The MLH1 NM_000249.4:c.688G>C (p.Glu230Gln; p.E230Q) variant has been reported in ClinVar as a variant of uncertain significance with four clinical laboratory submissions.1 This variant is present at very low frequency in population databases, including gnomAD v4.1 at 2/1576948 alleles (AF 1.26827e-06; grpmax FAF 2.9e-07) and gnomAD v2.1 at 1/31410 alleles (AF 3.1837e-05), which is below the MLH1 PM2_Supporting threshold of 0.00002 in gnomAD v4.2 No variant-specific calibrated functional assay result for p.Glu230Gln was identified in the reviewed mismatch repair functional assay references.3 For this MLH1 missense variant, the HCI prior probability is 0.0581, below the BP4 threshold of 0.11; REVEL is 0.627, BayesDel is 0.158729, and SpliceAI predicts no significant splice impact with a maximum delta score of 0.04.4
Final classification
Uncertain Significance - Conflicting Evidence
PM2BP4
MLH1
c.688G>C
p.Glu230Gln
This variant
The MLH1 NM_000249.4:c.688G>C (p.Glu230Gln; p.E230Q) variant has been reported in ClinVar as a variant of uncertain significance with four clinical laboratory submissions.
ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MLH1 Version 2.0.0 v2.0.0 criteria-combination framework: matched Rule31 (Benign.Supporting >=1 + Pathogenic.Supporting >=1) with applied criteria: PM2 supporting, BP4 supporting; maps to Uncertain Significance - Conflicting Evidence.
Classification rationale
PM2
BP4
Uncertain Significance - Conflicting Evidence
MLH1 c.688G>C
PM2 + BP4
→
Uncertain Significance - Conflicting Evidence
3
vcep_functional_assay_svi_documentation_mmroncokb ↗
4
hci_priorrevelbayesdelspliceai ↗cspec ↗
LYFE Sciences is an AI system, and it can make mistakes. Criteria
may be applied incorrectly, sources may be misread, and a confident-looking
classification can still be wrong. Double-check every criterion and
its underlying evidence before relying on any call.
Gene diagram
· NM_000249.4 · variants mapped to exon structure
MLH1
NM_000249.4
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 15 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 2
Strength
Supporting
Moderate
Strong
Very strong
PM2
supporting
Pathogenic
This variant is present at very low frequency in gnomAD v4.1 at 2/1576948 alleles (AF 1.26827e-06), which is below the MLH1 PM2_Supporting threshold of 0.00002.
gnomAD v4.1 AF 1.26827e-062 of 1576948 allelesThreshold <0.00002
BP4
supporting
Benign
For this MLH1 missense variant, the HCI prior probability is 0.0581, which is below the BP4 threshold of 0.11 and supports BP4_Supporting. REVEL is 0.627 and BayesDel is 0.158729, and SpliceAI predicts no significant splice impact with a maximum delta score of 0.04.
HCI prior 0.0581REVEL 0.627BayesDel 0.158729
Assessed · not applied
· 4 not met · 11 not assessed
Pathogenic
PVS1
This is a missense substitution, not a nonsense, frameshift, canonical +/-1,2 splice, initiation codon, or proven splice-abrogating variant, so PVS1 is not met under the MLH1-specific rules.
PS1
No previously established MLH1 pathogenic or likely pathogenic variant causing the same amino acid change with a different nucleotide change was identified in the available evidence, so PS1 was not applied.
PS2
No confirmed de novo occurrence data with the point-based evidence required by the MLH1 VCEP were identified, so PS2 was not assessed.
PS3
No variant-specific calibrated functional assay result for p.Glu230Gln was identified in the reviewed mismatch repair functional assay references, so PS3 was not applied.
PM3
No confirmed in trans observations with an established pathogenic MLH1 variant and no PM3 point-based evidence were identified, so PM3 was not assessed.
PM5
No eligible same-residue pathogenic or likely pathogenic missense comparator at codon 230 was established from the available evidence, so PM5 was not applied.
PP1
No segregation data with a calculable Bayes likelihood ratio were identified, so PP1 was not assessed.
PP3
For this MLH1 missense variant, the HCI prior probability is 0.0581, which is below the PP3 thresholds of >0.68 for Supporting and >0.81 for Moderate.
PP4
No tumor MSI, mismatch repair immunohistochemistry, or MLH1 promoter methylation data were identified to support the MLH1-specific PP4 phenotype rule, so PP4 was not assessed.
Benign
BA1
The gnomAD v4.1 grpmax filtering allele frequency is 2.9e-07, which is below the BA1 threshold of 0.001, so BA1 is not met.
BS1
The gnomAD v4.1 grpmax filtering allele frequency is 2.9e-07, which is below the BS1 range of 0.0001 to <0.001, so BS1 is not met.
BS2
No confirmed in trans co-occurrence with a known pathogenic MLH1 variant in an individual meeting the MLH1 VCEP BS2 conditions was identified, so BS2 was not assessed.
BS3
No variant-specific calibrated functional evidence showing retained mismatch repair function was identified in the reviewed functional assay references, so BS3 was not applied.
BS4
No non-segregation data with a calculable Bayes likelihood ratio were identified, so BS4 was not assessed.
BP5
No tumor findings meeting the MLH1-specific BP5 conditions, such as multiple MSS or inconsistent mismatch repair protein results or qualifying MLH1 methylation/BRAF evidence, were identified, so BP5 was not assessed.
N/A · 11
PS4 · PM1 · PM4 · PM6 · PP2 · PP5 · BP1 · BP2 · BP3 · BP6 · BP7
Research & evidence
Population frequency
gnomAD v4.1
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 1.26827e-06; MAF= 0.00013%, 2/1576948 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 1.74471e-06; MAF= 0.00017%, 2/1146320 alleles, homozygotes = 0); grpmax FAF= 2.9e-07.
v2.1
This variant is present in gnomAD v2.1 (AF= 3.1837e-05; MAF= 0.00318%, 1/31410 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 6.4792e-05; MAF= 0.00648%, 1/15434 alleles, homozygotes = 0).
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00013%
· 2 / 1,576,948
0 hom · FAF 2.9e-05%
0 hom · FAF 2.9e-05%
European (non-Finnish) 2 / 1,146,320 |
0.00017% |
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
0.0032%
· 1 / 31,410
0 hom
0 hom
European (non-Finnish) 1 / 15,434 |
0.0065% |
+ 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
ClinVar
This variant has been reported in ClinVar as Uncertain significance (4 clinical laboratories). (ClinVarID = 483554)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.04). REVEL score = 0.627. BayesDel score = 0.158729. HCI prior probability for pathogenicity = 0.0581. MAPP score = 4.41. Custom PP2 score = 0.715.
Functional
Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. MLH1, a DNA mismatch repair protein, is recurrently altered by deletion and mutation in various cancer types.
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.
Sources & reference links
Triaged references · 3 PMIDs not cited in assessment
25741868 ↗
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.
CLINVAR
25394175 ↗
A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment.
CLINVAR
28492532 ↗
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
CLINVAR