APOBEC1
protein-codingapolipoprotein B mRNA editing enzyme catalytic subunit 1, the group of Apolipoprotein B mRNA editing enzyme catalytic subunits
Gene summary
This gene encodes a member of the cytidine deaminase enzyme family. The encoded protein forms a multiple-protein editing holoenzyme with APOBEC1 complementation factor (ACF) and APOBEC1 stimulating protein (ASP). This holoenzyme is involved in the editing of C-to-U nucleotide bases in apolipoprotein B and neurofibromatosis-1 mRNAs. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2015]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~16.5 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 APOBEC1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001644.5. 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 | 22 | 1 | 23 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 22 | 2 | 0 | 24 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001635.2 | 5 | MANE Select | |
| Ensembl | ENSP00000229304.4 | 5 | MANE Select | |
| RefSeq | NP_001291495.1 | 5 | Standard | |
| RefSeq | NP_005880.2 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Metabolism of RNA
- Formation of the Editosome
- mRNA Editing: C to U Conversion
- mRNA Editing
Biological Process
- RNA processing
- mRNA processing
- lipid metabolic process
- triglyceride metabolic process
- response to osmotic stress
Molecular Function
- RNA binding
- mRNA binding
- cytidine deaminase activity
- cytosine deaminase activity
- protein binding
Cellular Component
- nucleus
- nucleoplasm
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000229304
- Coding exons
- 5
- Length
- 16504
- Individuals with no LoFs
- 124319
- Homozygous LoFs
- 6
- Heterozygous LoFs
- 1422
- Defined
- 125747
- p
- 0.00569
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.772 | 109 | 134 | 0.813 | 0.00000727 | 1554 |
| Missense (PolyPhen) | 30 | 39.643 | 0.75676 | 480 | ||
| Synonymous | 0.544 | 42 | 46.7 | 0.899 | 0.00000280 | 426 |
| Loss of Function | 0.0258 | 12 | 12.1 | 0.992 | 6.00e-7 | 125 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0027 | 0.0025 | notable |
| Latino/Admixed American | 0.0013 | 0.0012 | notable |
| Ashkenazi Jewish | 0.0035 | 0.0032 | notable |
| East Asian | 0.0012 | 0.0011 | notable |
| Finnish | 0.0026 | 0.0025 | notable |
| European (Non-Finnish) | 0.0096 | 0.0092 | notable |
| South Asian | 0.0063 | 0.0057 | notable |
| Other | 0.0040 | 0.0038 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalytic component of the apolipoprotein B mRNA editing enzyme complex which is responsible for the postranscriptional editing of a CAA codon for Gln to a UAA codon for stop in the APOB mRNA. Also involved in CGA (Arg) to UGA (Stop) editing in the NF1 mRNA. May also play a role in the epigenetic regulation of gene expression by participating in DNA demethylation. {ECO:0000269|PubMed:11727199}.;
Recessive Scores
- pRec
- 0.149
Intolerance Scores
- LoFtool
- 0.828
- RVIS EVS
- 1.13
- RVIS percentile EVS
- 92.16
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.921
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |