Is GATA2 p.Val70= (c.210C>T) pathogenic?

GATA2 p.Val70= (c.210C>T) is classified Likely benign in GATA2 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-09-03). Very rare (popmax 0.00224%, eas); Associated with monocytopenia with susceptibility to infections.

What condition is associated with GATA2 p.Val70= (c.210C>T)?

GATA2 p.Val70= (c.210C>T) is associated with monocytopenia with susceptibility to infections, deafness-lymphedema-leukemia syndrome (ClinVar).

How common is GATA2 p.Val70= (c.210C>T) in the general population?

GATA2 p.Val70= (c.210C>T) is very rare (popmax 0.00224%, eas) (gnomAD).

How is GATA2 deficiency spectrum inherited?

Typically Autosomal dominant, Not applicable (Orphanet). A genetic counselor can assess individual risk for a family.

GATA2 p.Val70=

c.210C>T · rs2107673388 · VCV1079711

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00224%, eas)

Conditions

monocytopenia with susceptibility to infections

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 2.3	GERP 0.26, phastCons 1
Overall
CADD	9.827	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00224% East Asian · 1/44,628 alleles

Overall 0.000124% 2/1,608,528 alleles · very rare exomes 2/1,456,146 · genomes 0/152,382 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00224%	44,628
European (non-Finnish)	8.49e-05%	1,178,248

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.Val70=
Coding: c.210C>T
MANE Select: NM_032638
dbSNP: rs2107673388
Type: single nucleotide variant
Location: chr3:128486822 (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

monocytopenia with susceptibility to infections — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: deafness-lymphedema-leukemia syndrome

For GATA2 deficiency spectrum (Orphanet):

Inheritance: Autosomal dominant, Not applicable
Onset: Adult

Similar variants

GATA2 p.Val70Phe Conflicting classifications of pathogenicity ★ ⚠ same residue
GATA2 p.Val70fs Pathogenic ★ 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-val70 (accessed [today's date]).

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