GeneBe

B3GNT4

UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 4, the group of Beta 3-glycosyltransferases

Basic information

Region (hg38): 12:122203681-122208952

Links

ENSG00000176383 ∙ NCBI:79369 ∙ OMIM:605864 ∙ HGNC:15683 ∙ Uniprot:Q9C0J1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the B3GNT4 gene.

  • not_specified (74 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the B3GNT4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000030765.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
0
missense
66
clinvar
8
clinvar
 74
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 66 8 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
B3GNT4protein_codingprotein_codingENST00000324189 25410
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
7.68e-70.29912549712491257470.000995
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-2.403402361.440.00001422419
Missense in Polyphen13585.3641.5815990
Synonymous-3.5014197.21.450.00000545826
Loss of Function0.3381011.20.8916.48e-7116

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001410.00141
Ashkenazi Jewish0.002190.00218
East Asian0.0004350.000435
Finnish0.00004730.0000462
European (Non-Finnish)0.001180.00117
Middle Eastern0.0004350.000435
South Asian0.001550.00147
Other0.0008250.000815

dbNSFP

Source: dbNSFP

Function
FUNCTION: Beta-1,3-N-acetylglucosaminyltransferase involved in the synthesis of poly-N-acetyllactosamine. Has activity for type 2 oligosaccharides. {ECO:0000269|PubMed:11042166}.;
Pathway
Glycosphingolipid biosynthesis - lacto and neolacto series - Homo sapiens (human);Metabolism of carbohydrates;Keratan sulfate biosynthesis;Keratan sulfate/keratin metabolism;Glycosaminoglycan metabolism;Post-translational protein modification;Metabolism of proteins;Metabolism;O-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Recessive Scores

pRec
0.153

Intolerance Scores

loftool
0.919
rvis_EVS
1.07
rvis_percentile_EVS
91.61

Haploinsufficiency Scores

pHI
0.140
hipred
N
hipred_score
0.170
ghis
0.413

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.225

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
B3gnt4
Phenotype

Gene ontology

Biological process
protein glycosylation;O-glycan processing;keratan sulfate biosynthetic process;poly-N-acetyllactosamine biosynthetic process
Cellular component
Golgi membrane;endoplasmic reticulum;Golgi apparatus;integral component of membrane
Molecular function
acetylgalactosaminyltransferase activity;UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity;N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity