UniProtKB/SwissProt variant VAR

Variant information

Variant position:

227

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 Leucine (L) to Proline (P) at position 227 (L227P, p.Leu227Pro).

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:

Similar physico-chemical property. Both residues are medium size and hydrophobic.

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

BLOSUM score:

-3

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; expresses protein level comparable to wild-type SMPD1 expressing cells; retains no enzyme activity.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs764317969 [ dbSNP | Ensembl ]

Sequence information

Variant position:

227

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:

TDLHWDHDYLEGTDPDCADP L CCRRGSGLPPASRPGAGYWG

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                         TDLHWDHDYLEGTDPDCADPLCCRRGSGLPPASRPGAGYWG

Mouse                         TDLHWDHEYLEGTDPYCADPLCCRRGSGWPPNSQKGAGFWG

Bovine                        TDLHWDHDYLEGTDPNCENPLCCRRDSGPPPASQPGAGYWG

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	208 – 208	Zinc 1
Metal binding	210 – 210	Zinc 1; via tele nitrogen
Disulfide bond	223 – 228
Mutagenesis	233 – 233	S -> A. No effect on sphingomyelin phosphodiesterase activity. No effect on endolysosome location. No effect on phosphorylation by PRKCD.
Beta strand	224 – 227

Literature citations

Acid sphingomyelinase: identification of nine novel mutations among Italian Niemann Pick type B patients and characterization of in vivo functional in-frame start codon.
Pittis M.G.; Ricci V.; Guerci V.I.; Marcais C.; Ciana G.; Dardis A.; Gerin F.; Stroppiano M.; Vanier M.T.; Filocamo M.; Bembi B.;
Hum. Mutat. 24:186-187(2004)
Cited for: VARIANTS NPDB PRO-105; PRO-227; CYS-246; THR-283; LYS-294 AND ILE-384;

Functional in vitro characterization of 14 SMPD1 mutations identified in Italian patients affected by Niemann Pick type B disease.
Dardis A.; Zampieri S.; Filocamo M.; Burlina A.; Bembi B.; Pittis M.G.;
Hum. Mutat. 26:164-164(2005)
Cited for: VARIANTS NPDB ALA-132 AND TYR-565; CHARACTERIZATION OF VARIANTS NPDB PRO-105; ALA-132; PRO-227; CYS-246; THR-283; TYR-565; HIS-602 AND PRO-602;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P17405: Variant p.Leu227Pro