PMS1

protein-coding

PMS1 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]

Previous symbols:
  • PMSL1

MANE transcript

NM_000534.5

Inheritance

AD

ClinVar variants

P:5U:136B:47

Top phenotype

Ovarian cancer

gnomAD constraint

pLI —, LoF o/e 0.76

Max pathogenic AF

—

Genomic locus

chr2:189,784,085-189,877,629

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~93.5 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Lynch syndromeNO_KNOWN

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

13 Conditions Cataloged
not specifiedTotal: 141
not providedTotal: 53
Ovarian cancerTotal: 8
Lynch syndrome 1Total: 8
PMS1-related disorderTotal: 5
Hereditary breast ovarian cancer syndromeTotal: 3
PMS1-related breast cancerTotal: 2
Polyp of colonTotal: 2

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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
15
clinvar
2
clinvar
19
missense
2
clinvar
119
clinvar
21
clinvar
9
clinvar
151
nonsense
8
clinvar
8
start loss
0
frameshift
1
clinvar
2
clinvar
5
clinvar
8
splice donor/acceptor (+/-2bp)
2
clinvar
2
Total141363611188

Highest pathogenic variant AF is 0.000095564916

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 127 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_000534.5RefSeqNP_000525.112MANE Select
ENST00000441310.7EnsemblENSP00000406490.312MANE Select
NM_001128143.2RefSeqNP_001121615.111Standard
NM_001128144.2RefSeqNP_001121616.111Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.6254414790.9200.00002346190
Missense (PolyPhen)139143.940.96571800
Synonymous1.611411670.8420.000008611669
Loss of Function1.483242.40.7550.00000225568

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000680.00068rare
Latino/Admixed American0.000820.00081rare
Ashkenazi Jewish0.00230.0023notable
East Asian0.000160.00016rare
Finnish0.0000930.000092rare
European (Non-Finnish)0.000470.00047rare
South Asian0.000460.00042rare
Other0.000660.00065rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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