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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q02880: Variant p.Ala490Pro

DNA topoisomerase 2-beta
Gene: TOP2B
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Variant information Variant position: help 490 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 Alanine (A) to Proline (P) at position 490 (A490P, p.Ala490Pro). 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 small size and hydrophobic (A) to medium size and hydrophobic (P) 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
Variant description: help In BILU; decreased protein abundance; severely decreased DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 490 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 1626 The length of the canonical sequence.
Location on the sequence: help GKHSLECTLILTEGDSAKSL A VSGLGVIGRDRYGVFPLRGK 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                         GKHSLECTLILTEGDSAKSLAVSGLGVIGRDRYGVFPLRGK

Mouse                         GKHSLECTLILTEGDSAKSLAVSGLGVIGRDRYGVFPLRGK

Chicken                       GKHSLDCTLILTEGDSAKSLAVSGLGVIGRDRYGVFPLRGK
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 2 – 1626 DNA topoisomerase 2-beta
Domain 476 – 593 Toprim
Binding site 482 – 482
Site 510 – 510 Interaction with DNA
Mutagenesis 482 – 482 E -> Q. Strongly reduced enzyme activity.
Mutagenesis 485 – 485 S -> A. Slightly reduced enzyme activity.
Mutagenesis 508 – 508 R -> E. Slightly reduced enzyme activity.
Mutagenesis 510 – 510 K -> E. Strongly reduced enzyme activity.
Helix 483 – 491



Literature citations
Topoisomerase 2beta mutation impairs early B-cell development.
Papapietro O.; Chandra A.; Eletto D.; Inglott S.; Plagnol V.; Curtis J.; Maes M.; Alisaac A.; Albuquerque A.S.; Basseres E.; Hermine O.; Picard C.; Fischer A.; Durandy A.; Kracker S.; Burns S.O.; Cuchet-Lourenco D.; Okkenhaug K.; Nejentsev S.;
Blood 135:1497-1501(2020)
Cited for: VARIANT BILU PRO-490; CHARACTERIZATION OF VARIANT BILU PRO-490; FUNCTION;
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.