GLB1L3

Summary

GLB1L3 (galactosidase beta 1 like 3, HGNC:25147) is a protein-coding gene on chromosome 11q25, encoding Beta-galactosidase-1-like protein 3 (Q8NCI6). Cleaves beta-linked terminal galactosyl residues from gangliosides, glycoproteins, and glycosaminoglycans.

Predicted to enable beta-galactosidase activity. Predicted to be involved in galactose catabolic process. Predicted to be active in vacuole.

Source: NCBI Gene 112937 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 123 total
• MANE Select transcript: NM_001080407

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25147
Approved symbol	GLB1L3
Name	galactosidase beta 1 like 3
Location	11q25
Locus type	gene with protein product
Status	Approved
Aliases	FLJ90231
Ensembl gene	ENSG00000166105
Ensembl biotype	protein_coding
Entrez	112937

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 12 protein_coding, 5 retained_intron, 1 nonsense_mediated_decay

ENST00000389887, ENST00000410100, ENST00000431683, ENST00000455971, ENST00000467068, ENST00000486034, ENST00000498012, ENST00000532985, ENST00000927556, ENST00000927557, ENST00000927558, ENST00000927559, ENST00000927560, ENST00000927561, ENST00000927562, ENST00000927563, ENST00000927564, ENST00000927565

RefSeq mRNA: 1 — MANE Select: NM_001080407 NM_001080407

CCDS: CCDS44780

Canonical transcript exons

ENST00000431683 — 20 exons

Exon	Start	End
ENSE00001140726	134311064	134311170
ENSE00001278318	134310571	134310651
ENSE00001507191	134309626	134309763
ENSE00001592509	134277700	134277912
ENSE00001610612	134277326	134277451
ENSE00001771930	134283737	134283845
ENSE00002144091	134276379	134276763
ENSE00002470840	134281377	134281445
ENSE00002491177	134282025	134282120
ENSE00003484893	134288798	134288890
ENSE00003494570	134292132	134292213
ENSE00003498605	134312816	134312887
ENSE00003531386	134314330	134314441
ENSE00003547893	134318877	134319564
ENSE00003565002	134307124	134307208
ENSE00003586567	134312349	134312489
ENSE00003622457	134293145	134293209
ENSE00003646551	134318631	134318747
ENSE00003654683	134313941	134314028
ENSE00003687869	134313396	134313474

Expression profiles

Bgee: expression breadth ubiquitous, 151 present calls, max score 82.86.

FANTOM5 (CAGE): breadth broad, TPM avg 0.8647 / max 40.4994, expressed in 241 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
117706	0.6627	213
206520	0.1311	76
206519	0.0709	42

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.86	gold quality
secondary oocyte	CL:0000655	82.43	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	81.78	gold quality
right hemisphere of cerebellum	UBERON:0014890	80.96	gold quality
cerebellar hemisphere	UBERON:0002245	80.90	gold quality
cerebellar cortex	UBERON:0002129	80.77	gold quality
primary visual cortex	UBERON:0002436	79.35	gold quality
prostate gland	UBERON:0002367	79.24	gold quality
cerebellum	UBERON:0002037	78.86	gold quality
Brodmann (1909) area 23	UBERON:0013554	77.56	gold quality
right frontal lobe	UBERON:0002810	77.20	gold quality
seminal vesicle	UBERON:0000998	76.74	gold quality
Brodmann (1909) area 9	UBERON:0013540	76.60	gold quality
oocyte	CL:0000023	75.50	silver quality
skin of leg	UBERON:0001511	73.47	gold quality
anterior cingulate cortex	UBERON:0009835	73.41	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	73.04	gold quality
right testis	UBERON:0004534	72.87	gold quality
prefrontal cortex	UBERON:0000451	72.10	gold quality
testis	UBERON:0000473	71.78	gold quality
skin of abdomen	UBERON:0001416	71.71	gold quality
left testis	UBERON:0004533	71.65	gold quality
middle temporal gyrus	UBERON:0002771	71.56	silver quality
superficial temporal artery	UBERON:0001614	71.48	gold quality
endothelial cell	CL:0000115	71.40	silver quality
nucleus accumbens	UBERON:0001882	71.40	gold quality
occipital lobe	UBERON:0002021	71.37	gold quality
zone of skin	UBERON:0000014	70.95	gold quality
neocortex	UBERON:0001950	70.02	gold quality
frontal cortex	UBERON:0001870	69.70	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-GEOD-83139	yes	4.05
E-MTAB-7008	no	191.86
E-ANND-3	no	5.13

Regulation

Is transcription factor: no

Cross-species orthologs

8 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:dkey-224e22.2	ENSDARG00000034941
danio_rerio	b3gat1b	ENSDARG00000055279
mus_musculus	Glb1l3	ENSMUSG00000031966
rattus_norvegicus	Glb1l3	ENSRNOG00000031469
drosophila_melanogaster	Gal	FBGN0001089
drosophila_melanogaster	Ect3	FBGN0260746
caenorhabditis_elegans		WBGENE00011832
caenorhabditis_elegans		WBGENE00019225

Paralogs (3): GLB1L2 (ENSG00000149328), GLB1L (ENSG00000163521), GLB1 (ENSG00000170266)

Protein

Protein identifiers

Beta-galactosidase-1-like protein 3 — Q8NCI6 (reviewed: Q8NCI6)

All UniProt accessions (2): Q8NCI6, H7C115

UniProt curated annotations — full annotation on UniProt →

Function. Cleaves beta-linked terminal galactosyl residues from gangliosides, glycoproteins, and glycosaminoglycans.

Similarity. Belongs to the glycosyl hydrolase 35 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q8NCI6-1	1	yes
Q8NCI6-2	2
Q8NCI6-4	4

RefSeq proteins (1): NP_001073876* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001944	Glycoside_Hdrlase_35	Family
IPR008979	Galactose-bd-like_sf	Homologous_superfamily
IPR017853	GH_hydrolase_sf	Homologous_superfamily
IPR026283	B-gal_1-like	Family
IPR031330	Gly_Hdrlase_35_cat	Domain
IPR048912	BetaGal1-like_ABD1	Domain
IPR048913	BetaGal_gal-bd	Domain

Pfam: PF01301, PF21317, PF21467

UniProt features (12 total): binding site 4, splice variant 3, active site 2, sequence variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NCI6-F1	91.82	0.89

Functional residue map

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

Catalytic / active sites (2): 227 (proton donor); 301 (nucleophile)

Ligand- & substrate-binding residues (4): 122; 168; 226; 368

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-2022857	Keratan sulfate degradation
R-HSA-2024101	CS/DS degradation
R-HSA-9840310	Glycosphingolipid catabolism

MSigDB gene sets: 61 (showing top): GOBP_MONOSACCHARIDE_CATABOLIC_PROCESS, GOBP_GALACTOSE_METABOLIC_PROCESS, GOBP_CARBOHYDRATE_METABOLIC_PROCESS, OCT1_06, GOBP_SMALL_MOLECULE_CATABOLIC_PROCESS, GOBP_CARBOHYDRATE_CATABOLIC_PROCESS, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, REACTOME_SPHINGOLIPID_METABOLISM, GOBP_MONOSACCHARIDE_METABOLIC_PROCESS, chr11q25, REACTOME_METABOLISM_OF_CARBOHYDRATES_AND_CARBOHYDRATE_DERIVATIVES, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_GLYCOSYL_BONDS, GSE13762_CTRL_VS_125_VITAMIND_DAY12_DC_UP, GSE13762_CTRL_VS_125_VITAMIND_DAY12_DC_DN, GOMF_HYDROLASE_ACTIVITY_HYDROLYZING_O_GLYCOSYL_COMPOUNDS

GO Biological Process (2): galactose catabolic process (GO:0019388), carbohydrate metabolic process (GO:0005975)

GO Molecular Function (4): beta-galactosidase activity (GO:0004565), hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553), hydrolase activity (GO:0016787), hydrolase activity, acting on glycosyl bonds (GO:0016798)

GO Cellular Component (1): vacuole (GO:0005773)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
Keratan sulfate/keratin metabolism	1
Chondroitin sulfate/dermatan sulfate metabolism	1
Glycosphingolipid metabolism	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
galactose metabolic process	1
hexose catabolic process	1
primary metabolic process	1
galactosidase activity	1
hydrolase activity, acting on glycosyl bonds	1
catalytic activity	1
hydrolase activity	1
cytoplasm	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

482 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GLB1L3	PATE3	B3GLJ2	626
GLB1L3	PATE2	Q6UY27	590
GLB1L3	PATE1	Q8WXA2	574
GLB1L3	MON1B	Q7L1V2	517
GLB1L3	CLPSL2	Q6UWE3	507
GLB1L3	SPINK14	Q6IE38	481
GLB1L3	HAPSTR1	Q14CZ0	415
GLB1L3	RNASE13	Q5GAN3	415
GLB1L3	ASB16	Q96NS5	387
GLB1L3	WFDC10A	Q9H1F0	379
GLB1L3	PATE4	P0C8F1	379
GLB1L3	RPL8	P25120	377
GLB1L3	NCAPD3	P42695	356
GLB1L3	NEMP1	O14524	354
GLB1L3	GSC2	O15499	346

IntAct

3 interactions, top by confidence:

A	B	Type	Score
GLB1L3	ZYG11B	psi-mi:“MI:0914”(association)	0.350
GLB1L3	UQCRQ	psi-mi:“MI:0914”(association)	0.350

BioGRID (14): HSPA5 (Affinity Capture-MS), ZYG11B (Affinity Capture-MS), DPP9 (Affinity Capture-MS), SIL1 (Affinity Capture-MS), ZYG11B (Affinity Capture-MS), SIL1 (Affinity Capture-MS), HSPD1 (Affinity Capture-MS), GLB1L3 (Positive Genetic), SIL1 (Affinity Capture-MS), ZYG11B (Affinity Capture-MS), HSPD1 (Affinity Capture-MS), UQCRQ (Affinity Capture-MS), COIL (Affinity Capture-MS), GLB1L3 (Positive Genetic)

ESM2 similar proteins: A2RSQ1, O19015, O22585, P10538, P16278, P23780, P45582, P48980, P49676, Q00662, Q0DGD7, Q0INM3, Q0IZZ8, Q3UPY5, Q58D55, Q5R7P4, Q5XIL5, Q60HF6, Q60V90, Q67VU7, Q6L6S1, Q6UWU2, Q75HQ3, Q7G3T8, Q7XFK2, Q7Y223, Q8GX69, Q8IW92, Q8NCI6, Q8RUV9, Q8VC60, Q8VZR2, Q93324, Q93Z24, Q95LV1, Q966W3, Q9C6W4, Q9FN08, Q9FZ29, Q9GV16

Diamond homologs: A1CE56, A1D199, A1D1Z9, A1DJ58, A1DM65, A2QA64, A2QAN3, A2QL84, A2RSQ1, A6RPN7, A7EBU5, A7EZS5, B0XMP7, B0XNY2, B0XXE7, B0Y752, B2W791, B6GW04, B6H5X9, B6QHA9, B6QLF0, B8N2I5, B8N6V7, B8NKI4, B8QGZ3, I0AIT9, O19015, P16278, P23780, P29853, P48982, Q0CMF3, Q0DGD7, Q2U6P1, Q2UCU3, Q2UMD5, Q3UPY5, Q4WG05, Q4WNE4, Q4WRD3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	102
Likely benign	13
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3390 predictions. Top by Δscore:

Variant	Effect	Δscore
11:134277408:G:GT	donor_gain	1.0000
11:134277913:G:GG	donor_gain	1.0000
11:134281376:GCTAT:G	acceptor_gain	1.0000
11:134281446:G:GG	donor_gain	1.0000
11:134288796:A:AG	acceptor_gain	1.0000
11:134288797:G:GA	acceptor_gain	1.0000
11:134288886:ACAAG:A	donor_loss	1.0000
11:134288887:CAAGG:C	donor_loss	1.0000
11:134288888:AAGG:A	donor_loss	1.0000
11:134288889:AGGT:A	donor_loss	1.0000
11:134288891:GT:G	donor_loss	1.0000
11:134288892:T:A	donor_loss	1.0000
11:134292211:G:GT	donor_gain	1.0000
11:134309621:TGCAG:T	acceptor_gain	1.0000
11:134309623:CAG:C	acceptor_gain	1.0000
11:134309624:A:AG	acceptor_gain	1.0000
11:134309624:AGA:A	acceptor_gain	1.0000
11:134309625:G:GG	acceptor_gain	1.0000
11:134309625:GA:G	acceptor_gain	1.0000
11:134309625:GAG:G	acceptor_gain	1.0000
11:134309735:G:GT	donor_gain	1.0000
11:134309735:G:T	donor_gain	1.0000
11:134309759:C:G	donor_gain	1.0000
11:134309780:T:TA	donor_gain	1.0000
11:134309781:A:AA	donor_gain	1.0000
11:134312347:A:AG	acceptor_gain	1.0000
11:134312348:G:GG	acceptor_gain	1.0000
11:134312348:GCCA:G	acceptor_gain	1.0000
11:134312485:CACAG:C	donor_loss	1.0000
11:134312486:ACAGG:A	donor_loss	1.0000

AlphaMissense

4291 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:134313985:T:C	F542L	0.976
11:134313987:T:A	F542L	0.976
11:134313987:T:G	F542L	0.976
11:134310625:T:C	L385P	0.971
11:134312428:T:C	L456P	0.966
11:134314427:T:C	F589L	0.965
11:134314429:C:A	F589L	0.965
11:134314429:C:G	F589L	0.965
11:134307175:T:A	W310R	0.963
11:134307175:T:C	W310R	0.963
11:134310586:T:C	L372P	0.961
11:134310586:T:A	L372H	0.956
11:134313418:T:C	L508P	0.955
11:134312817:T:A	V477E	0.953
11:134318673:G:T	G608W	0.952
11:134318644:G:A	G598E	0.951
11:134313409:T:C	L505P	0.947
11:134307177:G:C	W310C	0.946
11:134307177:G:T	W310C	0.946
11:134310615:T:G	Y382D	0.945
11:134318677:G:C	R609P	0.945
11:134309757:A:C	S365R	0.942
11:134309759:C:A	S365R	0.942
11:134309759:C:G	S365R	0.942
11:134310592:A:T	E374V	0.942
11:134312819:T:C	F478L	0.940
11:134312821:T:A	F478L	0.940
11:134312821:T:G	F478L	0.940
11:134313986:T:C	F542S	0.940
11:134277870:G:C	R107P	0.938

dbSNP variants (sampled 300 via entrez): RS1000002362 (11:134291865 C>T), RS1000073626 (11:134296865 A>T), RS1000089742 (11:134321556 T>C), RS1000116818 (11:134297626 C>T), RS1000147361 (11:134281310 G>A), RS1000177908 (11:134308945 T>TGGAGAGATGATTGC), RS1000180416 (11:134280971 C>T), RS1000226673 (11:134324424 A>C), RS1000283999 (11:134317540 A>T), RS1000333061 (11:134282172 A>C,T), RS1000381496 (11:134280640 A>G), RS1000515443 (11:134287999 C>T), RS1000688097 (11:134324027 C>G,T), RS1000745882 (11:134286649 C>A,T), RS1000866416 (11:134300629 C>G,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

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression	4
entinostat	increases expression, affects cotreatment	2
belinostat	increases expression, affects cotreatment	2
fluorene-9-bisphenol	increases expression	1
triphenyl phosphate	affects expression	1
terbufos	increases methylation	1
trichostatin A	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	increases expression, affects cotreatment	1
Resveratrol	decreases expression, affects cotreatment	1
Benzo(a)pyrene	increases methylation, decreases methylation	1
Copper	affects cotreatment, decreases expression	1
Diethylhexyl Phthalate	decreases expression	1
Fonofos	increases methylation	1
Niclosamide	decreases expression	1
Oxygen	decreases expression	1
Parathion	increases methylation	1
Silver	decreases expression	1
Antirheumatic Agents	decreases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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