GAL3ST1

protein-coding

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

Gene summary

Sulfonation, an important step in the metabolism of many drugs, xenobiotics, hormones, and neurotransmitters, is catalyzed by sulfotransferases. This gene encodes galactosylceramide sulfotransferase, which catalyzes the sulfation of membrane glycolipids including the final step in the synthesis of sulfatide, a major lipid component of the myelin sheath. This gene exhibits elevated expression in ovarian epithelial carcinoma and the encoded enzyme exhibits elevated activity in renal cell carcinoma. Mutations in this gene may be associated with reduced insulin resistance. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]

MANE transcript

NM_001318104.2

Inheritance

—

ClinVar variants

U:51B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.16

Max pathogenic AF

—

Genomic locus

chr22:30,554,635-30,574,665

External References & Databases

Ensembl (ENSG00000128242)

Transcript & Mutation Effects

hg38 • Region Span ~20.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GAL3ST1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 52

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001318104.2. 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						0
missense			51 clinvar	1 clinvar		52
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	51	1	0	52

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 97 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001318104.2	RefSeq	NP_001305033.1	2	MANE Select
ENST00000406361.6	Ensembl	ENSP00000385207.1	2	MANE Select
NM_001318103.2	RefSeq	NP_001305032.1	2	Standard
NM_001318105.2	RefSeq	NP_001305034.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ether lipid metabolism - Homo sapiens (human)
Sphingolipid metabolism - Homo sapiens (human)
Sphingolipid Metabolism
Gaucher Disease
Globoid Cell Leukodystrophy

Biological Process

protein N-linked glycosylation
galactosylceramide biosynthetic process
spermatogenesis
myelination

Molecular Function

galactosylceramide sulfotransferase activity
sulfotransferase activity

Cellular Component

Golgi membrane
integral component of plasma membrane
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000402321
Coding exons: 2
Length: 19953
Individuals with no LoFs: 125719
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125723
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.73	225	311	0.724	0.0000252	2741
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.182

Intolerance Scores

LoFtool: 0.203
RVIS EVS: 0.69
RVIS percentile EVS: 85.21

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.911

Gene Damage Prediction

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