B3GAT2

beta-1,3-glucuronyltransferase 2, the group of Beta-1,3-glucuronyltransferases

Basic information

Region (hg38): 6:70856679-70957060

Links

ENSG00000112309 ∙ NCBI:135152 ∙ OMIM:607497 ∙ HGNC:922 ∙ Uniprot:Q9NPZ5 ∙ 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 B3GAT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the B3GAT2 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			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			12	1		13
Total	0	0	34	1	0

Variants in B3GAT2

This is a list of pathogenic ClinVar variants found in the B3GAT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-70856916-G-T		not specified	Uncertain significance (Jan 23, 2023)
6-70857922-G-A		not specified	Uncertain significance (Jun 04, 2024)
6-70857940-C-G		not specified	Uncertain significance (Jan 25, 2024)
6-70857946-T-C		not specified	Uncertain significance (Dec 27, 2022)
6-70857990-T-C		not specified	Uncertain significance (Jun 01, 2023)
6-70858024-T-C		not specified	Uncertain significance (Dec 15, 2022)
6-70858047-A-G		not specified	Uncertain significance (Aug 12, 2021)
6-70858131-G-A		not specified	Uncertain significance (Mar 06, 2023)
6-70858131-G-C		not specified	Uncertain significance (Apr 11, 2023)
6-70858135-T-C		not specified	Uncertain significance (Aug 12, 2022)
6-70858186-T-C		not specified	Uncertain significance (May 16, 2022)
6-70860200-A-G		not specified	Likely benign (May 01, 2022)
6-70860242-C-A		not specified	Uncertain significance (Aug 10, 2021)
6-70860246-C-T		not specified	Uncertain significance (Apr 05, 2023)
6-70861692-G-A		not specified	Uncertain significance (Dec 03, 2021)
6-70861696-C-G		not specified	Uncertain significance (Jul 05, 2022)
6-70861698-T-G		not specified	Uncertain significance (Dec 14, 2021)
6-70861961-G-C		not specified	Uncertain significance (Mar 18, 2024)
6-70894226-C-A		not specified	Uncertain significance (Feb 06, 2023)
6-70894265-G-A		not specified	Uncertain significance (Feb 16, 2023)
6-70894272-T-A		not specified	Uncertain significance (Aug 04, 2023)
6-70955898-G-T		not specified	Uncertain significance (Apr 09, 2022)
6-70955927-C-T		not specified	Uncertain significance (Apr 20, 2023)
6-70955975-C-T		not specified	Uncertain significance (Nov 17, 2022)
6-70955979-G-C		not specified	Uncertain significance (Oct 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
B3GAT2	protein_coding	protein_coding	ENST00000230053	4	100360

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000333	0.594	125696	0	52	125748	0.000207

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.379	174	189	0.922	0.0000103	2026
Missense in Polyphen		52	80.083	0.64932		823
Synonymous	-0.451	88	82.8	1.06	0.00000460	703
Loss of Function	0.752	8	10.6	0.751	5.30e-7	109

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000541	0.000540
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.0000950	0.0000924
European (Non-Finnish)	0.000244	0.000237
Middle Eastern	0.0000545	0.0000544
South Asian	0.000238	0.000229
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the biosynthesis of L2/HNK-1 carbohydrate epitope on both glycolipids and glycoproteins. {ECO:0000250|UniProtKB:O35789}.
• Pathway: Mannose type O-glycan biosynthesis - Homo sapiens (human);Metabolism of carbohydrates;A tetrasaccharide linker sequence is required for GAG synthesis;Heparan sulfate/heparin (HS-GAG) metabolism;Chondroitin sulfate/dermatan sulfate metabolism;Glycosaminoglycan metabolism;Proteoglycan biosynthesis;glycoaminoglycan-protein linkage region biosynthesis;chondroitin sulfate biosynthesis;heparan sulfate biosynthesis;dermatan sulfate biosynthesis;Metabolism (Consensus)

Recessive Scores

• pRec: 0.162

Intolerance Scores

• loftool: 0.773
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.4

Haploinsufficiency Scores

• pHI: 0.254
• hipred: Y
• hipred_score: 0.643
• ghis: 0.484

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.181

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: B3gat2

Gene ontology

• Biological process: protein glycosylation;glycosaminoglycan metabolic process;chondroitin sulfate proteoglycan biosynthetic process
• Cellular component: Golgi membrane;integral component of membrane
• Molecular function: galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity;metal ion binding