B4GALNT1

Chr 12AR

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

Also known as: GALGT, GALNACT, GalNAc-T, SPG26

NCBI Gene: 2583ENSG00000135454UniProt: Q00973OMIM: 601873

The protein catalyzes the transfer of GalNAc to GM3 and GD3 gangliosides via beta-1,4 linkage to synthesize GM2 and GD2 gangliosides, functioning in the Golgi apparatus membrane. Mutations cause spastic paraplegia 26 through autosomal recessive inheritance. The pathogenic mechanism likely involves disrupted ganglioside biosynthesis leading to progressive spasticity of the lower limbs.

GeneReviewsOMIMResearchSummary from RefSeq, OMIM, UniProt
ARLOEUF 0.791 OMIM phenotype
Clinical Summary— B4GALNT1
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Gene-Disease Validity (ClinGen)
complex hereditary spastic paraplegia · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
38 unique Pathogenic / Likely Pathogenic· 143 VUS of 315 total submissions
Explore recent and relevant literature in Research Assistant →
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GeneReview available — B4GALNT1
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.79LOEUF
pLI 0.000
Z-score 2.31
OE 0.48 (0.30–0.79)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
0.92Z-score
OE missense 0.85 (0.77–0.94)
267 obs / 313.0 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.48 (0.30–0.79)
0≤0.351.4
Missense OE0.85 (0.77–0.94)
0≤0.61.4
Synonymous OE0.98
0≤1.21.6
LoF obs/exp: 11 / 23.0Missense obs/exp: 267 / 313.0Syn Z: 0.15

ClinVar Variant Classifications

315 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic23
Likely Pathogenic15
VUS143
Likely Benign104
Benign22
Conflicting2
23
Pathogenic
15
Likely Pathogenic
143
VUS
104
Likely Benign
22
Benign
2
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
19
0
4
0
23
Likely Pathogenic
11
2
2
0
15
VUS
0
131
10
2
143
Likely Benign
0
6
32
66
104
Benign
0
2
18
2
22
Conflicting
—2
Total301416670309

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

B4GALNT1 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 4 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