ARID4B

Chr 1

AT-rich interaction domain 4B

Also known as: BCAA, BRCAA1, RBBP1L1, RBP1L1, SAP180

NCBI Gene: 51742ENSG00000054267UniProt: Q4LE39

This gene encodes a protein with sequence similarity to retinoblastoma-binding protein-1. The encoded protein is a subunit of the histone deacetylase-dependant SIN3A transcriptional corepressor complex, which functions in diverse cellular processes including proliferation, differentiation, apoptosis, oncogenesis, and cell fate determination. The gene product is recognized by IgG antibody isolated from a breast cancer patient and appears to be a molecular marker associated with a broad range of human malignancies. Alternate transcriptional splice variants encoding different isoforms have been characterized. [provided by RefSeq, Jul 2008]

192
ClinVar variants
47
Pathogenic / LP
1.00
pLI score· haploinsufficient
0
Active trials
Clinical Summary— ARID4B
⚡
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.
📋
ClinVar Variants
47 Pathogenic / Likely Pathogenic· 138 VUS of 192 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.19LOEUF
pLI 1.000
Z-score 6.67
OE 0.09 (0.05–0.19)
Highly constrained

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

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
2.29Z-score
OE missense 0.75 (0.69–0.80)
480 obs / 643.5 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.09 (0.05–0.19)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.75 (0.69–0.80)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.91
0≤1.21.6
LoF obs/exp: 6 / 63.2Missense obs/exp: 480 / 643.5Syn Z: 1.09

ClinVar Variant Classifications

192 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic45
Likely Pathogenic2
VUS138
Likely Benign5
Benign1
Conflicting1
45
Pathogenic
2
Likely Pathogenic
138
VUS
5
Likely Benign
1
Benign
1
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
45
0
45
Likely Pathogenic
0
0
2
0
2
VUS
0
126
12
0
138
Likely Benign
0
3
1
1
5
Benign
0
0
0
1
1
Conflicting
—1
Total0129602192

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

View in ClinVar →

Protein Context — Lollipop Plot

ARID4B · protein map & ClinVar variants

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

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Downregulation of ARID4A and ARID4B promote tumor progression and directly regulated by microRNA-30d in patient with prostate cancer.
Liang YK et al.·J Cell Biochem
2018
ARID4B: An Orchestrator from Stem Cell Fate to Carcinogenesis.
Kandy RRK et al.·Cells
2025Review
Overexpression of ARID4B predicts poor survival in patients with hepatocellular carcinoma.
Wang R et al.·Hum Pathol
2018Cohort
Allelic variation and differential expression of the mSIN3A histone deacetylase complex gene Arid4b promote mammary tumor growth and metastasis.
Winter SF et al.·PLoS Genet
2012
Machine learning selection of basement membrane-associated genes and development of a predictive model for kidney fibrosis.
Yuan Z et al.·Sci Rep
2025Functional
Autoantibody targets in vaccine-associated narcolepsy.
Häggmark-Månberg A et al.·Autoimmunity
2016
MRCKα Is Dispensable for Breast Cancer Development in the MMTV-PyMT Model.
Kwa MQ et al.·Cells
2021Functional
Regulation of spermatogonial stem cell self-renewal and spermatocyte meiosis by Sertoli cell signaling.
Chen SR et al.·Reproduction
2015Review
Novel serum biomarkers for detection of excessive alcohol use.
Liangpunsakul S et al.·Alcohol Clin Exp Res
2015
Intragenic CNVs for epigenetic regulatory genes in intellectual disability: Survey identifies pathogenic and benign single exon changes.
Zahir FR et al.·Am J Med Genet A
2016
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools