GNAT2 p.Ala5=
c.15C>A · rs372507125 · VCV2724090
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,608,520)
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 5.1 | GERP -0.014, phastCons 1 |
| Overall | ||
| CADD | 9.315 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,608,520). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- GNAT2
- Protein
- p.Ala5=
- Coding
- c.15C>A
- MANE Select
- NM_001377295
- dbSNP
- rs372507125
- Type
- single nucleotide variant
- Location
- chr1:109612856 (GRCh38)
- Gene constraint
- LOEUF 1.176 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.21 · 2 PDB
- Residue 5
- the 'disordered' region
Similar variants
- GNAT2 p.Ala5Val Conflicting classifications of pathogenicity ★ ⚠ 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-ala5 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown