LPA

lipoprotein(a)

Basic information

Region (hg38): 6:160531481-160664275

Previous symbols: [ "LP" ]

Links

ENSG00000198670NCBI:4018OMIM:152200HGNC:6667Uniprot:P08519AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Lipoprotein A deficiency, congenitalARGeneralThe clinical relevance of the condition is unclearGeneral7726859; 10484779; 15523644; 16840570; 16267501; 20032323

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LPA gene.

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
clinvar
2
missense
106
clinvar
11
clinvar
5
clinvar
122
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
1
clinvar
2
clinvar
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)1879678
6-160531779-G-A not specified Uncertain significance (Jan 18, 2022)2396805
6-160531806-G-A Benign (Apr 20, 2019)1251319
6-160531871-A-G not specified Uncertain significance (Aug 08, 2023)2593152
6-160532649-C-T not specified Uncertain significance (Jan 11, 2023)2475517
6-160537897-C-T not specified Uncertain significance (Sep 01, 2021)2361798
6-160540037-G-A Likely benign (Feb 01, 2023)2657110
6-160540079-G-A not specified Uncertain significance (Nov 09, 2021)2215536
6-160540103-T-C not specified Uncertain significance (Nov 06, 2023)3119693
6-160540105-T-C LIPOPROTEIN(a) POLYMORPHISM Benign (Aug 07, 2020)975030
6-160540140-G-C not specified Uncertain significance (May 05, 2023)2544302
6-160540183-C-G not specified Uncertain significance (Jan 26, 2022)2273447
6-160541120-G-A not specified Uncertain significance (Feb 17, 2022)2277718
6-160541153-A-G Likely benign (Feb 01, 2023)2657111
6-160541179-A-G not specified Uncertain significance (Dec 14, 2023)3119692
6-160542742-C-T Uncertain significance (Nov 01, 2023)2673088
6-160542757-G-A not specified Uncertain significance (Jul 11, 2023)2610405
6-160542769-G-A not specified Uncertain significance (Jul 06, 2021)2388609
6-160545458-A-G not specified Uncertain significance (Mar 14, 2023)2496032
6-160545505-T-C not specified Uncertain significance (Sep 16, 2021)2325983
6-160545509-T-C not specified Likely benign (Apr 13, 2022)2346313
6-160545521-G-C not specified Uncertain significance (Oct 22, 2021)2256506
6-160545527-G-A Likely benign (Nov 01, 2023)2673089
6-160547791-T-A not specified Uncertain significance (Jan 23, 2023)2466244
6-160547809-A-G not specified Likely benign (Apr 12, 2022)2407824

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
LPAprotein_codingprotein_codingENST00000447678 39134893
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
6.59e-898.54e-19114094346113081257480.0475
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-3.2710157611.330.000041813062
Missense in Polyphen481333.061.44425596
Synonymous-6.194132811.470.00001674017
Loss of Function-2.7111890.21.310.000005621320

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.1260.123
Ashkenazi Jewish0.02900.0289
East Asian0.004170.00403
Finnish0.07800.0779
European (Non-Finnish)0.03890.0386
Middle Eastern0.004170.00403
South Asian0.04700.0454
Other0.04340.0429

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyHighMediumHigh
CancerHighMediumHigh

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