A4GALT

protein-coding

alpha 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]

Previous symbols:
  • P1

MANE transcript

NM_017436.7

Inheritance

AR, BG

ClinVar variants

P:1U:100B:35

Top phenotype

Blood group, P1PK system

gnomAD constraint

pLI —, LoF o/e 0.95

Max pathogenic AF

—

Genomic locus

chr22:42,692,121-42,721,298

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~29.2 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

A4GALT-related congenital disorder of glycosylationDEFINITIVE

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)

Blood group, P1PK systemBG

Manifestation: Hematologic

Intervention: Hematologic

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

Refs: 10993874Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to A4GALT variants in ClinVar

7 Conditions Cataloged
not providedTotal: 72
not specifiedTotal: 61
p phenotypeTotal: 6
Blood group, P1PK systemTotal: 4
A4GALT-related disorderTotal: 4
Infantile cortical hyperostosisTotal: 1
NOR polyagglutination syndromeTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
23
clinvar
4
clinvar
27
missense
1
clinvar
94
clinvar
5
clinvar
3
clinvar
103
nonsense
2
clinvar
2
start loss
0
frameshift
4
clinvar
4
splice donor/acceptor (+/-2bp)
0
Total10100287136
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 115 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_017436.7RefSeqNP_059132.11MANE Select
ENST00000642412.2EnsemblENSP00000494127.11MANE Select
NM_001318038.3RefSeqNP_001304967.11Standard
ENST00000249005.3EnsemblENSP00000249005.21Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.1872412331.030.00001762248
Missense (PolyPhen)7178.1160.9089877
Synonymous-0.9901241111.120.00000928750
Loss of Function0.14588.460.9463.72e-790

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000250.00025rare
Latino/Admixed American0.000120.00012rare
Ashkenazi Jewish00.0absent
East Asian0.000540.00038rare
Finnish00.0absent
European (Non-Finnish)0.0000990.000097rare
South Asian0.0000680.000065rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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