DHDDS p.Ile244=
c.732C>T · rs757277775 · VCV2815825
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
Conditions
1
retinitis pigmentosa 59
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.199 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.21 | GERP -2.4, phastCons 0.026 |
| Overall | ||
| CADD | 7.03 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,022 alleles
Overall
6.2e-05%
1/1,614,162 alleles · very rare
exomes 1/1,461,874 · genomes 0/152,288 · 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
- DHDDS
- Protein
- p.Ile244=
- Coding
- c.732C>T
- MANE Select
- NM_205861
- dbSNP
- rs757277775
- Type
- single nucleotide variant
- Location
- chr1:26460111 (GRCh38)
- Gene constraint
- LOEUF 0.536 · pLI 0.91 (gnomAD)
- Structure
- AlphaFold pLDDT 95.01 · 9 PDB
- Residue 244
- 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-ile244 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown