{"_id":"chr12:g.105189779T>G","_version":1,"chrom":"12","clingen":{"caid":"CA386375834"},"dbnsfp":{"_license":"http://bit.ly/2VLnQBz","aa":{"alt":"D","codon_degeneracy":[2,2,2,2],"codonpos":[3,3,3,3],"pos":[484,441,490,32],"ref":"E","refcodon":["GAA","GAA","GAA","GAA"]},"alfa":{"african":{"ac":0,"af":0.0,"an":2898},"african_american":{"ac":0,"af":0.0,"an":2784},"african_others":{"ac":0,"af":0.0,"an":114},"asian":{"ac":0,"af":0.0,"an":112},"east_asian":{"ac":0,"af":0.0,"an":86},"european":{"ac":0,"af":0.0,"an":9690},"latin_american_1":{"ac":0,"af":0.0,"an":146},"latin_american_2":{"ac":0,"af":0.0,"an":610},"other":{"ac":0,"af":0.0,"an":496},"other_asian":{"ac":0,"af":0.0,"an":26},"south_asian":{"ac":0,"af":0.0,"an":98},"total":{"ac":0,"af":0.0,"an":14050}},"alphamissense":{"pred":["B","B","B","B"],"rankscore":0.17911,"score":[0.0747,0.077,0.0784,0.1018]},"alt":"G","altai_neandertal":["T","T"],"ancestral_allele":"T","appris":"principal1","bayesdel":{"add_af":{"pred":"T","rankscore":0.21053,"score":-0.198279},"no_af":{"pred":"T","rankscore":0.20034,"score":-0.52259}},"bstatistic":{"converted_rankscore":0.59757,"score":682.0},"cadd":{"phred":15.7,"raw_rankscore":0.22621,"raw_score":1.779308},"chagyrskaya_neandertal":["T","T"],"chrom":"12","clinpred":{"pred":"T","rankscore":0.15696,"score":0.133446596936136},"dann":{"rankscore":0.38498,"score":0.9812872953392041},"denisova":["T","T"],"deogen2":{"pred":["T","T"],"rankscore":0.10596,"score":[0.011013,0.011963]},"eigen":{"phred_coding":1.149772,"raw_coding":-0.513661081515351,"raw_coding_rankscore":0.21637},"eigen-pc":{"phred_coding":1.412657,"raw_coding":-0.37772216035456,"raw_coding_rankscore":0.25663},"ensembl":{"geneid":["ENSG00000136044","ENSG00000136044","ENSG00000136044","ENSG00000136044"],"proteinid":["ENSP00000258530","ENSP00000444472","ENSP00000446917","ENSP00000446510"],"transcriptid":["ENST00000258530","ENST00000539978","ENST00000551662","ENST00000553109"]},"esm1b":{"pred":["T","T","T"],"rankscore":0.29517,"score":[-4.334,-4.315,-4.397]},"fathmm":{"converted_rankscore":0.25018,"pred":["T","T","T"],"score":[2.62,1.82,2.4]},"fathmm-mkl":{"coding_group":"AEFBI","coding_pred":"D","coding_rankscore":0.4987,"coding_score":0.89418},"fathmm-xf":{"coding_pred":"N","coding_rankscore":0.33529,"coding_score":0.209293},"fitcons":{"gm12878":{"confidence_value":0,"rankscore":0.59785,"score":0.653731},"h1-hesc":{"confidence_value":0,"rankscore":0.68683,"score":0.702456},"huvec":{"confidence_value":0,"rankscore":0.71501,"score":0.711},"integrated":{"confidence_value":0,"rankscore":0.52595,"score":0.67177}},"gencode_basic":["Y","Y","Y"],"genename":["APPL2","APPL2","APPL2","APPL2"],"genocanyon":{"rankscore":0.2272,"score":0.702671000681119},"gerp":{"91_mammals":{"rankscore":0.32201,"score":1.32}},"gerp++":{"nr":5.8,"rs":0.359,"rs_rankscore":0.15324},"gmvp":{"rankscore":0.14424,"score":0.14501257336759604},"hg18":{"end":104107687,"start":104107687},"hg19":{"end":105583557,"start":105583557},"hg38":{"end":105189779,"start":105189779},"hgvsc":["c.1323A>C","c.1470A>C","c.1452A>C","c.96A>C"],"hgvsp":["p.E441D","p.Glu441Asp","p.Glu490Asp","p.E490D","p.E484D","p.Glu32Asp","p.Glu484Asp"],"list-s2":{"pred":["T","T","T","T"],"rankscore":0.36981,"score":[0.748825,0.739826,0.748825,0.680032]},"lrt":{"converted_rankscore":0.29204,"omega":0.413505,"pred":"N","score":0.012361},"m-cap":{"pred":"T","rankscore":0.09211,"score":0.003912},"metalr":{"pred":"T","rankscore":0.12935,"score":0.0301},"metarnn":{"pred":["T","T","T","T"],"rankscore":0.20205,"score":[0.10852429,0.10852429,0.10852429,0.10852429]},"metasvm":{"pred":"T","rankscore":0.16921,"score":-1.0413},"mpc":{"rankscore":0.10528,"score":0.0931597170186},"mutationassessor":{"pred":"L","rankscore":0.26193,"score":1.04},"mutationtaster":{"aae":["E484D","E441D","E490D"],"converted_rankscore":0.39816,"model":["simple_aae","simple_aae","simple_aae"],"pred":["D","D","D"],"score":[0.97011,0.97011,0.981784]},"mutformer":{"rankscore":0.34494,"score":0.0055164},"mutpred":{"aa_change":"E484D","accession":"Q8NEU8","pred":{"mechanism":"Loss of glycosylation at P483","p_val":0.1749},"rankscore":0.2444,"score":0.286},"mvp":{"rankscore":0.44609,"score":[0.449860987313,0.449860987313,0.449860987313,0.449860987313]},"phactboost":{"rankscore":0.24739,"score":0.0111311022586291},"phastcons":{"100way_vertebrate":{"rankscore":0.28771,"score":0.715},"17way_primate":{"rankscore":0.54974,"score":0.972},"470way_mammalian":{"rankscore":0.29052,"score":0.952}},"phylop":{"100way_vertebrate":{"rankscore":0.09284,"score":-0.215},"17way_primate":{"rankscore":0.62972,"score":0.665},"470way_mammalian":{"rankscore":0.13619,"score":0.023}},"polyphen2":{"hdiv":{"pred":"B","rankscore":0.02946,"score":0.0},"hvar":{"pred":"B","rankscore":0.04355,"score":0.001}},"primateai":{"pred":"T","rankscore":0.33477,"score":0.4612159729},"provean":{"converted_rankscore":0.27259,"pred":["N","N","N","N"],"score":[-0.64,-0.89,-0.64,-1.04]},"ref":"T","reliability_index":10,"revel":{"rankscore":0.12962,"score":[0.047,0.047,0.047,0.047]},"rsid":"rs1362568061","sift":{"converted_rankscore":0.28646,"pred":["T","T","T","T"],"score":[0.202,0.207,0.186,0.114]},"sift4g":{"converted_rankscore":0.12072,"pred":["T","T","T","T"],"score":[0.509,0.519,0.509,0.475]},"siphy_29way":{"logodds_rankscore":0.00776,"logodds_score":0.6525,"pi":{"a":0.2895,"c":0.2682,"g":0.1116,"t":0.3308}},"tsl":[1,2,2,3],"uniprot":[{"acc":"Q8NEU8","entry":"DP13B_HUMAN"},{"acc":"Q8NEU8-2","entry":"DP13B_HUMAN"},{"acc":"Q8NEU8-3","entry":"DP13B_HUMAN"},{"acc":"H0YH86","entry":"H0YH86_HUMAN"}],"varity":{"er":{"rankscore":0.10508,"score":0.057625223},"er_loo":{"rankscore":0.10508,"score":0.057625223},"r":{"rankscore":0.08201,"score":0.047712304},"r_loo":{"rankscore":0.08201,"score":0.047712304}},"vep_canonical":"YES","vest4":{"rankscore":0.02759,"score":[0.049,0.056,0.047]},"vindijia_neandertal":["T","T"]},"dbsnp":{"_license":"http://bit.ly/2AqoLOc","alleles":[{"allele":"T","freq":{"dbgap_popfreq":1.0,"topmed":1.0}},{"allele":"G","freq":{"dbgap_popfreq":0.0,"topmed":0.0}}],"alt":"G","chrom":"12","dbsnp_build":156,"gene":{"geneid":55198,"is_pseudo":false,"name":"adaptor protein, phosphotyrosine interacting with PH domain and leucine zipper 2","rnas":[{"codon_aligned_transcript_change":{"deleted_sequence":"GAA","inserted_sequence":"GAA","position":1629,"seq_id":"NM_001251904.2"},"hgvs":"NM_001251904.2:c.1470=","protein":{"variant":{"spdi":{"deleted_sequence":"E","inserted_sequence":"E","position":489,"seq_id":"NP_001238833.1"}}},"protein_product":{"refseq":"NP_001238833.1"},"refseq":"NM_001251904.2","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"GAA","inserted_sequence":"GAA","position":1525,"seq_id":"NM_001251905.2"},"hgvs":"NM_001251905.2:c.1323=","protein":{"variant":{"spdi":{"deleted_sequence":"E","inserted_sequence":"E","position":440,"seq_id":"NP_001238834.1"}}},"protein_product":{"refseq":"NP_001238834.1"},"refseq":"NM_001251905.2","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"GAA","inserted_sequence":"GAA","position":1611,"seq_id":"NM_018171.5"},"hgvs":"NM_018171.5:c.1452=","protein":{"variant":{"spdi":{"deleted_sequence":"E","inserted_sequence":"E","position":483,"seq_id":"NP_060641.2"}}},"protein_product":{"refseq":"NP_060641.2"},"refseq":"NM_018171.5","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"GAA","inserted_sequence":"GAA","position":1629,"seq_id":"XM_006719472.2"},"hgvs":"XM_006719472.2:c.1470=","protein":{"variant":{"spdi":{"deleted_sequence":"E","inserted_sequence":"E","position":489,"seq_id":"XP_006719535.1"}}},"protein_product":{"refseq":"XP_006719535.1"},"refseq":"XM_006719472.2","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"GAA","inserted_sequence":"GAA","position":4570,"seq_id":"XM_011538530.4"},"hgvs":"XM_011538530.4:c.1431=","protein":{"variant":{"spdi":{"deleted_sequence":"E","inserted_sequence":"E","position":476,"seq_id":"XP_011536832.1"}}},"protein_product":{"refseq":"XP_011536832.1"},"refseq":"XM_011538530.4","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"GAA","inserted_sequence":"GAA","position":2829,"seq_id":"XM_011538531.4"},"hgvs":"XM_011538531.4:c.1341=","protein":{"variant":{"spdi":{"deleted_sequence":"E","inserted_sequence":"E","position":446,"seq_id":"XP_011536833.1"}}},"protein_product":{"refseq":"XP_011536833.1"},"refseq":"XM_011538531.4","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"GAA","inserted_sequence":"GAA","position":1543,"seq_id":"XM_011538532.4"},"hgvs":"XM_011538532.4:c.1341=","protein":{"variant":{"spdi":{"deleted_sequence":"E","inserted_sequence":"E","position":446,"seq_id":"XP_011536834.1"}}},"protein_product":{"refseq":"XP_011536834.1"},"refseq":"XM_011538532.4","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"GAA","inserted_sequence":"GAA","position":7942,"seq_id":"XM_017019551.3"},"hgvs":"XM_017019551.3:c.1413=","protein":{"variant":{"spdi":{"deleted_sequence":"E","inserted_sequence":"E","position":470,"seq_id":"XP_016875040.1"}}},"protein_product":{"refseq":"XP_016875040.1"},"refseq":"XM_017019551.3","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"GAA","inserted_sequence":"GAA","position":1611,"seq_id":"XM_017019554.2"},"hgvs":"XM_017019554.2:c.1452=","protein":{"variant":{"spdi":{"deleted_sequence":"E","inserted_sequence":"E","position":483,"seq_id":"XP_016875043.1"}}},"protein_product":{"refseq":"XP_016875043.1"},"refseq":"XM_017019554.2","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"GAA","inserted_sequence":"GAA","position":1819,"seq_id":"XM_047429062.1"},"hgvs":"XM_047429062.1:c.1341=","protein":{"variant":{"spdi":{"deleted_sequence":"E","inserted_sequence":"E","position":446,"seq_id":"XP_047285018.1"}}},"protein_product":{"refseq":"XP_047285018.1"},"refseq":"XM_047429062.1","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"GAA","inserted_sequence":"GAA","position":4570,"seq_id":"XM_047429063.1"},"hgvs":"XM_047429063.1:c.1431=","protein":{"variant":{"spdi":{"deleted_sequence":"E","inserted_sequence":"E","position":476,"seq_id":"XP_047285019.1"}}},"protein_product":{"refseq":"XP_047285019.1"},"refseq":"XM_047429063.1","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"GAA","inserted_sequence":"GAA","position":4552,"seq_id":"XM_047429064.1"},"hgvs":"XM_047429064.1:c.1413=","protein":{"variant":{"spdi":{"deleted_sequence":"E","inserted_sequence":"E","position":470,"seq_id":"XP_047285020.1"}}},"protein_product":{"refseq":"XP_047285020.1"},"refseq":"XM_047429064.1","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"GAA","inserted_sequence":"GAA","position":1525,"seq_id":"XM_047429065.1"},"hgvs":"XM_047429065.1:c.1323=","protein":{"variant":{"spdi":{"deleted_sequence":"E","inserted_sequence":"E","position":440,"seq_id":"XP_047285021.1"}}},"protein_product":{"refseq":"XP_047285021.1"},"refseq":"XM_047429065.1","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"protein_product":{"refseq":"XP_047285022.1"},"refseq":"XM_047429066.1","so":[{"accession":"SO:0002152","name":"genic_downstream_transcript_variant"}]}],"strand":"-","symbol":"APPL2"},"hg38":{"end":105189779,"start":105189779},"ref":"T","rsid":"rs1362568061","vartype":"snv"},"hg38":{"end":105189779,"start":105189779},"observed":true,"snpeff":{"_license":"http://bit.ly/2suyRKt","ann":[{"cdna":{"length":"3248","position":"1688"},"cds":{"length":"2013","position":"1470"},"effect":"missense_variant","feature_id":"NM_001251904.1","feature_type":"transcript","gene_id":"APPL2","genename":"APPL2","hgvs_c":"c.1470A>C","hgvs_p":"p.Glu490Asp","protein":{"length":"670","position":"490"},"putative_impact":"MODERATE","rank":"16","total":"21","transcript_biotype":"protein_coding"},{"cdna":{"length":"3273","position":"1713"},"cds":{"length":"1866","position":"1323"},"effect":"missense_variant","feature_id":"NM_001251905.1","feature_type":"transcript","gene_id":"APPL2","genename":"APPL2","hgvs_c":"c.1323A>C","hgvs_p":"p.Glu441Asp","protein":{"length":"621","position":"441"},"putative_impact":"MODERATE","rank":"16","total":"21","transcript_biotype":"protein_coding"},{"cdna":{"length":"3230","position":"1670"},"cds":{"length":"1995","position":"1452"},"effect":"missense_variant","feature_id":"NM_018171.3","feature_type":"transcript","gene_id":"APPL2","genename":"APPL2","hgvs_c":"c.1452A>C","hgvs_p":"p.Glu484Asp","protein":{"length":"664","position":"484"},"putative_impact":"MODERATE","rank":"16","total":"21","transcript_biotype":"protein_coding"}]},"vcf":{"alt":"G","position":"105189779","ref":"T"}}