FGD1 p.Pro877=
c.2631G>A · rs370717352 · VCV1794059
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0193%, nfe)
Conditions
1
Inborn genetic diseases
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 -1.3, phastCons 1 |
| Overall | ||
| CADD | 3.639 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0193%
European (non-Finnish) · 173/894,777 alleles
Filtering AF
0.0169%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0161%
Overall
0.0151%
183/1,209,418 alleles · ultra-rare
exomes 170/1,096,894 · genomes 13/112,524 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0193% | 5,172 |
| Remaining individualsnot grpmax-eligible | 0.0147% | 6,795 |
| Admixed American | 0.00437% | 22,877 |
| African / African-American | 0.00174% | 57,382 |
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.Pro877=
- Coding
- c.2631G>A
- MANE Select
- NM_004463
- dbSNP
- rs370717352
- Type
- single nucleotide variant
- Location
- chrX:54446364 (GRCh38)
- Structure
- AlphaFold pLDDT 66.18
- Residue 877
- the ph 2 domain
Similar variants
- FGD1 p.Arg519Cys Likely pathogenic ★★ same condition
- FGD1 p.Arg153Trp Uncertain significance ★★ same condition
- FGD1 p.Arg281Gln Uncertain significance ★★ ⚠ same condition
- FGD1 p.Arg522Ser Uncertain significance ★★ ⚠ same condition
- FGD1 p.Arg723Trp Uncertain significance ★★ ⚠ same condition
- FGD1 p.Asp191Asn Uncertain significance ★★ ⚠ same condition
- FGD1 p.Glu812= Uncertain significance ★★ same condition
- FGD1 p.Glu953Lys 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-pro877 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown