LGALS16

Summary

LGALS16 (galectin 16, HGNC:40039) is a protein-coding gene on chromosome 19q13.2, encoding Galectin-16 (A8MUM7). Binds lactose with high affinity.

Enables lactose binding activity. Involved in positive regulation of T cell apoptotic process. Predicted to be located in membrane.

Source: NCBI Gene 148003 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 32 total
• MANE Select transcript: NM_001190441

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:40039
Approved symbol	LGALS16
Name	galectin 16
Location	19q13.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000249861
Ensembl biotype	protein_coding
Entrez	148003

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 nonsense_mediated_decay

ENST00000392051, ENST00000594480

RefSeq mRNA: 1 — MANE Select: NM_001190441 NM_001190441

CCDS: CCDS54267

Canonical transcript exons

ENST00000392051 — 4 exons

Exon	Start	End
ENSE00002497394	39657883	39657959
ENSE00003187541	39655913	39655976
ENSE00003494719	39660395	39660647
ENSE00003692580	39658460	39658670

Expression profiles

Bgee: expression breadth broad, 23 present calls, max score 74.08.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0849 / max 99.4324, expressed in 15 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
175798	0.0760	14
175799	0.0090	1

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
placenta	UBERON:0001987	74.08	gold quality
cerebellar cortex	UBERON:0002129	49.74	gold quality
cerebellum	UBERON:0002037	49.67	gold quality
cerebellar hemisphere	UBERON:0002245	49.51	gold quality
right hemisphere of cerebellum	UBERON:0014890	49.05	gold quality
hypothalamus	UBERON:0001898	42.13	gold quality
sural nerve	UBERON:0015488	41.53	gold quality
adrenal tissue	UBERON:0018303	38.17	silver quality
substantia nigra	UBERON:0002038	38.16	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
anterior cingulate cortex	UBERON:0009835	33.03	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
prefrontal cortex	UBERON:0000451	30.28	gold quality
monocyte	CL:0000576	30.07	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
leukocyte	CL:0000738	29.85	gold quality
brain	UBERON:0000955	28.66	gold quality
liver	UBERON:0002107	28.35	gold quality
superior frontal gyrus	UBERON:0002661	28.16	silver quality
duodenum	UBERON:0002114	28.14	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	27.77	silver quality
frontal cortex	UBERON:0001870	27.75	gold quality
lymph node	UBERON:0000029	27.57	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-3929	yes	156.08
E-ANND-3	yes	2.79
E-MTAB-8060	no	1453.17

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

9 targeting LGALS16, 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-4690-5P	99.65	66.24	813
HSA-MIR-670-3P	99.03	68.88	2404
HSA-MIR-4650-3P	99.01	68.39	1062
HSA-MIR-3155A	98.16	66.09	965
HSA-MIR-3155B	98.16	66.09	965
HSA-MIR-484	98.16	66.92	1074
HSA-MIR-4778-5P	97.96	68.06	1634
HSA-MIR-6783-5P	97.67	67.21	1528
HSA-MIR-4689	96.97	65.79	1209

Literature-anchored findings (GeneRIF, showing 3)

• Human galectin-16 has a pseudo ligand binding site and plays a role in regulating c-Rel-mediated lymphocyte activity. (PMID:33011338)
• Expression, Regulation, and Functions of the Galectin-16 Gene in Human Cells and Tissues. (PMID:34944551)
• Insights into cAMP-dependent molecular mechanisms regulating expression and function of LGALS16 gene in choriocarcinoma JEG-3 cells. (PMID:38212900)

Cross-species orthologs

31 orthologs

Organism	Symbol	Gene ID
danio_rerio	lgals9l1	ENSDARG00000025903
danio_rerio	lgals9l3	ENSDARG00000041060
danio_rerio	lgals3b	ENSDARG00000044001
danio_rerio	si:ch211-10a23.2	ENSDARG00000060656
danio_rerio	lgals9l4	ENSDARG00000069058
danio_rerio	lgals9l5	ENSDARG00000087311
danio_rerio	si:dkey-95h12.2	ENSDARG00000092923
danio_rerio	lgals9l6	ENSDARG00000093059
mus_musculus	Lgals9	ENSMUSG00000001123
rattus_norvegicus	Lgals5	ENSRNOG00000012557
rattus_norvegicus	Lgals9	ENSRNOG00000012681
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), LGALS9B (ENSG00000170298), LGALS4 (ENSG00000171747), LGALS9C (ENSG00000171916), LGALS7B (ENSG00000178934), LGALS7 (ENSG00000205076), GRIFIN (ENSG00000275572)

Protein

Protein identifiers

Galectin-16 — A8MUM7 (reviewed: A8MUM7)

All UniProt accessions (2): A8MUM7, M0R108

UniProt curated annotations — full annotation on UniProt →

Function. Binds lactose with high affinity. Strong inducer of T-cell apoptosis.

Tissue specificity. Predominantly and highly expressed in the placenta where it is localized mainly in the syncytiotrophoblast and in the endothelia of fetal vessels. Also detected in the amnion and chorionic trophoblasts in fetal membranes.

RefSeq proteins (1): NP_001177370* (*=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 (17 total): strand 12, chain 1, domain 1, helix 1, sequence variant 1, turn 1

Structure

Experimental structures (PDB)

3 structures.

PDB	Method	Resolution (Å)
6LJQ	X-RAY DIFFRACTION	1.49
6LJP	X-RAY DIFFRACTION	2
6LJR	X-RAY DIFFRACTION	2

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A8MUM7-F1	94.65	0.89

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 21 (showing top): GOBP_POSITIVE_REGULATION_OF_LYMPHOCYTE_APOPTOTIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_LEUKOCYTE_APOPTOTIC_PROCESS, GOBP_REGULATION_OF_LEUKOCYTE_APOPTOTIC_PROCESS, GOBP_REGULATION_OF_LYMPHOCYTE_APOPTOTIC_PROCESS, GOBP_REGULATION_OF_T_CELL_APOPTOTIC_PROCESS, GOBP_LEUKOCYTE_APOPTOTIC_PROCESS, KUUSELO_PANCREATIC_CANCER_19Q13_AMPLIFICATION, GOBP_POSITIVE_REGULATION_OF_T_CELL_APOPTOTIC_PROCESS, GOBP_LYMPHOCYTE_APOPTOTIC_PROCESS, GOBP_T_CELL_APOPTOTIC_PROCESS, GOMF_OLIGOSACCHARIDE_BINDING, DESCARTES_MAIN_FETAL_TROPHOBLAST_GIANT_CELLS, DESCARTES_FETAL_PLACENTA_TROPHOBLAST_GIANT_CELLS, GOBP_REGULATION_OF_PROGRAMMED_CELL_DEATH, GOBP_POSITIVE_REGULATION_OF_PROGRAMMED_CELL_DEATH

GO Biological Process (2): apoptotic process (GO:0006915), positive regulation of T cell apoptotic process (GO:0070234)

GO Molecular Function (2): carbohydrate binding (GO:0030246), lactose binding (GO:0030395)

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
programmed cell death	1
apoptotic signaling pathway	1
execution phase of apoptosis	1
positive regulation of lymphocyte apoptotic process	1
T cell apoptotic process	1
regulation of T cell apoptotic process	1
binding	1
disaccharide binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

172 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LGALS16	LGALS1	P09382	459
LGALS16	EID2	Q8N6I1	444
LGALS16	ZNF320	A2RRD8	426
LGALS16	ZNF268	Q14587	408
LGALS16	C20orf96	Q9NUD7	399
LGALS16	CGB5	P01233	395
LGALS16	ZNF486	Q96H40	393
LGALS16	MYEOV	Q96EZ4	385
LGALS16	NEDD4	P46934	381
LGALS16	DYRK1B	Q9Y463	376
LGALS16	CCDC157	Q569K6	370
LGALS16	ZNF714	Q96N38	367
LGALS16	TLCD5	Q6ZRR5	356
LGALS16	XAGE3	Q8WTP9	348
LGALS16	KHDC1L	Q5JSQ8	348

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A3Q1N1R0, A4D1Z8, A8MUM7, D3ZGS3, O00214, O08573, O14727, O23547, O44126, O54891, O88644, O88879, P07583, P08520, P11762, P23668, P26788, P36573, P38552, P47967, P56180, P56217, P56470, P79238, P97400, P97840, Q01968, Q05315, Q09581, Q09605, Q29058, Q3MHZ8, Q62665, Q6DGJ1, Q6NVF0, Q801X7, Q8C726, Q8K419, Q8LEV3, Q8TCE9

Diamond homologs: A8MUM7, O00182, O08573, O54891, P38486, P38552, P47929, P79238, P97400, P97840, Q05315, Q29058, Q3B8N2, Q3MHZ8, Q3T0D6, Q6DKI2, Q8K419, Q8TCE9, Q9UHV8, A4D1Z8, O00214, O44126, O54974, O88644, P07583, P08520, P08699, P16110, P17931, P23668, P47845, P47953, P47967, P56217, P56470, P97590, Q09605, Q09610, Q1ECW6, Q29373

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	29
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

451 predictions. Top by Δscore:

Variant	Effect	Δscore
19:39655954:A:T	donor_gain	1.0000
19:39655977:G:GG	donor_gain	1.0000
19:39657960:G:GG	donor_gain	1.0000
19:39658451:T:TA	acceptor_gain	1.0000
19:39658455:CTCA:C	acceptor_loss	1.0000
19:39658456:TCA:T	acceptor_loss	1.0000
19:39658457:CA:C	acceptor_loss	1.0000
19:39658458:A:AG	acceptor_gain	1.0000
19:39658458:AG:A	acceptor_loss	1.0000
19:39658459:G:GA	acceptor_gain	1.0000
19:39658459:GC:G	acceptor_gain	1.0000
19:39658459:GCA:G	acceptor_gain	1.0000
19:39658459:GCAAC:G	acceptor_gain	1.0000
19:39658564:GTC:G	donor_gain	1.0000
19:39658666:ATGAG:A	donor_loss	1.0000
19:39658667:TGAGG:T	donor_loss	1.0000
19:39658670:GGTGA:G	donor_loss	1.0000
19:39658672:T:A	donor_loss	1.0000
19:39655972:TAACT:T	donor_gain	0.9900
19:39655974:ACT:A	donor_gain	0.9900
19:39655975:CT:C	donor_gain	0.9900
19:39655975:CTGT:C	donor_loss	0.9900
19:39655976:TGTGA:T	donor_loss	0.9900
19:39655977:G:T	donor_loss	0.9900
19:39655978:T:A	donor_loss	0.9900
19:39655979:GAGTT:G	donor_loss	0.9900
19:39657870:A:AG	acceptor_gain	0.9900
19:39658459:GCAA:G	acceptor_gain	0.9900
19:39658567:G:GG	donor_gain	0.9900
19:39658660:A:AG	donor_gain	0.9900

AlphaMissense

926 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:39660425:T:C	F112L	0.966
19:39660427:T:A	F112L	0.966
19:39660427:T:G	F112L	0.966
19:39658632:T:C	F89L	0.946
19:39658634:T:A	F89L	0.946
19:39658634:T:G	F89L	0.946
19:39657937:G:T	G24W	0.939
19:39658567:G:C	R67P	0.932
19:39658521:T:C	F52L	0.927
19:39658523:C:A	F52L	0.927
19:39658523:C:G	F52L	0.927
19:39658639:T:C	L91S	0.919
19:39660435:G:C	R115P	0.912
19:39657937:G:A	G24R	0.908
19:39657937:G:C	G24R	0.908
19:39658666:A:C	Y100S	0.908
19:39658581:T:A	W72R	0.907
19:39658581:T:C	W72R	0.907
19:39658522:T:C	F52S	0.905
19:39658531:G:C	R55P	0.901
19:39658486:T:C	F40S	0.900
19:39657926:T:A	V20E	0.899
19:39658480:T:A	V38E	0.897
19:39658665:T:C	Y100H	0.893
19:39657932:T:A	I22N	0.888
19:39658583:G:C	W72C	0.887
19:39658583:G:T	W72C	0.887
19:39658645:T:C	I93T	0.887
19:39658614:T:C	F83L	0.882
19:39658616:T:A	F83L	0.882

dbSNP variants (sampled 300 via entrez): RS1000178545 (19:39659379 C>A), RS1000341415 (19:39654117 A>T), RS1000484721 (19:39659648 A>G), RS1000520389 (19:39660685 C>A,T), RS1001266980 (19:39656855 T>G), RS1001717044 (19:39655399 G>C), RS1001871153 (19:39660734 A>T), RS1001915254 (19:39655233 T>TAAA), RS1002303732 (19:39656597 A>G), RS1003744964 (19:39657765 G>A,C), RS1004246021 (19:39656998 C>T), RS1005215000 (19:39658303 G>A), RS1005222891 (19:39658965 A>T), RS1005294326 (19:39657701 G>T), RS1007144033 (19:39654957 G>A,T)

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

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
ethyl-p-hydroxybenzoate	decreases expression	1
nordy	decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Coal	increases abundance, increases expression	1
Diethylhexyl Phthalate	increases expression	1
Rotenone	decreases expression	1
Smoke	increases abundance, increases expression	1

Clinical trials (associated diseases)

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