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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot O15270: Variant p.Val359Met

Serine palmitoyltransferase 2
Gene: SPTLC2
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Variant information Variant position: help 359 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 Valine (V) to Methionine (M) at position 359 (V359M, p.Val359Met). 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 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: 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 HSAN1C; partial loss of normal activity as measured by reduced formation of sphinganine; affects enzymatic affinity resulting in the accumulation of the alternative metabolite 1-deoxy-sphinganine. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 359 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 562 The length of the canonical sequence.
Location on the sequence: help AYLYLDEAHSIGALGPTGRG V VEYFGLDPEDVDVMMGTFTK 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                         AYLYLDEAHSIGALGPTGRGVVEYFGLDPEDVDVMMGTFTK

Mouse                         AYLYLDEAHSIGALGPSGRGVVDYFGLDPEDVDVMMGTFTK

Rat                           AYLYLDEAHSIGALGPSGRGVVDYFGLDPEDVDVMMGTFTK

Caenorhabditis elegans        AYLYLDEAHSIGAMGKTGKGVVEYWGCDPKDVDILMGTFTK

Slime mold                    CYLYIDEAHSIGALGKTGRGIVDYYGIDPKEIDILMGTYTK
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 – 562 Serine palmitoyltransferase 2
Modified residue 379 – 379 N6-(pyridoxal phosphate)lysine
Mutagenesis 378 – 378 T -> A. Decreased catalytic activity with L-serine and palmitoyl-CoA as substrates.
Mutagenesis 379 – 379 K -> A. Loss of catalytic activity with L-serine and palmitoyl-CoA as substrates.
Helix 359 – 363



Literature citations
Mutations in the SPTLC2 subunit of serine palmitoyltransferase cause hereditary sensory and autonomic neuropathy type I.
Rotthier A.; Auer-Grumbach M.; Janssens K.; Baets J.; Penno A.; Almeida-Souza L.; Van Hoof K.; Jacobs A.; De Vriendt E.; Schlotter-Weigel B.; Loscher W.; Vondracek P.; Seeman P.; De Jonghe P.; Van Dijck P.; Jordanova A.; Hornemann T.; Timmerman V.;
Am. J. Hum. Genet. 87:513-522(2010)
Cited for: FUNCTION; VARIANTS HSAN1C MET-359; VAL-382 AND PHE-504; CHARACTERIZATION OF VARIANTS HSAN1C MET-359; VAL-382 AND PHE-504;
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.