FGD1 p.Pro162=
c.486C>A · rs759337933 · VCV2441407
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0378%, sas)
Conditions
1
Aarskog-Scott syndrome, X-linked
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 1.6 | GERP -3.7, phastCons 1 |
| Overall | ||
| CADD | 6.729 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0378%
South Asian · 18/47,567 alleles
Filtering AF
0.0244%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0202%
Overall
0.00167%
18/1,079,717 alleles · ultra-rare
exomes 17/969,957 · genomes 1/109,760 · 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.Pro162=
- Coding
- c.486C>A
- MANE Select
- NM_004463
- dbSNP
- rs759337933
- Type
- single nucleotide variant
- Location
- chrX:54470756 (GRCh38)
- Structure
- AlphaFold pLDDT 66.18
- Residue 162
- the 'disordered' region
Similar variants
- FGD1 p.Arg193Ter Pathogenic/Likely pathogenic ★★ same condition
- FGD1 p.Arg519Cys Likely pathogenic ★★ same condition
- FGD1 p.Arg522His Pathogenic/Likely pathogenic ★★ same condition
- FGD1 p.Arg610Gln Pathogenic/Likely pathogenic ★★ same condition
- FGD1 p.Arg656Ter Pathogenic ★★ same condition
- FGD1 p.Arg910Ter Pathogenic/Likely pathogenic ★★ same condition
- FGD1 p.Arg408Trp Uncertain significance ★★ same condition
- FGD1 p.Arg883Trp 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-pro162 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown