Five-step scale from benign to pathogenic. This variant is pathogenic. Select a step to read what it means.
This variantScenario
BenignPathogenic
Pathogenic.A pathogenic classification under the recorded framework.
In plain language
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.
About MSH2
MSH2 is a tumor suppressor gene that encodes a key protein in the DNA mismatch repair system, which finds and fixes errors made during DNA replication. The MSH2 protein pairs with MSH6 or MSH3 to form complexes that recognize mismatched base pairs and trigger their repair. Inherited mutations in MSH2 cause Lynch syndrome (hereditary nonpolyposis colorectal cancer), predisposing to colorectal, endometrial, ovarian, and other cancers, and biallelic mutations cause constitutional mismatch repair deficiency. Loss of MSH2 function increases the mutation rate and drives tumor development, particularly in colorectal and endometrial cancers, and mismatch-repair-deficient tumors respond particularly well to immune checkpoint inhibitor therapies.
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01The reasoning
How it was classified
The recorded framework is ClinGen MSH2 VCEP v2.0. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
Recorded applied criteria
The applied criteria and their strengths are shown as assessed under the stated framework.
Met, Very Strong: nonsense p.Gln419Ter creates a premature termination codon at codon 419, within the VCEP's <= codon 891 window and predicted to trigger nonsense-mediated decay.
PM2Supporting
PM2 · supporting
Met, Supporting: c.1255C>T is absent from gnomAD v4.1 (AF=0), below the 0.00002 (<1 in 50,000 alleles) threshold.
PP3Supporting
PP3 · supporting
Met, Supporting: SpliceAI max delta 0.36 exceeds the >=0.2 threshold (predicted donor gain at intron 7 +6) per the VCEP PP3 rule. Flagged for human review: this SpliceAI-based support is mechanistically redundant with PVS1 for a nonsense variant.
PP5Supporting
PP5 · supporting
Met, Supporting: the InSiGHT expert panel classified this exact variant as Pathogenic in ClinVar (3-star).
Benign criteria applied · 0
No benign criterion marked as applied in the recorded assessment.
Recorded classification: Pathogenic
Pathogenic: PVS1 Very Strong (nonsense PTC at codon 419) plus PM2, PP3, and PP5 supporting satisfies InSiGHT MSH2 VCEP combination Rule4. PP3 carries a human-review flag for mechanistic redundancy with PVS1, but PVS1 + PM2 + PP5 alone still satisfies Rule4.
02The sources
Evidence at a glance
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1
gnomAD v2.1
Population frequency
Not recorded
gnomAD v4.1 allele counts were not recorded for this variant.
ACMG/AMP criteria under ClinGen MSH2 VCEP v2.0, with the data and sources behind each one.
28 criteria with recorded statuses: 4 met · 4 not met · 8 not assessed · 12 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Consequence/LoF group: c.1255C>T is a canonical-transcript nonsense change, NM_000251.3(NP_000242.1):p.(Gln419Ter), with germline LoF established for MSH2.
The InSiGHT MSH2 VCEP v2.0 specification directly governs PVS1: a nonsense/frameshift variant introducing a PTC at codon <=891 meets PVS1 at Very Strong strength; codon 419 qualifies, and the PVS1_Moderate window (codons 892-934) does not apply.
NMD is predicted (PTC in internal exon 8 of 16, upstream of the last exon-exon junction); the truncation removes >55% of the protein including the ATPase domain; no NMD-escape, distal-region, or population-LoF-enrichment downgrade applies.
PM4 and BP3 are declared Not Applicable by the governing VCEP specification and are also inapplicable on the merits (nonsense substitution, not an in-frame indel or repeat-region variant).
PMID:24278394 independently documents the exact variant as a germline MSH2 nonsense allele (p.Gln419*) in an MSI-H Lynch syndrome proband with MSH2 IHC loss, consistent with the predicted LoF consequence.
Governing framework: ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel specification for MSH2 v2.0 (cspec doc 1577628936, framework_mode=vcep, precedence rank 1). Generic ACMG/AMP is used only as fallback; no fallback was needed because the VCEP specification governs every criterion in this group.
Variant: NM_000251.3:c.1255C>T is a nonsense substitution NP_000242.1:p.(Gln419Ter) (premature termination codon at codon 419, exon 7, internal position c.1077-1276). It is not a missense change, so all codon/residue/domain criteria are judged at the applicability level first.
PS1: not_applicable - VCEP PS1 is scoped to predicted missense substitutions encoding the same amino acid change via a different nucleotide change (or same non-canonical splice nucleotide as a confirmed Pathogenic splice variant); this is a nonsense substitution and no alternate-nucleotide or splice-nucleotide comparator is documented.
PM1: not_applicable - VCEP explicitly declares PM1 Not Applicable (no recognized mutational hot spots; pathogenic variants generalized over all MMR domains).
PM5: not_applicable - VCEP PM5 requires a missense change at a residue with a different missense change classified P/LP by the VCEP; the variant is nonsense and pm5_candidates.json reports 0 same-residue candidates.
PP2: not_applicable - VCEP explicitly declares PP2 Not Applicable.
BP1: not_applicable - VCEP explicitly declares BP1 Not Applicable; MSH2 missense variants are a common disease mechanism so BP1 would not apply generically either.
No criterion in this group is met; all five are framework-level or variant-level not applicable, so this group contributes no pathogenic or benign evidence weight.
Governing framework: ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MSH2 Version 2.0 (CSpec doc 1577628936); generic ACMG not used because the VCEP specification applies.
PS2: not_assessed - no de novo occurrence or parental testing data for c.1255C>T in any source (PMID:24278394 reports the variant in a family-history-positive proband only; ClinVar submissions carry no de novo assertion).
PM6: not_applicable - declared Not Applicable by the InSiGHT MSH2 VCEP v2.0; assumed de novo evidence is scored under the PS2 point system.
PP1: not_assessed - no segregation/meioses data; combined Bayes likelihood ratio cannot be computed.
BS4: not_assessed - no non-segregation data (no pedigrees with lack of co-segregation); combined Bayes likelihood ratio cannot be computed.
No criterion in this group was inferred from another source's final classification (e.g., ClinVar/InSiGHT 'Pathogenic' for variation 90584 was used only as a pointer to literature, never as segregation or de novo evidence).
Functional group (PS3, BS3) evaluated under the ClinGen InSiGHT MSH2 v2.0 VCEP specification; both criteria are formally 'Applicable' but no variant-specific functional assay evidence exists.
PS3 not_assessed: no calibrated functional assay (functional odds), no flowchart-qualifying MMR lab assay, and no monoallelic-expression (puromycin) assay data for c.1255C>T in the case bundle, VCEP assay documentation, or any available full text.
BS3 not_assessed: no calibrated functional odds <=0.48, no proficient-function lab assay, and no NMD-inhibited RNA assay for c.1255C>T; the BS3 mRNA-aberration clause targets synonymous/intronic variants, not this nonsense variant.
The nonsense change p.(Gln419Ter) is expected to ablate MSH2 function and is handled by PVS1 (PTC <= codon 891 per VCEP) in another group; absence of functional assay data here should not be read as absence of pathogenicity.
Tumor MSI-H with MSH2 IHC loss for this variant (PMID:24278394) is tumor-phenotype evidence per the VCEP (PP4/BP5 domain) and was not used to satisfy PS3/BS3.
Governing framework: ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specification for MSH2 v2.0 (cspec doc 1577628936); generic ACMG/AMP not used because a gene-specific VCEP specification exists.
Variant: MSH2 c.1255C>T (NM_000251.3) = p.(Gln419Ter), a nonsense/null variant; PVS1-relevant but that is outside this group's scope.
PS4: not applicable - the InSiGHT MSH2 VCEP v2.0 explicitly does not use PS4/proband counting for MMR variant classification (tumor IHC evidence is captured under PP4); no case-control study for this variant exists in the bundle.
PP4: not assessed - no carrier-level tumor MSI or MMR IHC data is retrievable in this case (full texts do not mention the variant; ClinVar-cited case papers lack full text).
PP5: met at supporting - exact-variant ClinVar 3-star expert-panel classification Pathogenic by InSiGHT (VCV000090584 / SCV000107095) triggers the global PP5/BP6 rule despite the VCEP 'not applicable' flag (override flagged in warnings).
BP5: not assessed - no carrier-level tumor data showing MSS, intact MMR IHC, or IHC loss inconsistent with MSH2 is retrievable in this case.
BP6: not met - the only exact-variant expert-panel classification is Pathogenic (not benign); aggregate laboratory labels cannot trigger BP6.
Allelic group adjudication for NM_000251.3:c.1255C>T (p.Gln419Ter), MSH2, under the governing ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis EP Specification for MSH2 v2.0 (framework_mode = vcep; cspec found).
PM3: Applicable under the VCEP but not met. The rule requires co-occurrence with a known P/LP variant in the same gene in a CMMRD-consistent patient (1.0 point in trans, 0.5 point phase unknown). The only variant-specific observation in the collected evidence (PMID:24278394 Table 1, patient 1515#3442) is a single heterozygous Lynch syndrome carrier with no second MSH2 variant, no phase data, and no CMMRD features; total points = 0, below the 0.5 Supporting threshold. No biallelic/trans evidence was found in any available full text or database record.
BP2: Not applicable by explicit VCEP determination ('BS2 is used instead.'); generic ACMG BP2 is not applied because a governing VCEP specification takes precedence.
Inheritance mode consideration: Lynch syndrome 1 (MSH2) is autosomal dominant; biallelic MSH2 causes the recessive mismatch repair cancer syndrome (CMMRD). PM3-type evidence would require a documented biallelic/trans configuration, which is absent for this variant in the collected sources.
The variant's ClinVar Pathogenic classification (InSiGHT expert panel, 3-star, plus 6 clinical laboratories) was not used to support or refute PM3/BP2 (no inference of criteria from final classifications).
Variant NM_000251.3:c.1255C>T = p.(Gln419Ter) is a nonsense variant in MSH2 exon 7 (c.1077-1276), 21 nt upstream of the exon 7 donor; InSiGHT MSH2 VCEP v2.0 governs (framework_mode=vcep).
PP3 met at Supporting: SpliceAI max delta 0.36 (DS_DG 0.36, predicted donor-gain at intron 7 +6) >= 0.2 per Walker et al. 2023 (PMID 37352859) as adopted by the VCEP PP3 rule; missense HCI-prior paths not applicable (variant not in HCI table; nonsense allele). Flagged for human review because the variant is a nonsense variant and the splice prediction is mechanistically redundant with PVS1.
BP4 not applicable: VCEP BP4 rule covers missense (HCI prior <0.11) and intronic/synonymous (SpliceAI <=0.1) variants only; a nonsense variant falls outside both paths, and SpliceAI predicts splice impact (0.36) rather than no impact.
BP7 not applicable: variant is nonsense, not synonymous or intronic.
BayesDel noAF score 0.66 was retrieved but not used for PP3/BP4 because no verified published threshold is available to this pipeline (per calibration policy); REVEL score not found; aGVGD absent.
No double-counting: the single SpliceAI prediction (0.36) was used for PP3 only; BP4 and BP7 were not met from any prediction.
Governing framework: ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications for MSH2 v2.0 (CSPEC doc 1577628936); framework_mode=vcep, precedence_rank=1. Population criteria adjudicated against this specification, not generic ACMG/AMP.
Variant: MSH2 NM_000251.3:c.1255C>T, p.(Gln419Ter), a nonsense substitution in exon 7 (PTC at codon 419).
BA1 not met: gnomAD v4.1 Grpmax FAF = 0 (variant absent), below the 0.001 (0.1%) stand-alone benign threshold.
BS1 not met: gnomAD v4.1 Grpmax FAF = 0 (variant absent), below the 0.0001 (0.01%) lower bound of the benign-strong frequency band.
PM2 met at Supporting: variant absent from gnomAD v4.1, satisfying the VCEP PM2 threshold of AF <0.00002 (1 in 50,000 alleles); corroborated by absence in gnomAD v2.1 and gnomAD-Canada v1.0.
BS2 not assessed: the VCEP BS2 rule requires patient-level, phase-confirmed in-trans co-occurrence with a known pathogenic MSH2 variant in an adult Lynch syndrome patient without CMMRD; no such data exist in the case bundle. Flagged for human review.
No founder-pathogenic-variant considerations apply: all VCEP BA1/BS1 rules are frequency-threshold-driven and the variant has zero population frequency in every queried dataset.
No criteria match.
Met · 4
PVS1Very strongMet, Very Strong: nonsense p.Gln419Ter creates a premature termination codon at codon 419, within the VCEP's <= codon 891 window and predicted to trigger nonsense-mediated decay.
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Reasoning
Governing framework is the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel (MSH2 VCEP) specification v2.0 (cspec, precedence rank 1), which takes precedence over generic ACMG/AMP. The variant NM_000251.3:c.1255C>T is a single-nucleotide substitution creating a premature termination codon at amino acid 419 (CAG>TAG), i.e. nonsense change NP_000242.1:p.(Gln419Ter) (consequence_class: nonsense per pvs1_variant_assessment; not a splice-site variant). The VCEP PVS1 rule states: 'Nonsense/frameshift variant introducing Premature Termination Codon (PTC) <= codon 891 in MSH2' = PVS1 Very Strong. Codon 419 is well within the <=891 window and outside the PVS1_Moderate window (codons 892-934, i.e. the distal/last-exon region). Germline loss of function is an established MSH2 disease mechanism (pvs1_gene_context: pvs1_gene_gate = 'eligible', supported by the CSPEC's own PVS1 guidance). NMD expectation: the PTC is located in an internal exon (exon 8 of 16, per the canonical NM_000251.3 transcript), >50 nt upstream of the final exon-exon junction, so nonsense-mediated decay is predicted and no NMD-escape downgrade applies; the truncation removes >55% of the 934-amino-acid protein including the ATPase domain, so no 'non-critical distal region' or population-LoF-enrichment downgrade (PMC6185798 generic considerations) applies. The variant is absent from gnomAD v2.1/v4.1, consistent with a null allele. PMID:24278394 independently reports the exact variant as a germline MSH2 nonsense change (p.Gln419*) in a Lynch syndrome proband with an MSI-H tumor and MSH2 immunohistochemistry loss, corroborating the loss-of-function consequence. All VCEP PVS1 Very Strong conditions are met; no downgrade triggers identified.
Rule
Nonsense/frameshift variant introducing Premature Termination Codon (PTC) <= codon 891 in MSH2 (InSiGHT MSH2 VCEP v2.0, PVS1 Very Strong). Refer to Appendix for details.
Evidence considered
InSiGHT MSH2 VCEP v2.0 PVS1 rule: nonsense/frameshift introducing PTC <= codon 891 in MSH2 qualifies for PVS1 Very Strong; PVS1_Moderate reserved for PTC at codons 892-934 (cspec)
Variant is a nonsense change c.1255C>T p.(Gln419Ter) at codon 419, within the <=891 Very Strong window (pvs1_variant_assessment)
Gene-level PVS1 eligibility: germline LoF established for MSH2, pvs1_gene_gate = 'eligible' (pvs1_gene_context)
NMD expectation: PTC in internal exon 8 of 16, far upstream of last exon-exon junction; truncation removes ATPase domain and >55% of protein - no NMD-escape or distal-region downgrade
PMID:24278394 reports the exact variant as germline MSH2 nonsense p.Gln419* in an MSI-H, MSH2-IHC-loss Lynch syndrome proband, corroborating LoF consequence
Still missing
No patient-derived mRNA/NMD assay was reviewed; the PVS1 Very Strong call rests on the VCEP sequence-based rule (nonsense PTC <= codon 891) and predicted NMD, which the VCEP rule does not require to be experimentally confirmed for this variant class.
The local PVS1_DecisionTree_MMR.pdf appendix content was not machine-extracted (visual PDF); the CSPEC rule text itself is explicit and sufficient for this call.
PM2SupportingMet, Supporting: c.1255C>T is absent from gnomAD v4.1 (AF=0), below the 0.00002 (<1 in 50,000 alleles) threshold.
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Reasoning
VCEP PM2 (Supporting) is met when the allele frequency is absent/extremely rare, <0.00002 (<1 in 50,000 alleles) in the gnomAD v4 dataset. MSH2 c.1255C>T p.(Gln419Ter) is ABSENT from gnomAD v4.1 (variant chr2-47429920-C-T, search_status=absent; AF=0), which is below the 0.00002 threshold. Absence is corroborated by gnomAD v2.1 (2-47657059-C-T, absent) and gnomAD-Canada v1.0 (AC=0, AN=0, AF=0.0, hom=0). PM2_Supporting met.
Rule
Absent/extremely rare allele frequency <0.00002 (<1 in 50,000 alleles) in gnomAD v4 dataset
Evidence considered
gnomAD v4.1 direct variant query (https://gnomad.broadinstitute.org/variant/chr2-47429920-C-T?dataset=gnomad_r4) returned search_status=absent; AF=0 < 0.00002. Also absent from gnomAD v2.1 (2-47657059-C-T) and gnomAD-Canada v1.0 (AC=0, AN=0, AF=0.0). Threshold from ClinGen InSiGHT MSH2 v2.0 CSPEC (doc 1577628936): PM2 = allele frequency <0.00002 (1 in 50,000 alleles) in gnomAD v4, applied at Supporting strength.
PP3SupportingMet, Supporting: SpliceAI max delta 0.36 exceeds the >=0.2 threshold (predicted donor gain at intron 7 +6) per the VCEP PP3 rule. Flagged for human review: this SpliceAI-based support is mechanistically redundant with PVS1 for a nonsense variant.
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Reasoning
Governing framework: InSiGHT MSH2 VCEP v2.0 (cspec doc 1577628936). PP3 rule paths: (1) missense with HCI prior >0.81 (Moderate) or >0.68-0.81 (Supporting) - NOT applicable: NM_000251.3:c.1255C>T is a nonsense variant p.(Gln419Ter), and the HCI prior lookup table (vcep_hci_priors_msh2) does not contain this allele (variant_not_in_hci_table; the table covers missense substitutions only - c.1255C>A and c.1255C>G are present but are different alleles). (2) 'Predicted splice defect for non-canonical splicing nucleotides using SpliceAI with delta score >= 0.2 as per Walker et al 2023' - MET: SpliceAI max delta score = 0.36 (DS_DG = 0.36, predicted donor-gain 27 nt downstream of c.1255, i.e. intron 7 +6; DS_AL 0.02, DS_DL 0.01, DS_AG 0.0), which exceeds the >=0.2 threshold. The variant lies 21 nt 5' of the exon 7 donor junction (exon 7 = c.1077-1276), inside SpliceAI's high-confidence +/-50 bp window, and the predicted cryptic donor is at a non-canonical splicing nucleotide (intronic +6); the masked-score lookup setting recommended by the VCEP was used. PP3 applied at Supporting strength per the VCEP rule. Human review requested because: the variant is a nonsense variant whose primary loss-of-function mechanism is already captured by PVS1 (PTC at codon 419, <= codon 891), so the SpliceAI-based PP3 is supportive but mechanistically redundant (predicted donor-gain would also yield frameshift/NMD); the VCEP prohibits PVS1+PP3 stacking only for IVS +/-1/2 variants, not for nonsense variants, but confirm intended stacking with the PVS1 group.
Rule
PP3_Supporting: 'Predicted splice defect for non-canonical splicing nucleotides using SpliceAI with delta score >= 0.2 as per Walker et al 2023.' (InSiGHT MSH2 VCEP v2.0, cspec doc 1577628936)
Evidence considered
SpliceAI max delta score 0.36 (DS_DG 0.36, donor-gain predicted 27 nt downstream, intron 7 +6) >= 0.2 PP3 threshold as per Walker et al. 2023 (PMID 37352859), ClinGen SVI Splicing Subgroup recommendations (Am J Hum Genet 110:1046-1067), the publication named in the InSiGHT MSH2 VCEP v2.0 PP3 rule (cspec doc 1577628936).
InSiGHT MSH2 VCEP v2.0 PP3_Supporting rule: 'Predicted splice defect for non-canonical splicing nucleotides using SpliceAI with delta score >= 0.2 as per Walker et al 2023'; variant is 21 nt 5' of the exon 7 donor (exon 7 = c.1077-1276) and the predicted cryptic donor is at intronic +6.
HCI prior lookup (vcep_hci_priors_msh2): c.1255C>T absent from the MSH2 HCI prior table (variant_not_in_hci_table; table is missense-only, and neighboring alleles c.1255C>A / c.1255C>G with priors 0.002 / 0.001 are different substitutions) - missense HCI paths of PP3 are not applicable.
BayesDel noAF score 0.66 (bayesdel registry entry) was retrieved but treated as insufficiently calibrated for PP3: no verified published PP3/BP4 threshold is available to this pipeline, so the score was not used.
Still missing
Scope judgment: whether an exonic position 21 nt 5' of the exon 7 donor qualifies as a 'non-canonical splicing nucleotide' under the VCEP PP3 rule was interpreted positively because the SpliceAI-predicted cryptic donor (0.36) sits at intronic +6 and the variant is within SpliceAI's reliable +/-50 bp window; a human reviewer should confirm this reading.
Redundancy with PVS1: for this nonsense variant (p.Gln419Ter), PP3 via SpliceAI does not add an independent pathogenic mechanism (predicted donor-gain is also LoF); confirm the VCEP intends PP3 to be applied on top of PVS1 for nonsense variants before relying on it in the final combination.
Walker et al. 2023 (PMID 37352859) full text was not available in this case's publication set; the >=0.2 threshold is taken from the InSiGHT MSH2 VCEP v2.0 rule text, which names 'Walker et al 2023' and lists PMID 37352859 in its reference section.
REVEL score not found for this variant; aGVGD absent from the evidence bundle - no additional independent in silico lines were available.
PP5SupportingMet, Supporting: the InSiGHT expert panel classified this exact variant as Pathogenic in ClinVar (3-star).
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Reasoning
Expert panel International Society for Gastrointestinal Hereditary Tumours (InSiGHT) classified as Pathogenic.
Rule
Global PP5/BP6 rule (ClinVar 3-star expert-panel exact-variant classification -> PP5 supporting); overrides InSiGHT MSH2 VCEP v2.0 PP5 applicability = 'Not applicable for this VCEP'.
Evidence considered
ClinVar VCV000090584: exact variant NM_000251.3(MSH2):c.1255C>T (p.Gln419Ter); review status 'reviewed by expert panel' (3 stars); expert panel Pathogenic by InSiGHT (SCV000107095, germline, Lynch Syndrome, 2013-09-05); 6 clinical-laboratory Pathogenic submissions (aggregate labels, not used as PP5 trigger).
Global PP5/BP6 rule: exact-variant ClinVar 3-star expert-panel classification Pathogenic/Likely pathogenic -> PP5 supporting, VCEP 'not applicable' flag ignored.
ClinVar expert panel classification
Still missing
The underlying InSiGHT classification evidence (e.g. PMID 24362816 content) is not retrievable as full text in this case; the PP5 supporting strength reflects the 3-star expert-panel classification itself, not independently re-derived evidence.
PP5 is applied via the global 3-star expert-panel override although the governing VCEP marks PP5 'not applicable'; confirm this convention is intended for VCEP-managed genes.
PM3Not met: zero PM3 points, below the 0.5-point supporting minimum; no in-trans second pathogenic MSH2 variant or biallelic observation exists.
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Reasoning
Governing framework is the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis EP Specification for MSH2 v2.0 (cspec, doc 1577628936), which marks PM3 as Applicable with a points-based rule: co-occurrence with a known pathogenic/likely pathogenic sequence variant in the same gene (MSH2) in a patient with clinical features consistent with CMMRD per Aronson et al 2022; P/LP in trans = 1.0 point, P/LP with phase unknown = 0.5 points, summed across cases (>=4 points Very Strong; 2-3.5 Strong; 1-1.5 Moderate; 0.5 Supporting). The only variant-specific observation in the collected evidence is a single heterozygous carrier (PMID:24278394 Table 1, patient 1515#3442: MSI-H, MSH2 IHC loss, MSH2 c.1255C>T p.(Gln419*)); no second P/LP MSH2 variant, no phase testing, no CMMRD-consistent proband, and no biallelic/homozygous/compound-heterozygous observation is reported anywhere in the case bundle or in any available full text (PMID:24362816, PMID:15849733, PMID:15528792, PMID:11257106, PMID:10946232, PMID:23391514 all searched; variant absent from their available text). The variant is absent from gnomAD v2.1/v4.1/Canada, so no population-based homozygous carriers are documented either. Total PM3 points = 0, below the 0.5-point Supporting threshold; PM3 is therefore not met. The ClinVar Pathogenic classification (InSiGHT expert panel, 6 laboratories) was not used as PM3 evidence (no inference from final classifications).
Rule
Applicable. Points-based: P/LP in trans = 1.0 point; P/LP phase unknown = 0.5 points, in patients with clinical features consistent with CMMRD per Aronson et al 2022. Summed points: >=4 = Very Strong; 2-3.5 = Strong; 1-1.5 = Moderate; 0.5 = Supporting. (InSiGHT MSH2 VCEP v2.0)
Evidence considered
cspec (InSiGHT MSH2 VCEP v2.0) PM3 rule: 'Co-occurrence with a known pathogenic/likely pathogenic sequence variant in the same gene in a patient with clinical features consistent with CMMRD as per Aronson et al 2022... Pathogenic/Likely Pathogenic in trans: 1.0 point; Pathogenic/Likely Pathogenic - phase unknown: 0.5 points. Sum all cases with the above evidence to determine the PM3 strength.' Strength thresholds: >=4 points Very Strong; 2-3.5 Strong; 1-1.5 Moderate; 0.5 Supporting.
PMID:24278394 (De Lellis et al 2013), Table 1: patient 1515#3442 (Amsterdam criteria II), MSI-H, MSH2 IHC loss, germline MSH2 c.1255C>T (p.Gln419*) - single heterozygous Lynch syndrome observation; no second MSH2 variant, no phase information, no altered allele-specific expression reported for this patient; contributes 0 PM3 points.
clinvar (Variation 90584): ClinVar submission records (8 submissions, 6 clinical laboratories, InSiGHT expert panel Pathogenic) contain no trans/zygosity or biallelic observations for this variant; record consulted only to confirm absence of phase data, not to infer any criterion.
PMID:24362816 (Thompson et al 2014, InSiGHT LOVD classification paper): available full text contains no mention of c.1255C>T/p.Gln419* and no biallelic observation; negative search result.
PMID:15849733 (Mangold et al 2005, German HNPCC cohort): available full text contains no mention of c.1255C>T/p.Gln419* and no trans/biallelic observation; negative search result.
Still missing
The InSiGHT LOVD database (the authoritative repository for MMR variant observations and the source behind the InSiGHT expert-panel classification) was not queryable within this case bundle; a biallelic/trans observation for c.1255C>T recorded only in LOVD would not be captured here and cannot be fully excluded.
No parental/offspring phase testing data for any c.1255C>T carrier was available in the collected sources.
No proband with clinical features consistent with CMMRD (Aronson et al 2022 scoring table) carrying c.1255C>T plus a second MSH2 variant was identified in the collected evidence.
BA1Not met: allele frequency is 0 (absent from gnomAD v4.1), far below the >=0.001 (0.1%) BA1 threshold.
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Reasoning
VCEP BA1 (Stand Alone) requires gnomAD v4 Grpmax filtering allele frequency >= 0.001 (0.1%) with the variant excluded as a founder pathogenic variant. The variant MSH2 c.1255C>T p.(Gln419Ter) is ABSENT from gnomAD v4.1 (variant chr2-47429920-C-T, dataset=gnomad_r4; search_status=absent; AF effectively 0), far below the 0.001 threshold. The founder-variant exclusion clause is moot because no population frequency exists to exclude. BA1 not met.
Rule
GnomAD v4 Grpmax filtering allele frequency ≥ 0.001 (0.1%) and variant is excluded as founder pathogenic variant.
Evidence considered
gnomAD v4.1 direct variant query (https://gnomad.broadinstitute.org/variant/chr2-47429920-C-T?dataset=gnomad_r4) returned search_status=absent with no allele counts/frequencies; AF=0. Threshold from ClinGen InSiGHT MSH2 v2.0 CSPEC (doc 1577628936): BA1 = gnomAD v4 Grpmax FAF >= 0.001.
BS1Not met: allele frequency is 0 (absent from gnomAD v4.1), below the 0.0001-0.001 BS1 range.
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Reasoning
VCEP BS1 (Strong) requires gnomAD v4 Grpmax filtering allele frequency >= 0.0001 and < 0.001 (0.01-0.1%) with the variant excluded as a founder pathogenic variant. The variant is ABSENT from gnomAD v4.1 (search_status=absent; AF effectively 0), below the lower bound of 0.0001. BS1 not met.
Rule
GnomAD v4 Grpmax filtering allele frequency ≥ 0.0001 and < 0.001 (0.01-0.1%) and variant is excluded as founder pathogenic variant.
Evidence considered
gnomAD v4.1 direct variant query (https://gnomad.broadinstitute.org/variant/chr2-47429920-C-T?dataset=gnomad_r4) returned search_status=absent with no allele counts/frequencies; AF=0. Threshold from ClinGen InSiGHT MSH2 v2.0 CSPEC (doc 1577628936): BS1 = gnomAD v4 Grpmax FAF >= 0.0001 and < 0.001.
BP6Not met: the only ClinVar expert-panel classification for this exact variant is Pathogenic (InSiGHT), the opposite direction BP6 requires.
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Reasoning
The governing InSiGHT MSH2 VCEP v2.0 declares BP6 'Not applicable for this VCEP' (ClinGen SVI VCEP Review Committee recommendation). Under the pipeline's global PP5/BP6 rule, BP6 may only be triggered by an exact-variant ClinVar expert-panel classification of Benign/Likely benign; ordinary laboratory submissions, aggregate ClinVar labels, and non-expert assertions must never trigger BP6. For this exact variant (VCV000090584), the only expert-panel classification is Pathogenic (InSiGHT, SCV000107095) - the opposite direction - and no benign/likely-benign expert-panel assertion exists for c.1255C>T. The six clinical-laboratory submissions all assert Pathogenic and are aggregate laboratory labels, which cannot support BP6 under any interpretation. BP6 is therefore not met.
Rule
Global PP5/BP6 rule: BP6 only on exact-variant ClinVar 3-star expert-panel Benign/Likely benign classification; InSiGHT MSH2 VCEP v2.0 BP6 = 'Not applicable for this VCEP'. No benign expert-panel assertion exists -> not met.
Evidence considered
InSiGHT MSH2 VCEP v2.0: BP6 applicability = 'Not applicable for this VCEP'.
ClinVar VCV000090584: exact-variant expert-panel classification is Pathogenic (InSiGHT, SCV000107095); no expert-panel benign/likely-benign classification exists; 6 clinical-laboratory Pathogenic submissions are aggregate laboratory labels, not expert-panel assertions.
PS2Not assessed: no de novo occurrence data exist; no parental testing or de novo assertion is reported for c.1255C>T.
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Reasoning
No de novo occurrence data exists for MSH2 c.1255C>T (p.Gln419Ter) in any available source. The only variant-specific publication (PMID:24278394, De Lellis et al. 2013, Table 1) reports the variant in proband 334#1170 from an Amsterdam-criteria HNPCC family (positive family history) with an MSI-H tumor and loss of MSH2 expression by IHC; no parental testing, no maternity/paternity confirmation, and no de novo assertion are reported anywhere in the paper, and the ClinVar record (variation 90584, 3-star expert panel) carries no de novo assertions in its submissions. Under the InSiGHT MSH2 VCEP v2.0 PS2 point system (0.5-2 points per proband depending on parental confirmation and tumor MMR status), zero points can be assigned. Evidence is insufficient rather than affirmatively refuting: parental testing could still yield PS2 points.
Rule
InSiGHT MSH2 VCEP v2.0 PS2: >=4 de novo points = Very Strong; 2-3.5 = Strong; 1-1.5 = Moderate; 0.5 = Supporting. Points: 2 per proband for de novo with both maternity and paternity confirmed + MMR-deficient LS spectrum tumor (MSI/IHC consistent, no MLH1 methylation); 1 per proband for confirmed de novo + LS spectrum tumor without tumor data; 0.5 per proband for assumed de novo with maternity and/or paternity unconfirmed.
Evidence considered
InSiGHT MSH2 VCEP v2.0 (CSpec doc 1577628936) PS2 de novo point system: no qualifying de novo data present.
PMID:24278394 Table 1 lists MSH2 c.1255C>T (p.Gln419*) for proband/family 334#1170 (generation I) with MSI-H tumor and MSH2 loss by IHC; the paper reports no parental testing or de novo status.
ClinVar record (variation 90584, reviewed by expert panel, 3-star) and its submission PMID trail reviewed; no submission asserts de novo occurrence for this variant.
Still missing
No parental (maternity/paternity) testing results are available for any proband carrying c.1255C>T; no de novo occurrence is reported in PMID:24278394, the ClinVar submissions, or any other source in the case bundle.
If parental testing is performed and both parents are confirmed non-carriers, PS2 points should be assigned per the InSiGHT MSH2 VCEP v2.0 point system (2 points for confirmed de novo with MMR-deficient LS spectrum tumor; 1 point without tumor data; 0.5 points if parentage unconfirmed).
PS3Not assessed: no calibrated functional assay result exists for c.1255C>T; tumor MSI/IHC evidence belongs to PP4, not PS3.
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Reasoning
Governing framework is the ClinGen InSiGHT MSH2 v2.0 specification (cspec doc 1577628936, framework_mode=vcep): PS3_Strong requires calibrated functional assays with functional odds for pathogenicity >18.7; PS3_Moderate requires functional odds >4.3 and <=18.7, OR an MMR function defect meeting the functional assay flowchart, OR monoallelic expression with complete loss of expression (<10% of wild-type in cDNA without puromycin); PS3_Supporting requires calibrated functional odds >2.08 and <=4.3. No calibrated functional assay result exists for MSH2 c.1255C>T (p.Gln419Ter) in any available source. The SVI-curated functional assay documentation (vcep_functional_assay_svi_documentation_mmr) catalogues validated assays (Drost cell-free repair assay PMID 30504929/31965077 with <23% abnormal threshold for MLH1/MSH2; Thompson complementation/expression/localization assays PMID 24362816; Rath calibrated MLH1 assay PMID 36054288 with OddsPath_Functional >2.08; Jia/Scott MSH2 saturation mutagenesis PMID 33357406/36550560 with LOF score >0.4; Bouvet MNNG survival assay; Morak cDNA/FLT assay with allelic loss <=10%) but contains no variant-level rows and none of these assays tested c.1255C>T. None of the seven available full texts reports a functional assay or mRNA/allelic-expression (puromycin) assay for this variant. PMID:24278394 (De Lellis 2013) lists this variant in Table 1 (patient 1515#3442) with tumor MSI-H and MSH2 protein loss, but tumor MSI/IHC is tumor-phenotype evidence that the InSiGHT VCEP assigns to PP4/BP5, not PS3, and no ASE/RNA assay was performed for this patient. OncoKB's curated biological-effect label 'Likely Loss-of-function' is a curation annotation, not a validated functional assay, and cannot supply calibrated functional odds. Therefore PS3 is not assessed due to absence of any variant-specific validated functional assay evidence; the null effect of this nonsense variant is properly captured by PVS1 (PTC <= codon 891 per VCEP), which is outside this group.
Functional-assay-SVI-documentation-MMR.xlsx: validated MMR assay catalogue (thresholds, P/LP validation control counts, approved strength) - no variant rows, c.1255C>T absent
Functional-assay-flowchart.pdf (image-based; logic captured in cspec instructionsToUse): generic framework for historic protein/mRNA lab assays; no assay result exists for this variant to route
PMID:24278394 (De Lellis 2013): Table 1 reports c.1255C>T with tumor MSI-H and MSH2 IHC loss (patient 1515#3442); ASE not performed for this patient; tumor phenotype is PP4/BP5 evidence per VCEP, not PS3
PMID:24362816 (Thompson 2014): consulted as InSiGHT classification/functional-assay framework source; variant not mentioned in full text; no variant-level functional result reported
Still missing
No calibrated functional assay (functional odds for pathogenicity) result for c.1255C>T in any available source; none of the SVI-documented validated MMR assays (Drost 30504929/31965077, Thompson 24362816, Rath 36054288, Jia 33357406/Scott 36550560, Bouvet, Morak) tested this variant
No mRNA/allelic-expression assay with NMD inhibition (puromycin) performed for this variant; De Lellis 2013 ASE analysis (22 probands) did not include patient 1515 carrying c.1255C>T
Only variant-specific functional-adjacent datum is tumor MSI-H/MSH2-IHC loss (PMID:24278394), which the InSiGHT VCEP routes to PP4/BP5 and cannot substitute for a functional assay
PP1Not assessed: no co-segregation data exist; the only report describes a single proband with no meioses or segregation analysis.
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Reasoning
No co-segregation data exist for MSH2 c.1255C>T. The only variant-specific publication (PMID:24278394) reports the variant in a single proband (334#1170, family 1170) and provides no meioses, no pedigree co-segregation counts, and no segregation analysis; no other source in the case bundle reports segregation data. A combined Bayes likelihood ratio (COOL v3) therefore cannot be computed, so PP1 cannot be met at any strength. Note the variant is classified Pathogenic by the InSiGHT expert panel, but per instructions a final classification from another source was not used to infer segregation evidence.
Rule
InSiGHT MSH2 VCEP v2.0 PP1: combined Bayes likelihood ratio >18.7 in >=2 families = Strong; >4.3 and <=18.7 = Moderate; >2.08 and <=4.3 = Supporting (COOL v3; Belman et al. 2020, PMID 32773770).
Evidence considered
InSiGHT MSH2 VCEP v2.0 (CSpec doc 1577628936) PP1 rule: co-segregation with disease in pedigree(s) with combined Bayes likelihood ratio >18.7 in >=2 families = Strong; >4.3 and <=18.7 = Moderate; >2.08 and <=4.3 = Supporting; thresholds per Belman et al. 2020 (PMID 32773770), cited in the VCEP specification reference list.
PMID:24278394 Table 1: variant reported in proband 334#1170 of family 1170 (Amsterdam-criteria HNPCC cohort, generation I); the paper contains no segregation/meioses data for this variant.
Still missing
No segregation analysis available for c.1255C>T: no meioses, no affected/unaffected relative testing results, and no pedigree data permitting a combined Bayes likelihood ratio (COOL v3, per InSiGHT MSH2 VCEP v2.0 PP1 instructionsToUse).
Segregation testing in affected relatives across families would allow PP1 strength assignment (Supporting LR >2.08 to <=4.3; Moderate >4.3 to <=18.7; Strong >18.7 in >=2 families).
PP4Not assessed: no carrier-level tumor phenotype data (MSI or MMR IHC) were available for c.1255C>T.
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Reasoning
Under the governing InSiGHT MSH2 VCEP v2.0, PP4 is applicable and requires CRC/endometrial MSI-H tumors (standard 5-10 marker panel or tumor genome) and/or loss of MMR protein expression consistent with the variant location (MSH2/MSH6 loss for an MSH2 variant): 1 tumor = Supporting, 2 independent tumors = Moderate, >=3 independent tumors in >=2 families = Strong. No variant-specific tumor phenotype data (MSI status or MMR IHC) for carriers of c.1255C>T is present in the case evidence bundle. Full texts downloaded for this case (e.g. PMID 15849733, Mangold 2005, German HNPCC cohort with MSI tumor data) do not mention c.1255C>T / p.Gln419Ter; full-text files for PMID 24278394 and PMID 24362816 are empty (0 bytes). ClinVar-cited case-level papers (PMID 8581513 Miyaki; PMID 28874130 Rossi; PMID 31114938 Ben Sghaier; PMID 31588121 Ikenoue) are not in the source registry and have no full text in this case. The InSiGHT expert-panel submission (SCV000107095) exposes no evidence signals. With no retrievable tumor MSI/IHC evidence, PP4 cannot be assessed and is reported as not_assessed pending retrieval of carrier-level tumor phenotype data.
Rule
InSiGHT MSH2 VCEP v2.0 PP4: 1 MSI-H CRC/endometrial tumor and/or consistent MMR protein loss = Supporting; 2 independent tumors = Moderate; >=3 independent tumors in >=2 families = Strong.
Evidence considered
InSiGHT MSH2 VCEP v2.0 PP4 rule (Supporting: 1 CRC/endometrial MSI-H tumor and/or loss of MMR protein expression consistent with variant location; Moderate: 2 independent tumors; Strong: >=3 independent tumors in >=2 families) - used to define what evidence would satisfy PP4.
Searched all locally available full texts (PMID 15849733, 23391514, 15528792, 11257106, 10946232) for the exact variant (c.1255C>T, 1255, Gln419, Q419); no matches.
No tumor MSI status or MMR IHC data for c.1255C>T carriers is available in the case evidence bundle (needed for PP4 Supporting/Moderate/Strong tiers).
ClinVar-cited case papers with potential phenotype data (PMID 8581513, 28874130, 31114938, 31588121) are not in the source registry and have no full text in this case.
Local full-text files for PMID 24278394 and PMID 24362816 are empty (0 bytes) despite source registry marking them full_text_available.
BS2Not assessed: no in-trans co-occurrence or phase-confirmation data exist for any carrier of c.1255C>T.
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Reasoning
VCEP BS2 (Strong) is a patient-level co-occurrence criterion: it requires the variant to co-occur IN TRANS with a known pathogenic sequence variant in the same gene in a patient with colorectal cancer after age 45 (or another LS cancer above the median age of onset), with no previous/current evidence of CMMRD manifestations (Aronson et al 2022 scoring table), and with phase confirmed by testing parents or offspring. The case evidence bundle contains no proband phenotype, no co-occurrence observations, and no phase-confirmation data (no ClinVar submission text or literature record documents an in-trans second MSH2 pathogenic variant for a carrier of c.1255C>T). Therefore BS2 cannot be assessed from available evidence and is flagged for human review if patient-level data exist.
Rule
Co-occurrence in trans with a known pathogenic sequence variant in the same gene in a patient with colorectal cancer after age 45 (or other LS cancer above the median age of onset for that cancer in LS), and who has no previous or current evidence of clinical manifestations of CMMRD as per Aronson et al 2022 (Refer to 'Table for CMMRD diagnosis.pdf'). Confirmation of phase requires testing of parents or offspring.
Evidence considered
No data source in the case bundle contains co-occurrence/phase information; only the governing VCEP rule (ClinGen InSiGHT MSH2 v2.0 CSPEC doc 1577628936) defines what would be required for BS2.
Still missing
No patient-level co-occurrence data: absence of any documented phase-confirmed in-trans co-occurrence of c.1255C>T with a known pathogenic MSH2 variant in an adult Lynch syndrome patient without CMMRD. Requires proband genotype/phenotype records (cancer type and age at diagnosis, CMMRD exclusion per Aronson et al 2022, and parental/offspring phase testing) to adjudicate.
BS3Not assessed: no assay demonstrates proficient function for c.1255C>T, and the mRNA-aberration clause does not apply to nonsense variants.
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Reasoning
Under the ClinGen InSiGHT MSH2 v2.0 specification (cspec doc 1577628936), BS3_Strong requires calibrated functional assays with functional odds for pathogenicity <=0.05, OR for synonymous/intronic variants no associated mRNA aberration (splicing or allelic imbalance) determined with nonsense-mediated decay inhibition; BS3_Supporting requires calibrated functional odds >0.05 and <=0.48, OR variant-specific proficient function in protein and mRNA-based lab assays per the MMR functional assay flowchart. No calibrated functional assay result showing proficient function exists for c.1255C>T, and no protein/mRNA-based lab assay (e.g., cDNA/FLT analysis with puromycin) was performed for this variant in any available source (case bundle, VCEP assay documentation, or the seven available full texts). The BS3 mRNA-aberration clause is restricted to synonymous and intronic variants; this variant is a nonsense change (p.Gln419Ter), so that clause is inapplicable regardless. The only variant-specific datum, tumor MSI-H with MSH2 IHC loss in patient 1515#3442 (PMID:24278394), points away from proficient function and is tumor-phenotype evidence (PP4/BP5 domain per VCEP), not a benign-function assay. Accordingly BS3 is not assessed: there is no evidence of proficient function, and none is expected for a nonsense variant, but BS3 requires actual assay data rather than inference from variant type.
Evidence considered
InSiGHT MSH2 v2.0 BS3 rules (cspec): calibrated functional odds <=0.05 Strong (or no mRNA aberration for synonymous/intronic with NMD inhibition), >0.05-0.48 or proficient function per flowchart Supporting
Functional-assay-SVI-documentation-MMR.xlsx: validated assay catalogue with normal/abnormal thresholds and validation controls; c.1255C>T absent from all documented assays
Functional-assay-flowchart.pdf (image-based; logic captured in cspec): no variant-specific proficient-function assay result available to evaluate
PMID:24278394 (De Lellis 2013): tumor MSI-H/MSH2 IHC loss for this variant is inconsistent with proficient function and belongs to PP4/BP5 evidence, not BS3
PMID:24362816 (Thompson 2014): consulted as framework/classification source; variant not mentioned; no benign-function assay data for this variant
Still missing
No calibrated functional assay with functional odds <=0.05/<=0.48 for c.1255C>T (none of the SVI-documented validated assays tested this variant)
No protein or mRNA-based lab assay demonstrating proficient function (e.g., cDNA/FLT with NMD inhibition) performed for this variant
BS3 mRNA-aberration clause applies only to synonymous/intronic variants; variant is nonsense, and no RNA assay data exists regardless
BS4Not assessed: no non-segregation data exist; no affected non-carriers or unaffected carriers are reported for any pedigree.
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Reasoning
No non-segregation (lack of co-segregation) data exist for MSH2 c.1255C>T. No source in the case bundle reports affected non-carriers, unaffected carriers, or any pedigree for which a combined Bayes likelihood ratio <0.48 (Supporting) or <0.05 (Strong) could be computed. BS4 therefore cannot be assessed.
Rule
InSiGHT MSH2 VCEP v2.0 BS4: combined Bayes likelihood ratio <0.05 = Strong; >0.05 and <=0.48 = Supporting.
Evidence considered
InSiGHT MSH2 VCEP v2.0 (CSpec doc 1577628936) BS4 rule: lack of co-segregation with disease in pedigree(s) with combined Bayes likelihood ratio <0.05 = Strong; >0.05 and <=0.48 = Supporting (Belman et al. 2020, PMID 32773770, per VCEP reference list).
PMID:24278394 Table 1: proband-level report of the variant only; no non-segregation data present.
Still missing
No pedigrees with lack of co-segregation (affected non-carriers / unaffected carriers) reported for c.1255C>T in any available source.
Pedigree data with discordant meioses would be required to compute a combined Bayes likelihood ratio for BS4 (<0.05 = Strong; >0.05 and <=0.48 = Supporting).
BP5Not assessed: no tumor evidence of an alternative molecular basis (MSS, intact MMR IHC, BRAF V600E, or MLH1 methylation) was available.
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Reasoning
Under the governing InSiGHT MSH2 VCEP v2.0, BP5 is applicable and requires affirmative tumor evidence of an alternative molecular basis: Supporting = 2-3 tumors that are CRC/endometrial with MSS and/or no loss of MMR protein expression and/or LS-spectrum tumors with MMR protein loss inconsistent with the variant gene (or 1 BRAF V600E / MLH1-methylated MSI-H tumor with MLH1 loss); Strong = >=4 such tumors (or >=2 BRAF V600E / MLH1 methylation events). No such tumor data (MSS status, intact MMR IHC, IHC loss inconsistent with MSH2, BRAF V600E, or MLH1 promoter methylation) is available for c.1255C>T carriers in this case's evidence bundle, and none of the locally retrievable full texts mention the variant. The data gap is identical to PP4: carrier-level tumor phenotype data is not retrievable in this case, so BP5 cannot be assessed and is reported as not_assessed. There is no evidence suggesting BP5 would be met (the variant is a truncating null variant with an expert-panel Pathogenic classification).
InSiGHT MSH2 VCEP v2.0 BP5 rule (Supporting: 2-3 tumors with MSS and/or no loss of MMR protein expression and/or inconsistent MMR protein loss, or 1 BRAF V600E/MLH1 methylation event; Strong: >=4 tumors or >=2 BRAF V600E/MLH1 methylation events) - used to define what evidence would satisfy BP5.
Searched all locally available full texts for the exact variant (c.1255C>T, 1255, Gln419, Q419); no matches, hence no MSS/IHC data retrievable.
Still missing
No carrier-level tumor data (MSS, intact MMR IHC, IHC inconsistent with MSH2, BRAF V600E, MLH1 methylation) for c.1255C>T is available in the case evidence bundle (needed for BP5 Supporting/Strong tiers).
ClinVar-cited case papers (PMID 8581513, 28874130, 31114938, 31588121) are not in the source registry and have no full text in this case.
Local full-text files for PMID 24278394 and PMID 24362816 are empty (0 bytes) despite source registry marking them full_text_available.
Not applicable · 12· recorded as not applicableShow reasons ▾Hide reasons ▴PS1N/ANot applicable: PS1 covers missense substitutions or splice-nucleotide changes, and this is a nonsense change with no alternate-nucleotide comparator.
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Reasoning
Governing framework is the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel specification for MSH2 v2.0 (cspec doc 1577628936). Its PS1_Strong rule applies to 'A predicted missense substitution that encodes the same amino acid change with a different underlying nucleotide change previously established by this VCEP as Pathogenic (not a predicted or confirmed splice defect)', with the alternative clause covering variants at the same non-canonical splice nucleotide as a confirmed Pathogenic splice variant. The variant under review is a nonsense substitution NM_000251.3:c.1255C>T -> NP_000242.1:p.(Gln419Ter) (premature termination codon at codon 419, internal to exon 7, c.1077-1276), not a predicted missense substitution, and c.1255 is not a splice nucleotide. No alternate nucleotide change at c.1255 producing the same protein-level change p.Gln419Ter (e.g., c.1255C>A or c.1255C>G) is documented anywhere in the case bundle: ClinVar variation 90584 contains only c.1255C>T, pm5_candidates.json reports 0 same-residue candidates, and a search of all 7 downloaded full texts for '1255', 'Gln419', 'Q419', '419' returned no matches. PS1 is therefore not applicable to this variant class, and no comparator exists even under a generic same-amino-acid-change reading.
Rule
PS1_Strong (InSiGHT MSH2 VCEP v2.0): 'A predicted missense substitution that encodes the same amino acid change with a different underlying nucleotide change previously established by this VCEP as Pathogenic (not a predicted or confirmed splice defect). OR Variants affecting the same non-canonical splice nucleotide as a confirmed Pathogenic splice variant with similar or worse splicing in silico prediction using SpliceAI.'
Evidence considered
InSiGHT MSH2 VCEP v2.0 PS1 rule text (cspec doc 1577628936): PS1 scoped to predicted missense substitutions encoding the same amino acid change via a different nucleotide change previously established as Pathogenic by this VCEP, or to same non-canonical splice nucleotide as a confirmed Pathogenic splice variant.
pm5_candidates.json: 0 same-residue comparator candidates collected; eligible_for_classic_pm5_search=false because variant consequence class is nonsense.
ClinVar variation 90584: only c.1255C>T (p.Gln419Ter) recorded; no alternate nucleotide change at the same codon documented in any submission.
SpliceAI lookup: max delta score 0.36 (DS_DG 0.36); checked only to confirm the PS1 splice clause has no comparator, not used as standalone evidence.
Still missing
No alternate nucleotide change at c.1255 producing p.Gln419Ter (e.g., c.1255C>A/G) was identified in ClinVar, the evidence bundle, or available full texts; a database-level (InSiGHT/LOVD) check for alternate changes producing the same stop codon was not possible from this bundle.
PS1's splice-nucleotide clause cannot be evaluated because no confirmed Pathogenic splice variant at the same nucleotide is documented; SpliceAI max delta 0.36 (DS_DG 0.36) suggests possible donor-gain impact but no comparator variant exists.
PS4VCEPNot applicable: the InSiGHT MSH2 VCEP uses tumor IHC evidence under PP4 instead of PS4 proband counting.
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Reasoning
The governing framework is the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specification for MSH2 v2.0 (cspec doc 1577628936), which explicitly marks PS4 as 'Not applicable' with the instruction that, due to the availability of tumor IHC data for variant classification (see PP4), PS4 is not utilized for MMR variant classification using proband counting. Case-control enrichment data for this exact variant (c.1255C>T) are absent from the evidence bundle: no case-control OR/RR study is available, and the variant is absent from gnomAD v2.1/v4.1. One clinical laboratory submission (SCV001170797, Ambry) asserts detection of the variant in multiple individuals meeting Amsterdam criteria and cites PMID 8581513 (Miyaki 1995), but laboratory assertions were not used as independent PS4 evidence (never infer a criterion from another source's final classification), PMID 8581513 is not in the source registry, and no full text for it exists in this case. Accordingly PS4 is not applicable under the governing VCEP and is not assessed on generic ACMG grounds.
VCEP rule
InSiGHT MSH2 VCEP v2.0: PS4 applicability = Not applicable (proband counting not used for MMR variant classification).
Evidence considered
InSiGHT MSH2 VCEP v2.0 (cspec doc 1577628936): PS4 applicability = 'Not applicable'; instructionsToUse: 'Due to the availability of tumor IHC data for variant classification (see PP4), PS4 has not been utilized for MMR variant classification using proband counting.'
ClinVar VCV000090584 submission audit: Ambry SCV001170797 carries a PS4-style case-count assertion citing PMID 8581513; treated as laboratory assertion only, not independent evidence.
Still missing
No case-control enrichment study for c.1255C>T is available in the case evidence bundle (PS4 would in any case remain not applicable under the InSiGHT MSH2 VCEP v2.0).
PMID 8581513 (Miyaki 1995), cited by a clinical laboratory for this variant, is not in the source registry and has no full text in this case.
PM1VCEPNot applicable: the InSiGHT MSH2 VCEP recognizes no mutational hotspots for MSH2, and the variant is nonsense rather than missense.
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Reasoning
The governing InSiGHT MSH2 VCEP v2.0 specification explicitly declares PM1 'Not applicable' with the instruction: 'There are no recognized mutational hot spots that could be used for classification purposes. While there are functional domains in the MMR genes, the distribution of pathogenic variants is generalized over all the domains (unpublished data).' The VCEP therefore does not use the MMR functional domain schematic (MMR-Functional-domains.pdf, adapted from InSiGHT criteria v2.4) for PM1 classification. Additionally, the variant is a nonsense change (p.Gln419Ter), and PM1 is a missense/domain-location criterion. Per framework precedence, generic ACMG PM1 is not applied because an applicable VCEP specification exists and explicitly rules the criterion out.
VCEP rule
PM1 (InSiGHT MSH2 VCEP v2.0): declared Not Applicable - 'There are no recognized mutational hot spots that could be used for classification purposes. While there are functional domains in the MMR genes, the distribution of pathogenic variants is generalized over all the domains (unpublished data).'
Evidence considered
InSiGHT MSH2 VCEP v2.0 PM1 applicability declaration (cspec doc 1577628936): 'Not applicable' - no recognized mutational hot spots; pathogenic variant distribution generalized over all MMR functional domains (unpublished data).
VCEP MMR-Functional-domains.pdf (indexed for PM1): linear schematic of MMR domains by amino acid position; reviewed but the governing VCEP rules it out as PM1 evidence for MSH2.
PM4VCEPNot applicable: declared not applicable by the InSiGHT MSH2 VCEP, and a nonsense substitution causes truncation, not an in-frame length change.
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Reasoning
The governing InSiGHT MSH2 VCEP specification v2.0 (cspec) explicitly declares PM4 as 'Not Applicable' for MSH2, and the VCEP specification takes precedence over the generic ACMG/AMP framework. Independently, PM4 (protein length change due to in-frame insertion/deletion or stop-loss variant in a non-repeat region) is not relevant to this variant on the merits: c.1255C>T is a single-nucleotide nonsense substitution (p.Gln419Ter) that produces a truncated protein via a PTC rather than an altered-length in-frame protein, so no protein-length-change criterion applies. Not assessed under the generic framework because a governing gene-specific specification exists.
PM5N/ANot applicable: PM5 applies only to missense changes, and p.Gln419Ter is a nonsense substitution with no different missense change at codon 419.
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Reasoning
The governing InSiGHT MSH2 VCEP v2.0 PM5 rule applies to a 'Missense change at an amino acid residue where a different missense change was classified by this VCEP as Pathogenic on the protein level and not due to aberrant splicing', and only when PP3 is supporting for the missense change (PM5_Supporting if the other variant is Likely Pathogenic). The variant under review is a nonsense substitution (NM_000251.3:c.1255C>T -> p.Gln419Ter), not a missense change, so PM5 cannot apply at the variant level. Consistent with this, pm5_candidates.json reports eligible_for_classic_pm5_search=false ('variant consequence class (nonsense) is not missense'), 0 same-residue candidates, and recommendation level 'not_applicable'. No different missense change at MSH2 codon 419 is documented in the evidence bundle, ClinVar submissions, or any downloaded full text.
Rule
PM5 (InSiGHT MSH2 VCEP v2.0): 'Missense change at an amino acid residue where a different missense change was classified by this VCEP as Pathogenic on the protein level and not due to aberrant splicing. Only use PM5 if PP3 is supporting for the missense change. Use PM5_Supporting if other variant is Likely Pathogenic due to a missense alteration.'
Evidence considered
InSiGHT MSH2 VCEP v2.0 PM5 rule text (cspec doc 1577628936): applies to a missense change at a residue where a different missense change was classified Pathogenic/Likely Pathogenic by this VCEP, with PP3 supporting requirement.
pm5_candidates.json: eligible_for_classic_pm5_search=false because variant consequence class is nonsense; 0 same-residue candidates; recommendation 'not_applicable'.
Still missing
No different missense change at codon 419 (e.g., p.Gln419His, p.Gln419Arg) classified P/LP by this VCEP was found; a database-level (InSiGHT/LOVD/ClinVar) search for codon 419 missense comparators was not available in this bundle (pm5_candidates.json collected 0 candidates).
PM6VCEPNot applicable: the InSiGHT MSH2 VCEP captures unconfirmed de novo evidence within the PS2 point system rather than as PM6.
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Reasoning
The governing ClinGen InSiGHT MSH2 VCEP specification v2.0 (CSpec doc 1577628936) declares PM6 'Not applicable': assumed de novo evidence (maternity/paternity unconfirmed) is captured within the PS2 de novo point system (0.5 points per proband) rather than as a separate PM6 criterion. Therefore PM6 is not assessed under this framework.
VCEP rule
InSiGHT MSH2 VCEP v2.0: PM6 Not Applicable - assumed de novo variants are scored under the PS2 point system (0.5 points per proband with maternity and/or paternity unconfirmed).
Evidence considered
InSiGHT MSH2 VCEP v2.0 (CSpec doc 1577628936): PM6 applicability = 'Not applicable'; its instructionsToUse text states assumed de novo probands contribute 0.5 points to the PS2 point system, and that multiple probands meeting PS2/PS2_moderate and PM6/PM6_Strong criteria are combined under PS2/PS2_VeryStrong.
PP2VCEPNot applicable: the InSiGHT MSH2 VCEP declares PP2 not applicable, and this variant is nonsense, not missense.
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Reasoning
The governing InSiGHT MSH2 VCEP v2.0 specification explicitly declares PP2 'Not applicable' with the instruction: 'Missense variant in a gene with low rate of benign missense changes does not apply.' The VCEP does not apply PP2 for MSH2 variant classification. The variant is additionally a nonsense change (p.Gln419Ter), and PP2 is a gene-level missense-mechanism criterion. Generic ACMG PP2 is not used because the applicable VCEP specification governs and rules the criterion out.
VCEP rule
PP2 (InSiGHT MSH2 VCEP v2.0): declared Not Applicable - 'Missense variant in a gene with low rate of benign missense changes does not apply.'
Evidence considered
InSiGHT MSH2 VCEP v2.0 PP2 applicability declaration (cspec doc 1577628936): 'Not applicable' - 'Missense variant in a gene with low rate of benign missense changes does not apply.'
BP1VCEPNot applicable: the InSiGHT MSH2 VCEP declares BP1 not applicable, as missense is an established MSH2 mechanism.
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Reasoning
The governing InSiGHT MSH2 VCEP v2.0 specification explicitly declares BP1 'Not applicable' with the instruction: 'Missense variant in a gene where only loss of function causes disease is not applicable.' MSH2 is not a gene in which primarily truncating variants cause disease - missense variants are a well-established mechanism in Lynch syndrome - so BP1 does not apply at gene level either. The variant is also a nonsense change, and BP1 targets missense variants in truncation-only genes; it cannot be used to support a nonsense variant. Generic ACMG BP1 is not used because the applicable VCEP specification governs.
VCEP rule
BP1 (InSiGHT MSH2 VCEP v2.0): declared Not Applicable - 'Missense variant in a gene where only loss of function causes disease is not applicable.'
Evidence considered
InSiGHT MSH2 VCEP v2.0 BP1 applicability declaration (cspec doc 1577628936): 'Not applicable' - 'Missense variant in a gene where only loss of function causes disease is not applicable.'
BP2VCEPNot applicable: the InSiGHT MSH2 VCEP replaces BP2 with its BS2 rule ('BS2 is used instead').
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Reasoning
The governing ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis EP Specification for MSH2 v2.0 (cspec, doc 1577628936) explicitly marks BP2 as 'Not applicable' with the instruction 'BS2 is used instead.' The VCEP replaces BP2 (observed in trans with a pathogenic variant for a fully penetrant dominant disorder, or in cis with a pathogenic variant) with its own BS2 rule for trans co-occurrence in older-onset Lynch syndrome patients without CMMRD features. Under the applicable VCEP specification BP2 must not be applied, so it is not_applicable regardless of the absence of cis/trans observation data for this variant in the case bundle. No generic ACMG/AMP BP2 was applied because a governing VCEP specification exists and takes precedence.
VCEP rule
Not applicable - BS2 is used instead. (InSiGHT MSH2 VCEP v2.0)
Evidence considered
cspec (InSiGHT MSH2 VCEP v2.0) BP2 entry: applicability 'Not applicable', instructionsToUse 'BS2 is used instead.', originalACMGSummary '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.' - the VCEP explicitly disallows BP2 and substitutes BS2.
Still missing
No cis/trans phase observation data for c.1255C>T exists in the collected sources; if phase data became available, the VCEP-designated BS2 (not BP2) pathway would be the relevant rule and is outside this group's scope.
BP3VCEPNot applicable: the InSiGHT MSH2 VCEP declares BP3 not applicable, and a nonsense substitution is not an in-frame repeat-region indel.
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Reasoning
The governing InSiGHT MSH2 VCEP specification v2.0 (cspec) explicitly declares BP3 as 'Not Applicable' for MSH2, and the VCEP specification takes precedence over the generic ACMG/AMP framework. Independently, BP3 (in-frame indel in a repeat region without known function) cannot apply on the merits: c.1255C>T is a nonsense substitution (p.Gln419Ter), not an in-frame indel, and it does not lie in a repeat-region context (no repeat-region evidence exists in the case bundle). Not assessed under the generic framework because a governing gene-specific specification exists.
BP4N/ANot applicable: BP4's no-impact clauses target missense, intronic, or synonymous variants; c.1255C>T is exonic nonsense with SpliceAI delta 0.36.
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Reasoning
Governing framework: InSiGHT MSH2 VCEP v2.0 (cspec doc 1577628936). BP4 rule paths: (1) 'Missense variant with HCI-prior probability of pathogenicity <0.11' - NOT applicable: c.1255C>T is a nonsense variant p.(Gln419Ter) and is not present in the HCI prior lookup table (vcep_hci_priors_msh2, variant_not_in_hci_table; table covers missense substitutions only). (2) 'For intronic and synonymous variants: SpliceAI predicts no splicing impact with delta score <= 0.1 as per Walker et al 2023' - NOT applicable: the variant is an exonic nonsense variant (not intronic, not synonymous), and SpliceAI max delta is 0.36, which would not satisfy the <=0.1 no-impact threshold even if the scope were extended. BP4 is therefore not applicable to this variant class, and no computational evidence suggests a benign/no-impact effect for a truncating variant. No double-counting: the same SpliceAI prediction (0.36) was used only for PP3.
Rule
BP4_Supporting: 'Missense variant with HCI-prior probability of pathogenicity <0.11 as per https://hci-priors.hci.utah.edu/PRIORS OR For intronic and synonymous variants: SpliceAI predicts no splicing impact with delta score <= 0.1 as per Walker et al 2023.' (InSiGHT MSH2 VCEP v2.0, cspec doc 1577628936)
Evidence considered
InSiGHT MSH2 VCEP v2.0 BP4_Supporting rule: 'Missense variant with HCI-prior probability of pathogenicity <0.11 ... OR For intronic and synonymous variants: SpliceAI predicts no splicing impact with delta score <= 0.1 as per Walker et al 2023.' - neither path covers a nonsense exonic variant.
SpliceAI max delta score 0.36 - does not meet the <=0.1 no-splicing-impact BP4 threshold (Walker et al. 2023, PMID 37352859) even if the intronic/synonymous scope were extended to this variant.
HCI prior lookup (vcep_hci_priors_msh2): c.1255C>T absent from the MSH2 HCI prior table (variant_not_in_hci_table) - missense BP4 path not applicable.
BayesDel noAF score 0.66 (bayesdel registry entry) retrieved but not used: no verified published BP4 threshold available to this pipeline.
Still missing
No BP4-relevant evidence exists for this variant: HCI prior unavailable (nonsense variant not in table) and SpliceAI predicts splice impact (0.36), not absence of impact.
BayesDel noAF score 0.66 was not used: no verified published BP4 threshold is available to this pipeline.
BP7N/ANot applicable: BP7 covers synonymous or intronic variants at or beyond -21/+7, and c.1255C>T is an exonic nonsense change.
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Reasoning
Governing framework: InSiGHT MSH2 VCEP v2.0 (cspec doc 1577628936). BP7 rule: 'A synonymous (silent) or intronic variant at or beyond -21/+7 (5'/3' exonic).' NM_000251.3:c.1255C>T is a nonsense variant (p.Gln419Ter) located in the coding portion of exon 7 (c.1077-1276); it is neither synonymous nor intronic, so BP7 is not applicable.
Rule
BP7_Supporting: 'A synonymous (silent) or intronic variant at or beyond -21/+7 (5'/3' exonic).' (InSiGHT MSH2 VCEP v2.0, cspec doc 1577628936)
Evidence considered
InSiGHT MSH2 VCEP v2.0 BP7_Supporting rule: 'A synonymous (silent) or intronic variant at or beyond -21/+7 (5'/3' exonic). Variants may satisfy both BP7 and BP4.' - c.1255C>T (p.Gln419Ter) is a nonsense exonic variant, not synonymous or intronic.
Every interpreted variant in MSH2, mapped onto the exon structure of NM_000251.3. Select a row to find it on the plot.
MSH2NM_000251.3
Fetching transcript structure from UCSC…
Exons
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Transcript span
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Strand
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Variants mapped
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Source
UCSC ncbiRefSeqCurated
All variants in MSH2—Select a row to find it on the plot; use the link to open its page.
Protein
Location
Classification
Link
gnomAD v4.1Allele count data not recorded
gnomAD v2.1Allele count data not recorded
gnomAD-Canada v1.0Allele count data not recorded
Statements
gnomAD v4.1
Absent from gnomAD v4.1.
gnomAD v2.1
Absent from gnomAD v2.1.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
SpliceAI and Pangolin
SpliceAI acceptor lossat -98 bp
0.020
SpliceAI acceptor gainat +336 bp
0.000
SpliceAI donor lossat +21 bp
0.010
SpliceAI donor gainat -27 bp
0.360
Pangolin splice lossmagnitude shown
-0.150
Pangolin splice gain
0.170
Other predictors
REVEL
Not available
BayesDel
0.660
How the predictions were used
PP3SupportingMet, Supporting: SpliceAI max delta 0.36 exceeds the >=0.2 threshold (predicted donor gain at intron 7 +6) per the VCEP PP3 rule. Flagged for human review: this SpliceAI-based support is mechanistically redundant with PVS1 for a nonsense variant.
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Reasoning
Governing framework: InSiGHT MSH2 VCEP v2.0 (cspec doc 1577628936). PP3 rule paths: (1) missense with HCI prior >0.81 (Moderate) or >0.68-0.81 (Supporting) - NOT applicable: NM_000251.3:c.1255C>T is a nonsense variant p.(Gln419Ter), and the HCI prior lookup table (vcep_hci_priors_msh2) does not contain this allele (variant_not_in_hci_table; the table covers missense substitutions only - c.1255C>A and c.1255C>G are present but are different alleles). (2) 'Predicted splice defect for non-canonical splicing nucleotides using SpliceAI with delta score >= 0.2 as per Walker et al 2023' - MET: SpliceAI max delta score = 0.36 (DS_DG = 0.36, predicted donor-gain 27 nt downstream of c.1255, i.e. intron 7 +6; DS_AL 0.02, DS_DL 0.01, DS_AG 0.0), which exceeds the >=0.2 threshold. The variant lies 21 nt 5' of the exon 7 donor junction (exon 7 = c.1077-1276), inside SpliceAI's high-confidence +/-50 bp window, and the predicted cryptic donor is at a non-canonical splicing nucleotide (intronic +6); the masked-score lookup setting recommended by the VCEP was used. PP3 applied at Supporting strength per the VCEP rule. Human review requested because: the variant is a nonsense variant whose primary loss-of-function mechanism is already captured by PVS1 (PTC at codon 419, <= codon 891), so the SpliceAI-based PP3 is supportive but mechanistically redundant (predicted donor-gain would also yield frameshift/NMD); the VCEP prohibits PVS1+PP3 stacking only for IVS +/-1/2 variants, not for nonsense variants, but confirm intended stacking with the PVS1 group.
Rule
PP3_Supporting: 'Predicted splice defect for non-canonical splicing nucleotides using SpliceAI with delta score >= 0.2 as per Walker et al 2023.' (InSiGHT MSH2 VCEP v2.0, cspec doc 1577628936)
Evidence considered
SpliceAI max delta score 0.36 (DS_DG 0.36, donor-gain predicted 27 nt downstream, intron 7 +6) >= 0.2 PP3 threshold as per Walker et al. 2023 (PMID 37352859), ClinGen SVI Splicing Subgroup recommendations (Am J Hum Genet 110:1046-1067), the publication named in the InSiGHT MSH2 VCEP v2.0 PP3 rule (cspec doc 1577628936).
InSiGHT MSH2 VCEP v2.0 PP3_Supporting rule: 'Predicted splice defect for non-canonical splicing nucleotides using SpliceAI with delta score >= 0.2 as per Walker et al 2023'; variant is 21 nt 5' of the exon 7 donor (exon 7 = c.1077-1276) and the predicted cryptic donor is at intronic +6.
HCI prior lookup (vcep_hci_priors_msh2): c.1255C>T absent from the MSH2 HCI prior table (variant_not_in_hci_table; table is missense-only, and neighboring alleles c.1255C>A / c.1255C>G with priors 0.002 / 0.001 are different substitutions) - missense HCI paths of PP3 are not applicable.
BayesDel noAF score 0.66 (bayesdel registry entry) was retrieved but treated as insufficiently calibrated for PP3: no verified published PP3/BP4 threshold is available to this pipeline, so the score was not used.
Still missing
Scope judgment: whether an exonic position 21 nt 5' of the exon 7 donor qualifies as a 'non-canonical splicing nucleotide' under the VCEP PP3 rule was interpreted positively because the SpliceAI-predicted cryptic donor (0.36) sits at intronic +6 and the variant is within SpliceAI's reliable +/-50 bp window; a human reviewer should confirm this reading.
Redundancy with PVS1: for this nonsense variant (p.Gln419Ter), PP3 via SpliceAI does not add an independent pathogenic mechanism (predicted donor-gain is also LoF); confirm the VCEP intends PP3 to be applied on top of PVS1 for nonsense variants before relying on it in the final combination.
Walker et al. 2023 (PMID 37352859) full text was not available in this case's publication set; the >=0.2 threshold is taken from the InSiGHT MSH2 VCEP v2.0 rule text, which names 'Walker et al 2023' and lists PMID 37352859 in its reference section.
REVEL score not found for this variant; aGVGD absent from the evidence bundle - no additional independent in silico lines were available.
BP4N/ANot applicable: BP4's no-impact clauses target missense, intronic, or synonymous variants; c.1255C>T is exonic nonsense with SpliceAI delta 0.36.
Details ▾Hide ▴
Reasoning
Governing framework: InSiGHT MSH2 VCEP v2.0 (cspec doc 1577628936). BP4 rule paths: (1) 'Missense variant with HCI-prior probability of pathogenicity <0.11' - NOT applicable: c.1255C>T is a nonsense variant p.(Gln419Ter) and is not present in the HCI prior lookup table (vcep_hci_priors_msh2, variant_not_in_hci_table; table covers missense substitutions only). (2) 'For intronic and synonymous variants: SpliceAI predicts no splicing impact with delta score <= 0.1 as per Walker et al 2023' - NOT applicable: the variant is an exonic nonsense variant (not intronic, not synonymous), and SpliceAI max delta is 0.36, which would not satisfy the <=0.1 no-impact threshold even if the scope were extended. BP4 is therefore not applicable to this variant class, and no computational evidence suggests a benign/no-impact effect for a truncating variant. No double-counting: the same SpliceAI prediction (0.36) was used only for PP3.
Rule
BP4_Supporting: 'Missense variant with HCI-prior probability of pathogenicity <0.11 as per https://hci-priors.hci.utah.edu/PRIORS OR For intronic and synonymous variants: SpliceAI predicts no splicing impact with delta score <= 0.1 as per Walker et al 2023.' (InSiGHT MSH2 VCEP v2.0, cspec doc 1577628936)
Evidence considered
InSiGHT MSH2 VCEP v2.0 BP4_Supporting rule: 'Missense variant with HCI-prior probability of pathogenicity <0.11 ... OR For intronic and synonymous variants: SpliceAI predicts no splicing impact with delta score <= 0.1 as per Walker et al 2023.' - neither path covers a nonsense exonic variant.
SpliceAI max delta score 0.36 - does not meet the <=0.1 no-splicing-impact BP4 threshold (Walker et al. 2023, PMID 37352859) even if the intronic/synonymous scope were extended to this variant.
HCI prior lookup (vcep_hci_priors_msh2): c.1255C>T absent from the MSH2 HCI prior table (variant_not_in_hci_table) - missense BP4 path not applicable.
BayesDel noAF score 0.66 (bayesdel registry entry) retrieved but not used: no verified published BP4 threshold available to this pipeline.
Still missing
No BP4-relevant evidence exists for this variant: HCI prior unavailable (nonsense variant not in table) and SpliceAI predicts splice impact (0.36), not absence of impact.
BayesDel noAF score 0.66 was not used: no verified published BP4 threshold is available to this pipeline.
BP7N/ANot applicable: BP7 covers synonymous or intronic variants at or beyond -21/+7, and c.1255C>T is an exonic nonsense change.
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Reasoning
Governing framework: InSiGHT MSH2 VCEP v2.0 (cspec doc 1577628936). BP7 rule: 'A synonymous (silent) or intronic variant at or beyond -21/+7 (5'/3' exonic).' NM_000251.3:c.1255C>T is a nonsense variant (p.Gln419Ter) located in the coding portion of exon 7 (c.1077-1276); it is neither synonymous nor intronic, so BP7 is not applicable.
Rule
BP7_Supporting: 'A synonymous (silent) or intronic variant at or beyond -21/+7 (5'/3' exonic).' (InSiGHT MSH2 VCEP v2.0, cspec doc 1577628936)
Evidence considered
InSiGHT MSH2 VCEP v2.0 BP7_Supporting rule: 'A synonymous (silent) or intronic variant at or beyond -21/+7 (5'/3' exonic). Variants may satisfy both BP7 and BP4.' - c.1255C>T (p.Gln419Ter) is a nonsense exonic variant, not synonymous or intronic.
SpliceAI predicts possible splice impact for this variant (max delta score = 0.36). BayesDel score = 0.66.
7 paper records listed. 2 cited in the classification.
Cited in the classification
Integrative analysis of hereditary nonpolyposis colorectal cancer: the contribution of allele-specific expression and other assays to diagnostic algorithms.
De Lellis L et al. · 2013
De Lellis et al. (2013) report c.1255C>T (p.Gln419*) as a germline MSH2 nonsense variant in Lynch syndrome proband 1515#3442 (Amsterdam criteria II), detected by sequencing of 132 unrelated HNPCC probands. The patient's tumor was MSI-H with loss of MSH2 expression on immunohistochemistry (IHC). The variant is listed among the 27 loss-of-function nucleotide changes (nonsense and frameshift) introducing premature termination codons identified in the cohort. This independently corroborates that c.1255C>T is a germline, PTC-introducing nonsense allele in a classic MMR-deficient (MSI-H/MSH2-loss) Lynch syndrome context, consistent with the predicted loss-of-function consequence and NMD-expected truncation underlying PVS1.
Location Table 1 (Overview of MSI, IHC and mutational status in 132 HNPCC unrelated patients meeting AC), row for patient 1515#3442; supported by Results text: 'These included 27 loss-of-function nucleotide changes (nonsense and frameshift) introducing premature termination codons (PTCs)'
Context Germline screening (SSCP/DGGE, dHPLC, automated sequencing) of 132 unrelated AC-I/AC-II HNPCC probands with tumor MSI and MMR-protein IHC analyses; patient 1515#3442 had an MSI-H tumor and loss of MSH2 expression by IHC
Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database.
Thompson BA et al. · 2014 Feb
Thompson et al. 2014 describes the InSiGHT 5-tiered classification scheme applied to 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database. It was consulted as a negative screen for same-residue or alternate-nucleotide comparator evidence relevant to PS1/PM5 (e.g., an alternate nucleotide change producing p.Gln419Ter or a different missense change at codon 419 classified by InSiGHT). The exact variant c.1255C>T / p.Gln419Ter and codon 419 are not mentioned in the downloaded full text (variant-level tables are not part of the available text), so no comparator evidence for this group could be extracted.
Identification of a high-risk disease-causing constitutional mutation in a cancer patient guides the clinical management of the whole family, with implications for counselling, cancer treatment options, pre-symptomatic surveillance, and consideration of risk-reducing surgery and/or medication regimes.
Location Full text (publications/24362816.txt), opening paragraph; search of the downloaded text for '1255', 'Gln419', 'Q419', '419' returned no matches
Mutations associated with HNPCC predisposition -- Update of ICG-HNPCC/INSiGHT mutation database.
Peltomaki & Vasen 2004 (ICG-HNPCC/InSiGHT mutation database update) - general review noting rare instances of homozygosity and compound heterozygosity for MMR gene mutations associated with atypical tumor spectrum and constitutional mutator phenotype, but no variant-specific information on c.1255C>T and no biallelic observation for this variant.
Rare instances of homozygosity [29,38,40,41] or compound heterozygosity [4,13] for MMR gene mutations have been described. Homozygosity for MLH1 or MSH2 mutations is associated with atypical tumor spectrum (hematological malignancy and neurofibromatosis type 1) as well as constitutional mutator phenotype.
Discussion section, paragraph on homozygosity/compound heterozygosity of MMR mutations (Fig. 2 legend context)
Structural, molecular and cellular functions of MSH2 and MSH6 during DNA mismatch repair, damage signaling and other noncanonical activities.
Spectrum and frequencies of mutations in MSH2 and MLH1 identified in 1,721 German families suspected of hereditary nonpolyposis colorectal cancer.
Mangold E et al. · 2005
Mangold et al. 2005 reports the spectrum and frequencies of MSH2 and MLH1 mutations identified in 1,721 German families suspected of hereditary nonpolyposis colorectal cancer; it is cited in the ClinVar record for this variant. It was consulted as a negative screen for codon/residue comparator evidence (alternate nucleotide change producing p.Gln419Ter or other changes at MSH2 codon 419). The exact variant c.1255C>T / p.Gln419Ter and codon 419 are not mentioned in the downloaded full text, so no comparator evidence for this group could be extracted.
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
gnomAD v4.1
Absent from gnomAD v4.1.
gnomAD v2.1
Absent from gnomAD v2.1.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
ClinVar
This variant has been reported in ClinVar as Pathogenic (6 clinical laboratories) and as Pathogenic by International Society for Gastrointestinal Hereditary Tumours (InSiGHT) (expert panel). (ClinVarID = 90584)
In silico
SpliceAI predicts possible splice impact for this variant (max delta score = 0.36). BayesDel score = 0.66.
Functional
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
Somatic
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Cancer Hotspots
This variant does not lie in a statistically significant hotspot.
This variant was interpreted by pipeline 7.1.0.
The current version is 11.0.07.
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