IMPG2 p.Thr282Pro
c.844A>C · VCV3248835
Uncertain significance
No assertion criteria
Classification
Uncertain significance
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
AlphaMissense
likely benign
0.1943 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
1/3 damaging
AlphaMissense, REVEL, SaProt
Conditions
1
inherited retinal dystrophy
Computational evidence
| Protein change | ||
| AlphaMissense | 0.1943 | likely benign |
|---|---|---|
| REVEL | 0.097 | moderately benign-leaning |
| SaProt | LLR -12.16 | damaging |
| ⇒ SaProt calls this damaging; AlphaMissense and REVEL do not. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -0.11 | GERP -3.4, phastCons 0.81 |
| Regional constraint | o/e 0.98 | unconstrained · MANE · 93 kb · p 0.41 · regional, not allelic |
| Overall | ||
| CADD | 22.7 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
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
- IMPG2
- Protein
- p.Thr282Pro
- Coding
- c.844A>C
- MANE Select
- NM_016247
- Type
- single nucleotide variant
- Location
- chr3:101269558 (GRCh38)
- Gene constraint
- LOEUF 0.773 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.28
- Residue 282
- a UniProt-annotated variant site (in rp56); a UniProt-annotated variant site (in vmd5); the sea 1 domain
Similar variants
- IMPG2 p.Arg1088Ter Pathogenic/Likely pathogenic ★★ same condition
- IMPG2 p.Arg906Ter Pathogenic ★★ same condition
- IMPG2 p.Arg964Ter Pathogenic ★★ same condition
- IMPG2 p.Gln363Ter Pathogenic ★★ same condition
- IMPG2 p.Gln814Ter Pathogenic/Likely pathogenic ★★ same condition
- IMPG2 p.Gln856Ter Pathogenic ★★ same condition
- IMPG2 p.Glu1164Ter Pathogenic/Likely pathogenic ★★ same condition
- IMPG2 p.Glu226Ter 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/impg2-p-thr282pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown