GeneBe

APOBEC3F

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

Basic information

Region (hg38): 22:39040604-39055972

Links

ENSG00000128394 ∙ NCBI:200316 ∙ OMIM:608993 ∙ HGNC:17356 ∙ Uniprot:Q8IUX4 ∙ 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 APOBEC3F gene.

  • not_specified (51 variants)
  • not_provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APOBEC3F gene is commonly pathogenic or not. These statistics are base on transcript: NM_000145298.6. 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
clinvar
 2
missense
47
clinvar
7
clinvar
1
clinvar
 55
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 47 8 2
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
APOBEC3Fprotein_codingprotein_codingENST00000308521 713307
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.35e-70.8291257010471257480.000187
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.292752211.240.00001342478
Missense in Polyphen8579.6911.0666949
Synonymous-2.8211884.91.390.00000549654
Loss of Function1.501421.50.6520.00000123212

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002360.000235
Ashkenazi Jewish0.000.00
East Asian0.0001630.000163
Finnish0.00004620.0000462
European (Non-Finnish)0.0001820.000176
Middle Eastern0.0001630.000163
South Asian0.0004570.000457
Other0.0003260.000326

dbNSFP

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. Exhibits antiviral activity against vif-deficient HIV-1. 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 also against hepatitis B virus (HBV), equine infectious anemia virus (EIAV), xenotropic MuLV-related virus (XMRV) and simian foamy virus (SFV) and may inhibit the mobility of LTR and non-LTR retrotransposons. May also play a role in the epigenetic regulation of gene expression through the process of active DNA demethylation. {ECO:0000269|PubMed:15152192, ECO:0000269|PubMed:16378963, ECO:0000269|PubMed:16527742, ECO:0000269|PubMed:19458006, ECO:0000269|PubMed:20062055, ECO:0000269|PubMed:20219927, ECO:0000269|PubMed:20335265, ECO:0000269|PubMed:21496894, ECO:0000269|PubMed:21835787, ECO:0000269|PubMed:22807680, ECO:0000269|PubMed:22915799, ECO:0000269|PubMed:23097438, ECO:0000269|PubMed:23152537}.;
Pathway
Disease;hiv-1 defeats host-mediated resistance by cem15;Host Interactions of HIV factors;HIV Infection;Infectious disease;APOBEC3G mediated resistance to HIV-1 infection;Vif-mediated degradation of APOBEC3G (Consensus)

Recessive Scores

pRec
0.0507

Intolerance Scores

loftool
0.739
rvis_EVS
1.18
rvis_percentile_EVS
92.78

Haploinsufficiency Scores

pHI
hipred
N
hipred_score
0.356
ghis
0.498

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.220

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Gene ontology

Biological process
positive regulation of defense response to virus by host;cytidine deamination;negative regulation of transposition;base conversion or substitution editing;cytidine to uridine editing;negative regulation of viral genome replication;innate immune response;negative regulation of single stranded viral RNA replication via double stranded DNA intermediate;negative regulation of viral process;defense response to virus;DNA cytosine deamination;DNA demethylation
Cellular component
P-body;nucleus;cytoplasm;apolipoprotein B mRNA editing enzyme complex;ribonucleoprotein complex
Molecular function
RNA binding;cytidine deaminase activity;protein binding;zinc ion binding;identical protein binding