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Relevance to Autism

Cluster-detection analysis of an ASD-associated chromosome 2q linkage region that had been sequenced in three independent datasets revealed variants in the LRP2 gene that were associated with ASD in two of the datasets (the combined variable-threshold-test p value is 1.2 10(-5)). (Ionita-Laza et al., 2012). A de novo nonsense variant in the LRP2 gene was identified in an autistic proband following exome sequencing of 343 quad families from the Simons Simplex Collection (Iossifov et al., 2012).

Molecular Function

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.

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
Scan-statistic approach identifies clusters of rare disease variants in LRP2, a gene linked and associated with autism spectrum disorders, in three...
ASD
Positive Association
Genome-Wide Association Study for Autism Spectrum Disorder in Taiwanese Han Population.
ASD
Support
Large-scale discovery of novel genetic causes of developmental disorders.
ID, epilepsy/seizures
Microcephaly, hearing impairment
Support
High prevalence of multilocus pathogenic variation in neurodevelopmental disorders in the Turkish population
DD
Support
DD
Support
Synaptic, transcriptional and chromatin genes disrupted in autism.
ASD
Support
Next-Generation Sequencing in Korean Children With Autism Spectrum Disorder and Comorbid Epilepsy
ASD
ID, epilepsy/seizures
Support
Donnai-Barrow syndrome, DD
Autistic features, stereotypy, epilepsy/seizures
Support
Diagnostic exome sequencing in persons with severe intellectual disability.
ID
Epilepsy, ASD
Support
Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes
ASD
Support
Integrating de novo and inherited variants in 42
ASD
Support
De novo gene disruptions in children on the autistic spectrum.
ASD
Support
Mapping autosomal recessive intellectual disability: combined microarray and exome sequencing identifies 26 novel candidate genes in 192 consanguin...
ID
Support
Clinical Targeted Panel Sequencing Analysis in Clinical Evaluation of Children with Autism Spectrum Disorder in China
ASD
Support
Leveraging blood serotonin as an endophenotype to identify de novo and rare variants involved in autism.
ASD
Support
Mutational Landscape of Autism Spectrum Disorder Brain Tissue
ASD
Support
Excess of rare, inherited truncating mutations in autism.
ASD
Support
Prevalence and phenotypic impact of rare potentially damaging variants in autism spectrum disorder
ASD
Highly Cited
Mutations in LRP2, which encodes the multiligand receptor megalin, cause Donnai-Barrow and facio-oculo-acoustico-renal syndromes.
Recent Recommendation
Integrated systems analysis reveals a molecular network underlying autism spectrum disorders.
ASD

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN362R001 
 stop_gained 
 c.9550C>T 
 p.Arg3184Ter 
 De novo 
  
 Simplex 
 GEN362R002 
 synonymous_variant 
  
 p.(=) 
 Unknown 
  
  
 GEN362R003 
 missense_variant 
 NM_004525:c.6256G>C 
 p.Thr2086Ser 
 Unknown 
  
  
 GEN362R004 
 missense_variant 
 c.6160G>A 
 p.Asp2054Asn 
 Unknown 
  
  
 GEN362R005 
 missense_variant 
 c.6049G>A 
 p.Glu2017Lys 
 Unknown 
  
  
 GEN362R006 
 synonymous_variant 
  
 p.(=) 
 Unknown 
  
  
 GEN362R007 
 missense_variant 
 c.5932G>C 
 p.Glu1978Gln 
 Unknown 
  
  
 GEN362R008 
 missense_variant 
 c.5842G>A 
 p.Val1948Met 
 Unknown 
  
  
 GEN362R009 
 missense_variant 
 c.5792A>G 
 p.Gln1931Arg 
 Unknown 
  
  
 GEN362R010 
 missense_variant 
 c.4979G>A 
 p.Arg1660His 
 Unknown 
  
  
 GEN362R011 
 missense_variant 
 NM_004525.2:4978C>T 
 p.Arg1660Cys 
 Unknown 
  
  
 GEN362R012 
 missense_variant 
 c.4766G>A 
 p.Arg1589His 
 Unknown 
  
  
 GEN362R013 
 intron_variant 
 c.4692-35G>C 
  
 Unknown 
  
  
 GEN362R014 
 frameshift_variant 
 c.12437del 
 p.Gly4146GlufsTer2 
 De novo 
  
  
 GEN362R015 
 nonsynonymous_variant 
  
  
 Unknown 
  
 Unknown 
 GEN362R016 
 missense_variant 
 c.11107G>A 
 p.Asp3703Asn 
 Unknown 
  
 Unknown 
 GEN362R017 
 missense_variant 
 c.9929G>A 
 p.Arg3310His 
 Unknown 
  
 Unknown 
 GEN362R018 
 nonsynonymous_variant 
  
  
 Unknown 
  
 Unknown 
 GEN362R019 
 missense_variant 
 c.2933C>T 
 p.Thr978Met 
 Unknown 
  
 Unknown 
 GEN362R020 
 missense_variant 
 c.775G>C 
 p.Gly259Arg 
 Unknown 
  
 Unknown 
 GEN362R021 
 missense_variant 
 c.149C>G 
 p.Thr50Ser 
 Unknown 
  
 Unknown 
 GEN362R022a 
 missense_variant 
 c.11663G>A 
 p.Arg3888His 
 Familial 
 Maternal and Paternal 
 Simplex 
 GEN362R022b 
 missense_variant 
 c.5209C>T 
 p.Leu1737Phe 
 Familial 
 Maternal and Paternal 
 Simplex 
 GEN362R023a 
 missense_variant 
 c.6160G>A 
 p.Asp2054Asn 
 Familial 
 Maternal and Paternal 
 Simplex 
 GEN362R023b 
 missense_variant 
 c.6160G>A 
 p.Asp2054Asn 
 Familial 
 Maternal and Paternal 
 Simplex 
 GEN362R024 
 missense_variant 
 c.12137G>A 
 p.Arg4046Gln 
 De novo 
  
 Simplex 
 GEN362R025 
 missense_variant 
 c.10887C>G 
 p.His3629Gln 
 De novo 
  
  
 GEN362R026 
 missense_variant 
 c.10887C>G 
 p.His3629Gln 
 De novo 
  
 Simplex 
 GEN362R027a 
 missense_variant 
 c.11335G>A 
 p.Asp3779Asn 
 Familial 
 Both parents 
 Multiplex 
 GEN362R028 
 stop_gained 
 c.1093C>T 
 p.Arg365Ter 
 Familial 
 Paternal 
  
 GEN362R029 
 missense_variant 
 c.5314G>A 
 p.Val1772Ile 
 Unknown 
  
  
 GEN362R030 
 missense_variant 
 c.2944G>T 
 p.Gly982Cys 
 De novo 
  
 Simplex 
 GEN362R031 
 splice_site_variant 
 c.10393+1G>A 
  
 Unknown 
  
  
 GEN362R032 
 stop_gained 
 c.2320G>T 
 p.Gly774Ter 
 Unknown 
  
  
 GEN362R033 
 missense_variant 
 c.7931T>A 
 p.Val2644Glu 
 Unknown 
  
  
 GEN362R034 
 missense_variant 
 c.11938A>G 
 p.Thr3980Ala 
 Unknown 
  
  
 GEN362R035a 
 missense_variant 
 c.10836G>T 
 p.Gln3612His 
 Unknown 
  
  
 GEN362R035b 
 frameshift_variant 
 c.5406_5407del 
 p.His1802GlnfsTer39 
 Unknown 
  
  
 GEN362R036 
 frameshift_variant 
 c.11469_11472del 
 p.Cys3823TrpfsTer159 
 De novo 
  
  
 GEN362R037 
 missense_variant 
 c.4878T>A 
 p.Asp1626Glu 
 De novo 
  
  
 GEN362R038 
 missense_variant 
 c.3371A>G 
 p.Lys1124Arg 
 De novo 
  
  
 GEN362R039 
 missense_variant 
 c.4234C>T 
 p.Arg1412Trp 
 De novo 
  
 Simplex 
 GEN362R040 
 splice_site_variant 
 c.8452+1G>A 
  
 De novo 
  
  
 GEN362R041 
 missense_variant 
 c.4927C>T 
 p.Arg1643Trp 
 De novo 
  
  
 GEN362R042 
 synonymous_variant 
 c.2772G>A 
 p.Glu924%3D 
 De novo 
  
  
 GEN362R043 
 missense_variant 
 c.12926T>A 
 p.Leu4309Gln 
 De novo 
  
  
 GEN362R044 
 missense_variant 
 c.9911G>T 
 p.Arg3304Leu 
 De novo 
  
  
 GEN362R045 
 missense_variant 
 c.4403T>C 
 p.Ile1468Thr 
 De novo 
  
  
 GEN362R046 
 missense_variant 
 c.100C>T 
 p.Arg34Cys 
 De novo 
  
  
 GEN362R047a 
 missense_variant 
 c.6815G>A 
 p.Arg2272His 
 Familial 
 Maternal 
 Multiplex (monozygotic twins) 
  et al.  
 GEN362R047b 
 missense_variant 
 c.12725A>G 
 p.Asp4242Gly 
 Familial 
 Paternal 
 Multiplex (monozygotic twins) 
  et al.  
 GEN362R048a 
 missense_variant 
 c.11503C>T 
 p.Arg3835Cys 
 Familial 
 Both parents 
  
  et al.  

Common

Variant ID
Polymorphism
SNP ID
Allele Change
Residue Change
Population Origin
Population Stage
Author, Year
 GEN362C001 
 missense_variant 
 rs13391626 
 c.5825T>G;c.3536T>G;c.5840T>G;c.3551T>G 
 p.Val1942Gly;p.Val1179Gly;p.Val1947Gly;p.Val1184Gly 
 Seaver Autism Research Center & AGRE (397 ASD cases/450 controls) 
 Discovery 
 GEN362C002 
 gene_variant 
  
  
  
 Seaver Autism Research Center & AGRE (397 ASD cases/450 controls) 
 Discovery 
 GEN362C003 
 gene_variant 
  
  
  
 Seaver Autism Research Center & AGRE (397 ASD cases/450 controls) 
 Discovery 
 GEN362C004 
 gene_variant 
  
  
  
 Seaver Autism Research Center & AGRE (397 ASD cases/450 controls) 
 Discovery 
 GEN362C005 
 gene_variant 
  
  
  
 Seaver Autism Research Center & AGRE (397 ASD cases/450 controls) 
 Discovery 
 GEN362C006 
 gene_variant 
  
  
  
 Seaver Autism Research Center & AGRE (397 ASD cases/450 controls) 
 Discovery 
 GEN362C007 
 synonymous_variant 
 rs2075249 
 c.3054C>A;c.765C>A 
 p.(=) 
 ARRA-Broad (430 cases, 379 controls) 
 Discovery 
 GEN362C008 
 intron_variant 
 rs2075255 
 c.3550+18T>G;c.1261+18T>G 
  
 ARRA-Broad (430 cases, 379 controls) 
 Discovery 
 GEN362C009 
 synonymous_variant 
 rs831042 
 c.3660A>G;c.1371A>G 
 p.(=) 
 ARRA-Broad (430 cases, 379 controls) 
 Discovery 
 GEN362C010 
 intron_variant 
 rs2075254 
 c.3550+14C>T;c.1261+14C>T 
  
 ARRA-Broad (430 cases, 379 controls) 
 Discovery 
 GEN362C011 
 intron_variant 
 rs831041 
 c.3667+20A>C;c.1378+20A>C 
  
 ARRA-Broad (430 cases, 379 controls) 
 Discovery 
 GEN362C012 
 synonymous_variant 
 rs831043 
 c.3069A>G;c.780A>G 
 p.(=) 
 ARRA-Broad (430 cases, 379 controls) 
 Discovery 
 GEN362C013 
 synonymous_variant 
 rs2229267 
 c.4875T>C;c.2586T>C;c.4890T>C;c.2601T>C 
 p.(=) 
 ARRA-Broad (430 cases, 379 controls) 
 Discovery 
 GEN362C014 
 intron_variant 
 rs830973 
 c.4294+19C>T;c.2005+19C>T;c.4309+19C>T;c.2020+19C>T 
  
 ARRA-Broad (430 cases, 379 controls) 
 Discovery 
 GEN362C015 
 synonymous_variant 
 rs2241190 
 c.2460A>G;c.171A>G 
 p.(=) 
 ARRA-Broad (430 cases, 379 controls) 
 Discovery 
 GEN362C016 
 gene_variant 
  
  
  
 ARRA-Broad (430 cases, 379 controls) 
 Discovery 
 GEN362C017 
 intergenic_variant 
 rs13014164 
  
  
 315 ASD cases, 1115 healthy controls (Taiwanese Han) 
 Discovery 
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
2
Duplication
 1
 
2
Duplication
 1
 
2
Deletion
 1
 
2
Deletion
 1
 
2
Deletion
 19
 
2
Deletion
 3
 
2
Deletion
 1
 

No Animal Model Data Available


Interactor Symbol Interactor Name Interactor Organism Entrez ID Uniprot ID Interaction Type Evidence Reference
AMBN Ameloblastin 258 Q9NP70-2 IP; LC-MS/MS
Huttlin EL , et al. 2015
ANKS1B ankyrin repeat and sterile alpha motif domain containing 1B 56899 B7Z9I9 Y2H
Petersen HH , et al. 2003
ARHGAP19 Rho GTPase activating protein 19 84986 Q14CB8 IP; LC-MS/MS
Huttlin EL , et al. 2015
ATN1 atrophin 1 1822 P54259 Y2H
Lim J , et al. 2006
CCDC59 coiled-coil domain containing 59 29080 Q9P031 IP; LC-MS/MS
Huttlin EL , et al. 2015
CLU clusterin 1191 P10909 Affinity chromatography; Solid phase binding assay; Gel blot overlay assay
Kounnas MZ , et al. 1995
CTGF Connective tissue growth factor 1490 P29279 IP; LC-MS/MS
Huttlin EL , et al. 2015
DAB2 disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila) 1601 P98082 Y2H; GST; IP/WB
Oleinikov AV , et al. 2000
DLG2 discs, large homolog 2 (Drosophila) 1740 Q15700 Y2H; Surface plasmon resonance (SPR)
Larsson M , et al. 2003
DLG3 discs, large homolog 3 (Drosophila) 1741 Q92796 Y2H; Surface plasmon resonance (SPR)
Larsson M , et al. 2003
DLK2 Protein delta homolog 2 65989 Q6UY11-2 IP; LC-MS/MS
Huttlin EL , et al. 2015
EGFL6 EGF-like-domain, multiple 6 25975 Q8IUX8 IP; LC-MS/MS
Huttlin EL , et al. 2015
FAM19A3 Protein FAM19A3 284467 Q7Z5A8-2 IP; LC-MS/MS
Huttlin EL , et al. 2015
FAM19A4 Protein FAM19A4 151647 Q96LR4 IP; LC-MS/MS
Huttlin EL , et al. 2015
FGFRL1 fibroblast growth factor receptor-like 1 53834 A0PJ49 IP; LC-MS/MS
Huttlin EL , et al. 2015
FMR1 fragile X mental retardation 1 2332 G8JLE9 PAR-CLIP; RNA immunoprecipitation (RIP)
Ascano M Jr , et al. 2012
GC Vitamin D-binding protein 100008994 P53789 Affinity chromatography; Surface plasmon resonance (SPR)
Nykjaer A , et al. 2001
INSL6 Insulin-like peptide INSL6 11172 Q9Y581 IP; LC-MS/MS
Huttlin EL , et al. 2015
LCN2 lipocalin 2 3934 P80188 Surface plasmon resonance (SPR)
Hvidberg V , et al. 2005
LPA lipoprotein, Lp(a) 4018 P08519 Surface plasmon resonance (SPR)
Niemeier A , et al. 1999
LPL lipoprotein lipase 4023 P06858 Solid phase binding assay
Kounnas MZ , et al. 1993
LRP2BP LRP2 binding protein 55805 Q9P2M1 Y2H; GST; Surface plasmon resonance (SPR)
Petersen HH , et al. 2003
LRPAP1 low density lipoprotein receptor-related protein associated protein 1 4043 P30533 IP; LC-MS/MS
Huttlin EL , et al. 2015
MDK midkine (neurite growth-promoting factor 2) 4192 P21741 Affinity chromatography; MS; Solid phase I-125 binding assay
Muramatsu H , et al. 2000
MEPE Matrix extracellular phosphoglycoprotein 56955 Q9NQ76 IP; LC-MS/MS
Huttlin EL , et al. 2015
PDGFD Platelet-derived growth factor D 80310 Q9GZP0-2 IP; LC-MS/MS
Huttlin EL , et al. 2015
Ppara peroxisome proliferator activated receptor alpha 19013 P23204 Luciferase reporter assay; EMSA
Cabezas F , et al. 2011
Pparg peroxisome proliferator activated receptor gamma 19016 P37238 EMSA
Cabezas F , et al. 2011
RIBC2 RIB43A-like with coiled-coils protein 2 26150 Q9H4K1 IP; LC-MS/MS
Huttlin EL , et al. 2015
SOST Sclerostin 50964 Q9BQB4 IP; LC-MS/MS
Huttlin EL , et al. 2015
VIP VIP peptides 7432 P01282 IP; LC-MS/MS
Huttlin EL , et al. 2015
ZBTB48 zinc finger and BTB domain containing 48 3104 P10074 IP; LC-MS/MS
Huttlin EL , et al. 2015
ZFP41 Zinc finger protein 41 homolog 286128 Q8N8Y5 IP; LC-MS/MS
Huttlin EL , et al. 2015
ZNF224 zinc finger protein 224 7767 Q9NZL3 IP; LC-MS/MS
Huttlin EL , et al. 2015
ZNF264 zinc finger protein 264 9422 O43296 IP; LC-MS/MS
Huttlin EL , et al. 2015
ZNF408 zinc finger protein 408 79797 B4DXY4 IP; LC-MS/MS
Huttlin EL , et al. 2015
ZSCAN29 zinc finger and SCAN domain containing 29 146050 Q05BJ4 IP; LC-MS/MS
Huttlin EL , et al. 2015
Apba2 amyloid beta (A4) precursor protein-binding, family A, member 2 11784 P98084 Y2H
Gotthardt M , et al. 2000
Dab1 disabled 1 13131 P97318 Y2H; GST
Trommsdorff M , et al. 1998
DLG4 DLG4discs, large homolog 4 (Drosophila) 1742 P78352 Y2H; GST
Gotthardt M , et al. 2000
Fut4 fucosyltransferase 4 14345 Q11127 IP; MS
Hashii N , et al. 2009
GIPC1 GIPC PDZ domain containing family, member 1 10755 O14908 Y2H; GST
Gotthardt M , et al. 2000
Gprasp1 G protein-coupled receptor associated sorting protein 1 67298 Q5U4C1 Y2H; GST
Patrie KM , et al. 2001
Igf1 insulin-like growth factor 1 16000 E9PU89 IP/WB
Bols M , et al. 2010
ITGB1BP1 integrin beta 1 binding protein 1 9270 O14713 Y2H; GST
Gotthardt M , et al. 2000
Magi1 membrane associated guanylate kinase, WW and PDZ domain containing 1 14924 Q6RHR9 Y2H; GST
Patrie KM , et al. 2001
MAPK8IP1 mitogen-activated protein kinase 8 interacting protein 1 9479 Q6NUQ9 Y2H; GST
Gotthardt M , et al. 2000
MAPK8IP2 mitogen-activated protein kinase 8 interacting protein 2 23542 Q13387 Y2H; GST
Gotthardt M , et al. 2000
NOS1AP nitric oxide synthase 1 (neuronal) adaptor protein 9722 O75052 Y2H; GST
Gotthardt M , et al. 2000
NOS1AP nitric oxide synthase 1 (neuronal) adaptor protein 70729 Q9D3A8 Y2H; GST
Gotthardt M , et al. 2000
Pip5k1c phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma 18717 O70161 Y2H; GST
Gotthardt M , et al. 2000
Shh sonic hedgehog 20423 Q62226 GST
Christ A , et al. 2012
SYNJ2BP synaptojanin 2 binding protein 55333 P57105 Y2H; GST
Gotthardt M , et al. 2000
Tln1 talin 1 21894 P26039 Y2H
Gotthardt M , et al. 2000
Alb albumin 24186 P02770 in vitro binding assay; I-125 binding assay
Cui S , et al. 1996
Ankra2 ankyrin repeat, family A (RFXANK-like), 2 68558 Q6NZJ1 Y2H; GST; I-125 binding assay
Rader K , et al. 2000
Apoe apolipoprotein E 25728 P02650 Ligand binding assay
Veinbergs I , et al. 2001
B2m beta-2 microglobulin 24223 P07151 Ligand blotting
Orlando RA , et al. 1998
CST3 cystatin C 1471 P01034 Quartz-crystal microbalance
Kaseda R , et al. 2007
Cubn cubilin (intrinsic factor-cobalamin receptor) 80848 O70244 in vitro binding assay
Yammani RR , et al. 2001
Cycs cytochrome c, somatic 25309 P62898 Ligand blotting
Orlando RA , et al. 1998
Egf epidermal growth factor 25313 P07522 Ligand blotting
Orlando RA , et al. 1998
Irs1 insulin receptor substrate 1 25467 P35570 I-125 binding assay
Orlando RA , et al. 1998
Ldlrap1 low density lipoprotein receptor adaptor protein 1 500564 D3ZAR1 Y2H; GST; IP/WB
Nagai M , et al. 2003
Lrpap1 low density lipoprotein receptor-related protein associated protein 1 116565 Q99068 Solid phase binding assay; Ligand blotting
Orlando RA and Farquhar MG 1994
Lyz2 lysozyme 2 25211 Q6PDV1 Ligand blotting
Orlando RA , et al. 1998
Prl prolactin 24683 B5DEM6 Ligand blotting
Orlando RA , et al. 1998
Tg thyroglobulin 24826 G3V6V3 Solid phase binding assay
Zheng G , et al. 1998
Ttr transthyretin 24856 P02767 Ligand blotting
Sousa MM , et al. 2000
THBS1 thrombospondin 1 7057 P07996 Solid phase binding assay
Godyna S , et al. 1995
APOB N/A 100009101 N/A Ligand blotting; Solid phase binding assay
Chen Z , et al. 1999
APOH apolipoprotein H (beta-2-glycoprotein I) 350 P02749 Surface plasmon resonance (SPR)
Moestrup SK , et al. 1998
NHE-3 Sodium/hydrogen exchanger 3 100009430 P26432 IP/WB
Biemesderfer D , et al. 1999
PLAU plasminogen activator, urokinase 5328 P00749 Ligand blotting
Moestrup SK , et al. 1993
RBP1 retinol binding protein 1, cellular 5947 P09455 Surface plasmon resonance (SPR)
Christensen EI , et al. 1999
SERPINE1 serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1 5054 P05121 Ligand blotting
Moestrup SK , et al. 1993

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