DDR2 p.Ser53=
c.159A>G · rs765197646 · VCV1627153
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0346%, afr)
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 -0.31 | GERP -4 |
| Overall | ||
| CADD | 8.526 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0346%
African / African-American · 26/75,042 alleles
Filtering AF
0.0242%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0208%
Overall
0.00205%
33/1,613,632 alleles · ultra-rare
exomes 19/1,461,284 · genomes 14/152,348 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0346% | 2,886 |
| Admixed American | 0.00667% | 15,002 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,232 |
| European (non-Finnish) | 8.48e-05% | 1,179,670 |
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.Ser53=
- Coding
- c.159A>G
- MANE Select
- NM_006182
- dbSNP
- rs765197646
- Type
- single nucleotide variant
- Location
- chr1:162753171 (GRCh38)
- Gene constraint
- LOEUF 0.375 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 76.57 · 5 PDB
- Residue 53
- the f5/8 type c domain
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-ser53 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown