Whole exome sequencing identifies three novel mutations in ANTXR1 in families with GAPO syndrome

Abstract

GAPO syndrome (OMIM#230740) is the acronym for growth retardation, alopecia, pseudoanodontia, and optic atrophy. About 35 cases have been reported, making it among one of the rarest recessive conditions. Distinctive craniofacial features including alopecia, rarefaction of eyebrows and eyelashes, frontal bossing, high forehead, mid-facial hypoplasia, hypertelorism, and thickened eyelids and lips make GAPO syndrome a clinically recognizable phenotype. While this genomic study was in progress mutations in ANTXR1 were reported to cause GAPO syndrome. In our study we performed whole exome sequencing (WES) for five affected individuals from three Turkish kindreds segregating the GAPO trait. Exome sequencing analysis identified three novel homozygous mutations including; one frame-shift (c.1220_1221insT; p.Ala408Cysfs*2), one splice site (c.411A>G; p.Gln137Gln), and one non-synonymous (c.1150G>A; p.Gly384Ser) mutation in the ANTXR1 gene. Our studies expand the allelic spectrum in this rare condition and potentially provide insight into the role of ANTXR1 in the regulation of the extracellular matrix.

Keywords: ANTXR1; GAPO syndrome; whole exome sequencing.

FIG. 1

Facial appearance of patients with GAPO syndrome. Note that alopecia, relative macrocephaly, frontal bossing, low set and protruding ears, hypertelorism, thickened eyelids, sparse eyebrows and eyelashes, depressed nasal bridge, long philtrum, thick lips and micrognathia are the common craniofacial findings in all patients. A: Patient BAB5033 at age 12. B,C: Affected brothers in family HOU2034; BAB5141 at age 14 and BAB5142 at age 12. D,E: Frontal and lateral views of patient BAB5348 at age 42. F: Patient BAB5349 at age 37. Note that nodular lesions on scalp probably due to subcutaneous accumulation and extreme senile appearance in comparison with his age. This patient died 2 weeks after this photo was taken.

FIG. 2

Family pedigrees and segregation of the ANTXR1 mutations. The affected individuals are symbolized with black filled shapes and the locations of mutations are indicated with arrows. All parents are consanguineous. A: Family HOU2001 with one affected and one unaffected child. The affected patient BAB5033 has the homozygous (M/M) c.1220_1221insT variant while the parents and the unaffected sibling are heterozygous carriers (M/+). B: Family HOU2034 with three affected children. All the affected siblings BAB5141, BAB5142 and BAB5143 have the homozygous c.411A>G variant, while the parents are heterozygous carriers. C: Family HOU2085 consists of two related families with cousin marriages. Both affected male cousins BAB5348 and BAB5349 have the homozygous c.1150G>A variant and the unaffected brother of BAB5349 (BAB5350) is a heterozygous carrier. DNA samples from the parents were not available (NA) for segregation analyses.

FIG. 3

Gene structure and diagram of the functional domains of ANTXR1 and localization of the identified mutations. A: Demonstration of ANTXR1 exons. Asterisks indicate localization of previously described mutations in three different ethnicities (c.262C>T = Egyptian, c.505C>T = Czech, c.1435-12A>G = Sri Lankan). B: Conservation pattern and protein domains of ANTXR1 (564 aa). Conservation varies between 1 (variable) and 9 (conserved). Arrows indicate localization of the amino acid changes described in our study in three Turkish families. C: c.411A>G (p.Gln137Gln) mutation. G (blue) and GT (red) are substitution and canonical splicing donor site. D: c.1220_1221insT (p.Ala408Cysfs^*2) mutation. Inserted T is highlighted by blue.