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B3GALT4

gene
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Also known as beta3Gal-T4GalT4

Summary

B3GALT4 (beta-1,3-galactosyltransferase 4, HGNC:919) is a protein-coding gene on chromosome 6p21.32, encoding Beta-1,3-galactosyltransferase 4 (O96024). Involved in GM1/GD1B/GA1 ganglioside biosynthesis.

This gene is a member of the beta-1,3-galactosyltransferase (beta3GalT) gene family. This family encodes type II membrane-bound glycoproteins with diverse enzymatic functions using different donor substrates (UDP-galactose and UDP-N-acetylglucosamine) and different acceptor sugars (N-acetylglucosamine, galactose, N-acetylgalactosamine). The beta3GalT genes are distantly related to the Drosophila Brainiac gene and have the protein coding sequence contained in a single exon. The beta3GalT proteins also contain conserved sequences not found in the beta4GalT or alpha3GalT proteins. The carbohydrate chains synthesized by these enzymes are designated as type 1, whereas beta4GalT enzymes synthesize type 2 carbohydrate chains. The ratio of type 1:type 2 chains changes during embryogenesis. By sequence similarity, the beta3GalT genes fall into at least two groups: beta3GalT4 and 4 other beta3GalT genes (beta3GalT1-3, beta3GalT5). This gene is oriented telomere to centromere in close proximity to the ribosomal protein S18 gene. The functionality of the encoded protein is limited to ganglioseries glycolipid biosynthesis.

Source: NCBI Gene 8705 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 48 total
  • MANE Select transcript: NM_003782

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:919
Approved symbolB3GALT4
Namebeta-1,3-galactosyltransferase 4
Location6p21.32
Locus typegene with protein product
StatusApproved
Aliasesbeta3Gal-T4, GalT4
Ensembl geneENSG00000235863
Ensembl biotypeprotein_coding
OMIM603095
Entrez8705

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000451237, ENST00000606990

RefSeq mRNA: 1 — MANE Select: NM_003782 NM_003782

CCDS: CCDS34425

Canonical transcript exons

ENST00000383209 — 0 exons

Expression profiles

Bgee: expression breadth ubiquitous, 170 present calls, max score 87.56.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.8384 / max 178.4977, expressed in 1349 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
672643.43971162
672680.7891436
672630.4081218
672670.115524
672650.051613
672660.034410

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
lower esophagus mucosaUBERON:003583487.56gold quality
mucosa of transverse colonUBERON:000499186.81gold quality
granulocyteCL:000009486.12gold quality
left testisUBERON:000453385.90gold quality
right testisUBERON:000453485.07gold quality
olfactory segment of nasal mucosaUBERON:000538684.59gold quality
apex of heartUBERON:000209883.93gold quality
descending thoracic aortaUBERON:000234583.12gold quality
thoracic aortaUBERON:000151582.38gold quality
skin of legUBERON:000151182.34gold quality
ascending aortaUBERON:000149682.27gold quality
esophagus mucosaUBERON:000246982.17gold quality
monocyteCL:000057681.96gold quality
leukocyteCL:000073881.96gold quality
testisUBERON:000047381.91gold quality
transverse colonUBERON:000115781.89gold quality
right coronary arteryUBERON:000162581.72gold quality
mononuclear cellCL:000084281.67gold quality
skin of abdomenUBERON:000141681.64gold quality
mucosa of stomachUBERON:000119981.30gold quality
aortaUBERON:000094781.20gold quality
esophagusUBERON:000104381.05gold quality
popliteal arteryUBERON:000225080.73gold quality
tibial arteryUBERON:000761080.71gold quality
lower esophagusUBERON:001347380.54gold quality
left coronary arteryUBERON:000162680.52gold quality
lower esophagus muscularis layerUBERON:003583380.52gold quality
minor salivary glandUBERON:000183080.51gold quality
esophagogastric junction muscularis propriaUBERON:003584180.39gold quality
right adrenal glandUBERON:000123380.17gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no0.20

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

17 targeting B3GALT4, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-118499.9968.191458
HSA-MIR-103A-3P99.9869.141595
HSA-MIR-10799.9869.141595
HSA-MIR-6809-3P99.9171.453814
HSA-MIR-449699.8868.892236
HSA-MIR-2116-3P99.7464.32889
HSA-MIR-426199.5970.303415
HSA-MIR-6731-5P99.2867.422375
HSA-MIR-808599.2867.562362
HSA-MIR-7156-3P98.2567.66859
HSA-MIR-6747-3P97.7364.841596
HSA-MIR-92197.0966.45562
HSA-MIR-468996.9765.791209
HSA-MIR-6858-5P96.0564.591020
HSA-MIR-4774-5P95.9268.27827
HSA-MIR-286195.2465.471056
HSA-MIR-1211594.1966.37738

Literature-anchored findings (GeneRIF, showing 6)

  • We found beta3Gal-T4 and T5 enzymatic activity in ovarian cancer tissues, indicating that these enzymes are expressed at least in ovarian cancer (PMID:19225246)
  • Data showed that GM1/GD1b/GA1 synthase transfectant cells had definite reduction in cell growth and invasion. (PMID:20594196)
  • Induction of GM1a/GD1b synthase triggers complex ganglioside expression and alters neuroblastoma cell behavior; a new tumor cell model of ganglioside function (PMID:21519903)
  • Colorectal cancer (CRC) patients expressing both high B7-H3 and high B3GALT4 contributed to a significant decrease in overall survival. The expression of B3GALT4 in CRC is positively correlated with B7-H3 expression in vitro. B7-H3/B3GLAT4 may be used as dual prognostic biomarkers for CRC. (PMID:30131660)
  • In patients with late-onset Alzheimer disease, a number of differentially methylated postitions were hypomethylated in B3GALT4 compared with controls. (PMID:30372681)
  • B3GALT4 knockdown decreases GM1 ganglioside level and enhances vulnerability for neurodegeneration. (PMID:30611881)

Cross-species orthologs

18 orthologs

OrganismSymbolGene ID
danio_reriob3galt4ENSDARG00000076218
mus_musculusB3galt4ENSMUSG00000067370
rattus_norvegicusB3galt4ENSRNOG00000071248
drosophila_melanogasterCG8673FBGN0031986
drosophila_melanogasterCG8668FBGN0031988
caenorhabditis_elegansWBGENE00000267
caenorhabditis_elegansWBGENE00007104
caenorhabditis_elegansC47F8.3WBGENE00008159
caenorhabditis_elegansC47F8.5WBGENE00008161
caenorhabditis_elegansC47F8.6WBGENE00008162
caenorhabditis_elegansC54C8.3WBGENE00008291
caenorhabditis_elegansE03H4.11WBGENE00008478
caenorhabditis_elegansF14B6.4WBGENE00008785
caenorhabditis_elegansF14B6.6WBGENE00008787
caenorhabditis_elegansWBGENE00009849
caenorhabditis_elegansT09E11.10WBGENE00011659
caenorhabditis_elegansWBGENE00011665
caenorhabditis_elegansT15D6.5WBGENE00011780

Paralogs (15): B3GNT7 (ENSG00000156966), B3GALT2 (ENSG00000162630), B3GALNT2 (ENSG00000162885), B3GALNT1 (ENSG00000169255), B3GNT2 (ENSG00000170340), B3GALT1 (ENSG00000172318), B3GALT6 (ENSG00000176022), B3GNT4 (ENSG00000176383), B3GNT5 (ENSG00000176597), B3GNT8 (ENSG00000177191), B3GNT3 (ENSG00000179913), B3GALT5 (ENSG00000183778), B3GNT6 (ENSG00000198488), B3GALT9 (ENSG00000214654), B3GNT9 (ENSG00000237172)

Protein

Protein identifiers

Beta-1,3-galactosyltransferase 4 — O96024 (reviewed: O96024)

Alternative names: Gal-T2, Ganglioside galactosyltransferase, UDP-galactose:beta-N-acetyl-galactosamine-beta-1,3-galactosyltransferase

All UniProt accessions (2): O96024, Q5STJ7

UniProt curated annotations — full annotation on UniProt →

Function. Involved in GM1/GD1B/GA1 ganglioside biosynthesis.

Subcellular location. Golgi apparatus membrane.

Tissue specificity. Highly expressed in heart, skeletal muscle and pancreas and, to a lesser extent, in brain, placenta, kidney, liver and lung.

Pathway. Protein modification; protein glycosylation.

Similarity. Belongs to the glycosyltransferase 31 family.

RefSeq proteins (1): NP_003773* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002659Glyco_trans_31Family

Pfam: PF01762

Enzyme classification (BRENDA):

  • EC 2.4.1.62 — ganglioside galactosyltransferase (BRENDA: 11 organisms, 28 substrates, 17 inhibitors, 13 Km, 3 kcat entries)

Substrate kinetics (BRENDA)

5 substrates with measured Km, best-characterized 5. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
N-ACETYL-D-GALACTOSAMINYL-(N-ACETYLNEURAMINYL)-D0.01–0.185
UDP-GALACTOSE0.012–2.474
GALNACALPHA-FCHASE1.681
GALNACBETA-FCHASE3.181
UDP-GAL1.111

Catalyzed reactions (Rhea), 4 shown:

  • a ganglioside GM2 (d18:1(4E)) + UDP-alpha-D-galactose = a ganglioside GM1 (d18:1(4E)) + UDP + H(+) (RHEA:16773)
  • a ganglioside GA2 (d18:1(4E)) + UDP-alpha-D-galactose = a ganglioside GA1 (d18:1(4E)) + UDP + H(+) (RHEA:41960)
  • a ganglioside GD2 (d18:1(4E)) + UDP-alpha-D-galactose = a ganglioside GD1b (d18:1(4E)) + UDP + H(+) (RHEA:47568)
  • a ganglioside GM2 + UDP-alpha-D-galactose = a ganglioside GM1 + UDP + H(+) (RHEA:48280)

UniProt features (5 total): topological domain 2, chain 1, transmembrane region 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O96024-F184.890.60

Functional residue map

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

Glycosylation sites (1): 149

Function

Pathways and Gene Ontology

Reactome pathways

8 pathways

IDPathway
R-HSA-9037629Lewis blood group biosynthesis
R-HSA-9840309Glycosphingolipid biosynthesis
R-HSA-1430728Metabolism
R-HSA-1660662Glycosphingolipid metabolism
R-HSA-428157Sphingolipid metabolism
R-HSA-556833Metabolism of lipids
R-HSA-71387Metabolism of carbohydrates and carbohydrate derivatives
R-HSA-9033658Blood group systems biosynthesis

MSigDB gene sets: 148 (showing top): GOBP_OLIGOSACCHARIDE_METABOLIC_PROCESS, GOBP_GLYCOLIPID_BIOSYNTHETIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_CERAMIDE_BIOSYNTHETIC_PROCESS, GOBP_SPHINGOLIPID_METABOLIC_PROCESS, GOBP_AMIDE_METABOLIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, GOBP_AMIDE_BIOSYNTHETIC_PROCESS, GOBP_GLYCOSPHINGOLIPID_BIOSYNTHETIC_PROCESS, GOBP_CARBOHYDRATE_METABOLIC_PROCESS, GOBP_GANGLIOSIDE_BIOSYNTHETIC_PROCESS, GOBP_LIPID_METABOLIC_PROCESS, GOBP_OLIGOSACCHARIDE_BIOSYNTHETIC_PROCESS, GOBP_LIPID_BIOSYNTHETIC_PROCESS, BENPORATH_NOS_TARGETS

GO Biological Process (7): ganglioside biosynthetic process (GO:0001574), protein O-linked glycosylation (GO:0006493), glycosphingolipid biosynthetic process (GO:0006688), oligosaccharide biosynthetic process (GO:0009312), obsolete protein glycosylation (GO:0006486), lipid metabolic process (GO:0006629), carbohydrate derivative biosynthetic process (GO:1901137)

GO Molecular Function (5): N-acetyl-beta-D-glucosaminide beta-(1,3)-galactosyltransferase activity (GO:0008499), glycosyltransferase activity (GO:0016757), ganglioside galactosyltransferase activity (GO:0047915), transferase activity (GO:0016740), hexosyltransferase activity (GO:0016758)

GO Cellular Component (3): Golgi membrane (GO:0000139), Golgi apparatus (GO:0005794), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-6 pathways:

CategoryPathways
Metabolism2
Blood group systems biosynthesis1
Glycosphingolipid metabolism1
Sphingolipid metabolism1
Metabolism of lipids1
Metabolism of carbohydrates and carbohydrate derivatives1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
UDP-galactosyltransferase activity2
ganglioside metabolic process1
glycosphingolipid biosynthetic process1
ceramide biosynthetic process1
glycoprotein biosynthetic process1
glycosphingolipid metabolic process1
glycolipid biosynthetic process1
sphingolipid biosynthetic process1
oligosaccharide metabolic process1
carbohydrate biosynthetic process1
primary metabolic process1
biosynthetic process1
carbohydrate derivative metabolic process1
beta-1,3-galactosyltransferase activity1
transferase activity1
catalytic activity1
glycosyltransferase activity1
Golgi apparatus1
bounding membrane of organelle1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1
cellular anatomical structure1

Protein interactions and networks

STRING

793 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
B3GALT4A4GALTQ9NPC4866
B3GALT4WDR46O15213829
B3GALT4ST3GAL2Q16842757
B3GALT4B4GALNT1Q00973716
B3GALT4B4GALT6Q9UBX8701
B3GALT4RPS18P25232698
B3GALT4B4GALT5O43286660
B3GALT4ST8SIA5O15466645
B3GALT4ST3GAL5Q9UNP4645
B3GALT4UGCGQ16739593
B3GALT4C1GALT1Q9NS00578
B3GALT4ST8SIA1Q92185574
B3GALT4B4GALT4O60513544
B3GALT4PGAP4Q9BRR3507
B3GALT4ETFAP13804505

IntAct

7 interactions, top by confidence:

ABTypeScore
B3GALT4NOTCH1psi-mi:“MI:0915”(physical association)0.370
DAAM1B3GALT4psi-mi:“MI:0915”(physical association)0.370
B3GALT4METTL18psi-mi:“MI:0915”(physical association)0.370
B3GALT4DYNLL1psi-mi:“MI:0915”(physical association)0.370
B3GALT4psi-mi:“MI:0914”(association)0.350
B3GALT4DDX19Bpsi-mi:“MI:0915”(physical association)0.000

BioGRID (31): B3GALT4 (Two-hybrid), CACNA2D2 (Affinity Capture-MS), ABHD12 (Affinity Capture-MS), TUBA1A (Affinity Capture-MS), ENTPD2 (Affinity Capture-MS), TMEM165 (Affinity Capture-MS), PRSS8 (Affinity Capture-MS), ASIC1 (Affinity Capture-MS), CNPY3 (Affinity Capture-MS), PTDSS2 (Affinity Capture-MS), NPC1 (Affinity Capture-MS), TMX3 (Affinity Capture-MS), HFE (Affinity Capture-MS), HSPA5 (Affinity Capture-MS), GPR107 (Affinity Capture-MS)

ESM2 similar proteins: O08644, O15197, O88178, O96024, O97507, P00748, P0C0K6, P0C0K7, P98140, Q02853, Q04962, Q08345, Q08BL3, Q0V8J4, Q13444, Q3USF0, Q3V1N9, Q499S5, Q5EA85, Q5JCS9, Q5RAL7, Q5TJE8, Q66H69, Q6MG64, Q6ZMB0, Q7T3S5, Q7TNJ2, Q7YR43, Q7Z7M1, Q7Z7M8, Q864U6, Q8BYG9, Q8IU80, Q8IZF5, Q8IZY2, Q8K0J2, Q8N3T1, Q8NFL0, Q8R3I9, Q91V24

Diamond homologs: A8MXE2, O43825, O54904, O54905, O75752, O88178, O96024, Q1RLK6, Q5HZL5, Q5JCS9, Q5R5Y3, Q5RAL7, Q66H69, Q6AY39, Q6DE15, Q6P3P5, Q793U7, Q7JK24, Q7JK25, Q7JK26, Q7T3S5, Q864U6, Q864U8, Q8BGY6, Q8R3I9, Q920V1, Q95US5, Q99NB2, Q9BYG0, Q9C0J1, Q9JI67, Q9MYM7, Q9N293, Q9N294, Q9N295, Q9Y2A9, Q9Y2C3, Q9Y5Z6, Q9Z0F0, Q24157

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance33
Likely benign15
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1075 predictions. Top by Δscore:

VariantEffectΔscore
6:33279383:C:CTacceptor_gain1.0000
6:33279384:G:Tacceptor_gain1.0000
6:33279493:TTAC:Tdonor_loss1.0000
6:33279494:TAC:Tdonor_loss1.0000
6:33279495:A:AGdonor_loss1.0000
6:33279495:AC:Adonor_gain1.0000
6:33279496:C:CAdonor_loss1.0000
6:33279496:CC:Cdonor_gain1.0000
6:33279504:T:TAdonor_gain1.0000
6:33279520:T:TAdonor_gain1.0000
6:33279526:T:TAdonor_gain1.0000
6:33279606:TAGCC:Tacceptor_gain1.0000
6:33279609:CC:Cacceptor_gain1.0000
6:33279610:CC:Cacceptor_gain1.0000
6:33279610:CCT:Cacceptor_loss1.0000
6:33279747:AGGGG:Adonor_gain1.0000
6:33280422:CCTCA:Cdonor_loss1.0000
6:33280423:CTCA:Cdonor_loss1.0000
6:33280425:CACCT:Cdonor_loss1.0000
6:33280427:C:CAdonor_loss1.0000
6:33280427:CCTT:Cdonor_gain1.0000
6:33280518:GGCCC:Gacceptor_gain1.0000
6:33280519:GCCC:Gacceptor_gain1.0000
6:33280520:CCC:Cacceptor_gain1.0000
6:33280520:CCCC:Cacceptor_gain1.0000
6:33280521:CC:Cacceptor_gain1.0000
6:33280521:CCC:Cacceptor_gain1.0000
6:33280522:CC:Cacceptor_gain1.0000
6:33280522:CCTGA:Cacceptor_loss1.0000
6:33280523:C:CCacceptor_gain1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000382741 (6:33275295 T>A), RS1000984609 (6:33276833 C>G,T), RS1004002807 (6:33275630 T>C), RS1004113816 (6:33275637 G>A), RS1005085233 (6:33277149 G>A,C), RS1007920249 (6:33278937 G>C), RS1008321396 (6:33277237 AT>A), RS1008790390 (6:33278396 A>G), RS1008822964 (6:33277981 G>A), RS1010746931 (6:33277875 A>G), RS1011131495 (6:33278315 G>A,T), RS1011232859 (6:33278558 A>T), RS1011827603 (6:33277028 G>A), RS1011998223 (6:33277192 T>C), RS1012024701 (6:33277228 C>G,T)

Disease associations

OMIM: gene MIM:603095 | disease phenotypes: MIM:604571, MIM:612621

GenCC curated gene-disease

Mondo (2): MHC class I deficiency (MONDO:0011476), intellectual disability, autosomal dominant 5 (MONDO:0012960)

Orphanet (2): Immunodeficiency by defective expression of MHC class I (Orphanet:34592), SYNGAP1-related developmental and epileptic encephalopathy (Orphanet:544254)

HPO phenotypes

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

GWAS associations

3 associations (top):

StudyTraitp-value
GCST000132_6LDL cholesterol5.000000e-08
GCST004521_287Autism spectrum disorder or schizophrenia5.000000e-08
GCST005951_153Body mass index5.000000e-09

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004611low density lipoprotein cholesterol measurement
EFO:0004340body mass index

MeSH disease descriptors (1)

DescriptorNameTree numbers
C567234Mental Retardation, Autosomal Dominant 5 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

33 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects cotreatment, increases methylation, decreases expression, increases expression3
Valproic Acidaffects expression, decreases expression, increases expression, increases methylation3
propionaldehydedecreases expression2
butyraldehydedecreases expression2
pentanaldecreases expression2
Air Pollutantsdecreases expression, affects methylation, increases abundance2
Tretinoinincreases expression2
aristolochic acid Iincreases expression1
bisphenol Faffects cotreatment, increases expression1
deoxynivalenoldecreases expression1
n-hexanaldecreases expression1
sulforaphanedecreases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
caprylic aldehydedecreases expression1
heptanaldecreases expression1
di-n-butylphosphoric acidaffects expression1
jinfukangincreases expression1
Sunitinibdecreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Acetaminophenincreases expression1
Benzalkonium Compoundsaffects response to substance1
Benzo(a)pyreneincreases methylation1
Calcitriolaffects cotreatment, increases expression1
Cisplatinaffects response to substance1
Dexamethasoneaffects cotreatment, increases expression1
Indomethacinaffects cotreatment, increases expression1
Nitrogen Dioxideaffects methylation, increases abundance1
Silicon Dioxidedecreases expression1
Smokedecreases expression1
Testosteroneaffects cotreatment, increases expression1

Clinical trials (associated diseases)

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

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 75

This page pulls from 75 datasets indexed by BioBTree:

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