CSF1R p.Ala599=
c.1797C>T · VCV3616535
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00381%, nfe)
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 7.3 | GERP -1.1, phastCons 1 |
| Overall | ||
| CADD | 11.05 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00381%
European (non-Finnish) · 45/1,180,010 alleles
Filtering AF
0.00291%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0026%
Overall
0.00291%
47/1,613,650 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00381% | 26,222 |
| East Asian | 0.00223% | 44,852 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,482 |
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.Ala599=
- Coding
- c.1797C>T
- MANE Select
- NM_001288705
- Type
- single nucleotide variant
- Location
- chr5:150061552 (GRCh38)
- Gene constraint
- LOEUF 0.485 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 78.08 · 26 PDB
- Residue 599
- the protein kinase domain; a β-strand; a UniProt-annotated variant site (in banddos); a UniProt-annotated variant site (in hdls1)
Similar variants
- CSF1R p.Ala599Pro Uncertain significance ★ ⚠ same residue
- CSF1R p.Ala599Val Uncertain significance ★ ⚠ same residue
- CSF1R p.Ala780Val Likely pathogenic ★★ same type
- CSF1R p.Ala781Val Pathogenic ★★ same type
- CSF1R p.Arg676Ter Pathogenic ★★ same type
- CSF1R p.Arg777Gln Pathogenic ★★ same type
- CSF1R p.Arg777Trp Pathogenic/Likely pathogenic ★★ same type
- CSF1R p.Arg782Cys Pathogenic/Likely pathogenic ★★ 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/csf1r-p-ala599 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown