WBP4

WW domain binding protein 4, the group of Spliceosomal B complex

Basic information

Region (hg38): 13:41061509-41084006

Links

ENSG00000120688 ∙ NCBI:11193 ∙ OMIM:604981 ∙ HGNC:12739 ∙ Uniprot:O75554 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder with hypotonia, feeding difficulties, facial dysmorphism, and brain abnormalities (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopemental disorder with hypotonia, feeding difficulties, facial dysmorphism, and brain abnormalities	AR	Cardiovascular	Among other features, the condition can include congenital cardiac anomalies, and awareness may enable early identification and management	Cardiovascular; Craniofacial; Dermatologic; Musculoskeletal; Neurologic	37963460

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the WBP4 gene.

• not_specified (51 variants)
• not_provided (4 variants)
• Neurodevelopmental_disorder (4 variants)
• Neurodevelopmental_disorder_with_hypotonia,_feeding_difficulties,_facial_dysmorphism,_and_brain_abnormalities (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WBP4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000007187.5. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	1	1	3
missense			50	1		51
nonsense		1				1
start loss						0
frameshift		2				2
splice donor/acceptor (+/-2bp)		1				1
Total	0	4	51	2	1

Highest pathogenic variant AF is 0.000006578861

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WBP4	protein_coding	protein_coding	ENST00000379487	10	22728

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.98e-8	0.811	125682	0	61	125743	0.000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.237	171	180	0.950	0.00000805	2458
Missense in Polyphen		44	50.332	0.8742		706
Synonymous	-0.470	68	63.3	1.08	0.00000308	639
Loss of Function	1.50	15	22.7	0.661	9.54e-7	322

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000586	0.000583
Ashkenazi Jewish	0.00209	0.00209
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000144	0.000141
Middle Eastern	0.000109	0.000109
South Asian	0.000291	0.000261
Other	0.000654	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in pre-mRNA splicing as a component of the spliceosome (PubMed:9724750, PubMed:19592703, PubMed:28781166). May play a role in cross-intron bridging of U1 and U2 snRNPs in the mammalian A complex (PubMed:9724750). {ECO:0000269|PubMed:19592703, ECO:0000269|PubMed:28781166, ECO:0000269|PubMed:9724750}.
• Pathway: Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.397
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.75

Haploinsufficiency Scores

• pHI: 0.168
• hipred: Y
• hipred_score: 0.624
• ghis: 0.596

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.796

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wbp4

Gene ontology

• Biological process: mRNA splicing, via spliceosome;mRNA cis splicing, via spliceosome
• Cellular component: nucleus;nucleoplasm;nuclear speck;U2-type precatalytic spliceosome
• Molecular function: nucleic acid binding;protein binding;zinc ion binding;proline-rich region binding