Is GATA1 p.Pro50= (c.150G>A) pathogenic?

GATA1 p.Pro50= (c.150G>A) is classified Likely benign in GATA1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-05-02). Very rare (popmax 0.00538%, sas); Associated with Diamond-Blackfan anemia.

What condition is associated with GATA1 p.Pro50= (c.150G>A)?

GATA1 p.Pro50= (c.150G>A) is associated with Diamond-Blackfan anemia, GATA1-related cytopenia (ClinVar).

How common is GATA1 p.Pro50= (c.150G>A) in the general population?

GATA1 p.Pro50= (c.150G>A) is very rare (popmax 0.00538%, sas) (gnomAD).

How is Diamond-Blackfan anemia inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

GATA1 p.Pro50=

c.150G>A · rs782678694 · VCV767299

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00538%, sas)

Conditions

Diamond-Blackfan anemia

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 -1.7	GERP -2.6
Overall
CADD	1.217	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00538% South Asian · 3/55,741 alleles

Filtering AF 0.00143% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0011%

Overall 0.00216% 26/1,204,797 alleles · very rare exomes 24/1,093,029 · genomes 2/111,768 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00538%	18,580
Remaining individualsnot grpmax-eligible	0.00422%	23,709
East Asian	0.00297%	33,624
Admixed American	0.00221%	45,237
European (non-Finnish)	0.00213%	46,984

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: GATA1
Protein: p.Pro50=
Coding: c.150G>A
MANE Select: NM_002049
dbSNP: rs782678694
Type: single nucleotide variant
Location: chrX:48791259 (GRCh38)
Structure: AlphaFold pLDDT 59.48 · 1 PDB

Full GATA1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Diamond-Blackfan anemia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: GATA1-related cytopenia

For Diamond-Blackfan anemia (Orphanet):

Inheritance: Autosomal dominant
Onset: Childhood, Infancy, Neonatal
Prevalence: 1-9 / 1 000 000 (Europe)

Similar variants

GATA1 p.Pro50Arg Uncertain significance ★ ⚠ same residue
GATA1 p.Pro50Leu Uncertain significance ★ ⚠ same residue
GATA1 c.220+1G>A Pathogenic ★★ same condition
GATA1 c.220+2T>C Pathogenic/Likely pathogenic ★★ same condition
GATA1 p.Arg216Gln Pathogenic ★★ same condition
GATA1 p.Arg216Trp Likely pathogenic ★★ same condition
GATA1 p.Met1Thr Pathogenic/Likely pathogenic ★★ same condition
GATA1 p.Ser12Ter 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/gata1-p-pro50 (accessed [today's date]).

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