UniProtKB/SwissProt variant VAR

Variant information

Variant position:

172

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

Type of variant:

LB/B

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 Serine (S) at position 172 (R172S, p.Arg172Ser).

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 small size and polar (S)

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:

Found in patients with cartilagenous tumors.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs1057519736 [ dbSNP | Ensembl ]

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.

Type	Positions	Description
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

Mutant IDH1 Dysregulates the Differentiation of Mesenchymal Stem Cells in Association with Gene-Specific Histone Modifications to Cartilage- and Bone-Related Genes.
Jin Y.; Elalaf H.; Watanabe M.; Tamaki S.; Hineno S.; Matsunaga K.; Woltjen K.; Kobayashi Y.; Nagata S.; Ikeya M.; Kato T. Jr.; Okamoto T.; Matsuda S.; Toguchida J.;
PLoS ONE 10:E0131998-E0131998(2015)
Cited for: VARIANTS SER-172; THR-172 AND TRP-172; INVOLVEMENT IN DISEASE;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P48735: Variant p.Arg172Ser