UniProtKB/SwissProt variant VAR

Variant information

Variant position:

505

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 Serine (S) to Proline (P) at position 505 (S505P, p.Ser505Pro).

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 polar (S) 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

Variant description:

In MANSB; nearly complete loss of enzyme activity.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs121434334 [ dbSNP | Ensembl ]

Sequence information

Variant position:

505

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

Protein sequence length:

879

The length of the canonical sequence.

Location on the sequence:

YVKNIRELVLAGDKSRPFIT S SPTNGAETVAEAWVSQNPNS

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                         YVKNIRELVLAGDKSRPFITSSPTNGAETVAEAWVSQNPNS

Mouse                         YVKNIRKIVLSEDKSRPFIASSPTNGMKTMEEGWISYDPYS

Rat                           YVKTIREIVLSEDRSRPFIASSPTNGVKTMTEGWISKDPYS

Bovine                        YVKNIRTIVLEGDQTRPFITSSPTNGAKTIAEGWLSPNPYD

Goat                          YVKNIRTIVLEGDQTRPFIISSPTNGAKTTAEGWLSPNPYD

Caenorhabditis elegans        YQR-LAKIAKKVAPTIPFIMSSPSNGVETEEEGGVSKNPYD

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	18 – 879	Beta-mannosidase

Literature citations

Identification of two novel beta-mannosidosis-associated sequence variants: biochemical analysis of beta-mannosidase (MANBA) missense mutations.
Riise Stensland H.M.; Persichetti E.; Sorriso C.; Hansen G.M.; Bibi L.; Paciotti S.; Balducci C.; Beccari T.;
Mol. Genet. Metab. 94:476-480(2008)
Cited for: VARIANT MANSB PRO-505; CHARACTERIZATION OF VARIANTS MANSB TRP-182; GLU-392 AND PRO-505; CHARACTERIZATION OF VARIANT ILE-253; CATALYTIC ACTIVITY; MUTAGENESIS OF ARG-638; ARG-641 AND LEU-749;

The structure of mammalian beta-mannosidase provides insight into beta-mannosidosis and nystagmus.
Gytz H.; Liang J.; Liang Y.; Gorelik A.; Illes K.; Nagar B.;
FEBS J. 286:1319-1331(2019)
Cited for: CHARACTERIZATION OF VARIANTS MANSB TRP-182; GLU-392; 466-TRP--TYR-879 DEL AND PRO-505; FUNCTION; CATALYTIC ACTIVITY; PATHWAY; BIOPHYSICOCHEMICAL PROPERTIES;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot O00462: Variant p.Ser505Pro