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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P35498: Variant p.Phe1499Leu

Sodium channel protein type 1 subunit alpha
Gene: SCN1A
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Variant information Variant position: help 1499 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 Phenylalanine (F) to Leucine (L) at position 1499 (F1499L, p.Phe1499Leu). 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 large size and aromatic (F) to medium size and hydrophobic (L) 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 FHM3; changed voltage-gated sodium channel activity; right shift of the inactivation curve without major impact on activation. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 1499 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 IGVIIDNFNQQKKKFGGQDI F MTEEQKKYYNAMKKLGSKKP 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                         IGVIIDNFNQQKKKFGGQDIFMTEEQKKYYNAMKKLGSKKP

Mouse                         IGVIIDNFNQQKKKFGGQDIFMTEEQKKYYNAMKKLGSKKP

Rat                           IGVIIDNFNQQKKKFGGQDIFMTEEQKKYYNAMKKLGSKKP
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 1484 – 1541 Cytoplasmic
Repeat 1200 – 1514 III
Modified residue 1516 – 1516 Phosphoserine; by PKC



Literature citations
Comparative structural analysis of human Nav1.1 and Nav1.5 reveals mutational hotspots for sodium channelopathies.
Pan X.; Li Z.; Jin X.; Zhao Y.; Huang G.; Huang X.; Shen Z.; Cao Y.; Dong M.; Lei J.; Yan N.;
Proc. Natl. Acad. Sci. U.S.A. 118:0-0(2021)
Cited for: STRUCTURE BY ELECTRON MICROSCOPY (3.30 ANGSTROMS) IN COMPLEX WITH SCN4B; TOPOLOGY; DISULFIDE BONDS; GLYCOSYLATION AT ASN-338; ASN-1378; ASN-1392 AND ASN-1403; CHARACTERIZATION OF VARIANT DRVT VAL-1339 AND ARG-1658; CHARACTERIZATION OF VARIANT FMH3 LEU-1499; Elicited repetitive daily blindness: a new phenotype associated with hemiplegic migraine and SCN1A mutations.
Vahedi K.; Depienne C.; Le Fort D.; Riant F.; Chaine P.; Trouillard O.; Gaudric A.; Morris M.A.; LeGuern E.; Tournier-Lasserve E.; Bousser M.-G.;
Neurology 72:1178-1183(2009)
Cited for: VARIANTS FHM3 HIS-1489 AND LEU-1499;
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.