APOA2
apolipoprotein A2, the group of Apolipoproteins
Basic information
Region (hg38): 1:161222290-161223631
Links
Phenotypes
GenCC
Source:
- apolipoprotein A-II amyloidosis (Supportive), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Apolipoprotein A-II deficiency | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Cardiovascular | 2107739; 12522687; 24387992 |
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 APOA2 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 | 3 | |||||
| missense | 6 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 2 | 8 | 10 | |||
| non coding | 3 | |||||
| Total | 0 | 0 | 9 | 2 | 1 |
Variants in APOA2
This is a list of pathogenic ClinVar variants found in the APOA2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-161222407-A-T | Likely pathogenic (Nov 13, 2020) | |||
| 1-161222412-G-A | not specified | Uncertain significance (Apr 25, 2022) | ||
| 1-161222415-G-T | not specified | Uncertain significance (Apr 22, 2019) | ||
| 1-161222420-C-T | not specified • APOA2-related disorder | Benign (May 14, 2018) | ||
| 1-161222460-A-T | not specified | Uncertain significance (Jan 26, 2022) | ||
| 1-161222461-G-A | not specified | Benign (Dec 04, 2017) | ||
| 1-161222465-C-T | Apolipoprotein A-II deficiency | Uncertain significance (Jan 12, 2018) | ||
| 1-161222479-T-G | Apolipoprotein A-II deficiency • not specified | Uncertain significance (Aug 28, 2023) | ||
| 1-161222526-G-A | Apolipoprotein A-II deficiency • APOA2-related disorder | Benign (Jan 13, 2018) | ||
| 1-161222541-T-G | not specified | Likely benign (Aug 21, 2023) | ||
| 1-161222917-C-T | APOLIPOPROTEIN A-II DEFICIENCY, FAMILIAL, DUE TO APOA-II (HIROSHIMA) | Pathogenic (Apr 01, 1990) | ||
| 1-161222930-T-C | not specified | Uncertain significance (Apr 15, 2024) | ||
| 1-161222982-C-A | not specified | Uncertain significance (Sep 26, 2023) | ||
| 1-161222982-C-T | Apolipoprotein A-II deficiency • not specified | Uncertain significance (May 22, 2023) | ||
| 1-161223053-GCCCACACA-G | not specified | Benign (Jan 17, 2022) | ||
| 1-161223055-CCA-C | not specified • APOA2-related disorder | Benign (Jun 29, 2020) | ||
| 1-161223055-CCACA-C | Apolipoprotein A-II deficiency • not specified | Conflicting classifications of pathogenicity (Apr 19, 2021) | ||
| 1-161223055-CCACACA-C | Apolipoprotein A-II deficiency • not specified • APOA2-related disorder | Conflicting classifications of pathogenicity (Aug 12, 2019) | ||
| 1-161223055-CCACACACA-C | not specified | Benign (Sep 20, 2019) | ||
| 1-161223055-CCACACACACA-C | not specified • APOA2-related disorder | Benign (Aug 13, 2019) | ||
| 1-161223055-CCACACACACACA-C | not specified | Benign (Aug 13, 2019) | ||
| 1-161223055-CCACACACACACACACA-C | APOA2-related disorder | Likely benign (Oct 28, 2019) | ||
| 1-161223055-C-CCA | not specified | Benign (Dec 23, 2019) | ||
| 1-161223055-C-CCACA | Apolipoprotein A-II deficiency • not specified | Conflicting classifications of pathogenicity (Dec 22, 2021) | ||
| 1-161223055-C-CCACACA | not specified | Benign (Jun 12, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| APOA2 | protein_coding | protein_coding | ENST00000367990 | 3 | 1340 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0448 | 0.686 | 125732 | 0 | 9 | 125741 | 0.0000358 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.313 | 46 | 52.4 | 0.878 | 0.00000286 | 637 |
| Missense in Polyphen | 11 | 15.138 | 0.72666 | 207 | ||
| Synonymous | 0.0674 | 22 | 22.4 | 0.982 | 0.00000138 | 200 |
| Loss of Function | 0.568 | 2 | 3.07 | 0.651 | 1.29e-7 | 40 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000149 | 0.000149 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000352 | 0.0000352 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May stabilize HDL (high density lipoprotein) structure by its association with lipids, and affect the HDL metabolism.;
- Pathway
- Cholesterol metabolism - Homo sapiens (human);PPAR signaling pathway - Homo sapiens (human);Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha);PPAR Alpha Pathway;Nuclear Receptors Meta-Pathway;Dengue-2 Interactions with Complement and Coagulation Cascades;PPAR signaling pathway;Statin Pathway;Signaling by GPCR;Signal Transduction;Metabolism of fat-soluble vitamins;mechanism of gene regulation by peroxisome proliferators via ppara;Chylomicron assembly;Plasma lipoprotein assembly;Chylomicron remodeling;Post-translational protein phosphorylation;Post-translational protein modification;Metabolism of proteins;Metabolism;Transport of small molecules;Metabolism of vitamins and cofactors;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs);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
- 0.431
Intolerance Scores
- loftool
- 0.359
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.04
Haploinsufficiency Scores
- pHI
- 0.655
- hipred
- N
- hipred_score
- 0.276
- ghis
- 0.955
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.586
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Apoa2
- Phenotype
- growth/size/body region phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- retinoid metabolic process;acute inflammatory response;negative regulation of cytokine secretion involved in immune response;triglyceride metabolic process;phosphatidylcholine biosynthetic process;cholesterol metabolic process;phospholipid catabolic process;response to glucose;positive regulation of cholesterol esterification;negative regulation of very-low-density lipoprotein particle remodeling;viral process;protein oxidation;peptidyl-methionine modification;regulation of lipid metabolic process;regulation of intestinal cholesterol absorption;cholesterol transport;animal organ regeneration;regulation of protein stability;negative regulation of cholesterol transport;cholesterol efflux;phospholipid efflux;triglyceride-rich lipoprotein particle remodeling;chylomicron remodeling;low-density lipoprotein particle remodeling;high-density lipoprotein particle remodeling;chylomicron assembly;high-density lipoprotein particle assembly;high-density lipoprotein particle clearance;lipoprotein metabolic process;response to drug;cholesterol homeostasis;positive regulation of catalytic activity;response to estrogen;post-translational protein modification;reverse cholesterol transport;cellular protein metabolic process;positive regulation of interleukin-8 biosynthetic process;diacylglycerol catabolic process;negative regulation of lipid catabolic process;positive regulation of lipid catabolic process;response to glucocorticoid;negative regulation of lipase activity;negative regulation of cholesterol import;negative regulation of cholesterol transporter activity
- Cellular component
- extracellular region;early endosome;endoplasmic reticulum lumen;cytosol;very-low-density lipoprotein particle;high-density lipoprotein particle;spherical high-density lipoprotein particle;chylomicron;extracellular exosome;blood microparticle
- Molecular function
- lipid transporter activity;protein binding;phospholipid binding;high-density lipoprotein particle binding;lipid binding;cholesterol binding;cholesterol transporter activity;heat shock protein binding;phosphatidylcholine binding;apolipoprotein receptor binding;protein homodimerization activity;protein heterodimerization activity;lipase inhibitor activity;phosphatidylcholine-sterol O-acyltransferase activator activity;high-density lipoprotein particle receptor binding