Is SET p.Asp36del (c.105TGA[1]) pathogenic?

SET p.Asp36del (c.105TGA[1]) is classified Uncertain significance in SET (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-12). Associated with intellectual disability, autosomal dominant 58.

What condition is associated with SET p.Asp36del (c.105TGA[1])?

SET p.Asp36del (c.105TGA[1]) is associated with intellectual disability, autosomal dominant 58 (ClinVar).

SET p.Asp36del

c.105TGA[1] · VCV4540574

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

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 6.1	GERP 2, phastCons 1

Variant & gene context

Gene: SET
Protein: p.Asp36del
Coding: c.105TGA[1]
MANE Select: NM_003011
Type: Microsatellite
Location: chr9:128691201 (GRCh38)
Gene constraint: LOEUF 0.167 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 78.62 · 3 PDB
Residue 36: the 'disordered' region; the 'dimerization' 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.Asp36fs Pathogenic ★ same residue
SET p.Glu243fs Pathogenic ★ same condition
SET p.Ser140fs Pathogenic ★ same condition
SET p.Ser148fs Pathogenic ★ same condition
SET p.Thr85del Likely pathogenic 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

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-asp36del (accessed [today's date]).

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