SGCD p.Thr256=
c.768G>A · rs376141942 · VCV285465
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00668%, eas)
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 -0.31 | GERP -5.4, phastCons 0.011 |
| Overall | ||
| CADD | 5.422 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00668%
East Asian · 3/44,880 alleles
Filtering AF
0.00177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.000992%
16/1,613,410 alleles · very rare
exomes 14/1,461,246 · genomes 2/152,164 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00668% | 14,960 |
| European (non-Finnish) | 0.0011% | 90,732 |
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.Thr256=
- Coding
- c.768G>A
- MANE Select
- NM_000337
- dbSNP
- rs376141942
- Type
- single nucleotide variant
- Location
- chr5:156759285 (GRCh38)
- Gene constraint
- LOEUF 0.88 · pLI 0.05 (gnomAD)
- Structure
- AlphaFold pLDDT 81.43
Similar variants
- SGCD p.Thr256Met Conflicting classifications of pathogenicity ★ ⚠ same residue
- 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
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-thr256 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown