PLEC p.Pro808=
c.2424C>T · rs894090273 · VCV725918
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.61e-05%, 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 -4.6 | |
| Overall | ||
| CADD | 2.391 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.61e-05%
European (non-Finnish) · 1/1,161,114 alleles
Overall
6.36e-05%
1/1,572,956 alleles · very rare
exomes 1/1,420,608 · genomes 0/152,348 · 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
- PLEC
- Protein
- p.Pro808=
- Coding
- c.2424C>T
- MANE Select
- NM_201384
- dbSNP
- rs894090273
- Type
- single nucleotide variant
- Location
- chr8:143930417 (GRCh38)
- Gene constraint
- LOEUF 0.726 · pLI <0.01 (gnomAD)
- Residue 808
- an α-helix; the 'globular 1' region
Similar variants
- PLEC p.Pro808His Uncertain significance ★ same residue
- PLEC p.Arg1490Ter Pathogenic/Likely pathogenic ★★ same type
- PLEC p.Arg1973Trp Pathogenic ★★ ⚠ same type
- PLEC p.Arg2027Ter Pathogenic ★★ same type
- PLEC p.Arg2292Ter Pathogenic ★★ same type
- PLEC p.Arg2324Ter Pathogenic ★★ same type
- PLEC p.Arg2394Ter Pathogenic ★★ same type
- PLEC p.Arg559Ter Pathogenic ★★ 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/plec-p-pro808 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown