Is GATA6 p.Pro308= (c.924C>T) pathogenic?

GATA6 p.Pro308= (c.924C>T) is classified Likely benign in GATA6 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-18). Very rare (popmax 0.00259%, amr); Associated with atrioventricular septal defect 5.

What condition is associated with GATA6 p.Pro308= (c.924C>T)?

GATA6 p.Pro308= (c.924C>T) is associated with atrioventricular septal defect 5 (ClinVar).

How common is GATA6 p.Pro308= (c.924C>T) in the general population?

GATA6 p.Pro308= (c.924C>T) is very rare (popmax 0.00259%, amr) (gnomAD).

GATA6 p.Pro308=

c.924C>T · rs1431203656 · VCV1636884

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00259%, amr)

Conditions

atrioventricular septal defect 5

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.47	GERP 0.062, phastCons 1
Overall
CADD	12.45	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00259% Admixed American · 1/38,562 alleles

Filtering AF 0.00168% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00144%

Overall 0.00209% 30/1,437,754 alleles · very rare exomes 28/1,286,216 · genomes 2/151,538 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00259%	38,562
European (non-Finnish)	0.00245%	40,808
Remaining individualsnot grpmax-eligible	0.0018%	55,634
South Asian	0.00146%	68,720

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: GATA6
Protein: p.Pro308=
Coding: c.924C>T
MANE Select: NM_005257
dbSNP: rs1431203656
Type: single nucleotide variant
Location: chr18:22172068 (GRCh38)
Gene constraint: LOEUF 0.527 · pLI 0.95 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 53.48
Residue 308: the 'disordered' region

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

Disease context

atrioventricular septal defect 5 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

GATA6 p.Pro308His Conflicting classifications of pathogenicity ★ ⚠ same residue
GATA6 p.Pro308Leu Uncertain significance ★ ⚠ same residue
GATA6 c.1135+2T>C Likely pathogenic ★★ same condition
GATA6 p.Arg456Cys Pathogenic ★★ same condition
GATA6 p.Arg493Ter Pathogenic ★★ same condition
GATA6 p.Ala122Ser Uncertain significance ★★ ⚠ same condition
GATA6 p.Ala122Thr Uncertain significance ★★ ⚠ same condition
GATA6 p.Ala124Thr Uncertain significance ★★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/gata6-p-pro308 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown