SPRED1 p.Phe58=
c.174T>C · rs1595733589 · VCV758909
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Legius syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.88 | GERP -0.16, phastCons 1 |
| Overall | ||
| CADD | 9.48 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- SPRED1
- Protein
- p.Phe58=
- Coding
- c.174T>C
- MANE Select
- NM_152594
- dbSNP
- rs1595733589
- Type
- single nucleotide variant
- Location
- chr15:38299514 (GRCh38)
- Gene constraint
- LOEUF 0.496 · pLI 0.98 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 63.67 · 3 PDB
- Residue 58
- a β-strand; the wh1 domain
Similar variants
- SPRED1 p.Phe58Val Uncertain significance ★ ⚠ same residue
- SPRED1 p.Arg117Ter Pathogenic ★★ same condition
- SPRED1 p.Arg16Ter Pathogenic ★★ same condition
- SPRED1 p.Arg18Ter Pathogenic ★★ same condition
- SPRED1 p.Arg24Ter Pathogenic ★★ same condition
- SPRED1 p.Arg251Ter Pathogenic/Likely pathogenic ★★ same condition
- SPRED1 p.Arg325Ter Pathogenic/Likely pathogenic ★★ same condition
- SPRED1 p.Arg403Ter Pathogenic/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/spred1-p-phe58 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown