PSMB10

proteasome 20S subunit beta 10, the group of Proteasome

Basic information

Region (hg38): 16:67934506-67936864

Previous symbols: [ "MECL1" ]

Links

ENSG00000205220

∙ NCBI:5699 ∙ OMIM:176847 ∙ HGNC:9538 ∙ Uniprot:P40306 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

proteasome-associated autoinflammatory syndrome 5 (Limited), mode of inheritance: Unknown
immunodeficiency 121 with autoinflammation (Moderate), mode of inheritance: AD
proteasome-associated autoinflammatory syndrome 5 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Immunodeficiency 121 with autoinflammation; Proteasome-associated autoinflammatory syndrome 5	AD/AR	Allergy/Immunology/Infectious	Immunodeficiency 121 with autoinflammation involves severe immunodeficiency, and awareness may allow early and aggressive treatment of infections as well as preventative measures; HSCT has been described, but complications have been reported in multiple individuals; Proteasome-associated autoinflammatory syndrome 5 involves autoinflammatory manifestations, and medical management (eg, with steroids and methotrexate) has been described as beneficial	Allergy/Immunology/Infectious; Dermatologic	31783057; 38503300

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PSMB10 gene.

not_specified (28 variants)
Proteasome-associated_autoinflammatory_syndrome_5 (8 variants)
not_provided (6 variants)
Immunodeficiency_121_with_autoinflammation (3 variants)
PSMB10-related_disorder (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSMB10 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002801.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				4 clinvar		4
missense	5 clinvar		25 clinvar	4 clinvar		34
nonsense						0
start loss						0
frameshift	1 clinvar		1 clinvar			2
splice donor/acceptor (+/-2bp)	1 clinvar		1 clinvar			2
Total	7	0	27	8	0

Highest pathogenic variant AF is 0.0000459843

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSMB10	protein_coding	protein_coding	ENST00000358514	8	2586

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000177	0.445	125704	0	44	125748	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.694	139	164	0.848	0.00000795	1705
Missense in Polyphen		24	47.872	0.50133		494
Synonymous	0.0879	74	75.0	0.987	0.00000395	610
Loss of Function	0.630	10	12.4	0.807	5.30e-7	144

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00119	0.00116
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000927	0.0000924
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.000109	0.000109
South Asian	0.0000983	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: The proteasome is a multicatalytic proteinase complex which is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. The proteasome has an ATP-dependent proteolytic activity. This subunit is involved in antigen processing to generate class I binding peptides.;
Pathway: Proteasome - Homo sapiens (human);Proteasome Degradation;TLR NFkB;B cell receptor signaling;Post-translational protein modification;Metabolism of proteins;DroToll-like;Notch;Hedgehog;IL-1 NFkB;IL-1 p38;IL-1 JNK;TGF-beta super family signaling pathway canonical;TLR p38;UCH proteinases;Neddylation;Ub-specific processing proteases;JAK STAT pathway and regulation;Deubiquitination;TLR JNK;TNF;Wnt Canonical;Wnt Mammals;CD4 T cell receptor signaling-NFkB cascade;CD4 T cell receptor signaling (Consensus)

Recessive Scores

pRec: 0.191

Intolerance Scores

loftool: 0.693
rvis_EVS: -0.41
rvis_percentile_EVS: 26.23

Haploinsufficiency Scores

pHI: 0.678
hipred: Y
hipred_score: 0.595
ghis: 0.585

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.525

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Psmb10
Phenotype: homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); immune system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype;

Gene ontology

Biological process: cell morphogenesis;humoral immune response;proteasomal protein catabolic process;proteasomal ubiquitin-independent protein catabolic process;viral process;protein deubiquitination;T cell proliferation;proteasome-mediated ubiquitin-dependent protein catabolic process;post-translational protein modification
Cellular component: proteasome complex;nucleus;nucleoplasm;cytoplasm;cytosol;proteasome core complex;proteasome core complex, beta-subunit complex;spermatoproteasome complex
Molecular function: endopeptidase activity;threonine-type endopeptidase activity;protein binding