UniProtKB/SwissProt variant VAR

Variant information

Variant position:

28

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

Type of variant:

Unclassified

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 Alanine (A) to Threonine (T) at position 28 (A28T, p.Ala28Thr).

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 hydrophobic (A) to medium size and polar (T)

The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:

0

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:

Timothy syndrome (TS) [MIM:601005]: Disorder characterized by multiorgan dysfunction including lethal arrhythmias, webbing of fingers and toes, congenital heart disease, immune deficiency, intermittent hypoglycemia, cognitive abnormalities and autism. {ECO:0000269|PubMed:15454078, ECO:0000269|PubMed:15863612, ECO:0000269|PubMed:24728418, ECO:0000269|PubMed:25260352, ECO:0000269|PubMed:25633834, ECO:0000269|PubMed:26253506}. 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 TS; only with cardiac manifestation; unknown pathological significance; increased channel activity.

Any additional useful information about the variant.

Sequence information

Variant position:

28

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

Protein sequence length:

2221

The length of the canonical sequence.

Location on the sequence:

MYIPEENHQGSNYGSPRPAH A NMNANAAAGLAPEHIPTPGA

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                         MYIPEENH--------------------------QGSNYGSPRPAHANMNANAAAGLAPEHIPTPGA

Mouse                         MYVPEENH--------------------------QGSNYGS

Rat                           PYQPLSSCLSEDTERKFKGKVVHEAQLNCFYISPGGSNYGS

Rabbit                        AYQPLPSHLSAETESTCKGTVVHEAQLNHFYISPGGSNYGS

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 – 2221	Voltage-dependent L-type calcium channel subunit alpha-1C
Topological domain	1 – 124	Cytoplasmic
Alternative sequence	1 – 29	Missing. In isoform 16, isoform 17, isoform 18 and isoform 28.

Literature citations

Gain-of-function mutations in the calcium channel CACNA1C (Cav1.2) cause non-syndromic long-QT but not Timothy syndrome.
Wemhoener K.; Friedrich C.; Stallmeyer B.; Coffey A.J.; Grace A.; Zumhagen S.; Seebohm G.; Ortiz-Bonnin B.; Rinne S.; Sachse F.B.; Schulze-Bahr E.; Decher N.;
J. Mol. Cell. Cardiol. 80:186-195(2015)
Cited for: VARIANTS TS THR-28; GLY-860; THR-1186; VAL-1186; MET-1523; LYS-1544; ILE-1800 MET-1953 AND ILE-2097; CHARACTERIZATION OF VARIANTS TS THR-28; GLY-860; THR-1186; VAL-1186; MET-1523 AND LYS-1544; VARIANTS ARG-37; THR-304; LYS-477; SER-817; THR-1365; ILE-1755; GLY-1765; ASN-1787; MET-1835; ALA-1843; LYS-1948; CYS-1972; GLN-2056; ASN-2081; GLY-2122 AND SER-2174;

UniProtKB/Swiss-Prot Q13936: Variant p.Ala28Thr