Is GATA2 p.Pro335= (c.1005C>G) pathogenic?

GATA2 p.Pro335= (c.1005C>G) is classified Likely benign in GATA2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-02). Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with GATA2 p.Pro335= (c.1005C>G)?

GATA2 p.Pro335= (c.1005C>G) is associated with Inborn genetic diseases (ClinVar).

How common is GATA2 p.Pro335= (c.1005C>G) in the general population?

GATA2 p.Pro335= (c.1005C>G) is absent from gnomAD v4.1 (gnomAD).

GATA2 p.Pro335=

c.1005C>G · VCV4028499

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 0.49	GERP -2, phastCons 0.99
Overall
CADD	9.361	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: GATA2
Protein: p.Pro335=
Coding: c.1005C>G
MANE Select: NM_032638
Type: single nucleotide variant
Location: chr3:128483872 (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

Similar variants

GATA2 p.Pro335Ser Uncertain significance ★ ⚠ same residue
GATA2 p.Gln282Ter Pathogenic/Likely pathogenic ★★ same condition
GATA2 c.1017+532T>A Uncertain significance ★★ same condition
GATA2 c.-5C>T Uncertain significance ★★ same condition
GATA2 p.Ala103Val Uncertain significance ★★ ⚠ same condition
GATA2 p.Ala157Gly Uncertain significance ★★ ⚠ same condition
GATA2 p.Ala15Pro Uncertain significance ★★ ⚠ same condition
GATA2 p.Ala163Thr Uncertain significance ★★ ⚠ 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-pro335 (accessed [today's date]).

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