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UniProtKB/Swiss-Prot P09619: Variant p.Leu658Pro

Platelet-derived growth factor receptor beta
Chromosomal location: 5q31-q32
Variant information

Variant position:  658
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  Disease [Disclaimer]
The variants are classified into three categories: Disease, Polymorphism and Unclassified.
  • Disease: Variants implicated in disease according to literature reports.
  • Polymorphism: Variants not reported to be implicated in disease.
  • Unclassified: Variants with uncertain implication in disease according to literature reports. Evidence against or in favor of a pathogenic role is limited and/or conflicting.

Residue change:  From Leucine (L) to Proline (P) at position 658 (L658P, p.Leu658Pro).
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:  Similar physico-chemical property. Both residues are medium size and hydrophobic.
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  -3
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

Involvement in disease:  Basal ganglia calcification, idiopathic, 4 (IBGC4) [MIM:615007]: A form of basal ganglia calcification, an autosomal dominant condition characterized by symmetric calcification in the basal ganglia and other brain regions. Affected individuals can either be asymptomatic or show a wide spectrum of neuropsychiatric symptoms, including parkinsonism, dystonia, tremor, ataxia, dementia, psychosis, seizures, and chronic headache. Serum levels of calcium, phosphate, alkaline phosphatase and parathyroid hormone are normal. The neuropathological hallmark of the disease is vascular and pericapillary calcification, mainly of calcium phosphate, in the affected brain areas. {ECO:0000269|PubMed:23255827, ECO:0000269|PubMed:24065723, ECO:0000269|PubMed:26599395}. Note=The disease is caused by mutations affecting the gene represented in this entry.
The name and a short description of the disease associated with the variant. For more information about the disease, the user can refer to OMIM, following the link provided after the disease acronym.

Variant description:  In IBGC4; no effect on protein abundance; loss of PDGF beta receptor activity.
Any additional useful information about the variant.

Other resources:  
Links to websites of interest for the variant.

Sequence information

Variant position:  658
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  1106
The length of the canonical sequence.

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: 
The multiple alignment of the region surrounding the variant against various orthologous sequences.





Sequence annotation in neighborhood:  
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.

Chain 33 – 1106 Platelet-derived growth factor receptor beta
Topological domain 554 – 1106 Cytoplasmic
Domain 600 – 962 Protein kinase
Alternative sequence 337 – 1106 Missing. In isoform 2.

Literature citations

Functional characterization of germline mutations in PDGFB and PDGFRB in primary familial brain calcification.
Vanlandewijck M.; Lebouvier T.; Andaloussi Maee M.; Nahar K.; Hornemann S.; Kenkel D.; Cunha S.I.; Lennartsson J.; Boss A.; Heldin C.H.; Keller A.; Betsholtz C.;
PLoS ONE 10:E0143407-E0143407(2015)

Phenotypic spectrum of probable and genetically-confirmed idiopathic basal ganglia calcification.
Nicolas G.; Pottier C.; Charbonnier C.; Guyant-Marechal L.; Le Ber I.; Pariente J.; Labauge P.; Ayrignac X.; Defebvre L.; Maltete D.; Martinaud O.; Lefaucheur R.; Guillin O.; Wallon D.; Chaumette B.; Rondepierre P.; Derache N.; Fromager G.; Schaeffer S.; Krystkowiak P.; Verny C.; Jurici S.; Sauvee M.; Verin M.; Lebouvier T.; Rouaud O.; Thauvin-Robinet C.; Rousseau S.; Rovelet-Lecrux A.; Frebourg T.; Campion D.; Hannequin D.;
Brain 136:3395-3407(2013)
Cited for: VARIANTS IBGC4 PRO-658; TRP-987 AND VAL-1071;

Mutation of the PDGFRB gene as a cause of idiopathic basal ganglia calcification.
Nicolas G.; Pottier C.; Maltete D.; Coutant S.; Rovelet-Lecrux A.; Legallic S.; Rousseau S.; Vaschalde Y.; Guyant-Marechal L.; Augustin J.; Martinaud O.; Defebvre L.; Krystkowiak P.; Pariente J.; Clanet M.; Labauge P.; Ayrignac X.; Lefaucheur R.; Le Ber I.; Frebourg T.; Hannequin D.; Campion D.;
Neurology 80:181-187(2013)
Cited for: VARIANTS IBGC4 PRO-658 AND TRP-987;

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.