B3GALT2
Basic information
Region (hg38): 1:193178730-193186613
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (37 variants)
- not_provided (3 variants)
- Hyperparathyroidism_2_with_jaw_tumors (1 variants)
- Hyperparathyroidism_1 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the B3GALT2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003783.3. 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 | 3 | |||||
| missense | 38 | 39 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 38 | 4 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| B3GALT2 | protein_coding | protein_coding | ENST00000367434 | 1 | 7610 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.896 | 0.104 | 125724 | 0 | 6 | 125730 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.62 | 163 | 232 | 0.701 | 0.0000121 | 2787 |
| Missense in Polyphen | 37 | 79.159 | 0.46741 | 914 | ||
| Synonymous | -0.643 | 85 | 77.8 | 1.09 | 0.00000362 | 806 |
| Loss of Function | 3.26 | 2 | 16.1 | 0.124 | 0.00000100 | 179 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000615 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.000140 | 0.000139 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Beta-1,3-galactosyltransferase that transfers galactose from UDP-galactose to substrates with a terminal beta-N- acetylglucosamine (beta-GlcNAc) residue. Can also utilize substrates with a terminal galactose residue, albeit with lower efficiency. Involved in the biosynthesis of the carbohydrate moieties of glycolipids and glycoproteins. Inactive towards substrates with terminal alpha-N-acetylglucosamine (alpha-GlcNAc) or alpha-N-acetylgalactosamine (alpha-GalNAc) residues. {ECO:0000269|PubMed:9417100, ECO:0000269|PubMed:9582303}.;
- Pathway
- Glycosphingolipid biosynthesis - lacto and neolacto series - Homo sapiens (human)
(Consensus)
Recessive Scores
- pRec
- 0.117
Intolerance Scores
- loftool
- 0.257
- rvis_EVS
- -0.27
- rvis_percentile_EVS
- 34.32
Haploinsufficiency Scores
- pHI
- 0.288
- hipred
- Y
- hipred_score
- 0.654
- ghis
- 0.521
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.394
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- B3galt2
- Phenotype
- growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Gene ontology
- Biological process
- protein glycosylation;protein N-linked glycosylation;galactosylceramide biosynthetic process;oligosaccharide biosynthetic process
- Cellular component
- Golgi membrane;endoplasmic reticulum;Golgi apparatus;integral component of membrane
- Molecular function
- acetylgalactosaminyltransferase activity;UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity;glucosaminylgalactosylglucosylceramide beta-galactosyltransferase activity