IPO11 p.Leu112=
c.336C>G · rs34933123 · VCV768002
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.19%, afr)
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 0.73 | GERP -3.2, phastCons 1 |
| Overall | ||
| CADD | 4.131 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.19%
African / African-American · 2,395/75,024 alleles
Filtering AF
3.09%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.04%
Overall
0.167%
2,701/1,614,056 alleles · low-frequency
exomes 1,311/1,461,806 · genomes 1,390/152,250 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.19% | 31 |
| Remaining individualsnot grpmax-eligible | 0.229% | 437 |
| Admixed American | 0.225% | 445 |
| Middle Eastern | 0.148% | 674 |
| South Asian | 0.00549% | 18,213 |
| European (non-Finnish) | 0.00119% | 84,284 |
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
- IPO11
- Protein
- p.Leu112=
- Coding
- c.336C>G
- MANE Select
- NM_016338
- dbSNP
- rs34933123
- Type
- single nucleotide variant
- Location
- chr5:62451753 (GRCh38)
- Gene constraint
- LOEUF 0.598 · pLI 0.10 (gnomAD)
- Structure
- AlphaFold pLDDT 93.53
Similar variants
- IPO11 p.Thr409Ala Uncertain significance ★★ ⚠ same type
- IPO11 p.Ala726= Benign ★★ same type
- IPO11 p.Asn260Asp Benign ★★ same type
- IPO11 p.Leu246= Benign ★★ same type
- IPO11 p.Leu799= Benign ★★ same type
- IPO11 p.Ala110Val Uncertain significance ★ ⚠ same type
- IPO11 p.Ala332Thr Uncertain significance ★ ⚠ same type
- IPO11 p.Ala452Ser 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/ipo11-p-leu112 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown