Is PEX14 p.Pro10= (c.30G>C) pathogenic?

PEX14 p.Pro10= (c.30G>C) is classified Likely benign in PEX14 (ClinVar, Single submitter, 2 submitters; last evaluated 2025-09-18). Very rare (popmax 0.00672%, amr); Associated with peroxisome biogenesis disorder, complementation group K.

What condition is associated with PEX14 p.Pro10= (c.30G>C)?

PEX14 p.Pro10= (c.30G>C) is associated with peroxisome biogenesis disorder, complementation group K (ClinVar).

How common is PEX14 p.Pro10= (c.30G>C) in the general population?

PEX14 p.Pro10= (c.30G>C) is very rare (popmax 0.00672%, amr) (gnomAD).

PEX14 p.Pro10=

c.30G>C · rs1307415913 · VCV1111382

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00672%, amr)

Conditions

peroxisome biogenesis disorder, complementation group K

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 1.9	GERP 0.68, phastCons 1
Overall
CADD	15.13	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00672% Admixed American · 4/59,516 alleles

Filtering AF 0.00227% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00136%

Overall 0.000621% 10/1,610,080 alleles · very rare exomes 8/1,457,862 · genomes 2/152,218 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00672%	14,879
African / African-American	0.004%	24,969
South Asian	0.00333%	30,058

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: PEX14
Protein: p.Pro10=
Coding: c.30G>C
MANE Select: NM_004565
dbSNP: rs1307415913
Type: single nucleotide variant
Location: chr1:10474996 (GRCh38)
Gene constraint: LOEUF 0.542 · pLI 0.91 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 68.48 · 4 PDB
Residue 10: the 'disordered' region

Full PEX14 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

peroxisome biogenesis disorder, complementation group K — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PEX14 p.Pro10Arg Conflicting classifications of pathogenicity ★ ⚠ same residue
PEX14 p.Pro10Ser Uncertain significance ★ ⚠ same residue
PEX14 c.36+6G>T Uncertain significance ★★ same condition
PEX14 p.Ala102Thr Uncertain significance ★★ ⚠ same condition
PEX14 p.Ala254Val Uncertain significance ★★ ⚠ same condition
PEX14 p.Ala370Ser Uncertain significance ★★ ⚠ same condition
PEX14 p.Arg105Gln Uncertain significance ★★ ⚠ same condition
PEX14 p.Arg139Leu 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/pex14-p-pro10 (accessed [today's date]).

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