B3GAT1

beta-1,3-glucuronyltransferase 1, the group of Beta-1,3-glucuronyltransferases|CD molecules

Basic information

Region (hg38): 11:134378503-134412242

Previous symbols: [ "CD57", "LEU7" ]

Links

ENSG00000109956 ∙ NCBI:27087 ∙ OMIM:151290 ∙ HGNC:921 ∙ Uniprot:Q9P2W7 ∙ 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 B3GAT1 gene.

• Inborn genetic diseases (10 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the B3GAT1 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					1	1
missense			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	1

Variants in B3GAT1

This is a list of pathogenic ClinVar variants found in the B3GAT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-134381958-C-T		not specified	Uncertain significance (Jan 27, 2022)
11-134382740-G-T		not specified	Uncertain significance (Nov 21, 2022)
11-134382841-G-C		not specified	Uncertain significance (Oct 22, 2021)
11-134382947-G-A			Benign (Apr 17, 2018)
11-134382982-C-T		not specified	Uncertain significance (Nov 22, 2023)
11-134383693-T-G		not specified	Uncertain significance (Mar 16, 2022)
11-134383797-C-A		not specified	Uncertain significance (Feb 28, 2024)
11-134383907-G-C		not specified	Uncertain significance (May 23, 2023)
11-134383993-G-A		not specified	Uncertain significance (May 27, 2022)
11-134384014-G-A		not specified	Uncertain significance (Nov 22, 2021)
11-134384087-C-T		not specified	Uncertain significance (Jan 19, 2024)
11-134384090-A-G		not specified	Uncertain significance (Oct 07, 2022)
11-134384111-C-G		not specified	Uncertain significance (Sep 27, 2021)
11-134387563-G-A		not specified	Uncertain significance (Jul 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
B3GAT1	protein_coding	protein_coding	ENST00000524765	4	33415

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.135	0.861	125719	0	10	125729	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.42	138	244	0.565	0.0000182	2087
Missense in Polyphen		33	90.189	0.3659		860
Synonymous	-0.411	121	115	1.05	0.00000922	734
Loss of Function	2.51	4	14.2	0.281	9.24e-7	124

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000589	0.0000589
Ashkenazi Jewish	0.00	0.00
East Asian	0.000169	0.000163
Finnish	0.0000637	0.0000462
European (Non-Finnish)	0.0000370	0.0000352
Middle Eastern	0.000169	0.000163
South Asian	0.00	0.00
Other	0.000185	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the biosynthesis of L2/HNK-1 carbohydrate epitope on glycoproteins. Can also play a role in glycosaminoglycan biosynthesis. Substrates include asialo- orosomucoid (ASOR), asialo-fetuin, and asialo-neural cell adhesion molecule. Requires sphingomyelin for activity: stearoyl- sphingomyelin was the most effective, followed by palmitoyl- sphingomyelin and lignoceroyl-sphingomyelin. Activity was demonstrated only for sphingomyelin with a saturated fatty acid and not for that with an unsaturated fatty acid, regardless of the length of the acyl group. {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: 0.448

Intolerance Scores

• loftool: 0.375
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.58

Haploinsufficiency Scores

• pHI: 0.727
• hipred: Y
• hipred_score: 0.755
• ghis: 0.592

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.383

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: B3gat1
• 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: carbohydrate metabolic process;protein glycosylation;glycosaminoglycan metabolic process;chondroitin sulfate proteoglycan biosynthetic process
• Cellular component: Golgi membrane;extracellular region;endoplasmic reticulum membrane;integral component of membrane;intracellular membrane-bounded organelle
• Molecular function: UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity;galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity;metal ion binding