WSB1

WD repeat and SOCS box containing 1, the group of WD repeat domain containing

Basic information

Region (hg38): 17:27294076-27315926

Links

ENSG00000109046 ∙ NCBI:26118 ∙ OMIM:610091 ∙ HGNC:19221 ∙ Uniprot:Q9Y6I7 ∙ 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 WSB1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WSB1 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			29			29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	29	0	1

Variants in WSB1

This is a list of pathogenic ClinVar variants found in the WSB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-27294423-G-A		not specified	Uncertain significance (Aug 09, 2021)
17-27301802-A-G		not specified	Uncertain significance (Jan 23, 2023)
17-27301838-A-G		not specified	Uncertain significance (Dec 14, 2023)
17-27301839-A-G		not specified	Uncertain significance (Feb 15, 2023)
17-27301845-G-A		not specified	Uncertain significance (Dec 18, 2023)
17-27301851-G-A		not specified	Uncertain significance (Mar 24, 2023)
17-27301896-C-G		not specified	Uncertain significance (Jan 26, 2023)
17-27301905-A-G		not specified	Uncertain significance (Jun 22, 2024)
17-27303368-C-G		not specified	Uncertain significance (Jan 16, 2024)
17-27303432-A-G		not specified	Uncertain significance (Sep 14, 2022)
17-27303447-A-G		not specified	Uncertain significance (Jan 19, 2024)
17-27303483-T-C		not specified	Uncertain significance (Aug 12, 2021)
17-27303555-G-A		not specified	Uncertain significance (Apr 19, 2024)
17-27303603-A-G		not specified	Uncertain significance (Dec 07, 2021)
17-27303609-G-A		not specified	Uncertain significance (Oct 20, 2021)
17-27304780-G-T		not specified	Uncertain significance (Dec 31, 2023)
17-27304842-G-C		not specified	Uncertain significance (Dec 21, 2022)
17-27304843-A-T		not specified	Uncertain significance (Apr 26, 2023)
17-27306803-G-T		not specified	Uncertain significance (Dec 13, 2021)
17-27306839-C-T		not specified	Uncertain significance (Mar 25, 2024)
17-27306848-C-T		not specified	Uncertain significance (May 26, 2023)
17-27309105-C-G		not specified	Uncertain significance (Mar 29, 2024)
17-27309120-T-G		not specified	Uncertain significance (Apr 01, 2024)
17-27309188-A-G		not specified	Uncertain significance (Feb 09, 2023)
17-27309248-A-G		not specified	Uncertain significance (Jul 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WSB1	protein_coding	protein_coding	ENST00000262394	9	19556

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.423	0.577	125727	0	20	125747	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.251	229	240	0.954	0.0000129	2764
Missense in Polyphen		81	95.996	0.84379		1129
Synonymous	-0.0976	80	78.9	1.01	0.00000383	805
Loss of Function	3.45	5	22.8	0.220	0.00000122	254

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000304	0.000304
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000880	0.0000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable substrate-recognition component of a SCF-like ECS (Elongin-Cullin-SOCS-box protein) E3 ubiquitin ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. Recognizes type II iodothyronine deiodinase/DIO2. Confers constitutive instability to HIPK2 through proteasomal degradation. {ECO:0000269|PubMed:15601820, ECO:0000269|PubMed:15965468, ECO:0000269|PubMed:18093972}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation;Neddylation (Consensus)

Recessive Scores

• pRec: 0.181

Intolerance Scores

• loftool: 0.637
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24.19

Haploinsufficiency Scores

• pHI: 0.359
• hipred: Y
• hipred_score: 0.775
• ghis: 0.588

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.580

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wsb1

Gene ontology

• Biological process: protein polyubiquitination;biological_process;intracellular signal transduction;post-translational protein modification
• Cellular component: cytosol
• Molecular function: ubiquitin-protein transferase activity;protein binding