LMTK1 — 314 ClinVar variants

All ClinVar germline LMTK1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 273 flagged for review →

31 Likely benign · 283 Uncertain significance

Full LMTK1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 273

Variants where the independent computational evidence doesn't line up with the clinical picture — a QC signal for a second look, not a reclassification.

Predictors lean, ClinVar uncertain 249

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification. · showing the 150 best-reviewed of 249

Predictors split 24

The independent predictors disagree with each other — read with care.

All LMTK1 variants

Likely benign 31

p.Ala1191= Single submitter
p.Ala151Thr Single submitter
p.Ala600Val Single submitter
p.Ala637Pro Single submitter
p.Arg1019Gln Single submitter
p.Arg133His Single submitter
p.Arg675His Single submitter
p.Arg793Cys Single submitter
p.Arg978Gln Single submitter
p.Asp303= Single submitter
p.Gly1053Arg Single submitter
p.Gly744Ser Single submitter
p.Gly846Ser Single submitter
p.Pro1081Leu Single submitter
p.Pro1127Leu Single submitter
p.Pro721Gln Single submitter
p.Pro776Leu Single submitter
p.Pro795Ser Single submitter
p.Pro817= Single submitter
p.Ser1371Cys Single submitter
p.Ser252= Single submitter
p.Ser307Gly Single submitter
p.Thr499Ala Single submitter
p.Thr557Ile Single submitter
p.Thr84Ala Single submitter
p.Val120Leu Single submitter
p.Val311= Single submitter
p.Val439Ala Single submitter
p.Val667Ala Single submitter
p.Val799Ile Single submitter
p.Val835Ala Single submitter

Uncertain significance 283

p.Ala1020Asp Single submitter ⚠
p.Ala1153Ser Single submitter ⚠
p.Ala1191Val Single submitter ⚠
p.Ala1204Val Single submitter ⚠
p.Ala1367Asp Single submitter ⚠
p.Ala1374Ser Single submitter ⚠
p.Ala193Thr Single submitter ⚠
p.Ala21Thr Single submitter ⚠
p.Ala21Val Single submitter ⚠
p.Ala220Val Single submitter ⚠
p.Ala33Thr Single submitter ⚠
p.Ala348Glu Single submitter
p.Ala348Val Single submitter ⚠
p.Ala442Val Single submitter ⚠
p.Ala460Gly Single submitter ⚠
p.Ala487Val Single submitter ⚠
p.Ala492Val Single submitter ⚠
p.Ala507Asp Single submitter ⚠
p.Ala507Thr Single submitter ⚠
p.Ala521Gly Single submitter ⚠
p.Ala521Ser Single submitter
p.Ala538Val Single submitter ⚠
p.Ala540Ser Single submitter ⚠
p.Ala540Val Single submitter ⚠
p.Ala548Thr Single submitter ⚠
p.Ala558Val Single submitter ⚠
p.Ala569Thr Single submitter ⚠
p.Ala614Val Single submitter ⚠
p.Ala624Val Single submitter ⚠
p.Ala632Val Single submitter ⚠
p.Ala653Thr Single submitter ⚠
p.Ala669Val Single submitter ⚠
p.Ala672Asp Single submitter ⚠
p.Ala673Gly Single submitter ⚠
p.Ala837Val Single submitter ⚠
p.Ala855Thr Single submitter ⚠
p.Ala864Pro Single submitter ⚠
p.Ala881Ser Single submitter ⚠
p.Ala912Val Single submitter ⚠
p.Ala934Val Single submitter ⚠
p.Ala954Val Single submitter ⚠
p.Ala964Thr Single submitter ⚠
p.Ala964Val Single submitter ⚠
p.Ala967Val Single submitter ⚠
p.Arg110Cys Single submitter ⚠
p.Arg1132Gln Single submitter ⚠
p.Arg1205His Single submitter ⚠
p.Arg1227His Single submitter ⚠
p.Arg1250Gln Single submitter ⚠
p.Arg1279Trp Single submitter ⚠
p.Arg218Trp Single submitter ⚠
p.Arg246Cys Single submitter ⚠
p.Arg246His Single submitter ⚠
p.Arg370Cys Single submitter ⚠
p.Arg370His Single submitter ⚠
p.Arg415Gly Single submitter ⚠
p.Arg473Gln Single submitter ⚠
p.Arg485Cys Single submitter ⚠
p.Arg501Cys Single submitter ⚠
p.Arg608His Single submitter ⚠
p.Arg670Leu Single submitter ⚠
p.Arg679Leu Single submitter ⚠
p.Arg691Cys Single submitter ⚠
p.Arg691His Single submitter ⚠
p.Arg716Trp Single submitter ⚠
p.Arg793His Single submitter ⚠
p.Arg933Gln Single submitter ⚠
p.Arg978Gly Single submitter ⚠
p.Arg978Trp Single submitter ⚠
p.Arg993Gly Single submitter ⚠
p.Asn145Asp Single submitter ⚠
p.Asn845Ser Single submitter ⚠
p.Asp1172Glu Single submitter ⚠
p.Asp119Gly Single submitter ⚠
p.Asp1244Glu Single submitter ⚠
p.Asp1318Asn Single submitter ⚠
p.Asp1356Gly Single submitter ⚠
p.Asp1356Tyr Single submitter ⚠
p.Asp226Asn Single submitter ⚠
p.Asp456Asn Single submitter ⚠
p.Asp562Asn Single submitter ⚠
p.Asp562Tyr Single submitter ⚠
p.Asp563Asn Single submitter ⚠
p.Asp563Glu Single submitter ⚠
p.Asp565His Single submitter ⚠
p.Asp592Asn Single submitter ⚠
p.Asp626Asn Single submitter ⚠
p.Asp697Asn Single submitter ⚠
p.Asp76Asn Single submitter ⚠
p.Asp818Asn Single submitter ⚠
p.Asp873Asn Single submitter ⚠
p.Asp901Asn Single submitter ⚠
p.Cys635Arg Single submitter ⚠
p.Cys759Trp Single submitter ⚠
p.Gln1084Pro Single submitter ⚠
p.Gln1099His Single submitter ⚠
p.Gln1282His Single submitter ⚠
p.Gln152Arg Single submitter ⚠
p.Gln354Arg Single submitter ⚠
p.Gln503Pro Single submitter ⚠
p.Gln674Arg Single submitter ⚠
p.Gln737Pro Single submitter ⚠
p.Glu1004Lys Single submitter ⚠
p.Glu1054Lys Single submitter ⚠
p.Glu1082Ala Single submitter ⚠
p.Glu1116Val Single submitter ⚠
p.Glu1170Lys Single submitter ⚠
p.Glu1189Asp Single submitter ⚠
p.Glu1189Lys Single submitter ⚠
p.Glu1294Asp Single submitter ⚠
p.Glu1370Gly Single submitter ⚠
p.Glu383Lys Single submitter
p.Glu407Gln Single submitter ⚠
p.Glu488Asp Single submitter ⚠
p.Glu488Gln Single submitter ⚠
p.Glu504Ala Single submitter ⚠
p.Glu529Lys Single submitter ⚠
p.Glu536Gly Single submitter ⚠
p.Glu640Gln Single submitter ⚠
p.Glu66Lys Single submitter ⚠
p.Glu720Lys Single submitter ⚠
p.Glu72Lys Single submitter ⚠
p.Glu834Lys Single submitter ⚠
p.Glu852Lys Single submitter ⚠
p.Glu854Asp Single submitter ⚠
p.Glu948Lys Single submitter ⚠
p.Glu976Lys Single submitter ⚠
p.Glu988Asp Single submitter ⚠
p.Gly1016Asp Single submitter ⚠
p.Gly1017Arg Single submitter ⚠
p.Gly1022Arg Single submitter ⚠
p.Gly1031Glu Single submitter ⚠
p.Gly1135Asp Single submitter ⚠
p.Gly1149Ser Single submitter ⚠
p.Gly1289Ser Single submitter ⚠
p.Gly132Ser Single submitter ⚠
p.Gly420Asp Single submitter ⚠
p.Gly420Ser Single submitter ⚠
p.Gly429Asp Single submitter ⚠
p.Gly429Ser Single submitter ⚠
p.Gly462Ser Single submitter ⚠
p.Gly486Ser Single submitter ⚠
p.Gly497Ala Single submitter ⚠
p.Gly510Ser Single submitter ⚠
p.Gly514Ala Single submitter ⚠
p.Gly549Ser Single submitter ⚠
p.Gly566Ser Single submitter ⚠
p.Gly579Val Single submitter ⚠
p.Gly59Ser Single submitter ⚠
p.Gly61Arg Single submitter ⚠
p.Gly622Glu Single submitter ⚠
p.Gly630Ser Single submitter ⚠
p.Gly676Val Single submitter ⚠
p.Gly707Ser Single submitter ⚠
p.Gly725Glu Single submitter ⚠
p.Gly772Arg Single submitter ⚠
p.Gly791Arg Single submitter ⚠
p.Gly832Asp Single submitter ⚠
p.Gly878Ser Single submitter ⚠
p.Gly89Arg Single submitter
p.Gly916Asp Single submitter ⚠
p.Gly957Ala Single submitter ⚠
p.Gly970Arg Single submitter ⚠
p.Gly972Val Single submitter ⚠
p.His341Leu Single submitter ⚠
p.His775Tyr Single submitter ⚠
p.Ile1349Val Single submitter ⚠
p.Ile46Phe Single submitter ⚠
p.Leu1062Val Single submitter ⚠
p.Leu128Val Single submitter ⚠
p.Leu395Met Single submitter ⚠
p.Leu745Ile Single submitter ⚠
p.Leu951Phe Single submitter ⚠
p.Leu97Phe Single submitter ⚠
p.Leu983Phe Single submitter ⚠
p.Lys401Gln Single submitter ⚠
p.Lys57Gln Single submitter ⚠
p.Met223Val Single submitter ⚠
p.Phe1101Leu Single submitter ⚠
p.Phe1266Tyr Single submitter ⚠
p.Phe1313Ser Single submitter ⚠
p.Phe1334Leu Single submitter ⚠
p.Phe638Ser Single submitter ⚠
p.Phe638Val Single submitter ⚠
p.Phe871Ser Single submitter ⚠
p.Pro1021Ser Single submitter ⚠
p.Pro1033Leu Single submitter ⚠
p.Pro1081Gln Single submitter ⚠
p.Pro1081Ser Single submitter ⚠
p.Pro1086Leu Single submitter ⚠
p.Pro108Ser Single submitter ⚠
p.Pro1136Gln Single submitter ⚠
p.Pro1158Leu Single submitter ⚠
p.Pro1183Ala Single submitter ⚠
p.Pro1183Thr Single submitter ⚠
p.Pro1195Ala Single submitter
p.Pro1214Ser Single submitter ⚠
p.Pro1305Leu Single submitter ⚠
p.Pro1341Arg Single submitter ⚠
p.Pro22Leu Single submitter ⚠
p.Pro29Thr Single submitter ⚠
p.Pro339His Single submitter ⚠
p.Pro419Ser Single submitter ⚠
p.Pro426Arg Single submitter ⚠
p.Pro508Ser Single submitter ⚠
p.Pro517Ala Single submitter
p.Pro517Leu Single submitter ⚠
p.Pro554Leu Single submitter ⚠
p.Pro595Arg Single submitter ⚠
p.Pro642Leu Single submitter ⚠
p.Pro655Leu Single submitter ⚠
p.Pro655Ser Single submitter ⚠
p.Pro721Leu Single submitter ⚠
p.Pro739Leu Single submitter ⚠
p.Pro743Ser Single submitter ⚠
p.Pro758Ser Single submitter ⚠
p.Pro797Leu Single submitter ⚠
p.Pro800Leu Single submitter ⚠
p.Pro808Leu Single submitter ⚠
p.Pro820Ser Single submitter ⚠
p.Pro829Ser Single submitter ⚠
p.Pro82Arg Single submitter ⚠
p.Pro82Leu Single submitter ⚠
p.Pro909Leu Single submitter ⚠
p.Pro922Leu Single submitter ⚠
p.Ser1029Thr Single submitter ⚠
p.Ser1165Gly Single submitter ⚠
p.Ser1168Asn Single submitter ⚠
p.Ser1184Ile Single submitter ⚠
p.Ser1187Gly Single submitter ⚠
p.Ser1335Leu Single submitter
p.Ser183Arg Single submitter
p.Ser183Asn Single submitter ⚠
p.Ser322Pro Single submitter ⚠
p.Ser3Trp Single submitter ⚠
p.Ser446Phe Single submitter ⚠
p.Ser553Gly Single submitter ⚠
p.Ser567Asn Single submitter ⚠
p.Ser571Leu Single submitter ⚠
p.Ser598Arg Single submitter ⚠
p.Ser607Leu Single submitter ⚠
p.Ser611Leu Single submitter ⚠
p.Ser613Trp Single submitter ⚠
p.Ser650Asn Single submitter ⚠
p.Ser680Cys Single submitter ⚠
p.Ser710Arg Single submitter ⚠
p.Ser811Leu Single submitter ⚠
p.Ser815Arg Single submitter ⚠
p.Ser902Cys Single submitter ⚠
p.Ser968Leu Single submitter ⚠
p.Thr1008Ile Single submitter ⚠
p.Thr1030Ser Single submitter ⚠
p.Thr118Ala Single submitter ⚠
p.Thr1220Ser Single submitter ⚠
p.Thr1330Ala Single submitter ⚠
p.Thr1338Met Single submitter ⚠
p.Thr1344Met Single submitter ⚠
p.Thr196Met Single submitter ⚠
p.Thr262Met Single submitter ⚠
p.Thr335Lys Single submitter ⚠
p.Thr335Met Single submitter ⚠
p.Thr350Met Single submitter ⚠
p.Thr557Pro Single submitter ⚠
p.Thr714Asn Single submitter ⚠
p.Thr828Met Single submitter ⚠
p.Thr84Lys Single submitter ⚠
p.Thr863Met Single submitter ⚠
p.Thr98Met Single submitter ⚠
p.Val1043Ile Single submitter ⚠
p.Val1055Met Single submitter ⚠
p.Val112Ala Single submitter ⚠
p.Val1240Ile Single submitter ⚠
p.Val1339Leu Single submitter ⚠
p.Val164Met Single submitter ⚠
p.Val267Met Single submitter ⚠
p.Val285Ala Single submitter
p.Val312Met Single submitter ⚠
p.Val320Leu Single submitter
p.Val325Met Single submitter ⚠
p.Val631Ala Single submitter ⚠
p.Val631Met Single submitter ⚠
p.Val682Leu Single submitter ⚠
p.Val886Ala Single submitter ⚠