GATA5

Chr 20ADAR

GATA binding protein 5

Also known as: CHTD5, GATAS, bB379O24.1

NCBI Gene: 140628ENSG00000130700UniProt: Q9BWX5

GATA5 encodes a transcription factor containing two GATA-type zinc fingers that is required during cardiovascular development and plays an important role in smooth muscle cell diversity. Mutations cause multiple types of congenital heart defects with both autosomal dominant and autosomal recessive inheritance patterns reported. The gene shows moderate constraint against loss-of-function variants (LOEUF 0.629), consistent with its role in essential cardiac development.

Summary from RefSeq, OMIM, UniProt
Research Assistant →

Primary Disease Associations & Inheritance

Congenital heart defects, multiple types, 5MIM #617912
ADAR
0
Active trials
17
Pubs (1 yr)
1
P/LP submissions
—
P/LP missense
0.63
LOEUF
Multiple*
Mechanism· predicted
Clinical Summary— GATA5
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.24) despite low pLI — interpret in context.
📋
ClinVar Variants
1 unique Pathogenic / Likely Pathogenic· 185 VUS of 300 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.63LOEUF
pLI 0.285
Z-score 2.46
OE 0.24 (0.11–0.63)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
1.07Z-score
OE missense 0.78 (0.68–0.89)
146 obs / 187.3 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.24 (0.11–0.63)
0≤0.351.4
Missense OE0.78 (0.68–0.89)
0≤0.61.4
Synonymous OE1.00
0≤1.21.6
LoF obs/exp: 3 / 12.3Missense obs/exp: 146 / 187.3Syn Z: -0.03
DN
0.6164th %ile
GOF
0.3689th %ile
LOF
0.70top 10%

This gene has evidence for multiple mechanisms of pathogenicity (loss-of-function and dominant-negative). Both the Badonyi & Marsh prediction and the broader genomic evidence point to loss-of-function as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

LOFprediction above median
DN1 literature citation

Literature Evidence

DNThe expression of the mutant inhibited wild-type-induced activation of the ANF promoter, suggesting that the mutant functions in a dominant-negative manner.PMID:22961344

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

300 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic1
VUS185
Likely Benign109
Conflicting2
1
Pathogenic
185
VUS
109
Likely Benign
2
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
1
0
1
Likely Pathogenic
0
0
0
0
0
VUS
12
160
13
0
185
Likely Benign
0
1
31
77
109
Benign
0
0
0
0
0
Conflicting
—2
Total121614577297

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

View in ClinVar →

Protein Context — Lollipop Plot

GATA5 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
N6-methyladenosine-modified ACSM3 mitigates lipid accumulation and suppresses tumor progression in ccRCC via GATA5/HMGCS2 axis and mTORC1 signaling.
Sun K et al.·Int J Biol Macromol
2025
Single-cell epigenomic and transcriptomic analysis unveils the pivotal role of GATA5/ISL1+ fibroblasts in cardiac repair post-myocardial infarction.
Zhang S et al.·Cardiovasc Res
2025
Disruption of Notch1 and Gata5 in Mice Leads to Congenital Aortic Valve Disease.
Yasuhara J et al.·JACC Basic Transl Sci
2025Open Access
Transcription factor GATA5 enhances autophagy by modulating miR-2765 in Penaeus vannamei under ammonia nitrogen stress.
Wang F et al.·Int J Biol Macromol
2025
Whole-Exome Sequencing Identifies Novel GATA5/6 Variants in Right-Sided Congenital Heart Defects.
Zodanu GKE et al.·Int J Mol Sci
2025Open Access
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients