APOD
apolipoprotein D, the group of Lipocalins|Apolipoproteins
Basic information
Region (hg38): 3:195568704-195584033
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the APOD gene is commonly pathogenic or not.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 10 | 15 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 3 | 3 |
Variants in APOD
This is a list of pathogenic ClinVar variants found in the APOD region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-195568911-T-C | not specified | Likely benign (Jan 03, 2022) | ||
| 3-195569087-T-C | APOD-related disorder | Likely benign (Jul 27, 2020) | ||
| 3-195569100-C-T | not specified | Uncertain significance (Nov 08, 2021) | ||
| 3-195569120-G-A | not specified | Uncertain significance (Mar 06, 2023) | ||
| 3-195571307-G-C | not specified | Uncertain significance (Aug 13, 2021) | ||
| 3-195571337-C-G | not specified | Uncertain significance (Sep 20, 2023) | ||
| 3-195573869-C-T | Benign (Jan 01, 2023) | |||
| 3-195573917-G-A | not specified | Uncertain significance (Apr 18, 2023) | ||
| 3-195573929-A-C | APOD-related disorder | Benign (Jun 24, 2019) | ||
| 3-195573930-G-T | Likely benign (Jun 06, 2018) | |||
| 3-195573935-T-G | not specified | Uncertain significance (Dec 20, 2023) | ||
| 3-195573953-C-T | not specified | Uncertain significance (Mar 16, 2022) | ||
| 3-195579377-G-A | not specified | Uncertain significance (Jan 19, 2022) | ||
| 3-195579388-A-G | not specified | Uncertain significance (Oct 20, 2023) | ||
| 3-195579418-A-G | APOD-related disorder | Benign (Jul 04, 2019) | ||
| 3-195579431-G-C | not specified | Uncertain significance (Aug 02, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| APOD | protein_coding | protein_coding | ENST00000343267 | 4 | 15504 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000544 | 0.717 | 125717 | 0 | 30 | 125747 | 0.000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.176 | 102 | 107 | 0.952 | 0.00000601 | 1231 |
| Missense in Polyphen | 30 | 40.042 | 0.74921 | 482 | ||
| Synonymous | 0.157 | 47 | 48.4 | 0.971 | 0.00000337 | 373 |
| Loss of Function | 0.875 | 6 | 8.80 | 0.682 | 3.73e-7 | 103 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000383 | 0.000383 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000352 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000425 | 0.000425 |
| Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: APOD occurs in the macromolecular complex with lecithin- cholesterol acyltransferase. It is probably involved in the transport and binding of bilin. Appears to be able to transport a variety of ligands in a number of different contexts.;
- Pathway
- Transport of fatty acids;Transport of vitamins, nucleosides, and related molecules;SLC-mediated transmembrane transport;Transport of small molecules
(Consensus)
Recessive Scores
- pRec
- 0.418
Intolerance Scores
- loftool
- 0.776
- rvis_EVS
- 0.77
- rvis_percentile_EVS
- 87.01
Haploinsufficiency Scores
- pHI
- 0.0315
- hipred
- N
- hipred_score
- 0.381
- ghis
- 0.422
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.409
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Apod
- Phenotype
- nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- response to reactive oxygen species;angiogenesis;glucose metabolic process;lipid metabolic process;lipid transport;brain development;aging;negative regulation of platelet-derived growth factor receptor signaling pathway;peripheral nervous system axon regeneration;tissue regeneration;negative regulation of protein import into nucleus;response to drug;negative regulation of smooth muscle cell proliferation;response to axon injury;negative regulation of focal adhesion assembly;negative regulation of lipoprotein lipid oxidation;negative regulation of monocyte chemotactic protein-1 production;negative regulation of cytokine production involved in inflammatory response;negative regulation of smooth muscle cell-matrix adhesion;negative regulation of T cell migration
- Cellular component
- extracellular region;extracellular space;cytoplasm;endoplasmic reticulum;cytosolic ribosome;dendrite;neuronal cell body;perinuclear region of cytoplasm;extracellular exosome
- Molecular function
- lipid transporter activity;protein binding;cholesterol binding