Sugi Variant

Sugi Variant/GATA3

GATA3 — 499 ClinVar variants

All ClinVar germline GATA3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 168 flagged for review →

61 Pathogenic · 6 Pathogenic/Likely pathogenic · 36 Likely pathogenic · 18 Conflicting · 46 Benign · 14 Benign/Likely benign · 114 Likely benign · 204 Uncertain significance

Full GATA3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 168

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 9

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 110

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

Predictors split 48

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

All GATA3 variants

Pathogenic 61

  • c.1050+2T>C Multiple submitters hypoparathyroidism-deafness-renal disease syndrome
  • c.925-3_925-2del Multiple submitters hypoparathyroidism-deafness-renal disease syndrome
  • p.Ala136fs Multiple submitters hypoparathyroidism-deafness-renal disease syndrome
  • p.Arg306Ter Multiple submitters hypoparathyroidism-deafness-renal disease syndrome
  • p.Arg367Ter Multiple submitters GATA3-related disorder
  • p.Gly144fs Multiple submitters hypoparathyroidism-deafness-renal disease syndrome
  • p.Pro135fs Multiple submitters hypoparathyroidism-deafness-renal disease syndrome
  • p.Ser237fs Multiple submitters
  • c.1051-1G>C Single submitter end stage renal failure
  • c.778+1G>A Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • c.779-1G>C Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • p.Asp192fs Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • p.Cys264Ser Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • p.Cys321Ser Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • p.Gln7fs Single submitter
  • p.Glu263Ter Single submitter
  • p.Gly128fs Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • p.Gly203fs Single submitter
  • p.Gly232fs Single submitter
  • p.Gly279fs Single submitter
  • p.Gly281fs Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • p.His216fs Single submitter
  • p.Leu130fs Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • p.Leu190fs Single submitter
  • p.Leu196fs Single submitter Inborn genetic diseases
  • p.Leu344fs Single submitter
  • p.Leu50fs Single submitter
  • p.Leu94fs Single submitter
  • p.Phe151fs Single submitter
  • p.Pro29fs Single submitter
  • p.Pro87fs Single submitter
  • p.Ser110fs Single submitter
  • p.Ser142Ter Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • p.Ser172Ter Single submitter
  • p.Ser213Ter Single submitter
  • p.Thr245fs Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • p.Thr259fs Single submitter
  • p.Trp112Ter Single submitter
  • p.Trp275Ter Single submitter
  • p.Tyr133Ter Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • p.Tyr225Ter Single submitter Monogenic hearing loss
  • p.Tyr283Ter Single submitter
  • p.Tyr345Ter Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • p.Val132fs Single submitter Deafness, autosomal dominant
  • p.Val226fs Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • c.924+2delinsGCTTACTTCCC No assertion criteria hypoparathyroidism-deafness-renal disease syndrome
  • p.Ala109fs No assertion criteria hypoparathyroidism-deafness-renal disease syndrome
  • p.Arg353fs No assertion criteria hypoparathyroidism-deafness-renal disease syndrome
  • p.Arg353Ser No assertion criteria hypoparathyroidism-deafness-renal disease syndrome
  • p.Asp160fs No assertion criteria hypoparathyroidism-deafness-renal disease syndrome
  • p.Cys288Trp No assertion criteria hypoparathyroidism-deafness-renal disease syndrome
  • p.Cys318fs No assertion criteria hypoparathyroidism-deafness-renal disease syndrome
  • p.Cys342Tyr No assertion criteria hypoparathyroidism-deafness-renal disease syndrome
  • p.Glu228fs No assertion criteria hypoparathyroidism-deafness-renal disease syndrome
  • p.Leu301fs No assertion criteria hypoparathyroidism-deafness-renal disease syndrome
  • p.Met36fs No assertion criteria hypoparathyroidism-deafness-renal disease syndrome
  • p.Ser118fs No assertion criteria hypoparathyroidism-deafness-renal disease syndrome
  • p.Thr156fs No assertion criteria hypoparathyroidism-deafness-renal disease syndrome
  • p.Thr316_Ala319del No assertion criteria hypoparathyroidism-deafness-renal disease syndrome
  • p.Trp275Arg No assertion criteria hypoparathyroidism-deafness-renal disease syndrome
  • p.Tyr291fs No assertion criteria hypoparathyroidism-deafness-renal disease syndrome

Pathogenic/Likely pathogenic 6

  • c.924+1G>A Multiple submitters hypoparathyroidism-deafness-renal disease syndrome
  • p.Arg276Gln Multiple submitters GATA3-related disorder
  • p.Arg299Gln Multiple submitters hypoparathyroidism-deafness-renal disease syndrome
  • p.His145fs Multiple submitters hypoparathyroidism-deafness-renal disease syndrome
  • p.Met401fs Multiple submitters hypoparathyroidism-deafness-renal disease syndrome
  • p.Thr272Ile Multiple submitters Monogenic hearing loss

Likely pathogenic 36

  • p.Arg299Trp Multiple submitters Inborn genetic diseases
  • p.Ser166Ter Multiple submitters GATA3-related disorder
  • c.242-1G>C Single submitter
  • c.778+1_778+5del Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • c.778+1_778+7del Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • c.925-1G>A Single submitter
  • p.Ala176fs Single submitter GATA3-related disorder
  • p.Arg256fs Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • p.Arg276Trp Single submitter
  • p.Arg353Thr Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • p.Arg399fs Single submitter
  • p.Asn320Ser Single submitter
  • p.Asn52Ter Single submitter hearing loss disorder
  • p.Cys288Ser Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • p.Gln187Ter Single submitter GATA3-related disorder
  • p.Glu46Ter Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • p.Gly248fs Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • p.His149fs Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • p.His380fs Single submitter
  • p.Ile122fs Single submitter
  • p.Leu274Pro Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • p.Leu290Phe Single submitter Monogenic hearing loss
  • p.Leu355_Thr356insTer Single submitter GATA3-related disorder
  • p.Met205fs Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • p.Pro129fs Single submitter
  • p.Pro236fs Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • p.Ser12fs Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • p.Ser175Ter Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • p.Ser214fs Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • p.Trp112fs Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • p.Tyr283fs Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • p.Tyr345Cys Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • p.Tyr345His Single submitter
  • p.Tyr63fs Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • c.1050+2T>A No assertion criteria congenital anomaly of kidney and urinary tract
  • p.Ser32fs No assertion criteria GATA3-related disorder

Conflicting classifications of pathogenicity 18

  • p.Ala287Thr Single submitter hypoparathyroidism-deafness-renal disease syndrome ⚠
  • p.Arg277Ter Single submitter hypoparathyroidism-deafness-renal disease syndrome ⚠
  • p.Arg299Leu Single submitter hypoparathyroidism-deafness-renal disease syndrome ⚠
  • p.Arg330= Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • p.Asp160Glu Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • p.Asp278Asn Single submitter Dominant congenital non-syndromic sensorineural hearing loss ⚠
  • p.Cys264Arg Single submitter ⚠
  • p.Cys85Tyr Single submitter ⚠
  • p.His28Asn Single submitter GATA3-related disorder ⚠
  • p.Leu19= Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • p.Pro163= Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • p.Pro236Ala Single submitter hypoparathyroidism-deafness-renal disease syndrome ⚠
  • p.Pro29Leu Single submitter Inborn genetic diseases ⚠
  • p.Pro354Thr Single submitter hypoparathyroidism-deafness-renal disease syndrome ⚠
  • p.Pro422= Single submitter hypoparathyroidism-deafness-renal disease syndrome
  • p.Ser271Leu Single submitter hypoparathyroidism-deafness-renal disease syndrome ⚠
  • p.Thr120Met Single submitter hypoparathyroidism-deafness-renal disease syndrome ⚠
  • p.Thr421Met Single submitter hypoparathyroidism-deafness-renal disease syndrome ⚠

Benign 46

Benign/Likely benign 14

  • c.1050+19G>A Multiple submitters hypoparathyroidism-deafness-renal disease syndrome
  • c.-359G>A Multiple submitters hypoparathyroidism-deafness-renal disease syndrome
  • c.-48G>T Multiple submitters hypoparathyroidism-deafness-renal disease syndrome
  • c.*265dup Multiple submitters hypoparathyroidism-deafness-renal disease syndrome
  • c.*664C>T Multiple submitters hypoparathyroidism-deafness-renal disease syndrome
  • p.Ala207= Multiple submitters hypoparathyroidism-deafness-renal disease syndrome
  • p.Ala396Thr Multiple submitters hypoparathyroidism-deafness-renal disease syndrome
  • p.Asn393= Multiple submitters hypoparathyroidism-deafness-renal disease syndrome
  • p.Asp160= Multiple submitters hypoparathyroidism-deafness-renal disease syndrome
  • p.Gly246Ala Multiple submitters hypoparathyroidism-deafness-renal disease syndrome
  • p.Leu290= Multiple submitters hypoparathyroidism-deafness-renal disease syndrome
  • p.Ser110= Multiple submitters hypoparathyroidism-deafness-renal disease syndrome
  • p.Thr280= Multiple submitters hypoparathyroidism-deafness-renal disease syndrome
  • p.Val72= Multiple submitters hypoparathyroidism-deafness-renal disease syndrome

Likely benign 114

Uncertain significance 204