CSF1R p.Arg753Gln
c.2258G>A · rs560352241 · VCV352135
Computational evidence
| Protein change | ||
| AlphaMissense | 0.0666 | likely benign |
|---|---|---|
| REVEL | 0.089 | moderately benign-leaning |
| SaProt | LLR -4.02 | tolerated |
| ⇒ AlphaMissense, REVEL and SaProt all call this tolerated. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.1 | GERP -4.3 |
| Regional constraint | o/e 1.05 | unconstrained · MANE · 2,496 bp · p 0.56 · regional, not allelic |
| Overall | ||
| CADD | 9.526 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.299% | 335 |
| Middle Eastern | 0.0498% | 2,007 |
| Remaining individualsnot grpmax-eligible | 0.0176% | 5,682 |
| African / African-American | 0.004% | 25,010 |
| East Asian | 0.00223% | 44,884 |
| European (non-Finnish) | 0.00144% | 69,412 |
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
- CSF1R
- Protein
- p.Arg753Gln
- Coding
- c.2258G>A
- MANE Select
- NM_001288705
- dbSNP
- rs560352241
- Type
- single nucleotide variant
- Location
- chr5:150057348 (GRCh38)
- Gene constraint
- LOEUF 0.485 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 78.08 · 26 PDB
- Residue 753
- the protein kinase domain; an α-helix; a UniProt-annotated variant site (in banddos)
Similar variants
- CSF1R p.Arg753Trp Conflicting classifications of pathogenicity ★ ⚠ same residue
- CSF1R p.Arg777Gln Pathogenic ★★ same condition
- CSF1R p.Arg777Trp Pathogenic/Likely pathogenic ★★ same condition
- CSF1R p.Arg782Cys Pathogenic/Likely pathogenic ★★ same condition
- CSF1R p.Gln642Ter Pathogenic/Likely pathogenic ★★ same condition
- CSF1R p.Gly589Arg Pathogenic/Likely pathogenic ★★ same condition
- CSF1R p.Ile794Thr Pathogenic/Likely pathogenic ★★ same condition
- CSF1R p.Arg710Cys Uncertain significance ★★ ⚠ same condition
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/csf1r-p-arg753gln (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown