IDH2 c.419G>A, p.Arg140Gln

Reasoning

NM_002168.4:c.419G>A encodes p.Arg140Gln. The exact p.Arg140Gln variant is documented in disease cohorts and in ClinVar variation 14716 with Pathogenic submissions from 7 clinical laboratories and Likely pathogenic submissions from 5 laboratories. Independent reports explicitly identify IDH2 c.419G>A/p.Arg140Gln in AML and D-2-hydroxyglutaric aciduria type II. This establishes the same amino-acid change as a previously established pathogenic variant; the paper evidence also documents the protein-level change rather than a splice-only effect.

Rule

Same amino acid change as a previously established pathogenic variant regardless of nucleotide change. ... Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level.

Evidence considered

• ClinVar variation 14716, NM_002168.4(IDH2):c.419G>A (p.Arg140Gln): Pathogenic from 7 clinical laboratories and Likely pathogenic from 5 clinical laboratories; review status criteria provided, multiple submitters, no conflicts.
• Ding et al. 2013, PMID:20567020: Table 1 and results identify IDH2 c.G419A causing p.R140Q in 48 adults with AML.
• Kranendijk et al. 2011, PMID:21889589: five patient-derived D-2-HGA type II cell lines carried heterozygous IDH2 c.[419 G>A], p.[Arg140Gln].
• Andersson et al. 2011, PMID:21647154: pediatric AML cases included IDH2 R140Q, with matched remission samples supporting somatic occurrence.

Sources

Reasoning

PS3 is met at strong strength. The exact IDH2 p.Arg140Gln variant encoded by NM_002168.4:c.419G>A was evaluated in independent functional systems. In recombinant-protein assays, R140Q homodimers had minimal normal isocitrate-to-alpha-ketoglutarate activity, wild-type:R140Q heterodimers showed a 60% reduction versus wild-type homodimers, and the variant acquired increased NADPH-dependent conversion of alpha-ketoglutarate to 2-hydroxyglutarate (PMID:21647154). In five patient-derived D-2-hydroxyglutaric aciduria type II lymphoblast lines, the heterozygous variant produced 14.4 nmol per hour per mg protein versus 1.8 in healthy controls and 1.9 in type I controls, approximately eightfold higher activity, with intracellular D-2-hydroxyglutarate approximately 140-fold higher than controls; the findings persisted after long-term culture and storage (PMID:21889589). These orthogonal biochemical and cell-based assays include control comparators, directly measure the relevant neomorphic enzyme activity and metabolite, and consistently support abnormal IDH2 function for the exact variant.

Rule

Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.

Evidence considered

• Andersson et al. 2011 (PMID:21647154), biochemical characterization of IDH2 R140Q: recombinant R140Q homodimers showed minimal isocitrate-to-alpha-ketoglutarate activity; wild-type:R140Q heterodimers had 60% lower activity than wild-type homodimers; R140Q showed increased NADPH-dependent alpha-ketoglutarate-to-2-hydroxyglutarate conversion.
• Kranendijk et al. 2011 (PMID:21889589), patient-derived lymphoblast assay: five heterozygous IDH2 R140Q cell lines had mean reaction activity of 14.4 nmol per hour per mg protein versus 1.8 in healthy controls and 1.9 in D-2-HGA type I controls, with approximately 140-fold higher intracellular D-2-hydroxyglutarate; the signal persisted after long-term culture and storage.

Sources

Reasoning

PM2 is met at supporting strength under the supplied generic SVI threshold. The variant is rare but present in population controls: gnomAD v4.1 reports AF=4.39968e-05 (71/1,613,752 alleles; homozygotes=0), gnomAD v2.1 reports AF=3.18194e-05 (9/282,846; homozygotes=0), and gnomAD-Canada reports AF=0.000108625 (2/18,412). The maximum overall AF is below the supplied PM2 supporting cutoff of 0.0001 in gnomAD v2.1 and v4.1; the slightly higher Canada value does not negate the qualifying large reference datasets, and no VCEP-specific source restriction applies.

Rule

Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.

Evidence considered

• gnomAD v4.1: AF=4.39968e-05 from 71/1,613,752 alleles, homozygotes=0; highest population AF=5.16992e-05.
• gnomAD v2.1: AF=3.18194e-05 from 9/282,846 alleles, homozygotes=0; highest population AF=1.00281e-04 and grpmax FAF=2.293e-05.
• gnomAD-Canada v1.0: AF=0.000108625 from 2/18,412 alleles, homozygotes=0; this is a supplementary population dataset and is slightly above the supplied 0.0001 PM2 cutoff.
• The supplied generic PM2 supporting threshold is <=0.0001; gnomAD v2.1 and v4.1 satisfy it, while the variant is not absent from controls.

Sources

Reasoning

The variant is a missense SNV, NM_002168.4:c.419G>A (p.Arg140Gln), so the governing rule requires the missense REVEL path only; SpliceAI and BayesDel are not used for PP3/BP4 in this situation. REVEL is 0.891, which meets the published generic PP3 moderate threshold of >= 0.773 but not the strong threshold of >= 0.932. Therefore PP3 is met at moderate strength. The REVEL calibration is from Pejaver et al. 2022 (PMID:36413997).

Rule

PP3: Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). ... PP3 (moderate): >= 0.773 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)

Evidence considered

• Variant consequence: missense_variant; NM_002168.4:c.419G>A produces NP_002159.2:p.(Arg140Gln).
• Local REVEL predictor lookup: REVEL score 0.891 for NM_002168.4:c.419G>A.
• Generic ClinGen SVI REVEL calibration: PP3 moderate >= 0.773 and PP3 strong >= 0.932; Pejaver et al. 2022, PMID:36413997.
• SpliceAI max delta 0.004 and BayesDel 0.44497 were not used because the missense-specific governing path is REVEL only and BayesDel has no generic ACMG-strength calibration.

Sources

Reasoning

The reviewed variant-specific literature reports affected cohorts carrying IDH2 p.Arg140Gln/R140Q, including 7/78 AML patients in PMID:20171147, 4 pediatric AML cases in PMID:21647154, and 48/805 adults with AML in PMID:20567020. These are affected-only series or case observations, not case-control comparisons with unaffected or population controls. PMID:20692206 reports a CALGB AML cohort of 358 patients and states that R140Q was not associated with outcome differences, but provides no affected-versus-unaffected carrier counts for this variant. The literature_pass PS4 leads (PMID:23169492, PMID:24049096, PMID:25326635, PMID:34131312) were checked against the available packet evidence; none supplies a qualifying case-control estimate. Therefore no OR/RR and 95% CI can be computed, and the ACMG/AMP PS4 threshold (>5.0 with a confidence interval excluding 1.0) is not met.

Rule

The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. ... Note 1: Relative risk (RR) or odds ratio (OR), as obtained from case-control studies, is >5.0 and the confidence interval around the estimate of RR or OR does not include 1.0.

Evidence considered

• PMID:20171147 reports IDH2 R140Q in 7/78 serial AML patients and all five IDH2 mutations in an initial 18-sample normal-karyotype AML set; this is an affected-only series.
• PMID:21647154 reports R140Q in 4 pediatric AML cases within 227 AML and 288 ALL samples; it does not provide an unaffected-control comparison for the exact variant.
• PMID:20567020 reports c.G419A/p.R140Q in 48 of 805 adults with AML; the cohort is affected-only and supplies no control carrier count.
• PMID:20692206 discusses a CALGB study of 358 AML patients and R140Q outcome, but not a case-control prevalence comparison.
• The literature_pass PS4 index listed PMID:23169492, PMID:24049096, PMID:25326635, and PMID:34131312; the available packet contained no verified case-control counts, OR/RR, or 95% CI from those papers.
• No OR/RR was computed because no affected-versus-control carrier counts or matched-ancestry control frequency paired with a case frequency were available.

Still missing

• No matched affected-versus-unaffected carrier counts or case-control OR/RR with 95% CI were identified.

Sources

Reasoning

The available exact-variant ClinVar submission describes the de novo finding as having parental status confirmed by trio analysis, rather than as assumed de novo without confirmation. Therefore the evidence does not match the PM6 definition.

Rule

Assumed de novo, but without confirmation of paternity and maternity.

Evidence considered

• ClinVar exact-variant submission SCV002768187 reports de novo status with "parental status confirmed" by trio analysis; this is inconsistent with the unconfirmed-parentage requirement for PM6.

Sources

Reasoning

ClinVar variation 14716 contains exact-variant Pathogenic and Likely pathogenic submissions, but the record documents zero expert-panel submissions and only clinical-laboratory, OMIM, or single-submitter assertions. The required exact-variant ClinVar expert-panel classification is absent, so PP5 is not met.

Rule

Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation.

Evidence considered

• ClinVar variation 14716 exactly matches NM_002168.4:c.419G>A (p.Arg140Gln), but reports 0 expert-panel submissions and only clinical-laboratory, OMIM, or single-submitter assertions.
• The exact-variant ClinVar record reports Pathogenic/Likely pathogenic classifications, but those classifications are not expert-panel assertions and therefore cannot trigger PP5 under the specified rule.

Sources

Reasoning

The variant does not meet BA1. Its highest reported frequency in the supplied population datasets is 0.001201923 (1/832 alleles in the gnomAD-Canada Ashkenazi Jewish subset), far below the generic stand-alone threshold of 0.05; gnomAD v4.1 reports 4.39968e-05 overall and 5.16992e-05 in its highest-frequency population. The variant is an SNV, so the indel-calling caveat is not applicable.

Rule

Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.

Evidence considered

• gnomAD v4.1: 71/1,613,752 alleles, AF=4.39968e-05, homozygotes=0; highest gnomAD population AF=5.16992e-05 in European non-Finnish individuals.
• gnomAD v2.1: 9/282,846 alleles, AF=3.18194e-05, homozygotes=0; highest gnomAD population AF=1.00281e-04 in East Asian individuals.
• gnomAD-Canada v1.0: overall AF=0.000108625 (2/18,412 alleles), with the highest reported subset AF=0.001201923 (1/832 alleles) in the Ashkenazi Jewish subset.
• The generic BA1 stand-alone threshold supplied for this case is >=0.05.

Sources

Reasoning

The available frequencies do not establish BS1. The highest supplied frequency is 0.001201923 in a small Ashkenazi Jewish gnomAD-Canada subset, while the highest gnomAD v4.1 population frequency is 5.16992e-05; both are below the generic 0.01 default. No disease prevalence, penetrance, allelic heterogeneity, or gene-specific maximum-credible-allele-frequency calculation is supplied to show that this frequency is greater than expected for the disorder, and the ancestry-limited elevation is therefore not sufficient by itself.

Rule

Allele frequency is greater than expected for the disorder.

Evidence considered

• gnomAD-Canada v1.0: highest supplied subset AF=0.001201923 (1/832 alleles) in Ashkenazi Jewish individuals; overall AF=0.000108625.
• gnomAD v4.1: overall AF=4.39968e-05 and highest gnomAD population AF=5.16992e-05 in European non-Finnish individuals; homozygotes=0.
• The generic BS1 default supplied for this case is >=0.01, but the governing definition requires frequency greater than expected for the disorder; no prevalence, penetrance, allelic-heterogeneity, or maximum-credible-frequency inputs are supplied.
• Whiffin et al. 2017 (PMID:28518168) is the named publication for maximum-credible-allele-frequency calibration, but no case-specific calculation can be performed from the supplied inputs.

Sources

Reasoning

BS3 is not met. The available exact-variant functional studies do not show no damaging effect on protein function or splicing; instead, they show reduced normal IDH2 enzymatic activity and a gain of neomorphic 2-hydroxyglutarate production in recombinant assays and patient-derived lymphoblasts. No well-established benign functional result was identified for NM_002168.4:c.419G>A (p.Arg140Gln).

Rule

Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.

Evidence considered

• Andersson et al. 2011 (PMID:21647154), recombinant IDH2 R140Q assays showed a 60% reduction in wild-type:R140Q heterodimer normal activity and increased 2-hydroxyglutarate-producing activity.
• Kranendijk et al. 2011 (PMID:21889589), five patient-derived IDH2 R140Q lymphoblast lines showed approximately eightfold higher 2-hydroxyglutarate-producing reaction activity than healthy controls and approximately 140-fold higher intracellular D-2-hydroxyglutarate.

Sources

Reasoning

The variant is a missense SNV, NM_002168.4:c.419G>A (p.Arg140Gln), so BP4 is evaluated through the missense REVEL path only; its SpliceAI result cannot substitute for a non-supportive REVEL result. REVEL is 0.891, which is above the generic BP4 supporting cutoff of <= 0.29 and therefore does not support no impact. The result is not in a BP4 gray zone that can be rescued by SpliceAI. Therefore BP4 is not met.

Rule

BP4: Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc) ... BP4 (supporting): <= 0.29 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)

Evidence considered

• Variant consequence: missense_variant; NM_002168.4:c.419G>A produces NP_002159.2:p.(Arg140Gln).
• Local REVEL predictor lookup: REVEL score 0.891 for NM_002168.4:c.419G>A.
• Generic ClinGen SVI REVEL calibration: BP4 supporting <= 0.29; the observed REVEL score is above this cutoff.
• SpliceAI max delta 0.004 was not used because BP4 for a missense variant uses the REVEL path only.

Sources

Reasoning

ClinVar variation 14716 exactly matches the variant but has zero expert-panel submissions and no exact-variant expert-panel Benign or Likely benign classification. The available record is Pathogenic/Likely pathogenic from non-expert submissions, which cannot trigger BP6.

Rule

Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.

Evidence considered

• ClinVar variation 14716 exactly matches NM_002168.4:c.419G>A (p.Arg140Gln), reports 0 expert-panel submissions, and summarizes Pathogenic/Likely pathogenic submissions.
• No exact-variant ClinVar expert-panel Benign or Likely benign assertion is present; ordinary laboratory submissions and aggregate labels were not used to trigger BP6.

Sources

Reasoning

A ClinVar submission for the exact variant reports that it was de novo in the proband with parental status confirmed by trio analysis. However, the available record does not document the patient's disease phenotype, absence of family history, or separate confirmation of both maternity and paternity, so the complete PS2 definition cannot be established.

Rule

De novo (both maternity and paternity confirmed) in a patient with the disease and no family history.

Evidence considered

• ClinVar exact-variant submission SCV002768187 reports: "this variant has been shown to be de novo in the proband (parental status confirmed) (by trio analysis)".
• ClinVar submission audit identifies SCV000807283 as having origin "de novo", but this is a submission-level annotation and does not itself provide the missing patient phenotype or family-history documentation.

Still missing

• Patient-level clinical phenotype consistent with the disease is not documented in the available evidence.
• No-family-history status is not documented.
• The record does not explicitly separate confirmation of maternity and paternity.
• Original trio report or laboratory report is needed to verify the parental testing details.

Sources

Reasoning

The variant is p.Arg140Gln and the bundle reports a statistically significant IDH2 R140 cancer hotspot. However, the generic PM1 rule requires a mutational hotspot or critical, well-established functional domain without benign variation, and the governing instructions restrict somatic-hotspot use to a VCEP that names the source or hotspot route. No VCEP covers IDH2, vcep_materials.json has no domain table, and the available materials do not provide an auditable critical-domain definition together with absence of benign variation. The criterion therefore cannot be adjudicated from the supplied evidence.

Rule

Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation.

Evidence considered

• The case evidence reports CancerHotspots query IDH2 R140 as a statistically significant hotspot, but the extraction is marked partially parsed and no source_registry key exists for that source.
• vcep_materials.json reports no VCEP, no CSPEC, and an empty domain_tables object for IDH2.
• PMID:20171147 describes structural modeling of the IDH2 active site and recurrent R140Q, but it does not supply a complete critical-domain boundary or benign-variation exclusion for generic PM1.

Still missing

• An allowed generic ACMG/AMP basis for the somatic hotspot or an auditable critical functional domain at residue 140.
• Evidence that the relevant hotspot/domain lacks benign variation.

Sources

Reasoning

The residue-140 literature contains alternate missense observations, including IDH2 R140W in pediatric AML and IDH2 R140G in D-2-hydroxyglutaric aciduria type II. The supplied evidence does not establish either alternate change as pathogenic under the governing PM5 rule, and pm5_candidates.json contains no validated same-residue pathogenic comparator. Therefore PM5 cannot be applied or excluded conclusively.

Rule

Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before. ... Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level.

Evidence considered

• Andersson et al. 2011, PMID:21647154: pediatric AML results report IDH2 R140Q (N=4) and R140W (N=1), but the extract does not establish R140W as pathogenic.
• Kranendijk et al. 2011, PMID:21889589: the abstract and extract mention IDH2 R140Q and R140G in D-2-HGA type II, but the supplied extract does not establish R140G as pathogenic.
• pm5_candidates.json: total_candidates_seen=0, same_residue_candidates=0, and no expert-panel or non-expert majority pathogenic comparator was validated.

Still missing

• A different missense variant at Arg140 with an independently established pathogenic classification.

Sources

Reasoning

The available evidence contains no documented affected relatives carrying the variant, no informative meioses, and no family segregation analysis. A de novo submission annotation is not evidence of co-segregation in multiple affected family members.

Rule

Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease.

Still missing

• Pedigree and phenotype data for affected relatives are unavailable.
• Variant testing results for affected and unaffected relatives are unavailable.
• The number of informative meioses is unavailable.

Reasoning

IDH2 is a missense-affected metabolic enzyme in the supplied disease and cancer reports, but the case bundle does not provide a gene-level analysis demonstrating both a low rate of benign missense variation and missense variants as a common disease mechanism. No applicable quantitative or curated gene-level evidence was supplied for this criterion.

Rule

Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.

Evidence considered

• The supplied literature documents recurrent IDH2 missense mutations, but it does not provide the required gene-wide benign-missense rate and disease-mechanism assessment.

Still missing

• Gene-level benign-missense constraint or equivalent evidence showing a low rate of benign missense variation.
• Gene-level evidence that missense variants are a common mechanism of IDH2 disease.

Reasoning

The case materials identify the variant and relevant IDH2-associated diseases, but do not provide a patient phenotype or family history for the case being adjudicated. Without case-specific clinical findings, phenotype specificity cannot be evaluated.

Rule

Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.

Still missing

• Case-specific phenotype and family-history data are required.

Reasoning

BS2 was not assessed. The variant is present in gnomAD, including 71 alleles in gnomAD v4.1 with no homozygotes, and the supplied age histogram includes heterozygote observations in older age bins; however, these aggregate population data do not identify a specific healthy adult individual, establish the individual's clinical status, or demonstrate that full penetrance is expected at an early age for the relevant disorder.

Rule

BS2

Evidence considered

• gnomAD v4.1 reports 71/1,613,752 alleles and homozygotes=0; the supplied age histogram shows heterozygote observations in older age bins, but no individual-level phenotype or health status is provided.
• gnomAD v2.1 reports 9/282,846 alleles and homozygotes=0; it likewise does not identify a specific healthy adult carrier or establish phenotype status.

Still missing

• A documented healthy adult carrying the variant is not identified.
• The relevant disorder's inheritance, early-age full-penetrance expectation, and penetrance are not established in the supplied evidence.

Sources

Reasoning

The available evidence contains no documented affected family members who tested negative for the variant and no family-based non-segregation analysis. Therefore lack of segregation cannot be assessed.

Rule

Lack of segregation in affected members of a family.

Still missing

• Pedigree and phenotype data for affected relatives are unavailable.
• Variant test results for affected relatives are unavailable.
• Potential phenocopies or more than one pathogenic variant in the family cannot be evaluated.

Reasoning

The supplied evidence does not establish that IDH2 disease is caused primarily by truncating variants. Instead, it documents recurrent missense variants, but that observation alone does not satisfy or refute the gene-level BP1 requirement. A comprehensive gene-level disease-variant mechanism review is missing.

Rule

Missense variant in a gene for which primarily truncating variants are known to cause disease.

Evidence considered

• The supplied case evidence reports recurrent IDH2 missense variants but provides no comprehensive gene-level variant-spectrum analysis establishing a primarily truncating disease mechanism.

Still missing

• Gene-level evidence showing that primarily truncating variants are known to cause IDH2 disease.

Reasoning

The case evidence does not establish that IDH2 p.Arg140Gln is observed in trans with a pathogenic variant in a fully penetrant dominant disorder, or in cis with a pathogenic variant in any inheritance pattern. The available affected-patient study documents the queried variant as heterozygous but provides no paired pathogenic variant and no cis/trans phase result. Consequently BP2 cannot be assessed from the available evidence.

Rule

BP2: Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern.

Evidence considered

• Kranendijk et al. reported heterozygous IDH2 p.Arg140Gln in five patient-derived type II lymphoblast lines, but did not report a second pathogenic variant or phase information relevant to BP2.

Still missing

• A paired pathogenic variant and validated cis/trans phase information are required to evaluate BP2.

Sources

Reasoning

The available evidence reports IDH2 p.Arg140Gln in disease cohorts and functional studies, but does not document this variant in a case with an alternate molecular basis for disease. No qualifying BP5 case is available for adjudication.

Rule

Variant found in a case with an alternate molecular basis for disease.

Still missing

• A case report or cohort record documenting an alternate molecular diagnosis in the same affected case is required.