ASPNAT p.Ala227=
c.681G>A · rs138913660 · VCV731692
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0616%, nfe)
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 -1.9 | GERP -4.7 |
| Overall | ||
| CADD | 8.546 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0616%
European (non-Finnish) · 727/1,179,930 alleles
Filtering AF
0.0579%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0564%
Overall
0.0506%
816/1,612,244 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0616% | 1,623 |
| African / African-American | 0.0559% | 1,787 |
| Remaining individualsnot grpmax-eligible | 0.0528% | 1,893 |
| Admixed American | 0.02% | 5,001 |
| East Asian | 0.00223% | 44,888 |
| South Asian | 0.0011% | 91,076 |
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
- ASPNAT
- Protein
- p.Ala227=
- Coding
- c.681G>A
- MANE Select
- NM_178557
- dbSNP
- rs138913660
- Type
- single nucleotide variant
- Location
- chr4:2063899 (GRCh38)
- Structure
- AlphaFold pLDDT 81.36
- Residue 227
- the n-acetyltransferase domain
Similar variants
- ASPNAT c.541+8C>T Benign ★★ same type
- ASPNAT p.Ala35= Likely benign ★★ same type
- ASPNAT p.Gly263= Likely benign ★★ same type
- ASPNAT p.Pro56= Likely benign ★★ same type
- ASPNAT p.Ala125Thr Uncertain significance ★ ⚠ same type
- ASPNAT p.Ala225Thr Uncertain significance ★ ⚠ same type
- ASPNAT p.Ala22Val Uncertain significance ★ ⚠ same type
- ASPNAT p.Ala255Thr 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/aspnat-p-ala227 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown