IMPG2 p.Asp1189=
c.3567C>T · rs764568010 · VCV1661128
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00667%, amr)
Conditions
1
inherited retinal dystrophy
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.26 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.71 | GERP -5.2 |
| Overall | ||
| CADD | 2.066 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00667%
Admixed American · 4/59,970 alleles
Filtering AF
0.00226%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00135%
Overall
0.00161%
26/1,612,764 alleles · very rare
exomes 23/1,460,774 · genomes 3/151,990 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00667% | 14,993 |
| East Asian | 0.00446% | 22,435 |
| South Asian | 0.00439% | 22,754 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,191 |
| African / African-American | 0.00267% | 37,412 |
| European (non-Finnish) | 0.00102% | 98,333 |
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
- IMPG2
- Protein
- p.Asp1189=
- Coding
- c.3567C>T
- MANE Select
- NM_016247
- dbSNP
- rs764568010
- Type
- single nucleotide variant
- Location
- chr3:101229446 (GRCh38)
- Gene constraint
- LOEUF 0.773 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.28
- Residue 1189
- a UniProt-annotated variant site (in rp56); a UniProt-annotated variant site (in vmd5)
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-asp1189 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown