PSMF1

proteasome inhibitor subunit 1, the group of Proteasome

Basic information

Region (hg38): 20:1113239-1189415

Links

ENSG00000125818 ∙ NCBI:9491 ∙ OMIM:617858 ∙ HGNC:9571 ∙ Uniprot:Q92530 ∙ 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 PSMF1 gene.

• Inborn genetic diseases (27 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSMF1 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			13	2	1	16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1		1	2
non coding			12			12
Total	0	0	25	3	1

Variants in PSMF1

This is a list of pathogenic ClinVar variants found in the PSMF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-1118787-A-G		not specified	Uncertain significance (Oct 02, 2023)
20-1118889-G-C		not specified	Uncertain significance (Sep 27, 2022)
20-1125499-C-G		not specified	Uncertain significance (Feb 16, 2023)
20-1125500-G-A			Benign (May 24, 2018)
20-1125508-A-G		not specified	Likely benign (Nov 01, 2022)
20-1125586-A-G		not specified	Uncertain significance (Jun 21, 2023)
20-1127492-C-G		not specified	Uncertain significance (Mar 02, 2023)
20-1135153-G-A		not specified	Uncertain significance (Sep 01, 2021)
20-1135165-G-C		not specified	Uncertain significance (Sep 14, 2022)
20-1135174-C-T		not specified	Uncertain significance (Jun 30, 2022)
20-1135176-C-T		not specified	Uncertain significance (May 04, 2023)
20-1135177-C-T		not specified	Uncertain significance (Oct 05, 2023)
20-1135203-A-G		not specified	Uncertain significance (Jan 29, 2024)
20-1135221-C-T			Likely benign (May 24, 2018)
20-1135222-G-A		not specified	Uncertain significance (Dec 05, 2022)
20-1135242-G-A		not specified	Uncertain significance (Jul 13, 2021)
20-1135294-G-A		not specified	Uncertain significance (Jul 08, 2022)
20-1163148-G-A			Likely benign (Apr 12, 2018)
20-1163153-T-C			Benign (Dec 31, 2019)
20-1164323-G-A		not specified	Uncertain significance (Aug 21, 2023)
20-1164458-T-C		not specified	Uncertain significance (Aug 04, 2023)
20-1164466-A-T		not specified	Uncertain significance (Oct 13, 2021)
20-1165072-T-C		not specified	Uncertain significance (Sep 22, 2023)
20-1180910-C-A		not specified	Uncertain significance (Sep 30, 2022)
20-1180988-C-T		not specified	Uncertain significance (Jun 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSMF1	protein_coding	protein_coding	ENST00000335877	7	66691

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.31e-8	0.185	125713	0	35	125748	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0597	171	169	1.01	0.00000952	1749
Missense in Polyphen		55	56.567	0.97229		562
Synonymous	0.0833	67	67.9	0.987	0.00000373	563
Loss of Function	0.236	12	12.9	0.929	6.35e-7	149

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000337	0.000337
Ashkenazi Jewish	0.00	0.00
East Asian	0.000490	0.000489
Finnish	0.00	0.00
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.000490	0.000489
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays an important role in control of proteasome function. Inhibits the hydrolysis of protein and peptide substrates by the 20S proteasome. Also inhibits the activation of the proteasome by the proteasome regulatory proteins PA700 and PA28. {ECO:0000269|PubMed:10764772}.
• Pathway: Proteasome - Homo sapiens (human);Post-translational protein modification;Metabolism of proteins;UCH proteinases;Neddylation;Ub-specific processing proteases;Deubiquitination (Consensus)

Recessive Scores

• pRec: 0.0916

Intolerance Scores

• loftool: 0.905
• rvis_EVS: 0.42
• rvis_percentile_EVS: 77.06

Haploinsufficiency Scores

• pHI: 0.739
• hipred: Y
• hipred_score: 0.501
• ghis: 0.409

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.219

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Psmf1
• 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)

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;negative regulation of endopeptidase activity;protein deubiquitination;post-translational protein modification;negative regulation of proteasomal protein catabolic process
• Cellular component: nucleoplasm;endoplasmic reticulum;cytosol;proteasome core complex;membrane;perinuclear region of cytoplasm
• Molecular function: endopeptidase inhibitor activity;protein binding;protein homodimerization activity;protein heterodimerization activity;proteasome binding