IMPG2 p.Thr175=
c.525T>C · rs766687575 · VCV1646786
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0646%, eas)
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 · A>C here scores Δ0.27 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.7 | GERP -2.2, phastCons 0.96 |
| Overall | ||
| CADD | 8.044 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0646%
East Asian · 29/44,884 alleles
Filtering AF
0.0461%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0399%
Overall
0.00186%
30/1,613,160 alleles · ultra-rare
exomes 29/1,460,928 · genomes 1/152,232 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0646% | 1,548 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,450 |
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.Thr175=
- Coding
- c.525T>C
- MANE Select
- NM_016247
- dbSNP
- rs766687575
- Type
- single nucleotide variant
- Location
- chr3:101291487 (GRCh38)
- Gene constraint
- LOEUF 0.773 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.28
- Residue 175
- a UniProt-annotated variant site (in rp56)
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-thr175 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown