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UniProtKB/Swiss-Prot O15270: Variant p.Ile504Phe

Serine palmitoyltransferase 2
Gene: SPTLC2
Variant information

Variant position:  504
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  Disease [Disclaimer]
The variants are classified into three categories: Disease, Polymorphism and Unclassified.
  • Disease: Variants implicated in disease according to literature reports.
  • Polymorphism: Variants not reported to be implicated in disease.
  • Unclassified: Variants with uncertain implication in disease according to literature reports. Evidence against or in favor of a pathogenic role is limited and/or conflicting.

Residue change:  From Isoleucine (I) to Phenylalanine (F) at position 504 (I504F, p.Ile504Phe).
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 hydrophobic (I) to large size and aromatic (F)
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  0
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

Involvement in disease:  Neuropathy, hereditary sensory and autonomic, 1C (HSAN1C) [MIM:613640]: A form of hereditary sensory and autonomic neuropathy, a genetically and clinically heterogeneous group of disorders characterized by degeneration of dorsal root and autonomic ganglion cells, and by prominent sensory abnormalities with a variable degree of motor and autonomic dysfunction. The neurological phenotype is often complicated by severe infections, osteomyelitis, and amputations. HSAN1C symptoms include loss of touch and vibration in the feet, dysesthesia and severe panmodal sensory loss in the upper and lower limbs, distal lower limb sensory loss with ulceration and osteomyelitis, and distal muscle weakness. {ECO:0000269|PubMed:20920666, ECO:0000269|PubMed:23658386, ECO:0000269|PubMed:26573920}. Note=The disease is caused by mutations affecting the gene represented in this entry. SPTLC2 disease mutations cause a shift in the substrate specificity of SPT resulting in the alternative use of L-alanine and L-glycine over its canonical substrate L-serine. This leads to the production of 1-deoxysphingolipids that cannot be correctly metabolized (PubMed:23658386). {ECO:0000269|PubMed:23658386, ECO:0000269|PubMed:26573920}.
The name and a short description of the disease associated with the variant. For more information about the disease, the user can refer to OMIM, following the link provided after the disease acronym.

Variant description:  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:  
Links to websites of interest for the variant.



Sequence information

Variant position:  504
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  562
The length of the canonical sequence.

Location on the sequence:   REMLKRNIGVVVVGFPATPI  I ESRARFCLSAAHTKEILDTA
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                         REMLKRNIGVVVVGFPATPIIESRARFCLSAAHTKEILDTA

Mouse                         REMLKRNIGVVVVGFPATPIIESRARFCLSAAHTKEILDTA

Rat                           REMLKRNIGVVVVGFPATPIIESRARFCLSAAHTKEILDTA

Caenorhabditis elegans        REMLARNIGCVVVSFPATHMTEGRVRFCISAAHTKEQLDEV

Slime mold                    RLCLEKHIAVVVVGYPATPLTEPRTRFCISASHTIEDLDWA

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 1 – 562 Serine palmitoyltransferase 2


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.