UniProtKB/SwissProt variant VAR

Variant information

Variant position:

934

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 Cysteine (C) to Tryptophan (W) at position 934 (C934W, p.Cys934Trp).

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 medium size and polar (C) to large size and aromatic (W)

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

Involvement in disease:

Retinitis pigmentosa 39 (RP39) [MIM:613809]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269|PubMed:10775529, ECO:0000269|PubMed:12112664, ECO:0000269|PubMed:12427073, ECO:0000269|PubMed:15325563, ECO:0000269|PubMed:16098008, ECO:0000269|PubMed:17296898, ECO:0000269|PubMed:20507924, ECO:0000269|PubMed:21686329, ECO:0000269|PubMed:22334370, ECO:0000269|PubMed:24227914}. 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 RP39.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs201527662 [ dbSNP | Ensembl ]

Sequence information

Variant position:

934

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

Protein sequence length:

5202

The length of the canonical sequence.

Location on the sequence:

DPISGQCLCVPNRQGRRCNQ C QPGFYISPGNATGCLPCSCH

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                         DPISGQCLCVPNRQGRRCNQCQPGFYISPGNATGCLPCSCH

Mouse                         DPISGQCLCLPHRQGRRCEQCQPGFYSSPSNATGCLPCLCH

Rat                           DPVSGQCLCLPHRQERRCVQCQPGCYSSPSNATGCLPCLCH

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	32 – 5202	Usherin
Topological domain	32 – 5042	Extracellular
Domain	900 – 950	Laminin EGF-like 8
Glycosylation	944 – 944	N-linked (GlcNAc...) asparagine
Disulfide bond	934 – 948

Literature citations

Seven novel mutations in the long isoform of the USH2A gene in Chinese families with nonsyndromic retinitis pigmentosa and Usher syndrome Type II.
Xu W.; Dai H.; Lu T.; Zhang X.; Dong B.; Li Y.;
Mol. Vis. 17:1537-1552(2011)
Cited for: VARIANT RP39 TRP-934; VARIANT USH2A CYS-2744; VARIANTS THR-125; LYS-1486; THR-2106; THR-2169 AND ALA-3411;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot O75445: Variant p.Cys934Trp