Sugi Variant

Sugi Variant/CFAP53

CFAP53 — 160 ClinVar variants

All ClinVar germline CFAP53 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 105 flagged for review →

3 Pathogenic · 9 Likely pathogenic · 4 Conflicting · 9 Benign · 5 Benign/Likely benign · 33 Likely benign · 97 Uncertain significance

Full CFAP53 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 105

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 41

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

Predictors split 63

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

All CFAP53 variants

Pathogenic 3

  • c.778-2A>T Single submitter
  • p.Met335fs Single submitter heterotaxy, visceral, 6, autosomal
  • p.Arg41Ter No assertion criteria heterotaxy, visceral, 6, autosomal

Likely pathogenic 9

  • c.1213+1G>A Single submitter heterotaxy, visceral, 6, autosomal
  • c.1214-1G>A Single submitter heterotaxy, visceral, 6, autosomal
  • c.474-2A>G Single submitter heterotaxy, visceral, 6, autosomal
  • c.996+1G>C Single submitter heterotaxy, visceral, 6, autosomal
  • p.Gln293Ter Single submitter heterotaxy, visceral, 6, autosomal
  • p.Glu382Ter Single submitter heterotaxy, visceral, 6, autosomal
  • c.301_473+1del No assertion criteria dextrocardia
  • p.Glu96fs No assertion criteria CFAP53-related disorder
  • p.Val259= No assertion criteria Heterotaxy

Conflicting classifications of pathogenicity 4

Benign 9

  • c.474-18T>C Multiple submitters heterotaxy, visceral, 6, autosomal
  • c.778-12A>T Multiple submitters heterotaxy, visceral, 6, autosomal
  • p.Arg231Cys Multiple submitters heterotaxy, visceral, 6, autosomal ⚠
  • p.Arg304Gly Multiple submitters heterotaxy, visceral, 6, autosomal ⚠
  • p.Asn263= Multiple submitters heterotaxy, visceral, 6, autosomal
  • p.Glu294Lys Multiple submitters heterotaxy, visceral, 6, autosomal ⚠
  • p.Ile266= Multiple submitters heterotaxy, visceral, 6, autosomal
  • p.Leu313= Multiple submitters heterotaxy, visceral, 6, autosomal
  • p.Trp205Cys Multiple submitters heterotaxy, visceral, 6, autosomal ⚠

Benign/Likely benign 5

  • p.Arg102His Multiple submitters heterotaxy, visceral, 6, autosomal ⚠
  • p.Arg165His Multiple submitters heterotaxy, visceral, 6, autosomal ⚠
  • p.Arg39= Multiple submitters heterotaxy, visceral, 6, autosomal
  • p.Gln315= Multiple submitters heterotaxy, visceral, 6, autosomal
  • p.Lys19= Multiple submitters heterotaxy, visceral, 6, autosomal

Likely benign 33

  • p.Glu269= Multiple submitters
  • c.1213+13A>T Single submitter heterotaxy, visceral, 6, autosomal
  • c.1213+17C>A Single submitter heterotaxy, visceral, 6, autosomal
  • c.1213+18A>G Single submitter heterotaxy, visceral, 6, autosomal
  • c.1214-4T>G Single submitter
  • c.1316+20A>G Single submitter heterotaxy, visceral, 6, autosomal
  • c.299+11C>G Single submitter heterotaxy, visceral, 6, autosomal
  • c.300-4T>A Single submitter heterotaxy, visceral, 6, autosomal
  • c.474-6T>C Single submitter heterotaxy, visceral, 6, autosomal
  • c.69+9A>G Single submitter heterotaxy, visceral, 6, autosomal
  • p.Ala507= Single submitter heterotaxy, visceral, 6, autosomal
  • p.Arg145= Single submitter
  • p.Arg24Ile Single submitter heterotaxy, visceral, 6, autosomal
  • p.Arg42Cys Single submitter heterotaxy, visceral, 6, autosomal ⚠
  • p.Arg5= Single submitter
  • p.Asp305= Single submitter heterotaxy, visceral, 6, autosomal
  • p.Gln31= Single submitter
  • p.Gln319= Single submitter heterotaxy, visceral, 6, autosomal
  • p.Glu189= Single submitter heterotaxy, visceral, 6, autosomal
  • p.Glu353= Single submitter heterotaxy, visceral, 6, autosomal
  • p.Glu65Gly Single submitter heterotaxy, visceral, 6, autosomal ⚠
  • p.Gly89= Single submitter
  • p.His268= Single submitter heterotaxy, visceral, 6, autosomal
  • p.Leu292= Single submitter
  • p.Leu37= Single submitter heterotaxy, visceral, 6, autosomal
  • p.Leu372= Single submitter heterotaxy, visceral, 6, autosomal
  • p.Lys203Arg Single submitter Inborn genetic diseases
  • p.Lys281= Single submitter heterotaxy, visceral, 6, autosomal
  • p.Lys331= Single submitter heterotaxy, visceral, 6, autosomal
  • p.Lys375= Single submitter heterotaxy, visceral, 6, autosomal
  • p.Ser57Asn Single submitter Inborn genetic diseases
  • p.Val166= Single submitter heterotaxy, visceral, 6, autosomal
  • c.*4C>T No assertion criteria CFAP53-related disorder

Uncertain significance 97