SGCD p.Ser17=
c.51T>C · rs2127716489 · VCV1746033
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 8.49e-05%, nfe)
Conditions
2
Inborn genetic diseases
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 -7.2 | GERP -3.9 |
| Overall | ||
| CADD | 0.96 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.49e-05%
European (non-Finnish) · 1/1,178,474 alleles
Overall
6.21e-05%
1/1,610,826 alleles · very rare
exomes 1/1,458,564 · genomes 0/152,262 · 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
- SGCD
- Protein
- p.Ser17=
- Coding
- c.51T>C
- MANE Select
- NM_000337
- dbSNP
- rs2127716489
- Type
- single nucleotide variant
- Location
- chr5:156344536 (GRCh38)
- Gene constraint
- LOEUF 0.88 · pLI 0.05 (gnomAD)
- Structure
- AlphaFold pLDDT 81.43
Similar variants
- SGCD p.Arg165Ter Pathogenic ★★★ same condition
- SGCD p.Arg97Ter Pathogenic ★★★ same condition
- SGCD p.Arg31Trp Uncertain significance ★★★ ⚠ same condition
- SGCD p.Ile64Thr Uncertain significance ★★★ ⚠ same condition
- SGCD c.192+1G>A Likely pathogenic ★★ same condition
- SGCD c.294+1G>A Likely pathogenic ★★ same condition
- SGCD c.4-1G>T Likely pathogenic ★★ same condition
- SGCD p.Arg33Ter Pathogenic/Likely pathogenic ★★ 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/sgcd-p-ser17 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown