UniProtKB/SwissProt variant VAR

Variant information

Variant position:

1589

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

Type of variant:

Disease [Disclaimer]

The variants are classified into three categories: Disease, Polymorphism and Unclassified.

Disease: Variants implicated in disease according to literature reports.
Polymorphism: Variants not reported to be implicated in disease.
Unclassified: Variants with uncertain implication in disease according to literature reports. Evidence against or in favor of a pathogenic role is limited and/or conflicting.

Residue change:

From Tyrosine (Y) to Cysteine (C) at position 1589 (Y1589C, p.Tyr1589Cys).

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 large size and aromatic (Y) to medium size and polar (C)

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

Involvement in disease:

Seizures, benign familial infantile, 3 (BFIS3) [MIM:607745]: A form of benign familial infantile epilepsy, a neurologic disorder characterized by afebrile seizures occurring in clusters during the first year of life, without neurologic sequelae. BFIS3 inheritance is autosomal dominant. {ECO:0000269|PubMed:11371648, ECO:0000269|PubMed:12243921, ECO:0000269|PubMed:15048894, ECO:0000269|PubMed:16417554, ECO:0000269|PubMed:17021166, ECO:0000269|PubMed:17386050, ECO:0000269|PubMed:18479388, ECO:0000269|PubMed:20371507, ECO:0000269|PubMed:22612257, ECO:0000269|PubMed:23360469, ECO:0000269|PubMed:23758435, ECO:0000269|PubMed:25982755, ECO:0000269|PubMed:26291284, ECO:0000269|PubMed:29844171, ECO:0000269|PubMed:30144217}. Note=The disease is caused by mutations affecting the gene represented in this entry.

The name and a short description of the disease associated with the variant. For more information about the disease, the user can refer to OMIM, following the link provided after the disease acronym.

Variant description:

In BFIS3; increased voltage-gated sodium channel activity; depolarized shift of steady-state inactivation; increased persistent sodium current; slower fast inactivation; accelerated recovery of fast inactivation; gain of function.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs1553463119 [ dbSNP | Ensembl ]

Sequence information

Variant position:

1589

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:

VFIVLFTGECVLKLISLRYY Y FTIGWNIFDFVVVILSIVGM

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                         VFIVLFTGECVLKLISLRYYYFTIGWNIFDFVVVILSIVGM

Mouse                         VFIVLFTGECVLKLISLRHYYFTIGWNIFDFVVVILSIVGM

Rat                           VFIVLFTGECVLKLISLRHYYFTIGWNIFDFVVVILSIVGM

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	1581 – 1592	Cytoplasmic
Repeat	1513 – 1811	IV

Literature citations

An SCN2A mutation in a family with infantile seizures from Madagascar reveals an increased subthreshold Na(+) current.
Lauxmann S.; Boutry-Kryza N.; Rivier C.; Mueller S.; Hedrich U.B.; Maljevic S.; Szepetowski P.; Lerche H.; Lesca G.;
Epilepsia 54:E117-E121(2013)
Cited for: VARIANT BFIS3 CYS-1589; CHARACTERIZATION OF VARIANT BFIS3 CYS-1589;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q99250: Variant p.Tyr1589Cys