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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q969W0: Variant p.Thr51Ile

Serine palmitoyltransferase small subunit A
Gene: SPTSSA
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Variant information Variant position: help 51 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant: help 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: help From Threonine (T) to Isoleucine (I) at position 51 (T51I, p.Thr51Ile). 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: help 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: help -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: help In SPG90A; likely pathogenic; results in increased sphingolipid biosynthetic process due to impaired down-regulation of serine palmitoyltransferase (SPT) complex activity by ORMDL3. Any additional useful information about the variant.


Sequence information Variant position: help 51 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 71 The length of the canonical sequence.
Location on the sequence: help PWERTVFNSMLVSIVGMALY T GYVFMPQHIMAILHYFEIVQ 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: help The multiple alignment of the region surrounding the variant against various orthologous sequences. 
Human                         PWERTVFNSMLVSIVGMALYTGYVFMPQHIMAILHYFEIVQ

Mouse                         PWERTVFNSMLVSVVGMALYTGYVFMPQHIMAILHYFEIVQ

Rat                           PWERTVFNSMLVSVVGMALYTGYVFMPQHIMAILHYFEIVQ

Bovine                        PWERTVFNSMLVSIVGMALYTGYVFMPQHIMAILHYFEIVQ

Xenopus tropicalis            PWERTIFNSMLVSIVGMALYTGYIFMPQHILAILHYFEIVQ

Zebrafish                     PWERTIFNSLLISVAAMAVYTGYVFMPQHIMAILHYFEVVQ
Sequence annotation in neighborhood: help 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 1 – 71 Serine palmitoyltransferase small subunit A
Transmembrane 35 – 57 Helical
Mutagenesis 59 – 59 H -> L. Impaired down-regulation of SPT complex activity by ORMDL3.
Helix 31 – 54



Literature citations
SPTSSA variants alter sphingolipid synthesis and cause a complex hereditary spastic paraplegia.
Srivastava S.; Shaked H.M.; Gable K.; Gupta S.D.; Pan X.; Somashekarappa N.; Han G.; Mohassel P.; Gotkine M.; Doney E.; Goldenberg P.; Tan Q.K.G.; Gong Y.; Kleinstiver B.; Wishart B.; Cope H.; Pires C.B.; Stutzman H.; Spillmann R.C.; Sadjadi R.; Elpeleg O.; Lee C.H.; Bellen H.J.; Edvardson S.; Eichler F.; Dunn T.M.;
Brain 146:1420-1435(2023)
Cited for: VARIANT SPG90A ILE-51; INVOLVEMENT IN SPG90A AND SPG90B; CHARACTERIZATION OF VARIANT SPG90A ILE-51; MUTAGENESIS OF HIS-59;
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.