SGTA p.Ser235=
c.705G>A · rs186892404 · VCV712653
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.12%, amr)
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 · C>A here scores Δ0.23 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5.9 | GERP -5 |
| Overall | ||
| CADD | 0.443 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.12%
Admixed American · 1,275/60,018 alleles
Filtering AF
2.03%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.99%
Overall
0.0947%
1,529/1,613,994 alleles · low-frequency
exomes 1,387/1,461,662 · genomes 142/152,332 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 2.12% | 47 |
| East Asian | 0.423% | 236 |
| Remaining individualsnot grpmax-eligible | 0.0656% | 1,524 |
| South Asian | 0.00439% | 22,764 |
| African / African-American | 0.00267% | 37,517 |
| Finnishnot grpmax-eligible | 0.00156% | 64,012 |
| European (non-Finnish) | 0.00136% | 73,744 |
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
- SGTA
- Protein
- p.Ser235=
- Coding
- c.705G>A
- MANE Select
- NM_003021
- dbSNP
- rs186892404
- Type
- single nucleotide variant
- Location
- chr19:2759289 (GRCh38)
- Gene constraint
- LOEUF 0.747 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.86 · 5 PDB
Similar variants
- SGTA p.Pro72= Benign ★★ same type
- SGTA p.Ala10Thr Uncertain significance ★ ⚠ same type
- SGTA p.Ala42Val Uncertain significance ★ ⚠ same type
- SGTA p.Ala53Gly Uncertain significance ★ ⚠ same type
- SGTA p.Ala66Thr Uncertain significance ★ ⚠ same type
- SGTA p.Ala66Val Uncertain significance ★ ⚠ same type
- SGTA p.Arg302Pro Uncertain significance ★ ⚠ same type
- SGTA p.Gln275Ter 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/sgta-p-ser235 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown