ATIC p.Thr55=
c.165G>A · rs754454433 · VCV2085654
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0495%, mid)
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 -11 | GERP -4.3 |
| Overall | ||
| CADD | 0.144 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0495%
Middle Eastern · 3/6,062 alleles
Filtering AF
0.0134%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00718%
Overall
0.00663%
107/1,614,028 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0495% | 2,021 |
| Remaining individualsnot grpmax-eligible | 0.0176% | 5,682 |
| Admixed American | 0.0117% | 8,573 |
| South Asian | 0.00659% | 15,178 |
| European (non-Finnish) | 0.00627% | 15,945 |
| African / African-American | 0.00533% | 18,758 |
| East Asian | 0.00446% | 22,429 |
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.Thr55=
- Coding
- c.165G>A
- MANE Select
- NM_004044
- dbSNP
- rs754454433
- Type
- single nucleotide variant
- Location
- chr2:215318175 (GRCh38)
- Gene constraint
- LOEUF 1.044 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 97.46 · 5 PDB
- Residue 55
- the mgs-like domain; the 'imp cyclohydrolase' region; an α-helix
Similar variants
- ATIC p.Thr55Met 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.Ile491Val Uncertain significance ★★ ⚠ same type
- ATIC p.Val154Ala 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-thr55 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown