Genetic Analyses
Fluorescently labeled microsatellite markers located close to the respective genes (Table S1) excluded linkage of the disorder toGNPTAB (OMIM#607840), GNPTG (OMIM#607838), IDUA(OMIM#611542) and ARSB (OMIM#611542) for family NMD02. Analyses of the filtered exome data revealed three novel homozygous exonic variants located on chromosome 14q32 (Table S6) which also segregated with the phenotype in family NMD02 (Figure 1-2). OnlyTMEM251 variant c.133C>T;p.(Arg45Trp) was predicted to be damaging by all five prediction programs and affected an amino acid which was fully conserved in the orthologous proteins (Figure 3A). This variant was absent in all public databases and from 400 ethnically matched control chromosomes. The known genetic causes of various forms of mucopolysaccharidosis and mucolipidosis were also excluded by analyses of exome data for family NMD02 (Table S1).
We identified five regions of shared homozygosity located on different chromosomes from the exome data of the two affected individuals (Figure S1). Sequencing of the variants located in these regions revealed that only variants present on chromosome 14q32 (Table S2, Table S6 and data not shown) segregated with the phenotype with a LOD score of 3.2 atθ = 0. Moreover, no variants were identified by Sanger sequencing in those exons which were located within chromosome 14q32 region of shared homozygosity (Figure S1) and had not been covered by exome sequencing (Table S2).
Analysis of the trio exome sequencing data of family ID01 revealed one homozygous insertion variant c.215dupA;p.(Tyr72Ter) in TMEM251 in the patient, for which the parents were heterozygous carriers (Figure 1 and 2). None of the other 23 individuals from the pedigree were found to be homozygous for the variant. Moreover, this variant was absent from all public databases. The variant identified in family NMD02 was deposited in LOVD (#0000601066) and the variant identified in family ID01 was deposited in ClinVar (SCV000998897).