SCAPER: S-Phase Cyclin A-Associated Protein in the Endoplasmic Reticulum
A gene encoding a cyclin A/CDK2-associated protein implicated in ciliopathy and intellectual disability
Gene Information Card
| Symbol | SCAPER |
|---|---|
| Full Name | S-phase cyclin A-associated protein in the endoplasmic reticulum |
| Gene Type | protein-coding |
| Chromosomal Location | 15q24.3 |
| NCBI Gene ID | 49855 ncbi.nlm.nih.gov/gene/49855 |
| Ensembl ID | ENSG00000140386 |
| UniProt ID | Q9BY12 |
| OMIM ID | 611611 |
| HGNC ID | 1307 |
| Aliases | C15orf3, FLJ11184, ZNF291 |
Description
SCAPER (S-phase cyclin A-associated protein in the endoplasmic reticulum) is a protein-coding gene located on chromosome 15q24.3. The encoded protein localizes to the endoplasmic reticulum and interacts with cyclin A and CDK2, playing a role in cell cycle regulation. Biallelic loss-of-function mutations in SCAPER cause autosomal recessive intellectual disability with or without retinitis pigmentosa and ciliopathy features. The gene is widely expressed, with highest levels in the brain and retina.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Intellectual disability, autosomal recessive 76 (MRT76) | Loss-of-function mutations impair cyclin A/CDK2 signaling and ciliary function | OMIM #618429; ClinVar |
| Retinitis pigmentosa with or without intellectual disability | Disruption of SCAPER leads to photoreceptor degeneration and ciliary defects | OMIM #618429; PubMed studies |
| Ciliopathy (nephronophthisis-like) | SCAPER mutations affect primary cilia assembly and function | Case reports in ClinVar |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Brain | 12.5 | Medium |
| Retina | 15.2 | Medium |
| Testis | 8.3 | Low |
| Kidney | 6.1 | Low |
| Liver | 4.7 | Low |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| HEK293 | 10.2 | Embryonic kidney cells |
| SH-SY5Y | 14.8 | Neuroblastoma cell line |
| ARPE-19 | 16.5 | Retinal pigment epithelium cells |
| HeLa | 9.1 | Cervical cancer cells |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.226C>T (p.Arg76*) | Nonsense | Rare | Loss of function; premature stop codon |
| c.1045_1046del (p.Leu349Glufs*2) | Frameshift | Rare | Loss of function; truncated protein |
| c.1684C>T (p.Arg562Trp) | Missense | Rare | Likely loss of function; disrupts cyclin A binding |
Mutation functional classification
Loss of Function (LOF)
Biallelic loss-of-function mutations (nonsense, frameshift, splice-site) cause autosomal recessive intellectual disability and retinitis pigmentosa by impairing SCAPER's role in cell cycle and cilia.
Gain of Function (GOF)
No gain-of-function mutations reported for SCAPER.
Dominant Negative (DN)
No dominant-negative mutations reported for SCAPER.
View complete mutation data：
Gene Ontology (GO)
Pathways
• Cell Cycle
• G1/S Transition (Reactome R-HSA-69202)
• Cilium Assembly (Reactome R-HSA-5620924)
Protein Summary
The SCAPER protein (UniProt Q9BY12) is a 1,267-amino-acid polypeptide that localizes to the endoplasmic reticulum and centrosome. It contains a cyclin A/CDK2-binding domain and a zinc finger domain. SCAPER interacts with cyclin A and CDK2 to regulate cell cycle progression at the G1/S transition. It also localizes to the base of primary cilia and is required for ciliogenesis. Loss of SCAPER leads to cell cycle defects and impaired ciliary function, underlying the neurological and retinal phenotypes.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| SCAPER Knockout HEK293 Cell Line | EDJ-KQ15184 | Human | 49855 | Details Get a Quote |
| SCAPER Knockout HCT 116 Cell Line | EDJ-KQ17926 | Human | 49855 | Details Get a Quote |
| SCAPER Knockout A-549 Cell Line | EDJ-KQ47976 | Human | 49855 | Details Get a Quote |
| SCAPER Knockout HeLa Cell Line | EDJ-KQ47977 | Human | 49855 | Details Get a Quote |
