UBXN6

UBX domain protein 6, the group of UBX domain containing

Basic information

Region (hg38): 19:4444998-4457794

Previous symbols: [ "UBXD1" ]

Links

ENSG00000167671 ∙ NCBI:80700 ∙ OMIM:611946 ∙ HGNC:14928 ∙ Uniprot:Q9BZV1 ∙ 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 UBXN6 gene.

• Inborn genetic diseases (33 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBXN6 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			33			33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	1	0

Variants in UBXN6

This is a list of pathogenic ClinVar variants found in the UBXN6 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-4445530-C-T		not specified	Uncertain significance (Sep 07, 2022)
19-4445552-C-G		not specified	Uncertain significance (Jan 30, 2024)
19-4445554-C-T		not specified	Uncertain significance (Jun 18, 2021)
19-4445562-G-A		not specified	Uncertain significance (Aug 29, 2022)
19-4445584-C-T		not specified	Uncertain significance (Mar 29, 2022)
19-4445587-C-T		not specified	Uncertain significance (Mar 04, 2024)
19-4446159-C-A		not specified	Uncertain significance (Jul 25, 2023)
19-4446361-T-C		not specified	Uncertain significance (Jun 17, 2022)
19-4446381-C-T		not specified	Uncertain significance (Sep 16, 2021)
19-4446384-A-G		not specified	Uncertain significance (Sep 26, 2023)
19-4446388-C-G		not specified	Uncertain significance (Sep 16, 2021)
19-4446396-C-A		not specified	Uncertain significance (Apr 13, 2022)
19-4446396-C-T		not specified	Uncertain significance (Jun 21, 2023)
19-4446397-G-A		not specified	Uncertain significance (Jan 30, 2024)
19-4446539-T-C		not specified	Uncertain significance (Dec 02, 2022)
19-4446541-G-T		not specified	Uncertain significance (Dec 20, 2023)
19-4446567-G-T		not specified	Uncertain significance (Jan 04, 2024)
19-4446618-C-T		not specified	Uncertain significance (Oct 05, 2023)
19-4446621-G-A		not specified	Uncertain significance (May 17, 2023)
19-4446632-G-A		not specified	Uncertain significance (Jan 06, 2023)
19-4446651-T-C		not specified	Uncertain significance (Aug 02, 2021)
19-4446683-G-C		not specified	Uncertain significance (Jan 18, 2023)
19-4446686-G-C		not specified	Uncertain significance (Aug 23, 2021)
19-4446874-A-G		not specified	Uncertain significance (Oct 26, 2022)
19-4446891-G-A			Likely benign (Mar 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBXN6	protein_coding	protein_coding	ENST00000301281	11	12824

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000548	0.970	125695	0	51	125746	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.586	303	276	1.10	0.0000181	2804
Missense in Polyphen		83	89.63	0.92603		901
Synonymous	-1.61	156	132	1.18	0.00000990	876
Loss of Function	2.00	12	22.2	0.542	0.00000103	254

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000541	0.000536
Ashkenazi Jewish	0.000200	0.000198
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000190	0.000185
Middle Eastern	0.000218	0.000217
South Asian	0.000229	0.000229
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May negatively regulate the ATPase activity of VCP, an ATP-driven segregase that associates with different cofactors to control a wide variety of cellular processes (PubMed:26475856). As a cofactor of VCP, it may play a role in the transport of CAV1 to lysosomes for degradation (PubMed:21822278, PubMed:23335559). It may also play a role in endoplasmic reticulum-associated degradation (ERAD) of misfolded proteins (PubMed:19275885). Together with VCP and other cofactors, it may play a role in macroautophagy, regulating for instance the clearance of damaged lysosomes (PubMed:27753622). {ECO:0000269|PubMed:19275885, ECO:0000269|PubMed:21822278, ECO:0000269|PubMed:23335559, ECO:0000269|PubMed:26475856, ECO:0000269|PubMed:27753622}.
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.813
• rvis_EVS: -0.17
• rvis_percentile_EVS: 40.63

Haploinsufficiency Scores

• pHI: 0.0989
• hipred: Y
• hipred_score: 0.746
• ghis: 0.481

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.826

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ubxn6

Gene ontology

• Biological process: macroautophagy;endosome to lysosome transport via multivesicular body sorting pathway;ERAD pathway
• Cellular component: nucleus;cytoplasm;lysosomal membrane;microtubule organizing center;cytosol;extrinsic component of membrane;early endosome membrane;late endosome membrane;protein-containing complex;extracellular exosome
• Molecular function: protein binding