GNAS p.Ser96=
c.288C>T · VCV3346622
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000847%, nfe)
Conditions
1
GNAS-related disorder
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 1.8 | GERP 0.21, phastCons 1 |
| Overall | ||
| CADD | 8.565 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000847%
European (non-Finnish) · 10/1,179,986 alleles
Filtering AF
0.000429%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000312%
Overall
0.00062%
10/1,613,522 alleles · very rare
exomes 10/1,461,244 · genomes 0/152,278 · 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
- GNAS
- Protein
- p.Ser96=
- Coding
- c.288C>T
- MANE Select
- NM_000516 · reported on NM_016592
- Type
- single nucleotide variant
- Location
- chr20:58840394 (GRCh38)
- Gene constraint
- LOEUF 0.302 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 59.47 · 200 PDB
- Residue 96
- the 'disordered' region; the g-alpha domain; an α-helix
Similar variants
- GNAS p.Pro96Ala Uncertain significance ★ ⚠ same residue
- GNAS p.Pro96Ser Uncertain significance ⚠ same residue
- GNAS p.Ser96Ala Uncertain significance same residue
- GNAS p.Lys96Glu Likely pathogenic ★ same residue
- GNAS p.Ala102Val Pathogenic/Likely pathogenic ★★ same condition
- GNAS p.Arg165His Pathogenic/Likely pathogenic ★★ same condition
- GNAS p.Arg201Cys Pathogenic/Likely pathogenic ★★ same condition
- GNAS p.Arg258Gln Pathogenic/Likely pathogenic ★★ same condition
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/gnas-p-ser96 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown