SGPL1 p.Ser202=
c.606G>A · rs550769426 · VCV2176347
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0254%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.033 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.57 | GERP -4.4, phastCons 0.021 |
| Overall | ||
| CADD | 9.476 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0254%
East Asian · 10/39,410 alleles
Filtering AF
0.0137%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0104%
Overall
0.0044%
67/1,522,418 alleles · ultra-rare
exomes 64/1,370,278 · genomes 3/152,140 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0254% | 3,941 |
| South Asian | 0.00791% | 12,648 |
| African / African-American | 0.00419% | 23,861 |
| European (non-Finnish) | 0.00415% | 24,080 |
| Remaining individualsnot grpmax-eligible | 0.00172% | 58,062 |
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.Ser202=
- Coding
- c.606G>A
- MANE Select
- NM_003901
- dbSNP
- rs550769426
- Type
- single nucleotide variant
- Location
- chr10:70859490 (GRCh38)
- Gene constraint
- LOEUF 0.71 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.07 · 2 PDB
Similar variants
- 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
- SGPL1 p.Arg278Gly 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-ser202 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown