UniProtKB/SwissProt variant VAR

Variant information

Variant position:

53

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 53 (F53S, p.Phe53Ser).

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 LQT5; unknown pathological significance.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs199473355 [ dbSNP | Ensembl ]

Sequence information

Variant position:

53

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

Protein sequence length:

129

The length of the canonical sequence.

Location on the sequence:

RSPRSSDGKLEALYVLMVLG F FGFFTLGIMLSYIRSKKLEH

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                         RSPRSSDGKLEALYVLMVLGFFGFFTLGIMLSYIRSKKLEH

Mouse                         KSQLRDDSKLEALYILMVLGFFGFFTLGIMLSYIRSKKLEH

Rat                           RSQLRDDSKLEALYILMVLGFFGFFTLGIMLSYIRSKKLEH

Pig                           RSQLRDDSKLEALYILMVLGFFGFFTLGIMLSYIRSKKLEH

Rabbit                        RGPLGDDGQMEALYILMVLGFFGFFTLGIMLSYIRSQKLEH

Cat                           RSPGGDDSQLEALYILMVLGFFGFFTLGIMLSYIRSKKLEH

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 – 129	Potassium voltage-gated channel subfamily E member 1
Transmembrane	44 – 66	Helical
Mutagenesis	69 – 69	K -> H. Lowers current 2-fold and leads to faster deactivation of KCNQ1/KCNE1 channel.
Helix	46 – 71

Literature citations

Genetic testing in the long QT syndrome: development and validation of an efficient approach to genotyping in clinical practice.
Napolitano C.; Priori S.G.; Schwartz P.J.; Bloise R.; Ronchetti E.; Nastoli J.; Bottelli G.; Cerrone M.; Leonardi S.;
JAMA 294:2975-2980(2005)
Cited for: VARIANTS LQT5 HIS-36 AND SER-53;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P15382: Variant p.Phe53Ser