CENPP

centromere protein P, the group of Constitutive centromere associated network

Basic information

Region (hg38): 9:92325952-92620529

Links

ENSG00000188312 ∙ NCBI:401541 ∙ OMIM:611505 ∙ HGNC:32933 ∙ Uniprot:Q6IPU0 ∙ 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 CENPP gene.

• Inborn genetic diseases (69 variants)
• not provided (4 variants)
• Low-frequency hearing loss;Low-frequency sensorineural hearing impairment (1 variants)
• Osteoarthritis susceptibility 3 (1 variants)
• not specified (1 variants)
• Lumbar disk degeneration, susceptibility to (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CENPP 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			10
nonsense		1				1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			57	3	4	64
Total	0	1	67	3	4

Variants in CENPP

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

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

Position	Type	Phenotype	Significance	ClinVar
9-92332208-G-T		not specified	Uncertain significance (Dec 28, 2022)
9-92332224-A-T		not specified	Uncertain significance (Oct 03, 2022)
9-92332277-C-T		CENPP-related disorder	Likely benign (Jul 28, 2020)
9-92345730-A-T		not specified	Uncertain significance (Nov 14, 2023)
9-92345738-A-G		not specified	Uncertain significance (Oct 25, 2022)
9-92379770-G-C		not specified	Uncertain significance (Dec 21, 2022)
9-92379798-G-A		CENPP-related disorder	Likely benign (Apr 28, 2022)
9-92379847-T-G		not specified	Uncertain significance (Jun 01, 2023)
9-92385727-G-A		not specified	Uncertain significance (Nov 13, 2023)
9-92386262-T-C		not specified	Uncertain significance (Sep 14, 2023)
9-92393116-T-G		not specified	Uncertain significance (Jan 16, 2024)
9-92393149-C-T		not specified	Uncertain significance (Mar 16, 2022)
9-92393161-G-C		not specified	Uncertain significance (Feb 12, 2024)
9-92401118-G-A		not specified	Uncertain significance (Aug 01, 2022)
9-92401127-G-A		not specified	Uncertain significance (Feb 28, 2024)
9-92401159-A-T		not specified	Uncertain significance (Sep 20, 2023)
9-92403325-C-T		not specified	Uncertain significance (Mar 30, 2022)
9-92403329-A-T		not specified	Uncertain significance (May 27, 2022)
9-92415190-C-T		not specified	Uncertain significance (Sep 22, 2023)
9-92415316-T-C		not specified	Uncertain significance (Mar 28, 2022)
9-92415321-C-T		not specified	Uncertain significance (Nov 27, 2023)
9-92415345-T-C		not specified	Uncertain significance (Jan 18, 2023)
9-92415346-G-A		not specified	Uncertain significance (Feb 28, 2024)
9-92415350-A-T		not specified	Uncertain significance (Jan 03, 2022)
9-92415361-A-T		not specified	Uncertain significance (Feb 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CENPP	protein_coding	protein_coding	ENST00000375587	8	295050

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0463	0.949	125724	0	24	125748	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.320	138	149	0.926	0.00000766	1866
Missense in Polyphen		13	12.945	1.0042		160
Synonymous	0.0210	56	56.2	0.996	0.00000295	538
Loss of Function	2.47	5	15.5	0.322	7.44e-7	189

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)	0.000106	0.000105
Middle Eastern	0.00	0.00
South Asian	0.000406	0.000392
Other	0.00	0.00

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. {ECO:0000269|PubMed:16622420}.
• 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: 0.0755

Intolerance Scores

• loftool: 0.311
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.8

Haploinsufficiency Scores

• pHI: 0.0620
• hipred: Y
• hipred_score: 0.532
• ghis: 0.472

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.404

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cenpp

Gene ontology

• Biological process: CENP-A containing nucleosome assembly
• Cellular component: chromosome, centromeric region;nucleus;nucleoplasm;nucleolus;cytosol
• Molecular function: protein binding