ST3GAL2

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

Basic information

Region (hg38): 16:70375977-70439237

Previous symbols: [ "SIAT4B" ]

Links

ENSG00000157350NCBI:6483OMIM:607188HGNC:10863Uniprot:Q16842AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
1
clinvar
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)2225195
16-70381798-C-G not specified Uncertain significance (Apr 15, 2024)3322936
16-70381798-C-T not specified Uncertain significance (Nov 21, 2024)3449993
16-70381799-G-A not specified Uncertain significance (Aug 14, 2024)3449992
16-70381856-C-G not specified Uncertain significance (Feb 27, 2023)2489169
16-70388499-C-T not specified Uncertain significance (Feb 22, 2025)3801946
16-70388502-C-T not specified Uncertain significance (Feb 06, 2024)3170629
16-70395030-C-T not specified Uncertain significance (Feb 25, 2025)3801943
16-70395071-C-G not specified Uncertain significance (Oct 25, 2022)2319371
16-70395109-G-A not specified Uncertain significance (Sep 08, 2024)2344176
16-70395157-T-C not specified Uncertain significance (Feb 27, 2024)2398241
16-70395174-A-G Uncertain significance (-)91971
16-70395175-T-A not specified Uncertain significance (Jan 16, 2024)3170628
16-70398226-A-G not specified Uncertain significance (Aug 10, 2021)2216158
16-70398227-T-C not specified Uncertain significance (Dec 28, 2024)3801947
16-70398260-C-T not specified Likely benign (Oct 06, 2022)2317512
16-70398310-C-T not specified Uncertain significance (Oct 12, 2021)2223742
16-70398337-A-C not specified Uncertain significance (Jan 24, 2025)3801945
16-70398341-T-A not specified Uncertain significance (Sep 26, 2023)3170627
16-70398382-A-G not specified Uncertain significance (Dec 14, 2023)3170626
16-70398397-G-A not specified Uncertain significance (May 03, 2023)2509975
16-70398412-C-T not specified Uncertain significance (Mar 31, 2024)3322935
16-70398413-C-G not specified Uncertain significance (Aug 01, 2022)2304503
16-70398428-G-C not specified Uncertain significance (Jun 10, 2024)3322934
16-70398433-G-A not specified Uncertain significance (Aug 01, 2024)3449991

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ST3GAL2protein_codingprotein_codingENST00000393640 659803
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9420.0583125740071257470.0000278
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.701602330.6860.00001492319
Missense in Polyphen3992.0330.42376955
Synonymous-0.5831101021.070.00000718687
Loss of Function3.47217.80.1120.00000109155

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001230.000123
Ashkenazi Jewish0.000.00
East Asian0.00005750.0000544
Finnish0.00004900.0000462
European (Non-Finnish)0.00001770.0000176
Middle Eastern0.00005750.0000544
South Asian0.00003290.0000327
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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