PSME3IP1

proteasome activator subunit 3 interacting protein 1

Basic information

Region (hg38): 16:57152466-57186116

Previous symbols: [ "C16orf94", "FAM192A" ]

Links

ENSG00000172775 ∙ NCBI:80011 ∙ OMIM:617766 ∙ HGNC:29856 ∙ Uniprot:Q9GZU8 ∙ 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 PSME3IP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSME3IP1 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						0
missense			15			15
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	0	0

Variants in PSME3IP1

This is a list of pathogenic ClinVar variants found in the PSME3IP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-57154312-T-C		not specified	Uncertain significance (Apr 28, 2022)
16-57154318-C-T		not specified	Uncertain significance (Sep 17, 2021)
16-57154405-G-C		not specified	Uncertain significance (Aug 29, 2023)
16-57154467-A-T		not specified	Uncertain significance (Feb 11, 2025)
16-57154468-C-T		not specified	Uncertain significance (Dec 28, 2022)
16-57154484-C-T		not specified	Uncertain significance (Nov 08, 2021)
16-57167220-G-A		not specified	Uncertain significance (Feb 27, 2023)
16-57172265-G-C		not specified	Uncertain significance (May 15, 2023)
16-57172340-T-A		not specified	Uncertain significance (Jul 14, 2024)
16-57172345-T-A		not specified	Uncertain significance (Jun 12, 2023)
16-57172346-C-T		not specified	Uncertain significance (May 15, 2024)
16-57172367-T-C		not specified	Uncertain significance (Jun 05, 2024)
16-57172794-C-T		not specified	Uncertain significance (Oct 26, 2021)
16-57173785-G-A		not specified	Uncertain significance (Jan 27, 2025)
16-57173836-C-T		not specified	Uncertain significance (Sep 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSME3IP1	protein_coding	protein_coding	ENST00000309137	6	33651

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.195	0.803	124786	0	8	124794	0.0000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.31	95	138	0.686	0.00000731	1669
Missense in Polyphen		26	44.181	0.58848		567
Synonymous	0.511	50	54.8	0.912	0.00000309	471
Loss of Function	2.69	4	15.4	0.260	9.49e-7	168

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	0.0000928	0.0000928
European (Non-Finnish)	0.0000530	0.0000530
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes the association of the proteasome activator complex subunit PSME3 with the 20S proteasome and regulates its activity. Inhibits PSME3-mediated degradation of some proteasome substrates, probably by affecting their diffusion rate into the catalytic chamber of the proteasome. Also inhibits the interaction of PSME3 with COIL, inhibits accumulation of PSME3 in Cajal bodies and positively regulates the number of Cajal bodies in the nucleus. {ECO:0000269|PubMed:29934401}.

Intolerance Scores

• loftool: 0.196
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.64

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.595
• ghis: 0.517

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam192a

Gene ontology

• Biological process: negative regulation of protein binding;negative regulation of proteasomal protein catabolic process
• Cellular component: nucleus
• Molecular function: protein binding