PMS1
protein-codingPMS1 homolog 1, mismatch repair system component, the group of MutL homologs
Gene summary
This gene encodes a protein belonging to the DNA mismatch repair mutL/hexB family. This protein is thought to be involved in the repair of DNA mismatches, and it can form heterodimers with MLH1, a known DNA mismatch repair protein. Mutations in this gene cause hereditary nonpolyposis colorectal cancer type 3 (HNPCC3) either alone or in combination with mutations in other genes involved in the HNPCC phenotype, which is also known as Lynch syndrome. [provided by RefSeq, Jul 2008]
- PMSL1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~93.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0005835
Submitter: ClinGen
*PMS1* (formerly known as PMSL1) encodes a protein belonging to the DNA mismatch repair mutL/hexB family, suggesting its involvement in DNA mismatch repair. Per criteria outlined by the ClinGen Lumping and Splitting Working Group, there is no disease associated with *PMS1* in OMIM, although there was an early assertion of association with Lynch syndrome. Thus, it was curated for that disorder. **Summary of Genetic Evidence (Case Level):** 0 point Nicolaides et al., 1994, first reported a frameshift germline variant in *PMS1* associated with autosomal dominant hereditary non-polyposis colorectal cancer/Lynch syndrome (PMID: 8072530). However, conflicting findings were subsequently noted in another study (Liu et al., 2001, PMID:11691795), where the proband and her nephew with Lynch syndrome reported in PMID: 8072530, in fact, had a large deletion in *MSH2* but not *PMS1*. Liu et al. also failed to detect pathogenic germline mutations in *PMS1* from 84 families with Lynch syndrome. Another study also found no germline variants in PMS1 within 34 Lynch syndrome families (PMID: 8574961). **Summary of Experimental Evidence:** 0.5 point While a study highlighted the association of PMS1 with hMLH1 as a heterodimer (PMID: 10748105), Prolla et al. (PMID:9500552) generated mice deficient for the murine homologues of the human gene *PMS1* and showed that the mice did not develop tumors, and mouse embryonic fibroblast cells deficient for PMS1 showed no defeat in dinucleotide repeats and there was no significant difference of microsatellite instability in the mucosa of PMS-deficient mice compared to wildtypes. **Overall Summary:** Considering the lack of substantial association in both genetic and experimental studies, there is convincing evidence refuting the gene-disease relationship between *PMS1* and autosomal dominant Lynch syndrome. This gene-disease pair was originally evaluated as disputed on 5/22/2017 by Colon Cancer GCEP. This re-curation was approved by the ClinGen Hereditary Cancer GCEP on 8/25/2023 (SOP Version 9).
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PMS1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000534.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 15 | 2 | 19 | ||
| missense | 2 | 119 | 21 | 9 | 151 | |
| nonsense | 8 | 8 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 2 | 5 | 8 | ||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 1 | 4 | 136 | 36 | 11 | 188 |
Highest pathogenic variant AF is 0.000095564916
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000525.1 | 12 | MANE Select | |
| Ensembl | ENSP00000406490.3 | 12 | MANE Select | |
| RefSeq | NP_001121615.1 | 11 | Standard | |
| RefSeq | NP_001121616.1 | 11 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- mismatch repair
- response to drug
Molecular Function
- DNA binding
- ATP binding
- ATPase activity
- enzyme binding
- mismatched DNA binding
Cellular Component
- nucleus
- mismatch repair complex
- MutLalpha complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000441310
- Coding exons
- 12
- Length
- 93249
- Individuals with no LoFs
- 125611
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 137
- Defined
- 125748
- p
- 0.000545
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.625 | 441 | 479 | 0.920 | 0.0000234 | 6190 |
| Missense (PolyPhen) | 139 | 143.94 | 0.9657 | 1800 | ||
| Synonymous | 1.61 | 141 | 167 | 0.842 | 0.00000861 | 1669 |
| Loss of Function | 1.48 | 32 | 42.4 | 0.755 | 0.00000225 | 568 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00068 | 0.00068 | rare |
| Latino/Admixed American | 0.00082 | 0.00081 | rare |
| Ashkenazi Jewish | 0.0023 | 0.0023 | notable |
| East Asian | 0.00016 | 0.00016 | rare |
| Finnish | 0.000093 | 0.000092 | rare |
| European (Non-Finnish) | 0.00047 | 0.00047 | rare |
| South Asian | 0.00046 | 0.00042 | rare |
| Other | 0.00066 | 0.00065 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Probably involved in the repair of mismatches in DNA. {ECO:0000269|PubMed:10748105}.;
Recessive Scores
- pRec
- 0.0919
Intolerance Scores
- LoFtool
- 0.0827
- RVIS EVS
- 0.58
- RVIS percentile EVS
- 82.32
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.247
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |