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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot O75197: Variant p.Thr1540Met

Low-density lipoprotein receptor-related protein 5
Gene: LRP5
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Variant information Variant position: help 1540 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant: help LB/B The variants are classified into three categories: LP/P, LB/B and US.
  • LP/P: likely pathogenic or pathogenic.
  • LB/B: likely benign or benign.
  • US: uncertain significance

Residue change: help From Threonine (T) to Methionine (M) at position 1540 (T1540M, p.Thr1540Met). Indicates the amino acid change of the variant. The one-letter and three-letter codes for amino acids used in UniProtKB/Swiss-Prot are those adopted by the commission on Biochemical Nomenclature of the IUPAC-IUB.
Physico-chemical properties: help Change from medium size and polar (T) to medium size and hydrophobic (M) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score: help -1 The score within a Blosum matrix for the corresponding wild-type to variant amino acid change. The log-odds score measures the logarithm for the ratio of the likelihood of two amino acids appearing by chance. The Blosum62 substitution matrix is used. This substitution matrix contains scores for all possible exchanges of one amino acid with another:
  • Lowest score: -4 (low probability of substitution).
  • Highest score: 11 (high probability of substitution).
More information can be found on the following page

Polymorphism: help Genetic variations in LRP5 define the bone mineral density quantitative trait locus 1 (BMND1) [MIM:601884]. Variance in bone mineral density influences bone mass and contributes to size determination in the general population. Additional information on the polymorphism described.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 1540 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 1615 The length of the canonical sequence.
Location on the sequence: help NIPATARPYRPYIIRGMAPP T TPCSTDVCDSDYSASRWKAS The residue change on the sequence. Unless the variant is located at the beginning or at the end of the protein sequence, both residues upstream (20) and downstream (20) of the variant will be shown.
Residue conservation: help The multiple alignment of the region surrounding the variant against various orthologous sequences.
Human                         NIPATARPYRPYIIRGMAPPTTPCSTDVCDSDYSASRWKAS

Mouse                         GIPATARPYRPYVIRGMAPPTTPCSTDVCDSDYSTSRWKSS

Sequence annotation in neighborhood: help The regions or sites of interest surrounding the variant. In general the features listed are posttranslational modifications, binding sites, enzyme active sites, local secondary structure or other characteristics reported in the cited references. The "Sequence annotation in neighborhood" lines have a fixed format:
  • Type: the type of sequence feature.
  • Positions: endpoints of the sequence feature.
  • Description: contains additional information about the feature.
TypePositionsDescription
Chain 32 – 1615 Low-density lipoprotein receptor-related protein 5
Topological domain 1408 – 1615 Cytoplasmic
Motif 1538 – 1545 PPPSP motif B



Literature citations
Complexity of the genotype-phenotype correlation in familial exudative vitreoretinopathy with mutations in the LRP5 and/or FZD4 genes.
Qin M.; Hayashi H.; Oshima K.; Tahira T.; Hayashi K.; Kondo H.;
Hum. Mutat. 26:104-112(2005)
Cited for: VARIANTS EVR4 PHE-145; CYS-444; THR-522; MET-535; ARG-610; CYS-617; ALA-798 AND ASP-1121; VARIANTS VAL-97 AND MET-1540;
Disclaimer: Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. They are not in any way intended to be used as a substitute for professional medical advice, diagnostic, treatment or care.