PCGF5

polycomb group ring finger 5, the group of Polycomb group ring fingers|Ring finger proteins

Basic information

Region (hg38): 10:91163012-91284337

Previous symbols: [ "RNF159" ]

Links

ENSG00000180628 ∙ NCBI:84333 ∙ OMIM:617407 ∙ HGNC:28264 ∙ Uniprot:Q86SE9 ∙ 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 PCGF5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCGF5 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			5			5
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in PCGF5

This is a list of pathogenic ClinVar variants found in the PCGF5 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-91240535-G-A		not specified	Uncertain significance (Nov 27, 2023)
10-91248516-C-T		not specified	Uncertain significance (May 14, 2024)
10-91251340-A-T		not specified	Uncertain significance (Sep 20, 2023)
10-91251421-CAG-C			Uncertain significance (Apr 01, 2017)
10-91261332-A-G		not specified	Uncertain significance (May 30, 2024)
10-91264515-G-A		not specified	Uncertain significance (Apr 13, 2023)
10-91271641-C-T		not specified	Uncertain significance (Mar 30, 2024)
10-91278278-A-G		not specified	Uncertain significance (Jul 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCGF5	protein_coding	protein_coding	ENST00000336126	9	64181

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.980	0.0199	125646	0	3	125649	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.39	58	137	0.424	0.00000702	1696
Missense in Polyphen		8	43.286	0.18482		565
Synonymous	1.17	36	46.1	0.780	0.00000227	440
Loss of Function	3.82	2	20.8	0.0962	0.00000143	214

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000271	0.0000264
Middle Eastern	0.00	0.00
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 (PubMed:26151332). Within the PRC1-like complex, regulates RNF2 ubiquitin ligase activity (PubMed:26151332). Plays a redundant role with PCGF3 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:Q3UK78, ECO:0000269|PubMed:26151332}.
• Pathway: Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human);Gene expression (Transcription);RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known;Generic Transcription Pathway;RNA Polymerase II Transcription;Transcriptional regulation by RUNX1 (Consensus)

Recessive Scores

• pRec: 0.0716

Intolerance Scores

• loftool: 0.306
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.300
• hipred: Y
• hipred_score: 0.746
• ghis: 0.560

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.148

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Low	Medium
Primary Immunodeficiency	Medium	Low	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pcgf5

Gene ontology

• Biological process: histone H2A-K119 monoubiquitination;positive regulation of transcription by RNA polymerase II;inactivation of X chromosome by genetic imprinting
• Cellular component: X chromosome;nucleus;nucleoplasm;nucleolus;centrosome;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