UniProtKB/Swiss-Prot O14522: Variant p.Ala29Pro

Receptor-type tyrosine-protein phosphatase T
Gene: PTPRT
Feedback?

Variant information Variant position:

29 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 Alanine (A) to Proline (P) at position 29 (A29P, p.Ala29Pro). 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 small size and hydrophobic (A) to medium size and hydrophobic (P) 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
Other resources:

Links to websites of interest for the variant.

Variant rs2867655 [ dbSNP | Ensembl ]

Sequence information Variant position:

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

1441 The length of the canonical sequence.
Location on the sequence:

LSLLLRLQLPPLPGARAQSA A GGCSFDEHYSNCGYSVALGT 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                         LS----LLLRLQLPPLPGARAQSAAGGCSFDEHYSNCGYSVALGT

Mouse                         LCLLRLLLLGLQRPPLPGAGAQSAAGGCSFDEHYSNCGYSV

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	26 – 1441	Receptor-type tyrosine-protein phosphatase T
Topological domain	26 – 747	Extracellular

Literature citations
Identification and characterization of RPTP rho, a novel RPTP mu/kappa-like receptor protein tyrosine phosphatase whose expression is restricted to the central nervous system.
McAndrew P.E.; Frostholm A.; White R.A.; Rotter A.; Burghes A.H.M.;
Brain Res. Mol. Brain Res. 56:9-21(1998)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1); CHARACTERIZATION; VARIANT PRO-29; Construction and characterization of human brain cDNA libraries suitable for analysis of cDNA clones encoding relatively large proteins.
Ohara O.; Nagase T.; Ishikawa K.; Nakajima D.; Ohira M.; Seki N.; Nomura N.;
DNA Res. 4:53-59(1997)
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3); VARIANT PRO-29; 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 3); VARIANT PRO-29;

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.