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Comprehensive Research Report: CWC27 (SDCCAG10) Gene Function and Annotation

Gene Identity and Nomenclature

CWC27 (gene symbol: CWC27, UniProt: Q6UX04) encodes the spliceosome-associated protein CWC27 homolog in humans (rajiv2018structuralandfunctional pages 1-3). The protein is also known by several alternative names, including SDCCAG10 (Serologically Defined Colon Cancer Antigen 10), NY-CO-10, and Cyp54 (rajiv2018structuralandfunctional pages 1-3, jurkova2026humancyclophilins—anemerging pages 1-2). CWC27 belongs to the cyclophilin-type peptidyl-prolyl isomerase (PPIase) family and is classified among the eight human nuclear cyclophilins, also referred to as "spliceophilins" due to their association with the spliceosome (rajiv2018structuralandfunctional pages 1-3).

Protein Structure and Domains

Overall Architecture

The CWC27 protein consists of two distinct structural regions: an N-terminal cyclophilin-like domain (CLD) containing the characteristic PPIase fold, and a large C-terminal region composed of low-complexity, repetitive sequences (rajiv2018structuralandfunctional pages 1-3, rajiv2018structuralandfunctional pages 10-14). The N-terminal domain (~183 amino acids) adopts the canonical cyclophilin fold characterized by eight antiparallel β-sheets and two α-helices (rajiv2018structuralandfunctional pages 1-3). In contrast, the C-terminal extension (approximately 200 residues) is elongated, solvent-exposed, and largely unstructured, with its detailed function remaining incompletely characterized (rajiv2018structuralandfunctional pages 10-14, bertrand2022cwc27associatedwith pages 2-4).

Domain Organization and Functional Implications

The cyclophilin-like domain contains the conserved proline-binding pocket characteristic of the cyclophilin family. However, structural analysis reveals that CWC27 has undergone a critical substitution in the active site. While canonical cyclophilins possess a tryptophan residue (Trp121 in the reference cyclophilin PPIA) that is essential for catalytic activity, CWC27 harbors a glutamic acid substitution at position 122 (Glu122) in the S1 proline-binding pocket (rajiv2018structuralandfunctional pages 10-14, davis2010structuralandbiochemical pages 3-4). This substitution is key to understanding CWC27's non-catalytic function.

Molecular Function: An Inactive Cyclophilin

Lack of Peptidyl-Prolyl Isomerase Activity

Despite belonging to the cyclophilin family, CWC27 is catalytically inactive as a peptidyl-prolyl cis-trans isomerase (davis2010structuralandbiochemical pages 1-2, davis2010structuralandbiochemical pages 3-4, bertrand2022cwc27associatedwith pages 2-4). Comprehensive biochemical characterization of the human cyclophilin family demonstrated that CWC27 (SDCCAG10) lacks measurable PPIase activity against standard tetrapeptide substrates, a finding that distinguishes it from most other cyclophilins (davis2010structuralandbiochemical pages 1-2, davis2010structuralandbiochemical pages 3-4). This loss of catalytic function is directly attributable to the Glu122 substitution in the active site, which renders the enzyme incompetent for proline isomerization (rajiv2018structuralandfunctional pages 10-14).

Substrate Binding Capabilities

While CWC27 cannot catalyze prolyl isomerization, it retains the ability to bind proline-containing peptides (rajiv2018structuralandfunctional pages 10-14, bertrand2022cwc27associatedwith pages 2-4). This preserved binding capacity, despite loss of catalytic activity, suggests that CWC27 functions primarily through protein-protein interactions rather than enzymatic catalysis (breafernandez2019expandingtheclinical pages 1-3, bertrand2022cwc27associatedwith pages 2-4). Family-wide ligand binding studies confirm that CWC27 does not bind cyclosporin A (CsA), the canonical cyclophilin inhibitor, consistent with its altered active site architecture (davis2010structuralandbiochemical pages 3-4).

Cellular Localization

CWC27 is localized to the nucleus and cytosol, with its primary functional activity occurring in the nuclear compartment (jurkova2026humancyclophilins—anemerging pages 1-2). Consistent with other nuclear cyclophilins involved in splicing, CWC27 localizes to nuclear speckles, subnuclear domains enriched in splicing factors and pre-mRNA processing machinery (rajiv2018structuralandfunctional pages 1-3). This nuclear localization is essential for its role in pre-mRNA splicing and spliceosome function.

Role in Pre-mRNA Splicing and the Spliceosome

Integration into the Spliceosome Cycle

CWC27 functions as a splicing factor within the major spliceosome, the large ribonucleoprotein complex responsible for removing introns from precursor messenger RNAs (rajiv2018structuralandfunctional pages 1-3, bertrand2022cwc27associatedwith pages 1-2, wan2020howisprecursor pages 1-2). The spliceosome undergoes dynamic assembly through sequential stages: assembly (E, A, pre-B, B complexes), activation (Bact complex), catalysis (B, C, C complexes), and disassembly (P, ILS complexes) (wan2020howisprecursor pages 1-2). CWC27 is specifically enriched in the activated Bact spliceosome and is present with moderate abundance in the C complex, but is released prior to the stable formation of the B* complex (rajiv2018structuralandfunctional pages 10-14, zhan2024molecularbasisfor pages 1-2, wan2020howisprecursor pages 8-10).

Structural Positioning within the Spliceosome

Cryo-electron microscopy (cryo-EM) structures of human spliceosomes at near-atomic resolution have revealed the precise positioning of CWC27 within the Bact complex (rajiv2018structuralandfunctional pages 10-14, zhan2024molecularbasisfor pages 1-2, schmitzova2023structuralbasisof pages 1-2). In these structures, the cyclophilin-like domain of CWC27 makes contacts with several spliceosomal components, including PRPF8 (a central scaffolding protein), BUD31, RNF113 (RING finger protein 113), and U5 snRNP 200 kDa helicase (rajiv2018structuralandfunctional pages 10-14). These interactions position CWC27 at the spliceosome surface where it can coordinate recruitment and remodeling of additional factors during activation.

Interaction with CWC22 and EJC Assembly

A critical function of CWC27 is its formation of a heterodimer with CWC22, another spliceosomal protein (bertrand2022cwc27associatedwith pages 1-2, bertrand2022cwc27associatedwith pages 2-4, schlautmann2020adayin pages 3-5). The CWC27–CWC22 complex serves as a landing platform for recruiting eIF4A3, the DEAD-box RNA helicase that forms the core of the exon junction complex (EJC) (schlautmann2020adayin pages 1-3, schlautmann2020adayin pages 3-5). The EJC is a multi-protein complex deposited on mRNAs approximately 20-24 nucleotides upstream of exon-exon junctions following splicing, and it plays essential roles in downstream mRNA metabolism including export, translation, and nonsense-mediated decay (schlautmann2020adayin pages 1-3).

The sequential recruitment model proposes that CWC22 initially binds to the spliceosome alone, followed by CWC27 association to form the CWC27/CWC22 heterodimer, which then recruits eIF4A3 (schlautmann2020adayin pages 3-5). Following eIF4A3 recruitment, CWC27 dissociates from the spliceosome before complete EJC assembly, as its continued presence would sterically clash with RBM8A, another EJC core component (schlautmann2020adayin pages 3-5). This step-wise assembly pathway highlights CWC27's role as a transient assembly factor rather than a permanent spliceosome component.

Mechanistic Role in Spliceosome Activation

During the transition from the pre-catalytic B complex to the catalytically activated B* complex, the spliceosome undergoes extensive remodeling driven by ATP-dependent RNA helicases (wan2020howisprecursor pages 1-2, zhan2024molecularbasisfor pages 1-2, schmitzova2023structuralbasisof pages 1-2). CWC27 participates in this critical activation stage. Structural studies from 2023-2024 have provided detailed molecular choreography of this process. In the Bact complex, the branch site (BS) of the pre-mRNA is sequestered approximately 50 Å away from the 5' splice site and shielded by proteins including CWC27 (schmitzova2023structuralbasisof pages 1-2, wan2020howisprecursor pages 8-10). The DEAH-box helicase PRP2, assisted by its co-activator SPP2, pulls on the 3' end of the intron, leading to dissociation of the SF3a/SF3b complexes, RES complex, and importantly, both CWC24 and CWC27 (schmitzova2023structuralbasisof pages 1-2, wan2020howisprecursor pages 8-10). This remodeling allows the branch site to move into proximity with the 5' splice site for catalysis.

Recent 2024 studies capturing six intermediate states between B and B* complexes (pre-Bact, Bact-I, Bact-II, Bact-III, Bact-IV, and post-Bact) demonstrate that CWC27 is present in earlier Bact states but absent in later post-Bact intermediates, confirming its release during this critical transition (zhan2024molecularbasisfor pages 1-2).

In Vivo Functional Evidence

Mouse Model Validation

While CWC27's role in splicing was inferred from in vitro biochemical studies and structural analyses, direct in vivo validation came from studies of a mouse model carrying a frameshift mutation (Cwc27K338fs/K338fs) (bertrand2022cwc27associatedwith pages 1-2, bertrand2022cwc27associatedwith pages 4-6, bertrand2022cwc27associatedwith pages 2-4). This mouse model exhibits progressive retinal degeneration, with retinal dysfunction detectable by electroretinography at 3 months of age and photoreceptor loss evident at 4 months (bertrand2022cwc27associatedwith pages 2-4).

Splicing Defects in the Mutant Retina

RNA-sequencing analysis of the Cwc27K338fs/K338fs mouse retina provided the first direct evidence that CWC27 functions as a splicing factor in vivo (bertrand2022cwc27associatedwith pages 1-2, bertrand2022cwc27associatedwith pages 4-6). Compared to wild-type controls, the mutant retina exhibited 257 differential splicing events, with the most abundant defects being intron retention followed by exon skipping (bertrand2022cwc27associatedwith pages 4-6). These splicing pattern changes are consistent with those observed in other splicing factor-associated disease models, including retinitis pigmentosa caused by mutations in PRPF31, PRPF8, and other core spliceosomal components (bertrand2022cwc27associatedwith pages 1-2).

Gene ontology analysis revealed that differentially spliced genes in the mutant retina were enriched for visual physiology pathways and included several inherited retinal disease genes such as Cnga1 (cyclic nucleotide-gated channel alpha 1), Prpf6 (pre-mRNA processing factor 6), and Rpgrip1 (retinitis pigmentosa GTPase regulator interacting protein 1) (bertrand2022cwc27associatedwith pages 4-6). Single-cell RNA-sequencing demonstrated that rod photoreceptors and Müller glial cells showed the largest number of differentially expressed genes, with rod photoreceptors exhibiting downregulation of mitochondrial transcripts and Müller cells showing upregulation of inflammatory genes (bertrand2022cwc27associatedwith pages 4-6).

Disease Mechanism

The mouse model studies suggest that CWC27 loss leads to aberrant splicing, which in turn activates endoplasmic reticulum (ER) stress pathways, as evidenced by positive CHOP staining in the mutant retina (bertrand2022cwc27associatedwith pages 1-2, bertrand2022cwc27associatedwith pages 4-6). This ER stress response likely contributes to the progressive photoreceptor degeneration observed in the model. Importantly, the disease mechanism appears to stem from defective splicing rather than loss of cyclophilin enzymatic activity, given that CWC27 lacks PPIase activity (bertrand2022cwc27associatedwith pages 1-2, bertrand2022cwc27associatedwith pages 2-4).

Disease Associations: CWC27-Related Spliceosomopathy

Human Genetic Disorders

Biallelic deleterious variants in CWC27 cause a rare autosomal recessive condition classified as a spliceosomopathy (griffin2020spliceosomopathiesdiseasesand pages 1-7, breafernandez2019expandingtheclinical pages 1-3). The phenotypic spectrum includes retinal degeneration/retinitis pigmentosa as the cardinal feature, along with variable additional manifestations such as short stature, skeletal anomalies (including brachydactyly), neurological defects, hypergonadotropic hypogonadism, dental anomalies, and cataracts (griffin2020spliceosomopathiesdiseasesand pages 1-7, breafernandez2019expandingtheclinical pages 1-3).

Spliceosomopathies as a Disease Class

CWC27-related disorders belong to the broader category of spliceosomopathies, diseases caused by mutations in genes encoding spliceosome components (griffin2020spliceosomopathiesdiseasesand pages 1-7). A striking feature of spliceosomopathies is their tissue specificity despite the ubiquitous expression of spliceosomal proteins. For example, mutations in PRPF31, PRPF8, PRPF6, and SNRNP200 predominantly cause retinitis pigmentosa, while mutations in other spliceosomal genes cause myelodysplastic syndromes or craniofacial disorders such as mandibulofacial dysostosis (griffin2020spliceosomopathiesdiseasesand pages 1-7). The mechanisms underlying this tissue specificity remain an active area of investigation, but likely involve differential sensitivity of specific cell types to splicing perturbations, with photoreceptors being particularly vulnerable (bertrand2022cwc27associatedwith pages 1-2, griffin2020spliceosomopathiesdiseasesand pages 1-7).

Recent Developments (2023-2024)

Structural Biology Advances

Major advances in understanding CWC27 function have come from recent cryo-EM structural studies. Schmitzová et al. (2023) reported structures of the BAQR spliceosome, an intermediate stalled between PRP2 and Aquarius helicase actions, providing unprecedented detail on CWC27's interactions during catalytic activation (schmitzova2023structuralbasisof pages 1-2). Zhan et al. (2024) captured six distinct intermediate states of the human Bact complex, revealing the molecular choreography of spliceosome activation and the ordered flux of components including CWC27 (zhan2024molecularbasisfor pages 1-2).

Functional Genomics Insights

Rogalska et al. (2024) conducted transcriptome-wide analysis of splicing networks following systematic knockdown of 305 spliceosome components and regulators in human cancer cells. This study revealed that CWC27 knockdown, which links to exon junction complex assembly, produces specific splicing regulatory effects, confirming its specialized function within the core spliceosome machinery.

Therapeutic Implications

A comprehensive 2026 review by Jurkova et al. discusses human cyclophilins as an emerging class of drug targets (jurkova2026humancyclophilins—anemerging pages 1-2, jurkova2026humancyclophilins—anemerging pages 9-11). While CWC27's lack of PPIase activity makes it an unlikely target for traditional cyclophilin inhibitors like cyclosporin derivatives, understanding its role in splicing could inform therapeutic strategies for CWC27-related spliceosomopathies and potentially for modulating splicing in other disease contexts.

Summary Table of Key Properties

Table: This table summarizes the key molecular, biochemical, cellular, and disease-related properties of human CWC27 from the cited literature. It highlights why CWC27 is best understood as a catalytically inactive spliceosomal cyclophilin that helps organize splicing and EJC recruitment, with strong links to retinal degeneration.

Conclusions

CWC27 represents a fascinating example of molecular evolution within the cyclophilin family. Despite lacking catalytic peptidyl-prolyl isomerase activity due to a critical active site substitution (Glu122), CWC27 has been repurposed as a structural and scaffolding component of the spliceosome. Its primary function is to facilitate recruitment of the exon junction complex during pre-mRNA splicing through formation of a transient landing platform with CWC22. Loss of CWC27 function leads to widespread splicing defects, particularly intron retention and exon skipping, which cause tissue-specific pathology most prominently affecting the retina. The recent structural and functional characterization of CWC27 highlights the complexity of spliceosome assembly and the critical importance of non-catalytic factors in orchestrating this essential cellular process.

Key Research Papers (with URLs and dates):

1. Davis et al. (2010) - Structural and Biochemical Characterization of the Human Cyclophilin Family. PLoS Biology 8(7):e1000439. https://doi.org/10.1371/journal.pbio.1000439

2. Rajiv & Davis (2018) - Structural and Functional Insights into Human Nuclear Cyclophilins. Biomolecules 8(4):161. https://doi.org/10.3390/biom8040161

3. Brea-Fernández et al. (2019) - Expanding the clinical and molecular spectrum of the CWC27-related spliceosomopathy. Journal of Human Genetics 64:1133-1136. https://doi.org/10.1038/s10038-019-0664-7

4. Griffin & Saint-Jeannet (2020) - Spliceosomopathies: Diseases and mechanisms. Developmental Dynamics 249:1038-1046. https://doi.org/10.1002/dvdy.214

5. Wan et al. (2020) - How Is Precursor Messenger RNA Spliced by the Spliceosome? Annual Review of Biochemistry 89:333-358. https://doi.org/10.1146/annurev-biochem-013118-111024

6. Schlautmann & Gehring (2020) - A Day in the Life of the Exon Junction Complex. Biomolecules 10(6):866. https://doi.org/10.3390/biom10060866

7. Bertrand et al. (2022) - Cwc27, associated with retinal degeneration, functions as a splicing factor in vivo. Human Molecular Genetics 31(8):1278-1292. https://doi.org/10.1093/hmg/ddab319

8. Schmitzová et al. (2023) - Structural basis of catalytic activation in human splicing. Nature 617:842-850. https://doi.org/10.1038/s41586-023-06049-w (Published May 2023)

9. Zhan et al. (2024) - Molecular basis for the activation of human spliceosome. Nature Communications 15:6348. https://doi.org/10.1038/s41467-024-50785-0 (Published July 2024)

10. Rogalska et al. (2024) - Transcriptome-wide splicing network reveals specialized regulatory functions of the core spliceosome. Science 386(6721):551-560. https://doi.org/10.1126/science.adn8105 (Published November 2024)

11. Jurkova et al. (2026) - Human Cyclophilins—An Emerging Class of Drug Targets. Medicinal Research Reviews 46(2):475-512. https://doi.org/10.1002/med.70021 (Published October 2025, volume dated 2026)

References

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2. (jurkova2026humancyclophilins—anemerging pages 1-2): Katarina Jurkova, Hana Navratilova, Kamil Musilek, and Ondrej Benek. Human cyclophilins—an emerging class of drug targets. Medicinal Research Reviews, 46:475-512, Oct 2026. URL: https://doi.org/10.1002/med.70021, doi:10.1002/med.70021. This article has 1 citations and is from a domain leading peer-reviewed journal.

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8. (bertrand2022cwc27associatedwith pages 1-2): Renae Elaine Bertrand, Jun Wang, Yumei Li, Xuesen Cheng, Keqing Wang, Peter Stoilov, and Rui Chen. Cwc27, associated with retinal degeneration, functions as a splicing factor in vivo. Human molecular genetics, 31:1278-1292, Nov 2022. URL: https://doi.org/10.1093/hmg/ddab319, doi:10.1093/hmg/ddab319. This article has 19 citations and is from a domain leading peer-reviewed journal.

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Citations

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2. rajiv2018structuralandfunctional pages 10-14
3. davis2010structuralandbiochemical pages 3-4
4. wan2020howisprecursor pages 1-2
5. schlautmann2020adayin pages 1-3
6. schlautmann2020adayin pages 3-5
7. zhan2024molecularbasisfor pages 1-2
8. griffin2020spliceosomopathiesdiseasesand pages 1-7
9. schmitzova2023structuralbasisof pages 1-2
10. davis2010structuralandbiochemical pages 1-2
11. breafernandez2019expandingtheclinical pages 1-3
12. wan2020howisprecursor pages 8-10
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