DDR2 p.Ser667=
c.2001C>T · rs758442995 · VCV746044
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00195%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.24 | GERP -0.82, phastCons 0.98 |
| Overall | ||
| CADD | 6.328 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00195%
European (non-Finnish) · 23/1,180,002 alleles
Filtering AF
0.0013%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00108%
Overall
0.00149%
24/1,614,080 alleles · very rare
exomes 24/1,461,834 · genomes 0/152,246 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00195% | 51,304 |
| African / African-American | 0.00133% | 75,012 |
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.Ser667=
- Coding
- c.2001C>T
- MANE Select
- NM_006182
- dbSNP
- rs758442995
- Type
- single nucleotide variant
- Location
- chr1:162775796 (GRCh38)
- Gene constraint
- LOEUF 0.375 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 76.57 · 5 PDB
- Residue 667
- the protein kinase domain; an α-helix
Similar variants
- DDR2 p.Arg341Ter Pathogenic/Likely pathogenic ★★ same type
- DDR2 p.Arg611Ter Pathogenic/Likely pathogenic ★★ same type
- DDR2 p.Arg752Cys Likely pathogenic ★★ same type
- DDR2 p.Leu610Pro Pathogenic/Likely pathogenic ★★ same type
- DDR2 c.1728+6T>C Uncertain significance ★★ same type
- DDR2 c.-27-11G>C Uncertain significance ★★ same type
- DDR2 c.*48A>G Uncertain significance ★★ same type
- DDR2 p.Arg128His Uncertain significance ★★ ⚠ 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-ser667 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown