GeneBe

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.

  • not_specified (117 variants)
  • not_provided (1 variants)
  • Multiple_myeloma (1 variants)

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. These statistics are base on transcript: NM_000002892.4. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
0
missense
113
clinvar
4
clinvar
 117
nonsense
1
clinvar
 1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
1
clinvar
 1
Total 0 1 113 5 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ARID4Aprotein_codingprotein_codingENST00000355431 2375503
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.002.60e-812475459851257440.00394
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.455246260.8370.00003068339
Missense in Polyphen181279.540.647493624
Synonymous0.2952112170.9740.00001102189
Loss of Function7.06465.90.06070.00000360885

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.003140.00307
Ashkenazi Jewish0.009340.00817
East Asian0.00005540.0000544
Finnish0.003820.00370
European (Non-Finnish)0.005990.00562
Middle Eastern0.00005540.0000544
South Asian0.003020.00275
Other0.004400.00408

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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