ENOX2 p.Leu396=
c.1188C>T · rs770298882 · VCV764769
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.046%, mid)
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 -6.1 | GERP -4.1 |
| Overall | ||
| CADD | 0.188 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.046%
Middle Eastern · 2/4,352 alleles
Filtering AF
0.0262%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0222%
Overall
0.00248%
30/1,208,345 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.046% | 2,176 |
| South Asian | 0.0388% | 2,578 |
| East Asian | 0.00296% | 33,752 |
| Remaining individualsnot grpmax-eligible | 0.0021% | 47,581 |
| European (non-Finnish) | 0.000448% | 223,462 |
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
- ENOX2
- Protein
- p.Leu396=
- Coding
- c.1188C>T
- MANE Select
- NM_006375
- dbSNP
- rs770298882
- Type
- single nucleotide variant
- Location
- chrX:130637352 (GRCh38)
- Structure
- AlphaFold pLDDT 77.86
Similar variants
- ENOX2 c.1129+6G>A Benign ★★ same type
- ENOX2 c.-38-6023T>G Uncertain significance ★ ⚠ same type
- ENOX2 p.Arg129His Uncertain significance ★ ⚠ same type
- ENOX2 p.Arg139His Uncertain significance ★ ⚠ same type
- ENOX2 p.Arg156His Uncertain significance ★ ⚠ same type
- ENOX2 p.Arg190His Uncertain significance ★ ⚠ same type
- ENOX2 p.Arg190Leu Uncertain significance ★ ⚠ same type
- ENOX2 p.Arg208His Uncertain significance ★ ⚠ 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/enox2-p-leu396 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown