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UniProtKB/Swiss-Prot Q9H251: Variant p.Arg3Cys

Gene: CDH23
Variant information

Variant position:  3
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  Polymorphism
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 Cysteine (C) at position 3 (R3C, p.Arg3Cys).
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 medium size and polar (C)
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  -3
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

Other resources:  
Links to websites of interest for the variant.

Sequence information

Variant position:  3
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:   MG  R HVATSCHVAWLLVLISGCWG
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                         MGRHVATSCHVAWLLVLISGCWG

Mouse                         MRYSLVTCYAVLWLLMLVPGSWG

Rat                           MRHPPVTWCAMLWLLMLVSGSWG

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.

Signal peptide 1 – 23
Alternative sequence 1 – 2240 Missing. In isoform 7 and isoform 9.
Alternative sequence 1 – 24 MGRHVATSCHVAWLLVLISGCWGQ -> MRSWFQQDPMVGACTTGTRASHPK. In isoform 10 and isoform 11.

Literature citations

Mutation of CDH23, encoding a new member of the cadherin gene family, causes Usher syndrome type 1D.
Bolz H.; Von Brederlow B.; Ramirez A.; Bryda E.C.; Kutsche K.; Nothwang H.G.; Seeliger M.; Del C.-Salcedo Cabrera M.; Vila Caballero M.; Pelaez Molina O.; Gal A.; Kubisch C.;
Nat. Genet. 27:108-112(2001)
Cited for: NUCLEOTIDE SEQUENCE [MRNA]; FUNCTION; ALTERNATIVE SPLICING; TISSUE SPECIFICITY; VARIANTS USH1D MET-1281 DEL; HIS-1496 AND GLN-1746; VARIANTS CYS-3; ALA-490; ASN-496; THR-1222; CYS-1349; ASP-1351; THR-1575; SER-1671; ILE-1675; GLN-1804; SER-1999; LYS-2044; GLN-2358; LEU-2380; GLN-2588 AND LEU-3125;

The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment.
Clark H.F.; Gurney A.L.; Abaya E.; Baker K.; Baldwin D.T.; Brush J.; Chen J.; Chow B.; Chui C.; Crowley C.; Currell B.; Deuel B.; Dowd P.; Eaton D.; Foster J.S.; Grimaldi C.; Gu Q.; Hass P.E.; Heldens S.; Huang A.; Kim H.S.; Klimowski L.; Jin Y.; Johnson S.; Lee J.; Lewis L.; Liao D.; Mark M.R.; Robbie E.; Sanchez C.; Schoenfeld J.; Seshagiri S.; Simmons L.; Singh J.; Smith V.; Stinson J.; Vagts A.; Vandlen R.L.; Watanabe C.; Wieand D.; Woods K.; Xie M.-H.; Yansura D.G.; Yi S.; Yu G.; Yuan J.; Zhang M.; Zhang Z.; Goddard A.D.; Wood W.I.; Godowski P.J.; Gray A.M.;
Genome Res. 13:2265-2270(2003)

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;

Distribution and frequencies of CDH23 mutations in Japanese patients with non-syndromic hearing loss.
Wagatsuma M.; Kitoh R.; Suzuki H.; Fukuoka H.; Takumi Y.; Usami S.;
Clin. Genet. 72:339-344(2007)
Cited for: VARIANTS DFNB12 LEU-240; GLN-301; PRO-1716 AND TRP-2029; VARIANTS TRP-1417; ILE-1711; MET-1807; ASN-1876; ILE-1908; CYS-2171; PRO-2227; ILE-2283; PRO-2473; HIS-2489; VAL-2669; VAL-2801 AND CYS-3175;

Prevalence and clinical features of hearing loss patients with CDH23 mutations: a large cohort study.
Miyagawa M.; Nishio S.Y.; Usami S.;
PLoS ONE 7:E40366-E40366(2012)
Cited for: VARIANTS DFNB12 LEU-240; GLN-301; LYS-956; MET-1368; TRP-1417; ALA-1626; PRO-1716; TRP-2029; LYS-2287 AND LYS-2438; VARIANTS ASN-160; ILE-803; ILE-1415; GLY-1443; TRP-1588; ILE-1711; MET-1807; ASN-1876; ILE-1908; VAL-2130; CYS-2171; PRO-2227; PRO-2473; VAL-2669; VAL-2801; SER-2912 AND CYS-3175;

Disclaimer: Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. They are not in any way intended to be used as a substitute for professional medical advice, diagnostic, treatment or care.