LGALS9B

Summary

LGALS9B (galectin 9B, HGNC:24842) is a protein-coding gene on chromosome 17p11.2, encoding Galectin-9B (Q3B8N2). Binds galactosides. It is a selective cancer dependency (DepMap: 14.5% of cell lines).

This gene was initially thought to represent a pseudogene of galectin 9; however, this transcript has good exon-intron structure and encodes a predicted protein of the same size as and highly similar to galectin 9. This gene is one of two similar loci on chromosome 17p similar to galectin 9 and now thought to be protein-encoding. This gene is the more centromeric gene.

Source: NCBI Gene 284194 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 61 total
• Cancer dependency (DepMap): dependent in 14.5% of screened cell lines
• MANE Select transcript: NM_001367292

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24842
Approved symbol	LGALS9B
Name	galectin 9B
Location	17p11.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000170298
Ensembl biotype	protein_coding
Entrez	284194

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 5 protein_coding, 2 nonsense_mediated_decay, 2 retained_intron

ENST00000324290, ENST00000423676, ENST00000578481, ENST00000578724, ENST00000581490, ENST00000584703, ENST00000897461, ENST00000897462, ENST00000897463

RefSeq mRNA: 2 — MANE Select: NM_001367292 NM_001042685, NM_001367292

CCDS: CCDS42283, CCDS92280

Canonical transcript exons

ENST00000423676 — 11 exons

Exon	Start	End
ENSE00002337584	20460352	20460443
ENSE00002381735	20449395	20450119
ENSE00002684409	20467432	20467539
ENSE00003467583	20451481	20451643
ENSE00003468467	20455303	20455398
ENSE00003490919	20451795	20451883
ENSE00003504420	20452351	20452395
ENSE00003539649	20458183	20458384
ENSE00003581700	20456561	20456671
ENSE00003682389	20453572	20453607
ENSE00003683532	20453017	20453067

Expression profiles

Bgee: expression breadth ubiquitous, 120 present calls, max score 89.17.

Top tissues by expression

132 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
mucosa of transverse colon	UBERON:0004991	89.17	gold quality
esophagus mucosa	UBERON:0002469	86.60	gold quality
mucosa of stomach	UBERON:0001199	86.03	gold quality
rectum	UBERON:0001052	84.85	gold quality
lower esophagus mucosa	UBERON:0035834	82.57	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	81.37	gold quality
transverse colon	UBERON:0001157	77.39	gold quality
gall bladder	UBERON:0002110	76.58	gold quality
body of stomach	UBERON:0001161	75.73	gold quality
duodenum	UBERON:0002114	74.23	gold quality
stomach	UBERON:0000945	72.49	gold quality
blood	UBERON:0000178	72.14	gold quality
granulocyte	CL:0000094	71.93	gold quality
vagina	UBERON:0000996	70.52	gold quality
colonic epithelium	UBERON:0000397	68.34	gold quality
small intestine Peyer’s patch	UBERON:0003454	67.01	gold quality
small intestine	UBERON:0002108	66.59	gold quality
intestine	UBERON:0000160	64.51	gold quality
colon	UBERON:0001155	63.96	gold quality
vermiform appendix	UBERON:0001154	63.85	gold quality
esophagus	UBERON:0001043	63.64	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	59.94	gold quality
spleen	UBERON:0002106	59.09	gold quality
fundus of stomach	UBERON:0001160	58.28	gold quality
tonsil	UBERON:0002372	56.91	gold quality
lymph node	UBERON:0000029	56.43	gold quality
minor salivary gland	UBERON:0001830	54.76	gold quality
bone marrow	UBERON:0002371	54.45	gold quality
skin of leg	UBERON:0001511	54.26	gold quality
prostate gland	UBERON:0002367	53.62	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.18

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

7 targeting LGALS9B, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-1296-3P	99.72	64.04	636
HSA-MIR-1915-3P	99.58	66.79	1988
HSA-MIR-4505	99.27	67.81	2678
HSA-MIR-491-5P	99.13	65.98	1468
HSA-MIR-564	95.85	65.01	163
HSA-MIR-2861	95.24	65.47	1056

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 14.5% of screened cell lines.

Cross-species orthologs

23 orthologs

Organism	Symbol	Gene ID
danio_rerio	lgals3b	ENSDARG00000044001
danio_rerio	si:ch211-10a23.2	ENSDARG00000060656
danio_rerio	si:dkey-95h12.2	ENSDARG00000092923
drosophila_melanogaster	galectin	FBGN0031213
drosophila_melanogaster	CG11374	FBGN0031214
drosophila_melanogaster	CG13950	FBGN0031289
caenorhabditis_elegans		WBGENE00002264
caenorhabditis_elegans		WBGENE00002266
caenorhabditis_elegans		WBGENE00002269
caenorhabditis_elegans		WBGENE00002270
caenorhabditis_elegans		WBGENE00002271
caenorhabditis_elegans		WBGENE00004165
caenorhabditis_elegans	C27C7.5	WBGENE00007768
caenorhabditis_elegans	F46A8.3	WBGENE00009746
caenorhabditis_elegans	F46A8.4	WBGENE00009747
caenorhabditis_elegans	F46A8.5	WBGENE00009748
caenorhabditis_elegans	F46A8.8	WBGENE00009751
caenorhabditis_elegans		WBGENE00017080
caenorhabditis_elegans		WBGENE00018255
caenorhabditis_elegans		WBGENE00018649
caenorhabditis_elegans		WBGENE00018650
caenorhabditis_elegans		WBGENE00018651
caenorhabditis_elegans		WBGENE00235368

Paralogs (16): LGALS14 (ENSG00000006659), LGALS2 (ENSG00000100079), LGALS1 (ENSG00000100097), LGALS13 (ENSG00000105198), CLC (ENSG00000105205), LGALS8 (ENSG00000116977), LGALSL (ENSG00000119862), LGALS3 (ENSG00000131981), LGALS12 (ENSG00000133317), LGALS9 (ENSG00000168961), LGALS4 (ENSG00000171747), LGALS9C (ENSG00000171916), LGALS7B (ENSG00000178934), LGALS7 (ENSG00000205076), LGALS16 (ENSG00000249861), GRIFIN (ENSG00000275572)

Protein

Protein identifiers

Galectin-9B — Q3B8N2 (reviewed: Q3B8N2)

Alternative names: Galectin-9-like protein A

All UniProt accessions (3): Q3B8N2, J3QRN8, J3QSC5

UniProt curated annotations — full annotation on UniProt →

Function. Binds galactosides.

Miscellaneous. The LGALS9-like proteins are encoded by a duplicated regions on chromosome 17; there are at least 3 genes coding for galectin-9-like proteins.

Isoforms (2)

UniProt ID	Names	Canonical?
Q3B8N2-1	1	yes
Q3B8N2-2	2

RefSeq proteins (2): NP_001036150, NP_001354221* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001079	Galectin_CRD	Domain
IPR013320	ConA-like_dom_sf	Homologous_superfamily
IPR044156	Galectin-like	Family

Pfam: PF00337

UniProt features (10 total): sequence conflict 3, domain 2, binding site 2, chain 1, region of interest 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q3B8N2-F1	85.01	0.77

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (2): 82–88; 288–294

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 120 (showing top): GOBP_REGULATION_OF_CELL_ACTIVATION, GOBP_REGULATION_OF_LEUKOCYTE_PROLIFERATION, GOBP_REGULATION_OF_ALPHA_BETA_T_CELL_ACTIVATION, GOBP_NEGATIVE_REGULATION_OF_LEUKOCYTE_PROLIFERATION, GOBP_NEGATIVE_REGULATION_OF_CELL_CELL_ADHESION, GOBP_CELL_CELL_ADHESION, GOBP_NEGATIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS, GOBP_CD4_POSITIVE_ALPHA_BETA_T_CELL_ACTIVATION, GOBP_LEUKOCYTE_PROLIFERATION, GOBP_NEGATIVE_REGULATION_OF_TYPE_II_INTERFERON_PRODUCTION, GOBP_CYTOKINE_PRODUCTION, GOBP_REGULATION_OF_CD4_POSITIVE_ALPHA_BETA_T_CELL_ACTIVATION, GOBP_NEGATIVE_REGULATION_OF_T_CELL_PROLIFERATION, GOBP_ALPHA_BETA_T_CELL_ACTIVATION, GOBP_LEUKOCYTE_CELL_CELL_ADHESION

GO Biological Process (3): positive regulation of gene expression (GO:0010628), negative regulation of type II interferon production (GO:0032689), negative regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000562)

GO Molecular Function (3): galactoside binding (GO:0016936), carbohydrate binding (GO:0030246), protein binding (GO:0005515)

GO Cellular Component (2): nucleus (GO:0005634), cytosol (GO:0005829)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	2
gene expression	1
regulation of gene expression	1
positive regulation of macromolecule biosynthetic process	1
negative regulation of cytokine production	1
type II interferon production	1
regulation of type II interferon production	1
CD4-positive, alpha-beta T cell proliferation	1
negative regulation of alpha-beta T cell proliferation	1
negative regulation of CD4-positive, alpha-beta T cell activation	1
regulation of CD4-positive, alpha-beta T cell proliferation	1
carbohydrate derivative binding	1
intracellular membrane-bounded organelle	1
cytoplasm	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1014 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LGALS9B	HAVCR2	Q8TDQ0	999
LGALS9B	LAG3	P18627	991
LGALS9B	CLEC7A	Q9BXN2	983
LGALS9B	CTLA4	P16410	974
LGALS9B	TIGIT	Q495A1	950
LGALS9B	PDCD1	Q15116	947
LGALS9B	CD44	P16070	928
LGALS9B	CD274	Q9NZQ7	871
LGALS9B	TNFRSF9	Q07011	805
LGALS9B	BTLA	Q7Z6A9	800
LGALS9B	CEACAM1	P13688	796
LGALS9B	CD8A	P01732	778
LGALS9B	HSPB3	Q12988	764
LGALS9B	PTPRC	P08575	738
LGALS9B	TNFRSF14	Q92956	703

IntAct

34 interactions, top by confidence:

A	B	Type	Score
WWP2	LGALS9B	psi-mi:“MI:0915”(physical association)	0.740
LGALS9B	WWP2	psi-mi:“MI:0915”(physical association)	0.740
LGALS9B	DAB1	psi-mi:“MI:0915”(physical association)	0.560
PRTFDC1	LGALS9B	psi-mi:“MI:0915”(physical association)	0.560
DAB1	LGALS9B	psi-mi:“MI:0915”(physical association)	0.560
NTAQ1	LGALS9B	psi-mi:“MI:0915”(physical association)	0.560
LGALS9B	ABI2	psi-mi:“MI:0915”(physical association)	0.560
LGALS9B	ATPAF2	psi-mi:“MI:0915”(physical association)	0.560
QARS1	LGALS9B	psi-mi:“MI:0915”(physical association)	0.560
LONRF1	LGALS9B	psi-mi:“MI:0915”(physical association)	0.560
LGALS9B	NTAQ1	psi-mi:“MI:0915”(physical association)	0.560
NLRP12	LGALS9B	psi-mi:“MI:0915”(physical association)	0.370
PBK	LGALS9	psi-mi:“MI:0914”(association)	0.350
LGALS9	PODXL	psi-mi:“MI:0914”(association)	0.350
LGALS9B	ABCC4	psi-mi:“MI:0914”(association)	0.350
LGALS9	LGALS8	psi-mi:“MI:0914”(association)	0.350
LGALS9B	ABI2	psi-mi:“MI:0915”(physical association)	0.000
ATPAF2	LGALS9B	psi-mi:“MI:0915”(physical association)	0.000
QARS1	LGALS9B	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (49): LGALS9B (Two-hybrid), LGALS9B (Two-hybrid), LGALS9B (Two-hybrid), LGALS9B (Affinity Capture-MS), LGALS9B (Affinity Capture-MS), LGALS9B (Affinity Capture-MS), LGALS9B (Affinity Capture-MS), LGALS9B (Two-hybrid), LGALS9B (Two-hybrid), LGALS9B (Two-hybrid), LGALS9B (Two-hybrid), ATPAF2 (Two-hybrid), QARS (Two-hybrid), SLC12A7 (Affinity Capture-MS), LNPEP (Affinity Capture-MS)

ESM2 similar proteins: A8MUM7, C0HJQ1, C0HJR3, O00182, O00214, O08573, O44126, O54891, O54974, O55060, P05162, P07583, P09382, P11116, P11762, P16045, P23668, P36573, P38552, P47929, P47967, P48538, P56217, P56470, P61801, P81184, P97590, P97840, Q05315, Q09581, Q1ECW6, Q29058, Q3B8N2, Q3MHZ8, Q3T0D6, Q49I35, Q504A5, Q5R7M1, Q62665, Q68FJ4

Diamond homologs: A4D1Z8, C0HJQ1, C0HJR3, O00182, O88644, P08699, P09382, P11116, P16110, P47953, P47967, P97840, Q3B8N2, Q3MHZ8, Q3T0D6, Q49I35, Q6DGJ1, Q6DKI2, Q9D1U0, A8MUM7, O08573, O54891, P38486, P38552, P47929, P79238, P97400, Q05315, Q29058, Q8K419, Q8TCE9, Q9UHV8, O00214, O44126, O54974, P07583, P08520, P17931, P23668, P47845

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

61 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	54
Likely benign	6
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1665 predictions. Top by Δscore:

Variant	Effect	Δscore
17:20451475:CCTTA:C	donor_loss	1.0000
17:20451477:TTACC:T	donor_loss	1.0000
17:20451480:C:CG	donor_loss	1.0000
17:20451880:TCGG:T	acceptor_gain	1.0000
17:20451881:CGG:C	acceptor_gain	1.0000
17:20451881:CGGC:C	acceptor_gain	1.0000
17:20451884:C:CC	acceptor_gain	1.0000
17:20452349:A:AC	donor_gain	1.0000
17:20452350:C:CC	donor_gain	1.0000
17:20453010:GACTT:G	donor_loss	1.0000
17:20453011:ACTT:A	donor_loss	1.0000
17:20453012:CTTA:C	donor_loss	1.0000
17:20453013:TTAC:T	donor_loss	1.0000
17:20453014:TA:T	donor_loss	1.0000
17:20453015:A:AC	donor_gain	1.0000
17:20453015:A:T	donor_loss	1.0000
17:20453016:C:CC	donor_gain	1.0000
17:20453016:CA:C	donor_gain	1.0000
17:20453068:C:CC	acceptor_gain	1.0000
17:20453069:T:C	acceptor_loss	1.0000
17:20467430:A:AC	donor_gain	1.0000
17:20467431:C:CC	donor_gain	1.0000
17:20467431:CTGGG:C	donor_gain	1.0000
17:20450115:CACAC:C	acceptor_gain	0.9900
17:20450117:CAC:C	acceptor_gain	0.9900
17:20450118:ACCT:A	acceptor_loss	0.9900
17:20450121:T:G	acceptor_loss	0.9900
17:20451474:GCCTT:G	donor_loss	0.9900
17:20451479:A:AC	donor_gain	0.9900
17:20451480:C:CC	donor_gain	0.9900

AlphaMissense

2366 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:20451543:A:G	W288R	0.996
17:20451543:A:T	W288R	0.996
17:20451566:C:G	R280P	0.996
17:20451541:C:A	W288C	0.995
17:20451541:C:G	W288C	0.995
17:20451569:A:T	V279D	0.994
17:20451590:C:G	R272P	0.993
17:20451641:A:G	F255S	0.993
17:20451813:A:T	V248D	0.993
17:20451640:G:C	F255L	0.991
17:20451640:G:T	F255L	0.991
17:20451642:A:G	F255L	0.991
17:20451567:G:T	R280S	0.990
17:20451484:G:C	F307L	0.989
17:20451484:G:T	F307L	0.989
17:20451486:A:G	F307L	0.989
17:20458272:A:G	W82R	0.989
17:20458272:A:T	W82R	0.989
17:20451605:A:G	F267S	0.988
17:20451591:G:T	R272S	0.987
17:20451819:C:T	G246D	0.986
17:20450112:A:G	I311T	0.985
17:20458187:A:G	F110S	0.985
17:20458337:A:G	F60S	0.985
17:20451562:G:C	N281K	0.984
17:20451562:G:T	N281K	0.984
17:20451603:G:C	H268D	0.984
17:20451635:A:T	I257N	0.984
17:20450016:A:G	L343P	0.983
17:20458331:A:G	F62S	0.983

dbSNP variants (sampled 300 via entrez): RS1000263259 (17:20457741 A>G), RS1000809862 (17:20461184 C>T), RS1000862656 (17:20460795 C>T), RS1000963466 (17:20469488 T>A,C), RS1001214346 (17:20459752 A>C), RS1001266695 (17:20458984 A>G), RS1001432406 (17:20468667 G>A), RS1002115161 (17:20449197 C>T), RS1002221891 (17:20462756 G>C), RS1002272520 (17:20462055 G>A), RS1002572491 (17:20448944 G>T), RS1003226146 (17:20464934 G>A), RS1003277614 (17:20464527 A>G), RS1003629925 (17:20451364 T>C), RS1003882180 (17:20466973 G>C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Oxygen	increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Tretinoin	increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.