CETN3

centrin 3, the group of EF-hand domain containing

Basic information

Region (hg38): 5:90392257-90409766

Links

ENSG00000153140 ∙ NCBI:1070 ∙ OMIM:602907 ∙ HGNC:1868 ∙ Uniprot:O15182 ∙ 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 CETN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CETN3 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						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in CETN3

This is a list of pathogenic ClinVar variants found in the CETN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-90399384-T-C		not specified	Uncertain significance (Sep 15, 2021)
5-90399418-T-A		not specified	Uncertain significance (Apr 12, 2023)
5-90399486-T-C		not specified	Uncertain significance (Sep 01, 2021)
5-90399496-T-G		not specified	Uncertain significance (Aug 16, 2021)
5-90405723-G-A		not specified	Uncertain significance (Jul 27, 2024)
5-90405724-C-G		not specified	Uncertain significance (Feb 16, 2023)
5-90405727-C-T		not specified	Uncertain significance (Oct 22, 2021)
5-90405757-C-T		not specified	Uncertain significance (Jan 18, 2023)
5-90405782-C-G		not specified	Uncertain significance (Mar 02, 2023)
5-90407734-C-T		not specified	Uncertain significance (Feb 12, 2025)
5-90407764-T-C		not specified	Uncertain significance (Nov 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CETN3	protein_coding	protein_coding	ENST00000283122	5	17526

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000105	0.603	125566	0	182	125748	0.000724

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.389	73	83.0	0.880	0.00000382	1129
Missense in Polyphen		22	26.707	0.82377		357
Synonymous	-0.704	31	26.4	1.17	0.00000113	272
Loss of Function	0.694	7	9.28	0.754	5.39e-7	117

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00142	0.00142
Ashkenazi Jewish	0.00871	0.00857
East Asian	0.00	0.00
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000299	0.000290
Middle Eastern	0.00	0.00
South Asian	0.000105	0.0000980
Other	0.00262	0.00245

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a fundamental role in microtubule-organizing center structure and function.

Recessive Scores

• pRec: 0.136

Intolerance Scores

• loftool: 0.723
• rvis_EVS: 0.19
• rvis_percentile_EVS: 66.57

Haploinsufficiency Scores

• pHI: 0.957
• hipred: Y
• hipred_score: 0.842
• ghis: 0.629

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cetn3

Gene ontology

• Biological process: centrosome cycle;cell division
• Cellular component: nucleolus;centrosome;centriole
• Molecular function: calcium ion binding;protein binding