FOXG1 p.Pro486=
c.1458T>C · rs2138662412 · VCV1148030
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
FOXG1 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 4.4 | GERP -1.4, phastCons 1 |
| Overall | ||
| CADD | 10.49 | PHRED · no single calibrated threshold — expert panels disagree |
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
- FOXG1
- Protein
- p.Pro486=
- Coding
- c.1458T>C
- MANE Select
- NM_005249
- dbSNP
- rs2138662412
- Type
- single nucleotide variant
- Location
- chr14:28768737 (GRCh38)
- Gene constraint
- LOEUF 0.36 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 58.79 · 1 PDB
- Residue 486
- a UniProt-annotated variant site (in rttcv)
Disease context
FOXG1 disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor FOXG1 syndrome (Orphanet):
- Onset
- Neonatal
Similar variants
- FOXG1 p.Pro486Ser Uncertain significance ★ ⚠ same residue
- FOXG1 p.Arg230Leu Likely pathogenic ★★★ same condition
- FOXG1 p.Asn187Lys Pathogenic ★★★ same condition
- FOXG1 p.Asn236Asp Likely pathogenic ★★★ same condition
- FOXG1 p.Gly224Ser Likely pathogenic ★★★ same condition
- FOXG1 p.Gly250Ser Likely pathogenic ★★★ same condition
- FOXG1 p.Gly267Ser Pathogenic ★★★ same condition
- FOXG1 p.Ile207Thr 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/foxg1-p-pro486 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown