CETN3

protein-coding

centrin 3, the group of EF-hand domain containing

Gene summary

The protein encoded by this gene contains four EF-hand calcium binding domains, and is a member of the centrin protein family. Centrins are evolutionarily conserved proteins similar to the CDC31 protein of S. cerevisiae. Yeast CDC31 is located at the centrosome of interphase and mitotic cells, where it plays a fundamental role in centrosome duplication and separation. Multiple forms of the proteins similar to the yeast centrin have been identified in human and other mammalian cells, some of which have been shown to be associated with centrosome fractions. This protein appears to be one of the most abundant centrins associated with centrosome, which suggests a similar function to its yeast counterpart. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2014]

MANE transcript

NM_004365.4

Inheritance

—

ClinVar variants

U:18

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.75

Max pathogenic AF

—

Genomic locus

chr5:90,392,257-90,409,766

External References & Databases

Ensembl (ENSG00000153140)

Transcript & Mutation Effects

hg38 • Region Span ~17.5 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 CETN3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 15

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004365.4. 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			15 clinvar			15
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	18	0	0	18

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 36 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004365.4	RefSeq	NP_004356.2	5	MANE Select
ENST00000283122.8	Ensembl	ENSP00000283122.3	5	MANE Select
NM_001297765.2	RefSeq	NP_001284694.1	6	Standard
NM_001297768.2	RefSeq	NP_001284697.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

centrosome cycle
cell division

Molecular Function

calcium ion binding
protein binding

Cellular Component

nucleolus
centrosome
centriole

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000283122
Coding exons: 5
Length: 17526
Individuals with no LoFs: 125566
Homozygous LoFs: 0
Heterozygous LoFs: 182
Defined: 125748
p: 0.000724

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.389	73	83.0	0.880	0.00000382	1129
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.0012	0.0011	notable
Ashkenazi Jewish	0.0087	0.0086	notable
East Asian	0	0.0	absent
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00030	0.00029	rare
South Asian	0.00011	0.000098	rare
Other	0.0026	0.0024	notable

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.539

Gene Damage Prediction

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