GeneBe

LGALS9

galectin 9, the group of Galectins|Receptor ligands

Basic information

Region (hg38): 17:27629798-27649560

Links

ENSG00000168961 ∙ NCBI:3965 ∙ OMIM:601879 ∙ HGNC:6570 ∙ Uniprot:O00182 ∙ 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 LGALS9 gene.

  • not_specified (67 variants)
  • not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LGALS9 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000009587.3. 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.

EffectPLPVUSLBBSum
synonymous
0
missense
61
clinvar
6
clinvar
1
clinvar
 68
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 61 6 1
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
LGALS9protein_codingprotein_codingENST00000395473 1119763
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.000006550.9041256612851257480.000346
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.9121752120.8240.00001272329
Missense in Polyphen5264.0370.81203717
Synonymous0.1058687.30.9860.00000577697
Loss of Function1.601118.40.5989.57e-7191

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0005190.000519
Ashkenazi Jewish0.003970.00378
East Asian0.0002170.000217
Finnish0.0001850.000185
European (Non-Finnish)0.0002040.000202
Middle Eastern0.0002170.000217
South Asian0.0001320.000131
Other0.0006520.000652

dbNSFP

Source: dbNSFP

Function
FUNCTION: Binds galactosides (PubMed:18005988). Has high affinity for the Forssman pentasaccharide (PubMed:18005988). Ligand for HAVCR2/TIM3 (PubMed:16286920). Binding to HAVCR2 induces T-helper type 1 lymphocyte (Th1) death (PubMed:16286920). Also stimulates bactericidal activity in infected macrophages by causing macrophage activation and IL1B secretion which restricts intracellular bacterial growth (By similarity). Ligand for P4HB; the interaction retains P4HB at the cell surface of Th2 T-helper cells, increasing disulfide reductase activity at the plasma membrane, altering the plasma membrane redox state and enhancing cell migration (PubMed:21670307). Ligand for CD44; the interaction enhances binding of SMAD3 to the FOXP3 promoter, leading to up- regulation of FOXP3 expression and increased induced regulatory T (iTreg) cell stability and suppressive function (By similarity). Promotes ability of mesenchymal stromal cells to suppress T-cell proliferation (PubMed:23817958). Expands regulatory T-cells and induces cytotoxic T-cell apoptosis following virus infection (PubMed:20209097). Activates ERK1/2 phosphorylation inducing cytokine (IL-6, IL-8, IL-12) and chemokine (CCL2) production in mast and dendritic cells (PubMed:24465902, PubMed:16116184). Inhibits degranulation and induces apoptosis of mast cells (PubMed:24465902). Induces maturation and migration of dendritic cells (PubMed:25754930, PubMed:16116184). Inhibits natural killer (NK) cell function (PubMed:23408620). Can transform NK cell phenotype from peripheral to decidual during pregnancy (PubMed:25578313). Astrocyte derived galectin-9 enhances microglial TNF production (By similarity). May play a role in thymocyte-epithelial interactions relevant to the biology of the thymus. May provide the molecular basis for urate flux across cell membranes, allowing urate that is formed during purine metabolism to efflux from cells and serving as an electrogenic transporter that plays an important role in renal and gastrointestinal urate excretion (By similarity). Highly selective to the anion urate (By similarity). {ECO:0000250|UniProtKB:O08573, ECO:0000250|UniProtKB:P97840, ECO:0000269|PubMed:16116184, ECO:0000269|PubMed:16286920, ECO:0000269|PubMed:18005988, ECO:0000269|PubMed:18977853, ECO:0000269|PubMed:20209097, ECO:0000269|PubMed:21670307, ECO:0000269|PubMed:23408620, ECO:0000269|PubMed:23817958, ECO:0000269|PubMed:24465902, ECO:0000269|PubMed:25578313, ECO:0000269|PubMed:25754930}.;
Pathway
Uricosurics Pathway, Pharmacodynamics;Vitamin D Receptor Pathway;Signaling by Interleukins;Cytokine Signaling in Immune system;Immune System;Interleukin-2 family signaling (Consensus)

Recessive Scores

pRec
0.220

Intolerance Scores

loftool
0.890
rvis_EVS
0.8
rvis_percentile_EVS
87.54

Haploinsufficiency Scores

pHI
0.136
hipred
N
hipred_score
0.218
ghis
0.486

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.693

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Lgals9
Phenotype
endocrine/exocrine gland phenotype; immune system phenotype; hematopoietic system phenotype; skeleton phenotype;

Gene ontology

Biological process
natural killer cell tolerance induction;chemotaxis;inflammatory response;female pregnancy;positive regulation of gene expression;negative regulation of gene expression;response to lipopolysaccharide;regulation of interleukin-4 production;regulation of interleukin-5 production;negative regulation of chemokine production;negative regulation of interferon-gamma production;negative regulation of tumor necrosis factor production;positive regulation of interleukin-4 production;positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response;toll-like receptor 2 signaling pathway;toll-like receptor 4 signaling pathway;p38MAPK cascade;positive regulation of I-kappaB kinase/NF-kappaB signaling;negative regulation of mast cell degranulation;negative regulation of natural killer cell mediated cytotoxicity;negative regulation of activated T cell proliferation;positive regulation of viral entry into host cell;positive regulation of interleukin-1 beta secretion;positive regulation of NF-kappaB transcription factor activity;maternal process involved in female pregnancy;positive regulation of activated T cell autonomous cell death;ERK1 and ERK2 cascade;positive regulation of ERK1 and ERK2 cascade;response to interleukin-1;cellular response to interferon-gamma;positive regulation of transforming growth factor beta production;positive regulation of monocyte chemotactic protein-1 production;mature conventional dendritic cell differentiation;cellular response to virus;regulation of p38MAPK cascade;positive regulation of NIK/NF-kappaB signaling;positive regulation of interferon-gamma secretion;positive regulation of tumor necrosis factor secretion;positive regulation of interleukin-8 secretion;positive regulation of dendritic cell chemotaxis;negative regulation of CD4-positive, alpha-beta T cell proliferation;positive regulation of CD4-positive, alpha-beta T cell proliferation;positive regulation of interleukin-13 secretion;positive regulation of dendritic cell apoptotic process;positive regulation of interleukin-6 secretion;positive regulation of interleukin-10 secretion;positive regulation of interleukin-12 secretion;positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell;positive regulation of dendritic cell differentiation;positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway
Cellular component
extracellular space;nucleus;cytoplasm;cytosol
Molecular function
galactose binding;enzyme binding;carbohydrate binding;disaccharide binding