DDOST p.Ser414=
c.1242C>T · rs931915308 · VCV510876
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00891%, eas)
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 -1.1 | GERP -5.3 |
| Overall | ||
| CADD | 6.891 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00891%
East Asian · 4/44,890 alleles
Filtering AF
0.00298%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0018%
Overall
0.00192%
31/1,613,830 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00891% | 11,223 |
| European (non-Finnish) | 0.00195% | 51,304 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,474 |
| Finnishnot grpmax-eligible | 0.00157% | 63,850 |
| African / African-American | 0.00133% | 74,930 |
| South Asian | 0.0011% | 91,092 |
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.Ser414=
- Coding
- c.1242C>T
- MANE Select
- NM_005216
- dbSNP
- rs931915308
- Type
- single nucleotide variant
- Location
- chr1:20652457 (GRCh38)
- Gene constraint
- LOEUF 0.747 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 89.27 · 6 PDB
Similar variants
- 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
- DDOST p.Arg237His Uncertain significance ★★ ⚠ same type
- DDOST p.Arg280Cys 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-ser414 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown