PCGF2

polycomb group ring finger 2, the group of Ring finger proteins|Polycomb group ring fingers

Basic information

Region (hg38): 17:38733897-38749817

Previous symbols: [ "ZNF144", "RNF110" ]

Links

ENSG00000277258 ∙ NCBI:7703 ∙ OMIM:600346 ∙ HGNC:12929 ∙ Uniprot:P35227 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• turnpenny-fry syndrome (Limited), mode of inheritance: AD
• turnpenny-fry syndrome (Strong), mode of inheritance: AD
• turnpenny-fry syndrome (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Turnpenny-Fry syndrome	AD	Cardiovascular	The condition can involve congenital cardiac anomalies, and awareness may allow early management	Cardiovascular; Craniofacial; Musculoskeletal; Neurologic	25533962; 30343942

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PCGF2 gene.

• not provided (150 variants)
• Inborn genetic diseases (18 variants)
• Turnpenny-fry syndrome (6 variants)
• not specified (3 variants)
• Intellectual disability;Abnormality of the outer ear (1 variants)
• Global developmental delay (1 variants)
• PCGF2-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCGF2 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				31	6	37
missense		3	60	5	10	78
nonsense						0
start loss						0
frameshift			2			2
inframe indel			3			3
splice donor/acceptor (+/-2bp)						0
splice region			1	6	3	10
non coding			1	19	6	26
Total	0	3	66	55	22

Variants in PCGF2

This is a list of pathogenic ClinVar variants found in the PCGF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-38734160-C-T			Benign (Oct 01, 2022)
17-38735214-T-A		PCGF2-related disorder	Likely benign (Dec 23, 2019)
17-38735229-T-G		not specified	Uncertain significance (May 04, 2022)
17-38735231-AG-A		Wolfram syndrome 2 • Turnpenny-fry syndrome	Uncertain significance (Mar 25, 2024)
17-38735233-G-C		Inborn genetic diseases	Uncertain significance (Jul 07, 2023)
17-38735233-G-T		Inborn genetic diseases	Conflicting classifications of pathogenicity (Nov 17, 2022)
17-38735234-G-C			Uncertain significance (Oct 13, 2023)
17-38735240-C-T		Inborn genetic diseases	Likely benign (Aug 05, 2023)
17-38735241-G-A			Likely benign (Nov 26, 2023)
17-38735242-G-A			Uncertain significance (Oct 25, 2022)
17-38735247-G-A			Likely benign (Jan 22, 2024)
17-38735250-G-C			Uncertain significance (Oct 30, 2023)
17-38735253-G-A			Likely benign (Oct 06, 2023)
17-38735257-G-T		not specified	Uncertain significance (Feb 26, 2024)
17-38735267-G-A		Inborn genetic diseases	Uncertain significance (Apr 25, 2022)
17-38735267-G-C			Uncertain significance (Nov 27, 2023)
17-38735267-GC-G			Uncertain significance (Jan 24, 2023)
17-38735287-G-A			Uncertain significance (Jan 27, 2022)
17-38735309-T-A			Uncertain significance (Jun 05, 2022)
17-38735312-C-T		Inborn genetic diseases	Uncertain significance (Jul 12, 2022)
17-38735313-C-A			Likely benign (Oct 03, 2023)
17-38735314-C-T			Uncertain significance (Aug 16, 2022)
17-38735315-C-T			Uncertain significance (Jan 12, 2024)
17-38735316-G-A			Likely benign (Feb 11, 2022)
17-38735320-G-A		PCGF2-related disorder	Benign (Jan 18, 2024)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor. Binds specifically to the DNA sequence 5'-GACTNGACT-3'. Has tumor suppressor activity. May play a role in control of cell proliferation and/or neural cell development. Regulates proliferation of early T progenitor cells by maintaining expression of HES1. Also plays a role in antero- posterior specification of the axial skeleton and negative regulation of the self-renewal activity of hematopoietic stem cells (By similarity). 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). {ECO:0000250|UniProtKB:P23798, ECO:0000269|PubMed:26151332}.
• Pathway: Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human);Gene expression (Transcription);Transcriptional Regulation by E2F6;Generic Transcription Pathway;SUMOylation of DNA damage response and repair proteins;SUMOylation of chromatin organization proteins;SUMOylation of RNA binding proteins;Post-translational protein modification;SUMO E3 ligases SUMOylate target proteins;Metabolism of proteins;RNA Polymerase II Transcription;SUMOylation (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.332
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.15

Haploinsufficiency Scores

• pHI: 0.287
• hipred: Y
• hipred_score: 0.580

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.685

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcgf2
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; embryo phenotype; immune system phenotype; skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; digestive/alimentary phenotype; vision/eye phenotype; craniofacial phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;in utero embryonic development;chromatin silencing;anterior/posterior pattern specification;histone acetylation;histone H2A-K119 monoubiquitination;embryonic skeletal system morphogenesis;cellular response to hydrogen peroxide;negative regulation of G0 to G1 transition;negative regulation of apoptotic signaling pathway
• Cellular component: nuclear chromatin;sex chromatin;nucleus;nucleoplasm;nuclear body;PcG protein complex;PRC1 complex
• Molecular function: DNA binding;DNA-binding transcription factor activity;protein binding;metal ion binding;promoter-specific chromatin binding