PDCD10 p.Ile63del
c.183CAT[1] · rs1559953989 · VCV590671
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.2 | GERP -2.9, phastCons 1 |
Population frequency
dbSNP / gnomAD
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- PDCD10
- Protein
- p.Ile63del
- Coding
- c.183CAT[1]
- MANE Select
- NM_007217
- dbSNP
- rs1559953989
- Type
- Microsatellite
- Location
- chr3:167697089 (GRCh38)
- Gene constraint
- LOEUF 0.924 · pLI 0.64 (gnomAD)
- Structure
- AlphaFold pLDDT 90.82 · 10 PDB
- Residue 63
- an α-helix
Similar variants
- PDCD10 c.269_270delAG Likely pathogenic ★★ same type
- PDCD10 c.557+4_557+7del Pathogenic/Likely pathogenic ★★ same type
- PDCD10 p.Arg124fs Pathogenic ★★ same type
- PDCD10 p.Met92fs Pathogenic ★ same type
- PDCD10 p.Ile49del Uncertain significance ★ same type
- PDCD10 c.395+203_395+205del Benign ★ 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/pdcd10-p-ile63del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown