ATIC p.Gly481=
c.1443A>G · rs112288749 · VCV1600148
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.8%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.007 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · A>T here scores Δ0.28 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP -0.049 | GERP -4.8, phastCons 0.04 |
| Overall | ||
| CADD | 7.003 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.8%
European (non-Finnish) · 33,090/1,180,026 alleles
Filtering AF
2.78%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.77%
Overall
2.32%
37,422/1,614,178 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 2.8% | 36 |
| Finnishnot grpmax-eligible | 2.51% | 40 |
| Remaining individualsnot grpmax-eligible | 1.9% | 53 |
| Ashkenazi Jewishnot grpmax-eligible | 1.11% | 90 |
| Admixed American | 0.846% | 118 |
| Middle Eastern | 0.775% | 129 |
| African / African-American | 0.401% | 249 |
| South Asian | 0.382% | 262 |
| East Asian | 0.00668% | 14,962 |
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.Gly481=
- Coding
- c.1443A>G
- MANE Select
- NM_004044
- dbSNP
- rs112288749
- Type
- single nucleotide variant
- Location
- chr2:215346881 (GRCh38)
- Gene constraint
- LOEUF 1.044 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 97.46 · 5 PDB
- Residue 481
- the 'aicar formyltransferase' region
Similar variants
- 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.Ile491Val 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-gly481 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown