Greig Cephalopolysyndactyly Contiguous Gene Syndrome in a Congolese patient co-occurring with Sickle-Cell Anemia, and review of literature

Introduction

Greig cephalopolysyndactyly syndrome (GCPS) (MIM# 175700) is a rare genetic disorder characterized by craniofacial abnormalities (macrocephaly, frontal bossing, hypertelorism, broad nasal bridge) and abnormal limb development (pre- and postaxial foot/hand polydactyly, variable fingers/toes syndactyly, broad thumb and hallux). This may be associated with structural brain abnormalities such as corpus callosum abnormalities. Most of the patients have normal intelligence (Biesecker, 2008; Kozma et al., 2021). These clinical manifestations show both inter- and intra-familial variabilities (Schulz et al., 2008). Missense variants, as well as haploinsufficiency resulting from copy number losses, splicing or truncating variants elsewhere in the Gli-Kruppel Family Member 3 (GLI3) gene cause GCPS by loss of the DNA-binding capacity or activation of nonsense-mediated mRNA decay, or by the formation of an unstable or mislocalized protein (Biesecker, 2006). Chromosomal deletions, larger than 1 Mb, that encompasses GLI3 are referred to as Greig Cephalopolysyndactyly Contiguous Gene Syndrome (GCPS-CGS), and the clinical presentation is more severe than the classical GCPS. Patients with GCPS-CGS present complex neurobehavioral disorders with intellectual disability, severe developmental delay, and neurological features. The level of disability seems to be correlated to the size of the deletion (Biesecker, 2008; Johnston et al., 2003; Schulz et al., 2008).

To date, nearly 200 patients with GCPS have been reported (Kozma et al., 2021), including twenty-seven patients referred to as GCPS-CGS (Kozma et al., 2021; Zung et al., 2011). None of the reported patients are from Sub-Saharan Africa, where multiple overshadowing conditions such as infectious diseases or Sickle Cell Anemia (SCA) are frequent.

We present the phenotype of GCPS-CGS in the first patient from Sub-Saharan Africa, review the phenotype in previously reported patients and discuss the co-occurrence of SCA. The patient was recruited in the frame “Deciphering Developmental Disorders in Africa Project (DDD-Africa)” which aimed to study 500 individuals with unexplained Developmental Disorders (DD) in two Sub-Saharan countries (South Africa and DR Congo). This study was approved by the Ethical Committee of the Public Health School of the University of Kinshasa (ESP/CE/050/2018).

Clinical summary

The proband was an 8-year-old fourth-born girl referred to the genetic clinic for global developmental delay, limb anomalies, and dysmorphic facial appearance. She was born to unrelated young and healthy Congolese parents (age at birth: father, 33 years; mother, 30 years). She was born at term with macrosomia (birth weight was 4400 g = 99^th percentile) after an uneventful pregnancy and uncomplicated vaginal delivery. Parents could not recall birth OFC and height. Fully formed preaxial toe polydactyly (Figure 1 N-O) and rudimentary postaxial hand polydactyly (Figure 1 H-I) were observed at birth. She also had an anal bud, and no details were available. Before the age of 1 year, the patient underwent surgical resection of the foot preaxial polydactyly and anal bud. Her gross and fine motor development (walked at 4.5 years) and speech and language development (the first word “papa” at the age of 1 year and then regressed to complete absence of speech at the time of consultation) were delayed. She had stereotypical hand movements and had not acquired hygiene autonomy. At 6 years of age, she developed kyphoscoliosis (Figure 1 M), for which she was misdiagnosed with Pot disease (bone tuberculosis) despite negative bacteriological investigations. She was treated with anti-tuberculosis drugs for 6 months without improvement as she retained the spinal deformity. A Cardiac ultrasound performed at the age of 6 years was normal. In addition, she presented with fever and anemia, requiring blood transfusions during three separate episodes.

Figure 1.

Clinical photographs, Spine X-ray and Brain MRI of the patient

Clinical photographs of the patient at the age of 7 years: (A) macrocephaly, arched eyebrows, hypertelorism, epicanthus, convergent strabismus, wide nasal bridge, broad nose, short columella, deep philtrum, thick lips, pointed chin; (B-C) flat nasal bridge, short neck, Darwin-notch of helix at right; (D) incisors macrodontia; (F-I) long fingers, camptodactyly of 5th fingers, rudiment hands postaxial polydactyly, abnormal palmar dermatoglyphics; (P-Q) post-operative scar after surgical correction of foot preaxial polydactyly, toes camptodactyly 2–3, partial bilateral toes cutaneous syndactyly 1–4, toes clinodactyly (3–5 at left, 4–5 at right). Clinical photographs of the patient at the age of 8 years: (J) swollen left knee; (K) wide intermammillary distance, small umbilical hernia; (L) pronounced kyphoscoliosis. Brain MRI of the patient at the age of 8 years (E): obstructive quadriventricular hydrocephalus, agenesis of the corpus callosum, and supratentorial multiple system atrophy. Spine X-ray at the age of 6 years (M): thoracic kyphoscoliosis. Foot X-ray at the age of 1year (N-O): bilateral foot preaxial polydactyly.

At the evaluation (age, 7 years), macrocephaly was observed (OFC 54 cm = 98^th percentile). Height (118 cm = 30^th percentile) and weight (27.6 Kg = 87^th percentile) were normal, using the WHO growth charts. Dysmorphism evaluation (Figure 1) revealed macrocephaly, arched eyebrows, hypertelorism, epicanthus, convergent strabismus, wide and flat nasal bridge, broad nose, short columella, deep philtrum, thick lips, big central incisors, Darwin-notch of the helix at right, short neck, pointed chin, small umbilical hernia, long fingers, short proximal and long distal phalanges of the fingers, camptodactyly of 5th fingers, abnormal palmar dermatoglyphic, hands postaxial polydactyly, feet preaxial polydactyly, bilateral toes camptodactyly 2–3, partial bilateral toes syndactyly 1–4, toes clinodactyly (3–5 at left, 4–5 at right), and overlapping toes 2 of 3 on left.

When she returned for follow-up at the age of 8 years, we further noted a wide intermammillary distance and pronounced thoracic kyphoscoliosis (Figure 1 K-L). She exhibited difficulties in walking due to a painful and swollen left knee (Figure 1 J). IQ evaluation using Differential Ability Scales II (DAS II) concluded to severe cognitive disability and developmental cognitive age equal to 5 years old.

Brain MRI (Figure 1 E) identified obstructive quadriventricular hydrocephalus, absence of the corpus callosum, and supratentorial multiple system atrophy. Spine MRI imaging (not included) revealed a T12 benign wedge-shaped vertebral compression fracture with a mass effect of the posterosuperior corner on the spinal cord without signs of compression or syringomyelic cavity formation. Benign panvertebral spinal cord hyperplasia was also observed. Left Knee MRI (not included) revealed lateral meniscal dysplasia typical of a discoid meniscus associated with low abundance hydrarthrosis and absence of patellofemoral dysplasia.

Investigations

Trio-based Genome Sequencing (GS) performed using DRAGEN Germline Pipeline 3.2.8 (for calling SNVs and small CNVs) and WiseCondorX (for calling large CNVs) (Supplementary digital content, genetic analysis procedure, Supplemental Digital Content 1, http://links.lww.com/CD/A47), identified a de novo deletion of 5.84 Mb Seq[GRch38]del(7)(p14.1p12.3)chr7:g.41547763–47388635del including GLI3 gene, classified as pathogenic following the ACMG guidelines causing GCPS-CGS. This deletion includes 43 coding genes of which 10 (GLI3, BLVRA, PGAM2, AEBP1, GCK, CAMK2B, OGDH, CCM2, ADCY1 and NPC1L1) are linked to known phenotypes in OMIM (Supplemental Figure S1, Supplemental Digital Content 2, http://links.lww.com/CD/A48 and Table S1, Supplemental Digital Content 3, http://links.lww.com/CD/A49). This deletion was not present in either parent, confirming the de novo deletion (Figure 2). The deletion was confirmed using Chromosomal Micro Array (CMA). The minimum and maximum regions of deletion in the CMA were 41613473–47364514 and 47412204–41518989, respectively (Supplemental Figure S2, Supplemental Digital Content 4, http://links.lww.com/CD/A50).

Figure 2.

Visualization with WiseCondorX

In the Index, the ratio profile of chromosome 7 shows a loss on chromosome 7p14.1-p12.3, expands over a 5.8 Mb region between hg38 coordinates 41547763 and 47388635. Mother and Father are normal.

In addition, we identified a homozygous missense variant in HBB gene [NM_000518.5: c.20A>T (p.Glu7Val) (Chr11:5227002T>A; GRCh38)], both parents being heterozygous. It is a well-known pathogenic variant (rs334) that causes Sickle Cell Anemia (ClinVar accession number: RCV000016574.39). We concluded to a dual diagnosis of GCPS-CGS and Sickle Cell Anemia. The patient was referred to a specialized center for SCA, to the pediatric surgery unit for follow-up of scoliosis, to the neuropaediatric service, and special school for developmental delay.

Discussion

The phenotype in our patient matches the common presentation of the 27 patients with GCPS-CGS reported in the literature (Table 1 and Supplemental Table S2, Supplemental Digital Content 5, http://links.lww.com/CD/A51) (Kozma et al., 2021; Zung et al., 2011). The correlation between deletions greater than 1 Mb on the chromosome 7p14, including GLI3 gene, and severe neurodevelopmental features has been established (Johnston et al., 2003, 2007) and confirmed in 22 (81.5 %) patients (Table 1 and Supplemental Table S2, Supplemental Digital Content 5, http://links.lww.com/CD/A51). Twenty-six patients had a de novo inheritance pattern (Supplemental Table S2, Supplemental Digital Content 5, http://links.lww.com/CD/A51), which is consistent with the inherited pattern of GCPS-CGS (Biesecker, 2008; Johnston et al., 2003). The only inherited case was paternal (Schulz et al., 2008).

Table 1.

Phenotype evaluation of 27 patients reported in the literature with GCPS-CGS caused by deletion greater than 1 Mb, compared to our patient.

Phenotype	Our patient	Kozma et al., 2021	Niida et al., 2015	Démurger et al., 2015	Hurst et al., 2011	Zung et al., 2011	Schulz et al., 2008	Debeer et al., 2007	Johnston et al., 2003, 2007	Kroisel et al., 2001; Schwarzbraun et al., 2005	Zneimer et al., 2000	Williams et al., 1997	Number (%) of patients who presented those phenotypes
Total number of patients	1	1	1	2	3	1	1	2	9	5	1	1	27 (100)
Preaxial polydactyly	Y	1	1	2	2	1	1	2	9	5	-	1	25 (92.6)
Cutaneous syndactyly	Y	1	1	2	3	1	1	2	6	5	1	1	24 (88.9)
Severe developmental delay	Y	1	1	2	3	1	1	-	6	5	1	1	22 (81.5)
Brain anomaly	Y	1	1	2	2	1	1	-	6	4	-	1	19 (70.4)
Hypertelorism	Y	1	1	2	-	1	1	2	4	5	-	-	17 (62.9)
Intellectual disability (ID)	Y	1	-	-	2	1	1	2	4	5	-	-	16 (59.2)
Broad thumb/hallux	N	1	-	1	2	-	1	2	1	5	1	1	15 (55.5)
Macrocephaly	Y	1	1	-	-	1	1	-	3	4	-	1	12 (44.4)
Ophthalmologic anomaly	Y	1	-	2	2	-	1	-	1	2	1	1	11 (40.7)
Flat nasal bridge	Y	-	-	-	2	-	1	-	-	5	1	1	10 (37)
Wide nasal bridge	Y	1	-	-	2	1	-	2	-	-	-	1	7 (25.9)
Seizures	N	-	-	-	1	1	-	-	2	3	-	-	7 (25.9)
Heart defect	N	-	-	-	3	-	1	-	1	1	-	-	6 (22.2)
Macrosomia	Y	1	1	-	-	-	-	-	-	1	1	1	5 (18.5)
Frontal bossing	N	-	1	-	-	-	-	2	-	-	1	1	5 (18.5)
Downslanted palpebral fissures	N	-	-	-	-	-	-	-	-	5	-	-	5 (18.5)
Umbilical hernia	Y	1	-	-	-	-	1	-	-	2	-	1	5 (18.5)
Craniosynostosis	N	-	-	-	3	-	-	-	-	-	1	-	4 (14.8)
High forehead	N	-	-	-	-	1	-	2	-	-	-	-	3 (11.1)
Broad nose	Y	-	-	-	-	-	1	-	-	-	1	1	3 (11.1)
Inguinal hernia	N	-	-	1	-	-	1	-	1	-	-	-	3 (11.1)
Scaphocephaly	N	-	-	-	1	-	-	-	-	-	1	-	2 (7.4)
Trigonocephaly	N	-	-	-	2	-	-	-	-	-	-	-	2 (7.4)
Broad late closing cranial suture	N	-	-	-	1	-	-	-	-	-	1	-	2 (7.4)
Prominent metopic ridge	N	1	-	-	-	-	-	-	-	-	-	1	2 (7.4)
Postaxial polydactyly	Y	-	-	-	-	-	-	-	-	2	-	-	2 (7.4)
Abnormal behavior	Y	-	-	-	-	-	-	-	-	2	-	-	2 (7.4)
Camptodactyly	Y	-	-	-	-	-	-	-	-	-	-	-	0 (0)

Abbreviations: Y, present; N, absent.

Additional features found in our patient are broader (Supplemental Table S2, Supplemental Digital Content 5, http://links.lww.com/CD/A51), whereas the cases with broader additional features in the literature are those with a large deletion, except for Zneimer, whose size is not available (Supplemental Table S2, Supplemental Digital Content 5, http://links.lww.com/CD/A51) (Kozma et al., 2021). In our case, we could attribute that to the variable expressivity of contiguous genes (Fryns et al., 1981; Kozma et al., 2021; Zung et al., 2011) and their association with SCA, mostly in terms of musculoskeletal abnormalities (scoliosis, meniscal dysplasia), recurrent infections, and anemia. Both the morphology and clinical complications of SCA may overshadow a co-occurring disease and delay its diagnosis of either disease.

The co-occurrence of neurodevelopmental disorders and SCA has higher odds of reciprocally increasing the complications (Lance et al., 2021) making it difficult to determine the impact of each disease on part of the patient’s phenotype. With SCA, which is frequent in the Congolese environment, and its influence on the morphology of the patient and the severity of clinical features (Lumbala et al., 2022), highthroughput sequencing approaches such as GS are encouraged. Furthermore, GS proved to be an all-in-one approach for future genetic investigations in our patient. This allowed us to elucidate the clinical features of our patient (who was treated for a long time for chronic infectious disease, Tuberculosis) by highlighting these two diseases.

In conclusion, this report provides a clinical description with the expansion of the known phenotype and molecular profile of the first African patient with GCPS-CGS. She is setting an example of SCA overshadowing the clinical presentation of a rare disease and extending the diagnostic odyssey in Sub-Saharan Africa. In addition, this report demonstrates the benefits of GS in patients with multiple types of aberrations and diseases. Although our patient did not present many more signs attributable to the deletion of the other genes in the CNV segment, follow-up is still necessary.

Supplementary Material

Table S1. Genes deleted involved in known phenotype

• Table S1. Genes with known phenotypes within the 5.8 Mb deletion of 7p14 detected in the patient.

Out of these 10 coding genes, 5 (BLVRA, PGAM2, AEBP1, OGDH, and ADCY1) have autosomal recessive (AR) inheritance, 4 (GLI3, PGAM2, GCK, CAMK2B, and CCM2) have autosomal dominant inheritance and one gene (NPC1L1) has unclear inheritance.

Table S2. Literature review of patients with GCPS-CGS

• Table S2. Clinical evaluation and molecular results of the literature review of patients with GCPS-CGS caused by deletion greater than 1 Mb, compared to our patient.

Abbreviations: Y, present; N, absent; P, percentile; NA, not available; VSD, ventricular septal defect; ASD, atrial septal defect; PDA, patent ductus arteriosus; DORV, double outlet right ventricle; SVAS, supraventricular aortic stenosis; PS, pulmonary stenosis; CA, coarctation of the aorta; FB, foot bilateral; HB, hand bilateral; BH, broad halluces; BT, broad thumb; FC, finger camptodactyly; TC, toe camptodactyly; FS, finger syndactyly; TS, toe syndactyly; ID, Intellectual disability; ACC, corpus callosum agenesis; HCC, corpus callosum hypoplasia; VD, ventricular dilatation; CCM, cerebral cavernous malformation; CD, cerebellar dysgenesis, BA, brain atrophy; CH, cavernous hemangioma, GR, Growth retardation

• Genetic analysis procedure

Figure S2. CMA visualization of the deletion

• Figure S1. Overview of the 43 coding Genes on the deleted segment visualized via Moon platform.

• Figure S2. CMA visualization.

Chromosomal micro array confirmed the presence of this deletion previously identified with GS. The boundaries of the deletion provided by NGS analysis fall well between the limits of the maximum and minimum regions of deletion returned by the CMA. The maximum region of deletion is 47412204–41518989 (8.21 Mb), whereas the minimum deleted region is 41613473–47364514 (5.751 Mb).

Data availability

A summary of this patient, including the HPO and deletion, has been made available through DECIPHER (subject number 491020). Any other data and information may be obtained upon reasonable request from the corresponding author.