CBX4

chromobox 4, the group of Chromobox family

Basic information

Region (hg38): 17:79833156-79839440

Links

ENSG00000141582 ∙ NCBI:8535 ∙ OMIM:603079 ∙ HGNC:1554 ∙ Uniprot:O00257 ∙ 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 CBX4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CBX4 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			41			41
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	41	0	2

Variants in CBX4

This is a list of pathogenic ClinVar variants found in the CBX4 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-79833966-G-A		not specified	Uncertain significance (Aug 17, 2022)
17-79833994-G-A		not specified	Uncertain significance (Dec 03, 2021)
17-79834033-A-G		not specified	Uncertain significance (May 04, 2022)
17-79834049-G-T		not specified	Uncertain significance (Dec 21, 2023)
17-79834077-G-A		not specified	Uncertain significance (Apr 25, 2023)
17-79834118-T-TGCCGCC			Benign (May 21, 2018)
17-79834189-C-T		not specified	Uncertain significance (Jun 28, 2024)
17-79834194-T-G		not specified	Uncertain significance (Dec 25, 2024)
17-79834255-T-A		not specified	Uncertain significance (May 08, 2023)
17-79834258-C-T		not specified	Uncertain significance (Feb 13, 2024)
17-79834263-G-A		not specified	Uncertain significance (Jan 23, 2024)
17-79834285-G-A		not specified	Uncertain significance (Feb 06, 2023)
17-79834299-G-A		not specified	Uncertain significance (Aug 12, 2022)
17-79834303-G-A		not specified	Uncertain significance (Mar 01, 2024)
17-79834332-G-A		not specified	Uncertain significance (Feb 23, 2023)
17-79834396-C-G		not specified	Uncertain significance (Dec 19, 2023)
17-79834417-C-T		not specified	Uncertain significance (Nov 20, 2024)
17-79834442-G-T		not specified	Uncertain significance (May 17, 2023)
17-79834451-G-C		not specified	Uncertain significance (Dec 01, 2022)
17-79834459-G-C		not specified	Uncertain significance (Mar 27, 2023)
17-79834477-G-T		not specified	Uncertain significance (Sep 29, 2023)
17-79834501-A-G		not specified	Uncertain significance (Dec 16, 2023)
17-79834539-A-T		not specified	Uncertain significance (May 12, 2024)
17-79834582-C-A		not specified	Uncertain significance (Mar 18, 2024)
17-79834593-G-C		not specified	Uncertain significance (Feb 23, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CBX4	protein_coding	protein_coding	ENST00000269397	5	6274

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.982	0.0180	125704	0	2	125706	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.22	261	383	0.681	0.0000261	3626
Missense in Polyphen		68	140.89	0.48263		1431
Synonymous	0.228	176	180	0.978	0.0000141	1129
Loss of Function	3.55	1	16.6	0.0601	7.13e-7	222

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000893	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 SUMO-protein ligase which facilitates SUMO1 conjugation by UBE2I (PubMed:12679040). Involved in the sumoylation of HNRNPK, a p53/TP53 transcriptional coactivator, hence indirectly regulates p53/TP53 transcriptional activation resulting in p21/CDKN1A expression. Monosumoylates ZNF131 (PubMed:22825850). {ECO:0000269|PubMed:12679040, ECO:0000269|PubMed:22825850}.
• Pathway: Signal Transduction;Gene expression (Transcription);RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known;the prc2 complex sets long-term gene silencing through modification of histone tails;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;C-MYB transcription factor network;Intracellular signaling by second messengers;Transcriptional regulation by RUNX1;Regulation of retinoblastoma protein (Consensus)

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.0942
• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.73

Haploinsufficiency Scores

• pHI: 0.879
• hipred: Y
• hipred_score: 0.630
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.369

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cbx4
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; immune system phenotype; hematopoietic system 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)

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;chromatin organization;protein sumoylation;negative regulation of apoptotic process;negative regulation of transcription, DNA-templated
• Cellular component: nucleus;nucleoplasm;nuclear body;nuclear speck;PcG protein complex;PRC1 complex
• Molecular function: chromatin binding;transcription corepressor activity;single-stranded RNA binding;protein binding;SUMO transferase activity;enzyme binding;SUMO binding;methylated histone binding;transcription regulatory region DNA binding;phosphoprotein binding