DDOST p.Ser49=
c.147C>T · rs774852781 · VCV3051734
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00509%, nfe)
Conditions
1
DDOST-related disorder
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 3.5 | GERP -3.2, phastCons 1 |
| Overall | ||
| CADD | 12.02 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00509%
European (non-Finnish) · 60/1,179,928 alleles
Filtering AF
0.00402%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00362%
Overall
0.00397%
64/1,613,596 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00509% | 19,665 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,821 |
| South Asian | 0.0011% | 91,076 |
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
- DDOST
- Protein
- p.Ser49=
- Coding
- c.147C>T
- MANE Select
- NM_005216
- dbSNP
- rs774852781
- Type
- single nucleotide variant
- Location
- chr1:20661204 (GRCh38)
- Gene constraint
- LOEUF 0.747 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 89.27 · 6 PDB
- Residue 49
- a β-strand
Disease context
DDOST-related disorder
Similar variants
- DDOST c.*10G>A Likely benign same condition
- DDOST c.*3_*4dup Likely benign same condition
- DDOST p.Gln215His Pathogenic/Likely pathogenic ★★ ⚠ same type
- DDOST c.-18T>G Uncertain significance ★★ ⚠ same type
- DDOST p.Ala11Val Uncertain significance ★★ ⚠ same type
- DDOST p.Ala219Val Uncertain significance ★★ ⚠ same type
- DDOST p.Ala232Ser Uncertain significance ★★ ⚠ same type
- DDOST p.Ala415Thr Uncertain significance ★★ ⚠ 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/ddost-p-ser49 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown