B4GAT1
Basic information
Region (hg38): 11:66345374-66347629
Previous symbols: [ "B3GNT6", "B3GNT1" ]
Links
Phenotypes
GenCC
Source:
- 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:
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
- 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 | 76 | 80 | ||||
missense | 85 | 91 | ||||
nonsense | 2 | |||||
start loss | 1 | |||||
frameshift | 3 | |||||
inframe indel | 2 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 2 | 2 | ||||
non coding | 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) | |||
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) | ||
11-66346144-G-T | Inborn genetic diseases | Uncertain significance (Jun 19, 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) |
GnomAD
Source:
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:
- 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