PSMB11

proteasome subunit beta 11

Basic information

Region (hg38): 14:23042212-23044060

Links

ENSG00000222028 ∙ NCBI:122706 ∙ OMIM:611137 ∙ HGNC:31963 ∙ Uniprot:A5LHX3 ∙ 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 PSMB11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSMB11 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					1	1
missense			27	2	3	32
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	2	5

Variants in PSMB11

This is a list of pathogenic ClinVar variants found in the PSMB11 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-23042239-A-T		not specified	Uncertain significance (Dec 13, 2023)
14-23042265-A-T		not specified	Uncertain significance (Jul 14, 2023)
14-23042293-G-A		not specified	Likely benign (Aug 13, 2021)
14-23042314-C-G		not specified	Uncertain significance (Aug 09, 2021)
14-23042317-G-A		not specified	Uncertain significance (Mar 29, 2024)
14-23042322-T-G		not specified	Uncertain significance (Nov 17, 2023)
14-23042329-C-T		not specified	Uncertain significance (Jul 09, 2021)
14-23042345-G-T		not specified	Uncertain significance (Feb 28, 2024)
14-23042350-A-G		not specified	Uncertain significance (Mar 29, 2022)
14-23042370-G-A			Benign (Dec 31, 2019)
14-23042377-C-T		not specified	Uncertain significance (Oct 04, 2022)
14-23042392-G-A		not specified	Uncertain significance (Apr 25, 2022)
14-23042425-C-A			Uncertain significance (Oct 02, 2023)
14-23042425-C-T		not specified	Uncertain significance (May 11, 2022)
14-23042460-GC-G			Benign (Oct 30, 2018)
14-23042466-T-C		not specified	Likely benign (Mar 20, 2024)
14-23042476-T-A		not specified	Uncertain significance (Oct 12, 2021)
14-23042490-C-A		not specified	Uncertain significance (Feb 28, 2024)
14-23042554-G-A		not specified	Uncertain significance (Nov 17, 2022)
14-23042569-G-A			Likely benign (Mar 01, 2023)
14-23042583-G-A		not specified	Uncertain significance (Sep 01, 2021)
14-23042593-C-T		not specified	Uncertain significance (Nov 17, 2022)
14-23042688-C-T		not specified	Uncertain significance (Apr 25, 2022)
14-23042706-T-C		not specified	Uncertain significance (Apr 25, 2022)
14-23042711-C-T			Benign (Apr 17, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSMB11	protein_coding	protein_coding	ENST00000408907	1	1894

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000243	0.170	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0560	198	200	0.989	0.0000129	1884
Missense in Polyphen		76	87.153	0.87203		778
Synonymous	-0.315	86	82.4	1.04	0.00000521	676
Loss of Function	-0.354	8	6.99	1.14	2.98e-7	75

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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. Incorporated instead of PSMB5 or PSMB8, this unit reduces the chymotrypsin-like activity of the proteasome (By similarity). Plays a pivotal role in development of CD8-positive T cells (By similarity). {ECO:0000250}.
• Pathway: Proteasome - Homo sapiens (human);Post-translational protein modification;Metabolism of proteins;UCH proteinases;Neddylation;Ub-specific processing proteases;Deubiquitination (Consensus)

Intolerance Scores

• loftool: 0.536
• rvis_EVS: 0.11
• rvis_percentile_EVS: 62

Haploinsufficiency Scores

• pHI: 0.366
• hipred: N
• hipred_score: 0.357

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.714

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Psmb11
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: proteolysis;proteasomal protein catabolic process;proteasomal ubiquitin-independent protein catabolic process;protein deubiquitination;proteasome-mediated ubiquitin-dependent protein catabolic process;CD8-positive, alpha-beta T cell differentiation;post-translational protein modification
• Cellular component: nucleus;cytoplasm;cytosol;proteasome core complex;proteasome core complex, beta-subunit complex
• Molecular function: endopeptidase activity;threonine-type endopeptidase activity;peptidase activity