#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_Mutation_Status	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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
MSL3P1	151507	broad.mit.edu	37	2	234775941	234775941	+	RNA	SNP	A	A	G	rs213545	byFrequency	TCGA-WC-A87W-01A-11D-A39W-08	TCGA-WC-A87W-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5b97d5cc-c7d2-4d27-87cb-4c5090079458	addacac8-7364-409d-adce-53703cafaea2	g.chr2:234775941A>G	ENST00000438684.1	-	0	173					NR_024322.1		P0C860	MS3L2_HUMAN	male-specific lethal 3 homolog (Drosophila) pseudogene 1						chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)											CACTACTGTCAGAGGAACTGC	0.378													G|||	2788	0.556709	0.4244	0.6153	5008	,	,		18980	0.7232		0.6143	False		,,,				2504	0.4632					ENST00000438684.1																			0																																																			0							g.chr2:234775941A>G	BI831020		2q37.1	2011-03-21	2011-03-21	2011-03-21	ENSG00000224287	ENSG00000224287			17837	pseudogene	pseudogene			"""male-specific lethal 3-like 2 (Drosophila)"""	MSL3L2			Standard	NR_024322		Approved		uc010znf.2	P0C860	OTTHUMG00000059126		2.37:g.234775941A>G			Somatic						NR_024322.1		WXS	Illumina GAIIx	Phase_I					0	173	-									RNA	SNP	ENST00000438684.1	37																																																																																						0.378	MSL3P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000131002.2	NR_024322		4	11	0	0	0	1	0	4	11				
SCN11A	11280	broad.mit.edu	37	3	38938527	38938527	+	Missense_Mutation	SNP	G	G	T			TCGA-WC-A87W-01A-11D-A39W-08	TCGA-WC-A87W-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5b97d5cc-c7d2-4d27-87cb-4c5090079458	addacac8-7364-409d-adce-53703cafaea2	g.chr3:38938527G>T	ENST00000302328.3	-	14	2410	c.2212C>A	c.(2212-2214)Ccg>Acg	p.P738T	SCN11A_ENST00000444237.2_Missense_Mutation_p.P738T|SCN11A_ENST00000456224.3_Missense_Mutation_p.P738T|SCN11A_ENST00000450244.1_Missense_Mutation_p.P738T	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	738					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GGGCCTGTCGGGTTACAGAGT	0.502																																						ENST00000450244.1																			0				NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119						c.(2212-2214)Ccg>Acg		sodium channel, voltage-gated, type XI, alpha subunit	Cocaine(DB00907)						101.0	92.0	95.0					3																	38938527		2203	4300	6503	SO:0001583	missense	11280				response to drug	voltage-gated sodium channel complex	voltage-gated sodium channel activity	g.chr3:38938527G>T	AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10583	protein-coding gene	gene with protein product		604385	"""sodium channel, voltage-gated, type XI, alpha polypeptide"", ""sodium channel, voltage-gated, type XII, alpha"""	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.2212C>A	3.37:g.38938527G>T	ENSP00000307599:p.Pro738Thr		Somatic				SCN11A_ENST00000456224.3_Missense_Mutation_p.P738T|SCN11A_ENST00000444237.2_Missense_Mutation_p.P738T|SCN11A_ENST00000302328.3_Missense_Mutation_p.P738T	p.P738T			WXS	Illumina GAIIx	Phase_I	Q9UI33	SCNBA_HUMAN		Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	14	2410	-			738					A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Missense_Mutation	SNP	ENST00000302328.3	37	c.2212C>A	CCDS33737.1	.	.	.	.	.	.	.	.	.	.	G	0.972	-0.699833	0.03279	.	.	ENSG00000168356	ENST00000302328;ENST00000450244;ENST00000456224;ENST00000444237	D;D;D;D	0.96136	-3.92;-3.92;-3.87;-3.74	0.225	0.225	0.15325	Ion transport (1);	17.326200	0.00166	N	0.000001	D	0.95169	0.8434	M	0.86178	2.8	0.09310	N	1	B	0.14805	0.011	B	0.12837	0.008	T	0.80167	-0.1495	10	0.56958	D	0.05	.	5.9124	0.19035	1.0E-4:0.0:0.9999:0.0	.	738	Q9UI33	SCNBA_HUMAN	T	738	ENSP00000307599:P738T;ENSP00000400945:P738T;ENSP00000416757:P738T;ENSP00000408028:P738T	ENSP00000307599:P738T	P	-	1	0	SCN11A	38913531	0.000000	0.05858	0.002000	0.10522	0.021000	0.10359	-4.182000	0.00278	0.300000	0.22699	0.305000	0.20034	CCG		0.502	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139		17	31	1	0	2.4624e-09	1	2.4624e-09	17	31				
ITGA8	8516	broad.mit.edu	37	10	15701035	15701035	+	Missense_Mutation	SNP	G	G	A	rs148965352		TCGA-WC-A87W-01A-11D-A39W-08	TCGA-WC-A87W-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5b97d5cc-c7d2-4d27-87cb-4c5090079458	addacac8-7364-409d-adce-53703cafaea2	g.chr10:15701035G>A	ENST00000378076.3	-	10	1264	c.911C>T	c.(910-912)aCg>aTg	p.T304M		NM_003638.1	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8	304				T -> Y (in Ref. 5; AAA93514). {ECO:0000305}.	brain development (GO:0007420)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|metanephros development (GO:0001656)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|substrate adhesion-dependent cell spreading (GO:0034446)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|dendritic spine membrane (GO:0032591)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integrin alpha8-beta1 complex (GO:0034678)|integrin complex (GO:0008305)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	metal ion binding (GO:0046872)			NS(2)|breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(57)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	96						CGTCATATCCGTAGAGTTAAT	0.318													G|||	1	0.000199681	0.0	0.0	5008	,	,		16733	0.0		0.001	False		,,,				2504	0.0					ENST00000378076.3																			0				NS(2)|breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(57)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	96						c.(910-912)aCg>aTg		integrin, alpha 8		G	MET/THR	2,4404	4.2+/-10.8	0,2,2201	52.0	54.0	53.0		911	5.6	1.0	10	dbSNP_134	53	12,8584	9.1+/-34.3	0,12,4286	yes	missense	ITGA8	NM_003638.1	81	0,14,6487	AA,AG,GG		0.1396,0.0454,0.1077	probably-damaging	304/1064	15701035	14,12988	2203	4298	6501	SO:0001583	missense	8516				cell differentiation|cell-cell adhesion|cell-matrix adhesion|integrin-mediated signaling pathway|nervous system development	integrin complex	receptor activity	g.chr10:15701035G>A	L36531	CCDS31155.1	10p13	2010-03-23			ENSG00000077943	ENSG00000077943		"""Integrins"""	6144	protein-coding gene	gene with protein product		604063				7768999	Standard	XM_005252633		Approved		uc001ioc.1	P53708	OTTHUMG00000017733	ENST00000378076.3:c.911C>T	10.37:g.15701035G>A	ENSP00000367316:p.Thr304Met		Somatic					p.T304M	NM_003638.1	NP_003629	WXS	Illumina GAIIx	Phase_I	P53708	ITA8_HUMAN			10	1264	-			304	T -> Y (in Ref. 5; AAA93514).				B0YJ31|Q5VX94	Missense_Mutation	SNP	ENST00000378076.3	37	c.911C>T	CCDS31155.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	19.50	3.839816	0.71488	4.54E-4	0.001396	ENSG00000077943	ENST00000378076;ENST00000538044	T	0.24350	1.86	5.59	5.59	0.84812	.	0.139474	0.64402	D	0.000005	T	0.45756	0.1358	L	0.55834	1.745	0.53688	D	0.999976	D;D	0.89917	1.0;1.0	D;P	0.67103	0.949;0.891	T	0.22626	-1.0211	10	0.49607	T	0.09	.	16.2993	0.82801	0.0:0.0:1.0:0.0	.	289;304	F5H818;P53708	.;ITA8_HUMAN	M	304;289	ENSP00000367316:T304M	ENSP00000367316:T304M	T	-	2	0	ITGA8	15741041	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.825000	0.75293	2.634000	0.89283	0.563000	0.77884	ACG		0.318	ITGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046987.1	NM_003638		3	42	0	0	0	1	0	3	42				
RNF213	57674	broad.mit.edu	37	17	78332109	78332109	+	Silent	SNP	C	C	T			TCGA-WC-A87W-01A-11D-A39W-08	TCGA-WC-A87W-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5b97d5cc-c7d2-4d27-87cb-4c5090079458	addacac8-7364-409d-adce-53703cafaea2	g.chr17:78332109C>T	ENST00000582970.1	+	37	11027	c.10884C>T	c.(10882-10884)gtC>gtT	p.V3628V	RNF213_ENST00000336301.6_Silent_p.V1701V|CTD-2047H16.4_ENST00000575034.1_RNA|CTD-2047H16.4_ENST00000572151.1_RNA|RNF213_ENST00000508628.2_Silent_p.V3677V	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	3628					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			GGAAGCGGGTCCAAGGTGCTG	0.572																																						ENST00000582970.1																			0				NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130						c.(10882-10884)gtC>gtT		ring finger protein 213							70.0	61.0	64.0					17																	78332109		2203	4300	6503	SO:0001819	synonymous_variant	57674							g.chr17:78332109C>T	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.10884C>T	17.37:g.78332109C>T			Somatic				RNF213_ENST00000336301.6_Silent_p.V1701V|CTD-2047H16.4_ENST00000575034.1_RNA|CTD-2047H16.4_ENST00000572151.1_RNA|RNF213_ENST00000508628.2_Silent_p.V3677V	p.V3628V	NM_001256071.1	NP_001243000.1	WXS	Illumina GAIIx	Phase_I	Q9HCF4	ALO17_HUMAN	BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)		37	11027	+	all_neural(118;0.0538)		0					C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Silent	SNP	ENST00000582970.1	37	c.10884C>T	CCDS58606.1																																																																																				0.572	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		12	24	0	0	0	1	0	12	24				
GNA11	2767	broad.mit.edu	37	19	3118942	3118942	+	Missense_Mutation	SNP	A	A	T			TCGA-WC-A87W-01A-11D-A39W-08	TCGA-WC-A87W-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5b97d5cc-c7d2-4d27-87cb-4c5090079458	addacac8-7364-409d-adce-53703cafaea2	g.chr19:3118942A>T	ENST00000078429.4	+	5	868	c.626A>T	c.(625-627)cAg>cTg	p.Q209L	GNA11_ENST00000586180.1_3'UTR|AC005262.2_ENST00000585980.1_RNA|AC005262.3_ENST00000587701.1_RNA	NM_002067.2	NP_002058.2	P29992	GNA11_HUMAN	guanine nucleotide binding protein (G protein), alpha 11 (Gq class)	209					action potential (GO:0001508)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cellular response to pH (GO:0071467)|developmental pigmentation (GO:0048066)|heart development (GO:0007507)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|regulation of melanocyte differentiation (GO:0045634)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 2A serotonin receptor binding (GO:0031826)	p.Q209L(80)|p.Q209P(2)		endometrium(2)|eye(132)|kidney(1)|large_intestine(2)|lung(1)|meninges(5)|ovary(1)|prostate(1)|skin(16)	161		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.79e-05)|OV - Ovarian serous cystadenocarcinoma(105;2.68e-113)|Epithelial(107;1.22e-111)|all cancers(105;5.78e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00141)|STAD - Stomach adenocarcinoma(1328;0.181)		GTGGGGGGCCAGCGGTCGGAG	0.612			Mis		uveal melanoma																																	ENST00000078429.4				Dom	yes		19	19p13.3	2767	Mis	"""guanine nucleotide binding protein (G protein), alpha 11 (Gq class)"""			E			uveal melanoma		82	Substitution - Missense(82)	p.Q209L(80)|p.Q209P(2)	eye(69)|skin(8)|meninges(5)	endometrium(2)|eye(132)|kidney(1)|large_intestine(2)|lung(1)|meninges(5)|ovary(1)|prostate(1)|skin(16)	161						c.(625-627)cAg>cTg		guanine nucleotide binding protein (G protein), alpha 11 (Gq class)							104.0	89.0	94.0					19																	3118942		2203	4300	6503	SO:0001583	missense	2767				activation of phospholipase C activity by dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|platelet activation|protein ADP-ribosylation|regulation of action potential	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity	g.chr19:3118942A>T	AF493900	CCDS12103.1	19p13.3	2014-02-04			ENSG00000088256	ENSG00000088256			4379	protein-coding gene	gene with protein product		139313	"""hypocalciuric hypercalcemia 2"""	HHC2		1302014, 23802516	Standard	NM_002067		Approved	FBH, FBH2, FHH2	uc002lxd.3	P29992	OTTHUMG00000180631	ENST00000078429.4:c.626A>T	19.37:g.3118942A>T	ENSP00000078429:p.Gln209Leu		Somatic				GNA11_ENST00000586180.1_3'UTR|AC005262.3_ENST00000587701.1_RNA	p.Q209L	NM_002067.2	NP_002058.2	WXS	Illumina GAIIx	Phase_I	P29992	GNA11_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (162;6.79e-05)|OV - Ovarian serous cystadenocarcinoma(105;2.68e-113)|Epithelial(107;1.22e-111)|all cancers(105;5.78e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00141)|STAD - Stomach adenocarcinoma(1328;0.181)	5	868	+		Hepatocellular(1079;0.137)	209					O15109|Q14350|Q6IB00	Missense_Mutation	SNP	ENST00000078429.4	37	c.626A>T	CCDS12103.1	.	.	.	.	.	.	.	.	.	.	.	15.05	2.718086	0.48622	.	.	ENSG00000088256	ENST00000078429	D	0.91237	-2.81	3.26	3.26	0.37387	.	0.000000	0.64402	U	0.000006	D	0.96950	0.9004	H	0.99357	4.53	0.80722	D	1	D	0.59767	0.986	D	0.68483	0.958	D	0.96823	0.9605	10	0.87932	D	0	.	10.7338	0.46113	1.0:0.0:0.0:0.0	.	209	P29992	GNA11_HUMAN	L	209	ENSP00000078429:Q209L	ENSP00000078429:Q209L	Q	+	2	0	GNA11	3069942	1.000000	0.71417	0.438000	0.26821	0.027000	0.11550	9.104000	0.94239	1.256000	0.44068	0.379000	0.24179	CAG		0.612	GNA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452261.2	NM_002067		25	38	0	0	0	1	0	25	38				
FLG	2312	broad.mit.edu	37	1	152285621	152285621	+	Missense_Mutation	SNP	T	T	C	rs145627745	byFrequency	TCGA-WC-A87W-01A-11D-A39W-08	TCGA-WC-A87W-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5b97d5cc-c7d2-4d27-87cb-4c5090079458	addacac8-7364-409d-adce-53703cafaea2	g.chr1:152285621T>C	ENST00000368799.1	-	3	1776	c.1741A>G	c.(1741-1743)Acc>Gcc	p.T581A	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	581	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GAGTGCCTGGTGCCGTCTCCT	0.567									Ichthyosis																													ENST00000368799.1																			0				autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424						c.(1741-1743)Acc>Gcc		filaggrin							392.0	368.0	376.0					1																	152285621		2203	4300	6503	SO:0001583	missense	2312	Ichthyosis	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity	g.chr1:152285621T>C	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.1741A>G	1.37:g.152285621T>C	ENSP00000357789:p.Thr581Ala		Somatic				FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	p.T581A	NM_002016.1	NP_002007.1	WXS	Illumina GAIIx	Phase_I	P20930	FILA_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.206)		3	1776	-	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		581			Ser-rich.		Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	c.1741A>G	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	-	1.034	-0.680941	0.03353	.	.	ENSG00000143631	ENST00000368799;ENST00000392689	T	0.02498	4.27	2.15	-4.3	0.03710	.	.	.	.	.	T	0.00440	0.0014	N	0.14661	0.345	0.09310	N	1	B	0.32968	0.392	B	0.42062	0.374	T	0.35201	-0.9798	9	0.08837	T	0.75	.	0.4631	0.00519	0.1939:0.3015:0.2321:0.2724	.	581	P20930	FILA_HUMAN	A	581;113	ENSP00000357789:T581A	ENSP00000357789:T581A	T	-	1	0	FLG	150552245	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-6.125000	0.00079	-3.882000	0.00095	-1.828000	0.00595	ACC		0.567	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		33	224	0	0	0	1	0	33	224				
BRINP3	339479	broad.mit.edu	37	1	190067401	190067401	+	Missense_Mutation	SNP	A	A	G			TCGA-WC-A87W-01A-11D-A39W-08	TCGA-WC-A87W-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5b97d5cc-c7d2-4d27-87cb-4c5090079458	addacac8-7364-409d-adce-53703cafaea2	g.chr1:190067401A>G	ENST00000367462.3	-	8	2279	c.2048T>C	c.(2047-2049)cTg>cCg	p.L683P	BRINP3_ENST00000534846.1_Missense_Mutation_p.L581P	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	683					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)											CTGCAAAATCAGGTCCCGAAT	0.458																																						ENST00000367462.3																			0											c.(2047-2049)cTg>cCg		bone morphogenetic protein/retinoic acid inducible neural-specific 3							109.0	108.0	109.0					1																	190067401		2203	4300	6503	SO:0001583	missense	339479							g.chr1:190067401A>G	AB111893	CCDS1373.1	1q31.1	2013-09-18	2013-09-18	2013-09-18	ENSG00000162670	ENSG00000162670			22393	protein-coding gene	gene with protein product			"""family with sequence similarity 5, member C"""	FAM5C		16018821, 15193423	Standard	NM_199051		Approved	DBCCR1L, DBCCR1L1	uc001gse.1	Q76B58	OTTHUMG00000035533	ENST00000367462.3:c.2048T>C	1.37:g.190067401A>G	ENSP00000356432:p.Leu683Pro		Somatic				BRINP3_ENST00000534846.1_Missense_Mutation_p.L581P	p.L683P	NM_199051.1	NP_950252.1	WXS	Illumina GAIIx	Phase_I					8	2279	-			683					B3KVP1|B7Z260|O95726|Q2M330	Missense_Mutation	SNP	ENST00000367462.3	37	c.2048T>C	CCDS1373.1	.	.	.	.	.	.	.	.	.	.	A	14.39	2.521122	0.44866	.	.	ENSG00000162670	ENST00000367462;ENST00000534846	T;T	0.21734	2.24;1.99	5.62	4.48	0.54585	.	0.082989	0.49916	D	0.000129	T	0.29321	0.0730	M	0.70275	2.135	0.80722	D	1	P;P	0.41848	0.763;0.651	P;B	0.44359	0.447;0.174	T	0.02721	-1.1119	10	0.49607	T	0.09	.	10.9682	0.47424	0.8428:0.1572:0.0:0.0	.	581;683	B7Z260;Q76B58	.;FAM5C_HUMAN	P	683;581	ENSP00000356432:L683P;ENSP00000438022:L581P	ENSP00000356432:L683P	L	-	2	0	FAM5C	188334024	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	9.237000	0.95368	0.932000	0.37266	0.528000	0.53228	CTG		0.458	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1	NM_199051		4	71	0	0	0	1	0	4	71				
TRPM7	54822	broad.mit.edu	37	15	50866914	50866914	+	Missense_Mutation	SNP	T	T	A			TCGA-WC-A87W-01A-11D-A39W-08	TCGA-WC-A87W-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5b97d5cc-c7d2-4d27-87cb-4c5090079458	addacac8-7364-409d-adce-53703cafaea2	g.chr15:50866914T>A	ENST00000313478.7	-	35	5303	c.5022A>T	c.(5020-5022)gaA>gaT	p.E1674D	TRPM7_ENST00000560955.1_Missense_Mutation_p.E1673D|TRPM7_ENST00000561443.1_5'UTR	NM_017672.4	NP_060142.3	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel, subfamily M, member 7	1674	Alpha-type protein kinase. {ECO:0000255|PROSITE-ProRule:PRU00501}.				actomyosin structure organization (GO:0031032)|calcium ion transmembrane transport (GO:0070588)|calcium-dependent cell-matrix adhesion (GO:0016340)|cellular magnesium ion homeostasis (GO:0010961)|ion transmembrane transport (GO:0034220)|necroptotic process (GO:0070266)|protein autophosphorylation (GO:0046777)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(17)|lung(13)|ovary(4)|pancreas(1)|skin(4)|stomach(3)	52				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)		GTTGTTGAATTTCCTATAAAA	0.303																																						ENST00000313478.7																			0				breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(17)|lung(13)|ovary(4)|pancreas(1)|skin(4)|stomach(3)	52						c.(5020-5022)gaA>gaT		transient receptor potential cation channel, subfamily M, member 7							126.0	120.0	122.0					15																	50866914		1810	4071	5881	SO:0001583	missense	54822				cell death	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein serine/threonine kinase activity	g.chr15:50866914T>A	AF346629	CCDS42035.1, CCDS73725.1	15q21	2011-12-14				ENSG00000092439		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17994	protein-coding gene	gene with protein product		605692				11161216, 11385574, 16382100	Standard	XM_005254486		Approved	CHAK1, LTRPC7, TRP-PLIK	uc001zyt.4	Q96QT4		ENST00000313478.7:c.5022A>T	15.37:g.50866914T>A	ENSP00000320239:p.Glu1674Asp		Somatic				TRPM7_ENST00000560955.1_Missense_Mutation_p.E1673D|TRPM7_ENST00000561443.1_5'UTR	p.E1674D	NM_017672.4	NP_060142.3	WXS	Illumina GAIIx	Phase_I	Q96QT4	TRPM7_HUMAN		all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)	35	5303	-			1674			Alpha-type protein kinase.		Q6ZMF5|Q86VJ4|Q8NBW2|Q9BXB2|Q9NXQ2	Missense_Mutation	SNP	ENST00000313478.7	37	c.5022A>T	CCDS42035.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.472146	0.84533	.	.	ENSG00000092439	ENST00000313478	T	0.06371	3.31	5.25	5.25	0.73442	MHCK/EF2 kinase (3);Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.17408	0.0418	L	0.36672	1.1	0.58432	D	0.999995	D	0.89917	1.0	D	0.87578	0.998	T	0.00657	-1.1623	10	0.87932	D	0	-26.0928	15.3214	0.74124	0.0:0.0:0.0:1.0	.	1674	Q96QT4	TRPM7_HUMAN	D	1674	ENSP00000320239:E1674D	ENSP00000320239:E1674D	E	-	3	2	TRPM7	48654206	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	3.362000	0.52314	2.191000	0.70037	0.528000	0.53228	GAA		0.303	TRPM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418604.1	NM_017672		23	46	0	0	0	1	0	23	46				
MAGED1	9500	broad.mit.edu	37	X	51640905	51640905	+	Silent	SNP	A	A	G			TCGA-WC-A87W-01A-11D-A39W-08	TCGA-WC-A87W-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5b97d5cc-c7d2-4d27-87cb-4c5090079458	addacac8-7364-409d-adce-53703cafaea2	g.chrX:51640905A>G	ENST00000375722.1	+	7	1833	c.1581A>G	c.(1579-1581)caA>caG	p.Q527Q	MAGED1_ENST00000326587.7_Silent_p.Q527Q|MAGED1_ENST00000494718.1_3'UTR|MAGED1_ENST00000375695.2_Silent_p.Q583Q|MAGED1_ENST00000375772.3_Silent_p.Q527Q			Q9Y5V3	MAGD1_HUMAN	melanoma antigen family D, 1	527	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|circadian regulation of gene expression (GO:0032922)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of circadian rhythm (GO:0042752)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	transcription coactivator activity (GO:0003713)			breast(1)|endometrium(4)|large_intestine(10)|lung(13)|ovary(3)|upper_aerodigestive_tract(1)	32	Ovarian(276;0.236)					TTGGGATTCAACTGAAAGAAA	0.443										Multiple Myeloma(10;0.10)																												ENST00000375695.2																			0				breast(1)|endometrium(4)|large_intestine(10)|lung(13)|ovary(3)|upper_aerodigestive_tract(1)	32						c.(1747-1749)caA>caG		melanoma antigen family D, 1							52.0	46.0	48.0					X																	51640905		2203	4299	6502	SO:0001819	synonymous_variant	9500				apoptosis|induction of apoptosis by extracellular signals|negative regulation of epithelial cell proliferation|nerve growth factor receptor signaling pathway|regulation of transcription, DNA-dependent	cytoplasm|plasma membrane|protein complex	protein binding	g.chrX:51640905A>G	AF124440	CCDS14337.1, CCDS35279.1	Xp11.23	2008-08-01			ENSG00000179222	ENSG00000179222			6813	protein-coding gene	gene with protein product		300224				10409427	Standard	NM_006986		Approved	NRAGE, DLXIN-1	uc004dpn.3	Q9Y5V3	OTTHUMG00000021540	ENST00000375722.1:c.1581A>G	X.37:g.51640905A>G		Multiple Myeloma(10;0.10)	Somatic				MAGED1_ENST00000494718.1_3'UTR|MAGED1_ENST00000375722.1_Silent_p.Q527Q|MAGED1_ENST00000375772.3_Silent_p.Q527Q|MAGED1_ENST00000326587.7_Silent_p.Q527Q	p.Q583Q	NM_001005333.1	NP_001005333.1	WXS	Illumina GAIIx	Phase_I	Q9Y5V3	MAGD1_HUMAN			8	1902	+	Ovarian(276;0.236)		527			MAGE.		Q5VSH6|Q8IZ84|Q8WY92|Q9H352|Q9HBT4|Q9UF36	Silent	SNP	ENST00000375722.1	37	c.1749A>G	CCDS14337.1																																																																																				0.443	MAGED1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056593.1	NM_001005332		9	13	0	0	0	1	0	9	13				
PRB3	5544	broad.mit.edu	37	12	11420458	11420458	+	Missense_Mutation	SNP	C	C	T	rs28435564	byFrequency	TCGA-WC-A87W-01A-11D-A39W-08	TCGA-WC-A87W-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5b97d5cc-c7d2-4d27-87cb-4c5090079458	addacac8-7364-409d-adce-53703cafaea2	g.chr12:11420458C>T	ENST00000279573.7	-	3	860	c.725G>A	c.(724-726)cGt>cAt	p.R242H	PRB3_ENST00000381842.3_Intron|PRB3_ENST00000538488.1_Intron|PRB3_ENST00000440870.3_Intron			Q04118	PRB3_HUMAN	proline-rich protein BstNI subfamily 3	179	10 X 21 AA tandem repeats of [RH]-P-G-K- P-[EQ]-G-[PQS]-P-[PS]-Q-[GE]-G-N-[QK]- [SP]-[QR]-[GR]-P-P-P.|Pro-rich.				defense response to Gram-negative bacterium (GO:0050829)	extracellular region (GO:0005576)				breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(5)	25			OV - Ovarian serous cystadenocarcinoma(49;0.201)			CTTTCCTGGACGAGGTGGGGG	0.612													c|||	1688	0.337061	0.1861	0.4251	5008	,	,		4544	0.3571		0.4453	False		,,,				2504	0.3466					ENST00000279573.7																			0				breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(5)	25						c.(724-726)cGt>cAt		proline-rich protein BstNI subfamily 3							9.0	4.0	6.0					12																	11420458		1057	1581	2638	SO:0001583	missense	5544					extracellular region	Gram-negative bacterial cell surface binding	g.chr12:11420458C>T			12p13.2	2012-10-02				ENSG00000197870			9339	protein-coding gene	gene with protein product		168840				1894623	Standard	NM_006249		Approved	PRG	uc001qzs.3	Q04118		ENST00000279573.7:c.725G>A	12.37:g.11420458C>T	ENSP00000279573:p.Arg242His		Somatic				PRB3_ENST00000381842.3_Intron|PRB3_ENST00000538488.1_Intron|PRB3_ENST00000440870.3_Intron	p.R242H			WXS	Illumina GAIIx	Phase_I	Q04118	PRB3_HUMAN	OV - Ovarian serous cystadenocarcinoma(49;0.201)		3	860	-						10 X 21 AA tandem repeats of [RH]-P-G-K- P-[EQ]-G-[PQS]-P-[PS]-Q-[GE]-G-N-[QK]- [SP]-[QR]-[GR]-P-P-P.|Pro-rich.		Q15188|Q4VAY3|Q4VAY4|Q7M4M9|Q9UCT9	Missense_Mutation	SNP	ENST00000279573.7	37	c.725G>A																																																																																					0.612	PRB3-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000402119.5	NM_006249		4	13	0	0	0	1	0	4	13				
IGSF11	152404	broad.mit.edu	37	3	118824025	118824025	+	Silent	SNP	T	T	C			TCGA-WC-A87W-01A-11D-A39W-08	TCGA-WC-A87W-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5b97d5cc-c7d2-4d27-87cb-4c5090079458	addacac8-7364-409d-adce-53703cafaea2	g.chr3:118824025T>C	ENST00000425327.2	-	2	283	c.15A>G	c.(13-15)gaA>gaG	p.E5E	IGSF11_ENST00000354673.2_Silent_p.E5E|IGSF11_ENST00000441144.2_Silent_p.E5E			Q5DX21	IGS11_HUMAN	immunoglobulin superfamily, member 11	10					cell adhesion (GO:0007155)|regulation of growth (GO:0040008)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						AGAGCAAAAGTTCCACCAGAG	0.358																																						ENST00000354673.2																			0				autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						c.(13-15)gaA>gaG		immunoglobulin superfamily, member 11							110.0	106.0	107.0					3																	118824025		2203	4300	6503	SO:0001819	synonymous_variant	152404				cell adhesion|regulation of growth	integral to membrane|plasma membrane	receptor activity	g.chr3:118824025T>C	AB079879	CCDS2983.1, CCDS46891.1	3q21.2	2013-01-11			ENSG00000144847	ENSG00000144847		"""Immunoglobulin superfamily / I-set domain containing"""	16669	protein-coding gene	gene with protein product	"""cancer/testis antigen 119"""	608351				12207903	Standard	XM_006713516		Approved	BT-IgSF, MGC35227, Igsf13, VSIG3, CT119	uc003ebw.3	Q5DX21	OTTHUMG00000159387	ENST00000425327.2:c.15A>G	3.37:g.118824025T>C			Somatic				IGSF11_ENST00000441144.2_Silent_p.E5E|IGSF11_ENST00000425327.2_Silent_p.E5E	p.E5E	NM_152538.2	NP_689751.2	WXS	Illumina GAIIx	Phase_I	Q5DX21	IGS11_HUMAN			3	395	-			0					C9JZN0|Q8N4F1|Q8N7T8|Q8NDD2	Silent	SNP	ENST00000425327.2	37	c.15A>G	CCDS2983.1																																																																																				0.358	IGSF11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000355074.2			12	14	0	0	0	1	0	12	14				
KIAA1549	57670	broad.mit.edu	37	7	138552831	138552831	+	Missense_Mutation	SNP	C	C	T			TCGA-WC-A87W-01A-11D-A39W-08	TCGA-WC-A87W-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5b97d5cc-c7d2-4d27-87cb-4c5090079458	addacac8-7364-409d-adce-53703cafaea2	g.chr7:138552831C>T	ENST00000422774.1	-	15	4867	c.4819G>A	c.(4819-4821)Gtc>Atc	p.V1607I	KIAA1549_ENST00000242365.4_Missense_Mutation_p.V1557I|KIAA1549_ENST00000440172.1_Missense_Mutation_p.V1607I			Q9HCM3	K1549_HUMAN	KIAA1549	1607						integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						CAGCCGTTGACCTGGTGTTTC	0.552			O	BRAF	pilocytic astrocytoma																																NSCLC(119;1534 1718 44213 46230 50068)	ENST00000440172.1				Dom	yes		7	7q34	57670	O	KIAA1549			O	BRAF		pilocytic astrocytoma	KIAA1549/BRAF(703)	0				large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						c.(4819-4821)Gtc>Atc		KIAA1549							50.0	58.0	56.0					7																	138552831		2057	4191	6248	SO:0001583	missense	57670					integral to membrane		g.chr7:138552831C>T		CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.4819G>A	7.37:g.138552831C>T	ENSP00000416040:p.Val1607Ile		Somatic				KIAA1549_ENST00000242365.4_Missense_Mutation_p.V1557I|KIAA1549_ENST00000422774.1_Missense_Mutation_p.V1607I	p.V1607I	NM_001164665.1|NM_020910.2	NP_001158137.1|NP_065961.2	WXS	Illumina GAIIx	Phase_I	Q9HCM3	K1549_HUMAN			15	4867	-			1607					B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Missense_Mutation	SNP	ENST00000422774.1	37	c.4819G>A	CCDS56513.1	.	.	.	.	.	.	.	.	.	.	C	6.767	0.510352	0.12883	.	.	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.21734	1.99;2.0;2.0	4.53	3.64	0.41730	.	0.324362	0.32655	N	0.005815	T	0.04497	0.0123	N	0.00707	-1.245	0.26509	N	0.974629	B;B;B;B	0.29552	0.248;0.0;0.208;0.0	B;B;B;B	0.25884	0.064;0.001;0.038;0.001	T	0.37798	-0.9690	10	0.06625	T	0.88	.	8.2926	0.31967	0.0:0.8437:0.0:0.1563	.	1607;391;1607;391	Q9HCM3;Q9HCM3-4;Q9HCM3-2;Q9HCM3-3	K1549_HUMAN;.;.;.	I	1607;1557;1607	ENSP00000406661:V1607I;ENSP00000242365:V1557I;ENSP00000416040:V1607I	ENSP00000242365:V1557I	V	-	1	0	KIAA1549	138203371	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	1.542000	0.36137	2.493000	0.84123	0.655000	0.94253	GTC		0.552	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1			8	16	0	0	0	1	0	8	16				
FAM69B	138311	broad.mit.edu	37	9	139620492	139620492	+	IGR	SNP	A	A	G			TCGA-WC-A87W-01A-11D-A39W-08	TCGA-WC-A87W-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5b97d5cc-c7d2-4d27-87cb-4c5090079458	addacac8-7364-409d-adce-53703cafaea2	g.chr9:139620492A>G	ENST00000371692.4	+	0	1668				SNHG7_ENST00000414282.1_RNA|SNHG7_ENST00000416970.1_RNA|SNHG7_ENST00000391185.1_RNA|SNHG7_ENST00000436596.1_RNA|SNHG7_ENST00000362567.2_RNA|SNHG7_ENST00000447221.1_RNA	NM_152421.3	NP_689634.2	Q5VUD6	FA69B_HUMAN	family with sequence similarity 69, member B							endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				NS(1)|endometrium(3)|large_intestine(2)|lung(1)|prostate(1)	8	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;1.03e-05)|Epithelial(140;0.00013)		TCCCTCATGGAGCAAACCAGG	0.502																																						ENST00000414282.1																			0																																																	SO:0001628	intergenic_variant	0							g.chr9:139620492A>G		CCDS7004.1	9q34.3	2012-08-03			ENSG00000165716	ENSG00000165716			28290	protein-coding gene	gene with protein product		614543				21334309	Standard	NM_152421		Approved	MGC20262, C9orf136	uc004cik.3	Q5VUD6	OTTHUMG00000020940		9.37:g.139620492A>G			Somatic				SNHG7_ENST00000447221.1_RNA|SNHG7_ENST00000416970.1_RNA|SNHG7_ENST00000436596.1_RNA				WXS	Illumina GAIIx	Phase_I					0	451	-								Q5VUD7|Q8N5N0|Q8WYU5	RNA	SNP	ENST00000371692.4	37		CCDS7004.1																																																																																				0.502	FAM69B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055102.1	NM_152421		3	38	0	0	0	1	0	3	38				
NBEAL2	23218	broad.mit.edu	37	3	47033435	47033435	+	Splice_Site	SNP	A	A	T			TCGA-WC-A87W-01A-11D-A39W-08	TCGA-WC-A87W-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5b97d5cc-c7d2-4d27-87cb-4c5090079458	addacac8-7364-409d-adce-53703cafaea2	g.chr3:47033435A>T	ENST00000450053.3	+	9	1210	c.1031A>T	c.(1030-1032)aAg>aTg	p.K344M	NBEAL2_ENST00000292309.5_Splice_Site_p.K344M|NBEAL2_ENST00000383740.2_5'UTR	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	344					blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		CAGAACAGCAAGGTGGGTAGG	0.592																																						ENST00000450053.3																			0				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51						c.(1030-1032)aAg>aTg		neurobeachin-like 2							42.0	40.0	40.0					3																	47033435		2052	4202	6254	SO:0001630	splice_region_variant	23218						binding	g.chr3:47033435A>T	AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"""WD repeat domain containing"""	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.1032+1A>T	3.37:g.47033435A>T			Somatic				NBEAL2_ENST00000383740.2_5'UTR|NBEAL2_ENST00000292309.5_Splice_Site_p.K344M	p.K344M	NM_015175.2	NP_055990.1	WXS	Illumina GAIIx	Phase_I	Q6ZNJ1	NBEL2_HUMAN		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)	9	1210	+		Acute lymphoblastic leukemia(5;0.0534)	344					O60288|Q6P994|Q6UX91|Q8NAC9	Splice_Site	SNP	ENST00000450053.3	37	c.1031A>T	CCDS46817.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.506466	0.85282	.	.	ENSG00000160796	ENST00000292309;ENST00000450053;ENST00000296147	T;T	0.61980	0.06;0.06	4.13	4.13	0.48395	Armadillo-type fold (1);	.	.	.	.	T	0.74816	0.3766	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;0.994	D;P	0.69479	0.964;0.733	T	0.78135	-0.2322	9	0.87932	D	0	.	12.4731	0.55797	1.0:0.0:0.0:0.0	.	337;344	Q6ZNJ1-4;Q6ZNJ1	.;NBEL2_HUMAN	M	344;344;337	ENSP00000292309:K344M;ENSP00000415034:K344M	ENSP00000292309:K344M	K	+	2	0	NBEAL2	47008439	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	6.894000	0.75655	1.723000	0.51488	0.379000	0.24179	AAG		0.592	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064	Missense_Mutation	4	4	0	0	0	1	0	4	4				
PTPRG	5793	broad.mit.edu	37	3	61548042	61548054	+	Splice_Site	DEL	CCCCGGTGAGTGC	CCCCGGTGAGTGC	-	rs201903648|rs2365955	byFrequency	TCGA-WC-A87W-01A-11D-A39W-08	TCGA-WC-A87W-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5b97d5cc-c7d2-4d27-87cb-4c5090079458	addacac8-7364-409d-adce-53703cafaea2	g.chr3:61548042_61548054delCCCCGGTGAGTGC	ENST00000474889.1	+	1	458_462	c.81_85delCCCCGGTGAGTGC	c.(79-87)ttccccggt>ttgt	p.FPG27fs	PTPRG_ENST00000495879.1_3'UTR|PTPRG_ENST00000295874.10_Splice_Site_p.FPG27fs	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	27					brain development (GO:0007420)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of neuron projection development (GO:0010977)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.?(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|liver(2)|lung(15)|ovary(7)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	62				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		TCGTGTGCTTCCCCGGTGAGTGCCGGCCGCCGA	0.648																																						ENST00000474889.1																			1	Unknown(1)	p.?(1)	ovary(1)	NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|liver(2)|lung(15)|ovary(7)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	62						c.(79-87)ttccccggt>ttgt		protein tyrosine phosphatase, receptor type, G																																				SO:0001630	splice_region_variant	5793				transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	identical protein binding|transmembrane receptor protein tyrosine phosphatase activity	g.chr3:61548042_61548054delCCCCGGTGAGTGC	L09247	CCDS2895.1	3p21-p14	2013-02-11			ENSG00000144724	ENSG00000144724		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9671	protein-coding gene	gene with protein product		176886		PTPG		1711217	Standard	NM_002841		Approved	RPTPG	uc003dlb.3	P23470	OTTHUMG00000158660	ENST00000474889.1:c.85+1CCCCGGTGAGTGC>-	3.37:g.61548042_61548054delCCCCGGTGAGTGC			Somatic				PTPRG_ENST00000295874.10_Splice_Site_p.FPG27fs|PTPRG_ENST00000495879.1_3'UTR	p.FPG27fs	NM_002841.3	NP_002832.3	WXS	Illumina GAIIx	Phase_I	P23470	PTPRG_HUMAN		BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)	1	458_462	+			27					B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5	Splice_Site	DEL	ENST00000474889.1	37	c.81_85delCCCCGGTGAGTGC	CCDS2895.1																																																																																				0.648	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351674.1	NM_002841	Frame_Shift_Del	11	144						11	144	---	---	---	---
MIR7162	102466227	broad.mit.edu	37	15	62538522	62538523	+	RNA	INS	-	-	GA	rs3055695|rs540111016|rs370506651	byFrequency	TCGA-WC-A87W-01A-11D-A39W-08	TCGA-WC-A87W-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5b97d5cc-c7d2-4d27-87cb-4c5090079458	addacac8-7364-409d-adce-53703cafaea2	g.chr15:62538522_62538523insGA	ENST00000570077.1	-	0	693_694				AC126323.1_ENST00000408214.1_RNA																							GGGGGCTCCGGGTAGGGGTTCA	0.609																																						ENST00000570077.1																			0																																																			0							g.chr15:62538522_62538523insGA																													15.37:g.62538522_62538523insGA			Somatic								WXS	Illumina GAIIx	Phase_I					0	693_694	-									RNA	INS	ENST00000570077.1	37																																																																																						0.609	hsa-mir-7162.1-004	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000422143.1			2	4						2	4	---	---	---	---
PCGF2	7703	broad.mit.edu	37	17	36891521	36891521	+	Frame_Shift_Del	DEL	C	C	-			TCGA-WC-A87W-01A-11D-A39W-08	TCGA-WC-A87W-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5b97d5cc-c7d2-4d27-87cb-4c5090079458	addacac8-7364-409d-adce-53703cafaea2	g.chr17:36891521delC	ENST00000580830.1	-	12	1691	c.990delG	c.(988-990)gggfs	p.G330fs	PCGF2_ENST00000360797.2_Frame_Shift_Del_p.G330fs|PCGF2_ENST00000578109.1_3'UTR|PCGF2_ENST00000581345.1_Frame_Shift_Del_p.G330fs|PCGF2_ENST00000579882.1_3'UTR|PCGF2_ENST00000585100.1_3'UTR			P35227	PCGF2_HUMAN	polycomb group ring finger 2	330	Pro/Ser-rich.				anterior/posterior pattern specification (GO:0009952)|cellular response to hydrogen peroxide (GO:0070301)|embryonic skeletal system morphogenesis (GO:0048704)|histone acetylation (GO:0016573)|in utero embryonic development (GO:0001701)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	10	Breast(7;9.07e-22)					TCATCTTGCGCCCCCTGCTGG	0.627											OREG0024367	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000580830.1																			0				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	10						c.(988-990)gggfs		polycomb group ring finger 2							17.0	10.0	13.0					17																	36891521		2167	4257	6424	SO:0001589	frameshift_variant	7703				negative regulation of transcription from RNA polymerase II promoter	PcG protein complex	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr17:36891521delC	D13969	CCDS32638.1	17q12	2013-01-09	2005-01-17	2005-01-19		ENSG00000277258		"""RING-type (C3HC4) zinc fingers"", ""Polycomb group ring fingers"""	12929	protein-coding gene	gene with protein product		600346	"""ring finger protein 110"""	ZNF144, RNF110		8325509	Standard	NM_007144		Approved	MEL-18	uc002hqp.1	P35227		ENST00000580830.1:c.990delG	17.37:g.36891521delC	ENSP00000461961:p.Gly330fs		Somatic	OREG0024367	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	866	PCGF2_ENST00000581345.1_Frame_Shift_Del_p.G330fs|PCGF2_ENST00000585100.1_3'UTR|PCGF2_ENST00000360797.2_Frame_Shift_Del_p.G330fs|PCGF2_ENST00000579882.1_3'UTR|PCGF2_ENST00000578109.1_3'UTR	p.G330fs			WXS	Illumina GAIIx	Phase_I	P35227	PCGF2_HUMAN			12	1691	-	Breast(7;9.07e-22)		330			Pro/Ser-rich.		A6NGD8	Frame_Shift_Del	DEL	ENST00000580830.1	37	c.990delG	CCDS32638.1																																																																																				0.627	PCGF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442246.2	NM_007144		2	4						2	4	---	---	---	---
PPP1R15A	23645	broad.mit.edu	37	19	49377681	49377682	+	Frame_Shift_Ins	INS	-	-	G			TCGA-WC-A87W-01A-11D-A39W-08	TCGA-WC-A87W-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5b97d5cc-c7d2-4d27-87cb-4c5090079458	addacac8-7364-409d-adce-53703cafaea2	g.chr19:49377681_49377682insG	ENST00000200453.5	+	2	1460_1461	c.1191_1192insG	c.(1192-1194)gagfs	p.E398fs		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	398	4 X 34 AA approximate repeats.|Glu-rich.|Interaction with SMAD7.				apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		GAGAGGACACAGAGGAGGAGGA	0.53																																						ENST00000200453.5																			0				breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23						c.(1192-1194)gagfs		protein phosphatase 1, regulatory subunit 15A																																				SO:0001589	frameshift_variant	23645				apoptosis|cell cycle arrest|regulation of translation|response to DNA damage stimulus	endoplasmic reticulum	protein binding	g.chr19:49377681_49377682insG	U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14375	protein-coding gene	gene with protein product	"""growth arrest and DNA-damage-inducible 34"""	611048	"""protein phosphatase 1, regulatory (inhibitor) subunit 15A"""			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.1192dupG	19.37:g.49377682_49377682dupG	ENSP00000200453:p.Glu398fs		Somatic					p.E398fs	NM_014330.3	NP_055145.3	WXS	Illumina GAIIx	Phase_I	O75807	PR15A_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)	2	1460_1461	+		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)	398			4 X 34 AA approximate repeats.|Glu-rich.|Interaction with SMAD7.		B4DKQ3|Q6IA96|Q9NVU6	Frame_Shift_Ins	INS	ENST00000200453.5	37	c.1191_1192insG	CCDS12738.1																																																																																				0.530	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330		38	54						38	54	---	---	---	---
LZTS3	9762	broad.mit.edu	37	20	3145615	3145615	+	Frame_Shift_Del	DEL	C	C	-			TCGA-WC-A87W-01A-11D-A39W-08	TCGA-WC-A87W-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5b97d5cc-c7d2-4d27-87cb-4c5090079458	addacac8-7364-409d-adce-53703cafaea2	g.chr20:3145615delC	ENST00000329152.3	-	3	2904	c.1507delG	c.(1507-1509)gccfs	p.A503fs	LZTS3_ENST00000360342.3_Frame_Shift_Del_p.A457fs|LZTS3_ENST00000337576.5_Frame_Shift_Del_p.A457fs			O60299	LZTS3_HUMAN		503						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)											TCCAGGCTGGCCTGCTTGCTG	0.716																																						ENST00000329152.3																			0											c.(1507-1509)gccfs									6.0	6.0	6.0					20																	3145615		2119	4145	6264	SO:0001589	frameshift_variant	0							g.chr20:3145615delC																												ENST00000329152.3:c.1507delG	20.37:g.3145615delC	ENSP00000332123:p.Ala503fs		Somatic				LZTS3_ENST00000360342.3_Frame_Shift_Del_p.A457fs|LZTS3_ENST00000337576.5_Frame_Shift_Del_p.A457fs	p.A503fs			WXS	Illumina GAIIx	Phase_I					3	2904	-								A2A2Q7|D3DVX6|Q8IXX8	Frame_Shift_Del	DEL	ENST00000329152.3	37	c.1507delG	CCDS13049.1																																																																																				0.716	LZTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077715.2			2	4						2	4	---	---	---	---
