POLE2
protein-codingDNA polymerase epsilon 2, accessory subunit, the group of DNA polymerases
Gene summary
DNA polymerase epsilon, which is involved in DNA repair and replication, is composed of a large catalytic subunit and a small accessory subunit. The protein encoded by this gene represents the small subunit (B). Defects in this gene have been linked to colorectal cancer and to combined immunodeficiency. [provided by RefSeq, Jan 2017]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~44.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0800128
Submitter: ClinGen
*POLE2* was first reported in relation to combined immunodeficiency due to *POLE2* deficiency in 2016 (Frugoni et al., PMID: 26365386). *POLE2* deficiency is characterized by combined immunodeficiency, recurrent respiratory infections, agammaglobulinemia, absent NK cells, T cell lymphopenia and neutropenia, absent circulating B cells, increased effector memory T cells, undetectable TRECs, severe dyspnea with hypoxia, hepatomegaly, and hypothyroidism. The mechanism of pathogenicity appears to be homozygous loss of function. The curation of *POLE2* related to *POLE2* deficiency includes both case-level and experimental evidence. One variant, a canonical splice site variant has been reported in a single individual (PMID: 26365386). Heterozygous carriers from this single family were reportedly not identified to have any clinical features associated with *POLE2* deficiency. This gene-disease relationship is also supported by experimental evidence. Cell cycle proliferation studies on the patient’s peripheral blood leukocytes and fibroblasts showed abnormal cell cycle activity. This was partially rescued when cultured fibroblasts from the patient was transfected with wild type *POLE2*-containing vector (PMID: 26365386). It is unclear if abnormal cell cycle activity as a result of loss of *POLE2* is a mechanism for immunodeficiency. In summary, there is limited evidence to support this gene-disease relationship. Although more evidence is needed to support a causal role, no convincing evidence has emerged that contradicts the gene-disease relationship. This classification was approved by the ClinGen SCID/CID Gene Curation Expert Panel on the meeting date 05/16/2024 (SOP Version 9).
Inheritance Pattern: AR
Disease ID:MONDO:0015131
Submitter: PanelApp Australia
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to POLE2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002692.4. 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 | 10 | 58 | 2 | 70 | ||
| missense | 209 | 9 | 2 | 220 | ||
| nonsense | 8 | 8 | ||||
| start loss | 0 | |||||
| frameshift | 14 | 14 | ||||
| splice donor/acceptor (+/-2bp) | 13 | 13 | ||||
| Total | 0 | 0 | 254 | 67 | 4 | 325 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002683.2 | 19 | MANE Select | |
| Ensembl | ENSP00000216367.5 | 19 | MANE Select | |
| RefSeq | NP_001184259.1 | 18 | Standard | |
| RefSeq | NP_001184260.1 | 17 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| pole2 | Danio rerio | Structure: trunk Quality: necrotic abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Nucleotide excision repair - Homo sapiens (human)
- Pyrimidine metabolism - Homo sapiens (human)
- Base excision repair - Homo sapiens (human)
- HTLV-I infection - Homo sapiens (human)
- DNA replication - Homo sapiens (human)
Biological Process
- G1/S transition of mitotic cell cycle
- DNA replication
- DNA-dependent DNA replication
- DNA repair
- error-prone translesion synthesis
Molecular Function
- DNA binding
- DNA-directed DNA polymerase activity
- protein binding
Cellular Component
- nucleoplasm
- epsilon DNA polymerase complex
- nuclear body
- intracellular membrane-bounded organelle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000216367
- Coding exons
- 19
- Length
- 44868
- Individuals with no LoFs
- 125678
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 66
- Defined
- 125744
- p
- 0.000262
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.791 | 232 | 268 | 0.864 | 0.0000136 | 3432 |
| Missense (PolyPhen) | 56 | 76.44 | 0.7326 | 1017 | ||
| Synonymous | 0.0667 | 89 | 89.8 | 0.991 | 0.00000446 | 957 |
| Loss of Function | 2.60 | 16 | 31.8 | 0.503 | 0.00000163 | 408 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00032 | 0.00031 | rare |
| Latino/Admixed American | 0.000088 | 0.000087 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.00017 | 0.00016 | rare |
| Finnish | 0.00018 | 0.00018 | rare |
| European (Non-Finnish) | 0.00042 | 0.00041 | rare |
| South Asian | 0.000069 | 0.000065 | rare |
| Other | 0.00017 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Participates in DNA repair and in chromosomal DNA replication.;
Recessive Scores
- pRec
- 0.0896
Intolerance Scores
- LoFtool
- 0.830
- RVIS EVS
- 0.15
- RVIS percentile EVS
- 64.61
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.703
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |