CENPU

centromere protein U, the group of Constitutive centromere associated network

Basic information

Region (hg38): 4:184694085-184734130

Previous symbols: [ "MLF1IP" ]

Links

ENSG00000151725 ∙ NCBI:79682 ∙ OMIM:611511 ∙ HGNC:21348 ∙ Uniprot:Q71F23 ∙ 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 CENPU gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CENPU 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			26	4		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			7		1	8
Total	0	0	33	4	1

Variants in CENPU

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

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

Position	Type	Phenotype	Significance	ClinVar
4-184694537-ACAGATGAAG-A		PRIMPOL-related disorder	Benign (Apr 26, 2019)
4-184694538-C-G		not specified	Uncertain significance (Jun 24, 2022)
4-184694547-C-G		not specified	Uncertain significance (Dec 03, 2021)
4-184694573-C-G		not specified	Uncertain significance (Sep 29, 2022)
4-184694579-C-T		not specified	Uncertain significance (May 14, 2024)
4-184694615-G-T		not specified	Uncertain significance (Jul 27, 2024)
4-184694626-T-G		not specified	Uncertain significance (Jul 05, 2022)
4-184694634-G-C		not specified	Uncertain significance (Nov 17, 2023)
4-184694703-A-G		not specified	Uncertain significance (Dec 18, 2023)
4-184694750-G-C		not specified	Uncertain significance (Apr 07, 2023)
4-184695316-T-A		not specified	Uncertain significance (Jul 26, 2022)
4-184695319-T-C		not specified	Uncertain significance (Oct 06, 2024)
4-184695325-A-G		not specified	Uncertain significance (Nov 30, 2021)
4-184695331-C-T		not specified	Likely benign (Oct 25, 2022)
4-184695338-G-A		not specified	Uncertain significance (Feb 23, 2023)
4-184695347-C-T		not specified	Uncertain significance (May 11, 2022)
4-184695373-A-G		not specified	Uncertain significance (Jul 05, 2024)
4-184695397-T-C		not specified	Uncertain significance (Aug 01, 2022)
4-184697700-G-A		not specified	Uncertain significance (Sep 28, 2022)
4-184697727-C-T			Likely benign (Nov 03, 2017)
4-184697750-C-G		not specified	Uncertain significance (Feb 07, 2023)
4-184697796-G-C		not specified	Uncertain significance (Jan 19, 2024)
4-184700848-T-C		not specified	Uncertain significance (Aug 02, 2022)
4-184702136-G-A		not specified	Uncertain significance (Aug 10, 2021)
4-184702410-C-A			Likely benign (Nov 03, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CENPU	protein_coding	protein_coding	ENST00000281453	13	39516

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.79e-8	0.870	125671	0	75	125746	0.000298

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.462	232	213	1.09	0.0000107	2718
Missense in Polyphen		39	40.799	0.95592		614
Synonymous	-0.335	77	73.3	1.05	0.00000375	753
Loss of Function	1.63	15	23.5	0.638	0.00000106	326

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000434	0.000425
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000550	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000242	0.000237
Middle Eastern	0.0000550	0.0000544
South Asian	0.00117	0.00114
Other	0.000329	0.000326

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. Plays an important role in the correct PLK1 localization to the mitotic kinetochores. A scaffold protein responsible for the initial recruitment and maintenance of the kinetochore PLK1 population until its degradation. Involved in transcriptional repression. {ECO:0000269|PubMed:12941884, ECO:0000269|PubMed:16716197, ECO:0000269|PubMed:17081991}.
• 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;PLK1 signaling events (Consensus)

Recessive Scores

• pRec: 0.0782

Intolerance Scores

• rvis_EVS: 0.49
• rvis_percentile_EVS: 79.46

Haploinsufficiency Scores

• pHI: 0.565
• hipred: N
• hipred_score: 0.485
• ghis: 0.515

Essentials

• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cenpu
• Phenotype: growth/size/body region 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); embryo phenotype

Gene ontology

• Biological process: viral process;CENP-A containing nucleosome assembly;chordate embryonic development
• Cellular component: condensed chromosome kinetochore;nucleus;nucleoplasm;microtubule organizing center;cytosol
• Molecular function: protein binding