UniProtKB/SwissProt variant VAR

Variant information

Variant position:

242

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 Arginine (R) to Threonine (T) at position 242 (R242T, p.Arg242Thr).

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 (T)

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 AN1; the mutant homeodomain binds DNA as well as the wild-type homeodomain; the mutant does not modify the DNA-binding properties of the paired domain; the steady-state levels of the full-length mutant protein are higher than those of the wild-type one; a responsive promoter is activated to a higher extent by the mutant protein than by the wild-type protein; the presence of the mutation reduces sensitivity to trypsin digestion.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs121907927 [ dbSNP | Ensembl ]

Sequence information

Variant position:

242

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

Protein sequence length:

422

The length of the canonical sequence.

Location on the sequence:

IEALEKEFERTHYPDVFARE R LAAKIDLPEARIQVWFSNRR

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                         IEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRR

Mouse                         IEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRR

Rat                           IEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRR

Bovine                        IEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRR

Xenopus laevis                IEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRR

Zebrafish                     IEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRR

Drosophila                    IDSLEKEFERTHYPDVFARERLAGKIGLPEARIQVWFSNRR

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	1 – 422	Paired box protein Pax-6
DNA binding	210 – 269	Homeobox
Helix	237 – 246

Literature citations

National study of microphthalmia, anophthalmia, and coloboma (MAC) in Scotland: investigation of genetic aetiology.
Morrison D.; FitzPatrick D.; Hanson I.; Williamson K.; van Heyningen V.; Fleck B.; Jones I.; Chalmers J.; Campbell H.;
J. Med. Genet. 39:16-22(2002)
Cited for: VARIANT AN1 THR-242;

Molecular analysis of a human PAX6 homeobox mutant.
D'Elia A.V.; Puppin C.; Pellizzari L.; Pianta A.; Bregant E.; Lonigro R.; Tell G.; Fogolari F.; van Heyningen V.; Damante G.;
Eur. J. Hum. Genet. 14:744-751(2006)
Cited for: CHARACTERIZATION OF VARIANT AN1 THR-242;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P26367: Variant p.Arg242Thr