GATA4 p.Pro258=
c.774T>C · VCV3716997
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
atrioventricular septal defect 4
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 -10 | GERP -3.8 |
| Overall | ||
| CADD | 1.666 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- GATA4
- Protein
- p.Pro258=
- Coding
- c.774T>C
- MANE Select
- NM_001308093
- Type
- single nucleotide variant
- Location
- chr8:11749073 (GRCh38)
- Gene constraint
- LOEUF 0.468 · pLI 0.99 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 58.64 · 3 PDB
Similar variants
- GATA4 p.Pro258Leu Uncertain significance ★★ ⚠ same residue
- GATA4 p.Pro258Ser Uncertain significance ★★ ⚠ same residue
- GATA4 p.Pro258Arg 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
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-pro258 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown