PCGF1
polycomb group ring finger 1, the group of Ring finger proteins|Polycomb group ring fingers
Basic information
Region (hg38): 2:74505043-74507695
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCGF1 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 13 | 14 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 13 | 1 | 0 |
Variants in PCGF1
This is a list of pathogenic ClinVar variants found in the PCGF1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 2-74505352-C-T | not specified | Uncertain significance (Jul 05, 2023) | ||
| 2-74505383-G-A | not specified | Uncertain significance (May 05, 2023) | ||
| 2-74505394-A-G | not specified | Uncertain significance (Feb 14, 2025) | ||
| 2-74505404-C-T | not specified | Uncertain significance (Jul 31, 2024) | ||
| 2-74505559-G-A | not specified | Uncertain significance (Aug 16, 2022) | ||
| 2-74505562-T-C | not specified | Uncertain significance (Jun 02, 2023) | ||
| 2-74505567-C-T | not specified | Uncertain significance (Apr 04, 2024) | ||
| 2-74505602-G-A | not specified | Uncertain significance (Jul 05, 2023) | ||
| 2-74505745-C-T | not specified | Likely benign (Nov 27, 2024) | ||
| 2-74505958-C-T | not specified | Uncertain significance (Apr 04, 2024) | ||
| 2-74506007-T-C | not specified | Uncertain significance (Apr 13, 2022) | ||
| 2-74506194-C-A | not specified | Uncertain significance (Nov 25, 2024) | ||
| 2-74506211-A-C | not specified | Uncertain significance (Jan 23, 2025) | ||
| 2-74506733-G-A | not specified | Likely benign (Jan 21, 2025) | ||
| 2-74506848-C-T | not specified | Uncertain significance (Apr 23, 2024) | ||
| 2-74506877-C-A | not specified | Uncertain significance (Feb 27, 2024) | ||
| 2-74507142-C-A | not specified | Uncertain significance (Sep 06, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PCGF1 | protein_coding | protein_coding | ENST00000233630 | 9 | 3538 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.997 | 0.00287 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.11 | 78 | 151 | 0.517 | 0.00000901 | 1695 |
| Missense in Polyphen | 13 | 47.552 | 0.27338 | 525 | ||
| Synonymous | 0.333 | 51 | 54.1 | 0.942 | 0.00000282 | 471 |
| Loss of Function | 3.84 | 0 | 17.2 | 0.00 | 9.11e-7 | 187 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the Polycomb group (PcG) multiprotein BCOR complex, a complex required to maintain the transcriptionally repressive state of some genes, such as BCL6 and the cyclin- dependent kinase inhibitor, CDKN1A. Transcriptional repressor that may be targeted to the DNA by BCL6; this transcription repressor activity may be related to PKC signaling pathway. Represses CDKN1A expression by binding to its promoter, and this repression is dependent on the retinoic acid response element (RARE element). Promotes cell cycle progression and enhances cell proliferation as well. May have a positive role in tumor cell growth by down- regulating CDKN1A. 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). Regulates the expression of DPPA4 and NANOG in the NT2 embryonic carcinoma cells (PubMed:26687479). {ECO:0000269|PubMed:15620699, ECO:0000269|PubMed:16943429, ECO:0000269|PubMed:17088287, ECO:0000269|PubMed:26151332, ECO:0000269|PubMed:26687479}.;
- Pathway
- Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human)
(Consensus)
Recessive Scores
- pRec
- 0.106
Intolerance Scores
- loftool
- 0.151
- rvis_EVS
- 0.37
- rvis_percentile_EVS
- 74.95
Haploinsufficiency Scores
- pHI
- 0.388
- hipred
- Y
- hipred_score
- 0.775
- ghis
- 0.481
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.920
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pcgf1
- Phenotype
- mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Zebrafish Information Network
- Gene name
- pcgf1
- Affected structure
- head muscle
- Phenotype tag
- abnormal
- Phenotype quality
- delayed
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;chromatin silencing;regulation of transcription, DNA-templated;histone H2A monoubiquitination;histone H2A-K119 monoubiquitination
- Cellular component
- nucleus;nucleoplasm;PcG protein complex;PRC1 complex
- Molecular function
- protein binding;protein C-terminus binding;metal ion binding;promoter-specific chromatin binding