INPPL1 p.Pro153=
c.459C>T · rs113871062 · VCV784198
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.67%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.3 | GERP -1.8 |
| Overall | ||
| CADD | 1.502 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.67%
African / African-American · 1,251/75,010 alleles
Filtering AF
1.59%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.56%
Overall
0.0893%
1,440/1,612,854 alleles · low-frequency
exomes 768/1,460,558 · genomes 672/152,296 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.67% | 60 |
| Remaining individualsnot grpmax-eligible | 0.191% | 525 |
| Admixed American | 0.0919% | 1,088 |
| Middle Eastern | 0.0496% | 2,016 |
| South Asian | 0.0055% | 18,183 |
| European (non-Finnish) | 0.000594% | 168,485 |
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
- INPPL1
- Protein
- p.Pro153=
- Coding
- c.459C>T
- MANE Select
- NM_001567
- dbSNP
- rs113871062
- Type
- single nucleotide variant
- Location
- chr11:72228788 (GRCh38)
- Gene constraint
- LOEUF 0.776 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.75 · 11 PDB
- Residue 153
- the 'disordered' region
Similar variants
- INPPL1 c.2213-2A>C Pathogenic/Likely pathogenic ★★ same type
- INPPL1 p.Arg649Ter Pathogenic/Likely pathogenic ★★ same type
- INPPL1 p.Arg949Ter Pathogenic ★★ same type
- INPPL1 c.2326+9C>T Uncertain significance ★★ same type
- INPPL1 c.3686+3G>T Uncertain significance ★★ same type
- INPPL1 c.754-3C>T Uncertain significance ★★ same type
- INPPL1 p.Ala1245Ser Uncertain significance ★★ ⚠ same type
- INPPL1 p.Ala212Thr 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/inppl1-p-pro153 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown