Variant classification summary

NM_000249.3:c.676C>T

MLH1 · NP_000240.1:p.(Arg226Ter) · NM_000249.3

GRCh37: chr3:37053589 C>T · GRCh38: chr3:37012098 C>T

Gene: MLH1 Transcript: NM_000249.3

Final call

Pathogenic

PVS1 very strong PM2 supporting PM3 moderate PP4 moderate PP5 supporting

Variant details

Gene

MLH1

Transcript

NM_000249.3

Protein

NP_000240.1:p.(Arg226Ter)

gnomAD AF

6.230040507723381e-07 (v4.1)

ClinVar

Pathogenic

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

PVS1 (Very Strong): nonsense p.(Arg226Ter) introduces a premature stop at codon 226, before the InSiGHT codon-753 boundary, predicted to trigger nonsense-mediated decay.

2

PM2 (Supporting): gnomAD v4.1 allele frequency 6.23e-07 (1/1,605,126), more than 30-fold below the 0.00002 threshold.

3

PM3 (Moderate): homozygous CMMRD-affected carriers place the variant in trans with an identical known-pathogenic allele.

4

PP4 (Moderate): two independent MSI-H colorectal tumors show loss of MLH1 expression consistent with the variant.

5

PP5 (Supporting): the InSiGHT expert panel classified the exact variant Pathogenic (ClinVar 3-star).

6

Overall: Pathogenic per InSiGHT MLH1 v2.0 combination Rule 2 (PVS1 very strong plus two moderate criteria), independently confirmed by Rule 4 (PVS1 plus two supporting criteria).

Final determination: Rule2 of the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel MLH1 v2.0 criteria-combination framework is satisfied by the adjudicated criteria (1 Pathogenic.Very Strong = PVS1, plus >=2 Pathogenic.Moderate = PM3 and PP4), so the variant is classified as Pathogenic.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

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

Criterion	Status	Rationale	Evidence used
PVS1	Met	Met (Very Strong): nonsense p.(Arg226Ter) creates a premature stop at codon 226, well before the InSiGHT codon-753 boundary, predicted to trigger nonsense-mediated decay.	cspec vcep_pvs1_decisiontree_mmr pvs1_gene_context pvs1_variant_assessment PMID:11343035 PMID:10874307 spliceai gnomad_v4
PS1	N/A	Not applicable: c.676C>T is a nonsense change, while PS1 covers only missense substitutions and splice-nucleotide variants.	cspec spliceai
PS2	Not met	Not met: no de novo occurrence is documented; the only family with parental testing shows the variant was inherited from the affected mother.	PMID:11343035
PS3	Not met	Not met: no VCEP-approved calibrated functional assay was performed for this variant; available IVTT and IHC data are qualitative and not scoreable.	PMID:11343035 PMID:16216036 PMID:10874307 vcep_functional_assay_svi_documentation_mmr cspec
PS4	N/A	Not applicable: the InSiGHT MLH1 specification marks PS4 not applicable, and only single-family case reports, not case-control data, exist.
PM1	N/A	Not applicable: the InSiGHT MLH1 specification explicitly declares PM1 not applicable for this gene.	cspec
PM2	Met	Met (Supporting): gnomAD v4.1 allele frequency 6.23e-07 (1/1,605,126 alleles), more than 30-fold below the 0.00002 threshold, with zero homozygotes.	gnomad_v4 gnomad_v2 gnomad_canada cspec
PM3	Met	Met (Moderate): homozygous carriers affected with CMMRD place the variant in trans with an identical known-pathogenic allele (1.0 point). Flagged for human review: the homozygous-carrier source (PMID 17889038) could not be independently verified.	clinvar gnomad_v4 cspec
PM4	N/A	Not applicable: the InSiGHT specification marks PM4 not applicable, and the variant is a nonsense change, not an in-frame indel or stop-loss.	cspec
PM5	N/A	Not applicable: PM5 requires a missense change at a VCEP-classified residue, but c.676C>T is a nonsense variant.	cspec pm5_candidates PMID:10874307
PM6	N/A	Not applicable: per the InSiGHT specification, assumed de novo evidence is scored under PS2, and none is reported for this variant.
PP1	Not assessed	Not assessed: co-segregation is directionally positive in the one reported pedigree, but the ages needed for a defensible segregation likelihood ratio are unreported.	PMID:11343035 PMID:10874307
PP2	N/A	Not applicable: the InSiGHT MLH1 specification explicitly declares PP2 not applicable for this gene.	cspec
PP3	Not met	Not met: SpliceAI max delta 0.09 vs the 0.2 splice-defect threshold, and the HCI missense path does not apply to a nonsense variant.	spliceai cspec vcep_hci_priors_mlh1
PP4	Met	Met (Moderate): two independent MSI-H colorectal tumors with loss of MLH1 expression in carriers of this exact variant; three are required for Strong.	PMID:11343035 PMID:16216036
PP5	Met	Met (Supporting): the InSiGHT expert panel classified the exact variant Pathogenic (ClinVar 3-star submission).	clinvar
BA1	Not met	Not met: gnomAD v4.1 allele frequency 6.23e-07, more than 1000-fold below the 0.001 (0.1%) BA1 threshold.	gnomad_v4 gnomad_v2 gnomad_canada cspec
BS1	Not met	Not met: allele frequency 6.23e-07 is far below the 0.0001 (0.01%) BS1 floor, with zero homozygotes.	gnomad_v4 gnomad_v2 gnomad_canada cspec
BS2	Not met	Not met: no phase-confirmed trans co-occurrence with a known pathogenic variant in a later-onset colorectal cancer patient exists.	cspec gnomad_v4 gnomad_v2
BS3	Not met	Not met: no calibrated functional assay was performed, and the documented protein truncation and MLH1 loss contradict proficient function.	PMID:11343035 PMID:16216036 vcep_functional_assay_svi_documentation_mmr cspec
BS4	Not met	Not met: no affected non-carrier was found; both tested affected relatives carry the variant, consistent with co-segregation.	PMID:11343035
BP1	N/A	Not applicable: the InSiGHT specification declares BP1 not applicable; MLH1 missense variants are a well-established disease mechanism.	cspec
BP2	N/A	Not applicable: the InSiGHT specification uses BS2 in place of BP2, and no cis observation was found for this variant.	cspec
BP3	N/A	Not applicable: the InSiGHT specification marks BP3 not applicable, and the variant is a nonsense change, not an in-frame indel in a repeat region.	cspec
BP4	N/A	Not applicable: BP4 covers missense or intronic/synonymous variants, not an exonic nonsense change.	cspec vcep_hci_priors_mlh1 spliceai
BP5	Not met	Not met: both documented carrier tumors are MSI-H with MLH1 loss, the opposite of the benign tumor-phenotype direction BP5 requires.
BP6	Not met	Not met: the only expert-panel submission classifies the variant Pathogenic, not Benign.
BP7	N/A	Not applicable: BP7 covers synonymous or intronic variants, and c.676C>T is an exonic nonsense change.	cspec

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