B3GALT2

beta-1,3-galactosyltransferase 2, the group of Beta 3-glycosyltransferases

Basic information

Region (hg38): 1:193178729-193186613

Links

ENSG00000162630 ∙ NCBI:8707 ∙ OMIM:603018 ∙ HGNC:917 ∙ Uniprot:O43825 ∙ 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 B3GALT2 gene.

• Inborn genetic diseases (14 variants)
• Hyperparathyroidism 2 with jaw tumors (1 variants)
• Hyperparathyroidism 1 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the B3GALT2 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			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	0

Variants in B3GALT2

This is a list of pathogenic ClinVar variants found in the B3GALT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-193180308-G-A		Hyperparathyroidism 1	Uncertain significance (Apr 17, 2018)
1-193180313-C-G		not specified	Uncertain significance (May 11, 2022)
1-193180378-G-C		not specified	Uncertain significance (Apr 19, 2023)
1-193180556-C-T		not specified	Uncertain significance (Jul 12, 2022)
1-193180653-G-A		not specified	Uncertain significance (Apr 20, 2023)
1-193180684-A-T		not specified	Uncertain significance (Aug 22, 2023)
1-193180784-T-A		not specified	Uncertain significance (Jan 08, 2024)
1-193180956-G-A		not specified	Uncertain significance (Nov 08, 2022)
1-193180965-A-G		not specified	Uncertain significance (Mar 28, 2023)
1-193181011-T-G		not specified	Uncertain significance (Jan 23, 2024)
1-193181015-A-G		not specified	Uncertain significance (Jan 07, 2022)
1-193181160-G-A		not specified	Uncertain significance (Apr 04, 2023)
1-193181196-A-C		Hyperparathyroidism 2 with jaw tumors	Likely benign (Mar 11, 2015)
1-193181214-T-G		not specified	Uncertain significance (Sep 14, 2022)
1-193181224-C-A		not specified	Uncertain significance (Nov 18, 2022)
1-193181324-C-T		not specified	Uncertain significance (Sep 06, 2022)
1-193181369-C-T		not specified	Uncertain significance (Dec 07, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
B3GALT2	protein_coding	protein_coding	ENST00000367434	1	7610

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.896	0.104	125724	0	6	125730	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.62	163	232	0.701	0.0000121	2787
Missense in Polyphen		37	79.159	0.46741		914
Synonymous	-0.643	85	77.8	1.09	0.00000362	806
Loss of Function	3.26	2	16.1	0.124	0.00000100	179

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000140	0.000139
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Beta-1,3-galactosyltransferase that transfers galactose from UDP-galactose to substrates with a terminal beta-N- acetylglucosamine (beta-GlcNAc) residue. Can also utilize substrates with a terminal galactose residue, albeit with lower efficiency. 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:9417100, ECO:0000269|PubMed:9582303}.
• Pathway: Glycosphingolipid biosynthesis - lacto and neolacto series - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.257
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.32

Haploinsufficiency Scores

• pHI: 0.288
• hipred: Y
• hipred_score: 0.654
• ghis: 0.521

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.394

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: B3galt2
• Phenotype: growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

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