LRP2

protein-coding

LDL receptor related protein 2, the group of Low density lipoprotein receptors

Gene summary

The protein encoded by this gene, low density lipoprotein-related protein 2 (LRP2) or megalin, is a multi-ligand endocytic receptor that is expressed in many different tissues but primarily in absorptive epithilial tissues such as the kidney. This glycoprotein has a large amino-terminal extracellular domain, a single transmembrane domain, and a short carboxy-terminal cytoplasmic tail. The extracellular ligand-binding-domains bind diverse macromolecules including albumin, apolipoproteins B and E, and lipoprotein lipase. The LRP2 protein is critical for the reuptake of numerous ligands, including lipoproteins, sterols, vitamin-binding proteins, and hormones. This protein also has a role in cell-signaling; extracellular ligands include parathyroid horomones and the morphogen sonic hedgehog while cytosolic ligands include MAP kinase scaffold proteins and JNK interacting proteins. Recycling of this membrane receptor is regulated by phosphorylation of its cytoplasmic domain. Mutations in this gene cause Donnai-Barrow syndrome (DBS) and facio-oculoacoustico-renal syndrome (FOAR).[provided by RefSeq, Aug 2009]

MANE transcript

NM_004525.3

Inheritance

AR, AD

ClinVar variants

P:294U:1952B:1675

Top phenotype

Donnai-Barrow syndrome; Faciooculoacousticorenal syndrome

gnomAD constraint

pLI —, LoF o/e 0.2

Max pathogenic AF

—

Genomic locus

chr2:169,127,109-169,362,534

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~235.4 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Donnai-Barrow syndromeSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009104

Submitter: Orphanet

intellectual disabilityLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0001071

Submitter: G2P

Donnai-Barrow syndromeDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009104

Submitter: G2P

Donnai-Barrow syndromeDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009104

Submitter: Natera

Donnai-Barrow syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009104

Submitter: PanelApp Australia

Donnai-Barrow syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009104

Submitter: Labcorp Genetics (formerly Invitae)

Stickler syndromeMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0019354

Submitter: Genomics England PanelApp

congenital heart diseaseNO_KNOWN

Inheritance Pattern: AR

Disease ID:MONDO:0005453

Submitter: ClinGen

*LRP2* was first reported in relation to autosomal recessive congenital heart disease in 2020 (Theis JL et al., PMID: 33006316). Two unique variants (heterozygous missense) that have been reported in one proband in one publication are included in this curation (PMID: 33006316). However, these variants were not scored due to a high minor allele frequency in gnomAD v.4.This gene-disease relationship is supported by an animal model (PMID: 26822476). No evidence for a causal role for *LRP2* in autosomal recessive congenital heart disease has been reported. Although this gene-disease relationship is supported by an animal model, no reports have directly implicated the gene in humans.This classification was approved by the ClinGen Congenital Heart Disease GCEP on the meeting date September 9th, 2024 (SOP Version 11).

Clinical Genomic Database (CGD)

Donnai-Barrow syndrome; Faciooculoacousticorenal syndromeAR

Manifestation: Audiologic/Otolaryngologic; Craniofacial; Musculoskeletal; Ophthalmologic; Renal

Intervention: Audiologic/Otolaryngologic; General

Rationale: Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development

Refs: 8266995; 9475100; 12923867; 17632512; 18553518; 20301732Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LRP2 variants in ClinVar

17 Conditions Cataloged
not providedTotal: 4251
Donnai-Barrow syndromeTotal: 1289
not specifiedTotal: 634
Inborn genetic diseasesTotal: 591
LRP2-related disorderTotal: 332
Intellectual disabilityTotal: 20
Hearing impairmentTotal: 4
DSD incomplete virilizationTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004525.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
28
clinvar
1468
clinvar
8
clinvar
1504
missense
13
clinvar
1907
clinvar
188
clinvar
11
clinvar
2119
nonsense
94
clinvar
34
clinvar
1
clinvar
129
start loss
0
frameshift
65
clinvar
24
clinvar
1
clinvar
90
splice donor/acceptor (+/-2bp)
5
clinvar
59
clinvar
15
clinvar
79
Total16413019521656193921

Highest pathogenic variant AF is 0.000086969565

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_004525.3RefSeqNP_004516.279MANE Select
ENST00000649046.1EnsemblENSP00000496870.179MANE Select
ENST00000443831.1EnsemblENSP00000409813.123Standard
ENST00000443831.2EnsemblENSP00000409813.123Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
lrp2aDanio rerio

Structure: posterior segment eye

Quality: increased depth

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Thyroid hormone synthesis - Homo sapiens (human)
  • Cholesterol metabolism - Homo sapiens (human)
  • Hedgehog signaling pathway - Homo sapiens (human)
  • HH-Ncore
  • Vitamin B12 Metabolism

Biological Process

  • retinoid metabolic process
  • neural tube closure
  • secondary heart field specification
  • outflow tract septum morphogenesis
  • ventricular compact myocardium morphogenesis

Molecular Function

  • low-density lipoprotein particle receptor activity
  • calcium ion binding
  • protein binding
  • drug binding
  • SH3 domain binding

Cellular Component

  • lysosome
  • lysosomal membrane
  • endoplasmic reticulum
  • Golgi apparatus
  • plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000263816
Coding exons
79
Length
235577
Individuals with no LoFs
125661
Homozygous LoFs
0
Heterozygous LoFs
87
Defined
125748
p
0.000346
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.0722422.53e+30.8840.00014631104
Missense (PolyPhen)65310110.6459212688
Synonymous-0.7799519211.030.00005538418
Loss of Function11.6472410.1950.00001412805

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000180.00018rare
Latino/Admixed American0.000260.00026rare
Ashkenazi Jewish0.000600.00060rare
East Asian0.000270.00027rare
Finnish0.000510.00051rare
European (Non-Finnish)0.000380.00038rare
South Asian0.000260.00026rare
Other0.000330.00033rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Multiligand endocytic receptor (By similarity). Acts together with CUBN to mediate endocytosis of high-density lipoproteins (By similarity). Mediates receptor-mediated uptake of polybasic drugs such as aprotinin, aminoglycosides and polymyxin B (By similarity). In the kidney, mediates the tubular uptake and clearance of leptin (By similarity). Also mediates transport of leptin across the blood-brain barrier through endocytosis at the choroid plexus epithelium (By similarity). Endocytosis of leptin in neuronal cells is required for hypothalamic leptin signaling and leptin-mediated regulation of feeding and body weight (By similarity). Mediates endocytosis and subsequent lysosomal degradation of CST3 in kidney proximal tubule cells (By similarity). Mediates renal uptake of 25-hydroxyvitamin D3 in complex with the vitamin D3 transporter GC/DBP (By similarity). Mediates renal uptake of metallothionein-bound heavy metals (PubMed:15126248). Together with CUBN, mediates renal reabsorption of myoglobin (By similarity). Mediates renal uptake and subsequent lysosomal degradation of APOM (By similarity). Plays a role in kidney selenium homeostasis by mediating renal endocytosis of selenoprotein SEPP1 (By similarity). Mediates renal uptake of the antiapoptotic protein BIRC5/survivin which may be important for functional integrity of the kidney (PubMed:23825075). Mediates renal uptake of matrix metalloproteinase MMP2 in complex with metalloproteinase inhibitor TIMP1 (By similarity). Mediates endocytosis of Sonic hedgehog protein N-product (ShhN), the active product of SHH (By similarity). Also mediates ShhN transcytosis (By similarity). In the embryonic neuroepithelium, mediates endocytic uptake and degradation of BMP4, is required for correct SHH localization in the ventral neural tube and plays a role in patterning of the ventral telencephalon (By similarity). Required at the onset of neurulation to sequester SHH on the apical surface of neuroepithelial cells of the rostral diencephalon ventral midline and to control PTCH1-dependent uptake and intracellular trafficking of SHH (By similarity). During neurulation, required in neuroepithelial cells for uptake of folate bound to the folate receptor FOLR1 which is necessary for neural tube closure (By similarity). In the adult brain, negatively regulates BMP signaling in the subependymal zone which enables neurogenesis to proceed (By similarity). In astrocytes, mediates endocytosis of ALB which is required for the synthesis of the neurotrophic factor oleic acid (By similarity). Involved in neurite branching (By similarity). During optic nerve development, required for SHH- mediated migration and proliferation of oligodendrocyte precursor cells (By similarity). Mediates endocytic uptake and clearance of SHH in the retinal margin which protects retinal progenitor cells from mitogenic stimuli and keeps them quiescent (By similarity). Plays a role in reproductive organ development by mediating uptake in reproductive tissues of androgen and estrogen bound to the sex hormone binding protein SHBG (By similarity). Mediates endocytosis of angiotensin-2 (By similarity). Also mediates endocytosis of angiotensis 1-7 (By similarity). Binds to the complex composed of beta-amyloid protein 40 and CLU/APOJ and mediates its endocytosis and lysosomal degradation (By similarity). Required for embryonic heart development (By similarity). Required for normal hearing, possibly through interaction with estrogen in the inner ear (By similarity). {ECO:0000250|UniProtKB:A2ARV4, ECO:0000250|UniProtKB:C0HL13, ECO:0000250|UniProtKB:P98158, ECO:0000269|PubMed:15126248, ECO:0000269|PubMed:23825075}.;
Disease
DISEASE: Donnai-Barrow syndrome (DBS) [MIM:222448]: Rare autosomal recessive disorder characterized by major malformations including agenesis of the corpus callosum, congenital diaphragmatic hernia, facial dysmorphology, ocular anomalies, sensorineural hearing loss and developmental delay. The FOAR syndrome was first described as comprising facial anomalies, ocular anomalies, sensorineural hearing loss, and proteinuria. DBS and FOAR were first described as distinct disorders but the classic distinguishing features between the 2 disorders were presence of proteinuria and absence of diaphragmatic hernia and corpus callosum anomalies in FOAR. Early reports noted that the 2 disorders shared many phenotypic features and may be identical. Although there is variability in the expression of some features (e.g., agenesis of the corpus callosum and proteinuria), DBS and FOAR are now considered to represent the same entity. {ECO:0000269|PubMed:17632512}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.542

Intolerance Scores

LoFtool
0.00434
RVIS EVS
3.32
RVIS percentile EVS
99.42

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.949

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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