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. 2014 Jun 5;94(6):898-904.
doi: 10.1016/j.ajhg.2014.04.015. Epub 2014 May 15.

Neu-Laxova syndrome, an inborn error of serine metabolism, is caused by mutations in PHGDH

Ranad Shaheen  1 , Zuhair Rahbeeni  2 , Amal Alhashem  3 , Eissa Faqeih  4 , Qi Zhao  5 , Yong Xiong  5 , Agaadir Almoisheer  1 , Sarah M Al-Qattan  1 , Halima A Almadani  6 , Noufa Al-Onazi  3 , Badi S Al-Baqawi  7 , Mohammad Ali Saleh  4 , Fowzan S Alkuraya  8
Affiliations

Neu-Laxova syndrome, an inborn error of serine metabolism, is caused by mutations in PHGDH

Ranad Shaheen et al. Am J Hum Genet. .

Abstract

Neu-Laxova syndrome (NLS) is a rare autosomal-recessive disorder characterized by severe fetal growth restriction, microcephaly, a distinct facial appearance, ichthyosis, skeletal anomalies, and perinatal lethality. The pathogenesis of NLS remains unclear despite extensive clinical and pathological phenotyping of the >70 affected individuals reported to date, emphasizing the need to identify the underlying genetic etiology, which remains unknown. In order to identify the cause of NLS, we conducted a positional-mapping study combining autozygosity mapping and whole-exome sequencing in three consanguineous families affected by NLS. Surprisingly, the NLS-associated locus identified in this study was solved at the gene level to reveal mutations in PHGDH, which is known to be mutated in individuals with microcephaly and developmental delay. PHGDH encodes the first enzyme in the phosphorylated pathway of de novo serine synthesis, and complete deficiency of its mouse ortholog recapitulates many of the key features of NLS. This study shows that NLS represents the extreme end of a known inborn error of serine metabolism and highlights the power of genomic sequencing in revealing the unsuspected allelic nature of apparently distinct clinical entities.

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Figures

Figure 1
Figure 1
Pedigrees and Clinical Images of the Study Families The index individual is indicated in each pedigree by an arrow, and asterisks denote individuals whose DNA was available for analysis. Abbreviations are as follows: NND, neonatal death; and SB, stillbirth. (A) A babygram imaging of the index individual from family 2 shows small distorted calvarial bones without gross vertebral or tubular bone deformity. (B) A photograph of the index individual from family 3 shows microcephaly, generalized colloidon-like ichthyosis, a sloping forehead, a broad nose, large ears, a short neck, spastic long fingers, and fixed contractures of the extremities. (C and D) Axial (C) and sagittal (D) MRI of the index individual from family 3 shows a markedly atrophic and small brain with significant ventriculomegaly but normal appearance of the brainstem.
Figure 2
Figure 2
Identification of a NLS-Associated Locus on Chromosome 1 (A) AgileMultiIdeogram showing the chromosome 1 ROH (dark blue) shared among the index individuals from each of the three families. (B) Combined genome-wide linkage analysis of the three families revealed a single maximal peak (LOD score = ∼3.9) on chromosome 1, and AutoSNPa output shows the critical interval at chr1: 119,695,451–120,492,822 (boxed in blue) within the shared ROH. The identical haplotype between individual II:1 in family 1 and individual II:4 in family 2 is denoted by black lines, whereas the red lines in individual II:1 from family 3 denote divergence in haplotype. (C) Upper panel: sequence chromatogram of the two missense mutations (control tracing is shown for comparison, and the location of each mutation is denoted by an asterisk). Lower Panel: schematic of PHGDH and the locations of the two homozygous missense substitutions identified in the three families (previously reported substitutions in individuals with PHGDH deficiency are shown in blue for comparison).
Figure 3
Figure 3
The Two Substituted Amino Acid Residues Are Located in an Important Region of PHGDH (A) Gly140 (G140, red sphere) and Arg163 (R163, green stick) are located at the PHGDH dimer interface (molecule 1 in salmon, molecule 2 in cyan, two substrates in sticks). The dimer is important for the optimal function of PHGDH. Details of the boxed regions are shown in (B) and (C). (B) The p.Gly140Arg (Gly140 in red, Arg in purple) substitution would cause steric clash (marked by a “X”) and introduce extra positive charge at the dimer interface, which would most likely weaken the dimerization by steric hindrance and electrostatic repulsion from two nearby positively charged residues (Lys289 [K289] and Arg230 [R230] in sticks). (C) Arg163 (R163) participates in a water (HOH)-coordinated hydrogen-bonding and salt bridge network at the dimerization interface (Glu108 [E108], Glu159 [E159], and Phe167 [F167] are shown as sticks, and the interaction network is shown as black dashed lines). The p.Arg163Gln substitution might be detrimental to the integrity of this network and weaken dimerization. Also, the loss of the positive charge by the Arg-to-Gln substitution would perturb the surface charge distribution. (D) Arg135 (R135, purple; involved in the previously reported p.Arg135Trp substitution in PHGDH deficiency) and Arg54 (R54, pink sticks) interact with the tail of the substrate malate (MLT, pink sticks) by providing two salt bridges (black dashed lines). The p.Arg135Trp substitution (gray sticks) would eliminate one of the salt bridges and weaken the overall electrostatic attraction. Some activity presumably remains given that Arg54 might still hold the MLT substrate in position. Furthermore, Arg135 does not interact with other protein side chains, and there is enough space to accommodate a Trp substitution, so the p.Arg135Trp substitution might not perturb the overall protein structure and function significantly. (E) Multisequence-alignment orthologs of the two missense substitutions. The affected glycine and arginine residues (boxed in red) are absolutely conserved across species down to C. elegans and plant.
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