#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
CHEK2	11200	broad.mit.edu	37	22	29091787	29091787	+	Nonsense_Mutation	SNP	G	G	C			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr22:29091787G>C	ENST00000405598.1	-	12	1361	c.1170C>G	c.(1168-1170)taC>taG	p.Y390*	CHEK2_ENST00000328354.6_Nonsense_Mutation_p.Y390*|CHEK2_ENST00000382578.1_Nonsense_Mutation_p.Y299*|CHEK2_ENST00000382580.2_Nonsense_Mutation_p.Y433*|CHEK2_ENST00000348295.3_Nonsense_Mutation_p.Y361*|CHEK2_ENST00000544772.1_Nonsense_Mutation_p.Y169*|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000403642.1_Nonsense_Mutation_p.Y299*|CHEK2_ENST00000402731.1_Nonsense_Mutation_p.Y361*|CHEK2_ENST00000464581.1_5'Flank|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000404276.1_Nonsense_Mutation_p.Y390*			O96017	CHK2_HUMAN	checkpoint kinase 2	390	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|T-loop/activation segment.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						CAGGCGCCAAGTAGGTGGGGG	0.423			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																														ENST00000544772.1			yes	Rec		familial breast cancer	22	22q12.1	11200	F	CHK2 checkpoint homolog (S. pombe)			E		breast			0				central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						c.(505-507)taC>taG	Direct reversal of damage;Other conserved DNA damage response genes	checkpoint kinase 2							56.0	57.0	57.0					22																	29091787		2203	4300	6503	SO:0001587	stop_gained	11200				cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	g.chr22:29091787G>C	AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"""CHK2 (checkpoint, S.pombe) homolog"", ""CHK2 checkpoint homolog (S. pombe)"""	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.1170C>G	22.37:g.29091787G>C	ENSP00000386087:p.Tyr390*					CHEK2_ENST00000403642.1_Nonsense_Mutation_p.Y299*|CHEK2_ENST00000405598.1_Nonsense_Mutation_p.Y390*|CHEK2_ENST00000348295.3_Nonsense_Mutation_p.Y361*|CHEK2_ENST00000402731.1_Nonsense_Mutation_p.Y361*|CHEK2_ENST00000382580.2_Nonsense_Mutation_p.Y433*|CHEK2_ENST00000382578.1_Nonsense_Mutation_p.Y299*|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000328354.6_Nonsense_Mutation_p.Y390*|CHEK2_ENST00000404276.1_Nonsense_Mutation_p.Y390*	p.Y169*	NM_001257387.1	NP_001244316.1	O96017	CHK2_HUMAN			12	1943	-			390			FHA.		A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Nonsense_Mutation	SNP	ENST00000405598.1	37	c.507C>G	CCDS13843.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	48|48	14.325224|14.325224	0.99790|0.99790	.|.	.|.	ENSG00000183765|ENSG00000183765	ENST00000434810|ENST00000348295;ENST00000382578;ENST00000544772;ENST00000328354;ENST00000404276;ENST00000405598;ENST00000382580;ENST00000403642;ENST00000402731	.|.	.|.	.|.	5.89|5.89	2.09|2.09	0.27110|0.27110	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.27027|.	0.0662|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.15809|.	-1.0424|.	4|.	.|0.02654	.|T	.|1	-30.0052|-30.0052	7.6633|7.6633	0.28415|0.28415	0.4602:0.0:0.5398:0.0|0.4602:0.0:0.5398:0.0	.|.	.|.	.|.	.|.	S|X	134|361;299;169;390;390;390;433;299;361	.|.	.|ENSP00000329178:Y390X	T|Y	-|-	2|3	0|2	CHEK2|CHEK2	27421787|27421787	0.999000|0.999000	0.42202|0.42202	0.797000|0.797000	0.32132|0.32132	0.912000|0.912000	0.54170|0.54170	0.561000|0.561000	0.23515|0.23515	0.499000|0.499000	0.27970|0.27970	0.650000|0.650000	0.86243|0.86243	ACT|TAC		0.423	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735		8	95	0	0	0	0.335167	0	8	95				
SP140	11262	broad.mit.edu	37	2	231135315	231135315	+	Missense_Mutation	SNP	G	G	A			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr2:231135315G>A	ENST00000392045.3	+	15	1573	c.1459G>A	c.(1459-1461)Gca>Aca	p.A487T	SP140_ENST00000343805.6_Missense_Mutation_p.A427T|SP140_ENST00000417495.3_Missense_Mutation_p.A373T|SP140_ENST00000486687.2_Missense_Mutation_p.A411T|SP140_ENST00000350136.5_Missense_Mutation_p.A356T|SP140_ENST00000420434.3_Missense_Mutation_p.A460T	NM_007237.4	NP_009168.4	Q13342	SP140_HUMAN	SP140 nuclear body protein	487					defense response (GO:0006952)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		TGTGGATATTGCAAACAACTC	0.308																																						ENST00000392045.3																			0				NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12						c.(1459-1461)Gca>Aca		SP140 nuclear body protein							73.0	67.0	69.0					2																	231135315		1798	4067	5865	SO:0001583	missense	11262				defense response	cytoplasm|nuclear envelope|nucleolus|nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr2:231135315G>A	U63420	CCDS33392.1, CCDS42831.1, CCDS63149.1, CCDS63150.1, CCDS63151.1	2q37.1	2013-01-28			ENSG00000079263	ENSG00000079263		"""Zinc fingers, PHD-type"""	17133	protein-coding gene	gene with protein product		608602				8695863, 8910577, 12368356	Standard	NM_001005176		Approved	LYSP100-B, LYSP100-A	uc002vql.3	Q13342	OTTHUMG00000153670	ENST00000392045.3:c.1459G>A	2.37:g.231135315G>A	ENSP00000375899:p.Ala487Thr					SP140_ENST00000417495.3_Missense_Mutation_p.A373T|SP140_ENST00000486687.2_Missense_Mutation_p.A411T|SP140_ENST00000420434.3_Missense_Mutation_p.A460T|SP140_ENST00000350136.5_Missense_Mutation_p.A356T|SP140_ENST00000343805.6_Missense_Mutation_p.A427T	p.A487T	NM_007237.4	NP_009168.4	Q13342	LY10_HUMAN		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)	15	1573	+		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)	487					E7ESH9|E7EUR5|E9PFJ6|Q0VGE5|Q13341|Q3KR17|Q4ZG66|Q53TG1|Q6NSG4|Q92881|Q96TG3	Missense_Mutation	SNP	ENST00000392045.3	37	c.1459G>A	CCDS42831.1	.	.	.	.	.	.	.	.	.	.	G	4.033	0.003742	0.07866	.	.	ENSG00000079263	ENST00000486687;ENST00000350136;ENST00000392045;ENST00000417495;ENST00000343805;ENST00000420434	T;T;T;T;T	0.58210	0.56;0.89;0.63;0.35;0.64	2.98	0.0753	0.14399	.	.	.	.	.	T	0.26159	0.0638	N	0.14661	0.345	0.09310	N	1	P;B;B;B	0.36048	0.534;0.079;0.435;0.016	B;B;B;B	0.29353	0.068;0.019;0.101;0.014	T	0.11966	-1.0566	9	0.21014	T	0.42	-3.8702	5.5523	0.17097	0.3948:0.0:0.6052:0.0	.	460;373;427;487	E7EUR5;E7ESH9;E9PFJ6;Q13342	.;.;.;LY10_HUMAN	T	411;356;487;373;427;460	ENSP00000440107:A411T;ENSP00000345846:A356T;ENSP00000375899:A487T;ENSP00000342096:A427T;ENSP00000398210:A460T	ENSP00000342096:A427T	A	+	1	0	SP140	230843559	0.026000	0.19158	0.000000	0.03702	0.001000	0.01503	-0.063000	0.11655	0.013000	0.14918	-0.145000	0.13849	GCA		0.308	SP140-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000332015.1	NM_007237		12	141	0	0	0	0.500413	0	12	141				
LOC101927079	101927079	broad.mit.edu	37	15	22332570	22332570	+	RNA	SNP	T	T	C	rs551210093		TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr15:22332570T>C	ENST00000558896.1	+	0	377																											CCCATGCTCATCTGCTCCAAT	0.398																																						ENST00000558896.1																			0																																																			0							g.chr15:22332570T>C																													15.37:g.22332570T>C														0	377	+									RNA	SNP	ENST00000558896.1	37																																																																																						0.398	RP11-69H14.6-001	KNOWN	basic	sense_overlapping	sense_overlapping	OTTHUMT00000417625.1			4	239	0	0	0	0.150653	0	4	239				
GYS1	2997	broad.mit.edu	37	19	49488755	49488755	+	Silent	SNP	G	G	A			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr19:49488755G>A	ENST00000323798.3	-	5	982	c.786C>T	c.(784-786)acC>acT	p.T262T	GYS1_ENST00000540532.1_Silent_p.T182T|GYS1_ENST00000541188.1_Silent_p.T182T|GYS1_ENST00000263276.6_Silent_p.T198T|GYS1_ENST00000544287.1_Intron|GYS1_ENST00000457974.1_5'Flank	NM_002103.4	NP_002094.2	P13807	GYS1_HUMAN	glycogen synthase 1 (muscle)	262					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|heart development (GO:0007507)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|inclusion body (GO:0016234)|membrane (GO:0016020)	glucose binding (GO:0005536)|glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000164)|all cancers(93;0.000226)|GBM - Glioblastoma multiforme(486;0.00561)|Epithelial(262;0.0286)		CCTCGATGGCGGTGATCTGGG	0.582																																						ENST00000323798.3																			0				breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						c.(784-786)acC>acT		glycogen synthase 1 (muscle)							127.0	96.0	107.0					19																	49488755		2203	4300	6503	SO:0001819	synonymous_variant	2997				glucose metabolic process|glycogen biosynthetic process	cytosol	glycogen (starch) synthase activity|protein binding	g.chr19:49488755G>A		CCDS12747.1, CCDS54292.1	19q13.3	2013-02-22			ENSG00000104812	ENSG00000104812	2.4.1.11	"""Glycosyltransferase group 1 domain containing"""	4706	protein-coding gene	gene with protein product		138570		GYS			Standard	NM_002103		Approved	GSY	uc002plp.3	P13807	OTTHUMG00000150723	ENST00000323798.3:c.786C>T	19.37:g.49488755G>A						GYS1_ENST00000540532.1_Silent_p.T182T|GYS1_ENST00000541188.1_Silent_p.T182T|GYS1_ENST00000263276.6_Silent_p.T198T|GYS1_ENST00000544287.1_Intron	p.T262T	NM_002103.4	NP_002094.2	P13807	GYS1_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.000164)|all cancers(93;0.000226)|GBM - Glioblastoma multiforme(486;0.00561)|Epithelial(262;0.0286)	5	982	-		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)	262					Q9BTT9	Silent	SNP	ENST00000323798.3	37	c.786C>T	CCDS12747.1																																																																																				0.582	GYS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319791.1	NM_002103		3	74	0	0	0	0.115264	0	3	74				
PSMB7	5695	broad.mit.edu	37	9	127177679	127177679	+	Missense_Mutation	SNP	G	G	A	rs143961480		TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr9:127177679G>A	ENST00000259457.3	-	1	39	c.26C>T	c.(25-27)cCa>cTa	p.P9L	PSMB7_ENST00000498485.1_5'Flank|PSMB7_ENST00000536392.1_Missense_Mutation_p.P9L	NM_002799.3	NP_002790.1	Q99436	PSB7_HUMAN	proteasome (prosome, macropain) subunit, beta type, 7	9					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|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 polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)			breast(1)|endometrium(1)|kidney(1)|lung(1)|pancreas(1)	5						TCCAACTGGTGGAGCATACAC	0.607											OREG0019476	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000536392.1																			0				breast(1)|endometrium(1)|kidney(1)|lung(1)|pancreas(1)	5						c.(25-27)cCa>cTa		proteasome (prosome, macropain) subunit, beta type, 7		G	LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	43.0	43.0	43.0		26	2.3	0.0	9	dbSNP_134	43	0,8600		0,0,4300	no	missense	PSMB7	NM_002799.2	98	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	9/278	127177679	1,13005	2203	4300	6503	SO:0001583	missense	5695				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|interspecies interaction between organisms|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex	threonine-type endopeptidase activity	g.chr9:127177679G>A	AJ420455	CCDS6855.1	9q34.11-q34.12	2008-02-05			ENSG00000136930	ENSG00000136930		"""Proteasome (prosome, macropain) subunits"""	9544	protein-coding gene	gene with protein product		604030				8811196	Standard	NM_002799		Approved	Z	uc004boj.4	Q99436	OTTHUMG00000021042	ENST00000259457.3:c.26C>T	9.37:g.127177679G>A	ENSP00000259457:p.Pro9Leu		OREG0019476	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1555	PSMB7_ENST00000259457.3_Missense_Mutation_p.P9L	p.P9L			Q99436	PSB7_HUMAN			1	42	-			9					B4E0P1|Q5TBG6|Q96AG8|Q9BWA7	Missense_Mutation	SNP	ENST00000259457.3	37	c.26C>T	CCDS6855.1	.	.	.	.	.	.	.	.	.	.	G	9.026	0.986104	0.18889	2.27E-4	0.0	ENSG00000136930	ENST00000259457;ENST00000536392;ENST00000441097	T;T;T	0.32753	1.44;1.44;1.44	6.17	2.28	0.28536	.	0.692388	0.14648	N	0.306794	T	0.15912	0.0383	N	0.13168	0.305	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.30966	-0.9960	10	0.10377	T	0.69	-32.2283	10.5372	0.45011	0.0713:0.4231:0.5056:0.0	.	9;9	B4E0P1;Q99436	.;PSB7_HUMAN	L	9	ENSP00000259457:P9L;ENSP00000440247:P9L;ENSP00000393157:P9L	ENSP00000259457:P9L	P	-	2	0	PSMB7	126217500	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.406000	0.21032	0.165000	0.19558	-0.150000	0.13652	CCA		0.607	PSMB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055525.1	NM_002799		3	76	0	0	0	0.115264	0	3	76				
XRN2	22803	broad.mit.edu	37	20	21346221	21346221	+	Missense_Mutation	SNP	G	G	A			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr20:21346221G>A	ENST00000377191.3	+	26	2430	c.2335G>A	c.(2335-2337)Gca>Aca	p.A779T	XRN2_ENST00000430571.2_Missense_Mutation_p.A703T|XRN2_ENST00000539513.1_Missense_Mutation_p.A725T	NM_012255.3	NP_036387.2	Q9H0D6	XRN2_HUMAN	5'-3' exoribonuclease 2	779					cell growth (GO:0016049)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA catabolic process (GO:0006401)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA processing (GO:0006396)|spermatogenesis (GO:0007283)	aggresome (GO:0016235)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|5'-3' exoribonuclease activity (GO:0004534)|nuclease activity (GO:0004518)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(6)|large_intestine(10)|lung(12)|ovary(1)|skin(5)	39						AAAGCCAGCAGCAGTACTGAA	0.438																																						ENST00000377191.3																			0				endometrium(5)|kidney(6)|large_intestine(10)|lung(12)|ovary(1)|skin(5)	39						c.(2335-2337)Gca>Aca		5'-3' exoribonuclease 2							96.0	95.0	96.0					20																	21346221		2203	4300	6503	SO:0001583	missense	22803				cell growth|DNA catabolic process, exonucleolytic|mRNA processing|regulation of transcription, DNA-dependent|RNA catabolic process|spermatogenesis|transcription termination, DNA-dependent	nucleolus	5'-3' exoribonuclease activity|nucleic acid binding|protein binding|zinc ion binding	g.chr20:21346221G>A	AF064257	CCDS13144.1	20p11.2-p11.1	2011-09-12			ENSG00000088930	ENSG00000088930	3.1.13.-		12836	protein-coding gene	gene with protein product		608851				10409438	Standard	NM_012255		Approved		uc002wsf.1	Q9H0D6	OTTHUMG00000032025	ENST00000377191.3:c.2335G>A	20.37:g.21346221G>A	ENSP00000366396:p.Ala779Thr					XRN2_ENST00000430571.2_Missense_Mutation_p.A703T|XRN2_ENST00000539513.1_Missense_Mutation_p.A725T	p.A779T	NM_012255.3	NP_036387.2	Q9H0D6	XRN2_HUMAN			26	2430	+			779					Q3L8N4|Q6KGZ9|Q9BQL1|Q9NTW0|Q9NXS6|Q9UL53	Missense_Mutation	SNP	ENST00000377191.3	37	c.2335G>A	CCDS13144.1	.	.	.	.	.	.	.	.	.	.	G	11.20	1.569493	0.28003	.	.	ENSG00000088930	ENST00000377191;ENST00000430571;ENST00000539513	T;T;T	0.18338	2.22;2.22;2.22	5.95	0.00139	0.14046	.	0.422063	0.29572	N	0.011779	T	0.05456	0.0144	N	0.02011	-0.69	0.19300	N	0.999978	B	0.02656	0.0	B	0.01281	0.0	T	0.40308	-0.9570	10	0.22706	T	0.39	-0.1946	9.8893	0.41281	0.3764:0.4698:0.1538:0.0	.	779	Q9H0D6	XRN2_HUMAN	T	779;703;725	ENSP00000366396:A779T;ENSP00000413548:A703T;ENSP00000441113:A725T	ENSP00000366396:A779T	A	+	1	0	XRN2	21294221	1.000000	0.71417	0.956000	0.39512	0.422000	0.31414	1.577000	0.36515	0.132000	0.18615	-0.768000	0.03414	GCA		0.438	XRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078273.2	NM_012255		3	103	0	0	0	0.115264	0	3	103				
TSSC2	650368	broad.mit.edu	37	11	3427845	3427845	+	RNA	SNP	C	C	T			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr11:3427845C>T	ENST00000529482.1	+	0	962									tumor suppressing subtransferable candidate 2 pseudogene																		CTTCAAGTGGCAGGAGCAGAA	0.587																																						ENST00000529482.1																			0																																																			0							g.chr11:3427845C>T			11p15.4	2014-06-05	2008-06-30		ENSG00000223756	ENSG00000223756			12384	pseudogene	pseudogene	"""tumor-supressing STF cDNA 2"", ""asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase) (ALG1) pseudogene"""	608999	"""tumor suppressing subtransferable candidate 2"""			9403053	Standard	NR_024248		Approved				OTTHUMG00000011705		11.37:g.3427845C>T														0	962	+									RNA	SNP	ENST00000529482.1	37																																																																																						0.587	TSSC2-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000392020.1			4	67	0	0	0	0.150653	0	4	67				
GON4L	54856	broad.mit.edu	37	1	155796629	155796629	+	Splice_Site	SNP	C	C	T			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr1:155796629C>T	ENST00000368331.1	-	3	744	c.696G>A	c.(694-696)atG>atA	p.M232I	GON4L_ENST00000361040.5_Splice_Site_p.M232I|GON4L_ENST00000471341.1_5'UTR|GON4L_ENST00000437809.1_Splice_Site_p.M232I|GON4L_ENST00000271883.5_Splice_Site_p.M232I	NM_001282858.1|NM_001282860.1	NP_001269787.1|NP_001269789.1	Q3T8J9	GON4L_HUMAN	gon-4-like (C. elegans)	232					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	45	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					AAAGCCTACCCATTGGAATGA	0.383																																						ENST00000437809.1																			0				NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	45						c.e3+1		gon-4-like (C. elegans)							81.0	80.0	81.0					1																	155796629		2203	4300	6503	SO:0001630	splice_region_variant	54856				regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding	g.chr1:155796629C>T	AB046826	CCDS1121.1, CCDS44242.1, CCDS60296.1	1q22	2013-10-31	2006-11-08	2006-02-16	ENSG00000116580	ENSG00000116580			25973	protein-coding gene	gene with protein product		610393	"""gon-4 homolog (C.elegans)"""	GON4		16545939, 21454521	Standard	XM_005245283		Approved	FLJ20203, GON-4	uc001fly.1	Q3T8J9	OTTHUMG00000014106	ENST00000368331.1:c.697+1G>A	1.37:g.155796629C>T						GON4L_ENST00000471341.1_5'UTR|GON4L_ENST00000361040.5_Splice_Site_p.M232_splice|GON4L_ENST00000271883.5_Splice_Site_p.M232_splice|GON4L_ENST00000368331.1_Splice_Site_p.M232_splice	p.M232_splice			Q3T8J9	GON4L_HUMAN			3	818	-	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)		232					B7ZBL4|Q14C93|Q3T8J8|Q5VYZ5|Q5W0D5|Q6AWA6|Q6P1Q6|Q7Z3L3|Q8IY79|Q9BQI1|Q9HCG6	Splice_Site	SNP	ENST00000368331.1	37	c.697_splice		.	.	.	.	.	.	.	.	.	.	C	10.23	1.292817	0.23564	.	.	ENSG00000116580	ENST00000437809;ENST00000368331;ENST00000271883;ENST00000539959;ENST00000361040	T;T;T;T	0.11385	2.98;2.98;2.98;2.78	4.47	2.38	0.29361	.	0.300219	0.27851	N	0.017588	T	0.01905	0.0060	L	0.27053	0.805	0.21802	N	0.999533	B;B;B;B	0.19706	0.022;0.001;0.022;0.038	B;B;B;B	0.18871	0.023;0.003;0.006;0.014	T	0.46048	-0.9219	10	0.17832	T	0.49	.	6.628	0.22841	0.1984:0.5914:0.2102:0.0	.	232;232;232;232	A4PB68;Q3T8J9-2;Q3T8J9;Q3T8J9-3	.;.;GON4L_HUMAN;.	I	232	ENSP00000396117:M232I;ENSP00000357315:M232I;ENSP00000271883:M232I;ENSP00000354322:M232I	ENSP00000271883:M232I	M	-	3	0	GON4L	154063253	0.990000	0.36364	1.000000	0.80357	0.993000	0.82548	0.449000	0.21744	1.202000	0.43218	0.491000	0.48974	ATG		0.383	GON4L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_032292	Missense_Mutation	5	77	0	0	0	0.217242	0	5	77				
PTCH1	5727	broad.mit.edu	37	9	98229625	98229625	+	Missense_Mutation	SNP	G	G	A			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr9:98229625G>A	ENST00000331920.6	-	15	2632	c.2333C>T	c.(2332-2334)aCg>aTg	p.T778M	PTCH1_ENST00000429896.2_Missense_Mutation_p.T627M|PTCH1_ENST00000437951.1_Missense_Mutation_p.T712M|PTCH1_ENST00000375274.2_Missense_Mutation_p.T777M|PTCH1_ENST00000421141.1_Missense_Mutation_p.T627M|PTCH1_ENST00000430669.2_Missense_Mutation_p.T712M|PTCH1_ENST00000418258.1_Missense_Mutation_p.T627M	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	778					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)	p.T778M(2)|p.T777M(1)		NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				TACAATGTCCGTAAGGTCCAG	0.473																																						ENST00000430669.2																			3	Substitution - Missense(3)	p.T778M(2)|p.T777M(1)	large_intestine(3)	NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490	GRCh37	CI972684	PTCH1	I		c.(2134-2136)aCg>aTg		patched 1							103.0	103.0	103.0					9																	98229625		2203	4300	6503	SO:0001583	missense	5727				embryonic limb morphogenesis|negative regulation of multicellular organism growth|protein processing|regulation of smoothened signaling pathway|smoothened signaling pathway	integral to plasma membrane	hedgehog receptor activity	g.chr9:98229625G>A	AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"""patched (Drosophila) homolog"", ""patched homolog (Drosophila)"", ""patched homolog 1 (Drosophila)"""	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.2333C>T	9.37:g.98229625G>A	ENSP00000332353:p.Thr778Met					PTCH1_ENST00000429896.2_Missense_Mutation_p.T627M|PTCH1_ENST00000421141.1_Missense_Mutation_p.T627M|PTCH1_ENST00000375274.2_Missense_Mutation_p.T777M|PTCH1_ENST00000418258.1_Missense_Mutation_p.T627M|PTCH1_ENST00000437951.1_Missense_Mutation_p.T712M|PTCH1_ENST00000331920.6_Missense_Mutation_p.T778M	p.T712M			Q13635	PTC1_HUMAN			15	2720	-		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)	778					A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Missense_Mutation	SNP	ENST00000331920.6	37	c.2135C>T	CCDS6714.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.742987	0.89573	.	.	ENSG00000185920	ENST00000331920;ENST00000437951;ENST00000421141;ENST00000418258;ENST00000375275;ENST00000430669;ENST00000429896;ENST00000375274	D;D;D;D;D;D;D	0.90732	-2.72;-2.71;-2.7;-2.7;-2.71;-2.7;-2.72	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	D	0.94535	0.8240	M	0.71036	2.16	0.80722	D	1	D;D;D	0.69078	0.997;0.994;0.996	P;P;P	0.61592	0.891;0.803;0.883	D	0.94031	0.7301	10	0.52906	T	0.07	-14.1169	19.894	0.96945	0.0:0.0:1.0:0.0	.	712;777;778	Q13635-3;Q13635-2;Q13635	.;.;PTC1_HUMAN	M	778;712;627;627;214;712;627;777	ENSP00000332353:T778M;ENSP00000389744:T712M;ENSP00000399981:T627M;ENSP00000396135:T627M;ENSP00000410287:T712M;ENSP00000414823:T627M;ENSP00000364423:T777M	ENSP00000332353:T778M	T	-	2	0	PTCH1	97269446	1.000000	0.71417	0.970000	0.41538	0.973000	0.67179	9.476000	0.97823	2.700000	0.92200	0.591000	0.81541	ACG		0.473	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264		4	152	0	0	0	0.150653	0	4	152				
E2F3	1871	broad.mit.edu	37	6	20402610	20402610	+	Silent	SNP	C	C	T			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr6:20402610C>T	ENST00000346618.3	+	1	213	c.147C>T	c.(145-147)gcC>gcT	p.A49A	E2F3_ENST00000535432.1_5'Flank	NM_001949.4	NP_001940.1	O00716	E2F3_HUMAN	E2F transcription factor 3	49	Poly-Ala.				mitotic cell cycle (GO:0000278)|Notch signaling pathway (GO:0007219)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(3)	7	all_cancers(95;0.154)|all_epithelial(95;0.0585)|Breast(50;0.146)|Ovarian(93;0.148)		OV - Ovarian serous cystadenocarcinoma(7;0.0068)|all cancers(50;0.0148)|Epithelial(50;0.0562)			ccgccgccgccgctgccgccg	0.741																																						ENST00000346618.3																			0				central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(3)	7						c.(145-147)gcC>gcT		E2F transcription factor 3							14.0	21.0	18.0					6																	20402610		2127	4171	6298	SO:0001819	synonymous_variant	1871				G1 phase of mitotic cell cycle|G2 phase of mitotic cell cycle|transcription initiation from RNA polymerase II promoter	transcription factor complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity	g.chr6:20402610C>T	Y10479	CCDS4545.1, CCDS58999.1	6p22	2008-08-29			ENSG00000112242	ENSG00000112242			3115	protein-coding gene	gene with protein product		600427				8246996	Standard	NM_001949		Approved		uc003nda.2	O00716	OTTHUMG00000016389	ENST00000346618.3:c.147C>T	6.37:g.20402610C>T							p.A49A	NM_001949.4	NP_001940.1	O00716	E2F3_HUMAN	OV - Ovarian serous cystadenocarcinoma(7;0.0068)|all cancers(50;0.0148)|Epithelial(50;0.0562)		1	213	+	all_cancers(95;0.154)|all_epithelial(95;0.0585)|Breast(50;0.146)|Ovarian(93;0.148)		49			Poly-Ala.		Q15000|Q68DT0|Q9BZ44	Silent	SNP	ENST00000346618.3	37	c.147C>T	CCDS4545.1																																																																																				0.741	E2F3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043828.1			3	75	0	0	0	0.115264	0	3	75				
SNURF	8926	broad.mit.edu	37	15	25230184	25230184	+	Intron	SNP	G	G	A			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr15:25230184G>A	ENST00000551312.2	+	6	1184				SNHG14_ENST00000551361.1_RNA|SNHG14_ENST00000551631.2_RNA|SNORD64_ENST00000386683.1_RNA|SNHG14_ENST00000459433.1_RNA|SNORD108_ENST00000459332.1_RNA			Q9Y675	SNURF_HUMAN	SNRPN upstream reading frame							nucleus (GO:0005634)				breast(2)|large_intestine(2)|lung(1)	5		all_cancers(20;1.4e-21)|Breast(32;0.000625)		all cancers(64;3.48e-07)|Epithelial(43;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0142)		ACTATCTGCAGGAATTTATTT	0.373																																						ENST00000551631.2																			0																																																	SO:0001627	intron_variant	0							g.chr15:25230184G>A		CCDS10016.1	15q11.2	2013-08-27			ENSG00000214265	ENSG00000214265			11171	protein-coding gene	gene with protein product						10318933	Standard	NM_022804		Approved		uc001ywu.3	Q9Y675	OTTHUMG00000129181	ENST00000551312.2:c.213+2600G>A	15.37:g.25230184G>A						SNHG14_ENST00000551361.1_RNA		NR_001293.1						0	887	+								A6NCW2	RNA	SNP	ENST00000551312.2	37		CCDS10016.1																																																																																				0.373	SNURF-002	KNOWN	basic|appris_candidate_longest|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000413842.1	NM_005678		3	61	0	0	0	0.115264	0	3	61				
NRAS	4893	broad.mit.edu	37	1	115256529	115256529	+	Missense_Mutation	SNP	T	T	C	rs11554290	byFrequency	TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr1:115256529T>C	ENST00000369535.4	-	3	435	c.182A>G	c.(181-183)cAa>cGa	p.Q61R		NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	61			Q -> K (in CMNS and NCMS; somatic mutation). {ECO:0000269|PubMed:23392294}.|Q -> R (in CMNS, NCMS and KNEN; also found in lung carcinoma cell and melanoma; dbSNP:rs11554290). {ECO:0000269|PubMed:18633438, ECO:0000269|PubMed:22499344, ECO:0000269|PubMed:23392294, ECO:0000269|PubMed:3276402}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.Q61R(817)|p.Q61L(175)|p.Q61P(23)|p.Q61K(1)		NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTACTCTTCTTGTCCAGCTGT	0.458	Q61L(C3A_LIVER)|Q61L(HEPG2_LIVER)|Q61L(HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(IPC298_SKIN)|Q61L(KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(MELJUSO_SKIN)|Q61L(MHHES1_BONE)|Q61L(MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61P(TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(HT1197_URINARY_TRACT)|Q61R(KMS27_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(KU1919_URINARY_TRACT)|Q61R(NCIH2347_LUNG)|Q61R(ONS76_CENTRAL_NERVOUS_SYSTEM)|Q61R(SKMEL2_SKIN)|Q61R(SW1271_LUNG)|Q61R(TT2609C02_THYROID)	50	Mis		"""melanoma, MM, AML, thyroid"""				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																												ENST00000369535.4	Q61L(C3A_LIVER)|Q61L(HEPG2_LIVER)|Q61L(HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(IPC298_SKIN)|Q61L(KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(MELJUSO_SKIN)|Q61L(MHHES1_BONE)|Q61L(MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61P(TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(HT1197_URINARY_TRACT)|Q61R(KMS27_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(KU1919_URINARY_TRACT)|Q61R(NCIH2347_LUNG)|Q61R(ONS76_CENTRAL_NERVOUS_SYSTEM)|Q61R(SKMEL2_SKIN)|Q61R(SW1271_LUNG)|Q61R(TT2609C02_THYROID)	50		Dom	yes		1	1p13.2	4893	Mis	neuroblastoma RAS viral (v-ras) oncogene homolog			"""L, E"""			"""melanoma, MM, AML, thyroid"""		1016	Substitution - Missense(1016)	p.Q61R(817)|p.Q61L(175)|p.Q61P(23)|p.Q61K(1)	skin(466)|thyroid(279)|haematopoietic_and_lymphoid_tissue(124)|NS(50)|large_intestine(27)|lung(17)|urinary_tract(11)|adrenal_gland(7)|liver(7)|breast(7)|soft_tissue(4)|testis(3)|endometrium(3)|ovary(3)|central_nervous_system(2)|pancreas(2)|eye(1)|prostate(1)|meninges(1)|autonomic_ganglia(1)	NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085						c.(181-183)cAa>cGa		neuroblastoma RAS viral (v-ras) oncogene homolog							180.0	156.0	164.0					1																	115256529		2203	4300	6503	SO:0001583	missense	4893	Noonan syndrome	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	Golgi membrane|plasma membrane	GTP binding|GTPase activity	g.chr1:115256529T>C	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.182A>G	1.37:g.115256529T>C	ENSP00000358548:p.Gln61Arg	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)					p.Q61R	NM_002524.4	NP_002515.1	P01111	RASN_HUMAN		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	3	435	-	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)	61		Q -> K (in neuroblastoma cell).|Q -> R (in lung carcinoma cell and melanoma; dbSNP:rs11554290).			Q14971|Q15104|Q15282	Missense_Mutation	SNP	ENST00000369535.4	37	c.182A>G	CCDS877.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.004139	0.74932	.	.	ENSG00000213281	ENST00000369535	D	0.83673	-1.75	5.08	5.08	0.68730	Small GTP-binding protein domain (1);	0.000000	0.53938	U	0.000043	D	0.86489	0.5945	M	0.92604	3.325	0.80722	D	1	B	0.28512	0.214	B	0.39590	0.304	D	0.88255	0.2919	10	0.66056	D	0.02	.	15.0132	0.71565	0.0:0.0:0.0:1.0	rs11554290;rs11554290	61	P01111	RASN_HUMAN	R	61	ENSP00000358548:Q61R	ENSP00000358548:Q61R	Q	-	2	0	NRAS	115058052	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.761000	0.85260	2.120000	0.65058	0.533000	0.62120	CAA		0.458	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033395.2	NM_002524		85	172	0	0	0	0.870114	0	85	172				
DIRAS2	54769	broad.mit.edu	37	9	93375575	93375575	+	Missense_Mutation	SNP	C	C	A			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr9:93375575C>A	ENST00000375765.3	-	2	923	c.535G>T	c.(535-537)Gac>Tac	p.D179Y		NM_017594.3	NP_060064.2	Q96HU8	DIRA2_HUMAN	DIRAS family, GTP-binding RAS-like 2	179					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)	p.D179N(1)		kidney(1)|large_intestine(6)|lung(3)|skin(2)	12						TTTTTCCCGTCGATCTGGAGA	0.547																																						ENST00000375765.3																			1	Substitution - Missense(1)	p.D179N(1)	skin(1)	kidney(1)|large_intestine(6)|lung(3)|skin(2)	12						c.(535-537)Gac>Tac		DIRAS family, GTP-binding RAS-like 2							166.0	149.0	155.0					9																	93375575		2203	4300	6503	SO:0001583	missense	0				small GTPase mediated signal transduction	intracellular|plasma membrane	GTP binding|GTPase activity	g.chr9:93375575C>A	AB076889	CCDS6687.1	9q22.32	2014-05-09			ENSG00000165023	ENSG00000165023			19323	protein-coding gene	gene with protein product		607863				12194967	Standard	NM_017594		Approved	Di-Ras2, DKFZp761C07121	uc004aqx.1	Q96HU8	OTTHUMG00000020196	ENST00000375765.3:c.535G>T	9.37:g.93375575C>A	ENSP00000364919:p.Asp179Tyr						p.D179Y	NM_017594.3	NP_060064.2	Q96HU8	DIRA2_HUMAN			2	923	-			179					B3KVM2	Missense_Mutation	SNP	ENST00000375765.3	37	c.535G>T	CCDS6687.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.277498	0.80580	.	.	ENSG00000165023	ENST00000375765	T	0.70164	-0.46	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	T	0.69033	0.3066	L	0.29908	0.895	0.80722	D	1	D	0.57257	0.979	P	0.55303	0.773	T	0.70521	-0.4849	10	0.54805	T	0.06	.	18.3183	0.90229	0.0:1.0:0.0:0.0	.	179	Q96HU8	DIRA2_HUMAN	Y	179	ENSP00000364919:D179Y	ENSP00000364919:D179Y	D	-	1	0	DIRAS2	92415395	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	7.473000	0.81007	2.884000	0.98904	0.655000	0.94253	GAC		0.547	DIRAS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053012.1			3	58	1	0	0.115264	0.115264	0.123123	3	58				
PCDHGB4	8641	broad.mit.edu	37	5	140768722	140768722	+	Missense_Mutation	SNP	A	A	G			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr5:140768722A>G	ENST00000519479.1	+	1	1271	c.1271A>G	c.(1270-1272)gAt>gGt	p.D424G	PCDHGB3_ENST00000576222.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_003736.2|NM_018925.2|NM_032098.1	NP_003727.1|NP_061748.1|NP_115269.1	Q9UN71	PCDGG_HUMAN	protocadherin gamma subfamily B, 4	424	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(9)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(2)	37			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGGCAACAGATCGGGGCAAG	0.448																																						ENST00000519479.1																			0				endometrium(9)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(2)	37						c.(1270-1272)gAt>gGt									120.0	126.0	124.0					5																	140768722		1954	4154	6108	SO:0001583	missense	0							g.chr5:140768722A>G	AF152520	CCDS54928.1, CCDS75337.1	5q31	2010-01-26				ENSG00000253953		"""Cadherins / Protocadherins : Clustered"""	8711	other	protocadherin	"""fibroblast cadherin FIB2"", ""cadherin 20"""	603058				10380929	Standard	NM_003736		Approved	FIB2, CDH20, PCDH-GAMMA-B4		Q9UN71		ENST00000519479.1:c.1271A>G	5.37:g.140768722A>G	ENSP00000428288:p.Asp424Gly					PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA4_ENST00000571252.1_Intron	p.D424G	NM_003736.2|NM_018925.2|NM_032098.1	NP_003727.1|NP_061748.1|NP_115269.1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		1	1271	+								O15099|Q2M267|Q9UN64	Missense_Mutation	SNP	ENST00000519479.1	37	c.1271A>G	CCDS54928.1	.	.	.	.	.	.	.	.	.	.	.	14.92	2.680233	0.47886	.	.	ENSG00000253953	ENST00000519479	T	0.68765	-0.35	5.14	5.14	0.70334	Cadherin (4);Cadherin-like (1);	.	.	.	.	D	0.90669	0.7073	H	0.99884	4.89	0.35060	D	0.761495	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.97373	0.9977	9	0.87932	D	0	.	15.0172	0.71594	1.0:0.0:0.0:0.0	.	424;424	Q9UN71-2;Q9UN71	.;PCDGG_HUMAN	G	424	ENSP00000428288:D424G	ENSP00000428288:D424G	D	+	2	0	PCDHGB4	140748906	1.000000	0.71417	0.064000	0.19789	0.032000	0.12392	8.808000	0.91939	2.078000	0.62432	0.529000	0.55759	GAT		0.448	PCDHGB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374745.1	NM_003736		7	191	0	0	0	0.278610	0	7	191				
KIAA0895L	653319	broad.mit.edu	37	16	67211930	67211930	+	Silent	SNP	G	G	A			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr16:67211930G>A	ENST00000290881.7	-	7	2160	c.1234C>T	c.(1234-1236)Ctg>Ttg	p.L412L	KIAA0895L_ENST00000563902.1_Silent_p.L412L|KIAA0895L_ENST00000563831.2_Intron|KIAA0895L_ENST00000561621.1_Silent_p.C408C			Q68EN5	K895L_HUMAN	KIAA0895-like	412										breast(2)|endometrium(5)|kidney(2)|large_intestine(3)|lung(2)|prostate(2)|skin(1)	17						AGTGAGGTCAGCAACGGGAAA	0.607																																						ENST00000290881.7																			0				breast(2)|endometrium(5)|kidney(2)|large_intestine(3)|lung(2)|prostate(2)|skin(1)	17						c.(1234-1236)Ctg>Ttg		KIAA0895-like							53.0	51.0	51.0					16																	67211930		2006	4184	6190	SO:0001819	synonymous_variant	653319							g.chr16:67211930G>A	AK092303	CCDS42177.1	16q22.1	2008-11-27				ENSG00000196123			34408	protein-coding gene	gene with protein product							Standard	NM_001040715		Approved	LOC653319	uc002ert.3	Q68EN5		ENST00000290881.7:c.1234C>T	16.37:g.67211930G>A						KIAA0895L_ENST00000561621.1_Silent_p.C408C|KIAA0895L_ENST00000563831.2_Intron|KIAA0895L_ENST00000561679.1_Silent_p.L257L|KIAA0895L_ENST00000563902.1_Silent_p.L412L	p.L412L			Q68EN5	K895L_HUMAN			7	2160	-			412					A2VCS8|Q8N3H9|Q8NAQ5|Q96IE5	Silent	SNP	ENST00000290881.7	37	c.1234C>T	CCDS42177.1																																																																																				0.607	KIAA0895L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421193.4	NM_001040715		3	88	0	0	0	0.115264	0	3	88				
RANGAP1	5905	broad.mit.edu	37	22	41650402	41650402	+	Silent	SNP	C	C	T			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr22:41650402C>T	ENST00000455915.2	-	10	2639	c.1170G>A	c.(1168-1170)gaG>gaA	p.E390E	RANGAP1_ENST00000356244.3_Silent_p.E390E|RANGAP1_ENST00000407260.4_Silent_p.E335E|RANGAP1_ENST00000405486.1_Silent_p.E390E			P46060	RAGP1_HUMAN	Ran GTPase activating protein 1	390	Asp/Glu-rich (highly acidic).				mitotic cell cycle (GO:0000278)|negative regulation of protein export from nucleus (GO:0046826)|positive regulation of Ran GTPase activity (GO:0032853)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear pore (GO:0005643)|perinuclear region of cytoplasm (GO:0048471)	Ran GTPase activator activity (GO:0005098)	p.E390E(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						cctcctcctcctcttcttcct	0.562																																						ENST00000455915.2																			1	Substitution - coding silent(1)	p.E390E(1)	kidney(1)	breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						c.(1168-1170)gaG>gaA		Ran GTPase activating protein 1							233.0	159.0	184.0					22																	41650402		2203	4300	6503	SO:0001819	synonymous_variant	5905				mitotic prometaphase|signal transduction	condensed chromosome kinetochore|cytosol|nuclear membrane|nuclear pore|soluble fraction|spindle pole	protein binding|Ran GTPase activator activity	g.chr22:41650402C>T	X82260	CCDS14012.1	22q13	2013-01-17			ENSG00000100401	ENSG00000100401			9854	protein-coding gene	gene with protein product		602362	"""segregation distorter homolog (Drosophila)"""	SD		7878053	Standard	NM_002883		Approved	Fug1, KIAA1835	uc003azu.3	P46060	OTTHUMG00000150940	ENST00000455915.2:c.1170G>A	22.37:g.41650402C>T						RANGAP1_ENST00000356244.3_Silent_p.E390E|RANGAP1_ENST00000407260.4_Silent_p.E335E|RANGAP1_ENST00000405486.1_Silent_p.E390E	p.E390E			P46060	RAGP1_HUMAN			10	2639	-			390			Asp/Glu-rich (highly acidic).		Q96JJ2	Silent	SNP	ENST00000455915.2	37	c.1170G>A	CCDS14012.1																																																																																				0.562	RANGAP1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320606.1	NM_002883		4	45	0	0	0	0.150653	0	4	45				
PDE1A	5136	broad.mit.edu	37	2	183387037	183387037	+	Missense_Mutation	SNP	G	G	T			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr2:183387037G>T	ENST00000410103.1	-	2	150	c.67C>A	c.(67-69)Cag>Aag	p.Q23K	PDE1A_ENST00000358139.2_Missense_Mutation_p.Q23K|PDE1A_ENST00000456212.1_Missense_Mutation_p.Q23K|PDE1A_ENST00000331935.6_Missense_Mutation_p.Q23K|PDE1A_ENST00000536095.1_5'UTR|PDE1A_ENST00000435564.1_Missense_Mutation_p.Q23K	NM_001003683.2	NP_001003683.1	P54750	PDE1A_HUMAN	phosphodiesterase 1A, calmodulin-dependent	23					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of smooth muscle cell apoptotic process (GO:0034391)|regulation of smooth muscle cell proliferation (GO:0048660)|signal transduction (GO:0007165)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|calcium- and calmodulin-regulated 3',5'-cyclic-GMP phosphodiesterase activity (GO:0048101)|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			endometrium(5)|large_intestine(3)|lung(12)|ovary(1)|pancreas(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(2)	35			OV - Ovarian serous cystadenocarcinoma(117;0.061)		Bepridil(DB01244)|Caffeine(DB00201)|Felodipine(DB01023)|Nicardipine(DB00622)	TTTTCAGTCTGTTCTCCTGTA	0.398																																						ENST00000435564.1																			0				endometrium(5)|large_intestine(3)|lung(12)|ovary(1)|pancreas(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(2)	35						c.(67-69)Cag>Aag		phosphodiesterase 1A, calmodulin-dependent							147.0	147.0	147.0					2																	183387037		2202	4300	6502	SO:0001583	missense	0				activation of phospholipase C activity|nerve growth factor receptor signaling pathway|platelet activation	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding	g.chr2:183387037G>T		CCDS2285.1, CCDS33344.1, CCDS58741.1, CCDS74612.1	2q32.1	2008-03-18			ENSG00000115252	ENSG00000115252	3.1.4.17	"""Phosphodiesterases"""	8774	protein-coding gene	gene with protein product		171890				8557689, 11342109	Standard	NM_005019		Approved		uc010zfq.2	P54750	OTTHUMG00000132596	ENST00000410103.1:c.67C>A	2.37:g.183387037G>T	ENSP00000387037:p.Gln23Lys					PDE1A_ENST00000536095.1_5'UTR|PDE1A_ENST00000358139.2_Missense_Mutation_p.Q23K|PDE1A_ENST00000331935.6_Missense_Mutation_p.Q23K|PDE1A_ENST00000456212.1_Missense_Mutation_p.Q23K|PDE1A_ENST00000410103.1_Missense_Mutation_p.Q23K	p.Q23K	NM_001258312.1|NM_005019.4	NP_001245241.1|NP_005010.2	P54750	PDE1A_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.061)		1	267	-			23					D3DPG5|Q86VZ0|Q9C0K8|Q9C0K9|Q9C0L0|Q9C0L1|Q9C0L2|Q9C0L3|Q9C0L4|Q9UFX3	Missense_Mutation	SNP	ENST00000410103.1	37	c.67C>A	CCDS33344.1	.	.	.	.	.	.	.	.	.	.	G	9.327	1.059621	0.19987	.	.	ENSG00000115252	ENST00000435564;ENST00000331935;ENST00000410103;ENST00000358139;ENST00000456212	T;T;T;T;T	0.70045	-0.43;-0.43;-0.44;-0.44;-0.45	5.73	5.73	0.89815	.	0.667620	0.14105	N	0.341135	T	0.56659	0.2000	L	0.46157	1.445	0.31181	N	0.702087	B;P	0.35033	0.349;0.481	B;B	0.33454	0.079;0.164	T	0.55573	-0.8120	10	0.10636	T	0.68	.	12.2252	0.54455	0.0775:0.0:0.9225:0.0	.	23;23	P54750;P54750-4	PDE1A_HUMAN;.	K	23	ENSP00000410309:Q23K;ENSP00000331574:Q23K;ENSP00000387037:Q23K;ENSP00000350858:Q23K;ENSP00000408874:Q23K	ENSP00000331574:Q23K	Q	-	1	0	PDE1A	183095282	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.010000	0.57117	2.714000	0.92807	0.591000	0.81541	CAG		0.398	PDE1A-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000334356.1			23	123	1	0	5.61819e-17	0.693898	6.77064e-17	23	123				
CROCCP2	84809	broad.mit.edu	37	1	16957414	16957414	+	lincRNA	SNP	C	C	T	rs2296161	byFrequency	TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr1:16957414C>T	ENST00000412962.1	-	0	264							Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2						centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)											AAGTGCAGGGCGGAGAGAATC	0.706																																						ENST00000412962.1																			0																																																			0							g.chr1:16957414C>T	AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908			28170	pseudogene	pseudogene			"""ciliary rootlet coiled-coil, rootletin-like 1"""	CROCCL1		12477932	Standard	NR_026752		Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884		1.37:g.16957414C>T														0	264	-								Q8NF65|Q96FR5|Q9BRE8	RNA	SNP	ENST00000412962.1	37																																																																																						0.706	CROCCP2-003	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000092784.1	NR_026752.1		3	27	0	0	0	0.115264	0	3	27				
PRPF38B	55119	broad.mit.edu	37	1	109235326	109235326	+	Missense_Mutation	SNP	C	C	T			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr1:109235326C>T	ENST00000370025.4	+	1	382	c.113C>T	c.(112-114)gCg>gTg	p.A38V	PRPF38B_ENST00000370021.1_5'UTR|PRPF38B_ENST00000370022.5_Missense_Mutation_p.A38V|PRPF38B_ENST00000467302.1_3'UTR	NM_018061.2	NP_060531.2	Q5VTL8	PR38B_HUMAN	pre-mRNA processing factor 38B	38					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			NS(1)|kidney(3)|large_intestine(5)|lung(8)|prostate(1)|skin(1)	19		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0149)|Lung(183;0.0888)|COAD - Colon adenocarcinoma(174;0.113)|Epithelial(280;0.161)		ACCAAGCCGGCGGTCTCCGGC	0.667																																						ENST00000370025.4																			0				NS(1)|kidney(3)|large_intestine(5)|lung(8)|prostate(1)|skin(1)	19						c.(112-114)gCg>gTg		pre-mRNA processing factor 38B							47.0	37.0	40.0					1																	109235326		2202	4299	6501	SO:0001583	missense	55119				mRNA processing|RNA splicing	spliceosomal complex		g.chr1:109235326C>T	AL833950	CCDS788.1	1p13.3	2013-10-03	2013-10-03		ENSG00000134186	ENSG00000134186			25512	protein-coding gene	gene with protein product			"""PRP38 pre-mRNA processing factor 38 (yeast) domain containing B"""				Standard	NM_018061		Approved	FLJ10330, NET1	uc001dvv.4	Q5VTL8	OTTHUMG00000010991	ENST00000370025.4:c.113C>T	1.37:g.109235326C>T	ENSP00000359042:p.Ala38Val					PRPF38B_ENST00000370021.1_5'UTR|PRPF38B_ENST00000370022.5_Missense_Mutation_p.A38V|PRPF38B_ENST00000467302.1_3'UTR	p.A38V	NM_018061.2	NP_060531.2	Q5VTL8	PR38B_HUMAN		Colorectal(144;0.0149)|Lung(183;0.0888)|COAD - Colon adenocarcinoma(174;0.113)|Epithelial(280;0.161)	1	382	+		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)	38					Q05DD6|Q32Q58|Q5VTL9|Q6PK39|Q7Z6E2|Q86WF3|Q8IWG9|Q9NW40	Missense_Mutation	SNP	ENST00000370025.4	37	c.113C>T	CCDS788.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.080998	0.76528	.	.	ENSG00000134186	ENST00000370025;ENST00000370022	.	.	.	5.64	2.67	0.31697	.	0.165964	0.53938	N	0.000048	T	0.21631	0.0521	N	0.19112	0.55	0.80722	D	1	B	0.11235	0.004	B	0.06405	0.002	T	0.05903	-1.0857	9	0.36615	T	0.2	.	9.2823	0.37735	0.0:0.7481:0.1194:0.1324	.	38	Q5VTL8	PR38B_HUMAN	V	38	.	ENSP00000359039:A38V	A	+	2	0	PRPF38B	109036849	1.000000	0.71417	0.987000	0.45799	0.969000	0.65631	3.893000	0.56243	0.755000	0.32990	0.462000	0.41574	GCG		0.667	PRPF38B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030231.1	NM_018061		4	49	0	0	0	0.150653	0	4	49				
PRPF3	9129	broad.mit.edu	37	1	150307507	150307507	+	Missense_Mutation	SNP	G	G	A			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr1:150307507G>A	ENST00000324862.6	+	7	995	c.830G>A	c.(829-831)cGc>cAc	p.R277H	PRPF3_ENST00000414970.2_Missense_Mutation_p.R228H|PRPF3_ENST00000543398.1_Missense_Mutation_p.R142H|PRPF3_ENST00000467329.1_3'UTR	NM_004698.2	NP_004689.1	O43395	PRPF3_HUMAN	pre-mRNA processing factor 3	277					mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U4/U6 x U5 tri-snRNP complex (GO:0046540)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Lung NSC(24;5.57e-29)|Breast(34;0.000844)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)	Colorectal(1306;0.0149)		CTGACACACCGCATGCCTACT	0.458																																					Ovarian(168;1070 2670 5178 20729)	ENST00000324862.6																			0				breast(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						c.(829-831)cGc>cAc		pre-mRNA processing factor 3							116.0	93.0	101.0					1																	150307507		2203	4300	6503	SO:0001583	missense	9129				nuclear mRNA splicing, via spliceosome	Cajal body|cytoplasm|nuclear speck|spliceosomal complex	protein binding	g.chr1:150307507G>A	AF001947	CCDS951.1	1q21.1	2013-07-16	2013-06-10		ENSG00000117360	ENSG00000117360			17348	protein-coding gene	gene with protein product		607301	"""retinitis pigmentosa 18 (autosomal dominant)"", ""PRP3 pre-mRNA processing factor 3 homolog (yeast)"", ""PRP3 pre-mRNA processing factor 3 homolog (S. cerevisiae)"""	RP18			Standard	NM_004698		Approved	Prp3, hPrp3, SNRNP90	uc001eum.4	O43395	OTTHUMG00000012807	ENST00000324862.6:c.830G>A	1.37:g.150307507G>A	ENSP00000315379:p.Arg277His					PRPF3_ENST00000414970.2_Missense_Mutation_p.R228H|PRPF3_ENST00000543398.1_Missense_Mutation_p.R142H|PRPF3_ENST00000467329.1_3'UTR	p.R277H	NM_004698.2	NP_004689.1	O43395	PRPF3_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.171)	Colorectal(1306;0.0149)	7	995	+	Lung NSC(24;5.57e-29)|Breast(34;0.000844)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Colorectal(459;0.171)		277					B4DSY9|O43446|Q5VT54	Missense_Mutation	SNP	ENST00000324862.6	37	c.830G>A	CCDS951.1	.	.	.	.	.	.	.	.	.	.	G	16.90	3.249198	0.59103	.	.	ENSG00000117360	ENST00000324862;ENST00000414970;ENST00000543398	T;T	0.77750	-1.12;-1.1	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.66446	0.2790	M	0.68952	2.095	0.80722	D	1	B;B	0.22080	0.064;0.064	B;B	0.14578	0.011;0.011	T	0.65187	-0.6229	10	0.13853	T	0.58	-5.0451	20.0822	0.97779	0.0:0.0:1.0:0.0	.	228;277	E7EVD1;O43395	.;PRPF3_HUMAN	H	277;228;142	ENSP00000315379:R277H;ENSP00000387844:R228H	ENSP00000315379:R277H	R	+	2	0	PRPF3	148574131	1.000000	0.71417	0.989000	0.46669	0.998000	0.95712	9.511000	0.98006	2.826000	0.97356	0.563000	0.77884	CGC		0.458	PRPF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035836.1	NM_004698		3	51	0	0	0	0.115264	0	3	51				
MCTP2	55784	broad.mit.edu	37	15	94858758	94858758	+	Splice_Site	SNP	G	G	A			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr15:94858758G>A	ENST00000357742.4	+	3	529	c.529G>A	c.(529-531)Gta>Ata	p.V177I	MCTP2_ENST00000543482.1_Splice_Site_p.V177I|MCTP2_ENST00000331706.4_5'UTR|MCTP2_ENST00000451018.3_Splice_Site_p.V177I	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	177					calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|liver(1)|lung(12)|ovary(1)|pancreas(1)|skin(9)|stomach(2)	49	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)			ATCTGTGCAGGTACCGGGGGA	0.512																																						ENST00000357742.4																			0				autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|liver(1)|lung(12)|ovary(1)|pancreas(1)|skin(9)|stomach(2)	49						c.e3-1		multiple C2 domains, transmembrane 2							90.0	73.0	79.0					15																	94858758		2197	4298	6495	SO:0001630	splice_region_variant	55784				calcium-mediated signaling	integral to membrane|membrane fraction	calcium ion binding	g.chr15:94858758G>A	AK002037	CCDS32338.1, CCDS53975.1, CCDS53976.1	15q26.2	2006-02-08				ENSG00000140563			25636	protein-coding gene	gene with protein product						15528213	Standard	NM_018349		Approved	FLJ11175, FLJ33303	uc002btj.3	Q6DN12		ENST00000357742.4:c.529-1G>A	15.37:g.94858758G>A						MCTP2_ENST00000543482.1_Splice_Site_p.V177_splice|MCTP2_ENST00000451018.3_Splice_Site_p.V177_splice|MCTP2_ENST00000331706.4_5'UTR	p.V177_splice	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)		3	529	+	Lung NSC(78;0.0821)|all_lung(78;0.148)		177					A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Splice_Site	SNP	ENST00000357742.4	37	c.528_splice	CCDS32338.1	.	.	.	.	.	.	.	.	.	.	G	0.970	-0.700359	0.03279	.	.	ENSG00000140563	ENST00000543482;ENST00000556363;ENST00000451018;ENST00000357742	T;T;T	0.69806	-0.43;-0.21;-0.06	6.07	-0.562	0.11781	C2 calcium/lipid-binding domain, CaLB (1);	1.003210	0.08035	N	0.994205	T	0.43277	0.1240	N	0.08118	0	0.80722	D	1	B;B;B;B;B	0.12013	0.002;0.0;0.0;0.001;0.005	B;B;B;B;B	0.04013	0.0;0.0;0.0;0.0;0.001	T	0.14615	-1.0466	9	.	.	.	.	10.6672	0.45736	0.5048:0.0:0.4952:0.0	.	177;177;177;177;177	F5H415;Q6DN12-2;Q6DN12;B7Z6H2;G3V2J2	.;.;MCTP2_HUMAN;.;.	I	177	ENSP00000438521:V177I;ENSP00000395109:V177I;ENSP00000350377:V177I	.	V	+	1	0	MCTP2	92659762	0.001000	0.12720	0.028000	0.17463	0.042000	0.13812	-0.286000	0.08399	-0.285000	0.09089	-0.290000	0.09829	GTA		0.512	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349	Missense_Mutation	3	39	0	0	0	0.150653	0	3	39				
KDM6B	23135	broad.mit.edu	37	17	7750709	7750709	+	Missense_Mutation	SNP	G	G	C			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr17:7750709G>C	ENST00000448097.2	+	10	1527	c.1196G>C	c.(1195-1197)aGc>aCc	p.S399T	KDM6B_ENST00000254846.5_Missense_Mutation_p.S399T			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	399	Pro-rich.				cardiac muscle cell differentiation (GO:0055007)|cellular response to hydrogen peroxide (GO:0070301)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|mesodermal cell differentiation (GO:0048333)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)	p.S399T(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|skin(5)	37						ACCACCACcagcagcagcagt	0.672																																						ENST00000254846.5																			1	Substitution - Missense(1)	p.S399T(1)	lung(1)	central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|skin(5)	37						c.(1195-1197)aGc>aCc		lysine (K)-specific demethylase 6B							45.0	54.0	51.0					17																	7750709		2203	4300	6503	SO:0001583	missense	23135				inflammatory response	nucleus	metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	g.chr17:7750709G>C	AB002344	CCDS32552.1	17p13.1	2011-07-01	2009-04-17	2009-04-17		ENSG00000132510		"""Chromatin-modifying enzymes / K-demethylases"""	29012	protein-coding gene	gene with protein product		611577	"""jumonji domain containing 3"", ""jumonji domain containing 3, histone lysine demethylase"""	JMJD3		10662545, 9205841	Standard	NM_001080424		Approved	KIAA0346	uc002giw.1	O15054		ENST00000448097.2:c.1196G>C	17.37:g.7750709G>C	ENSP00000412513:p.Ser399Thr					KDM6B_ENST00000448097.2_Missense_Mutation_p.S399T	p.S399T	NM_001080424.1	NP_001073893.1	O15054	KDM6B_HUMAN			10	1585	+			399			Pro-rich.		C9IZ40|Q96G33	Missense_Mutation	SNP	ENST00000448097.2	37	c.1196G>C		.	.	.	.	.	.	.	.	.	.	G	4.000	-0.002662	0.07819	.	.	ENSG00000132510	ENST00000254846;ENST00000448097	T;T	0.08458	3.09;3.09	2.79	0.726	0.18248	.	0.509864	0.16624	N	0.206341	T	0.03434	0.0099	N	0.08118	0	0.20196	N	0.999927	B	0.11235	0.004	B	0.13407	0.009	T	0.45205	-0.9277	10	0.05351	T	0.99	-5.8581	10.8708	0.46883	0.0:0.4056:0.5944:0.0	.	399	O15054-1	.	T	399	ENSP00000254846:S399T;ENSP00000412513:S399T	ENSP00000254846:S399T	S	+	2	0	KDM6B	7691434	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	1.396000	0.34531	0.250000	0.21479	-0.234000	0.12200	AGC		0.672	KDM6B-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440248.1	XM_043272		4	167	0	0	0	0.150653	0	4	167				
TUBB8P7	197331	broad.mit.edu	37	16	90162555	90162555	+	RNA	SNP	C	C	T	rs532637415	byFrequency	TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr16:90162555C>T	ENST00000564451.1	+	0	1908				TUBB8P7_ENST00000567960.1_RNA					tubulin, beta 8 class VIII pseudogene 7																		ATGCCACGGCCGAGGAGGAGG	0.522																																						ENST00000567960.1																			0																																																			0							g.chr16:90162555C>T			16q24.3	2013-02-18			ENSG00000261812	ENSG00000261812			42345	pseudogene	pseudogene							Standard	NG_002334		Approved				OTTHUMG00000172847		16.37:g.90162555C>T						TUBB8P7_ENST00000564451.1_RNA								0	1291	+									RNA	SNP	ENST00000564451.1	37																																																																																						0.522	TUBB8P7-004	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000420856.1	NG_002334		4	192	0	0	0	0.217242	0	4	192				
CELF2	10659	broad.mit.edu	37	10	11299727	11299727	+	Missense_Mutation	SNP	G	G	A			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr10:11299727G>A	ENST00000379261.4	+	5	501	c.409G>A	c.(409-411)Gga>Aga	p.G137R	CELF2_ENST00000417956.2_Missense_Mutation_p.G113R|CELF2_ENST00000354897.3_Missense_Mutation_p.G113R|CELF2_ENST00000609692.1_Missense_Mutation_p.G113R|CELF2_ENST00000450189.1_Missense_Mutation_p.G144R|CELF2_ENST00000315874.4_Missense_Mutation_p.G113R|CELF2_ENST00000427450.1_Missense_Mutation_p.G113R|CELF2_ENST00000399850.3_Missense_Mutation_p.G113R|CELF2_ENST00000542579.1_Missense_Mutation_p.G144R|CELF2_ENST00000416382.2_Missense_Mutation_p.G137R|CELF2_ENST00000537122.1_Missense_Mutation_p.G26R|CELF2_ENST00000608830.1_Missense_Mutation_p.G113R|CELF2_ENST00000354440.2_Missense_Mutation_p.G113R	NM_001025077.2	NP_001020248.1	O95319	CELF2_HUMAN	CUGBP, Elav-like family member 2	137	Necessary for RNA-binding, TNNT2 exon 5 and NMDA R1 exon 21 inclusion.|RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|regulation of heart contraction (GO:0008016)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	16						ATTGTTCATAGGAATGGTATC	0.418																																						ENST00000379261.4																			0				breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	16						c.(409-411)Gga>Aga		CUGBP, Elav-like family member 2							88.0	89.0	88.0					10																	11299727		1931	4141	6072	SO:0001583	missense	10659				mRNA processing|regulation of heart contraction	cytoplasm|nucleus	nucleotide binding|protein binding|RNA binding	g.chr10:11299727G>A	U69546	CCDS41488.1, CCDS44354.1, CCDS44355.1, CCDS44356.1	10p13	2013-02-12	2010-02-19	2010-02-19	ENSG00000048740	ENSG00000048740		"""RNA binding motif (RRM) containing"""	2550	protein-coding gene	gene with protein product		602538	"""CUG triplet repeat, RNA-binding protein 2"", ""CUG triplet repeat, RNA binding protein 2"""	CUGBP2		7869393, 9887331	Standard	NM_006561		Approved	Etr-3, NAPOR-2, BRUNOL3	uc001ikl.4	O95319	OTTHUMG00000017668	ENST00000379261.4:c.409G>A	10.37:g.11299727G>A	ENSP00000368563:p.Gly137Arg					CELF2_ENST00000537122.1_Missense_Mutation_p.G26R|CELF2_ENST00000354440.2_Missense_Mutation_p.G113R|CELF2_ENST00000427450.1_Missense_Mutation_p.G113R|CELF2_ENST00000450189.1_Missense_Mutation_p.G144R|CELF2_ENST00000354897.3_Missense_Mutation_p.G113R|CELF2_ENST00000416382.2_Missense_Mutation_p.G137R|CELF2_ENST00000399850.3_Missense_Mutation_p.G113R|CELF2_ENST00000315874.3_Missense_Mutation_p.G113R|CELF2_ENST00000542579.1_Missense_Mutation_p.G144R|CELF2_ENST00000417956.2_Missense_Mutation_p.G113R	p.G137R	NM_001025077.2	NP_001020248.1	O95319	CELF2_HUMAN			5	501	+			137			Necessary for RNA-binding, TNNT2 exon 5 and NMDA R1 exon 21 inclusion.|RRM 2.		B7ZAN9|Q7KYU4|Q8N499|Q92950|Q96NW9|Q96RQ5|Q96RQ6|Q9UL67	Missense_Mutation	SNP	ENST00000379261.4	37	c.409G>A	CCDS44354.1	.	.	.	.	.	.	.	.	.	.	G	30	5.057691	0.93846	.	.	ENSG00000048740	ENST00000379261;ENST00000416382;ENST00000450189;ENST00000542579;ENST00000399850;ENST00000417956;ENST00000315874;ENST00000354440;ENST00000354897;ENST00000427450;ENST00000537122	T;T;T;T;T;T;T;T;T;T	0.10573	2.86;2.86;2.86;2.86;2.86;2.86;2.86;2.86;2.86;2.86	5.49	5.49	0.81192	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.35595	0.0937	M	0.73372	2.23	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0	T	0.05354	-1.0890	10	0.87932	D	0	-7.3231	19.3698	0.94480	0.0:0.0:1.0:0.0	.	121;137;132;144;132;137	B4DDE7;B4DS31;B2RA86;E9PC62;O95319-3;O95319	.;.;.;.;.;CELF2_HUMAN	R	137;137;144;144;113;113;113;113;113;113;26	ENSP00000368563:G137R;ENSP00000406451:G137R;ENSP00000389951:G144R;ENSP00000443926:G144R;ENSP00000382743:G113R;ENSP00000404834:G113R;ENSP00000315328:G113R;ENSP00000346426:G113R;ENSP00000388530:G113R;ENSP00000438884:G26R	ENSP00000315328:G113R	G	+	1	0	CELF2	11339733	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.745000	0.98856	2.555000	0.86185	0.655000	0.94253	GGA		0.418	CELF2-201	KNOWN	basic|CCDS	protein_coding	protein_coding				10	72	0	0	0	0.387290	0	10	72				
RAPGEF6	51735	broad.mit.edu	37	5	130825338	130825338	+	Missense_Mutation	SNP	C	C	A			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr5:130825338C>A	ENST00000509018.1	-	15	1946	c.1741G>T	c.(1741-1743)Gta>Tta	p.V581L	RAPGEF6_ENST00000296859.6_Missense_Mutation_p.V581L|RAPGEF6_ENST00000512052.1_Missense_Mutation_p.V296L|CTC-432M15.3_ENST00000514667.1_Missense_Mutation_p.V631L|RAPGEF6_ENST00000308008.6_Missense_Mutation_p.V581L|RAPGEF6_ENST00000510071.1_Missense_Mutation_p.V581L|RAPGEF6_ENST00000307984.5_Missense_Mutation_p.V581L|RAPGEF6_ENST00000507093.1_Missense_Mutation_p.V581L	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	Rap guanine nucleotide exchange factor (GEF) 6	581	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143, ECO:0000305}.				positive regulation of GTPase activity (GO:0043547)|Ras protein signal transduction (GO:0007265)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP-dependent protein binding (GO:0030742)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		TGTCCATTTACTTCCATAATC	0.259																																					Melanoma(168;435 1955 13113 13877 23213)	ENST00000509018.1																			0				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31						c.(1741-1743)Gta>Tta		Rap guanine nucleotide exchange factor (GEF) 6							42.0	44.0	43.0					5																	130825338		2201	4291	6492	SO:0001583	missense	51735				Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction	cytoplasm|plasma membrane	GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding	g.chr5:130825338C>A	AF117947	CCDS34225.1, CCDS54897.1, CCDS54898.1, CCDS54899.1, CCDS54900.1	5q31.1	2008-02-05	2004-03-01	2004-03-02	ENSG00000158987	ENSG00000158987			20655	protein-coding gene	gene with protein product		610499	"""PDZ domain containing guanine nucleotide exchange factor (GEF) 2"""	PDZGEF2		11524421, 12095257	Standard	NM_016340		Approved	RA-GEF-2, PDZ-GEF2	uc010jdi.2	Q8TEU7	OTTHUMG00000162683	ENST00000509018.1:c.1741G>T	5.37:g.130825338C>A	ENSP00000421684:p.Val581Leu					RAPGEF6_ENST00000307984.5_Missense_Mutation_p.V581L|RAPGEF6_ENST00000512052.1_Missense_Mutation_p.V296L|RAPGEF6_ENST00000507093.1_Missense_Mutation_p.V581L|RAPGEF6_ENST00000296859.6_Missense_Mutation_p.V581L|FNIP1_ENST00000514667.1_Missense_Mutation_p.V631L|RAPGEF6_ENST00000510071.1_Missense_Mutation_p.V581L|RAPGEF6_ENST00000308008.6_Missense_Mutation_p.V581L	p.V581L	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)	15	1946	-			581			PDZ.		A3KN82|A5PLL6|B7ZML2|E9PDV7|Q8NI21|Q8TEU6|Q96PC1	Missense_Mutation	SNP	ENST00000509018.1	37	c.1741G>T	CCDS34225.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.353524	0.82243	.	.	ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000217128	ENST00000509018;ENST00000307984;ENST00000507093;ENST00000296859;ENST00000358714;ENST00000512052;ENST00000308008;ENST00000510071;ENST00000514667	T;T;T;T;T;T;T;T	0.37752	1.18;1.18;1.18;1.18;1.18;1.18;1.18;1.18	5.93	5.93	0.95920	PDZ/DHR/GLGF (4);Ras guanine nucleotide exchange factor, domain (1);	0.069079	0.64402	D	0.000019	T	0.49643	0.1569	L	0.47190	1.495	0.80722	D	1	P;P;P;P;P;P;P	0.50272	0.933;0.933;0.918;0.835;0.933;0.918;0.87	P;P;P;P;P;P;P	0.53102	0.718;0.718;0.596;0.612;0.718;0.596;0.718	T	0.44298	-0.9337	10	0.87932	D	0	.	20.3368	0.98748	0.0:1.0:0.0:0.0	.	581;581;581;296;631;581;581	A3KN82;B7ZML2;Q8TEU7-2;D6RE77;E9PCH4;Q8TEU7-3;Q8TEU7	.;.;.;.;.;.;RPGF6_HUMAN	L	581;581;581;581;581;296;581;581;631	ENSP00000421684:V581L;ENSP00000309298:V581L;ENSP00000426081:V581L;ENSP00000296859:V581L;ENSP00000426910:V296L;ENSP00000311419:V581L;ENSP00000425389:V581L;ENSP00000426948:V631L	ENSP00000426948:V631L	V	-	1	0	RAPGEF6;FNIP1	130853237	1.000000	0.71417	1.000000	0.80357	0.814000	0.46013	2.969000	0.49232	2.805000	0.96524	0.655000	0.94253	GTA		0.259	RAPGEF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370059.1	NM_016340		3	34	1	0	0.115264	0.115264	0.123123	3	34				
QPRT	23475	broad.mit.edu	37	16	29708392	29708392	+	Missense_Mutation	SNP	G	G	A	rs147793931	byFrequency	TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr16:29708392G>A	ENST00000395384.4	+	3	786	c.625G>A	c.(625-627)Gtg>Atg	p.V209M	QPRT_ENST00000562473.1_Missense_Mutation_p.V61M|QPRT_ENST00000219771.7_3'UTR	NM_014298.3	NP_055113.2	Q15274	NADC_HUMAN	quinolinate phosphoribosyltransferase	209					NAD biosynthetic process (GO:0009435)|NAD metabolic process (GO:0019674)|protein oligomerization (GO:0051259)|quinolinate catabolic process (GO:0034213)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	nicotinate-nucleotide diphosphorylase (carboxylating) activity (GO:0004514)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)	9					Niacin(DB00627)	GCAGGAGGCCGTGCAGGCAGC	0.657																																						ENST00000395384.4																			0				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)	9						c.(625-627)Gtg>Atg		quinolinate phosphoribosyltransferase	Niacin(DB00627)	G	MET/VAL	1,4393		0,1,2196	26.0	24.0	24.0		625	-6.6	0.0	16	dbSNP_134	24	2,8598		0,2,4298	yes	missense	QPRT	NM_014298.3	21	0,3,6494	AA,AG,GG		0.0233,0.0228,0.0231	possibly-damaging	209/298	29708392	3,12991	2197	4300	6497	SO:0001583	missense	23475				protein oligomerization|quinolinate catabolic process|water-soluble vitamin metabolic process	cytosol	nicotinate-nucleotide diphosphorylase (carboxylating) activity|protein homodimerization activity	g.chr16:29708392G>A	D78177	CCDS10651.1	16p11.2	2008-07-31	2008-07-31		ENSG00000103485	ENSG00000103485	2.4.2.19		9755	protein-coding gene	gene with protein product	"""nicotinate-nucleotide pyrophosphorylase (carboxylating)"""	606248				9473669	Standard	NM_014298		Approved	QPRTase	uc002dto.3	Q15274	OTTHUMG00000097770	ENST00000395384.4:c.625G>A	16.37:g.29708392G>A	ENSP00000378782:p.Val209Met					QPRT_ENST00000219771.7_3'UTR|QPRT_ENST00000562473.1_Missense_Mutation_p.V61M	p.V209M	NM_014298.3	NP_055113.2	Q15274	NADC_HUMAN			3	786	+			209					Q53XW7|Q96G22|Q9BSG6	Missense_Mutation	SNP	ENST00000395384.4	37	c.625G>A	CCDS10651.1	.	.	.	.	.	.	.	.	.	.	.	9.382	1.073194	0.20147	2.28E-4	2.33E-4	ENSG00000103485	ENST00000219771;ENST00000395384	T	0.30714	1.52	4.97	-6.57	0.01842	Aldolase-type TIM barrel (1);Quinolinate phosphoribosyl transferase, C-terminal (2);	1.175030	0.06391	N	0.717076	T	0.21103	0.0508	L	0.49350	1.555	0.09310	N	1	B	0.25563	0.129	B	0.20767	0.031	T	0.35500	-0.9786	10	0.44086	T	0.13	-19.2333	4.0328	0.09716	0.0796:0.3559:0.151:0.4134	.	209	Q15274	NADC_HUMAN	M	64;209	ENSP00000378782:V209M	ENSP00000219771:V64M	V	+	1	0	QPRT	29615893	0.000000	0.05858	0.000000	0.03702	0.549000	0.35272	-1.062000	0.03468	-0.707000	0.05022	0.491000	0.48974	GTG		0.657	QPRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215011.2	NM_014298		3	31	0	0	0	0.150653	0	3	31				
FRMPD4	9758	broad.mit.edu	37	X	12734288	12734288	+	Missense_Mutation	SNP	A	A	G			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chrX:12734288A>G	ENST00000380682.1	+	15	2216	c.1710A>G	c.(1708-1710)atA>atG	p.I570M		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	570					positive regulation of synapse structural plasticity (GO:0051835)	cytoskeleton (GO:0005856)|dendritic spine (GO:0043197)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						AAGCCCAGATAACATACATAG	0.468																																						ENST00000380682.1																			0				breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						c.(1708-1710)atA>atG		FERM and PDZ domain containing 4							127.0	117.0	120.0					X																	12734288		2203	4300	6503	SO:0001583	missense	9758				positive regulation of synapse structural plasticity	cytoskeleton|dendritic spine	phosphatidylinositol-4,5-bisphosphate binding|protein binding	g.chrX:12734288A>G	AB002314	CCDS35201.1	Xp22.31	2006-02-09	2006-02-09	2006-02-09	ENSG00000169933	ENSG00000169933			29007	protein-coding gene	gene with protein product		300838	"""PDZ domain containing 10"""	PDZK10, PDZD10		9205841	Standard	NM_014728		Approved	KIAA0316	uc004cuz.2	Q14CM0	OTTHUMG00000021138	ENST00000380682.1:c.1710A>G	X.37:g.12734288A>G	ENSP00000370057:p.Ile570Met						p.I570M	NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN			15	2216	+			570					A8K0X9|O15032	Missense_Mutation	SNP	ENST00000380682.1	37	c.1710A>G	CCDS35201.1	.	.	.	.	.	.	.	.	.	.	A	11.12	1.546416	0.27652	.	.	ENSG00000169933	ENST00000380682;ENST00000429478;ENST00000304087	T	0.26223	1.75	5.47	-1.94	0.07571	.	0.273852	0.41712	D	0.000827	T	0.14141	0.0342	L	0.36672	1.1	0.21950	N	0.999458	B;B	0.23540	0.017;0.087	B;B	0.14023	0.004;0.01	T	0.08806	-1.0704	10	0.44086	T	0.13	.	4.2688	0.10776	0.2865:0.4953:0.0989:0.1193	.	562;570	B7ZLE1;Q14CM0	.;FRPD4_HUMAN	M	570;561;559	ENSP00000370057:I570M	ENSP00000304583:I559M	I	+	3	3	FRMPD4	12644209	0.914000	0.31030	0.773000	0.31616	0.996000	0.88848	0.196000	0.17176	-0.792000	0.04480	0.430000	0.28490	ATA		0.468	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	XM_045712		10	201	0	0	0	0.361761	0	10	201				
PNCK	139728	broad.mit.edu	37	X	152936612	152936612	+	Silent	SNP	G	G	A			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chrX:152936612G>A	ENST00000370150.1	-	8	826	c.648C>T	c.(646-648)agC>agT	p.S216S	PNCK_ENST00000393831.2_Silent_p.S239S|PNCK_ENST00000340888.3_Silent_p.S216S|PNCK_ENST00000475172.1_5'Flank|PNCK_ENST00000370145.4_Silent_p.S233S|PNCK_ENST00000447676.2_Silent_p.S299S|PNCK_ENST00000370142.1_Silent_p.S239S			Q6P2M8	KCC1B_HUMAN	pregnancy up-regulated nonubiquitous CaM kinase	216	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			breast(2)|lung(3)|skin(1)	6	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GCTCAGGGTCGCTCTCGTCGT	0.602																																						ENST00000393831.2																			0				breast(2)|lung(3)|skin(1)	6						c.(715-717)agC>agT		pregnancy up-regulated nonubiquitous CaM kinase							61.0	60.0	60.0					X																	152936612		2203	4300	6503	SO:0001819	synonymous_variant	139728					cytoplasm|nucleus	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity	g.chrX:152936612G>A	BC033746	CCDS35503.2, CCDS48189.1	Xq28	2013-10-14	2013-10-14		ENSG00000130822	ENSG00000130822			13415	protein-coding gene	gene with protein product		300680	"""pregnancy upregulated non-ubiquitously expressed CaM kinase"", ""pregnancy up-regulated non-ubiquitously expressed CaM kinase"""			12477932	Standard	NM_001039582		Approved	MGC45419, CaMK1b	uc011myu.2	Q6P2M8	OTTHUMG00000024216	ENST00000370150.1:c.648C>T	X.37:g.152936612G>A						PNCK_ENST00000447676.2_Silent_p.S299S|PNCK_ENST00000370150.1_Silent_p.S216S|PNCK_ENST00000340888.3_Silent_p.S216S|PNCK_ENST00000370142.1_Silent_p.S239S|PNCK_ENST00000370145.4_Silent_p.S233S	p.S239S	NM_001039582.3	NP_001034671.3	Q6P2M8	KCC1B_HUMAN			8	1151	-	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)		216			Protein kinase.		B4DJR8|B4E1A6|B7WPG0|D3DWU7|Q8N4R0	Silent	SNP	ENST00000370150.1	37	c.717C>T																																																																																					0.602	PNCK-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000061044.2	NM_198452		51	124	0	0	0	0.870114	0	51	124				
DISC1	27185	broad.mit.edu	37	1	231885806	231885806	+	Missense_Mutation	SNP	C	C	T			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr1:231885806C>T	ENST00000602281.1	+	4	1305	c.1252C>T	c.(1252-1254)Cgt>Tgt	p.R418C	DISC1_ENST00000537876.1_Missense_Mutation_p.R418C|DISC1_ENST00000602873.1_Missense_Mutation_p.R68C|DISC1_ENST00000366637.3_5'UTR|DISC1_ENST00000535983.1_Missense_Mutation_p.R418C|DISC1_ENST00000366636.4_Missense_Mutation_p.R418C|DISC1_ENST00000439617.2_Missense_Mutation_p.R418C|DISC1_ENST00000366633.3_Missense_Mutation_p.R418C|DISC1_ENST00000539444.1_Missense_Mutation_p.R418C|TSNAX-DISC1_ENST00000602962.1_3'UTR	NM_001164542.1|NM_001164544.1	NP_001158014.1|NP_001158016.1	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1	418	Interaction with TRAF3IP1.				canonical Wnt signaling pathway (GO:0060070)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cerebral cortex radially oriented cell migration (GO:0021799)|microtubule cytoskeleton organization (GO:0000226)|mitochondrial calcium ion homeostasis (GO:0051560)|neuron migration (GO:0001764)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neuron projection development (GO:0010975)|regulation of synapse maturation (GO:0090128)|TOR signaling (GO:0031929)	cell junction (GO:0030054)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	15		all_cancers(173;0.0208)|Prostate(94;0.0975)				TGCCTTGCGCCGTGGGGCCAC	0.527																																						ENST00000439617.2																			0				breast(1)|cervix(1)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	15						c.(1252-1254)Cgt>Tgt		disrupted in schizophrenia 1							69.0	70.0	70.0					1																	231885806		2203	4300	6503	SO:0001583	missense	27185				microtubule cytoskeleton organization|neuron migration|positive regulation of neuroblast proliferation|positive regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway	centrosome|microtubule	protein binding	g.chr1:231885806C>T	AF222980	CCDS31055.1, CCDS31056.1, CCDS53482.1, CCDS53483.1, CCDS53484.1, CCDS59205.1, CCDS59206.1, CCDS59207.1	1q42.1	2008-02-05			ENSG00000162946	ENSG00000162946			2888	protein-coding gene	gene with protein product		605210				10814723	Standard	NM_001164550		Approved		uc010pxh.2	Q9NRI5	OTTHUMG00000037835	ENST00000602281.1:c.1252C>T	1.37:g.231885806C>T	ENSP00000473425:p.Arg418Cys					DISC1_ENST00000539444.1_Missense_Mutation_p.R418C|DISC1_ENST00000602281.1_Missense_Mutation_p.R418C|TRAX_ENST00000602962.1_3'UTR|DISC1_ENST00000535983.1_Missense_Mutation_p.R418C|DISC1_ENST00000537876.1_Missense_Mutation_p.R418C|DISC1_ENST00000366637.3_5'UTR|DISC1_ENST00000366633.3_Missense_Mutation_p.R418C|DISC1_ENST00000602873.1_Missense_Mutation_p.R68C|DISC1_ENST00000366636.4_Missense_Mutation_p.R418C	p.R418C	NM_001164537.1|NM_001164540.1|NM_018662.2	NP_001158009.1|NP_001158012.1|NP_061132.2	Q9NRI5	DISC1_HUMAN			4	1305	+		all_cancers(173;0.0208)|Prostate(94;0.0975)	418			Interaction with TRAF3IP1.		A6NLH2|C4P091|C4P095|C4P0A1|C4P0A3|C4P0B3|C4P0B6|C4P0C1|C9J6D0|O75045|Q5VT44|Q5VT45|Q8IXJ0|Q8IXJ1|Q9BX19|Q9NRI3|Q9NRI4	Missense_Mutation	SNP	ENST00000602281.1	37	c.1252C>T	CCDS59205.1	.	.	.	.	.	.	.	.	.	.	.	17.40	3.379182	0.61735	.	.	ENSG00000162946	ENST00000439617;ENST00000366637;ENST00000366636;ENST00000366638;ENST00000532576;ENST00000535983;ENST00000537876;ENST00000366633;ENST00000539444;ENST00000295051;ENST00000535944	T;T;T;T;T;T;T;T	0.18657	2.61;2.44;2.44;2.23;2.61;2.25;2.24;2.2	4.32	0.511	0.16989	.	2.081170	0.03736	N	0.254267	T	0.31827	0.0809	L	0.36672	1.1	0.09310	N	1	D;D;D;D;D;D;D;D;D;D;B;D;D;D;D;D;D;D;D	0.89917	1.0;0.976;1.0;0.999;1.0;0.999;0.998;1.0;0.996;0.999;0.006;0.998;0.999;0.999;1.0;0.998;1.0;0.998;0.998	P;B;D;P;D;P;P;D;P;P;B;P;P;P;P;P;P;P;P	0.65874	0.899;0.431;0.911;0.827;0.939;0.827;0.731;0.939;0.55;0.827;0.002;0.731;0.827;0.827;0.899;0.731;0.899;0.731;0.731	T	0.12760	-1.0535	10	0.87932	D	0	-0.4317	3.0663	0.06215	0.0:0.4068:0.2221:0.3712	.	450;418;450;418;418;418;418;418;68;418;418;418;418;418;418;418;418;418;418	C4P096;C4P094;E2QRA4;C4P0A3;C4P098;C4P0A1;C4P0A4;A6NLH2;C4P0C1;C4P0A5;C4P095;C4P0B6;C4P0C4;C4P0B1;A7E2W8;Q5T409;Q9NRI5-2;Q9NRI5;Q9NRI5-3	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;DISC1_HUMAN;.	C	418;418;418;450;418;418;418;418;418;418;418	ENSP00000403888:R418C;ENSP00000355596:R418C;ENSP00000443996:R418C;ENSP00000440909:R418C;ENSP00000355593:R418C;ENSP00000440953:R418C;ENSP00000295051:R418C;ENSP00000441193:R418C	ENSP00000295051:R418C	R	+	1	0	DISC1	229952429	0.000000	0.05858	0.000000	0.03702	0.483000	0.33249	-0.337000	0.07852	0.063000	0.16370	0.655000	0.94253	CGT		0.527	DISC1-019	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467451.1	NM_018662		5	94	0	0	0	0.217242	0	5	94				
ITPR1	3708	broad.mit.edu	37	3	4824425	4824425	+	Splice_Site	SNP	G	G	C			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr3:4824425G>C	ENST00000443694.2	+	47	6465	c.6465G>C	c.(6463-6465)caG>caC	p.Q2155H	ITPR1_ENST00000354582.6_Splice_Site_p.Q2155H|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000357086.4_Splice_Site_p.Q2122H|ITPR1_ENST00000456211.2_Splice_Site_p.Q2107H|ITPR1_ENST00000302640.8_Splice_Site_p.Q2155H|ITPR1_ENST00000423119.2_Splice_Site_p.Q2122H			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	2170					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	TAGCCCATCAGGTATGATCTC	0.527																																						ENST00000354582.6																			0				NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106						c.e49+1		inositol 1,4,5-trisphosphate receptor, type 1							72.0	80.0	77.0					3																	4824425		2080	4188	6268	SO:0001630	splice_region_variant	3708				activation of phospholipase C activity|cell death|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	endoplasmic reticulum membrane|integral to membrane|platelet dense granule membrane|platelet dense tubular network membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|intracellular ligand-gated calcium channel activity|phosphatidylinositol binding|protein binding	g.chr3:4824425G>C	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"""Ion channels / Inositol triphosphate receptors"""	6180	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 94"""	147265	"""spinocerebellar ataxia 15"", ""spinocerebellar ataxia 16"", ""spinocerebellar ataxia 29"""	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.6465+1G>C	3.37:g.4824425G>C						ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000456211.2_Splice_Site_p.Q2107_splice|ITPR1_ENST00000443694.2_Splice_Site_p.Q2155_splice|ITPR1_ENST00000423119.2_Splice_Site_p.Q2122_splice|ITPR1_ENST00000357086.4_Splice_Site_p.Q2122_splice|ITPR1_ENST00000302640.8_Splice_Site_p.Q2155_splice	p.Q2155_splice			Q14643	ITPR1_HUMAN		Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	49	6815	+			2170					E7EPX7|E9PDE9|Q14660|Q99897	Splice_Site	SNP	ENST00000443694.2	37	c.6465_splice	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	G	15.13	2.743139	0.49151	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000426160;ENST00000357086;ENST00000456211;ENST00000443694	D;D;D;D;D;D	0.92495	-3.05;-3.05;-3.05;-3.05;-3.04;-3.05	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	D	0.96002	0.8698	M	0.79475	2.455	0.80722	D	1	D;D	0.76494	0.993;0.999	P;D	0.72982	0.907;0.979	D	0.96302	0.9222	10	0.66056	D	0.02	.	18.6784	0.91537	0.0:0.0:1.0:0.0	.	2170;2122	Q14643;G5E9P1	ITPR1_HUMAN;.	H	2170;2155;2155;2122;616;2122;2107;2155	ENSP00000306253:Q2155H;ENSP00000346595:Q2155H;ENSP00000405934:Q2122H;ENSP00000349597:Q2122H;ENSP00000397885:Q2107H;ENSP00000401671:Q2155H	ENSP00000306253:Q2155H	Q	+	3	2	ITPR1	4799425	1.000000	0.71417	1.000000	0.80357	0.055000	0.15305	5.514000	0.67043	2.407000	0.81776	0.655000	0.94253	CAG		0.527	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222	Missense_Mutation	4	42	0	0	0	0.184627	0	4	42				
GEMIN5	25929	broad.mit.edu	37	5	154315560	154315560	+	Missense_Mutation	SNP	C	C	A			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr5:154315560C>A	ENST00000285873.7	-	3	425	c.350G>T	c.(349-351)tGg>tTg	p.W117L		NM_001252156.1|NM_015465.4	NP_001239085.1|NP_056280.2	Q8TEQ6	GEMI5_HUMAN	gem (nuclear organelle) associated protein 5	117					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|protein complex assembly (GO:0006461)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)	poly(A) RNA binding (GO:0044822)|snRNA binding (GO:0017069)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			TCGAGGAGACCAATGTAATGT	0.328																																						ENST00000285873.7																			0				breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38						c.(349-351)tGg>tTg		gem (nuclear organelle) associated protein 5							74.0	69.0	71.0					5																	154315560		2203	4300	6503	SO:0001583	missense	25929				ncRNA metabolic process|protein complex assembly|spliceosomal snRNP assembly	Cajal body|cytosol|spliceosomal complex	protein binding|snRNA binding	g.chr5:154315560C>A	AK022748	CCDS4330.1	5q34	2013-01-10			ENSG00000082516	ENSG00000082516		"""WD repeat domain containing"""	20043	protein-coding gene	gene with protein product		607005				11714716	Standard	NM_015465		Approved		uc003lvx.3	Q8TEQ6	OTTHUMG00000130189	ENST00000285873.7:c.350G>T	5.37:g.154315560C>A	ENSP00000285873:p.Trp117Leu						p.W117L	NM_001252156.1|NM_015465.4	NP_001239085.1|NP_056280.2	Q8TEQ6	GEMI5_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00112)		3	425	-	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	117					Q14CV0|Q8WWV4|Q969W4|Q9H9K3|Q9UFI5	Missense_Mutation	SNP	ENST00000285873.7	37	c.350G>T	CCDS4330.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.856694	0.91433	.	.	ENSG00000082516	ENST00000285873	T	0.67171	-0.25	5.77	5.77	0.91146	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.83202	0.5203	M	0.79475	2.455	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.994	D	0.84175	0.0436	10	0.72032	D	0.01	-9.5783	19.9983	0.97395	0.0:1.0:0.0:0.0	.	117;117	B7ZLC9;Q8TEQ6	.;GEMI5_HUMAN	L	117	ENSP00000285873:W117L	ENSP00000285873:W117L	W	-	2	0	GEMIN5	154295753	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.231000	0.78106	2.724000	0.93272	0.561000	0.74099	TGG		0.328	GEMIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252507.1			8	41	1	0	0.0581538	0.335167	0.0650768	8	41				
OR4K5	79317	broad.mit.edu	37	14	20389468	20389468	+	Missense_Mutation	SNP	A	A	C			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr14:20389468A>C	ENST00000315915.4	+	1	728	c.703A>C	c.(703-705)Aag>Cag	p.K235Q		NM_001005483.1	NP_001005483.1	Q8NGD3	OR4K5_HUMAN	olfactory receptor, family 4, subfamily K, member 5	235						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|liver(1)|lung(27)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	47	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TGCAATGGCAAAGGCATTTTC	0.418																																						ENST00000315915.4																			0				central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|liver(1)|lung(27)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	47						c.(703-705)Aag>Cag		olfactory receptor, family 4, subfamily K, member 5							258.0	271.0	267.0					14																	20389468		2203	4300	6503	SO:0001583	missense	79317				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr14:20389468A>C	BK004355	CCDS32024.1	14q11.22	2012-08-09				ENSG00000176281		"""GPCR / Class A : Olfactory receptors"""	14745	protein-coding gene	gene with protein product						14983052	Standard	NM_001005483		Approved		uc010tkw.2	Q8NGD3		ENST00000315915.4:c.703A>C	14.37:g.20389468A>C	ENSP00000319511:p.Lys235Gln						p.K235Q	NM_001005483.1	NP_001005483.1	Q8NGD3	OR4K5_HUMAN	Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)	1	728	+	all_cancers(95;0.00108)		235					Q6IFA7	Missense_Mutation	SNP	ENST00000315915.4	37	c.703A>C	CCDS32024.1	.	.	.	.	.	.	.	.	.	.	.	11.23	1.577984	0.28180	.	.	ENSG00000176281	ENST00000315915	T	0.00372	7.73	4.52	3.37	0.38596	GPCR, rhodopsin-like superfamily (1);	0.117100	0.37393	N	0.002107	T	0.01976	0.0062	H	0.99732	4.735	0.22610	N	0.998935	D	0.89917	1.0	D	0.79108	0.992	T	0.35919	-0.9769	10	0.87932	D	0	.	8.3313	0.32189	0.9041:0.0:0.0959:0.0	.	235	Q8NGD3	OR4K5_HUMAN	Q	235	ENSP00000319511:K235Q	ENSP00000319511:K235Q	K	+	1	0	OR4K5	19459308	1.000000	0.71417	0.024000	0.17045	0.005000	0.04900	6.139000	0.71728	0.760000	0.33108	-0.253000	0.11424	AAG		0.418	OR4K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409867.1	NM_001005483		21	541	0	0	0	0.608945	0	21	541				
UBASH3B	84959	broad.mit.edu	37	11	122680513	122680513	+	Silent	SNP	G	G	A			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr11:122680513G>A	ENST00000284273.5	+	14	2244	c.1869G>A	c.(1867-1869)caG>caA	p.Q623Q		NM_032873.4	NP_116262.2	Q8TF42	UBS3B_HUMAN	ubiquitin associated and SH3 domain containing B	623	Protein tyrosine phosphatase. {ECO:0000250}.				negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein kinase activity (GO:0006469)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(11)|prostate(1)|skin(2)|stomach(2)	26		Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104)		BRCA - Breast invasive adenocarcinoma(274;1.37e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0463)		GAATATGGCAGCTGACAGATC	0.443																																						ENST00000284273.5																			0				breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(11)|prostate(1)|skin(2)|stomach(2)	26						c.(1867-1869)caG>caA		ubiquitin associated and SH3 domain containing B							82.0	83.0	83.0					11																	122680513		2202	4299	6501	SO:0001819	synonymous_variant	84959					cytoplasm|nucleus	protein tyrosine phosphatase activity	g.chr11:122680513G>A	AB075839	CCDS31694.1	11q24.1	2010-04-28	2010-04-28		ENSG00000154127	ENSG00000154127			29884	protein-coding gene	gene with protein product	"""SH3 domain-containing 70 kDa protein, suppressor of T-cell receptor signaling 1, nm23-phosphorylated unknown substrate"""	609201				11853319, 12370296	Standard	NM_032873		Approved	KIAA1959, STS-1	uc001pyi.4	Q8TF42	OTTHUMG00000166025	ENST00000284273.5:c.1869G>A	11.37:g.122680513G>A							p.Q623Q	NM_032873.4	NP_116262.2	Q8TF42	UBS3B_HUMAN		BRCA - Breast invasive adenocarcinoma(274;1.37e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0463)	14	2244	+		Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104)	623			Protein tyrosine phosphatase (By similarity).		Q53GT5|Q53GT8|Q8NBV7|Q96IG9|Q96NZ2	Silent	SNP	ENST00000284273.5	37	c.1869G>A	CCDS31694.1																																																																																				0.443	UBASH3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387499.1	NM_032873		3	110	0	0	0	0.150653	0	3	110				
SLC12A4	6560	broad.mit.edu	37	16	67979074	67979074	+	Missense_Mutation	SNP	C	C	A			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr16:67979074C>A	ENST00000316341.3	-	23	3222	c.3082G>T	c.(3082-3084)Gtc>Ttc	p.V1028F	SLC12A4_ENST00000338335.3_3'UTR|SLC12A4_ENST00000572037.1_Missense_Mutation_p.V980F|CTC-479C5.17_ENST00000590594.1_lincRNA|SLC12A4_ENST00000537830.2_Missense_Mutation_p.V1022F|SLC12A4_ENST00000541864.2_Missense_Mutation_p.V997F|SLC12A4_ENST00000422611.2_Missense_Mutation_p.V1030F|LCAT_ENST00000264005.5_5'Flank|SLC12A4_ENST00000576616.1_Missense_Mutation_p.V1028F	NM_001145961.1|NM_005072.4	NP_001139433.1|NP_005063.1	Q9UP95	S12A4_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 4	1028					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(2)|ovary(2)|prostate(4)|skin(2)|urinary_tract(3)	29		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)	Bumetanide(DB00887)|Potassium Chloride(DB00761)	GTGACAATGACTTCATTGAGC	0.577																																						ENST00000422611.2																			0				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(2)|ovary(2)|prostate(4)|skin(2)|urinary_tract(3)	29						c.(3088-3090)Gtc>Ttc		solute carrier family 12 (potassium/chloride transporter), member 4	Bumetanide(DB00887)|Potassium Chloride(DB00761)						139.0	127.0	131.0					16																	67979074		2198	4300	6498	SO:0001583	missense	6560				cell volume homeostasis|potassium ion transport|sodium ion transport	integral to plasma membrane|membrane fraction	potassium:chloride symporter activity	g.chr16:67979074C>A		CCDS10855.1, CCDS54030.1, CCDS54031.1, CCDS54032.1	16q22.1	2013-07-18	2013-07-18		ENSG00000124067	ENSG00000124067		"""Solute carriers"""	10913	protein-coding gene	gene with protein product		604119				8663127	Standard	NM_005072		Approved	KCC1	uc010ceu.2	Q9UP95	OTTHUMG00000137535	ENST00000316341.3:c.3082G>T	16.37:g.67979074C>A	ENSP00000318557:p.Val1028Phe					SLC12A4_ENST00000572037.1_Missense_Mutation_p.V980F|SLC12A4_ENST00000338335.3_3'UTR|SLC12A4_ENST00000537830.2_Missense_Mutation_p.V1022F|SLC12A4_ENST00000541864.2_Missense_Mutation_p.V997F|SLC12A4_ENST00000576616.1_Missense_Mutation_p.V1028F|SLC12A4_ENST00000316341.3_Missense_Mutation_p.V1028F	p.V1030F	NM_001145962.1	NP_001139434.1	Q9UP95	S12A4_HUMAN		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)	22	3127	-		Ovarian(137;0.192)	1028					B4DF69|B4DR04|B4DZ82|B7ZAV0|F5H066|F5H0S9|F5H3C0|O60632|O75893|Q13953|Q96LD5	Missense_Mutation	SNP	ENST00000316341.3	37	c.3088G>T	CCDS10855.1	.	.	.	.	.	.	.	.	.	.	C	34	5.343899	0.95807	.	.	ENSG00000124067	ENST00000422611;ENST00000541864;ENST00000537830;ENST00000316341	T;T;T;T	0.67171	-0.25;-0.25;-0.25;-0.25	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	D	0.85279	0.5660	M	0.90145	3.09	0.80722	D	1	D;P;D;P;D;P	0.63046	0.973;0.956;0.992;0.947;0.974;0.911	P;P;D;P;D;P	0.64042	0.73;0.714;0.921;0.805;0.913;0.643	D	0.87188	0.2232	10	0.87932	D	0	.	20.3593	0.98849	0.0:1.0:0.0:0.0	.	1030;1022;997;1022;1028;1028	F5H3C0;B4DF30;F5H066;F5H0S9;Q9UP95-2;Q9UP95	.;.;.;.;.;S12A4_HUMAN	F	1030;997;1022;1028	ENSP00000395983:V1030F;ENSP00000438334:V997F;ENSP00000445962:V1022F;ENSP00000318557:V1028F	ENSP00000318557:V1028F	V	-	1	0	SLC12A4	66536575	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.487000	0.81328	2.822000	0.97130	0.557000	0.71058	GTC		0.577	SLC12A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268864.4	NM_005072		4	146	1	0	0.00116845	0.217242	0.00137292	4	146				
LOC728323	728323	broad.mit.edu	37	2	243056967	243056967	+	RNA	DEL	T	T	-			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr2:243056967delT	ENST00000456398.1	+	0	413																											CAGTGCTATCTTATGAAATAA	0.299																																						ENST00000456398.1																			0																																																			0							g.chr2:243056967delT																													2.37:g.243056967delT														0	413	+									RNA	DEL	ENST00000456398.1	37																																																																																						0.299	AC093642.5-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000322444.2			4	8						4	8	---	---	---	---
MSH3	4437	broad.mit.edu	37	5	79950742	79950750	+	In_Frame_Del	DEL	CCCCCAGCT	CCCCCAGCT	-	rs144629981|rs3045983|rs557874766|rs1047489	byFrequency	TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr5:79950742_79950750delCCCCCAGCT	ENST00000265081.6	+	1	276_284	c.196_204delCCCCCAGCT	c.(196-204)cccccagctdel	p.PPA66del	DHFR_ENST00000439211.2_5'UTR|DHFR_ENST00000511032.1_5'Flank|DHFR_ENST00000504396.1_5'Flank|DHFR_ENST00000505337.1_5'Flank|DHFR_ENST00000513048.1_5'Flank	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	66					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		gCCCCCAGCGCCCCCAGCTCCCGCCTTCC	0.732								Mismatch excision repair (MMR)						1174	0.234425	0.2874	0.2061	5008	,	,		7173	0.0565		0.2535	False		,,,				2504	0.3466				Melanoma(88;1010 1399 13793 26548 36275)	ENST00000265081.6																			0				NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						c.(196-204)del	Mismatch excision repair (MMR)	mutS homolog 3			,	1105,2179		342,421,879					,	4.0	1.0		dbSNP_102	4	1941,4615		567,807,1904	no	coding,utr-5	DHFR,MSH3	NM_002439.3,NM_000791.3	,	909,1228,2783	A1A1,A1R,RR		29.6065,33.648,30.9553	,	,		3046,6794				SO:0001651	inframe_deletion	4437				maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments	MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding	g.chr5:79950742_79950750delCCCCCAGCT	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"""Divergent upstream protein"", ""Mismatch repair protein 1"""	600887	"""mutS (E. coli) homolog 3"", ""mutS homolog 3 (E. coli)"""				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.196_204delCCCCCAGCT	5.37:g.79950742_79950750delCCCCCAGCT	ENSP00000265081:p.Pro66_Ala68del					DHFR_ENST00000439211.2_5'UTR	p.PPA66del	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)	1	276_284	+		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)	66					A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	In_Frame_Del	DEL	ENST00000265081.6	37	c.196_204delCCCCCAGCT	CCDS34195.1																																																																																				0.732	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		2	4						2	4	---	---	---	---
HLA-DRB6	3128	broad.mit.edu	37	6	32523362	32523363	+	RNA	INS	-	-	GATA	rs142676080|rs190692498		TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr6:32523362_32523363insGATA	ENST00000411500.1	-	0	458					NR_001298.1				major histocompatibility complex, class II, DR beta 6 (pseudogene)																		AAAGCAATGTGGATAAAGGGAC	0.431																																						ENST00000411500.1																			0																																																			0							g.chr6:32523362_32523363insGATA	L76566		6p21.3	2011-07-08			ENSG00000229391	ENSG00000229391		"""Histocompatibility complex"""	4954	pseudogene	pseudogene						1529427, 10436177	Standard	NR_001298		Approved		uc003obn.1		OTTHUMG00000031028		6.37:g.32523363_32523366dupGATA								NR_001298.1						0	458	-									RNA	INS	ENST00000411500.1	37																																																																																						0.431	HLA-DRB6-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000272900.1	NR_001298		4	4						4	4	---	---	---	---
GIGYF1	64599	broad.mit.edu	37	7	100284335	100284337	+	In_Frame_Del	DEL	CCT	CCT	-			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr7:100284335_100284337delCCT	ENST00000275732.5	-	7	1838_1840	c.629_631delAGG	c.(628-633)gagggc>ggc	p.E210del	GIGYF1_ENST00000471340.2_Intron	NM_022574.4	NP_072096.2	O75420	PERQ1_HUMAN	GRB10 interacting GYF protein 1	210	Poly-Glu.				insulin-like growth factor receptor signaling pathway (GO:0048009)			p.E210delE(1)		central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)					CTCCAGCTGCcctcctcctcctc	0.7																																						ENST00000275732.5																			1	Deletion - In frame(1)	p.E210delE(1)	large_intestine(1)	central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23						c.(628-633)ggc>g		GRB10 interacting GYF protein 1				14,2,4238		0,0,14,0,2,2111						5.0	1.0			29	36,2,8190		0,0,36,0,2,4076	no	codingComplex	GIGYF1	NM_022574.4		0,0,50,0,4,6187	A1A1,A1A2,A1R,A2A2,A2R,RR		0.4618,0.3761,0.4326				50,4,12428				SO:0001651	inframe_deletion	64599							g.chr7:100284335_100284337delCCT	AF053356	CCDS34708.1	7q22	2008-02-11	2008-02-11	2008-02-11	ENSG00000146830	ENSG00000146830			9126	protein-coding gene	gene with protein product	"""GYF domain containing 1"""	612064	"""PERQ amino acid rich, with GYF domain 1"""	PERQ1		9799793, 12771153	Standard	NM_022574		Approved	GYF1	uc003uwg.1	O75420	OTTHUMG00000157036	ENST00000275732.5:c.629_631delAGG	7.37:g.100284344_100284346delCCT	ENSP00000275732:p.Glu210del					GIGYF1_ENST00000471340.2_Intron	p.EG210del	NM_022574.4	NP_072096.2	O75420	PERQ1_HUMAN			7	1838_1840	-	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)		210			Poly-Glu.		Q6Y7W7|Q8WZ38	In_Frame_Del	DEL	ENST00000275732.5	37	c.629_631delAGG	CCDS34708.1																																																																																				0.700	GIGYF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347205.2	NM_022574		7	75						7	75	---	---	---	---
AL162419.1	0	broad.mit.edu	37	9	4378426	4378427	+	RNA	INS	-	-	T			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr9:4378426_4378427insT	ENST00000408803.1	-	0	67_68																											GTTTGTTTATATTTTTTTCTTT	0.307																																						ENST00000408803.1																			0																																																			0							g.chr9:4378426_4378427insT																													9.37:g.4378433_4378433dupT														0	67_68	-									RNA	INS	ENST00000408803.1	37																																																																																						0.307	AL162419.1-201	NOVEL	basic	miRNA	miRNA				2	4						2	4	---	---	---	---
ZMIZ1	57178	broad.mit.edu	37	10	81072446	81072446	+	Frame_Shift_Del	DEL	C	C	-			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr10:81072446delC	ENST00000334512.5	+	25	3716	c.3144delC	c.(3142-3144)gacfs	p.D1048fs	ZMIZ1_ENST00000446377.2_Frame_Shift_Del_p.D114fs	NM_020338.3	NP_065071.1	Q9ULJ6	ZMIZ1_HUMAN	zinc finger, MIZ-type containing 1	1048					artery morphogenesis (GO:0048844)|cell aging (GO:0007569)|developmental growth (GO:0048589)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)|vitellogenesis (GO:0007296)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(1)	30	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)			CTTATCTGGACCCCCCCGACC	0.557																																						ENST00000334512.5																			0				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(1)	30						c.(3142-3144)gafs		zinc finger, MIZ-type containing 1							193.0	181.0	185.0					10																	81072446		2203	4300	6503	SO:0001589	frameshift_variant	57178				transcription, DNA-dependent	cytoplasm|nuclear speck	zinc ion binding	g.chr10:81072446delC	AB033050	CCDS7357.1	10q22.3	2012-11-30	2006-10-24	2006-10-24	ENSG00000108175	ENSG00000108175		"""Zinc fingers, MIZ-type"""	16493	protein-coding gene	gene with protein product		607159	"""retinoic acid induced 17"""	RAI17		15626329	Standard	NM_020338		Approved	RP11-519K18.1, KIAA1224, FLJ13541, hZIMP10, Zimp10, MIZ	uc001kaf.2	Q9ULJ6	OTTHUMG00000018560	ENST00000334512.5:c.3144delC	10.37:g.81072446delC	ENSP00000334474:p.Asp1048fs					ZMIZ1_ENST00000446377.2_Frame_Shift_Del_p.D114fs	p.D1048fs	NM_020338.3	NP_065071.1	Q9ULJ6	ZMIZ1_HUMAN	Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)		25	3716	+	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		1048					Q5JSH9|Q7Z7E6	Frame_Shift_Del	DEL	ENST00000334512.5	37	c.3144delC	CCDS7357.1																																																																																				0.557	ZMIZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048944.2	NM_020338		7	541						7	541	---	---	---	---
DGKZ	8525	broad.mit.edu	37	11	46387931	46387933	+	In_Frame_Del	DEL	CCT	CCT	-			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr11:46387931_46387933delCCT	ENST00000454345.1	+	2	250_252	c.125_127delCCT	c.(124-129)gcctcc>gcc	p.S45del	DGKZ_ENST00000343674.6_Intron|DGKZ_ENST00000543978.1_Intron|DGKZ_ENST00000456247.2_Intron|DGKZ_ENST00000527911.1_Intron|DGKZ_ENST00000528615.1_Intron|DGKZ_ENST00000532868.2_Intron|DGKZ_ENST00000318201.8_Intron|DGKZ_ENST00000421244.2_Intron|DGKZ_ENST00000525434.1_3'UTR|DGKZ_ENST00000395574.3_Intron	NM_001105540.1	NP_001099010.1	Q13574	DGKZ_HUMAN	diacylglycerol kinase, zeta	45					blood coagulation (GO:0007596)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|mitotic G1 DNA damage checkpoint (GO:0031571)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of Ras protein signal transduction (GO:0046580)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|enzyme inhibitor activity (GO:0004857)|lipid kinase activity (GO:0001727)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein C-terminus binding (GO:0008022)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|pancreas(1)|prostate(1)|skin(1)	25				GBM - Glioblastoma multiforme(35;0.0259)|Lung(87;0.141)		GCTGGGCAGGCCTCCTCCTCACT	0.759																																						ENST00000454345.1																			0				central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|pancreas(1)|prostate(1)|skin(1)	25						c.(124-129)gcc>g		diacylglycerol kinase, zeta			,,,,,,	7,3395		2,3,1696					,,,,,,	3.4	1.0			6	41,7245		7,27,3609	no	intron,intron,intron,intron,intron,intron,coding	DGKZ	NM_201533.3,NM_201532.2,NM_003646.3,NM_001199268.1,NM_001199267.1,NM_001199266.1,NM_001105540.1	,,,,,,	9,30,5305	A1A1,A1R,RR		0.5627,0.2058,0.4491	,,,,,,	,,,,,,		48,10640				SO:0001651	inframe_deletion	8525				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell migration|intracellular signal transduction|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of mitotic cell cycle|platelet activation	cytoplasm|lamellipodium|nucleus|plasma membrane	ATP binding|diacylglycerol kinase activity|lipid kinase activity|metal ion binding|protein binding|protein C-terminus binding	g.chr11:46387931_46387933delCCT	U51477	CCDS7918.1, CCDS41640.1, CCDS44579.1, CCDS44580.1, CCDS55757.1, CCDS55758.1, CCDS55759.1, CCDS44579.2	11p11.2	2010-11-24	2010-11-24		ENSG00000149091	ENSG00000149091	2.7.1.107		2857	protein-coding gene	gene with protein product		601441	"""diacylglycerol kinase, zeta 104kDa"""			8626588	Standard	NM_003646		Approved	DAGK5, hDGKzeta, DGK-ZETA, DAGK6	uc001ncn.1	Q13574	OTTHUMG00000166437	ENST00000454345.1:c.125_127delCCT	11.37:g.46387937_46387939delCCT	ENSP00000412178:p.Ser45del					DGKZ_ENST00000543978.1_Intron|DGKZ_ENST00000525434.1_3'UTR|DGKZ_ENST00000343674.6_Intron|DGKZ_ENST00000456247.2_Intron|DGKZ_ENST00000528615.1_Intron|DGKZ_ENST00000318201.8_Intron|DGKZ_ENST00000421244.2_Intron|DGKZ_ENST00000527911.1_Intron|DGKZ_ENST00000395574.3_Intron|DGKZ_ENST00000532868.2_Intron	p.AS42del	NM_001105540.1	NP_001099010.1	Q13574	DGKZ_HUMAN		GBM - Glioblastoma multiforme(35;0.0259)|Lung(87;0.141)	2	250_252	+			42					B7Z2M9|B7Z6M3|E9PPW4|F6UCU9|G3V0F6|J3KNJ6|O00542|Q6ZVG7|Q8IVW9	In_Frame_Del	DEL	ENST00000454345.1	37	c.125_127delCCT	CCDS41640.1																																																																																				0.759	DGKZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389772.1	NM_001105540		6	3						6	3	---	---	---	---
RAB40C	57799	broad.mit.edu	37	16	677579	677580	+	Frame_Shift_Ins	INS	-	-	C			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr16:677579_677580insC	ENST00000248139.3	+	6	1006_1007	c.803_804insC	c.(802-807)agccccfs	p.SP268fs	RAB40C_ENST00000539661.1_Frame_Shift_Ins_p.SP268fs|RAB40C_ENST00000535977.1_Frame_Shift_Ins_p.SP268fs|RAB40C_ENST00000538492.1_Frame_Shift_Ins_p.SP268fs	NM_021168.4	NP_066991.3	Q96S21	RB40C_HUMAN	RAB40C, member RAS oncogene family	268					protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)	p.Q271fs*7(1)		NS(1)|endometrium(2)|large_intestine(1)|lung(1)|prostate(1)	6		Hepatocellular(780;0.0218)				CCACCCCAGAGCCCCCCCCAGA	0.678																																					Melanoma(123;1631 1690 28262 44104 44957)	ENST00000535977.1																			1	Insertion - Frameshift(1)	p.Q271fs*7(1)	large_intestine(1)	NS(1)|endometrium(2)|large_intestine(1)|lung(1)|prostate(1)	6						c.(802-804)accfs		RAB40C, member RAS oncogene family																																				SO:0001589	frameshift_variant	57799				protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding	g.chr16:677579_677580insC	Z84779	CCDS10413.1	16p13.3	2008-07-28	2003-10-14		ENSG00000197562	ENSG00000197562		"""RAB, member RAS oncogene"""	18285	protein-coding gene	gene with protein product			"""RAS-like, family 8, member C"""	RASL8C		11697911, 18485483	Standard	NM_021168		Approved	RARL	uc021szv.1	Q96S21	OTTHUMG00000047854	ENST00000248139.3:c.811dupC	16.37:g.677587_677587dupC	ENSP00000248139:p.Ser268fs					RAB40C_ENST00000248139.3_Frame_Shift_Ins_p.T268fs|RAB40C_ENST00000539661.1_Frame_Shift_Ins_p.T268fs|RAB40C_ENST00000538492.1_Frame_Shift_Ins_p.T268fs	p.T268fs	NM_001172663.1	NP_001166134.1	Q96S21	RB40C_HUMAN			7	1025_1026	+		Hepatocellular(780;0.0218)	268					A2IDE2|D3DU54|O60795|Q4TT41|Q5PXE8|Q6PIU5	Frame_Shift_Ins	INS	ENST00000248139.3	37	c.803_804insC	CCDS10413.1																																																																																				0.678	RAB40C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109079.4	NM_021168		7	135						7	135	---	---	---	---
SMG1P3	100271836	broad.mit.edu	37	16	21469994	21469994	+	RNA	DEL	A	A	-			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr16:21469994delA	ENST00000520823.2	-	0	749				snoU13_ENST00000459321.1_RNA																							ACTGTACATTAAAAAAAAAAA	0.294																																						ENST00000520823.2																			0																																																			0							g.chr16:21469994delA																													16.37:g.21469994delA														0	749	-									RNA	DEL	ENST00000520823.2	37																																																																																						0.294	CTD-2547E10.2-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000378302.2			3	4						3	4	---	---	---	---
AFG3L1P	172	broad.mit.edu	37	16	90053824	90053824	+	RNA	DEL	G	G	-			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr16:90053824delG	ENST00000437774.1	+	0	731					NR_003226.1				AFG3-like AAA ATPase 1, pseudogene																		aggtggaggaggtggaggagg	0.622																																						ENST00000437774.1																			0																																																			0							g.chr16:90053824delG	AJ001495		16q24.3	2013-10-17	2013-10-17	2010-10-28	ENSG00000223959	ENSG00000223959		"""ATPases / AAA-type"""	314	pseudogene	pseudogene		603020	"""AFG3 ATPase family gene 3-like 1 (S. cerevisiae), pseudogene"", ""AFG3 ATPase family member 3-like 1 (S. cerevisiae), pseudogene"""	AFG3, AFG3L1		9545647, 11549317	Standard	NR_003228		Approved		uc002fpz.1		OTTHUMG00000138987		16.37:g.90053824delG								NR_003226.1						0	731	+									RNA	DEL	ENST00000437774.1	37																																																																																						0.622	AFG3L1P-004	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000316791.1	NR_003226		2	4						2	4	---	---	---	---
HOXB7	3217	broad.mit.edu	37	17	46685277	46685277	+	Frame_Shift_Del	DEL	T	T	-			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chr17:46685277delT	ENST00000239165.7	-	2	679	c.581delA	c.(580-582)aagfs	p.K194fs	HOXB-AS3_ENST00000467155.2_RNA|HOXB6_ENST00000484302.2_5'Flank|HOXB-AS3_ENST00000491264.1_RNA|HOXB-AS3_ENST00000466037.2_RNA|HOXB-AS3_ENST00000494420.1_RNA|HOXB-AS3_ENST00000487849.3_RNA|HOXB6_ENST00000225648.3_5'Flank|HOXB7_ENST00000567101.2_5'UTR	NM_004502.3	NP_004493.3	P09629	HXB7_HUMAN	homeobox B7	194				K -> N (in Ref. 7; AAB19469). {ECO:0000305}.	anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|multicellular organismal development (GO:0007275)|myeloid cell differentiation (GO:0030099)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	8						CTTGTTCTCCTTTTTCCACTT	0.592																																						ENST00000239165.7																			0				NS(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	8						c.(580-582)agfs		homeobox B7							103.0	113.0	109.0					17																	46685277		2203	4300	6503	SO:0001589	frameshift_variant	3217					nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr17:46685277delT		CCDS11532.1	17q21.32	2013-05-22	2005-12-22					"""Homeoboxes / ANTP class : HOXL subclass"""	5118	protein-coding gene	gene with protein product		142962	"""homeo box B7"""	HOX2, HOX2C		1973146, 1358459	Standard	NM_004502		Approved		uc002inv.3	P09629	OTTHUMG00000170231	ENST00000239165.7:c.581delA	17.37:g.46685277delT	ENSP00000239165:p.Lys194fs					HOXB7_ENST00000567101.1_5'UTR	p.K194fs	NM_004502.3	NP_004493.3	P09629	HXB7_HUMAN			2	679	-			194	K -> N (in Ref. 7; AAB19469).				A8K3N8|Q15957|Q53FN3|Q96BQ6	Frame_Shift_Del	DEL	ENST00000239165.7	37	c.581delA	CCDS11532.1																																																																																				0.592	HOXB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358097.3			8	497						8	497	---	---	---	---
HS6ST2	90161	broad.mit.edu	37	X	131762582	131762582	+	Frame_Shift_Del	DEL	A	A	-			TCGA-BJ-A3PT-01A-12D-A21Z-08	TCGA-BJ-A3PT-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	08d1b350-92cd-4a94-91f6-68734dd228f7	ca1e236e-e01e-44f2-931b-0840aa54a37f	g.chrX:131762582delA	ENST00000370836.2	-	4	1902	c.1487delT	c.(1486-1488)ttgfs	p.L496fs	HS6ST2_ENST00000521489.1_Frame_Shift_Del_p.L536fs|HS6ST2_ENST00000406696.3_Frame_Shift_Del_p.L222fs|HS6ST2_ENST00000370833.2_Frame_Shift_Del_p.L390fs	NM_147175.3	NP_671704.3	Q96MM7	H6ST2_HUMAN	heparan sulfate 6-O-sulfotransferase 2	496					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	heparan sulfate 6-O-sulfotransferase activity (GO:0017095)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(2)	9	Acute lymphoblastic leukemia(192;0.000127)					ATACCTCTGCAAAAAAAGGTC	0.453																																						ENST00000370836.2																			0				central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(2)	9						c.(1486-1488)tgfs		heparan sulfate 6-O-sulfotransferase 2							155.0	153.0	154.0					X																	131762582		1937	4110	6047	SO:0001589	frameshift_variant	90161					integral to membrane	sulfotransferase activity	g.chrX:131762582delA	AB067776	CCDS48169.1, CCDS48170.1	Xq26.2	2008-02-05			ENSG00000171004	ENSG00000171004		"""Sulfotransferases, membrane-bound"""	19133	protein-coding gene	gene with protein product		300545				10644753	Standard	NM_147175		Approved		uc011mvd.1	Q96MM7	OTTHUMG00000022430	ENST00000370836.2:c.1487delT	X.37:g.131762582delA	ENSP00000359873:p.Leu496fs					HS6ST2_ENST00000370837.1_Frame_Shift_Del_p.L350fs|HS6ST2_ENST00000406696.3_Frame_Shift_Del_p.L222fs|HS6ST2_ENST00000521489.1_Frame_Shift_Del_p.L536fs|HS6ST2_ENST00000370833.2_Frame_Shift_Del_p.L390fs	p.L496fs	NM_147175.3	NP_671704.3	Q96MM7	H6ST2_HUMAN			4	1902	-	Acute lymphoblastic leukemia(192;0.000127)		496					B9WRT4|B9WRT5|E9PDY5|Q2TB13|Q4VC07|Q6PIC4|Q86SM9|Q8N3T4|Q8NBN4|Q96SJ4	Frame_Shift_Del	DEL	ENST00000370836.2	37	c.1487delT	CCDS48169.1																																																																																				0.453	HS6ST2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058332.3	NM_147174		16	433						16	433	---	---	---	---
