IMPG1 p.Asp423=
c.1269C>T · rs758038128 · VCV1156378
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00891%, eas)
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 -0.32 | GERP -3.3 |
| Overall | ||
| CADD | 3.856 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00891%
East Asian · 4/44,876 alleles
Filtering AF
0.00347%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00229%
Overall
0.00322%
52/1,613,266 alleles · very rare
exomes 43/1,461,112 · genomes 9/152,154 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00891% | 11,219 |
| Admixed American | 0.00834% | 11,993 |
| African / African-American | 0.00801% | 12,482 |
| Finnishnot grpmax-eligible | 0.00469% | 21,335 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,226 |
| European (non-Finnish) | 0.00263% | 38,046 |
| South Asian | 0.0011% | 91,058 |
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.Asp423=
- Coding
- c.1269C>T
- MANE Select
- NM_001563
- dbSNP
- rs758038128
- Type
- single nucleotide variant
- Location
- chr6:76002940 (GRCh38)
- Gene constraint
- LOEUF 1.217 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 59.26
Similar variants
- IMPG1 p.Asp423Glu Uncertain significance ★ ⚠ same residue
- IMPG1 p.Asp423Tyr 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
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-asp423 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown