CWC27
protein-codingCWC27 spliceosome associated cyclophilin, the group of Cyclophilin peptidylprolyl isomerases|Spliceosomal C complex|Spliceosomal Bact complex|Spliceosomal P complex|NTC associated proteins
Gene summary
Predicted to enable peptidyl-prolyl cis-trans isomerase activity. Predicted to be involved in mRNA splicing, via spliceosome. Located in nucleoplasm. Part of U2-type precatalytic spliceosome and catalytic step 2 spliceosome. [provided by Alliance of Genome Resources, Jun 2026]
- SDCCAG10
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~336.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0009598
Submitter: ClinGen
*CWC27* was first reported in relation to retinitis pigmentosa with or without skeletal anomalies in 2017 (Xu et al., PMID: 28285769). Metaphyseal chondrodysplasia-retinitis pigmentosa syndrome is characterized by retinal degeneration (average onset of night blindness of 10 years of age, followed by restriction of visual fields), brachydactyly (affects primarily the distal phalanges), craniofacial abnormalities (include frontal bossing, downslanting palpebral fissures, large columella, hypoplastic nares, micrognathia, and large low-set ears), short stature, and neurologic defects. Per criteria outlined by the ClinGen Lumping & Splitting Working Group, no differences were found in molecular mechanism (loss-of-function) and inheritance pattern (autosomal recessive) among the reported cases with or without skeletal features. As a result, diverse cases have been curated under the lumped disease term *CWC27*-related retinopathy with or without syndromic features. This curation includes ten variants (five nonsense, three frameshift, and two disrupting splicing) that have collectively been reported in ten probands in four publications (PMID: 28285769, PMID: 36718996, PMID: 31481716, PMID: 34828430). The variants segregated fully with disease, and were not found in the heterozygous state. The mechanism of pathogenicity is reported to be loss-of-function. This gene-disease association is also supported by experimental evidence. CWC27 encodes a member of the cyclophilin family of peptidyl-prolyl cis-trans isomerases. However, the N-terminal peptidyl-prolyl isomerase domain lacks catalytic activity due to its lack of a conserved active-site tryptophan, and is instead predicted to be a proline-binding protein. Three mouse models have been created; *Cwc27K338fs/K338fs* and two versions of *Cwc27* knockout, where all three models recapitulated the ocular phenotypes observed in human subjects (PMID: 28285769). The *Cwc27K338fs/K338fs* mouse, which carried the equivalent of the hypomorphic C-terminally truncating human allele p.Val335Serfs13, showed late onset ocular defects with no significant embryonic lethality compared to the more severe phenotype observed in the two *Cwc27* knockout mouse models (high embryonic lethality, growth retardation, ocular defects, and craniofacial/limb defects). The decreased severity of the phenotype may be explained by incomplete loss of expression of *Cwc27* (PMID: 28285769). In summary, *CWC27* is Definitively associated with *CWC27*-related retinopathy with or without syndromic features. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time without the emergence of conflicting evidence. This classification was approved by the ClinGen Retina Gene Curation Expert Panel on July 3rd, 2025 (SOP Version 11).
Inheritance Pattern: AR
Disease ID:MONDO:0009598
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0009598
Submitter: Labcorp Genetics (formerly Invitae)
Clinical Genomic Database (CGD)
Manifestation: Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CWC27 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_005869.4. 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 | 1 | 1 | 67 | 2 | 71 | |
| missense | 157 | 4 | 161 | |||
| nonsense | 11 | 1 | 12 | |||
| start loss | 0 | |||||
| frameshift | 15 | 8 | 3 | 26 | ||
| splice donor/acceptor (+/-2bp) | 1 | 11 | 7 | 19 | ||
| Total | 28 | 19 | 169 | 71 | 2 | 289 |
Highest pathogenic variant AF is 0.000024589397
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005860.2 | 14 | MANE Select | |
| Ensembl | ENSP00000370460.2 | 14 | MANE Select | |
| RefSeq | NP_001284573.1 | 13 | Standard | |
| RefSeq | NP_001284574.1 | 11 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Metabolism of RNA
- mRNA Splicing - Major Pathway
- mRNA Splicing
- Processing of Capped Intron-Containing Pre-mRNA
Biological Process
- mRNA splicing, via spliceosome
- protein peptidyl-prolyl isomerization
- protein folding
Molecular Function
- peptidyl-prolyl cis-trans isomerase activity
- cyclosporin A binding
Cellular Component
- nucleus
- nucleoplasm
- catalytic step 1 spliceosome
- catalytic step 2 spliceosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000381070
- Coding exons
- 14
- Length
- 249834
- Individuals with no LoFs
- 125710
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 38
- Defined
- 125748
- p
- 0.000151
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.762 | 193 | 225 | 0.857 | 0.0000113 | 3109 |
| Missense (PolyPhen) | 60 | 82.088 | 0.73092 | 1096 | ||
| Synonymous | 1.41 | 60 | 75.6 | 0.793 | 0.00000369 | 802 |
| Loss of Function | 1.94 | 14 | 24.4 | 0.575 | 0.00000114 | 360 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00051 | 0.00049 | rare |
| Latino/Admixed American | 0.000070 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00023 | 0.00022 | rare |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.00017 | 0.00017 | rare |
| South Asian | 0.000068 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: As part of the spliceosome, plays a role in pre-mRNA splicing (PubMed:29360106). Probable inactive PPIase with no peptidyl-prolyl cis-trans isomerase activity (PubMed:20676357). {ECO:0000269|PubMed:20676357, ECO:0000269|PubMed:29360106}.;
- Disease
- DISEASE: Retinitis pigmentosa with or without skeletal anomalies (RPSKA) [MIM:250410]: An autosomal recessive disease characterized by retinal degeneration, brachydactyly, short stature, craniofacial dysmorphism, and neurologic defects. Retinal defects are consistent with retinitis pigmentosa in most patients. Neurologic manifestations include mild-to-moderate intellectual disability and psychomotor retardation. {ECO:0000269|PubMed:28285769}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Intolerance Scores
- LoFtool
- 0.843
- RVIS EVS
- -0.29
- RVIS percentile EVS
- 33.2
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.283
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |