Is SET p.Asp211del (c.628GAT[1]) pathogenic?

SET p.Asp211del (c.628GAT[1]) is classified Uncertain significance in SET (ClinVar, Single submitter, 1 submitter; last evaluated 2023-09-22).

SET p.Asp211del

c.628GAT[1] · VCV4904858

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

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 1.3	GERP -0.96, phastCons 1

Variant & gene context

Gene: SET
Protein: p.Asp211del
Coding: c.628GAT[1]
MANE Select: NM_003011
Type: Microsatellite
Location: chr9:128693773 (GRCh38)
Gene constraint: LOEUF 0.167 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 78.62 · 3 PDB
Residue 211: a turn; the 'earmuff domain' region

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

Similar variants

SET p.Asp264del Likely benign ★★ same type
SET p.Glu243fs Pathogenic ★ same type
SET p.Ser140fs Pathogenic ★ same type
SET p.Ser148fs Pathogenic ★ same type
SET c.811-6_811-3del Uncertain significance ★ same type
SET p.Asp36del Uncertain significance ★ same type
SET p.Glu229del Uncertain significance ★ same type
SET c.810+65TA[11] Benign ★ 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-asp211del (accessed [today's date]).

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