MINDY1
protein-codingMINDY lysine 48 deubiquitinase 1, the group of MINDY deubiquitinases
Gene summary
Enables K48-linked deubiquitinase activity; K48-linked polyubiquitin modification-dependent protein binding activity; and cysteine-type carboxypeptidase activity. Predicted to be involved in proteolysis. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]
- FAM63A
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~11.8 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 MINDY1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001376665.1. 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 | 3 | 1 | 4 | |||
| missense | 68 | 3 | 71 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 77 | 4 | 0 | 81 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001363594.1 | 9 | MANE Select | |
| Ensembl | ENSP00000507359.1 | 9 | MANE Select | |
| RefSeq | NP_001035307.2 | 9 | Standard | |
| RefSeq | NP_001156730.3 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- biological_process
- protein K48-linked deubiquitination
Molecular Function
- thiol-dependent ubiquitin-specific protease activity
- protein binding
- cysteine-type carboxypeptidase activity
- K48-linked polyubiquitin modification-dependent protein binding
- Lys48-specific deubiquitinase activity
Cellular Component
- nucleus
- nucleoplasm
- cytosol
- nuclear body
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000361738
- Coding exons
- 10
- Length
- 11827
- Individuals with no LoFs
- 125650
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 97
- Defined
- 125747
- p
- 0.000386
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.21 | 233 | 291 | 0.800 | 0.0000160 | 3351 |
| Missense (PolyPhen) | 85 | 116.08 | 0.73223 | 1435 | ||
| Synonymous | -1.26 | 139 | 121 | 1.15 | 0.00000691 | 1062 |
| Loss of Function | 0.419 | 25 | 27.4 | 0.913 | 0.00000153 | 270 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00037 | 0.00037 | rare |
| Latino/Admixed American | 0.00088 | 0.00087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00044 | 0.00044 | rare |
| Finnish | 0.000094 | 0.000092 | rare |
| European (Non-Finnish) | 0.00035 | 0.00034 | rare |
| South Asian | 0.00023 | 0.00023 | rare |
| Other | 0.00082 | 0.00081 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Hydrolase that can specifically remove 'Lys-48'-linked conjugated ubiquitin from proteins. Has exodeubiquitinase activity and has a preference for long polyubiquitin chains. May play a regulatory role at the level of protein turnover. {ECO:0000269|PubMed:27292798, ECO:0000269|PubMed:28082312}.;
Recessive Scores
- pRec
- 0.0637
Intolerance Scores
- RVIS EVS
- 0.46
- RVIS percentile EVS
- 78.69
Essentials
- Essential (gene trap)
- N