FGF23 p.Ser29=
c.87C>T · rs1209745441 · VCV1581044
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.016 | GERP -3, phastCons 0.32 |
| Overall | ||
| CADD | 7.673 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,030 alleles
Overall
6.2e-05%
1/1,612,982 alleles · very rare
exomes 0/1,460,770 · genomes 1/152,212 · joint denominator
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
- FGF23
- Protein
- p.Ser29=
- Coding
- c.87C>T
- MANE Select
- NM_020638
- dbSNP
- rs1209745441
- Type
- single nucleotide variant
- Location
- chr12:4379496 (GRCh38)
- Gene constraint
- LOEUF 1.608 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.94 · 6 PDB
- Residue 29
- an α-helix
Similar variants
- 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
- FGF23 p.Ala236Pro 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-ser29 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown