LNPEP

leucyl and cystinyl aminopeptidase, the group of Aminopeptidases|M1 metallopeptidases

Basic information

Region (hg38): 5:96935394-97037513

Links

ENSG00000113441 ∙ NCBI:4012 ∙ OMIM:151300 ∙ HGNC:6656 ∙ Uniprot:Q9UIQ6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LNPEP gene.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			53	1		54
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	53	1	0

Variants in LNPEP

This is a list of pathogenic ClinVar variants found in the LNPEP region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-96979222-G-A		not specified	Uncertain significance (Jun 28, 2023)
5-96979307-G-A		not specified	Uncertain significance (Jun 24, 2022)
5-96979351-G-A		not specified	Uncertain significance (Nov 18, 2023)
5-96979384-G-A		not specified	Uncertain significance (Jul 06, 2021)
5-96979413-C-T		not specified	Uncertain significance (Dec 21, 2023)
5-96979455-G-A		not specified	Uncertain significance (Jul 19, 2023)
5-96979486-C-T		not specified	Uncertain significance (Jun 17, 2024)
5-96979496-G-A		not specified	Uncertain significance (Jan 26, 2022)
5-96979537-G-T		not specified	Uncertain significance (Nov 09, 2021)
5-96979540-G-T		not specified	Uncertain significance (May 30, 2024)
5-96979552-A-C		not specified	Uncertain significance (Nov 03, 2022)
5-96979561-T-C		not specified	Uncertain significance (Oct 27, 2021)
5-96979710-G-A		not specified	Uncertain significance (Jul 15, 2021)
5-96979761-A-T		not specified	Uncertain significance (Feb 05, 2024)
5-96979854-G-A		not specified	Uncertain significance (Feb 10, 2022)
5-96979885-A-T		not specified	Uncertain significance (May 12, 2024)
5-96979917-A-G		not specified	Uncertain significance (Feb 27, 2023)
5-96979923-A-G		not specified	Uncertain significance (Jun 11, 2021)
5-96979930-A-C		not specified	Uncertain significance (Mar 01, 2023)
5-96985111-G-A		not specified	Uncertain significance (Jun 10, 2024)
5-96985112-C-T		not specified	Uncertain significance (Mar 05, 2024)
5-96986551-G-A		not specified	Likely benign (May 11, 2022)
5-96986578-G-A		not specified	Uncertain significance (Jun 10, 2022)
5-96986638-A-G		not specified	Uncertain significance (Jan 19, 2022)
5-96986645-T-A		not specified	Uncertain significance (Apr 12, 2022)

GnomAD

Source: gnomAD

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: dbNSFP

• 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