UBXN1

UBX domain protein 1, the group of UBX domain containing

Basic information

Region (hg38): 11:62676498-62679117

Links

ENSG00000162191 ∙ NCBI:51035 ∙ OMIM:616378 ∙ HGNC:18402 ∙ Uniprot:Q04323 ∙ 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 UBXN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBXN1 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		1
missense			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	21	2	0

Variants in UBXN1

This is a list of pathogenic ClinVar variants found in the UBXN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-62676746-C-A		not specified	Uncertain significance (Dec 14, 2024)
11-62676752-C-T		not specified	Uncertain significance (Jul 19, 2023)
11-62676774-C-G		not specified	Uncertain significance (Nov 08, 2024)
11-62676871-A-T		not specified	Uncertain significance (Jan 29, 2024)
11-62676912-C-G			Likely benign (Feb 01, 2023)
11-62676960-G-C		not specified	Uncertain significance (Oct 07, 2022)
11-62676965-C-T		not specified	Uncertain significance (Oct 26, 2022)
11-62676966-G-A		not specified	Uncertain significance (Jan 09, 2023)
11-62677528-C-G		not specified	Uncertain significance (Jan 24, 2023)
11-62677531-T-C		not specified	Uncertain significance (Jan 22, 2025)
11-62677541-C-T		not specified	Uncertain significance (Mar 28, 2022)
11-62677573-G-A		not specified	Uncertain significance (Aug 27, 2024)
11-62677621-A-G		not specified	Uncertain significance (Jul 23, 2024)
11-62677811-G-C		not specified	Uncertain significance (Nov 17, 2022)
11-62677957-C-A		not specified	Uncertain significance (Oct 03, 2023)
11-62678065-C-T		not specified	Uncertain significance (Nov 08, 2024)
11-62678342-T-C		not specified	Uncertain significance (Jan 20, 2025)
11-62678346-T-C		not specified	Uncertain significance (Aug 16, 2021)
11-62678384-C-A		not specified	Uncertain significance (Jul 13, 2021)
11-62678410-TACAA-T			Likely benign (Dec 01, 2022)
11-62678521-G-C		not specified	Uncertain significance (Jan 29, 2024)
11-62678538-G-A			Likely benign (Feb 01, 2023)
11-62678596-A-G		not specified	Uncertain significance (Jun 11, 2024)
11-62678711-C-G		not specified	Uncertain significance (May 20, 2024)
11-62678720-C-T		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBXN1	protein_coding	protein_coding	ENST00000294119	8	2598

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.728	0.272	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.838	160	193	0.830	0.0000116	1983
Missense in Polyphen		55	77.16	0.7128		814
Synonymous	-1.25	82	68.8	1.19	0.00000352	637
Loss of Function	3.20	3	17.4	0.172	8.50e-7	194

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	0.0000949	0.0000924
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ubiquitin-binding protein that plays a role in the modulation of innate immune response. Blocks both the RIG-I-like receptors (RLR) and NF-kappa-B pathways. Following viral infection, UBXN1 is induced and recruited to the RLR component MAVS. In turn, interferes with MAVS oligomerization, and disrupts the MAVS/TRAF3/TRAF6 signalosome. This function probably serves as a brake to prevent excessive RLR signaling (PubMed:23545497). Interferes with the TNFalpha-triggered NF-kappa-B pathway by interacting with cellular inhibitors of apoptosis proteins (cIAPs) and thereby inhibiting their recruitment to TNFR1 (PubMed:25681446). Prevents also the activation of NF-kappa-B by associating with CUL1 and thus inhibiting NF-kappa-B inhibitor alpha/NFKBIA degradation that remains bound to NF-kappa-B (PubMed:28152074). Interacts with the BRCA1-BARD1 heterodimer and regulates its activity. Specifically binds 'Lys-6'-linked polyubiquitin chains. Interaction with autoubiquitinated BRCA1 leads to the inhibition of the E3 ubiquitin-protein ligase activity of the BRCA1-BARD1 heterodimer (PubMed:20351172). Component of a complex required to couple deglycosylation and proteasome-mediated degradation of misfolded proteins in the endoplasmic reticulum that are retrotranslocated in the cytosol. {ECO:0000269|PubMed:20351172, ECO:0000269|PubMed:23545497, ECO:0000269|PubMed:25681446, ECO:0000269|PubMed:28152074}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Asparagine N-linked glycosylation;N-glycan trimming in the ER and Calnexin/Calreticulin cycle (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.415
• rvis_EVS: 0.48
• rvis_percentile_EVS: 79.04

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.701
• ghis: 0.404

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.567

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ubxn1

Gene ontology

• Biological process: protein folding;viral process;negative regulation of protein ubiquitination;negative regulation of proteasomal ubiquitin-dependent protein catabolic process;proteasome-mediated ubiquitin-dependent protein catabolic process;negative regulation of protein K48-linked deubiquitination;negative regulation of ERAD pathway;negative regulation of ubiquitin-specific protease activity
• Cellular component: nucleus;cytoplasm;endoplasmic reticulum;cytosol;dendrite;VCP-NPL4-UFD1 AAA ATPase complex;neuronal cell body
• Molecular function: protein binding;polyubiquitin modification-dependent protein binding;ubiquitin protein ligase binding;K48-linked polyubiquitin modification-dependent protein binding;ubiquitin binding;ATPase binding;K6-linked polyubiquitin modification-dependent protein binding;proteasome regulatory particle binding