CWC27

CWC27 spliceosome associated cyclophilin, the group of Cyclophilin peptidylprolyl isomerases|Spliceosomal C complex|Spliceosomal Bact complex|Spliceosomal P complex|NTC associated proteins

Basic information

Region (hg38): 5:64766367-65102412

Previous symbols: [ "SDCCAG10" ]

Links

ENSG00000153015NCBI:10283OMIM:617170HGNC:10664Uniprot:Q6UX04AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • metaphyseal chondrodysplasia-retinitis pigmentosa syndrome (Strong), mode of inheritance: AR
  • metaphyseal chondrodysplasia-retinitis pigmentosa syndrome (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Retinitis pigmentosa with or without skeletal anomaliesARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCraniofacial; Musculoskeletal; Neurologic; Ophthalmologic28285769

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CWC27 gene.

  • not provided (23 variants)
  • Metaphyseal chondrodysplasia-retinitis pigmentosa syndrome (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CWC27 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
3
clinvar
50
clinvar
3
clinvar
56
missense
134
clinvar
2
clinvar
2
clinvar
138
nonsense
8
clinvar
1
clinvar
9
start loss
0
frameshift
14
clinvar
1
clinvar
2
clinvar
17
inframe indel
2
clinvar
2
splice donor/acceptor (+/-2bp)
1
clinvar
8
clinvar
9
splice region
1
10
21
6
38
non coding
54
clinvar
13
clinvar
67
Total 23 9 141 106 19

Highest pathogenic variant AF is 0.0000197

Variants in CWC27

This is a list of pathogenic ClinVar variants found in the CWC27 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
5-64769116-G-A Metaphyseal chondrodysplasia-retinitis pigmentosa syndrome Benign (Jul 30, 2021)1255435
5-64769156-A-G Uncertain significance (Dec 18, 2023)1403669
5-64769160-ACATC-A Pathogenic (Aug 10, 2022)1441533
5-64769162-A-G Uncertain significance (Aug 09, 2022)970063
5-64769166-A-C Uncertain significance (Jul 17, 2023)1056737
5-64769178-C-T Uncertain significance (Jul 05, 2022)1489931
5-64769179-G-A Likely benign (Jul 03, 2022)2013633
5-64769189-G-A Likely pathogenic (Feb 27, 2022)2103908
5-64769196-C-T Likely benign (Dec 12, 2021)2061233
5-64769204-A-G Likely benign (Feb 24, 2022)1102934
5-64774673-G-T Likely benign (May 27, 2022)1999483
5-64774691-G-A Uncertain significance (Nov 01, 2022)1053548
5-64774697-T-C Likely benign (Dec 26, 2023)749565
5-64774701-A-G Uncertain significance (Jul 06, 2022)854246
5-64774704-C-G Uncertain significance (Jun 05, 2022)2150347
5-64774708-A-C Likely benign (Jan 21, 2024)1978499
5-64774719-T-C Uncertain significance (Oct 04, 2021)1007615
5-64774723-CAT-C Pathogenic (Jul 26, 2022)843649
5-64774724-A-C Uncertain significance (Jun 04, 2022)1444829
5-64774734-G-C Inborn genetic diseases Uncertain significance (Jun 29, 2023)2607427
5-64774742-G-T Pathogenic (Aug 09, 2022)1454227
5-64774747-T-C Likely benign (Jan 09, 2024)1643820
5-64774748-C-A Uncertain significance (Jul 21, 2022)1059307
5-64774748-C-T Uncertain significance (Jul 19, 2022)1360521
5-64774764-A-AT Pathogenic (Nov 26, 2022)2816802

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CWC27protein_codingprotein_codingENST00000381070 14249834
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
4.56e-70.9581257100381257480.000151
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.7621932250.8570.00001133109
Missense in Polyphen6082.0880.730921096
Synonymous1.416075.60.7930.00000369802
Loss of Function1.941424.40.5750.00000114360

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0005780.000562
Ashkenazi Jewish0.000.00
East Asian0.0002250.000217
Finnish0.0001390.000139
European (Non-Finnish)0.0001710.000167
Middle Eastern0.0002250.000217
South Asian0.00006810.0000653
Other0.000.00

dbNSFP

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.;
Pathway
Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Intolerance Scores

loftool
0.843
rvis_EVS
-0.29
rvis_percentile_EVS
33.2

Haploinsufficiency Scores

pHI
0.0721
hipred
N
hipred_score
0.436
ghis
0.613

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.283

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Cwc27
Phenotype
reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process
mRNA splicing, via spliceosome;protein peptidyl-prolyl isomerization;protein folding
Cellular component
nucleus;nucleoplasm;catalytic step 1 spliceosome;catalytic step 2 spliceosome
Molecular function
peptidyl-prolyl cis-trans isomerase activity;cyclosporin A binding