Variant classification summary

NM_000249.3:c.551C>G

MLH1 · NP_000240.1:p.(Ser184Ter) · NM_000249.3

GRCh37: chr3:37053316 C>G · GRCh38: chr3:37011825 C>G

Gene: MLH1 Transcript: NM_000249.3

Final call

VUS

PVS1 very strong PM2 supporting

Variant details

Gene

MLH1

Transcript

NM_000249.3

Protein

NP_000240.1:p.(Ser184Ter)

gnomAD AF

ClinVar

Pathogenic

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000249.3:c.551C>G (p.Ser184Ter) is a nonsense variant that introduces a premature termination codon at codon 184 of MLH1, well before the VCEP threshold of codon 753, meeting PVS1_VeryStrong.

2

The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases, meeting PM2_Supporting under the InSiGHT VCEP threshold of <0.00002 allele frequency.

3

ClinVar reports this variant as Pathogenic with 3 clinical laboratory submissions, classified as criteria provided, single submitter. However, under the InSiGHT VCEP, PP5 and BP6 are not applicable, and ClinVar classification alone does not independently satisfy other criteria.

4

No variant-specific functional studies, patient phenotype data, co-segregation data, or de novo observations were identified in the available literature or case materials.

Final determination: No criteria-combination rule matched the adjudicated criteria in the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MLH1 Version 2.0 v2.0 framework, so the variant remains a Variant of Uncertain Significance pending human review.

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	NM_000249.3:c.551C>G is a nonsense variant that introduces a premature termination codon at codon 184 (p.Ser184Ter), well before codon 753 of MLH1. Under the InSiGHT VCEP v2.0 PVS1 rules, nonsense variants introducing a PTC at or before codon 753 qualify for PVS1_VeryStrong. Loss of function is an established disease mechanism for MLH1 in Lynch syndrome.	cspec
PS1	N/A	PS1 under the InSiGHT VCEP is defined for missense substitutions that encode the same amino acid change with a different nucleotide change, or for splice variants affecting the same non-canonical splice nucleotide. This variant is a nonsense substitution (p.Ser184Ter), not a missense change, and does not meet the VCEP PS1 criteria.	cspec
PS2	Not met	No de novo observations have been reported for this variant in the available evidence. No publications, ClinVar submissions, or database entries document a confirmed de novo occurrence.
PS3	Not met	No variant-specific functional assay data is available for NM_000249.3:c.551C>G in the calibrated MMR functional assay documentation or the literature. The variant is a nonsense change predicted to cause loss of function via NMD, but this is captured under PVS1; PS3 requires experimental functional evidence which is absent. OncoKB lists the variant as Likely Oncogenic / Likely Loss-of-function but provides no associated PMIDs with functional data.	oncokb
PS4	N/A	PS4 is not applicable under the InSiGHT VCEP v2.0. The VCEP states: '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.'	cspec
PS5	N/A	PS5 is not a defined criterion in the ACMG/AMP 2015 framework, the ClinGen SVI recommendations, or the InSiGHT VCEP v2.0 specifications for MLH1. No evidence can be evaluated under this criterion.
PM1	N/A	PM1 is not applicable under the InSiGHT VCEP v2.0. The VCEP states: '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.'	cspec
PM2	Met	NM_000249.3:c.551C>G is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 population databases. Under the InSiGHT VCEP v2.0, PM2_Supporting is met when the variant allele frequency is <0.00002 (<1 in 50,000 alleles) in gnomAD v4, which is satisfied by complete absence.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	N/A	PM5 under the InSiGHT VCEP v2.0 is defined for missense changes at an amino acid residue where a different missense change has been classified as pathogenic/likely pathogenic. NM_000249.3:c.551C>G is a nonsense variant (p.Ser184Ter), not a missense change, and therefore does not satisfy the VCEP PM5 criteria.	cspec
PM6	N/A	PM6 is not applicable under the InSiGHT VCEP v2.0. The VCEP directs users to use PS2 for de novo evidence instead (instructions: 'Please see PS2').	cspec
PP1	Not met	No co-segregation data is available for this variant in the case materials. No pedigrees or segregation analysis were provided or identified in the literature.
PP2	N/A	PP2 is not applicable under the InSiGHT VCEP v2.0. The VCEP states: 'Missense variant in a gene with low rate of benign missense changes does not apply.' Additionally, this variant is a nonsense change, not a missense.	cspec
PP3	N/A	PP3 under the InSiGHT VCEP v2.0 is defined for missense variants (HCI prior probability for pathogenicity) or predicted splice defects for non-canonical splice nucleotides (SpliceAI delta score ≥ 0.2). This variant is a nonsense substitution (p.Ser184Ter) creating a premature termination codon. It is not a missense variant (HCI prior not applicable) and SpliceAI predicts no splice impact (max delta 0.00). The VCEP PP3 rules do not apply to nonsense variants.	cspec spliceai
PP4	Not met	No patient-specific phenotype data (MSI status, IHC, tumor type) is available for this variant in the case materials. PP4 under the InSiGHT VCEP requires at least one CRC/Endometrial MSI-H tumor and/or loss of MMR protein expression consistent with the variant location.
PP5	N/A	PP5 is not applicable for this VCEP. The InSiGHT VCEP v2.0 states: 'This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.'	cspec
BA1	Not met	BA1 under the InSiGHT VCEP v2.0 requires a gnomAD v4 Grpmax filtering allele frequency ≥ 0.001 (0.1%). This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada. The frequency threshold for BA1 is not met.	gnomad_v2 gnomad_v4
BS1	Not met	BS1 under the InSiGHT VCEP v2.0 requires a gnomAD v4 Grpmax filtering allele frequency ≥ 0.0001 and < 0.001 (0.01-0.1%) with exclusion of founder pathogenic variants. This variant is absent from all gnomAD datasets. The frequency threshold for BS1 is not met.	gnomad_v2 gnomad_v4
BS2	Not met	BS2 under the InSiGHT VCEP v2.0 requires co-occurrence in trans with a known pathogenic variant in a patient with colorectal cancer after age 45 without CMMRD features. No such co-occurrence data is available for this variant.
BS3	Not met	No variant-specific functional data demonstrating a benign or normal functional effect is available. The calibrated MMR functional assay documentation does not include this variant, and no publications report functional studies showing normal MMR function for p.Ser184Ter.
BS4	Not met	No co-segregation or lack-of-segregation data is available for this variant. No family pedigrees with Bayes likelihood ratios are present in the case materials.
BP1	N/A	BP1 is not applicable under the InSiGHT VCEP v2.0. The VCEP states: 'Missense variant in a gene where only loss of function causes disease is not applicable.' This variant is a nonsense change causing loss of function.	cspec
BP2	N/A	BP2 is not applicable under the InSiGHT VCEP v2.0. The VCEP states: 'BS2 is used instead.'	cspec
BP4	N/A	BP4 under the InSiGHT VCEP v2.0 is defined for missense variants with HCI prior <0.11 or intronic/synonymous variants with SpliceAI delta ≤ 0.1. This variant is a nonsense substitution (p.Ser184Ter) creating a premature termination codon. Neither VCEP BP4 rule applies; SpliceAI delta of 0.00 for a nonsense variant does not constitute evidence of no impact.	cspec spliceai
BP5	Not met	No tumor data demonstrating MSS status, retained MMR protein expression, or an alternate molecular basis for disease is available for this variant. BP5 under the InSiGHT VCEP requires tumor evidence inconsistent with pathogenic MMR deficiency.
BP6	N/A	BP6 is not applicable for this VCEP. The InSiGHT VCEP v2.0 states: 'This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.'	cspec
BP7	N/A	BP7 under the InSiGHT VCEP v2.0 applies to synonymous (silent) or intronic variants. NM_000249.3:c.551C>G is a nonsense variant (p.Ser184Ter), not a synonymous or intronic change, and therefore does not qualify for BP7.	cspec

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