FGF14 p.Phe54=
c.162C>T · rs764122877 · VCV2793311
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0516%, amr)
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 4.9 | GERP 1.5, phastCons 1 |
| Overall | ||
| CADD | 14.04 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0516%
Admixed American · 31/60,036 alleles
Filtering AF
0.0374%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0325%
Overall
0.00229%
37/1,613,960 alleles · ultra-rare
exomes 37/1,461,638 · genomes 0/152,322 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0516% | 1,937 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,625 |
| South Asian | 0.0022% | 45,545 |
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
- FGF14
- Protein
- p.Phe54=
- Coding
- c.162C>T
- MANE Select
- NM_004115
- dbSNP
- rs764122877
- Type
- single nucleotide variant
- Location
- chr13:101916484 (GRCh38)
- Gene constraint
- LOEUF 0.482 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 79.77
Similar variants
- FGF14 p.Phe54fs Likely pathogenic ★ same residue
- FGF14 c.408+1G>A Likely pathogenic ★★ same type
- FGF14 p.Ala90Gly Uncertain significance ★★ ⚠ same type
- FGF14 p.Arg186Ter Uncertain significance ★★ same type
- FGF14 p.Arg207Gln Uncertain significance ★★ ⚠ same type
- FGF14 p.Arg59Gly Uncertain significance ★★ same type
- FGF14 p.Gln117Arg Uncertain significance ★★ ⚠ same type
- FGF14 p.His86Asn 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/fgf14-p-phe54 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown