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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P52701: Variant p.Leu1354Gln

DNA mismatch repair protein Msh6
Gene: MSH6
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Variant information Variant position: help 1354 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant: help US 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 Leucine (L) to Glutamine (Q) at position 1354 (L1354Q, p.Leu1354Gln). 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 medium size and hydrophobic (L) to medium size and polar (Q) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score: help -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

Variant description: help In CRC and LYNCH5; uncertain significance; normal mismatch repair activity. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 1354 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 1360 The length of the canonical sequence.
Location on the sequence: help REVCLASERSTVDAEAVHKL L TLIKEL 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                         REVCLASER-----------------------------STVDAEAVHKLLTLIKEL-----

Mouse                         REVCLATEK------------------

Chicken                       RFLCRVVDG------------------

Drosophila                    AKIVAATAG------------------

Slime mold                    HGTISRSKLV-----------------

Baker's yeast                 GEVVSVPGGLQSDFVRIAYGDGLKNTK

Fission yeast                 SDDIALMSDF-----------------

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 – 1360 DNA mismatch repair protein Msh6
Alternative sequence 1069 – 1360 Missing. In isoform GTBP-alt.
Helix 1347 – 1359



Literature citations
Verification of the three-step model in assessing the pathogenicity of mismatch repair gene variants.
Kansikas M.; Kariola R.; Nystroem M.;
Hum. Mutat. 32:107-115(2011)
Cited for: CHARACTERIZATION OF VARIANTS LYNCH5 LEU-128; ILE-144; ARG-566; LEU-623; THR-728; GLY-881 DELINS LYS-SER; THR-1087; HIS-1095; LYS-1193 AND GLN-1354; CHARACTERIZATION OF VARIANT ARG-1087; FUNCTION; Two mismatch repair gene mutations found in a colon cancer patient - which one is pathogenic?
Kariola R.; Otway R.; Loennqvist K.E.; Raevaara T.E.; Macrae F.; Vos Y.J.; Kohonen-Corish M.; Hofstra R.M.W.; Nystroem-Lahti M.;
Hum. Genet. 112:105-109(2003)
Cited for: VARIANTS CRC HIS-1095 AND GLN-1354; Mismatch repair analysis of inherited MSH2 and/or MSH6 variation pairs found in cancer patients.
Kantelinen J.; Kansikas M.; Candelin S.; Hampel H.; Smith B.; Holm L.; Kariola R.; Nystrom M.;
Hum. Mutat. 33:1294-1301(2012)
Cited for: CHARACTERIZATION OF VARIANTS PRO-435; PRO-585; THR-677; ALA-878; HIS-1095 AND GLN-1354;
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.