SETBP1 p.Pro1529=
c.4587C>T · VCV3690265
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 9.12e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.9 | GERP -3.1 |
| Overall | ||
| CADD | 1.035 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
9.12e-05%
European (non-Finnish) · 1/1,096,698 alleles
Overall
6.95e-05%
1/1,438,932 alleles · very rare
exomes 1/1,289,130 · genomes 0/149,802 · joint denominator
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- SETBP1
- Protein
- p.Pro1529=
- Coding
- c.4587C>T
- MANE Select
- NM_015559
- Type
- single nucleotide variant
- Location
- chr18:45063494 (GRCh38)
- Gene constraint
- LOEUF 0.143 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 43.30
- Residue 1529
- the 'disordered' region; the '3 x 8 aa tandem repeats of p-p-l-p-p-p-p-p' region
Similar variants
- SETBP1 p.Pro1529Ser Uncertain significance ★ ⚠ same residue
- SETBP1 p.Pro1529del Uncertain significance ★ same residue
- SETBP1 p.Pro1529dup Uncertain significance ★ same residue
- SETBP1 p.Arg530Ter Pathogenic ★★ same type
- SETBP1 p.Arg544Ter Pathogenic/Likely pathogenic ★★ same type
- SETBP1 p.Arg589Ter Pathogenic ★★ same type
- SETBP1 p.Arg625Ter Pathogenic ★★ same type
- SETBP1 p.Arg626Ter 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/setbp1-p-pro1529 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown