GNAS p.Pro98=
c.294C>T · rs1800902 · VCV1205855
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Common
common (popmax 10.8%, afr) — too common for a highly-penetrant pathogenic allele
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 -0.82 | GERP -2.4, phastCons 0.009 |
| Overall | ||
| CADD | 11.53 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
10.8%
African / African-American · 8,101/74,978 alleles
Filtering AF
10.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 10.5%
Overall
3.3%
53,165/1,613,458 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 10.8% | 9 |
| South Asian | 4.09% | 24 |
| Remaining individualsnot grpmax-eligible | 3.52% | 28 |
| European (non-Finnish) | 3.1% | 32 |
| Middle Eastern | 2.89% | 35 |
| Admixed American | 1.92% | 52 |
| Ashkenazi Jewishnot grpmax-eligible | 1.4% | 72 |
| Finnishnot grpmax-eligible | 1.03% | 97 |
| East Asian | 0.357% | 280 |
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.Pro98=
- Coding
- c.294C>T
- MANE Select
- NM_000516 · reported on NM_016592
- dbSNP
- rs1800902
- Type
- single nucleotide variant
- Location
- chr20:58840400 (GRCh38)
- Gene constraint
- LOEUF 0.302 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 59.47 · 200 PDB
- Residue 98
- the 'disordered' region; the g-alpha domain; an α-helix
Similar variants
- GNAS c.139+1G>C Pathogenic ★★ same type
- GNAS c.139+2T>C Pathogenic ★★ same type
- GNAS c.312+5G>A Pathogenic ★★ same type
- GNAS c.432+1G>A Pathogenic ★★ same type
- GNAS c.433-2A>C Pathogenic/Likely pathogenic ★★ same type
- GNAS p.Ala102Thr Pathogenic/Likely pathogenic ★★ same type
- GNAS p.Ala102Val Pathogenic/Likely pathogenic ★★ same type
- GNAS p.Arg160Cys Pathogenic/Likely pathogenic ★★ 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/gnas-p-pro98 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown