#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
NOS2	4843	broad.mit.edu	37	17	26106045	26106045	+	Missense_Mutation	SNP	C	C	T	rs200623027		TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr17:26106045C>T	ENST00000313735.6	-	10	1275	c.1042G>A	c.(1042-1044)Gcc>Acc	p.A348T		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	348					arginine catabolic process (GO:0006527)|blood coagulation (GO:0007596)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|circadian rhythm (GO:0007623)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|peptidyl-cysteine S-nitrosylation (GO:0018119)|phagosome maturation (GO:0090382)|positive regulation of guanylate cyclase activity (GO:0031284)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of leukocyte mediated cytotoxicity (GO:0001912)|positive regulation of vasodilation (GO:0045909)|regulation of cell proliferation (GO:0042127)|regulation of cellular respiration (GO:0043457)|regulation of insulin secretion (GO:0050796)|response to bacterium (GO:0009617)|response to hypoxia (GO:0001666)|superoxide metabolic process (GO:0006801)	cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	arginine binding (GO:0034618)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric-oxide synthase activity (GO:0004517)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|tetrahydrobiopterin binding (GO:0034617)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(28)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	56					Dexamethasone(DB01234)|Doxorubicin(DB00997)|L-Arginine(DB00125)|L-Citrulline(DB00155)|Miconazole(DB01110)|Triflusal(DB08814)	GCAGGCAGGGCGTACCACTTT	0.502																																						ENST00000313735.6																			0				autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(28)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	56						c.(1042-1044)Gcc>Acc		nitric oxide synthase 2, inducible	Dexamethasone(DB01234)|Hydrocortisone(DB00741)|L-Arginine(DB00125)|L-Citrulline(DB00155)						61.0	59.0	60.0					17																	26106045		2203	4300	6503	SO:0001583	missense	4843				arginine catabolic process|defense response to Gram-negative bacterium|innate immune response in mucosa|nitric oxide biosynthetic process|peptidyl-cysteine S-nitrosylation|platelet activation|positive regulation of killing of cells of other organism|positive regulation of leukocyte mediated cytotoxicity|regulation of cellular respiration|regulation of insulin secretion|superoxide metabolic process	cytosol|nucleus	arginine binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|protein homodimerization activity|tetrahydrobiopterin binding	g.chr17:26106045C>T	U20141	CCDS11223.1	17q11.2	2014-06-12	2008-09-16	2008-09-16	ENSG00000007171	ENSG00000007171	1.14.13.39		7873	protein-coding gene	gene with protein product		163730	"""nitric oxide synthase 2A (inducible, hepatocytes)"""	NOS2A		7682706	Standard	NM_000625		Approved	iNOS, NOS, HEP-NOS	uc002gzu.3	P35228	OTTHUMG00000132445	ENST00000313735.6:c.1042G>A	17.37:g.26106045C>T	ENSP00000327251:p.Ala348Thr						p.A348T	NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN			10	1275	-			348					A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Missense_Mutation	SNP	ENST00000313735.6	37	c.1042G>A	CCDS11223.1	.	.	.	.	.	.	.	.	.	.	C	33	5.208239	0.95033	.	.	ENSG00000007171	ENST00000313735;ENST00000379105;ENST00000302153	T	0.35048	1.33	5.68	5.68	0.88126	Nitric oxide synthase, oxygenase domain (2);	0.126462	0.52532	D	0.000069	T	0.59972	0.2233	M	0.90425	3.115	0.54753	D	0.99998	D;D	0.71674	0.998;0.993	P;P	0.56612	0.681;0.802	T	0.68062	-0.5508	10	0.72032	D	0.01	.	12.1439	0.54012	0.0:0.9224:0.0:0.0776	.	348;348	F8WEM3;P35228	.;NOS2_HUMAN	T	348;309;348	ENSP00000327251:A348T	ENSP00000305638:A348T	A	-	1	0	NOS2	23130172	0.999000	0.42202	0.837000	0.33122	0.980000	0.70556	4.073000	0.57570	2.683000	0.91414	0.561000	0.74099	GCC		0.502	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1	NM_000625		19	47	0	0	0	1	0	19	47				
DCAF5	8816	broad.mit.edu	37	14	69521532	69521532	+	Missense_Mutation	SNP	T	T	C			TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr14:69521532T>C	ENST00000341516.5	-	9	2018	c.1871A>G	c.(1870-1872)gAc>gGc	p.D624G	DCAF5_ENST00000556847.1_Missense_Mutation_p.D542G|DCAF5_ENST00000554215.1_Missense_Mutation_p.D542G|DCAF5_ENST00000553293.1_5'Flank|DCAF5_ENST00000557386.1_Missense_Mutation_p.D623G	NM_001284206.1|NM_001284207.1|NM_003861.2	NP_001271135.1|NP_001271136.1|NP_003852.1	Q96JK2	DCAF5_HUMAN	DDB1 and CUL4 associated factor 5	624					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|mitochondrion (GO:0005739)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|upper_aerodigestive_tract(2)	29						GGAGGAGAGGTCATCCACTTT	0.522																																						ENST00000341516.5																			0				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|upper_aerodigestive_tract(2)	29						c.(1870-1872)gAc>gGc		DDB1 and CUL4 associated factor 5							140.0	133.0	136.0					14																	69521532		2203	4300	6503	SO:0001583	missense	8816					CUL4 RING ubiquitin ligase complex		g.chr14:69521532T>C	AB058727	CCDS32106.1, CCDS61480.1, CCDS61481.1, CCDS73646.1	14q23-q24.1	2013-01-09	2009-07-17	2009-07-17				"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	20224	protein-coding gene	gene with protein product		603812	"""WD repeat domain 22"""	WDR22		9740667, 9521877	Standard	NM_003861		Approved	BCRP2, D14S1461E, BCRG2, KIAA1824	uc001xkp.3	Q96JK2		ENST00000341516.5:c.1871A>G	14.37:g.69521532T>C	ENSP00000341351:p.Asp624Gly					DCAF5_ENST00000556847.1_Missense_Mutation_p.D542G|DCAF5_ENST00000557386.1_Missense_Mutation_p.D623G|DCAF5_ENST00000554215.1_Missense_Mutation_p.D542G	p.D624G	NM_003861.2	NP_003852.1	Q96JK2	DCAF5_HUMAN			9	2018	-			624					B2RN31|G3V4J7|O60559|Q8N3V3|Q8N3V5	Missense_Mutation	SNP	ENST00000341516.5	37	c.1871A>G	CCDS32106.1	.	.	.	.	.	.	.	.	.	.	T	19.77	3.888555	0.72524	.	.	ENSG00000139990	ENST00000341516;ENST00000554215;ENST00000556847;ENST00000557386	T;T;T;T	0.76316	-1.01;-0.87;-0.87;-0.45	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.81098	0.4752	L	0.34521	1.04	0.80722	D	1	D;D	0.65815	0.995;0.991	P;P	0.62089	0.898;0.793	T	0.83299	-0.0029	10	0.66056	D	0.02	-21.0249	15.2825	0.73797	0.0:0.0:0.0:1.0	.	623;624	G3V4J7;Q96JK2	.;DCAF5_HUMAN	G	624;542;542;623	ENSP00000341351:D624G;ENSP00000451551:D542G;ENSP00000452052:D542G;ENSP00000451845:D623G	ENSP00000341351:D624G	D	-	2	0	DCAF5	68591285	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.937000	0.75898	2.005000	0.58758	0.459000	0.35465	GAC		0.522	DCAF5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414806.2	NM_003861		11	88	0	0	0	1	0	11	88				
SLC16A3	9123	broad.mit.edu	37	17	80195392	80195392	+	Missense_Mutation	SNP	T	T	C			TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr17:80195392T>C	ENST00000581287.1	+	3	3068	c.746T>C	c.(745-747)gTg>gCg	p.V249A	SLC16A3_ENST00000582743.1_Missense_Mutation_p.V249A|SLC16A3_ENST00000392341.1_Missense_Mutation_p.V249A|SLC16A3_ENST00000392339.1_Missense_Mutation_p.V249A	NM_001206951.1|NM_001206952.1	NP_001193880.1|NP_001193881.1	O15427	MOT4_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 3	249					blood coagulation (GO:0007596)|cellular metabolic process (GO:0044237)|leukocyte migration (GO:0050900)|monocarboxylic acid transport (GO:0015718)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	actin cytoskeleton (GO:0015629)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|poly(A) RNA binding (GO:0044822)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			endometrium(2)|kidney(1)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9	Breast(20;0.00285)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.227)		OV - Ovarian serous cystadenocarcinoma(97;0.00463)|BRCA - Breast invasive adenocarcinoma(99;0.0149)		Gamma Hydroxybutyric Acid(DB01440)|Niacin(DB00627)|Pyruvic acid(DB00119)	CCCGTGTTCGTGGTGAGCTAC	0.682																																					Pancreas(52;652 1135 19190 37282 52456)	ENST00000581287.1																			0				endometrium(2)|kidney(1)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9						c.(745-747)gTg>gCg		solute carrier family 16 (monocarboxylate transporter), member 3	Pyruvic acid(DB00119)						31.0	35.0	33.0					17																	80195392		2202	4298	6500	SO:0001583	missense	9123				blood coagulation|leukocyte migration|organic anion transport|pyruvate metabolic process	actin cytoskeleton|integral to plasma membrane|membrane fraction|nuclear membrane	secondary active monocarboxylate transmembrane transporter activity|symporter activity	g.chr17:80195392T>C	U81800	CCDS11804.1	17q25.3	2013-07-18	2013-07-18		ENSG00000141526	ENSG00000141526		"""Solute carriers"""	10924	protein-coding gene	gene with protein product		603877	"""solute carrier family 16 (monocarboxylic acid transporters), member 3"", ""solute carrier family 16, member 3 (monocarboxylic acid transporter 4)"""			9425115	Standard	NM_004207		Approved	MCT3, MCT4	uc021ufm.1	O15427	OTTHUMG00000178832	ENST00000581287.1:c.746T>C	17.37:g.80195392T>C	ENSP00000463978:p.Val249Ala					SLC16A3_ENST00000392339.1_Missense_Mutation_p.V249A|SLC16A3_ENST00000392341.1_Missense_Mutation_p.V249A|SLC16A3_ENST00000582743.1_Missense_Mutation_p.V249A	p.V249A	NM_001206951.1|NM_001206952.1	NP_001193880.1|NP_001193881.1	O15427	MOT4_HUMAN	OV - Ovarian serous cystadenocarcinoma(97;0.00463)|BRCA - Breast invasive adenocarcinoma(99;0.0149)		3	3068	+	Breast(20;0.00285)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.227)		249					B3KXG8|Q2M1P8	Missense_Mutation	SNP	ENST00000581287.1	37	c.746T>C	CCDS11804.1	.	.	.	.	.	.	.	.	.	.	T	16.66	3.185724	0.57909	.	.	ENSG00000141526	ENST00000392341;ENST00000392339	T;T	0.58060	0.36;0.36	5.68	5.68	0.88126	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.63604	0.2525	M	0.76002	2.32	0.58432	D	0.999999	P;P	0.46578	0.866;0.88	P;P	0.49252	0.489;0.604	T	0.69105	-0.5233	10	0.87932	D	0	.	15.1101	0.72349	0.0:0.0:0.0:1.0	.	249;249	Q53G91;O15427	.;MOT4_HUMAN	A	249	ENSP00000376152:V249A;ENSP00000376150:V249A	ENSP00000376150:V249A	V	+	2	0	SLC16A3	77788681	1.000000	0.71417	0.997000	0.53966	0.914000	0.54420	7.956000	0.87863	2.173000	0.68751	0.528000	0.53228	GTG		0.682	SLC16A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443498.1	NM_004207		7	34	0	0	0	1	0	7	34				
PHYH	5264	broad.mit.edu	37	10	13325695	13325695	+	Missense_Mutation	SNP	G	G	A	rs104894178	byFrequency	TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr10:13325695G>A	ENST00000263038.4	-	7	881	c.823C>T	c.(823-825)Cgg>Tgg	p.R275W	PHYH_ENST00000396920.3_Missense_Mutation_p.R258W|PHYH_ENST00000396913.2_Missense_Mutation_p.R175W	NM_006214.3	NP_006205.1	O14832	PAHX_HUMAN	phytanoyl-CoA 2-hydroxylase	275			R -> Q (in RD; total loss of activity; dbSNP:rs28939674). {ECO:0000269|PubMed:10767344}.|R -> W (in RD; total loss of activity; dbSNP:rs28939671). {ECO:0000269|PubMed:10767344, ECO:0000269|PubMed:9326939}.		cellular lipid metabolic process (GO:0044255)|fatty acid alpha-oxidation (GO:0001561)|isoprenoid metabolic process (GO:0006720)|methyl-branched fatty acid metabolic process (GO:0097089)|small molecule metabolic process (GO:0044281)	mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	cofactor binding (GO:0048037)|electron carrier activity (GO:0009055)|L-ascorbic acid binding (GO:0031418)|metal ion binding (GO:0046872)|phytanoyl-CoA dioxygenase activity (GO:0048244)			NS(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	25		Ovarian(717;0.0448)			Antihemophilic Factor(DB00025)|Vitamin C(DB00126)	CTTACCTTCCGGAATCCCTGG	0.423																																						ENST00000396920.3																			0				NS(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	25	GRCh37	CM971176	PHYH	M	rs104894178	c.(772-774)Cgg>Tgg		phytanoyl-CoA 2-hydroxylase	Antihemophilic Factor(DB00025)|Vitamin C(DB00126)	G	TRP/ARG,TRP/ARG	0,4406		0,0,2203	122.0	120.0	120.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	523,823	0.6	1.0	10	dbSNP_132	120	3,8597	3.0+/-9.4	0,3,4297	no	missense,missense	PHYH	NM_001037537.1,NM_006214.3	101,101	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	probably-damaging,probably-damaging	175/239,275/339	13325695	3,13003	2203	4300	6503	SO:0001583	missense	5264				fatty acid alpha-oxidation|nervous system development	peroxisomal matrix	electron carrier activity|L-ascorbic acid binding|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|phytanoyl-CoA dioxygenase activity|protein binding	g.chr10:13325695G>A		CCDS7097.1, CCDS41489.1	10p13	2010-04-27	2006-01-09		ENSG00000107537	ENSG00000107537	1.14.11.18		8940	protein-coding gene	gene with protein product	"""Refsum disease"", ""phytanoyl-CoA dioxygenase"""	602026	"""phytanoyl-CoA hydroxylase (Refsum disease)"", ""phytanoyl-CoA hydroxylase"""			9326939	Standard	XM_005252469		Approved	PAHX, RD, PHYH1	uc001imf.3	O14832	OTTHUMG00000017693	ENST00000263038.4:c.823C>T	10.37:g.13325695G>A	ENSP00000263038:p.Arg275Trp					PHYH_ENST00000396913.2_Missense_Mutation_p.R175W|PHYH_ENST00000263038.4_Missense_Mutation_p.R275W	p.R258W			O14832	PAHX_HUMAN			7	1176	-		Ovarian(717;0.0448)	275					A8MTS8|B1ALH5	Missense_Mutation	SNP	ENST00000263038.4	37	c.772C>T	CCDS7097.1	.	.	.	.	.	.	.	.	.	.	G	16.67	3.187110	0.57909	0.0	3.49E-4	ENSG00000107537	ENST00000396913;ENST00000263038;ENST00000396920;ENST00000453759	D;D;D;D	0.99042	-5.36;-5.36;-5.36;-5.36	5.86	0.573	0.17363	.	0.000000	0.85682	D	0.000000	D	0.99245	0.9737	H	0.94808	3.585	0.80722	A	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99391	1.0925	9	0.87932	D	0	-15.0804	6.327	0.21248	0.0608:0.1057:0.4182:0.4153	rs28939671	258;275	B1ALH6;O14832	.;PAHX_HUMAN	W	175;275;258;175	ENSP00000380121:R175W;ENSP00000263038:R275W;ENSP00000380126:R258W;ENSP00000412525:R175W	ENSP00000263038:R275W	R	-	1	2	PHYH	13365701	1.000000	0.71417	0.965000	0.40720	0.300000	0.27592	2.191000	0.42640	-0.145000	0.11294	0.591000	0.81541	CGG		0.423	PHYH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046845.2			16	96	0	0	0	1	0	16	96				
GTF2IRD2P1	401375	broad.mit.edu	37	7	72664015	72664015	+	RNA	SNP	C	C	G	rs202030378|rs372212945	byFrequency	TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr7:72664015C>G	ENST00000425256.1	-	0	885									GTF2I repeat domain containing 2 pseudogene 1																		ATACCACCCCCGGGGCATGCC	0.507																																						ENST00000425256.1																			0																																																			0							g.chr7:72664015C>G	AY312852		7q11.23	2010-03-19	2010-02-09	2010-02-09	ENSG00000214544	ENSG00000214544			33127	pseudogene	pseudogene			"""GTF2I repeat domain containing 2 pseudogene"""	GTF2IRD2P		15100712	Standard	NG_033736		Approved		uc003txs.1		OTTHUMG00000156803		7.37:g.72664015C>G								NR_002164.1						0	885	-									RNA	SNP	ENST00000425256.1	37																																																																																						0.507	GTF2IRD2P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000345921.1	NR_002164		4	16	0	0	0	1	0	4	16				
GNL3	26354	broad.mit.edu	37	3	52720844	52720845	+	Splice_Site	DNP	GT	GT	TC			TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr3:52720844_52720845GT>TC	ENST00000418458.1	+	2	245		c.e2+1		SNORD19_ENST00000391191.1_RNA|GNL3_ENST00000394799.2_Splice_Site|PBRM1_ENST00000394830.3_5'Flank|GNL3_ENST00000460073.1_Intron|SNORD19B_ENST00000516978.1_RNA	NM_014366.4|NM_206826.1	NP_055181.3|NP_996562.1	Q9BVP2	GNL3_HUMAN	guanine nucleotide binding protein-like 3 (nucleolar)						cell proliferation (GO:0008283)|GTP catabolic process (GO:0006184)|regulation of cell proliferation (GO:0042127)|ribosome biogenesis (GO:0042254)	extracellular space (GO:0005615)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(3)|large_intestine(3)|lung(2)	12				BRCA - Breast invasive adenocarcinoma(193;6.75e-05)|Kidney(197;0.000611)|KIRC - Kidney renal clear cell carcinoma(197;0.000773)|OV - Ovarian serous cystadenocarcinoma(275;0.048)		CCAAAAAAAGGTAAGTGTAGTG	0.386																																						ENST00000394799.2																			0				breast(4)|endometrium(3)|large_intestine(3)|lung(2)	12						c.e2+1|c.e2+2		guanine nucleotide binding protein-like 3 (nucleolar)																																				SO:0001630	splice_region_variant	26354				regulation of cell proliferation	nucleolus	GTP binding|protein binding	g.chr3:52720844G>T|g.chr3:52720845T>C	AK027514	CCDS2861.1, CCDS43100.1	3p21.1	2005-01-10			ENSG00000163938	ENSG00000163938			29931	protein-coding gene	gene with protein product		608011				11085516, 12464630	Standard	NM_014366		Approved	C77032, E2IG3, MGC800, NS, nucleostemin	uc003dfd.3	Q9BVP2	OTTHUMG00000158752	Exception_encountered	3.37:g.52720844_52720845delinsTC						GNL3_ENST00000460073.1_Intron|GNL3_ENST00000418458.1_Splice_Site		NM_206825.1	NP_996561.1	Q9BVP2	GNL3_HUMAN		BRCA - Breast invasive adenocarcinoma(193;6.75e-05)|Kidney(197;0.000611)|KIRC - Kidney renal clear cell carcinoma(197;0.000773)|OV - Ovarian serous cystadenocarcinoma(275;0.048)	2	246	+								B2RDC1|Q5PU80|Q96SV6|Q96SV7|Q9UJY0	Splice_Site	SNP	ENST00000418458.1	37		CCDS2861.1																																																																																				0.386	GNL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352032.1	NM_014366	Intron	7	32|30	1|0	0	3.09899e-07|0	1	3.25791e-07|0	7	30				
PKHD1	5314	broad.mit.edu	37	6	51947999	51947999	+	Missense_Mutation	SNP	G	G	A	rs137852944		TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr6:51947999G>A	ENST00000371117.3	-	3	382	c.107C>T	c.(106-108)aCg>aTg	p.T36M	PKHD1_ENST00000340994.4_Missense_Mutation_p.T36M	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	36	IPT/TIG 1; atypical.		T -> M (in ARPKD; common mutation; dbSNP:rs28939383). {ECO:0000269|PubMed:11898128, ECO:0000269|PubMed:11919560, ECO:0000269|PubMed:12506140, ECO:0000269|PubMed:12846734, ECO:0000269|PubMed:12874454, ECO:0000269|PubMed:15108281}.		cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					TGTGATCCACGTTCCCCCTGC	0.393													G|||	1	0.000199681	0.0	0.0	5008	,	,		22118	0.0		0.0	False		,,,				2504	0.001					ENST00000371117.3																			0				NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	GRCh37	CM020490	PKHD1	M	rs137852944	c.(106-108)aCg>aTg		polycystic kidney and hepatic disease 1 (autosomal recessive)		G	MET/THR,MET/THR	1,4405	2.1+/-5.4	0,1,2202	141.0	117.0	125.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	107,107	5.5	0.9	6	dbSNP_133	125	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	PKHD1	NM_138694.3,NM_170724.2	81,81	0,4,6499	AA,AG,GG		0.0349,0.0227,0.0308	probably-damaging,probably-damaging	36/4075,36/3397	51947999	4,13002	2203	4300	6503	SO:0001583	missense	5314				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity	g.chr6:51947999G>A	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.107C>T	6.37:g.51947999G>A	ENSP00000360158:p.Thr36Met					PKHD1_ENST00000340994.4_Missense_Mutation_p.T36M	p.T36M	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN			3	382	-	Lung NSC(77;0.0605)		36		T -> M (in ARPKD; common mutation; dbSNP:rs28939383).	IPT/TIG 1; atypical.		Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	c.107C>T	CCDS4935.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	21.3	4.127301	0.77549	2.27E-4	3.49E-4	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.91996	-2.75;-2.95	5.51	5.51	0.81932	.	0.000000	0.64402	D	0.000003	D	0.94716	0.8295	M	0.63843	1.955	0.33698	A	0.614121	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.972	D	0.95125	0.8250	9	0.87932	D	0	.	16.5687	0.84605	0.0:0.0:1.0:0.0	rs28939383	36;36	P08F94-2;P08F94	.;PKHD1_HUMAN	M	36	ENSP00000360158:T36M;ENSP00000341097:T36M	ENSP00000341097:T36M	T	-	2	0	PKHD1	52055958	1.000000	0.71417	0.940000	0.37924	0.981000	0.71138	5.608000	0.67654	2.605000	0.88082	0.563000	0.77884	ACG		0.393	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		4	75	0	0	0	1	0	4	75				
CACNG2	10369	broad.mit.edu	37	22	36960572	36960572	+	Silent	SNP	C	C	T			TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr22:36960572C>T	ENST00000300105.6	-	4	1779	c.798G>A	c.(796-798)acG>acA	p.T266T	RP5-1119A7.17_ENST00000562756.1_RNA	NM_006078.3	NP_006069.1	Q9Y698	CCG2_HUMAN	calcium channel, voltage-dependent, gamma subunit 2	266					membrane depolarization (GO:0051899)|membrane hyperpolarization (GO:0060081)|neuromuscular junction development (GO:0007528)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	18						TGGAGATCTCCGTGGACGGCA	0.667																																						ENST00000300105.6																			0				breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	18						c.(796-798)acG>acA		calcium channel, voltage-dependent, gamma subunit 2							69.0	73.0	72.0					22																	36960572		2203	4300	6503	SO:0001819	synonymous_variant	10369				membrane depolarization|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity	g.chr22:36960572C>T	AF096322	CCDS13931.1	22q13.1	2006-08-01			ENSG00000166862	ENSG00000166862		"""Calcium channel subunits"""	1406	protein-coding gene	gene with protein product		602911					Standard	NM_006078		Approved	stargazin, MGC138502, MGC138504	uc003aps.2	Q9Y698	OTTHUMG00000030612	ENST00000300105.6:c.798G>A	22.37:g.36960572C>T							p.T266T	NM_006078.3	NP_006069.1	Q9Y698	CCG2_HUMAN			4	1779	-			266					Q2M1M1|Q5TGT3|Q9UGZ7	Silent	SNP	ENST00000300105.6	37	c.798G>A	CCDS13931.1																																																																																				0.667	CACNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075500.2			5	72	0	0	0	1	0	5	72				
MLLT3	4300	broad.mit.edu	37	9	20414352	20414352	+	Silent	SNP	G	G	A			TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr9:20414352G>A	ENST00000380338.4	-	5	778	c.492C>T	c.(490-492)agC>agT	p.S164S	MLLT3_ENST00000429426.2_Silent_p.S161S|MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000475957.1_5'UTR	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3	164	Poly-Ser.				anterior/posterior pattern specification (GO:0009952)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of transcription, DNA-templated (GO:0006355)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		tactgctgctgctgctgctgc	0.537			T	MLL	ALL																																	ENST00000380338.4				Dom	yes		9	9p22	4300	T	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 (AF9)"""			L	MLL		ALL		0				central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66						c.(490-492)agC>agT		myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3																																				SO:0001819	synonymous_variant	4300				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding	g.chr9:20414352G>A	L13744	CCDS6494.1	9p22	2008-02-05	2001-11-28		ENSG00000171843	ENSG00000171843			7136	protein-coding gene	gene with protein product		159558	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 3"""			8506309, 8414510	Standard	NM_001286691		Approved	AF-9, AF9, YEATS3	uc003zoe.2	P42568	OTTHUMG00000019650	ENST00000380338.4:c.492C>T	9.37:g.20414352G>A						MLLT3_ENST00000475957.1_5'UTR|MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S161S	p.S164S	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN		GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)	5	778	-			164			Poly-Ser.		B1AMQ2|B2R7B3|B7Z755|D3DRJ8|Q8IVB0	Silent	SNP	ENST00000380338.4	37	c.492C>T	CCDS6494.1																																																																																				0.537	MLLT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051872.1	NM_004529		5	50	0	0	0	1	0	5	50				
PER2	8864	broad.mit.edu	37	2	239181795	239181795	+	Missense_Mutation	SNP	C	C	G			TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr2:239181795C>G	ENST00000254657.3	-	5	765	c.486G>C	c.(484-486)gaG>gaC	p.E162D	PER2_ENST00000440245.1_Missense_Mutation_p.E162D|PER2_ENST00000355768.2_Missense_Mutation_p.E162D|PER2_ENST00000254658.3_Missense_Mutation_p.E162D	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	162					circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|fatty acid metabolic process (GO:0006631)|gluconeogenesis (GO:0006094)|glycogen biosynthetic process (GO:0005978)|histone H3 deacetylation (GO:0070932)|lactate biosynthetic process (GO:0019249)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of DNA-templated transcription, termination (GO:0060567)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of glutamate uptake involved in transmission of nerve impulse (GO:0051946)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of vasoconstriction (GO:0019229)|response to ischemia (GO:0002931)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	pre-mRNA binding (GO:0036002)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|ubiquitin binding (GO:0043130)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)		AGGGGTGACCCTCGCTGGACA	0.567																																						ENST00000254657.3																			0				NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						c.(484-486)gaG>gaC		period circadian clock 2							83.0	68.0	73.0					2																	239181795		2203	4300	6503	SO:0001583	missense	8864				circadian rhythm|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding|signal transducer activity	g.chr2:239181795C>G	AB002345	CCDS2528.1	2q37.3	2012-12-13	2012-12-13		ENSG00000132326	ENSG00000132326			8846	protein-coding gene	gene with protein product		603426	"""period (Drosophila) homolog 2"", ""period homolog 2 (Drosophila)"""			9427249, 17218255	Standard	NM_022817		Approved	KIAA0347	uc002vyc.3	O15055	OTTHUMG00000152884	ENST00000254657.3:c.486G>C	2.37:g.239181795C>G	ENSP00000254657:p.Glu162Asp					PER2_ENST00000440245.1_Missense_Mutation_p.E162D|PER2_ENST00000355768.2_Missense_Mutation_p.E162D|PER2_ENST00000254658.3_Missense_Mutation_p.E162D	p.E162D	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)	5	765	-		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)	162					A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	Missense_Mutation	SNP	ENST00000254657.3	37	c.486G>C	CCDS2528.1	.	.	.	.	.	.	.	.	.	.	C	10.37	1.331319	0.24167	.	.	ENSG00000132326	ENST00000254657;ENST00000254658;ENST00000440245;ENST00000355768	T;T;T;T	0.50548	2.75;0.74;1.84;0.74	4.81	0.632	0.17705	.	0.470425	0.25189	N	0.032465	T	0.52853	0.1760	L	0.42245	1.32	0.27718	N	0.945222	B;D;B;B	0.64830	0.228;0.994;0.008;0.008	B;D;B;B	0.70716	0.117;0.97;0.044;0.029	T	0.43294	-0.9400	10	0.33141	T	0.24	-18.5789	9.1613	0.37023	0.0:0.4539:0.4559:0.0902	.	162;162;162;162	F5GYD5;B4DH14;O15055-2;O15055	.;.;.;PER2_HUMAN	D	162	ENSP00000254657:E162D;ENSP00000254658:E162D;ENSP00000397516:E162D;ENSP00000348013:E162D	ENSP00000254657:E162D	E	-	3	2	PER2	238846534	0.996000	0.38824	0.101000	0.21167	0.613000	0.37349	0.724000	0.25954	0.529000	0.28599	0.655000	0.94253	GAG		0.567	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257167.1	NM_022817		3	34	0	0	0	1	0	3	34				
MCMBP	79892	broad.mit.edu	37	10	121591577	121591577	+	Silent	SNP	G	G	A			TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr10:121591577G>A	ENST00000360003.3	-	15	1918	c.1749C>T	c.(1747-1749)aaC>aaT	p.N583N	MCMBP_ENST00000466047.1_5'UTR|MCMBP_ENST00000369077.3_Silent_p.N581N	NM_001256378.1|NM_001256379.1|NM_024834.3	NP_001243307.1|NP_001243308.1|NP_079110.1	Q9BTE3	MCMBP_HUMAN	minichromosome maintenance complex binding protein	583					DNA-dependent DNA replication (GO:0006261)|mitotic nuclear division (GO:0007067)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(2)|skin(2)	21						TCTGAGGGTCGTTCTTCCGCA	0.423																																						ENST00000360003.3																			0				breast(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(2)|skin(2)	21						c.(1747-1749)aaC>aaT		minichromosome maintenance complex binding protein							152.0	122.0	132.0					10																	121591577		2203	4300	6503	SO:0001819	synonymous_variant	79892				cell division|DNA-dependent DNA replication|mitosis|S phase of mitotic cell cycle|sister chromatid cohesion	nucleus	chromatin binding	g.chr10:121591577G>A	BC007219	CCDS7617.1, CCDS58099.1	10q26.13	2013-10-11	2011-01-05	2011-01-05	ENSG00000197771	ENSG00000197771			25782	protein-coding gene	gene with protein product		610909	"""chromosome 10 open reading frame 119"""	C10orf119		17296731	Standard	NM_024834		Approved	FLJ13081, MCM-BP	uc001ler.3	Q9BTE3	OTTHUMG00000019159	ENST00000360003.3:c.1749C>T	10.37:g.121591577G>A						MCMBP_ENST00000466047.1_5'UTR|MCMBP_ENST00000369077.3_Silent_p.N581N	p.N583N	NM_001256378.1|NM_001256379.1|NM_024834.3	NP_001243307.1|NP_001243308.1|NP_079110.1	Q9BTE3	MCMBP_HUMAN			15	1918	-			583					B3KSP7|Q6IA56|Q9BVT9|Q9H916	Silent	SNP	ENST00000360003.3	37	c.1749C>T	CCDS7617.1																																																																																				0.423	MCMBP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050684.1	NM_024834		10	44	0	0	0	1	0	10	44				
PDP1	54704	broad.mit.edu	37	8	94934324	94934324	+	Missense_Mutation	SNP	C	C	G			TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr8:94934324C>G	ENST00000297598.4	+	2	306	c.37C>G	c.(37-39)Cgt>Ggt	p.R13G	PDP1_ENST00000517764.1_Missense_Mutation_p.R13G|PDP1_ENST00000396200.3_Missense_Mutation_p.R38G|PDP1_ENST00000520728.1_Missense_Mutation_p.R13G	NM_001161781.1|NM_018444.3	NP_001155253.1|NP_060914.2	Q9P0J1	PDP1_HUMAN	pyruvate dehyrogenase phosphatase catalytic subunit 1	13					cellular metabolic process (GO:0044237)|peptidyl-threonine dephosphorylation (GO:0035970)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	[pyruvate dehydrogenase (lipoamide)] phosphatase activity (GO:0004741)|metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|liver(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)	18						TCCTCTCATCCGTAACTGTGA	0.473																																						ENST00000396200.3																			0				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|liver(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)	18						c.(112-114)Cgt>Ggt		pyruvate dehyrogenase phosphatase catalytic subunit 1							167.0	151.0	157.0					8																	94934324		2203	4300	6503	SO:0001583	missense	54704				pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix|protein serine/threonine phosphatase complex	[pyruvate dehydrogenase (lipoamide)] phosphatase activity	g.chr8:94934324C>G	AF155661	CCDS6259.1, CCDS55262.1	8q22.1	2012-04-17	2009-06-12	2009-06-12	ENSG00000164951	ENSG00000164951	3.1.3.43	"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	9279	protein-coding gene	gene with protein product		605993	"""protein phosphatase 2C, magnesium-dependent, catalytic subunit"""	PPM2C		8396421	Standard	NM_001161779		Approved	PDP, PDH	uc003ygf.3	Q9P0J1		ENST00000297598.4:c.37C>G	8.37:g.94934324C>G	ENSP00000297598:p.Arg13Gly					PDP1_ENST00000517764.1_Missense_Mutation_p.R13G|PDP1_ENST00000520728.1_Missense_Mutation_p.R13G|PDP1_ENST00000297598.4_Missense_Mutation_p.R13G	p.R38G	NM_001161779.1	NP_001155251.1	Q9P0J1	PDP1_HUMAN			3	388	+			13					B3KX71|J3KPU0|Q5U5K1	Missense_Mutation	SNP	ENST00000297598.4	37	c.112C>G	CCDS6259.1	.	.	.	.	.	.	.	.	.	.	C	11.55	1.673522	0.29693	.	.	ENSG00000164951	ENST00000297598;ENST00000520614;ENST00000520728;ENST00000518107;ENST00000396200;ENST00000518573;ENST00000517764;ENST00000518827;ENST00000521144	T;T;T;T	0.53423	0.69;0.69;0.62;0.69	6.16	6.16	0.99307	.	0.135816	0.47093	D	0.000251	T	0.39911	0.1096	L	0.44542	1.39	0.44323	D	0.997203	P;B	0.39737	0.685;0.206	B;B	0.32393	0.145;0.019	T	0.40059	-0.9583	10	0.72032	D	0.01	-15.1349	15.5636	0.76269	0.1378:0.8622:0.0:0.0	.	64;13	B4DYX8;Q9P0J1	.;PDP1_HUMAN	G	13;13;13;13;38;13;13;13;13	ENSP00000297598:R13G;ENSP00000428317:R13G;ENSP00000379503:R38G;ENSP00000430380:R13G	ENSP00000297598:R13G	R	+	1	0	PDP1	95003500	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.978000	0.56881	2.937000	0.99478	0.650000	0.86243	CGT		0.473	PDP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378415.2	NM_018444		10	56	0	0	0	1	0	10	56				
CLASP2	23122	broad.mit.edu	37	3	33557515	33557515	+	Splice_Site	SNP	C	C	T			TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr3:33557515C>T	ENST00000468888.2	-	36	4180	c.4134G>A	c.(4132-4134)gaG>gaA	p.E1378E	CLASP2_ENST00000480013.1_Splice_Site_p.E1157E|CLASP2_ENST00000359576.5_Splice_Site_p.E1369E|CLASP2_ENST00000307312.7_Splice_Site_p.E859E|CLASP2_ENST00000461133.3_Splice_Site_p.E1137E|CLASP2_ENST00000399362.4_Splice_Site_p.E1377E|CLASP2_ENST00000539981.1_3'UTR			O75122	CLAP2_HUMAN	cytoplasmic linker associated protein 2	1158					axon guidance (GO:0007411)|establishment or maintenance of cell polarity (GO:0007163)|fucosylation (GO:0036065)|microtubule anchoring (GO:0034453)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)|regulation of microtubule polymerization or depolymerization (GO:0031110)|regulation of microtubule-based process (GO:0032886)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)|microtubule plus-end binding (GO:0051010)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	48						GGTAACTTACCTCCTTATGAG	0.318																																						ENST00000399362.4																			0				breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	48						c.e36+1		cytoplasmic linker associated protein 2							101.0	95.0	97.0					3																	33557515		1833	4086	5919	SO:0001630	splice_region_variant	23122							g.chr3:33557515C>T	AB014527		3p24.3	2013-01-18			ENSG00000163539	ENSG00000163539			17078	protein-coding gene	gene with protein product		605853				9734811, 10899121	Standard	NM_015097		Approved	KIAA0627	uc021wvc.1	O75122	OTTHUMG00000156489	ENST00000468888.2:c.4134+1G>A	3.37:g.33557515C>T						CLASP2_ENST00000307312.7_Splice_Site_p.E859_splice|CLASP2_ENST00000480013.1_Splice_Site_p.E1157_splice|CLASP2_ENST00000359576.5_Splice_Site_p.E1369_splice|CLASP2_ENST00000539981.1_3'UTR|CLASP2_ENST00000461133.3_Splice_Site_p.E1137_splice|CLASP2_ENST00000468888.2_Splice_Site_p.E1378_splice	p.E1377_splice	NM_015097.2	NP_055912.2	B2RTR1	B2RTR1_HUMAN			36	4484	-			1379					Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	Splice_Site	SNP	ENST00000468888.2	37	c.4131_splice		.	.	.	.	.	.	.	.	.	.	C	13.53	2.263991	0.39995	.	.	ENSG00000163539	ENST00000487553	.	.	.	5.03	5.03	0.67393	.	.	.	.	.	T	0.74450	0.3718	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.73344	-0.4012	4	.	.	.	-18.7248	18.5544	0.91079	0.0:1.0:0.0:0.0	.	.	.	.	R	153	.	.	G	-	1	0	CLASP2	33532519	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	5.556000	0.67307	2.611000	0.88343	0.563000	0.77884	GGG		0.318	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000344320.4	NM_001207044	Silent	4	18	0	0	0	1	0	4	18				
CACNG5	27091	broad.mit.edu	37	17	64880940	64880940	+	Intron	SNP	C	C	A			TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr17:64880940C>A	ENST00000533854.1	+	6	807				CACNG5_ENST00000169565.3_Nonsense_Mutation_p.Y244*|CACNG5_ENST00000307139.3_Intron			Q9UF02	CCG5_HUMAN	calcium channel, voltage-dependent, gamma subunit 5						regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ion transmembrane transporter activity (GO:0015075)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)|skin(2)	24			BRCA - Breast invasive adenocarcinoma(6;1.61e-08)			CACTGTCTTACCTTTCTGGGT	0.602																																						ENST00000169565.3																			0				NS(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)|skin(2)	24						c.(730-732)taC>taA		calcium channel, voltage-dependent, gamma subunit 5							97.0	79.0	85.0					17																	64880940		2203	4300	6503	SO:0001627	intron_variant	27091				regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|postsynaptic density|postsynaptic membrane	voltage-gated calcium channel activity	g.chr17:64880940C>A	AF148220	CCDS11665.1	17q24	2004-02-16				ENSG00000075429		"""Calcium channel subunits"""	1409	protein-coding gene	gene with protein product		606405				10613843	Standard	NM_145811		Approved		uc010wqj.2	Q9UF02		ENST00000533854.1:c.571-160C>A	17.37:g.64880940C>A						CACNG5_ENST00000533854.1_Intron|CACNG5_ENST00000307139.3_Intron	p.Y244*			Q9UF02	CCG5_HUMAN	BRCA - Breast invasive adenocarcinoma(6;1.61e-08)		4	732	+			0	SAGVMSVYLFMKRYTAEDMYRPHPGFYRPRLSNCSDYSGQF LHPDAWVRGRSPSDISSEASLQMNSNYPALLKCPDYDQMSS SPC -> VKPVTLSMDRLGLGTAPLSRGEWGWGRRDIPQPF WTPDHPLYFPSSSQNVSLSYLSGSPPARMSPGPCSCPHVHF PPHSSCVLCRPQPREMRQAPAASPSSAVFSL (in Ref. 1; AAF03089).				A8K2A6|Q547R3|Q8WXS7|Q9UHM3	Nonsense_Mutation	SNP	ENST00000533854.1	37	c.732C>A	CCDS11665.1	.	.	.	.	.	.	.	.	.	.	C	11.60	1.685861	0.29962	.	.	ENSG00000075429	ENST00000169565	.	.	.	2.89	1.85	0.25348	.	1.382030	0.05535	N	0.564742	.	.	.	.	.	.	0.37943	D	0.932394	.	.	.	.	.	.	.	.	.	.	.	.	.	-1.047	7.5936	0.28035	0.0:0.7342:0.2658:0.0	.	.	.	.	X	244	.	.	Y	+	3	2	CACNG5	62311402	0.002000	0.14202	0.001000	0.08648	0.104000	0.19210	0.353000	0.20130	0.731000	0.32448	0.603000	0.83216	TAC		0.602	CACNG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389882.1	NM_014404, NM_145811		17	40	1	0	3.52763e-06	1	3.61582e-06	17	40				
ADAMTS8	11095	broad.mit.edu	37	11	130281313	130281313	+	Splice_Site	SNP	G	G	A	rs201797398		TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr11:130281313G>A	ENST00000257359.6	-	6	2455	c.1749C>T	c.(1747-1749)gaC>gaT	p.D583D		NM_007037.4	NP_008968.4	Q9UP79	ATS8_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 8	583	Cys-rich.				negative regulation of cell proliferation (GO:0008285)|phosphate ion transmembrane transport (GO:0035435)	proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)|low-affinity phosphate transmembrane transporter activity (GO:0009673)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.D583D(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	10	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.039)|Lung(977;0.213)		GGTAATTACCGTCAGGGGGGC	0.582													G|||	1	0.000199681	0.0	0.0	5008	,	,		17916	0.001		0.0	False		,,,				2504	0.0					ENST00000257359.6																			1	Substitution - coding silent(1)	p.D583D(1)	prostate(1)	central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	10						c.e6+1		ADAM metallopeptidase with thrombospondin type 1 motif, 8		G		0,3950		0,0,1975	56.0	61.0	59.0		1749	-3.8	0.0	11		59	4,8242		0,4,4119	no	coding-synonymous-near-splice	ADAMTS8	NM_007037.4		0,4,6094	AA,AG,GG		0.0485,0.0,0.0328		583/890	130281313	4,12192	1975	4123	6098	SO:0001630	splice_region_variant	11095				negative regulation of cell proliferation|proteolysis	proteinaceous extracellular matrix	heparin binding|integrin binding|low affinity phosphate transmembrane transporter activity|metalloendopeptidase activity|zinc ion binding	g.chr11:130281313G>A	AF060153	CCDS41732.1	11q25	2008-07-18	2005-08-19		ENSG00000134917	ENSG00000134917		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	224	protein-coding gene	gene with protein product		605175	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 8"""			10438512	Standard	NM_007037		Approved	METH2, FLJ41712, ADAM-TS8	uc001qgg.4	Q9UP79	OTTHUMG00000165656	ENST00000257359.6:c.1750+1C>T	11.37:g.130281313G>A							p.D583_splice	NM_007037.4	NP_008968.4	Q9UP79	ATS8_HUMAN		OV - Ovarian serous cystadenocarcinoma(99;0.039)|Lung(977;0.213)	6	2455	-	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)	583			Cys-rich.		Q9NZS0	Splice_Site	SNP	ENST00000257359.6	37	c.1750_splice	CCDS41732.1																																																																																				0.582	ADAMTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385636.1	NM_007037	Silent	3	23	0	0	0	1	0	3	23				
MAP7D1	55700	broad.mit.edu	37	1	36641841	36641841	+	Missense_Mutation	SNP	G	G	A			TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr1:36641841G>A	ENST00000373151.2	+	7	1108	c.892G>A	c.(892-894)Gat>Aat	p.D298N	MAP7D1_ENST00000373150.4_Missense_Mutation_p.D298N|MAP7D1_ENST00000373148.4_5'Flank|MAP7D1_ENST00000316156.4_Missense_Mutation_p.D261N|MAP7D1_ENST00000474796.1_3'UTR	NM_018067.3	NP_060537.3	Q3KQU3	MA7D1_HUMAN	MAP7 domain containing 1	298					microtubule cytoskeleton organization (GO:0000226)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)				breast(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	19		Myeloproliferative disorder(586;0.0393)				CAGCATCGTGGATCGTCTGAT	0.677																																						ENST00000316156.4																			0				breast(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	19						c.(781-783)Gat>Aat		MAP7 domain containing 1							23.0	26.0	25.0					1																	36641841		2164	4285	6449	SO:0001583	missense	55700					cytoplasm|spindle		g.chr1:36641841G>A	AK096341	CCDS30673.1, CCDS65492.1, CCDS65493.1	1p34.3	2008-02-05	2007-02-08	2007-02-08	ENSG00000116871	ENSG00000116871			25514	protein-coding gene	gene with protein product			"""proline arginine rich coiled coil 1"", ""arginine/proline rich coiled-coil 1"""	PARCC1, RPRC1		10574461	Standard	XM_005271024		Approved	FLJ10350, FLJ39022	uc001bzz.3	Q3KQU3	OTTHUMG00000007714	ENST00000373151.2:c.892G>A	1.37:g.36641841G>A	ENSP00000362244:p.Asp298Asn					MAP7D1_ENST00000474796.1_3'UTR|MAP7D1_ENST00000373151.2_Missense_Mutation_p.D298N|MAP7D1_ENST00000373150.4_Missense_Mutation_p.D298N	p.D261N			Q3KQU3	MA7D1_HUMAN			6	1234	+		Myeloproliferative disorder(586;0.0393)	298					D3DPS4|Q7L8J5|Q8N905|Q8TAK0|Q9HBQ2|Q9NW29|Q9ULN3	Missense_Mutation	SNP	ENST00000373151.2	37	c.781G>A	CCDS30673.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.310631	0.81358	.	.	ENSG00000116871	ENST00000316156;ENST00000373150;ENST00000373151	T;T;T	0.05580	3.42;3.42;3.42	5.3	5.3	0.74995	.	0.000000	0.39475	N	0.001360	T	0.12390	0.0301	L	0.27053	0.805	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.81914	0.993;0.995;0.982	T	0.05305	-1.0893	10	0.02654	T	1	-18.67	17.499	0.87726	0.0:0.0:1.0:0.0	.	261;298;298	Q3KQU3-2;Q3KQU3-4;Q3KQU3	.;.;MA7D1_HUMAN	N	261;298;298	ENSP00000320228:D261N;ENSP00000362243:D298N;ENSP00000362244:D298N	ENSP00000320228:D261N	D	+	1	0	MAP7D1	36414428	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.379000	0.97198	2.454000	0.82982	0.655000	0.94253	GAT		0.677	MAP7D1-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382095.1	NM_018067		5	6	0	0	0	1	0	5	6				
EMR2	30817	broad.mit.edu	37	19	14866467	14866467	+	Splice_Site	SNP	C	C	T	rs142367407		TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr19:14866467C>T	ENST00000315576.3	-	13	1866	c.1415G>A	c.(1414-1416)cGt>cAt	p.R472H	EMR2_ENST00000594294.1_Splice_Site_p.R423H|EMR2_ENST00000353005.1_Splice_Site_p.R330H|EMR2_ENST00000346057.1_Splice_Site_p.R423H|EMR2_ENST00000595839.1_Splice_Site_p.R330H|EMR2_ENST00000601345.1_Splice_Site_p.R461H|EMR2_ENST00000596991.2_Splice_Site_p.R461H|EMR2_ENST00000353876.1_Splice_Site_p.R379H|EMR2_ENST00000392965.3_Splice_Site_p.R472H|EMR2_ENST00000392967.2_Splice_Site_p.R461H|EMR2_ENST00000392964.3_Intron|EMR2_ENST00000594076.1_Splice_Site_p.R379H	NM_013447.3	NP_038475.2	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 2	472					cell adhesion (GO:0007155)|cell migration (GO:0016477)|G-protein coupled receptor signaling pathway (GO:0007186)|granulocyte chemotaxis (GO:0071621)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	48						AGCACTCACACGGTGGGAGAA	0.577																																						ENST00000315576.3																			0				breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	48						c.e13+1		egf-like module containing, mucin-like, hormone receptor-like 2		C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	162.0	145.0	151.0		1415,1268,1136,989,1382,1235,1103	-7.9	0.0	19	dbSNP_134	151	0,8600		0,0,4300	yes	missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice	EMR2	NM_013447.2,NM_152916.1,NM_152917.1,NM_152918.1,NM_152919.1,NM_152920.1,NM_152921.1	29,29,29,29,29,29,29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign,benign,benign,benign,benign,benign	472/824,423/775,379/731,330/682,461/813,412/764,368/720	14866467	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	30817				cell adhesion|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity	g.chr19:14866467C>T	AF114491	CCDS32935.1, CCDS59361.1	19p13.1	2014-08-08	2003-11-26			ENSG00000127507		"""CD molecules"", ""-"", ""GPCR / Class B : Orphans"""	3337	protein-coding gene	gene with protein product		606100	"""egf-like module containing, mucin-like, hormone receptor-like sequence 2"""				Standard	NM_013447		Approved	CD312	uc002mzp.2	Q9UHX3		ENST00000315576.3:c.1416+1G>A	19.37:g.14866467C>T						EMR2_ENST00000392967.2_Splice_Site_p.R461_splice|EMR2_ENST00000392964.3_Intron|EMR2_ENST00000353876.1_Splice_Site_p.R379_splice|EMR2_ENST00000595839.1_Splice_Site_p.R330_splice|EMR2_ENST00000596991.2_Splice_Site_p.R461_splice|EMR2_ENST00000594294.1_Splice_Site_p.R423_splice|EMR2_ENST00000594076.1_Splice_Site_p.R379_splice|EMR2_ENST00000353005.1_Splice_Site_p.R330_splice|EMR2_ENST00000346057.1_Splice_Site_p.R423_splice|EMR2_ENST00000392965.3_Splice_Site_p.R472_splice|EMR2_ENST00000601345.1_Splice_Site_p.R461_splice	p.R472_splice	NM_013447.2	NP_038475.2	Q9UHX3	EMR2_HUMAN			13	1866	-			472					B4DQ96|E7ESD7|E9PBR1|E9PEL6|E9PFQ5|E9PG91|Q8NG96|Q9Y4B1	Splice_Site	SNP	ENST00000315576.3	37	c.1416_splice	CCDS32935.1	.	.	.	.	.	.	.	.	.	.	C	7.738	0.700673	0.15106	2.27E-4	0.0	ENSG00000127507	ENST00000315576;ENST00000392967;ENST00000346057;ENST00000353876;ENST00000353005;ENST00000392965	T;T;T;T;T;T	0.77229	-0.95;-1.08;-0.48;0.31;1.04;1.18	3.94	-7.88	0.01178	.	.	.	.	.	T	0.51007	0.1649	N	0.14661	0.345	0.09310	N	1	P;B;D;B;B;B;B;B	0.57899	0.951;0.121;0.981;0.002;0.121;0.037;0.283;0.132	B;B;B;B;B;B;B;B	0.41036	0.197;0.024;0.346;0.008;0.024;0.011;0.018;0.094	T	0.54675	-0.8258	9	0.35671	T	0.21	.	3.5975	0.08012	0.1165:0.3757:0.3524:0.1554	.	472;379;472;330;423;472;472;461	E7ESD7;Q9UHX3-4;A0JNV7;Q9UHX3-5;Q9UHX3-3;A8K6W1;Q9UHX3;Q9UHX3-2	.;.;.;.;.;.;EMR2_HUMAN;.	H	472;461;423;379;330;472	ENSP00000319883:R472H;ENSP00000376694:R461H;ENSP00000263380:R423H;ENSP00000319454:R379H;ENSP00000319838:R330H;ENSP00000376692:R472H	ENSP00000319883:R472H	R	-	2	0	EMR2	14727467	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	-4.163000	0.00282	-2.001000	0.00964	-1.420000	0.01111	CGT		0.577	EMR2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466502.2		Missense_Mutation	12	67	0	0	0	1	0	12	67				
KRTAP9-4	85280	broad.mit.edu	37	17	39406130	39406130	+	Missense_Mutation	SNP	G	G	A	rs201060748		TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr17:39406130G>A	ENST00000334109.2	+	1	192	c.158G>A	c.(157-159)cGc>cAc	p.R53H		NM_033191.2	NP_149461.2	Q9BYQ2	KRA94_HUMAN	keratin associated protein 9-4	53	15 X 5 AA repeats of C-C-[RQVGE]-[SPTN]- [TASPF].					keratin filament (GO:0045095)		p.R53H(4)		breast(1)|large_intestine(1)|lung(11)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			CCTTGCTGCCGCCCAACTTGC	0.642													.|||	1	0.000199681	0.0	0.0	5008	,	,		19351	0.0		0.001	False		,,,				2504	0.0					ENST00000334109.2																			4	Substitution - Missense(4)	p.R53H(4)	lung(3)|upper_aerodigestive_tract(1)	breast(1)|large_intestine(1)|lung(11)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18						c.(157-159)cGc>cAc		keratin associated protein 9-4							60.0	49.0	53.0					17																	39406130		2203	4299	6502	SO:0001583	missense	85280					keratin filament		g.chr17:39406130G>A	AJ406948	CCDS11386.1	17q21.2	2013-06-25			ENSG00000241595	ENSG00000241595		"""Keratin associated proteins"""	18902	protein-coding gene	gene with protein product						11279113	Standard	NM_033191		Approved	KAP9.4	uc002hwi.3	Q9BYQ2	OTTHUMG00000133438	ENST00000334109.2:c.158G>A	17.37:g.39406130G>A	ENSP00000334922:p.Arg53His						p.R53H	NM_033191.2	NP_149461.2	Q9BYQ2	KRA94_HUMAN	STAD - Stomach adenocarcinoma(17;0.000397)		1	192	+		Breast(137;0.000496)	53			15 X 5 AA repeats of C-C-[RQVGE]-[SPTN]- [TASPF].		Q0VAE3	Missense_Mutation	SNP	ENST00000334109.2	37	c.158G>A	CCDS11386.1	.	.	.	.	.	.	.	.	.	.	.	2.344	-0.350422	0.05173	.	.	ENSG00000241595	ENST00000334109	T	0.01099	5.34	2.57	-5.14	0.02875	.	.	.	.	.	T	0.01254	0.0041	L	0.57536	1.79	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.39099	-0.9630	9	0.40728	T	0.16	.	2.8899	0.05673	0.2815:0.2222:0.4039:0.0924	.	53	Q9BYQ2	KRA94_HUMAN	H	53	ENSP00000334922:R53H	ENSP00000334922:R53H	R	+	2	0	KRTAP9-4	36659656	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-2.235000	0.01202	-3.785000	0.00107	-2.699000	0.00136	CGC		0.642	KRTAP9-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257306.1			4	69	0	0	0	1	0	4	69				
TUBB8P7	197331	broad.mit.edu	37	16	90162513	90162513	+	RNA	SNP	T	T	C			TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr16:90162513T>C	ENST00000564451.1	+	0	1866				TUBB8P7_ENST00000567960.1_RNA					tubulin, beta 8 class VIII pseudogene 7									p.N415N(2)									GCAACATGAATGACCTGGTGT	0.537																																						ENST00000567960.1																			2	Substitution - coding silent(2)	p.N415N(2)	prostate(1)|kidney(1)																																																0							g.chr16:90162513T>C			16q24.3	2013-02-18			ENSG00000261812	ENSG00000261812			42345	pseudogene	pseudogene							Standard	NG_002334		Approved				OTTHUMG00000172847		16.37:g.90162513T>C						TUBB8P7_ENST00000564451.1_RNA								0	1249	+									RNA	SNP	ENST00000564451.1	37																																																																																						0.537	TUBB8P7-004	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000420856.1	NG_002334		4	95	0	0	0	1	0	4	95				
GPHN	10243	broad.mit.edu	37	14	67555762	67555762	+	Missense_Mutation	SNP	G	G	A			TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr14:67555762G>A	ENST00000315266.5	+	11	2229	c.1108G>A	c.(1108-1110)Gca>Aca	p.A370T	GPHN_ENST00000543237.1_Missense_Mutation_p.A416T|GPHN_ENST00000478722.1_Missense_Mutation_p.A403T|GPHN_ENST00000544752.2_3'UTR|GPHN_ENST00000305960.9_Missense_Mutation_p.A339T	NM_001024218.1	NP_001019389.1	Q9NQX3	GEPH_HUMAN	gephyrin	370	MPT adenylyltransferase.				establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycine receptor clustering (GO:0072579)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|molybdopterin adenylyltransferase activity (GO:0061598)|molybdopterin molybdotransferase activity (GO:0061599)|transferase activity (GO:0016740)			large_intestine(8)|liver(1)|ovary(2)|stomach(1)	12		all_cancers(7;0.0476)|all_hematologic(31;0.0116)		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)		CCCCTTCCCAGCATCAGTAAA	0.348			T	MLL	AL																																	ENST00000478722.1				Dom	yes		14	14q24	10243	T	gephyrin (GPH)			L	MLL		AL		0				large_intestine(8)|liver(1)|ovary(2)|stomach(1)	12						c.(1207-1209)Gca>Aca		gephyrin							88.0	83.0	84.0					14																	67555762		2203	4300	6503	SO:0001583	missense	10243				Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process	cell junction|cytoplasm|cytoskeleton|postsynaptic membrane	ATP binding|metal ion binding|nucleotidyltransferase activity	g.chr14:67555762G>A	AB037806	CCDS9777.1, CCDS32103.1	14q23.3	2008-04-22			ENSG00000171723	ENSG00000171723			15465	protein-coding gene	gene with protein product		603930				1319186, 10325225, 18403029	Standard	XM_005267250		Approved	KIAA1385	uc001xix.3	Q9NQX3	OTTHUMG00000029785	ENST00000315266.5:c.1108G>A	14.37:g.67555762G>A	ENSP00000312771:p.Ala370Thr					GPHN_ENST00000543237.1_Missense_Mutation_p.A416T|GPHN_ENST00000315266.5_Missense_Mutation_p.A370T|GPHN_ENST00000544752.2_3'UTR|GPHN_ENST00000305960.9_Missense_Mutation_p.A339T	p.A403T	NM_020806.4	NP_065857.1	Q9NQX3	GEPH_HUMAN		Epithelial(1;1.73e-08)|all cancers(60;3.15e-07)|OV - Ovarian serous cystadenocarcinoma(108;0.000275)|BRCA - Breast invasive adenocarcinoma(234;0.00323)|Colorectal(3;0.0938)|KIRC - Kidney renal clear cell carcinoma(182;0.184)	12	2328	+		all_cancers(7;0.0476)|all_hematologic(31;0.0116)	370			MPT adenylyltransferase.		Q9H4E9|Q9P2G2	Missense_Mutation	SNP	ENST00000315266.5	37	c.1207G>A	CCDS32103.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.592390	0.86953	.	.	ENSG00000171723	ENST00000315266;ENST00000478722;ENST00000543237;ENST00000305960	.	.	.	5.77	4.88	0.63580	MoeA, N-terminal and linker domain (2);	0.047628	0.85682	D	0.000000	T	0.75302	0.3831	M	0.62016	1.91	0.80722	D	1	P;D;P;D	0.76494	0.826;0.999;0.914;0.996	P;D;P;D	0.71414	0.555;0.973;0.763;0.929	T	0.76138	-0.3069	9	0.46703	T	0.11	-6.3225	14.5922	0.68373	0.0709:0.0:0.9291:0.0	.	339;416;370;403	F8W7D6;F5H039;Q9NQX3;Q9NQX3-2	.;.;GEPH_HUMAN;.	T	370;403;416;339	.	ENSP00000303019:A339T	A	+	1	0	GPHN	66625515	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.054000	0.93866	1.442000	0.47568	0.655000	0.94253	GCA		0.348	GPHN-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000074299.2	NM_020806		16	41	0	0	0	1	0	16	41				
SPOP	8405	broad.mit.edu	37	17	47679302	47679302	+	Missense_Mutation	SNP	G	G	A			TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr17:47679302G>A	ENST00000393328.2	-	10	1270	c.905C>T	c.(904-906)gCt>gTt	p.A302V	SPOP_ENST00000503676.1_Missense_Mutation_p.A302V|SPOP_ENST00000393331.3_Missense_Mutation_p.A302V|SPOP_ENST00000347630.2_Missense_Mutation_p.A302V|SPOP_ENST00000504102.1_Missense_Mutation_p.A302V	NM_003563.3	NP_003554.1	O43791	SPOP_HUMAN	speckle-type POZ protein	302	Important for homodimerization.				glucose homeostasis (GO:0042593)|positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902237)|positive regulation of type B pancreatic cell apoptotic process (GO:2000676)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	Cul3-RING ubiquitin ligase complex (GO:0031463)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	ubiquitin protein ligase binding (GO:0031625)			endometrium(18)|kidney(1)|large_intestine(3)|liver(1)|lung(4)|ovary(3)|prostate(33)	63						AATTTCTGCAGCGTTCTCCAC	0.488										Prostate(2;0.17)																												ENST00000393331.3																			0				endometrium(18)|kidney(1)|large_intestine(3)|liver(1)|lung(4)|ovary(3)|prostate(33)	63						c.(904-906)gCt>gTt		speckle-type POZ protein							134.0	125.0	128.0					17																	47679302		2203	4300	6503	SO:0001583	missense	8405				mRNA processing	nucleus	protein binding	g.chr17:47679302G>A	AJ000644	CCDS11551.1	17q21.33	2013-01-09			ENSG00000121067	ENSG00000121067		"""BTB/POZ domain containing"""	11254	protein-coding gene	gene with protein product		602650				9414087	Standard	NM_001007227		Approved	TEF2, BTBD32	uc002ipg.3	O43791	OTTHUMG00000161496	ENST00000393328.2:c.905C>T	17.37:g.47679302G>A	ENSP00000377001:p.Ala302Val	Prostate(2;0.17)				SPOP_ENST00000393328.2_Missense_Mutation_p.A302V|SPOP_ENST00000347630.2_Missense_Mutation_p.A302V|SPOP_ENST00000504102.1_Missense_Mutation_p.A302V|SPOP_ENST00000503676.1_Missense_Mutation_p.A302V	p.A302V	NM_001007226.1|NM_001007227.1	NP_001007227.1|NP_001007228.1	O43791	SPOP_HUMAN			11	1375	-			302			Homodimerization.		B2R6S3|D3DTW7|Q53HJ1	Missense_Mutation	SNP	ENST00000393328.2	37	c.905C>T	CCDS11551.1	.	.	.	.	.	.	.	.	.	.	G	15.98	2.993408	0.54041	.	.	ENSG00000121067	ENST00000393328;ENST00000393331;ENST00000347630;ENST00000504102;ENST00000503536;ENST00000503676;ENST00000513872	T;T;T;T;T	0.61980	0.06;0.06;0.06;0.06;0.06	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.37865	0.1019	N	0.05230	-0.09	0.80722	D	1	B	0.27068	0.167	B	0.15052	0.012	T	0.42548	-0.9445	10	0.02654	T	1	-13.7413	18.9609	0.92677	0.0:0.0:1.0:0.0	.	302	O43791	SPOP_HUMAN	V	302;302;302;302;186;302;255	ENSP00000377001:A302V;ENSP00000377004:A302V;ENSP00000240327:A302V;ENSP00000425905:A302V;ENSP00000420908:A302V	ENSP00000240327:A302V	A	-	2	0	SPOP	45034301	1.000000	0.71417	0.412000	0.26496	0.987000	0.75469	5.217000	0.65252	2.818000	0.97014	0.591000	0.81541	GCT		0.488	SPOP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365154.2	NM_003563		4	92	0	0	0	1	0	4	92				
HTR1E	3354	broad.mit.edu	37	6	87725081	87725081	+	Missense_Mutation	SNP	C	C	T			TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr6:87725081C>T	ENST00000305344.5	+	2	732	c.29C>T	c.(28-30)gCc>gTc	p.A10V		NM_000865.2	NP_000856.1	P28566	5HT1E_HUMAN	5-hydroxytryptamine (serotonin) receptor 1E, G protein-coupled	10					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP metabolic process (GO:0030815)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(3)|endometrium(2)|kidney(3)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(3)	41		all_cancers(76;7.11e-06)|Acute lymphoblastic leukemia(125;1.2e-09)|Prostate(29;3.51e-09)|all_hematologic(105;7.43e-06)|all_epithelial(107;0.00819)		BRCA - Breast invasive adenocarcinoma(108;0.055)	Aripiprazole(DB01238)|Clozapine(DB00363)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ketamine(DB01221)|Loxapine(DB00408)|Methysergide(DB00247)|Olanzapine(DB00334)|Quetiapine(DB01224)|Ziprasidone(DB00246)	ACCACAGAGGCCAGCATGGCT	0.468																																						ENST00000305344.4																			0				breast(3)|endometrium(2)|kidney(3)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(3)	41						c.(28-30)gCc>gTc		5-hydroxytryptamine (serotonin) receptor 1E, G protein-coupled	Eletriptan(DB00216)						118.0	100.0	106.0					6																	87725081		2203	4300	6503	SO:0001583	missense	3354				G-protein signaling, coupled to cyclic nucleotide second messenger|synaptic transmission	integral to plasma membrane	protein binding|serotonin binding|serotonin receptor activity	g.chr6:87725081C>T		CCDS5006.1	6q14-q15	2013-06-19	2012-02-03		ENSG00000168830	ENSG00000168830		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5291	protein-coding gene	gene with protein product		182132	"""5-hydroxytryptamine (serotonin) receptor 1E"""			1608964	Standard	NM_000865		Approved	5-HT1E	uc003pli.3	P28566	OTTHUMG00000015154	ENST00000305344.5:c.29C>T	6.37:g.87725081C>T	ENSP00000307766:p.Ala10Val					HTR1E_ENST00000369584.1_Missense_Mutation_p.A10V	p.A10V	NM_000865.2	NP_000856.1	P28566	5HT1E_HUMAN		BRCA - Breast invasive adenocarcinoma(108;0.055)	2	732	+		all_cancers(76;7.11e-06)|Acute lymphoblastic leukemia(125;1.2e-09)|Prostate(29;3.51e-09)|all_hematologic(105;7.43e-06)|all_epithelial(107;0.00819)	10					E1P503|Q9P1Y1	Missense_Mutation	SNP	ENST00000305344.5	37	c.29C>T	CCDS5006.1	.	.	.	.	.	.	.	.	.	.	C	3.811	-0.039769	0.07497	.	.	ENSG00000168830	ENST00000305344;ENST00000369584	T;T	0.66815	-0.23;-0.23	3.87	2.96	0.34315	.	0.232319	0.26499	U	0.024026	T	0.23171	0.0560	N	0.08118	0	0.29603	N	0.847498	B	0.17038	0.02	B	0.10450	0.005	T	0.12243	-1.0555	10	0.25106	T	0.35	.	11.2122	0.48806	0.1837:0.8163:0.0:0.0	.	10	P28566	5HT1E_HUMAN	V	10	ENSP00000307766:A10V;ENSP00000358597:A10V	ENSP00000307766:A10V	A	+	2	0	HTR1E	87781800	0.972000	0.33761	0.971000	0.41717	0.270000	0.26580	2.219000	0.42899	0.910000	0.36722	0.508000	0.49915	GCC		0.468	HTR1E-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472488.2	NM_000865		6	20	0	0	0	1	0	6	20				
L3MBTL3	84456	broad.mit.edu	37	6	130387569	130387569	+	Silent	SNP	C	C	T	rs139205810	byFrequency	TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr6:130387569C>T	ENST00000529410.1	+	13	1415	c.936C>T	c.(934-936)gaC>gaT	p.D312D	L3MBTL3_ENST00000368139.2_Silent_p.D287D|L3MBTL3_ENST00000361794.2_Silent_p.D312D|L3MBTL3_ENST00000368136.2_Silent_p.D312D|L3MBTL3_ENST00000533560.1_Silent_p.D287D|L3MBTL3_ENST00000526019.1_Silent_p.D287D			Q96JM7	LMBL3_HUMAN	l(3)mbt-like 3 (Drosophila)	312					chromatin modification (GO:0016568)|erythrocyte maturation (GO:0043249)|granulocyte differentiation (GO:0030851)|macrophage differentiation (GO:0030225)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				cervix(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|skin(4)|stomach(1)|urinary_tract(1)	43				GBM - Glioblastoma multiforme(226;0.0266)|OV - Ovarian serous cystadenocarcinoma(155;0.154)		TGAATGCAGACGCTCTGGATA	0.403																																						ENST00000529410.1																			0				cervix(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|skin(4)|stomach(1)|urinary_tract(1)	43						c.(934-936)gaC>gaT		l(3)mbt-like 3 (Drosophila)		C	,	2,4404	4.2+/-10.8	0,2,2201	90.0	90.0	90.0		861,936	-10.8	0.4	6	dbSNP_134	90	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	L3MBTL3	NM_001007102.2,NM_032438.2	,	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	,	287/756,312/781	130387569	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	84456				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus		g.chr6:130387569C>T	AB058701	CCDS34537.1, CCDS34538.1	6q23	2013-01-10			ENSG00000198945	ENSG00000198945		"""Sterile alpha motif (SAM) domain containing"""	23035	protein-coding gene	gene with protein product							Standard	NM_032438		Approved	KIAA1798	uc003qbt.3	Q96JM7	OTTHUMG00000015554	ENST00000529410.1:c.936C>T	6.37:g.130387569C>T						L3MBTL3_ENST00000361794.2_Silent_p.D312D|L3MBTL3_ENST00000368136.2_Silent_p.D312D|L3MBTL3_ENST00000368139.2_Silent_p.D287D|L3MBTL3_ENST00000526019.1_Silent_p.D287D|L3MBTL3_ENST00000533560.1_Silent_p.D287D	p.D312D			Q96JM7	LMBL3_HUMAN		GBM - Glioblastoma multiforme(226;0.0266)|OV - Ovarian serous cystadenocarcinoma(155;0.154)	13	1415	+			312					Q4VXE1|Q5VUM9|Q6P9B5	Silent	SNP	ENST00000529410.1	37	c.936C>T	CCDS34537.1																																																																																				0.403	L3MBTL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042195.2	XM_027074		18	79	0	0	0	1	0	18	79				
SPEN	23013	broad.mit.edu	37	1	16257885	16257885	+	Missense_Mutation	SNP	C	C	T			TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr1:16257885C>T	ENST00000375759.3	+	11	5354	c.5150C>T	c.(5149-5151)gCg>gTg	p.A1717V		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	1717					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		ATGATGCCTGCGGGTGTTGAG	0.582																																						ENST00000375759.3																			0				NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149						c.(5149-5151)gCg>gTg		spen family transcriptional repressor							131.0	141.0	138.0					1																	16257885		2203	4300	6503	SO:0001583	missense	23013				interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding	g.chr1:16257885C>T		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"""RNA binding motif (RRM) containing"""	17575	protein-coding gene	gene with protein product		613484	"""SPEN homolog, transcriptional regulator (Drosophila)"", ""spen homolog, transcriptional regulator (Drosophila)"""			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.5150C>T	1.37:g.16257885C>T	ENSP00000364912:p.Ala1717Val						p.A1717V	NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)	11	5354	+		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)	1717					Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	37	c.5150C>T	CCDS164.1	.	.	.	.	.	.	.	.	.	.	C	10.57	1.386326	0.25031	.	.	ENSG00000065526	ENST00000375759	T	0.08458	3.09	5.16	-10.3	0.00346	.	.	.	.	.	T	0.03871	0.0109	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39292	-0.9621	9	0.24483	T	0.36	13.0822	10.7435	0.46166	0.0:0.2075:0.1581:0.6344	.	1717	Q96T58	MINT_HUMAN	V	1717	ENSP00000364912:A1717V	ENSP00000364912:A1717V	A	+	2	0	SPEN	16130472	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.713000	0.01883	-3.293000	0.00194	-0.444000	0.05651	GCG		0.582	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		25	109	0	0	0	1	0	25	109				
GMPPB	29925	broad.mit.edu	37	3	49759417	49759417	+	Missense_Mutation	SNP	C	C	T			TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr3:49759417C>T	ENST00000480687.1	-	9	1048	c.932G>A	c.(931-933)cGc>cAc	p.R311H	AMIGO3_ENST00000320431.7_5'Flank|GMPPB_ENST00000308388.6_Missense_Mutation_p.R311H|AMIGO3_ENST00000535833.1_5'UTR|GMPPB_ENST00000308375.6_Missense_Mutation_p.R311H			Q9Y5P6	GMPPB_HUMAN	GDP-mannose pyrophosphorylase B	311					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|mannose-1-phosphate guanylyltransferase activity (GO:0004475)			endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|skin(1)	6				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CACGCGGCAGCGCCAGCCCAC	0.662																																						ENST00000480687.1																			0				endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|skin(1)	6						c.(931-933)cGc>cAc		GDP-mannose pyrophosphorylase B							66.0	59.0	62.0					3																	49759417		2203	4300	6503	SO:0001583	missense	29925				dolichol-linked oligosaccharide biosynthetic process|GDP-mannose biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine		GTP binding|mannose-1-phosphate guanylyltransferase activity	g.chr3:49759417C>T	AF135421	CCDS2802.1, CCDS2803.1	3p21.31	2008-02-05			ENSG00000173540	ENSG00000173540	2.7.7.22		22932	protein-coding gene	gene with protein product		615320					Standard	NM_013334		Approved	KIAA1851	uc003cxl.1	Q9Y5P6	OTTHUMG00000158151	ENST00000480687.1:c.932G>A	3.37:g.49759417C>T	ENSP00000418565:p.Arg311His					GMPPB_ENST00000308388.6_Missense_Mutation_p.R311H|GMPPB_ENST00000308375.6_Missense_Mutation_p.R311H|AMIGO3_ENST00000535833.1_5'UTR	p.R311H			Q9Y5P6	GMPPB_HUMAN		BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)	9	1048	-			311					A8K6N5|Q9H7U3	Missense_Mutation	SNP	ENST00000480687.1	37	c.932G>A	CCDS2803.1	.	.	.	.	.	.	.	.	.	.	C	14.62	2.589875	0.46214	.	.	ENSG00000173540	ENST00000480687;ENST00000308375;ENST00000308388	T;T;T	0.73897	-0.76;-0.79;-0.76	4.98	4.98	0.66077	.	0.042701	0.85682	D	0.000000	T	0.64450	0.2599	N	0.25825	0.765	0.58432	D	0.999997	B;B	0.11235	0.003;0.004	B;B	0.10450	0.005;0.001	T	0.58875	-0.7559	10	0.33940	T	0.23	-28.5085	17.425	0.87524	0.0:1.0:0.0:0.0	.	311;311	Q9Y5P6-2;Q9Y5P6	.;GMPPB_HUMAN	H	311	ENSP00000418565:R311H;ENSP00000309092:R311H;ENSP00000311130:R311H	ENSP00000309092:R311H	R	-	2	0	GMPPB	49734421	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.790000	0.55461	2.579000	0.87056	0.561000	0.74099	CGC		0.662	GMPPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350291.1	NM_013334		6	25	0	0	0	1	0	6	25				
PODNL1	79883	broad.mit.edu	37	19	14043545	14043545	+	Silent	SNP	G	G	A	rs373284026		TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr19:14043545G>A	ENST00000339560.5	-	8	1785	c.1512C>T	c.(1510-1512)caC>caT	p.H504H	PODNL1_ENST00000538517.2_Silent_p.H413H|PODNL1_ENST00000538371.2_Silent_p.H502H|PODNL1_ENST00000254320.3_Silent_p.H422H	NM_024825.3	NP_079101.3	Q6PEZ8	PONL1_HUMAN	podocan-like 1	504						proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(19;5.26e-23)			TGTTTGGGACGTGGCAGGGCA	0.577																																						ENST00000538517.2																			0				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|skin(1)	8						c.(1237-1239)caC>caT		podocan-like 1			,,	0,4298		0,0,2149	54.0	60.0	58.0		1506,1239,1512	-1.8	0.0	19		58	1,8363		0,1,4181	no	coding-synonymous,coding-synonymous,coding-synonymous	PODNL1	NM_001146254.1,NM_001146255.1,NM_024825.3	,,	0,1,6330	AA,AG,GG		0.012,0.0,0.0079	,,	502/511,413/422,504/513	14043545	1,12661	2149	4182	6331	SO:0001819	synonymous_variant	79883					proteinaceous extracellular matrix		g.chr19:14043545G>A	AK027100	CCDS12300.1, CCDS54225.1, CCDS54226.1	19p13.12	2008-02-05							26275	protein-coding gene	gene with protein product						12477932	Standard	NM_024825		Approved	FLJ23447, SLRR5B	uc010xnj.2	Q6PEZ8		ENST00000339560.5:c.1512C>T	19.37:g.14043545G>A						PODNL1_ENST00000254320.3_Silent_p.H422H|PODNL1_ENST00000538371.2_Silent_p.H502H|PODNL1_ENST00000339560.5_Silent_p.H504H	p.H413H	NM_001146255.1	NP_001139727.1	Q6PEZ8	PONL1_HUMAN	OV - Ovarian serous cystadenocarcinoma(19;5.26e-23)		6	1483	-			504			Leu-rich.		B7Z564|Q9H5G9	Silent	SNP	ENST00000339560.5	37	c.1239C>T	CCDS12300.1																																																																																				0.577	PODNL1-003	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457967.1	NM_024825		4	72	0	0	0	1	0	4	72				
CAPN2	824	broad.mit.edu	37	1	223900386	223900386	+	Frame_Shift_Del	DEL	C	C	-			TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr1:223900386delC	ENST00000295006.5	+	1	353	c.44delC	c.(43-45)gccfs	p.A15fs	CAPN2_ENST00000433674.2_Intron	NM_001748.4	NP_001739	P17655	CAN2_HUMAN	calpain 2, (m/II) large subunit	15					blastocyst development (GO:0001824)|cellular response to amino acid stimulus (GO:0071230)|myoblast fusion (GO:0007520)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of cytoskeleton organization (GO:0051493)|response to hypoxia (GO:0001666)	chromatin (GO:0000785)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|cytoskeletal protein binding (GO:0008092)			breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|stomach(3)	29				GBM - Glioblastoma multiforme(131;0.109)		CGGGAGGCGGCCGAGGGGCTG	0.711																																						ENST00000295006.5																			0				breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|stomach(3)	29						c.(43-45)gcfs		calpain 2, (m/II) large subunit							15.0	17.0	16.0					1																	223900386		2176	4265	6441	SO:0001589	frameshift_variant	824				proteolysis	cytoplasm|plasma membrane		g.chr1:223900386delC	J04700	CCDS31035.1, CCDS53478.1	1q41-q42	2013-01-10			ENSG00000162909	ENSG00000162909	3.4.22.52	"""EF-hand domain containing"""	1479	protein-coding gene	gene with protein product		114230				2852952, 2539381	Standard	NM_001748		Approved	mCANP, CANPml, CANPL2	uc001hob.4	P17655	OTTHUMG00000037376	ENST00000295006.5:c.44delC	1.37:g.223900386delC	ENSP00000295006:p.Ala15fs					CAPN2_ENST00000433674.2_Intron	p.A15fs	NM_001748.4	NP_001739.2	P17655	CAN2_HUMAN		GBM - Glioblastoma multiforme(131;0.109)	1	353	+			15					A6NDG7|B7ZA96|E7ES58|Q16738|Q6PJT3|Q8WU26|Q9HBB1	Frame_Shift_Del	DEL	ENST00000295006.5	37	c.44delC	CCDS31035.1																																																																																				0.711	CAPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090973.1	NM_001748		2	4						2	4	---	---	---	---
SRGAP3	9901	broad.mit.edu	37	3	9032419	9032420	+	Frame_Shift_Ins	INS	-	-	G			TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr3:9032419_9032420insG	ENST00000383836.3	-	21	3089_3090	c.2662_2663insC	c.(2662-2664)cggfs	p.R888fs	SRGAP3_ENST00000360413.3_Frame_Shift_Ins_p.R864fs	NM_014850.3	NP_055665.1	O43295	SRGP3_HUMAN	SLIT-ROBO Rho GTPase activating protein 3	888					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)		SRGAP3/RAF1(6)	breast(1)|endometrium(2)|kidney(21)|large_intestine(7)|lung(13)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	54				OV - Ovarian serous cystadenocarcinoma(96;0.0563)		GGCAGCAGCCCGGGGTGGTGTG	0.703			T	RAF1	pilocytic astrocytoma																																	ENST00000383836.3				Dom	yes		3	3p25.3	9901	T	SLIT-ROBO Rho GTPase activating protein 3			M	RAF1		pilocytic astrocytoma	SRGAP3/RAF1(6)	0				breast(1)|endometrium(2)|kidney(21)|large_intestine(7)|lung(13)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	54						c.(2662-2664)ggcfs		SLIT-ROBO Rho GTPase activating protein 3																																				SO:0001589	frameshift_variant	9901				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding	g.chr3:9032419_9032420insG	AB007871	CCDS2572.1, CCDS33689.1	3p25.3	2011-07-04	2004-11-12	2004-11-12	ENSG00000196220	ENSG00000196220		"""Rho GTPase activating proteins"""	19744	protein-coding gene	gene with protein product		606525	"""SLIT-ROBO Rho GTPase activating protein 2"""	SRGAP2		12195014	Standard	NM_014850		Approved	KIAA0411, MEGAP, WRP, ARHGAP14	uc003brf.2	O43295	OTTHUMG00000090589	ENST00000383836.3:c.2663dupC	3.37:g.9032423_9032423dupG	ENSP00000373347:p.Arg888fs					SRGAP3_ENST00000360413.3_Frame_Shift_Ins_p.G864fs	p.G888fs	NM_014850.3	NP_055665.1	O43295	SRGP2_HUMAN		OV - Ovarian serous cystadenocarcinoma(96;0.0563)	21	3089_3090	-			888					Q8IX13|Q8IZV8	Frame_Shift_Ins	INS	ENST00000383836.3	37	c.2662_2663insC	CCDS2572.1																																																																																				0.703	SRGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207137.3			3	5						3	5	---	---	---	---
DBR1	51163	broad.mit.edu	37	3	137880741	137880743	+	In_Frame_Del	DEL	TCG	TCG	-	rs376362448|rs2622736	byFrequency	TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr3:137880741_137880743delTCG	ENST00000260803.4	-	8	1776_1778	c.1623_1625delCGA	c.(1621-1626)gacgat>gat	p.541_542DD>D	DBR1_ENST00000505015.2_In_Frame_Del_p.307_308DD>D	NM_016216.3	NP_057300.2	Q9UK59	DBR1_HUMAN	debranching RNA lariats 1	541					mRNA splicing, via spliceosome (GO:0000398)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|RNA splicing, via transesterification reactions (GO:0000375)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA lariat debranching enzyme activity (GO:0008419)			NS(1)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	15						TTAAGCTGCATCGTCATCATCAT	0.394																																						ENST00000260803.4																			0				NS(1)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	15						c.(1621-1626)gat>ga		debranching RNA lariats 1																																				SO:0001651	inframe_deletion	51163					nucleus	metal ion binding|RNA lariat debranching enzyme activity	g.chr3:137880741_137880743delTCG	AF180919	CCDS33863.1	3q22.3	2013-05-01	2013-05-01		ENSG00000138231	ENSG00000138231			15594	protein-coding gene	gene with protein product		607024	"""debranching enzyme (S. Cerevisiae) homolog 1"", ""debranching enzyme homolog 1 (S. cerevisiae)"""			10982890	Standard	NM_016216		Approved		uc003erv.3	Q9UK59	OTTHUMG00000159824	ENST00000260803.4:c.1623_1625delCGA	3.37:g.137880741_137880743delTCG	ENSP00000260803:p.Asp542del					DBR1_ENST00000505015.2_In_Frame_Del_p.DD307del	p.DD541del	NM_016216.3	NP_057300.2	Q9UK59	DBR1_HUMAN			8	1776_1778	-			541					Q96GH0|Q9NXQ6	In_Frame_Del	DEL	ENST00000260803.4	37	c.1623_1625delCGA	CCDS33863.1																																																																																				0.394	DBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357585.1			7	97						7	97	---	---	---	---
MIR9-2	407047	broad.mit.edu	37	5	87980814	87980816	+	RNA	DEL	GAG	GAG	-			TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr5:87980814_87980816delGAG	ENST00000510274.1	+	0	46																											ggaggaggaagaggaggaggagg	0.581																																						ENST00000510274.1																			0																																																			0							g.chr5:87980814_87980816delGAG																													5.37:g.87980823_87980825delGAG														0	46	+									RNA	DEL	ENST00000510274.1	37																																																																																						0.581	CTC-467M3.1-001	KNOWN	basic	antisense	antisense	OTTHUMT00000369794.1			2	4						2	4	---	---	---	---
MCC	4163	broad.mit.edu	37	5	112824048	112824049	+	In_Frame_Ins	INS	-	-	GCC	rs35336557|rs531679771|rs370593160	byFrequency	TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr5:112824048_112824049insGCC	ENST00000408903.3	-	1	478_479	c.63_64insGGC	c.(61-66)ggcagc>ggcGGCagc	p.21_22insG		NM_001085377.1	NP_001078846	P23508	CRCM_HUMAN	mutated in colorectal cancers	0					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(4)|kidney(3)|large_intestine(15)|liver(2)|lung(8)|ovary(2)|pancreas(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		ctgctgccgctgccgccgccgc	0.738														1663	0.332069	0.0227	0.3487	5008	,	,		8489	0.5208		0.3668	False		,,,				2504	0.5082					ENST00000408903.3																			0				endometrium(4)|kidney(3)|large_intestine(15)|liver(2)|lung(8)|ovary(2)|pancreas(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						c.(61-66)gggcgg>ggGGCgcgg		mutated in colorectal cancers																																				SO:0001652	inframe_insertion	4163				negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|Wnt receptor signaling pathway	cytoplasm|nucleus|plasma membrane	protein binding|receptor activity	g.chr5:112824048_112824049insGCC		CCDS4111.1, CCDS43351.1	5q21-q22	2013-01-10			ENSG00000171444	ENSG00000171444		"""EF-hand domain containing"""	6935	protein-coding gene	gene with protein product		159350				1848370	Standard	NM_002387		Approved		uc003kql.4	P23508	OTTHUMG00000128804	ENST00000408903.3:c.61_63dupGGC	5.37:g.112824055_112824057dupGCC	ENSP00000386227:p.Gly22_Gly23dup						p.21_22GR>GAR	NM_001085377.1	NP_001078846.1	P23508	CRCM_HUMAN		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)	1	478_479	-		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)	549					D3DT05|Q6ZR04	In_Frame_Ins	INS	ENST00000408903.3	37	c.63_64insGGC	CCDS43351.1																																																																																				0.738	MCC-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370839.1	NM_001085377		5	9						5	9	---	---	---	---
MUC17	140453	broad.mit.edu	37	7	100684307	100684308	+	In_Frame_Ins	INS	-	-	CTC			TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr7:100684307_100684308insCTC	ENST00000306151.4	+	3	9674_9675	c.9610_9611insCTC	c.(9610-9612)tct>tCTCct	p.3204_3205insP		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3204	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					AGCCACTTCATCTACAACTGCT	0.5																																						ENST00000306151.4																			0				NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343						c.(9610-9612)tac>CTCtac		mucin 17, cell surface associated																																				SO:0001652	inframe_insertion	140453					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity	g.chr7:100684307_100684308insCTC	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	Exception_encountered	7.37:g.100684307_100684308insCTC	ENSP00000302716:p.Ser3204_Thr3205insPro						p.3203_3204insL	NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN			3	9674_9675	+	Lung NSC(181;0.136)|all_lung(186;0.182)		3203			59 X approximate tandem repeats.|Ser-rich.		O14761|Q685J2|Q8TDH7	In_Frame_Ins	INS	ENST00000306151.4	37	c.9610_9611insCTC	CCDS34711.1																																																																																				0.500	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		7	263						7	263	---	---	---	---
BABAM1	29086	broad.mit.edu	37	19	17375158	17375158	+	IGR	DEL	T	T	-			TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chr19:17375158delT	ENST00000598188.1	+	0	0				USHBP1_ENST00000252597.3_Splice_Site|USHBP1_ENST00000598570.1_Splice_Site|USHBP1_ENST00000431146.2_Splice_Site			Q9NWV8	BABA1_HUMAN	BRISC and BRCA1 A complex member 1						chromatin modification (GO:0016568)|double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|positive regulation of DNA repair (GO:0045739)|protein K63-linked deubiquitination (GO:0070536)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRISC complex (GO:0070552)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	5						CGTCAACCCCTAAAACCACAG	0.582																																						ENST00000252597.3																			0				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(10)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44						c.e2-2		Usher syndrome 1C binding protein 1				0,4246		0,0,2123	18.0	17.0	17.0			2.2	0.0	19		18	3,8223		0,3,4110	no	splice-3	USHBP1	NM_031941.3		0,3,6233	A1A1,A1R,RR		0.0365,0.0,0.0241			17375158	3,12469	2195	4288	6483	SO:0001628	intergenic_variant	83878						PDZ domain binding	g.chr19:17375158delT	AK000578	CCDS46012.1, CCDS74310.1	19p13.11	2011-02-21	2011-02-21	2011-01-31	ENSG00000105393	ENSG00000105393			25008	protein-coding gene	gene with protein product	"""Mediator of Rap80 Interactions and Targeting 40 kD"", ""new component of the BRCA1 A complex"""	612766	"""chromosome 19 open reading frame 62"""	C19orf62		11042152	Standard	NM_001288756		Approved	FLJ20571, HSPC142, NBA1, MERIT40	uc002nfv.3	Q9NWV8			19.37:g.17375158delT						USHBP1_ENST00000598570.1_Splice_Site|USHBP1_ENST00000431146.2_Splice_Site		NM_031941.3	NP_114147.2	Q8N6Y0	USBP1_HUMAN			2	126	-								A8MQT0|B4DRY9|B4DVR1|Q6FIA0|Q9P018	Splice_Site	DEL	ENST00000598188.1	37		CCDS46012.1																																																																																				0.582	BABAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463469.1	NM_014173		3	3						3	3	---	---	---	---
PQBP1	10084	broad.mit.edu	37	X	48759668	48759669	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chrX:48759668_48759669delAG	ENST00000376563.1	+	5	651_652	c.451_452delAG	c.(451-453)agafs	p.R151fs	PQBP1_ENST00000473764.1_3'UTR|PQBP1_ENST00000396763.1_Frame_Shift_Del_p.R151fs|PQBP1_ENST00000447146.2_Frame_Shift_Del_p.R151fs|PQBP1_ENST00000218224.4_Frame_Shift_Del_p.R151fs|PQBP1_ENST00000376566.4_Intron|PQBP1_ENST00000247140.4_Intron	NM_001032381.1|NM_001032382.1|NM_001032383.1|NM_001167989.1	NP_001027553.1|NP_001027554.1|NP_001027555.1|NP_001161461.1	O60828	PQBP1_HUMAN	polyglutamine binding protein 1	151	7 X 2 AA tandem repeats of [DE]-R.|Arg-rich.|Intrinsically disordered.				alternative mRNA splicing, via spliceosome (GO:0000380)|neuron projection development (GO:0031175)|regulation of dendrite morphogenesis (GO:0048814)|regulation of RNA splicing (GO:0043484)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|neuronal ribonucleoprotein granule (GO:0071598)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ribonucleoprotein complex binding (GO:0043021)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(2)	11						CAAGGTAGACAGAGAGAGAGAG	0.619																																						ENST00000218224.4																			0				breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(2)	11						c.(451-453)afs		polyglutamine binding protein 1			,,,,,,,,	60,3659		4,23,29,1565,506					,,,,,,,,	-6.6	0.0			44	111,6368		9,35,58,2312,1709	no	intron,frameshift,intron,frameshift,frameshift,frameshift,frameshift,frameshift,frameshift	PQBP1	NM_144495.2,NM_005710.2,NM_001167992.1,NM_001167990.1,NM_001167989.1,NM_001032384.1,NM_001032383.1,NM_001032382.1,NM_001032381.1	,,,,,,,,	13,58,87,3877,2215	A1A1,A1R,A1,RR,R		1.7132,1.6133,1.6768	,,,,,,,,	,,,,,,,,		171,10027				SO:0001589	frameshift_variant	10084				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|transcription coactivator activity	g.chrX:48759668_48759669delAG	AJ005893	CCDS14309.1, CCDS55412.1	Xp11.23	2014-01-31			ENSG00000102103	ENSG00000102103			9330	protein-coding gene	gene with protein product		300463	"""Sutherland-Haan X-linked mental retardation syndrome"", ""mental retardation, X-linked 55"", ""mental retardation, X-linked 2 (non-dysmorphic)"""	RENS1, MRXS8, SHS, MRX55, MRX2		9875212, 15024694, 14634649	Standard	NM_144495		Approved		uc004dlg.3	O60828	OTTHUMG00000024128	ENST00000376563.1:c.451_452delAG	X.37:g.48759678_48759679delAG	ENSP00000365747:p.Arg151fs					PQBP1_ENST00000396763.1_Frame_Shift_Del_p.R151fs|PQBP1_ENST00000376563.1_Frame_Shift_Del_p.R151fs|PQBP1_ENST00000376566.4_Intron|PQBP1_ENST00000247140.4_Intron|PQBP1_ENST00000447146.2_Frame_Shift_Del_p.R151fs|PQBP1_ENST00000473764.1_3'UTR	p.R151fs	NM_005710.2	NP_005701.1	O60828	PQBP1_HUMAN			4	705_706	+			151			7 X 2 AA tandem repeats of [DE]-R.|Arg-rich.		Q4VY25|Q4VY26|Q4VY27|Q4VY29|Q4VY30|Q4VY34|Q4VY35|Q4VY36|Q4VY37|Q4VY38|Q9GZP2|Q9GZU4|Q9GZZ4	Frame_Shift_Del	DEL	ENST00000376563.1	37	c.451_452delAG	CCDS14309.1																																																																																				0.619	PQBP1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060777.1	NM_001032381.1		2	4						2	4	---	---	---	---
ATRX	546	broad.mit.edu	37	X	76938946	76938956	+	Frame_Shift_Del	DEL	TTAATTGGGGA	TTAATTGGGGA	-	rs375129029		TCGA-V1-A9OY-01A-11D-A41K-08	TCGA-V1-A9OY-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	9454b4b6-985f-4e62-bbe9-1e61cf2e786b	7273e5ac-35e8-4188-bc14-ee745c353554	g.chrX:76938946_76938956delTTAATTGGGGA	ENST00000373344.5	-	9	2006_2016	c.1792_1802delTCCCCAATTAA	c.(1792-1803)tccccaattaaafs	p.SPIK598fs	ATRX_ENST00000395603.3_Frame_Shift_Del_p.SPIK560fs|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	598					ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						ATCAGCACCTTTAATTGGGGAATTAGAAAGG	0.355			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																															ENST00000373344.5				Rec	yes		X	Xq21.1	546	"""Mis, F, N"""	alpha thalassemia/mental retardation syndrome X-linked	yes	ATR-X (alpha thalassemia/mental retardation) syndrome	E			"""Pancreatic neuroendocrine tumors, paediatric GBM"""		1	Unknown(1)	p.?(1)	bone(1)	bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						c.(1792-1803)afs		alpha thalassemia/mental retardation syndrome X-linked	Phosphatidylserine(DB00144)																																			SO:0001589	frameshift_variant	546				DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding	g.chrX:76938946_76938956delTTAATTGGGGA	U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.1792_1802delTCCCCAATTAA	X.37:g.76938946_76938956delTTAATTGGGGA	ENSP00000362441:p.Ser598fs					ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Frame_Shift_Del_p.SPIK560fs	p.SPIK598fs	NM_000489.3	NP_000480.2	P46100	ATRX_HUMAN			9	2006_2016	-			598					D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Frame_Shift_Del	DEL	ENST00000373344.5	37	c.1792_1802delTCCCCAATTAA	CCDS14434.1																																																																																				0.355	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		58	121						58	121	---	---	---	---
