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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 applied · 22 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
BP4 supporting Benign
Multiple lines of computational evidence suggest no impact on the gene product: REVEL score 0.068 (strongly benign-leaning), BayesDel score -0.421 (benign-leaning), and SpliceAI max delta score 0.04 (no predicted splicing impact). All three concordant in silico predictors support a benign interpretation.
REVEL: 0.068 (benign-leaningthreshold for pathogenic typically >0.5). BayesDel: -0.421 (negative score indicates benign). SpliceAI max delta: 0.04 (no splicing alteration predictedthreshold for effect typically ≥0.2).
Assessed · not applied
Pathogenic
PS1 No established pathogenic variant at amino acid residue E1213 with the same amino acid change (Glu1213Lys) was identified in ClinVar or the literature to satisfy PS1 criteria.
PS2 No de novo occurrence of NM_001040108.2:c.3637G>A has been reported in the literature or population databases.
PS3 No variant-specific functional studies (in vitro or in vivo) demonstrating a deleterious effect were identified for MLH3 p.Glu1213Lys.
PS4 The variant is present in gnomAD population databases at low frequency (v2.1: 0.0113%; v4.1: 0.0144%) with no evidence of statistically significant enrichment in affected individuals over controls.
PM1 Residue Glu1213 lies in the C-terminal region of MLH3 outside well-defined functional domains.
PM2 The variant is present in gnomAD population databases (v2.1: 32/282,848 alleles, AF=0.0113%; v4.1: 232/1,612,714 alleles, AF=0.0144%).
PM5 No pathogenic missense variant at the same amino acid residue (Glu1213) has been identified.
PM6 No de novo occurrence of this variant has been reported in the literature or databases.
PP1 No published co-segregation studies involving NM_001040108.2:c.3637G>A in families with MLH3-associated disease were identified.
PP2 Insufficient evidence to determine whether MLH3 has a low rate of benign missense variation and whether missense variants are a common mechanism of disease.
PP3 Multiple lines of computational evidence do not support a deleterious effect.
PP4 No specific patient phenotype or family history data were available for assessment.
PP5 ClinVar classification for this variant is Uncertain Significance (5 clinical laboratories, criteria provided, single submitter).
Benign
BA1 gnomAD v2.1 allele frequency is 0.0113% (32/282,848 alleles) and v4.1 allele frequency is 0.0144% (232/1,612,714 alleles).
BS1 gnomAD v2.1 allele frequency is 0.0113% and v4.1 allele frequency is 0.0144%.
BS2 The variant is observed in heterozygous state in gnomAD (32 alleles in v2.1, 232 alleles in v4.1, zero homozygotes), but individual-level clinical confirmation of healthy adult status is not available.
BS3 No well-established in vitro or in vivo functional studies demonstrating no damaging effect on MLH3 protein function or splicing were identified for this variant.
BS4 No family segregation data are available for this variant.
BP1 While biallelic MLH3 loss-of-function (truncating) variants are associated with polyposis predisposition (PMID:30573798), MLH3 is not established as a gene where primarily truncating variants cause disease to the exclusion of missense variants.
BP2 No observation of this variant in trans with a known pathogenic MLH3 variant in a healthy individual has been reported.
BP5 No case has been identified in which this variant is found alongside an alternate molecular basis for disease.
BP6 No reputable source has classified this variant as benign.
N/A · 5 PVS1 · PM3 · PM4 · BP3 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
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.
v2.1
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.
🇨🇦 CA
This variant is absent from gnomAD-Canada.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.014% · 232 / 1,612,714
0 hom · FAF 0.015%
European (Finnish)
20 / 63,958
0.031%
European (non-Finnish)
201 / 1,178,786
0.017%
Remaining individuals
4 / 62,460
0.0064%
African/African American
4 / 75,002
0.0053%
Ashkenazi Jewish
1 / 29,592
0.0034%
Admixed American
1 / 60,022
0.0017%
South Asian
1 / 91,044
0.0011%
+ 3 not observed (Amish, East Asian, Middle Eastern)
gnomAD v2.1
0.011% · 32 / 282,848
0 hom · FAF 0.014%
Remaining individuals
2 / 7,226
0.028%
European (Finnish)
5 / 25,088
0.02%
European (non-Finnish)
24 / 129,196
0.019%
African/African American
1 / 24,964
0.004%
+ 4 not observed (Admixed American, Ashkenazi Jewish, East Asian, South Asian)
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
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.
Sources & reference links
7Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 11 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
20301390 ↗ Lynch Syndrome. CLINVAR
24493721 ↗ American Society of Clinical Oncology Expert Statement: collection and use of a cancer family history for oncology providers. CLINVAR
26389258 ↗ Cancer Genetics Risk Assessment and Counseling (PDQ®): Health Professional Version. CLINVAR
26389505 ↗ Genetics of Colorectal Cancer (PDQ®): Health Professional Version. CLINVAR
33451724 ↗ Endometrial cancer: A society of gynecologic oncology evidence-based review and recommendations, part II. CLINVAR
33516529 ↗ Endometrial cancer: A society of gynecologic oncology evidence-based review and recommendations. CLINVAR
34043773 ↗ European guidelines from the EHTG and ESCP for Lynch syndrome: an updated third edition of the Mallorca guidelines based on gene and gender. CLINVAR
24905773 ↗ Endometrial cancer: a review and current management strategies: part I. CLINVAR
24929052 ↗ Endometrial cancer: a review and current management strategies: part II. CLINVAR
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR