GAL3ST2

galactose-3-O-sulfotransferase 2, the group of Sulfotransferases, membrane bound

Basic information

Region (hg38): 2:241776822-241804287

Links

ENSG00000154252 ∙ NCBI:64090 ∙ OMIM:608237 ∙ HGNC:24869 ∙ Uniprot:Q9H3Q3 ∙ 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 GAL3ST2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GAL3ST2 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		1	44	3		48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	44	3	0

Variants in GAL3ST2

This is a list of pathogenic ClinVar variants found in the GAL3ST2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-241776969-T-A		not specified	Uncertain significance (Apr 12, 2022)
2-241776974-G-A		not specified	Uncertain significance (Sep 10, 2024)
2-241776985-G-A		not specified	Conflicting classifications of pathogenicity (Dec 31, 2019)
2-241799073-G-A		not specified	Likely benign (Jan 03, 2022)
2-241799117-G-A		not specified	Uncertain significance (Jul 14, 2024)
2-241799133-C-T		not specified	Uncertain significance (Dec 03, 2021)
2-241801810-C-T		not specified	Uncertain significance (Aug 20, 2024)
2-241801827-T-C		not specified	Uncertain significance (Apr 19, 2024)
2-241801834-A-C		not specified	Uncertain significance (Oct 12, 2022)
2-241801858-C-T			Likely pathogenic (Aug 21, 2014)
2-241801861-T-C		not specified	Uncertain significance (Dec 18, 2023)
2-241801938-G-A		not specified	Uncertain significance (Aug 26, 2024)
2-241801942-A-G		not specified	Uncertain significance (Nov 06, 2024)
2-241801962-C-T		not specified	Uncertain significance (Oct 02, 2023)
2-241801974-G-A		not specified	Uncertain significance (Mar 15, 2024)
2-241801977-G-A		not specified	Uncertain significance (Jan 26, 2023)
2-241803351-A-G		not specified	Uncertain significance (Nov 17, 2022)
2-241803411-G-A		not specified	Uncertain significance (Feb 14, 2023)
2-241803442-C-T		not specified	Likely benign (Sep 07, 2022)
2-241803519-C-G		not specified	Uncertain significance (Jun 16, 2023)
2-241803592-G-C		not specified	Uncertain significance (Aug 23, 2021)
2-241803648-G-A		not specified	Uncertain significance (Nov 09, 2024)
2-241803651-G-A		not specified	Uncertain significance (Jul 05, 2023)
2-241803667-C-G		not specified	Uncertain significance (Aug 30, 2022)
2-241803672-G-C		not specified	Uncertain significance (Jun 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GAL3ST2	protein_coding	protein_coding	ENST00000192314	4	27384

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.93e-11	0.0118	124763	7	825	125595	0.00332

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0524	219	217	1.01	0.0000127	2489
Missense in Polyphen		80	83.862	0.95395		1064
Synonymous	0.768	98	108	0.906	0.00000692	865
Loss of Function	-1.07	14	10.3	1.36	5.40e-7	103

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00456	0.00437
Ashkenazi Jewish	0.00558	0.00468
East Asian	0.000132	0.000109
Finnish	0.000522	0.000508
European (Non-Finnish)	0.00622	0.00538
Middle Eastern	0.000132	0.000109
South Asian	0.000797	0.000719
Other	0.00495	0.00392

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transfers a sulfate group to the hydroxyl group at C3 of non-reducing beta-galactosyl residues. Acts both on type 1 (Gal- beta-1,3-GlcNAc) and type 2 (Gal-beta-1,4-GlcNAc) chains with similar efficiency.
• Pathway: Metapathway biotransformation Phase I and II (Consensus)

Recessive Scores

• pRec: 0.109

Haploinsufficiency Scores

• pHI: 0.0636
• hipred: N
• hipred_score: 0.285
• ghis: 0.409

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.162

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gal3st2c

Gene ontology

• Biological process: biological_process;glycolipid biosynthetic process
• Cellular component: membrane;integral component of membrane;Golgi cisterna membrane
• Molecular function: galactosylceramide sulfotransferase activity;protein binding;sulfotransferase activity