ATIC p.Ser338=
c.1014T>C · rs201424787 · VCV730029
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0648%, eas)
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 -1.2 | GERP -3.4, phastCons 0.001 |
| Overall | ||
| CADD | 6.67 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0648%
East Asian · 29/44,780 alleles
Filtering AF
0.0462%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.04%
Overall
0.00267%
43/1,608,360 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0648% | 1,544 |
| Remaining individualsnot grpmax-eligible | 0.0209% | 4,796 |
| African / African-American | 0.00133% | 74,946 |
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.Ser338=
- Coding
- c.1014T>C
- MANE Select
- NM_004044
- dbSNP
- rs201424787
- Type
- single nucleotide variant
- Location
- chr2:215336040 (GRCh38)
- Gene constraint
- LOEUF 1.044 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 97.46 · 5 PDB
- Residue 338
- the 'aicar formyltransferase' region; a β-strand
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-ser338 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown