ARID4A

AT-rich interaction domain 4A, the group of AT-rich interaction domain containing

Basic information

Region (hg38): 14:58298504-58373887

Previous symbols: [ "RBBP1" ]

Links

ENSG00000032219 ∙ NCBI:5926 ∙ OMIM:180201 ∙ HGNC:9885 ∙ Uniprot:P29374 ∙ 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 ARID4A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARID4A 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						0
missense			46	2		48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	46	2	0

Variants in ARID4A

This is a list of pathogenic ClinVar variants found in the ARID4A region.

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

Position	Type	Phenotype	Significance	ClinVar
14-58301685-G-A		not specified	Uncertain significance (Oct 19, 2024)
14-58318574-C-T		not specified	Uncertain significance (Jun 10, 2024)
14-58318798-C-T		not specified	Uncertain significance (Apr 06, 2024)
14-58328267-A-G		not specified	Uncertain significance (Dec 02, 2024)
14-58328274-A-G		not specified	Uncertain significance (Jun 27, 2022)
14-58329538-G-A		not specified	Uncertain significance (Sep 22, 2023)
14-58329539-C-A		not specified	Uncertain significance (Sep 22, 2023)
14-58329568-C-G		not specified	Uncertain significance (Mar 07, 2023)
14-58329572-A-G		not specified	Likely benign (Nov 12, 2021)
14-58330037-A-T		not specified	Uncertain significance (Dec 22, 2023)
14-58330048-A-C		not specified	Uncertain significance (Oct 05, 2023)
14-58330065-A-G		not specified	Uncertain significance (Jul 16, 2024)
14-58346423-A-G		not specified	Uncertain significance (Oct 12, 2024)
14-58346456-A-G		not specified	Uncertain significance (Aug 30, 2022)
14-58346465-A-G		not specified	Uncertain significance (Oct 26, 2022)
14-58347670-A-T		not specified	Uncertain significance (Oct 29, 2021)
14-58347684-A-C		not specified	Uncertain significance (Feb 15, 2023)
14-58347730-A-G		not specified	Uncertain significance (Apr 07, 2023)
14-58347756-A-G		not specified	Uncertain significance (Jan 04, 2022)
14-58347801-G-C		not specified	Uncertain significance (Oct 12, 2024)
14-58347826-T-A		not specified	Uncertain significance (Sep 07, 2022)
14-58351121-G-A		not specified	Uncertain significance (Jul 26, 2022)
14-58351139-G-A		not specified	Uncertain significance (Oct 22, 2021)
14-58353680-G-A		not specified	Uncertain significance (Jul 27, 2024)
14-58353796-C-G		not specified	Uncertain significance (Jan 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARID4A	protein_coding	protein_coding	ENST00000355431	23	75503

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	2.60e-8	124754	5	985	125744	0.00394

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.45	524	626	0.837	0.0000306	8339
Missense in Polyphen		181	279.54	0.64749		3624
Synonymous	0.295	211	217	0.974	0.0000110	2189
Loss of Function	7.06	4	65.9	0.0607	0.00000360	885

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00314	0.00307
Ashkenazi Jewish	0.00934	0.00817
East Asian	0.0000554	0.0000544
Finnish	0.00382	0.00370
European (Non-Finnish)	0.00599	0.00562
Middle Eastern	0.0000554	0.0000544
South Asian	0.00302	0.00275
Other	0.00440	0.00408

dbNSFP

Source: dbNSFP

• Function: FUNCTION: DNA-binding protein which modulates activity of several transcription factors including RB1 (retinoblastoma-associated protein) and AR (androgen receptor) (By similarity). May function as part of an mSin3A repressor complex (PubMed:14581478). Has no intrinsic transcriptional activity (By similarity). 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 ARID4B (By similarity). Involved in spermatogenesis, together with ARID4B, where it acts as a transcriptional coactivator for AR 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 (By similarity). 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:F8VPQ2, ECO:0000269|PubMed:14581478}.
• Pathway: HDACs deacetylate histones;Chromatin modifying enzymes;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.211

Intolerance Scores

• loftool: 0.351
• rvis_EVS: -1.19
• rvis_percentile_EVS: 5.85

Haploinsufficiency Scores

• pHI: 0.626
• hipred: Y
• hipred_score: 0.775
• ghis: 0.624

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.898

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arid4a
• Phenotype: immune system phenotype; renal/urinary system phenotype; skeleton 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); 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); neoplasm; respiratory system phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype

Gene ontology

• Biological process: regulation of gene expression by genetic imprinting;regulation of transcription by RNA polymerase II;spermatogenesis;histone deacetylation;histone H4-K20 trimethylation;histone H3-K9 trimethylation;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;erythrocyte development;histone H3-K4 trimethylation;establishment of Sertoli cell barrier
• Cellular component: nucleus;nucleoplasm;cytosol;plasma membrane;transcriptional repressor complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;histone deacetylase activity;transcription regulatory region DNA binding