ARID5B

AT-rich interaction domain 5B, the group of AT-rich interaction domain containing

Basic information

Region (hg38): 10:61901684-62096944

Links

ENSG00000150347 ∙ NCBI:84159 ∙ OMIM:608538 ∙ HGNC:17362 ∙ Uniprot:Q14865 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• isolated cleft palate (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ARID5B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARID5B 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				11	3	14
missense			48		2	50
nonsense						0
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	50	11	5

Variants in ARID5B

This is a list of pathogenic ClinVar variants found in the ARID5B region.

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

Position	Type	Phenotype	Significance	ClinVar
10-61902146-T-TC		ARID5B-related disorder	Likely benign (Jun 24, 2019)
10-61902172-C-A		not specified	Uncertain significance (Jan 26, 2022)
10-61902274-G-A		ARID5B-related disorder	Uncertain significance (Dec 05, 2022)
10-61902277-C-A		not specified	Uncertain significance (Sep 30, 2021)
10-61940196-C-T		not specified	Uncertain significance (Jun 26, 2024)
10-61940243-G-C		not specified	Uncertain significance (Oct 03, 2022)
10-61940248-T-G		not specified	Uncertain significance (Jan 30, 2024)
10-61940281-C-T		ARID5B-related disorder	Likely benign (Nov 26, 2019)
10-61940340-A-G		not specified	Uncertain significance (Jan 10, 2022)
10-61940366-G-A		not specified	Uncertain significance (Mar 01, 2023)
10-61940387-C-A		not specified	Uncertain significance (Aug 21, 2023)
10-61940393-G-C		not specified	Uncertain significance (Feb 06, 2024)
10-62000114-G-T		not specified	Uncertain significance (Nov 10, 2024)
10-62000216-C-T		ARID5B-related disorder	Likely benign (Mar 29, 2019)
10-62000222-G-A		not specified	Uncertain significance (Dec 10, 2024)
10-62000246-C-T		not specified	Uncertain significance (Sep 17, 2021)
10-62000268-A-C		not specified	Uncertain significance (Mar 12, 2024)
10-62050925-A-G		ARID5B-related disorder	Likely benign (Jul 07, 2023)
10-62050938-A-G		not specified	Uncertain significance (Apr 23, 2024)
10-62050975-A-G		not specified	Uncertain significance (Jan 06, 2023)
10-62057266-G-C		not specified	Uncertain significance (Mar 28, 2023)
10-62057274-G-C		ARID5B-related disorder	Uncertain significance (May 31, 2024)
10-62057275-G-C		not specified	Uncertain significance (Aug 09, 2021)
10-62069690-A-AT		ARID5B-related disorder	Likely benign (Sep 27, 2024)
10-62085803-AC-A		8 conditions	Uncertain significance (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARID5B	protein_coding	protein_coding	ENST00000279873	10	195645

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	9.62e-7	125667	0	3	125670	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.60	478	667	0.717	0.0000365	7817
Missense in Polyphen		216	334.27	0.64618		3970
Synonymous	0.212	274	278	0.984	0.0000171	2311
Loss of Function	5.94	1	43.0	0.0233	0.00000206	579

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.0000996	0.0000993
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription coactivator that binds to the 5'-AATA[CT]- 3' core sequence and plays a key role in adipogenesis and liver development. Acts by forming a complex with phosphorylated PHF2, which mediates demethylation at Lys-336, leading to target the PHF2-ARID5B complex to target promoters, where PHF2 mediates demethylation of dimethylated 'Lys-9' of histone H3 (H3K9me2), followed by transcription activation of target genes. The PHF2- ARID5B complex acts as a coactivator of HNF4A in liver. Required for adipogenesis: regulates triglyceride metabolism in adipocytes by regulating expression of adipogenic genes. Overexpression leads to induction of smooth muscle marker genes, suggesting that it may also act as a regulator of smooth muscle cell differentiation and proliferation. Represses the cytomegalovirus enhancer. {ECO:0000269|PubMed:21532585}.
• Disease: DISEASE: Note=Defects in ARID5B may be a cause of susceptibility to coronary atherosclerosis in the Japanese population.; DISEASE: Leukemia, acute lymphoblastic (ALL) [MIM:613065]: A subtype of acute leukemia, a cancer of the white blood cells. ALL is a malignant disease of bone marrow and the most common malignancy diagnosed in children. The malignant cells are lymphoid precursor cells (lymphoblasts) that are arrested in an early stage of development. The lymphoblasts replace the normal marrow elements, resulting in a marked decrease in the production of normal blood cells. Consequently, anemia, thrombocytopenia, and neutropenia occur to varying degrees. The lymphoblasts also proliferate in organs other than the marrow, particularly the liver, spleen, and lymphnodes. {ECO:0000269|PubMed:19684603, ECO:0000269|PubMed:19684604, ECO:0000269|PubMed:20042726, ECO:0000269|PubMed:20054350, ECO:0000269|PubMed:20189245, ECO:0000269|PubMed:20460642, ECO:0000269|PubMed:21098271}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
• Pathway: Mesodermal Commitment Pathway;FTO Obesity Variant Mechanism;Pathways Affected in Adenoid Cystic Carcinoma;HDMs demethylate histones;Chromatin modifying enzymes;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.0665
• rvis_EVS: -1.04
• rvis_percentile_EVS: 7.83

Haploinsufficiency Scores

• pHI: 0.790
• hipred: Y
• hipred_score: 0.728
• ghis: 0.524

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.545

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arid5b
• Phenotype: renal/urinary system phenotype; skeleton phenotype; immune system phenotype; digestive/alimentary phenotype; limbs/digits/tail phenotype; hematopoietic system phenotype; 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype; muscle phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;kidney development;liver development;regulation of transcription by RNA polymerase II;male gonad development;female gonad development;post-embryonic development;fibroblast migration;histone demethylation;adrenal gland development;multicellular organism growth;fat cell differentiation;negative regulation of transcription, DNA-templated;platelet-derived growth factor receptor signaling pathway;cell development;muscle organ morphogenesis;skeletal system morphogenesis;positive regulation of DNA-binding transcription factor activity;roof of mouth development;face morphogenesis;adipose tissue development;fat pad development;positive regulation of nucleic acid-templated transcription;cellular response to leukemia inhibitory factor
• Cellular component: nucleus;nucleoplasm
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;transcription coactivator activity;protein binding;histone demethylase activity;transcription regulatory region DNA binding