PEX5L

protein-coding

peroxisomal biogenesis factor 5 like, the group of Tetratricopeptide repeat domain containing

Gene summary

Enables peroxisome matrix targeting signal-1 binding activity and small GTPase binding activity. Predicted to be involved in protein import into peroxisome matrix, docking. Predicted to act upstream of or within maintenance of protein location and regulation of membrane potential. Located in cytosol. Part of signaling receptor complex. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_016559.3

Inheritance

—

ClinVar variants

U:60

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.3

Max pathogenic AF

—

Genomic locus

chr3:179,794,958-180,037,053

External References & Databases

Ensembl (ENSG00000114757)

Transcript & Mutation Effects

hg38 • Region Span ~242.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PEX5L variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 56

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016559.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			57 clinvar			57
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	60	0	0	60

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 63 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016559.3	RefSeq	NP_057643.1	15	MANE Select
ENST00000467460.6	Ensembl	ENSP00000419975.1	15	MANE Select
NM_001256750.2	RefSeq	NP_001243679.1	15	Standard
NM_001256751.2	RefSeq	NP_001243680.1	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Peroxisome - Homo sapiens (human)

Biological Process

protein import into peroxisome matrix, docking
regulation of cAMP-mediated signaling

Molecular Function

peroxisome targeting sequence binding
peroxisome matrix targeting signal-1 binding
small GTPase binding

Cellular Component

peroxisomal membrane
cytosol
receptor complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000467460
Coding exons: 15
Length: 242096
Individuals with no LoFs: 125703
Homozygous LoFs: 0
Heterozygous LoFs: 45
Defined: 125748
p: 0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.85	193	341	0.566	0.0000181	4078
Missense (PolyPhen)		61	141.25	0.43187		1629
Synonymous	0.368	129	134	0.960	0.00000797	1189
Loss of Function	3.98	11	37.2	0.296	0.00000180	443

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00072	0.00061	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00016	0.00016	rare
South Asian	0.000067	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Accessory subunit of hyperpolarization-activated cyclic nucleotide-gated (HCN) channels, regulating their cell-surface expression and cyclic nucleotide dependence. {ECO:0000250}.;

Recessive Scores

pRec: 0.145

Intolerance Scores

LoFtool: 0.168
RVIS EVS: -0.98
RVIS percentile EVS: 8.8

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.465

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium