CSF1R p.Tyr886=
c.2658C>T · rs1361443175 · VCV750092
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.22 | acceptor loss, 3 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.86 | GERP -4.8 |
| Overall | ||
| CADD | 2.115 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/59,704 alleles
Overall
0.000137%
2/1,458,452 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 59,704 |
| European (non-Finnish) | 8.49e-05% | 1,178,220 |
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.Tyr886=
- Coding
- c.2658C>T
- MANE Select
- NM_001288705
- dbSNP
- rs1361443175
- Type
- single nucleotide variant
- Location
- chr5:150054427 (GRCh38)
- Gene constraint
- LOEUF 0.485 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 78.08 · 26 PDB
- Residue 886
- the protein kinase domain; an α-helix; a UniProt-annotated variant site (in banddos)
Similar variants
- CSF1R p.Tyr886His 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
- CSF1R p.Arg782His 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-tyr886 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown