Sugi Variant

Sugi Variant/GATA6

GATA6 — 760 ClinVar variants

All ClinVar germline GATA6 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 384 flagged for review →

36 Pathogenic · 1 Pathogenic/Likely pathogenic · 23 Likely pathogenic · 22 Conflicting · 8 Benign · 15 Benign/Likely benign · 216 Likely benign · 439 Uncertain significance

Full GATA6 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 384

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 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 283

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 283

Predictors split 90

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

All GATA6 variants

Pathogenic 36

  • p.Arg456Cys Multiple submitters Inborn genetic diseases
  • p.Arg493Ter Multiple submitters atrioventricular septal defect 5
  • c.1136-2A>G Single submitter Autosomal dominant GATA6-related disorders
  • p.Arg456Leu Single submitter pancreatic hypoplasia-diabetes-congenital heart disease syndrome
  • p.Arg479Gly Single submitter
  • p.Cys414Ter Single submitter
  • p.Gln120Ter Single submitter atrioventricular septal defect 5
  • p.Gln149Ter Single submitter pancreatic hypoplasia-diabetes-congenital heart disease syndrome
  • p.Gln206Ter Single submitter atrioventricular septal defect 5
  • p.Gln309fs Single submitter
  • p.Gln363Ter Single submitter pancreatic hypoplasia-diabetes-congenital heart disease syndrome
  • p.Glu355Ter Single submitter Autosomal dominant GATA6-related disorders
  • p.Glu460Ter Single submitter
  • p.Glu486fs Single submitter atrioventricular septal defect 5
  • p.Gly238Ter Single submitter Abnormal cardiovascular system morphology
  • p.Gly244fs Single submitter conotruncal heart malformations
  • p.Gly280Ter Single submitter atrioventricular septal defect 5
  • p.Gly375fs Single submitter pancreatic hypoplasia-diabetes-congenital heart disease syndrome
  • p.Gly441Ter Single submitter atrioventricular septal defect 5
  • p.Leu384fs Single submitter atrioventricular septal defect 5
  • p.Lys473fs Single submitter atrioventricular septal defect 5
  • p.Lys494fs Single submitter
  • p.Lys496Ter Single submitter atrioventricular septal defect 5
  • p.Pro357fs Single submitter
  • p.Pro369fs Single submitter pancreatic hypoplasia-diabetes-congenital heart disease syndrome
  • p.Trp8Ter Single submitter tetralogy of fallot
  • p.Tyr310fs Single submitter Inborn genetic diseases
  • p.Tyr340Ter Single submitter tetralogy of fallot
  • p.Val358fs Single submitter Abnormal cardiovascular system morphology
  • p.Asn466Asp No assertion criteria pancreatic hypoplasia-diabetes-congenital heart disease syndrome
  • p.Asn466His No assertion criteria persistent truncus arteriosus
  • p.Lys500fs No assertion criteria GATA6-related disorder
  • p.Lys502fs No assertion criteria pancreatic hypoplasia-diabetes-congenital heart disease syndrome
  • p.Met483fs No assertion criteria pancreatic hypoplasia-diabetes-congenital heart disease syndrome
  • p.Ser266fs No assertion criteria pancreatic hypoplasia-diabetes-congenital heart disease syndrome
  • p.Thr452Ala No assertion criteria pancreatic hypoplasia-diabetes-congenital heart disease syndrome

Pathogenic/Likely pathogenic 1

  • p.Arg456His Multiple submitters pancreatic hypoplasia-diabetes-congenital heart disease syndrome

Likely pathogenic 23

  • c.1135+2T>C Multiple submitters tetralogy of fallot
  • c.1135+1G>A Single submitter pancreatic hypoplasia-diabetes-congenital heart disease syndrome
  • c.1302+5G>A Single submitter GATA6-related disorders
  • c.1429-2A>G Single submitter atrioventricular septal defect 5
  • c.1620+2T>C Single submitter Inborn genetic diseases
  • p.Arg493fs Single submitter GATA6-related disorders
  • p.Asp231fs Single submitter pancreatic hypoplasia-diabetes-congenital heart disease syndrome
  • p.Cys468Tyr Single submitter
  • p.Gln309Ter Single submitter GATA6-related disorders
  • p.Gly250fs Single submitter GATA6-related disorders
  • p.Gly469Arg Single submitter pancreatic hypoplasia-diabetes-congenital heart disease syndrome
  • p.Gly50Ter Single submitter pancreatic hypoplasia-diabetes-congenital heart disease syndrome
  • p.Leu80fs Single submitter pancreatic hypoplasia-diabetes-congenital heart disease syndrome
  • p.Pro226fs Single submitter GATA6-related disorder
  • p.Pro234fs Single submitter dilated cardiomyopathy
  • p.Ser294Arg Single submitter pancreatic hypoplasia-diabetes-congenital heart disease syndrome
  • p.Ser314Ter Single submitter GATA6-related disorders
  • p.Ser77Ter Single submitter GATA6-related disorders
  • p.Thr453Asn Single submitter neutropenia, severe congenital, 8, autosomal dominant
  • p.Trp401Ter Single submitter GATA6-related disorders
  • p.Val189fs Single submitter GATA6-related congenital heart disease with or without pancreatic hypoplasia or diabetes
  • p.Val372fs Single submitter pancreatic hypoplasia-diabetes-congenital heart disease syndrome
  • p.Ser511Cys No assertion criteria atypical coarctation of aorta ⚠

Conflicting classifications of pathogenicity 22

Benign 8

Benign/Likely benign 15

  • c.1135+9C>G Multiple submitters atrioventricular septal defect 5
  • c.1516+17G>A Multiple submitters atrioventricular septal defect 5
  • c.1516+19C>T Multiple submitters atrioventricular septal defect 5
  • c.1620+6T>C Multiple submitters atrioventricular septal defect 5
  • p.Ala178Val Multiple submitters monogenic diabetes
  • p.Ala284Gly Multiple submitters monogenic diabetes
  • p.Asn458= Multiple submitters Inborn genetic diseases
  • p.Asp524= Multiple submitters atrioventricular septal defect 5
  • p.Glu551= Multiple submitters atrioventricular septal defect 5
  • p.Gly15Arg Multiple submitters monogenic diabetes
  • p.His333del Multiple submitters atrioventricular septal defect 5
  • p.His333dup Multiple submitters atrioventricular septal defect 5
  • p.Pro74= Multiple submitters atrioventricular septal defect 5
  • p.Thr450= Multiple submitters atrioventricular septal defect 5
  • p.Thr534= Multiple submitters atrioventricular septal defect 5

Likely benign 216

  • c.1135+16C>T Multiple submitters atrioventricular septal defect 5
  • c.1516+10C>T Multiple submitters atrioventricular septal defect 5
  • c.1516+20G>A Multiple submitters atrioventricular septal defect 5
  • c.-37-259C>T Multiple submitters
  • c.-37-38G>C Multiple submitters
  • p.Ala124= Multiple submitters atrioventricular septal defect 5
  • p.Ala21Gly Multiple submitters atrioventricular septal defect 5
  • p.Ala256= Multiple submitters atrioventricular septal defect 5
  • p.Ala283= Multiple submitters atrioventricular septal defect 5
  • p.Ala285= Multiple submitters atrioventricular septal defect 5
  • p.Ala315= Multiple submitters atrioventricular septal defect 5
  • p.Asn214= Multiple submitters atrioventricular septal defect 5
  • p.Glu68Val Multiple submitters atrioventricular septal defect 5
  • p.Gly207= Multiple submitters atrioventricular septal defect 5
  • p.Gly224= Multiple submitters atrioventricular septal defect 5
  • p.Gly238= Multiple submitters atrioventricular septal defect 5
  • p.Gly245= Multiple submitters conotruncal heart malformations
  • p.Gly289= Multiple submitters atrioventricular septal defect 5
  • p.Gly61= Multiple submitters atrioventricular septal defect 5
  • p.Leu136= Multiple submitters atrioventricular septal defect 5
  • p.Leu300= Multiple submitters atrioventricular septal defect 5
  • p.Leu79= Multiple submitters atrioventricular septal defect 5
  • p.Pro11= Multiple submitters atrioventricular septal defect 5
  • p.Pro141= Multiple submitters atrioventricular septal defect 5
  • p.Pro159= Multiple submitters atrioventricular septal defect 5
  • p.Pro350= Multiple submitters atrioventricular septal defect 5
  • p.Pro94= Multiple submitters atrioventricular septal defect 5
  • p.Thr67= Multiple submitters atrioventricular septal defect 5
  • p.Val259= Multiple submitters atrioventricular septal defect 5
  • p.Val99= Multiple submitters atrioventricular septal defect 5
  • c.1135+12G>C Single submitter atrioventricular septal defect 5
  • c.1135+14dup Single submitter atrioventricular septal defect 5
  • c.1135+19G>T Single submitter atrioventricular septal defect 5
  • c.1135+7G>A Single submitter atrioventricular septal defect 5
  • c.1135+9C>T Single submitter atrioventricular septal defect 5
  • c.1136-14C>T Single submitter atrioventricular septal defect 5
  • c.1136-19C>A Single submitter atrioventricular septal defect 5
  • c.1136-20_1136-16del Single submitter atrioventricular septal defect 5
  • c.1136-26G>A Single submitter
  • c.1136-296G>T Single submitter
  • c.1302+12C>T Single submitter atrioventricular septal defect 5
  • c.1302+149G>C Single submitter
  • c.1302+14G>A Single submitter atrioventricular septal defect 5
  • c.1302+20_1302+52del Single submitter atrioventricular septal defect 5
  • c.1303-13G>T Single submitter atrioventricular septal defect 5
  • c.1303-19G>A Single submitter atrioventricular septal defect 5
  • c.1303-6T>C Single submitter atrioventricular septal defect 5
  • c.1303-8G>C Single submitter atrioventricular septal defect 5
  • c.1428+10G>A Single submitter atrioventricular septal defect 5
  • c.1428+217C>A Single submitter
  • c.1428+9T>A Single submitter atrioventricular septal defect 5
  • c.1429-111C>T Single submitter
  • c.1429-17A>G Single submitter atrioventricular septal defect 5
  • c.1429-18T>C Single submitter atrioventricular septal defect 5
  • c.1516+15A>G Single submitter atrioventricular septal defect 5
  • c.1516+20G>C Single submitter atrioventricular septal defect 5
  • c.1620+13A>G Single submitter
  • c.1620+18A>T Single submitter atrioventricular septal defect 5
  • c.1620+19T>C Single submitter atrioventricular septal defect 5
  • c.1620+283T>C Single submitter
  • c.1620+7A>T Single submitter atrioventricular septal defect 5
  • c.1621-12C>G Single submitter atrioventricular septal defect 5
  • c.1621-14C>T Single submitter atrioventricular septal defect 5
  • c.1621-15C>T Single submitter atrioventricular septal defect 5
  • c.1621-16C>G Single submitter
  • c.1621-17T>C Single submitter atrioventricular septal defect 5
  • c.1621-20G>T Single submitter atrioventricular septal defect 5
  • c.-19G>A Single submitter
  • c.*41C>T Single submitter
  • p.Ala100= Single submitter atrioventricular septal defect 5
  • p.Ala134= Single submitter
  • p.Ala152= Single submitter
  • p.Ala153= Single submitter atrioventricular septal defect 5
  • p.Ala16= Single submitter atrioventricular septal defect 5
  • p.Ala165= Single submitter atrioventricular septal defect 5
  • p.Ala175= Single submitter atrioventricular septal defect 5
  • p.Ala178= Single submitter atrioventricular septal defect 5
  • p.Ala181= Single submitter atrioventricular septal defect 5
  • p.Ala19= Single submitter atrioventricular septal defect 5
  • p.Ala216= Single submitter atrioventricular septal defect 5
  • p.Ala242= Single submitter atrioventricular septal defect 5
  • p.Ala246= Single submitter atrioventricular septal defect 5
  • p.Ala255= Single submitter atrioventricular septal defect 5
  • p.Ala257= Single submitter atrioventricular septal defect 5
  • p.Ala284= Single submitter atrioventricular septal defect 5
  • p.Ala29= Single submitter atrioventricular septal defect 5
  • p.Ala302= Single submitter atrioventricular septal defect 5
  • p.Ala316= Single submitter atrioventricular septal defect 5
  • p.Ala316Pro Single submitter atrioventricular septal defect 5
  • p.Ala351= Single submitter atrioventricular septal defect 5
  • p.Ala368= Single submitter atrioventricular septal defect 5
  • p.Ala459= Single submitter atrioventricular septal defect 5
  • p.Ala549= Single submitter atrioventricular septal defect 5
  • p.Ala578= Single submitter atrioventricular septal defect 5
  • p.Ala593= Single submitter atrioventricular septal defect 5
  • p.Ala595= Single submitter atrioventricular septal defect 5
  • p.Ala96= Single submitter atrioventricular septal defect 5
  • p.Arg262= Single submitter atrioventricular septal defect 5
  • p.Arg306= Single submitter atrioventricular septal defect 5
  • p.Arg317= Single submitter
  • p.Arg388= Single submitter atrioventricular septal defect 5
  • p.Arg403= Single submitter atrioventricular septal defect 5
  • p.Arg433= Single submitter atrioventricular septal defect 5
  • p.Arg48= Single submitter atrioventricular septal defect 5
  • p.Arg52= Single submitter atrioventricular septal defect 5
  • p.Arg585= Single submitter atrioventricular septal defect 5
  • p.Asn273= Single submitter atrioventricular septal defect 5
  • p.Asn412= Single submitter atrioventricular septal defect 5
  • p.Asn466= Single submitter atrioventricular septal defect 5
  • p.Asp404= Single submitter atrioventricular septal defect 5
  • p.Cys390= Single submitter atrioventricular septal defect 5
  • p.Cys444= Single submitter atrioventricular septal defect 5
  • p.Cys526= Single submitter atrioventricular septal defect 5
  • p.Cys590= Single submitter atrioventricular septal defect 5
  • p.Cys60= Single submitter atrioventricular septal defect 5
  • p.Gln206= Single submitter atrioventricular septal defect 5
  • p.Glu460= Single submitter atrioventricular septal defect 5
  • p.Gly101= Single submitter atrioventricular septal defect 5
  • p.Gly103= Single submitter atrioventricular septal defect 5
  • p.Gly133= Single submitter atrioventricular septal defect 5
  • p.Gly158= Single submitter atrioventricular septal defect 5
  • p.Gly209= Single submitter atrioventricular septal defect 5
  • p.Gly243= Single submitter atrioventricular septal defect 5
  • p.Gly250= Single submitter atrioventricular septal defect 5
  • p.Gly253= Single submitter atrioventricular septal defect 5
  • p.Gly274= Single submitter atrioventricular septal defect 5
  • p.Gly288= Single submitter
  • p.Gly292= Single submitter atrioventricular septal defect 5
  • p.Gly296= Single submitter atrioventricular septal defect 5
  • p.Gly304= Single submitter
  • p.Gly375= Single submitter atrioventricular septal defect 5
  • p.Gly415= Single submitter atrioventricular septal defect 5
  • p.Gly567= Single submitter atrioventricular septal defect 5
  • p.Gly571= Single submitter
  • p.Gly6= Single submitter atrioventricular septal defect 5
  • p.His171= Single submitter atrioventricular septal defect 5
  • p.His222= Single submitter atrioventricular septal defect 5
  • p.His333= Single submitter atrioventricular septal defect 5
  • p.Ile428= Single submitter
  • p.Leu112= Single submitter atrioventricular septal defect 5
  • p.Leu113= Single submitter atrioventricular septal defect 5
  • p.Leu114= Single submitter atrioventricular septal defect 5
  • p.Leu151= Single submitter atrioventricular septal defect 5
  • p.Leu205= Single submitter atrioventricular septal defect 5
  • p.Leu362= Single submitter atrioventricular septal defect 5
  • p.Leu380= Single submitter atrioventricular septal defect 5
  • p.Leu381= Single submitter atrioventricular septal defect 5
  • p.Leu384= Single submitter atrioventricular septal defect 5
  • p.Leu427= Single submitter atrioventricular septal defect 5
  • p.Leu574= Single submitter atrioventricular septal defect 5
  • p.Leu78= Single submitter atrioventricular septal defect 5
  • p.Lys419= Single submitter atrioventricular septal defect 5
  • p.Phe169= Single submitter atrioventricular septal defect 5
  • p.Phe263= Single submitter atrioventricular septal defect 5
  • p.Phe88= Single submitter atrioventricular septal defect 5
  • p.Pro144= Single submitter atrioventricular septal defect 5
  • p.Pro186= Single submitter
  • p.Pro199= Single submitter atrioventricular septal defect 5
  • p.Pro202= Single submitter atrioventricular septal defect 5
  • p.Pro212= Single submitter atrioventricular septal defect 5
  • p.Pro234= Single submitter atrioventricular septal defect 5
  • p.Pro267= Single submitter
  • p.Pro269= Single submitter atrioventricular septal defect 5
  • p.Pro270= Single submitter atrioventricular septal defect 5
  • p.Pro279= Single submitter atrioventricular septal defect 5
  • p.Pro308= Single submitter atrioventricular septal defect 5
  • p.Pro318= Single submitter atrioventricular septal defect 5
  • p.Pro334= Single submitter atrioventricular septal defect 5
  • p.Pro369= Single submitter atrioventricular septal defect 5
  • p.Pro371= Single submitter atrioventricular septal defect 5
  • p.Pro430= Single submitter atrioventricular septal defect 5
  • p.Pro463= Single submitter atrioventricular septal defect 5
  • p.Pro532= Single submitter atrioventricular septal defect 5
  • p.Pro544= Single submitter atrioventricular septal defect 5
  • p.Pro555= Single submitter atrioventricular septal defect 5
  • p.Pro577= Single submitter atrioventricular septal defect 5
  • p.Pro87= Single submitter atrioventricular septal defect 5
  • p.Pro91= Single submitter atrioventricular septal defect 5
  • p.Pro97= Single submitter atrioventricular septal defect 5
  • p.Ser107= Single submitter atrioventricular septal defect 5
  • p.Ser155= Single submitter atrioventricular septal defect 5
  • p.Ser185= Single submitter atrioventricular septal defect 5
  • p.Ser229= Single submitter atrioventricular septal defect 5
  • p.Ser232= Single submitter atrioventricular septal defect 5
  • p.Ser254= Single submitter atrioventricular septal defect 5
  • p.Ser260= Single submitter atrioventricular septal defect 5
  • p.Ser266= Single submitter atrioventricular septal defect 5
  • p.Ser287= Single submitter
  • p.Ser312= Single submitter atrioventricular septal defect 5
  • p.Ser335= Single submitter atrioventricular septal defect 5
  • p.Ser385= Single submitter atrioventricular septal defect 5
  • p.Ser387= Single submitter atrioventricular septal defect 5
  • p.Ser41= Single submitter atrioventricular septal defect 5
  • p.Ser43= Single submitter atrioventricular septal defect 5
  • p.Ser443= Single submitter atrioventricular septal defect 5
  • p.Ser47= Single submitter atrioventricular septal defect 5
  • p.Ser539= Single submitter atrioventricular septal defect 5
  • p.Ser558= Single submitter atrioventricular septal defect 5
  • p.Ser563= Single submitter atrioventricular septal defect 5
  • p.Ser576= Single submitter atrioventricular septal defect 5
  • p.Ser583= Single submitter atrioventricular septal defect 5
  • p.Ser588= Single submitter atrioventricular septal defect 5
  • p.Thr123= Single submitter atrioventricular septal defect 5
  • p.Thr192= Single submitter atrioventricular septal defect 5
  • p.Thr322= Single submitter atrioventricular septal defect 5
  • p.Thr530= Single submitter atrioventricular septal defect 5
  • p.Thr581= Single submitter atrioventricular septal defect 5
  • p.Thr62= Single submitter atrioventricular septal defect 5
  • p.Tyr188= Single submitter atrioventricular septal defect 5
  • p.Tyr235= Single submitter atrioventricular septal defect 5
  • p.Tyr265= Single submitter atrioventricular septal defect 5
  • p.Val293= Single submitter atrioventricular septal defect 5
  • p.Val391= Single submitter atrioventricular septal defect 5
  • p.Ala173= No assertion criteria GATA6-related disorder
  • p.Ala180= No assertion criteria GATA6-related disorder
  • p.Ala182= No assertion criteria GATA6-related disorder

Uncertain significance 439

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