Mutations in the cyclin family member FAM58A cause an X-linked dominant disorder characterized by syndactyly, telecanthus and anogenital and renal malformations.

Abstract

We identified four girls with a consistent constellation of facial dysmorphism and malformations previously reported in a single mother-daughter pair. Toe syndactyly, telecanthus and anogenital and renal malformations were present in all affected individuals; thus, we propose the name 'STAR syndrome' for this disorder. Using array CGH, qPCR and sequence analysis, we found causative mutations in FAM58A on Xq28 in all affected individuals, suggesting an X-linked dominant inheritance pattern for this recognizable syndrome.

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Mutations in the cyclin family
member FAM58A cause
an X-linked dominant disorder
characterized by syndactyly,
telecanthus and anogenital
and renal malformations
Sheila Unger1,2,12, Detlef Bo ¨hm3,12, Frank J Kaiser4,
Silke Kaulfu?5, Wiktor Borozdin3, Karin Buiting6,
Peter Burfeind5, Johann Bo ¨hm1, Francisco Barrionuevo1,
Alexander Craig1, Kristi Borowski7, Kim Keppler-Noreuil7,
Thomas Schmitt-Mechelke8, Bernhard Steiner9, Deborah Bartholdi9,
Johannes Lemke9, Geert Mortier10, Richard Sandford11,
Bernhard Zabel1,2, Andrea Superti-Furga2& Ju ¨rgen Kohlhase3
We identified four girls with a consistent constellation of
facial dysmorphism and malformations previously reported in
a single mother–daughter pair. Toe syndactyly, telecanthus and
anogenital and renal malformations were present in all affected
individuals; thus, we propose the name ‘STAR syndrome’ for
this disorder. Using array CGH, qPCR and sequence analysis,
we found causative mutations in FAM58A on Xq28 in all
affected individuals, suggesting an X-linked dominant
inheritance pattern for this recognizable syndrome.
We identified four unrelated girls with anogenital and renal malfor-
mations, dysmorphic facial features, normal intellect and syndactyly of
toes. A similar combination of features had been reported previously
in a mother–daughter pair1(Table 1 and Supplementary Note
online). These authors noted clinical overlap with Townes-Brocks
syndrome but suggested that the phenotype represented a separate
autosomal dominant entity (MIM601446). Here we define the
cardinal features of this syndrome as a characteristic facial appearance
with apparent telecanthus and broad tripartite nasal tip, variable
syndactyly of toes 2–5, hypoplastic labia, anal atresia and urogenital
malformations (Fig. 1a–h). We also observed a variety of other
features (Table 1).
On the basis of the phenotypic overlap with Townes-Brocks,
Okihiro and Feingold syndromes, we analyzed SALL1 (ref. 2), SALL4
(ref. 3) and MYCN4but found no mutations in any of these genes
(Supplementary Methods online). Next, we carried out genome-
wide high-resolution oligonucleotide array comparative genomic
hybridization (CGH)5analysis (Supplementary Methods) of genomic
DNA from the most severely affected individual (case 1, with lower
lid coloboma, epilepsy and syringomyelia) and identified a hetero-
zygous deletion of 37.9–50.7 kb on Xq28, which removed exons 1 and
2 of FAM58A (Fig. 1i,j). Using real-time PCR, we confirmed the
deletion in the child and excluded it in her unaffected parents
(Supplementary Fig. 1a online, Supplementary Methods and
Supplementary Table 1 online). Through CGH with a customized
oligonucleotide array enriched in probes for Xq28, followed by break-
point cloning, we defined the exact deletion size as 40,068 bp
(g.152,514,164_152,554,231del(chromosome X, NCBI Build 36.2);
Fig. 1j and Supplementary Figs. 2,3 online). The deletion removes
the coding regions of exons 1 and 2 as well as intron 1 (2,774 bp),
492 bp of intron 2, and 36,608 bp of 5¢ sequence, including the 5¢ UTR
and the entire KRT18P48 pseudogene (NCBI gene ID 340598).
Paternity was proven using routine methods. We did not find deletions
overlapping FAM58A in the available copy number variation
(CNV) databases.
Subsequently, we carried out qPCR analysis of the three
other affected individuals (cases 2, 3 and 4) and the mother-daughter
pair from the literature (cases 5 and 6). In case 3, we detected
a de novo heterozygous deletion of 1.1–10.3 kb overlapping exon 5
(Supplementary Fig. 1b online). Using Xq28-targeted array CGH
and breakpoint cloning, we identified a deletion of 4,249 bp
(g.152,504,123_152,508,371del(chromosome X, NCBI Build 36.2);
Fig. 1j and Supplementary Figs. 2,3), which removed 1,265 bp
of intron 4, all of exon 5, including the 3¢ UTR, and 2,454 bp
of 3¢ sequence.
We found heterozygous FAM58A point mutations in the remaining
cases (Fig. 1j, Supplementary Fig. 2, Supplementary Methods
and Supplementary Table 1). In case 2, we identified the mutation
555+1G4A, affecting the splice donor site of intron 4. In case
4, we identified the frameshift mutation 201dupT, which immediately
results in a premature stop codon N68XfsX1. In cases 5 and 6,
we detected the mutation 556-1G4A, which alters the splice
acceptor site of intron 4. We validated the point mutations
and deletions by independent rounds of PCR and sequencing
or by qPCR. We confirmed paternity and de novo status of
the point mutations and deletions in all sporadic cases. None
of the mutations were seen in the DNA of 60 unaffected female
Received 10 October 2007; accepted 2 January 2008; published online 24 February 2008; doi:10.1038/ng.86
1Institute of Human Genetics,2Centre for Pediatrics and Adolescent Medicine, University of Freiburg, Freiburg, D-79106 Freiburg, Germany.3Center for Human
Genetics Freiburg, D-79100 Freiburg, Freiburg, Germany.4Institut fu ¨r Humangenetik, Universita ¨tsklinikum Schleswig-Holstein, Campus Lu ¨beck, D-23538 Lu ¨beck,
Germany.5Institut fu ¨r Humangenetik, Universita ¨t Go ¨ttingen, D-37073 Go ¨ttingen, Germany.6Institut fu ¨r Humangenetik, Universita ¨tsklinikum Essen, D-45122 Essen,
Germany.7Division of Medical Genetics, University of Iowa Hospitals and Clinics, Iowa City, Iowa 52242, USA.8Abteilung Neuropa ¨diatrie, Kinderspital, CH-6000
Luzern, Switzerland.9Institut fu ¨r Medizinische Genetik, Universita ¨t Zu ¨rich, CH-8603 Schwerzenbach, Switzerland.10Center for Medical Genetics, Ghent University
Hospital, B-9000 Ghent, Belgium.11Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke’s Hospital,
Cambridge CB2 OXY, UK.12These authors contributed equally to this work. Correspondence should be addressed to J.K. (jkohlhase@humangenetik-freiburg.de).
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controls, and no larger deletions involving FAM58A were found
in 93 unrelated array-CGH investigations.
By analyzing X-chromosome inactivation (Supplementary Meth-
ods and Supplementary Fig. 4 online), we found complete skewing
of X inactivation in cases 1 and 3–6 and almost complete skewing in
case 2, suggesting that cells carrying the mutation on the active
X chromosome have a growth disadvantage during fetal development.
Using RT-PCR on RNA from lymphoblastoid cells of case 2 (Supple-
mentary Fig. 2), we did not find any aberrant splice products as
additional evidence that the mutated allele is inactivated. Further-
more, FAM58A is subjected to X inactivation6. In cases 1 and 3, the
parental origin of the deletions could not be determined, as a result of
lack of informative SNPs. Case 5, the mother of case 6, gave birth to
two boys, both clinically unaffected (samples not available). We cannot
exclude that the condition is lethal in males. No fetal losses were
reported from any of the families.
The function of FAM58A is unknown. The gene consists of five
coding exons, and the 642-bp coding region encodes a protein of 214
amino acids. GenBank lists a mRNA length of 1,257 bp for the
reference sequence (NM_152274.2). Expression of the gene (by EST
data) was found in 27 of 48 adult tissues including kidney, colon,
cervix and uterus, but not heart (NCBI expression viewer, UniGene
Hs.496943). Expression was also noted in 24 of 26 listed tumor tissues
as well as in embryo and fetus. Genes homologous to FAM58A (NCBI
HomoloGene: 13362) are found on the X chromosome in the
chimpanzee and the dog. The zebrafish has a similar gene on
chromosome 23. However, in the mouse and rat, there are no true
homologs. These species have similar but intronless genes on chromo-
somes 11 (mouse) and 10 (rat), most likely arising from a retro-
transposon insertion event. On the murine X chromosome, the
flanking genes Atp2b3 and Dusp9 are conserved, but only remnants
of the FAM58A sequence can be detected.
