IMPG2 p.His1073=
c.3219C>T · rs752500181 · VCV1115361
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.127%, sas)
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 -0.66 | GERP -5.5 |
| Overall | ||
| CADD | 7.686 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.127%
South Asian · 116/91,024 alleles
Filtering AF
0.109%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.101%
Overall
0.00831%
134/1,613,362 alleles · rare
exomes 129/1,461,742 · genomes 5/151,620 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.127% | 785 |
| Middle Eastern | 0.0165% | 6,060 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,497 |
| East Asian | 0.0067% | 14,934 |
| African / African-American | 0.00134% | 74,784 |
| European (non-Finnish) | 0.000678% | 147,483 |
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.His1073=
- Coding
- c.3219C>T
- MANE Select
- NM_016247
- dbSNP
- rs752500181
- Type
- single nucleotide variant
- Location
- chr3:101232795 (GRCh38)
- Gene constraint
- LOEUF 0.773 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.28
- Residue 1073
- a UniProt-annotated variant site (in rp56); a UniProt-annotated variant site (in vmd5); the egf-like 2 domain
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-his1073 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown