NM_000251.3:c.1571G>A

MSH2 · NP_000242.1:p.(Arg524His) · NM_000251.3

GRCh37: chr2:47693857 G>A · GRCh38: chr2:47466718 G>A

Gene: MSH2 Transcript: NM_000251.3

Final call

PM2 supporting PM5 supporting PP3 supporting BS3 strong

Variant details

Gene

MSH2

Transcript

NM_000251.3

Protein

NP_000242.1:p.(Arg524His)

gnomAD AF

1.3632217639593909e-05 (v4.1)

ClinVar

Uncertain significance

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

All three criteria assigned to the consequence/loss-of-function group are not applicable to NM_000251.3:c.1571G>A because the variant is a single-nucleotide missense substitution, NP_000242.1:p.(Arg524His), and not a null or length-altering allele.

The governing ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis EP specification for MSH2 v2.0 is the framework applied (framework_mode = vcep, official cspec v2.0); it explicitly sets PM4 and BP3 to 'Not Applicable' for MSH2 and confines PVS1 to nonsense/frameshift at or before codon 891, large single/multi-exon genomic alterations, IVS +/-1 or +/-2 splice variants with exon skipping/cryptic-site use, and mRNA-confirmed splice aberrations.

The MMR PVS1 decision tree contains only nonsense/frameshift, GT-AG 1,2 splice site, deletion, duplication and initiation-codon branches; a missense change reaches no PVS1 node, so no strength tier (very strong/strong/moderate/supporting) is assignable and strength is returned as null.

Splice-mediated null mechanisms were positively excluded rather than presumed: c.1571 lies internal to MSH2 exon 10 (exon 10 spans c.1511-c.1661), not at a splice-consensus or exon-terminal position, and SpliceAI max delta is 0.038, below the >=0.2 delta this VCEP uses for a predicted splice defect.

Neither governing VCEP file (PVS1_DecisionTree_MMR.pdf, VCEP-pilot-variants---MMR.xlsx) contains any variant-specific entry or pre-assigned code for c.1571G>A, p.Arg524His or p.R524H; this is documented in each criterion's gaps_remaining and reflects absent table rows rather than absent evidence.

Variant scope: NM_000251.3:c.1571G>A is an exonic missense substitution, NP_000242.1:p.(Arg524His), in MSH2 exon 10 (chr2:47466718 G>A, GRCh38).

Governing framework: ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel specification to the ACMG/AMP guidelines for MSH2 v2.0 (CSPEC doc 1577628936), which takes precedence over generic ACMG/AMP. It scopes PS1 and PM5 as applicable and declares PM1, PP2 and BP1 not applicable for MSH2.

PS1 not met: codon 524 is CGT, and the only single-nucleotide substitution in that codon encoding histidine (CAT) is the observed c.1571G>A; the other five substitutions give Ser/Gly/Cys/Pro/Leu and the third-base changes are synonymous Arg. PS1 requires a different nucleotide change encoding the same amino-acid change, so the criterion cannot be satisfied for this variant, and no VCEP-established Pathogenic p.Arg524His classification exists.

PM5 met at supporting: a different missense change at the same residue, NM_000251.3:c.1571G>C (p.Arg524Pro), is classified Likely pathogenic by expert-panel review in ClinVar (VCV000001759; InSiGHT submission, Guidelines v2.4, 'Abrogated function & 2 MSI-H tumours'), on protein-level grounds rather than as a splice defect, and the VCEP's PP3 precondition is satisfied for this variant (HCI prior 0.7525, PP3_Supporting band >0.68 and <=0.81). Because the comparator is Likely Pathogenic rather than Pathogenic, the specification directs PM5_Supporting.

PM1 not applicable: the MSH2 v2.0 specification states there are no recognised mutational hotspots usable for classification and that pathogenic variants are distributed across all MMR functional domains; the declared PM1 file (MMR-Functional-domains.pdf) contains only its figure caption with no extractable domain coordinates, vcep_materials.json's authoritative domain_tables key is empty for MSH2, and CancerHotspots returns no hotspot row for MSH2 R524.

PP2 and BP1 not applicable: the same specification removes both criteria for MSH2 (PP2: low benign-missense-rate premise does not apply; BP1: missense change in a gene where only loss of function causes disease), and BP1 additionally fails structurally because this variant is missense, not truncating.

Net contribution of this group: PM5_Supporting only; PS1 not met; PM1, PP2 and BP1 out of scope under the governing specification.

Variant scope: NM_000251.3:c.1571G>A is an exonic missense substitution, NP_000242.1:p.(Arg524His); only the two functional evidence codes PS3 and BS3 were adjudicated, and both were judged on protein-level MMR function.

Governing framework: ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel specification to the ACMG/AMP guidelines for MSH2 v2.0 (CSPEC). Its PS3 and BS3 rules are expressed as calibrated functional-assay bands (PS3: odds >18.7 Strong, >4.3 and <=18.7 Moderate, >2.08 and <=4.3 Supporting; BS3: odds <=0.05 Strong, >0.05 and <=0.48 Supporting), with secondary flowchart arms for MMR function defect (PS3_Moderate), complete loss of monoallelic expression (PS3_Moderate) and variant-specific proficient function (BS3_Supporting). The VCEP index declares two files as governing PS3/BS3, and both were searched in full.

Governing files: neither Functional-assay-SVI-documentation-MMR.xlsx nor Functional-assay-flowchart.pdf contains an entry for this variant, so no pre-assigned code exists. The documentation is still decisive as calibration data: it approves and calibrates the assay that does carry variant-level data for p.Arg524His - the Jia/Scott massively parallel MSH2 loss-of-function screen (PMID 33357406; 36550560), normal readout LOF <=0, abnormal readout LOF >0.4, 22 P/LP and 26 B/LB validation controls, proposed strength 'PS3, BS3'.

Decisive functional result: p.Arg524His scores LOF -0.72 in that VCEP-approved calibrated assay, i.e. a normal, non-loss-of-function readout (below the <=0 normal cutoff and the paper's own a priori cutoff of 0; well below the >0.4 abnormal cutoff). Neighbouring substitutions at the same codon do score as loss of function in the same assay (R524P +3.33, R524D +3.02), so the negative readout is informative for this residue rather than a gap in the map.

Net contribution of this group: BS3 is met (benign, variant-specific proficient function from a VCEP-calibrated assay; strong per the assay table's proposed-strength row, and at least supporting on the flowchart path), and PS3 is not met - no available functional readout for this variant is abnormal, so no pathogenic functional evidence is contributed. No functional evidence conflicts with the benign direction of this code. Where the strength sits between supporting and strong is a weighting question only; the code itself (BS3 met, PS3 not met) is stable under either reading and is flagged in warnings.

Governing framework is the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specification for MSH2 v2.0 (cspec), which is gene- and disease-specific and therefore overrides generic ACMG/AMP defaults for this group.

PS4: marked Not Applicable by the VCEP; tumor IHC/PP4 replaces proband counting for MMR genes.

PP4: not met - 0 documented CRC/endometrial MSI-H tumors (with MSI on a standard 5-10 marker panel or tumor genome and/or MSH2/MSH6-consistent protein loss) versus >=1 required for PP4_Supporting.

BP5: not met - 0 documented MSS / no-MMR-loss / inconsistent-IHC tumors versus >=2 (or >=4 for Strong) required by the VCEP's tumor-based BP5 rule.

PP5/BP6: neither triggered - ClinVar variation 182564 has zero expert-panel submissions and only 1-star single-submitter records with conflicting classifications; both criteria are additionally listed as Not Applicable by the VCEP.

Net effect of this group on the MSH2 c.1571G>A (p.R524H) classification: no pathogenic and no benign phenotype/prevalence assertions are contributed.

No tumor phenotype data (MSI/MSS, IHC, BRAF V600E, MLH1 methylation) and no proband cancer history exist in the case materials, which is the reason PP4 and BP5 are unevaluable beyond 'not met' rather than scorable.

Neither allelic criterion contributes evidence for MSH2 c.1571G>A (p.Arg524His). BP2 is Not Applicable in the governing InSiGHT MSH2 v2.0 specification, which directs use of BS2 instead, so the criterion cannot be applied to this gene.

PM3 is Applicable in the same specification but is points-based and requires a patient with CMMRD-consistent clinical features carrying a known pathogenic/likely pathogenic MSH2 variant in trans (1.0 point) or with unknown phase (0.5 points). This case contains no proband, no second MSH2 variant, no phase determination and no CMMRD-consistent clinical or tumour data, and no retrieved publication names the variant, so zero points accrue and PM3 is not met.

Variant scope: NM_000251.3:c.1571G>A is an exonic missense substitution, NP_000242.1:p.(Arg524His), so PP3/BP4 were evaluated on the protein-impact path and BP7 was treated as out of scope.

Governing framework: ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel specification to the ACMG/AMP guidelines for MSH2 v2.0 (CSPEC). For MSH2 missense variants this specification defines PP3 and BP4 by the HCI prior probability for pathogenicity (PP3_Moderate >0.81; PP3_Supporting >0.68 and <=0.81; BP4_Supporting <0.11), and the gene's VCEP index declares HCI-PRIORS-MSH2.txt as the governing supporting file for those two criteria.

Governing lookup result: the HCI-PRIORS table contains an exact row for c.1571G>A / p.R524H (exon 10, DBID MSH2_03461, reference PMID22949387) with prior probability 0.7525. That value sits in the supporting pathogenic band, so PP3 is met at Supporting strength and BP4 is not met.

Single-path discipline: the available SpliceAI result (max delta 0.038) was not used for PP3/BP4, because a missense substitution takes computational evidence from the protein-impact path only and a clean splice prediction is neither PP3 nor BP4 support for it. REVEL 0.918 was noted but not double-counted, since the gene-specific HCI-prior rule governs for MSH2 missense variants.

Population evidence for NM_000251.3:c.1571G>A (p.Arg524His): the variant is extremely rare but not absent — gnomAD v4.1 total AF 1.36322e-05 (22/1,613,824 alleles) with joint grpmax filtering AF 1.03e-05, and gnomAD v2.1 AF 1.06093e-05 (3/282,770 alleles).

PM2 is met at Supporting strength under the InSiGHT MSH2 v2.0 threshold (< 0.00002 in gnomAD v4); PM2_Supporting is the strength used throughout the VCEP's own pilot classifications.

Neither benign frequency code is met: BA1 (>= 0.001) and BS1 (>= 0.0001) both fail by ~97-fold and ~10-fold respectively on the VCEP-designated gnomAD v4 grpmax filtering AF of 1.03e-05, as do the gnomAD v2.1 result, the gnomAD v2.1/v3.1 non-cancer subsets and every gnomAD v4.1 subpopulation (maximum 3.12402e-05, European Finnish).

Zero homozygotes are reported in every dataset; for a dominant, high-penetrance mismatch-repair gene this is consistent with pathogenicity rather than benignity and provides no prevalence/penetrance argument for BA1/BS1.

gnomAD-Canada v1.0 (a non-gnomAD HostSeq cohort) gives a 2-allele European non-Finnish grpmax filtering AF of 1.7036e-04 that crosses the BS1 threshold; this is flagged for human review but does not satisfy BS1, which the VCEP defines on gnomAD v4.

BS2 is a patient-level co-occurrence/CMMRD rule rather than a frequency rule and is not assessable here: no phase, zygosity, parental-testing or second MSH2 variant information exists in this case.

Net effect on the combined classification: the population group contributes PM2_Supporting only; no stand-alone or strong benign population evidence is available.

Final determination: Rule24 in the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MSH2 Version 2.0 v2.0 criteria-combination framework is satisfied by the adjudicated criteria, so the variant is classified as Uncertain Significance - Conflicting Evidence.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	Not applicable: c.1571G>A is a missense substitution (p.Arg524His), not a null variant, and reaches no PVS1 node in the InSiGHT MSH2 v2.0 rules.	cspec vcep_pvs1_decisiontree_mmr vcep_hci_priors_msh2 spliceai
PS1	Not met	Not met: codon 524 is CGT and only the observed c.1571G>A (CGT>CAT) encodes His, so no alternate nucleotide change gives p.Arg524His.	cspec clinvar vcep_hci_priors_msh2 vcep_vcep_pilot_variants_mmr
PS2	Not assessed	Not assessed: no proband or parental-testing data exists, so no de novo points can be assigned against the >=0.5-point VCEP minimum.	cspec clinvar PMID:25741868
PS3	Not met	Not met: R524H scores LOF -0.72 in the VCEP-approved calibrated MSH2 screen, a normal readout below the >0.4 abnormal threshold.	vcep_functional_assay_svi_documentation_mmr vcep_functional_assay_flowchart
PS4	N/A	Not applicable: the InSiGHT MSH2 v2.0 specification states PS4 is not used for MMR variants, as tumor evidence is captured by PP4 instead.	cspec
PM1	N/A	Not applicable: the governing InSiGHT MSH2 v2.0 specification declares PM1 not applicable because MSH2 pathogenic variants are spread across all functional domains.	cspec vcep_mmr_functional_domains vcep_output
PM2	Met	Met at supporting: gnomAD v4.1 AF 1.36e-05 (grpmax filtering 1.03e-05) is below the VCEP PM2 threshold of < 0.00002.	cspec gnomad_v4 gnomad_v2 gnomad_canada
PM3	Not met	Not met: no MSH2 trans co-occurrence is documented, and CSPEC v2.0 PM3 needs at least 0.5 points from a CMMRD-consistent patient.	cspec vcep_table_for_cmmrd_diagnosis clinvar
PM4	N/A	Not applicable: the InSiGHT MSH2 v2.0 specification marks PM4 Not Applicable, and c.1571G>A is a missense substitution with no protein-length change.	cspec vcep_hci_priors_msh2 vcep_vcep_pilot_variants_mmr
PM5	Met	Met at supporting: same-residue p.Arg524Pro (c.1571G>C) is expert-panel Likely pathogenic, which with PP3 supporting (HCI prior 0.7525) gives PM5_Supporting.	cspec clinvar vcep_vcep_pilot_variants_mmr pm5_candidates hci_prior vcep_hci_priors_msh2
PM6	N/A	Not applicable: the MSH2 v2.0 VCEP marks PM6 not applicable, with assumed de novo evidence scored under PS2 instead.	cspec clinvar
PP1	Not assessed	Not assessed: no pedigree or co-segregation data exists, so the combined Bayes likelihood ratio required for PP1 (>=2.08) cannot be computed.	cspec clinvar PMID:27363726 PMID:11598466
PP2	N/A	Not applicable: the governing InSiGHT MSH2 v2.0 specification declares PP2 not applicable, as its low-benign-missense-rate premise does not apply to MSH2.	cspec
PP3	Met	Met at supporting: VCEP-declared HCI prior for MSH2 c.1571G>A p.Arg524His is 0.7525, inside the >0.68-0.81 PP3_Supporting band.	cspec hci_prior vcep_hci_priors_msh2
PP4	Not met	Not met: zero MSI-H colorectal/endometrial tumors documented versus the >=1 required for PP4_Supporting (0 >= 1? no).	cspec vcep_table_for_cmmrd_diagnosis vcep_vcep_pilot_variants_mmr
PP5	Not met	Not met: no expert-panel ClinVar classification exists for c.1571G>A (13 single-submitter records, 1 star, conflicting), and the VCEP lists PP5 as not for use.	cspec clinvar
BA1	Not met	Not met: gnomAD v4.1 grpmax filtering AF 1.03e-05 is ~97-fold below the VCEP BA1 stand-alone threshold of >= 0.001.	cspec gnomad_v4 gnomad_v2 gnomad_canada
BS1	Not met	Not met: gnomAD v4.1 grpmax filtering AF 1.03e-05 is ~10-fold below the VCEP BS1 threshold of >= 0.0001.	cspec gnomad_v4 gnomad_v2 gnomad_canada
BS2	Not assessed	Not assessed: no phase, zygosity or in-trans second MSH2 variant data exists for this variant, which the VCEP BS2 rule requires.	cspec vcep_vcep_pilot_variants_mmr vcep_table_for_cmmrd_diagnosis clinvar
BS3	Met	Met at strong: R524H scores LOF -0.72 (normal, threshold <=0) in the VCEP-approved calibrated MSH2 assay, whose proposed strength is BS3.	vcep_functional_assay_svi_documentation_mmr vcep_functional_assay_flowchart
BS4	Not assessed	Not assessed: no pedigree data exists, so the combined Bayes likelihood ratio of <=0.48 required for BS4 cannot be computed.	cspec clinvar PMID:27363726
BP1	N/A	Not applicable: the governing InSiGHT MSH2 v2.0 specification declares BP1 not applicable, and this variant is a missense change rather than a truncating variant.	cspec clinvar
BP2	N/A	Not applicable: InSiGHT MSH2 v2.0 sets BP2 to Not Applicable at all strengths and directs that BS2 be used instead.	cspec
BP3	N/A	Not applicable: the InSiGHT MSH2 v2.0 specification marks BP3 Not Applicable, and c.1571G>A is a single-nucleotide missense change, not an in-frame indel.	cspec vcep_hci_priors_msh2 vcep_vcep_pilot_variants_mmr
BP4	Not met	Not met: VCEP missense BP4 requires an HCI prior <0.11, but this variant's HCI prior is 0.7525.	cspec hci_prior vcep_hci_priors_msh2
BP5	Not met	Not met: zero MSS/no-MMR-loss or inconsistent-IHC tumors documented versus the >=2 needed for BP5_Supporting (0 >= 2? no).	cspec
BP6	Not met	Not met: no expert-panel Benign/Likely benign ClinVar classification for this variant (13 single-submitter records, 1 star, conflicting); the VCEP also lists BP6 as not for use.	cspec clinvar
BP7	N/A	Not applicable: c.1571G>A encodes the missense change p.Arg524His, outside BP7's synonymous/deep-intronic scope.	cspec

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