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GeneBe

LPA

lipoprotein(a)

Basic information

Region (hg38): 6:160531481-160664275

Previous symbols: [ "LP" ]

Links

ENSG00000198670NCBI:4018OMIM:152200HGNC:6667Uniprot:P08519AlphaFoldGenCCjaxSfariGnomADPubmed

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.

  • 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)link
6-160531779-G-A Inborn genetic diseases Uncertain significance (Jan 18, 2022)link
6-160531806-G-A Benign (Apr 20, 2019)link
6-160531871-A-G Inborn genetic diseases Uncertain significance (Aug 08, 2023)link
6-160532649-C-T Inborn genetic diseases Uncertain significance (Jan 11, 2023)link
6-160537897-C-T Inborn genetic diseases Uncertain significance (Sep 01, 2021)link
6-160540079-G-A Inborn genetic diseases Uncertain significance (Nov 09, 2021)link
6-160540105-T-C LIPOPROTEIN(a) POLYMORPHISM Benign (Aug 07, 2020)link
6-160540140-G-C Inborn genetic diseases Uncertain significance (May 05, 2023)link
6-160540183-C-G Inborn genetic diseases Uncertain significance (Jan 26, 2022)link
6-160541120-G-A Inborn genetic diseases Uncertain significance (Feb 17, 2022)link
6-160542757-G-A Inborn genetic diseases Uncertain significance (Jul 11, 2023)link
6-160542769-G-A Inborn genetic diseases Uncertain significance (Jul 06, 2021)link
6-160545458-A-G Inborn genetic diseases Uncertain significance (Mar 14, 2023)link
6-160545505-T-C Inborn genetic diseases Uncertain significance (Sep 16, 2021)link
6-160545509-T-C Inborn genetic diseases Likely benign (Apr 13, 2022)link
6-160545521-G-C Inborn genetic diseases Uncertain significance (Oct 22, 2021)link
6-160547791-T-A Inborn genetic diseases Uncertain significance (Jan 23, 2023)link
6-160547809-A-G Inborn genetic diseases Likely benign (Apr 12, 2022)link
6-160547881-C-T Inborn genetic diseases Uncertain significance (Jul 26, 2022)link
6-160547886-A-G Inborn genetic diseases Uncertain significance (Nov 22, 2022)link
6-160547936-G-A Myofibrillar myopathy 6 Benign/Likely benign (Dec 15, 2020)link
6-160548507-A-T Inborn genetic diseases Uncertain significance (Apr 13, 2022)link
6-160548552-G-C Abnormal bleeding;Thrombocytopenia Uncertain significance (May 01, 2020)link
6-160548597-A-G Benign (Oct 15, 2020)link

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