CSF1R p.Val31=
c.93C>T · rs41424646 · VCV1166659
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.168%, amr)
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 -6.6 | GERP -4.4 |
| Overall | ||
| CADD | 0.044 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.168%
Admixed American · 101/60,018 alleles
Filtering AF
0.142%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.132%
Overall
0.0321%
518/1,614,056 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.168% | 594 |
| African / African-American | 0.127% | 790 |
| Middle Eastern | 0.0825% | 1,212 |
| Remaining individualsnot grpmax-eligible | 0.0368% | 2,717 |
| European (non-Finnish) | 0.0241% | 4,155 |
| South Asian | 0.00988% | 10,118 |
| Finnishnot grpmax-eligible | 0.00156% | 64,046 |
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.Val31=
- Coding
- c.93C>T
- MANE Select
- NM_001288705
- dbSNP
- rs41424646
- Type
- single nucleotide variant
- Location
- chr5:150080981 (GRCh38)
- Gene constraint
- LOEUF 0.485 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 78.08 · 26 PDB
- Residue 31
- the ig-like c2-type 1 domain; a β-strand
Similar variants
- CSF1R p.Val31Asp Uncertain significance ★ ⚠ same residue
- 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
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-val31 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown