DHDDS p.Asp34=
c.102C>T · rs577531413 · VCV1460528
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.005%, amr)
Conditions
1
retinitis pigmentosa 59
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 -0.17 | GERP -4, phastCons 0.7 |
| Overall | ||
| CADD | 11.86 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.005%
Admixed American · 3/60,014 alleles
Filtering AF
0.00145%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00123%
Overall
0.00192%
31/1,613,970 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.005% | 20,005 |
| East Asian | 0.00446% | 22,441 |
| European (non-Finnish) | 0.00212% | 47,195 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,496 |
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.Asp34=
- Coding
- c.102C>T
- MANE Select
- NM_205861
- dbSNP
- rs577531413
- Type
- single nucleotide variant
- Location
- chr1:26438206 (GRCh38)
- Gene constraint
- LOEUF 0.536 · pLI 0.91 (gnomAD)
- Structure
- AlphaFold pLDDT 95.01 · 9 PDB
- Residue 34
- a binding site
Similar variants
- DHDDS p.Asp34Glu Likely pathogenic same residue
- DHDDS p.Asp34fs Pathogenic ★ same residue
- 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
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-asp34 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown