#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_BAM_File	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_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	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_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	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_NormalRefReads_WU	i_NormalVAF_WU	i_NormalVarReads_WU	i_ORegAnno_bin	i_RNARefReads_WU	i_RNAVAF_WU	i_RNAVarReads_WU	i_Start_position_hg18	i_TumorRefReads_WU	i_TumorVAF_WU	i_TumorVarReads_WU	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	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_deletion_substructures	i_domain	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_name	i_gene_type	i_havana_transcript	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_type	i_ucsc_cons	i_variant
RCC2	55920	genome.wustl.edu	37	1	17740033	17740033	+	Splice_Site	SNP	C	C	T			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b94e2b78-8092-49af-9c9e-7fd612b89793	22830365-9194-4c33-98d3-294740f281eb	g.chr1:17740033C>T	ENST00000375436.4	-	9	1394	c.1207G>A	c.(1207-1209)Ggt>Agt	p.G403S	AC004824.1_ENST00000583469.1_RNA|RCC2_ENST00000375433.3_Splice_Site_p.G403S	NM_018715.3	NP_061185.1	Q9P258	RCC2_HUMAN	regulator of chromosome condensation 2	403					chromosome passenger complex localization to kinetochore (GO:0072356)|endosome organization (GO:0007032)|focal adhesion assembly (GO:0048041)|integrin-mediated signaling pathway (GO:0007229)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of GTPase activity (GO:0034260)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of attachment of spindle microtubules to kinetochore (GO:0051987)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|regulation of cell migration (GO:0030334)	chromosome, centromeric core domain (GO:0034506)|cytosol (GO:0005829)|microtubule (GO:0005874)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|Rac GTPase binding (GO:0048365)			breast(2)|endometrium(1)|kidney(3)|large_intestine(7)|lung(4)	17		Colorectal(325;0.000147)|Breast(348;0.00122)|Renal(390;0.00145)|all_lung(284;0.0054)|Lung NSC(340;0.00566)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00492)|BRCA - Breast invasive adenocarcinoma(304;7.69e-06)|COAD - Colon adenocarcinoma(227;1.19e-05)|Kidney(64;0.000189)|KIRC - Kidney renal clear cell carcinoma(64;0.00273)|STAD - Stomach adenocarcinoma(196;0.0135)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.19)		AATCACTAACCCACTTCACTG	0.557																																						dbGAP											0			1											75.0	77.0	77.0					1																	17740033		2203	4300	6503	17612620	SO:0001630	splice_region_variant	0				CCDS181.1	1p36.13	2010-05-05			ENSG00000179051	ENSG00000179051			30297	protein-coding gene	gene with protein product		609587				10819331, 12919680	Standard	NM_018715		Approved	TD-60	uc001bal.3	Q9P258	OTTHUMG00000002513	ENST00000375436.4:c.1207+1G>A	1.37:g.17740033C>T		255	2.65	7		36	37.93	22	17612620	62	40.38	42	Q8IVL9|Q9BSN6|Q9NPV8	Missense_Mutation	SNP	HMMPfam_RCC1,PatternScan_RCC1_1,PatternScan_RCC1_2,superfamily_RCC1/BLIP-II	p.G403S	ENST00000375436.4	37	c.1207	CCDS181.1	1	.	.	.	.	.	.	.	.	.	.	C	35	5.453539	0.96223	.	.	ENSG00000179051	ENST00000375436;ENST00000375433	D;D	0.87179	-2.22;-2.22	5.4	5.4	0.78164	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.85682	D	0.000000	D	0.95130	0.8422	M	0.92122	3.275	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.95814	0.8844	9	.	.	.	-13.7292	18.1015	0.89507	0.0:1.0:0.0:0.0	.	403	Q9P258	RCC2_HUMAN	S	403	ENSP00000364585:G403S;ENSP00000364582:G403S	.	G	-	1	0	RCC2	17612620	1.000000	0.71417	1.000000	0.80357	0.831000	0.47069	7.637000	0.83313	2.687000	0.91594	0.655000	0.94253	GGT	-	superfamily_RCC1/BLIP-II		0.557	RCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RCC2	protein_coding	OTTHUMT00000007144.1	C	NM_018715	Missense_Mutation	17612620	-1	no_errors	NM_018715.1	genbank	human	validated	54_36p	missense	SNP	1.000	T
ALG6	29929	genome.wustl.edu	37	1	63876887	63876887	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b94e2b78-8092-49af-9c9e-7fd612b89793	22830365-9194-4c33-98d3-294740f281eb	g.chr1:63876887G>A	ENST00000371108.4	+	8	870	c.565G>A	c.(565-567)Ggg>Agg	p.G189R	ALG6_ENST00000263440.4_Missense_Mutation_p.G191R	NM_013339.3	NP_037471.2	Q9Y672	ALG6_HUMAN	ALG6, alpha-1,3-glucosyltransferase	189					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucosyltransferase activity (GO:0046527)			endometrium(1)|large_intestine(4)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						CGACCTCCTAGGGTCACTGGC	0.378																																						dbGAP											0			1											201.0	199.0	199.0					1																	63876887		2203	4300	6503	63649475	SO:0001583	missense	0			AF063604	CCDS30735.1	1p31.3	2013-03-01	2013-03-01		ENSG00000088035	ENSG00000088035	2.4.1.267		23157	protein-coding gene	gene with protein product	"""dolichyl-P-Glc:Man(9)GlcNAc(2)-PP-dolichol alpha- 1->3-glucosyltransferase"""	604566	"""asparagine-linked glycosylation 6 homolog (yeast, alpha-1,3-glucosyltransferase)"", ""asparagine-linked glycosylation 6, alpha-1,3-glucosyltransferase homolog (S. cerevisiae)"""			10359825, 11875054	Standard	NM_013339		Approved		uc021oof.1	Q9Y672	OTTHUMG00000009140	ENST00000371108.4:c.565G>A	1.37:g.63876887G>A	ENSP00000360149:p.Gly189Arg	169	0.59	1		18	32.14	9	63649475	74	37.29	44	B3KMU2|Q5SXR9|Q9H3I0	Missense_Mutation	SNP	HMMPfam_Alg6_Alg8	p.G189R	ENST00000371108.4	37	c.565	CCDS30735.1	1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.532750	0.85812	.	.	ENSG00000088035	ENST00000371108;ENST00000263440	D;D	0.84800	-1.9;-1.9	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	D	0.93861	0.8036	M	0.91038	3.17	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.94204	0.7452	10	0.66056	D	0.02	-12.9908	19.6786	0.95946	0.0:0.0:1.0:0.0	.	191	A2A2G4	.	R	189;191	ENSP00000360149:G189R;ENSP00000263440:G191R	ENSP00000263440:G191R	G	+	1	0	ALG6	63649475	1.000000	0.71417	0.994000	0.49952	0.681000	0.39784	9.226000	0.95229	2.738000	0.93877	0.591000	0.81541	GGG	-	HMMPfam_Alg6_Alg8		0.378	ALG6-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	ALG6	protein_coding	OTTHUMT00000025330.2	G	NM_013339		63649475	+1	no_errors	NM_013339.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
DYSF	8291	genome.wustl.edu	37	2	71909662	71909662	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b94e2b78-8092-49af-9c9e-7fd612b89793	22830365-9194-4c33-98d3-294740f281eb	g.chr2:71909662G>A	ENST00000258104.3	+	54	6336	c.6059G>A	c.(6058-6060)cGc>cAc	p.R2020H	DYSF_ENST00000413539.2_Missense_Mutation_p.R2051H|DYSF_ENST00000409651.1_Missense_Mutation_p.R2052H|DYSF_ENST00000429174.2_Missense_Mutation_p.R2041H|DYSF_ENST00000409366.1_Missense_Mutation_p.R2042H|DYSF_ENST00000409762.1_Missense_Mutation_p.R2037H|DYSF_ENST00000479049.2_3'UTR|DYSF_ENST00000409744.1_Missense_Mutation_p.R2028H|DYSF_ENST00000409582.3_Missense_Mutation_p.R2058H|DYSF_ENST00000410020.3_Missense_Mutation_p.R2059H|DYSF_ENST00000410041.1_Missense_Mutation_p.R2038H|DYSF_ENST00000394120.2_Missense_Mutation_p.R2021H	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	2020					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						GCTTCCAGGCGCCCCGACACC	0.567																																						dbGAP											0			2											142.0	117.0	125.0					2																	71909662		2203	4300	6503	71763170	SO:0001583	missense	0			AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.6059G>A	2.37:g.71909662G>A	ENSP00000258104:p.Arg2020His	427	3.80	17		22	48.84	21	71763170	135	38.46	85	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Missense_Mutation	SNP	HMMPfam_C2,HMMSmart_SM00239,HMMSmart_SM00693,HMMSmart_SM00694,superfamily_C2 domain (Calcium/lipid-binding domain CaLB),HMMPfam_FerA,HMMPfam_FerB,HMMPfam_FerI	p.R2020H	ENST00000258104.3	37	c.6059	CCDS1918.1	2	.	.	.	.	.	.	.	.	.	.	G	33	5.207308	0.95033	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	D;D;D;D;D;D;D;D;D;D;D	0.89875	-2.58;-2.58;-2.56;-2.55;-2.58;-2.58;-2.58;-2.55;-2.55;-2.56;-2.58	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	D	0.95576	0.8562	M	0.90870	3.155	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	0.999;0.999;0.999;0.999;0.999;1.0;1.0;1.0;1.0;0.999;0.999;1.0;0.999;0.999;0.999	D	0.96407	0.9301	10	0.87932	D	0	-19.5122	16.3717	0.83364	0.0:0.0:1.0:0.0	.	784;2052;2059;2042;2007;2038;2028;2037;2027;2051;2058;2041;2006;2021;2020	B7Z8G4;O75923-8;O75923-13;O75923-10;O75923-9;O75923-11;O75923-12;O75923-5;O75923-6;O75923-2;O75923-7;O75923-4;O75923-3;O75923-14;O75923	.;.;.;.;.;.;.;.;.;.;.;.;.;.;DYSF_HUMAN	H	2051;2037;2058;2041;2020;2052;2021;2028;2042;2059;2038	ENSP00000407046:R2051H;ENSP00000387137:R2037H;ENSP00000386547:R2058H;ENSP00000398305:R2041H;ENSP00000258104:R2020H;ENSP00000386683:R2052H;ENSP00000377678:R2021H;ENSP00000386285:R2028H;ENSP00000386512:R2042H;ENSP00000386881:R2059H;ENSP00000386617:R2038H	ENSP00000258104:R2020H	R	+	2	0	DYSF	71763170	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.780000	0.99024	2.514000	0.84764	0.655000	0.94253	CGC	-	NULL		0.567	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	DYSF	protein_coding	OTTHUMT00000251970.3	G	NM_003494		71763170	+1	no_errors	NM_003494.1	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
CADPS	8618	genome.wustl.edu	37	3	62484930	62484930	+	Silent	SNP	C	C	G			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	C	C	C	G	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b94e2b78-8092-49af-9c9e-7fd612b89793	22830365-9194-4c33-98d3-294740f281eb	g.chr3:62484930C>G	ENST00000383710.4	-	18	2962	c.2613G>C	c.(2611-2613)cgG>cgC	p.R871R	CADPS_ENST00000283269.9_Silent_p.R888R|CADPS_ENST00000357948.3_Silent_p.R848R	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	871	Interaction with DRD2.				catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		GAGTGATTAACCGGCCTACAT	0.408																																						dbGAP											0			3											131.0	118.0	123.0					3																	62484930		2203	4300	6503	62459970	SO:0001819	synonymous_variant	0			U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"""Pleckstrin homology (PH) domain containing"""	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.2613G>C	3.37:g.62484930C>G		248	1.57	4		NA	NA	NA	62459970	115	35.75	64	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Silent	SNP	HMMPfam_C2,HMMPfam_PH,HMMSmart_SM00233,HMMPfam_DUF1041,superfamily_PH domain-like	p.R871	ENST00000383710.4	37	c.2613	CCDS46858.1	3	.	.	.	.	.	.	.	.	.	.	C	4.637	0.118344	0.08881	.	.	ENSG00000163618	ENST00000491424	.	.	.	5.71	-3.32	0.04973	.	.	.	.	.	T	0.52354	0.1729	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50127	-0.8864	4	.	.	.	.	9.0428	0.36327	0.0:0.4188:0.3063:0.275	.	.	.	.	L	178	.	.	V	-	1	0	CADPS	62459970	0.355000	0.24921	0.977000	0.42913	0.977000	0.68977	-0.554000	0.06006	-0.551000	0.06175	-1.320000	0.01293	GTT	-	HMMPfam_DUF1041		0.408	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	CADPS	protein_coding	OTTHUMT00000351951.5	C	NM_003716, NM_183393, NM_183394		62459970	-1	no_errors	NM_003716.3	genbank	human	reviewed	54_36p	silent	SNP	0.921	G
KLHDC3	116138	genome.wustl.edu	37	6	42984974	42984974	+	Missense_Mutation	SNP	T	T	C			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b94e2b78-8092-49af-9c9e-7fd612b89793	22830365-9194-4c33-98d3-294740f281eb	g.chr6:42984974T>C	ENST00000326974.4	+	2	239	c.44T>C	c.(43-45)gTg>gCg	p.V15A	KLHDC3_ENST00000332245.8_Missense_Mutation_p.V15A|KLHDC3_ENST00000244670.8_5'UTR	NM_057161.3	NP_476502.1	Q9BQ90	KLDC3_HUMAN	kelch domain containing 3	15					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|reciprocal meiotic recombination (GO:0007131)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)	chromatin binding (GO:0003682)			cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9			Colorectal(64;0.00237)|all cancers(41;0.0034)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0539)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			CCCCGCAGGGTGAACCATGCT	0.612																																						dbGAP											0			6											88.0	96.0	94.0					6																	42984974		2203	4300	6503	43092952	SO:0001583	missense	0			AB055925	CCDS4880.1	6p21.1	2003-06-12			ENSG00000124702	ENSG00000124702			20704	protein-coding gene	gene with protein product		611248				12444059, 12606021	Standard	NM_057161		Approved	PEAS, hPeas, dJ20C7.3	uc003otl.3	Q9BQ90	OTTHUMG00000014714	ENST00000326974.4:c.44T>C	6.37:g.42984974T>C	ENSP00000313995:p.Val15Ala	383	5.39	23		56	41.67	40	43092952	40	36.92	24	A8K2W9	Missense_Mutation	SNP	HMMPfam_Kelch_1,superfamily_Galactose oxidase central domain,HMMPfam_Kelch_2	p.V15A	ENST00000326974.4	37	c.44	CCDS4880.1	6	.	.	.	.	.	.	.	.	.	.	T	23.1	4.370653	0.82573	.	.	ENSG00000124702	ENST00000326974;ENST00000432243;ENST00000394096;ENST00000332245	T;T	0.65549	-0.16;2.3	5.15	5.15	0.70609	Kelch-type beta propeller (1);	0.000000	0.64402	D	0.000001	T	0.73110	0.3545	M	0.75615	2.305	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.999	T	0.74999	-0.3472	10	0.45353	T	0.12	.	15.2822	0.73794	0.0:0.0:0.0:1.0	.	15;15;15	E7ENU0;E7ERR0;Q9BQ90	.;.;KLDC3_HUMAN	A	15	ENSP00000313995:V15A;ENSP00000331562:V15A	ENSP00000313995:V15A	V	+	2	0	KLHDC3	43092952	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.627000	0.83176	2.067000	0.61834	0.533000	0.62120	GTG	-	superfamily_Galactose oxidase central domain,HMMPfam_Kelch_2		0.612	KLHDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KLHDC3	protein_coding	OTTHUMT00000040570.1	T	NM_057161		43092952	+1	no_errors	NM_057161.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	C
PKHD1	5314	genome.wustl.edu	37	6	51619690	51619690	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b94e2b78-8092-49af-9c9e-7fd612b89793	22830365-9194-4c33-98d3-294740f281eb	g.chr6:51619690C>T	ENST00000371117.3	-	56	8964	c.8689G>A	c.(8689-8691)Gtc>Atc	p.V2897I	PKHD1_ENST00000340994.4_Missense_Mutation_p.V2897I	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	2897					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)					GAGCTAAGGACTATTTTGTCA	0.453																																						dbGAP											0			6											160.0	149.0	152.0					6																	51619690		2203	4300	6503	51727649	SO:0001583	missense	0			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.8689G>A	6.37:g.51619690C>T	ENSP00000360158:p.Val2897Ile	314	2.79	9		NA	NA	NA	51727649	126	35.71	70	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	HMMPfam_TIG,HMMSmart_SM00429,HMMSmart_SM00710,superfamily_Pectin lyase-like,superfamily_E set domains,HMMPfam_G8	p.V2897I	ENST00000371117.3	37	c.8689	CCDS4935.1	6	.	.	.	.	.	.	.	.	.	.	C	13.08	2.131335	0.37630	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.83163	-1.69;-1.69	5.63	-0.264	0.12950	.	0.270222	0.30949	N	0.008541	T	0.74906	0.3778	M	0.76328	2.33	0.09310	N	1	P;D;P	0.52996	0.911;0.957;0.816	P;P;B	0.48795	0.514;0.59;0.152	T	0.71272	-0.4642	10	0.66056	D	0.02	.	9.2177	0.37358	0.0:0.5652:0.0:0.4348	.	2897;2897;2897	A8MVM9;P08F94-2;P08F94	.;.;PKHD1_HUMAN	I	2897	ENSP00000360158:V2897I;ENSP00000341097:V2897I	ENSP00000341097:V2897I	V	-	1	0	PKHD1	51727649	0.007000	0.16637	0.019000	0.16419	0.431000	0.31685	-0.051000	0.11885	-0.051000	0.13334	-0.123000	0.14984	GTC	-	NULL		0.453	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PKHD1	protein_coding	OTTHUMT00000040893.1	C	NM_138694		51727649	-1	no_errors	NM_138694.3	genbank	human	reviewed	54_36p	missense	SNP	0.252	T
SCAF8	22828	genome.wustl.edu	37	6	155154044	155154044	+	Missense_Mutation	SNP	G	G	T			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b94e2b78-8092-49af-9c9e-7fd612b89793	22830365-9194-4c33-98d3-294740f281eb	g.chr6:155154044G>T	ENST00000367178.3	+	20	3907	c.3331G>T	c.(3331-3333)Ggt>Tgt	p.G1111C	TIAM2_ENST00000461783.3_5'UTR|SCAF8_ENST00000367186.4_Missense_Mutation_p.G1177C|SCAF8_ENST00000417268.1_Missense_Mutation_p.G1111C	NM_014892.3	NP_055707.3	Q9UPN6	SCAF8_HUMAN	SR-related CTD-associated factor 8	1111					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase core enzyme binding (GO:0043175)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(15)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	46						ACCGGTCTATGGTGGTCCAAA	0.468																																						dbGAP											0			6											64.0	71.0	68.0					6																	155154044		2203	4300	6503	155195736	SO:0001583	missense	0			AB029039	CCDS5247.1, CCDS69226.1, CCDS75541.1	6q25.1-q25.3	2013-02-12	2011-01-10	2011-01-10	ENSG00000213079	ENSG00000213079		"""RNA binding motif (RRM) containing"""	20959	protein-coding gene	gene with protein product			"""RNA binding motif protein 16"""	RBM16		10470851	Standard	NM_001286189		Approved	KIAA1116	uc003qpz.3	Q9UPN6	OTTHUMG00000015877	ENST00000367178.3:c.3331G>T	6.37:g.155154044G>T	ENSP00000356146:p.Gly1111Cys	163	1.81	3		53	27.03	20	155195736	115	17.27	24	B7Z888|Q5TBU6|Q6NSK3|Q9BQN8|Q9BX43	Missense_Mutation	SNP	HMMPfam_RRM_1,HMMSmart_RRM,HMMSmart_RPR,HMMPfam_DUF618,superfamily_ENTH_VHS,superfamily_SSF54928	p.G1111C	ENST00000367178.3	37	c.3331	CCDS5247.1	6	.	.	.	.	.	.	.	.	.	.	G	12.89	2.074327	0.36566	.	.	ENSG00000213079;ENSG00000213079;ENSG00000213079;ENSG00000146426	ENST00000367178;ENST00000417268;ENST00000367186;ENST00000528928	T;T;T	0.58210	0.35;0.35;0.35	5.73	2.95	0.34219	.	0.353900	0.25363	U	0.031205	T	0.25754	0.0627	L	0.27053	0.805	0.80722	D	1	P;P;P	0.49696	0.927;0.927;0.927	B;B;B	0.43623	0.425;0.425;0.425	T	0.05886	-1.0858	10	0.66056	D	0.02	.	10.4632	0.44592	0.2155:0.0:0.7845:0.0	.	1156;1177;1111	B7Z876;B7Z888;Q9UPN6	.;.;SCAF8_HUMAN	C	1111;1111;1177;72	ENSP00000356146:G1111C;ENSP00000413098:G1111C;ENSP00000356154:G1177C	ENSP00000356146:G1111C	G	+	1	0	TIAM2;SCAF8	155195736	1.000000	0.71417	0.119000	0.21687	0.912000	0.54170	4.901000	0.63259	0.337000	0.23665	-0.126000	0.14955	GGT	-	NULL		0.468	SCAF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RBM16	protein_coding	OTTHUMT00000042798.1	G	NM_014892		155195736	+1	no_errors	NM_014892.3	genbank	human	validated	54_36p	missense	SNP	0.996	T
SDK1	221935	genome.wustl.edu	37	7	4014056	4014056	+	Missense_Mutation	SNP	G	G	A	rs147156647		TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b94e2b78-8092-49af-9c9e-7fd612b89793	22830365-9194-4c33-98d3-294740f281eb	g.chr7:4014056G>A	ENST00000404826.2	+	13	2012	c.1873G>A	c.(1873-1875)Gtg>Atg	p.V625M	SDK1_ENST00000389531.3_Missense_Mutation_p.V625M	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	625	Ig-like C2-type 6.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		GTCTAGGATCGTGGTGGAGAA	0.552																																						dbGAP											0			7						G	MET/VAL	0,4406		0,0,2203	135.0	107.0	116.0		1873	0.2	0.1	7	dbSNP_134	116	1,8599	1.2+/-3.3	0,1,4299	no	missense	SDK1	NM_152744.3	21	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	625/2214	4014056	1,13005	2203	4300	6503	3980582	SO:0001583	missense	0			AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19307	protein-coding gene	gene with protein product		607216	"""sidekick homolog 1 (chicken)"", ""sidekick homolog 1, cell adhesion molecule (chicken)"""			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.1873G>A	7.37:g.4014056G>A	ENSP00000385899:p.Val625Met	169	8.15	15		NA	NA	NA	3980582	27	41.30	19	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,HMMPfam_I-set,HMMPfam_ig,superfamily_Immunoglobulin	p.V625M	ENST00000404826.2	37	c.1873	CCDS34590.1	7	.	.	.	.	.	.	.	.	.	.	G	5.409	0.260610	0.10239	0.0	1.16E-4	ENSG00000146555	ENST00000404826;ENST00000389531	T;T	0.67698	-0.28;-0.28	5.35	0.18	0.15068	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.413260	0.21746	N	0.069747	T	0.41743	0.1172	L	0.33093	0.98	0.09310	N	1	P	0.35807	0.522	B	0.27715	0.082	T	0.28776	-1.0033	10	0.44086	T	0.13	.	0.8736	0.01219	0.3264:0.29:0.2361:0.1476	.	625	Q7Z5N4	SDK1_HUMAN	M	625	ENSP00000385899:V625M;ENSP00000374182:V625M	ENSP00000374182:V625M	V	+	1	0	SDK1	3980582	0.006000	0.16342	0.113000	0.21522	0.207000	0.24258	0.352000	0.20113	-0.039000	0.13602	-0.244000	0.11960	GTG	-	HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_ig,superfamily_Immunoglobulin		0.552	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SDK1	protein_coding	OTTHUMT00000323702.1	G	NM_152744		3980582	+1	no_errors	NM_152744.1	genbank	human	validated	54_36p	missense	SNP	0.004	A
TRPM3	80036	genome.wustl.edu	37	9	73218347	73218347	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b94e2b78-8092-49af-9c9e-7fd612b89793	22830365-9194-4c33-98d3-294740f281eb	g.chr9:73218347C>T	ENST00000377111.2	-	19	2914	c.2671G>A	c.(2671-2673)Gtg>Atg	p.V891M	TRPM3_ENST00000408909.2_Missense_Mutation_p.V750M|TRPM3_ENST00000358082.3_Missense_Mutation_p.V753M|TRPM3_ENST00000396292.4_Missense_Mutation_p.V763M|TRPM3_ENST00000377106.1_Missense_Mutation_p.V763M|TRPM3_ENST00000396285.1_Missense_Mutation_p.V738M|TRPM3_ENST00000396280.5_Missense_Mutation_p.V740M|TRPM3_ENST00000423814.3_Missense_Mutation_p.V918M|TRPM3_ENST00000377105.1_Missense_Mutation_p.V750M|TRPM3_ENST00000357533.2_Missense_Mutation_p.V895M|TRPM3_ENST00000377110.3_Missense_Mutation_p.V891M|TRPM3_ENST00000360823.2_Missense_Mutation_p.V753M	NM_001007471.2	NP_001007472.2	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	916					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						TTCACTAACACGATATAGTTG	0.493																																						dbGAP											0			9											105.0	88.0	94.0					9																	73218347		2203	4300	6503	72408167	SO:0001583	missense	0			AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17992	protein-coding gene	gene with protein product	"""melastatin 2"""	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377111.2:c.2671G>A	9.37:g.73218347C>T	ENSP00000366315:p.Val891Met	506	1.75	9		NA	NA	NA	72408167	115	38.17	71	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Missense_Mutation	SNP	HMMPfam_Ion_trans	p.V891M	ENST00000377111.2	37	c.2671		9	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.5|24.5	4.539032|4.539032	0.85917|0.85917	.|.	.|.	ENSG00000083067|ENSG00000083067	ENST00000396280|ENST00000377111;ENST00000377110;ENST00000377106;ENST00000360823;ENST00000377105;ENST00000357533;ENST00000408909;ENST00000396285;ENST00000396292;ENST00000358082;ENST00000423814	.|T;T;T;T;T;T;T;T;T;T;T	.|0.63913	.|-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07	5.59|5.59	5.59|5.59	0.84812|0.84812	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.81216|0.81216	0.4776|0.4776	M|M	0.80332|0.80332	2.49|2.49	0.48762|0.48762	D|D	0.999708|0.999708	.|D;D;D;D;D;D;D;D	.|0.89917	.|1.0;0.968;0.999;0.999;1.0;1.0;0.976;0.997	.|D;P;D;D;D;D;P;P	.|0.77557	.|0.99;0.651;0.981;0.96;0.978;0.975;0.674;0.818	T|T	0.82196|0.82196	-0.0577|-0.0577	5|10	.|0.56958	.|D	.|0.05	-23.9162|-23.9162	19.6085|19.6085	0.95589|0.95589	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|891;891;881;895;753;750;863;738	.|Q9HCF6-2;Q9HCF6-10;Q9HCF6-4;A2A3F7;A2A3F4;G5E9G1;Q9HCF6-8;A2A3F3	.|.;.;.;.;.;.;.;.	H|M	739|891;891;763;753;750;895;750;738;763;753;918	.|ENSP00000366315:V891M;ENSP00000366314:V891M;ENSP00000366310:V763M;ENSP00000354066:V753M;ENSP00000366309:V750M;ENSP00000350140:V895M;ENSP00000386127:V750M;ENSP00000379581:V738M;ENSP00000379587:V763M;ENSP00000350791:V753M;ENSP00000389542:V918M	.|ENSP00000350140:V895M	R|V	-|-	2|1	0|0	TRPM3|TRPM3	72408167|72408167	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	4.911000|4.911000	0.63328|0.63328	2.629000|2.629000	0.89072|0.89072	0.637000|0.637000	0.83480|0.83480	CGT|GTG	-	NULL		0.493	TRPM3-007	NOVEL	basic|exp_conf	protein_coding	TRPM3	protein_coding	OTTHUMT00000214157.5	C	NM_206945		72408167	-1	no_errors	NM_001007471.1	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
DYNC2H1	79659	genome.wustl.edu	37	11	102980403	102980403	+	Missense_Mutation	SNP	T	T	G			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	T	T	T	G	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b94e2b78-8092-49af-9c9e-7fd612b89793	22830365-9194-4c33-98d3-294740f281eb	g.chr11:102980403T>G	ENST00000375735.2	+	1	244	c.100T>G	c.(100-102)Tgc>Ggc	p.C34G	DYNC2H1_ENST00000334267.7_Missense_Mutation_p.C34G|DYNC2H1_ENST00000398093.3_Missense_Mutation_p.C34G	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	34	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		GCCACTGTTGTGCAACTGTCT	0.517																																						dbGAP											0			11											85.0	82.0	83.0					11																	102980403		1968	4164	6132	102485613	SO:0001583	missense	0			AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"""Cytoplasmic dyneins"""	2962	protein-coding gene	gene with protein product		603297	"""dynein, cytoplasmic, heavy polypeptide 2"""	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.100T>G	11.37:g.102980403T>G	ENSP00000364887:p.Cys34Gly	231	4.55	11		NA	NA	NA	102485613	71	29.70	30	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	HMMSmart_SM00382,HMMPfam_Dynein_heavy,HMMPfam_AAA_5,HMMPfam_DHC_N1,HMMPfam_DHC_N2,superfamily_P-loop containing nucleoside triphosphate hydrolases	p.C34G	ENST00000375735.2	37	c.100	CCDS53701.1	11	.	.	.	.	.	.	.	.	.	.	T	8.934	0.964209	0.18583	.	.	ENSG00000187240	ENST00000375735;ENST00000334267;ENST00000398093	T;T;T	0.28069	1.77;1.63;1.77	5.63	-11.3	0.00108	.	0.812540	0.09108	U	0.847418	T	0.09158	0.0226	N	0.08118	0	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.12837	-1.0532	10	0.19590	T	0.45	.	4.5833	0.12269	0.2668:0.444:0.1737:0.1155	.	34;34;34	Q8NCM8-3;Q8NCM8;Q8NCM8-2	.;DYHC2_HUMAN;.	G	34	ENSP00000364887:C34G;ENSP00000334021:C34G;ENSP00000381167:C34G	ENSP00000334021:C34G	C	+	1	0	DYNC2H1	102485613	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.048000	0.01406	-1.778000	0.01282	-0.353000	0.07706	TGC	-	NULL		0.517	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DYNC2H1	protein_coding	OTTHUMT00000387196.1	T	XM_370652		102485613	+1	no_errors	NM_001080463.1	genbank	human	provisional	54_36p	missense	SNP	0.000	G
TMCO5A	145942	genome.wustl.edu	37	15	38243365	38243365	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b94e2b78-8092-49af-9c9e-7fd612b89793	22830365-9194-4c33-98d3-294740f281eb	g.chr15:38243365C>T	ENST00000319669.4	+	11	899	c.797C>T	c.(796-798)aCc>aTc	p.T266I	TMCO5A_ENST00000540944.1_Intron|TMCO5A_ENST00000559502.1_Intron	NM_152453.2	NP_689666.2	Q8N6Q1	TMC5A_HUMAN	transmembrane and coiled-coil domains 5A	266						integral component of membrane (GO:0016021)		p.T266I(1)		central_nervous_system(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(2)	15						GGCAGGAGCACCTTGTGGAAG	0.428																																						dbGAP											1	Substitution - Missense(1)	skin(1)	15											129.0	113.0	118.0					15																	38243365		2200	4297	6497	36030657	SO:0001583	missense	0			BC029221	CCDS10046.1	15q14	2008-06-10	2008-06-10	2008-06-10	ENSG00000166069	ENSG00000166069			28558	protein-coding gene	gene with protein product			"""transmembrane and coiled-coil domains 5"""	TMCO5		12477932	Standard	NM_152453		Approved	MGC35118	uc001zjw.3	Q8N6Q1	OTTHUMG00000129787	ENST00000319669.4:c.797C>T	15.37:g.38243365C>T	ENSP00000327234:p.Thr266Ile	214	3.59	8		NA	NA	NA	36030657	77	44.20	61	Q8NA63	Missense_Mutation	SNP	NULL	p.T266I	ENST00000319669.4	37	c.797	CCDS10046.1	15	.	.	.	.	.	.	.	.	.	.	C	8.105	0.777553	0.16120	.	.	ENSG00000166069	ENST00000319669	.	.	.	4.63	0.625	0.17665	.	0.683800	0.13041	N	0.418491	T	0.13286	0.0322	N	0.04018	-0.295	0.22918	N	0.998561	B	0.02656	0.0	B	0.01281	0.0	T	0.20207	-1.0282	9	0.26408	T	0.33	-0.0556	2.3945	0.04386	0.2093:0.2412:0.0:0.5495	.	266	Q8N6Q1	TMC5A_HUMAN	I	266	.	ENSP00000327234:T266I	T	+	2	0	TMCO5A	36030657	0.860000	0.29831	0.429000	0.26710	0.843000	0.47879	0.446000	0.21694	0.260000	0.21731	-0.438000	0.05819	ACC	-	NULL		0.428	TMCO5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TMCO5A	protein_coding	OTTHUMT00000252012.1	C	NM_152453		36030657	+1	no_errors	NM_152453.2	genbank	human	provisional	54_36p	missense	SNP	0.332	T
SMG1	23049	genome.wustl.edu	37	16	18849950	18849950	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b94e2b78-8092-49af-9c9e-7fd612b89793	22830365-9194-4c33-98d3-294740f281eb	g.chr16:18849950C>T	ENST00000446231.2	-	43	7419	c.7007G>A	c.(7006-7008)aGa>aAa	p.R2336K	SMG1_ENST00000389467.3_Missense_Mutation_p.R2336K			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	2336	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						ATCCAGATGTCTGTCTCCAAG	0.368																																						dbGAP											0			16											129.0	119.0	122.0					16																	18849950		1866	4115	5981	18757451	SO:0001583	missense	0			AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"""phosphatidylinositol 3-kinase-related kinase"""	607032	"""smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"""			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.7007G>A	16.37:g.18849950C>T	ENSP00000402515:p.Arg2336Lys	229	4.18	10		56	43.43	43	18757451	93	33.57	47	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	HMMPfam_HEAT,HMMPfam_PI3_PI4_kinase,HMMSmart_SM00146,HMMPfam_FATC,superfamily_Protein kinase-like (PK-like),superfamily_ARM repeat,PatternScan_PI3_4_KINASE_2	p.R2336K	ENST00000446231.2	37	c.7007	CCDS45430.1	16	.	.	.	.	.	.	.	.	.	.	C	26.7	4.765517	0.90020	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	D;D	0.98901	-5.22;-5.22	5.87	5.87	0.94306	Protein kinase-like domain (1);Armadillo-type fold (1);Phosphatidylinositol 3/4-kinase, conserved site (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.000000	0.85682	D	0.000000	D	0.99591	0.9852	H	0.98818	4.34	0.44908	D	0.997929	P;D	0.57257	0.902;0.979	P;D	0.74023	0.87;0.982	D	0.97739	1.0207	10	0.87932	D	0	.	20.5827	0.99408	0.0:1.0:0.0:0.0	.	2196;2336	Q96Q15-2;Q96Q15	.;SMG1_HUMAN	K	2336	ENSP00000402515:R2336K;ENSP00000374118:R2336K	ENSP00000374118:R2336K	R	-	2	0	SMG1	18757451	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.419000	0.80179	2.941000	0.99782	0.655000	0.94253	AGA	-	HMMPfam_PI3_PI4_kinase,HMMSmart_SM00146,superfamily_Protein kinase-like (PK-like),PatternScan_PI3_4_KINASE_2		0.368	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	SMG1	protein_coding	OTTHUMT00000391817.1	C	NM_015092		18757451	-1	no_errors	NM_015092.4	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
EEF2	1938	genome.wustl.edu	37	19	3982568	3982568	+	Intron	SNP	A	A	T			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	A	A	A	T	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b94e2b78-8092-49af-9c9e-7fd612b89793	22830365-9194-4c33-98d3-294740f281eb	g.chr19:3982568A>T	ENST00000309311.6	-	5	701				SNORD37_ENST00000384048.1_RNA|EEF2_ENST00000600720.1_5'Flank	NM_001961.3	NP_001952.1	P13639	EF2_HUMAN	eukaryotic translation elongation factor 2						cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|hematopoietic progenitor cell differentiation (GO:0002244)|positive regulation of gene expression (GO:0010628)|positive regulation of translation (GO:0045727)|translation (GO:0006412)|translational elongation (GO:0006414)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation activator activity (GO:0008494)|translation elongation factor activity (GO:0003746)			endometrium(4)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|GBM - Glioblastoma multiforme(1328;0.0223)|STAD - Stomach adenocarcinoma(1328;0.18)		AGTCATCACGAATAGGGGGGC	0.577																																					Colon(165;1804 1908 4071 6587 18799)	dbGAP											0			19											32.0	31.0	31.0					19																	3982568		876	1991	2867	3933568	SO:0001627	intron_variant	0			Z11692	CCDS12117.1	19p13.3	2012-09-20			ENSG00000167658	ENSG00000167658			3214	protein-coding gene	gene with protein product	"""polypeptidyl-tRNA translocase"""	130610		EF2		2610926, 6427766	Standard	NM_001961		Approved	EEF-2	uc002lze.3	P13639		ENST00000309311.6:c.613-146T>A	19.37:g.3982568A>T		106	7.02	8		4	42.86	3	3933568	12	42.86	9	B2RMP5|D6W618|Q58J86	RNA	SNP	-	NULL	ENST00000309311.6	37	NULL	CCDS12117.1	19																																																																																			-	-		0.577	EEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SNORD37	protein_coding	OTTHUMT00000457615.2	A	NM_001961		3933568	-1	no_errors	NR_002602.1	genbank	human	provisional	54_36p	rna	SNP	0.000	T
HAO1	54363	genome.wustl.edu	37	20	7866398	7866398	+	Silent	SNP	C	C	T			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b94e2b78-8092-49af-9c9e-7fd612b89793	22830365-9194-4c33-98d3-294740f281eb	g.chr20:7866398C>T	ENST00000378789.3	-	6	978	c.927G>A	c.(925-927)aaG>aaA	p.K309K		NM_017545.2	NP_060015.1	Q9UJM8	HAOX1_HUMAN	hydroxyacid oxidase (glycolate oxidase) 1	309	FMN hydroxy acid dehydrogenase. {ECO:0000255|PROSITE-ProRule:PRU00683}.				cellular nitrogen compound metabolic process (GO:0034641)|fatty acid alpha-oxidation (GO:0001561)|glycolate catabolic process (GO:0046296)|glyoxylate metabolic process (GO:0046487)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	(S)-2-hydroxy-acid oxidase activity (GO:0003973)|FMN binding (GO:0010181)|glycolate oxidase activity (GO:0008891)|glyoxylate oxidase activity (GO:0047969)|long-chain-(S)-2-hydroxy-long-chain-acid oxidase activity (GO:0052853)|medium-chain-(S)-2-hydroxy-acid oxidase activity (GO:0052854)|receptor binding (GO:0005102)|very-long-chain-(S)-2-hydroxy-acid oxidase activity (GO:0052852)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36						CAAACACAGCCTTGGCGCCAA	0.473																																						dbGAP											0			20											123.0	124.0	124.0					20																	7866398		2203	4300	6503	7814398	SO:0001819	synonymous_variant	0			AL021879	CCDS13100.1	20p12	2005-01-10			ENSG00000101323	ENSG00000101323	1.1.3.15		4809	protein-coding gene	gene with protein product		605023		GOX1		9891009	Standard	NM_017545		Approved	GOX	uc002wmw.1	Q9UJM8	OTTHUMG00000031841	ENST00000378789.3:c.927G>A	20.37:g.7866398C>T		379	5.01	20		NA	NA	NA	7814398	142	35.45	78	Q14CQ0|Q9UPZ0|Q9Y3I7	Silent	SNP	HMMPfam_FMN_dh,PatternScan_FMN_HYDROXY_ACID_DH_1,superfamily_FMN-linked oxidoreductases	p.K309	ENST00000378789.3	37	c.927	CCDS13100.1	20																																																																																			-	HMMPfam_FMN_dh,superfamily_FMN-linked oxidoreductases		0.473	HAO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HAO1	protein_coding	OTTHUMT00000077926.2	C			7814398	-1	no_errors	NM_017545.2	genbank	human	reviewed	54_36p	silent	SNP	0.990	T
DNMT3B	1789	genome.wustl.edu	37	20	31386387	31386387	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b94e2b78-8092-49af-9c9e-7fd612b89793	22830365-9194-4c33-98d3-294740f281eb	g.chr20:31386387C>T	ENST00000328111.2	+	15	1933	c.1612C>T	c.(1612-1614)Cgc>Tgc	p.R538C	DNMT3B_ENST00000456297.2_Missense_Mutation_p.R442C|DNMT3B_ENST00000348286.2_Missense_Mutation_p.R518C|DNMT3B_ENST00000201963.3_Missense_Mutation_p.R530C|DNMT3B_ENST00000353855.2_Missense_Mutation_p.R518C|DNMT3B_ENST00000443239.3_Missense_Mutation_p.R476C|DNMT3B_ENST00000375623.4_3'UTR|DNMT3B_ENST00000344505.4_Missense_Mutation_p.R518C	NM_006892.3	NP_008823.1	Q9UBC3	DNM3B_HUMAN	DNA (cytosine-5-)-methyltransferase 3 beta	538	ADD. {ECO:0000255|PROSITE- ProRule:PRU00865}.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation on cytosine within a CG sequence (GO:0010424)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of neuron differentiation (GO:0045666)|protein complex localization (GO:0031503)|regulation of gene expression by genetic imprinting (GO:0006349)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA-methyltransferase activity (GO:0009008)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)|unmethylated CpG binding (GO:0045322)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(16)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CGTCCTGCGGCGCCGGAAGGA	0.642																																						dbGAP											0			20											43.0	47.0	46.0					20																	31386387		2203	4300	6503	30850048	SO:0001583	missense	0				CCDS13204.1, CCDS13205.1, CCDS13206.1, CCDS13207.1, CCDS56183.1, CCDS56184.1	20q11.2	2014-09-17			ENSG00000088305	ENSG00000088305			2979	protein-coding gene	gene with protein product		602900				9662389, 10433969	Standard	NM_006892		Approved		uc002wyc.3	Q9UBC3	OTTHUMG00000032226	ENST00000328111.2:c.1612C>T	20.37:g.31386387C>T	ENSP00000328547:p.Arg538Cys	126	5.26	7		18	61.70	29	30850048	44	37.14	26	A2A2E2|B4DSM8|B4DSU1|E1P5M6|E1P5M7|E7EN63|E9PBF2|Q9UBD4|Q9UJQ5|Q9UKA6|Q9UNE5|Q9Y5R9|Q9Y5S0	Missense_Mutation	SNP	HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT	p.R538C	ENST00000328111.2	37	c.1612	CCDS13205.1	20	.	.	.	.	.	.	.	.	.	.	C	33	5.255438	0.95336	.	.	ENSG00000088305	ENST00000328111;ENST00000353855;ENST00000348286;ENST00000443239;ENST00000456297;ENST00000344505;ENST00000201963	T;T;T;T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2;-1.2;-1.2;-1.2	5.76	5.76	0.90799	Zinc finger, FYVE/PHD-type (1);	0.056575	0.64402	D	0.000001	D	0.89188	0.6644	M	0.79926	2.475	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.91635	0.977;0.985;0.972;0.99;0.99;0.99;0.999	D	0.89576	0.3817	10	0.87932	D	0	-29.4349	19.3309	0.94288	0.0:1.0:0.0:0.0	.	442;476;237;530;518;518;538	E9PBF2;E7EN63;B3KM53;Q9UBC3-6;Q9UBC3-3;Q9UBC3-2;Q9UBC3	.;.;.;.;.;.;DNM3B_HUMAN	C	538;518;518;476;442;518;530	ENSP00000328547:R538C;ENSP00000313397:R518C;ENSP00000337764:R518C;ENSP00000403169:R476C;ENSP00000412305:R442C;ENSP00000345105:R518C;ENSP00000201963:R530C	ENSP00000201963:R530C	R	+	1	0	DNMT3B	30850048	1.000000	0.71417	1.000000	0.80357	0.791000	0.44710	5.897000	0.69831	2.880000	0.98712	0.650000	0.86243	CGC	-	superfamily_FYVE/PHD zinc finger		0.642	DNMT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DNMT3B	protein_coding	OTTHUMT00000078643.2	C	NM_006892		30850048	+1	no_errors	NM_006892.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
U2AF1	7307	genome.wustl.edu	37	21	44524456	44524456	+	Missense_Mutation	SNP	G	G	T	rs371769427		TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b94e2b78-8092-49af-9c9e-7fd612b89793	22830365-9194-4c33-98d3-294740f281eb	g.chr21:44524456G>T	ENST00000291552.4	-	2	193	c.101C>A	c.(100-102)tCt>tAt	p.S34Y	U2AF1_ENST00000486519.1_5'UTR|U2AF1_ENST00000459639.1_5'UTR|U2AF1_ENST00000380276.2_Missense_Mutation_p.S34Y|U2AF1_ENST00000398137.1_5'UTR	NM_006758.2	NP_006749.1	Q01081	U2AF1_HUMAN	U2 small nuclear RNA auxiliary factor 1	34					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.S34F(45)|p.S34Y(12)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(111)|large_intestine(2)|lung(7)|prostate(2)|skin(1)	126						GTGCAACCGAGAGCACCTGTC	0.358			Mis		"""CLL, MDS"""																																	dbGAP		Dom	yes		21	21q22.3	7307	U2 small nuclear RNA auxiliary factor 1		L	57	Substitution - Missense(57)	haematopoietic_and_lymphoid_tissue(43)|lung(12)|endometrium(2)	21											67.0	64.0	65.0					21																	44524456		2203	4300	6503	43397525	SO:0001583	missense	0			BC001177	CCDS13694.1, CCDS33574.1, CCDS42948.1	21q22.3	2014-09-17	2006-04-11		ENSG00000160201	ENSG00000160201		"""RNA binding motif (RRM) containing"""	12453	protein-coding gene	gene with protein product		191317	"""U2(RNU2) small nuclear RNA auxiliary factor binding protein"", ""U2(RNU2) small nuclear RNA auxiliary factor 1"""	U2AFBP		8660980, 7956352	Standard	NM_006758		Approved	U2AF35, RNU2AF1, RN	uc002zdb.1	Q01081	OTTHUMG00000086836	ENST00000291552.4:c.101C>A	21.37:g.44524456G>T	ENSP00000291552:p.Ser34Tyr	142	0.70	1		67	49.62	66	43397525	19	45.71	16	Q701P4|Q71RF1	Missense_Mutation	SNP	HMMPfam_RRM_1,HMMSmart_RRM,HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1,superfamily_SSF54928	p.S34Y	ENST00000291552.4	37	c.101	CCDS13694.1	21	.	.	.	.	.	.	.	.	.	.	G	28.9	4.962845	0.92791	.	.	ENSG00000160201	ENST00000380276;ENST00000291552	T;T	0.46063	0.88;0.88	5.47	5.47	0.80525	Zinc finger, CCCH-type (3);	0.000000	0.85682	D	0.000000	T	0.77239	0.4101	H	0.96430	3.82	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.997;0.997	D	0.84864	0.0821	10	0.87932	D	0	-15.7954	19.3169	0.94218	0.0:0.0:1.0:0.0	.	34;34;34	Q69YM7;Q01081;Q701P4	.;U2AF1_HUMAN;.	Y	34	ENSP00000369629:S34Y;ENSP00000291552:S34Y	ENSP00000291552:S34Y	S	-	2	0	U2AF1	43397525	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.864000	0.92294	2.560000	0.86352	0.563000	0.77884	TCT	-	HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1		0.358	U2AF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	U2AF1	protein_coding	OTTHUMT00000195541.1	G	NM_006758		43397525	-1	no_errors	NM_001025203.1	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
NIPSNAP1	8508	genome.wustl.edu	37	22	29966426	29966426	+	Missense_Mutation	SNP	T	T	C	rs538441678		TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b94e2b78-8092-49af-9c9e-7fd612b89793	22830365-9194-4c33-98d3-294740f281eb	g.chr22:29966426T>C	ENST00000216121.7	-	2	448	c.194A>G	c.(193-195)aAg>aGg	p.K65R		NM_001202502.1|NM_003634.3	NP_001189431.1|NP_003625.2	Q9BPW8	NIPS1_HUMAN	nipsnap homolog 1 (C. elegans)	65					sensory perception of pain (GO:0019233)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|synaptic membrane (GO:0097060)	neurotransmitter binding (GO:0042165)	p.?(1)		large_intestine(2)|lung(2)|skin(1)	5						GGTTTCCTTCTTGGACAGCAG	0.547													T|||	1	0.000199681	0.0	0.0014	5008	,	,		18865	0.0		0.0	False		,,,				2504	0.0					dbGAP											1	Unknown(1)	lung(1)	22											77.0	72.0	74.0					22																	29966426		2203	4300	6503	28296426	SO:0001583	missense	0			AJ001258	CCDS13860.1	22q12	2013-09-12	2001-11-28		ENSG00000184117	ENSG00000184117			7827	protein-coding gene	gene with protein product	"""4-nitrophenylphosphatase domain and non-neuronal SNAP25-like 1"""	603249	"""NIPSNAP, C. elegans, homolog 1"""			9661659	Standard	NM_003634		Approved		uc003afx.4	Q9BPW8	OTTHUMG00000151294	ENST00000216121.7:c.194A>G	22.37:g.29966426T>C	ENSP00000216121:p.Lys65Arg	764	2.55	20		19	38.71	12	28296426	100	42.53	74	B2RAY3|O43800	Missense_Mutation	SNP	HMMPfam_NIPSNAP	p.K65R	ENST00000216121.7	37	c.194	CCDS13860.1	22	.	.	.	.	.	.	.	.	.	.	T	26.2	4.713000	0.89112	.	.	ENSG00000184117	ENST00000216121	T	0.61510	0.1	4.48	4.48	0.54585	Dimeric alpha-beta barrel (1);	0.000000	0.85682	D	0.000000	T	0.70762	0.3261	M	0.75884	2.315	0.58432	D	0.999999	D;D	0.76494	0.996;0.999	D;D	0.63703	0.917;0.917	T	0.68808	-0.5311	10	0.20046	T	0.44	-6.5541	13.9248	0.63955	0.0:0.0:0.0:1.0	.	45;65	B4DQI7;Q9BPW8	.;NIPS1_HUMAN	R	65	ENSP00000216121:K65R	ENSP00000216121:K65R	K	-	2	0	NIPSNAP1	28296426	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.522000	0.81844	2.014000	0.59158	0.374000	0.22700	AAG	-	NULL		0.547	NIPSNAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NIPSNAP1	protein_coding	OTTHUMT00000322117.1	T			28296426	-1	no_errors	NM_003634.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	C
BCHE	590	genome.wustl.edu	37	3	165548476	165548476	+	Frame_Shift_Del	DEL	G	G	-	rs374198965		TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	G	G	G	-	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	b94e2b78-8092-49af-9c9e-7fd612b89793	22830365-9194-4c33-98d3-294740f281eb	g.chr3:165548476delG	ENST00000264381.3	-	2	512	c.346delC	c.(346-348)ctcfs	p.L116fs	BCHE_ENST00000540653.1_Intron	NM_000055.2	NP_000046.1	P06276	CHLE_HUMAN	butyrylcholinesterase	116					cellular protein metabolic process (GO:0044267)|choline metabolic process (GO:0019695)|cocaine metabolic process (GO:0050783)|learning (GO:0007612)|negative regulation of cell proliferation (GO:0008285)|negative regulation of synaptic transmission (GO:0050805)|neuroblast differentiation (GO:0014016)|response to alkaloid (GO:0043279)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|synaptic transmission, cholinergic (GO:0007271)	blood microparticle (GO:0072562)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)	acetylcholinesterase activity (GO:0003990)|beta-amyloid binding (GO:0001540)|catalytic activity (GO:0003824)|choline binding (GO:0033265)|cholinesterase activity (GO:0004104)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(34)|ovary(4)|pancreas(2)|stomach(1)	55					Aclidinium(DB08897)|Ambenonium(DB01122)|Bambuterol(DB01408)|Chloroprocaine(DB01161)|Chlorphenesin(DB00856)|Chlorpromazine(DB00477)|Choline(DB00122)|Cinchocaine(DB00527)|Cisplatin(DB00515)|Clevidipine(DB04920)|Cyclopentolate(DB00979)|Decamethonium(DB01245)|Demecarium(DB00944)|Diethylcarbamazine(DB00711)|Dipivefrin(DB00449)|Doxacurium chloride(DB01135)|Drospirenone(DB01395)|Echothiophate(DB01057)|Edrophonium(DB01010)|Ephedrine(DB01364)|Ethopropazine(DB00392)|Galantamine(DB00674)|Hexafluronium(DB00941)|Irinotecan(DB00762)|Isoflurophate(DB00677)|Malathion(DB00772)|Mefloquine(DB00358)|Mirabegron(DB08893)|Mivacurium(DB01226)|Neostigmine(DB01400)|Nizatidine(DB00585)|Oxybuprocaine(DB00892)|Pancuronium(DB01337)|Pegvisomant(DB00082)|Pentagastrin(DB00183)|Perindopril(DB00790)|Pipecuronium(DB01338)|Pralidoxime(DB00733)|Procainamide(DB01035)|Procaine(DB00721)|Pyridostigmine(DB00545)|Ramipril(DB00178)|Rivastigmine(DB00989)|Succinylcholine(DB00202)|Sulpiride(DB00391)|Terbutaline(DB00871)|Triamcinolone(DB00620)|Triflupromazine(DB00508)|Trimethaphan(DB01116)	TCTTCACTGAGGTCAGTGTTT	0.383																																						dbGAP											0			3											83.0	88.0	87.0					3																	165548476		2203	4300	6503	167031170	SO:0001589	frameshift_variant	0			M16541	CCDS3198.1	3q26.1-q26.2	2013-07-10			ENSG00000114200	ENSG00000114200	3.1.1.8		983	protein-coding gene	gene with protein product		177400	"""cholinesterase 1"", ""cholinesterase (serum) 2"""	CHE1, CHE2		1769657, 2318303	Standard	NM_000055		Approved	E1	uc003fem.4	P06276	OTTHUMG00000158131	ENST00000264381.3:c.346delC	3.37:g.165548476delG	ENSP00000264381:p.Leu116fs	128	0.00	0		0	0.00	0	167031170	83	28.45	33	A8K7P8	Frame_Shift_Del	DEL	HMMPfam_COesterase,HMMPfam_AChE_tetra,PatternScan_CARBOXYLESTERASE_B_2,PatternScan_CARBOXYLESTERASE_B_1,superfamily_SSF53474	p.L116fs	ENST00000264381.3	37	c.346	CCDS3198.1	3																																																																																			-	HMMPfam_COesterase,superfamily_SSF53474		0.383	BCHE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BCHE	protein_coding	OTTHUMT00000350254.1	G			167031170	-1	no_errors	NM_000055.2	genbank	human	reviewed	54_36p	frame_shift_del	DEL	0.974	-
