SETBP1 p.Asp353Val
c.1058_1059delinsTC · rs2145095402 · VCV1199493
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
Conditions
2
Schinzel-Giedion syndrome
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 9.4 | GERP 1.6, phastCons 1 |
| Regional constraint | o/e 1.09 | unconstrained · MANE · 249 kb · p 0.047 · regional, not allelic |
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
- SETBP1
- Protein
- p.Asp353Val
- Coding
- c.1058_1059delinsTC
- MANE Select
- NM_015559
- dbSNP
- rs2145095402
- Type
- Indel
- Location
- chr18:44950398 (GRCh38)
- Gene constraint
- LOEUF 0.143 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 43.30
- Residue 353
- the 'disordered' region
Similar variants
- SETBP1 p.Asp353Gly Uncertain significance ★ ⚠ same residue
- SETBP1 p.Asp353His Uncertain significance ★ ⚠ same residue
- SETBP1 p.Asp353= Likely benign ★ same residue
- SETBP1 p.Asn1225_Glu1227delinsThrLysLeuLeuArgGln Uncertain significance same condition
- SETBP1 p.Arg530Ter Pathogenic ★★ same condition
- SETBP1 p.Arg544Ter Pathogenic/Likely pathogenic ★★ same condition
- SETBP1 p.Arg589Ter Pathogenic ★★ same condition
- SETBP1 p.Arg625Ter 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/setbp1-p-asp353val (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown