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Amish Lethal Microcephaly

Synonyms: Amish Microcephaly, MCPHA
, MD
Genetic Disease Research Branch
National Human Genome Research Institute
National Institutes of Health
Bethesda, Maryland

Initial Posting: ; Last Update: December 7, 2017.

Summary

Clinical characteristics.

Amish lethal microcephaly is characterized by severe congenital microcephaly and highly elevated 2-ketoglutarate or lactic acidosis. The occipitofrontal circumference is typically more than two standard deviations (occasionally >6 SD) below the mean; anterior and posterior fontanels are closed at birth and facial features are distorted. The average life span of an affected infant is between five and six months among the Lancaster Amish, although an affected Amish-Mennonite child was reported to be living with severe developmental delay at age seven years.

Diagnosis/testing.

The diagnosis of Amish lethal microcephaly is established in a proband with typical clinical findings and/or identification of biallelic pathogenic variants in SLC25A19 by molecular genetic testing. All affected individuals within the Old Order Amish population are homozygous for the same single-base pair substitution.

Management.

Treatment of manifestations: Treatment is supportive only. Phenobarbital has been used to treat a few children with seizures. Physical therapy may alleviate contractures or other secondary neurologic manifestations. Infectious illnesses are managed to minimize acidosis.

Genetic counseling.

Amish lethal microcephaly is inherited in an autosomal recessive manner. At conception, each sib of an affected individual has a 25% chance of being affected, a 50% chance of being an asymptomatic carrier, and a 25% chance of being unaffected and not a carrier. Carrier testing for at-risk family members and prenatal testing or preimplantation diagnosis for pregnancies at increased risk are possible once the pathogenic variants have been identified in the family.

Diagnosis

Suggestive Findings

Amish lethal microcephaly should be suspected in individuals with the following findings:

  • Severe microcephaly:
    • Present at birth
    • Occipitofrontal circumference typically >2 SD (occasionally >6 SD) below the mean
  • Highly elevated (≥10-fold increased) levels of the urinary organic acid 2-ketoglutarate OR lactic acidosis

Note that the clinical criteria for this disorder are based solely on the manifestations in the Old Order Amish kindreds from southeastern Pennsylvania and a single non-Amish patient clinical report. The spectrum of the disorder may be larger than currently appreciated.

Establishing the Diagnosis

The diagnosis of Amish lethal microcephaly is established in a proband with typical clinical findings and/or identification of biallelic pathogenic variants in SLC25A19 by molecular genetic testing (see Table 1).

Molecular genetic testing approaches can include single-gene testing, use of a multigene panel, and more comprehensive genomic testing:

  • Single-gene testing. Sequence analysis of SLC25A19 is performed first and followed by gene-targeted deletion/duplication analysis if only one or no pathogenic variant is found. Note: No deletions or duplications involving SLC25A19 as causative of Amish lethal microcephaly have been reported.
    Targeted analysis for the c.530G>C pathogenic variant can be performed first in individuals of Amish ancestry.
  • A multigene panel that includes SLC25A19 and other genes of interest (see Differential Diagnosis) may also be considered. Note: (1) The genes included in the panel and the diagnostic sensitivity of the testing used for each gene vary by laboratory and over time. (2) Some multigene panels may include genes not associated with the condition discussed in this GeneReview; thus, clinicians need to determine which multigene panel provides the best opportunity to identify the genetic cause of the condition at the most reasonable cost while limiting identification of pathogenic variants in genes that do not explain the underlying phenotype. (3) Methods used in a panel may include sequence analysis, deletion/duplication analysis, and/or other non-sequencing-based tests.
    For an introduction to multigene panels click here. More detailed information for clinicians ordering genetic tests can be found here.
  • More comprehensive genomic testing (when available) including exome sequencing and genome sequencing may be considered. Such testing may provide or suggest a diagnosis not previously considered (e.g., mutation of a different gene or genes that results in a similar clinical presentation). For an introduction to comprehensive genomic testing click here. More detailed information for clinicians ordering genomic testing can be found here.

Table 1.

Molecular Genetic Testing Used in Amish Lethal Microcephaly

Gene 1Test MethodProportion of Pathogenic Variants 2 Detectable by This Method
SLC25A19Sequence analysis 3100% 4
Gene-targeted deletion/duplication analysis 5Unknown 6
1.
2.

See Molecular Genetics for information on allelic variants detected in this gene.

3.

Sequence analysis detects variants that are benign, likely benign, of uncertain significance, likely pathogenic, or pathogenic. Pathogenic variants may include small intragenic deletions/insertions and missense, nonsense, and splice site variants; typically, exon or whole-gene deletions/duplications are not detected. For issues to consider in interpretation of sequence analysis results, click here.

4.

To date, all individuals with Amish microcephaly have the c.530G>C variant.

5.

Gene-targeted deletion/duplication analysis detects intragenic deletions or duplications. Methods that may be used include: quantitative PCR, long-range PCR, multiplex ligation-dependent probe amplification (MLPA), and a gene-targeted microarray designed to detect single-exon deletions or duplications.

6.

No data on detection rate of gene-targeted deletion/duplication analysis are available.

Clinical Characteristics

Clinical Description

Amish lethal microcephaly (MCPHA) is a distinct disorder with little variability in its presentation, at least among the Old Order Amish from Lancaster County, Pennsylvania [Kelley et al 2002] and the single reported patient from outside of this area [Siu et al 2010].

Microcephaly. Affected infants have severe microcephaly at birth.

  • The cranial vault is extremely underdeveloped as a result of the small brain size.
  • Anterior and posterior fontanels are closed, and ridging from premature sutural fusion may be evident.
  • MRI imaging has not been done in most affected individuals; partial absence of the corpus callosum and closed spinal dysraphism were identified by imaging in the individual reported by Siu et al [2010].
  • The facial features are distorted as a result of the profound microcephaly.
  • Many affected infants have difficulty maintaining body temperature.
  • The Amish individuals died quite young. The single affected individual described by Siu et al [2010] had irritability and profound developmental delay. The Amish patients were able to breast/bottle feed early on, but developed severe irritability and seizures.

Non-CNS physical anomalies

  • Moderate micrognathia is seen.
  • Mild hepatomegaly has been observed in several affected individuals, usually during acute illnesses associated with metabolic acidosis.
  • 2-ketoglutaric acidosis has been demonstrated in a number of Amish infants with this disorder (a variable finding).

Prognosis. After the first two or three months of life, increasing irritability of unknown causes commonly develops [Kelley et al 2002]. Although no changes in physical or neurologic examination accompany the irritability, the Lancaster Amish children are more likely to die within 24-48 hours of developing their next viral illness.

The average life span of an affected infant is between five and six months among the Lancaster Amish; the affected Amish-Mennonite child reported by Siu et al [2010] was alive (albeit with severe developmental delay) at age seven years.

Neuropathology. A partial autopsy of an affected infant age four months gave insight into the neuropathology of the disorder [Strauss et al 2002]. The severity of the malformation was more pronounced in the anterior portion of the brain. Frontal lobes are smooth and rudimentary. Increasing convolution and lamination progress occipitotemporally. Regions that are most hypoplastic are most disorganized histologically.

No pathology on the case reported by Siu et al [2010] has been available.

Genotype-Phenotype Correlations

With a single pathogenic variant identified in all known individuals with MCPHA and little variation in clinical presentation, no conclusions about genotype-phenotype correlation can be made at this time.

Prevalence

MCPHA has been found primarily in the Old Order Amish who have ancestors in Lancaster County, Pennsylvania. At least 61 affected infants have been born to 33 nuclear families in the past 40 years. In this population, incidence is approximately one in 500 births. There are typically three or more births of infants with MCPHA per year in this population.

The report of Siu et al [2010] shows that the phenotype is not limited to the Old Order Amish population, although prevalence is difficult to estimate.

Differential Diagnosis

Microcephaly has a wide variety of causative factors. It can be syndromic or isolated, environmental or genetic, congenital or acquired [Battaglia & Carey 2003]. A metabolic screen (including urine organic acids, plasma amino acids, lactate, pyruvate, and electrolytes) is indicated for all children with congenital microcephaly. Further specific evaluations are performed as indicated based on the results of this screen. Elevated alpha-ketoglutarate may be seen in other disorders as well.

Microcephaly. The differential diagnosis for isolated congenital microcephaly includes single-gene disorders inherited in an autosomal recessive manner.

Primary autosomal recessive microcephalies are a group of nonsyndromic disorders characterized by a small-sized brain which are not associated with gross anomalies of brain architecture or malformations in other organ systems. Associated genes include ASPM, CDK5RAP2, CENPJ, CEP152, MCPH1, STIL, and WDR62.

The degree of microcephaly is much greater in Amish lethal microcephaly than in any of these other genetically defined microcephaly syndromes. Additionally, 2-ketoglutaric aciduria has not been reported as a finding with these disorders.

Microcephaly may also be inherited in an autosomal dominant manner and possibly in an X-linked manner, though most of the causative genes have not been identified [Battaglia & Carey 2003]. Members of a three-generation family with microcephaly were found to have a heterozygous pathogenic variant in WDFY3 [Kadir et al 2016].

Alpha-ketoglutarate. Elevated levels of urinary alpha-ketoglutarate may also be seen in individuals with pathogenic variants in the alpha-ketoglutarate dehydrogenase complex, but this phenotype does not typically present with microcephaly [Dunckelmann et al 2000].

Increased levels of urinary 2-ketoglutarate are common in a wide variety of disorders of mitochondrial dysfunction, including those caused by mutation of both mtDNA and nuclear DNA genes.

Among other genetic malformation syndromes, a similar level of urinary 2-ketoglutarate is also characteristic of the autosomal recessive form of DOORS (deafness, onychodystrophy, osteodystrophy, intellectual disability [formerly known as mental retardation] seizures) syndrome, associated with biallelic pathogenic variants in TBC1D24 (see TBC1D24-Related Disorders).

Management

Evaluation Following Initial Diagnosis

To establish the extent of disease in an individual diagnosed with Amish lethal microcephaly (MCPHA), the following evaluations are recommended if they have not already been completed:

  • Appropriate imaging studies. Given that the fontanels are typically closed or overriding, MRI is more useful than ultrasound. Computed tomography can be used, but has lower resolution.
  • Consultation with a clinical geneticist, biochemical geneticist, and/or genetic counselor. Care coordination is important in managing affected infants as it is necessary to provide appropriate comfort care given the uniformly poor prognosis.

Treatment of Manifestations

This disorder is fatal within the first year of life in children of the Old Order Amish of Lancaster County, Pennsylvania. No intervention – including mitochondrial vitamin treatment – has shown promise for treatment or amelioration in this population. However, most experience with this disorder is based on the Old Order Amish; therefore, most clinical experience is based on a single allele. It is now known that this same allele can manifest in a more mild form [Siu et al 2010]. In this case, it was shown that a ketogenic diet improved the acidosis.

Seizures have occurred in some affected infants; the few children who were treated responded well to phenobarbital.

Physical therapy may be considered if the affected child develops contractures or other secondary neurologic manifestations. The patients respond to benzodiazepine anxiolytics.

Support and respite for the family may be needed during the stressful terminal irritability phase of the disease, which can last for several weeks.

In general, a palliative approach to care is appropriate. Within the Old Order Amish, care within the extended family is sufficient. Non-Amish patients may be considered for pediatric hospice care.

Prevention of Primary Manifestations

Routine childhood illnesses should be managed to minimize the acidosis associated with acute illnesses. Many affected infants in the Lancaster Amish population have died during metabolic exacerbations associated with an intercurrent infectious illness.

Agents/Circumstances to Avoid

Good handwashing and avoidance of contact with individuals with communicable respiratory diseases is appropriate.

Evaluation of Relatives at Risk

Prior to genetic testing, or while it is under way, urine and plasma amino acids and pyruvate and lactate levels should be considered.

See Genetic Counseling for issues related to testing of at-risk relatives for genetic counseling purposes.

Therapies Under Investigation

Search ClinicalTrials.gov for access to information on clinical studies for a wide range of diseases and conditions. Note: There may not be clinical trials for this disorder.

Genetic Counseling

Genetic counseling is the process of providing individuals and families with information on the nature, inheritance, and implications of genetic disorders to help them make informed medical and personal decisions. The following section deals with genetic risk assessment and the use of family history and genetic testing to clarify genetic status for family members. This section is not meant to address all personal, cultural, or ethical issues that individuals may face or to substitute for consultation with a genetics professional. —ED.

Mode of Inheritance

Amish lethal microcephaly (MCPHA) is inherited in an autosomal recessive manner.

Risk to Family Members

Parents of a proband

  • The parents of an affected individual are obligate heterozygotes (i.e., carriers of one SLC25A19 pathogenic variant).
  • Heterozygotes (carriers) are asymptomatic, have normal urinary excretion of 2-ketoglutarate, and are not at risk of developing the disorder.

Sibs of a proband

  • At conception, each sib of an affected individual has a 25% chance of being affected, a 50% chance of being an asymptomatic carrier, and a 25% chance of being unaffected and not a carrier.
  • Heterozygotes (carriers) are asymptomatic and are not at risk of developing the disorder.

Offspring of a proband. MCPHA is lethal before reproductive age.

Other family member. The risk to each sib of the proband's parents of being a carrier is at least 50% and may be 67% (2/3) if the proband's parent had an affected sib.

Carrier (Heterozygote) Detection

Carrier testing for at-risk family members requires prior identification of the SLC25A19 pathogenic variants in the family.

Related Genetic Counseling Issues

Family planning

  • The optimal time for determination of genetic risk, clarification of carrier status, and discussion of the availability of prenatal testing is before pregnancy.
  • It is appropriate to offer genetic counseling (including discussion of potential risks to offspring and reproductive options) to young adults who are carriers or are at risk of being carriers.

DNA banking is the storage of DNA (typically extracted from white blood cells) for possible future use. Because it is likely that testing methodology and our understanding of genes, allelic variants, and diseases will improve in the future, consideration should be given to banking DNA of affected individuals.

Prenatal Testing and Preimplantation Genetic Diagnosis

Molecular genetic testing. Once the SLC25A19 pathogenic variants have been identified in an affected family member, prenatal testing for a pregnancy at increased risk and preimplantation genetic diagnosis for Amish lethal microcephaly are possible.

Fetal ultrasound examination. Three fetal ultrasound examinations performed after 20 weeks' gestation in two pregnancies of babies ultimately found to have MCPHA revealed marked deceleration of head growth [Kelley et al 2002]. The sensitivity and specificity of fetal ultrasound for the prenatal diagnosis of Amish lethal microcephaly has not been evaluated.

Biochemical genetic testing. Prenatal diagnosis by measurement of 2-ketoglutarate in amniotic fluid has also not been evaluated.

Resources

GeneReviews staff has selected the following disease-specific and/or umbrella support organizations and/or registries for the benefit of individuals with this disorder and their families. GeneReviews is not responsible for the information provided by other organizations. For information on selection criteria, click here.

  • Medline Plus
  • National Institute of Neurological Disorders and Stroke (NINDS)
    PO Box 5801
    Bethesda MD 20824
    Phone: 800-352-9424 (toll-free); 301-496-5751; 301-468-5981 (TTY)

Molecular Genetics

Information in the Molecular Genetics and OMIM tables may differ from that elsewhere in the GeneReview: tables may contain more recent information. —ED.

Table A.

Amish Lethal Microcephaly: Genes and Databases

Data are compiled from the following standard references: gene from HGNC; chromosome locus from OMIM; protein from UniProt. For a description of databases (Locus Specific, HGMD, ClinVar) to which links are provided, click here.

Table B.

OMIM Entries for Amish Lethal Microcephaly (View All in OMIM)

606521SOLUTE CARRIER FAMILY 25 (MITOCHONDRIAL THIAMINE PYROPHOSPHATE CARRIER), MEMBER 19; SLC25A19
607196MICROCEPHALY, AMISH TYPE; MCPHA

Gene structure. SLC25A19 contains nine exons that span 16.5 kb [Iacobazzi et al 2001]. Translation begins in exon 4 and there is evidence of alternate splicing of the three untranslated 5' exons. For a detailed summary of gene and protein information, see Table A, Gene.

Pathogenic variants. One known pathogenic variant results in Amish lethal microcephaly (MCPHA) [Rosenberg et al 2002]. A single-nucleotide substitution that predicts p.Gly177Ala (see Table 2, OMIM 606521) was found homozygous in affected individuals. This substitution has not been observed in the population [exac.broadinstitute.org]. For more information, see Table A.

Table 2.

SLC25A19 Variants Discussed in This GeneReview

DNA Nucleotide ChangePredicted Protein ChangeReference Sequences
c.373G>Ap.Gly125SerNM_021734​.4
NP_068380​.3
c.530G>Cp.Gly177Ala

Note on variant classification: Variants listed in the table have been provided by the author. GeneReviews staff have not independently verified the classification of variants.

Note on nomenclature: GeneReviews follows the standard naming conventions of the Human Genome Variation Society (varnomen​.hgvs.org). See Quick Reference for an explanation of nomenclature.

Normal gene product. The protein encoded by SLC25A19 contains three predicted mitochondrial carrier motifs. These motifs are characteristic of proteins, including the 2-ketoglutarate transporter, found in the inner mitochondrial membrane [Dolce et al 2001]. Functional analysis using bacterially expressed protein reconstituted in proteoliposomes revealed that DNC can catalyze the transport of deoxynucleotide diphosphates, deoxynucleotide triphosphates, and dideoxynucleotide triphosphates in exchange for dNDPs, ADP, or ATP. However, studies showed that this is not the primary physiologic function of this protein [Lindhurst et al 2006]. Transport assays revealed that the SLC25A19 protein also catalyzes the exchange of thiamine pyrophosphate (ThPP) and thiamine monophosphate (ThMP). ThPP is a co-factor for the pyruvate dehydrogenase (PDH) and the alpha-ketoglutarate dehydrogenase (KGDH) complexes that are both found in the mitochondria, and are key enzymes in oxidative metabolism.

Abnormal gene product. A bacterially expressed human SLC25A19 protein containing the p.Gly177Ala substitution reconstituted in proteoliposomes was unable to catalyze the exchange of α-S35dATP for ADP, ThPP or ThMP at 37°C and had reduced activity at 25°C [Rosenberg et al 2002].

Knockout mouse embryos homozygous for a null allele of Slc25a19 have a neural tube closure defect, yolk sac erythropoiectic failure, and elevated alpha-ketoglutarate in the amniotic fluid, and are lethal by embryonic day 12 [Lindhurst et al 2006]. Fibroblasts generated from E10.5 mouse embryos had normal levels of mitochondrial ribo- and deoxyribonucleoside triphosphates, but ThPP and ThMP were not detectable in their mitochondria. Ribo- and deoxyriboncleoside triphosphate levels were also normal in mitochondria of lymphoblasts from individuals with MCPHA; ThPP and ThMP levels were markedly reduced, indicating that the p.Gly177Ala substitution is a hypomorphic allele. Activity of the PDH and KGDH complexes was greatly reduced in both the mouse and human cells, which explains the alpha-ketoglutaric aciduria in individuals with MCPHA and emphasizes the importance of oxidative metabolism in early embryogenesis. These findings provide a basis for understanding how a pathogenic variant in this transporter can cause metabolic acidosis with elevated alpha-ketoglutarate.

The findings in the child with severe microcephaly, partial absence of the corpus callosum, and closed spinal dysraphism reported by Siu et al [2010] parallel the mouse model of MCPHA [Lindhurst et al 2006].

References

Literature Cited

  • Battaglia A, Carey JC. Microcephaly. In: Rudolph CD, Rudolph AM, eds. Rudolph's Pediatrics. 21 ed. New York, NY: McGraw-Hill; 2003:784-6.
  • Dolce V, Fiermonte G, Runswick MJ, Palmieri F, Walker JE. The human mitochondrial deoxynucleotide carrier and its role in the toxicity of nucleoside antivirals. Proc Natl Acad Sci U S A. 2001;98:2284–8. [PMC free article: PMC30130] [PubMed: 11226231]
  • Dunckelmann RJ, Ebinger F, Schulze A, Wanders RJ, Rating D, Mayatepek E. 2-ketoglutarate dehydrogenase deficiency with intermittent 2-ketoglutaric aciduria. Neuropediatrics. 2000;31:35–8. [PubMed: 10774994]
  • Iacobazzi V, Ventura M, Fiermonte G, Prezioso G, Rocchi M, Palmieri F. Genomic organization and mapping of the gene (SLC25A19) encoding the human mitochondrial deoxynucleotide carrier (DNC). Cytogenet Cell Genet. 2001;93:40–2. [PubMed: 11474176]
  • Kadir R, Harel T, Markus B, Perez Y, Bakhrat A, Cohen I, Volodarsky M, Feintsein-Linial M, Chervinski E, Zlotogora J, Sivan S, Birnbaum RY, Abdu U, Shalev S, Birk OS. ALFY-controlled DVL3 autophagy regulates Wnt signaling, determining human brain size. PLoS Genet. 2016;12:e1005919. [PMC free article: PMC4805177] [PubMed: 27008544]
  • Kelley RI, Robinson D, Puffenberger EG, Strauss KA, Morton DH. Amish lethal microcephaly: a new metabolic disorder with severe congenital microcephaly and 2-ketoglutaric aciduria. Am J Med Genet. 2002;112:318–26. [PubMed: 12376931]
  • Lindhurst MJ, Fiermonte G, Song S, Struys E, De Leonardis F, Schwartzberg PL, Chen A, Castegna A, Verhoeven N, Mathews CK, Palmieri F, Biesecker LG. Knockout of Slc25a19 causes mitochondrial thiamine pyrophosphate depletion, embryonic lethality, CNS malformations, and anemia. Proc Natl Acad Sci U S A. 2006;103:15927–32. [PMC free article: PMC1595310] [PubMed: 17035501]
  • Rosenberg MJ, Agarwala R, Bouffard G, Davis J, Fiermonte G, Hilliard MS, Koch T, Kalikin LM, Makalowska I, Morton DH, Petty EM, Weber JL, Palmieri F, Kelley RI, Schäffer AA, Biesecker LG. Mutant deoxynucleotide carrier is associated with congenital microcephaly. Nat Genet. 2002;32:175–9. [PubMed: 12185364]
  • Siu VM, Ratko S, Prasad AN, Prasad C, Rupar CA. Amish microcephaly: Long-term survival and biochemical characterization. Am J Med Genet A. 2010;152A:1747–51. [PubMed: 20583149]
  • Spiegel R, Shaag A, Edvardson S, Mandel H, Stepensky P, Shalev SA, Horovitz Y, Pines O, Elpeleg O. SLC25A19 mutation as a cause of neuropathy and bilateral striatal necrosis. Ann Neurol. 2009;66:419–24. [PubMed: 19798730]
  • Strauss KA, Pfannl R, Morton DH. The neuropathology of Amish lethal microcephaly. Am J Hum Genet. 2002;71S:260.

Chapter Notes

Author Notes

Dr. Biesecker is a clinical geneticist and human geneticist trained at the University of Michigan, now based at the National Human Genome Research Institute at the NIH.

Author History

Leslie G Biesecker, MD (2003-present)
Marjorie J Lindhurst, PhD; National Human Genome Research Institute (2003-2017)

Revision History

  • 7 December 2017 (ha) Comprehensive update posted live
  • 16 June 2011 (me) Comprehensive update posted live
  • 5 May 2009 (me) Comprehensive update posted
  • 20 December 2005 (me) Comprehensive update posted live
  • 4 September 2003 (me) Review posted live
  • 24 June 2003 (mjl) Original submission

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