UniProtKB/SwissProt variant VAR

Variant information

Variant position:

125

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 Tyrosine (Y) to Aspartate (D) at position 125 (Y125D, p.Tyr125Asp).

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 aromatic (Y) to medium size and acidic (D)

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

Variant description:

In SBHX.

Any additional useful information about the variant.

Sequence information

Variant position:

125

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

Protein sequence length:

365

The length of the canonical sequence.

Location on the sequence:

YTIDGSRKIGSMDELEEGES Y VCSSDNFFKKVEYTKNVNPN

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                         YTIDGSRKIGSMDELEEGESYVCSS-------------DNFFKKVE-------------YTKNVNP--------N

Mouse                         YTIDGSRKIGSMDELEEGESYVCSS-------------DNF

Rat                           YTIDGSRKIGSMDELEEGESYVCSS-------------DNF

Slime mold                    YSMD-KKRIQDIKDFVDGHHYICCGAEPLNTEVIPKGIQDI

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 – 365	Neuronal migration protein doublecortin
Domain	53 – 139	Doublecortin 1
Modified residue	110 – 110	Phosphoserine; by PKC
Modified residue	115 – 115	Phosphoserine; by CK2, MARK1 and PKA
Beta strand	124 – 131

Literature citations

Doublecortin is the major gene causing X-linked subcortical laminar heterotopia (SCLH).
Des Portes V.; Francis F.; Pinard J.-M.; Desguerre I.; Moutard M.-L.; Snoeck I.; Meiners L.C.; Capron F.; Cusmai R.; Ricci S.; Motte J.; Echenne B.; Ponsot G.; Dulac O.; Chelly J.; Beldjord C.;
Hum. Mol. Genet. 7:1063-1070(1998)
Cited for: VARIANTS SBHX ASP-125; GLU-223 AND THR-250;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot O43602: Variant p.Tyr125Asp