B4GAT1

beta-1,4-glucuronyltransferase 1

Basic information

Region (hg38): 11:66345374-66347629

Previous symbols: [ "B3GNT6", "B3GNT1" ]

Links

ENSG00000174684NCBI:11041OMIM:605517HGNC:15685Uniprot:O43505AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

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

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 13ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingMusculoskeletal; Neurologic; Ophthalmologic23359570

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the B4GAT1 gene.

  • Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the B4GAT1 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
3
clinvar
76
clinvar
1
clinvar
80
missense
2
clinvar
85
clinvar
4
clinvar
91
nonsense
1
clinvar
1
clinvar
2
start loss
1
clinvar
1
frameshift
3
clinvar
3
inframe indel
1
clinvar
1
clinvar
2
splice donor/acceptor (+/-2bp)
0
splice region
2
2
non coding
8
clinvar
8
Total 1 3 94 88 1

Variants in B4GAT1

This is a list of pathogenic ClinVar variants found in the B4GAT1 region.

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

Position Type Phenotype Significance ClinVar
11-66345856-G-A Likely benign (Sep 22, 2018)1186329
11-66346055-G-A Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 Likely benign (Sep 14, 2023)1100478
11-66346057-G-A Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 Uncertain significance (Oct 13, 2023)1396950
11-66346062-GGA-G Uncertain significance (Apr 26, 2018)524131
11-66346080-G-A Likely pathogenic (Sep 21, 2021)242670
11-66346088-C-T Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 Likely benign (Jun 30, 2023)1640300
11-66346090-C-A Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 Pathogenic (Apr 29, 2021)1252009
11-66346091-C-T not specified • Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 Likely benign (Dec 01, 2023)420656
11-66346097-G-C Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 Uncertain significance (May 07, 2022)1972892
11-66346115-CTTA-C Likely pathogenic (Jul 25, 2017)503771
11-66346121-G-A Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 Likely benign (Dec 08, 2021)779773
11-66346129-T-C Likely pathogenic (Sep 21, 2021)242669
11-66346136-C-T Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 • B4GAT1-related disorder Benign/Likely benign (Jan 11, 2024)474248
11-66346144-G-T Inborn genetic diseases Uncertain significance (Jun 19, 2024)3259557
11-66346145-G-A Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 Likely benign (Sep 14, 2018)752667
11-66346145-G-C Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 Likely benign (Sep 12, 2023)2570802
11-66346146-G-C Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 Uncertain significance (Feb 24, 2021)1438892
11-66346151-G-C Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 Benign/Likely benign (Jan 18, 2024)541281
11-66346160-C-T Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 Likely benign (Aug 09, 2022)1939915
11-66346161-G-C Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 Uncertain significance (Aug 31, 2021)423075
11-66346175-C-T Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 Uncertain significance (Sep 05, 2021)1371352
11-66346179-T-A Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 Uncertain significance (Jul 19, 2022)2420919
11-66346181-A-C Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 Likely benign (Apr 28, 2021)1532187
11-66346187-G-T Uncertain significance (Apr 01, 2023)2641988
11-66346197-T-C Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 Uncertain significance (Sep 17, 2021)1413052

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
B4GAT1protein_codingprotein_codingENST00000311181 22321
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.006940.9771257170131257300.0000517
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.901612450.6580.00001422633
Missense in Polyphen4983.1270.58946855
Synonymous2.22841140.7360.00000668877
Loss of Function2.12614.80.4068.06e-7142

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002900.0000290
Ashkenazi Jewish0.00009950.0000993
East Asian0.000.00
Finnish0.00005710.0000462
European (Non-Finnish)0.00007940.0000703
Middle Eastern0.000.00
South Asian0.00003920.0000327
Other0.0001630.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Beta-1,4-glucuronyltransferase involved in O- mannosylation of alpha-dystroglycan (DAG1). Transfers a glucuronic acid (GlcA) residue onto a xylose (Xyl) acceptor to produce the glucuronyl-beta-1,4-xylose-beta disaccharide primer, which is further elongated by LARGE1, during synthesis of phosphorylated O- mannosyl glycan (PubMed:25279699, PubMed:25279697). Phosphorylated O-mannosyl glycan is a carbohydrate is a carbohydrate structure present in alpha-dystroglycan (DAG1), which is required for binding laminin G-like domain-containing extracellular proteins with high affinity (PubMed:25279699, PubMed:25279697). Required for axon guidance; via its function in O-mannosylation of alpha- dystroglycan (DAG1) (By similarity). {ECO:0000250|UniProtKB:Q8BWP8, ECO:0000269|PubMed:19587235, ECO:0000269|PubMed:23359570, ECO:0000269|PubMed:25279697, ECO:0000269|PubMed:25279699}.;
Pathway
Mannose type O-glycan biosynthesis - 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;terminal <i>O</i>-glycans residues modification;O-linked glycosylation (Consensus)

Recessive Scores

pRec
0.123

Haploinsufficiency Scores

pHI
hipred
N
hipred_score
0.285
ghis
0.713

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap
N
gene_indispensability_pred
gene_indispensability_score

Mouse Genome Informatics

Gene name
B4gat1
Phenotype
muscle phenotype; homeostasis/metabolism phenotype; immune system phenotype; cellular phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); 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);

Zebrafish Information Network

Gene name
b4gat1
Affected structure
muscle
Phenotype tag
abnormal
Phenotype quality
disorganized

Gene ontology

Biological process
protein O-linked glycosylation;axon guidance;keratan sulfate biosynthetic process;poly-N-acetyllactosamine biosynthetic process;protein O-linked mannosylation
Cellular component
Golgi membrane;Golgi apparatus;integral component of Golgi membrane;extracellular exosome
Molecular function
protein binding;N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity;glucuronosyltransferase activity;metal ion binding