SBDS p.Asp110=
c.330C>T · VCV4159836
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000339%, nfe)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.52 | GERP -1.4, phastCons 0.99 |
| Overall | ||
| CADD | 7.085 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000339%
European (non-Finnish) · 4/1,179,940 alleles
Filtering AF
7.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.4e-05%
Overall
0.000248%
4/1,614,014 alleles · very rare
exomes 4/1,461,752 · genomes 0/152,262 · 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
- SBDS
- Protein
- p.Asp110=
- Coding
- c.330C>T
- MANE Select
- NM_016038
- Type
- single nucleotide variant
- Location
- chr7:66993346 (GRCh38)
- Gene constraint
- LOEUF 1.08 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.97 · 6 PDB
- Residue 110
- an α-helix
Similar variants
- SBDS p.Lys33Thr Pathogenic/Likely pathogenic ★★ same condition
- SBDS p.Arg22Cys Uncertain significance ★★ ⚠ same condition
- SBDS p.Asp246Asn Uncertain significance ★★ ⚠ same condition
- SBDS p.Cys216Tyr Uncertain significance ★★ ⚠ same condition
- SBDS p.Ile111Val Uncertain significance ★★ ⚠ same condition
- SBDS p.Ile224Thr Uncertain significance ★★ ⚠ same condition
- SBDS p.Lys240Arg Uncertain significance ★★ ⚠ same condition
- SBDS p.Thr129Ser Uncertain significance ★★ 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/sbds-p-asp110 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown