MSH2

Final classification

Pathogenic

MSH2 c.1255C>T · p.Gln419Ter

MSH2

PVS1 (Very Strong): nonsense p.Gln419Ter creates a premature termination codon within the VCEP's <= codon 891 window, predicted to trigger nonsense-mediated decay.

Gene

MSH2

Transcript

NM_000251.3

HGVS · transcript:coding

NM_000251.3:c.1255C>T

Consequence

N/A

GRCh38

chr2:47429920 C>T

GRCh37

chr2:47657059 C>T

Basis 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. ▾

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.

Classification rationale

PVS1PM2PP3PP5 Pathogenic

MSH2 c.1255C>T

PVS1 (Very Strong): nonsense p.Gln419Ter creates a premature termination codon within the VCEP's <= codon 891 window, predicted to trigger nonsense-mediated decay. PM2 (Supporting): absent from gnomAD v4.1, below the <0.00002 population-frequency threshold. PP3 (Supporting): SpliceAI max delta 0.36 exceeds the >=0.2 predicted-splice-defect threshold (flagged for human review as redundant with PVS1). PP5 (Supporting): this exact variant is classified Pathogenic by the InSiGHT expert panel in ClinVar (3-star). Overall: Pathogenic per InSiGHT MSH2 VCEP combination Rule4 (1 Very Strong + at least 2 Supporting).

PVS1 + PM2 + PP3 + PP5 → Pathogenic

Gene diagram · NM_000251.3 · variants mapped to exon structure

MSH2 NM_000251.3

Fetching transcript structure from UCSC…

Applied criteria · 4 applied · 12 assessed

Applied · 4

Strength Supporting Moderate Strong Very strong

✓

PVS1 very strong Pathogenic

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.

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)

cspec ↗PMID:24278394 ↗

✓

PM2 supporting Pathogenic

Met, Supporting: c.1255C>T is absent from gnomAD v4.1 (AF=0), below the 0.00002 (<1 in 50,000 alleles) threshold.

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.

gnomad_v4 ↗gnomad_v2 ↗gnomad_canada ↗cspec ↗

✓

PP3 supporting review Pathogenic

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.

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.

spliceai ↗cspec ↗

✓

PP5 supporting Pathogenic

Met, Supporting: the InSiGHT expert panel classified this exact variant as Pathogenic in ClinVar (3-star).

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

clinvar ↗

Assessed · not applied

Pathogenic

PS2 Not assessed: no de novo occurrence data exist; no parental testing or de novo assertion is reported for c.1255C>T.

PS3 Not assessed: no calibrated functional assay result exists for c.1255C>T; tumor MSI/IHC evidence belongs to PP4, not PS3.

PM3 Not met: zero PM3 points, below the 0.5-point supporting minimum; no in-trans second pathogenic MSH2 variant or biallelic observation exists.

PP1 Not assessed: no co-segregation data exist; the only report describes a single proband with no meioses or segregation analysis.

PP4 Not assessed: no carrier-level tumor phenotype data (MSI or MMR IHC) were available for c.1255C>T.

Benign

BA1 Not met: allele frequency is 0 (absent from gnomAD v4.1), far below the >=0.001 (0.1%) BA1 threshold.

BS1 Not met: allele frequency is 0 (absent from gnomAD v4.1), below the 0.0001-0.001 BS1 range.

BS2 Not assessed: no in-trans co-occurrence or phase-confirmation data exist for any carrier of c.1255C>T.

BS3 Not assessed: no assay demonstrates proficient function for c.1255C>T, and the mRNA-aberration clause does not apply to nonsense variants.

BS4 Not assessed: no non-segregation data exist; no affected non-carriers or unaffected carriers are reported for any pedigree.

BP5 Not assessed: no tumor evidence of an alternative molecular basis (MSS, intact MMR IHC, BRAF V600E, or MLH1 methylation) was available.

BP6 Not met: the only ClinVar expert-panel classification for this exact variant is Pathogenic (InSiGHT), the opposite direction BP6 requires.

N/A · 12 PS1 · PS4 · PM1 · PM4 · PM5 · PM6 · PP2 · BP1 · BP2 · BP3 · BP4 · BP7

Research & evidence

Population frequency · supports pathogenic

gnomAD v4.1

gnomAD v2.1

v4.1

Absent from gnomAD v4.1.

v2.1

Absent from gnomAD v2.1.

🇨🇦 CA

Absent from gnomAD-Canada v1.0.

Allele frequency by ancestry

three datasets · side by side

gnomAD v4.1

Absent · 0 / ?
0 hom

Not observed in any ancestry group.

gnomAD v2.1

Absent · 0 / ?
0 hom

Not observed in any ancestry group.

gnomAD Canada 🇨🇦

Absent · 0 / ?
0 hom

Not observed in any ancestry group.

gnomAD v4 ↗ gnomAD v2 ↗ gnomAD 🇨🇦 ↗

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)

ClinVar ↗

In silico

SpliceAI predicts possible splice impact for this variant (max delta score = 0.36). BayesDel score = 0.66.

SpliceAI ↗

Functional Likely Oncogenic

OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.

OncoKB ↗

COSMIC

Cancer hotspots

Somatic evidence Not in COSMIC / hotspots

COSMIC

This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).

Hotspots

This variant does not lie in a statistically significant hotspot.

COSMIC ↗ Hotspots ↗

Literature · how each cited paper was used

2papers cited

Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 5 further PMIDs triaged but not cited — see Sources & References.

Integrative analysis of hereditary nonpolyposis colorectal cancer: the contribution of allele-specific expression and other assays to diagnostic algorithms.

PMID 24278394 ↗ · De Lellis L et al. · 2013 CLINVAR · functional

Searched

c.1255C>T1255p.Gln419*Q419Gln419

Found

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.

Variant

✓ Names this variant — characterised directly

Applied to

→PVS1 very strong

Reports the exact variant as a germline MSH2 nonsense change (p.Gln419*) introducing a PTC in an MSI-H, MSH2-IHC-loss Lynch syndrome proband - corroborates the predicted loss-of-function (nonsense) consequence evaluated under PVS1.

1515#3442 II MSI-H MSH2 MSH2 c.1255CT (p.Gln419*)

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 · full text

Rule & framework references · cited for criterion definitions, not variant evidence

24362816 ↗ Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database.

Sources & reference links

9Sources

CSpec VCEP

ClinVar

gnomAD v2.1

gnomAD v4.1

gnomAD-Canada

SpliceAI

OncoKB

COSMIC

Cancer hotspots

Triaged references · 5 PMIDs not cited in assessment

10946232 ↗ Structure and function of mismatch repair proteins. ONCOKB

11257106 ↗ Deficient DNA mismatch repair: a common etiologic factor for colon cancer. ONCOKB

15528792 ↗ Mutations associated with HNPCC predisposition -- Update of ICG-HNPCC/INSiGHT mutation database. ONCOKB

23391514 ↗ Structural, molecular and cellular functions of MSH2 and MSH6 during DNA mismatch repair, damage signaling and other noncanonical activities. ONCOKB

15849733 ↗ Spectrum and frequencies of mutations in MSH2 and MLH1 identified in 1,721 German families suspected of hereditary nonpolyposis colorectal cancer. CLINVAR