ATIC p.Ile491=
c.1473C>T · VCV3616704
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000763%, 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 -4.5 | GERP -5.7 |
| Overall | ||
| CADD | 5.95 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000763%
European (non-Finnish) · 9/1,180,010 alleles
Filtering AF
0.000359%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00026%
Overall
0.000616%
9/1,461,862 alleles · very rare
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
- ATIC
- Protein
- p.Ile491=
- Coding
- c.1473C>T
- MANE Select
- NM_004044
- Type
- single nucleotide variant
- Location
- chr2:215346911 (GRCh38)
- Gene constraint
- LOEUF 1.044 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 97.46 · 5 PDB
- Residue 491
- the 'aicar formyltransferase' region; an α-helix
Similar variants
- ATIC p.Ile491Val Uncertain significance ★★ ⚠ same residue
- ATIC c.688+3A>G Uncertain significance ★★ same type
- ATIC p.Ala140Thr Uncertain significance ★★ ⚠ same type
- ATIC p.Ala183Glu Uncertain significance ★★ ⚠ same type
- ATIC p.Ala510Thr Uncertain significance ★★ ⚠ same type
- ATIC p.His584Arg Uncertain significance ★★ ⚠ same type
- ATIC p.Val154Ala Uncertain significance ★★ ⚠ same type
- FN1 p.Ala2470Pro 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/atic-p-ile491 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown