Is PEX16 p.Pro210= (c.630C>T) pathogenic?

PEX16 p.Pro210= (c.630C>T) is classified Likely benign in PEX16 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-02). Very rare (popmax 0.00801%, afr); Associated with peroxisome biogenesis disorder.

What condition is associated with PEX16 p.Pro210= (c.630C>T)?

PEX16 p.Pro210= (c.630C>T) is associated with peroxisome biogenesis disorder (ClinVar).

How common is PEX16 p.Pro210= (c.630C>T) in the general population?

PEX16 p.Pro210= (c.630C>T) is very rare (popmax 0.00801%, afr) (gnomAD).

PEX16 p.Pro210=

c.630C>T · rs760707150 · VCV2910772

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00801%, afr)

Conditions

peroxisome biogenesis disorder

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 -1.6	GERP -5.1
Overall
CADD	0.343	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00801% African / African-American · 6/74,944 alleles

Filtering AF 0.00347% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00228%

Overall 0.000435% 7/1,610,414 alleles · very rare exomes 3/1,458,180 · genomes 4/152,234 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00801%	12,491
European (non-Finnish)	8.47e-05%	1,180,011

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: PEX16
Protein: p.Pro210=
Coding: c.630C>T
MANE Select: NM_004813
dbSNP: rs760707150
Type: single nucleotide variant
Location: chr11:45914380 (GRCh38)
Gene constraint: LOEUF 0.957 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 83.07
Residue 210: the 'disordered' region

Full PEX16 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

Similar variants

PEX16 p.Pro210Leu Uncertain significance ★★ ⚠ same residue
PEX16 c.888-1G>C Likely pathogenic ★★ same condition
PEX16 p.Arg176Ter Pathogenic ★★ same condition
PEX16 p.Arg227Trp Likely pathogenic ★★ same condition
PEX16 p.Arg287Cys Pathogenic/Likely pathogenic ★★ same condition
PEX16 p.Arg287His Pathogenic/Likely pathogenic ★★ ⚠ same condition
PEX16 c.225+3G>A Uncertain significance ★★ same condition
PEX16 p.Ala114Thr 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/pex16-p-pro210 (accessed [today's date]).

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