APOC2
apolipoprotein C2, the group of Apolipoproteins
Basic information
Region (hg38): 19:44946035-44949565
Links
Phenotypes
GenCC
Source:
- familial apolipoprotein C-II deficiency (Strong), mode of inheritance: AR
- familial apolipoprotein C-II deficiency (Strong), mode of inheritance: Semidominant
- familial apolipoprotein C-II deficiency (Strong), mode of inheritance: AR
- familial apolipoprotein C-II deficiency (Supportive), mode of inheritance: AR
- familial apolipoprotein C-II deficiency (Definitive), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Apolipoprotein C-II deficiency (Hyperlipoproteinemia, type Ib) | AR | Cardiovascular; Gastrointestinal | Depending on the severity of disease, individuals may present with manifestations ranging from neonatal encephalopathy to episodic acute pancreatitis, and dietary measures (eg, with low-fat diet, and medium-chain triglyceride supplementation in infancy) can be beneficial to help control lipid abnormalities, including decreasing the risk of episodes of acute pancreatitis; Treatment of acute pancreatitis involves fasting with low-calorie infusion, but serum triglycerides can also be rapidly decreased in emergent situations through normal plasma transfusion; Medical treatment (eg, with fibrates) may be beneficial in adults | Cardiovascular; Gastrointestinal; Neurologic | 565877; 213719; 227429; 6101731; 6475985; 3944267; 3467353; 3171393; 3225819; 1479292; 2477392; 2501098; 7815420; 10225669; 12049186; 12783430; 16153625; 22129523 |
ClinVar
This is a list of variants' phenotypes submitted to
- Cardiovascular_phenotype (58 variants)
- not_provided (45 variants)
- Familial_apolipoprotein_C-II_deficiency (38 variants)
- not_specified (4 variants)
- APOC2-related_disorder (2 variants)
- APOLIPOPROTEIN_C-II_(PARIS) (1 variants)
- APOLIPOPROTEIN_C-II_(HAMBURG) (1 variants)
- APOLIPOPROTEIN_C-II_(BARI) (1 variants)
- APOLIPOPROTEIN_C-II_(AFRICAN) (1 variants)
- APOLIPOPROTEIN_C-II_(PADOVA) (1 variants)
- APOLIPOPROTEIN_C-II_(WAKAYAMA) (1 variants)
- APOLIPOPROTEIN_C-II_(SAN_FRANCISCO) (1 variants)
- APOLIPOPROTEIN_C-II_(TORONTO) (1 variants)
- APOLIPOPROTEIN_C-II_(ST._MICHAEL) (1 variants)
- APOLIPOPROTEIN_C-II_(AUCKLAND) (1 variants)
- Apolipoprotein_c-ii_variant (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the APOC2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000483.5. 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 | 29 | 29 | ||||
| missense | 34 | 43 | ||||
| nonsense | 9 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 6 | |||||
| splice donor/acceptor (+/-2bp) | 2 | |||||
| Total | 10 | 8 | 35 | 37 | 0 |
Highest pathogenic variant AF is 0.0000371767
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| APOC2 | protein_coding | protein_coding | ENST00000590360 | 3 | 3580 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.402 | 0.563 | 125738 | 0 | 8 | 125746 | 0.0000318 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.329 | 44 | 50.6 | 0.870 | 0.00000263 | 642 |
| Missense in Polyphen | 12 | 15.355 | 0.7815 | 202 | ||
| Synonymous | 0.277 | 21 | 22.7 | 0.926 | 0.00000136 | 204 |
| Loss of Function | 1.67 | 1 | 5.06 | 0.198 | 3.19e-7 | 45 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000116 | 0.000116 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000176 | 0.0000176 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of chylomicrons, very low-density lipoproteins (VLDL), low-density lipoproteins (LDL), and high-density lipoproteins (HDL) in plasma. Plays an important role in lipoprotein metabolism as an activator of lipoprotein lipase. Both proapolipoprotein C-II and apolipoprotein C-II can activate lipoprotein lipase. In normolipidemic individuals, it is mainly distributed in the HDL, whereas in hypertriglyceridemic individuals, predominantly found in the VLDL and LDL. {ECO:0000269|PubMed:2209608, ECO:0000303|PubMed:22304839}.;
- Disease
- DISEASE: Hyperlipoproteinemia 1B (HLPP1B) [MIM:207750]: Autosomal recessive trait characterized by hypertriglyceridemia, xanthomas, and increased risk of pancreatitis and early atherosclerosis. {ECO:0000269|PubMed:8323539}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Cholesterol metabolism - Homo sapiens (human);Statin Pathway, Pharmacodynamics;MECP2 and Associated Rett Syndrome;Plasma lipoprotein assembly, remodeling, and clearance;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
- 0.103
Intolerance Scores
- loftool
- 0.464
- rvis_EVS
- 0.77
- rvis_percentile_EVS
- 86.95
Haploinsufficiency Scores
- pHI
- 0.0828
- hipred
- N
- hipred_score
- 0.146
- ghis
- 0.564
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.372
Mouse Genome Informatics
- Gene name
- Apoc2
- Phenotype
- homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- apoc2
- Affected structure
- macrophage
- Phenotype tag
- abnormal
- Phenotype quality
- increased amount
Gene ontology
- Biological process
- retinoid metabolic process;positive regulation of phospholipase activity;positive regulation of triglyceride catabolic process;positive regulation of very-low-density lipoprotein particle remodeling;negative regulation of very-low-density lipoprotein particle clearance;lipid catabolic process;negative regulation of cholesterol transport;cholesterol efflux;phospholipid efflux;triglyceride-rich lipoprotein particle remodeling;chylomicron remodeling;very-low-density lipoprotein particle remodeling;high-density lipoprotein particle remodeling;chylomicron assembly;chylomicron remnant clearance;high-density lipoprotein particle clearance;response to drug;cholesterol homeostasis;lipoprotein transport;negative regulation of catalytic activity;reverse cholesterol transport;positive regulation of fatty acid biosynthetic process;negative regulation of lipid metabolic process;negative regulation of receptor-mediated endocytosis;positive regulation of lipoprotein lipase activity;positive regulation of phospholipid catabolic process;triglyceride homeostasis
- Cellular component
- extracellular region;extracellular space;early endosome;very-low-density lipoprotein particle;low-density lipoprotein particle;intermediate-density lipoprotein particle;spherical high-density lipoprotein particle;chylomicron
- Molecular function
- lipid binding;phospholipase activator activity;protein homodimerization activity;phospholipase binding;lipase inhibitor activity;lipoprotein lipase activator activity