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UniProtKB/Swiss-Prot P48735: Variant p.Arg172Met

Isocitrate dehydrogenase [NADP], mitochondrial
Gene: IDH2
Variant information

Variant position:  172
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 Arginine (R) to Methionine (M) at position 172 (R172M, p.Arg172Met).
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 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:  Glioma (GLM) [MIM:137800]: Gliomas are benign or malignant central nervous system neoplasms derived from glial cells. They comprise astrocytomas and glioblastoma multiforme that are derived from astrocytes, oligodendrogliomas derived from oligodendrocytes and ependymomas derived from ependymocytes. {ECO:0000269|PubMed:19228619, ECO:0000269|PubMed:25495392}. Note=The gene represented in this entry is involved in disease pathogenesis.
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 GLM; somatic mutation; reduces enzymatic activity.
Any additional useful information about the variant.

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



Sequence information

Variant position:  172
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  452
The length of the canonical sequence.

Location on the sequence:   IICKNIPRLVPGWTKPITIG  R HAHGDQYKATDFVADRAGTF
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                         IICKNIPRLVPGWTKPITIGRHAHGDQYKATDFVADRAGTF

Mouse                         IICKNIPRLVPGWTKPITIGRHAHGDQYKATDFVVDRAGTF

Rat                           IICKNIPRLVPGWTKPITIGRHAHGDQYKATDFVVDRAGMF

Bovine                        IICKNIPRLVPGWTKPITIGRHAHGDQYKATDFVVDRAGTF

Slime mold                    IICKNLPLLVPGWKKPIIIGRHAHGDQYKATDFVVNGPGKL

Baker's yeast                 IVIPRIPRLVPRWEKPIIIGRHAHGDQYKATDTLIPGPGSL

Fission yeast                 ILIKNIPKYIPGWTNPICIGRHAFGDQYKSTDLVASGPGKL

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 40 – 452 Isocitrate dehydrogenase [NADP], mitochondrial
Binding site 172 – 172 Substrate
Site 179 – 179 Critical for catalysis
Modified residue 155 – 155 N6-acetyllysine
Modified residue 166 – 166 N6-acetyllysine; alternate
Modified residue 166 – 166 N6-succinyllysine; alternate
Modified residue 180 – 180 N6-acetyllysine; alternate
Modified residue 180 – 180 N6-succinyllysine; alternate
Beta strand 169 – 173


Literature citations

IDH1 and IDH2 mutations in gliomas.
Yan H.; Parsons D.W.; Jin G.; McLendon R.; Rasheed B.A.; Yuan W.; Kos I.; Batinic-Haberle I.; Jones S.; Riggins G.J.; Friedman H.; Friedman A.; Reardon D.; Herndon J.; Kinzler K.W.; Velculescu V.E.; Vogelstein B.; Bigner D.D.;
N. Engl. J. Med. 360:765-773(2009)
Cited for: VARIANTS GLM GLY-172; LYS-172 AND MET-172; CHARACTERIZATION OF VARIANTS GLM GLY-172; LYS-172 AND MET-172;

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.