UniProtKB/Swiss-Prot Q99250: Variant p.Gly1460Arg

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

1460 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 Glycine (G) to Arginine (R) at position 1460 (G1460R, p.Gly1460Arg). 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:

Change from glycine (G) to large size and basic (R) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score:

-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:

Found in a patient with non-syndromic intellectual disability and epilepsy; likely pathogenic. Any additional useful information about the variant.

Sequence information Variant position:

1460 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:

QPKYEDNLYMYLYFVIFIIF G SFFTLNLFIGVIIDNFNQQK 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                         QPKYEDNLYMYLYFVIFIIFGSFFTLNLFIGVIIDNFNQQK

Mouse                         QPKYEDNLYMYLYFVIFIIFGSFFTLNLFIGVIIDNFNQQK

Rat                           QPKYEDNLYMYLYFVIFIIFGSFFTLNLFIGVIIDNFNQQK

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
Transmembrane	1448 – 1469	Helical; Name=S6 of repeat III
Repeat	1190 – 1504	III
Site	1443 – 1443	Binds Mu-conotoxin KIIIA
Turn	1460 – 1462

Literature citations
Nonsyndromic intellectual disability with novel heterozygous SCN2A mutation and epilepsy.
Yokoi T.; Enomoto Y.; Tsurusaki Y.; Naruto T.; Kurosawa K.;
Hum. Genome Var. 5:20-20(2018)
Cited for: VARIANT ARG-1460;

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.