PEX5L

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

Basic information

Region (hg38): 3:179794957-180037053

Links

ENSG00000114757 ∙ NCBI:51555 ∙ OMIM:611058 ∙ HGNC:30024 ∙ Uniprot:Q8IYB4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PEX5L gene.

• Inborn genetic diseases (14 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PEX5L gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in PEX5L

This is a list of pathogenic ClinVar variants found in the PEX5L region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-179801904-T-G		not specified	Uncertain significance (Sep 16, 2021)
3-179801931-G-C		not specified	Uncertain significance (Oct 03, 2022)
3-179808316-T-C		not specified	Uncertain significance (Dec 19, 2022)
3-179808390-T-C		not specified	Uncertain significance (Jan 23, 2024)
3-179809643-A-C		not specified	Uncertain significance (Dec 07, 2021)
3-179811861-A-C		not specified	Uncertain significance (Jul 09, 2021)
3-179819873-G-A		not specified	Uncertain significance (Sep 16, 2021)
3-179819883-C-G		not specified	Uncertain significance (Dec 03, 2021)
3-179819924-C-T		not specified	Uncertain significance (Jun 06, 2023)
3-179859135-C-T		not specified	Uncertain significance (Dec 20, 2021)
3-179874377-C-A		not specified	Uncertain significance (Jan 04, 2024)
3-179875375-G-T		not specified	Uncertain significance (Aug 08, 2023)
3-179875404-C-T		not specified	Uncertain significance (Sep 17, 2021)
3-179875420-G-T		not specified	Uncertain significance (Oct 27, 2022)
3-179879946-G-C		not specified	Uncertain significance (Jan 29, 2024)
3-179879988-G-A		not specified	Uncertain significance (Aug 01, 2022)
3-179887705-G-A		not specified	Uncertain significance (Nov 01, 2022)
3-179898195-T-G		not specified	Uncertain significance (May 27, 2022)
3-179898210-T-C		not specified	Uncertain significance (Dec 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PEX5L	protein_coding	protein_coding	ENST00000467460	15	242096

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00799	0.992	125703	0	45	125748	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.85	193	341	0.566	0.0000181	4078
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000965	0.000964
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000163	0.000158
Middle Eastern	0.00	0.00
South Asian	0.0000670	0.0000653
Other	0.00	0.00

dbNSFP

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}.
• Pathway: Peroxisome - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.145

Intolerance Scores

• loftool: 0.168
• rvis_EVS: -0.98
• rvis_percentile_EVS: 8.8

Haploinsufficiency Scores

• pHI: 0.158
• hipred: Y
• hipred_score: 0.576
• ghis: 0.591

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.465

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pex5l
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: protein import into peroxisome matrix, docking;regulation of cAMP-mediated signaling
• Cellular component: peroxisomal membrane;cytosol;receptor complex
• Molecular function: peroxisome targeting sequence binding;peroxisome matrix targeting signal-1 binding;small GTPase binding