SPATA21
protein-codingspermatogenesis associated 21, the group of EF-hand domain containing
Gene summary
Predicted to enable calcium ion binding activity. [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 ~50.3 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 SPATA21 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_198546.1. 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 | 0 | |||||
| missense | 71 | 7 | 78 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 71 | 7 | 0 | 78 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_940948.1 | 11 | MANE Select | |
| Ensembl | ENSP00000335612.1 | 11 | MANE Select | |
| RefSeq | NP_001340278.1 | 9 | Standard | |
| Ensembl | ENSP00000364727.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Molecular Function
- calcium ion binding
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000335496
- Coding exons
- 11
- Length
- 50308
- Individuals with no LoFs
- 125647
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 99
- Defined
- 125746
- p
- 0.000394
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.00793 | 274 | 274 | 1.00 | 0.0000161 | 3022 |
| Missense (PolyPhen) | 37 | 47.332 | 0.78171 | 643 | ||
| Synonymous | -0.806 | 121 | 110 | 1.10 | 0.00000652 | 933 |
| Loss of Function | -0.328 | 25 | 23.3 | 1.07 | 0.00000109 | 271 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00037 | 0.00037 | rare |
| Latino/Admixed American | 0.00079 | 0.00078 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00093 | 0.00092 | rare |
| Finnish | 0.000093 | 0.000092 | rare |
| European (Non-Finnish) | 0.00031 | 0.00031 | rare |
| South Asian | 0.00033 | 0.00033 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in the differentiation of haploid spermatids. {ECO:0000250}.;
Intolerance Scores
- LoFtool
- 0.882
- RVIS EVS
- 1.31
- RVIS percentile EVS
- 94.04
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0665
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |