B4GALNT1

beta-1,4-N-acetyl-galactosaminyltransferase 1, the group of Beta 4-glycosyltransferases

Basic information

Region (hg38): 12:57623409-57633239

Previous symbols: [ "GALGT", "SPG26" ]

Links

ENSG00000135454NCBI:2583OMIM:601873HGNC:4117Uniprot:Q00973AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • 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: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Spastic paraplegia 26, autosomal recessiveARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingNeurologic23746551

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the B4GALNT1 gene.

  • 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
3
clinvar
70
clinvar
5
clinvar
78
missense
3
clinvar
2
clinvar
123
clinvar
6
clinvar
3
clinvar
137
nonsense
6
clinvar
6
start loss
0
frameshift
7
clinvar
3
clinvar
10
inframe indel
3
clinvar
3
splice donor/acceptor (+/-2bp)
7
clinvar
7
splice region
6
9
1
16
non coding
1
clinvar
23
clinvar
20
clinvar
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)1686495
12-57624885-T-G Likely benign (Nov 01, 2022)2643143
12-57625419-C-T not specified Conflicting classifications of pathogenicity (Aug 01, 2024)1686497
12-57625736-C-T Likely benign (Aug 01, 2024)3341588
12-57626577-A-G Benign (Jun 26, 2018)1242221
12-57626742-C-T not specified • B4GALNT1-related disorder Benign (Nov 18, 2016)387791
12-57626748-T-G Inborn genetic diseases Uncertain significance (Aug 15, 2023)2592593
12-57626789-C-G Spastic paraplegia Likely benign (Aug 10, 2023)1953285
12-57626790-C-G Spastic paraplegia Conflicting classifications of pathogenicity (Apr 26, 2024)848217
12-57626799-G-A not specified • Spastic paraplegia Benign (Aug 01, 2024)235331
12-57626801-C-T Spastic paraplegia • Hereditary spastic paraplegia 26 • Inborn genetic diseases Uncertain significance (Nov 27, 2023)835530
12-57626805-T-C Spastic paraplegia Uncertain significance (Jun 13, 2022)2037088
12-57626813-G-A Spastic paraplegia Likely benign (Dec 22, 2023)2070214
12-57626813-G-C Spastic paraplegia Uncertain significance (Aug 05, 2022)2043253
12-57626832-C-T Spastic paraplegia Pathogenic (Feb 22, 2023)1074269
12-57626833-G-A Hereditary spastic paraplegia 26 Pathogenic (-)989144
12-57626837-C-T Spastic paraplegia Likely benign (Nov 07, 2023)2716703
12-57626843-G-A Spastic paraplegia Likely benign (Jun 19, 2022)699702
12-57626856-C-G Inborn genetic diseases Uncertain significance (Jul 13, 2021)2219604
12-57626858-G-A Spastic paraplegia Likely benign (May 20, 2022)2082932
12-57626868-G-C Spastic paraplegia Pathogenic (Sep 20, 2022)2110770
12-57626876-A-G Spastic paraplegia Likely benign (Nov 08, 2022)2043284
12-57626891-G-A Spastic paraplegia Likely benign (Apr 14, 2023)1954451
12-57626891-G-C Spastic paraplegia • B4GALNT1-related disorder Benign/Likely benign (Dec 18, 2023)383660
12-57626900-A-AT Spastic paraplegia Pathogenic (Feb 08, 2019)852385

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
B4GALNT1protein_codingprotein_codingENST00000341156 109946
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00003930.9911257270211257480.0000835
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.9242673130.8530.00001943350
Missense in Polyphen72109.760.655971069
Synonymous0.1541331350.9830.000008381173
Loss of Function2.311123.00.4790.00000113236

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003290.000236
Ashkenazi Jewish0.00009920.0000992
East Asian0.0001690.000163
Finnish0.000.00
European (Non-Finnish)0.00005280.0000527
Middle Eastern0.0001690.000163
South Asian0.0001340.000131
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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