LMLN
protein-codingleishmanolysin like peptidase
Gene summary
This gene encodes a zinc-metallopeptidase. The encoded protein may play a role in cell migration and invasion. Studies of a similar protein in Drosophila indicate a potential role in mitotic progression. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2009]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~83.5 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 LMLN variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001136049.3. 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 | 2 | 1 | 1 | 4 | ||
| missense | 67 | 2 | 69 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 69 | 3 | 1 | 73 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001129521.3 | 17 | MANE Select | |
| Ensembl | ENSP00000410926.3 | 17 | MANE Select | |
| RefSeq | NP_149018.3 | 16 | Standard | |
| Ensembl | ENSP00000328829.5 | 16 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| lmln | Danio rerio | Structure: melanocyte Quality: dispersed abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- proteolysis
- cell cycle
- cell adhesion
- cell division
Molecular Function
- metalloendopeptidase activity
- peptidase activity
- metal ion binding
Cellular Component
- cytoplasm
- lipid droplet
- cytosol
- focal adhesion
- membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000420910
- Coding exons
- 17
- Length
- 83521
- Individuals with no LoFs
- 125619
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 128
- Defined
- 125748
- p
- 0.000513
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.90 | 282 | 387 | 0.729 | 0.0000200 | 4503 |
| Missense (PolyPhen) | 69 | 126.95 | 0.5435 | 1515 | ||
| Synonymous | 0.300 | 140 | 145 | 0.968 | 0.00000793 | 1319 |
| Loss of Function | 2.22 | 29 | 45.1 | 0.643 | 0.00000250 | 496 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00056 | 0.00055 | rare |
| Latino/Admixed American | 0.00069 | 0.00067 | rare |
| Ashkenazi Jewish | 0.0043 | 0.0043 | notable |
| East Asian | 0.00034 | 0.00033 | rare |
| Finnish | 0.000093 | 0.000092 | rare |
| European (Non-Finnish) | 0.00028 | 0.00027 | rare |
| South Asian | 0.00043 | 0.00039 | rare |
| Other | 0.00067 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Metalloprotease. {ECO:0000250|UniProtKB:Q9VH19}.;
Recessive Scores
- pRec
- 0.454
Intolerance Scores
- LoFtool
- 0.894
- RVIS EVS
- -0.49
- RVIS percentile EVS
- 22.65
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.513
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |