Variant
PMS2 L42_E44del
NM_000535.7(PMS2):c.123_131del (p.Leu42_Glu44del)
- p.Leu42_Glu44del
- p.L42_E44del
- rs863224676
- ClinVar classification
- Pathogenic/likely pathogenic
- Review status
- 2 stars out of 4criteria provided, multiple submitters, no conflicts
- Last evaluated
- 29 July 2024
Data current to ClinVar release 2026-10-12 · Dante Labs data release 2026.10.16-c6eea6bfFacts last changed 16 October 2026
This page as data
Add .json to the page's address, or ask for application/json, to read it as JSON.
library(jsonlite)
url <- "https://dantelabs.com/genes/pms2/variants/l42-e44del.json"
page <- fromJSON(url)
page$variant$nameSummary
L42_E44del is an in-frame variant in PMS2: it adds or removes one or more amino acids without shifting how the rest of the gene's code is read. ClinVar classifies it as likely pathogenic for Lynch Syndrome (criteria provided, multiple submitters, no conflicts). ClinVar also lists it under 1 more condition.
ClinVar classifications
| Condition | Classification | Review status | Submissions | Last evaluated |
|---|---|---|---|---|
| Lynch SyndromeClinVar VCV000216449 (opens in a new tab) | Likely pathogenic | 2 stars out of 4criteria provided, multiple submitters, no conflicts | 2 submissions | 29 July 2024 |
| Lynch syndrome 4ClinVar VCV000216449 (opens in a new tab) | Pathogenic/likely pathogenic | 2 stars out of 4criteria provided, multiple submitters, no conflicts | 3 submissions | 27 March 2026 |
Classifications as ClinVar records them in release 2026-10-12. ClinVar updates them as evidence is reviewed.
Where it lies in PMS2
L42_E44del lies in exon 2 of the 15 in PMS2's MANE Select transcript, NM_000535.7.
Molecular details
| Gene | PMS2 |
|---|---|
| Transcript | NM_000535.7MANE Select |
| Coding DNA change (HGVS c.) | c.123_131del |
| Protein change (HGVS p.) | p.Leu42_Glu44delp.L42_E44del |
| Predicted consequence | In-frame insertion or deletiondisruptive_inframe_deletion (opens in a new tab) |
| Predicted impact | Moderate |
| Position (GRCh38) | chr7:6005923 TTCTACTAAC>T |
| Position (GRCh37) | chr7:6045554 TTCTACTAAC>T |
| dbSNP ID | rs863224676 (opens in a new tab) |
| ClinVar Variation ID | VCV000216449 (opens in a new tab) |
| ClinVar Allele ID | 212611 |
| ClinGen Allele Registry ID | CA336478 (opens in a new tab) |
| ClinVar name | NM_000535.7(PMS2):c.123_131del (p.Leu42_Glu44del) |
PMS2 L42_E44del in other databases
Reports that look at this variant (1)
These Genome Test condition reports include L42_E44del among the variants they look at.
| Report | Conditions | Inheritance |
|---|---|---|
| Lynch Syndrome | Lynch Syndrome | Autosomal dominant |
Other variants in PMS2
- c.1A>GLikely pathogenic3 stars out of 4
- c.24-12_107delinsAAATPathogenic3 stars out of 4
- c.163+2T>CLikely pathogenic3 stars out of 4
- c.164-2A>GLikely pathogenic3 stars out of 4
- c.164-518_803+252delinsCGPathogenic3 stars out of 4
- c.251-2A>GLikely pathogenic3 stars out of 4
- c.538-478_705+456delPathogenic3 stars out of 4
- c.705+1G>TLikely pathogenic3 stars out of 4
- c.989-2A>GLikely pathogenic3 stars out of 4
- c.989-296_1144+706delPathogenic3 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). PMS2 L42_E44del (c.123_131del, rs863224676) (Version 2026.10.16-c6eea6bf). Retrieved 17 October 2026, from https://dantelabs.com/genes/pms2/variants/l42-e44del
Dante Labs. PMS2 L42_E44del (c.123_131del, rs863224676) [Internet]. Version 2026.10.16-c6eea6bf. 16 October 2026 [cited 17 October 2026]. Available from: https://dantelabs.com/genes/pms2/variants/l42-e44del
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