Is GATA2 p.Pro22= (c.66C>G) pathogenic?

GATA2 p.Pro22= (c.66C>G) is classified Benign/Likely benign in GATA2 (ClinVar, Multiple submitters, 10 submitters; last evaluated 2026-01-29). Rare (popmax 0.841%, afr); Associated with Inborn genetic diseases.

What condition is associated with GATA2 p.Pro22= (c.66C>G)?

GATA2 p.Pro22= (c.66C>G) is associated with Inborn genetic diseases, deafness-lymphedema-leukemia syndrome, monocytopenia with susceptibility to infections (ClinVar).

How common is GATA2 p.Pro22= (c.66C>G) in the general population?

GATA2 p.Pro22= (c.66C>G) is rare (popmax 0.841%, afr) (gnomAD).

GATA2 p.Pro22=

c.66C>G · rs113384352 · VCV257567

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 10 submitters

gnomAD v4.1

Rare

rare (popmax 0.841%, 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 0.06	GERP -1, phastCons 0.67
Overall
CADD	9.692	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.841% African / African-American · 631/75,004 alleles

Filtering AF 0.787% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.765%

Overall 0.0445% 717/1,611,640 alleles · rare exomes 341/1,459,334 · genomes 376/152,306 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.841%	119
Remaining individualsnot grpmax-eligible	0.0786%	1,272
Admixed American	0.0601%	1,663
European (non-Finnish)	8.48e-05%	1,179,048

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.Pro22=
Coding: c.66C>G
MANE Select: NM_032638
dbSNP: rs113384352
Type: single nucleotide variant
Location: chr3:128486966 (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 hereditary neoplastic syndrome

Similar variants

GATA2 p.Pro22Ala Uncertain significance ★★ ⚠ same residue
GATA2 p.Pro22Leu Uncertain significance ★★ ⚠ same residue
GATA2 p.Pro22Ser Uncertain significance ★★ ⚠ same residue
GATA2 p.Pro22Thr Uncertain significance ★★ ⚠ same residue
GATA2 p.Pro22Arg Uncertain significance ★ ⚠ same residue
GATA2 p.Pro22His Uncertain significance ★ ⚠ same residue
GATA2 c.1017+572C>T Pathogenic/Likely pathogenic ★★ same condition
GATA2 c.1018-1G>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-pro22 (accessed [today's date]).

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