PDCD10 p.Leu33=
c.99A>G · rs369606517 · VCV1768874
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00134%, afr)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.108 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.25 | acceptor loss, 2 bp away · masked 0 · deltas |
| Constraint at this position | ||
| Conservation | phyloP 5.1 | GERP 2.3, phastCons 1 |
| Overall | ||
| CADD | 15.29 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00134%
African / African-American · 1/74,664 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000187%
3/1,601,940 alleles · very rare
exomes 1/1,449,742 · genomes 2/152,198 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00134% | 74,664 |
| European (non-Finnish) | 0.000171% | 585,007 |
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
- PDCD10
- Protein
- p.Leu33=
- Coding
- c.99A>G
- MANE Select
- NM_007217
- dbSNP
- rs369606517
- Type
- single nucleotide variant
- Location
- chr3:167704893 (GRCh38)
- Gene constraint
- LOEUF 0.924 · pLI 0.64 (gnomAD)
- Structure
- AlphaFold pLDDT 90.82 · 10 PDB
- Residue 33
- an α-helix
Similar variants
- PDCD10 p.Asn104Ser Uncertain significance ★★ ⚠ same condition
- PDCD10 p.Leu44Arg Uncertain significance ★★ ⚠ same condition
- PDCD10 p.Phe76Val Uncertain significance ★★ ⚠ same condition
- PDCD10 p.Tyr27Cys Uncertain significance ★★ ⚠ same condition
- PDCD10 p.Ala46= Likely benign ★★ same condition
- PDCD10 p.Phe127= Likely benign ★★ same condition
- PDCD10 p.Val72Leu Benign/Likely benign ★★ same condition
- PDCD10 p.Asn156Lys 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/pdcd10-p-leu33 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown