EXO1
protein-codingexonuclease 1, the group of Exonucleases
Gene summary
This gene encodes a protein with 5' to 3' exonuclease activity as well as an RNase H activity. It is similar to the Saccharomyces cerevisiae protein Exo1 which interacts with Msh2 and which is involved in mismatch repair and recombination. Alternative splicing of this gene results in three transcript variants encoding two different isoforms. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~47.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0005835
Submitter: ClinGen
Exonuclease 1 (EXO1) is a 5’ to 3’ exonuclease, which is required for both DNA mismatch repair and DNA double-strand break (DSB) repair. Although there is no disease associated with *EXO1* in OMIM, 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 In 2001, Wu et al. (PMID: 11375940) first proposed the association of germline *EXO1* variants in autosomal dominant Lynch syndrome by reporting 13 variants (splice site and missense) detected in 14 families with HNPCC or atypical HNPCC. This study also found that these variants did not occur in more than 200 control individuals. However, this study did not exclude germline MLH1, MSH2, and MSH6 mutations from the patients or use large control populations. Co-segregation of EXO1 variants with disease in these families was not tested. Additionally, the results from the first study were questioned by two subsequent publications (PMID: 12517792, 14756672), in which the authors confirmed that several variants observed in the patients with Lynch syndrome in the Wu et al. study were also observed in controls with similar frequencies, including the truncating variant previously proposed to be a disease-causing mutation. In addition, Alam et al. (PMID: 14623461) identified nine individuals carrying heterozygous germline deletions of 1q42.3 that include *EXO1* gene. Theses individuals had multiple cutaneous and uterine leiomyomatosis, but they did not develop colorectal cancer or other Lynch syndrome spectrum cancers. No microsatellite instability (MSI) was detected from the *EXO1*-null skin leiomyomata tissues either. **Overall Summary:** Considering the lack of substantial association in both genetic and experimental studies, there is convincing evidence refuting the gene-disease relationship between *EXO1* and autosomal dominant Lynch syndrome. This gene-disease pair was originally evaluated as disputed on 6/8/2017 by Colon Cancer GCEP. This re-curation was approved by the ClinGen Hereditary Cancer GCEP on 5/26/2023 (SOP Version 9).
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to EXO1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_130398.4. 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 | 1 | 36 | 1 | 38 | ||
| missense | 95 | 18 | 6 | 119 | ||
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 3 | 4 | |||
| splice donor/acceptor (+/-2bp) | 2 | 1 | 3 | |||
| Total | 0 | 1 | 103 | 55 | 7 | 166 |
Highest pathogenic variant AF is 0.0000043374057
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_569082.2 | 13 | MANE Select | |
| Ensembl | ENSP00000355506.3 | 13 | MANE Select | |
| RefSeq | NP_001306153.1 | 13 | Standard | |
| RefSeq | NP_003677.4 | 13 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Mismatch repair - Homo sapiens (human)
- Mismatch repair
- Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta)
- Mismatch Repair
- HDR through Single Strand Annealing (SSA)
Biological Process
- DNA replication
- DNA repair
- mismatch repair
- DNA recombination
- RNA phosphodiester bond hydrolysis, endonucleolytic
Molecular Function
- DNA binding
- RNA-DNA hybrid ribonuclease activity
- exonuclease activity
- protein binding
- 5'-3' exonuclease activity
Cellular Component
- nucleus
- nucleoplasm
- plasma membrane
- nuclear body
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000366548
- Coding exons
- 13
- Length
- 47182
- Individuals with no LoFs
- 125279
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 467
- Defined
- 125748
- p
- 0.00187
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -1.03 | 500 | 439 | 1.14 | 0.0000228 | 5542 |
| Missense (PolyPhen) | 130 | 132.84 | 0.97859 | 1684 | ||
| Synonymous | -0.859 | 182 | 168 | 1.08 | 0.00000950 | 1617 |
| Loss of Function | 1.92 | 25 | 37.7 | 0.662 | 0.00000205 | 485 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0011 | 0.0011 | notable |
| Latino/Admixed American | 0.0021 | 0.0021 | notable |
| Ashkenazi Jewish | 0.00050 | 0.00050 | rare |
| East Asian | 0.00016 | 0.00016 | rare |
| Finnish | 0.00083 | 0.00083 | rare |
| European (Non-Finnish) | 0.0028 | 0.0028 | notable |
| South Asian | 0.00059 | 0.00059 | rare |
| Other | 0.0021 | 0.0021 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: 5'->3' double-stranded DNA exonuclease which may also possess a cryptic 3'->5' double-stranded DNA exonuclease activity. Functions in DNA mismatch repair (MMR) to excise mismatch- containing DNA tracts directed by strand breaks located either 5' or 3' to the mismatch. Also exhibits endonuclease activity against 5'-overhanging flap structures similar to those generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Required for somatic hypermutation (SHM) and class switch recombination (CSR) of immunoglobulin genes. Essential for male and female meiosis. {ECO:0000269|PubMed:10364235, ECO:0000269|PubMed:10608837, ECO:0000269|PubMed:11809771, ECO:0000269|PubMed:11842105, ECO:0000269|PubMed:12414623, ECO:0000269|PubMed:12704184, ECO:0000269|PubMed:14636568, ECO:0000269|PubMed:14676842, ECO:0000269|PubMed:15225546, ECO:0000269|PubMed:15886194, ECO:0000269|PubMed:16143102, ECO:0000269|PubMed:9685493}.;
Recessive Scores
- pRec
- 0.261
Intolerance Scores
- LoFtool
- 0.974
- RVIS EVS
- 3.14
- RVIS percentile EVS
- 99.3
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.699
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | High | Medium | High |
| Cancer | High | Medium | High |