ARID2

Chr 12AD

AT-rich interaction domain 2

Also known as: BAF200, CSS6, SMARCF3, ZIPZAP, p200

NCBI Gene: 196528ENSG00000189079UniProt: Q68CP9OMIM: 609539

This gene encodes a member of the AT-rich interactive domain (ARID)-containing family of DNA-binding proteins. Members of the ARID family have roles in embryonic patterning, cell lineage gene regulation, cell cycle control, transcriptional regulation and chromatin structure modification. This protein functions as a subunit of the polybromo- and BRG1-associated factor or PBAF (SWI/SNF-B) chromatin remodeling complex which facilitates ligand-dependent transcriptional activation by nuclear receptors. Mutations in this gene are associated with hepatocellular carcinomas. A pseudogene of this gene is found on chromosome1. [provided by RefSeq, Dec 2016]

OMIMResearchGenerating clinical summary…
LOFmechanismADLOEUF 0.101 OMIM phenotype
Clinical Summary— ARID2
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Gene-Disease Validity (ClinGen)
Coffin-Siris 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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Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint?
0.10LOEUF
pLI 1.000
Z-score 8.00
OE 0.04 (0.02–0.10)
Highly constrained

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

Missense Constraint?
2.73Z-score
OE missense 0.75 (0.71–0.80)
720 obs / 958.1 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?
LoF OE?0.04 (0.02–0.10)
0≤0.351.4
Missense OE?0.75 (0.71–0.80)
0≤0.61.4
Synonymous OE?1.13
0≤1.21.6
LoF obs/exp: 3 / 80.4Missense obs/exp: 720 / 958.1Syn Z: -1.89
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
strongARID2-related Coffin-Siris like disorderLOFAD

This gene — mechanism propensity

DN
0.2199th %ile
GOF
0.14100th %ile
LOF
0.83top 5%

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

LOFprediction above median · 1 literature citation · LOEUF 0.10 · ClinGen HI: Sufficient evidence for dosage pathogenicity

Literature Evidence

LOFThe phenotypes of 22 patients with either an ARID2 heterozygous mutation or haploinsufficiency were reviewed.1

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

References

  1. 1.PMID 33051312 ↗

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

ARID2 · protein map & ClinVar variants

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

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