UniProtKB/SwissProt variant VAR

Variant information

Variant position:

7188

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

Type of variant:

Disease [Disclaimer]

The variants are classified into three categories: Disease, Polymorphism and Unclassified.

Disease: Variants implicated in disease according to literature reports.
Polymorphism: Variants not reported to be implicated in disease.
Unclassified: Variants with uncertain implication in disease according to literature reports. Evidence against or in favor of a pathogenic role is limited and/or conflicting.

Residue change:

From Cysteine (C) to Glycine (G) at position 7188 (C7188G, p.Cys7188Gly).

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 (C) to glycine (G)

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

Involvement in disease:

Lissencephaly 9 with complex brainstem malformation (LIS9) [MIM:618325]: A form of lissencephaly, a disorder of cortical development characterized by agyria or pachygyria and disorganization of the clear neuronal lamination of normal six-layered cortex. LIS9 is an autosomal dominant form clinically characterized by global developmental delay apparent since infancy, impaired intellectual development with poor or absent speech, and sometimes abnormal or involuntary movements. Brain imaging shows malformation of the brainstem, in addition to pachygyria and lissencephaly. {ECO:0000269|PubMed:30471716}. Note=The disease is caused by mutations affecting the gene represented in this entry.

The name and a short description of the disease associated with the variant. For more information about the disease, the user can refer to OMIM, following the link provided after the disease acronym.

Variant description:

In LIS9.

Any additional useful information about the variant.

Sequence information

Variant position:

7188

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

Protein sequence length:

7388

The length of the canonical sequence.

Location on the sequence:

MVRVGGGWMALDEFLVKNDP C RARGRTNIELREKFILPEGA

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                         MVRVGGGWMALDEFLVKNDPCRARGRTNIELREKFILPEGA

Mouse                         MVRVGGGWMALDEFLVKNDPCRARGRTNIELREKFILPEGA

Rat                           MVRVGGGWMALDEFLVKNDPCRARGRTNIELREKFILPEGA

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 – 7388	Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5
Domain	7117 – 7189	GAR
Region	7117 – 7388	C-terminal tail
Helix	7187 – 7192

Literature citations

MACF1 mutations encoding highly conserved zinc-binding residues of the GAR domain cause defects in neuronal migration and axon guidance.
Dobyns W.B.; Aldinger K.A.; Ishak G.E.; Mirzaa G.M.; Timms A.E.; Grout M.E.; Dremmen M.H.G.; Schot R.; Vandervore L.; van Slegtenhorst M.A.; Wilke M.; Kasteleijn E.; Lee A.S.; Barry B.J.; Chao K.R.; Szczaluba K.; Kobori J.; Hanson-Kahn A.; Bernstein J.A.; Carr L.; D'Arco F.; Miyana K.; Okazaki T.; Saito Y.; Sasaki M.; Das S.; Wheeler M.M.; Bamshad M.J.; Nickerson D.A.; Engle E.C.; Verheijen F.W.; Doherty D.; Mancini G.M.S.;
Am. J. Hum. Genet. 103:1009-1021(2018)
Cited for: INVOLVEMENT IN LIS9; VARIANTS LIS9 ARG-6664; PHE-7135; TYR-7186; GLY-7188 AND PHE-7188;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q9UPN3: Variant p.Cys7188Gly