ST6GALNAC3

ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 3, the group of Sialyltransferases

Basic information

Region (hg38): 1:76074745-76634603

Previous symbols: [ "SIAT7C" ]

Links

ENSG00000184005 ∙ NCBI:256435 ∙ OMIM:610133 ∙ HGNC:19343 ∙ Uniprot:Q8NDV1 ∙ 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 ST6GALNAC3 gene.

• Inborn genetic diseases (13 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ST6GALNAC3 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	0

Variants in ST6GALNAC3

This is a list of pathogenic ClinVar variants found in the ST6GALNAC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-76074876-A-G		not specified	Uncertain significance (Dec 15, 2022)
1-76313809-A-G		not specified	Uncertain significance (Jan 29, 2024)
1-76313862-C-T		not specified	Uncertain significance (Jan 23, 2023)
1-76313863-G-A		not specified	Uncertain significance (Jun 22, 2021)
1-76313930-A-G		not specified	Uncertain significance (Jun 05, 2023)
1-76313936-C-A		not specified	Uncertain significance (Oct 25, 2023)
1-76412234-C-T		not specified	Uncertain significance (Mar 11, 2022)
1-76412245-A-C		not specified	Uncertain significance (Sep 16, 2022)
1-76412269-C-T		not specified	Uncertain significance (Nov 06, 2023)
1-76412353-G-A		not specified	Uncertain significance (Dec 21, 2023)
1-76412372-T-C		not specified	Uncertain significance (Sep 22, 2022)
1-76627490-C-T		not specified	Uncertain significance (Jan 29, 2024)
1-76627519-G-A		not specified	Uncertain significance (Jan 05, 2022)
1-76628689-T-A		not specified	Uncertain significance (Oct 12, 2021)
1-76628690-C-A		not specified	Uncertain significance (Oct 12, 2021)
1-76628708-T-C		not specified	Uncertain significance (Apr 11, 2023)
1-76628784-A-T		not specified	Uncertain significance (Nov 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ST6GALNAC3	protein_coding	protein_coding	ENST00000328299	5	559883

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000264	0.937	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.449	161	178	0.905	0.00000952	2010
Missense in Polyphen		48	74.611	0.64333		843
Synonymous	0.275	61	63.8	0.956	0.00000359	568
Loss of Function	1.67	8	15.0	0.534	8.29e-7	175

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000123	0.000123
Middle Eastern	0.0000546	0.0000544
South Asian	0.00	0.00
Other	0.000349	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the biosynthesis of ganglioside GD1A from GM1B. Transfers CMP-NeuAc with an alpha-2,6-linkage to GalNAc residue on NeuAc-alpha-2,3-Gal-beta-1,3-GalNAc of glycoproteins and glycolipids. ST6GalNAcIII prefers glycolipids to glycoproteins (By similarity). {ECO:0000250}.
• Pathway: Glycosphingolipid biosynthesis - ganglio series - Homo sapiens (human);Globo Sphingolipid Metabolism;Post-translational protein modification;Metabolism of proteins;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: 0.104

Intolerance Scores

• loftool: 0.686
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.91

Haploinsufficiency Scores

• pHI: 0.291
• hipred: N
• hipred_score: 0.443
• ghis: 0.503

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.316

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: St6galnac3

Gene ontology

• Biological process: ganglioside biosynthetic process;protein glycosylation;glycosylceramide metabolic process;glycosphingolipid metabolic process;glycoprotein metabolic process;sialylation
• Cellular component: Golgi membrane;nucleoplasm;integral component of membrane
• Molecular function: alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity;sialyltransferase activity;(alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl-galactosaminide 6-alpha-sialyltransferase activity