LGALS9
galectin 9, the group of Galectins|Receptor ligands
Basic information
Region (hg38): 17:27629798-27649560
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
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.
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 | 30 | 33 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 30 | 2 | 1 |
Variants in LGALS9
This is a list of pathogenic ClinVar variants found in the LGALS9 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-27631277-C-A | not specified | Uncertain significance (Oct 05, 2023) | ||
| 17-27631287-G-A | not specified | Uncertain significance (Jan 02, 2024) | ||
| 17-27631287-G-T | not specified | Uncertain significance (Jun 12, 2023) | ||
| 17-27638317-A-T | not specified | Uncertain significance (May 23, 2023) | ||
| 17-27640654-G-A | not specified | Uncertain significance (Jun 29, 2022) | ||
| 17-27640666-A-G | not specified | Uncertain significance (Apr 01, 2022) | ||
| 17-27640667-C-T | not specified | Uncertain significance (Aug 08, 2023) | ||
| 17-27640673-A-C | not specified | Uncertain significance (May 02, 2023) | ||
| 17-27640693-G-A | not specified | Uncertain significance (May 09, 2023) | ||
| 17-27640732-C-T | not specified | Uncertain significance (Sep 27, 2021) | ||
| 17-27642278-G-A | not specified | Uncertain significance (Mar 07, 2024) | ||
| 17-27642293-G-A | not specified | Uncertain significance (Sep 28, 2022) | ||
| 17-27642323-T-C | not specified | Uncertain significance (May 01, 2024) | ||
| 17-27642332-C-T | not specified | Uncertain significance (Mar 05, 2024) | ||
| 17-27643562-C-T | not specified | Likely benign (Mar 19, 2024) | ||
| 17-27643579-C-T | not specified | Uncertain significance (May 18, 2023) | ||
| 17-27643603-A-G | not specified | Uncertain significance (Apr 06, 2024) | ||
| 17-27643609-C-T | not specified | Uncertain significance (Jan 05, 2022) | ||
| 17-27645339-C-T | not specified | Uncertain significance (Dec 03, 2021) | ||
| 17-27645347-A-T | not specified | Uncertain significance (Oct 24, 2023) | ||
| 17-27645879-A-T | not specified | Uncertain significance (Dec 16, 2023) | ||
| 17-27646551-C-A | not specified | Uncertain significance (Oct 06, 2022) | ||
| 17-27646577-C-A | not specified | Likely benign (May 21, 2024) | ||
| 17-27647031-C-T | not specified | Uncertain significance (Jul 27, 2021) | ||
| 17-27647109-G-T | not specified | Uncertain significance (Jun 05, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LGALS9 | protein_coding | protein_coding | ENST00000395473 | 11 | 19763 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00000655 | 0.904 | 125661 | 2 | 85 | 125748 | 0.000346 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.912 | 175 | 212 | 0.824 | 0.0000127 | 2329 |
| Missense in Polyphen | 52 | 64.037 | 0.81203 | 717 | ||
| Synonymous | 0.105 | 86 | 87.3 | 0.986 | 0.00000577 | 697 |
| Loss of Function | 1.60 | 11 | 18.4 | 0.598 | 9.57e-7 | 191 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000519 | 0.000519 |
| Ashkenazi Jewish | 0.00397 | 0.00378 |
| East Asian | 0.000217 | 0.000217 |
| Finnish | 0.000185 | 0.000185 |
| European (Non-Finnish) | 0.000204 | 0.000202 |
| Middle Eastern | 0.000217 | 0.000217 |
| South Asian | 0.000132 | 0.000131 |
| Other | 0.000652 | 0.000652 |
dbNSFP
Source:
- 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
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
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