B3GNT2

UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2, the group of Beta 3-glycosyltransferases|MicroRNA protein coding host genes

Basic information

Region (hg38): 2:62196115-62224731

Previous symbols: [ "B3GNT1" ]

Links

ENSG00000170340 ∙ NCBI:10678 ∙ OMIM:605581 ∙ HGNC:15629 ∙ Uniprot:Q9NY97 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 (Moderate), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the B3GNT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the B3GNT2 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					2	2
missense			17		2	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	4

Variants in B3GNT2

This is a list of pathogenic ClinVar variants found in the B3GNT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-62222293-A-G		B3GNT2-related disorder	Likely benign (Jul 22, 2021)
2-62222341-G-A		not specified	Uncertain significance (Jun 30, 2024)
2-62222346-A-G		not specified	Uncertain significance (Jan 05, 2022)
2-62222374-T-C		not specified	Uncertain significance (Feb 07, 2025)
2-62222381-C-G		not specified	Uncertain significance (Jul 06, 2021)
2-62222421-C-G		not specified	Uncertain significance (Feb 22, 2025)
2-62222422-C-T		not specified	Uncertain significance (Jan 22, 2025)
2-62222462-C-A		not specified	Uncertain significance (Mar 15, 2024)
2-62222463-G-C		B3GNT2-related disorder	Likely benign (Sep 04, 2019)
2-62222467-G-A		not specified	Uncertain significance (Oct 05, 2023)
2-62222486-A-G		not specified	Uncertain significance (Dec 14, 2021)
2-62222509-G-A		not specified	Uncertain significance (Nov 24, 2024)
2-62222529-G-A		B3GNT2-related disorder	Benign (Dec 31, 2019)
2-62222531-C-T		not specified	Uncertain significance (May 18, 2023)
2-62222614-A-G		not specified	Uncertain significance (Oct 25, 2023)
2-62222624-C-T		not specified	Uncertain significance (Aug 12, 2021)
2-62222628-T-A			Benign (Dec 03, 2018)
2-62222628-T-G			Benign (Dec 31, 2019)
2-62222638-A-G		not specified	Uncertain significance (Mar 11, 2022)
2-62222705-G-A		not specified	Uncertain significance (Aug 06, 2024)
2-62222716-G-A		not specified	Uncertain significance (Jan 24, 2025)
2-62222777-C-A		not specified	Uncertain significance (Jan 23, 2024)
2-62222781-A-G			Benign (Jun 26, 2018)
2-62223166-G-A		not specified	Uncertain significance (Jul 27, 2022)
2-62223172-A-G		not specified	Uncertain significance (Dec 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
B3GNT2	protein_coding	protein_coding	ENST00000301998	1	28619

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.887	0.113	125687	0	2	125689	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.28	168	221	0.759	0.0000121	2644
Missense in Polyphen		37	88.579	0.41771		1057
Synonymous	0.154	89	90.9	0.979	0.00000553	753
Loss of Function	2.87	1	11.5	0.0871	6.38e-7	145

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000621	0.0000617
Ashkenazi Jewish	0.0000992	0.0000992
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-N-acetylglucosaminyltransferase involved in the synthesis of poly-N-acetyllactosamine. Catalyzes the initiation and elongation of poly-N-acetyllactosamine chains. Shows a marked preference for Gal(beta1-4)Glc(NAc)-based acceptors (PubMed:9892646). Probably constitutes the main polylactosamine synthase. {ECO:0000269|PubMed:11042166, ECO:0000269|PubMed:25279697, ECO:0000269|PubMed:9892646}.
• Pathway: 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;Glycosphingolipid biosynthesis - neolactoseries;Glycosaminoglycan metabolism;Post-translational protein modification;Metabolism of proteins;Metabolism;O-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.123

Intolerance Scores

• loftool: 0.207
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.35

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.654
• ghis: 0.601

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: K
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: B3gnt2
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; growth/size/body region phenotype; craniofacial phenotype; cellular phenotype; taste/olfaction phenotype

Gene ontology

• Biological process: protein glycosylation;axon guidance;sensory perception of smell;O-glycan processing;keratan sulfate biosynthetic process;poly-N-acetyllactosamine biosynthetic process;cellular response to leukemia inhibitory factor
• Cellular component: Golgi membrane;endoplasmic reticulum;Golgi apparatus;integral component of membrane
• Molecular function: protein binding;acetylgalactosaminyltransferase activity;UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity;N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity