PM1 (supporting): p.Arg172 is the critical active site residue of IDH2, a well-characterized functional domain and statistically significant mutational hotspot where somatic missense mutations produce neomorphic enzyme activity converting α-ketoglutarate to 2-hydroxyglutarate. OncoKB classifies R172S as oncogenic, and PMID:24403254 confirmed R172S as a recurrent somatic mutation in 3/12 osteosarcoma patients.1 PM2 (supporting): NM_002168.3:c.516G>C is absent from gnomAD v2.1 and extremely rare in gnomAD v4.1 (AF = 6.19 × 10⁻⁷; 1/1,614,224 alleles; 0 homozygotes), far below the PM2 threshold of <0.1%.2 Two supporting criteria for pathogenicity (PM1_supporting + PM2_supporting) are met with no benign criteria met. Per the generic ACMG/AMP 2015 classification combination rules (PMID:25741868), this combination does not reach the threshold for Likely Pathogenic (minimum requires ≥1 moderate and ≥4 supporting, or ≥2 moderate and ≥2 supporting, or ≥1 strong and ≥2 supporting). The variant is classified as a Variant of Uncertain Significance (VUS).3
IDH2
Final classification
VUS
IDH2 c.516G>C · p.Arg172Ser
IDH2
PM1 (supporting): p.Arg172 is the critical active site residue of IDH2, a well-characterized functional domain and statistically significant mutational hotspot where somatic missense mutations produce neomorphic enzyme activity converting α-ketoglutarate to 2-hydroxyglutarate. OncoKB classifies R172S as oncogenic, and PMID:24403254 confirmed R172S as a recurrent somatic mutation in 3/12 osteosarcoma patients.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 supporting, PM2 supporting; combination = 2 supporting, which maps to VUS.
Classification rationale
PM1PM2
VUS
IDH2 c.516G>C
PM1 + PM2
→
VUS
Gene diagram
· NM_002168.3 · variants mapped to exon structure
IDH2
NM_002168.3
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 21 assessed
Applied · 2
Strength
Supporting
Moderate
Strong
Very strong
✓
PM1
supporting
Pathogenic
p.Arg172 is the critical active site residue of IDH2, analogous to IDH1 R132. This residue is a well-characterized functional domain where somatic missense mutations (R172K, R172M, R172W, R172G, R172S) produce neomorphic enzyme activity converting α-ketoglutarate to the oncometabolite 2-hydroxyglutarate. The residue is in a statistically significant mutational hotspot (cancerhotspots.org), OncoKB classifies R172S as oncogenic, and PMID:24403254 confirmed R172S as a recurrent somatic mutation in osteosarcoma (3/12 patients).
Residue R172 is the IDH2 active sitea critical functional domain.Statistically significant hotspot at cancerhotspots.org.
✓
PM2
supporting
Pathogenic
NM_002168.3:c.516G>C is absent from gnomAD v2.1 and extremely rare in gnomAD v4.1 (AF = 6.19 × 10⁻⁷; 1/1,614,224 alleles; 0 homozygotes). The highest subpopulation frequency is in Ashkenazi Jewish (AF = 3.38 × 10⁻⁵; 1/29,606 alleles). Allele frequency is far below the PM2 threshold of <0.1% in all populations, consistent with a rare variant.
gnomAD v2.1: absent.gnomAD v4.1: AF = 6.19e-07 (1/1614
Assessed · not applied
Pathogenic
PS1
No evidence that a different nucleotide change at c.516 leading to the same p.Arg172Ser amino acid substitution has been established as pathogenic.
PS2
No de novo data available for this variant.
PS3
No variant-specific functional assay demonstrating a deleterious effect for p.Arg172Ser (R172S) was identified.
PS4
No case-control data comparing variant prevalence in affected individuals versus controls.
PM5
No same-residue pathogenic comparator with a different amino acid change was identified in ClinVar.
PM6
No de novo data available.
PP1
No co-segregation data available.
PP2
IDH2 disease mechanism is predominantly gain-of-function/neomorphic via missense mutations at specific active site residues (R172, R140), not a gene where a low rate of benign missense variation and high missense constraint is the defining feature.
PP3
In silico predictions are mixed and do not provide multiple lines of computational support for a deleterious effect.
PP4
No patient phenotype or clinical data available for this variant.
PP5
ClinVar classification for this variant (VariationID 375985) is risk factor with review status 'no assertion criteria provided' (0-star).
Benign
BA1
Variant allele frequency in gnomAD v4.1 is 6.19 × 10⁻⁷ (0.00006%), far below the BA1 threshold of >1%.
BS1
Variant allele frequency in gnomAD v4.1 is 6.19 × 10⁻⁷ (0.00006%), far below the BS1 threshold of >0.3%.
BS2
No data on observation of this variant in healthy adults.
BS3
Well-established functional studies (PMID:20171147, PMID:23264629) demonstrate that IDH2 R172 mutations produce a neomorphic gain-of-function — converting α-ketoglutarate to the oncometabolite 2-hydroxyglutarate — rather than showing no damaging effect.
BS4
No segregation data available to demonstrate lack of co-segregation with disease.
BP1
IDH2 disease mechanism is predominantly gain-of-function/neomorphic via specific missense mutations at active site residues.
BP2
No data on observation in trans with a pathogenic variant.
BP4
Computational evidence does not support a benign interpretation.
BP5
No data indicating this variant is found in a case with an alternate molecular basis for disease.
BP6
ClinVar classification is risk factor, not benign.
N/A · 3
PVS1 · BP3 · BP7
Research & evidence
Population frequency
gnomAD v4.1
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 6.19493e-07; MAF= 0.00006%, 1/1614224 alleles, homozygotes = 0) and has highest observed frequency in the Ashkenazi Jewish population (AF= 3.37769e-05; MAF= 0.00338%, 1/29606 alleles, homozygotes = 0).
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
6.2e-05%
· 1 / 1,614,224
0 hom
0 hom
Ashkenazi Jewish 1 / 29,606 |
0.0034% |
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, African/African American, European (non-Finnish))
gnomAD v2.1
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
ClinVar
This variant has been reported in ClinVar but submission details could not be extracted. (ClinVarID = 375985)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.567. BayesDel score = 0.31655.
Functional
Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; curated oncogenicity label: Oncogenic.
COSMIC
Cancer hotspots
Somatic evidence
Hotspot
COSMIC
This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV57468772, n = 35 times).
Hotspots
This variant lies in a statistically significant hotspot.
Literature · how each cited paper was used
1papers cited
Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 4 further PMIDs triaged but not cited — see Sources & References.
Isocitrate dehydrogenase 2 mutation is a frequent event in osteosarcoma detected by a multi-specific monoclonal antibody MsMab-1.
Searched
c.516G>Cp.Arg172SerR172SIDH2-R172S
Found
Identified IDH2-R172S in 3 of 12 (25%) osteosarcoma patients by direct DNA sequencing (AGG>AGT). Developed and validated MsMab-1 multi-specific monoclonal antibody that detects IDH2-R172S by ELISA, Western blot, and immunohistochemistry. No morphological difference, growth difference, or cell migration difference was observed between IDH2-WT and IDH2-R172S transfected U-2 OS osteosarcoma cells at 2 days post-transfection. MsMab-1 stained 9 of 32 (28.1%) osteosarcomas on tissue microarray.
Variant
✓ Names this variant — characterised directly
Applied to
→PM1 supports · met
Why
Confirms R172S as a recurrent somatic mutation at the IDH2 active site residue. Supports PM1 domain-level application but functional data (no growth/migration difference) are insufficient for PS3.
This article describes the IDH2-R172S mutation in 3 of 12 (25%) osteosarcoma patients, which was detected by direct DNA sequencing. Furthermore, MsMab-1 stained nine of 32 (28.1%) osteosarcomas in a tissue microarray.
Location Introduction (describes R172S in osteosarcoma); Results, Mutational analysis section (3/12 patients, Fig 1); Results, Specificity of MsMab-1 section (ELISA Tables 3-4, Western blot Fig 2); Results, Immunohistochemical analysis (Fig 3); Discussion paragraphs 1-3. · Context Direct DNA sequencing of osteosarcoma FFPE tissue; ELISA with synthetic IDH2 peptides; Western blot using CHO and U-2 OS cells transfected with IDH2-R172S; immunohistochemistry on osteosarcoma tissue microarray · full text
Sources & reference links
Triaged references · 4 PMIDs not cited in assessment
20171147 ↗
The common feature of leukemia-associated IDH1 and IDH2 mutations is a neomorphic enzyme activity converting alpha-ketoglutarate to 2-hydroxyglutarate.
ONCOKB
20567020 ↗
IDH1 and IDH2 mutations are frequent genetic alterations in acute myeloid leukemia and confer adverse prognosis in cytogenetically normal acute myeloid leukemia with NPM1 mutation without FLT3 internal tandem duplication.
ONCOKB
23264629 ↗
The potential for isocitrate dehydrogenase mutations to produce 2-hydroxyglutarate depends on allele specificity and subcellular compartmentalization.
ONCOKB
28193778 ↗
AG-221, a First-in-Class Therapy Targeting Acute Myeloid Leukemia Harboring Oncogenic IDH2 Mutations.
ONCOKB