DGUOK p.Ser28=
c.84C>T · rs2466941733 · VCV2848648
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000169%, nfe)
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 -2.7 | GERP -4.2 |
| Overall | ||
| CADD | 6.611 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000169%
European (non-Finnish) · 2/1,180,036 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,612,202 alleles · very rare
exomes 2/1,459,800 · genomes 0/152,402 · 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
- DGUOK
- Protein
- p.Ser28=
- Coding
- c.84C>T
- MANE Select
- NM_080916
- dbSNP
- rs2466941733
- Type
- single nucleotide variant
- Location
- chr2:73926994 (GRCh38)
- Gene constraint
- LOEUF 1.115 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 87.27 · 1 PDB
Similar variants
- DGUOK p.Ser28fs Pathogenic ★ same residue
- DGUOK c.443+1G>A Pathogenic ★★ same type
- DGUOK c.444-62C>A Pathogenic/Likely pathogenic ★★ same type
- DGUOK p.Arg118Cys Pathogenic/Likely pathogenic ★★ same type
- DGUOK p.Arg118His Pathogenic/Likely pathogenic ★★ same type
- DGUOK p.Arg142Lys Pathogenic/Likely pathogenic ★★ same type
- DGUOK p.Asp255Tyr Pathogenic/Likely pathogenic ★★ ⚠ same type
- DGUOK p.Gln197= Pathogenic/Likely pathogenic ★★ 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/dguok-p-ser28 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown