WAC — 416 ClinVar variants

All ClinVar germline WAC variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 141 flagged for review →

80 Pathogenic · 6 Pathogenic/Likely pathogenic · 32 Likely pathogenic · 11 Conflicting · 40 Benign · 4 Benign/Likely benign · 83 Likely benign · 160 Uncertain significance

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

⚑ Evidence disagreements 141

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 7

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

Predicted LoF vs a conflicting call 1

ClinVar submitters conflict, and it's a predicted loss-of-function change in a gene where LoF causes disease — flagged for review, not resolved (verify NMD-escape for C-terminal truncations). Non-missense.

Predictors lean, ClinVar uncertain 103

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

Predictors split 30

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

All WAC variants

Pathogenic 80

  • c.1746+2T>C Multiple submitters Neurodevelopmental delay
  • p.Arg151Ter Multiple submitters DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Arg47Ter Multiple submitters DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Arg513Ter Multiple submitters DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Arg550Ter Multiple submitters Inborn genetic diseases
  • p.Arg85fs Multiple submitters Paediatric disorders
  • p.Asn387fs Multiple submitters
  • p.Gln170Ter Multiple submitters WAC-related neurodevelopmental disorder
  • p.Gln193Ter Multiple submitters DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Glu88fs Multiple submitters Inborn genetic diseases
  • p.His104fs Multiple submitters DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Ser110Ter Multiple submitters DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Thr224fs Multiple submitters DeSanto-Shinawi syndrome due to WAC point mutation
  • c.1165+2T>C Single submitter
  • c.1438-1G>T Single submitter
  • c.1556+1G>A Single submitter
  • c.1747-1G>A Single submitter
  • c.382-2A>G Single submitter
  • c.498-2A>G Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Ala285fs Single submitter
  • p.Arg10fs Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Arg305fs Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Arg622fs Single submitter
  • p.Arg89fs Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Asn461fs Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Asp126fs Single submitter Inborn genetic diseases
  • p.Asp502Ter Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Gln156fs Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Gln156Ter Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Gln350Ter Single submitter DeSanto-Shinawi syndrome
  • p.Gln358fs Single submitter
  • p.Gln358Ter Single submitter
  • p.Gln435Ter Single submitter
  • p.Gln492fs Single submitter WAC-related disorder
  • p.Gln492Ter Single submitter
  • p.Gln545fs Single submitter DeSanto-Shinawi syndrome
  • p.Gln545Ter Single submitter
  • p.Gln9Ter Single submitter
  • p.Glu162fs Single submitter neurodevelopmental disorder
  • p.His102fs Single submitter Inborn genetic diseases
  • p.His570fs Single submitter
  • p.His597fs Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.His84fs Single submitter
  • p.Ile220fs Single submitter
  • p.Ile469fs Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Ile568fs Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Leu419fs Single submitter
  • p.Lys161fs Single submitter
  • p.Lys290fs Single submitter
  • p.Lys68fs Single submitter
  • p.Pro264fs Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Pro332fs Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Pro368fs Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Pro52fs Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Ser105fs Single submitter
  • p.Ser118fs Single submitter
  • p.Ser125Ter Single submitter Inborn genetic diseases
  • p.Ser198fs Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Ser286fs Single submitter
  • p.Ser316Ter Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Ser38fs Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Ser412fs Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Ser446_Pro447insAsnIleTer Single submitter
  • p.Ser481Ter Single submitter Paediatric disorders
  • p.Ser523fs Single submitter
  • p.Ser551fs Single submitter WAC-related disorder
  • p.Ser584Ter Single submitter Inborn genetic diseases
  • p.Ser76fs Single submitter
  • p.Thr391fs Single submitter
  • p.Trp135Ter Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Tyr148Ter Single submitter
  • p.Tyr95Ter Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Val298fs Single submitter
  • p.Val612fs Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Val86fs Single submitter
  • c.1557-184_1747-188del No assertion criteria DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Asp90fs No assertion criteria DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Gln618Ter No assertion criteria DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Trp574Ter No assertion criteria DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Tyr69Ter No assertion criteria DeSanto-Shinawi syndrome due to WAC point mutation

Pathogenic/Likely pathogenic 6

  • c.1437+1G>A Multiple submitters Shwachman-Diamond syndrome
  • p.Arg613Ter Multiple submitters Neurodevelopmental abnormality
  • p.Arg622Ter Multiple submitters DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Gln400Ter Multiple submitters
  • p.Ser101Ter Multiple submitters DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Ser449Ter Multiple submitters DeSanto-Shinawi syndrome due to WAC point mutation

Likely pathogenic 32

  • c.381+1G>T Multiple submitters DeSanto-Shinawi syndrome due to WAC point mutation
  • c.1556+2T>G Single submitter
  • c.1746+1G>A Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • c.1747-2A>G Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • c.275-1G>A Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • c.497+2T>G Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • c.610+2T>G Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Ala201fs Single submitter WAC-related disorder
  • p.Arg169fs Single submitter neurodevelopmental disorder
  • p.Arg47fs Single submitter WAC-related disorder
  • p.Asp186fs Single submitter
  • p.Gln23Ter Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Gln271Ter Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Gln504Ter Single submitter WAC-related disorder
  • p.Glu158fs Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Gly91fs Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.His530fs Single submitter
  • p.Ile420fs Single submitter WAC-related disorder
  • p.Met58fs Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Pro36fs Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Pro512fs Single submitter WAC-related disorder
  • p.Ser279Ter Single submitter WAC-related disorder
  • p.Ser427fs Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Ser470fs Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Ser493fs Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Thr333fs Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Thr417fs Single submitter WAC-related disorder
  • p.Thr482fs Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Tyr147fs Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Tyr450fs Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Tyr450Ter Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Asn607fs No assertion criteria

Conflicting classifications of pathogenicity 11

  • c.274+3G>A Single submitter Inborn genetic diseases
  • c.381+4_381+7del Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Arg47Gln Single submitter DeSanto-Shinawi syndrome due to WAC point mutation ⚠
  • p.Asn434Ser Single submitter Inborn genetic diseases ⚠
  • p.Gln487Pro Single submitter Inborn genetic diseases ⚠
  • p.Gln624Ter Single submitter DeSanto-Shinawi syndrome due to WAC point mutation ⚠
  • p.Pro557Ala Single submitter Inborn genetic diseases ⚠
  • p.Thr482Ala Single submitter DeSanto-Shinawi syndrome due to WAC point mutation ⚠
  • p.Val154Ile Single submitter DeSanto-Shinawi syndrome due to WAC point mutation
  • p.Val381Met Single submitter Inborn genetic diseases ⚠
  • p.Val542Ile Single submitter Inborn genetic diseases ⚠

Benign 40

Benign/Likely benign 4

Likely benign 83

Uncertain significance 160