LTN1 — 217 ClinVar variants

All ClinVar germline LTN1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 186 flagged for review →

2 Benign · 15 Likely benign · 200 Uncertain significance

Full LTN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 186

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 167

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 167

Predictors split 19

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

All LTN1 variants

Benign 2

p.Ala500Val Multiple submitters
p.Glu462Asp Multiple submitters

Likely benign 15

p.Ala444Thr Single submitter
p.Arg1065Cys Single submitter
p.Arg608Gln Single submitter
p.Arg628Gln Single submitter
p.Gln288= Single submitter
p.Ile1101Val Single submitter
p.Ile1296Val Single submitter
p.Ile1322Leu Single submitter
p.Ile311Val Single submitter
p.Leu881= Single submitter
p.Met632Val Single submitter
p.Phe1206= Single submitter
p.Ser511= Single submitter
p.Thr473Met Single submitter
p.Thr807Ala Single submitter

Uncertain significance 200

c.64G>A Single submitter
c.-15G>T Single submitter
c.-26C>T Single submitter
c.-30A>G Single submitter
c.-35G>A Single submitter
c.-9A>G Single submitter
p.Ala1028Ser Single submitter ⚠
p.Ala1672Val Single submitter ⚠
p.Ala22Val Single submitter
p.Ala391Gly Single submitter ⚠
p.Ala507Pro Single submitter ⚠
p.Ala644Val Single submitter ⚠
p.Ala658Val Single submitter ⚠
p.Arg1065Pro Single submitter ⚠
p.Arg1099Gln Single submitter ⚠
p.Arg1112Gly Single submitter ⚠
p.Arg119His Single submitter
p.Arg120His Single submitter ⚠
p.Arg1366Thr Single submitter ⚠
p.Arg1504Trp Single submitter
p.Arg1633Gln Single submitter
p.Arg20Gln Single submitter ⚠
p.Arg223Gln Single submitter ⚠
p.Arg285Cys Single submitter ⚠
p.Arg349Leu Single submitter ⚠
p.Arg353Gln Single submitter ⚠
p.Arg353Trp Single submitter ⚠
p.Arg675Gly Single submitter ⚠
p.Arg690Gln Single submitter ⚠
p.Arg690Trp Single submitter ⚠
p.Arg698Ile Single submitter ⚠
p.Arg70Trp Single submitter ⚠
p.Arg974Ile Single submitter ⚠
p.Asn1209His Single submitter ⚠
p.Asn1298Ser Single submitter ⚠
p.Asn485Ser Single submitter ⚠
p.Asn829Asp Single submitter ⚠
p.Asn905Thr Single submitter ⚠
p.Asp1182Tyr Single submitter ⚠
p.Asp196Asn Single submitter ⚠
p.Asp443Asn Single submitter ⚠
p.Asp543Val Single submitter ⚠
p.Asp673Gly Single submitter ⚠
p.Asp693Gly Single submitter ⚠
p.Asp739Asn Single submitter ⚠
p.Asp739His Single submitter ⚠
p.Asp790Asn Single submitter ⚠
p.Asp936Glu Single submitter ⚠
p.Asp985His Single submitter ⚠
p.Cys1275Phe Single submitter ⚠
p.Cys1455Ser Single submitter ⚠
p.Cys1455Tyr Single submitter ⚠
p.Cys1472Tyr Single submitter ⚠
p.Cys555Tyr Single submitter ⚠
p.Cys854Arg Single submitter ⚠
p.Gln1055Lys Single submitter ⚠
p.Gln1371Arg Single submitter ⚠
p.Gln674Arg Single submitter ⚠
p.Glu1083Gly Single submitter ⚠
p.Glu1532Asp Single submitter ⚠
p.Glu1587Asp Single submitter ⚠
p.Glu249Asp Single submitter ⚠
p.Glu396Lys Single submitter ⚠
p.Glu551Asp Single submitter ⚠
p.Glu567Val Single submitter ⚠
p.Glu591Ala Single submitter ⚠
p.Glu933Gln Single submitter ⚠
p.Glu935Gly Single submitter ⚠
p.Gly1724Ser Single submitter ⚠
p.Gly454Glu Single submitter ⚠
p.Gly537Ala Single submitter ⚠
p.Gly635Ala Single submitter ⚠
p.Gly635Arg Single submitter ⚠
p.Gly679Asp Single submitter ⚠
p.His1084Arg Single submitter ⚠
p.His1109Tyr Single submitter ⚠
p.His1187Arg Single submitter ⚠
p.His1403Tyr Single submitter ⚠
p.His453Arg Single submitter ⚠
p.His613Asn Single submitter
p.His967Pro Single submitter ⚠
p.Ile1127Met Single submitter ⚠
p.Ile1170Leu Single submitter ⚠
p.Ile1222Thr Single submitter ⚠
p.Ile1304Val Single submitter ⚠
p.Ile1444Val Single submitter ⚠
p.Ile1461Thr Single submitter ⚠
p.Ile1484Met Single submitter ⚠
p.Ile1593Thr Single submitter ⚠
p.Ile1646Thr Single submitter ⚠
p.Ile1649Arg Single submitter ⚠
p.Ile305Val Single submitter ⚠
p.Ile359Met Single submitter ⚠
p.Ile419Thr Single submitter ⚠
p.Ile502Val Single submitter ⚠
p.Ile57Val Single submitter ⚠
p.Ile600Thr Single submitter ⚠
p.Ile600Val Single submitter ⚠
p.Ile684Val Single submitter ⚠
p.Ile740Val Single submitter ⚠
p.Ile944Leu Single submitter ⚠
p.Ile991Leu Single submitter ⚠
p.Leu1047Arg Single submitter ⚠
p.Leu1067Arg Single submitter ⚠
p.Leu1090Phe Single submitter ⚠
p.Leu1280Phe Single submitter ⚠
p.Leu1389Ser Single submitter ⚠
p.Leu1519Val Single submitter ⚠
p.Leu235Val Single submitter ⚠
p.Leu25Phe Single submitter ⚠
p.Leu355Pro Single submitter ⚠
p.Leu460Phe Single submitter ⚠
p.Leu582Trp Single submitter ⚠
p.Leu614Pro Single submitter ⚠
p.Leu647Val Single submitter ⚠
p.Leu741Val Single submitter ⚠
p.Leu752Phe Single submitter ⚠
p.Leu800Phe Single submitter ⚠
p.Leu863Met Single submitter ⚠
p.Leu882Met Single submitter ⚠
p.Leu932Val Single submitter ⚠
p.Leu939Ile Single submitter ⚠
p.Lys1056Thr Single submitter ⚠
p.Lys1178Glu Single submitter ⚠
p.Lys1667Arg Single submitter ⚠
p.Lys1707Arg Single submitter ⚠
p.Lys1740fs Single submitter neurodevelopmental disorder
p.Lys178Arg Single submitter ⚠
p.Lys378Asn Single submitter ⚠
p.Lys533Glu Single submitter ⚠
p.Lys783Gln Single submitter ⚠
p.Lys806Asn Single submitter ⚠
p.Lys983Asn Single submitter ⚠
p.Met1248Thr Single submitter ⚠
p.Met1578Val Single submitter ⚠
p.Met632Thr Single submitter ⚠
p.Met696Ile Single submitter ⚠
p.Met696Leu Single submitter ⚠
p.Met696Thr Single submitter ⚠
p.Met963Val Single submitter ⚠
p.Phe1287Ser Single submitter ⚠
p.Phe1310Leu Single submitter ⚠
p.Phe678Ser Single submitter ⚠
p.Pro1132Ser Single submitter ⚠
p.Pro1300His Single submitter ⚠
p.Pro1300Leu Single submitter
p.Pro180Leu Single submitter ⚠
p.Pro505Ala Single submitter ⚠
p.Pro949Leu Single submitter ⚠
p.Ser1071Leu Single submitter ⚠
p.Ser1179Asn Single submitter ⚠
p.Ser1237Phe Single submitter ⚠
p.Ser1237Tyr Single submitter ⚠
p.Ser1259Gly Single submitter ⚠
p.Ser1508Gly Single submitter ⚠
p.Ser1612Phe Single submitter ⚠
p.Ser373Phe Single submitter ⚠
p.Ser394Leu Single submitter ⚠
p.Ser410Thr Single submitter ⚠
p.Ser623Phe Single submitter ⚠
p.Ser640Asn Single submitter ⚠
p.Ser759Thr Single submitter ⚠
p.Ser762Pro Single submitter ⚠
p.Ser911Ala Single submitter ⚠
p.Ser934Asn Single submitter ⚠
p.Thr1060Met Single submitter ⚠
p.Thr1177Ala Single submitter ⚠
p.Thr1177Ile Single submitter ⚠
p.Thr1351Met Single submitter ⚠
p.Thr1381Ala Single submitter ⚠
p.Thr1463Ile Single submitter ⚠
p.Thr1529Ile Single submitter ⚠
p.Thr1543Asn Single submitter ⚠
p.Thr1631Ala Single submitter ⚠
p.Thr1640Ile Single submitter ⚠
p.Thr1640Ser Single submitter ⚠
p.Thr400Ile Single submitter ⚠
p.Thr569Arg Single submitter ⚠
p.Thr619Ile Single submitter ⚠
p.Thr706Ile Single submitter ⚠
p.Trp1307Arg Single submitter ⚠
p.Tyr1558Cys Single submitter ⚠
p.Tyr828Cys Single submitter ⚠
p.Tyr830Cys Single submitter ⚠
p.Val1008Phe Single submitter ⚠
p.Val121Ile Single submitter ⚠
p.Val1401Leu Single submitter ⚠
p.Val1452Ile Single submitter ⚠
p.Val1458Gly Single submitter ⚠
p.Val1626Ile Single submitter ⚠
p.Val1673Ala Single submitter ⚠
p.Val334Ile Single submitter ⚠
p.Val358Phe Single submitter ⚠
p.Val512Ala Single submitter ⚠
p.Val556Ile Single submitter ⚠
p.Val594Ala Single submitter
p.Val642Ile Single submitter ⚠
p.Val68Ala Single submitter ⚠
p.Val68Leu Single submitter ⚠
p.Val708Met Single submitter ⚠