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.

not_specified (36 variants)
not_provided (1 variants)

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. These statistics are base on transcript: NM_000006927.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			35 clinvar	1 clinvar		36
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	35	2	0

Loading clinvar variants...

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