UniProtKB/SwissProt variant VAR

Variant information

Variant position:

571

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 Leucine (L) to Isoleucine (I) at position 571 (L571I, p.Leu571Ile).

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:

Similar physico-chemical property. Both residues are medium size and hydrophobic.

The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:

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:

Normal DNA mismatch repair activity.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs63750055 [ dbSNP | Ensembl ]

Sequence information

Variant position:

571

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:

CHSNQEDTGCKFRVLPQPTN L ATPNTKRFKKEEILSSSDIC

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                         CHSNQEDTGCKFRVLPQPTNLATPNTKRFKKEEILSSSDIC

Mouse                         QSLKPEDHGYQCKALPL-ARLSPTNAKRFKTEERPSNVNIS

Chicken                       HKLNRVNDCNNQTNLPQEATNSLPRVRRFKNEADDFKAGIH

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
Modified residue	573 – 573	Phosphothreonine
Alternative sequence	184 – 862	Missing. In isoform 4.
Alternative sequence	269 – 669	Missing. In isoform 2.
Alternative sequence	560 – 572	CKFRVLPQPTNLA -> LKTGPSDPRTSMN. In isoform 3.

Literature citations

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;

Comprehensive mutation analysis of PMS2 in a large cohort of probands suspected of lynch syndrome or constitutional mismatch repair deficiency syndrome.
van der Klift H.M.; Mensenkamp A.R.; Drost M.; Bik E.C.; Vos Y.J.; Gille H.J.; Redeker B.E.; Tiersma Y.; Zonneveld J.B.; Garcia E.G.; Letteboer T.G.; Olderode-Berends M.J.; van Hest L.P.; van Os T.A.; Verhoef S.; Wagner A.; van Asperen C.J.; Ten Broeke S.W.; Hes F.J.; de Wind N.; Nielsen M.; Devilee P.; Ligtenberg M.J.; Wijnen J.T.; Tops C.M.;
Hum. Mutat. 37:1162-1179(2016)
Cited for: VARIANTS MMRCS ILE-46; THR-66; TRP-107; GLY-115; PRO-205; VAL-263; LYS-307; SER-437; GLN-479; VAL-488; GLN-504; ILE-585 AND LEU-815; CHARACTERIZATION OF VARIANTS MMRCS ILE-46; THR-66; TRP-107; GLY-115; LYS-307; SER-437; VAL-488; GLN-504 AND LEU-815; VARIANTS VAL-18; GLU-60; SER-470; LEU-563; ILE-571 AND SER-775; CHARACTERIZATION OF VARIANTS SER-470 AND SER-775;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P54278: Variant p.Leu571Ile