LRP10

gene
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Also known as DKFZP564C1940MGC8675LRP9MST087MSTP087

Summary

LRP10 (LDL receptor related protein 10, HGNC:14553) is a protein-coding gene on chromosome 14q11.2, encoding Low-density lipoprotein receptor-related protein 10 (Q7Z4F1). Probable receptor, which is involved in the internalization of lipophilic molecules and/or signal transduction.

This gene encodes a low density lipoprotein receptor family protein. A similar protein in mouse is thought to play a role in the uptake of apolipoprotein E-containing lipoproteins.

Source: NCBI Gene 26020 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 127 total
  • MANE Select transcript: NM_014045

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:14553
Approved symbolLRP10
NameLDL receptor related protein 10
Location14q11.2
Locus typegene with protein product
StatusApproved
AliasesDKFZP564C1940, MGC8675, LRP9, MST087, MSTP087
Ensembl geneENSG00000197324
Ensembl biotypeprotein_coding
OMIM609921
Entrez26020

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 14 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000359591, ENST00000470660, ENST00000546834, ENST00000551466, ENST00000553002, ENST00000908030, ENST00000908031, ENST00000908032, ENST00000908033, ENST00000908034, ENST00000908035, ENST00000912553, ENST00000912554, ENST00000912555, ENST00000960874, ENST00000960875

RefSeq mRNA: 2 — MANE Select: NM_014045 NM_001329226, NM_014045

CCDS: CCDS86372, CCDS9578

Canonical transcript exons

ENST00000359591 — 7 exons

ExonStartEnd
ENSE000010313922287668922876818
ENSE000010994252287331122873446
ENSE000011500472287535522876372
ENSE000011500712287273822872782
ENSE000012587002287694022881713
ENSE000012587052287174022872337
ENSE000035431532287505522875245

Expression profiles

Bgee: expression breadth ubiquitous, 284 present calls, max score 99.25.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 93.2966 / max 1503.2833, expressed in 1821 samples.

FANTOM5 promoters (16 alternative TSS)

Promoter IDTPM avgSamples expressed
13884945.40721807
13884828.18731800
1388563.63191348
1388522.75701137
1388502.66071189
1388602.65781092
1388512.15161094
1388552.02241055
1388591.2086713
1388580.6753421

Top tissues by expression

289 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
stromal cell of endometriumCL:000225599.25gold quality
deciduaUBERON:000245098.60gold quality
right coronary arteryUBERON:000162598.41gold quality
pancreatic ductal cellCL:000207998.40gold quality
mucosa of stomachUBERON:000119998.38gold quality
popliteal arteryUBERON:000225098.23gold quality
tibial arteryUBERON:000761098.23gold quality
aortaUBERON:000094798.20gold quality
gall bladderUBERON:000211098.18gold quality
descending thoracic aortaUBERON:000234598.18gold quality
thoracic aortaUBERON:000151598.16gold quality
ascending aortaUBERON:000149698.13gold quality
type B pancreatic cellCL:000016998.08gold quality
pharyngeal mucosaUBERON:000035598.08gold quality
coronary arteryUBERON:000162197.85gold quality
left coronary arteryUBERON:000162697.84gold quality
lower esophagus mucosaUBERON:003583497.81gold quality
esophagus mucosaUBERON:000246997.80gold quality
gingivaUBERON:000182897.77gold quality
bloodUBERON:000017897.74gold quality
saphenous veinUBERON:000731897.67gold quality
epithelium of esophagusUBERON:000197697.66gold quality
esophagusUBERON:000104397.65gold quality
cartilage tissueUBERON:000241897.64gold quality
gingival epitheliumUBERON:000194997.61gold quality
penisUBERON:000098997.60gold quality
cervix squamous epitheliumUBERON:000692297.56gold quality
urethraUBERON:000005797.54gold quality
lower esophagusUBERON:001347397.51gold quality
lower esophagus muscularis layerUBERON:003583397.50gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 18)

  • LRP10 may interfere with the formation of the beta-catenin/TCF complex and/or its binding to target DNA in the nucleus, and that the extracellular domain of LRP10 is critical for inhibition of the canonical Wnt/beta-catenin signaling pathway. (PMID:20093106)
  • Increased expression of LRP10 in human neuroblastoma SH-SY5Y cells induces the accumulation of mature APP in the Golgi and reduces its presence at the cell surface and its processing into Abeta. (PMID:22734645)
  • In Mayer-Rokitansky-Kuster-Hauser syndrome in monoztgotic twins, LRP10 was identified as one of the candidate genes. (PMID:25492683)
  • Our findings implicate LRP10 gene defects in the development of inherited forms of alpha-synucleinopathies (PMID:29887161)
  • Genetic screening of the LRP10 gene in our cohort may provide independent, albeit limited, evidence for the pathogenicity of LRP10 in familial Parkinson disease. (PMID:30964957)
  • p.Tyr307Asn variant is pathogenic for PD and PDD in the southwest Dutch population. (PMID:31147221)
  • Analysis of p.Tyr307Asn variant in the LRP10 gene in Parkinson’s disease in southern Spain. (PMID:32409252)
  • LRP10 variants in progressive supranuclear palsy. (PMID:32527607)
  • Clinical and Pathological Phenotypes of LRP10 Variant Carriers with Dementia. (PMID:32597809)
  • Rare, pathogenic variants in LRP10 are associated with amyotrophic lateral sclerosis in patients from mainland China. (PMID:32690342)
  • Mutation analysis of LRP10 in a large Chinese familial Parkinson disease cohort. (PMID:32950273)
  • LRP10 Mutations May Correlate with Sporadic Parkinson’s Disease in China. (PMID:33118139)
  • LRP10 interacts with SORL1 in the intracellular vesicle trafficking pathway in non-neuronal brain cells and localises to Lewy bodies in Parkinson’s disease and dementia with Lewy bodies. (PMID:33913039)
  • Screening of LRP10 mutations in Parkinson’s disease patients from Italy. (PMID:34216936)
  • Role of LRP10 in Parkinson’s disease in a Taiwanese cohort. (PMID:34246039)
  • Genetic analysis of the LRP10 gene in Chinese patients with Parkinson’s disease. (PMID:36434476)
  • LRP10 and alpha-synuclein transmission in Lewy body diseases. (PMID:38315424)
  • Lrp10 suppresses IL7R limiting CD8 T cell homeostatic expansion and anti-tumor immunity. (PMID:38956225)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriolrp10ENSDARG00000054539
mus_musculusLrp10ENSMUSG00000022175
rattus_norvegicusLrp10ENSRNOG00000011592
drosophila_melanogasterarrFBGN0000119

Paralogs (14): LRP6 (ENSG00000070018), LRP2 (ENSG00000081479), NID2 (ENSG00000087303), NID1 (ENSG00000116962), LRP1 (ENSG00000123384), LDLR (ENSG00000130164), LRP3 (ENSG00000130881), LRP4 (ENSG00000134569), EGF (ENSG00000138798), LRP12 (ENSG00000147650), VLDLR (ENSG00000147852), LRP8 (ENSG00000157193), LRP5 (ENSG00000162337), LRP1B (ENSG00000168702)

Protein

Protein identifiers

Low-density lipoprotein receptor-related protein 10Q7Z4F1 (reviewed: Q7Z4F1)

All UniProt accessions (2): Q7Z4F1, H0YHW7

UniProt curated annotations — full annotation on UniProt →

Function. Probable receptor, which is involved in the internalization of lipophilic molecules and/or signal transduction. May be involved in the uptake of lipoprotein APOE in liver.

Subcellular location. Membrane. Coated pit.

Tissue specificity. Expressed in blood leukocyte, lung, placenta, small intestine, liver, kidney, spleen, thymus, colon, skeletal muscle and heart.

Similarity. Belongs to the LDLR family.

Isoforms (2)

UniProt IDNamesCanonical?
Q7Z4F1-11yes
Q7Z4F1-22

RefSeq proteins (2): NP_001316155, NP_054764* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000859CUB_domDomain
IPR002172LDrepeatLR_classA_rptRepeat
IPR023415LDLR_class-A_CSConserved_site
IPR035914Sperma_CUB_dom_sfHomologous_superfamily
IPR036055LDL_receptor-like_sfHomologous_superfamily
IPR050685LDLRFamily

Pfam: PF00057, PF00431

UniProt features (40 total): disulfide bond 15, domain 6, glycosylation site 4, sequence conflict 3, compositionally biased region 2, topological domain 2, sequence variant 2, signal peptide 1, chain 1, region of interest 1, modified residue 1, transmembrane region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q7Z4F1-F167.840.17

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 596

Disulfide bonds (15): 28–57, 80–98, 140–152, 147–165, 159–174, 192–220, 308–331, 315–344, 338–353, 356–374, 363–387, 381–396, 399–411, 406–424, 418–433

Glycosylation sites (4): 56, 111, 193, 299

Function

Pathways and Gene Ontology

Reactome pathways

6 pathways

IDPathway
R-HSA-975634Retinoid metabolism and transport
R-HSA-1430728Metabolism
R-HSA-196854Metabolism of vitamins and cofactors
R-HSA-2187338Visual phototransduction
R-HSA-6806667Metabolism of fat-soluble vitamins
R-HSA-9709957Sensory Perception

MSigDB gene sets: 195 (showing top): MYOGENIN_Q6, AREB6_01, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_EAR_DEVELOPMENT, BLALOCK_ALZHEIMERS_DISEASE_UP, KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_DN, GOBP_LIPID_METABOLIC_PROCESS, AACTTT_UNKNOWN, E12_Q6, GOBP_SENSORY_ORGAN_DEVELOPMENT, ACEVEDO_LIVER_CANCER_UP, GOBP_IMPORT_INTO_CELL, GOBP_LIPID_LOCALIZATION, GOBP_ENDOCYTOSIS, ACACTCC_MIR122A

GO Biological Process (5): lipid metabolic process (GO:0006629), lipid transport (GO:0006869), endocytosis (GO:0006897), inner ear development (GO:0048839), vesicle-mediated transport (GO:0016192)

GO Molecular Function (2): low-density lipoprotein particle receptor activity (GO:0005041), protein binding (GO:0005515)

GO Cellular Component (3): plasma membrane (GO:0005886), clathrin-coated pit (GO:0005905), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-5 pathways:

CategoryPathways
Visual phototransduction1
Metabolism of fat-soluble vitamins1
Metabolism1
Sensory Perception1
Metabolism of vitamins and cofactors1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
transport2
membrane2
primary metabolic process1
lipid localization1
vesicle budding from membrane1
membrane invagination1
vesicle-mediated transport1
import into cell1
ear development1
anatomical structure development1
cellular process1
low-density lipoprotein particle binding1
lipoprotein particle receptor activity1
binding1
cell periphery1
endomembrane system1
cellular anatomical structure1

Protein interactions and networks

STRING

898 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LRP10APOEP02649797
LRP10APPP05067612
LRP10TMEM230Q96A57599
LRP10FAM163AQ96GL9553
LRP10PRKNO60260491
LRP10ZFAND4Q86XD8456
LRP10LRP11Q86VZ4434
LRP10LRCH1Q9Y2L9427
LRP10EIF3KQ9UBQ5426
LRP10DNAJC13O75165420
LRP10VLDLRP98155411
LRP10SLC14A1Q13336398
LRP10VPS13CQ709C8398
LRP10AXIN1O15169396
LRP10GSK3BP49841394

IntAct

199 interactions, top by confidence:

ABTypeScore
TRDNTMEM223psi-mi:“MI:0914”(association)0.640
SLC20A1LIN7Apsi-mi:“MI:0914”(association)0.640
P2RX4FAM20Bpsi-mi:“MI:0914”(association)0.640
PDGFRBPIK3R2psi-mi:“MI:0914”(association)0.610
BCL2L2LRP10psi-mi:“MI:0915”(physical association)0.560
MIPLRP10psi-mi:“MI:0915”(physical association)0.560
LRP10EBPpsi-mi:“MI:0915”(physical association)0.560
LRP10psi-mi:“MI:0915”(physical association)0.560
LRP10TMEM179Bpsi-mi:“MI:0915”(physical association)0.560
LRP10MGST3psi-mi:“MI:0915”(physical association)0.560
LRP10BCL2L2psi-mi:“MI:0915”(physical association)0.560
NOTOLRP10psi-mi:“MI:0915”(physical association)0.560
LRP10TMEM237psi-mi:“MI:0915”(physical association)0.560
SLC14A2LRP10psi-mi:“MI:0915”(physical association)0.560
LRP10ST6GALNAC6psi-mi:“MI:0915”(physical association)0.560
SLC10A1LRP10psi-mi:“MI:0915”(physical association)0.560
LRP10MRPS18Bpsi-mi:“MI:0915”(physical association)0.560
EBPLRP10psi-mi:“MI:0915”(physical association)0.560
PLEKHO1LRP10psi-mi:“MI:0915”(physical association)0.560
LRP10CISD2psi-mi:“MI:0915”(physical association)0.560
LRP10psi-mi:“MI:0915”(physical association)0.560
GORABLRP10psi-mi:“MI:0915”(physical association)0.560

BioGRID (163): LRP10 (Affinity Capture-MS), LRP10 (Affinity Capture-MS), LRP10 (Affinity Capture-MS), LRP10 (Affinity Capture-MS), LRP10 (Affinity Capture-MS), LRP10 (Affinity Capture-MS), LRP10 (Affinity Capture-MS), LRP10 (Affinity Capture-MS), LRP10 (Affinity Capture-MS), LRP10 (Affinity Capture-MS), LRP10 (Affinity Capture-MS), LRP10 (Affinity Capture-MS), LRP10 (Affinity Capture-MS), LRP10 (Affinity Capture-MS), LRP10 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GTW7, A0A1D5NSK0, A0A1L8HYT7, A0A286YEC0, D3ZT86, D3ZWJ9, D4A929, F8W3R9, G7PWZ3, I6M4H4, O08852, O43157, O43278, O75074, O88204, P17813, P49000, P59383, Q04912, Q17R55, Q499Z3, Q4R3B7, Q4TUC0, Q5ND34, Q62190, Q63961, Q6AXX1, Q76MJ5, Q7TN88, Q7TQH7, Q7Z442, Q7Z4F1, Q80W87, Q80YN4, Q866Y3, Q86VZ4, Q8BHW9, Q8BMN4, Q8BYI8, Q8BZT7

Diamond homologs: A2VEC9, E9Q6D8, G3V928, O57382, O57460, O70244, O75074, O88204, O88307, P0DSP1, P13497, P42674, P48740, P98063, P98064, P98070, P98157, P98165, Q04833, Q07954, Q20176, Q4A3R3, Q5R662, Q62381, Q6F3F9, Q7M761, Q7RTZ1, Q7TQH7, Q7Z407, Q7Z408, Q7Z4F1, Q80T79, Q811M5, Q86SQ4, Q8BQH6, Q8BUJ9, Q8CHN8, Q8JI28, Q8K1S7, Q8NCW0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

127 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance90
Likely benign14
Benign9

Top pathogenic / likely-pathogenic (0)

SpliceAI

990 predictions. Top by Δscore:

VariantEffectΔscore
14:22873306:TCCA:Tacceptor_loss1.0000
14:22873307:CCA:Cacceptor_loss1.0000
14:22873308:CA:Cacceptor_loss1.0000
14:22873309:A:ACacceptor_loss1.0000
14:22873309:A:AGacceptor_gain1.0000
14:22873309:AGCTT:Aacceptor_gain1.0000
14:22873310:G:GTacceptor_gain1.0000
14:22873310:GC:Gacceptor_gain1.0000
14:22873310:GCTT:Gacceptor_gain1.0000
14:22873310:GCTTG:Gacceptor_gain1.0000
14:22873443:TCAGG:Tdonor_loss1.0000
14:22873444:CAGG:Cdonor_loss1.0000
14:22873445:AGGT:Adonor_loss1.0000
14:22873447:G:Adonor_loss1.0000
14:22873448:T:Gdonor_loss1.0000
14:22875052:TAG:Tacceptor_loss1.0000
14:22875053:A:ACacceptor_loss1.0000
14:22875190:C:Gdonor_gain1.0000
14:22875241:CCAAG:Cdonor_loss1.0000
14:22875242:CAAGG:Cdonor_loss1.0000
14:22875243:AAG:Adonor_loss1.0000
14:22875244:AGGTA:Adonor_loss1.0000
14:22875246:GTAG:Gdonor_loss1.0000
14:22875247:T:Gdonor_loss1.0000
14:22876687:A:AGacceptor_gain1.0000
14:22876688:G:GGacceptor_gain1.0000
14:22876688:GC:Gacceptor_gain1.0000
14:22876814:ATGAT:Adonor_gain1.0000
14:22876815:TGAT:Tdonor_gain1.0000
14:22876816:GAT:Gdonor_gain1.0000

AlphaMissense

4523 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
14:22875974:G:CW342C1.000
14:22875974:G:TW342C1.000
14:22876159:T:GF404C1.000
14:22876196:G:CW416C1.000
14:22876196:G:TW416C1.000
14:22876218:T:AC424S1.000
14:22876219:G:AC424Y1.000
14:22876219:G:CC424S1.000
14:22876293:A:CS449R1.000
14:22876295:C:AS449R1.000
14:22876295:C:GS449R1.000
14:22876760:T:CL499P1.000
14:22876763:T:AI500N1.000
14:22876796:T:GF511C1.000
14:22875614:G:CW222C0.999
14:22875614:G:TW222C0.999
14:22875655:T:CF236S0.999
14:22875840:T:CF298L0.999
14:22875841:T:CF298S0.999
14:22875841:T:GF298C0.999
14:22875842:C:AF298L0.999
14:22875842:C:GF298L0.999
14:22875846:G:CA300P0.999
14:22875847:C:AA300D0.999
14:22875852:T:GY302D0.999
14:22875978:T:AC344S0.999
14:22875978:T:CC344R0.999
14:22875979:G:AC344Y0.999
14:22875979:G:CC344S0.999
14:22875979:G:TC344F0.999

dbSNP variants (sampled 300 via entrez): RS1000268552 (14:22875064 G>A,C), RS1000587796 (14:22876543 G>C), RS1000942014 (14:22879681 T>C), RS1001287870 (14:22870323 G>A), RS1001308106 (14:22881252 G>A,C), RS1001371508 (14:22880041 G>A), RS1001479780 (14:22875287 C>T), RS1001490526 (14:22875766 C>A,G,T), RS1001799756 (14:22869979 C>A), RS1001815877 (14:22882202 G>C), RS1002101220 (14:22881903 C>G,T), RS1002282880 (14:22870109 T>C), RS1003126226 (14:22876449 G>A), RS1003158657 (14:22876739 C>G,T), RS1003492137 (14:22878123 C>A)

Disease associations

OMIM: gene MIM:609921 | disease phenotypes: MIM:600057

GenCC curated gene-disease

Mondo (2): myoepithelial tumor (MONDO:0002380), bladder exstrophy-epispadias-cloacal exstrophy complex (MONDO:0700039)

Orphanet (1): Classic bladder exstrophy (Orphanet:93930)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

2 associations (top):

StudyTraitp-value
GCST010483_2Cardiovascular death, myocardial infarction or stroke in response to clopidogrel treatment5.000000e-06
GCST90002398_216Neutrophil count3.000000e-09

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0006919cardiovascular event measurement
EFO:0004833neutrophil count

MeSH disease descriptors (1)

DescriptorNameTree numbers
D009208MyoepitheliomaC04.557.435.585

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

57 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, increases methylation10
Benzo(a)pyreneincreases expression5
trichostatin Aaffects cotreatment, increases expression3
Acetaminophendecreases expression, increases expression3
Tretinoinincreases expression3
Aflatoxin B1affects expression, increases expression3
sodium arseniteincreases expression2
mercuric bromideincreases expression, affects cotreatment2
Phenylmercuric Acetateaffects cotreatment, increases expression2
Tetrachlorodibenzodioxinincreases expression2
Cyclosporineincreases expression2
bisphenol Faffects cotreatment, increases expression1
methylmercuric chlorideincreases expression1
triphenyl phosphateaffects expression1
bisphenol Aaffects expression1
sulforaphaneincreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
butyraldehydedecreases expression1
cupric chlorideincreases expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
erucylphospho-N,N,N-trimethylpropylammoniumincreases expression1
dorsomorphinaffects cotreatment, increases expression1
jinfukangaffects cotreatment, increases expression1
(+)-JQ1 compounddecreases expression1
MT19c compounddecreases expression1
Temozolomidedecreases expression1
Air Pollutantsaffects expression, increases abundance1
Atrazineincreases expression1
Azathioprineincreases expression1

Cellosaurus cell lines

1 cell lines: 1 induced pluripotent stem cell

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_D0HGLCPHi003-AInduced pluripotent stem cellMale

Clinical trials (associated diseases)

5 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT03600649PHASE1UNKNOWNClinical Trial of SP-2577 (Seclidemstat) in Patients With Relapsed or Refractory Ewing or Ewing-related Sarcomas
NCT05266196PHASE1/PHASE2UNKNOWNA Rollover Protocol to Allow for Continued Access to the LSD1 Inhibitor Seclidemstat (SP-2577)
NCT06239272PHASE1/PHASE2RECRUITINGNRSTS2021, A Risk Adapted Study Evaluating Maintenance Pazopanib, Limited Margin, Dose-Escalated Radiation Therapy and Selinexor in Non-Rhabdomyosarcoma Soft Tissue Sarcoma (NRSTS)
NCT06625190PHASE1/PHASE2RECRUITINGAlpha/Beta T and B Cell Depletion With Zoledronic Acid for Solid Tumors
NCT06244420Not specifiedCOMPLETEDMalignant Myoepithelioma of Bone and Soft Tissues: Diagnostic Imaging and Histology in Relation to Prognosis