GAL3ST4

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

Basic information

Region (hg38): 7:100159244-100168617

Links

ENSG00000197093 ∙ NCBI:79690 ∙ OMIM:608235 ∙ HGNC:24145 ∙ Uniprot:Q96RP7 ∙ 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 GAL3ST4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GAL3ST4 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					1	1
missense			41	5	3	49
nonsense			1	1		2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	42	6	5

Variants in GAL3ST4

This is a list of pathogenic ClinVar variants found in the GAL3ST4 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-100159975-G-C		not specified	Uncertain significance (Jan 03, 2022)
7-100159985-C-A		not specified	Uncertain significance (Nov 10, 2022)
7-100160019-G-C		not specified	Uncertain significance (Mar 25, 2024)
7-100160031-C-T		not specified	Uncertain significance (Oct 26, 2022)
7-100160075-T-C		not specified	Uncertain significance (Jun 07, 2024)
7-100160116-G-A		not specified	Uncertain significance (Dec 20, 2023)
7-100160116-G-T		not specified	Uncertain significance (Oct 03, 2023)
7-100160158-C-T		not specified	Uncertain significance (May 03, 2023)
7-100160160-C-G		not specified	Uncertain significance (Mar 19, 2024)
7-100160190-C-T		not specified	Uncertain significance (Mar 25, 2024)
7-100160206-C-T		not specified	Uncertain significance (Jun 24, 2022)
7-100160217-G-A		not specified	Uncertain significance (Feb 07, 2023)
7-100160226-C-T		not specified	Uncertain significance (Feb 23, 2023)
7-100160236-C-T		not specified	Uncertain significance (Jan 19, 2024)
7-100160251-G-A		not specified	Uncertain significance (Mar 31, 2024)
7-100160257-A-G		not specified	Uncertain significance (Oct 20, 2021)
7-100160307-G-C		not specified	Uncertain significance (May 31, 2022)
7-100160316-C-T		not specified	Uncertain significance (Jan 09, 2024)
7-100160331-C-T			Benign (Dec 31, 2019)
7-100160332-G-A			Benign (Mar 29, 2018)
7-100160383-G-A		not specified	Uncertain significance (May 13, 2024)
7-100160410-C-T		not specified	Uncertain significance (Jan 19, 2024)
7-100160417-G-A			Benign (Dec 21, 2017)
7-100160467-C-T		not specified	Uncertain significance (Apr 20, 2024)
7-100160484-A-G		not specified	Uncertain significance (Jul 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GAL3ST4	protein_coding	protein_coding	ENST00000360039	3	9507

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.23e-12	0.0671	125524	1	223	125748	0.000891

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0161	292	293	0.997	0.0000184	3079
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00709	0.00687
Ashkenazi Jewish	0.00	0.00
East Asian	0.000454	0.000435
Finnish	0.0000948	0.0000924
European (Non-Finnish)	0.000328	0.000325
Middle Eastern	0.000454	0.000435
South Asian	0.00167	0.00163
Other	0.000663	0.000652

dbNSFP

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}.
• Pathway: TYROBP Causal Network;Metapathway biotransformation Phase I and II (Consensus)

Recessive Scores

• pRec: 0.0934

Intolerance Scores

• loftool: 0.627
• rvis_EVS: 1.07
• rvis_percentile_EVS: 91.67

Haploinsufficiency Scores

• pHI: 0.101
• hipred: N
• hipred_score: 0.170
• ghis: 0.438

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.266

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gal3st4

Gene ontology

• Biological process: sulfur compound metabolic process;cell-cell signaling;glycoprotein metabolic process;glycolipid biosynthetic process;oligosaccharide metabolic process;proteoglycan biosynthetic process
• Cellular component: membrane;integral component of membrane;Golgi cisterna membrane;extracellular exosome
• Molecular function: galactosylceramide sulfotransferase activity;3'-phosphoadenosine 5'-phosphosulfate binding;galactose 3-O-sulfotransferase activity;proteoglycan sulfotransferase activity