GAL3ST1

galactose-3-O-sulfotransferase 1, the group of Sulfotransferases, membrane bound

Basic information

Region (hg38): 22:30554635-30574665

Links

ENSG00000128242 ∙ NCBI:9514 ∙ OMIM:602300 ∙ HGNC:24240 ∙ Uniprot:Q99999 ∙ 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 GAL3ST1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GAL3ST1 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			16	1	1	18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	1

Variants in GAL3ST1

This is a list of pathogenic ClinVar variants found in the GAL3ST1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-30555061-C-G		not specified	Uncertain significance (Dec 07, 2021)
22-30555062-T-G		not specified	Uncertain significance (Dec 07, 2021)
22-30555175-G-T		not specified	Likely benign (Jan 26, 2022)
22-30555206-C-A		not specified	Uncertain significance (Sep 25, 2023)
22-30555240-G-C		not specified	Uncertain significance (Dec 19, 2023)
22-30555332-G-T		not specified	Uncertain significance (Jun 17, 2024)
22-30555454-C-G		not specified	Uncertain significance (Jan 17, 2023)
22-30555657-C-T		not specified	Uncertain significance (Dec 06, 2021)
22-30555686-A-G		not specified	Uncertain significance (Jan 27, 2022)
22-30555689-G-A		not specified	Uncertain significance (Jun 21, 2023)
22-30555702-G-T		not specified	Uncertain significance (Mar 01, 2024)
22-30555757-G-C		not specified	Uncertain significance (Nov 09, 2022)
22-30555861-C-A		not specified	Uncertain significance (Aug 17, 2021)
22-30556027-G-C		not specified	Uncertain significance (Jul 25, 2023)
22-30557275-C-T		not specified	Uncertain significance (Aug 16, 2022)
22-30557308-C-T			Benign (Feb 24, 2021)
22-30557335-C-T		not specified	Uncertain significance (Sep 01, 2021)
22-30557370-G-A		not specified	Uncertain significance (Jul 19, 2022)
22-30557374-T-G		not specified	Uncertain significance (May 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GAL3ST1	protein_coding	protein_coding	ENST00000402321	2	19953

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.666	0.333	125719	0	4	125723	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.73	225	311	0.724	0.0000252	2741
Missense in Polyphen		66	130.94	0.50404		1268
Synonymous	-0.740	155	144	1.08	0.0000124	871
Loss of Function	2.71	2	12.2	0.164	7.15e-7	116

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000178	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the sulfation of membrane glycolipids. Seems to prefer beta-glycosides at the non-reducing termini of sugar chains attached to a lipid moiety. Catalyzes the synthesis of galactosylceramide sulfate (sulfatide), a major lipid component of the myelin sheath and of monogalactosylalkylacylglycerol sulfate (seminolipid), present in spermatocytes (By similarity). Also acts on lactosylceramide, galactosyl 1-alkyl-2-sn-glycerol and galactosyl diacylglycerol (in vitro). {ECO:0000250, ECO:0000269|PubMed:8830034}.
• Pathway: Ether lipid metabolism - Homo sapiens (human);Sphingolipid metabolism - Homo sapiens (human);Sphingolipid Metabolism;Gaucher Disease;Globoid Cell Leukodystrophy;Metachromatic Leukodystrophy (MLD);Fabry disease;Krabbe disease;Sphingolipid Metabolism;Metapathway biotransformation Phase I and II;Glycosphingolipid biosynthesis - ganglioseries;Glycosphingolipid metabolism (Consensus)

Recessive Scores

• pRec: 0.182

Intolerance Scores

• loftool: 0.203
• rvis_EVS: 0.69
• rvis_percentile_EVS: 85.21

Haploinsufficiency Scores

• pHI: 0.229
• hipred: Y
• hipred_score: 0.566
• ghis: 0.434

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.911

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gal3st1
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); renal/urinary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: protein N-linked glycosylation;galactosylceramide biosynthetic process;spermatogenesis;myelination
• Cellular component: Golgi membrane;integral component of plasma membrane;membrane
• Molecular function: galactosylceramide sulfotransferase activity;sulfotransferase activity