FAR1 p.Arg480=
c.1440C>T · rs567066123 · VCV710940
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0867%, 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 0.41 | GERP 1.2, phastCons 0.99 |
| Overall | ||
| CADD | 9.026 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0867%
Admixed American · 52/59,968 alleles
Filtering AF
0.0679%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0611%
Overall
0.00422%
68/1,612,448 alleles · ultra-rare
exomes 49/1,460,448 · genomes 19/152,000 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0867% | 1,153 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,608 |
| European (non-Finnish) | 0.00102% | 98,232 |
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.Arg480=
- Coding
- c.1440C>T
- MANE Select
- NM_032228
- dbSNP
- rs567066123
- Type
- single nucleotide variant
- Location
- chr11:13728666 (GRCh38)
- Gene constraint
- LOEUF 0.595 · pLI 0.57 (gnomAD)
- Structure
- AlphaFold pLDDT 94.13
- Residue 480
- a UniProt-annotated variant site (in cspsd; increased ether lipid biosynthetic process in patient cells; increased far1 protein levels in patient cells due to impaired down-regulation by plasmalogen); a UniProt-annotated variant site (in cspsd); 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 p.Arg480Cys Pathogenic/Likely pathogenic ★★ ⚠ same residue
- FAR1 p.Arg480His Pathogenic/Likely pathogenic ★★ same residue
- FAR1 p.Arg480Leu Pathogenic ★★ same residue
- FAR1 p.Arg480Ser Likely pathogenic ★ same residue
- FAR1 c.-7-2A>G Likely 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
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-arg480 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown