Is SET p.Asp247del (c.739_741del) pathogenic?

SET p.Asp247del (c.739741del) is classified Uncertain significance in SET (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-08-05). Associated with SET-related disorder.

What condition is associated with SET p.Asp247del (c.739_741del)?

SET p.Asp247del (c.739_741del) is associated with SET-related disorder (ClinVar).

SET p.Asp247del

c.739_741del · VCV3344904

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

Conditions

SET-related disorder

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 4.5	GERP 1.1, phastCons 1
Region caveats
Repeat context	tandem	GA-rich low complexity · ambiguous alignment · confidence, not pathogenicity

Variant & gene context

Gene: SET
Protein: p.Asp247del
Coding: c.739_741del
MANE Select: NM_003011
Type: Deletion
Location: chr9:128693971 (GRCh38)
Gene constraint: LOEUF 0.167 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 78.62 · 3 PDB
Residue 247: a UniProt-annotated variant site (in mrd58); the 'disordered' region

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

Disease context

SET-related disorder

Similar variants

SET c.664-5_664-4del Likely benign same condition
SET p.Gln39Ter Pathogenic ★ same condition
SET p.His196Arg Uncertain significance ★ ⚠ same condition
SET p.Asp202Gly Uncertain significance ⚠ same condition
SET p.Ser197= Likely benign same condition
SET p.Arg44fs Pathogenic/Likely pathogenic ★★ same type
SET c.493-3_504del Pathogenic ★ same type
SET p.Asp36fs Pathogenic ★ same type

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-asp247del (accessed [today's date]).

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