ARID5A

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

Basic information

Region (hg38): 2:96536742-96552634

Links

ENSG00000196843 ∙ NCBI:10865 ∙ OMIM:611583 ∙ HGNC:17361 ∙ Uniprot:Q03989 ∙ 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 ARID5A gene.

• Inborn genetic diseases (22 variants)
• ARID5A-related condition (2 variants)
• not specified (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARID5A 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			24			24
nonsense						0
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	0	0

Variants in ARID5A

This is a list of pathogenic ClinVar variants found in the ARID5A region.

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

Position	Type	Phenotype	Significance	ClinVar
2-96549362-G-T		not specified	Uncertain significance (Apr 18, 2023)
2-96549437-GCC-G		not specified	Uncertain significance (Sep 11, 2023)
2-96549440-CCA-C		not specified	Uncertain significance (Sep 11, 2023)
2-96550662-A-G		not specified	Uncertain significance (Oct 31, 2023)
2-96550684-G-A		not specified	Uncertain significance (Nov 02, 2023)
2-96550699-C-T		not specified	Uncertain significance (Mar 29, 2022)
2-96550707-G-A		not specified	Uncertain significance (Jan 17, 2023)
2-96551095-C-A		ARID5A-related disorder	Likely benign (Feb 13, 2024)
2-96551109-G-A		ARID5A-related disorder	Likely benign (Jan 29, 2021)
2-96551155-G-T		not specified	Uncertain significance (Dec 01, 2022)
2-96551186-G-A		not specified	Uncertain significance (Jan 03, 2024)
2-96551217-T-A		not specified	Uncertain significance (Mar 29, 2022)
2-96551307-A-G		not specified	Uncertain significance (Dec 22, 2023)
2-96551370-G-A		not specified	Uncertain significance (Aug 30, 2021)
2-96551376-G-A		not specified	Uncertain significance (Jun 11, 2021)
2-96551391-C-T		not specified	Uncertain significance (Dec 15, 2023)
2-96551394-C-T		not specified	Uncertain significance (Nov 21, 2022)
2-96551396-C-A		not specified	Uncertain significance (Jun 09, 2022)
2-96551421-C-T		not specified	Uncertain significance (Apr 18, 2023)
2-96551439-T-C		ARID5A-related disorder	Likely benign (Apr 17, 2023)
2-96551514-C-T		not specified	Uncertain significance (Feb 28, 2023)
2-96551552-G-A		not specified	Uncertain significance (Dec 16, 2023)
2-96551574-C-T		not specified	Uncertain significance (Feb 05, 2024)
2-96551576-G-A		not specified	Uncertain significance (Feb 12, 2024)
2-96551639-C-A		not specified	Uncertain significance (Sep 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARID5A	protein_coding	protein_coding	ENST00000357485	7	15896

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.945	0.0548	125670	0	10	125680	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.67	253	340	0.745	0.0000199	3803
Missense in Polyphen		58	96.777	0.59931		1045
Synonymous	1.17	137	156	0.881	0.0000102	1251
Loss of Function	3.49	2	18.0	0.111	8.44e-7	242

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000970	0.0000952
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000579	0.0000544
Finnish	0.0000470	0.0000462
European (Non-Finnish)	0.0000474	0.0000440
Middle Eastern	0.0000579	0.0000544
South Asian	0.0000362	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to AT-rich stretches in the modulator region upstream of the human cytomegalovirus major intermediate early gene enhancer. May act as repressor and down-regulate enhancer- dependent gene expressison (PubMed:8649988). May positively regulate chondrocyte-specific transcription such as of COL2A1 in collaboration with SOX9 and positively regulate histone H3 acetylation at chondrocyte-specific genes. May stimulate early- stage chondrocyte differentiation and inhibit later stage differention (By similarity). Can repress ESR1-mediated transcriptional activation; proposed to act as corepressor for selective nuclear hormone receptors (PubMed:15941852). As RNA- binding protein involved in the regulation of inflammatory response by stabilizing selective inflammation-related mRNAs, such as IL6, STAT3 and TBX21. Binds to stem loop structures located in the 3'UTRs of IL6, STAT3 and TBX21 mRNAs; at least for STAT3 prevents binding of ZC3H12A to the mRNA stem loop structure thus inhibiting its degradation activity. Contributes to elevated IL6 levels possibly implicated in autoimmunity processes. IL6- dependent stabilization of STAT3 mRNA may promote differentiation of naive CD4+ T-cells into T-helper Th17 cells. In CD4+ T-cells may also inhibit RORC-induced Th17 cell differentiation independently of IL6 signaling. Stabilization of TBX21 mRNA contributes to elevated interferon-gamma secretion in Th1 cells possibly implicated in the establishment of septic shock (By similarity). {ECO:0000250|UniProtKB:Q3U108, ECO:0000269|PubMed:15941852, ECO:0000269|PubMed:8649988}.

Recessive Scores

• pRec: 0.0971

Intolerance Scores

• loftool: 0.0510
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.64

Haploinsufficiency Scores

• pHI: 0.0967
• hipred: N
• hipred_score: 0.435
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.298

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arid5a
• Phenotype: homeostasis/metabolism phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase II;innate immune response;negative regulation of transcription, DNA-templated;cellular response to estrogen stimulus
• Cellular component: nucleus;nucleoplasm;nucleolus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;transcription corepressor activity;RNA binding;protein binding;transcription factor binding;estrogen receptor binding;sequence-specific DNA binding;transcription regulatory region DNA binding;retinoid X receptor binding;thyroid hormone receptor binding;androgen receptor binding