APOC3
apolipoprotein C3, the group of Apolipoproteins
Basic information
Region (hg38): 11:116829706-116833072
Links
Phenotypes
GenCC
Source:
- cholesterol-ester transfer protein deficiency (Supportive), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Apolipoprotein C-III deficiency | AD | General | The clinical applicability of Hyperalophalipoproteinemia 2 is unclear, though variants may be related to lower triglyceride levels and protection against cardiovascular disease | Cardiovascular | 2914370; 2022742; 16813599; 19074352; 24941081; 24941082; 25225788 |
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 APOC3 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 | 12 | 13 | ||||
| missense | 19 | 19 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 1 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| splice region | 0 | |||||
| non coding | 11 | 19 | ||||
| Total | 0 | 0 | 20 | 21 | 12 |
Variants in APOC3
This is a list of pathogenic ClinVar variants found in the APOC3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| APOC3 | protein_coding | protein_coding | ENST00000227667 | 3 | 3367 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0100 | 0.622 | 125050 | 2 | 528 | 125580 | 0.00211 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.0576 | 59 | 57.8 | 1.02 | 0.00000336 | 634 |
| Missense in Polyphen | 13 | 15.133 | 0.85903 | 196 | ||
| Synonymous | 0.310 | 24 | 26.0 | 0.923 | 0.00000186 | 197 |
| Loss of Function | 0.356 | 3 | 3.74 | 0.801 | 2.45e-7 | 34 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00338 | 0.00336 |
| Ashkenazi Jewish | 0.00199 | 0.00199 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.000833 | 0.000832 |
| European (Non-Finnish) | 0.00285 | 0.00285 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.00196 | 0.00190 |
| Other | 0.00326 | 0.00327 |
dbNSFP
Source:
- Function
- FUNCTION: Component of triglyceride-rich very low density lipoproteins (VLDL) and high density lipoproteins (HDL) in plasma (PubMed:18201179, PubMed:22510806). Plays a multifaceted role in triglyceride homeostasis (PubMed:18201179, PubMed:22510806). Intracellularly, promotes hepatic very low density lipoprotein 1 (VLDL1) assembly and secretion; extracellularly, attenuates hydrolysis and clearance of triglyceride-rich lipoproteins (TRLs) (PubMed:18201179, PubMed:22510806). Impairs the lipolysis of TRLs by inhibiting lipoprotein lipase and the hepatic uptake of TRLs by remnant receptors (PubMed:18201179, PubMed:22510806). Formed of several curved helices connected via semiflexible hinges, so that it can wrap tightly around the curved micelle surface and easily adapt to the different diameters of its natural binding partners (PubMed:18408013). {ECO:0000269|PubMed:18408013, ECO:0000303|PubMed:18201179, ECO:0000303|PubMed:22510806}.;
- Disease
- DISEASE: Hyperalphalipoproteinemia 2 (HALP2) [MIM:614028]: A condition characterized by high levels of high density lipoprotein (HDL) and increased HDL cholesterol levels. {ECO:0000269|PubMed:2022742}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Cholesterol metabolism - Homo sapiens (human);PPAR signaling pathway - Homo sapiens (human);Statin Pathway, Pharmacodynamics;PPAR Alpha Pathway;Nuclear Receptors Meta-Pathway;PPAR signaling pathway;Statin Pathway;Signaling by GPCR;Signal Transduction;Metabolism of fat-soluble vitamins;Chylomicron assembly;Plasma lipoprotein assembly;Chylomicron remodeling;HDL remodeling;Metabolism;Transport of small molecules;Metabolism of vitamins and cofactors;Plasma lipoprotein assembly, remodeling, and clearance;Retinoid metabolism and transport;G alpha (i) signalling events;Plasma lipoprotein remodeling;Visual phototransduction;GPCR downstream signalling
(Consensus)
Recessive Scores
- pRec
- 0.731
Intolerance Scores
- loftool
- 0.606
- rvis_EVS
- 0.37
- rvis_percentile_EVS
- 74.95
Haploinsufficiency Scores
- pHI
- 0.331
- hipred
- N
- hipred_score
- 0.146
- ghis
- 0.986
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.967
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Apoc3
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); normal phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- retinoid metabolic process;triglyceride metabolic process;G protein-coupled receptor signaling pathway;negative regulation of triglyceride catabolic process;negative regulation of very-low-density lipoprotein particle remodeling;negative regulation of very-low-density lipoprotein particle clearance;negative regulation of high-density lipoprotein particle clearance;negative regulation of low-density lipoprotein particle clearance;triglyceride catabolic process;regulation of Cdc42 protein signal transduction;cholesterol efflux;phospholipid efflux;chylomicron remodeling;high-density lipoprotein particle remodeling;chylomicron assembly;very-low-density lipoprotein particle assembly;chylomicron remnant clearance;lipoprotein metabolic process;cholesterol homeostasis;reverse cholesterol transport;negative regulation of fatty acid biosynthetic process;negative regulation of lipid metabolic process;negative regulation of receptor-mediated endocytosis;negative regulation of lipid catabolic process;negative regulation of lipoprotein lipase activity;negative regulation of cholesterol import;triglyceride homeostasis
- Cellular component
- extracellular region;extracellular space;early endosome;very-low-density lipoprotein particle;intermediate-density lipoprotein particle;spherical high-density lipoprotein particle;chylomicron;collagen-containing extracellular matrix;extracellular exosome
- Molecular function
- phospholipid binding;cholesterol binding;enzyme regulator activity;lipase inhibitor activity;high-density lipoprotein particle receptor binding