APOBEC1
Basic information
Region (hg38): 12:7649400-7665908
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (23 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the APOBEC1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001644.5. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 22 | 23 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 22 | 2 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| APOBEC1 | protein_coding | protein_coding | ENST00000229304 | 5 | 16504 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.68e-8 | 0.128 | 124319 | 6 | 1422 | 125747 | 0.00569 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.772 | 109 | 134 | 0.813 | 0.00000727 | 1554 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00396 | 0.00381 |
| Ashkenazi Jewish | 0.00347 | 0.00318 |
| East Asian | 0.00115 | 0.00114 |
| Finnish | 0.00262 | 0.00245 |
| European (Non-Finnish) | 0.00960 | 0.00921 |
| Middle Eastern | 0.00115 | 0.00114 |
| South Asian | 0.00632 | 0.00570 |
| Other | 0.00404 | 0.00375 |
dbNSFP
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}.;
- Pathway
- Metabolism of RNA;Formation of the Editosome;mRNA Editing: C to U Conversion;mRNA Editing
(Consensus)
Recessive Scores
- pRec
- 0.149
Intolerance Scores
- loftool
- 0.828
- rvis_EVS
- 1.13
- rvis_percentile_EVS
- 92.16
Haploinsufficiency Scores
- pHI
- 0.125
- hipred
- N
- hipred_score
- 0.213
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.921
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Apobec1
- Phenotype
- homeostasis/metabolism phenotype; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan);
Gene ontology
- Biological process
- RNA processing;mRNA processing;lipid metabolic process;triglyceride metabolic process;response to osmotic stress;cytidine deamination;response to zinc ion;response to gamma radiation;cytidine to uridine editing;mRNA modification;cellular response to insulin stimulus;regulation of cell population proliferation;lipoprotein biosynthetic process;lipoprotein transport;positive regulation of catalytic activity;response to ethanol;mRNA stabilization;response to calcium ion;defense response to virus;DNA cytosine deamination;DNA demethylation;negative regulation of triglyceride metabolic process;negative regulation of methylation-dependent chromatin silencing;positive regulation of mRNA modification
- Cellular component
- nucleus;nucleoplasm;cytoplasm
- Molecular function
- RNA binding;mRNA binding;cytidine deaminase activity;cytosine deaminase activity;protein binding;enzyme activator activity;zinc ion binding;AU-rich element binding;protein domain specific binding;ribonucleoprotein complex binding