UniProtKB/SwissProt variant VAR

Variant information

Variant position:

4439

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

Type of variant:

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:

From Threonine (T) to Isoleucine (I) at position 4439 (T4439I, p.Thr4439Ile).

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 (T) to medium size and hydrophobic (I)

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

Variant description:

In USH2A.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs753330544 [ dbSNP | Ensembl ]

Sequence information

Variant position:

4439

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:

FSLVACTNGGCTASVSKSAW T MEALPENMDSPTLQVTGSES

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                         FSLVACTNGGCTASVSKSAWTMEALPENMDSPTLQVTGSES

Mouse                         ISLVACTSGGCTASRTTSAWTKEAPPENMDPPTLHITGPES

Rat                           VSLVACTKGGCTASRVASAWTMEAPPEDMDPPTLHVMGPES

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	4358 – 4445	Fibronectin type-III 29
Alternative sequence	1547 – 5202	Missing. In isoform 2.

Literature citations

PDZD7 is a modifier of retinal disease and a contributor to digenic Usher syndrome.
Ebermann I.; Phillips J.B.; Liebau M.C.; Koenekoop R.K.; Schermer B.; Lopez I.; Schafer E.; Roux A.F.; Dafinger C.; Bernd A.; Zrenner E.; Claustres M.; Blanco B.; Nurnberg G.; Nurnberg P.; Ruland R.; Westerfield M.; Benzing T.; Bolz H.J.;
J. Clin. Invest. 120:1812-1823(2010)
Cited for: INTERACTION WITH PDZD7; VARIANT USH2A ILE-4439;

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; ASP-2265-ASP-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; CYS-4115; LEU-4433; VAL-4624 AND TRP-5031;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot O75445: Variant p.Thr4439Ile