GATA3 p.Pro44=
c.132G>A · VCV3664697
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.231%, mid)
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 -2.8 |
| Overall | ||
| CADD | 7.352 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.231%
Middle Eastern · 14/6,062 alleles
Filtering AF
0.14%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.112%
Overall
0.00207%
33/1,592,572 alleles · rare
exomes 31/1,440,352 · genomes 2/152,220 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.231% | 433 |
| Admixed American | 0.00347% | 28,807 |
| African / African-American | 0.00268% | 37,257 |
| European (non-Finnish) | 0.0012% | 83,555 |
| South Asian | 0.00114% | 87,552 |
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
- GATA3
- Protein
- p.Pro44=
- Coding
- c.132G>A
- MANE Select
- NM_001002295
- Type
- single nucleotide variant
- Location
- chr10:8055787 (GRCh38)
- Gene constraint
- LOEUF 0.376 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 58.51 · 3 PDB
- Residue 44
- the 'interaction with tbx21' region
Similar variants
- GATA3 c.1050+2T>C Pathogenic ★★ same type
- GATA3 c.924+1G>A Pathogenic/Likely pathogenic ★★ same type
- GATA3 p.Arg276Gln Pathogenic/Likely pathogenic ★★ same type
- GATA3 p.Arg299Gln Pathogenic/Likely pathogenic ★★ same type
- GATA3 p.Arg299Trp Likely pathogenic ★★ same type
- GATA3 p.Arg306Ter Pathogenic ★★ same type
- GATA3 p.Arg367Ter Pathogenic ★★ same type
- GATA3 p.Ser166Ter Likely pathogenic ★★ same type
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/gata3-p-pro44 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown