LRPAP1

LDL receptor related protein associated protein 1

Basic information

Region (hg38): 4:3503612-3532446

Previous symbols: [ "A2MRAP", "RAP" ]

Links

ENSG00000163956NCBI:4043OMIM:104225HGNC:6701Uniprot:P30533AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • myopia 23, autosomal recessive (Definitive), mode of inheritance: AR
  • myopia 23, autosomal recessive (Strong), mode of inheritance: AR
  • myopia 23, autosomal recessive (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Myopia 23, autosomal recessiveARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingOphthalmologic23830514; 25525168

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LRPAP1 gene.

  • not_specified (77 variants)
  • not_provided (18 variants)
  • LRPAP1-related_disorder (12 variants)
  • Myopia_23,_autosomal_recessive (4 variants)
  • Prostate_cancer (1 variants)
  • Rare_isolated_myopia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRPAP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002337.4. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
4
clinvar
5
clinvar
9
missense
73
clinvar
10
clinvar
3
clinvar
86
nonsense
1
clinvar
1
start loss
0
frameshift
3
clinvar
1
clinvar
4
splice donor/acceptor (+/-2bp)
0
Total 3 2 73 14 8

Highest pathogenic variant AF is 0.00000143082

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
LRPAP1protein_codingprotein_codingENST00000500728 826184
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
4.50e-70.6261257180301257480.000119
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.032722281.190.00001472303
Missense in Polyphen8579.6511.0672902
Synonymous-1.071221081.130.00000798681
Loss of Function1.051216.60.7217.08e-7198

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002120.000212
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.000.00
European (Non-Finnish)0.0001330.000123
Middle Eastern0.0001090.000109
South Asian0.0003040.000294
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Molecular chaperone for LDL receptor-related proteins that may regulate their ligand binding activity along the secretory pathway. {ECO:0000269|PubMed:7774585}.;
Disease
DISEASE: Myopia 23, autosomal recessive (MYP23) [MIM:615431]: A refractive error of the eye, in which parallel rays from a distant object come to focus in front of the retina, vision being better for near objects than for far. {ECO:0000269|PubMed:23830514}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Cholesterol metabolism - Homo sapiens (human);integrin signaling pathway;Reelin signaling pathway;Lissencephaly gene (LIS1) in neuronal migration and development;Signaling events mediated by the Hedgehog family (Consensus)

Recessive Scores

pRec
0.123

Intolerance Scores

loftool
0.551
rvis_EVS
0.6
rvis_percentile_EVS
82.83

Haploinsufficiency Scores

pHI
0.128
hipred
N
hipred_score
0.197
ghis
0.422

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.802

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Lrpap1
Phenotype
endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); renal/urinary system phenotype;

Gene ontology

Biological process
negative regulation of receptor internalization;negative regulation of very-low-density lipoprotein particle clearance;negative regulation of protein binding;transcytosis;regulation of receptor-mediated endocytosis;negative regulation of cell death;extracellular negative regulation of signal transduction;negative regulation of amyloid-beta clearance;positive regulation of amyloid-beta clearance
Cellular component
extracellular region;endosome;endoplasmic reticulum;endoplasmic reticulum-Golgi intermediate compartment;Golgi apparatus;Golgi lumen;cis-Golgi network;plasma membrane;cell surface;endosome lumen;rough endoplasmic reticulum lumen
Molecular function
amyloid-beta binding;signaling receptor binding;protein binding;heparin binding;lipase binding;receptor antagonist activity;low-density lipoprotein particle receptor binding;very-low-density lipoprotein particle receptor binding