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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q99250: Variant p.Leu1563Val

Sodium channel protein type 2 subunit alpha
Gene: SCN2A
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Variant information Variant position: help 1563 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 Valine (V) at position 1563 (L1563V, p.Leu1563Val). 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 Similar physico-chemical property. Both residues are medium size and hydrophobic. 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 BFIS3; increased voltage-gated sodium channel activity; impaired fast inactivation; no effect on kinetics of activation or inactivation; no effect on voltage dependence of activation; gain of function. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 1563 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 2005 The length of the canonical sequence.
Location on the sequence: help LNMVTMMVETDDQSQEMTNI L YWINLVFIVLFTGECVLKLI 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                         LNMVTMMVETDDQSQEMTNILYWINLVFIVLFTGECVLKLI

Mouse                         LNMVTMMVETDDQSQEMTNILYWINLVFIVLFTGECVLKLI

Rat                           LNMVTMMVETDDQSQEMTNILYWINLVFIVLFTGECVLKLI

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 – 2005 Sodium channel protein type 2 subunit alpha
Transmembrane 1562 – 1580 Helical; Name=S2 of repeat IV
Repeat 1513 – 1811 IV
Helix 1557 – 1584



Literature citations
Sodium-channel defects in benign familial neonatal-infantile seizures.
Heron S.E.; Crossland K.M.; Andermann E.; Phillips H.A.; Hall A.J.; Bleasel A.; Shevell M.; Mercho S.; Seni M.H.; Guiot M.C.; Mulley J.C.; Berkovic S.F.; Scheffer I.E.;
Lancet 360:851-852(2002)
Cited for: VARIANTS BFIS3 PHE-1330 AND VAL-1563; Effects in neocortical neurons of mutations of the Na(v)1.2 Na+ channel causing benign familial neonatal-infantile seizures.
Scalmani P.; Rusconi R.; Armatura E.; Zara F.; Avanzini G.; Franceschetti S.; Mantegazza M.;
J. Neurosci. 26:10100-10109(2006)
Cited for: CHARACTERIZATION OF VARIANTS BFIS3 GLN-223; GLN-1319; PHE-1330 AND VAL-1563; FUNCTION; TRANSPORTER ACTIVITY; SUBCELLULAR LOCATION; Impaired NaV1.2 function and reduced cell surface expression in benign familial neonatal-infantile seizures.
Misra S.N.; Kahlig K.M.; George A.L. Jr.;
Epilepsia 49:1535-1545(2008)
Cited for: CHARACTERIZATION OF VARIANTS BFIS3 GLN-1319; PHE-1330 AND VAL-1563; Dynamic action potential clamp predicts functional separation in mild familial and severe de novo forms of SCN2A epilepsy.
Berecki G.; Howell K.B.; Deerasooriya Y.H.; Cilio M.R.; Oliva M.K.; Kaplan D.; Scheffer I.E.; Berkovic S.F.; Petrou S.;
Proc. Natl. Acad. Sci. U.S.A. 115:E5516-E5525(2018)
Cited for: VARIANTS DEE11 GLN-853 AND GLN-1882; CHARACTERIZATION OF VARIANTS DEE11 GLN-853 AND GLN-1882; VARIANT BFIS3 VAL-1563; CHARACTERIZATION OF VARIANT BFIS3 VAL-1563; FUNCTION; TRANSPORTER ACTIVITY; SUBCELLULAR LOCATION;
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.