NLN

neurolysin, the group of M3 metallopeptidase family

Basic information

Region (hg38): 5:65722205-65871725

Previous symbols: [ "AGTBP" ]

Links

ENSG00000123213 ∙ NCBI:57486 ∙ OMIM:611530 ∙ HGNC:16058 ∙ Uniprot:Q9BYT8 ∙ 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 NLN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NLN 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			37	1		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	37	1	1

Variants in NLN

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

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

Position	Type	Phenotype	Significance	ClinVar
5-65758596-T-C		not specified	Uncertain significance (Nov 08, 2022)
5-65758631-G-A		not specified	Uncertain significance (May 05, 2023)
5-65758649-G-A		not specified	Uncertain significance (Jul 13, 2021)
5-65758686-C-T		not specified	Uncertain significance (Jun 30, 2022)
5-65758742-G-A		not specified	Uncertain significance (Dec 28, 2022)
5-65758758-T-G		not specified	Uncertain significance (Jan 24, 2023)
5-65762960-T-A		not specified	Uncertain significance (Nov 03, 2022)
5-65763017-C-A		not specified	Uncertain significance (Oct 06, 2021)
5-65763026-C-G		not specified	Uncertain significance (Dec 11, 2023)
5-65763044-T-C		not specified	Uncertain significance (Mar 15, 2024)
5-65763049-C-T		not specified	Uncertain significance (May 21, 2024)
5-65763050-G-A		not specified	Uncertain significance (Mar 31, 2024)
5-65777436-G-A		not specified	Uncertain significance (Jan 20, 2023)
5-65781375-A-C		not specified	Uncertain significance (Dec 03, 2021)
5-65781384-G-T		not specified	Uncertain significance (Jan 24, 2024)
5-65781408-C-T		not specified	Uncertain significance (Aug 01, 2022)
5-65785782-C-G		not specified	Uncertain significance (Apr 26, 2024)
5-65785827-A-G		not specified	Uncertain significance (Oct 14, 2023)
5-65785844-A-T		not specified	Uncertain significance (Dec 16, 2023)
5-65785847-C-T		not specified	Uncertain significance (Jun 10, 2024)
5-65785892-C-T		not specified	Uncertain significance (Jul 26, 2022)
5-65788144-T-G		not specified	Uncertain significance (Aug 12, 2021)
5-65788331-A-G		not specified	Uncertain significance (Feb 15, 2023)
5-65788415-C-A		not specified	Uncertain significance (Apr 07, 2022)
5-65788475-T-A		not specified	Uncertain significance (Nov 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NLN	protein_coding	protein_coding	ENST00000380985	13	149531

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.91e-12	0.918	125660	0	87	125747	0.000346

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.249	369	383	0.964	0.0000194	4646
Missense in Polyphen		111	106.46	1.0427		1277
Synonymous	1.59	116	140	0.829	0.00000799	1296
Loss of Function	2.03	24	37.4	0.642	0.00000214	445

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000515	0.000514
Ashkenazi Jewish	0.00	0.00
East Asian	0.000224	0.000217
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000488	0.000484
Middle Eastern	0.000224	0.000217
South Asian	0.000431	0.000425
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolyzes oligopeptides such as neurotensin, bradykinin and dynorphin A. {ECO:0000250}.
• Pathway: Renin-angiotensin system - Homo sapiens (human);Signaling by GPCR;Signal Transduction;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding (Consensus)

Recessive Scores

• pRec: 0.144

Intolerance Scores

• loftool: 0.936
• rvis_EVS: -0.35
• rvis_percentile_EVS: 29.43

Haploinsufficiency Scores

• pHI: 0.392
• hipred: N
• hipred_score: 0.448
• ghis: 0.594

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0490

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Nln
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: regulation of gluconeogenesis;proteolysis;peptide metabolic process;regulation of skeletal muscle fiber differentiation
• Cellular component: extracellular region;mitochondrial intermembrane space;plasma membrane
• Molecular function: metalloendopeptidase activity;peptide binding;metal ion binding