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SPATA7
spermatogenesis associated 7
SPATA7 is located on the long (q) arm of chromosome 14, at band 14q31.3. Arm ratio per GRCh38 - banding schematic.
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Overview
SPATA7 (spermatogenesis associated 7) encodes a protein localised to the connecting cilium of photoreceptor cells in the retina. Despite its name referencing spermatogenesis, the gene's primary clinical significance relates to vision, where it plays an essential role in maintaining photoreceptor structure and function. The protein is concentrated at the junction between the inner and outer segments of rod and cone cells, where it contributes to the organisation and stability of this specialised ciliary structure. Pathogenic variants in SPATA7 disrupt photoreceptor architecture, leading to progressive retinal degeneration and severe visual impairment, often manifesting in infancy or early childhood.
What the gene does
The SPATA7 protein functions within the connecting cilium of photoreceptor cells, a narrow bridge that links the metabolically active inner segment to the light-sensing outer segment. This ciliary structure is critical for transporting proteins and other molecules between the two compartments, a process essential for photoreceptor maintenance and visual function. SPATA7 appears to contribute to the structural integrity of the cilium and may participate in organising protein complexes at this site. Research suggests the protein helps anchor or stabilise components within the ciliary region, ensuring proper trafficking of visual pigments and phototransduction proteins to the outer segment. Without functional SPATA7, photoreceptors cannot maintain their architecture effectively, leading to progressive degeneration of both rod and cone cells and consequent vision loss.
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Chromosome location
SPATA7 is located on the long arm of chromosome 14 at position 14q31.3. The gene spans multiple exons encoding a 599-amino-acid protein. This chromosomal region contains several other genes, but SPATA7 is the sole gene in this locus associated with inherited retinal disease.
Protein structure
The SPATA7 protein comprises 599 amino acids with a predicted disordered region spanning amino acids 163 to 205. Disordered regions often facilitate protein-protein interactions and provide flexibility in molecular assemblies, which may be relevant to SPATA7's role in organising ciliary structures. The protein lacks well-characterised enzymatic domains, consistent with a structural or scaffolding function at the photoreceptor cilium. Further experimental characterisation of additional functional motifs is ongoing.
Key variants
Pathogenic variants in SPATA7 are typically loss-of-function changes, including nonsense mutations, frameshift deletions, and splice-site alterations that disrupt protein production or function. The inheritance pattern for SPATA7-related retinal disease is autosomal recessive, meaning two pathogenic variants (one inherited from each parent) are required for clinical manifestation. Carriers with a single pathogenic variant generally do not experience vision problems. The spectrum of reported pathogenic variants is distributed across the gene, with no single predominant mutation hotspot identified to date.
Sample of pathogenic variants
10 pathogenic / likely-pathogenic variants from ClinVar, ranked by review status (expert-panel-reviewed first). This is a sample; recurrent founder variants in a specific population may not appear here - see the full ClinVar listing via the link above.
| Variant (HGVS) | Protein change | Classification | Evidence | Associated condition |
|---|---|---|---|---|
c.1102_1103del | p.Leu368fs | Pathogenic/Likely pathogenic | ★★☆☆ | SPATA7-related disorder |
c.1126_1127del | p.Thr375_Asp376insTer | Pathogenic | ★★☆☆ | Leber congenital amaurosis 3 |
c.1199_1203del | p.Asn400fs | Pathogenic/Likely pathogenic | ★★☆☆ | SPATA7-related disorder |
c.224del | p.Ser75fs | Pathogenic/Likely pathogenic | ★★☆☆ | SPATA7-related disorder |
c.265_268del | p.Leu89fs | Pathogenic/Likely pathogenic | ★★☆☆ | SPATA7-related disorder |
c.296_297del | p.Glu99fs | Pathogenic | ★★☆☆ | Leber congenital amaurosis 3 |
c.419del | p.Met140fs | Pathogenic/Likely pathogenic | ★★☆☆ | SPATA7-related disorder |
c.487A>T | p.Lys163Ter | Pathogenic | ★★☆☆ | Retinal dystrophy |
c.699_700del | p.Phe233_Ser234insTer | Pathogenic | ★★☆☆ | Leber congenital amaurosis |
c.808del | p.Asp270fs | Pathogenic/Likely pathogenic | ★★☆☆ | Leber congenital amaurosis 3 |
Evidence stars indicate ClinVar review status. Individual variant interpretation should always be performed by a qualified clinical laboratory - many variants remain classified as Variants of Uncertain Significance (VUS) pending more research.
Associated conditions
Pathogenic variants in SPATA7 cause inherited retinal dystrophies, most commonly Leber congenital amaurosis (LCA) and early-onset severe retinal dystrophy. LCA represents one of the most severe forms of inherited retinal degeneration, typically presenting in the first months of life with profound visual impairment, nystagmus (involuntary eye movements), and markedly reduced or absent electrical responses on electroretinography. Individuals with SPATA7-related retinal disease generally experience progressive degeneration of both rod and cone photoreceptors, leading to severe visual disability from early childhood. The phenotype can vary in severity, with some individuals showing a slightly later onset or slower progression, but most affected individuals have significant lifelong visual impairment.
No disease links recorded for this gene in our reference set.
UK clinical status
SPATA7 is included on the NHS Genomic Medicine Service Retinal Disorders panel with green (definitive evidence) classification under version R32. This designation reflects robust clinical and research evidence linking the gene to inherited retinal disease, and confirms that SPATA7 testing is appropriate for individuals presenting with early-onset retinal dystrophy or suspected Leber congenital amaurosis within NHS diagnostic pathways.
Sources: NHS GMS PanelApp · Genomics England PanelApp · NHS National Genomic Test Directory
Frequently asked questions
What does SPATA7 stand for?
SPATA7 stands for spermatogenesis associated 7. Despite the name suggesting a role in male fertility, the gene's primary clinical significance relates to retinal function, where it is essential for photoreceptor cell structure in the eye.
How is SPATA7-related retinal disease inherited?
SPATA7-related retinal disease follows an autosomal recessive inheritance pattern. An individual must inherit two pathogenic variants, one from each parent, to develop the condition. Carriers with one pathogenic variant typically have normal vision.
At what age do symptoms of SPATA7-related retinal disease usually appear?
Symptoms typically appear in infancy or early childhood, often within the first year of life. Affected individuals may present with severe visual impairment, nystagmus, and lack of visual responsiveness from a very early age.