PEX7 p.Pro168=
c.504T>C · rs770113657 · VCV1094399
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0028%, nfe)
Conditions
1
peroxisome biogenesis disorder 9B
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.15 | GERP 0.43, phastCons 0.99 |
| Overall | ||
| CADD | 8.082 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0028%
European (non-Finnish) · 33/1,177,972 alleles
Filtering AF
0.002%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00176%
Overall
0.00205%
33/1,611,650 alleles · very rare
exomes 33/1,459,382 · genomes 0/152,268 · 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
- PEX7
- Protein
- p.Pro168=
- Coding
- c.504T>C
- MANE Select
- NM_000288
- dbSNP
- rs770113657
- Type
- single nucleotide variant
- Location
- chr6:136846159 (GRCh38)
- Gene constraint
- LOEUF 0.941 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.54
Similar variants
- PEX7 p.Pro168fs Likely pathogenic ★ same residue
- PEX7 p.Pro168Ala Uncertain significance ⚠ same residue
- PEX7 c.130+1G>A Pathogenic ★★ same condition
- PEX7 c.131-1G>A Likely pathogenic ★★ same condition
- PEX7 c.188+1G>A Pathogenic/Likely pathogenic ★★ same condition
- PEX7 c.188+1G>C Pathogenic/Likely pathogenic ★★ same condition
- PEX7 c.340-1G>T Likely pathogenic ★★ same condition
- PEX7 c.634-2A>G Pathogenic/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/pex7-p-pro168 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown