#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
MIPEP	4285	broad.mit.edu	37	13	24444199	24444199	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr13:24444199C>T	ENST00000382172.3	-	6	837	c.739G>A	c.(739-741)Gat>Aat	p.D247N		NM_005932.3	NP_005923	Q99797	MIPEP_HUMAN	mitochondrial intermediate peptidase	247					protein processing involved in protein targeting to mitochondrion (GO:0006627)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|liver(1)|lung(12)|prostate(2)|skin(1)	27		all_cancers(29;1.83e-22)|all_epithelial(30;8.75e-19)|all_lung(29;9.17e-18)|Lung SC(185;0.0225)|Breast(139;0.14)		all cancers(112;0.00389)|Epithelial(112;0.0266)|OV - Ovarian serous cystadenocarcinoma(117;0.0717)|Lung(94;0.207)|GBM - Glioblastoma multiforme(144;0.232)		ATGATATGATCCCCAGCAGAT	0.393																																						ENST00000382172.3																			0				breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|liver(1)|lung(12)|prostate(2)|skin(1)	27						c.(739-741)Gat>Aat		mitochondrial intermediate peptidase							180.0	151.0	161.0					13																	24444199		2203	4300	6503	SO:0001583	missense	4285				protein processing involved in protein targeting to mitochondrion|proteolysis	mitochondrial matrix	metal ion binding|metalloendopeptidase activity	g.chr13:24444199C>T		CCDS9303.1	13q12	2011-01-17			ENSG00000027001	ENSG00000027001	3.4.24.59		7104	protein-coding gene	gene with protein product		602241				9073519	Standard	NM_005932		Approved	MIP	uc001uox.4	Q99797	OTTHUMG00000016573	ENST00000382172.3:c.739G>A	13.37:g.24444199C>T	ENSP00000371607:p.Asp247Asn						p.D247N	NM_005932.3	NP_005923.2	Q99797	MIPEP_HUMAN		all cancers(112;0.00389)|Epithelial(112;0.0266)|OV - Ovarian serous cystadenocarcinoma(117;0.0717)|Lung(94;0.207)|GBM - Glioblastoma multiforme(144;0.232)	6	837	-		all_cancers(29;1.83e-22)|all_epithelial(30;8.75e-19)|all_lung(29;9.17e-18)|Lung SC(185;0.0225)|Breast(139;0.14)	247					Q5JV15|Q5T9Q9|Q96G65	Missense_Mutation	SNP	ENST00000382172.3	37	c.739G>A	CCDS9303.1	.	.	.	.	.	.	.	.	.	.	C	8.790	0.930368	0.18131	.	.	ENSG00000027001	ENST00000382172	T	0.08546	3.08	5.92	-1.26	0.09376	Neurolysin/Thimet oligopeptidase, domain 2 (1);	0.753644	0.13890	N	0.355715	T	0.06917	0.0176	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.26916	-1.0089	10	0.37606	T	0.19	.	13.8677	0.63598	0.0:0.2461:0.0:0.7539	.	247	Q99797	MIPEP_HUMAN	N	247	ENSP00000371607:D247N	ENSP00000371607:D247N	D	-	1	0	MIPEP	23342199	0.001000	0.12720	0.000000	0.03702	0.010000	0.07245	0.746000	0.26275	-0.644000	0.05465	-0.145000	0.13849	GAT		0.393	MIPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044169.1			49	51	0	0	0	0.870114	0	49	51				
IGF2R	3482	broad.mit.edu	37	6	160501242	160501242	+	Missense_Mutation	SNP	C	C	T	rs368781979		TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr6:160501242C>T	ENST00000356956.1	+	39	5916	c.5768C>T	c.(5767-5769)gCg>gTg	p.A1923V		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	1923	Fibronectin type-II. {ECO:0000255|PROSITE-ProRule:PRU00479}.				insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	GAGAGCAGGGCGAAGCTGTGG	0.557																																						ENST00000356956.1																			0				breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95						c.(5767-5769)gCg>gTg		insulin-like growth factor 2 receptor		C	VAL/ALA	0,4406		0,0,2203	130.0	116.0	121.0		5768	4.8	0.0	6		121	1,8599	1.2+/-3.3	0,1,4299	no	missense	IGF2R	NM_000876.2	64	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	1923/2492	160501242	1,13005	2203	4300	6503	SO:0001583	missense	3482				receptor-mediated endocytosis	cell surface|endocytic vesicle|endosome|integral to plasma membrane|lysosomal membrane|trans-Golgi network transport vesicle	glycoprotein binding|insulin-like growth factor receptor activity|phosphoprotein binding|transporter activity	g.chr6:160501242C>T	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"""CD molecules"""	5467	protein-coding gene	gene with protein product	"""cation-independent mannose-6 phosphate receptor"""	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.5768C>T	6.37:g.160501242C>T	ENSP00000349437:p.Ala1923Val						p.A1923V	NM_000876.2	NP_000867.2	P11717	MPRI_HUMAN		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	39	5916	+		Breast(66;0.000777)|Ovarian(120;0.0305)	1923			Fibronectin type-II.		Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	37	c.5768C>T	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	C	8.172	0.791869	0.16258	0.0	1.16E-4	ENSG00000197081	ENST00000356956	T	0.50548	0.74	5.63	4.77	0.60923	Mannose-6-phosphate receptor, binding (1);Fibronectin, type II, collagen-binding (5);Kringle-like fold (1);	0.593695	0.17810	N	0.161239	T	0.18800	0.0451	L	0.41710	1.295	0.09310	N	1	B	0.20671	0.047	B	0.08055	0.003	T	0.09314	-1.0680	10	0.46703	T	0.11	-6.6753	8.0398	0.30515	0.1949:0.7243:0.0:0.0808	.	1923	P11717	MPRI_HUMAN	V	1923	ENSP00000349437:A1923V	ENSP00000349437:A1923V	A	+	2	0	IGF2R	160421232	0.001000	0.12720	0.000000	0.03702	0.010000	0.07245	1.355000	0.34068	1.519000	0.48950	0.561000	0.74099	GCG		0.557	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		45	49	0	0	0	0.853193	0	45	49				
GATA3	2625	broad.mit.edu	37	10	8100437	8100437	+	Silent	SNP	G	G	A			TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr10:8100437G>A	ENST00000346208.3	+	3	866	c.411G>A	c.(409-411)tcG>tcA	p.S137S	GATA3_ENST00000379328.3_Silent_p.S137S|GATA3_ENST00000461472.1_3'UTR			P23771	GATA3_HUMAN	GATA binding protein 3	137	Poly-Ser.				anatomical structure formation involved in morphogenesis (GO:0048646)|anatomical structure morphogenesis (GO:0009653)|aortic valve morphogenesis (GO:0003180)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cardiac right ventricle morphogenesis (GO:0003215)|cell fate determination (GO:0001709)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|cellular response to interferon-alpha (GO:0035457)|cellular response to interleukin-4 (GO:0071353)|cellular response to tumor necrosis factor (GO:0071356)|defense response (GO:0006952)|developmental growth (GO:0048589)|ear development (GO:0043583)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|interferon-gamma secretion (GO:0072643)|interleukin-4 secretion (GO:0072602)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|lymphocyte migration (GO:0072676)|male gonad development (GO:0008584)|mast cell differentiation (GO:0060374)|mesenchymal to epithelial transition (GO:0060231)|mesonephros development (GO:0001823)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell motility (GO:2000146)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell proliferation involved in mesonephros development (GO:2000607)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation (GO:2000703)|negative regulation of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation (GO:2000734)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct formation (GO:0072179)|nephric duct morphogenesis (GO:0072178)|neuron migration (GO:0001764)|norepinephrine biosynthetic process (GO:0042421)|otic vesicle development (GO:0071599)|parathyroid gland development (GO:0060017)|parathyroid hormone secretion (GO:0035898)|pharyngeal system development (GO:0060037)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-13 secretion (GO:2000667)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of interleukin-5 secretion (GO:2000664)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of signal transduction (GO:0009967)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of thyroid hormone generation (GO:2000611)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ureteric bud formation (GO:0072107)|post-embryonic development (GO:0009791)|pro-T cell differentiation (GO:0002572)|regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043370)|regulation of cellular response to X-ray (GO:2000683)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of establishment of cell polarity (GO:2000114)|regulation of histone H3-K27 methylation (GO:0061085)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to gamma radiation (GO:0010332)|response to virus (GO:0009615)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)|T cell receptor signaling pathway (GO:0050852)|T-helper 2 cell differentiation (GO:0045064)|thymic T cell selection (GO:0045061)|thymus development (GO:0048538)|TOR signaling (GO:0031929)|transcription from RNA polymerase II promoter (GO:0006366)|type IV hypersensitivity (GO:0001806)|ureter maturation (GO:0035799)|ureteric bud formation (GO:0060676)|uterus development (GO:0060065)|ventricular septum development (GO:0003281)	nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer sequence-specific DNA binding (GO:0001158)|HMG box domain binding (GO:0071837)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)			NS(1)|breast(44)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(24)|ovary(3)|skin(2)	87						CCCCGGCCTCGTCCTCCTCCT	0.716			"""F, N, S"""		breast		"""HDR syndrome (HYPOPARATHYROIDISM, SENSORINEURAL DEAFNESS, AND RENAL DISEASE)"""																															ENST00000379328.3				Rec	yes		10	10p15	2625	"""F, N, S"""	GATA binding protein 3	yes	"""HDR syndrome (HYPOPARATHYROIDISM, SENSORINEURAL DEAFNESS, AND RENAL DISEASE)"""	E			breast		0				NS(1)|breast(44)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(24)|ovary(3)|skin(2)	87						c.(409-411)tcG>tcA		GATA binding protein 3							42.0	54.0	50.0					10																	8100437		2203	4300	6503	SO:0001819	synonymous_variant	2625				aortic valve morphogenesis|blood coagulation|canonical Wnt receptor signaling pathway involved in metanephric kidney development|cardiac right ventricle morphogenesis|cell fate determination|cellular response to interferon-alpha|cellular response to interleukin-4|cellular response to tumor necrosis factor|defense response|ear development|lymphocyte migration|male gonad development|mesenchymal to epithelial transition|mesonephros development|negative regulation of cell cycle|negative regulation of cell motility|negative regulation of cell proliferation involved in mesonephros development|negative regulation of endothelial cell apoptosis|negative regulation of fat cell differentiation|negative regulation of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation|negative regulation of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation|negative regulation of inflammatory response|negative regulation of mammary gland epithelial cell proliferation|nephric duct formation|norepinephrine biosynthetic process|pharyngeal system development|phosphatidylinositol 3-kinase cascade|positive regulation of endothelial cell migration|positive regulation of interleukin-13 secretion|positive regulation of interleukin-4 production|positive regulation of interleukin-5 secretion|positive regulation of protein kinase B signaling cascade|positive regulation of T cell differentiation|positive regulation of thyroid hormone generation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription regulatory region DNA binding|positive regulation of ureteric bud formation|regulation of cellular response to X-ray|regulation of cytokine biosynthetic process|regulation of nephron tubule epithelial cell differentiation|response to estrogen stimulus|response to virus|sympathetic nervous system development|T cell receptor signaling pathway|TOR signaling cascade|ureteric bud formation|uterus development|ventricular septum development	nuclear chromatin|nucleolus|nucleoplasm	core promoter proximal region sequence-specific DNA binding|core promoter sequence-specific DNA binding|E-box binding|HMG box domain binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription|transcription coactivator activity|transcription factor binding|zinc ion binding	g.chr10:8100437G>A	X55122	CCDS7083.1, CCDS31143.1	10p15	2013-01-25	2001-11-28		ENSG00000107485	ENSG00000107485		"""GATA zinc finger domain containing"""	4172	protein-coding gene	gene with protein product		131320	"""GATA-binding protein 3"""			2050118, 15087456	Standard	NM_002051		Approved	HDR	uc001ijz.3	P23771	OTTHUMG00000017640	ENST00000346208.3:c.411G>A	10.37:g.8100437G>A						GATA3_ENST00000346208.3_Silent_p.S137S|GATA3_ENST00000461472.1_3'UTR	p.S137S	NM_001002295.1|NM_002051.2	NP_001002295.1|NP_002042.1	P23771	GATA3_HUMAN			3	979	+			137			Poly-Ser.		Q5VWG7|Q5VWG8|Q96J16	Silent	SNP	ENST00000346208.3	37	c.411G>A	CCDS7083.1																																																																																				0.716	GATA3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046719.1	NM_001002295		31	37	0	0	0	0.779181	0	31	37				
MYO3A	53904	broad.mit.edu	37	10	26359114	26359114	+	Silent	SNP	T	T	C			TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr10:26359114T>C	ENST00000265944.5	+	13	1411	c.1245T>C	c.(1243-1245)taT>taC	p.Y415Y	MYO3A_ENST00000543632.1_Silent_p.Y415Y	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	415	Myosin motor.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						ACTTAGGATATCAATCTATGA	0.318																																						ENST00000265944.5																			0				NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						c.(1243-1245)taT>taC		myosin IIIA							65.0	66.0	66.0					10																	26359114		2202	4299	6501	SO:0001819	synonymous_variant	53904				protein autophosphorylation|response to stimulus|sensory perception of sound|visual perception	cytoplasm|filamentous actin|filopodium|myosin complex	actin binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|plus-end directed microfilament motor activity|protein serine/threonine kinase activity	g.chr10:26359114T>C	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"""Myosins / Myosin superfamily : Class III"""	7601	protein-coding gene	gene with protein product		606808	"""deafness, autosomal recessive 30"""	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.1245T>C	10.37:g.26359114T>C						MYO3A_ENST00000543632.1_Silent_p.Y415Y	p.Y415Y	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN			13	1411	+			415			Myosin head-like.		Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Silent	SNP	ENST00000265944.5	37	c.1245T>C	CCDS7148.1																																																																																				0.318	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		4	65	0	0	0	0.184627	0	4	65				
CYP26B1	56603	broad.mit.edu	37	2	72359586	72359586	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr2:72359586C>T	ENST00000001146.2	-	6	1512	c.1309G>A	c.(1309-1311)Ggt>Agt	p.G437S	CYP26B1_ENST00000412253.1_Missense_Mutation_p.G246S|CYP26B1_ENST00000546307.1_Missense_Mutation_p.G362S	NM_001277742.1|NM_019885.2	NP_001264671.1|NP_063938.1	Q9NR63	CP26B_HUMAN	cytochrome P450, family 26, subfamily B, polypeptide 1	437					bone morphogenesis (GO:0060349)|cell fate determination (GO:0001709)|cellular response to retinoic acid (GO:0071300)|cornification (GO:0070268)|embryonic limb morphogenesis (GO:0030326)|establishment of skin barrier (GO:0061436)|male meiosis (GO:0007140)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|oxidation-reduction process (GO:0055114)|positive regulation of gene expression (GO:0010628)|positive regulation of tongue muscle cell differentiation (GO:2001037)|proximal/distal pattern formation (GO:0009954)|retinoic acid catabolic process (GO:0034653)|retinoic acid receptor signaling pathway (GO:0048384)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|tongue morphogenesis (GO:0043587)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|retinoic acid 4-hydroxylase activity (GO:0008401)|retinoic acid binding (GO:0001972)			breast(1)|kidney(3)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)	28						GTCCGGACACCGCCACCGAAC	0.647																																						ENST00000001146.2																			0				breast(1)|kidney(3)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)	28						c.(1309-1311)Ggt>Agt		cytochrome P450, family 26, subfamily B, polypeptide 1							69.0	59.0	63.0					2																	72359586		2203	4300	6503	SO:0001583	missense	56603				cell fate determination|embryonic limb morphogenesis|male meiosis|negative regulation of retinoic acid receptor signaling pathway|proximal/distal pattern formation|retinoic acid catabolic process|spermatogenesis|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	electron carrier activity|heme binding|retinoic acid 4-hydroxylase activity|retinoic acid binding	g.chr2:72359586C>T		CCDS1919.1, CCDS62934.1	2p12	2006-11-24			ENSG00000003137	ENSG00000003137		"""Cytochrome P450s"""	20581	protein-coding gene	gene with protein product		605207				10545224	Standard	NM_019885		Approved	P450RAI-2	uc002sih.2	Q9NR63	OTTHUMG00000129756	ENST00000001146.2:c.1309G>A	2.37:g.72359586C>T	ENSP00000001146:p.Gly437Ser					CYP26B1_ENST00000546307.1_Missense_Mutation_p.G362S|CYP26B1_ENST00000412253.1_Missense_Mutation_p.G246S	p.G437S	NM_001277742.1|NM_019885.2	NP_001264671.1|NP_063938.1	Q9NR63	CP26B_HUMAN			6	1512	-			437					B2R8M7|B7Z2K6|B7Z2P4|B7Z3B8|E4W5W7|Q32MC0|Q53TW1|Q9NP41	Missense_Mutation	SNP	ENST00000001146.2	37	c.1309G>A	CCDS1919.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.864064	0.91511	.	.	ENSG00000003137	ENST00000001146;ENST00000412253;ENST00000546307	D;D;D	0.98849	-5.18;-5.18;-5.18	5.64	4.74	0.60224	Cytochrome P450, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99333	0.9766	M	0.93594	3.435	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.98720	1.0708	10	0.87932	D	0	-31.7115	15.4221	0.75022	0.0:0.8603:0.1397:0.0	.	362;420;437	B7Z2K6;B7Z2P4;Q9NR63	.;.;CP26B_HUMAN	S	437;246;362	ENSP00000001146:G437S;ENSP00000401465:G246S;ENSP00000443304:G362S	ENSP00000001146:G437S	G	-	1	0	CYP26B1	72213094	1.000000	0.71417	0.578000	0.28575	0.697000	0.40408	7.813000	0.86123	1.476000	0.48215	0.655000	0.94253	GGT		0.647	CYP26B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251969.1	NM_019885		16	15	0	0	0	0.557998	0	16	15				
SCN1A	6323	broad.mit.edu	37	2	166872165	166872165	+	Missense_Mutation	SNP	C	C	T	rs146374754		TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr2:166872165C>T	ENST00000303395.4	-	17	3501	c.3502G>A	c.(3502-3504)Gta>Ata	p.V1168I	AC010127.3_ENST00000595268.1_RNA|SCN1A_ENST00000375405.3_Missense_Mutation_p.V1157I|AC010127.3_ENST00000595647.1_RNA|SCN1A_ENST00000409050.1_Missense_Mutation_p.V1140I|SCN1A_ENST00000423058.2_Missense_Mutation_p.V1168I|AC010127.3_ENST00000597623.1_RNA			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1168					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GGTTCCACTACGGGCTGTTCT	0.413																																						ENST00000423058.2																			0				NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200						c.(3502-3504)Gta>Ata		sodium channel, voltage-gated, type I, alpha subunit	Lamotrigine(DB00555)|Levetiracetam(DB01202)|Phenacemide(DB01121)|Phenytoin(DB00252)|Topiramate(DB00273)|Zonisamide(DB00909)	C	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	0,4406		0,0,2203	145.0	135.0	138.0		3502,3418,3502,3469	3.6	0.8	2	dbSNP_134	138	1,8597	1.2+/-3.3	0,1,4298	no	missense,missense,missense,missense	SCN1A	NM_001165963.1,NM_001165964.1,NM_001202435.1,NM_006920.4	29,29,29,29	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign,benign	1168/2010,1140/1982,1168/2010,1157/1999	166872165	1,13003	2203	4299	6502	SO:0001583	missense	6323					voltage-gated sodium channel complex	voltage-gated sodium channel activity	g.chr2:166872165C>T	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10585	protein-coding gene	gene with protein product		182389	"""febrile convulsions 3"""	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.3502G>A	2.37:g.166872165C>T	ENSP00000303540:p.Val1168Ile					AC010127.3_ENST00000597623.1_RNA|AC010127.3_ENST00000595647.1_RNA|SCN1A_ENST00000409050.1_Missense_Mutation_p.V1140I|SCN1A_ENST00000375405.3_Missense_Mutation_p.V1157I|SCN1A_ENST00000303395.4_Missense_Mutation_p.V1168I	p.V1168I	NM_001165963.1|NM_001202435.1	NP_001159435.1|NP_001189364.1	P35498	SCN1A_HUMAN			17	3519	-			1168					E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	37	c.3502G>A	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	C	13.61	2.290024	0.40494	0.0	1.16E-4	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.83419	-1.72;-1.72;-1.72;-1.72	5.42	3.63	0.41609	Sodium ion transport-associated (1);	0.251153	0.27686	N	0.018261	T	0.72645	0.3486	L	0.38692	1.165	0.23293	N	0.997963	P;B;P	0.36712	0.566;0.003;0.484	B;B;B	0.37267	0.124;0.003;0.245	T	0.58567	-0.7614	10	0.18710	T	0.47	.	9.3209	0.37964	0.0:0.7803:0.0:0.2197	.	1157;1140;1168	P35498-2;E9PG49;P35498	.;.;SCN1A_HUMAN	I	1168;1168;1157;1140	ENSP00000407030:V1168I;ENSP00000303540:V1168I;ENSP00000364554:V1157I;ENSP00000386312:V1140I	ENSP00000303540:V1168I	V	-	1	0	SCN1A	166580411	1.000000	0.71417	0.812000	0.32479	0.893000	0.52053	2.644000	0.46613	0.668000	0.31126	-0.373000	0.07131	GTA		0.413	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		47	78	0	0	0	0.870114	0	47	78				
BBS1	582	broad.mit.edu	37	11	66294278	66294278	+	Splice_Site	SNP	G	G	A	rs200116631	byFrequency	TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr11:66294278G>A	ENST00000318312.7	+	13	1390	c.1339G>A	c.(1339-1341)Gcc>Acc	p.A447T	BBS1_ENST00000529766.1_3'UTR|BBS1_ENST00000393994.2_Splice_Site_p.A318T|CTD-3074O7.11_ENST00000419755.3_Splice_Site_p.A484T|ZDHHC24_ENST00000526986.1_Intron|BBS1_ENST00000455748.2_Splice_Site_p.A350T	NM_024649.4	NP_078925.3	Q8NFJ9	BBS1_HUMAN	Bardet-Biedl syndrome 1	447					cilium assembly (GO:0042384)|Golgi to plasma membrane protein transport (GO:0043001)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	BBSome (GO:0034464)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	patched binding (GO:0005113)|RNA polymerase II repressing transcription factor binding (GO:0001103)|smoothened binding (GO:0005119)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(2)|urinary_tract(1)	28						GGCTGGCACCGGTGAGCCTCA	0.622									Bardet-Biedl syndrome				G|||	2	0.000399361	0.0015	0.0	5008	,	,		20063	0.0		0.0	False		,,,				2504	0.0				GBM(152;173 2612 9770 10137)	ENST00000419755.3																			0											c.e13+1									94.0	94.0	94.0					11																	66294278		2200	4295	6495	SO:0001630	splice_region_variant	0		Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome				g.chr11:66294278G>A	AF503941	CCDS8142.1	11q13	2013-01-08			ENSG00000174483	ENSG00000174483			966	protein-coding gene	gene with protein product		209901				9039982, 12567324	Standard	NM_024649		Approved	FLJ23590	uc001oij.1	Q8NFJ9	OTTHUMG00000167110	ENST00000318312.7:c.1339+1G>A	11.37:g.66294278G>A						ZDHHC24_ENST00000526986.1_Intron|BBS1_ENST00000455748.2_Splice_Site_p.A350_splice|BBS1_ENST00000529766.1_3'UTR|BBS1_ENST00000318312.7_Splice_Site_p.A447_splice|BBS1_ENST00000393994.2_Splice_Site_p.A318_splice	p.A484_splice							13	1528	+								Q32MM9|Q32MN0|Q96SN4	Splice_Site	SNP	ENST00000318312.7	37	c.1450_splice	CCDS8142.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	3.830	-0.036025	0.07497	.	.	ENSG00000256349;ENSG00000174483;ENSG00000174483;ENSG00000174483	ENST00000419755;ENST00000318312;ENST00000455748;ENST00000393994	D;D;D;D	0.96885	-4.09;-4.16;-3.97;-3.88	4.54	3.61	0.41365	.	.	.	.	.	D	0.90776	0.7104	L	0.28344	0.845	0.80722	D	1	B;P;B;B;B;B	0.34864	0.04;0.473;0.417;0.326;0.035;0.176	B;B;B;B;B;B	0.30716	0.009;0.036;0.119;0.032;0.02;0.023	D	0.87671	0.2541	9	0.14656	T	0.56	.	12.3202	0.54981	0.0:0.0:0.8289:0.1711	.	122;350;318;335;447;484	B4DH75;E7EQH1;Q32MM9;Q4G0L2;Q8NFJ9;Q8NFJ9-2	.;.;.;.;BBS1_HUMAN;.	T	484;447;350;318	ENSP00000398526:A484T;ENSP00000317469:A447T;ENSP00000405764:A350T;ENSP00000377563:A318T	ENSP00000317469:A447T	A	+	1	0	BBS1;CTD-3074O7.11	66050854	1.000000	0.71417	0.914000	0.36105	0.014000	0.08584	4.819000	0.62664	1.212000	0.43366	-0.182000	0.12963	GCC		0.622	BBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393235.2		Missense_Mutation	6	111	0	0	0	0.248553	0	6	111				
HELZ	9931	broad.mit.edu	37	17	65105677	65105677	+	Silent	SNP	A	A	G			TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr17:65105677A>G	ENST00000358691.5	-	29	4210	c.4044T>C	c.(4042-4044)gcT>gcC	p.A1348A	HELZ_ENST00000580168.1_Silent_p.A1349A	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	1348						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					GTGCGTGGGGAGCAGGAAGGG	0.473																																						ENST00000358691.5																			0				NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						c.(4042-4044)gcT>gcC		helicase with zinc finger							194.0	195.0	195.0					17																	65105677		2003	4170	6173	SO:0001819	synonymous_variant	9931							g.chr17:65105677A>G	D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"""Zinc fingers, CCCH-type domain containing"""	16878	protein-coding gene	gene with protein product	"""down-regulated in human cancers"""	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.4044T>C	17.37:g.65105677A>G						HELZ_ENST00000580168.1_Silent_p.A1349A	p.A1348A	NM_014877.3	NP_055692.2					29	4210	-	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)							I6L9H4	Silent	SNP	ENST00000358691.5	37	c.4044T>C	CCDS42374.1																																																																																				0.473	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		43	41	0	0	0	0.859065	0	43	41				
PDK1	5163	broad.mit.edu	37	2	173423525	173423525	+	Missense_Mutation	SNP	C	C	G			TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr2:173423525C>G	ENST00000282077.3	+	2	468	c.286C>G	c.(286-288)Ctc>Gtc	p.L96V	AC093818.1_ENST00000436922.1_RNA|AC093818.1_ENST00000444919.1_RNA|AC093818.1_ENST00000450443.1_RNA|PDK1_ENST00000410055.1_Missense_Mutation_p.L96V|AC093818.1_ENST00000442417.1_RNA|PDK1_ENST00000543905.1_Missense_Mutation_p.L20V|Y_RNA_ENST00000362996.1_RNA|PDK1_ENST00000392571.2_Missense_Mutation_p.L96V|PDK1_ENST00000544863.1_5'UTR			Q15118	PDK1_HUMAN	pyruvate dehydrogenase kinase, isozyme 1	96				L -> R (in Ref. 3; BAH14173). {ECO:0000305}.	cell proliferation (GO:0008283)|cellular metabolic process (GO:0044237)|glucose metabolic process (GO:0006006)|hypoxia-inducible factor-1alpha signaling pathway (GO:0097411)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of glucose metabolic process (GO:0010906)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)			central_nervous_system(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)	16			OV - Ovarian serous cystadenocarcinoma(117;0.12)			AGAAATAAGTCTCCTTCCAGA	0.393									Autosomal Dominant Polycystic Kidney Disease																													ENST00000410055.1																			0				central_nervous_system(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)	16						c.(286-288)Ctc>Gtc		pyruvate dehydrogenase kinase, isozyme 1							117.0	115.0	116.0					2																	173423525		2203	4300	6503	SO:0001583	missense	5163	Autosomal Dominant Polycystic Kidney Disease	Familial Cancer Database	ADPKD	glucose metabolic process|peptidyl-histidine phosphorylation|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate|small GTPase mediated signal transduction	mitochondrial matrix	ATP binding|pyruvate dehydrogenase (acetyl-transferring) kinase activity|two-component sensor activity	g.chr2:173423525C>G	L42450	CCDS2250.1, CCDS63059.1	2q31.1	2008-05-23	2005-11-16		ENSG00000152256	ENSG00000152256			8809	protein-coding gene	gene with protein product		602524	"""pyruvate dehydrogenase kinase, isoenzyme 1"""			7499431	Standard	NR_103731		Approved		uc002uhs.3	Q15118	OTTHUMG00000132285	ENST00000282077.3:c.286C>G	2.37:g.173423525C>G	ENSP00000282077:p.Leu96Val					PDK1_ENST00000282077.2_Missense_Mutation_p.L96V|PDK1_ENST00000544863.1_5'UTR|PDK1_ENST00000543905.1_Missense_Mutation_p.L20V|PDK1_ENST00000392571.2_Missense_Mutation_p.L96V	p.L96V	NM_002610.3	NP_002601.1	Q15118	PDK1_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.12)		2	386	+			96					B2R6T1|B7Z937|D3DPD8|E9PD65|Q308M4	Missense_Mutation	SNP	ENST00000282077.3	37	c.286C>G	CCDS2250.1	.	.	.	.	.	.	.	.	.	.	C	16.40	3.111310	0.56398	.	.	ENSG00000152256	ENST00000443353;ENST00000543905;ENST00000282077;ENST00000392571;ENST00000410055;ENST00000416991;ENST00000439519	T;T;T;T;T;T;T	0.31510	1.49;1.49;1.49;1.49;1.49;1.49;1.49	5.7	5.7	0.88788	Branched-chain alpha-ketoacid dehydrogenase kinase/Pyruvate dehydrogenase kinase, N-terminal (3);	0.063440	0.64402	D	0.000003	T	0.48607	0.1509	M	0.92604	3.325	0.80722	D	1	B;P	0.36874	0.286;0.572	B;P	0.46026	0.223;0.501	T	0.49995	-0.8879	10	0.15066	T	0.55	-19.6975	9.6268	0.39754	0.0:0.8074:0.0:0.1926	.	96;96	Q15118;E9PD65	PDK1_HUMAN;.	V	20;20;96;96;96;38;20	ENSP00000399558:L20V;ENSP00000438567:L20V;ENSP00000282077:L96V;ENSP00000376352:L96V;ENSP00000386985:L96V;ENSP00000399160:L38V;ENSP00000388366:L20V	ENSP00000282077:L96V	L	+	1	0	PDK1	173131771	1.000000	0.71417	1.000000	0.80357	0.894000	0.52154	1.881000	0.39638	2.703000	0.92315	0.655000	0.94253	CTC		0.393	PDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255380.3	NM_002610		32	41	0	0	0	0.729181	0	32	41				
TRIM28	10155	broad.mit.edu	37	19	59059532	59059532	+	Missense_Mutation	SNP	G	G	T			TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr19:59059532G>T	ENST00000253024.5	+	7	1375	c.1086G>T	c.(1084-1086)ttG>ttT	p.L362F	TRIM28_ENST00000341753.6_Missense_Mutation_p.L280F	NM_005762.2	NP_005753.1	Q13263	TIF1B_HUMAN	tripartite motif containing 28	362	Interaction with MAGEC2.|Leucine zipper alpha helical coiled-coil region.|RBCC domain.				convergent extension involved in axis elongation (GO:0060028)|DNA repair (GO:0006281)|embryonic placenta morphogenesis (GO:0060669)|epithelial to mesenchymal transition (GO:0001837)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of DNA repair (GO:0045739)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein sumoylation (GO:0016925)|protein ubiquitination (GO:0016567)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|Krueppel-associated box domain binding (GO:0035851)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)		CAGCCCTTTTGCTTTCTAAGA	0.532																																						ENST00000253024.5																			0				biliary_tract(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|urinary_tract(1)	19						c.(1084-1086)ttG>ttT		tripartite motif containing 28							180.0	177.0	178.0					19																	59059532		2203	4300	6503	SO:0001583	missense	10155				epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent	nucleoplasm	chromo shadow domain binding|ligase activity|transcription corepressor activity|zinc ion binding	g.chr19:59059532G>T		CCDS12985.1	19q13.4	2014-06-13	2011-01-25			ENSG00000130726		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, PHD-type"""	16384	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 157"""	601742	"""tripartite motif-containing 28"""			11331580, 11226167	Standard	NM_005762		Approved	TIF1B, KAP1, TF1B, RNF96, PPP1R157	uc002qtg.1	Q13263		ENST00000253024.5:c.1086G>T	19.37:g.59059532G>T	ENSP00000253024:p.Leu362Phe					TRIM28_ENST00000341753.6_Missense_Mutation_p.L280F	p.L362F	NM_005762.2	NP_005753.1	Q13263	TIF1B_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (67;0.0434)|all cancers(4;1.39e-13)|Epithelial(4;1.01e-10)|OV - Ovarian serous cystadenocarcinoma(4;2.34e-09)|GBM - Glioblastoma multiforme(193;0.0102)|Lung(386;0.179)	7	1375	+		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)	362			Leucine zipper alpha helical coiled-coil region.|RBCC domain.		O00677|Q7Z632|Q93040|Q96IM1	Missense_Mutation	SNP	ENST00000253024.5	37	c.1086G>T	CCDS12985.1	.	.	.	.	.	.	.	.	.	.	G	18.53	3.644737	0.67358	.	.	ENSG00000130726	ENST00000253024;ENST00000341753	T;T	0.80033	-1.01;-1.33	5.12	4.08	0.47627	B-box, C-terminal (1);	0.000000	0.56097	D	0.000029	D	0.86535	0.5956	L	0.57536	1.79	0.45427	D	0.998408	D;D	0.76494	0.999;0.998	D;D	0.87578	0.998;0.996	D	0.87273	0.2287	10	0.87932	D	0	-19.2018	11.6439	0.51250	0.0877:0.0:0.9123:0.0	.	280;362	Q13263-2;Q13263	.;TIF1B_HUMAN	F	362;280	ENSP00000253024:L362F;ENSP00000342232:L280F	ENSP00000253024:L362F	L	+	3	2	TRIM28	63751344	1.000000	0.71417	0.930000	0.37139	0.956000	0.61745	1.688000	0.37690	1.297000	0.44761	0.555000	0.69702	TTG		0.532	TRIM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467074.1	NM_005762		6	195	1	0	0.0293803	0.248553	0.0306861	6	195				
ARHGAP25	9938	broad.mit.edu	37	2	69002506	69002506	+	Missense_Mutation	SNP	C	C	T	rs201284610	byFrequency	TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr2:69002506C>T	ENST00000295381.3	+	2	634	c.215C>T	c.(214-216)gCg>gTg	p.A72V	ARHGAP25_ENST00000467265.1_Missense_Mutation_p.A72V|ARHGAP25_ENST00000409202.3_Missense_Mutation_p.A72V|ARHGAP25_ENST00000544262.1_Missense_Mutation_p.A46V|ARHGAP25_ENST00000409030.3_Missense_Mutation_p.A65V|ARHGAP25_ENST00000497079.1_Missense_Mutation_p.A65V|ARHGAP25_ENST00000456116.2_3'UTR|ARHGAP25_ENST00000409220.1_Missense_Mutation_p.A65V	NM_001007231.2	NP_001007232.2	P42331	RHG25_HUMAN	Rho GTPase activating protein 25	72	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(20)|ovary(3)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	52						GTGCTGAGGGCGCAGCAGCTC	0.592													C|||	2	0.000399361	0.0015	0.0	5008	,	,		17936	0.0		0.0	False		,,,				2504	0.0					ENST00000295381.3																			0				breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(20)|ovary(3)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	52						c.(214-216)gCg>gTg		Rho GTPase activating protein 25							116.0	122.0	120.0					2																	69002506		2203	4300	6503	SO:0001583	missense	9938				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity	g.chr2:69002506C>T	D29642	CCDS33214.1, CCDS46312.1, CCDS33214.2, CCDS54363.1, CCDS54364.1	2p13.3	2013-01-10			ENSG00000163219	ENSG00000163219		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	28951	protein-coding gene	gene with protein product		610587				7584044	Standard	NM_001007231		Approved	KIAA0053	uc010fdg.3	P42331	OTTHUMG00000152621	ENST00000295381.3:c.215C>T	2.37:g.69002506C>T	ENSP00000295381:p.Ala72Val					ARHGAP25_ENST00000544262.1_Missense_Mutation_p.A46V|ARHGAP25_ENST00000409030.3_Missense_Mutation_p.A65V|ARHGAP25_ENST00000497079.1_Missense_Mutation_p.A65V|ARHGAP25_ENST00000467265.1_Missense_Mutation_p.A72V|ARHGAP25_ENST00000456116.2_3'UTR|ARHGAP25_ENST00000409202.3_Missense_Mutation_p.A72V|ARHGAP25_ENST00000409220.1_Missense_Mutation_p.A65V	p.A72V	NM_001007231.2	NP_001007232.2	P42331	RHG25_HUMAN			2	634	+			72			PH.		A8K2Y1|B7Z498|E9PFQ7|G5E9G2|Q8IXQ2	Missense_Mutation	SNP	ENST00000295381.3	37	c.215C>T		1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	15.89	2.965662	0.53507	.	.	ENSG00000163219	ENST00000544262;ENST00000295381;ENST00000409202;ENST00000467265;ENST00000409030;ENST00000409220;ENST00000482106;ENST00000497079	T;T;T;T;T;T;T	0.12255	2.7;2.7;2.7;2.7;2.7;2.7;2.7	5.58	4.69	0.59074	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.168528	0.52532	D	0.000076	T	0.13157	0.0319	L	0.42245	1.32	0.26473	N	0.975242	P;B;P;P;P;P;B	0.49090	0.919;0.221;0.767;0.767;0.767;0.767;0.346	B;B;B;B;B;B;B	0.41917	0.37;0.06;0.098;0.098;0.098;0.066;0.058	T	0.14392	-1.0474	10	0.37606	T	0.19	.	12.1387	0.53986	0.0:0.6502:0.3498:0.0	.	72;46;72;65;65;65;72	E9PFQ7;B7Z8K7;P42331-4;G5E9G2;P42331-3;P42331-2;P42331	.;.;.;.;.;.;RHG25_HUMAN	V	46;72;72;72;65;65;65;65	ENSP00000439917:A46V;ENSP00000295381:A72V;ENSP00000386911:A72V;ENSP00000420583:A72V;ENSP00000386863:A65V;ENSP00000386241:A65V;ENSP00000417139:A65V	ENSP00000295381:A72V	A	+	2	0	ARHGAP25	68856010	0.999000	0.42202	0.858000	0.33744	0.448000	0.32197	3.334000	0.52097	2.613000	0.88420	0.563000	0.77884	GCG		0.592	ARHGAP25-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014882		4	92	0	0	0	0.150653	0	4	92				
CLK4	57396	broad.mit.edu	37	5	178039445	178039445	+	Silent	SNP	C	C	T			TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr5:178039445C>T	ENST00000316308.4	-	9	1191	c.1023G>A	c.(1021-1023)cgG>cgA	p.R341R		NM_020666.2	NP_065717.1	Q9HAZ1	CLK4_HUMAN	CDC-like kinase 4	341	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(2)	21	all_cancers(89;0.000969)|Renal(175;0.000159)|all_epithelial(37;0.000451)|Lung NSC(126;0.00545)|all_lung(126;0.00918)	all_cancers(40;0.0272)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.235)		CTCTGTAGTGCCGGGTAGACA	0.408																																						ENST00000316308.4																			0				breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(2)	21						c.(1021-1023)cgG>cgA		CDC-like kinase 4							80.0	71.0	74.0					5																	178039445		2203	4300	6503	SO:0001819	synonymous_variant	57396					nucleus	ATP binding|protein serine/threonine kinase activity|protein tyrosine kinase activity	g.chr5:178039445C>T	AF294429	CCDS4437.1	5q35	2008-05-02			ENSG00000113240	ENSG00000113240		"""CDC-like kinases"""	13659	protein-coding gene	gene with protein product		607969				11170754	Standard	NM_020666		Approved		uc003mjf.1	Q9HAZ1	OTTHUMG00000130893	ENST00000316308.4:c.1023G>A	5.37:g.178039445C>T							p.R341R	NM_020666.2	NP_065717.1	Q9HAZ1	CLK4_HUMAN	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.235)	9	1191	-	all_cancers(89;0.000969)|Renal(175;0.000159)|all_epithelial(37;0.000451)|Lung NSC(126;0.00545)|all_lung(126;0.00918)	all_cancers(40;0.0272)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	341			Protein kinase.			Silent	SNP	ENST00000316308.4	37	c.1023G>A	CCDS4437.1																																																																																				0.408	CLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253479.2			3	58	0	0	0	0.115264	0	3	58				
NBPF1	55672	broad.mit.edu	37	1	16918653	16918653	+	Splice_Site	SNP	C	C	T			TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr1:16918653C>T	ENST00000430580.2	-	6	853		c.e6+1			NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1							cytoplasm (GO:0005737)									UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		TCTTAACTTACTGTTGTGAAA	0.418																																						ENST00000430580.2																			0											c.e6+1		neuroblastoma breakpoint family, member 1																																				SO:0001630	splice_region_variant	55672					cytoplasm		g.chr1:16918653C>T	AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481		"""neuroblastoma breakpoint family"""	26088	protein-coding gene	gene with protein product		610501				11214970, 16079250	Standard	NM_017940		Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.34+1G>A	1.37:g.16918653C>T								NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)	6	853	-								Q8N4E8|Q9C0H0	Splice_Site	SNP	ENST00000430580.2	37																																																																																						0.418	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000106436.3	NM_017940	Intron	4	46	0	0	0	0.184627	0	4	46				
PXDNL	137902	broad.mit.edu	37	8	52359639	52359639	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr8:52359639C>T	ENST00000356297.4	-	12	1550	c.1450G>A	c.(1450-1452)Ggc>Agc	p.G484S	PXDNL_ENST00000543296.1_Missense_Mutation_p.G484S	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	484	Ig-like C2-type 3.				hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				TCATATTGGCCTTGATCGTGC	0.468																																						ENST00000356297.4																			0				NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48						c.(1450-1452)Ggc>Agc		peroxidasin homolog (Drosophila)-like							155.0	151.0	152.0					8																	52359639		2024	4183	6207	SO:0001583	missense	137902				hydrogen peroxide catabolic process	extracellular space	heme binding|peroxidase activity	g.chr8:52359639C>T		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"""Immunoglobulin superfamily / I-set domain containing"""	26359	protein-coding gene	gene with protein product	"""polysomal ribonuclease 1 homolog (Xenopus)"""	615904	"""peroxidasin homolog-like (Drosophila)"""			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.1450G>A	8.37:g.52359639C>T	ENSP00000348645:p.Gly484Ser					PXDNL_ENST00000543296.1_Missense_Mutation_p.G484S	p.G484S	NM_144651.4	NP_653252.3	A1KZ92	PXDNL_HUMAN			12	1550	-		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)	484			Ig-like C2-type 3.		B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	c.1450G>A	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.342424	0.81911	.	.	ENSG00000147485	ENST00000356297;ENST00000543296	T;T	0.80994	-1.44;-1.44	4.02	4.02	0.46733	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.92821	0.7717	H	0.98068	4.14	0.42647	D	0.993435	D	0.89917	1.0	D	0.91635	0.999	D	0.94464	0.7679	9	0.72032	D	0.01	.	11.6306	0.51173	0.0:1.0:0.0:0.0	.	484	A1KZ92	PXDNL_HUMAN	S	484	ENSP00000348645:G484S;ENSP00000444865:G484S	ENSP00000348645:G484S	G	-	1	0	PXDNL	52522192	1.000000	0.71417	0.951000	0.38953	0.780000	0.44128	3.400000	0.52594	1.775000	0.52247	0.467000	0.42956	GGC		0.468	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		5	221	0	0	0	0.184627	0	5	221				
TP53	7157	broad.mit.edu	37	17	7579362	7579362	+	Missense_Mutation	SNP	A	A	C	rs587783063		TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr17:7579362A>C	ENST00000269305.4	-	4	514	c.325T>G	c.(325-327)Ttc>Gtc	p.F109V	TP53_ENST00000455263.2_Missense_Mutation_p.F109V|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Missense_Mutation_p.F109V|TP53_ENST00000413465.2_Missense_Mutation_p.F109V|TP53_ENST00000359597.4_Missense_Mutation_p.F109V|TP53_ENST00000445888.2_Missense_Mutation_p.F109V	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	109	Interaction with HIPK1. {ECO:0000250}.|Interaction with WWOX.|Required for interaction with ZNF385A.		F -> C (in sporadic cancers; somatic mutation).|F -> L (in a sporadic cancer; somatic mutation).|F -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.Q100fs*37(3)|p.G59fs*23(3)|p.F109fs*16(3)|p.G108_F109delGF(2)|p.F109_R110delFR(2)|p.V73fs*9(1)|p.G105_T125del21(1)|p.Y107fs*44(1)|p.W91fs*13(1)|p.Y103_G112>C(1)|p.P13fs*18(1)|p.S33fs*23(1)|p.Y107fs*38(1)|p.F109V(1)|p.Y103_L111>L(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CCCAGACGGAAACCGTAGCTG	0.612		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	ENST00000420246.2		111	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	"""Mis, N, F"""	tumor protein p53			"""L, E, M, O"""		"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""	"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""		31	Deletion - Frameshift(12)|Whole gene deletion(8)|Deletion - In frame(5)|Insertion - Frameshift(3)|Complex - deletion inframe(2)|Substitution - Missense(1)	p.0?(8)|p.Q100fs*37(3)|p.G59fs*23(3)|p.F109fs*16(3)|p.G108_F109delGF(2)|p.F109_R110delFR(2)|p.V73fs*9(1)|p.G105_T125del21(1)|p.Y107fs*44(1)|p.W91fs*13(1)|p.Y103_G112>C(1)|p.P13fs*18(1)|p.S33fs*23(1)|p.Y107fs*38(1)|p.F109V(1)|p.Y103_L111>L(1)	ovary(6)|upper_aerodigestive_tract(5)|bone(4)|breast(4)|lung(3)|large_intestine(2)|central_nervous_system(2)|liver(2)|stomach(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185						c.(325-327)Ttc>Gtc	Other conserved DNA damage response genes	tumor protein p53							62.0	59.0	60.0					17																	7579362		2203	4300	6503	SO:0001583	missense	7157	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	g.chr17:7579362A>C	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.325T>G	17.37:g.7579362A>C	ENSP00000269305:p.Phe109Val	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)				TP53_ENST00000445888.2_Missense_Mutation_p.F109V|TP53_ENST00000359597.4_Missense_Mutation_p.F109V|TP53_ENST00000413465.2_Missense_Mutation_p.F109V|TP53_ENST00000455263.2_Missense_Mutation_p.F109V|TP53_ENST00000269305.4_Missense_Mutation_p.F109V	p.F109V	NM_001126114.2|NM_001276696.1	NP_001119586.1|NP_001263625.1	P04637	P53_HUMAN		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	4	457	-		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)	109		F -> C (in sporadic cancers; somatic mutation).|F -> L (in a sporadic cancer; somatic mutation).|F -> S (in sporadic cancers; somatic mutation).	Interaction with HIPK1 (By similarity).|Interaction with WWOX.		Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	c.325T>G	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	19.13	3.768678	0.69878	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000508793;ENST00000503591	D;D;D;D;D;D;D;D	0.99842	-7.1;-7.1;-7.1;-7.1;-7.1;-7.1;-7.1;-7.1	4.75	4.75	0.60458	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.104685	0.64402	D	0.000004	D	0.99796	0.9913	M	0.90977	3.165	0.44247	D	0.997097	D;D;D;D;D;D;D	0.89917	1.0;0.988;0.999;0.999;0.999;0.992;0.998	D;D;D;D;D;D;D	0.97110	1.0;0.914;0.994;0.997;0.996;0.994;0.974	D	0.97852	1.0275	10	0.87932	D	0	-31.6488	7.201	0.25881	0.9017:0.0:0.0983:0.0	.	70;109;109;109;109;109;109	B4E095;E7EMR6;P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	V	109	ENSP00000410739:F109V;ENSP00000352610:F109V;ENSP00000269305:F109V;ENSP00000398846:F109V;ENSP00000391127:F109V;ENSP00000391478:F109V;ENSP00000424104:F109V;ENSP00000426252:F109V	ENSP00000269305:F109V	F	-	1	0	TP53	7520087	1.000000	0.71417	0.861000	0.33841	0.921000	0.55340	4.618000	0.61211	2.125000	0.65367	0.533000	0.62120	TTC		0.612	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		54	7	0	0	0	0.870114	0	54	7				
CAMK1D	57118	broad.mit.edu	37	10	12803041	12803041	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr10:12803041G>A	ENST00000378847.3	+	4	731	c.394G>A	c.(394-396)Gtg>Atg	p.V132M	CAMK1D_ENST00000378845.1_Missense_Mutation_p.V132M	NM_153498.2	NP_705718.1	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID	132	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				inflammatory response (GO:0006954)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis (GO:0050766)|positive regulation of respiratory burst (GO:0060267)|regulation of dendrite development (GO:0050773)|regulation of granulocyte chemotaxis (GO:0071622)	calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|stomach(1)	16				GBM - Glioblastoma multiforme(1;3.16e-05)		CTTGGACGCCGTGTACTATCT	0.577																																						ENST00000378847.3																			0				endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|stomach(1)	16						c.(394-396)Gtg>Atg		calcium/calmodulin-dependent protein kinase ID							86.0	71.0	76.0					10																	12803041		2203	4300	6503	SO:0001583	missense	57118					calcium- and calmodulin-dependent protein kinase complex|cytoplasm|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity	g.chr10:12803041G>A	AF286366	CCDS7091.1, CCDS7092.1	10p13	2003-11-05			ENSG00000183049	ENSG00000183049			19341	protein-coding gene	gene with protein product		607957				11050006	Standard	XM_006717481		Approved	CKLiK	uc001ilo.3	Q8IU85	OTTHUMG00000017683	ENST00000378847.3:c.394G>A	10.37:g.12803041G>A	ENSP00000368124:p.Val132Met					CAMK1D_ENST00000378845.1_Missense_Mutation_p.V132M	p.V132M	NM_153498.2	NP_705718.1	Q8IU85	KCC1D_HUMAN		GBM - Glioblastoma multiforme(1;3.16e-05)	4	731	+			132			Protein kinase.		B0YIY0|Q9HD31	Missense_Mutation	SNP	ENST00000378847.3	37	c.394G>A	CCDS7091.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.882980	0.91740	.	.	ENSG00000183049	ENST00000378847;ENST00000378845	T;T	0.41400	1.0;1.0	5.71	5.71	0.89125	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.057688	0.64402	D	0.000002	T	0.66228	0.2768	M	0.72118	2.19	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.986	T	0.68032	-0.5516	10	0.87932	D	0	-28.48	18.8366	0.92165	0.0:0.0:1.0:0.0	.	132;132	Q8IU85;Q5SQQ7	KCC1D_HUMAN;.	M	132	ENSP00000368124:V132M;ENSP00000368122:V132M	ENSP00000368122:V132M	V	+	1	0	CAMK1D	12843047	1.000000	0.71417	0.960000	0.40013	0.837000	0.47467	9.869000	0.99810	2.684000	0.91462	0.655000	0.94253	GTG		0.577	CAMK1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046820.1	NM_020397		12	21	0	0	0	0.411799	0	12	21				
HNF1B	6928	broad.mit.edu	37	17	36059196	36059196	+	Silent	SNP	G	G	A			TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr17:36059196G>A	ENST00000225893.4	-	8	1900	c.1539C>T	c.(1537-1539)taC>taT	p.Y513Y	HNF1B_ENST00000561193.1_Silent_p.Y487Y|HNF1B_ENST00000427275.2_Intron|HNF1B_ENST00000560016.1_Intron	NM_000458.2|NM_001165923.1	NP_000449.1|NP_001159395.1	P35680	HNF1B_HUMAN	HNF1 homeobox B	513					anterior/posterior pattern specification (GO:0009952)|branching morphogenesis of an epithelial tube (GO:0048754)|embryonic digestive tract morphogenesis (GO:0048557)|endocrine pancreas development (GO:0031018)|endodermal cell fate specification (GO:0001714)|epithelial cell proliferation (GO:0050673)|genitalia development (GO:0048806)|hepatoblast differentiation (GO:0061017)|hindbrain development (GO:0030902)|inner cell mass cell differentiation (GO:0001826)|insulin secretion (GO:0030073)|kidney development (GO:0001822)|mesonephric duct formation (GO:0072181)|negative regulation of mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis (GO:0061296)|negative regulation of mesenchymal cell apoptotic process involved in metanephros development (GO:1900212)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephric nephron tubule development (GO:0039020)|pronephros development (GO:0048793)|regulation of branch elongation involved in ureteric bud branching (GO:0072095)|regulation of endodermal cell fate specification (GO:0042663)|regulation of pronephros size (GO:0035565)|regulation of Wnt signaling pathway (GO:0030111)|response to glucose (GO:0009749)|ureteric bud elongation (GO:0060677)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(6)|kidney(3)|large_intestine(2)|liver(1)|lung(3)|ovary(3)|prostate(1)|skin(2)	28		Breast(25;0.00765)|Ovarian(249;0.15)	STAD - Stomach adenocarcinoma(1;0.0142)			GCTTGTGTGCGTACACTGGAG	0.532																																					Colon(71;102 1179 9001 27917 43397)	ENST00000225893.4																			0				breast(2)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(6)|kidney(3)|large_intestine(2)|liver(1)|lung(3)|ovary(3)|prostate(1)|skin(2)	28						c.(1537-1539)taC>taT		HNF1 homeobox B							96.0	87.0	90.0					17																	36059196		2203	4300	6503	SO:0001819	synonymous_variant	6928				endocrine pancreas development|genitalia development|kidney development|positive regulation of transcription initiation from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|pronephric nephron tubule development|regulation of pronephros size	nucleus	DNA binding|protein homodimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr17:36059196G>A	BC017714	CCDS11324.1, CCDS58538.1	17q12	2014-05-06	2007-08-24	2007-08-24	ENSG00000108753	ENSG00000275410		"""Homeoboxes / HNF class"""	11630	protein-coding gene	gene with protein product		189907	"""transcription factor 2, hepatic; LF-B3; variant hepatic nuclear factor"""	TCF2		1677179, 10484768	Standard	NM_000458		Approved	LFB3, VHNF1, HNF1beta, MODY5	uc002hok.4	P35680	OTTHUMG00000188478	ENST00000225893.4:c.1539C>T	17.37:g.36059196G>A						HNF1B_ENST00000561193.1_Silent_p.Y487Y|HNF1B_ENST00000560016.1_Intron|HNF1B_ENST00000427275.2_Intron	p.Y513Y	NM_000458.2|NM_001165923.1	NP_000449.1|NP_001159395.1	P35680	HNF1B_HUMAN	STAD - Stomach adenocarcinoma(1;0.0142)		8	1900	-		Breast(25;0.00765)|Ovarian(249;0.15)	513					B4DKM3|E0YMJ9	Silent	SNP	ENST00000225893.4	37	c.1539C>T	CCDS11324.1																																																																																				0.532	HNF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256807.3	NM_000458		6	38	0	0	0	0.278610	0	6	38				
AMOTL2	51421	broad.mit.edu	37	3	134079238	134079238	+	Silent	SNP	T	T	G			TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr3:134079238T>G	ENST00000422605.2	-	7	1759	c.1593A>C	c.(1591-1593)ccA>ccC	p.P531P	AMOTL2_ENST00000249883.5_Silent_p.P531P|AMOTL2_ENST00000514516.1_Silent_p.P589P|AMOTL2_ENST00000513145.1_Silent_p.P529P			Q9Y2J4	AMOL2_HUMAN	angiomotin like 2	531					hippo signaling (GO:0035329)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|tight junction (GO:0005923)				endometrium(8)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	19						TGCTACCACCTGGGGCACCTG	0.632																																						ENST00000514516.1																			0				endometrium(8)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	19						c.(1765-1767)ccA>ccC		angiomotin like 2							30.0	31.0	31.0					3																	134079238		2203	4298	6501	SO:0001819	synonymous_variant	51421							g.chr3:134079238T>G	AF175966	CCDS33860.1, CCDS63783.1, CCDS63784.1	3q21-q22	2008-07-18			ENSG00000114019	ENSG00000114019			17812	protein-coding gene	gene with protein product	"""Leman coiled-coil protein"", ""angiomotin-like protein 2"""	614658					Standard	NM_016201		Approved	LCCP	uc003eqg.1	Q9Y2J4	OTTHUMG00000159777	ENST00000422605.2:c.1593A>C	3.37:g.134079238T>G						AMOTL2_ENST00000422605.2_Silent_p.P531P|AMOTL2_ENST00000513145.1_Silent_p.P529P|AMOTL2_ENST00000249883.5_Silent_p.P531P	p.P589P	NM_001278683.1	NP_001265612.1	Q9Y2J4	AMOL2_HUMAN			7	1945	-			531					A8K6F1|B7Z5Q1|E9PHW3|Q53EP1|Q96F99|Q9UKB4	Silent	SNP	ENST00000422605.2	37	c.1767A>C																																																																																					0.632	AMOTL2-014	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000358149.1	NM_016201		4	10	0	0	0	0.217242	0	4	10				
CBX5	23468	broad.mit.edu	37	12	54635636	54635636	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr12:54635636C>T	ENST00000439541.2	-	5	604	c.479G>A	c.(478-480)tGt>tAt	p.C160Y	CBX5_ENST00000209875.4_Missense_Mutation_p.C160Y|CBX5_ENST00000550411.1_Missense_Mutation_p.C160Y	NM_001127321.1	NP_001120793.1	P45973	CBX5_HUMAN	chromobox homolog 5	160	Chromo 2; shadow subtype. {ECO:0000255|PROSITE-ProRule:PRU00053}.|Interaction with ASXL1.				blood coagulation (GO:0007596)|negative regulation of transcription, DNA-templated (GO:0045892)|viral process (GO:0016032)	chromocenter (GO:0010369)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|kinetochore (GO:0000776)|nuclear envelope (GO:0005635)|nuclear heterochromatin (GO:0005720)|nuclear pericentric heterochromatin (GO:0031618)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|methylated histone binding (GO:0035064)|protein binding, bridging (GO:0030674)|repressing transcription factor binding (GO:0070491)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)	8						AATTTGTGGACATTTCACATT	0.398																																					Colon(153;588 2459 18334 48613)	ENST00000209875.4																			0				endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)	8						c.(478-480)tGt>tAt		chromobox homolog 5							203.0	183.0	190.0					12																	54635636		2203	4300	6503	SO:0001583	missense	23468				blood coagulation|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|nuclear centromeric heterochromatin|nuclear envelope|nucleolus|transcriptional repressor complex	methylated histone residue binding|protein binding, bridging|repressing transcription factor binding	g.chr12:54635636C>T	U26311	CCDS8875.1	12q13.13	2010-07-06	2010-06-24		ENSG00000094916	ENSG00000094916			1555	protein-coding gene	gene with protein product	"""HP1 alpha homolog (Drosophila)"""	604478	"""chromobox homolog 5 (Drosophila HP1 alpha)"", ""chromobox homolog 5 (HP1 alpha homolog, Drosophila)"""			8663349	Standard	NM_012117		Approved	HP1Hs-alpha, HP1, HP1-ALPHA	uc001sfj.4	P45973		ENST00000439541.2:c.479G>A	12.37:g.54635636C>T	ENSP00000401009:p.Cys160Tyr					CBX5_ENST00000550411.1_Missense_Mutation_p.C160Y|CBX5_ENST00000439541.2_Missense_Mutation_p.C160Y	p.C160Y	NM_012117.2	NP_036249.1	P45973	CBX5_HUMAN			5	615	-			160			Chromo 2; shadow subtype.		B2R8T9	Missense_Mutation	SNP	ENST00000439541.2	37	c.479G>A	CCDS8875.1	.	.	.	.	.	.	.	.	.	.	C	17.82	3.483358	0.63962	.	.	ENSG00000094916	ENST00000209875;ENST00000439541;ENST00000550489;ENST00000550411	T;T;T	0.53640	0.61;0.61;0.61	5.17	4.28	0.50868	Chromo shadow (1);Chromo domain-like (1);Chromo domain/shadow (2);Chromo shadow, subgroup (1);	0.076920	0.64402	D	0.000001	T	0.69557	0.3124	M	0.83692	2.655	0.80722	D	1	D;P	0.54397	0.966;0.887	D;P	0.74348	0.983;0.733	T	0.75153	-0.3418	10	0.87932	D	0	-3.0526	13.2707	0.60159	0.1595:0.8405:0.0:0.0	.	159;160	G3V1X9;P45973	.;CBX5_HUMAN	Y	160;160;159;160	ENSP00000209875:C160Y;ENSP00000401009:C160Y;ENSP00000449207:C160Y	ENSP00000209875:C160Y	C	-	2	0	CBX5	52921903	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.321000	0.79088	1.546000	0.49388	0.655000	0.94253	TGT		0.398	CBX5-004	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000405468.1	NM_012117		45	71	0	0	0	0.847076	0	45	71				
IDH1	3417	broad.mit.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000446179.1_Missense_Mutation_p.R132H|IDH1_ENST00000345146.2_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)	ENST00000415913.1				Dom	yes		2	2q33.3	3417	Mis	"""isocitrate dehydrogenase 1 (NADP+), soluble"""			O			gliobastoma		2835	Substitution - Missense(2834)|Complex - compound substitution(1)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(1)	NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887						c.(394-396)cGt>cAt		isocitrate dehydrogenase 1 (NADP+), soluble							79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle	cytosol|peroxisomal matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity	g.chr2:209113112C>T		CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His					IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_Missense_Mutation_p.R132H	p.R132H			O75874	IDHC_HUMAN		Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)	4	776	-			132		R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate).|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).			Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	c.395G>A	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			24	34	0	0	0	0.624587	0	24	34				
FAM134B	54463	broad.mit.edu	37	5	16475174	16475174	+	Silent	SNP	C	C	T	rs369353830		TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr5:16475174C>T	ENST00000306320.9	-	9	1256	c.1170G>A	c.(1168-1170)acG>acA	p.T390T	FAM134B_ENST00000399793.2_Silent_p.T249T	NM_001034850.2	NP_001030022.1	Q9H6L5	F134B_HUMAN	family with sequence similarity 134, member B	390					sensory perception of pain (GO:0019233)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(2)|skin(1)	16						CTGCTGATTGCGTCTCTTTGC	0.493																																						ENST00000306320.9																			0				breast(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(2)|skin(1)	16						c.(1168-1170)acG>acA		family with sequence similarity 134, member B		C	,	1,3993		0,1,1996	176.0	174.0	174.0		1170,747	2.5	0.0	5		174	0,8360		0,0,4180	no	coding-synonymous,coding-synonymous	FAM134B	NM_001034850.1,NM_019000.3	,	0,1,6176	TT,TC,CC		0.0,0.025,0.0081	,	390/498,249/357	16475174	1,12353	1997	4180	6177	SO:0001819	synonymous_variant	54463				sensory perception of pain	cis-Golgi network|endoplasmic reticulum|integral to membrane		g.chr5:16475174C>T	BC053326	CCDS43304.1, CCDS43305.1	5p15.1	2014-09-17			ENSG00000154153	ENSG00000154153			25964	protein-coding gene	gene with protein product		613114				19838196, 24327336	Standard	NM_001034850		Approved	FLJ20152	uc003jfs.3	Q9H6L5	OTTHUMG00000161788	ENST00000306320.9:c.1170G>A	5.37:g.16475174C>T						FAM134B_ENST00000399793.2_Silent_p.T249T	p.T390T	NM_001034850.2	NP_001030022.1	Q9H6L5	F134B_HUMAN			9	1256	-			390					Q69YN8|Q9H6K6|Q9H764|Q9NXM8	Silent	SNP	ENST00000306320.9	37	c.1170G>A	CCDS43304.1																																																																																				0.493	FAM134B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000366090.1	NM_001034850		37	48	0	0	0	0.796494	0	37	48				
WASH3P	374666	broad.mit.edu	37	15	102515299	102515299	+	RNA	SNP	G	G	A	rs201972834		TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr15:102515299G>A	ENST00000557932.1	+	0	1145				DDX11L9_ENST00000562189.1_RNA			C4AMC7	WASH3_HUMAN	WAS protein family homolog 3 pseudogene						Arp2/3 complex-mediated actin nucleation (GO:0034314)|endosomal transport (GO:0016197)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|recycling endosome (GO:0055037)|WASH complex (GO:0071203)	alpha-tubulin binding (GO:0043014)	p.G374S(10)		central_nervous_system(1)|endometrium(6)|kidney(11)|prostate(5)|stomach(1)|urinary_tract(1)	25						TGGGGGCATCGGCAAGGCCAA	0.652																																						ENST00000557932.1																			10	Substitution - Missense(10)	p.G374S(10)	kidney(7)|prostate(2)|endometrium(1)	central_nervous_system(1)|endometrium(6)|kidney(11)|prostate(5)|stomach(1)|urinary_tract(1)	25																																														0							g.chr15:102515299G>A			15q26.3	2014-03-20	2008-01-16	2008-01-16	ENSG00000185596	ENSG00000185596		"""WAS protein homologs"""	24362	pseudogene	pseudogene			"""family with sequence similarity 39, member D pseudogene"""	FAM39DP		11701968, 18159949	Standard	NR_003659		Approved	FLJ25222	uc002cdi.3	C4AMC7	OTTHUMG00000172275		15.37:g.102515299G>A														0	1145	+									RNA	SNP	ENST00000557932.1	37			.	.	.	.	.	.	.	.	.	.	g	2.376	-0.343229	0.05243	.	.	ENSG00000185596	ENST00000338304;ENST00000398121	.	.	.	1.01	1.01	0.19927	.	0.000000	0.85682	D	0.000000	T	0.41926	0.1180	.	.	.	.	.	.	.	.	.	.	.	.	T	0.51044	-0.8755	4	.	.	.	-23.1056	7.9382	0.29941	0.0:0.0:1.0:0.0	.	.	.	.	S	383;374	.	.	G	+	1	0	WASH3P	100332822	1.000000	0.71417	0.997000	0.53966	0.230000	0.25150	8.205000	0.89743	0.863000	0.35553	0.184000	0.17185	GGC		0.652	WASH3P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417608.1	NM_199163		8	10	0	0	0	0.278610	0	8	10				
FPGT	8790	broad.mit.edu	37	1	74670899	74670899	+	Missense_Mutation	SNP	C	C	A	rs371902734		TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr1:74670899C>A	ENST00000609362.1	+	4	1205	c.1168C>A	c.(1168-1170)Cca>Aca	p.P390T	FPGT-TNNI3K_ENST00000557284.2_Intron|FPGT-TNNI3K_ENST00000370893.1_Intron|FPGT-TNNI3K_ENST00000370895.1_Intron|FPGT-TNNI3K_ENST00000370899.3_Intron|FPGT_ENST00000524915.1_Intron|FPGT_ENST00000370898.3_Missense_Mutation_p.P403T|TNNI3K_ENST00000370891.2_Intron|FPGT-TNNI3K_ENST00000533006.1_Intron|FPGT_ENST00000534056.1_Intron|FPGT_ENST00000370894.5_Missense_Mutation_p.F117L	NM_003838.4	NP_003829.3	O14772	FPGT_HUMAN	fucose-1-phosphate guanylyltransferase	390					fucose metabolic process (GO:0006004)	cytoplasm (GO:0005737)	catalytic activity (GO:0003824)|fucose-1-phosphate guanylyltransferase activity (GO:0047341)|GTP binding (GO:0005525)			breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	39						TAGTATCTTTCCAGATATACC	0.388																																						ENST00000370898.2																			0				breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	39						c.(1168-1170)Cca>Aca		fucose-1-phosphate guanylyltransferase							59.0	61.0	60.0					1																	74670899		2203	4299	6502	SO:0001583	missense	8790							g.chr1:74670899C>A	AF017445	CCDS663.1, CCDS663.2	1p31.1	2013-09-24			ENSG00000254685	ENSG00000254685	2.7.7.30		3825	protein-coding gene	gene with protein product		603609				9804772	Standard	NM_003838		Approved	GFPP		O14772	OTTHUMG00000009571	ENST00000609362.1:c.1168C>A	1.37:g.74670899C>A	ENSP00000476680:p.Pro390Thr					FPGT-TNNI3K_ENST00000557284.1_Intron|FPGT_ENST00000534056.1_Intron|FPGT-TNNI3K_ENST00000370899.3_Intron|FPGT_ENST00000524915.1_Intron|TNNI3K_ENST00000370891.2_Intron|FPGT-TNNI3K_ENST00000370895.1_Intron|TNNI3K_ENST00000370893.1_Intron|FPGT_ENST00000370894.4_Missense_Mutation_p.F117L	p.P390T	NM_001199328.1|NM_003838.3	NP_001186257.1|NP_003829.2					4	1205	+								A6NMH3|B4DRX2|B4E2Y7|E9PNQ2|Q8N5J7	Missense_Mutation	SNP	ENST00000609362.1	37	c.1168C>A	CCDS663.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	2.010|2.010	-0.427306|-0.427306	0.04701|0.04701	.|.	.|.	ENSG00000254685|ENSG00000254685	ENST00000370894|ENST00000370898	.|T	.|0.34472	.|1.36	5.91|5.91	4.0|4.0	0.46444|0.46444	.|L-fucokinase (1);	.|.	.|.	.|.	.|.	T|T	0.19327|0.19327	0.0464|0.0464	M|M	0.74881|0.74881	2.28|2.28	0.35909|0.35909	D|D	0.830986|0.830986	.|P;B	.|0.38420	.|0.63;0.43	.|B;B	.|0.38428	.|0.273;0.259	T|T	0.05886|0.05886	-1.0858|-1.0858	6|9	0.32370|0.27082	T|T	0.25|0.32	.|.	6.0053|6.0053	0.19542|0.19542	0.1316:0.6515:0.0:0.2169|0.1316:0.6515:0.0:0.2169	.|.	.|15;390	.|B4E2Y7;O14772	.|.;FPGT_HUMAN	L|T	117|390	.|ENSP00000359935:P390T	ENSP00000359931:F117L|ENSP00000359935:P390T	F|P	+|+	3|1	2|0	TNNI3K|TNNI3K	74443487|74443487	0.000000|0.000000	0.05858|0.05858	0.254000|0.254000	0.24359|0.24359	0.434000|0.434000	0.31775|0.31775	-0.082000|-0.082000	0.11304|0.11304	0.789000|0.789000	0.33779|0.33779	0.655000|0.655000	0.94253|0.94253	TTC|CCA		0.388	FPGT-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				11	65	1	0	1.58986e-06	0.361761	1.77913e-06	11	65				
LMCD1	29995	broad.mit.edu	37	3	8590439	8590439	+	Silent	SNP	C	C	T			TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr3:8590439C>T	ENST00000157600.3	+	4	805	c.573C>T	c.(571-573)agC>agT	p.S191S	LMCD1-AS1_ENST00000439407.1_RNA|LMCD1_ENST00000397386.3_Silent_p.S79S|LMCD1_ENST00000454244.1_Silent_p.S118S|LMCD1_ENST00000535732.1_Silent_p.S191S	NM_014583.2	NP_055398.1	Q9NZU5	LMCD1_HUMAN	LIM and cysteine-rich domains 1	191	PET. {ECO:0000255|PROSITE- ProRule:PRU00636}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|regulation of cardiac muscle hypertrophy (GO:0010611)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(2)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)	16				OV - Ovarian serous cystadenocarcinoma(96;0.124)		AATATAAGAGCGAGGCCCTCG	0.587																																						ENST00000157600.3																			0				breast(2)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)	16						c.(571-573)agC>agT		LIM and cysteine-rich domains 1							93.0	100.0	98.0					3																	8590439		2203	4300	6503	SO:0001819	synonymous_variant	29995				positive regulation of calcineurin-NFAT signaling pathway|regulation of cardiac muscle hypertrophy|transcription, DNA-dependent	cytoplasm|extracellular space|nucleus	transcription corepressor activity|zinc ion binding	g.chr3:8590439C>T	AF169284	CCDS33688.1, CCDS63533.1, CCDS63534.1	3p26-p24	2008-07-18			ENSG00000071282	ENSG00000071282			6633	protein-coding gene	gene with protein product	"""dyxin"""	604859				10662546	Standard	NM_001278233		Approved		uc003bqq.4	Q9NZU5	OTTHUMG00000154971	ENST00000157600.3:c.573C>T	3.37:g.8590439C>T						LMCD1_ENST00000454244.1_Silent_p.S118S|LMCD1_ENST00000397386.3_Silent_p.S79S|LMCD1-AS1_ENST00000439407.1_RNA|LMCD1_ENST00000535732.1_Silent_p.S191S	p.S191S	NM_014583.2	NP_055398.1	Q9NZU5	LMCD1_HUMAN		OV - Ovarian serous cystadenocarcinoma(96;0.124)	4	805	+			191			PET.		B4DG80	Silent	SNP	ENST00000157600.3	37	c.573C>T	CCDS33688.1																																																																																				0.587	LMCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337854.1	NM_014583		32	66	0	0	0	0.750413	0	32	66				
CXorf21	80231	broad.mit.edu	37	X	30578233	30578233	+	Silent	SNP	T	T	C			TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chrX:30578233T>C	ENST00000378962.3	-	3	562	c.240A>G	c.(238-240)agA>agG	p.R80R		NM_025159.2	NP_079435.1	Q9HAI6	CX021_HUMAN	chromosome X open reading frame 21	80										kidney(1)|large_intestine(3)|lung(13)|ovary(1)|stomach(1)|urinary_tract(1)	20						GCACTGTGACTCTCTGACTTC	0.453																																						ENST00000378962.3																			0				kidney(1)|large_intestine(3)|lung(13)|ovary(1)|stomach(1)|urinary_tract(1)	20						c.(238-240)agA>agG		chromosome X open reading frame 21							168.0	162.0	164.0					X																	30578233		2202	4300	6502	SO:0001819	synonymous_variant	80231							g.chrX:30578233T>C	BC020611	CCDS14224.1	Xp21.3	2006-04-12			ENSG00000120280	ENSG00000120280			25667	protein-coding gene	gene with protein product						12477932	Standard	NM_025159		Approved	FLJ11577	uc004dcg.2	Q9HAI6	OTTHUMG00000021325	ENST00000378962.3:c.240A>G	X.37:g.30578233T>C							p.R80R	NM_025159.2	NP_079435.1	Q9HAI6	CX021_HUMAN			3	562	-			80						Silent	SNP	ENST00000378962.3	37	c.240A>G	CCDS14224.1																																																																																				0.453	CXorf21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056164.1	NM_025159		6	183	0	0	0	0.248553	0	6	183				
ZDHHC7	55625	broad.mit.edu	37	16	85010046	85010046	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr16:85010046C>T	ENST00000313732.4	-	8	1182	c.830G>A	c.(829-831)gGg>gAg	p.G277E	ZDHHC7_ENST00000564466.1_Missense_Mutation_p.G314E|ZDHHC7_ENST00000569488.1_5'Flank	NM_017740.2	NP_060210.2	Q9NXF8	ZDHC7_HUMAN	zinc finger, DHHC-type containing 7	277					peptidyl-L-cysteine S-palmitoylation (GO:0018230)|protein palmitoylation (GO:0018345)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			large_intestine(6)|lung(4)	10						TGAGGGGGGCCCCCCAAAGAC	0.572																																						ENST00000313732.4																			0				large_intestine(6)|lung(4)	10						c.(829-831)gGg>gAg		zinc finger, DHHC-type containing 7							47.0	58.0	54.0					16																	85010046		2199	4300	6499	SO:0001583	missense	55625					integral to membrane	acyltransferase activity|protein binding|zinc ion binding	g.chr16:85010046C>T	AK000286	CCDS10950.1, CCDS45538.1	16q23.1	2010-02-09			ENSG00000153786	ENSG00000153786		"""Zinc fingers, DHHC-type"""	18459	protein-coding gene	gene with protein product	"""Sertoli cell gene with zinc finger domain-&#946;"""	614604					Standard	NM_017740		Approved	FLJ10792, ZNF370, FLJ20279, SERZ-B, SERZ1	uc002fiq.2	Q9NXF8	OTTHUMG00000137645	ENST00000313732.4:c.830G>A	16.37:g.85010046C>T	ENSP00000315604:p.Gly277Glu					ZDHHC7_ENST00000564466.1_Missense_Mutation_p.G314E	p.G277E	NM_017740.2	NP_060210.2	Q9NXF8	ZDHC7_HUMAN			8	1182	-			277					D3DUM1|Q8WV42|Q9NVD8	Missense_Mutation	SNP	ENST00000313732.4	37	c.830G>A	CCDS10950.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.802021	0.90538	.	.	ENSG00000153786	ENST00000313732;ENST00000344861	T;T	0.57107	1.41;0.42	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.58595	0.2133	M	0.68593	2.085	0.80722	D	1	P;P	0.48998	0.837;0.918	B;P	0.47827	0.373;0.558	T	0.53258	-0.8464	10	0.12766	T	0.61	-24.6769	19.0039	0.92843	0.0:1.0:0.0:0.0	.	314;277	Q9NXF8-2;Q9NXF8	.;ZDHC7_HUMAN	E	277;314	ENSP00000315604:G277E;ENSP00000341681:G314E	ENSP00000315604:G277E	G	-	2	0	ZDHHC7	83567547	1.000000	0.71417	0.971000	0.41717	0.908000	0.53690	5.906000	0.69900	2.808000	0.96608	0.561000	0.74099	GGG		0.572	ZDHHC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269087.1	NM_017740		13	20	0	0	0	0.500413	0	13	20				
HPS1	3257	broad.mit.edu	37	10	100185433	100185433	+	Missense_Mutation	SNP	A	A	C			TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr10:100185433A>C	ENST00000325103.6	-	13	1433	c.1200T>G	c.(1198-1200)gaT>gaG	p.D400E	HPS1_ENST00000361490.4_Missense_Mutation_p.D400E|HPS1_ENST00000467246.1_5'UTR	NM_000195.3	NP_000186.2	Q92902	HPS1_HUMAN	Hermansky-Pudlak syndrome 1	400					blood coagulation (GO:0007596)|eye pigmentation (GO:0048069)|lysosome organization (GO:0007040)|melanocyte differentiation (GO:0030318)|positive regulation of natural killer cell activation (GO:0032816)|retina development in camera-type eye (GO:0060041)|secretion of lysosomal enzymes (GO:0033299)|visual perception (GO:0007601)	BLOC-3 complex (GO:0031085)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	protein dimerization activity (GO:0046983)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.234)		Epithelial(162;3.87e-12)|all cancers(201;5.63e-10)		TGGAGAAGCCATCCATCAGCT	0.692									Hermansky-Pudlak syndrome		OREG0020430	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000325103.6																			0				breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23						c.(1198-1200)gaT>gaG		Hermansky-Pudlak syndrome 1							26.0	30.0	29.0					10																	100185433		2203	4299	6502	SO:0001583	missense	3257	Hermansky-Pudlak syndrome	Familial Cancer Database	HPS, HPS1-8	lysosome organization|response to stimulus|visual perception	cytoplasmic membrane-bounded vesicle|integral to plasma membrane|lysosome|membrane fraction|soluble fraction	protein dimerization activity	g.chr10:100185433A>C	U79136	CCDS7475.1, CCDS7476.1	10q23.1-q23.3	2014-06-18		2002-05-01	ENSG00000107521	ENSG00000107521			5163	protein-coding gene	gene with protein product		604982	"""Hermansky-Pudlak syndrome"""	HPS		8541858, 7573033	Standard	NM_182639		Approved		uc021pwv.1	Q92902	OTTHUMG00000018876	ENST00000325103.6:c.1200T>G	10.37:g.100185433A>C	ENSP00000326649:p.Asp400Glu		OREG0020430	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1349	HPS1_ENST00000467246.1_5'UTR|HPS1_ENST00000361490.4_Missense_Mutation_p.D400E	p.D400E	NM_000195.3	NP_000186.2	Q92902	HPS1_HUMAN		Epithelial(162;3.87e-12)|all cancers(201;5.63e-10)	13	1433	-		Colorectal(252;0.234)	400					A8MRT2|O15402|O15502|Q5TAA3|Q8WXE5	Missense_Mutation	SNP	ENST00000325103.6	37	c.1200T>G	CCDS7475.1	.	.	.	.	.	.	.	.	.	.	A	9.118	1.008161	0.19199	.	.	ENSG00000107521	ENST00000325103;ENST00000361490;ENST00000407891;ENST00000359632	T;T;T	0.32023	1.47;1.47;1.47	5.38	-0.352	0.12598	.	0.103213	0.64402	N	0.000003	T	0.28400	0.0702	M	0.64997	1.995	0.80722	D	1	B;B;B;B	0.24483	0.013;0.048;0.104;0.048	B;B;B;B	0.34536	0.034;0.054;0.185;0.054	T	0.04621	-1.0938	10	0.27785	T	0.31	.	6.5186	0.22262	0.6898:0.1199:0.1904:0.0	.	38;367;400;400	Q658M9;Q92902-2;Q8WXE5;D3DR62	.;.;.;.	E	400;400;367;195	ENSP00000326649:D400E;ENSP00000355310:D400E;ENSP00000352652:D195E	ENSP00000326649:D400E	D	-	3	2	HPS1	100175423	0.230000	0.23740	0.909000	0.35828	0.023000	0.10783	-0.297000	0.08276	-0.318000	0.08665	-0.379000	0.06801	GAT		0.692	HPS1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049776.1	NM_000195, NM_182637, NM_182638, NM_182639		15	23	0	0	0	0.479597	0	15	23				
HSPG2	3339	broad.mit.edu	37	1	22174482	22174482	+	Silent	SNP	G	G	A			TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr1:22174482G>A	ENST00000374695.3	-	60	7921	c.7842C>T	c.(7840-7842)atC>atT	p.I2614I	HSPG2_ENST00000430507.1_3'UTR	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2614	Ig-like C2-type 11.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GGATGGTGACGATGAGCGAGG	0.662																																						ENST00000374695.3																			0				breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127						c.(7840-7842)atC>atT		heparan sulfate proteoglycan 2	Becaplermin(DB00102)|Palifermin(DB00039)						88.0	82.0	84.0					1																	22174482		2203	4300	6503	SO:0001819	synonymous_variant	3339				angiogenesis|cell adhesion|lipid metabolic process|lipoprotein metabolic process	basement membrane|extracellular space|plasma membrane	protein C-terminus binding	g.chr1:22174482G>A	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.7842C>T	1.37:g.22174482G>A						HSPG2_ENST00000430507.1_3'UTR	p.I2614I	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	60	7921	-		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)	2614			Ig-like C2-type 11.		Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	c.7842C>T	CCDS30625.1																																																																																				0.662	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		6	40	0	0	0	0.217242	0	6	40				
TAT	6898	broad.mit.edu	37	16	71610262	71610262	+	Silent	SNP	G	G	A			TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr16:71610262G>A	ENST00000355962.4	-	2	190	c.57C>T	c.(55-57)gaC>gaT	p.D19D	RP11-432I5.1_ENST00000561529.1_RNA	NM_000353.2	NP_000344.1	P17735	ATTY_HUMAN	tyrosine aminotransferase	19					2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|L-phenylalanine catabolic process (GO:0006559)|response to glucocorticoid (GO:0051384)|response to mercury ion (GO:0046689)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|L-phenylalanine:2-oxoglutarate aminotransferase activity (GO:0080130)|L-tyrosine:2-oxoglutarate aminotransferase activity (GO:0004838)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(3)	29		Ovarian(137;0.125)		Kidney(780;0.0157)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)	TGACATGCACGTCCAGAATTG	0.522																																					Melanoma(198;542 2142 10292 21661 50033)|Esophageal Squamous(48;487 1013 5572 44395 52594)	ENST00000355962.4																			0				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(3)	29						c.(55-57)gaC>gaT		tyrosine aminotransferase	L-Glutamic Acid(DB00142)|L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)|Pyridoxal Phosphate(DB00114)						113.0	112.0	112.0					16																	71610262		2198	4300	6498	SO:0001819	synonymous_variant	6898				2-oxoglutarate metabolic process|glutamate metabolic process|L-phenylalanine catabolic process|tyrosine catabolic process	cytosol	1-aminocyclopropane-1-carboxylate synthase activity|L-tyrosine:2-oxoglutarate aminotransferase activity|pyridoxal phosphate binding	g.chr16:71610262G>A		CCDS10903.1	16q22.1	2012-10-02			ENSG00000198650	ENSG00000198650	2.6.1.5		11573	protein-coding gene	gene with protein product		613018					Standard	NM_000353		Approved		uc002fap.2	P17735	OTTHUMG00000137590	ENST00000355962.4:c.57C>T	16.37:g.71610262G>A						RP11-432I5.1_ENST00000561529.1_RNA	p.D19D	NM_000353.2	NP_000344.1	P17735	ATTY_HUMAN		Kidney(780;0.0157)	2	190	-		Ovarian(137;0.125)	19					B2R8I1|D3DWS2	Silent	SNP	ENST00000355962.4	37	c.57C>T	CCDS10903.1																																																																																				0.522	TAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268989.1			5	56	0	0	0	0.184627	0	5	56				
USP25	29761	broad.mit.edu	37	21	17246819	17246819	+	Missense_Mutation	SNP	T	T	C			TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr21:17246819T>C	ENST00000285679.6	+	22	3142	c.2773T>C	c.(2773-2775)Tca>Cca	p.S925P	USP25_ENST00000285681.2_Missense_Mutation_p.S957P|USP25_ENST00000351097.5_Missense_Mutation_p.S320P|USP25_ENST00000400183.2_Missense_Mutation_p.S995P	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	925					cellular protein modification process (GO:0006464)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|proteolysis (GO:0006508)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|SUMO binding (GO:0032183)|ubiquitin-specific protease activity (GO:0004843)	p.S925P(1)		breast(4)|endometrium(6)|kidney(2)|large_intestine(13)|liver(5)|lung(14)|ovary(4)|prostate(1)|skin(1)|urinary_tract(2)	52				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)		AGAATTGATATCACATTATAG	0.328																																						ENST00000285681.2																			1	Substitution - Missense(1)	p.S925P(1)	breast(1)	breast(4)|endometrium(6)|kidney(2)|large_intestine(13)|liver(5)|lung(14)|ovary(4)|prostate(1)|skin(1)|urinary_tract(2)	52						c.(2869-2871)Tca>Cca		ubiquitin specific peptidase 25							155.0	161.0	159.0					21																	17246819		2203	4299	6502	SO:0001583	missense	29761				protein modification process|ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin thiolesterase activity|ubiquitin-specific protease activity	g.chr21:17246819T>C	AF170562	CCDS33515.1, CCDS63336.1, CCDS63337.1	21q11.2	2011-02-24	2005-08-08		ENSG00000155313	ENSG00000155313		"""Ubiquitin-specific peptidases"""	12624	protein-coding gene	gene with protein product		604736	"""ubiquitin specific protease 25"""			12838346, 10612803	Standard	NM_013396		Approved	USP21	uc002yjy.1	Q9UHP3	OTTHUMG00000074343	ENST00000285679.6:c.2773T>C	21.37:g.17246819T>C	ENSP00000285679:p.Ser925Pro					USP25_ENST00000400183.2_Missense_Mutation_p.S995P|USP25_ENST00000351097.5_Missense_Mutation_p.S320P|USP25_ENST00000285679.6_Missense_Mutation_p.S925P	p.S957P			Q9UHP3	UBP25_HUMAN		Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)	23	3238	+			925					C0LSZ0|Q6DHZ9|Q9H9W1	Missense_Mutation	SNP	ENST00000285679.6	37	c.2869T>C	CCDS33515.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.192781	0.78902	.	.	ENSG00000155313	ENST00000285681;ENST00000285679;ENST00000351097;ENST00000400183	T;T;T;T	0.32515	1.86;1.87;1.45;1.86	5.71	4.54	0.55810	.	0.115906	0.64402	D	0.000016	T	0.35335	0.0928	L	0.44542	1.39	0.38696	D	0.952878	P;P;P;P	0.50369	0.934;0.889;0.823;0.791	P;P;P;B	0.48952	0.491;0.521;0.596;0.255	T	0.26916	-1.0089	10	0.66056	D	0.02	.	12.9389	0.58331	0.0:0.0:0.1355:0.8645	.	995;320;957;925	Q9UHP3-3;Q96B65;Q9UHP3-1;Q9UHP3	.;.;.;UBP25_HUMAN	P	957;925;320;995	ENSP00000285681:S957P;ENSP00000285679:S925P;ENSP00000299574:S320P;ENSP00000383044:S995P	ENSP00000285679:S925P	S	+	1	0	USP25	16168690	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	5.885000	0.69736	0.972000	0.38314	0.377000	0.23210	TCA		0.328	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1			30	162	0	0	0	0.750413	0	30	162				
LGI4	163175	broad.mit.edu	37	19	35616158	35616158	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr19:35616158G>A	ENST00000310123.3	-	9	2072	c.1553C>T	c.(1552-1554)gCt>gTt	p.A518V	LGI4_ENST00000493050.1_5'UTR|LGI4_ENST00000392225.3_3'UTR	NM_139284.2	NP_644813.1	Q8N135	LGI4_HUMAN	leucine-rich repeat LGI family, member 4	518					adult locomotory behavior (GO:0008344)|glial cell proliferation (GO:0014009)|myelination in peripheral nervous system (GO:0022011)|neuron maturation (GO:0042551)	extracellular space (GO:0005615)				endometrium(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	all_lung(56;7.56e-09)|Lung NSC(56;1.1e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849)			AAAGCAAGCAGCAAAGAGGAA	0.647																																						ENST00000310123.3																			0				endometrium(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10						c.(1552-1554)gCt>gTt		leucine-rich repeat LGI family, member 4							61.0	62.0	62.0					19																	35616158		2203	4300	6503	SO:0001583	missense	163175					extracellular region		g.chr19:35616158G>A	AJ487519	CCDS12444.1	19q13.13	2008-07-03			ENSG00000153902	ENSG00000153902			18712	protein-coding gene	gene with protein product		608303				12023020	Standard	NM_139284		Approved		uc002nxx.2	Q8N135	OTTHUMG00000044558	ENST00000310123.3:c.1553C>T	19.37:g.35616158G>A	ENSP00000312273:p.Ala518Val					LGI4_ENST00000392225.3_3'UTR|LGI4_ENST00000493050.1_5'UTR	p.A518V	NM_139284.2	NP_644813.1	Q8N135	LGI4_HUMAN	Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849)		9	2072	-	all_lung(56;7.56e-09)|Lung NSC(56;1.1e-08)|Esophageal squamous(110;0.162)		518					B2RN53|B9EGS7|Q5M8T1	Missense_Mutation	SNP	ENST00000310123.3	37	c.1553C>T	CCDS12444.1	.	.	.	.	.	.	.	.	.	.	G	17.34	3.365241	0.61513	.	.	ENSG00000153902	ENST00000310123;ENST00000437421	T	0.68181	-0.31	5.15	5.15	0.70609	.	0.177142	0.38164	N	0.001799	T	0.61899	0.2384	L	0.45352	1.415	0.80722	D	1	P	0.42908	0.793	B	0.41374	0.355	T	0.64474	-0.6399	10	0.44086	T	0.13	.	16.1241	0.81380	0.0:0.0:1.0:0.0	.	518	Q8N135	LGI4_HUMAN	V	518;519	ENSP00000312273:A518V	ENSP00000312273:A518V	A	-	2	0	LGI4	40307998	1.000000	0.71417	0.975000	0.42487	0.954000	0.61252	6.056000	0.71111	2.404000	0.81709	0.484000	0.47621	GCT		0.647	LGI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103963.1			3	36	0	0	0	0.115264	0	3	36				
CHDC2	286464	broad.mit.edu	37	X	36091355	36091355	+	Missense_Mutation	SNP	C	C	A			TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chrX:36091355C>A	ENST00000313548.4	+	4	476	c.290C>A	c.(289-291)tCt>tAt	p.S97Y		NM_173695.2	NP_775966.1	Q8N9S7	CHDC2_HUMAN	calponin homology domain containing 2	97						integral component of membrane (GO:0016021)											CAATTCCTTTCTCTTGAGGAA	0.433																																						ENST00000378660.1																			0											c.(289-291)tCt>tAt		calponin homology domain containing 2							105.0	92.0	97.0					X																	36091355		2202	4300	6502	SO:0001583	missense	286464							g.chrX:36091355C>A	AK093920	CCDS14238.1	Xp21.1	2014-08-07	2012-11-28	2012-11-28	ENSG00000176034	ENSG00000176034			26708	protein-coding gene	gene with protein product			"""chromosome X open reading frame 59"""	CXorf59			Standard	NM_173695		Approved	FLJ36601, RP13-11B7.1	uc004ddk.1	Q8N9S7	OTTHUMG00000021351	ENST00000313548.4:c.290C>A	X.37:g.36091355C>A	ENSP00000324767:p.Ser97Tyr					CHDC2_ENST00000313548.4_Missense_Mutation_p.S97Y	p.S97Y							4	478	+									Missense_Mutation	SNP	ENST00000313548.4	37	c.290C>A	CCDS14238.1	.	.	.	.	.	.	.	.	.	.	C	1.060	-0.673054	0.03403	.	.	ENSG00000176034	ENST00000378660;ENST00000313548	.	.	.	4.9	-2.23	0.06930	.	0.733108	0.11267	N	0.581945	T	0.20659	0.0497	N	0.19112	0.55	0.09310	N	1	B	0.15930	0.015	B	0.12156	0.007	T	0.34725	-0.9817	9	0.02654	T	1	-0.0788	9.4981	0.38999	0.0:0.2793:0.0:0.7207	.	97	Q8N9S7	CX059_HUMAN	Y	97	.	ENSP00000324767:S97Y	S	+	2	0	CXorf59	36001276	0.469000	0.25846	0.000000	0.03702	0.028000	0.11728	-0.688000	0.05150	-0.529000	0.06358	0.529000	0.55759	TCT		0.433	CHDC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173695		27	63	1	0	3.73988e-18	0.706142	4.28718e-18	27	63				
TBC1D21	161514	broad.mit.edu	37	15	74178445	74178445	+	Silent	SNP	C	C	T			TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr15:74178445C>T	ENST00000300504.2	+	7	689	c.606C>T	c.(604-606)ggC>ggT	p.G202G	TBC1D21_ENST00000562056.1_Silent_p.G165G|TBC1D21_ENST00000535547.2_Silent_p.G166G	NM_153356.1	NP_699187.1	Q8IYX1	TBC21_HUMAN	TBC1 domain family, member 21	202	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.					acrosomal vesicle (GO:0001669)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(2)|large_intestine(2)|lung(6)|ovary(3)|skin(1)|stomach(1)|urinary_tract(1)	17						TCAACATTGGCGTGGCCAAGA	0.572																																						ENST00000300504.2																			0				breast(1)|endometrium(2)|large_intestine(2)|lung(6)|ovary(3)|skin(1)|stomach(1)|urinary_tract(1)	17						c.(604-606)ggC>ggT		TBC1 domain family, member 21							219.0	146.0	170.0					15																	74178445		2198	4297	6495	SO:0001819	synonymous_variant	161514					intracellular	Rab GTPase activator activity	g.chr15:74178445C>T	BC033516	CCDS10252.1, CCDS66822.1	15q24	2013-07-09			ENSG00000167139	ENSG00000167139			28536	protein-coding gene	gene with protein product	"""male germ cell-specific expressed, containing a RabGAP domain"""					21128978	Standard	XR_243080		Approved	MGC34741, MgcRabGAP	uc002avz.3	Q8IYX1	OTTHUMG00000137594	ENST00000300504.2:c.606C>T	15.37:g.74178445C>T						TBC1D21_ENST00000535547.2_Silent_p.G166G|TBC1D21_ENST00000562056.1_Silent_p.G165G	p.G202G	NM_153356.1	NP_699187.1	Q8IYX1	TBC21_HUMAN			7	689	+			202			Rab-GAP TBC.		B9A6M2	Silent	SNP	ENST00000300504.2	37	c.606C>T	CCDS10252.1																																																																																				0.572	TBC1D21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268994.1	NM_153356		3	41	0	0	0	0.115264	0	3	41				
ACACA	31	broad.mit.edu	37	17	35640173	35640173	+	Missense_Mutation	SNP	T	T	C			TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr17:35640173T>C	ENST00000394406.2	-	5	684	c.494A>G	c.(493-495)aAt>aGt	p.N165S	ACACA_ENST00000360679.3_Missense_Mutation_p.N107S|ACACA_ENST00000353139.5_Missense_Mutation_p.N202S|ACACA_ENST00000335166.5_Missense_Mutation_p.N87S	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	165	Biotin carboxylation.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	CTCACCTGCATTGGCTTTAAG	0.408																																					Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)	ENST00000353139.5																			0				NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83						c.(604-606)aAt>aGt		acetyl-CoA carboxylase alpha	Biotin(DB00121)						139.0	112.0	121.0					17																	35640173		2203	4300	6503	SO:0001583	missense	31				acetyl-CoA metabolic process|energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|triglyceride biosynthetic process	cytosol	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding	g.chr17:35640173T>C	U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 1"""	200350	"""acetyl-Coenzyme A carboxylase alpha"""	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.494A>G	17.37:g.35640173T>C	ENSP00000377928:p.Asn165Ser					ACACA_ENST00000394406.2_Missense_Mutation_p.N165S|ACACA_ENST00000360679.3_Missense_Mutation_p.N107S|ACACA_ENST00000335166.5_Missense_Mutation_p.N87S	p.N202S	NM_198834.1|NM_198839.1	NP_942131.1|NP_942136.1	Q13085	ACACA_HUMAN			5	1086	-		Breast(25;0.00157)|Ovarian(249;0.15)	165			Biotin carboxylation.		B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Missense_Mutation	SNP	ENST00000394406.2	37	c.605A>G	CCDS11317.1	.	.	.	.	.	.	.	.	.	.	T	32	5.159511	0.94686	.	.	ENSG00000132142	ENST00000353139;ENST00000360679;ENST00000394406;ENST00000452074;ENST00000335166;ENST00000456066	D;D;D;D	0.92299	-3.01;-3.01;-3.01;-3.01	5.84	5.84	0.93424	Pre-ATP-grasp fold (1);PreATP-grasp-like fold (1);Biotin carboxylation domain (1);Carbamoyl-phosphate synthase, large subunit, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.95648	0.8585	M	0.77313	2.365	0.80722	D	1	D;D;D	0.64830	0.983;0.994;0.992	D;D;P	0.64595	0.91;0.927;0.84	D	0.95993	0.8987	10	0.72032	D	0.01	-20.1772	16.226	0.82293	0.0:0.0:0.0:1.0	.	202;165;107	Q13085-4;Q13085;Q13085-2	.;ACACA_HUMAN;.	S	202;107;165;189;87;87	ENSP00000344789:N202S;ENSP00000353898:N107S;ENSP00000377928:N165S;ENSP00000335323:N87S	ENSP00000335323:N87S	N	-	2	0	ACACA	32714286	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.997000	0.88414	2.230000	0.72887	0.528000	0.53228	AAT		0.408	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		14	37	0	0	0	0.479597	0	14	37				
HNRNPH2	3188	broad.mit.edu	37	X	100667035	100667035	+	Missense_Mutation	SNP	G	G	T			TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chrX:100667035G>T	ENST00000316594.5	+	2	137	c.59G>T	c.(58-60)tGg>tTg	p.W20L	RPL36A-HNRNPH2_ENST00000409170.3_3'UTR	NM_001032393.2|NM_001199973.1|NM_001199974.1|NM_019597.4	NP_001027565.1|NP_001186902.1|NP_001186903.1|NP_062543.1	P55795	HNRH2_HUMAN	heterogeneous nuclear ribonucleoprotein H2 (H')	20	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|large_intestine(2)|lung(6)|skin(1)	12						GGCCTACCCTGGTCCTGCTCA	0.527																																						ENST00000316594.5																			0				breast(3)|large_intestine(2)|lung(6)|skin(1)	12						c.(58-60)tGg>tTg		heterogeneous nuclear ribonucleoprotein H2 (H')							144.0	114.0	124.0					X																	100667035		2203	4300	6503	SO:0001583	missense	3188				nuclear mRNA splicing, via spliceosome	actin cytoskeleton|cytoplasm|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding	g.chrX:100667035G>T	U01923	CCDS14485.1	Xq22	2013-02-12		2008-04-18	ENSG00000126945	ENSG00000126945		"""RNA binding motif (RRM) containing"""	5042	protein-coding gene	gene with protein product		300610		HNRPH2		7499401	Standard	NM_019597		Approved	hnRNPH', FTP3, HNRPH'	uc004ehn.3	P55795	OTTHUMG00000022029	ENST00000316594.5:c.59G>T	X.37:g.100667035G>T	ENSP00000361927:p.Trp20Leu					RPL36A-HNRNPH2_ENST00000409170.3_3'UTR	p.W20L	NM_001032393.2|NM_001199973.1|NM_001199974.1|NM_019597.4	NP_001027565.1|NP_001186902.1|NP_001186903.1|NP_062543.1	P55795	HNRH2_HUMAN			2	137	+			20			RRM 1.		A1L400|Q9HHA7	Missense_Mutation	SNP	ENST00000316594.5	37	c.59G>T	CCDS14485.1	.	.	.	.	.	.	.	.	.	.	G	18.74	3.687870	0.68271	.	.	ENSG00000126945	ENST00000457902;ENST00000316594	T	0.28069	1.63	5.1	5.1	0.69264	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.62159	0.2405	M	0.88105	2.93	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.70547	-0.4842	10	0.87932	D	0	-4.2278	15.2312	0.73390	0.0:0.0:1.0:0.0	.	20	P55795	HNRH2_HUMAN	L	20	ENSP00000361927:W20L	ENSP00000361927:W20L	W	+	2	0	HNRNPH2	100553691	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.634000	0.74290	2.275000	0.75901	0.600000	0.82982	TGG		0.527	HNRNPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057556.1	NM_019597		5	90	1	0	0.014758	0.184627	0.0157642	5	90				
LOC101928372	101928372	broad.mit.edu	37	1	160905975	160905975	+	lincRNA	DEL	T	T	-	rs368373384	byFrequency	TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr1:160905975delT	ENST00000427339.1	-	0	0				RP11-544M22.1_ENST00000356006.3_RNA																							cttcttcttcttttttttttt	0.393													|||unknown(HR)	181	0.0361422	0.1278	0.0144	5008	,	,		16599	0.0		0.001	False		,,,				2504	0.001					ENST00000356006.3																			0																																																			0							g.chr1:160905975delT																													1.37:g.160905975delT														0	629	+									RNA	DEL	ENST00000427339.1	37																																																																																						0.393	RP11-312J18.6-001	KNOWN	basic|exp_conf	lincRNA	lincRNA	OTTHUMT00000071456.1			2	4						2	4	---	---	---	---
KIF1A	547	broad.mit.edu	37	2	241702180	241702180	+	Frame_Shift_Del	DEL	T	T	-	rs531766047		TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr2:241702180delT	ENST00000320389.7	-	22	2203	c.2045delA	c.(2044-2046)tacfs	p.Y683fs	KIF1A_ENST00000498729.2_Frame_Shift_Del_p.Y692fs	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A	683					anterograde axon cargo transport (GO:0008089)|ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			NS(1)|central_nervous_system(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(25)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	66		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		CTCCGGGTAGTACCTGGAGTC	0.617																																						ENST00000498729.2																			0				NS(1)|central_nervous_system(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(25)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	66						c.(2071-2073)tcfs		kinesin family member 1A							42.0	46.0	44.0					2																	241702180		2107	4226	6333	SO:0001589	frameshift_variant	547				anterograde axon cargo transport	cytoplasm|microtubule|nucleus	ATP binding|microtubule motor activity	g.chr2:241702180delT	AF004425	CCDS46561.1, CCDS58757.1	2q37.2	2014-09-17	2004-01-09	2004-01-14	ENSG00000130294	ENSG00000130294		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	888	protein-coding gene	gene with protein product		601255	"""axonal transport of synaptic vesicles"", ""chromosome 2 open reading frame 20"", ""spastic paraplegia 30 (autosomal recessive)"""	ATSV, C2orf20, SPG30		7539720, 10323250, 22258533	Standard	NM_001244008		Approved	UNC104	uc010fzk.3	Q12756	OTTHUMG00000151940	ENST00000320389.7:c.2045delA	2.37:g.241702180delT	ENSP00000322791:p.Tyr683fs					KIF1A_ENST00000320389.7_Frame_Shift_Del_p.Y683fs	p.Y692fs	NM_001244008.1	NP_001230937.1	Q12756	KIF1A_HUMAN		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)	23	2318	-		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)	683					B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Frame_Shift_Del	DEL	ENST00000320389.7	37	c.2072delA	CCDS46561.1																																																																																				0.617	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3	NM_138483		2	4						2	4	---	---	---	---
POU4F2	5458	broad.mit.edu	37	4	147560458	147560466	+	In_Frame_Del	DEL	GGCGGCGGC	GGCGGCGGC	-	rs189899086|rs72269802		TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr4:147560458_147560466delGGCGGCGGC	ENST00000281321.3	+	1	414_422	c.166_174delGGCGGCGGC	c.(166-174)ggcggcggcdel	p.GGG65del	AC093887.1_ENST00000584185.1_RNA	NM_004575.2	NP_004566.2	Q12837	PO4F2_HUMAN	POU class 4 homeobox 2	65	Poly-Gly.				axon extension (GO:0048675)|axon guidance (GO:0007411)|intracellular estrogen receptor signaling pathway (GO:0030520)|MAPK cascade (GO:0000165)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|retinal ganglion cell axon guidance (GO:0031290)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	33	all_hematologic(180;0.151)					CGCTggtggtggcggcggcggcggcggcg	0.761																																						ENST00000281321.3																			0				NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	33						c.(166-174)del		POU class 4 homeobox 2																																				SO:0001651	inframe_deletion	5458				estrogen receptor signaling pathway|MAPKKK cascade|negative regulation of transcription from RNA polymerase II promoter	nuclear speck	RNA polymerase II core promoter proximal region sequence-specific DNA binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription	g.chr4:147560458_147560466delGGCGGCGGC	U06233	CCDS34074.1	4q31.22	2011-06-20	2007-07-13					"""Homeoboxes / POU class"""	9219	protein-coding gene	gene with protein product		113725	"""POU domain, class 4, transcription factor 2"", ""POU domain class 4, transcription factor 2"""	BRN3B		8332509	Standard	NM_004575		Approved	Brn-3b	uc003ikv.3	Q12837		ENST00000281321.3:c.166_174delGGCGGCGGC	4.37:g.147560467_147560475delGGCGGCGGC	ENSP00000281321:p.Gly65_Gly67del					AC093887.1_ENST00000584185.1_RNA	p.GGG65del	NM_004575.2	NP_004566.2	Q12837	PO4F2_HUMAN			1	414_422	+	all_hematologic(180;0.151)		65			Poly-Gly.		B1PJR6|B2RC84|Q13883|Q14987	In_Frame_Del	DEL	ENST00000281321.3	37	c.166_174delGGCGGCGGC	CCDS34074.1																																																																																				0.761	POU4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367020.1	NM_004575		5	7						5	7	---	---	---	---
FAM66B	100128890	broad.mit.edu	37	8	7191540	7191541	+	lincRNA	DEL	CA	CA	-	rs376658666		TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr8:7191540_7191541delCA	ENST00000606573.1	-	0	703									family with sequence similarity 66, member B																		GGGGTGcacgcacacacacaca	0.53																																						ENST00000606573.1																			0																																																			0							g.chr8:7191540_7191541delCA			8p23.1	2013-07-05			ENSG00000215374	ENSG00000215374		"""Long non-coding RNAs"""	28890	non-coding RNA	RNA, long non-coding							Standard	NR_027423		Approved				OTTHUMG00000165383		8.37:g.7191550_7191551delCA														0	703	-									RNA	DEL	ENST00000606573.1	37																																																																																						0.530	FAM66B-002	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000470344.1	NR_027423		7	47						7	47	---	---	---	---
C16orf74	404550	broad.mit.edu	37	16	85743879	85743881	+	In_Frame_Del	DEL	GCT	GCT	-	rs374238893		TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chr16:85743879_85743881delGCT	ENST00000284245.4	-	3	244_246	c.61_63delAGC	c.(61-63)agcdel	p.S21del	C16orf74_ENST00000602675.1_5'UTR|C16orf74_ENST00000602758.1_Intron|C16orf74_ENST00000602583.1_In_Frame_Del_p.S9del|C16orf74_ENST00000602914.1_Intron|C16orf74_ENST00000602766.1_5'UTR|C16orf74_ENST00000602719.1_In_Frame_Del_p.S21del	NM_206967.2	NP_996850.1	Q96GX8	CP074_HUMAN	chromosome 16 open reading frame 74	21																	CCTCGTCGTGGCTGCTGCTGCTG	0.635																																						ENST00000602583.1																			0											c.(25-27)del		chromosome 16 open reading frame 74																																				SO:0001651	inframe_deletion	404550							g.chr16:85743879_85743881delGCT	BC009078	CCDS45540.1	16q24.1	2014-05-28			ENSG00000154102	ENSG00000154102			23362	protein-coding gene	gene with protein product							Standard	NM_206967		Approved	MGC17624	uc002fjc.4	Q96GX8	OTTHUMG00000183875	ENST00000284245.4:c.61_63delAGC	16.37:g.85743888_85743890delGCT	ENSP00000284245:p.Ser21del					C16orf74_ENST00000602675.1_5'UTR|C16orf74_ENST00000602914.1_Intron|C16orf74_ENST00000284245.4_In_Frame_Del_p.S21del|C16orf74_ENST00000602719.1_In_Frame_Del_p.S21del|C16orf74_ENST00000602758.1_Intron|C16orf74_ENST00000602766.1_5'UTR	p.S9del			Q96GX8	CP074_HUMAN			1	575_577	-			21						In_Frame_Del	DEL	ENST00000284245.4	37	c.25_27delAGC	CCDS45540.1																																																																																				0.635	C16orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467253.1	NM_206967		2	4						2	4	---	---	---	---
ATRX	546	broad.mit.edu	37	X	76939340	76939343	+	Frame_Shift_Del	DEL	CTAC	CTAC	-			TCGA-DU-6407-01A-13D-1705-08	TCGA-DU-6407-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f92a34fa-014e-4b41-a6d0-3b46b8c8a3ee	4a5655ba-0f40-4c74-9534-23eb5df3ad4d	g.chrX:76939340_76939343delCTAC	ENST00000373344.5	-	9	1619_1622	c.1405_1408delGTAG	c.(1405-1410)gtagatfs	p.VD469fs	ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Frame_Shift_Del_p.VD431fs	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	469					ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						TGCTCACTATCTACCTGTTTTCTT	0.358			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																															ENST00000373344.5				Rec	yes		X	Xq21.1	546	"""Mis, F, N"""	alpha thalassemia/mental retardation syndrome X-linked	yes	ATR-X (alpha thalassemia/mental retardation) syndrome	E			"""Pancreatic neuroendocrine tumors, paediatric GBM"""		1	Unknown(1)	p.?(1)	bone(1)	bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						c.(1405-1410)atfs		alpha thalassemia/mental retardation syndrome X-linked	Phosphatidylserine(DB00144)																																			SO:0001589	frameshift_variant	546				DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding	g.chrX:76939340_76939343delCTAC	U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.1405_1408delGTAG	X.37:g.76939340_76939343delCTAC	ENSP00000362441:p.Val469fs					ATRX_ENST00000395603.3_Frame_Shift_Del_p.VD431fs|ATRX_ENST00000480283.1_5'UTR	p.VD469fs	NM_000489.3	NP_000480.2	P46100	ATRX_HUMAN			9	1619_1622	-			469					D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Frame_Shift_Del	DEL	ENST00000373344.5	37	c.1405_1408delGTAG	CCDS14434.1																																																																																				0.358	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		132	279						132	279	---	---	---	---
