SPICE1

Chr 3

spindle and centriole associated protein 1

Also known as: CCDC52, SPICE

Involved in metaphase chromosome alignment; mitotic spindle assembly; and regulation of centriole replication. Located in intracellular membrane-bounded organelle; microtubule cytoskeleton; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2025]

OMIMResearchGenerating clinical summary…
DNmechanismLOEUF 0.89
Clinical SummarySPICE1
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
131 VUS of 159 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint?
0.89LOEUF
pLI 0.000
Z-score 2.15
OE 0.66 (0.490.89)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?
0.35Z-score
OE missense 0.95 (0.881.03)
439 obs / 460.0 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.66 (0.490.89)
00.351.4
Missense OE?0.95 (0.881.03)
00.61.4
Synonymous OE?0.94
01.21.6
LoF obs/exp: 30 / 45.7Missense obs/exp: 439 / 460.0Syn Z: 0.60

This gene — mechanism propensity

DN
0.6454th %ile
GOF
0.5856th %ile
LOF
0.4233th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

159 submitted variants in ClinVar

Classification Summary

VUS131
Likely Benign13
131
VUS
13
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
0
0
0
Likely Pathogenic
0
0
0
0
0
VUS
0
131
0
0
131
Likely Benign
0
11
0
2
13
Benign
0
0
0
0
0
Total014202144

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

30 pathogenic / likely-pathogenic (of 33) ClinVar copy-number / structural variants overlap SPICE1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →

Protein Context — Lollipop Plot

SPICE1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →