PDGFRB p.Arg685=
c.2055C>A · VCV4684869
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00153%, 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 1.2 | GERP -1.2, phastCons 1 |
| Overall | ||
| CADD | 7.905 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00153%
European (non-Finnish) · 18/1,179,884 alleles
Filtering AF
0.000953%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000787%
Overall
0.00118%
19/1,613,658 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00153% | 65,549 |
| African / African-American | 0.00133% | 74,942 |
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.Arg685=
- Coding
- c.2055C>A
- MANE Select
- NM_002609
- Type
- single nucleotide variant
- Location
- chr5:150123170 (GRCh38)
- Gene constraint
- LOEUF 0.504 · pLI 0.94 (gnomAD)
- Structure
- AlphaFold pLDDT 72.96 · 9 PDB
- Residue 685
- the protein kinase domain
Similar variants
- PDGFRB p.Arg685His Uncertain significance ★ ⚠ same residue
- PDGFRB p.Arg685Cys Benign ★ same residue
- PDGFRB p.Arg561Cys Pathogenic ★★ ⚠ same type
- PDGFRB p.Asn666His Pathogenic/Likely pathogenic ★★ same type
- PDGFRB p.Asn666Lys Pathogenic/Likely pathogenic ★★ same type
- PDGFRB p.Asn666Ser Pathogenic/Likely pathogenic ★★ same type
- PDGFRB p.Pro560Leu Pathogenic/Likely pathogenic ★★ same type
- PDGFRB p.Pro584Arg 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/pdgfrb-p-arg685 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown