#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
BTN2A3P	54718	broad.mit.edu	37	6	26422353	26422353	+	RNA	SNP	C	C	T	rs571530750	byFrequency	TCGA-SP-A6QG-01A-12D-A35I-08	TCGA-SP-A6QG-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc3443dd-2a18-4c31-b14e-d87edca616ff	d94a0f0a-e850-4bfb-b531-1259d30edbd6	g.chr6:26422353C>T	ENST00000466808.2	+	0	7							Q96KV6	BT2A3_HUMAN	butyrophilin, subfamily 2, member A3, pseudogene							integral component of membrane (GO:0016021)		p.P3S(2)									GCTCATGGAACCAGCTGCTGC	0.622													C|||	7	0.00139776	0.0023	0.0	5008	,	,		16376	0.001		0.0	False		,,,				2504	0.0031					ENST00000466808.2																			2	Substitution - Missense(2)	p.P3S(2)	endometrium(1)|kidney(1)																																																54718							g.chr6:26422353C>T	AL021917		6p22.1	2014-01-14	2011-09-06	2011-09-06	ENSG00000124549	ENSG00000124549		"""Butyrophilins"""	13229	pseudogene	pseudogene		613592	"""butyrophilin, subfamily 2, member A3"""	BTN2A3			Standard	NR_027795		Approved	BTN2.3	uc011dkl.1	Q96KV6	OTTHUMG00000014453		6.37:g.26422353C>T														0	7	+								A6NEF4	RNA	SNP	ENST00000466808.2	37																																																																																						0.622	BTN2A3P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000040118.4	NR_027795		4	89	0	0	0	1	0	4	89				
ARHGAP10	79658	broad.mit.edu	37	4	148653479	148653479	+	Silent	SNP	C	C	T			TCGA-SP-A6QG-01A-12D-A35I-08	TCGA-SP-A6QG-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc3443dd-2a18-4c31-b14e-d87edca616ff	d94a0f0a-e850-4bfb-b531-1259d30edbd6	g.chr4:148653479C>T	ENST00000336498.3	+	1	266	c.27C>T	c.(25-27)agC>agT	p.S9S		NM_024605.3	NP_078881.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 10	0					establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			autonomic_ganglia(2)|endometrium(5)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		TGGAGTTCAGCGACTGCTACC	0.672																																						ENST00000336498.3																			0				autonomic_ganglia(2)|endometrium(5)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33						c.(25-27)agC>agT		Rho GTPase activating protein 10							30.0	30.0	30.0					4																	148653479		2203	4300	6503	SO:0001819	synonymous_variant	79658				apoptosis|filopodium assembly|regulation of apoptosis|small GTPase mediated signal transduction	cytosol|perinuclear region of cytoplasm|plasma membrane	cytoskeletal adaptor activity|SH3 domain binding	g.chr4:148653479C>T	BC047914	CCDS34075.1	4q31.23	2013-09-20			ENSG00000071205	ENSG00000071205		"""Rho GTPase activating proteins"""	26099	protein-coding gene	gene with protein product		609746				8288572	Standard	NM_024605		Approved	FLJ20896, FLJ41791, GRAF2	uc003ilf.3	A1A4S6	OTTHUMG00000161460	ENST00000336498.3:c.27C>T	4.37:g.148653479C>T							p.S9S	NM_024605.3	NP_078881.3	A1A4S6	RHG10_HUMAN		GBM - Glioblastoma multiforme(119;0.0423)	1	266	+	all_hematologic(180;0.151)	Renal(17;0.0166)	9			BAR.		Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Silent	SNP	ENST00000336498.3	37	c.27C>T	CCDS34075.1																																																																																				0.672	ARHGAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365005.1	NM_024605		4	41	0	0	0	1	0	4	41				
ADCY9	115	broad.mit.edu	37	16	4015941	4015941	+	Silent	SNP	C	C	T	rs146633008	byFrequency	TCGA-SP-A6QG-01A-12D-A35I-08	TCGA-SP-A6QG-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc3443dd-2a18-4c31-b14e-d87edca616ff	d94a0f0a-e850-4bfb-b531-1259d30edbd6	g.chr16:4015941C>T	ENST00000294016.3	-	11	4435	c.3897G>A	c.(3895-3897)acG>acA	p.T1299T		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	1299					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						CCTTGGCCTGCGTGCTGCTGT	0.567													C|||	2	0.000399361	0.0008	0.0	5008	,	,		19847	0.001		0.0	False		,,,				2504	0.0					ENST00000294016.3																			0				breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						c.(3895-3897)acG>acA		adenylate cyclase 9		C		1,4393	2.1+/-5.4	0,1,2196	95.0	88.0	90.0		3897	-11.3	0.0	16	dbSNP_134	90	0,8600		0,0,4300	no	coding-synonymous	ADCY9	NM_001116.3		0,1,6496	TT,TC,CC		0.0,0.0228,0.0077		1299/1354	4015941	1,12993	2197	4300	6497	SO:0001819	synonymous_variant	115				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding	g.chr16:4015941C>T	AF036927	CCDS32382.1	16p13.3	2013-02-04				ENSG00000162104	4.6.1.1	"""Adenylate cyclases"""	240	protein-coding gene	gene with protein product		603302				9628827	Standard	NM_001116		Approved	AC9	uc002cvx.3	O60503		ENST00000294016.3:c.3897G>A	16.37:g.4015941C>T							p.T1299T	NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN			11	4435	-			1299	QHQLSISPDIRVQVDGSIGRSPTDEIANLVPSVQYVDKTSL GSDSSTQAKDAHLSPKRPWKEPVKAEERGRFGKAIEKDDCD ETGIEEANELTKLNVSKSV -> APAVHLPRHPRPGGWQHR TVSHRRDCQPGAFCPVCGQDISGF (in Ref. 1; AAC24201).				A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Silent	SNP	ENST00000294016.3	37	c.3897G>A	CCDS32382.1																																																																																				0.567	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1			3	68	0	0	0	1	0	3	68				
ABCF2	10061	broad.mit.edu	37	7	150915186	150915186	+	Missense_Mutation	SNP	A	A	G	rs548630362		TCGA-SP-A6QG-01A-12D-A35I-08	TCGA-SP-A6QG-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc3443dd-2a18-4c31-b14e-d87edca616ff	d94a0f0a-e850-4bfb-b531-1259d30edbd6	g.chr7:150915186A>G	ENST00000287844.2	-	11	1428	c.1319T>C	c.(1318-1320)cTg>cCg	p.L440P	ABCF2_ENST00000222388.2_Missense_Mutation_p.L440P|ABCF2_ENST00000473874.1_5'Flank	NM_007189.1	NP_009120.1	Q9UG63	ABCF2_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 2	440	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|large_intestine(4)|lung(15)|ovary(1)|skin(2)	24			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TAGCAGCTTCAGAAGAGTTGA	0.517													A|||	1	0.000199681	0.0	0.0	5008	,	,		19946	0.0		0.0	False		,,,				2504	0.001					ENST00000287844.2																			0				breast(1)|central_nervous_system(1)|large_intestine(4)|lung(15)|ovary(1)|skin(2)	24						c.(1318-1320)cTg>cCg		ATP-binding cassette, sub-family F (GCN20), member 2							136.0	114.0	121.0					7																	150915186		2203	4300	6503	SO:0001583	missense	10061					ATP-binding cassette (ABC) transporter complex|mitochondrial envelope	ATP binding|ATPase activity|transporter activity	g.chr7:150915186A>G	AJ005016	CCDS5922.1, CCDS5923.1	7q36.1	2012-03-14			ENSG00000033050	ENSG00000033050		"""ATP binding cassette transporters / subfamily F"""	71	protein-coding gene	gene with protein product		612510				8894702	Standard	NM_007189		Approved	EST133090, ABC28, M-ABC1, HUSSY-18	uc003wjo.1	Q9UG63	OTTHUMG00000154570	ENST00000287844.2:c.1319T>C	7.37:g.150915186A>G	ENSP00000287844:p.Leu440Pro					ABCF2_ENST00000222388.2_Missense_Mutation_p.L440P	p.L440P	NM_007189.1	NP_009120.1	Q9UG63	ABCF2_HUMAN	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	11	1428	-			440			ABC transporter 2.		O60864|Q75MJ0|Q75MJ1|Q96TE8	Missense_Mutation	SNP	ENST00000287844.2	37	c.1319T>C	CCDS5923.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.527414	0.85706	.	.	ENSG00000033050	ENST00000222388;ENST00000287844	D;D	0.95788	-3.81;-3.81	5.49	5.49	0.81192	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.85682	D	0.000000	D	0.98620	0.9538	H	0.98238	4.18	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.79108	0.987;0.992	D	0.99667	1.0995	10	0.87932	D	0	-2.4219	14.7613	0.69607	1.0:0.0:0.0:0.0	.	440;440	Q9UG63;Q75MJ1	ABCF2_HUMAN;.	P	440	ENSP00000222388:L440P;ENSP00000287844:L440P	ENSP00000222388:L440P	L	-	2	0	ABCF2	150546119	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	8.543000	0.90651	2.078000	0.62432	0.482000	0.46254	CTG		0.517	ABCF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336086.1	NM_005692		5	76	0	0	0	1	0	5	76				
VPS13B	157680	broad.mit.edu	37	8	100479757	100479757	+	Silent	SNP	C	C	T			TCGA-SP-A6QG-01A-12D-A35I-08	TCGA-SP-A6QG-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc3443dd-2a18-4c31-b14e-d87edca616ff	d94a0f0a-e850-4bfb-b531-1259d30edbd6	g.chr8:100479757C>T	ENST00000358544.2	+	24	3672	c.3561C>T	c.(3559-3561)gtC>gtT	p.V1187V	VPS13B_ENST00000395996.1_Silent_p.V1187V|VPS13B_ENST00000357162.2_Silent_p.V1187V	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	1187					protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			CTCTAGCTGTCACGTCTCAAA	0.438																																					Colon(161;2205 2542 7338 31318)	ENST00000395996.1																			0				NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193						c.(3559-3561)gtC>gtT		vacuolar protein sorting 13 homolog B (yeast)							234.0	204.0	214.0					8																	100479757		2203	4300	6503	SO:0001819	synonymous_variant	157680				protein transport			g.chr8:100479757C>T	AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"""Cohen syndrome 1"""	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.3561C>T	8.37:g.100479757C>T						VPS13B_ENST00000358544.2_Silent_p.V1187V|VPS13B_ENST00000357162.2_Silent_p.V1187V	p.V1187V			Q7Z7G8	VP13B_HUMAN	OV - Ovarian serous cystadenocarcinoma(57;0.00636)		24	3672	+	Breast(36;3.73e-07)		1187					C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Silent	SNP	ENST00000358544.2	37	c.3561C>T	CCDS6280.1																																																																																				0.438	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		31	127	0	0	0	1	0	31	127				
GTPBP2	54676	broad.mit.edu	37	6	43589788	43589788	+	Silent	SNP	G	G	A			TCGA-SP-A6QG-01A-12D-A35I-08	TCGA-SP-A6QG-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc3443dd-2a18-4c31-b14e-d87edca616ff	d94a0f0a-e850-4bfb-b531-1259d30edbd6	g.chr6:43589788G>A	ENST00000307126.5	-	11	1583	c.1584C>T	c.(1582-1584)caC>caT	p.H528H	GTPBP2_ENST00000476510.1_5'UTR|GTPBP2_ENST00000307114.7_Silent_p.H440H	NM_019096.3	NP_061969.3			GTP binding protein 2											breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(3)|prostate(1)|skin(2)|urinary_tract(1)	18	all_cancers(18;9.36e-06)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000501)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)			CGTTGCCCACGTGTACTGTCA	0.552																																					GBM(116;405 1620 28302 32150 44768)	ENST00000307126.5																			0				breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(3)|prostate(1)|skin(2)|urinary_tract(1)	18						c.(1582-1584)caC>caT		GTP binding protein 2							210.0	171.0	184.0					6																	43589788		2203	4300	6503	SO:0001819	synonymous_variant	54676						GTP binding|GTPase activity	g.chr6:43589788G>A	AB024574	CCDS4903.1, CCDS69124.1	6p21	2008-07-28			ENSG00000172432	ENSG00000172432			4670	protein-coding gene	gene with protein product		607434				10833435, 11054535	Standard	NM_019096		Approved		uc003ovs.3	Q9BX10	OTTHUMG00000014744	ENST00000307126.5:c.1584C>T	6.37:g.43589788G>A						GTPBP2_ENST00000307114.7_Silent_p.H440H|GTPBP2_ENST00000476510.1_5'UTR	p.H528H	NM_019096.3	NP_061969.3	Q9BX10	GTPB2_HUMAN	all cancers(41;0.000501)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)		11	1583	-	all_cancers(18;9.36e-06)|Lung NSC(15;0.00161)|all_lung(25;0.004)		528						Silent	SNP	ENST00000307126.5	37	c.1584C>T	CCDS4903.1	.	.	.	.	.	.	.	.	.	.	g	5.020	0.189428	0.09547	.	.	ENSG00000172432	ENST00000419497;ENST00000432918	.	.	.	5.79	-6.95	0.01628	.	.	.	.	.	T	0.51873	0.1700	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.66002	-0.6031	4	.	.	.	-15.7491	18.0049	0.89207	0.6017:0.0:0.3983:0.0	.	.	.	.	C	97	.	.	R	-	1	0	GTPBP2	43697766	0.663000	0.27448	0.274000	0.24659	0.923000	0.55619	-0.185000	0.09684	-2.203000	0.00744	-1.723000	0.00705	CGT		0.552	GTPBP2-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040679.1			4	117	0	0	0	1	0	4	117				
EP400	57634	broad.mit.edu	37	12	132547087	132547087	+	Silent	SNP	G	G	A	rs12366766	byFrequency	TCGA-SP-A6QG-01A-12D-A35I-08	TCGA-SP-A6QG-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc3443dd-2a18-4c31-b14e-d87edca616ff	d94a0f0a-e850-4bfb-b531-1259d30edbd6	g.chr12:132547087G>A	ENST00000333577.4	+	48	8392	c.8283G>A	c.(8281-8283)caG>caA	p.Q2761Q	EP400_ENST00000389562.2_Silent_p.Q2724Q|EP400_ENST00000330386.6_Silent_p.Q2644Q|EP400_ENST00000332482.4_Silent_p.Q2688Q|EP400_ENST00000389561.2_Silent_p.Q2725Q			Q96L91	EP400_HUMAN	E1A binding protein p400	2761	Interaction with ZNF42. {ECO:0000250}.|Poly-Gln.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.Q2724Q(16)|p.Q2725Q(1)		NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		agcagcagcagcaacaacagc	0.562													G|||	37	0.00738818	0.0038	0.0072	5008	,	,		15585	0.002		0.0149	False		,,,				2504	0.0102					ENST00000333577.4																			17	Substitution - coding silent(17)	p.Q2724Q(16)|p.Q2725Q(1)	prostate(4)|kidney(4)|central_nervous_system(3)|lung(3)|endometrium(2)|urinary_tract(1)	NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161						c.(8281-8283)caG>caA		E1A binding protein p400							28.0	31.0	30.0					12																	132547087		2199	4282	6481	SO:0001819	synonymous_variant	57634				histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent	NuA4 histone acetyltransferase complex|nuclear speck	ATP binding|DNA binding|helicase activity	g.chr12:132547087G>A	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"""trinucleotide repeat containing 12"""	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.8283G>A	12.37:g.132547087G>A						EP400_ENST00000332482.4_Silent_p.Q2688Q|EP400_ENST00000389562.2_Silent_p.Q2724Q|EP400_ENST00000330386.6_Silent_p.Q2644Q|EP400_ENST00000389561.2_Silent_p.Q2725Q	p.Q2761Q			Q96L91	EP400_HUMAN		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)	48	8392	+	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)	2761			Interaction with ZNF42 (By similarity).|Poly-Gln.		O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	37	c.8283G>A																																																																																					0.562	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		4	52	0	0	0	1	0	4	52				
NEBL	10529	broad.mit.edu	37	10	21158716	21158716	+	Nonsense_Mutation	SNP	G	G	A	rs370153729		TCGA-SP-A6QG-01A-12D-A35I-08	TCGA-SP-A6QG-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc3443dd-2a18-4c31-b14e-d87edca616ff	d94a0f0a-e850-4bfb-b531-1259d30edbd6	g.chr10:21158716G>A	ENST00000377122.4	-	6	931	c.535C>T	c.(535-537)Cga>Tga	p.R179*	NEBL_ENST00000417816.2_Intron|NEBL_ENST00000377159.4_Intron|NEBL_ENST00000377119.1_Nonsense_Mutation_p.R179*	NM_006393.2	NP_006384.1	O76041	NEBL_HUMAN	nebulette	179					cardiac muscle thin filament assembly (GO:0071691)	extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|filamin binding (GO:0031005)|structural constituent of muscle (GO:0008307)|tropomyosin binding (GO:0005523)	p.R179*(1)		NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						ATGTCTGGTCGGTCAAGTTCT	0.368																																						ENST00000377122.4																			1	Substitution - Nonsense(1)	p.R179*(1)	endometrium(1)	NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						c.(535-537)Cga>Tga		nebulette		G	,stop/ARG,	1,4405	2.1+/-5.4	0,1,2202	227.0	187.0	200.0		,535,	3.6	1.0	10		200	0,8600		0,0,4300	no	intron,stop-gained,intron	NEBL	NM_001173484.1,NM_006393.2,NM_213569.2	,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,	,179/1015,	21158716	1,13005	2203	4300	6503	SO:0001587	stop_gained	10529				regulation of actin filament length		actin binding|structural constituent of muscle	g.chr10:21158716G>A	Y16241	CCDS7133.1, CCDS7134.1	10p12	2014-09-17			ENSG00000078114	ENSG00000078114			16932	protein-coding gene	gene with protein product		605491				9733644, 10470015	Standard	NM_213569		Approved		uc001iqi.3	O76041	OTTHUMG00000017788	ENST00000377122.4:c.535C>T	10.37:g.21158716G>A	ENSP00000366326:p.Arg179*					NEBL_ENST00000377119.1_Nonsense_Mutation_p.R179*|NEBL_ENST00000377159.4_Intron|NEBL_ENST00000417816.2_Intron	p.R179*	NM_006393.2	NP_006384.1	O76041	NEBL_HUMAN			6	931	-			179					B0YJ45|Q2TBD0|Q70I54|Q9UIC4	Nonsense_Mutation	SNP	ENST00000377122.4	37	c.535C>T	CCDS7134.1	.	.	.	.	.	.	.	.	.	.	G	37	6.026689	0.97216	2.27E-4	0.0	ENSG00000078114	ENST00000377122;ENST00000377119	.	.	.	5.97	3.61	0.41365	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.9103	0.58177	0.0:0.0:0.2679:0.7321	.	.	.	.	X	179	.	ENSP00000366323:R179X	R	-	1	2	NEBL	21198722	1.000000	0.71417	0.969000	0.41365	0.250000	0.25880	3.246000	0.51414	0.491000	0.27793	-0.262000	0.10625	CGA		0.368	NEBL-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047113.1	NM_006393		4	125	0	0	0	1	0	4	125				
MLLT3	4300	broad.mit.edu	37	9	20414343	20414343	+	Silent	SNP	A	A	G	rs372894655	byFrequency	TCGA-SP-A6QG-01A-12D-A35I-08	TCGA-SP-A6QG-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc3443dd-2a18-4c31-b14e-d87edca616ff	d94a0f0a-e850-4bfb-b531-1259d30edbd6	g.chr9:20414343A>G	ENST00000380338.4	-	5	787	c.501T>C	c.(499-501)agT>agC	p.S167S	MLLT3_ENST00000475957.1_5'UTR|MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S164S	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3	167	Poly-Ser.				anterior/posterior pattern specification (GO:0009952)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of transcription, DNA-templated (GO:0006355)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)		p.S167S(19)		central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		tgctgctgctactgctgctgc	0.532			T	MLL	ALL								A|||	612	0.122204	0.1505	0.1066	5008	,	,		12422	0.0833		0.0716	False		,,,				2504	0.1871					ENST00000380338.4				Dom	yes		9	9p22	4300	T	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 (AF9)"""			L	MLL		ALL		19	Substitution - coding silent(19)	p.S167S(19)	lung(8)|kidney(5)|endometrium(3)|central_nervous_system(1)|urinary_tract(1)|prostate(1)	central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66						c.(499-501)agT>agC		myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3							8.0	15.0	13.0					9																	20414343		1537	3257	4794	SO:0001819	synonymous_variant	4300				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding	g.chr9:20414343A>G	L13744	CCDS6494.1	9p22	2008-02-05	2001-11-28		ENSG00000171843	ENSG00000171843			7136	protein-coding gene	gene with protein product		159558	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 3"""			8506309, 8414510	Standard	NM_001286691		Approved	AF-9, AF9, YEATS3	uc003zoe.2	P42568	OTTHUMG00000019650	ENST00000380338.4:c.501T>C	9.37:g.20414343A>G						MLLT3_ENST00000429426.2_Silent_p.S164S|MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000475957.1_5'UTR	p.S167S	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN		GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)	5	787	-			167			Poly-Ser.		B1AMQ2|B2R7B3|B7Z755|D3DRJ8|Q8IVB0	Silent	SNP	ENST00000380338.4	37	c.501T>C	CCDS6494.1																																																																																				0.532	MLLT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051872.1	NM_004529		5	83	0	0	0	1	0	5	83				
PCDHGA4	56111	broad.mit.edu	37	5	140737040	140737040	+	Missense_Mutation	SNP	C	C	T	rs375569568		TCGA-SP-A6QG-01A-12D-A35I-08	TCGA-SP-A6QG-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc3443dd-2a18-4c31-b14e-d87edca616ff	d94a0f0a-e850-4bfb-b531-1259d30edbd6	g.chr5:140737040C>T	ENST00000571252.1	+	1	2273	c.2273C>T	c.(2272-2274)tCc>tTc	p.S758F	PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_5'Flank	NM_018917.2	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4	758					homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CACGAGGTCTCCCTCACCGCG	0.602																																						ENST00000571252.1																			0				endometrium(1)|kidney(1)|lung(3)	5						c.(2272-2274)tCc>tTc				C	,,,PHE/SER,,PHE/SER	1,4405		0,1,2202	85.0	90.0	88.0		,,,2273,,2273	3.7	0.3	5		88	0,8600		0,0,4300	no	intron,intron,intron,missense,intron,missense	PCDHGB1,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018922.2,NM_032053.1	,,,155,,155	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,,,,	,,,758/932,,758/821	140737040	1,13005	2203	4300	6503	SO:0001583	missense	56111							g.chr5:140737040C>T	AF152511	CCDS58979.1, CCDS58979.2, CCDS75331.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8702	other	protocadherin		606291				10380929	Standard	NM_018917		Approved	PCDH-GAMMA-A4		Q9Y5G9		ENST00000571252.1:c.2273C>T	5.37:g.140737040C>T	ENSP00000458570:p.Ser758Phe					PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron	p.S758F	NM_018917.2	NP_061740.1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		1	2273	+								Q9Y5D3	Missense_Mutation	SNP	ENST00000571252.1	37	c.2273C>T	CCDS58979.1																																																																																				0.602	PCDHGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437959.1	NM_018917		14	135	0	0	0	1	0	14	135				
MICU3	286097	broad.mit.edu	37	8	16962937	16962937	+	Silent	SNP	C	C	G			TCGA-SP-A6QG-01A-12D-A35I-08	TCGA-SP-A6QG-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc3443dd-2a18-4c31-b14e-d87edca616ff	d94a0f0a-e850-4bfb-b531-1259d30edbd6	g.chr8:16962937C>G	ENST00000318063.5	+	11	1143	c.1101C>G	c.(1099-1101)ctC>ctG	p.L367L	MICU3_ENST00000519866.1_3'UTR	NM_181723.2	NP_859074.1	Q86XE3	MICU3_HUMAN	mitochondrial calcium uptake family, member 3	367						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)										TGGATAATCTCCAAACAGAAG	0.313																																						ENST00000318063.5																			0											c.(1099-1101)ctC>ctG		mitochondrial calcium uptake family, member 3							40.0	39.0	40.0					8																	16962937		2193	4295	6488	SO:0001819	synonymous_variant	286097							g.chr8:16962937C>G	BC032868	CCDS5999.1	8p22	2013-03-26	2013-03-26	2013-03-14	ENSG00000155970	ENSG00000155970		"""EF-hand domain containing"""	27820	protein-coding gene	gene with protein product		610633	"""EF hand domain family A2"", ""EF-hand domain family, member A2"""	EFHA2		23409044	Standard	NM_181723		Approved	DKFZp313A0139	uc003wxd.2	Q86XE3	OTTHUMG00000096965	ENST00000318063.5:c.1101C>G	8.37:g.16962937C>G						MICU3_ENST00000519866.1_3'UTR	p.L367L	NM_181723.2	NP_859074.1					11	1143	+								Q8IYZ3	Silent	SNP	ENST00000318063.5	37	c.1101C>G	CCDS5999.1	.	.	.	.	.	.	.	.	.	.	C	5.850	0.340982	0.11069	.	.	ENSG00000155970	ENST00000519044	.	.	.	4.9	-1.78	0.07957	.	.	.	.	.	T	0.38719	0.1051	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.25363	-1.0134	4	.	.	.	-6.8235	1.0634	0.01605	0.2984:0.2351:0.2808:0.1857	.	.	.	.	C	212	.	.	S	+	2	0	EFHA2	17007308	0.877000	0.30153	0.978000	0.43139	0.988000	0.76386	-0.083000	0.11286	-0.480000	0.06803	-0.291000	0.09656	TCC		0.313	MICU3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214031.1	NM_181723		8	58	0	0	0	1	0	8	58				
ZEB2	9839	broad.mit.edu	37	2	145147119	145147119	+	Nonsense_Mutation	SNP	C	C	A			TCGA-SP-A6QG-01A-12D-A35I-08	TCGA-SP-A6QG-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc3443dd-2a18-4c31-b14e-d87edca616ff	d94a0f0a-e850-4bfb-b531-1259d30edbd6	g.chr2:145147119C>A	ENST00000558170.2	-	10	4728	c.3544G>T	c.(3544-3546)Gaa>Taa	p.E1182*	ZEB2_ENST00000409487.3_Nonsense_Mutation_p.E1182*|ZEB2_ENST00000539609.3_Nonsense_Mutation_p.E1158*|ZEB2_ENST00000303660.4_Nonsense_Mutation_p.E1182*	NM_014795.3	NP_055610.1	O60315	ZEB2_HUMAN	zinc finger E-box binding homeobox 2	1182	Glu-rich (acidic).				cell proliferation in forebrain (GO:0021846)|developmental pigmentation (GO:0048066)|hippocampus development (GO:0021766)|melanocyte migration (GO:0097324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of melanosome organization (GO:1903056)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|phosphatase regulator activity (GO:0019208)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(6)|large_intestine(23)|lung(45)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	107				BRCA - Breast invasive adenocarcinoma(221;0.112)		GTCTCTTCTTCATCTCGTATC	0.478																																					Melanoma(33;1235 1264 5755 16332)	ENST00000558170.2																			0				breast(3)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(6)|large_intestine(23)|lung(45)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	107						c.(3544-3546)Gaa>Taa		zinc finger E-box binding homeobox 2							265.0	250.0	255.0					2																	145147119		2203	4300	6503	SO:0001587	stop_gained	9839					cytoplasm|nucleolus	phosphatase regulator activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|SMAD binding|zinc ion binding	g.chr2:145147119C>A	AB011141	CCDS2186.1, CCDS54403.1	2q22.3	2013-01-08	2007-02-15	2007-02-15	ENSG00000169554	ENSG00000169554		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	14881	protein-coding gene	gene with protein product	"""SMAD interacting protein 1"""	605802	"""zinc finger homeobox 1b"""	ZFHX1B			Standard	NM_014795		Approved	KIAA0569, SIP-1, SIP1	uc002tvu.3	O60315	OTTHUMG00000131834	ENST00000558170.2:c.3544G>T	2.37:g.145147119C>A	ENSP00000454157:p.Glu1182*					ZEB2_ENST00000409487.3_Nonsense_Mutation_p.E1182*|ZEB2_ENST00000303660.4_Nonsense_Mutation_p.E1182*|ZEB2_ENST00000539609.3_Nonsense_Mutation_p.E1158*	p.E1182*	NM_014795.3	NP_055610.1	O60315	ZEB2_HUMAN		BRCA - Breast invasive adenocarcinoma(221;0.112)	10	4728	-			1182			Glu-rich (acidic).		A0JP09|B7Z2P2|F5H814|Q9UED1	Nonsense_Mutation	SNP	ENST00000558170.2	37	c.3544G>T	CCDS2186.1	.	.	.	.	.	.	.	.	.	.	C	43	10.404943	0.99399	.	.	ENSG00000169554	ENST00000539609;ENST00000303660;ENST00000409487	.	.	.	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-11.7048	19.7945	0.96474	0.0:1.0:0.0:0.0	.	.	.	.	X	1158;1182;1182	.	ENSP00000302501:E1182X	E	-	1	0	ZEB2	144863589	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.776000	0.85560	2.746000	0.94184	0.591000	0.81541	GAA		0.478	ZEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254778.5	NM_014795		4	109	1	0	1.23904e-05	1	1.23904e-05	4	109				
CDC27	996	broad.mit.edu	37	17	45234323	45234323	+	Silent	SNP	T	T	C			TCGA-SP-A6QG-01A-12D-A35I-08	TCGA-SP-A6QG-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc3443dd-2a18-4c31-b14e-d87edca616ff	d94a0f0a-e850-4bfb-b531-1259d30edbd6	g.chr17:45234323T>C	ENST00000066544.3	-	7	891	c.798A>G	c.(796-798)cgA>cgG	p.R266R	CDC27_ENST00000446365.2_Silent_p.R205R|CDC27_ENST00000527547.1_Silent_p.R266R|CDC27_ENST00000528748.1_5'Flank|CDC27_ENST00000531206.1_Silent_p.R266R	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	266					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						CTAATAAACTTCGACCAGTTT	0.358																																						ENST00000066544.3																			0				NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						c.(796-798)cgA>cgG		cell division cycle 27							60.0	65.0	63.0					17																	45234323		2200	4293	6493	SO:0001819	synonymous_variant	996				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule	protein phosphatase binding	g.chr17:45234323T>C	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.798A>G	17.37:g.45234323T>C						CDC27_ENST00000446365.2_Silent_p.R205R|CDC27_ENST00000531206.1_Silent_p.R266R|CDC27_ENST00000527547.1_Silent_p.R266R	p.R266R	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN			7	891	-			266					G3V1C4|Q16349|Q96F35	Silent	SNP	ENST00000066544.3	37	c.798A>G	CCDS11509.1																																																																																				0.358	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2			8	73	0	0	0	1	0	8	73				
STAC3	246329	broad.mit.edu	37	12	57643383	57643383	+	Missense_Mutation	SNP	A	A	G			TCGA-SP-A6QG-01A-12D-A35I-08	TCGA-SP-A6QG-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc3443dd-2a18-4c31-b14e-d87edca616ff	d94a0f0a-e850-4bfb-b531-1259d30edbd6	g.chr12:57643383A>G	ENST00000332782.2	-	2	238	c.37T>C	c.(37-39)Tcc>Ccc	p.S13P	STAC3_ENST00000546246.2_Intron|STAC3_ENST00000554578.1_Intron	NM_145064.1	NP_659501.1	Q96MF2	STAC3_HUMAN	SH3 and cysteine rich domain 3	13					intracellular signal transduction (GO:0035556)|neuromuscular synaptic transmission (GO:0007274)|skeletal muscle contraction (GO:0003009)|skeletal muscle fiber development (GO:0048741)		identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(10)|ovary(2)|skin(1)	18						GCTGGGAAGGAGGGCTTAGGG	0.537																																						ENST00000332782.2																			0				breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(10)|ovary(2)|skin(1)	18						c.(37-39)Tcc>Ccc		SH3 and cysteine rich domain 3							68.0	65.0	66.0					12																	57643383		2203	4300	6503	SO:0001583	missense	246329				intracellular signal transduction		identical protein binding|metal ion binding	g.chr12:57643383A>G	AK057013	CCDS8936.1, CCDS66405.1, CCDS66406.1	12q13.3	2014-08-12			ENSG00000185482	ENSG00000185482			28423	protein-coding gene	gene with protein product		615521				12477932	Standard	NM_001286257		Approved	MGC2793	uc009zpl.2	Q96MF2	OTTHUMG00000171271	ENST00000332782.2:c.37T>C	12.37:g.57643383A>G	ENSP00000329200:p.Ser13Pro					STAC3_ENST00000554578.1_Intron|STAC3_ENST00000546246.2_Intron	p.S13P	NM_145064.1	NP_659501.1	Q96MF2	STAC3_HUMAN			2	238	-			13					B4DUK9|Q96HU5	Missense_Mutation	SNP	ENST00000332782.2	37	c.37T>C	CCDS8936.1	.	.	.	.	.	.	.	.	.	.	A	13.85	2.360164	0.41801	.	.	ENSG00000185482	ENST00000332782;ENST00000553489	D;D	0.94793	-1.55;-3.52	5.07	1.48	0.22813	.	0.350840	0.21144	N	0.079440	T	0.82066	0.4956	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.71368	-0.4614	10	0.02654	T	1	-14.5002	6.5772	0.22573	0.6062:0.0:0.3938:0.0	.	13	Q96MF2	STAC3_HUMAN	P	13	ENSP00000329200:S13P;ENSP00000452299:S13P	ENSP00000329200:S13P	S	-	1	0	STAC3	55929650	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.825000	0.39081	0.386000	0.24997	0.528000	0.53228	TCC		0.537	STAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412724.2	NM_145064		4	50	0	0	0	1	0	4	50				
TRMT2B	79979	broad.mit.edu	37	X	100297190	100297190	+	Missense_Mutation	SNP	G	G	A			TCGA-SP-A6QG-01A-12D-A35I-08	TCGA-SP-A6QG-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc3443dd-2a18-4c31-b14e-d87edca616ff	d94a0f0a-e850-4bfb-b531-1259d30edbd6	g.chrX:100297190G>A	ENST00000372936.3	-	3	861	c.89C>T	c.(88-90)cCc>cTc	p.P30L	TRMT2B_ENST00000478422.1_Intron|TRMT2B_ENST00000372939.1_Missense_Mutation_p.P30L|TRMT2B_ENST00000338687.7_Missense_Mutation_p.P30L|TRMT2B-AS1_ENST00000443801.2_RNA|TRMT2B_ENST00000372931.5_Missense_Mutation_p.P30L|TRMT2B_ENST00000545398.1_Missense_Mutation_p.P30L|TRMT2B_ENST00000372935.1_Missense_Mutation_p.P30L	NM_024917.5	NP_079193.2	Q96GJ1	TRM2_HUMAN	tRNA methyltransferase 2 homolog B (S. cerevisiae)	30						mitochondrion (GO:0005739)	S-adenosylmethionine-dependent tRNA (m5U54) methyltransferase activity (GO:0030697)			breast(3)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	24						GGCATACCAGGGAAGCAGTCC	0.502																																						ENST00000338687.7																			0				breast(3)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	24						c.(88-90)cCc>cTc		tRNA methyltransferase 2 homolog B (S. cerevisiae)							93.0	81.0	85.0					X																	100297190		2203	4300	6503	SO:0001583	missense	79979						tRNA (uracil-5-)-methyltransferase activity	g.chrX:100297190G>A	BC020116	CCDS14477.1, CCDS55464.1	Xq22.1	2012-06-12	2012-06-12	2008-09-17	ENSG00000188917	ENSG00000188917			25748	protein-coding gene	gene with protein product			"""chromosome X open reading frame 34"""	CXorf34		14702039	Standard	NM_024917		Approved	FLJ12687	uc004egq.3	Q96GJ1	OTTHUMG00000022017	ENST00000372936.3:c.89C>T	X.37:g.100297190G>A	ENSP00000362027:p.Pro30Leu					TRMT2B_ENST00000545398.1_Missense_Mutation_p.P30L|TRMT2B_ENST00000478422.1_Intron|TRMT2B_ENST00000372935.1_Missense_Mutation_p.P30L|TRMT2B_ENST00000372936.3_Missense_Mutation_p.P30L|TRMT2B_ENST00000372931.5_Missense_Mutation_p.P30L|TRMT2B_ENST00000372939.1_Missense_Mutation_p.P30L	p.P30L			Q96GJ1	TRM2_HUMAN			3	894	-			30					A6NDG5|A6NEI9|A6NMG6|Q5JPF0|Q5JVY6|Q96HU7|Q96IH9|Q9H9K2	Missense_Mutation	SNP	ENST00000372936.3	37	c.89C>T	CCDS14477.1	.	.	.	.	.	.	.	.	.	.	G	6.872	0.530349	0.13127	.	.	ENSG00000188917	ENST00000338687;ENST00000545398;ENST00000372939;ENST00000372935;ENST00000372936;ENST00000372931	T;T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;1.03;1.03	4.71	0.569	0.17340	.	1.061280	0.07366	N	0.884909	T	0.37156	0.0993	M	0.66939	2.045	0.09310	N	1	B;B;B	0.11235	0.004;0.002;0.002	B;B;B	0.14578	0.011;0.005;0.005	T	0.45659	-0.9246	10	0.72032	D	0.01	-25.6958	0.832	0.01132	0.2213:0.1827:0.4059:0.1902	.	30;30;30	Q96GJ1-3;F2Z384;Q96GJ1	.;.;TRM2_HUMAN	L	30	ENSP00000340970:P30L;ENSP00000438134:P30L;ENSP00000362030:P30L;ENSP00000362026:P30L;ENSP00000362027:P30L;ENSP00000362022:P30L	ENSP00000340970:P30L	P	-	2	0	TRMT2B	100183846	0.207000	0.23482	0.007000	0.13788	0.059000	0.15707	0.400000	0.20932	0.130000	0.18549	0.513000	0.50165	CCC		0.502	TRMT2B-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057512.1	NM_024917		18	44	0	0	0	1	0	18	44				
HOXB3	3213	broad.mit.edu	37	17	46629486	46629486	+	Silent	SNP	G	G	A			TCGA-SP-A6QG-01A-12D-A35I-08	TCGA-SP-A6QG-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc3443dd-2a18-4c31-b14e-d87edca616ff	d94a0f0a-e850-4bfb-b531-1259d30edbd6	g.chr17:46629486G>A	ENST00000470495.1	-	1	1798	c.351C>T	c.(349-351)tgC>tgT	p.C117C	HOXB3_ENST00000485909.2_Intron|HOXB3_ENST00000311626.4_Silent_p.C117C|HOXB-AS3_ENST00000465846.2_RNA|HOXB3_ENST00000489475.1_Silent_p.C44C|HOXB3_ENST00000490677.1_Intron|HOXB-AS1_ENST00000508688.1_RNA|HOXB-AS1_ENST00000435312.1_RNA|HOXB-AS1_ENST00000502764.2_RNA|HOXB3_ENST00000472863.1_Silent_p.C44C|HOXB3_ENST00000476342.1_Silent_p.C117C|HOXB3_ENST00000460160.1_Intron|HOXB3_ENST00000498678.1_Silent_p.C117C			P14651	HXB3_HUMAN	homeobox B3	117					angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|cartilage development (GO:0051216)|definitive hemopoiesis (GO:0060216)|embryonic skeletal system morphogenesis (GO:0048704)|face development (GO:0060324)|glossopharyngeal nerve morphogenesis (GO:0021615)|hematopoietic progenitor cell differentiation (GO:0002244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of neurogenesis (GO:0050767)|rhombomere development (GO:0021546)|thyroid gland development (GO:0030878)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(2)|large_intestine(2)|lung(16)|prostate(4)|upper_aerodigestive_tract(1)	30						TGCCGGGACCGCACTTTGGGG	0.617																																						ENST00000470495.1																			0				breast(1)|endometrium(4)|kidney(2)|large_intestine(2)|lung(16)|prostate(4)|upper_aerodigestive_tract(1)	30						c.(349-351)tgC>tgT		homeobox B3							164.0	184.0	177.0					17																	46629486		2203	4300	6503	SO:0001819	synonymous_variant	3213				angiogenesis	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr17:46629486G>A		CCDS11528.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120093	ENSG00000120093		"""Homeoboxes / ANTP class : HOXL subclass"""	5114	protein-coding gene	gene with protein product		142966	"""homeo box B3"""	HOX2, HOX2G		1973146, 1358459	Standard	XM_006721854		Approved		uc002ino.3	P14651	OTTHUMG00000159922	ENST00000470495.1:c.351C>T	17.37:g.46629486G>A						HOXB3_ENST00000485909.2_Intron|HOXB-AS3_ENST00000465846.2_RNA|HOXB3_ENST00000311626.4_Silent_p.C117C|HOXB3_ENST00000498678.1_Silent_p.C117C|HOXB3_ENST00000476342.1_Silent_p.C117C|HOXB3_ENST00000472863.1_Silent_p.C44C|HOXB3_ENST00000490677.1_Intron|HOXB3_ENST00000460160.1_Intron|HOXB3_ENST00000489475.1_Silent_p.C44C	p.C117C			P14651	HXB3_HUMAN			1	1798	-			117					A8K567|B7Z5N8|B7Z5P8|B7ZAD0|D3DTV3|O95615|P17484	Silent	SNP	ENST00000470495.1	37	c.351C>T	CCDS11528.1																																																																																				0.617	HOXB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358261.1			6	298	0	0	0	1	0	6	298				
UBN1	29855	broad.mit.edu	37	16	4910691	4910693	+	In_Frame_Del	DEL	AGA	AGA	-			TCGA-SP-A6QG-01A-12D-A35I-08	TCGA-SP-A6QG-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc3443dd-2a18-4c31-b14e-d87edca616ff	d94a0f0a-e850-4bfb-b531-1259d30edbd6	g.chr16:4910691_4910693delAGA	ENST00000396658.4	+	6	1401_1403	c.698_700delAGA	c.(697-702)gagaag>gag	p.K238del	UBN1_ENST00000262376.6_In_Frame_Del_p.K238del|UBN1_ENST00000545171.1_In_Frame_Del_p.K238del|UBN1_ENST00000590769.1_In_Frame_Del_p.K238del	NM_016936.3	NP_058632.2	Q9NPG3	UBN1_HUMAN	ubinuclein 1	238	Lys-rich.				chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of phosphatase activity (GO:0010923)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|tight junction (GO:0005923)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K234E(1)		NS(1)|endometrium(6)|kidney(4)|large_intestine(10)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38						GCCAGTAAGGAGAAGAAGAAGAA	0.453																																						ENST00000396658.4																			1	Substitution - Missense(1)	p.K234E(1)	large_intestine(1)	NS(1)|endometrium(6)|kidney(4)|large_intestine(10)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38						c.(697-702)gag>g		ubinuclein 1																																				SO:0001651	inframe_deletion	29855				chromatin modification|interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter	PML body|tight junction	DNA binding|sequence-specific DNA binding transcription factor activity	g.chr16:4910691_4910693delAGA	AF108460	CCDS10525.1, CCDS73822.1	16p13.3	2010-11-09			ENSG00000118900	ENSG00000118900			12506	protein-coding gene	gene with protein product		609771				10725330	Standard	XM_005255277		Approved		uc002cyb.3	Q9NPG3	OTTHUMG00000129531	ENST00000396658.4:c.698_700delAGA	16.37:g.4910700_4910702delAGA	ENSP00000379894:p.Lys238del					UBN1_ENST00000262376.6_In_Frame_Del_p.EK233del|UBN1_ENST00000590769.1_In_Frame_Del_p.EK233del|UBN1_ENST00000545171.1_In_Frame_Del_p.EK233del	p.EK233del	NM_016936.3	NP_058632.2	Q9NPG3	UBN1_HUMAN			6	1401_1403	+			233			Lys-rich.		B7Z6D3|D3DUE8|Q13079|Q9P1P7	In_Frame_Del	DEL	ENST00000396658.4	37	c.698_700delAGA	CCDS10525.1																																																																																				0.453	UBN1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251719.1	NM_016936		9	215						9	215	---	---	---	---
NPIPA8	101059953	broad.mit.edu	37	16	18441114	18441116	+	Splice_Site	DEL	CAC	CAC	-			TCGA-SP-A6QG-01A-12D-A35I-08	TCGA-SP-A6QG-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc3443dd-2a18-4c31-b14e-d87edca616ff	d94a0f0a-e850-4bfb-b531-1259d30edbd6	g.chr16:18441114_18441116delCAC	ENST00000339303.5	-	1	15		c.e1+1					P0DM63	NPIA8_HUMAN	nuclear pore complex interacting protein family, member A8																		CGGCCATACTCACCACTGGGACT	0.709																																						ENST00000339303.5																			0											c.e1+1		nuclear pore complex interacting protein family, member A8																																				SO:0001630	splice_region_variant	101059953							g.chr16:18441114_18441116delCAC		CCDS61865.1	16p12.3	2013-06-11			ENSG00000214940	ENSG00000214940			41983	protein-coding gene	gene with protein product	"""morpheus gene family member 9"""					11586358	Standard	NM_001282511		Approved	LCR16a9		P0DM63	OTTHUMG00000166284	ENST00000339303.5:c.4043+1GTG>-	16.37:g.18441117_18441119delCAC														1	15	-									Splice_Site	DEL	ENST00000339303.5	37																																																																																						0.709	NPIPA8-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding			Intron	5	11						5	11	---	---	---	---
LINC00482	284185	broad.mit.edu	37	17	79279019	79279020	+	lincRNA	INS	-	-	C	rs185100858|rs3215153	byFrequency	TCGA-SP-A6QG-01A-12D-A35I-08	TCGA-SP-A6QG-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc3443dd-2a18-4c31-b14e-d87edca616ff	d94a0f0a-e850-4bfb-b531-1259d30edbd6	g.chr17:79279019_79279020insC	ENST00000332012.5	-	0	573_574					NR_038080.1		Q8N8I6	CQ055_HUMAN	long intergenic non-protein coding RNA 482																		CCCAGGCACAGCCCCTGAGGCA	0.673													CCCC|CCCC|CCCCC|insertion	348	0.0694888	0.0091	0.0389	5008	,	,		17826	0.1379		0.0944	False		,,,				2504	0.0767					ENST00000332012.5																			0																	70,3778		6,58,1860						1.4	0.0		dbSNP_106	9	743,7211		62,619,3296	no	intergenic				68,677,5156	A1A1,A1R,RR		9.3412,1.8191,6.8887				813,10989						284185							g.chr17:79279019_79279020insC	AK096740		17q25.3	2012-10-12	2011-09-01	2011-09-01	ENSG00000185168	ENSG00000185168		"""Long non-coding RNAs"""	26816	non-coding RNA	RNA, long non-coding			"""chromosome 17 open reading frame 55"""	C17orf55			Standard	NR_038080		Approved	FLJ39421	uc002kac.1	Q8N8I6			17.37:g.79279023_79279023dupC								NR_038080.1						0	573_574	-									RNA	INS	ENST00000332012.5	37																																																																																						0.673	LINC00482-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000439605.1	NM_178519		5	9						5	9	---	---	---	---
SRPX	8406	broad.mit.edu	37	X	38079976	38079978	+	In_Frame_Del	DEL	GCA	GCA	-	rs35523939|rs72249350|rs139109693		TCGA-SP-A6QG-01A-12D-A35I-08	TCGA-SP-A6QG-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc3443dd-2a18-4c31-b14e-d87edca616ff	d94a0f0a-e850-4bfb-b531-1259d30edbd6	g.chrX:38079976_38079978delGCA	ENST00000378533.3	-	1	174_176	c.68_70delTGC	c.(67-72)ctgcgc>cgc	p.L23del	SRPX_ENST00000538295.1_In_Frame_Del_p.L23del|SRPX_ENST00000432886.2_In_Frame_Del_p.L23del|SRPX_ENST00000544439.1_In_Frame_Del_p.L23del|RP13-43E11.1_ENST00000423919.1_RNA|TM4SF2_ENST00000465127.1_Intron|SRPX_ENST00000343800.6_Intron	NM_006307.4	NP_006298.1	P78539	SRPX_HUMAN	sushi-repeat containing protein, X-linked	23			Missing. {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:8634709, ECO:0000269|PubMed:9162095}.		autophagy (GO:0006914)|cell adhesion (GO:0007155)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|phagolysosome assembly (GO:0001845)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|response to endoplasmic reticulum stress (GO:0034976)	autophagic vacuole (GO:0005776)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)		p.L23delL(2)		autonomic_ganglia(1)|breast(2)|endometrium(5)|large_intestine(5)|lung(10)|prostate(2)	25						GGCGGGACGCgcagcagcagcag	0.729											OREG0019726	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		636	0.168477	0.1657	0.1398	3775	,	,		8591	0.0129		0.2028	False		,,,				2504	0.1053					ENST00000378533.3																			2	Deletion - In frame(2)	p.L23delL(2)	prostate(2)	autonomic_ganglia(1)|breast(2)|endometrium(5)|large_intestine(5)|lung(10)|prostate(2)	25						c.(67-72)cgc>c		sushi-repeat containing protein, X-linked																																				SO:0001651	inframe_deletion	8406				cell adhesion	cell surface|membrane		g.chrX:38079976_38079978delGCA	U78093	CCDS14245.1, CCDS55400.1, CCDS55401.1, CCDS55402.1	Xp21.1	2011-01-25	2011-01-25		ENSG00000101955	ENSG00000101955			11309	protein-coding gene	gene with protein product		300187	"""sushi-repeat-containing protein, X chromosome"", ""sushi-repeat-containing protein, X-linked"""			8634708, 8634709	Standard	NM_006307		Approved	ETX1	uc004ddy.2	P78539	OTTHUMG00000021362	ENST00000378533.3:c.68_70delTGC	X.37:g.38079985_38079987delGCA	ENSP00000367794:p.Leu23del		OREG0019726	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	875	SRPX_ENST00000544439.1_In_Frame_Del_p.LR23del|TM4SF2_ENST00000465127.1_Intron|SRPX_ENST00000432886.2_In_Frame_Del_p.LR23del|SRPX_ENST00000538295.1_In_Frame_Del_p.LR23del|SRPX_ENST00000343800.6_Intron	p.LR23del	NM_006307.4	NP_006298.1	P78539	SRPX_HUMAN			1	174_176	-			23		Missing.			A8K065|B3KWP8|B4DDB8|B4DQH5|F5H4D7|G3V1L0|Q4VX66|Q99652|Q99913	In_Frame_Del	DEL	ENST00000378533.3	37	c.68_70delTGC	CCDS14245.1																																																																																				0.729	SRPX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056243.1	NM_006307		4	8						4	8	---	---	---	---
FAM120C	54954	broad.mit.edu	37	X	54209302	54209303	+	In_Frame_Ins	INS	-	-	GGCGGC			TCGA-SP-A6QG-01A-12D-A35I-08	TCGA-SP-A6QG-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fc3443dd-2a18-4c31-b14e-d87edca616ff	d94a0f0a-e850-4bfb-b531-1259d30edbd6	g.chrX:54209302_54209303insGGCGGC	ENST00000375180.2	-	1	385_386	c.329_330insGCCGCC	c.(328-330)ccc>ccGCCGCCc	p.110_110P>PPP	FAM120C_ENST00000328235.4_In_Frame_Ins_p.110_110P>PPP|FAM120C_ENST00000477084.1_In_Frame_Ins_p.110_110P>PPP|FAM120C_ENST00000497680.1_5'Flank	NM_017848.4	NP_060318.3	Q9NX05	F120C_HUMAN	family with sequence similarity 120C	110							poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28						GCAGCTGAGGGGGCGGCGGCGG	0.748														77	0.0203974	0.0045	0.0159	3775	,	,		9228	0.0		0.0467	False		,,,				2504	0.0133					ENST00000375180.2																			0				breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28						c.(328-330)ccc>cGCCGCCcc		family with sequence similarity 120C																																				SO:0001652	inframe_insertion	54954							g.chrX:54209302_54209303insGGCGGC	AY150025	CCDS14356.1, CCDS55421.1, CCDS75987.1	Xp11.22	2011-04-13	2006-07-04	2006-07-04	ENSG00000184083	ENSG00000184083			16949	protein-coding gene	gene with protein product		300741	"""chromosome X open reading frame 17"""	CXorf17		14585507	Standard	XM_006724589		Approved	ORF34, FLJ20506	uc004dsz.4	Q9NX05	OTTHUMG00000021625	ENST00000375180.2:c.324_329dupGCCGCC	X.37:g.54209303_54209308dupGGCGGC	ENSP00000364324:p.ProPro110dup					FAM120C_ENST00000477084.1_In_Frame_Ins_p.109_110insRR|FAM120C_ENST00000328235.4_In_Frame_Ins_p.109_110insRR	p.109_110insRR	NM_017848.4	NP_060318.3	Q9NX05	F120C_HUMAN			1	385_386	-			109					B2RMT7	In_Frame_Ins	INS	ENST00000375180.2	37	c.329_330insGCCGCC	CCDS14356.1																																																																																				0.748	FAM120C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056795.2	NM_017848		3	5						3	5	---	---	---	---
