FAR1 p.Leu413=
c.1237C>T · rs2500154247 · VCV2812271
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00017%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.22 | donor loss · deltas |
|---|---|---|
| Pangolin | Δ0.25 | loss · gain 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP -0.83, phastCons 0.98 |
| Overall | ||
| CADD | 7.806 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00017%
European (non-Finnish) · 2/1,175,762 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000125%
2/1,602,970 alleles · very rare
exomes 2/1,450,752 · genomes 0/152,218 · 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
- FAR1
- Protein
- p.Leu413=
- Coding
- c.1237C>T
- MANE Select
- NM_032228
- dbSNP
- rs2500154247
- Type
- single nucleotide variant
- Location
- chr11:13721839 (GRCh38)
- Gene constraint
- LOEUF 0.595 · pLI 0.57 (gnomAD)
- Structure
- AlphaFold pLDDT 94.13
- Residue 413
- 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-leu413 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown