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
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
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 | |||||
| missense | 13 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 13 | 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 (May 20, 2024) | ||
| 11-134382740-G-T | not specified | Uncertain significance (Nov 21, 2022) | ||
| 11-134382841-G-C | not specified | Uncertain significance (Oct 22, 2021) | ||
| 11-134382939-G-C | not specified | Uncertain significance (Apr 29, 2024) | ||
| 11-134382947-G-A | Benign (Apr 17, 2018) | |||
| 11-134382982-C-T | not specified | Uncertain significance (Nov 22, 2023) | ||
| 11-134382992-C-G | not specified | Uncertain significance (Mar 15, 2024) | ||
| 11-134383693-T-G | not specified | Uncertain significance (Mar 16, 2022) | ||
| 11-134383797-C-A | not specified | Uncertain significance (Feb 28, 2024) | ||
| 11-134383834-C-A | not specified | Uncertain significance (Nov 24, 2024) | ||
| 11-134383907-G-C | not specified | Uncertain significance (May 23, 2023) | ||
| 11-134383924-C-T | not specified | Uncertain significance (Aug 01, 2024) | ||
| 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) | ||
| 11-134384144-G-C | not specified | Uncertain significance (Apr 08, 2024) | ||
| 11-134387563-G-A | not specified | Uncertain significance (Jul 09, 2021) | ||
| 11-134387620-C-T | not specified | Uncertain significance (Oct 04, 2024) |
GnomAD
Source:
| 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:
- 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