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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P35498: Variant p.Leu1649Gln

Sodium channel protein type 1 subunit alpha
Gene: SCN1A
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Variant information Variant position: help 1649 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 Leucine (L) to Glutamine (Q) at position 1649 (L1649Q, p.Leu1649Gln). 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 (L) to medium size and polar (Q) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score: help -2 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. Any additional useful information about the variant.


Sequence information Variant position: help 1649 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 FVSPTLFRVIRLARIGRILR L IKGAKGIRTLLFALMMSLPA 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                         FVSPTLFRVIRLARIGRILRLIKGAKGIRTLLFALMMSLPA

Mouse                         FVSPTLFRVIRLARIGRILRLIKGAKGIRTLLFALMMSLPA

Rat                           FVSPTLFRVIRLARIGRILRLIKGAKGIRTLLFALMMSLPA
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
Transmembrane 1637 – 1655 Helical; Name=S4 of repeat IV
Repeat 1523 – 1821 IV
Helix 1647 – 1651



Literature citations
The novel p.L1649Q mutation in the SCN1A epilepsy gene is associated with familial hemiplegic migraine: genetic and functional studies. Mutation in brief #957. Online.
Vanmolkot K.R.; Babini E.; de Vries B.; Stam A.H.; Freilinger T.; Terwindt G.M.; Norris L.; Haan J.; Frants R.R.; Ramadan N.M.; Ferrari M.D.; Pusch M.; van den Maagdenberg A.M.; Dichgans M.;
Hum. Mutat. 28:522-522(2007)
Cited for: VARIANT FHM3 GLN-1649;
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.