Sugi Variant

Sugi Variant/ATP7A

ATP7A — 2221 ClinVar variants

All ClinVar germline ATP7A variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 857 flagged for review →

128 Pathogenic · 11 Pathogenic/Likely pathogenic · 116 Likely pathogenic · 174 Conflicting · 86 Benign · 48 Benign/Likely benign · 806 Likely benign · 852 Uncertain significance

Full ATP7A gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 857

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 3

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

Predictors agree, ClinVar conflicts 107

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

Predicted LoF vs a conflicting call 4

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 525

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 525

Predictors split 218

The independent predictors disagree with each other — read with care. · showing the 150 best-reviewed of 218

All ATP7A variants

Pathogenic 128

Pathogenic/Likely pathogenic 11

Likely pathogenic 116

Conflicting classifications of pathogenicity 174

Benign 86

Benign/Likely benign 48

  • c.1947-3A>G Multiple submitters X-linked distal spinal muscular atrophy type 3
  • c.2406+20C>T Multiple submitters Menkes disease
  • c.2407-14G>T Multiple submitters Menkes disease
  • c.3801+6T>C Multiple submitters Inborn genetic diseases
  • c.4226+11T>C Multiple submitters Inborn genetic diseases
  • c.610+19A>G Multiple submitters Menkes disease
  • p.Ala1145Val Multiple submitters Inborn genetic diseases
  • p.Ala159Thr Multiple submitters Inborn genetic diseases
  • p.Ala337Thr Multiple submitters Menkes disease
  • p.Ala94= Multiple submitters occipital horn syndrome
  • p.Arg1295Trp Multiple submitters Inborn genetic diseases ⚠
  • p.Arg1423= Multiple submitters History of neurodevelopmental disorder
  • p.Arg590= Multiple submitters Menkes disease
  • p.Arg590Gly Multiple submitters Inborn genetic diseases
  • p.Arg844Cys Multiple submitters Inborn genetic diseases ⚠
  • p.Asn1197Asp Multiple submitters Inborn genetic diseases
  • p.Asp747= Multiple submitters occipital horn syndrome
  • p.Cys288= Multiple submitters Ehlers-Danlos syndrome
  • p.Cys903= Multiple submitters Inborn genetic diseases
  • p.Gln104= Multiple submitters Ehlers-Danlos syndrome
  • p.Gln704Arg Multiple submitters occipital horn syndrome
  • p.Glu1205Gln Multiple submitters Inborn genetic diseases
  • p.Glu1207= Multiple submitters Menkes disease
  • p.Glu840Val Multiple submitters occipital horn syndrome
  • p.Gly70Asp Multiple submitters X-linked distal spinal muscular atrophy type 3
  • p.His1051= Multiple submitters Menkes disease
  • p.His1070= Multiple submitters Inborn genetic diseases
  • p.Ile1150Thr Multiple submitters Menkes disease
  • p.Ile1464Val Multiple submitters Inborn genetic diseases
  • p.Ile189Val Multiple submitters Inborn genetic diseases ⚠
  • p.Leu1032= Multiple submitters Menkes disease
  • p.Leu1402= Multiple submitters Menkes disease
  • p.Lys109= Multiple submitters Ehlers-Danlos syndrome
  • p.Lys644Arg Multiple submitters intellectual disability
  • p.Pro539Thr Multiple submitters Menkes disease ⚠
  • p.Pro59= Multiple submitters Ehlers-Danlos syndrome
  • p.Pro80Leu Multiple submitters Ehlers-Danlos syndrome
  • p.Ser1160= Multiple submitters Ehlers-Danlos syndrome
  • p.Ser1463= Multiple submitters Inborn genetic diseases
  • p.Ser164Asn Multiple submitters Inborn genetic diseases
  • p.Thr1414Ile Multiple submitters Menkes disease
  • p.Thr818Ala Multiple submitters Inborn genetic diseases ⚠
  • p.Tyr215= Multiple submitters Menkes disease
  • p.Tyr608Cys Multiple submitters Inborn genetic diseases
  • p.Val1401Leu Multiple submitters occipital horn syndrome ⚠
  • p.Val579= Multiple submitters Ehlers-Danlos syndrome
  • p.Val767Leu Multiple submitters Inborn genetic diseases
  • p.Val869= Multiple submitters Menkes disease

Likely benign 806

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

Uncertain significance 852

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