CYP24A1 p.Phe14=
c.42C>T · VCV4766715
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0137%, sas)
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 1.7 | GERP -2.7, phastCons 1 |
| Overall | ||
| CADD | 7.811 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0137%
South Asian · 12/87,338 alleles
Filtering AF
0.00791%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00616%
Overall
0.000886%
14/1,580,860 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0137% | 7,278 |
| European (non-Finnish) | 0.000172% | 583,033 |
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
- CYP24A1
- Protein
- p.Phe14=
- Coding
- c.42C>T
- MANE Select
- NM_000782
- Type
- single nucleotide variant
- Location
- chr20:54173538 (GRCh38)
- Gene constraint
- LOEUF 1.507 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 89.03
Similar variants
- CYP24A1 p.Arg159Gln Pathogenic/Likely pathogenic ★★ same type
- CYP24A1 p.Arg159Trp Pathogenic/Likely pathogenic ★★ same type
- CYP24A1 p.Arg223Ter Pathogenic ★★ same type
- CYP24A1 p.Arg396Gln Pathogenic/Likely pathogenic ★★ same type
- CYP24A1 p.Arg396Trp Pathogenic/Likely pathogenic ★★ same type
- CYP24A1 p.Arg466Ter Pathogenic ★★ same type
- CYP24A1 p.Gln347Ter Pathogenic/Likely pathogenic ★★ same type
- CYP24A1 p.Gln442Ter Pathogenic/Likely pathogenic ★★ 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/cyp24a1-p-phe14 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown