ST3GAL6

Chr 3

ST3 beta-galactoside alpha-2,3-sialyltransferase 6

Also known as: SIAT10, ST3GALVI

NCBI Gene: 10402 ENSG00000064225 UniProt: Q9Y274 OMIM: 607156

This enzyme transfers sialic acid residues to terminal galactose on glycoproteins and glycolipids, synthesizing selectin ligands essential for neutrophil recruitment during inflammation and lymphocyte homing to lymph nodes. Biallelic mutations cause autosomal recessive intellectual disability with seizures and dysmorphic features, typically manifesting in infancy or early childhood. The gene shows very low constraint against loss-of-function variants, consistent with recessive inheritance requiring biallelic mutations for disease manifestation.

OMIM ResearchSummary from RefSeq, UniProt

The protein encoded by this gene is a member of the sialyltransferase family. Members of this family are enzymes that transfer sialic acid from the activated cytidine 5'-monophospho-N-acetylneuraminic acid to terminal positions on sialylated glycolipids (gangliosides) or to the N- or O-linked sugar chains of glycoproteins. This protein has high specificity for neolactotetraosylceramide and neolactohexaosylceramide as glycolipid substrates and may contribute to the formation of selectin ligands and sialyl Lewis X, a carbohydrate important for cell-to-cell recognition and a blood group antigen. [provided by RefSeq, Apr 2016]

OMIM ResearchGenerating clinical summary…

LOEUF 1.20

Clinical Summary— ST3GAL6

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

35 VUS of 43 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.20LOEUF

pLI 0.000

Z-score 0.93

OE 0.76 (0.50–1.20)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.91Z-score

OE missense 0.81 (0.70–0.93)

141 obs / 174.8 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.76 (0.50–1.20)

0≤0.351.4

Missense OE?0.81 (0.70–0.93)

0≤0.61.4

Synonymous OE?1.05

0≤1.21.6

LoF obs/exp: 14 / 18.3Missense obs/exp: 141 / 174.8Syn Z: -0.34

ClinVar Variant Classifications

43 submitted variants in ClinVar

ClinVar

Classification Summary

VUS35

Likely Benign1

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Total
Pathogenic	0	0
Likely Pathogenic	0	0
VUS	35	35
Likely Benign	1	1
Benign	0	0
Total	36	36

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

View in ClinVar →

10 pathogenic / likely-pathogenic (of 15) ClinVar copy-number / structural variants overlap ST3GAL6 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →