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

No genCC data.

ClinVar

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

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.

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
missense			20			20
nonsense		1				1
start loss						0
frameshift		2				2
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region						0
non coding						0
Total	0	4	20	0	1

Variants in WBP4

This is a list of pathogenic ClinVar variants found in the WBP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-41065203-A-G		not specified	Uncertain significance (Aug 29, 2022)
13-41065216-A-T		not specified	Uncertain significance (Jul 06, 2021)
13-41065240-C-T		not specified	Uncertain significance (Nov 06, 2023)
13-41065241-C-T			Benign (Feb 26, 2018)
13-41065257-G-C		not specified	Uncertain significance (May 05, 2023)
13-41065281-G-C		not specified	Uncertain significance (Apr 20, 2024)
13-41065289-TA-T		not specified	Benign/Likely benign (-)
13-41068612-C-T		not specified	Uncertain significance (Jan 26, 2023)
13-41068705-G-A		not specified	Uncertain significance (Feb 28, 2024)
13-41068705-G-C		not specified	Uncertain significance (Jun 16, 2024)
13-41071526-G-A		Neurodevelopmental disorder	Likely pathogenic (May 01, 2023)
13-41071551-G-T		not specified	Uncertain significance (Feb 06, 2024)
13-41072788-G-A		not specified	Uncertain significance (Feb 27, 2024)
13-41072793-GA-G		Neurodevelopmental disorder • Neurodevelopmental disorder with hypotonia, feeding difficulties, facial dysmorphism, and brain abnormalities	Likely pathogenic (May 01, 2023)
13-41072800-T-G		not specified	Uncertain significance (Sep 27, 2021)
13-41076122-T-G		not specified	Uncertain significance (Oct 03, 2022)
13-41076149-C-G		Neurodevelopmental disorder	Likely pathogenic (May 01, 2023)
13-41076157-C-A		not specified	Uncertain significance (Aug 12, 2021)
13-41076173-G-T		not specified	Uncertain significance (Jun 09, 2022)
13-41076202-T-G		not specified	Uncertain significance (Oct 26, 2022)
13-41076220-C-T		not specified	Uncertain significance (Apr 27, 2022)
13-41076232-T-C		not specified	Uncertain significance (Mar 28, 2024)
13-41080688-C-A		not specified	Uncertain significance (Oct 26, 2022)
13-41080706-C-G		not specified	Uncertain significance (Aug 17, 2021)
13-41080708-G-T		not specified	Uncertain significance (May 13, 2022)

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