UniProtKB/SwissProt variant VAR

Variant information

Variant position:

1754

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 Phenylalanine (F) to Serine (S) at position 1754 (F1754S, p.Phe1754Ser).

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 (F) to small size and polar (S)

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:

In DEE13; unknown pathological significance.

Any additional useful information about the variant.

Sequence information

Variant position:

1754

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

Protein sequence length:

1980

The length of the canonical sequence.

Location on the sequence:

GDCGNPSVGIFFFVSYIIIS F LIVVNMYIAIILENFSVATE

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                         GDCGNPSVGIFFFVSYIIISFLIVVNMYIAIILENFSVATE

Mouse                         GDCGNPSVGIFFFVSYIIISFLIVVNMYIAIILENFSVATE

Rat                           GDCGNPSVGIFFFVSYIIISFLIVVNMYIAIILENFSVATE

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 – 1980	Sodium channel protein type 8 subunit alpha
Transmembrane	1743 – 1765	Helical; Name=S6 of repeat IV
Repeat	1504 – 1801	IV
Alternative sequence	1284 – 1980	Missing. In isoform 4.

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 DEE13 THR-408; SER-1323; VAL-1327; SER-1754 AND PRO-1865;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q9UQD0: Variant p.Phe1754Ser