CWC15

CWC15 spliceosome associated protein homolog, the group of NTC associated proteins|NineTeen complex|Spliceosomal C complex

Basic information

Region (hg38): 11:94962620-94973586

Links

ENSG00000150316 ∙ NCBI:51503 ∙ ∙ HGNC:26939 ∙ Uniprot:Q9P013 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CWC15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CWC15 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						0
missense			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in CWC15

This is a list of pathogenic ClinVar variants found in the CWC15 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-94972063-T-C		not specified	Uncertain significance (Dec 27, 2023)
11-94972079-G-A		not specified	Uncertain significance (Aug 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CWC15	protein_coding	protein_coding	ENST00000279839	7	10990

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.978	0.0223	123741	0	2	123743	0.00000808

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.12	45	107	0.422	0.00000523	1488
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000559	0.0000559
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000559	0.0000559
South Asian	0.0000331	0.0000331
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• 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}.
• Pathway: Spliceosome - Homo sapiens (human);Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.113

Haploinsufficiency Scores

• pHI: 0.304
• hipred: Y
• hipred_score: 0.673

Essentials

• gene_indispensability_pred: E
• gene_indispensability_score: 0.909

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Low	Low
Primary Immunodeficiency	Medium	Low	Medium
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Cwc15

Gene ontology

• Biological process: mRNA splicing, via spliceosome;mRNA cis splicing, via spliceosome
• Cellular component: nucleus;nucleoplasm;spliceosomal complex;mitochondrion;nuclear speck;U2-type catalytic step 2 spliceosome;catalytic step 2 spliceosome
• Molecular function: RNA binding;protein binding