LNPEP
leucyl and cystinyl aminopeptidase, the group of Aminopeptidases|M1 metallopeptidases
Basic information
Region (hg38): 5:96935394-97037513
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (112 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the LNPEP gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005575.3. 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 | 0 | |||||
| missense | 109 | 112 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 109 | 3 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LNPEP | protein_coding | protein_coding | ENST00000231368 | 18 | 102122 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.000427 | 125721 | 0 | 22 | 125743 | 0.0000875 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.44 | 432 | 525 | 0.823 | 0.0000254 | 6724 |
| Missense in Polyphen | 141 | 194.72 | 0.72412 | 2591 | ||
| Synonymous | 0.706 | 179 | 191 | 0.935 | 0.00000937 | 1930 |
| Loss of Function | 5.87 | 7 | 53.2 | 0.132 | 0.00000281 | 645 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000322 | 0.000322 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000626 | 0.0000615 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.0000656 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Release of an N-terminal amino acid, cleaves before cysteine, leucine as well as other amino acids. Degrades peptide hormones such as oxytocin, vasopressin and angiotensin III, and plays a role in maintaining homeostasis during pregnancy. May be involved in the inactivation of neuronal peptides in the brain. Cleaves Met-enkephalin and dynorphin. Binds angiotensin IV and may be the angiotensin IV receptor in the brain. {ECO:0000269|PubMed:11389728, ECO:0000269|PubMed:11707427, ECO:0000269|PubMed:1731608}.;
- Pathway
- Renin-angiotensin system - Homo sapiens (human);Vesicle-mediated transport;Membrane Trafficking;TCR;Immune System;Adaptive Immune System;Endosomal/Vacuolar pathway;Antigen processing-Cross presentation;Class I MHC mediated antigen processing & presentation;Translocation of GLUT4 to the plasma membrane;Insulin-mediated glucose transport
(Consensus)
Recessive Scores
- pRec
- 0.305
Intolerance Scores
- loftool
- 0.358
- rvis_EVS
- 0.18
- rvis_percentile_EVS
- 66.24
Haploinsufficiency Scores
- pHI
- 0.0765
- hipred
- Y
- hipred_score
- 0.696
- ghis
- 0.578
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.820
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Lnpep
- Phenotype
- homeostasis/metabolism 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan);
Gene ontology
- Biological process
- protein polyubiquitination;antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent;proteolysis;cell-cell signaling;female pregnancy;protein catabolic process;peptide catabolic process;SMAD protein signal transduction;negative regulation of cold-induced thermogenesis
- Cellular component
- extracellular region;cytoplasm;lysosomal membrane;cytosol;integral component of plasma membrane;membrane;cytoplasmic vesicle membrane;early endosome lumen;perinuclear region of cytoplasm
- Molecular function
- aminopeptidase activity;protein binding;metallopeptidase activity;zinc ion binding;peptide binding;metalloaminopeptidase activity