PSMD6

proteasome 26S subunit, non-ATPase 6, the group of Proteasome

Basic information

Region (hg38): 3:64010549-64024010

Links

ENSG00000163636

∙ NCBI:9861 ∙ OMIM:617857 ∙ HGNC:9564 ∙ Uniprot:Q15008 ∙ 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 PSMD6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSMD6 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			12 clinvar			12
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in PSMD6

This is a list of pathogenic ClinVar variants found in the PSMD6 region.

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

Position	Phenotype	Significance	ClinVar
3-64010763-G-T	not specified	Uncertain significance (Jun 12, 2023)	2559710
3-64010930-C-T	not specified	Uncertain significance (Aug 16, 2021)	2374128
3-64013557-G-A		Uncertain significance (Feb 01, 2023)	2498933
3-64018626-G-A	not specified	Uncertain significance (Aug 21, 2023)	2619788
3-64018679-A-G	not specified	Uncertain significance (Mar 18, 2024)	3311006
3-64018694-G-A	not specified	Uncertain significance (May 16, 2024)	3311010
3-64018823-C-T	not specified	Uncertain significance (Dec 08, 2023)	3220459
3-64018839-T-G	not specified	Uncertain significance (Jan 10, 2022)	2280733
3-64018873-G-C	not specified	Uncertain significance (May 13, 2024)	3311009
3-64018951-T-C	not specified	Uncertain significance (Apr 09, 2024)	3311004
3-64019000-G-A	not specified	Uncertain significance (Feb 27, 2023)	2489657
3-64019348-A-C	not specified	Uncertain significance (Dec 07, 2021)	2410412
3-64022359-T-C	not specified	Uncertain significance (Dec 09, 2023)	3220458
3-64022407-G-C	not specified	Uncertain significance (Apr 20, 2024)	3311008
3-64022455-T-C	not specified	Uncertain significance (Feb 05, 2024)	3220457
3-64022800-G-GTTCT	See cases	Uncertain significance (Mar 14, 2020)	930281
3-64023287-C-T	not specified	Uncertain significance (Apr 25, 2023)	2516419
3-64023302-C-T	not specified	Uncertain significance (Jun 04, 2024)	3311005
3-64023329-G-T	not specified	Uncertain significance (Sep 17, 2021)	3220460
3-64023331-T-G	not specified	Uncertain significance (Apr 13, 2023)	2536770

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSMD6	protein_coding	protein_coding	ENST00000295901	8	13434

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.995	0.00482	125675	0	10	125685	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.26	163	215	0.759	0.0000112	2542
Missense in Polyphen		41	76.848	0.53352		961
Synonymous	-1.08	91	78.8	1.15	0.00000397	728
Loss of Function	3.96	1	20.2	0.0495	0.00000110	255

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000626	0.0000626
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000711	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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. {ECO:0000269|PubMed:1317798}.;
Pathway: Epstein-Barr virus infection - Homo sapiens (human);Proteasome - Homo sapiens (human);Proteasome Degradation;Parkin-Ubiquitin Proteasomal System pathway;TLR NFkB;Neutrophil degranulation;B cell receptor signaling;Post-translational protein modification;Metabolism of proteins;DroToll-like;Notch;Hedgehog;Innate Immune System;Immune System;IL-1 NFkB;IL-1 p38;IL-1 JNK;TGF-beta super family signaling pathway canonical;TLR p38;UCH proteinases;Neddylation;Ub-specific processing proteases;JAK STAT pathway and regulation;Deubiquitination;TNFalpha;TLR JNK;TNF;Wnt Canonical;Wnt Mammals;CD4 T cell receptor signaling-NFkB cascade;CD4 T cell receptor signaling (Consensus)

Recessive Scores

pRec: 0.159

Intolerance Scores

loftool: 0.106
rvis_EVS: -0.6
rvis_percentile_EVS: 17.91

Haploinsufficiency Scores

pHI: 0.962
hipred: Y
hipred_score: 0.825
ghis: 0.536

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.846

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Psmd6
Phenotype

Zebrafish Information Network

Gene name: psmd6
Affected structure: midbrain hindbrain boundary
Phenotype tag: abnormal
Phenotype quality: hemorrhagic

Gene ontology

Biological process: proteolysis;protein deubiquitination;proteasome-mediated ubiquitin-dependent protein catabolic process;neutrophil degranulation;post-translational protein modification;regulation of catalytic activity
Cellular component: proteasome complex;extracellular region;nucleoplasm;cytosol;proteasome regulatory particle;proteasome accessory complex;secretory granule lumen;ficolin-1-rich granule lumen
Molecular function: protein binding;ATPase activity;enzyme regulator activity