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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q9NY46: Variant p.Val1769Ala

Sodium channel protein type 3 subunit alpha
Gene: SCN3A
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Variant information Variant position: help 1769 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 Alanine (A) at position 1769 (V1769A, p.Val1769Ala). 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 hydrophobic (V) to small size and hydrophobic (A) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score: help 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
Variant description: help In DEE62; prominent gain of channel function, with markedly increased amplitude of the slowly inactivating current component. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 1769 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 2000 The length of the canonical sequence.
Location on the sequence: help FFFVSYIIISFLVVVNMYIA V ILENFSVATEESAEPLSEDD 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                         FFFVSYIIISFLVVVNMYIAVILENFSVATEESAEPLSEDD

Mouse                         FFFVSYIIISFLVVVNMYIAVILENFSVATEESAEPLSEDD

Rat                           FFFVSYIIISFLVVVNMYIAVILENFSVATEESAEPLSEDD
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 – 2000 Sodium channel protein type 3 subunit alpha
Transmembrane 1745 – 1770 Helical; Name=S6 of repeat IV
Repeat 1508 – 1806 IV
Helix 1744 – 1777



Literature citations
Mutations in SCN3A cause early infantile epileptic encephalopathy.
Zaman T.; Helbig I.; Bozovic I.B.; DeBrosse S.D.; Bergqvist A.C.; Wallis K.; Medne L.; Maver A.; Peterlin B.; Helbig K.L.; Zhang X.; Goldberg E.M.;
Ann. Neurol. 83:703-717(2018)
Cited for: INVOLVEMENT IN DEE62; VARIANTS DEE62 THR-875; LEU-1333; CYS-1642; ALA-1769 AND GLN-1799; CHARACTERIZATION OF VARIANTS DEE62 THR-875; LEU-1333; CYS-1642; ALA-1769 AND GLN-1799; FUNCTION;
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.