DGUOK p.Arg142=
c.426G>A · rs1205047368 · VCV2728742
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0044%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.60 | donor loss, 1 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.5 | GERP -2, phastCons 1 |
| Overall | ||
| CADD | 9.058 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0044%
South Asian · 4/90,854 alleles
Filtering AF
0.00143%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000893%
Overall
0.00031%
5/1,612,516 alleles · very rare
exomes 4/1,460,336 · genomes 1/152,180 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0044% | 22,713 |
| European (non-Finnish) | 8.48e-05% | 1,179,632 |
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.Arg142=
- Coding
- c.426G>A
- MANE Select
- NM_080916
- dbSNP
- rs1205047368
- Type
- single nucleotide variant
- Location
- chr2:73946889 (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 142
- a UniProt-annotated variant site (in mtdps3); a β-strand; a binding site
Similar variants
- DGUOK p.Arg142Lys Pathogenic/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.Asp255Tyr Pathogenic/Likely pathogenic ★★ ⚠ same type
- DGUOK p.Gln197= Pathogenic/Likely pathogenic ★★ same type
- DGUOK p.Gln79Ter 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-arg142 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown