Is PEX7 p.Asn79= (c.237C>T) pathogenic?

PEX7 p.Asn79= (c.237C>T) is classified Likely benign in PEX7 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-10-23). Ultra-rare (popmax 0.0283%, amr); Associated with peroxisome biogenesis disorder 9B.

What condition is associated with PEX7 p.Asn79= (c.237C>T)?

PEX7 p.Asn79= (c.237C>T) is associated with peroxisome biogenesis disorder 9B (ClinVar).

How common is PEX7 p.Asn79= (c.237C>T) in the general population?

PEX7 p.Asn79= (c.237C>T) is ultra-rare (popmax 0.0283%, amr) (gnomAD).

PEX7 p.Asn79=

c.237C>T · rs752745963 · VCV1149769

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0283%, amr)

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 -4.5	GERP -3.5
Overall
CADD	5.989	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0283% Admixed American · 17/59,974 alleles

Filtering AF 0.018% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0147%

Overall 0.00341% 55/1,613,824 alleles · ultra-rare exomes 46/1,461,816 · genomes 9/152,008 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0283%	3,528
Remaining individualsnot grpmax-eligible	0.008%	12,501
European (non-Finnish)	0.00263%	38,063
African / African-American	0.00133%	74,916
South Asian	0.0011%	91,050

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.Asn79=
Coding: c.237C>T
MANE Select: NM_000288
dbSNP: rs752745963
Type: single nucleotide variant
Location: chr6:136826367 (GRCh38)
Gene constraint: LOEUF 0.941 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.54

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.Asn79Ser 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
PEX7 c.634-2A>G Pathogenic/Likely pathogenic ★★ same condition
PEX7 c.748-2A>G 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-asn79 (accessed [today's date]).

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