GATA2 p.Phe173=
c.519C>T · rs748950881 · VCV1666451
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 6.26e-05%)
Conditions
3
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3 | GERP -0.54, phastCons 1 |
| Overall | ||
| CADD | 10.27 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.26e-05%
Overall
6.26e-05%
1/1,597,116 alleles · very rare
exomes 1/1,444,924 · genomes 0/152,192 · 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.Phe173=
- Coding
- c.519C>T
- MANE Select
- NM_032638
- dbSNP
- rs748950881
- Type
- single nucleotide variant
- Location
- chr3:128486079 (GRCh38)
- Gene constraint
- LOEUF 0.335 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 57.11 · 2 PDB
- Residue 173
- the 'disordered' region
Similar variants
- GATA2 p.Phe173Leu 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
- GATA2 c.1143+2T>A Pathogenic/Likely pathogenic ★★ same condition
- GATA2 p.Ala372Thr Likely pathogenic ★★ same condition
- GATA2 p.Arg204Ter 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-phe173 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown