ROR1 p.Val648=
c.1944C>T · rs747850753 · VCV2779085
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00666%, amr)
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 -1.6 | GERP -7.9 |
| Overall | ||
| CADD | 0.966 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00666%
Admixed American · 4/60,028 alleles
Filtering AF
0.00225%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00135%
Overall
0.000372%
6/1,614,200 alleles · very rare
exomes 6/1,461,882 · genomes 0/152,318 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00666% | 15,007 |
| European (non-Finnish) | 0.000169% | 590,019 |
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
- ROR1
- Protein
- p.Val648=
- Coding
- c.1944C>T
- MANE Select
- NM_005012
- dbSNP
- rs747850753
- Type
- single nucleotide variant
- Location
- chr1:64177985 (GRCh38)
- Gene constraint
- LOEUF 0.326 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 69.17 · 5 PDB
- Residue 648
- the protein kinase domain
Similar variants
- ROR1 p.Ala596Ser Uncertain significance ★★ ⚠ same type
- ROR1 p.Ala833Ser Uncertain significance ★★ ⚠ same type
- ROR1 p.Ala923Gly Uncertain significance ★★ ⚠ same type
- ROR1 p.Ala923Thr Uncertain significance ★★ ⚠ same type
- ROR1 p.Ala935Val Uncertain significance ★★ ⚠ same type
- ROR1 p.Arg25His Uncertain significance ★★ ⚠ same type
- ROR1 p.Arg429Gln Uncertain significance ★★ same type
- ROR1 p.Arg474Cys 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/ror1-p-val648 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown