PEX11A

peroxisomal biogenesis factor 11 alpha, the group of Peroxins

Basic information

Region (hg38): 15:89677763-89690783

Links

ENSG00000166821 ∙ NCBI:8800 ∙ OMIM:603866 ∙ HGNC:8852 ∙ Uniprot:O75192 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• peroxisome biogenesis disorder (No Known Disease Relationship), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PEX11A gene.

• Inborn genetic diseases (24 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PEX11A 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				1		1
missense			23	2		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	3	0

Variants in PEX11A

This is a list of pathogenic ClinVar variants found in the PEX11A region.

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

Position	Type	Phenotype	Significance	ClinVar
15-89677777-T-G			Benign (Jun 19, 2021)
15-89683382-G-A		not specified	Uncertain significance (Nov 07, 2022)
15-89683398-C-G		not specified	Uncertain significance (Jun 05, 2023)
15-89683403-G-T		not specified	Uncertain significance (Jun 26, 2023)
15-89683430-T-C		not specified	Likely benign (Jun 23, 2021)
15-89683456-A-G		not specified	Uncertain significance (Dec 14, 2023)
15-89683463-C-G		not specified	Uncertain significance (Sep 16, 2021)
15-89683508-T-G		not specified	Uncertain significance (Dec 01, 2022)
15-89683510-T-G		not specified	Uncertain significance (May 10, 2022)
15-89683607-C-T		not specified	Uncertain significance (Feb 15, 2023)
15-89683608-C-G		not specified	Likely benign (Feb 28, 2024)
15-89683641-T-A			Likely benign (Mar 01, 2023)
15-89683648-T-A		not specified	Uncertain significance (Sep 17, 2021)
15-89683663-C-G		not specified	Uncertain significance (Jun 10, 2022)
15-89683684-A-C		not specified	Uncertain significance (Dec 28, 2022)
15-89683706-G-C		not specified	Uncertain significance (Dec 21, 2023)
15-89683727-G-C			Likely benign (Mar 01, 2023)
15-89683762-C-T		not specified	Uncertain significance (Feb 15, 2023)
15-89683799-C-T		not specified	Uncertain significance (Jul 13, 2021)
15-89683874-G-A		not specified	Uncertain significance (Aug 17, 2021)
15-89683884-G-T		not specified	Uncertain significance (Jan 18, 2022)
15-89683897-A-G		not specified	Uncertain significance (Feb 10, 2023)
15-89683915-T-C		not specified	Uncertain significance (Jul 11, 2023)
15-89686436-C-T		not specified	Uncertain significance (Feb 13, 2023)
15-89686451-C-T		not specified	Uncertain significance (Sep 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PEX11A	protein_coding	protein_coding	ENST00000300056	3	13020

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.45e-7	0.314	125697	0	49	125746	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.100	132	135	0.976	0.00000691	1593
Missense in Polyphen		32	42.349	0.75563		573
Synonymous	0.0749	50	50.7	0.987	0.00000236	510
Loss of Function	0.372	10	11.4	0.881	7.56e-7	115

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000399	0.000398
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.000266	0.000264
Middle Eastern	0.000381	0.000381
South Asian	0.0000980	0.0000980
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in peroxisomal proliferation and may regulate peroxisomes division (PubMed:9792670). May mediate binding of coatomer proteins to the peroxisomal membrane (By similarity). Promotes membrane protrusion and elongation on the peroxisomal surface (PubMed:20826455). {ECO:0000250|UniProtKB:O70597, ECO:0000269|PubMed:20826455, ECO:0000269|PubMed:9792670}.
• Pathway: Peroxisome - Homo sapiens (human);Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha) (Consensus)

Recessive Scores

• pRec: 0.130

Intolerance Scores

• loftool: 0.738
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24

Haploinsufficiency Scores

• pHI: 0.0710
• hipred: N
• hipred_score: 0.251
• ghis: 0.545

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.939

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pex11a
• Phenotype: growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); liver/biliary system phenotype

Gene ontology

• Biological process: peroxisome organization;signal transduction;peroxisome membrane biogenesis;peroxisome fission;regulation of lipid metabolic process;regulation of peroxisome size;brown fat cell differentiation
• Cellular component: peroxisome;peroxisomal membrane;integral component of peroxisomal membrane;protein-containing complex
• Molecular function: protein binding;protein homodimerization activity