IMPG1 p.Ser487=
c.1461T>C · rs1405322605 · VCV3027856
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0245%, 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 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.16 | GERP -0.23 |
| Overall | ||
| CADD | 1.55 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0245%
East Asian · 11/44,872 alleles
Filtering AF
0.0137%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0106%
Overall
0.000682%
11/1,613,992 alleles · ultra-rare
exomes 11/1,461,682 · genomes 0/152,310 · joint denominator
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
- IMPG1
- Protein
- p.Ser487=
- Coding
- c.1461T>C
- MANE Select
- NM_001563
- dbSNP
- rs1405322605
- Type
- single nucleotide variant
- Location
- chr6:75950925 (GRCh38)
- Gene constraint
- LOEUF 1.217 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 59.26
Similar variants
- IMPG1 c.498-1G>C Likely pathogenic ★★ same condition
- IMPG1 p.Trp126Ter Pathogenic/Likely pathogenic ★★ same condition
- IMPG1 p.Arg580Cys Uncertain significance ★★ same condition
- IMPG1 p.Glu695Lys Uncertain significance ★★ ⚠ same condition
- IMPG1 p.His337Arg Uncertain significance ★★ ⚠ same condition
- IMPG1 p.Leu268Ile Uncertain significance ★★ ⚠ same condition
- IMPG1 p.Lys282Asn Uncertain significance ★★ ⚠ same condition
- IMPG1 p.Met57Val Uncertain significance ★★ ⚠ 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/impg1-p-ser487 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown