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.

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.

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						0
missense			13	1	1	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	13	1	1

Variants in APOBEC2

This is a list of pathogenic ClinVar variants found in the APOBEC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-41053352-C-A		not specified	Uncertain significance (Jun 29, 2023)
6-41053370-C-T		not specified	Uncertain significance (Dec 13, 2023)
6-41053381-G-A		not specified	Uncertain significance (Sep 29, 2022)
6-41061332-C-T		not specified	Uncertain significance (Oct 26, 2022)
6-41061346-C-G		not specified	Uncertain significance (Dec 17, 2023)
6-41061455-C-T		not specified	Uncertain significance (Aug 03, 2022)
6-41061494-G-A		not specified	Uncertain significance (Jun 26, 2023)
6-41061542-C-T		not specified	Uncertain significance (Dec 20, 2023)
6-41061559-G-C		not specified	Uncertain significance (Dec 13, 2022)
6-41061701-C-G		not specified	Uncertain significance (Mar 02, 2023)
6-41061791-T-C			Benign (Jul 31, 2018)
6-41061804-A-G		not specified	Uncertain significance (Jan 24, 2024)
6-41061818-A-G		not specified	Likely benign (Dec 06, 2022)
6-41061839-T-A		not specified	Uncertain significance (Jan 10, 2022)
6-41061842-G-A		not specified • EBV-positive nodal T- and NK-cell lymphoma	Uncertain significance (Feb 12, 2024)

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