CENPO

centromere protein O, the group of Constitutive centromere associated network

Basic information

Region (hg38): 2:24793135-24822376

Links

ENSG00000138092 ∙ NCBI:79172 ∙ OMIM:611504 ∙ HGNC:28152 ∙ Uniprot:Q9BU64 ∙ 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 CENPO gene.

• Inborn genetic diseases (13 variants)
• not provided (6 variants)
• BODY MASS INDEX QUANTITATIVE TRAIT LOCUS 19 (1 variants)
• ADCY3-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CENPO 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	2		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4	2	3	9
Total	0	0	14	4	3

Variants in CENPO

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

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

Position	Type	Phenotype	Significance	ClinVar
2-24793181-GGGTGGTCGCGGTGAGTGTGCAAGGCCGC-G		Neurodevelopmental disorder with early-onset parkinsonism and behavioral abnormalities	Pathogenic (Mar 13, 2024)
2-24793188-C-G		not specified	Uncertain significance (Mar 02, 2023)
2-24793189-G-A		PTRHD1-related disorder	Likely benign (Aug 28, 2019)
2-24793221-G-A		Neurodevelopmental disorder with early-onset parkinsonism and behavioral abnormalities	Pathogenic (Mar 13, 2024)
2-24793223-C-T		Parkinsonian disorder • Neurodevelopmental disorder with early-onset parkinsonism and behavioral abnormalities	Pathogenic (Dec 14, 2021)
2-24793237-C-G		PTRHD1-related disorder	Likely benign (Aug 13, 2019)
2-24793251-G-T		PTRHD1-related disorder	Benign (Jun 14, 2019)
2-24793296-A-G		not specified	Uncertain significance (Feb 21, 2024)
2-24793336-C-G		PTRHD1-related disorder	Uncertain significance (Feb 08, 2024)
2-24799719-T-A		not specified	Uncertain significance (Aug 08, 2022)
2-24799722-C-T		not specified	Uncertain significance (Feb 17, 2023)
2-24799797-C-T		not specified	Uncertain significance (May 27, 2022)
2-24799798-G-A		not specified	Likely benign (Mar 07, 2023)
2-24799809-G-A		not specified	Likely benign (Mar 16, 2022)
2-24799821-G-A		not specified	Uncertain significance (Nov 01, 2021)
2-24799828-G-A		not specified	Uncertain significance (Dec 08, 2021)
2-24799842-A-C		not specified	Likely benign (Oct 02, 2023)
2-24815518-G-T		not specified	Uncertain significance (Aug 02, 2023)
2-24815519-C-A		not specified	Uncertain significance (Jan 22, 2024)
2-24815604-C-T		not specified	Uncertain significance (Jul 09, 2021)
2-24816805-G-A		not specified	Uncertain significance (Jul 25, 2023)
2-24817672-G-T		not specified	Uncertain significance (Apr 25, 2022)
2-24817739-C-G		not specified	Uncertain significance (Feb 06, 2024)
2-24817757-C-T		not specified	Uncertain significance (Jan 24, 2024)
2-24817779-A-C		not specified	Uncertain significance (Dec 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CENPO	protein_coding	protein_coding	ENST00000380834	6	29241

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.89e-9	0.239	125594	1	153	125748	0.000613

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.404	148	163	0.911	0.00000874	1925
Missense in Polyphen		31	40.723	0.76123		552
Synonymous	-0.707	73	65.7	1.11	0.00000335	604
Loss of Function	0.619	15	17.8	0.842	0.00000121	179

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00325	0.00325
Ashkenazi Jewish	0.00398	0.00398
East Asian	0.000217	0.000217
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.000217	0.000217
South Asian	0.000297	0.000294
Other	0.00147	0.00147

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the CENPA-CAD (nucleosome distal) complex, a complex recruited to centromeres which is involved in assembly of kinetochore proteins, mitotic progression and chromosome segregation. May be involved in incorporation of newly synthesized CENPA into centromeres via its interaction with the CENPA-NAC complex. Modulates the kinetochore-bound levels of NDC80 complex. {ECO:0000269|PubMed:16622420, ECO:0000269|PubMed:16716197, ECO:0000269|PubMed:16932742, ECO:0000269|PubMed:18007590}.
• Pathway: Signal Transduction;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;RHO GTPases Activate Formins;Nucleosome assembly;RHO GTPase Effectors;Signaling by Rho GTPases;Chromosome Maintenance;Deposition of new CENPA-containing nucleosomes at the centromere;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Cell Cycle, Mitotic (Consensus)

Recessive Scores

• pRec: 0.0640

Intolerance Scores

• loftool: 0.879
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.61

Haploinsufficiency Scores

• pHI: 0.0963
• hipred: N
• hipred_score: 0.438
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.799

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cenpo
• Phenotype: homeostasis/metabolism 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)

Gene ontology

• Biological process: CENP-A containing nucleosome assembly
• Cellular component: condensed nuclear chromosome kinetochore;condensed nuclear chromosome, centromeric region;nucleus;nucleoplasm;cytosol;Mis6-Sim4 complex
• Molecular function: protein binding