PDXK p.Ser89=
c.267G>A · VCV4946398
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00267%, 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 -0.43 | GERP -3.6, phastCons 0.041 |
| Overall | ||
| CADD | 10.89 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00267%
African / African-American · 2/74,870 alleles
Filtering AF
0.000443%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000166%
Overall
0.000744%
12/1,613,378 alleles · very rare
exomes 11/1,461,256 · genomes 1/152,122 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00267% | 37,435 |
| East Asian | 0.00223% | 44,878 |
| South Asian | 0.0022% | 45,535 |
| Admixed American | 0.00167% | 59,988 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,462 |
| European (non-Finnish) | 0.000424% | 235,911 |
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
- PDXK
- Protein
- p.Ser89=
- Coding
- c.267G>A
- MANE Select
- NM_003681
- Type
- single nucleotide variant
- Location
- chr21:43743743 (GRCh38)
- Gene constraint
- LOEUF 0.597 · pLI 0.77 (gnomAD)
- Structure
- AlphaFold pLDDT 95.83 · 10 PDB
- Residue 89
- an α-helix
Similar variants
- PDXK p.Ala228Thr Pathogenic ★★ ⚠ same type
- PDXK p.Ala211Thr Uncertain significance ★★ ⚠ same type
- PDXK p.Ala37Val Uncertain significance ★★ ⚠ same type
- PDXK p.Gly281Glu Uncertain significance ★★ ⚠ same type
- PDXK p.Met126Thr Uncertain significance ★★ ⚠ same type
- PDXK c.142+3058C>T Likely benign ★★ same type
- PDXK c.143-116A>G Benign ★★ same type
- PDXK c.143-202G>A 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/pdxk-p-ser89 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown