ROR2 p.Pro590=
c.1770C>T · rs372398011 · VCV259430
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0329%, sas)
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 -8.8 | GERP -3.8 |
| Overall | ||
| CADD | 0.131 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0329%
South Asian · 30/91,078 alleles
Filtering AF
0.0237%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0205%
Overall
0.00589%
95/1,613,990 alleles · ultra-rare
exomes 89/1,461,794 · genomes 6/152,196 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0329% | 3,036 |
| European (non-Finnish) | 0.005% | 20,001 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,244 |
| Finnishnot grpmax-eligible | 0.00313% | 31,976 |
| African / African-American | 0.00267% | 37,474 |
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
- ROR2
- Protein
- p.Pro590=
- Coding
- c.1770C>T
- MANE Select
- NM_004560
- dbSNP
- rs372398011
- Type
- single nucleotide variant
- Location
- chr9:91724724 (GRCh38)
- Gene constraint
- LOEUF 0.543 · pLI 0.35 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 69.09 · 6 PDB
- Residue 590
- the protein kinase domain; an α-helix
Similar variants
- ROR2 p.Pro590Ser Uncertain significance ★ ⚠ same residue
- ROR2 c.175+1G>A Likely pathogenic ★★ same type
- ROR2 p.Arg119Ter Pathogenic ★★ same type
- ROR2 p.Arg397Ter Pathogenic ★★ same type
- ROR2 p.Arg442Ter Pathogenic ★★ same type
- ROR2 p.Arg528Ter Pathogenic/Likely pathogenic ★★ same type
- ROR2 c.175+3G>T Uncertain significance ★★ same type
- ROR2 c.-102G>T 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/ror2-p-pro590 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown