SPICE1

protein-coding

spindle and centriole associated protein 1

Gene summary

Involved in metaphase chromosome alignment; mitotic spindle assembly; and regulation of centriole replication. Located in microtubule cytoskeleton. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

CCDC52

MANE transcript

NM_144718.4

Inheritance

—

ClinVar variants

U:136B:13

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.66

Max pathogenic AF

—

Genomic locus

chr3:113,442,718-113,515,187

External References & Databases

Ensembl (ENSG00000163611)

Transcript & Mutation Effects

hg38 • Region Span ~72.5 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 SPICE1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 143

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_144718.4. 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				2 clinvar		2
missense			135 clinvar	11 clinvar		146
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	136	13	0	149

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 43 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_144718.4	RefSeq	NP_653319.1	17	MANE Select
ENST00000295872.8	Ensembl	ENSP00000295872.4	17	MANE Select
NM_001331078.2	RefSeq	NP_001318007.1	17	Standard
NM_001331079.2	RefSeq	NP_001318008.2	17	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of centriole replication
cell division
metaphase plate congression
mitotic spindle assembly

Molecular Function

protein binding

Cellular Component

centrosome
centriole
spindle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000295872
Coding exons: 17
Length: 72470
Individuals with no LoFs: 125669
Homozygous LoFs: 0
Heterozygous LoFs: 79
Defined: 125748
p: 0.000314

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.348	439	460	0.954	0.0000247	5570
Missense (PolyPhen)		132	141.97	0.92978		1772
Synonymous	0.597	149	159	0.940	0.00000810	1663
Loss of Function	2.15	30	45.7	0.656	0.00000237	541

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00033	0.00032	rare
Ashkenazi Jewish	0.00040	0.00040	rare
East Asian	0.00044	0.00044	rare
Finnish	0.00018	0.00018	rare
European (Non-Finnish)	0.00030	0.00030	rare
South Asian	0.00037	0.00036	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Regulator required for centriole duplication, for proper bipolar spindle formation and chromosome congression in mitosis. {ECO:0000269|PubMed:20736305}.;

Intolerance Scores

RVIS EVS: 0.25
RVIS percentile EVS: 69.66

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): H
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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