B4GALNT3

Chr 12

beta-1,4-N-acetyl-galactosaminyltransferase 3

NCBI Gene: 283358ENSG00000139044UniProt: Q6L9W6

B4GALNT3 transfers N-acetylgalactosamine (GalNAc) onto glucosyl residues to form N,N-prime-diacetyllactosediamine (LacdiNAc, or LDN), a unique terminal structure of cell surface N-glycans (Ikehara et al., 2006 [PubMed 16728562]).[supplied by OMIM, Aug 2008]

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0
Active trials
5
Pubs (1 yr)
0
P/LP submissions
—
P/LP missense
0.78
LOEUF
DN
Mechanism· predicted
Clinical Summary— B4GALNT3
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.78LOEUF
pLI 0.000
Z-score 2.92
OE 0.58 (0.43–0.78)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
0.71Z-score
OE missense 0.92 (0.85–0.98)
544 obs / 592.7 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.58 (0.43–0.78)
0≤0.351.4
Missense OE0.92 (0.85–0.98)
0≤0.61.4
Synonymous OE0.98
0≤1.21.6
LoF obs/exp: 32 / 55.4Missense obs/exp: 544 / 592.7Syn Z: 0.26
DN
0.6745th %ile
GOF
0.4875th %ile
LOF
0.3260th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

B4GALNT3 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Comprehensive Analysis of GDF10 Methylation Site-Associated Genes as Prognostic Markers for Endometrial Cancer
Fan J et al.·J Oncol
2022
Glyco-engineered HEK 293-F cell lines for the production of therapeutic glycoproteins with human N-glycosylation and improved pharmacokinetics.
Uhler R et al.·Glycobiology
2021
GWAS meta-analysis followed by Mendelian randomization revealed potential control mechanisms for circulating alpha-Klotho levels
Gergei I et al.·Hum Mol Genet
2022Functional
Vitamin D receptor in osteoblast lineage cells mediates increased sclerostin circulation and decreased bone formation in hypervitaminosis D.
Liu Z et al.·J Steroid Biochem Mol Biol
2025
Genome-Wide Association Study of 2,093 Cases With Idiopathic Polyneuropathy and 445,256 Controls Identifies First Susceptibility Loci
Winsvold BS et al.·Front Neurol
2021Cohort
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients