SGPL1 p.Ser151=
c.453T>C · rs774918873 · VCV1941892
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.064 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -7.1 | GERP -5.3 |
| Overall | ||
| CADD | 2.132 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/59,886 alleles
Filtering AF
0.000689%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000539%
Overall
0.00093%
15/1,612,898 alleles · very rare
exomes 14/1,460,730 · genomes 1/152,168 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 59,886 |
| European (non-Finnish) | 0.00119% | 84,245 |
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
- SGPL1
- Protein
- p.Ser151=
- Coding
- c.453T>C
- MANE Select
- NM_003901
- dbSNP
- rs774918873
- Type
- single nucleotide variant
- Location
- chr10:70857657 (GRCh38)
- Gene constraint
- LOEUF 0.71 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.07 · 2 PDB
Similar variants
- SGPL1 p.Ser151Asn Uncertain significance ★ ⚠ same residue
- SGPL1 p.Arg222Gln Pathogenic ★★ same type
- SGPL1 p.Arg495Ter Pathogenic ★★ same type
- SGPL1 p.Arg505Ter Pathogenic ★★ same type
- SGPL1 p.Tyr331Ter Pathogenic ★★ same type
- SGPL1 p.Tyr416Cys Likely pathogenic ★★ same type
- SGPL1 p.Ala316Thr Uncertain significance ★★ ⚠ same type
- SGPL1 p.Ala492Ser 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/sgpl1-p-ser151 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown