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…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.25

LOEUF

—

Mechanism

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

Background carrier burden — how many people carry a rare variant somewhere in SPATC1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 45

834 rare PASS variants

Rare truncating (LoF)

1 in 350

136 rare PASS variants

Rare synonymous (reference)

1 in 94

385 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SPATC1. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 58	1 in 480
South Asian	~43k	1 in 38	1 in 450
Remaining (unassigned)	~30k	1 in 47	1 in 250
European (Finnish)	~27k	1 in 130	1 in 510
Admixed American	~22k	1 in 37	1 in 870
African / African American	~21k	1 in 36	1 in 830
East Asian	~20k	1 in 47	1 in 450
Ashkenazi Jewish	~13k	1 in 340	1 in 1,500
Middle Eastern	~2,884	1 in 50	≈ 1 in 2,900

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 5 of 5 coding exons well covered in gnomAD exomes. Genomes: 4 of 5 (exon 3 below).? see exons ↓