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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P50479: Variant p.Gly259Cys

PDZ and LIM domain protein 4
Gene: PDLIM4
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Variant information Variant position: help 259 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 Glycine (G) to Cysteine (C) at position 259 (G259C, p.Gly259Cys). 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 glycine (G) to medium size and polar (C) 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

Polymorphism: help Genetic variations in PDLIM4 may be correlated with bone mineral density (BMD). Low BMD is a risk factor for osteoporotic fracture. Osteoporosis is characterized by reduced bone mineral density, disruption of bone microarchitecture, and the alteration of the amount and variety of non-collagenous proteins in bone. Osteoporotic bones are more at risk of fracture. Additional information on the polymorphism described.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 259 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 330 The length of the canonical sequence.
Location on the sequence: help ASKLGAPLSGLQGLPECTRC G HGIVGTIVKARDKLYHPECF 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                         ASKLGAPLSGLQGLPECTRCGHGIVGTIVKARDKLYHPECF

Mouse                         ASKLGAPLSGLQGLPECTRCGHGIVGTIVKARDKLYHPECF

Rat                           ASKLGAPLSGLQGLPECTRCGHGIVGTIVKARDKLYHPECF

Bovine                        ASKLGAPLSGLQGLPECTRCGHGIVGTIVKARDKLYHPECF

Chicken                       GPKLGAAMSGLQMLPECTRCGNGIVGTIVKARDKLYHPECF

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 1 – 330 PDZ and LIM domain protein 4
Domain 253 – 312 LIM zinc-binding
Alternative sequence 225 – 330 DWPGPGGPRNLKPTASKLGAPLSGLQGLPECTRCGHGIVGTIVKARDKLYHPECFMCSDCGLNLKQRGYFFLDERLYCESHAKARVKPPEGYDVVAVYPNAKVELV -> APSSRHGTSSTIPSASCAVTAA. In isoform 2.



Literature citations
Submission
Scharm B.; Schaefer R.;
Cited for: NUCLEOTIDE SEQUENCE (ISOFORM 1); VARIANTS CYS-142 AND CYS-259;
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.