PSMG2

proteasome assembly chaperone 2

Basic information

Region (hg38): 18:12658043-12728945

Previous symbols: [ "TNFSF5IP1" ]

Links

ENSG00000128789 ∙ NCBI:56984 ∙ OMIM:609702 ∙ HGNC:24929 ∙ Uniprot:Q969U7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• proteasome-associated autoinflammatory syndrome 4 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Proteasome-associated autoinflammatory syndrome 4	AR	Allergy/Immunology/Infectious	The condition involves autoinflammatory manifestations, and medical management (eg, with JAK inhibitors) has been described as resulting in clinical improvement	Allergy/Immunology/Infectious; Neurologic	30664889

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PSMG2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSMG2 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	34	1	36
missense			92	5	5	102
nonsense			3			3
start loss			2			2
frameshift			4			4
inframe indel						0
splice donor/acceptor (+/-2bp)			5			5
splice region			2	5	1	8
non coding			42	22	6	70
Total	0	0	149	61	12

Variants in PSMG2

This is a list of pathogenic ClinVar variants found in the PSMG2 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-12673378-C-T		not specified	Uncertain significance (Nov 11, 2024)
18-12673379-G-A		not specified	Uncertain significance (Sep 26, 2024)
18-12673414-G-A		not specified	Uncertain significance (Dec 02, 2024)
18-12673471-C-T		Short stature	Likely pathogenic (Nov 18, 2001)
18-12674558-G-A		not specified	Uncertain significance (Jan 23, 2025)
18-12674650-T-C		not specified	Uncertain significance (Jan 08, 2025)
18-12674671-G-A		not specified	Uncertain significance (Jun 17, 2024)
18-12674674-C-T		not specified	Uncertain significance (Nov 10, 2024)
18-12674707-A-G		not specified	Uncertain significance (Feb 01, 2025)
18-12674721-C-A		not specified	Uncertain significance (Jun 10, 2024)
18-12678137-A-C		not specified	Uncertain significance (Aug 04, 2023)
18-12678176-A-G		not specified	Uncertain significance (Jan 08, 2025)
18-12678230-G-A		not specified	Uncertain significance (Nov 12, 2024)
18-12678249-C-T		not specified	Uncertain significance (Aug 04, 2022)
18-12678326-C-T		not specified	Uncertain significance (Sep 20, 2023)
18-12678404-A-T		not specified	Uncertain significance (Jan 10, 2023)
18-12678436-G-C		not specified	Uncertain significance (Feb 28, 2025)
18-12680717-T-C		not specified	Uncertain significance (May 08, 2024)
18-12680725-G-A		not specified	Uncertain significance (Oct 19, 2024)
18-12680794-C-G		not specified	Uncertain significance (May 31, 2024)
18-12686290-G-A		not specified	Uncertain significance (Jul 17, 2023)
18-12686353-T-C		not specified	Uncertain significance (Dec 02, 2022)
18-12686399-C-T		Short stature	Uncertain significance (Nov 18, 2001)
18-12686425-A-G		not specified	Uncertain significance (Feb 04, 2025)
18-12686436-T-A		CEP76-related disorder	Likely benign (Mar 12, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSMG2	protein_coding	protein_coding	ENST00000317615	7	67003

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.38e-7	0.291	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.442	127	142	0.896	0.00000742	1706
Missense in Polyphen		31	34.939	0.88726		451
Synonymous	-0.616	54	48.5	1.11	0.00000242	514
Loss of Function	0.413	11	12.6	0.874	5.29e-7	172

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000457	0.000449
Ashkenazi Jewish	0.00	0.00
East Asian	0.000165	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000108	0.000105
Middle Eastern	0.000165	0.000163
South Asian	0.000132	0.000131
Other	0.000168	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Chaperone protein which promotes assembly of the 20S proteasome as part of a heterodimer with PSMG1. The PSMG1-PSMG2 heterodimer binds to the PSMA5 and PSMA7 proteasome subunits, promotes assembly of the proteasome alpha subunits into the heteroheptameric alpha ring and prevents alpha ring dimerization. {ECO:0000269|PubMed:16251969, ECO:0000269|PubMed:17707236}.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.300
• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.46

Haploinsufficiency Scores

• pHI: 0.243
• hipred: Y
• hipred_score: 0.626
• ghis: 0.474

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.469

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Psmg2

Gene ontology

• Biological process: mitotic spindle assembly checkpoint;negative regulation of apoptotic process;proteasome assembly
• Cellular component: nucleus;cytosol
• Molecular function: protein binding