UniProtKB/Swiss-Prot Q99250: Variant p.Val424Met

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

424 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant:

US 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 Valine (V) to Methionine (M) at position 424 (V424M, p.Val424Met). 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:

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:

Found in a patient with early-onset seizures and Rett-like features, including autistic behavior, limited hand function with chorea and profound intellectual disability; likely pathogenic. Any additional useful information about the variant.

Sequence information Variant position:

424 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:

FFVLVIFLGSFYLINLILAV V AMAYEEQNQATLEEAEQKEA 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                         FFVLVIFLGSFYLINLILAVVAMAYEEQNQATLEEAEQKEA

Mouse                         FFVLVIFLGSFYLINLILAVVAMAYEEQNQATLEEAEQKEA

Rat                           FFVLVIFLGSFYLINLILAVVAMAYEEQNQATLEEAEQKEA

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.

Type	Positions	Description
Chain	1 – 2005	Sodium channel protein type 2 subunit alpha
Topological domain	423 – 759	Cytoplasmic
Repeat	111 – 456	I
Helix	415 – 440

Literature citations
The therapeutic implication of a novel SCN2A mutation associated early-onset epileptic encephalopathy with Rett-like features.
Liang J.S.; Lin L.J.; Yang M.T.; Wang J.S.; Lu J.F.;
Brain Dev. 39:877-881(2017)
Cited for: VARIANT MET-424;

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.