Is PEX13 p.Phe179Val (c.535T>G) pathogenic?

PEX13 p.Phe179Val (c.535T>G) is classified Uncertain significance in PEX13 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-02). AlphaMissense: ambiguous (0.4353); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with PEX13 p.Phe179Val (c.535T>G)?

PEX13 p.Phe179Val (c.535T>G) is associated with Inborn genetic diseases (ClinVar).

How common is PEX13 p.Phe179Val (c.535T>G) in the general population?

PEX13 p.Phe179Val (c.535T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about PEX13 p.Phe179Val (c.535T>G)?

AlphaMissense predicts ambiguous (score 0.4353) — an in-silico prediction, not a clinical call.

PEX13 p.Phe179Val

c.535T>G · VCV4627288

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4353 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.4353	ambiguous
REVEL	0.462	indeterminate
SaProt	LLR -9.37	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.9	GERP 1.7, phastCons 1
Regional constraint	o/e 1.12	unconstrained · MANE · 31 kb · p 0.0078 · regional, not allelic
Overall
CADD	22.2	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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: PEX13
Protein: p.Phe179Val
Coding: c.535T>G
MANE Select: NM_002618
Type: single nucleotide variant
Location: chr2:61031861 (GRCh38)
Gene constraint: LOEUF 1.159 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 65.62 · 3 PDB
Residue 179: the 'targeting to peroxisomes' region; the 'interaction with pex19' region

Full PEX13 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PEX13 p.Ala2Pro Uncertain significance ★★ ⚠ same condition
PEX13 p.Ala364Thr Uncertain significance ★★ ⚠ same condition
PEX13 p.Arg189Trp Uncertain significance ★★ ⚠ same condition
PEX13 p.Gln4Pro Uncertain significance ★★ ⚠ same condition
PEX13 p.Glu378Lys Uncertain significance ★★ ⚠ same condition
PEX13 p.Gly128Arg Uncertain significance ★★ ⚠ same condition
PEX13 p.Gly216Ala Uncertain significance ★★ ⚠ same condition
PEX13 p.Ile291Val 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/pex13-p-phe179val (accessed [today's date]).

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