GATA1

Chr XXLR

GATA binding protein 1

Also known as: CNSHA9, ERYF1, GATA-1, GF-1, GF1, HAEADA, NF-E1, NFE1

NCBI Gene: 2623 ENSG00000102145 UniProt: P15976 OMIM: 305371

This transcription factor serves as a master regulator for red blood cell development and controls the switch from fetal to adult hemoglobin production. Mutations cause X-linked recessive hematologic disorders including dyserythropoietic anemia, thrombocytopenia, and beta-thalassemia, often presenting with combined blood cell abnormalities affecting red cells and platelets. The gene is highly constrained against loss-of-function variants (pLI 0.95, LOEUF 0.32), reflecting its critical role in hematopoiesis.

GeneReviews OMIM ResearchSummary from RefSeq, OMIM, UniProt

This gene encodes a protein which belongs to the GATA family of transcription factors. The protein plays an important role in erythroid development by regulating the switch of fetal hemoglobin to adult hemoglobin. Mutations in this gene have been associated with X-linked dyserythropoietic anemia and thrombocytopenia. [provided by RefSeq, Jul 2008]

GeneReviews OMIM ResearchGenerating clinical summary…

LOFmechanismXLRLOEUF 0.325 OMIM phenotypes

Clinical Summary— GATA1

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Gene-Disease Validity (ClinGen)

GATA1-Related X-Linked Cytopenia · XLDefinitive

Definitive — sufficient evidence for diagnostic panels

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Population Constraint (gnomAD)

Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.95). One damaged copy is likely sufficient to cause disease.

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ClinVar Variants

71 unique Pathogenic / Likely Pathogenic· 190 VUS of 422 total submissions

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Clinical Trials

2 active or recruiting trials — potential therapeutic options may be available

Explore recent and relevant literature in Research Assistant →

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GeneReview available — GATA1

Authoritative clinical overview · Recommended first read

Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

LoF intolerant — likely haploinsufficient

LoF Constraint?

0.32LOEUF

pLI 0.948

Z-score 2.83

OE 0.00 (0.00–0.32)

Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?

1.14Z-score

OE missense 0.76 (0.66–0.88)

133 obs / 175.3 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.00 (0.00–0.32)

0≤0.351.4

Missense OE?0.76 (0.66–0.88)

0≤0.61.4

Synonymous OE?0.98

0≤1.21.6

LoF obs/exp: 0 / 9.3Missense obs/exp: 133 / 175.3Syn Z: 0.11

This gene — mechanism propensity

0.3495th %ile

GOF

0.2994th %ile

LOF

0.88top 5%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · 80% of P/LP variants are LoF · LOEUF 0.32

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

422 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic53

Likely Pathogenic18

VUS190

Likely Benign106

Benign26

Conflicting23

Pathogenic

Likely Pathogenic

190

VUS

106

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	44	7	1	1	53
Likely Pathogenic	13	5	0	0	18
VUS	6	170	11	3	190
Likely Benign	0	13	17	76	106
Benign	0	11	5	10	26
Conflicting	—				23
Total	63	206	34	90	416

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

72 pathogenic / likely-pathogenic (of 82) ClinVar copy-number / structural variants overlap GATA1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →