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.

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.

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	2
missense			19	3	1	23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	4	2

Variants in APOBEC3F

This is a list of pathogenic ClinVar variants found in the APOBEC3F region.

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

Position	Type	Phenotype	Significance	ClinVar
22-39040967-C-A		not specified	Uncertain significance (Dec 21, 2022)
22-39043004-C-G		not specified	Uncertain significance (Apr 25, 2022)
22-39044944-T-C		not specified	Uncertain significance (Mar 29, 2024)
22-39044965-G-C		not specified	Uncertain significance (Jan 03, 2024)
22-39045049-A-G		not specified	Uncertain significance (Aug 10, 2021)
22-39045067-G-A		not specified	Uncertain significance (Apr 12, 2022)
22-39045152-G-A		not specified	Uncertain significance (Nov 08, 2022)
22-39045199-G-C		not specified	Uncertain significance (Jun 18, 2024)
22-39045213-C-A		not specified	Uncertain significance (Jan 18, 2022)
22-39045429-A-C			Likely benign (Jul 09, 2018)
22-39045501-C-A		not specified	Uncertain significance (May 25, 2022)
22-39045512-T-C		not specified	Uncertain significance (Apr 23, 2024)
22-39045521-G-A		not specified	Uncertain significance (Jan 22, 2024)
22-39049431-G-A			Benign (Aug 01, 2018)
22-39049480-C-T		not specified	Uncertain significance (Jan 31, 2022)
22-39049546-C-G		not specified	Uncertain significance (Mar 21, 2023)
22-39049553-C-G		not specified	Uncertain significance (Dec 15, 2022)
22-39049553-C-T		not specified	Uncertain significance (Mar 21, 2023)
22-39049555-T-C		not specified	Uncertain significance (Mar 21, 2023)
22-39052137-C-T			Likely benign (Jul 13, 2018)
22-39052141-C-G		not specified	Uncertain significance (May 06, 2022)
22-39052233-A-G		not specified	Uncertain significance (Jan 10, 2023)
22-39052270-A-G			Benign (Jul 26, 2018)
22-39052305-C-T		not specified	Uncertain significance (Jul 08, 2022)
22-39052345-G-C		not specified	Uncertain significance (Feb 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APOBEC3F	protein_coding	protein_coding	ENST00000308521	7	13307

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.35e-7	0.829	125701	0	47	125748	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.29	275	221	1.24	0.0000134	2478
Missense in Polyphen		85	79.691	1.0666		949
Synonymous	-2.82	118	84.9	1.39	0.00000549	654
Loss of Function	1.50	14	21.5	0.652	0.00000123	212

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000236	0.000235
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000182	0.000176
Middle Eastern	0.000163	0.000163
South Asian	0.000457	0.000457
Other	0.000326	0.000326

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

• 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

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

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