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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:Q3KNV8AlphaFoldGenCCjaxSfariGnomADPubmed

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 (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)link
4-743576-A-G Inborn genetic diseases Uncertain significance (Sep 22, 2022)link
4-744660-A-G Inborn genetic diseases Uncertain significance (Jun 18, 2021)link
4-761316-G-A Inborn genetic diseases Uncertain significance (Aug 04, 2023)link
4-761356-G-A Benign (Mar 30, 2018)link
4-761398-C-T Benign (Mar 30, 2018)link
4-765023-C-T See cases Uncertain significance (Oct 10, 2018)link

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