ARID4B

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

Basic information

Region (hg38): 1:235131634-235328219

Previous symbols: [ "RBP1L1" ]

Links

ENSG00000054267 ∙ NCBI:51742 ∙ OMIM:609696 ∙ HGNC:15550 ∙ Uniprot:Q4LE39 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ARID4B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARID4B gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	2
missense			69	4		73
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	69	6	1

Variants in ARID4B

This is a list of pathogenic ClinVar variants found in the ARID4B region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-235131741-C-T		not specified	Uncertain significance (Jul 16, 2021)
1-235131774-T-G		not specified	Uncertain significance (Dec 27, 2023)
1-235131777-A-C		not specified	Uncertain significance (May 09, 2023)
1-235131778-G-C		not specified	Uncertain significance (Aug 27, 2024)
1-235131786-G-A		not specified	Uncertain significance (Apr 01, 2024)
1-235131807-C-T		not specified	Uncertain significance (Feb 03, 2025)
1-235131830-T-A		not specified	Uncertain significance (Jul 10, 2024)
1-235131867-A-C		not specified	Uncertain significance (Jul 13, 2022)
1-235131883-G-T		not specified	Uncertain significance (Dec 01, 2022)
1-235131889-A-C		not specified	Uncertain significance (Feb 01, 2025)
1-235131924-C-A		not specified	Uncertain significance (Dec 02, 2022)
1-235131948-A-T		not specified	Uncertain significance (Jan 23, 2024)
1-235131949-T-G		not specified	Uncertain significance (Dec 28, 2022)
1-235131972-A-G		not specified	Uncertain significance (Aug 16, 2021)
1-235131978-A-C		not specified	Uncertain significance (Jan 03, 2024)
1-235131985-C-T		not specified	Uncertain significance (Mar 19, 2024)
1-235135692-A-C		not specified	Uncertain significance (Jul 26, 2024)
1-235135713-A-G		not specified	Uncertain significance (Apr 29, 2024)
1-235135714-C-T		not specified	Uncertain significance (Apr 12, 2023)
1-235135723-T-G		not specified	Uncertain significance (Aug 22, 2023)
1-235135741-A-G		not specified	Uncertain significance (Mar 07, 2025)
1-235135761-T-C		not specified	Uncertain significance (Jan 09, 2024)
1-235137905-C-G		not specified	Uncertain significance (Apr 01, 2024)
1-235138106-G-A		not specified	Uncertain significance (Jan 30, 2024)
1-235138112-G-A		not specified	Uncertain significance (Oct 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARID4B	protein_coding	protein_coding	ENST00000264183	23	196586

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000195	125730	0	17	125747	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.29	480	644	0.746	0.0000311	8681
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000475	0.000471
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000565	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000269	0.0000264
Middle Eastern	0.0000565	0.0000544
South Asian	0.0000367	0.0000327
Other	0.00	0.00

dbNSFP

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}.
• Pathway: 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;Negative epigenetic regulation of rRNA expression;Epigenetic regulation of gene expression;Gene expression (Transcription);HDACs deacetylate histones;Chromatin modifying enzymes;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.259

Intolerance Scores

• loftool: 0.444
• rvis_EVS: -0.44
• rvis_percentile_EVS: 24.63

Haploinsufficiency Scores

• pHI: 0.653
• hipred: Y
• hipred_score: 0.783
• ghis: 0.635

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.786

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arid4b
• Phenotype: endocrine/exocrine gland phenotype; growth/size/body region phenotype; cellular phenotype; immune system phenotype; homeostasis/metabolism phenotype; liver/biliary system phenotype; respiratory system phenotype; neoplasm; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); skeleton phenotype; renal/urinary system phenotype

Gene ontology

• Biological process: regulation of gene expression by genetic imprinting;regulation of transcription by RNA polymerase II;spermatogenesis;biological_process;histone deacetylation;histone H4-K20 trimethylation;histone H3-K9 trimethylation;positive regulation of transcription by RNA polymerase II;establishment of Sertoli cell barrier
• Cellular component: cellular_component;nucleus;nucleoplasm;cytoplasm
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;molecular_function;histone deacetylase activity;protein binding;transcription regulatory region DNA binding