AMZ1
protein-codingarchaelysin family metallopeptidase 1, the group of M54 metallopeptidase family
Gene summary
Predicted to enable metal ion binding activity and metallopeptidase activity. Predicted to be involved in proteolysis. [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 ~96.0 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 AMZ1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001384743.1. 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 | 8 | ||
| missense | 140 | 15 | 5 | 160 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 143 | 17 | 9 | 169 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001371672.1 | 6 | MANE Select | |
| Ensembl | ENSP00000506962.1 | 6 | MANE Select | |
| RefSeq | NP_001271284.1 | 5 | Standard | |
| RefSeq | NP_001308695.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- proteolysis
Molecular Function
- peptidase activity
- metallopeptidase activity
- zinc ion binding
Cellular Component
- cellular_component
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000312371
- Coding exons
- 6
- Length
- 95979
- Individuals with no LoFs
- 125608
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 127
- Defined
- 125736
- p
- 0.000509
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -3.59 | 485 | 308 | 1.58 | 0.0000208 | 3143 |
| Missense (PolyPhen) | 122 | 82.009 | 1.4876 | 885 | ||
| Synonymous | -4.68 | 212 | 141 | 1.50 | 0.0000103 | 1032 |
| Loss of Function | -2.36 | 28 | 17.4 | 1.61 | 8.33e-7 | 189 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0018 | 0.0017 | notable |
| Latino/Admixed American | 0.00047 | 0.00046 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00039 | 0.00038 | rare |
| Finnish | 0.00020 | 0.00018 | rare |
| European (Non-Finnish) | 0.00055 | 0.00052 | rare |
| South Asian | 0.00039 | 0.00036 | rare |
| Other | 0.00050 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Zinc metalloprotease. Exhibits aminopeptidase activity against neurogranin in vitro. Does not hydrolyze angiotensin-2. {ECO:0000269|PubMed:15972818}.;
Recessive Scores
- pRec
- 0.106
Intolerance Scores
- RVIS EVS
- 0.26
- RVIS percentile EVS
- 69.84
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.263
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |