Is PEX7 p.Thr14= (c.42G>A) pathogenic?

PEX7 p.Thr14= (c.42G>A) is classified Likely benign in PEX7 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-04). Very rare (popmax 0.00257%, eas); Associated with peroxisome biogenesis disorder 9B.

What condition is associated with PEX7 p.Thr14= (c.42G>A)?

PEX7 p.Thr14= (c.42G>A) is associated with peroxisome biogenesis disorder 9B (ClinVar).

How common is PEX7 p.Thr14= (c.42G>A) in the general population?

PEX7 p.Thr14= (c.42G>A) is very rare (popmax 0.00257%, eas) (gnomAD).

PEX7 p.Thr14=

c.42G>A · rs1253900568 · VCV1147081

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00257%, eas)

Conditions

peroxisome biogenesis disorder 9B

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 0.74	GERP 0.74, phastCons 1
Overall
CADD	12.02	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00257% East Asian · 1/38,850 alleles

Filtering AF 0.000562% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000444%

Overall 0.000857% 13/1,517,444 alleles · very rare exomes 12/1,365,434 · genomes 1/152,010 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00257%	38,850
European (non-Finnish)	0.00105%	94,963

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: PEX7
Protein: p.Thr14=
Coding: c.42G>A
MANE Select: NM_000288
dbSNP: rs1253900568
Type: single nucleotide variant
Location: chr6:136822707 (GRCh38)
Gene constraint: LOEUF 0.941 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.54
Residue 14: a UniProt-annotated variant site (in pbd9b)

Full PEX7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

peroxisome biogenesis disorder 9B — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PEX7 p.Thr14Pro Pathogenic/Likely pathogenic ★★ ⚠ same residue
PEX7 p.Thr14Met Uncertain significance ★ ⚠ same residue
PEX7 p.Thr14_Pro15insLeuArgThr Uncertain significance ★ same residue
PEX7 c.130+1G>A Pathogenic ★★ same condition
PEX7 c.131-1G>A Likely pathogenic ★★ same condition
PEX7 c.188+1G>A Pathogenic/Likely pathogenic ★★ same condition
PEX7 c.188+1G>C Pathogenic/Likely pathogenic ★★ same condition
PEX7 c.340-1G>T Likely pathogenic ★★ 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/pex7-p-thr14 (accessed [today's date]).

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