CWC27

protein-coding

CWC27 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]

Previous symbols:
  • SDCCAG10

MANE transcript

NM_005869.4

Inheritance

AR

ClinVar variants

P:47U:169B:73

Top phenotype

Retinitis pigmentosa with or without skeletal anomalies

gnomAD constraint

pLI —, LoF o/e 0.57

Max pathogenic AF

—

Genomic locus

chr5:64,766,368-65,102,412

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~336.0 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

metaphyseal chondrodysplasia-retinitis pigmentosa syndromeDEFINITIVE

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).

metaphyseal chondrodysplasia-retinitis pigmentosa syndromeDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009598

Submitter: G2P

metaphyseal chondrodysplasia-retinitis pigmentosa syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009598

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Retinitis pigmentosa with or without skeletal anomaliesAR

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

Refs: 28285769Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CWC27 variants in ClinVar

8 Conditions Cataloged
not providedTotal: 369
Inborn genetic diseasesTotal: 51
Metaphyseal chondrodysplasia-retinitis pigmentosa syndromeTotal: 20
CWC27-related disorderTotal: 13
Retinal dystrophyTotal: 10
not specifiedTotal: 3
Retinitis pigmentosaTotal: 2
Optic atrophyTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
clinvar
67
clinvar
2
clinvar
71
missense
157
clinvar
4
clinvar
161
nonsense
11
clinvar
1
clinvar
12
start loss
0
frameshift
15
clinvar
8
clinvar
3
clinvar
26
splice donor/acceptor (+/-2bp)
1
clinvar
11
clinvar
7
clinvar
19
Total2819169712289

Highest pathogenic variant AF is 0.000024589397

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 40 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_005869.4RefSeqNP_005860.214MANE Select
ENST00000381070.8EnsemblENSP00000370460.214MANE Select
NM_001297644.1RefSeqNP_001284573.113Standard
NM_001297645.2RefSeqNP_001284574.111Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.7621932250.8570.00001133109
Missense (PolyPhen)6082.0880.730921096
Synonymous1.416075.60.7930.00000369802
Loss of Function1.941424.40.5750.00000114360

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000510.00049rare
Latino/Admixed American0.0000700.000058rare
Ashkenazi Jewish00.0absent
East Asian0.000230.00022rare
Finnish0.000140.00014rare
European (Non-Finnish)0.000170.00017rare
South Asian0.0000680.000065rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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