APOLD1
protein-codingapolipoprotein L domain containing 1, the group of MicroRNA protein coding host genes
Gene summary
APOLD1 is an endothelial cell early response protein that may play a role in regulation of endothelial cell signaling and vascular function (Regard et al., 2004 [PubMed 15102925]).[supplied by OMIM, Dec 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~104.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0021181
Submitter: ClinGen
The APOLD1 gene encodes an endothelial cell early response protein induced after ischemia and expected to regulate endothelial cell signaling and vascular function One variant, c.145_146delinsTA (p.Arg49Ter) in APOLD1 was reported in 4 members of a family with an unclassified bleeding disorder (Stritt et al., PMID:35638551). This variant results from a combination in cis of the common c.146G>A; p.R49Q (rs4763876) and the rare missense c.145C>T; p.R49W (rs757476941) nucleotide substitution in APOLD1. The mechanism of disorder is not completely clear, however, it has been proposed that loss of APOLD1 results in dysmorphic endothelial cells with reduced cell-cell junctions and increased permeability, potentially leading to a bleeding disorder. Evidence supporting this gene-disease relationship includes genetic evidences (case-level data) and experimental evidences (expression; functional alteration in non-patient cells, non-human model organisms). Summary of Case Level Data: 1.5 POINTS Variants in this gene have been reported in 4 probands in 1 publication (PMID: 35638551). Affected patients show an unusual type of spontaneous and trauma-related bleeding defect as they have normal coagulation and platelet function test parameters and do not respond to classical treatment with tranexamic acid or platelet transfusion. The use of vasodilators or aspirin worsened their bleeding tendency, and they developed microcirculatory symptoms, such as livedo reticularis after the administration of desmopressin and Raynaud syndrome. Summary of Experimental Data: 3.5 POINTS Regard B et al. showed that APOLD1 is rapidly induced in endothelial cells of cerebral vessels by seizures. APOLD1 mRNA is expressed in capillaries and in the cells lining the inner surface of veins and arteries, suggesting expression by endothelial cells (PMID 15102925). Stritt et al. showed that APOLD1 localizes to cell-cell junctions and Weibel-Palade bodies in endothelial cells and in platelet alpha granules (PMID 35638551). The same authors showed that APOLD1 silencing causes increase in cell size, altered shape, endothelial cell junction dismantling (reduction in the tight junction protein CLDN5 and PECAM1), markedly enhanced fibronectin fibrillogenesis and actin stress fiber formation, reminiscent of endothelial cell activation, and increased endothelial permeability to FITC-dextran. Fan et al demonstrated that Apold1 KO mice show impaired angiogenesis in the ischemic stroke border zone (PMID:36933174). In summary, we obtained limited association of APOLD1 with unclassified bleeding disorder. This classification was approved by the ClinGen Hemostasis Thrombosis Working Group on DATE (SOP Version 10).
Inheritance Pattern: AD
Disease ID:MONDO:0958229
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Hematologic
Intervention: Hematologic
Rationale: The condition can involve increased risk of bleeding, and awareness may allow preventive measures (such as related to surgical situations) and early management of bleeding episodes
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to APOLD1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_030817.3. 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 | 58 | 58 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 58 | 0 | 0 | 58 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_110444.3 | 2 | MANE Select | |
| Ensembl | ENSP00000348998.4 | 2 | MANE Select | |
| RefSeq | NP_001123887.1 | 2 | Standard | |
| Ensembl | ENSP00000324277.6 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- angiogenesis
- response to hypoxia
- lipid transport
- cell differentiation
- endothelial cell activation
Molecular Function
- lipid binding
Cellular Component
- extracellular region
- nucleoplasm
- cytosol
- plasma membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000326765
- Coding exons
- 2
- Length
- 104059
- Individuals with no LoFs
- 125728
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 18
- Defined
- 125746
- p
- 0.0000716
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.449 | 120 | 135 | 0.891 | 0.00000717 | 1694 |
| Missense (PolyPhen) | 47 | 52.527 | 0.89477 | 699 | ||
| Synonymous | 1.18 | 51 | 62.9 | 0.811 | 0.00000340 | 631 |
| Loss of Function | 0.103 | 6 | 6.28 | 0.956 | 2.70e-7 | 73 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000047 | 0.000046 | rare |
| European (Non-Finnish) | 0.000099 | 0.000097 | rare |
| South Asian | 0.00017 | 0.00016 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May be involved in angiogenesis. May play a role in activity-dependent changes of brain vasculature. May affect blood- brain permeability. {ECO:0000269|PubMed:15102925}.;
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- H
- Indispensability pred.
- N
- Indispensability score
- 0.410
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |