POLB

DNA polymerase beta, the group of DNA polymerases

Basic information

Region (hg38): 8:42338453-42371808

Links

ENSG00000070501 ∙ NCBI:5423 ∙ OMIM:174760 ∙ HGNC:9174 ∙ Uniprot:P06746 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the POLB gene.

• Inborn genetic diseases (7 variants)

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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	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)
8-42357354-C-T		not specified	Uncertain significance (Dec 13, 2023)
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)
8-42371595-G-A		not specified	Uncertain significance (Oct 03, 2022)
8-42371652-G-A		not specified	Uncertain significance (Oct 29, 2021)

GnomAD

Source: gnomAD

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: dbNSFP

• 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