Clinical utility gene card for: acrodermatitis enteropathica – update 2015

UPDATE TO: _European Journal of Human Genetics_ (2012) 20, doi:10.1038/ejhg.2011.227; published online 14 December 2011 1. DISEASE CHARACTERISTICS 1.1 NAME OF THE DISEASE (SYNONYMS)

Acrodermatitis enteropathica (AEZ). 1.2 OMIM# OF THE DISEASE 201100. 1.3 NAME OF THE ANALYZED GENES OR DNA/CHROMOSOME SEGMENTS SLC39A4.1 1.4 OMIM# OF THE GENE(S) 607059. 1.5 VARIANT SPECTRUM

AEZ is a rare autosomal recessive form of zinc deficiency. Individuals with a genuine AEZ have either homozygous or compound heterozygous variants of _SLC39A4_. Thirty-four variants clearly

affecting _SLC39A4_ function have been reported so far: 16 missense, four nonsense, three splice-site, and 11 frameshifting indels.2, 3, 4 Seven additional variants of unknown significance

were also reported,3 among which three can be considered likely deleterious—two missense and a splice-site variant. No hotspot-variant region is observed, as alterations are evenly

distributed all along the 12 exons. Except for a few cases where a founder effect is suspected, most of the variants affecting _SLC39A4_ function are private. All published variants that

affect _SLC39A4_ function and variants of unknown significance will be available soon in the public LOVD database under construction that is dedicated to _SLC39A4_ (www.LOVD.nl/SLC39A4). 1.6

ANALYTICAL METHODS Single-nucleotide variants and indels are detected by bidirectional sequencing of the 12 exons of _SLC39A4_ and their flanking intronic sequences, using either Sanger

sequencing of PCR products or high-throughput sequencing (HTS) targeting the regions of interest with a recommended minimal read depth of 30 × and preferably of at least 100 ×. Whole exome5

or even whole-genome sequencing may also be used for variant detection, provided the sequence quality meets diagnostic requirements. Larger deletions or duplications involving at least one

exon can be found by analysis of HTS data or they can be screened by a quantitative method such as quantitative multiplex PCR of short fluorescent fragments or multiplex ligation-dependent

probe amplification. 1.7 ANALYTICAL VALIDATION The first level of validation is the sequencing of both strands. Any suspected new variant present on both strands is then submitted to an

internal validation through analysis of variants found in previous patients; it is also compared with public variant databases (eg, dbSNP (http://www.ncbi.nlm.nih.gov/SNP/), Exome Variant

Server (http://evs.gs.washington.edu/niehsExome/), 1000 genomes (http://www.1000genomes.org/), ExAC Browser (http://exac.broadinstitute.org/), or LOVD (www.LOVD.nl/SLC39A4)) and its

potential deleterious effect on _SLC39A4_ function is searched through prediction by bioinformatic tools. Single-nucleotide variants or copy-number variations identified through HTS have to

be confirmed by Sanger sequencing or by a quantitative method, respectively. Whenever possible, segregation between the variant and the phenotype should be assessed by testing

affected/unaffected relatives and obligatory carriers in the family, to exclude possible variants that would not affect _SLC39A4_ function. 1.8 ESTIMATED FREQUENCY OF THE DISEASE (INCIDENCE

AT BIRTH (BIRTH PREVALENCE) OR POPULATION PREVALENCE) The only data available in literature indicates an incidence of 1:500 000 births in Denmark6

(http://www.orpha.net/orphacom/cahiers/docs/GB/Prevalence_of_rare_diseases_by_alphabetical_list.pdf). This is consistent with the frequency of rare variants known to affect or potentially

affecting _SLC39A4_ function, which are released in public variant database, considering an autosomal recessive mode of inheritance. An unofficial study conducted in France in the late 90s

identified 15 families. The frequency seems artificially much higher in countries of the Mediterranean basin, probably because of a founder effect due to a higher incidence of consanguinity.

1.9 IF APPLICABLE, PREVALENCE IN THE ETHNIC GROUP OF INVESTIGATED PERSON Not applicable. 1.10 DIAGNOSTIC SETTING Comment: AEZ is an autosomal recessive syndrome of severe permanent zinc

deficiency due to a malabsorption of zinc by a defective zinc transporter, SLC39A4 (or ZIP4), expressed mainly in the brush border of jejunum and duodenum enterocytes.1 _(Differential)

diagnostics—_Testing of _SLC39A4_ is indicated in patients who developed clinical symptoms and biological signs of a severe zinc deficiency, at birth or after weaning (clinical and

biological features are described in section 3.1.2). The identification of a molecular anomaly in _SLC39A4_ gives definitive proof of AEZ and enables its distinction from transient forms of

zinc deficiency that can: (1) have a genetic component, such as the transient neonatal zinc deficiency (TNZD) caused by variant affecting _SLC30A2_ function, which reduces milk zinc

concentration in nursing mothers of exclusively breastfed infants,4, 7 or (2) be acquired by an unbalanced diet too rich in phytates—found notably in cereals—by total parenteral nutrition or

prematurity. In a few cases, genetic testing may also differentiate AEZ from biotin deficiency, atopic dermatitis, or rare genodermatoses mimicking AEZ (Küry _et al._ manuscript under

preparation), especially when biochemical results are ambiguous (see 3.1.3). _Predictive testing—_it is not applicable in most cases, because AEZ symptoms and signs occurs in the perinatal

period. The value of the genetic test would therefore rather be considered diagnostic than predictive. _Prenatal—_it is technically feasible, but it is not recommended. Zinc supplementation

can indeed be applied immediately in a newborn suspected of AEZ on the basis of a zinc dosage (see 3.1.2). Besides, the risk for the mother inherent to prenatal testing cannot be neglected.

Genetic testing comes in a second time, in order to confirm clinical diagnosis. 2. TEST CHARACTERISTICS 2.1 ANALYTICAL SENSITIVITY (PROPORTION OF POSITIVE TESTS IF THE GENOTYPE IS PRESENT)

Theoretically 100% if variants affecting _SLC39A4_ function are localized within exons or flanking introns sequences, which encompasses at least 80% of this type of variants. 2.2 ANALYTICAL

SPECIFICITY (PROPORTION OF NEGATIVE TESTS IF THE GENOTYPE IS NOT PRESENT) 100%. 2.3 CLINICAL SENSITIVITY (PROPORTION OF POSITIVE TESTS IF THE DISEASE IS PRESENT) The clinical sensitivity can

be dependent on variable factors such as age or family history. In such cases a general statement should be given, even if quantification can only be made case by case. Overall, variants

affecting _SLC39A4_ function are observed in about 48% of the index cases tested: ~40% of the patients are homozygotes or compound heterozygotes, whereas 8% are heterozygotes only.8 In these

last ones, we cannot exclude the presence of a second anomaly in unexplored regions of the _SLC39A4_ gene (intronic, promoting, untranslated or even regulatory regions) or in another gene

directly involved in zinc homeostasis.9 Besides, the participation of epigenetic events such as methylation or miRNA regulation cannot be ruled out either. The same hypotheses are also

valuable to explain the failure in variant detection in about 52% of the patients.9 In addition, the difficulty—or even sometimes the impossibility—to distinguish congenital zinc deficiency

AEZ from acquired zinc deficiency largely accounts for these negative tests; except for the age at onset, which can be much later in acquired zinc deficiency, both entities share indeed the

same clinical features. A few other negative tests are attributable to the partial clinical overlap between AEZ and biotin deficiency, atopic dermatitis or exceedingly rare genodermatoses

(Küry _et al._ manuscript under preparation). 2.4 CLINICAL SPECIFICITY (PROPORTION OF NEGATIVE TESTS IF THE DISEASE IS NOT PRESENT) The clinical specificity can be dependent on variable

factors such as age or family history. In such cases a general statement should be given, even if a quantification can only be made case by case. 100%. 2.5 POSITIVE CLINICAL PREDICTIVE VALUE

(LIFE TIME RISK TO DEVELOP THE DISEASE IF THE TEST IS POSITIVE) If homozygous or compound heterozygous variants affecting _SLC39A4_ function are identified in still asymptomatic breastfed

children—their zinc deficiency is masked by zinc from maternal milk—the risk to develop AEZ after weaning is 100%. 2.6 NEGATIVE CLINICAL PREDICTIVE VALUE (PROBABILITY NOT TO DEVELOP THE

DISEASE IF THE TEST IS NEGATIVE) Assume an increased risk based on family history for a non-affected person. Allelic and locus heterogeneity may need to be considered. Index case in that

family had been tested: When a variant affecting _SLC39A4_ function is identified in the index case, the negative predictive value is 100%. Index case in that family had not been tested: Not

applicable. 3. CLINICAL UTILITY 3.1 (DIFFERENTIAL) DIAGNOSTICS: THE TESTED PERSON IS CLINICALLY AFFECTED (To be answered if in 1.10 ‘A’ was marked) 3.1.1 CAN A DIAGNOSIS BE MADE OTHER THAN

THROUGH A GENETIC TEST? 3.1.2. DESCRIBE THE BURDEN OF ALTERNATIVE DIAGNOSTIC METHODS TO THE PATIENT Diagnosis can be established by the concomitant presence of characteristic clinical

features and biological signs. Historically, AEZ was defined by a triad of symptoms, including a periacral and periorificial dermatitis, an alopecia and a diarrhea.10 In practical terms,

this pathognomonic triad is seen in only 25% of the cases.11 The most constant clinical symptoms are cutaneous lesions (first eczematous, then quickly erosive, psoriasiform or

vesiculopustulous) always located at least in periorificial areas, and very frequently associated with acral lesions. Secondary fungal and bacterial infections, erosions of the buccal

mucosa, integument disorders (alopecia and nail dystrophy), diarrhea, neuropsychiatric symptoms (irritability, apathy or psychomotor delay), and failure to thrive are also frequently

reported.11 The characteristic biological sign of AEZ is a decrease in body zinc levels, usually assessed by a dosage of zinc plasma or serum levels; low levels of zinc-dependent enzymes,

such as alkaline phosphatase, are also observed. Consequently, a key element in the diagnosis of AEZ is the excellent responsiveness of zinc deficiency symptoms and signs to oral zinc

supplementation; all of them should indeed resolve within days/weeks. It is worth noting, however, that such a responsiveness to zinc therapy is also observed in transient neonatal zinc

deficiency (TNZD), in which maternal milk does not provide enough zinc to meet the infant’s needs, despite a normal intestinal absorption.7 Eventually, interruption of zinc therapy may help

to distinguish between inherited (AEZ) and acquired zinc deficiency, as, on the one hand, a relapse is always observed in AEZ, whereas, on the other hand, no further supplementation is

required after weaning in TNZD. 3.1.3 HOW IS THE COST EFFECTIVENESS OF ALTERNATIVE DIAGNOSTIC METHODS TO BE JUDGED? Establishing a diagnosis of AEZ is not very easy, because of the rarity of

the disease, which often leads to a long diagnostic delay. Moreover, clinical and biochemical diagnostic methods are rarely sufficient to establish a definitive diagnosis of AEZ, notably

because acquired zinc deficiency causes are varied and not always obvious to determine.12, 13 More rarely, biotinidase deficiency and atopic dermatitis are sometimes misdiagnosed as AEZ,

especially when zinc levels are found subnormal and symptoms seem zinc responsive. Such situations can be considered as exceptions, but they nevertheless illustrate the difficulty to rely

upon zinc dosage and clinical features only, all the more that true AEZ patients also happen to exhibit very marginal decreases in plasma zinc levels. As a matter of fact, zinc homeostasis

is so tightly regulated that even the slightest biochemical abnormality can stress a more profound zinc deficiency. Methods for zinc dosage and definition of standard values for zinc levels

are not harmonized either between laboratories/countries, which can induce misinterpretation of biochemical results. In any case, the ultimate diagnostic proof of AEZ is therefore brought by

the identification of a molecular anomaly in _SLC39A4_. 3.1.4 WILL DISEASE MANAGEMENT BE INFLUENCED BY THE RESULT OF A GENETIC TEST? 3.2 PREDICTIVE SETTING: THE TESTED PERSON IS CLINICALLY

UNAFFECTED BUT CARRIES AN INCREASED RISK BASED ON FAMILY HISTORY (To be answered if in 1.10 ‘B’ was marked) 3.2.1 WILL THE RESULT OF A GENETIC TEST INFLUENCE LIFESTYLE AND PREVENTION? If the

test result is POSITIVE (please describe). Not applicable. If the test result is NEGATIVE (please describe). Not applicable. 3.2.2 WHICH OPTIONS IN VIEW OF LIFESTYLE AND PREVENTION DOES A

PERSON AT-RISK HAVE IF NO GENETIC TEST HAS BEEN DONE (PLEASE DESCRIBE)? Not applicable. 3.3 GENETIC RISK ASSESSMENT IN FAMILY MEMBERS OF A DISEASED PERSON (To be answered if in 1.10 ‘C’ was

marked) 3.3.1 DOES THE RESULT OF A GENETIC TEST RESOLVE THE GENETIC SITUATION IN THAT FAMILY? Yes; given the autosomal recessive mode of inheritance, newborns can be evaluated immediately

after birth for the disorder. 3.3.2 CAN A GENETIC TEST IN THE INDEX PATIENT SAVE GENETIC OR OTHER TESTS IN FAMILY MEMBERS? No. 3.3.3 DOES A POSITIVE GENETIC TEST RESULT IN THE INDEX PATIENT

ENABLE A PREDICTIVE TEST IN A FAMILY MEMBER? Yes. 3.4 PRENATAL DIAGNOSIS (To be answered if in 1.10 ‘D’ was marked) 3.4.1 DOES A POSITIVE GENETIC TEST RESULT IN THE INDEX PATIENT ENABLE A

PRENATAL DIAGNOSIS? Not applicable. 4. IF APPLICABLE, FURTHER CONSEQUENCES OF TESTING Please assume that the result of a genetic test has no immediate medical consequences. Is there any

evidence that a genetic test is nevertheless useful for the patient or his/her relatives? (Please describe) Results of _SLC39A4_ genetic testing may have no immediate medical consequence,

because zinc supplementation has almost always been proposed to patients prior to the request for genetic analysis. Yet, in addition to its influence on disease management in homozygotes or

compound heterozygotes (see section 3.1.4), the results of _SLC39A4_ genetic testing may also have consequences for their relatives. Variant carriers are worth detecting, as heterozygous

carriers of a variant affecting function would be hypersensitive to zinc deficiency.14 Their zinc status should therefore be regularly followed up to prevent possible symptoms of zinc

deficiency. Besides, genetic testing of _SLC39A4_ may avoid zinc oversupplementation and secondary copper or iron deficiency in transiently zinc-deficient neonates, who do not need any

further zinc therapy after weaning. Of note, in TNZD, a biallelic or heterozygous variant affecting _SLC30A2_ function is present in the lactating mother, which induces AEZ-like zinc

deficiency in the breastfed infant.4, 7 Beyond _SLC39A4_ screening, additional genetic testings are therefore required for this other form of zinc deficiency, and they may be considered for

possible alternative inherited forms of AEZ-like entities suspected to be due to variants in zinc transporters or metallothioneins.9 This suggests a genetic heterogeneity and the need for

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_Hum Mol Genet_ 2007; 16: 1391–1399. Article  CAS  Google Scholar  Download references ACKNOWLEDGEMENTS This work was supported by EuroGentest2 (Unit 2: ‘Genetic testing as part of health

care’), a Coordination Action under FP7 (Grant Agreement Number 261469) and the European Society of Human Genetics. SK, SS and SB are partially supported by a donation from the laboratory

LABCATAL for their fundamental research on AEZ. AUTHOR INFORMATION AUTHORS AND AFFILIATIONS * CHU de Nantes, Service de Génétique Médicale, Nantes, France Sébastien Küry, Sébastien Schmitt 

& Stéphane Bézieau * Hôpital Charles Nicolle, Service de Dermatologie, Tunis, Tunisia Monia Kharfi * Laboratoire LABCATAL, Montrouge, France Eric Blouin Authors * Sébastien Küry View

author publications You can also search for this author inPubMed Google Scholar * Monia Kharfi View author publications You can also search for this author inPubMed Google Scholar * Eric

Blouin View author publications You can also search for this author inPubMed Google Scholar * Sébastien Schmitt View author publications You can also search for this author inPubMed Google

Scholar * Stéphane Bézieau View author publications You can also search for this author inPubMed Google Scholar CORRESPONDING AUTHOR Correspondence to Sébastien Küry. ETHICS DECLARATIONS

COMPETING INTERESTS The authors declare no conflict of interest. RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Küry, S., Kharfi, M., Blouin, E. _et

al._ Clinical utility gene card for: acrodermatitis enteropathica – update 2015. _Eur J Hum Genet_ 24, 779 (2016). https://doi.org/10.1038/ejhg.2015.203 Download citation * Received: 09

March 2015 * Revised: 29 July 2015 * Accepted: 14 August 2015 * Published: 07 October 2015 * Issue Date: May 2016 * DOI: https://doi.org/10.1038/ejhg.2015.203 SHARE THIS ARTICLE Anyone you

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