SPAG11A
protein-codingsperm associated antigen 11A
Gene summary
Involved in antimicrobial humoral immune response mediated by antimicrobial peptide. Predicted to be located in extracellular region. [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 ~21.0 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 SPAG11A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001395484.1. 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 | 1 | 1 | ||||
| missense | 6 | 1 | 7 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 6 | 2 | 0 | 8 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001382413.1 | 3 | MANE Select | |
| Ensembl | ENSP00000496500.1 | 3 | MANE Select | |
| RefSeq | NP_001075021.2 | 4 | Standard | |
| RefSeq | NP_001350655.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- defense response to bacterium
- antimicrobial humoral immune response mediated by antimicrobial peptide
Cellular Component
- extracellular region
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000326558
- Coding exons
- 4
- Length
- 20992
- Individuals with no LoFs
- 124260
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 8
- Defined
- 124268
- p
- 0.0000322
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.142 | 37 | 34.7 | 1.07 | 0.00000185 | 654 |
| Missense (PolyPhen) | 10 | 9.723 | 1.0285 | 189 | ||
| Synonymous | -0.299 | 12 | 10.8 | 1.12 | 4.96e-7 | 211 |
| Loss of Function | -1.29 | 5 | 2.71 | 1.84 | 1.14e-7 | 58 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000091 | 0.000088 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.0000099 | 0.0000089 | rare |
| South Asian | 0.00016 | 0.00013 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May have antimicrobial activity. May also play a role sperm maturation, storage, and protection. {ECO:0000250|UniProtKB:Q8VBV2}.;
Essentials
- Essential (CRISPR)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.178