SGPL1 p.Phe75=
c.225T>C · VCV3695062
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000509%, nfe)
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 0.4 | GERP 0.17, phastCons 1 |
| Overall | ||
| CADD | 6.977 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000509%
European (non-Finnish) · 6/1,179,824 alleles
Filtering AF
0.000183%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00012%
Overall
0.000372%
6/1,613,828 alleles · very rare
exomes 5/1,461,606 · genomes 1/152,222 · 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
- SGPL1
- Protein
- p.Phe75=
- Coding
- c.225T>C
- MANE Select
- NM_003901
- Type
- single nucleotide variant
- Location
- chr10:70851174 (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-phe75 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown