ST3GAL1

ST3 beta-galactoside alpha-2,3-sialyltransferase 1, the group of Sialyltransferases

Basic information

Region (hg38): 8:133454847-133571940

Previous symbols: [ "SIAT4A" ]

Links

ENSG00000008513 ∙ NCBI:6482 ∙ OMIM:607187 ∙ HGNC:10862 ∙ Uniprot:Q11201 ∙ 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 ST3GAL1 gene.

• Inborn genetic diseases (6 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ST3GAL1 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					2	2
missense			6		1	7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	6	0	3

Variants in ST3GAL1

This is a list of pathogenic ClinVar variants found in the ST3GAL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-133459772-C-T		not specified	Uncertain significance (Aug 30, 2021)
8-133459777-A-C		not specified	Uncertain significance (Nov 22, 2023)
8-133459813-G-A		not specified	Uncertain significance (Sep 29, 2023)
8-133459838-C-T		not specified	Uncertain significance (Nov 10, 2022)
8-133459873-G-A		not specified	Uncertain significance (Jan 23, 2024)
8-133461892-T-A		not specified	Likely benign (Feb 27, 2024)
8-133461898-A-G		not specified	Uncertain significance (Jan 26, 2022)
8-133463467-T-C			Benign (Jun 04, 2018)
8-133464796-G-A		not specified	Uncertain significance (Apr 19, 2023)
8-133464866-C-T		not specified	Uncertain significance (Nov 29, 2023)
8-133465935-A-G			Benign (Jun 26, 2018)
8-133475754-C-T			Benign (Jun 26, 2018)
8-133475832-T-C		not specified	Likely benign (Nov 09, 2023)
8-133475833-G-A			Benign (Apr 03, 2018)
8-133475931-T-C		not specified	Uncertain significance (Dec 12, 2023)
8-133475948-A-C		not specified	Uncertain significance (Jan 27, 2022)
8-133476021-C-T		not specified	Uncertain significance (Oct 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ST3GAL1	protein_coding	protein_coding	ENST00000319914	6	117093

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.583	0.417	125735	0	7	125742	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.30	161	215	0.751	0.0000132	2244
Missense in Polyphen		63	91.966	0.68503		955
Synonymous	0.313	90	93.9	0.959	0.00000651	662
Loss of Function	2.97	3	15.7	0.191	8.28e-7	161

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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 on sugar chains O-linked to Thr or Ser and also as a terminal sequence on certain gangliosides. SIAT4A and SIAT4B sialylate the same acceptor substrates but exhibit different Km values. {ECO:0000250|UniProtKB:P54751}.
• 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: 0.144

Intolerance Scores

• loftool: 0.351
• rvis_EVS: 0.29
• rvis_percentile_EVS: 71.5

Haploinsufficiency Scores

• pHI: 0.129
• hipred: Y
• hipred_score: 0.646
• ghis: 0.417

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.242

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: St3gal1
• Phenotype: hematopoietic system phenotype; normal phenotype; immune system phenotype

Gene ontology

• Biological process: N-acetylneuraminate metabolic process;cellular protein modification process;protein phosphorylation;protein N-linked glycosylation;O-glycan processing;keratan sulfate biosynthetic process;sialylation
• Cellular component: Golgi membrane;membrane;integral component of membrane;Golgi cisterna membrane;extracellular exosome
• Molecular function: beta-galactoside (CMP) alpha-2,3-sialyltransferase activity