INPP5E p.Pro69=
c.207C>T · VCV3348509
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00174%, nfe)
Conditions
1
INPP5E-related disorder
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 2.8 | GERP -0.21, phastCons 0.99 |
| Overall | ||
| CADD | 7.697 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00174%
European (non-Finnish) · 20/1,147,944 alleles
Filtering AF
0.00114%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000925%
Overall
0.0013%
20/1,538,606 alleles · very rare
exomes 19/1,386,452 · genomes 1/152,154 · joint denominator
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
- INPP5E
- Protein
- p.Pro69=
- Coding
- c.207C>T
- MANE Select
- NM_019892
- Type
- single nucleotide variant
- Location
- chr9:136439213 (GRCh38)
- Structure
- AlphaFold pLDDT 88.46
Disease context
INPP5E-related disorder
Similar variants
- INPP5E p.Pro69Arg Uncertain significance ★ ⚠ same residue
- INPP5E c.937-2A>G Pathogenic/Likely pathogenic ★★ same condition
- INPP5E p.Arg435Gln Pathogenic/Likely pathogenic ★★ same condition
- INPP5E p.Arg435Trp Pathogenic/Likely pathogenic ★★ same condition
- INPP5E p.Arg557His Pathogenic/Likely pathogenic ★★ same condition
- INPP5E p.Tyr543Ter Pathogenic ★★ same condition
- INPP5E p.Val303Met Pathogenic/Likely pathogenic ★★ same condition
- INPP5E p.Arg351Cys Uncertain significance ★★ ⚠ same condition
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/inpp5e-p-pro69 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown