UniProtKB/Swiss-Prot O75445: Variant p.Met3868Val

Usherin
Gene: USH2A
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Variant information Variant position:

3868 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant:

LB/B 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:

From Methionine (M) to Valine (V) at position 3868 (M3868V, p.Met3868Val). 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
Other resources:

Links to websites of interest for the variant.

Variant rs35309576 [ dbSNP | Ensembl ]

Sequence information Variant position:

3868 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:

QNGSCGVSSRMFVKTPEAAP M DLNSPVLKALGSACIEIKWM 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                         QNGSCGVSSRMFVKTPEAAPMDLNSPVLKALGSACIEIKWM

Mouse                         QNGGCGVSPGTYVRTLEAAPVGLMPPLLKALGSSCIEVKWM

Rat                           QEG-CGVSPGTHVRTLEAAPVGLMPPLLKALGSHCIEVKWT

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	3866 – 3963	Fibronectin type-III 24
Glycosylation	3849 – 3849	N-linked (GlcNAc...) asparagine
Alternative sequence	1547 – 5202	Missing. In isoform 2.

Literature citations
Identification of 14 novel mutations in the long isoform of USH2A in Spanish patients with Usher syndrome type II.
Aller E.; Jaijo T.; Beneyto M.; Najera C.; Oltra S.; Ayuso C.; Baiget M.; Carballo M.; Antinolo G.; Valverde D.; Moreno F.; Vilela C.; Collado D.; Perez-Garrigues H.; Navea A.; Millan J.M.;
J. Med. Genet. 43:E55-E55(2006)
Cited for: VARIANTS USH2A ASP-2249; HIS-2354; ARG-3251; ARG-3267; TYR-3472 INS; MET-3571; MET-4337 AND LEU-4818; VARIANTS ARG-713; PHE-1572; THR-1665; THR-2106; THR-2169; ALA-2238; GLN-2875; PHE-2886; SER-3099; ASN-3144; ALA-3411 AND VAL-3868; Spectrum of USH2A mutations in Scandinavian patients with Usher syndrome type II.
Dreyer B.; Brox V.; Tranebjaerg L.; Rosenberg T.; Sadeghi A.M.; Moeller C.; Nilssen O.;
Hum. Mutat. 29:451-451(2008)
Cited for: VARIANTS USH2A TYR-163; ARG-268; CYS-303; TRP-334; HIS-346; ILE-352; ARG-536; PHE-759; LEU-1212; 2265-GLU-TYR-2266 DELINS ASP; GLY-3124; THR-3504; ARG-3521; ILE-4054; ARG-4232; ILE-4439; CYS-4487; HIS-4592 AND ARG-4795; VARIANTS THR-125; MET-230; ASP-478; SER-595; VAL-644; ARG-713; PRO-1349; LYS-1486; PHE-1572; THR-1665; CYS-1757; ASN-2080; ASN-2086; THR-2106; THR-2169; ALA-2238; HIS-2292; ALA-2562; GLN-2875; PHE-2886; LYS-3088; SER-3099; ALA-3115; ASN-3144; ASP-3199; ALA-3411; LEU-3590; ILE-3835; VAL-3868; THR-3893; LEU-4433; VAL-4624 AND TRP-5031; Identification of 11 novel mutations in USH2A among Japanese patients with Usher syndrome type 2.
Nakanishi H.; Ohtsubo M.; Iwasaki S.; Hotta Y.; Mizuta K.; Mineta H.; Minoshima S.;
Clin. Genet. 76:383-391(2009)
Cited for: VARIANTS USH2A PRO-180; TYR-691; SER-1369 DEL; ARG-2752; GLY-3515; MET-3571 AND CYS-3747; VARIANTS LYS-1486; THR-2106; THR-2169; GLN-2875; PHE-2886; ALA-3115; ASP-3199; ALA-3411; ILE-3835; VAL-3868; ARG-4203; HIS-4493; VAL-4611; GLU-4838; GLN-4848 AND GLU-5026; Novel mutations in the long isoform of the USH2A gene in patients with Usher syndrome type II or non-syndromic retinitis pigmentosa.
McGee T.L.; Seyedahmadi B.J.; Sweeney M.O.; Dryja T.P.; Berson E.L.;
J. Med. Genet. 47:499-506(2010)
Cited for: VARIANTS USH2A THR-1836; GLY-1953; ASN-2080; ARG-2116; PHE-2128; TYR-2128; THR-2196; ALA-2238; PRO-2260; HIS-2292; ALA-2562; PRO-2639; SER-2786; 3263-ILE--GLY-3269 DEL; LYS-3448; ILE-3462; CYS-3479; SER-3529; MET-3844; LYS-3904; ARG-4174; ARG-4269; LEU-4433; 4445-GLU--SER-4449 DELINS ASP-LEU; HIS-4570; GLU-4662; ARG-4692; ARG-4763; ARG-4808; ARG-4817 AND MET-4918; VARIANTS RP39 SER-1978; TYR-2237; HIS-2573; LYS-2930; TYR-3358; TYR-3384; PRO-3606; SER-3618; HIS-3719; LYS-4094; HIS-4192; ASN-4248; VAL-4447; PRO-4840; MET-4844; HIS-5143; ILE-5145 AND GLY-5188; VARIANTS PHE-1572; THR-1665; THR-2169; GLN-2875; SER-3099; ASN-3144; ALA-3411; VAL-3868; ASP-4778; GLU-4838; GLN-4848 AND GLU-5026;

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.