APOBEC3D
protein-codingapolipoprotein B mRNA editing enzyme catalytic subunit 3D, 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 a group of related genes 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 and inhibit retroviruses, such as HIV, by deaminating cytosine residues in nascent retroviral cDNA. [provided by RefSeq, Jul 2008]
- APOBEC3E
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~12.2 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 APOBEC3D variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_152426.4. 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 | 2 | 2 | ||||
| missense | 72 | 4 | 76 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 76 | 4 | 0 | 80 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_689639.2 | 7 | MANE Select | |
| Ensembl | ENSP00000216099.7 | 7 | MANE Select | |
| RefSeq | NP_001350710.1 | 4 | Standard | |
| Ensembl | ENSP00000388017.2 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- cytidine deamination
- negative regulation of transposition
- cytidine to uridine editing
- innate immune response
- negative regulation of single stranded viral RNA replication via double stranded DNA intermediate
Molecular Function
- RNA binding
- cytidine deaminase activity
- zinc ion binding
Cellular Component
- P-body
- nucleus
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000216099
- Coding exons
- 7
- Length
- 18914
- Individuals with no LoFs
- 125631
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 116
- Defined
- 125747
- p
- 0.000461
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -1.09 | 279 | 232 | 1.20 | 0.0000142 | 2566 |
| Missense (PolyPhen) | 65 | 62.098 | 1.0467 | 774 | ||
| Synonymous | -0.551 | 93 | 86.5 | 1.08 | 0.00000511 | 698 |
| Loss of Function | -0.817 | 25 | 21.0 | 1.19 | 0.00000114 | 211 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0015 | 0.0015 | notable |
| Latino/Admixed American | 0.00026 | 0.00026 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.0021 | 0.0021 | notable |
| European (Non-Finnish) | 0.00022 | 0.00022 | rare |
| South Asian | 0.00020 | 0.00020 | rare |
| Other | 0.00033 | 0.00033 | 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 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. May inhibit the mobility of LTR and non-LTR retrotransposons. {ECO:0000269|PubMed:12859895, ECO:0000269|PubMed:20062055, ECO:0000269|PubMed:21835787, ECO:0000269|PubMed:22807680, ECO:0000269|PubMed:23097438, ECO:0000269|PubMed:23152537}.;
Recessive Scores
- pRec
- 0.0492
Intolerance Scores
- LoFtool
- 0.792
- RVIS EVS
- -0.16
- RVIS percentile EVS
- 42.06
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.00463
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |