Is GATA2 p.Ala342= (c.1026C>T) pathogenic?

GATA2 p.Ala342= (c.1026C>T) is classified Likely benign in GATA2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-25). Very rare (popmax 0.0022%, sas); Associated with deafness-lymphedema-leukemia syndrome.

What condition is associated with GATA2 p.Ala342= (c.1026C>T)?

GATA2 p.Ala342= (c.1026C>T) is associated with deafness-lymphedema-leukemia syndrome, monocytopenia with susceptibility to infections (ClinVar).

How common is GATA2 p.Ala342= (c.1026C>T) in the general population?

GATA2 p.Ala342= (c.1026C>T) is very rare (popmax 0.0022%, sas) (gnomAD).

GATA2 p.Ala342=

c.1026C>T · rs758279649 · VCV1990309

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.0022%, 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 5	GERP -3.8, phastCons 1
Overall
CADD	12.4	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0022% South Asian · 2/91,088 alleles

Filtering AF 0.000365% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000136%

Overall 0.000124% 2/1,613,520 alleles · very rare exomes 2/1,461,272 · genomes 0/152,248 · 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.Ala342=
Coding: c.1026C>T
MANE Select: NM_032638
dbSNP: rs758279649
Type: single nucleotide variant
Location: chr3:128481936 (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.Ala342Ser Uncertain significance ★★ same residue
GATA2 p.Ala342Thr Uncertain significance ★★ ⚠ same residue
GATA2 p.Ala342Val Uncertain significance ★★ ⚠ same residue
GATA2 p.Ala342dup Uncertain significance ★★ same residue
GATA2 p.Ala342del Pathogenic ★ same residue
GATA2 p.Ala342fs Pathogenic ★ same residue
GATA2 p.Ala342_Arg343insThrAla Uncertain significance ★ same residue
GATA2 c.1017+572C>T 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-ala342 (accessed [today's date]).

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