SBDS p.Ser61=
c.183T>C · rs200346194 · VCV1267216
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
rare (popmax 0.117%, amr)
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 | all four deltas below 0.2 · A>C here scores Δ0.37 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.88 | GERP -3.6, phastCons 0.99 |
| Overall | ||
| CADD | 12.61 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.117%
Admixed American · 70/59,960 alleles
Filtering AF
0.0947%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0867%
Overall
0.0532%
859/1,613,162 alleles · rare
exomes 702/1,460,878 · genomes 157/152,284 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.117% | 857 |
| East Asian | 0.0847% | 1,181 |
| South Asian | 0.0758% | 1,319 |
| Remaining individualsnot grpmax-eligible | 0.0608% | 1,644 |
| European (non-Finnish) | 0.0488% | 2,051 |
| Finnishnot grpmax-eligible | 0.0422% | 2,371 |
| African / African-American | 0.04% | 2,500 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0338% | 2,960 |
| Middle Eastern | 0.033% | 3,030 |
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.Ser61=
- Coding
- c.183T>C
- MANE Select
- NM_016038
- dbSNP
- rs200346194
- Type
- single nucleotide variant
- Location
- chr7:66994287 (GRCh38)
- Gene constraint
- LOEUF 1.08 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.97 · 6 PDB
- Residue 61
- a turn
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-ser61 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown