IMPG2 p.Arg1200=
c.3600A>G · rs139944942 · VCV709664
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.214%, afr)
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 0.1 | GERP -2, phastCons 0.97 |
| Overall | ||
| CADD | 8.295 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.214%
African / African-American · 160/74,784 alleles
Filtering AF
0.187%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.177%
Overall
0.0119%
192/1,611,142 alleles · rare
exomes 107/1,459,582 · genomes 85/151,560 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.214% | 467 |
| Remaining individualsnot grpmax-eligible | 0.0289% | 3,460 |
| Admixed American | 0.0133% | 7,493 |
| South Asian | 0.0022% | 45,474 |
| European (non-Finnish) | 0.000339% | 294,854 |
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.Arg1200=
- Coding
- c.3600A>G
- MANE Select
- NM_016247
- dbSNP
- rs139944942
- Type
- single nucleotide variant
- Location
- chr3:101229413 (GRCh38)
- Gene constraint
- LOEUF 0.773 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.28
- Residue 1200
- a UniProt-annotated variant site (in rp56); a UniProt-annotated variant site (in vmd5)
Similar variants
- IMPG2 c.1240-1G>A Likely pathogenic ★★ same type
- IMPG2 c.1240-2A>G Pathogenic/Likely pathogenic ★★ same type
- IMPG2 c.502-2A>G Likely pathogenic ★★ same type
- IMPG2 c.583+1G>C Pathogenic/Likely pathogenic ★★ same type
- IMPG2 c.667-1G>A Pathogenic/Likely pathogenic ★★ same type
- IMPG2 c.828+1G>A Pathogenic/Likely pathogenic ★★ same type
- IMPG2 c.829-1G>T Pathogenic/Likely pathogenic ★★ same type
- IMPG2 c.829-2A>T Pathogenic/Likely pathogenic ★★ same type
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-arg1200 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown