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Revista de investigación clínica

versión On-line ISSN 2564-8896versión impresa ISSN 0034-8376

Rev. invest. clín. vol.74 no.6 Ciudad de México nov./dic. 2022  Epub 23-Ene-2023

https://doi.org/10.24875/ric.22000234 

Original articles

Severe Congenital Neutropenia Type 4: A Rare Disease Harboring a G6pc3 Gene Pathogenic Variant Particular to the Mexican Population

Larissa López-Rodríguez1 

Yevgeniya Svyryd1 

Edmar O. Benítez-Alonso1 

Pamela Rivero-García1 

Leonora Luna-Muñoz1 

Osvaldo M. Mutchinick1  * 

1Department of Genetics, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico


ABSTRACT

Background:

Severe congenital neutropenia type 4 (SCN4) is a rare autosomal recessive granulopoiesis disorder caused by G6PC3 gene pathogenic variants. The estimated prevalence is 1/10,000,000 people. Over 90% of patients present a syndromic form with variable multisystemic involvement, including congenital heart defects, increased visibility of superficial veins (IVSV), inflammatory bowel disease, and congenital urogenital defects as prominent symptoms.

Objectives:

The objective of the study was to study non-hematological phenotypic findings that suggest a clinical diagnosis of SCN4.

Methods:

We examined medical records of patients diagnosed with neutropenia from January 2000 to December 2020, selecting cases with non-hematologic manifestations for phenotypic description and G6PC3 gene sequencing.

Results:

We found 11 cases with non-hematologic features: congenital heart defects in 8, IVSV in 6, inflammatory bowel disease in 4, urogenital defects in 4, and similar facial appearance. In addition, Sanger sequencing confirmed 3 homozygous cases for the c.210delC variant, a compound heterozygous harboring this variant, and a c.199_218+1 deletion.

Conclusions:

Our findings of the c.210delC variant in very close geographical settings, to date, have only been reported among Mexicans, and a mutual uncommon surname in two families strongly supports a founder effect for the variant in the studied population. Furthermore, the described non-hematologic symptoms in patients with severe primary neutropenia should be explored, confirming SCN4 by investigating G6PC3 gene mutations.

Keywords Neutropenia; Severe congenital neutropenia; Severe congenital neutropenia type 4; G6PC3 mutations

INTRODUCTION

Neutropenia is a wide-range hematopoiesis disorder characterized by granulopoiesis arrest at the promyelocyte maturation stage with peripheral blood absolute neutrophil count below 1500/µL or below 500/µL in severe neutropenia, for a normal range of 2500-6000/µL. Severe congenital neutropenia (SCN) includes a heterogeneous group of disorders of hematopoiesis deficient mature neutrophils1. SCN type 4 (SCN4) is a rare disease characterized by the presence of SCN, associated with non-hematologic multisystemic traits, that was simultaneously described by Dursun et al. (2009) and Boztug et al. (2009), identifying both groups of authors the underlying genetic cause2,3. The characteristic non-hematological manifestations include increased visibility of superficial veins (IVSV), congenital heart defects, and urogenital anomalies. In addition, less frequent findings are thrombocytopenia, failure to thrive, inner ear hearing loss, and endocrine disorders such as growth hormone deficiency, delayed puberty, and cutis laxa4,5. As a group, SCN has an estimated prevalence of 6/1,000,000 individuals; in contrast, SCN4 has a prevalence of 1/10,000,000 people6. The gene G6PC3, located in 17q21, encodes the ubiquitously expressed glucose 6-phosphatase-β enzyme (G6Pase-β or G6PC3)7,8.

G6PC3 catalyzes the final step of glycogenolysis, hydrolyzing the glucose-6-phosphate to glucose and inorganic phosphate in the endoplasmic reticulum (ER) (4). The biallelic G6PC3 gene variants trigger energy homeostasis impairment, failure in 1,5-anhydroglucitol-6-phosphate elimination, ER stress, and elevated apoptosis rate, causing dysfunctional neutrophils and SCN49,10.

Although SCN comprises a heterogeneous group of rare genetic diseases, SCN4 occurs mainly as a syndromic entity, including severe neutropenia and variable multisystemic non-hematologic features. In this respect, only seven cases of nonsyndromic neutropenia related to G6PC3 deficiency have been reported, all younger than 18 years when diagnosed4,11-13. Hence, the rarity of the disease, around one in 10 million people, and the identification of 11 patients suggestive of SCN4 in an adult tertiary medical center, prompted us to define the phenotypic, molecular, and geographical distribution characteristics of this apparent cluster in the Mexican population.

METHODS

Patient population

We conducted an observational retrospective study by reviewing the electronic medical records of patients with neutropenia (ICD-10 code D.70) seen from January 2000 to December 2020 at the National Institute of Medical Sciences and Nutrition “Salvador Zubiran” (Mexico City, Mexico). Syndromic neutropenia cases included at least one associated non-hematological disorder, such as IVSV, congenital heart defects, urogenital anomalies, and inflammatory bowel disease. Cases of secondary neutropenia due to other hematological or non-hematological disorders were excluded from the study.

Informed consent for study participation, molecular analysis, manuscript, and photographs publication is available from all the patients. The Institutional Review Board approved the study on May 21, 2021, (GEN-3729-21-22-1).

Clinical-genetic inclusion procedure

All patients included in the study were selected through a two-steps process by an experienced geneticist and a resident in medical genetics: (1) scrutiny from medical records of all cases with a diagnosis of neutropenia; and (2) a genetic assessment interview with each patient, including clinical exam, laboratory results, sociodemographic characteristics, pedigree construction, pre-test genetic counseling, signed consent approval and, from the patient and family members that accepted, a whole blood sample for the molecular study. Patients with phenotypic characteristics of other genetic or unrelated disorders were excluded from the study.

Molecular analysis

The DNA samples from all patients underwent direct Sanger sequencing of the whole coding region of the G6PC3 gene (RefSeq NM_138387.4). The primer sequences for G6PC3 (exon 1-6) were taken from a previous report2 and ordered from Integrated DNA Technologies (IDT, Coralville, Iowa, USA). We used HotStarTaq Master Mix Kit for fragment amplification under manufacturer standard conditions (QIAGEN, Hilden, Germany). The primer sequences and annealing temperatures are exhibited in Table S1. The PCR products were sequenced using a BigDye Terminator v3.1 Cycle Sequencing kit on an ABI Prism 3500 Genetic Analyzer under the procedure indicated by the manufacturer (Applied Biosystems, ThermoFisher Scientific, CA, USA). Sequence analysis was performed using the Unipro UGENE (version 39.0)14.

RESULTS

Patients

Eleven patients with neutropenia and non-hematologic traits were included in the study. The sex ratio female-to-male was 4:1. The current median age was 38.5 years (21-68 years); the median age at diagnosis was 32 years, although with a wide range (1 month-58 years). Regarding family backgrounds, patients 5 and 6 had first-degree relatives with recurrent infections, a sister and daughter, respectively, and patient 11 had two sisters with leukopenia.

Hematological findings

A varied hematological diagnosis was present in the four cases that were subsequently confirmed to have G6PC3 gene pathogenic variants (PV), showing neutropenia, cyclic neutropenia, pancytopenia, and medullary aplasia (Table 1 and Fig. 1). Of the remaining seven cases, two presented severe neutropenia and two cyclic neutropenia. Other diagnoses were mild neutropenia, cytopenia, and medullary aplasia, one each.

Table 1. Clinical description of patients with G6PC3 gene pathogenic variants 

Characteristics P1 P2 P3 P4
Sex Female Male Female Male
Age 25 37 28 19
Consanguinity Denied Denied Denied Denied
ANC (cells/mm3) 375–4051 84–20,942 297–4384 300–11,500
Lymphocytes (cells/mm3) 175–825* 171–780* 257–884* 300*–5,814
Platelets (×109/L) 245-573 17-257 91-448 45-499
Height (cm) 1.34 1.62 1.57 1.57
Dysmorphic features Triangular face, midface hypoplasia, depressed nasal bridge, thick lips, and prognathism Round face, midface hypoplasia, depressed nasal bridge, thick lips, and prognathism Round face, midface hypoplasia, depressed nasal bridge, thick lips, and prognathism Round face, midface hypoplasia, thick lips prognathism
Congenital heart defects ASD ASD ASD ASD
Skeletal findings Scoliosis None None Pectus carinatum and scoliosis
Increased visibility of superficial veins pattern Upper and lower limbs Upper and lower limbs Chest, upper and lower limbs Absent
Endocrine findings Delayed bone age, central thyroid dysfunction Hypergonado-tropic hypogonadism None None
Bone marrow findings Not available Hypercellular marrow with myeloid hyperplasia Increased megakaryocytes Hypocellular marrow with megaloblastic changes in myeloid cell line
Other findings Delayed psychomotor development, juvenile rheumatoid arthritis (JRA), and Crohn's disease Crohn’s disease
46, XY
Chronic diarrhea Delayed psychomotor development
46, XY
Genotype Compound heterozygous
[c.210delC] + [c.199_218+1del]
Homozygous
[c.210delC]
Homozygous
[c.210delC]
Homozygous
[c.210delC]

*Values in the range of lymphocytopenia; Values in the range of thrombocytopenia; ASD: atrial septal defect.

Figure 1. Absolute Neutrophilic Count (ANC) in G6PC3 deficient patients. Long dashes indicate the threshold of 1500 cells/uL, below which ANC corresponds to neutropenia; short dashes indicate the threshold of 500 cells/uL, corresponding to severe neutropenia. Spikes are coincident with remission episodes. 

Non-hematological findings

The most frequent non-hematological findings in the patients were cardiovascular disorders in 8/11 cases (77.7%), atrial septal defects (ASD) in four patients, and a persistent cardiac murmur in the other 4. Furthermore, seven patients (63.6%) showed peripheral vascular system-associated symptoms, of which 6 had IVSV, and one showed peripheral venous insufficiency. In addition, four patients had anomalies of the urogenital tract (36.4%). A similar number of cases (36.4%) presented inflammatory bowel disease, Crohn’s disease in 2, and ulcerative colitis in one. Figure 2 shows the combined non-hematological manifestations of each of the 11 patients.

Figure 2. Non-hematological manifestations observed in patients with syndromic neutropenia. Height below the third percentile. 

Molecular findings

Sanger sequencing of the G6PC3 gene confirmed the clinical diagnosis of SCN4 in 4 of the 11 patients analyzed (Fig. 3). Patient one was a compound heterozygous for the c.210delC variant (rs769441127; NC_000017.11:g.44071174) and a 21bp deletion c.199_218+1del (rs1597905369; NC_000017.11:g.44071159-44071179del), predicted to impact the canonical splice site region between exon and intron 1. The remaining three cases were homozygous for the frame shift pathogenic c.210delC variant creating a premature stop codon, just 46 amino acids after the deletion site, giving place to a truncated protein of 115 amino acid residues (NP_612396.1: p.(Phe71Serfs*46)) that presumed to suffer the nonsense-mediated decay of the transcript9. Segregation analysis was available for patients 1, 2, and 4. The 21bp deletion of compound heterozygous (patient 1) was inherited from the mother and the 1bp deletion from the father. Both parents of patients 2 and 4 were carriers of the c.210delC variant. Cascade testing in the family of patient 2 confirmed homozygosity for the c.210delC variant in 2 cousins of the index patient. One is a 24-year-old female with recurrent aphtha, cardiac murmur, and inguinal hernia, and her brother, 16 y. o., with recurrent upper airway infections and bilateral cryptorchidism. Although in the family of patient three, parents and siblings rejected genotyping, the mother and the father should be both heterozygous for the c.210delC variant because patient three is homozygous for it.

Figure 3. Electropherograms of the G6PC3 reference sequence and the two identified pathogenic variants. Homozygous c.210delC in patients 2, 3, and 4, and compound heterozygous c.210delC c.199_218+1del variants in patient 1.
The first variant was inherited from the father and the second from the mother. 

Clinical description of positive cases

Table 1 compares the clinical findings observed in patients with a confirmed molecular diagnosis. Figure 1 shows the heterogeneous behavior of the magnitude of neutropenia over time in these four patients with the G6PC3 gene variants described.

Additional clinical findings observed in the cases with confirmed SCN4

Patient 1

Female, 25 y.o., born to an at-term uneventful pregnancy from healthy parents denying consanguinity. No other family member was affected (Fig. 4A). Soon after birth, a urinary infection required hospitalization for 4 days, solved without complications. The heart murmur, diagnosed at birth as an ASD and later developing to pulmonary arterial hypertension, was surgically repaired at age 14. She showed failure to thrive, delayed psychomotor development, recurrent infections during childhood with fever, cyclic neutropenia, and later, symptoms of juvenile rheumatoid arthritis. When first seen by us, she showed short stature of 134 cm (< 3rd centile), a head circumference of 49 cm (< 3rd centile), with an upper/lower segment ratio of 0.90 and arm span/height ratio of 0.94. She had a triangular face, retrognathia, mild frontal bossing, hypotelorism, low nasal bridge, short philtrum, downturned mouth corners, midface hypoplasia, IVSV of the upper and lower limbs, scoliosis, bilateral clinodactyly of the fifth finger, amenorrhea, central thyroid dysfunction, and growth hormone release defect. She was diagnosed with cyclic neutropenia and nonregenerative hypochromic microcytic anemia secondary to iron deficiency. A colon biopsy performed due to chronic diarrhea showed a focal zone of fibrosis, active inflammation in the terminal ileum, collapsed loops, and mesenteric adenomegaly diagnosed as Crohn’s disease.

Figure 4. Sequencing analysis results and genealogies of G6PC3 mutation positive. Family pedigrees illustrate the four cases in which a pathogenic variant (PV) in the G6PC3 gene was present. In addition, segregation analysis and cascade testing were done to determine the parental origin of variants and carriers in three families. Circles represent females; squares indicate males; arrows refer to probands; fully shaded figures represent SCN4 patients, symbols with a black dot inside represent PV carriers. *Family members who underwent genetic testing. Arabic numerals-individual identifiers; Roman numerals-generations. 

Patient 2

Male, 37 y.o., born to an at-term uneventful pregnancy of probably consanguineous healthy parents from a rural community (933 inhabitants); and a family history of a female second cousin who died at age 18 of severe neutropenia and Crohn’s disease (Fig. 4B). At birth, he presented neutropenia, later diagnosed as cyclic neutropenia. He has bilateral cryptorchidism, surgically repaired at age 8. He has short stature (162 cm, p < 5), dysmorphic face features (Table 1), an IVSV pattern of the upper and lower limbs, acute kidney pain, kidney stones, and hypercalciuria. He presented intense-generalized abdominal pain and episodic diarrhea in late adolescence. A colon biopsy at age 19 showed acute severe ulcerative colitis and rectum with chronic proctitis diagnosed as Crohn’s disease, treated surgically, and currently having an ileostomy. Incidentally, the patient was diagnosed with ASD at the same age, which was repaired. Sex hormone analysis confirmed hypogonadotropic hypogonadism, with a 46, XY normal karyotype. He is currently on and off granulocyte colony-stimulating factor treatment.

Patient 3

Female, 28 y.o., born to an at-term uneventful pregnancy of unknown consanguinity of healthy parents (Fig. 4C). She presented cytopenia, recurrent otitis media, and upper airway infections during childhood. At age 19, she started with episodic diarrhea and intense-generalized abdominal pain, mild neutropenia, thrombocytopenia, and lymphopenia. On genetic evaluation, she presented dysmorphic features (Table 1), with upper and lower limbs showing IVSV. Echocardiography at 28 years of age confirmed an ASD and mitral and aortic insufficiency.

Patient 4

Male 19 y.o., born to an at-term uneventful pregnancy and ignored consanguinity of healthy parents (Fig. 4D). He had recurrent upper-airway infections, hypotonia, and gastroesophageal reflux during the neonatal period. Recurrent upper airway infections and idiopathic neutropenia continue as current symptoms. At age 16, he underwent surgical repair of a previously diagnosed ASD. Imaging studies confirmed thoracic 2-4 vertebral fusion and dextroscoliosis. He also presented dysmorphic features and Pectus carinatum (Table 1).

Interestingly, even though patients denied or ignored kinship and consanguinity, the information on geographic family origin from the father of patient 1, both parents of patient 2, and the father of patient 3 confirmed that they are all from neighboring towns of the same state (patient 1, Ixtlahuaca; patient 2, Jiquipilco; patient 3, Toluca; patient 4, Chalco). Furthermore, the distances between locations show geographical proximity: Ixtlahuaca-Jiquipilco 14 km, Ixtlahuaca-Toluca 34 km, Jiquipilco-Toluca 31 km, and Chalco-Toluca-Ixtlahuaca-Jiquipilco, 77–97 km. This strongly suggests a founder effect for the G6PC3 gene c.210delC variant. Moreover, sharing an uncommon surname by two of the families further supports the possibility of a common ancestor, probably for all families.

DISCUSSION

We conducted a phenotypic, biochemical, and genetic analysis in 11 patients with severe cyclic congenital neutropenia. Sanger sequencing identified two previously rare reported G6PC3 gene PVs in 4 of the 11 patients with non-hematologic traits (36.4%). Patient 1 had a rare splice donor site variant (c.199_218+1del), which has only once been submitted to the ClinVar database (ID: 691994), in a patient with pulmonary arterial hypertension, leukopenia, and an ASD, probably having SCN4, although not specified in the report15. The c.210delC variant has been well characterized as pathogenic and has only been described in patients of Hispanic descent5,16. Interestingly, 31 heterozygous carriers for the c.210delC variant are reported in the gnomeAD database, all in Latino/Admixed Americans17; in addition, 395 alleles were identified in 92,041 individuals (184,082 alleles) of Native Mexican ancestry, with a prevalence of 0.00215 in the Mexico City Prospective Study (MCPS) database18.

Furthermore, in the same database, this variant has the highest frequency of all PV of the G6PC3 gene, with a prevalence of 0.00143 in 138,200 DNA-sequenced samples. Interestingly, the c.210delC variant was only found in individuals confirmed to be of Native Mexican ancestry but not in Mexicans with an admixture of African, Asian or European ancestry18. Although our patients denied inter-family relationships, the family residences of patients 1, 2, and 3 are within a 35 km distance, which makes it possible that these families share a common ancestor, also supported by the fact that two of the families share an uncommon surname. In another study of Mexican patients, Velez-Tirado et al. reported 5 patients carrying this variant; 3 of them were homozygotes, and although they denied consanguinity, the authors mentioned that they might come from geographically close communities16. Our findings and the above reports strongly support that the c.210delC variant is particular to the Mexican population and sheds light on a possible founder effect5,16-18.

We describe four patients with sequencing diagnoses of G6PC3 gene PV, 3 of which are homozygous for the c.210delC nonsense variant. Although the disease is known as SCN4, the blood analysis findings in these patients show that the hematological phenotype is much broader. Furthermore, our patients (Table 1) fulfilled the criteria for SCN and cyclic neutropenia, as all showed variable degrees of severe neutropenia associated with periods of remission and affected platelet and lymphocytes cell lines. Regarding non-hematological abnormalities, congenital heart defects were the most frequent, as others have noticed16,19. We found that in all positive cases presented with ASD, these defects usually occurred as soft murmurs or were asymptomatic for a long time, making them a common undiagnosed abnormality20. In our group of patients, IVSV was a relatively common finding. Although patient four did not show this anomaly, veins may probably become more prominent with age5, being this finding present in two-thirds of patients16.

Regarding patients without G6PC3 PV, despite the unspecific diagnosis of a heart murmur, none of these patients had an ASD, as observed in the four patients with a G6PC3 PV, which has been frequently associated with mutations in this gene16. Although 3/7 had IVSV, in our sample of cases, it seems not to be a defining phenotypic marker of the syndromic SCN4. In addition, except for one patient with ulcerative colitis, no other patients showed gastrointestinal symptomatology. The common aspect in both groups was the heterogeneous character of hematologic manifestations. It is of note that SCNs are a group of heterogeneous diseases with different inheritance and multigene etiology1. Therefore, the syndromic form is probably not always exclusively due to mutations in the G6PC3 gene.

G6PC3 deficiency due to pathogenic and probably PV of the G6PC3 gene is considered within the group of rare diseases. The 127 reported cases of SCN4 worldwide present 53 different G6PC3 PV. Of these, 22 are missense (41.5%), 22 nonsense or frame shift (41.5%), 6 splice site variants (11.3%), and 3 in-frame deletions (5.7%); gene location and detailed characteristics of each one is shown in figure 5 and table 2. Most described cases are in the pediatric age group, and in most, a diagnosis has been reached via WES, meaning that clinical diagnosis is rarely suspected; therefore, it is possible that SCN4 may be underdiagnosed. The 4 patients reported herein reached adulthood without a diagnosis, until now. An early confirmed diagnosis can diminish complications such as Crohn’s disease, believed to be caused by intrinsic defects in hematopoietic cells, with inadequate control of gut microbiota, secondary to reduced survival and function of neutrophils, leading to a dysregulated inflammatory response; this association is not specific to G6PC3 deficiency21. There are more than 240 risk genes for IBD, including Crohn’s disease; however, the pathogenic mechanism of contribution is not well understood. IBD is an immune-mediated disorder, and several identified genes participate in regulating and maintaining the local immune response to viruses and bacteria. The particular genetic background may predispose to altered immunoglobulin production, enhancement of specific cytokine expression, and subsequent tissue inflammation22. Crohn’s disease or another IBD may not be influenced directly by G6PC3 mutations but is aggravated by neutropenia. In addition, well-timed allogeneic hematopoietic stem cell transplantation has been proven beneficial in the remission of inflammatory bowel disease symptomatology23.

Table 2. Compilation of G6PC3 mutations reported in cases with SCN4 

Exon NM_138387.4 NP_612396.1 Short MC GRCh38 chr17 dbSNP ClinVar Interpr. MT CADD Ref.
1 c.[130C>T] p.[Pro44Ser] P44S MS 44071095 rs775224457 189781 P DC 28 1-5
1 c.[131C>T] p.[Pro44Leu] P44L MS 44071096 rs762019955 na na DC 29 6-8
1 c.[141C>G] p.[Tyr47Ter] Y47* N 44071106 rs118203970 1039 P DC 37 6,8,9
1 c.[144C>A] p.[Tyr48Ter] Y48* N 44071109 rs1194477276 632283 likely-P DC 34 10,11
1 c.[175T>C] p.[Trp59Arg] W59R MS 44071140 rs752966267 853860 US DC 32 8,12
1 c.[190_210]delACCGAGTGGCTCAACCTCATC p.[Thr64_Ile70del] T64_I70del IFD 44071155- 44071175 na na na DC na 2,3
1 c.[194A>C] p.[Glu65Ala] E65A MS 44071159 rs745318917 na na DC 31 7,13
1 c.[207delC] p.[Ile70fsTer46] I70fs* FS 44071172 na na na DC na 14
1 c.[207dup] p.[Ile70fsTer17] I70fs* FS 44071171- 44071172 rs1191239079 691992 P DC 33 6
1 c.[210delC] p.[Phe71fsTer46] F71fs FS 44071175 rs769441127 189782 P DC 35 6,15 This publication
1 c.[214delA] p.[Lys72fsTer45] K72fs* FS 44071179 rs1177939839 na na DC na 16
1 c.[218+1G>A] p.? p.? SDL 44071184 na 1430600 P DC 35 6,17
1 c.199_218+1delCTCAACCTCATCTTCAAGTGG p.? p.? SD 44071159-44071179 rs1597905369 691994 P DC na This publication
2 c.[249G>A] p.Trp83Ter W83* N 44074190 na na na DC 39 18
2 c.[257delA] p.[Glu86Glyfs*31] E86Gfs* FS 44074198 na na na DC na 19
2 c.[282delA] p.[Ala95fsTer22] A95fs* FS 44074223 na na na DC na 5
2 c.[295C>T] p.[Gln199Ter] Q99* N 44074236 na na na DC 38 20
3 c.[326-1G>C] p.? p.? SAL 44074679 na na na DC 33 7
3 c.[346A>G] p.[Met116Val] M116V MS 44074700 rs267606834 1042 P DC 25 21
3 c.[347T>C] p.[Met116Thr] M116T MS 44074701 na na na DC 26 1,5
3 c.[347T>A] p.[Met116Lys] M116K MS 44074701 na na na DC 28 22
3 c.[348G>A] p.[Met116Ile] M116I MS 44074702 rs1373865222 na na DC 30 6
3 c.[353C>G] p.[Thr118Arg] T118R MS 44074707 rs766706036 na na DC 25 14
3 c.[372delC] p.[Ile125*] I125* N 44074726 na na na DC na 23
3 c.[373_375delATA] p.[Ile125del] I125del IFD 44074727-44074729 na na na DC na 11
3 c.[394C>T] p.[Gln132Ter] Q132* N 44074748 na na na DC 36 7,24
3 c.[416G>T] p.[Ser139Ile] S139I MS 44074770 na na na DC 39 6,25
4 c.[417-1G>A] p.? p.? SAL 44074968 rs763408993 na na DC 34 26
4 c.[421delT] p.[Trp141fsTer2] W141fs* FS 44074973 na na na DC na 15
4 c.[461T>C] p.[Leu154Pro] L154P MS 44075013 na na na DC 28 27
4 c.[481C>T] p.[Arg161Ter] R161* N 44075033 rs1056739194 na na DC 35 15,18
4 c.[482G>A] p.[Arg161Gln] R161Q MS 44075034 rs1485073209 na na DC 27 6
4 c.[482G>C] p.[Arg161Pro] R161P MS 44075034 na 1679807 US DC 26 28
4 c.[535+1G>A] p.? p.? SS 44075088 na na na DC 34 7,24
5 c.[554T>C] p.[Leu185Pro] L185P MS 44075328 rs118203969 1038 P DC 24 15
5 c.[565C>T] p.[Arg189Ter] R189* N 44075339 rs745582203 653016 P DC 36 6,8,18
5 c.[566G>A] p.[Arg189Gln] R189Q MS 44075340 rs140294222 262367 US DC 18 22
5 c.[596A>G] p.[Tyr199Cys] Y199C MS 44075370 rs1597910284 na na DC 27 20
5 c.[623T>G] p.[Leu208Arg] L208R MS 44075397 na na na 26 3
5 c.[677+1G>A] p.? p.? SS 44075452 rs778208850 1066709 likely-P DC 34 10
6 c.[1000_1001delAT] p.[Met334fs] M334fs FS 44076002-44076003 na na na DC na 1
6 c.[680_684delinsT] p.[Ser227Leufs*3] S227Lfs* FS 44075682-44075685 na na na DC na 11
6 c.[757C>T] p.[Arg253Cys] R253C MS 44075759 rs765927570 960968 likely-P/US DC 31 29
6 c.[758G>A] p.[Arg253His] R253H MS 44075760 rs118203968 1037 P DC 31 10,18,20,22,30
6 c.[935dupT] p.[Asn313fs] N313fs+39aa FS 44075933-44075934 rs797044567 189784 P DC na 6,7,10,26,27
+38 AA FS
44075767 rs748931188 1342134 P DC 33 7,33-36
6 c.[766_768delGGG] p.[Gly256del] G256del IFD 44075768-44075770 na na na DC na 20
6 c.[778G>C] p.[Gly260Arg] G260R MS 44075780 rs200478425 30874 P/US DC 28 6,10,14,18,22,26,33,34
6 c.[779G>A] p.[Gly260Asp] G260D MS 44075781 na na na DC 27 6
6 c.[829C>T] p.[Gln277Ter] Q277* N 44075831 rs148559256 189783 P DC 33 6,10,35,36
6 c.[882_903dup] p.[His302GlyfsTer92] H302Gfs* FS 44075884-44075905 na na na DC na 5
6 c.[765_766delAG] p.[Ala257CysfsTer129] A257Cfs*+38aa FS 44075767 rs748931188 1342134 P DC 33 7,33-36
+39 aa FS 44075933-44075934 rs797044567 189784 P DC na 6,7,10,26,27
6 c.[960delG] p.[Trp320CysfsTer4] W320Cfs* FS 44075961 na na na DC na 32
6 c.[974T>G] p.[Leu325Arg] L325R MS 44075976 na na na DC 25 37

