GNAT2 p.Pro288=
c.864A>C · VCV3648469
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 -2.2 | GERP -4.2 |
| Overall | ||
| CADD | 5.229 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- GNAT2
- Protein
- p.Pro288=
- Coding
- c.864A>C
- MANE Select
- NM_001377295
- Type
- single nucleotide variant
- Location
- chr1:109603961 (GRCh38)
- Gene constraint
- LOEUF 1.176 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.21 · 2 PDB
- Residue 288
- the g-alpha domain
Similar variants
- GNAT2 p.Pro288Thr Uncertain significance ★ ⚠ same residue
- GNAT2 p.Arg105Ter Pathogenic/Likely pathogenic ★★ same type
- GNAT2 p.Arg161Ter Pathogenic ★★ same type
- GNAT2 p.Arg313Ter Pathogenic ★★ same type
- GNAT2 p.Gln58Ter Pathogenic/Likely pathogenic ★★ same type
- GNAT2 c.118+5G>A Uncertain significance ★★ same type
- GNAT2 c.590+6T>C Uncertain significance ★★ same type
- GNAT2 c.-53-78G>A 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/gnat2-p-pro288 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown