UniProtKB/SwissProt variant VAR

Variant information

Variant position:

20

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 Arginine (R) to Glutamine (Q) at position 20 (R20Q, p.Arg20Gln).

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 (R) to medium size and polar (Q)

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:

No effect on protein abundance; no effect on subcellular localization; normal DNA mismatch repair activity.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs10254120 [ dbSNP | Ensembl ]

Sequence information

Variant position:

20

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:

MERAESSSTEPAKAIKPID R KSVHQICSGQVVLSLSTAVK

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                         MERAESSSTEPAKAIKPIDRKSVHQICSGQVVLSLSTAVK

Mouse                         MEQTEGVSTECAKAIKPIDGKSVHQICSGQVILSLSTAVK

Chicken                       MEEAAPCS-EPAKTIKRIDRESVHRICSGQVVLSLGTAVK

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.

Type	Positions	Description
Chain	1 – 862	Mismatch repair endonuclease PMS2

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;

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;

Refining the role of PMS2 in Lynch syndrome: germline mutational analysis improved by comprehensive assessment of variants.
Borras E.; Pineda M.; Cadinanos J.; Del Valle J.; Brieger A.; Hinrichsen I.; Cabanillas R.; Navarro M.; Brunet J.; Sanjuan X.; Musulen E.; van der Klift H.; Lazaro C.; Plotz G.; Blanco I.; Capella G.;
J. Med. Genet. 50:552-563(2013)
Cited for: VARIANT HNPCC4 ILE-46; VARIANTS GLN-20; SER-470; SER-597 AND SER-775; CHARACTERIZATION OF VARIANT HNPCC4 ILE-46; CHARACTERIZATION OF VARIANTS GLN-20 AND SER-470; MUTAGENESIS OF ASP-70; FUNCTION; SUBCELLULAR LOCATION;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P54278: Variant p.Arg20Gln