956T>C	M59040	CCDS7897.1, CCDS31455.1, CCDS31456.1, CCDS31457.1, CCDS31458.1, CCDS55754.1, CCDS55755.1	11p13	2014-07-18	2006-03-28		ENSG00000026508	ENSG00000026508		"""CD molecules"", ""Blood group antigens"", ""Proteoglycans / Cell surface : Other"""	1681	protein-coding gene	gene with protein product	"""hematopoietic cell E- and L-selectin ligand"", ""chondroitin sulfate proteoglycan 8"""	107269	"""CD44 antigen (homing function and Indian blood group system)"""	MIC4, MDU2, MDU3		2454887	Standard	NM_001202555		Approved	IN, MC56, Pgp1, CD44R, HCELL, CSPG8	uc001mvu.3	P16070	OTTHUMG00000044388	ENST00000428726.2:c.1770T>C	11.37:g.35232956T>C						CD44_ENST00000449691.2_Silent_p.T547T|RP1-68D18.4_ENST00000528869.1_RNA|CD44_ENST00000437706.2_Intron|CD44_ENST00000434472.2_Silent_p.T277T|CD44_ENST00000433892.2_Silent_p.T341T|CD44_ENST00000433354.2_Silent_p.T562T|CD44_ENST00000526669.2_Intron|CD44_ENST00000415148.2_Silent_p.T547T|CD44_ENST00000360158.4_Intron|CD44_ENST00000352818.4_Intron|CD44_ENST00000278386.6_Intron|CD44_ENST00000263398.6_Intron	p.T590T	NM_000610.3	NP_000601.3	P16070	CD44_HUMAN	STAD - Stomach adenocarcinoma(6;0.00731)		14	1893	+	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)	590			Stem.		A5YRN9|B6EAT9|D3DR12|D3DR13|O95370|P22511|Q04858|Q13419|Q13957|Q13958|Q13959|Q13960|Q13961|Q13967|Q13968|Q13980|Q15861|Q16064|Q16065|Q16066|Q16208|Q16522|Q86T72|Q86Z27|Q8N694|Q92493|Q96J24|Q9H5A5|Q9UC28|Q9UC29|Q9UC30|Q9UCB0|Q9UJ36	Silent	SNP	ENST00000428726.2	37	c.1770T>C	CCDS7897.1																																																																																				0.398	CD44-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388927.1	NM_000610		8	262	0	0	0	0.038147	0	8	262				
GPATCH1	55094	broad.mit.edu	37	19	33592467	33592467	+	Missense_Mutation	SNP	T	T	C			TCGA-DJ-A13P-01A-11D-A10S-08	TCGA-DJ-A13P-10A-01D-A10S-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d67fb1e-4411-4aca-8d9a-f76dad5e03fb	541aed7f-ed74-4214-b7d3-85c7dc551738	g.chr19:33592467T>C	ENST00000170564.2	+	9	1381	c.1067T>C	c.(1066-1068)tTa>tCa	p.L356S		NM_018025.2	NP_060495.2	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	356					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|prostate(4)|skin(4)	40	Esophageal squamous(110;0.137)					TCTAAACCTTTATCTTCTAAG	0.308																																					Pancreas(67;88 1713 4567 18227)	ENST00000170564.2																			0				breast(4)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|prostate(4)|skin(4)	40						c.(1066-1068)tTa>tCa		G patch domain containing 1							109.0	105.0	106.0					19																	33592467		2203	4300	6503	SO:0001583	missense	55094					catalytic step 2 spliceosome	nucleic acid binding	g.chr19:33592467T>C	AF434677	CCDS12428.1	19q13.12	2013-01-28		2006-12-13		ENSG00000076650		"""G patch domain containing"""	24658	protein-coding gene	gene with protein product	"""evolutionarily conserved G patch domain containing"""			GPATC1		12477932	Standard	NM_018025		Approved	ECGP, FLJ10206, FLJ38686	uc002nug.1	Q9BRR8		ENST00000170564.2:c.1067T>C	19.37:g.33592467T>C	ENSP00000170564:p.Leu356Ser						p.L356S	NM_018025.2	NP_060495.2	Q9BRR8	GPTC1_HUMAN			9	1381	+	Esophageal squamous(110;0.137)		356					Q8IZV6|Q8N3B7|Q9NW94	Missense_Mutation	SNP	ENST00000170564.2	37	c.1067T>C	CCDS12428.1	.	.	.	.	.	.	.	.	.	.	T	5.798	0.331483	0.10956	.	.	ENSG00000076650	ENST00000170564	T	0.12774	2.65	5.64	4.62	0.57501	.	0.397513	0.28317	N	0.015793	T	0.06872	0.0175	N	0.20574	0.59	0.80722	D	1	B	0.13145	0.007	B	0.15052	0.012	T	0.26815	-1.0092	10	0.09338	T	0.73	-13.0817	5.3243	0.15898	0.0:0.2264:0.0:0.7736	.	356	Q9BRR8	GPTC1_HUMAN	S	356	ENSP00000170564:L356S	ENSP00000170564:L356S	L	+	2	0	GPATCH1	38284307	0.985000	0.35326	1.000000	0.80357	0.991000	0.79684	2.197000	0.42696	2.278000	0.76064	0.523000	0.50628	TTA		0.308	GPATCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450834.1	NM_018025		3	93	0	0	0	0.009096	0	3	93				
ZNF733P	643955	broad.mit.edu	37	7	62752443	62752443	+	RNA	SNP	G	G	C	rs372167638		TCGA-DJ-A13P-01A-11D-A10S-08	TCGA-DJ-A13P-10A-01D-A10S-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d67fb1e-4411-4aca-8d9a-f76dad5e03fb	541aed7f-ed74-4214-b7d3-85c7dc551738	g.chr7:62752443G>C	ENST00000331425.6	-	0	992					NR_003952.1				zinc finger protein 733, pseudogene																		CTTATGTCTAGTAAGGTTTGA	0.438																																						ENST00000331425.6																			0																																																			0							g.chr7:62752443G>C			7q11.21	2012-04-20	2012-04-20	2012-04-20	ENSG00000185037	ENSG00000185037			32473	pseudogene	pseudogene			"""zinc finger protein 733"""	ZNF733			Standard	NR_003952		Approved		uc011kdj.2		OTTHUMG00000156270		7.37:g.62752443G>C								NR_003952.1						0	992	-									RNA	SNP	ENST00000331425.6	37																																																																																						0.438	ZNF733P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000343679.1			6	26	0	0	0	0.021553	0	6	26				
HOXC12	3228	broad.mit.edu	37	12	54348806	54348806	+	Silent	SNP	G	G	T			TCGA-DJ-A13P-01A-11D-A10S-08	TCGA-DJ-A13P-10A-01D-A10S-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d67fb1e-4411-4aca-8d9a-f76dad5e03fb	541aed7f-ed74-4214-b7d3-85c7dc551738	g.chr12:54348806G>T	ENST00000243103.3	+	1	189	c.93G>T	c.(91-93)gcG>gcT	p.A31A	AC012531.23_ENST00000603432.1_lincRNA	NM_173860.1	NP_776272.1	P31275	HXC12_HUMAN	homeobox C12	31					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)	12						ACTTCCGCGCGTCCGGGGCGC	0.652																																						ENST00000243103.3																			0				large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)	12						c.(91-93)gcG>gcT		homeobox C12							31.0	38.0	35.0					12																	54348806		2203	4300	6503	SO:0001819	synonymous_variant	3228				multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr12:54348806G>T	AF328962	CCDS8866.1	12q13.13	2011-06-20	2005-12-22		ENSG00000123407	ENSG00000123407		"""Homeoboxes / ANTP class : HOXL subclass"""	5124	protein-coding gene	gene with protein product		142975	"""homeo box C12"""	HOX3, HOX3F, HOC3F		1973146, 1358459	Standard	NM_173860		Approved		uc010soq.2	P31275	OTTHUMG00000160010	ENST00000243103.3:c.93G>T	12.37:g.54348806G>T							p.A31A	NM_173860.1	NP_776272.1	P31275	HXC12_HUMAN			1	189	+			31					Q9BXJ6	Silent	SNP	ENST00000243103.3	37	c.93G>T	CCDS8866.1																																																																																				0.652	HOXC12-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358868.2	NM_173860		6	45	1	0	5.18039e-06	0.038147	5.52575e-06	6	45				
OFD1	8481	broad.mit.edu	37	X	13778527	13778527	+	Nonsense_Mutation	SNP	A	A	T			TCGA-DJ-A13P-01A-11D-A10S-08	TCGA-DJ-A13P-10A-01D-A10S-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d67fb1e-4411-4aca-8d9a-f76dad5e03fb	541aed7f-ed74-4214-b7d3-85c7dc551738	g.chrX:13778527A>T	ENST00000340096.6	+	16	2275	c.1948A>T	c.(1948-1950)Aga>Tga	p.R650*	OFD1_ENST00000380567.1_Nonsense_Mutation_p.R510*|OFD1_ENST00000490265.1_3'UTR|OFD1_ENST00000380550.3_Nonsense_Mutation_p.R610*	NM_003611.2	NP_003602.1	O75665	OFD1_HUMAN	oral-facial-digital syndrome 1	650	Mediates homooligomerization.|Mediates the interaction with SDCCAG8.				axoneme assembly (GO:0035082)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation (GO:2000314)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|gamma-tubulin binding (GO:0043015)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	25						AAAGGCTTTCAGAAGTTACCA	0.478																																						ENST00000380567.1																			0				breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	25						c.(1528-1530)Aga>Tga		oral-facial-digital syndrome 1							74.0	71.0	72.0					X																	13778527		2203	4300	6503	SO:0001587	stop_gained	8481				cilium movement involved in determination of left/right asymmetry|G2/M transition of mitotic cell cycle	centriole|cilium|cytosol|microtubule basal body|nuclear membrane	alpha-tubulin binding|gamma-tubulin binding	g.chrX:13778527A>T	Y15164	CCDS14157.1	Xp22	2014-06-18			ENSG00000046651	ENSG00000046651			2567	protein-coding gene	gene with protein product		300170	"""retinitis pigmentosa 23 (X-linked recessive)"""	CXorf5, RP23		9722947, 9215688, 22619378	Standard	NM_003611		Approved	71-7A, JBTS10	uc004cvp.4	O75665	OTTHUMG00000021159	ENST00000340096.6:c.1948A>T	X.37:g.13778527A>T	ENSP00000344314:p.Arg650*					OFD1_ENST00000490265.1_3'UTR|OFD1_ENST00000380550.3_Nonsense_Mutation_p.R610*|OFD1_ENST00000340096.6_Nonsense_Mutation_p.R650*	p.R510*			O75665	OFD1_HUMAN			17	2400	+			650					B9ZVU5|O75666|Q4VAK4	Nonsense_Mutation	SNP	ENST00000340096.6	37	c.1528A>T	CCDS14157.1	.	.	.	.	.	.	.	.	.	.	.	47	13.480964	0.99744	.	.	ENSG00000046651	ENST00000380550;ENST00000340096;ENST00000380567	.	.	.	5.67	2.2	0.27929	.	0.217516	0.45606	D	0.000357	.	.	.	.	.	.	0.54753	D	0.999987	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.9488	8.5217	0.33279	0.3763:0.5098:0.0:0.1139	.	.	.	.	X	610;650;510	.	ENSP00000344314:R650X	R	+	1	2	OFD1	13688448	0.994000	0.37717	0.002000	0.10522	0.906000	0.53458	2.282000	0.43461	0.053000	0.16036	0.430000	0.28490	AGA		0.478	OFD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055808.1	NM_003611		42	138	0	0	0	0.086207	0	42	138				
ZFYVE26	23503	broad.mit.edu	37	14	68248225	68248225	+	Missense_Mutation	SNP	A	A	G			TCGA-DJ-A13P-01A-11D-A10S-08	TCGA-DJ-A13P-10A-01D-A10S-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d67fb1e-4411-4aca-8d9a-f76dad5e03fb	541aed7f-ed74-4214-b7d3-85c7dc551738	g.chr14:68248225A>G	ENST00000347230.4	-	22	4532	c.4394T>C	c.(4393-4395)cTg>cCg	p.L1465P	ZFYVE26_ENST00000555452.1_Missense_Mutation_p.L1465P	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	1465					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		CACGGGAAACAGGTATTGCCA	0.498																																						ENST00000347230.4																			0				NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94						c.(4393-4395)cTg>cCg		zinc finger, FYVE domain containing 26							95.0	92.0	93.0					14																	68248225		2203	4300	6503	SO:0001583	missense	23503				cell cycle|cell death|cytokinesis|double-strand break repair via homologous recombination	centrosome|midbody	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding	g.chr14:68248225A>G	AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"""Zinc fingers, FYVE domain containing"""	20761	protein-coding gene	gene with protein product	"""spastizin"", ""FYVE-CENT"""	612012	"""spastic paraplegia 15 (complicated, autosomal recessive)"""	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.4394T>C	14.37:g.68248225A>G	ENSP00000251119:p.Leu1465Pro					ZFYVE26_ENST00000555452.1_Missense_Mutation_p.L1465P	p.L1465P	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN		all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)	22	4532	-			1465					B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	ENST00000347230.4	37	c.4394T>C	CCDS9788.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.540998	0.85917	.	.	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000555452	T;T	0.37752	1.35;1.18	5.83	5.83	0.93111	.	0.000000	0.64402	D	0.000001	T	0.60881	0.2303	M	0.69823	2.125	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.64428	-0.6410	10	0.87932	D	0	-9.2215	16.2025	0.82095	1.0:0.0:0.0:0.0	.	1465;1465	G3V2D8;Q68DK2	.;ZFY26_HUMAN	P	1465;1444;1465	ENSP00000251119:L1465P;ENSP00000450603:L1465P	ENSP00000251119:L1465P	L	-	2	0	ZFYVE26	67317978	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.679000	0.91220	2.231000	0.72958	0.459000	0.35465	CTG		0.498	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346		3	157	0	0	0	0.115264	0	3	157				
HNRNPDL	9987	broad.mit.edu	37	4	83349287	83349287	+	Missense_Mutation	SNP	G	G	A			TCGA-DJ-A13P-01A-11D-A10S-08	TCGA-DJ-A13P-10A-01D-A10S-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d67fb1e-4411-4aca-8d9a-f76dad5e03fb	541aed7f-ed74-4214-b7d3-85c7dc551738	g.chr4:83349287G>A	ENST00000295470.5	-	3	833	c.658C>T	c.(658-660)Ccc>Tcc	p.P220S	ENOPH1_ENST00000273920.3_5'Flank|HNRNPDL_ENST00000349655.4_Missense_Mutation_p.P101S|ENOPH1_ENST00000509635.1_5'Flank|HNRNPDL_ENST00000502762.1_Missense_Mutation_p.P220S|HNRNPDL_ENST00000602300.1_Missense_Mutation_p.P101S|HNRNPDL_ENST00000514511.1_Intron	NM_001207000.1|NM_031372.3	NP_001193929.1|NP_112740.1	O14979	HNRDL_HUMAN	heterogeneous nuclear ribonucleoprotein D-like	220	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				regulation of gene expression (GO:0010468)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|single-stranded DNA binding (GO:0003697)										GCCCTTTTGGGATCTATCAAT	0.373																																						ENST00000295470.5																			0											c.(658-660)Ccc>Tcc		heterogeneous nuclear ribonucleoprotein D-like							96.0	99.0	98.0					4																	83349287		2203	4300	6503	SO:0001583	missense	9987							g.chr4:83349287G>A	D89092	CCDS3593.1, CCDS75153.1	4q21.22	2013-06-12		2013-06-12	ENSG00000152795	ENSG00000152795		"""RNA binding motif (RRM) containing"""	5037	protein-coding gene	gene with protein product		607137		HNRPDL		10072754, 9524220	Standard	NM_001207000		Approved	JKTBP, laAUF1	uc003hmr.3	O14979	OTTHUMG00000130299	ENST00000295470.5:c.658C>T	4.37:g.83349287G>A	ENSP00000295470:p.Pro220Ser					HNRNPDL_ENST00000514511.1_Intron|HNRNPDL_ENST00000349655.4_Missense_Mutation_p.P101S|HNRNPDL_ENST00000602300.1_Missense_Mutation_p.P101S|HNRNPDL_ENST00000502762.1_Missense_Mutation_p.P220S	p.P220S	NM_001207000.1|NM_031372.3	NP_001193929.1|NP_112740.1					3	833	-								Q6SPF2|Q7KZ74|Q7KZ75|Q96IM0|Q96S43	Missense_Mutation	SNP	ENST00000295470.5	37	c.658C>T	CCDS3593.1	.	.	.	.	.	.	.	.	.	.	g	20.5	4.001272	0.74818	.	.	ENSG00000152795	ENST00000295470;ENST00000502762;ENST00000349655	T;T;T	0.74106	-0.81;-0.81;-0.81	6.17	5.32	0.75619	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.000000	0.85682	D	0.000000	D	0.86117	0.5856	M	0.81341	2.54	0.80722	D	1	D;B	0.65815	0.995;0.249	D;B	0.69142	0.962;0.186	D	0.87197	0.2238	10	0.87932	D	0	.	15.9972	0.80260	0.065:0.0:0.935:0.0	.	101;220	O14979-3;O14979	.;HNRDL_HUMAN	S	220;220;101	ENSP00000295470:P220S;ENSP00000422040:P220S;ENSP00000338552:P101S	ENSP00000295470:P220S	P	-	1	0	HNRPDL	83568311	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.373000	0.97168	2.941000	0.99782	0.655000	0.94253	CCC		0.373	HNRNPDL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252644.1	NM_005463		6	120	0	0	0	0.021553	0	6	120				
ANXA1	301	broad.mit.edu	37	9	75775259	75775259	+	Silent	SNP	A	A	G			TCGA-DJ-A13P-01A-11D-A10S-08	TCGA-DJ-A13P-10A-01D-A10S-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d67fb1e-4411-4aca-8d9a-f76dad5e03fb	541aed7f-ed74-4214-b7d3-85c7dc551738	g.chr9:75775259A>G	ENST00000376911.1	+	4	1233	c.351A>G	c.(349-351)caA>caG	p.Q117Q	ANXA1_ENST00000257497.6_Silent_p.Q117Q			P04083	ANXA1_HUMAN	annexin A1	117					alpha-beta T cell differentiation (GO:0046632)|arachidonic acid secretion (GO:0050482)|cell surface receptor signaling pathway (GO:0007166)|cellular component movement (GO:0006928)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to hydrogen peroxide (GO:0070301)|endocrine pancreas development (GO:0031018)|estrous cycle phase (GO:0060206)|gliogenesis (GO:0042063)|hepatocyte differentiation (GO:0070365)|inflammatory response (GO:0006954)|insulin secretion (GO:0030073)|keratinocyte differentiation (GO:0030216)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of apoptotic process (GO:0043066)|negative regulation of catalytic activity (GO:0043086)|negative regulation of interleukin-8 secretion (GO:2000483)|neutrophil clearance (GO:0097350)|neutrophil homeostasis (GO:0001780)|peptide cross-linking (GO:0018149)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of neutrophil apoptotic process (GO:0033031)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of vesicle fusion (GO:0031340)|regulation of cell proliferation (GO:0042127)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to interleukin-1 (GO:0070555)|response to peptide hormone (GO:0043434)|response to X-ray (GO:0010165)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cilium (GO:0005929)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|phospholipase A2 inhibitor activity (GO:0019834)|phospholipid binding (GO:0005543)|protein binding, bridging (GO:0030674)|receptor binding (GO:0005102)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(5)	8		all_epithelial(88;2.54e-11)		OV - Ovarian serous cystadenocarcinoma(323;2.82e-06)|GBM - Glioblastoma multiforme(74;0.0325)	Amcinonide(DB00288)|Dexamethasone(DB01234)|Hydrocortisone(DB00741)	CTCCAGCGCAATTTGATGCTG	0.428																																						ENST00000376911.1																			0				breast(1)|central_nervous_system(1)|large_intestine(1)|lung(5)	8						c.(349-351)caA>caG		annexin A1	Alclometasone(DB00240)|Amcinonide(DB00288)|Beclomethasone(DB00394)|Betamethasone(DB00443)|Clobetasol(DB01013)|Clocortolone(DB00838)|Desonide(DB01260)|Desoximetasone(DB00547)|Dexamethasone(DB01234)|Diflorasone(DB00223)|Flumethasone Pivalate(DB00663)|Halobetasol Propionate(DB00596)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol Etabonate(DB00873)|Methylprednisolone(DB00959)|Mometasone(DB00764)|Prednicarbate(DB01130)|Prednisone(DB00635)|Rimexolone(DB00896)|Triamcinolone(DB00620)						107.0	107.0	107.0					9																	75775259		2203	4300	6503	SO:0001819	synonymous_variant	301				alpha-beta T cell differentiation|anti-apoptosis|cell surface receptor linked signaling pathway|cellular component movement|inflammatory response|keratinocyte differentiation|lipid metabolic process|peptide cross-linking|positive regulation of vesicle fusion	basolateral plasma membrane|cilium|cornified envelope|cytoplasm|extracellular region|nucleus	calcium ion binding|calcium-dependent phospholipid binding|phospholipase A2 inhibitor activity|protein binding, bridging|receptor binding|structural molecule activity	g.chr9:75775259A>G	X05908	CCDS6645.1	9q21.13	2013-02-25			ENSG00000135046	ENSG00000135046		"""Annexins"", ""Endogenous ligands"""	533	protein-coding gene	gene with protein product		151690		ANX1, LPC1		2936963	Standard	NM_000700		Approved		uc004ajf.1	P04083	OTTHUMG00000020016	ENST00000376911.1:c.351A>G	9.37:g.75775259A>G						ANXA1_ENST00000257497.6_Silent_p.Q117Q	p.Q117Q			P04083	ANXA1_HUMAN		OV - Ovarian serous cystadenocarcinoma(323;2.82e-06)|GBM - Glioblastoma multiforme(74;0.0325)	4	1233	+		all_epithelial(88;2.54e-11)	117						Silent	SNP	ENST00000376911.1	37	c.351A>G	CCDS6645.1																																																																																				0.428	ANXA1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052665.1	NM_000700		3	152	0	0	0	0.009096	0	3	152				
LRRTM4	80059	broad.mit.edu	37	2	77746748	77746748	+	Missense_Mutation	SNP	C	C	T			TCGA-DJ-A13P-01A-11D-A10S-08	TCGA-DJ-A13P-10A-01D-A10S-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d67fb1e-4411-4aca-8d9a-f76dad5e03fb	541aed7f-ed74-4214-b7d3-85c7dc551738	g.chr2:77746748C>T	ENST00000409093.1	-	3	583	c.247G>A	c.(247-249)Ggc>Agc	p.G83S	LRRTM4_ENST00000409282.1_Missense_Mutation_p.G84S|LRRTM4_ENST00000409911.1_Missense_Mutation_p.G84S|LRRTM4_ENST00000409088.3_Missense_Mutation_p.G83S|LRRTM4_ENST00000409884.1_Missense_Mutation_p.G83S			Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4	83					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|regulation of presynaptic membrane organization (GO:1901629)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)		p.G83C(2)		autonomic_ganglia(1)|endometrium(1)|large_intestine(6)|lung(49)|ovary(2)|pancreas(3)|prostate(1)|upper_aerodigestive_tract(1)	64				Colorectal(11;0.059)		TGGTTAAGGCCGGCAAACTGA	0.403																																						ENST00000409088.3																			2	Substitution - Missense(2)	p.G83C(2)	lung(2)	autonomic_ganglia(1)|endometrium(1)|large_intestine(6)|lung(49)|ovary(2)|pancreas(3)|prostate(1)|upper_aerodigestive_tract(1)	64						c.(247-249)Ggc>Agc		leucine rich repeat transmembrane neuronal 4							131.0	124.0	126.0					2																	77746748		1902	4115	6017	SO:0001583	missense	80059					integral to membrane		g.chr2:77746748C>T	AK122612	CCDS46346.1, CCDS46347.1, CCDS74530.1	2p12	2008-02-05			ENSG00000176204	ENSG00000176204			19411	protein-coding gene	gene with protein product		610870				12676565	Standard	NM_024993		Approved	FLJ12568	uc002snr.3	Q86VH4	OTTHUMG00000152842	ENST00000409093.1:c.247G>A	2.37:g.77746748C>T	ENSP00000386357:p.Gly83Ser					LRRTM4_ENST00000409911.1_Missense_Mutation_p.G84S|LRRTM4_ENST00000409282.1_Missense_Mutation_p.G84S|LRRTM4_ENST00000409884.1_Missense_Mutation_p.G83S|LRRTM4_ENST00000409093.1_Missense_Mutation_p.G83S	p.G83S	NM_024993.4	NP_079269.4	Q86VH4	LRRT4_HUMAN		Colorectal(11;0.059)	3	661	-			83					Q4FZ98|Q6UXJ7	Missense_Mutation	SNP	ENST00000409093.1	37	c.247G>A	CCDS46346.1	.	.	.	.	.	.	.	.	.	.	C	10.64	1.406729	0.25378	.	.	ENSG00000176204	ENST00000409911;ENST00000409884;ENST00000409093;ENST00000409088;ENST00000409282	T;T;T;T;T	0.58940	0.3;0.3;0.3;0.3;0.3	5.96	5.07	0.68467	.	0.154837	0.64402	N	0.000013	T	0.39627	0.1085	N	0.20881	0.62	0.58432	D	0.999991	P;B;B	0.37985	0.613;0.307;0.143	B;B;B	0.32211	0.142;0.087;0.057	T	0.24584	-1.0156	10	0.25106	T	0.35	.	12.6798	0.56916	0.0:0.9182:0.0:0.0818	.	84;83;83	Q4KMX1;Q86VH4-2;Q86VH4	.;.;LRRT4_HUMAN	S	84;83;83;83;84	ENSP00000387228:G84S;ENSP00000387297:G83S;ENSP00000386357:G83S;ENSP00000386236:G83S;ENSP00000386286:G84S	ENSP00000386236:G83S	G	-	1	0	LRRTM4	77600256	0.999000	0.42202	1.000000	0.80357	0.999000	0.98932	3.893000	0.56243	1.486000	0.48398	0.655000	0.94253	GGC		0.403	LRRTM4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328225.1	NM_024993		4	122	0	0	0	0.009096	0	4	122				
FAM64A	54478	broad.mit.edu	37	17	6348539	6348539	+	Missense_Mutation	SNP	G	G	A			TCGA-DJ-A13P-01A-11D-A10S-08	TCGA-DJ-A13P-10A-01D-A10S-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d67fb1e-4411-4aca-8d9a-f76dad5e03fb	541aed7f-ed74-4214-b7d3-85c7dc551738	g.chr17:6348539G>A	ENST00000250056.8	+	2	192	c.109G>A	c.(109-111)Gag>Aag	p.E37K	FAM64A_ENST00000576056.1_Missense_Mutation_p.E37K|FAM64A_ENST00000570337.2_Missense_Mutation_p.E37K|FAM64A_ENST00000572447.1_Missense_Mutation_p.E37K|FAM64A_ENST00000571373.1_Missense_Mutation_p.E37K|FAM64A_ENST00000572595.2_Missense_Mutation_p.E37K	NM_001195228.1	NP_001182157.1	Q9BSJ6	FA64A_HUMAN	family with sequence similarity 64, member A	37					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7				COAD - Colon adenocarcinoma(228;0.141)		CAGCCATCAGGAGACCTCTGT	0.647																																						ENST00000572447.1																			0				breast(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7						c.(109-111)Gag>Aag		family with sequence similarity 64, member A							28.0	29.0	29.0					17																	6348539		2203	4300	6503	SO:0001583	missense	54478					nucleolus	protein binding	g.chr17:6348539G>A		CCDS32541.1, CCDS56016.1	17p13.2	2013-10-11			ENSG00000129195	ENSG00000129195			25483	protein-coding gene	gene with protein product	"""CALM interacting protein expressed in thymus and spleen"""					19383357, 16491119	Standard	NM_019013		Approved	FLJ10156, FLJ10491, CATS	uc002gcw.2	Q9BSJ6	OTTHUMG00000177832	ENST00000250056.8:c.109G>A	17.37:g.6348539G>A	ENSP00000250056:p.Glu37Lys					FAM64A_ENST00000576056.1_Missense_Mutation_p.E37K|FAM64A_ENST00000572595.2_Missense_Mutation_p.E37K|FAM64A_ENST00000571373.1_Missense_Mutation_p.E37K|FAM64A_ENST00000250056.8_Missense_Mutation_p.E37K|FAM64A_ENST00000570337.2_Missense_Mutation_p.E37K	p.E37K	NM_019013.2	NP_061886.2	Q9BSJ6	FA64A_HUMAN		COAD - Colon adenocarcinoma(228;0.141)	2	218	+			37					Q96CT4|Q9NVV1|Q9NWB5	Missense_Mutation	SNP	ENST00000250056.8	37	c.109G>A	CCDS56016.1	.	.	.	.	.	.	.	.	.	.	G	14.26	2.482282	0.44147	.	.	ENSG00000129195	ENST00000250056;ENST00000308855	T	0.56444	0.46	5.08	3.08	0.35506	.	0.712790	0.12957	N	0.425350	T	0.41236	0.1150	L	0.43152	1.355	0.09310	N	1	P;B	0.38048	0.616;0.447	B;B	0.39617	0.305;0.168	T	0.16600	-1.0397	10	0.14252	T	0.57	-9.026	6.7574	0.23523	0.0941:0.1788:0.7271:0.0	.	37;37	Q9BSJ6;Q9BSJ6-2	FA64A_HUMAN;.	K	37	ENSP00000250056:E37K	ENSP00000250056:E37K	E	+	1	0	FAM64A	6289263	0.177000	0.23109	0.002000	0.10522	0.022000	0.10575	2.085000	0.41634	0.725000	0.32318	0.655000	0.94253	GAG		0.647	FAM64A-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000439156.1	NM_019013		22	32	0	0	0	0.069288	0	22	32				
LAMA5	3911	broad.mit.edu	37	20	60886750	60886750	+	Silent	SNP	C	C	T	rs374794377		TCGA-DJ-A13P-01A-11D-A10S-08	TCGA-DJ-A13P-10A-01D-A10S-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d67fb1e-4411-4aca-8d9a-f76dad5e03fb	541aed7f-ed74-4214-b7d3-85c7dc551738	g.chr20:60886750C>T	ENST00000252999.3	-	71	9792	c.9726G>A	c.(9724-9726)ccG>ccA	p.P3242P	LAMA5_ENST00000492698.1_5'Flank	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	3242	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|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)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			GGAGGAGCCTCGGGGGCCCCT	0.667																																						ENST00000252999.3																			0				breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81						c.(9724-9726)ccG>ccA		laminin, alpha 5	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	T		2,4316		0,2,2157	9.0	9.0	9.0		9726	-6.7	0.0	20		9	2,8526		0,2,4262	no	coding-synonymous	LAMA5	NM_005560.3		0,4,6419	TT,TC,CC		0.0235,0.0463,0.0311		3242/3696	60886750	4,12842	2159	4264	6423	SO:0001819	synonymous_variant	3911				angiogenesis|cell proliferation|cell recognition|cytoskeleton organization|endothelial cell differentiation|focal adhesion assembly|integrin-mediated signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex	integrin binding	g.chr20:60886750C>T	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.9726G>A	20.37:g.60886750C>T							p.P3242P	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	BRCA - Breast invasive adenocarcinoma(19;4.36e-06)		71	9792	-	Breast(26;1.57e-08)		3242			Laminin G-like 3.		Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	c.9726G>A	CCDS33502.1																																																																																				0.667	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		5	5	0	0	0	0.021553	0	5	5				
PHEX	5251	broad.mit.edu	37	X	22112115	22112115	+	Silent	SNP	T	T	G			TCGA-DJ-A13P-01A-11D-A10S-08	TCGA-DJ-A13P-10A-01D-A10S-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d67fb1e-4411-4aca-8d9a-f76dad5e03fb	541aed7f-ed74-4214-b7d3-85c7dc551738	g.chrX:22112115T>G	ENST00000379374.4	+	7	1312	c.747T>G	c.(745-747)ctT>ctG	p.L249L	PHEX_ENST00000535894.1_Silent_p.L152L|PHEX_ENST00000475778.1_3'UTR|PHEX_ENST00000537599.1_Silent_p.L249L	NM_000444.4	NP_000435.3	P78562	PHEX_HUMAN	phosphate regulating endopeptidase homolog, X-linked	249					bone mineralization (GO:0030282)|cell-cell signaling (GO:0007267)|cellular protein modification process (GO:0006464)|organophosphate metabolic process (GO:0019637)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|cervix(2)|endometrium(2)|large_intestine(12)|liver(1)|lung(19)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	42						GGGATGCCCTTTACAAGTTCA	0.413																																						ENST00000379374.4																			0				breast(1)|cervix(2)|endometrium(2)|large_intestine(12)|liver(1)|lung(19)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	42						c.(745-747)ctT>ctG		phosphate regulating endopeptidase homolog, X-linked							174.0	159.0	164.0					X																	22112115		2203	4300	6503	SO:0001819	synonymous_variant	5251				biomineral tissue development|cell-cell signaling|protein modification process|proteolysis|skeletal system development	integral to plasma membrane	aminopeptidase activity|metalloendopeptidase activity|zinc ion binding	g.chrX:22112115T>G	U82970	CCDS14204.1	Xp22.2-p22.1	2008-07-31	2008-07-31		ENSG00000102174	ENSG00000102174			8918	protein-coding gene	gene with protein product		300550	"""phosphate regulating gene with homologies to endopeptidases on the X chromosome (hypophosphatemia, vitamin D resistant rickets)"""	HYP, HPDR		7550339, 9070861	Standard	NM_000444		Approved	PEX, HPDR1, HYP1, XLH	uc004dah.3	P78562	OTTHUMG00000021241	ENST00000379374.4:c.747T>G	X.37:g.22112115T>G						PHEX_ENST00000475778.1_3'UTR|PHEX_ENST00000537599.1_Silent_p.L249L|PHEX_ENST00000535894.1_Silent_p.L152L	p.L249L	NM_000444.4	NP_000435.3	P78562	PHEX_HUMAN			7	1312	+			249					O00678|Q13646|Q2M325|Q93032|Q99827	Silent	SNP	ENST00000379374.4	37	c.747T>G	CCDS14204.1																																																																																				0.413	PHEX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056035.1	NM_000444		23	233	0	0	0	0.091800	0	23	233				
TBC1D5	9779	broad.mit.edu	37	3	17349528	17349528	+	Missense_Mutation	SNP	A	A	G			TCGA-DJ-A13P-01A-11D-A10S-08	TCGA-DJ-A13P-10A-01D-A10S-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d67fb1e-4411-4aca-8d9a-f76dad5e03fb	541aed7f-ed74-4214-b7d3-85c7dc551738	g.chr3:17349528A>G	ENST00000253692.7	-	14	2758	c.1094T>C	c.(1093-1095)gTa>gCa	p.V365A	TBC1D5_ENST00000429383.4_Missense_Mutation_p.V365A|TBC1D5_ENST00000446818.2_Missense_Mutation_p.V365A|TBC1D5_ENST00000414318.2_5'UTR|TBC1D5_ENST00000429924.2_Missense_Mutation_p.V317A	NM_014744.2	NP_055559.1	Q92609	TBCD5_HUMAN	TBC1 domain family, member 5	365						retromer complex (GO:0030904)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	36						GATATAATCTACTAAACCCAG	0.463																																						ENST00000253692.7																			0				NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	36						c.(1093-1095)gTa>gCa		TBC1 domain family, member 5							81.0	78.0	79.0					3																	17349528		2203	4300	6503	SO:0001583	missense	9779					intracellular	protein binding|Rab GTPase activator activity	g.chr3:17349528A>G	D86965	CCDS33714.1, CCDS46770.1	3p24.3	2013-07-09			ENSG00000131374	ENSG00000131374			19166	protein-coding gene	gene with protein product		615740				19531583	Standard	NM_014744		Approved	KIAA0210	uc003cbe.3	Q92609	OTTHUMG00000155488	ENST00000253692.7:c.1094T>C	3.37:g.17349528A>G	ENSP00000253692:p.Val365Ala					TBC1D5_ENST00000429924.2_Missense_Mutation_p.V317A|TBC1D5_ENST00000446818.2_Missense_Mutation_p.V365A|TBC1D5_ENST00000414318.2_5'UTR|TBC1D5_ENST00000429383.4_Missense_Mutation_p.V365A	p.V365A	NM_014744.2	NP_055559.1	Q92609	TBCD5_HUMAN			14	2758	-			365					A6NP25|C9JP52	Missense_Mutation	SNP	ENST00000253692.7	37	c.1094T>C	CCDS33714.1	.	.	.	.	.	.	.	.	.	.	A	17.55	3.417639	0.62622	.	.	ENSG00000131374	ENST00000253692;ENST00000429383;ENST00000446818;ENST00000429924	T;T;T;T	0.11385	2.78;2.78;2.78;2.78	5.55	5.55	0.83447	Rab-GAP/TBC domain (3);	0.000000	0.85682	D	0.000000	T	0.23766	0.0575	L	0.41710	1.295	0.80722	D	1	B;P;P	0.51240	0.372;0.943;0.94	P;P;P	0.62014	0.74;0.854;0.897	T	0.00415	-1.1753	10	0.66056	D	0.02	-17.9645	15.6976	0.77512	1.0:0.0:0.0:0.0	.	317;365;365	C9J3F6;C9JP52;Q92609	.;.;TBCD5_HUMAN	A	365;365;365;317	ENSP00000253692:V365A;ENSP00000398127:V365A;ENSP00000402935:V365A;ENSP00000411925:V317A	ENSP00000253692:V365A	V	-	2	0	TBC1D5	17324532	1.000000	0.71417	0.113000	0.21522	0.443000	0.32047	9.173000	0.94815	2.115000	0.64714	0.477000	0.44152	GTA		0.463	TBC1D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340301.3	NM_014744		3	83	0	0	0	0.115264	0	3	83				
STXBP5	134957	broad.mit.edu	37	6	147685192	147685192	+	Missense_Mutation	SNP	C	C	T			TCGA-DJ-A13P-01A-11D-A10S-08	TCGA-DJ-A13P-10A-01D-A10S-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d67fb1e-4411-4aca-8d9a-f76dad5e03fb	541aed7f-ed74-4214-b7d3-85c7dc551738	g.chr6:147685192C>T	ENST00000321680.6	+	25	2971	c.2971C>T	c.(2971-2973)Cgg>Tgg	p.R991W	STXBP5_ENST00000367481.3_Missense_Mutation_p.R955W|STXBP5_ENST00000179882.6_Missense_Mutation_p.R646W|STXBP5_ENST00000367480.3_Missense_Mutation_p.R938W	NM_001127715.2	NP_001121187.1	Q5T5C0	STXB5_HUMAN	syntaxin binding protein 5 (tomosyn)	991					exocytosis (GO:0006887)|negative regulation of exocytosis (GO:0045920)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|synapse (GO:0045202)	syntaxin-1 binding (GO:0017075)	p.R955W(1)|p.R991W(1)		breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(21)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	42		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)		TACCAATATGCGGATAGCCAG	0.363																																						ENST00000367481.3																			2	Substitution - Missense(2)	p.R955W(1)|p.R991W(1)	kidney(2)	breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(21)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	42						c.(2863-2865)Cgg>Tgg		syntaxin binding protein 5 (tomosyn)							189.0	181.0	184.0					6																	147685192		2203	4300	6503	SO:0001583	missense	0				exocytosis|positive regulation of exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|nicotinic acetylcholine-gated receptor-channel complex|synaptic vesicle	syntaxin-1 binding	g.chr6:147685192C>T	AK055484	CCDS5211.1, CCDS47499.1	6q24.3	2013-01-10			ENSG00000164506	ENSG00000164506		"""WD repeat domain containing"""	19665	protein-coding gene	gene with protein product		604586				9620695, 14767561	Standard	NM_139244		Approved	tomosyn, LLGL3	uc010khz.2	Q5T5C0	OTTHUMG00000015766	ENST00000321680.6:c.2971C>T	6.37:g.147685192C>T	ENSP00000321826:p.Arg991Trp					STXBP5_ENST00000367480.3_Missense_Mutation_p.R938W|STXBP5_ENST00000321680.6_Missense_Mutation_p.R991W|STXBP5_ENST00000179882.6_Missense_Mutation_p.R646W	p.R955W	NM_139244.4	NP_640337.3	Q5T5C0	STXB5_HUMAN		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)	23	2971	+		Ovarian(120;0.0164)	991					Q14DF3|Q5T5C1|Q5T5C2|Q8NBG8|Q96NG9	Missense_Mutation	SNP	ENST00000321680.6	37	c.2863C>T	CCDS47499.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.218984	0.79464	.	.	ENSG00000164506	ENST00000367481;ENST00000321680;ENST00000367480;ENST00000179882	T;T;T;T	0.26518	1.73;1.73;1.73;1.73	5.84	2.77	0.32553	Lethal giant larvae (Lgl)-like, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.39784	0.1091	M	0.81682	2.555	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.999	T	0.43556	-0.9384	10	0.72032	D	0.01	.	11.1257	0.48317	0.2422:0.6922:0.0:0.0656	.	955;991;646	Q5T5C0-2;Q5T5C0;B3KXX0	.;STXB5_HUMAN;.	W	955;991;938;646	ENSP00000356451:R955W;ENSP00000321826:R991W;ENSP00000356450:R938W;ENSP00000179882:R646W	ENSP00000179882:R646W	R	+	1	2	STXBP5	147726885	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.045000	0.57368	0.793000	0.33875	-0.182000	0.12963	CGG		0.363	STXBP5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042606.1			5	296	0	0	0	0.029380	0	5	296				
NEO1	4756	broad.mit.edu	37	15	73528814	73528814	+	Missense_Mutation	SNP	A	A	G			TCGA-DJ-A13P-01A-11D-A10S-08	TCGA-DJ-A13P-10A-01D-A10S-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d67fb1e-4411-4aca-8d9a-f76dad5e03fb	541aed7f-ed74-4214-b7d3-85c7dc551738	g.chr15:73528814A>G	ENST00000339362.5	+	9	1865	c.1418A>G	c.(1417-1419)tAc>tGc	p.Y473C	NEO1_ENST00000558964.1_Missense_Mutation_p.Y473C|NEO1_ENST00000560262.1_Missense_Mutation_p.Y473C|NEO1_ENST00000261908.6_Missense_Mutation_p.Y473C|NEO1_ENST00000560352.1_3'UTR			Q92859	NEO1_HUMAN	neogenin 1	473	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|iron ion homeostasis (GO:0055072)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of transcription, DNA-templated (GO:0006355)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(9)|lung(26)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	57						AACCTTACCTACTCTGTGTTC	0.562																																						ENST00000339362.5																			0				NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(9)|lung(26)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	57						c.(1417-1419)tAc>tGc		neogenin 1							181.0	149.0	160.0					15																	73528814		2198	4297	6495	SO:0001583	missense	4756				axon guidance|cell adhesion|positive regulation of muscle cell differentiation	Golgi apparatus|integral to plasma membrane|nucleus		g.chr15:73528814A>G	U61262	CCDS10247.1, CCDS53957.1, CCDS58378.1	15q22.3-q23	2014-06-20	2010-06-24		ENSG00000067141	ENSG00000067141		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7754	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 2"""	601907	"""neogenin (chicken) homolog 1"""			9121761	Standard	NM_002499		Approved	NGN, HsT17534, IGDCC2, NTN1R2	uc002avm.4	Q92859	OTTHUMG00000133509	ENST00000339362.5:c.1418A>G	15.37:g.73528814A>G	ENSP00000341198:p.Tyr473Cys					NEO1_ENST00000560352.1_3'UTR|NEO1_ENST00000560262.1_Missense_Mutation_p.Y473C|NEO1_ENST00000261908.6_Missense_Mutation_p.Y473C|NEO1_ENST00000558964.1_Missense_Mutation_p.Y473C	p.Y473C			Q92859	NEO1_HUMAN			9	1865	+			473			Fibronectin type-III 1.		B7ZKM9|B7ZKN0|O00340|Q17RX1	Missense_Mutation	SNP	ENST00000339362.5	37	c.1418A>G	CCDS10247.1	.	.	.	.	.	.	.	.	.	.	A	19.25	3.791756	0.70452	.	.	ENSG00000067141	ENST00000339362;ENST00000379842;ENST00000261908	T;T	0.75050	-0.9;-0.9	6.05	6.05	0.98169	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.054961	0.85682	D	0.000000	D	0.90438	0.7006	H	0.95645	3.7	0.80722	D	1	P;D;D;D	0.76494	0.804;0.999;0.979;0.991	P;D;D;D	0.79784	0.669;0.993;0.968;0.947	D	0.93073	0.6484	10	0.87932	D	0	-12.0065	16.5932	0.84781	1.0:0.0:0.0:0.0	.	473;473;211;473	B7ZKM9;B7ZKN0;E7EUX3;Q92859	.;.;.;NEO1_HUMAN	C	473;211;473	ENSP00000341198:Y473C;ENSP00000261908:Y473C	ENSP00000261908:Y473C	Y	+	2	0	NEO1	71315867	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.077000	0.76814	2.320000	0.78422	0.528000	0.53228	TAC		0.562	NEO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257472.2	NM_002499		4	239	0	0	0	0.021553	0	4	239				
BMS1P20	96610	broad.mit.edu	37	22	22664141	22664141	+	RNA	SNP	G	G	A	rs369590722		TCGA-DJ-A13P-01A-11D-A10S-08	TCGA-DJ-A13P-10A-01D-A10S-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d67fb1e-4411-4aca-8d9a-f76dad5e03fb	541aed7f-ed74-4214-b7d3-85c7dc551738	g.chr22:22664141G>A	ENST00000426066.1	+	0	664					NR_027293.1				BMS1 pseudogene 20																		AAATTTGAAGGTGCTGTGATT	0.448																																						ENST00000426066.1																			0																																																			0							g.chr22:22664141G>A			22q11.22	2013-09-20			ENSG00000236850	ENSG00000236850			49153	pseudogene	pseudogene							Standard	XR_430414		Approved				OTTHUMG00000151046		22.37:g.22664141G>A								NR_027293.1						0	664	+									RNA	SNP	ENST00000426066.1	37																																																																																						0.448	BMS1P20-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000473090.1			4	100	0	0	0	0.009096	0	4	100				
CLCN6	1185	broad.mit.edu	37	1	11888618	11888618	+	Missense_Mutation	SNP	G	G	C			TCGA-DJ-A13P-01A-11D-A10S-08	TCGA-DJ-A13P-10A-01D-A10S-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d67fb1e-4411-4aca-8d9a-f76dad5e03fb	541aed7f-ed74-4214-b7d3-85c7dc551738	g.chr1:11888618G>C	ENST00000346436.6	+	12	1110	c.1058G>C	c.(1057-1059)tGt>tCt	p.C353S	CLCN6_ENST00000376487.3_Missense_Mutation_p.C331S|CLCN6_ENST00000312413.6_Intron|CLCN6_ENST00000376492.3_Intron|CLCN6_ENST00000376496.3_Missense_Mutation_p.C353S	NM_001286.3	NP_001277	P51797	CLCN6_HUMAN	chloride channel, voltage-sensitive 6	353					cell volume homeostasis (GO:0006884)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|response to mechanical stimulus (GO:0009612)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|voltage-gated chloride channel activity (GO:0005247)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(4)	36	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		ACATTCAACTGTCTGAACAAG	0.537																																						ENST00000346436.6																			0				cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(4)	36						c.(1057-1059)tGt>tCt		chloride channel, voltage-sensitive 6							177.0	188.0	184.0					1																	11888618		2203	4300	6503	SO:0001583	missense	1185				cell volume homeostasis|signal transduction	endosome membrane|integral to membrane	antiporter activity|ATP binding|voltage-gated chloride channel activity	g.chr1:11888618G>C	X83378	CCDS138.1, CCDS57972.1	1p36	2012-09-26	2012-02-23		ENSG00000011021	ENSG00000011021		"""Ion channels / Chloride channels : Voltage-sensitive"""	2024	protein-coding gene	gene with protein product		602726	"""chloride channel 6"""			8543009	Standard	NM_001286		Approved	CLC-6, KIAA0046, ClC-6	uc001ate.5	P51797	OTTHUMG00000002299	ENST00000346436.6:c.1058G>C	1.37:g.11888618G>C	ENSP00000234488:p.Cys353Ser					CLCN6_ENST00000376496.3_Missense_Mutation_p.C353S|CLCN6_ENST00000312413.6_Intron|CLCN6_ENST00000376492.3_Intron|CLCN6_ENST00000376487.3_Missense_Mutation_p.C331S	p.C353S	NM_001286.3	NP_001277.1	P51797	CLCN6_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)	12	1110	+	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)	353					A8K1T4|B4DGT7|F8W9R3|O60818|O60819|O60820|O60821|P78520|P78521|Q17R81|Q5SNW2|Q5SNW3|Q5SNX1|Q5SNX2|Q5SNX3|Q99427|Q99428|Q99429	Missense_Mutation	SNP	ENST00000346436.6	37	c.1058G>C	CCDS138.1	.	.	.	.	.	.	.	.	.	.	G	15.40	2.821060	0.50633	.	.	ENSG00000011021	ENST00000346436;ENST00000376487;ENST00000376496	D;D;D	0.93659	-3.26;-3.26;-3.26	6.07	6.07	0.98685	Chloride channel, core (2);	0.000000	0.85682	D	0.000000	D	0.86443	0.5934	N	0.05414	-0.055	0.80722	D	1	B;B	0.17465	0.022;0.011	B;B	0.15052	0.006;0.012	T	0.80511	-0.1350	10	0.20046	T	0.44	-19.9849	19.6321	0.95713	0.0:0.0:1.0:0.0	.	331;353	F8W9R3;P51797	.;CLCN6_HUMAN	S	353;331;353	ENSP00000234488:C353S;ENSP00000365670:C331S;ENSP00000365679:C353S	ENSP00000234488:C353S	C	+	2	0	CLCN6	11811205	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.476000	0.97823	2.884000	0.98904	0.655000	0.94253	TGT		0.537	CLCN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006639.2	NM_001286		4	399	0	0	0	0.014758	0	4	399				
PPOX	5498	broad.mit.edu	37	1	161140206	161140206	+	Missense_Mutation	SNP	G	G	C			TCGA-DJ-A13P-01A-11D-A10S-08	TCGA-DJ-A13P-10A-01D-A10S-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d67fb1e-4411-4aca-8d9a-f76dad5e03fb	541aed7f-ed74-4214-b7d3-85c7dc551738	g.chr1:161140206G>C	ENST00000367999.4	+	10	1261	c.995G>C	c.(994-996)gGa>gCa	p.G332A	PPOX_ENST00000535223.1_Intron|PPOX_ENST00000352210.5_Missense_Mutation_p.G332A|B4GALT3_ENST00000470882.1_5'Flank|PPOX_ENST00000432542.2_Missense_Mutation_p.G77A|PPOX_ENST00000544598.1_Intron|PPOX_ENST00000495483.1_3'UTR	NM_001122764.1	NP_001116236.1	P50336	PPOX_HUMAN	protoporphyrinogen oxidase	332			G -> A (in VP; abolishes activity; impairs protein folding and/or stability). {ECO:0000269|PubMed:18570668, ECO:0000269|PubMed:23430901}.		heme biosynthetic process (GO:0006783)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound biosynthetic process (GO:0006779)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)	integral component of mitochondrial inner membrane (GO:0031305)|intrinsic component of mitochondrial inner membrane (GO:0031304)|mitochondrial intermembrane space (GO:0005758)|mitochondrial membrane (GO:0031966)	flavin adenine dinucleotide binding (GO:0050660)|oxygen-dependent protoporphyrinogen oxidase activity (GO:0004729)			breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(3)	15	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			CAGGGATTTGGACATTTGGTG	0.557																																						ENST00000367999.4																			0				breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(3)	15						c.(994-996)gGa>gCa		protoporphyrinogen oxidase							88.0	82.0	84.0					1																	161140206		2203	4300	6503	SO:0001583	missense	5498				heme biosynthetic process	intrinsic to mitochondrial inner membrane|mitochondrial intermembrane space	flavin adenine dinucleotide binding|oxygen-dependent protoporphyrinogen oxidase activity	g.chr1:161140206G>C	BC002357	CCDS1221.1	1q22	2008-02-05			ENSG00000143224	ENSG00000143224	1.3.3.4		9280	protein-coding gene	gene with protein product		600923	"""variegate porphyria"""	VP		8575762, 10457135	Standard	NM_000309		Approved	PPO	uc001fyg.2	P50336	OTTHUMG00000034342	ENST00000367999.4:c.995G>C	1.37:g.161140206G>C	ENSP00000356978:p.Gly332Ala					PPOX_ENST00000544598.1_Intron|PPOX_ENST00000535223.1_Intron|PPOX_ENST00000432542.2_Missense_Mutation_p.G77A|PPOX_ENST00000352210.5_Missense_Mutation_p.G332A|PPOX_ENST00000495483.1_3'UTR	p.G332A	NM_001122764.1	NP_001116236.1	P50336	PPOX_HUMAN	BRCA - Breast invasive adenocarcinoma(70;0.00275)		10	1261	+	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		332					D3DVG0|Q5VTW8	Missense_Mutation	SNP	ENST00000367999.4	37	c.995G>C	CCDS1221.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.56|18.56	3.650072|3.650072	0.67472|0.67472	.|.	.|.	ENSG00000143224|ENSG00000143224	ENST00000537523;ENST00000537829|ENST00000352210;ENST00000367999;ENST00000435935;ENST00000432542	.|D;D;D	.|0.99748	.|-6.62;-6.62;-6.62	5.43|5.43	5.43|5.43	0.79202|0.79202	.|Amine oxidase (1);	.|0.110089	.|0.64402	.|D	.|0.000008	D|D	0.99796|0.99796	0.9913|0.9913	M|M	0.93720|0.93720	3.45|3.45	0.48040|0.48040	D|D	0.999574|0.999574	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;0.999	.|D;D;D;D	.|0.97110	.|1.0;0.999;0.962;0.972	D|D	0.97274|0.97274	0.9913|0.9913	5|10	.|0.72032	.|D	.|0.01	-8.1151|-8.1151	14.6179|14.6179	0.68562|0.68562	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|77;3;170;332	.|B4DQQ7;Q96SE3;B3KT30;P50336	.|.;.;.;PPOX_HUMAN	H|A	85;55|332;332;299;77	.|ENSP00000343943:G332A;ENSP00000356978:G332A;ENSP00000396841:G77A	.|ENSP00000343943:G332A	D|G	+|+	1|2	0|0	PPOX|PPOX	159406830|159406830	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.963000|0.963000	0.63663|0.63663	7.747000|7.747000	0.85070|0.85070	2.823000|2.823000	0.97156|0.97156	0.650000|0.650000	0.86243|0.86243	GAC|GGA		0.557	PPOX-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082993.1	NM_000309		3	104	0	0	0	0.115264	0	3	104				
MCMDC2	157777	broad.mit.edu	37	8	67834750	67834750	+	IGR	SNP	G	G	A			TCGA-DJ-A13P-01A-11D-A10S-08	TCGA-DJ-A13P-10A-01D-A10S-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d67fb1e-4411-4aca-8d9a-f76dad5e03fb	541aed7f-ed74-4214-b7d3-85c7dc551738	g.chr8:67834750G>A	ENST00000422365.2	+	0	5096				SNHG6_ENST00000364849.1_RNA|SNORD87_ENST00000522478.1_RNA	NM_173518.4	NP_775789.3	Q4G0Z9	MCMD2_HUMAN	minichromosome maintenance domain containing 2						DNA replication (GO:0006260)		ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(2)|kidney(2)|lung(5)	9						ACCTCAGCTGGGTAAACGGCA	0.308																																						ENST00000364849.1																			0																				78.0	78.0	78.0					8																	67834750		876	1991	2867	SO:0001628	intergenic_variant	0							g.chr8:67834750G>A	BC034576	CCDS6197.2, CCDS47868.1, CCDS47869.1	8q13.1	2012-04-13	2012-04-13	2012-04-13	ENSG00000178460	ENSG00000178460			26368	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 45"""	C8orf45			Standard	NM_173518		Approved	FLJ25692	uc003xwz.4	Q4G0Z9	OTTHUMG00000157068		8.37:g.67834750G>A						SNORD87_ENST00000522478.1_RNA		NR_002598.1						0	40	-								B4DYZ3|B4DZM4|B4E293|Q6P533|Q7Z3P4	RNA	SNP	ENST00000422365.2	37		CCDS6197.2																																																																																				0.308	MCMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347350.1	NM_173518		4	112	0	0	0	0.009096	0	4	112				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-DJ-A13P-01A-11D-A10S-08	TCGA-DJ-A13P-10A-01D-A10S-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d67fb1e-4411-4aca-8d9a-f76dad5e03fb	541aed7f-ed74-4214-b7d3-85c7dc551738	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	81	0	0	0	0.139131	0	49	81				
C5orf42	65250	broad.mit.edu	37	5	37169637	37169637	+	Missense_Mutation	SNP	T	T	A			TCGA-DJ-A13P-01A-11D-A10S-08	TCGA-DJ-A13P-10A-01D-A10S-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d67fb1e-4411-4aca-8d9a-f76dad5e03fb	541aed7f-ed74-4214-b7d3-85c7dc551738	g.chr5:37169637T>A	ENST00000508244.1	-	33	6582	c.6489A>T	c.(6487-6489)ttA>ttT	p.L2163F	C5orf42_ENST00000274258.7_Missense_Mutation_p.L1043F|C5orf42_ENST00000425232.2_Missense_Mutation_p.L2163F			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	2163						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			TTAATTGACATAAAGGAATAC	0.368																																						ENST00000274258.7																			0				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79						c.(3127-3129)ttA>ttT		chromosome 5 open reading frame 42							66.0	69.0	68.0					5																	37169637		2203	4300	6503	SO:0001583	missense	65250							g.chr5:37169637T>A		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.6489A>T	5.37:g.37169637T>A	ENSP00000421690:p.Leu2163Phe					C5orf42_ENST00000425232.2_Missense_Mutation_p.L2163F|C5orf42_ENST00000508244.1_Missense_Mutation_p.L2163F	p.L1043F			E9PH94	E9PH94_HUMAN	COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)		34	6716	-	all_lung(31;0.000616)		2163					A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	c.3129A>T	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	T	16.40	3.112594	0.56398	.	.	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	T;T;T;T	0.27402	1.71;1.71;1.67;1.69	5.39	-4.43	0.03568	.	1.265550	0.05870	N	0.624454	T	0.17408	0.0418	N	0.20986	0.625	0.09310	N	1	B;B	0.14438	0.005;0.01	B;B	0.11329	0.004;0.006	T	0.29941	-0.9995	10	0.45353	T	0.12	.	4.4666	0.11692	0.4596:0.2531:0.0:0.2873	.	2163;1043	E9PH94;Q9H799	.;CE042_HUMAN	F	2163;2163;1043;1211;1043	ENSP00000421690:L2163F;ENSP00000389014:L2163F;ENSP00000274258:L1043F;ENSP00000424223:L1211F	ENSP00000274258:L1043F	L	-	3	2	C5orf42	37205394	0.001000	0.12720	0.000000	0.03702	0.436000	0.31835	0.039000	0.13884	-0.668000	0.05296	0.533000	0.62120	TTA		0.368	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		40	63	0	0	0	0.117977	0	40	63				
KMT2A	4297	broad.mit.edu	37	11	118374769	118374769	+	Missense_Mutation	SNP	A	A	T			TCGA-DJ-A13P-01A-11D-A10S-08	TCGA-DJ-A13P-10A-01D-A10S-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d67fb1e-4411-4aca-8d9a-f76dad5e03fb	541aed7f-ed74-4214-b7d3-85c7dc551738	g.chr11:118374769A>T	ENST00000389506.5	+	27	8153	c.8153A>T	c.(8152-8154)gAt>gTt	p.D2718V	KMT2A_ENST00000534358.1_Missense_Mutation_p.D2721V|KMT2A_ENST00000354520.4_Missense_Mutation_p.D2680V			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	2718		Cleavage; by TASP1, site 2.			anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										TCACAGTTGGATGGTGTTGAT	0.428																																						ENST00000534358.1																			0											c.(8161-8163)gAt>gTt		lysine (K)-specific methyltransferase 2A							71.0	65.0	67.0					11																	118374769		2200	4296	6496	SO:0001583	missense	4297							g.chr11:118374769A>T	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7132	protein-coding gene	gene with protein product		159555	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)"", ""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"""	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.8153A>T	11.37:g.118374769A>T	ENSP00000374157:p.Asp2718Val					KMT2A_ENST00000354520.4_Missense_Mutation_p.D2680V|KMT2A_ENST00000389506.5_Missense_Mutation_p.D2718V	p.D2721V	NM_001197104.1|NM_005933.3	NP_001184033.1|NP_005924.2					27	8185	+								E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Missense_Mutation	SNP	ENST00000389506.5	37	c.8162A>T	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	A	13.60	2.287019	0.40494	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313	D;D;D	0.92595	-3.07;-3.07;-3.01	5.51	5.51	0.81932	.	0.098878	0.64402	D	0.000002	D	0.95401	0.8507	M	0.67569	2.06	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.95809	0.8840	10	0.87932	D	0	.	15.794	0.78394	1.0:0.0:0.0:0.0	.	2721;2718	E9PQG7;Q03164	.;MLL1_HUMAN	V	2721;2718;2680;1628	ENSP00000436786:D2721V;ENSP00000374157:D2718V;ENSP00000346516:D2680V	ENSP00000346516:D2680V	D	+	2	0	MLL	117879979	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	8.650000	0.91073	2.317000	0.78254	0.459000	0.35465	GAT		0.428	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		5	64	0	0	0	0.021553	0	5	64				
DLGAP3	58512	broad.mit.edu	37	1	35370150	35370151	+	Frame_Shift_Ins	INS	-	-	C			TCGA-DJ-A13P-01A-11D-A10S-08	TCGA-DJ-A13P-10A-01D-A10S-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d67fb1e-4411-4aca-8d9a-f76dad5e03fb	541aed7f-ed74-4214-b7d3-85c7dc551738	g.chr1:35370150_35370151insC	ENST00000373347.1	-	3	1102_1103	c.834_835insG	c.(832-837)aggcccfs	p.P279fs	DLGAP3_ENST00000495979.1_5'Flank|DLGAP3_ENST00000235180.4_Frame_Shift_Ins_p.P279fs			O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated protein 3	279					cell-cell signaling (GO:0007267)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)	beta-amyloid binding (GO:0001540)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(23)|ovary(4)|prostate(3)|skin(3)|urinary_tract(1)	46		Myeloproliferative disorder(586;0.0393)				TCCCCAGGGGGCCTCCCACCCG	0.673																																						ENST00000373347.1																			0				central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(23)|ovary(4)|prostate(3)|skin(3)|urinary_tract(1)	46						c.(832-837)agccccfs		discs, large (Drosophila) homolog-associated protein 3																																				SO:0001589	frameshift_variant	58512				cell-cell signaling	cell junction|postsynaptic density|postsynaptic membrane		g.chr1:35370150_35370151insC	AF131778	CCDS30670.1	1p35.3-p34.1	2008-02-05			ENSG00000116544	ENSG00000116544			30368	protein-coding gene	gene with protein product		611413				8619474, 9110174	Standard	NM_001080418		Approved	SAPAP3, DAP3	uc001byc.3	O95886	OTTHUMG00000004049	ENST00000373347.1:c.835dupG	1.37:g.35370152_35370152dupC	ENSP00000362444:p.Pro279fs					DLGAP3_ENST00000235180.4_Frame_Shift_Ins_p.S278fs	p.S278fs			O95886	DLGP3_HUMAN			3	1102_1103	-		Myeloproliferative disorder(586;0.0393)	278					Q5TDD5|Q9H3X7	Frame_Shift_Ins	INS	ENST00000373347.1	37	c.834_835insG	CCDS30670.1																																																																																				0.673	DLGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011554.1	NM_021234		7	162						7	162	---	---	---	---
LOC403323	403323	broad.mit.edu	37	9	66545695	66545695	+	lincRNA	DEL	A	A	-	rs368616794|rs199855162|rs56683069		TCGA-DJ-A13P-01A-11D-A10S-08	TCGA-DJ-A13P-10A-01D-A10S-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d67fb1e-4411-4aca-8d9a-f76dad5e03fb	541aed7f-ed74-4214-b7d3-85c7dc551738	g.chr9:66545695delA	ENST00000445604.2	-	0	669																											CTGTAAGAGGAAAAAAAAACA	0.373																																						ENST00000445604.2																			0																																																			0							g.chr9:66545695delA																													9.37:g.66545695delA														0	669	-									RNA	DEL	ENST00000445604.2	37																																																																																						0.373	RP11-262H14.3-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000037074.2			4	5						4	5	---	---	---	---
ZNF268	10795	broad.mit.edu	37	12	133780834	133780834	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DJ-A13P-01A-11D-A10S-08	TCGA-DJ-A13P-10A-01D-A10S-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d67fb1e-4411-4aca-8d9a-f76dad5e03fb	541aed7f-ed74-4214-b7d3-85c7dc551738	g.chr12:133780834delC	ENST00000536435.2	+	6	2892	c.2562delC	c.(2560-2562)cacfs	p.H854fs	ZNF268_ENST00000536899.2_3'UTR|ZNF268_ENST00000537565.1_Frame_Shift_Del_p.H693fs|ZNF268_ENST00000542986.2_3'UTR|ZNF268_ENST00000541009.2_3'UTR|ZNF268_ENST00000228289.5_Frame_Shift_Del_p.H854fs	NM_001165885.1|NM_003415.2	NP_001159357.1|NP_003406.1	Q14587	ZN268_HUMAN	zinc finger protein 268	854					cell differentiation (GO:0030154)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein heterodimerization activity (GO:0043497)|regulation of transcription, DNA-templated (GO:0006355)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(3)|endometrium(4)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(1)|skin(1)	24	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.000215)|all_epithelial(31;0.096)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		TTCTTGTACACCAGAGAATGC	0.413																																						ENST00000536435.2																			0				NS(2)|breast(3)|endometrium(4)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(1)|skin(1)	24						c.(2560-2562)cafs		zinc finger protein 268							142.0	138.0	139.0					12																	133780834		692	1591	2283	SO:0001589	frameshift_variant	10795					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr12:133780834delC	X78926	CCDS45012.1, CCDS53851.1, CCDS53852.1, CCDS53853.1, CCDS53854.1, CCDS59239.1, CCDS59240.1	12q24.33	2013-01-08				ENSG00000090612		"""Zinc fingers, C2H2-type"", ""-"""	13061	protein-coding gene	gene with protein product		604753				7865130	Standard	NM_003415		Approved	HZF3	uc010tcf.2	Q14587	OTTHUMG00000167946	ENST00000536435.2:c.2562delC	12.37:g.133780834delC	ENSP00000444412:p.His854fs					ZNF268_ENST00000536899.2_3'UTR|ZNF268_ENST00000541009.2_3'UTR|ZNF268_ENST00000228289.5_Frame_Shift_Del_p.H854fs|ZNF268_ENST00000542986.2_3'UTR|ZNF268_ENST00000537565.1_Frame_Shift_Del_p.H693fs	p.H854fs	NM_001165885.1|NM_003415.2	NP_001159357.1|NP_003406.1	Q14587	ZN268_HUMAN		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)	6	2892	+	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.000215)|all_epithelial(31;0.096)	854					Q8TDG8|Q96RH4|Q9BZJ9	Frame_Shift_Del	DEL	ENST00000536435.2	37	c.2562delC	CCDS45012.1																																																																																				0.413	ZNF268-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397191.2	NM_152943		2	4						2	4	---	---	---	---
CSPG4P5	114817	broad.mit.edu	37	15	84958415	84958426	+	RNA	DEL	CGAGGACATTGG	CGAGGACATTGG	-	rs535146949|rs548644616|rs373234755	byFrequency	TCGA-DJ-A13P-01A-11D-A10S-08	TCGA-DJ-A13P-10A-01D-A10S-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d67fb1e-4411-4aca-8d9a-f76dad5e03fb	541aed7f-ed74-4214-b7d3-85c7dc551738	g.chr15:84958415_84958426delCGAGGACATTGG	ENST00000558801.1	-	0	6303_6314									DNM1 pseudogene 51																		TCGGGCACCACGAGGACATTGGTGAGGACAGG	0.557														177	0.0353435	0.0015	0.0403	5008	,	,		20334	0.0198		0.0905	False		,,,				2504	0.0368					ENST00000558801.1																			0																																																			0							g.chr15:84958415_84958426delCGAGGACATTGG			15q25.2	2013-05-16			ENSG00000259297	ENSG00000235370			48500	pseudogene	pseudogene							Standard			Approved				OTTHUMG00000172438		15.37:g.84958415_84958426delCGAGGACATTGG														0	6303_6314	-									RNA	DEL	ENST00000558801.1	37																																																																																						0.557	DNM1P51-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000471721.1			5	6						5	6	---	---	---	---
RP11-266O8.1	0	broad.mit.edu	37	15	93976693	93976694	+	lincRNA	INS	-	-	GTGT	rs61308508|rs12899357|rs113111170		TCGA-DJ-A13P-01A-11D-A10S-08	TCGA-DJ-A13P-10A-01D-A10S-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d67fb1e-4411-4aca-8d9a-f76dad5e03fb	541aed7f-ed74-4214-b7d3-85c7dc551738	g.chr15:93976693_93976694insGTGT	ENST00000543286.1	+	0	545																											CCTAAAtgtgcgtgtgtgtgtg	0.475																																						ENST00000543286.1																			0																																																			0							g.chr15:93976693_93976694insGTGT																													15.37:g.93976698_93976701dupGTGT														0	545	+									RNA	INS	ENST00000543286.1	37																																																																																						0.475	RP11-266O8.1-003	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000415156.1			2	4						2	4	---	---	---	---
CDC27	996	broad.mit.edu	37	17	45219612	45219612	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DJ-A13P-01A-11D-A10S-08	TCGA-DJ-A13P-10A-01D-A10S-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d67fb1e-4411-4aca-8d9a-f76dad5e03fb	541aed7f-ed74-4214-b7d3-85c7dc551738	g.chr17:45219612delA	ENST00000066544.3	-	11	1454	c.1361delT	c.(1360-1362)ctafs	p.L454fs	CDC27_ENST00000446365.2_Frame_Shift_Del_p.L393fs|CDC27_ENST00000527547.1_Frame_Shift_Del_p.L454fs|CDC27_ENST00000531206.1_Frame_Shift_Del_p.L460fs	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	454					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TGCTTTTTGTAGATTAAAGGC	0.308																																						ENST00000066544.3																			0				NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						c.(1360-1362)cafs		cell division cycle 27							30.0	30.0	30.0					17																	45219612		2201	4295	6496	SO:0001589	frameshift_variant	996				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule	protein phosphatase binding	g.chr17:45219612delA	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.1361delT	17.37:g.45219612delA	ENSP00000066544:p.Leu454fs					CDC27_ENST00000531206.1_Frame_Shift_Del_p.L460fs|CDC27_ENST00000527547.1_Frame_Shift_Del_p.L454fs|CDC27_ENST00000446365.2_Frame_Shift_Del_p.L393fs	p.L454fs	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN			11	1454	-			454					G3V1C4|Q16349|Q96F35	Frame_Shift_Del	DEL	ENST00000066544.3	37	c.1361delT	CCDS11509.1																																																																																				0.308	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2			10	87						10	87	---	---	---	---
CTC-559E9.6	0	broad.mit.edu	37	19	19944580	19944580	+	RNA	DEL	T	T	-	rs372322378		TCGA-DJ-A13P-01A-11D-A10S-08	TCGA-DJ-A13P-10A-01D-A10S-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d67fb1e-4411-4aca-8d9a-f76dad5e03fb	541aed7f-ed74-4214-b7d3-85c7dc551738	g.chr19:19944580delT	ENST00000591884.1	+	0	520																											ATGTTTAATCttttttttttt	0.378																																						ENST00000591884.1																			0																																																			0							g.chr19:19944580delT																													19.37:g.19944580delT														0	520	+									RNA	DEL	ENST00000591884.1	37																																																																																						0.378	CTC-559E9.6-003	KNOWN	basic	antisense	processed_transcript	OTTHUMT00000460786.1			3	5						3	5	---	---	---	---
CD3EAP	10849	broad.mit.edu	37	19	45911859	45911861	+	In_Frame_Del	DEL	GAA	GAA	-			TCGA-DJ-A13P-01A-11D-A10S-08	TCGA-DJ-A13P-10A-01D-A10S-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d67fb1e-4411-4aca-8d9a-f76dad5e03fb	541aed7f-ed74-4214-b7d3-85c7dc551738	g.chr19:45911859_45911861delGAA	ENST00000309424.3	+	3	1121_1123	c.633_635delGAA	c.(631-636)cggaag>cgg	p.K217del	ERCC1_ENST00000300853.3_3'UTR|CD3EAP_ENST00000589804.1_In_Frame_Del_p.K219del|PPP1R13L_ENST00000418234.2_5'Flank|ERCC1_ENST00000423698.2_3'UTR|ERCC1_ENST00000588738.1_5'Flank	NM_012099.1	NP_036231.1	O15446	RPA34_HUMAN	CD3e molecule, epsilon associated protein	217	Poly-Lys.				rRNA transcription (GO:0009303)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|RNA polymerase I transcription factor complex (GO:0000120)	DNA-directed RNA polymerase activity (GO:0003899)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	11		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0251)		TGGATGTGCGGAAGAAGAAGAAG	0.581																																						ENST00000309424.3																			0				breast(2)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	11						c.(631-636)cgg>cg		CD3e molecule, epsilon associated protein			,,	0,144,4118		0,0,0,13,118,2000					,,	-5.6	0.0			66	5,183,8058		0,0,5,3,177,3938	no	codingComplex,utr-3,utr-3	ERCC1,CD3EAP	NM_012099.1,NM_001983.3,NM_001166049.1	,,	0,0,5,16,295,5938	A1A1,A1A2,A1R,A2A2,A2R,RR		2.2799,3.3787,2.6543	,,	,,		5,327,12176				SO:0001651	inframe_deletion	10849				rRNA transcription|transmembrane receptor protein tyrosine kinase signaling pathway	chromosome|RNA polymerase I transcription factor complex	DNA-directed RNA polymerase activity	g.chr19:45911859_45911861delGAA	U86751	CCDS12661.1, CCDS74397.1	19q13.3	2008-02-05	2006-03-28			ENSG00000117877			24219	protein-coding gene	gene with protein product	"""CD3 epsilon associated protein"", ""antisense to ERCC 1"""	107325	"""CD3e antigen, epsilon polypeptide associated protein"""			10373416, 9426281, 15226435	Standard	XM_005258425		Approved	ASE-1, CAST, PAF49	uc002pbq.1	O15446		ENST00000309424.3:c.633_635delGAA	19.37:g.45911868_45911870delGAA	ENSP00000310966:p.Lys217del					ERCC1_ENST00000423698.2_3'UTR|CD3EAP_ENST00000589804.1_In_Frame_Del_p.RK213del|ERCC1_ENST00000300853.3_3'UTR	p.RK211del	NM_012099.1	NP_036231.1	O15446	RPA34_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.0251)	3	1121_1123	+		all_neural(266;0.224)|Ovarian(192;0.231)	211					Q32N11|Q7Z5U2|Q9UPF6	In_Frame_Del	DEL	ENST00000309424.3	37	c.633_635delGAA	CCDS12661.1																																																																																				0.581	CD3EAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459538.1	NM_012099		7	220						7	220	---	---	---	---
SLC9B1P1	100128190	broad.mit.edu	37	Y	13501672	13501674	+	In_Frame_Del	DEL	AAT	AAT	-	rs373544976		TCGA-DJ-A13P-01A-11D-A10S-08	TCGA-DJ-A13P-10A-01D-A10S-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	2d67fb1e-4411-4aca-8d9a-f76dad5e03fb	541aed7f-ed74-4214-b7d3-85c7dc551738	g.chrY:13501672_13501674delAAT	ENST00000331172.6	-	4	534_536	c.535_537delATT	c.(535-537)attdel	p.I179del				A6NJY1	SL9P1_HUMAN	solute carrier family 9, subfamily B (NHA1, cation proton antiporter 1), member 1 pseudogene 1	164						integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)										TCTTACCAACAATATTTGATTCA	0.241																																						ENST00000331172.6																			0											c.(535-537)del																																						SO:0001651	inframe_deletion	0							g.chrY:13501672_13501674delAAT			Yq11.21	2013-07-15	2012-03-22	2011-07-26	ENSG00000183704	ENSG00000183704		"""Solute carriers"""	37492	pseudogene	pseudogene			"""Na+/H+ exchanger domain containing 1 pseudogene 1"", ""solute carrier family 9, subfamily B (cation proton antiporter 2), member 1 pseudogene 1"""	NHEDC1P1			Standard	NG_023008		Approved			A6NJY1		ENST00000331172.6:c.535_537delATT	Y.37:g.13501672_13501674delAAT	ENSP00000331938:p.Ile179del						p.I179del							4	534_536	-									In_Frame_Del	DEL	ENST00000331172.6	37	c.535_537delATT																																																																																					0.241	SLC9B1P1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NG_023008		5	2						5	2	---	---	---	---
