FGD1 p.Ser290=
c.870G>A · VCV4755236
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0036%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.3 | GERP -4.2 |
| Overall | ||
| CADD | 7.634 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0036%
South Asian · 2/55,572 alleles
Filtering AF
0.000597%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000223%
Overall
0.000166%
2/1,203,954 alleles · very rare
exomes 2/1,090,479 · genomes 0/113,475 · 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
- FGD1
- Protein
- p.Ser290=
- Coding
- c.870G>A
- MANE Select
- NM_004463
- Type
- single nucleotide variant
- Location
- chrX:54470247 (GRCh38)
- Structure
- AlphaFold pLDDT 66.18
- Residue 290
- the 'disordered' region
Similar variants
- FGD1 p.Arg193Ter Pathogenic/Likely pathogenic ★★ same type
- FGD1 p.Arg443Cys Pathogenic/Likely pathogenic ★★ same type
- FGD1 p.Arg519Cys Likely pathogenic ★★ same type
- FGD1 p.Arg522His Pathogenic/Likely pathogenic ★★ same type
- FGD1 p.Arg567Ter Pathogenic/Likely pathogenic ★★ same type
- FGD1 p.Arg610Gln Pathogenic/Likely pathogenic ★★ same type
- FGD1 p.Arg656Ter Pathogenic ★★ same type
- FGD1 p.Arg910Ter Pathogenic/Likely pathogenic ★★ 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/fgd1-p-ser290 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown