EXO1

protein-coding

exonuclease 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

NM_130398.4

Inheritance

AD

ClinVar variants

P:1U:103B:62

Top phenotype

EXO1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.66

Max pathogenic AF

—

Genomic locus

chr1:241,847,967-241,895,148

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~47.2 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

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

4 Conditions Cataloged
not specifiedTotal: 141
EXO1-related disorderTotal: 28
not providedTotal: 27
Hereditary breast ovarian cancer syndromeTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
36
clinvar
1
clinvar
38
missense
95
clinvar
18
clinvar
6
clinvar
119
nonsense
2
clinvar
2
start loss
0
frameshift
1
clinvar
3
clinvar
4
splice donor/acceptor (+/-2bp)
2
clinvar
1
clinvar
3
Total01103557166

Highest pathogenic variant AF is 0.0000043374057

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 49 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_130398.4RefSeqNP_569082.213MANE Select
ENST00000366548.8EnsemblENSP00000355506.313MANE Select
NM_001319224.2RefSeqNP_001306153.113Standard
NM_003686.4RefSeqNP_003677.413Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-1.035004391.140.00002285542
Missense (PolyPhen)130132.840.978591684
Synonymous-0.8591821681.080.000009501617
Loss of Function1.922537.70.6620.00000205485

Population LoF Frequency

PopulationCAFp-valueStatus
African0.00110.0011notable
Latino/Admixed American0.00210.0021notable
Ashkenazi Jewish0.000500.00050rare
East Asian0.000160.00016rare
Finnish0.000830.00083rare
European (Non-Finnish)0.00280.0028notable
South Asian0.000590.00059rare
Other0.00210.0021notable

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyHighMediumHigh
CancerHighMediumHigh
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