Starting
Initialising…
0%
MLH3
Final classification
VUS
MLH3 c.3637G>A · p.Glu1213Lys
MLH3

NM_001040108.2:c.3637G>A (p.Glu1213Lys) is a missense variant in exon 6 of MLH3, a mismatch repair gene associated with Lynch syndrome and polyposis predisposition.

Gene
MLH3
Transcript
NM_001040108.2
HGVS · transcript:coding
NM_001040108.2:c.3637G>A
Consequence
N/A
GRCh38
chr14:75038346 C>T
GRCh37
chr14:75505049 C>T
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: BP4 supporting benign; combination = 1 supporting benign, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: BP4 supporting benign; combination = 1 supporting benign, which maps to VUS.
Classification rationale
BP4 VUS
MLH3 c.3637G>A

NM_001040108.2:c.3637G>A (p.Glu1213Lys) is a missense variant in exon 6 of MLH3, a mismatch repair gene associated with Lynch syndrome and polyposis predisposition.1 This variant is present in gnomAD population databases at low frequency: v2.1 AF=0.0113% (32/282,848 alleles) and v4.1 AF=0.0144% (232/1,612,714 alleles), with no homozygotes observed. It does not meet BA1 (>1%), BS1 (>0.3%), or PM2 (absent/extremely low) population frequency thresholds.2 ClinVar reports this variant as Uncertain Significance based on submissions from 5 clinical laboratories (ClinVar variation ID 847280). No expert panel review or pathogenic classification is available.3 Multiple in silico predictors concordantly suggest a benign effect: REVEL score 0.068, BayesDel score -0.421, and SpliceAI max delta 0.04, supporting BP4 (supporting benign).4 No variant-specific functional studies, segregation data, de novo occurrences, case-control enrichment, or pathogenic comparator variants at the same residue were identified. No publications specifically mention this variant. The only met criterion is BP4 (supporting benign). No pathogenic or other benign criteria are met. The evidence is insufficient to classify this variant beyond Uncertain Significance under generic ACMG/AMP 2015 rules.5

BP4 VUS
1 pvs1_variant_assessment
4 revelbayesdelspliceai ↗
5 generic_acmg_combination_rules
Gene diagram · NM_001040108.2 · variants mapped to exon structure
MLH3 NM_001040108.2
Fetching transcript structure from UCSC…
Applied criteria · 1 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      Population frequency
      Overall AF
      232 / 1,612,714
      0.014%
      Highest · European (Finnish)
      0.031%
      Homozygotes
      0
      grpmax FAF
      0.015%
      Allele frequency by ancestry — gnomAD v4.1
      observed in 6 of 9 groups
      AncestryAllele countFrequencyHomozygotes
      European (Finnish) 20 / 63,958 0.031% 0
      European (non-Finnish) 201 / 1,178,786 0.017% 0
      African/African American 4 / 75,002 0.0053% 0
      Ashkenazi Jewish 1 / 29,592 0.0034% 0
      Admixed American 1 / 60,022 0.0017% 0
      South Asian 1 / 91,044 0.0011% 0
      Amish 0 / 912
      East Asian 0 / 44,878
      Middle Eastern 0 / 6,060
      This variant is present in gnomAD v4.1 (AF= 0.000143857; MAF= 0.01439%, 232/1612714 alleles, homozygotes = 0) and has highest observed frequency in the European (Finnish) population (AF= 0.000312705; MAF= 0.03127%, 20/63958 alleles, homozygotes = 0); grpmax FAF= 0.00015121.
      Overall AF
      32 / 282,848
      0.011%
      Highest · Remaining individuals
      0.028%
      Homozygotes
      0
      grpmax FAF
      0.014%
      Allele frequency by ancestry — gnomAD v2.1
      observed in 4 of 8 groups
      AncestryAllele countFrequencyHomozygotes
      Remaining individuals 2 / 7,226 0.028% 0
      European (Finnish) 5 / 25,088 0.02% 0
      European (non-Finnish) 24 / 129,196 0.019% 0
      African/African American 1 / 24,964 0.004% 0
      Admixed American 0 / 35,438
      Ashkenazi Jewish 0 / 10,370
      East Asian 0 / 19,954
      South Asian 0 / 30,612
      This variant is present in gnomAD v2.1 (AF= 0.000113135; MAF= 0.01131%, 32/282848 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 0.000276778; MAF= 0.02768%, 2/7226 alleles, homozygotes = 0); grpmax FAF= 0.00013731.
      This variant is absent from gnomAD-Canada.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (5 clinical laboratories). (ClinVarID = 847280)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.04). REVEL score = 0.068. BayesDel score = -0.421174.
      Functional / OncoKB screenshot
      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. MLH3, a DNA mismatch repair protein, is infrequently altered in cancer.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      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.
      Literature · 11 PMIDs triaged · 8 high-priority
      11papers screened
      Papers triaged by theme: functional/splicing/segregation/case_observation. high_priority_papers include abstract snippets. Use these to support PS3/BS3/PS4/PP1/PP3/PP5.
      25741868 ↗ functional
      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.
      The American College of Medical Genetics and Genomics (ACMG) previously developed guidance for the interpretation of sequence variants.(1) In the past decade, sequencing technology has evolved rapidly with the advent of high-throughput next-generation sequencing. By adopting and leveraging next-generation sequencing, clinical laboratories are now performing an ever-increasing catalogue of genetic
      BS3PP5PS3PS4
      20301390 ↗ case observation
      Untitled reference
      PP5PS4
      24493721 ↗ case observation
      American Society of Clinical Oncology Expert Statement: collection and use of a cancer family history for oncology providers.
      PP5PS4
      26389258 ↗ case observation
      Untitled reference
      PP5PS4
      26389505 ↗ case observation
      Untitled reference
      PP5PS4
      33451724 ↗ hotspot domain
      Endometrial cancer: A society of gynecologic oncology evidence-based review and recommendations, part II.
      In 2014, the Society of Gynecologic Oncology's Clinical Practice Committee published a clinical update reviewing the treatment of women with endometrial cancer. At that time, there had been significant advances in the diagnosis, work-up, surgical management, and available treatment options allowing for more optimal care of affected women. This manuscript, Part II in a two-part series, includes spe
      PM1PP5PS4
      33516529 ↗ case observation
      Endometrial cancer: A society of gynecologic oncology evidence-based review and recommendations.
      In 2014, the Society of Gynecologic Oncology's Clinical Practice Committee published a clinical update reviewing the treatment of women with endometrial cancer. At that time, there had been significant advances in the diagnosis, work-up, surgical management, and available treatment options allowing for more optimal care of affected women. Despite these advances, the incidence of endometrial cancer
      PP5PS4
      34043773 ↗ case observation
      European guidelines from the EHTG and ESCP for Lynch syndrome: an updated third edition of the Mallorca guidelines based on gene and gender.
      Lynch syndrome is the most common genetic predisposition for hereditary cancer but remains underdiagnosed. Large prospective observational studies have recently increased understanding of the effectiveness of colonoscopic surveillance and the heterogeneity of cancer risk between genotypes. The need for gene- and gender-specific guidelines has been acknowledged. The European Hereditary Tumour Group
      PP5PS4
      24905773 ↗ background review
      Endometrial cancer: a review and current management strategies: part I.
      PP5PS4
      24929052 ↗ background review
      Endometrial cancer: a review and current management strategies: part II.
      PP5PS4
      28492532 ↗ background review
      Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
      PP5PS4
      Sources & reference links
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots