POLR2L
protein-codingRNA polymerase II, I and III subunit L, the group of RNA polymerase subunits
Gene summary
This gene encodes a subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. The product of this gene contains four conserved cysteines characteristic of an atypical zinc-binding domain. Like its counterpart in yeast, this subunit may be shared by the other two DNA-directed RNA polymerases. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~5.2 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 POLR2L variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_021128.5. 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 | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 11 | 0 | 0 | 11 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_066951.1 | 2 | MANE Select | |
| Ensembl | ENSP00000324124.4 | 2 | MANE Select | |
| Ensembl | ENSP00000432807.1 | 2 | Standard | |
| Ensembl | ENSP00000564752.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- 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)
Biological Process
- mRNA splicing, via spliceosome
- transcription-coupled nucleotide-excision repair
- regulation of transcription by RNA polymerase I
- transcription initiation from RNA polymerase I promoter
- termination of RNA polymerase I transcription
Molecular Function
- RNA polymerase I activity
- RNA polymerase II activity
- RNA polymerase III activity
- DNA binding
- DNA-directed 5'-3' RNA polymerase activity
Cellular Component
- nucleus
- nucleoplasm
- RNA polymerase II, core complex
- RNA polymerase III complex
- RNA polymerase I complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000322028
- Coding exons
- 2
- Length
- 5190
- Individuals with no LoFs
- 124999
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 6
- Defined
- 125005
- p
- 0.0000240
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.0828 | 39 | 40.5 | 0.963 | 0.00000252 | 411 |
| Missense (PolyPhen) | 4 | 4.8504 | 0.82467 | 72 | ||
| Synonymous | -2.33 | 30 | 17.6 | 1.71 | 9.38e-7 | 135 |
| Loss of Function | -1.10 | 4 | 2.23 | 1.79 | 9.43e-8 | 28 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000073 | 0.000062 | rare |
| Latino/Admixed American | 0.000031 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000047 | 0.000046 | rare |
| European (Non-Finnish) | 0.000010 | 0.0000089 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
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 a 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, POLR2L/RBP10 is part of the core element with the central large cleft (By similarity). {ECO:0000250, ECO:0000269|PubMed:9852112}.;
Recessive Scores
- pRec
- 0.363
Intolerance Scores
- LoFtool
- 0.164
- RVIS EVS
- -0.05
- RVIS percentile EVS
- 49.39
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- N
- Indispensability score
- 0.463
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Low | Low | Low |