Is PEX16 p.Arg287= (c.861C>T) pathogenic?

PEX16 p.Arg287= (c.861C>T) is classified Uncertain significance in PEX16 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-13). Absent from gnomAD v4.1; Associated with peroxisome biogenesis disorder 8A (Zellweger).

What condition is associated with PEX16 p.Arg287= (c.861C>T)?

PEX16 p.Arg287= (c.861C>T) is associated with peroxisome biogenesis disorder 8A (Zellweger) (ClinVar).

How common is PEX16 p.Arg287= (c.861C>T) in the general population?

PEX16 p.Arg287= (c.861C>T) is absent from gnomAD v4.1 (gnomAD).

PEX16 p.Arg287=

c.861C>T · rs747883612 · VCV877671

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

peroxisome biogenesis disorder 8A (Zellweger)

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 0.63	GERP 1.2, phastCons 1
Overall
CADD	6.009	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: PEX16
Protein: p.Arg287=
Coding: c.861C>T
MANE Select: NM_004813
dbSNP: rs747883612
Type: single nucleotide variant
Location: chr11:45913845 (GRCh38)
Gene constraint: LOEUF 0.957 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 83.07
Residue 287: the 'interaction with pex19' region

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

Disease context

peroxisome biogenesis disorder 8A (Zellweger) — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PEX16 p.Arg287Cys Pathogenic/Likely pathogenic ★★ same residue
PEX16 p.Arg287His Pathogenic/Likely pathogenic ★★ ⚠ same residue
PEX16 p.Arg176Ter Pathogenic ★★ same condition
PEX16 p.Arg227Gln Uncertain significance ★★ same condition
PEX16 p.Arg271Gln Uncertain significance ★★ ⚠ same condition
PEX16 p.Arg293Cys Uncertain significance ★★ ⚠ same condition
PEX16 p.Asn180Lys Uncertain significance ★★ ⚠ same condition
PEX16 p.Leu206Val 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-arg287 (accessed [today's date]).

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