CEP295

protein-coding

centrosomal protein 295, the group of Small nucleolar RNA protein coding host genes

Gene summary

Enables microtubule binding activity. Involved in several processes, including centriole replication; positive regulation of protein acetylation; and regulation of centrosome duplication. Located in cytoplasm and microtubule cytoskeleton. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

KIAA1731

MANE transcript

NM_033395.2

Inheritance

ClinVar variants

P:8U:407B:49

Top phenotype

Seckel syndrome 11

gnomAD constraint

pLI —, LoF o/e 0.38

Max pathogenic AF

—

Genomic locus

chr11:93,661,682-93,730,358

External References & Databases

Ensembl (ENSG00000166004)

Transcript & Mutation Effects

hg38 • Region Span ~68.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

Clinical Genomic Database (CGD)

Seckel syndrome 11AR

Manifestation: Cardiovascular; Craniofacial; Genitourinary; Musculoskeletal; Neurologic; Ophthalmologic; Renal

Intervention: Cardiovascular

Rationale: Among other findings, the condition can include congenital cardiac anomalies, and awareness may allow early intervention and management

Refs: 38154379

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CEP295 variants in ClinVar

6 Conditions Cataloged

not specifiedTotal: 397

not providedTotal: 42

Seckel syndrome 11Total: 9

CEP295-related conditionTotal: 7

Meckel-Gruber syndromeTotal: 1

Fetal anomalies with a likely genetic causeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_033395.2. 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			5 clinvar	6 clinvar	7 clinvar	18
missense	1 clinvar		390 clinvar	25 clinvar	11 clinvar	427
nonsense	2 clinvar	1 clinvar	2 clinvar			5
start loss			1 clinvar			1
frameshift	2 clinvar	2 clinvar	6 clinvar			10
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	5	3	407	31	18	464

Highest pathogenic variant AF is 0.000030906707

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_033395.2	RefSeq	NP_203753.1	29	MANE Select
ENST00000325212.11	Ensembl	ENSP00000316681.6	29	MANE Select
ENST00000529185.1	Ensembl	ENSP00000433198.1	2	Standard
ENST00000530425.1	Ensembl	ENSP00000431853.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of centrosome duplication
regulation of centriole replication
positive regulation of protein acetylation
positive regulation of centriole elongation
positive regulation of establishment of protein localization

Molecular Function

microtubule binding

Cellular Component

cytoplasm
centrosome
centriole
cytosol
cytoskeleton

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000325212
Coding exons: 29
Length: 68718
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.66	999	1.16e+3	0.863	0.0000548	17046
Missense (PolyPhen)		206	263.21	0.78265		4377
Synonymous	2.75	355	427	0.831	0.0000207	4828
Loss of Function	6.13	43	113	0.379	0.00000560	1597

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Centriole-enriched microtubule-binding protein involved in centriole biogenesis (PubMed:20844083, PubMed:25131205, PubMed:27185865). Essential for the generation of the distal portion of new-born centrioles in a CENPJ- and CEP120-mediated elongation dependent manner during the cell cycle S/G2 phase after formation of the initiating cartwheel structure (PubMed:27185865). Required for the recruitment of centriolar proteins, such as POC1B, POC5 and CEP135, into the distal portion of centrioles (PubMed:27185865). Also required for centriole-to-centrosome conversion during mitotic progression, but is dispensable for cartwheel removal or centriole disengagement (PubMed:25131205). Binds to and stabilizes centriolar microtubule (PubMed:27185865). {ECO:0000269|PubMed:20844083, ECO:0000269|PubMed:25131205, ECO:0000269|PubMed:27185865}.;

Recessive Scores

pRec: 0.0830

Intolerance Scores

RVIS EVS: 5.12
RVIS percentile EVS: 99.83

Essentials

Essential (gene trap): E