Variant
MSH2 L559X
NM_000251.3(MSH2):c.1676del (p.Leu559Ter)
- p.Leu559Ter
- p.L559*
- rs63750633
- ClinVar classification
- Pathogenic
- Review status
- 3 stars out of 4reviewed by expert panel
- Last evaluated
- 5 September 2013
- Expert panel
- International Society for Gastrointestinal Hereditary Tumours (InSiGHT)
Data current to ClinVar release 2026-10-12 · Dante Labs data release 2026.10.16-c6eea6bfFacts last changed 16 October 2026
Reference genomeGRCh38hg38
Positions on gene and variant pages follow this choice, in this browser.
Summary
L559X is a nonsense variant in MSH2: it creates an early stop signal, so the protein the gene encodes is predicted to be cut short. ClinVar classifies it as pathogenic for Lynch Syndrome (reviewed by expert panel).
ClinVar classifications
| Condition | Classification | Review status | Submissions | Last evaluated |
|---|---|---|---|---|
| Lynch SyndromeClinVar VCV000090743 (opens in a new tab) | Pathogenic | 3 stars out of 4reviewed by expert panel | 1 submission | 5 September 2013 |
Classifications as ClinVar records them in release 2026-10-12. ClinVar updates them as evidence is reviewed.
Where it lies in MSH2
L559X lies in exon 11 of the 16 in MSH2's MANE Select transcript, NM_000251.3.
Molecular details
| Gene | MSH2 |
|---|---|
| Transcript | NM_000251.3MANE Select |
| Coding DNA change (HGVS c.) | c.1676del |
| Protein change (HGVS p.) | p.Leu559Terp.L559* |
| Predicted consequence | Nonsense (stop gained)stop_gained (opens in a new tab) |
| Predicted impact | High |
| Position (GRCh38) | chr2:47470976 CT>C |
| Position (GRCh37) | chr2:47698115 CT>C |
| dbSNP ID | rs63750633 (opens in a new tab) |
| ClinVar Variation ID | VCV000090743 (opens in a new tab) |
| ClinVar Allele ID | 96218 |
| ClinGen Allele Registry ID | CA018970 (opens in a new tab) |
| ClinVar name | NM_000251.3(MSH2):c.1676del (p.Ser558_Leu559insTer) |
MSH2 L559X in other databases
Reports that look at this variant (1)
These Genome Test condition reports include L559X among the variants they look at.
| Report | Conditions | Inheritance |
|---|---|---|
| Lynch Syndrome | Lynch Syndrome | Autosomal dominant |
Other variants in MSH2
- A123Vfs*51Pathogenic3 stars out of 4
- A230Lfs*16Pathogenic3 stars out of 4
- A230Sfs*2Pathogenic3 stars out of 4
- A266Qfs*8Pathogenic3 stars out of 4
- A370Qfs*3Pathogenic3 stars out of 4
- A398Gfs*19Pathogenic3 stars out of 4
- A499Cfs*14Pathogenic3 stars out of 4
- A500Pfs*26Pathogenic3 stars out of 4
- A573Pfs*17Pathogenic3 stars out of 4
- A636PPathogenic3 stars out of 4
Limitations
This page describes publicly available information about a genetic variant. It is not a diagnosis, and it says nothing about whether you or anyone else carries this variant.
Classifications come from ClinVar and change as new evidence is reviewed. A classification here may differ from the one in ClinVar today, or from the one a laboratory reports.
Whole genome sequencing with short reads can miss or miscall some variants, particularly in repeated or highly similar stretches of DNA and in large insertions, deletions or rearrangements.
If you have questions about a variant in your own results or in your family, talk to a genetic counsellor or your doctor.
Sources & credits
- Classifications from ClinVar (release 2026-10-12), National Center for Biotechnology Information.
- Condition terms from the Mondo Disease Ontology (release 2026-10-06), used under CC BY 4.0.
- Gene symbols and names from the HUGO Gene Nomenclature Committee (release 2026-10-16).
- Allele identifiers from the ClinGen Allele Registry (release 2026-10-16-c4908f54).
- Reference SNP identifiers from dbSNP (release b157), National Center for Biotechnology Information.
- Gene–disease links from the Gene Curation Coalition, GenCC (release 2026-10-16).
- Difficult regions from the Genome in a Bottle Consortium (release v3.6).
- Transcripts from MANE (release v1.5), NCBI and EMBL-EBI.
- Predicted consequences from mehari (release 0.11.0), with transcript models from cdot.
- Built from Dante Labs data release 2026.10.16-c6eea6bf of 16 October 2026.
Cite this page
Dante Labs. (16 October 2026). MSH2 L559X (c.1676del, rs63750633) (Version 2026.10.16-c6eea6bf). Retrieved 16 October 2026, from https://dantelabs.com/genes/msh2/variants/l559x
Dante Labs. MSH2 L559X (c.1676del, rs63750633) [Internet]. Version 2026.10.16-c6eea6bf. 16 October 2026 [cited 16 October 2026]. Available from: https://dantelabs.com/genes/msh2/variants/l559x
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