UniProtKB/SwissProt variant VAR

Variant information

Variant position:

498

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

Type of variant:

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:

From Arginine (R) to Leucine (L) at position 498 (R498L, p.Arg498Leu).

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 hydrophobic (L)

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:

In LPRD1.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs397507542 [ dbSNP | Ensembl ]

Sequence information

Variant position:

498

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

Protein sequence length:

593

The length of the canonical sequence.

Location on the sequence:

IIREKGVDCDIDVPKTIQMV R SQRSGMVQTEAQYRFIYMAV

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                         IIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAV

Mouse                         IIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAV

Rat                           IIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAV

Chicken                       IIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAV

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	2 – 593	Tyrosine-protein phosphatase non-receptor type 11
Domain	247 – 517	Tyrosine-protein phosphatase
Binding site	506 – 506
Alternative sequence	461 – 593	Missing. In isoform 3.
Helix	490 – 498

Literature citations

Clinical and molecular analysis of 30 patients with multiple lentigines LEOPARD syndrome.
Sarkozy A.; Conti E.; Digilio M.C.; Marino B.; Morini E.; Pacileo G.; Wilson M.; Calabro R.; Pizzuti A.; Dallapiccola B.;
J. Med. Genet. 41:E68-E68(2004)
Cited for: VARIANTS LPRD1 CYS-279; SER-279; ALA-464; MET-468; TRP-498; LEU-498 AND PRO-506;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q06124: Variant p.Arg498Leu