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): 5:64766368-65102412

Previous symbols: [ "SDCCAG10" ]

Links

ENSG00000153015

∙ NCBI:10283 ∙ OMIM:617170 ∙ HGNC:10664 ∙ Uniprot:Q6UX04 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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

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 ClinVar and linked to the CWC27 gene.

not_provided (348 variants)
Inborn_genetic_diseases (47 variants)
Metaphyseal_chondrodysplasia-retinitis_pigmentosa_syndrome (19 variants)
CWC27-related_disorder (13 variants)
Retinal_dystrophy (10 variants)
not_specified (3 variants)
Optic_atrophy (1 variants)
Retinitis_pigmentosa (1 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. These statistics are base on transcript: NM_000005869.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous	1 clinvar		1 clinvar	59 clinvar	2 clinvar	63
missense			149 clinvar	4 clinvar		153
nonsense	11 clinvar					11
start loss						0
frameshift	13 clinvar	7 clinvar	3 clinvar			23
splice donor/acceptor (+/-2bp)	1 clinvar	11 clinvar				12
Total	26	18	153	63	2

Highest pathogenic variant AF is 0.000024589397

Loading clinvar variants...

GnomAD

Source: gnomAD

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: 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

	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