MRE11
protein-codingMRE11 homolog, double strand break repair nuclease, the group of BRCA1 C complex|MRN complex|MicroRNA protein coding host genes
Gene summary
This gene encodes a nuclear protein involved in homologous recombination, telomere length maintenance, and DNA double-strand break repair. By itself, the protein has 3' to 5' exonuclease activity and endonuclease activity. The protein forms a complex with the RAD50 homolog; this complex is required for nonhomologous joining of DNA ends and possesses increased single-stranded DNA endonuclease and 3' to 5' exonuclease activities. In conjunction with a DNA ligase, this protein promotes the joining of noncomplementary ends in vitro using short homologies near the ends of the DNA fragments. This gene has a pseudogene on chromosome 3. Alternative splicing of this gene results in two transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
- MRE11A
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~78.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0024557
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0024557
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0007254
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0008315
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0024557
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0024557
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0024557
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0016419
Submitter: ClinGen
MRE11 (also known as MRE11A) is part of the MRN (MRE11-RAD50-NBN) complex and is involved in repairing double strand breaks in DNA. Bi-allelic mutations in MRE11 are associated with the recessive Ataxia-telangiectasia-like disorder 1. Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we have split MRE11 into two separate curations - one for the recessive Ataxia-telangiectasia-like disorder 1 and the second for hereditary breast cancer (refute the association with breast cancer) described here. Evidence refuting this gene-disease relationship includes case-control data, while experimental data supports the role of MRE11 in DNA damage repair. **Summary of Case-Control Data: 0 POINTS** This gene-disease relationship has been studied in at least 4 case-control studies at the aggregate variant level and 1 case-control cohort at the single variant level. In 2021, two large case-control studies [CARRIERS (PMID: 33471974) and BCAC (PMID: 33471991); both with more than 32 thousand cases and controls] did not identify a significant association of aggregate loss of function (LOF) variants in MRE11 and breast cancer. Likewise, another large case-control study published in 2017 (Couch et al. PMID: 28418444) screened breast cancer cases from commercial laboratories and did not find significant association of pathogenic mutations in MRE11 with breast cancer. Two more case-control studies with smaller case and control sizes also showed no association of LOF or missense MRE11 variants with breast cancer (PMID: 29368209 and 29678143). **Summary of Experimental Data: 1 POINTS** While case control studies did not support the gene-disease association, there is experimental evidence showing the role of MRE11 in double-strand DNA break repair (0.5 point, PMID:9651580). Another study reported reduced MRE11 expression in breast cancer tissues (0.5 point, PMID:14511253). **Overall Summary:** In summary, given the lack of significant association in large breast cancer case-control studies to date, there is convincing evidence refuting the association between MRE11 and autosomal dominant hereditary breast cancer, which significantly outweighs the evidence supporting the association. This gene-disease pair was originally evaluated as disputed by the Breast/Ovarian Cancer GCEP on 10/25/2017. This re-curation was approved by the ClinGen Hereditary Diseases GCEP on 2/17/2023 (SOP Version 9).
Inheritance Pattern: AD
Disease ID:MONDO:0016248
Submitter: ClinGen
MRE11 (previously known as MRE11A) constitutes a part of the MRN complex and encodes a nuclear protein involved in DNA double-strand break repair. Paull and Gellert in 1998 first reported the role of MRE11 in this pathway, while Heikkinen et al. in 2003 identified the first monoallelic germline variant in this gene in an ovarian cancer patient. MRE11 has been also linked to MRE11-related ataxia with oculomotor apraxia (autosomal recessive) and hereditary breast cancer (autosomal dominant), which were curated separately. Per criteria outlined by the ClinGen Lumping and Splitting Working Group, curations to refute or dispute can be split when needed. This curation focuses on refuting the association with familial ovarian cancer. Evidence curated in this gene-disease relationship includes case level and case-control data (0 Point), and experimental data (1 Point). Five studies (PMIDs: 14684699, 22006311, 29348823, 30441849, 31742824) identified MRE11 germline variants in ovarian cancer patients predominantly through multi-gene panel testing. However, the absence of co-segregation analysis in these studies raises uncertainties regarding whether the variants segregated with cancer. In two of these cases (Walsh et al., 2011 and Koczkowska et al., 2018), carriers were identified with concomitant BRCA1 or BRCA2 mutations, a known gene associated with ovarian cancer. Additionally, the pathogenicity of the MRE11 variants in these studies remains inconclusive due to the lack of supporting functional data. Importantly, multiple large case-control studies (PMIDs: 26720728, 28888541, 31406321, 33510186) presented no significant differences in MRE11 variant frequencies between cases and controls. Experimentally, Paull and Gellert (PMID: 9705271) demonstrated the specific enzymatic activities of MRE11 and its collaboration with RAD50 in repairing DNA double-strand breaks, emphasizing their roles in nonhomologous end-joining processes. Additionally, Zhong et al. (PMID: 10426999) found an interaction between BRCA1 and hRad50, forming a complex with hMre11 and p95/nibrin, suggesting BRCA1's cellular responses to DNA damage may be mediated by this complex. However, experimental studies establishing the specific association between MRE11 and familial ovarian cancer are lacking. In summary, given the lack of significant association in large ovarian cancer case-control studies to date, there is convincing evidence refuting the association between MRE11 and autosomal dominant familial ovarian cancer, which significantly outweighs the evidence supporting the association. This gene-disease pair was originally evaluated as disputed by the Breast/Ovarian Cancer GCEP on 10/25/2017. This re-curation as refuted was approved by the ClinGen Hereditary Cancer GCEP on 12/15/2023 (SOP Version 10).
Clinical Genomic Database (CGD)
Manifestation: Dermatologic; Neurologic; Oncologic; Ophthalmologic
Intervention: Oncologic
Rationale: Awareness of the risk of malignancy may allow early surveillance, preventive measures, and early diagnosis and treatment of disease
Comments: Individuals with Ataxia-telangiectasia-like disorder 1 may be at increased risk for malignancy, though the data are unclear
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to MRE11 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_005591.4. 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 | 8 | 475 | 5 | 489 | |
| missense | 1 | 4 | 1218 | 56 | 2 | 1281 |
| nonsense | 20 | 27 | 3 | 50 | ||
| start loss | 1 | 1 | 2 | |||
| frameshift | 41 | 40 | 4 | 85 | ||
| splice donor/acceptor (+/-2bp) | 2 | 57 | 7 | 66 | ||
| Total | 64 | 130 | 1241 | 531 | 7 | 1973 |
Highest pathogenic variant AF is 0.000093581664
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005582.1 | 19 | MANE Select | |
| Ensembl | ENSP00000325863.4 | 19 | MANE Select | |
| RefSeq | NP_001317276.1 | 19 | Standard | |
| RefSeq | NP_001427389.1 | 20 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Homologous recombination - Homo sapiens (human)
- Cellular senescence - Homo sapiens (human)
- Non-homologous end-joining - Homo sapiens (human)
- miRNA Regulation of DNA Damage Response
- Homologous recombination
Biological Process
- regulation of mitotic recombination
- telomere maintenance
- double-strand break repair via homologous recombination
- DNA double-strand break processing
- DNA replication
Molecular Function
- single-stranded DNA endodeoxyribonuclease activity
- DNA binding
- double-stranded DNA binding
- ATP-dependent DNA helicase activity
- nuclease activity
Cellular Component
- chromosome, telomeric region
- nuclear chromosome, telomeric region
- nucleus
- nucleoplasm
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000323929
- Coding exons
- 19
- Length
- 74180
- Individuals with no LoFs
- 125633
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 115
- Defined
- 125748
- p
- 0.000457
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.130 | 378 | 385 | 0.981 | 0.0000202 | 4714 |
| Missense (PolyPhen) | 89 | 105.63 | 0.84258 | 1389 | ||
| Synonymous | -0.966 | 138 | 124 | 1.11 | 0.00000624 | 1263 |
| Loss of Function | 2.40 | 26 | 43.0 | 0.605 | 0.00000240 | 498 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00037 | 0.00037 | rare |
| Latino/Admixed American | 0.00041 | 0.00040 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.00044 | 0.00044 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00053 | 0.00053 | rare |
| South Asian | 0.00069 | 0.00069 | rare |
| Other | 0.00065 | 0.00065 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Component of the MRN complex, which plays a central role in double-strand break (DSB) repair, DNA recombination, maintenance of telomere integrity and meiosis. The complex possesses single-strand endonuclease activity and double-strand- specific 3'-5' exonuclease activity, which are provided by MRE11. RAD50 may be required to bind DNA ends and hold them in close proximity. This could facilitate searches for short or long regions of sequence homology in the recombining DNA templates, and may also stimulate the activity of DNA ligases and/or restrict the nuclease activity of MRE11 to prevent nucleolytic degradation past a given point (PubMed:9651580, PubMed:9590181, PubMed:9705271, PubMed:11741547, PubMed:29670289). The complex may also be required for DNA damage signaling via activation of the ATM kinase (PubMed:15064416). In telomeres the MRN complex may modulate t- loop formation (PubMed:10888888). {ECO:0000269|PubMed:10888888, ECO:0000269|PubMed:11741547, ECO:0000269|PubMed:15064416, ECO:0000269|PubMed:29670289, ECO:0000269|PubMed:9590181, ECO:0000269|PubMed:9705271}.;
- Disease
- DISEASE: Ataxia-telangiectasia-like disorder 1 (ATLD1) [MIM:604391]: A rare disorder characterized by progressive cerebellar ataxia, dysarthria, abnormal eye movements, and absence of telangiectasia. ATLD patients show normal levels of total IgG, IgA and IgM, although there may be reduced levels of specific functional antibodies. At the cellular level, ATLD exhibits hypersensitivity to ionizing radiation and radioresistant DNA synthesis. {ECO:0000269|PubMed:10612394}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=Defects in MRE11 can be a cause of nephronophthisis- related ciliopathies (NPHP-RC), a group of recessive diseases that affect kidney, retina and brain. A homozygous truncating mutation MRE11 has been found in patients with cerebellar vermis hypoplasia, ataxia and dysarthria. {ECO:0000269|PubMed:22863007}.;
Recessive Scores
- pRec
- 0.503
Intolerance Scores
- RVIS EVS
- 0.04
- RVIS percentile EVS
- 57.41
Essentials
- Essential (gene trap)
- H