PDK2 p.Ser42=
c.126C>T · rs11546968 · VCV791201
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.24%, 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 0.84 | GERP -4.4, phastCons 1 |
| Overall | ||
| CADD | 15.3 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.24%
African / African-American · 928/75,030 alleles
Filtering AF
1.17%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.14%
Overall
0.104%
1,671/1,613,758 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.24% | 81 |
| Middle Eastern | 0.297% | 337 |
| Admixed American | 0.198% | 504 |
| Remaining individualsnot grpmax-eligible | 0.149% | 672 |
| European (non-Finnish) | 0.0431% | 2,318 |
| South Asian | 0.00439% | 22,769 |
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
- PDK2
- Protein
- p.Ser42=
- Coding
- c.126C>T
- MANE Select
- NM_002611
- dbSNP
- rs11546968
- Type
- single nucleotide variant
- Location
- chr17:50097430 (GRCh38)
- Gene constraint
- LOEUF 0.92 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.16 · 38 PDB
Similar variants
- PDK2 p.Arg74= Benign ★★ same type
- PDK2 p.Ala337Thr Uncertain significance ★ ⚠ same type
- PDK2 p.Ala378Val Uncertain significance ★ ⚠ same type
- PDK2 p.Arg162Cys Uncertain significance ★ ⚠ same type
- PDK2 p.Arg291Gln Uncertain significance ★ ⚠ same type
- PDK2 p.Arg405Cys Uncertain significance ★ ⚠ same type
- PDK2 p.Asn69Lys Uncertain significance ★ ⚠ same type
- PDK2 p.Asp114Gly 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/pdk2-p-ser42 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown