LGMN
legumain
Basic information
Region (hg38): 14:92703807-92748679
Previous symbols: [ "PRSC1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (66 variants)
- not_provided (2 variants)
- High_myopia (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the LGMN gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005606.7. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 65 | 67 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 65 | 2 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LGMN | protein_coding | protein_coding | ENST00000393218 | 13 | 44896 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000405 | 0.998 | 125722 | 0 | 26 | 125748 | 0.000103 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.22 | 204 | 259 | 0.787 | 0.0000146 | 2867 |
| Missense in Polyphen | 21 | 57.472 | 0.3654 | 668 | ||
| Synonymous | 0.537 | 100 | 107 | 0.934 | 0.00000745 | 797 |
| Loss of Function | 2.75 | 10 | 24.8 | 0.404 | 0.00000113 | 289 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000213 | 0.000213 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000546 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000179 | 0.000176 |
| Middle Eastern | 0.0000546 | 0.0000544 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Has a strict specificity for hydrolysis of asparaginyl bonds. Can also cleave aspartyl bonds slowly, especially under acidic conditions. Required for normal lysosomal protein degradation in renal proximal tubules. Required for normal degradation of internalized EGFR. Plays a role in the regulation of cell proliferation via its role in EGFR degradation (By similarity). May be involved in the processing of proteins for MHC class II antigen presentation in the lysosomal/endosomal system. {ECO:0000250, ECO:0000269|PubMed:23776206}.;
- Pathway
- Antigen processing and presentation - Homo sapiens (human);Lysosome - Homo sapiens (human);Trafficking and processing of endosomal TLR;Toll-Like Receptors Cascades;MHC class II antigen presentation;Innate Immune System;Immune System;Adaptive Immune System
(Consensus)
Recessive Scores
- pRec
- 0.325
Intolerance Scores
- loftool
- 0.829
- rvis_EVS
- -0.02
- rvis_percentile_EVS
- 52.09
Haploinsufficiency Scores
- pHI
- 0.189
- hipred
- N
- hipred_score
- 0.406
- ghis
- 0.530
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.521
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Lgmn
- Phenotype
- liver/biliary system phenotype; hematopoietic system phenotype; limbs/digits/tail phenotype; immune system phenotype; homeostasis/metabolism phenotype; renal/urinary system phenotype; skeleton phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); cellular phenotype;
Zebrafish Information Network
- Gene name
- lgmn
- Affected structure
- vertebra
- Phenotype tag
- abnormal
- Phenotype quality
- increased occurrence
Gene ontology
- Biological process
- renal system process;proteolysis;vacuolar protein processing;memory;positive regulation of cell population proliferation;associative learning;response to acidic pH;negative regulation of gene expression;antigen processing and presentation of exogenous peptide antigen via MHC class II;receptor catabolic process;cellular response to hepatocyte growth factor stimulus;negative regulation of multicellular organism growth;vitamin D metabolic process;negative regulation of neuron apoptotic process;positive regulation of mitotic cell cycle;proteolysis involved in cellular protein catabolic process;cellular response to calcium ion;positive regulation of monocyte chemotaxis;dendritic spine organization;activation of cysteine-type endopeptidase activity;self proteolysis;positive regulation of long-term synaptic potentiation;negative regulation of ERBB signaling pathway;cellular response to amyloid-beta;positive regulation of endothelial cell chemotaxis
- Cellular component
- extracellular region;cytoplasm;lysosome;late endosome;endolysosome lumen;lysosomal lumen;apical part of cell;perinuclear region of cytoplasm;extracellular exosome
- Molecular function
- cysteine-type endopeptidase activity;peptidase activity;tau protein binding