FLAD1 p.Arg12=
c.36G>A · rs747083416 · VCV2871110
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00153%, 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 -0.51 | GERP -2.9 |
| Overall | ||
| CADD | 1.741 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00153%
European (non-Finnish) · 18/1,179,762 alleles
Filtering AF
0.000954%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000787%
Overall
0.00112%
18/1,613,666 alleles · very rare
exomes 17/1,461,478 · genomes 1/152,188 · 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
- FLAD1
- Protein
- p.Arg12=
- Coding
- c.36G>A
- MANE Select
- NM_025207
- dbSNP
- rs747083416
- Type
- single nucleotide variant
- Location
- chr1:154983730 (GRCh38)
- Gene constraint
- LOEUF 0.809 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.34 · 2 PDB
Similar variants
- FLAD1 p.Arg12Lys Uncertain significance ★ ⚠ same residue
- FLAD1 p.Arg148Ter Pathogenic ★★ same type
- FLAD1 p.Arg249Ter Pathogenic ★★ same type
- FLAD1 p.Arg530Cys Pathogenic/Likely pathogenic ★★ ⚠ same type
- FLAD1 p.Cys136Ter Pathogenic/Likely pathogenic ★★ same type
- FLAD1 c.1365-3A>G Uncertain significance ★★ same type
- FLAD1 p.Arg137Gln Uncertain significance ★★ ⚠ same type
- FLAD1 p.Arg137Trp 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/flad1-p-arg12 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown