FLAD1 p.Pro203=
c.609C>T · rs776874328 · VCV1529086
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00161%, 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 -1.5 | GERP -2.7 |
| Overall | ||
| CADD | 5.888 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00161%
European (non-Finnish) · 19/1,180,020 alleles
Filtering AF
0.00103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00083%
Overall
0.0013%
21/1,614,174 alleles · very rare
exomes 21/1,461,886 · genomes 0/152,288 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00161% | 62,106 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,512 |
| Finnishnot grpmax-eligible | 0.00156% | 64,032 |
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.Pro203=
- Coding
- c.609C>T
- MANE Select
- NM_025207
- dbSNP
- rs776874328
- Type
- single nucleotide variant
- Location
- chr1:154988341 (GRCh38)
- Gene constraint
- LOEUF 0.809 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.34 · 2 PDB
- Residue 203
- the 'fad diphosphatase' region; an α-helix
Similar variants
- 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
- FLAD1 p.Arg169His 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-pro203 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown