About MLH1
No gene-level summary was recorded for this case.
Previous versions
Variant interpretation report
MLH1 c.677G>A, p.(Arg226Gln)
Classification
Pathogenic
Variant description:
No variant summary was recorded for this case.
Five-step scale from benign to pathogenic. This variant is pathogenic. Select a step to read what it means.
Pathogenic.A pathogenic classification under the recorded framework.
In plain language
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.
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.
01The reasoning
How it was classified
The recorded framework is ClinGen MLH1 VCEP v2.0.0. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
Recorded applied criteria
The applied criteria and their strengths are shown as assessed under the stated framework.
Pathogenic evidence criteria: 5
Benign evidence criteria: 0
Pathogenic criteria applied · 5
PVS1Very strong
PVS1 · very strong
c.677G>A (last nucleotide of exon 8) results in complete exon 8 skipping (r.589_677del) as demonstrated by patient mRNA analysis in two independent studies, leading to a frameshift and premature termination codon subject to nonsense-mediated decay. The variant allele produces no full-length or reference transcript. Confirmed in an affected sibling carrying the same variant.
PM2Supporting
PM2 · supporting
c.677G>A is present in gnomAD v4.1 at an allele frequency of 6.23e-7 (1/1,604,126 alleles, 0 homozygotes), which is below the VCEP PM2_Supporting threshold of <0.00002 (<1 in 50,000 alleles). The variant is absent from gnomAD v2.1 and gnomAD-Canada.
PP3Supporting
PP3 · supporting
SpliceAI predicts a splicing defect for this variant (max delta score = 0.44), meeting the VCEP PP3_Supporting threshold of delta ≥0.2 for non-canonical splicing nucleotides. The HCI prior probability of 0.4702 does not meet the missense PP3 thresholds (>0.68).
PP4Supporting
PP4 · supporting
One CRC tumor from a carrier of c.677G>A demonstrated MSI-H (5/5 microsatellite markers) and loss of MLH1 protein expression by immunohistochemistry (Pagenstecher et al. 2006). This meets VCEP PP4_Supporting criteria: 1 CRC with MSI-H and MMR protein loss consistent with variant location.
PP5Supporting
PP5 · supporting
Expert panel International Society for Gastrointestinal Hereditary Tumours (InSiGHT) classified as Pathogenic.
Benign criteria applied · 0
No benign criterion marked as applied in the recorded assessment.
Recorded classification: Pathogenic
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.
02The sources
Evidence at a glance
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1
gnomAD v2.1
Population frequency
1 / 1,604,126 alleles
gnomAD v4.1: 1 / 1,604,126 alleles. Recorded AF 6.23392e-07. Recorded homozygote count 0.
gnomAD v2.1
Absent from gnomAD v2.1.
SpliceAI score
0.440 maximum delta
Recorded SpliceAI maximum delta score: 0.440. Refer to the recorded PP3/BP4 rationale for interpretation.
ClinVar submissions
18 reported laboratory submissions
18 Pathogenic.
Functional evidence
Statement recorded
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.
No listed criterion applied
OncoKB ↗
COSMIC
Cancer Hotspots
Somatic evidence
7 recorded samples
This variant has previously been reported in somatic cancers (COSMIC; COSV51619014, n = 7 times).
Cancer Hotspots
This variant does not lie in a statistically significant hotspot.
Context only
For specialists
Technical detail
ACMG/AMP criteria under ClinGen MLH1 VCEP v2.0.0, with the data and sources behind each one.
27 criteria with recorded statuses: 5 met · 7 not met · 4 not assessed · 11 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Met
Not met
Not assessed
Not applicable
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.
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.
PP3_Supporting: SpliceAI predicts splicing impact (max delta = 0.44), meeting VCEP threshold (delta ≥0.2) for non-canonical splice position.
PP4_Supporting: One CRC tumor from a carrier demonstrates MSI-H (5/5 markers) with loss of MLH1 protein expression by IHC.
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.
No criteria match.
Met · 5
PVS1 Very strongc.677G>A (last nucleotide of exon 8) results in complete exon 8 skipping (r.589_677del) as demonstrated by patient mRNA analysis in two independent studies, leading to a frameshift and premature termination codon subject to nonsense-mediated decay. The variant allele produces no full-length or reference transcript. Confirmed in an affected sibling carrying the same variant. Details ▾Hide ▴
Evidence considered
- Sharp et al. 2004: RT-PCR from patient lymphocytes shows c.677G>A causes complete skipping of exon 8 (89bp deletion)
- frameshift
- and absence of mutant transcript from full-length product. Identical result in affected sister.
- Pagenstecher et al. 2006: Confirmed complete exon skipping for c.677G>A by mRNA analysis. Patient 916 with CRC at 31 years
- MSI 5/5
- MLH1 loss by IHC
- segregation with disease confirmed.
Sources
PM2 Supportingc.677G>A is present in gnomAD v4.1 at an allele frequency of 6.23e-7 (1/1,604,126 alleles, 0 homozygotes), which is below the VCEP PM2_Supporting threshold of <0.00002 (<1 in 50,000 alleles). The variant is absent from gnomAD v2.1 and gnomAD-Canada. Details ▾Hide ▴
Evidence considered
- gnomAD v4.1: AF = 6.23e-7
- 1/1
- 604
- 126 alleles
- homozygotes = 0
- gnomAD v2.1: absent
- gnomAD-Canada: absent
- VCEP PM2_Supporting threshold: AF < 0.00002
Sources
PP3 SupportingSpliceAI predicts a splicing defect for this variant (max delta score = 0.44), meeting the VCEP PP3_Supporting threshold of delta ≥0.2 for non-canonical splicing nucleotides. The HCI prior probability of 0.4702 does not meet the missense PP3 thresholds (>0.68). Details ▾Hide ▴
Evidence considered
- SpliceAI: max delta = 0.44 (≥0.2 threshold for PP3_Supporting)
- HCI prior: 0.4702 (not ≥0.68 for missense PP3_Supporting
- not >0.81 for PP3_Moderate)
Sources
PP4 SupportingOne CRC tumor from a carrier of c.677G>A demonstrated MSI-H (5/5 microsatellite markers) and loss of MLH1 protein expression by immunohistochemistry (Pagenstecher et al. 2006). This meets VCEP PP4_Supporting criteria: 1 CRC with MSI-H and MMR protein loss consistent with variant location. Details ▾Hide ▴
Evidence considered
- Pagenstecher et al. 2006
- Table 1
- patient 916: CRC at 31 years
- MSI 5/5 markers
- MLH1 loss by IHC.
Sources
Not met · 7 · evaluated, threshold not reached
BA1 gnomAD v4.1 allele frequency is 6.23e-7, well below the VCEP BA1 stand-alone benign threshold of ≥0.001 (0.1%). Details ▾Hide ▴
Evidence considered
- gnomAD v4.1 AF = 6.23e-7
- far below BA1 threshold of 0.001.
Sources
BS1 gnomAD v4.1 allele frequency is 6.23e-7, below the VCEP BS1 strong benign threshold range of ≥0.0001 and <0.001. Details ▾Hide ▴
BS3 All identified functional evidence demonstrates a damaging effect on splicing (complete exon 8 skipping). No well-established functional studies show normal MMR activity or benign protein function for this variant. Details ▾Hide ▴
Evidence considered
- Sharp et al. 2004: c.677G>A causes complete exon 8 skipping
- frameshift.
- Pagenstecher et al. 2006: Confirmed aberrant splicing.
Sources
BS4 Pagenstecher et al. (2006) report co-segregation of c.677G>A with disease, which is inconsistent with BS4 (lack of co-segregation). No published reports demonstrate absence of co-segregation for this variant. Details ▾Hide ▴
Evidence considered
- Pagenstecher et al. 2006 reports co-segregation with disease (Yes)
- which is the opposite of what BS4 requires.
Sources
PMID:16341550 ↗16341550
BP4 HCI prior probability of pathogenicity is 0.4702, far above the VCEP BP4_Supporting threshold of <0.11. SpliceAI delta score of 0.44 predicts splicing impact (≥0.1), further contraindicating BP4. Details ▾Hide ▴
Evidence considered
- HCI prior: 0.4702 (>>0.11 threshold for BP4_Supporting)
- SpliceAI max delta: 0.44 (>>0.1 threshold for no splicing impact)
Sources
BP5 The available tumor evidence shows MSI-H with loss of MLH1 protein expression (Pagenstecher et al. 2006), which is inconsistent with BP5 requirements for MSS tumors with intact MMR protein expression. Details ▾Hide ▴
Evidence considered
- Pagenstecher et al. 2006: Patient 916 tumor showed MSI-H (5/5) and MLH1 loss
- opposite of BP5 criteria.
Sources
PMID:16341550 ↗16341550
BP7 c.677G>A is a missense (non-synonymous) coding variant, not a synonymous or intronic variant. BP7 requires a synonymous (silent) or intronic variant at or beyond -21/+7 exonic positions. Details ▾Hide ▴
Not assessed · 4 · no assessment recorded
PS2 No confirmed de novo occurrence of c.677G>A has been identified in ClinVar submissions, the published literature reviewed, or the InSiGHT LOVD database. PS2 requires confirmed de novo observations with maternity/paternity confirmation. Details ▾Hide ▴
Still missing
- No de novo data available for this variant.
Sources
15300854163415501265556814871975
PS3 Variant was not found in the VCEP-calibrated functional assay documentation (Functional-assay-SVI-documentation-MMR.xlsx). Putative functional evidence from PMID:12362047 (yeast-based MMR assay) could not be verified as the full-text was not available for review. PS3 requires calibrated functional odds per the VCEP framework. Details ▾Hide ▴
Evidence considered
- VCEP functional assay spreadsheet queried
- variant not listed.
- Exploratory search identified PMID:12362047 as potentially containing functional data
- but full-text not available for verification.
Still missing
- Calibrated functional assay data not available in VCEP documentation. PMID:12362047 full-text needed to verify functional evidence.
PP1 Pagenstecher et al. (2006) report co-segregation of c.677G>A with disease ('Yes') in one family, but provide insufficient detail (number of meioses, pedigree structure, affected/unaffected counts) to calculate a Bayes Likelihood Ratio per VCEP PP1 rules. VCEP PP1 requires a combined LR >2.08 for Supporting, >4.3 for Moderate, or >18.7 for Strong. Specific segregation quantification is needed. Details ▾Hide ▴
Evidence considered
- Pagenstecher et al. 2006: Table 1
- patient 916 reports 'Segregation of the mutation with the disease: Yes' but without quantified LR.
Still missing
- Detailed segregation data (pedigree
- number of meioses) needed to calculate Bayes LR for PP1 strength assignment.
Sources
PMID:16341550 ↗16341550
BS2 No evidence of co-occurrence in trans with a known pathogenic MLH1 variant in a patient without clinical manifestations of CMMRD was identified in the reviewed literature. Details ▾Hide ▴
Still missing
- BS2 requires specific co-occurrence data with confirmed phase.
Sources
15300854163415501265556814871975
Not applicable · 11· recorded as not applicable Show reasons ▾Hide reasons ▴
PS1 N/ANo alternative nucleotide substitution encodes p.Arg226Gln. The known variant c.677G>T at the same position encodes p.Arg226Leu, a different amino acid change, and therefore does not satisfy the PS1 requirement for same amino acid change via a different nucleotide. Details ▾Hide ▴
No further detail was recorded.
PS4 VCEPVCEP ClinGen InSiGHT MMR specifications (v2.0.0) explicitly mark PS4 as Not Applicable for this gene. Details ▾Hide ▴
PM1 VCEPVCEP ClinGen InSiGHT MMR specifications (v2.0.0) explicitly mark PM1 as Not Applicable for MLH1. Details ▾Hide ▴
PM5 N/Ac.677G>A has been demonstrated to cause complete exon 8 skipping via patient mRNA analysis, acting as a splicing defect rather than a missense change at the protein level. VCEP PM5 requires a missense change at the amino acid residue not due to aberrant splicing. As the pathogenic mechanism is splicing aberration, not an expressed missense protein, PM5 is not applicable. Details ▾Hide ▴
Evidence considered
- Sharp et al. 2004: c.677G>A causes exon 8 skipping
- no full-length transcript from mutant allele.
- Pagenstecher et al. 2006: Confirmed complete exon skipping.
Sources
PM6 VCEPVCEP ClinGen InSiGHT MMR specifications (v2.0.0) explicitly mark PM6 as Not Applicable for MLH1. Details ▾Hide ▴
PP2 VCEPVCEP ClinGen InSiGHT MMR specifications (v2.0.0) explicitly mark PP2 as Not Applicable for MLH1. Details ▾Hide ▴
BP1 VCEPVCEP ClinGen InSiGHT MMR specifications (v2.0.0) explicitly mark BP1 as Not Applicable for MLH1. Details ▾Hide ▴
BP2 VCEPVCEP ClinGen InSiGHT MMR specifications (v2.0.0) explicitly mark BP2 as Not Applicable for MLH1. Details ▾Hide ▴
BP3 VCEPIn-frame deletion/insertion not present; variant is a single nucleotide substitution. Skipped per workflow directive. Details ▾Hide ▴
No further detail was recorded.
BP6 VCEPVCEP ClinGen InSiGHT MMR specifications (v2.0.0) explicitly mark BP6 as Not Applicable as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee. Details ▾Hide ▴
PS5 N/AThe VCEP framework deprecates PP5 (reputable source reporting) as Not Applicable. PS5 is analogous and not specified in the CSPEC rule set. Sufficient primary evidence is available for independent evaluation, making reliance on external assertions unnecessary. Details ▾Hide ▴
Sources
Identifiers
- Gene
- MLH1
- Transcript
- NM_000249.4
- Coding (HGVS c.)
- NM_000249.4:c.677G>A
- Protein (HGVS p.)
- NP_000240.1:p.(Arg226Gln)
- GRCh38
- chr3:37012099 G>A
- GRCh37
- chr3:37053590 G>A
- ClinVar
- 187313, 90318, 90319
- COSMIC
- COSV51619014
Gene diagram
Every interpreted variant in MLH1, mapped onto the exon structure of NM_000249.4. Select a row to find it on the plot.
MLH1NM_000249.4
Fetching transcript structure from UCSC…
Exons
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Transcript span
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Strand
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Variants mapped
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Source
UCSC ncbiRefSeqCurated
All variants in MLH1
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Select a row to find it on the plot; use the link to open its page.
| Protein | Location | Classification | Link |
|---|
gnomAD v4.1
1 / 1,604,126 alleles
AF 6.23e-07 · 0 homozygotes
gnomAD v2.1
Allele count data not recorded
gnomAD-Canada v1.0
0 / 0 alleles
AF 0 · 0 homozygotes · FAF 0
By genetic ancestry
gnomAD v4.1
AF 6.2e-07 · 1 / 1,604,126 alleles · 0 hom
| European (non-Finnish)1 / 1,170,848 | 8.5e-07 |
0 alternate alleles recorded in 9 other groups: Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American.
gnomAD-Canada
AF 0 · 0 / 0 alleles · 0 hom
Statements
gnomAD v4.1
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).
gnomAD v2.1
Absent from gnomAD v2.1.
SpliceAI and Pangolin
Other predictors
- REVEL
- 0.198
- BayesDel
- 0.384
How the predictions were used
PP3 SupportingSpliceAI predicts a splicing defect for this variant (max delta score = 0.44), meeting the VCEP PP3_Supporting threshold of delta ≥0.2 for non-canonical splicing nucleotides. The HCI prior probability of 0.4702 does not meet the missense PP3 thresholds (>0.68). Details ▾Hide ▴
Evidence considered
- SpliceAI: max delta = 0.44 (≥0.2 threshold for PP3_Supporting)
- HCI prior: 0.4702 (not ≥0.68 for missense PP3_Supporting
- not >0.81 for PP3_Moderate)
Sources
BP4 HCI prior probability of pathogenicity is 0.4702, far above the VCEP BP4_Supporting threshold of <0.11. SpliceAI delta score of 0.44 predicts splicing impact (≥0.1), further contraindicating BP4. Details ▾Hide ▴
Evidence considered
- HCI prior: 0.4702 (>>0.11 threshold for BP4_Supporting)
- SpliceAI max delta: 0.44 (>>0.1 threshold for no splicing impact)
Sources
BP7 c.677G>A is a missense (non-synonymous) coding variant, not a synonymous or intronic variant. BP7 requires a synonymous (silent) or intronic variant at or beyond -21/+7 exonic positions. Details ▾Hide ▴
Statement
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.
9 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata. None of the listed paper records explicitly indicates that the variant is named.
Recorded publications
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PMID 12655568 ↗Novel MLH1 and MSH2 germline mutations in the first HNPCC families identified in Slovakia.Bartosova Z et al. · 2003No paper-specific finding is recorded.
-
PMID 14871975 ↗Microsatellite instability, immunohistochemistry, and additional PMS2 staining in suspected hereditary nonpolyposis colorectal cancer.de Jong AE et al. · 2004No paper-specific finding is recorded.
-
PMID 15300854 ↗RNA analysis reveals splicing mutations and loss of expression defects in MLH1 and BRCA1.Sharp A et al. · 2004No paper-specific finding is recorded.
-
PMID 15309712 ↗Clinical features and mismatch repair gene mutation screening in Chinese patients with hereditary nonpolyposis colorectal carcinoma.Liu SR et al. · 2004No paper-specific finding is recorded.
-
PMID 16341550 ↗Aberrant splicing in MLH1 and MSH2 due to exonic and intronic variants.Pagenstecher C et al. · 2006No paper-specific finding is recorded.
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PMID 16451135 ↗Germline MSH2 and MLH1 mutational spectrum including large rearrangements in HNPCC families from Poland (update study).Kurzawski G et al. · 2006No paper-specific finding is recorded.
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PMID 17453009 ↗Patients with an unexplained microsatellite instable tumour have a low risk of familial cancer.Overbeek LI et al. · 2007No paper-specific finding is recorded.
-
PMID 17569143 ↗Germline MLH1 and MSH2 mutational spectrum including frequent large genomic aberrations in Hungarian hereditary non-polyposis colorectal cancer families: implications for genetic testing.No paper-specific finding is recorded.
-
PMID 28492532 ↗Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.No paper-specific finding is recorded.
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
gnomAD v4.1
1 / 1,604,126 recorded alleles
Open source ↗
gnomAD v2.1
Captured gnomAD v2.1 source record
Open source ↗
SpliceAI Lookup
Recorded maximum delta 0.440
Open source ↗
ClinVar
18 Pathogenic
Open source ↗
COSMIC
Captured COSMIC source record
Open source ↗
Cancer hotspots
Captured Cancer Hotspots source record
Open source ↗
OncoKB
Captured OncoKB source record
Open source ↗
ClinGen CSpec
Captured ClinGen CSpec source record
Open source ↗
All source links
- ClinGen CSpec ↗cspec.genome.network/cspec/ui/svi/doc/1564688410
- ClinVar ↗www.ncbi.nlm.nih.gov/clinvar/variation/90318/
- gnomAD v2.1 ↗gnomad.broadinstitute.org/variant/3-37053590-G-A?dataset=gnomad_r2_1
- gnomAD v4.1 ↗gnomad.broadinstitute.org/variant/chr3-37012099-G-A?dataset=gnomad_r4
- SpliceAI Lookup ↗spliceailookup.broadinstitute.org/#variant=NM_000249.4%3Ac.677G…
- OncoKB ↗www.oncokb.org/gene/MLH1/R226Q
- COSMIC ↗cancer.sanger.ac.uk/cosmic/mutation/overview?id=124265256
- Cancer hotspots ↗www.cancerhotspots.org/
Statements for reports
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
gnomAD v4.1
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).
gnomAD v2.1
Absent from gnomAD v2.1.
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
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.
Somatic
This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV51619014, n = 7 times).
Cancer Hotspots
This variant does not lie in a statistically significant hotspot.