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UniProtKB/Swiss-Prot P46976: Variant p.Thr83Met

Glycogenin-1
Gene: GYG1
Variant information

Variant position:  83
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 Threonine (T) to Methionine (M) at position 83 (T83M, p.Thr83Met).
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 (M)
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

Involvement in disease:  Glycogen storage disease 15 (GSD15) [MIM:613507]: A metabolic disorder resulting in muscle weakness, associated with the glycogen depletion in skeletal muscle, and cardiac arrhythmia, associated with the accumulation of abnormal storage material in the heart. The skeletal muscle shows a marked predominance of slow-twitch, oxidative muscle fibers and mitochondrial proliferation. {ECO:0000269|PubMed:20357282, ECO:0000269|PubMed:22160680}. 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 GSD15; loss of autoglucosylation.
Any additional useful information about the variant.

Other resources:  
Links to websites of interest for the variant.



Sequence information

Variant position:  83
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  350
The length of the canonical sequence.

Location on the sequence:   VLDSGDSAHLTLMKRPELGV  T LTKLHCWSLTQYSKCVFMDA
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                         VLDSGDSAHLTLMKRPELGVTLTKLHCWSLTQYSKCVFMDA

Mouse                         VLDSGDSAHLTLMKRPELGITLTKLHCWSLTQYSKCVFMDA

Rat                           VLDSGDSAHLTLMKRPELGITLTKLHCWSLTQYSKCVFMDA

Rabbit                        ILDSGDSAHLTLMKRPELGVTLTKLHCWSLTQYSKCVFMDA

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.

TypePositionsDescription
Chain 2 – 350 Glycogenin-1
Metal binding 102 – 102 Manganese
Binding site 77 – 77 Substrate
Site 86 – 86 Important for catalytic activity
Helix 80 – 91


Literature citations

Conformational plasticity of glycogenin and its maltosaccharide substrate during glycogen biogenesis.
Chaikuad A.; Froese D.S.; Berridge G.; von Delft F.; Oppermann U.; Yue W.W.;
Proc. Natl. Acad. Sci. U.S.A. 108:21028-21033(2011)
Cited for: X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS) OF 1-262 OF WILD-TYPE AND VARIANT GSD15 MET-83 IN COMPLEXES WITH MANGANESE; UDP AND UDP-ALPHA-D-GLUCOSE; FUNCTION; CATALYTIC ACTIVITY; SUBUNIT; PATHWAY; GLYCOSYLATION AT TYR-195; COFACTOR; MUTAGENESIS OF TYR-195; CHARACTERIZATION OF VARIANT GSD15 MET-83;

Glycogenin-1 deficiency and inactivated priming of glycogen synthesis.
Moslemi A.R.; Lindberg C.; Nilsson J.; Tajsharghi H.; Andersson B.; Oldfors A.;
N. Engl. J. Med. 362:1203-1210(2010)
Cited for: VARIANT GSD15 MET-83; CHARACTERIZATION OF VARIANT GSD15 MET-83;

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.