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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q9BXM7: Variant p.Pro399Leu

Serine/threonine-protein kinase PINK1, mitochondrial
Gene: PINK1
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Variant information Variant position: help 399 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant: help LP/P [Disclaimer] 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 Proline (P) to Leucine (L) at position 399 (P399L, p.Pro399Leu). 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 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: help -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
Variant description: help Found in early-onset Parkinson disease with digenic inheritance; likely pathogenic; the patient also has mutation S-39 in PARK7; decreases PRKN and SNCAIP ubiquitination and degradation. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 399 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 581 The length of the canonical sequence.
Location on the sequence: help WLVIADFGCCLADESIGLQL P FSSWYVDRGGNGCLMAPEVS 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                         WLVIADFGCCLADESIGLQLPFSSWYVDRGGNGCLMAPEVS

Mouse                         WLVISDFGCCLADQHVGLRLPFNSSSVERGGNGSLMAPEVS

Rat                           WLVISDFGCCLADERVGLQLPFNSSSVERGGNGSLMAPEVS

Caenorhabditis elegans        QLVVADFGCALA--CDNWQVDYESDEVSLGGNAKTKAPEIA

Drosophila                    VLVLSDFGCCLADKVHGLRLPYVSHDVDKGGNAALMAPEIF
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 78 – 581 Serine/threonine-protein kinase PINK1, mitochondrial
Topological domain 111 – 581 Cytoplasmic
Domain 156 – 511 Protein kinase
Modified residue 402 – 402 Phosphoserine; by autocatalysis
Mutagenesis 384 – 384 D -> A. Abolishes MFN2 phosphorylation and interaction with PRKN; when associated with A-219 and A-362. Loss of enzyme activity and impaired localization of PRKN to mitochondria; when associated with M-219 and A-362.
Mutagenesis 384 – 384 D -> N. Loss of activity. Abolishes Drp1 phosphorylation. No effect on localization to mitochondria.



Literature citations
Parkin, PINK1, and DJ-1 form a ubiquitin E3 ligase complex promoting unfolded protein degradation.
Xiong H.; Wang D.; Chen L.; Choo Y.S.; Ma H.; Tang C.; Xia K.; Jiang W.; Ronai Z.; Zhuang X.; Zhang Z.;
J. Clin. Invest. 119:650-660(2009)
Cited for: FUNCTION; COMPONENT OF A COMPLEX COMPOSED OF PRKN; PARK7 AND PINK1; SUBCELLULAR LOCATION; PROTEOLYTIC CLEAVAGE; CHARACTERIZATION OF VARIANTS PARK6 ASP-309 AND MET-313; CHARACTERIZATION OF VARIANT LEU-399; Association of PINK1 and DJ-1 confers digenic inheritance of early-onset Parkinson's disease.
Tang B.; Xiong H.; Sun P.; Zhang Y.; Wang D.; Hu Z.; Zhu Z.; Ma H.; Pan Q.; Xia J.-H.; Xia K.; Zhang Z.;
Hum. Mol. Genet. 15:1816-1825(2006)
Cited for: VARIANT LEU-399;
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.