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GeneE
10 sources retrieved · Most recent: April 2026 · Index updated 15 days ago
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B3GALT6
beta-1,3-galactosyltransferase 6
Chromosome 1 · 1p36.33
NCBI Gene: 126792Ensembl: ENSG00000176022.7HGNC: HGNC:17978UniProt: Q96L58
40PubMed Papers
23Diseases
0Drugs
37Pathogenic Variants
CLINICAL
OMIM Disease Gene
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
Golgi apparatusmembranegalactosylxylosylprotein 3-beta-galactosyltransferase activityglycosaminoglycan biosynthetic processspondyloepimetaphyseal dysplasia with joint laxity, type 1, with or without fracturesEhlers-Danlos syndrome, spondylodysplastic type, 2Ehlers-Danlos syndrome, progeroid typespondyloepimetaphyseal dysplasia with joint laxity
✦AI Summary

B3GALT6 encodes β1,3-galactosyltransferase 6, a Golgi-localized glycosyltransferase that catalyzes the transfer of galactose from UDP-galactose to galactose-β1,4-xylose residues in the linker region of glycosaminoglycans (GAGs), particularly heparan sulfate and chondroitin sulfate 1. This enzyme is essential for proteoglycan biosynthesis, functioning as the third sugar-adding enzyme in the GAG linkage region 2. B3GALT6 mutations cause spondylodysplastic Ehlers-Danlos syndrome and spondyloepimetaphyseal dysplasia, characterized by severe musculoskeletal abnormalities, craniofacial dysmorphism, and connective tissue fragility 13. These pathogenic mutations reduce protein abundance and eliminate galactosyltransferase activity, leading to deficient GAG synthesis and ultrastructural collagen fibril disorganization 1. Loss of B3GALT6 function results in impaired collagen maturation and altered tissue biomechanics 3. Beyond skeletal disease, B3GALT6 promotes dormant breast cancer cell survival and recurrence through heparan sulfate-mediated FGF signaling, predicting poor patient outcomes 4. Additionally, sulfated GAGs produced via B3GALT6 serve as cellular targets for Candida albicans candidalysin toxin, with therapeutic potential through exogenous GAG supplementation 5.

Sources cited
1
B3GALT6 encodes a linker region glycosyltransferase; biallelic mutations cause spondylodysplastic EDS with GAG synthesis deficiency and collagen fibril abnormalities
PMID: 29931299
2
B3GALT6 knockout zebrafish recapitulate human β3GalT6-deficiency phenotypes with craniofacial dysmorphism, skeletal dysplasia, and disturbed collagen organization
PMID: 33363150
3
B3GALT6 mutations cause spondylodysplastic EDS through impaired collagen maturation and defective collagen XII glycosylation affecting tissue structure
PMID: 40857410
4
B3GALT6-mediated heparan sulfate biosynthesis promotes dormant breast cancer cell survival and recurrence via FGF signaling axis
PMID: 38065100
5
B3GALT6 produces sulfated GAGs that serve as cellular targets for Candida albicans candidalysin toxin; exogenous sulfated GAGs protect epithelial cells
PMID: 39285260
Disease Associationsⓘ23
spondyloepimetaphyseal dysplasia with joint laxity, type 1, with or without fracturesOpen Targets
0.82Strong
Ehlers-Danlos syndrome, spondylodysplastic type, 2Open Targets
0.80Strong
Ehlers-Danlos syndrome, progeroid typeOpen Targets
0.70Strong
spondyloepimetaphyseal dysplasia with joint laxityOpen Targets
0.70Moderate
Al-Gazali syndromeOpen Targets
0.67Moderate
Ehlers-Danlos syndromeOpen Targets
0.56Moderate
B3GALT6-congenital disorder of glycosylationOpen Targets
0.37Weak
Disproportionate short statureOpen Targets
0.37Weak
Ehlers-Danlos syndrome, spondylodysplastic typeOpen Targets
0.37Weak
Spondyloepiphyseal dysplasia and spondyloepimetaphyseal dysplasiaOpen Targets
0.37Weak
spondyloepiphyseal dysplasiaOpen Targets
0.27Weak
genetic disorderOpen Targets
0.19Weak
hair colorOpen Targets
0.05Suggestive
asthmaOpen Targets
0.03Suggestive
Nasal Cavity PolypOpen Targets
0.02Suggestive
ankylosing spondylitisOpen Targets
0.02Suggestive
Crohn's diseaseOpen Targets
0.02Suggestive
psoriasisOpen Targets
0.02Suggestive
sclerosing cholangitisOpen Targets
0.02Suggestive
ulcerative colitisOpen Targets
0.02Suggestive
Al-Gazali syndromeUniProt
Ehlers-Danlos syndrome, spondylodysplastic type, 2UniProt
Spondyloepimetaphyseal dysplasia with joint laxity, 1, with or without fracturesUniProt
Pathogenic Variants37
NM_080605.4(B3GALT6):c.1A>G (p.Met1Val)Pathogenic
Spondyloepimetaphyseal dysplasia with joint laxity, type 1, with or without fractures|not provided|Spondyloepimetaphyseal dysplasia with joint laxity;Ehlers-Danlos syndrome, spondylodysplastic type, 2|B3GALT6-related disorder|Ehlers-Danlos syndrome, spondylodysplastic type, 2
★★☆☆2025→ Residue 1
NM_080605.4(B3GALT6):c.513_520del (p.Glu174fs)Pathogenic
Ehlers-Danlos syndrome, spondylodysplastic type, 2;Spondyloepimetaphyseal dysplasia with joint laxity|not provided|B3GALT6-related disorder|Ehlers-Danlos syndrome, spondylodysplastic type, 2
★★☆☆2025→ Residue 174
NM_080605.4(B3GALT6):c.2T>C (p.Met1Thr)Pathogenic
Ehlers-Danlos syndrome, spondylodysplastic type, 2;Spondyloepimetaphyseal dysplasia with joint laxity|not provided|B3GALT6-congenital disorder of glycosylation
★★☆☆2025→ Residue 1
NM_080605.4(B3GALT6):c.925T>A (p.Ser309Thr)Pathogenic
Ehlers-Danlos syndrome, spondylodysplastic type, 2|not provided|Spondyloepimetaphyseal dysplasia with joint laxity;Ehlers-Danlos syndrome, spondylodysplastic type, 2
★★☆☆2025→ Residue 309
NM_080605.4(B3GALT6):c.556T>C (p.Phe186Leu)Pathogenic
Spondyloepimetaphyseal dysplasia with joint laxity, type 1, with or without fractures|Spondyloepimetaphyseal dysplasia with joint laxity, type 1, with fractures|Ehlers-Danlos syndrome, spondylodysplastic type, 2|not provided
★★☆☆2024→ Residue 186
NM_080605.4(B3GALT6):c.766C>T (p.Arg256Trp)Pathogenic
Ehlers-Danlos syndrome, spondylodysplastic type, 2
★★☆☆2023→ Residue 256
NM_080605.4(B3GALT6):c.1A>T (p.Met1Leu)Pathogenic
Fetal anomalies with a likely genetic cause
★☆☆☆2026→ Residue 1
NM_080605.4(B3GALT6):c.197_253del (p.Ala66_Arg84del)Pathogenic
Ehlers-Danlos syndrome, spondylodysplastic type, 2;Spondyloepimetaphyseal dysplasia with joint laxity
★☆☆☆2025→ Residue 66
NM_080605.4(B3GALT6):c.2T>G (p.Met1Arg)Likely pathogenic
Ehlers-Danlos syndrome, spondylodysplastic type, 2
★☆☆☆2025→ Residue 1
NM_080605.4(B3GALT6):c.117dup (p.Arg40fs)Pathogenic
Ehlers-Danlos syndrome, spondylodysplastic type, 2;Spondyloepimetaphyseal dysplasia with joint laxity
★☆☆☆2025→ Residue 40
NM_080605.4(B3GALT6):c.200C>T (p.Pro67Leu)Pathogenic
Spondyloepimetaphyseal dysplasia with joint laxity, type 1, with or without fractures|Spondyloepimetaphyseal dysplasia with joint laxity;Ehlers-Danlos syndrome, spondylodysplastic type, 2
★☆☆☆2025→ Residue 67
NM_080605.4(B3GALT6):c.577A>T (p.Lys193Ter)Pathogenic
Ehlers-Danlos syndrome, spondylodysplastic type, 2;Spondyloepimetaphyseal dysplasia with joint laxity
★☆☆☆2025→ Residue 193
NM_080605.4(B3GALT6):c.251_257del (p.Arg84fs)Pathogenic
Ehlers-Danlos syndrome, spondylodysplastic type, 2;Spondyloepimetaphyseal dysplasia with joint laxity
★☆☆☆2025→ Residue 84
NM_080605.4(B3GALT6):c.460A>T (p.Lys154Ter)Pathogenic
Ehlers-Danlos syndrome, spondylodysplastic type, 2;Spondyloepimetaphyseal dysplasia with joint laxity
★☆☆☆2025→ Residue 154
NM_080605.4(B3GALT6):c.521_528del (p.Glu174fs)Pathogenic
Ehlers-Danlos syndrome, spondylodysplastic type, 2;Spondyloepimetaphyseal dysplasia with joint laxity
★☆☆☆2025→ Residue 174
NM_080605.4(B3GALT6):c.84C>G (p.Tyr28Ter)Pathogenic
Ehlers-Danlos syndrome, spondylodysplastic type, 2;Spondyloepimetaphyseal dysplasia with joint laxity
★☆☆☆2025→ Residue 28
NC_000001.11:g.1232202_1232288delPathogenic
Ehlers-Danlos syndrome, spondylodysplastic type, 2;Spondyloepimetaphyseal dysplasia with joint laxity
★☆☆☆2024
NM_080605.4(B3GALT6):c.636C>G (p.Tyr212Ter)Pathogenic
Spondyloepimetaphyseal dysplasia with joint laxity;Ehlers-Danlos syndrome, spondylodysplastic type, 2
★☆☆☆2024→ Residue 212
NM_080605.4(B3GALT6):c.1A>C (p.Met1Leu)Pathogenic
Al-Gazali syndrome;Spondyloepimetaphyseal dysplasia with joint laxity, type 1, with or without fractures;Ehlers-Danlos syndrome, spondylodysplastic type, 2
★☆☆☆2024→ Residue 1
NM_080605.4(B3GALT6):c.235A>G (p.Thr79Ala)Pathogenic
Ehlers-Danlos syndrome, spondylodysplastic type, 2;Spondyloepimetaphyseal dysplasia with joint laxity
★☆☆☆2024→ Residue 79
View on ClinVar ↗
Related Genes
FAM20BProtein interaction81%XYLT2Protein interaction75%UBE2J2Protein interaction75%CHST14Protein interaction72%XYLT1Protein interaction69%B4GALT7Protein interaction63%
Tissue Expression6 tissues
Liver
100%
Heart
70%
Lung
61%
Ovary
60%
Brain
55%
Bone Marrow
18%
Gene Interaction Network
Click a node to explore
B3GALT6FAM20BXYLT2UBE2J2CHST14XYLT1B4GALT7
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt Q96L58
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
1.99LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF2.54 [1.51–1.99]
RankingsWhere B3GALT6 stands among ~20K protein-coding genes
  • #10,135of 20,598
    Most Researched40
  • #1,627of 5,498
    Most Pathogenic Variants37
  • #17,834of 17,882
    Most Constrained (LOEUF)1.99
Genes detectedB3GALT6
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
B3GALT6 promotes dormant breast cancer cell survival and recurrence by enabling heparan sulfate-mediated FGF signaling.
PMID: 38065100
Cancer Cell · 2024
1.00
2
Sulfated glycosaminoglycans are host epithelial cell targets of the Candida albicans toxin candidalysin.
PMID: 39285260
Nat Microbiol · 2024
0.90
3
PMID: 33363150
Front Cell Dev Biol · 2020
0.80
4
B3GALT6 mutations lead to compromised connective tissue biomechanics in Ehlers-Danlos syndrome.
PMID: 40857410
JCI Insight · 2025
0.70
5
Mutant
PMID: 35734427
Front Genet · 2022
0.60