PEX6 p.Pro560=
c.1680C>G · rs372998833 · VCV1683500
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
2
megalencephaly
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 -0.24 | GERP -0.65, phastCons 0.007 |
| Overall | ||
| CADD | 3.321 | 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
- PEX6
- Protein
- p.Pro560=
- Coding
- c.1680C>G
- MANE Select
- NM_000287
- dbSNP
- rs372998833
- Type
- single nucleotide variant
- Location
- chr6:42968298 (GRCh38)
- Gene constraint
- LOEUF 0.799 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.87
Disease context
megalencephaly — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsAlso linked: leukodystrophy
Similar variants
- PEX6 c.1130+1G>A Likely pathogenic ★★ same type
- PEX6 c.1233+1G>A Likely pathogenic ★★ same type
- PEX6 c.1688+1G>A Pathogenic ★★ same type
- PEX6 c.1689-1G>A Likely pathogenic ★★ same type
- PEX6 c.1885-1G>A Likely pathogenic ★★ same type
- PEX6 c.1961+1G>A Likely pathogenic ★★ same type
- PEX6 c.1962-1G>A Pathogenic/Likely pathogenic ★★ same type
- PEX6 c.2094+1G>A Likely 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/pex6-p-pro560 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown