IMPG1 p.Ser398=
c.1194T>G · VCV3683280
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00168%, amr)
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 0.33 | GERP -2.6, phastCons 0.001 |
| Overall | ||
| CADD | 0.637 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00168%
Admixed American · 1/59,616 alleles
Overall
6.2e-05%
1/1,612,782 alleles · very rare
exomes 1/1,460,442 · genomes 0/152,340 · 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.Ser398=
- Coding
- c.1194T>G
- MANE Select
- NM_001563
- Type
- single nucleotide variant
- Location
- chr6:76003892 (GRCh38)
- Gene constraint
- LOEUF 1.217 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 59.26
Similar variants
- IMPG1 p.Ser398Pro Uncertain significance ★ ⚠ same residue
- IMPG1 c.1212+2T>C Likely pathogenic ★★ same type
- IMPG1 c.1291+1G>T Pathogenic/Likely pathogenic ★★ same type
- IMPG1 c.1824+1G>A Pathogenic/Likely pathogenic ★★ same type
- IMPG1 c.498-1G>C Likely pathogenic ★★ same type
- IMPG1 c.807+1G>A Pathogenic/Likely pathogenic ★★ same type
- IMPG1 c.807+2T>A Pathogenic/Likely pathogenic ★★ same type
- IMPG1 p.Arg507Ter 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/impg1-p-ser398 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown