CWC27
Basic information
Region (hg38): 5:64766367-65102412
Previous symbols: [ "SDCCAG10" ]
Links
Phenotypes
GenCC
Source:
- metaphyseal chondrodysplasia-retinitis pigmentosa syndrome (Strong), mode of inheritance: AR
- metaphyseal chondrodysplasia-retinitis pigmentosa syndrome (Definitive), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Retinitis pigmentosa with or without skeletal anomalies | AR | General | 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 | Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic | 28285769 |
ClinVar
This is a list of variants' phenotypes submitted to
- 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 | 50 | 56 | ||||
missense | 134 | 138 | ||||
nonsense | 9 | |||||
start loss | 0 | |||||
frameshift | 14 | 17 | ||||
inframe indel | 2 | |||||
splice donor/acceptor (+/-2bp) | 9 | |||||
splice region | 1 | 10 | 21 | 6 | 38 | |
non coding | 54 | 13 | 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) | ||
5-64769156-A-G | Uncertain significance (Dec 18, 2023) | |||
5-64769160-ACATC-A | Pathogenic (Aug 10, 2022) | |||
5-64769162-A-G | Uncertain significance (Aug 09, 2022) | |||
5-64769166-A-C | Uncertain significance (Jul 17, 2023) | |||
5-64769178-C-T | Uncertain significance (Jul 05, 2022) | |||
5-64769179-G-A | Likely benign (Jul 03, 2022) | |||
5-64769189-G-A | Likely pathogenic (Feb 27, 2022) | |||
5-64769196-C-T | Likely benign (Dec 12, 2021) | |||
5-64769204-A-G | Likely benign (Feb 24, 2022) | |||
5-64774673-G-T | Likely benign (May 27, 2022) | |||
5-64774691-G-A | Uncertain significance (Nov 01, 2022) | |||
5-64774697-T-C | Likely benign (Dec 26, 2023) | |||
5-64774701-A-G | Uncertain significance (Jul 06, 2022) | |||
5-64774704-C-G | Uncertain significance (Jun 05, 2022) | |||
5-64774708-A-C | Likely benign (Jan 21, 2024) | |||
5-64774719-T-C | Uncertain significance (Oct 04, 2021) | |||
5-64774723-CAT-C | Pathogenic (Jul 26, 2022) | |||
5-64774724-A-C | Uncertain significance (Jun 04, 2022) | |||
5-64774734-G-C | Inborn genetic diseases | Uncertain significance (Jun 29, 2023) | ||
5-64774742-G-T | Pathogenic (Aug 09, 2022) | |||
5-64774747-T-C | Likely benign (Jan 09, 2024) | |||
5-64774748-C-A | Uncertain significance (Jul 21, 2022) | |||
5-64774748-C-T | Uncertain significance (Jul 19, 2022) | |||
5-64774764-A-AT | Pathogenic (Nov 26, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
CWC27 | protein_coding | protein_coding | ENST00000381070 | 14 | 249834 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
4.56e-7 | 0.958 | 125710 | 0 | 38 | 125748 | 0.000151 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.762 | 193 | 225 | 0.857 | 0.0000113 | 3109 |
Missense in 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 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000578 | 0.000562 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000225 | 0.000217 |
Finnish | 0.000139 | 0.000139 |
European (Non-Finnish) | 0.000171 | 0.000167 |
Middle Eastern | 0.000225 | 0.000217 |
South Asian | 0.0000681 | 0.0000653 |
Other | 0.00 | 0.00 |
dbNSFP
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.;
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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