DHDDS p.Trp238Ter
c.714G>A · rs2124501559 · VCV1400385
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
retinitis pigmentosa 59
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| NMD | predicted | premature termination codon in exon 8 of 9 |
| REVEL | 0.42 | indeterminate |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 39.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- DHDDS
- Protein
- p.Trp238Ter
- Coding
- c.714G>A
- MANE Select
- NM_205861
- dbSNP
- rs2124501559
- Type
- single nucleotide variant
- Location
- chr1:26460093 (GRCh38)
- Gene constraint
- LOEUF 0.536 · pLI 0.91 (gnomAD)
- Structure
- AlphaFold pLDDT 95.01 · 9 PDB
- Residue 238
- a UniProt-annotated variant site (in rp59; in a patient with congenital disorder of glycosylation); an α-helix
Similar variants
- DHDDS c.658-2A>G Likely pathogenic ★★ same condition
- DHDDS p.Arg205Gln Pathogenic ★★ same condition
- DHDDS p.Arg211Gln Pathogenic ★★ same condition
- DHDDS p.Arg37Cys Pathogenic ★★ same condition
- DHDDS p.Arg37His Pathogenic/Likely pathogenic ★★ same condition
- DHDDS p.Arg37Ser Pathogenic ★★ same condition
- DHDDS p.Gly35Glu Pathogenic/Likely pathogenic ★★ same condition
- DHDDS p.Lys42Glu Pathogenic ★★ ⚠ same condition
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/dhdds-p-trp238ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown