UniProtKB/SwissProt variant VAR

Variant information

Variant position:

1333

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 Serine (S) to Tyrosine (Y) at position 1333 (S1333Y, p.Ser1333Tyr).

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 small size and polar (S) to large size and aromatic (Y)

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 LQT3 and SIDS.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs199473604 [ dbSNP | Ensembl ]

Sequence information

Variant position:

1333

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

Protein sequence length:

2016

The length of the canonical sequence.

Location on the sequence:

ALSRFEGMRVVVNALVGAIP S IMNVLLVCLIFWLIFSIMGV

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                         ALSRFEGMRVVVNALVGAIPSIMNVLLVCLIFWLIFSIMGV

Mouse                         ALSRFEGMRVVVNALVGAIPSIMNVLLVCLIFWLIFSIMGV

Rat                           ALSRFEGMRVVVNALVGAIPSIMNVLLVCLIFWLIFSIMGV

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 – 2016	Sodium channel protein type 5 subunit alpha
Topological domain	1317 – 1333	Cytoplasmic
Repeat	1187 – 1501	III
Helix	1332 – 1356

Literature citations

Spectrum of pathogenic mutations and associated polymorphisms in a cohort of 44 unrelated patients with long QT syndrome.
Millat G.; Chevalier P.; Restier-Miron L.; Da Costa A.; Bouvagnet P.; Kugener B.; Fayol L.; Gonzalez Armengod C.; Oddou B.; Chanavat V.; Froidefond E.; Perraudin R.; Rousson R.; Rodriguez-Lafrasse C.;
Clin. Genet. 70:214-227(2006)
Cited for: VARIANTS LQT3 VAL-9; GLN-225; ARG-639; TYR-1333; TRP-1609 AND ASN-1819;

Biophysical characterization of a new SCN5A mutation S1333Y in a SIDS infant linked to long QT syndrome.
Huang H.; Millat G.; Rodriguez-Lafrasse C.; Rousson R.; Kugener B.; Chevalier P.; Chahine M.;
FEBS Lett. 583:890-896(2009)
Cited for: VARIANT SIDS TYR-1333;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q14524: Variant p.Ser1333Tyr