POLE3
DNA polymerase epsilon 3, accessory subunit, the group of Chromatin accessibility complex|ATAC complex|DNA polymerases
Basic information
Region (hg38): 9:113407235-113410675
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the POLE3 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 8 | 0 | 0 |
Variants in POLE3
This is a list of pathogenic ClinVar variants found in the POLE3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 9-113408843-C-G | not specified | Uncertain significance (Feb 01, 2023) | ||
| 9-113408864-C-T | not specified | Uncertain significance (Aug 13, 2021) | ||
| 9-113408892-C-A | not specified | Uncertain significance (Sep 17, 2021) | ||
| 9-113408924-C-T | not specified | Uncertain significance (Dec 11, 2023) | ||
| 9-113408974-C-A | not specified | Uncertain significance (Aug 02, 2023) | ||
| 9-113410107-G-A | not specified | Uncertain significance (Jun 30, 2022) | ||
| 9-113410128-C-T | not specified | Uncertain significance (Aug 16, 2022) | ||
| 9-113410136-G-A | not specified | Uncertain significance (Sep 22, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| POLE3 | protein_coding | protein_coding | ENST00000374171 | 4 | 3438 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0307 | 0.823 | 125729 | 0 | 18 | 125747 | 0.0000716 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.144 | 79 | 82.7 | 0.956 | 0.00000422 | 972 |
| Missense in Polyphen | 24 | 27.605 | 0.8694 | 315 | ||
| Synonymous | -0.699 | 39 | 33.8 | 1.15 | 0.00000178 | 251 |
| Loss of Function | 1.13 | 3 | 5.99 | 0.501 | 2.50e-7 | 81 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000177 | 0.000177 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000981 | 0.0000879 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000326 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Forms a complex with DNA polymerase epsilon subunit CHRAC1 and binds naked DNA, which is then incorporated into chromatin, aided by the nucleosome-remodeling activity of ISWI/SNF2H and ACF1.;
- Pathway
- 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);Purine metabolism - Homo sapiens (human);Pyrimidine metabolism;HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA);DNA Repair;DNA Double-Strand Break Repair;Homology Directed Repair;Purine metabolism;Activation of the pre-replicative complex;Mitotic G1-G1/S phases;DNA replication initiation;DNA Replication;Pyrimidine metabolism;Synthesis of DNA;S Phase;PCNA-Dependent Long Patch Base Excision Repair;Resolution of AP sites via the multiple-nucleotide patch replacement pathway;Resolution of Abasic Sites (AP sites);Base Excision Repair;Telomere C-strand synthesis initiation;Telomere C-strand (Lagging Strand) Synthesis;Extension of Telomeres;Telomere Maintenance;Chromosome Maintenance;G1/S Transition;Recognition of DNA damage by PCNA-containing replication complex;DNA Replication Pre-Initiation;M/G1 Transition;Termination of translesion DNA synthesis;Translesion synthesis by Y family DNA polymerases bypasses lesions on DNA template;DNA Damage Bypass;Cell Cycle;Dual Incision in GG-NER;Gap-filling DNA repair synthesis and ligation in GG-NER;Global Genome Nucleotide Excision Repair (GG-NER);Cell Cycle, Mitotic;Dual incision in TC-NER;Gap-filling DNA repair synthesis and ligation in TC-NER;Transcription-Coupled Nucleotide Excision Repair (TC-NER);Nucleotide Excision Repair;HDR through Homologous Recombination (HRR)
(Consensus)
Recessive Scores
- pRec
- 0.250
Intolerance Scores
- loftool
- 0.507
- rvis_EVS
- -0.12
- rvis_percentile_EVS
- 44.54
Haploinsufficiency Scores
- pHI
- 0.347
- hipred
- Y
- hipred_score
- 0.774
- ghis
- 0.655
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.994
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pole3
- Phenotype
Gene ontology
- Biological process
- G1/S transition of mitotic cell cycle;DNA replication;cellular response to DNA damage stimulus;CENP-A containing nucleosome assembly;nucleosome mobilization;histone H3 acetylation;heterochromatin assembly involved in chromatin silencing;cellular response to gamma radiation;DNA biosynthetic process
- Cellular component
- nucleus;nucleoplasm;Ada2/Gcn5/Ada3 transcription activator complex;epsilon DNA polymerase complex
- Molecular function
- DNA binding;DNA-directed DNA polymerase activity;histone acetyltransferase activity;protein binding;protein heterodimerization activity