UniProtKB/SwissProt variant VAR

Variant information

Variant position:

387

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 Cysteine (C) to Arginine (R) at position 387 (C387R, p.Cys387Arg).

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 medium size and polar (C) to large size and basic (R)

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 NPDA.

Any additional useful information about the variant.

Sequence information

Variant position:

387

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:

GFYALSPYPGLRLISLNMNF C SRENFWLLINSTDPAGQLQW

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                         GFYALSPYPGLRLISLNMNFCSRENFWLLINSTDPAGQLQW

Mouse                         GFYALTPRPGLRLISLNMNFCSRENFWLLINSTDPAGQLQW

Bovine                        GFYALSPRPGLRLISLNMNFCSRENFWLLINSTDPAGQLQW

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
Glycosylation	397 – 397	N-linked (GlcNAc...) asparagine
Disulfide bond	387 – 433
Alternative sequence	365 – 420	Missing. In isoform 3.
Alternative sequence	377 – 420	Missing. In isoform 2.
Mutagenesis	397 – 397	N -> G. Reduces sphingomyelin phosphodiesterase activity. No effect on secretion.
Helix	384 – 387

Literature citations

Identification of seven novel SMPD1 mutations causing Niemann-Pick disease types A and B.
Irun P.; Mallen M.; Dominguez C.; Rodriguez-Sureda V.; Alvarez-Sala L.A.; Arslan N.; Bermejo N.; Guerrero C.; Perez de Soto I.; Villalon L.; Giraldo P.; Pocovi M.;
Clin. Genet. 84:356-361(2013)
Cited for: VARIANTS NPDA ARG-228 AND ARG-387; VARIANTS NPDB CYS-230; SER-247; HIS-378; TRP-476; SER-492; PHE-599 AND ARG-610 DEL;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P17405: Variant p.Cys387Arg