GLE1 — 718 ClinVar variants

All ClinVar germline GLE1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 120 flagged for review →

60 Pathogenic · 23 Pathogenic/Likely pathogenic · 59 Likely pathogenic · 20 Conflicting · 29 Benign · 4 Benign/Likely benign · 383 Likely benign · 140 Uncertain significance

Full GLE1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 120

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 vs ClinVar 1

ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.

Predictors agree, ClinVar conflicts 8

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

Predictors lean, ClinVar uncertain 89

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

Predictors split 22

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

All GLE1 variants

Pathogenic 60

Pathogenic/Likely pathogenic 23

  • p.Ala365fs Multiple submitters
  • p.Arg133Ter Multiple submitters Lethal congenital contractural syndrome Finnish type
  • p.Arg282Ter Multiple submitters Lethal congenital contractural syndrome Finnish type
  • p.Arg313Ter Multiple submitters Lethal congenital contractural syndrome Finnish type
  • p.Arg569His Multiple submitters Lethal congenital contractural syndrome Finnish type
  • p.Arg584Trp Multiple submitters Lethal congenital contractural syndrome Finnish type ⚠
  • p.Arg590Ter Multiple submitters Lethal congenital contractural syndrome Finnish type
  • p.Gln121fs Multiple submitters lethal arthrogryposis-anterior horn cell disease syndrome
  • p.Gln252fs Multiple submitters Lethal congenital contractural syndrome Finnish type
  • p.Gln352Ter Multiple submitters Lethal congenital contractural syndrome Finnish type
  • p.Gln379fs Multiple submitters Lethal congenital contractural syndrome Finnish type
  • p.Gln563fs Multiple submitters GLE1-related disorder
  • p.Gln591Ter Multiple submitters Lethal congenital contractural syndrome Finnish type
  • p.Gln636Ter Multiple submitters Lethal congenital contractural syndrome Finnish type
  • p.Gln81Ter Multiple submitters lethal congenital contracture syndrome 1
  • p.Glu38Ter Multiple submitters Lethal congenital contractural syndrome Finnish type
  • p.Leu402fs Multiple submitters lethal arthrogryposis-anterior horn cell disease syndrome
  • p.Lys336fs Multiple submitters Lethal congenital contractural syndrome Finnish type
  • p.Thr660fs Multiple submitters Lethal congenital contractural syndrome Finnish type
  • p.Trp150Ter Multiple submitters lethal arthrogryposis-anterior horn cell disease syndrome
  • p.Trp51Ter Multiple submitters Lethal congenital contractural syndrome Finnish type
  • p.Val158fs Multiple submitters lethal congenital contracture syndrome 1
  • p.Val228fs Multiple submitters Lethal congenital contractural syndrome Finnish type

Likely pathogenic 59

  • c.1881+1G>T Multiple submitters lethal arthrogryposis-anterior horn cell disease syndrome
  • c.1964+2T>C Multiple submitters Lethal congenital contractural syndrome Finnish type
  • c.2029-1G>A Multiple submitters Lethal congenital contractural syndrome Finnish type
  • p.Gln257fs Multiple submitters Lethal congenital contractural syndrome Finnish type
  • p.Gln673fs Multiple submitters lethal congenital contracture syndrome 1
  • p.Gly143fs Multiple submitters lethal arthrogryposis-anterior horn cell disease syndrome
  • p.Gly597Asp Multiple submitters Lethal congenital contractural syndrome Finnish type
  • c.100-1G>A Single submitter Lethal congenital contractural syndrome Finnish type
  • c.1129+1G>C Single submitter
  • c.1130-1G>C Single submitter
  • c.1242+1G>A Single submitter
  • c.1243-2A>G Single submitter
  • c.1312+1G>A Single submitter
  • c.1312+2T>C Single submitter
  • c.1456-1G>A Single submitter lethal congenital contracture syndrome 1
  • c.1647-1G>C Single submitter
  • c.1776+2T>G Single submitter
  • c.1777-1G>C Single submitter
  • c.1881+2T>C Single submitter
  • c.1964+2T>G Single submitter
  • c.1965-1G>C Single submitter
  • c.1965-1G>T Single submitter Lethal congenital contractural syndrome Finnish type
  • c.1965-2A>G Single submitter
  • c.321+2T>G Single submitter
  • c.322-1G>A Single submitter
  • c.432+2T>C Single submitter
  • c.581+1G>T Single submitter
  • c.581+2T>C Single submitter
  • c.642+1G>A Single submitter
  • c.643-2A>G Single submitter
  • c.897+1G>A Single submitter Lethal congenital contractural syndrome Finnish type
  • p.Ala578fs Single submitter Lethal congenital contractural syndrome Finnish type
  • p.Gln151Ter Single submitter
  • p.Gln154Ter Single submitter Lethal congenital contractural syndrome Finnish type
  • p.Gln185fs Single submitter lethal arthrogryposis-anterior horn cell disease syndrome
  • p.Gln252Ter Single submitter Lethal congenital contractural syndrome Finnish type
  • p.Gln327Ter Single submitter lethal congenital contracture syndrome 1
  • p.Gln354Ter Single submitter Lethal congenital contractural syndrome Finnish type
  • p.Gln399fs Single submitter GLE1-related disorder
  • p.Gln477Ter Single submitter Lethal congenital contractural syndrome Finnish type
  • p.Glu177fs Single submitter Lethal congenital contractural syndrome Finnish type
  • p.Glu341Ter Single submitter lethal congenital contracture syndrome 1
  • p.His525fs Single submitter Lethal congenital contractural syndrome Finnish type
  • p.Ile428fs Single submitter Lethal congenital contractural syndrome Finnish type
  • p.Ile502fs Single submitter Lethal congenital contractural syndrome Finnish type
  • p.Leu218fs Single submitter lethal arthrogryposis-anterior horn cell disease syndrome
  • p.Leu633fs Single submitter Lethal congenital contractural syndrome Finnish type
  • p.Leu679fs Single submitter Lethal congenital contractural syndrome Finnish type
  • p.Lys347Ter Single submitter Lethal congenital contractural syndrome Finnish type
  • p.Lys559fs Single submitter lethal congenital contracture syndrome 1
  • p.Lys649fs Single submitter Lethal congenital contractural syndrome Finnish type
  • p.Met1fs Single submitter Lethal congenital contractural syndrome Finnish type
  • p.Met1Val Single submitter Lethal congenital contractural syndrome Finnish type
  • p.Pro89fs Single submitter lethal congenital contracture syndrome 1
  • p.Ser571Ter Single submitter lethal congenital contracture syndrome 1
  • p.Ser75Ter Single submitter lethal arthrogryposis-anterior horn cell disease syndrome
  • p.Trp602Ter Single submitter
  • p.Val128fs Single submitter
  • p.Val492fs Single submitter Lethal congenital contractural syndrome Finnish type

Conflicting classifications of pathogenicity 20

  • c.1130-15T>C Single submitter lethal congenital contracture syndrome 1
  • c.1243-5G>A Single submitter lethal congenital contracture syndrome 1
  • c.1882-8C>G Single submitter lethal arthrogryposis-anterior horn cell disease syndrome
  • c.1964+8G>T Single submitter lethal arthrogryposis-anterior horn cell disease syndrome
  • c.2028+1G>A Single submitter Lethal congenital contractural syndrome Finnish type
  • c.2029-5A>G Single submitter lethal arthrogryposis-anterior horn cell disease syndrome
  • c.643-4A>G Single submitter lethal congenital contracture syndrome 1
  • c.-45T>C Single submitter lethal arthrogryposis-anterior horn cell disease syndrome
  • p.Asp18Glu Single submitter lethal arthrogryposis-anterior horn cell disease syndrome ⚠
  • p.Asp275Asn Single submitter lethal arthrogryposis-anterior horn cell disease syndrome ⚠
  • p.Cys39Tyr Single submitter lethal congenital contracture syndrome 1 ⚠
  • p.Leu149= Single submitter
  • p.Phe695Ser Single submitter ⚠
  • p.Pro2Arg Single submitter lethal arthrogryposis-anterior horn cell disease syndrome ⚠
  • p.Pro363Ser Single submitter Inborn genetic diseases ⚠
  • p.Pro613Thr Single submitter Inborn genetic diseases ⚠
  • p.Ser465Thr Single submitter lethal arthrogryposis-anterior horn cell disease syndrome ⚠
  • p.Tyr547= Single submitter lethal arthrogryposis-anterior horn cell disease syndrome
  • p.Val132Ile Single submitter Inborn genetic diseases ⚠
  • p.Val56Ile Single submitter Inborn genetic diseases ⚠

Benign 29

Benign/Likely benign 4

  • c.433-15A>C Multiple submitters lethal arthrogryposis-anterior horn cell disease syndrome
  • c.897+16G>A Multiple submitters
  • p.Glu334Lys Multiple submitters lethal arthrogryposis-anterior horn cell disease syndrome ⚠
  • p.Tyr577= Multiple submitters lethal congenital contracture syndrome 1

Likely benign 383

Showing the top 300 by review status; the full set is in the sitemap.

Uncertain significance 140

  • c.-108C>A Multiple submitters lethal arthrogryposis-anterior horn cell disease syndrome
  • c.-81C>T Multiple submitters lethal arthrogryposis-anterior horn cell disease syndrome
  • p.Arg227Cys Multiple submitters Inborn genetic diseases ⚠
  • p.Arg26Gly Multiple submitters Inborn genetic diseases ⚠
  • p.Arg575His Multiple submitters Inborn genetic diseases ⚠
  • p.Asp474Glu Multiple submitters Inborn genetic diseases ⚠
  • p.Met191Ile Multiple submitters Inborn genetic diseases ⚠
  • p.Pro357Ala Multiple submitters Inborn genetic diseases ⚠
  • p.Pro370Leu Multiple submitters Inborn genetic diseases ⚠
  • p.Pro43Ser Multiple submitters Inborn genetic diseases ⚠
  • p.Val464Ala Multiple submitters ⚠
  • c.1881+5G>A Single submitter
  • c.321+13T>G Single submitter lethal arthrogryposis-anterior horn cell disease syndrome
  • c.433-15A>G Single submitter
  • c.-34G>A Single submitter lethal congenital contracture syndrome 1
  • c.-51G>A Single submitter lethal arthrogryposis-anterior horn cell disease syndrome
  • c.-84A>C Single submitter lethal arthrogryposis-anterior horn cell disease syndrome
  • c.*111T>C Single submitter lethal arthrogryposis-anterior horn cell disease syndrome
  • c.*390C>T Single submitter lethal arthrogryposis-anterior horn cell disease syndrome
  • c.*540G>A Single submitter
  • c.*640C>T Single submitter lethal arthrogryposis-anterior horn cell disease syndrome
  • c.*708T>C Single submitter lethal arthrogryposis-anterior horn cell disease syndrome
  • c.*782C>G Single submitter lethal arthrogryposis-anterior horn cell disease syndrome
  • c.*962C>T Single submitter lethal congenital contracture syndrome 1
  • p.Ala165Pro Single submitter Inborn genetic diseases ⚠
  • p.Ala250Val Single submitter lethal arthrogryposis-anterior horn cell disease syndrome ⚠
  • p.Ala425Ser Single submitter Inborn genetic diseases ⚠
  • p.Ala503Thr Single submitter Inborn genetic diseases ⚠
  • p.Ala632Thr Single submitter ⚠
  • p.Ala91Ser Single submitter Inborn genetic diseases ⚠
  • p.Ala91Val Single submitter Inborn genetic diseases ⚠
  • p.Arg188Trp Single submitter Inborn genetic diseases ⚠
  • p.Arg196Ile Single submitter Inborn genetic diseases ⚠
  • p.Arg21Cys Single submitter ⚠
  • p.Arg237Trp Single submitter Inborn genetic diseases ⚠
  • p.Arg244Cys Single submitter Inborn genetic diseases ⚠
  • p.Arg244Leu Single submitter Inborn genetic diseases ⚠
  • p.Arg246Gln Single submitter lethal arthrogryposis-anterior horn cell disease syndrome ⚠
  • p.Arg282Gln Single submitter Inborn genetic diseases ⚠
  • p.Arg313Gln Single submitter Inborn genetic diseases ⚠
  • p.Arg316Gln Single submitter lethal congenital contracture syndrome 1 ⚠
  • p.Arg316Trp Single submitter lethal congenital contracture syndrome 1 ⚠
  • p.Arg319Trp Single submitter ⚠
  • p.Arg31Trp Single submitter Inborn genetic diseases ⚠
  • p.Arg338Ser Single submitter Inborn genetic diseases ⚠
  • p.Arg462Cys Single submitter lethal congenital contracture syndrome 1 ⚠
  • p.Arg603His Single submitter ⚠
  • p.Arg670Leu Single submitter ⚠
  • p.Arg697Cys Single submitter GLE1-related disorder ⚠
  • p.Arg697His Single submitter Inborn genetic diseases ⚠
  • p.Asn409Asp Single submitter Inborn genetic diseases ⚠
  • p.Asp186Glu Single submitter Inborn genetic diseases ⚠
  • p.Asp186Tyr Single submitter Inborn genetic diseases ⚠
  • p.Asp27His Single submitter Inborn genetic diseases ⚠
  • p.Asp34Asn Single submitter Inborn genetic diseases ⚠
  • p.Asp518Glu Single submitter lethal congenital contracture syndrome 1 ⚠
  • p.Cys678Tyr Single submitter Inborn genetic diseases
  • p.Gln121Glu Single submitter Inborn genetic diseases ⚠
  • p.Gln242His Single submitter Inborn genetic diseases ⚠
  • p.Gln285His Single submitter Inborn genetic diseases ⚠
  • p.Gln477Arg Single submitter Inborn genetic diseases ⚠
  • p.Gln477Lys Single submitter Inborn genetic diseases ⚠
  • p.Gln81His Single submitter Inborn genetic diseases ⚠
  • p.Glu192Gly Single submitter ⚠
  • p.Glu224Asp Single submitter Inborn genetic diseases ⚠
  • p.Glu234Lys Single submitter Inborn genetic diseases ⚠
  • p.Glu240Gly Single submitter lethal arthrogryposis-anterior horn cell disease syndrome ⚠
  • p.Glu310Lys Single submitter lethal congenital contracture syndrome 1 ⚠
  • p.Glu443Ala Single submitter Inborn genetic diseases ⚠
  • p.Glu489Lys Single submitter amyotrophic lateral sclerosis ⚠
  • p.Glu612Val Single submitter lethal congenital contracture syndrome 1 ⚠
  • p.Gly508Val Single submitter Inborn genetic diseases ⚠
  • p.Gly5Asp Single submitter Inborn genetic diseases ⚠
  • p.Gly601Val Single submitter Inborn genetic diseases ⚠
  • p.Gly666Val Single submitter ⚠
  • p.His523Tyr Single submitter Inborn genetic diseases ⚠
  • p.His594Asp Single submitter Inborn genetic diseases
  • p.Ile293Phe Single submitter Inborn genetic diseases ⚠
  • p.Ile385Val Single submitter Inborn genetic diseases ⚠
  • p.Ile418Val Single submitter Inborn genetic diseases ⚠
  • p.Ile656Thr Single submitter Inborn genetic diseases ⚠
  • p.Ile669Lys Single submitter
  • p.Leu315Pro Single submitter Inborn genetic diseases ⚠
  • p.Leu36Val Single submitter Inborn genetic diseases ⚠
  • p.Leu468Ile Single submitter Inborn genetic diseases ⚠
  • p.Leu468Phe Single submitter ⚠
  • p.Leu519Arg Single submitter Inborn genetic diseases ⚠
  • p.Leu544Ser Single submitter Inborn genetic diseases ⚠
  • p.Lys127Arg Single submitter Inborn genetic diseases ⚠
  • p.Lys176Arg Single submitter Inborn genetic diseases ⚠
  • p.Lys568Asn Single submitter Inborn genetic diseases ⚠
  • p.Met191Thr Single submitter Inborn genetic diseases ⚠
  • p.Met398Thr Single submitter Inborn genetic diseases ⚠
  • p.Met60Val Single submitter ⚠
  • p.Phe404Ser Single submitter ⚠
  • p.Phe690Cys Single submitter Inborn genetic diseases ⚠
  • p.Phe84Leu Single submitter Inborn genetic diseases ⚠
  • p.Pro429Ala Single submitter
  • p.Pro456Arg Single submitter Inborn genetic diseases ⚠
  • p.Ser162Leu Single submitter lethal congenital contracture syndrome 1 ⚠
  • p.Ser17Phe Single submitter Inborn genetic diseases ⚠
  • p.Ser413Asn Single submitter Inborn genetic diseases ⚠
  • p.Ser434Cys Single submitter Inborn genetic diseases ⚠
  • p.Ser531Pro Single submitter Inborn genetic diseases ⚠
  • p.Ser693Phe Single submitter amyotrophic lateral sclerosis ⚠
  • p.Ser698Phe Single submitter ⚠
  • p.Thr106Ala Single submitter Inborn genetic diseases ⚠
  • p.Thr106Ile Single submitter Inborn genetic diseases ⚠
  • p.Thr10Ala Single submitter Inborn genetic diseases ⚠
  • p.Val274Ile Single submitter Inborn genetic diseases ⚠
  • c.1129+9C>T No assertion criteria Lethal congenital contractural syndrome Finnish type
  • c.1242+4G>C No assertion criteria Lethal congenital contractural syndrome Finnish type
  • c.1777-10C>T No assertion criteria Lethal congenital contractural syndrome Finnish type
  • c.1964+5C>G No assertion criteria Lethal congenital contractural syndrome Finnish type
  • c.642+6A>G No assertion criteria Lethal congenital contractural syndrome Finnish type
  • c.99+6C>T No assertion criteria Lethal congenital contractural syndrome Finnish type
  • c.-10T>C No assertion criteria Lethal congenital contractural syndrome Finnish type
  • p.Arg156Trp No assertion criteria Lethal congenital contractural syndrome Finnish type ⚠
  • p.Arg244His No assertion criteria Lethal congenital contractural syndrome Finnish type ⚠
  • p.Asp263= No assertion criteria Lethal congenital contractural syndrome Finnish type
  • p.Asp395His No assertion criteria Lethal congenital contractural syndrome Finnish type ⚠
  • p.Gln423= No assertion criteria Lethal congenital contractural syndrome Finnish type
  • p.Glu163Gln No assertion criteria lethal arthrogryposis-anterior horn cell disease syndrome ⚠
  • p.Gly541Val No assertion criteria Lethal congenital contractural syndrome Finnish type ⚠
  • p.Ile294Met No assertion criteria Lethal congenital contractural syndrome Finnish type ⚠
  • p.Leu187Phe No assertion criteria Lethal congenital contractural syndrome Finnish type ⚠
  • p.Leu216Phe No assertion criteria Lethal congenital contractural syndrome Finnish type ⚠
  • p.Leu271Pro No assertion criteria Lethal congenital contractural syndrome Finnish type ⚠
  • p.Leu519= No assertion criteria Lethal congenital contractural syndrome Finnish type
  • p.Lys127Thr No assertion criteria lethal arthrogryposis-anterior horn cell disease syndrome ⚠
  • p.Lys214= No assertion criteria Lethal congenital contractural syndrome Finnish type
  • p.Lys527= No assertion criteria Lethal congenital contractural syndrome Finnish type
  • p.Lys568Arg No assertion criteria Lethal congenital contractural syndrome Finnish type ⚠
  • p.Met611Ile No assertion criteria Lethal congenital contractural syndrome Finnish type ⚠
  • p.Met665Arg No assertion criteria Lethal congenital contractural syndrome Finnish type ⚠
  • p.Pro533Ala No assertion criteria Lethal congenital contractural syndrome Finnish type ⚠
  • p.Ser301Arg No assertion criteria Lethal congenital contractural syndrome Finnish type ⚠
  • p.Ser494Cys No assertion criteria Lethal congenital contractural syndrome Finnish type ⚠
  • p.Thr10= No assertion criteria Lethal congenital contractural syndrome Finnish type
  • p.Val380Ala No assertion criteria lethal arthrogryposis-anterior horn cell disease syndrome ⚠