UniProtKB/Swiss-Prot P01034: Variant p.Ala25Thr

• Variant information
• Sequence information
• Literature citations
• All

Variant information

Variant position: 25 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant: LP/P [Disclaimer: Variants classification is intended for research purposes only, not for clinical and diagnostic use. The label disease variant is assigned according to literature reports on probable disease-association that can be based on theoretical reasons. This label must not be considered as a definitive proof for the pathogenic role of a variant.] 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 Threonine (T) at position 25 (A25T, p.Ala25Thr). 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 polar (T) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score: 0 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 ARMD11; likely benign; alters processing and glycosylation. Any additional useful information about the variant.
Other resources: Links to websites of interest for the variant.

• Variant rs1064039 [ dbSNP | Ensembl ]

Sequence information

Variant position: 25 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: 146 The length of the canonical sequence.
Location on the sequence: LRAPLLLLAILAVALAVSPA A GSSPGKPPRLVGGPMDASVE 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.
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
Signal peptide	1 – 26
Site	37 – 37	Reactive site
Modified residue	43 – 43	Phosphoserine; by FAM20C
Mutagenesis	25 – 25	A -> S. Shows a dual distribution to the Golgi apparatus and to the mitochondria.

Literature citations

The human cystatin C gene (CST3) is a member of the cystatin gene family which is localized on chromosome 20.
Saitoh E.; Sabatini L.M.; Eddy R.L.; Shows T.B.; Azen E.A.; Isemura S.; Sanada K.;
Biochem. Biophys. Res. Commun. 162:1324-1331(1989)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]; VARIANT ARMD11 THR-25; Enrichment of glycopeptides for glycan structure and attachment site identification.
Nilsson J.; Rueetschi U.; Halim A.; Hesse C.; Carlsohn E.; Brinkmalm G.; Larson G.;
Nat. Methods 6:809-811(2009)
Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS]; STRUCTURE OF CARBOHYDRATES; CHARACTERIZATION OF VARIANT ARMD11 THR-25; CST3 genotype associated with exudative age related macular degeneration.
Zurdel J.; Finckh U.; Menzer G.; Nitsch R.M.; Richard G.;
Br. J. Ophthalmol. 86:214-219(2002)
Cited for: VARIANT ARMD11 THR-25;