PEX11G

protein-coding

peroxisomal biogenesis factor 11 gamma, the group of Peroxins

Gene summary

The protein encoded by this gene is a member of the PEX11 family. This family is reported to regulate the number and size of peroxisomes in evolutionarily distant organisms. The protein encoded by this gene may induce clustering of peroxisomes. Alternative splicing results in multiple transcript variants that encode different protein isoforms. [provided by RefSeq, Jul 2012]

MANE transcript

NM_080662.4

Inheritance

AR

ClinVar variants

U:67B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.03

Max pathogenic AF

—

Genomic locus

chr19:7,476,875-7,497,449

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~20.6 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

peroxisome biogenesis disorderNO_KNOWN

Inheritance Pattern: AR

Disease ID:MONDO:0019234

Submitter: ClinGen

The relationship between PEX11G and Peroxisome Biogenesis Disorder, an autosomal recessive disorder, was evaluated using the ClinGen Clinical Validity Framework as of May, 2020. PEX11G is a member of the PEX11 family, which is composed of membrane elongation factors involved in regulation of peroxisome maintenance and proliferation. PEX11G has not been reported in relation to human disease, to the best of our knowledge. PMID: 26935981 reports that a homozygous PEX11G variant was identified by whole exome sequencing in a patient with mevalonate kinase deficiency. Two heterozygous variants in MVK as well as variants in other genes were detected in this patient. The authors suggest the PEX11G variant may be a modifier and implicated in the blurred vision phenotype in the patient. Of note, this variant is reported in gnomAD v2.1.1 at the highest MAF of 0.03814 in the non-Finnish European population with 62 homozygotes. Therefore, the PEX11G variant is not considered to be contributing towards any phenotype in the patient. In summary, no convincing evidence for a causal role for PEX11G in autosomal recessive peroxisome biogenesis disorder in humans has been reported (SOP Version 7).

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PEX11G variants in ClinVar

2 Conditions Cataloged
not specifiedTotal: 62
not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_080662.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
2
clinvar
1
clinvar
3
missense
63
clinvar
1
clinvar
64
nonsense
0
start loss
0
frameshift
1
clinvar
1
splice donor/acceptor (+/-2bp)
2
clinvar
2
Total00672170
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 31 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_080662.4RefSeqNP_542393.15MANE Select
ENST00000221480.6EnsemblENSP00000221480.15MANE Select
NM_001270539.2RefSeqNP_001257468.15Standard
NM_001300881.2RefSeqNP_001287810.14Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Peroxisome - Homo sapiens (human)
  • Beta Oxidation of Very Long Chain Fatty Acids
  • Adrenoleukodystrophy, X-linked
  • Carnitine-acylcarnitine translocase deficiency

Biological Process

  • peroxisome fission
  • regulation of peroxisome size

Molecular Function

  • protein binding

Cellular Component

  • peroxisome
  • integral component of peroxisomal membrane
  • intrinsic component of peroxisomal membrane
  • protein-containing complex

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000221480
Coding exons
5
Length
20575
Individuals with no LoFs
125659
Homozygous LoFs
0
Heterozygous LoFs
81
Defined
125740
p
0.000322
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.3491401291.090.000008221441
Missense (PolyPhen)5544.3761.2394549
Synonymous0.9074957.80.8480.00000349525
Loss of Function-0.07651110.71.036.23e-7107

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000250.00025rare
Latino/Admixed American0.0000600.000058rare
Ashkenazi Jewish00.0absent
East Asian0.00150.0015notable
Finnish0.0000470.000046rare
European (Non-Finnish)0.000230.00022rare
South Asian0.000730.00069rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Promotes membrane protrusion and elongation on the peroxisomal surface. {ECO:0000269|PubMed:20826455}.;

Recessive Scores

pRec
0.107

Intolerance Scores

LoFtool
0.836
RVIS EVS
0.33
RVIS percentile EVS
73.27

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.883

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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