APOBEC2

protein-coding

apolipoprotein B mRNA editing enzyme catalytic subunit 2, the group of Apolipoprotein B mRNA editing enzyme catalytic subunits

Gene summary

Enables cytidine deaminase activity. Involved in positive regulation of gene expression via chromosomal CpG island demethylation. Acts upstream of or within cytidine to uridine editing. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_006789.4

Inheritance

—

ClinVar variants

U:30B:3

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.47

Max pathogenic AF

—

Genomic locus

chr6:41,053,202-41,064,891

External References & Databases

Ensembl (ENSG00000124701)

Transcript & Mutation Effects

hg38 • Region Span ~11.7 kb

Loading mutation effect viewer...

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 APOBEC2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 30

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

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006789.4. 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				1 clinvar		1
missense			30 clinvar	1 clinvar	1 clinvar	32
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	30	2	1	33

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006789.4	RefSeq	NP_006780.1	2	MANE Select
ENST00000244669.3	Ensembl	ENSP00000244669.2	2	MANE Select
ENST00000899065.1	Ensembl	ENSP00000569124.1	2	Standard
ENST00001038519.1	Ensembl	ENSP00000708336.1	2	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
apobec2b	Danio rerio	Structure: Muller cell Quality: cellular potency abnormal

Gene / Model

Organism

Observed Phenotype

apobec2b

Danio rerio

Structure: Muller cell

Quality: cellular potency

abnormal

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

mRNA processing
cytidine deamination
cytidine to uridine editing
mRNA modification
DNA demethylation

Molecular Function

RNA binding
cytidine deaminase activity
identical protein binding
metal ion binding

Cellular Component

nucleus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000244669
Coding exons: 2
Length: 11208
Individuals with no LoFs: 125731
Homozygous LoFs: 0
Heterozygous LoFs: 16
Defined: 125747
p: 0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.214	136	129	1.05	0.00000749	1462
Missense (PolyPhen)		43	47.647	0.90248		569
Synonymous	-0.821	62	54.3	1.14	0.00000312	436
Loss of Function	1.45	4	8.59	0.466	4.33e-7	100

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000079	0.000079	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probable C to U editing enzyme whose physiological substrate is not yet known. Does not display detectable apoB mRNA editing. Has a low intrinsic cytidine deaminase activity. May play a role in the epigenetic regulation of gene expression through the process of active DNA demethylation. {ECO:0000269|PubMed:17187054, ECO:0000269|PubMed:21496894}.;

Recessive Scores

pRec: 0.120

Intolerance Scores

LoFtool: 0.603
RVIS EVS: 0.55
RVIS percentile EVS: 81.38

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.996

Gene Damage Prediction

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