GAL3ST3

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

Basic information

Region (hg38): 11:66040765-66049161

Links

ENSG00000175229 ∙ NCBI:89792 ∙ OMIM:608234 ∙ HGNC:24144 ∙ Uniprot:Q96A11 ∙ 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 GAL3ST3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GAL3ST3 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					5	5
missense			47		1	48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					6	6
Total	0	0	47	0	12

Variants in GAL3ST3

This is a list of pathogenic ClinVar variants found in the GAL3ST3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-66042292-C-T			Benign (Nov 11, 2018)
11-66042404-C-A			Benign (Nov 11, 2018)
11-66042507-T-C			Uncertain significance (Nov 03, 2019)
11-66042550-G-A		not specified	Uncertain significance (Nov 09, 2024)
11-66042557-G-A		not specified	Uncertain significance (Feb 14, 2023)
11-66042559-T-C		not specified	Uncertain significance (Feb 05, 2025)
11-66042572-G-T		not specified	Uncertain significance (Jan 24, 2024)
11-66042574-T-G			Benign (Nov 11, 2018)
11-66042577-G-A		not specified	Uncertain significance (Aug 22, 2023)
11-66042578-G-A		not specified	Uncertain significance (Mar 08, 2025)
11-66042580-C-A		not specified	Uncertain significance (Dec 28, 2024)
11-66042581-G-A		not specified	Uncertain significance (Jan 02, 2025)
11-66042593-C-T		not specified	Uncertain significance (Jul 27, 2021)
11-66042596-C-T		not specified	Uncertain significance (Mar 20, 2024)
11-66042598-C-T		not specified	Uncertain significance (Mar 31, 2023)
11-66042604-T-G		not specified	Uncertain significance (Mar 24, 2023)
11-66042610-T-G		not specified	Uncertain significance (Mar 24, 2023)
11-66042638-C-T		not specified	Uncertain significance (Sep 27, 2024)
11-66042641-C-T		not specified	Uncertain significance (Jan 29, 2024)
11-66042689-C-T		not specified	Uncertain significance (Apr 15, 2024)
11-66042703-T-C		not specified	Uncertain significance (Dec 15, 2023)
11-66042724-C-G		not specified	Uncertain significance (Dec 14, 2024)
11-66042738-C-T			Benign (Nov 11, 2018)
11-66042768-G-A			Benign (Jun 09, 2021)
11-66042788-C-T		not specified	Uncertain significance (Feb 14, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GAL3ST3	protein_coding	protein_coding	ENST00000312006	2	7229

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.93e-8	0.0738	125474	0	23	125497	0.0000916

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.774	262	300	0.874	0.0000242	2698
Missense in Polyphen		115	126.64	0.90811		1180
Synonymous	0.858	132	145	0.909	0.0000127	943
Loss of Function	-0.442	11	9.53	1.15	4.09e-7	114

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000337	0.000332
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000147	0.000139
European (Non-Finnish)	0.0000918	0.0000882
Middle Eastern	0.00	0.00
South Asian	0.0000332	0.0000327
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transfers a sulfate to position 3 of non-reducing beta- galactosyl residues in N-glycans and core2-branched O-glycans. Has high activity towards Gal-beta-1,4-GlcNAc, Gal-beta-1,4(Fuc-alpha- 1,3)GlcNAc and lower activity towards Gal-beta-1,3(Fuc-alpha- 1,4)GlcNAc. {ECO:0000269|PubMed:11323440, ECO:0000269|PubMed:11356829}.
• Pathway: Metapathway biotransformation Phase I and II (Consensus)

Recessive Scores

• pRec: 0.110

Haploinsufficiency Scores

• pHI: 0.156
• hipred: Y
• hipred_score: 0.544
• ghis: 0.551

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.201

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gal3st3

Gene ontology

• Biological process: monosaccharide metabolic process;sulfur compound metabolic process;glycolipid biosynthetic process;oligosaccharide metabolic process;proteoglycan biosynthetic process;poly-N-acetyllactosamine metabolic process
• Cellular component: integral component of membrane;Golgi cisterna membrane
• Molecular function: galactosylceramide sulfotransferase activity;carbohydrate binding;3'-phosphoadenosine 5'-phosphosulfate binding;galactose 3-O-sulfotransferase activity;proteoglycan sulfotransferase activity