MPND
protein-codingMPN domain containing, the group of JAMM/MPN+ metallopeptidase family
Gene summary
Predicted to enable metallopeptidase activity and polyubiquitin modification-dependent protein binding activity. Predicted to be involved in double-strand break repair. Predicted to be part of BRCA1-A complex and BRISC complex. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~16.6 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 MPND variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001300862.2. 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 | 0 | |||||
| missense | 101 | 3 | 104 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 101 | 3 | 0 | 104 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001287791.1 | 13 | MANE Select | |
| Ensembl | ENSP00000471735.1 | 13 | MANE Select | |
| RefSeq | NP_001153318.1 | 11 | Standard | |
| RefSeq | NP_116257.2 | 12 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| mpnd | Danio rerio | Structure: head Quality: decreased size abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- proteolysis
Molecular Function
- metallopeptidase activity
- metal ion binding
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000262966
- Coding exons
- 12
- Length
- 16560
- Individuals with no LoFs
- 124732
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 40
- Defined
- 124772
- p
- 0.000160
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.310 | 214 | 227 | 0.942 | 0.0000140 | 2979 |
| Missense (PolyPhen) | 77 | 81.307 | 0.94703 | 872 | ||
| Synonymous | -0.503 | 110 | 103 | 1.06 | 0.00000699 | 961 |
| Loss of Function | 1.97 | 10 | 19.4 | 0.516 | 8.25e-7 | 269 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00026 | 0.00026 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0011 | 0.0011 | notable |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000080 | 0.000079 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Probable protease. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.0965
Intolerance Scores
- LoFtool
- 0.226
- RVIS EVS
- 0.17
- RVIS percentile EVS
- 65.96
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.895
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |