SBDS p.Ile29=
c.87C>T · VCV3792706
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00667%, afr)
Conditions
1
Inborn genetic diseases
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 3.9 | GERP 0.78, phastCons 1 |
| Overall | ||
| CADD | 13.48 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00667%
African / African-American · 5/74,942 alleles
Filtering AF
0.00255%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00161%
Overall
0.00031%
5/1,614,002 alleles · very rare
exomes 2/1,461,752 · genomes 3/152,250 · 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.Ile29=
- Coding
- c.87C>T
- MANE Select
- NM_016038
- Type
- single nucleotide variant
- Location
- chr7:66995331 (GRCh38)
- Gene constraint
- LOEUF 1.08 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.97 · 6 PDB
- Residue 29
- a β-strand
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-ile29 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown