LVRN

laeverin, the group of Aminopeptidases|M1 metallopeptidases

Basic information

Region (hg38): 5:115962453-116027619

Links

ENSG00000172901 ∙ NCBI:206338 ∙ OMIM:610046 ∙ HGNC:26904 ∙ Uniprot:Q6Q4G3 ∙ 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 LVRN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LVRN 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				2	2	4
missense			42	3	1	46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	5	3

Variants in LVRN

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

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

Position	Type	Phenotype	Significance	ClinVar
5-115962628-C-A		not specified	Uncertain significance (Mar 29, 2023)
5-115962654-C-G		not specified	Uncertain significance (Feb 15, 2023)
5-115962654-C-T		not specified	Uncertain significance (Feb 21, 2024)
5-115962720-G-A		not specified	Uncertain significance (Dec 11, 2023)
5-115962796-C-A		not specified	Uncertain significance (Jul 19, 2023)
5-115962799-C-G		not specified	Uncertain significance (May 27, 2022)
5-115962805-G-A		not specified	Uncertain significance (May 24, 2024)
5-115962846-G-C		not specified	Uncertain significance (Jun 24, 2022)
5-115962883-C-A		not specified	Uncertain significance (Sep 26, 2023)
5-115962981-G-C		not specified	Uncertain significance (Mar 11, 2022)
5-115962993-C-A		not specified	Uncertain significance (May 01, 2024)
5-115962993-C-T		not specified	Uncertain significance (Jul 11, 2022)
5-115963002-G-T		not specified	Uncertain significance (Oct 16, 2023)
5-115963017-A-G		not specified	Uncertain significance (Nov 08, 2022)
5-115963083-G-A		not specified	Uncertain significance (May 14, 2024)
5-115963093-G-A		not specified	Uncertain significance (Mar 31, 2024)
5-115963142-C-G			Likely benign (Jul 01, 2022)
5-115963153-T-A		not specified	Uncertain significance (May 10, 2024)
5-115963164-C-G		not specified	Likely benign (Nov 15, 2021)
5-115963175-A-T		not specified	Uncertain significance (Dec 27, 2022)
5-115963176-T-C		not specified	Uncertain significance (Feb 03, 2022)
5-115963222-A-G		not specified	Uncertain significance (May 23, 2023)
5-115963225-A-T		not specified	Uncertain significance (Nov 15, 2021)
5-115963268-G-C		not specified	Uncertain significance (Nov 17, 2023)
5-115983348-G-A		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LVRN	protein_coding	protein_coding	ENST00000357872	20	65166

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.30e-17	0.734	124695	1	1052	125748	0.00420

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.883	578	521	1.11	0.0000251	6469
Missense in Polyphen		168	171.48	0.97972		2210
Synonymous	0.142	198	201	0.987	0.0000103	1854
Loss of Function	1.97	33	47.7	0.692	0.00000203	598

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00697	0.00693
Ashkenazi Jewish	0.00523	0.00497
East Asian	0.000607	0.000598
Finnish	0.00430	0.00407
European (Non-Finnish)	0.00359	0.00344
Middle Eastern	0.000607	0.000598
South Asian	0.00981	0.00932
Other	0.00443	0.00424

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Metalloprotease which may be important for placentation by regulating biological activity of key peptides at the embryo- maternal interface. On synthetic substrates it shows a marked preference for Leu-4-methylcoumaryl-7-amide (Leu-MCA) over Met- MCA, Arg-LCA and Lys-LCA. Cleaves the N-terminal amino acid of several peptides such as angiotensin-3, kisspeptin-10 and endokinin C. {ECO:0000269|PubMed:17525158}.

Intolerance Scores

• rvis_EVS: 1.37
• rvis_percentile_EVS: 94.46

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.280
• ghis: 0.386

Essentials

• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Mouse Genome Informatics

• Gene name: Lvrn

Gene ontology

• Biological process: proteolysis;peptide catabolic process
• Cellular component: cytoplasm;plasma membrane;integral component of membrane
• Molecular function: zinc ion binding;peptide binding;metalloaminopeptidase activity