IMPG2 p.Ile689fs
c.2065del · VCV4963516
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
IMPG2-related disorders
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 13 of 19 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 4.3 | GERP -0.81, phastCons 0.98 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- IMPG2
- Protein
- p.Ile689fs
- Coding
- c.2065del
- MANE Select
- NM_016247
- Type
- Deletion
- Location
- chr3:101244266 (GRCh38)
- Gene constraint
- LOEUF 0.773 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.28
- Residue 689
- a UniProt-annotated variant site (in rp56); a UniProt-annotated variant site (in vmd5)
Disease context
IMPG2-related disorders
Similar variants
- IMPG2 p.Asn755_Tyr756insTer Pathogenic/Likely pathogenic ★★ same condition
- IMPG2 p.Glu914fs Pathogenic/Likely pathogenic ★★ same condition
- IMPG2 p.Phe437fs Pathogenic/Likely pathogenic ★★ same condition
- IMPG2 p.Ser804_Ala805insTer Pathogenic/Likely pathogenic ★★ same condition
- IMPG2 c.666+3_666+16del Likely pathogenic ★ same condition
- IMPG2 p.Asn953fs Likely pathogenic ★ same condition
- IMPG2 p.Asp195fs Likely pathogenic ★ same condition
- IMPG2 p.Gly897fs 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-ile689fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown