B3GAT1

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

Basic information

Region (hg38): 11:134378504-134412242

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.

not_specified (30 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. These statistics are base on transcript: NM_000054025.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			31 clinvar			31
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	31	0	1

Loading clinvar variants...

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