PSMC6

proteasome 26S subunit, ATPase 6, the group of AAA ATPases|Proteasome

Basic information

Region (hg38): 14:52707178-52728590

Links

ENSG00000100519

∙ NCBI:5706 ∙ OMIM:602708 ∙ HGNC:9553 ∙ Uniprot:P62333 ∙ 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 PSMC6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSMC6 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 clinvar		1
missense			4 clinvar			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1 clinvar			1
Total	0	0	5	1	0

Variants in PSMC6

This is a list of pathogenic ClinVar variants found in the PSMC6 region.

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

Position	Phenotype	Significance	ClinVar
14-52707190-G-A	not specified	Uncertain significance (Nov 09, 2023)	3220414
14-52707193-A-C	not specified	Uncertain significance (Mar 29, 2023)	2530978
14-52707200-A-G	not specified	Uncertain significance (Oct 25, 2024)	3426964
14-52707208-C-T	not specified	Uncertain significance (Feb 14, 2024)	3220415
14-52707211-C-T	not specified	Uncertain significance (Apr 07, 2022)	2206877
14-52707216-C-T		Likely benign (Jul 06, 2018)	717661
14-52708333-C-A	not specified	Uncertain significance (May 13, 2024)	3310979
14-52723976-A-G	not specified	Uncertain significance (Jan 10, 2023)	3220413

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSMC6	protein_coding	protein_coding	ENST00000445930	14	21416

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00338	125554	2	191	125747	0.000768

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.32	85	225	0.377	0.0000115	2633
Missense in Polyphen		11	72.223	0.15231		868
Synonymous	0.157	73	74.7	0.977	0.00000373	746
Loss of Function	4.32	2	25.6	0.0782	0.00000134	320

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00644	0.00637
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00213	0.00213
European (Non-Finnish)	0.000301	0.000299
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000327
Other	0.000655	0.000652

dbNSFP

Source: dbNSFP

Function: FUNCTION: Component of the 26S proteasome, a multiprotein complex involved in the ATP-dependent degradation of ubiquitinated proteins. This complex plays a key role in the maintenance of protein homeostasis by removing misfolded or damaged proteins, which could impair cellular functions, and by removing proteins whose functions are no longer required. Therefore, the proteasome participates in numerous cellular processes, including cell cycle progression, apoptosis, or DNA damage repair. PSMC6 belongs to the heterohexameric ring of AAA (ATPases associated with diverse cellular activities) proteins that unfolds ubiquitinated target proteins that are concurrently translocated into a proteolytic chamber and degraded into peptides. {ECO:0000269|PubMed:1317798}.;
Pathway: Epstein-Barr virus infection - Homo sapiens (human);Proteasome - Homo sapiens (human);Proteasome Degradation;Parkin-Ubiquitin Proteasomal System pathway;Post-translational protein modification;Metabolism of proteins;UCH proteinases;Neddylation;Ub-specific processing proteases;Deubiquitination (Consensus)

Intolerance Scores

loftool: 0.118
rvis_EVS: -0.12
rvis_percentile_EVS: 44.89

Haploinsufficiency Scores

pHI: 0.999
hipred: Y
hipred_score: 0.831
ghis: 0.629

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Psmc6
Phenotype

Zebrafish Information Network

Gene name: psmc6
Affected structure: anatomical system
Phenotype tag: abnormal
Phenotype quality: quality

Gene ontology

Biological process: ubiquitin-dependent protein catabolic process;protein deubiquitination;ubiquitin-dependent ERAD pathway;post-translational protein modification;positive regulation of RNA polymerase II transcriptional preinitiation complex assembly;positive regulation of proteasomal protein catabolic process
Cellular component: proteasome complex;nucleus;nucleoplasm;cytosol;proteasome regulatory particle, base subcomplex;membrane;proteasome accessory complex;cytosolic proteasome complex;extracellular exosome
Molecular function: protein binding;ATP binding;ATPase activity;protein binding, bridging;proteasome-activating ATPase activity;identical protein binding