Is GATA2 p.Pro267= (c.801C>T) pathogenic?

GATA2 p.Pro267= (c.801C>T) is classified Likely benign in GATA2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-10-16). Very rare (popmax 0.00661%, nfe); Associated with deafness-lymphedema-leukemia syndrome.

What condition is associated with GATA2 p.Pro267= (c.801C>T)?

GATA2 p.Pro267= (c.801C>T) is associated with deafness-lymphedema-leukemia syndrome, monocytopenia with susceptibility to infections (ClinVar).

How common is GATA2 p.Pro267= (c.801C>T) in the general population?

GATA2 p.Pro267= (c.801C>T) is very rare (popmax 0.00661%, nfe) (gnomAD).

GATA2 p.Pro267=

c.801C>T · rs376351188 · VCV539729

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00661%, nfe)

Conditions

deafness-lymphedema-leukemia syndrome

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 -20	GERP -3.4
Overall
CADD	0.013	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00661% European (non-Finnish) · 78/1,179,966 alleles

Filtering AF 0.00538% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00498%

Overall 0.00502% 81/1,613,904 alleles · very rare exomes 75/1,461,704 · genomes 6/152,200 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00661%	15,128
African / African-American	0.00267%	37,460
Remaining individualsnot grpmax-eligible	0.0016%	62,478

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.Pro267=
Coding: c.801C>T
MANE Select: NM_032638
dbSNP: rs376351188
Type: single nucleotide variant
Location: chr3:128485797 (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

deafness-lymphedema-leukemia syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: monocytopenia with susceptibility to infections

Similar variants

GATA2 p.Pro267Arg Uncertain significance ★★ ⚠ same residue
GATA2 p.Pro267His Uncertain significance ★★ ⚠ same residue
GATA2 p.Pro267Leu Uncertain significance ★ ⚠ same residue
GATA2 p.Pro267Ala 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-pro267 (accessed [today's date]).

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