PCGF3

polycomb group ring finger 3, the group of Ring finger proteins|Polycomb group ring fingers

Basic information

Region (hg38): 4:705748-770089

Previous symbols: [ "RNF3" ]

Links

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

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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	2
missense			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	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
4-733708-G-A		not specified	Uncertain significance (Jan 16, 2025)
4-733716-C-A		not specified	Uncertain significance (Oct 01, 2024)
4-733732-C-T		not specified	Uncertain significance (Feb 28, 2024)
4-733733-G-A		not specified	Uncertain significance (Mar 18, 2024)
4-733786-A-G		not specified	Uncertain significance (Jul 26, 2024)
4-743525-C-T		not specified	Uncertain significance (Apr 23, 2024)
4-743533-A-C		not specified	Uncertain significance (Jul 14, 2021)
4-743576-A-G		not specified	Uncertain significance (Sep 22, 2022)
4-744617-G-A		not specified	Uncertain significance (Dec 02, 2024)
4-744617-G-C		not specified	Uncertain significance (May 21, 2024)
4-744660-A-G		not specified	Uncertain significance (Jun 18, 2021)
4-744687-A-G		not specified	Uncertain significance (Mar 01, 2024)
4-761290-CCTGGAG-C			Uncertain significance (Mar 06, 2024)
4-761316-G-A		not specified	Uncertain significance (Aug 04, 2023)
4-761339-C-T		not specified	Uncertain significance (Sep 10, 2024)
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)
4-766036-C-T		not specified	Uncertain significance (Jan 23, 2024)

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