APOL3
protein-codingapolipoprotein L3, the group of Apolipoproteins
Gene summary
This gene is a member of the apolipoprotein L gene family, and it is present in a cluster with other family members on chromosome 22. The encoded protein is found in the cytoplasm, where it may affect the movement of lipids, including cholesterol, and/or allow the binding of lipids to organelles. In addition, expression of this gene is up-regulated by tumor necrosis factor-alpha in endothelial cells lining the normal and atherosclerotic iliac artery and aorta. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2015]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~26.4 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 APOL3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_145639.2. 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 | 1 | 1 | ||||
| missense | 50 | 6 | 4 | 60 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 50 | 7 | 4 | 61 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_663614.1 | 3 | MANE Select | |
| Ensembl | ENSP00000415779.3 | 3 | MANE Select | |
| RefSeq | NP_001380516.1 | 3 | Standard | |
| RefSeq | NP_001380517.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- lipid transport
- inflammatory response
- lipoprotein metabolic process
- positive regulation of I-kappaB kinase/NF-kappaB signaling
Molecular Function
- lipid transporter activity
- lipid binding
Cellular Component
- extracellular region
- cytoplasm
- membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000349314
- Coding exons
- 3
- Length
- 25854
- Individuals with no LoFs
- 122099
- Homozygous LoFs
- 436
- Heterozygous LoFs
- 3203
- Defined
- 125738
- p
- 0.0146
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0414 | 228 | 226 | 1.01 | 0.0000123 | 2569 |
| Missense (PolyPhen) | 56 | 68.556 | 0.81685 | 801 | ||
| Synonymous | -0.879 | 101 | 90.4 | 1.12 | 0.00000494 | 857 |
| Loss of Function | 0.0582 | 5 | 5.14 | 0.972 | 2.17e-7 | 64 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.22 | 0.22 | notable |
| Latino/Admixed American | 0.0081 | 0.0080 | notable |
| Ashkenazi Jewish | 0.0055 | 0.0055 | notable |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00065 | 0.00052 | rare |
| South Asian | 0.00026 | 0.00026 | rare |
| Other | 0.0075 | 0.0075 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May affect the movement of lipids in the cytoplasm or allow the binding of lipids to organelles.;
Intolerance Scores
- LoFtool
- 0.851
- RVIS EVS
- 1.18
- RVIS percentile EVS
- 92.78
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0738
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |