Is GATA2 p.Pro137= (c.411A>G) pathogenic?

GATA2 p.Pro137= (c.411A>G) is classified Likely benign in GATA2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-11-19). Very rare (popmax 0.00234%, sas); Associated with Inborn genetic diseases.

What condition is associated with GATA2 p.Pro137= (c.411A>G)?

GATA2 p.Pro137= (c.411A>G) is associated with Inborn genetic diseases, deafness-lymphedema-leukemia syndrome, monocytopenia with susceptibility to infections (ClinVar).

How common is GATA2 p.Pro137= (c.411A>G) in the general population?

GATA2 p.Pro137= (c.411A>G) is very rare (popmax 0.00234%, sas) (gnomAD).

GATA2 p.Pro137=

c.411A>G · rs1286155488 · VCV1623730

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00234%, sas)

Conditions

Inborn genetic diseases

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 -3	GERP -2.8
Overall
CADD	3.194	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00234% South Asian · 2/85,320 alleles

Filtering AF 0.000389% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000146%

Overall 0.000256% 4/1,562,720 alleles · very rare exomes 4/1,411,030 · genomes 0/151,690 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00234%	42,660
Remaining individualsnot grpmax-eligible	0.00165%	60,536
European (non-Finnish)	8.67e-05%	1,154,009

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.Pro137=
Coding: c.411A>G
MANE Select: NM_032638
dbSNP: rs1286155488
Type: single nucleotide variant
Location: chr3:128486187 (GRCh38)
Gene constraint: LOEUF 0.335 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 57.11 · 2 PDB
Residue 137: the 'disordered' region

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

Similar variants

GATA2 p.Pro137Ser Uncertain significance ★★ ⚠ same residue
GATA2 p.Pro137Leu 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-pro137 (accessed [today's date]).

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