PEX11B

peroxisomal biogenesis factor 11 beta, the group of Peroxins

Basic information

Region (hg38): 1:145911350-145918717

Links

ENSG00000131779 ∙ NCBI:8799 ∙ OMIM:603867 ∙ HGNC:8853 ∙ Uniprot:O96011 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• peroxisome biogenesis disorder 14B (Definitive), mode of inheritance: AR
• peroxisome biogenesis disorder 14B (Strong), mode of inheritance: AR
• peroxisome biogenesis disorder 14B (Strong), mode of inheritance: AR
• Zellweger spectrum disorders (Supportive), mode of inheritance: AR
• peroxisome biogenesis disorder (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Peroxisome biogenesis factor disorder 14B	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Biochemical; Craniofacial; Gastrointestinal; Genitourinary; Musculoskeletal; Neurologic; Renal	22581968

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PEX11B gene.

• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PEX11B 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			3	53	1	57
missense			107	1		108
nonsense		4	1			5
start loss		1	1			2
frameshift	2	1				3
inframe indel			3			3
splice donor/acceptor (+/-2bp)		1				1
splice region			4	6		10
non coding				22	4	26
Total	2	7	115	76	5

Highest pathogenic variant AF is 0.00000657

Variants in PEX11B

This is a list of pathogenic ClinVar variants found in the PEX11B region.

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

Position	Type	Phenotype	Significance	ClinVar
1-145912155-G-A		PEX11B-related disorder	Likely benign (Aug 29, 2023)
1-145912169-T-G			Uncertain significance (Sep 19, 2022)
1-145912170-G-A			Likely benign (Jul 15, 2022)
1-145912174-C-A			Uncertain significance (Apr 19, 2022)
1-145912174-C-T		Peroxisome biogenesis disorder 14B • Inborn genetic diseases	Uncertain significance (Nov 04, 2023)
1-145912175-G-A		Peroxisome biogenesis disorder 14B	Uncertain significance (Aug 15, 2022)
1-145912181-A-G		Inborn genetic diseases	Uncertain significance (Sep 24, 2024)
1-145912184-G-T		Inborn genetic diseases	Uncertain significance (Dec 21, 2023)
1-145912191-T-C			Likely benign (Mar 23, 2023)
1-145912195-G-T			Uncertain significance (Jun 13, 2022)
1-145912202-T-C			Uncertain significance (Nov 01, 2023)
1-145912215-G-T			Uncertain significance (Sep 18, 2017)
1-145912220-C-T		Inborn genetic diseases	Uncertain significance (May 23, 2023)
1-145912221-G-A		PEX11B-related disorder	Likely benign (Aug 16, 2023)
1-145912221-G-C			Likely benign (Jul 17, 2023)
1-145912224-G-A			Likely benign (Sep 05, 2023)
1-145912230-A-G			Likely benign (Jan 24, 2023)
1-145912238-C-T			Uncertain significance (Apr 09, 2018)
1-145912240-A-G			Uncertain significance (Aug 16, 2022)
1-145912245-A-C			Likely benign (Dec 17, 2022)
1-145912250-C-T			Uncertain significance (Mar 28, 2022)
1-145912252-C-A			Uncertain significance (Dec 11, 2023)
1-145912255-C-T			Uncertain significance (Sep 05, 2023)
1-145912256-G-A		Peroxisome biogenesis disorder 14B	Uncertain significance (Dec 19, 2024)
1-145912260-G-C			Likely benign (Oct 28, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PEX11B	protein_coding	protein_coding	ENST00000369306	4	7479

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000133	0.863	125722	0	25	125747	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.305	156	146	1.07	0.00000837	1603
Missense in Polyphen		60	53.775	1.1158		638
Synonymous	0.898	49	57.7	0.850	0.00000290	596
Loss of Function	1.36	8	13.4	0.599	9.37e-7	126

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000235	0.000235
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000897	0.0000879
Middle Eastern	0.000164	0.000163
South Asian	0.000131	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in peroxisomal proliferation (PubMed:9792670). May regulate peroxisome division by recruiting the dynamin-related GTPase DNM1L to the peroxisomal membrane (PubMed:12618434). Promotes membrane protrusion and elongation on the peroxisomal surface (PubMed:20826455). {ECO:0000269|PubMed:12618434, ECO:0000269|PubMed:20826455, ECO:0000269|PubMed:9792670}.
• Disease: DISEASE: Peroxisome biogenesis disorder 14B (PBD14B) [MIM:614920]: An autosomal recessive peroxisome biogenesis disorder characterized clinically by mild intellectual disability, congenital cataracts, progressive hearing loss, and polyneuropathy. Additionally, recurrent migraine-like episodes following mental stress or physical exertion, not a common feature in peroxisome disorders, are observed. {ECO:0000269|PubMed:22581968}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Peroxisome - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.191

Intolerance Scores

• loftool: 0.877
• rvis_EVS: -0.27
• rvis_percentile_EVS: 33.97

Haploinsufficiency Scores

• pHI: 0.350
• hipred: Y
• hipred_score: 0.576
• ghis: 0.534

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.980

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pex11b
• 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; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton 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); craniofacial phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: peroxisome organization;signal transduction;peroxisome fission;regulation of peroxisome size;protein homooligomerization
• Cellular component: mitochondrion;peroxisome;peroxisomal membrane;integral component of peroxisomal membrane;membrane;protein-containing complex
• Molecular function: protein binding;protein homodimerization activity