APOBEC2

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

Basic information

Region (hg38): 6:41053202-41064891

Links

ENSG00000124701

∙ NCBI:10930 ∙ OMIM:604797 ∙ HGNC:605 ∙ Uniprot:Q9Y235 ∙ 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 APOBEC2 gene.

not_specified (28 variants)
EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APOBEC2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006789.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			26 clinvar	1 clinvar	1 clinvar	28
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	26	2	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APOBEC2	protein_coding	protein_coding	ENST00000244669	2	11208

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0171	0.898	125731	0	16	125747	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.214	136	129	1.05	0.00000749	1462
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000792	0.0000791
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

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}.;
Pathway: Metabolism of RNA;Formation of the Editosome;mRNA Editing: C to U Conversion;mRNA Editing (Consensus)

Recessive Scores

pRec: 0.120

Intolerance Scores

loftool: 0.603
rvis_EVS: 0.55
rvis_percentile_EVS: 81.38

Haploinsufficiency Scores

pHI: 0.705
hipred: N
hipred_score: 0.398
ghis: 0.420

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.996

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Apobec2
Phenotype: muscle phenotype; growth/size/body region phenotype; skeleton phenotype; normal phenotype;

Zebrafish Information Network

Gene name: apobec2b
Affected structure: Muller cell
Phenotype tag: abnormal
Phenotype quality: cellular potency

Gene ontology

Biological process: mRNA processing;cytidine deamination;cytidine to uridine editing;mRNA modification;DNA demethylation
Cellular component: nucleus;cytoplasm
Molecular function: RNA binding;cytidine deaminase activity;identical protein binding;metal ion binding