#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
PRDM9	56979	broad.mit.edu	37	5	23522839	23522839	+	Missense_Mutation	SNP	C	C	T			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr5:23522839C>T	ENST00000296682.3	+	8	909	c.727C>T	c.(727-729)Ccc>Tcc	p.P243S		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	243					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						CCTCAGTCTGCCCCCAGGGCT	0.577										HNSCC(3;0.000094)																												ENST00000296682.3																			0				NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						c.(727-729)Ccc>Tcc		PR domain containing 9							53.0	51.0	52.0					5																	23522839		2203	4300	6503	SO:0001583	missense	56979				meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleoplasm	histone-lysine N-methyltransferase activity|nucleic acid binding|zinc ion binding	g.chr5:23522839C>T	AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"""-"", ""Zinc fingers, C2H2-type"""	13994	protein-coding gene	gene with protein product	"""PR-domain containing protein 9"""	609760	"""minisatellite binding protein 3, 115kDa"", ""minisatellite binding protein 3 (115kD)"""	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.727C>T	5.37:g.23522839C>T	ENSP00000296682:p.Pro243Ser	HNSCC(3;0.000094)					p.P243S	NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN			8	909	+			243					B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	c.727C>T	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	C	16.01	3.002194	0.54254	.	.	ENSG00000164256	ENST00000296682;ENST00000253473	D	0.86769	-2.17	4.02	4.02	0.46733	.	0.000000	0.36200	N	0.002726	D	0.94456	0.8216	M	0.93854	3.465	0.58432	D	0.999996	D	0.89917	1.0	D	0.80764	0.994	D	0.95312	0.8413	10	0.87932	D	0	-21.1566	12.0507	0.53505	0.0:1.0:0.0:0.0	.	243	Q9NQV7	PRDM9_HUMAN	S	243;37	ENSP00000296682:P243S	ENSP00000253473:P37S	P	+	1	0	PRDM9	23558596	1.000000	0.71417	0.990000	0.47175	0.193000	0.23685	3.875000	0.56108	1.952000	0.56665	0.597000	0.82753	CCC		0.577	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227		29	58	0	0	0	1	0	29	58				
SCN5A	6331	broad.mit.edu	37	3	38622756	38622756	+	Missense_Mutation	SNP	C	C	A	rs199473181		TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr3:38622756C>A	ENST00000333535.4	-	17	3043	c.2894G>T	c.(2893-2895)cGc>cTc	p.R965L	SCN5A_ENST00000423572.2_Missense_Mutation_p.R965L|SCN5A_ENST00000455624.2_Missense_Mutation_p.R965L|SCN5A_ENST00000449557.2_Missense_Mutation_p.R965L|SCN5A_ENST00000414099.2_Missense_Mutation_p.R965L|SCN5A_ENST00000443581.1_Missense_Mutation_p.R965L|SCN5A_ENST00000425664.1_Missense_Mutation_p.R965L|SCN5A_ENST00000450102.2_Missense_Mutation_p.R965L|SCN5A_ENST00000451551.2_Missense_Mutation_p.R965L|SCN5A_ENST00000413689.1_Missense_Mutation_p.R965L			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	965			R -> C (in BRGDA1; steady state inactivation shifted to a more negative potential; slower recovery from inactivation). {ECO:0000269|PubMed:11901046, ECO:0000269|PubMed:19272188}.		AV node cell to bundle of His cell communication (GO:0086067)|brainstem development (GO:0003360)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cardiac ventricle development (GO:0003231)|cellular response to calcium ion (GO:0071277)|cerebellum development (GO:0021549)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during SA node cell action potential (GO:0086046)|neuronal action potential (GO:0019228)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of action potential (GO:0045760)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|telencephalon development (GO:0021537)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	ankyrin binding (GO:0030506)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)	p.R965H(2)		NS(3)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|lung(27)|ovary(6)|pancreas(3)|prostate(10)|skin(9)|upper_aerodigestive_tract(4)	107	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909)	CCTCTGGATGCGGGCCAGGGC	0.627																																						ENST00000413689.1																			2	Substitution - Missense(2)	p.R965H(2)	lung(2)	NS(3)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|lung(27)|ovary(6)|pancreas(3)|prostate(10)|skin(9)|upper_aerodigestive_tract(4)	107	GRCh37	CM067021	SCN5A	M		c.(2893-2895)cGc>cTc		sodium channel, voltage-gated, type V, alpha subunit	Benzonatate(DB00868)|Bepridil(DB01244)|Carbamazepine(DB00564)|Cocaine(DB00907)|Dibucaine(DB00527)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lamotrigine(DB00555)|Lidocaine(DB00281)|Mephenytoin(DB00532)|Mexiletine(DB00379)|Mibefradil(DB01388)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine(DB00908)|Riluzole(DB00740)|Tocainide(DB01056)|Verapamil(DB00661)						24.0	26.0	26.0					3																	38622756		2028	4212	6240	SO:0001583	missense	6331				blood circulation|cellular response to calcium ion|muscle contraction|regulation of heart contraction	sarcolemma|voltage-gated sodium channel complex	protein binding|voltage-gated sodium channel activity	g.chr3:38622756C>A	AJ310893	CCDS46796.1, CCDS46797.1, CCDS46798.1, CCDS46799.1, CCDS54569.1, CCDS54570.1	3p21	2014-09-17	2007-01-23		ENSG00000183873	ENSG00000183873		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10593	protein-coding gene	gene with protein product	"""long QT syndrome 3"""	600163	"""sodium channel, voltage-gated, type V, alpha (long QT syndrome 3)"""	CMD1E		7842012, 15466643, 16382098	Standard	NM_198056		Approved	Nav1.5, LQT3, HB1, HBBD, PFHB1, IVF, HB2, HH1, SSS1, CDCD2, CMPD2, ICCD	uc021wvl.1	Q14524	OTTHUMG00000156166	ENST00000333535.4:c.2894G>T	3.37:g.38622756C>A	ENSP00000328968:p.Arg965Leu					SCN5A_ENST00000425664.1_Missense_Mutation_p.R965L|SCN5A_ENST00000451551.2_Missense_Mutation_p.R965L|SCN5A_ENST00000443581.1_Missense_Mutation_p.R965L|SCN5A_ENST00000450102.2_Missense_Mutation_p.R965L|SCN5A_ENST00000414099.2_Missense_Mutation_p.R965L|SCN5A_ENST00000423572.2_Missense_Mutation_p.R965L|SCN5A_ENST00000455624.2_Missense_Mutation_p.R965L|SCN5A_ENST00000333535.4_Missense_Mutation_p.R965L|SCN5A_ENST00000449557.2_Missense_Mutation_p.R965L	p.R965L	NM_001099404.1|NM_001160160.1	NP_001092874.1|NP_001153632.1	Q14524	SCN5A_HUMAN		KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	17	3087	-	Medulloblastoma(35;0.163)		965		R -> C (in BRS1; steady state inactivation shifted to a more negative potential; slower recovery from inactivation).			A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Missense_Mutation	SNP	ENST00000333535.4	37	c.2894G>T	CCDS46796.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.046611	0.93740	.	.	ENSG00000183873	ENST00000414099;ENST00000423572;ENST00000413689;ENST00000451551;ENST00000443581;ENST00000425664;ENST00000333535;ENST00000455624;ENST00000450102;ENST00000449557	D;D;D;D;D;D;D;D;D;D	0.98105	-4.72;-4.72;-4.72;-4.72;-4.72;-4.72;-4.72;-4.72;-4.72;-4.72	4.59	4.59	0.56863	Sodium ion transport-associated (1);	0.000000	0.85682	D	0.000000	D	0.98915	0.9632	M	0.90814	3.15	0.58432	D	0.999992	D;D;D;D;D;D;D	0.89917	0.998;0.999;0.997;0.998;0.998;1.0;0.997	D;D;D;D;D;D;D	0.91635	0.97;0.997;0.95;0.97;0.97;0.999;0.95	D	0.99709	1.1006	10	0.87932	D	0	.	17.6188	0.88075	0.0:1.0:0.0:0.0	.	965;965;965;965;965;965;965	E9PEF3;E9PHB6;Q14524-6;E9PG18;Q14524;Q14524-2;E9PEK2	.;.;.;.;SCN5A_HUMAN;.;.	L	965	ENSP00000398962:R965L;ENSP00000398266:R965L;ENSP00000410257:R965L;ENSP00000388797:R965L;ENSP00000397915:R965L;ENSP00000416634:R965L;ENSP00000328968:R965L;ENSP00000399524:R965L;ENSP00000403355:R965L;ENSP00000413996:R965L	ENSP00000328968:R965L	R	-	2	0	SCN5A	38597760	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.651000	0.83577	2.399000	0.81585	0.655000	0.94253	CGC		0.627	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056		4	47	1	0	1	1	1	4	47				
PCDH19	57526	broad.mit.edu	37	X	99662844	99662844	+	Missense_Mutation	SNP	G	G	A			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chrX:99662844G>A	ENST00000373034.4	-	1	2427	c.752C>T	c.(751-753)tCg>tTg	p.S251L	PCDH19_ENST00000420881.2_Missense_Mutation_p.S251L|PCDH19_ENST00000255531.7_Missense_Mutation_p.S251L	NM_001184880.1	NP_001171809.1	Q8TAB3	PCD19_HUMAN	protocadherin 19	251	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(5)|endometrium(11)|kidney(1)|large_intestine(14)|liver(1)|lung(23)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	68						GTTGGGAGGCGAGTTTTCTGG	0.602																																						ENST00000373034.4																			0				breast(5)|endometrium(11)|kidney(1)|large_intestine(14)|liver(1)|lung(23)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	68						c.(751-753)tCg>tTg		protocadherin 19							143.0	145.0	145.0					X																	99662844		2188	4272	6460	SO:0001583	missense	57526				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chrX:99662844G>A	AB037734	CCDS43976.1, CCDS48141.1, CCDS55462.1	Xq22.1	2014-06-28			ENSG00000165194	ENSG00000165194		"""Cadherins / Protocadherins : Non-clustered"""	14270	protein-coding gene	gene with protein product		300460	"""epilepsy, female restricted, with mental retardation (Juberg-Hellman syndrome)"""	EFMR		11549318, 18469813, 19752159	Standard	NM_020766		Approved	KIAA1313, EIEE9	uc010nmz.3	Q8TAB3	OTTHUMG00000022000	ENST00000373034.4:c.752C>T	X.37:g.99662844G>A	ENSP00000362125:p.Ser251Leu					PCDH19_ENST00000255531.7_Missense_Mutation_p.S251L|PCDH19_ENST00000420881.2_Missense_Mutation_p.S251L	p.S251L	NM_001184880.1	NP_001171809.1	Q8TAB3	PCD19_HUMAN			1	2427	-			251			Cadherin 3.		B0LDS4|E9PAM6|Q5JTG1|Q5JTG2|Q68DT7|Q9P2N3	Missense_Mutation	SNP	ENST00000373034.4	37	c.752C>T	CCDS55462.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.503820	0.85176	.	.	ENSG00000165194	ENST00000420881;ENST00000373034;ENST00000255531	T;T;T	0.52754	0.65;0.65;0.65	5.95	5.95	0.96441	Cadherin (4);Cadherin-like (1);	0.115858	0.64402	D	0.000012	T	0.55337	0.1914	L	0.48986	1.54	0.80722	D	1	P;P;P	0.49253	0.859;0.903;0.921	B;P;P	0.51193	0.207;0.532;0.662	T	0.45673	-0.9245	10	0.26408	T	0.33	.	19.254	0.93938	0.0:0.0:1.0:0.0	.	251;251;251	Q8TAB3;Q8TAB3-2;E9PAM6	PCD19_HUMAN;.;.	L	251	ENSP00000400327:S251L;ENSP00000362125:S251L;ENSP00000255531:S251L	ENSP00000255531:S251L	S	-	2	0	PCDH19	99549500	1.000000	0.71417	0.992000	0.48379	0.913000	0.54294	9.869000	0.99810	2.498000	0.84270	0.513000	0.50165	TCG		0.602	PCDH19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057479.2	NM_020766		74	209	0	0	0	1	0	74	209				
MS4A1	931	broad.mit.edu	37	11	60233595	60233595	+	Missense_Mutation	SNP	A	A	C			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr11:60233595A>C	ENST00000534668.1	+	5	827	c.538A>C	c.(538-540)Acc>Ccc	p.T180P	MS4A1_ENST00000389939.2_Missense_Mutation_p.T180P|MS4A1_ENST00000345732.4_Missense_Mutation_p.T180P|MS4A1_ENST00000532073.1_Missense_Mutation_p.T180P|MS4A1_ENST00000528313.1_Intron	NM_152866.2	NP_690605.1	P11836	CD20_HUMAN	membrane-spanning 4-domains, subfamily A, member 1	180					B cell proliferation (GO:0042100)|humoral immune response (GO:0006959)	external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	MHC class II protein complex binding (GO:0023026)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(10)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	24					Ibritumomab(DB00078)|Obinutuzumab(DB08935)|Rituximab(DB00073)|Tositumomab(DB00081)	CTCCCCATCTACCCAATACTG	0.373																																						ENST00000534668.1																			0				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(10)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						c.(538-540)Acc>Ccc		membrane-spanning 4-domains, subfamily A, member 1	Ibritumomab(DB00078)|Rituximab(DB00073)|Tositumomab(DB00081)						133.0	124.0	127.0					11																	60233595		2203	4300	6503	SO:0001583	missense	931				B cell activation|immune response	integral to plasma membrane		g.chr11:60233595A>C	M27394	CCDS31570.1	11q12-q13.1	2014-09-17				ENSG00000156738		"""CD molecules"""	7315	protein-coding gene	gene with protein product		112210		CD20		2448768	Standard	NM_152866		Approved	B1, Bp35, MS4A2	uc001npq.3	P11836		ENST00000534668.1:c.538A>C	11.37:g.60233595A>C	ENSP00000433277:p.Thr180Pro					MS4A1_ENST00000345732.4_Missense_Mutation_p.T180P|MS4A1_ENST00000528313.1_Intron|MS4A1_ENST00000389939.2_Missense_Mutation_p.T180P|MS4A1_ENST00000532073.1_Missense_Mutation_p.T180P	p.T180P	NM_152866.2	NP_690605.1	P11836	CD20_HUMAN			5	827	+			180					A6NMS4|B4DT24|P08984|Q13963	Missense_Mutation	SNP	ENST00000534668.1	37	c.538A>C	CCDS31570.1	.	.	.	.	.	.	.	.	.	.	A	13.68	2.309700	0.40895	.	.	ENSG00000156738	ENST00000345732;ENST00000532073;ENST00000534668;ENST00000389939	T;T;T;T	0.02395	4.31;4.31;4.31;4.31	5.13	-0.594	0.11664	.	2.028640	0.01840	N	0.035231	T	0.03095	0.0091	N	0.21373	0.66	0.09310	N	1	P;P	0.48911	0.917;0.856	P;P	0.45195	0.473;0.473	T	0.33979	-0.9847	10	0.33940	T	0.23	1.7403	4.3771	0.11275	0.4794:0.2225:0.2981:0.0	.	180;180	E9PKH8;P11836	.;CD20_HUMAN	P	180	ENSP00000314620:T180P;ENSP00000433519:T180P;ENSP00000433277:T180P;ENSP00000374589:T180P	ENSP00000314620:T180P	T	+	1	0	MS4A1	59990171	0.000000	0.05858	0.000000	0.03702	0.060000	0.15804	0.334000	0.19787	0.062000	0.16340	0.533000	0.62120	ACC		0.373	MS4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395402.1			16	224	0	0	0	1	0	16	224				
CEP170B	283638	broad.mit.edu	37	14	105361169	105361169	+	Silent	SNP	A	A	C			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr14:105361169A>C	ENST00000414716.3	+	19	4767	c.4539A>C	c.(4537-4539)tcA>tcC	p.S1513S	CEP170B_ENST00000453495.1_Silent_p.S1549S|CEP170B_ENST00000556508.1_Silent_p.S1478S|CEP170B_ENST00000418279.1_Silent_p.S1443S	NM_001112726.2	NP_001106197.1	Q9Y4F5	C170B_HUMAN	centrosomal protein 170B	1548						cytoplasm (GO:0005737)|microtubule (GO:0005874)		p.S1513S(3)|p.S1479S(3)|p.S1478S(1)									GCCCACCCTCACCCGCCTCAG	0.711																																						ENST00000453495.1																			7	Substitution - coding silent(7)	p.S1513S(3)|p.S1479S(3)|p.S1478S(1)	prostate(3)|kidney(2)|central_nervous_system(2)								c.(4645-4647)tcA>tcC		centrosomal protein 170B							11.0	15.0	14.0					14																	105361169		1915	4097	6012	SO:0001819	synonymous_variant	283638							g.chr14:105361169A>C	AB006622	CCDS45175.1, CCDS45176.1, CCDS45176.2	14q32.33	2014-02-20	2012-11-30	2012-11-30	ENSG00000099814	ENSG00000099814			20362	protein-coding gene	gene with protein product	"""Cep170-related"""		"""KIAA0284"""	KIAA0284		23087211	Standard	NM_015005		Approved	FAM68C, Cep170R	uc010axb.4	Q9Y4F5	OTTHUMG00000170763	ENST00000414716.3:c.4539A>C	14.37:g.105361169A>C						CEP170B_ENST00000556508.1_Silent_p.S1478S|CEP170B_ENST00000418279.1_Silent_p.S1443S|CEP170B_ENST00000414716.3_Silent_p.S1513S	p.S1549S							19	4875	+								Q2KHR7|Q86TI7	Silent	SNP	ENST00000414716.3	37	c.4647A>C	CCDS45175.1																																																																																				0.711	CEP170B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000410289.2	NM_001112726		9	24	0	0	0	1	0	9	24				
USP48	84196	broad.mit.edu	37	1	22030798	22030798	+	Silent	SNP	C	C	T			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr1:22030798C>T	ENST00000308271.9	-	20	3120	c.2472G>A	c.(2470-2472)gtG>gtA	p.V824V	USP48_ENST00000529637.1_Silent_p.V836V|USP48_ENST00000374732.3_Silent_p.V362V|USP48_ENST00000400301.1_Silent_p.V824V	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48	824	DUSP 3. {ECO:0000255|PROSITE- ProRule:PRU00613}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			NS(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(14)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		TTACATCTCCCACTTCAATTC	0.358																																						ENST00000308271.9																			0				NS(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(14)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						c.(2470-2472)gtG>gtA		ubiquitin specific peptidase 48							92.0	93.0	93.0					1																	22030798		2203	4300	6503	SO:0001819	synonymous_variant	84196				ubiquitin-dependent protein catabolic process	mitochondrion|nucleus	cysteine-type peptidase activity|ubiquitin thiolesterase activity	g.chr1:22030798C>T	AF502942	CCDS30623.1, CCDS44084.1	1p36.12	2008-02-05	2005-08-08	2004-04-07	ENSG00000090686	ENSG00000090686		"""Ubiquitin-specific peptidases"""	18533	protein-coding gene	gene with protein product			"""ubiquitin specific protease 31"", ""ubiquitin specific protease 48"""	USP31		12838346	Standard	XM_005246009		Approved	FLJ23277, FLJ11328, FLJ20103, FLJ23054, MGC14879	uc001bfb.3	Q86UV5	OTTHUMG00000007798	ENST00000308271.9:c.2472G>A	1.37:g.22030798C>T						USP48_ENST00000400301.1_Silent_p.V824V|USP48_ENST00000374732.3_Silent_p.V362V|USP48_ENST00000529637.1_Silent_p.V836V	p.V824V	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)	20	3120	-		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)	824			DUSP 3.		B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Silent	SNP	ENST00000308271.9	37	c.2472G>A	CCDS30623.1																																																																																				0.358	USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021372.1	NM_032236		69	112	0	0	0	1	0	69	112				
DSG1	1828	broad.mit.edu	37	18	28919761	28919761	+	Missense_Mutation	SNP	G	G	A			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr18:28919761G>A	ENST00000257192.4	+	11	1672	c.1460G>A	c.(1459-1461)gGt>gAt	p.G487D		NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	487	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell-cell junction assembly (GO:0007043)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|protein stabilization (GO:0050821)|response to progesterone (GO:0032570)|single organismal cell-cell adhesion (GO:0016337)	apical plasma membrane (GO:0016324)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)|toxic substance binding (GO:0015643)			NS(2)|central_nervous_system(2)|endometrium(5)|kidney(7)|large_intestine(11)|lung(36)|ovary(3)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	76			OV - Ovarian serous cystadenocarcinoma(10;0.00559)			CAAAGTTTTGGTAATGACGAC	0.328																																						ENST00000257192.4																			0				NS(2)|central_nervous_system(2)|endometrium(5)|kidney(7)|large_intestine(11)|lung(36)|ovary(3)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	76						c.(1459-1461)gGt>gAt		desmoglein 1							77.0	79.0	78.0					18																	28919761		2203	4300	6503	SO:0001583	missense	1828				calcium-dependent cell-cell adhesion|cell-cell junction assembly|cellular component disassembly involved in apoptosis|homophilic cell adhesion|protein stabilization	cytosol|desmosome|integral to membrane|internal side of plasma membrane	calcium ion binding|gamma-catenin binding|toxin binding	g.chr18:28919761G>A	X56654	CCDS11896.1	18q12.1	2014-05-13			ENSG00000134760	ENSG00000134760		"""Cadherins / Major cadherins"""	3048	protein-coding gene	gene with protein product		125670		DSG		1889810	Standard	NM_001942		Approved	CDHF4	uc002kwp.3	Q02413	OTTHUMG00000131983	ENST00000257192.4:c.1460G>A	18.37:g.28919761G>A	ENSP00000257192:p.Gly487Asp						p.G487D	NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	OV - Ovarian serous cystadenocarcinoma(10;0.00559)		11	1672	+			487			Cadherin 4.		B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	c.1460G>A	CCDS11896.1	.	.	.	.	.	.	.	.	.	.	g	2.756	-0.258975	0.05791	.	.	ENSG00000134760	ENST00000257192	T	0.60299	0.2	5.03	-1.19	0.09585	Cadherin (2);	0.574961	0.16718	N	0.202362	T	0.50326	0.1609	M	0.73962	2.25	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.46219	-0.9207	10	0.51188	T	0.08	.	5.9414	0.19196	0.4416:0.1347:0.4237:0.0	.	487	Q02413	DSG1_HUMAN	D	487	ENSP00000257192:G487D	ENSP00000257192:G487D	G	+	2	0	DSG1	27173759	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.678000	0.05209	-0.405000	0.07599	-2.354000	0.00241	GGT		0.328	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942		8	138	0	0	0	1	0	8	138				
UACA	55075	broad.mit.edu	37	15	70961406	70961406	+	Silent	SNP	G	G	A			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr15:70961406G>A	ENST00000322954.6	-	16	1802	c.1617C>T	c.(1615-1617)acC>acT	p.T539T	UACA_ENST00000539319.1_Silent_p.T430T|UACA_ENST00000560441.1_Silent_p.T524T|UACA_ENST00000379983.2_Silent_p.T526T	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	539					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of protein import into nucleus (GO:0042307)|response to UV (GO:0009411)	apoptosome (GO:0043293)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)		p.T526T(1)|p.T539T(1)		breast(2)|endometrium(7)|kidney(4)|large_intestine(13)|lung(17)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	50						TCAGTTCCTCGGTTAGTCTGT	0.383																																						ENST00000322954.6																			2	Substitution - coding silent(2)	p.T526T(1)|p.T539T(1)	lung(2)	breast(2)|endometrium(7)|kidney(4)|large_intestine(13)|lung(17)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	50						c.(1615-1617)acC>acT		uveal autoantigen with coiled-coil domains and ankyrin repeats							182.0	170.0	174.0					15																	70961406		2199	4297	6496	SO:0001819	synonymous_variant	55075					cytoskeleton|extracellular region		g.chr15:70961406G>A	AF322916	CCDS10235.1, CCDS32280.1	15q22-q24	2013-01-10			ENSG00000137831	ENSG00000137831		"""Ankyrin repeat domain containing"""	15947	protein-coding gene	gene with protein product		612516				11162650, 10997877	Standard	NM_001008224		Approved	FLJ10128, KIAA1561	uc002asr.3	Q9BZF9	OTTHUMG00000133363	ENST00000322954.6:c.1617C>T	15.37:g.70961406G>A						UACA_ENST00000560441.1_Silent_p.T524T|UACA_ENST00000379983.2_Silent_p.T526T|UACA_ENST00000539319.1_Silent_p.T430T	p.T539T	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN			16	1802	-			539					G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Silent	SNP	ENST00000322954.6	37	c.1617C>T	CCDS10235.1																																																																																				0.383	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2			15	355	0	0	0	1	0	15	355				
SLC22A6	9356	broad.mit.edu	37	11	62744652	62744652	+	Nonsense_Mutation	SNP	C	C	T			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr11:62744652C>T	ENST00000377871.3	-	9	1835	c.1569G>A	c.(1567-1569)tgG>tgA	p.W523*	SLC22A6_ENST00000458333.2_Intron|SLC22A6_ENST00000421062.2_Nonsense_Mutation_p.W479*|SLC22A6_ENST00000537349.1_5'Flank|SLC22A6_ENST00000360421.4_Intron	NM_004790.4|NM_153278.2	NP_004781.2|NP_695010.1	Q4U2R8	S22A6_HUMAN	solute carrier family 22 (organic anion transporter), member 6	523					alpha-ketoglutarate transport (GO:0015742)|organic anion transport (GO:0015711)|protein homooligomerization (GO:0051260)|renal tubular secretion (GO:0097254)|response to methotrexate (GO:0031427)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	chloride ion binding (GO:0031404)|inorganic anion exchanger activity (GO:0005452)|organic anion transmembrane transporter activity (GO:0008514)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(18)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36					Acetaminophen(DB00316)|Acetazolamide(DB00819)|Acetylcysteine(DB06151)|Acetylsalicylic acid(DB00945)|Aciclovir(DB00787)|Adefovir Dipivoxil(DB00718)|Aminohippurate(DB00345)|Aminophenazone(DB01424)|Amoxicillin(DB01060)|Antipyrine(DB01435)|Aspartame(DB00168)|Benzylpenicillin(DB01053)|Bromodiphenhydramine(DB01237)|Bumetanide(DB00887)|Captopril(DB01197)|Carbenicillin(DB00578)|Carprofen(DB00821)|Caspofungin(DB00520)|Cefacetrile(DB01414)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefazolin(DB01327)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Cefotiam(DB00229)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftriaxone(DB01212)|Cephalexin(DB00567)|Chloramphenicol(DB00446)|Chlorothiazide(DB00880)|Chlorpropamide(DB00672)|Cidofovir(DB00369)|Cilastatin(DB01597)|Cimetidine(DB00501)|Cinoxacin(DB00827)|Cloxacillin(DB01147)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Cyclothiazide(DB00606)|Dabrafenib(DB08912)|Diclofenac(DB00586)|Didanosine(DB00900)|Diflunisal(DB00861)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Doxycycline(DB00254)|Enalapril(DB00584)|Ethacrynic acid(DB00903)|Etodolac(DB00749)|Fluorescein(DB00693)|Flurbiprofen(DB00712)|Folic Acid(DB00158)|Foscarnet(DB00529)|Furosemide(DB00695)|Ganciclovir(DB01004)|Gentamicin(DB00798)|Glyburide(DB01016)|Hydrochlorothiazide(DB00999)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Lamivudine(DB00709)|Levofloxacin(DB01137)|Losartan(DB00678)|Meclofenamic acid(DB00939)|Methazolamide(DB00703)|Methotrexate(DB00563)|Minocycline(DB01017)|Nafcillin(DB00607)|Nalidixic Acid(DB00779)|Naproxen(DB00788)|Nateglinide(DB00731)|Norfloxacin(DB01059)|Novobiocin(DB01051)|Ofloxacin(DB01165)|Oxytetracycline(DB00595)|Phenylbutazone(DB00812)|Piperacillin(DB00319)|Piroxicam(DB00554)|Pravastatin(DB00175)|Probenecid(DB01032)|Riboflavin(DB00140)|Salicylic acid(DB00936)|Stavudine(DB00649)|Streptomycin(DB01082)|Sulindac(DB00605)|Tenofovir(DB00300)|Tetracycline(DB00759)|Tolbutamide(DB01124)|Tolmetin(DB00500)|Trifluridine(DB00432)|Valaciclovir(DB00577)|Valproic Acid(DB00313)|Vancomycin(DB00512)|Zalcitabine(DB00943)|Zidovudine(DB00495)	gagTGGGGGCCCACCTGCTCT	0.607																																						ENST00000377871.3																			0				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(18)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36						c.(1567-1569)tgG>tgA		solute carrier family 22 (organic anion transporter), member 6							72.0	74.0	74.0					11																	62744652		2201	4298	6499	SO:0001587	stop_gained	9356				alpha-ketoglutarate transport	basolateral plasma membrane|integral to plasma membrane|membrane fraction	inorganic anion exchanger activity|protein binding	g.chr11:62744652C>T	AF057039	CCDS8041.1, CCDS31591.1, CCDS44631.1, CCDS44632.1	11q12.3	2013-07-15			ENSG00000197901	ENSG00000197901		"""Solute carriers"""	10970	protein-coding gene	gene with protein product		607582				9762842, 9950961	Standard	NM_004790		Approved	ROAT1, PAHT, OAT1	uc001nwk.3	Q4U2R8	OTTHUMG00000167767	ENST00000377871.3:c.1569G>A	11.37:g.62744652C>T	ENSP00000367102:p.Trp523*					SLC22A6_ENST00000458333.2_Intron|SLC22A6_ENST00000421062.2_Nonsense_Mutation_p.W479*|SLC22A6_ENST00000360421.4_Intron	p.W523*	NM_004790.4|NM_153278.2	NP_004781.2|NP_695010.1	Q4U2R8	S22A6_HUMAN			9	1835	-			523					A8MY93|B2D0R6|O95187|O95742|Q7LDA0|Q8N192|Q9NQA6|Q9NQC2|Q9UBG6|Q9UEQ8	Nonsense_Mutation	SNP	ENST00000377871.3	37	c.1569G>A	CCDS31591.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.980466	0.92982	.	.	ENSG00000197901	ENST00000377871;ENST00000421062	.	.	.	4.48	0.513	0.17000	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	.	6.4495	0.21896	0.0:0.5215:0.0:0.4785	.	.	.	.	X	523;479	.	ENSP00000367102:W523X	W	-	3	0	SLC22A6	62501228	0.005000	0.15991	0.192000	0.23308	0.502000	0.33828	-0.130000	0.10498	-0.014000	0.14175	0.561000	0.74099	TGG		0.607	SLC22A6-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396186.1	NM_004790		8	213	0	0	0	1	0	8	213				
CCDC33	80125	broad.mit.edu	37	15	74625122	74625122	+	Missense_Mutation	SNP	G	G	A	rs374632000		TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr15:74625122G>A	ENST00000398814.3	+	16	2305	c.1874G>A	c.(1873-1875)cGg>cAg	p.R625Q	CCDC33_ENST00000558821.1_Missense_Mutation_p.R218Q|CCDC33_ENST00000321288.5_Missense_Mutation_p.R828Q|CCDC33_ENST00000268082.4_Missense_Mutation_p.R218Q	NM_025055.3	NP_079331.3	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33	828										breast(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						GCGAAGCTGCGGACGGAGCTG	0.602																																						ENST00000321288.5																			0				breast(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						c.(2482-2484)cGg>cAg		coiled-coil domain containing 33		G	GLN/ARG,GLN/ARG	0,3918		0,0,1959	72.0	80.0	78.0		1874,653	3.0	0.7	15		78	1,8297		0,1,4148	no	missense,missense	CCDC33	NM_025055.3,NM_182791.2	43,43	0,1,6107	AA,AG,GG		0.0121,0.0,0.0082	possibly-damaging,possibly-damaging	625/756,218/368	74625122	1,12215	1959	4149	6108	SO:0001583	missense	80125						protein binding	g.chr15:74625122G>A	BC025689	CCDS42058.1, CCDS42059.1, CCDS73753.1	15q24.1	2009-08-06				ENSG00000140481			26552	protein-coding gene	gene with protein product	"""cancer/testis antigen 61"""					12477932	Standard	NM_025055		Approved	FLJ32855, CT61	uc002axo.4	Q8N5R6		ENST00000398814.3:c.1874G>A	15.37:g.74625122G>A	ENSP00000381795:p.Arg625Gln					CCDC33_ENST00000268082.4_Missense_Mutation_p.R218Q|CCDC33_ENST00000558821.1_Missense_Mutation_p.R218Q|CCDC33_ENST00000398814.3_Missense_Mutation_p.R625Q	p.R828Q			Q8N5R6	CCD33_HUMAN			18	2483	+			828					A8K3U4|A8MPQ6|A8MV61|A8MVU9|B3KQ49|Q8TAX6|Q9H5Q6	Missense_Mutation	SNP	ENST00000398814.3	37	c.2483G>A	CCDS42058.1	.	.	.	.	.	.	.	.	.	.	G	10.65	1.409417	0.25378	0.0	1.21E-4	ENSG00000140481	ENST00000321288;ENST00000398814;ENST00000321374;ENST00000268082	T;T;T;T	0.36340	1.26;1.67;1.37;1.49	5.04	3.04	0.35103	.	0.250853	0.29699	N	0.011436	T	0.20780	0.0500	L	0.45581	1.43	0.18873	N	0.999988	B;B;P;B	0.40834	0.232;0.36;0.73;0.36	B;B;B;B	0.21360	0.023;0.034;0.026;0.034	T	0.16394	-1.0404	10	0.33141	T	0.24	.	6.9978	0.24793	0.0908:0.0:0.7382:0.171	.	218;218;828;625	Q8N5R6-4;Q8N5R6-5;C9JFX2;Q8N5R6-6	.;.;.;.	Q	828;625;218;218	ENSP00000325012:R828Q;ENSP00000381795:R625Q;ENSP00000325661:R218Q;ENSP00000268082:R218Q	ENSP00000268082:R218Q	R	+	2	0	CCDC33	72412175	1.000000	0.71417	0.730000	0.30809	0.186000	0.23388	2.500000	0.45381	1.137000	0.42214	0.543000	0.68304	CGG		0.602	CCDC33-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419491.2	NM_182791		14	191	0	0	0	1	0	14	191				
LOC101927755	101927755	broad.mit.edu	37	17	58066651	58066651	+	lincRNA	SNP	C	C	T	rs376360537		TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr17:58066651C>T	ENST00000586209.1	+	0	158																											ACTGGTAAAGCTGTTTAAGAG	0.333																																						ENST00000586209.1																			0																																																			0							g.chr17:58066651C>T																													17.37:g.58066651C>T														0	158	+									RNA	SNP	ENST00000586209.1	37																																																																																						0.333	RP11-178C3.2-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000449162.1			3	39	0	0	0	1	0	3	39				
GPR141	353345	broad.mit.edu	37	7	37780775	37780775	+	Silent	SNP	C	C	T			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr7:37780775C>T	ENST00000447769.1	+	4	1069	c.780C>T	c.(778-780)agC>agT	p.S260S	EPDR1_ENST00000476620.1_Intron|GPR141_ENST00000461610.1_Intron|GPR141_ENST00000334425.1_Silent_p.S260S			Q7Z602	GP141_HUMAN	G protein-coupled receptor 141	260						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(13)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						CCTGTAACAGCAAGGTTGCAT	0.383																																						ENST00000447769.1																			0				NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(13)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						c.(778-780)agC>agT		G protein-coupled receptor 141							165.0	160.0	162.0					7																	37780775		2203	4300	6503	SO:0001819	synonymous_variant	353345					integral to membrane|plasma membrane	G-protein coupled receptor activity	g.chr7:37780775C>T	AY288420	CCDS5451.1	7p14.1	2012-08-21			ENSG00000187037	ENSG00000187037		"""GPCR / Class A : Orphans"""	19997	protein-coding gene	gene with protein product		609045				12679517, 14623098	Standard	NM_181791		Approved	PGR13	uc003tfm.1	Q7Z602	OTTHUMG00000102105	ENST00000447769.1:c.780C>T	7.37:g.37780775C>T						GPR141_ENST00000334425.1_Silent_p.S260S|EPDR1_ENST00000476620.1_Intron|GPR141_ENST00000461610.1_Intron	p.S260S			Q7Z602	GP141_HUMAN			4	1069	+			260					A4D1X7|Q0VAR5|Q86SP3	Silent	SNP	ENST00000447769.1	37	c.780C>T	CCDS5451.1																																																																																				0.383	GPR141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219943.2	NM_181791		5	262	0	0	0	1	0	5	262				
IDH1	3417	broad.mit.edu	37	2	209113113	209113113	+	Missense_Mutation	SNP	G	G	A	rs121913499		TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr2:209113113G>A	ENST00000415913.1	-	4	775	c.394C>T	c.(394-396)Cgt>Tgt	p.R132C	IDH1_ENST00000446179.1_Missense_Mutation_p.R132C|IDH1_ENST00000345146.2_Missense_Mutation_p.R132C	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.R132C(446)|p.R132G(125)|p.R132S(106)|p.G131_R132>VL(1)|p.R132V(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)		TAAGCATGACGACCTATGATG	0.398			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		679	Substitution - Missense(678)|Complex - compound substitution(1)	p.R132C(446)|p.R132G(125)|p.R132S(106)|p.G131_R132>VL(1)|p.R132V(1)	haematopoietic_and_lymphoid_tissue(280)|central_nervous_system(181)|bone(177)|biliary_tract(21)|soft_tissue(12)|large_intestine(2)|skin(2)|autonomic_ganglia(1)|endometrium(1)|NS(1)|prostate(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>Tgt		isocitrate dehydrogenase 1 (NADP+), soluble							81.0	74.0	76.0					2																	209113113		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.chr2:209113113G>A		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.394C>T	2.37:g.209113113G>A	ENSP00000390265:p.Arg132Cys					IDH1_ENST00000345146.2_Missense_Mutation_p.R132C|IDH1_ENST00000446179.1_Missense_Mutation_p.R132C	p.R132C			O75874	IDHC_HUMAN		Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)	4	775	-			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.394C>T	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.550898	0.86127	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.87029	-2.2;-2.2;-2.2;-2.2	5.57	5.57	0.84162	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.94049	0.8093	H	0.99379	4.54	0.80722	D	1	B	0.29862	0.259	B	0.31245	0.126	D	0.94048	0.7315	10	0.87932	D	0	-20.0399	19.5341	0.95242	0.0:0.0:1.0:0.0	.	132	O75874	IDHC_HUMAN	C	132	ENSP00000260985:R132C;ENSP00000410513:R132C;ENSP00000390265:R132C;ENSP00000391075:R132C	ENSP00000260985:R132C	R	-	1	0	IDH1	208821358	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	7.074000	0.76791	2.616000	0.88540	0.555000	0.69702	CGT		0.398	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			64	124	0	0	0	1	0	64	124				
VAC14	55697	broad.mit.edu	37	16	70834803	70834803	+	Start_Codon_SNP	SNP	T	T	C			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr16:70834803T>C	ENST00000261776.5	-	1	261	c.1A>G	c.(1-3)Atg>Gtg	p.M1V	RP11-424M24.5_ENST00000574178.1_lincRNA	NM_018052.3	NP_060522.3	Q08AM6	VAC14_HUMAN	Vac14 homolog (S. cerevisiae)	1					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of lipid kinase activity (GO:0043550)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|PAS complex (GO:0070772)	receptor activity (GO:0004872)			breast(2)|endometrium(2)|kidney(10)|large_intestine(1)|lung(10)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	33		Ovarian(137;0.0699)				TCGGGGTTCATGGTGGCAGCT	0.697																																						ENST00000261776.5																			0				breast(2)|endometrium(2)|kidney(10)|large_intestine(1)|lung(10)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	33						c.(1-3)Atg>Gtg		Vac14 homolog (S. cerevisiae)																																				SO:0001582	initiator_codon_variant	55697				interspecies interaction between organisms	endoplasmic reticulum|endosome membrane|microsome	protein binding|receptor activity	g.chr16:70834803T>C	AK056433	CCDS10896.1	16q22.1	2010-03-23	2005-02-09		ENSG00000103043	ENSG00000103043			25507	protein-coding gene	gene with protein product		604632	"""Tax1 (human T-cell leukemia virus type I) binding protein 2"""	TAX1BP2		15542851, 12719380	Standard	NM_018052		Approved	FLJ10305, ArPIKfyve	uc002ezm.3	Q08AM6	OTTHUMG00000137583	ENST00000261776.5:c.1A>G	16.37:g.70834803T>C	ENSP00000261776:p.Met1Val						p.M1V	NM_018052.3	NP_060522.3	Q08AM6	VAC14_HUMAN			1	261	-		Ovarian(137;0.0699)	1					B3KPJ5|B3KSM8|Q13174|Q6IA12|Q7L4Y1|Q9BW96|Q9H6V6	Translation_Start_Site	SNP	ENST00000261776.5	37	c.1A>G	CCDS10896.1	.	.	.	.	.	.	.	.	.	.	T	18.00	3.525433	0.64747	.	.	ENSG00000103043	ENST00000261776	.	.	.	4.74	4.74	0.60224	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.77638	0.4160	.	.	.	0.80722	D	1	P	0.52842	0.956	D	0.65010	0.931	T	0.81226	-0.1029	8	0.87932	D	0	-36.2039	14.061	0.64800	0.0:0.0:0.0:1.0	.	1	Q08AM6	VAC14_HUMAN	V	1	.	ENSP00000261776:M1V	M	-	1	0	VAC14	69392304	1.000000	0.71417	1.000000	0.80357	0.725000	0.41563	5.378000	0.66190	1.985000	0.57927	0.374000	0.22700	ATG		0.697	VAC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268973.3	NM_018052	Missense_Mutation	4	83	0	0	0	1	0	4	83				
EPB42	2038	broad.mit.edu	37	15	43512971	43512971	+	Intron	SNP	G	G	A			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr15:43512971G>A	ENST00000441366.2	-	1	236				EPB42_ENST00000540029.1_Intron|EPB42_ENST00000300215.3_Missense_Mutation_p.A18V	NM_000119.2|NM_001114134.1	NP_000110.2|NP_001107606.1	P16452	EPB42_HUMAN	erythrocyte membrane protein band 4.2						cell morphogenesis (GO:0000902)|erythrocyte maturation (GO:0043249)|hemoglobin metabolic process (GO:0020027)|iron ion homeostasis (GO:0055072)|peptide cross-linking (GO:0018149)|regulation of cell shape (GO:0008360)|spleen development (GO:0048536)	cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)|structural constituent of cytoskeleton (GO:0005200)			endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.7e-07)		TGCGGGGGCTGCATACAGTCC	0.582																																						ENST00000300215.3																			0				endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						c.(52-54)gCa>gTa		erythrocyte membrane protein band 4.2							132.0	128.0	129.0					15																	43512971		2203	4299	6502	SO:0001627	intron_variant	2038				erythrocyte maturation|peptide cross-linking|regulation of cell shape	cytoplasm|cytoskeleton|plasma membrane	ATP binding|protein binding|protein-glutamine gamma-glutamyltransferase activity|structural constituent of cytoskeleton	g.chr15:43512971G>A	M60298	CCDS10093.1, CCDS45249.1	15q15-q21	2013-05-02			ENSG00000166947	ENSG00000166947		"""Transglutaminases"""	3381	protein-coding gene	gene with protein product	"""Erythrocyte surface protein band 4.2"""	177070				1284644	Standard	NM_000119		Approved	PA, MGC116735, MGC116737	uc001zrb.4	P16452	OTTHUMG00000130701	ENST00000441366.2:c.10+42C>T	15.37:g.43512971G>A						EPB42_ENST00000441366.2_Intron|EPB42_ENST00000540029.1_Intron	p.A18V			P16452	EPB42_HUMAN		GBM - Glioblastoma multiforme(94;8.7e-07)	1	510	-		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)	0					Q4KKX0|Q4VB97	Missense_Mutation	SNP	ENST00000441366.2	37	c.53C>T	CCDS45249.1	.	.	.	.	.	.	.	.	.	.	G	15.51	2.856159	0.51376	.	.	ENSG00000166947	ENST00000300215	D	0.85955	-2.05	3.5	2.37	0.29283	.	10.230900	0.00166	N	0.000007	T	0.67869	0.2939	.	.	.	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.62854	-0.6766	9	0.05959	T	0.93	-0.1817	5.0058	0.14288	0.8515:0.0:0.1485:0.0	.	18	P16452-2	.	V	18	ENSP00000300215:A18V	ENSP00000300215:A18V	A	-	2	0	EPB42	41300263	0.004000	0.15560	0.005000	0.12908	0.006000	0.05464	0.829000	0.27449	0.546000	0.28920	-0.379000	0.06801	GCA		0.582	EPB42-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432219.1	NM_000119		5	323	0	0	0	1	0	5	323				
SEC23IP	11196	broad.mit.edu	37	10	121663645	121663645	+	Silent	SNP	C	C	T			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr10:121663645C>T	ENST00000369075.3	+	4	1029	c.957C>T	c.(955-957)taC>taT	p.Y319Y	SEC23IP_ENST00000543134.1_Silent_p.Y108Y	NM_007190.3	NP_009121.1	Q9Y6Y8	S23IP_HUMAN	SEC23 interacting protein	319	Interaction with SEC23A.				acrosome assembly (GO:0001675)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|single fertilization (GO:0007338)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear endoplasmic reticulum (GO:0097038)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	36		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)		all cancers(201;0.00515)		GAGGGCGCTACGATGTTTACC	0.488																																						ENST00000369075.3																			0				NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	36						c.(955-957)taC>taT		SEC23 interacting protein							112.0	104.0	107.0					10																	121663645		2203	4300	6503	SO:0001819	synonymous_variant	11196				Golgi organization|intracellular protein transport	endoplasmic reticulum|ER to Golgi transport vesicle membrane|ER-Golgi intermediate compartment	metal ion binding	g.chr10:121663645C>T	AB019435	CCDS7618.1	10q26.11-q26.12	2013-01-10			ENSG00000107651	ENSG00000107651		"""Sterile alpha motif (SAM) domain containing"""	17018	protein-coding gene	gene with protein product						10400679	Standard	NM_007190		Approved	p125	uc001leu.2	Q9Y6Y8	OTTHUMG00000019161	ENST00000369075.3:c.957C>T	10.37:g.121663645C>T						SEC23IP_ENST00000543134.1_Silent_p.Y108Y	p.Y319Y	NM_007190.3	NP_009121.1	Q9Y6Y8	S23IP_HUMAN		all cancers(201;0.00515)	4	1029	+		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)	319			Interaction with SEC23A.		D3DRD2|Q8IXH5|Q9BUK5	Silent	SNP	ENST00000369075.3	37	c.957C>T	CCDS7618.1	.	.	.	.	.	.	.	.	.	.	C	8.230	0.804528	0.16467	.	.	ENSG00000107651	ENST00000442952	.	.	.	5.33	-7.45	0.01374	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-13.9946	17.8598	0.88777	0.0:0.2151:0.0:0.7849	.	.	.	.	X	85	.	.	R	+	1	2	SEC23IP	121653635	0.008000	0.16893	0.315000	0.25238	0.794000	0.44872	-1.264000	0.02847	-1.568000	0.01670	-0.251000	0.11542	CGA		0.488	SEC23IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050688.1			56	116	0	0	0	1	0	56	116				
ROBO2	6092	broad.mit.edu	37	3	77526572	77526572	+	Silent	SNP	A	A	G			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr3:77526572A>G	ENST00000461745.1	+	3	1296	c.396A>G	c.(394-396)cgA>cgG	p.R132R	ROBO2_ENST00000332191.8_Silent_p.R132R|ROBO2_ENST00000487694.3_Silent_p.R148R	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	132					apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		CAGTGTTACGAGATGACTTCC	0.463																																						ENST00000461745.1																			0				NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117						c.(394-396)cgA>cgG		roundabout, axon guidance receptor, homolog 2 (Drosophila)							137.0	129.0	132.0					3																	77526572		1864	4098	5962	SO:0001819	synonymous_variant	6092				apoptosis involved in luteolysis|axon midline choice point recognition|cellular response to hormone stimulus|homophilic cell adhesion|metanephros development|negative regulation of negative chemotaxis|negative regulation of synaptogenesis|olfactory bulb interneuron development|positive regulation of axonogenesis|retinal ganglion cell axon guidance|ureteric bud development	axolemma|cell surface|integral to membrane	axon guidance receptor activity|identical protein binding	g.chr3:77526572A>G	AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	10250	protein-coding gene	gene with protein product		602431	"""roundabout (axon guidance receptor, Drosophila) homolog 2"""			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.396A>G	3.37:g.77526572A>G						ROBO2_ENST00000332191.8_Silent_p.R132R|ROBO2_ENST00000487694.3_Silent_p.R148R	p.R132R	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN		Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)	3	1296	+			132					O43608|Q19AB4|Q19AB5	Silent	SNP	ENST00000461745.1	37	c.396A>G	CCDS43109.1																																																																																				0.463	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		20	275	0	0	0	1	0	20	275				
ZXDB	158586	broad.mit.edu	37	X	57619097	57619097	+	Missense_Mutation	SNP	G	G	A			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chrX:57619097G>A	ENST00000374888.1	+	1	829	c.616G>A	c.(616-618)Ggg>Agg	p.G206R		NM_007157.3	NP_009088.1	P98169	ZXDB_HUMAN	zinc finger, X-linked, duplicated B	206					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.G206R(2)		NS(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(2)|skin(6)	27						CCAGCAGCCCGGGTGTCTGAT	0.711																																						ENST00000374888.1																			2	Substitution - Missense(2)	p.G206R(2)	lung(1)|prostate(1)	NS(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(2)|skin(6)	27						c.(616-618)Ggg>Agg		zinc finger, X-linked, duplicated B							12.0	14.0	13.0					X																	57619097		2186	4257	6443	SO:0001583	missense	158586				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding	g.chrX:57619097G>A	L14788	CCDS35313.1	Xp11.1	2013-01-08			ENSG00000198455	ENSG00000198455		"""Zinc fingers, C2H2-type"""	13199	protein-coding gene	gene with protein product		300236				8268913	Standard	NM_007157		Approved	ZNF905	uc004dvd.3	P98169	OTTHUMG00000021685	ENST00000374888.1:c.616G>A	X.37:g.57619097G>A	ENSP00000364023:p.Gly206Arg						p.G206R	NM_007157.3	NP_009088.1	P98169	ZXDB_HUMAN			1	829	+			206					A8K151|Q9UBB3	Missense_Mutation	SNP	ENST00000374888.1	37	c.616G>A	CCDS35313.1	.	.	.	.	.	.	.	.	.	.	.	0	-2.654782	0.00108	.	.	ENSG00000198455	ENST00000374888	T	0.11063	2.81	2.65	1.78	0.24846	.	0.160870	0.29602	N	0.011697	T	0.04452	0.0122	N	0.12182	0.205	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.41787	-0.9489	10	0.15952	T	0.53	.	4.3042	0.10938	0.3435:0.0:0.6565:0.0	.	206	P98169	ZXDB_HUMAN	R	206	ENSP00000364023:G206R	ENSP00000364023:G206R	G	+	1	0	ZXDB	57635822	0.000000	0.05858	0.002000	0.10522	0.045000	0.14185	-0.287000	0.08388	0.520000	0.28426	0.556000	0.70494	GGG		0.711	ZXDB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056922.1	NM_007157		3	32	0	0	0	1	0	3	32				
CMA1	1215	broad.mit.edu	37	14	24974844	24974844	+	Silent	SNP	G	G	A			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr14:24974844G>A	ENST00000250378.3	-	5	651	c.622C>T	c.(622-624)Ctg>Ttg	p.L208L	CMA1_ENST00000206446.4_Silent_p.L97L|RP11-80A15.1_ENST00000555109.1_Intron	NM_001836.3	NP_001827.1	P23946	CMA1_HUMAN	chymase 1, mast cell	208	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				angiotensin maturation (GO:0002003)|cellular protein metabolic process (GO:0044267)|cellular response to glucose stimulus (GO:0071333)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|interleukin-1 beta biosynthetic process (GO:0050720)|midbrain development (GO:0030901)|peptide metabolic process (GO:0006518)|positive regulation of angiogenesis (GO:0045766)|regulation of inflammatory response (GO:0050727)	extracellular region (GO:0005576)|intracellular (GO:0005622)	peptide binding (GO:0042277)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			kidney(1)|lung(8)|pancreas(1)|prostate(1)	11				GBM - Glioblastoma multiforme(265;0.0271)		CCAGCACACAGAAGAGGGCCC	0.612																																						ENST00000250378.3																			0				kidney(1)|lung(8)|pancreas(1)|prostate(1)	11						c.(622-624)Ctg>Ttg		chymase 1, mast cell							52.0	56.0	55.0					14																	24974844		2203	4300	6503	SO:0001819	synonymous_variant	1215				interleukin-1 beta biosynthetic process|proteolysis	extracellular region	serine-type endopeptidase activity	g.chr14:24974844G>A		CCDS9630.1	14q12	2012-08-30			ENSG00000092009	ENSG00000092009	3.4.21.39		2097	protein-coding gene	gene with protein product		118938				8468056	Standard	NM_001836		Approved		uc001wpp.1	P23946	OTTHUMG00000140181	ENST00000250378.3:c.622C>T	14.37:g.24974844G>A						CMA1_ENST00000206446.4_Silent_p.L97L|RP11-80A15.1_ENST00000555109.1_Intron	p.L208L	NM_001836.3	NP_001827.1	P23946	CMA1_HUMAN		GBM - Glioblastoma multiforme(265;0.0271)	5	651	-			208			Peptidase S1.		B5BUM8|Q16018|Q3SY36|Q3SY37|Q9UDH5	Silent	SNP	ENST00000250378.3	37	c.622C>T	CCDS9630.1																																																																																				0.612	CMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276535.2			8	142	0	0	0	1	0	8	142				
FRMD7	90167	broad.mit.edu	37	X	131216554	131216554	+	Splice_Site	SNP	C	C	A			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chrX:131216554C>A	ENST00000298542.4	-	9	917	c.742G>T	c.(742-744)Gtg>Ttg	p.V248L	FRMD7_ENST00000370879.1_Splice_Site_p.V128L|FRMD7_ENST00000464296.1_Splice_Site_p.V233L	NM_194277.2	NP_919253.1	Q6ZUT3	FRMD7_HUMAN	FERM domain containing 7	248	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				regulation of neuron projection development (GO:0010975)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24	Acute lymphoblastic leukemia(192;0.000127)					TTGCACAACACCTGTATAAAC	0.448																																						ENST00000298542.4																			0				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24						c.e9-1		FERM domain containing 7							119.0	107.0	111.0					X																	131216554		2203	4300	6503	SO:0001630	splice_region_variant	90167				regulation of neuron projection development	cytoskeleton|growth cone|neuronal cell body	binding	g.chrX:131216554C>A	AL161984	CCDS35397.1	Xq26.2	2014-09-17	2006-09-01	2006-09-01	ENSG00000165694	ENSG00000165694			8079	protein-coding gene	gene with protein product		300628	"""nystagmus 1, congenital"""	NYS, NYS1		2063919, 17013395	Standard	NM_194277		Approved	FLJ43346	uc004ewn.3	Q6ZUT3	OTTHUMG00000022421	ENST00000298542.4:c.742-1G>T	X.37:g.131216554C>A						FRMD7_ENST00000464296.1_Splice_Site_p.V233_splice|FRMD7_ENST00000370879.1_Splice_Site_p.V128_splice	p.V248_splice	NM_194277.2	NP_919253.1	Q6ZUT3	FRMD7_HUMAN			9	917	-	Acute lymphoblastic leukemia(192;0.000127)		248			FERM.		C0LLJ3|Q5JX99	Splice_Site	SNP	ENST00000298542.4	37	c.741_splice	CCDS35397.1	.	.	.	.	.	.	.	.	.	.	C	11.22	1.574369	0.28092	.	.	ENSG00000165694	ENST00000370879;ENST00000298542;ENST00000464296	D;D;D	0.86497	-2.13;-2.13;-2.13	5.2	5.2	0.72013	FERM, C-terminal PH-like domain (1);FERM domain (1);Pleckstrin homology-type (1);	0.598709	0.16454	N	0.213725	T	0.79470	0.4451	L	0.29908	0.895	0.37055	D	0.897782	P;P	0.36837	0.571;0.485	B;B	0.34991	0.121;0.193	T	0.81072	-0.1098	10	0.41790	T	0.15	.	10.6459	0.45619	0.0:0.9098:0.0:0.0902	.	233;248	Q6ZUT3-2;Q6ZUT3	.;FRMD7_HUMAN	L	128;248;233	ENSP00000359916:V128L;ENSP00000298542:V248L;ENSP00000417996:V233L	ENSP00000298542:V248L	V	-	1	0	FRMD7	131044235	0.987000	0.35691	0.999000	0.59377	0.617000	0.37484	1.422000	0.34826	2.306000	0.77630	0.544000	0.68410	GTG		0.448	FRMD7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355031.1	NM_194277	Missense_Mutation	11	297	1	0	4.68919e-08	1	5.12539e-08	11	297				
OR4F6	390648	broad.mit.edu	37	15	102346232	102346232	+	Missense_Mutation	SNP	A	A	G			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr15:102346232A>G	ENST00000328882.4	+	1	331	c.310A>G	c.(310-312)Atc>Gtc	p.I104V		NM_001005326.1	NP_001005326.1	Q8NGB9	OR4F6_HUMAN	olfactory receptor, family 4, subfamily F, member 6	104						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|large_intestine(1)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	22	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.00039)|Lung(145;0.17)|LUSC - Lung squamous cell carcinoma(107;0.187)			GATCTTCTTTATCCATGCAGT	0.458																																						ENST00000328882.4																			0				breast(1)|large_intestine(1)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						c.(310-312)Atc>Gtc		olfactory receptor, family 4, subfamily F, member 6							198.0	184.0	189.0					15																	102346232		2203	4300	6503	SO:0001583	missense	390648				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr15:102346232A>G	AC025234	CCDS32341.1	15q26.3	2014-02-19	2002-02-28		ENSG00000184140	ENSG00000184140		"""GPCR / Class A : Olfactory receptors"""	15372	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily F, member 12"""	OR4F12			Standard	NM_001005326		Approved		uc010utr.2	Q8NGB9	OTTHUMG00000172267	ENST00000328882.4:c.310A>G	15.37:g.102346232A>G	ENSP00000327525:p.Ile104Val						p.I104V	NM_001005326.1	NP_001005326.1	Q8NGB9	OR4F6_HUMAN	OV - Ovarian serous cystadenocarcinoma(32;0.00039)|Lung(145;0.17)|LUSC - Lung squamous cell carcinoma(107;0.187)		1	331	+	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		104					B9EH28|Q6IF95	Missense_Mutation	SNP	ENST00000328882.4	37	c.310A>G	CCDS32341.1	.	.	.	.	.	.	.	.	.	.	.	2.830	-0.242820	0.05906	.	.	ENSG00000184140	ENST00000328882	T	0.00487	7.05	4.64	3.47	0.39725	GPCR, rhodopsin-like superfamily (1);	0.111909	0.39615	N	0.001318	T	0.00178	0.0005	N	0.01824	-0.7	0.09310	N	1	B	0.20671	0.047	B	0.18871	0.023	T	0.32402	-0.9908	10	0.21540	T	0.41	.	4.6817	0.12738	0.7051:0.196:0.0989:0.0	.	104	Q8NGB9	OR4F6_HUMAN	V	104	ENSP00000327525:I104V	ENSP00000327525:I104V	I	+	1	0	OR4F6	100163755	0.000000	0.05858	0.802000	0.32245	0.187000	0.23431	-0.858000	0.04281	0.856000	0.35383	0.482000	0.46254	ATC		0.458	OR4F6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417593.1			13	465	0	0	0	1	0	13	465				
SSTR1	6751	broad.mit.edu	37	14	38679188	38679188	+	Silent	SNP	C	C	G			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr14:38679188C>G	ENST00000267377.2	+	3	1211	c.594C>G	c.(592-594)acC>acG	p.T198T		NM_001049.2	NP_001040.1	P30872	SSR1_HUMAN	somatostatin receptor 1	198					cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cerebellum development (GO:0021549)|digestion (GO:0007586)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glutamate receptor signaling pathway (GO:0007215)|negative regulation of cell proliferation (GO:0008285)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29	Hepatocellular(127;0.213)|Esophageal squamous(585;0.22)		Lung(238;3.93e-06)|LUAD - Lung adenocarcinoma(48;2.62e-05)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.00444)	Octreotide(DB00104)|Pasireotide(DB06663)	TCTCTCGCACCGCGGCCAACA	0.637																																						ENST00000267377.2																			0				breast(1)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29						c.(592-594)acC>acG		somatostatin receptor 1	Octreotide(DB00104)						76.0	73.0	74.0					14																	38679188		2203	4300	6503	SO:0001819	synonymous_variant	0				digestion|G-protein signaling, coupled to cyclic nucleotide second messenger|negative regulation of cell proliferation|response to nutrient	integral to plasma membrane	somatostatin receptor activity	g.chr14:38679188C>G		CCDS9666.1	14q13	2012-08-08			ENSG00000139874	ENSG00000139874		"""GPCR / Class A : Somatostatin receptors"""	11330	protein-coding gene	gene with protein product		182451				8449518	Standard	NM_001049		Approved		uc001wul.1	P30872	OTTHUMG00000140249	ENST00000267377.2:c.594C>G	14.37:g.38679188C>G							p.T198T	NM_001049.2	NP_001040.1	P30872	SSR1_HUMAN	Lung(238;3.93e-06)|LUAD - Lung adenocarcinoma(48;2.62e-05)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.00444)	3	1211	+	Hepatocellular(127;0.213)|Esophageal squamous(585;0.22)		198						Silent	SNP	ENST00000267377.2	37	c.594C>G	CCDS9666.1																																																																																				0.637	SSTR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409930.2			7	98	0	0	0	1	0	7	98				
C1orf95	375057	broad.mit.edu	37	1	226784542	226784542	+	Missense_Mutation	SNP	G	G	A			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr1:226784542G>A	ENST00000366788.3	+	2	347	c.242G>A	c.(241-243)cGc>cAc	p.R81H	C1orf95_ENST00000366789.4_Missense_Mutation_p.R81H	NM_001003665.3	NP_001003665.1	Q69YW2	STUM_HUMAN	chromosome 1 open reading frame 95	81						integral component of membrane (GO:0016021)				large_intestine(1)|lung(4)|ovary(3)	8	Breast(184;0.133)	Prostate(94;0.0885)		GBM - Glioblastoma multiforme(131;0.113)		TGCGGGGCCCGCACCGACCTC	0.617																																						ENST00000366788.3																			0				large_intestine(1)|lung(4)|ovary(3)	8						c.(241-243)cGc>cAc		chromosome 1 open reading frame 95							123.0	114.0	117.0					1																	226784542		2203	4300	6503	SO:0001583	missense	375057					integral to membrane		g.chr1:226784542G>A	AF035308	CCDS31044.1	1q42.12	2012-06-26			ENSG00000203685	ENSG00000203685			30491	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_001003665		Approved	DKFZp761P211	uc021pjw.1	Q69YW2	OTTHUMG00000037583	ENST00000366788.3:c.242G>A	1.37:g.226784542G>A	ENSP00000355752:p.Arg81His					C1orf95_ENST00000366789.4_Missense_Mutation_p.R81H	p.R81H	NM_001003665.3	NP_001003665.1	Q69YW2	CA095_HUMAN		GBM - Glioblastoma multiforme(131;0.113)	2	347	+	Breast(184;0.133)	Prostate(94;0.0885)	81					A6NGL2	Missense_Mutation	SNP	ENST00000366788.3	37	c.242G>A	CCDS31044.1	.	.	.	.	.	.	.	.	.	.	G	31	5.067341	0.93898	.	.	ENSG00000203685	ENST00000366788;ENST00000366789	.	.	.	5.68	5.68	0.88126	.	0.068968	0.56097	D	0.000023	T	0.71970	0.3403	L	0.46157	1.445	0.53688	D	0.999979	D	0.69078	0.997	P	0.58391	0.838	T	0.72776	-0.4191	9	0.59425	D	0.04	1.0745	19.3828	0.94543	0.0:0.0:1.0:0.0	.	81	Q69YW2	CA095_HUMAN	H	81	.	ENSP00000355752:R81H	R	+	2	0	C1orf95	224851165	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.623000	0.83113	2.669000	0.90835	0.561000	0.74099	CGC		0.617	C1orf95-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091634.1	NM_001003665		5	266	0	0	0	1	0	5	266				
RP11-156P1.3	0	broad.mit.edu	37	17	45128812	45128812	+	RNA	SNP	C	C	T			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr17:45128812C>T	ENST00000575173.1	-	0	418				LRRC37A17P_ENST00000570478.1_RNA																							AGTCCTGTTTCTGTGTGGATT	0.373																																						ENST00000575173.1																			0																																																			0							g.chr17:45128812C>T																													17.37:g.45128812C>T														0	418	-									RNA	SNP	ENST00000575173.1	37																																																																																						0.373	RP11-156P1.3-009	KNOWN	basic	lincRNA	processed_transcript	OTTHUMT00000440924.1			5	91	0	0	0	1	0	5	91				
IGHV4OR15-8	28317	broad.mit.edu	37	15	22473151	22473151	+	RNA	SNP	G	G	T	rs553444566	byFrequency	TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr15:22473151G>T	ENST00000557788.2	-	0	119							A6NJ16	IV4F8_HUMAN	immunoglobulin heavy variable 4/OR15-8 (non-functional)							extracellular region (GO:0005576)											AGACAACGCAGGTGAGGGACA	0.612																																						ENST00000557788.2																			0																																																			0							g.chr15:22473151G>T	Z29598		15q11.2	2012-02-20	2008-09-15		ENSG00000259261	ENSG00000259261		"""Immunoglobulins / IGH orphons"""	5658	other	immunoglobulin gene			"""immunoglobulin heavy variable 4/OR15-8"", ""V-set and immunoglobulin domain containing 6"""	VSIG6		7951227	Standard			Approved	IGHV4/OR15-8, IGHV4OR158		A6NJ16	OTTHUMG00000171934		15.37:g.22473151G>T														0	119	-									RNA	SNP	ENST00000557788.2	37																																																																																						0.612	IGHV4OR15-8-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene	OTTHUMT00000415968.2			11	523	1	0	1.58986e-06	1	1.69826e-06	11	523				
ADAMTS12	81792	broad.mit.edu	37	5	33576786	33576786	+	Silent	SNP	C	C	T			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr5:33576786C>T	ENST00000504830.1	-	19	3680	c.3345G>A	c.(3343-3345)tcG>tcA	p.S1115S	ADAMTS12_ENST00000504582.1_5'Flank|ADAMTS12_ENST00000352040.3_Silent_p.S1030S	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	1115	Spacer 2.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						GGCCTCCCTCCGAGGTAGGAC	0.493										HNSCC(64;0.19)																												ENST00000504830.1																			0				NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						c.(3343-3345)tcG>tcA		ADAM metallopeptidase with thrombospondin type 1 motif, 12							92.0	88.0	89.0					5																	33576786		2203	4300	6503	SO:0001819	synonymous_variant	81792				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding	g.chr5:33576786C>T	AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14605	protein-coding gene	gene with protein product		606184	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"""			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.3345G>A	5.37:g.33576786C>T		HNSCC(64;0.19)				ADAMTS12_ENST00000352040.3_Silent_p.S1030S	p.S1115S	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN			19	3680	-			1115			Spacer 2.		A2RRN9|A5D6V6|Q6UWL3	Silent	SNP	ENST00000504830.1	37	c.3345G>A	CCDS34140.1																																																																																				0.493	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		4	176	0	0	0	1	0	4	176				
TIMELESS	8914	broad.mit.edu	37	12	56815192	56815192	+	Silent	SNP	C	C	T			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr12:56815192C>T	ENST00000553532.1	-	23	2961	c.2811G>A	c.(2809-2811)gtG>gtA	p.V937V	TIMELESS_ENST00000229201.4_Silent_p.V936V|TIMELESS_ENST00000554616.1_Silent_p.V434V					timeless circadian clock											NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						GCCGCTCAGCCACCAGCCCCA	0.517																																						ENST00000229201.4																			0				NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						c.(2806-2808)gtG>gtA		timeless circadian clock							118.0	115.0	116.0					12																	56815192		2203	4300	6503	SO:0001819	synonymous_variant	8914				cell division|circadian rhythm|detection of abiotic stimulus|mitosis|morphogenesis of an epithelium|negative regulation of transcription, DNA-dependent|regulation of S phase|response to DNA damage stimulus|transcription, DNA-dependent	nuclear chromatin		g.chr12:56815192C>T	AF098162	CCDS8918.1	12q13.3	2012-12-14	2012-12-14		ENSG00000111602	ENSG00000111602			11813	protein-coding gene	gene with protein product	"""Tof1 homolog (S. cerevisiae)"", ""timeless circadian clock 1"""	603887	"""timeless (Drosophila) homolog"", ""timeless homolog (Drosophila)"""			9856465	Standard	NM_003920		Approved	hTIM, TIM, TIM1	uc001slf.2	Q9UNS1	OTTHUMG00000170600	ENST00000553532.1:c.2811G>A	12.37:g.56815192C>T						TIMELESS_ENST00000554616.1_Silent_p.V434V|TIMELESS_ENST00000553532.1_Silent_p.V937V	p.V936V	NM_003920.3	NP_003911.2	Q9UNS1	TIM_HUMAN			23	2962	-			937						Silent	SNP	ENST00000553532.1	37	c.2808G>A	CCDS8918.1																																																																																				0.517	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920		14	247	0	0	0	1	0	14	247				
ECM1	1893	broad.mit.edu	37	1	150483973	150483973	+	Missense_Mutation	SNP	C	C	T			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr1:150483973C>T	ENST00000369047.4	+	7	874	c.749C>T	c.(748-750)tCg>tTg	p.S250L	ECM1_ENST00000369049.4_Missense_Mutation_p.S277L|ECM1_ENST00000346569.6_Intron|ECM1_ENST00000470432.1_3'UTR	NM_004425.3	NP_004416.2	Q16610	ECM1_HUMAN	extracellular matrix protein 1	250	2 X approximate repeats.				angiogenesis (GO:0001525)|biomineral tissue development (GO:0031214)|inflammatory response (GO:0006954)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of peptidase activity (GO:0010466)|ossification (GO:0001503)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of T cell migration (GO:2000404)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type 2 immune response (GO:0002828)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	enzyme binding (GO:0019899)|laminin binding (GO:0043236)|protease binding (GO:0002020)|protein C-terminus binding (GO:0008022)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|urinary_tract(1)	22	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.29e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			GCCGAGTTCTCGGTCAAGACC	0.632																																					Melanoma(156;1696 2560 11093 19685)	ENST00000369047.4																			0				NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|urinary_tract(1)	22						c.(748-750)tCg>tTg		extracellular matrix protein 1							81.0	80.0	80.0					1																	150483973		2203	4300	6503	SO:0001583	missense	1893				angiogenesis|biomineral tissue development|negative regulation of bone mineralization|negative regulation of peptidase activity|ossification|positive regulation of angiogenesis|positive regulation of endothelial cell proliferation|positive regulation of I-kappaB kinase/NF-kappaB cascade	proteinaceous extracellular matrix	laminin binding|protease binding|protein C-terminus binding|signal transducer activity	g.chr1:150483973C>T	U68186	CCDS953.1, CCDS954.1, CCDS55632.1	1q21	2008-02-05			ENSG00000143369	ENSG00000143369			3153	protein-coding gene	gene with protein product		602201				9367673, 9501329	Standard	NM_004425		Approved		uc001eus.3	Q16610	OTTHUMG00000012806	ENST00000369047.4:c.749C>T	1.37:g.150483973C>T	ENSP00000358043:p.Ser250Leu					ECM1_ENST00000346569.6_Intron|ECM1_ENST00000369049.4_Missense_Mutation_p.S277L|ECM1_ENST00000470432.1_3'UTR	p.S250L	NM_004425.3	NP_004416.2	Q16610	ECM1_HUMAN	UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.29e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)		7	874	+	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		250			2 X approximate repeats.		A8K8S0|B4DW49|B4DY60|O43266|Q5T5G4|Q5T5G5|Q5T5G6|Q8IZ60	Missense_Mutation	SNP	ENST00000369047.4	37	c.749C>T	CCDS953.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.053897	0.75960	.	.	ENSG00000143369	ENST00000369049;ENST00000369047	T;T	0.79141	-1.24;-1.24	4.29	4.29	0.51040	.	0.565129	0.18027	N	0.154048	D	0.83193	0.5201	M	0.68952	2.095	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.997;0.997;0.998	D	0.84586	0.0664	10	0.87932	D	0	-6.4312	12.4287	0.55561	0.0:1.0:0.0:0.0	.	277;250;250	Q16610-4;C8CHS3;Q16610	.;.;ECM1_HUMAN	L	277;250	ENSP00000358045:S277L;ENSP00000358043:S250L	ENSP00000358043:S250L	S	+	2	0	ECM1	148750597	0.996000	0.38824	1.000000	0.80357	0.995000	0.86356	2.268000	0.43338	2.403000	0.81681	0.561000	0.74099	TCG		0.632	ECM1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035832.2	NM_004425		5	190	0	0	0	1	0	5	190				
URB2	9816	broad.mit.edu	37	1	229773923	229773923	+	Missense_Mutation	SNP	C	C	T			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr1:229773923C>T	ENST00000258243.2	+	4	3699	c.3563C>T	c.(3562-3564)gCc>gTc	p.A1188V		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	1188						aggresome (GO:0016235)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(6)	73						TTCTTTTTGGCCCCAGAACTG	0.453																																						ENST00000258243.2																			0				breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(6)	73						c.(3562-3564)gCc>gTc		URB2 ribosome biogenesis 2 homolog (S. cerevisiae)							139.0	141.0	141.0					1																	229773923		2203	4300	6503	SO:0001583	missense	9816					nucleolus		g.chr1:229773923C>T	D50923	CCDS31052.1	1q42.13	2009-11-06	2008-10-01	2008-10-01	ENSG00000135763	ENSG00000135763			28967	protein-coding gene	gene with protein product	"""nucleolar preribosomal-associated protein 1"""		"""KIAA0133"""	KIAA0133		8590280	Standard	NM_014777		Approved	NPA2, NET10	uc001hts.1	Q14146	OTTHUMG00000039464	ENST00000258243.2:c.3563C>T	1.37:g.229773923C>T	ENSP00000258243:p.Ala1188Val						p.A1188V	NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN			4	3699	+			1188					Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	37	c.3563C>T	CCDS31052.1	.	.	.	.	.	.	.	.	.	.	C	8.994	0.978342	0.18812	.	.	ENSG00000135763	ENST00000258243	T	0.31510	1.49	5.65	2.62	0.31277	.	0.428662	0.26867	N	0.022082	T	0.12689	0.0308	N	0.11560	0.145	0.09310	N	1	B	0.13145	0.007	B	0.14578	0.011	T	0.16247	-1.0409	9	.	.	.	-6.9435	4.6092	0.12392	0.1749:0.588:0.0:0.2371	.	1188	Q14146	URB2_HUMAN	V	1188	ENSP00000258243:A1188V	.	A	+	2	0	URB2	227840546	0.001000	0.12720	0.297000	0.24988	0.954000	0.61252	0.399000	0.20916	1.549000	0.49425	0.585000	0.79938	GCC		0.453	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777		5	306	0	0	0	1	0	5	306				
COL1A2	1278	broad.mit.edu	37	7	94054923	94054923	+	Splice_Site	SNP	G	G	A			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr7:94054923G>A	ENST00000297268.6	+	43	3254	c.2783G>A	c.(2782-2784)gGc>gAc	p.G928D		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	928					blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	TCTTCACAGGGCAACCCTGGG	0.493										HNSCC(75;0.22)																												ENST00000297268.6																		COL1A2/PLAG1(3)	0				NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115						c.e43-1		collagen, type I, alpha 2	Collagenase(DB00048)						92.0	83.0	86.0					7																	94054923		2203	4300	6503	SO:0001630	splice_region_variant	1278				axon guidance|blood vessel development|collagen fibril organization|leukocyte migration|odontogenesis|platelet activation|regulation of blood pressure|Rho protein signal transduction|skeletal system development|skin morphogenesis|transforming growth factor beta receptor signaling pathway	collagen type I|extracellular space|plasma membrane	extracellular matrix structural constituent|identical protein binding|platelet-derived growth factor binding|protein binding, bridging	g.chr7:94054923G>A	Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"""Collagens"""	2198	protein-coding gene	gene with protein product	"""alpha 2(I)-collagen"", ""alpha-2 collagen type I"", ""type I procollagen"", ""collagen I, alpha-2 polypeptide"", ""collagen of skin, tendon and bone, alpha-2 chain"""	120160	"""osteogenesis imperfecta type IV"""	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.2782-1G>A	7.37:g.94054923G>A		HNSCC(75;0.22)					p.G928_splice	NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	STAD - Stomach adenocarcinoma(171;0.0031)		43	3254	+	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		928					P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Splice_Site	SNP	ENST00000297268.6	37	c.2781_splice	CCDS34682.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.466298	0.84425	.	.	ENSG00000164692	ENST00000297268;ENST00000545487	D	0.99176	-5.52	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	D	0.99661	0.9874	H	0.98754	4.32	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97473	1.0042	10	0.87932	D	0	.	19.5787	0.95455	0.0:0.0:1.0:0.0	.	928	P08123	CO1A2_HUMAN	D	928;929	ENSP00000297268:G928D	ENSP00000297268:G928D	G	+	2	0	COL1A2	93892859	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	9.657000	0.98554	2.941000	0.99782	0.655000	0.94253	GGC		0.493	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089	Missense_Mutation	4	89	0	0	0	1	0	4	89				
SEL1L2	80343	broad.mit.edu	37	20	13850848	13850848	+	Splice_Site	SNP	C	C	T	rs569791808		TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr20:13850848C>T	ENST00000284951.5	-	13	1180	c.1106G>A	c.(1105-1107)gGc>gAc	p.G369D	SEL1L2_ENST00000378072.5_Splice_Site_p.G369D|SEL1L2_ENST00000486903.1_5'UTR			Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 (C. elegans)	369						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	51						GATTGCATTGCCCTAGAAGAG	0.338													C|||	1	0.000199681	0.0	0.0	5008	,	,		16827	0.0		0.0	False		,,,				2504	0.001					ENST00000284951.5																			0				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	51						c.e13-1		sel-1 suppressor of lin-12-like 2 (C. elegans)							67.0	69.0	68.0					20																	13850848		1804	4073	5877	SO:0001630	splice_region_variant	80343					integral to membrane	binding	g.chr20:13850848C>T	AL137678	CCDS59443.1	20p12.1	2011-03-31	2006-11-24	2006-11-24	ENSG00000101251	ENSG00000101251			15897	protein-coding gene	gene with protein product		614289	"""chromosome 20 open reading frame 50"""	C20orf50			Standard	NM_001271539		Approved	DKFZp434C1826	uc010zrl.3	Q5TEA6	OTTHUMG00000031910	ENST00000284951.5:c.1105-1G>A	20.37:g.13850848C>T						SEL1L2_ENST00000486903.1_5'UTR|SEL1L2_ENST00000378072.5_Splice_Site_p.G369_splice	p.G369_splice			Q5TEA6	SE1L2_HUMAN			13	1180	-			369					B4DXX5	Splice_Site	SNP	ENST00000284951.5	37	c.1104_splice		.	.	.	.	.	.	.	.	.	.	C	17.77	3.470633	0.63625	.	.	ENSG00000101251	ENST00000378072;ENST00000284951	T;T	0.58506	0.33;0.33	5.45	4.51	0.55191	Tetratricopeptide-like helical (1);	0.000000	0.56097	D	0.000029	T	0.77432	0.4129	M	0.88906	2.99	0.80722	D	1	P;D	0.89917	0.943;1.0	P;D	0.97110	0.874;1.0	T	0.80091	-0.1527	9	.	.	.	-1.6905	10.1881	0.43011	0.0:0.9082:0.0:0.0918	.	369;369	B4DXX5;Q5TEA6	.;SE1L2_HUMAN	D	369	ENSP00000367312:G369D;ENSP00000284951:G369D	.	G	-	2	0	SEL1L2	13798848	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	6.093000	0.71422	1.309000	0.44985	0.557000	0.71058	GGC		0.338	SEL1L2-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078067.3	NM_025229	Missense_Mutation	12	153	0	0	0	1	0	12	153				
PTPDC1	138639	broad.mit.edu	37	9	96859944	96859944	+	Missense_Mutation	SNP	G	G	A	rs202171045		TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr9:96859944G>A	ENST00000375360.3	+	7	1274	c.934G>A	c.(934-936)Gaa>Aaa	p.E312K	PTPDC1_ENST00000288976.3_Missense_Mutation_p.E364K	NM_001253830.1|NM_177995.2	NP_001240759.1|NP_818931.1	A2A3K4	PTPC1_HUMAN	protein tyrosine phosphatase domain containing 1	312					cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)		protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.E364K(1)|p.E312K(1)		endometrium(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	32						GGATGTGTCCGAAGGACCTGG	0.468													.|||	1	0.000199681	0.0008	0.0	5008	,	,		21811	0.0		0.0	False		,,,				2504	0.0					ENST00000375360.3																			2	Substitution - Missense(2)	p.E364K(1)|p.E312K(1)	skin(2)	endometrium(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	32						c.(934-936)Gaa>Aaa		protein tyrosine phosphatase domain containing 1		G	LYS/GLU,LYS/GLU	1,4405		0,1,2202	83.0	78.0	80.0		934,1090	1.2	0.0	9		80	0,8600		0,0,4300	no	missense,missense	PTPDC1	NM_177995.1,NM_152422.3	56,56	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign	312/755,364/807	96859944	1,13005	2203	4300	6503	SO:0001583	missense	138639						protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	g.chr9:96859944G>A	BC051654	CCDS6707.1, CCDS6708.1, CCDS75860.1	9q22.32	2011-06-09			ENSG00000158079	ENSG00000158079		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"""	30184	protein-coding gene	gene with protein product	"""protein tyrosine phosphatase PTP9Q22"""					14702039	Standard	NM_152422		Approved	PTP9Q22, FLJ37312	uc010mrj.2	A2A3K4	OTTHUMG00000020258	ENST00000375360.3:c.934G>A	9.37:g.96859944G>A	ENSP00000364509:p.Glu312Lys					PTPDC1_ENST00000288976.3_Missense_Mutation_p.E364K	p.E312K	NM_001253830.1|NM_177995.2	NP_001240759.1|NP_818931.1	A2A3K4	PTPC1_HUMAN			7	1274	+			312					Q5T3M4|Q6NXE8|Q8IWM1|Q8N1X4|Q8N9F5	Missense_Mutation	SNP	ENST00000375360.3	37	c.934G>A	CCDS6707.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	.	5.336	0.247379	0.10130	2.27E-4	0.0	ENSG00000158079	ENST00000375360;ENST00000288976	T;T	0.14022	2.54;2.54	5.82	1.22	0.21188	.	0.534966	0.22894	N	0.054349	T	0.10809	0.0264	L	0.43152	1.355	0.09310	N	1	B;B;B;B	0.20671	0.047;0.046;0.047;0.047	B;B;B;B	0.15870	0.009;0.014;0.006;0.006	T	0.21348	-1.0248	10	0.41790	T	0.15	-1.8842	8.2023	0.31432	0.2216:0.1402:0.6381:0.0	.	366;364;366;312	E7EN59;A2A3K4-2;A8K0X7;A2A3K4	.;.;.;PTPC1_HUMAN	K	312;364	ENSP00000364509:E312K;ENSP00000288976:E364K	ENSP00000288976:E364K	E	+	1	0	PTPDC1	95899765	0.939000	0.31865	0.001000	0.08648	0.014000	0.08584	2.281000	0.43452	0.317000	0.23160	-0.136000	0.14681	GAA		0.468	PTPDC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000215007.1	NM_177995, NM_152422		4	229	0	0	0	1	0	4	229				
SSX9	280660	broad.mit.edu	37	X	48164214	48164214	+	RNA	SNP	C	C	A			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chrX:48164214C>A	ENST00000608568.1	-	0	155					NR_073393.1		Q7RTT3	SSX9_HUMAN	synovial sarcoma, X breakpoint 9						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|kidney(2)|lung(2)|prostate(1)|stomach(1)	8						GTCACCTCACCTTTTGGATCT	0.557																																						ENST00000376909.1																			0				breast(1)|endometrium(1)|kidney(2)|lung(2)|prostate(1)|stomach(1)	8						c.e2+1									219.0	192.0	201.0					X																	48164214		2203	4299	6502			0							g.chrX:48164214C>A	BK000689		Xp11.23	2013-01-16			ENSG00000204648	ENSG00000204648			19655	other	unknown		300544				12216073	Standard	NR_073393		Approved		uc031tjk.1	Q7RTT3	OTTHUMG00000021490		X.37:g.48164214C>A						SSX9_ENST00000407081.2_Splice_Site_p.K23_splice	p.K23_splice							2	131	-									Splice_Site	SNP	ENST00000608568.1	37	c.69_splice		.	.	.	.	.	.	.	.	.	.	c	12.36	1.913243	0.33815	.	.	ENSG00000204648	ENST00000376909;ENST00000407081	T;T	0.00808	5.67;5.67	1.51	1.51	0.23008	Krueppel-associated box (2);Krueppel-associated box-related (1);	0.142073	0.32736	N	0.005712	T	0.02380	0.0073	.	.	.	0.09310	N	1	D	0.59357	0.985	D	0.63192	0.912	T	0.40942	-0.9536	8	.	.	.	.	5.9294	0.19130	0.0:1.0:0.0:0.0	.	23	Q7RTT3	SSX9_HUMAN	N	23	ENSP00000366107:K23N;ENSP00000385293:K23N	.	K	-	3	2	SSX9	48049158	0.960000	0.32886	0.050000	0.19076	0.096000	0.18686	2.412000	0.44609	1.040000	0.40099	0.171000	0.16805	AAG		0.557	SSX9-002	KNOWN	basic	retained_intron	pseudogene	OTTHUMT00000472372.1	NR_073393		10	445	1	0	1.61879e-10	1	1.8115e-10	10	445				
ACVRL1	94	broad.mit.edu	37	12	52310011	52310011	+	Missense_Mutation	SNP	G	G	T			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr12:52310011G>T	ENST00000388922.4	+	8	1523	c.1240G>T	c.(1240-1242)Gtg>Ttg	p.V414L	ACVRL1_ENST00000550683.1_Missense_Mutation_p.V428L|ACVRL1_ENST00000419526.2_Missense_Mutation_p.V240L	NM_000020.2	NP_000011.2	P37023	ACVL1_HUMAN	activin A receptor type II-like 1	414	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|angiogenesis (GO:0001525)|artery development (GO:0060840)|blood circulation (GO:0008015)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|blood vessel maturation (GO:0001955)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|cellular response to transforming growth factor beta stimulus (GO:0071560)|endothelial tube morphogenesis (GO:0061154)|in utero embryonic development (GO:0001701)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of focal adhesion assembly (GO:0051895)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of blood pressure (GO:0008217)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of DNA replication (GO:0006275)|regulation of endothelial cell proliferation (GO:0001936)|regulation of transcription, DNA-templated (GO:0006355)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|venous blood vessel development (GO:0060841)|wound healing, spreading of epidermal cells (GO:0035313)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)	activin binding (GO:0048185)|activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type I (GO:0005025)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	20				BRCA - Breast invasive adenocarcinoma(357;0.0991)	Adenosine triphosphate(DB00171)	CCGGACCATCGTGAATGGTGA	0.622																																						ENST00000550683.1																			0				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	20						c.(1282-1284)Gtg>Ttg		activin A receptor type II-like 1	Adenosine triphosphate(DB00171)						55.0	50.0	52.0					12																	52310011		2203	4300	6503	SO:0001583	missense	94				blood vessel endothelial cell proliferation involved in sprouting angiogenesis|blood vessel maturation|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of endothelial cell migration|negative regulation of focal adhesion assembly|positive regulation of BMP signaling pathway|positive regulation of transcription, DNA-dependent|regulation of blood pressure|regulation of blood vessel endothelial cell migration|regulation of DNA replication|regulation of endothelial cell proliferation|transforming growth factor beta receptor signaling pathway|wound healing, spreading of epidermal cells	cell surface|integral to plasma membrane	activin binding|activin receptor activity, type I|ATP binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity	g.chr12:52310011G>T	L17075	CCDS31804.1	12q13.13	2014-09-17			ENSG00000139567	ENSG00000139567			175	protein-coding gene	gene with protein product		601284		ACVRLK1, ORW2		8397373, 8640225	Standard	NM_000020		Approved	HHT2, ALK1, HHT	uc001rzk.3	P37023	OTTHUMG00000169507	ENST00000388922.4:c.1240G>T	12.37:g.52310011G>T	ENSP00000373574:p.Val414Leu					ACVRL1_ENST00000388922.4_Missense_Mutation_p.V414L|ACVRL1_ENST00000419526.2_Missense_Mutation_p.V240L	p.V428L	NM_001077401.1	NP_001070869.1	P37023	ACVL1_HUMAN		BRCA - Breast invasive adenocarcinoma(357;0.0991)	7	1383	+			414			Protein kinase.		A6NGA8	Missense_Mutation	SNP	ENST00000388922.4	37	c.1282G>T	CCDS31804.1	.	.	.	.	.	.	.	.	.	.	G	8.379	0.837128	0.16891	.	.	ENSG00000139567	ENST00000388922;ENST00000267008;ENST00000550683;ENST00000548659;ENST00000419526	D;D;D	0.92858	-3.12;-3.12;-3.12	4.98	2.13	0.27403	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.559465	0.15026	N	0.284715	T	0.81187	0.4770	N	0.04018	-0.295	0.34036	D	0.654428	B;B	0.19200	0.034;0.005	B;B	0.26310	0.068;0.032	T	0.74867	-0.3518	10	0.28530	T	0.3	.	9.6568	0.39930	0.2331:0.0:0.7669:0.0	.	240;414	E7EN07;P37023	.;ACVL1_HUMAN	L	414;414;428;240;240	ENSP00000373574:V414L;ENSP00000447884:V428L;ENSP00000392492:V240L	ENSP00000267008:V414L	V	+	1	0	ACVRL1	50596278	0.201000	0.23410	0.940000	0.37924	0.283000	0.27025	1.190000	0.32126	0.371000	0.24564	0.563000	0.77884	GTG		0.622	ACVRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404520.2			3	45	1	0	1	1	1	3	45				
PLEKHA6	22874	broad.mit.edu	37	1	204214034	204214034	+	Silent	SNP	C	C	A			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr1:204214034C>A	ENST00000272203.3	-	15	2446	c.2130G>T	c.(2128-2130)gtG>gtT	p.V710V	PLEKHA6_ENST00000414478.1_Silent_p.V730V	NM_014935.4	NP_055750.2	Q9Y2H5	PKHA6_HUMAN	pleckstrin homology domain containing, family A member 6	710										breast(2)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)			GAGAGCCCGACACCAGTGAAA	0.627																																						ENST00000272203.3																			0				breast(2)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						c.(2128-2130)gtG>gtT		pleckstrin homology domain containing, family A member 6							11.0	12.0	12.0					1																	204214034		2181	4279	6460	SO:0001819	synonymous_variant	22874							g.chr1:204214034C>A	AB023186	CCDS1444.1	1q32	2013-01-10			ENSG00000143850	ENSG00000143850		"""Pleckstrin homology (PH) domain containing"""	17053	protein-coding gene	gene with protein product		607771				11001876	Standard	NM_014935		Approved	PEPP3, KIAA0969	uc001hau.4	Q9Y2H5	OTTHUMG00000036057	ENST00000272203.3:c.2130G>T	1.37:g.204214034C>A						PLEKHA6_ENST00000414478.1_Silent_p.V730V	p.V710V	NM_014935.4	NP_055750.2	Q9Y2H5	PKHA6_HUMAN	KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)		15	2446	-	all_cancers(21;0.0222)|Breast(84;0.179)		710					A7MD51|Q5VTI6	Silent	SNP	ENST00000272203.3	37	c.2130G>T	CCDS1444.1																																																																																				0.627	PLEKHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087889.3	NM_014935		3	7	1	0	0.00024832	1	0.000259356	3	7				
INTS4	92105	broad.mit.edu	37	11	77629973	77629973	+	Missense_Mutation	SNP	G	G	C			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr11:77629973G>C	ENST00000534064.1	-	15	1850	c.1816C>G	c.(1816-1818)Caa>Gaa	p.Q606E		NM_033547.3	NP_291025.3	Q96HW7	INT4_HUMAN	integrator complex subunit 4	606					snRNA processing (GO:0016180)	integrator complex (GO:0032039)			INTS4/GAB2(2)	NS(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(5)|upper_aerodigestive_tract(1)	32	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)			GGATCCTCTTGAGGTATGATG	0.493																																						ENST00000534064.1																		INTS4/GAB2(2)	0				NS(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(5)|upper_aerodigestive_tract(1)	32						c.(1816-1818)Caa>Gaa		integrator complex subunit 4							98.0	97.0	97.0					11																	77629973		2200	4292	6492	SO:0001583	missense	92105				snRNA processing	integrator complex	protein binding	g.chr11:77629973G>C	BC015664	CCDS31644.1	11q14.1	2006-04-26			ENSG00000149262	ENSG00000149262			25048	protein-coding gene	gene with protein product		611348				16239144	Standard	NM_033547		Approved	INT4, MGC16733, MST093	uc001oys.3	Q96HW7	OTTHUMG00000166629	ENST00000534064.1:c.1816C>G	11.37:g.77629973G>C	ENSP00000434466:p.Gln606Glu						p.Q606E	NM_033547.3	NP_291025.3	Q96HW7	INT4_HUMAN	Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)		15	1850	-	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		606					Q2YD62|Q6PJG4|Q7Z4E7|Q96G32|Q96GA1|Q9BRC0	Missense_Mutation	SNP	ENST00000534064.1	37	c.1816C>G	CCDS31644.1	.	.	.	.	.	.	.	.	.	.	G	5.021	0.189597	0.09547	.	.	ENSG00000149262	ENST00000534064;ENST00000354849	.	.	.	4.45	4.45	0.53987	.	0.386187	0.27836	N	0.017650	T	0.39682	0.1087	N	0.19112	0.55	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.33599	-0.9862	9	0.02654	T	1	-0.4425	17.3058	0.87194	0.0:0.0:1.0:0.0	.	606	Q96HW7	INT4_HUMAN	E	606;457	.	ENSP00000346913:Q457E	Q	-	1	0	INTS4	77307621	0.997000	0.39634	0.826000	0.32828	0.652000	0.38707	3.587000	0.53957	2.317000	0.78254	0.650000	0.86243	CAA		0.493	INTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390927.1	NM_033547		89	141	0	0	0	1	0	89	141				
RP11-431K24.1	0	broad.mit.edu	37	1	8118037	8118037	+	lincRNA	DEL	T	T	-			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr1:8118037delT	ENST00000445300.1	+	0	815																											ccttccttccttccttccttc	0.438																																						ENST00000445300.1																			0																																																			0							g.chr1:8118037delT																													1.37:g.8118037delT														0	815	+									RNA	DEL	ENST00000445300.1	37																																																																																						0.438	RP11-431K24.1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000004926.1			3	4						3	4	---	---	---	---
AGAP2	116986	broad.mit.edu	37	12	58121782	58121782	+	Frame_Shift_Del	DEL	C	C	-			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr12:58121782delC	ENST00000547588.1	-	15	2703	c.2704delG	c.(2704-2706)gtcfs	p.V902fs	AGAP2_ENST00000257897.3_Frame_Shift_Del_p.V546fs|AGAP2-AS1_ENST00000542466.2_3'UTR|RP11-571M6.8_ENST00000548410.2_RNA	NM_001122772.2	NP_001116244.1	Q99490	AGAP2_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	902	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				axon guidance (GO:0007411)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|large_intestine(7)|lung(20)|prostate(3)|skin(1)|stomach(1)	48						ATGGCCTGGACCCAGGCATCC	0.567																																						ENST00000257897.3																			0				breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|large_intestine(7)|lung(20)|prostate(3)|skin(1)|stomach(1)	48						c.(1636-1638)tcfs		ArfGAP with GTPase domain, ankyrin repeat and PH domain 2							155.0	143.0	147.0					12																	58121782		2203	4300	6503	SO:0001589	frameshift_variant	116986				axon guidance|negative regulation of neuron apoptosis|negative regulation of protein catabolic process|protein transport|regulation of ARF GTPase activity|small GTPase mediated signal transduction	mitochondrion|nucleolus	ARF GTPase activator activity|GTP binding|zinc ion binding	g.chr12:58121782delC	AF413077	CCDS8951.1, CCDS44932.1	12q13.2	2013-05-30	2008-09-22	2008-09-22	ENSG00000135439	ENSG00000135439		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16921	protein-coding gene	gene with protein product		605476	"""centaurin, gamma 1"""	CENTG1			Standard	NM_001122772		Approved		uc001spq.3	Q99490	OTTHUMG00000170285	ENST00000547588.1:c.2704delG	12.37:g.58121782delC	ENSP00000449241:p.Val902fs					AGAP2_ENST00000547588.1_Frame_Shift_Del_p.V902fs|AGAP2-AS1_ENST00000542466.2_3'UTR	p.V546fs	NM_014770.3	NP_055585.1	Q99490	AGAP2_HUMAN			14	1721	-			902			G domain.		A8K9F7|O00578|Q548E0|Q8IWU3	Frame_Shift_Del	DEL	ENST00000547588.1	37	c.1636delG	CCDS44932.1																																																																																				0.567	AGAP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408367.1	NM_014770		7	271						7	271	---	---	---	---
RBM25	58517	broad.mit.edu	37	14	73572607	73572608	+	Frame_Shift_Del	DEL	AG	AG	-	rs150988201		TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr14:73572607_73572608delAG	ENST00000261973.7	+	11	1480_1481	c.1195_1196delAG	c.(1195-1197)agafs	p.R399fs	RBM25_ENST00000527432.1_Frame_Shift_Del_p.R399fs	NM_021239.2	NP_067062.1	P49756	RBM25_HUMAN	RNA binding motif protein 25	399	Arg-rich.|Glu-rich.|Necessary for nuclear speckle localization.				mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of apoptotic process (GO:0042981)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(6)|ovary(2)|pancreas(1)	31				BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)		agagcgggaaagagagagagag	0.446																																						ENST00000261973.7																			0				breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(6)|ovary(2)|pancreas(1)	31						c.(1195-1197)afs		RNA binding motif protein 25																																				SO:0001589	frameshift_variant	58517				apoptosis|mRNA processing|regulation of alternative nuclear mRNA splicing, via spliceosome|RNA splicing	cytoplasm|nuclear speck	mRNA binding|nucleotide binding|protein binding	g.chr14:73572607_73572608delAG	BX647116	CCDS32113.1	14q24.3	2013-02-12	2004-04-23	2004-04-29	ENSG00000119707	ENSG00000119707		"""RNA binding motif (RRM) containing"""	23244	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 94"""	612427	"""RNA-binding region (RNP1, RRM) containing 7"""	RNPC7		9847074, 7596406	Standard	NM_021239		Approved	S164, fSAP94, NET52, Snu71	uc001xno.3	P49756	OTTHUMG00000167540	ENST00000261973.7:c.1195_1196delAG	14.37:g.73572617_73572618delAG	ENSP00000261973:p.Arg399fs					RBM25_ENST00000527432.1_Frame_Shift_Del_p.R399fs	p.R399fs	NM_021239.2	NP_067062.1	P49756	RBM25_HUMAN		BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)	11	1480_1481	+			399			Arg-rich.|Glu-rich.|Necessary for nuclear speckle localization.		A0PJL9|B2RNA8|B3KT03|Q2TA72|Q5XJ17|Q6P665|Q9H6A1|Q9UEQ5|Q9UIE9	Frame_Shift_Del	DEL	ENST00000261973.7	37	c.1195_1196delAG	CCDS32113.1																																																																																				0.446	RBM25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394966.1	XM_027330		7	68						7	68	---	---	---	---
ZFHX3	463	broad.mit.edu	37	16	72991713	72991715	+	In_Frame_Del	DEL	CCA	CCA	-	rs4788682	byFrequency	TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr16:72991713_72991715delCCA	ENST00000268489.5	-	2	3002_3004	c.2330_2332delTGG	c.(2329-2334)gtggct>gct	p.V777del	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	777	Poly-Ala.		V -> A (in dbSNP:rs4788682). {ECO:0000269|PubMed:7592926}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.V777V(1)		NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				gccgccgcagccaccgccgccgc	0.635																																						ENST00000268489.5																			1	Substitution - coding silent(1)	p.V777V(1)	lung(1)	NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153						c.(2329-2334)gct>g		zinc finger homeobox 3			,	1706,1886		582,542,672					,	5.5	0.1			17	4240,2792		1606,1028,882	no	coding,intron	ZFHX3	NM_006885.3,NM_001164766.1	,	2188,1570,1554	A1A1,A1R,RR		39.7042,47.4944,44.0324	,	,		5946,4678				SO:0001651	inframe_deletion	463				muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation	transcription factor complex	enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding	g.chr16:72991713_72991715delCCA	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.2330_2332delTGG	16.37:g.72991713_72991715delCCA	ENSP00000268489:p.Val777del					ZFHX3_ENST00000397992.5_Intron	p.VA777del	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN			2	3002_3004	-		Ovarian(137;0.13)	777		V -> A (in dbSNP:rs4788682).	Poly-Ala.		D3DWS8|O15101|Q13719	In_Frame_Del	DEL	ENST00000268489.5	37	c.2330_2332delTGG	CCDS10908.1																																																																																				0.635	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		9	209						9	209	---	---	---	---
TERF2IP	54386	broad.mit.edu	37	16	75690204	75690206	+	In_Frame_Del	DEL	GAA	GAA	-			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr16:75690204_75690206delGAA	ENST00000300086.4	+	3	992_994	c.895_897delGAA	c.(895-897)gaadel	p.E304del		NM_018975.3	NP_061848.2	Q9NYB0	TE2IP_HUMAN	telomeric repeat binding factor 2, interacting protein	304	Asp/Glu-rich (acidic).				negative regulation of DNA recombination at telomere (GO:0048239)|negative regulation of telomere maintenance (GO:0032205)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protection from non-homologous end joining at telomere (GO:0031848)|protein localization to chromosome, telomeric region (GO:0070198)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of transcription, DNA-templated (GO:0006355)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)|telomere maintenance via telomere lengthening (GO:0010833)|transcription, DNA-templated (GO:0006351)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear chromosome (GO:0000228)|nuclear chromosome, telomeric region (GO:0000784)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)	5						TGATgaggaggaagaagaagaag	0.424																																						ENST00000300086.4																			0				central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)	5						c.(895-897)del		telomeric repeat binding factor 2, interacting protein				1,182,4081		0,0,1,0,182,1949						-3.9	1.0			71	0,377,7877		0,0,0,1,375,3751	no	codingComplex	TERF2IP	NM_018975.3		0,0,1,1,557,5700	A1A1,A1A2,A1R,A2A2,A2R,RR		4.5675,4.2917,4.4736				1,559,11958				SO:0001651	inframe_deletion	54386				negative regulation of DNA recombination at telomere|negative regulation of telomere maintenance|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|protection from non-homologous end joining at telomere|protein localization to chromosome, telomeric region|regulation of double-strand break repair via homologous recombination|telomere maintenance via telomerase|transcription, DNA-dependent	cytoplasm|nuclear telomere cap complex|nucleoplasm	DNA binding|protein binding	g.chr16:75690204_75690206delGAA	AK000669	CCDS32491.1	16q23.1	2012-10-03			ENSG00000166848	ENSG00000166848			19246	protein-coding gene	gene with protein product		605061				10850490	Standard	NM_018975		Approved	RAP1	uc002fet.2	Q9NYB0	OTTHUMG00000177136	ENST00000300086.4:c.895_897delGAA	16.37:g.75690213_75690215delGAA	ENSP00000300086:p.Glu304del						p.E304del	NM_018975.3	NP_061848.2	Q9NYB0	TE2IP_HUMAN			3	992_994	+			304			Asp/Glu-rich (acidic).		B4DQN4|Q4W4Y2|Q8WYZ3|Q9NWR2	In_Frame_Del	DEL	ENST00000300086.4	37	c.895_897delGAA	CCDS32491.1																																																																																				0.424	TERF2IP-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000435519.1	NM_018975		9	164						9	164	---	---	---	---
MIR3687-2	103504728	broad.mit.edu	37	21	9825838	9825839	+	RNA	INS	-	-	GCG	rs372061766|rs369177681|rs563875271	byFrequency	TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr21:9825838_9825839insGCG	ENST00000577708.1	+	0	0				MIR3648_ENST00000581792.1_RNA	NR_037458.1																						cggccgcgactgcggcggcggt	0.842																																						ENST00000581792.1																			0																																																			0							g.chr21:9825838_9825839insGCG																													21.37:g.9825845_9825847dupGCG								NR_037421.1						0	7_8	+									RNA	INS	ENST00000577708.1	37																																																																																						0.842	MIR3687-201	KNOWN	basic	miRNA	miRNA				4	4						4	4	---	---	---	---
XKR3	150165	broad.mit.edu	37	22	17264884	17264884	+	Frame_Shift_Del	DEL	A	A	-			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chr22:17264884delA	ENST00000331428.5	-	4	1107	c.1005delT	c.(1003-1005)attfs	p.I335fs		NM_175878.3	NP_787074.2	Q5GH77	XKR3_HUMAN	XK, Kell blood group complex subunit-related family, member 3	335						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(6)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				GTCTCCCGTCAATTATTTTGT	0.408																																						ENST00000331428.5																			0				central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(6)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						c.(1003-1005)atfs		XK, Kell blood group complex subunit-related family, member 3							52.0	48.0	49.0					22																	17264884		1515	3484	4999	SO:0001589	frameshift_variant	150165					integral to membrane|plasma membrane		g.chr22:17264884delA	AY989815	CCDS42975.1	22q11.1	2007-01-16	2006-01-12		ENSG00000172967	ENSG00000172967			28778	protein-coding gene	gene with protein product		611674	"""X Kell blood group precursor-related family, member 3"""			16431037	Standard	NM_175878		Approved	MGC57211, XTES	uc002zlv.3	Q5GH77	OTTHUMG00000143726	ENST00000331428.5:c.1005delT	22.37:g.17264884delA	ENSP00000331704:p.Ile335fs						p.I335fs	NM_175878.3	NP_787074.2	Q5GH77	XKR3_HUMAN			4	1107	-	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)	335					B2RPN1|Q52PG8|Q8N7E1	Frame_Shift_Del	DEL	ENST00000331428.5	37	c.1005delT	CCDS42975.1																																																																																				0.408	XKR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289789.1	NM_175878		90	42						90	42	---	---	---	---
ATRX	546	broad.mit.edu	37	X	76937477	76937480	+	Frame_Shift_Del	DEL	TCTC	TCTC	-			TCGA-S9-A6U1-01A-21D-A33T-08	TCGA-S9-A6U1-10A-01D-A33W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b195ecbd-19d9-44f9-87b6-f3cee5b93490	119a0ced-acee-46e4-8534-c42b39d35197	g.chrX:76937477_76937480delTCTC	ENST00000373344.5	-	9	3482_3485	c.3268_3271delGAGA	c.(3268-3273)gagaagfs	p.EK1090fs	ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Frame_Shift_Del_p.EK1052fs	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	1090					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						CACCTTTTCTTCTCTCTACCATAT	0.377			"""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.(3268-3273)agfs		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:76937477_76937480delTCTC	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.3268_3271delGAGA	X.37:g.76937477_76937480delTCTC	ENSP00000362441:p.Glu1090fs					ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Frame_Shift_Del_p.EK1052fs	p.EK1090fs	NM_000489.3	NP_000480.2	P46100	ATRX_HUMAN			9	3482_3485	-			1090					D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Frame_Shift_Del	DEL	ENST00000373344.5	37	c.3268_3271delGAGA	CCDS14434.1																																																																																				0.377	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		221	438						221	438	---	---	---	---
