Is GATA2 p.Pro93= (c.279G>A) pathogenic?

GATA2 p.Pro93= (c.279G>A) is classified Conflicting classifications of pathogenicity in GATA2 (ClinVar, Conflicting submitters, 7 submitters; last evaluated 2026-01-28). Rare (popmax 0.147%, afr); Associated with Inborn genetic diseases.

What condition is associated with GATA2 p.Pro93= (c.279G>A)?

GATA2 p.Pro93= (c.279G>A) is associated with Inborn genetic diseases, deafness-lymphedema-leukemia syndrome, monocytopenia with susceptibility to infections (ClinVar).

How common is GATA2 p.Pro93= (c.279G>A) in the general population?

GATA2 p.Pro93= (c.279G>A) is rare (popmax 0.147%, afr) (gnomAD).

GATA2 p.Pro93=

c.279G>A · rs142993548 · VCV241722

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 7 submitters

gnomAD v4.1

Rare

rare (popmax 0.147%, afr)

Conditions

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 -9.4	GERP -2.7
Overall
CADD	1.48	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.147% African / African-American · 110/74,952 alleles

Filtering AF 0.124% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.116%

Overall 0.0139% 222/1,598,488 alleles · rare exomes 137/1,446,266 · genomes 85/152,222 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.147%	681
South Asian	0.106%	945
Remaining individualsnot grpmax-eligible	0.021%	4,770
Admixed American	0.0105%	9,546

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.Pro93=
Coding: c.279G>A
MANE Select: NM_032638
dbSNP: rs142993548
Type: single nucleotide variant
Location: chr3:128486319 (GRCh38)
Gene constraint: LOEUF 0.335 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 57.11 · 2 PDB

Full GATA2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: deafness-lymphedema-leukemia syndrome monocytopenia with susceptibility to infections

Similar variants

GATA2 p.Pro93Gln Uncertain significance ★★ ⚠ same residue
GATA2 p.Pro93Leu Uncertain significance ★ ⚠ same residue
GATA2 p.Pro93Ser 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

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-pro93 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown