LMTK3 — 220 ClinVar variants

All ClinVar germline LMTK3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 183 flagged for review →

5 Benign · 9 Likely benign · 206 Uncertain significance

Full LMTK3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 183

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 162

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 162

Predictors split 21

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

All LMTK3 variants

Benign 5

p.Leu314= Multiple submitters
p.Leu354= Multiple submitters
c.4366+8A>C Single submitter
c.646-9C>G Single submitter
p.Thr203= Single submitter

Likely benign 9

p.Pro22= Multiple submitters
c.794+9G>C Single submitter
p.Arg1227Lys Single submitter
p.Glu138= Single submitter
p.Pro495= Single submitter
p.Pro753= Single submitter
p.Ser600= Single submitter
p.Thr1033Met Single submitter
p.Glu1287del No assertion criteria LMTK3-related disorder

Uncertain significance 206

c.-35G>T Single submitter
c.-44G>A Single submitter
c.-45C>T Single submitter
c.-6G>T Single submitter
p.Ala1040Asp Single submitter ⚠
p.Ala1055Thr Single submitter ⚠
p.Ala1055Val Single submitter ⚠
p.Ala1060Thr Single submitter ⚠
p.Ala1071Val Single submitter ⚠
p.Ala1135Ser Single submitter ⚠
p.Ala1168Val Single submitter ⚠
p.Ala1260Ser Single submitter ⚠
p.Ala1261Pro Single submitter ⚠
p.Ala1265Ser Single submitter ⚠
p.Ala1268Gly Single submitter ⚠
p.Ala1270Glu Single submitter ⚠
p.Ala1292Val Single submitter ⚠
p.Ala1293Ser Single submitter ⚠
p.Ala1297Thr Single submitter ⚠
p.Ala1320Glu Single submitter ⚠
p.Ala1320Thr Single submitter ⚠
p.Ala1323Thr Single submitter ⚠
p.Ala1375Thr Single submitter ⚠
p.Ala1449Val Single submitter ⚠
p.Ala288Thr Single submitter
p.Ala29Asp Single submitter ⚠
p.Ala381Pro Single submitter ⚠
p.Ala496Val Single submitter ⚠
p.Ala529Val Single submitter ⚠
p.Ala566Pro Single submitter ⚠
p.Ala585Val Single submitter ⚠
p.Ala677Val Single submitter ⚠
p.Ala688Ser Single submitter ⚠
p.Ala690fs Single submitter
p.Ala723Gly Single submitter ⚠
p.Ala726fs Single submitter
p.Ala728Pro Single submitter ⚠
p.Ala728Val Single submitter ⚠
p.Ala752Pro Single submitter ⚠
p.Ala762Val Single submitter ⚠
p.Ala775Thr Single submitter ⚠
p.Ala882Val Single submitter ⚠
p.Arg1010Lys Single submitter ⚠
p.Arg1017Gly Single submitter ⚠
p.Arg1054Thr Single submitter ⚠
p.Arg1202Lys Single submitter ⚠
p.Arg1453Gln Single submitter ⚠
p.Arg220His Single submitter
p.Arg32Gln Single submitter ⚠
p.Arg443Pro Single submitter ⚠
p.Arg490Gly Single submitter ⚠
p.Arg64fs Single submitter
p.Arg685Trp Single submitter ⚠
p.Arg714Gln Single submitter ⚠
p.Arg747Gln Single submitter ⚠
p.Arg747Trp Single submitter ⚠
p.Arg820Trp Single submitter ⚠
p.Arg848Leu Single submitter ⚠
p.Arg867Pro Single submitter ⚠
p.Arg883Trp Single submitter ⚠
p.Arg969Lys Single submitter ⚠
p.Asn1460Ser Single submitter ⚠
p.Asp1196Glu Single submitter ⚠
p.Asp1282Asn Single submitter ⚠
p.Asp1418His Single submitter ⚠
p.Asp217Ala Single submitter ⚠
p.Asp428Glu Single submitter ⚠
p.Asp455fs Single submitter
p.Asp558Glu Single submitter ⚠
p.Asp707Asn Single submitter ⚠
p.Asp829Ala Single submitter ⚠
p.Gln189Ter Single submitter
p.Glu1201Val Single submitter ⚠
p.Glu1264Asp Single submitter ⚠
p.Glu1281Lys Single submitter ⚠
p.Glu1287Asp Single submitter ⚠
p.Glu1289Lys Single submitter ⚠
p.Glu1414Gln Single submitter
p.Glu1441Asp Single submitter ⚠
p.Glu675Lys Single submitter ⚠
p.Glu78Gly Single submitter
p.Glu826Ala Single submitter ⚠
p.Glu975Gly Single submitter ⚠
p.Gly1044Arg Single submitter ⚠
p.Gly1096Arg Single submitter ⚠
p.Gly1096Trp Single submitter ⚠
p.Gly1113Ser Single submitter ⚠
p.Gly1118Asp Single submitter ⚠
p.Gly1124Ser Single submitter ⚠
p.Gly1125Asp Single submitter ⚠
p.Gly1186Ser Single submitter ⚠
p.Gly1195Arg Single submitter ⚠
p.Gly1219Glu Single submitter ⚠
p.Gly1278Glu Single submitter ⚠
p.Gly1408Asp Single submitter ⚠
p.Gly492Arg Single submitter ⚠
p.Gly492Trp Single submitter
p.Gly493Glu Single submitter ⚠
p.Gly609Ser Single submitter ⚠
p.Gly630Glu Single submitter ⚠
p.Gly633Glu Single submitter ⚠
p.Gly647Ser Single submitter ⚠
p.Gly746Arg Single submitter ⚠
p.Gly780Cys Single submitter ⚠
p.Gly810Ala Single submitter ⚠
p.Gly811Trp Single submitter
p.Gly913Arg Single submitter ⚠
p.Gly947Arg Single submitter ⚠
p.Gly985Arg Single submitter ⚠
p.His695Gln Single submitter ⚠
p.Leu1150Pro Single submitter ⚠
p.Leu1212Trp Single submitter ⚠
p.Leu133Val Single submitter
p.Leu1440Pro Single submitter ⚠
p.Leu173Val Single submitter ⚠
p.Leu222Val Single submitter ⚠
p.Leu454fs Single submitter
p.Leu542Trp Single submitter ⚠
p.Leu588Ile Single submitter ⚠
p.Leu588Val Single submitter ⚠
p.Lys1203Arg Single submitter ⚠
p.Met864Ile Single submitter ⚠
p.Phe1243Leu Single submitter ⚠
p.Phe1431Cys Single submitter ⚠
p.Phe732Ser Single submitter ⚠
p.Pro1048Gln Single submitter ⚠
p.Pro1077Gln Single submitter ⚠
p.Pro1146Gln Single submitter ⚠
p.Pro1149Leu Single submitter ⚠
p.Pro1152Leu Single submitter ⚠
p.Pro1205Ala Single submitter ⚠
p.Pro1248Leu Single submitter ⚠
p.Pro1294Ala Single submitter ⚠
p.Pro1312Leu Single submitter ⚠
p.Pro1376Arg Single submitter ⚠
p.Pro1376Ser Single submitter ⚠
p.Pro1383Gln Single submitter ⚠
p.Pro1383Leu Single submitter ⚠
p.Pro1424Ala Single submitter ⚠
p.Pro1427Leu Single submitter ⚠
p.Pro1450Thr Single submitter ⚠
p.Pro172Thr Single submitter ⚠
p.Pro25Ser Single submitter ⚠
p.Pro34Ser Single submitter ⚠
p.Pro38Ala Single submitter
p.Pro420Arg Single submitter ⚠
p.Pro421Leu Single submitter ⚠
p.Pro434Ser Single submitter ⚠
p.Pro450Leu Single submitter ⚠
p.Pro499Ala Single submitter ⚠
p.Pro559Arg Single submitter ⚠
p.Pro559Ser Single submitter ⚠
p.Pro567Arg Single submitter ⚠
p.Pro567Thr Single submitter ⚠
p.Pro596Thr Single submitter ⚠
p.Pro612Leu Single submitter ⚠
p.Pro661Thr Single submitter ⚠
p.Pro670Arg Single submitter ⚠
p.Pro704His Single submitter ⚠
p.Pro724Ala Single submitter ⚠
p.Pro724Arg Single submitter ⚠
p.Pro724His Single submitter ⚠
p.Pro730Ala Single submitter ⚠
p.Pro749Ser Single submitter ⚠
p.Pro750Leu Single submitter ⚠
p.Pro754Arg Single submitter ⚠
p.Pro754Leu Single submitter ⚠
p.Pro755Ala Single submitter ⚠
p.Pro755Arg Single submitter ⚠
p.Pro755His Single submitter ⚠
p.Pro755Ser Single submitter ⚠
p.Pro756Ser Single submitter ⚠
p.Pro808Gln Single submitter ⚠
p.Pro825His Single submitter
p.Pro845Leu Single submitter ⚠
p.Pro901Leu Single submitter ⚠
p.Ser1063fs Single submitter
p.Ser1404Ile Single submitter ⚠
p.Ser187Arg Single submitter ⚠
p.Ser265Arg Single submitter ⚠
p.Ser501Leu Single submitter ⚠
p.Ser656Asn Single submitter ⚠
p.Ser709Leu Single submitter ⚠
p.Ser727Leu Single submitter ⚠
p.Ser858Asn Single submitter ⚠
p.Ser999Arg Single submitter ⚠
p.Thr1015Met Single submitter ⚠
p.Thr1021Asn Single submitter ⚠
p.Thr1021Ile Single submitter ⚠
p.Thr1095Ser Single submitter ⚠
p.Thr1141Arg Single submitter ⚠
p.Thr1189Met Single submitter ⚠
p.Thr1385Ala Single submitter ⚠
p.Thr1385Met Single submitter ⚠
p.Thr799Asn Single submitter
p.Thr859Met Single submitter ⚠
p.Trp692Arg Single submitter ⚠
p.Val1313Ala Single submitter
p.Val1436Ile Single submitter ⚠
p.Val534Met Single submitter
p.Val580Met Single submitter ⚠
p.Val628Ile Single submitter ⚠
p.Val689Ile Single submitter ⚠
p.Val689Leu Single submitter ⚠
p.Val909Asp Single submitter ⚠
p.Val988Leu Single submitter ⚠