ST3GAL2

ST3 beta-galactoside alpha-2,3-sialyltransferase 2, the group of Sialyltransferases

Basic information

Region (hg38): 16:70375977-70439237

Previous symbols: [ "SIAT4B" ]

Links

ENSG00000157350 ∙ NCBI:6483 ∙ OMIM:607188 ∙ HGNC:10863 ∙ Uniprot:Q16842 ∙ 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 ST3GAL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ST3GAL2 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			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	0

Variants in ST3GAL2

This is a list of pathogenic ClinVar variants found in the ST3GAL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-70381732-A-G		not specified	Uncertain significance (Aug 17, 2021)
16-70381798-C-G		not specified	Uncertain significance (Apr 15, 2024)
16-70381798-C-T		not specified	Uncertain significance (Nov 21, 2024)
16-70381799-G-A		not specified	Uncertain significance (Aug 14, 2024)
16-70381856-C-G		not specified	Uncertain significance (Feb 27, 2023)
16-70388499-C-T		not specified	Uncertain significance (Feb 22, 2025)
16-70388502-C-T		not specified	Uncertain significance (Feb 06, 2024)
16-70395030-C-T		not specified	Uncertain significance (Feb 25, 2025)
16-70395071-C-G		not specified	Uncertain significance (Oct 25, 2022)
16-70395109-G-A		not specified	Uncertain significance (Sep 08, 2024)
16-70395157-T-C		not specified	Uncertain significance (Feb 27, 2024)
16-70395174-A-G			Uncertain significance (-)
16-70395175-T-A		not specified	Uncertain significance (Jan 16, 2024)
16-70398226-A-G		not specified	Uncertain significance (Aug 10, 2021)
16-70398227-T-C		not specified	Uncertain significance (Dec 28, 2024)
16-70398260-C-T		not specified	Likely benign (Oct 06, 2022)
16-70398310-C-T		not specified	Uncertain significance (Oct 12, 2021)
16-70398337-A-C		not specified	Uncertain significance (Jan 24, 2025)
16-70398341-T-A		not specified	Uncertain significance (Sep 26, 2023)
16-70398382-A-G		not specified	Uncertain significance (Dec 14, 2023)
16-70398397-G-A		not specified	Uncertain significance (May 03, 2023)
16-70398412-C-T		not specified	Uncertain significance (Mar 31, 2024)
16-70398413-C-G		not specified	Uncertain significance (Aug 01, 2022)
16-70398428-G-C		not specified	Uncertain significance (Jun 10, 2024)
16-70398433-G-A		not specified	Uncertain significance (Aug 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ST3GAL2	protein_coding	protein_coding	ENST00000393640	6	59803

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.942	0.0583	125740	0	7	125747	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.70	160	233	0.686	0.0000149	2319
Missense in Polyphen		39	92.033	0.42376		955
Synonymous	-0.583	110	102	1.07	0.00000718	687
Loss of Function	3.47	2	17.8	0.112	0.00000109	155

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000575	0.0000544
Finnish	0.0000490	0.0000462
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.0000575	0.0000544
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Responsible for the synthesis of the sequence NeuAc- alpha-2,3-Gal-beta-1,3-GalNAc- found in terminal carbohydrate groups of certain glycoproteins, oligosaccharides and glycolipids. SIAT4A and SIAT4B sialylate the same acceptor substrates but exhibit different Km values. {ECO:0000250|UniProtKB:Q11204}.
• Pathway: Glycosphingolipid biosynthesis - ganglio series - Homo sapiens (human);Mucin type O-glycan biosynthesis - Homo sapiens (human);Glycosphingolipid biosynthesis - globo and isoglobo series - Homo sapiens (human);Glycosaminoglycan biosynthesis - keratan sulfate - Homo sapiens (human);Ganglio Sphingolipid Metabolism;Globo Sphingolipid Metabolism;Metabolism of carbohydrates;Keratan sulfate biosynthesis;Keratan sulfate/keratin metabolism;Glycosaminoglycan metabolism;Post-translational protein modification;Metabolism of proteins;Glycosphingolipid biosynthesis - ganglioseries;Glycosphingolipid biosynthesis - globoseries;Metabolism;mucin core 1 and core 2 <i>O</i>-glycosylation;O-Glycan biosynthesis;Sialic acid metabolism;Synthesis of substrates in N-glycan biosythesis;Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein;Asparagine N-linked glycosylation;Termination of O-glycan biosynthesis;O-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.140

Intolerance Scores

• loftool: 0.237
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.93

Haploinsufficiency Scores

• pHI: 0.224
• hipred: Y
• hipred_score: 0.673
• ghis: 0.658

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.886

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: St3gal2
• Phenotype: immune system phenotype; normal phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: protein glycosylation;glycoprotein biosynthetic process;glycolipid biosynthetic process;oligosaccharide biosynthetic process;O-glycan processing;keratan sulfate biosynthetic process;lipid glycosylation;sialylation;protein sialylation
• Cellular component: Golgi membrane;extracellular region;integral component of membrane;Golgi cisterna membrane
• Molecular function: beta-galactoside (CMP) alpha-2,3-sialyltransferase activity;monosialoganglioside sialyltransferase activity