PCGF1

polycomb group ring finger 1, the group of Ring finger proteins|Polycomb group ring fingers

Basic information

Region (hg38): 2:74505043-74507695

Links

ENSG00000115289NCBI:84759OMIM:610231HGNC:17615Uniprot:Q9BSM1AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PCGF1 gene.

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
clinvar
1
clinvar
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)2588164
2-74505383-G-A not specified Uncertain significance (May 05, 2023)2544615
2-74505394-A-G not specified Uncertain significance (Feb 14, 2025)3886871
2-74505404-C-T not specified Uncertain significance (Jul 31, 2024)3415683
2-74505559-G-A not specified Uncertain significance (Aug 16, 2022)2374315
2-74505562-T-C not specified Uncertain significance (Jun 02, 2023)2555860
2-74505567-C-T not specified Uncertain significance (Apr 04, 2024)3305105
2-74505602-G-A not specified Uncertain significance (Jul 05, 2023)2592940
2-74505745-C-T not specified Likely benign (Nov 27, 2024)3415682
2-74505958-C-T not specified Uncertain significance (Apr 04, 2024)3305104
2-74506007-T-C not specified Uncertain significance (Apr 13, 2022)2283867
2-74506194-C-A not specified Uncertain significance (Nov 25, 2024)3415684
2-74506211-A-C not specified Uncertain significance (Jan 23, 2025)3886870
2-74506733-G-A not specified Likely benign (Jan 21, 2025)3886869
2-74506848-C-T not specified Uncertain significance (Apr 23, 2024)3305106
2-74506877-C-A not specified Uncertain significance (Feb 27, 2024)3210183
2-74507142-C-A not specified Uncertain significance (Sep 06, 2022)2310187

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PCGF1protein_codingprotein_codingENST00000233630 93538
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9970.0028700000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.11781510.5170.000009011695
Missense in Polyphen1347.5520.27338525
Synonymous0.3335154.10.9420.00000282471
Loss of Function3.84017.20.009.11e-7187

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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