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 Coffin-Siris Syndrome 6 and multiple cancers. [provided by RefSeq, Jul 2026]

GeneReviewsOMIMResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Coffin-Siris syndrome 6MIM #617808
AD

Clinical highlights

Gene-disease validity (ClinGen)
Coffin-Siris syndrome · ADDefinitivesufficient evidence for diagnostic panels
Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype) and the gene is intolerant of it in the population — truncating, frameshift and canonical splice variants carry more prior weight here than missense.Curated gene-level mechanism — a prior for triage, not a per-variant call.
1
Active trials
56
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.10
LOEUF· LoF intol.
LOF
Mechanism· G2P
📖
GeneReview available — ARID2
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?
0.10LOEUF
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

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