A3GALT2

alpha 1,3-galactosyltransferase 2, the group of Glycosyltransferase family 6

Basic information

Region (hg38): 1:33306766-33321098

Previous symbols: [ "A3GALT2P" ]

Links

ENSG00000184389

∙ NCBI:127550 ∙ OMIM:619850 ∙ HGNC:30005 ∙ Uniprot:U3KPV4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the A3GALT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the A3GALT2 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						0
missense				1 clinvar		1
nonsense						0
start loss						0
frameshift					1 clinvar	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	1	1

Variants in A3GALT2

This is a list of pathogenic ClinVar variants found in the A3GALT2 region.

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

Position	Significance	ClinVar
1-33307191-C-T	Likely benign (Apr 01, 2023)	2638619
1-33307198-G-T	Benign (Mar 01, 2025)	3777911
1-33312068-TAGTC-T	Benign (Nov 01, 2023)	2638620

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
A3GALT2	protein_coding	protein_coding	ENST00000442999	5	14333

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.28e-10	0.0280	119682	51	3633	123366	0.0150

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0464	170	172	0.990	0.0000110	2110
Missense in Polyphen		41	38.657	1.0606		523
Synonymous	0.126	77	78.4	0.982	0.00000555	697
Loss of Function	-0.553	14	11.9	1.17	5.14e-7	134

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0134	0.0133
Ashkenazi Jewish	0.00900	0.00900
East Asian	0.0000556	0.0000556
Finnish	0.0108	0.0109
European (Non-Finnish)	0.0246	0.0243
Middle Eastern	0.0000556	0.0000556
South Asian	0.00803	0.00794
Other	0.0146	0.0147

dbNSFP

Source: dbNSFP

Function: FUNCTION: Synthesizes the galactose-alpha(1,3)-galactose group on the glycosphingolipid isoglobotrihexosylceramide or isogloboside 3 (iGb3) by catalyzing the transfer of galactose from UDP-Galactose to its acceptor molecule Gal-beta-1,4-Glc-ceramide. Can also catalyze the addition of galactose to iGb3 itself to form polygalactose structures. {ECO:0000305|PubMed:23378701}.;
Pathway: Glycosphingolipid biosynthesis - globo and isoglobo series - Homo sapiens (human);Ganglio Sphingolipid Metabolism;Globo Sphingolipid Metabolism (Consensus)

Recessive Scores

pRec: 0.0960

Haploinsufficiency Scores

pHI: 0.106
hipred: N
hipred_score: 0.271
ghis

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: A3galt2
Phenotype

Gene ontology

Biological process: carbohydrate metabolic process;glycosphingolipid biosynthetic process;lipid glycosylation
Cellular component: Golgi apparatus;integral component of membrane;vesicle;Golgi cisterna membrane
Molecular function: alpha-1,3-galactosyltransferase activity;transferase activity, transferring glycosyl groups;metal ion binding;N-acetyllactosaminide 3-alpha-galactosyltransferase activity