ARID3A

AT-rich interaction domain 3A, the group of AT-rich interaction domain containing

Basic information

Region (hg38): 19:925781-975939

Previous symbols: [ "DRIL1" ]

Links

ENSG00000116017 ∙ NCBI:1820 ∙ OMIM:603265 ∙ HGNC:3031 ∙ Uniprot:Q99856 ∙ 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 ARID3A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARID3A 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				2	3	5
missense			35	3	1	39
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	36	5	4

Variants in ARID3A

This is a list of pathogenic ClinVar variants found in the ARID3A region.

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

Position	Type	Phenotype	Significance	ClinVar
19-929579-G-A		not specified	Likely benign (Dec 12, 2023)
19-929598-C-T		not specified	Uncertain significance (Nov 15, 2024)
19-929637-G-A		not specified	Uncertain significance (Apr 20, 2024)
19-929640-C-T		not specified	Uncertain significance (Nov 07, 2022)
19-929641-G-A		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
19-929647-G-A		not specified	Uncertain significance (Jun 13, 2023)
19-929652-G-C		not specified	Uncertain significance (Aug 20, 2024)
19-929655-C-T		not specified	Uncertain significance (Aug 13, 2021)
19-929658-G-A		not specified	Uncertain significance (Nov 03, 2022)
19-929673-C-T		not specified	Uncertain significance (Sep 20, 2024)
19-929676-G-A		not specified	Uncertain significance (Jul 25, 2024)
19-929686-G-A		not specified	Uncertain significance (Mar 06, 2023)
19-929694-C-T		not specified	Uncertain significance (Jan 09, 2024)
19-929763-G-A			Benign (Apr 24, 2018)
19-929763-G-T		not specified	Uncertain significance (Dec 05, 2023)
19-929784-C-T		not specified	Uncertain significance (Feb 22, 2023)
19-929791-C-T		not specified	Uncertain significance (Jul 14, 2021)
19-929805-G-A		not specified	Likely benign (Nov 13, 2023)
19-929812-G-A		not specified	Likely benign (Nov 13, 2023)
19-929824-C-T		not specified	Uncertain significance (May 02, 2024)
19-929889-G-A		not specified	Uncertain significance (Jun 11, 2024)
19-929895-A-G		not specified	Uncertain significance (Nov 20, 2024)
19-932431-G-A		not specified	Uncertain significance (Jan 08, 2024)
19-932458-G-A		not specified	Uncertain significance (Dec 02, 2022)
19-932458-G-T		not specified	Uncertain significance (Jun 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARID3A	protein_coding	protein_coding	ENST00000263620	8	50159

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.991	0.00935	124671	0	2	124673	0.00000802

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.27	296	364	0.813	0.0000248	3732
Missense in Polyphen		36	98.303	0.36622		999
Synonymous	-1.23	184	164	1.12	0.0000125	1243
Loss of Function	4.04	2	22.8	0.0876	0.00000128	244

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000117	0.0000998
East Asian	0.0000548	0.0000546
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000548	0.0000546
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor which may be involved in the control of cell cycle progression by the RB1/E2F1 pathway and in B-cell differentiation. {ECO:0000269|PubMed:11812999, ECO:0000269|PubMed:12692263}.
• Pathway: TP53 Regulates Transcription of Cell Cycle Genes;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest;TP53 Regulates Transcription of Cell Cycle Genes;Transcriptional Regulation by TP53;Direct p53 effectors (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.352
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.64

Haploinsufficiency Scores

• pHI: 0.333
• hipred: Y
• hipred_score: 0.831
• ghis: 0.516

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.982

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arid3a
• 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); normal 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; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; skeleton phenotype; immune system phenotype; limbs/digits/tail 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); growth/size/body region phenotype; cellular phenotype

Gene ontology

• Biological process: DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;cytosol;intracellular membrane-bounded organelle;membrane raft
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;chromatin binding;protein binding;protein homodimerization activity