# A PMM2-CDG caused by an A108V mutation associated with a heterozygous 70 kilobases deletion case report

Elodie Lebredonchel, A. Riquet, D. Neut, F. Broly, G. Matthijs, André Klein,

Francois Foulquier

► To cite this version:

Elodie Lebredonchel, A. Riquet, D. Neut, F. Broly, G. Matthijs, et al.. A PMM2-CDG caused by an A108V mutation associated with a heterozygous 70 kilobases deletion case report. Italian Journal of Pediatrics, 2022, Italian Journal of Pediatrics, 48 (1), 10.1186/s13052-022-01355-x. hal-03857602

HAL Id: hal-03857602

https://hal.univ-lille.fr/hal-03857602

Submitted on 17 Nov 2022

HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d'enseignement et de
recherche français ou étrangers, des laboratoires
publics ou privés.

<figure><img src="image_1.png" /></figure>

Distributed under a Creative Commons Attribution 4.0 International License
CASE REPORT

Open Access

<figure><img src="image_2.png" /></figure>

Check for
updates

# A PMM2-CDG caused by an A108V mutation associated with a heterozygous 70 kilobases deletion case report

E. Lebredonchel<fnref n="1" />,²* ID, A. Riquet³, D. Neut⁴, F. Broly⁵, G. Matthijs⁶, A. Klein<fnref n="1" />,²† and F. Foulquier<fnref n="1" />†

## Abstract

**Background:** Congenital Disorders of Glycosylation (CDG) are a large group of inborn errors of metabolism with more than 140 different CDG types reported to date (1). The first characterized, PMM2-CDG, with an autosomal recessive transmission, is also the most frequent. The *PMM2* gene encodes a phosphomannomutase. Here, a novel genetic variation causing PMM2-CDG is reported.

**Case presentation:** We report the case of a French child, from healthy and unrelated parents, presenting congenital ataxia with hypotonia, hyperlaxity, inverted nipples, as well as altered coagulation parameters and liver function. Transferrin isoelectrofocusing revealed a typical type I CDG profile. Direct Sanger sequencing and quantitative PCR of *PMM2* revealed a unique and novel genotype. On one allele, the patient was heterozygote with a known missense variant NM_000303.3(PMM2):c.323C > T, p.Ala108Val in exon 4. On the second allele, whole genome sequencing (WGS) indicated the presence of a novel heterozygous 70 kb deletion.

**Conclusion:** We report in the present paper the largest known heterozygous deletion of a *PMM2* gene. The observation reveals the impact of a precise diagnostic on genetic counselling: by using WGS, an erroneous conclusion of homozygosity in the case of a relatively rare variant could be avoided, and an index patient with healthy and unrelated parents correctly identified.

**Keywords:** CDG, PMM2, Deletion mutation, PMM2-CDG, Whole genome sequencing

## Background

Congenital Disorders of Glycosylation (CDG) are a rapidly expanding family of genetic diseases. Today, 140 different CDG subtypes have been reported [1] categorized in 2 groups: CDG-I, affecting steps before the oligosaccharide precursor transfer in the endoplasmic reticulum, and CDG-II, affecting the steps following the transfer, mostly in the Golgi apparatus. The

first patient cases were reported 40 years ago by Jaeken et al., [2]. Mutations in *PMM2* (OMIM 601,785), a gene on chromosome 16p13 encoding a phosphomannomutase were shown to be responsible for the disease. This enzyme catalyzes the conversion in the cytosol of mannose-6-P to mannose-1-P, necessary for the synthesis of donor substrates for glycosylation, GDP-mannose, and Dol-P-mannose.

First named CDG-Ia then changed into PMM2-CDG in 2009 [3], the disease is thought to represent 70% of the total CDG cases, with an estimated incidence around 1:20 000 [4]. The spectrum of clinical phenotypes and severity is broad and is characterized with mainly a psychomotor development impairment associated with cerebellar hypoplasia, hypotonia, dysmorphia, and coagulopathy

<footnote>†A. Klein and F. Foulquier equally contributed to this work.</footnote>

<footnote>*Correspondence: elodie.lebredonchel@chu-lille.fr</footnote>

<footnote n="1">¹ UMR 8576, Univ. Lille, CNRS, UGSF - Unité de Glycobiologie Structurale Et Fonctionnelle, 59000 Lille, France
Full list of author information is available at the end of the article</footnote>
[5]. The lethality rate in the first 4 years of life is about 20%. Beyond childhood, PMM2-CDG patients have a good life expectancy [6]. The number of *PMM2* mutations classified in HGMD (https://my.qiagendigitalinsights.com) is 142, most of these, 113, are missense mutations and the most frequent is p.Arg141His (R141H) [7]. We report the particular genotype of a PMM2-CDG patient with a heterozygous p.Ala108Val (A108V) mutation on one allele and a first-described > 70 kb-deletion on the other allele.

## Case presentation

We report the case of a PMM2-CDG French child of Caucasian descent. She was born at term with a length of 48 cm for 3.110 kg, after uncomplicated pregnancy with vaginal delivery. The AGPAR score was 10 both at 1 min and 5 min and the newborn screening results were normal. The parents are unrelated and the 6-years older brother is healthy. Parents reported abnormal abrupt movements of the child after birth that stopped spontaneously.

Biologically, at 9 months of age, elevated transaminases $TGO=50$ UI/L, $TGP=51$ [normal values 10–35 UI/L] and normal coagulation parameters with $ATIIIA=63\%$ [normal values 80–120%] and $FXI$ 53% at the lower limit [normal values 50–150%] were assayed. The cytology and the thyroid function were normal.

The clinical examination at 9 months of age revealed ataxia, hypotonia, hyperlaxity, strabismus, esotropia, feeding difficulties, and inverted nipples. The child was calm and exclusively breastfed with an absence of facial dysmorphia and no sleeping disorders. At that time, the girl presented an inability to reach a seated posture. The diagnosis of CDG was oriented by an abnormal pattern in serum transferrin isoelectrofocusing [8] with an elevation of asialo- and disialo-transferrin, typical from a type I CDG (Fig. 1). Brain MRI revealed cerebellar abnormalities with vermis hypoplasia. The child finally reaches a seated posture at 11 months of age.

## Genetic testing

Direct Sanger sequencing of the 8 exons of *PMM2* reported a seemingly homozygous variant rs200203569 NM_000303.3(PMM2): c.323C > T in exon 4. The variant leads to a missense substitution of alanine 108 to proline (p.Ala108Pro), commonly named A108V, known to be pathogenic (ClinVar, SIFT, Mutation Taster). The A108V mutation is quite rare and is often associated with R141H, the most common deleterious *PMM2* mutation, in compound heterozygous patients [9]. A homozygous presentation of R141H variant is thought

to be incompatible with life as no case was reported so far [10]. For the A108V variant, the gnomAD (2.1) website reports a frequency of 0.0012% in the overall population. To our knowledge, no homozygous A108V patient is reported in the literature and, as the parents were unrelated, further genetic explorations were conducted. Direct Sanger sequencing of *PMM2* of the paternal DNA reported a heterozygous A108V mutation while no mutation was found in the mother. At the time of the genetic exploration, the seemingly second variant could have been either due to the de novo variant or to the absence of sequence at the same location on the other allele. A quantitative PCR (qPCR) of the 13 exons was performed, showing a reduction of the DNA of the gene by 50% in the mother and the proband from exon

<figure><img src="image_3.png" /><figcaption>**Fig. 1** Distribution of transferrin glycoforms via transferrin isoelectrofocusing of the patient compared to a control. Numbers 0, 2, 3, 4, 5, and 6 indicate the migration position of the asialo-, disialo-, trisialo-, tetrasialo-, pentasialo-, and hexasialotransferrin forms respectively</figcaption></figure>
<figure><img src="image_4.png" /></figure>

3 to exon 8, the last exon of *PMM2* (Fig. 2). The hypothesis of the de novo variant was rejected as the heterozygous deletion in *PMM2* gene was found. To evaluate the extent of the deletion that goes beyond *PMM2* gene, Whole Genome Sequencing (WGS) was performed. WGS was preferred to CGH array to accurately determine the exact position of the breakpoints. WGS allowed to delineate the deletion of 70,453 bp in position chr16:8,897,826–8,968,278 (Fig. 3). In the HGMD database, the largest deletion reported is 28 kb-long.

The deletion also affects a part of *CARHSP1* (Calcium Regulated Hear Stable Protein 1) (OMIM: 616,885) gene that plays a role in TNF mRNA stabilization, seemingly not affecting the phenotype.

## Discussion and conclusions

In the present study, we described the case of a PMM2-CDG patient with congenital ataxia. The genotype identified in the child is novel. The clinical course was relatively mild for a child with PMM2-CDG as the child does not present facial dysmorphia. Given that the maternal mutation could not be detected upon Sanger sequencing, further investigations were performed to precise the genetic transmission of the disease.

A108V mutation was first described in France [7] and the effect on the enzyme activity is unknown.

When associated to a mutation in R141H the remaining phosphomannomutase activity in leucocytes is 0.09% [11].

Quantitative PCR and WGS allowed to identify a large deletion on the maternal allele. A new deletion of 70,453 bp in position chr16:8,897,826–8,968,278 could be accurately detected with WGS including 6 exons of *PMM2* and a part of *CARHSP1* gene. Knockout of CARHSP1 has demonstrated the role of CARHSP1 as a TNF-α mRNA stability enhancer [12]. GnomAD database reports various loss of function heterozygote mutation for CARHSP1, indicating that the observed pathology is mainly due to the phosphomannomutase defect.

To our knowledge, this is the largest *PMM2* deletion reported so far. Our example illustrates the usefulness of WGS in the case of an apparent homozygous variant in an unrelated family. Wherever possible, compound heterozygosity has to be confirmed with a parental genetic study. As the disease transmission for the couple is 25%, an antenatal diagnostic can now be proposed for future pregnancies.

This case underlines the importance of the correlation between the phenotype description and the genetic study, especially in disorders with a wide phenotypic spectrum like PMM2-CDG [13], where it is
<figure><img src="image_5.png" /></figure>

essential for a correct diagnosis to search thoroughly over the appearances.

In case of strong suspicion of PMM2-CDG based on the clinical phenotypes and despite the absence of transferrin abnormalities, the molecular analysis should be performed to avoid any diagnostic deadlocks.

**Abbreviations**

CDG: Congenital Disorder of Glycosylation; PMM2: Phosphomannomutase 2;

WGS: Whole Genome Sequencing; Bp: Base pair.

**Acknowledgements**

We thank the patient's parents for their kind participation and support.

**Authors' contributions**

Reported the case: N.D, R.A, Conducted the analyses: L.E, B.F, Analysed the data: L.E, B.F, Wrote the paper: L.E, FF, K.A, MG. All authors read and approved the final manuscript.

**Funding**

This work was supported by the Agence Nationale de la Recherche (ANR: Solv-CDG).

**Availability of data and materials**

The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request.

**Declarations**

**Ethics approval and consent to participate**

Informed consent for genetic testing has been sign by the parent of the index case and is available on request. Not ethic committee is required in the context of a unique case report in the country were the analyses were made.

All methods were performed in accordance with the ethical standards as laid down in the Declaration of Helsinki and its later amendments or comparable ethical standards.

**Consent for publication**

Informed consent was obtained from parents to publish data on the patient.

**Competing interests**

The authors have declared that no competing interests exist.

**Author details**

¹UMR 8576, Univ. Lille, CNRS, UGSF - Unité de Glycobiologie Structurale Et Fonctionnelle, 59000 Lille, France. ²Centre de Biologie Et Pathologie, Lille Medical Center, University of Lille, UAM de glycopathologies, 59000 Lille, France.

³Lille University Hospital Center Paediatrics, 59000 Lille, France. ⁴Cabinet de Pédiatrie, 93 Rue de la Paix, 62200 Boulogne-sur-Mer City, France. ⁵Centre Hospitalier Régional Universitaire de Lille Centre de Biologie Pathologie, 59000 Lille, France. ⁶Laboratory for Molecular Diagnosis, Center for Human Genetics, 3000 Leuven, KU, Belgium.

Received: 7 January 2022 Accepted: 27 August 2022

Published online: 11 October 2022
## References

1. Ondruskova N, Cechova A, Hansikova H, Honzik T, Jaeken J. Congenital disorders of glycosylation: Still « hot » in 2020. Biochim Biophys Acta Gen Subj janv. 2021;1865(1):129751.

2. Jaeken J, Vanderschueren-Lodeweyckx M, Casaer P, Snoeck L, Corbeel L, Eggermont E, et al. Familial psychomotor retardation with markedly fluctuating serum prolactin, FSH and GH levels, partial TBG-deficiency, increased serum arylsulphatase A and increased CSF protein: a new syndrome?: 90. Pediatric Research févr. 1980;14(2):179-179.

3. Aebi M, Helenius A, Schenk B, Barone R, Fiumara A, Berger EG, et al. Carbohydrate-deficient glycoprotein syndromes become congenital disorders of glycosylation: an updated nomenclature for CDG. First International Workshop on CDGS. Glycoconj J. 1999;16(11):669-71.

4. Schollen E, Kjaergaard S, Legius E, Schwartz M, Matthijs G. Lack of Hardy-Weinberg equilibrium for the most prevalent PMM2 mutation in CDG-la (congenital disorders of glycosylation type Ia). Eur J Hum Genet mai. 2000;8(5):367-71.

5. Jaeken J, Stibler H, Hagberg B. The carbohydrate-deficient glycoprotein syndrome. A new inherited multisystemic disease with severe nervous system involvement. Acta Paediatr Scand Suppl. 1991;375:1-71.

6. Pajusalu S, Vals MA, Mihkla L, Šamarina U, Kahre T, Õunap K. The Estimated Prevalence of N-Linked Congenital Disorders of Glycosylation Across Various Populations Based on Allele Frequencies in General Population Databases. Front Genet. 2021;12:719437. https://doi.org/10.3389/fgene. 2021.719437.

7. Matthijs G, Schollen E, Bjursell C, Erlandson A, Freeze H, Imtiaz F, et al. Mutations in PMM2 that cause congenital disorders of glycosylation, type Ia (CDG-la). Hum Mutat. 2000;16(5):386-94.

8. Stibler H, Beaugé F, Bjørneboe A, Aufrère G. Transferrin microheterogeneity in rats treated chronically with ethanol. Pharmacol Toxicol avr. 1989;64(4):383-5.

9. Le Bizec C, Vuillaumier-Barrot S, Barnier A, Dupré T, Durand G, Seta N. A new insight into PMM2 mutations in the French population. Hum Mutat mai. 2005;25(5):504-5.

10. Matthijs G, Schollen E, Van Schaftingen E, Cassiman JJ, Jaeken J. Lack of Homozygotes for the Most Frequent Disease Allele in Carbohydrate-Deficient Glycoprotein Syndrome Type 1A. Am J Human Genetics. 1998;62(3):542-50.

11. Matthijs G, Schollen E, Pardon E, Veiga-Da-Cunha M, Jaeken J, Cassiman JJ, et al. Mutations in PMM2, a phosphomannomutase gene on chromosome 16p13 in carbohydrate-deficient glycoprotein type I syndrome (Jaeken syndrome). Nat Genet. 1997;16(1):88-92.

12. Pfeiffer JR, McAvoy BL, Fecteau RE, Deleault KM, Brooks SA. CARHSP1 is required for effective tumor necrosis factor alpha mRNA stabilization and localizes to processing bodies and exosomes. Mol Cell Biol janv. 2011;31(2):277-86.

13. Vuillaumier-Barrot S, Isidor B, Dupré T, Le Bizec C, David A, Seta N. Expanding the Spectrum of PMM2-CDG Phenotype. In: SSIEM, éditeur. JIMD Reports - Case and Research Reports, 2012/2 [Internet]. Berlin, Heidelberg: Springer Berlin Heidelberg; 2011. p. 123-5. (JIMD Reports; vol. 5). Available on:https://doi.org/10.1007/8904_2011_114 Cité 2022 avr 29

## Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Ready to submit your research? Choose BMC and benefit from:

* fast, convenient online submission

* thorough peer review by experienced researchers in your field

* rapid publication on acceptance

* support for research data, including large and complex data types

* gold Open Access which fosters wider collaboration and increased citations

* maximum visibility for your research: over 100M website views per year

At BMC, research is always in progress.

Learn more biomedcentral.com/submissions

<figure><img src="image_6.png" /></figure>