SPSB2

splA/ryanodine receptor domain and SOCS box containing 2

Basic information

Region (hg38): 12:6870935-6889358

Links

ENSG00000111671 ∙ NCBI:84727 ∙ OMIM:611658 ∙ HGNC:29522 ∙ Uniprot:Q99619 ∙ 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 SPSB2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPSB2 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			27			27
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	27	0	1

Variants in SPSB2

This is a list of pathogenic ClinVar variants found in the SPSB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-6871214-T-C		not specified	Uncertain significance (Sep 03, 2024)
12-6871251-C-T		not specified	Uncertain significance (Apr 22, 2022)
12-6871256-C-T		not specified	Uncertain significance (May 21, 2024)
12-6871263-C-A		not specified	Uncertain significance (Nov 12, 2024)
12-6871291-G-C		not specified	Uncertain significance (Oct 01, 2024)
12-6871328-GAGA-G			Benign (Nov 20, 2017)
12-6872256-A-G		not specified	Uncertain significance (Mar 03, 2025)
12-6872301-G-T		not specified	Uncertain significance (Apr 08, 2024)
12-6872345-T-A		not specified	Uncertain significance (Jun 26, 2024)
12-6872346-A-T		not specified	Uncertain significance (Mar 28, 2023)
12-6872349-T-A		not specified	Uncertain significance (Aug 21, 2024)
12-6872357-A-G		not specified	Uncertain significance (Oct 06, 2024)
12-6872385-T-C		not specified	Uncertain significance (Dec 17, 2023)
12-6872391-G-C		not specified	Uncertain significance (Aug 17, 2021)
12-6872457-C-T		not specified	Uncertain significance (Mar 12, 2024)
12-6872463-G-A		not specified	Uncertain significance (Nov 07, 2024)
12-6872492-C-T		not specified	Uncertain significance (Oct 12, 2021)
12-6872546-T-C		not specified	Uncertain significance (Dec 01, 2022)
12-6872565-C-G		not specified	Uncertain significance (May 30, 2024)
12-6872579-A-C		not specified	Uncertain significance (Jul 13, 2021)
12-6872639-A-T		not specified	Uncertain significance (Sep 27, 2022)
12-6872642-C-A		not specified	Uncertain significance (May 30, 2024)
12-6872667-G-A		not specified	Uncertain significance (Feb 05, 2024)
12-6872674-A-C		not specified	Uncertain significance (Dec 03, 2021)
12-6872744-C-T		not specified	Uncertain significance (Mar 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPSB2	protein_coding	protein_coding	ENST00000524270	2	18424

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0214	0.914	125637	0	104	125741	0.000414

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.610	172	151	1.14	0.00000767	1641
Missense in Polyphen		70	59.837	1.1698		684
Synonymous	-0.223	72	69.6	1.03	0.00000333	589
Loss of Function	1.58	4	9.14	0.437	3.95e-7	97

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000593	0.000590
Ashkenazi Jewish	0.00	0.00
East Asian	0.000872	0.000870
Finnish	0.000606	0.000601
European (Non-Finnish)	0.000386	0.000378
Middle Eastern	0.000872	0.000870
South Asian	0.000392	0.000392
Other	0.000489	0.000489

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)

Intolerance Scores

• loftool: 0.726
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.64

Haploinsufficiency Scores

• pHI: 0.0797
• hipred: N
• hipred_score: 0.242
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.824

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spsb2
• Phenotype: homeostasis/metabolism phenotype; hematopoietic system phenotype

Gene ontology

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