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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P43246: Variant p.Gly162Arg

DNA mismatch repair protein Msh2
Gene: MSH2
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Variant information Variant position: help 162 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 Glycine (G) to Arginine (R) at position 162 (G162R, p.Gly162Arg). 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 large size and basic (R) 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; associated with an abnormal subcellular localization pattern; affects protein stability; loss of protein expression. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 162 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 SASIGVVGVKMSAVDGQRQV G VGYVDSIQRKLGLCEFPDND 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                         SASIGVVGVKMSAV-DGQRQVGVGYVDSIQRKLGLCEFPDND

Mouse                         SASVGVMGIKMAVV-DGQRHVGVGYVDSTQRKLGLCEFPEN

Rat                           ATSIGIMGIKLSTV-DGQRQVGVGDVDSTQRKLGLCEFPDN

Bovine                        SASIGVVGVKMSTV-DGQRQVGVGYVDSTQRKLGLCEFPDN

Drosophila                    LVGNSIISLLVKLDGGGQRRVGVASVEQNDCKFQLLEFLDD

Slime mold                    EGSV-MMALKVTRE-KGSIVFGISFGDATFKTIGVSQFMDN

Baker's yeast                 SIIIASLKVQWNSQ-DGNCIIGVAFIDTTAYKVGMLDIVDN

Fission yeast                 SVSSVLLAVTTRVK-QDQRIIGVAFIDPILKKLGVSEFVDS

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 160 – 167



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; Gene symbol: MSH2. Disease: hereditary nonpolyposis colorectal cancer.
Kohonen-Corish M.R.J.; Otway R.; Tetlow N.; Hornby J.; Doe W.F.;
Hum. Genet. 116:539-539(2005)
Cited for: VARIANT LYNCH1 ARG-162; 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; MSH2 missense mutations and HNPCC syndrome: pathogenicity assessment in a human expression system.
Belvederesi L.; Bianchi F.; Galizia E.; Loretelli C.; Bracci R.; Catalani R.; Amati M.; Cellerino R.;
Hum. Mutat. 29:E296-E309(2008)
Cited for: CHARACTERIZATION OF VARIANTS LYNCH1 ARG-162; HIS-167 AND SER-359;
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.