ST6GAL1

ST6 beta-galactoside alpha-2,6-sialyltransferase 1, the group of Sialyltransferases

Basic information

Region (hg38): 3:186930325-187078553

Previous symbols: [ "SIAT1" ]

Links

ENSG00000073849 ∙ NCBI:6480 ∙ OMIM:109675 ∙ HGNC:10860 ∙ Uniprot:P15907 ∙ 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 ST6GAL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ST6GAL1 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 ST6GAL1

This is a list of pathogenic ClinVar variants found in the ST6GAL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-187042771-T-C		not specified	Uncertain significance (Mar 20, 2023)
3-187042772-C-G		not specified	Uncertain significance (Jan 24, 2024)
3-187042915-C-T		not specified	Uncertain significance (Nov 08, 2022)
3-187042942-G-A		not specified	Uncertain significance (Nov 09, 2024)
3-187043083-A-G		not specified	Uncertain significance (Dec 19, 2023)
3-187043124-C-T		not specified	Uncertain significance (Aug 02, 2022)
3-187043172-G-C		not specified	Uncertain significance (Mar 03, 2022)
3-187051255-A-G		not specified	Uncertain significance (Oct 29, 2024)
3-187051308-G-A		not specified	Uncertain significance (Nov 13, 2024)
3-187051321-C-A		not specified	Uncertain significance (Dec 16, 2023)
3-187051332-C-G		not specified	Uncertain significance (Mar 04, 2024)
3-187072891-A-C		not specified	Uncertain significance (May 05, 2023)
3-187072892-A-G		not specified	Uncertain significance (Mar 08, 2024)
3-187072931-A-G		not specified	Uncertain significance (Feb 27, 2023)
3-187075579-A-G		not specified	Uncertain significance (Sep 14, 2022)
3-187075618-T-A		not specified	Uncertain significance (Dec 04, 2024)
3-187075736-G-A		not specified	Uncertain significance (Jul 30, 2024)
3-187075772-C-T		not specified	Uncertain significance (Apr 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ST6GAL1	protein_coding	protein_coding	ENST00000169298	5	148068

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.234	0.765	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.15	177	226	0.784	0.0000121	2701
Missense in Polyphen		33	55.197	0.59786		629
Synonymous	0.432	82	87.1	0.941	0.00000453	760
Loss of Function	2.78	4	16.0	0.250	6.88e-7	203

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000616	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000676	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transfers sialic acid from CMP-sialic acid to galactose- containing acceptor substrates. {ECO:0000269|PubMed:21081508, ECO:0000269|PubMed:23999306}.
• Pathway: N-Glycan biosynthesis - Homo sapiens (human);Other types of O-glycan biosynthesis - Homo sapiens (human);Globo Sphingolipid Metabolism;Post-translational protein modification;N-Glycan antennae elongation;N-glycan antennae elongation in the medial/trans-Golgi;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;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;N-Glycan biosynthesis;Termination of O-glycan biosynthesis;O-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.163

Intolerance Scores

• loftool: 0.120
• rvis_EVS: -0.78
• rvis_percentile_EVS: 12.77

Haploinsufficiency Scores

• pHI: 0.669
• hipred: Y
• hipred_score: 0.520
• ghis: 0.618

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.720

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: St6gal1
• Phenotype: hematopoietic system phenotype; normal phenotype; immune system phenotype; digestive/alimentary phenotype

Gene ontology

• Biological process: N-acetylneuraminate metabolic process;humoral immune response;O-glycan processing;protein N-linked glycosylation via asparagine;sialylation
• Cellular component: Golgi membrane;extracellular region;integral component of membrane;Golgi cisterna membrane
• Molecular function: beta-galactoside alpha-2,6-sialyltransferase activity;protein binding;sialyltransferase activity;protein homodimerization activity