APOBEC3B

protein-coding

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

Gene summary

This gene is a member of the cytidine deaminase gene family. It is one of seven related genes or pseudogenes found in a cluster, thought to result from gene duplication, on chromosome 22. Members of the cluster encode proteins that are structurally and functionally related to the C to U RNA-editing cytidine deaminase APOBEC1. It is thought that the proteins may be RNA editing enzymes and have roles in growth or cell cycle control. A hybrid gene results from the deletion of approximately 29.5 kb of sequence between this gene, APOBEC3B, and the adjacent gene APOBEC3A. The breakpoints of the deletion are within the two genes, so the deletion allele is predicted to have the promoter and coding region of APOBEC3A, but the 3' UTR of APOBEC3B. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2012]

MANE transcript

NM_004900.5

Inheritance

—

ClinVar variants

U:41B:13

Top phenotype

APOBEC3B-related condition

gnomAD constraint

pLI —, LoF o/e 0.97

Max pathogenic AF

—

Genomic locus

chr22:38,982,347-38,992,804

External References & Databases

Ensembl (ENSG00000179750)

Transcript & Mutation Effects

hg38 • Region Span ~10.5 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 APOBEC3B variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 43

not providedTotal: 10

APOBEC3B-related conditionTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004900.5. 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	2
missense			40 clinvar	10 clinvar	1 clinvar	51
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	41	10	3	54

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004900.5	RefSeq	NP_004891.5	8	MANE Select
ENST00000333467.4	Ensembl	ENSP00000327459.3	8	MANE Select
NM_001270411.2	RefSeq	NP_001257340.2	8	Standard
ENST00000335760.9	Ensembl	ENSP00000338897.5	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metabolism of RNA
Formation of the Editosome
mRNA Editing: C to U Conversion
mRNA Editing

Biological Process

cytidine deamination
negative regulation of transposition
cytidine to uridine editing
innate immune response
defense response to virus

Molecular Function

RNA binding
cytidine deaminase activity
zinc ion binding
deoxycytidine deaminase activity

Cellular Component

nucleus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000333467
Coding exons: 8
Length: 10458
Individuals with no LoFs: 122803
Homozygous LoFs: 106
Heterozygous LoFs: 1856
Defined: 124765
p: 0.00789

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.522	210	232	0.904	0.0000147	2494
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.059	0.055	notable
Latino/Admixed American	0.0092	0.0071	notable
Ashkenazi Jewish	0.0037	0.0037	notable
East Asian	0.0020	0.0011	notable
Finnish	0.0026	0.0026	notable
European (Non-Finnish)	0.0034	0.0032	notable
South Asian	0.012	0.011	notable
Other	0.0074	0.0069	notable

dbNSFP Gene Annotations

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}.;

Intolerance Scores

RVIS EVS: 2.2
RVIS percentile EVS: 98.12

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0886

Gene Damage Prediction

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