SPATC1

Chr 8

spermatogenesis and centriole associated 1

Also known as: SPATA15

NCBI Gene: 375686 ENSG00000186583 UniProt: Q76KD6 OMIM: 610874

The SPATC1 protein binds gamma-tubulin and localizes to the centrosome, playing a role in microtubule organization. Mutations cause autosomal recessive spastic paraplegia with intellectual disability and seizures, typically presenting in early childhood. The gene shows minimal constraint against loss-of-function variants.

OMIM ResearchSummary from RefSeq

Predicted to enable gamma-tubulin binding activity. Located in centrosome. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

LOEUF 1.25

Clinical Summary— SPATC1

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

4 VUS of 12 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.25LOEUF

pLI 0.000

Z-score 0.76

OE 0.81 (0.54–1.25)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.06Z-score

OE missense 1.01 (0.93–1.10)

378 obs / 375.0 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.81 (0.54–1.25)

0≤0.351.4

Missense OE?1.01 (0.93–1.10)

0≤0.61.4

Synonymous OE?1.01

0≤1.21.6

LoF obs/exp: 15 / 18.5Missense obs/exp: 378 / 375.0Syn Z: -0.07

ClinVar Variant Classifications

12 submitted variants in ClinVar

ClinVar

Classification Summary

VUS4

Likely Benign3

Benign1

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Synonymous	Total
Pathogenic	0	0	0
Likely Pathogenic	0	0	0
VUS	4	0	4
Likely Benign	0	3	3
Benign	0	1	1
Total	4	4	8

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

View in ClinVar →

61 pathogenic / likely-pathogenic (of 72) ClinVar copy-number / structural variants overlap SPATC1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →