MINDY2
protein-codingMINDY lysine 48 deubiquitinase 2, the group of MINDY deubiquitinases
Gene summary
Enables peptidase activity and polyubiquitin modification-dependent protein binding activity. Predicted to be involved in chromatin remodeling and proteolysis. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]
- FAM63B
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~90.7 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 MINDY2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001040450.3. 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 | 95 | 3 | 98 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 96 | 3 | 0 | 99 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001035540.1 | 9 | MANE Select | |
| Ensembl | ENSP00000452885.1 | 9 | MANE Select | |
| RefSeq | NP_001035543.1 | 9 | Standard | |
| Ensembl | ENSP00000326194.5 | 6 | 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
- cysteine-type carboxypeptidase activity
- K48-linked polyubiquitin modification-dependent protein binding
- K63-linked polyubiquitin modification-dependent protein binding
- K11-linked polyubiquitin modification-dependent protein binding
Cellular Component
- nucleoplasm
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000559228
- Coding exons
- 9
- Length
- 90709
- Individuals with no LoFs
- 124765
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 29
- Defined
- 124794
- p
- 0.000116
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.559 | 361 | 332 | 1.09 | 0.0000161 | 4041 |
| Missense (PolyPhen) | 104 | 127.68 | 0.81451 | 1700 | ||
| Synonymous | -2.34 | 164 | 130 | 1.26 | 0.00000648 | 1202 |
| Loss of Function | 2.83 | 13 | 29.6 | 0.439 | 0.00000150 | 339 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000071 | 0.000065 | rare |
| Latino/Admixed American | 0.00027 | 0.00026 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000056 | 0.000056 | rare |
| Finnish | 0.000093 | 0.000093 | rare |
| European (Non-Finnish) | 0.00010 | 0.000097 | rare |
| South Asian | 0.00018 | 0.00016 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Hydrolase that can remove 'Lys-48'-linked conjugated ubiquitin from proteins (PubMed:27292798). Binds to polyubiquitin chains of different linkage types, including 'Lys-6', 'Lys-11', 'Lys-29', 'Lys-33', 'Lys-48' and 'Lys-63' (PubMed:28082312). May play a regulatory role at the level of protein turnover (PubMed:27292798). {ECO:0000269|PubMed:27292798, ECO:0000269|PubMed:28082312}.;
Intolerance Scores
- RVIS EVS
- -0.13
- RVIS percentile EVS
- 43.91
Essentials
- Essential (gene trap)
- N