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NM_002439.5:c.2006G>A
p.Arg669Gln · MSH3
ACMG/AMP
0%
complete
Final classification
VUS
PM2BP4
MSH3
c.2006G>A
p.Arg669Gln
missense · exon 14

MSH3 encodes a protein that partners with MSH2 to form MutS beta, a key component of the DNA mismatch repair system that recognizes and corrects errors made during DNA replication. It acts as a tumor suppressor: loss of MSH3 function leads to mismatch repair deficiency, an elevated mutation rate, and increased cancer risk, and the gene is frequently altered in mismatch repair-deficient colorectal cancers. Defects in MSH3 are linked to susceptibility to endometrial cancer, and inherited mutations are associated with an autosomal recessive form of familial adenomatous polyposis, with minimal evidence for a role in Lynch syndrome. Tumors with mismatch repair deficiency, including those involving MSH3, tend to respond well to immune checkpoint inhibitor therapies.

This variant

MSH3 encodes the MSH2-partner protein MutS beta, whose loss impairs DNA mismatch repair and is associated with autosomal recessive familial adenomatous polyposis and mismatch-repair-deficient cancers.

Transcript
NM_002439.5
HGVS · transcript:coding
NM_002439.5:c.2006G>A
GRCh38
chr5:80768042 G>A
GRCh37
chr5:80063861 G>A
VUS: PM2 supporting for rarity plus BP4 supporting for a low REVEL score do not satisfy a generic ACMG/AMP pathogenic or benign combination rule.
Classification rationale
PM2 BP4 VUS
MSH3 c.2006G>A missense · exon 14

PM2 supporting: gnomAD v4.1 shows an allele frequency of 4.46249e-05 with zero homozygotes. BP4 supporting: REVEL score 0.202 is below the generic BP4 threshold of 0.29.

PM2 + BP4 → VUS
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_002439.5 · variants mapped to exon structure
MSH3 NM_002439.5
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 22 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
Met at supporting: gnomAD v4.1 AF 4.46249e-05 is below the generic PM2 threshold of 0.0001, with zero homozygotes.
Default all-comers gnomAD v4.1 reports AF=4.46249e-05 from 72/1,613,448 alleles, with zero homozygotes.Default all-comers gnomAD v2.1 reports AF=2.38798e-05 from 6/251,258 alleles, with zero homozygotes.Concordant non-cancer subsets report AF=2.1122e-05 in gnomAD v2.1 non-cancer exomes and AF=2.70933e-05 in gnomAD v3.1 non-cancer genomes, with zero homozygotes in both.
BP4 supporting Benign
Met at supporting strength: REVEL score 0.202 is below the BP4 threshold of 0.29 for missense variants.
The normalized consequence is missense, NM_002439.5:c.2006G>A (p.Arg669Gln), so REVEL is the applicable BP4 path and SpliceAI is not used.REVEL score: 0.202; generic ClinGen SVI calibration assigns BP4 supporting at <=0.29, moderate at <=0.183, and strong at <=0.016 (Pejaver et al. 2022, PMID:36413997).
Assessed · not applied · 5 not met · 17 not assessed
Pathogenic
PS1 Not assessed: no validated alternate-codon variant producing the same p.Arg669Gln amino-acid change was identified.
PS2 Not assessed: no confirmed proband de novo observation or parental testing showing absence of NM_002439.5:c.2006G>A in both biological parents.
PS3 Not assessed: no validated variant-specific functional assay or controlled biological readout demonstrating that MSH3 p.Arg669Gln impairs function was identified.
PS4 Not assessed: no case-control counts, enrichment statistic, or variant-specific affected-patient cohort is available for c.2006G>A.
PM1 Not assessed: no MSH3-approved domain table or validated critical functional-region annotation places p.Arg669 in a PM1-qualifying region.
PM3 Not assessed: no affected-proband biallelic observation or confirmed in-trans pathogenic MSH3 variant is documented.
PM5 Not assessed: zero validated pathogenic or likely pathogenic alternate missense variants at MSH3 residue Arg669 were identified.
PM6 Not assessed: no affected proband with a presumed de novo NM_002439.5:c.2006G>A result and no supporting parental or family evidence is reported.
PP1 Not assessed: no informative affected relatives, non-carriers, meioses, or phenotype-concordant family segregation data are available.
PP2 Not assessed: MSH3 loss-of-function evidence is present, but no gene-specific missense-rate data establish PP2 eligibility.
PP3 Not met: REVEL score 0.202 is below the PP3 supporting threshold of 0.644 for missense variants.
PP4 Not assessed: no patient phenotype or family history sufficiently specific for an MSH3-related disease is documented.
PP5 Not met: ClinVar reports 0 expert-panel submissions, and no exact-variant Pathogenic or Likely pathogenic expert-panel classification exists.
Benign
BA1 Not met: gnomAD v4.1 allele frequency 4.46249e-05 is far below the generic BA1 threshold of 0.05.
BS1 Not met: the highest gnomAD v4.1 frequency is 4.46249e-05, below the generic BS1 threshold of 0.01.
BS2 Not assessed: gnomAD shows zero homozygotes, but available heterozygotes lack individual phenotype data needed to establish BS2.
BS3 Not assessed: no validated variant-specific assay with controlled, disease-relevant results showing normal MSH3 function was identified.
BS4 Not assessed: no tested affected relatives lacking NM_002439.5:c.2006G>A and no informative non-segregation observation are documented.
BP1 Not assessed: MSH3 loss-of-function evidence alone does not prove that pathogenic missense variants are uncommon enough for BP1.
BP2 Not assessed: no documented cis co-occurrence with a pathogenic or likely pathogenic MSH3 variant is available.
BP5 Not assessed: no confirmed alternate molecular or clinical explanation is documented to account for the relevant phenotype independently of this variant.
BP6 Not met: ClinVar reports 0 expert-panel submissions, so the two single-submitter Likely benign assertions cannot trigger BP6.
N/A · 4 PVS1 · 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= 4.46249e-05; MAF= 0.00446%, 72/1613448 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 6.66889e-05; MAF= 0.00667%, 4/59980 alleles, homozygotes = 0); grpmax FAF= 4.347e-05.
v2.1
This variant is present in gnomAD v2.1 (AF= 2.38798e-05; MAF= 0.00239%, 6/251258 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 8.67303e-05; MAF= 0.00867%, 3/34590 alleles, homozygotes = 0); grpmax FAF= 2.298e-05.
🇨🇦 CA
Not available in gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.0045% · 72 / 1,613,448
0 hom · FAF 0.0043%
Admixed American
4 / 59,980
0.0067%
European (non-Finnish)
64 / 1,179,766
0.0054%
East Asian
1 / 44,844
0.0022%
South Asian
2 / 91,064
0.0022%
African/African American
1 / 74,778
0.0013%
+ 5 not observed (Remaining individuals, European (Finnish), Amish, Middle Eastern, Ashkenazi Jewish)
gnomAD v2.1
0.0024% · 6 / 251,258
0 hom · FAF 0.0023%
Admixed American
3 / 34,590
0.0087%
African/African American
1 / 16,244
0.0062%
European (non-Finnish)
2 / 113,578
0.0018%
+ 5 not observed (Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, 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 (8 clinical laboratories) and as Likely benign (2 clinical laboratories). (ClinVarID = 654902)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02). REVEL score = 0.202. BayesDel score = -0.379204.
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. MSH3, a DNA mismatch repair protein, is frequently mutated in colorectal cancers.
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 previously been reported in somatic cancers (COSMIC; COSV99434793, n = 1 times).
Hotspots
This variant does not lie in a statistically significant hotspot.
Literature · how each cited paper was used
1papers cited
Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 7 further PMIDs triaged but not cited — see Sources & references.
Rule & framework references · cited for criterion definitions, not variant evidence
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.
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 7 PMIDs not cited in assessment
24905773 ↗ Endometrial cancer: a review and current management strategies: part I. CLINVAR
24929052 ↗ Endometrial cancer: a review and current management strategies: part II. 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
26467025 ↗ A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders. CLINVAR
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. 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