POLR2B
RNA polymerase II subunit B, the group of RNA polymerase subunits
Basic information
Region (hg38): 4:56977722-57031158
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 POLR2B 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 | 1 | |||||
| missense | 17 | 17 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 17 | 1 | 0 |
Variants in POLR2B
This is a list of pathogenic ClinVar variants found in the POLR2B region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 4-56986356-A-G | not specified | Uncertain significance (Oct 01, 2024) | ||
| 4-56986390-C-T | not specified | Uncertain significance (Dec 05, 2022) | ||
| 4-56990839-G-A | not specified | Uncertain significance (Mar 19, 2024) | ||
| 4-56990876-C-T | not specified | Uncertain significance (Oct 05, 2023) | ||
| 4-56994759-C-T | not specified | Uncertain significance (Jul 17, 2024) | ||
| 4-57006910-C-T | not specified | Uncertain significance (May 22, 2023) | ||
| 4-57006977-A-C | not specified | Uncertain significance (Oct 24, 2024) | ||
| 4-57010791-A-T | Uncertain significance (Jan 08, 2024) | |||
| 4-57010803-G-C | not specified | Uncertain significance (Aug 02, 2022) | ||
| 4-57010866-T-C | not specified | Uncertain significance (Nov 07, 2023) | ||
| 4-57010876-A-C | Likely benign (Mar 01, 2024) | |||
| 4-57010878-C-T | not specified | Uncertain significance (May 20, 2024) | ||
| 4-57011036-A-T | not specified | Uncertain significance (Dec 13, 2023) | ||
| 4-57015611-A-G | not specified | Uncertain significance (Jun 02, 2023) | ||
| 4-57017173-T-C | not specified | Uncertain significance (Jan 24, 2024) | ||
| 4-57017210-C-T | Tracheoesophageal fistula | Likely pathogenic (Jul 01, 2019) | ||
| 4-57017637-G-A | not specified | Uncertain significance (Jan 19, 2024) | ||
| 4-57020910-A-G | not specified | Uncertain significance (Aug 04, 2023) | ||
| 4-57022228-A-G | not specified | Uncertain significance (Nov 30, 2021) | ||
| 4-57022236-A-T | not specified | Uncertain significance (Sep 15, 2021) | ||
| 4-57023423-C-T | not specified | Uncertain significance (Jul 30, 2024) | ||
| 4-57023570-G-A | not specified | Uncertain significance (Dec 15, 2022) | ||
| 4-57023666-G-A | not specified | Uncertain significance (May 21, 2024) | ||
| 4-57023744-G-A | not specified | Uncertain significance (Dec 13, 2023) | ||
| 4-57030386-G-A | not specified | Uncertain significance (Dec 08, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| POLR2B | protein_coding | protein_coding | ENST00000381227 | 25 | 53447 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.524 | 0.476 | 125702 | 0 | 46 | 125748 | 0.000183 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 6.62 | 182 | 661 | 0.275 | 0.0000354 | 7741 |
| Missense in Polyphen | 53 | 321.41 | 0.1649 | 3665 | ||
| Synonymous | 1.01 | 194 | 213 | 0.912 | 0.0000109 | 2174 |
| Loss of Function | 5.76 | 14 | 63.5 | 0.220 | 0.00000342 | 783 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00104 | 0.00104 |
| Ashkenazi Jewish | 0.0000993 | 0.0000992 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.0000924 | 0.0000924 |
| European (Non-Finnish) | 0.000124 | 0.000123 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.000230 | 0.000229 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB2 is part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template (By similarity). {ECO:0000250, ECO:0000269|PubMed:9852112}.;
- Pathway
- Pyrimidine metabolism - Homo sapiens (human);Huntington,s disease - Homo sapiens (human);RNA polymerase - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);Pyrimidine metabolism;Eukaryotic Transcription Initiation;FGFR2 alternative splicing;Signaling by FGFR2;DNA Repair;Disease;RNA Pol II CTD phosphorylation and interaction with CE during HIV infection;Signal Transduction;Formation of the HIV-1 Early Elongation Complex;Gene expression (Transcription);Signaling by FGFR;Formation of HIV-1 elongation complex containing HIV-1 Tat;Tat-mediated elongation of the HIV-1 transcript;Abortive elongation of HIV-1 transcript in the absence of Tat;HIV Transcription Elongation;HIV elongation arrest and recovery;Formation of HIV elongation complex in the absence of HIV Tat;Pausing and recovery of HIV elongation;Generic Transcription Pathway;Tat-mediated HIV elongation arrest and recovery;Pausing and recovery of Tat-mediated HIV elongation;Transcription of the HIV genome;Late Phase of HIV Life Cycle;HIV Life Cycle;HIV Infection;RNA Polymerase II HIV Promoter Escape;RNA Polymerase II Pre-transcription Events;RNA Polymerase II Transcription Initiation;RNA Polymerase II Transcription Initiation And Promoter Clearance;RNA Pol II CTD phosphorylation and interaction with CE;Viral Messenger RNA Synthesis;Influenza Viral RNA Transcription and Replication;Formation of RNA Pol II elongation complex ;Influenza Life Cycle;Influenza Infection;HIV Transcription Initiation;RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription;Metabolism of RNA;Infectious disease;Purine metabolism;RNA Polymerase II Transcription Elongation;mRNA Splicing - Major Pathway;Pyrimidine metabolism;RNA Polymerase II Promoter Escape;RNA Polymerase II Transcription Pre-Initiation And Promoter Opening;TP53 Regulates Transcription of DNA Repair Genes;Signaling by Nuclear Receptors;Transcriptional Regulation by TP53;mRNA Capping;Formation of the Early Elongation Complex;Estrogen-dependent gene expression;Transcriptional regulation by small RNAs;Signaling by Receptor Tyrosine Kinases;ESR-mediated signaling;Formation of TC-NER Pre-Incision Complex;mRNA Splicing - Minor Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA;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;Gene Silencing by RNA
(Consensus)
Recessive Scores
- pRec
- 0.493
Intolerance Scores
- loftool
- rvis_EVS
- -1
- rvis_percentile_EVS
- 8.32
Haploinsufficiency Scores
- pHI
- 0.358
- hipred
- Y
- hipred_score
- 0.793
- ghis
- 0.711
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.531
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Polr2b
- Phenotype
Zebrafish Information Network
- Gene name
- polr2b
- Affected structure
- head
- Phenotype tag
- abnormal
- Phenotype quality
- flat
Gene ontology
- Biological process
- mRNA splicing, via spliceosome;transcription-coupled nucleotide-excision repair;transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;transcription elongation from RNA polymerase II promoter;7-methylguanosine mRNA capping;fibroblast growth factor receptor signaling pathway;RNA metabolic process;snRNA transcription by RNA polymerase II;regulation of gene silencing by miRNA
- Cellular component
- nuclear chromosome, telomeric region;nucleus;nucleoplasm;RNA polymerase II, core complex;membrane
- Molecular function
- RNA polymerase II activity;DNA binding;chromatin binding;RNA binding;DNA-directed 5'-3' RNA polymerase activity;protein binding;ribonucleoside binding;metal ion binding