AMMECR1: a single point mutation causes developmental delay, midface hypoplasia and elliptocytosis.
Deletions in the Xq22.3-Xq23 region, inclusive ofCOL4A5, have been associated with a contiguous gene deletion syndrome characterised byAlport syndrome with intellectual disability (Mental retardation),Midface hypoplasia andElliptocytosis (AMME). The extrarenal biological and clinical significance of neighbouring genes to the Alport locus has been largely speculative. We sought to discover a genetic cause for two half-brothers presenting with nephrocalcinosis, early speech and language delay and midface hypoplasia with submucous cleft palate and bifid uvula.



Whole exome sequencing was undertaken on maternal half-siblings. In-house genomic analysis included extraction of all shared variants on the X chromosome in keeping with X-linked inheritance. Patient-specific mutants were transfected into three cell lines and microscopically visualised to assess the nuclear expression pattern of the mutant protein.



In the affected half-brothers, we identified a hemizygous novel non-synonymous variant of unknown significance inAMMECR1(c.G530A; p.G177D), a gene residing in the AMME disease locus. Transfected cell lines with the p.G177D mutation showed aberrant nuclear localisation patterns when compared with the wild type. Blood films revealed the presence of elliptocytes in the older brother.



Our study shows that a single missense mutation inAMMECR1causes a phenotype of midface hypoplasia, mild intellectual disability and the presence of elliptocytes, previously reported as part of a contiguous gene deletion syndrome. Functional analysis confirms mutant-specific protein dysfunction. We conclude thatAMMECR1is a critical gene in the pathogenesis of AMME, causing midface hypoplasia and elliptocytosis and contributing to early speech and language delay, infantile hypotonia and hearing loss, and may play a role in dysmorphism, nephrocalcinosis and submucous cleft palate.
Human Genetics & Genomic Medicine, University of Southampton, Duthie Building (Mailpoint 808), Southampton General Hospital, Southampton, UK.
Gaia
G
Andreoletti
Human Genetics & Genomic Medicine, University of Southampton, Duthie Building (Mailpoint 808), Southampton General Hospital, Southampton, UK.
Eleanor G
EG
Seaby
Centre for Human Development, Stem Cells and Regeneration HDH, University of Southampton, IDS Building, Southampton General Hospital, Southampton, UK.
Jennifer M
JM
Dewing
Centre for Human Development, Stem Cells and Regeneration HDH, University of Southampton, IDS Building, Southampton General Hospital, Southampton, UK.
Ita
I
O'Kelly
Human Genetics & Genomic Medicine, University of Southampton, Duthie Building (Mailpoint 808), Southampton General Hospital, Southampton, UK.|Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Princess Anne Hospital, Southampton, UK.
Katherine
K
Lachlan
Wessex Regional Paediatric Nephro-Urology Service, Southampton Children's Hospital, Southampton, UK.
Rodney D
0000-0001-7426-0188
RD
Gilbert
Human Genetics & Genomic Medicine, University of Southampton, Duthie Building (Mailpoint 808), Southampton General Hospital, Southampton, UK.
Sarah
S
Ennis
D001483:Base Sequence; D002658:Developmental Disabilities / Q000235:genetics* / Q000503:physiopathology; D004612:Elliptocytosis, Hereditary / Q000235:genetics* / Q000503:physiopathology; D059472:Exome / Q000235:genetics; D020022:Genetic Predisposition to Disease; D005838:Genotype; D006801:Humans; D009394:Nephritis, Hereditary / Q000235:genetics* / Q000503:physiopathology; D010375:Pedigree; D010641:Phenotype; D017354:Point Mutation; D011506:Proteins / Q000235:genetics*
C118927:AMMECR1 protein, human; D011506:Proteins
Clinical genetics; Complex traits; Diagnosis; Molecular genetics