LPA
Basic information
Region (hg38): 6:160531481-160664275
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
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.
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 | 2 | |||||
missense | 106 | 11 | 122 | |||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 3 | |||||
splice region | 4 | 4 | ||||
non coding | 0 | |||||
Total | 0 | 0 | 107 | 13 | 7 |
Variants in LPA
This is a list of pathogenic ClinVar variants found in the LPA region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
6-160531748-C-T | Benign (Nov 01, 2022) | |||
6-160531779-G-A | not specified | Uncertain significance (Jan 18, 2022) | ||
6-160531806-G-A | Benign (Apr 20, 2019) | |||
6-160531871-A-G | not specified | Uncertain significance (Aug 08, 2023) | ||
6-160532649-C-T | not specified | Uncertain significance (Jan 11, 2023) | ||
6-160537897-C-T | not specified | Uncertain significance (Sep 01, 2021) | ||
6-160540037-G-A | Likely benign (Feb 01, 2023) | |||
6-160540079-G-A | not specified | Uncertain significance (Nov 09, 2021) | ||
6-160540103-T-C | not specified | Uncertain significance (Nov 06, 2023) | ||
6-160540105-T-C | LIPOPROTEIN(a) POLYMORPHISM | Benign (Aug 07, 2020) | ||
6-160540140-G-C | not specified | Uncertain significance (May 05, 2023) | ||
6-160540183-C-G | not specified | Uncertain significance (Jan 26, 2022) | ||
6-160541120-G-A | not specified | Uncertain significance (Feb 17, 2022) | ||
6-160541153-A-G | Likely benign (Feb 01, 2023) | |||
6-160541179-A-G | not specified | Uncertain significance (Dec 14, 2023) | ||
6-160542742-C-T | Uncertain significance (Nov 01, 2023) | |||
6-160542757-G-A | not specified | Uncertain significance (Jul 11, 2023) | ||
6-160542769-G-A | not specified | Uncertain significance (Jul 06, 2021) | ||
6-160545458-A-G | not specified | Uncertain significance (Mar 14, 2023) | ||
6-160545505-T-C | not specified | Uncertain significance (Sep 16, 2021) | ||
6-160545509-T-C | not specified | Likely benign (Apr 13, 2022) | ||
6-160545521-G-C | not specified | Uncertain significance (Oct 22, 2021) | ||
6-160545527-G-A | Likely benign (Nov 01, 2023) | |||
6-160547791-T-A | not specified | Uncertain significance (Jan 23, 2023) | ||
6-160547809-A-G | not specified | Likely benign (Apr 12, 2022) |
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