CENPT

centromere protein T, the group of Constitutive centromere associated network

Basic information

Region (hg38): 16:67828157-67847811

Previous symbols: [ "C16orf56" ]

Links

ENSG00000102901 ∙ NCBI:80152 ∙ OMIM:611510 ∙ HGNC:25787 ∙ Uniprot:Q96BT3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• short stature and microcephaly with genital anomalies (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Short stature and microcephaly with genital anomalies	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Endocrine; Genitourinary; Musculoskeletal; Neurologic; Ophthalmologic	29228025

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CENPT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CENPT 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				4	1	5
missense			31	7	5	43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding		1	46	63	13	123
Total	0	1	77	74	19

Variants in CENPT

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

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

Position	Type	Phenotype	Significance	ClinVar
16-67828301-G-A		not specified	Uncertain significance (May 16, 2022)
16-67828322-C-T		not specified	Uncertain significance (Jul 02, 2024)
16-67828343-C-T		not specified	Uncertain significance (Mar 18, 2024)
16-67828356-C-T		not specified	Uncertain significance (Nov 10, 2024)
16-67828383-G-A			Likely benign (Apr 30, 2018)
16-67828478-G-C		not specified	Uncertain significance (Nov 30, 2022)
16-67828511-T-C		not specified	Uncertain significance (Nov 18, 2024)
16-67828517-G-A		not specified	Likely benign (Aug 08, 2024)
16-67828533-A-C		not specified	Uncertain significance (Jul 14, 2021)
16-67828558-T-A		not specified	Uncertain significance (Aug 08, 2023)
16-67828688-G-A		not specified	Uncertain significance (Dec 16, 2023)
16-67828712-G-A		not specified	Uncertain significance (Apr 15, 2024)
16-67828728-G-A		not specified	Uncertain significance (Jul 06, 2024)
16-67828748-C-G		not specified	Uncertain significance (Aug 28, 2024)
16-67828757-T-A		not specified	Uncertain significance (Jan 24, 2023)
16-67828784-G-T		not specified	Uncertain significance (Jan 23, 2024)
16-67828791-G-A		not specified	Uncertain significance (Mar 20, 2023)
16-67828803-G-C		CENPT-related disorder	Benign (Jan 28, 2020)
16-67828829-G-A		not specified	Uncertain significance (Jul 16, 2024)
16-67828838-G-A		not specified	Uncertain significance (Jul 22, 2024)
16-67829427-C-T		not specified	Uncertain significance (Dec 13, 2022)
16-67829438-G-A		CENPT-related disorder	Likely benign (Feb 18, 2022)
16-67829504-G-A		not specified	Likely benign (Dec 17, 2021)
16-67829548-T-C		Short stature and microcephaly with genital anomalies	Benign (Jul 22, 2021)
16-67829764-C-T		Short stature and microcephaly with genital anomalies	Pathogenic (Nov 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CENPT	protein_coding	protein_coding	ENST00000562787	13	19655

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000585	0.994	124773	0	35	124808	0.000140

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.136	312	319	0.979	0.0000179	3549
Missense in Polyphen		84	83.931	1.0008		984
Synonymous	0.172	129	132	0.981	0.00000760	1215
Loss of Function	2.45	13	26.7	0.487	0.00000139	300

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000321	0.000316
Ashkenazi Jewish	0.0000993	0.0000993
East Asian	0.000111	0.000111
Finnish	0.000439	0.000417
European (Non-Finnish)	0.000103	0.0000971
Middle Eastern	0.000111	0.000111
South Asian	0.000208	0.000196
Other	0.00	0.00

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. Part of a nucleosome- associated complex that binds specifically to histone H3- containing nucleosomes at the centromere, as opposed to nucleosomes containing CENPA. Component of the heterotetrameric CENP-T-W-S-X complex that binds and supercoils DNA, and plays an important role in kinetochore assembly. CENPT has a fundamental role in kinetochore assembly and function. It is one of the inner kinetochore proteins, with most further proteins binding downstream. Required for normal chromosome organization and normal progress through mitosis. {ECO:0000269|PubMed:16716197, ECO:0000269|PubMed:21529714, ECO:0000269|PubMed:21695110}.
• 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: 0.0660

Intolerance Scores

• loftool: 0.592
• rvis_EVS: 1.29
• rvis_percentile_EVS: 93.84

Haploinsufficiency Scores

• pHI: 0.0493
• hipred: N
• hipred_score: 0.233
• ghis: 0.423

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.271

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cenpt

Gene ontology

• Biological process: mitotic cell cycle;regulation of transcription by RNA polymerase II;chromosome segregation;CENP-A containing nucleosome assembly;chromosome organization;cell division;kinetochore assembly
• Cellular component: chromosome, centromeric region;kinetochore;condensed chromosome kinetochore;nucleus;nucleoplasm;cytosol;nuclear body
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;protein heterodimerization activity