UniProtKB/Swiss-Prot P07339: Variant p.Ala58Val

Cathepsin D
Gene: CTSD
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Variant information Variant position:

58 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 Valine (V) at position 58 (A58V, p.Ala58Val). 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 (V) 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
Polymorphism:

The Val-58 allele is significantly overrepresented in demented patients (11.8%) compared with non-demented controls (4.9%). Carriers of the Val-58 allele have a 3.1-fold increased risk for developing AD than non-carriers. Additional information on the polymorphism described.
Variant description:

Associated with increased risk for AD; possibly influences secretion and intracellular maturation. Any additional useful information about the variant.
Other resources:

Links to websites of interest for the variant.

Variant rs17571 [ dbSNP | Ensembl ]

Sequence information Variant position:

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

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

EVGGSVEDLIAKGPVSKYSQ A VPAVTEGPIPEVLKNYMDAQ 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                         EVGGSVEDLIAKGPVSKYSQAVPAVTEG---PIPEVLKNYMDAQ

                              ELGGPVEDLIAKGPISKYAQGAPAVTGG---PIPEMLRNYM

Mouse                         EVGGSVEDLILKGPITKYSMQSSPKTTE---PVSELLKNYL

Rat                           EVGGSVEDLILKGPITKYSMQSSPRTKE---PVSELLKNYL

Pig                           ---------------------------G---PIPEVLKNYM

Bovine                        EAAGXVXXLIAKGPISKYATGEPAVRQG---PIPELLKNYM

Chicken                       EVGSEIPDMNAITQFLKFKLGFADLAE----PTPEILKNYM

Slime mold                    RVP------------QKWSNRLSALNAGTTIPISD----FE

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
Propeptide	21 – 64	Activation peptide
Glycosylation	63 – 63	O-linked (GalNAc...) threonine

Literature citations
A genetic variation of cathepsin D is a major risk factor for Alzheimer's disease.
Papassotiropoulos A.; Bagli M.; Kurz A.; Kornhuber J.; Forstl H.; Maier W.; Pauls J.; Lautenschlager N.; Heun R.;
Ann. Neurol. 47:399-403(2000)
Cited for: VARIANT VAL-58;

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.