GATA3 p.Pro148=
c.444G>A · VCV4906508
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00322%, nfe)
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 -1.9 | GERP -0.45 |
| Overall | ||
| CADD | 9.132 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00322%
European (non-Finnish) · 38/1,179,702 alleles
Filtering AF
0.00239%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0021%
Overall
0.00261%
42/1,611,814 alleles · very rare
exomes 37/1,459,786 · genomes 5/152,028 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00322% | 31,045 |
| Finnishnot grpmax-eligible | 0.00321% | 31,198 |
| East Asian | 0.00223% | 44,866 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,438 |
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.Pro148=
- Coding
- c.444G>A
- MANE Select
- NM_001002295
- Type
- single nucleotide variant
- Location
- chr10:8058507 (GRCh38)
- Gene constraint
- LOEUF 0.376 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 58.51 · 3 PDB
- Residue 148
- the 'interaction with tbx21' region; the 'disordered' 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-pro148 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown