NM_001040108.2:c.3637G>A

MLH3 · NP_001035197.1:p.(Glu1213Lys) · NM_001040108.2

GRCh37: chr14:75505049 C>T · GRCh38: chr14:75038346 C>T

Gene: MLH3 Transcript: NM_001040108.2

Final call

VUS

BP4 supporting benign

Variant details

Gene

MLH3

Transcript

NM_001040108.2

Protein

NP_001035197.1:p.(Glu1213Lys)

gnomAD AF

0.00014385687728884353 (v4.1)

ClinVar

Uncertain significance

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

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.

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.

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.

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).

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.

Final determination: Generic ACMG/AMP 2015 fallback rules do not meet benign, likely benign, likely pathogenic, or pathogenic combination thresholds, so the variant is classified as Variant of Uncertain Significance.

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	N/A	Missense variant (p.Glu1213Lys); does not fall into null-variant buckets (nonsense, frameshift, canonical ±1,2 splice consensus) per ClinGen SVI PVS1 recommendations (PMC6185798).	pvs1_generic_framework pvs1_variant_assessment
PS1	Not assessed	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.	clinvar
PS2	Not met	No de novo occurrence of NM_001040108.2:c.3637G>A has been reported in the literature or population databases. PS2 requires confirmation of de novo status with confirmed maternity and paternity.
PS3	Not met	No variant-specific functional studies (in vitro or in vivo) demonstrating a deleterious effect were identified for MLH3 p.Glu1213Lys. OncoKB reports unknown oncogenic effect with no variant-specific functional evidence curated.	oncokb
PS4	Not met	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. No case-control studies report this variant.	gnomad_v2 gnomad_v4
PS5	Not assessed	No different pathogenic variant at the same nucleotide position (c.3637) has been established. PS5 requires a different pathogenic nucleotide change at the same position.	clinvar
PM1	Not met	Residue Glu1213 lies in the C-terminal region of MLH3 outside well-defined functional domains. The variant does not lie in a statistically significant mutational hotspot (hotspots screen negative). No critical functional domain identified at this position.
PM2	Not met	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%). It is not absent from population controls; PM2 requires absence or extremely low frequency in population databases.	gnomad_v2 gnomad_v4
PM5	Not met	No pathogenic missense variant at the same amino acid residue (Glu1213) has been identified. Automated PM5 candidate harvesting returned no candidates.	pm5_candidates
PM6	Not met	No de novo occurrence of this variant has been reported in the literature or databases. PM6 requires confirmed de novo status without confirmation of paternity and maternity.
PP1	Not assessed	No published co-segregation studies involving NM_001040108.2:c.3637G>A in families with MLH3-associated disease were identified. PP1 requires demonstration of co-segregation with disease in multiple affected family members.
PP2	Not assessed	Insufficient evidence to determine whether MLH3 has a low rate of benign missense variation and whether missense variants are a common mechanism of disease. MLH3 is not a well-characterized gene for PP2 application in generic ACMG framework.
PP3	Not met	Multiple lines of computational evidence do not support a deleterious effect. REVEL score 0.068 (benign-leaning), BayesDel score -0.421 (benign-leaning), and SpliceAI max delta 0.04 (no predicted splicing impact). PP3 requires computational evidence supporting a deleterious effect.	revel bayesdel spliceai
PP4	Not assessed	No specific patient phenotype or family history data were available for assessment. PP4 requires that the patient's phenotype or family history is highly specific for a disease with a single genetic etiology.
PP5	Not met	ClinVar classification for this variant is Uncertain Significance (5 clinical laboratories, criteria provided, single submitter). No reputable source has classified this variant as pathogenic. PP5 requires a reputable source to report the variant as pathogenic.	clinvar
BA1	Not met	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). Neither exceeds the BA1 threshold of >1% for a standing-alone benign criterion.	gnomad_v2 gnomad_v4
BS1	Not met	gnomAD v2.1 allele frequency is 0.0113% and v4.1 allele frequency is 0.0144%. Neither exceeds the BS1 threshold of >0.3% for a strong benign population frequency criterion.	gnomad_v2 gnomad_v4
BS2	Not assessed	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. MLH3-associated disease may exhibit recessive inheritance with incomplete penetrance, complicating direct BS2 application without clinical context.	gnomad_v2 gnomad_v4
BS3	Not met	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. BS3 requires direct functional evidence of a benign effect.	oncokb
BS4	Not assessed	No family segregation data are available for this variant. BS4 requires lack of segregation in affected members of a family; this cannot be assessed without family genotype and phenotype data.
BP1	Not met	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. Missense variants have been reported in association with MLH3-related phenotypes.	pvs1_gene_context
BP2	Not met	No observation of this variant in trans with a known pathogenic MLH3 variant in a healthy individual has been reported. gnomAD shows zero homozygotes for this variant.	gnomad_v2 gnomad_v4
BP3	N/A	BP3 applies to in-frame deletions/insertions in repetitive regions; this is a missense substitution.
BP4	Met	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 bayesdel spliceai
BP5	Not met	No case has been identified in which this variant is found alongside an alternate molecular basis for disease. BP5 requires a variant to be found in a case with an established alternate molecular cause.
BP6	Not met	No reputable source has classified this variant as benign. ClinVar classification is Uncertain Significance (5 clinical laboratories). BP6 requires a reputable source to report the variant as benign.	clinvar
BP7	N/A	This is a missense variant (c.3637G>A, p.Glu1213Lys), not a synonymous (silent) variant. BP7 applies exclusively to synonymous variants.
PM3	N/A	Skipped per case instructions; no biallelic observation data assessed.
PM4	N/A	Variant is a missense substitution, not an in-frame deletion or insertion. PM4 applies only to protein-length-altering variants.

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