GATA4 p.Pro342=
c.1026T>C · rs56206007 · VCV239095
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.08%, afr)
Conditions
2
Cardiovascular phenotype
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.02 | GERP -0.78, phastCons 0.85 |
| Overall | ||
| CADD | 7.443 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.08%
African / African-American · 2,315/75,056 alleles
Filtering AF
2.98%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.94%
Overall
0.162%
2,615/1,614,200 alleles · low-frequency
exomes 1,204/1,461,874 · genomes 1,411/152,326 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.08% | 32 |
| Remaining individualsnot grpmax-eligible | 0.21% | 477 |
| Admixed American | 0.203% | 492 |
| Middle Eastern | 0.115% | 866 |
| South Asian | 0.00549% | 18,217 |
| European (non-Finnish) | 0.00297% | 33,715 |
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.Pro342=
- Coding
- c.1026T>C
- MANE Select
- NM_001308093
- dbSNP
- rs56206007
- Type
- single nucleotide variant
- Location
- chr8:11756960 (GRCh38)
- Gene constraint
- LOEUF 0.468 · pLI 0.99 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 58.64 · 3 PDB
- Residue 342
- the 'disordered' region
Similar variants
- GATA4 p.Pro342Leu 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-pro342 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown