LPA
lipoprotein(a)
Basic information
Region (hg38): 6:160531481-160664275
Previous symbols: [ "LP" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
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
- Inborn genetic diseases (51 variants)
- not provided (6 variants)
- LIPOPROTEIN(a) POLYMORPHISM (3 variants)
- Lipoprotein(a) deficiency, congenital (2 variants)
- not specified (1 variants)
- Abnormal bleeding;Thrombocytopenia (1 variants)
- Myofibrillar myopathy 6 (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.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 0 | |||||
missense | 48 | 3 | 5 | 56 | ||
nonsense | 1 | 1 | 2 | |||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice variant | 1 | 1 | 2 | 4 | ||
non coding | 1 | 1 | ||||
Total | 1 | 0 | 50 | 4 | 8 |
Highest pathogenic variant AF is 0.0000197
Variants in LPA
This is a list of pathogenic ClinVar variants found in the LPA region.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
6-160531748-C-T | Benign (Nov 01, 2022) | |||
6-160531779-G-A | Inborn genetic diseases | Uncertain significance (Jan 18, 2022) | ||
6-160531806-G-A | Benign (Apr 20, 2019) | |||
6-160531871-A-G | Inborn genetic diseases | Uncertain significance (Aug 08, 2023) | ||
6-160532649-C-T | Inborn genetic diseases | Uncertain significance (Jan 11, 2023) | ||
6-160537897-C-T | Inborn genetic diseases | Uncertain significance (Sep 01, 2021) | ||
6-160540079-G-A | Inborn genetic diseases | Uncertain significance (Nov 09, 2021) | ||
6-160540105-T-C | LIPOPROTEIN(a) POLYMORPHISM | Benign (Aug 07, 2020) | ||
6-160540140-G-C | Inborn genetic diseases | Uncertain significance (May 05, 2023) | ||
6-160540183-C-G | Inborn genetic diseases | Uncertain significance (Jan 26, 2022) | ||
6-160541120-G-A | Inborn genetic diseases | Uncertain significance (Feb 17, 2022) | ||
6-160542757-G-A | Inborn genetic diseases | Uncertain significance (Jul 11, 2023) | ||
6-160542769-G-A | Inborn genetic diseases | Uncertain significance (Jul 06, 2021) | ||
6-160545458-A-G | Inborn genetic diseases | Uncertain significance (Mar 14, 2023) | ||
6-160545505-T-C | Inborn genetic diseases | Uncertain significance (Sep 16, 2021) | ||
6-160545509-T-C | Inborn genetic diseases | Likely benign (Apr 13, 2022) | ||
6-160545521-G-C | Inborn genetic diseases | Uncertain significance (Oct 22, 2021) | ||
6-160547791-T-A | Inborn genetic diseases | Uncertain significance (Jan 23, 2023) | ||
6-160547809-A-G | Inborn genetic diseases | Likely benign (Apr 12, 2022) | ||
6-160547881-C-T | Inborn genetic diseases | Uncertain significance (Jul 26, 2022) | ||
6-160547886-A-G | Inborn genetic diseases | Uncertain significance (Nov 22, 2022) | ||
6-160547936-G-A | Myofibrillar myopathy 6 | Benign/Likely benign (Dec 15, 2020) | ||
6-160548507-A-T | Inborn genetic diseases | Uncertain significance (Apr 13, 2022) | ||
6-160548552-G-C | Abnormal bleeding;Thrombocytopenia | Uncertain significance (May 01, 2020) | ||
6-160548597-A-G | Benign (Oct 15, 2020) |
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