IMPG2 p.Ser403fs
c.1208_1218del · VCV3248992
Likely pathogenic
No assertion criteria
Classification
Likely pathogenic
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
inherited retinal dystrophy
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 11 of 19 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.28 | GERP -5.5, phastCons 0.001 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- IMPG2
- Protein
- p.Ser403fs
- Coding
- c.1208_1218del
- MANE Select
- NM_016247
- Type
- Deletion
- Location
- chr3:101253717 (GRCh38)
- Gene constraint
- LOEUF 0.773 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.28
- Residue 403
- a UniProt-annotated variant site (in rp56); a UniProt-annotated variant site (in vmd5)
Similar variants
- IMPG2 p.Ser804_Ala805insTer Pathogenic/Likely pathogenic ★★ same condition
- IMPG2 c.887+430_908+274del Likely pathogenic ★ same condition
- IMPG2 p.Gln1201fs Likely pathogenic ★ same condition
- IMPG2 p.Gln30fs Likely pathogenic ★ same condition
- IMPG2 p.Ser403Ter Pathogenic ★ same residue
- IMPG2 p.Tyr715fs Pathogenic ★ same condition
- IMPG2 p.Gly606fs Pathogenic same condition
- IMPG2 p.Arg1088Ter 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-ser403fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown