PEX7 p.Ala9fs
c.26del · VCV3593203
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
2
rhizomelic chondrodysplasia punctata type 1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 1 of 10 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 9.5 | GERP 1, phastCons 1 |
| Region caveats | ||
| Repeat context | tandem | G-rich low complexity · ambiguous alignment · confidence, not pathogenicity |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- PEX7
- Protein
- p.Ala9fs
- Coding
- c.26del
- MANE Select
- NM_000288
- Type
- Deletion
- Location
- chr6:136822691 (GRCh38)
- Gene constraint
- LOEUF 0.941 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.54
Disease context
rhizomelic chondrodysplasia punctata type 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsAlso linked: peroxisome biogenesis disorder 9B
For Rhizomelic chondrodysplasia punctata (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Antenatal, Neonatal
- Prevalence
- 1-9 / 1 000 000 (Europe)
Similar variants
- PEX7 p.Ala9Glu Uncertain significance ★ ⚠ same residue
- PEX7 p.Ala9Val Uncertain significance ★ ⚠ same residue
- PEX7 p.Ala9= Likely benign ★ same residue
- PEX7 c.116_130+20del Likely pathogenic ★★ same condition
- PEX7 c.363_526+230del Likely pathogenic ★★ same condition
- PEX7 p.Glu211fs Likely pathogenic ★★ same condition
- PEX7 p.Phe61fs Pathogenic/Likely pathogenic ★★ same condition
- PEX7 p.Phe71fs 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/pex7-p-ala9fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown