Sugi Variant

Sugi Variant/GRIN2A

GRIN2A — 2347 ClinVar variants

All ClinVar germline GRIN2A variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 957 flagged for review →

115 Pathogenic · 46 Pathogenic/Likely pathogenic · 140 Likely pathogenic · 198 Conflicting · 141 Benign · 44 Benign/Likely benign · 691 Likely benign · 972 Uncertain significance

Full GRIN2A gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 957

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 8

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

Predictors agree, ClinVar conflicts 135

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

Predicted LoF vs a conflicting call 5

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 638

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 638

Predictors split 171

The independent predictors disagree with each other — read with care. · showing the 150 best-reviewed of 171

All GRIN2A variants

Pathogenic 115

Pathogenic/Likely pathogenic 46

  • c.1007+1G>A Multiple submitters GRIN2A-Related Disorders
  • c.1123-2A>G Multiple submitters Landau-Kleffner syndrome
  • c.1497+1G>T Multiple submitters Landau-Kleffner syndrome
  • c.2168+1G>C Multiple submitters epilepsy
  • c.2346_2356+8del Multiple submitters Landau-Kleffner syndrome
  • p.Ala635Thr Multiple submitters Inborn genetic diseases
  • p.Ala716Thr Multiple submitters Landau-Kleffner syndrome
  • p.Ala727Thr Multiple submitters Landau-Kleffner syndrome
  • p.Ala818Glu Multiple submitters Landau-Kleffner syndrome
  • p.Ala818Val Multiple submitters Landau-Kleffner syndrome
  • p.Arg244fs Multiple submitters Landau-Kleffner syndrome
  • p.Arg518Cys Multiple submitters Landau-Kleffner syndrome
  • p.Arg518His Multiple submitters Landau-Kleffner syndrome
  • p.Arg681Ter Multiple submitters Landau-Kleffner syndrome
  • p.Arg695Gln Multiple submitters neurodevelopmental disorder
  • p.Asn614Ser Multiple submitters GRIN2A-related complex neurodevelopmental disorder
  • p.Asn648Ser Multiple submitters Landau-Kleffner syndrome
  • p.Asp731Asn Multiple submitters Landau-Kleffner syndrome
  • p.Asp776Tyr Multiple submitters Landau-Kleffner syndrome
  • p.Cys436Arg Multiple submitters Landau-Kleffner syndrome
  • p.Gln163Ter Multiple submitters Landau-Kleffner syndrome
  • p.Glu58Ter Multiple submitters Landau-Kleffner syndrome
  • p.Gly483Arg Multiple submitters Landau-Kleffner syndrome
  • p.Gly498Ser Multiple submitters Landau-Kleffner syndrome
  • p.Gly760Ser Multiple submitters Landau-Kleffner syndrome
  • p.Ile654Thr Multiple submitters Landau-Kleffner syndrome ⚠
  • p.Ile694Thr Multiple submitters Landau-Kleffner syndrome
  • p.Leu248fs Multiple submitters Landau-Kleffner syndrome
  • p.Leu611Gln Multiple submitters Landau-Kleffner syndrome
  • p.Leu649Val Multiple submitters Landau-Kleffner syndrome
  • p.Leu812Met Multiple submitters Landau-Kleffner syndrome
  • p.Lys454fs Multiple submitters Landau-Kleffner syndrome
  • p.Met1Thr Multiple submitters Landau-Kleffner syndrome
  • p.Met817Arg Multiple submitters Landau-Kleffner syndrome
  • p.Met817Thr Multiple submitters Landau-Kleffner syndrome
  • p.Met817Val Multiple submitters Landau-Kleffner syndrome
  • p.Phe210fs Multiple submitters Landau-Kleffner syndrome
  • p.Ser1341fs Multiple submitters Landau-Kleffner syndrome
  • p.Ser1459Gly Multiple submitters early-onset epileptic encephalopathy and intellectual disability due to GRIN2A mutation ⚠
  • p.Ser511Leu Multiple submitters Landau-Kleffner syndrome
  • p.Ser554Arg Multiple submitters intellectual disability
  • p.Thr513Ile Multiple submitters Landau-Kleffner syndrome
  • p.Thr531Met Multiple submitters GRIN2A-Related Disorders
  • p.Thr690Lys Multiple submitters Landau-Kleffner syndrome
  • p.Trp372Ter Multiple submitters GRIN2A-Related Disorders
  • p.Trp558Ser Multiple submitters Landau-Kleffner syndrome

Likely pathogenic 140

Conflicting classifications of pathogenicity 198

Benign 141

Benign/Likely benign 44

  • c.1122+16T>A Multiple submitters Landau-Kleffner syndrome
  • c.1329-9T>G Multiple submitters Landau-Kleffner syndrome
  • c.1652-13T>C Multiple submitters Landau-Kleffner syndrome
  • c.1652-14C>G Multiple submitters Landau-Kleffner syndrome
  • c.2007+10C>T Multiple submitters Landau-Kleffner syndrome
  • c.2007+15C>T Multiple submitters Landau-Kleffner syndrome
  • c.2007+16T>C Multiple submitters Landau-Kleffner syndrome
  • c.2008-14C>T Multiple submitters Landau-Kleffner syndrome
  • c.-19+8C>T Multiple submitters Landau-Kleffner syndrome
  • c.-34C>A Multiple submitters Landau-Kleffner syndrome
  • p.Arg1022Cys Multiple submitters Landau-Kleffner syndrome
  • p.Arg920= Multiple submitters Landau-Kleffner syndrome
  • p.Asn1041= Multiple submitters Landau-Kleffner syndrome
  • p.Asn1076Lys Multiple submitters Inborn genetic diseases
  • p.Asn75= Multiple submitters Inborn genetic diseases
  • p.Asp102= Multiple submitters Landau-Kleffner syndrome
  • p.Asp294= Multiple submitters Landau-Kleffner syndrome
  • p.Gln1265His Multiple submitters Landau-Kleffner syndrome
  • p.Glu1156Asp Multiple submitters Landau-Kleffner syndrome
  • p.Gly1197= Multiple submitters Landau-Kleffner syndrome
  • p.Gly951Val Multiple submitters Landau-Kleffner syndrome
  • p.His223= Multiple submitters Inborn genetic diseases
  • p.His381Tyr Multiple submitters Inborn genetic diseases
  • p.Ile313= Multiple submitters Inborn genetic diseases
  • p.Ile750= Multiple submitters Inborn genetic diseases
  • p.Ile876Asn Multiple submitters Landau-Kleffner syndrome ⚠
  • p.Leu898= Multiple submitters Inborn genetic diseases
  • p.Lys221Arg Multiple submitters Inborn genetic diseases
  • p.Pro273= Multiple submitters Landau-Kleffner syndrome
  • p.Pro314= Multiple submitters Landau-Kleffner syndrome
  • p.Pro336Ser Multiple submitters Landau-Kleffner syndrome
  • p.Ser1198= Multiple submitters Landau-Kleffner syndrome
  • p.Thr1064= Multiple submitters Landau-Kleffner syndrome
  • p.Thr1064Ala Multiple submitters Inborn genetic diseases
  • p.Thr1082= Multiple submitters Inborn genetic diseases
  • p.Thr141Met Multiple submitters Inborn genetic diseases
  • p.Thr300= Multiple submitters Inborn genetic diseases
  • p.Thr301= Multiple submitters Inborn genetic diseases
  • p.Thr543= Multiple submitters Landau-Kleffner syndrome
  • p.Thr759= Multiple submitters Landau-Kleffner syndrome
  • p.Tyr321= Multiple submitters Inborn genetic diseases
  • p.Tyr730= Multiple submitters Inborn genetic diseases
  • p.Val417= Multiple submitters Inborn genetic diseases
  • p.Val967Leu Multiple submitters Inborn genetic diseases

Likely benign 691

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

Uncertain significance 972

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