MC: molecular consequence; MT: mutation Tester prediction; MS: missense; N: nonsense; FS: frameshift; IFD-in-frame deletion; SDL: splicing donor lost; SD: splicing donor; SAL: splicing acceptor lost; SS: splicing site; P: pathogenic; na: not available; US: uncertain significance; DC: disease causing; CADD: Combined Annotation Dependent Depletion score. References mentioned in this table are placed in the Suplementary Data.

Figure 5. G6PC3 reported pathogenic variants (PV) in patients with SCN4. (A) the absolute frequency of unrelated patients (one per family) of known PV in confirmed SCN4 cases reported in the literature consulted in Scholar Google. (B) illustration of known G6PC3 PV presented on the protein with structural domains indicated. The red rectangle encloses a pathogenic variant found only in the Mexican population. All variant details and references can be found in Table II and Appendix S1, respectively. 

It is known that SCN is a heterogeneous disease with multigene involvement and diverse inheritance patterns, as well as variable phenotypic manifestations, being ELANE (neutrophil elastase gene) PV responsible in most cases with the disease. However, such a form of SCN occurs without specific non-hematological manifestations1. Moreover, only two Mexican patients were reported with PV in ELANE and were sporadic24. Meanwhile, five identified SCN patients were found to have genetic alterations on G6PC316. Therefore, the characterization of non-hematologic SCN-associated multisystemic external and internal abnormalities in the patients in this study shed light on defining the SCN4 syndromic form of the disease.

The findings in the four patients, mainly those present in the three patients homozygous for the c.210delC variant, do not allow to propose a definitive genotype-phenotype correlation, even though patients share the same congenital heart defect and other phenotypic features, such as IVSV, gastrointestinal, and characteristic facial appearance. Regarding the rest of the systems involved, findings were heterogeneous, which may represent, to some extent, a variable expression of this pathogenic variant, although other yet unknown modifying factors may affect the occurrence of non-hematological manifestations.

Finally, the present uniqueness of the c.210delC variant in Hispanics of Mexican descent, the regional proximity of the families’ residence, and the sharing of an uncommon surname between the members of two of the families, strongly support the possibility of ignored consanguinity, an ancient common ancestor, and a founder effect for this G6PC3 gene variant.

Our study showed that searching for non-hematological features in patients with severe neutropenia could identify cases with G6PC3 PV. Therefore, it is highly recommended that patients with primary neutropenia be examined mainly for congenital heart defects, peripheral vascular system anomalies, inflammatory bowel disease, urogenital defects, and facial appearance, to guide genetic testing for decision-making. Furthermore, our findings suggest this disorder may have a higher prevalence in Mexicans than has been described, most probably due to a founder effect of the c.210delC pathogenic variant, particular to the Mexican population.

SUPPLEMENTARY DATA

Supplementary data are available at Revista de Investigación Clínica online (10.24875/RIC.22000234). These data are provided by the corresponding author and published online for the benefit of the reader. The contents of supplementary data are the sole responsibility of the authors.

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Received: September 13, 2022; Accepted: October 26, 2022

* Corresponding author: Osvaldo M. Mutchinick E-mail: osvaldo@unam.mx

Contributed equally to this work as first authors.

Creative Commons License Instituto Nacional de Cardiología Ignacio Chávez. Published by Permanyer. This is an open access article under the CC BY-NC-ND license