CSF1R p.Leu331=
c.993G>A · rs768818550 · VCV1620863
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00585%, nfe)
Conditions
1
CSF1R-related disorder
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 -0.5 | GERP -3.2, phastCons 0.05 |
| Overall | ||
| CADD | 4.07 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00585%
European (non-Finnish) · 69/1,180,014 alleles
Filtering AF
0.0047%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00431%
Overall
0.00434%
70/1,614,002 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00585% | 17,102 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,488 |
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.Leu331=
- Coding
- c.993G>A
- MANE Select
- NM_001288705
- dbSNP
- rs768818550
- Type
- single nucleotide variant
- Location
- chr5:150073390 (GRCh38)
- Gene constraint
- LOEUF 0.485 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 78.08 · 26 PDB
- Residue 331
- the ig-like c2-type 4 domain
Similar variants
- CSF1R p.Arg777Gln Pathogenic ★★ same condition
- CSF1R p.Arg777Trp Pathogenic/Likely pathogenic ★★ same condition
- CSF1R p.Arg782Cys Pathogenic/Likely pathogenic ★★ same condition
- CSF1R p.Gln642Ter Pathogenic/Likely pathogenic ★★ same condition
- CSF1R p.Gly589Arg Pathogenic/Likely pathogenic ★★ same condition
- CSF1R p.Ile794Thr Pathogenic/Likely pathogenic ★★ same condition
- CSF1R p.Arg710Cys Uncertain significance ★★ ⚠ same condition
- CSF1R p.Asp439Ala Uncertain significance ★★ ⚠ 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-leu331 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown