NAT1 p.Ile3=
c.9T>C · VCV4899646
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00102%, 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 -3.4 | |
| Overall | ||
| CADD | 5.555 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00102%
European (non-Finnish) · 12/1,178,748 alleles
Filtering AF
0.000543%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000429%
Overall
0.000744%
12/1,611,912 alleles · very rare
exomes 9/1,459,724 · genomes 3/152,188 · joint denominator
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
- NAT1
- Protein
- p.Ile3=
- Coding
- c.9T>C
- MANE Select
- NM_000662
- Type
- single nucleotide variant
- Location
- chr8:18222056 (GRCh38)
- Gene constraint
- LOEUF 1.906 · pLI 0.15 (gnomAD)
- Structure
- AlphaFold pLDDT 98.20 · 2 PDB
- Residue 3
- an α-helix
Similar variants
- NAT1 p.Val149Ile Benign ★★ same type
- NAT1 p.Arg127Cys Uncertain significance ★ ⚠ same type
- NAT1 p.Arg127His Uncertain significance ★ ⚠ same type
- NAT1 p.Arg197Gly Uncertain significance ★ ⚠ same type
- NAT1 p.Asn272Ser Uncertain significance ★ ⚠ same type
- NAT1 p.Asn39Lys Uncertain significance ★ ⚠ same type
- NAT1 p.Asp142Tyr Uncertain significance ★ ⚠ same type
- NAT1 p.Asp179Asn 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/nat1-p-ile3 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown