IPO9 p.Gln558=
c.1674G>A · rs61743350 · VCV791229
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.09%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.20 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 6.7 | GERP 1, phastCons 1 |
| Overall | ||
| CADD | 13.53 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.09%
African / African-American · 820/74,994 alleles
Filtering AF
1.03%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.01%
Overall
0.0574%
927/1,614,046 alleles · low-frequency
exomes 471/1,461,868 · genomes 456/152,178 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.09% | 91 |
| Remaining individualsnot grpmax-eligible | 0.0608% | 1,645 |
| Middle Eastern | 0.0495% | 2,021 |
| Admixed American | 0.035% | 2,857 |
| South Asian | 0.022% | 4,554 |
| European (non-Finnish) | 0.00212% | 47,201 |
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
- IPO9
- Protein
- p.Gln558=
- Coding
- c.1674G>A
- MANE Select
- NM_018085
- dbSNP
- rs61743350
- Type
- single nucleotide variant
- Location
- chr1:201866778 (GRCh38)
- Gene constraint
- LOEUF 0.31 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 88.37 · 7 PDB
- Residue 558
- an α-helix
Similar variants
- IPO9 p.Ala10Val Uncertain significance ★ ⚠ same type
- IPO9 p.Ala131Val Uncertain significance ★ ⚠ same type
- IPO9 p.Ala166Pro Uncertain significance ★ ⚠ same type
- IPO9 p.Ala342Gly Uncertain significance ★ ⚠ same type
- IPO9 p.Ala418Gly Uncertain significance ★ ⚠ same type
- IPO9 p.Ala425Thr Uncertain significance ★ ⚠ same type
- IPO9 p.Ala498Ser Uncertain significance ★ ⚠ same type
- IPO9 p.Ala508Asp Uncertain significance ★ 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/ipo9-p-gln558 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown