IMPG2 p.Ser839=
c.2517G>A · rs765258879 · VCV3027554
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00891%, 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 | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.2 | GERP -2.5, phastCons 1 |
| Overall | ||
| CADD | 11.71 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00891%
East Asian · 4/44,892 alleles
Filtering AF
0.00347%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00229%
Overall
0.00143%
23/1,614,024 alleles · very rare
exomes 19/1,461,854 · genomes 4/152,170 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00891% | 11,223 |
| African / African-American | 0.00801% | 12,484 |
| South Asian | 0.00329% | 30,359 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,490 |
| European (non-Finnish) | 0.000763% | 131,113 |
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.Ser839=
- Coding
- c.2517G>A
- MANE Select
- NM_016247
- dbSNP
- rs765258879
- Type
- single nucleotide variant
- Location
- chr3:101243814 (GRCh38)
- Gene constraint
- LOEUF 0.773 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.28
- Residue 839
- a UniProt-annotated variant site (in rp56); a UniProt-annotated variant site (in vmd5)
Similar variants
- IMPG2 p.Ser839Leu Uncertain significance ★★ ⚠ same residue
- 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
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-ser839 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown