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UniProtKB/Swiss-Prot P54278: Variant p.Lys541Glu

Mismatch repair endonuclease PMS2
Gene: PMS2
Variant information

Variant position:  541
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  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:  From Lysine (K) to Glutamate (E) at position 541 (K541E, p.Lys541Glu).
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:  Change from large size and basic (K) to medium size and acidic (E)
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  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:  Normal DNA mismatch repair activity.
Any additional useful information about the variant.

Other resources:  
Links to websites of interest for the variant.



Sequence information

Variant position:  541
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  862
The length of the canonical sequence.

Location on the sequence:   ASSPGDRGSQEHVDSQEKAP  K TDDSFSDVDCHSNQEDTGCK
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: 
The multiple alignment of the region surrounding the variant against various orthologous sequences.

Human                         ASSPGDRGSQEHVDS---QEKAPKTDDSFSDVDCHSNQEDTGCK

Mouse                         VSSLEDRPSQETINC-------GDLDCRPPGTGQSLKPEDH

Chicken                       FCSSEEQHQNEYLKTVGHSEKSLECDIQVLGTEHKLNRVND

Sequence annotation in neighborhood:  
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 – 862 Mismatch repair endonuclease PMS2
Alternative sequence 184 – 862 Missing. In isoform 4.
Alternative sequence 269 – 669 Missing. In isoform 2.


Literature citations

Mutations of two PMS homologues in hereditary nonpolyposis colon cancer.
Nicolaides N.C.; Papadopoulos N.; Liu B.; Wei Y.-F.; Carter K.C.; Ruben S.M.; Rosen C.A.; Haseltine W.H.; Fleischmann R.D.; Fraser C.M.; Adams M.D.; Venter J.C.; Dunlop M.G.; Hamilton S.R.; Petersen G.M.; de la Chapelle A.; Vogelstein B.; Kinzler K.W.;
Nature 371:75-80(1994)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANTS GLN-20 AND GLU-541;

PMS2 mRNA, nirs splice variants.
Tabata Y.; Sameshima E.; Hayashi A.; Iida K.; Mitsuyama M.; Kanai S.; Furuya T.; Saito T.;
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1; 2; 3 AND 4); VARIANT GLU-541;

Submission
Bronner C.E.; Baker S.M.; Morrison P.T.; Warren G.; Smith L.G.; Lescoe M.K.; Kane M.F.; Earibino C.; Lipford J.; Lindblom A.; Tannergaard P.; Bollag R.J.; Godwin A.R.; Ward D.C.; Nordenskjoeld M.; Fishel R.; Kolodner R.D.; Liskay R.M.;
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1); VARIANTS SER-470 AND GLU-541;

Complete sequencing and characterization of 21,243 full-length human cDNAs.
Ota T.; Suzuki Y.; Nishikawa T.; Otsuki T.; Sugiyama T.; Irie R.; Wakamatsu A.; Hayashi K.; Sato H.; Nagai K.; Kimura K.; Makita H.; Sekine M.; Obayashi M.; Nishi T.; Shibahara T.; Tanaka T.; Ishii S.; Yamamoto J.; Saito K.; Kawai Y.; Isono Y.; Nakamura Y.; Nagahari K.; Murakami K.; Yasuda T.; Iwayanagi T.; Wagatsuma M.; Shiratori A.; Sudo H.; Hosoiri T.; Kaku Y.; Kodaira H.; Kondo H.; Sugawara M.; Takahashi M.; Kanda K.; Yokoi T.; Furuya T.; Kikkawa E.; Omura Y.; Abe K.; Kamihara K.; Katsuta N.; Sato K.; Tanikawa M.; Yamazaki M.; Ninomiya K.; Ishibashi T.; Yamashita H.; Murakawa K.; Fujimori K.; Tanai H.; Kimata M.; Watanabe M.; Hiraoka S.; Chiba Y.; Ishida S.; Ono Y.; Takiguchi S.; Watanabe S.; Yosida M.; Hotuta T.; Kusano J.; Kanehori K.; Takahashi-Fujii A.; Hara H.; Tanase T.-O.; Nomura Y.; Togiya S.; Komai F.; Hara R.; Takeuchi K.; Arita M.; Imose N.; Musashino K.; Yuuki H.; Oshima A.; Sasaki N.; Aotsuka S.; Yoshikawa Y.; Matsunawa H.; Ichihara T.; Shiohata N.; Sano S.; Moriya S.; Momiyama H.; Satoh N.; Takami S.; Terashima Y.; Suzuki O.; Nakagawa S.; Senoh A.; Mizoguchi H.; Goto Y.; Shimizu F.; Wakebe H.; Hishigaki H.; Watanabe T.; Sugiyama A.; Takemoto M.; Kawakami B.; Yamazaki M.; Watanabe K.; Kumagai A.; Itakura S.; Fukuzumi Y.; Fujimori Y.; Komiyama M.; Tashiro H.; Tanigami A.; Fujiwara T.; Ono T.; Yamada K.; Fujii Y.; Ozaki K.; Hirao M.; Ohmori Y.; Kawabata A.; Hikiji T.; Kobatake N.; Inagaki H.; Ikema Y.; Okamoto S.; Okitani R.; Kawakami T.; Noguchi S.; Itoh T.; Shigeta K.; Senba T.; Matsumura K.; Nakajima Y.; Mizuno T.; Morinaga M.; Sasaki M.; Togashi T.; Oyama M.; Hata H.; Watanabe M.; Komatsu T.; Mizushima-Sugano J.; Satoh T.; Shirai Y.; Takahashi Y.; Nakagawa K.; Okumura K.; Nagase T.; Nomura N.; Kikuchi H.; Masuho Y.; Yamashita R.; Nakai K.; Yada T.; Nakamura Y.; Ohara O.; Isogai T.; Sugano S.;
Nat. Genet. 36:40-45(2004)
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1); VARIANTS SER-470 AND GLU-541;

The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).
The MGC Project Team;
Genome Res. 14:2121-2127(2004)
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1); VARIANTS GLU-541 AND ILE-622;

Heterozygous mutations in PMS2 cause hereditary nonpolyposis colorectal carcinoma (Lynch syndrome).
Hendriks Y.M.; Jagmohan-Changur S.; van der Klift H.M.; Morreau H.; van Puijenbroek M.; Tops C.; van Os T.; Wagner A.; Ausems M.G.; Gomez E.; Breuning M.H.; Broecker-Vriends A.H.; Vasen H.F.; Wijnen J.T.;
Gastroenterology 130:312-322(2006)
Cited for: VARIANTS HNPCC4 ILE-585 AND ILE-622; VARIANTS VAL-18; GLN-20; SER-470; LYS-485; GLU-541; SER-597 AND ALA-857;

Inactivation of DNA mismatch repair by variants of uncertain significance in the PMS2 gene.
Drost M.; Koppejan H.; de Wind N.;
Hum. Mutat. 34:1477-1480(2013)
Cited for: CHARACTERIZATION OF VARIANTS VAL-18; GLN-20; ALA-41; GLU-60; THR-423; LYS-485; ALA-511; MET-511; GLU-541; LEU-563; ILE-571; SER-597 AND ALA-857; CHARACTERIZATION OF VARIANTS HNPCC4 ASN-46; ILE-46; PRO-205; GLU-207; VAL-263; GLN-479; ILE-622; ALA-663; LYS-705; ASP-750; ARG-797 AND TYR-843; MUTAGENESIS OF GLU-41 AND TYR-519;

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.