SETD5 p.Glu359=
c.1077G>A · rs2041379870 · VCV981663
Likely pathogenic
No assertion criteria
Classification
Likely pathogenic
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Chromatinopathy
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.73 | pathogenic-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.82 | donor loss · deltas |
| Pangolin | Δ0.73 | loss · gain 0.01 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 2, phastCons 1 |
| Overall | ||
| CADD | 21.8 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- SETD5
- Protein
- p.Glu359=
- Coding
- c.1077G>A
- MANE Select
- NM_001080517
- dbSNP
- rs2041379870
- Type
- single nucleotide variant
- Location
- chr3:9442245 (GRCh38)
- Gene constraint
- LOEUF 0.376 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 47.10
- Residue 359
- the set domain
Disease context
Chromatinopathy
Similar variants
- SETD5 p.Glu359Gly Uncertain significance ★ ⚠ same residue
- SETD5 p.Arg1174Ter Pathogenic/Likely pathogenic ★★ same condition
- SETD5 p.Arg445Ter Pathogenic ★★ same condition
- SETD5 p.Arg768Ter Pathogenic ★★ same condition
- SETD5 p.Gln1058Ter Pathogenic/Likely pathogenic ★★ same condition
- SETD5 p.Gln272Ter Pathogenic/Likely pathogenic ★★ same condition
- SETD5 p.Tyr391Cys Likely pathogenic ★★ same condition
- SETD5 p.Ala259Thr Uncertain significance ★★ ⚠ 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/setd5-p-glu359 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown