PEX19 p.Ser149=
c.447G>A · rs749234062 · VCV1672305
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00568%, nfe)
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 | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.4 | GERP -5 |
| Overall | ||
| CADD | 2.3 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00568%
European (non-Finnish) · 67/1,179,990 alleles
Filtering AF
0.00453%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00417%
Overall
0.00446%
72/1,614,086 alleles · very rare
exomes 72/1,461,838 · genomes 0/152,248 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00568% | 17,612 |
| East Asian | 0.00446% | 22,443 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,252 |
| Admixed American | 0.00167% | 60,022 |
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.Ser149=
- Coding
- c.447G>A
- MANE Select
- NM_002857
- dbSNP
- rs749234062
- Type
- single nucleotide variant
- Location
- chr1:160282186 (GRCh38)
- Gene constraint
- LOEUF 1.066 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.95 · 5 PDB
Similar variants
- PEX19 p.Ser149Leu 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-ser149 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown