CBX6

chromobox 6, the group of Chromobox family

Basic information

Region (hg38): 22:38861422-38872249

Links

ENSG00000183741 ∙ NCBI:23466 ∙ OMIM:617438 ∙ HGNC:1556 ∙ Uniprot:O95503 ∙ 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 CBX6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CBX6 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			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	1	0

Variants in CBX6

This is a list of pathogenic ClinVar variants found in the CBX6 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-38866235-C-A		not specified	Uncertain significance (Nov 23, 2024)
22-38866324-C-G		not specified	Uncertain significance (Mar 21, 2023)
22-38866348-T-C		not specified	Uncertain significance (Feb 13, 2024)
22-38866364-T-A		not specified	Uncertain significance (Nov 15, 2024)
22-38866367-C-T		not specified	Uncertain significance (Oct 10, 2023)
22-38866391-G-A		not specified	Uncertain significance (Jan 22, 2025)
22-38866415-C-G		not specified	Uncertain significance (Feb 09, 2025)
22-38866420-G-T		not specified	Uncertain significance (Dec 12, 2023)
22-38866537-G-A		not specified	Uncertain significance (Nov 19, 2022)
22-38866540-G-C		not specified	Uncertain significance (May 23, 2023)
22-38866545-G-C		not specified	Uncertain significance (Mar 06, 2023)
22-38866574-G-C		not specified	Uncertain significance (May 25, 2022)
22-38866581-G-T		not specified	Uncertain significance (Apr 20, 2023)
22-38866595-A-G		not specified	Uncertain significance (Mar 13, 2023)
22-38866601-G-A		not specified	Uncertain significance (Oct 30, 2023)
22-38866645-T-C		not specified	Uncertain significance (Feb 19, 2025)
22-38866714-G-T		not specified	Uncertain significance (Jul 14, 2021)
22-38866767-C-T		not specified	Uncertain significance (Feb 23, 2023)
22-38866768-A-C		not specified	Uncertain significance (May 08, 2024)
22-38866850-G-A		not specified	Uncertain significance (Nov 22, 2021)
22-38866936-C-T		not specified	Uncertain significance (Jul 12, 2023)
22-38867027-C-A		not specified	Uncertain significance (Feb 28, 2024)
22-38867029-T-A		not specified	Uncertain significance (Oct 26, 2022)
22-38867031-C-A			Likely benign (Jan 01, 2025)
22-38867063-T-G		not specified	Uncertain significance (Feb 07, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CBX6	protein_coding	protein_coding	ENST00000407418	5	10865

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.976	0.0243	120482	0	2	120484	0.00000830

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.31	172	281	0.612	0.0000198	2557
Missense in Polyphen		28	61.336	0.4565		516
Synonymous	0.443	128	135	0.951	0.0000106	908
Loss of Function	3.13	0	11.4	0.00	4.89e-7	146

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000764	0.0000672
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000967	0.00000930
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 (PubMed:21282530). 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. Possibly contributes to the target selectivity of the PRC1 complex by binding specific regions of chromatin (PubMed:18927235). Recruitment to chromatin might occur in an H3K27me3-independent fashion (By similarity). May have a PRC1-independent function in embryonic stem cells (By similarity). {ECO:0000250|UniProtKB:Q9DBY5, ECO:0000269|PubMed:18927235, 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;Cellular Senescence;Cellular responses to stress;RNA Polymerase II Transcription;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: 0.0906

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.664
• ghis: 0.408

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.591

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cbx6
• Phenotype: muscle phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland 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; immune system phenotype; skeleton phenotype; embryo phenotype; respiratory system phenotype; liver/biliary 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); normal phenotype

Zebrafish Information Network

• Gene name: cbx6b
• Affected structure: definitive hemopoiesis
• Phenotype tag: abnormal
• Phenotype quality: decreased occurrence

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;chromatin organization;neuron projection development
• Cellular component: heterochromatin;nucleus;nucleoplasm;plasma membrane;cytoplasmic side of plasma membrane;filopodium;dendrite;growth cone;PcG protein complex;neuronal cell body
• Molecular function: single-stranded RNA binding;protein binding