DGUOK p.Phe54=
c.162T>C · rs1241473255 · VCV2843871
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · T>A here scores Δ0.31 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.3 | GERP 0.033, phastCons 1 |
| Overall | ||
| CADD | 10.86 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,540 alleles
Overall
6.2e-05%
1/1,613,664 alleles · very rare
exomes 1/1,461,322 · genomes 0/152,342 · 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.Phe54=
- Coding
- c.162T>C
- MANE Select
- NM_080916
- dbSNP
- rs1241473255
- Type
- single nucleotide variant
- Location
- chr2:73938929 (GRCh38)
- Gene constraint
- LOEUF 1.115 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 87.27 · 1 PDB
- Residue 54
- an α-helix
Similar variants
- DGUOK p.Phe54fs Likely 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-phe54 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown