APOBEC3B

apolipoprotein B mRNA editing enzyme catalytic subunit 3B, the group of Apolipoprotein B mRNA editing enzyme catalytic subunits|Minor histocompatibility antigens

Basic information

Region (hg38): 22:38982347-38992804

Links

ENSG00000179750 ∙ NCBI:9582 ∙ OMIM:607110 ∙ HGNC:17352 ∙ Uniprot:Q9UH17 ∙ 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 APOBEC3B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APOBEC3B 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	2
missense			11	4		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	4	2

Variants in APOBEC3B

This is a list of pathogenic ClinVar variants found in the APOBEC3B region.

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

Position	Type	Phenotype	Significance	ClinVar
22-38984080-C-G		not specified	Uncertain significance (Aug 10, 2021)
22-38984126-C-T			Benign (Jun 28, 2018)
22-38984140-A-G		not specified	Uncertain significance (Mar 29, 2023)
22-38984152-A-G		not specified	Uncertain significance (Jul 06, 2021)
22-38984190-C-T			Likely benign (-)
22-38984232-G-T			Uncertain significance (-)
22-38985899-A-C		not specified	Benign (-)
22-38985962-T-G			Likely benign (Jul 01, 2023)
22-38986299-A-C		not specified	Likely benign (Oct 02, 2023)
22-38986390-C-T		not specified	Uncertain significance (May 20, 2024)
22-38986391-G-A		not specified	Likely benign (Jan 16, 2024)
22-38989481-C-G		not specified	Uncertain significance (Sep 12, 2023)
22-38989505-T-C			Benign (Nov 16, 2018)
22-38989518-C-T			Likely benign (-)
22-38989590-A-G			Uncertain significance (-)
22-38991404-C-A		not specified	Uncertain significance (May 26, 2024)
22-38991407-T-A		not specified	Uncertain significance (May 26, 2024)
22-38991446-T-A		not specified	Uncertain significance (Feb 28, 2024)
22-38991454-C-A		not specified	Uncertain significance (Jun 03, 2022)
22-38991525-G-A		not specified	Uncertain significance (Mar 01, 2023)
22-38991587-C-T		not specified	Uncertain significance (Aug 30, 2022)
22-38992041-G-C			Likely benign (-)
22-38992066-C-T		not specified	Uncertain significance (Oct 29, 2021)
22-38992067-G-A			Likely benign (-)
22-38992084-C-G		not specified	Uncertain significance (Apr 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APOBEC3B	protein_coding	protein_coding	ENST00000333467	8	10458

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.21e-16	0.0132	122803	106	1856	124765	0.00789

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.522	210	232	0.904	0.0000147	2494
Missense in Polyphen		85	109.36	0.77723		1305
Synonymous	-0.829	100	90.0	1.11	0.00000569	685
Loss of Function	0.158	24	24.9	0.966	0.00000135	245

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0682	0.0642
Ashkenazi Jewish	0.00372	0.00368
East Asian	0.00202	0.00115
Finnish	0.00261	0.00255
European (Non-Finnish)	0.00341	0.00322
Middle Eastern	0.00202	0.00115
South Asian	0.0122	0.0110
Other	0.00742	0.00693

dbNSFP

Source: dbNSFP

• Function: FUNCTION: DNA deaminase (cytidine deaminase) which acts as an inhibitor of retrovirus replication and retrotransposon mobility via deaminase-dependent and -independent mechanisms. After the penetration of retroviral nucleocapsids into target cells of infection and the initiation of reverse transcription, it can induce the conversion of cytosine to uracil in the minus-sense single-strand viral DNA, leading to G-to-A hypermutations in the subsequent plus-strand viral DNA. The resultant detrimental levels of mutations in the proviral genome, along with a deamination- independent mechanism that works prior to the proviral integration, together exert efficient antiretroviral effects in infected target cells. Selectively targets single-stranded DNA and does not deaminate double-stranded DNA or single-or double- stranded RNA. Exhibits antiviral activity against simian immunodeficiency virus (SIV), hepatitis B virus (HBV) and human T- cell leukemia virus type 1 (HTLV-1) and may inhibit the mobility of LTR and non-LTR retrotransposons. {ECO:0000269|PubMed:12859895, ECO:0000269|PubMed:15466872, ECO:0000269|PubMed:16060832, ECO:0000269|PubMed:16527742, ECO:0000269|PubMed:20062055, ECO:0000269|PubMed:22457529}.
• Pathway: Metabolism of RNA;Formation of the Editosome;mRNA Editing: C to U Conversion;mRNA Editing (Consensus)

Intolerance Scores

• rvis_EVS: 2.2
• rvis_percentile_EVS: 98.12

Haploinsufficiency Scores

• pHI: 0.114
• hipred: N
• hipred_score: 0.218
• ghis: 0.408

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0886

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Apobec3
• Phenotype: hematopoietic 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); normal phenotype; neoplasm; immune system phenotype

Gene ontology

• Biological process: cytidine deamination;negative regulation of transposition;cytidine to uridine editing;innate immune response;defense response to virus;DNA demethylation
• Cellular component: nucleus;cytoplasm
• Molecular function: RNA binding;cytidine deaminase activity;zinc ion binding;deoxycytidine deaminase activity