LPA
Basic information
Region (hg38): 6:160531482-160664275
Previous symbols: [ "LP" ]
Links
Phenotypes
GenCC
Source:
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Lipoprotein A deficiency, congenital | AR | General | The clinical relevance of the condition is unclear | General | 7726859; 10484779; 15523644; 16840570; 16267501; 20032323 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (245 variants)
- not_provided (19 variants)
- LPA-related_disorder (3 variants)
- Thrombocytopenia (1 variants)
- LIPOPROTEIN(a)_QUANTITATIVE_TRAIT_LOCUS (1 variants)
- Abnormal_bleeding (1 variants)
- Myofibrillar_myopathy_6 (1 variants)
- LIPOPROTEIN(a)_POLYMORPHISM (1 variants)
- Lipoprotein(a)_deficiency,_congenital (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the LPA gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005577.4. 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 | 4 | |||||
missense | 232 | 21 | 256 | |||
nonsense | 3 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 2 | |||||
Total | 1 | 1 | 234 | 25 | 4 |
Highest pathogenic variant AF is 0.0000421395
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
LPA | protein_coding | protein_coding | ENST00000447678 | 39 | 134893 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
6.59e-89 | 8.54e-19 | 114094 | 346 | 11308 | 125748 | 0.0475 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -3.27 | 1015 | 761 | 1.33 | 0.0000418 | 13062 |
Missense in Polyphen | 481 | 333.06 | 1.4442 | 5596 | ||
Synonymous | -6.19 | 413 | 281 | 1.47 | 0.0000167 | 4017 |
Loss of Function | -2.71 | 118 | 90.2 | 1.31 | 0.00000562 | 1320 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.126 | 0.123 |
Ashkenazi Jewish | 0.0290 | 0.0289 |
East Asian | 0.00417 | 0.00403 |
Finnish | 0.0780 | 0.0779 |
European (Non-Finnish) | 0.0389 | 0.0386 |
Middle Eastern | 0.00417 | 0.00403 |
South Asian | 0.0470 | 0.0454 |
Other | 0.0434 | 0.0429 |
dbNSFP
Source:
- Function
- FUNCTION: Apo(a) is the main constituent of lipoprotein(a) (Lp(a)). It has serine proteinase activity and is able of autoproteolysis. Inhibits tissue-type plasminogen activator 1. Lp(a) may be a ligand for megalin/Gp 330. {ECO:0000269|PubMed:2531657}.;
- Pathway
- Cholesterol metabolism - Homo sapiens (human);LDL remodeling;Transport of small molecules;Plasma lipoprotein assembly, remodeling, and clearance;Plasma lipoprotein remodeling;amb2 Integrin signaling
(Consensus)
Haploinsufficiency Scores
- pHI
- 0.0757
- hipred
- N
- hipred_score
- 0.335
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.678
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | High | Medium | High |
Cancer | High | Medium | High |
Gene ontology
- Biological process
- proteolysis;lipid metabolic process;lipid transport;blood circulation;negative regulation of endopeptidase activity;low-density lipoprotein particle remodeling
- Cellular component
- extracellular region;plasma lipoprotein particle
- Molecular function
- fibronectin binding;serine-type endopeptidase activity;endopeptidase inhibitor activity;protein binding;heparin binding;apolipoprotein binding