PEX5L

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

Basic information

Region (hg38): 3:179794958-180037053

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.

not_specified (50 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. These statistics are base on transcript: NM_000016559.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			50 clinvar			50
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	50	0	0

Loading clinvar variants...

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