PEX1 c.357+1G>A
Likely pathogenic
No assertion criteria
Classification
Likely pathogenic
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
Consequence
canonical splice-site (±1/±2)
predicted LoF
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,599,574)
Conditions
1
peroxisome biogenesis disorder 1A (Zellweger)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Consequence | canonical splice-site (±1/±2) | predicted loss-of-function |
|---|---|---|
| Splicing | ||
| Splice region | donor +1 | canonical splice dinucleotide (donor +1) · inside the BP7-excluded zone |
| SpliceAI | Δ0.94 | donor loss · deltas |
| Pangolin | Δ0.80 | loss · gain 0.40 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 7.7 | GERP 2.1, phastCons 1 |
| Non-coding constraint | Z 0.55 | 1 kb window · o/e 0.96 · regional · uncalibrated |
| Overall | ||
| CADD | 34.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,599,574). 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.357+1G>A
- MANE Select
- NM_000466
- dbSNP
- rs866144313
- Type
- single nucleotide variant
- Location
- chr7:92518994 (GRCh38)
- Gene constraint
- LOEUF 0.746 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.19
Similar variants
- PEX1 c.1239+1G>T Pathogenic ★★ same condition
- PEX1 c.130-1G>T 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
- PEX1 c.2719-2A>G 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/pex1-c-357-plus-1g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown