A4GALT

alpha 1,4-galactosyltransferase (P blood group), the group of Alpha 1,4-glycosyltransferases|Blood group antigens

Basic information

Region (hg38): 22:42692120-42721298

Previous symbols: [ "P1" ]

Links

ENSG00000128274 ∙ NCBI:53947 ∙ OMIM:607922 ∙ HGNC:18149 ∙ Uniprot:Q9NPC4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Blood group, P1PK system	BG	Hematologic	Variants associated with a blood group may be important in specific situations (eg, related to transfusion)	Hematologic	10993874

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the A4GALT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the A4GALT 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				17	6	23
missense			48	3	4	55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	48	20	10

Variants in A4GALT

This is a list of pathogenic ClinVar variants found in the A4GALT region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
22-42692896-G-A			Likely benign (Jun 22, 2023)
22-42692922-T-TG		p phenotype	Affects (Jan 01, 2002)
22-42692930-T-C		not specified	Uncertain significance (Jun 06, 2023)
22-42692934-G-A			Uncertain significance (Jun 20, 2022)
22-42692957-G-A			Uncertain significance (Jul 05, 2022)
22-42692965-C-T		A4GALT-related disorder	Benign (Jan 31, 2024)
22-42692966-G-A		not specified	Uncertain significance (Jan 27, 2022)
22-42692981-G-A		not specified	Uncertain significance (Aug 07, 2023)
22-42692995-C-G		not specified	Uncertain significance (Jun 22, 2023)
22-42693016-A-G			Likely benign (Dec 22, 2023)
22-42693038-G-A			Uncertain significance (Jan 22, 2024)
22-42693046-C-G		not specified	Uncertain significance (Sep 27, 2021)
22-42693049-G-C		A4GALT-related disorder	Benign (Jan 31, 2024)
22-42693060-C-A			Likely benign (Dec 07, 2023)
22-42693137-G-T		not specified	Uncertain significance (Feb 28, 2023)
22-42693148-G-C			Likely benign (Jan 22, 2024)
22-42693154-G-C		not specified	Uncertain significance (Oct 05, 2023)
22-42693169-C-T		p phenotype	Affects (Mar 29, 2002)
22-42693176-T-C			Uncertain significance (Dec 25, 2021)
22-42693185-C-T		not specified	Uncertain significance (May 26, 2023)
22-42693193-C-T			Likely benign (Jun 28, 2022)
22-42693200-G-A		p phenotype	Uncertain significance (Dec 09, 2023)
22-42693249-G-A			Uncertain significance (Feb 13, 2023)
22-42693282-C-T			Uncertain significance (Oct 24, 2022)
22-42693283-G-A			Benign (Jan 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
A4GALT	protein_coding	protein_coding	ENST00000401850	1	29178

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000767	0.311	125708	0	28	125736	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.187	241	233	1.03	0.0000176	2248
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000366	0.000362
Ashkenazi Jewish	0.00	0.00
East Asian	0.000544	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.0000987	0.0000967
Middle Eastern	0.000544	0.000381
South Asian	0.0000679	0.0000653
Other	0.00	0.00

dbNSFP

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.
• Pathway: Glycosphingolipid biosynthesis - globo and isoglobo series - Homo sapiens (human);Glycosphingolipid biosynthesis - lacto and neolacto series - Homo sapiens (human);Globo Sphingolipid Metabolism (Consensus)

Recessive Scores

• pRec: 0.222

Intolerance Scores

• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.34

Haploinsufficiency Scores

• pHI: 0.102
• hipred: N
• hipred_score: 0.242
• ghis: 0.595

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.101

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: A4galt
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); homeostasis/metabolism phenotype

Gene ontology

• Biological process: globoside biosynthetic process;protein glycosylation;glycosphingolipid biosynthetic process;plasma membrane organization
• Cellular component: membrane;integral component of Golgi membrane
• Molecular function: galactosyltransferase activity;toxic substance binding;lactosylceramide 4-alpha-galactosyltransferase activity