UniProtKB/SwissProt variant VAR

Variant information

Variant position:

453

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 Alanine (A) to Aspartate (D) at position 453 (A453D, p.Ala453Asp).

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 acidic (D)

The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:

-2

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 NPDB.

Any additional useful information about the variant.

Sequence information

Variant position:

453

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

Protein sequence length:

631

The length of the canonical sequence.

Location on the sequence:

CLKSWSWNYYRIVARYENTL A AQFFGHTHVDEFEVFYDEET

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                         CLKSWSWNYYRIVARYENTLAAQFFGHTHVDEFEVFYDEET

Mouse                         CLKSWSWNYYKIIARYENTLAGQFFGHTHVDEFEIFYDEET

Bovine                        CLKSWSWNYYRIVERYENTLAGQFFGHTHVDEFEVFYDEET

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	47 – 631	Sphingomyelin phosphodiesterase
Metal binding	459 – 459	Zinc 2; via pros nitrogen
Metal binding	461 – 461	Zinc 1; via tele nitrogen
Beta strand	452 – 457

Literature citations

A novel missense mutation of the SMPD1 gene in a Taiwanese patient with type B Niemann-Pick disease.
Lan M.Y.; Lin S.J.; Chen Y.F.; Peng C.H.; Liu Y.F.;
Ann. Hematol. 88:695-697(2009)
Cited for: VARIANTS NPDB ARG-332 AND ASP-453;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P17405: Variant p.Ala453Asp