ACGS Best Practice Guidelines for Variant Classification in Rare Disease 2020, a supplementary practical guidelines, is based on the Standards and Guidelines for the Interpretation of Sequence Variations issued by the American Society for Medical Genetics and Genomics (ACMG) and the Association of Molecular Pathology (AMP) in 2015 by the British Medical Genetics Society under the Clinical Genomics Society (ACGS), and has integrated the detailed rules of standards developed by the ClinGen Sequence Variant Interpretation (SVI) Working Group by 2020. The further development of the ACMG/AMP guidelines is currently undertaken by the ClinGen SVI working group in the United States, which focuses on the classification of high penetrance and protein coding variants. ClinGen has established many expert panels on variants for specific diseases which required various evidence thresholds and is currently developing disease/gene specific guidelines. The British Medical Genetics Society has collected and integrated information on the guidelines for sequence variation classification and their extended rules, forming its own "2020 ACGS Best Practice Guidelines for Rare Disease Variation Classification" and is regularly updating it. The author has translated and summarized it for the reference of Chinese Medical Genetics Practitioners.
Humans ; Genetic Testing ; Genetic Variation ; Genome, Human ; Rare Diseases/genetics* ; China

OBJECTIVE: To summarize the clinical features and biological characteristics of Helsmoortel Van der Aa syndrome (HVDAS) due to hotspot mutations of the ADNP gene in order to facilitate early diagnosis. METHODS: Clinical data and result of genetic testing for a girl with HVDAS due to hotspot mutation of the ADNP gene was summarized. Related literature was also reviewed. RESULTS: The patient, a 2-year-old girl, had presented with growth retardation, facial dysmorphism, psychomotor and language delay and recurrent respiratory infections. Whole exome sequencing revealed that she has harbored a heterozygous c.2496_2499delTAAA (p.Asn832Lysfs*81) variant of the ADNP gene, which was not found in either of her parents. CONCLUSION Although the typical features of the HVDAS have included intellectual disability and autism spectrum disorders, growth retardation and premature primary tooth eruption may also be present. In addition, the phenotypic difference among individuals carrying hot spot variants of the ADNP gene was not prominent.
Humans ; Female ; Child, Preschool ; Intellectual Disability/genetics* ; Homeodomain Proteins/genetics* ; Nerve Tissue Proteins/genetics* ; Abnormalities, Multiple/genetics* ; Mutation ; Rare Diseases ; Growth Disorders/genetics*

A boy, aged 6 years, attended the hospital due to global developmental delay for 6 years and recurrent fever and convulsions for 5 years. The boy was found to have delayed mental and motor development at the age of 3 months and experienced recurrent fever and convulsions since the age of 1 year, with intermittent canker sores and purulent tonsillitis. During the fever period, blood tests showed elevated white blood cell count, C-reactive protein, and erythrocyte sedimentation rate, which returned to normal after the fever subsides. Electroencephalography showed epilepsy, and genetic testing showed compound heterozygous mutations in the GPAA1 gene. The boy was finally diagnosed with glycosylphosphatidylinositol biosynthesis deficiency 15 (GPIBD15) and periodic fever. The patient did not respond well to antiepileptic treatment, but showed successful fever control with glucocorticoid therapy. This article reports the first case of GPIBD15 caused by GPAA1 gene mutation in China and summarizes the genetic features, clinical features, diagnosis, and treatment of this disease, which provides a reference for the early diagnosis and treatment of GPIBD15.
Humans ; Male ; Fever ; Glycosylphosphatidylinositols/genetics* ; Membrane Glycoproteins/genetics* ; Mutation ; Rare Diseases ; Seizures ; Child

OBJECTIVE: To explore the genetic basis for a child manifesting with intellectual disability, language delay and autism spectrum disorder. METHODS: Genomic DNA was extracted from peripheral blood samples of the child and his family members, and subjected to whole exome sequencing. Candidate variants were verified by Sanger sequencing and interpreted according to the guidelines of the American College of Medical Genetics and Genomics. RESULTS: The child was found to harbor a heterozygous c.568C>T (p.Q190X) nonsense variant of the ADNP gene, which was not detected in either parent by Sanger sequencing. CONCLUSION The clinical and genetic testing both suggested that the child has Helsmoortel-van der Aa syndrome due to ADNP gene mutation, which is extremely rare in China.
Abnormalities, Multiple/genetics* ; Autism Spectrum Disorder/genetics* ; Autistic Disorder/genetics* ; Child ; Heterozygote ; Homeodomain Proteins/genetics* ; Humans ; Intellectual Disability/genetics* ; Mutation ; Nerve Tissue Proteins/genetics* ; Rare Diseases

OBJECTIVE: To analyze the clinical characteristics and genetic etiology of a child with Helsmoortel-Van der Aa syndrome (HVDAS). METHODS: Genetic testing was carried out for the child and his parents, and the clinical phenotypes and genetic variants of reported cases were summarized through literature review. RESULTS: The child has featured peculiar facies, accompanied by autism spectrum disorder, intellectual disability and motor retardation, and curving of the second toes, which was unreported previously. Genetic testing revealed that the child has harbored a heterozygous c.2157C>G (p.Tyr719*) variant of the ADNP gene, which was not found in either parent. Based on the guidelines of the American College of Medical Genetics and Genomics, this variant was rated as pathogenic. Among 80 HVDAS cases described in the literature, most had various degrees of behavioral abnormalities, intellectual disability, language retardation and motor retardation, with common features involving the nervous system, gastrointestinal system and eye. Variants of the ADNP gene mainly included frameshift variants and nonsense variants, with the hotspot variants including p.Tyr719*, p.Asn832lysfs*81 and p.Arg730*. CONCLUSION The clinical phenotype of the child is closely correlated with the heterozygous variant of the ADNP gene, which expanded the phenotypic spectrum of HVDAS. As HVDAS may involve multiple systems and have high phenotypic heterogeneity, genetic testing technology can facilitate accurately diagnose.
Abnormalities, Multiple/genetics* ; Autism Spectrum Disorder/genetics* ; Autistic Disorder/genetics* ; Homeodomain Proteins/genetics* ; Humans ; Intellectual Disability/genetics* ; Mutation ; Nerve Tissue Proteins/genetics* ; Rare Diseases/complications*

OBJECTIVE: To investigate the genetic etiology, clinical diagnosis and treatment of a child with pancytopenia, failure to thrive and pulmonary infection. METHODS: Peripheral blood samples of the child and her parents were collected. Genomic DNA was extracted. Genetic variants associated with hematological diseases were detected by high-throughput sequencing. RESULTS: Three variants of TCN2 gene were found, one of which located in exon 5 upstream(c.581-8A>T), the parents has carried this variant; one in exon 6 (c.924_927del), the variant was originated from the mother; one in exon 7 (c.973C>T), the variant has ocurred de novo. The variants pathogenic analysis combined with clinical manifestation, pancytopenia, the increase in methylmalonic acid level and increased homocysteine, the child was diagnosed with transcobalaminIIdeficiency. The patient presented with respiratory infection, which was confirmed to be pneumocystosis by lung radioscopy and pathogenic high-throughput sequencing of broncho-alveolar lavage fluid. The patient presented with acute respiratory distress syndrome during the treatment with intramuscular injection of vitamin B CONCLUSION We reported a case of Chinese child with TCNII deficiency due to novel gene variant, and analyzed the pathogenicity of the three variants. The treatment of TCNII deficiency with cobalamin should be individualized.
Amino Acid Metabolism, Inborn Errors ; Child ; Female ; Genetic Testing ; Humans ; Rare Diseases ; Transcobalamins/genetics* ; Vitamin B 12

A boy, aged 1 year and 6 months, was found to have persistent positive urine glucose at the age of 4 months, with polydipsia, polyuria, and growth retardation. Laboratory examinations suggested that the boy had low specific weight urine, anemia, hypokalemia, hyponatremia, hypomagnesemia, metabolic acidosis, glycosuria, acidaminuria, increased fractional excretion of potassium, and decreased tubular reabsorption of phosphate. X-ray examinations of the head, thorax, and right hand showed changes of renal rickets. The slit-lamp examination showed a large number of cystine crystals in the cornea. The genetic testing showed a suspected pathogenic homozygous mutation of the
Amino Acid Transport Systems, Neutral/genetics* ; Cornea ; Cystinosis/genetics* ; Humans ; Hypokalemia ; Infant ; Male ; Mutation ; Rare Diseases

OBJECTIVE: To explore the clinical features and genetic diagnosis of two cases with rare diseases and X chromosome abnormalities. METHODS: Multiple ligation-dependent probe amplification (MLPA) and karyotype analysis were carried out on an 8-year-old girl who was diagnosed with Duchenne muscular dystrophy. Karyotype analysis and PCR assay for SRY and AZF genes were carried out for a-2-month-old male infant with short penis. RESULTS: The girl, who featured short stature and cubitus valgus, was diagnosed as Turner syndrome with a karyotype of 46,X,i(Xq). The male infant was detected with a karyotype of 45,X, with presence of SRY gene but absence of AZF gene. CONCLUSION Both cases may be associated with abnormalities of X chromosome. Genetic testing can facilitate early diagnosis and clinical intervention for such patients.
Chromosomes, Human, X ; Humans ; Infant ; Karyotyping ; Male ; Muscular Dystrophy, Duchenne ; genetics ; Rare Diseases ; Turner Syndrome ; genetics

High-Throughput Nucleotide Sequencing ; Humans ; Rare Diseases ; genetics

Potocki-Shaffer syndrome (PSS, OMIM #601224) is a rare contiguous gene deletion syndrome caused by haploinsufficiency of genes located on the 11p11.2p12. Affected individuals have a number of characteristic features including multiple exostoses, biparietal foramina, abnormalities of genitourinary system, hypotonia, developmental delay, and intellectual disability. We report here on the first Korean case of an 8-yr-old boy with PSS diagnosed by high resolution microarray. Initial evaluation was done at age 6 months because of a history of developmental delay, hypotonia, and dysmorphic face. Coronal craniosynostosis and enlarged parietal foramina were found on skull radiographs. At age 6 yr, he had severe global developmental delay. Multiple exostoses of long bones were detected during a radiological check-up. Based on the clinical and radiological features, PSS was highly suspected. Subsequently, chromosomal microarray analysis identified an 8.6 Mb deletion at 11p11.2 [arr 11p12p11.2 (Chr11:39,204,770-47,791,278)x1]. The patient continued rehabilitation therapy for profound developmental delay. The progression of multiple exostosis has being monitored. This case confirms and extends data on the genetic basis of PSS. In clinical and radiologic aspect, a patient with multiple exostoses accompanying with syndromic features, including craniofacial abnormalities and mental retardation, the diagnosis of PSS should be considered.
Child ; Chromosome Deletion ; Chromosome Disorders/diagnosis/*genetics/radiography ; Chromosome Mapping ; Chromosomes, Human, Pair 11/genetics/radiography ; Craniofacial Abnormalities/genetics ; Developmental Disabilities/genetics ; Exostoses, Multiple Hereditary/diagnosis/*genetics/radiography ; Humans ; Male ; Muscle Hypotonia/genetics ; Oligonucleotide Array Sequence Analysis ; Rare Diseases/*genetics ; Republic of Korea