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

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 8.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_003846.3	NP_003837.1	4	yes	-
ENST00000369306.8	ENSP00000358312.3	4	yes	-
NM_001184795.1	NP_001171724.1	4	-	-
ENST00000428634.1	ENSP00000414018.1	1	-	-

Phenotypes

GenCC

Source: genCC

• peroxisome biogenesis disorder 14B (Strong), mode of inheritance: AR
• peroxisome biogenesis disorder (Definitive), mode of inheritance: AR
• peroxisome biogenesis disorder 14B (Strong), mode of inheritance: AR
• Zellweger spectrum disorders (Supportive), mode of inheritance: AR
• peroxisome biogenesis disorder 14B (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 (228 variants)
• Inborn_genetic_diseases (41 variants)
• Peroxisome_biogenesis_disorder_14B (19 variants)
• PEX11B-related_disorder (14 variants)
• not_specified (3 variants)
• Peroxisome_biogenesis_disorder (1 variants)
• Radial_aplasia-thrombocytopenia_syndrome (1 variants)
• See_cases (1 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. These statistics are base on transcript: NM_003846.3. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			4	63	1	68
missense			122	3		125
nonsense	1	6	1			8
start loss		2				2
frameshift	2	4				6
splice donor/acceptor (+/-2bp)		2				2
Total	3	14	127	66	1

Highest pathogenic variant AF is 0.000009916012

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
		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

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

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