POLR1E
protein-codingRNA polymerase I subunit E, the group of RNA polymerase subunits
Gene summary
Predicted to enable DNA binding activity and RNA polymerase I general transcription initiation factor binding activity. Involved in nucleolar large rRNA transcription by RNA polymerase I; transcription elongation by RNA polymerase I; and transcription initiation at RNA polymerase I promoter. Located in fibrillar center and nucleoplasm. Part of RNA polymerase I complex. [provided by Alliance of Genome Resources, Jun 2026]
- PRAF1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~17.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to POLR1E variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_022490.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 53 | 1 | 54 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 57 | 1 | 0 | 58 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_071935.1 | 12 | MANE Select | |
| Ensembl | ENSP00000367029.4 | 12 | MANE Select | |
| RefSeq | NP_001269695.1 | 10 | Standard | |
| Ensembl | ENSP00000367023.3 | 11 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Pyrimidine metabolism - Homo sapiens (human)
- RNA polymerase - Homo sapiens (human)
- Purine metabolism - Homo sapiens (human)
- Pyrimidine metabolism
- Eukaryotic Transcription Initiation
Biological Process
- RNA polymerase I preinitiation complex assembly
- transcription initiation from RNA polymerase I promoter
- termination of RNA polymerase I transcription
- positive regulation of gene expression, epigenetic
Molecular Function
- RNA polymerase I activity
- RNA polymerase I general transcription initiation factor binding
- DNA binding
Cellular Component
- fibrillar center
- nucleus
- nucleoplasm
- nucleolus
- RNA polymerase I complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000377798
- Coding exons
- 12
- Length
- 17763
- Individuals with no LoFs
- 125687
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 61
- Defined
- 125748
- p
- 0.000243
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.741 | 204 | 236 | 0.864 | 0.0000127 | 2747 |
| Missense (PolyPhen) | 33 | 50.305 | 0.656 | 593 | ||
| Synonymous | 1.55 | 72 | 90.8 | 0.793 | 0.00000513 | 788 |
| Loss of Function | 1.87 | 14 | 23.9 | 0.587 | 0.00000142 | 270 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00031 | 0.00031 | rare |
| Latino/Admixed American | 0.00026 | 0.00026 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.00032 | 0.00032 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. Appears to be involved in the formation of the initiation complex at the promoter by mediating the interaction between Pol I and UBTF/UBF (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.108
Intolerance Scores
- LoFtool
- 0.862
- RVIS EVS
- 0.42
- RVIS percentile EVS
- 77.16
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.980
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |