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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

ENSG00000185619NCBI:10336OMIM:617543HGNC:10066Uniprot:Q3KNV8AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PCGF3 gene.

  • Inborn genetic diseases (4 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.

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
2
clinvar
2
missense
5
clinvar
5
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 5 0 2

Variants in PCGF3

This is a list of pathogenic ClinVar variants found in the PCGF3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
4-733732-C-T not specified Uncertain significance (Feb 28, 2024)3210189
4-743533-A-C not specified Uncertain significance (Jul 14, 2021)2232970
4-743576-A-G not specified Uncertain significance (Sep 22, 2022)2313060
4-744660-A-G not specified Uncertain significance (Jun 18, 2021)2233484
4-744687-A-G not specified Uncertain significance (Mar 01, 2024)3210188
4-761316-G-A not specified Uncertain significance (Aug 04, 2023)2615900
4-761356-G-A Benign (Mar 30, 2018)785081
4-761398-C-T Benign (Mar 30, 2018)769626
4-765023-C-T See cases Uncertain significance (Oct 10, 2018)930979
4-766036-C-T not specified Uncertain significance (Jan 23, 2024)3210190

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PCGF3protein_codingprotein_codingENST00000362003 864892
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9530.0467124783021247850.00000801
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.10781510.5180.000009231610
Missense in Polyphen852.5780.15216560
Synonymous-1.618063.61.260.00000468413
Loss of Function3.22114.00.07135.93e-7181

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.00005660.0000556
Finnish0.000.00
European (Non-Finnish)0.000008830.00000883
Middle Eastern0.00005660.0000556
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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