B4GAT1

beta-1,4-glucuronyltransferase 1

Basic information

Region (hg38): 11:66345373-66347629

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

Links

ENSG00000174684 ∙ NCBI:11041 ∙ OMIM:605517 ∙ HGNC:15685 ∙ Uniprot:O43505 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 13	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Musculoskeletal; Neurologic; Ophthalmologic	23359570

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 (161 variants)
• not provided (35 variants)
• not specified (16 variants)
• Inborn genetic diseases (7 variants)
• B4GAT1-related condition (2 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	69	1	73
missense		2	85	4		91
nonsense	1		1			2
start loss			1			1
frameshift			3			3
inframe indel		1	1			2
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding				7		7
Total	1	3	94	80	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)
11-66346055-G-A		Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13	Likely benign (Sep 14, 2023)
11-66346057-G-A		Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13	Uncertain significance (Oct 13, 2023)
11-66346062-GGA-G			Uncertain significance (Apr 26, 2018)
11-66346080-G-A			Likely pathogenic (Sep 21, 2021)
11-66346088-C-T		Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13	Likely benign (Jun 30, 2023)
11-66346090-C-A		Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13	Pathogenic (Apr 29, 2021)
11-66346091-C-T		not specified • Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13	Likely benign (Dec 01, 2023)
11-66346097-G-C		Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13	Uncertain significance (May 07, 2022)
11-66346115-CTTA-C			Likely pathogenic (Jul 25, 2017)
11-66346121-G-A		Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13	Likely benign (Dec 08, 2021)
11-66346129-T-C			Likely pathogenic (Sep 21, 2021)
11-66346136-C-T		Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 • B4GAT1-related disorder	Benign/Likely benign (Jan 11, 2024)
11-66346145-G-A		Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13	Likely benign (Sep 14, 2018)
11-66346145-G-C		Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13	Likely benign (Sep 12, 2023)
11-66346146-G-C		Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13	Uncertain significance (Feb 24, 2021)
11-66346151-G-C		Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13	Benign/Likely benign (Jan 18, 2024)
11-66346160-C-T		Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13	Likely benign (Aug 09, 2022)
11-66346161-G-C		Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13	Uncertain significance (Aug 31, 2021)
11-66346175-C-T		Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13	Uncertain significance (Sep 05, 2021)
11-66346179-T-A		Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13	Uncertain significance (Jul 19, 2022)
11-66346181-A-C		Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13	Likely benign (Apr 28, 2021)
11-66346187-G-T			Uncertain significance (Apr 01, 2023)
11-66346197-T-C		Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13	Uncertain significance (Sep 17, 2021)
11-66346201-G-T		Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13	Uncertain significance (Dec 28, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
B4GAT1	protein_coding	protein_coding	ENST00000311181	2	2321

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00694	0.977	125717	0	13	125730	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.90	161	245	0.658	0.0000142	2633
Missense in Polyphen		49	83.127	0.58946		855
Synonymous	2.22	84	114	0.736	0.00000668	877
Loss of Function	2.12	6	14.8	0.406	8.06e-7	142

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.0000995	0.0000993
East Asian	0.00	0.00
Finnish	0.0000571	0.0000462
European (Non-Finnish)	0.0000794	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.0000392	0.0000327
Other	0.000163	0.000163

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

• hipred: N
• hipred_score: 0.285
• ghis: 0.713

Essentials

• essential_gene_gene_trap: N

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