B4GALT4
Basic information
Region (hg38): 3:119211732-119240946
Links
Phenotypes
GenCC
Source:
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 B4GALT4 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 | 0 | |||||
| missense | 10 | 11 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 1 | 0 |
Variants in B4GALT4
This is a list of pathogenic ClinVar variants found in the B4GALT4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-119212631-C-T | not specified | Uncertain significance (May 23, 2023) | ||
| 3-119216289-T-C | not specified | Uncertain significance (Feb 05, 2024) | ||
| 3-119218738-C-A | not specified | Uncertain significance (Dec 20, 2023) | ||
| 3-119218760-A-C | not specified | Uncertain significance (Feb 28, 2024) | ||
| 3-119224094-T-C | not specified | Uncertain significance (Aug 02, 2021) | ||
| 3-119224130-T-C | not specified | Uncertain significance (May 17, 2023) | ||
| 3-119224136-G-A | not specified | Uncertain significance (Mar 24, 2023) | ||
| 3-119224170-C-T | not specified | Uncertain significance (Oct 02, 2023) | ||
| 3-119226910-G-T | not specified | Uncertain significance (Dec 19, 2023) | ||
| 3-119229900-G-A | not specified | Uncertain significance (Aug 21, 2023) | ||
| 3-119229959-G-T | not specified | Likely benign (Jan 17, 2024) | ||
| 3-119229975-G-C | not specified | Uncertain significance (Mar 30, 2024) | ||
| 3-119230002-T-G | not specified | Uncertain significance (May 12, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| B4GALT4 | protein_coding | protein_coding | ENST00000483209 | 6 | 29372 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 5.83e-7 | 0.683 | 125723 | 0 | 25 | 125748 | 0.0000994 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.19 | 143 | 189 | 0.757 | 0.00000995 | 2258 |
| Missense in Polyphen | 56 | 80.052 | 0.69955 | 944 | ||
| Synonymous | 0.334 | 69 | 72.6 | 0.950 | 0.00000390 | 643 |
| Loss of Function | 1.14 | 12 | 17.1 | 0.702 | 9.60e-7 | 201 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000908 | 0.0000905 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000219 | 0.000217 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000134 | 0.000132 |
| Middle Eastern | 0.000219 | 0.000217 |
| South Asian | 0.0000987 | 0.0000980 |
| Other | 0.000167 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Responsible for the synthesis of complex-type N-linked oligosaccharides in many glycoproteins as well as the carbohydrate moieties of glycolipids. {ECO:0000269|PubMed:9792633}.;
- Pathway
- Glycosphingolipid biosynthesis - lacto and neolacto series - Homo sapiens (human);Glycosaminoglycan biosynthesis - keratan sulfate - Homo sapiens (human);Metabolism of carbohydrates;Keratan sulfate biosynthesis;Keratan sulfate/keratin metabolism;Glycosaminoglycan metabolism;Post-translational protein modification;N-Glycan antennae elongation;N-glycan antennae elongation in the medial/trans-Golgi;Metabolism of proteins;Metabolism;Galactose metabolism;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation
(Consensus)
Recessive Scores
- pRec
- 0.125
Intolerance Scores
- loftool
- 0.659
- rvis_EVS
- 0.26
- rvis_percentile_EVS
- 70.26
Haploinsufficiency Scores
- pHI
- 0.500
- hipred
- N
- hipred_score
- 0.379
- ghis
- 0.408
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.118
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- B4galt4
- Phenotype
Gene ontology
- Biological process
- carbohydrate metabolic process;protein glycosylation;membrane lipid metabolic process;keratan sulfate biosynthetic process
- Cellular component
- Golgi membrane;Golgi apparatus;integral component of membrane;Golgi cisterna membrane
- Molecular function
- beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity;N-acetyllactosamine synthase activity;galactosyltransferase activity;metal ion binding