SPSB4

splA/ryanodine receptor domain and SOCS box containing 4

Basic information

Region (hg38): 3:141051347-141148611

Links

ENSG00000175093 ∙ NCBI:92369 ∙ OMIM:611660 ∙ HGNC:30630 ∙ Uniprot:Q96A44 ∙ 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 SPSB4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPSB4 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			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in SPSB4

This is a list of pathogenic ClinVar variants found in the SPSB4 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-141066133-A-G		not specified	Uncertain significance (Jun 29, 2023)
3-141066141-G-A		not specified	Uncertain significance (Jan 02, 2024)
3-141066178-A-G		not specified	Uncertain significance (Apr 04, 2024)
3-141066187-G-A		not specified	Uncertain significance (May 23, 2024)
3-141066211-G-A		not specified	Uncertain significance (Oct 20, 2023)
3-141066211-G-C		not specified	Uncertain significance (Mar 19, 2024)
3-141066350-G-C		not specified	Uncertain significance (Apr 09, 2024)
3-141066424-G-A		not specified	Uncertain significance (Apr 15, 2024)
3-141066471-C-A		not specified	Uncertain significance (Jul 11, 2023)
3-141066496-C-T		not specified	Uncertain significance (Dec 15, 2023)
3-141066561-G-C		not specified	Uncertain significance (May 11, 2022)
3-141066621-C-G		not specified	Uncertain significance (Dec 18, 2023)
3-141066670-G-T		not specified	Uncertain significance (Sep 14, 2022)
3-141066672-T-C		not specified	Uncertain significance (Dec 15, 2023)
3-141066693-C-G		not specified	Uncertain significance (Apr 28, 2022)
3-141066699-G-A		not specified	Uncertain significance (May 05, 2023)
3-141066747-G-T		not specified	Uncertain significance (Apr 20, 2023)
3-141066767-A-C		not specified	Uncertain significance (Jan 31, 2022)
3-141066777-C-G		not specified	Uncertain significance (Jun 24, 2022)
3-141066792-C-G		not specified	Uncertain significance (Feb 28, 2024)
3-141147160-T-G		not specified	Uncertain significance (Nov 29, 2021)
3-141147171-C-T		not specified	Uncertain significance (Feb 28, 2023)
3-141147204-C-T		not specified	Uncertain significance (Apr 05, 2023)
3-141147205-G-A		not specified	Uncertain significance (Sep 26, 2023)
3-141147229-C-T		not specified	Uncertain significance (Jul 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPSB4	protein_coding	protein_coding	ENST00000310546	2	97210

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000418	0.661	125715	0	4	125719	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.869	135	167	0.810	0.0000126	1688
Missense in Polyphen		36	53.529	0.67254		614
Synonymous	0.542	71	77.1	0.921	0.00000601	599
Loss of Function	0.744	6	8.32	0.722	5.86e-7	76

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000911	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable substrate recognition component of a SCF-like ECS (Elongin BC-CUL2/5-SOCS-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. {ECO:0000269|PubMed:15601820}.
• 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: 0.140

Haploinsufficiency Scores

• pHI: 0.780
• hipred: Y
• hipred_score: 0.728
• ghis: 0.477

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.752

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spsb4

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;protein ubiquitination;intracellular signal transduction;regulation of circadian rhythm;proteasome-mediated ubiquitin-dependent protein catabolic process;post-translational protein modification;positive regulation of protein polyubiquitination
• Cellular component: cytosol;SCF ubiquitin ligase complex
• Molecular function: ubiquitin-protein transferase activity;protein binding;protein binding, bridging involved in substrate recognition for ubiquitination