CSF1R p.Ser935=
c.2805C>T · rs147476583 · VCV352124
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.11%, amr)
Conditions
1
leukoencephalopathy, hereditary diffuse, with spheroids
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.004 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.7 | GERP -1.1 |
| Overall | ||
| CADD | 0.747 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.11%
Admixed American · 665/59,810 alleles
Filtering AF
1.04%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.01%
Overall
0.0526%
848/1,611,690 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 1.11% | 90 |
| Ashkenazi Jewishnot grpmax-eligible | 0.115% | 870 |
| Remaining individualsnot grpmax-eligible | 0.0673% | 1,485 |
| Middle Eastern | 0.0661% | 1,514 |
| African / African-American | 0.032% | 3,122 |
| South Asian | 0.0176% | 5,674 |
| East Asian | 0.0112% | 8,949 |
| European (non-Finnish) | 0.00475% | 21,048 |
| Finnishnot grpmax-eligible | 0.00313% | 31,917 |
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.Ser935=
- Coding
- c.2805C>T
- MANE Select
- NM_001288705
- dbSNP
- rs147476583
- Type
- single nucleotide variant
- Location
- chr5:150054183 (GRCh38)
- Gene constraint
- LOEUF 0.485 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 78.08 · 26 PDB
- Residue 935
- the 'disordered' region; a UniProt-annotated variant site (in banddos)
Similar variants
- CSF1R p.Ser935Gly Uncertain significance ★ ⚠ same residue
- CSF1R p.Ala781Val Pathogenic ★★ same condition
- CSF1R p.Arg777Gln Pathogenic ★★ same condition
- CSF1R p.Arg777Trp Pathogenic/Likely pathogenic ★★ same condition
- CSF1R p.Arg782Cys Pathogenic/Likely pathogenic ★★ same condition
- CSF1R p.Arg782His Pathogenic/Likely pathogenic ★★ same condition
- CSF1R p.Gln481Ter Pathogenic ★★ same condition
- CSF1R p.Gln877Ter Likely pathogenic ★★ 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-ser935 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown