CENPK

centromere protein K, the group of Constitutive centromere associated network

Basic information

Region (hg38): 5:65517766-65563168

Links

ENSG00000123219 ∙ NCBI:64105 ∙ OMIM:611502 ∙ HGNC:29479 ∙ Uniprot:Q9BS16 ∙ 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 CENPK gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CENPK 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in CENPK

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

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

Position	Type	Phenotype	Significance	ClinVar
5-65518479-T-G		not specified	Uncertain significance (Aug 05, 2024)
5-65518503-C-T		not specified	Uncertain significance (Sep 17, 2021)
5-65518506-G-C		not specified	Uncertain significance (May 29, 2024)
5-65518513-C-A		not specified	Uncertain significance (Jun 02, 2023)
5-65518602-T-C		not specified	Uncertain significance (Nov 14, 2023)
5-65518623-T-C		not specified	Uncertain significance (Dec 07, 2021)
5-65521509-G-T		not specified	Uncertain significance (Jun 03, 2022)
5-65528553-T-C		not specified	Uncertain significance (Jul 17, 2024)
5-65529010-G-A		not specified	Uncertain significance (Apr 20, 2023)
5-65529129-T-C		not specified	Uncertain significance (Feb 14, 2023)
5-65529147-T-A		not specified	Uncertain significance (May 30, 2023)
5-65551590-C-G		not specified	Uncertain significance (Nov 21, 2022)
5-65551594-G-A		not specified	Uncertain significance (Feb 07, 2025)
5-65551635-A-T		not specified	Uncertain significance (Nov 07, 2023)
5-65552501-T-C		not specified	Uncertain significance (Nov 16, 2022)
5-65554804-A-G		not specified	Uncertain significance (Feb 13, 2025)
5-65554812-C-A		not specified	Uncertain significance (Aug 12, 2021)
5-65554876-G-A		not specified	Uncertain significance (Sep 14, 2024)
5-65554901-G-C		not specified	Uncertain significance (Jun 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CENPK	protein_coding	protein_coding	ENST00000396679	9	45406

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.08e-11	0.0445	125646	0	59	125705	0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.128	133	129	1.03	0.00000612	1777
Missense in Polyphen		37	41.936	0.8823		622
Synonymous	0.207	44	45.8	0.961	0.00000231	453
Loss of Function	-0.0699	16	15.7	1.02	6.58e-7	227

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000141	0.000130
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000680	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000372	0.000343
Middle Eastern	0.0000680	0.0000544
South Asian	0.000576	0.000490
Other	0.000170	0.000163

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. Acts in coordination with KNL1 to recruit the NDC80 complex to the outer kinetochore. {ECO:0000269|PubMed:16622420, ECO:0000269|PubMed:16716197, ECO:0000269|PubMed:18045986}.
• 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: 0.175

Intolerance Scores

• loftool: 0.536
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.23

Haploinsufficiency Scores

• pHI: 0.532
• hipred: Y
• hipred_score: 0.518
• ghis: 0.581

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.616

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cenpk

Gene ontology

• Biological process: CENP-A containing nucleosome assembly;kinetochore assembly
• Cellular component: condensed chromosome kinetochore;nucleoplasm;cytosol
• Molecular function: protein binding