CSF1R p.Ser139=
c.417G>A · rs61753457 · VCV768045
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.51%, afr)
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 -20 | GERP -3.6 |
| Overall | ||
| CADD | 0.236 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.51%
African / African-American · 1,135/75,046 alleles
Filtering AF
1.44%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.41%
Overall
0.0781%
1,261/1,613,848 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.51% | 66 |
| Remaining individualsnot grpmax-eligible | 0.123% | 812 |
| Admixed American | 0.0683% | 1,464 |
| South Asian | 0.0011% | 91,090 |
| European (non-Finnish) | 0.000593% | 168,577 |
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.Ser139=
- Coding
- c.417G>A
- MANE Select
- NM_001288705
- dbSNP
- rs61753457
- Type
- single nucleotide variant
- Location
- chr5:150080227 (GRCh38)
- Gene constraint
- LOEUF 0.485 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 78.08 · 26 PDB
- Residue 139
- a β-strand; a disulfide bond; the ig-like c2-type 2 domain
Similar variants
- 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
- CSF1R p.Gln481Ter 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-ser139 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown