GATAD2B

Chr 1AD

GATA zinc finger domain containing 2B

Also known as: GANDS, MRD18, P66beta, p68

NCBI Gene: 57459ENSG00000143614UniProt: Q8WXI9OMIM: 614998

This gene encodes a transcriptional repressor that functions as a component of the histone deacetylase NuRD complex, which remodels chromatin and represses gene expression. Mutations cause GAND syndrome, characterized by intellectual disability and dysmorphic features, inherited in an autosomal dominant pattern. The gene is highly constrained against loss-of-function variants (pLI 1.0, LOEUF 0.097), indicating that even single functional copies are critical for normal development.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismADLOEUF 0.101 OMIM phenotype
Clinical Summary— GATAD2B
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Gene-Disease Validity (ClinGen)
severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome · ADDefinitive

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 1.00). One damaged copy is likely sufficient to cause disease.
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ClinVar Variants
53 unique Pathogenic / Likely Pathogenic· 223 VUS of 500 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Dual constrained — LoF & missense intolerant
LoF Constraint
0.10LOEUF
pLI 1.000
Z-score 5.13
OE 0.00 (0.00–0.10)
Highly constrained

Among the most LoF-intolerant genes (~top 3%)

Missense Constraint
3.16Z-score
OE missense 0.52 (0.46–0.59)
182 obs / 347.9 exp
Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios
LoF OE0.00 (0.00–0.10)
0≤0.351.4
Missense OE0.52 (0.46–0.59)
0≤0.61.4
Synonymous OE1.01
0≤1.21.6
LoF obs/exp: 0 / 30.6Missense obs/exp: 182 / 347.9Syn Z: -0.12
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveGATAD2B-related nonspecific severe intellectual disabilityLOFAD
DN
0.2299th %ile
GOF
0.1799th %ile
LOF
0.89top 5%

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

LOFprediction above median · 1 literature citation · 81% of P/LP variants are LoF · LOEUF 0.10

Literature Evidence

LOFGATAD2B loss-of-function mutations cause a recognisable syndrome with intellectual disability and are associated with learning deficits and synaptic undergrowth in DrosophilaPMID:23644463

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

500 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic35
Likely Pathogenic18
VUS223
Likely Benign163
Benign31
Conflicting15
35
Pathogenic
18
Likely Pathogenic
223
VUS
163
Likely Benign
31
Benign
15
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
26
2
7
0
35
Likely Pathogenic
17
1
0
0
18
VUS
4
200
14
5
223
Likely Benign
0
3
60
100
163
Benign
0
1
30
0
31
Conflicting
—15
Total47207111105485

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

View in ClinVar →

Protein Context — Lollipop Plot

GATAD2B · 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
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