APOBEC3G
apolipoprotein B mRNA editing enzyme catalytic subunit 3G, the group of Apolipoprotein B mRNA editing enzyme catalytic subunits
Basic information
Region (hg38): 22:39077067-39087743
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the APOBEC3G 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 | 19 | 19 | ||||
| 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 | 0 | 0 |
Variants in APOBEC3G
This is a list of pathogenic ClinVar variants found in the APOBEC3G region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 22-39078950-G-A | not specified | Uncertain significance (Jan 25, 2023) | ||
| 22-39079002-C-T | not specified | Uncertain significance (Sep 25, 2023) | ||
| 22-39080960-G-A | not specified | Uncertain significance (Apr 19, 2023) | ||
| 22-39080967-G-A | not specified | Uncertain significance (Nov 10, 2022) | ||
| 22-39080975-C-G | not specified | Uncertain significance (Jun 16, 2023) | ||
| 22-39080985-G-C | not specified | Uncertain significance (Oct 03, 2022) | ||
| 22-39081125-C-T | not specified | Uncertain significance (Jan 24, 2023) | ||
| 22-39083738-A-G | not specified | Uncertain significance (Dec 02, 2022) | ||
| 22-39083857-C-G | not specified | Uncertain significance (Jun 05, 2024) | ||
| 22-39086341-T-G | not specified | Uncertain significance (May 23, 2023) | ||
| 22-39086357-G-T | not specified | Uncertain significance (Dec 03, 2021) | ||
| 22-39086361-T-C | not specified | Uncertain significance (Dec 12, 2023) | ||
| 22-39086387-T-G | not specified | Uncertain significance (Dec 02, 2022) | ||
| 22-39086437-C-A | not specified | Uncertain significance (May 26, 2022) | ||
| 22-39086478-C-T | not specified | Uncertain significance (May 24, 2023) | ||
| 22-39086481-G-A | not specified | Uncertain significance (Jun 29, 2022) | ||
| 22-39086519-C-T | not specified | Uncertain significance (Dec 14, 2023) | ||
| 22-39086541-C-A | not specified | Uncertain significance (Jan 19, 2024) | ||
| 22-39087050-G-T | not specified | Uncertain significance (Oct 10, 2023) | ||
| 22-39087092-A-G | not specified | Uncertain significance (Mar 30, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| APOBEC3G | protein_coding | protein_coding | ENST00000407997 | 8 | 46825 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 5.67e-21 | 0.000217 | 125493 | 2 | 253 | 125748 | 0.00101 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.151 | 227 | 233 | 0.972 | 0.0000137 | 2569 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00101 | 0.000999 |
| Ashkenazi Jewish | 0.00119 | 0.00119 |
| East Asian | 0.000163 | 0.000163 |
| Finnish | 0.000185 | 0.000185 |
| European (Non-Finnish) | 0.000714 | 0.000712 |
| Middle Eastern | 0.000163 | 0.000163 |
| South Asian | 0.00431 | 0.00426 |
| Other | 0.000652 | 0.000652 |
dbNSFP
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}.;
- Pathway
- Dual hijack model of Vif in HIV infection;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
- 0.0568
Intolerance Scores
- loftool
- 0.860
- rvis_EVS
- 0.07
- rvis_percentile_EVS
- 58.96
Haploinsufficiency Scores
- pHI
- hipred
- N
- hipred_score
- 0.401
- ghis
- 0.615
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.894
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;viral process;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;cytosol;apolipoprotein B mRNA editing enzyme complex;ribonucleoprotein complex
- Molecular function
- RNA binding;cytidine deaminase activity;protein binding;zinc ion binding;dCTP deaminase activity;identical protein binding;protein homodimerization activity;deoxycytidine deaminase activity