FAR1 p.Phe507=
c.1521C>T · rs147721857 · VCV1669811
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0112%, nfe)
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 0.83 | GERP 0.42, phastCons 0.99 |
| Overall | ||
| CADD | 8.688 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0112%
European (non-Finnish) · 132/1,178,478 alleles
Filtering AF
0.00962%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00905%
Overall
0.00837%
135/1,611,946 alleles · ultra-rare
exomes 128/1,459,972 · genomes 7/151,974 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0112% | 8,928 |
| African / African-American | 0.004% | 24,975 |
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
- FAR1
- Protein
- p.Phe507=
- Coding
- c.1521C>T
- MANE Select
- NM_032228
- dbSNP
- rs147721857
- Type
- single nucleotide variant
- Location
- chr11:13728747 (GRCh38)
- Gene constraint
- LOEUF 0.595 · pLI 0.57 (gnomAD)
- Structure
- AlphaFold pLDDT 94.13
- Residue 507
- the 'necessary and sufficient for pex19-mediated localization into peroxisome membrane' region; a UniProt-annotated variant site (in pfcrd; results in a complete loss of enzyme activity)
Similar variants
- FAR1 c.-7-2A>G Likely pathogenic ★★ same type
- FAR1 p.Arg480Cys Pathogenic/Likely pathogenic ★★ ⚠ same type
- FAR1 p.Arg480His Pathogenic/Likely pathogenic ★★ same type
- FAR1 p.Arg480Leu Pathogenic ★★ same type
- FAR1 c.546-13A>G Uncertain significance ★★ same type
- FAR1 p.Ala361Val Uncertain significance ★★ ⚠ same type
- FAR1 p.Arg133Gln Uncertain significance ★★ ⚠ same type
- FAR1 p.Arg160Cys 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/far1-p-phe507 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown