SPACA9
protein-codingsperm acrosome associated 9
Gene summary
Enables microtubule binding activity. Involved in axoneme assembly. Located in axonemal microtubule; cytosol; and sperm end piece. [provided by Alliance of Genome Resources, Jun 2026]
- C9orf9
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~12.2 kbGenCC 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 SPACA9 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001316897.2. 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 | 1 | 1 | ||||
| missense | 4 | 4 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 5 | 0 | 0 | 5 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001303826.1 | 3 | MANE Select | |
| Ensembl | ENSP00000348659.5 | 3 | MANE Select | |
| RefSeq | NP_001303827.1 | 3 | Standard | |
| RefSeq | NP_001303829.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Molecular Function
- protein binding
- calcium-dependent protein binding
Cellular Component
- acrosomal vesicle
- nucleus
- cytoplasmic microtubule
- ciliary basal body
- sperm flagellum
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000350499
- Coding exons
- 4
- Length
- 12175
- Individuals with no LoFs
- 125631
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 117
- Defined
- 125748
- p
- 0.000465
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.362 | 118 | 107 | 1.10 | 0.00000680 | 1119 |
| Missense (PolyPhen) | 53 | 44.598 | 1.1884 | 447 | ||
| Synonymous | -0.377 | 50 | 46.7 | 1.07 | 0.00000339 | 305 |
| Loss of Function | 0.298 | 7 | 7.90 | 0.886 | 4.33e-7 | 88 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00043 | 0.00043 | rare |
| Latino/Admixed American | 0.0012 | 0.0012 | notable |
| Ashkenazi Jewish | 0.0019 | 0.0019 | notable |
| East Asian | 0.00016 | 0.00016 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00032 | 0.00032 | rare |
| South Asian | 0.00016 | 0.00016 | rare |
| Other | 0.0010 | 0.00098 | notable |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.101
Intolerance Scores
- RVIS EVS
- -0.43
- RVIS percentile EVS
- 25.15
Essentials
- Essential (gene trap)
- N