CWC15
protein-codingCWC15 spliceosome associated protein homolog, the group of NTC associated proteins|NineTeen complex|Spliceosomal C complex
Gene summary
Predicted to enable RNA binding activity. Involved in mRNA splicing, via spliceosome. Located in nuclear speck. Part of U2-type catalytic step 2 spliceosome. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~11.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CWC15 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_016403.4. 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 | ||||
| missense | 6 | 6 | ||||
| nonsense | 0 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 9 | 0 | 0 | 9 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_057487.2 | 6 | MANE Select | |
| Ensembl | ENSP00000475615.2 | 6 | MANE Select | |
| RefSeq | NP_001350300.1 | 6 | Standard | |
| RefSeq | NP_001350301.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Spliceosome - Homo sapiens (human)
- Metabolism of RNA
- mRNA Splicing - Major Pathway
- mRNA Splicing
- Processing of Capped Intron-Containing Pre-mRNA
Biological Process
- mRNA splicing, via spliceosome
- mRNA cis splicing, via spliceosome
Molecular Function
- RNA binding
- protein binding
Cellular Component
- nucleus
- nucleoplasm
- spliceosomal complex
- mitochondrion
- nuclear speck
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000279839
- Coding exons
- 7
- Length
- 10990
- Individuals with no LoFs
- 123741
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 2
- Defined
- 123743
- p
- 0.00000808
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.12 | 45 | 107 | 0.422 | 0.00000523 | 1488 |
| Missense (PolyPhen) | 9 | 34.668 | 0.25961 | 457 | ||
| Synonymous | -0.342 | 38 | 35.4 | 1.07 | 0.00000168 | 394 |
| Loss of Function | 3.16 | 0 | 11.7 | 0.00 | 6.51e-7 | 153 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000056 | 0.000056 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in pre-mRNA splicing as component of the spliceosome (PubMed:28502770, PubMed:28076346). Component of the PRP19-CDC5L complex that forms an integral part of the spliceosome and is required for activating pre-mRNA splicing. {ECO:0000269|PubMed:20176811, ECO:0000269|PubMed:28076346, ECO:0000269|PubMed:28502770}.;
Recessive Scores
- pRec
- 0.113
Essentials
- Indispensability pred.
- E
- Indispensability score
- 0.909
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Low | Low | Low |