Is GATA4 p.Ser90= (c.270C>T) pathogenic?

GATA4 p.Ser90= (c.270C>T) is classified Likely benign in GATA4 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-05-06). Very rare (popmax 0.00152%, afr); Associated with Cardiovascular phenotype.

What condition is associated with GATA4 p.Ser90= (c.270C>T)?

GATA4 p.Ser90= (c.270C>T) is associated with Cardiovascular phenotype, atrioventricular septal defect 4 (ClinVar).

How common is GATA4 p.Ser90= (c.270C>T) in the general population?

GATA4 p.Ser90= (c.270C>T) is very rare (popmax 0.00152%, afr) (gnomAD).

GATA4 p.Ser90=

c.270C>T · rs1800007382 · VCV2812302

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00152%, afr)

Conditions

Cardiovascular phenotype

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 0.93	GERP -1.6, phastCons 0.97
Overall
CADD	10.99	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00152% African / African-American · 1/65,606 alleles

Overall 7.35e-05% 1/1,361,034 alleles · very rare exomes 0/1,209,050 · genomes 1/151,984 · joint denominator

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: GATA4
Protein: p.Ser90=
Coding: c.270C>T
MANE Select: NM_001308093
dbSNP: rs1800007382
Type: single nucleotide variant
Location: chr8:11708582 (GRCh38)
Gene constraint: LOEUF 0.468 · pLI 0.99 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 58.64 · 3 PDB
Residue 90: the 'disordered' region

Full GATA4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: atrioventricular septal defect 4

Similar variants

GATA4 p.Ser90Thr Uncertain significance ★★ ⚠ same residue
GATA4 p.Arg231Ter Pathogenic ★★ same condition
GATA4 p.Arg284His Pathogenic/Likely pathogenic ★★ same condition
GATA4 p.Gly297Ser Pathogenic/Likely pathogenic ★★ same condition
GATA4 c.1001-3C>T Uncertain significance ★★ same condition
GATA4 c.912+5G>A Uncertain significance ★★ same condition
GATA4 c.913-5T>G Uncertain significance ★★ same condition
GATA4 p.Ala131Gly 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/gata4-p-ser90 (accessed [today's date]).

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