LMTK2 — 229 ClinVar variants

All ClinVar germline LMTK2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 200 flagged for review →

6 Benign · 14 Likely benign · 209 Uncertain significance

Full LMTK2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 200

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 172

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 172

Predictors split 28

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

All LMTK2 variants

Benign 6

p.Ala1383= Multiple submitters
p.Pro1113= Multiple submitters
p.Ser910Ile Multiple submitters
p.Tyr1032= Multiple submitters
p.Ala1008= Single submitter
p.Ala1104= Single submitter

Likely benign 14

p.Arg454= Single submitter
p.Arg939Gln Single submitter
p.Asp1244Glu Single submitter
p.Asp1360Asn Single submitter
p.Glu898Lys Single submitter
p.Gly1212Ser Single submitter
p.Gly1390Ser Single submitter
p.Gly497Ala Single submitter
p.Gly526Ser Single submitter
p.Ile1491Met Single submitter
p.Pro1180Leu Single submitter
p.Pro1259= Single submitter
p.Thr1239Ala Single submitter
p.Thr1458Ala Single submitter

Uncertain significance 209

p.Ala1155Val Single submitter ⚠
p.Ala1183Val Single submitter ⚠
p.Ala1242Val Single submitter ⚠
p.Ala1284Thr Single submitter ⚠
p.Ala1284Val Single submitter ⚠
p.Ala1300Thr Single submitter ⚠
p.Ala1338Val Single submitter ⚠
p.Ala1383Val Single submitter ⚠
p.Ala207Val Single submitter ⚠
p.Ala21Val Single submitter ⚠
p.Ala224Val Single submitter ⚠
p.Ala255Thr Single submitter ⚠
p.Ala399Val Single submitter ⚠
p.Ala428Thr Single submitter ⚠
p.Ala480Thr Single submitter ⚠
p.Ala570Val Single submitter ⚠
p.Ala962Thr Single submitter ⚠
p.Arg1083Lys Single submitter ⚠
p.Arg1101Pro Single submitter ⚠
p.Arg1221Cys Single submitter ⚠
p.Arg1299Trp Single submitter ⚠
p.Arg1331Gln Single submitter ⚠
p.Arg1456Gln Single submitter ⚠
p.Arg1470Gln Single submitter ⚠
p.Arg227Leu Single submitter ⚠
p.Arg234Pro Single submitter ⚠
p.Arg244Lys Single submitter ⚠
p.Arg411Gln Single submitter
p.Arg454Trp Single submitter ⚠
p.Arg489Cys Single submitter ⚠
p.Arg691Cys Single submitter ⚠
p.Arg828Gln Single submitter ⚠
p.Arg895Gln Single submitter ⚠
p.Arg8Trp Single submitter ⚠
p.Arg911Gly Single submitter ⚠
p.Asn1240His Single submitter ⚠
p.Asn175Asp Single submitter ⚠
p.Asn278Ser Single submitter ⚠
p.Asn345His Single submitter ⚠
p.Asn345Lys Single submitter ⚠
p.Asn345Ser Single submitter ⚠
p.Asn434Thr Single submitter ⚠
p.Asn658Asp Single submitter ⚠
p.Asn722Asp Single submitter ⚠
p.Asn730Lys Single submitter ⚠
p.Asn927Ser Single submitter ⚠
p.Asp1080Asn Single submitter ⚠
p.Asp1110Glu Single submitter ⚠
p.Asp1213Asn Single submitter ⚠
p.Asp1343Asn Single submitter ⚠
p.Asp1343Glu Single submitter ⚠
p.Asp1360Gly Single submitter ⚠
p.Asp1360Val Single submitter ⚠
p.Asp1426Glu Single submitter ⚠
p.Asp1426Val Single submitter ⚠
p.Asp357Gly Single submitter ⚠
p.Asp484Asn Single submitter ⚠
p.Asp528Tyr Single submitter ⚠
p.Asp541Ala Single submitter ⚠
p.Asp603Gly Single submitter ⚠
p.Asp653Asn Single submitter ⚠
p.Asp663Asn Single submitter ⚠
p.Asp703Gly Single submitter ⚠
p.Asp792Asn Single submitter ⚠
p.Cys204Arg Single submitter ⚠
p.Gln1144His Single submitter ⚠
p.Gln122Arg Single submitter ⚠
p.Gln856Arg Single submitter ⚠
p.Gln884Ter Single submitter
p.Glu1143Lys Single submitter ⚠
p.Glu1197Lys Single submitter ⚠
p.Glu1216Lys Single submitter ⚠
p.Glu1262Lys Single submitter ⚠
p.Glu1315Gln Single submitter ⚠
p.Glu1347Lys Single submitter ⚠
p.Glu1407Asp Single submitter
p.Glu1407Lys Single submitter ⚠
p.Glu155Lys Single submitter ⚠
p.Glu215Gln Single submitter ⚠
p.Glu248Gln Single submitter ⚠
p.Glu36Gln Single submitter ⚠
p.Glu488Lys Single submitter ⚠
p.Glu629Lys Single submitter ⚠
p.Glu851Lys Single submitter ⚠
p.Glu920Asp Single submitter ⚠
p.Gly1063Ser Single submitter ⚠
p.Gly1063Val Single submitter ⚠
p.Gly127Arg Single submitter ⚠
p.Gly1281Arg Single submitter ⚠
p.Gly1385Ser Single submitter ⚠
p.Gly1390Asp Single submitter ⚠
p.Gly1396Val Single submitter ⚠
p.Gly520Arg Single submitter ⚠
p.Gly627Val Single submitter ⚠
p.Gly659Arg Single submitter ⚠
p.Gly683Ser Single submitter ⚠
p.His1169Arg Single submitter ⚠
p.His1250Asp Single submitter ⚠
p.His1304Arg Single submitter ⚠
p.His404Arg Single submitter ⚠
p.His741Tyr Single submitter ⚠
p.Ile1261Thr Single submitter ⚠
p.Ile166Val Single submitter ⚠
p.Ile681Lys Single submitter ⚠
p.Ile848Thr Single submitter ⚠
p.Leu1010Val Single submitter ⚠
p.Leu1067Pro Single submitter ⚠
p.Leu1141Phe Single submitter ⚠
p.Leu13Val Single submitter ⚠
p.Leu1437Phe Single submitter ⚠
p.Leu1437Pro Single submitter ⚠
p.Leu198Val Single submitter ⚠
p.Leu277Phe Single submitter
p.Leu392Val Single submitter ⚠
p.Leu699Phe Single submitter ⚠
p.Leu834Phe Single submitter ⚠
p.Lys1020Asn Single submitter ⚠
p.Lys1245Glu Single submitter ⚠
p.Lys1374Glu Single submitter ⚠
p.Lys168Thr Single submitter ⚠
p.Lys258Arg Single submitter ⚠
p.Lys302Glu Single submitter ⚠
p.Lys641Glu Single submitter ⚠
p.Lys733Asn Single submitter ⚠
p.Lys942Asn Single submitter ⚠
p.Lys956Arg Single submitter ⚠
p.Met233Leu Single submitter ⚠
p.Met655Lys Single submitter ⚠
p.Met797Ile Single submitter ⚠
p.Phe121Leu Single submitter ⚠
p.Pro1024Ser Single submitter ⚠
p.Pro1069Leu Single submitter ⚠
p.Pro111Thr Single submitter
p.Pro1121Leu Single submitter ⚠
p.Pro1125Ser Single submitter ⚠
p.Pro1142Leu Single submitter ⚠
p.Pro1201Ser Single submitter ⚠
p.Pro1317Ser Single submitter ⚠
p.Pro1342His Single submitter ⚠
p.Pro1372Ala Single submitter ⚠
p.Pro1398Ser Single submitter ⚠
p.Pro1454Leu Single submitter ⚠
p.Pro1463Leu Single submitter ⚠
p.Pro534Leu Single submitter
p.Pro538Ala Single submitter ⚠
p.Pro569Ser Single submitter ⚠
p.Pro816Leu Single submitter ⚠
p.Pro826Leu Single submitter ⚠
p.Pro831Ala Single submitter ⚠
p.Pro850Ala Single submitter ⚠
p.Pro91Arg Single submitter ⚠
p.Ser1076Leu Single submitter ⚠
p.Ser1199Cys Single submitter ⚠
p.Ser119Leu Single submitter ⚠
p.Ser1203Arg Single submitter ⚠
p.Ser1310Trp Single submitter ⚠
p.Ser1474Cys Single submitter ⚠
p.Ser1482Pro Single submitter ⚠
p.Ser330Gly Single submitter ⚠
p.Ser435Gly Single submitter ⚠
p.Ser490Ile Single submitter ⚠
p.Ser513Leu Single submitter ⚠
p.Ser559Asn Single submitter ⚠
p.Ser642Leu Single submitter ⚠
p.Ser647Gly Single submitter ⚠
p.Ser696Asn Single submitter ⚠
p.Ser810Cys Single submitter ⚠
p.Ser871Leu Single submitter ⚠
p.Ser878Arg Single submitter ⚠
p.Ser886Phe Single submitter ⚠
p.Ser901Pro Single submitter ⚠
p.Ser917Gly Single submitter ⚠
p.Thr1059Met Single submitter ⚠
p.Thr1091Met Single submitter ⚠
p.Thr1179Met Single submitter ⚠
p.Thr1217Arg Single submitter ⚠
p.Thr1228Met Single submitter ⚠
p.Thr1232Met Single submitter ⚠
p.Thr1363Ala Single submitter ⚠
p.Thr1410Ile Single submitter ⚠
p.Thr1432Arg Single submitter ⚠
p.Thr1458Met Single submitter ⚠
p.Thr582Ser Single submitter ⚠
p.Thr761Met Single submitter ⚠
p.Thr843Ala Single submitter ⚠
p.Thr872Ala Single submitter ⚠
p.Thr893Ile Single submitter ⚠
p.Thr973Asn Single submitter ⚠
p.Tyr1032Ter Single submitter
p.Tyr1100His Single submitter ⚠
p.Tyr139His Single submitter ⚠
p.Tyr329Cys Single submitter ⚠
p.Tyr551Cys Single submitter ⚠
p.Val1005Ile Single submitter ⚠
p.Val110Leu Single submitter
p.Val125Ala Single submitter ⚠
p.Val162Ile Single submitter ⚠
p.Val167Leu Single submitter ⚠
p.Val167Met Single submitter ⚠
p.Val205Ile Single submitter ⚠
p.Val213Met Single submitter ⚠
p.Val420Ile Single submitter ⚠
p.Val43Phe Single submitter ⚠
p.Val509Asp Single submitter ⚠
p.Val595Ile Single submitter ⚠
p.Val716Ala Single submitter ⚠
p.Val716Ile Single submitter ⚠
p.Val849Phe Single submitter ⚠
p.Cys217_Asp218delinsTer No assertion criteria prostate cancer