Sugi Variant

Sugi Variant/ATP1A3

ATP1A3 — 1327 ClinVar variants

All ClinVar germline ATP1A3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 460 flagged for review →

70 Pathogenic · 23 Pathogenic/Likely pathogenic · 79 Likely pathogenic · 66 Conflicting · 41 Benign · 36 Benign/Likely benign · 505 Likely benign · 507 Uncertain significance

Full ATP1A3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 460

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 21

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

Predicted LoF vs a conflicting call 7

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 255

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 255

Predictors split 176

The independent predictors disagree with each other — read with care. · showing the 150 best-reviewed of 176

All ATP1A3 variants

Pathogenic 70

Pathogenic/Likely pathogenic 23

  • p.Ala320Pro Multiple submitters dystonia 12
  • p.Arg756Cys Multiple submitters alternating hemiplegia of childhood 2
  • p.Arg756His Multiple submitters developmental and epileptic encephalopathy 99
  • p.Asp609Tyr Multiple submitters alternating hemiplegia of childhood 2
  • p.Asp742Tyr Multiple submitters dystonia 12
  • p.Glu277Lys Multiple submitters dystonia 12
  • p.Glu324Gly Multiple submitters cerebellar ataxia-areflexia-pes cavus-optic atrophy-sensorineural hearing loss syndrome
  • p.Gly325Asp Multiple submitters cerebellar ataxia-areflexia-pes cavus-optic atrophy-sensorineural hearing loss syndrome
  • p.Gly803Asp Multiple submitters dystonia 12
  • p.Gly89Ala Multiple submitters dystonia 12
  • p.Gly947Trp Multiple submitters cerebellar ataxia-areflexia-pes cavus-optic atrophy-sensorineural hearing loss syndrome
  • p.Ile318Met Multiple submitters alternating hemiplegia of childhood 2
  • p.Ile777Asn Multiple submitters ATP1A3-associated neurological disorder
  • p.Leu326Arg Multiple submitters dystonia 12
  • p.Leu715Pro Multiple submitters developmental and epileptic encephalopathy 99
  • p.Pro323Ser Multiple submitters cerebellar ataxia-areflexia-pes cavus-optic atrophy-sensorineural hearing loss syndrome
  • p.Pro775Leu Multiple submitters Inborn genetic diseases
  • p.Pro808Leu Multiple submitters dystonia 12
  • p.Ser137del Multiple submitters ATP1A3-associated neurological disorder
  • p.Ser772Asn Multiple submitters dystonia 12
  • p.Thr360Arg Multiple submitters dystonia 12
  • p.Val129Met Multiple submitters Juvenile onset psychosis
  • p.Val919del Multiple submitters developmental and epileptic encephalopathy 99

Likely pathogenic 79

Conflicting classifications of pathogenicity 66

Benign 41

Benign/Likely benign 36

  • c.1192+3G>A Multiple submitters alternating hemiplegia of childhood 2
  • c.1192+6C>T Multiple submitters developmental and epileptic encephalopathy 99
  • c.1193-4C>G Multiple submitters developmental and epileptic encephalopathy 99
  • c.154-5C>G Multiple submitters developmental and epileptic encephalopathy 99
  • c.1943+12A>T Multiple submitters developmental and epileptic encephalopathy 99
  • c.2419-6G>A Multiple submitters dystonia 12
  • c.2419-7C>T Multiple submitters alternating hemiplegia of childhood 2
  • c.6+3A>G Multiple submitters Inborn genetic diseases
  • c.994-4C>G Multiple submitters developmental and epileptic encephalopathy 99
  • c.*106T>C Multiple submitters developmental and epileptic encephalopathy 99
  • c.*315G>A Multiple submitters alternating hemiplegia of childhood 2
  • p.Ala635= Multiple submitters developmental and epileptic encephalopathy 99
  • p.Ala69= Multiple submitters alternating hemiplegia of childhood 2
  • p.Ala813= Multiple submitters dystonia 12
  • p.Arg64= Multiple submitters cerebellar ataxia-areflexia-pes cavus-optic atrophy-sensorineural hearing loss syndrome
  • p.Asn119= Multiple submitters alternating hemiplegia of childhood 2
  • p.Asp565= Multiple submitters alternating hemiplegia of childhood 2
  • p.Asp742= Multiple submitters dystonia 12
  • p.Asp992= Multiple submitters dystonia 12
  • p.Ile96= Multiple submitters cerebellar ataxia-areflexia-pes cavus-optic atrophy-sensorineural hearing loss syndrome
  • p.Leu303= Multiple submitters developmental and epileptic encephalopathy 99
  • p.Leu853= Multiple submitters alternating hemiplegia of childhood 2
  • p.Phe946= Multiple submitters developmental and epileptic encephalopathy 99
  • p.Pro789= Multiple submitters alternating hemiplegia of childhood 2
  • p.Pro962= Multiple submitters dystonia 12
  • p.Ser509= Multiple submitters developmental and epileptic encephalopathy 99
  • p.Thr222= Multiple submitters dystonia 12
  • p.Thr262= Multiple submitters alternating hemiplegia of childhood 2
  • p.Thr272= Multiple submitters alternating hemiplegia of childhood 2
  • p.Thr360= Multiple submitters alternating hemiplegia of childhood 2
  • p.Thr377= Multiple submitters developmental and epileptic encephalopathy 99
  • p.Thr658= Multiple submitters alternating hemiplegia of childhood 2
  • p.Thr778= Multiple submitters cerebellar ataxia-areflexia-pes cavus-optic atrophy-sensorineural hearing loss syndrome
  • p.Tyr121= Multiple submitters alternating hemiplegia of childhood 2
  • p.Val247= Multiple submitters alternating hemiplegia of childhood 2
  • p.Val378= Multiple submitters alternating hemiplegia of childhood 2

Likely benign 505

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

Uncertain significance 507

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