FAM58A contains a cyclin-box-fold domain, a protein-binding
domain found in cyclins with a role in cell cycle and transcription
control. No human phenotype resulting from a cyclin gene mutation
has yet been reported. Homozygous knockout mice for Ccnd1
(encoding cyclin D1) are viable but small and have reduced lifespan.
They also have dystrophic changes of the retina, likely as a result of
decreased cell proliferation and degeneration of photoreceptor cells
during embryogenesis7,8.
Cyclin D1 colocalizes with SALL4 in the nucleus, and both proteins
cooperatively mediate transcriptional repression9. As the phenotype of
our cases overlaps considerably with that of Townes-Brocks syndrome
caused by SALL1 mutations1, we carried out co-immunoprecipitation
to find out if SALL1 or SALL4 would interact with FAM58A in a
manner similar to that observed for SALL4 and cyclin D1. We found
that FAM58A interacts with SALL1 but not with SALL4 (Supplemen-
tary Fig. 5 online), supporting the hypothesis that FAM58A and
SALL1 participate in the same developmental pathway.
How do FAM58A mutations lead to STAR syndrome? Growth
retardation (all cases; Table 1) and retinal abnormalities (three
cases) are reminiscent of the reduced body size and retinal anomalies
in cyclin D1 knockout mice7,8. Therefore, a proliferation defect
might be partly responsible for STAR syndrome. To address
this question, we carried out a knockdown of FAM58A mRNA
followed by a proliferation assay. Transfection of HEK293 cells
with three different FAM58A-specific RNAi oligonucleotides resulted
in a significant reduction of both FAM58A mRNA expression
and proliferation of transfected cells (Supplementary Methods and
Supplementary Fig. 6 online), supporting the link between FAM58A
and cell proliferation.
Table 1 Clinical features in STAR syndrome cases
Feature
Case 1
Case 2
Case 3
Case 4
Case 5
Case 6
Feingold
syndrome
Okihiro
syndrome
Townes-Brocks
syndrome
Telecanthus
X
X
X
X
No
No
Lop ears
X
X
X
X
No
No (low set)
(X)
X
Clinodactyly 5th finger
X
X
X
X
X
X
X
Syndactyly of toes (not 2–3)
X
X
X
X
X
X
X
Rare
Occasional
Anal atresia
X
X
X
X
X
X
Reported in
1 individual
Occasional
X
Genital anomaly (external)
Hpl. labia
Hpl. labia
Hpl. labia
Hpl. labia
Clitoromeg.
Clitoromeg.
Rare
Genital anomaly (internal)
Dupl. vagina + uterus
Dupl. vagina, bic. uterus
None
None
Rare
Renal anomaly
Sol. kidney
Cros. fused kidneys
Pelv. kidney, ESRD
Sol. kidney, ESRD
Rare
Occasional
X
Urinary tract anomaly
VU reflux
Hydronephr., VU reflux,
megaureter
VU reflux
Hydronephr.,
small bladder
VU reflux
Radial ray anomaly
X
X
X
Congenital heart disease
PFO, peripheral pulm.
artery stenosis
Bicusp. aortic valve,
valv. pulm. stenosis
ASD
Rare
Occasional
Occasional
Height (percentile)
3rd
o3rd
o3rd
5th
o3rd
o3rd
Eyes
Macular hypoplasia
Dystr. retina, –5D myopia
Normal
Craniosynostosis
Cor., lambd.
sagittal
Abbreviations: asym., asymmetrical; bic., bicornuate; bicusp., bicuspid; bif., bifid; clitoromeg., clitoromegaly; cor., coronal; cros., crossed; dupl., duplicated; ESDR, end-stage renal disease; hpl., hypoplastic; hydronephr., hydronephrosis;
lambd., lambdoid; PFO, persistent formane ovale; pelv., pelvic; pulm., pulmonary; sol., solitary; valv., valvular; VU, vesicourethral. An ‘‘X’’ denotes a trait present in the respective case or typically observed in the overlapping syndromes.
More detailed information, especially on cases 5 and 6, is contained in the Supplementary Note.
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We found that loss-of-function mutations of FAM58A result in a
rather homogeneous clinical phenotype. The additional anomalies in
case 1 are likely to result from an effect of the 40-kb deletion on
expression of a neighboring gene, possibly ATP2B3 or DUSP9. How-
ever, we cannot exclude that the homogeneous phenotype results from
an ascertainment bias and that FAM58A mutations, including
missense changes, could result in a broader spectrum of malforma-
tions. The genes causing the overlapping phenotypes of STAR syn-
drome and Townes-Brocks syndrome seem to act in the same pathway.
Of note, MYCN, a gene mutated in Feingold syndrome, is a direct
regulator of cyclin D2 (refs. 10,11); thus, it is worth exploring whether
the phenotypic similarities between Feingold and STAR syndrome
might be explained by direct regulation of FAM58A by MYCN.
FAM58A is located approximately 0.56 Mb centromeric to MECP2
on Xq28. Duplications overlapping both MECP2 and FAM58A have
been described and are not associated with a clinical phenotype in
females12, but no deletions overlapping both MECP2 and FAM58A
have been observed to date13. Although other genes between FAM58A
and MECP2 have been implicated in brain development, FAM58A and
MECP2 are the only genes in this region known to result in X-linked
dominant phenotypes; thus, deletion of both genes on the same allele
might be lethal in both males and females.
Note: Supplementary information is available on the Nature Genetics website.
ACKNOWLEDGMENTS
We thank the research subjects and their families for their participation, generosity
and patience. We thank G. Scherer for critical discussion, P. Hermanns and
B. Ro ¨sler for help with cell cultures, and C. Lich for technical assistance.
J.K. received funding from the Deutsche Forschungsgemeinschaft (grant no.
Ko1850/6-1,6-2).
AUTHOR CONTRIBUTIONS
S.U. contributed to the clinical evalutation of cases, syndrome delineation
and subject enrollment in the study. D.B. performed array CGH, mutation
analysis and qPCR. W.B. performed mutation analysis on MYCN, SALL1
and SALL4 and FAM58A breakpoint cloning. F.J.K. performed co-immuno-
precipitation studies. K. Buiting performed X-chromosome inactivation studies.
S.K. and P.B. performed cell culture studies, siRNA knockdown experiments
and proliferation assays, and contributed to the manuscript. J.B., F.B.
and A.C. cloned expression constructs and performed RT-PCR. K.
Borowski, K.K.-N., G.M., T.S.-M., B.S., D. Bartholdi, R.S., B.Z., and
A.S.-F contributed to subject enrollment and clinical evaluation. S.U., D.B.,
J.B., F.J.K., K.Bu., S.K., P.B., R.S., G.M. and A.S.-F. also contributed to the
manuscript. J.K. oversaw all aspects of the research and wrote major parts
of the manuscript.
Published online at http://www.nature.com/naturegenetics
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reprintsandpermissions
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Figure 1 Clinical and molecular characterization of STAR syndrome. (a–f) Facial appearances of cases 1–3 (apparent telecanthus, dysplastic ears and thin
upper lips; a,c,e), and toe syndactyly 2–5, 3–5 or 4–5 (b,d,f) in these cases illustrate recognizable features of STAR syndrome (specific parental consent has
been obtained for publication of these photographs). Anal atresia and hypoplastic labia are not shown. (g,h) X-ray films of the feet of case 2 showing only
four rays on the left and delta-shaped 4th and 5th metatarsals on the right (h; compare to clinical picture in d). (i) Array-CGH data. Log2ratio represents
copy number loss of six probes spanning between 37.9 and 50.7 kb, with one probe positioned within FAM58A. The deletion does not remove parts of other
functional genes. (j) Schematic structure of FAM58A and position of the mutations. FAM58A has five coding exons (boxes). The cyclin domain (green) is
encoded by exons 2–4. The horizontal arrow indicates the deletion extending 5¢ in case 1, which includes exons 1 and 2, whereas the horizontal line below
exon 5 indicates the deletion found in case 3, which removes exon 5 and some 3¢ sequence. The pink horizontal bars above the boxes indicate the
amplicons used for qPCR and sequencing (one alternative exon 5 amplicon is not indicated because of space constraints). The mutation 201dupT (case 4)
results in an immediate stop codon, and the 555+1G4A and 555-1G4A splice mutations in cases 2, 5 and 6 are predicted to be deleterious because they
alter the conserved splice donor and acceptor site of intron 4, respectively.
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