UniProtKB/Swiss-Prot Q12923: Variant p.Ile2458Val

Tyrosine-protein phosphatase non-receptor type 13
Gene: PTPN13
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Variant information Variant position:

2458 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 Isoleucine (I) to Valine (V) at position 2458 (I2458V, p.Ile2458Val). 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:

3 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 substrate affinity. Any additional useful information about the variant.
Other resources:

Links to websites of interest for the variant.

Variant rs34226837 [ dbSNP | Ensembl ]

Sequence information Variant position:

2458 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length:

2485 The length of the canonical sequence.
Location on the sequence:

DLVRCMRLQRHGMVQTEDQY I FCYQVILYVLTRLQAEEEQK 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                         DLVRCMRLQRHGMVQTEDQYIFCYQVILYVLTRLQAEEEQK

Mouse                         DLVRCMRLQRHGMVQTEGQYVFCYQVILYVLTHLQAEEQKA

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 – 2485	Tyrosine-protein phosphatase non-receptor type 13
Domain	2213 – 2467	Tyrosine-protein phosphatase
Binding site	2452 – 2452
Mutagenesis	2444 – 2444	R -> E. Loss of catalytic activity.
Mutagenesis	2444 – 2444	R -> K. Reduces substrate affinity 7 fold.
Mutagenesis	2444 – 2444	R -> Q. Strongly decreases catalytic activity.
Mutagenesis	2448 – 2448	H -> A. Reduces substrate affinity 2 fold.
Mutagenesis	2449 – 2449	G -> V. Loss of catalytic activity.
Mutagenesis	2474 – 2474	E -> D. No effect on substrate affinity.
Helix	2454 – 2475

Literature citations
Crystal structure of the PTPL1/FAP-1 human tyrosine phosphatase mutated in colorectal cancer: evidence for a second phosphotyrosine substrate recognition pocket.
Villa F.; Deak M.; Bloomberg G.B.; Alessi D.R.; van Aalten D.M.;
J. Biol. Chem. 280:8180-8187(2005)
Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF 2163-2477; FUNCTION; CATALYTIC ACTIVITY; MUTAGENESIS OF ASP-2154; ARG-2205; GLN-2221; MET-2307; CYS-2408; ARG-2444; HIS-2448; GLY-2449 AND GLU-2474; CHARACTERIZATION OF VARIANT VAL-2458;

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.