PSMF1

proteasome inhibitor subunit 1, the group of Proteasome

Basic information

Region (hg38): 20:1113240-1189415

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.

• not_specified (42 variants)
• not_provided (4 variants)
• Complex_neurodevelopmental_disorder_with_motor_features (1 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. These statistics are base on transcript: NM_000006814.5. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	2
missense			42	2	1	45
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	42	3	2

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