POLE2

protein-coding

DNA 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

NM_002692.4

Inheritance

AR

ClinVar variants

U:254B:71

Top phenotype

POLE2-related disorder

gnomAD constraint

pLI —, LoF o/e 0.5

Max pathogenic AF

—

Genomic locus

chr14:49,643,555-49,688,422

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~44.9 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

combined immunodeficiency due to POLE2 deficiencyLIMITED

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).

combined immunodeficiencyLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0015131

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to POLE2 variants in ClinVar

3 Conditions Cataloged
not providedTotal: 418
not specifiedTotal: 97
POLE2-related disorderTotal: 11

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.

EffectPLPVUSLBBSum
synonymous
10
clinvar
58
clinvar
2
clinvar
70
missense
209
clinvar
9
clinvar
2
clinvar
220
nonsense
8
clinvar
8
start loss
0
frameshift
14
clinvar
14
splice donor/acceptor (+/-2bp)
13
clinvar
13
Total00254674325
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 24 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_002692.4RefSeqNP_002683.219MANE Select
ENST00000216367.10EnsemblENSP00000216367.519MANE Select
NM_001197330.2RefSeqNP_001184259.118Standard
NM_001197331.3RefSeqNP_001184260.117Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
pole2Danio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.7912322680.8640.00001363432
Missense (PolyPhen)5676.440.73261017
Synonymous0.06678989.80.9910.00000446957
Loss of Function2.601631.80.5030.00000163408

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000320.00031rare
Latino/Admixed American0.0000880.000087rare
Ashkenazi Jewish0.0000990.000099rare
East Asian0.000170.00016rare
Finnish0.000180.00018rare
European (Non-Finnish)0.000420.00041rare
South Asian0.0000690.000065rare
Other0.000170.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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