Variant
PMS2 E109Gfs*30
NM_000535.7(PMS2):c.325dup (p.Glu109GlyfsTer30)
- p.Glu109GlyfsTer30
- p.E109Gfs*30
- rs587781716
- ClinVar classification
- Pathogenic
- Review status
- 2 stars out of 4criteria provided, multiple submitters, no conflicts
- Last evaluated
- 20 September 2023
Data current to ClinVar release 2026-10-19 · Dante Labs data release 2026.10.21-311f020eFacts last changed 21 October 2026
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E109Gfs*30 is a frameshift variant in PMS2: it adds or removes DNA letters in a way that shifts how the rest of the gene's code is read. ClinVar classifies it as pathogenic for Lynch syndrome 4 (criteria provided, multiple submitters, no conflicts).
ClinVar classifications
| Condition | Classification | Review status | Submissions | Last evaluated |
|---|---|---|---|---|
| Lynch syndrome 4ClinVar VCV000233300 (opens in a new tab) | Pathogenic | 2 stars out of 4criteria provided, multiple submitters, no conflicts | 4 submissions | 20 September 2023 |
Classifications as ClinVar records them in release 2026-10-19. ClinVar updates them as evidence is reviewed.
ACMG/AMP criteria
The ACMG/AMP criteria E109Gfs*30 meets, from its predicted effect in PMS2, gnomAD and ClinVar.
| Criterion | Strength | Points | Rests on |
|---|---|---|---|
| PVS1Null variant where loss of function causes disease | Very strong | +8 | frameshift_variant on NM_000535.7Expected to cause nonsense-mediated decay |
| PP5A reputable source reports it as pathogenic | Supporting | Not counted | ClinVar: Pathogenic (criteria provided, multiple submitters, no conflicts) |
On these criteria alone: +8 points, likely pathogenic.
Assessed automatically, without functional, computational or family evidence. Not a clinical classification.
Population frequency
How often E109Gfs*30 is seen among the people whose exomes and genomes gnomAD 4.1 brings together.
| Dataset | Allele frequency | Allele count | Homozygotes | Commonest in |
|---|---|---|---|---|
| gnomAD exomesFailed gnomAD's quality filters | 0.00049%1 in 206,160 | 7 of 1,443,120 | 0 | South Asian: 0.0058% |
| gnomAD genomes | 0.0026%1 in 37,995 | 4 of 151,980 | 0 | South Asian: 0.021% |
Figures from gnomAD 4.1, as gnomAD publishes them. Groups are genetic ancestry groups as gnomAD infers them. They describe the variant in gnomAD's populations, not anyone's result.
Molecular details
| Gene | PMS2 |
|---|---|
| Transcript | NM_000535.7MANE Select |
| Coding DNA change (HGVS c.) | c.325dup |
| Protein change (HGVS p.) | p.Glu109GlyfsTer30p.E109Gfs*30 |
| Predicted consequence | Frameshiftframeshift_variant (opens in a new tab)frameshift_truncation (opens in a new tab) |
| Predicted impact | High |
| Position (GRCh38) | chr7:6003717 T>TC |
| Position (GRCh37) | chr7:6043348 T>TC |
| dbSNP ID | rs587781716 (opens in a new tab) |
| ClinVar Variation ID | VCV000233300 (opens in a new tab) |
| ClinVar Allele ID | 233589 |
| ClinGen Allele Registry ID | CA4150133 (opens in a new tab) |
| ClinVar name | NM_000535.7(PMS2):c.325dup (p.Glu109fs) |
PMS2 E109Gfs*30 in other databases
Reports that look at this variant (1)
These Genome Test condition reports include E109Gfs*30 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 2026-10-19), 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 2026-10-21-c4908f54).
- Reference SNP identifiers from dbSNP (release b157), National Center for Biotechnology Information.
- Gene–disease links from the Gene Curation Coalition, GenCC (release 2026-10-21).
- 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 2026.10.21-311f020e of 21 October 2026.
Cite this page
Dante Labs. (21 October 2026). PMS2 E109Gfs*30 (c.325dup, rs587781716) (Version 2026.10.21-311f020e). Retrieved 21 October 2026, from https://dantelabs.com/genes/pms2/variants/e109gfs30
Dante Labs. PMS2 E109Gfs*30 (c.325dup, rs587781716) [Internet]. Version 2026.10.21-311f020e. 21 October 2026 [cited 21 October 2026]. Available from: https://dantelabs.com/genes/pms2/variants/e109gfs30
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