CENPBD1P

CENPB DNA-binding domain containing 1, pseudogene

Basic information

Region (hg38): 16:89969983-89971922

Previous symbols: [ "CENPBD1" ]

Links

ENSG00000177946 ∙ NCBI:92806 ∙ ∙ HGNC:28272 ∙ Uniprot:B2RD01 ∙ 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 CENPBD1P gene.

• Inborn genetic diseases (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CENPBD1P 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			5	2		7
Total	0	0	5	2	0

Variants in CENPBD1P

This is a list of pathogenic ClinVar variants found in the CENPBD1P region.

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

Position	Type	Phenotype	Significance	ClinVar
16-89971382-T-A		not specified	Uncertain significance (Jul 19, 2022)
16-89971448-C-T		not specified	Likely benign (Apr 13, 2022)
16-89971455-C-T		not specified	Uncertain significance (Sep 02, 2024)
16-89971458-C-G		not specified	Uncertain significance (Feb 28, 2025)
16-89971483-T-G		not specified	Uncertain significance (Jun 02, 2023)
16-89971496-C-T		not specified	Uncertain significance (Jan 04, 2024)
16-89971537-C-A		not specified	Uncertain significance (Jan 23, 2023)
16-89971546-T-C		not specified	Uncertain significance (Oct 29, 2024)
16-89971552-C-A		not specified	Uncertain significance (Jan 09, 2024)
16-89971555-T-G		not specified	Uncertain significance (Jul 16, 2024)
16-89971583-G-C		not specified	Uncertain significance (Jan 16, 2025)
16-89971592-C-T		not specified	Likely benign (Feb 07, 2023)
16-89971595-C-G		not specified	Uncertain significance (Aug 28, 2024)
16-89971607-C-T		not specified	Uncertain significance (Jul 14, 2024)
16-89971623-G-T		not specified	Uncertain significance (Dec 03, 2024)
16-89971705-G-T		not specified	Uncertain significance (Dec 13, 2022)
16-89971739-C-T		not specified	Uncertain significance (Jan 04, 2024)
16-89971748-C-A		not specified	Uncertain significance (Apr 12, 2024)
16-89971781-C-T		not specified	Uncertain significance (Nov 30, 2022)
16-89971828-C-T		not specified	Uncertain significance (Oct 10, 2023)
16-89971842-T-G		not specified	Uncertain significance (Oct 30, 2023)
16-89971843-T-G		not specified	Uncertain significance (Dec 27, 2023)
16-89971862-C-G		not specified	Uncertain significance (Feb 19, 2025)
16-89971873-C-A		not specified	Uncertain significance (Feb 12, 2025)
16-89971892-C-G		not specified	Uncertain significance (Aug 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CENPBD1P	protein_coding	protein_coding	ENST00000314994	1	2737

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.283	0.500	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0522	112	110	1.01	0.00000658	1220
Missense in Polyphen		20	25.552	0.78271		326
Synonymous	1.66	30	44.0	0.682	0.00000287	357
Loss of Function	0.152	0	0.0268	0.00	9.19e-10	1

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

Intolerance Scores

• loftool: 0.747
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.56

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146
• ghis: 0.524

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Gene ontology

• Cellular component: nucleus
• Molecular function: DNA binding