NAXE p.Glu71=
c.213G>A · rs777720826 · VCV755239
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0022%, sas)
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 4.9 | GERP 2.4, phastCons 1 |
| Overall | ||
| CADD | 12.64 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0022%
South Asian · 2/91,084 alleles
Filtering AF
0.000365%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000137%
Overall
0.000186%
3/1,614,140 alleles · very rare
exomes 2/1,461,888 · genomes 1/152,252 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0022% | 45,542 |
| European (non-Finnish) | 8.47e-05% | 1,180,058 |
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
- NAXE
- Protein
- p.Glu71=
- Coding
- c.213G>A
- MANE Select
- NM_144772
- dbSNP
- rs777720826
- Type
- single nucleotide variant
- Location
- chr1:156592131 (GRCh38)
- Gene constraint
- LOEUF 1.079 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.71
- Residue 71
- a UniProt-annotated variant site (found in a patient with progressive myoclonus epilepsy and developmental delay; uncertain significance); the yjef n-terminal domain
Similar variants
- NAXE c.664+2T>A Likely pathogenic ★★ same type
- NAXE p.Ser43Ter Pathogenic ★★ same type
- NAXE p.Arg197Gln Uncertain significance ★★ ⚠ same type
- NAXE p.Arg254Cys Uncertain significance ★★ same type
- NAXE p.Glu64Ala Uncertain significance ★★ ⚠ same type
- NAXE p.Leu86Pro Uncertain significance ★★ ⚠ same type
- NAXE p.Ser79Arg Uncertain significance ★★ ⚠ same type
- NAXE p.Val68Leu 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/naxe-p-glu71 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown