PVS1_VeryStrong: c.677G>A (last nucleotide of exon 8) produces no full-length transcript; patient mRNA analysis demonstrates complete exon 8 skipping (r.589_677del), frameshift, and NMD in two independent studies.1 PM2_Supporting: Extremely rare in population databases — gnomAD v4.1 AF = 6.23e-7 (1/1,604,126 alleles), absent from v2.1 and gnomAD-Canada, meeting VCEP threshold <0.00002.2 PP3_Supporting: SpliceAI predicts splicing impact (max delta = 0.44), meeting VCEP threshold (delta ≥0.2) for non-canonical splice position.3 PP4_Supporting: One CRC tumor from a carrier demonstrates MSI-H (5/5 markers) with loss of MLH1 protein expression by IHC.4 Evidence for pathogenicity includes confirmed RNA-level splicing aberration causing frameshift, extreme population rarity, in silico splice prediction, and tumor phenotype consistent with MMR deficiency.5
MLH1
Final classification
Pathogenic
MLH1 c.677G>A · p.Arg226Gln
MLH1
PVS1_VeryStrong: c.677G>A (last nucleotide of exon 8) produces no full-length transcript; patient mRNA analysis demonstrates complete exon 8 skipping (r.589_677del), frameshift, and NMD in two independent studies.
ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MLH1 Version 2.0.0 v2.0.0 criteria-combination framework: matched Rule4 (1 Pathogenic.Very Strong + Pathogenic.Supporting >=2) with applied criteria: PVS1 very strong, PM2 supporting, PP3 supporting, PP4 supporting, PP5 supporting; maps to Pathogenic.
Classification rationale
PVS1PM2PP3PP4PP5
Pathogenic
MLH1 c.677G>A
PVS1 + PM2 + PP3 + PP4 + PP5
→
Pathogenic
Gene diagram
· NM_000249.4 · variants mapped to exon structure
MLH1
NM_000249.4
Fetching transcript structure from UCSC…
Applied criteria · 5 met · select any tile
Met
Not met
Not assessed
N/A
Strength
very strong
supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
—
—
—
Rationale
Select a criterion.
Sources
Evidence used
Gaps remaining
Rule
—
Research & evidence
Population frequency · supports pathogenic
gnomAD v4.1
gnomAD v2.1
Population frequency
Overall AF
1 / 1,604,126
6.2e-05%
Highest · European (non-Finnish)
8.5e-05%
Homozygotes
0
Allele frequency by ancestry — gnomAD v4.1
observed in 1 of 9 groups
| Ancestry | Allele count | Frequency | Homozygotes |
|---|---|---|---|
| European (non-Finnish) | 1 / 1,170,848 | 8.5e-05% | 0 |
| Admixed American | 0 / 59,994 | — | — |
| European (Finnish) | 0 / 63,948 | — | — |
| Amish | 0 / 910 | — | — |
| East Asian | 0 / 44,840 | — | — |
| Middle Eastern | 0 / 6,046 | — | — |
| South Asian | 0 / 90,932 | — | — |
| Ashkenazi Jewish | 0 / 29,556 | — | — |
| African/African American | 0 / 74,806 | — | — |
“
This variant is present in gnomAD v4.1 (AF= 6.23392e-07; MAF= 0.00006%, 1/1604126 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.54082e-07; MAF= 0.00009%, 1/1170848 alleles, homozygotes = 0).
“
Absent from gnomAD v2.1.
“
This variant is absent from gnomAD-Canada.
ClinVar
This variant has been reported in ClinVar as Pathogenic (18 clinical laboratories) and as Pathogenic by International Society for Gastrointestinal Hereditary Tumours (InSiGHT) (expert panel). (ClinVarID = 90318)
In silico
SpliceAI predicts possible splice impact for this variant (max delta score = 0.44). REVEL score = 0.198. BayesDel score = 0.384087. HCI prior probability for pathogenicity = 0.4702. MAPP score = 11.7. Custom PP2 score = 0.821.
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. MLH1, a DNA mismatch repair protein, is recurrently altered by deletion and mutation in various cancer types.
COSMIC
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; COSV51619014, n = 7 times).
Hotspots
This variant does not lie in a statistically significant hotspot.
Literature · 45 PMIDs triaged · 8 high-priority
45papers screened
Papers triaged by theme: functional/splicing/segregation/case_observation. high_priority_papers include abstract snippets. Use these to support PS3/BS3/PS4/PP1/PP3/PP5.
12655568 ↗
splicing rna
Novel MLH1 and MSH2 germline mutations in the first HNPCC families identified in Slovakia.
Hereditary nonpolyposis colorectal cancer (HNPCC) is a dominantly-inherited cancer predisposition syndrome, in which the susceptibility to cancer of the colon, endometrium and ovary is linked to germline mutations in DNA mismatch repair (MMR) genes. We have recently initiated a cancer prevention program in suspected HNPCC families in the Slovak Republic. The first ten families fulfilling Amsterdam
BP7PP3PP5PS4PVS1
14871975 ↗
functional
Microsatellite instability, immunohistochemistry, and additional PMS2 staining in suspected hereditary nonpolyposis colorectal cancer.
Immunohistochemistry (IHC) and microsatellite instability (MSI) analysis can be used to identify patients with a possible DNA mismatch repair defect [hereditary nonpolyposis colorectal carcinoma (HNPCC)]. The Bethesda criteria have been proposed to select families for determination of MSI. The aims of this study were to assess the yield of MSI analysis in families suspected for HNPCC, to compare t
BS3PP5PS3PS4
15300854 ↗
splicing rna
RNA analysis reveals splicing mutations and loss of expression defects in MLH1 and BRCA1.
The classical paradigm of mutation screening seeks to relate alterations in DNA sequence to their effect at the protein level. However, the majority of missense mutations are problematic as their pathological significance is often unclear. In order to test the hypothesis that many missense mutations primarily cause defects at the RNA rather than the protein level, we have performed retrospective R
BP7PP3PP5PS4PVS1
15309712 ↗
segregation
Clinical features and mismatch repair gene mutation screening in Chinese patients with hereditary nonpolyposis colorectal carcinoma.
Hereditary nonpolyposis colorectal cancer (HNPCC) is an autosomal dominantly-inherited cancer-susceptibility syndrome that confers an increased risk for colorectal cancer and a variety of other tumors at a young age. It has been associated with germline mutations in five mismatch repair (MMR) genes (hMSH2, hMLH1, hPMS1, hPMS2, and hMSH6/GTBP). The great majority of germline mutations were found in
BS4PP1PP5PS4
16341550 ↗
splicing rna
Aberrant splicing in MLH1 and MSH2 due to exonic and intronic variants.
Single base substitutions in DNA mismatch repair genes which are predicted to lead either to missense or silent mutations, or to intronic variants outside the highly conserved splicing region are often found in hereditary nonpolyposis colorectal cancer (HNPCC) families. In order to use the variants for predictive testing in persons at risk, their pathogenicity has to be evaluated. There is growing
BP7PP3PP5PS4PVS1
16451135 ↗
functional
Germline MSH2 and MLH1 mutational spectrum including large rearrangements in HNPCC families from Poland (update study).
Germline mutations in the DNA mismatch repair genes MSH2 and MLH1 account for a significant proportion of hereditary non-polyposis colorectal cancer (HNPCC) families. One approach by which development of an efficient DNA-testing procedure can be implemented is to describe the nature and frequency of common mutations in particular ethnic groups. Two hundred and twenty-six patients from families mat
BS3PP5PS3PS4
17453009 ↗
functional
Patients with an unexplained microsatellite instable tumour have a low risk of familial cancer.
The cancer risk is unknown for those families in which a microsatellite instable tumour is neither explained by MLH1 promoter methylation nor by a germline mutation in a mismatch repair (MMR) gene. Such information is essential for genetic counselling. Families suspected of Lynch syndrome (n = 614) were analysed for microsatellite instability, MLH1 promoter methylation and/or germline mutations in
BS3PP5PS3PS4
17569143 ↗
functional
Germline MLH1 and MSH2 mutational spectrum including frequent large genomic aberrations in Hungarian hereditary non-polyposis colorectal cancer families: implications for genetic testing.
To analyze the prevalence of germline MLH1 and MSH2 gene mutations and evaluate the clinical characteristics of Hungarian hereditary non-polyposis colorectal cancer (HNPCC) families. Thirty-six kindreds were tested for mutations using conformation sensitive gel electrophoreses, direct sequencing and also screening for genomic rearrangements applying multiplex ligation-dependent probe amplification
BS3PP5PS3PS4
28492532 ↗
background review
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
PS3PS4
Sources & reference links