About MLH1
No gene-level summary was recorded for this case.
Previous versions
Variant interpretation report
MLH1 c.1989G>A, p.(Glu663=)
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. 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: 3
Benign evidence criteria: 0
Pathogenic criteria applied · 3
PVS1Very strong
PVS1 · very strong
c.1989G>A at the last nucleotide of exon 17 disrupts the splice donor consensus. Patient mRNA analysis in two independent laboratories (Terdiman 2001, Tang 2009) confirms exon 17 skipping, which is out-of-frame (93 bp) and predicted to introduce a premature termination codon subject to NMD. This matches the InSiGHT VCEP PVS1_Very_Strong rule for variants where mRNA from patient constitutional samples demonstrates splicing aberration leading to premature stop codon, confirmed by an independent laboratory.
PM2Supporting
PM2 · supporting
c.1989G>A is absent from gnomAD v2.1 (exomes), gnomAD v4.1 (exomes/genomes), and gnomAD-Canada v1.0. This satisfies the InSiGHT VCEP PM2_Supporting threshold of allele frequency < 0.00002 (absent/extremely rare in gnomAD v4).
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 v2.0 criteria-combination framework: matched Rule4 (1 Pathogenic.Very Strong + Pathogenic.Supporting >=2) with applied criteria: PVS1 very strong, PM2 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
Not recorded
gnomAD v4.1 allele counts were not recorded for this variant.
gnomAD v2.1
Absent from gnomAD v2.1.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
SpliceAI score
0.000 maximum delta
Recorded SpliceAI maximum delta score: 0.000. Refer to the recorded PP3/BP4 rationale for interpretation.
No listed criterion applied
SpliceAI ↗
ClinVar submissions
4 reported laboratory submissions
4 Likely pathogenic. ClinVar API review status: reviewed by expert panel.
Functional evidence
Statement recorded
OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
No listed criterion applied
OncoKB ↗
COSMIC
Cancer Hotspots
Somatic evidence
No matching record reported
This variant has not previously been reported in somatic cancers (COSMIC).
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, with the data and sources behind each one.
27 criteria with recorded statuses: 3 met · 6 not met · 8 not assessed · 10 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Met
Not met
Not assessed
Not applicable
PVS1_Very_Strong: c.1989G>A at the last nucleotide of exon 17 results in exon 17 skipping confirmed by patient mRNA analysis in two independent laboratories (Terdiman 2001, Tang 2009). Exon 17 skipping (93 bp, out-of-frame) introduces a premature termination codon predicted to undergo NMD.
PM2_Supporting: c.1989G>A is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, meeting the InSiGHT VCEP threshold of < 0.00002 (< 1 in 50,000 alleles).
Final classification: Pathogenic. Per InSiGHT VCEP MLH1 v2.0 combining rules (Rule 1): 1 PVS1_Very_Strong yields a Pathogenic classification. This is concordant with the ClinVar InSiGHT Expert Panel classification of Pathogenic (ClinVar ID 89979).
No criteria match.
Met · 3
PVS1 Very strongc.1989G>A at the last nucleotide of exon 17 disrupts the splice donor consensus. Patient mRNA analysis in two independent laboratories (Terdiman 2001, Tang 2009) confirms exon 17 skipping, which is out-of-frame (93 bp) and predicted to introduce a premature termination codon subject to NMD. This matches the InSiGHT VCEP PVS1_Very_Strong rule for variants where mRNA from patient constitutional samples demonstrates splicing aberration leading to premature stop codon, confirmed by an independent laboratory. Details ▾Hide ▴
Evidence considered
- c.1989G>A at last base of exon 17 (splice donor position -1)
- mRNA assay from two independent laboratories confirms exon 17 skipping
- Exon 17 is 93 bp
- skipping disrupts reading frame leading to premature termination codon
- Terdiman 2001 (PMID:11208710): two independent families (2AN7
- 5EJ9) with exon 17 skipping by mRNA analysis
- Tang 2009 (PMID:19419416): independent confirmation of aberrant splicing from c.1989G>A
Sources
PM2 Supportingc.1989G>A is absent from gnomAD v2.1 (exomes), gnomAD v4.1 (exomes/genomes), and gnomAD-Canada v1.0. This satisfies the InSiGHT VCEP PM2_Supporting threshold of allele frequency < 0.00002 (absent/extremely rare in gnomAD v4). Details ▾Hide ▴
Evidence considered
- Absent from gnomAD v2.1
- Absent from gnomAD v4.1
- Absent from gnomAD-Canada v1.0
Sources
Not met · 6 · evaluated, threshold not reached
PP3 VCEP PP3 for MLH1 requires either a missense variant with HCI prior >0.68 (not applicable; this is a synonymous variant not in the HCI table) or a predicted splice defect with SpliceAI delta >= 0.2 (SpliceAI max delta = 0.00, no splice impact predicted). Neither condition is satisfied. Details ▾Hide ▴
Evidence considered
- HCI prior: variant not found in MLH1 HCI lookup table
- SpliceAI max delta score: 0.00 (no predicted splice impact)
Sources
BA1 VCEP BA1 requires gnomAD v4 grpmax filtering allele frequency >= 0.001 (0.1%). c.1989G>A is absent from gnomAD. The BA1 threshold is not satisfied. Details ▾Hide ▴
BS1 VCEP BS1 requires gnomAD v4 grpmax filtering allele frequency >= 0.0001 and < 0.001. c.1989G>A is absent from gnomAD. The BS1 threshold is not satisfied. Details ▾Hide ▴
BS3 VCEP BS3 requires calibrated functional assays with odds for pathogenicity <= 0.05, or variant-specific proficient function in protein/mRNA assays. The experimental data available shows the opposite: patient mRNA assays in two independent laboratories confirm exon 17 skipping (a loss-of-function splicing defect). No evidence of normal or proficient function exists for this variant. Details ▾Hide ▴
Evidence considered
- Patient mRNA shows exon 17 skipping
- confirming loss of function
- No evidence of normal splicing or proficient MMR function
Sources
BP4 VCEP BP4 for synonymous variants requires SpliceAI delta score <= 0.1 predicting no splicing impact. SpliceAI delta = 0.00 satisfies this threshold in silico. However, direct experimental evidence from patient mRNA (Terdiman 2001, Tang 2009) demonstrates that c.1989G>A does cause exon 17 skipping. In silico prediction is overridden by experimental data showing a splicing defect. Details ▾Hide ▴
Evidence considered
- SpliceAI delta = 0.00 (predicted no impact)
- Patient mRNA analysis confirms exon 17 skipping (contradicts in silico prediction)
Sources
BP7 VCEP BP7 applies to synonymous or intronic variants at or beyond -21/+7 from the splice junction. c.1989G>A is at the last nucleotide of exon 17, which is position -1 of the splice donor consensus. This position is within the splice consensus region, not at or beyond -21/+7. Furthermore, patient mRNA confirms this variant does affect splicing (exon 17 skipping), precluding BP7 application. Details ▾Hide ▴
Evidence considered
- c.1989 is the last nucleotide of exon 17 (position -1 of splice donor)
- Patient mRNA confirms exon 17 skipping
Sources
Not assessed · 8 · no assessment recorded
PS2 No de novo data available in the evidence package. VCEP PS2 requires de novo point accumulation based on confirmed parentage. Details ▾Hide ▴
Still missing
- No de novo testing data available
PS3 The VCEP-calibrated functional assay spreadsheet (Functional-assay-SVI-documentation-MMR.xlsx) does not list c.1989G>A. No calibrated functional odds ratio data is available for this variant. The functional consequence of this variant is a splicing defect (exon 17 skipping), which is captured under PVS1 rather than PS3. Details ▾Hide ▴
Still missing
- No calibrated functional assay data with odds ratios available for this variant
Sources
vcep_functional_assay_svi_documentation_mmr
PP1 No co-segregation data provided. VCEP PP1 requires Bayes likelihood ratio from pedigree analysis. Details ▾Hide ▴
Still missing
- No co-segregation data available
PP4 No tumor data (MSI status, IHC for MMR protein expression) provided in the evidence package. VCEP PP4 requires MSI-H tumors with MMR protein expression loss consistent with the variant location. Details ▾Hide ▴
Still missing
- No tumor MSI/IHC data available
BS2 No evidence of co-occurrence in trans with a known pathogenic MLH1 variant. VCEP BS2 requires confirmed trans co-occurrence in a CRC patient after age 45 without CMMRD features. Details ▾Hide ▴
Still missing
- No co-occurrence data available
BS4 No segregation data available. VCEP BS4 requires Bayes likelihood ratio for lack of co-segregation. Details ▾Hide ▴
Still missing
- No segregation data available
BP5 No tumor data (MSS status, MMR protein expression by IHC) provided. VCEP BP5 requires MSS tumors or inconsistent MMR protein loss in the tumor. Details ▾Hide ▴
Still missing
- No tumor data available
PS5 No evidence provided to evaluate PS5. No reported de novo variant observations for this specific variant. Details ▾Hide ▴
Still missing
- No PS5 evidence provided
Not applicable · 10· recorded as not applicable Show reasons ▾Hide reasons ▴
PS1 N/APS1 requires a predicted missense substitution encoding the same amino acid change with a different nucleotide change. c.1989G>A is a synonymous variant (p.Glu663=) with no amino acid change. Details ▾Hide ▴
No further detail was recorded.
PS4 VCEPPS4 is not applicable per InSiGHT VCEP MLH1 v2.0 specifications. Details ▾Hide ▴
Sources
PM1 VCEPPM1 is not applicable per InSiGHT VCEP MLH1 v2.0 specifications. Details ▾Hide ▴
Sources
PM5 N/AVCEP PM5 requires a missense change at an amino acid residue where a different missense change was classified as Pathogenic. c.1989G>A is a synonymous variant (p.Glu663=), not a missense change. Details ▾Hide ▴
No further detail was recorded.
PM6 VCEPPM6 is not applicable per InSiGHT VCEP MLH1 v2.0 specifications. Details ▾Hide ▴
Sources
PP2 VCEPPP2 is not applicable per InSiGHT VCEP MLH1 v2.0 specifications. Details ▾Hide ▴
Sources
BP1 VCEPBP1 is not applicable per InSiGHT VCEP MLH1 v2.0 specifications. Details ▾Hide ▴
Sources
BP2 VCEPBP2 is not applicable per InSiGHT VCEP MLH1 v2.0 specifications. Details ▾Hide ▴
Sources
BP3 VCEPIn-frame indels in repetitive regions without known function; not applicable to a single-nucleotide substitution. Details ▾Hide ▴
No further detail was recorded.
BP6 VCEPBP6 is not applicable per InSiGHT VCEP MLH1 v2.0 specifications. Details ▾Hide ▴
Sources
Identifiers
- Gene
- MLH1
- Transcript
- NM_000249.4
- Coding (HGVS c.)
- NM_000249.4:c.1989G>A
- Protein (HGVS p.)
- NP_000240.1:p.(Glu663=)
- GRCh38
- chr3:37048609 G>A
- GRCh37
- chr3:37090100 G>A
- ClinVar
- 382746, 89979
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
Allele count data not recorded
gnomAD v2.1
Allele count data not recorded
gnomAD-Canada v1.0
Allele count data not recorded
Statements
gnomAD v4.1
Absent from gnomAD v4.1.
gnomAD v2.1
Absent from gnomAD v2.1.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
SpliceAI and Pangolin
Other predictors
- REVEL
- Not available
- BayesDel
- Not available
How the predictions were used
PP3 VCEP PP3 for MLH1 requires either a missense variant with HCI prior >0.68 (not applicable; this is a synonymous variant not in the HCI table) or a predicted splice defect with SpliceAI delta >= 0.2 (SpliceAI max delta = 0.00, no splice impact predicted). Neither condition is satisfied. Details ▾Hide ▴
Evidence considered
- HCI prior: variant not found in MLH1 HCI lookup table
- SpliceAI max delta score: 0.00 (no predicted splice impact)
Sources
BP4 VCEP BP4 for synonymous variants requires SpliceAI delta score <= 0.1 predicting no splicing impact. SpliceAI delta = 0.00 satisfies this threshold in silico. However, direct experimental evidence from patient mRNA (Terdiman 2001, Tang 2009) demonstrates that c.1989G>A does cause exon 17 skipping. In silico prediction is overridden by experimental data showing a splicing defect. Details ▾Hide ▴
Evidence considered
- SpliceAI delta = 0.00 (predicted no impact)
- Patient mRNA analysis confirms exon 17 skipping (contradicts in silico prediction)
Sources
BP7 VCEP BP7 applies to synonymous or intronic variants at or beyond -21/+7 from the splice junction. c.1989G>A is at the last nucleotide of exon 17, which is position -1 of the splice donor consensus. This position is within the splice consensus region, not at or beyond -21/+7. Furthermore, patient mRNA confirms this variant does affect splicing (exon 17 skipping), precluding BP7 application. Details ▾Hide ▴
Evidence considered
- c.1989 is the last nucleotide of exon 17 (position -1 of splice donor)
- Patient mRNA confirms exon 17 skipping
Sources
Statement
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
9 paper records listed. 2 cited in the classification.
Cited in the classification
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PMID 11208710 ↗Efficient detection of hereditary nonpolyposis colorectal cancer gene carriers by screening for tumor microsatellite instability before germline genetic testing.Terdiman JP et al. · 2001 Janc.1989G>A at the splice donor of MLH1 exon 17 identified in two independent HNPCC/Lynch syndrome families (2AN7, 5EJ9). mRNA analysis from patient lymphocytes confirmed exon 17 skipping in both families.→ PVS1 Names this variant
Source detail
1989G A, Splice donor, Exon skipping (M)
Location Table listing mutations with mRNA assay results for MLH1 exon 17
Context RT-PCR mRNA analysis from patient lymphocyte-derived RNA; exon skipping detected by gel electrophoresis
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PMID 19419416 ↗Germ line MLH1 and MSH2 mutations in Taiwanese Lynch syndrome families: characterization of a founder genomic mutation in the MLH1 gene.Tang R et al. · 2009 Aprc.1989G>A in MLH1 exon 17 reported in a Taiwanese Lynch syndrome family. Aberrant splicing confirmed as the functional consequence.→ PVS1 Names this variant
Source detail
c.1989G.A, 663, Aberrant splicing
Location Table summarizing MLH1 mutations identified in Taiwanese Lynch syndrome families
Context Mutation screening by DHPLC and DNA sequencing in 93 Taiwanese families fulfilling Amsterdam criteria II
Other recorded publications
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PMID 10480359 ↗Prevalence of germline mutations of hMLH1, hMSH2, hPMS1, hPMS2, and hMSH6 genes in 75 French kindreds with nonpolyposis colorectal cancer.Wang Q et al. · 1999Prevalence study of germline MMR gene mutations in 75 French HNPCC kindreds. c.1989G>A was not identified in full-text search.Does not name this variant
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PMID 16395668 ↗Systematic mRNA analysis for the effect of MLH1 and MSH2 missense and silent mutations on aberrant splicing.Auclair J et al. · 2006Studied c.1989G>T (p.Glu663Asp), a missense variant at the same nucleotide position (c.1989) in MLH1 exon 17. Confirmed exon 17 skipping by patient mRNA and minigene assay. Provides mechanistic context that the last nucleotide of exon 17 (G of GAGgt) is critical for splice donor function; substitutions at this position disrupt splicing regardless of whether they change the amino acid.Does not name this variant
Quoted passage
c.1989G4T, pGlu663Asp, GAGgt GATgt, Exon 17 skipping
Table 1 and Results section
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PMID 17576681 ↗Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.Buratti E et al. · 2007Computational analysis of 346 aberrant 5' splice sites in human disease genes. c.1989G>A was not identified in full-text search.Does not name this variant
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PMID 18561205 ↗A large fraction of unclassified variants of the mismatch repair genes MLH1 and MSH2 is associated with splicing defects.Tournier I et al. · 2008Studied c.1989G>T (p.Glu663Asp), a missense variant at the same nucleotide position in MLH1 exon 17. Minigene splicing assay confirmed exon 17 skipping and cryptic donor site activation.Does not name this variant
Quoted passage
c.1989G4T (p.Glu663Asp), Missense (DS), Exon 17 skipping 1 Cryptic DS activation
Table 1: MLH1 and MSH2 Variants Tested in the pCAS Ex Vivo Splicing Assay
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PMID 21404117 ↗Missense variants in hMLH1 identified in patients from the German HNPCC consortium and functional studies.Hardt K et al. · 2011Functional characterization of 88 MLH1 missense variants from the German HNPCC consortium using yeast two-hybrid and dominant negative mutator effect assays. c.1989G>A is synonymous and was not among the missense variants studied.Does not name this variant
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PMID 21615986 ↗Distinct mutations in MLH1 and MSH2 genes in hereditary non-polyposis colorectal cancer (HNPCC) families from China.Wei W et al. · 2011No paper-specific finding is recorded.
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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
Captured gnomAD v4.1 source record
Open source ↗
gnomAD v2.1
Captured gnomAD v2.1 source record
Open source ↗
SpliceAI Lookup
Recorded maximum delta 0.000
Open source ↗
ClinVar
4 Likely 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/89979/
- gnomAD v2.1 ↗gnomad.broadinstitute.org/variant/3-37090100-G-A?dataset=gnomad_r2_1
- gnomAD v4.1 ↗gnomad.broadinstitute.org/variant/chr3-37048609-G-A?dataset=gnomad_r4
- gnomAD-Canada ↗http://192.168.4.76:8001/variant/3-37048609-G-A
- SpliceAI Lookup ↗spliceailookup.broadinstitute.org/#variant=NM_000249.4%3Ac.1989…
- OncoKB ↗www.oncokb.org/gene/MLH1/E663=
- COSMIC ↗cancer.sanger.ac.uk/cosmic/search?q=MLH1+c.1989G%3EA
- 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
Absent from gnomAD v4.1.
gnomAD v2.1
Absent from gnomAD v2.1.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
ClinVar
This variant has been reported in ClinVar as Likely pathogenic (4 clinical laboratories) and as Pathogenic by International Society for Gastrointestinal Hereditary Tumours (InSiGHT) (expert panel). (ClinVarID = 89979)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
Functional
OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
Somatic
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Cancer Hotspots
This variant does not lie in a statistically significant hotspot.