A PIGH mutation leading to GPI deficiency is associated with developmental delay and autism

We identified an individual with a homozygous missense variant (p.Ser103Pro) in a conserved residue of the glycosylphosphatidylinositol (GPI) biosynthesis gene PIGH. This gene encodes an essential component of the phosphatidylinositol N‐acetylglucosaminyltransferase complex, in the first step of the biosynthesis of GPI, a glycolipid anchor added to more than one hundred human proteins, several being critical for embryogenesis and neurological functions. The affected individual had hypotonia, moderate developmental delay, and autism. Unlike other reported individuals with GPI deficiency, the proband did not have epilepsy; however, he did have two episodes of febrile seizures. He had normal alkaline phosphatase and no brachytelephalangy. Upon analysis of the surface expression of GPI‐anchored proteins on granulocytes, he was demonstrated to have GPI deficiency. This suggests that PIGH mutations may cause a syndrome with developmental delay and autism, but without an epileptic encephalopathy, and should increase the awareness of the potentially deleterious nature of biallelic variants in this gene.     

Exome reports A de novo GNB2 variant associated with global developmental delay,intellectual disability,and dysmorphic features

Heterotrimeric G proteins are composed of α, β, and γ subunits and are involved in integrating signals between receptors and effector proteins. The 5 human Gβ proteins (encoded by GNB1, GNB2, GNB3, GNB4, and GNB5) are highly similar. Variants in GNB1 were identified as a genetic cause of developmental delay. De novo variant in GNB2 has recently been reported as a cause of sinus node dysfunction and atrioventricular block but not as a cause of developmental delay. Trio-based whole-exome sequencing was performed on an individual with global developmental delay, muscle hypotonia, multiple congenital joint contractures and dysmorphism such as brachycephalus, thick eyebrows, thin upper lip, micrognathia, prominent chin, and bilateral tapered fingers. We identified a de novo GNB2 variant c.229G>A, p.(Gly77Arg). Notably, pathogenic substitutions of the homologous Gly77 residue including an identical variant (p.Gly77Arg, p.Gly77Val, p.Gly77Ser, p.Gly77Ala) of GNB1, a paralog of GNB2, was reported in individuals with global developmental delay and hypotonia. Clinical features of our case overlap with those of GNB1 variants. Our study suggests that a GNB2 variant may be associated with syndromic global developmental delay.     

Aminoacylation-defective bi-allelic mutations in human EPRS1 associated with psychomotor developmental delay,epilepsy, and deafness

Aminoacyl-tRNA synthetases are enzymes that ensure accurate protein synthesis. Variants of the dual-functional cytoplasmic human glutamyl-prolyl-tRNA synthetase, EPRS1, have been associated with leukodystrophy, diabetes and bone disease. Here, we report compound heterozygous variants in EPRS1 in a 4-year-old female patient presenting with psychomotor developmental delay, seizures and deafness. Functional studies of these two missense mutations support major defects in enzymatic function in vitro and contributed to confirmation of the diagnosis.     

DNAH2 is a novel candidate gene associated with multiple morphological abnormalities of the sperm flagella

Multiple morphological abnormalities of flagella (MMAF) is one kind of severe teratozoospermia. Gene mutations reported in previous works only revealed the pathogenesis of approximately half of the MMAF cases, and more genetic defects in MMAF need to be explored. In the present study, we performed a genetic analysis on Han Chinese men with MMAF using whole-exome sequencing. After filtering out the cases with known gene mutations, we identified five novel mutation sites in the DNAH2 gene in three cases from three families. These mutations were validated through Sanger sequencing and absent in all control individuals. In silico analysis revealed that these DNAH2 variations are deleterious. The spermatozoa with DNAH2 mutations showed severely disarranged axonemal structures with mitochondrial sheath defection. The DNAH2 protein level was significantly decreased and inner dynein arms were absent in the spermatozoa of patients. ICSI treatment was performed for two MMAF patients with DNAH2 mutations and the associated couples successfully achieved pregnancy, indicating good nuclear quality of the sperm from the DNAH2 mutant patients. Together, these data suggest that the DNAH2 mutation can cause severe sperm flagella defects that damage sperm motility. These results provide a novel genetic pathogeny for the human MMAF phenotype.     

Sorting nexin 27 (SNX27) variants associated with seizures,developmental delay,behavioral disturbance,and subcortical brain abnormalities

Sorting nexin 27 (SNX27) influences the composition of the cellular membrane via regulation of selective endosomal recycling. Molecular analysis indicates that SNX27 regulates numerous cellular processes through promiscuous interactions with its receptor cargos. SNX27 deficient (Snx27 ^−/−) mice exhibit reduced embryonic survival, marked postnatal growth restriction and lethality. Haploinsufficient mice (Snx27 ^+/−) show a less severe phenotype, with deficits in learning, memory, synaptic transmission and neuronal plasticity. One family previously reported with a homozygous SNX27 frameshift variant (c.515_516del;p.His172Argfs*6), exhibited infantile intractable myoclonic epilepsy, axial hypotonia, startle-like movements, cardiac septal defects, global developmental delay, failure to thrive, recurrent chest infections, persistent hypoxemia and early death secondary to respiratory failure. Here, we report two additional patients with compound heterozygous SNX27 variants, that are predicted to be damaging: (a) c.510C>G;p.Tyr170* and c.1295G>A;p.Cys432Tyr, and (b) c.782dupT;p.Leu262Profs*6 and c.989G>A;p.Arg330His. They exhibit global developmental delay, behavioral disturbance, epilepsy, some dysmorphic features and subcortical white matter abnormalities. In addition, possible connective tissue involvement was noted. Epilepsy, developmental delays and subcortical white matter abnormalities appear to be core features of SNX27-related disorders. We correlate the observed phenotype with available in vitro, in vivo and proteomic data and suggest additional possible molecular mediators of SNX27-related pathology.     

一例Sifrim-Hitz-Weiss综合征患儿的临床与CHD4基因变异分析

目的探讨一例Sifrim-Hitz-Weiss综合征(Sifrim-Hitz-Weiss syndrome,SIHIWES)患儿的基因型与表型的对应关系。方法收集先证者及其父母的外周血样,提取基因组DNA,采用全外显子测序对先证者进行检测,并应用Sanger测序对先证者及父母进行验证。结果先证者为一例2岁女性患儿,表现为全面发育迟缓、智力障碍、特殊面容等。其产前表现为NT增厚,颅面部异常和胎动减少等。全外显子测序发现患儿CHD4基因发生了致病性变异NM_001273:c.2989C>G(p.Leu997Val)(GRCh37/hg19)。与以往报道的SIHIWES的临床表型相比,该患儿产前临床特征未有描述,而产后某些新的表型包括眼底检查结果和某些特殊面容如左右耳不对称、眼睑下垂、长人中和嘴角下斜等也呈现出来。结论本文研究结果扩展了CHD4基因变异谱,并丰富了SIHIWES的临床表型谱。     

TSGA10 is a novel candidate gene associated with acephalic spermatozoa

Acephalic spermatozoa is a rare teratozoospermia associated with male infertility. However, the pathogenesis of this disorder remains unclear. Here, we report a 27 years old infertile male from a consanguineous family, who presented with 99% headless sperm in his ejaculate. Electron microscopic and immunofluorescence analysis suggested breakage at the midpiece of the patient's sperm cells. Subsequent whole‐exome sequencing analysis identified a homozygous deletion within TSGA10 (c.211delG; p.A71Hfs*12), which resulted in the production of truncated TSGA10 protein. TSGA10 is a testis‐specific protein that localized to the midpiece in the spermatozoa of a normal control; however, immunostaining failed to detect TSGA10 protein in the patient's sperm. Western blot analysis also showed complete absence of TSGA10 protein in the patient. One cycle of in vitro fertilization‐assisted reproduction was conducted, but pregnancy was not achieved after embryo transfer, possibly due to poor embryo quality. Therefore, we speculate that the presence of rare sequence variants within TSGA10 may be associated with acephalic spermatozoa in humans.     

A homozygous variant disrupting the PIGH start‐codon is associated with developmental delay,epilepsy, and microcephaly

Defective glycosylphosphatidylinositol (GPI)‐anchor biogenesis can cause a spectrum of predominantly neurological problems. For eight genes critical to this biological process, disease associations are not yet reported. Scanning exomes from 7,833 parent–child trios and 1,792 singletons from the DDD study for biallelic variants in this gene‐set uncovered a rare PIGH variant in a boy with epilepsy, microcephaly, and behavioral difficulties. Although only 2/2 reads harbored this c.1A > T transversion, the presence of ～25 Mb autozygosity at this locus implied homozygosity, which was confirmed using Sanger sequencing. A similarly‐affected sister was also homozygous. FACS analysis of PIGH‐deficient CHO cells indicated that cDNAs with c.1A > T could not efficiently restore expression of GPI‐APs. Truncation of PIGH protein was consistent with the utilization of an in‐frame start‐site at codon 63. In summary, we describe siblings harboring a homozygous c.1A > T variant resulting in defective GPI‐anchor biogenesis and highlight the importance of exploring low‐coverage variants within autozygous regions.     

PPP1R21 homozygous null variants associated with developmental delay,muscle weakness,distinctive facial features,and brain abnormalities

We present 3 children with homozygous null variants in the PPP1R21 gene. A 3‐year‐old girl had profound developmental delay, hypotonia and weakness, poor feeding, recurrent chest infections and respiratory failure, rotatory nystagmus, absent reflexes, and a homozygous nonsense variant c.2089C>T (p.Arg697*). A 2‐year‐old boy had profound developmental delay, weakness and hypotonia, recurrent chest infections and respiratory distress, undescended testes, rotatory nystagmus, hyporeflexia, and a homozygous nonsense variant c.427C>T (p.Arg143*). An 11‐year‐old girl with profound developmental delay, weakness and hypotonia, stereotypic movements, growth failure, hyporeflexia, and a homozygous frameshift variant c.87_88delAG (p.Gly30Cysfs*4). In addition, these children shared common facial features (thick eyebrows, hypertelorism, broad nasal bridge, short nose with upturned nasal tip and broad low‐hanging columella, thick lips, low‐set ears, and coarse facies with excessive facial hair), and brain abnormalities (cerebellar vermis hypoplasia, ventricular dilatation, and reduced white matter volume). Although PPP1R21 has not yet been linked to human disease, the consistency in the phenotype of individuals from unrelated families, the nature of the variants which result in truncated proteins, and the expected vital role for PPP1R21 in cellular function, all support that PPP1R21 is a novel disease‐associated gene responsible for the phenotype observed in these individuals.     

单纯17q25.3拷贝数重复导致全面性发育迟缓和多发性先天异常一例

目的探讨单纯17q25.3拷贝数重复的临床特征、遗传方式及基因型与表型的关系。方法应用全外显子测序、染色体微阵列、染色体核型分析、荧光原位杂交技术联合对先证者及其家系成员进行分析。结果先证者为一例4岁的多发性先天异常男性患儿,表现为全面性发育迟缓、矮小、智力障碍、脑发育不良、小头、特殊面容、肌张力低下、注意力缺陷多动障碍、共济失调、骨骼和心血管异常等。全外显子测序和染色体微阵列分析鉴定其在染色体17q25.3→qter发生5.7 Mb拷贝数重复,可能为患儿致病的原因。荧光原位杂交证实先证者该拷贝数重复是遗传自携带该片段平衡易位的母亲,其外祖母和舅舅也为该片段平衡易位携带者,而小姨未见异常。结论本研究结果丰富了单纯17q25.3拷贝数重复的临床表型谱,为遗传咨询提供了依据,并初步提示了P4HB、ACTG1、BAIAP2及TBCD基因为17q25.3拷贝数重复候选基因。     

SHORT syndrome with microcephaly and developmental delay

We report a boy with typical clinical features of SHORT syndrome alongside a significant microcephaly and severe developmental delay associated with a de novo single nucleotide missense DNA variant resulting in a single amino acid change in codon 486 of the PIK3R1 gene (PIK3R1 c.1456G>A (p.Ala486Thr)). Our report strikingly coincides with another recently published case from Brazil, describing a 23-year-old woman with the same de novo PIK3R1 DNA variant, who also exhibits SHORT syndrome with severe secondary microcephaly and intellectual disability. On review of the literature, we have identified further cases of PIK3R1-related SHORT Syndrome with a similar phenotype. We note all these cases (including ours) have variants located in the -inter SH2 domain (iSH2); we speculate that pathogenic iSH2 located PIK3R1 variants are associated with a different and otherwise unreported clinical picture of SHORT syndrome that presents with microcephaly and/or significant developmental delay/intellectual disability. The pathogenic mechanism of why these variants apparently lead to a different clinical picture of SHORT syndrome remains unknown.     

ERI1: A case report of an autosomal recessive syndrome associated with developmental delay and distal limb abnormalities

ERI1 is an evolutionary conserved 3′–5′ exonuclease with an important function in multiple RNA processing pathways. Although the molecular mechanisms in which ERI1 is involved have been studied extensively in model organisms, the pathology associated with ERI1 variants in humans has remained elusive because no case has been reported so far. Here, we present a case of a female patient with a homozygous nonsense variant in ERI1 gene. The patient exhibits mild intellectual disability, eyelid ptosis, and anomalies in her hands and feet (brachydactyly, clinodactyly, dysplastic/short nail of halluces, brachytelephalangy, short metacarpals, and toe syndactyly). This case report is the first of its kind and is invaluable for understanding ERI1 pathology in humans.     

A novel homozygous splice-site variant of NCAPD2 gene identified in two siblings with primary microcephaly: The second case report

Here we describe the second case of primary microcephaly caused by a novel homozygous splice-site variant at the NCAPD2 gene. The proband was born with microcephaly, and developed intellectual disability. Whole exome sequencing identified a canonical splice-site variant, c.3477+2T>C, at the NCAPD2 gene. Sanger sequencing showed that the proband and her sibling, a symptomatic fetus, carried a homozygous c.3477+2T>C variant, while the unaffected parents were heterozygous and her younger brother had wild-type alleles. To date, only one case of primary microcephaly with a homozygous splice-site pathogenic variant at the NCAPD2 gene has been reported. Our study of two siblings provides additional evidence that NCAPD2 is a causative gene of primary microcephaly. This finding adds new knowledge in the etiology of microcephaly and contributes to more accurate counseling of affected families.