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Intellectual disability

Gene: PMPCB

Green List (high evidence)
PMPCB (peptidase, mitochondrial processing beta subunit)
EnsemblGeneIds (GRCh38): ENSG00000105819
EnsemblGeneIds (GRCh37): ENSG00000105819
OMIM: 603131, Gene2Phenotype
PMPCB is in 8 panels

2 reviews

Catherine Snow (Genomics England)

Green List (high evidence)

PMPCB identified by Konstantinos Varvagiannis following publication by Vögtle et al. (2018 - PMID: 29576218) who identified 5 individuals from 4 unrelated families (in one case consanguineous) who have biallelic pathogenic PMPCB variants.
PMPCB is in OMIM and Gene2Phenotype with relevant phenotype. Individuals reported have stagnation in their development before onset of symptoms including, delayed psychomotor development and ID. PMPCB is Green on relevant Mitochondrial disorders panel (Version 2.1). As phenotype of DD is relevant to ID panel PMPCB is classified as Green.
Created: 24 Oct 2019, 3:36 p.m. | Last Modified: 24 Oct 2019, 3:39 p.m.
Panel Version: 2.1083

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Publications

Created: 24 Oct 2019, 3:36 p.m.
Last Modified: 24 Oct 2019, 3:39 p.m.
Panel version: 2.1082

Konstantinos Varvagiannis (Other)

Green List (high evidence)

Biallelic pathogenic PMPCB variants cause, Multiple mitochondrial dysfunctions syndrome 6 (MIM 617954).

5 relevant individuals from 4 unrelated families (in one case consanguineous) have been reported by Vögtle et al. (2018 - PMID: 29576218).

Onset of symptoms (eg. hypotonia) often preceded a period of developmental regression/stagnation which was common in all individuals and occurred within the first 2 years of life, usually following febrile illness. In all cases neurological features were severe (lack of ambulation/speech). Seizures were observed in 4 individuals from 3 families, with onset at the age of 11-24m. MRI images demonstrated T2 signal hyperintensities of the basal ganglia with cerebellar and cerebral atrophy in some. Deterioration with early death was reported on three occasions, though some years after symptom onset.

Following exclusion of other diagnoses in some cases (eg. aCGH, epilepsy panel), WES identified biallelic PMPCB missense variants, supported by Sanger confirmation and segregation studies. The following variants were reported (NM_004279.2):
- c.523C>T (p.Arg175Cys) in trans with c.601G>C (p.Ala201Pro) [Fam A and B]
- c.524G>A (p.Arg175His) in trans with c.530T>G (p.Val177Gly) [Fam C]
- c.1265T>C (p.Ile422Thr) in homozygous state [Fam D with 2 affected sibs]

The gene encodes the catalytic (beta) subunit of the mitochondrial processing protease (MPP) which is responsible for the cleavage/maturation of nuclear-encoded mitochondrial precursor proteins after their import in mitochondria. The alpha subunit is encoded by PMPCA (green rating proposed for this panel).

Extensive studies demonstrated (perhaps a better summary provided by OMIM):
- Reduced PMPCB protein levels in mitochondria isolated from patient fibroblasts or patient-derived pluripotent stem cells.
- Frataxin maturation was impaired with accumulation of the intermediate form and lower amounts of mature FXN, indicating decrease in MPP activity.
- Analysis of the homologous Mas1 S. cerevisiae mutants was carried out, with the exception of Ile422Thr (corresponding to Mas1 - Ile398Thr), the introduction of which did not yield viable yeast strains. Homologous mutations led to a temperature-sensitive phenotype with accumulation of immature/unprocessed precursor proteins and decrease of mature/processed forms both in vivo or in organello (following isolation of mitochondria). Under conditions of heat stress, Mas1 mutations decreased biogenesis of Fe-S clusters.
- Respiratory chain complexes I-III contain Fe-S clusters. In muscle biopsy from an affected individual, complex II activity was significantly reduced (although this was not the case in fibroblasts or liver biopsy). Dysfunction of mitochondrial and cytosolic Fe-S cluster-dependent enzymes (eg. aconitase) was also shown in muscle tissue.

Regression/stagnation with seizures/non-achievement of milestones may justify testing for an ID / epilepsy gene panel. In addition, metabolic studies or mitochondrial respiratory chain complex studies were sometimes non-informative (lactate elevated in 3/5 subjects) or not carried out at all / in relevant tissues (muscle biopsy in 2 individuals, fibroblasts/liver biopsy did not demonstrate reduced complex activity when tested).

PMPCB is included in the ID gene panel of Radboudumc, as well as the SysID database. The gene is included in the DD panel of G2P associated with "Neurodegeneration in Early Childhood" (disease confidence : probable).

As a result, PMPCB can be considered for inclusion in both epilepsy and ID panels as green (or amber).
Sources: Literature, Radboud University Medical Center, Nijmegen
Created: 26 Sep 2019, 12:18 a.m. | Last Modified: 26 Sep 2019, 5:41 p.m.
Panel Version: 2.1046

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Multiple mitochondrial dysfunctions syndrome 6, 617954

Publications

Variants in this GENE are reported as part of current diagnostic practice

Created: 26 Sep 2019, 12:18 a.m.
Last Modified: 26 Sep 2019, 5:41 p.m.
Panel version: 2.1046

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Phenotypes
  • Multiple mitochondrial dysfunctions syndrome 6 OMIM:617954
  • multiple mitochondrial dysfunctions syndrome 6 MONDO:0054785
OMIM
603131
Clinvar variants
Variants in PMPCB
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

11 May 2021, Gel status: 3

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for gene: PMPCB were changed from Multiple mitochondrial dysfunctions syndrome 6, 617954 to Multiple mitochondrial dysfunctions syndrome 6 OMIM:617954; multiple mitochondrial dysfunctions syndrome 6 MONDO:0054785

24 Oct 2019, Gel status: 3

Set publications

Catherine Snow (Genomics England)

Publications for gene: PMPCB were set to

24 Oct 2019, Gel status: 3

Entity classified by Genomics England curator

Catherine Snow (Genomics England)

Gene: pmpcb has been classified as Green List (High Evidence).

26 Sep 2019, Gel status: 0

Created, Added New Source, Set mode of inheritance, Set Phenotypes, Set penetrance

Konstantinos Varvagiannis (Other)

gene: PMPCB was added gene: PMPCB was added to Intellectual disability. Sources: Literature,Radboud University Medical Center, Nijmegen Mode of inheritance for gene: PMPCB was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: PMPCB were set to Multiple mitochondrial dysfunctions syndrome 6, 617954 Penetrance for gene: PMPCB were set to Complete Review for gene: PMPCB was set to GREEN gene: PMPCB was marked as current diagnostic