B3GNT7
protein-codingUDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7, the group of Beta 3-glycosyltransferases
Gene summary
Enables N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity. Involved in keratan sulfate proteoglycan biosynthetic process. Predicted to be located in membrane. Predicted to be active in Golgi membrane. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~13.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to B3GNT7 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_145236.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 52 | 3 | 55 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 52 | 4 | 0 | 56 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_660279.1 | 2 | MANE Select | |
| Ensembl | ENSP00000287590.5 | 2 | MANE Select | |
| Ensembl | ENSP00000519481.1 | 4 | Standard | |
| Ensembl | ENSP00000519481.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Glycosaminoglycan biosynthesis - keratan sulfate - Homo sapiens (human)
- Metabolism of carbohydrates
- Keratan sulfate biosynthesis
- Keratan sulfate/keratin metabolism
- Glycosaminoglycan metabolism
Biological Process
- protein glycosylation
- O-glycan processing
- keratan sulfate biosynthetic process
- poly-N-acetyllactosamine biosynthetic process
Molecular Function
- acetylgalactosaminyltransferase activity
- UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity
- N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity
Cellular Component
- Golgi membrane
- endoplasmic reticulum
- Golgi apparatus
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000287590
- Coding exons
- 2
- Length
- 5622
- Individuals with no LoFs
- 124620
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 15
- Defined
- 124635
- p
- 0.0000602
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.19 | 221 | 277 | 0.799 | 0.0000195 | 2587 |
| Missense (PolyPhen) | 65 | 111.86 | 0.58108 | 1074 | ||
| Synonymous | -0.401 | 141 | 135 | 1.04 | 0.0000104 | 850 |
| Loss of Function | 2.79 | 2 | 12.7 | 0.157 | 6.24e-7 | 128 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00013 | 0.00013 | rare |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000036 | 0.000035 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0.00052 | 0.00050 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May be involved in keratane sulfate biosynthesis. Transfers N-acetylgalactosamine on to keratan sulfate-related glycans. May play a role in preventing cells from migrating out of the original tissues and invading surrounding tissues. {ECO:0000269|PubMed:12061784}.;
Recessive Scores
- pRec
- 0.105
Intolerance Scores
- LoFtool
- 0.354
- RVIS EVS
- -0.05
- RVIS percentile EVS
- 50.34
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.220
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |