CEP97

protein-coding

centrosomal protein 97

Gene summary

Predicted to enable U2 snRNA binding activity and calmodulin binding activity. Involved in negative regulation of cilium assembly and regulation of mitotic spindle assembly. Located in centriole and centrosome. Part of protein-containing complex. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

LRRIQ2

MANE transcript

NM_024548.4

Inheritance

—

ClinVar variants

P:1U:234B:85

Top phenotype

Global developmental delay

gnomAD constraint

pLI —, LoF o/e 0.58

Max pathogenic AF

—

Genomic locus

chr3:101,724,534-101,770,562

External References & Databases

Ensembl (ENSG00000182504)

Transcript & Mutation Effects

hg38 • Region Span ~46.0 kb

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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 CEP97 variants in ClinVar

4 Conditions Cataloged

not providedTotal: 284

not specifiedTotal: 115

Global developmental delayTotal: 1

Intellectual disabilityTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024548.4. 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			3 clinvar	61 clinvar	6 clinvar	70
missense		1 clinvar	214 clinvar	15 clinvar	3 clinvar	233
nonsense			2 clinvar			2
start loss						0
frameshift			9 clinvar			9
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	1	234	76	9	320

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024548.4	RefSeq	NP_078824.2	11	MANE Select
ENST00000341893.8	Ensembl	ENSP00000342510.3	11	MANE Select
NM_001303401.2	RefSeq	NP_001290330.1	11	Standard
NM_001410784.1	RefSeq	NP_001397713.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Anchoring of the basal body to the plasma membrane
Cilium Assembly
Organelle biogenesis and maintenance

Biological Process

ciliary basal body-plasma membrane docking
regulation of mitotic spindle assembly
negative regulation of cilium assembly

Molecular Function

protein binding
calmodulin binding

Cellular Component

centrosome
microtubule organizing center
cytosol
protein-containing complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000341893
Coding exons: 11
Length: 46638
Individuals with no LoFs: 125684
Homozygous LoFs: 0
Heterozygous LoFs: 64
Defined: 125748
p: 0.000255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.682	410	451	0.910	0.0000225	5676
Missense (PolyPhen)		84	101.84	0.82482		1293
Synonymous	0.758	157	170	0.926	0.00000849	1663
Loss of Function	2.53	24	41.6	0.577	0.00000211	492

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00026	0.00023	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00055	0.00054	rare
Finnish	0.00028	0.00028	rare
European (Non-Finnish)	0.00027	0.00026	rare
South Asian	0.00013	0.00013	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Acts as a key negative regulator of ciliogenesis in collaboration with CCP110 by capping the mother centriole thereby preventing cilia formation. Required for recruitment of CCP110 to the centrosome. {ECO:0000269|PubMed:17719545}.;

Recessive Scores

pRec: 0.0988

Intolerance Scores

RVIS EVS: -0.6
RVIS percentile EVS: 18.21

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.862

Gene Damage Prediction

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