DDR2 p.Pro559=
c.1677C>T · rs1350936433 · VCV3053424
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
Conditions
1
DDR2-related disorder
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 0.57 | GERP 0.001, phastCons 0.99 |
| Overall | ||
| CADD | 11.45 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,034 alleles
Overall
6.19e-05%
1/1,614,210 alleles · very rare
exomes 1/1,461,884 · genomes 0/152,326 · 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
- DDR2
- Protein
- p.Pro559=
- Coding
- c.1677C>T
- MANE Select
- NM_006182
- dbSNP
- rs1350936433
- Type
- single nucleotide variant
- Location
- chr1:162772196 (GRCh38)
- Gene constraint
- LOEUF 0.375 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 76.57 · 5 PDB
Disease context
DDR2-related disorder
Similar variants
- DDR2 p.Arg341Ter Pathogenic/Likely pathogenic ★★ same condition
- DDR2 p.Ser460Leu Uncertain significance ⚠ same condition
- DDR2 c.*8A>G Likely benign same condition
- DDR2 p.Ile409= Likely benign same condition
- DDR2 p.Phe558= Likely benign same condition
- DDR2 p.Arg611Ter Pathogenic/Likely pathogenic ★★ same type
- DDR2 p.Arg752Cys Likely pathogenic ★★ same type
- DDR2 p.Leu610Pro Pathogenic/Likely 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/ddr2-p-pro559 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown