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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P35498: Variant p.Thr1250Met

Sodium channel protein type 1 subunit alpha
Gene: SCN1A
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Variant information Variant position: help 1250 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 Methionine (M) at position 1250 (T1250M, p.Thr1250Met). 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 (M) 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 GEFSP2. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 1250 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 2009 The length of the canonical sequence.
Location on the sequence: help LSSGALAFEDIYIDQRKTIK T MLEYADKVFTYIFILEMLLK 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                         LSSGALAFEDIYIDQRKTIKTMLEYADKVFTYIFILEMLLK

Mouse                         LSSGALAFEDIYIDQRKTIKTMLEYADKVFTYIFILEMLLK

Rat                           LSSGALAFEDIYIDQRKTIKTMLEYADKVFTYIFILEMLLK
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 – 2009 Sodium channel protein type 1 subunit alpha
Topological domain 1238 – 1250 Extracellular
Repeat 1200 – 1514 III
Helix 1249 – 1280



Literature citations
Mutational analysis of the SCN1A, SCN1B and GABRG2 genes in 150 Italian patients with idiopathic childhood epilepsies.
Orrico A.; Galli L.; Grosso S.; Buoni S.; Pianigiani R.; Balestri P.; Sorrentino V.;
Clin. Genet. 75:579-581(2009)
Cited for: VARIANTS GLN-542 AND PHE-790; VARIANT FEB3A ASP-1308; VARIANT DRVT CYS-1648; VARIANTS GEFSP2 THR-899; ILE-976; ASN-1249 AND MET-1250; POSSIBLE INVOLVEMENT IN PANAYIOTOPOULOS SYNDROME;
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.