SGPL1 p.Pro299=
c.897T>C · rs535148757 · VCV1949424
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00267%, afr)
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 -6.4 | GERP -5.6 |
| Overall | ||
| CADD | 1.571 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00267%
African / African-American · 2/74,942 alleles
Filtering AF
0.000443%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000166%
Overall
0.000186%
3/1,611,080 alleles · very rare
exomes 2/1,458,726 · genomes 1/152,354 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00267% | 37,471 |
| Admixed American | 0.00167% | 59,796 |
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.Pro299=
- Coding
- c.897T>C
- MANE Select
- NM_003901
- dbSNP
- rs535148757
- Type
- single nucleotide variant
- Location
- chr10:70871134 (GRCh38)
- Gene constraint
- LOEUF 0.71 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.07 · 2 PDB
- Residue 299
- an α-helix
Similar variants
- SGPL1 p.Pro299Ser 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-pro299 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown