ST3GAL6

ST3 beta-galactoside alpha-2,3-sialyltransferase 6, the group of Sialyltransferases

Basic information

Region (hg38): 3:98732236-98821201

Previous symbols: [ "SIAT10" ]

Links

ENSG00000064225 ∙ NCBI:10402 ∙ OMIM:607156 ∙ HGNC:18080 ∙ Uniprot:Q9Y274 ∙ 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 ST3GAL6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ST3GAL6 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in ST3GAL6

This is a list of pathogenic ClinVar variants found in the ST3GAL6 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-98768448-G-T		not specified	Uncertain significance (Dec 02, 2022)
3-98768517-C-T		not specified	Uncertain significance (Aug 02, 2021)
3-98770902-G-A		not specified	Uncertain significance (Aug 13, 2021)
3-98772842-C-T		not specified	Uncertain significance (Jun 23, 2021)
3-98772880-G-A		not specified	Uncertain significance (Jul 09, 2021)
3-98788149-C-T		not specified	Uncertain significance (Aug 17, 2021)
3-98788164-C-G		not specified	Uncertain significance (Nov 18, 2022)
3-98788199-G-A		not specified	Uncertain significance (Sep 17, 2021)
3-98788387-G-A		not specified	Uncertain significance (Jun 18, 2021)
3-98788387-G-T		not specified	Uncertain significance (Jun 03, 2024)
3-98791844-C-T		not specified	Uncertain significance (Jun 03, 2024)
3-98791850-C-T		not specified	Uncertain significance (Jan 17, 2024)
3-98791991-A-G		not specified	Uncertain significance (Sep 09, 2021)
3-98793720-A-G		not specified	Uncertain significance (Jan 29, 2024)
3-98793732-A-C		not specified	Uncertain significance (Mar 21, 2023)
3-98793733-A-G		not specified	Uncertain significance (Oct 13, 2023)
3-98799502-T-C		not specified	Uncertain significance (Aug 02, 2021)
3-98799515-G-T		not specified	Uncertain significance (Dec 19, 2022)
3-98799538-C-T		not specified	Uncertain significance (May 15, 2024)
3-98799553-T-C		not specified	Uncertain significance (Feb 06, 2023)
3-98799566-C-T		not specified	Uncertain significance (Dec 16, 2022)
3-98799682-G-A		not specified	Uncertain significance (Dec 05, 2022)
3-98799686-T-C		DCBLD2-related disorder	Likely benign (Feb 25, 2022)
3-98799701-C-T		not specified	Uncertain significance (Jan 23, 2024)
3-98799724-C-T		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ST3GAL6	protein_coding	protein_coding	ENST00000394162	9	88966

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.33e-8	0.469	125628	0	113	125741	0.000449

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.908	141	175	0.807	0.00000858	2182
Missense in Polyphen		46	65.829	0.69878		838
Synonymous	-0.339	68	64.5	1.05	0.00000351	609
Loss of Function	0.934	14	18.3	0.765	0.00000101	235

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000512	0.000511
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00185	0.00185
European (Non-Finnish)	0.000284	0.000281
Middle Eastern	0.000109	0.000109
South Asian	0.000687	0.000686
Other	0.000991	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the synthesis of sialyl-paragloboside, a precursor of sialyl-Lewis X determinant. Has a alpha-2,3- sialyltransferase activity toward Gal-beta1,4-GlcNAc structure on glycoproteins and glycolipids. Has a restricted substrate specificity, it utilizes Gal-beta1,4-GlcNAc on glycoproteins, and neolactotetraosylceramide and neolactohexaosylceramide, but not lactotetraosylceramide, lactosylceramide or asialo-GM1.
• Pathway: Glycosphingolipid biosynthesis - lacto and neolacto series - Homo sapiens (human);Signal Transduction;Metabolism of carbohydrates;Keratan sulfate biosynthesis;Keratan sulfate/keratin metabolism;Glycosphingolipid biosynthesis - neolactoseries;Glycosaminoglycan metabolism;Post-translational protein modification;Metabolism of proteins;Metabolism;Pre-NOTCH Processing in Golgi;Pre-NOTCH Expression and Processing;Signaling by NOTCH;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: 0.149

Intolerance Scores

• loftool: 0.762
• rvis_EVS: -0.2
• rvis_percentile_EVS: 38.82

Haploinsufficiency Scores

• pHI: 0.468
• hipred: N
• hipred_score: 0.313
• ghis: 0.455

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.109

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: St3gal6
• Phenotype: hematopoietic system phenotype; immune system phenotype; cellular phenotype

Gene ontology

• Biological process: cellular protein modification process;protein glycosylation;glycolipid metabolic process;glycolipid biosynthetic process;oligosaccharide metabolic process;keratan sulfate biosynthetic process;cellular response to interleukin-6;sialylation
• Cellular component: Golgi membrane;integral component of membrane;extracellular exosome
• Molecular function: beta-galactoside (CMP) alpha-2,3-sialyltransferase activity;sialyltransferase activity;beta-galactoside alpha-2,3-sialyltransferase activity