GATA3 p.Pro42=
c.126G>C · VCV3902342
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 -9.4 | GERP -2.8 |
| Overall | ||
| CADD | 0.487 | 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
- GATA3
- Protein
- p.Pro42=
- Coding
- c.126G>C
- MANE Select
- NM_001002295
- Type
- single nucleotide variant
- Location
- chr10:8055781 (GRCh38)
- Gene constraint
- LOEUF 0.376 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 58.51 · 3 PDB
- Residue 42
- the 'interaction with tbx21' region
Similar variants
- GATA3 p.Pro42Ser Uncertain significance ★ ⚠ same residue
- 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
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-pro42 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown