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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P43246: Variant p.Cys697Phe

DNA mismatch repair protein Msh2
Gene: MSH2
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Variant information Variant position: help 697 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 Cysteine (C) to Phenylalanine (F) at position 697 (C697F, p.Cys697Phe). 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 polar (C) to large size and aromatic (F) 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 LYNCH1; decreased mismatch repair activity; loss of protein expression; confers multiple biochemical defects. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 697 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 934 The length of the canonical sequence.
Location on the sequence: help TYIRQTGVIVLMAQIGCFVP C ESAEVSIVDCILARVGAGDS 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                         TYIRQTGVIVLMAQIGCFVPCESAEVSIVDCILARVGAGDS

Mouse                         TYIRQTGVIVLMAQIGCFVPCESAEVSIVDCILARVGAGDS

Rat                           TYIRQTGVIVLMAQIGCFVPCESAEVSIVDCILARVGAGDS

Bovine                        TYIRQTGVVVLMAQIGCFVPCEWAEVSIVDCILARVGAGDS

Drosophila                    TYIRSVGTAVLMAHIGAFVPCSLATISMVDSILGRVGASDN

Slime mold                    TFIRQVGLIVLMAQIGCFVPAQKATIAVVDCILSRVGAGDS

Baker's yeast                 TYIRQVGVISLMAQIGCFVPCEEAEIAIVDAILCRVGAGDS

Fission yeast                 TYIRQVGVITVMAQIGCPVPCEVADLDIIDAILARVGASDS

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 – 934 DNA mismatch repair protein Msh2
Beta strand 695 – 703



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 LYNCH1 PRO-33; MET-44; VAL-45; SER-127; MET-145; ASP-161; ARG-162; ARG-164; PRO-173; ARG-187; PRO-187; VAL-272; TYR-333; LEU-519; ASN-603; PRO-636; ALA-674; VAL-688; PHE-697; 745-ILE-ILE-746 DEL; LYS-749; THR-834; GLY-886 AND GLU-923; CHARACTERIZATION OF VARIANTS ASP-322 AND ILE-722; FUNCTION; Hereditary nonpolyposis colorectal cancer (HNPCC): eight novel germline mutations in hMSH2 or hMLH1 genes.
Wehner M.; Buschhausen L.; Lamberti C.; Kruse R.; Caspari R.; Propping P.; Friedl W.;
Hum. Mutat. 10:241-244(1997)
Cited for: VARIANT LYNCH1 PHE-697; VARIANT ASP-322; Mutator phenotypes of common polymorphisms and missense mutations in MSH2.
Drotschmann K.; Clark A.B.; Kunkel T.A.;
Curr. Biol. 9:907-910(1999)
Cited for: CHARACTERIZATION OF VARIANTS ASP-322; PHE-390; LYS-419; TYR-506; PRO-524; LEU-622 AND PHE-697; Pathogenicity of MSH2 missense mutations is typically associated with impaired repair capability of the mutated protein.
Ollila S.; Sarantaus L.; Kariola R.; Chan P.; Hampel H.; Holinski-Feder E.; Macrae F.; Kohonen-Corish M.; Gerdes A.-M.; Peltomaeki P.; Mangold E.; de la Chapelle A.; Greenblatt M.; Nystroem M.;
Gastroenterology 131:1408-1417(2006)
Cited for: VARIANTS LYNCH1 PRO-33; ASP-161; ARG-162; ARG-164; PRO-173; PRO-187; TYR-333; ASN-603; PRO-636; PHE-697; 745-ILE-ILE-746 DEL AND LYS-749; VARIANTS VAL-272; THR-834 AND GLU-923; CHARACTERIZATION OF VARIANTS LYNCH1 PRO-33; ASP-161; ARG-162; ARG-164; PRO-173; PRO-187; TYR-333; ASN-603; PRO-636; PHE-697; 745-ILE-ILE-746 DEL AND LYS-749; CHARACTERIZATION OF VARIANTS VAL-272; THR-834 AND GLU-923; Mechanisms of pathogenicity in human MSH2 missense mutants.
Ollila S.; Dermadi Bebek D.; Jiricny J.; Nystroem M.;
Hum. Mutat. 29:1355-1363(2008)
Cited for: CHARACTERIZATION OF VARIANTS LYNCH1 PRO-33; SER-127; ASP-161; ARG-162; ARG-164; PRO-173; PRO-187; VAL-272; TYR-333; ASN-603; PRO-636; ALA-674; PHE-697; 745-ILE-ILE-746 DEL; LYS-749; THR-834 AND GLU-923; CHARACTERIZATION OF VARIANT ASP-322; Functional analysis of HNPCC-related missense mutations in MSH2.
Lutzen A.; de Wind N.; Georgijevic D.; Nielsen F.C.; Rasmussen L.J.;
Mutat. Res. 645:44-55(2008)
Cited for: CHARACTERIZATION OF VARIANTS LYNCH1 HIS-167; THR-305: LEU-622; ARG-639; ARG-674; PHE-697 AND THR-834; A rapid and cell-free assay to test the activity of lynch syndrome-associated MSH2 and MSH6 missense variants.
Drost M.; Zonneveld J.B.; van Hees S.; Rasmussen L.J.; Hofstra R.M.; de Wind N.;
Hum. Mutat. 33:488-494(2012)
Cited for: CHARACTERIZATION OF VARIANTS LYNCH1 MET-44; VAL-45; HIS-167; THR-305; PHE-390; ASN-596 DEL; ARG-639; ARG-674; PHE-697; PHE-723 AND GLY-886; CHARACTERIZATION OF VARIANTS ASP-165; HIS-177; VAL-272; LEU-385; LEU-519; ALA-675; GLU-759; VAL-805; GLY-843 AND LEU-860;
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.