CBX7

chromobox 7, the group of Chromobox family

Basic information

Region (hg38): 22:39120167-39152680

Links

ENSG00000100307 ∙ NCBI:23492 ∙ OMIM:608457 ∙ HGNC:1557 ∙ Uniprot:O95931 ∙ 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 CBX7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CBX7 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						0
missense			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	0

Variants in CBX7

This is a list of pathogenic ClinVar variants found in the CBX7 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-39133944-G-A		not specified	Uncertain significance (May 09, 2023)
22-39133959-T-C		not specified	Likely benign (Nov 10, 2022)
22-39134006-G-A		not specified	Uncertain significance (Mar 06, 2023)
22-39134031-C-T		not specified	Uncertain significance (Mar 02, 2023)
22-39134036-A-G		not specified	Uncertain significance (Feb 15, 2023)
22-39134038-G-T		not specified	Uncertain significance (May 05, 2023)
22-39134042-G-A		not specified	Uncertain significance (May 07, 2024)
22-39134404-C-T		not specified	Uncertain significance (Apr 15, 2024)
22-39134416-G-C		not specified	Uncertain significance (Oct 06, 2021)
22-39134437-C-T		not specified	Uncertain significance (Mar 30, 2024)
22-39134454-A-G		not specified	Uncertain significance (Sep 03, 2024)
22-39134455-C-T		not specified	Uncertain significance (Jan 23, 2024)
22-39134524-G-A		not specified	Uncertain significance (Aug 09, 2021)
22-39134644-T-C		not specified	Uncertain significance (Mar 01, 2024)
22-39134745-T-C		not specified	Uncertain significance (Oct 09, 2024)
22-39138655-G-C		Malignant tumor of prostate	Uncertain significance (-)
22-39138674-T-C		not specified	Uncertain significance (Nov 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CBX7	protein_coding	protein_coding	ENST00000216133	6	32508

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.685	0.314	125731	0	4	125735	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.30	108	153	0.704	0.0000101	1575
Missense in Polyphen		24	43.668	0.5496		421
Synonymous	-0.382	76	71.9	1.06	0.00000524	516
Loss of Function	2.75	2	12.5	0.161	6.77e-7	148

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000967	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000990	0.0000980
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. 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. Promotes histone H3 trimethylation at 'Lys-9' (H3K9me3). Binds to trimethylated lysine residues in histones, and possibly also other proteins. Regulator of cellular lifespan by maintaining the repression of CDKN2A, but not by inducing telomerase activity. {ECO:0000269|PubMed:19636380, ECO:0000269|PubMed:21047797, ECO:0000269|PubMed:21060834, ECO:0000269|PubMed:21282530}.

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.181
• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.686
• hipred: Y
• hipred_score: 0.594
• ghis: 0.607

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cbx7
• Phenotype: cellular phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland phenotype; neoplasm

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;chromatin organization
• Cellular component: nuclear chromatin;nucleus;nucleoplasm;cytosol;PcG protein complex;PRC1 complex
• Molecular function: protein binding