Alazami syndrome in an Afghani girl: A case report and review of literature

Purpose: Alazami syndrome is a rare autosomal recessive disorder with core phenotypic manifestations of short stature, mild facial dysmorphism, and global developmental delay evolving to severe intellectual disability. Homozygous loss-of-function mutations in LARP7 gene, which encodes a chaperone protein of the noncoding RNA 7SK, have been detected in patients with Alazami syndrome. Since its first description in 2012, only six families with Alazami syndrome have been reported to date. This case is reported to expand the phenotypic description to include small kidneys.

Methods: The patient was referred for Clinical Genetics evaluation at Rady Children’s Hospital San Diego due to intellectual disability and growth delay. Whole exome sequencing was performed (GeneDx) after informed consent.

Result: Whole exome sequencing identified a homozygous pathogenic variant in exon 12 of LARP 7(c.1620_1623delACAG; p.Ala542Aspfs*15), conferring a diagnosis of Alazami syndrome. The clinical features of a 16-year-old Afghani girl with Alazami syndrome are reported and compared to features of previously reported Alazami syndrome cases. In addition to sharing many features of previously reported cases, the subject of this report also had small kidneys and pre-hypertension.

Conclusion: This case report broadens the phenotype of Alazami syndrome to include small kidneys and behavioral problems related to anxiety.

Introduction

Alazami syndrome (OMIM: 615071) is a genetic disorder caused by homozygous or compound heterozygous mutations in LARP7, which encodes a chaperone of the 7SK noncoding (nc) RNA [1]. Alazami et al., [2], first described this syndrome in a large consanguineous Saudi Arabian family, where ten affected children showed primordial dwarfism (PD) having growth parameters at least 3.5 SD below the mean, severe intellectual disability, and facial dysmorphism consisting of malar hypoplasia, short philtrum, triangular face, deep-seated eyes, broad nose, narrow palpebral fissures, and microstomia [1-3]. Additionally, some nonspecific skeletal abnormalities such as scoliosis and mild epiphyseal changes in proximal phalanges without clear dysplasia were observed [2]. Genome-wide linkage analysis of affected individuals, their parents, and some of the unaffected siblings detected an extended 26.5- Mb homozygous region between SNPs surrounding chromosome 4q24-4q28.2 among all patients but not in unaffected relatives. Molecular functional studies and sequencing of a list of candidate genes in this region showeda homozygous 7 bp duplication in exon 8 of LARP 7 gene (c.1024_1030dupAAGGATA, p.T344Kfs*9), causing a frameshift mutation that resulted in premature truncation of the peptide [2]. A complete absence of LARP7 protein was also observed in the patients suggesting that mutation produced a null phenotype [2].

Najmabadi et al., [4], conducted a large study including 136 consanguineousIranianfamilies with autosomal-recessive intellectual disability and microcephaly and determined the etiology to be a frameshift mutation (Lys276fs) in LARP 7. Furthermore, Ling et al., [3], detected compound heterozygous frameshift variants in LARP7: c.213_214dup (p.Ser72fs) and c.651_655del (p.Lys219fs) in a 2-year old Caucasian girl with Alazami syndrome. Hollink et al., [1], reported two unrelated Alazami syndrome patients with homozygous loss-of-function variants in LARP7. Dateki et al., [5], reported another patient with Alazami syndrome having unique compound heterozygous mutations in LARP7 [5]. Recently Imbert-Bouteille M et al., [6], reported two sisters with Alazami syndrome with homozygous frameshift variant in exon7 of LARP7:c.524_525ins (p.Ala176Leufs).

Herein we report a new case of Alazami syndrome with a homozygous 4-bp deletion in exon 12 of LARP7. The clinical features of the patient in the present case report are compared with other previously reported Alazami syndrome patients to portray further phenotypic manifestations related to this syndrome.

Case Presentation

The patient wasa 16-year-old girl of Afghan origin with primary complaints of intellectual disability, growth and motor development delay, and dysmorphic facial features, who was referred for outpatient clinical genetics consultation. She was the product of a consanguineous union, and there was a family history of intellectual disability in a paternal aunt and paternal grandmother. Mother reported poor fetal movement, a 7 kg weight loss and depression during the pregnancy. She was delivered at term by cesarean section weighing1.8 kg. Although her growth in the neonatal period was normal, her psychomotor development was delayed and she was able to talk and walk at 3 years age. She is unable to speak full sentences and usually gives one-word answers, fails to follow commands, requires assistance to get dressed, and shows situational anxiety.Physical examination revealed a height of 144.5 cm (z=-2.82) and head circumference of 51.8 (z=-2.5) with narrow, prominent forehead and low posterior hairline. Her nose was broad with a bulbous tip. She had a short philtrum, widely spaced teeth, deeply set eyes, malar flattening and mildly short palpebral fissures (2.5cm) (Figure1). Finger pads were prominent, and the great toes were shorter than the second toes. Streaky hyperpigmentation was observed on her right lateral chest and back of the legs. There was a grey macule on the dorsum of her left hand. She could walk steadily with a wide-based gait but was unable to run. She has hyperopia and strabismus, but is noncompliant with wearing spectacles.

Figure 1: Narrow, prominent forehead, low posterior hair line, broad nose with a bulbous tip, a short philtrum, widely spaced teeth, deeply set eyes, malar flattening and mildly short palpebral fissures.

Renal ultrasound with Doppler detected a small left kidney (4thcentile); DMSA scan showed equal flow of blood in both the kidneys and normal renal function. Due to strong family history of hypertension, amlodipine was started for prehypertension. Echocardiogram was normal. Audiological evaluation revealed mild conductive hearing loss in both ears. An oligonucleotide SNP microarray showed regions of homozygosity totaling at least 103 Mb, consistent with parental first-cousin relationship, and a 109 kb microdeletion of chromosome 16q21, interpreted as a variant of uncertain significance.

Whole exome sequencing analysis revealed a homozygous 4 bp deletion in exon 12 of LARP7, resulting in a frameshift and creating a premature stop codon (c.1620_1623delACAG; p.A542Nfs*15). Her parents were heterozygous for the c.1620_1623delACAG variant in the LARP7 (Table 1).

Discussion

We presentan additional case of Alazami syndrome characterized by severe intellectual disability, mild facial dysmorphism, mild short stature, and microcephaly due to a novel homozygous frameshift loss-of-function variant in LARP7. LARP7 belongs to the La Autoantigen related protein family and is responsible for regulation of 7SK-mediated transcription by binding to the 3’-terminal domain of 7SK RNA and becoming an intrinsic part of it [7]. LARP7inhibits RNA Polymerase II-transcribed genes by means of the 7SK small ribonucleoprotein (snRNP) system [8]. 7SK snRNP controls the function of the positive transcription elongation factor P-TEFb that facilitates transcription elongation mediated by RNA Polymerase-II. 7SK snRNP sequesters with P-TEFb and inactivates it by inhibiting its kinase activity [9]. Inactive P-TEFb prevents RNA Polymerase-II phosphorylation and elongation of transcripts [2,7,8]. Thus, depletion of 7SK RNA might be expected to result in growth delay. In fact, loss of LARP7 protein expression due to mutation of LARP7 gene and consequent reduction in the level of 7SK RNA [8], was detected in the affected individuals of the Saudi family [1,2]. Okamura et al., [9], identified gene-specific as well as celltype-specific transcription activation in mouse embryos due to 7SK snRNP mediated regulation of P-TEFb activity, thus proposing LARP-7 mediated transcription regulation incites cell cycle progression in actively proliferating primordial germ cells (PGCs), which proliferate excessively in early mammalian embryos. In addition, Dai et al., [10], determined that knockdown of LARP 7 downregulatesLin28, a positive regulator of organismal growth, causing premature differentiation of embryonic stem cells, resulting in growth deficiency.

All cases of Alazami syndrome have been due to homozygous or compound heterozygous frameshift variants in LARP7 [1-6]. The mutational mechanism is loss-of-function presumably due tononsense-mediated mRNA decay [1,5]. Consistent features among nearly all cases include global developmental delay evolving to severe intellectual disability, growth retardation, and dysmorphic facial features [1-3,5,6]. The patient presented herein has distinct facial features, highly impaired motor skills and language skills. Recently Dateki et al., [5], reported a Japanese patient with Alazami syndrome having compound heterozygous mutation in LARP7and showing facial features as well as intellectual and motor developmental delayquite similar to our patient, suggesting these manifestations are the most consistentfeatures of Alazami syndrome.

Some cases have had normal prenatal growth but considerable postnatal growth restriction [3,5]. Our patient’s final adult height is not as significantly impaired as the initial case descriptions [2,3,6] and not in the range typical for primordial dwarfism, and more in accordance with the growth reported byHollink et al., [1] and Dateki et al. [5].

Behavioral abnormalities have been reported in Alazami syndrome.Hyperactive behavior was reported by Hollink et al., [1], in one patient and in both patients reported by Imbert-Bouteille M et al., [6]. Furthermore, anxiety, frequent tantrums, and hypersensitivity to stimuli were observed in the patient reported by Ling et al., [3]. Our patient exhibits situational anxiety. These findings suggest that behavioral abnormalitiesare an important feature ofAlazami syndrome.

Our patient has pre-hypertension with a family history of early-onset of hypertension.Additionally, our patient possesses small-sized kidneys (between 4-14% tile). To date, only one other patient has exhibited this feature: Holahan et al., [11], reported small sized kidneys (between 5-10%). Whether the small kidney size is a congenital defect or acquiredand whether this phenotype belongs to the spectrum of billaelicLARP7 mutations remain to be determined.

With more widespread use of WES, we anticipate that the diagnosis of Alazami syndrome will be made in additional patients of all racial/ethnic backgrounds, and we expect the clinical spectrum to continue to broaden.

1. Hollink IH, Alfadhel M, Al-Wakeel AS (2016) Broadening the phenotypic spectrum of pathogenic LARP7 variants: two cases with intellectual disability, variable growth retardation and distinct facial features. J Hum Genet 61: 229-233. Link: https://bit.ly/2XqLoQF
2. Alazami AM, Al-Owain M, Alzahrani F (2012) Loss of function mutation in LARP7, chaperone of 7SK ncRNA, causes a syndrome of facial dysmorphism, intellectual disability, and primordial dwarfism. Hum Mutat 33: 1429-1434. Link: https://bit.ly/325HFXL
3. Ling TT, Sorrentino S (2016) Compound heterozygous variants in the LARP7 gene as a cause of Alazami syndrome in a Caucasian female with significant failure to thrive, short stature, and developmental disability. Am J Med Genet A 170A: 217-219. Link: https://bit.ly/2KZPbOg
4. Najmabadi H, Hu H, Garshasbi M, Zemojtel T, Abedini SS, et al. (2011) Deep sequencing reveals 50 novel genes for recessive cognitive disorder. Nature 478: 57-63. Link: https://bit.ly/2LATuzm
5. Dateki S, Kitajima T, Kihara T, Watanabe S, Yoshiura K-C, et al. (2018) Novel compound heterozygous variants in the LARP7 gene in a patient with Alazami syndrome. Hum Gen Var 5: 18014. Link: https://bit.ly/2RTaEJF
6. Imbert-Bouteille M, Mau Them FT, Thevenon J (2019) LARP7 variants and further delineation of the Alazami syndrome phenotypic spectrum among primordial dwarfisms: 2 sisters. Eur J Med Genet 62: 161-166. Link: https://bit.ly/2XqLHuY
7. Markert A, Grimm M, Martinez J (2008) The La-related protein LARP7 is a component of the 7SK ribonucleoprotein and affects transcription of cellular and viral polymerase II genes. EMBO Rep 9: 569-575. Link: https://bit.ly/2KXY4rH
8. Krueger BJ, Jeronimo C, Roy BB (2008) LARP7 is a stable component of the 7SK snRNP while P-TEFb, HEXIM1 and hnRNP A1 are reversibly associated. Nucleic Acids Res 36: 2219-2229. Link: https://bit.ly/326AFd1
9. Okamura D, Maeda I, Taniguchi H (2012) Cell cycle gene-specific control of transcription has a critical role in proliferation of primordial germ cells. Genes Dev 26: 2477-2482. Link: https://bit.ly/2YwnHD7
10. Dai Q, Luan G, Deng L (2014) Primordial dwarfism gene maintains Lin28 expression to safeguard embryonic stem cells from premature differentiation. Cell Rep 7: 735-746. Link: https://bit.ly/2NvHQrT
11. Holohan B, Kim W, Lai TP (2016) Impaired telomere maintenance in Alazami syndrome patients with LARP7 deficiency. BMC Genomics 17: 749. Link: https://bit.ly/2NydCER