SETD2 p.Glu1985del
c.5949_5951del · rs2107638020 · VCV1184104
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
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 0.41 | phastCons 0.99 |
Population frequency
dbSNP / gnomAD
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- SETD2
- Protein
- p.Glu1985del
- Coding
- c.5949_5951del
- MANE Select
- NM_014159
- dbSNP
- rs2107638020
- Type
- Deletion
- Location
- chr3:47083829 (GRCh38)
- Gene constraint
- LOEUF 0.176 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 43.81 · 43 PDB
- Residue 1985
- a UniProt-annotated variant site (in aml; uncertain significance; somatic mutation); a UniProt-annotated variant site (in all; uncertain significance; somatic mutation); the 'disordered' region
Similar variants
- SETD2 p.Glu1985Asp Uncertain significance ★ ⚠ same residue
- SETD2 c.5015+39_5015+40del Benign ★★ same type
- SETD2 c.6110-27_6110-26del Benign/Likely benign ★★ same type
- SETD2 p.Asn1856fs Likely pathogenic ★ same type
- SETD2 p.Gly1687fs Likely pathogenic ★ same type
- SETD2 p.Gly1726fs Pathogenic ★ same type
- SETD2 p.Lys1486fs Pathogenic ★ same type
- SETD2 p.Ser2238fs 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/setd2-p-glu1985del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown