#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
JUP	3728	broad.mit.edu	37	17	39915087	39915087	+	Silent	SNP	G	G	A			TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr17:39915087G>A	ENST00000393931.3	-	9	1651	c.1533C>T	c.(1531-1533)tgC>tgT	p.C511C	JUP_ENST00000310706.5_Silent_p.C511C|JUP_ENST00000393930.1_Silent_p.C511C|JUP_ENST00000540235.1_Intron	NM_002230.2	NP_002221.1	P14923	PLAK_HUMAN	junction plakoglobin	511					adherens junction organization (GO:0034332)|atrioventricular valve morphogenesis (GO:0003181)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell-cell junction organization (GO:0045216)|cellular response to indole-3-methanol (GO:0071681)|cytoskeletal anchoring at plasma membrane (GO:0007016)|desmosome assembly (GO:0002159)|detection of mechanical stimulus (GO:0050982)|ectoderm development (GO:0007398)|endothelial cell-cell adhesion (GO:0071603)|establishment of protein localization to plasma membrane (GO:0090002)|gastrulation (GO:0007369)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of Wnt signaling pathway involved in heart development (GO:0003308)|nervous system development (GO:0007399)|oocyte development (GO:0048599)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein heterooligomerization (GO:0051291)|regulation of cell proliferation (GO:0042127)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|skin development (GO:0043588)|ventricular cardiac muscle cell action potential (GO:0086005)	actin cytoskeleton (GO:0015629)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|gamma-catenin-TCF7L2 complex (GO:0071665)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|cadherin binding (GO:0045296)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|structural constituent of cell wall (GO:0005199)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)	23		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)		GGTTGGCTGGGCACAGGGCCA	0.622																																					Colon(16;42 520 6044 17852 28530)	ENST00000393931.3																			0				breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)	23						c.(1531-1533)tgC>tgT		junction plakoglobin							28.0	30.0	29.0					17																	39915087		2203	4300	6503	SO:0001819	synonymous_variant	3728				adherens junction organization|atrioventricular valve morphogenesis|cell migration|cell morphogenesis|cellular response to indole-3-methanol|cytoskeletal anchoring at plasma membrane|detection of mechanical stimulus|ectoderm development|endothelial cell-cell adhesion|gastrulation|morphogenesis of embryonic epithelium|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of Wnt receptor signaling pathway involved in heart development|nervous system development|oocyte development|positive regulation of protein import into nucleus|positive regulation of sequence-specific DNA binding transcription factor activity|skin development	actin cytoskeleton|Axin-APC-beta-catenin-GSK3B complex|basolateral plasma membrane|catenin complex|desmosome|fascia adherens|gamma-catenin-TCF7L2 complex|internal side of plasma membrane|nucleus|protein-DNA complex|Z disc|zonula adherens	alpha-catenin binding|cadherin binding|protein homodimerization activity|protein kinase binding|protein phosphatase binding|RPTP-like protein binding|specific RNA polymerase II transcription factor activity|transcription coactivator activity	g.chr17:39915087G>A	AF233882	CCDS11407.1	17q21	2014-09-17	2004-08-09		ENSG00000173801	ENSG00000173801		"""Armadillo repeat containing"""	6207	protein-coding gene	gene with protein product		173325	"""catenin (cadherin-associated protein), gamma 80kDa"""	CTNNG		1889810, 7604000	Standard	NM_021991		Approved	DP3, PDGB, PKGB, DPIII	uc002hxs.2	P14923	OTTHUMG00000133494	ENST00000393931.3:c.1533C>T	17.37:g.39915087G>A						JUP_ENST00000310706.5_Silent_p.C511C|JUP_ENST00000393930.1_Silent_p.C511C|JUP_ENST00000540235.1_Intron	p.C511C	NM_002230.2	NP_002221.1	P14923	PLAK_HUMAN	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)	9	1651	-		Breast(137;0.000162)	511					Q15093|Q15151|Q7L3S5|Q86W21|Q9BWC4|Q9HCX9	Silent	SNP	ENST00000393931.3	37	c.1533C>T	CCDS11407.1																																																																																				0.622	JUP-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257406.1			3	11	0	0	0	1	0	3	11				
SLX4	84464	broad.mit.edu	37	16	3639059	3639059	+	Missense_Mutation	SNP	G	G	A	rs149362820	byFrequency	TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr16:3639059G>A	ENST00000294008.3	-	12	5220	c.4580C>T	c.(4579-4581)cCg>cTg	p.P1527L		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	1527	Interaction with MUS81.|Interaction with PLK1 and TERF2-TERF2IP.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						CATCTGGGCCGGAGGAGGGGT	0.622								Direct reversal of damage																														ENST00000294008.3																			0				breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						c.(4579-4581)cCg>cTg	Direct reversal of damage	SLX4 structure-specific endonuclease subunit		G	LEU/PRO	1,4393	2.1+/-5.4	0,1,2196	78.0	92.0	87.0		4580	-11.1	0.0	16	dbSNP_134	87	0,8600		0,0,4300	no	missense	SLX4	NM_032444.2	98	0,1,6496	AA,AG,GG		0.0,0.0228,0.0077	benign	1527/1835	3639059	1,12993	2197	4300	6497	SO:0001583	missense	84464				DNA double-strand break processing involved in repair via single-strand annealing|double-strand break repair via homologous recombination|nucleotide-excision repair	Slx1-Slx4 complex	enzyme activator activity|protein binding	g.chr16:3639059G>A	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.4580C>T	16.37:g.3639059G>A	ENSP00000294008:p.Pro1527Leu						p.P1527L	NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN			12	5220	-			1527			Interaction with MUS81.|Interaction with PLK1 and TERF2-TERF2IP.		Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	c.4580C>T	CCDS10506.2	.	.	.	.	.	.	.	.	.	.	G	9.261	1.043181	0.19748	2.28E-4	0.0	ENSG00000188827	ENST00000294008	T	0.00832	5.64	5.56	-11.1	0.00147	.	1.094360	0.07130	N	0.845311	T	0.00356	0.0011	N	0.03154	-0.405	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.47837	-0.9086	10	0.02654	T	1	.	4.1615	0.10285	0.2232:0.2975:0.3825:0.0968	.	1527	Q8IY92	SLX4_HUMAN	L	1527	ENSP00000294008:P1527L	ENSP00000294008:P1527L	P	-	2	0	SLX4	3579060	0.008000	0.16893	0.000000	0.03702	0.000000	0.00434	0.081000	0.14823	-2.737000	0.00381	-1.140000	0.01884	CCG		0.622	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444		4	190	0	0	0	1	0	4	190				
ZCCHC5	203430	broad.mit.edu	37	X	77912605	77912605	+	Missense_Mutation	SNP	C	C	T	rs369311059		TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chrX:77912605C>T	ENST00000321110.1	-	2	1608	c.1313G>A	c.(1312-1314)cGt>cAt	p.R438H		NM_152694.2	NP_689907.1	Q8N8U3	ZCHC5_HUMAN	zinc finger, CCHC domain containing 5	438							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(1)|prostate(1)|skin(1)	37						TTTGTGCCAACGGACCCATTC	0.547																																						ENST00000321110.1																			0				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(1)|prostate(1)|skin(1)	37						c.(1312-1314)cGt>cAt		zinc finger, CCHC domain containing 5		C	HIS/ARG	2,3833		0,2,1630,571	136.0	103.0	114.0		1313	-2.2	0.0	X		114	0,6728		0,0,2428,1872	no	missense	ZCCHC5	NM_152694.2	29	0,2,4058,2443	TT,TC,CC,C		0.0,0.0522,0.0189	benign	438/476	77912605	2,10561	2203	4300	6503	SO:0001583	missense	203430						nucleic acid binding|zinc ion binding	g.chrX:77912605C>T	AK096184	CCDS14440.1	Xq13.3	2008-02-05			ENSG00000179300	ENSG00000179300		"""Zinc fingers, CCHC domain containing"""	22997	protein-coding gene	gene with protein product						15716091, 16093683	Standard	NM_152694		Approved	FLJ38865, Mar3, Mart3, ZHC5	uc004edc.1	Q8N8U3	OTTHUMG00000021892	ENST00000321110.1:c.1313G>A	X.37:g.77912605C>T	ENSP00000316794:p.Arg438His						p.R438H	NM_152694.2	NP_689907.1	Q8N8U3	ZCHC5_HUMAN			2	1608	-			438					B2RMZ0|Q5JQE9	Missense_Mutation	SNP	ENST00000321110.1	37	c.1313G>A	CCDS14440.1	.	.	.	.	.	.	.	.	.	.	C	0.038	-1.298223	0.01364	5.22E-4	0.0	ENSG00000179300	ENST00000321110	T	0.25749	1.78	3.2	-2.2	0.06994	.	.	.	.	.	T	0.16385	0.0394	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21109	-1.0255	9	0.44086	T	0.13	.	8.1248	0.30992	0.0:0.4658:0.0:0.5342	.	438	Q8N8U3	ZCHC5_HUMAN	H	438	ENSP00000316794:R438H	ENSP00000316794:R438H	R	-	2	0	ZCCHC5	77799261	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.973000	0.03798	-0.802000	0.04421	-1.585000	0.00851	CGT		0.547	ZCCHC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057319.1	NM_152694		9	23	0	0	0	1	0	9	23				
GH1	2688	broad.mit.edu	37	17	61995130	61995130	+	Missense_Mutation	SNP	G	G	A			TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr17:61995130G>A	ENST00000323322.5	-	4	488	c.446C>T	c.(445-447)aCg>aTg	p.T149M	GH1_ENST00000342364.4_Intron|GH1_ENST00000458650.2_Missense_Mutation_p.T134M|CSHL1_ENST00000392824.4_Intron|GH1_ENST00000351388.4_Missense_Mutation_p.T109M	NM_000515.3	NP_000506.2	P01241	SOMA_HUMAN	growth hormone 1	149					bone maturation (GO:0070977)|glucose transport (GO:0015758)|growth hormone receptor signaling pathway (GO:0060396)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|response to estradiol (GO:0032355)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)|growth hormone receptor binding (GO:0005131)|metal ion binding (GO:0046872)|prolactin receptor binding (GO:0005148)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)	19						CCCCATCAGCGTTTGGATGCC	0.567																																						ENST00000323322.5																			0				breast(3)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)	19						c.(445-447)aCg>aTg		growth hormone 1							64.0	66.0	65.0					17																	61995130		2203	4300	6503	SO:0001583	missense	2688				glucose transport|growth hormone receptor signaling pathway|JAK-STAT cascade|positive regulation of activation of JAK2 kinase activity|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of MAP kinase activity|positive regulation of multicellular organism growth|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|response to estradiol stimulus	extracellular space	growth factor activity|growth hormone receptor binding|hormone activity|metal ion binding|prolactin receptor binding	g.chr17:61995130G>A	M13438	CCDS11653.1, CCDS11654.1, CCDS45760.1	17q22-q24	2014-01-30				ENSG00000259384		"""Endogenous ligands"""	4261	protein-coding gene	gene with protein product	"""pituitary growth hormone"", ""somatotropin"""	139250				6306568	Standard	XM_005257218		Approved	GH-N, GHN, GH, hGH-N	uc002jdj.3	P01241		ENST00000323322.5:c.446C>T	17.37:g.61995130G>A	ENSP00000312673:p.Thr149Met					GH1_ENST00000458650.2_Missense_Mutation_p.T134M|CSHL1_ENST00000392824.4_Intron|GH1_ENST00000351388.4_Missense_Mutation_p.T109M|GH1_ENST00000342364.4_Intron	p.T149M	NM_000515.3	NP_000506.2	P01241	SOMA_HUMAN			4	488	-			149					A6NEF6|Q14405|Q16631|Q5EB53|Q9HBZ1|Q9UMJ7|Q9UNL5	Missense_Mutation	SNP	ENST00000323322.5	37	c.446C>T	CCDS11653.1	.	.	.	.	.	.	.	.	.	.	g	12.26	1.885264	0.33255	.	.	ENSG00000204414	ENST00000323322;ENST00000458650;ENST00000351388	D;D;D	0.90844	-2.2;-2.2;-2.74	2.86	2.86	0.33363	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.335977	0.30820	N	0.008804	D	0.92414	0.7592	M	0.76727	2.345	0.80722	D	1	P;D;D	0.76494	0.905;0.999;0.999	B;P;P	0.55011	0.223;0.766;0.766	D	0.92625	0.6111	10	0.62326	D	0.03	.	11.5436	0.50679	0.0:0.0:1.0:0.0	.	109;149;134	A6NEF6;P01241;B1A4G7	.;SOMA_HUMAN;.	M	149;134;109	ENSP00000312673:T149M;ENSP00000408486:T134M;ENSP00000343791:T109M	ENSP00000312673:T149M	T	-	2	0	GH1	59348862	1.000000	0.71417	0.815000	0.32552	0.069000	0.16628	4.820000	0.62671	1.594000	0.50039	0.298000	0.19748	ACG		0.567	GH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417708.1	NM_000515		5	79	0	0	0	1	0	5	79				
RPL10A	4736	broad.mit.edu	37	6	35437258	35437258	+	Nonsense_Mutation	SNP	G	G	T	rs11266793		TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr6:35437258G>T	ENST00000322203.6	+	4	289	c.262G>T	c.(262-264)Gag>Tag	p.E88*	RPL10A_ENST00000467020.1_3'UTR	NM_007104.4	NP_009035.3	P62906	RL10A_HUMAN	ribosomal protein L10a	88					anatomical structure morphogenesis (GO:0009653)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|large_intestine(2)|ovary(1)	4						CATGGACATCGAGGCGCTGAA	0.552																																						ENST00000322203.6																			0				breast(1)|large_intestine(2)|ovary(1)	4						c.(262-264)Gag>Tag		ribosomal protein L10a							45.0	46.0	46.0					6																	35437258		2203	4300	6503	SO:0001587	stop_gained	4736				anatomical structure morphogenesis|endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosol|large ribosomal subunit	RNA binding|structural constituent of ribosome	g.chr6:35437258G>T	U12404	CCDS4806.1	6p21.31	2011-04-06			ENSG00000198755	ENSG00000198755		"""L ribosomal proteins"""	10299	protein-coding gene	gene with protein product		615660		NEDD6		7609734, 9647638	Standard	NM_007104		Approved	Csa-19, L10A	uc003okp.1	P62906	OTTHUMG00000014566	ENST00000322203.6:c.262G>T	6.37:g.35437258G>T	ENSP00000363018:p.Glu88*					RPL10A_ENST00000467020.1_3'UTR	p.E88*	NM_007104.4	NP_009035.3	P62906	RL10A_HUMAN			4	289	+			88					B2R801|P52859|P53025|Q5TZT6|Q8J013	Nonsense_Mutation	SNP	ENST00000322203.6	37	c.262G>T	CCDS4806.1	.	.	.	.	.	.	.	.	.	.	G	34	5.412615	0.96072	.	.	ENSG00000198755	ENST00000322203	.	.	.	4.88	4.88	0.63580	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	16.623	0.84934	0.0:0.0:1.0:0.0	rs11266793	.	.	.	X	88	.	ENSP00000363018:E88X	E	+	1	0	RPL10A	35545236	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.791000	0.99081	2.255000	0.74692	0.455000	0.32223	GAG		0.552	RPL10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040283.1	NM_007104		9	22	1	0	0.000442599	1	0.000469424	9	22				
USP33	23032	broad.mit.edu	37	1	78187835	78187835	+	Missense_Mutation	SNP	G	G	T			TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr1:78187835G>T	ENST00000370793.1	-	14	1875	c.1529C>A	c.(1528-1530)cCt>cAt	p.P510H	USP33_ENST00000357428.1_Missense_Mutation_p.P510H|USP33_ENST00000370794.3_Missense_Mutation_p.P479H|USP33_ENST00000370792.3_Missense_Mutation_p.P510H	NM_015017.4	NP_055832.3	Q8TEY7	UBP33_HUMAN	ubiquitin specific peptidase 33	510	USP.				axon guidance (GO:0007411)|cell migration (GO:0016477)|centrosome duplication (GO:0051298)|endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell body (GO:0044297)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|VCB complex (GO:0030891)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|prostate(2)|urinary_tract(1)	44						TTCCTTGCCAGGAATTGGCAA	0.408																																					Melanoma(152;72 1870 11110 26780 42647)	ENST00000370793.1																			0				breast(1)|central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|prostate(2)|urinary_tract(1)	44						c.(1528-1530)cCt>cAt		ubiquitin specific peptidase 33							103.0	100.0	101.0					1																	78187835		2203	4300	6503	SO:0001583	missense	23032				axon guidance|cell migration|endocytosis|protein K48-linked deubiquitination|protein K63-linked deubiquitination|regulation of G-protein coupled receptor protein signaling pathway|ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm|VCB complex	cysteine-type endopeptidase activity|G-protein-coupled receptor binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding	g.chr1:78187835G>T	AF383173	CCDS678.1, CCDS679.1, CCDS680.1	1p31	2008-02-05	2005-08-08		ENSG00000077254	ENSG00000077254		"""Ubiquitin-specific peptidases"""	20059	protein-coding gene	gene with protein product		615146	"""ubiquitin specific protease 33"""			12838346	Standard	NM_015017		Approved	KIAA1097, VDU1	uc001dht.4	Q8TEY7	OTTHUMG00000009651	ENST00000370793.1:c.1529C>A	1.37:g.78187835G>T	ENSP00000359829:p.Pro510His					USP33_ENST00000370792.3_Missense_Mutation_p.P510H|USP33_ENST00000370794.3_Missense_Mutation_p.P479H|USP33_ENST00000357428.1_Missense_Mutation_p.P510H	p.P510H	NM_015017.4	NP_055832.3	Q8TEY7	UBP33_HUMAN			14	1875	-			510					Q8TEY6|Q96AV6|Q9H9F0|Q9UPQ5	Missense_Mutation	SNP	ENST00000370793.1	37	c.1529C>A	CCDS678.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.5|24.5	4.538009|4.538009	0.85917|0.85917	.|.	.|.	ENSG00000077254|ENSG00000077254	ENST00000481579|ENST00000370794;ENST00000370793;ENST00000357428;ENST00000370792	.|T;T;T;T	.|0.38077	.|3.85;1.16;1.16;3.85	5.0|5.0	5.0|5.0	0.66597|0.66597	.|Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.55784|0.55784	0.1942|0.1942	M|M	0.75447|0.75447	2.3|2.3	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.91635	.|0.998;0.998;0.999	T|T	0.59958|0.59958	-0.7356|-0.7356	5|10	.|0.62326	.|D	.|0.03	.|.	18.6877|18.6877	0.91571|0.91571	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|510;479;510	.|Q8TEY7-3;Q8TEY7-2;Q8TEY7	.|.;.;UBP33_HUMAN	M|H	115|479;510;510;510	.|ENSP00000359830:P479H;ENSP00000359829:P510H;ENSP00000350009:P510H;ENSP00000359828:P510H	.|ENSP00000350009:P510H	L|P	-|-	1|2	2|0	USP33|USP33	77960423|77960423	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	9.476000|9.476000	0.97823|0.97823	2.494000|2.494000	0.84150|0.84150	0.467000|0.467000	0.42956|0.42956	CTG|CCT		0.408	USP33-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000026923.2	NM_015017		6	92	1	0	5.9392e-07	1	6.496e-07	6	92				
SLFN5	162394	broad.mit.edu	37	17	33592770	33592770	+	Nonsense_Mutation	SNP	C	C	T	rs146569957		TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr17:33592770C>T	ENST00000299977.4	+	5	2687	c.2539C>T	c.(2539-2541)Cga>Tga	p.R847*	SLFN5_ENST00000542451.1_3'UTR	NM_144975.3	NP_659412.3	Q08AF3	SLFN5_HUMAN	schlafen family member 5	847					cell differentiation (GO:0030154)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(8)|liver(2)|lung(6)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	34		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0191)		CAGTGTCTGTCGATTTTCAGG	0.493																																						ENST00000299977.4																			0				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(8)|liver(2)|lung(6)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	34						c.(2539-2541)Cga>Tga		schlafen family member 5							81.0	76.0	77.0					17																	33592770		2203	4300	6503	SO:0001587	stop_gained	162394				cell differentiation		ATP binding	g.chr17:33592770C>T	BX647942	CCDS32619.1	17q12	2006-04-05				ENSG00000166750			28286	protein-coding gene	gene with protein product		614952				9846487	Standard	NM_144975		Approved	MGC19764	uc002hjf.4	Q08AF3		ENST00000299977.4:c.2539C>T	17.37:g.33592770C>T	ENSP00000299977:p.Arg847*					SLFN5_ENST00000542451.1_3'UTR	p.R847*	NM_144975.3	NP_659412.3	Q08AF3	SLFN5_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (308;0.0191)	5	2687	+		Ovarian(249;0.17)	847					Q08AF2|Q8WU54|Q96A82	Nonsense_Mutation	SNP	ENST00000299977.4	37	c.2539C>T	CCDS32619.1	.	.	.	.	.	.	.	.	.	.	c	37	6.464966	0.97590	.	.	ENSG00000166750	ENST00000299977	.	.	.	3.28	1.07	0.20283	.	0.282623	0.19067	N	0.123584	.	.	.	.	.	.	0.21719	N	0.999573	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.6604	0.28400	0.4591:0.5408:0.0:0.0	.	.	.	.	X	847	.	ENSP00000299977:R847X	R	+	1	2	SLFN5	30616883	0.000000	0.05858	0.256000	0.24389	0.509000	0.34042	0.076000	0.14712	0.167000	0.19631	0.655000	0.94253	CGA		0.493	SLFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448649.2	NM_144975		7	63	0	0	0	1	0	7	63				
RTF1	23168	broad.mit.edu	37	15	41769659	41769659	+	Silent	SNP	C	C	T			TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr15:41769659C>T	ENST00000389629.4	+	14	1698	c.1686C>T	c.(1684-1686)taC>taT	p.Y562Y		NM_015138.4	NP_055953.3	Q92541	RTF1_HUMAN	Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	562					DNA-templated transcription, initiation (GO:0006352)|endodermal cell fate commitment (GO:0001711)|histone H3-K4 trimethylation (GO:0080182)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|single-stranded DNA binding (GO:0003697)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)	18		all_cancers(109;1.79e-19)|all_epithelial(112;8.18e-17)|Lung NSC(122;3.16e-11)|all_lung(180;8.14e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;1.15e-16)|GBM - Glioblastoma multiforme(113;1.81e-06)|BRCA - Breast invasive adenocarcinoma(123;0.119)		CCCACAGTTACATCAACCAGC	0.458																																						ENST00000389629.4																			0				central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)	18						c.(1684-1686)taC>taT		Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)							114.0	109.0	111.0					15																	41769659		2203	4300	6503	SO:0001819	synonymous_variant	23168				histone modification|regulation of transcription, DNA-dependent|transcription initiation, DNA-dependent	nucleoplasm	protein binding|single-stranded DNA binding	g.chr15:41769659C>T	D87440	CCDS32200.2	15q14	2004-03-03	2005-07-20	2005-07-20	ENSG00000137815	ENSG00000137815			28996	protein-coding gene	gene with protein product		611633	"""KIAA0252"""	KIAA0252		15632063	Standard	NM_015138		Approved		uc001zny.3	Q92541	OTTHUMG00000133744	ENST00000389629.4:c.1686C>T	15.37:g.41769659C>T							p.Y562Y	NM_015138.4	NP_055953.3	Q92541	RTF1_HUMAN		OV - Ovarian serous cystadenocarcinoma(18;1.15e-16)|GBM - Glioblastoma multiforme(113;1.81e-06)|BRCA - Breast invasive adenocarcinoma(123;0.119)	14	1698	+		all_cancers(109;1.79e-19)|all_epithelial(112;8.18e-17)|Lung NSC(122;3.16e-11)|all_lung(180;8.14e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)	562					Q96BX6	Silent	SNP	ENST00000389629.4	37	c.1686C>T	CCDS32200.2																																																																																				0.458	RTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258111.1	NM_015138		22	64	0	0	0	1	0	22	64				
SLC12A1	6557	broad.mit.edu	37	15	48527104	48527104	+	Missense_Mutation	SNP	G	G	A	rs150258541		TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr15:48527104G>A	ENST00000558405.1	+	8	1132	c.1118G>A	c.(1117-1119)cGc>cAc	p.R373H	SLC12A1_ENST00000380993.3_Missense_Mutation_p.R373H|SLC12A1_ENST00000330289.6_Missense_Mutation_p.R373H|SLC12A1_ENST00000559723.1_3'UTR|SLC12A1_ENST00000396577.3_Missense_Mutation_p.R373H			Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1	373					cell death (GO:0008219)|chemical homeostasis (GO:0048878)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|kidney development (GO:0001822)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:potassium:chloride symporter activity (GO:0008511)	p.R373H(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1)	59		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Potassium Chloride(DB00761)|Quinethazone(DB01325)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	TTTGGGCCACGCTTCACAAAG	0.393													G|||	1	0.000199681	0.0	0.0	5008	,	,		17317	0.0		0.001	False		,,,				2504	0.0					ENST00000396577.3																			1	Substitution - Missense(1)	p.R373H(1)	large_intestine(1)	NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1)	59						c.(1117-1119)cGc>cAc		solute carrier family 12 (sodium/potassium/chloride transporter), member 1	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Metolazone(DB00524)|Potassium Chloride(DB00761)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	G	HIS/ARG,HIS/ARG	0,4396		0,0,2198	97.0	100.0	99.0		1118,1118	3.2	1.0	15	dbSNP_134	99	4,8590	3.7+/-12.6	0,4,4293	yes	missense,missense	SLC12A1	NM_000338.2,NM_001184832.1	29,29	0,4,6491	AA,AG,GG		0.0465,0.0,0.0308	benign,benign	373/1100,373/1100	48527104	4,12986	2198	4297	6495	SO:0001583	missense	6557				potassium ion transport|sodium ion transport	integral to membrane|membrane fraction	sodium:potassium:chloride symporter activity	g.chr15:48527104G>A		CCDS10129.2, CCDS53940.1	15q15-q21	2013-07-18	2013-07-18		ENSG00000074803	ENSG00000074803		"""Solute carriers"""	10910	protein-coding gene	gene with protein product		600839				8640224	Standard	NM_000338		Approved	NKCC2	uc010bem.3	Q13621	OTTHUMG00000131495	ENST00000558405.1:c.1118G>A	15.37:g.48527104G>A	ENSP00000453409:p.Arg373His					SLC12A1_ENST00000559723.1_3'UTR|SLC12A1_ENST00000558405.1_Missense_Mutation_p.R373H|SLC12A1_ENST00000330289.6_Missense_Mutation_p.R373H|SLC12A1_ENST00000380993.3_Missense_Mutation_p.R373H	p.R373H	NM_001184832.1	NP_001171761.1	Q13621	S12A1_HUMAN		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	9	1333	+		all_lung(180;0.00219)	373					A8JYA2|E9PDW4	Missense_Mutation	SNP	ENST00000558405.1	37	c.1118G>A	CCDS10129.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	15.66	2.899566	0.52227	0.0	4.65E-4	ENSG00000074803	ENST00000428362;ENST00000380993;ENST00000396577;ENST00000330289	D;D;D	0.98747	-5.11;-5.11;-5.11	5.06	3.16	0.36331	Amino acid permease domain (1);	0.150320	0.56097	D	0.000021	D	0.92489	0.7615	N	0.02674	-0.535	0.24190	N	0.995552	B;B;B	0.29085	0.02;0.232;0.126	B;B;B	0.29598	0.029;0.104;0.099	D	0.88249	0.2915	10	0.87932	D	0	.	5.3133	0.15843	0.4013:0.0:0.5987:0.0	.	373;373;373	Q8IUN5;E9PDW4;Q13621	.;.;S12A1_HUMAN	H	186;373;373;373	ENSP00000370381:R373H;ENSP00000379822:R373H;ENSP00000331550:R373H	ENSP00000331550:R373H	R	+	2	0	SLC12A1	46314396	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.706000	0.47135	1.270000	0.44297	0.467000	0.42956	CGC		0.393	SLC12A1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417131.1			5	47	0	0	0	1	0	5	47				
SCFD1	23256	broad.mit.edu	37	14	31097463	31097463	+	Missense_Mutation	SNP	G	G	A			TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr14:31097463G>A	ENST00000458591.2	+	2	337	c.110G>A	c.(109-111)aGc>aAc	p.S37N	SCFD1_ENST00000421551.3_Missense_Mutation_p.A8T|SCFD1_ENST00000541123.1_5'UTR|SCFD1_ENST00000544052.2_Intron|SCFD1_ENST00000396629.2_Intron	NM_016106.3	NP_057190.2	Q8WVM8	SCFD1_HUMAN	sec1 family domain containing 1	37					post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|regulation of ER to Golgi vesicle-mediated transport (GO:0060628)|response to hypoxia (GO:0001666)|response to toxic substance (GO:0009636)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle docking involved in exocytosis (GO:0006904)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|Golgi transport complex (GO:0017119)|Golgi-associated vesicle (GO:0005798)|plasma membrane (GO:0005886)	syntaxin binding (GO:0019905)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)	13	Hepatocellular(127;0.0877)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)	GBM - Glioblastoma multiforme(265;0.0181)		ATTAAAAACAGCACAGGAGAA	0.318																																						ENST00000458591.2																			0				endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)	13						c.(109-111)aGc>aAc		sec1 family domain containing 1							98.0	101.0	100.0					14																	31097463		2203	4299	6502	SO:0001583	missense	23256				post-Golgi vesicle-mediated transport|protein transport|regulation of ER to Golgi vesicle-mediated transport|response to toxin|retrograde vesicle-mediated transport, Golgi to ER|vesicle docking involved in exocytosis	cis-Golgi network|endoplasmic reticulum membrane|Golgi cisterna membrane|Golgi-associated vesicle|plasma membrane	syntaxin-5 binding	g.chr14:31097463G>A	AF110646	CCDS9639.1, CCDS45092.1, CCDS58308.1	14q12	2006-04-04	2004-01-15	2004-01-16	ENSG00000092108	ENSG00000092108			20726	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 163"""	C14orf163			Standard	NM_016106		Approved	RA410, KIAA0917, STXBP1L2, SLY1	uc001wqm.2	Q8WVM8	OTTHUMG00000029420	ENST00000458591.2:c.110G>A	14.37:g.31097463G>A	ENSP00000390783:p.Ser37Asn					SCFD1_ENST00000544052.2_Intron|SCFD1_ENST00000421551.3_Missense_Mutation_p.A8T|SCFD1_ENST00000396629.2_Intron|SCFD1_ENST00000541123.1_5'UTR	p.S37N	NM_016106.3	NP_057190.2	Q8WVM8	SCFD1_HUMAN	LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)	GBM - Glioblastoma multiforme(265;0.0181)	2	337	+	Hepatocellular(127;0.0877)		37					A8K2Z5|B7Z4U7|B7Z594|O60754|O94990|Q7Z529|Q9BZI3|Q9UNL3|Q9Y6A8	Missense_Mutation	SNP	ENST00000458591.2	37	c.110G>A	CCDS9639.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.21|12.21	1.871056|1.871056	0.33069|0.33069	.|.	.|.	ENSG00000092108|ENSG00000092108	ENST00000421551|ENST00000458591;ENST00000557076	D|T;T	0.82984|0.29142	-1.67|1.67;1.58	5.54|5.54	4.46|4.46	0.54185|0.54185	.|.	.|0.100816	.|0.64402	.|D	.|0.000004	T|T	0.16128|0.16128	0.0388|0.0388	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	P|B	0.35527|0.02656	0.507|0.0	B|B	0.30495|0.04013	0.116|0.001	T|T	0.08066|0.08066	-1.0740|-1.0740	9|10	0.29301|0.18276	T|T	0.29|0.48	-25.2101|-25.2101	14.3584|14.3584	0.66752|0.66752	0.0837:0.0:0.9163:0.0|0.0837:0.0:0.9163:0.0	.|.	8|37	B7Z738|Q8WVM8	.|SCFD1_HUMAN	T|N	8|37;12	ENSP00000388078:A8T|ENSP00000390783:S37N;ENSP00000450755:S12N	ENSP00000388078:A8T|ENSP00000309417:S45N	A|S	+|+	1|2	0|0	SCFD1|SCFD1	30167214|30167214	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.962000|0.962000	0.63368|0.63368	4.551000|4.551000	0.60740|0.60740	2.601000|2.601000	0.87937|0.87937	0.655000|0.655000	0.94253|0.94253	GCA|AGC		0.318	SCFD1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276612.3	NM_182835		15	65	0	0	0	1	0	15	65				
MACF1	23499	broad.mit.edu	37	1	39750842	39750842	+	Missense_Mutation	SNP	A	A	T			TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr1:39750842A>T	ENST00000372915.3	+	11	1321	c.1234A>T	c.(1234-1236)Atg>Ttg	p.M412L	MACF1_ENST00000545844.1_Missense_Mutation_p.M412L|MACF1_ENST00000539005.1_Missense_Mutation_p.M412L|MACF1_ENST00000567887.1_Missense_Mutation_p.M444L|MACF1_ENST00000361689.2_Missense_Mutation_p.M412L|MACF1_ENST00000317713.7_Missense_Mutation_p.M412L|MACF1_ENST00000564288.1_Missense_Mutation_p.M407L			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	412					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			CATCATAGAGATGCTGGAACG	0.473																																						ENST00000564288.1																			0				breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203						c.(1219-1221)Atg>Ttg		microtubule-actin crosslinking factor 1							157.0	154.0	155.0					1																	39750842		2203	4300	6503	SO:0001583	missense	23499				cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding	g.chr1:39750842A>T	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"""EF-hand domain containing"""	13664	protein-coding gene	gene with protein product	"""actin cross-linking factor"", ""620 kDa actin binding protein"", ""macrophin 1"", ""trabeculin-alpha"", ""actin cross-linking family protein 7"""	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.1234A>T	1.37:g.39750842A>T	ENSP00000362006:p.Met412Leu					MACF1_ENST00000372915.3_Missense_Mutation_p.M412L|MACF1_ENST00000539005.1_Missense_Mutation_p.M412L|MACF1_ENST00000545844.1_Missense_Mutation_p.M412L|MACF1_ENST00000361689.2_Missense_Mutation_p.M412L|MACF1_ENST00000567887.1_Missense_Mutation_p.M444L|MACF1_ENST00000317713.7_Missense_Mutation_p.M412L	p.M407L			Q9UPN3	MACF1_HUMAN	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)		12	1996	+	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	412					B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37	c.1219A>T		.	.	.	.	.	.	.	.	.	.	A	19.05	3.751208	0.69533	.	.	ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000524432;ENST00000530262;ENST00000372900	T;T;T;T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19;-0.19;-0.19;-0.19	5.82	5.82	0.92795	.	.	.	.	.	T	0.64571	0.2610	M	0.80422	2.495	0.80722	D	1	B;B	0.28880	0.001;0.226	B;B	0.29524	0.001;0.103	T	0.62450	-0.6852	9	0.17832	T	0.49	.	16.1814	0.81903	1.0:0.0:0.0:0.0	.	412;377	F8W8Q1;Q9UPN3-3	.;.	L	412;412;412;412;412;370;561;572	ENSP00000439537:M412L;ENSP00000362006:M412L;ENSP00000354573:M412L;ENSP00000313438:M412L;ENSP00000444364:M412L;ENSP00000435070:M370L;ENSP00000437059:M561L	ENSP00000313438:M412L	M	+	1	0	MACF1	39523429	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.339000	0.96797	2.234000	0.73211	0.533000	0.62120	ATG		0.473	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		26	82	0	0	0	1	0	26	82				
MLLT3	4300	broad.mit.edu	37	9	20414280	20414280	+	Silent	SNP	G	G	A			TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr9:20414280G>A	ENST00000380338.4	-	5	850	c.564C>T	c.(562-564)agC>agT	p.S188S	MLLT3_ENST00000475957.1_5'UTR|MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S185S	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3	188	Poly-Ser.				anterior/posterior pattern specification (GO:0009952)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of transcription, DNA-templated (GO:0006355)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)		p.S188S(1)		central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		TGGTActactgctgctgctgc	0.502			T	MLL	ALL																																	ENST00000380338.4				Dom	yes		9	9p22	4300	T	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 (AF9)"""			L	MLL		ALL		1	Substitution - coding silent(1)	p.S188S(1)	large_intestine(1)	central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66						c.(562-564)agC>agT		myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3							77.0	84.0	82.0					9																	20414280		2203	4300	6503	SO:0001819	synonymous_variant	4300				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding	g.chr9:20414280G>A	L13744	CCDS6494.1	9p22	2008-02-05	2001-11-28		ENSG00000171843	ENSG00000171843			7136	protein-coding gene	gene with protein product		159558	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 3"""			8506309, 8414510	Standard	NM_001286691		Approved	AF-9, AF9, YEATS3	uc003zoe.2	P42568	OTTHUMG00000019650	ENST00000380338.4:c.564C>T	9.37:g.20414280G>A						MLLT3_ENST00000475957.1_5'UTR|MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S185S	p.S188S	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN		GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)	5	850	-			188			Poly-Ser.		B1AMQ2|B2R7B3|B7Z755|D3DRJ8|Q8IVB0	Silent	SNP	ENST00000380338.4	37	c.564C>T	CCDS6494.1																																																																																				0.502	MLLT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051872.1	NM_004529		4	166	0	0	0	1	0	4	166				
PHF14	9678	broad.mit.edu	37	7	11075358	11075358	+	Missense_Mutation	SNP	C	C	T			TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr7:11075358C>T	ENST00000403050.3	+	8	1999	c.1547C>T	c.(1546-1548)tCc>tTc	p.S516F	PHF14_ENST00000445996.2_Missense_Mutation_p.S231F	NM_014660.3	NP_055475.2	O94880	PHF14_HUMAN	PHD finger protein 14	516					lung alveolus development (GO:0048286)|negative regulation of mesenchymal cell proliferation involved in lung development (GO:2000791)|negative regulation of platelet-derived growth factor receptor-alpha signaling pathway (GO:2000584)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(2)|breast(1)|endometrium(4)|kidney(5)|large_intestine(5)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	35				UCEC - Uterine corpus endometrioid carcinoma (126;0.205)		GCTCTACAGTCCTATTGTAAA	0.368																																						ENST00000403050.3																			0				NS(2)|breast(1)|endometrium(4)|kidney(5)|large_intestine(5)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	35						c.(1546-1548)tCc>tTc		PHD finger protein 14							186.0	183.0	184.0					7																	11075358		1861	4103	5964	SO:0001583	missense	9678						zinc ion binding	g.chr7:11075358C>T	AB018326	CCDS47542.1	7p21.3	2013-01-28			ENSG00000106443	ENSG00000106443		"""Zinc fingers, PHD-type"""	22203	protein-coding gene	gene with protein product						9872452	Standard	NM_014660		Approved	KIAA0783	uc003sry.2	O94880	OTTHUMG00000150463	ENST00000403050.3:c.1547C>T	7.37:g.11075358C>T	ENSP00000385795:p.Ser516Phe					PHF14_ENST00000445996.2_Missense_Mutation_p.S231F	p.S516F	NM_014660.3	NP_055475.2	O94880	PHF14_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (126;0.205)	8	1999	+			516					A7MCZ3|B4DI82	Missense_Mutation	SNP	ENST00000403050.3	37	c.1547C>T	CCDS47542.1	.	.	.	.	.	.	.	.	.	.	C	16.76	3.211509	0.58343	.	.	ENSG00000106443	ENST00000403050;ENST00000445996	T;T	0.71579	-0.22;-0.58	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	T	0.76615	0.4012	N	0.19112	0.55	0.80722	D	1	D;D;D;D	0.71674	0.994;0.99;0.998;0.998	D;D;D;D	0.78314	0.989;0.974;0.991;0.991	T	0.77872	-0.2426	10	0.54805	T	0.06	.	20.4581	0.99154	0.0:1.0:0.0:0.0	.	231;231;516;516	O94880-2;B4DG57;A8MSQ1;O94880	.;.;.;PHF14_HUMAN	F	516;231	ENSP00000385795:S516F;ENSP00000403907:S231F	ENSP00000385795:S516F	S	+	2	0	PHF14	11041883	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.800000	0.85949	2.835000	0.97688	0.650000	0.86243	TCC		0.368	PHF14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318212.1	NM_014660		37	135	0	0	0	1	0	37	135				
OR5P2	120065	broad.mit.edu	37	11	7817803	7817803	+	Silent	SNP	C	C	T			TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr11:7817803C>T	ENST00000329434.2	-	1	717	c.687G>A	c.(685-687)ggG>ggA	p.G229G	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	229						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CCTTGTGGTGCCCCTCAGTGG	0.483																																						ENST00000329434.2																			0				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22						c.(685-687)ggG>ggA		olfactory receptor, family 5, subfamily P, member 2							115.0	117.0	116.0					11																	7817803		2104	4292	6396	SO:0001819	synonymous_variant	120065				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:7817803C>T	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.687G>A	11.37:g.7817803C>T						RP11-35J10.5_ENST00000527565.1_lincRNA	p.G229G	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN		Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	1	717	-			229					Q3MIS8	Silent	SNP	ENST00000329434.2	37	c.687G>A	CCDS7782.1																																																																																				0.483	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444		4	74	0	0	0	1	0	4	74				
TNFAIP6	7130	broad.mit.edu	37	2	152222683	152222683	+	Missense_Mutation	SNP	C	C	T	rs373227124		TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr2:152222683C>T	ENST00000243347.3	+	3	421	c.346C>T	c.(346-348)Cgt>Tgt	p.R116C	MIR4773-1_ENST00000585225.1_RNA	NM_007115.3	NP_009046.2	P98066	TSG6_HUMAN	tumor necrosis factor, alpha-induced protein 6	116	Link. {ECO:0000255|PROSITE- ProRule:PRU00323}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|inflammatory response (GO:0006954)|signal transduction (GO:0007165)		hyaluronic acid binding (GO:0005540)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.131)	Hyaluronan(DB08818)	TTATGGAATCCGTCTCAATAG	0.428																																						ENST00000243347.3																			0				endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13						c.(346-348)Cgt>Tgt		tumor necrosis factor, alpha-induced protein 6		C	CYS/ARG	0,4406		0,0,2203	117.0	113.0	115.0		346	5.2	1.0	2		115	1,8599	1.2+/-3.3	0,1,4299	no	missense	TNFAIP6	NM_007115.3	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	116/278	152222683	1,13005	2203	4300	6503	SO:0001583	missense	7130				cell adhesion|cell-cell signaling|inflammatory response|signal transduction		hyaluronic acid binding	g.chr2:152222683C>T		CCDS2193.1	2q23.3	2008-11-18			ENSG00000123610	ENSG00000123610			11898	protein-coding gene	gene with protein product		600410				1730767, 8568267, 15060082	Standard	NM_007115		Approved	TSG6, TSG-6	uc002txk.3	P98066	OTTHUMG00000131884	ENST00000243347.3:c.346C>T	2.37:g.152222683C>T	ENSP00000243347:p.Arg116Cys						p.R116C	NM_007115.3	NP_009046.2	P98066	TSG6_HUMAN		BRCA - Breast invasive adenocarcinoma(221;0.131)	3	421	+			116			Link.		Q53TI7|Q8WWI9	Missense_Mutation	SNP	ENST00000243347.3	37	c.346C>T	CCDS2193.1	.	.	.	.	.	.	.	.	.	.	C	14.22	2.470789	0.43942	0.0	1.16E-4	ENSG00000123610	ENST00000243347	T	0.35421	1.31	5.15	5.15	0.70609	C-type lectin fold (1);Link (3);C-type lectin-like (1);	0.000000	0.85682	D	0.000000	T	0.72053	0.3413	H	0.94423	3.535	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.80935	-0.1160	10	0.72032	D	0.01	.	18.9653	0.92694	0.0:1.0:0.0:0.0	.	116	P98066	TSG6_HUMAN	C	116	ENSP00000243347:R116C	ENSP00000243347:R116C	R	+	1	0	TNFAIP6	151930929	1.000000	0.71417	0.998000	0.56505	0.082000	0.17680	4.539000	0.60657	2.526000	0.85167	0.563000	0.77884	CGT		0.428	TNFAIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254834.2	NM_007115		16	56	0	0	0	1	0	16	56				
BMS1P20	96610	broad.mit.edu	37	22	22663087	22663087	+	RNA	SNP	A	A	G	rs1054158|rs71318762	byFrequency	TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr22:22663087A>G	ENST00000426066.1	+	0	526					NR_027293.1				BMS1 pseudogene 20																		GCTGCCACATAAGTTGTCCTT	0.303													.|||	3161	0.63119	0.9652	0.4726	5008	,	,		8984	0.4077		0.5219	False		,,,				2504	0.635					ENST00000426066.1																			0																																																			0							g.chr22:22663087A>G			22q11.22	2013-09-20			ENSG00000236850	ENSG00000236850			49153	pseudogene	pseudogene							Standard	XR_430414		Approved				OTTHUMG00000151046		22.37:g.22663087A>G								NR_027293.1						0	526	+									RNA	SNP	ENST00000426066.1	37																																																																																						0.303	BMS1P20-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000473090.1			4	40	0	0	0	1	0	4	40				
CDH23	64072	broad.mit.edu	37	10	73544680	73544680	+	Silent	SNP	C	C	T			TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr10:73544680C>T	ENST00000224721.6	+	42	5555	c.5550C>T	c.(5548-5550)aaC>aaT	p.N1850N		NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	1845	Cadherin 17. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						TGGACATCAACGACAACGACC	0.597																																						ENST00000224721.6																			0				NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						c.(5548-5550)aaC>aaT		cadherin-related 23							84.0	89.0	87.0					10																	73544680		2184	4279	6463	SO:0001819	synonymous_variant	64072				calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding	g.chr10:73544680C>T	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.5550C>T	10.37:g.73544680C>T							p.N1850N	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN			42	5555	+			1845			Cadherin 17.		C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	37	c.5550C>T																																																																																					0.597	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		12	27	0	0	0	1	0	12	27				
C17orf47	284083	broad.mit.edu	37	17	56620062	56620062	+	Missense_Mutation	SNP	G	G	A			TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr17:56620062G>A	ENST00000321691.3	-	1	1667	c.1486C>T	c.(1486-1488)Cca>Tca	p.P496S	RP11-112H10.4_ENST00000578022.1_RNA|RP11-112H10.4_ENST00000580589.1_RNA|SEPT4_ENST00000412945.3_5'Flank|SEPT4_ENST00000457347.2_5'Flank|RP11-112H10.4_ENST00000580769.1_RNA	NM_001038704.2	NP_001033793	Q8NEP4	CQ047_HUMAN	chromosome 17 open reading frame 47	496										NS(1)|breast(2)|endometrium(1)|kidney(4)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	24	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TCACTCAGTGGTGCCCAACTT	0.493																																						ENST00000321691.3																			0				NS(1)|breast(2)|endometrium(1)|kidney(4)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	24						c.(1486-1488)Cca>Tca		chromosome 17 open reading frame 47							251.0	253.0	253.0					17																	56620062		2203	4300	6503	SO:0001583	missense	284083							g.chr17:56620062G>A		CCDS32691.1	17q23.2	2012-10-11			ENSG00000181013	ENSG00000181013			26844	protein-coding gene	gene with protein product							Standard	NM_001038704		Approved	FLJ40121	uc002iwq.2	Q8NEP4	OTTHUMG00000179244	ENST00000321691.3:c.1486C>T	17.37:g.56620062G>A	ENSP00000354874:p.Pro496Ser					RP11-112H10.4_ENST00000580769.1_RNA|RP11-112H10.4_ENST00000578022.1_RNA|RP11-112H10.4_ENST00000580589.1_RNA	p.P496S	NM_001038704.2	NP_001033793.2	Q8NEP4	CQ047_HUMAN			1	1667	-	Medulloblastoma(34;0.127)|all_neural(34;0.237)		496					Q8N821	Missense_Mutation	SNP	ENST00000321691.3	37	c.1486C>T	CCDS32691.1	.	.	.	.	.	.	.	.	.	.	G	2.887	-0.230423	0.05983	.	.	ENSG00000181013	ENST00000321691	T	0.31510	1.49	5.6	0.954	0.19595	.	0.428023	0.22489	N	0.059400	T	0.17109	0.0411	L	0.29908	0.895	0.09310	N	1	P	0.41393	0.748	B	0.40101	0.319	T	0.06899	-1.0801	10	0.30078	T	0.28	-5.9125	3.1278	0.06413	0.3059:0.0:0.5045:0.1896	.	496	Q8NEP4	CQ047_HUMAN	S	496	ENSP00000354874:P496S	ENSP00000354874:P496S	P	-	1	0	C17orf47	53975061	0.000000	0.05858	0.114000	0.21550	0.051000	0.14879	0.488000	0.22371	0.741000	0.32674	-0.258000	0.10820	CCA		0.493	C17orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445443.1	NM_001038704		17	330	0	0	0	1	0	17	330				
HEATR6	63897	broad.mit.edu	37	17	58143748	58143748	+	Splice_Site	SNP	C	C	T			TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr17:58143748C>T	ENST00000184956.6	-	9	1255		c.e9-1		HEATR6_ENST00000585976.1_Splice_Site	NM_022070.4	NP_071353.4	Q6AI08	HEAT6_HUMAN	HEAT repeat containing 6								poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	44	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)			TTGGTAAGACCTTTCATAACC	0.284																																						ENST00000184956.6																			0				NS(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	44						c.e9-1		HEAT repeat containing 6							34.0	36.0	35.0					17																	58143748		2202	4299	6501	SO:0001630	splice_region_variant	63897						binding	g.chr17:58143748C>T	BX640819	CCDS11623.1	17q23.2	2007-05-01				ENSG00000068097			24076	protein-coding gene	gene with protein product	"""amplified in breast cancer 1"""					12755490	Standard	NM_022070		Approved	ABC1, FLJ22087	uc002iyk.1	Q6AI08		ENST00000184956.6:c.1239-1G>A	17.37:g.58143748C>T						HEATR6_ENST00000585976.1_Splice_Site		NM_022070.4	NP_071353.4	Q6AI08	HEAT6_HUMAN	BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)		9	1255	-	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)							B3KXP3|Q6MZX1|Q6MZY2|Q8TDM9|Q9H6B3|Q9H6M7	Splice_Site	SNP	ENST00000184956.6	37		CCDS11623.1	.	.	.	.	.	.	.	.	.	.	.	23.1	4.371763	0.82573	.	.	ENSG00000068097	ENST00000184956;ENST00000393017	.	.	.	5.81	5.81	0.92471	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.5152	0.95160	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	HEATR6	55498530	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	7.067000	0.76741	2.937000	0.99478	0.650000	0.86243	.		0.284	HEATR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449165.1	NM_022070	Intron	5	19	0	0	0	1	0	5	19				
PIP5K1B	8395	broad.mit.edu	37	9	71509360	71509360	+	Missense_Mutation	SNP	C	C	T			TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr9:71509360C>T	ENST00000265382.3	+	8	882	c.577C>T	c.(577-579)Cca>Tca	p.P193S	PIP5K1B_ENST00000541509.1_Missense_Mutation_p.P193S	NM_003558.2	NP_003549.1	O14986	PI51B_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type I, beta	193	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)|uropod (GO:0001931)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)			breast(1)|large_intestine(2)|stomach(1)	4				Lung(182;0.133)		CAACGTTTTGCCACGCTCCAT	0.408																																						ENST00000265382.3																			0				breast(1)|large_intestine(2)|stomach(1)	4						c.(577-579)Cca>Tca		phosphatidylinositol-4-phosphate 5-kinase, type I, beta							99.0	89.0	92.0					9																	71509360		2203	4300	6503	SO:0001583	missense	8395					endomembrane system|membrane|uropod	1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|protein binding	g.chr9:71509360C>T	U78579	CCDS6624.1, CCDS65063.1	9q13	2008-02-05			ENSG00000107242	ENSG00000107242			8995	protein-coding gene	gene with protein product		602745				9177790, 8841185	Standard	NM_003558		Approved	STM7, MSS4	uc004agu.4	O14986	OTTHUMG00000019976	ENST00000265382.3:c.577C>T	9.37:g.71509360C>T	ENSP00000265382:p.Pro193Ser					PIP5K1B_ENST00000541509.1_Missense_Mutation_p.P193S	p.P193S	NM_003558.2	NP_003549.1	O14986	PI51B_HUMAN		Lung(182;0.133)	8	882	+			193			PIPK.		A8K9L9|B4DIG7|P78518|P78519|Q5T5K6|Q5T5K8|Q5T5K9|Q5VZ00|Q7KYT5|Q8NHQ5|Q92749	Missense_Mutation	SNP	ENST00000265382.3	37	c.577C>T	CCDS6624.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.110538	0.77210	.	.	ENSG00000107242	ENST00000541509;ENST00000377290;ENST00000265382;ENST00000419747	T;T	0.35421	1.31;1.31	5.82	5.82	0.92795	Phosphatidylinositol-4-phosphate 5-kinase, core (2);Phosphatidylinositol-4-phosphate 5-kinase, core, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.52757	0.1754	M	0.64676	1.99	0.80722	D	1	P	0.37423	0.594	P	0.48334	0.574	T	0.51521	-0.8695	10	0.87932	D	0	-14.2947	20.1143	0.97922	0.0:1.0:0.0:0.0	.	193	O14986	PI51B_HUMAN	S	193;193;193;140	ENSP00000438082:P193S;ENSP00000265382:P193S	ENSP00000265382:P193S	P	+	1	0	PIP5K1B	70699180	1.000000	0.71417	0.539000	0.28077	0.963000	0.63663	7.669000	0.83911	2.765000	0.95021	0.650000	0.86243	CCA		0.408	PIP5K1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052561.2	NM_003558		4	101	0	0	0	1	0	4	101				
BMS1P20	96610	broad.mit.edu	37	22	22663086	22663086	+	RNA	SNP	T	T	G	rs1054157|rs71318762	byFrequency	TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr22:22663086T>G	ENST00000426066.1	+	0	525					NR_027293.1				BMS1 pseudogene 20																		AGCTGCCACATAAGTTGTCCT	0.299													.|||	3161	0.63119	0.9652	0.4726	5008	,	,		9186	0.4077		0.5219	False		,,,				2504	0.635					ENST00000426066.1																			0																																																			0							g.chr22:22663086T>G			22q11.22	2013-09-20			ENSG00000236850	ENSG00000236850			49153	pseudogene	pseudogene							Standard	XR_430414		Approved				OTTHUMG00000151046		22.37:g.22663086T>G								NR_027293.1						0	525	+									RNA	SNP	ENST00000426066.1	37																																																																																						0.299	BMS1P20-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000473090.1			4	41	0	0	0	1	0	4	41				
MTMR6	9107	broad.mit.edu	37	13	25848214	25848214	+	Missense_Mutation	SNP	T	T	C			TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr13:25848214T>C	ENST00000381801.5	-	2	897	c.136A>G	c.(136-138)Acc>Gcc	p.T46A	MTMR6_ENST00000540661.1_Missense_Mutation_p.T46A	NM_004685.3	NP_004676.3	Q9Y217	MTMR6_HUMAN	myotubularin related protein 6	46					peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|potassium ion transmembrane transport (GO:0071805)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	calcium-activated potassium channel activity (GO:0015269)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(5)|stomach(3)	36		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.00927)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.164)		CTTACCCAGGTTTCTTTTTGA	0.338																																						ENST00000381801.5																			0				breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(5)|stomach(3)	36						c.(136-138)Acc>Gcc		myotubularin related protein 6							122.0	121.0	122.0					13																	25848214		2203	4300	6503	SO:0001583	missense	9107					cytoplasm|nuclear envelope	calcium-activated potassium channel activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity	g.chr13:25848214T>C	AF072928	CCDS9313.1	13q12	2011-06-09			ENSG00000139505	ENSG00000139505		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7453	protein-coding gene	gene with protein product		603561				9736772	Standard	NM_004685		Approved		uc001uqf.4	Q9Y217	OTTHUMG00000016606	ENST00000381801.5:c.136A>G	13.37:g.25848214T>C	ENSP00000371221:p.Thr46Ala					MTMR6_ENST00000540661.1_Missense_Mutation_p.T46A	p.T46A	NM_004685.3	NP_004676.3	Q9Y217	MTMR6_HUMAN		all cancers(112;0.00927)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.164)	2	897	-		Lung SC(185;0.0225)|Breast(139;0.0351)	46					B2RBB5|B3KSB4|Q5JRG6|Q86TB7|Q86YH4|Q96P80	Missense_Mutation	SNP	ENST00000381801.5	37	c.136A>G	CCDS9313.1	.	.	.	.	.	.	.	.	.	.	T	13.05	2.121574	0.37436	.	.	ENSG00000139505	ENST00000540661;ENST00000541021;ENST00000381801	D;D	0.82081	-1.57;-1.57	5.17	5.17	0.71159	Pleckstrin homology-type (1);	0.051129	0.85682	D	0.000000	D	0.84316	0.5445	M	0.85630	2.765	0.80722	D	1	B;B	0.12013	0.003;0.005	B;B	0.18561	0.021;0.022	T	0.81174	-0.1053	10	0.27082	T	0.32	.	15.305	0.73985	0.0:0.0:0.0:1.0	.	46;46	Q9Y217;Q9Y217-2	MTMR6_HUMAN;.	A	46	ENSP00000443161:T46A;ENSP00000371221:T46A	ENSP00000371221:T46A	T	-	1	0	MTMR6	24746214	1.000000	0.71417	1.000000	0.80357	0.451000	0.32288	4.226000	0.58606	2.075000	0.62263	0.482000	0.46254	ACC		0.338	MTMR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044225.1	NM_004685		27	73	0	0	0	1	0	27	73				
FAM86EP	348926	broad.mit.edu	37	4	3948570	3948570	+	RNA	SNP	G	G	T	rs191853620	byFrequency	TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr4:3948570G>T	ENST00000313946.8	-	0	1232				AC226119.5_ENST00000281228.8_RNA					family with sequence similarity 86, member E, pseudogene																		GGAGCCCGCTGGTGCTCCCGG	0.622																																						ENST00000281228.8																			0																																																			0							g.chr4:3948570G>T			4p16.3	2011-07-01			ENSG00000251669	ENSG00000251669			28017	pseudogene	pseudogene						12477932	Standard	NR_024253		Approved		uc011bvu.2		OTTHUMG00000159867		4.37:g.3948570G>T						FAM86EP_ENST00000313946.8_RNA								0	815	-									RNA	SNP	ENST00000313946.8	37																																																																																						0.622	FAM86EP-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000357822.1			3	52	1	0	0.004672	1	0.00480941	3	52				
AADAT	51166	broad.mit.edu	37	4	170988533	170988533	+	Missense_Mutation	SNP	T	T	C	rs368676033		TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr4:170988533T>C	ENST00000337664.4	-	9	1183	c.907A>G	c.(907-909)Ata>Gta	p.I303V	AADAT_ENST00000509167.1_Missense_Mutation_p.I307V|AADAT_ENST00000353187.2_Missense_Mutation_p.I303V|AADAT_ENST00000515480.1_Missense_Mutation_p.I303V	NM_016228.3	NP_057312.1	Q8N5Z0	AADAT_HUMAN	aminoadipate aminotransferase	303					2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|kynurenine metabolic process (GO:0070189)|L-kynurenine metabolic process (GO:0097052)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	mitochondrial matrix (GO:0005759)	2-aminoadipate transaminase activity (GO:0047536)|kynurenine-oxoglutarate transaminase activity (GO:0016212)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|pancreas(1)|stomach(1)	11		Prostate(90;0.00601)|Renal(120;0.0183)|all_neural(102;0.122)|Melanoma(52;0.17)		GBM - Glioblastoma multiforme(119;0.0355)|LUSC - Lung squamous cell carcinoma(193;0.118)		AGCTGTGATATCATGAGCTAA	0.333																																						ENST00000337664.4																			0				breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|pancreas(1)|stomach(1)	11						c.(907-909)Ata>Gta		aminoadipate aminotransferase	L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)						80.0	78.0	79.0					4																	170988533		2203	4300	6503	SO:0001583	missense	51166				2-oxoglutarate metabolic process|biosynthetic process|glutamate metabolic process|lysine catabolic process	mitochondrial matrix	2-aminoadipate transaminase activity|kynurenine-oxoglutarate transaminase activity|protein homodimerization activity	g.chr4:170988533T>C	AF097994	CCDS3814.1, CCDS75209.1	4q33	2010-12-09			ENSG00000109576	ENSG00000109576	2.6.1.39		17929	protein-coding gene	gene with protein product	"""kynurenine aminotransferase II"", ""L kynurenine/alpha aminoadipate aminotransferase"""	611754				12126930, 10441733	Standard	NM_182662		Approved	KATII, KAT2	uc003isr.3	Q8N5Z0	OTTHUMG00000160912	ENST00000337664.4:c.907A>G	4.37:g.170988533T>C	ENSP00000336808:p.Ile303Val					AADAT_ENST00000353187.2_Missense_Mutation_p.I303V|AADAT_ENST00000509167.1_Missense_Mutation_p.I307V|AADAT_ENST00000515480.1_Missense_Mutation_p.I303V	p.I303V	NM_016228.3	NP_057312.1	Q8N5Z0	AADAT_HUMAN		GBM - Glioblastoma multiforme(119;0.0355)|LUSC - Lung squamous cell carcinoma(193;0.118)	9	1183	-		Prostate(90;0.00601)|Renal(120;0.0183)|all_neural(102;0.122)|Melanoma(52;0.17)	303					B3KP84|Q9UL02	Missense_Mutation	SNP	ENST00000337664.4	37	c.907A>G	CCDS3814.1	.	.	.	.	.	.	.	.	.	.	T	1.656	-0.512739	0.04200	.	.	ENSG00000109576	ENST00000337664;ENST00000515480;ENST00000509167;ENST00000353187	D;D;D;D	0.88975	-2.45;-2.45;-2.45;-2.45	5.8	-3.64	0.04515	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.321314	0.36703	N	0.002444	T	0.70263	0.3204	N	0.04820	-0.15	0.21802	N	0.99953	B;B	0.02656	0.0;0.0	B;B	0.09377	0.003;0.004	T	0.57940	-0.7724	10	0.02654	T	1	-9.224	15.3238	0.74144	0.0:0.2187:0.0:0.7813	.	307;303	Q8N5Z0-2;Q8N5Z0	.;AADAT_HUMAN	V	303;303;307;303	ENSP00000336808:I303V;ENSP00000423341:I303V;ENSP00000423190:I307V;ENSP00000226840:I303V	ENSP00000336808:I303V	I	-	1	0	AADAT	171225108	0.061000	0.20836	0.003000	0.11579	0.239000	0.25481	-0.444000	0.06854	-0.550000	0.06183	0.460000	0.39030	ATA		0.333	AADAT-004	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000362952.1	NM_016228		14	35	0	0	0	1	0	14	35				
KDM5A	5927	broad.mit.edu	37	12	416835	416835	+	Missense_Mutation	SNP	G	G	A			TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr12:416835G>A	ENST00000399788.2	-	23	4077	c.3715C>T	c.(3715-3717)Cgg>Tgg	p.R1239W	KDM5A_ENST00000382815.4_Missense_Mutation_p.R1239W	NM_001042603.1	NP_001036068.1	P29375	KDM5A_HUMAN	lysine (K)-specific demethylase 5A	1239					chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|multicellular organismal development (GO:0007275)|negative regulation of histone deacetylase activity (GO:1901726)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.R1239W(2)		NS(2)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(29)|ovary(1)|prostate(5)|skin(6)|stomach(1)|urinary_tract(2)	77						TCAGGCAACCGTACGGGCAAC	0.512			T	NUP98	AML																																	ENST00000399788.2				Dom	yes		12	12p11	5927	T	"""lysine (K)-specific demethylase 5A, JARID1A"""			L	NUP98		AML		2	Substitution - Missense(2)	p.R1239W(2)	large_intestine(2)	NS(2)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(29)|ovary(1)|prostate(5)|skin(6)|stomach(1)|urinary_tract(2)	77						c.(3715-3717)Cgg>Tgg		lysine (K)-specific demethylase 5A							76.0	76.0	76.0					12																	416835		1921	4126	6047	SO:0001583	missense	5927				chromatin modification|multicellular organismal development|positive regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	cytoplasm|nucleolus	DNA binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr12:416835G>A		CCDS41736.1	12p13.33	2013-01-28	2009-04-06	2009-04-06	ENSG00000073614	ENSG00000073614		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	9886	protein-coding gene	gene with protein product		180202	"""retinoblastoma-binding protein 2"", ""Jumonji, AT rich interactive domain 1A (RBBP2-like)"", ""jumonji, AT rich interactive domain 1A"""	RBBP2, JARID1A		1857421	Standard	NM_001042603		Approved		uc001qif.1	P29375	OTTHUMG00000168055	ENST00000399788.2:c.3715C>T	12.37:g.416835G>A	ENSP00000382688:p.Arg1239Trp					KDM5A_ENST00000382815.4_Missense_Mutation_p.R1239W	p.R1239W	NM_001042603.1	NP_001036068.1	P29375	KDM5A_HUMAN			23	4077	-			1239					A8MV76|Q4LE72|Q86XZ1	Missense_Mutation	SNP	ENST00000399788.2	37	c.3715C>T	CCDS41736.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.011070	0.75046	.	.	ENSG00000073614	ENST00000399788;ENST00000382815	T;T	0.01209	5.17;5.17	5.66	4.71	0.59529	.	0.000000	0.85682	D	0.000000	T	0.05044	0.0135	L	0.56199	1.76	0.58432	D	0.999999	D;D	0.67145	0.993;0.996	P;D	0.68353	0.832;0.957	T	0.34551	-0.9824	10	0.87932	D	0	-14.4907	15.3118	0.74039	0.0:0.0:0.8315:0.1685	.	1239;1239	P29375;P29375-2	KDM5A_HUMAN;.	W	1239	ENSP00000382688:R1239W;ENSP00000372265:R1239W	ENSP00000372265:R1239W	R	-	1	2	KDM5A	287096	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	3.803000	0.55560	1.354000	0.45846	0.585000	0.79938	CGG		0.512	KDM5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397812.1	NM_005056		3	54	0	0	0	1	0	3	54				
KRT12	3859	broad.mit.edu	37	17	39021060	39021060	+	Missense_Mutation	SNP	C	C	A			TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr17:39021060C>A	ENST00000251643.4	-	3	828	c.805G>T	c.(805-807)Gat>Tat	p.D269Y	RP5-1110E20.1_ENST00000579136.1_RNA	NM_000223.3	NP_000214.1	Q99456	K1C12_HUMAN	keratin 12	269	Coil 1B.|Rod.				visual perception (GO:0007601)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(2)	15		Breast(137;0.000301)			Griseofulvin(DB00400)	TGACTCACATCCTCGTGGTTC	0.507																																						ENST00000251643.4																			0				central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(2)	15						c.(805-807)Gat>Tat		keratin 12							110.0	110.0	110.0					17																	39021060		2203	4300	6503	SO:0001583	missense	3859				visual perception	intermediate filament	structural molecule activity	g.chr17:39021060C>A		CCDS11378.1	17q21.2	2013-06-20	2008-08-01		ENSG00000187242	ENSG00000187242		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6414	protein-coding gene	gene with protein product	"""Meesmann corneal dystrophy"""	601687				9171831, 16831889	Standard	NM_000223		Approved	K12	uc002hvk.2	Q99456	OTTHUMG00000133369	ENST00000251643.4:c.805G>T	17.37:g.39021060C>A	ENSP00000251643:p.Asp269Tyr						p.D269Y	NM_000223.3	NP_000214.1	Q99456	K1C12_HUMAN			3	828	-		Breast(137;0.000301)	269			Coil 1B.|Rod.		B2R9E0	Missense_Mutation	SNP	ENST00000251643.4	37	c.805G>T	CCDS11378.1	.	.	.	.	.	.	.	.	.	.	C	16.75	3.208733	0.58343	.	.	ENSG00000187242	ENST00000251643	T	0.80393	-1.37	5.96	5.96	0.96718	Filament (1);	0.152024	0.30584	N	0.009310	T	0.80691	0.4671	L	0.55213	1.73	0.37334	D	0.91011	P	0.43938	0.822	B	0.41174	0.349	D	0.84518	0.0626	10	0.87932	D	0	.	20.422	0.99049	0.0:1.0:0.0:0.0	.	269	Q99456	K1C12_HUMAN	Y	269	ENSP00000251643:D269Y	ENSP00000251643:D269Y	D	-	1	0	KRT12	36274586	1.000000	0.71417	0.997000	0.53966	0.166000	0.22503	4.964000	0.63701	2.832000	0.97577	0.655000	0.94253	GAT		0.507	KRT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257214.2	NM_000223		18	106	1	0	2.94398e-08	1	3.32385e-08	18	106				
ALK	238	broad.mit.edu	37	2	29498076	29498076	+	Missense_Mutation	SNP	T	T	C			TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr2:29498076T>C	ENST00000389048.3	-	11	2836	c.1930A>G	c.(1930-1932)Atc>Gtc	p.I644V	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	644					activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	TTCTGCAGGATCTTGTCCTCT	0.498			"""T, Mis, A"""	"""NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"""	"""ALCL, NSCLC, Neuroblastoma"""	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																													ENST00000389048.3			yes	Dom	yes	Familial neuroblastoma	2	2p23	238	"""T, Mis, A"""	anaplastic lymphoma kinase (Ki-1)			"""L, E, M"""	"""NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"""	neuroblastoma	"""ALCL, NSCLC, Neuroblastoma"""	ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	0				NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340						c.(1930-1932)Atc>Gtc		anaplastic lymphoma receptor tyrosine kinase	Adenosine triphosphate(DB00171)						90.0	90.0	90.0					2																	29498076		2203	4300	6503	SO:0001583	missense	238	Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity	g.chr2:29498076T>C	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"""CD molecules"""	427	protein-coding gene	gene with protein product		105590	"""anaplastic lymphoma kinase (Ki-1)"""			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.1930A>G	2.37:g.29498076T>C	ENSP00000373700:p.Ile644Val					ALK_ENST00000431873.1_Intron	p.I644V	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN			11	2836	-	Acute lymphoblastic leukemia(172;0.155)		644					Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Missense_Mutation	SNP	ENST00000389048.3	37	c.1930A>G	CCDS33172.1	.	.	.	.	.	.	.	.	.	.	T	1.398	-0.579027	0.03854	.	.	ENSG00000171094	ENST00000389048	T	0.76316	-1.01	4.97	-4.02	0.04034	.	0.726416	0.12099	N	0.499632	T	0.58750	0.2144	L	0.40543	1.245	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.40459	-0.9562	9	.	.	.	.	1.7268	0.02923	0.1384:0.3326:0.1427:0.3863	.	644	Q9UM73	ALK_HUMAN	V	644	ENSP00000373700:I644V	.	I	-	1	0	ALK	29351580	0.000000	0.05858	0.006000	0.13384	0.033000	0.12548	-1.210000	0.02999	-1.091000	0.03065	-0.379000	0.06801	ATC		0.498	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		11	52	0	0	0	1	0	11	52				
LPHN3	23284	broad.mit.edu	37	4	62800613	62800613	+	Missense_Mutation	SNP	G	G	A			TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr4:62800613G>A	ENST00000514591.1	+	13	2293	c.1964G>A	c.(1963-1965)aGa>aAa	p.R655K	LPHN3_ENST00000504896.1_Missense_Mutation_p.R655K|LPHN3_ENST00000508078.1_3'UTR|LPHN3_ENST00000545650.1_Missense_Mutation_p.R655K|LPHN3_ENST00000507164.1_Missense_Mutation_p.R723K|LPHN3_ENST00000508946.1_Missense_Mutation_p.R655K|LPHN3_ENST00000508693.1_Missense_Mutation_p.R723K|LPHN3_ENST00000514157.1_Missense_Mutation_p.R655K|LPHN3_ENST00000506746.1_Missense_Mutation_p.R723K|LPHN3_ENST00000507625.1_Missense_Mutation_p.R723K|LPHN3_ENST00000511324.1_Missense_Mutation_p.R723K|LPHN3_ENST00000509896.1_Missense_Mutation_p.R723K|LPHN3_ENST00000514996.1_Missense_Mutation_p.R655K|LPHN3_ENST00000512091.2_Missense_Mutation_p.R655K|LPHN3_ENST00000506700.1_Missense_Mutation_p.R655K|LPHN3_ENST00000506720.1_Missense_Mutation_p.R723K			Q9HAR2	LPHN3_HUMAN	latrophilin 3	642					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						AATGCATGGAGAGACCTGACT	0.483																																						ENST00000512091.1																			0				breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						c.(1963-1965)aGa>aAa		latrophilin 3							87.0	92.0	90.0					4																	62800613		2079	4219	6298	SO:0001583	missense	23284				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding	g.chr4:62800613G>A	AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"""-"", ""GPCR / Class B : Orphans"""	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.1964G>A	4.37:g.62800613G>A	ENSP00000422533:p.Arg655Lys					LPHN3_ENST00000506720.1_Missense_Mutation_p.R723K|LPHN3_ENST00000508946.1_Missense_Mutation_p.R655K|LPHN3_ENST00000545650.1_Missense_Mutation_p.R655K|LPHN3_ENST00000509896.1_Missense_Mutation_p.R723K|LPHN3_ENST00000506700.1_Missense_Mutation_p.R655K|LPHN3_ENST00000514591.1_Missense_Mutation_p.R655K|LPHN3_ENST00000507625.1_Missense_Mutation_p.R723K|LPHN3_ENST00000508078.1_3'UTR|LPHN3_ENST00000508693.1_Missense_Mutation_p.R723K|LPHN3_ENST00000506746.1_Missense_Mutation_p.R723K|LPHN3_ENST00000507164.1_Missense_Mutation_p.R723K|LPHN3_ENST00000511324.1_Missense_Mutation_p.R723K|LPHN3_ENST00000514996.1_Missense_Mutation_p.R655K|LPHN3_ENST00000514157.1_Missense_Mutation_p.R655K|LPHN3_ENST00000504896.1_Missense_Mutation_p.R655K	p.R655K			Q9HAR2	LPHN3_HUMAN			13	2711	+			642					E9PE04|O94867|Q9NWK5	Missense_Mutation	SNP	ENST00000514591.1	37	c.1964G>A	CCDS54768.1	.	.	.	.	.	.	.	.	.	.	G	8.931	0.963424	0.18583	.	.	ENSG00000150471	ENST00000512091;ENST00000514591;ENST00000509896;ENST00000511324;ENST00000506700;ENST00000534975;ENST00000545650;ENST00000295349;ENST00000280009;ENST00000507164;ENST00000508693;ENST00000507625;ENST00000514157;ENST00000504896;ENST00000508946;ENST00000506720;ENST00000506746;ENST00000514996	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.09538	2.97;2.97;2.97;2.97;2.97;2.97;2.97;2.97;2.97;2.97;2.97;2.97;2.97;2.97;2.97	5.43	4.58	0.56647	Domain of unknown function DUF3497 (1);	0.139364	0.64402	N	0.000005	T	0.09512	0.0234	L	0.38531	1.155	0.47778	D	0.999514	P;P;P	0.38617	0.64;0.64;0.587	B;B;B	0.40602	0.334;0.334;0.225	T	0.02868	-1.1100	10	0.02654	T	1	.	14.1765	0.65544	0.0714:0.0:0.9286:0.0	.	655;642;655	E9PE04;Q9HAR2;Q9HAR2-2	.;LPHN3_HUMAN;.	K	655;655;723;723;655;642;655;642;655;723;723;723;655;655;655;723;723;655	ENSP00000423388:R655K;ENSP00000422533:R655K;ENSP00000423787:R723K;ENSP00000425033:R723K;ENSP00000424120:R655K;ENSP00000439831:R655K;ENSP00000421476:R723K;ENSP00000424030:R723K;ENSP00000421372:R723K;ENSP00000425201:R655K;ENSP00000423434:R655K;ENSP00000421627:R655K;ENSP00000420931:R723K;ENSP00000425884:R723K;ENSP00000424258:R655K	ENSP00000280009:R655K	R	+	2	0	LPHN3	62483208	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	4.748000	0.62148	1.518000	0.48934	0.650000	0.86243	AGA		0.483	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			5	35	0	0	0	1	0	5	35				
RBM27	54439	broad.mit.edu	37	5	145641086	145641086	+	Missense_Mutation	SNP	G	G	T			TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr5:145641086G>T	ENST00000265271.5	+	13	2073	c.1907G>T	c.(1906-1908)gGt>gTt	p.G636V	RBM27_ENST00000506502.1_Missense_Mutation_p.G581V	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	636	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCTTTTAAGGGTGACCCAGAA	0.368																																						ENST00000265271.5																			0				NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39						c.(1906-1908)gGt>gTt		RNA binding motif protein 27							84.0	76.0	79.0					5																	145641086		1568	3582	5150	SO:0001583	missense	54439				mRNA processing	cytoplasm|nuclear speck	nucleotide binding|RNA binding|zinc ion binding	g.chr5:145641086G>T	AL833706	CCDS43378.1	5q32	2013-01-09				ENSG00000091009		"""Zinc fingers, CCCH-type domain containing"", ""RNA binding motif (RRM) containing"""	29243	protein-coding gene	gene with protein product	"""acidic rich RS domain containing 1"""					10718198, 15741184	Standard	NM_018989		Approved	KIAA1311, ARRS1, Psc1, ZC3H18	uc003lnz.4	Q9P2N5		ENST00000265271.5:c.1907G>T	5.37:g.145641086G>T	ENSP00000265271:p.Gly636Val					RBM27_ENST00000506502.1_Missense_Mutation_p.G581V	p.G636V	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		13	2073	+			636			RRM.		Q8IYW9	Missense_Mutation	SNP	ENST00000265271.5	37	c.1907G>T	CCDS43378.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.166200	0.78339	.	.	ENSG00000091009	ENST00000265271	T	0.52526	0.66	5.5	5.5	0.81552	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.147962	0.46758	D	0.000279	T	0.63988	0.2558	M	0.72894	2.215	0.80722	D	1	D;D	0.63046	0.992;0.992	D;D	0.67548	0.952;0.952	T	0.65693	-0.6106	10	0.56958	D	0.05	-14.8224	10.5156	0.44887	0.1179:0.0:0.8821:0.0	.	636;581	Q9P2N5;B3KY61	RBM27_HUMAN;.	V	636	ENSP00000265271:G636V	ENSP00000265271:G636V	G	+	2	0	RBM27	145621279	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.256000	0.78350	2.593000	0.87608	0.561000	0.74099	GGT		0.368	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128		4	65	1	0	0.00909568	1	0.00909568	4	65				
OTUD3	23252	broad.mit.edu	37	1	20220960	20220960	+	Missense_Mutation	SNP	C	C	T			TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr1:20220960C>T	ENST00000375120.3	+	3	471	c.470C>T	c.(469-471)gCc>gTc	p.A157V	OTUD3_ENST00000466697.1_3'UTR	NM_015207.1	NP_056022.1	Q5T2D3	OTUD3_HUMAN	OTU deubiquitinase 3	157	OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.				protein K11-linked deubiquitination (GO:0035871)|protein K6-linked deubiquitination (GO:0044313)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|kidney(2)|large_intestine(4)|lung(1)|skin(1)	9		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000276)|Lung NSC(340;0.000338)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.12e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000142)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.000408)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		CAACTTAATGCCCCTTTGTGG	0.418																																						ENST00000375120.3																			0				breast(1)|kidney(2)|large_intestine(4)|lung(1)|skin(1)	9						c.(469-471)gCc>gTc		OTU domain containing 3							135.0	127.0	130.0					1																	20220960		1868	4107	5975	SO:0001583	missense	23252							g.chr1:20220960C>T	AB007928	CCDS41279.1	1p36.13	2014-02-24	2014-02-24		ENSG00000169914	ENSG00000169914		"""OTU domain containing"""	29038	protein-coding gene	gene with protein product		611758	"""OTU domain containing 3"""			9455484, 23827681	Standard	NM_015207		Approved	KIAA0459, DUBA4	uc001bcs.4	Q5T2D3	OTTHUMG00000002696	ENST00000375120.3:c.470C>T	1.37:g.20220960C>T	ENSP00000364261:p.Ala157Val					OTUD3_ENST00000466697.1_3'UTR	p.A157V	NM_015207.1	NP_056022.1	Q5T2D3	OTUD3_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.12e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000142)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.000408)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	3	471	+		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000276)|Lung NSC(340;0.000338)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)	157			OTU.		O75047	Missense_Mutation	SNP	ENST00000375120.3	37	c.470C>T	CCDS41279.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.042099	0.75732	.	.	ENSG00000169914	ENST00000375120	T	0.43294	0.95	5.92	5.92	0.95590	Ovarian tumour, otubain (2);	0.195144	0.53938	D	0.000041	T	0.46600	0.1401	L	0.59436	1.845	0.45005	D	0.998023	P	0.47191	0.891	P	0.47346	0.544	T	0.27938	-1.0059	10	0.31617	T	0.26	.	13.8063	0.63233	0.1531:0.8468:0.0:0.0	.	157	Q5T2D3	OTUD3_HUMAN	V	157	ENSP00000364261:A157V	ENSP00000364261:A157V	A	+	2	0	OTUD3	20093547	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.941000	0.56607	2.804000	0.96469	0.655000	0.94253	GCC		0.418	OTUD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007655.1			3	47	0	0	0	1	0	3	47				
C5orf45	51149	broad.mit.edu	37	5	179264450	179264450	+	Nonsense_Mutation	SNP	G	G	A			TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr5:179264450G>A	ENST00000292586.6	-	7	1063	c.973C>T	c.(973-975)Cga>Tga	p.R325*	C5orf45_ENST00000518235.1_Intron|C5orf45_ENST00000520698.1_Intron|C5orf45_ENST00000518219.1_3'UTR|C5orf45_ENST00000523084.1_Nonsense_Mutation_p.R191*|C5orf45_ENST00000403396.2_Intron|SQSTM1_ENST00000389805.4_3'UTR|SQSTM1_ENST00000376929.3_3'UTR|C5orf45_ENST00000376931.2_Nonsense_Mutation_p.R270*|C5orf45_ENST00000523267.1_5'UTR	NM_016175.3	NP_057259.2	Q6NTE8	CE045_HUMAN	chromosome 5 open reading frame 45	325										breast(2)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12						CGTGTGGGTCGAGGATTCTGT	0.547																																						ENST00000292586.6																			0				breast(2)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12						c.(973-975)Cga>Tga		chromosome 5 open reading frame 45							175.0	177.0	177.0					5																	179264450		2203	4300	6503	SO:0001587	stop_gained	51149							g.chr5:179264450G>A		CCDS34318.1, CCDS34319.1	5q35.3	2008-07-10			ENSG00000161010	ENSG00000161010			30817	protein-coding gene	gene with protein product	"""truncated calcium binding protein"""						Standard	NM_016175		Approved	MGC65027, MGC78537, DKFZp686L2452, LOC51149	uc003mla.3	Q6NTE8	OTTHUMG00000163490	ENST00000292586.6:c.973C>T	5.37:g.179264450G>A	ENSP00000292586:p.Arg325*					C5orf45_ENST00000523267.1_5'UTR|C5orf45_ENST00000523084.1_Nonsense_Mutation_p.R191*|C5orf45_ENST00000403396.2_Intron|C5orf45_ENST00000518219.1_3'UTR|SQSTM1_ENST00000389805.4_3'UTR|SQSTM1_ENST00000376929.3_3'UTR|C5orf45_ENST00000518235.1_Intron|C5orf45_ENST00000376931.2_Nonsense_Mutation_p.R270*|C5orf45_ENST00000520698.1_Intron	p.R325*	NM_016175.3	NP_057259.2	Q6NTE8	CE045_HUMAN			7	1063	-			325					B5MD09|E9PAK6|Q7Z3D8|Q9BUC1|Q9UN54	Nonsense_Mutation	SNP	ENST00000292586.6	37	c.973C>T	CCDS34319.1	.	.	.	.	.	.	.	.	.	.	G	16.41	3.116392	0.56505	.	.	ENSG00000161010	ENST00000376931;ENST00000523084;ENST00000292586	.	.	.	4.49	0.156	0.14910	.	0.669254	0.13497	N	0.383506	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	0.2007	1.634	0.02738	0.1905:0.3013:0.3545:0.1538	.	.	.	.	X	270;191;325	.	ENSP00000292586:R325X	R	-	1	2	C5orf45	179197056	0.002000	0.14202	0.000000	0.03702	0.003000	0.03518	0.441000	0.21611	-0.100000	0.12241	0.462000	0.41574	CGA		0.547	C5orf45-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373760.2	NM_016175		4	204	0	0	0	1	0	4	204				
RP11-649A16.1	0	broad.mit.edu	37	3	146995076	146995077	+	RNA	INS	-	-	A			TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr3:146995076_146995077insA	ENST00000473299.1	-	0	132																											TTCTGGACTGtaaaaaaaaaaa	0.292																																						ENST00000473299.1																			0																																																			0							g.chr3:146995076_146995077insA																													3.37:g.146995087_146995087dupA														0	132	-									RNA	INS	ENST00000473299.1	37																																																																																						0.292	RP11-649A16.1-001	KNOWN	basic	antisense	antisense	OTTHUMT00000355522.1			4	4						4	4	---	---	---	---
BMPR1B	658	broad.mit.edu	37	4	96046274	96046275	+	Splice_Site	INS	-	-	A			TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr4:96046274_96046275insA	ENST00000515059.1	+	8	868		c.e8+2		BMPR1B_ENST00000264568.4_Splice_Site|BMPR1B_ENST00000394931.1_Splice_Site|BMPR1B_ENST00000440890.2_Splice_Site	NM_001203.2	NP_001194.1	O00238	BMR1B_HUMAN	bone morphogenetic protein receptor, type IB						BMP signaling pathway (GO:0030509)|cartilage condensation (GO:0001502)|chondrocyte differentiation (GO:0002062)|dorsal/ventral pattern formation (GO:0009953)|eye development (GO:0001654)|inflammatory response (GO:0006954)|limb morphogenesis (GO:0035108)|ovarian cumulus expansion (GO:0001550)|ovulation cycle (GO:0042698)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cell differentiation (GO:0045597)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of osteoblast differentiation (GO:0045669)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|retinal ganglion cell axon guidance (GO:0031290)|skeletal system development (GO:0001501)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta receptor activity, type I (GO:0005025)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.51e-07)		CCTCTGCTGGTATGAGAAGAAC	0.421																																						ENST00000515059.1																			0				breast(3)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31						c.e8+2		bone morphogenetic protein receptor, type IB																																				SO:0001630	splice_region_variant	658				BMP signaling pathway|cartilage condensation|eye development|limb morphogenesis|ovarian cumulus expansion|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	receptor complex	ATP binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta receptor activity	g.chr4:96046274_96046275insA	D89675	CCDS3642.1, CCDS58919.1	4q23-q24	2008-02-05			ENSG00000138696	ENSG00000138696		"""CD molecules"""	1077	protein-coding gene	gene with protein product		603248				8140412, 9730621	Standard	NM_001203		Approved	ALK6, CDw293	uc031sgn.1	O00238	OTTHUMG00000130991	ENST00000515059.1:c.585+2->A	4.37:g.96046275_96046275dupA						BMPR1B_ENST00000394931.1_Splice_Site|BMPR1B_ENST00000440890.2_Splice_Site|BMPR1B_ENST00000264568.4_Splice_Site		NM_001203.2	NP_001194.1	O00238	BMR1B_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;6.51e-07)	8	868	+		Hepatocellular(203;0.114)						B2R953|B4DSV1|P78366	Splice_Site	INS	ENST00000515059.1	37		CCDS3642.1																																																																																				0.421	BMPR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253609.3	NM_001203	Intron	11	36						11	36	---	---	---	---
RRP36	88745	broad.mit.edu	37	6	42989414	42989419	+	In_Frame_Del	DEL	GCCGGG	GCCGGG	-	rs200886831|rs551189349|rs199544375		TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr6:42989414_42989419delGCCGGG	ENST00000244496.5	+	1	32_37	c.22_27delGCCGGG	c.(22-27)gccgggdel	p.AG14del		NM_033112.2	NP_149103.1	Q96EU6	RRP36_HUMAN	ribosomal RNA processing 36 homolog (S. cerevisiae)	14					ribosomal small subunit biogenesis (GO:0042274)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.A8_G9delAG(2)		NS(1)|breast(1)|central_nervous_system(1)|large_intestine(5)|lung(1)|ovary(1)|prostate(1)	11						TAACTAccgcgccggggccggggccg	0.777																																						ENST00000244496.5																			2	Deletion - In frame(2)	p.A8_G9delAG(2)	prostate(1)|central_nervous_system(1)	NS(1)|breast(1)|central_nervous_system(1)|large_intestine(5)|lung(1)|ovary(1)|prostate(1)	11						c.(22-27)del		ribosomal RNA processing 36 homolog (S. cerevisiae)																																				SO:0001651	inframe_deletion	88745				ribosomal small subunit biogenesis|rRNA processing	nucleolus		g.chr6:42989414_42989419delGCCGGG	BC011933	CCDS34453.1	6p21.1	2010-07-06	2010-07-06	2010-07-06	ENSG00000124541	ENSG00000124541			21374	protein-coding gene	gene with protein product		613475	"""chromosome 6 open reading frame 153"""	C6orf153		20038530	Standard	NM_033112		Approved	dJ20C7.4	uc003otp.1	Q96EU6	OTTHUMG00000014715	ENST00000244496.5:c.22_27delGCCGGG	6.37:g.42989420_42989425delGCCGGG	ENSP00000244496:p.Ala14_Gly15del						p.AG14del	NM_033112.2	NP_149103.1	Q96EU6	RRP36_HUMAN			1	32_37	+			14					Q9BRF6|Q9P0C8	In_Frame_Del	DEL	ENST00000244496.5	37	c.22_27delGCCGGG	CCDS34453.1																																																																																				0.777	RRP36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040572.1	NM_033112		3	6						3	6	---	---	---	---
ZIC2	7546	broad.mit.edu	37	13	100635008	100635010	+	In_Frame_Del	DEL	CCA	CCA	-	rs375069774		TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr13:100635008_100635010delCCA	ENST00000376335.3	+	1	983_985	c.690_692delCCA	c.(688-693)gcccac>gcc	p.H239del		NM_007129.3	NP_009060.2	O95409	ZIC2_HUMAN	Zic family member 2	239	Necessary for interaction with MDFIC and transcriptional activation or repression. {ECO:0000250}.|Poly-His.		H -> HH. {ECO:0000269|PubMed:15221788}.|Missing. {ECO:0000269|PubMed:15221788}.		brain development (GO:0007420)|developmental pigmentation (GO:0048066)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|retinal ganglion cell axon guidance (GO:0031290)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(2)|liver(2)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					CAGCCGCGGCccaccaccaccac	0.621																																					Pancreas(97;119 1522 31925 44771 48764)	ENST00000376335.3																			0				large_intestine(2)|liver(2)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						c.(688-693)gcc>gc		Zic family member 2																																				SO:0001651	inframe_deletion	7546				brain development|negative regulation of transcription, DNA-dependent|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|visual perception	cytoplasm|nucleus	chromatin DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr13:100635008_100635010delCCA	AF104902	CCDS9495.1	13q32	2013-01-08	2011-05-19		ENSG00000043355	ENSG00000043355		"""Zinc fingers, C2H2-type"""	12873	protein-coding gene	gene with protein product	"""Zinc finger protein of the cerebellum 2"""	603073	"""Zic family member 2 (odd-paired Drosophila homolog)"", ""Zic family member 2 (odd-paired homolog, Drosophila)"""			9771712	Standard	NM_007129		Approved	HPE5	uc001von.3	O95409	OTTHUMG00000017279	ENST00000376335.3:c.690_692delCCA	13.37:g.100635017_100635019delCCA	ENSP00000365514:p.His239del						p.AH230del	NM_007129.3	NP_009060.2	O95409	ZIC2_HUMAN			1	983_985	+	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)		230			Necessary for interaction with MDFIC and transcriptional activation or repression (By similarity).|Poly-Ala.		Q5VYA9|Q9H309	In_Frame_Del	DEL	ENST00000376335.3	37	c.690_692delCCA	CCDS9495.1																																																																																				0.621	ZIC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045618.2	NM_007129		8	73						8	73	---	---	---	---
SEPT1	1731	broad.mit.edu	37	16	30393855	30393855	+	5'UTR	DEL	G	G	-	rs201701101	byFrequency	TCGA-KK-A7B1-01A-11D-A32B-08	TCGA-KK-A7B1-11A-12D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c866d486-7422-4b92-89e2-f77933384d64	d47e6a60-b436-4ee5-b201-819ac01c600b	g.chr16:30393855delG	ENST00000571393.1	-	0	180				SEPT1_ENST00000321367.3_Frame_Shift_Del_p.G46fs|SEPT1_ENST00000570039.1_5'Flank|SEPT1_ENST00000605106.1_Frame_Shift_Del_p.G4fs			Q8WYJ6	SEPT1_HUMAN	septin 1						cell cycle (GO:0007049)|cell division (GO:0051301)	septin complex (GO:0031105)	GTP binding (GO:0005525)			breast(2)|endometrium(1)|large_intestine(3)|lung(15)|ovary(1)|skin(1)|urinary_tract(1)	24			Colorectal(24;0.193)			CCATGACTCCGCCAGCCATCA	0.642																																						ENST00000321367.3																			0				breast(2)|endometrium(1)|large_intestine(3)|lung(15)|ovary(1)|skin(1)|urinary_tract(1)	24						c.(133-135)ggfs		septin 1							29.0	24.0	26.0					16																	30393855		2195	4298	6493	SO:0001623	5_prime_UTR_variant	1731				cell cycle|cell division	microtubule organizing center|septin complex	GTP binding|protein binding	g.chr16:30393855delG	AF308288	CCDS10678.1, CCDS10678.2, CCDS10678.3	16p11.2	2013-01-21		2001-09-10	ENSG00000180096	ENSG00000180096	3.1.5.1	"""Septins"""	2879	protein-coding gene	gene with protein product		612897		DIFF6		8697812	Standard	NM_052838		Approved	PNUTL3	uc002dxy.4	Q8WYJ6	OTTHUMG00000176984	ENST00000571393.1:c.-7C>-	16.37:g.30393855delG						SEPT1_ENST00000605106.1_Frame_Shift_Del_p.G4fs|SEPT1_ENST00000571393.1_5'UTR	p.G46fs	NM_052838.4	NP_443070.5	Q8WYJ6	SEPT1_HUMAN	Colorectal(24;0.193)		2	180	-			0					B4DVE6|Q658T1|Q8NEZ1|Q96EL4|Q9H285	Frame_Shift_Del	DEL	ENST00000571393.1	37	c.135delC																																																																																					0.642	SEPT1-201	KNOWN	basic	protein_coding	protein_coding		NM_052838		2	4						2	4	---	---	---	---
