PCGF5
protein-codingpolycomb group ring finger 5, the group of Polycomb group ring fingers|Ring finger proteins
Gene summary
Predicted to enable histone H2AK119 ubiquitin ligase activity. Acts upstream of or within positive regulation of transcription by RNA polymerase II. Located in centrosome and nucleoplasm. Part of PcG protein complex. [provided by Alliance of Genome Resources, Jun 2026]
- RNF159
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~121.3 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 PCGF5 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_032373.5. 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 | 1 | 1 | ||||
| missense | 19 | 19 | ||||
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 27 | 0 | 0 | 27 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_115749.2 | 9 | MANE Select | |
| Ensembl | ENSP00000337500.5 | 9 | MANE Select | |
| RefSeq | NP_001243478.1 | 9 | Standard | |
| RefSeq | NP_001244030.1 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human)
- Gene expression (Transcription)
- RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known
- Generic Transcription Pathway
- RNA Polymerase II Transcription
Biological Process
- histone H2A-K119 monoubiquitination
- positive regulation of transcription by RNA polymerase II
- inactivation of X chromosome by genetic imprinting
Molecular Function
- RNA polymerase II regulatory region sequence-specific DNA binding
- DNA-binding transcription factor activity
- protein binding
- metal ion binding
Cellular Component
- X chromosome
- nucleus
- nucleoplasm
- nucleolus
- centrosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000336126
- Coding exons
- 9
- Length
- 64181
- Individuals with no LoFs
- 125646
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 3
- Defined
- 125649
- p
- 0.0000119
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.39 | 58 | 137 | 0.424 | 0.00000702 | 1696 |
| Missense (PolyPhen) | 8 | 43.286 | 0.18482 | 565 | ||
| Synonymous | 1.17 | 36 | 46.1 | 0.780 | 0.00000227 | 440 |
| Loss of Function | 3.82 | 2 | 20.8 | 0.0962 | 0.00000143 | 214 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000027 | 0.000026 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Component of a Polycomb group (PcG) multiprotein PRC1- like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones; it mediates monoubiquitination of histone H2A 'Lys-119', rendering chromatin heritably changed in its expressibility (PubMed:26151332). Within the PRC1-like complex, regulates RNF2 ubiquitin ligase activity (PubMed:26151332). Plays a redundant role with PCGF3 as part of a PRC1-like complex that mediates monoubiquitination of histone H2A 'Lys-119' on the X chromosome and is required for normal silencing of one copy of the X chromosome in XX females (By similarity). {ECO:0000250|UniProtKB:Q3UK78, ECO:0000269|PubMed:26151332}.;
Recessive Scores
- pRec
- 0.0716
Intolerance Scores
- LoFtool
- 0.306
- RVIS EVS
- -0.16
- RVIS percentile EVS
- 41.25
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.148
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Medium |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |