PEX19 p.Asp281=
c.843T>C · rs1479324430 · VCV2822036
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
Conditions
1
peroxisome biogenesis disorder 12A (Zellweger)
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 0.9 | GERP -2.2, phastCons 0.98 |
| Overall | ||
| CADD | 6.547 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/75,060 alleles
Filtering AF
0.000183%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00012%
Overall
0.000479%
7/1,461,848 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00133% | 75,060 |
| European (non-Finnish) | 0.000508% | 196,666 |
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
- PEX19
- Protein
- p.Asp281=
- Coding
- c.843T>C
- MANE Select
- NM_002857
- dbSNP
- rs1479324430
- Type
- single nucleotide variant
- Location
- chr1:160279608 (GRCh38)
- Gene constraint
- LOEUF 1.066 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.95 · 5 PDB
- Residue 281
- an α-helix
Similar variants
- PEX19 p.Asp281Gly Uncertain significance ★ ⚠ same residue
- PEX19 c.346+2T>C Likely pathogenic ★★ same condition
- PEX19 p.Leu94Ter Likely pathogenic ★★ same condition
- PEX19 p.Lys193Ter Pathogenic/Likely pathogenic ★★ same condition
- PEX19 p.Ser54Leu Pathogenic ★★ ⚠ same condition
- PEX19 c.*1335G>T Uncertain significance ★★ same condition
- PEX19 c.*864C>T Uncertain significance ★★ same condition
- PEX19 p.Ala14Pro Uncertain significance ★★ ⚠ 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/pex19-p-asp281 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown