GPT2 p.Pro428=
c.1284A>G · rs150249768 · VCV718832
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.133%, nfe)
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 -12 | GERP -3.2 |
| Overall | ||
| CADD | 0.439 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.133%
European (non-Finnish) · 1,568/1,180,034 alleles
Filtering AF
0.127%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.125%
Overall
0.101%
1,636/1,614,122 alleles · rare
exomes 1,544/1,461,880 · genomes 92/152,242 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.133% | 753 |
| Remaining individualsnot grpmax-eligible | 0.0784% | 1,275 |
| Admixed American | 0.0133% | 7,501 |
| African / African-American | 0.012% | 8,329 |
| Finnishnot grpmax-eligible | 0.00312% | 32,022 |
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
- GPT2
- Protein
- p.Pro428=
- Coding
- c.1284A>G
- MANE Select
- NM_133443
- dbSNP
- rs150249768
- Type
- single nucleotide variant
- Location
- chr16:46924460 (GRCh38)
- Gene constraint
- LOEUF 0.677 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.89 · 1 PDB
Similar variants
- GPT2 p.Arg92Ter Pathogenic/Likely pathogenic ★★ same type
- GPT2 p.Arg110Trp Uncertain significance ★★ ⚠ same type
- GPT2 p.Gly324Glu Uncertain significance ★★ ⚠ same type
- GPT2 p.Ile197Val Uncertain significance ★★ ⚠ same type
- GPT2 p.Phe446Ser Uncertain significance ★★ ⚠ same type
- GPT2 p.Ser124Thr Uncertain significance ★★ ⚠ same type
- GPT2 p.Tyr182Phe Uncertain significance ★★ ⚠ same type
- GPT2 p.Val163Met 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/gpt2-p-pro428 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown