Is ST3GAL3 p.Pro288= (c.864C>T) pathogenic?

ST3GAL3 p.Pro288= (c.864C>T) is classified Likely benign in ST3GAL3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-01-30). Absent from gnomAD v4.1; Associated with early-infantile DEE.

What condition is associated with ST3GAL3 p.Pro288= (c.864C>T)?

ST3GAL3 p.Pro288= (c.864C>T) is associated with early-infantile DEE (ClinVar).

How common is ST3GAL3 p.Pro288= (c.864C>T) in the general population?

ST3GAL3 p.Pro288= (c.864C>T) is absent from gnomAD v4.1 (gnomAD).

ST3GAL3 p.Pro288=

c.864C>T · rs2528472671 · VCV2802342

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

early-infantile DEE

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.243	benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.082	GERP -1.9, phastCons 0.93
Overall
CADD	9.101	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: ST3GAL3
Protein: p.Pro288=
Coding: c.864C>T
MANE Select: NM_006279
dbSNP: rs2528472671
Type: single nucleotide variant
Location: chr1:43920523 (GRCh38)
Gene constraint: LOEUF 0.573 · pLI 0.48 (gnomAD)
Structure: AlphaFold pLDDT 90.87
Residue 288: a disulfide bond

Full ST3GAL3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

early-infantile DEE — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ST3GAL3 c.166+1G>A Pathogenic/Likely pathogenic ★★ same condition
ST3GAL3 p.Arg261Ter Pathogenic/Likely pathogenic ★★ same condition
ST3GAL3 c.118+5G>A Uncertain significance ★★ same condition
ST3GAL3 c.397+6T>G Uncertain significance ★★ same condition
ST3GAL3 p.Ala281Thr Uncertain significance ★★ ⚠ same condition
ST3GAL3 p.Arg115Leu Uncertain significance ★★ ⚠ same condition
ST3GAL3 p.Arg147His Uncertain significance ★★ ⚠ same condition
ST3GAL3 p.Arg159Cys Uncertain significance ★★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/st3gal3-p-pro288 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown