PEX1 c.129+7T>C
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,553,556)
Conditions
1
Zellweger spectrum disorders
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +7 | near-intronic (+7 nt from the splice site) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 3.3 | GERP 1.4, phastCons 0.66 |
| Non-coding constraint | Z 2.44 | 1 kb window · o/e 0.86 · regional · uncalibrated |
| Overall | ||
| CADD | 13.17 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,553,556). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- PEX1
- Coding
- c.129+7T>C
- MANE Select
- NM_000466
- dbSNP
- rs765006313
- Type
- single nucleotide variant
- Location
- chr7:92528300 (GRCh38)
- Gene constraint
- LOEUF 0.746 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.19
Disease context
Zellweger spectrum disorders — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Zellweger syndrome (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Neonatal
Similar variants
- PEX1 c.1239+1G>T Pathogenic ★★ same condition
- PEX1 c.130-1G>T Pathogenic/Likely pathogenic ★★ same condition
- PEX1 c.130-2A>G Pathogenic/Likely pathogenic ★★ same condition
- PEX1 c.130-2A>T Pathogenic/Likely pathogenic ★★ same condition
- PEX1 c.1483+1G>A Pathogenic ★★ same condition
- PEX1 c.1587+1G>A Likely pathogenic ★★ same condition
- PEX1 c.1670+1G>A Pathogenic/Likely pathogenic ★★ same condition
- PEX1 c.1670+1G>T 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/pex1-c-129-plus-7t-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown