CWC22

CWC22 spliceosome associated protein homolog, the group of MIF4G domain containing proteins|Spliceosomal Bact complex|Spliceosomal P complex|NTC associated proteins|Spliceosomal C complex

Basic information

Region (hg38): 2:179944876-180007297

Links

ENSG00000163510 ∙ NCBI:57703 ∙ OMIM:615186 ∙ HGNC:29322 ∙ Uniprot:Q9HCG8 ∙ 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 CWC22 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CWC22 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				1	1	2
missense			73	4	1	78
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region						0
non coding						0
Total	0	0	73	5	3

Variants in CWC22

This is a list of pathogenic ClinVar variants found in the CWC22 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-179945146-G-C		not specified	Uncertain significance (Sep 04, 2024)
2-179945154-T-C		not specified	Uncertain significance (Nov 17, 2023)
2-179945179-T-C		not specified	Uncertain significance (Feb 10, 2025)
2-179945230-C-T		not specified	Uncertain significance (May 09, 2023)
2-179945238-T-C		not specified	Uncertain significance (Aug 27, 2024)
2-179945248-T-C		not specified	Uncertain significance (May 01, 2024)
2-179945259-C-T		not specified	Uncertain significance (Jan 16, 2025)
2-179945269-C-G		not specified	Uncertain significance (Nov 07, 2022)
2-179945281-T-C		not specified	Uncertain significance (Aug 01, 2024)
2-179945317-T-C		not specified	Uncertain significance (Jan 23, 2023)
2-179945330-G-C		not specified	Uncertain significance (Jul 30, 2024)
2-179945349-T-C		not specified	Uncertain significance (Feb 10, 2022)
2-179945350-G-A		not specified	Uncertain significance (Jun 26, 2023)
2-179945387-T-A		not specified	Uncertain significance (Jul 06, 2022)
2-179945409-T-C		not specified	Uncertain significance (Jan 25, 2023)
2-179945463-C-T		not specified	Likely benign (Dec 06, 2021)
2-179945490-T-C		not specified	Likely benign (Feb 01, 2025)
2-179945542-A-C		not specified	Uncertain significance (Mar 26, 2024)
2-179945634-T-A			Benign (Feb 25, 2018)
2-179945641-T-C		not specified	Uncertain significance (Mar 12, 2024)
2-179945656-T-C		not specified	Uncertain significance (Feb 13, 2024)
2-179945671-C-T		not specified	Uncertain significance (Jul 06, 2021)
2-179945683-T-C		not specified	Uncertain significance (Mar 20, 2023)
2-179945720-G-A			Benign (Apr 01, 2025)
2-179950552-C-G		not specified	Uncertain significance (Dec 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CWC22	protein_coding	protein_coding	ENST00000410053	19	62238

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000899	0.999	124581	0	52	124633	0.000209

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.02	384	444	0.864	0.0000226	5985
Missense in Polyphen		62	94.665	0.65494		1316
Synonymous	0.898	138	152	0.907	0.00000770	1574
Loss of Function	4.50	15	48.9	0.306	0.00000301	635

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000278	0.000274
Ashkenazi Jewish	0.0000996	0.0000994
East Asian	0.0000557	0.0000556
Finnish	0.000604	0.000603
European (Non-Finnish)	0.000258	0.000257
Middle Eastern	0.0000557	0.0000556
South Asian	0.00	0.00
Other	0.000166	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for pre-mRNA splicing and for exon-junction complex (EJC) assembly. Hinders EIF4A3 from non-specifically binding RNA and escorts it to the splicing machinery to promote EJC assembly on mature mRNAs. Through its role in EJC assembly, required for nonsense-mediated mRNA decay. {ECO:0000269|PubMed:22959432, ECO:0000269|PubMed:22961380, ECO:0000269|PubMed:23236153}.
• Pathway: Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.164

Intolerance Scores

• loftool: 0.897
• rvis_EVS: 0.07
• rvis_percentile_EVS: 59.11

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.650
• ghis: 0.573

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.298

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cwc22

Gene ontology

• Biological process: mRNA splicing, via spliceosome;regulation of mRNA splicing, via spliceosome
• Cellular component: nucleoplasm;spliceosomal complex;cytosol;nuclear speck;U2-type catalytic step 1 spliceosome;U2-type catalytic step 2 spliceosome;catalytic step 2 spliceosome
• Molecular function: RNA binding;protein binding