ST3GAL1

Chr 8

ST3 beta-galactoside alpha-2,3-sialyltransferase 1

Also known as: Gal-NAc6S, SIAT4A, SIATFL, ST3GalA, ST3GalA.1, ST3GalIA, 1, ST3O

NCBI Gene: 6482 ENSG00000008513 UniProt: Q11201 OMIM: 607187

The ST3GAL1 protein is a sialyltransferase that catalyzes the transfer of sialic acid to galactose-containing glycoproteins and glycolipids, playing a critical role in terminal sialylation of mucin-type O-glycans and regulation of CD8+ T cell survival. Mutations cause autosomal recessive intellectual disability with seizures, developmental delay, and T cell immunodeficiency. The gene shows moderate constraint against loss-of-function variants (LOEUF 0.495), consistent with its essential role in glycosylation and immune function.

OMIM ResearchSummary from RefSeq, UniProt

The protein encoded by this gene is a type II membrane protein that catalyzes the transfer of sialic acid from CMP-sialic acid to galactose-containing substrates. The encoded protein is normally found in the Golgi but can be proteolytically processed to a soluble form. Correct glycosylation of the encoded protein may be critical to its sialyltransferase activity. This protein, which is a member of glycosyltransferase family 29, can use the same acceptor substrates as does sialyltransferase 4B. Two transcript variants encoding the same protein have been found for this gene. Other transcript variants may exist, but have not been fully characterized yet. [provided by RefSeq, Jul 2008]

OMIM ResearchGenerating clinical summary…

LOEUF 0.49

Clinical Summary— ST3GAL1

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Population Constraint (gnomAD)

Moderately constrained gene (pLI 0.58) — some intolerance to loss-of-function variants.

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ClinVar Variants

37 VUS of 58 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

0.49LOEUF

pLI 0.583

Z-score 2.97

OE 0.19 (0.09–0.49)

Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?

1.30Z-score

OE missense 0.75 (0.66–0.85)

161 obs / 214.5 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.19 (0.09–0.49)

0≤0.351.4

Missense OE?0.75 (0.66–0.85)

0≤0.61.4

Synonymous OE?0.96

0≤1.21.6

LoF obs/exp: 3 / 15.7Missense obs/exp: 161 / 214.5Syn Z: 0.31

ClinVar Variant Classifications

58 submitted variants in ClinVar

ClinVar

Classification Summary

VUS37

Likely Benign3

Benign3

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	0	0	0
Likely Pathogenic	0	0	0	0
VUS	37	0	0	37
Likely Benign	2	1	0	3
Benign	1	0	2	3
Total	40	1	2	43

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

53 pathogenic / likely-pathogenic (of 60) ClinVar copy-number / structural variants overlap ST3GAL1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →