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UniProtKB/Swiss-Prot P17405: Variant p.Thr258Ile

Sphingomyelin phosphodiesterase
Gene: SMPD1
Variant information

Variant position:  258
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 Threonine (T) to Isoleucine (I) at position 258 (T258I, p.Thr258Ile).
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 (T) to medium size and hydrophobic (I)
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 NPDB.
Any additional useful information about the variant.



Sequence information

Variant position:  258
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:   ASRPGAGYWGEYSKCDLPLR  T LESLLSGLGPAGPFDMVYWT
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                         ASRPGAGYWGEYSKCDLPLRTLESLLSGLGPAGPFDMVYWT

Mouse                         NSQKGAGFWGEYSKCDLPLRTLESLLKGLGPAGPFEMVYWT

Bovine                        ASQPGAGYWGEYSKCDLPLRTLESLLSGLGPAGPFDMVYWT

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.

TypePositionsDescription
Chain 47 – 631 Sphingomyelin phosphodiesterase
Mutagenesis 250 – 250 S -> A. No effect on sphingomyelin phosphodiesterase activity. No effect on endolysosome location. No effect on phosphorylation by PRKCD.
Helix 256 – 264


Literature citations

SMPD1 mutation update: database and comprehensive analysis of published and novel variants.
Zampieri S.; Filocamo M.; Pianta A.; Lualdi S.; Gort L.; Coll M.J.; Sinnott R.; Geberhiwot T.; Bembi B.; Dardis A.;
Hum. Mutat. 37:139-147(2016)
Cited for: VARIANTS NPDB ILE-258; GLN-476; ASP-577; ARG-598 AND CYS-610; VARIANT NPDA PHE-482 DEL; REVIEW ON VARIANTS;

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.