PDK3 p.Val193=
c.579G>A · rs1438877046 · VCV2660192
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000114%, nfe)
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 0.62 | GERP -4.7, phastCons 1 |
| Overall | ||
| CADD | 2.126 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000114%
European (non-Finnish) · 1/880,657 alleles
Overall
8.37e-05%
1/1,194,287 alleles · very rare
exomes 1/1,080,903 · genomes 0/113,384 · 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
- PDK3
- Protein
- p.Val193=
- Coding
- c.579G>A
- MANE Select
- NM_005391
- dbSNP
- rs1438877046
- Type
- single nucleotide variant
- Location
- chrX:24505282 (GRCh38)
- Structure
- AlphaFold pLDDT 91.32 · 5 PDB
- Residue 193
- the histidine kinase domain; an α-helix
Similar variants
- PDK3 p.Val193Leu Uncertain significance ★ ⚠ same residue
- PDK3 p.Val193Met Uncertain significance ★ ⚠ same residue
- PDK3 c.320+6T>C Uncertain significance ★★ same type
- PDK3 p.Ala360Val Uncertain significance ★★ ⚠ same type
- PDK3 p.Arg378Cys Uncertain significance ★★ same type
- PDK3 p.Asp188Asn Uncertain significance ★★ ⚠ same type
- PDK3 p.Ile113Thr Uncertain significance ★★ ⚠ same type
- PDK3 p.Leu112Pro 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/pdk3-p-val193 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown