PCGF3
polycomb group ring finger 3, the group of Ring finger proteins|Polycomb group ring fingers
Basic information
Region (hg38): 4:705747-770089
Previous symbols: [ "RNF3" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (3 variants)
- not provided (2 variants)
- See cases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCGF3 gene is commonly pathogenic or not.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 2 | 2 | ||||
missense | 4 | 4 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice variant | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 4 | 0 | 2 |
Variants in PCGF3
This is a list of pathogenic ClinVar variants found in the PCGF3 region.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
4-743533-A-C | Inborn genetic diseases | Uncertain significance (Jul 14, 2021) | ||
4-743576-A-G | Inborn genetic diseases | Uncertain significance (Sep 22, 2022) | ||
4-744660-A-G | Inborn genetic diseases | Uncertain significance (Jun 18, 2021) | ||
4-761316-G-A | Inborn genetic diseases | Uncertain significance (Aug 04, 2023) | ||
4-761356-G-A | Benign (Mar 30, 2018) | |||
4-761398-C-T | Benign (Mar 30, 2018) | |||
4-765023-C-T | See cases | Uncertain significance (Oct 10, 2018) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PCGF3 | protein_coding | protein_coding | ENST00000362003 | 8 | 64892 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.953 | 0.0467 | 124783 | 0 | 2 | 124785 | 0.00000801 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.10 | 78 | 151 | 0.518 | 0.00000923 | 1610 |
Missense in Polyphen | 8 | 52.578 | 0.15216 | 560 | ||
Synonymous | -1.61 | 80 | 63.6 | 1.26 | 0.00000468 | 413 |
Loss of Function | 3.22 | 1 | 14.0 | 0.0713 | 5.93e-7 | 181 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000566 | 0.0000556 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.00000883 | 0.00000883 |
Middle Eastern | 0.0000566 | 0.0000556 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
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. Within the PRC1-like complex, regulates RNF2 ubiquitin ligase activity (PubMed:26151332). Plays a redundant role with PCGF5 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:Q8BTQ0, ECO:0000269|PubMed:26151332}.;
- Pathway
- Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human)
(Consensus)
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- loftool
- 0.334
- rvis_EVS
- -0.3
- rvis_percentile_EVS
- 32.62
Haploinsufficiency Scores
- pHI
- 0.197
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.632
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.398
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pcgf3
- Phenotype
- hematopoietic system phenotype; immune system phenotype;
Gene ontology
- Biological process
- regulation of transcription, DNA-templated;histone H2A-K119 monoubiquitination;inactivation of X chromosome by genetic imprinting
- Cellular component
- X chromosome;nucleus;nucleoplasm;PcG protein complex;PRC1 complex
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity;protein binding;metal ion binding