UniProtKB/SwissProt variant VAR

Variant information

Variant position:

2833

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 Arginine (R) to Glycine (G) at position 2833 (R2833G, p.Arg2833Gly).

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 basic (R) to glycine (G)

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:

Usher syndrome 1D (USH1D) [MIM:601067]: USH is a genetically heterogeneous condition characterized by the association of retinitis pigmentosa with sensorineural deafness. Age at onset and differences in auditory and vestibular function distinguish Usher syndrome type 1 (USH1), Usher syndrome type 2 (USH2) and Usher syndrome type 3 (USH3). USH1 is characterized by profound congenital sensorineural deafness, absent vestibular function and prepubertal onset of progressive retinitis pigmentosa leading to blindness. {ECO:0000269|PubMed:11138009, ECO:0000269|PubMed:12075507, ECO:0000269|PubMed:15660226, ECO:0000269|PubMed:16679490, ECO:0000269|PubMed:18429043}. 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 USH1D; atypical.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs760130862 [ dbSNP | Ensembl ]

Sequence information

Variant position:

2833

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

Protein sequence length:

3354

The length of the canonical sequence.

Location on the sequence:

PPRGPSPTLDLVADLTLQEV R VVLEDINDQPPRFTKAEYTA

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                         PPRGPSPTLDLVADLTLQEVRVVLEDINDQPPRFTKAEYTA

Mouse                         PPRGPSPALDLLTDLTLQEVRVVLEDINDQPPRFTKAEYTA

Rat                           PPRGPSPALDLLTDLTLQEVRVVLEDINDQPPRFTKAEYTA

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	24 – 3354	Cadherin-23
Topological domain	24 – 3064	Extracellular
Domain	2729 – 2846	Cadherin 26
Alternative sequence	25 – 3127	Missing. In isoform 10 and isoform 11.
Alternative sequence	531 – 3354	Missing. In isoform 5.
Alternative sequence	1213 – 3354	Missing. In isoform 6.

Literature citations

CDH23 mutation and phenotype heterogeneity: a profile of 107 diverse families with Usher syndrome and nonsyndromic deafness.
Astuto L.M.; Bork J.M.; Weston M.D.; Askew J.W.; Fields R.R.; Orten D.J.; Ohliger S.J.; Riazuddin S.; Morell R.J.; Khan S.; Riazuddin S.; Kremer H.; van Hauwe P.; Moller C.G.; Cremers C.W.R.J.; Ayuso C.; Heckenlively J.R.; Rohrschneider K.; Spandau U.; Greenberg J.; Ramesar R.; Reardon W.; Bitoun P.; Millan J.; Legge R.; Friedman T.B.; Kimberling W.J.;
Am. J. Hum. Genet. 71:262-275(2002)
Cited for: VARIANTS DFNB12 GLY-124; SER-452; GLN-480; GLN-582; TRP-1060; ASP-1186; PRO-1586; LYS-1595; ASN-1846; TRP-2465 AND HIS-2608; VARIANTS USH1D PRO-484; ARG-1206; ALA-1209; GLY-2517; SER-2744; GLY-2833 AND HIS-3175; VARIANTS CYS-3; ALA-490; ASN-496; THR-1222; GLN-1437; MET-1620; ILE-1675; GLN-1804; ILE-1887; SER-1999; LYS-2044; GLN-2066; ILE-2283; GLN-2358; LEU-2380; GLN-2588; GLU-2933; ASN-2954 AND SER-2962;

UniProtKB/Swiss-Prot Q9H251: Variant p.Arg2833Gly