PSMG4

proteasome assembly chaperone 4

Basic information

Region (hg38): 6:3231402-3303373

Previous symbols: [ "C6orf86" ]

Links

ENSG00000180822 ∙ NCBI:389362 ∙ OMIM:617550 ∙ HGNC:21108 ∙ Uniprot:Q5JS54 ∙ 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 PSMG4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSMG4 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2	1		3
Total	0	0	8	1	0

Variants in PSMG4

This is a list of pathogenic ClinVar variants found in the PSMG4 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-3232126-C-T			Likely benign (Jul 01, 2023)
6-3259039-T-C		not specified	Likely benign (Jun 18, 2024)
6-3259074-A-G		not specified	Uncertain significance (Dec 17, 2021)
6-3259090-A-G		not specified	Uncertain significance (Nov 09, 2021)
6-3259110-G-A		not specified	Uncertain significance (Dec 06, 2022)
6-3259123-C-T		not specified	Uncertain significance (Dec 07, 2023)
6-3259143-G-C		not specified	Uncertain significance (May 13, 2024)
6-3263706-C-T		not specified	Uncertain significance (Nov 05, 2021)
6-3264222-G-C		not specified	Uncertain significance (Oct 24, 2023)
6-3264227-G-A		not specified	Uncertain significance (Nov 22, 2021)
6-3264247-G-A		not specified	Likely benign (Sep 16, 2021)
6-3267653-G-A		not specified	Uncertain significance (Feb 23, 2023)
6-3273069-T-A		not specified	Uncertain significance (Apr 07, 2022)
6-3273111-C-G		not specified	Uncertain significance (Feb 27, 2023)
6-3273137-T-C		not specified	Uncertain significance (Jul 20, 2021)
6-3273147-C-T		not specified	Uncertain significance (Jun 07, 2024)
6-3273185-T-G		not specified	Uncertain significance (Feb 13, 2024)
6-3273219-C-T		not specified	Uncertain significance (Jun 22, 2023)
6-3273379-C-T			Benign (Aug 07, 2018)
6-3273382-G-A			Benign (Dec 31, 2019)
6-3283860-C-G			Likely benign (Aug 01, 2022)
6-3283860-C-T			Benign (Oct 09, 2018)
6-3283869-G-C		not specified	Uncertain significance (Feb 15, 2023)
6-3283940-C-T		not specified	Likely benign (Feb 13, 2023)
6-3283971-C-T		not specified	Uncertain significance (Jun 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSMG4	protein_coding	protein_coding	ENST00000419065	4	71971

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00187	0.502	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.954	36	56.1	0.642	0.00000308	1033
Missense in Polyphen		8	19.386	0.41267		421
Synonymous	0.747	19	23.6	0.804	0.00000151	313
Loss of Function	0.102	4	4.23	0.946	1.78e-7	74

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Chaperone protein which promotes assembly of the 20S proteasome.

Intolerance Scores

• rvis_EVS: 0.72
• rvis_percentile_EVS: 85.92

Haploinsufficiency Scores

• ghis: 0.658

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.166

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Psmg4

Gene ontology

• Biological process: proteasome assembly