B4GALT6
Basic information
Region (hg38): 18:31622246-31685836
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 B4GALT6 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 | 12 | 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 | 12 | 0 | 1 |
Variants in B4GALT6
This is a list of pathogenic ClinVar variants found in the B4GALT6 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 18-31625661-T-C | not specified | Uncertain significance (Nov 18, 2022) | ||
| 18-31626295-T-C | not specified | Uncertain significance (Jan 23, 2024) | ||
| 18-31626362-C-T | not specified | Uncertain significance (Dec 06, 2022) | ||
| 18-31638675-C-T | not specified | Uncertain significance (Jun 24, 2022) | ||
| 18-31638715-T-C | not specified | Uncertain significance (Feb 10, 2022) | ||
| 18-31645408-C-T | not specified | Uncertain significance (Dec 07, 2023) | ||
| 18-31645456-T-C | not specified | Uncertain significance (Oct 26, 2021) | ||
| 18-31666268-G-A | not specified | Uncertain significance (Jan 03, 2024) | ||
| 18-31684333-T-C | Benign (May 24, 2018) | |||
| 18-31684360-A-T | not specified | Uncertain significance (Sep 01, 2021) | ||
| 18-31684372-T-A | not specified | Uncertain significance (Oct 06, 2021) | ||
| 18-31684392-T-C | not specified | Uncertain significance (Jul 15, 2021) | ||
| 18-31684417-G-A | not specified | Uncertain significance (Aug 19, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| B4GALT6 | protein_coding | protein_coding | ENST00000306851 | 9 | 63590 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.908 | 0.0922 | 125735 | 0 | 10 | 125745 | 0.0000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.70 | 149 | 220 | 0.677 | 0.0000117 | 2530 |
| Missense in Polyphen | 37 | 73.576 | 0.50288 | 750 | ||
| Synonymous | 0.692 | 70 | 77.8 | 0.900 | 0.00000440 | 693 |
| Loss of Function | 3.63 | 3 | 20.9 | 0.144 | 0.00000113 | 248 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000123 | 0.000123 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000530 | 0.0000527 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000660 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Required for the biosynthesis of glycosphingolipids. {ECO:0000269|PubMed:1551920, ECO:0000269|PubMed:3099851}.;
- Pathway
- Sphingolipid metabolism - Homo sapiens (human);Sphingolipid Metabolism;Gaucher Disease;Globoid Cell Leukodystrophy;Metachromatic Leukodystrophy (MLD);Fabry disease;Krabbe disease;Sphingolipid Metabolism;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;Glycosphingolipid biosynthesis - globoseries;Metabolism;Glycosphingolipid metabolism;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;O-linked glycosylation of mucins;O-linked glycosylation
(Consensus)
Recessive Scores
- pRec
- 0.267
Intolerance Scores
- loftool
- 0.424
- rvis_EVS
- 0.19
- rvis_percentile_EVS
- 67.03
Haploinsufficiency Scores
- pHI
- 0.614
- hipred
- Y
- hipred_score
- 0.728
- ghis
- 0.472
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.865
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- B4galt6
- Phenotype
- normal phenotype; cellular phenotype;
Gene ontology
- Biological process
- lactosylceramide biosynthetic process;carbohydrate metabolic process;protein glycosylation;keratan sulfate biosynthetic process
- Cellular component
- Golgi membrane;integral component of membrane;Golgi cisterna membrane
- Molecular function
- beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity;galactosyltransferase activity;metal ion binding