Somatic STK11 mosaicism in a Turkish patient with Peutz-Jeghers syndrome.

Peutz-Jeghers syndrome (PJS) is an autosomal dominant disorder, caused by germline variants in the serine/threonine kinase 11 (STK11) gene. However, mosaic variants in STK11 gene have been rarely described. A 25-year-old woman diagnosed with PJS due to multiple hamartomatous polyps in the gastrointestinal tract was referred to our clinic. In the molecular diagnosis, the patient was evaluated using the STK11 gene sequence analysis and multiplex ligation-dependent probe amplification (MLPA) method, which suggested no pathogenic variant to account for the clinical picture. Given that the clinical findings of the patient were consistent with those of PJS, the raw data from next-generation sequencing (NGS) were re-examined for mosaicism which led to the detection of a novel mosaic c.920 + 1G > T variant in STK11 gene with a rate of 23% (1860x). Deep read-level NGS was performed on buccal mucosa and polyp samples to determine mosaicism levels in other tissues. Variant frequencies were 29% (710x) and 31% (1301x), respectively. Mosaicism should be considered in cases with clear clinical diagnostic criteria, such as PJS, where the pathogenic variant cannot be detected by sequence analysis and MLPA methods. Identification of mosaicism in these patients is very important as it can have an impact on patient follow-up and genetic counseling for relatives.

Secondary findings in genes related to cancer phenotypes in Turkish exome sequencing data from 2020 individuals.

Big data generated from exome sequencing (ES) and genome sequencing (GS) analyses can be used to detect actionable and high-penetrance variants that are not directly associated with the primary diagnosis of patients but can guide their clinical follow-up and treatment. Variants that are classified as pathogenic/likely pathogenic and are clinically significant but not directly associated with the primary diagnosis of patients are defined as secondary findings (SF). The aim of this study was to examine the frequency and variant spectrum of cancer-related SF in 2020 Turkish ES data and to discuss the importance of the presence of cancer-related SF in at-risk family members in terms of genetic counseling and follow-up. A total of 2020 patients from 2020 different families were evaluated by ES. SF were detected in 28 unrelated cases (1.38%), and variants in BRCA2 (11 patients) and MLH1 (4 patients) genes were observed most frequently. A total of 21 different variants were identified, with 4 of them (c.9919_9932del and c.3653del in the BRCA2 gene, c.2002A>G in the MSH2 gene, c.26_29del in the TMEM127 gene) being novel variations. In three different families, c.1189C>T (p.Gln397*) variation in BRCA2 gene was detected, suggesting that this may be a common variant in the Turkish population. This study represents the largest cohort conducted in the Turkish population, examining the frequency and variant spectrum of cancer-related SF. With the identification of frequent variations and the detection of novel variations, the findings of this study have contributed to the variant spectrum. Genetic testing conducted in family members is presented as real-life data, showcasing the implications in terms of counseling, monitoring, and treatment through case examples.

The first Turkish family with a novel biallelic missense variant of the ALKBH8 gene: A study on the clinical and variant spectrum of ALKBH8-related intellectual developmental disorders.

ABH8, the protein encoded by the ALKBH8 gene, modifies tRNAs by methylating their anticodon wobble uridine residues. The variations in the ALKBH8 gene are associated with the "intellectual developmental disorder, autosomal recessive type 71" (MIM: 618504) phenotype in the OMIM database. This phenotype is characterized by global developmental delay, facial dysmorphic features, and psychiatric problems. To date, 12 patients from five distinct families carrying variants of the ALKBH8 gene have been reported in the literature. In the present study, we report the first Turkish family harboring a novel homozygous missense variant, NM_138775.3:c.1874G > C (p.Arg625Pro), in the last exon of the ALKBH8 gene. Two affected siblings in this family showed signs of global developmental delay and intellectual disability. Based on the dysmorphological assessment of the cases, fifth finger clinodactyly and fetal fingertip pads were prominent, in addition to the dysmorphic findings similar to those reported in previous studies. Minor dysmorphic limb anomalies in relation to this phenotype have not yet been previously reported in the literature. Our computational studies revealed the potential deleterious effects of the Arg-to-Pro substitution on the structure and stability of the ABH8 methyltransferase domain. In the present report, the first Turkish family with an ultrarare disease associated with the ALKBH8 gene was reported, and a novel deleterious variant in the ALKBH8 gene and additional clinical features that were not reported with this condition have been reported.

Expanding the clinical and immunological phenotypes of PAX1-deficient SCID and CID patients.

Paired box 1 (PAX1) deficiency has been reported in a small number of patients diagnosed with otofaciocervical syndrome type 2 (OFCS2). We described six new patients who demonstrated variable clinical penetrance. Reduced transcriptional activity of pathogenic variants confirmed partial or complete PAX1 deficiency. Thymic aplasia and hypoplasia were associated with impaired T cell immunity. Corrective treatment was required in 4/6 patients. Hematopoietic stem cell transplantation resulted in poor immune reconstitution with absent naïve T cells, contrasting with the superior recovery of T cell immunity after thymus transplantation. Normal ex vivo differentiation of PAX1-deficient CD34+ cells into mature T cells demonstrated the absence of a hematopoietic cell-intrinsic defect. New overlapping features with DiGeorge syndrome included primary hypoparathyroidism (n = 5) and congenital heart defects (n = 2), in line with PAX1 expression during early embryogenesis. Our results highlight new features of PAX1 deficiency, which are relevant to improving early diagnosis and identifying patients requiring corrective treatment.

Novel, homozygous RAB3GAP1 c.2606 + 1G>A, p.Glu830ValfsTer9 variant and chromosome 3q29 duplication in a Turkish individual with Warburg micro syndrome.

Warburg micro syndrome (WARBM) is a rare, autosomal recessive, neurodevelopmental disorder characterized by microcephaly, cortical dysplasia, corpus callosum hypoplasia, congenital hypotonia leading to subsequent spastic quadriplegia, severe developmental delay and hypogenitalism. Ophthalmologic findings that may affect any ocular segment including characteristic, small, atonic pupils. WARBM is known to be caused by biallelic, pathogenic variants in at least five genes although additional genetic loci may exist. The RAB3GAP1 c.748 + 1G>A, p.Asp250CysfsTer24 founder variant has been described in families of Turkish ancestry. We report the clinical and molecular findings in three, unrelated, Turkish families with WARBM. A novel c.974-2A>G variant causing WARBM in three siblings of Turkish descent was found. Functional studies of the novel, c.2606 + 1G>A variant in patients' mRNA revealed skipping of exon 22 which results in a premature stop codon in exon 23. However, the clinical consequences of this variant are blended given that the individual also had a maternally inherited chromosome 3q29 microduplication.

De novo Pure Partial Trisomy 6p Associated with Facial Dysmorphism, Developmental Delay, Brain Anomalies, and Primary Congenital Hypothyroidism.

Introduction: Partial trisomy 6p is a rare chromosomal anomaly, characterized by low birth weight, developmental delay, craniofacial abnormalities, feeding difficulties, congenital heart defects, and renal abnormalities. Some of the partial trisomy 6p cases reported in the literature included partial monosomy of another chromosome. This is often due to the fact that one of the parents is a balanced translocation carrier, thereby making it difficult to determine the genotype-phenotype relationship. Pure partial trisomy 6p cases are even rarer and may occur as a result of a marker chromosome, tandem or inverted duplication, and interchromosomal insertion. Case Presentation: In this study, we evaluated the physical characteristics and genetic data of a 2-year-old girl with developmental delay and facial dysmorphic features. Dysmorphology assessment revealed the presence of a prominent forehead, short and narrow palpebral fissures, blepharoptosis, convex nasal ridge, hemangioma on the left eyelid, high-arched palate, retromicrognathia, and low-set ears. The patient‧s G-banded karyotype was 46,XX,der(2)t(2;6)(q37.3;p22.1). Upon SNP-array analysis, aimed to determine the origin of the extra chromosomal material detected in chromosome 2 of the patient, there was a de novo 27.5-Mb duplication at 6p, arr[GRCh37] 6p25.3p22.1(204,909_27,835,272)×3, interpreted to be pathogenic. Conclusion: We present this case report to clarify the clinical findings of a rare chromosomal anomaly, discuss the genes that may be related to the phenotype and contribute to the literature in terms of knowledge regarding genotype-phenotype correlation.

Multigene Panel Testing in Turkish Hereditary Cancer Syndrome Patients.

Objective: Hereditary cancer syndromes (HCSs) are a heterogenous group of disorders caused by germline pathogenic variations in various genes that function in cell growth and proliferation. This study aimed to describe the germline variations in patients with hereditary cancer using multigene panels. Methods: The molecular and clinical findings of 218 patients with HCS were evaluated. In addition, 25 HCS-related genes were sequenced using a multigene panel, and variations were classified according to the American College of Medical Genetics and Genomics (ACMG) criteria. In total, 218 HCS patients predominantly with breast, colorectal, ovarian, gastric, and endometrium cancers were included. Results: Pathogenic variations in 12 distinct genes were detected in 36 of 218 (16.5%) cases. In this study, the most affected gene was the ATM gene, in which pathogenic variations were detected in 8 of 218 cases, followed by CHEK2 (3.2%), MUTYH (3.2%), BRIP1 (1.8%), BARD1 (0.9%), TP53 (0.9%), PALB2 (0.4%), MLH1 (0.4%), MSH2 (0.4%), PMS2 (0.4%), RAD50 (0.4%), and RAD51C (0.4%). Conclusions: This study contributes to genotype-phenotype correlation in HCSs and expands the variation spectrum by introducing three novel pathogenic variations. The wide spectrum of the gene pathogenic variations detected and the presence of multiple gene defects in the same patient make the multigene panel testing a valuable tool in detecting the hereditary forms of cancer and providing effective genetic counseling and family specific screening strategies. Amaç: Herediter kanser sendromlari (HCS) hücre büyümesi ve proliferasyonunda görevli genlerde saptanan germline mutasyonlardan kaynaklanan heterojen bir grup hastaliktir. Bu çalismada kalitimsal kanser sendrom ön tanisiyla degerlendirilen olgularda çoklu gen paneli ile germ hatti varyasyonlarinin degerlendirilmesi planlanmistir. Yöntemler: Kalitimsal kanser sendromu düsünülen 218 olgudan periferik kandan DNA izolasyonu sonrasi HCS ile iliskili 25 gen multigen panel kullanilarak dizilendi ve varyasyonlar American College of Medical Genetics and Genomics (ACMG) kriterlerine göre degerlendirildi. Bulgular: Meme, kolorektal, over, gastrik ve endometriyum kanseri basta olmak üzere toplam 218 herediter kanser sendromlu olgu degerlendirildi. Tüm çalisma grubu incelendiginde en sik ATM gen varyasyonlari (8/218, %3,6) tespit edildi ve bunu siklik sirasina göre CHEK2 (%3,2), MUTYH (%3,2), BRIP1 (%1,8), BARD1 (%0,9), TP53 (%0,9), PALB2 (%0,4), MLH1 (%0,4), MSH2 (%0,4), PMS2 (%0,4), RAD50 (%0,4), RAD51C (%0,4) varyasyonlari takip etmekteydi. Sonuçlar: Bu çalismada farkli kanser türlerinde kalitimsal kansere yol açan genler analiz edilmis ve fenotiple iliskisi degerlendirilmistir. Ayrica bu çalismada ilk kez saptanan üç yeni varyasyon ile literatüre katki saglanmaktadir. Patojenik varyasyon tespit edilen genlerin genis dagilimi ve ayni hastada birden fazla genetik varyasyonun varligi düsünüldügünde, uygun genetik danisma ve aileye özgü tarama planlamasi yapmak için çoklu gen taramasi kalitimsal kanser hastalarinin degerlendirilmesinde hizli ve etkin bir yöntem olarak görünmektedir.

Two New Cases of Primary Microcephaly with Neuronal Migration Defect Caused by Truncating Mutations in the ASPM Gene.

Autosomal recessive primary microcephaly (MCPH) is a uncommon disorder due to congenital deficiency in the development of the cerebral cortex, characterized by a head circumference below 2 SD. MCPH is a group of diseases with genetic heterogeneity and has been reported by the Online Mendelian Inheritance In Man® (OMIM) database and associated with 25 different genes. It is known that MCPH cases are most frequently associated with abnormal spindle-like, microcephaly-associated (ASPM) gene mutations. The ASPM protein consists of an N-terminal 81 IQ (isoleucine-glutamine) domain, a calponin-homology domain, and a C-terminal domain. It interacts with calmodulin and calmodulin-related proteins via the IQ domain and acts as a part in mitotic spindle function. The basic characteristics of cases with ASPM gene mutations are microcephaly (below -3 SD) present before 1 year of age, intellectual disability, and the absence of other congenital anomalies. Macroscopic organization of the brain is preserved in cases with ASPM mutation, and a decrease in brain volume, particularly gray matter volume loss and a simplified gyral pattern are observed. Cortical migration defects are a very rare finding in patients with ASPM mutations. In the present study, we aimed to discuss the clinical and genetic findings in 2 cases with cortical dysplasia in which truncated variants in the ASPM gene were detected, particularly in terms of genotype-phenotype correlation in comparison with the literature.

Autosomal Recessive Primary Microcephaly (MCPH) and Novel Pathogenic Variants in ASPM and WDR62 Genes.

Introduction: Autosomal recessive primary microcephaly (MCPH) is a disorder characterized by congenital microcephaly and intellectual disability without extra-central nervous system malformation. MCPH is a disease with heterogeneity in genotype and phenotype. For this reason, it is important to determine the genetic causes and genotype-phenotype relationship in MCPH, which causes lifelong impairment. In this study, we aimed to evaluate the clinical, genetic, and brain imaging findings of cases diagnosed with MCPH. Methods: Electroencephalogram and brain magnetic resonance imaging were performed for all cases. We evaluated genetic results of the 39 families including cases with suspected MCPH diagnosis. Results: Genetic diagnosis related to MCPH was provided in 11/39 (28.2%) of these families including 13/41 cases (31.7%). Variants of the WDR62 gene were the most common (61.5%) cause, and variants of the ASPM gene were the second most common cause (38.5%). We have found 6 novel variants and 4 previously reported variants in ASPM and WDR62 genes. Main brain imaging findings in our cases were lissencephaly, polymicrogyria, schizencephaly, pachygyria, and cortical dysplasia. Genetic counseling in 2 families whose genetic diagnosis was determined prevented them from having another child with MCPH. Discussion/Conclusion: Detection and reporting of novel variants is an important step in eliminating this disorder by providing families with appropriate genetic counseling.

Differential Diagnosis of Acromegaly: Pachydermoperiostosis Two New Cases from Turkey

Pachydermoperiostosis (PDP), also known as primary hypertrophic osteoarthropathy, is a rare genetic disorder characterized by pachyderma and periostosis. Acromegaly is a condition caused by excessive secretion of growth hormone (GH) leading to elevated insulin-like growth factor 1 levels, and is characterised by somatic overgrowth and physical disfigurement, notably affecting hands and feet. We present two cases referred with an initial diagnosis of acromegaly that were ultimately diagnosed as PDP. Case 1: A 17 year-old boy presented with enlargement in both feet and hands, finger clubbing, swelling in knee joints, knee pain, coarsening of facial skin lines and forehead skin, and excessive sweating which increased gradually over five years. There were prominent skin folds on the forehead, face, and eyelids. Also, there was an enlargement in both hands and clubbing of the fingers. There was marked swelling in the knee joints and ankles. Genetic analysis revealed a novel homozygous variant NM_005630: c.31C>T (p.Q11*) in the SLCO2A1 gene. Case 2: A 16 year-old boy presented with coarsening of forehead skin and scalp, excessive sweating, and pain in the elbow and knee over three years. Skin folds were prominent on the forehead and scalp. Genetic analysis revealed a homozygous variant NM_005630.2:c.86delG (p.G29Afs*48) in the SLCO2A1 gene. Such clinical presentation contemporaneous with normal GH level and prominent radiological abnormalities prompted the diagnosis of PDP. In conclusion, PDP is a very rare osteoarthrodermopathic disorder with clinical and radiographic presentation that may mimic acromegaly. In the evaluation of patients with acromegaloid appearance, PDP should be considered as a differential diagnosis.

Biallelic Mutations in DNAJB11 are Associated with Prenatal Polycystic Kidney Disease in a Turkish Family.

Polycystic kidney disease (PKD) is a life-threatening condition resulting in end-stage renal disease. Two major forms of PKD are defined according to the inheritance pattern. Autosomal dominant PKD (ADPKD) is characterized by renal cysts, where nearly half of the patients suffers from renal failure in the 7th decade of life. Autosomal recessive PKD (ARPKD) is a rarer and more severe form presenting in childhood. Whole-exome sequencing (WES) analyses was performed to investigate molecular causes of the disease in the fetus. In this study, we present 2 fetuses prenatally diagnosed with PKD in a consanguineous family. WES analysis of the second fetus revealed a homozygous variant (c.740+1G>A) in DNAJB11 which is related to ADPKD. This study reveals that DNAJB11 biallelic mutations may cause an antenatal severe form of ARPKD and contributes to understanding the DNAJB11-related ADPKD phenotype. The possibility of ARPKD due to biallelic mutations in ADPKD genes should be considered in genetic counseling.

Meckel-Gruber Syndrome: Clinical and Molecular Genetic Profiles in Two Fetuses and Review of the Current Literature.

Background: Meckel-Gruber syndrome (MKS; OMIM No. 249000) is a rare, in utero lethal disease characterized by occipital encephalocele, polycystic kidneys, and polydactyly. Methodology and Results: In this study, two fetuses diagnosed as having MKS in the prenatal period were evaluated on the basis of ultrasonographic findings, postmortem autopsy findings, and molecular genetic analyses. Using exome sequencing analyses a novel homozygous frameshift variant (NM_015631: c.530delA, p.Lys177Argfs*47) was detected at exon 4 of TCTN3 gene in case 1, and a novel homozygous synonymous variant (NM_025114: c.180G>A, p Lys60Lys) was detected at exon 3 of CEP290 gene in case 2. Case 1 is the first reported case in the literature, which showed the typical MKS clinical feature with a novel frameshift variation in the TCTN3 gene. The variant in case 2 is the first reported synonymous variant of CEP290 gene in the literature, which has been shown to affect splicing in a functional study at the RNA level. Conclusion: TCTN3 gene variants that were rarely associated with the typical MKS phenotype and all cases with these variations have been discussed in the context of genotype-phenotype. The detection of the first synonymous variant of CEP290 gene and the demonstration of its effect on splicing by a functional study are likely to contribute to the molecular etiology of MKS.

Secondary findings in 622 Turkish clinical exome sequencing data.

CES (Clinical Exome Sequencing) is a method that we use to diagnose rare diseases with nonspesific clinical features. Besides primary indication for testing genetic information may be detected about diseases which have not yet emerged. ACMG guidelines recommend to report pathogenic variations in medically actionable 59 genes. In this study we evaluated CES data of 622 cases which were tested for various indications. According to ACMG recommendations 59 genes were screened for reportable variations. The detected variations were reviewed using distinct databases and ACMG variation classification guidelines. Among 622 cases 13 (2.1%) had reportable variations including oncogenetic, cardiogenetic disorders, and malignant hyperthermia susceptibility-related genes. In 15 cases (2.4%) heterozygous pathogenic and likely pathogenic variations were detected in genes showing autosomal recessive inheritance. Ten novel variations causing truncated protein or splicing defect were reported. We detected 11 variations having conflicting interpretations in databases and 30 novel variations, predicted as likely pathogenic via insilico analysis tools which further evaluations are needed. As to our knowledge this is the first study investigating secondary findings in Turkish population. To extract the information that may lead to prevent severe morbidities and mortalities from big data is a valuable and lifesaving effort. Results of this study will contrbute to existing knowledge about secondary findings in exome sequencing and will be a pioneer for studies in Turkish population.

The Spectrum of Low-Density Lipoprotein Receptor Mutations in a Large Turkish Cohort of Patients with Familial Hypercholesterolemia.

Background: Monogenic hypercholesterolemia with Mendelian inheritance is a heterogeneous group of diseases that are characterized by elevated plasma low-density lipoprotein cholesterol (LDL-C) levels, and the most common form of this disorder is autosomal-dominant familial hypercholesterolemia (FH). Methods: A total of 104 index cases with the clinical diagnosis of FH were included in this study. Low-density lipoprotein receptor (LDLR) was sequenced using the Sanger sequencing method. Results: Pathogenic/likely pathogenic variants were detected in LDLR in 55 of the 104 cases (mutation detection rate = 52.8%). Thirty different variants were detected in LDLR, three of which were novel. The total cholesterol and LDL-C values of the patients in the group of premature termination codon (PTC) mutation carriers were significantly higher than those of the patients in the group of non-PTC mutation carriers. A total of 87 patients (17 pediatric and 70 adult cases) were diagnosed with cascade genetic screening. Statin treatment was recommended to all 87 patients and was accepted and initiated in 70 of these patients. Conclusions: This study is the largest patient cohort that evaluated FH cases in the Turkish population. Herein, we revealed the LDLR mutation spectrum for a Turkish population and compared the cases in the context of genotype-phenotype correlation. Genetic screening of individuals with suspected FH not only helps to establish their diagnosis, but also facilitates early diagnosis and treatment initiation in other family members through cascade screening.

Novel clinical features and pleiotropic effect in three unrelated patients with LMNA variant.

LMNA gene encodes A-type lamins and the encoded proteins join the structure of the nuclear lamina and affect the processes of nuclear homeostasis, DNA replication, repair, transcription, and apoptosis. LMNA variants cause a heterogeneous group of diseases known as laminopathies. Phenotypes associated with LMNA variants mainly affect the heart, skeleton, skin, bones, and nervous system. The affected tissues may vary depending on the site of the variant on the gene and the variation type. Complex phenotypes may also occur in some cases, in which findings of premature aging, cardiomyopathy, mandibuloacral dysplasia, lipodystrophy, renal involvement, metabolic involvement, and myopathy coexist. The pleiotropic effect of LMNA variants can result in heterogeneous phenotypes. In this study, we aimed to describe atypical phenotypic characteristics in a patient with familial partial lipodystrophy type 2 associated with LMNA variant, another with mandibuloacral dysplasia, and a third patient with a complex phenotype as well as discuss them in the context of their relationship with the genotype.

A large Turkish pedigree with multiple endocrine neoplasia type 1 syndrome carrying a rare mutation: c.1680_1683 del TGAG.

BACKGROUND AND AIMS: Multiple endocrine neoplasia type 1 (MEN1) is an autosomal dominant syndrome characterized by tumors arising from endocrine glands with no specific genotype-phenotype correlation. Herein, we report the largest Turkish kindred with MEN1 inherited a scarce MEN1 mutation gene. MATERIALS AND METHODS: Sixty-four year-old man, referred to our gastroenterology outpatient clinic for evaluation of pancreatic mass lesion, was diagnosed with MEN1-syndrome after endoscopic ultrasound guided sampling of the mass revealing pancreatic neuroendocrine tumor (pNET), and accompanying primary hyperparathyroidism (PHPT) and pituitary tumor. Genetic analysis by whole gene Sanger sequencing of MEN1 gene identified a frame-shift mutation in exon 10 (c.1680_1683delTGAG). All the relatives of the index case were proposed for clinical and genetic evaluation for MEN1-syndrome. RESULTS: Of the 25 relatives of the index case, 17 were diagnosed MEN1-syndrome. Eighteen members among all relatives consented to genetic analysis and 11 had the same mutation as the index case. All the mutation positive members had MEN1, while none of mutation negative subjects had any sign of MEN1-syndrome. The frequencies of PHPT, pNET and pituitary tumors in this kindred were 94.1% (16/17), 29.4% (5/17) and 29.4% (5/17) respectively. CONCLUSION: We report rare MEN1 gene mutation which was descibed in a single sporadic patient before. It inherited in at least three generations of a large family, which has proven strong dominant effect on MEN1 phenotype. Further researches may be conducted to clarify potential candidacy of this mutation, as a hotspot for MEN1 patients, especially in Turkish population.

Low DHEAS Concentration in a Girl Presenting with Short Stature and Premature Pubarche: A Novel PAPSS2 Gene Mutation.

OBJECTIVE: Dehydroepiandrosterone (DHEA) sulfotransferase (SULT2A1) converts DHEA to DHEA sulfate (DHEAS) which prevents bioactive androgen excess. This enzymatic reaction requires PAPS (3'-phospho-adenosine-5'-phosphosulfate) biosynthesis mediated by PAPS synthase 2 (PAPSS2). Here, we report a patient presenting with short stature and premature pubarche due to a novel homozygous mutation in the PAPPS2 gene. CASE REPORT: A 7.5-year-old girl was referred for short stature. She was born at term with a birth weight of 2,850 g and her parents were first cousins. At presentation, her height was 113.0 cm (-2.1 SDS) and weight was 28.3 kg (+0.9 SDS), her arm span was 115.0 cm, and upper to lower segment ratio was 1.2. Her pubic hair and breast development were at Tanner stage III and I, respectively. Radiographs revealed mild lumbar scoliosis and platyspondyly and irregular vertebral endplates in the thoracolumbar region. Her serum DHEAS was low (39 ng/mL). The plasma DHEAS/DHEA ratio was significantly decreased on 2 separate measurements (4.4 and 19.8; normal range 31-345). PAPSS2 gene analysis identified a homozygous p.L440Wfs*12 (c.1318_1330 delCTACTACACCCTC) variant. This is the first report of a large deletion leading to a frameshift effect in the PAPSS2 gene and a truncated PAPSS2 protein. CONCLUSION: We describe the third case with PAPSS2 deficiency presenting with premature pubarche, and the first large deletion in the PAPSS2 gene. Although PAPSS2 deficiency is a rare cause of premature pubarche and adrenal androgen excess, it should be considered, especially in cases with disproportionate short stature and clinical hyperandrogenism associated with low plasma DHEAS concentration.