CBX7

protein-coding

chromobox 7, the group of Chromobox family

Gene summary

This gene encodes a protein that contains the CHROMO (CHRomatin Organization MOdifier) domain. The encoded protein is a component of the Polycomb repressive complex 1 (PRC1), and is thought to control the lifespan of several normal human cells. [provided by RefSeq, Oct 2016]

MANE transcript

NM_175709.5

Inheritance

—

ClinVar variants

U:35B:3

Top phenotype

Prostate cancer

gnomAD constraint

pLI —, LoF o/e 0.16

Max pathogenic AF

—

Genomic locus

chr22:39,120,167-39,152,680

External References & Databases

Ensembl (ENSG00000100307)

Transcript & Mutation Effects

hg38 • Region Span ~32.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CBX7 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 31

not providedTotal: 1

Prostate cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_175709.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar		3
missense			31 clinvar	2 clinvar		33
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	35	3	0	38

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 44 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_175709.5	RefSeq	NP_783640.1	6	MANE Select
ENST00000216133.10	Ensembl	ENSP00000216133.5	6	MANE Select
NM_001346743.2	RefSeq	NP_001333672.1	6	Standard
NM_001346744.2	RefSeq	NP_001333673.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of transcription by RNA polymerase II
chromatin organization

Molecular Function

protein binding

Cellular Component

nuclear chromatin
nucleus
nucleoplasm
cytosol
PcG protein complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000216133
Coding exons: 6
Length: 32508
Individuals with no LoFs: 125731
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125735
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.30	108	153	0.704	0.0000101	1575
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000097	0.0000088	rare
South Asian	0.000099	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.801

Gene Damage Prediction

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