GNAT2 p.Ser44=
c.132A>G · VCV3619736
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00144%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · T>G here scores Δ0.35 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.61 | GERP -4.2, phastCons 0.055 |
| Overall | ||
| CADD | 11.6 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00144%
European (non-Finnish) · 17/1,179,778 alleles
Filtering AF
0.000878%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000718%
Overall
0.00105%
17/1,613,880 alleles · very rare
exomes 17/1,461,578 · genomes 0/152,302 · joint denominator
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
- GNAT2
- Protein
- p.Ser44=
- Coding
- c.132A>G
- MANE Select
- NM_001377295
- Type
- single nucleotide variant
- Location
- chr1:109610494 (GRCh38)
- Gene constraint
- LOEUF 1.176 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.21 · 2 PDB
- Residue 44
- a binding site; the g-alpha domain; the 'g1 motif' region
Similar variants
- 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
- GNAT2 p.Ala152Thr 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-ser44 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown