FXYD2 p.Pro18=
c.54G>A · rs773683745 · VCV2176285
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0447%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -9.8 | GERP -3.7 |
| Overall | ||
| CADD | 1.757 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0447%
East Asian · 20/44,764 alleles
Filtering AF
0.0295%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0247%
Overall
0.00248%
40/1,610,472 alleles · ultra-rare
exomes 38/1,458,450 · genomes 2/152,022 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0447% | 2,238 |
| Middle Eastern | 0.0165% | 6,058 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,350 |
| European (non-Finnish) | 0.00144% | 69,363 |
| South Asian | 0.00111% | 89,898 |
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
- FXYD2
- Protein
- p.Pro18=
- Coding
- c.54G>A
- MANE Select
- NM_001680
- dbSNP
- rs773683745
- Type
- single nucleotide variant
- Location
- chr11:117822689 (GRCh38)
- Gene constraint
- LOEUF 1.239 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.04 · 4 PDB
Similar variants
- FXYD2 p.Arg27His Uncertain significance ★★ ⚠ same type
- FXYD2 p.Arg51Cys Uncertain significance ★★ ⚠ same type
- FXYD2 p.Arg59Lys Uncertain significance ★★ ⚠ same type
- FXYD2 c.139+279A>G Benign ★★ same type
- FXYD2 c.139+85T>C Benign ★★ same type
- FXYD2 c.139+9G>A Likely benign ★★ same type
- FXYD2 c.140-164A>G Benign ★★ same type
- FXYD2 c.19+227T>C Benign ★★ 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/fxyd2-p-pro18 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown