Back
NM_000179.3:c.3787C>T
p.Arg1263Cys · MSH6
0%
complete
Final classification
VUS
BP4
MSH6
c.3787C>T
p.Arg1263Cys
missense · exon 8

MSH6 encodes a protein in the DNA mismatch repair system, which fixes errors made during DNA replication. Partnering with MSH2, it forms a complex that recognizes and helps correct mismatched DNA bases, keeping the genetic code stable. Inherited mutations in MSH6 cause Lynch syndrome (hereditary nonpolyposis colorectal cancer), raising the risk of colorectal, endometrial, ovarian, and other cancers, while mutations in both copies lead to constitutional mismatch repair deficiency. Because faulty mismatch repair drives tumor development and produces microsatellite instability, MSH6 acts as a tumor suppressor, and cancers with such repair defects often respond well to immune checkpoint inhibitor therapy.

This variant

MSH6 encodes a DNA mismatch-repair protein that partners with MSH2 to maintain genomic stability; inherited pathogenic variants cause Lynch syndrome, while biallelic variants cause constitutional mismatch repair deficiency.

Transcript
NM_000179.3
HGVS · transcript:coding
NM_000179.3:c.3787C>T
GRCh38
chr2:47806344 C>T
GRCh37
chr2:48033483 C>T
VUS: BP4 (supporting) was the only applied criterion, and no ClinGen InSiGHT MSH6 pathogenic or benign combination rule was satisfied.
Classification rationale
BP4 VUS
MSH6 c.3787C>T missense · exon 8

BP4 supporting: MSH6 HCI prior 0.0236 is below the VCEP threshold of <0.11. VUS: no pathogenic or benign combination rule was satisfied by the adjudicated criteria.

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_000179.3 · variants mapped to exon structure
MSH6 NM_000179.3
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 15 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 · 1
Strength Supporting Moderate Strong Very strong
BP4 supporting Benign
Met, supporting: MSH6 HCI prior 0.0236 is below the governing BP4 threshold of <0.11 for missense variants.
The governing MSH6 CSPEC specifies BP4 supporting for a missense variant with HCI prior probability <0.11.The exact HCI lookup entry for c.3787C>T / p.R1263C reports pathogenicity probability 0.0236, which meets the governing MSH6 BP4 supporting rule.REVEL score 0.594 does not meet the generic BP4 supporting cutoff <=0.29; that calibration is from Pejaver et al. 2022 (PMID:36413997).
Assessed · not applied · 6 not met · 9 not assessed
Pathogenic
PS1 Not met: no alternate-nucleotide p.Arg1263Cys comparator is established as Pathogenic by the MSH6 VCEP.
PS2 Not assessed: no proband-level de novo observation, parental confirmation, or qualifying Lynch syndrome-spectrum tumor evidence is documented for this variant.
PS3 Not assessed: no variant-specific calibrated functional odds, MMR function-defect assay, or monoallelic-expression result is available for p.Arg1263Cys.
PM2 Not met: gnomAD v4.1 total AF is 2.3545e-05, above the VCEP PM2 threshold of 0.00002 despite grpmax FAF 1.994e-05.
PM3 Not assessed: no documented CMMRD proband, second pathogenic MSH6 variant, or phase evidence is available to assign the VCEP's PM3 points.
PM5 Not met: zero same-residue Arg1263 comparator candidates were found, and HCI prior 0.0236 is below the PP3 Supporting threshold of >0.68.
PP1 Not assessed: no pedigree genotypes, meioses, or combined Bayes likelihood ratio are documented to compare with the PP1 supporting threshold of >2.08.
PP3 Not met: HCI prior 0.0236 and REVEL 0.594 are below the MSH6 PP3 supporting thresholds of >0.68 and >=0.644, respectively.
PP4 Not assessed: no tumor MSI, tumor-genome, or MMR IHC result is documented to compare with the PP4 phenotype-specific rule.
Benign
BA1 Not met: gnomAD v4.1 grpmax FAF is 1.994e-05, below the VCEP BA1 threshold of 0.0022.
BS1 Not met: gnomAD v4.1 grpmax FAF is 1.994e-05, below the VCEP BS1 lower threshold of 0.00022.
BS2 Not assessed: no qualifying in-trans co-occurrence, cancer age, CMMRD assessment, or phase-confirmation evidence is documented.
BS3 Not assessed: no variant-specific calibrated functional odds or qualifying proficient protein, mRNA, or NMD-controlled RNA assay is available for p.Arg1263Cys.
BS4 Not assessed: no non-segregating pedigree data or combined Bayes likelihood ratio is documented to compare with the BS4 strong threshold of <0.05.
BP5 Not assessed: the required tumor count and MSS, MMR-IHC, BRAF V600E, or MLH1-methylation evidence are not documented.
N/A · 12 PVS1 · PS4 · PM1 · PM4 · PM6 · PP2 · PP5 · BP1 · BP2 · BP3 · BP6 · 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= 2.3545e-05; MAF= 0.00235%, 38/1613930 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 4.00545e-05; MAF= 0.00401%, 3/74898 alleles, homozygotes = 0); grpmax FAF= 1.994e-05.
v2.1
This variant is present in gnomAD v2.1 (AF= 1.76919e-05; MAF= 0.00177%, 5/282616 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 3.10121e-05; MAF= 0.00310%, 4/128982 alleles, homozygotes = 0); grpmax FAF= 7.02e-06.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.0024% · 38 / 1,613,930
0 hom · FAF 0.002%
African/African American
3 / 74,898
0.004%
European (non-Finnish)
33 / 1,179,996
0.0028%
Admixed American
1 / 59,976
0.0017%
South Asian
1 / 91,088
0.0011%
+ 6 not observed (Remaining individuals, European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish)
gnomAD v2.1
0.0018% · 5 / 282,616
0 hom · FAF 0.0007%
European (non-Finnish)
4 / 128,982
0.0031%
Admixed American
1 / 35,410
0.0028%
+ 6 not observed (African/African American, 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 (10 clinical laboratories) and as Likely benign (2 clinical laboratories) and as Uncertain Significance (1 clinical laboratory). (ClinVarID = 89461)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02). REVEL score = 0.594. BayesDel score = 0.306998. HCI prior probability for pathogenicity = 0.0236. MAPP score = 10.25. Custom PP2 score = 0.046.
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. MSH6, a DNA mismatch repair protein, is frequently mutated in colorectal, small bowel, and endometrial 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; COSV52284241, n = 3 times).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 8 PMIDs not cited in assessment
23621914 ↗ CoDP: predicting the impact of unclassified genetic variants in MSH6 by the combination of different properties of the protein. CLINVAR
24905773 ↗ Endometrial cancer: a review and current management strategies: part I. CLINVAR
25452455 ↗ Hereditary colorectal cancer syndromes: American Society of Clinical Oncology Cl CLINVAR
25583476 ↗ Mutational landscape of gastric adenocarcinoma in Chinese: implications for prognosis and therapy. CLINVAR
25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint co CLINVAR
26333163 ↗ Classification of Amino Acid Substitutions in Mismatch Repair Proteins Using PON-MMR2. CLINVAR
26389210 ↗ Genetics of Breast and Gynecologic Cancers (PDQ®): Health Professional Version. CLINVAR
26467025 ↗ A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mende CLINVAR