CSF1R p.Pro510=
c.1530G>A · VCV3358844
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00989%, sas)
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 -9.1 | GERP -4.2 |
| Overall | ||
| CADD | 0.217 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00989%
South Asian · 9/91,012 alleles
Filtering AF
0.00514%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00376%
Overall
0.0013%
21/1,612,536 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00989% | 10,112 |
| African / African-American | 0.00267% | 37,454 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,446 |
| European (non-Finnish) | 0.000763% | 131,082 |
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.Pro510=
- Coding
- c.1530G>A
- MANE Select
- NM_001288705
- Type
- single nucleotide variant
- Location
- chr5:150068311 (GRCh38)
- Gene constraint
- LOEUF 0.485 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 78.08 · 26 PDB
- Residue 510
- a UniProt-annotated variant site (in banddos)
Similar variants
- CSF1R p.Pro510Leu Benign/Likely benign ★★ same residue
- CSF1R p.Pro510Ala Benign ★ same residue
- 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
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-pro510 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown