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UniProtKB/Swiss-Prot P01127: Variant p.Leu9Arg

Platelet-derived growth factor subunit B
Gene: PDGFB
Chromosomal location: 22q13.1
Variant information

Variant position:  9
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 Arginine (R) at position 9 (L9R, p.Leu9Arg).
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:  Change from medium size and hydrophobic (L) to large size and basic (R)
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  -2
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, 5 (IBGC5) [MIM:615483]: 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:23913003, 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 IBGC5; loss of protein expression.
Any additional useful information about the variant.



Sequence information

Variant position:  9
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  241
The length of the canonical sequence.

Location on the sequence:   MNRCWALF  L SLCCYLRLVSAEGDPIPEEL
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.

Human                         MNRCWALFLSLCCYLRLVSAEGDPIPEEL

                              MNRCWALFLSLCCYLRLVSAEGDPIPEEL

Mouse                         MNRCWALFLPLCCYLRLVSAEGDPIPEEL

Sheep                         MNRCWALFLSLCCYLRLVSAEGDPIPEEL

Cat                           MNRCWALFLSLCCYLRLVSAEGDPIPEEL

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.

TypePositionsDescription
Signal peptide 1 – 20
Alternative sequence 1 – 21 MNRCWALFLSLCCYLRLVSAE -> MFIMGL. 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)
Cited for: CHARACTERIZATION OF VARIANTS IBGC5 ARG-9 AND PRO-119; FUNCTION;

Mutations in the gene encoding PDGF-B cause brain calcifications in humans and mice.
Keller A.; Westenberger A.; Sobrido M.J.; Garcia-Murias M.; Domingo A.; Sears R.L.; Lemos R.R.; Ordonez-Ugalde A.; Nicolas G.; da Cunha J.E.; Rushing E.J.; Hugelshofer M.; Wurnig M.C.; Kaech A.; Reimann R.; Lohmann K.; Dobricic V.; Carracedo A.; Petrovic I.; Miyasaki J.M.; Abakumova I.; Mae M.A.; Raschperger E.; Zatz M.; Zschiedrich K.; Klepper J.; Spiteri E.; Prieto J.M.; Navas I.; Preuss M.; Dering C.; Jankovic M.; Paucar M.; Svenningsson P.; Saliminejad K.; Khorshid H.R.; Novakovic I.; Aguzzi A.; Boss A.; Le Ber I.; Defer G.; Hannequin D.; Kostic V.S.; Campion D.; Geschwind D.H.; Coppola G.; Betsholtz C.; Klein C.; Oliveira J.R.;
Nat. Genet. 45:1077-1082(2013)
Cited for: VARIANTS IBGC5 ARG-9 AND PRO-119;

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.