A4GALT
protein-codingalpha 1,4-galactosyltransferase (P blood group), the group of Alpha 1,4-glycosyltransferases|Blood group antigens
Gene summary
The protein encoded by this gene catalyzes the transfer of galactose to lactosylceramide to form globotriaosylceramide, which has been identified as the P(k) antigen of the P blood group system. This protein, a type II membrane protein found in the Golgi, is also required for the synthesis of the bacterial verotoxins receptor. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2015]
- P1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~29.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0100587
Submitter: ClinGen
*A4GALT* was first reported in relation to autosomal recessive congenital disorder of glycosylation in 2000 (Steffensen et al., PMID: 10747952). *A4GALT*-congenital disorder of glycosylation presents as the blood group phenotype p null. Persons affected with this condition may present with no phenotype beyond abnormal agglutination in standard blood group serological testing or may present with recurrent spontaneous abortion or congenital hemolytic anemia. Per criteria outlined by the ClinGen Lumping and Splitting guidelines, we found a difference in molecular mechanism. Therefore, the following disease entities have been split into multiple disease entities, congenital disorder of glycosylation and NOR polyagglutination syndrome. The split curation for autosomal recessive NOR polyagglutination syndrome will be curated separately. 14 variants (missense, in-frame indel, nonsense, frameshift) that have been reported in 13 probands in 6 publications (PMIDs: 12823750, 15142124, 10747952, 10993874, 11896312, 27612185) are included in this curation. More evidence is available in the literature, but the maximum score for genetic evidence (12 pts) has been reached. The mechanism of pathogenicity is known to be loss of function. This gene-disease relationship is also supported by in vitro functional assays. (PMIDs: 23927681, 18067504). In summary, there is definitive evidence supporting the relationship between *A4GALT* and autosomal recessive congenital disorder of glycosylation. This has been repeatedly demonstrated in both the research and clinical diagnostic settings and has been upheld over time. This classification was approved by the ClinGen Congenital Disorders of Glycosylation GCEP on the meeting date May 21, 2025 (SOP Version 11).
Clinical Genomic Database (CGD)
Manifestation: Hematologic
Intervention: Hematologic
Rationale: Variants associated with a blood group may be important in specific situations (eg, related to transfusion)
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to A4GALT variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_017436.7. 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.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 23 | 4 | 27 | |||
| missense | 1 | 94 | 5 | 3 | 103 | |
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 4 | 4 | ||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 1 | 0 | 100 | 28 | 7 | 136 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_059132.1 | 1 | MANE Select | |
| Ensembl | ENSP00000494127.1 | 1 | MANE Select | |
| RefSeq | NP_001304967.1 | 1 | Standard | |
| Ensembl | ENSP00000249005.2 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Glycosphingolipid biosynthesis - globo and isoglobo series - Homo sapiens (human)
- Glycosphingolipid biosynthesis - lacto and neolacto series - Homo sapiens (human)
- Globo Sphingolipid Metabolism
Biological Process
- globoside biosynthetic process
- protein glycosylation
- glycosphingolipid biosynthetic process
- plasma membrane organization
Molecular Function
- galactosyltransferase activity
- toxic substance binding
- lactosylceramide 4-alpha-galactosyltransferase activity
Cellular Component
- membrane
- integral component of Golgi membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000401850
- Coding exons
- 1
- Length
- 29178
- Individuals with no LoFs
- 125708
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 28
- Defined
- 125736
- p
- 0.000111
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.187 | 241 | 233 | 1.03 | 0.0000176 | 2248 |
| Missense (PolyPhen) | 71 | 78.116 | 0.9089 | 877 | ||
| Synonymous | -0.990 | 124 | 111 | 1.12 | 0.00000928 | 750 |
| Loss of Function | 0.145 | 8 | 8.46 | 0.946 | 3.72e-7 | 90 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00054 | 0.00038 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000099 | 0.000097 | rare |
| South Asian | 0.000068 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Necessary for the biosynthesis of the Pk antigen of blood histogroup P. Catalyzes the transfer of galactose to lactosylceramide and galactosylceramide. Necessary for the synthesis of the receptor for bacterial verotoxins.;
Recessive Scores
- pRec
- 0.222
Intolerance Scores
- RVIS EVS
- -0.29
- RVIS percentile EVS
- 33.34
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.101
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |