GATA2 p.Pro183=
c.549T>A · VCV4842570
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 6.3e-05%)
Conditions
1
Inborn genetic diseases
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 -12 | GERP -3.4 |
| Overall | ||
| CADD | 0.073 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.3e-05%
Overall
6.3e-05%
1/1,586,496 alleles · very rare
exomes 0/1,435,544 · genomes 1/150,952 · joint denominator
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
- GATA2
- Protein
- p.Pro183=
- Coding
- c.549T>A
- MANE Select
- NM_032638
- Type
- single nucleotide variant
- Location
- chr3:128486049 (GRCh38)
- Gene constraint
- LOEUF 0.335 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 57.11 · 2 PDB
- Residue 183
- the 'disordered' region
Similar variants
- GATA2 p.Pro183Leu Uncertain significance ★ ⚠ same residue
- GATA2 p.Gln282Ter Pathogenic/Likely pathogenic ★★ same condition
- GATA2 c.1017+532T>A Uncertain significance ★★ same condition
- GATA2 c.-5C>T Uncertain significance ★★ same condition
- GATA2 p.Ala103Val Uncertain significance ★★ ⚠ same condition
- GATA2 p.Ala157Gly Uncertain significance ★★ ⚠ same condition
- GATA2 p.Ala15Pro Uncertain significance ★★ ⚠ same condition
- GATA2 p.Ala163Thr 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/gata2-p-pro183 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown