STS p.Gly56=
c.168G>C · VCV4948675
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 -0.76 | GERP 1.5 |
| Overall | ||
| CADD | 2.629 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- STS
- Protein
- p.Gly56=
- Coding
- c.168G>C
- MANE Select
- NM_001320752
- Type
- single nucleotide variant
- Location
- chrX:7257272 (GRCh38)
- Structure
- AlphaFold pLDDT 94.31 · 2 PDB
- Residue 56
- an α-helix
Similar variants
- STS p.Gly56Val Uncertain significance ★ ⚠ same residue
- STS p.Gly354Arg Likely pathogenic ★★ same type
- STS p.Arg381Ser Uncertain significance ★★ ⚠ same type
- STS p.Asp397Asn Uncertain significance ★★ ⚠ same type
- STS c.1082-55C>T Likely benign ★★ same type
- STS c.1082-76G>A Benign ★★ same type
- STS c.1241+15G>C Benign ★★ same type
- STS c.138-9T>G Likely benign ★★ 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/sts-p-gly56 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown