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UniProtKB/Swiss-Prot Q99250: Variant p.Leu1650Pro

Sodium channel protein type 2 subunit alpha
Gene: SCN2A
Variant information

Variant position:  1650
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  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:  From Leucine (L) to Proline (P) at position 1650 (L1650P, p.Leu1650Pro).
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:  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:  -3
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:  In DEE11; also found in patients with familial episodic ataxia and impairment of speech development.
Any additional useful information about the variant.



Sequence information

Variant position:  1650
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  2005
The length of the canonical sequence.

Location on the sequence:   LARIGRILRLIKGAKGIRTL  L FALMMSLPALFNIGLLLFLV
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: 
The multiple alignment of the region surrounding the variant against various orthologous sequences.

Human                         LARIGRILRLIKGAKGIRTLLFALMMSLPALFNIGLLLFLV

Mouse                         LARIGRILRLIKGAKGIRTLLFALMMSLPALFNIGLLLFLV

Rat                           LARIGRILRLIKGAKGIRTLLFALMMSLPALFNIGLLLFLV

Sequence annotation in neighborhood:  
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
Topological domain 1641 – 1659 Cytoplasmic
Repeat 1513 – 1811 IV
Helix 1646 – 1654


Literature citations

Improving diagnosis and broadening the phenotypes in early-onset seizure and severe developmental delay disorders through gene panel analysis.
Trump N.; McTague A.; Brittain H.; Papandreou A.; Meyer E.; Ngoh A.; Palmer R.; Morrogh D.; Boustred C.; Hurst J.A.; Jenkins L.; Kurian M.A.; Scott R.H.;
J. Med. Genet. 53:310-317(2016)
Cited for: VARIANTS DEE11 MET-873; ILE-987; LYS-999; VAL-999; GLN-1260; GLU-1260; 1435-ARG--LYS-2005 DEL; PRO-1479; PRO-1650; PHE-1829 AND GLN-1882;

Dominant SCN2A Mutation Causes Familial Episodic Ataxia and Impairment of Speech Development.
Fazeli W.; Becker K.; Herkenrath P.; Duechting C.; Koerber F.; Landgraf P.; Nuernberg P.; Altmueller J.; Thiele H.; Koy A.; Liebau M.C.; Simon T.; Doetsch J.; Cirak S.;
Neuropediatrics 49:379-384(2018)
Cited for: VARIANT PRO-1650;

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.