Sugi Variant

Sugi Variant/LMAN1

LMAN1 — 227 ClinVar variants

All ClinVar germline LMAN1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 91 flagged for review →

9 Pathogenic · 1 Pathogenic/Likely pathogenic · 5 Likely pathogenic · 6 Conflicting · 35 Benign · 9 Benign/Likely benign · 16 Likely benign · 146 Uncertain significance

Full LMAN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 91

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 agree, ClinVar conflicts 1

ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.

Predictors lean, ClinVar uncertain 72

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.

Predictors split 18

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

All LMAN1 variants

Pathogenic 9

  • p.Arg117Ter Single submitter factor V and factor VIII, combined deficiency of, type 1
  • p.Arg202Ter Single submitter retinitis pigmentosa 7
  • p.Arg456Ter Single submitter factor V and factor VIII, combined deficiency of, type 1
  • p.Asn180fs Single submitter
  • p.Asn452_Leu453insTer Single submitter LMAN1-related disorder
  • c.1149+2T>C No assertion criteria factor V and factor VIII, combined deficiency of, type 1
  • p.Asp31fs No assertion criteria factor V and factor VIII, combined deficiency of, type 1
  • p.Gln266fs No assertion criteria factor V and factor VIII, combined deficiency of, type 1
  • p.Met1Thr No assertion criteria factor V and factor VIII, combined deficiency of, type 1

Pathogenic/Likely pathogenic 1

  • p.Lys302Ter Multiple submitters factor V and factor VIII, combined deficiency of, type 1

Likely pathogenic 5

  • c.478-11_483delinsATTTTTTTAGGAAAAA Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.535_539+2del Single submitter
  • p.Arg5fs Single submitter factor V and factor VIII, combined deficiency of, type 1
  • p.Gly30fs Single submitter factor V and factor VIII, combined deficiency of, type 1
  • p.Pro274= Single submitter factor V and factor VIII, combined deficiency of, type 1

Conflicting classifications of pathogenicity 6

  • c.1221-4T>C Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.477+10T>C Single submitter factor V and factor VIII, combined deficiency of, type 1
  • p.Leu9= Single submitter factor V and factor VIII, combined deficiency of, type 1
  • p.Pro464= Single submitter factor V and factor VIII, combined deficiency of, type 1
  • p.Ser282= Single submitter factor V and factor VIII, combined deficiency of, type 1
  • p.Val393Ala Single submitter factor V deficiency ⚠

Benign 35

Benign/Likely benign 9

  • c.1374+20C>T Multiple submitters
  • c.214+7C>T Multiple submitters factor V and factor VIII, combined deficiency of, type 1
  • c.478-17G>A Multiple submitters
  • c.539+5GT[3] Multiple submitters
  • p.Ala249= Multiple submitters
  • p.Arg117= Multiple submitters factor V and factor VIII, combined deficiency of, type 1
  • p.Leu133= Multiple submitters
  • p.Pro312= Multiple submitters factor V and factor VIII, combined deficiency of, type 1
  • p.Val487= Multiple submitters

Likely benign 16

Uncertain significance 146

  • c.*57G>A Multiple submitters factor V and factor VIII, combined deficiency of, type 1
  • p.Lys440Arg Multiple submitters factor V and factor VIII, combined deficiency of, type 1 ⚠
  • p.Phe293Ile Multiple submitters Inborn genetic diseases ⚠
  • p.Pro464Arg Multiple submitters factor V and factor VIII, combined deficiency of, type 1 ⚠
  • p.Pro471Leu Multiple submitters Inborn genetic diseases ⚠
  • p.Pro65Leu Multiple submitters Inborn genetic diseases ⚠
  • p.Thr478= Multiple submitters factor V and factor VIII, combined deficiency of, type 1
  • c.477+3A>G Single submitter LMAN1-related disorder
  • c.478-15T>C Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.539+3A>G Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.-5C>T Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*1164A>G Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*1168C>T Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*1271A>G Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*1298A>G Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*1300C>T Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*1305A>G Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*1332C>G Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*1390T>C Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*1390T>G Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*1556C>G Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*1565C>T Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*1616A>G Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*1631A>G Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*185A>T Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*1862A>G Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*1970T>G Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*1988C>T Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*2021A>C Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*2044A>G Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*2099C>T Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*210G>A Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*21T>G Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*2259A>T Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*2359A>G Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*2541T>C Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*2602G>T Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*2637T>C Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*2650G>A Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*2670G>C Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*2893G>A Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*2923C>T Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*319A>G Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*416C>T Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*424T>G Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*480A>G Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*48G>A Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*492T>C Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*571T>C Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*652T>C Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*753T>C Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*763T>A Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*794A>G Single submitter factor V and factor VIII, combined deficiency of, type 1
  • c.*939C>T Single submitter factor V and factor VIII, combined deficiency of, type 1
  • p.Ala11Thr Single submitter Inborn genetic diseases ⚠
  • p.Ala141Pro Single submitter Inborn genetic diseases
  • p.Ala183Thr Single submitter Inborn genetic diseases ⚠
  • p.Ala240Thr Single submitter Inborn genetic diseases ⚠
  • p.Ala2Val Single submitter Inborn genetic diseases ⚠
  • p.Ala83Thr Single submitter Inborn genetic diseases ⚠
  • p.Arg10Pro Single submitter Inborn genetic diseases ⚠
  • p.Arg10Trp Single submitter Inborn genetic diseases ⚠
  • p.Arg195His Single submitter Inborn genetic diseases ⚠
  • p.Arg329Gln Single submitter Inborn genetic diseases ⚠
  • p.Arg340His Single submitter Inborn genetic diseases ⚠
  • p.Arg350= Single submitter factor V and factor VIII, combined deficiency of, type 1
  • p.Arg350Trp Single submitter Inborn genetic diseases ⚠
  • p.Arg401Lys Single submitter Inborn genetic diseases ⚠
  • p.Arg44His Single submitter Inborn genetic diseases
  • p.Arg45Cys Single submitter Inborn genetic diseases ⚠
  • p.Arg81Gln Single submitter ⚠
  • p.Asn171Ser Single submitter factor V and factor VIII, combined deficiency of, type 1 ⚠
  • p.Asn180Lys Single submitter factor V and factor VIII, combined deficiency of, type 1 ⚠
  • p.Asn196Asp Single submitter Inborn genetic diseases ⚠
  • p.Asn218Ser Single submitter Inborn genetic diseases ⚠
  • p.Asp155Gly Single submitter Inborn genetic diseases ⚠
  • p.Asp155His Single submitter factor V and factor VIII, combined deficiency of, type 1 ⚠
  • p.Asp278Asn Single submitter Inborn genetic diseases ⚠
  • p.Asp301Asn Single submitter Inborn genetic diseases ⚠
  • p.Asp313Glu Single submitter Inborn genetic diseases ⚠
  • p.Asp36Glu Single submitter Inborn genetic diseases ⚠
  • p.Asp36His Single submitter factor V and factor VIII, combined deficiency of, type 1 ⚠
  • p.Gln173Glu Single submitter Inborn genetic diseases ⚠
  • p.Gln315His Single submitter Inborn genetic diseases ⚠
  • p.Gln333Glu Single submitter Inborn genetic diseases ⚠
  • p.Gln455Arg Single submitter Inborn genetic diseases ⚠
  • p.Gln59His Single submitter Inborn genetic diseases
  • p.Glu105Lys Single submitter Inborn genetic diseases ⚠
  • p.Glu299Lys Single submitter Inborn genetic diseases ⚠
  • p.Glu358Gly Single submitter Inborn genetic diseases ⚠
  • p.Gly158Val Single submitter Inborn genetic diseases ⚠
  • p.Gly182Arg Single submitter Inborn genetic diseases ⚠
  • p.Gly219Ser Single submitter Inborn genetic diseases ⚠
  • p.Gly316Arg Single submitter Inborn genetic diseases ⚠
  • p.Gly337Arg Single submitter Inborn genetic diseases ⚠
  • p.His311Gln Single submitter Inborn genetic diseases ⚠
  • p.His480Tyr Single submitter Inborn genetic diseases ⚠
  • p.His69Gln Single submitter Inborn genetic diseases ⚠
  • p.Ile168Val Single submitter Inborn genetic diseases ⚠
  • p.Ile174Thr Single submitter Inborn genetic diseases ⚠
  • p.Ile238Val Single submitter Inborn genetic diseases ⚠
  • p.Ile322Leu Single submitter Inborn genetic diseases ⚠
  • p.Ile322Val Single submitter Inborn genetic diseases ⚠
  • p.Ile437Thr Single submitter factor V and factor VIII, combined deficiency of, type 1 ⚠
  • p.Ile493Val Single submitter Inborn genetic diseases ⚠
  • p.Ile74Leu Single submitter Inborn genetic diseases ⚠
  • p.Leu314Phe Single submitter Inborn genetic diseases ⚠
  • p.Leu343Phe Single submitter Inborn genetic diseases ⚠
  • p.Leu453Ile Single submitter factor V and factor VIII, combined deficiency of, type 1 ⚠
  • p.Leu57Val Single submitter factor V and factor VIII, combined deficiency of, type 1
  • p.Leu9Phe Single submitter ⚠
  • p.Lys279Asn Single submitter Inborn genetic diseases ⚠
  • p.Lys302Glu Single submitter ⚠
  • p.Lys440Asn Single submitter Inborn genetic diseases ⚠
  • p.Met215Ile Single submitter Inborn genetic diseases ⚠
  • p.Met458Thr Single submitter Inborn genetic diseases ⚠
  • p.Met497Thr Single submitter Inborn genetic diseases ⚠
  • p.Phe293Leu Single submitter Inborn genetic diseases ⚠
  • p.Phe296Leu Single submitter Inborn genetic diseases ⚠
  • p.Phe436Val Single submitter Inborn genetic diseases ⚠
  • p.Phe509Leu Single submitter factor V and factor VIII, combined deficiency of, type 1 ⚠
  • p.Phe510Ile Single submitter Inborn genetic diseases ⚠
  • p.Phe510Tyr Single submitter Inborn genetic diseases ⚠
  • p.Phe52Cys Single submitter Inborn genetic diseases ⚠
  • p.Pro15Leu Single submitter Inborn genetic diseases ⚠
  • p.Pro200Leu Single submitter Inborn genetic diseases ⚠
  • p.Pro270Ala Single submitter Inborn genetic diseases ⚠
  • p.Pro277Ala Single submitter Inborn genetic diseases ⚠
  • p.Pro378Ser Single submitter Inborn genetic diseases ⚠
  • p.Pro471Ser Single submitter factor V and factor VIII, combined deficiency of, type 1 ⚠
  • p.Pro55Leu Single submitter Inborn genetic diseases ⚠
  • p.Ser282Leu Single submitter Inborn genetic diseases ⚠
  • p.Thr213Ile Single submitter factor V and factor VIII, combined deficiency of, type 1 ⚠
  • p.Thr221= Single submitter factor V and factor VIII, combined deficiency of, type 1
  • p.Thr268Pro Single submitter Inborn genetic diseases ⚠
  • p.Thr276Ile Single submitter Inborn genetic diseases ⚠
  • p.Thr478Met Single submitter Inborn genetic diseases ⚠
  • p.Thr95Ile Single submitter ⚠
  • p.Trp126Leu Single submitter Inborn genetic diseases ⚠
  • p.Tyr199= Single submitter factor V and factor VIII, combined deficiency of, type 1
  • p.Val13Leu Single submitter Inborn genetic diseases ⚠
  • p.Val259Ile Single submitter factor V and factor VIII, combined deficiency of, type 1 ⚠
  • p.Val414Ile Single submitter Inborn genetic diseases ⚠
  • p.Val490Ile Single submitter Inborn genetic diseases ⚠
  • p.Val64Met Single submitter Inborn genetic diseases ⚠
  • p.Val82Leu Single submitter Inborn genetic diseases ⚠