IMPG2 p.Ser1151=
c.3453A>C · rs767843952 · VCV2961032
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00834%, amr)
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 -2.8 | GERP -4 |
| Overall | ||
| CADD | 2.203 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00834%
Admixed American · 5/59,988 alleles
Filtering AF
0.00323%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00207%
Overall
0.00031%
5/1,613,898 alleles · very rare
exomes 4/1,461,716 · genomes 1/152,182 · 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
- IMPG2
- Protein
- p.Ser1151=
- Coding
- c.3453A>C
- MANE Select
- NM_016247
- dbSNP
- rs767843952
- Type
- single nucleotide variant
- Location
- chr3:101229560 (GRCh38)
- Gene constraint
- LOEUF 0.773 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.28
- Residue 1151
- 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-ser1151 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown