Is PEX19 p.Glu294= (c.882A>G) pathogenic?

PEX19 p.Glu294= (c.882A>G) is classified Likely benign in PEX19 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-08-11). Very rare (popmax 8.48e-05%, nfe); Associated with Inborn genetic diseases.

What condition is associated with PEX19 p.Glu294= (c.882A>G)?

PEX19 p.Glu294= (c.882A>G) is associated with Inborn genetic diseases (ClinVar).

How common is PEX19 p.Glu294= (c.882A>G) in the general population?

PEX19 p.Glu294= (c.882A>G) is very rare (popmax 8.48e-05%, nfe) (gnomAD).

PEX19 p.Glu294=

c.882A>G · rs1571135088 · VCV728251

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 8.48e-05%, nfe)

Conditions

Inborn genetic diseases

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 0.54	GERP -3, phastCons 1
Overall
CADD	7.636	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.48e-05% European (non-Finnish) · 1/1,179,782 alleles

Overall 6.2e-05% 1/1,613,906 alleles · very rare exomes 1/1,461,604 · genomes 0/152,302 · 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: PEX19
Protein: p.Glu294=
Coding: c.882A>G
MANE Select: NM_002857
dbSNP: rs1571135088
Type: single nucleotide variant
Location: chr1:160279569 (GRCh38)
Gene constraint: LOEUF 1.066 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 71.95 · 5 PDB

Full PEX19 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PEX19 p.Ala14Pro Uncertain significance ★★ ⚠ same condition
PEX19 p.Ala37Val Uncertain significance ★★ ⚠ same condition
PEX19 p.Ala95Asp Uncertain significance ★★ ⚠ same condition
PEX19 p.Asp163Gly Uncertain significance ★★ ⚠ same condition
PEX19 p.Asp30Asn Uncertain significance ★★ ⚠ same condition
PEX19 p.Gln122Arg Uncertain significance ★★ ⚠ same condition
PEX19 p.Gln123Glu Uncertain significance ★★ ⚠ same condition
PEX19 p.Gln72Arg 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-glu294 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown