CENPK

protein-coding

centromere protein K, the group of Constitutive centromere associated network

Gene summary

CENPK is a subunit of a CENPH (MIM 605607)-CENPI (MIM 300065)-associated centromeric complex that targets CENPA (MIM 117139) to centromeres and is required for proper kinetochore function and mitotic progression (Okada et al., 2006 [PubMed 16622420]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_022145.5

Inheritance

—

ClinVar variants

U:33B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.02

Max pathogenic AF

—

Genomic locus

chr5:65,517,766-65,563,168

External References & Databases

Ensembl (ENSG00000123219)

Transcript & Mutation Effects

hg38 • Region Span ~45.4 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CENPK variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 33

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_022145.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			33 clinvar	2 clinvar		35
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	33	2	0	35

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 75 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_022145.5	RefSeq	NP_071428.2	9	MANE Select
ENST00000396679.6	Ensembl	ENSP00000379911.1	9	MANE Select
NM_001267038.2	RefSeq	NP_001253967.1	9	Standard
NM_001349367.2	RefSeq	NP_001336296.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

CENP-A containing nucleosome assembly
kinetochore assembly

Molecular Function

protein binding

Cellular Component

condensed chromosome kinetochore
nucleoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000396679
Coding exons: 9
Length: 45406
Individuals with no LoFs: 125646
Homozygous LoFs: 0
Heterozygous LoFs: 59
Defined: 125705
p: 0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.128	133	129	1.03	0.00000612	1777
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000073	0.000062	rare
Latino/Admixed American	0.000068	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000068	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00037	0.00034	rare
South Asian	0.00058	0.00049	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.175

Intolerance Scores

LoFtool: 0.536
RVIS EVS: 0.31
RVIS percentile EVS: 72.23

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Indispensability pred.: E
Indispensability score: 0.616

Gene Damage Prediction

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