SPATA13
protein-codingspermatogenesis associated 13, the group of Pleckstrin homology domain containing|MicroRNA protein coding host genes|Dbl family Rho GEFs
Gene summary
Enables guanyl-nucleotide exchange factor activity and identical protein binding activity. Involved in cell migration; plasma membrane bounded cell projection assembly; and regulation of cell migration. Located in several cellular components, including filopodium; lamellipodium; and ruffle membrane. [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 ~55.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0001868
Submitter: ClinGen
*SPATA13* was first reported in relation to autosomal dominant primary angle closure glaucoma (PACG) in 2020 (Waseem et al., PMID: 32339198). PACG disorders include physical obstruction of the aqueous humor outflow channels, elevation of internal eye pressure, ocular hypertension, plateau iris configuration, iridocorneal angle closure, drainage angle damage, and end-organ glaucomatous damage. *SPATA13 *contains 1,339 amino acids and 14 exons, and functions as a guanine nucleotide exchange factor. There is only one disease assertion made for *SPATA13*; Primary Angle Closure Glaucoma (618880). Summary of Genetic Evidence (2.1 points): One 9-base-pair deletion was found in all affected individuals (n=12) from one family in one publication (PMID: 32339198). The mechanism of pathogenicity appears to be loss of function. Summary of Experimental Evidence (0 points): This gene-disease relationship is supported by an expression study (PMID: 32339198) revealing expression of SPATA13 in eye tissue including the human iris, ciliary epithelium, retinal pigment epithelium, retina and lens; however, the study also suggested a ubiquitous expression pattern of *SPATA13,* confirmed by GTex (https://gtexportal.org/home/gene/SPATA13). In summary, there is limited evidence to support this gene-disease relationship. Although more evidence is needed to support a causal role, no convincing evidence has emerged that contradicts the gene-disease relationship.
Inheritance Pattern: AD
Disease ID:MONDO:0001868
Submitter: PanelApp Australia
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SPATA13 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001166271.3. 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 | 2 | 10 | 12 | |||
| missense | 206 | 17 | 3 | 226 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 209 | 27 | 3 | 239 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001159743.1 | 12 | MANE Select | |
| Ensembl | ENSP00000371542.3 | 12 | MANE Select | |
| RefSeq | NP_001273721.1 | 14 | Standard | |
| RefSeq | NP_001273722.1 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Regulation of actin cytoskeleton - Homo sapiens (human)
- Regulation of RAC1 activity
- Regulation of CDC42 activity
Biological Process
- cell migration
- lamellipodium assembly
- regulation of cell migration
- regulation of Rho protein signal transduction
- filopodium assembly
Molecular Function
- guanyl-nucleotide exchange factor activity
- protein binding
- Rac guanyl-nucleotide exchange factor activity
Cellular Component
- nucleoplasm
- cytoplasm
- cytosol
- lamellipodium
- filopodium
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000424834
- Coding exons
- 12
- Length
- 327269
- Individuals with no LoFs
- 125720
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 28
- Defined
- 125748
- p
- 0.000111
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.03 | 636 | 797 | 0.798 | 0.0000500 | 8391 |
| Missense (PolyPhen) | 147 | 248.91 | 0.59057 | 2629 | ||
| Synonymous | 1.78 | 288 | 329 | 0.875 | 0.0000217 | 2551 |
| Loss of Function | 4.50 | 14 | 47.4 | 0.295 | 0.00000235 | 552 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0.00030 | 0.00030 | rare |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.00016 | 0.00016 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Acts as guanine nucleotide exchange factor (GEF) for RHOA, RAC1 and CDC42 GTPases. Regulates cell migration and adhesion assembly and disassembly through a RAC1, PI3K, RHOA and AKT1-dependent mechanism. Increases both RAC1 and CDC42 activity, but decreases the amount of active RHOA. Required for MMP9 up- regulation via the JNK signaling pathway in colorectal tumor cells. Involved in tumor angiogenesis and may play a role in intestinal adenoma formation and tumor progression. {ECO:0000269|PubMed:17145773, ECO:0000269|PubMed:17599059, ECO:0000269|PubMed:19151759, ECO:0000269|PubMed:19893577, ECO:0000269|PubMed:19934221}.;
Recessive Scores
- pRec
- 0.112
Intolerance Scores
- LoFtool
- 0.257
- RVIS EVS
- 2.01
- RVIS percentile EVS
- 97.67
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.214
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |