ST6GAL2

ST6 beta-galactoside alpha-2,6-sialyltransferase 2, the group of Sialyltransferases

Basic information

Region (hg38): 2:106801599-106887108

Previous symbols: [ "SIAT2" ]

Links

ENSG00000144057 ∙ NCBI:84620 ∙ OMIM:608472 ∙ HGNC:10861 ∙ Uniprot:Q96JF0 ∙ 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 ST6GAL2 gene.

• Inborn genetic diseases (20 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ST6GAL2 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			18	2		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	18	2	0

Variants in ST6GAL2

This is a list of pathogenic ClinVar variants found in the ST6GAL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-106806809-A-G		not specified	Uncertain significance (Dec 12, 2023)
2-106806845-C-T		not specified	Uncertain significance (Aug 13, 2021)
2-106830129-C-A		not specified	Uncertain significance (Mar 01, 2024)
2-106832581-G-A		not specified	Uncertain significance (Feb 07, 2023)
2-106832649-G-C		not specified	Uncertain significance (Jan 17, 2024)
2-106834081-T-G		not specified	Uncertain significance (Nov 16, 2022)
2-106843207-G-C		not specified	Likely benign (Sep 19, 2023)
2-106843224-G-C		not specified	Uncertain significance (Jul 12, 2023)
2-106843245-C-T		not specified	Likely benign (Oct 26, 2022)
2-106843249-C-A		not specified	Uncertain significance (May 25, 2022)
2-106843296-A-T		not specified	Uncertain significance (May 18, 2022)
2-106843400-T-C		not specified	Uncertain significance (Mar 12, 2024)
2-106843442-C-T		not specified	Uncertain significance (Jun 11, 2021)
2-106843470-T-C		not specified	Uncertain significance (Dec 01, 2022)
2-106843494-C-G		not specified	Uncertain significance (Sep 12, 2023)
2-106843583-A-G		not specified	Uncertain significance (Nov 15, 2021)
2-106843664-C-T		not specified	Uncertain significance (May 16, 2022)
2-106843681-C-G		not specified	Uncertain significance (Aug 17, 2021)
2-106843695-C-A		not specified	Uncertain significance (Jul 08, 2022)
2-106843697-C-G		not specified	Uncertain significance (Jun 16, 2023)
2-106843847-G-C		not specified	Uncertain significance (May 05, 2023)
2-106843848-A-T		not specified	Uncertain significance (May 05, 2023)
2-106843851-G-A		not specified	Likely benign (Oct 06, 2021)
2-106843895-A-G		not specified	Uncertain significance (Sep 06, 2022)
2-106843942-C-A		not specified	Uncertain significance (Oct 29, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ST6GAL2	protein_coding	protein_coding	ENST00000409382	5	85509

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00566	0.990	125723	0	25	125748	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.211	324	335	0.968	0.0000221	3427
Missense in Polyphen		106	133.58	0.7935		1409
Synonymous	0.326	141	146	0.966	0.0000107	1072
Loss of Function	2.49	7	18.6	0.376	8.94e-7	205

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000876	0.0000876
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000142	0.000139
European (Non-Finnish)	0.000120	0.000114
Middle Eastern	0.0000544	0.0000544
South Asian	0.000131	0.000131
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transfers sialic acid from the donor of substrate CMP- sialic acid to galactose containing acceptor substrates. Has alpha-2,6-sialyltransferase activity toward oligosaccharides that have the Gal-beta-1,4-GlcNAc sequence at the non-reducing end of their carbohydrate groups, but it has weak or no activities toward glycoproteins and glycolipids. {ECO:0000269|PubMed:12235148}.
• Pathway: N-Glycan biosynthesis - Homo sapiens (human);Other types of O-glycan biosynthesis - Homo sapiens (human);Globo Sphingolipid Metabolism;Post-translational protein modification;Metabolism of proteins;terminal <i>O</i>-glycans residues modification;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 (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.795
• rvis_EVS: 1.73
• rvis_percentile_EVS: 96.6

Haploinsufficiency Scores

• pHI: 0.181
• hipred: N
• hipred_score: 0.418
• ghis: 0.398

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.136

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: St6gal2

Gene ontology

• Biological process: protein glycosylation;oligosaccharide metabolic process;sialylation
• Cellular component: Golgi membrane;integral component of membrane;Golgi cisterna membrane
• Molecular function: beta-galactoside alpha-2,6-sialyltransferase activity