APOBEC3G
protein-codingapolipoprotein B mRNA editing enzyme catalytic subunit 3G, the group of Apolipoprotein B mRNA editing enzyme catalytic subunits
Gene summary
This gene is a member of the cytidine deaminase gene family. It is one of seven related genes or pseudogenes found in a cluster, thought to result from gene duplication, on chromosome 22. Members of the cluster encode proteins that are structurally and functionally related to the C to U RNA-editing cytidine deaminase APOBEC1. The protein encoded by this gene catalyzes site-specific deamination of both RNA and single-stranded DNA. The encoded protein has been found to be a specific inhibitor of human immunodeficiency virus-1 (HIV-1) infectivity. [provided by RefSeq, Mar 2017]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~10.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to APOBEC3G variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_021822.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 36 | 2 | 38 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 36 | 2 | 0 | 38 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_068594.1 | 8 | MANE Select | |
| Ensembl | ENSP00000385057.3 | 8 | MANE Select | |
| RefSeq | NP_001336365.1 | 7 | Standard | |
| RefSeq | NP_001336366.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Dual hijack model of Vif in HIV infection
- Disease
- hiv-1 defeats host-mediated resistance by cem15
- Host Interactions of HIV factors
- HIV Infection
Biological Process
- positive regulation of defense response to virus by host
- cytidine deamination
- negative regulation of transposition
- viral process
- base conversion or substitution editing
Molecular Function
- RNA binding
- cytidine deaminase activity
- protein binding
- zinc ion binding
- dCTP deaminase activity
Cellular Component
- P-body
- nucleus
- cytoplasm
- cytosol
- apolipoprotein B mRNA editing enzyme complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000407997
- Coding exons
- 8
- Length
- 46825
- Individuals with no LoFs
- 125493
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 253
- Defined
- 125748
- p
- 0.00101
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.151 | 227 | 233 | 0.972 | 0.0000137 | 2569 |
| Missense (PolyPhen) | 75 | 75.993 | 0.98694 | 1003 | ||
| Synonymous | 0.00267 | 86 | 86.0 | 1.00 | 0.00000514 | 672 |
| Loss of Function | -0.985 | 28 | 22.9 | 1.22 | 0.00000119 | 243 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00075 | 0.00074 | rare |
| Latino/Admixed American | 0.00026 | 0.00026 | rare |
| Ashkenazi Jewish | 0.0012 | 0.0012 | notable |
| East Asian | 0.00016 | 0.00016 | rare |
| Finnish | 0.00019 | 0.00018 | rare |
| European (Non-Finnish) | 0.00071 | 0.00071 | rare |
| South Asian | 0.0043 | 0.0043 | notable |
| Other | 0.00065 | 0.00065 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: DNA deaminase (cytidine deaminase) which acts as an inhibitor of retrovirus replication and retrotransposon mobility via deaminase-dependent and -independent mechanisms. Exhibits potent 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 simian immunodeficiency viruses (SIVs), hepatitis B virus (HBV), equine infectious anemia virus (EIAV), xenotropic MuLV-related virus (XMRV) and simian foamy virus (SFV). May inhibit the mobility of LTR and non-LTR retrotransposons. {ECO:0000269|PubMed:12167863, ECO:0000269|PubMed:12808465, ECO:0000269|PubMed:12808466, ECO:0000269|PubMed:12809610, ECO:0000269|PubMed:12859895, ECO:0000269|PubMed:12970355, ECO:0000269|PubMed:14528300, ECO:0000269|PubMed:14557625, ECO:0000269|PubMed:15031497, ECO:0000269|PubMed:16378963, ECO:0000269|PubMed:16527742, ECO:0000269|PubMed:18288108, ECO:0000269|PubMed:19458006, ECO:0000269|PubMed:20219927, ECO:0000269|PubMed:20335265, ECO:0000269|PubMed:21123384, ECO:0000269|PubMed:21835787, ECO:0000269|PubMed:22791714, ECO:0000269|PubMed:22807680, ECO:0000269|PubMed:22915799, ECO:0000269|PubMed:23097438, ECO:0000269|PubMed:23152537}.;
Recessive Scores
- pRec
- 0.0568
Intolerance Scores
- LoFtool
- 0.860
- RVIS EVS
- 0.07
- RVIS percentile EVS
- 58.96
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.894
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |