STX3 p.Ser97=
c.291C>T · rs148104403 · VCV714776
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.669%, sas)
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 -0.34 | GERP -2.2, phastCons 0.1 |
| Overall | ||
| CADD | 11.81 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.669%
South Asian · 609/91,042 alleles
Filtering AF
0.625%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.607%
Overall
0.0904%
1,458/1,612,696 alleles · rare
exomes 1,342/1,460,426 · genomes 116/152,270 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.669% | 149 |
| Middle Eastern | 0.561% | 178 |
| Remaining individualsnot grpmax-eligible | 0.112% | 892 |
| Admixed American | 0.0883% | 1,133 |
| European (non-Finnish) | 0.0576% | 1,736 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0203% | 4,933 |
| African / African-American | 0.00666% | 15,004 |
| Finnishnot grpmax-eligible | 0.00312% | 32,014 |
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
- STX3
- Protein
- p.Ser97=
- Coding
- c.291C>T
- MANE Select
- NM_004177
- dbSNP
- rs148104403
- Type
- single nucleotide variant
- Location
- chr11:59790520 (GRCh38)
- Gene constraint
- LOEUF 0.748 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.60
Similar variants
- STX3 p.Arg247Ter Pathogenic ★★ same type
- STX3 p.Ala10Val Uncertain significance ★★ ⚠ same type
- STX3 p.Ala219Pro Uncertain significance ★★ ⚠ same type
- STX3 p.Ala279Thr Uncertain significance ★★ ⚠ same type
- STX3 p.Arg125Trp Uncertain significance ★★ ⚠ same type
- STX3 p.Arg197Leu Uncertain significance ★★ ⚠ same type
- STX3 p.Arg4Cys Uncertain significance ★★ ⚠ same type
- STX3 p.Arg92Gln 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/stx3-p-ser97 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown