CSF1R p.Pro54del
c.159_161del · VCV4768338
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00263%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.5 | GERP -4.4, phastCons 0.006 |
| Overall | ||
| CADD | 1.824 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00263%
European (non-Finnish) · 31/1,180,012 alleles
Filtering AF
0.00188%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00164%
Overall
0.00192%
31/1,614,002 alleles · very rare
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.Pro54del
- Coding
- c.159_161del
- MANE Select
- NM_001288705
- Type
- Deletion
- Location
- chr5:150080913 (GRCh38)
- Gene constraint
- LOEUF 0.485 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 78.08 · 26 PDB
- Residue 54
- a disulfide bond; the ig-like c2-type 1 domain; an α-helix
Similar variants
- CSF1R p.Pro54Arg Uncertain significance ★ ⚠ same residue
- CSF1R p.Pro54= Likely benign ★ same residue
- CSF1R p.Pro54Ser Likely benign ★ same residue
- CSF1R p.Arg931_Ser939del Uncertain significance ★★ same type
- CSF1R p.Ser929_Ser935del Uncertain significance ★★ same type
- CSF1R c.2655-18_2655-16del Likely benign ★★ same type
- CSF1R c.1969+115_1969+116del Pathogenic ★ same type
- CSF1R p.Gln426fs 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-pro54del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown