GeneBe

B4GALNT2

protein-coding

beta-1,4-N-acetyl-galactosaminyltransferase 2, the group of Beta 4-glycosyltransferases

Gene summary

B4GALNT2 catalyzes the last step in the biosynthesis of the human Sd(a) antigen through the addition of an N-acetylgalactosamine residue via a beta-1,4 linkage to a subterminal galactose residue substituted with an alpha-2,3-linked sialic acid. B4GALNT2 also catalyzes the last step in the biosynthesis of the Cad antigen (Montiel et al., 2003 [PubMed 12678917]).[supplied by OMIM, Mar 2008]

Previous symbols:
  • GALGT2

MANE transcript

NM_001159387.2

Inheritance

BG

ClinVar variants

U:77B:9

Top phenotype

Sid blood group antigen

gnomAD constraint

pLI —, LoF o/e 1.05

Max pathogenic AF

—

Genomic locus

chr17:49,132,460-49,176,840

External References & Databases

Ensembl (ENSG00000167080)NCBI Gene (124872)OMIM (111730)HGNC:24136GenCCUniProt (Q8NHY0)AlphaFoldClinVar (B4GALNT2)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~44.4 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

Clinical Genomic Database (CGD)

Sid blood group antigenBG

Manifestation: Hematologic

Intervention: Hematologic

Rationale: Variants associated with a blood group may be important in specific situations (eg, related to transfusion)

Refs: N/ASource: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to B4GALNT2 variants in ClinVar

3 Conditions Cataloged
not specifiedTotal: 95
not providedTotal: 3
BLOOD GROUP, SID SYSTEMTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001159387.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
2
clinvar
 2
missense
75
clinvar
5
clinvar
1
clinvar
 81
nonsense
1
clinvar
 1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
2
clinvar
 2
Total00777286
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001159387.2RefSeqNP_001152859.111MANE Select
ENST00000393354.7EnsemblENSP00000377022.311MANE Select
NM_001159388.2RefSeqNP_001152860.110Standard
NM_153446.3RefSeqNP_703147.211Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Post-translational protein modification
  • Metabolism of proteins
  • Asparagine N-linked glycosylation

Biological Process

  • UDP-N-acetylglucosamine metabolic process
  • protein N-linked glycosylation via asparagine
  • UDP-N-acetylgalactosamine metabolic process
  • negative regulation of cell-cell adhesion
  • lipid glycosylation

Molecular Function

  • acetylgalactosaminyltransferase activity

Cellular Component

  • Golgi membrane
  • integral component of membrane
  • integral component of Golgi membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000300404
Coding exons
11
Length
37530
Individuals with no LoFs
125249
Homozygous LoFs
2
Heterozygous LoFs
497
Defined
125748
p
0.00199
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.3892973160.9380.00001763655
Missense (PolyPhen)110103.161.06631210
Synonymous0.1521311330.9830.000008031149
Loss of Function-0.2352523.81.050.00000116269

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0160.016notable
Latino/Admixed American0.000840.00084rare
Ashkenazi Jewish0.00360.0036notable
East Asian0.000660.00065rare
Finnish0.0000940.000092rare
European (Non-Finnish)0.00130.0013notable
South Asian0.000360.00036rare
Other0.00130.0013notable

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Involved in the synthesis of the Sd(a) antigen (Sia- alpha2,3-[GalNAc-beta1,4]Gal-beta1,4-GlcNAc), a carbohydrate determinant expressed on erythrocytes, the colonic mucosa and other tissues. Transfers a beta-1,4-linked GalNAc to the galactose residue of an alpha-2,3-sialylated chain. {ECO:0000269|PubMed:12678917, ECO:0000269|PubMed:14688233}.;

Recessive Scores

pRec
0.284

Intolerance Scores

LoFtool
0.975
RVIS EVS
0.8
RVIS percentile EVS
87.69

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
N
Indispensability score
0.226

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium
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