GATA6 p.Val293=
c.879G>A · rs1311556193 · VCV1567445
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0216%, sas)
Conditions
1
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 1.8 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 7.669 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0216%
South Asian · 6/27,836 alleles
Filtering AF
0.00931%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00635%
Overall
0.000721%
9/1,248,432 alleles · ultra-rare
exomes 7/1,097,088 · genomes 2/151,344 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0216% | 4,639 |
| African / African-American | 0.00311% | 32,139 |
| European (non-Finnish) | 0.0001% | 999,670 |
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.Val293=
- Coding
- c.879G>A
- MANE Select
- NM_005257
- dbSNP
- rs1311556193
- Type
- single nucleotide variant
- Location
- chr18:22172023 (GRCh38)
- Gene constraint
- LOEUF 0.527 · pLI 0.95 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 53.48
- Residue 293
- the 'disordered' region
Similar variants
- 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
- GATA6 p.Ala134Asp Uncertain significance ★★ ⚠ same condition
- GATA6 p.Ala134Thr 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-val293 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown