FGF23 p.Thr239=
c.717G>T · rs1865047897 · VCV1961456
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 0.15 | GERP -1.2 |
| Overall | ||
| CADD | 0.838 | 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
- FGF23
- Protein
- p.Thr239=
- Coding
- c.717G>T
- MANE Select
- NM_020638
- dbSNP
- rs1865047897
- Type
- single nucleotide variant
- Location
- chr12:4370382 (GRCh38)
- Gene constraint
- LOEUF 1.608 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.94 · 6 PDB
- Residue 239
- a UniProt-annotated variant site (in)
Similar variants
- FGF23 p.Thr239Met Benign ★★ same residue
- FGF23 p.Arg179Gln Pathogenic ★★ ⚠ same type
- FGF23 p.Arg179Trp Pathogenic/Likely pathogenic ★★ same type
- FGF23 p.Gln54His Likely pathogenic ★★ ⚠ same type
- FGF23 p.Gly123Trp Pathogenic/Likely pathogenic ★★ same type
- FGF23 p.Ser129Pro Pathogenic/Likely pathogenic ★★ same type
- FGF23 p.Ala202Val Uncertain significance ★★ ⚠ same type
- FGF23 p.Ala213Thr Uncertain significance ★★ ⚠ 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/fgf23-p-thr239 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown