UniProtKB/SwissProt variant VAR

Variant information

Variant position:

1562

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 Valine (V) to Methionine (M) at position 1562 (V1562M, p.Val1562Met).

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:

Similar physico-chemical property. Both residues are medium size and hydrophobic.

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

BLOSUM score:

1

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:

Spinocerebellar ataxia 29 (SCA29) [MIM:117360]: An autosomal dominant, congenital spinocerebellar ataxia characterized by early motor delay, hypotonia and mild cognitive delay. Affected individuals develop a very slowly progressive or non-progressive gait and limb ataxia associated with cerebellar atrophy on brain imaging. Additional variable features include nystagmus, dysarthria, and tremor. {ECO:0000269|PubMed:22986007, ECO:0000269|PubMed:26770814}. 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 SCA29.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs397514535 [ dbSNP | Ensembl ]

Sequence information

Variant position:

1562

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

Protein sequence length:

2758

The length of the canonical sequence.

Location on the sequence:

VESCIRVLSDVAKSRAIAIP V DLDSQVNNLFLKSHSIVQKT

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                         VESCIRVLSDVAKSRAIAIPVDLDSQVNNLFLKSHSIVQKT

Mouse                         VESCIRVLSDVAKSRAIAIPVDLDSQVNNLFLKSHNIVQKT

Rat                           VESCIRVLSDVAKSRAIAIPVDLDSQVNNLFLKSHNIVQKT

Bovine                        VESCIRVLSDVAKSRAIAIPVDLDSQVNNLFLKSHNLVQKT

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 – 2758	Inositol 1,4,5-trisphosphate receptor type 1
Topological domain	1 – 2282	Cytoplasmic
Cross	1581 – 1581	Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)

Literature citations

Missense mutations in ITPR1 cause autosomal dominant congenital nonprogressive spinocerebellar ataxia.
Huang L.; Chardon J.W.; Carter M.T.; Friend K.L.; Dudding T.E.; Schwartzentruber J.; Zou R.; Schofield P.W.; Douglas S.; Bulman D.E.; Boycott K.M.;
Orphanet J. Rare Dis. 7:67-67(2012)
Cited for: VARIANTS SCA29 ASP-602 AND MET-1562;

ITPR1 gene p.Val1553Met mutation in Russian family with mild Spinocerebellar ataxia.
Shadrina M.I.; Shulskaya M.V.; Klyushnikov S.A.; Nikopensius T.; Nelis M.; Kivistik P.A.; Komar A.A.; Limborska S.A.; Illarioshkin S.N.; Slominsky P.A.;
Cerebellum Ataxias 3:2-2(2016)
Cited for: VARIANT SCA29 MET-1562;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q14643: Variant p.Val1562Met