CENPB

centromere protein B, the group of DNA transposon derived genes|Helix-turn-helix CENPB type domain containing

Basic information

Region (hg38): 20:3783851-3786740

Links

ENSG00000125817 ∙ NCBI:1059 ∙ OMIM:117140 ∙ HGNC:1852 ∙ Uniprot:P07199 ∙ 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 CENPB gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CENPB 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			31			31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	1	0

Variants in CENPB

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

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

Position	Type	Phenotype	Significance	ClinVar
20-3784720-C-G		not specified	Uncertain significance (Jul 17, 2024)
20-3784722-T-C		not specified	Uncertain significance (Apr 20, 2023)
20-3784878-C-T		not specified	Uncertain significance (Oct 17, 2023)
20-3785005-C-A		not specified	Uncertain significance (Oct 26, 2021)
20-3785008-G-C			Likely benign (Nov 01, 2022)
20-3785117-C-T		not specified	Uncertain significance (Dec 22, 2023)
20-3785129-C-A		not specified	Uncertain significance (Mar 06, 2023)
20-3785143-C-G		not specified	Uncertain significance (Oct 05, 2023)
20-3785168-C-T		not specified	Uncertain significance (Jun 05, 2023)
20-3785174-C-A		not specified	Uncertain significance (Jan 03, 2025)
20-3785209-C-G		not specified	Uncertain significance (Nov 03, 2022)
20-3785219-C-T		not specified	Uncertain significance (Feb 14, 2023)
20-3785228-T-A		not specified	Uncertain significance (Oct 04, 2024)
20-3785342-G-A		not specified	Uncertain significance (Jan 10, 2023)
20-3785472-G-C		not specified	Uncertain significance (Oct 13, 2023)
20-3785490-G-T		not specified	Uncertain significance (Jan 25, 2023)
20-3785520-C-A		not specified	Uncertain significance (Aug 04, 2024)
20-3785525-C-G		not specified	Uncertain significance (Jan 08, 2025)
20-3785537-A-G		not specified	Uncertain significance (Mar 29, 2024)
20-3785538-A-C		not specified	Uncertain significance (Mar 29, 2024)
20-3785592-G-C		not specified	Uncertain significance (Feb 06, 2023)
20-3785595-C-T		not specified	Uncertain significance (May 23, 2023)
20-3785640-C-A		not specified	Uncertain significance (Oct 12, 2021)
20-3785656-C-A		not specified	Uncertain significance (Jan 25, 2023)
20-3785693-T-C		not specified	Uncertain significance (Oct 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CENPB	protein_coding	protein_coding	ENST00000379751	1	2840

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00366	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.73	212	357	0.593	0.0000206	3811
Missense in Polyphen		17	38.045	0.44684		434
Synonymous	-0.0715	170	169	1.01	0.0000110	1232
Loss of Function	3.77	0	16.5	0.00	7.41e-7	202

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Interacts with centromeric heterochromatin in chromosomes and binds to a specific 17 bp subset of alphoid satellite DNA, called the CENP-B box (PubMed:11726497). May organize arrays of centromere satellite DNA into a higher-order structure which then directs centromere formation and kinetochore assembly in mammalian chromosomes (Probable). {ECO:0000269|PubMed:11726497, ECO:0000305}.
• Pathway: FOXM1 transcription factor network (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.102
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.69

Haploinsufficiency Scores

• pHI: 0.619
• hipred: Y
• hipred_score: 0.681
• ghis: 0.556

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.994

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cenpb
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; reproductive 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); normal phenotype

Gene ontology

• Cellular component: chromosome, centromeric region;condensed nuclear chromosome, centromeric region;chromosome;nuclear body;nuclear pericentric heterochromatin
• Molecular function: chromatin binding;satellite DNA binding;centromeric DNA binding;sequence-specific DNA binding