FMO4 p.Gln402=
c.1206A>G · rs45445497 · VCV722743
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.64%, eas)
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 -0.003 | GERP -2.3, phastCons 0.001 |
| Overall | ||
| CADD | 1.771 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.64%
East Asian · 733/44,828 alleles
Filtering AF
1.54%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.5%
Overall
0.0506%
817/1,613,134 alleles · low-frequency
exomes 708/1,460,848 · genomes 109/152,286 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.64% | 61 |
| Remaining individualsnot grpmax-eligible | 0.08% | 1,250 |
| South Asian | 0.0209% | 4,793 |
| Middle Eastern | 0.0165% | 6,058 |
| European (non-Finnish) | 0.00119% | 84,227 |
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
- FMO4
- Protein
- p.Gln402=
- Coding
- c.1206A>G
- MANE Select
- NM_002022
- dbSNP
- rs45445497
- Type
- single nucleotide variant
- Location
- chr1:171337381 (GRCh38)
- Gene constraint
- LOEUF 1.329 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.52
Similar variants
- FMO4 c.1180+3A>G Uncertain significance ★★ same type
- FMO4 p.Gly372Ser Likely benign ★★ same type
- FMO4 p.Leu221His Likely benign ★★ same type
- FMO4 p.Ser534Pro Benign ★★ same type
- FMO4 p.Ala159Asp Uncertain significance ★ ⚠ same type
- FMO4 p.Arg116Ser Uncertain significance ★ ⚠ same type
- FMO4 p.Arg186Cys Uncertain significance ★ ⚠ same type
- FMO4 p.Arg205Gln 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/fmo4-p-gln402 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown