PEX7 p.His154=
c.462T>C · rs753312829 · VCV1159666
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
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 -1 | GERP 0.51, phastCons 0.004 |
| Overall | ||
| CADD | 1.136 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,070 alleles
Filtering AF
6.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.000248%
4/1,613,712 alleles · very rare
exomes 4/1,461,424 · genomes 0/152,288 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0011% | 91,070 |
| European (non-Finnish) | 0.000254% | 393,226 |
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.His154=
- Coding
- c.462T>C
- MANE Select
- NM_000288
- dbSNP
- rs753312829
- Type
- single nucleotide variant
- Location
- chr6:136846117 (GRCh38)
- Gene constraint
- LOEUF 0.941 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.54
Similar variants
- 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
- PEX7 c.748-2A>G Likely pathogenic ★★ same condition
- PEX7 c.803+1G>A 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-his154 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown