B4GALT3

beta-1,4-galactosyltransferase 3, the group of Beta 4-glycosyltransferases

Basic information

Region (hg38): 1:161171310-161177968

Links

ENSG00000158850 ∙ NCBI:8703 ∙ OMIM:604014 ∙ HGNC:926 ∙ Uniprot:O60512 ∙ 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 B4GALT3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the B4GALT3 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	0

Variants in B4GALT3

This is a list of pathogenic ClinVar variants found in the B4GALT3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-161171836-C-A		not specified	Uncertain significance (Aug 16, 2021)
1-161171881-G-A		not specified	Uncertain significance (Feb 06, 2024)
1-161171902-G-A		not specified	Uncertain significance (Sep 01, 2024)
1-161171907-G-A		not specified	Uncertain significance (May 08, 2023)
1-161171922-G-C		not specified	Uncertain significance (Feb 15, 2023)
1-161171979-G-A		not specified	Uncertain significance (Sep 13, 2023)
1-161172025-G-C		not specified	Uncertain significance (Jul 10, 2024)
1-161172040-T-G		not specified	Uncertain significance (Sep 10, 2024)
1-161172265-C-A		not specified	Uncertain significance (Nov 09, 2024)
1-161172294-T-C		not specified	Uncertain significance (Jun 27, 2023)
1-161173650-T-C		not specified	Uncertain significance (May 23, 2023)
1-161173681-C-T		not specified	Uncertain significance (May 11, 2022)
1-161173895-C-T		not specified	Uncertain significance (Apr 07, 2023)
1-161173905-G-A		not specified	Uncertain significance (Sep 09, 2024)
1-161174036-G-A		not specified	Uncertain significance (May 01, 2024)
1-161175066-C-T		not specified	Uncertain significance (Jul 17, 2023)
1-161175082-G-A		not specified	Uncertain significance (Jul 05, 2023)
1-161175172-G-A		not specified	Uncertain significance (Mar 31, 2024)
1-161175220-C-A		not specified	Uncertain significance (Jul 16, 2024)
1-161175859-G-A		not specified	Uncertain significance (Dec 01, 2022)
1-161175938-A-T		not specified	Likely benign (Jun 05, 2024)
1-161175942-C-T		not specified	Uncertain significance (Nov 10, 2022)
1-161176044-A-G		not specified	Uncertain significance (Jun 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
B4GALT3	protein_coding	protein_coding	ENST00000319769	6	6188

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0114	0.987	125728	0	19	125747	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.46	188	253	0.742	0.0000165	2494
Missense in Polyphen		48	88.254	0.54389		949
Synonymous	0.486	88	94.0	0.936	0.00000480	883
Loss of Function	2.76	7	20.5	0.342	0.00000148	182

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000323	0.000323
European (Non-Finnish)	0.0000528	0.0000527
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Responsible for the synthesis of complex-type N-linked oligosaccharides in many glycoproteins as well as the carbohydrate moieties of glycolipids.
• Pathway: N-Glycan biosynthesis - Homo sapiens (human);Other types of O-glycan biosynthesis - Homo sapiens (human);Mannose type O-glycan biosynthesis - Homo sapiens (human);Glycosphingolipid biosynthesis - lacto and neolacto series - Homo sapiens (human);Glycosaminoglycan biosynthesis - keratan sulfate - Homo sapiens (human);Metabolism of carbohydrates;Keratan sulfate biosynthesis;Keratan sulfate/keratin metabolism;Glycosaminoglycan metabolism;Post-translational protein modification;N-Glycan antennae elongation;N-glycan antennae elongation in the medial/trans-Golgi;Metabolism of proteins;Metabolism;terminal <i>O</i>-glycans residues modification;Galactose metabolism;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;N-Glycan biosynthesis (Consensus)

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.626
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.91

Haploinsufficiency Scores

• pHI: 0.306
• hipred: N
• hipred_score: 0.476
• ghis: 0.569

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.895

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: B4galt3

Gene ontology

• Biological process: carbohydrate metabolic process;protein glycosylation;galactosylceramide biosynthetic process;keratan sulfate biosynthetic process
• Cellular component: Golgi membrane;Golgi apparatus;cytosol;integral component of membrane;Golgi cisterna membrane;extracellular exosome
• Molecular function: beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity;N-acetyllactosamine synthase activity;galactosyltransferase activity;metal ion binding