ARID4B

protein-coding

AT-rich interaction domain 4B, the group of MicroRNA protein coding host genes|AT-rich interaction domain containing

Gene summary

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]

Previous symbols:

RBP1L1

MANE transcript

NM_016374.6

Inheritance

—

ClinVar variants

U:146B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.09

Max pathogenic AF

—

Genomic locus

chr1:235,131,634-235,328,219

External References & Databases

Ensembl (ENSG00000054267)

Transcript & Mutation Effects

hg38 • Region Span ~196.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ARID4B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 131

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016374.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar	1 clinvar	4
missense			131 clinvar	4 clinvar		135
nonsense			1 clinvar			1
start loss						0
frameshift			3 clinvar			3
splice donor/acceptor (+/-2bp)			9 clinvar			9
Total	0	0	146	5	1	152

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 30 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016374.6	RefSeq	NP_057458.4	23	MANE Select
ENST00000264183.9	Ensembl	ENSP00000264183.3	23	MANE Select
NM_001206794.2	RefSeq	NP_001193723.1	23	Standard
NM_031371.4	RefSeq	NP_112739.2	22	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

miR-targeted genes in leukocytes - TarBase
miR-targeted genes in lymphocytes - TarBase
miR-targeted genes in muscle cell - TarBase
Pathways Affected in Adenoid Cystic Carcinoma
NoRC negatively regulates rRNA expression

Biological Process

regulation of gene expression by genetic imprinting
regulation of transcription by RNA polymerase II
spermatogenesis
biological_process
histone deacetylation

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
molecular_function
histone deacetylase activity
protein binding
transcription regulatory region DNA binding

Cellular Component

cellular_component
nucleus
nucleoplasm
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000264183
Coding exons: 23
Length: 196586
Individuals with no LoFs: 125730
Homozygous LoFs: 0
Heterozygous LoFs: 17
Defined: 125747
p: 0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.29	480	644	0.746	0.0000311	8681
Missense (PolyPhen)		187	323.61	0.57786		4362
Synonymous	1.09	204	225	0.908	0.0000112	2311
Loss of Function	6.67	6	63.2	0.0950	0.00000328	893

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0.00035	0.00023	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000057	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000027	0.000026	rare
South Asian	0.000037	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Acts as a transcriptional repressor (PubMed:12724404). May function in the assembly and/or enzymatic activity of the Sin3A corepressor complex or in mediating interactions between the complex and other regulatory complexes (PubMed:12724404). Plays a role in the regulation of epigenetic modifications at the PWS/AS imprinting center near the SNRPN promoter, where it might function as part of a complex with RB1 and ARID4A. Involved in spermatogenesis, together with ARID4A, where it functions as a transcriptional coactivator for AR (androgen receptor) and enhances expression of genes required for sperm maturation. Regulates expression of the tight junction protein CLDN3 in the testis, which is important for integrity of the blood-testis barrier. Plays a role in myeloid homeostasis where it regulates the histone methylation state of bone marrow cells and expression of various genes involved in hematopoiesis. May function as a leukemia suppressor (By similarity). {ECO:0000250|UniProtKB:A2CG63, ECO:0000269|PubMed:12724404}.;

Recessive Scores

pRec: 0.259

Intolerance Scores

LoFtool: 0.444
RVIS EVS: -0.44
RVIS percentile EVS: 24.63

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.786

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium