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Relevance to Autism

De novo missense variants in the LRP1 gene have been observed in ASD probands from the Autism Sequencing Consortium and the Simons Simplex Collection (DeRubeis et al., 2014; Iossifov et al., 2014). Whole-exome sequencing of 20 high-functioning autism families in Torrico et al., 2019 identified a de novo splice-site variant in LRP1 that resulted in in-frame skipping of exon 29 and reduced cytokine expression in proband-derived immortalized lymphocyte cell lines. Torrico et al., 2019 also demonstrated that de novo variants in LRP1 are associated with ASD (P=0.039) and schizophrenia (P=0.008), common variants in LRP1 show gene-based association in schizophrenia (P=6.6E-07) and in a meta-analysis across seven psychiatric disorders (P=1.2E-05), and LRP1 exhibits an increased burden of ultra-rare pathogenic variants in a cohort of ASD probands from the ARRA Autism Sequencing Collaboration compared to controls (35 variants in 1778 ASD probands vs. 64 variants in 7875 controls; P-value of 1.2E-05).

Molecular Function

This gene encodes a member of the low-density lipoprotein receptor family of proteins. The encoded preproprotein is proteolytically processed by furin to generate 515 kDa and 85 kDa subunits that form the mature receptor (PMID: 8546712). This receptor is involved in several cellular processes, including intracellular signaling, lipid homeostasis, and clearance of apoptotic cells. In addition, the encoded protein is necessary for the alpha 2-macroglobulin-mediated clearance of secreted amyloid precursor protein and beta-amyloid, the main component of amyloid plaques found in Alzheimer patients.

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
Synaptic, transcriptional and chromatin genes disrupted in autism.
ASD
Support
The contribution of de novo coding mutations to autism spectrum disorder
ASD
Support
Integrating de novo and inherited variants in 42
ASD
Support
Mutational Landscape of Autism Spectrum Disorder Brain Tissue
ASD
Support
Recent ultra-rare inherited variants implicate new autism candidate risk genes
ASD
Support
Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes
ASD
Recent Recommendation
Truncating variant burden in high-functioning autism and pleiotropic effects of LRP1 across psychiatric phenotypes
ASD
SCZ

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN1088R001 
 missense_variant 
 c.11452G>A 
 p.Gly3818Ser 
 De novo 
  
  
 GEN1088R002 
 missense_variant 
 c.4966G>T 
 p.Asp1656Tyr 
 De novo 
  
 Simplex 
 GEN1088R003 
 missense_variant 
 c.10190A>G 
 p.Asn3397Ser 
 De novo 
  
 Simplex 
 GEN1088R004 
 splice_site_variant 
 c.5203A>G 
 p.Thr1735Ala 
 De novo 
  
 Simplex 
 GEN1088R005 
 frameshift_variant 
 A>AG 
 p.Glu104GluTer 
 Unknown 
  
  
 GEN1088R006 
 missense_variant 
 c.430G>C 
 p.Asp144His 
 Unknown 
  
  
 GEN1088R007 
 missense_variant 
 c.1364G>A 
 p.Arg455Gln 
 Unknown 
  
  
 GEN1088R008 
 missense_variant 
 c.4446T>A 
 p.Phe1482Leu 
 Unknown 
  
  
 GEN1088R009 
 missense_variant 
 c.5144A>G 
 p.Lys1715Arg 
 Unknown 
  
  
 GEN1088R010 
 missense_variant 
 c.5674T>C 
 p.Phe1892Leu 
 Unknown 
  
  
 GEN1088R011 
 missense_variant 
 c.5875G>A 
 p.Val1959Met 
 Unknown 
  
  
 GEN1088R012 
 missense_variant 
 c.6214C>T 
 p.Arg2072Trp 
 Unknown 
  
  
 GEN1088R013 
 missense_variant 
 c.6394G>A 
 p.Val2132Met 
 Unknown 
  
  
 GEN1088R014 
 missense_variant 
 c.6498C>G 
 p.Cys2166Trp 
 Unknown 
  
  
 GEN1088R015 
 missense_variant 
 c.6923C>T 
 p.Thr2308Met 
 Unknown 
  
  
 GEN1088R016 
 missense_variant 
 c.7542C>G 
 p.Asp2514Glu 
 Unknown 
  
  
 GEN1088R017 
 missense_variant 
 c.8104G>A 
 p.Ala2702Thr 
 Unknown 
  
  
 GEN1088R018 
 missense_variant 
 c.8936C>T 
 p.Thr2979Met 
 Unknown 
  
  
 GEN1088R019 
 missense_variant 
 c.9136G>A 
 p.Gly3046Arg 
 Unknown 
  
  
 GEN1088R020 
 missense_variant 
 c.9395A>G 
 p.Asn3132Ser 
 Unknown 
  
  
 GEN1088R021 
 missense_variant 
 c.9434G>A 
 p.Arg3145His 
 Unknown 
  
  
 GEN1088R022 
 missense_variant 
 c.10274G>A 
 p.Arg3425His 
 Unknown 
  
  
 GEN1088R023 
 missense_variant 
 c.11432C>G 
 p.Ser3811Trp 
 Unknown 
  
  
 GEN1088R024 
 missense_variant 
 c.11954C>T 
 p.Ala3985Val 
 Unknown 
  
  
 GEN1088R025 
 missense_variant 
 c.408C>G 
 p.Asn136Lys 
 De novo 
  
  
 GEN1088R026 
 stop_gained 
 c.13339C>T 
 p.Arg4447Ter 
 Familial 
  
 Simplex 
 GEN1088R027 
 stop_gained 
 c.9379G>T 
 p.Glu3127Ter 
 Familial 
  
 Simplex 
 GEN1088R028 
 stop_gained 
 c.5008C>T 
 p.Arg1670Ter 
 Familial 
  
 Simplex 
 GEN1088R029 
 missense_variant 
 c.10424G>A 
 p.Arg3475Gln 
 Unknown 
  
  
 GEN1088R030 
 missense_variant 
 c.8719T>A 
 p.Ser2907Thr 
 De novo 
  
 Simplex 
 GEN1088R031 
 synonymous_variant 
 c.9144C>T 
 p.Asn3048%3D 
 De novo 
  
 Simplex 
 GEN1088R032 
 splice_site_variant 
 c.4362-1G>A 
  
 De novo 
  
  
 GEN1088R033 
 missense_variant 
 c.4390G>A 
 p.Asp1464Asn 
 De novo 
  
  
 GEN1088R034 
 synonymous_variant 
 c.7785T>A 
 p.Ser2595%3D 
 De novo 
  
  
 GEN1088R035 
 missense_variant 
 c.8104G>A 
 p.Ala2702Thr 
 De novo 
  
  
 GEN1088R036 
 missense_variant 
 c.8914C>T 
 p.Arg2972Trp 
 De novo 
  
  
 GEN1088R037 
 missense_variant 
 c.10847A>G 
 p.Asp3616Gly 
 De novo 
  
  
 GEN1088R038 
 missense_variant 
 c.11819G>A 
 p.Arg3940His 
 De novo 
  
  
 GEN1088R039 
 missense_variant 
 c.12051G>C 
 p.Trp4017Cys 
 De novo 
  
  
 GEN1088R040 
 synonymous_variant 
 c.180C>T 
 p.Ala60%3D 
 De novo 
  
 Simplex 
 GEN1088R041 
 synonymous_variant 
 c.1083C>T 
 p.Leu361%3D 
 De novo 
  
 Simplex 
 GEN1088R042 
 missense_variant 
 c.10023C>G 
 p.Cys3341Trp 
 De novo 
  
 Simplex 
 GEN1088R043 
 missense_variant 
 c.3998C>T 
 p.Thr1333Ile 
 De novo 
  
  
 GEN1088R044 
 frameshift_variant 
 c.7344_7354del 
 p.His2448GlnfsTer27 
 De novo 
  
 Multiplex 
 GEN1088R045 
 frameshift_variant 
 c.11935_11936del 
 p.Asp3980CysfsTer3 
 Familial 
 Maternal 
 Multiplex 

Common

No Common Variants Available
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
12
Duplication
 1
 
12
Duplication
 2
 
12
Deletion-Duplication
 9
 
12
Deletion
 4
 
12
Deletion
 2
 
12
Deletion
 1
 

No Animal Model Data Available

 

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