Is GATA2 p.Phe467= (c.1401C>T) pathogenic?

GATA2 p.Phe467= (c.1401C>T) is classified Likely benign in GATA2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-05-22). Ultra-rare (popmax 0.0619%, sas); Associated with deafness-lymphedema-leukemia syndrome.

What condition is associated with GATA2 p.Phe467= (c.1401C>T)?

GATA2 p.Phe467= (c.1401C>T) is associated with deafness-lymphedema-leukemia syndrome, monocytopenia with susceptibility to infections (ClinVar).

How common is GATA2 p.Phe467= (c.1401C>T) in the general population?

GATA2 p.Phe467= (c.1401C>T) is ultra-rare (popmax 0.0619%, sas) (gnomAD).

GATA2 p.Phe467=

c.1401C>T · rs534807053 · VCV698663

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0619%, sas)

Conditions

deafness-lymphedema-leukemia syndrome

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 -3.3	GERP -2.9
Overall
CADD	0.829	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0619% South Asian · 55/88,804 alleles

Filtering AF 0.0488% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0441%

Overall 0.00619% 99/1,600,468 alleles · ultra-rare exomes 91/1,448,128 · genomes 8/152,340 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0619%	1,615
East Asian	0.0179%	5,588
Remaining individualsnot grpmax-eligible	0.00646%	15,474
African / African-American	0.00534%	18,728
European (non-Finnish)	0.00239%	41,843

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.Phe467=
Coding: c.1401C>T
MANE Select: NM_032638
dbSNP: rs534807053
Type: single nucleotide variant
Location: chr3:128481061 (GRCh38)
Gene constraint: LOEUF 0.335 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 57.11 · 2 PDB
Residue 467: the 'disordered' region

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.Phe467del Uncertain significance ★★ same residue
GATA2 p.Phe467Ile Uncertain significance ★ ⚠ same residue
GATA2 p.Phe467Leu 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-phe467 (accessed [today's date]).

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