CSF1R p.Lys357Ter
c.1069A>T · rs767475362 · VCV1333351
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
leukoencephalopathy, hereditary diffuse, with spheroids
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| NMD | predicted | premature termination codon in exon 6 of 21 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.4 | GERP -0.43 |
| Overall | ||
| CADD | 34.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CSF1R
- Protein
- p.Lys357Ter
- Coding
- c.1069A>T
- MANE Select
- NM_001288705
- dbSNP
- rs767475362
- Type
- single nucleotide variant
- Location
- chr5:150073314 (GRCh38)
- Gene constraint
- LOEUF 0.485 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 78.08 · 26 PDB
- Residue 357
- the ig-like c2-type 4 domain
Similar variants
- 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
- CSF1R p.Glu633Lys 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-lys357ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown