WSB2

WD repeat and SOCS box containing 2, the group of WD repeat domain containing

Basic information

Region (hg38): 12:118032687-118062430

Links

ENSG00000176871 ∙ NCBI:55884 ∙ ∙ HGNC:19222 ∙ Uniprot:Q9NYS7 ∙ 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 WSB2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WSB2 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				2	1	3
missense			15	1	1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	3	2

Variants in WSB2

This is a list of pathogenic ClinVar variants found in the WSB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-118034206-C-T		not specified	Uncertain significance (Jan 16, 2024)
12-118034329-G-C		not specified	Uncertain significance (Mar 20, 2023)
12-118035287-C-T		not specified	Uncertain significance (Jun 02, 2023)
12-118035293-T-C		not specified	Uncertain significance (Jun 29, 2023)
12-118035305-C-T		not specified	Uncertain significance (Dec 11, 2023)
12-118036386-T-C		not specified	Uncertain significance (Apr 19, 2024)
12-118036424-G-A			Likely benign (Jun 01, 2022)
12-118036433-G-A			Benign (Jul 04, 2018)
12-118038289-G-A		not specified	Uncertain significance (Nov 09, 2021)
12-118038300-A-G			Likely benign (Jan 01, 2023)
12-118042862-T-C		not specified	Uncertain significance (Jan 10, 2023)
12-118042916-T-C			Benign (Jul 04, 2018)
12-118043202-C-T			Likely benign (Jan 01, 2023)
12-118043222-C-T		not specified	Uncertain significance (Sep 16, 2021)
12-118043229-A-G		not specified	Uncertain significance (Jul 29, 2022)
12-118043243-G-T		not specified	Uncertain significance (Nov 09, 2022)
12-118043273-C-G		not specified	Uncertain significance (Jan 04, 2024)
12-118043298-G-C		not specified	Uncertain significance (Mar 04, 2024)
12-118043322-G-A		not specified	Uncertain significance (Aug 02, 2021)
12-118043324-C-T		not specified	Uncertain significance (Aug 17, 2021)
12-118052428-C-G		not specified	Uncertain significance (Mar 24, 2023)
12-118062151-G-A			Benign (Jul 04, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WSB2	protein_coding	protein_coding	ENST00000315436	9	29524

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.929	0.0706	125739	0	8	125747	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.14	144	237	0.608	0.0000137	2636
Missense in Polyphen		25	82.329	0.30366		892
Synonymous	-0.541	109	102	1.07	0.00000671	801
Loss of Function	3.72	3	21.7	0.138	0.00000108	232

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be a 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. {ECO:0000250}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Neddylation (Consensus)

Recessive Scores

• pRec: 0.0814

Intolerance Scores

• loftool: 0.356
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.13

Haploinsufficiency Scores

• pHI: 0.0739
• hipred: Y
• hipred_score: 0.768
• ghis: 0.443

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.757

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wsb2
• Phenotype: homeostasis/metabolism phenotype; craniofacial phenotype; growth/size/body region phenotype; skeleton phenotype; vision/eye phenotype; limbs/digits/tail phenotype; reproductive system phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: protein ubiquitination;intracellular signal transduction;post-translational protein modification
• Cellular component: cytosol