Reclassification of Two MLH1 Variants of Uncertain Significance Utilizing Clinical and Functional Data
ABSTRACT Background Pathogenic variants in the mismatch repair genes are associated with an elevated lifetime risk of colorectal cancer (CRC). We previously identified two variants of uncertain significance (VUS) in the MLH1 gene, c.696_698del, p.(Cys233del) and c.1919C > G, p.(Pro640Arg), in Dan...
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Wiley
2024-11-01
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| Series: | Molecular Genetics & Genomic Medicine |
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| Online Access: | https://doi.org/10.1002/mgg3.70026 |
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| author | Jane Hübertz Frederiksen Ulf Birkedal Sarah Bachmann Elisabeth Victoria Eliesen Lene Juel Rasmussen Katja Venborg Pedersen Lana Al‐Zehhawi Susanne E. Boonen Lotte Krogh Karina Rønlund Lise Graversen Jannie Assenholt Kjeld Schmiegelow Karin Wadt Anne‐Marie Gerdes Thomas v. O. Hansen |
| author_facet | Jane Hübertz Frederiksen Ulf Birkedal Sarah Bachmann Elisabeth Victoria Eliesen Lene Juel Rasmussen Katja Venborg Pedersen Lana Al‐Zehhawi Susanne E. Boonen Lotte Krogh Karina Rønlund Lise Graversen Jannie Assenholt Kjeld Schmiegelow Karin Wadt Anne‐Marie Gerdes Thomas v. O. Hansen |
| author_sort | Jane Hübertz Frederiksen |
| collection | DOAJ |
| description | ABSTRACT Background Pathogenic variants in the mismatch repair genes are associated with an elevated lifetime risk of colorectal cancer (CRC). We previously identified two variants of uncertain significance (VUS) in the MLH1 gene, c.696_698del, p.(Cys233del) and c.1919C > G, p.(Pro640Arg), in Danish families with numerous occurrences of CRC. Methods To reclassify the variants we collected clinical data, initiated tumor and co‐segregation analysis, and performed RNA splicing analysis, subcellular localization, and protein stability studies. Results The functional analysis revealed that the c.696_698del, p.(Cys233del) variant had an effect at the RNA level, on subcellular localization, and on protein stability, while the c.1919C > G, p.(Pro640Arg) variant showed decreased expression in localization studies and decreased protein stability. These results suggest both variants disrupt DNA mismatch repair. Conclusion By applying all collected data and functional results we propose to reclassify the c.696_698del, p.(Cys233del) and the c.1919C > G, p.(Pro640Arg) variants as likely pathogenic (class 4) using MMR gene‐specific ACMG/AMP guidelines. Consequently, the two MLH1 variants can now be used for risk assessment of variant carriers, while family members without the variants can be excluded from intensified cancer surveillance and follow population recommendations. |
| format | Article |
| id | doaj-art-3138d238b0bc48cdadc8df08238a908f |
| institution | Kabale University |
| issn | 2324-9269 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | Wiley |
| record_format | Article |
| series | Molecular Genetics & Genomic Medicine |
| spelling | doaj-art-3138d238b0bc48cdadc8df08238a908f2024-11-27T06:54:36ZengWileyMolecular Genetics & Genomic Medicine2324-92692024-11-011211n/an/a10.1002/mgg3.70026Reclassification of Two MLH1 Variants of Uncertain Significance Utilizing Clinical and Functional DataJane Hübertz Frederiksen0Ulf Birkedal1Sarah Bachmann2Elisabeth Victoria Eliesen3Lene Juel Rasmussen4Katja Venborg Pedersen5Lana Al‐Zehhawi6Susanne E. Boonen7Lotte Krogh8Karina Rønlund9Lise Graversen10Jannie Assenholt11Kjeld Schmiegelow12Karin Wadt13Anne‐Marie Gerdes14Thomas v. O. Hansen15Department of Clinical Genetics, Rigshospitalet Copenhagen University Hospital Copenhagen DenmarkDepartment of Clinical Genetics, Rigshospitalet Copenhagen University Hospital Copenhagen DenmarkDepartment of Clinical Genetics, Rigshospitalet Copenhagen University Hospital Copenhagen DenmarkDepartment of Clinical Genetics, Rigshospitalet Copenhagen University Hospital Copenhagen DenmarkCenter for Healthy Aging, Department of Cellular and Molecular Medicine University of Copenhagen Copenhagen DenmarkDepartment of Clinical Genetics, Hospital Littlebelt University of Southern Denmark Vejle DenmarkDepartment of Clinical Genetics, Zealand University Hospital Region Zealand Roskilde DenmarkDepartment of Clinical Genetics Odense University Hospital Odense DenmarkDepartment of Clinical Genetics Odense University Hospital Odense DenmarkDepartment of Clinical Genetics, Hospital Littlebelt University of Southern Denmark Vejle DenmarkDepartment of Clinical Genetics Aarhus University Hospital Aarhus DenmarkMOMA Aarhus DenmarkDepartment of Pediatrics and Adolescent Medicine Copenhagen University Hospital Copenhagen DenmarkDepartment of Clinical Genetics, Rigshospitalet Copenhagen University Hospital Copenhagen DenmarkDepartment of Clinical Genetics, Rigshospitalet Copenhagen University Hospital Copenhagen DenmarkDepartment of Clinical Genetics, Rigshospitalet Copenhagen University Hospital Copenhagen DenmarkABSTRACT Background Pathogenic variants in the mismatch repair genes are associated with an elevated lifetime risk of colorectal cancer (CRC). We previously identified two variants of uncertain significance (VUS) in the MLH1 gene, c.696_698del, p.(Cys233del) and c.1919C > G, p.(Pro640Arg), in Danish families with numerous occurrences of CRC. Methods To reclassify the variants we collected clinical data, initiated tumor and co‐segregation analysis, and performed RNA splicing analysis, subcellular localization, and protein stability studies. Results The functional analysis revealed that the c.696_698del, p.(Cys233del) variant had an effect at the RNA level, on subcellular localization, and on protein stability, while the c.1919C > G, p.(Pro640Arg) variant showed decreased expression in localization studies and decreased protein stability. These results suggest both variants disrupt DNA mismatch repair. Conclusion By applying all collected data and functional results we propose to reclassify the c.696_698del, p.(Cys233del) and the c.1919C > G, p.(Pro640Arg) variants as likely pathogenic (class 4) using MMR gene‐specific ACMG/AMP guidelines. Consequently, the two MLH1 variants can now be used for risk assessment of variant carriers, while family members without the variants can be excluded from intensified cancer surveillance and follow population recommendations.https://doi.org/10.1002/mgg3.70026ACMG/AMP classificationLynch syndromeMLH1nuclear localizationprotein stabilityRNA splicing analysis |
| spellingShingle | Jane Hübertz Frederiksen Ulf Birkedal Sarah Bachmann Elisabeth Victoria Eliesen Lene Juel Rasmussen Katja Venborg Pedersen Lana Al‐Zehhawi Susanne E. Boonen Lotte Krogh Karina Rønlund Lise Graversen Jannie Assenholt Kjeld Schmiegelow Karin Wadt Anne‐Marie Gerdes Thomas v. O. Hansen Reclassification of Two MLH1 Variants of Uncertain Significance Utilizing Clinical and Functional Data Molecular Genetics & Genomic Medicine ACMG/AMP classification Lynch syndrome MLH1 nuclear localization protein stability RNA splicing analysis |
| title | Reclassification of Two MLH1 Variants of Uncertain Significance Utilizing Clinical and Functional Data |
| title_full | Reclassification of Two MLH1 Variants of Uncertain Significance Utilizing Clinical and Functional Data |
| title_fullStr | Reclassification of Two MLH1 Variants of Uncertain Significance Utilizing Clinical and Functional Data |
| title_full_unstemmed | Reclassification of Two MLH1 Variants of Uncertain Significance Utilizing Clinical and Functional Data |
| title_short | Reclassification of Two MLH1 Variants of Uncertain Significance Utilizing Clinical and Functional Data |
| title_sort | reclassification of two mlh1 variants of uncertain significance utilizing clinical and functional data |
| topic | ACMG/AMP classification Lynch syndrome MLH1 nuclear localization protein stability RNA splicing analysis |
| url | https://doi.org/10.1002/mgg3.70026 |
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