MSH3 c.316C>G, p.(Gln106Glu)

Reasoning

The variant is rare in large population databases and has no observed homozygotes: AF 0.000148697 in gnomAD v4.1 and AF 0.0000671796 in gnomAD v2.1, with the highest reported subpopulation AF 0.000196605 and 0 homozygotes in gnomAD v4.1. This is compatible with PM2 at supporting strength under the generic non-VCEP rare-frequency approach, but the case lacks a formal MSH3-specific maximum credible allele-frequency model incorporating disease prevalence, penetrance, and the confirmed recessive disease mechanism; human review is therefore retained.

Rule

Generic ACMG/AMP PM2: variant absent from or present at an extremely low frequency in population databases, accounting for disease mechanism and expected maximum allele frequency. Applied here at supporting strength using the generic non-VCEP rare-frequency threshold of <0.1%; no MSH3-specific rule was available.

Evidence considered

• gnomAD v4.1: AF 0.000148697 (240/1,614,020 alleles), maximum reported subpopulation AF 0.000196605, and homozygotes = 0.
• gnomAD v2.1: AF 0.0000671796 (19/282,824 alleles), maximum reported subpopulation AF 0.000139381, and homozygotes = 0.
• The variant is present but extremely rare rather than absent; the available generic approach permits supporting PM2 for a rare variant below 0.1% when no applicable gene-specific specification is available.
• gnomAD-Canada v1.0 was not available because the query timed out; this is a data-availability limitation, not evidence that the variant is absent.

Still missing

• No MSH3-specific VCEP/CSPEC rule or validated maximum credible allele-frequency threshold was available.
• No formal disease-prevalence, penetrance, or inheritance-based frequency calculation was supplied for this missense allele.
• gnomAD-Canada v1.0 was unavailable for this variant because the query timed out.

Sources

Reasoning

MSH3 NM_002439.5:c.316C>G is a missense variant encoding p.(Gln106Glu). No applicable VCEP/CSPEC rule was found, so the generic missense path uses REVEL only. The REVEL score is 0.176, which is below the BP4 threshold of <0.250; BP4 is met at supporting strength.

Rule

Generic ACMG/AMP fallback, missense path: REVEL <0.250 supports BP4; REVEL 0.176 meets that threshold.

Evidence considered

• The case evidence identifies this as the missense change NP_002430.3:p.(Gln106Glu) and reports REVEL 0.176.
• No MSH3 VCEP/CSPEC or other gene-specific PP3/BP4 framework was available; the generic ACMG fallback therefore applies.
• For generic missense assessment, this laboratory applies calibrated REVEL thresholds: >0.750 for PP3 and <0.250 for BP4. The published ClinGen SVI calibration is PMID:36413997.

Sources

Reasoning

MSH3 NM_002439.5:c.316C>G is a missense variant encoding p.(Gln106Glu). No applicable VCEP/CSPEC rule was found, so the generic missense path uses REVEL only. The REVEL score is 0.176, below the PP3 threshold of >0.750; PP3 is not met.

Rule

Generic ACMG/AMP fallback, missense path: REVEL >0.750 supports PP3; REVEL 0.176 does not meet that threshold.

Evidence considered

• The case evidence identifies this as the missense change NP_002430.3:p.(Gln106Glu) and reports REVEL 0.176.
• No MSH3 VCEP/CSPEC or other gene-specific PP3/BP4 framework was available; the generic ACMG fallback therefore applies.
• For generic missense assessment, this laboratory applies calibrated REVEL thresholds: >0.750 for PP3 and <0.250 for BP4. The published ClinGen SVI calibration is PMID:36413997.

Sources

Reasoning

ClinVar has no exact-variant expert-panel submission classified Pathogenic or Likely pathogenic. The record contains only single-submitter laboratory assertions (predominantly uncertain significance and one likely benign assertion), which are ineligible for PP5.

Rule

Apply PP5 only for an exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification.

Evidence considered

• The ClinVar submission audit for NM_002439.5(MSH3):c.316C>G reports zero expert-panel submissions; the aggregate record is uncertain significance with single-submitter laboratory assertions.

Still missing

• An exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification.

Sources

Reasoning

The variant is not sufficiently common for a stand-alone benign frequency criterion. gnomAD v4.1 reports AF 0.000148697 (240/1,614,020 alleles), maximum population AF 0.000196605 in European non-Finnish individuals, and no homozygotes; gnomAD v2.1 reports AF 0.0000671796. These frequencies are far below the generic BA1 threshold of 1%.

Rule

Generic ACMG/AMP BA1: allele frequency >=1% in a population database can support stand-alone benign evidence. No applicable MSH3-specific VCEP/CSPEC was available.

Evidence considered

• gnomAD v4.1: 240/1,614,020 alleles, AF 0.000148697; highest reported subpopulation AF 0.000196605 in European (non-Finnish) individuals; homozygotes = 0.
• gnomAD v2.1: 19/282,824 alleles, AF 0.0000671796; highest reported subpopulation AF 0.000139381; homozygotes = 0.
• Generic ACMG/AMP population interpretation: a frequency of at least 1% is required for BA1; the observed frequency is orders of magnitude lower.

Sources

Reasoning

The observed allele frequency does not exceed the expected maximum frequency for a pathogenic MSH3 variant under the available generic population thresholds. gnomAD v4.1 AF is 0.000148697, with maximum reported subpopulation AF 0.000196605; both are below 0.3%.

Rule

Generic ACMG/AMP BS1: allele frequency greater than expected for the disorder but below the BA1 threshold. In this generic non-VCEP assessment, AF >0.3% is used as the benign-frequency screening threshold; the observed AF does not reach it.

Evidence considered

• gnomAD v4.1 reports AF 0.000148697 overall and 0.000196605 in the highest-frequency reported subpopulation, European (non-Finnish).
• gnomAD v2.1 reports AF 0.0000671796 overall and 0.000139381 in European (non-Finnish) individuals.
• The observed frequencies are below the generic non-VCEP BS1 screening threshold of 0.3%; no disease-prevalence/penetrance model in the case materials establishes a lower BS1 threshold.

Sources

Reasoning

No homozygous individuals are reported in either gnomAD v2.1 or gnomAD v4.1. Therefore, the required observation of the variant in healthy adults in a homozygous state is absent.

Rule

Generic ACMG/AMP BS2: observation of the variant in a healthy adult individual in the homozygous state, or in a hemizygous state for an X-linked disorder, supports benign evidence. No such observation is present.

Evidence considered

• gnomAD v2.1 reports total homozygotes = 0 and European non-Finnish homozygotes = 0.
• gnomAD v4.1 reports total homozygotes = 0 and European non-Finnish homozygotes = 0.
• The population datasets do not provide the homozygous healthy-adult observation required for BS2; absence of homozygotes is not positive BS2 evidence.

Sources

Reasoning

ClinVar has no exact-variant expert-panel submission classified Benign or Likely benign. The single laboratory Likely benign assertion is not an expert-panel assertion and is ineligible for BP6.

Rule

Apply BP6 only for an exact-variant ClinVar expert-panel Benign or Likely benign classification.

Evidence considered

• The ClinVar submission audit for NM_002439.5(MSH3):c.316C>G reports zero expert-panel submissions; one Likely benign assertion is from a single clinical laboratory.

Still missing

• An exact-variant ClinVar expert-panel Benign or Likely benign classification.

Sources

Reasoning

The variant is MSH3 p.Gln106Glu (Q106E). The reviewed case literature does not document a pathogenic or likely pathogenic variant producing the same amino-acid change at this codon, and no validated same-amino-acid comparator is present in the evidence bundle. The available evidence is therefore insufficient to apply PS1.

Rule

PS1 requires a well-established pathogenic missense variant causing the same amino-acid change as the variant under assessment.

Evidence considered

• The case variant is NM_002439.5:c.316C>G, NP_002430.3:p.(Gln106Glu), and ClinVar contains only uncertain-significance and one likely-benign submissions without an expert-panel classification.
• PMID:28944238 reports other MSH3 variants but does not report c.316C>G, p.Q106E, or a same-amino-acid substitution at residue 106.

Still missing

• No confirmed pathogenic or likely pathogenic same-amino-acid substitution at MSH3 residue 106 was identified in the supplied evidence.

Sources

Reasoning

No case-level evidence documents that NM_002439.5:c.316C>G (p.Gln106Glu) is de novo in a proband. The bundle contains no proband-parent genotype comparison, validated parental testing, maternity/paternity confirmation, or mosaicism assessment sufficient to apply PS2.

Rule

Generic ACMG/AMP PS2 requires a confirmed de novo variant in an affected individual with confirmed parentage; strength depends on the quality and completeness of de novo evidence. No applicable MSH3-specific specification was retrieved.

Evidence considered

• The case summary identifies the variant as MSH3 c.316C>G (p.Gln106Glu), but provides no family, parental-testing, or de novo observation data.
• The paper-extract bundle reports that the fetched literature provides no variant-specific case-level or segregation data for this variant.

Still missing

• Proband and both parental genotypes are not documented.
• No confirmed maternity/paternity and no assessment for parental mosaicism are provided.
• No case-level phenotype and inheritance context is provided to assess whether a de novo event would be relevant.

Sources

Reasoning

No validated variant-specific functional assay demonstrating a damaging effect was identified. The available literature extracts either do not mention MSH3 c.316C>G (p.Gln106Glu) or provide only general variant-classification, cancer, or gene-panel context without functional results, assay controls, or biologically relevant measurements for this variant.

Rule

Generic ACMG/AMP PS3: functional studies supportive of a damaging effect may support PS3 only when the assay is well established, appropriately controlled, and biologically relevant; no such variant-specific evidence is available here.

Evidence considered

• The case bundle identifies no applicable MSH3-specific VCEP or gene-specific functional specification; generic ACMG/AMP criteria are therefore used.
• The extracted full-text literature contains no variant-specific MSH3 p.Gln106Glu functional assay result, control set, or quantitative assay calibration.
• The ClinVar record reports conflicting single-submitter classifications and does not itself constitute functional evidence.

Still missing

• A validated assay directly testing MSH3 p.Gln106Glu function is needed.
• The assay should include appropriate wild-type, pathogenic, and benign controls and demonstrate biological relevance to MSH3 mismatch-repair activity.
• Independent replication or a calibrated quantitative functional framework is unavailable.

Sources

Reasoning

No exact-variant case-control enrichment evidence is available. The only retrieved colorectal cancer case-control paper examined MSH3 but did not report c.316C>G (p.Gln106Glu), so it cannot supply affected-carrier or control-carrier counts for this variant.

Rule

Generic ACMG/AMP PS4: apply only when variant prevalence is significantly increased in affected individuals compared with controls.

Evidence considered

• PMID:28944238 sequenced 1,231 colorectal cancer cases and 93 unaffected controls, but its pre-computed extraction found no mention of MSH3 c.316C>G or p.(Gln106Glu); the reported MSH3 carrier observations concern other variants.

Still missing

• A variant-specific case-control dataset or a rigorously ascertained series reporting c.316C>G carrier counts in affected individuals and controls, with statistical analysis.

Sources

Reasoning

No applicable MSH3 VCEP or gene-specific framework was supplied. vcep_materials.json has no MSH3 domain_tables entry, so there is no authoritative approved critical-domain list to check. The supplied hotspot result is negative, but that does not establish that residue 106 is outside every possible functional domain. PM1 cannot be adjudicated from the available evidence.

Rule

PM1 requires a variant located in a mutational hot spot or critical and well-established functional domain without benign variation.

Evidence considered

• vcep_materials.json reports no CSPEC/VCEP materials and an empty domain_tables object for MSH3.
• The supplied hotspot assessment reports that MSH3 Q106 is not in a statistically significant hotspot; this is insufficient by itself to exclude other critical functional-domain evidence.

Still missing

• No MSH3-specific VCEP domain table or complete validated critical-domain annotation was available.
• No variant-specific functional or statistically significant hotspot evidence was supplied for residue 106.

Reasoning

No applicable MSH3-specific VCEP framework is available, so the generic ACMG/AMP PM3 rule was used. The case bundle contains no affected-proband observation for NM_002439.5:c.316C>G (p.Gln106Glu) in a recessive phenotype, no confirmed pathogenic variant in trans, and no phase or parental testing information. Population, ClinVar, and general gene-level literature records do not establish allelic phase or a qualifying affected-proband observation; therefore PM3 cannot be applied.

Rule

Generic ACMG/AMP PM3: pathogenic or likely pathogenic variants observed in trans with the variant under assessment in affected individuals support a recessive disease mechanism; apply only when the affected-proband observation and phase are sufficiently established.

Evidence considered

• The applicable generic ACMG/AMP framework is PMID:25741868 because the bundle reports no MSH3-specific VCEP or gene-specific framework.
• The case bundle identifies the variant as NM_002439.5:c.316C>G (NP_002430.3:p.(Gln106Glu)) but provides no affected-proband, compound-heterozygous, trans-phase, parental, or segregation observation for this exact variant.
• The reviewed exact-variant literature extraction for PMID:28944238 states that the variant was not mentioned and provides no case-level or segregation data; the other extracted papers likewise provide no exact-variant allelic evidence.

Still missing

• Affected-proband case data for this exact variant are unavailable.
• No confirmed pathogenic/likely pathogenic allele in trans is documented.
• No parental testing, haplotype, or other phase information is documented.
• The inheritance model and biallelic disease context for this individual are not documented.

Sources

Reasoning

The supplied PM5 candidate summary identified no same-residue comparator candidates and explicitly states that classic PM5 semantics could not be confirmed. The literature extraction for the relevant MSH3 cohort also does not report p.Q106E or another substitution at residue 106. There is insufficient evidence to apply PM5.

Rule

PM5 requires a novel missense change at a residue where a different missense change is established as pathogenic.

Evidence considered

• The PM5 candidate summary reports zero same-residue candidates and instructs that PM5 should not be applied from that artifact alone.
• PMID:28944238 lists several other MSH3 variants, but none is at residue 106 and the paper does not establish a pathogenic comparator for this codon.

Still missing

• No confirmed pathogenic or likely pathogenic missense variant at MSH3 residue 106 was identified.

Sources

Reasoning

No case-level evidence documents a presumed de novo occurrence of this variant. There is no report of an affected proband with negative parental testing or other evidence permitting PM6.

Rule

Generic ACMG/AMP PM6 may be used for a presumed de novo variant when parentage and/or parental testing is insufficient for PS2; presumed de novo status must still be supported by case-level evidence. No applicable MSH3-specific specification was retrieved.

Evidence considered

• The consolidated case-evidence bundle contains no documented presumed de novo observation for MSH3 c.316C>G (p.Gln106Glu).
• The paper-extract bundle reports no variant-specific segregation or case-level data for this variant.

Still missing

• No affected-proband case report with parental testing is available.
• No information is provided about whether either parent was tested or found negative.
• No parentage, phenotype, or meiosis-related case details are available.

Sources

Reasoning

No affected relatives carrying this variant, informative meioses, pedigree, or quantitative segregation observations are documented. Therefore, segregation with disease cannot be evaluated and PP1 cannot be applied.

Rule

Generic ACMG/AMP PP1 supports pathogenicity when a variant co-segregates with disease in affected family members; strength may increase with multiple informative meioses. No applicable MSH3-specific specification was retrieved.

Evidence considered

• The case summary and evidence bundle contain no family segregation data for MSH3 c.316C>G (p.Gln106Glu).
• The paper-extract bundle reports that the exact variant has no variant-specific segregation or case-level evidence in the fetched literature.

Still missing

• No pedigree or family structure is provided.
• No affected-relative genotypes or phenotype assessments are provided.
• No informative meioses or segregation likelihood/counts are available.

Sources

Reasoning

The bundle supports MSH3 as a gene in which loss-of-function disease mechanism has been described, but it does not provide a validated gene-specific missense-enrichment rule or demonstrate that missense variation is a rare mechanism for disease in the applicable disorder. The presence of several MSH3 missense variants in one sequencing cohort is not sufficient to establish PP2.

Rule

PP2 requires that missense variants be a common mechanism of disease in the gene and that the assessed missense variant is in a gene where pathogenic missense variation is enriched relative to benign missense variation, according to an applicable specification.

Evidence considered

• PMID:28944238 describes several MSH3 missense variants in a targeted colorectal-cancer susceptibility cohort, but does not establish missense depletion, a disease-specific missense mechanism, or a PP2 rule for MSH3.
• The case materials describe an MSH3 loss-of-function mechanism, but no applicable VCEP framework or quantitative missense-enrichment evidence is available.

Still missing

• No gene-specific missense-enrichment analysis or validated MSH3 PP2 specification was supplied.
• The available MSH3 missense observations do not establish that missense variants are a rare cause of disease.

Sources

Reasoning

No patient-level phenotype for an exact-variant carrier is available, and the reported colorectal cancer context is not demonstrated to be highly specific for MSH3-related disease. The retrieved colorectal cancer cohort does not report this variant.

Rule

Generic ACMG/AMP PP4: apply only when the patient's phenotype or family history is highly specific for a disease with a single genetic etiology.

Evidence considered

• The extraction for PMID:28944238 states that c.316C>G/p.(Gln106Glu) is not mentioned; its MSH3 observations are for other variants, so the paper provides no phenotype evidence for this exact variant.

Still missing

• Clinically detailed exact-variant carrier data showing a phenotype highly specific for the relevant MSH3-associated condition and excluding plausible alternative etiologies.

Sources

Reasoning

No validated variant-specific functional assay demonstrating preserved MSH3 function was identified. The available literature extracts do not report a benign functional result for MSH3 c.316C>G (p.Gln106Glu), and no assay controls, biological relevance, or calibrated benign threshold are available to support BS3.

Rule

Generic ACMG/AMP BS3: well-established functional studies showing no damaging effect may support BS3 only when the assay is well established, appropriately controlled, and biologically relevant; no such variant-specific evidence is available here.

Evidence considered

• The case bundle identifies no applicable MSH3-specific VCEP or gene-specific functional specification; generic ACMG/AMP criteria are therefore used.
• The extracted full-text literature contains no variant-specific MSH3 p.Gln106Glu functional assay result demonstrating preserved function.
• Population presence and computational scores are not functional evidence and were not used to assess BS3.

Still missing

• A validated assay directly testing MSH3 p.Gln106Glu and showing preserved function is needed.
• The assay should include appropriate wild-type, pathogenic, and benign controls and a predefined benign-function threshold.
• Independent replication or a calibrated quantitative functional framework is unavailable.

Sources

Reasoning

No tested unaffected relatives who lack the variant, no informative non-segregation observations, and no phenotype-appropriate family analysis are documented. The available population and ClinVar summaries do not constitute BS4 evidence.

Rule

Generic ACMG/AMP BS4 supports benignity when a variant fails to segregate with disease in affected or appropriately assessed family members; informative phenotypes and genotypes are required. No applicable MSH3-specific specification was retrieved.

Evidence considered

• The consolidated bundle contains no family-level non-segregation evidence for MSH3 c.316C>G (p.Gln106Glu).
• Presence of the variant in gnomAD and mixed single-submitter ClinVar classifications does not establish non-segregation in an informative family and was not used for BS4.

Still missing

• No unaffected relatives with documented genotype and adequate age/phenotype information are reported.
• No informative meioses demonstrating lack of segregation are available.
• No family-level assessment addresses reduced penetrance, phenocopies, or phenotype misclassification.

Sources

Reasoning

Although the supplied materials support an MSH3 loss-of-function disease mechanism, they do not establish that the relevant disease is caused predominantly by truncating variants or provide a gene-specific BP1 rule. Therefore BP1 cannot be applied solely from the gene-level mechanism summary.

Rule

BP1 requires a missense variant in a gene for which primarily truncating variants are known to cause disease, with the gene-specific disease mechanism appropriately established.

Evidence considered

• The case materials characterize MSH3 loss of function as a supported disease mechanism, but do not provide a validated BP1 specification or demonstrate a predominantly truncating disease spectrum.
• PMID:28944238 reports multiple MSH3 missense variants in a targeted cohort without establishing whether missense variants are generally benign or whether truncating variants predominate among pathogenic variants.

Still missing

• No MSH3-specific framework or sufficiently comprehensive variant-spectrum analysis showing that disease is predominantly caused by truncating variants was supplied.
• The available cohort paper reports MSH3 missense variants but does not define the pathogenic variant spectrum for BP1.

Sources

Reasoning

No applicable MSH3-specific VCEP framework is available, so the generic ACMG/AMP BP2 rule was used. The case bundle contains no reliable observation of NM_002439.5:c.316C>G (p.Gln106Glu) in cis with a pathogenic variant or in trans with a benign/likely benign variant, and no phase information. The mere presence of the variant in ClinVar or population databases is not BP2 evidence.

Rule

Generic ACMG/AMP BP2: the variant is observed in trans with a pathogenic/likely pathogenic variant for a dominant disorder, or in cis with a pathogenic/likely pathogenic variant for a recessive disorder; apply only when the comparator allele, inheritance context, and phase are established.

Evidence considered

• The applicable generic ACMG/AMP framework is PMID:25741868 because the bundle reports no MSH3-specific VCEP or gene-specific framework.
• The case bundle provides no affected-individual genotype showing this exact variant with a second allele, and no cis/trans phase, parental testing, haplotype, or family segregation information.
• The exact-variant literature extraction for PMID:28944238 reports no p.Gln106Glu observation or segregation data, and the remaining extracted publications do not supply qualifying allelic evidence.
• ClinVar records the exact variant but do not document the individual-level phase or co-occurring allele required for BP2; ClinVar classification labels were not used as evidence for this criterion.

Still missing

• No individual-level observation with a second variant is documented for this exact variant.
• No pathogenic/likely pathogenic or benign/likely benign comparator allele is documented in the same individual.
• No cis/trans phase determination is documented.
• No phenotype and inheritance context is available to support a BP2 observation.

Sources

Reasoning

No evidence shows that an exact-variant carrier with the relevant phenotype also has a separate pathogenic molecular diagnosis that fully explains that phenotype.

Rule

Generic ACMG/AMP BP5: apply only when a variant is found in a case with an alternate molecular basis for the disease.

Evidence considered

• The reviewed case-evidence bundle contains no exact-variant co-occurrence or alternate molecular-diagnosis report.

Still missing

• Case-level molecular and phenotypic data documenting an alternate pathogenic diagnosis that fully accounts for the presenting phenotype in an exact-variant carrier.