ALG3 — 250 ClinVar variants

All ClinVar germline ALG3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 107 flagged for review →

17 Pathogenic · 4 Pathogenic/Likely pathogenic · 17 Likely pathogenic · 16 Conflicting · 6 Benign · 5 Benign/Likely benign · 69 Likely benign · 116 Uncertain significance

Full ALG3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 107

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 2

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

Predictors lean, ClinVar uncertain 58

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

Predictors split 47

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

All ALG3 variants

Pathogenic 17

  • p.Arg266Cys Multiple submitters ALG3-congenital disorder of glycosylation
  • p.Trp396Ter Multiple submitters ALG3-congenital disorder of glycosylation
  • c.606-2A>C Single submitter ALG3-congenital disorder of glycosylation
  • p.Arg287Ter Single submitter ALG3-congenital disorder of glycosylation
  • p.Asn346Ser Single submitter ALG3-congenital disorder of glycosylation ⚠
  • p.Asn397fs Single submitter ALG3-congenital disorder of glycosylation
  • p.Gln16fs Single submitter ALG3-congenital disorder of glycosylation
  • p.Gln23Ter Single submitter ALG3-congenital disorder of glycosylation
  • p.Gln331Ter Single submitter Inborn genetic diseases
  • p.His297fs Single submitter ALG3-congenital disorder of glycosylation
  • p.Pro39fs Single submitter ALG3-congenital disorder of glycosylation
  • p.Trp24Ter Single submitter ALG3-congenital disorder of glycosylation
  • c.163_196+3del No assertion criteria ALG3-congenital disorder of glycosylation
  • p.Arg385Thr No assertion criteria ALG3-congenital disorder of glycosylation
  • p.Gly118Asp No assertion criteria ALG3-congenital disorder of glycosylation
  • p.Met157Lys No assertion criteria ALG3-congenital disorder of glycosylation
  • p.Trp421Ter No assertion criteria ALG3-congenital disorder of glycosylation

Pathogenic/Likely pathogenic 4

  • p.Arg171Gln Multiple submitters ALG3-congenital disorder of glycosylation
  • p.Arg354His Multiple submitters ALG3-congenital disorder of glycosylation
  • p.Gly55= Multiple submitters ALG3-congenital disorder of glycosylation
  • p.Met1Thr Multiple submitters ALG3-congenital disorder of glycosylation

Likely pathogenic 17

  • c.444+1G>T Multiple submitters ALG3-congenital disorder of glycosylation
  • p.Arg354Cys Multiple submitters ALG3-congenital disorder of glycosylation
  • p.Asn174Ser Multiple submitters ALG3-congenital disorder of glycosylation ⚠
  • p.Ile69Thr Multiple submitters ALG3-congenital disorder of glycosylation
  • c.296+4A>G Single submitter ALG3-congenital disorder of glycosylation
  • c.444+1G>A Single submitter ALG3-congenital disorder of glycosylation
  • c.444+2T>G Single submitter ALG3-congenital disorder of glycosylation
  • p.Arg163His Single submitter ALG3-congenital disorder of glycosylation
  • p.Arg171Trp Single submitter ALG3-congenital disorder of glycosylation
  • p.Cys307Ter Single submitter congenital disorder of glycosylation
  • p.Gly96Arg Single submitter ALG3-congenital disorder of glycosylation
  • p.Leu189Pro Single submitter
  • p.Leu223fs Single submitter
  • p.Lys72fs Single submitter ALG3-congenital disorder of glycosylation
  • p.Tyr106fs Single submitter
  • p.Tyr74Cys Single submitter ALG3-congenital disorder of glycosylation
  • p.Leu137_Leu138insValPheLeuLeu No assertion criteria ALG3-congenital disorder of glycosylation

Conflicting classifications of pathogenicity 16

  • c.297-6T>C Single submitter ALG3-congenital disorder of glycosylation
  • c.606-10C>T Single submitter ALG3-congenital disorder of glycosylation
  • c.606-8C>T Single submitter ALG3-congenital disorder of glycosylation
  • c.933-4C>T Single submitter ALG3-congenital disorder of glycosylation
  • p.Ala17= Single submitter ALG3-congenital disorder of glycosylation
  • p.Ala282Val Single submitter ALG3-congenital disorder of glycosylation ⚠
  • p.Arg117Pro Single submitter ALG3-congenital disorder of glycosylation ⚠
  • p.Arg117Ter Single submitter ALG3-congenital disorder of glycosylation
  • p.Gln359= Single submitter ALG3-congenital disorder of glycosylation
  • p.Gly16Trp Single submitter ALG3-congenital disorder of glycosylation
  • p.Leu232= Single submitter ALG3-congenital disorder of glycosylation
  • p.Leu342Ile Single submitter ALG3-congenital disorder of glycosylation ⚠
  • p.Lys22= Single submitter ALG3-congenital disorder of glycosylation
  • p.Ser259= Single submitter ALG3-congenital disorder of glycosylation
  • p.Tyr74= Single submitter ALG3-congenital disorder of glycosylation
  • p.Val362Ile Single submitter ALG3-congenital disorder of glycosylation ⚠

Benign 6

Benign/Likely benign 5

  • c.727-50T>C Multiple submitters
  • p.Cys159= Multiple submitters ALG3-congenital disorder of glycosylation
  • p.Ile107Val Multiple submitters ALG3-congenital disorder of glycosylation
  • p.Pro424= Multiple submitters ALG3-congenital disorder of glycosylation
  • p.Pro424Leu Multiple submitters ALG3-congenital disorder of glycosylation

Likely benign 69

  • c.1010-292C>T Multiple submitters
  • c.52+196G>T Multiple submitters
  • c.605+124C>T Multiple submitters
  • c.933-29T>C Multiple submitters
  • p.Ile392= Multiple submitters ALG3-congenital disorder of glycosylation
  • p.Leu223= Multiple submitters ALG3-congenital disorder of glycosylation
  • p.Leu98= Multiple submitters ALG3-congenital disorder of glycosylation
  • p.Pro369= Multiple submitters ALG3-congenital disorder of glycosylation
  • c.1009+14T>G Single submitter ALG3-congenital disorder of glycosylation
  • c.1010-137G>A Single submitter
  • c.1155-9C>T Single submitter ALG3-congenital disorder of glycosylation
  • c.196+16G>A Single submitter ALG3-congenital disorder of glycosylation
  • c.196+19del Single submitter ALG3-congenital disorder of glycosylation
  • c.196+8C>T Single submitter
  • c.296+13A>C Single submitter ALG3-congenital disorder of glycosylation
  • c.296+20T>C Single submitter ALG3-congenital disorder of glycosylation
  • c.296+9G>C Single submitter ALG3-congenital disorder of glycosylation
  • c.297-11T>C Single submitter ALG3-congenital disorder of glycosylation
  • c.297-19A>G Single submitter ALG3-congenital disorder of glycosylation
  • c.445-17C>T Single submitter ALG3-congenital disorder of glycosylation
  • c.445-19T>C Single submitter ALG3-congenital disorder of glycosylation
  • c.52+9G>A Single submitter
  • c.605+9C>T Single submitter ALG3-congenital disorder of glycosylation
  • c.606-18C>T Single submitter ALG3-congenital disorder of glycosylation
  • c.726+10T>A Single submitter
  • c.932+10G>A Single submitter ALG3-congenital disorder of glycosylation
  • c.932+7A>G Single submitter ALG3-congenital disorder of glycosylation
  • c.933-20_933-17del Single submitter ALG3-congenital disorder of glycosylation
  • p.Ala239= Single submitter ALG3-congenital disorder of glycosylation
  • p.Ala296= Single submitter ALG3-congenital disorder of glycosylation
  • p.Ala414= Single submitter ALG3-congenital disorder of glycosylation
  • p.Arg10= Single submitter ALG3-congenital disorder of glycosylation
  • p.Arg193= Single submitter ALG3-congenital disorder of glycosylation
  • p.Arg6= Single submitter ALG3-congenital disorder of glycosylation
  • p.Arg8= Single submitter
  • p.Asn210= Single submitter ALG3-congenital disorder of glycosylation
  • p.Glu38= Single submitter
  • p.Glu8= Single submitter
  • p.Gly230= Single submitter ALG3-congenital disorder of glycosylation
  • p.Gly390= Single submitter ALG3-congenital disorder of glycosylation
  • p.Gly80= Single submitter ALG3-congenital disorder of glycosylation
  • p.Ile107= Single submitter ALG3-congenital disorder of glycosylation
  • p.Ile338= Single submitter ALG3-congenital disorder of glycosylation
  • p.Leu181= Single submitter ALG3-congenital disorder of glycosylation
  • p.Leu213= Single submitter ALG3-congenital disorder of glycosylation
  • p.Leu283= Single submitter
  • p.Leu306= Single submitter ALG3-congenital disorder of glycosylation
  • p.Leu36= Single submitter
  • p.Leu380= Single submitter ALG3-congenital disorder of glycosylation
  • p.Leu418= Single submitter ALG3-congenital disorder of glycosylation
  • p.Phe104= Single submitter ALG3-congenital disorder of glycosylation
  • p.Phe152= Single submitter ALG3-congenital disorder of glycosylation
  • p.Phe168= Single submitter ALG3-congenital disorder of glycosylation
  • p.Phe183= Single submitter ALG3-congenital disorder of glycosylation
  • p.Phe214= Single submitter ALG3-congenital disorder of glycosylation
  • p.Pro248= Single submitter ALG3-congenital disorder of glycosylation
  • p.Pro335= Single submitter ALG3-congenital disorder of glycosylation
  • p.Pro376= Single submitter
  • p.Ser11= Single submitter ALG3-congenital disorder of glycosylation
  • p.Ser315= Single submitter ALG3-congenital disorder of glycosylation
  • p.Ser405= Single submitter ALG3-congenital disorder of glycosylation
  • p.Thr273= Single submitter ALG3-congenital disorder of glycosylation
  • p.Val211= Single submitter ALG3-congenital disorder of glycosylation
  • c.1154+5C>T No assertion criteria ALG3-related disorder
  • c.*5C>T No assertion criteria ALG3-related disorder
  • p.Gln5= No assertion criteria ALG3-related disorder
  • p.Glu18= No assertion criteria ALG3-related disorder
  • p.His62= No assertion criteria ALG3-related disorder
  • p.Val180= No assertion criteria ALG3-related disorder

Uncertain significance 116