SPATA6
protein-codingspermatogenesis associated 6
Gene summary
Predicted to enable myosin light chain binding activity. Predicted to be involved in motile cilium assembly and spermatogenesis. Predicted to be located in extracellular region and motile cilium. Predicted to be active in sperm head-tail coupling apparatus. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~176.8 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 SPATA6 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_019073.4. 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 | 81 | 81 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 85 | 1 | 0 | 86 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_061946.1 | 13 | MANE Select | |
| Ensembl | ENSP00000360913.3 | 13 | MANE Select | |
| RefSeq | NP_001273167.1 | 13 | Standard | |
| RefSeq | NP_001273168.1 | 12 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- multicellular organism development
- spermatogenesis
- cell differentiation
- motile cilium assembly
Molecular Function
- myosin light chain binding
Cellular Component
- extracellular region
- sperm connecting piece
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000371847
- Coding exons
- 13
- Length
- 176802
- Individuals with no LoFs
- 125661
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 86
- Defined
- 125748
- p
- 0.000346
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.199 | 251 | 260 | 0.965 | 0.0000137 | 3167 |
| Missense (PolyPhen) | 153 | 153.59 | 0.99618 | 1899 | ||
| Synonymous | 1.15 | 83 | 97.5 | 0.851 | 0.00000539 | 900 |
| Loss of Function | -0.411 | 30 | 27.7 | 1.08 | 0.00000149 | 360 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.00077 | 0.00072 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00044 | 0.00044 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00033 | 0.00033 | rare |
| South Asian | 0.00037 | 0.00033 | rare |
| Other | 0.00053 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Required for formation of the sperm connecting piece during spermiogenesis. Sperm connecting piece is essential for linking the developing flagellum to the head during late spermiogenesis. May be involved in myosin-based microfilament transport through interaction with myosin subunits. {ECO:0000250|UniProtKB:Q3U6K5}.;
Recessive Scores
- pRec
- 0.104
Intolerance Scores
- LoFtool
- 0.962
- RVIS EVS
- -0.31
- RVIS percentile EVS
- 32.15
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.240
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | High |