B4GALNT1
Basic information
Region (hg38): 12:57623409-57633239
Previous symbols: [ "GALGT", "SPG26" ]
Links
Phenotypes
GenCC
Source:
- hereditary spastic paraplegia 26 (Moderate), mode of inheritance: AR
- hereditary spastic paraplegia 26 (Strong), mode of inheritance: AR
- hereditary spastic paraplegia 26 (Supportive), mode of inheritance: AR
- complex hereditary spastic paraplegia (Definitive), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Spastic paraplegia 26, autosomal recessive | 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 | Neurologic | 23746551 |
ClinVar
This is a list of variants' phenotypes submitted to
- Spastic paraplegia (10 variants)
- Hereditary spastic paraplegia 26 (5 variants)
- not provided (1 variants)
- Inborn genetic diseases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the B4GALNT1 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 | 70 | 78 | ||||
missense | 123 | 137 | ||||
nonsense | 6 | |||||
start loss | 0 | |||||
frameshift | 10 | |||||
inframe indel | 3 | |||||
splice donor/acceptor (+/-2bp) | 7 | |||||
splice region | 6 | 9 | 1 | 16 | ||
non coding | 23 | 20 | 44 | |||
Total | 16 | 12 | 130 | 99 | 28 |
Highest pathogenic variant AF is 0.00000659
Variants in B4GALNT1
This is a list of pathogenic ClinVar variants found in the B4GALNT1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
12-57624077-G-A | not specified | Conflicting classifications of pathogenicity (Nov 01, 2022) | ||
12-57624885-T-G | Likely benign (Nov 01, 2022) | |||
12-57625419-C-T | not specified | Conflicting classifications of pathogenicity (Aug 01, 2024) | ||
12-57625736-C-T | Likely benign (Aug 01, 2024) | |||
12-57626577-A-G | Benign (Jun 26, 2018) | |||
12-57626742-C-T | not specified • B4GALNT1-related disorder | Benign (Nov 18, 2016) | ||
12-57626748-T-G | Inborn genetic diseases | Uncertain significance (Aug 15, 2023) | ||
12-57626789-C-G | Spastic paraplegia | Likely benign (Aug 10, 2023) | ||
12-57626790-C-G | Spastic paraplegia | Conflicting classifications of pathogenicity (Apr 26, 2024) | ||
12-57626799-G-A | not specified • Spastic paraplegia | Benign (Aug 01, 2024) | ||
12-57626801-C-T | Spastic paraplegia • Hereditary spastic paraplegia 26 • Inborn genetic diseases | Uncertain significance (Nov 27, 2023) | ||
12-57626805-T-C | Spastic paraplegia | Uncertain significance (Jun 13, 2022) | ||
12-57626813-G-A | Spastic paraplegia | Likely benign (Dec 22, 2023) | ||
12-57626813-G-C | Spastic paraplegia | Uncertain significance (Aug 05, 2022) | ||
12-57626832-C-T | Spastic paraplegia | Pathogenic (Feb 22, 2023) | ||
12-57626833-G-A | Hereditary spastic paraplegia 26 | Pathogenic (-) | ||
12-57626837-C-T | Spastic paraplegia | Likely benign (Nov 07, 2023) | ||
12-57626843-G-A | Spastic paraplegia | Likely benign (Jun 19, 2022) | ||
12-57626856-C-G | Inborn genetic diseases | Uncertain significance (Jul 13, 2021) | ||
12-57626858-G-A | Spastic paraplegia | Likely benign (May 20, 2022) | ||
12-57626868-G-C | Spastic paraplegia | Pathogenic (Sep 20, 2022) | ||
12-57626876-A-G | Spastic paraplegia | Likely benign (Nov 08, 2022) | ||
12-57626891-G-A | Spastic paraplegia | Likely benign (Apr 14, 2023) | ||
12-57626891-G-C | Spastic paraplegia • B4GALNT1-related disorder | Benign/Likely benign (Dec 18, 2023) | ||
12-57626900-A-AT | Spastic paraplegia | Pathogenic (Feb 08, 2019) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
B4GALNT1 | protein_coding | protein_coding | ENST00000341156 | 10 | 9946 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0000393 | 0.991 | 125727 | 0 | 21 | 125748 | 0.0000835 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.924 | 267 | 313 | 0.853 | 0.0000194 | 3350 |
Missense in Polyphen | 72 | 109.76 | 0.65597 | 1069 | ||
Synonymous | 0.154 | 133 | 135 | 0.983 | 0.00000838 | 1173 |
Loss of Function | 2.31 | 11 | 23.0 | 0.479 | 0.00000113 | 236 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000329 | 0.000236 |
Ashkenazi Jewish | 0.0000992 | 0.0000992 |
East Asian | 0.000169 | 0.000163 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000528 | 0.0000527 |
Middle Eastern | 0.000169 | 0.000163 |
South Asian | 0.000134 | 0.000131 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in the biosynthesis of gangliosides GM2, GD2 and GA2. {ECO:0000269|PubMed:1601877}.;
- Disease
- DISEASE: Spastic paraplegia 26, autosomal recessive (SPG26) [MIM:609195]: A form of spastic paraplegia, a neurodegenerative disorder characterized by a slow, gradual, progressive weakness and spasticity of the lower limbs. Rate of progression and the severity of symptoms are quite variable. Initial symptoms may include difficulty with balance, weakness and stiffness in the legs, muscle spasms, and dragging the toes when walking. In some forms of the disorder, bladder symptoms (such as incontinence) may appear, or the weakness and stiffness may spread to other parts of the body. SPG26 is a complicated form characterized by onset in the first 2 decades of life of gait abnormalities due to lower limb spasticity and muscle weakness. Some patients have upper limb involvement. Additional features include intellectual disability, peripheral neuropathy, dysarthria, cerebellar signs, extrapyramidal signs, and cortical atrophy. The disorder is slowly progressive. {ECO:0000269|PubMed:23746551}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Glycosphingolipid biosynthesis - ganglio series - Homo sapiens (human);Ganglio Sphingolipid Metabolism;Metabolism of Spingolipids in ER and Golgi apparatus;Metabolism of lipids;Glycosphingolipid biosynthesis - ganglioseries;Metabolism;Glycosphingolipid metabolism;Sphingolipid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.247
Intolerance Scores
- loftool
- 0.489
- rvis_EVS
- 0.26
- rvis_percentile_EVS
- 70.52
Haploinsufficiency Scores
- pHI
- 0.122
- hipred
- Y
- hipred_score
- 0.711
- ghis
- 0.521
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.336
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- B4galnt1
- Phenotype
- hematopoietic system phenotype; reproductive 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); respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); renal/urinary system phenotype; immune system 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); endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- ganglioside biosynthetic process;carbohydrate metabolic process;glycosphingolipid metabolic process;spermatogenesis;lipid storage;lipid glycosylation
- Cellular component
- Golgi membrane;plasma membrane;membrane;integral component of Golgi membrane
- Molecular function
- (N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase activity