FGD1 p.Ser92=
c.276T>G · rs2522741347 · VCV3067587
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,186,837)
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 3.8 | GERP -0.41, phastCons 1 |
| Overall | ||
| CADD | 12.39 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,186,837). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- FGD1
- Protein
- p.Ser92=
- Coding
- c.276T>G
- MANE Select
- NM_004463
- dbSNP
- rs2522741347
- Type
- single nucleotide variant
- Location
- chrX:54495157 (GRCh38)
- Structure
- AlphaFold pLDDT 66.18
- Residue 92
- the 'disordered' region
Similar variants
- FGD1 p.Ser92_Tyr93insTer Pathogenic ★ same residue
- 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
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-ser92 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown