NAA15 p.Ala808=
c.2424C>T · VCV3606434
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00134%, afr)
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 2.2 | GERP -0.5, phastCons 1 |
| Overall | ||
| CADD | 11.33 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00134%
African / African-American · 1/74,864 alleles
Filtering AF
0.000615%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000474%
Overall
0.000868%
14/1,613,714 alleles · very rare
exomes 13/1,461,666 · genomes 1/152,048 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00134% | 74,864 |
| European (non-Finnish) | 0.0011% | 90,762 |
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
- NAA15
- Protein
- p.Ala808=
- Coding
- c.2424C>T
- MANE Select
- NM_057175
- Type
- single nucleotide variant
- Location
- chr4:139387907 (GRCh38)
- Gene constraint
- LOEUF 0.438 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 89.66 · 12 PDB
- Residue 808
- an α-helix; a UniProt-annotated variant site (in mrd50); the 'interaction with hypk' region
Similar variants
- NAA15 p.Ala808Val Uncertain significance ★ ⚠ same residue
- NAA15 c.1087+2T>G Pathogenic ★★ same type
- NAA15 c.1410+1G>A Pathogenic/Likely pathogenic ★★ same type
- NAA15 c.1539+1G>A Pathogenic/Likely pathogenic ★★ same type
- NAA15 c.1753+1G>T Pathogenic/Likely pathogenic ★★ same type
- NAA15 c.1947+1G>A Pathogenic/Likely pathogenic ★★ same type
- NAA15 c.908-2A>G Pathogenic ★★ same type
- NAA15 p.Ala585Thr Likely pathogenic ★★ ⚠ 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/naa15-p-ala808 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown