UBXN6
protein-codingUBX domain protein 6, the group of UBX domain containing
Gene summary
Enables ATPase binding activity. Involved in several processes, including ERAD pathway; endosome to lysosome transport via multivesicular body sorting pathway; and protein unfolding. Located in bounding membrane of organelle and cytosol. Part of endosome and protein-containing complex. [provided by Alliance of Genome Resources, Jun 2026]
- UBXD1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~12.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to UBXN6 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_025241.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 103 | 103 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 6 | 6 | ||||
| Total | 0 | 0 | 109 | 1 | 0 | 110 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_079517.1 | 11 | MANE Select | |
| Ensembl | ENSP00000301281.5 | 11 | MANE Select | |
| RefSeq | NP_001164562.1 | 10 | Standard | |
| Ensembl | ENSP00000378246.2 | 10 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Protein processing in endoplasmic reticulum - Homo sapiens (human)
Biological Process
- macroautophagy
- endosome to lysosome transport via multivesicular body sorting pathway
- ERAD pathway
Molecular Function
- protein binding
Cellular Component
- nucleus
- cytoplasm
- lysosomal membrane
- microtubule organizing center
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000301281
- Coding exons
- 11
- Length
- 12824
- Individuals with no LoFs
- 125695
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 51
- Defined
- 125746
- p
- 0.000203
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.586 | 303 | 276 | 1.10 | 0.0000181 | 2804 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00018 | rare |
| Latino/Admixed American | 0.00035 | 0.00035 | rare |
| Ashkenazi Jewish | 0.00020 | 0.00020 | rare |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00019 | 0.00018 | rare |
| South Asian | 0.00023 | 0.00023 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- 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}.;
Recessive Scores
- pRec
- 0.105
Intolerance Scores
- LoFtool
- 0.813
- RVIS EVS
- -0.17
- RVIS percentile EVS
- 40.63
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.826
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |