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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot O75445: Variant p.Thr4425Met

Usherin
Gene: USH2A
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Variant information Variant position: help 4425 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant: help LP/P [Disclaimer] The variants are classified into three categories: LP/P, LB/B and US.
  • LP/P: likely pathogenic or pathogenic.
  • LB/B: likely benign or benign.
  • US: uncertain significance

Residue change: help From Threonine (T) to Methionine (M) at position 4425 (T4425M, p.Thr4425Met). 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: help Change from medium size and polar (T) to medium size and hydrophobic (M) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score: help -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

Variant description: help In USH2A and RP39; associated with C-4115. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 4425 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 5202 The length of the canonical sequence.
Location on the sequence: help CLLVSHLQPYSQYNFSLVAC T NGGCTASVSKSAWTMEALPE 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: help The multiple alignment of the region surrounding the variant against various orthologous sequences.
Human                         CLLVSHLQPYSQYNFSLVACTNGGCTASVSKSAWTMEALPE

Mouse                         SFLLSNLQPSTQYNISLVACTSGGCTASRTTSAWTKEAPPE

Rat                           SLLLSNLRPFTQYNVSLVACTKGGCTASRVASAWTMEAPPE

Sequence annotation in neighborhood: help 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.
TypePositionsDescription
Chain 32 – 5202 Usherin
Topological domain 32 – 5042 Extracellular
Domain 4358 – 4445 Fibronectin type-III 29
Glycosylation 4418 – 4418 N-linked (GlcNAc...) asparagine
Alternative sequence 1547 – 5202 Missing. In isoform 2.



Literature citations
Identification of 51 novel exons of the Usher syndrome type 2A (USH2A) gene that encode multiple conserved functional domains and that are mutated in patients with Usher syndrome type II.
Van Wijk E.; Pennings R.J.E.; Te Brinke H.; Claassen A.; Yntema H.G.; Hoefsloot L.H.; Cremers F.P.M.; Cremers C.W.R.J.; Kremer H.;
Am. J. Hum. Genet. 74:738-744(2004)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1); TISSUE SPECIFICITY; VARIANTS USH2A CYS-4115 AND MET-4425; Molecular and in silico analyses of the full-length isoform of usherin identify new pathogenic alleles in Usher type II patients.
Baux D.; Larrieu L.; Blanchet C.; Hamel C.; Ben Salah S.; Vielle A.; Gilbert-Dussardier B.; Holder M.; Calvas P.; Philip N.; Edery P.; Bonneau D.; Claustres M.; Malcolm S.; Roux A.-F.;
Hum. Mutat. 28:781-789(2007)
Cited for: VARIANTS USH2A GLU-218; PHE-280; LYS-284; TRP-334; GLN-334; HIS-346; ILE-352; PHE-759; GLU-1833; SER-2795; ARG-3282; MET-3571; GLU-3895; MET-3976; CYS-4115 AND MET-4425; VARIANT PHE-1572; Next-generation genetic testing for retinitis pigmentosa.
Neveling K.; Collin R.W.; Gilissen C.; van Huet R.A.; Visser L.; Kwint M.P.; Gijsen S.J.; Zonneveld M.N.; Wieskamp N.; de Ligt J.; Siemiatkowska A.M.; Hoefsloot L.H.; Buckley M.F.; Kellner U.; Branham K.E.; den Hollander A.I.; Hoischen A.; Hoyng C.; Klevering B.J.; van den Born L.I.; Veltman J.A.; Cremers F.P.; Scheffer H.;
Hum. Mutat. 33:963-972(2012)
Cited for: VARIANTS RP39 PHE-419; PHE-759; CYS-1859; HIS-2460; TYR-3358; ARG-3669; CYS-4115; HIS-4192 AND MET-4425;
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.