POLR2E
RNA polymerase II, I and III subunit E, the group of RNA polymerase subunits
Basic information
Region (hg38): 19:1086574-1095380
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 POLR2E 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 | 9 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 9 | 0 | 1 |
Variants in POLR2E
This is a list of pathogenic ClinVar variants found in the POLR2E region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-1089544-T-A | not specified | Uncertain significance (Oct 10, 2023) | ||
| 19-1089545-T-C | not specified | Uncertain significance (Oct 10, 2023) | ||
| 19-1089910-G-A | not specified | Uncertain significance (Mar 07, 2024) | ||
| 19-1089944-C-G | not specified | Uncertain significance (Jun 24, 2022) | ||
| 19-1090933-A-G | not specified | Uncertain significance (Feb 27, 2023) | ||
| 19-1091812-T-C | not specified | Uncertain significance (Oct 17, 2024) | ||
| 19-1091909-T-C | Short stature | Pathogenic (Nov 18, 2001) | ||
| 19-1093907-G-C | not specified | Uncertain significance (Apr 17, 2023) | ||
| 19-1093977-C-T | Benign (Jun 21, 2018) | |||
| 19-1093981-C-T | not specified | Uncertain significance (Jan 30, 2024) | ||
| 19-1093990-C-T | not specified | Uncertain significance (Aug 13, 2021) | ||
| 19-1094078-G-A | not specified | Likely benign (Jul 25, 2023) | ||
| 19-1095308-T-G | not specified | Uncertain significance (Aug 28, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| POLR2E | protein_coding | protein_coding | ENST00000215587 | 7 | 9005 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 7.21e-9 | 0.148 | 125597 | 0 | 56 | 125653 | 0.000223 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.353 | 129 | 141 | 0.916 | 0.00000926 | 1364 |
| Missense in Polyphen | 43 | 44.117 | 0.97468 | 410 | ||
| Synonymous | -2.31 | 80 | 57.7 | 1.39 | 0.00000393 | 401 |
| Loss of Function | 0.212 | 13 | 13.9 | 0.939 | 7.62e-7 | 142 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00166 | 0.00165 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000218 | 0.000218 |
| Finnish | 0.0000927 | 0.0000924 |
| European (Non-Finnish) | 0.000146 | 0.000141 |
| Middle Eastern | 0.000218 | 0.000218 |
| South Asian | 0.000131 | 0.000131 |
| 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. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, POLR2E/RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process (By similarity). {ECO:0000250, ECO:0000269|PubMed:9852112}.;
- Pathway
- Pyrimidine metabolism - Homo sapiens (human);Huntington,s disease - Homo sapiens (human);Cytosolic DNA-sensing pathway - 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;B-WICH complex positively regulates rRNA expression;Positive epigenetic regulation of rRNA expression;DNA Repair;Disease;RNA Pol II CTD phosphorylation and interaction with CE during HIV infection;NoRC negatively regulates rRNA expression;Negative epigenetic regulation of rRNA expression;Signal Transduction;Formation of the HIV-1 Early Elongation Complex;Epigenetic regulation of gene expression;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;RNA Polymerase I Promoter Clearance;Influenza Infection;HIV Transcription Initiation;RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription;Metabolism of RNA;Infectious disease;Purine metabolism;RNA Polymerase I Transcription Termination;RNA Polymerase I Transcription;RNA Polymerase II Transcription Elongation;mRNA Splicing - Major Pathway;RNA Polymerase I Transcription Initiation;RNA Polymerase I Promoter Escape;Pyrimidine metabolism;RNA Polymerase II Promoter Escape;RNA Polymerase I Chain Elongation;RNA Polymerase III Transcription Termination;RNA Polymerase II Transcription Pre-Initiation And Promoter Opening;RNA Polymerase III Chain Elongation;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;RNA Polymerase III Abortive And Retractive Initiation;RNA Polymerase III Transcription Initiation From Type 1 Promoter;RNA Polymerase III Transcription Initiation From Type 2 Promoter;ESR-mediated signaling;RNA Polymerase III Transcription Initiation From Type 3 Promoter;RNA Polymerase III Transcription Initiation;RNA Polymerase III Transcription;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
- 0.322
Intolerance Scores
- loftool
- 0.525
- rvis_EVS
- -0.43
- rvis_percentile_EVS
- 25.37
Haploinsufficiency Scores
- pHI
- 0.441
- hipred
- N
- hipred_score
- 0.473
- ghis
- 0.616
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.991
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Polr2e
- Phenotype
Gene ontology
- Biological process
- mRNA splicing, via spliceosome;transcription-coupled nucleotide-excision repair;transcription initiation from RNA polymerase I promoter;termination of RNA polymerase I transcription;transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;transcription elongation from RNA polymerase II promoter;7-methylguanosine mRNA capping;transcription by RNA polymerase III;fibroblast growth factor receptor signaling pathway;viral process;RNA metabolic process;snRNA transcription by RNA polymerase II;positive regulation of gene expression, epigenetic;regulation of gene silencing by miRNA
- Cellular component
- nucleus;nucleoplasm;RNA polymerase II, core complex;RNA polymerase III complex;RNA polymerase I complex;cytosol
- Molecular function
- RNA polymerase I activity;RNA polymerase II activity;RNA polymerase III activity;DNA binding;DNA-directed 5'-3' RNA polymerase activity;protein binding