PCGF6

polycomb group ring finger 6, the group of Polycomb group ring fingers|Ring finger proteins

Basic information

Region (hg38): 10:103302796-103351144

Previous symbols: [ "RNF134" ]

Links

ENSG00000156374 ∙ NCBI:84108 ∙ OMIM:607816 ∙ HGNC:21156 ∙ Uniprot:Q9BYE7 ∙ 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 PCGF6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCGF6 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				1		1
missense			21			21
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	21	1	1

Variants in PCGF6

This is a list of pathogenic ClinVar variants found in the PCGF6 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-103314206-T-C		not specified	Uncertain significance (Jun 07, 2023)
10-103314211-C-T		not specified	Uncertain significance (Jun 02, 2024)
10-103326608-C-T		not specified	Uncertain significance (May 13, 2024)
10-103326631-G-A		not specified	Uncertain significance (Jun 22, 2021)
10-103333938-G-A		not specified	Uncertain significance (May 20, 2024)
10-103345028-T-G		not specified	Uncertain significance (Jun 13, 2024)
10-103345062-T-C			Likely benign (May 30, 2018)
10-103345069-C-T		not specified	Uncertain significance (Jan 19, 2022)
10-103345096-G-T		not specified	Uncertain significance (Mar 19, 2024)
10-103345121-G-C		not specified	Uncertain significance (May 06, 2024)
10-103347250-C-G		not specified	Uncertain significance (Aug 11, 2022)
10-103347398-C-T		not specified	Uncertain significance (Mar 20, 2023)
10-103347406-T-C		not specified	Uncertain significance (Apr 12, 2023)
10-103348798-T-C		not specified	Uncertain significance (Jun 24, 2022)
10-103348966-T-G		not specified	Uncertain significance (Dec 21, 2021)
10-103348987-G-A		not specified	Uncertain significance (May 23, 2023)
10-103348987-G-C		not specified	Uncertain significance (Feb 07, 2023)
10-103350808-C-G		not specified	Uncertain significance (Mar 21, 2023)
10-103350841-G-A		not specified	Uncertain significance (Dec 15, 2023)
10-103350846-C-A		not specified	Uncertain significance (Aug 16, 2021)
10-103350889-G-A		not specified	Uncertain significance (Feb 05, 2024)
10-103350892-A-G		not specified	Uncertain significance (Jun 06, 2022)
10-103350930-G-A		not specified	Uncertain significance (Mar 25, 2024)
10-103350948-G-C		not specified	Uncertain significance (Mar 02, 2023)
10-103350963-G-T		not specified	Uncertain significance (Aug 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCGF6	protein_coding	protein_coding	ENST00000369847	10	48339

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000515	0.971	125698	0	13	125711	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.779	141	170	0.832	0.00000832	2236
Missense in Polyphen		13	17.804	0.73017		216
Synonymous	0.136	58	59.3	0.978	0.00000276	676
Loss of Function	1.97	10	19.3	0.517	0.00000105	248

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000304	0.0000304
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000890	0.0000879
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor (PubMed:12167161). May modulate the levels of histone H3K4Me3 by activating KDM5D histone demethylase (PubMed:17320162). 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:12167161). Within the PRC1-like complex, regulates RNF2 ubiquitin ligase activity (PubMed:26151332). {ECO:0000269|PubMed:12167161, ECO:0000269|PubMed:17320162, 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;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.709
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• pHI: 0.542
• hipred: Y
• hipred_score: 0.727
• ghis: 0.651

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.743

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcgf6

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;histone H2A-K119 monoubiquitination;negative regulation of transcription, DNA-templated;inactivation of X chromosome by genetic imprinting;negative regulation of G0 to G1 transition
• Cellular component: nucleus;nucleoplasm;PcG protein complex;PRC1 complex
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;protein binding;metal ion binding