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

ENSG00000185619 ∙ NCBI:10336 ∙ OMIM:617543 ∙ HGNC:10066 ∙ Uniprot:Q3KNV8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed

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)
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: gnomAD

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: 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

	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