GATA2 p.Val181=
c.543G>A · rs547329727 · VCV1664448
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0198%, sas)
Conditions
3
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 -0.59 | GERP -3.4, phastCons 0.019 |
| Overall | ||
| CADD | 8.242 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0198%
South Asian · 18/91,068 alleles
Filtering AF
0.0127%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0106%
Overall
0.00124%
20/1,613,664 alleles · ultra-rare
exomes 18/1,461,452 · genomes 2/152,212 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0198% | 5,059 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,243 |
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.Val181=
- Coding
- c.543G>A
- MANE Select
- NM_032638
- dbSNP
- rs547329727
- Type
- single nucleotide variant
- Location
- chr3:128486055 (GRCh38)
- Gene constraint
- LOEUF 0.335 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 57.11 · 2 PDB
- Residue 181
- the 'disordered' region
Similar variants
- GATA2 p.Val181Leu Uncertain significance ★★ ⚠ same residue
- GATA2 p.Val181Met Uncertain significance ★★ ⚠ same residue
- GATA2 p.Val181Glu Uncertain significance ★ ⚠ same residue
- GATA2 p.Val181Gly Uncertain significance ★ ⚠ same residue
- GATA2 c.1017+572C>T Pathogenic/Likely pathogenic ★★ same condition
- GATA2 c.1018-1G>T Pathogenic/Likely pathogenic ★★ same condition
- GATA2 c.1018-2A>G Pathogenic/Likely pathogenic ★★ same condition
- GATA2 c.1018-2A>T Pathogenic ★★ 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-val181 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown