Is GATA2 p.Ser71= (c.213C>T) pathogenic?

GATA2 p.Ser71= (c.213C>T) is classified Likely benign in GATA2 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-12-10). Ultra-rare (popmax 0.0119%, amr); Associated with Inborn genetic diseases.

What condition is associated with GATA2 p.Ser71= (c.213C>T)?

GATA2 p.Ser71= (c.213C>T) is associated with Inborn genetic diseases, deafness-lymphedema-leukemia syndrome, monocytopenia with susceptibility to infections (ClinVar).

How common is GATA2 p.Ser71= (c.213C>T) in the general population?

GATA2 p.Ser71= (c.213C>T) is ultra-rare (popmax 0.0119%, amr) (gnomAD).

GATA2 p.Ser71=

c.213C>T · rs759513417 · VCV412748

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0119%, amr)

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 4.9	GERP 1.3, phastCons 1
Overall
CADD	13.51	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0119% Admixed American · 7/58,908 alleles

Filtering AF 0.00552% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00386%

Overall 0.000622% 10/1,607,650 alleles · ultra-rare exomes 3/1,455,398 · genomes 7/152,252 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0119%	8,415
Remaining individualsnot grpmax-eligible	0.00322%	31,097
African / African-American	0.00133%	74,918

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.Ser71=
Coding: c.213C>T
MANE Select: NM_032638
dbSNP: rs759513417
Type: single nucleotide variant
Location: chr3:128486819 (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.Ser71Ala Uncertain significance ★ ⚠ same residue
GATA2 p.Ser71Tyr 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-ser71 (accessed [today's date]).

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