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Intellectual disability

Gene: PMPCA

Amber List (moderate evidence)

PMPCA (peptidase, mitochondrial processing alpha subunit)
EnsemblGeneIds (GRCh38): ENSG00000165688
EnsemblGeneIds (GRCh37): ENSG00000165688
OMIM: 613036, Gene2Phenotype
PMPCA is in 11 panels

2 reviews

Rebecca Foulger (Genomics England curator)

Comment on list classification: Updated rating from Grey to Amber. PMPCA was added and rated Green by Konstantinos Varvagiannis. Although there are sufficient (3) literature cases overall, the phenotype is variable across cases: 3 families with a possible Founder variant in PMID:25808372, no ID reported in PMID:26657514, 1 family in PMID:27148589 and 1 individual in PMID:30617178. Therefore rated Amber awaiting further cases.
Created: 24 Oct 2019, 9:27 a.m. | Last Modified: 24 Oct 2019, 9:27 a.m.
Panel Version: 2.1070
Summary of evidence (see Konstantinos Varvagiannis' reviews for full details):
PMID: 25808372 (Jobling et al, 2015): All 17 patients (4 families) present with non-progressive cerebellar ataxia, and the majority have intellectual disability of variable severity. ID was seen in Families 1-3 (all Lebanese and all with the same A377T variant, suggesting Founder effect). ID was not recorded in the single patient from Family 4 (French) with Ser96Leu variant.

PMID:26657514 (Choquet et al., 2016) report an additional family wiht a PMPCA variant. The authors note that in contrast to the Jopling study, ID was not observed in their families, and patients have a milder disease course.

PMID:27148589 (Joshi et al., 2016) describe 2 Lebanese cousins with developmental delay amongst their phenotypes and compound het variants in PMPCA. Unaffected siblings were wild type or heterozygous for a single variant.

PMID:30617178 (Rubegni et al., 2019) report a 7 year old boy with global DD and a homozygous Arg185Trp variant in PMPCA.
Created: 24 Oct 2019, 9:13 a.m. | Last Modified: 24 Oct 2019, 9:13 a.m.
Panel Version: 2.1069

Konstantinos Varvagiannis (Other)

Green List (high evidence)

Biallelic pathogenic PMPCA variants cause Spinocerebellar ataxia, autosomal recessive 2 (SCAR2 - MIM 213200). More than 20 individuals from several unrelated families have been reported. At least 6 different pathogenic variants have been identified. Loss of PMPCA function is the suggested mechanism. ID is a feature of the disorder.

PMPCA encodes the α-subunit of mitochondrial processing peptidase (αMPP), a heterodimeric enzyme responsible for the cleavage of nuclear-encoded mitochondrial precursor proteins after import in the mitochondria (summary by Jobling et al and OMIM).

Arguments for involvement of the gene include the highly similar phenotype, segregation studies, expression of the gene in fetal and relevant adult tissues (in brain/cerebellum/cerebellar vermis), lower protein levels demonstrated for some variants, abnormal processing of frataxin (in line with the role of αMPP) demonstrated in most cases, rescue of the maturation defect upon transduction of wt PMPCA cDNA, disruption of REDOX balance in patient cells, etc.

Relevant studies are summarized below.

PMPCA is included in gene panels for ID offered by several diagnostic laboratories (incl. Radboud UMC, GeneDx, etc) and listed as a confirmed ID gene in SysID. It is not associated with any phenotype in G2P.

As a result, this gene can be considered for inclusion in the current panel probably as green (or amber).

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[1] - Jobling et al. (2015 - PMID: 25808372) described the phenotype of 17 individuals from 4 families, all presenting with non-progressive cerebellar ataxia and the majority with ID of variable severity (15/17 - relevant to the current panel). Individuals from 3 of the families - all of Lebanese origin - were homozygous for NM_015160.3:c.1129G>A (p.Ala377Thr). A further similarly affected subject was compound heterozygous for c.287C>T (p.Ser96Leu) and c.1543G>A (p.Gly515Arg).

The homozygous variant in the first family was found within a 2.85 Mb linkage region on chr 9q34. An additional variant within this region (in CAMSAP1) was discarded following results in other families of the same origin.

Semi-quantitative RT-PCR demonstrated fetal expression of the PMPCA as well as relatively higher expression in adult brain, cerebellum and cerebellar vermis.

As for Ala377Thr, protein levels were shown to be lowest in affected individuals (LCLs, fibroblasts) and low - though somewhat higher - in carrier parents (LCL) compared to controls. RT-PCR on total RNA from LCLs did not show evidence of abnormal transcripts/additional splicing defect. Localization of mutant protein and morphology of mitochondrial reticulum was similar to controls. Maturation of frataxin - the protein depleted in Friedreich ataxia - was shown to be abnormal in patient lymphoblasts, compatible with the role of αMPP. In line with abnormal mitochondrial function, REDOX balance was increased in patient cells.

[2] - Choquet et al. (2016 - PMID: 26657514) reported on 2 sibs - born to distantly related parents. The authors noted a phenotype corresponding to SCAR2 although the presentation was somewhat milder, intellectual disability was not a feature (despite some learning difficulties in one) and ataxia was progressive. WES demonstrated homozygosity for NM_015160:c.766G>A (p.Val256Met). Western blot in patient lymphoblasts showed αMPP levels similar to carriers and controls. Abnormal maturation (accumulation of specific isoforms) was shown for frataxin.

[3] - Joshi et al. (2016 - PMID: 27148589) described the phenotype of 2 cousins belonging to a large Lebanese pedigree. Presentation in both was compatible with multisystem involvement incl. profound global DD, severe hypotonia, weakness, respiratory insufficiency, blindness suggestive of mitochondrial disorder. mtDNA, analyses of mitochondrial focused nuclear gene panel and aCGH were non-diagnostic. Both subjects were compound heterozygous for NM_015160.3:c.1066G>A (p.Gly356Ser) and c.1129G>A (p.Ala377Thr) following WES, with compatible segregation studies within the family. Western blot revealed PMPCA levels similar to control. Reduction of PMPCA staining and abnormally enlarged mitochondria were observed upon immunofluorescence in patient fibroblasts. Frataxin processing was abnormal. Lentiviral transduction of patient fibroblasts with wt PMPCA cDNA, led to increased PMPCA levels and correction of frataxin processing.

[4] - Rubegni et al. (2019 - PMID: 30617178) report on a 7-y.o. boy with global DD, spastic-ataxic gait and 'low IQ'. MRI images were suggestive of cerebellar atrophy with hyperintensity in the striatum. The child was homozygous for c.553C>T / p.Arg185Trp (reference not specified, although the variant would be compatible with NM_015160.3).
Sources: Literature, Radboud University Medical Center, Nijmegen
Created: 23 Sep 2019, 3:23 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Spinocerebellar ataxia, autosomal recessive 2 (MIM 213200)

Publications

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

History Filter Activity

24 Oct 2019, Gel status: 2

Entity classified by Genomics England curator

Rebecca Foulger (Genomics England curator)

Gene: pmpca has been classified as Amber List (Moderate Evidence).

23 Sep 2019, Gel status: 0

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

Konstantinos Varvagiannis (Other)

gene: PMPCA was added gene: PMPCA was added to Intellectual disability. Sources: Literature,Radboud University Medical Center, Nijmegen Mode of inheritance for gene: PMPCA was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: PMPCA were set to 25808372; 26657514; 27148589; 30617178 Phenotypes for gene: PMPCA were set to Spinocerebellar ataxia, autosomal recessive 2 (MIM 213200) Penetrance for gene: PMPCA were set to Complete Review for gene: PMPCA was set to GREEN gene: PMPCA was marked as current diagnostic