B3GALT1

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

Basic information

Region (hg38): 2:167293001-167874045

Links

ENSG00000172318 ∙ NCBI:8708 ∙ OMIM:603093 ∙ HGNC:916 ∙ Uniprot:Q9Y5Z6 ∙ 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 B3GALT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the B3GALT1 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			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	0

Variants in B3GALT1

This is a list of pathogenic ClinVar variants found in the B3GALT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-167869112-A-G		not specified	Likely benign (Feb 02, 2022)
2-167869124-A-C		not specified	Uncertain significance (May 24, 2024)
2-167869130-T-C		not specified	Uncertain significance (Feb 27, 2023)
2-167869160-C-A		not specified	Uncertain significance (Jan 05, 2022)
2-167869160-C-G		not specified	Uncertain significance (Jan 31, 2022)
2-167869203-C-G		not specified	Uncertain significance (Sep 01, 2021)
2-167869214-A-T		not specified	Uncertain significance (Oct 02, 2023)
2-167869337-A-T		not specified	Uncertain significance (Oct 03, 2023)
2-167869388-C-T		not specified	Uncertain significance (Aug 16, 2021)
2-167869409-C-T		not specified	Uncertain significance (Jan 26, 2023)
2-167869427-G-T		not specified	Uncertain significance (Jun 16, 2023)
2-167869577-AT-A		Malignant tumor of prostate	Uncertain significance (-)
2-167869592-G-A		not specified	Uncertain significance (Sep 17, 2021)
2-167869626-C-T		not specified	Uncertain significance (Nov 03, 2023)
2-167869658-G-A		not specified	Uncertain significance (Jan 19, 2024)
2-167869896-A-G			Uncertain significance (Jun 02, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
B3GALT1	protein_coding	protein_coding	ENST00000392690	1	55370

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0102	0.949	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.58	125	186	0.673	0.00000966	2173
Missense in Polyphen		19	60.719	0.31292		722
Synonymous	-0.814	76	67.5	1.13	0.00000368	617
Loss of Function	1.77	5	11.5	0.436	8.00e-7	121

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Beta-1,3-galactosyltransferase that transfers galactose from UDP-alpha-D-galactose to substrates with a terminal beta-N- acetylglucosamine (beta-GlcNAc) residue. Involved in the biosynthesis of the carbohydrate moieties of glycolipids and glycoproteins. Inactive towards substrates with terminal alpha-N- acetylglucosamine (alpha-GlcNAc) or alpha-N-acetylgalactosamine (alpha-GalNAc) residues. {ECO:0000269|PubMed:9582303}.
• Pathway: Glycosphingolipid biosynthesis - lacto and neolacto series - Homo sapiens (human);Ganglio Sphingolipid Metabolism;Metabolism of Spingolipids in ER and Golgi apparatus (Consensus)

Recessive Scores

• pRec: 0.149

Intolerance Scores

• loftool: 0.290
• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.11

Haploinsufficiency Scores

• pHI: 0.211
• hipred: Y
• hipred_score: 0.605
• ghis: 0.536

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.926

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: B3galt1

Gene ontology

• Biological process: protein glycosylation;protein N-linked glycosylation;galactosylceramide biosynthetic process;oligosaccharide biosynthetic process;lipid glycosylation
• 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;glucosaminylgalactosylglucosylceramide beta-galactosyltransferase activity