LGMN

legumain

Basic information

Region (hg38): 14:92703807-92748679

Previous symbols: [ "PRSC1" ]

Links

ENSG00000100600 ∙ NCBI:5641 ∙ OMIM:602620 ∙ HGNC:9472 ∙ Uniprot:Q99538 ∙ 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 LGMN gene.

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.

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					1	1
missense			30	2		32
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	30	2	2

Variants in LGMN

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

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

Position	Type	Phenotype	Significance	ClinVar
14-92704348-T-C		not specified	Uncertain significance (Oct 04, 2022)
14-92704631-A-G			Benign (Dec 31, 2019)
14-92704662-C-G		not specified	Uncertain significance (Jun 22, 2024)
14-92704680-C-T		not specified	Uncertain significance (Oct 05, 2022)
14-92704688-T-C		High myopia	Uncertain significance (Dec 17, 2018)
14-92706569-C-T		not specified	Uncertain significance (Oct 14, 2021)
14-92706587-C-T		not specified	Uncertain significance (Jun 26, 2023)
14-92706625-C-T		not specified	Uncertain significance (Jun 29, 2023)
14-92709682-C-T		not specified	Uncertain significance (Dec 11, 2023)
14-92709747-C-T		not specified	Uncertain significance (Apr 22, 2022)
14-92709763-A-G		not specified	Uncertain significance (Nov 23, 2022)
14-92709767-C-T		not specified	Uncertain significance (Dec 06, 2022)
14-92709773-T-C		not specified	Uncertain significance (Nov 09, 2021)
14-92709790-T-A		not specified	Uncertain significance (Apr 09, 2024)
14-92709808-G-A		not specified	Uncertain significance (Oct 02, 2023)
14-92709815-G-A		not specified	Uncertain significance (Jan 30, 2024)
14-92711661-T-G		not specified	Uncertain significance (Mar 01, 2023)
14-92711679-C-T		not specified	Uncertain significance (Dec 20, 2021)
14-92711699-G-A		not specified	Uncertain significance (Oct 12, 2021)
14-92711708-A-G		not specified	Uncertain significance (Oct 05, 2023)
14-92711713-G-A			Benign (Dec 31, 2019)
14-92711721-T-C		not specified	Uncertain significance (May 27, 2022)
14-92711934-T-G		not specified	Uncertain significance (Sep 16, 2021)
14-92712861-T-C		not specified	Uncertain significance (May 04, 2022)
14-92713827-C-T		not specified	Likely benign (Aug 28, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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