CBX8

chromobox 8, the group of Chromobox family

Basic information

Region (hg38): 17:79792131-79801683

Links

ENSG00000141570 ∙ NCBI:57332 ∙ OMIM:617354 ∙ HGNC:15962 ∙ Uniprot:Q9HC52 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CBX8 gene.

• Inborn genetic diseases (9 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CBX8 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	0

Variants in CBX8

This is a list of pathogenic ClinVar variants found in the CBX8 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-79794692-C-A		not specified	Uncertain significance (Jun 12, 2023)
17-79794823-C-T		not specified	Uncertain significance (Nov 02, 2021)
17-79794979-C-T		not specified	Uncertain significance (Feb 28, 2024)
17-79795054-C-T		not specified	Uncertain significance (Sep 14, 2022)
17-79795195-G-A		not specified	Uncertain significance (Apr 08, 2022)
17-79795291-G-C		not specified	Uncertain significance (Aug 15, 2023)
17-79795333-G-A		not specified	Uncertain significance (Jul 12, 2023)
17-79795356-C-T		not specified	Uncertain significance (Aug 02, 2021)
17-79795357-G-A		not specified	Uncertain significance (Mar 24, 2023)
17-79795362-C-G		not specified	Uncertain significance (May 25, 2022)
17-79795376-G-A			Likely benign (Oct 01, 2022)
17-79795500-A-G		not specified	Uncertain significance (Oct 20, 2023)
17-79795557-G-A		not specified	Uncertain significance (Jan 19, 2024)
17-79796278-C-T		not specified	Uncertain significance (May 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CBX8	protein_coding	protein_coding	ENST00000269385	5	9552

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.993	0.00729	125737	0	6	125743	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.938	198	239	0.829	0.0000146	2444
Missense in Polyphen		32	49.729	0.64349		543
Synonymous	-1.78	124	101	1.22	0.00000619	820
Loss of Function	3.84	1	19.1	0.0524	0.00000139	180

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000991	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000295	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000188	0.000163

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. {ECO:0000269|PubMed:21282530}.
• Pathway: Signal Transduction;Gene expression (Transcription);RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known;Generic Transcription Pathway;Oxidative Stress Induced Senescence;SUMOylation of DNA damage response and repair proteins;Cellular Senescence;SUMOylation of chromatin organization proteins;Cellular responses to stress;SUMOylation of RNA binding proteins;Post-translational protein modification;SUMO E3 ligases SUMOylate target proteins;Metabolism of proteins;RNA Polymerase II Transcription;SUMOylation;Cellular responses to external stimuli;Regulation of PTEN gene transcription;PTEN Regulation;PIP3 activates AKT signaling;Intracellular signaling by second messengers;Transcriptional regulation by RUNX1 (Consensus)

Recessive Scores

• pRec: 0.175

Intolerance Scores

• loftool: 0.165
• rvis_EVS: 0
• rvis_percentile_EVS: 53.73

Haploinsufficiency Scores

• pHI: 0.926
• hipred: Y
• hipred_score: 0.749
• ghis: 0.528

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.975

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cbx8
• Phenotype: cellular phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;positive regulation of cell population proliferation;histone ubiquitination;positive regulation of collagen biosynthetic process;positive regulation of DNA repair;regulation of catalytic activity;cellular response to hydrogen peroxide
• Cellular component: nuclear chromatin;heterochromatin;nucleus;nucleoplasm;PcG protein complex;PRC1 complex
• Molecular function: single-stranded RNA binding;protein binding;methylated histone binding;ubiquitin-protein transferase activator activity