CSF1R p.Ala781=
c.2343G>A · rs55804445 · VCV2415885
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00801%, afr)
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 0.97 | GERP -4, phastCons 1 |
| Overall | ||
| CADD | 4.691 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00801%
African / African-American · 6/74,922 alleles
Filtering AF
0.00347%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00229%
Overall
0.00167%
27/1,614,024 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00801% | 12,487 |
| Finnishnot grpmax-eligible | 0.00312% | 32,005 |
| Admixed American | 0.00167% | 59,998 |
| European (non-Finnish) | 0.00153% | 65,558 |
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.Ala781=
- Coding
- c.2343G>A
- MANE Select
- NM_001288705
- dbSNP
- rs55804445
- Type
- single nucleotide variant
- Location
- chr5:150056318 (GRCh38)
- Gene constraint
- LOEUF 0.485 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 78.08 · 26 PDB
- Residue 781
- the protein kinase domain; an α-helix; a UniProt-annotated variant site (in banddos); a UniProt-annotated variant site (in hdls1); a UniProt-annotated variant site (in hdls1; impairs autophosphorylation upon stimulation with csf1)
Similar variants
- CSF1R p.Ala781Val Pathogenic ★★ same residue
- CSF1R p.Ala781Gly Uncertain significance ★ ⚠ same residue
- CSF1R p.Ala781Glu Pathogenic 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
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-ala781 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown