SPSB3

splA/ryanodine receptor domain and SOCS box containing 3

Basic information

Region (hg38): 16:1776711-1793700

Previous symbols: [ "C16orf31" ]

Links

ENSG00000162032 ∙ NCBI:90864 ∙ OMIM:611659 ∙ HGNC:30629 ∙ Uniprot:Q6PJ21 ∙ 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 SPSB3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPSB3 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			30	1		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	3	1

Variants in SPSB3

This is a list of pathogenic ClinVar variants found in the SPSB3 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-1777104-C-T		not specified	Uncertain significance (Apr 06, 2024)
16-1777108-G-C		not specified	Uncertain significance (Apr 07, 2022)
16-1777134-G-A		not specified	Uncertain significance (Jan 06, 2023)
16-1777141-G-C		not specified	Uncertain significance (Aug 13, 2021)
16-1777156-C-T		not specified	Uncertain significance (Jun 22, 2021)
16-1777164-G-A		not specified	Uncertain significance (Aug 01, 2022)
16-1777179-G-C		not specified	Uncertain significance (Dec 19, 2022)
16-1777195-G-C		not specified	Uncertain significance (Feb 14, 2023)
16-1777197-C-T		not specified	Uncertain significance (Feb 05, 2024)
16-1777259-C-T			Likely benign (Mar 05, 2018)
16-1777273-C-T		not specified	Uncertain significance (Jun 17, 2024)
16-1777290-G-A		not specified	Uncertain significance (May 17, 2023)
16-1777300-G-A		not specified	Uncertain significance (Jan 19, 2024)
16-1777345-C-A		not specified	Uncertain significance (Apr 04, 2023)
16-1777359-C-T		not specified	Uncertain significance (Nov 09, 2021)
16-1777404-G-A		not specified	Uncertain significance (Apr 12, 2023)
16-1777415-C-G		not specified	Uncertain significance (Feb 06, 2024)
16-1777748-T-C		not specified	Uncertain significance (Mar 20, 2024)
16-1777816-A-T		not specified	Uncertain significance (Dec 27, 2022)
16-1777825-C-T		not specified	Uncertain significance (Jul 12, 2022)
16-1777852-C-G		not specified	Uncertain significance (Jul 12, 2022)
16-1777999-G-A		not specified	Uncertain significance (Jan 29, 2024)
16-1778005-C-T		not specified	Likely benign (Dec 20, 2023)
16-1778021-C-T		not specified	Uncertain significance (Sep 01, 2021)
16-1778022-C-T			Likely benign (Apr 11, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPSB3	protein_coding	protein_coding	ENST00000566339	6	16989

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0361	0.957	125374	0	19	125393	0.0000758

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.785	219	254	0.862	0.0000180	2310
Missense in Polyphen		59	94.844	0.62208		849
Synonymous	-3.16	156	113	1.38	0.00000866	720
Loss of Function	2.37	5	14.8	0.337	7.19e-7	156

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000136	0.000133
Middle Eastern	0.000110	0.000109
South Asian	0.0000327	0.0000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.123

Intolerance Scores

• loftool: 0.480
• rvis_EVS: -0.44
• rvis_percentile_EVS: 24.46

Haploinsufficiency Scores

• pHI: 0.0950
• hipred: Y
• hipred_score: 0.654
• ghis: 0.522

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.980

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spsb3

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;protein ubiquitination;proteasome-mediated ubiquitin-dependent protein catabolic process;post-translational protein modification
• Cellular component: cytosol;SCF ubiquitin ligase complex
• Molecular function: ubiquitin-protein transferase activity;protein binding