POLB
DNA polymerase beta, the group of DNA polymerases
Basic information
Region (hg38): 8:42338454-42371808
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 POLB 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 | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 0 | 0 |
Variants in POLB
This is a list of pathogenic ClinVar variants found in the POLB region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 8-42339017-G-T | not specified | Uncertain significance (May 26, 2023) | ||
| 8-42352553-A-G | not specified | Uncertain significance (May 18, 2022) | ||
| 8-42355531-A-G | not specified | Uncertain significance (Nov 28, 2023) | ||
| 8-42357198-C-G | not specified | Uncertain significance (Aug 10, 2024) | ||
| 8-42357354-C-T | not specified | Uncertain significance (Dec 13, 2023) | ||
| 8-42361297-G-A | not specified | Uncertain significance (May 13, 2024) | ||
| 8-42361315-A-G | not specified | Uncertain significance (Jun 10, 2024) | ||
| 8-42361317-G-T | not specified | Uncertain significance (Jan 26, 2022) | ||
| 8-42361342-T-G | not specified | Uncertain significance (Jan 03, 2024) | ||
| 8-42369304-A-G | not specified | Uncertain significance (Aug 09, 2021) | ||
| 8-42369323-G-T | not specified | Uncertain significance (Oct 12, 2022) | ||
| 8-42369859-A-G | not specified | Uncertain significance (Nov 24, 2024) | ||
| 8-42371595-G-A | not specified | Uncertain significance (Oct 03, 2022) | ||
| 8-42371652-G-A | not specified | Uncertain significance (Oct 29, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| POLB | protein_coding | protein_coding | ENST00000265421 | 14 | 33355 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000340 | 0.989 | 125733 | 0 | 14 | 125747 | 0.0000557 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.57 | 119 | 178 | 0.669 | 0.00000890 | 2210 |
| Missense in Polyphen | 28 | 48.661 | 0.57541 | 614 | ||
| Synonymous | 0.458 | 55 | 59.5 | 0.924 | 0.00000275 | 584 |
| Loss of Function | 2.26 | 11 | 22.6 | 0.487 | 0.00000110 | 290 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000905 | 0.0000905 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000976 | 0.0000967 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases. {ECO:0000269|PubMed:11805079, ECO:0000269|PubMed:21362556, ECO:0000269|PubMed:9207062, ECO:0000269|PubMed:9572863}.;
- Pathway
- Base excision repair - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Nucleotide Metabolism;DNA Repair;Post-translational protein modification;Metabolism of proteins;Purine metabolism;Pyrimidine metabolism;POLB-Dependent Long Patch Base Excision Repair;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;Ub-specific processing proteases;Deubiquitination;Abasic sugar-phosphate removal via the single-nucleotide replacement pathway;Resolution of AP sites via the single-nucleotide replacement pathway;APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway
(Consensus)
Recessive Scores
- pRec
- 0.313
Intolerance Scores
- loftool
- 0.782
- rvis_EVS
- -0.07
- rvis_percentile_EVS
- 48.12
Haploinsufficiency Scores
- pHI
- 0.295
- hipred
- Y
- hipred_score
- 0.572
- ghis
- 0.594
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.973
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Polb
- Phenotype
- integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype; vision/eye phenotype; craniofacial phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; respiratory system phenotype; immune system phenotype; renal/urinary system phenotype; skeleton phenotype; hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary phenotype;
Zebrafish Information Network
- Gene name
- polb
- Affected structure
- anatomical system
- Phenotype tag
- abnormal
- Phenotype quality
- quality
Gene ontology
- Biological process
- DNA repair;base-excision repair;base-excision repair, base-free sugar-phosphate removal;base-excision repair, gap-filling;base-excision repair, DNA ligation;pyrimidine dimer repair;nucleotide-excision repair, DNA gap filling;double-strand break repair via nonhomologous end joining;inflammatory response;cellular response to DNA damage stimulus;salivary gland morphogenesis;aging;intrinsic apoptotic signaling pathway in response to DNA damage;response to gamma radiation;somatic hypermutation of immunoglobulin genes;protein deubiquitination;response to ethanol;lymph node development;spleen development;homeostasis of number of cells;neuron apoptotic process;response to hyperoxia;immunoglobulin heavy chain V-D-J recombination;DNA biosynthetic process
- Cellular component
- nucleus;nucleoplasm;cytoplasm;microtubule;spindle microtubule;protein-containing complex
- Molecular function
- damaged DNA binding;DNA-directed DNA polymerase activity;DNA-(apurinic or apyrimidinic site) endonuclease activity;protein binding;microtubule binding;lyase activity;enzyme binding;metal ion binding