Sugi Variant

Sugi Variant/WDFY3

WDFY3 — 1110 ClinVar variants

All ClinVar germline WDFY3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 477 flagged for review →

37 Pathogenic · 8 Pathogenic/Likely pathogenic · 55 Likely pathogenic · 12 Conflicting · 45 Benign · 2 Benign/Likely benign · 157 Likely benign · 794 Uncertain significance

Full WDFY3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 477

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 agree, ClinVar conflicts 5

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

Predicted LoF vs a conflicting call 3

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 396

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 396

Predictors split 71

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

All WDFY3 variants

Pathogenic 37

Pathogenic/Likely pathogenic 8

  • p.Arg1128Ter Multiple submitters microcephaly 18, primary, autosomal dominant
  • p.Arg1865Ter Multiple submitters Inborn genetic diseases
  • p.Arg2428Ter Multiple submitters Inborn genetic diseases
  • p.Arg2673Ter Multiple submitters microcephaly 18, primary, autosomal dominant
  • p.Arg3166Ter Multiple submitters microcephaly 18, primary, autosomal dominant
  • p.Glu281Ter Multiple submitters Neurodevelopmental delay
  • p.Phe2957fs Multiple submitters Neurodevelopmental delay
  • p.Pro820fs Multiple submitters WDFY3-related disorder

Likely pathogenic 55

  • p.Arg2491Ter Multiple submitters
  • p.Arg2823Trp Multiple submitters Neurodevelopmental delay
  • p.Asn250Ser Multiple submitters Neurodevelopmental delay ⚠
  • c.8098-1G>C Single submitter microcephaly 18, primary, autosomal dominant
  • c.8901+1G>A Single submitter microcephaly 18, primary, autosomal dominant
  • c.8902-2A>G Single submitter microcephaly 18, primary, autosomal dominant
  • c.957-2A>G Single submitter microcephaly 18, primary, autosomal dominant
  • c.9726+1del Single submitter Neurodevelopmental delay
  • p.Arg2261Ter Single submitter
  • p.Arg2386Ter Single submitter intellectual disability, autosomal dominant 1
  • p.Arg2697fs Single submitter Autosomal dominant WDFY3-related disorders
  • p.Arg2763Ter Single submitter microcephaly 18, primary, autosomal dominant
  • p.Arg2823Gln Single submitter
  • p.Arg2829fs Single submitter microcephaly 18, primary, autosomal dominant
  • p.Arg491fs Single submitter microcephaly 18, primary, autosomal dominant
  • p.Arg929Ter Single submitter microcephaly 18, primary, autosomal dominant
  • p.Asp2323fs Single submitter microcephaly 18, primary, autosomal dominant
  • p.Asp2578fs Single submitter Autosomal dominant WDFY3-related disorders
  • p.Asp3006fs Single submitter Neurodevelopmental delay
  • p.Asp3238fs Single submitter Neurodevelopmental delay
  • p.Cys314fs Single submitter microcephaly 18, primary, autosomal dominant
  • p.Gln2112Leu Single submitter
  • p.Gln3121Ter Single submitter syndromic intellectual disability
  • p.Gln883Ter Single submitter neurodevelopmental disorder
  • p.Gly2553Arg Single submitter Inborn genetic diseases
  • p.Gly2558Ser Single submitter Neurodevelopmental delay
  • p.Gly2815Val Single submitter prostate cancer
  • p.His1135Tyr Single submitter neurodevelopmental disorder ⚠
  • p.His3309fs Single submitter WDFY3-related disorder
  • p.Ile1351fs Single submitter WDFY3-related disorder
  • p.Ile2955Thr Single submitter
  • p.Ile339fs Single submitter complex neurodevelopmental disorder
  • p.Leu1346Ter Single submitter microcephaly 18, primary, autosomal dominant
  • p.Leu2898fs Single submitter microcephaly 18, primary, autosomal dominant
  • p.Leu470Ter Single submitter microcephaly 18, primary, autosomal dominant
  • p.Lys1705fs Single submitter Macrocephaly
  • p.Lys1981fs Single submitter Autosomal dominant WDFY3-related disorders
  • p.Phe689fs Single submitter microcephaly 18, primary, autosomal dominant
  • p.Pro2626His Single submitter
  • p.Ser1942Leu Single submitter microcephaly 18, primary, autosomal dominant
  • p.Ser2459fs Single submitter Neurodevelopmental delay
  • p.Ser664fs Single submitter Neurodevelopmental delay
  • p.Ser97Ter Single submitter microcephaly 18, primary, autosomal dominant
  • p.Thr1281fs Single submitter
  • p.Thr1977fs Single submitter microcephaly 18, primary, autosomal dominant
  • p.Thr2663fs Single submitter microcephaly 18, primary, autosomal dominant
  • p.Trp1815Ter Single submitter Autosomal dominant WDFY3-related disorders
  • p.Trp2204Arg Single submitter Neurodevelopmental delay
  • p.Trp3437Ter Single submitter WDFY3-related disorder
  • p.Tyr2435Ter Single submitter microcephaly 18, primary, autosomal dominant
  • p.Val1322fs Single submitter WDFY3-related disorder
  • c.6993+2T>C No assertion criteria WDFY3-related disorder
  • p.Arg978Ter No assertion criteria autism spectrum disorder
  • p.Leu557Pro No assertion criteria microcephaly 18, primary, autosomal dominant
  • p.Ser423Ter No assertion criteria

Conflicting classifications of pathogenicity 12

Benign 45

Benign/Likely benign 2

  • c.3487+8dup Multiple submitters microcephaly 18, primary, autosomal dominant
  • p.His2230= Multiple submitters

Likely benign 157

Uncertain significance 794

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