PDGFRB p.Asp1034=
c.3102C>T · rs569140859 · VCV1585392
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 -0.82 | GERP -4.4 |
| Overall | ||
| CADD | 5.154 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Ashkenazi Jewishnot grpmax-eligible | 0.101% | 987 |
| African / African-Americangrpmax | 0.00934% | 10,708 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,496 |
| East Asian | 0.00669% | 14,945 |
| South Asian | 0.0033% | 30,345 |
| Admixed American | 0.00167% | 59,984 |
| European (non-Finnish) | 0.00119% | 84,249 |
Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.
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
- PDGFRB
- Protein
- p.Asp1034=
- Coding
- c.3102C>T
- MANE Select
- NM_002609
- dbSNP
- rs569140859
- Type
- single nucleotide variant
- Location
- chr5:150117653 (GRCh38)
- Gene constraint
- LOEUF 0.504 · pLI 0.94 (gnomAD)
- Structure
- AlphaFold pLDDT 72.96 · 9 PDB
- Residue 1034
- the 'disordered' region
Disease context
acroosteolysis-keloid-like lesions-premature aging syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsAlso linked: basal ganglia calcification, idiopathic, 4skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndromeinfantile myofibromatosis
For Acroosteolysis-keloid-like lesions-premature aging syndrome (Orphanet):
- Inheritance
- Autosomal dominant
- Onset
- Infancy, Neonatal
Similar variants
- PDGFRB p.Arg561Cys Pathogenic ★★ ⚠ same condition
- PDGFRB p.Asn666His Pathogenic/Likely pathogenic ★★ same condition
- PDGFRB p.Asn666Lys Pathogenic/Likely pathogenic ★★ same condition
- PDGFRB p.Asn666Ser Pathogenic/Likely pathogenic ★★ same condition
- PDGFRB p.Pro560Leu Pathogenic/Likely pathogenic ★★ same condition
- PDGFRB p.Pro584Arg Pathogenic ★★ same condition
- PDGFRB p.Trp566Arg Pathogenic ★★ same condition
- PDGFRB p.Ala513Thr 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/pdgfrb-p-asp1034 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown