POLR2M
protein-codingRNA polymerase II subunit M, the group of RNA polymerase subunits
Gene summary
This gene encodes a subunit of a specific form of RNA polymerase II termed Pol II(G). The encoded protein may act as a negative regulator of transcriptional activation by the Mediator complex. Alternative splicing results in multiple transcript variants. There is a pseudogene for this gene on chromosome 4. Readthrough transcription between this gene and the neighboring upstream gene MYZAP (myocardial zonula adherens protein) is represented with GeneID 145781. [provided by RefSeq, Oct 2013]
- GRINL1A
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~76.1 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 POLR2M variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015532.5. 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 | 2 | 2 | ||||
| missense | 58 | 6 | 2 | 66 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 58 | 8 | 2 | 68 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_056347.1 | 4 | MANE Select | |
| Ensembl | ENSP00000299638.3 | 4 | MANE Select | |
| RefSeq | NP_001018112.1 | 4 | Standard | |
| Ensembl | ENSP00000369930.4 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- RNA biosynthetic process
- intracellular signal transduction
- maintenance of ER location
Molecular Function
- DNA-directed 5'-3' RNA polymerase activity
Cellular Component
- nuclear envelope
- RNA polymerase II, holoenzyme
- neuronal cell body
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000299638
- Coding exons
- 4
- Length
- 190730
- Individuals with no LoFs
- 125669
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 8
- Defined
- 125677
- p
- 0.0000318
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.845 | 240 | 206 | 1.17 | 0.0000112 | 2406 |
| Missense (PolyPhen) | 66 | 62.234 | 1.0605 | 800 | ||
| Synonymous | -0.266 | 81 | 78.0 | 1.04 | 0.00000421 | 713 |
| Loss of Function | 2.30 | 5 | 14.4 | 0.347 | 7.58e-7 | 179 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000046 | 0.000044 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.102
Intolerance Scores
- RVIS EVS
- 0.31
- RVIS percentile EVS
- 72.6
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Low | Low | Low |