CENPN

centromere protein N, the group of Constitutive centromere associated network

Basic information

Region (hg38): 16:81006552-81033114

Previous symbols: [ "C16orf60" ]

Links

ENSG00000166451 ∙ NCBI:55839 ∙ OMIM:611509 ∙ HGNC:30873 ∙ Uniprot:Q96H22 ∙ 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 CENPN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CENPN 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			24	3		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	3	0

Variants in CENPN

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

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

Position	Type	Phenotype	Significance	ClinVar
16-81011993-G-A		not specified	Uncertain significance (Jul 06, 2021)
16-81012064-G-A		not specified	Uncertain significance (Dec 06, 2021)
16-81012075-G-C		not specified	Uncertain significance (Jan 10, 2023)
16-81014142-C-T		not specified	Likely benign (Jul 15, 2021)
16-81014146-C-G		not specified	Uncertain significance (Apr 24, 2024)
16-81017329-T-C		not specified	Likely benign (Feb 05, 2024)
16-81017333-A-C		not specified	Uncertain significance (Sep 06, 2022)
16-81017343-C-T		not specified	Uncertain significance (Jan 23, 2024)
16-81017782-T-G		not specified	Uncertain significance (May 11, 2022)
16-81020104-C-A		not specified	Uncertain significance (Sep 26, 2023)
16-81020167-A-T		not specified	Uncertain significance (Oct 22, 2021)
16-81020205-T-C		not specified	Uncertain significance (Jul 14, 2022)
16-81020209-A-G		not specified	Uncertain significance (Sep 30, 2021)
16-81020233-C-T		not specified	Uncertain significance (Apr 25, 2022)
16-81020263-C-T		not specified	Uncertain significance (Mar 06, 2023)
16-81022615-A-C		not specified	Uncertain significance (Nov 08, 2022)
16-81022662-C-G		not specified	Uncertain significance (Jul 15, 2021)
16-81022675-A-G		not specified	Uncertain significance (Nov 17, 2022)
16-81022679-T-C		not specified	Uncertain significance (May 23, 2024)
16-81022684-A-C		not specified	Uncertain significance (Dec 19, 2023)
16-81024737-C-T		not specified	Uncertain significance (Nov 08, 2021)
16-81024742-C-T		not specified	Uncertain significance (Dec 15, 2023)
16-81024748-C-A		not specified	Uncertain significance (Aug 02, 2022)
16-81026579-A-G		not specified	Likely benign (Jan 29, 2024)
16-81026585-C-G		not specified	Uncertain significance (Jul 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CENPN	protein_coding	protein_coding	ENST00000393335	10	26617

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00442	0.994	125733	0	14	125747	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.426	202	186	1.09	0.00000949	2333
Missense in Polyphen		64	65.929	0.97075		882
Synonymous	-1.36	81	66.8	1.21	0.00000367	629
Loss of Function	2.81	8	22.3	0.358	0.00000129	235

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)	0.0000884	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.000103	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the CENPA-NAC (nucleosome-associated) complex, a complex that plays a central role in assembly of kinetochore proteins, mitotic progression and chromosome segregation. The CENPA-NAC complex recruits the CENPA-CAD (nucleosome distal) complex and may be involved in incorporation of newly synthesized CENPA into centromeres. CENPN is the first protein to bind specifically to CENPA nucleosomes and the direct binding of CENPA nucleosomes by CENPN is required for centromere assembly. Required for chromosome congression and efficiently align the chromosomes on a metaphase plate. {ECO:0000269|PubMed:16622419, ECO:0000269|PubMed:16716197, ECO:0000269|PubMed:18007590, ECO:0000269|PubMed:19543270}.
• 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: 0.0811

Intolerance Scores

• rvis_EVS: 1.13
• rvis_percentile_EVS: 92.23

Haploinsufficiency Scores

• pHI: 0.243
• hipred: N
• hipred_score: 0.230
• ghis: 0.499

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.463

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cenpn

Zebrafish Information Network

• Gene name: cenpn
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: atrophied

Gene ontology

• Biological process: chromosome segregation;CENP-A containing nucleosome assembly;kinetochore assembly
• Cellular component: condensed chromosome kinetochore;nucleus;nucleoplasm;cytosol