PSMG1

proteasome assembly chaperone 1

Basic information

Region (hg38): 21:39174769-39183488

Previous symbols: [ "DSCR2" ]

Links

ENSG00000183527 ∙ NCBI:8624 ∙ OMIM:605296 ∙ HGNC:3043 ∙ Uniprot:O95456 ∙ 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 PSMG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSMG1 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			15	1	2	18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	2	2

Variants in PSMG1

This is a list of pathogenic ClinVar variants found in the PSMG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-39175629-C-G			Benign (Feb 25, 2018)
21-39177451-A-C		not specified	Uncertain significance (Aug 30, 2021)
21-39177512-C-T		not specified	Uncertain significance (Sep 17, 2021)
21-39177536-T-C		not specified	Likely benign (Oct 04, 2022)
21-39178464-C-T		not specified	Uncertain significance (Sep 12, 2023)
21-39178465-G-A			Likely benign (Jun 23, 2018)
21-39178470-C-T		not specified	Uncertain significance (Dec 23, 2022)
21-39178513-G-C		not specified	Uncertain significance (Sep 23, 2023)
21-39178550-G-A		not specified	Uncertain significance (Mar 17, 2023)
21-39178580-T-A		not specified	Uncertain significance (Jun 24, 2022)
21-39178595-C-T		not specified	Uncertain significance (Jan 23, 2024)
21-39178607-A-C		not specified	Uncertain significance (Oct 29, 2021)
21-39178608-T-C			Benign (May 08, 2018)
21-39178614-T-A		not specified	Uncertain significance (Aug 02, 2022)
21-39179951-T-A		not specified	Uncertain significance (Oct 14, 2021)
21-39180292-T-C		not specified	Uncertain significance (Mar 23, 2022)
21-39180355-G-A		not specified	Uncertain significance (Dec 19, 2023)
21-39183348-G-A		not specified	Uncertain significance (Dec 21, 2023)
21-39183348-G-C		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSMG1	protein_coding	protein_coding	ENST00000331573	7	9083

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000342	0.954	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.501	128	145	0.883	0.00000697	1849
Missense in Polyphen		47	51.078	0.92015		660
Synonymous	0.594	51	56.7	0.900	0.00000307	544
Loss of Function	1.79	8	15.6	0.512	7.89e-7	188

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000294	0.0000294
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000655	0.0000544
Finnish	0.0000470	0.0000462
European (Non-Finnish)	0.0000821	0.0000791
Middle Eastern	0.0000655	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Chaperone protein which promotes assembly of the 20S proteasome as part of a heterodimer with PSMG2. 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: 0.116

Intolerance Scores

• loftool: 0.816
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.7

Haploinsufficiency Scores

• pHI: 0.0967
• hipred: Y
• hipred_score: 0.661
• ghis: 0.563

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.132

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Psmg1
• Phenotype: embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; normal 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype

Gene ontology

• Biological process: cerebellar granule cell precursor proliferation;proteasome assembly;proteasome core complex assembly
• Cellular component: nucleus;nucleoplasm;cytoplasm;endoplasmic reticulum;Golgi apparatus;cytosol
• Molecular function: protein binding;proteasome binding