PEX19 p.Ala62=
c.186C>A · rs758869711 · VCV2981123
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0418%, sas)
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 1.9 | GERP -1.7, phastCons 1 |
| Overall | ||
| CADD | 7.082 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0418%
South Asian · 38/91,010 alleles
Filtering AF
0.0312%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0276%
Overall
0.00242%
39/1,613,196 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0418% | 2,395 |
| African / African-American | 0.00134% | 74,876 |
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.Ala62=
- Coding
- c.186C>A
- MANE Select
- NM_002857
- dbSNP
- rs758869711
- Type
- single nucleotide variant
- Location
- chr1:160283104 (GRCh38)
- Gene constraint
- LOEUF 1.066 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.95 · 5 PDB
- Residue 62
- the 'disordered' region; the 'necessary for pex19 function on peroxisome biogenesis' region
Similar variants
- 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
- PEX19 p.Ala234Ser 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-ala62 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown