GAL3ST4

protein-coding

galactose-3-O-sulfotransferase 4, the group of Sulfotransferases, membrane bound

Gene summary

This gene encodes a member of the galactose-3-O-sulfotransferase protein family. The product of this gene catalyzes sulfonation by transferring a sulfate to the C-3' position of galactose residues in O-linked glycoproteins. This enzyme is highly specific for core 1 structures, with asialofetuin, Gal-beta-1,3-GalNAc and Gal-beta-1,3 (GlcNAc-beta-1,6)GalNAc being good substrates. [provided by RefSeq, Jul 2008]

MANE transcript

NM_024637.5

Inheritance

—

ClinVar variants

U:99B:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.91

Max pathogenic AF

—

Genomic locus

chr7:100,159,244-100,168,617

External References & Databases

Ensembl (ENSG00000197093)

Transcript & Mutation Effects

hg38 • Region Span ~9.4 kb

Loading mutation effect viewer...

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 GAL3ST4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 100

not providedTotal: 9

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024637.5. 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			1 clinvar		1 clinvar	2
missense			96 clinvar	7 clinvar	3 clinvar	106
nonsense			2 clinvar	1 clinvar		3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	99	8	4	111

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024637.5	RefSeq	NP_078913.3	3	MANE Select
ENST00000360039.9	Ensembl	ENSP00000353142.4	3	MANE Select
ENST00000411994.1	Ensembl	ENSP00000414733.1	2	Standard
ENST00000411994.2	Ensembl	ENSP00000414733.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

TYROBP Causal Network
Metapathway biotransformation Phase I and II

Biological Process

sulfur compound metabolic process
cell-cell signaling
glycoprotein metabolic process
glycolipid biosynthetic process
oligosaccharide metabolic process

Molecular Function

galactosylceramide sulfotransferase activity
3'-phosphoadenosine 5'-phosphosulfate binding
galactose 3-O-sulfotransferase activity
proteoglycan sulfotransferase activity

Cellular Component

membrane
integral component of membrane
Golgi cisterna membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000360039
Coding exons: 3
Length: 9507
Individuals with no LoFs: 125524
Homozygous LoFs: 1
Heterozygous LoFs: 223
Defined: 125748
p: 0.000891

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0161	292	293	0.997	0.0000184	3079
Missense (PolyPhen)		126	115.67	1.0893		1257
Synonymous	0.389	113	118	0.955	0.00000650	1091
Loss of Function	0.368	19	20.8	0.913	0.00000155	165

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0065	0.0062	notable
Latino/Admixed American	0.00064	0.00064	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00045	0.00044	rare
Finnish	0.000095	0.000092	rare
European (Non-Finnish)	0.00033	0.00033	rare
South Asian	0.0017	0.0016	notable
Other	0.00066	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Catalyzes the transfer of sulfate to beta-1,3-linked galactose residues in O-linked glycoproteins. Good substrates include asialofetuin, Gal-beta-1,3-GalNAc and Gal-beta-1,3 (GlcNAc-beta-1,6)GalNAc. {ECO:0000269|PubMed:11333265}.;

Recessive Scores

pRec: 0.0934

Intolerance Scores

LoFtool: 0.627
RVIS EVS: 1.07
RVIS percentile EVS: 91.67

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.266

Gene Damage Prediction

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