NAXE p.Thr55=
c.165G>A · rs201370740 · VCV1600546
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.17%, eas)
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 -2.8 | GERP -4.8 |
| Overall | ||
| CADD | 2.172 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.17%
East Asian · 525/44,806 alleles
Filtering AF
1.09%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.06%
Overall
0.0348%
562/1,613,242 alleles · low-frequency
exomes 506/1,460,920 · genomes 56/152,322 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.17% | 85 |
| Remaining individualsnot grpmax-eligible | 0.0512% | 1,952 |
| South Asian | 0.0022% | 45,538 |
| Admixed American | 0.00167% | 60,008 |
| European (non-Finnish) | 0.00017% | 589,880 |
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.Thr55=
- Coding
- c.165G>A
- MANE Select
- NM_144772
- dbSNP
- rs201370740
- Type
- single nucleotide variant
- Location
- chr1:156591969 (GRCh38)
- Gene constraint
- LOEUF 1.079 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.71
- Residue 55
- a UniProt-annotated variant site (found in a patient with progressive myoclonus epilepsy and developmental delay; uncertain significance)
Similar variants
- NAXE p.Thr55Met Uncertain significance ★ ⚠ same residue
- 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
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-thr55 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown