Is GATA2 p.Pro5= (c.15C>T) pathogenic?

GATA2 p.Pro5= (c.15C>T) is classified Likely benign in GATA2 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-12-13). No allele count reported in gnomAD v4.1 (AN 1,590,028); Associated with deafness-lymphedema-leukemia syndrome.

What condition is associated with GATA2 p.Pro5= (c.15C>T)?

GATA2 p.Pro5= (c.15C>T) is associated with deafness-lymphedema-leukemia syndrome, monocytopenia with susceptibility to infections (ClinVar).

How common is GATA2 p.Pro5= (c.15C>T) in the general population?

GATA2 p.Pro5= (c.15C>T) is no allele count reported in gnomAD v4.1 (AN 1,590,028) (gnomAD).

GATA2 p.Pro5=

c.15C>T · rs1573858 · VCV2040952

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,590,028)

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 -6.5	GERP -2.3
Overall
CADD	2.651	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,590,028). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: GATA2
Protein: p.Pro5=
Coding: c.15C>T
MANE Select: NM_032638
dbSNP: rs1573858
Type: single nucleotide variant
Location: chr3:128487017 (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.Pro5Arg Uncertain significance ★★ same residue
GATA2 p.Pro5Leu 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

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-pro5 (accessed [today's date]).

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