Sugi Variant

Sugi Variant/ATP2B1

ATP2B1 — 282 ClinVar variants

All ClinVar germline ATP2B1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 194 flagged for review →

16 Pathogenic · 1 Pathogenic/Likely pathogenic · 32 Likely pathogenic · 4 Conflicting · 5 Benign · 15 Likely benign · 209 Uncertain significance

Full ATP2B1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 194

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 3

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 147

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

Predictors split 42

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

All ATP2B1 variants

Pathogenic 16

Pathogenic/Likely pathogenic 1

  • p.Arg597Ter Multiple submitters neurodevelopmental disorder

Likely pathogenic 32

  • c.1130-2A>C Single submitter intellectual developmental disorder, autosomal dominant 66
  • c.1829+1G>A Single submitter
  • c.209-2A>G Single submitter
  • c.3060+2T>G Single submitter periventricular nodular heterotopia
  • c.406+1G>A Single submitter intellectual developmental disorder, autosomal dominant 66
  • c.661+2dup Single submitter
  • p.Ala1072Val Single submitter intellectual developmental disorder, autosomal dominant 66 ⚠
  • p.Ala330Pro Single submitter ATP2B1-related disorder ⚠
  • p.Ala438fs Single submitter
  • p.Ala841fs Single submitter intellectual developmental disorder, autosomal dominant 66
  • p.Asp239Gly Single submitter neurodevelopmental disorder
  • p.Glu824Lys Single submitter neurodevelopmental disorder
  • p.Glu987Ter Single submitter intellectual developmental disorder, autosomal dominant 30, with speech delay and behavioral abnormalities
  • p.Gly1073fs Single submitter intellectual developmental disorder, autosomal dominant 66
  • p.His459Arg Single submitter intellectual developmental disorder, autosomal dominant 66
  • p.Ile1021Thr Single submitter Inborn genetic diseases
  • p.Ile829del Single submitter ATP2B1-related disorder
  • p.Leu892_Ile893insTer Single submitter intellectual developmental disorder, autosomal dominant 66
  • p.Lys574fs Single submitter
  • p.Lys952fs Single submitter intellectual developmental disorder, autosomal dominant 66
  • p.Phe126fs Single submitter intellectual developmental disorder, autosomal dominant 66
  • p.Ser1034Ter Single submitter intellectual developmental disorder, autosomal dominant 66
  • p.Ser1037Ter Single submitter neurodevelopmental disorder
  • p.Ser837fs Single submitter intellectual developmental disorder, autosomal dominant 66
  • p.Thr264Ile Single submitter neurodevelopmental disorder
  • p.Thr425Lys Single submitter neurodevelopmental disorder
  • p.Thr675fs Single submitter
  • p.Thr714Pro Single submitter intellectual developmental disorder, autosomal dominant 66
  • p.Trp153Ter Single submitter neurodevelopmental disorder
  • p.Tyr917fs Single submitter intellectual developmental disorder, autosomal dominant 66
  • p.Val636fs Single submitter intellectual developmental disorder, autosomal dominant 66
  • p.Ser853Ter No assertion criteria autism

Conflicting classifications of pathogenicity 4

  • p.Arg789Cys Single submitter intellectual developmental disorder, autosomal dominant 66 ⚠
  • p.Arg846Ter Single submitter ATP2B1-related disorder ⚠
  • p.Arg991Gln Single submitter intellectual developmental disorder, autosomal dominant 66 ⚠
  • p.Val980Leu Single submitter isolated Pierre-Robin syndrome ⚠

Benign 5

Likely benign 15

Uncertain significance 209