ARID3B

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

Basic information

Region (hg38): 15:74541206-74598131

Links

ENSG00000179361 ∙ NCBI:10620 ∙ OMIM:612457 ∙ HGNC:14350 ∙ Uniprot:Q8IVW6 ∙ 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 ARID3B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARID3B 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					3	3
missense			20	1		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	1	3

Variants in ARID3B

This is a list of pathogenic ClinVar variants found in the ARID3B region.

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

Position	Type	Phenotype	Significance	ClinVar
15-74543949-C-G		not specified	Uncertain significance (May 11, 2022)
15-74543985-C-G		not specified	Uncertain significance (May 09, 2024)
15-74543987-G-C		not specified	Uncertain significance (Mar 15, 2024)
15-74544097-C-T		not specified	Uncertain significance (Feb 16, 2023)
15-74544324-C-G		not specified	Uncertain significance (Dec 01, 2022)
15-74544333-A-G		not specified	Uncertain significance (Sep 30, 2024)
15-74544375-C-T		not specified	Uncertain significance (Sep 17, 2021)
15-74544411-A-G		not specified	Uncertain significance (Jan 09, 2024)
15-74544426-G-A		not specified	Uncertain significance (Jan 23, 2024)
15-74544433-C-T		not specified	Uncertain significance (Jun 18, 2021)
15-74544439-T-C		not specified	Uncertain significance (Sep 25, 2024)
15-74572877-T-C		not specified	Uncertain significance (Jul 13, 2022)
15-74572931-A-G		not specified	Uncertain significance (Apr 08, 2023)
15-74573186-G-A		not specified	Likely benign (Feb 11, 2022)
15-74589834-C-A			Benign (Nov 15, 2017)
15-74589911-G-A			Benign (Jan 05, 2018)
15-74591251-C-T		not specified	Uncertain significance (Oct 04, 2022)
15-74591254-C-T		not specified	Uncertain significance (May 02, 2024)
15-74591311-G-A		not specified	Uncertain significance (Oct 29, 2024)
15-74591317-G-A		not specified	Uncertain significance (Oct 25, 2022)
15-74591318-G-C		not specified	Uncertain significance (Oct 03, 2022)
15-74591598-C-T		not specified	Uncertain significance (May 16, 2022)
15-74591623-C-G		not specified	Uncertain significance (Mar 30, 2024)
15-74591643-C-G		not specified	Uncertain significance (Oct 20, 2023)
15-74591649-G-A		not specified	Uncertain significance (Sep 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARID3B	protein_coding	protein_coding	ENST00000346246	8	56955

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.380	0.620	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.27	267	332	0.804	0.0000193	3610
Missense in Polyphen		81	127.97	0.63294		1383
Synonymous	-0.629	142	133	1.07	0.00000789	1166
Loss of Function	3.39	5	22.3	0.224	0.00000110	254

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000302	0.0000302
Ashkenazi Jewish	0.00	0.00
East Asian	0.000114	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000363	0.0000352
Middle Eastern	0.000114	0.000109
South Asian	0.0000985	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor which may be involved in neuroblastoma growth and malignant transformation. Favors nuclear targeting of ARID3A. {ECO:0000269|PubMed:16951138, ECO:0000269|PubMed:17400556}.

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.369
• rvis_EVS: -0.22
• rvis_percentile_EVS: 37.43

Haploinsufficiency Scores

• pHI: 0.266
• hipred: Y
• hipred_score: 0.728
• ghis: 0.545

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.985

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arid3b
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; embryo 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; hematopoietic system 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); craniofacial phenotype; cellular phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: biological_process;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;RNA polymerase II proximal promoter sequence-specific DNA binding;RNA polymerase II distal enhancer sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;protein binding