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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P35498: Variant p.Val1390Met

Sodium channel protein type 1 subunit alpha
Gene: SCN1A
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Variant information Variant position: help 1390 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 Methionine (M) at position 1390 (V1390M, p.Val1390Met). 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 DRVT; some patients have a borderline DRVT phenotype. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 1390 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 AGKFYHCINTTTGDRFDIED V NNHTDCLKLIERNETARWKN 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                         AGKFYHCINTTTGDRFDIEDVNNHTDCLKLIERNETARWKN

Mouse                         AGKFYHCVNTTTGDIFEISEVNNHSDCLKLIERNETARWKN

Rat                           AGKFYHCVNTTTGDTFEITEVNNHSDCLKLIERNETARWKN
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 1367 – 1418 Extracellular
Repeat 1200 – 1514 III
Glycosylation 1378 – 1378 N-linked (GlcNAc...) asparagine
Glycosylation 1392 – 1392 N-linked (GlcNAc...) asparagine
Glycosylation 1403 – 1403 N-linked (GlcNAc...) asparagine



Literature citations
Significant correlation of the SCN1A mutations and severe myoclonic epilepsy in infancy.
Ohmori I.; Ouchida M.; Ohtsuka Y.; Oka E.; Shimizu K.;
Biochem. Biophys. Res. Commun. 295:17-23(2002)
Cited for: VARIANTS DRVT CYS-902; CYS-931; PRO-1265; PHE-1289 DEL; MET-1390; ARG-1434; ARG-1450; CYS-1648 AND ARG-1674 AND ILE-1909; VARIANT THR-1067; The spectrum of SCN1A-related infantile epileptic encephalopathies.
Harkin L.A.; McMahon J.M.; Iona X.; Dibbens L.; Pelekanos J.T.; Zuberi S.M.; Sadleir L.G.; Andermann E.; Gill D.; Farrell K.; Connolly M.; Stanley T.; Harbord M.; Andermann F.; Wang J.; Batish S.D.; Jones J.G.; Seltzer W.K.; Gardner A.; Sutherland G.; Berkovic S.F.; Mulley J.C.; Scheffer I.E.;
Brain 130:843-852(2007)
Cited for: VARIANTS CYS-393; PRO-395; GLU-422; GLY-626; VAL-1480; SER-1543; GLN-1636 AND HIS-1657; VARIANTS DRVT HIS-79; CYS-84; TRP-101; ARG-199; THR-239; LEU-403; ASN-413; GLY-674; PRO-783; GLU-944; LEU-945; GLU-950; ASP-1238; MET-1390; GLY-1396; PRO-1441; VAL-1545; CYS-1596; GLN-1645; VAL-1707; ARG-1721 AND THR-1922; VARIANT GEFSP2 VAL-973; VARIANT DEE6B MET-226; Analysis of SCN1A mutation and parental origin in patients with Dravet syndrome.
Sun H.; Zhang Y.; Liu X.; Ma X.; Yang Z.; Qin J.; Jiang Y.; Qi Y.; Wu X.;
J. Hum. Genet. 55:421-427(2010)
Cited for: VARIANTS DRVT SER-90; THR-91; TRP-101; GLN-101; THR-239; ARG-259; HIS-393; TYR-939; GLY-952; LYS-1210; PRO-1260; PRO-1287; MET-1335; MET-1390; GLU-1433; GLU-1586 AND THR-1783;
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.