Is SET p.Thr85del (c.250ACA[1]) pathogenic?

SET p.Thr85del (c.250ACA[1]) is classified Likely pathogenic in SET (ClinVar, No assertion criteria, 1 submitter). Associated with intellectual disability, autosomal dominant 58.

What condition is associated with SET p.Thr85del (c.250ACA[1])?

SET p.Thr85del (c.250ACA[1]) is associated with intellectual disability, autosomal dominant 58 (ClinVar).

SET p.Thr85del

c.250ACA[1] · VCV4819999

Likely pathogenic No assertion criteria

Classification

Likely pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

Conditions

intellectual disability, autosomal dominant 58

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.9	GERP 2, phastCons 1

Variant & gene context

Gene: SET
Protein: p.Thr85del
Coding: c.250ACA[1]
MANE Select: NM_003011
Type: Microsatellite
Location: chr9:128691975 (GRCh38)
Gene constraint: LOEUF 0.167 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 78.62 · 3 PDB
Residue 85: an α-helix; the 'earmuff domain' region

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

Disease context

intellectual disability, autosomal dominant 58 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SET p.Glu243fs Pathogenic ★ same condition
SET p.Ser140fs Pathogenic ★ same condition
SET p.Ser148fs Pathogenic ★ same condition
SET p.Asp36del Uncertain significance ★ same condition
SET c.663+5G>C Pathogenic ★★ same condition
SET p.Arg44fs Pathogenic/Likely pathogenic ★★ same condition
SET p.Gln69fs Pathogenic/Likely pathogenic ★★ same condition
SET p.His105Tyr Likely pathogenic ★★ 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/set-p-thr85del (accessed [today's date]).

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