{"_id":"chr7:g.44189428T>G","_version":1,"cadd":{"_license":"http://bit.ly/2TIuab9","alt":"G","anc":"T","annotype":"CodingTranscript","bstatistic":749,"chmm":{"bivflnk":0.0,"enh":0.0,"enhbiv":0.008,"het":0.0,"quies":0.488,"reprpc":0.039,"reprpcwk":0.268,"tssa":0.0,"tssaflnk":0.0,"tssbiv":0.0,"tx":0.016,"txflnk":0.0,"txwk":0.094,"znfrpts":0.0},"chrom":7,"consdetail":"missense","consequence":"NON_SYNONYMOUS","consscore":7,"cpg":0.08,"dna":{"helt":-0.98,"mgw":-0.33,"prot":2.72,"roll":0.16},"encode":{"exp":0.84,"h3k27ac":4.0,"h3k4me1":4.0,"h3k4me3":4.0,"nucleo":1.1,"occ":1,"p_val":{"comb":12.65,"ctcf":1.14,"dnas":9.58,"faire":4.6,"mycp":0.0,"polii":0.0},"sig":{"ctcf":0.08,"dnase":0.23,"faire":0.04,"myc":0.0,"polii":0.0}},"exon":"6/10","fitcons":0.527649,"gc":0.53,"gene":{"ccds_id":"CCDS5480.1","cds":{"cdna_pos":775,"cds_pos":613,"rel_cdna_pos":0.32,"rel_cds_pos":0.44},"feature_id":"ENST00000345378","gene_id":"ENSG00000106633","genename":"GCK","prot":{"domain":"ndomain","protpos":205,"rel_prot_pos":0.44}},"gerp":{"n":5.96,"rs":522.8,"rs_pval":3.90346e-139,"s":5.96},"grantham":68,"isderived":"TRUE","isknownvariant":"FALSE","istv":"TRUE","length":0,"mapability":{"20bp":1,"35bp":1},"min_dist_tse":4697,"min_dist_tss":9447,"mutindex":-68,"naa":"H","oaa":"N","phast_cons":{"mammalian":0.996,"primate":0.983,"vertebrate":1.0},"phred":26.4,"phylop":{"mammalian":2.282,"primate":0.53,"vertebrate":5.144},"polyphen":{"cat":"probably_damaging","val":1},"pos":44189428,"rawscore":5.576242,"ref":"T","segway":"R5","sift":{"cat":"deleterious","val":0},"tf":{"bs":1,"bs_peaks":1,"bs_peaks_max":29.2839},"type":"SNV"},"chrom":"7","dbnsfp":{"_license":"http://bit.ly/2VLnQBz","aa":{"alt":"H","codon_degeneracy":[0,0,0,0,0],"codonpos":[1,1,1,1,1],"pos":[203,204,203,205,187],"ref":"N","refcodon":["AAT","AAT","AAT","AAT","AAT"]},"alphamissense":{"pred":["P","P","P","P"],"rankscore":0.96595,"score":[0.9911,0.9969,0.9875,0.9961]},"alt":"G","altai_neandertal":["T","T"],"ancestral_allele":"T","appris":"principal1","bayesdel":{"add_af":{"pred":"D","rankscore":0.87627,"score":0.364991},"no_af":{"pred":"D","rankscore":0.87467,"score":0.286508}},"bstatistic":{"converted_rankscore":0.60868,"score":671.0},"chagyrskaya_neandertal":["T","T"],"chrom":"7","clinpred":{"pred":"D","rankscore":0.97717,"score":0.999512195587158},"dann":{"rankscore":0.80453,"score":0.9969843685013309},"denisova":["T","T"],"deogen2":{"pred":"D","rankscore":0.99911,"score":0.985718},"eigen":{"phred_coding":14.43863,"raw_coding":1.01618538624655,"raw_coding_rankscore":0.96221},"eigen-pc":{"phred_coding":15.81647,"raw_coding":0.944841149428356,"raw_coding_rankscore":0.97247},"ensembl":{"geneid":["ENSG00000106633","ENSG00000106633","ENSG00000106633","ENSG00000106633","ENSG00000106633"],"proteinid":["ENSP00000482149","ENSP00000384247","ENSP00000379142","ENSP00000223366","ENSP00000402840"],"transcriptid":["ENST00000616242","ENST00000403799","ENST00000395796","ENST00000345378","ENST00000437084"]},"esm1b":{"pred":["D","D","D","D"],"rankscore":0.81663,"score":[-11.275,-11.373,-11.275,-11.351]},"eve":{"class10_pred":"U","class20_pred":"U","class25_pred":"U","class30_pred":"U","class40_pred":"P","class50_pred":"P","class60_pred":"P","class70_pred":"P","class75_pred":"P","class80_pred":"P","class90_pred":"P","rankscore":0.90709,"score":0.8378618243455772},"fathmm":{"converted_rankscore":0.99769,"pred":["D","D","D","D"],"score":[-6.71,-6.71,-6.71,-6.71]},"fathmm-mkl":{"coding_group":"AEFDGBCI","coding_pred":"D","coding_rankscore":0.67711,"coding_score":0.96139},"fathmm-xf":{"coding_pred":"D","coding_rankscore":0.97739,"coding_score":0.957911},"fitcons":{"gm12878":{"confidence_value":0,"rankscore":0.14657,"score":0.547309},"h1-hesc":{"confidence_value":0,"rankscore":0.34648,"score":0.602189},"huvec":{"confidence_value":0,"rankscore":0.1498,"score":0.542086},"integrated":{"confidence_value":0,"rankscore":0.28877,"score":0.554377}},"gencode_basic":["Y","Y","Y","Y","Y"],"genename":["GCK","GCK","GCK","GCK","GCK"],"genocanyon":{"rankscore":0.74766,"score":0.999999999999455},"gerp":{"91_mammals":{"rankscore":0.72823,"score":3.87}},"gerp++":{"nr":5.96,"rs":5.96,"rs_rankscore":0.96695},"gmvp":{"rankscore":0.99892,"score":0.9989325382635766},"hg18":{"end":44155953,"start":44155953},"hg19":{"end":44189428,"start":44189428},"hg38":{"end":44149829,"start":44149829},"hgvsc":["c.610A>C","c.613A>C","c.607A>C","c.559A>C"],"hgvsp":["p.Asn187His","p.N204H","p.Asn203His","p.N187H","p.N205H","p.N203H","p.Asn204His","p.Asn205His"],"interpro":{"domain":["Hexokinase, N-terminal","Hexokinase, N-terminal"]},"list-s2":{"pred":["D","D","D","D"],"rankscore":0.93712,"score":[0.981402,0.981402,0.981402,0.981402]},"lrt":{"converted_rankscore":0.8433,"omega":0.0,"pred":"D","score":0.0},"m-cap":{"pred":"D","rankscore":0.98223,"score":0.774925},"metalr":{"pred":"D","rankscore":0.9985,"score":0.9935},"metarnn":{"pred":["D","D","D","D","D"],"rankscore":0.99577,"score":[0.9906851,0.9906851,0.9906851,0.9906851,0.9906851]},"metasvm":{"pred":"D","rankscore":0.96264,"score":0.9411},"mpc":{"rankscore":0.96251,"score":2.26841461588},"mutationassessor":{"pred":"H","rankscore":0.97701,"score":4.175},"mutationtaster":{"aae":["N204H","N203H","N205H","N187H"],"converted_rankscore":0.81001,"model":["simple_aae","simple_aae","simple_aae","simple_aae"],"pred":["D","D","D","D"],"score":[1.0,1.0,1.0,1.0]},"mutformer":{"rankscore":0.99646,"score":0.99971777},"mutpred":{"aa_change":"N204H","accession":"P35557","pred":{"mechanism":"Gain of catalytic residue at N204","p_val":0.1769},"rankscore":0.99232,"score":0.942},"mvp":{"rankscore":0.99194,"score":[0.992022809967,0.992022809967,0.992022809967,0.992022809967,0.992022809967]},"phactboost":{"rankscore":0.94565,"score":0.998514476149206},"phastcons":{"100way_vertebrate":{"rankscore":0.71638,"score":1.0},"17way_primate":{"rankscore":0.56436,"score":0.976},"470way_mammalian":{"rankscore":0.68203,"score":1.0}},"phylop":{"100way_vertebrate":{"rankscore":0.88732,"score":8.017},"17way_primate":{"rankscore":0.62972,"score":0.665},"470way_mammalian":{"rankscore":0.70197,"score":7.833}},"polyphen2":{"hdiv":{"pred":["D","D","D","D"],"rankscore":0.90584,"score":[1.0,1.0,1.0,1.0]},"hvar":{"pred":["D","D","D","D"],"rankscore":0.97372,"score":[1.0,1.0,1.0,1.0]}},"primateai":{"pred":"D","rankscore":0.83268,"score":0.808536529541},"provean":{"converted_rankscore":0.82141,"pred":["D","D","D","D"],"score":[-4.89,-4.89,-4.89,-4.98]},"ref":"T","reliability_index":10,"revel":{"rankscore":0.99157,"score":[0.953,0.953,0.953,0.953]},"sift":{"converted_rankscore":0.91255,"pred":["D","D","D","D"],"score":[0.0,0.0,0.0,0.0]},"sift4g":{"converted_rankscore":0.92824,"pred":["D","D","D","D","D"],"score":[0.0,0.0,0.0,0.0,0.001]},"siphy_29way":{"logodds_rankscore":0.81175,"logodds_score":16.1219,"pi":{"a":0.0,"c":0.0,"g":0.0,"t":1.0}},"tsl":[5,1,1,2,5],"uniprot":[{"acc":"P35557-3","entry":"HXK4_HUMAN"},{"acc":"P35557","entry":"HXK4_HUMAN"},{"acc":"P35557-3","entry":"HXK4_HUMAN"},{"acc":"P35557-2","entry":"HXK4_HUMAN"},{"acc":"C9JQD1","entry":"C9JQD1_HUMAN"}],"varity":{"er":{"rankscore":0.96773,"score":0.92536557},"er_loo":{"rankscore":0.96774,"score":0.92536557},"r":{"rankscore":0.97187,"score":0.9590819},"r_loo":{"rankscore":0.97187,"score":0.9590819}},"vep_canonical":"YES","vest4":{"rankscore":0.96758,"score":[0.958,0.958,0.958,0.958,0.934]},"vindijia_neandertal":["T","T"]},"hg19":{"end":44189428,"start":44189428},"snpeff":{"_license":"http://bit.ly/2suyRKt","ann":[{"cdna":{"length":"2434","position":"781"},"cds":{"length":"1401","position":"613"},"effect":"missense_variant","feature_id":"NM_033507.1","feature_type":"transcript","gene_id":"GCK","genename":"GCK","hgvs_c":"c.613A>C","hgvs_p":"p.Asn205His","protein":{"length":"466","position":"205"},"putative_impact":"MODERATE","rank":"6","total":"10","transcript_biotype":"protein_coding"},{"cdna":{"length":"2558","position":"905"},"cds":{"length":"1395","position":"607"},"effect":"missense_variant","feature_id":"NM_033508.1","feature_type":"transcript","gene_id":"GCK","genename":"GCK","hgvs_c":"c.607A>C","hgvs_p":"p.Asn203His","protein":{"length":"464","position":"203"},"putative_impact":"MODERATE","rank":"7","total":"11","transcript_biotype":"protein_coding"},{"cdna":{"length":"2733","position":"1080"},"cds":{"length":"1398","position":"610"},"effect":"missense_variant","feature_id":"NM_000162.3","feature_type":"transcript","gene_id":"GCK","genename":"GCK","hgvs_c":"c.610A>C","hgvs_p":"p.Asn204His","protein":{"length":"465","position":"204"},"putative_impact":"MODERATE","rank":"6","total":"10","transcript_biotype":"protein_coding"},{"effect":"sequence_feature","feature_id":"NM_033507.1","feature_type":"miscellaneous-region:Hexokinase_large_subdomain","gene_id":"GCK","genename":"GCK","hgvs_c":"c.613A>C","putative_impact":"LOW","rank":"6","total":"10","transcript_biotype":"protein_coding"},{"effect":"sequence_feature","feature_id":"NM_033507.1","feature_type":"miscellaneous-region:Substrate_binding","gene_id":"GCK","genename":"GCK","hgvs_c":"c.613A>C","putative_impact":"LOW","rank":"6","total":"10","transcript_biotype":"protein_coding"},{"effect":"sequence_feature","feature_id":"NM_033508.1","feature_type":"miscellaneous-region:Hexokinase_large_subdomain","gene_id":"GCK","genename":"GCK","hgvs_c":"c.607A>C","putative_impact":"LOW","rank":"7","total":"11","transcript_biotype":"protein_coding"},{"effect":"sequence_feature","feature_id":"NM_033508.1","feature_type":"miscellaneous-region:Substrate_binding","gene_id":"GCK","genename":"GCK","hgvs_c":"c.607A>C","putative_impact":"LOW","rank":"7","total":"11","transcript_biotype":"protein_coding"},{"effect":"sequence_feature","feature_id":"NM_000162.3","feature_type":"miscellaneous-region:Hexokinase_large_subdomain","gene_id":"GCK","genename":"GCK","hgvs_c":"c.610A>C","putative_impact":"LOW","rank":"6","total":"10","transcript_biotype":"protein_coding"},{"effect":"sequence_feature","feature_id":"NM_000162.3","feature_type":"miscellaneous-region:Substrate_binding","gene_id":"GCK","genename":"GCK","hgvs_c":"c.610A>C","putative_impact":"LOW","rank":"6","total":"10","transcript_biotype":"protein_coding"}]},"vcf":{"alt":"G","position":"44189428","ref":"T"}}