WBP11

WW domain binding protein 11, the group of Spliceosomal B complex|Protein phosphatase 1 regulatory subunits|Cilia and flagella associated

Basic information

Region (hg38): 12:14784582-14803486

Links

ENSG00000084463 ∙ NCBI:51729 ∙ OMIM:618083 ∙ HGNC:16461 ∙ Uniprot:Q9Y2W2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• vertebral, cardiac, tracheoesophageal, renal, and limb defects (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Vertebral, cardiac, tracheoesophageal, renal, and limb defects	AD	Audiologic/Otolaryngologic; Cardiovascular	Individuals have been described with hearing impairment, and early recognition and treatment of hearing impairment may improve outcomes, including speech and language development; Individuals have been described with congenital cardiac anomalies, some of which required intervention, and awareness may allow surveillance and early management	Audiologic/Otolaryngologic; Cardiovascular; Craniofacial; Gastrointestinal; Musculoskeletal; Pulmonary; Neurologic; Renal	33276377

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the WBP11 gene.

• WBP11 spliceosomopathy (3 variants)
• Vertebral, cardiac, tracheoesophageal, renal, and limb defects (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WBP11 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			35	2		37
nonsense	2	2	1			5
start loss						0
frameshift	1	2	1			4
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding					1	1
Total	3	4	38	2	1

Variants in WBP11

This is a list of pathogenic ClinVar variants found in the WBP11 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-14787171-G-A		Inborn genetic diseases	Uncertain significance (Nov 03, 2023)
12-14787187-CCT-C		Inborn genetic diseases	Uncertain significance (Jun 02, 2021)
12-14787199-T-C		Inborn genetic diseases	Uncertain significance (Jun 07, 2024)
12-14787204-G-A		Inborn genetic diseases	Uncertain significance (May 24, 2023)
12-14787275-C-G		Inborn genetic diseases	Uncertain significance (Nov 14, 2023)
12-14787399-G-C		Inborn genetic diseases	Uncertain significance (Jun 16, 2024)
12-14787431-A-AG		WBP11 spliceosomopathy • Vertebral, cardiac, tracheoesophageal, renal, and limb defects	Pathogenic (Jun 01, 2020)
12-14787450-G-T		Inborn genetic diseases	Uncertain significance (Feb 21, 2024)
12-14787451-G-T		Inborn genetic diseases	Uncertain significance (Dec 01, 2022)
12-14787465-G-T		Inborn genetic diseases	Uncertain significance (Jul 11, 2023)
12-14787469-G-GC		Vertebral, cardiac, tracheoesophageal, renal, and limb defects	Pathogenic (-)
12-14787486-G-A			Uncertain significance (Apr 21, 2022)
12-14787498-C-A		Inborn genetic diseases	Uncertain significance (Sep 12, 2023)
12-14789046-C-T			Uncertain significance (Feb 01, 2023)
12-14789047-G-A			Uncertain significance (Feb 01, 2024)
12-14789091-C-T		Inborn genetic diseases	Uncertain significance (Dec 08, 2023)
12-14790467-C-A			Uncertain significance (Feb 02, 2023)
12-14790513-CAGGTGGTGGTCCAAG-C			Uncertain significance (Feb 15, 2023)
12-14790528-G-A			Uncertain significance (Feb 14, 2024)
12-14790552-G-A			Likely benign (Feb 01, 2023)
12-14790562-C-G			Uncertain significance (Dec 01, 2022)
12-14790573-G-C		WBP11-related disorder	Uncertain significance (Dec 01, 2022)
12-14790584-G-A		Inborn genetic diseases	Uncertain significance (Jul 26, 2022)
12-14790617-G-A		Inborn genetic diseases	Conflicting classifications of pathogenicity (Apr 01, 2024)
12-14790661-C-G		Inborn genetic diseases	Uncertain significance (Apr 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WBP11	protein_coding	protein_coding	ENST00000261167	11	17065

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000564	125712	0	4	125716	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.98	205	365	0.561	0.0000201	4132
Missense in Polyphen		12	31.723	0.37827		410
Synonymous	1.43	100	120	0.834	0.00000567	1329
Loss of Function	5.09	1	32.1	0.0311	0.00000226	332

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000577	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000978	0.00000879
Middle Eastern	0.0000577	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Activates pre-mRNA splicing. May inhibit PP1 phosphatase activity. {ECO:0000269|PubMed:10593949, ECO:0000269|PubMed:11375989, ECO:0000269|PubMed:14640981}.
• 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: 0.116

Intolerance Scores

• loftool: 0.0185
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.57

Haploinsufficiency Scores

• pHI: 0.587
• hipred: Y
• hipred_score: 0.785
• ghis: 0.622

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.486

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wbp11

Gene ontology

• Biological process: mRNA splicing, via spliceosome;rRNA processing;mRNA cis splicing, via spliceosome
• Cellular component: nucleus;nucleoplasm;cytosol;intracellular membrane-bounded organelle
• Molecular function: single-stranded DNA binding;RNA binding;protein binding;WW domain binding