APOBEC3A

apolipoprotein B mRNA editing enzyme catalytic subunit 3A, the group of Apolipoprotein B mRNA editing enzyme catalytic subunits

Basic information

Region (hg38): 22:38952741-38963184

Links

ENSG00000128383 ∙ NCBI:200315 ∙ OMIM:607109 ∙ HGNC:17343 ∙ Uniprot:P31941 ∙ 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 APOBEC3A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APOBEC3A 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				1		1
missense			5	1		6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	2	0

Variants in APOBEC3A

This is a list of pathogenic ClinVar variants found in the APOBEC3A region.

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

Position	Type	Phenotype	Significance	ClinVar
22-38959558-C-T		not specified	Uncertain significance (May 28, 2024)
22-38959615-T-A		not specified	Uncertain significance (Sep 16, 2021)
22-38959618-G-A		not specified	Uncertain significance (Jun 01, 2023)
22-38959638-T-C			Likely benign (Apr 01, 2022)
22-38961417-C-T		not specified	Likely benign (Sep 29, 2022)
22-38961418-G-A		not specified	Uncertain significance (Dec 01, 2022)
22-38961534-G-A		not specified	Uncertain significance (May 26, 2024)
22-38962182-C-A		not specified	Uncertain significance (Aug 02, 2022)
22-38962199-C-T		not specified	Uncertain significance (Nov 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APOBEC3A	protein_coding	protein_coding	ENST00000402255	5	10443

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00105	0.837	125702	5	41	125748	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.363	132	121	1.09	0.00000735	1310
Missense in Polyphen		29	34.466	0.84142		461
Synonymous	0.0764	48	48.7	0.986	0.00000319	363
Loss of Function	1.20	6	10.1	0.592	4.33e-7	110

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000444	0.000338
Ashkenazi Jewish	0.00	0.00
East Asian	0.000273	0.000272
Finnish	0.0000529	0.0000462
European (Non-Finnish)	0.000131	0.0000879
Middle Eastern	0.000273	0.000272
South Asian	0.000894	0.000784
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: DNA deaminase (cytidine deaminase) with restriction activity against viruses, foreign DNA and mobility of retrotransposons. Exhibits antiviral activity against adeno- associated virus (AAV) and human T-cell leukemia virus type 1 (HTLV-1) and may inhibit the mobility of LTR and non-LTR retrotransposons. Selectively targets single-stranded DNA and can deaminate both methylcytosine and cytosine in foreign DNA. Can induce somatic hypermutation in the nuclear and mitochondrial DNA. May also play a role in the epigenetic regulation of gene expression through the process of active DNA demethylation. {ECO:0000269|PubMed:10469298, ECO:0000269|PubMed:12859895, ECO:0000269|PubMed:16527742, ECO:0000269|PubMed:19461882, ECO:0000269|PubMed:20062055, ECO:0000269|PubMed:20615867, ECO:0000269|PubMed:21123384, ECO:0000269|PubMed:21368204, ECO:0000269|PubMed:21460793, ECO:0000269|PubMed:21496894, ECO:0000269|PubMed:22457529, ECO:0000269|PubMed:22896697}.
• Pathway: Metabolism of RNA;Formation of the Editosome;mRNA Editing: C to U Conversion;mRNA Editing (Consensus)

Intolerance Scores

• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.12

Haploinsufficiency Scores

• pHI: 0.0369
• hipred: N
• hipred_score: 0.218
• ghis: 0.448

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.749

Gene Damage Prediction

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

Gene ontology

• Biological process: cytidine deamination;negative regulation of transposition;cytidine to uridine editing;clearance of foreign intracellular DNA by conversion of DNA cytidine to uridine;negative regulation of viral genome replication;innate immune response;defense response to virus;DNA cytosine deamination;cellular response to xenobiotic stimulus;DNA demethylation
• Cellular component: nucleus;cytoplasm
• Molecular function: RNA binding;cytidine deaminase activity;protein binding;zinc ion binding;deoxycytidine deaminase activity