IPO8 p.Arg1002=
c.3004C>A · rs151232989 · VCV2498550
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.223 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.3 | phastCons 0.94 |
| Overall | ||
| CADD | 8.231 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- IPO8
- Protein
- p.Arg1002=
- Coding
- c.3004C>A
- MANE Select
- NM_006390
- dbSNP
- rs151232989
- Type
- single nucleotide variant
- Location
- chr12:30631907 (GRCh38)
- Gene constraint
- LOEUF 0.575 · pLI 0.15 (gnomAD)
- Structure
- AlphaFold pLDDT 87.59
- Residue 1002
- a UniProt-annotated variant site (in viss; undetectable protein levels in either patient's fibroblasts or patient's epstein-barr virus-immortalized b cell lines); a UniProt-annotated variant site (in viss); a UniProt-annotated variant site (in viss; undetectable protein levels in patient's fibroblasts, although mrna levels seem unaffected)
Similar variants
- IPO8 p.Arg1002Trp Uncertain significance ★★ ⚠ same residue
- IPO8 p.Arg1002Gln Uncertain significance ★ ⚠ same residue
- IPO8 c.2900-1G>A Pathogenic/Likely pathogenic ★★ same type
- IPO8 p.Arg474Ter Pathogenic ★★ same type
- IPO8 p.Arg803Ter Pathogenic/Likely pathogenic ★★ same type
- IPO8 p.Trp259Ter Pathogenic ★★ same type
- IPO8 p.Ala877Asp Uncertain significance ★★ ⚠ same type
- IPO8 p.Ala941Val 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/ipo8-p-arg1002 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown