SPON1
protein-codingspondin 1
Gene summary
Predicted to be an extracellular matrix structural constituent. Predicted to be involved in cell adhesion. Predicted to act upstream of or within negative regulation of amyloid-beta formation; positive regulation of amyloid precursor protein catabolic process; and positive regulation of protein processing. Located in extracellular matrix and obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~305.4 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 SPON1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006108.4. 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 | 4 | 4 | ||||
| missense | 64 | 1 | 65 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 6 | 6 | ||||
| Total | 0 | 0 | 74 | 1 | 0 | 75 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006099.2 | 16 | MANE Select | |
| Ensembl | ENSP00000460236.1 | 16 | MANE Select | |
| Ensembl | ENSP00000553736.1 | 15 | Standard | |
| Ensembl | ENSP00000553736.1 | 15 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Post-translational protein modification
- Metabolism of proteins
- O-glycosylation of TSR domain-containing proteins
- O-linked glycosylation
Biological Process
- cell adhesion
- positive regulation of protein processing
- positive regulation of protein binding
- negative regulation of amyloid-beta formation
- positive regulation of amyloid precursor protein catabolic process
Molecular Function
- extracellular matrix structural constituent
- protein binding
- metal ion binding
- LBD domain binding
Cellular Component
- extracellular space
- endoplasmic reticulum lumen
- extracellular matrix
- collagen-containing extracellular matrix
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Cell adhesion protein that promotes the attachment of spinal cord and sensory neuron cells and the outgrowth of neurites in vitro. May contribute to the growth and guidance of axons in both the spinal cord and the PNS (By similarity). Major factor for vascular smooth muscle cell. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.235