SBDS p.Ala116=
c.348A>C · VCV3437521
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00534%, 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 -1.7 | GERP -3.7 |
| Overall | ||
| CADD | 5.272 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00534%
African / African-American · 4/74,934 alleles
Filtering AF
0.00175%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00104%
Overall
0.000248%
4/1,614,042 alleles · very rare
exomes 1/1,461,820 · genomes 3/152,222 · 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.Ala116=
- Coding
- c.348A>C
- MANE Select
- NM_016038
- Type
- single nucleotide variant
- Location
- chr7:66993328 (GRCh38)
- Gene constraint
- LOEUF 1.08 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.97 · 6 PDB
- Residue 116
- a β-strand
Similar variants
- SBDS p.Ala116Val Uncertain significance ★ ⚠ same residue
- 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
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-ala116 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown