ARID3A

protein-coding

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

Gene summary

This gene encodes a member of the ARID (AT-rich interaction domain) family of DNA binding proteins. It was found by homology to the Drosophila dead ringer gene, which is important for normal embryogenesis. Other ARID family members have roles in embryonic patterning, cell lineage gene regulation, cell cycle control, transcriptional regulation, and possibly in chromatin structure modification. [provided by RefSeq, Jul 2008]

Previous symbols:

DRIL1

MANE transcript

NM_005224.3

Inheritance

—

ClinVar variants

U:114B:13

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.09

Max pathogenic AF

—

Genomic locus

chr19:925,781-975,939

External References & Databases

Ensembl (ENSG00000116017)

Transcript & Mutation Effects

hg38 • Region Span ~50.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ARID3A variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 114

not providedTotal: 6

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005224.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar	3 clinvar	5
missense			109 clinvar	7 clinvar	1 clinvar	117
nonsense			3 clinvar			3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	114	9	4	127

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005224.3	RefSeq	NP_005215.1	8	MANE Select
ENST00000263620.8	Ensembl	ENSP00000263620.2	8	MANE Select
ENST00000457152.3	Ensembl	ENSP00000440911.2	3	Standard
ENST00000587532.5	Ensembl	ENSP00000464969.3	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
positive regulation of transcription by RNA polymerase II

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

Cellular Component

nucleus
nucleoplasm
cytosol
intracellular membrane-bounded organelle
membrane raft

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000263620
Coding exons: 8
Length: 50159
Individuals with no LoFs: 124671
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 124673
p: 0.00000802

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.27	296	364	0.813	0.0000248	3732
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.00012	0.00010	rare
East Asian	0.000055	0.000055	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.111

Intolerance Scores

LoFtool: 0.352
RVIS EVS: -0.42
RVIS percentile EVS: 25.64

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.982

Gene Damage Prediction

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