FGD1 p.Ser205=
c.615C>T · rs1358668677 · VCV3038061
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00358%, nfe)
Conditions
1
FGD1-related disorder
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 3.2 | GERP -0.08, phastCons 1 |
| Overall | ||
| CADD | 2.95 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00358%
European (non-Finnish) · 32/893,184 alleles
Filtering AF
0.00259%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00222%
Overall
0.00265%
32/1,206,084 alleles · very rare
exomes 32/1,095,154 · genomes 0/110,930 · 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.Ser205=
- Coding
- c.615C>T
- MANE Select
- NM_004463
- dbSNP
- rs1358668677
- Type
- single nucleotide variant
- Location
- chrX:54470627 (GRCh38)
- Structure
- AlphaFold pLDDT 66.18
- Residue 205
- a modified residue (phosphoserine); a UniProt-annotated variant site (in aas); the 'disordered' region
Disease context
FGD1-related disorder
Similar variants
- FGD1 p.Ser205Ile Uncertain significance ★ ⚠ same residue
- FGD1 p.Ser205Gly Likely benign ★ same residue
- FGD1 p.Arg443Cys Pathogenic/Likely pathogenic ★★ same condition
- FGD1 p.Arg567Ter Pathogenic/Likely pathogenic ★★ same condition
- FGD1 p.Arg610Gln Pathogenic/Likely pathogenic ★★ same condition
- FGD1 c.2046+1G>A Likely pathogenic ★ same condition
- FGD1 p.Cys761Phe Likely pathogenic ★ same condition
- FGD1 p.Cys782Trp Uncertain significance ★ ⚠ same condition
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-ser205 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown