POP4
protein-codingPOP4 homolog, ribonuclease P/MRP subunit
Gene summary
This gene encodes one of the protein subunits of the small nucleolar ribonucleoprotein complexes: the endoribonuclease for mitochondrial RNA processing complex and the ribonuclease P complex. The encoded protein is localized to the nucleus and associates directly with the RNA component of these complexes. This protein is involved in processing of precursor RNAs. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2009]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~11.0 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 POP4 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006627.3. 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 | 43 | 3 | 46 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 48 | 3 | 0 | 51 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006618.1 | 7 | MANE Select | |
| Ensembl | ENSP00000465213.1 | 7 | MANE Select | |
| Ensembl | ENSP00000221770.3 | 3 | Standard | |
| Ensembl | ENSP00000468215.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Ribosome biogenesis in eukaryotes - Homo sapiens (human)
- RNA transport - Homo sapiens (human)
- tRNA processing
- Metabolism of RNA
- tRNA processing in the nucleus
Biological Process
- tRNA 5'-leader removal
- rRNA processing
- tRNA processing
- RNA phosphodiester bond hydrolysis, endonucleolytic
Molecular Function
- ribonuclease MRP activity
- RNA binding
- ribonuclease P activity
- protein binding
- ribonuclease P RNA binding
Cellular Component
- ribonuclease MRP complex
- nucleoplasm
- nucleolus
- ribonuclease P complex
- multimeric ribonuclease P complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000585603
- Coding exons
- 7
- Length
- 13221
- Individuals with no LoFs
- 125711
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 37
- Defined
- 125748
- p
- 0.000147
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.132 | 129 | 133 | 0.968 | 0.00000837 | 1424 |
| Missense (PolyPhen) | 26 | 36.785 | 0.70681 | 450 | ||
| Synonymous | -0.773 | 61 | 53.8 | 1.13 | 0.00000341 | 410 |
| Loss of Function | 1.03 | 9 | 13.0 | 0.693 | 6.50e-7 | 149 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00014 | 0.00014 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00016 | 0.00016 | rare |
| Finnish | 0.000092 | 0.000092 | rare |
| European (Non-Finnish) | 0.00019 | 0.00019 | rare |
| South Asian | 0.00016 | 0.00016 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Part of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. May function with RPP38 to coordinate the nucleolar targeting and/or assembly of RNase P.;
Recessive Scores
- pRec
- 0.125
Intolerance Scores
- LoFtool
- 0.405
- RVIS EVS
- -0.03
- RVIS percentile EVS
- 51.66
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.889
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |