GPT2 p.Pro125=
c.375C>T · rs2548966808 · VCV3045890
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
GPT2-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 1.3 | GERP 0.73, phastCons 1 |
| Overall | ||
| CADD | 12.77 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- GPT2
- Protein
- p.Pro125=
- Coding
- c.375C>T
- MANE Select
- NM_133443
- dbSNP
- rs2548966808
- Type
- single nucleotide variant
- Location
- chr16:46900723 (GRCh38)
- Gene constraint
- LOEUF 0.677 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.89 · 1 PDB
- Residue 125
- a β-strand
Disease context
GPT2-related disorder
Similar variants
- GPT2 c.333+1G>A Likely pathogenic ★ same condition
- 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
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-pro125 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown